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Small Ubiquitin-like MOdifiers (SUMOs) are a family of 3 proteins (SUMO1,2,3) that are reversibly conjugated to lysine residues of target proteins via a glycine-lysine isopeptide bond (reviewed in Hay 2013, Hannoun et al. 2010, Gareau and Lima 2010, Wilkinson and Henley 2010, Wang and Dasso 2009). Proteomic methods have yielded estimates of hundreds of target proteins. Targets are mostly located in the nucleus and therefore SUMOylation disproportionately affects gene expression. SUMOs are initially translated as proproteins possessing extra amino acid residues at the C-terminus which are removed by the SUMO processing endoproteases SENP1,2,5 (Hay 2007). Different SENPs have significantly different efficiencies with different SUMOs. The processing exposes a glycine residue at the C-terminus that is activated by ATP-dependent thiolation at cysteine-173 of UBA2 in a complex with SAE1, the E1 complex. The SUMO is transferred from E1 to cysteine-93 of a single E2 enzyme, UBC9 (UBE2I). UBC9 with or, in some cases, without an E3 ligase conjugates the glycine C-terminus of SUMO to an epsilon amino group of a lysine residue on the target protein. SUMO2 and SUMO3 may then be further polymerized, forming chains. SUMO1 is unable to form polymers. Conjugated SUMO can act as a biinding site for proteins possessing SUMO interaction motifs (SIMs) and can also directly affect the formation of complexes between the target protein and other proteins. Conjugated SUMOs are removed by cleavage of the isopeptide bond by processing enzymes SENP1,2,3,5. The processing enzymes SENP6 and SENP7 edit chains of SUMO2 and SUMO3.
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The initial translation products of SUMO1, SUMO2, and SUMO3 are precursors that have extra amino acid residues at the C-terminus (reviewed in Wang and Dasso 2009, Wilkinson and Henley 2010, Hannoun et al. 2010, Gareau and Lima 2010, Hay 2007). SUMO1 has 4 extra residues, SUMO2 has 2 extra residues, and SUMO3 has 11 extra residues. Proteolytic cleavage by SUMO peptidases (SENPs) removes the propeptide and leaves diglycine residues at the C-terminus. Each SENP has distinct preferences for certain SUMOs. SENP1 has highest activity on SUMO1; SENP2 and SENP5 have highest activity on SUMO2 (Shen et al. 2006, Reverter and Lima 2006, Mikolajczyk et al. 2007). SENP1 and SENP2 are predominantly nucleoplasmic (Bailey and O'Hare 2004, Kim et al. 2005, Zhang et al. 2002, Hang and Dasso 2002, Itahana et al. 2006) and SENP5 is predominantly nucleolar (Di Bacco et al. 2006, Gong and Yeh 2006), therefore the processing reactions are believed to occur in the nucleus. The processed SUMO is then activated by formation of a thioester bond with a cysteine residue of an E1 enzyme, UBA2 (SAE2) in a complex with SAE1. SUMO is then transferred from the E1 enzyme to an E2 enzyme, UBC9 (UBE2I).
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S-methyl-5-thio-?-D-ribose 1-phosphate(2?)
ChEBI:58533 S-methyl-5-thio-?-D-ribose 1-phosphate(2?)
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The UBA2:SAE1 complex catalyzes the formation of a thioester bond between SUMO3 and cysteine-173 of UBA2 (Tatham et al. 2001, Werner et al. 2009). ATP reacts with the C-terminal glycine residue of SUMO3 to yield pyrophosphate and a transient intermediate, SUMO3 adenylate, which then reacts with the thiol group of the cysteine residue on UBA2.
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The UBA2:SAE1 complex catalyzes the formation of a thioester linkage between the C-terminal glycine of the mature SUMO and a cysteine residue (cysteine-173) in UBA2 (SAE2) (reviewed in Wang and Dasso 2009, Wilkinson and Henley 2010, Hannoun et al. 2010, Gareau and Lima 2010). During the process the C-terminal glycine residue of SUMO is reacted with ATP to yield pyrophosphate and a transient intermediate, SUMO adenylate. The SUMO adenylate then reacts with the thiol group of the cysteine residue of UBA2 (Olsen et al. 2010).
The UBA2:SAE1 complex catalyzes the formation of a thioester bond between SUMO1 and cysteine-173 of UBA2 (Desterro et al. 1999, Okuma et al. 1999, Werner et al. 2009, Olsen et al. 2010, Wang and Chen 2010). ATP reacts with the C-terminal glycine residue of SUMO1 to yield pyrophosphate and a transient intermediate, SUMO1 adenylate, which then reacts with the thiol group of the cysteine residue on UBA2.
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The UBA2:SAE1 complex catalyzes the formation of a thioester bond between SUMO2 and cysteine-173 of UBA2 (Tatham et al. 2001, Werner et al. 2009). ATP reacts with the C-terminal glycine residue of SUMO2 to yield pyrophosphate and a transient intermediate, SUMO2 adenylate, which then reacts with the thiol group of the cysteine residue on UBA2.
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SUMO3 is transferred from cysteine-173 of UBA2 to cysteine-93 of UBC9 (UBE2I) in a transthiolation reaction (Tatham et al. 2001, Werner et al. 2009).
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SUMO is transferred from cysteine-173 of UBA2 to cysteine-93 of UBC9 (UBE2I) in a transthiolation reaction (reviewed in Wang and Dasso 2009, Wilkinson and Henley 2010, Hannoun et al. 2010, Gareau and Lima 2010). UBC9 is the only known E2 enzyme for SUMO and on certain substrates such as RanGAP1 may act without the requirement of an E3 ligase.
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SUMO1 is transferred from cysteine-173 of UBA2 to cysteine-93 of UBC9 (UBE2I) in a transthiolation reaction (Desterro et al. 1999, Okuma et al. 1999, Tatham et al. 2003, Lois and Lima 2005, Wang et al. 2007, Werner et al. 2009). The UbL domain of E1 recruits E2 into proximity for the transfer of SUMO (Lois and Lima 2005, Wang et al. 2009),
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SUMO2 is transferred from cysteine-173 of UBA2 to cysteine-93 of UBC9 (UBE2I) in a transthiolation reaction (Tatham et al. 2001, Werner et al. 2009).
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The generation of insulin-containing secretory granules from proinsulin in the lumen of the endoplasmic reticulum (ER) can be described in 4 steps: formation of intramolecular disulfide bonds, formation of proinsulin-zinc-calcium complexes, proteolytic cleavage of proinsulin to yield insulin, translocation of the granules across the cytosol to the plasma membrane. Transcription of the human insulin gene INS is activated by 4 important transcription factors: Pdx-1, MafA, Beta2/NeuroD1, and E47. The transcription factors interact with each other at the promoters of the insulin gene and act synergistically to promote transcription. Expression of the transcription factors is upregulated in response to glucose. The preproinsulin mRNA is translated by ribosomes at the rough endoplasmic reticulum (ER) and the preproinsulin enters the secretion pathway by virtue of its signal peptide, which is cleaved during translation to yield proinsulin. Evidence indicates that the preproinsulin mRNA is stabilized by glucose. In the process annotated in detail here, within the ER, three intramolecular disulfide bonds form between cysteine residues in the proinsulin. Formation of the bonds is the spontaneous result of the conformation of proinsulin and the oxidizing environment of the ER, which is maintained by Ero1-like alpha The cystine bonded proinsulin then moves via vesicles from the ER to the Golgi Complex. High concentrations of zinc are maintained in the Golgi by zinc transporters ZnT5, ZnT6, and ZnT7 and the proinsulin forms complexes with zinc and calcium. Proinsulin-zinc-calcium complexes bud in vesicles from the trans-Golgi to form immature secretory vesicles (secretory granules) in the cytosol. Within the immature granules the endoproteases Prohormone Convertase 1/3 and Prohormone Convertase 2 cleave at two sites of the proinsulin and Carboxypeptidase E removes a further 4 amino acid residues to yield the cystine-bonded A and B chains of mature insulin and the C peptide, which will also be secreted with the insulin. The insulin-zinc-calcium complexes form insoluble crystals within the granule The insulin-containing secretory granules are then translocated across the cytosol to the inner surface of the plasma membrane. Translocation occurs initially by attachment of the granules to Kinesin-1, which motors along microtubules, and then by attachment to Myosin Va, which motors along the microfilaments of the cortical actin network. A pancreatic beta cell contains about 10000 insulin granules of which about 1000 are docked at the plasma membrane and 50 are readily releasable in immediate response to stimulation by glucose or other secretogogues. Docking is due to interaction between the Exocyst proteins EXOC3 on the granule membrane and EXOC4 on the plasma membrane. Exocytosis is accomplished by interaction between SNARE-type proteins Syntaxin 1A and Syntaxin 4 on the plasma membrane and Synaptobrevin-2/VAMP2 on the granule membrane. Exocytosis is a calcium-dependent process due to interaction of the calcium-binding membrane protein Synaptotagmin V/IX with the SNARE-type proteins.
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Cloning and molecular analysis of the human citrate synthase gene
Expression, purification and characterization of human glutamate dehydrogenase (GDH) allosteric regulatory mutations
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After translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the body. These modifications include the internal peptide bond cleavages that activate proenzymes, the attachment of oligosaccharide moieties to membrane-bound and secreted proteins, the attachment of lipid or glycolipid moieties that serve to anchor proteins to cellular membranes, and the vitamin K-dependent attachment of carboxyl groups to glutamate residues.
Structure of the Rho family GTP-binding protein Cdc42 in complex with the multifunctional regulator RhoGDI
A comparison of the substrate specificity of MAPKAP kinase-2 and MAPKAP kinase-3 and their activation by cytokines and cellular stress
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As inferred from the yeast TIM23 complex, the human TIMM23 complex resides in the inner membrane of the mitochondrion and transfers precursor proteins to the inner membrane. The TIMM23 complex appears to adopt different configurations (and perhaps different subunit compositions) depending on whether the substrate is destined for the inner membrane or the matrix. Here we refer to the TIMM23 SORT complex as the configuration that delivers inner membrane proteins. The TIMM21 subunit is required for this activity. In yeast, the N-terminal presequences of precursors first interact with TIM50 and TIM23 (TIMM50 and TIMM23 in human). The TIM17 and TIM23 subunits (TIMM17 and TIMM23 in human) form a channel and are required to initiate translocation of precursors. In yeast experimentally verified substrates of the TIM23 SORT complex targeted to the inner membrane include CYB2, DLD (LDHD in human), ATP9 (ATP5G1 in human), COQ2, TIM54 (TIMM54 in human), COX4, COX5A, and ATP2 (ATP5B in human). Many other inner membrane proteins are believed to be substrates of the TIMM23 complex.
As inferred from yeast, the alpha subunit of the mitochondrial processing peptidase (MPP) binds presequences of mitochondrial precursors and the beta subunit cleaves the presequence. After cleavage, proteins destined for the inner membrane are released laterally from TIMM23 SORT into the membrane.
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As inferred from the yeast TIM23 complex, the human TIMM23 complex resides in the inner membrane of the mitochondrion and transfers precursor proteins to the inner membrane. The presequences of proteins targeted to the inner membrane are transferred to the matrix where they are cleaved. Sequences in the mature regions of the proteins then interact with the TIMM23 complex to halt transfer across the inner membrane and the proteins are released laterally into the inner membrane. TIMM21 is required. In yeast experimentally verified substrates of the TIM23 complex targeted to the inner membrane include CYB2, DLD (LDHD in human), ATP9 (ATP5G1 in human), COQ2, TIM54 (TIMM54 in human), COX4, COX5A, and ATP2 (ATP5B in human). Many other inner membrane proteins are believed to be substrates of the TIMM23 complex.
As inferred from the yeast TIM23 complex, the human TIMM23 complex resides in the inner membrane of the mitochondrion and transfers precursor proteins to the matrix. The TIMM23 complex appears to adopt different configurations (and perhaps different subunit compositions) depending on whether the substrate is destined for the inner membrane or the matrix. Here we refer to the TIMM23 PAM complex as the configuration that delivers inner membrane proteins. The PAM17 subcomplex is required for this activity. The N-terminal presequence of precursors first interacts with TIMM50 and TIMM23. The TIMM17 and TIMM23 subunits form a channel and are required to initiate translocation of precursors. In yeast experimentally verified substrates of TIM23:PAM include Hsp60 (HSP60 in human) and Yfh1 (Frataxin, FXN in human). Many other matrix proteins are believed to be substrates of the TIMM23 complex.
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As inferred from yeast, the alpha subunit of the mitochondrial processing peptidase (MPP) binds presequences of mitochondrial precursors and the beta subunit cleaves the presequence. After cleavage, proteins destined for the matrix are drawn into the matrix by ATP-dependent interaction with mtHSP70 (HSPA9, homolog of yeast SSC1) of the PAM complex.
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As inferred from the yeast TIM23 complex, the human TIMM23 complex transports precursor proteins across the inner membrane and into the matrix. As in yeast, subunits TIMM50, TIMM17, and TIMM23 are probably necessary for initiating translocation while the PAM complex with mtHSP70 (HSPA9, yeast SSC1) provides the motive force that drives the transport. mtHSP70 binding to the precursor pulls the protein into the matrix in a reaction requiring ATP hydrolysis. The yeast reaction appears to use a Brownian ratchet mechanism (Yamano et al. 2008). In yeast experimentally verified substrates of TIM23 PAM include Hsp60 (HSP60 in human) and Yfh1 (Frataxin, FXN in human). Many other matrix proteins are believed to be substrates of the TIMM23 complex
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A human mitochondrion contains about 1500 proteins, more than 99% of which are encoded in the nucleus, synthesized in the cytosol and imported into the mitochondrion. Proteins are targeted to four locations (outer membrane, intermembrane space, inner membrane, and matrix) and must be sorted accordingly (reviewed in Kutik et al. 2007, Milenkovic et al. 2007, Bolender et al. 2008, Endo and Yamano 2009). Newly synthesized proteins are transported from the cytosol across the outer membrane by the TOMM40:TOMM70 complex. Proteins that contain presequences first interact with the TOMM20 subunit of the complex while proteins that contain internal targeting elements first interact with the TOMM70 subunit. After initial interaction the protein is conducted across the outer membrane by TOMM40 subunits. In yeast some proteins such as Aco1, Atp1, Cit1, Idh1, and Atp2 have both presequences that interact with TOM20 and mature regions that interact with TOM70 (Yamamoto et al. 2009). After passage across the outer membrane, proteins may be targeted to the outer membrane via the SAMM50 complex, to the inner membrane via the TIMM22 or TIMM23 complexes (reviewed in van der Laan et al. 2010), to the matrix via the TIMM23 complex (reviewed in van der Laan et al. 2010), or proteins may fold and remain in the intermembrane space (reviewed in Stojanovski et al. 2008, Deponte and Hell 2009, Sideris and Tokatlidis 2010). Presequences on matrix and inner membrane proteins cause interaction with TIMM23 complexes; internal targeting sequences cause outer membrane proteins to interact with the SAMM50 complex and inner membrane proteins to interact with the TIMM22 complex. While in the intermembrane space hydrophobic proteins are chaperoned by the TIMM8:TIMM13 complex and/or the TIMM9:TIMM10:FXC1 complex.
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The human gene SLC30A5 encodes the zinc transporter ZnT5. This protein is widely expressed but is most abundant in pancreatic beta cells (Kambe T et al, 2002). In these cells, ZnT5 mediates the transport of zinc into secretory granules that contain insulin.
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Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol
This event has been computationally inferred from an event that has been demonstrated in another species. The inference is based on the homology mapping in Ensembl Compara. Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are inferred to the other species. High level events are also inferred for these events to allow for easier navigation. More details and caveats of the event inference in Reactome. For details on the Ensembl Compara system see also: Gene orthology/paralogy prediction method.
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Peptide hormones are cleaved from larger precursors in the secretory system (endoplasmic reticulum, Golgi apparatus, secretory granules) of the cell. After secretion peptide hormones are modified and degraded by extracellular proteases.
The BIP (HSPA5) gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
Microbial biotin protein ligases aid in understanding holocarboxylase synthetase deficiency
Signal transduction pathways used by NLR-type innate immune receptors
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The CTDSP2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The DCTN1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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Phosphorylation of the C-terminal region causes a loop in the C-terminus to change position, enabling access to an ADP-binding pocket. Phosphorylated IRE1-alpha dimers bind ADP in preference to ATP.
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The ATP6VOD1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The dissociation of the IRE1-alpha:BiP heterodimer liberates IRE1-alpha, which forms homodimers. Dimer formation is initiated by interaction between the N-terminal, luminal domains.
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Dimerization of the N-terminal luminal regions of IRE1-alpha brings the cytosolic C-terminal regions in proximity. The C-terminal region possesses kinase activity and the homodimer trans-autophosphorylates. From homology with Saccharomyces IRE1-alpha the phosphorylation of human IRE1-alpha is believed to be at Ser724.
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The N-terminal fragment of ATF6-alpha contains a bZIP domain and binds the sequence CCACG in ER Stress Response Elements (ERSEs). ATF6-alpha binds ERSEs together with the heterotrimeric transcription factor NF-Y, which binds the sequence CCAAT in the ERSEs, and together the two factors activate transcription of ER stress-responsive genes. Evidence from overexpression and knockdowns indicates that ATF6-alpha is a potent activator but its homolog ATF6-beta is not and ATF6-beta may actually reduce expression of ER stress proteins.
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ATF6-alpha is a transmembrane protein that normally resides in the Endoplasmic Reticulum (ER) membrane. Here its luminal C-terminal domain is associated with BiP, shielding 2 Golgi-targeting regions and thus keeping ATF6-alpha in the ER. Upon interaction of BiP with unfolded proteins in the ER, ATF6-alpha dissociates and transits to the Golgi where it is cleaved by the S1P and S2P proteases that reside in the Golgi, releasing the N-terminal domain of ATF6-alpha into the cytosol. After transiting to the nucleus, the N-terminal domain acts as a transcription factor to activate genes encoding chaperones.
A tandemly repeated sequence at the termini of the extrachromosomal ribosomal RNA genes in Tetrahymena
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Histone-modifying enzymes: regulators of developmental decisions and drivers of human disease
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The DDX11 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The DNAJB11 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The EDEM gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The GSK3A gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The HYOU1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
A module of negative feedback regulators defines growth factor signaling
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The KDELR3 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The FKBP14 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The GAP gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The GFPT1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The GOSR2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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Xbp-1 (S) binds the sequence CCACG in ER Stress Responsive Elements (ERSE, consensus sequence CCAAT (N)9 CCACG) located upstream from many genes. The ubiquitous transcription factor NF-Y, a heterotrimer, binds the CCAAT portion of the ERSE and together the IRE1-alpha: NF-Y complex activates transcription of a set of chaperone genes including DNAJB9, EDEM, RAMP4, p58IPK, and others. This results in an increase in protein folding activity in the ER.
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The YIF1A gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The WIPI1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The Sec31A gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The Aspariagine Synthetase (ASNS) gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
IRE1-alpha is a single-pass transmembrane protein that resides in the endoplasmic reticulum (ER) membrane. The C-terminus of IRE1-alpha is located in the cytosol; the N-terminus is located in the ER lumen. In unstressed cells IRE1-alpha exists in an inactive heterodimeric complex with BiP such that BiP in the ER lumen binds the N-terminal region of IRE1-alpha. Upon accumulation of unfolded proteins in the ER, BiP binds the unfolded protein and the IRE1-alpha:BiP complex dissociates. The dissociated IRE1-alpha then forms homodimers. Initially the luminal N-terminal regions pair. This is followed by trans-autophosphorylation of IRE1-alpha at Ser724 in the cytosolic C-terminal region. The phosphorylation causes a conformational change that allows the dimer to bind ADP, causing a further conformational change to yield back-to-back pairing of the cytosolic C-terminal regions of IRE1-alpha. The fully paired IRE1-alpha homodimer has endoribonuclease activity and cleaves the mRNA encoding Xbp-1. A 26 residue polyribonucleotide is released and the 5' and 3' fragments of the original Xbp-1 mRNA are rejoined. The spliced Xbp-1 message encodes Xbp-1 (S), a potent activator of transcription. Xbp-1 (S) together with the ubiquitous transcription factor NF-Y bind the ER Stress Responsive Element (ERSE) in a number of genes encoding chaperones. Recent data suggest that the IRE1-alpha homodimer can also cleave specific subsets of mRNAs, including the insulin (INS) mRNA in pancreatic beta cells.
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Constitutive activation of fibroblast growth factor receptor 3 by mutations responsible for the lethal skeletal dysplasia thanatophoric dysplasia type I
The SRPRB gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The SRPR gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The PPP2R5B gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The PDIA6 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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GABA is loaded into the synaptic vesicle by inihibitory amino acid transport, VIAAT or VGAT.
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Acetylcholine neurotransmitter release cycle involves syntheis of choline, loading of clathrin scultpted synaptic vesicles, docking and priming of the acetyl choline loaded synaptic vesicles and then release of acetylcholine. This cycle occurs in neurons of central nervous system (CNS), peripheral, autonomic and somatic nervous system. In the CNS, the acetylcholine is released by the presynaptic neurons into the synaptic cleft where the released acetylcholine is accessible to acetylcholine receptors located on the postsynaptic neurons.
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Succinate semialdehyde dehydrogenase (SSADH) converts succinate semialdehyde, in a final step of GABA degradation, into succinate. SSADH uses one water molecule and one molecule of NAD+ per molecule of succinyate semialdehyde.
GABA is converted to succinate semialdehyde by 4-aminobutyrate aminotransferase
GABA is metabolized to succinated by the serial action of two enzymes, 4-aminobutyrate aminotransferase and suucinate semialdehyde dehydrogenase.
Enzyme-substrate intermediate formation at lysine 329 of human deoxyhypusine synthase
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MISCELLANEOUS Present with 13000 molecules/cell in log phase SD medium.SIMILARITY Belongs to the archaeal RpoD/eukaryotic RPB3 RNA polymerase subunit family.
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ATF4 is a transcription factor and activates expression of IL-8, MCP1, IGFBP-1, CHOP, HERP1 and ATF3.
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The Unfolded Protein Response (UPR) is a regulatory system that protects the Endoplasmic Reticulum (ER) from overload. The UPR is provoked by the accumulation of improperly folded protein in the ER during times of unusually high secretion activity. Analysis of mutants with altered UPR, however, shows that the UPR is also required for normal development and function of secretory cells. One level at which the URP operates is transcriptional and translational regulation: mobilization of ATF6 and IRE1 leads to increased transcription of genes encoding chaperones, and mobilization of PERK (pancreatic eIF2alpha kinase, EIF2AK3) leads to phosphorylation of the translation initiation factor eIF2alpha and global down-regulation of protein synthesis. These three regulatory pathways are annotated here.
PERK (EIF2AK3) is a single-pass transmembrane protein located in the endoplasmic reticulum (ER) membrane such that the N-terminus of PERK is luminal and the C-terminus is cytosolic. PERK is maintained in an inactive form by interaction of its luminal domain with BiP, an ER chaperone. BiP also binds unfolded proteins and so BiP dissociates from PERK when unfolded proteins accumulate in the ER. Dissociated PERK monomers spontaneously form homodimers and the homodimeric form of PERK possesses kinase activity in its cytosolic C-terminal domain. The kinase specifically phosphorylates the translation factor eIF2alpha at Ser52, resulting in an arrest of translation. Thus translation of proteins targeted to the ER is downregulated. The translation arrest also causes depletion of Cyclin D1, a rapidly turned over protein. The depletion of Cyclin D1 in turn causes arrest of the cell cycle in G1 phase.
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In the cytosol, choline O-acetyltransferase (CHAT) acetylates choline (Cho) to produce acetylcholine (AcCho) (Toussaint 1992). AcCho is synthesised in the cytoplasm of cholinergic neurons from acetyl-CoA and Cho by CHAT enzyme.
Protein metabolism comprises the pathways of translation, post-translational modification and protein folding.
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The molecular dissection of Fc gamma receptor mediated phagocytosis
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Mutations in orthologous genes in human spondyloepimetaphyseal dysplasia and the brachymorphic mouse
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Sequence differences between human muscle and liver cDNAs for UDPglucose pyrophosphorylase and kinetic properties of the recombinant enzymes expressed in Escherichia coli.
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Mutations in a gene encoding a novel protein tyrosine phosphatase cause progressive myoclonus epilepsy
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Regulation of the members of the mammalian heat shock factor family
Conformational transition associated with E1-E2 interaction in small ubiquitin-like modifications
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Novel aspects of heat shock factors: DNA recognition, chromatin modulation and gene expression
The SUMO-specific protease SENP5 is required for cell division
Crystal structure of the human monoacylglycerol lipase, a key actor in endocannabinoid signaling
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Isolation and functional expression of human COQ2, a gene encoding a polyprenyl transferase involved in the synthesis of CoQ
Structural analysis of the GLUT1 facilitative glucose transporter (review).
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Comparison of messenger RNA distribution for 60 proteins in fat cells vs the nonfat cells of human omental adipose tissue
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Differential regulation of zinc efflux transporters ZnT-1, ZnT-5 and ZnT-7 gene expression by zinc levels: a real-time RT-PCR study
Targeting purine and pyrimidine metabolism in human apicomplexan parasites
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Cellular signalling mechanisms of neural cell adhesion molecules
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Reactions for the synthesis of the small nucleotide-linked sugar substrates that are used in the synthesis of the N-glycan precursor and in the later steps of glycosylation are annotated here. All these nucleotide-linked sugar donors are synthesized in the cytosol; however, to participate in the later reactions of N-glycan precursor biosynthesis (when the glycan is oriented toward the lumen of the endoplasmic reticulum (ER)), these substrates must be attached to a dolichyl-phosphate molecule and then flipped toward the luminal side of the ER, through a mechanism which is still not known but which involves a different protein than the one that mediates the flipping of the LLO itself (Sanyal et al. 2008). Two of the genes encoding enzymes involved in these reactions, MPI and PMM2, are known to be associated with Congenital Disorders of Glycosylation (CDG) diseases of type I. Of these, CDG-Ia, associated with defects in PMM2, is the most frequent CDG disease reported.
Dolichyl-phosphate-glucose functions as a donor of glucose groups in reactions including three steps of N-glycan precursor biosynthesis. Dolichyl-phosphate-glucose itself is synthesized from UDP-glucose and dolichol phosphate on the cytosolic face of the endoplasmic reticulum membrane, then flipped to the luminal surface of that membrane.
A second N-acetylglucosamine is added to the N-glycan precursor via a beta-1,4 linkage. This reaction is catalyzed by the ALG13:ALG14 complex, in which ALG13 functions as the catalyst and ALG14 functions as a membrane anchor which recruits ALG13 to the cytosolic face of ER (Gao XD et al, 2005).
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In the first step of N-glycan precursor (LLO) synthesis, N-acetylglucosamine is added, via an alpha-1,3 linkage, to a molecule of dolichyl phosphate, producing N-acetyl-D-glucosaminyl-diphosphodolichol (Eckert et al. 1998). This reaction is catalyzed by DPAGT1 (ALG7 in yeast), mutations in which are associated with CDG disorder type I-J (Wu et al. 2003). The dolichyl phosphate acts as an anchor for the LLO, so that subsequent sugar-addition reactions take place on a sugar anchored in the ER membrane.
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A mannose is added to the N-glycan precursor via a beta-1,4 linkage. The reaction is catalyzed by ALG1 (Takahashi T et al, 2000). Defects in ALG1 lead to congenital disorder of glycosylation type 1K (CDG1K) (Schwarz et al. 2004; Kranz et al. 2004; Grubenmann et al. 2004).
A second mannose is added to the N-glycan precursor via an alpha-1,3 linkage. The reaction is catalyzed by the mannosyltransferase ALG2. This is a bifunctional enzyme with both alpha 1,3- and alpha 1,6-mannosyltransferase activities. In humans, only the alpha 1,3 activity used in this reaction has been elucidated (Thiel et al. 2003). Defects in ALG2 are the cause of ALG2-CDG (CDG-1i; MIM:607906) (Thiel et al. 2003).
A third mannose is added to the N-glycan precursor by ALG2 using its alpha1,6-mannosyltransferase activity. This has been demonstrated experimentally in yeast (O'Reilly MK et al, 2006; Kämpf M et al, 2009); the human reaction is inferred by homology. Defects in ALG2 are the cause for CDG1I (Thiel C et al, 2003).
A fourth mannose is added to the N-glycan precursor by ALG11. The addition of the fifth mannose, also by ALG11, is the last step occurring on the cytosolic side of the ER membrane (Cipollo JF et al, 2001). Both these reactions are alpha1,2 mannose additions.
The precursor of the N-glycan sugar, now in the form of (GlcNAc)2 (Man)5 (PP-Dol), is flipped across the ER membrane, moving it from the cytosolic side into the ER lumen. The exact mechanism of this translocation is not well understood: the protein RFT1 is known to be involved (Helenius et al. 2002), along with an unknown flippase, which is distinct from the one that flips the Dol-P linked precursors (Dol-P-Mannose and Dol-P-glucose) (Sanyal et al. 2008). Defects in RFT1 are associated with Congenital Disorder of Glycosylation 1N (CDG1N) (Haeuptle et al. 2008).
The sixth mannose is added to the N-glycan precursor. This reaction occurs in the ER lumen and uses a different mannose donor (dolichyl-phosphate-mannose) than the previous steps. It has been proposed that ALG3, along with all the mannosyl- and glucosyltransferases in the N-glycan biosynthesis pathway that use dolichyl-phosphate-mannose or dolichyl-phosphate-glucose as donor, derive from duplications of a common ancestral enzyme (Oriol et al. 2002). Defects in ALG3 are associated with Congenital Disorder of Glycosylation 1D (CDG1D) (Sun et al. 2005).
The seventh mannose is added to the N-glycan precursor. This reaction occurs in the ER lumen and uses dolichyl phosphate D-mannose as the mannose donor with ALG9 mediating the reaction. Defects in ALG9 are the cause of congenital disorder of glycosylation type 1L (CDG1L) (Frank CG et al, 2004; Weinstein M et al, 2005). For many years ALG9 has been thought to be involved in bipolar affective disorder (Baysal BE et al, 2002), but this hypothesis has been proven wrong (Baysal BE et al, 2006).
The second glucose (supplied from the donor dolichol-phosphate-glucose) is added to the N-glycan precursor, mediated by ALG8 (Schollen E et al, 2004). Defects in ALG8 are the cause of congenital disorder of glycosylation type 1H (CDG1H) (Schollen E et al, 2004; Sun L et al, 2005).
The first glucose is added to the N-glycan precursor, mediated by ALG6. Defects in ALG6 are associated with CDG-Ic disorder (Imbach T et al, 1999; Sun L et al, 2005). The donor is a dolichol-phosphate-glucose (synthesized by ALG5).
The last mannose is added to the N-glycan precursor. This reaction occurs in the ER lumen, uses Dolichyl phosphate D-mannose as the mannose donor, and is catalyzed by ALG9. Defects in ALG9 are the cause of congenital disorder of glycosylation type 1L (CDG1L) (Frank CG et al, 2004; Weinstein M et al, 2005). For many years ALG9 was thought to be involved in bipolar affective disorder (Baysal BE et al, 2002), but this hypothesis has been proven wrong (Baysal BE et al, 2006).
The eighth mannose is added to the N-glycan precursor. This reaction occurs in the ER lumen and uses dolichyl phosphate D-mannose as a mannose donor. Defects in ALG12 are the cause of congenital disorder of glycosylation type 1G (CDG1G) (Chantret I et al, 2002).
The ARE-dependent mRNA-destabilizing activity of BRF1 is regulated by protein kinase B
After the glycosylated precursor is attached to the protein, the outer alpha-1,2-linked glucose is removed by glucosidase I (MOGS, GCS1 in yeast). This is a mandatory step for the protein folding control and glycan extension, and defects in MOGS are associated with congenital disorder of glycosylation type IIb (CDGIIb) (De Praeter et al. 2000, Völker et al. 2002).
The enzyme ER Man I can slowly trim up to four of the mannoses on the N-glycan on unfolded proteins accumulated in the ER. This step describes the removal of the mannose in the B position (Gonzalez et al, 1999: Hirao et al, 2006).
The last glucose is added to the N-glycan precursor. This reaction occurs inside the ER lumen and uses Dol-P-Glc as the glucose donor. In yeast, this reaction is catalyzed by ALG10 (Burda P and Aebi M,1998); however, this gene is duplicated in primates (Ciccarelli FD et al, 2005; Table 1), leading to two homologues, ALG10A and ALG10B, and to date there is no clear evidence to say which of these two paralogues (or both) is responsible for catalyzing this reaction in humans. No Congenital Disorders of Glycosylations are known to be associated with either gene.
N-linked glycosylation commences with the 14-step synthesis of a dolichol lipid-linked oligosaccharide (LLO) consisting of 14 sugars (2 core GlcNAcs, 9 mannoses and 3 terminal GlcNAcs). This pathway is highly conserved in eukaryotes, and a closely related pathway is found in many eubacteria and Archaea. Mutations in the genes associated with N-glycan precursor synthesis lead to a diverse group of disorders collectively known as Congenital Disorders of Glycosylation (type I and II) (Sparks et al. 1993). The phenotypes of these disorders reflect the important role that N-glycosylation has during development, controlling the folding and the properties of proteins in the secretory pathway, and proteins that mediate cell-to-cell interactions or timing of development.
The enzyme ER Man I can slowly trim up to four of the mannoses on the N-glycan on unfolded proteins accumulated in the ER. This step describes the removal of the mannose in the C position (Hirao et al, 2006).
Proteins with major folding defects are extracted from futile folding cycles in the calnexin chaperone system and the ER Quality Control Compartment, and are translocated back to the citosol for degradation. The N-glycan is used as a signal to distinguish proteins to be degraded, upon recognition by EDEM1, EDEM2 and EDEM3, three ER-stress-induced members of the glycosyl hydrolase 47 family (see Olivari S, Molinari M 2007 for a review) and OS9 (Mikami K, 2010; Hosokawa N, 2009).
The enzymes UGGT1 and UGGT2 are able to distinguish proteins with minor folding defects in the ERQC and reglucosylate them, by adding a glucose on the alpha 1,3 branch (Arnold SM et al, 2000; Arnold SM et al, 2003). The major affinity of these enzymes for proteins with minor folding defects has been demonstrated, but the exact mechanism that enable them to distinguish proteins with major and minor defects is still unknown (Pearse BR et al, 2008).
The unfolded protein is recognized by a chaperon protein (calnexin or calreticulin) and the folding process starts. The binding of these protein requires a mono-glucosylated glycan (Caramelo JJ and Parodi AJ, 2008), but in certain cases can occur even in the absence of glycosylation (Ireland BS et al, 2008).
Proteins that are released from the CNX or CRT complex with folding defects accumulate in a compartment of the ER called ERQC (Kamhi-Nesher et al. 2001). Here, the enzymes UGGG1 or UGGG2 are able to recognize glycoproteins with minor folding process and re-add the glucose on the alpha,1,3 branch; this is a signal for the transport of these glycoproteins back to the ER, where they can interact again with CNX or CRT in order to achieve a correct folding. At the same time that the glycoprotein is in the ERQC, the enzyme ER mannosidase I progressively removes the mannoses in position 1A, 2A, B, C on N-glycans; when the mannose on 1A is trimmed, UGGG1/UGGG2 is no longer able to re-add the glucose, and therefore the protein is destined for degradation. For years it has been thought that the removal of the mannose in position B of the N-glycan was the signal to direct proteins to degradation. However, this mechanism has been described better by Avezov et al (Avezov et al. 2008) and it has been demonstrated that even glycoproteins with Man8 or Man7 glycans can be re-glucosylated and interact again with CNX or CRT. For a review on this topic, see Lederkremer 2009 and Maattanen P et al, 2010.
Removal of the second mannose on the alpha 1,3 branch (Frenzel Z et al, 2003).
The enzyme ER Man I can slowly trim up to four of the mannoses on the N-glycan on unfolded proteins accumulated in the ER. This step describes the removal of the mannose in the A position (Hirao et al, 2006; Frenkel et al, 2003).
After being synthesized in the ER membrane the 14-sugars lipid-linked oligosaccharide is co-translationally transferred to an unfolded protein, as described in the previous steps. After this point the N-glycan is progressively trimmed of the three glucoses and some of the mannoses before the protein is transported to the cis-Golgi. The role of these trimming reactions is that the N-glycan attached to an unfolded glycoprotein in the ER assume the role of 'tags' that direct the interactions of the glycoprotein with different elements that mediate its folding. The removal of the two outer glucoses leads to an N-glycan with only one glucose, which is a signal for the binding of either one of two chaperone proteins, calnexin (CNX) and calreticulin (CRT). These chaperones provide an environment where the protein can fold more easily. The interaction with these proteins is not transient and is terminated by the trimming of the last remaining glucose, after which the glycoprotein is released from CNX or CRT and directed to the ER Quality Control compartment (ERQC) if it still has folding defects, or transported to the Golgi if the folding is correct. The involvement of N-glycans in the folding quality control of proteins in the ER explains why this form of glycosylation is so important, and why defects in the enzymes involved in these reactions are frequently associated with congenital diseases. However, there are many unknown points in this process, as it is known that even proteins without N-glycosylation sites can be folded properly (Caramelo JJ and Parodi AJ, 2008).
Sar1p-GTP recruits the cytoplasmic Sec23p-Sec24p complex. Though not represented in the subsequent steps, Sec23p-Sec24p would bind to members of the p24 protein family of possible cargo receptors, and together with Sar1p bind the appropiate v-SNARE, and Rab-GTP.
Sar1p-GTP hydrolysis is increased 15-30-fold by Sec23p. Sar1p-GDP is released as a result of this hydrolysis and used in further vesicle sculpting cycles. Sar1p-GTP hydrolysis occurs at two critical points during the cycle, first (as represented here) as a proofreading step, insuring that the cargo is loaded. Later in the cycle Sar1p-GTP hydrolysis triggers the uncoating of the budded vesicle.
Cyclin A- and cyclin E-Cdk complexes shuttle between the nucleus and the cytoplasm
Cytosolic Sec13p-Sec31p complexes bind to pre-bound Sec23p-Sec24p complexes.
The SUMO1 precursor has 4 extra residues at the C-terminus which can be removed endoproteolytically by either SENP1, SENP2, or SENP5 (Zheng and Au, 2005, Mikolajczyk et al. 2007). The order of processing activity is: SENP1 greater than SENP2 greater than SENP5 (Mikolajczyk et al. 2007). Both SENP1 and SENP2 shuttle between the nucleus and cytoplasmic and both are predominantly nucleoplasmic (Bailey and O'Hare 2004, Kim et al. 2005, Zhang et al. 2002, Hang and Dasso 2002, Itahana et al. 2006).
N-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley et al. 2009). An early study in 1999 revealed that about 50% of the proteins in the Swiss-Prot database at the time were N-glycosylated (Apweiler et al. 1999). It is now established that the majority of the proteins in the secretory pathway require glycosylation in order to achieve proper folding. The addition of an N-glycan to a protein can have several roles (Shental-Bechor & Levy 2009). First, glycans enhance the solubility and stability of the proteins in the ER, the golgi and on the outside of the cell membrane, where the composition of the medium is strongly hydrophilic and where proteins, that are mostly hydrophobic, have difficulty folding properly. Second, N-glycans are used as signal molecules during the folding and transport process of the protein: they have the role of labels to determine when a protein must interact with a chaperon, be transported to the golgi, or targeted for degradation in case of major folding defects. Third, and most importantly, N-glycans on completely folded proteins are involved in a wide range of processes: they help determine the specificity of membrane receptors in innate immunity or in cell-to-cell interactions, they can change the properties of hormones and secreted proteins, or of the proteins in the vesicular system inside the cell. All N-linked glycans are derived from a common 14-sugar oligosaccharide synthesized in the ER, which is attached co-translationally to a protein while this is being translated inside the reticulum. The process of the synthesis of this glycan, known as Synthesis of the N-glycan precursor or LLO, constitutes one of the most conserved pathways in eukaryotes, and has been also observed in some eubacteria. The attachment usually happens on an asparagine residue within the consensus sequence asparagine-X-threonine by an complex called oligosaccharyl transferase (OST). After being attached to an unfolded protein, the glycan is used as a label molecule in the folding process (also known as Calnexin/Calreticulin cycle) (Lederkremer 2009). The majority of the glycoproteins in the ER require at least one glycosylated residue in order to achieve proper folding, even if it has been shown that a smaller portion of the proteins in the ER can be folded without this modification. Once the glycoprotein has achieved proper folding, it is transported via the cis-Golgi through all the Golgi compartments, where the glycan is further modified according to the properties of the glycoprotein. This process involves relatively few enzymes but due to its combinatorial nature, can lead to several millions of different possible modifications. The exact topography of this network of reactions has not been established yet, representing one of the major challenges after the sequencing of the human genome (Hossler et al. 2006). Since N-glycosylation is involved in an great number of different processes, from cell-cell interaction to folding control, mutations in one of the genes involved in glycan assembly and/or modification can lead to severe development problems (often affecting the central nervous system). All the diseases in genes involved in glycosylation are collectively known as Congenital Disorders of Glycosylation (CDG) (Sparks et al. 2003), and classified as CDG type I for the genes in the LLO synthesis pathway, and CDG type II for the others.
Receptor-mediated endocytosis of cobalamin (vitamin B12)
At least two mechanisms of transport of proteins from the ER to the Golgi have been described. One is a general flow requiring no export signals (Wieland et al, 1987; Marti­nez-Menarguez et al, 1999). The other is mediated by LMAN1/MCFD2, mannose-binding lectins that recognize a glycan signal (Zhang B et al, 2003).
Secretory cargo destined to be secreted or to arrive at the plasma membrane (PM) leaves the ER via distinct exit sites. This cargo is destined for the Golgi apparatus.
COPII components (known as Sec13p, Sec23p, Sec24p, Sec31p, and Sar1p in yeast) traffic cargo from the endoplasmic reticulum to the Golgi apparatus. COPII-coated vesicles were originally discovered in the yeast Saccharomyces cerevisiae using genetic approaches coupled with a cell-free assay. The mammalian counterpart of this pathway is represented here. Newly synthesized proteins destined for secretion are sorted into COPII-coated vesicles at specialized regions of the ER. These vesicles leave the ER, become uncoated and subsequently fuse with the Golgi apparatus membrane.
Vesicle uncoating is triggered by Sar1p-GTP hydrolysis leaving only the vesicle cargo and the v-SNARE to target the vesicle to the Golgi membrane.
Once loaded the vesicles become fully sculpted, pinch off from the ER and bud into the cytosol.
Components and dynamics of DNA replication complexes in S. cerevisiae: redistribution of MCM proteins and Cdc45p during S phase.
Nucleocytoplasmic shuttling modulates activity and ubiquitination-dependent turnover of SUMO-specific protease 2
SUMO1, 2, and 3 are initially expressed as propeptides containing extra residues at the C-terminus. (SUMO1 has 4 residues, SUMO2 has 2 residues, and SUMO3 has 11 residues,) SENP1, 2, and 5 are endoproteases that process the precursors to produce the mature peptides (reviewed in Wang and Dasso 2009, Wilkinson and Henley 2010, Hannoun et al. 2010, Gareau and Lima 2010). SENP1 processes SUMO1 with greater efficiency than SUMO2 or SUMO3. SENP2 and SENP5 process SUMO2 with greater efficiency than SUMO1 or SUMO3 (Gong and Yeh 2006, Mikolajczyk et al. 2007). SENP1 shuttles between the cytosol and nuceoplasm and is predominantly nuclear (Bailey and O'hare 2004, Kim et al. 2005). SENP2 also shuttles (Itahana et al. 2006) and is mainly located on nucleoplasmic filaments of the nuclear pore complex (Hang and Dasso 2002, Zhang et al. 2002). SENP5 is located mostly in the nucleolus (Di Bacco et al. 2006, Gong and Yeh 2006).
The SUMO2 precursor has 2 extra residues at the C-terminus which can be removed endoproteolytically by SENP1, SENP2, or SENP5 (Zheng and Au, 2005, Gong and Yeh 2006, Mikolajczyk et al. 2007). The order of processing activity is: SENP1 greater than SENP2 greater than SENP5 (Mikolajczyk et al. 2007). SENP2 and SENP5 have highest activity on SUMO2, however the processing activity of SENP1 is higher overall (Mikolajczyk et al. 2007). SENP1 and SENP2 shuttle between the nucleus and cytosol and are predominantly nuclear (Bailey and O'Hare 2004, Kim et al. 2005, Zhang et al. 2002, Hang and Dasso 2002, Itahana et al. 2006). SENP5 is located in the nucleolus (Di Bacco et al. 2006, Gong and Yeh 2006).
The SUMO3 precursor has 11 extra residues at the C-terminus which can be removed endoproteolytically by SENP1, SENP2, or SENP5 (Zheng and Au, 2005, Gong and Yeh 2006, Mikolajczyk et al. 2007). The order of processing activity is: SENP1 greater than SENP2 greater than SENP5 (Mikolajczyk et al. 2007). Overall, processing of SUMO3 is the lowest of any SUMO (Mikolajczyk et al. 2007). SENP1 and SENP2 shuttle between the nucleus and cytosol and are predominantly nuclear (Bailey and O'Hare 2004, Kim et al. 2005, Zhang et al. 2002, Hang and Dasso 2002, Itahana et al. 2006). SENP5 is located in the nucleolus (Di Bacco et al. 2006, Gong and Yeh 2006).
D-2-hydroxyglutaric acidaemia: identification of a new enzyme, D-2-hydroxyglutarate dehydrogenase, localized in mitochondria
Complex III releases superoxide to both sides of the inner mitochondrial membrane
Conservation of the Caenorhabditis elegans timing gene clk-1 from yeast to human: a gene required for ubiquinone biosynthesis with potential implications for aging
Human peroxiredoxin 5 is a peroxynitrite reductase
Regulation of origin recognition complex conformation and ATPase activity: differential effects of single-stranded and double-stranded DNA binding.
Mechanism of the eukaryotic chaperonin: protein folding in the chamber of secrets
Identification of two mammalian reductases involved in the two-carbon fatty acyl elongation cascade
Molecular cloning of a novel member of the eukaryotic polypeptide chain-releasing factors (eRF). Its identification as eRF3 interacting with eRF1.
The ERBB4/HER4 receptor tyrosine kinase regulates gene expression by functioning as a STAT5A nuclear chaperone
Human Na+ -coupled citrate transporter: primary structure, genomic organization, and transport function
Identification of human PMP34 as a peroxisomal ATP transporter
Genetic defects of folate and cobalamin metabolism
Association of the human SUMO-1 protease SENP2 with the nuclear pore
Mutations in COX15 produce a defect in the mitochondrial heme biosynthetic pathway, causing early-onset fatal hypertrophic cardiomyopathy
Aquaporins in the hepatobiliary tract. Which, where and what they do in health and disease
Telomere C-strand (Lagging Strand) Synthesis
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CCNB:p-T14-CDK1 (name copied from entity in Homo sapiens)
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CCNB:CDK1 (name copied from entity in Homo sapiens)
RNA primer-DNA primer:origin duplex with DNA damage (name copied from entity in Homo sapiens)
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MAD2*CDC20 complex (name copied from entity in Homo sapiens)
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Cyclin B:Cdk1 complex (name copied from entity in Homo sapiens)
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Multiple forms of an inositol polyphosphate 5-phosphatase form signaling complexes with Shc and Grb2
Cyclin B1:phospho-Cdc2 ( Thr 14) (name copied from entity in Homo sapiens)
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RNA primer-DNA primer:origin duplex:PCNA (name copied from entity in Homo sapiens)
phospho-Cdc25C:14-3-3 protein complex (name copied from entity in Homo sapiens)
Ub-p-S123-CDC25A (name copied from entity in Homo sapiens)
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Structural relationships and the classification of aminoacyl-tRNA synthetases
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Redox-dependent regulation of the conformation and function of human heat shock factor 1
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Enzymatic activities of the human AGPAT isoform 3 and isoform 5: localization of AGPAT5 to mitochondria
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Localization of MCM2-7, Cdc45, and GINS to the site of DNA unwinding during eukaryotic DNA replication
PMP70, the 70-kDa peroxisomal membrane protein: a member of the ATP-binding cassette transporters
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Reverse transcriptase motifs in the catalytic subunit of telomerase
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Identification, purification, and partial characterization of a novel Mr 28,000 integral membrane protein from erythrocytes and renal tubules
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Cell cycle-regulated trafficking of human telomerase to telomeres
ChEBI:58548 S-methyl-5-thio-D-ribulose 1-phosphate(2?)
S-methyl-5-thio-D-ribulose 1-phosphate(2?)
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Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways
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A novel PtdIns3P and PtdIns(3,5)P2 phosphatase with an inactivating variant in centronuclear myopathy
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Structure/function studies of human beta-cell glucokinase. Enzymatic properties of a sequence polymorphism, mutations associated with diabetes, and other site-directed mutants.
Molecular basis of signaling specificity of insulin and IGF receptors: neglected corners and recent advances
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Note: the coordinates are copied over from Homo sapiens.
Isocitrate dehydrogenase 2 (NADP), mitochondrial
Isocitrate dehydrogenase (NAD) subunit alpha, mitochondrial precursor
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The eEF1B complex binds to eEF1A and regulates its activity by catalyzing the release of GDP. Subsequently, GTP is able to bind eEF1A allowing the formation of the ternary complex (eEF1A-GTP-aa-tRNA).In metazoans eEF1 protein family is composed of four subunits: eEF1A and eEF1B alpha, beta, and gamma (formerly EF-1alpha, EF-1beta, EF-1delta, and EF-1gamma, respectively). Both eEF1B alpha and eEF1B beta function as nucleotide exchange proteins. eEF1B gamma associates with eEF1B alpha and stimulates its exchange activity. This process is illustrated below with a GTP molecule in white and eEF1A protein in yellow.The three subunits of eEF1B are also shown.
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At the beginning of this reaction, 1 molecule of 'eEF2', and 1 molecule of 'GTP' are present. At the end of this reaction, 1 molecule of 'eEF2:GTP' is present. This reaction takes place in the 'cytosol'.
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The mechanism of a peptide bond requires the movement of three protons. First the deprotonation of the ammonium ion generates a reactive amine, allowing a nucleophilic attack on the carbonyl group. This is followed by the loss of a proton from the reaction intermediate, only to be taken up by the oxygen on the leaving group (from the end of the amino acid chain bound to the tRNA in the P-site). The peptide bond formation results in the net loss of one water molecule, leaving a deacylated-tRNA in the P-site, and a nascent polypeptide chain one amino acid larger in the A-site. For the purpose of illustration, the figures used in the section show one amino acid being added to a peptidyl-tRNA with a growing peptide chain.
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The A- and P-sites of the ribosome positions the aa-tRNA and peptidyl-tRNA such that a nucleophilic attack can occur between the amine group of the A-site aa-tRNA and the carbonyl group of the growing peptide chain on the P-site tRNA, resulting in the formation of a peptide bond. The carboxyl end of the peptide chain is uncoupled from the tRNA molecule in the P-site and forms a new peptide bond with the amino acid that is in the A-site. This process is illustrated below with: a peptidyl-tRNA with a growing peptide,a deacylated tRNA with an -OH and a ribosome with A,P and E sites to accommodate these three forms of tRNA.
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Following peptide bond formation, GTP-bound eEF2 catalyzes the translocation of the deacylated tRNA in the P-site and the peptidyl-tRNA in the A-site (the pre-translocation state) into the E- and P- sites (the post-translocation state), respectively. Thus, the mRNA advances by three bases to expose the next codon in the A-site. After translocation, GDP-bound eEF2 leaves the ribosome to allow another round of elongation. eEF2 is reactivated by the release of GDP and binds GTP for subsequent rounds. This process is illustrated below with a peptidyl-tRNA with a growing peptide, a deacylated tRNA with an -OH and a ribosome with A,P and E sites to accommodate these three forms of tRNA is also shown.
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Once the correct codon-anticodon match occurs between the mRNA and aa-tRNA, the decoding event triggers GTP hydrolysis on eEF1A. The resulting conformational change releases the aa-tRNA to the A-site, and GDP bound form eEF1A is released from the ribosome. Insight into the mechanics of this system has been obtained from earlier works with rabbit reticulocytes and the E.coli system. This process is illustrated below with: an amino acyl-tRNA with an amino acid, a peptidyl-tRNA with a growing peptide and a ribosome with A,P and E sites to accommodate these two forms of tRNA.
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Once the correct codon-anticodon match occurs between the mRNA and aa-tRNA, the decoding event triggers GTP hydrolysis on eEF1A. The resulting conformational change releases the aa-tRNA to the A-site, and GDP bound form of eEF1A is released from the ribosome. This process is illustrated below with: an amino acyl-tRNA with an amino acid,a peptidyl-tRNA with a growing peptide and a ribosome with A,P and E sites to accommodate these two forms of tRNA.
The cycle of elongation starts with an empty ribosomal A-site and the peptidyl-tRNA in the P-site. eEF1A is activated by GTP binding and allows for the subsequent binding of aminoacyl-tRNA (aa-tRNA).This process is illustrated below with a GTP molecule in white and eEF1A protein in yellow.
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The binding of eEF1A:GTP to aminoacyl tRNA (aa-tRNA) results in the formation of a ternary complex (eEF1A:GTP:aa-tRNA). Human eEF1A and rabbit eEF1A are 100% identical, and prokaryotic homologue of eEF1A (EF-Tu) shows 59% identity in the GTP-binding domain.This process is illustrated below with: a GTP molecule in white and eEF1A protein in yellow.
Citrate synthase, mitochondrial precursor
Phosphate incorporation during glycogen synthesis and Lafora disease
The process for translation of a protein destined for the endoplasmic reticulum (ER) branches from the canonical cytoslic translation process at the point when a nascent polypeptide containing a hydrophobic signal sequence is exposed on the surface of the cytosolic ribosome:mRNA:peptide complex. The signal sequence mediates the interaction of this complex with a cytosolic signal recognition particle (SRP) to form a complex which in turn docks with an SRP receptor complex on the ER membrane. There the ribosome complex is transferred from the SRP complex to a translocon complex embedded in the ER membrane and reoriented so that the nascent polypeptide protrudes through a pore in the translocon into the ER lumen. Translation, which had been halted by SRP binding, now resumes, the signal peptide is cleaved from the polypeptide, and elongation proceeds, with the growing polypeptide oriented into the ER lumen.
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Isocitrate dehydrogenase (NAD) subunit gamma, mitochondrial precursor
Isocitrate dehydrogenase (NAD) subunit beta, mitochondrial precursor
Aconitate hydratase, mitochondrial precursor
Dihydrolipoamide dehydrogenase, mitochondrial
Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex
Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor
70 kDa mitochondrial autoantigen of primary biliary cirrhosis
Biosynthesis of delta-aminolevulinic acid and the regulation of heme formation by immature erythroid cells in man
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Many cuts to ruin: a comprehensive update of caspase substrates
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Phosphorylation of Gz in human platelets. Selectivity and site of modification
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Protein synthesis is accomplished through the process of translation of an mRNA sequence into a polypeptide chain. This process can be divided into three distinct stages: initiation, elongation and termination. During the initiation phase, the two subunits of the ribosome are brought together to the translation start site on the mRNA where the polypeptide chain is to begin. Extension of the polypeptide chain occurs when a specific aminoacyl-tRNA, as determined by the template mRNA, binds an elongating ribosome. The protein chain is released from the ribosome when any one of three stop codons in the relevant reading frame on the mRNA is reached. Individual reactions at each one of these stages are catalyzed by a number of initiation, elongation and release factors, respectively.
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Gene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are processed. Most annotation is centered on the generation of messenger RNAs (mRNAs) by regulated RNA polymerase II (PolII) transcription, although the activities of PolI and PolIII are also covered briefly, as are some aspects of microRNA generation and function. Aspects of mRNA synthesis annotated here include the assembly of transcription factor complexes and their role in targeting specific genes for transcription, PolII-mediated transcription (RNA synthesis) itself, and the co- and post-translational processing of this RNA, via capping, splicing, and 3'-cleavage and polyadenylation to yield mature mRNA molecules that are exported from the nucleus. mRNA editing and nonsense-mediated decay are also annotated. Processes leading to mRNA breakdown are described: deadenylation-dependent mRNA decay, microRNA-mediated RNA cleavage, and regulation of mRNA stability by proteins that bind AU-rich elements. Other pathways included here are tRNA aminoacylation and snRNP assembly.
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Many biosynthetic reactions are coupled to the cleavage of ATP to yield AMP and pyrophosphate. These reactions are typically freely reversible when carried out with purified substrates and enzymes in vitro. In vivo, however, the pyrophosphate is rapdily and essentially irreversibly hydrolyzed by a ubiquitous inorganic pyrophosphatase. This hydrolysis has the effect of pulling the first reaction strongly in the direction of biosynthesis, at the expense of two high-energy phosphate bonds. Studies of human cells have identified two forms of the enzyme, one localized to the cytosol and the other to the mitochondrial matrix (Raja et al. 1981).
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During the synthesis of actin and tubulin, the nascent ribosome-associated chains bind to the heteromeric chaperone protein, prefoldin (PFD) (Hansen et al., 1999).
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Please note that this reaction was inferred from experiments performed using Saccharomyces cerevisiae.
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The arrival of any of the three stop codons (UAA, UAG and UGA) into the ribosomal A-site triggers the binding of a release factor (RF) to the ribosome and subsequent polypeptide chain release. In eukaryotes, the RF is composed of two proteins, eRF1 and eRF3. eRF1 is responsible for the hydrolysis of the peptidyl-tRNA, while eRF3 provides a GTP-dependent function. The ribosome releases the mRNA and dissociates into its two complex subunits, which can reassemble on another molecule to begin a new round of protein synthesis. It should be noted that at present, there is no factor identified in eukaryotes that would be the functional equivalent of the bacterial ribosome release (or recycling) factor, RRF, that catalyzes dissociation of the ribosome from the mRNA following release of the polypeptide
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At the beginning of this reaction, 1 molecule of 'eEF1B alpha', 1 molecule of 'eEF1B gamma', and 1 molecule of 'eEF1B beta' are present. At the end of this reaction, 1 molecule of 'eEF1B complex' is present. This reaction takes place in the 'cytosol'.
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The translation elongation cycle adds one amino acid at a time to a growing polypeptide according to the sequence of codons found in the mRNA. The next available codon on the mRNA is exposed in the aminoacyl-tRNA (aa-tRNA) binding site (A site) on the 30S subunit. A: Ternary complexes of aa -tRNA:eEF1A:GTP enter the ribosome and enable the anticodon of the tRNA to make a codon/anticodon interaction with the A-site codon of the mRNA. B: Upon cognate recognition, the eEF1A:GTP is brought into the GTPase activating center of the ribosome, GTP is hydrolyzed and eEF1A:GDP leaves the ribosome. C: The peptidyl transferase center of ribosome catalyses the formation of a peptide bond between the incoming amino acid and the peptide found in the peptidyl-tRNA binding site (P site). D: In the pre-translocation state of the ribosome, the eEF2:GTP enters the ribosome, physically translocating the peptidyl-tRNA out of the A site to P site and leaves the ribosome eEF2:GDP. This action of eEF2:GTP accounts for the precise movement of the mRNA by 3 nucleotides.Consequently, deacylated tRNA is shifted to the E site. A ribosome associated ATPase activity is proposed to stimulate the release of deacylated tRNA from the E site subsequent to translocation (Elskaya et al., 1991). In this post-translocation state, the ribosome is now ready to receive a new ternary complex. This process is illustrated below with: an amino acyl-tRNA with an amino acid, a peptidyl-tRNA with a growing peptide, a deacylated tRNA with an -OH, and a ribosome with A,P and E sites to accommodate these three forms of tRNA.
Pyruvate dehydrogenase E1 component beta subunit, mitochondrial precursor
pyruvate dehydrogenase E1 beta apoprotein
pyruvate dehydrogenase E1 alpha apoprotein
Pyruvate dehydrogenase E1 component alpha subunit, somatic form, mitochondrial precursor
Identification of the gene responsible for methylmalonic aciduria and homocystinuria, cblC type
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The 80S ribosome bound to the mRNA moves along the mRNA molecule from its initial site to the initiation codon and forms a 48S complex, in which the initiation codon is base paired to the anticodon of the Met-tRNAi. Proper recognition of the AUG initiation codon depends on base pairing with the anticodon of the Met-tRNAi and requires eIF1, eIF1A, eIF2 and eIF5.
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The AUG initiation codon in the mRNA is recognized by base pairing with the anticodon of the Met-tRNAi. This reaction requires eIF1, eIF1A, eIF2 and eIF5.
Reviews in molecular biology and biotechnology: transmembrane signaling by G protein-coupled receptors
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The mRNA-bound ribosomal complex moves along the 5'-untranslated region (5'-UTR) of the mRNA from its initial site to the initiation codon to form a 48S complex, in which the initiation codon (AUG) is base paired to the anticodon of the Met-tRNAi. It is not known whether eIF4A (or another ATPase, such as DED1) facilitates scanning by melting mRNA secondary structures or by actively propelling the ribosome.
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The ternary complex forms upon binding of the initiator methionyl-tRNA to the active eIF2:GTP complex.
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The ternary complex (Met-tRNAi:eIF2:GTP) binds to the complex formed by the 40S subunit, eIF3 and eIF1A, to form the 43S complex. eIF1A promotes binding of the ternary complex to the 40S subunit within 43S. The initiator methionyl-tRNA from the ternary complex is positioned at the ribosomal P site.
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Activation of eIF2 through direct binding of GTP.
Insulin-responsive human adipocytes express two glucose transporter isoforms and target them to different vesicles
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The factor eIF4E within the eIF4F (cap-binding) complex directly binds the 5'-cap on eukaryotic mRNAs. Note that the mRNA is in complex with cytoplasmic proteins constituting an mRNP complex.
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The cap-binding complex is constituted by the initiation factors eIF4A, eIF4G and eIF4E. First, eIF4E must be released from the inactive eIF4E:4E-BP complex. Then eIF4A interacts with eIF4G, and eIF4E binds to the amino-terminal domain of eIF4G, resulting in the formation of the cap-binding complex eIF4F. eIF4A together with eIF4B or eIF4H is thought to unwind RNA secondary structures near the 5'-end of the mRNA. The translation initiation complex is formed when the 43S complex binds the cap-bound mRNA.
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Binding of the methionyl-tRNA initiator to the active eIF2:GTP complex results in the formation of the ternary complex. Subsequently, this Met-tRNAi:eIF2:GTP (ternary) complex binds to the complex formed by the 40S subunit, eIF3 and eIF1A, to form the 43S complex.
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eIF4A interacts with eIF4G, and eIF4E interacts with the amino-terminal domain of eIF4G to form the cap-binding complex eIF4F.
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Identification and characterization of human glucose transporter-like protein-9 (GLUT9): alternative splicing alters trafficking
Glucose-sensing mechanisms in pancreatic beta-cells
Philos Trans R Soc Lond B Biol Sci 360:2211-25
ADP,ATP carrier protein, liver isoform T2
Ubiquinone biosynthesis protein COQ7 homolog
2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial ecNumber2.1.1.201/ecNumber
ADP,ATP carrier protein, fibroblast isoform
ADP,ATP carrier protein, heart/skeletal muscle isoform T1
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The SRP receptor in the the endoplasmic reticulum (ER) membrane binds via its alpha subunit to the the SRP54 subunit of the Signal Recognition Particle (SRP), which itself is bound to a ribosome:mRNA:polypeptide complex. This interaction tethers the ribosome to the ER membrane, oriented so that the nacent polypeptide will traverse the ER membrane and enter the ER lumen. This process has been characterized in detail in cultured canine cells; this human event is inferred by homology from its canine counterpart.
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The synthesis of a protein destined for the endoplasmic reticulum starts with the canonical events of cytosolic translation initiation and proceeds to the point where a nascent polypeptide chain containing a signal sequence protrudes from the mRNA:ribosome complex. Merrick (2010) provides an overview of these events.
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Once the 60S subunit joins the translation initiation complex, eIF5B hydrolyzes its GTP and is released from the now 80S monosome. The fully assembled 80s ribosome is now ready to start elongation of the polypeptide chain.
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Joining of the 60S subunit to form the 80S ribosome is catalyzed by the presence of GTP-bound eIF5B.
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Hydrolysis of eIF2-GTP occurs after the Met-tRNAi has recognized the AUG. This reaction is catalyzed by eIF5 (or eIF5B) and is thought to cause dissociation of all other initiation factors and allow joining of the large 60S ribosomal subunit. The 60S subunit joins - a reaction catalyzed by eIF5 or eIF5B - resulting in a translation-competent 80S ribosome. Following 60S subunit joining, eIF5B hydrolyzes its GTP and is released from the 80S ribosome, which is now ready to start elongating the polypeptide chain.
Inactive eIF2:GDP binds eIF2B to form an eIF2:GDP:eIF2B intermediate.
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eIF2B is a guanine nucleotide releasing factor that is required to cause GDP release so that a new GTP molecule can bind and activate eIF2, so that it can be reused.
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The active eIF2:GTP complex may be formed by direct binding of GTP to free eIF2 or by GDP-GTP exchange on the eIF2:GDP:eIF2B complex. The eIF2:GDP complex binds eIF2B forming an eIF2:GDP:eIF2B intermediate complex. eIF2B is a guanine nucleotide releasing factor required to cause GDP release so that a new GTP molecule can bind and activate eIF2. Phosphorylated eIF2:GDP sequesters all eIF2B as an inactive complex, and thus, reuse of eIF2 is inhibited as a consequence of the tight bond it forms with eIF2B, which prevents nucleotide exchange. Therefore, in the absence of free eIF2B, excess eIF2 remains in its inactive GDP-bound form and protein synthesis slows dramatically.
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Translation initiation is a complex process in which the Met-tRNAi initiator, 40S, and 60S ribosomal subunits are assembled by eukaryotic initiation factors (eIFs) into an 80S ribosome at the start codon of an mRNA. The basic mechanism for this process can be described as a series of five steps: 1) formation of a pool of free 40S subunits, 2) formation of the ternary complex (Met-tRNAi/eIF2/GTP), and subsequently, the 43S complex (comprising the 40S subunit, Met-tRNAi/eIF2/GTP, eIF3 and eIF1A), 3) activation of the mRNA upon binding of the cap-binding complex eIF4F, and factors eIF4A, eIF4B and eIF4H, with subsequent binding to the 43S complex, 4) ribosomal scanning and start codon recognition, and 5) GTP hydrolysis and joining of the 60S ribosomal subunit.
A J-protein is an essential subunit of the presequence translocase-associated protein import motor of mitochondria
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Initiation of translation in the majority of eukaryotic cellular mRNAs depends on the 5'-cap (m7GpppN) and involves ribosomal scanning of the 5' untranslated region (5'-UTR) for an initiating AUG start codon. Therefore, this mechanism is often called cap-dependent translation initiation. Proximity to the cap, as well as the nucleotides surrounding an AUG codon, influence the efficiency of the start site recognition during the scanning process. However, if the recognition site is poor enough, scanning ribosomal subunits will ignore and skip potential starting AUGs, a phenomenon called leaky scanning. Leaky scanning allows a single mRNA to encode several proteins that differ in their amino-termini. Merrick (2010) provides an overview of this process and hghlights several features of it that remain incompletely understood. Several eukaryotic cell and viral mRNAs initiate translation by an alternative mechanism that involves internal initiation rather than ribosomal scanning. These mRNAs contain complex nucleotide sequences, called internal ribosomal entry sites, where ribosomes bind in a cap-independent manner and start translation at the closest downstream AUG codon. Initiation on several viral and cellular mRNAs is cap-independent and is mediated by binding of the ribosome to internal ribosome entry site (IRES) elements. These elements are often found in characteristically long structured regions on the 5'-UTR of an mRNA that may or may not have regulatory upstream open reading frames (uORFs). Both of these features on the 5'-end of the mRNA hinder ribosomal scanning, and thus promote a cap-independent translation initiation mechanism. IRESs act as specific translational enhancers that allow translation initiation to occur in response to specific stimuli and under the control of different trans-acting factors, as for example when cap-dependent protein synthesis is shut off during viral infection. Such regulatory elements have been identified in the mRNAs of growth factors, protooncogenes, angiogenesis factors, and apoptosis regulators, which are translated under a variety of stress conditions, including hypoxia, serum deprivation, irradiation and apoptosis. Thus, cap-independent translational control might have evolved to regulate cellular responses in acute but transient stress conditions that would otherwise lead to cell death, while the same mechanism is of major importance for viral mRNAs to bypass the shutting-off of host protein synthesis after infection. Encephalomyocarditis virus (EMCV) and hepatitis C virus exemplify two distinct mechanisms of IRES-mediated initiation. In contrast to cap-dependent initiation, the eIF4A and eIF4G subunits of eIF4F bind immediately upstream of the EMCV initiation codon and promote binding of a 43S complex. Accordingly, EMCV initiation does not involve scanning and does not require eIF1, eIF1A, and the eIF4E subunit of eIF4F. Nonetheless, initiation on some EMCV-like IRESs requires additional non-canonical initiation factors, which alter IRES conformation and promote binding of eIF4A/eIF4G. Initiation on the hepatitis C virus IRES is simpler: a 43S complex containing only eIF2 and eIF3 binds directly to the initiation codon as a result of specific interaction of the IRES and the 40S subunit.
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Ubiquinone biosynthesis monooxygenase COQ6 ecNumber1.14.13.-/ecNumber
Hexaprenyldihydroxybenzoate methyltransferase, mitochondrial ecNumber2.1.1.114/ecNumber
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Aggregation states of mitochondrial malate dehydrogenase
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Genomic basis of mucopolysaccharidosis type IIID (MIM 252940) revealed by sequencing of GNS encoding N-acetylglucosamine-6-sulfatase
Glycosylphosphatidyl inositol (GPI) acts as a membrane anchor for many cell surface proteins. GPI is synthesized in the endoplasmic reticulum. In humans, a single pathway consisting of eleven reactions appears to be responsible for the synthesis of the major GPI species involved in membrane protein anchoring. As a nascent protein fated to become GPI-anchored moves into the lumen of the endoplasmic reticulum, it is attacked by a transamidase complex that cleaves it near its carboxy terminus and attaches an acylated GPI moiety. The GPI moiety is deacylated, yielding a protein-GPI conjugate that can be efficiently transported to the Golgi apparatus.
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Glycosylphosphatidyl inositol (GPI) acts as a membrane anchor for many cell surface proteins. GPI is synthesized in the endoplasmic reticulum. In humans, a single pathway consisting of nine reactions appears to be responsible for the synthesis of the major GPI species involved in membrane protein anchoring. This pathway is shown in the figure. Two additional reactions, not shown, allow the synthesis of variant forms of GPI, one with an additional mannose residue and one with an additional ethanolamine (Tauron et al. 2004; Shishioh et al. 2005). These variant GPI molecules may be used for tissue-specific protein modifications, or may function independently. The steps of GPI synthesis were first identified by isolating large numbers of mutant cell lines that had lost the ability to express GPI anchored proteins on their surfaces. Somatic cell hybrid analyses of these lines allowed the definition of complementation groups corresponding to distinct mutated genes, and cDNAs corresponding to normal forms of these genes were identified on the basis of their abilities to restore normal cell surface protein expression in mutant cells. Co-precipitation experiments with tagged cloned proteins have allowed the identification of additional proteins involved in GPI anchor biosynthesis.
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Most human GPI anchors have ethanolamine phosphate groups attached to their first and third mannose residues, but GPI anchors with ethanolamine phosphates attached to all three mannose residues have also been identified. Addition of the third ethanolamine phosphate can be catalyzed by a complex of PIG-F and a newly described human protein, GPI7. The donor of the ethanolamine phosphate for this reaction is unknown (Shishioh et al. 2005).
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The final step in the main pathway for the synthesis of GPI moieties in human cells is the addition of an ethanolamine phosphate to the third mannose residue of the glycolipid, donated by phosphatidylethanolamine. This reaction has been experimentally characterized in the mouse, where studies with mutated cell lines defective in GPI biosynthesis have established the role of two proteins, PIG-F and PIG-O, in this reaction (Hong et al. 2000). While a human PIG-F protein has been identified and shown to be involved in this event (Inoue et al. 1993), the human event has not been fully characterized and is therefore annotated here as inferred from studies of the mouse event.
Redox function of tetrahydrobiopterin and effect of L-arginine on oxygen binding in endothelial nitric oxide synthase
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In the eighth reaction of GPI synthesis, a third mannose residue is added, catalyzed by PIG-B (Takahashi et al. 1996).
Purification, characterization, and cDNA cloning of an AU-rich element RNA-binding protein, AUF1
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Dolichol is a polyisoprenol lipid comprised of five-carbon isoprene units linked linearly in a head-to-tail fashion. Almost all eukaryotic membranes contain dolichol and its phosphorylated form is used in the N-glycosylation of proteins where it is used as an anchor for the N-glycan sugar to the ER membrane, and as an initiation point for the synthesis. Dolichol biosynthesis occurs on the cytoplasmic face of the ER membrane, which is where N-glycosylation occurs too, so is perfectly placed to serve as a substrate for this process. Dolichyl phosphate can be obtained either from direct phosphorylation of dolichol, formed in a series of reactions from mevalonate 5-pyrophosphate, or a salvage reaction by de-phosphorylation of dolichyl diphosphate, released at the end of N-glycan biosynthesis (Cantagrel & Lefeber 2011).
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In the last step of the N-glycan precursor biosynthesis pathway, the mature N-glycan (Glc3Man9GlcNAc2) is removed from the dolichyl diphosphate (DOLDP) molecule upon which it has been synthesized and attached to a nascent protein. The released DOLDP molecule is de-phosphorylated by dolichyl diphosphatase 1 (DOLPP1) to dolichyl phosphate (DOLP). DOLP is thus salvaged and be used as substrate for the synthesis of another N-glycan oligosaccharide (Wedgwood & Strominger 1980).
Targeting, import, and dimerization of a mammalian mitochondrial ATP binding cassette (ABC) transporter, ABCB10 (ABC-me)
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Dolichol kinase (DOLK, TMEM15) mediates the phosphorylation of dolichol (DCHOL) to form dolichyl phosphate (DOLP) in the ER membrane (Fernandez et al. 2002). Defects in DOLK cause congenital disorder of glycosylation type 1M (CDG1M aka dolichol kinase deficiency; MIM:610768), a severe mutisystem disorder characterised by under-glycosylated serum glycoproteins which results in nervous system under-development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. Death occurs in early life (Kranz et al. 2007).
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The ER membrane-associated enzyme dehydrodolichyl diphosphate synthase (DHDDS) mediates the sequential head-to-tail cis addition of multiple isopentyl pyrophosphate (IPP) molecules to farnesyl pyrophosphate (E,E-FPP) to produce polyprenol pyrophosphate (pPPP) (Shridas et al. 2003). Dolichol in humans contain homologues ranging from 17-23 isoprene units, the most common homologues contain 19 or 20 isoprene units (Freeman et al. 1980). Defects in DHDDS cause retinitis pigmentosa 59 (RP59; MIM:613861), a pigment retinopathy, characterised by retinal pigment deposits (visible on fundus examination) and primary loss of rod photoreceptors followed by secondary loss of cone photoreceptors. Sufferers typically have night vision blindness and loss of mid to peripheral vision. As the condition progresses, they lose far peripheral vision and eventually central vision (Zuchner et al. 2011).
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Mevalonate pyrophosphate decarboxylase (MPD) decarboxylates mevalonate-5-pyrophosphate (MVA5PP) into isopentenyl pyrophosphate (IPPP) while hydrolysing ATP to ADP and orthophosphate (Toth & Huwyler 1996).
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Expression, characterization, and tissue distribution of a new cellular selenium-dependent glutathione peroxidase, GSHPx-GI
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Cytosolic UAP1 catalyzes the reaction of N-acetyl-D-glucosamine 1-phosphate (GlcNAc1P) and UTP to UDP-N-acetyl-D-glucosamine and pyrophosphate. Structural studies indicate that the active form of the enzyme is a dimer (Peneff C et al, 2001).
Cytosolic PGM3 catalyzes the isomerization of N-acetyl-D-glucosamine 6-phosphate (GlcNAc6P) to form N-acetyl-D-glucosamine 1-phosphate (GlcNAc1P) (Pang H et al, 2002).
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Mannose-6-phosphate isomerase (MPI) isomerizes fructose 6-phosphate (Fru6P) to mannose 6-phosphate (Man6P) (Proudfoot et al. 1994). Defects in this gene are associated with congenital disorder of glycosylation type 1B (CDG1B). Oral administration of mannose is an efficient therapy against this defect (Schollen et al. 2000).
UDP-acetylglucosamine acts as a donor for the first two steps of the N-glycan precursor biosynthesis pathway, and is later used as a substrate for further modifications after the precursor has been attached to the protein. It is synthesized from fructose 6-phosphate, glutamine, acetyl-CoA, and UTP in four steps.
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Cytosolic GNPNAT1 catalyzes the reaction of glucosamine 6-phosphate and acetyl-CoA to form N-acetyl-glucosamine 6-phosphate (GlcNAc6P) and CoA-SH. Structural studies indicate that the active form of the enzyme is a dimer (Wang J et al, 2008).
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Glucosamine-fructose 6-phosphate aminotransferases 1 and 2 (GFPT1,2) are the first and rate-limiting enzymes in the hexosamine synthesis pathway, and thus formation of hexosamines like N-acetylglucosamine (GlcNAc). These enzymes probably plays a role in limiting the availability of substrates for the N- and O- linked glycosylation of proteins (McKnight et al. 1992, Oki et al. 1999). GFPT1 and 2 are required for normal functioning of neuromuscular synaptic transmission. Defects in GFPT1 leads to altered muscle fibre morphology and impaired neuromuscular junction development (Senderek et al. 2011).
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Mannose 1-phosphate is converted to GDP-Mannose by mannose-1-phosphate guanyltransferase alpha and beta forms (GMPPA/B). This enzyme had originally been characterized from rat and bovine sources (Verachtert H et al, 1966) and more recently from pig (Ning B and Elbein AD, 2000).
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Phosphomannomutases 1 and 2 (PMM1 and PMM2) catalyze the isomerization of mannose 6-phosphate (Man6P) to mannose 1-phosphate (Man1P) in the cytosol of cells (Wada & Sakamoto 1997, Matthijs et al. 1997). Mutations in the PMM2 gene are one of the causes of Jaeken syndrome. a disease of glycosylation, type CDGIa. (Matthijs et al. 1997b).
The functional human dihydrofolate reductase gene
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Dolichyl-phosphate beta-glucosyltransferase (ALG5) associated with the endoplasmic reticulum (ER) membrane catalyzes the reaction of cytosolic UDP-glucose with dolichyl phosphate exposed on the cytosolic face of the ER membrane to form Dolichyl-P-glucose with its glucose moiety oriented toward the cytosol (Imbach T et al, 1999).
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GDP-mannose is the mannose donor for the first 5 mannose addition reactions in the N-glycan precursor synthesis, and also for the synthesis of Dolichyl-phosphate-mannose involved in other mannose transfer reactions. It is synthesized from fructose 6-phosphate and GTP in three steps.
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ChEBI:60125 N-epsilon-(1-(1-carboxy)ethyl)lysine
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The interaction between CCT and unfolded target proteins is thought to occur when CCT is in its ADP-bound state. ADP is then exchanged for ATP in CCT.
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Unfolded actins and tubulins bound to prefoldin are transferred to CCT via a docking mechanism (McCormack and Willison, 2001).
Unfolded actins and tubulins compete efficiently for binding to TriC/CCT and their chaperonin binding sites appear to be at least in part overlapping (Melki et al., 1993).
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Nucleotide-independent transfer of beta-actin from prefoldin to CCT occurs when prefoldin binds to CCT (Vainberg et al., 1998). Following ATP- dependent folding within CCT (Gao et al., 1992), beta-actin is released as a soluble, monomeric protein.
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TriC/CCT forms a binary complex with unfolded alpha- or beta-tubulin (Frydman et al., 1992; Gao et al., 1993). The tubulin folding intermediates produced by TriC are unstable (Gao et al., 1993). Five additional protein cofactors (cofactor A-E) are required for the generation of properly folded alpha- and beta-tubulin and for the formation of alpha/beta-tubulin heterodimers (Gao et al., 1993) (Tian et al., 1997, Cowan and Lewis 2001).
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Group II chaperonins enclose substrate proteins following substrate binding through the formation of a "built- in" lid over the central cavity. Upon ATP binding, lid formation is triggered by the transition state of ATP hydrolysis (Meyer, et al., 2003). In the case of CCT-mediated tubulin folding, one or more rounds of ATP hydrolysis are likely required before the association of non-exchangeable GTP with chaperonin-bound alpha tubulin.
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TRiC has broad recognition specificities, but in the cell it interacts with only a defined set of substrates (Yam et al. 2008). Many of its substrates that are targeted during biosynthesis are conserved between mammals and yeast (Yam et al. 2008).
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CCT/TRiC facilitates folding of newly translated SK1 into its mature active form (Zebol et al., 2008)
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In the case of actin and tubulin folding, and perhaps other substrates, the emerging polypeptide chain is transferred from the ribosome to TRiC via Prefoldin (Vainberg et al., 1998).
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Anoctamins are a family of Ca2+ activated Cl- channels
Heterotrimerization of heat-shock factors 1 and 2 provides a transcriptional switch in response to distinct stimuli
Due to the crowded envirnoment within the cell, many proteins must interact with molecular chaperones to attain their native conformation (reviewed in Young et al., 2004). Chaperones recognize and associate with proteins in their non-native state and facilitate their folding by stabilizing the conformation of productive folding intermediates. Chaperones that take part broadly in de novo protein folding, such as the Hsp70s and the chaperonins, facilitate the folding process through cycles of substrate binding and release regulated by their ATPase activity (see Young et al., 2004; Spiess et al., 2004; Bigotti and Clarke, 2008).
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The eukaryotic chaperonin TCP-1 ring complex (TRiC/ CCT) plays an essential role in the folding of a subset of proteins prominent among which are the actins and tubulins (reviewed in Altschuler and Willison, 2008). CCT/TRiC is an example of a type II chaperonin, defined (in contrast to type I) as functioning in the absence of a cochaperonin. TriC/CCT is a multisubunit toroidal complex that forms a cylinder containing two back-to-back stacked rings enclosing a cavity where substrate folding occurs in an ATP dependent process (reviewed in Altschuler and Willison, 2008 ). CCT/TriC contains eight paralogous subunits that are conserved throughout eukaryotic organisms (Leroux and Hartl 2000; Archibald et al. 2001; Valpuesta et al. 2002). CCT-mediated folding of non-native substrate protein involves capture through hydrophobic contacts with multiple chaperonin subunits followed by transfer of the protein into the central ring cavity where it folds. Although folding is initiated within this central cavity, only 5%-20% of proteins that are released have partitioned to the native state. The remaining portion is then recaptured by other chaperonin molecules (Cowan and Lewis 2001). This cycling process may be repeated multiple times before a target protein partitions to the native state. In the cell, binding to CCT occurs via presentation of target protein bound to upstream chaperones. During translation, the emerging polypeptide chain may be transferred from the ribosome to CCT via the chaperone Prefoldin (Vainberg et al., 1998) or the Hsp70 chaperone machinery (Melville et al., 2003). While the majority of CCT substrates ultimately partition to the native state as soluble, monomeric proteins, alpha and beta tubulin are unusual in that they require additional cofactors that are required to assemble the tubulin heterodimer (Cowan and Lewis 2001).
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The reaction of EIF5A, spermidine, and NAD+ to form EIF5A(Dhp), 1,3-diaminopropane, and NADH + H+ is reversible in vitro. Under physiological conditions, the reverse reaction is probably minimized by the rapid, irreversible conversion of FIF5A(Dhp) to EIF5A(Hyp).
Cytosolic deoxyhypusine synthase catalyzes the reaction of EIF5A protein, spermidine, and NAD+ to convert lysine-50 of EIF5A to deoxyhypusine, generating 1,3-diaminopropane and NADH + H+ in the process (Park 2006). Although the reaction is reversible, the reverse reaction is probably minimized under physiological conditions by the rapid, irreversible conversion of EIF5A(Dhp) to EIF5A(Hyp).
Cytosolic eIF5A undergoes a unique two-step post-translational modification at Lys 50 via deoxyhypusine (Dhp) to hypusine (Hyp). In the first step deoxyhypusine synthase transfers the aminobutyl group of spermidine to the epsilon-amino group of lysine 50, using NAD+ as a cofactor. Hydroxylation of the C2 of the newly added moiety in the second step is catalyzed by deoxyhypusine hydroxylase/monooxygenase with molecular oxygen as the source. The molecular function of eIF5A is unknown, but the protein is required for viability in eukaryotic cells and its normal function requires hypusinylation. eIF5A is the only protein known to undergo hypusinylation (Park 2006).
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Cytosolic deoxyhypusine hydroxylase catalyzes the irreversible conversion of peptidyl-deoxyhypusine to peptidyl-hypusine. The only known substrate for this enzyme is the modified lysine at residue 50 of eIF5A (Kang et al. 2007; Kim et al. 2006).
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In the second step of GPI synthesis, N-acetylglucosaminyl-PI is hydrolyzed to yield glucosaminyl-PI and acetate. The phosphatidylinositol (PI) derivatives involved in this reaction are located in the endoplasmic reticulum membrane, as is the PIG-L enzyme that catalyzes it (Sharma et al. 1999; Pottekat and Menon 2004).
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After translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the body. These modifications include the vitamin K-dependent attachment of carboxyl groups to glutamate residues and the conversion of lysine residues to hypusine.
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In the sixth step of GPI synthesis, a phosphoethanolamine group is transferred from phosphatidylethanolamine onto the first mannose of the GPI precursor. The human protein that catalyzes this reaction was first identified because it could complement a yeast mutant strain defective for GPI synthesis (Gaynor et al. 1999); its specific function in phosphoethanolamine transfer is inferred from functional studies of the homologous mouse protein (Hong et al. 1999). The reaction is annotated here with phosphatidylethanolamine as the donor of the phosphoethanolamine group on the basis of studies in yeast (Imhof et al. 2000).
In the fourth step of GPI synthesis, an acyl group (typically palmitate) is transferred from acyl CoA to glucosaminyl-PI. Mutagenesis and cloning studies suggest that a single protein, PIG-W, catalyzes this reaction (Murakami et al. 2003).
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Argonaute proteins: mediators of RNA silencing
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HDAC6 controls major cell response pathways to cytotoxic accumulation of protein aggregates
In vivo disposal of phenylalanine in phenylketonuria: a study of two siblings
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carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase
CAD protein (Includes: Glutamine-dependent carbamoyl-phosphate synthase (EC 6.3.5.5); Aspartate carbamoyltransferase (EC 2.1.3.2); Dihydroorotase (EC 3.5.2.3))
Glutamine-dependent carbamoyl-phosphate synthase
uridine monophosphate synthetase (orotate phosphoribosyl transferase and orotidine-5'-decarboxylase)
Uridine 5'-monophosphate synthase (UMP synthase) (Includes: Orotate phosphoribosyltransferase (EC 2.4.2.10) (OPRtase); Orotidine 5'- phosphate decarboxylase (EC 4.1.1.23) (OMPdecase))
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AMP deaminase 2 (EC 3.5.4.6) (AMP deaminase isoform L)
AMP deaminase 1 (EC 3.5.4.6) (Myoadenylate deaminase) (AMP deaminase isoform M)
Purine nucleoside phosphorylase (EC 2.4.2.1) (Inosine phosphorylase) (PNP)
AMP deaminase 3 (EC 3.5.4.6) (AMP deaminase isoform E) (Erythrocyte AMP deaminase)
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'NF-Y (name copied from entity in Homo sapiens) [nucleoplasm]' positively regulates 'Expression of BIP (78 kDa Glucose-regulated protein, GRP78, HSPA5)'
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Profiling of promoter occupancy by PPAR{alpha} in human hepatoma cells via ChIP-chip analysis
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MD-2: the Toll 'gatekeeper' in endotoxin signalling
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IMP (inosine monophosphate) dehydrogenase 1
Inosine-5'-monophosphate dehydrogenase 1 (EC 1.1.1.205) (IMP dehydrogenase 1) (IMPDH-I) (IMPD 1)
Inosine-5'-monophosphate dehydrogenase 1
Adenylosuccinate synthetase (EC 6.3.4.4) (IMP--aspartate ligase) (AdSS) (AMPSase)
AUF1 monomers form dimers which bind the U-rich sequences in AU-rich elements of mRNAs. Binding of the mRNA causes the dimers of AUF1 to form tetramers. Nonphosphorylated AUF1 isoform p40 causes the mRNA to form a rigid structure whereas p40 that is phosphorylated at serines 83 and 87 does not. This difference may cause nonphosphorylated p40 to fail to destabilize the bound mRNA.
In this module, the biology of various types of regulatory non-coding RNAs are described. Currently, biogenesis and functions of small interfering RNAs (siRNAs) and microRNAs are annotated.
Ubiquitin-dependent proteolysis of AUF1 and nuclease-dependent destruction of AUF1-bound mRNA are coupled in an unknown way. It is possible that ubiquitinated AUF1 targets other members of the AUF1 and signal transduction regulated complex (ASTRC), such as polyA-binding protein, for degradation and this renders the mRNA susceptible to nucleases.
AUF1 is ubiquitinated at unknown sites. The number of ubiquitin molecules conjugated to AUF1 and their linkage is unknown. Ubiquitination is required for subsequent degradation of both AUF1 and the mRNA bound by AUF1. It is uncertain if AUF1 is in a larger complex when it is ubiquitinated.
Biogenesis of microRNAs (miRNAs) can be summarized in five steps (reviewed in Ketting 2011, Nowotny and Yang 2009, Kim et al. 2009, Chua et al. 2009, Hannon and He 2004): 1. Transcription. miRNA transcripts may come from autonomously transcribed genes, they may be contained in cotranscripts with other genes, or they may be located in introns of host genes. Most miRNAs are transcribed by RNA polymerase II, however a few miRNAs originate as RNA polymerase III cotranscripts with neighboring repetitive elements. The initial transcript, termed a primary microRNA (pri-miRNA), contains an imperfectly double-stranded region within a hairpin loop. Longer sequences extend from the 5' and 3' ends of the hairpin and may also contain double-stranded regions. 2. Cleavage by Drosha. The 5' and 3' ends of the pri-miRNA are removed during endoribonucleolytic cleavage by the Drosha nuclease in a complex with the RNA-binding protein DGCR8 (the Microprocessor complex). The cleavage product is a short hairpin of about 60 to 70 nt called the pre-microRNA (pre-miRNA). 3. Nuclear export by Exportin-5. The resulting pre-miRNA is bound by Exportin-5 in a complex with Ran and GTP. The complex translocates the pre-miRNA through the nuclear pore into the cytoplasm. 4. Cleavage by Dicer. Once in the cytoplasm the pre-miRNA is bound and cleaved by the Dicer ribonuclease in complex with the RNA-binding protein TRBP (TAR binding protein). The product is an imperfectly double-stranded miRNA of about 21 to 23 nucleotides. At this stage the double-stranded miRNA has protruding single-stranded 3' ends of 2-3 nt. 5. Strand selection and incorporation into RNA-Induced Silencing Complex (RISC). At this stage the miRNA has two strands: the passenger strand, which will be removed and degraded, and the guide strand, which will be retained and guides the RISC to target mRNAs. An Argonaute protein is already bound to the Dicer:miRNA complex or subsequently binds the complex (the order is unknown). The human genome encodes 4 Argonaute proteins (AGO1 (EIF2C1), AGO2 (EIF2C2), AGO3 (EIF2C3), AGO4 (EIF2C4)), however only AGO2 (EIF2C2) can cleave target mRNAs with perfect or nearly perfect complementarity to the guide miRNA. In mammalian cells, such endogenous interactions are very rare; most miRNAs only cause translational repression. For complexes that contain AGO2, cleavage of the passenger strand of the double-stranded miRNA accompanies removal of the passenger strand. Complexes containing other Argonautes may use a helicase to remove the passenger strand but this is not fully known. The resulting single-stranded miRNA (the guide strand) remains in a complex containing Argonaute, Dicer, TRBP, and other proteins termed the RNA-induced Silencing Complex (RISC). The full set of proteins composing RISC is not yet known.
Tristetraprolin (TTP) binds UUAUUUAUU motifs in the AU-rich elements of mRNAs. TTP binds Transportin-1 (Importin beta-2) which plays a role in shuttling TTP between P-bodies and stress granules.
AUF1 (hnRNP D0) dimers bind U-rich regions of AU-rich elements (AREs) in the 3' untranslated regions of mRNAs. The binding causes AUF1 dimers to assemble into higher order tetrameric complexes. Diphosphorylated AUF1 bound to RNA recruits additional proteins, including eIF4G, polyA-binding protein, Hsp, Hsc70, Hsp27, NSEP-1, NSAP-1, and IMP-2 which target the mRNA and AUF1 for degradation. Unphosphorylated AUF1 is thought to be less able to recruit additional proteins. AUF1 also interacts directly or indirectly with HuR and the RNA-induced silencing complex (RISC). AUF1 complexed with RNA and other proteins is ubiquitinated and targeted for destruction by the proteasome while the bound mRNA is degraded. Inhibition of ubiquitin addition to AUF1 blocks mRNA degradation. The mechanism by which ubiquitin-dependent proteolysis is coupled to mRNA degradation is unknown. At least 4 isoforms of AUF1 exist: p45 (45 kDa) contains all exons, p42 lacks exon 2, p40 lacks exon 7, and p37 lacks exons 2 and 7. The presence of exon 7 in p42 and p45 seems to block ubiquitination while the absence of exon 7 (p37 and p40) targets AUF1 for ubiquitination and destabilizes bound RNAs. Lack of exon 2 (p37 and p42) is associated with higher affinity for RNA and 14-3-3sigma (SFN). AUF1 binds and destabilizes mRNAs encoding Interleukin-1 beta (IL1B), Tumor Necrosis Factor alpha (TNFA), Cyclin-dependent kinase inhibitor 1 (CDNK1A, p21), Cyclin-D1 (CCND1), Granulocyte-macrophage colony stimulating factor (GM-CSF, CSF2), inducible Nitric oxide synthase (iNOS, NOS2), Proto-oncogene cFos (FOS), Myc proto-oncogene (MYC), Apoptosis regulator Bcl-2 (BCL2).
Butyrate response factor 1 (BRF1) binds AU-rich elements in the 3' untranslated region of mRNAs.
BRF1 is phosphorylated at Serine92 and Serine203 by Protein kinase B/AKT. Protein kinase B is activated by phosphatidylinositol 3-kinase. Phosphorylation of BRF1 does not interfere with the ability of BRF1 to bind RNA or interact with enzymes that catalyze RNA degradation therefore larger complexes may contain phosphorylated BRF1.
Butyrate Response Factor 1 (BRF1, ZFP36L1, not to be confused with transcription factor IIIB) binds AU-rich elements in the 3' region of mRNAs. After binding, BRF1 recruits exonucleases (XRN1 and the exosome) and decapping enzymes (DCP1a and DCP2) to hydrolyze the RNA. The ability of BRF1 to direct RNA degradation is controlled by phosphorylation of BRF1. Protein kinase B/AKT1 phosphorylates BRF1 at serines 92 and 203. Phosphorylated BRF1 can still bind RNA but is sequestered by binding 14-3-3 protein, preventing BRF1 from destabilizing RNA. BRF1 is also phosphorylated by MK2 at serines 54, 92, 203, and at an unknown site in the C-terminus. It is unknown if this particular phosphorylated form of BRF1 binds 14-3-3.
p53-Independent G1/S DNA damage checkpoint
Phosphoribosylformylglycinamidine synthase
Formylglycinamide ribotide amidotransferase
phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase
Trifunctional purine biosynthetic protein adenosine-3 (Includes: Phosphoribosylamine--glycine ligase (EC 6.3.4.13) (GARS) (Glycinamide ribonucleotide synthetase) (Phosphoribosylglycinamide synthetase); Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1) (AIRS) (Phosphoribosyl-aminoimidazole synthetase) (AIR synthase); Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) (GART) (GAR transformylase) (5'-phosphoribosylglycinamide transformylase))
Trifunctional purine biosynthetic protein adenosine-3
5'-phosphoribosylglycinamide transformylase
Phosphoribosylformylglycinamidine cyclo-ligase
Phosphoribosylglycinamide formyltransferase
Phosphoribosyl-aminoimidazole synthetase
Bifunctional purine biosynthesis protein PURH (Includes: Phosphoribosylaminoimidazolecarboxamide formyltransferase (EC 2.1.2.3) (AICAR transformylase); IMP cyclohydrolase (EC 3.5.4.10) (Inosinicase) (IMP synthetase) (ATIC))
5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase
Bifunctional purine biosynthesis protein PURH
Phosphoribosylaminoimidazolecarboxamide formyltransferase
HuR binds AU-rich elements of mRNAs. Bound HuR can form oligomers on longer AU-rich elements. Phosphorylated HuR binds mRNA more tightly than unphosphorylated HuR does.
HuR phosphorylated on ser221 and ser318 binds AU-rich regions of mRNAs. Phosphorylation on ser318 appears to affect RNA binding and phosphorylation of ser221 affects nucleocytoplasmic shuttling.
HuR (ELAV1) phosphorylated on serine221 and serine158 binds COX-2 mRNA in the nucleus. The phosphorylation of serine 158 appears to affect RNA-binding while phosphorylation on serine 221 affects nucleocytoplasmic shuffling.
Protein kinase C delta (PKCdelta) phosphorylates HuR (ELAVL1) at serine 221 and serine 318.
Glutamine phosphoribosylpyrophosphate amidotransferase
Amidophosphoribosyltransferase precursor (EC 2.4.2.14) (Glutamine phosphoribosylpyrophosphate amidotransferase) (ATASE) (GPAT)
Amidophosphoribosyltransferase precursor
phosphoribosyl pyrophosphate amidotransferase
Protein kinase C alpha (PKCalpha) phosphorylates HuR (ELAVL1) on serine221 and serine 158.
Tristetraproline (TTP) binds RNAs that contain AU-rich elements and recruits enzymes that degrade RNA. TTP interacts with the exosome (3' to 5' exonuclease), XRN1 (5' to 3' exonuclease), and the decapping enzymes DCP1 and DCP2a. The activity of TTP is regulated by phosphorylation. MK2 phosphorylates TTP, which then binds 14-3-3.The interaction with 14-3-3 prevents phosphorylated TTP from entering stress granules and stabilizes mRNA bound by phosphorylated TTP. Tristetraproline is known to bind AU-rich elements in the following mRNAs: Tumor necrosis factor alpha (TNFA), Granulocyte-macrophage colony stimulating factor (CSF2, GM-CSF), Interleukin-2 (IL-2), and Proto-oncogene C-FOS (FOS, c-fos). Mice deficient in TTP exhibit arthritis, weight loss, skin lesions, autoimmunity, and myeloid hyperplasia.
80S monosomes dissociate into 40S and 60S ribosomal subunits. eIF1A promotes this dissociation.
The 80S ribosome dissociates into free 40S (small) and 60S (large) ribosomal subunits. Each ribosomal subunit is constituted by several individual ribosomal proteins and rRNA.
HuR (ELAVL1) is a ubiquitous protein that binds AU-rich elements in mRNAs and acts to stabilize the mRNAs. HuR activity is controlled by phosphorylation, with PKC alpha and PCK delta enhancing the ability of HuR to bind and stabilize mRNAs. Binding of mRNAs occurs in the nucleus and HuR then interacts with the CRM1 export pathway to transfer the mRNA to the cytoplasm. The mechanism by which HuR shields the mRNA from degradation is unknown. HuR also regulates translation of some mRNAs, in some cases repressing translation and in some cases enhancing translation of bound mRNAs by recruiting them to polysomes. HuR binds and regulates mRNAs encoding Cyclooxygenase-2 (COX2, PTGS2), Cyclin A (CCNA, CCNA2), Cyclin D1 (CCND1), Cyclin B1 (CCNB1), CD83 antigen (CD83), and proto-oncogene c-Fos (FOS). HuR is a member of a family of proteins that also contains HuD (ELAVL4), HuB (ELAVL2), and HuC (ELAVL3). HuB, HuC, and HuD are specifically expressed in neural tissue. HuR participates in apoptosis. During lethal stress HuR becomes mostly cytoplasmic and is a target of Caspase-3 and Caspase-7. The cleavage products of HuR in turn promote apoptosis.
RNA elements rich in adenine and uracil residues (AU-rich elements) bind specific proteins which either target the RNA for degradation or, more rarely, stabilize the RNA. The activity of the AU-element binding proteins is regulated, usually by phosphorylation but also by subcellular localization.
Electron Transfer Flavoprotein beta subunit
Succinate dehydrogenase (ubiquinone) iron-sulfur protein, mitochondrial
Succinate Dehydrogenase complex subunit B
Succinate Dehydrogenase complex subunit C
Succinate-ubiquinone oxidoreductase cytochrome B large subunit
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor
Enzymatic, metabolic and secretory patterns in human islets of type 2 (non-insulin-dependent) diabetic patients
InsP3-mediated intracellular calcium signalling is altered by expression of synaptojanin-1
Succinate Dehydrogenase complex subunit A
Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial
Essential role of Mia40 in import and assembly of mitochondrial intermembrane space proteins
2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor
alpha-ketoglutarate dehydrogenase E1 apoenzyme
Transcription termination by RNA polymerase III in fission yeast. A genetic and biochemically tractable model system.
Mitochondrial protein import: recognition of internal import signals of BCS1 by the TOM complex
Molecular mechanisms involved in the regulation of the endothelial nitric oxide synthase
Am J Physiol Regul Integr Comp Physiol 284:R1-12
Familial hyperlysinemias. Purification and characterization of the bifunctional aminoadipic semialdehyde synthase with lysine-ketoglutarate reductase and saccharopine dehydrogenase activities.
Structure and sequence of the human sulphamidase gene
Mitochondrial aquaporin-8 knockdown in human hepatoma HepG2 cells causes ROS-induced mitochondrial depolarization and loss of viability
Phosphorylation of serine 230 promotes inducible transcriptional activity of heat shock factor 1
MISCELLANEOUS Present with 8680 molecules/cell in log phase SD medium.SIMILARITY Belongs to the archaeal RpoL/eukaryotic RPB11/RPC19 RNA polymerase subunit family.
Transport to the Golgi and subsequent modification
ATP-dependent interaction of human mismatch repair proteins and dual role of PCNA in mismatch repair
Insulin signalling and the regulation of glucose and lipid metabolism
Functional properties and genomics of glucose transporters
KDM3B is the H3K9 demethylase involved in transcriptional activation of lmo2 in leukemia
ER-mediated phagocytosis: a new membrane for new functions
Primary structure of human triosephosphate isomerase
Characterization of the human mitochondrial methionyl-tRNA synthetase
Purification and properties of uroporphyrinogen I synthase from human erythrocytes. Identification of stable enzyme-substrate intermediates.
Is the mammalian serine palmitoyltransferase a high-molecular-mass complex?
Mechanisms of the TRIF-induced interferon-stimulated response element and NF-kappaB activation and apoptosis pathways
Mechanism of porphobilinogen synthase. Requirement of Zn2+ for enzyme activity.
The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci
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Transcriptional regulation of white adipocyte differentiation
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NGF signalling via TRKA from the plasma membrane
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Euplotes telomerase: evidence for limited base-pairing during primer elongation and dGTP as an effector of translocation
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Requirement of the DEAD-Box protein ded1p for messenger RNA translation.
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In addition to the methylation of the 5'-cap, there is methylation of internal nucleotides in the mRNA. This methylation can occur in translated and untranslated regions. One to three methyl groups have been seen per mRNA molecule, but methylation is non-stoichiometric. The most frequent methylation observed is at the N6 position of adenosine. The function of mRNA internal methylation, if any, is unknown.
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The 5'-ends of all eukaryotic pre-mRNAs studied thus far are converted to cap structures. The cap is thought to influence splicing of the first intron, and is bound by 'cap-binding' proteins, CBP80 and CBP20, in the nucleus. The cap is important for translation initiation, and it also interacts with the poly(A)terminus, via proteins, resulting in circularization of the mRNA to facilitate multiple rounds of translation. The cap is also important for mRNA stability, protecting it from 5' to 3' nucleases, and is required for mRNA export to the cytoplasm. The capping reaction usually occurs very rapidly on nascent transcripts; after the synthesis of only a few nucleotides by RNA polymerase II. The capping reaction involves the conversion of the 5'-end of the nascent transcript from a triphosphate to a diphosphate by a RNA 5'-triphosphatase, followed by the addition of a guanosine monophosphate by the mRNA guanylyltransferase, to form a 5'-5'-triphosphate linkage. This cap is then methylated by 2'-O-methyltransferases.
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At the beginning of this reaction, 1 molecule of 'CBP80', and 1 molecule of 'CBP20' are present. At the end of this reaction, 1 molecule of 'Cap Binding Complex (CBC)' is present. This reaction takes place in the 'nucleus'.
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The cap binding complex binds to the methylated GMP cap on the nascent mRNA transcript.
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At the beginning of this reaction, 1 molecule of 'ATAC C Complex with lariat containing 5'-end cleaved mRNA' is present. At the end of this reaction, 1 molecule of 'U6 ATAC snRNP', 1 molecule of 'post exon ligation complex', 1 molecule of 'U12 snRNP', 1 molecule of 'U11 snRNP', and 1 molecule of 'U5 snRNP' are present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'ATAC C Complex' is present. At the end of this reaction, 1 molecule of 'ATAC C Complex with lariat containing 5'-end cleaved mRNA' is present. This reaction takes place in the 'nucleus'.
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At the beginning of this reaction, 1 molecule of 'ATAC B Complex' is present. At the end of this reaction, 1 molecule of 'U4 ATAC snRNP', and 1 molecule of 'ATAC C Complex' are present. This reaction takes place in the 'nucleus'.
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The U4atac/U6atac enters the spliceosome and U6atac snRNA forms base pairing interactions with the 5' ss and also forms base pairing interactions with U12 and U4atac is partially displaced. U5 snRNP, the only snRNP common to both the major and minor splicing pathways, also joins the spliceosome to form the B complex and interacts with nucleotides within the 3' end of the exon flanking the 5' ss.
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In the final step of the capping reaction, the methyltransferase takes a methyl group from S-adenosyl-methionine to the N7 position of the cap guanine. N7G-methyltransferase (MT) mediated reaction can be represented as: GpppN(pN)n + S-adenosylmethionine (Adomet) ->m7GpppN(pN)n + S-adenosylhomocysteine (Adohcy).
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GMP capped mRNA transcript dissociates from GT for further modification.
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METAP1:2Co2+ (name copied from entity in Homo sapiens)
METAP2:2Co2+ (name copied from entity in Homo sapiens)
Activation of DNA-binding activity in an apparently cytoplasmic precursor of the NF-kappa B transcription factor
DSIF complex (name copied from entity in Homo sapiens)
FACT complex (name copied from entity in Homo sapiens)
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pol II open pre-initiation complex (name copied from entity in Homo sapiens)
TFIIE (name copied from entity in Homo sapiens)
RNA Polymerase II (unphosphorylated):TFIIF complex (name copied from entity in Homo sapiens)
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RNA Polymerase II holoenzyme complex (unphosphorylated) (name copied from entity in Homo sapiens)
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TFIIF (name copied from entity in Homo sapiens)
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NARS (cytosolic asparaginyl tRNA synthetase) catalyzes the reaction of asparagine, tRNA(Asn), and ATP to form Asn-tRNA(Asn), AMP, and pyrophosphate. The enzyme is a class I tRNA synthetase (Beaulande et al. 1998).
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5808.1
AARS (cytosolic alanyl tRNA synthetase) catalyzes the reaction of alanine, tRNA(ala), and ATP to form Ala tRNA(Ala), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a monomer (Shiba et al. 1995). A mutation in the editing domain of the mouse Aars gene results in misincorporation of non-cognate amino acids into cellular proteins. This is associated with protein misfolding in Purkinje cells and a phenotype consistent with human ataxia (Lee et al. 2006).
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5610669
GARS (cytosolic glycyl tRNA synthetase) catalyzes the reaction of glycine, tRNA(Gly), and ATP to form Gly tRNA(Gly), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a dimer. Cytosolic and mitochondrial glycyl tRNA synthetase enzymes are both encoded by the same gene; the cytosolic protein lacks an aminoterminal 54 residue sequence found in the mitochondrial protein. Mutations in GARS are associated with Charcot Marie Tooth disease and distal spinal muscular atrophy, two diseases characterized by axonal dysfunction (Antonellis et al. 2006)
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5203.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5393.1
CARS (cytosolic cysteinyl tRNA synthetase) catalyzes the reaction of cysteine, tRNA(cys), and ATP to form Cys-tRNA(Cys), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is a homomultimer, probably a dimer (Davidson et al. 2001).
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FARS (cytosolic phenylalanyl tRNA synthetase) catalyzes the reaction of phenylalanine, tRNA(Phe), and ATP to form Phe-tRNA(Phe), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a heterotetramer of two alpha and two beta subunits (Moor et al. 2002).
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HARS (cytosolic histidyl tRNA synthetase) catalyzes the reaction of histidine, tRNA(His), and ATP to form His-tRNA(His), AMP, and pyrophosphate (Lee et al. 2002).
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SARS (cytosolic seryl tRNA synthetase) catalyzes the reaction of serine, tRNA(Ser), and ATP to form Ser-tRNA(Ser), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a homodimer (Hartlein and Cusack 1995; Vincent et al. 1997).
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The splicing of a subset of pre-mRNA introns occurs by a second pathway, designated the AT-AC or U12-dependent splicing pathway. AT-AC introns have highly conserved, non-canonical splice sites that are removed by the AT-AC spliceosome, which contains distinct snRNAs (U11, U12, U4atac, U6atac) that are structurally and functionally analogous to the major spliceosome. U5 snRNA as well as many of the protein factors appear to be conserved between the two spliceosomes.
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Co-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per gene, which cannot serve as splicing substrates until both 5' and 3' ends of each intron are synthesized. Thus the time that it takes for pol II to synthesize each intron defines a minimal time and distance along the gene in which splicing factors can be recruited. The time that it takes for pol II to reach the end of the gene defines the maximal time in which splicing could occur co-transcriptionally. Thus, the kinetics of transcription can affect the kinetics of splicing.Any covalent change in a primary (nascent) mRNA transcript is mRNA Processing. For successful gene expression, the primary mRNA transcript needs to be converted to a mature mRNA prior to its translation into polypeptide. Eucaryotic mRNAs undergo a series of complex processing reactions; these begin on nascent transcripts as soon as a few ribonucleotides have been synthesized during transcription by RNA Polymerase II, through the export of the mature mRNA to the cytoplasm, and culminate with mRNA turnover in the cytoplasm.
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The process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing. Most of the mRNA is spliced by the major pathway, involving the U1, U2, U4, U5 and U6 snRNPs. A minor fraction, about 1 %, of the mRNAs are spliced via the U12 dependent pathway.
TFIIA (name copied from entity in Homo sapiens)
TFIIH (name copied from entity in Homo sapiens)
An integrated genomic analysis of human glioblastoma multiforme
pol II promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF complex (name copied from entity in Homo sapiens)
pol II promoter:TFIID:TFIIA:TFIIB complex (name copied from entity in Homo sapiens)
TFIID (name copied from entity in Homo sapiens)
pol II closed pre-initiation complex (name copied from entity in Homo sapiens)
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Pol II initiation complex (name copied from entity in Homo sapiens)
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Phosphoinositides in cell regulation and membrane dynamics
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RNA Polymearse II:NTP:TFIIF complex (name copied from entity in Homo sapiens)
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pol II promoter:TFIID complex (name copied from entity in Homo sapiens)
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pol II promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF:TFIIE complex (name copied from entity in Homo sapiens)
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_226461.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=111341
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5790.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5610762
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DARS2 (mitochondrial aspartyl tRNA synthetase) catalyzes the reaction of aspartate, mitochondrial tRNA(Asp), and ATP to form Asp tRNA(Asp), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a homodimer (Bonnefond et al. 2005). Homozygosity for DARS2 mutations is associated with leukoencephalopathy with brainstem and spinal cord involvement plus lactate elevation (Scheper et al 2007).
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NARS2 (mitochondrial asparaginyl tRNA synthetase) catalyzes the reaction of asparagine, mitochondrial tRNA(Asn), and ATP to form Asn-tRNA(Asn), AMP, and pyrophosphate. The NARS2 gene has been identified by computational analysis of the human genome sequence; its function has been inferred from those of the biochemically characterized mitochondrial aspartyl and tyrosyl tRNA synthetases (Bonnefond et al. 2005).
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RARS2 (mitochondrial arginyl tRNA synthetase) catalyzes the reaction of arginine, mitochondrial tRNA(Arg), and ATP to form Arg tRNA(Arg), AMP, and pyrophosphate. The enzyme is a class I tRNA synthetase. Homozygosity for RARS2 mutations has been associated with pontocerebellar hypoplasia â a disease characterized by a severe reduction in cerebellum and brainstem size (Edvardson et al. 2007).
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AARS2 (mitochondrial alanyl tRNA synthetase) catalyzes the reaction of alanine, mitochondrial tRNA(Ala), and ATP to form Ala-tRNA(Ala), AMP, and pyrophosphate. The AARS2 gene has been identified by computational analysis of the human genome sequence; its function has been inferred from those of the biochemically characterized mitochondrial aspartyl and tyrosyl tRNA synthetases (Bonnefond et al. 2005).
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Cytosolic tRNA synthetases catalyze the reactions of tRNAs encoded in the nuclear genome, their cognate amino acids, and ATP to form aminoacyl-tRNAs, AMP, and pyrophosphate. Eight of the tRNA synthetases, those specific for arginine, aspartate, glutamate and proline, glutamine, isoleucine, leucine, lysine, and methionine, associate to form a complex with three accessory proteins. Each of the component synthetases is active in vitro as a purified protein; complex formation is thought to channel aminoacylated tRNAs more efficiently to the site of protein synthesis in mRNA:ribosome complexes (Quevillon et al. 1999; Wolfe et al. 2003, 2005).
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Cytosolic PPA1 (pyrophosphatase (inorganic) 1) catalyzes the hydrolysis of pyrophosphate to yield two molecules of orthophosphate. The enzyme, a homodimer, requires Mg++ for activity (Fisher et al. 1974; Pynes and Younathan 1967; Thuiller et al. 1978).
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VARS (cytosolic valyl tRNA synthetase) catalyzes the reaction of valine, tRNA(Val), and ATP to form Val-tRNA(Val), AMP, and pyrophosphate. The enzyme is a class I tRNA synthetase (Vilalta et al. 1993).
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YARS (cytosolic tyrosyl tRNA synthetase) catalyzes the reaction of tyrosine, tRNA(Tyr), and ATP to form Tyr tRNA(Tyr), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is a homodimer (Yang et al. 2003). Mutations in the YARS gene are associated with dominant-intermediate Charcot-Marie-Tooth disease â a form of peripheral neuropathy characterized by axon and Schwann cell dysfunction (Jordanova et al. 2006).
WARS (cytosolic tryptophanyl tRNA synthetase) catalyzes the reaction of tryptophan, tRNA(Trp), and ATP to form Trp-tRNA(Trp), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is a homodimer (Bange et al. 1992; Rubin et al. 1991; Yu et al. 2004).
TARS (cytosolic threonyl tRNA synthetase) catalyzes the reaction of threonine, tRNA(Thr), and ATP to form Thr-tRNA(Thr), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a homodimer (Pan et al. 1982).
Facilitated recycling pathway for RNA polymerase III.
pol II transcription complex containing 4 nucleotide long transcript (name copied from entity in Homo sapiens)
pol II transcription complex containing 9 nucleotide long transcript (name copied from entity in Homo sapiens)
pol II transcription complex containing 11 nucleotide long transcript (name copied from entity in Homo sapiens)
Pol II transcription complex containing extruded transcript to +30 (name copied from entity in Homo sapiens)
Pol II Initiation complex with phosphodiester-PPi intermediate (name copied from entity in Homo sapiens)
pol II transcription complex (name copied from entity in Homo sapiens)
pol II transcription complex containing 3 Nucleotide long transcript (name copied from entity in Homo sapiens)
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_164897.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_164290.1
Pol II transcription complex with (ser5) phosphorylated CTD containing extruded transcript to +30 (name copied from entity in Homo sapiens)
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RNA polymerase II (phosphorylated):TFIIF complex (name copied from entity in Homo sapiens)
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_23113.2
RNA Polymerase II holoenzyme complex (phosphorylated) (name copied from entity in Homo sapiens)
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_164236.2
Isolation and characterization of the human pyruvate kinase M gene
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PARS2 (mitochondrial prolyl tRNA synthetase) catalyzes the reaction of proline, mitochondrial tRNA(Pro), and ATP to form Pro-tRNA(Pro), AMP, and pyrophosphate. The PARS2 gene has been identified by computational analysis of the human genome sequence; its function has been inferred from those of the biochemically characterized mitochondrial aspartyl and tyrosyl tRNA synthetases (Bonnefond et al. 2005).
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4570.2
KARS (mitochondrial lysyl tRNA synthetase) catalyzes the reaction of lysine, tRNA(Lys), and ATP to form Lys-tRNA(Lys), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a homodimer. The same gene encodes both cytosolic and mitochondrial KARS enzymes (Shiba et al. 1997).
5,10-methylenetetrahydrofolate polyglutamate
5,10-methylenetetrahydrofolate polyglutamate macromolecule
5,10-methylenetetrahydrofolate polyglutamate macromolecule [ChEBI:60473]
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LARS2 (mitochondrial leucyl tRNA synthetase) catalyzes the reaction of leucine, mitochondrial tRNA(Leu), and ATP to form Leu-tRNA(Leu), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is a monomer (Bullard et al. 2000).
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FARS2 (mitochondrial phenylalanyl tRNA synthetase) catalyzes the reaction of phenylalanine, mitochondrial tRNA(Phe), and ATP to form Phe-tRNA(Phe), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a monomer (Bullard et al. 1999).
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MARS2 (mitochondrial methionyl tRNA synthetase) catalyzes the reaction of methionine, mitochondrial tRNA(Met), and ATP to form Met-tRNA(Met), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is a monomer (Spencer et al. 2004).
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GARS (mitochondrial glycyl tRNA synthetase) catalyzes the reaction of glycine, tRNA(Gly), and ATP to form Gly-tRNA(Gly), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a dimer. Cytosolic and mitochondrial glycyl tRNA synthetase enzymes are both encoded by the same gene; the cytosolic protein lacks an aminoterminal 54-residue sequence found in the mitochondrial protein. Mutations in GARS are associated with Charcot-Marie-Tooth disease (Antonellis et al. 2007).
QARS (mitochondrial glutaminyl tRNA synthetase) catalyzes the reaction of glutamine, tRNA(Gln), and ATP to form Gln-tRNA(Gln), AMP, and pyrophosphate. The enzyme is a class I tRNA synthetase. The same gene encodes both the cytosolic and mitochondrial QARS enzymes (Lamour et al. 1994).
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IARS2 (mitochondrial isoleucyl tRNA synthetase) catalyzes the reaction of isoleucine, mitochondrial tRNA(Ile), and ATP to form Ile-tRNA(Ile), AMP, and pyrophosphate. The enzyme is a class I tRNA synthetase (Degoul et al. 1995).
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HARS2 (mitochondrial histidyl tRNA synthetase) catalyzes the reaction of histidine, mitochondrial tRNA(His), and ATP to form His-tRNA(His), AMP, and pyrophosphate. The enzyme is a class II tRNA synthetase (O'Hanlon et al. 1995).
EARS2 (mitochondrial glutamyl tRNA synthetase) catalyzes the reaction of glutamate, mitochondrial tRNA(Glu), and ATP to form Glu-tRNA(Glu), AMP, and pyrophosphate. The EARS2 gene has been identified by computational analysis of the human genome sequence; its function has been inferred from those of the biochemically characterized mitochondrial aspartyl and tyrosyl tRNA synthetases (Bonnefond et al. 2005).
RNA Polymerase II holoenzyme complex (hypophosphorylated):TFIIF complex (name copied from entity in Homo sapiens)
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RNA Pol II (hypophosphorylated) complex bound to DSIF protein (name copied from entity in Homo sapiens)
RNA Polymerase II (phosphorylated):TFIIF:capped pre-mRNA (name copied from entity in Homo sapiens)
RNA Pol II (hypophosphorylated):capped pre-mRNA complex (name copied from entity in Homo sapiens)
capped pre-mRNA:CBC:RNA Pol II (phosphorylated) complex (name copied from entity in Homo sapiens)
Cap Binding Complex (CBC) (name copied from entity in Homo sapiens)
RNA Pol II with phosphorylated CTD: CE complex (name copied from entity in Homo sapiens)
CE:Pol II CTD:Spt5 complex (name copied from entity in Homo sapiens)
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_237484.1
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_243664.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1362385
RBBP7:Replicative histone H3 (name copied from entity in Homo sapiens)
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Capping complex (initial) (name copied from entity in Homo sapiens)
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=83947
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5362.2
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Capping complex (hydrolyzed) (name copied from entity in Homo sapiens)
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The general transcription factor TFIIF has a high affinity for the RNA Polymerase II holoenzyme. TFIIF stabilizes the preinitiation complex, and suppresses non-specific binding of RNA Pol II to DNA, and is thus critical for start site recognition.
The binding of TFIIH completes the assembly of the preinitiation complex (PIC) for RNA Polymerase II transcription. Although RNA polymerase binds the TATA box on the promoter DNA, no initiation of transcription occurs until TFIIH is bound to the PIC. TFIIH is the only factor with known enzymatic activities.
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At the beginning of this reaction, 1 molecule of 'pol II open pre-initiation complex', and 2 molecules of 'NTP' are present. At the end of this reaction, 1 molecule of 'Pol II initiation complex' is present. This reaction takes place in the 'nucleus'.
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The catalytic mechanism of guanine nucleotide exchange factor action and competitive inhibition by phosphorylated eukaryotic initiation factor 2.
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At the beginning of this reaction, 1 molecule of 'Pol II initiation complex' is present. At the end of this reaction, 1 molecule of 'Pol II Initiation complex with phosphodiester-PPi intermediate' is present. This reaction takes place in the 'nucleus'.
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After assembly of the complete RNA polymerase II-preinitiation complex, the next step is separation of the two DNA strands. This isomerization step is known as the closed-to-open complex transition and occurs prior to the initiation of mRNA synthesis. In the RNA polymerase II system this step requires the hydrolysis of ATP or dATP into Pi and ADP or dADP (in contrast to the other RNA polymerase systems) and is catalyzed by the XPB subunit of TFIIH. The region of the promoter, which becomes single-stranded , spans from ââ¬â10 to +2 relative to the transcription start site. Negative supercoiling in the promoter region probably induces transient opening events and can alleviate requirement of TFIIE, TFIIH and ATP-hydrolysis for open complex formation. ATP is also used in this step by the cdk7-subunit of TFIIH to phosphorylate the heptad repeats of the C-terminal domain of the largest subunit of RNA polymerase II (RPB1) on serine-2
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Formation of the third phosphodiester bond creates a 4-nt product. This commits the initiation complex to promoter escape. The short 4-nt transcript is still loosely associated with the RNA polymerase II initiation complex and can dissociate to yield abortive products, which are not further extended. Inhibition of ATP-hydrolysis by TFIIH does not lead to collapse of the open region any longer. The transcription complex has lost the sensitivity to single-stranded oligo-nucleotide inhibition. However, ATP-hydrolysis and TFIIH are required for efficient promoter escape. The open region (ââ¬Åtranscription bubbleââ¬Â) expands concomitant with the site of RNA-extension. In this case this region spans positions -9 to +4.
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Formation of the second phosphodiester bond creates a 3-nt product. This short transcript is still loosely associated with the RNA polymerase II initiation complex and can dissociate to yield abortive products, which are not further extended. The transcription complex still requires continued ATP-hydrolysis by TFIIH and remains sensitive to single-stranded oligo-nucleotide inhibition. The open region (ââ¬Åtranscription bubbleââ¬Â) expands concomitant with the site of RNA-extension. In this case this region spans positions -9 to +3.
U4 ATAC snRNP:U6 ATAC snRNP (name copied from entity in Homo sapiens)
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Formation of the open complex exposes the template strand to the catalytic center of the RNA polymerase II enzyme. This facilitates formation of the first phosphodiester bond, which marks transcription initiation. As a result of this, the TFIIB basal transcription factor dissociates from the initiation complex. The open transcription initiation complex is unstable and can revert to the closed state. Initiation at this stage requires continued (d)ATP-hydrolysis by TFIIH. Dinucleotide transcripts are not stably associated with the transcription complex. Upon dissociation they form abortive products. The transcription complex is also sensitive to inhibition by small oligo-nucleotides. Dinucleotides complementary to position -1 and +1 in the template can also direct first phosphodiester bond formation. This reaction is independent on the basal transcription factors TFIIE and TFIIH and does not involve open complex formation. This reaction is sensitive to inhibition by single-stranded oligonucleotides.
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At the beginning of this reaction, 1 molecule of 'Pol II Initiation complex with phosphodiester-PPi intermediate' is present. At the end of this reaction, 1 molecule of 'pyrophosphate', and 1 molecule of 'pol II transcription complex' are present. This reaction takes place in the 'nucleus'.
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Initial-rate kinetics of human NMN-adenylyltransferases: substrate and metal ion specificity, inhibition by products and multisubstrate analogues, and isozyme contributions to NAD+ biosynthesis
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Covalent CE:GMP intermediate complex (name copied from entity in Homo sapiens)
Capping complex (intermediate) (name copied from entity in Homo sapiens)
Capping complex (with freed 5'- GMP) (name copied from entity in Homo sapiens)
Capping complex (GpppN..) (name copied from entity in Homo sapiens)
capped, methylated pre-mRNA:CBC Complex (name copied from entity in Homo sapiens)
mRNA capping factors (name copied from entity in Homo sapiens)
U4 ATAC:U5:U6 ATAC Complex (name copied from entity in Homo sapiens)
mRNA (N6-adenosine)-methyltransferase (name copied from entity in Homo sapiens)
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U6 ATAC snRNP (name copied from entity in Homo sapiens)
snRNP Sm core complex (name copied from entity in Homo sapiens)
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Human spermidine synthase gene: structure and chromosomal localization
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Formation of phosphodiester bonds nine and ten creates RNA products, which do not dissociate from the RNA pol II initiation complex. The transcription complex has enter the productive elongation phase. TFIIH and ATP-hydrolysis are required for efficient promoter escape. The open region (ââ¬Åtranscription bubbleââ¬Â) expands concomitant with the site of RNA-extension. The region upstream from the transcription start site (-9 to -3) collapses to the double-stranded state. TFIIH remains associated to the RNA pol II initiation complex.
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RNA polymerase II transcription complexes are susceptible to transcriptional stalling and arrest, when extending nascent transcripts to 30-nt. This susceptibility depends on presence on down-stream DNA, the particular DNA-sequence of the template and presence of transcription factors. Transcription factor TFIIH remains associated to the RNA pol II elongation complex until position +30. At this stage transcription elongation factor TFIIS can rescue stalled transcription elongation complexes. The transcription bubble varies between 13- and 22-nt in size.
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RNA Polymerase II promoter escape occurs after the first phosphodiester bond has been created.
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At the beginning of this reaction, 1 molecule of 'Pol II transcription complex containing transcript to +30' is present. At the end of this reaction, 1 molecule of 'Pol II transcription complex containing extruded transcript to +30' is present. This reaction takes place in the 'nucleus'.
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Phosphorylation of serine 5 residue at the CTD of pol II largest subunit is an important step signaling the end of initiation and escape into processive elongation processes. Cdk7 protein subunit of TFIIH phosphorylates RNA Pol II CTD serine 5 residues on its heptad repeats.
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At the beginning of this reaction, 1 molecule of 'mRNA capping enzyme', and 1 molecule of 'Pol II transcription complex with (ser5) phosphorylated CTD containing extruded transcript to +30' are present. At the end of this reaction, 1 molecule of 'RNA Pol II with phosphorylated CTD: CE complex' is present. This reaction takes place in the 'nucleus'.
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The capping enzyme interacts with the Spt5 subunit of transcription elongation factor DSIF. This interaction may couple the capping reaction with promoter escape or elongation, thereby acting as a ââ¬Åcheckpointââ¬Â to assure that capping has occurred before the polymerase proceeds to make the rest of the transcript.
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At the beginning of this reaction, 1 molecule of 'RNA Pol II with phosphorylated CTD: CE complex' is present. At the end of this reaction, 1 molecule of 'RNA Pol II with phosphorylated CTD: CE complex with activated GT' is present. This reaction takes place in the 'nucleus'.
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To facilitate co-transcriptional capping, and thereby restrict the cap structure to RNAs made by RNA polymerase II, the capping enzymes bind directly to the RNA polymerase II. The C-terminal domain of the largest Pol II subunit contains several phosphorylation sites on its heptapeptide repeats. The capping enzyme guanylyltransferase and the methyltransferase bind specifically to CTD phosphorylated at Serine 5 within the CTD. Kinase subunit of TFIIH, Cdk7, catalyzes this phosphorylation event that occurs near the promoter. In addition, it has been shown that binding of capping enzyme to the Serine-5 phosphorylated CTD stimulates guanylyltransferase activity in vitro.
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U12 snRNP (name copied from entity in Homo sapiens)
ATAC A Complex (name copied from entity in Homo sapiens)
U5 snRNP (name copied from entity in Homo sapiens)
U4 ATAC snRNP (name copied from entity in Homo sapiens)
ATAC C Complex (name copied from entity in Homo sapiens)
ATAC B Complex (name copied from entity in Homo sapiens)
U11 snRNP (name copied from entity in Homo sapiens)
SF3B (name copied from entity in Homo sapiens)
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post exon ligation complex (name copied from entity in Homo sapiens)
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CARS dimer (name copied from entity in Homo sapiens)
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GARS dimer (name copied from entity in Homo sapiens)
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Cloning and characterization of DPPL1 and DPPL2, representatives of a novel type of mammalian phosphatidate phosphatase
All characterised lysine demethylases other than KDM1A belong to the jumonji C-domain (JmjC) containing family, members of the Cupin superfamily of mononuclear Fe (II)-dependent oxygenases. They require 2-oxoglutarate (2-OG) and molecular oxygen as co-substrates, producing succinate and carbon dioxide. This hydroxylation-based mechanism does not require a protonatable lysine epsilon-amine group and consequently JmjC-containing demethylases are able to demethylate tri-, di- and monomethylated lyines. The first reported JmjC-containing demethylases were KDM2A and KDM2B (JHDM1A/B, FBXL11/10). These demethylate lysine-37 of histone H3 when mono- or di-methylated (H3K36Me1/2) (Tsukada et al. 2006). KDM4A (JHDM3A) can demethylate mono-, di and trimethylated lysine-37 of histone H3 (Klose et al. 2006).
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All characterized lysine demethylases other than KDM1A belong to the jumonjiC domain (JmjC) containing family.The JmjC KDMs are members of the Cupin superfamily of mononuclear Fe (II) dependent oxygenases, which are characterized by the presence of a double-stranded beta-helix core fold. The JmjC KDMs require 2 oxoglutarate (2 OG) and molecular oxygen as co substrates, producing, along with formaldehyde, succinate and carbon dioxide. This hydroxylation based mechanism does not require a protonatable lysine epsilon-amine group and consequently JmjC containing demethylases are able to catalyse demethylateion of tri , di and monomethylated lysines. KDM3A (JHDM2A), KDM3B (JHDM2B), KDM7A (JHDM1D), PHF8 (JHDM1E) and PHF2 when complexed with ARID5B (Wen et al. 2010, Baba et al. 2011) are specific for mono or di-methylated lysine-10 on histone H3 (H3K9Me1/2) (Yamane et al. 2006, Kim et al. 2012, Horton et al. 2010, Huang et al. 2010, Loenarz et al. 2008, Feng et al. 2010, Fortschegger et al. 2010, Qi et al. 2010).
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Transcription by RNA Polymerase I, RNA Polymerase III and transcription from mitochondrial promoters.
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Transcription elongation by RNA polymerase II (RNAPII) is controlled by a number of trans-acting transcription elongation factors as well as by cis-acting elements. Transcription elongation is a rate-limiting step for proper mRNA production in which the phosphorylation of Pol II CTD is a crucial biochemical event. The role of CTD phosphorylation in transcription by Pol II is greatly impaired by protein kinase inhibitors such as 5,6-dichloro-1- ribofuranosylbenzimidazole (DRB), which block CTD phosphorylation and induce arrest of elongating Pol II. DRB-sensitive activation Pol II CTD during elongation has enabled the isolation of two sets of factors -Negative Elongation Factors (NELF) and DRB sensitivity inducing factor (DSIF). P-Tefb is a DRB-sensitive, cyclin-dependent CTD kinase composed of Cdk9 that carries out Serine-2 phosphorylation of Pol II CTD during elongation. The mechanism by which DSIF, NELF and P-TEFb act together in Pol II-regulated elongation is yet to be fully understood. Various biochemical evidences point to a model in which DSIF and NELF negatively regulate elongation through interactions with polymerase containing a hypophosphorylated CTD. Subsequent phosphorylation of the Pol II CTD by P-Tefb might promote elongation by inhibiting interactions of DSIF and NELF with the elongation complex.
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The mechanisms governing the process of elongation during eukaryotic mRNA synthesis are being unraveled by recent studies. These studies have led to the expected discovery of a diverse collection of transcription factors that directly regulate the activities of RNA Polymerase II and unexpected discovery of roles for many elongation factors in other basic processes like DNA repair, recombination, etc. The transcription machinery and structural features of the major RNA polymerases are conserved across species. The genes active during elongation fall under different classes like, housekeeping, cell-cycle regulated, development and differentiation specific genes etc. The list of genes involved in elongation has been growing in recent times, and include: -TFIIS,DSIF, NELF, P-Tefb etc. that are involved in drug induced or sequence-dependent arrest - TFIIF, ELL, elongin, elongator etc. that are involved in increasing the catalytic rate of elongation by altering the Km and/or the Vmax of Pol II -FACT, Paf1 and other factors that are involved chromatin modification - DNA repair proteins, RNA processing and export factors, the 19S proteasome and a host of other factors like Spt5-Spt5, Paf1, and NELF complexes, FCP1P etc. (Arndt and Kane, 2003). Elongation also represents processive phase of transcription in which the activities of several mRNA processing factors are coupled to transcription through their binding to RNA polymerase (Pol II). One of the key events that enables this interaction is the differential phosphorylation of Pol II CTD. Phosphorylation pattern of CTD changes during transcription, most significantly at the beginning and during elongation process. TFIIH-dependent Ser5 phosphorylation is observed primarily at promoter regions while P-Tefb mediated Ser2 phosphorylation is seen mainly in the coding regions, during elongation. Experimental evidence suggests a dynamic association of RNA processing factors with differently modified forms of the polymerase during the transcription cycle. (Komarnitsky et al., 2000). [Komarnitsky et al 2000, Arndt & Kane 2003, Shilatifard et al 2003]
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FCP1 dephosphorylates RNAP II in ternary elongation complexes as well as in solution and, therefore, is thought to function in the recycling of RNAP II during the transcription cycle. Biochemical experiments suggest that human FCP1 targets CTDs that are phosphorylated at serine 2 (CTD-serine 2) and/or CTD-serine 5. It is also observed to stimulate elongation independent of its catalytic activity. Dephosphorylation of Ser2 - phosphorylated Pol II results in hypophosphorylated form that disengages capping enzymes (CE).
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DSIF is a heterodimer consisting of hSPT4 (human homolog of yeast Spt4- p14) and hSPT5 (human homolog of yeast Spt5-p160). DSIF association with Pol II may be enabled by Spt5 binding to Pol II creating a scaffold for NELF binding (Wada et al.,1998). Spt5 subunit of DSIF can be phosphorylated by P-TEFb.
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All characterized lysine demethylases other than KDM1A belong to the jumonjiC domain (JmjC) containing family.The JmjC KDMs are members of the Cupin superfamily of mononuclear Fe (II) dependent oxygenases, which are characterized by the presence of a double-stranded beta-helix core fold. The JmjC KDMs require 2 oxoglutarate (2 OG) and molecular oxygen as co substrates, producing, along with formaldehyde, succinate and carbon dioxide. This hydroxylation based mechanism does not require a protonatable lysine epsilon-amine group and consequently JmjC containing demethylases are able to demethylate tri , di and monomethylated lysines. KDM5A-D (JARID1A-D) catalyse the demethylation of di- or tri-methylated lysine-5 of histone H3 (H3K4Me2/3) (Christensen et al. 2007, Klose et al. 2007, Lee et al. 2007, Secombe et al. 2007, Seward et al. 2007, Iwase et al. 2007).
All characterized lysine demethylases other than KDM1A belong to the jumonjiC domain (JmjC) containing family.The JmjC KDMs are members of the Cupin superfamily of mononuclear Fe (II) dependent oxygenases, which are characterized by the presence of a double-stranded beta-helix core fold. The JmjC KDMs require 2 oxoglutarate (2 OG) and molecular oxygen as co substrates, producing, along with formaldehyde, succinate and carbon dioxide. This hydroxylation based mechanism does not require a protonatable lysine e amine group and consequently JmjC containing demethylases are able to demethylate tri , di and monomethylated lysines. KDM4A-D (JMJD2A-D/JHDM3A-D) catalyse the demethylation of di- or tri-methylated histone H3 at lysine-10 (H3K9Me2/3) (Cloos et al. 2006, Fodor et al. 2006, Whetstine et al. 2007), with a strong preference for Me3 (Whetstine et al. 2007). KDM4A (JHDM3A) can also demethylate lysine-37 of histone H3 (H3K36Me2/3) (Klose et al. 2006).
PPA1 dimer (name copied from entity in Homo sapiens)
YARS dimer (name copied from entity in Homo sapiens)
DARS2 dimer (name copied from entity in Homo sapiens)
SARS dimer (name copied from entity in Homo sapiens)
Release of apoptotic factors from the mitochondria
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FARS A2B2 tetramer (name copied from entity in Homo sapiens)
WARS dimer (name copied from entity in Homo sapiens)
TARS dimer (name copied from entity in Homo sapiens)
All characterized lysine demethylases other than KDM1A belong to the jumonjiC domain (JmjC) containing family.The JmjC KDMs are members of the Cupin superfamily of mononuclear Fe (II) dependent oxygenases, which are characterized by the presence of a double-stranded beta-helix core fold. The JmjC KDMs require 2 oxoglutarate (2 OG) and molecular oxygen as co substrates, producing, along with formaldehyde, succinate and carbon dioxide. This hydroxylation based mechanism does not require a protonatable lysine e amine group and consequently JmjC containing demethylases are able to demethylate tri , di and monomethylated lysines. KDM6A (UTX), KDM6B (JMJD3) and KDM7A (JHDM1D) catalyse the demethylation of di or tri-methylated lysine-28 of histone H3 (H3K27Me2/3) (Agger et al. 2007, Cho et al. 2007, De Santra et al. 2007, Hong et al. 2007, Lan et al. 2007, Lee et al. 2007, Horton et al. 2010, Huang et al. 2010).
Chromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance of the physical structure of eukaryotic chromatin. These processes include histone modification, DNA modification, and transcription. The modifications are bound by specific proteins that alter the conformation of chromatin.
The capping enzyme binds the 5'-end of the nascent transcript soon after it is synthesized on the DNA template, and results in the formation of the capping complex along with the C-terminal domain of RNA polymerase II, and Spt5.
After the capping complex is formed, the RNA triphosphatase activity of the capping enzyme hydrolyzes the 5'-end phosphate group of the nascent mRNA transcript to a diphosphate. The RNA triphosphatase (RTP) domain of mammalian capping enzyme is a member of a superfamily of phosphatases that include the protein tyrosine phosphatases, some lipid phosphatases, and several nucleic acid phosphatases. This family uses a conserved nucleophilic cysteine residue to attack the target phosphate. A transient phospho-cysteinyl enzyme intermediate is then hydrolyzed to regenerate the enzyme active site. It should be noted that while higher eukaryotic capping enzymes use PTP-like triphosphatase domains, the yeast triphosphatases are a completely different class of enzymes. The yeast RTPs are metal-dependent phosphatases. RNA 5'-triphosphatase (RTP) catalyzed first reaction can be represented as:pppN(pN)n + GTP -> ppN(pN)n + Pi; (n=20-25)
A highly conserved lysine within the guanylyltransferase (GT) site of the mRNA capping enzyme attacks the alpha-phosphate of GTP. An enzyme-GMP covalent intermediate is formed.
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Histone lysine demethylases (KDMs) are able to reverse N-methylations of histones and probably other proteins. To date KDMs have been demonstrated to catalyse demethylation of N-epsilon methylated lysine residues. Biochemically there are two distinct groups of N-epsilon methylated lysine demethylases with different catalytic mechanisms, both of which result in methyl group oxidation to produce formaldhyde. KDM1A, formerly known as Lysine Specific Demethylase 1 (LSD1), belongs to the flavin adenine dinucleotide (FAD)-dependent amino oxidase family. The KDM1A reaction mechanism requires a protonatable lysine epsilon-amine group, not available in trimethylated lysines, which consequently are not KDM1 substrates. Other KDMs belong to the Jumonji C (JmjC) -domain containing family. These are members of the Cupin superfamily of mononuclear Fe (II)-dependent oxygenases, which are characterised by the presence of a double-stranded beta-helix core fold. They require 2-oxoglutarate (2OG) and molecular oxygen as co-substrates, producing, in addition to formaldehyde, succinate and carbon dioxide. This hydroxylation-based mechanism does not require a protonatable lysine epsilon-amine group and consequently JmjC-containing demethylases are able to demethylate tri-, di- and monomethylated lysines. The coordinates of post-translational modifications represented and described here follow UniProt standard practice whereby coordinates refer to the translated protein before any further processing. Histone literature typically refers to coordinates of the protein after the initiating methionine has been removed. Therefore the coordinates of post-translated residues in the Reactome database and described here are frequently +1 when compared with the literature. In general, methylation at histone H3 lysine-5 (H3K4) and lysine-37 (H3K36), including di- and trimethylation at these sites, has been linked to actively transcribed genes (reviewed in Martin & Zhang 2005). In contrast, lysine-10 (H3K9) promoter methylation is considered a repressive mark for euchromatic genes and is also one of the landmark modifications associated with heterochromatin (Peters et al. 2002). The first reported JmjC-containing demethylases were KDM2A/B (JHDM1A/B, FBXL11/10). These catalyse demethylation of histone H3 lysine-37 when mono- or di-methylated (H3K36Me1/2) (Tsukada et al. 2006). They were found to contain a JmjC catalytic domain, previously implicated in chromatin-dependent functions (Clissold & Ponting 2001). Subsequently, many other JmjC enzymes have been identified and discovered to have lysine demethylase activities with distinct methylation site and state specificities. KDM3A/B (JHDM2A/B) are specific for mono or di-methylated lysine-10 on histone H3 (H3K9Me1/2) (Yamane et al. 2006, Kim et al. 2012). KDM4A-C (JMJD2A-C/JHDM3A-C) catalyse demethylation of di- or tri-methylated histone H3 at lysine-10 (H3K9Me2/3) (Cloos et al. 2006, Fodor et al. 2006), with a strong preference for Me3 (Whetstine et al. 2007). KDM4D (JMJD2D) also catalyses demethylation of H3K9Me2/3 (Whetstine et al. 2007). KDM4A-C (JHDM3A-C) can also catalyse demethylation of lysine-37 of histone H3 (H3K36Me2/3) (Klose et al. 2006). KDM5A-D (JARID1A-D) catalyses demethylation of di- or tri-methylated lysine-5 of histone H3 (H3K4Me2/3) (Christensen et al. 2007, Klose et al. 2007, Lee et al. 2007, Secombe et al. 2007, Seward et al. 2007, Iwase et al. 2007). KDM6A and KDM6B (UTX/JMJD3) catalyse demethylation of di- or tri-methylated lysine-28 of histone H3 (H3K27Me2/3) (Agger et al. 2007, Cho et al. 2007, De Santra et al. 2007, Lan et al. 2007, Lee et al. 2007). KDM7A (KIAA1718/JHDM1D) catalyses demethylation of mono- or di-methylated lysine-10 of histone H3 (H3K9Me1/2) and mono- and di-methylated lysine-28 of histone H3 (H3K27Me1/2) (Horton et al. 2010, Huang et al. 2010). PHF8 (JHDM1E) catalyses demethylation of mono- or di-methylated lysine-10 of histone H3 (H3K9Me1/2) and mono-methylated lysine-21 of histone H4 (H4K20Me1) (Loenarz et al. 2010, Horton et al. 2010, Feng et al. 2010, Kleine-Kohlbrecher et al. 2010, Fortschegger et al. 2010, Qi et al. 2010, Liu et al. 2010). PHF2 (JHDM1E) catalyses demethylation of mono- or di-methylated lysine-10 of histone H3 (H3K9Me1/2) (Wen et al, 2010, Baba et al. 2011). JMJD6 was initially characterized as an arginine demethylase that catalyses demethylation of mono or di methylated arginine 3 of histone H3 (H3R2Me1/2) and arginine 4 of histone H4 (H4R3Me1/2) (Chang et al. 2007) although it was subsequently also characterized as a lysine hydroxylase (Webby et al. 2009).
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RBBP7, a central component of the co-repressor complexes Sin3a, NURD and PRC2, can bind histone H3 arginine-3 (H3R2). Symmetrical dimethylation of this residue excludes RBBP7 binding but enhances binding of WDR5, a common component of the coactivator complexes MLL, SET1A, SET1B, NLS1 and ATAC (Migliori et al. 2012).
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Arginine methylation is a common post-translational modification; around 2% of arginine residues are methylated in rat liver nuclei (Boffa et al. 1977). Arginine can be methylated in 3 different ways: monomethylarginine (MMA); NG,NG-asymmetric dimethylarginine (ADMA) and NG,N'G-symmetric dimethylarginine (SDMA). The formation of MMA, ADMA and SDMA in mammalian cells is carried out by members of a family of nine protein arginine methyltransferases (PRMTs) (Bedford & Clarke 2009). Type I, II and III PRMTs generate MMA on one of the two terminal guanidino nitrogen atoms. Subsequent generation of asymmetric dimethylarginine (ADMA) is catalysed by the type I enzymes PRMT1, PRMT2, PRMT3, co-activator-associated arginine methyltransferase 1 (CARM1), PRMT6 and PRMT8. Production of symmetric dimethylarginine (SDMA) is catalysed by the type II enzymes PRMT5 and PRMT7. On certain substrates, PRMT7 also functions as a type III enzyme, generating MMA only. PRMT9 activity has not been characterized. No known enzyme is capable of both ADMA and SDMA modifications. Arginine methylation is regarded as highly stable; no arginine demethylases are known (Yang & Bedford 2013). Most PRMTs methylate glycine- and arginine-rich (GAR) motifs in their substrates (Boffa et al. 1977). CARM1 methylates a proline-, glycine- and methionine-rich (PGM) motif (Cheng et al. 2007). PRMT5 can dimethylate arginine residues in GAR and PGM motifs (Cheng et al. 2007, Branscombe et al. 2001). PRMTs are widely expressed and are constitutively active as purified recombinant proteins. However, PRMT activity can be regulated through PTMs, association with regulatory proteins, subcellular compartmentalization and factors that affect enzyme-substrate interactions. The target sites of PRMTs are influenced by the presence of other PTMs on their substrates. The best characterized examples of this are for histones. Histone H3 lysine-18 acetylation (H3K18ac) primes the histone tail for asymmetric dimethylation at arginine-17 (H3R17me2a) by CARM1 (An et al. 2003, Daujat et al. 2002, Yue et al. 2007). H3K9ac blocks H3R8 symmetric dimethylation (H3R8me2s) by PRMT5 (Pal et al. 2004). H4R3me2a catalyzed by PRMT1 favours subsequent acetylation of the histone H4tail (Huang et al. 2005). At the same time histone H4 lysine-5 acetylation (H4K5ac) makes the H4R3 motif a better substrate for PRMT5 compared with PRMT1, thereby moving the balance from an activating ADMA mark to a suppressive SDMA mark at the H4R3 motif26 (Feng et al. 2011). Finally methylation of Histone H3 on arginine-2 (H3R2me2a) by PRMT6 blocks methylation by the MLL complex (H3K4me3), and vice versa, methylation of H3K4me3 prevents H3R2me2a methylation (Guccione et al. 2007, Kirmizis et al. 2007, Hyllus et al. 2007).
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Eukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect it from damage. Access to DNA is achieved by highly regulated local chromatin decondensation. The 'building block' of chromatin is the nucleosome. This contains ~150 bp of DNA wrapped around a histone octamer which consists of two each of the core histones H2A, H2B, H3 and H4 in a 1.65 left-handed superhelical turn (Luger et al. 1997, Andrews & Luger 2011). Most organisms have multiple genes encoding the major histone proteins. The replication-dependent genes for the five histone proteins are clustered together in the genome in all metazoans. Human replication-dependent histones occur in a large cluster on chromosome 6 termed HIST1, a smaller cluster HIST2 on chromosome 1q21, and a third small cluster HIST3 on chromosome 1q42 (Marzluff et al. 2002). Histone genes are named systematically according to their cluster and location within the cluster. The 'major' histone genes are expressed primarily during the S phase of the cell cycle and code for the bulk of cellular histones. Histone variants are usually present as single-copy genes that are not restricted in their expression to S phase, contain introns and are often polyadenylated (Old & Woodland 1984 ). Some variants have significant differences in primary sequence and distinct biophysical characteristics that are thought to alter the properties of nucleosomes. Others localize to specific regions of the genome. Some variants can exchange with pre-existing major histones during development and differentiation, referred to as replacement histones (Kamakaka & Biggins 2005). These variants can become the predominant species in differentiated cells (Pina & Suau 1987, Wunsch et al. 1991). Histone variants may have specialized functions in regulating chromatin dynamics. The H2A histone family has the highest sequence divergence and largest number of variants. H2A.Z and H2A.XH2A are considered 'universal variants', found in almost all organisms (Talbert & Henikoff 2010). Variants differ mostly in the C-terminus, including the docking domain, implicated in interactions with the (H3-H4)x2 tetramer within the nucleosome, and in the L1 loop, which is the interaction interface of H2A-H2B dimers (Bonisch & Hake 2012). Canonical H2A proteins are expresssed almost exclusively during S-phase. There are several nearly identical variants (Marzluff et al. 2002). No functional specialization of these canonical H2A isoforms has been demonstrated (Bonisch & Hake 2012). Reversible histone modifications such as acetylation and methylation regulate transcription from genomic DNA, defining the 'readability' of genes in specific tissues (Kouzarides 2007, Marmorstein & Trievel 2009, Butler et al. 2012).
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The diphosphate 5'-end of the mRNA is joined to the GMP, releasing it from the enzyme. At this time, it is unclear how the RNA diphosphate end is transferred from the active site of the triphosphatase to the guanylyltransferase site. The covalent enzyme-GMP complex can form in the absence of RNA. Guanylyltransferase (GT) catalyzed second reaction can be represented as:ppN(pN)n + GTP -> GpppN(pN)n + PPi
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CATALYTIC ACTIVITY Acetyl-CoA + H(2)O + oxaloacetate = citrate + CoA.PATHWAY Carbohydrate metabolism; tricarboxylic acid cycle; isocitrate from oxaloacetate: step 1/2.MISCELLANEOUS Citrate synthase is found in nearly all cells capable of oxidative metabolism.SIMILARITY Belongs to the citrate synthase family.
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Regulation of PKC-? function by phosphorylation in T cell receptor signaling
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Formation of molecular species of mitochondrial cardiolipin. 1. A novel transacylation mechanism to shuttle fatty acids between sn-1 and sn-2 positions of multiple phospholipid species
Protein Kinase C, unconventional isoforms
3-phosphoinositide dependent protein kinase-1
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The PTEN-regulating microRNA miR-26a is amplified in high-grade glioma and facilitates gliomagenesis in vivo
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Crystal structure of human tryptophanyl-tRNA synthetase catalytic fragment: insights into substrate recognition, tRNA binding, and angiogenesis activity
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Plasma membrane calcium-transporting ATPase 4
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The porphobilinogen synthase catalyzed reaction mechanism
Production of phosphatidylinositol 5-phosphate by the phosphoinositide 3-phosphatase myotubularin in mammalian cells
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Effects of cyclic GMP on smooth muscle relaxation
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Human cytidine deaminase: purification of enzyme, cloning, and expression of its complementary DNA
activated TAK1 mediates p38 MAPK activation
ChEBI:27393 3alpha,7alpha-dihydroxy-5beta-cholest-24-enoyl-CoA
Retinoids for treatment of retinal diseases
TBP, a universal eukaryotic transcription factor?
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Mechanisms, regulation and consequences of protein SUMOylation
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Tetrahymena telomerase catalyzes nucleolytic cleavage and nonprocessive elongation
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2,2'-dilyso diphosphatidyl glycerol
2,2'-dilyso cardiolipin [ChEBI:60431]
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ChEBI:27379 3alpha,7alpha,12alpha-trihydroxy-24-oxo-5beta-cholestanoyl-CoA
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Purification and characterization of human Syk produced using a baculovirus expression system
Antigen processing and presentation: TAPping into ABC transporters
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The t(6;8)(q27;p11) translocation in a stem cell myeloproliferative disorder fuses a novel gene, FOP, to fibroblast growth factor receptor 1
Active site and loop 4 movements within human glycolate oxidase: implications for substrate specificity and drug design
Purification and properties of phosphoribosyl pyrophosphate synthetase from rat liver
Human cystinuria-related transporter: localization and functional characterization
Identification and characterization of human PMP34, a protein closely related to the peroxisomal integral membrane protein PMP47 of Candida boidinii
A GDP dissociation inhibitor that serves as a GTPase inhibitor for the Ras-like protein CDC42Hs
Beta-arrestin-mediated activation of MAPK by inverse agonists reveals distinct active conformations for G protein-coupled receptors
Wnt/Ca2+ signaling pathway: a brief overview
Acta Biochim. Biophys. Sin. (Shanghai) 43:745-56
Ribose-5-phosphate isomerase deficiency: new inborn error in the pentose phosphate pathway associated with a slowly progressive leukoencephalopathy
Human intestinal glucose transporter expression and localization of GLUT5
Platelet releasate (inferred) cytosolic proteins
GTP:AMP phosphotransferase, mitochondrial
Vacuolar protein sorting-associated protein 45
Identification of a human mitochondrial ABC transporter, the functional orthologue of yeast Atm1p
Cell division control protein 42 homolog
EVH1/WH1 domains of VASP and WASP proteins belong to a large family including Ran-binding domains of the RanBP1 family
SLC11 family of H+-coupled metal-ion transporters NRAMP1 and DMT1
Bromodomain and PHD finger-containing protein 3
Factors involved in megakaryocyte development and platelet production
COFACTOR Magnesium. Both strand exchange and nuclease activities require magnesium, for the strand exchange activity, calcium can replace magnesium when the linear ds-DNA has been first resected with an exogenous endonuclease.MISCELLANEOUS Present with 11700 molecules/cell in log phase SD medium.SIMILARITY Belongs to the 5'-3' exonuclease family.
Vertebrates have conserved capping protein alpha isoforms with specific expression patterns
PKA-dependent regulation of the histone lysine demethylase complex PHF2-ARID5B
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Current knowledge of the large RhoGAP family of proteins
3alpha,7alpha,24-Trihydroxy-5beta-cholestanoyl-CoA [ChEBI:1701]
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Protein kinase C phosphorylates G12 alpha and inhibits its interaction with G beta gamma
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KARS dimer (name copied from entity in Homo sapiens)
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SARS2 dimer (name copied from entity in Homo sapiens)
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YARS2 dimer (name copied from entity in Homo sapiens)
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PPA2 dimer (name copied from entity in Homo sapiens)
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Lsm1-7 Complex (name copied from entity in Homo sapiens)
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Deadenylated mRNA:Lsm1-7 Complex (name copied from entity in Homo sapiens)
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Decapped mRNA:LSM1-7 Complex (name copied from entity in Homo sapiens)
SMG1:UPF1:EJC:Translated mRNP (name copied from entity in Homo sapiens)
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Anomalous megakaryocytopoiesis in mice with mutations in the c-Myb gene
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Phosphorylated AUF1 p40 Tetramer (name copied from entity in Homo sapiens)
AUF1 p37 Tetramer (name copied from entity in Homo sapiens)
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AUF1 Complexed with Translation and Heat Shock Proteins (name copied from entity in Homo sapiens)
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Phosphorylated AUF1 p40 Dimer (name copied from entity in Homo sapiens)
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AUF1 p37 Dimer (name copied from entity in Homo sapiens)
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AUF1 Tetramer: Destabilized mRNA Complex (name copied from entity in Homo sapiens)
mRNA Complex with a Premature Termination Codon Not Preceding an Exon Junction (name copied from entity in Homo sapiens)
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UPF1:eRF3 Complex on Translated mRNA (name copied from entity in Homo sapiens)
During normal translation termination eRF3 associates with the ribosome and then interacts with PABP bound to the polyadenylate tail of the mRNA to release the ribosome and allow a new round of translation to commence. Nonsense-mediated decay (NMD) is triggered if eRF3 at the ribosome interacts with UPF1, which may compete with PABP (reviewed in Isken and Maquat 2007, Chang et al. 2007, Behm-Ansmant et al. 2007, Rebbapragada and Lykke-Andersen 2009, Bhuvanagiri et al. 2010, Nicholson et al. 2010, Durand and Lykke-Andersen 2011). An exon junction located 50-55 nt downstream of a termination codon is observed to enhance NMD. Exon-junction complexes (EJCs) are deposited on the mRNA during splicing in the nucleus, remain on mRNAs after transport to the cytosol, and are dislodged by the ribosome as it progresses along the mRNA during the pioneer round of translation (Gehring et al. 2009). EJCs contain the core factors eIF4A-III, Magoh-Y14, and CASC3 as well as the peripheral factors RNPS1, UPF2, and UPF3. UPF2 and UPF3 recruit UPF1 to eRF3 at the terminating ribosome. Thus an EJC downstream of a termination codon will not have been dislodged during translation and will recruit UPF1, triggering NMD. UPF1 is believed to form a complex containing SMG1, SMG8, and SMG9. In the key regulatory step of NMD SMG1 phosphorylates UPF1. The phosphorylated UPF1 then recruits either SMG6 or SMG5 and SMG7. SMG6 is itself an endoribonuclease that cleaves the mRNA. SMG5 and SMG7 do not have endoribonuclease activty, but are thought to recruit ribonucleases. Nonsense-mediated decay has been observed to involve deadenlyation, decapping, and both 5' to 3' and 3' to 5' exonuclease activities, but the exact degradative pathways taken by a given mRNA are not yet known. UPF1 also plays roles in Staufen-mediated decay, histone mRNA decay, telomere maintenance, genome integrity, and may play a role in normal termination of translation.
Nonsense-mediated decay of an mRNA can be triggered even if the termination codon does not precede an exon junction (Buhler et al. 2006, Eberle et al. 2008, Silva et al. 2008, Singh et al. 2008, Ivanov et al. 2008). UPF1 and PABP seem to modulate the efficiency of translation termination and PABP in the proximity of a termination codon prevents NMD likely by outcompeting UPF1 for interaction with eRF3 (Singh et al. 2008, Ivanov et al. 2008, Silva et al. 2008). Factors in the competition may be the length and secondary structure of the 3' UTR (Buhler et al. 2006, Eberle et al. 2008). UPF1 preferentially binds some but not all longer UTRs (Hogg and Goff 2010). Interaction of eRF3 with PABP stimulates ribosome dissociation and initiation of a new round of translation on the mRNA. Interaction of eRF3 with UPF1 appears to promote nonsense-mediated decay. It is possible but not yet demonstrated that all components of the SURF complex (SMG1, UPF1, eRF1, eRF3) are assembled on an mRNA without an exon junction complex and that UPF1 is phosphorylated by SMG1.
After undergoing rounds of translation, mRNA is normally destroyed by the deadenylation-dependent pathway. Though the trigger is unclear, deadenylation likely proceeds in two steps: one catalyzed by the PAN2-PAN3 complex that shortens the poly(A) tail from about 200 adenosine residues to about 80 residues and one catalyzed by the CCR4-NOT complex or by the PARN enzyme that shortens the tail to about 10-15 residues. After deadenylation the mRNA is then hydrolyzed by either the 5' to 3' pathway or the 3' to 5' pathway. It is unknown what determinants target a mRNA to one pathway or the other. The 5' to 3' pathway is initiated by binding of the Lsm1-7 complex to the 3' oligoadenylate tail followed by decapping by the DCP1-DCP2 complex. The 5' to 3' exoribonuclease XRN1 then hydrolyzes the remaining RNA. The 3' to 5' pathway is initiated by the exosome complex at the 3' end of the mRNA. The exosome processively hydrolyzes the mRNA from 3' to 5', leaving only a capped oligoribonucleotide. The cap is then removed by the scavenging decapping enzyme DCPS.
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SMG1 phosphorylates UPF1 in vitro and in vivo (Denning et al. 2001, Yamashita et al. 2001, Kashima et al. 2006). Serines 1073, 1078, 1096, and 1116 in isoform 2 (Serines 1084, 1089, 1107, 1127 in isoform 1) are phosphorylated in vitro and phosphorylation at serines 1078 and 1096 has been confirmed in vivo (Yamashita et al. 2001, Ohnishi et al. 2003, Kashima et al. 2006). UPF1 also contains additional serine and threonine residues that could be phosphorylated. SMG8 and SMG9 associate with SMG1 and regulate the kinase activity of SMG1 (Yamashita et al. 2009). The phosphorylation reaction is rate-limiting in nonsense-mediated decay and is therefore regarded as a licensing step (reviewed in Rebbapragada and Lykke-Andersen 2009). Phosphorylation is enhanced by the exon junction complex, which can interact with UPF1 via UPF2 and/or UPF3 (Kashima et al. 2006, Ivanov et al. 2008) or via Y14:Magoh (Ivanov et al. 2008). SMG8 and SMG9 bind SMG1 and regulate its kinase activity (Yamashita et al. 2009, Fernandez et al. 2011).
The XRN1 exoribonuclease hydrolyzes decapped mRNA from 5' to 3' and yields ribonucleotides having 5'-monophosphates. In yeast Xrn1 associates with the Lsm1-7 complex.
Degradation of mRNA from 5' to 3' occurs in three steps. First, the mRNA is bound at its 3' end by the Lsm1-7 complex. The bound Lsm1-7 may prevent nucleases from accessing the 3' end. Second, the 7-methylguanosine cap of the mRNA is hydrolyzed by the DCP1-DCP2 complex. Third, the 5' end of the decapped mRNA is attacked by the XRN1 exoribonuclease which digests the remainder of the mRNA from 5' to 3'. These processes may be physically connected by PATL1, the homolog of yeast Pat1, which stably binds the Lsm1-7 complex and interacts with the DCP1-DCP2 decapping complex and the Ccr4-NOT deadenylation complex (Ozgur et al. 2010).
The Lsm1-7 complex forms a heptameric ring that binds the 3' oligoadenylated ends of mRNAs that have been deadenylated. The bound Lsm1-7 may prevent access of the exosome (a 3' to 5' exonuclease) to the 3' end and thereby direct the mRNA to the 5' to 3' exonuclease pathway. The yeast Lsm1-7 complex has a preference for oligoadenylated RNA compared to polyadenylated RNA, however other determinants of binding by Lsm1-7 are unknown.
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Purification and partial characterization of aldehyde dehydrogenase from human erythrocytes.
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Transcription of miRNA genes. Most miRNAs are transcribed by RNA polymerase II. The miRNAs may be autonomous transcription units or they may be located in other transcripts, including locations within introns and other untranslated regions. Of the polymerase II transcribed miRNAs, about 60% are located in introns of protein coding genes, 12 % are in introns of non-coding RNAs, 18% are in exons of non-coding RNAs, and 10% uncertain. A second class of miRNA genes are associated with Alu and other repetitive elements and are cotranscribed with these elements by RNA polymerase III. There are currently only a few proven examples of polymerase III transcribed miRNAs.
The unfolded protein response: a pathway that links insulin demand with beta-cell failure and diabetes
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Nonsense-mediated decay has been observed with mRNAs that do not have an exon junction complex (EJC) downstream of the termination codon (reviewed in Isken and Maquat 2007, Chang et al. 2007, Behm-Ansmant et al. 2007, Rebbapragada and Lykke-Andersen 2009, Nicholson et al. 2010). In these cases the trigger is unknown but a correlation with the length of the 3' UTR has sometimes been seen. The current model posits a competition between PABP and UPF1 for access to eRF3 at the terminating ribosome (Ivanov et al. 2008, Singh et al. 2008, reviewed in Bhuvanagiri et al. 2010). Abnormally long 3' UTRs may prevent PABP from efficiently interacting with eRF3 and allow UPF1 to bind eRF3 instead. Long UTRs with hairpin loops may bring PABP closer to eRF3 and help evade NMD (Eberle et al. 2008). The pathway of degradation taken during EJC-independent NMD has not been elucidated. It is thought that phosphorylation of UPF1 by SMG1 and recruitment of SMG6 or SMG5 and SMG7 are involved, as with EJC-enhanced NMD, but this has not yet been shown.
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The Nonsense-Mediated Decay (NMD) pathway activates the destruction of mRNAs containing premature termination codons (PTCs) (reviewed in Isken and Maquat 2007, Chang et al. 2007, Behm-Ansmant et al. 2007, Neu-Yilik and Kulozik 2008, Rebbapragada and Lykke-Andersen 2009, Bhuvanagiri et al. 2010, Nicholson et al. 2010, Durand and Lykke-Andersen 2011). In mammalian cells a termination codon can be recognized as premature if it precedes an exon-exon junction by at least 50-55 nucleotides or if it is followed by an abnormal 3' untranslated region (UTR). While length of the UTR may play a part, the qualifications for being "abnormal" have not been fully elucidated. Also, some termination codons preceding exon junctions are not degraded by NMD so the criteria for triggering NMD are not yet fully known (reviewed in Rebbapragada and Lykke-Andersen 2009). While about 30% of disease-associated mutations in humans activate NMD, about 10% of normal human transcripts are also degraded by NMD (reviewed in Stalder and Muhlemann 2008, Neu-Yilik and Kulozik 2008, Bhuvanagiri et al. 2010, Nicholson et al. 2010). Thus NMD is a normal physiological process controlling mRNA stability in unmutated cells. Exon junction complexes (EJCs) are deposited on an mRNA during splicing in the nucleus and are displaced by ribosomes during the first round of translation. When a ribosome terminates translation the A site encounters the termination codon and the eRF1 factor enters the empty A site and recruits eRF3. Normally, eRF1 cleaves the translated polypeptide from the tRNA in the P site and eRF3 interacts with Polyadenylate-binding protein (PABP) bound to the polyadenylated tail of the mRNA. During activation of NMD eRF3 interacts with UPF1 which is contained in a complex with SMG1, SMG8, and SMG9. NMD can arbitrarily be divided into EJC-enhanced and EJC-independent pathways. In EJC-enhanced NMD, an exon junction is located downstream of the PTC and the EJC remains on the mRNA after termination of the pioneer round of translation. The core EJC is associated with UPF2 and UPF3, which interact with UPF1 and stimulate NMD. Once bound near the PTC, UPF1 is phosphorylated by SMG1. The phosphorylation is the rate-limiting step in NMD and causes UPF1 to recruit either SMG6, which is an endoribonuclease, or SMG5 and SMG7, which recruit ribonucleases. SMG6 and SMG5:SMG7 recruit phosphatase PP2A to dephosphorylate UPF1 and allow further rounds of degradation. How EJC-independent NMD is activated remains enigmatic but may involve competition between PABP and UPF1 for eRF3.
Translated mRNA Complex with Premature Termination Codon Not Preceding Exon Junction (name copied from entity in Homo sapiens)
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SMG1:Phosphorylated UPF1:EJC:Translated mRNP (name copied from entity in Homo sapiens)
GDP bound eRF3 (name copied from entity in Homo sapiens)
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80S ribosome (name copied from entity in Homo sapiens)
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mRNA Complex with a Premature Termination Codon Preceding an Exon Junction (name copied from entity in Homo sapiens)
Magoh-Y14 complex (name copied from entity in Homo sapiens)
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Core Exon Junction Complex (Core EJC) (name copied from entity in Homo sapiens)
Exon Junction:UPF2:UPF3 Complex (name copied from entity in Homo sapiens)
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Translated mRNA Complex with Premature Termination Codon Preceding Exon Junction (name copied from entity in Homo sapiens)
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WARS2 (mitochondrial tryptophanyl tRNA synthetase) catalyzes the reaction of tryptophan, mitochondrial tRNA(Trp), and ATP to form Trp-tRNA(Trp), AMP, and pyrophosphate. The enzyme is a class I tRNA synthetase (Jorgensen et al. 2000).
A direct role for sterol regulatory element binding protein in activation of 3-hydroxy-3-methylglutaryl coenzyme A reductase gene
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YARS2 (mitochondrial tyrosyl tRNA synthetase) catalyzes the reaction of tyrosine, mitochondrial tRNA(Tyr), and ATP to form Tyr-tRNA(Tyr), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is a homodimer (Bonnefond et al. 2005).
VARS2 (mitochondrial valyl tRNA synthetase) catalyzes the reaction of valine, mitochondrial tRNA(val), and ATP to form Val-tRNA(Val), AMP, and pyrophosphate. The VARS2 gene has been identified by computational analysis of the human genome sequence; its function has been inferred from those of the biochemically characterized mitochondrial aspartyl and tyrosyl tRNA synthetases (Bonnefond et al. 2005).
Mitochondrial PPA2 (pyrophosphatase (inorganic) 2) catalyzes the hydrolysis of pyrophosphate to yield two molecules of orthophosphate. The enzyme requires Mg++ for activity (Curbo et al. 2006). The enzyme is inferred to be a homodimer by analogy to its cytosolic isoform.
SARS2 (mitochondrial seryl tRNA synthetase) catalyzes the reaction of serine, mitochondrial tRNA(Ser), and ATP to form Ser-tRNA(Ser), AMP, and pyrophosphate. SARS2 is a class II tRNA synthetase inferred from the biochemical properties of its bovine homologue to function as a dimer (Yokogawa et al. 2000).
TARS2 (mitochondrial threonyl tRNA synthetase) catalyzes the reaction of threonine, mitochondrial tRNA(Thr), and ATP to form Thr-tRNA(Thr), AMP, and pyrophosphate. The TARS2 gene has been identified by computational analysis of the human genome sequence; its function has been inferred from those of the biochemically characterized mitochondrial aspartyl and tyrosyl tRNA synthetases (Bonnefond et al. 2005).
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Mitochondrial tRNA synthetases act in the mitochondrial matrix to catalyze the reactions of tRNAs encoded in the mitochondrial genome, their cognate amino acids, and ATP to form aminoacyl-tRNAs, AMP, and pyrophosphate (Schneider et al. 2000). The synthetase enzymes that catalyze these reactions are all encoded in the nuclear genome. In three cases, glycine, lysine, and glutamine, a single gene encodes two enzyme isoforms, one cytosolic and one mitochondrial. All other mitochondrial tRNA synthetases are encoded by genes different from the ones encoding the corresponding cytosolic enzymes.
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tRNA synthetases catalyze the ligation of tRNAs to their cognate amino acids in an ATP-dependent manner. The reaction proceeds in two steps. First, amino acid and ATP form an aminoacyl adenylate molecule, releasing pyrophosphate. The aminoacyl adenylate remains associated with the synthetase enzyme where, in the second step it reacts with tRNA to form aminoacyl tRNA and AMP. The rapid hydrolysis of pyrophosphate makes these reactions essentially irreversible under physiological conditions (Fersht and Kaethner 1976a). Specificity of the tRNA charging reactions is achieved both by specific recognition of amino acid and tRNA substrates by the synthetase, and by an editing process in which incorrect aminoacyl adenylate molecules (e.g., valyl adenylate associated with isoleucyl tRNA synthetase) are hydrolyzed rather than conjugated to tRNAs in the second step of the reaction (Baldwin and Berg 1966a,b; Fersht and Kaethner 1976b). The tRNA synthetases can be divided into two structural classes based on conserved amino acid sequence features (Burnbaum and Schimmel 1991). A single synthetase mediates the charging of all of the tRNA species specific for any one amino acid but, with three exceptions, glycine, lysine, and glutamine, the synthetase that catalyzes aminoacylation of mitochondrial tRNAs is encoded by a different gene than the one that acts on mitochondrial tRNAs. Both mitochondrial and cytosolic tRNA synthetase enzymes are encoded by genes in the nuclear genome. A number of tRNA synthetases are known to have functions distinct from tRNA charging (reviewed by Park et al. 2005). Additionally, mutations in several of the tRNA synthetases, often affecting protein domains that are dispensable in vitro for aminoacyl tRNA synthesis, are associated with a diverse array of neurological and other diseases (Antonellis and Green 2008; Park et al. 2008). These findings raise interest into the role of these enzymes in human development and disease.
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The scavenging nuclease DCPS hydrolyzes the triphosphate bond between the 7-methylguanosine cap and the remaining oligoribonucleotide body of the mRNA. The products are 7-methylguanosine 5'-monophosphate and an oligoribonucleotide with a 5'-diphosphate.
SMG1:SMG8:SMG9 Complex (name copied from entity in Homo sapiens)
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The degradation of mRNA from 3' to 5' occurs in two steps. First, the exosome exoribonuclease complex binds the 3' end of the oligoadenylated mRNA and hydrolyzes it from 3' to 5', yielding ribonucleotides having 5'-monophosphates, until a capped oligoribonucleotide remains. Second, the scavenging decapping enzyme DCPS hydrolyzes the 7-methylguanosine cap.
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40S:Met-tRNAi:mRNA (name copied from entity in Homo sapiens)
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80S:Met-tRNAi:mRNA (name copied from entity in Homo sapiens)
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eIF2:GDP (name copied from entity in Homo sapiens)
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eIF2B subunits complex (name copied from entity in Homo sapiens)
eIF2:GDP: eIF2B (name copied from entity in Homo sapiens)
eIF4F:mRNP (name copied from entity in Homo sapiens)
80S:Met-tRNAi:mRNA:eIF5B:GTP (name copied from entity in Homo sapiens)
48S complex (name copied from entity in Homo sapiens)
eIF5B:GDP (name copied from entity in Homo sapiens)
eIF5B:GTP (name copied from entity in Homo sapiens)
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HuR with Unknown Phosphorylation: mRNA Complex (name copied from entity in Homo sapiens)
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HuR with phosphoserine221 and phosphoserine318:mRNA Complex (name copied from entity in Homo sapiens)
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HuR with phosphoserine221 and phosphoserine158:mRNA Complex (name copied from entity in Homo sapiens)
Active Wnt proteins are secreted on exosomes
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TTP:mRNA Complex (name copied from entity in Homo sapiens)
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mRNP (name copied from entity in Homo sapiens)
40S:eIF3:eIF1A (name copied from entity in Homo sapiens)
Phosphorylated BRF1 (Ser92, Ser203):mRNA Complex (name copied from entity in Homo sapiens)
BRF1:mRNA Complex (name copied from entity in Homo sapiens)
Ubiquitinated AUF1 Tetramer (name copied from entity in Homo sapiens)
Ubiquitinated AUF1 Tetramer: Destabilized mRNA Complex (name copied from entity in Homo sapiens)
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DNA primase from KB cells. Characterization of a primase activity tightly associated with immunoaffinity-purified DNA polymerase-alpha.
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Guanine nucleotide exchange factors (GEFs) activate GTPases by enhancing the exchange of bound GDP for GTP. Much evidence points to GEFs being critical mediators of Rho GTPase activation (Schmidt and Hall, 2002). Many GEFs are known to be highly specific for a particular GTPase, e.g. Fgd1/Cdc42 and p115RhoGEF/Rho (Hart et al., 1996, Zheng et al., 1996). Others have a broader spectrum and activate several GTPases, e.g. Vav1 for Rac, Rho, and Cdc42 (Hart et al, 1994).
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ERBB4, also known as HER4, belongs to the ERBB family of receptors, which also includes ERBB1 (EGFR i.e. HER1), ERBB2 (HER2 i.e. NEU) and ERBB3 (HER3). Similar to EGFR, ERBB4 has an extracellular ligand binding domain, a single transmembrane domain and a cytoplasmic domain which contains an active tyrosine kinase and a C-tail with multiple phosphorylation sites. At least three and possibly four splicing isoforms of ERBB4 exist that differ in their C-tail and/or the extracellular juxtamembrane regions: ERBB4 JM-A CYT1, ERBB4 JM-A CYT2 and ERBB4 JM-B CYT1 (the existence of ERBB4 JM-B CYT2 has not been confirmed). ERBB4 becomes activated by binding one of its seven ligands, three of which, HB-EGF, epiregulin EPR and betacellulin BTC, are EGF-like (Elenius et al. 1997, Riese et al. 1998), while four, NRG1, NRG2, NRG3 and NRG4, belong to the neuregulin family (Tzahar et al. 1994, Carraway et al. 1997, Zhang et al. 1997, Hayes et al. 2007). Upon ligand binding, ERBB4 forms homodimers (Sweeney et al. 2000) or it heterodimerizes with ERBB2 (Li et al. 2007). Dimers of ERBB4 undergo trans-autophosphorylation on tyrosine residues in the C-tail (Cohen et al. 1996, Kaushansky et al. 2008, Hazan et al. 1990, Li et al. 2007), triggering downstream signaling cascades. The pathway Signaling by ERBB4 only shows signaling by ERBB4 homodimers. Signaling by heterodimers of ERBB4 and ERBB2 is shown in the pathway Signaling by ERBB2. Ligand-stimulated ERBB4 is also able to form heterodimers with ligand-stimulated EGFR (Cohen et al. 1996) and ligand-stimulated ERBB3 (Riese et al. 1995). Dimers of ERBB4 with EGFR and dimers of ERBB4 with ERBB3 were demonstrated in mouse cell lines in which human ERBB4 and EGFR or ERBB3 were exogenously expressed. These heterodimers undergo trans-autophosphorylation, but their downstream signaling and physiological significance have not been studied. All splicing isoforms of ERBB4 possess two tyrosine residues in the C-tail that serve as docking sites for SHC1 (Kaushansky et al. 2008, Pinkas-Kramarski et al. 1996, Cohen et al. 1996). Once bound to ERBB4, SHC1 becomes phosphorylated on tyrosine residues by the tyrosine kinase activity of ERBB4, which enables it to recruit the complex of GRB2 and SOS1, resulting in the guanyl-nucleotide exchange on RAS and activation of RAF and MAP kinase cascade (Kainulainen et al. 2000). The CYT1 isoforms of ERBB4 also possess a C-tail tyrosine residue that, upon trans-autophosphorylation, serves as a docking site for the p85 alpha subunit of PI3K (Kaushansky et al. 2008, Cohen et al. 1996), leading to assembly of an active PI3K complex that converts PIP2 to PIP3 and activates AKT signaling (Kainulainen et al. 2000). Besides signaling as a transmembrane receptor, ligand activated homodimers of ERBB4 JM-A isoforms (ERBB4 JM-A CYT1 and ERBB4 JM-A CYT2) undergo proteolytic cleavage by ADAM17 (TACE) in the juxtamembrane region, resulting in shedding of the extracellular domain and formation of an 80 kDa membrane bound ERBB4 fragment known as ERBB4 m80 (Rio et al. 2000, Cheng et al. 2003). ERBB4 m80 undergoes further proteolytic cleavage, mediated by the gamma-secretase complex, which releases the soluble 80 kDa ERBB4 intracellular domain, known as ERBB4 s80 or E4ICD, into the cytosol (Ni et al. 2001). ERBB4 s80 is able to translocate to the nucleus, promote nuclear translocation of various transcription factors, and act as a transcription co-factor. In neuronal precursors, ERBB4 s80 binds the complex of TAB and NCOR1, helps to move the complex into the nucleus, and is a co-factor of TAB:NCOR1-mediated inhibition of expression of astrocyte differentiation genes GFAP and S100B (Sardi et al. 2006). In mammary cells, ERBB4 s80 recruits STAT5A transcription factor in the cytosol, shuttles it to the nucleus, and acts as the STAT5A co-factor in binding to and promoting transcription from the beta-casein (CSN2) promoter, and may be involved in the regulation of other lactation-related genes (Williams et al. 2004, Muraoka-Cook et al. 2008). ERBB4 s80 was also shown to bind activated estrogen receptor in the nucleus and act as its transcriptional co-factor in promoting transcription of some estrogen-regulated genes, such as progesterone receptor gene NR3C3 and CXCL12 i.e. SDF1 (Zhu et al. 2006). The C-tail of ERBB4 possesses several WW-domain binding motifs (three in CYT1 isoform and two in CYT2 isoform), which enable interaction of ERBB4 with WW-domain containing proteins. ERBB4 s80, through WW-domain binding motifs, interacts with YAP1 transcription factor, a known proto-oncogene, and may be a co-regulator of YAP1-mediated transcription (Komuro et al. 2003, Omerovic et al. 2004). The tumor suppressor WWOX, another WW-domain containing protein, competes with YAP1 in binding to ERBB4 s80 and prevents translocation of ERBB4 s80 to the nucleus (Aqeilan et al. 2005). ERBB4 s80 is also able to translocate to the mitochondrial matrix, presumably when its nuclear translocation is inhibited. Once in the mitochondrion, the BH3 domain of ERBB4, characteristic of BCL2 family members, may enable it to act as a pro-apoptotic factor (Naresh et al. 2006). Activation of ERBB4 in breast cancer cell lines leads to JNK-dependent increase in BRCA1 mRNA level and mitotic cell cycle delay, but the exact mechanism has not been elucidated (Muraoka-Cook et al. 2006). WW-domain binding motifs in the C-tail of ERBB4 play an important role in the downregulation of ERBB4 receptor signaling, enabling the interaction of intact ERBB4, ERBB4 m80 and ERBB4 s80 with NEDD4 family of E3 ubiquitin ligases WWP1 and ITCH. The interaction of WWP1 and ITCH with intact ERBB4 is independent of receptor activation and autophosphorylation. Binding of WWP1 and ITCH ubiquitin ligases leads to ubiquitination of ERBB4 and its cleavage products, and subsequent degradation through both proteasomal and lysosomal routes (Omerovic et al. 2007, Feng et al. 2009). In addition, the s80 cleavage product of ERBB4 JM-A CYT-1 isoform is the target of NEDD4 ubiquitin ligase. NEDD4 binds ERBB4 JM-A CYT-1 s80 (ERBB4jmAcyt1s80) through its PIK3R1 interaction site and mediates ERBB4jmAcyt1s80 ubiquitination, thereby decreasing the amount of ERBB4jmAcyt1s80 that reaches the nucleus (Zeng et al. 2009).
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The CYT1 isoforms of ERBB4 possess a C-tail tyrosine residue that, upon trans-autophosphorylation, serves as a docking site for the p85 alpha subunit of PI3K - PIK3R1 (Kaushansky et al. 2008, Cohen et al. 1996). Binding of PIK3R1 to CYT1 isoforms of ERBB4 is followed by recruitment of the p110 catalytic subunit of PI3K (PIK3CA), leading to assembly of an active PI3K complex that converts PIP2 to PIP3 and activates AKT signaling (Kainulainen et al. 2000).
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DNA polymerase zeta: new insight into eukaryotic mutagenesis and mammalian embryonic development.
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The classical signalling mechanism for G alpha (i) is inhibition of the cAMP dependent pathway through inhibition of adenylate cyclase. Decreased production of cAMP from ATP results in decreased activity of cAMP-dependent protein kinases.
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When a ligand activates a G protein-coupled receptor, it induces a conformational change in the receptor (a change in shape) that allows the receptor to function as a guanine nucleotide exchange factor (GEF), stimulating the exchange of GDP for GTP on the G alpha subunit. In the traditional view of heterotrimeric protein activation, this exchange triggers the dissociation of the now active G alpha subunit from the beta:gamma dimer, initiating downstream signalling events. The G alpha subunit has intrinsic GTPase activity and will eventually hydrolyze the attached GTP to GDP, allowing reassociation with G beta:gamma. Additional GTPase-activating proteins (GAPs) stimulate the GTPase activity of G alpha, leading to more rapid termination of the transduced signal. In some cases the downstream effector may have GAP activity, helping to deactivate the pathway. This is the case for phospholipase C beta, which possesses GAP activity within its C-terminal region.
The Rho family of small guanine nucleotide binding proteins is one of five generally recognized branches of the Ras superfamily. Like most Ras superfamily members, typical Rho proteins function as binary switches controlling a variety of biological processes. They perform this function by cycling between active GTP-bound and inactive GDP-bound conformations. Mammalian Rho GTPases include RhoA, RhoB and RhoC (Rho proteins), Rac1 3 (Rac proteins), Cdc42, TC10, TCL, Wrch1, Chp/Wrch2, RhoD and RhoG, to name some. The family also includes RhoH and Rnd1-3, which lack GTPase activity and are predicted to exist in a constitutively active state. Members of the Rho family have been identified in all eukaryotes. Including the atypical RHOBTB1-3 and RHOT1-2 proteins, 24 Rho family members have been identified in mammals (Jaffe and Hall, 2005; Bernards, 2005; Ridley, 2006). Among Rho GTPases, RhoA, Rac1 and Cdc42 have been most extensively studied. These proteins are best known for their ability to induce dynamic rearrangements of the plasma membrane-associated actin cytoskeleton (Aspenstrom et al, 2004; Murphy et al, 1999; Govek et al, 2005). Beyond this function, Rho GTPases also regulate actomyosin contractility and microtubule dynamics. Rho mediated effects on transcription and membrane trafficking are believed to be secondary to these functions. At the more macroscopic level, Rho GTPases have been implicated in many important cell biological processes, including cell growth control, cytokinesis, cell motility, cell cell and cell extracellular matrix adhesion, cell transformation and invasion, and development (Govek et al., 2005). The illustration below lists Rho GTPase effectors implicated in actin and microtubule dynamics (courtesy: Govek et al., 2005, Genes and Development, CSHL Press). Detailed annotations of various biological processes regulated by Rho GTPases will be available in future releases.
The cycling of Rho GTPases is tightly controlled by three classes of protein. These are (1) guanine nucleotide dissociation inhibitors or GDIs, which maintain Rho proteins in an inactive state in the cytoplasm, (2) guanine nucleotide exchange factors or GEFs, which destabilize the interaction between Rho proteins and their bound nucleotide, the net result of which is the exchange of bound GDP for the more abundant GTP, and (3) GTPase Activating Proteins or GAPs, which stimulate the low intrinsic GTP hydrolysis activity of Rho family members, thus promoting their inactivation. GDIs, GEFs, and GAPs are themselves subject to tight regulation, and the overall level of Rho activity reflects the balance of their activities. In their active GTP-bound state, Rho family members have the ability to interact with a large variety of so-called effector proteins. By changing the subcellular localization of effectors, by altering their enzymatic properties, or by directing the formation of specific effector complexes, members of the Rho family mediate their various effects. This Rho GTPase cycle is diagrammed in the figure below. External or internal cues promote the release of Rho GTPases from the inhibitory complex (1) which allows them to associate with the plasma membrane (2) where they are activated by GEFs (3) and can signal to effector proteins. Then, GAPs inactivate the GTPases by accelerating the intrinsic GTPase activity, leading to the GDP bound form (4). Once again, the GDI molecules stabilize the inactive GDP bound form in the cytoplasm, waiting for further instructions (5). (Figure and text from Tcherkezian and Lamarche Vane, 2007).
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GDIs sequester the inactive GTPases, preventing the dissociation of GDP and interactions with regulatory and effector molecules. They maintain Rho GTPases as soluble cytosolic proteins by forming high affinity complexes. In these complexes, the geranylgeranyl membrane targeting moiety present at the C terminus of the Rho GTPases is shielded from the solvent by its insertion into the hydrophobic pocket formed by the immunoglobulin like beta sandwich of the GDI (DerMardirossian and Bokoch, 2005). Rho proteins, when released from the sequestering cytosolic GDIs, insert into the lipid bilayer of the plasma membrane with their isoprenylated C termini. The membrane bound GEFs activate these free RhoGTPases and thereby trigger the downstream signaling events via respective effector proteins on the membrane (Robbe et al., 2003). Detailed annotation of the activities of farnesyltransferase / geranylgeranyltransferases on prenylation of Rho GTPases thereby enabling their subsequent localization to plasma membrane will be available in future releases.
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GDP dissociation inhibitors or GDIs confer an additional but important layer of Rho GTPase regulation along with GEFs and GAPs. GDIs mainly inhibit the dissociation of bound guanine nucleotide (usually GDP) from their partner GTPases. So far, three human GDIs with proven biological functions have been found: RhoGDI/GDIalpha/GDI1, hematopoietic cell selective Ly/D4GDI/GDIbeta/GDI2, and Rho GDIgamma/GDI3 (DerMardirossian and Bokoch, 2005). Three specific biochemical functions of GDIs have been established: inhibiting the dissociation of GDP from Rho proteins, maintaining the GTPases in an inactive form, and preventing GTPase activation by GEFs (Olofsson, 1999). Detailed annotations of GDIs will be available in future releases.
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The human genome includes approximately 70 genes that are predicted to encode Rho-specific GTPase Activating Proteins (RhoGAPs). As in the case of GEFs, some RhoGAPs are believed to be highly specific, whereas others are more promiscuous with respect to their target GTPases. Increasing evidence suggests that GAPs are also regulated by external cues in addition to being signal terminators leading to Rho GTPase inactivation. These proteins play important role in many Rho mediated signaling pathways. Some known GAPs include p190 A, cdGAP, ARAP3, MgcRacGAP, Chimaerin, Nadrin, TCGAP, DLC 1, 2, ArhGAP6, Myosin IXA. These and other GAPs have been implicated in many processes, such as exocytosis, endocytosis, cytokinesis, cell differentiation, migration, neuronal morphogenesis, angiogenesis and tumor suppression. Detailed annotations of the biological role of GAPs in Rho mediated signaling will be available in future releases.
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eRF3-GTP:eRF1:peptidyl-tRNA:mRNA:80S Ribosome Complex
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eRF3-GDP:eRF1:peptidyl-tRNA:mRNA:80S Ribosome Complex
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eRF3-GDP:eRF1:tRNA:mRNA:80S Ribosome Complex
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RFC Heteropentamer:RNA primer-DNA primer:G-strand extended telomere end duplex:PCNA homotrimer (name copied from entity in Homo sapiens)
RNA primer-DNA primer:G-strand extended telomere:PCNA (name copied from entity in Homo sapiens)
Accurate cleavage and polyadenylation of exogenous RNA substrate.
RNA primer-DNA primer:G-strand extended telomere (name copied from entity in Homo sapiens)
RFC Heteropentamer:RNA primer-DNA primer:G-strand extended telomere end (name copied from entity in Homo sapiens)
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G alpha z (Lounsbury et al. 1991) and G alpha 12 (Kozasa & Gilman, 1996) are excellent in vitro substrates for all three subtypes of protein kinase C (PKC). Activation of PKC in intact platelets by agents such as thrombin, thromboxane A2 (TXA2) analogues and phorbol esters leads to rapid and near-stoichiometric phosphorylation of G alpha z (Carlson et al. 1989). The primary site of G alpha z phosphorylation is Ser-27 (Lounsbury et al. 1993). This phosphorylation blocks the interaction of G alpha z with Gbeta:gamma suggesting that it is a regulatory mechanism for attenuating signalling by preventing subunit reassociation.
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The classic signalling route for G alpha (q) is activation of phospholipase C beta thereby triggering phosphoinositide hydrolysis, calcium mobilization and protein kinase C activation. This provides a path to calcium-regulated kinases and phosphatases, GEFs, MAP kinase cassettes and other proteins that mediate cellular responses ranging from granule secretion, integrin activation, and aggregation in platelets. Gq participates in many other signalling events including direct interaction with RhoGEFs that stimulate RhoA activity and inhibition of PI3K. Both in vitro and in vivo, the G-protein Gq seems to be the predominant mediator of the activation of platelets.
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The heterotrimeric G protein Gz, is a member of the Gi family. Unlike other Gi family members it lacks an ADP ribosylation site cysteine four residues from the carboxyl terminus and is thus pertussis toxin-insensitive. It inhibits adenylyl cyclase types I, V and VI. G alpha (z) interacts with the Rap1 GTPase activating protein (Rap1GAP) to attenuate Rap1 signaling. Like all G-proteins Gz has an intrinsic GTPase activity, but this activity tends to be lower for the pertussis toxin insensitive G-proteins, most strikingly so for Gz, whose kcat value for GTP hydrolysis is 200-fold lower than those of Gs or Gi (Grazziano et al. 1989). Gz knockout mice have disrupted platelet aggregation at physiological concentrations of epinephrine and responses to several neuroactive drugs are altered (Yang et al. 2000).
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Slow intrisinc GTPase activity results in an inactivation of the alpha-i subunit by hydrolyzing GTP to GDP.
G protein-coupled receptors (GPCRs) are classically defined as the receptor, G-protein and downstream effectors, the alpha subunit of the G-protein being the primary signaling molecule. However, it has become clear that this greatly oversimplifies the complexities of GPCR signaling (see Gurevich & Gurevich, 2008). The beta:gamma G-protein dimer is also involved in downstream signaling (Smrcka, 2008), and some receptors form part of metastable complexes of receptor and accessory proteins such as the arrestins. GPCRs are involved in many diverse signaling events (Kristiansen 2004), using a variety of pathways that include modulation of adenylyl cyclase, phospholipase C, the mitogen activated protein kinases (MAPKs), extracellular signal regulated kinase (ERK) c-Jun-NH2-terminal kinase (JNK) and p38 MAPK.
The G12/13 family is probably the least well characterized subtype, partly because G12/13 coupling is difficult to determine when compared with the other subtypes which predominantly rely on assay technologies that measure intracellular calcium. The G12/13 family are best known for their involvement in the processes of cell proliferation and morphology, such as stress fiber and focal adhesion formation. Interactions with Rho guanine nucleotide exchange factors (RhoGEFs) are thought to mediate many of these processes. (Buhl et al.1995, Sugimoto et al. 2003). Activation of Rho or the regulation of events through Rho is often taken as evidence of G12/13 signaling. Receptors that are coupled with G12/13 invariably couple with one or more other G protein subtypes, usually Gq.
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The classical role of the G-protein beta/gamma dimer was believed to be the inactivation of the alpha subunit, Gbeta/gamma was viewed as a negative regulator of Galpha signalling. It is now known that Gbeta/gamma subunits can directly modulate many effectors, including some also regulated by G alpha.
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PI3K gamma (PI3KG) is a heterodimer consisting of a p110 catalytic subunit associated with a regulatory p101 or p84 subunit. PI3KG is most highly expressed in neutrophils, where the p101 form predominates (approximately 95%). G beta:gamma recruits PI3KG to the plasma membrane, both activating PI3KG and providing access to its substrate PIP2, which is converted to PIP3.
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PKC-theta (open): DAG (name copied from entity in Homo sapiens)
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GLUT4 tetramer (name copied from entity in Homo sapiens)
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PDK1:PIP2,PIP3 (name copied from entity in Homo sapiens)
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phospho p38:phospho MEF2 (name copied from entity in Homo sapiens)
CPSF:capped intronless pre-mRNA:CBC complex (name copied from entity in Homo sapiens)
CPSF (name copied from entity in Homo sapiens)
capped intronless pre-mRNA:CBC complex (name copied from entity in Homo sapiens)
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Downstream signaling events of B Cell Receptor (BCR)
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Platelet-derived Growth Factor (PDGF) is a potent stimulator of growth and motility of connective tissue cells such as fibroblasts and smooth muscle cells as well as other cells such as capillary endothelial cells and neurons.The PDGF family of growth factors is composed of four different polypeptide chains encoded by four different genes. The classical PDGF chains, PDGF-A and PDGF-B, and more recently discovered PDGF-C and PDGF-D. The four PDGF chains assemble into disulphide-bonded dimers via homo- or heterodimerization, and five different dimeric isoforms have been described so far; PDGF-AA, PDGF-AB, PDGF-BB, PDGF-CC and PDGF-DD. It is notable that no heterodimers involving PDGF-C and PDGF-D chains have been described. PDGF exerts its effects by binding to, and activating, two protein tyrosine kinase (PTK) receptors, alpha and beta. These receptors dimerize and undergo autophosphorylation. The phosphorylation sites then attract downstream effectors to transduct the signal into the cell.
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The free radical nitric oxide (NO), produced by endothelial NO synthase (eNOS), is an important vasoactive substance in normal vascular biology and pathophysiology. It plays an important role in vascular functions such as vascular dilation and angiogenesis (Murohara et al. 1998, Ziche at al. 1997). NO has been reported to be a downstream mediator in the angiogenic response mediated by VEGF, but the mechanism by which NO promotes neovessel formation is not clear (Babaei & Stewart 2002). Persistent vasodilation and increase in vascular permeability in the existing vasculature is observed during the early steps of angiogenesis, suggesting that these hemodynamic changes are indispensable during an angiogenic processes. NO production by VEGF can occur either through the activation of PI3K or through a PLC-gamma dependent manner. Once activated both pathways converge on AKT phosphorylation of eNOS, releasing NO (Lin & Sessa 2006). VEGF also regulates vascular permeability by promoting VE-cadherin endocytosis at the cell surface through a VEGFR-2SrcVav2RacPAK signalling axis.
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Nitric oxide (NO) is produced from L-arginine by the family of nitric oxide synthases (NOS) enzymes, forming the free radical NO and citrulline as byproduct. The cofactor tetrahydrobiopterin (BH4) is an essential requirement for the delivery of an electron to the intermediate in the catalytic cycle of NOS.
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The cofactor tetrahydrobiopterin (BH4) ensures endothelial nitric oxide synthase (eNOS) couples electron transfer to L-arginine oxidation (Berka et al. 2004). During catalysis, electrons derived from NADPH transfer to the flavins FAD and FMN in the reductase domain of eNOS and then on to the ferric heme in the oxygenase domain of eNOS. BH4 can donate an electron to intermediates in this electron transfer and is oxidised in the process, forming the BH3 radical. This radical can be reduced back to BH4 by iron, completing the cycle and forming ferrous iron again. Heme reduction enables O2 binding and L-arginine oxidation to occur within the oxygenase domain (Stuehr et al. 2009).
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HSP90 serves as a scaffold to promote productive interaction between AKT1 and eNOS. Due to the proximity of these proteins once complexed with HSP90, AKT1 phosphorylates eNOS at Ser1177. When Ser1177 is phosphorylated, the level of NO production is elevated two- to three-fold above basal level.
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PKC contains a N-terminal C2 like domain, a pseudosubstrate (PS), DAG binding (C1) domain and a C-terminal kinase domain. The PS sequence resembles an ideal substrate with the exception that it contains an alanine residue instead of a substrate serine residue. It is bound to the kinase domain in the resting state. As a result, PKC is maintained in a closed inactive state, inaccessible to cellular substrates. On stimulation of receptors there is an increase in intracellular calcium and diacylglycerol (DAG) levels which leads to the activation of PKC and its translocation from the cytosol to the plasma membrane. PKCs tether to the plasma membrane through DAG binding to the C1 domain. This confers a high-affinity interaction between PKC and the membrane, leading to a massive conformational change that releases the PS domain from the catalytic site, the system becomes both competent and accessible (Colon-Gonzalez & Kazanietz 2006).
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After phosphorylation by PDK1, PKC undergoes autophosphorylation at two sites important for PKC activity, one in the turn motif (Thr-642 in PKCB) and the second in the hydrophobic phosphorylation motif (Ser-661 in PKCB). These phosphorylations render the enzyme catalytically competent but still inactive; diacylglycerol (DAG) and calcium are required for full activation.
Protein kinase C (PKC) activation enhances angiogenesis by participating in the intracellular signaling of vascular endothelial growth factor (VEGF) in endothelial cells. VEGF can activate several PKC isoforms including alpha, beta, delta and zeta isoforms. Their activation is preceded by the activation of PLC gamma (Suzuma et al. 2002, Xia et al. 1996, Takahashi et al. 1999, Wellner et al. 1999). Before Protein kinase C (PKC) is competent to respond to second messengers it must first be phosphorylated at three conserved positions: the activation loop and two positions at the carboxyl terminus of the protein (Dutil et al. 1998). The phosphorylation of the activation loop appears to occur first and is mediated by phosphoinositide dependent protein kinases (PDKs). PDK1 phosphorylates PKCs at a critical Thr (T) residue in the activation loop, a requirement for PKC to gain catalytic competency (Toker 2003).
CDC42 is involved in the formation of filopodia with potential functions in guidance and migration in response to a VEGF gradient. CDC42 is activated downstream of VEGFR2 and involved in the formation of stress fibres by contributing to the activation of the p38 pathway. The activation of CDC42 may rely on FYN activity but the precise mechanism that leads to activation is not known (Lamalice et al. 2004, 2006).
CCNB1:p-T14,Y15,T161-CDK1 (name copied from entity in Homo sapiens)
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p-4S-CCNB1:p-T161-CDK1 (name copied from entity in Homo sapiens)
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VEGF mediated activation of ERK1/2 depends on the activity of PKC. Sphingosine kinase 1 (SPHK1) has been identified as the connecting link between PKC and Ras activation. Activated SPHK1 does not activate Ras-GEF directly but rather modulates Ras-GAP activity to favour Ras activation. VEGF-mediated stimulation of SPHK1 results from the direct phosphorylation of SPHK1 by PKC (Shu et al. 2002). S225 in SPHK1 may be the target site of phosphorylation (Piston et al. 2003).
CCNB1:p-T14,T161-CDK1 (name copied from entity in Homo sapiens)
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CAK (name copied from entity in Homo sapiens)
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Bestrophin and TMEM16-Ca(2+) activated Cl(-) channels with different functions
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Cyclin B2:phospho-Cdc2(Thr 14, Thr 161) (name copied from entity in Homo sapiens)
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Alcohol dehydrogenases, aldehyde dehydrogenases, and related enzymes
Cyclin B1:phospho-Cdc2(Thr 161, Thr 14, Tyr 15) (name copied from entity in Homo sapiens)
phospho-cyclin B1(CRS):phosph-Cdc2(Thr 161) (name copied from entity in Homo sapiens)
CCNB1:p-T14-CDK1 (name copied from entity in Homo sapiens)
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Cloning and identification of amino acid residues of human phospholipase C delta 1 essential for catalysis
Angiogenesis is the formation of new blood vessels from preexisting vasculature. One of the most important proangiogenic factors is vascular endothelial growth factor (VEGF). VEGF exerts its biologic effect through interaction with transmembrane tyrosine kinase receptors VEGFR, selectively expressed on vascular endothelial cells. VEGFA signaling through VEGFR2 is the major pathway that activates angiogenesis by inducing the proliferation, survival, sprouting and migration of endothelial cells (ECs), and also by increasing endothelial permeability (Lohela et al. 2009, Shibuya & Claesson-Welsh 2006, Claesson-Welsh & Welsh, 2013). The critical role of VEGFR2 in vascular development is highlighted by the fact that VEGFR2-/- mice die at E8.5-9.5 due to defective development of blood islands, endothelial cells and haematopoietic cells (Shalaby et al. 1995).
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VEGFR2 stimulates ERK not via GRB2-SOS-RAS, but via pY1175-dependent phosphorylation of PLC gamma and subsequent activation of PKCs. PKC plays an important mediatory role in the proliferative Ras/Raf/MEK/ERK pathway. PKC alpha can intersect the Ras/Raf/MEK/ERK cascade at the level of Ras (Clark et al. 2004) or downstream of Ras through direct phosphorylation of Raf (Kolch et al. 1993). VEGF stimulation leads to Ras activation in a Ras-guanine nucleotide exchange factor (GEF) independent mechanism. It rather relies on modulating the regulation of Ras-GTPase activating protein (GAP) than regulation of Ras-GEFS (Wu et al. 2003).
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Stem cell factor (SCF) is a growth factor with membrane bound and soluble forms. It is expressed by fibroblasts and endothelial cells throughout the body, promoting proliferation, migration, survival and differentiation of hematopoetic progenitors, melanocytes and germ cells.(Linnekin 1999, Ronnstrand 2004, Lennartsson and Ronnstrand 2006). The receptor for SCF is KIT, a tyrosine kinase receptor (RTK) closely related to the receptors for platelet derived growth factor receptor, colony stimulating factor 1 (Linnekin 1999) and Flt3 (Rosnet et al. 1991). Four isoforms of c-Kit have been identified in humans. Alternative splicing results in isoforms of KIT differing in the presence or absence of four residues (GNNK) in the extracellular region. This occurs due to the use of an alternate 5' splice donor site. These GNNK+ and GNNK- variants are co-expressed in most tissues; the GNNK- form predominates and was more strongly tyrosine-phosphorylated and more rapidly internalized (Ronnstrand 2004). There are also splice variants that arise from alternative usage of splice acceptor site resulting in the presence or absence of a serine residue (Crosier et al., 1993). Finally, there is an alternative shorter transcript of KIT expressed in postmeiotic germ cells in the testis which encodes a truncated KIT consisting only of the second part of the kinase domain and thus lackig the extracellular and transmembrane domains as well as the first part of the kinase domain (Rossi et al. 1991). Binding of SCF homodimers to KIT results in KIT homodimerization followed by activation of its intrinsic tyrosine kinase activity. KIT stimulation activates a wide array of signalling pathways including MAPK, PI3K and JAK/STAT (Reber et al. 2006, Ronnstrand 2004). Defects of KIT in humans are associated with different genetic diseases and also in several types of cancers like mast cell leukaemia, germ cell tumours, certain subtypes of malignant melanoma and gastrointestinal tumours.
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In normal development vascular endothelial growth factors (VEGFs) are crucial regulators of vascular development during embryogenesis (vasculogenesis) and blood-vessel formation in the adult (angiogenesis). In tumor progression, activation of VEGF pathways promotes tumor vascularization, facilitating tumor growth and metastasis. Abnormal VEGF function is also associated with inflammatory diseases including atherosclerosis, and hyperthyroidism. The members of the VEGF and VEGF-receptor protein families have distinct but overlapping ligand-receptor specificities, cell-type expression, and function. VEGF-receptor activation in turn regulates a network of signaling processes in the body that promote endothelial cell growth, migration and survival (Hicklin and Ellis, 2005; Shibuya and Claesson-Welsh, 2006). Molecular features of the VGF signaling cascades are outlined in the figure below (from Olsson et al. 2006; Nature Publishing Group). Tyrosine residues in the intracellular domains of VEGF receptors 1, 2,and 3 are indicated by dark blue boxes; residues susceptible to phosphorylation are numbered. A circled R indicates that phosphorylation is regulated by cell state (VEGFR2), by ligand binding (VEGFR1), or by heterodimerization (VEGFR3). Specific phosphorylation sites (boxed numbers) bind signaling molecules (dark blue ovals), whose interaction with other cytosolic signaling molecules (light blue ovals) leads to specific cellular (pale blue boxes) and tissue-level (pink boxes) responses in vivo. Signaling cascades whose molecular details are unclear are indicated by dashed arrows. DAG, diacylglycerol; EC, endothelial cell; eNOS, endothelial nitric oxide synthase; FAK, focal adhesion kinase; HPC, hematopoietic progenitor cell; HSP27, heat-shock protein-27; MAPK, mitogen-activated protein kinase; MEK, MAPK and ERK kinase; PI3K, phosphatidylinositol 3' kinase; PKC, protein kinase C; PLCgamma, phospholipase C-gamma; Shb, SH2 and beta-cells; TSAd, T-cell-specific adaptor. In the current release, the first events in these cascades - the interactions between VEGF proteins and their receptors - are annotated. Details of signaling events and their biological outcome, concisely illustrated in the image below, will be available in future versions of this pathway.
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ERBB2:EGFR and ERBB2:ERBB4 can directly recruit GRB2:SOS1 complex through phosphorylated C-tail tyrosines of EGFR (Y1068 and Y1086) and ERBB2 (Y1139) that serve as docking sites for GRB2 (Xie et al. 1995, Sepp-Lorenzino et al. 1996), which, again, results in SOS1-mediated guanyl-nucleotide exchange on RAS and activation of RAF and MAP kinases (Janes et al. 1994, Sepp-Lorenzino et al. 1996).
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All ERBB2 heterodimers, ERBB2:EGFR, ERBB2:ERBB3 and ERBB2:ERBB4, are able to activate RAF/MAP kinase cascade by recruiting SHC1 (Pinkas-Kramarski et al. 1996, Sepp-Lorenzino et al. 1996) to phosphorylated C-tail tyrosine residues in either EGFR (Y1148 and Y1173), ERBB2 (Y1196, Y1221, Y1222 and Y1248), ERBB3 (Y1328) or ERBB4 (Y1188 and Y1242 in JM-A CYT1 isoform, Y1178 and Y1232 in JM-B CYT1 isoform, Y1172 and Y1226 in JM-A CYT2 isoform). SHC1 recruitment is followed by phosphorylation (Segatto et al. 1993, Soler et al. 1994), and the phosphorylated SHC1 recruits GRB2:SOS1 complex (Xie et al. 1995), which leads to SOS1-mediated guanyl-nucleotide exchange on RAS (Xie et al. 1995) and downstream activation of RAF and MAP kinases.
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Activation of PLCG1 signaling is observed only in the presence of ERBB2:EGFR heterodimers, with PLCG1 binding to phosphorylated tyrosine Y992 and Y1173 in the C-tail of EGFR (Chattopadhyay et al. 1999), and potentially Y1023 in the C-tail of ERBB2 (Fazioli et al. 1991, Cohen et al. 1996).
ERBB2:ERBB3 and ERBB2:ERBB4cyt1 heterodimers activate PI3K signaling by direct binding of PI3K regulatory subunit p85 (Yang et al. 2007, Cohen et al. 1996, Kaushansky et al. 2008) to phosphorylated tyrosine residues in the C-tail of ERBB3 (Y1054, Y1197, Y1222, Y1224, Y1276 and Y1289) and ERBB4 CYT1 isoforms (Y1056 in JM-A CYT1 isoform and Y1046 in JM-B CYT1 isoform). Regulatory subunit p85 subsequently recruits catalytic subunit p110 of PI3K, resulting in the formation of active PI3K, conversion of PIP2 to PIP3, and PIP3-mediated activation of AKT signaling (Junttila et al. 2009, Kainulainen et al. 2000). Heterodimers of ERBB2 and EGFR recruit PI3K indirectly, through GRB2:GAB1 complex (Jackson et al. 2004), which again leads to PIP3-mediated activation of AKT signaling.
All splicing isoforms of ERBB4 possess two tyrosine residues in the C-tail that serve as docking sites for SHC1 (Kaushansky et al. 2008, Pinkas-Kramarski et al. 1996, Cohen et al. 1996). Once bound to ERBB4, SHC1 becomes phosphorylated on tyrosine residues by the tyrosine kinase activity of ERBB4, which enables it to recruit the complex of GRB2 and SOS1, resulting in the guanyl-nucleotide exchange on RAS and activation of RAF and MAP kinase cascade (Kainulainen et al. 2000).
ERBB2, also known as HER2 or NEU, is a receptor tyrosine kinase (RTK) belonging to the EGFR family. ERBB2 possesses an extracellular domain that does not bind any known ligand, contrary to other EGFR family members, a single transmembrane domain, and an intracellular domain consisting of an active kinase and a C-tail with multiple tyrosine phosphorylation sites. Inactive ERBB2 is associated with a chaperone heat shock protein 90 (HSP90) and its co-chaperone CDC37 (Xu et al. 2001, Citri et al. 2004, Xu et al. 2005). In addition, ERBB2 is associated with ERBB2IP (also known as ERBIN or LAP2), a protein responsible for proper localization of ERBB2. In epithelial cells, ERBB2IP restricts expression of ERBB2 to basolateral plasma membrane regions (Borg et al. 2000). ERBB2 becomes activated by forming a heterodimer with another ligand-activated EGFR family member, either EGFR, ERBB3 or ERBB4, which is accompanied by dissociation of chaperoning proteins HSP90 and CDC37 (Citri et al. 2004), as well as ERBB2IP (Borg et al. 2000) from ERBB2. ERBB2 heterodimers function to promote cell proliferation, cell survival and differentiation, depending on the cellular context. ERBB2 can also be activated by homodimerization when it is overexpressed, in cancer for example. In cells expressing both ERBB2 and EGFR, EGF stimulation of EGFR leads to formation of both ERBB2:EGFR heterodimers (Wada et al. 1990, Karunagaran et al. 1996) and EGFR homodimers. Heterodimers of ERBB2 and EGFR trans-autophosphorylate on twelve tyrosine residues, six in the C-tail of EGFR and six in the C-tail of ERBB2 - Y1023, Y1139, Y1196, Y1221, Y1222 and Y1248 (Margolis et al. 1989, Hazan et al. 1990,Walton et al. 1990, Helin et al. 1991, Ricci et al. 1995, Pinkas-Kramarski 1996). Phosphorylated tyrosine residues in the C-tail of EGFR and ERBB2 serve as docking sites for downstream signaling molecules. Three key signaling pathways activated by ERBB2:EGFR heterodimers are RAF/MAP kinase cascade, PI3K-induced AKT signaling, and signaling by phospholipase C gamma (PLCG1). Downregulation of EGFR signaling is mediated by ubiquitin ligase CBL, and is shown under Signaling by EGFR. In cells expressing ERBB2 and ERBB3, ERBB3 activated by neuregulin NRG1 or NRG2 binding (Tzahar et al. 1994) forms a heterodimer with ERBB2 (Pinkas-Kramarski et al. 1996, Citri et al. 2004). ERBB3 is the only EGFR family member with no kinase activity, and can only function in heterodimers, with ERBB2 being its preferred heterodimerization partner. After heterodimerization, ERBB2 phosphorylates ten tyrosine residues in the C-tail of ERBB3, Y1054, Y1197, Y1199, Y1222, Y1224, Y1260, Y1262, Y1276, Y1289 and Y1328 (Prigent et al. 1994, Pinkas-Kramarski et al. 1996, Vijapurkar et al. 2003, Li et al. 2007) that subsequently serve as docking sites for downstream signaling molecules, resulting in activation of PI3K-induced AKT signaling and RAF/MAP kinase cascade. Signaling by ERBB3 is downregulated by the action of RNF41 ubiquitin ligase, also known as NRDP1. In cells expressing ERBB2 and ERBB4, ligand stimulated ERBB4 can either homodimerize or form heterodimers with ERBB2 (Li et al. 2007), resulting in trans-autophosphorylation of ERBB2 and ERBB4 on C-tail tyrosine residues that will subsequently serve as docking sites for downstream signaling molecules, leading to activation of RAF/MAP kinase cascade and, in the case of ERBB4 CYT1 isoforms, PI3K-induced AKT signaling (Hazan et al. 1990, Cohen et al. 1996, Li et al. 2007, Kaushansky et al. 2008). Signaling by ERBB4 is downregulated by the action of WWP1 and ITCH ubiquitin ligases, and is shown under Signaling by ERBB4.
DNA polymerase alpha:primase:DNA polymerase alpha:G-strand extended telomere end (name copied from entity in Homo sapiens)
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DNA polymerase epsilon:G-strand extended telomere end (name copied from entity in Homo sapiens)
Telomerase RNP:Telomeric Chromosome End with an Additional single Stranded Telomere repeat (name copied from entity in Homo sapiens)
Telomerase Holoenzyme:Telomeric RNP End with Two Additional Single Stranded Telomere Repeats (name copied from entity in Homo sapiens)
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RNA primer:G-strand extended telomere end:DNA polymerase alpha:primase complex (name copied from entity in Homo sapiens)
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Purification and properties of human cytosolic folylpoly-gamma-glutamate synthetase and organization, localization, and differential splicing of its gene
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SCF-beta-TrCP:phospho-Emi1 complexes (name copied from entity in Homo sapiens)
The yeast mitochondrial protein import receptor Mas20p binds precursor proteins through electrostatic interaction with the positively charged presequence
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Telomerase RNP (name copied from entity in Homo sapiens)
Telomerase RNP Bound and base-paired to the Telomeric Chromosome End (name copied from entity in Homo sapiens)
SCF-beta-TrCP1 complex (name copied from entity in Homo sapiens)
SCF-associated multiubiquitinated Emi1complexes (name copied from entity in Homo sapiens)
RIT and RIN are two small guanine nucleotide binding proteins that share more than 50% sequence identity with RAS, including highly conserved core effector domains. Unlike RAS, the C termini of RIT and RIN lack a typical prenylation motif (CAAX, XXCC, or CXC) required for the association of RAS proteins with the plasma membrane. RIT is expressed in all tissues, whereas RIN is neuron-specific. They have similar signalling properties and are activated by NGF through unknown exchange factors. They signal to ERKs and p38 MAP kinase. They mainly lead to p38 activation via the BRAF-MEK kinase cascade.
The adaptor protein Frs2 (Fibroblast growth factor receptor substrate 2) can mediate the prolonged activation of the MAPK (ERK) cascade.
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Besides signalling through the tyrosine kinase receptors TRK A, B, and C, the mature neurotrophins NGF, BDNF, and NT3/4 signal through their common receptor p75NTR. NGF binding to p75NTR activates a number of downstream signalling events controlling survival, death, proliferation, and axonogenesis, according to the cellular context. p75NTR is devoid of enzymatic activity, and signals by recruiting other proteins to its own intracellular domain. p75 interacting proteins include NRIF, TRAF2, 4, and 6, NRAGE, necdin, SC1, NADE, RhoA, Rac, ARMS, RIP2, FAP and PLAIDD. Here we annotate only the proteins for which a clear involvement in p75NTR signalling was demonstrated. A peculiarity of p75NTR is the ability to bind the pro-neurotrophins proNGF and proBDNF. Proneurotrophins do not associate with TRK receptors, whereas they efficiently signal cell death by apoptosis through p75NTR. The biological action of neurotrophins is thus regulated by proteolytic cleavage, with proforms preferentially activating p75NTR, mediating apoptosis, and mature forms activating TRK receptors, to promote survival. Moreover, the two receptors are utilised to differentially modulate neuronal plasticity. For instance, proBDNF-p75NTR signalling facilitates LTD, long term depression, in the hippocampus (Woo NH, et al, 2005), while BDNF-TRKB signalling promotes LTP (long term potentiation). Many biological observations indicate a functional interaction between p75NTR and TRKA signaling pathways.
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Signalling through Shc adaptor proteins appears to be identical for both NGF and EGF. It leads to a fast, but transient, MAPK/ERK activation, which is insufficient to explain the prolonged activation of MAPK found in NGF-treated cells.
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Sphingomyielinase promotes the conversion of sphingomyelin to ceramide. Ceramide can activate JNK and other targets. The molecular details of the p75NTR-activated ceramide signalling cascade are only partially understood.
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In certain cell types, ligand binding to p75NTR leads to ceramide production, which can mediate either cell survival (e.g. in noecotical subplate neurons) or apoptosis (e.g. in oligodendrocytes). Low levels of ceramide are also able to stimulate axonal outgrowth in hippocampal neurons.
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p75NTR is a key regulator of neuronal apoptosis, both during development and after injury. Apoptosis is triggered by binding of either mature neurotrophin or proneurotrophin (proNGF, proBDNF). ProNGF is at least 10 times more potent than mature NGF in inducing apoptosis. TRKA signalling protects neurons from apoptosis. The molecular mechanisms involved in p75NTR-apoptosis are not well understood. The death signalling requires activation of c-JUN N-terminal Kinase (JNK), as well as transcriptional events. JNK activation appears to involve the receptor interacting proteins TRAF6, NRAGE, and Rac. The transcription events are thought to be regulated by another p75-interacting protein, NRIF. Two other p75-interacting proteins, NADE and Necdin, have been implicated in apoptosis, but their role is less clear.
PAK1 dimer (name copied from entity in Homo sapiens)
RAC1/CDC42:PAK dimer (name copied from entity in Homo sapiens)
p-5Y-PKC-theta:DAG (name copied from entity in Homo sapiens)
TIRAP/Mal, TRIF and TRAM. Differential utilization of these TIR
PKA tetramer (name copied from entity in Homo sapiens)
RAC1/CDC42:p-S144,T423-PAK (name copied from entity in Homo sapiens)
active PKC (alpha, gamma, delta) (name copied from entity in Homo sapiens)
cAMP:PKA regulatory subunit (name copied from entity in Homo sapiens)
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Neurotrophins utilize multiple pathways to activate ERKs (ERK1 and ERK2), a subgroup of the large MAP kinase (MAPK) family, from the plasma membrane. The major signalling pathways to ERKs are via RAS, ocurring from caveolae in the plasma membrane or from clathrin-coated vesicles, and via RAP1, taking place in early endosomes. Whereas RAS activation by NGF is transient, RAP1 activation by NGF is sustained for hours.
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After NGF binding, activated Trk receptors provide multiple docking sites for adaptor proteins and enzymes. Two docking proteins, the Ankyrin-Rich Membrane Spanning protein (ARMS/Kidins220) and Fibroblast growth factor receptor substrate 2 (Frs2), target signaling molecules in response to NGF stimulation and link receptor activation with the MAP kinase (also called the Extracellular signal-Regulated Kinase cascade, ERK) cascade, an essential process for growth factor-induced cell proliferation and differentiation. A feature of NGF signaling is the sustained activation of the MAPK cascade. This is achieved by the small G protein, Rap1 which binds to and activates B-Raf, an activator of the MAPK cascade. Rap1 is a member of the Ras family of G proteins and like all G proteins, Rap1 is in an inactive state when bound to GDP and is active when bound to GTP. A specific GEF (guanine nucleotide exchange factor) called C3G can activate Rap1 by exchanging GDP for GTP.
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ARMS (Ankyrin-Rich Membrane Spanning/Kidins 220) is a 220kD tetraspanning adaptor protein which becomes rapidly tyrosine phosphorylated by active Trk receptors. ARMS is another adaptor protein which is involved in the activation of Rap1 and the subsequent prolonged activation of the MAPK cascade.
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On phosphorylation, ERK5 translocates to the nucleus.
The location of neurotrophin stimulation appears to determine the nature of the transcriptional response through differential uses of individual MAP kinases. The ERK5 pathway has a unique function in retrograde signalling; in contrast, ERK1/2, which mediate nuclear responses following direct cell body stimulation, does not transmit a retrograde signal. Following neurotrophin stimulation of distal axons, phosphorylated TRK receptors are endocytosed and transported to the cell bodies, where MEK5 phosphorylates ERK5, leading to ERK5 nuclear translocation, phosphorylation of transcription factors, and neuronal survival. In contrast, neurotrophin stimulation of the cell bodies causes concurrent activation and nuclear transport of ERK1/2 as well as ERK5. Several distinctive features of the ERK5 pathway might be important for retrograde signalling. The ERK5 cascade does not depend on activation of the G-protein RAS. Instead, this pathway may use other G-proteins such as RAP that are associated with vesicles, or may not require any G-protein intermediate. Another distinctive feature is that the MEK5 isoform, which is expressed in the nervous system, exhibits a punctate staining pattern, suggesting a vesicular localization. ERK5 itself significantly differs from ERK1/2, and its substrate specificity also differs from ERK1/2. For instance, ERK5 directly activates transcription factors, including MEF2, that are not phosphorylated by ERK1/2. Conversely, ERK1/2, but not ERK5, activate transcription factors such as ELK1 and MITF.
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An important function of the kinase cascade triggered by neurotrophins is to induce the phosphorylation and activation of transcription factors in the nucleus to initiate new programs of gene expression. Transcription factors directly activated by neurotrophin signalling are responsible for induction of immediate-early genes, many of which are transcription factors. These in turn are involved in the induction of delayed-early genes.
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Trk receptors signal from the plasma membrane and from intracellular membranes, particularly from early endosomes. Signalling from the plasma membrane is fast but transient; signalling from endosomes is slower but long lasting. Signalling from the plasma membrane is annotated here. TRK signalling leads to proliferation in some cell types and neuronal differentiation in others. Proliferation is the likely outcome of short term signalling, as observed following stimulation of EGFR (EGF receptor). Long term signalling via TRK receptors, instead, was clearly shown to be required for neuronal differentiation in response to neurotrophins.
The activation of phosphlipase C-gamma (PLC-gamma) and subsequent mobilization of calcium from intracellular stores are essential for neurotrophin secretion. PLC-gamma is activated through the phosphorylation by TrkA receptor kinase and this form hydrolyses PIP2 to generate inositol tris-phosphate (IP3) and diacylglycerol (DAG). IP3 promotes the release of Ca2+ from internal stores and this results in activation of enzymes such as protein kinase C and Ca2+ calmodulin-regulated protein kinases.
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Several guanine exchange factors (GEFs) for the Rho family of GTPases contain PH domains that bind to PIP3. RhoA protein activation is a mechanism whereby PI3K acts independently of AKT.
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PI3K/AKT signalling is a major regulator of neuron survival. It blocks cell death by both impinging on the cytoplasmic cell death machinery and by regulating the expression of genes involved in cell death and survival. In addition, it may also use metabolic pathways to regulate cell survival.The PI3K/AKT pathway also affects axon diameter and branching (Marcus et al, 2002) and regulates small G proteins like RhoA (Vanhaesebroeck, B and Waterman, MD, 1999), which control the behaviour of the F-actin cytoskeleton. Moreover, through its connection with the TOR pathway, it promotes translation of a subset of mRNAs.
Extracellular signal-regulated kinase 5 (ERK5) is a member of the mitogen-activated protein kinase family. ERK5 is twice the size of the ERK1/2, containing a conserved amino terminal kinase domain that is 53% identical to ERK1/2, and a unique carboxyterminal region which contains potential binding sites for signalling molecules such as CRK, PI3 kinase and SRC. The second proline-rich region may interact with actin, targeting the kinase to a specific location in the cell. In contrast to ERK1 and ERK2, which are activated by neurotrophins (NTs), cAMP, and neuronal activity in neurons, ERK5 appears to be activated only by neurotrophins. The small GTPase Rap1 and the MEKK2 or MEKK3 kinases are critical upstream signaling molecules mediating neurotrophin stimulation of ERK5 in neurons. MEKK2 or MEKK3 activate MEK5, which appears to be localised in intracellular vesicles. MEK5 then activates ERK5. Once phosphorylated, ERK5 translocates to the nucleus.
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Activated mTORC1 (name copied from entity in Homo sapiens)
V-ATPase:ATP6AP1 (name copied from entity in Homo sapiens)
PIP3:AKT2 complex (name copied from entity in Homo sapiens)
PIP3:PDK1 complex (name copied from entity in Homo sapiens)
p-AMPK heterotrimer:AMP (name copied from entity in Homo sapiens)
AMPK heterotrimer (name copied from entity in Homo sapiens)
p-AMPK heterotrimer (name copied from entity in Homo sapiens)
Toll-like receptor 3: a link between toll-like receptor, interferon and viruses
Rheb:GTP (name copied from entity in Homo sapiens)
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The role of autophosphorylation sites on PDGF receptors are to provide docking sites for downstream signal transduction molecules which contain SH2 domains. The SH2 domain is a conserved motif of around 100 amino acids that can bind a phosphorylated tyrosine residue. These downstream molecules are activated upon binding to, or phosphorylated by, the receptor kinases intrinsic to PDGF receptors. Some of the dowstream molecules are themselves enzymes, such as phosphatidylinositol 3'-kinase (PI3K), phospholipase C (PLC-gamma), the Src family of tyrosine kinases, the tyrosine phosphatase SHP2, and a GTPase activating protein (GAP) for Ras. Others such as Grb2 are adaptor molecules which link the receptor with downstream catalytic molecules.
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Neurotrophins (NGF, BDNF, NT-3, NT-4/5) play pivotal roles in survival, differentiation, and plasticity of neurons in the peripheral and central nervous system. They are produced, and secreted in minute amounts, by a variety of tissues. They signal through two types of receptors: TRK tyrosine kinase receptors (TRKA, TRKB, TRKC), which specifically interact with the different neurotrophins, and p75NTR, which interacts with all neurotrophins. TRK receptors are reported in a variety of tissues in addition to neurons. p75NTRs are also widespread. Neurotrophins and their receptors are synthesized as several different splice variants, which differ in terms of their biological activities. The nerve growth factor (NGF) was the first growth factor to be identified and has served as a model for studying the mechanisms of action of neurotrophins and growth factors. The mechanisms by which NGF generates diverse cellular responses have been studied extensively in the rat pheochromocytoma cell line PC12. When exposed to NGF, PC12 cells exit the cell cycle and differentiate into sympathetic neuron-like cells. Current data show that signalling by the other neurotrophins is similar to NGF signalling.
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Mutations of the Down-regulated in adenoma (DRA) gene cause congenital chloride diarrhoea
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Regulation of the cyclin E gene by transcription factor E2F1
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Active PKC theta bound to DAG (name copied from entity in Homo sapiens)
p-Y90-PKC-theta:DAG (name copied from entity in Homo sapiens)
AKT:PIP3 (name copied from entity in Homo sapiens)
PDPK1:PIP3 (name copied from entity in Homo sapiens)
TORC2 complex (name copied from entity in Homo sapiens)
p-S-AKT:PIP3 (name copied from entity in Homo sapiens)
CDC42:GTP (name copied from entity in Homo sapiens)
p-S-AKT:PDPK1:PIP3 (name copied from entity in Homo sapiens)
PAK bound to Rac1 and Cdc42 (name copied from entity in Homo sapiens)
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PAK1-3 dimer (name copied from entity in Homo sapiens)
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PIP3:PDK1:active AKT (name copied from entity in Homo sapiens)
TAP (name copied from entity in Homo sapiens)
PDPK1:PIP2 (name copied from entity in Homo sapiens)
PP2A (name copied from entity in Homo sapiens)
Molecular scanning of insulin-responsive glucose transporter (GLUT4) gene in NIDDM subjects
CDC42:GDP (name copied from entity in Homo sapiens)
AGE adducts:Peptide:AGER-1,2,3 (name copied from entity in Homo sapiens)
Characterization of a human lysophosphatidic acid acyltransferase that is encoded by a gene located in the class III region of the human major histocompatibility complex
AGE adducts:Peptide (name copied from entity in Homo sapiens)
SUGT1:HSP90 (name copied from entity in Homo sapiens)
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CDC42-GTP:WASP/N-WASP (name copied from entity in Homo sapiens)
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Heterotrimeric G protein activation by G-protein-coupled receptors
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The copper chaperone for superoxide dismutase
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Constitutive receptor activation by Crouzon syndrome mutations in fibroblast growth factor receptor (FGFR)2 and FGFR2/Neu chimeras
Active N-SMase:Mg2+ (name copied from entity in Homo sapiens)
PIP3:RhoA (name copied from entity in Homo sapiens)
ATP6V1G dimer (name copied from entity in Homo sapiens)
ATP6V1A trimer (name copied from entity in Homo sapiens)
eNOS:CaM:HSP90:p-AKT1 (name copied from entity in Homo sapiens)
eNOS:CaM:HSP90 (name copied from entity in Homo sapiens)
ATP6V1B trimer (name copied from entity in Homo sapiens)
ATP6V1 (name copied from entity in Homo sapiens)
ATP6V0C hexamer (name copied from entity in Homo sapiens)
ATP6V0 (name copied from entity in Homo sapiens)
MISCELLANEOUS Present with 5300 molecules/cell in log phase SD medium.SIMILARITY Belongs to the archaeal RpoN/eukaryotic RPB10 RNA polymerase subunit family.
Requirement of PIG-F and PIG-O for transferring phosphoethanolamine to the third mannose in glycosylphosphatidylinositol
Cell signalling diversity of the Gqalpha family of heterotrimeric G proteins
Coenzyme Q biosynthesis: Coq6 is required for the C5-hydroxylation reaction and substrate analogs rescue Coq6 deficiency
Human TLR9 confers responsiveness to bacterial DNA via species-specific CpG motif recognition
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Processive DNA helicase activity of the minichromosome maintenance proteins 4, 6, and 7 complex requires forked DNA structures
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Identification and expression of a cDNA for human hydroxypyruvate/glyoxylate reductase
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Enzymic properties of different types of human erythrocyte glucose-6-phosphate dehydrogenase, with characterization of two new genetic variants
Jmjd2b antagonizes H3K9 trimethylation at pericentric heterochromatin in mammalian cells
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Homo sapiens dullard protein phosphatase shows a preference for the insulin-dependent phosphorylation site of lipin1
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Porcupine homolog is required for canonical Wnt signaling and gastrulation in mouse embryos
Purification and properties of carnitine acetyltransferase from human liver
Execution of nonsense-mediated mRNA decay: what defines a substrate?
Role of gastrin peptides in carcinogenesis
Purification of deoxyribonucleic acid polymerase delta from calf thymus: partial characterization of physical properties.
A bridging [4Fe-4S] cluster and nucleotide binding are essential for function of the Cfd1-Nbp35 complex as a scaffold in iron-sulfur protein maturation
Human GMP synthetase. Protein purification, cloning, and functional expression of cDNA
Identification of TTP mRNA targets in human dendritic cells reveals TTP as a critical regulator of dendritic cell maturation
The predicted ATP-binding domains in the hexose transporter GLUT1 critically affect transporter activity.
From hematopoietic stem cells to platelets
Intramolecular disulfide bond is a critical check point determining degradative fates of ATP-binding cassette (ABC) transporter ABCG2 protein
Advanced glycosylation endproduct receptor signaling
Rho GTPases have diverse effects on the organization of the actin filament system
H2S biogenesis by human cystathionine gamma-lyase leads to the novel sulfur metabolites lanthionine and homolanthionine and is responsive to the grade of hyperhomocysteinemia
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Cloning, sequencing and expression of a cDNA encoding mammalian valyl-tRNA synthetase
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Epidermal growth factor receptors harboring kinase domain mutations associate with the heat shock protein 90 chaperone and are destabilized following exposure to geldanamycins
Human Myt1 is a cell cycle-regulated kinase that inhibits Cdc2 but not Cdk2 activity
Regulation and dysregulation of aquaporins in water balance disorders
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Vitamin C: biosynthesis, recycling and degradation in mammals
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The X-linked mental retardation gene SMCX/JARID1C defines a family of histone H3 lysine 4 demethylases
The structure of human mitochondrial branched-chain aminotransferase.
Acta Crystallogr D Biol Crystallogr 57:506-15
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The retinoblastoma binding protein RBP2 is an H3K4 demethylase
RBP2 belongs to a family of demethylases, specific for tri-and dimethylated lysine 4 on histone 3
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The role of aminoacyl-tRNA synthetases in genetic diseases
G-protein alpha:GDP (name copied from entity in Homo sapiens)
G protein alpha:GTP complex (name copied from entity in Homo sapiens)
Protein Kinase C, alpha type: DAG (name copied from entity in Homo sapiens)
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Activated PLC beta 1/4 (name copied from entity in Homo sapiens)
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VPS35:VPS29:VPS26 (name copied from entity in Homo sapiens)
Oligomeric structure of the multifunctional protein CAD that initiates pyrimidine biosynthesis in mammalian cells
WLS:retromer (name copied from entity in Homo sapiens)
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activated PKC alpha (name copied from entity in Homo sapiens)
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Purification and some properties of inorganic pyrophosphatase from human erythrocytes
pT298-NLK dimer (name copied from entity in Homo sapiens)
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Although TBP (TATA box binding factor) is necessary and sufficient for initiation of basal transcription, the other subunits of the general transcription factor TFIID, the TBP-associated factors, are required for response to transcriptional activators. TBP binds to the TATA box (a core promoter element), and bends the DNA 80 degrees toward the major groove. This conformation of TBP-TATA box provides the proper topology for the binding of the general transcription factor TFIIB. Transcriptional activators function by affecting the kinetics of binding of TBP to the promoter DNA.
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The general transcription factor TFIIB is a single polypeptide of approximately 35 kDa. There is a Zn-binding domain near the N terminus of TFIIB, and the C-terminal domain encompasses two imperfect repeats; between the N and C termini is a phylogenetically conserved region. The C terminus interacts with TBP and RNA Polymerase II, whereas the N terminus interacts with factor TFIIF and RNA polymerase II. TFIIB is a sequence-specific factor, and it interacts with the BRE element within the promoter. TFIIB interacts with the Rpb1 subunit of RNA polymerase II to define transcription strat sites. Several activators directly bind TFIIB, and stimulate transcription. The N-terminus and the C-terminus can participate in intramolecular interactions, and this can be disrupted by specific activators by causing a conformational change in TFIIB. TFIIA also binds the preinitiation complex along with TFIIB. However, TFIIA is not required for accurate initiation, but rather functions as a coactivator of transcription.
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The mucopolysaccharidoses: a success of molecular medicine
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Leptin (LEP, OB, OBS), a circulating adipokine, and its receptor LEPR (DB, OBR) control food intake and energy balance and are implicated in obesity-related diseases (recently reviewed in Amitani et al. 2013, Dunmore and Brown 2013, Cottrell and Mercer 2012, La Cava 2012, Marroqui et al. 2012, Paz-Filho et al. 2012, Denver et al. 2011, Lee 2011, Marino et al. 2011, Morton and Schwartz 2011, Scherer and Buettner 2011, Shan and Yeo 2011, Wauman and Tavernier 2011, Dardeno et al. 2010, Bjorbaek 2009, Morris and Rui 2009, Myers et al. 2008), including cancer (Guo et al. 2012), inflammation (Newman and Gonzalez-Perez 2013, Iikuni et al. 2008), and angiogenesis (Gonzalez-Perez et al. 2013). The identification of spontaneous mutations in the leptin gene (ob or LEP) and the leptin receptor gene (Ob-R, db or LEPR) genes in mice opened up a new field in obesity research. Leptin was discovered as the product of the gene affected by the ob (obesity) mutation, which causes obesity in mice. Likewise LEPR is the product of the gene affected by the db (diabetic) mutation. Leptin binding to LEPR induces canonical (JAK2/STATs; MAPK/ERK 1/2, PI-3K/AKT) and non-canonical signaling pathways (PKC, JNK, p38 MAPK and AMPK) in diverse cell types. The binding of leptin to the long isoform of LEPR (OB-Rl) initiates a phosphorylation cascade that results in transcriptional activation of target genes by STAT5 and STAT3 and activation of the PI3K pathway(not shown here), the MAPK/ERK pathway, and the mTOR/S6K pathway. Shorter LEPR isoforms with truncated intracellular domains are unable to activate the STAT pathway, but can transduce signals by way of activation of JAK2, IRS-1 or ERKs, including MAPKs. LEPR is constitutively bound to the JAK2 kinase. Binding of LEP to LEPR causes a conformational change in LEPR that activates JAK2 autophosphorylation followed by phosphorylation of LEPR by JAK2. Phosphorylated LEPR binds STAT3, STAT5, and SHP2 which are then phosphorylated by JAK2. Phosphorylated JAK2 binds SH2B1 which then binds IRS1/2, resulting in phosphorylation of IRS1/2 by JAK2. Phosphorylated STAT3 and STAT5 dimerize and translocate to the nucleus where they activate transcription of target genes (Jovanovic et al. 2010). SHP2 activates the MAPK pathway. IRS1/2 activate the PI3K/AKT pathway which may be the activator of mTOR/S6K. Several isoforms of LEPR have been identified (reviewed in Gorska et al. 2010). The long isoform (LEPRb, OBRb) is expressed in the hypothalamus and all types of immune cells. It is the only isoform known to fully activate signaling pathways in response to leptin. Shorter isoforms (LEPRa, LEPRc, LEPRd, and a soluble isoform LEPRe) are able to interact with JAK kinases and activate other pathways, however their roles in energy homeostasis are not fully characterized.
Signal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such as hormones and growth factors, or reacting to other types of stimuli, such as light. Stimulation of transmembrane receptors leads to their conformational change which propagates the signal to the intracellular environment by activating downstream signaling cascades. Depending on the cellular context, this may impact cellular proliferation, differentiation, and survival. On the organism level, signal transduction regulates overall growth and behavior. Receptor tyrosine kinases (RTKs) transmit extracellular signals by phosphorylating their protein partners on conserved tyrosine residues. Some of the best studied RTKs are EGFR (reviewed in Avraham and Yarden, 2011), FGFR (reviewed in Eswarakumar et al, 2005), insulin receptor (reviewed in Saltiel and Kahn, 2001), NGF (reviewed in Reichardt, 2006), PDGF (reviewed in Andrae et al, 2008) and VEGF (reviewed in Xie et al, 2004). RTKs frequently activate downstream signaling through RAF/MAP kinases (reviewed in McKay and Morrison, 2007 and Wellbrock et al 2004), AKT (reviewed in Manning and Cantley, 2007) and PLC- gamma (reviewed in Patterson et al), which ultimately results in changes in gene expression and cellular metabolism. Receptor serine/threonine kinases of the TGF-beta family, such as TGF-beta receptors (reviewed in Kang et al. 2009) and BMP receptors (reviewed in Miyazono et al. 2009), transmit extracellular signals by phosphorylating regulatory SMAD proteins on conserved serine and threonine residues. This leads to formation of complexes of regulatory SMADs and SMAD4, which translocate to the nucleus where they act as transcription factors. WNT receptors transmit their signal through beta-catenin. In the absence of ligand, beta-catenin is constitutively degraded in a ubiquitin-dependent manner. WNT receptor stimulation releases beta-catenin from the destruction complex, allowing it to translocate to the nucleus where it acts as a transcriptional regulator (reviewed in MacDonald et al, 2009 and Angers and Moon, 2009). WNT receptors were originally classified as G-protein coupled receptors (GPCRs). Although they are structurally related, GPCRs primarily transmit their signals through G-proteins, which are trimers of alpha, beta and gamma subunits. When a GPCR is activated, it acts as a guanine nucleotide exchange factor, catalyzing GDP to GTP exchange on the G-alpha subunit of the G protein and its dissociation from the gamma-beta heterodimer. The G-alpha subunit regulates the activity of adenylate cyclase, while the gamma-beta heterodimer can activate AKT and PLC signaling (reviewed in Rosenbaum et al. 2009, Oldham and Hamm 2008, Ritter and Hall 2009). NOTCH receptors are activated by transmembrane ligands expressed on neighboring cells, which results in cleavage of NOTCH receptor and release of its intracellular domain. NOTCH intracellular domain translocates to the nucleus where it acts as a transcription factor (reviewed in Kopan and Ilagan, 2009). Integrins are activated by extracellular matrix components, such as fibronectin and collagen, leading to conformational change and clustering of integrins on the cell surface. This results in activation of integrin-linked kinase and other cytosolic kinases and, in co-operation with RTK signaling, regulates survival, proliferation and cell shape and adhesion (reviewed in Hehlgans et al, 2007) . Besides inducing changes in gene expression and cellular metabolism, extracellular signals that trigger the activation of Rho GTP-ases can trigger changes in the organization of cytoskeleton, thereby regulating cell polarity and cell-cell junctions (reviewed in Citi et al, 2011).
The visual pigment (rhodopsin in rods) consists of an 11-cis-retinal (11cRAL) chromophore covalently attached to a GPCR opsin family member via a Schiff base linkage. Upon photon absorption, 11cRAL isomerizes to all trans retinal (atRAL), changing the conformation of opsin to a form that can activate the regulatory G protein transducin (Gt). The alpha subunit of Gt activates phosphodiesterase which hydrolyses cGMP to 5'-GMP. A high level of cGMP keeps cGMP-gated cation channels open, so lower cGMP levels close these channels and hyperpolarize the cell. The hyperpolarization spreads passively to the synapse located at the opposite end of the rod, where it subsequently closes voltage-gated calcium channels. Vesicular release of the neurotransmitter glutamate subsides as the intracellular calcium levels drop. This diminution of neurotransmitter release relays the light signal to postsynaptic neurons. The events below describe activation, inactivation, recovery and regulation of the phototransduction cascade in rods (Burns & Pugh 2010, Korenbrot 2012, Smith 2010).
Visual phototransduction is the process by which photon absorption by visual pigment molecules in photoreceptor cells is converted to an electrical cellular response. The events in this process are photochemical, biochemical and electrophysiological and are highly conserved across many species. This process occurs in two types of photoreceptors in the retina, rods and cones. Each type consists of two parts, the outer segment which detects a photon signal and the inner segment which contains the necessary machinery for cell metabolism. Each type of cell functions differently. Rods are very light sensitive but their flash response is slow so they work best in twilight conditions but are not good at detecting objects moving quickly. Cones are less light-sensitive and have a fast flash response so they work best in daylight conditions and are better at detecting fast moving objects than rods. The visual pigment consists of a chromophore (11-cis-retinal, 11cRAL, A1) covalently attached to a GPCR opsin family member. The linkage is via a Schiff base forming retinylidene protein. Upon photon absorption, 11cRAL isomerises to all-trans retinal (atRAL), changing the conformation of opsin to an activated form which can activate the regulatory G protein transducin (Gt). The alpha subunit of Gt activates phosphodiesterase which hydrolyses cGMP to 5'-GMP. As high level of cGMP keep cGMP-gated sodium channels open, the lowering of cGMP levels closes these channels which causes hyperpolarization of the cell and subsequently, closure of voltage-gated calcium channels. As calcium levels drop, the level of the neurotransmitter glutamate also drops causing depolarization of the cell. This effectively relays the light signal to postsynaptic neurons as electrical signal (Burns & Pugh 2010, Korenbrot 2012, Pugh & Lamb 1993). 11cRAL cannot be synthesised in vertebrates. Vitamin A from many dietary sources is the precursor for 11cRAL. It is taken from food in the form of esters such as retinyl acetate or palmitate or one of four caretenoids (alpha-carotene, beta-carotene, gamma-carotene and beta-cryptoxanthin). Retinoids are transported from the gut to be stored in liver, until required by target organs such as the eye (Harrison & Hussain 2001, Harrison 2005). In the eye, in the form 11cRAL, it is used in the retinoid (visual) cycle to initiate phototransduction and for visual pigment regeneration to ready the photoreceptor for the next phototransduction event (von Lintig 2012, Blomhoff & Blomhoff 2006, von Lintig et al. 2010, D'Ambrosio et al. 2011, Wang & Kefalov 2011, Kefalov 2012, Wolf 2004).
At the beginning of this reaction, 1 molecule of 'pol II open pre-initiation complex' is present. At the end of this reaction, 1 molecule of 'pol II closed pre-initiation complex' is present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'SUPT5H protein', and 1 molecule of 'SPT4H1 protein' are present. At the end of this reaction, 1 molecule of 'DSIF complex' is present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'FACT 140 kDa subunit', and 1 molecule of 'FACT 80 kDa subunit' are present. At the end of this reaction, 1 molecule of 'FACT complex' is present. This reaction takes place in the 'nucleus'.
RhoGTPase:GDP (name copied from entity in Homo sapiens)
Inactivated RhoGTPase:GDP:GDI complex (name copied from entity in Homo sapiens)
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RhoGTPase:GTP (name copied from entity in Homo sapiens)
p(S27)-G protein alpha (z):GTP (name copied from entity in Homo sapiens)
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G-protein alpha (z):GTP (name copied from entity in Homo sapiens)
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G-protein alpha (i):GDP (name copied from entity in Homo sapiens)
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G-protein alpha (i): GTP (name copied from entity in Homo sapiens)
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2-Hexaprenyl-6-methoxyphenol [ChEBI:1109]
RhoA/B/C:GTP (name copied from entity in Homo sapiens)
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RhoA,B,C:GDP (name copied from entity in Homo sapiens)
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G-protein alpha (z):GDP (name copied from entity in Homo sapiens)
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All eukaryotic proteins synthesized in the cytosol are initiated by methionine (Met). For the maturation of many proteins, the removal of N-terminal Met is essential and is mediated by methionine-aminopeptidases (METAPs). In human, there are two forms, METAP1 and 2 (Arfin et al. 1995). These enzymes utilise 2 cobalt ions (Co2+) as cofactors (Addlagatta et al. 2005, Hu et al. 2006, Marino et al. 2007).
Receptor-to-effector signaling through G proteins: roles for beta gamma dimers as well as alpha subunits
After removal of the N-terminal methionine (Met) residue, the enzymes glycylpeptide N-tetradecanoyltransferase 1 and 2 (NMT1 and 2) mediate the transfer of the myristoyl (MYS) group from myristoyl-CoA to the now N-terminal glycine (Gly) residue of transducin's alpha subunit (GNAT1) (Glover et al. 1997, Giang & Cravatt 1998). Myristoylation is thought to aid enzyme function and localization. Evidence from chicken experiments suggest non-myristoylated proteins do not bind to membranes (Kamps et al. 1986).
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To terminate the single photon response and restore the system to its basal state, the three activated intermediates in phototransduction, rhodopsin (MII), transducin alpha subunit with GTP bound (GNAT1-GTP) and phosphodiesterase 6 (PDE6) all need to be efficiently deactivated. In addition, the cGMP concentrations must be restored to support reopening of the CNG channels. This section describes the inactivation and recovery events of the activated intermediates involved in phototransduction (Burns & Pugh 2010, Korenbrot 2012).
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Phosphorylated IGF1R binds and phosphorylates SHC1 (reviewed in Pavelic et al. 2007, Chitnis et al. 2008, Maki et al. 2010, Parrella et al. 2010, Siddle et al. 2012). Phosphorylated SHC then binds GRB:SOS, which activates RAS-RAF-MAPK signaling.
The phosphorylated type 1 insulin-like growth factor receptor phosphorylates IR1, IRS2, IRS4 and possibly other IRS/DOK family members (reviewed in Pavelic et al. 2007, Chitnis et al. 2008, Maki et al. 2010, Parrella et al. 2010, Siddle et al. 2012). The phosphorylated IRS proteins serve as scaffolds that bind the effector molecules PI3K and GRB2:SOS. PI3K then activates PKB (AKT) signaling while GRB2:SOS activates RAS-RAF-MAPK signaling.
After autophosphorylation the type 1 insulin-like growth factor receptor (IGF1R) binds and phosphorylates scaffold proteins, IRS1/2/4 and SHC1, which in turn bind effectors possessing enzymatic activity (recently reviewed in Pavelic et al. 2007, Chitnis et al. 2008, Maki et al. 2010, Parrella et al. 2010, and Siddle et al. 2012). IRS1/2/4 can bind both PI3K (via the p85 subunit of PI3K) and the GRB2:SOS complex. PI3K activates PKB (AKT, AKT1) signaling. GRB:SOS stimulates RAS to exchange GDP for GTP leading to activation of RAF and MAPK.
Binding of IGF1 (IGF-I) or IGF2 (IGF-II) to the extracellular alpha peptides of the type 1 insulin-like growth factor receptor (IGF1R) triggers the activation of two major signaling pathways: the SOS-RAS-RAF-MAPK (ERK) pathway and the PI3K-PKB (AKT) pathway (recently reviewed in Pavelic et al. 2007, Chitnis et al. 2008, Maki et al. 2010, Parella et al. 2010, Annunziata et al. 2011, Siddle et al. 2012, Holzenberger 2012).
The outer segment of photoreceptor cells is shed every 10-14 days to be completely replaced. The shed material is phagocytosed and transferred to the retinal pigment epithelium (RPE). Diretinoid-pyridinium-phosphatidylethanolamine (A2PE) can be hydrolysed to diretinoid-pyridinium-ethanolamine (A2E), a prominent constituent of lipofuscin (the material deposited in retinal tissue which accumulates over time and is implicated in macular degeneration). Evidence suggests this happens before transfer to RPE cells as part of the phagocytosed outer segment. A2E has been detected in outer segments (Ben-Shabat et al. 2002) and an N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D (NAPEPLD) activity detected in rat, mouse and human proteins (Okamoto et al. 2004, Ueda et al. 2005, Wang et al. 2006). This activity has been shown to hydrolyse A2PE to A2E in bovine outer segments before phagocytosis and transfer to RPE cells, suggesting A2PE is hydrolysed to A2E in photoreceptor outer segment membranes (Sparrow et al. 2003, Salvador & Giusto 1998).
Lipofuscin is a yellow-brown pigment grain composed mainly of lipids but also sugars and certain metals. Accumulation of lipofuscin is associated with degenerative diseases such as Alzheimer's disease, Parkinson's disease, chronic obstructive pulmonary disease and retinal macular degeneration. A prominent component of lipofuscin in retinal pigment epithelial (RPE) cells is the bisretinoid A2E (di-retinoid-pyridinium-ethanolamine), the end-product of the condensation of 2 molecules of all-trans-retinal (atRAL) and phosphatidylethanolamine (PE) in photoreceptor outer disc membranes. Once formed, A2E is phagocytosed, together with outer segments (Kevany & Palczewski 2010), to RPE where it accumulates. There is no evidence as yet to indicate that A2E can be catabolised (Sparrow et al. 2012, Sparrow et al. 2010). A simplified biosynthetic pathway for A2E is described here.
The retinoid cycle (also referred to as the visual cycle) is the process by which the visual chromophore 11-cis-retinal (11cRAL) is released from light-activated opsins in the form all-trans-retinal and isomerized back to its 11-cis isomer ready for another photoisomerization reaction. This process involves oxidation, reduction and isomerization reactions and take place in the retinal pigment epithelium (RPE) and photoreceptor segments of the eye (von Lintig 2012, Blomhoff & Blomhoff 2006, von Lintig et al. 2010, D'Ambrosio et al. 2011). This section describes the retinoid cycle in rods during dark/twilight conditions.
Active Calmodulin (name copied from entity in Homo sapiens)
palmitoylated, myristoylated eNOS dimer (name copied from entity in Homo sapiens)
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Cdc42-GDP (name copied from entity in Homo sapiens)
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DAG:active PKC:Ca+2 (name copied from entity in Homo sapiens)
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A DNA helicase activity is associated with an MCM4, -6, and -7 protein complex.
p-S1177-eNOS dimer (name copied from entity in Homo sapiens)
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p-S1177-eNOS:CaM:HSP90:p-AKT1 (name copied from entity in Homo sapiens)
p-S1177-eNOS:CaM:HSP90:p-AKT1:BH4 (name copied from entity in Homo sapiens)
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4xCa2+:CaM (name copied from entity in Homo sapiens)
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Humans and mice have 19 identified WNT proteins that were originally classified as either 'canonical' or 'non-canonical' depending upon whether they were able to transform the mouse mammary epithelial cell line C57MG and to induce secondary axis formation in Xenopus (Wong et al, 1994; Du et al, 1995). So-called canonical WNTs, including Wnt1, 3, 3a and 7, initiate signaling pathways that destabilize the destruction complex and allow beta-catenin to accumulate and translocate to the nucleus where it promotes transcription (reviewed in Saito-Diaz et al, 2013). Non-canonical WNTs, including Wnt 2, 4, 5a, 5b, 6, 7b, and Wnt11 activate beta-catenin-independent responses that regulate many aspects of morphogenesis and development, often by impinging on the cytoskeleton (reviewed in van Amerongen, 2012). Two of the main beta-catenin-independent pathways are the Planar Cell Polarity (PCP) pathway, which controls the establishment of polarity in the plane of a field of cells, and the WNT/Ca2+ pathway, which promotes the release of intracellular calcium and regulates numerous downstream effectors (reviewed in Gao, 2012; De, 2011).
WNT signaling pathways control a wide range of developmental and adult process in metozoans including cell proliferation, cell fate decisions, cell polarity and stem cell maintenance (reviewed in Saito-Diaz et al, 2013; MacDonald et al, 2009). The pathway is named for the WNT ligands, a large family of secreted cysteine-rich glycoproteins. At least 19 WNT members have been identified in humans and mice with distinct expression patterns during development (reviewed in Willert and Nusse, 2012). These ligands can activate at least three different downstream signaling cascades depending on which receptors they engage. In the so-called 'canonical' WNT signaling pathway, WNT ligands bind one of the 10 human Frizzled (FZD) receptors in conjunction with the LRP5/6 co-receptors to activate a transcriptional cascade that controls processes such as cell fate, proliferation and self-renenwal of stem cells. Engagement of the FZD-LRP receptor by WNT ligand results in the stabilization and translocation of cytosolic beta-catenin to the nucleus where it is a co-activator for LEF (lymphoid enhancer-binding factor)- and TCF (T cell factor) -dependent transcription. In the absence of WNT ligand, cytosolic beta-catenin is phosphorylated by a degradation complex consisting of glycogen synthase kinase 3 (GSK3), casein kinase 1 (CK1), Axin and Adenomatous polyposis coli (APC), and subsequently ubiquitinated and degraded by the 26S proteasome (reviewed in Saito-Diaz et al, 2013; Kimmelman and Xu, 2006). In addition to the beta-catenin-dependent transcriptional response, WNT signaling can also activate distinct non-transcriptional pathways that regulate cell migration and polarity. These beta-catenin-independent 'non-canonical' pathways signal through Frizzled receptors independently of LRP5/6, or occur through the tyrosine kinase receptors ROR and RYK (reviewed in Veeman et al, 2003; James et al, 2009). Non-canonical WNT pathways are best studied in Drosophila where the planar cell polarity (PCP) pathway controls the orientation of wing hairs and eye facets, but are also involved in processes such as convergent extension, neural tube closure, inner ear development and hair orientation in vertebrates and mammals(reviewed in Seifert and Mlodzik, 2007; Simons and Mlodzik, 2008). In the PCP pathway, binding of WNT ligand to the FZD receptor leads to activation of small Rho GTPases and JNK, which regulate the cytoskeleton and coordinate cell migration and polarity (reviewed in Lai et al, 2009; Schlessinger et al, 2009). In some cases, a FZD-WNT interaction increases intracellular calcium concentration and activates CaMK II and PKC; this WNT calcium pathway promotes cell migration and inhibits the canonical beta-catenin dependent transcriptional pathway (reviewed in Kuhl et al, 2000; Kohn and Moon, 2005; Rao et al 2010). Binding of WNT to ROR or RYK receptors also regulates cell migration, apparently through activation of JNK or SRC kinases, respectively, however the details of these pathways remain to be worked out (reviewed in Minami et al, 2010). Although the WNT signaling pathways were originally viewed as discrete, linear pathways controlled by defined subsets of 'canonical' or 'non-canonical' ligands and receptors, the emerging evidence is challenging this notion. Instead, the specificity and the downstream response appear to depend on the particular cellular context and vary with species, tissue and stage of development (reviewed in van Amerongen and Nusse, 2009; Rao et al, 2010).
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Dimerization and autophosphorylation at T298 is required for NLK nuclear localization (Ishitani et al, 2011).
Dock180 and ELMO1 proteins cooperate to promote evolutionarily conserved Rac-dependent cell migration
A number of so called non-canonical WNT ligands have been shown to promote intracellular calcium release upon FZD binding. This beta-catenin-independent WNT pathway acts through heterotrimeric G proteins and promotes calcium release through phophoinositol signaling and activation of phosphodiesterase (PDE). Downstream effectors include the calcium/calmodulin-dependent kinase II (CaMK2) and PKC (reviewed in De, 2011). The WNT Ca2+ pathway is important in dorsoventral polarity, convergent extension and organ formation in vertebrates and also has roles in negatively regulating 'canonical' beta-catenin-dependent transcription. Non-canonical WNT Ca2+ signaling is also implicated in inflammatory response and cancer (reviewed in Kohn and Moon, 2005; Sugimura and Li, 2010).
19 WNT proteins have been identified in human cells. The WNTs are members of a conserved metazoan family of secreted morphogens that activate several signaling pathways in the responding cell: the canonical (beta-catenin) WNT signaling cascade and several non-canonical pathways, including the planar cell polarity (PCP), the regulation of intracellular calcium signaling and activation of JNK kinases. WNT proteins exist in a gradient outside the secreting cell and are able to act over both short and long ranges to promote proliferation, changes in cell migration and polarity and tissue homeostasis, among others (reviewed in Saito-Diaz et al, 2012; Willert and Nusse, 2012). The WNTs are ~40kDa proteins with 23 conserved cysteine residues in the N-terminal that may form intramolecular disulphide bonds. They also contain an N-terminal signal sequence and a number of N-linked glycosylation sites (Janda et al, 2012). In addition to being glycosylated, WNTs are also lipid-modified in the endoplasmic reticulum by a WNT-specific O-acyl-transferase, Porcupine (PORCN), contributing to their characteristic hydrophobicity. PORCN-dependent palmitoylation is required for the secretion of WNT as well as its signaling activity, as either depletion of PORCN or mutation of the conserved serine acylation site results in the intracellular accumulation of WNT ligand (Takada et al, 2006; Barrott et al, 2011; Biechele et al, 2011; reviewed in Willert and Nusse, 2012). Secretion of WNT requires a number of other dedicated factors including the sorting receptor Wntless (WLS) (also knownas Evi, Sprinter, and GPR177), which binds WNT and escorts it to the cell surface (Banziger et al, 2006; Bartscherer et al, 2006; Goodman et al, 2006). A WNT-specific retromer containing SNX3 is subsequently required for the recycling of WLS back to the Golgi (reviewed in Herr et al, 2012; Johannes and Wunder, 2011). Once at the cell surface, WNT makes extensive contacts with components of the extracellular matrix such as heparan sulphate proteoglycans (HSPGs) and may be bound by any of a number of regulatory proteins, including WIFs and SFRPs. The diffusion of the WNT ligand may be aided by its packing either into WNT multimers, exosomes or onto lipoprotein particles to shield the hydrophobic lipid adducts from the aqueous extracellular environment (Gross et al, 2012; Luga et al, 2012, Korkut et al, 2009; reviewed in Willert and Nusse, 2012).
Ectopic expression of Xwnt5a or Rfz2 in Xenopus embryos results in PKC translocation to the plasma membrane in a G-protein-dependent manner (Sheldahl et al, 1999; reviewed in Kuhl et al, 2000). PKC activation in response to WNT5A has also been demonstrated in human metastatic melanoma cell lines, contributing to cytoskeletal reorganization leading to invasiveness and motility as well as promoting the epithelial to mesenchymal transition (Weeraratna et al, 2002; Dissanyake et al, 2007; O'Connell et al, 2009)
G protein-coupled receptors (GPCRs; 7TM receptors; seven transmembrane domain receptors; heptahelical receptors; G protein-linked receptors [GPLR]) are the largest family of transmembrane receptors in humans, accounting for more than 1% of the protein-coding capacity of the human genome. All known GPCRs share a common architecture of seven membrane-spanning helices connected by intra- and extracellular loops. The extracellular loops contain two highly-conserved cysteine residues that form disulphide bonds to stabilize the structure of the receptor. They recognize diverse messengers such as light, odorants, small molecules, hormones and neurotransmitters. Most GPCRs act as guanine nucleotide exchange factors; activated by ligand binding, they promote GDP-GTP exchange on associated heterotrimeric guanine nucleotide-binding (G) proteins. There are two models for GPCR-G Protein interactions: 1) ligand-GPCR binding first, then binding to G Proteins; 2) "Pre-coupling" of GPCRs and G Proteins before ligand binding (review Oldham WM and Hamm HE, 2008). These in turn activate effector enzymes or ion channels. GPCRs are involved in a range of physiological roles which include the visual sense, smell, behavioural regulation, functions of the autonomic nervous system and regulation of the immune system and inflammation. GPCRs are divided into 6 classes based on sequence homology and functional similarity; the main mammalian families are classes A/1-C/3; Class A/1 (Rhodopsin-like) Class B/2 (Secretin receptor family) Class C/3 (Metabotropic glutamate/pheromones) Class D/4 (fungal mating pheromone receptors) Class E/5 (cAMP receptors) Class F/6 (Frizzled/Smoothened) Here, those Class A/1 (Rhodopsin-like) receptors that bind peptide ligands have been annotated. The binding events mediated by other classes of receptors, as well as the downstream events triggered by receptor-ligand interactions will be annotated in future releases of Reactome.
Retromer is believed to escort WLS from the early endosome back to the Golgi for subsequent rounds of WNT secretion (reviewed in Johannes and Wunder, 2011; Willert and Nusse, 2012 ).
Gastrin, through the action of diacylglycerol produced from downstream G alpha (q) events, transactivates EGFR via a PKC-mediated pathway by activation of MMP3 (Matrix Metalloproteinase 3) which allows formation of mature HBEGF (heparin-binding epidermal growth factor) by cleaving pro-HBEGF. Mature HBEGF is then free to bind the EGFR, resulting in EGFR activation (Dufresne et al. 2006, Liebmann 2011).
Gastrin is a hormone whose main function is to stimulate secretion of hydrochloric acid by the gastric mucosa, which results in gastrin formation inhibition. This hormone also acts as a mitogenic factor for gastrointestinal epithelial cells. Gastrin has two biologically active peptide forms, G34 and G17.Gastrin gene expression is upregulated in both a number of pre-malignant conditions and in established cancer through a variety of mechanisms. Depending on the tissue where it is expressed and the level of expression, differential processing of the polypeptide product leads to the production of different biologically active peptides. In turn, acting through the classical gastrin cholecystokinin B receptor CCK-BR, its isoforms and alternative receptors, these peptides trigger signalling pathways which influence the expression of downstream genes that affect cell survival, angiogenesis and invasion (Wank 1995, de Weerth et al. 1999, Grabowska & Watson 2007)
Functional properties of a Drosophila homolog of the E2F1 gene
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Diacylglycerol, produced by PLC beta-mediated PIP2 hydrolysis in G alpha (q) signalling, remains in the plasma membrane and binds Protein Kinase C alpha (PKC-alpha), causing PKC-alpha to translocate from the cytosol to the plasma membrane. PKC-alpha is thereby activated and phosphorylates target proteins.
The phospholipase C (PLC) family of enzymes is both diverse and complex. The isoforms beta, gamma and delta (each have subtypes) make up the members of this family. PLC hydrolyzes phosphatidylinositol bisphosphate (PIP2) into two second messengers, inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG). IP3 mobilizes intracellular calcium stores while DAG activates protein kinase C isoforms which are involved in regulatory functions.
When dissociated Galpha-GTP and Gbeta-gamma can activate or inhibit different signalling cascades and effector proteins. The precise pathways depends on the identity of the alpha and beta/gamma subtypes.
Dopamine- and cAMP-regulated phosphoprotein, Mr 32 kDa (DARPP-32), was identified as a major target for dopamine and protein kinase A (PKA) in striatum. Recent advances now indicate that regulation DARPP-32 phosphorylation provides a mechanism for integrating information arriving at dopaminoceptive neurons, in multiple brain regions, via a variety of neurotransmitters, neuromodulators, neuropeptides, and steroid hormones. Activation of PKA or PKG stimulates DARPP-32 phosphorylation at Thr34, converting DARPP-32 into a potent inhibitor of protein phosphatase-1 (PP-1). DARPP-32 is also phosphorylated at Thr75 by Cdk5, converting DARPP-32 into an inhibitor of PKA. Thus, DARPP-32 has the unique property of being a dual-function protein, acting either as an inhibitor of PP-1 or of PKA.
Opioids are chemical substances similar to opiates, the active substances found in opium (morphine, codeine etc.). Opioid action is mediated by the receptors for endogenous opioids; peptides such as the enkephalins, the endorphins or the dynorphins. Opioids possess powerful analgesic and sedative effects, and are widely used as pain-killers. Their main side-effect is the rapid establishment of a strong addiction. Opioids receptors are G-protein coupled receptors (GPCR). There are four classes of receptors: mu (MOR), kappa (KOR) and delta (DOR), and the nociceptin receptor (NOP).
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The active form of G protein alpha subunit q (Gq-alpha) was found to activate phospholipase C beta-1 (PLC-beta1), in investigations using bovine membranes. Subsequently, all 4 human isoforms have been shown to be activated by Gq, though activation of PLCbeta-4 is limited. In recombinant assays, several activated rat G alpha q family members were found to stimulate human PLC-beta isoforms with the same rank order of decreasing potency. PLC-beta1 stimulation was slightly more than for PLC-beta3; PLC-beta3 stimulation was 10-fold greater than for beta-2. PLC-beta2 is expressed specifically in hematopoietic cells. PLC-beta acts directly on Gq to accelerate hydrolysis of bound GTP, thus PLC-betas are GTPase activating proteins (GAPs). The crystal structure of the C-terminal region from Turkey PLC-beta, revealed a novel fold composed almost entirely of three long helices forming a coiled-coil that dimerizes along its long axis in an antiparallel orientation. The extent of the dimer interface and gel exclusion chromatography data suggest that PLC-betas are functionally dimeric.
The phospholipase C (PLC) family of enzymes is both diverse and complex. The isoforms beta, gamma and delta (each have subtypes) make up the members of this family. One type, PLC-beta1, hydrolyzes phosphatidylinositol bisphosphate (PIP2) into two second messengers, inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG). IP3 mobilizes intracellular calcium stores while DAG activates protein kinase C isoforms which are involved in regulatory functions.
PLC-beta1 is a GTPase-activating protein (GAP) for Gq-alpha, exchanging GTP for GDP and releasing the alpha subunit to cycle back to the membrane and reassociate with the beta-gamma subunits. Between itself and the receptor, they regulate the amplitude of the PLC signal and the rates of signal initiation and termination.
Calcium, as the ion Ca2+, is essential in many biological processes. The majority of Ca2+ in many organisms is bound to phosphates which form skeletal structures and also buffer Ca2+ levels in extracellular fluids (typically 1 millimolar). Intracellular free Ca2+, by contrast, is 10,000 times lower than the outside of the cell (typically 10 micromolar). This concentration gradient is used to import Ca2+ into cells where it acts as a second messenger.
Receptor activated heterotrimeric G proteins consist of the Galpha and the tightly associated Gbeta-gamma subunits. When a ligand binds to a G protein-coupled receptor, it stabilises a conformation with an high affinity for the G-protein bound to GDP. GDP is then exchanged for GTP on the Galpha subunit. This exchange triggers the dissociation of the Galpha subunit from the Gbeta-gamma dimer and the receptor. Galpha-GTP and Gbeta-gamma, can then modulate different signalling cascades and effector proteins, while the receptor is able to activate another G protein, resulting in an amplification cascade. The Galpha subunit will eventually hydrolyze the attached GTP to GDP by its inherent enzymatic activity, allowing it to reassociate with Gbeta-gamma and start a new cycle.
Mitochondrial disulfide bond formation is driven by intersubunit electron transfer in Erv1 and proofread by glutathione
Retinoic acid activation of peroxisome proliferation-activated receptor delta represses obesity and insulin resistance
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Mechanistic studies on phosphopantothenoylcysteine decarboxylase: trapping of an enethiolate intermediate with a mechanism-based inactivating agent
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A histone H3 lysine 27 demethylase regulates animal posterior development
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Indoleamine 2,3-dioxygenase. Purification and some properties
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Astrocytic Glutamate-Glutamine Uptake And Metabolism
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Selective inhibition of 2-AG hydrolysis enhances endocannabinoid signaling in hippocampus
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The MRN complex: coordinating and mediating the response to broken chromosomes.
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Enzymatic hydration of leukotriene A4. Purification and characterization of a novel epoxide hydrolase from human erythrocytes
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Cleavage of 5-hydroxyluracil by UNG2 glycosylase
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Cleavage of thymine glycol by hNTH1 glycosylase
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Binding of Pol eta to lesioned DNA template
Binding of REV1 to lesioned DNA template
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Misinsertion of bases opposite to the lesion by HREV1
Cleavage of formamidopyrimidine by hNTH1 glycosylase
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Cleavage of cytosine glycol by hNTH1 glycosylase
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Cleavage of dihydrouracil by hNTH1 glycosylase
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Identification of the signal directing Tim9 and Tim10 into the intermembrane space of mitochondria
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Stimulation of the cell death response by PAK-2p34
Insertion of correct bases opposite to the lesion by Pol eta
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Association of RAD51 with RAD52:DNA double-strand break ends
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Association of RAD51 with the resected ends of the DNA double-strand break
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Ligation of DNA and formation of Holliday structures following repair synthesis
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The mechanism of PAK activation. Autophosphorylation events in both regulatory and kinase domains control activity
Intermolecular autophosphorylation of ATM within dimeric ATM complexes
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Dissociation of dimeric phospho-ATM complexes
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Association of RAD52 with ssDNA at resected ends of double-strand break
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5535.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29896
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2670.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_255759.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608447
Role of the vascular endothelial growth factor pathway in tumor growth and angiogenesis
A flavin-dependent monooxygenase involved in ubiquinone/ubiquinol biosynthesis, Coq6 (Heeringa et al. 2011) catalyses the C5-hydroxylation of 3-hexaprenyl-4-hydroxybenzoic acid (HHB) to 3,4-dihydroxy-5-hexaprenylbenzoic acid (DHHB) (Ozeir et al. 2011, Gin et al. 2003). Coq6 is a peripheral membrane protein that localizes to the matrix side of the inner mitochondrial membrane (Gin et al. 2003). Ferredoxin, Yah1 and the ferredoxin reductase, Arh1 may be the in vivo source of electrons for Coq6 and additionally required for this reaction (Ozeir et al. 2011).
hOGG1 glycosylase mediated recognition and binding of an 8-oxo guanine opposite to a cytosine
Cellular regulation of endothelial nitric oxide synthase
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Aminophospholipids are transported from in the internal to the external side of the plasma membrane
P-type ATPases type IV transport internal-facing APLs to external side of the plasma membrane
Probable phospholipid-transporting ATPase ID
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P-type ATPases type IV transport external-facing APLs to internal side of the plasma membrane
P-type ATPase type IV subfamily transporters may mediate phospholipid transfer
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611252
Probable phospholipid-transporting ATPase IG
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Cytosolic Cl- is transported to extracellular region by ANOs
ANOs transport cytosolic Cl- to extracellular region
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DMQ6H2 is hydroxylated to DeMQ6H2 by Cat5
Catabolite repression protein Cat5 aka ubiquinone biosynthesis protein catalyses the hydroxylation of 2-hexaprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQ6H2) to 3-demethylubiquinol-6 (DeMQ6H2) (Marbois & Clarke 1996, Tran et al. 2006).
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617195
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113601
Raf and akt mediate distinct aspects of sensory axon growth
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611258
The MCM2-7 complex is the putative replicative helicase that unwinds replication forks. While an S.erevisiae MCM hexameric complex consisting of one copy of each of the six subunits has been reconstituted in vitro from purified subunits (Davey et al. 2003), an active helicase can be assembled with three of the six MCM proteins, MCM4, MCM6 and MCM7, in human (Ishimi,1997), S. pombe (Lee and Hurwitz, 2001) and S. cerevisiae (Kaplan et al., 2003). However, this in vitro reaction may not represent the in vivo situation. In vivo experiments suggest that all six subunits are required at the replication fork (Labib et al., 2000; reviewed by Tye and Sawyer, 2000).
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Probable phospholipid-transporting ATPase IC
2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial (Coq5) catalyses the C-methyltransferase conversion of 2-hexaprenyl-6-methoxy-1,4-benzoquinol (MDMQ6H2) to 2-hexaprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQ6H2) (Barkovich et al. 1997).
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2882.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611259
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617191
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617192
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617189
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617190
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5616783
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617188
Identification of 3-methoxy-4-hydroxy-5-hexaprenylbenzoic acid as a new intermediate in ubiquinone biosynthesis by Saccharomyces cerevisiae
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_252256.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_96459.4
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ATF6 activated by proteolysis binds in the presence of NF-Y (CBF) directly to the cis-acting element responsible for the mammalian unfolded protein response
Lysophospholipid acyltransferases and arachidonate recycling in human neutrophils
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2731008
Cancer-associated IDH1 mutations produce 2-hydroxyglutarate
UNG glycosylase mediated recognition and binding of an uracil opposite to a guanine
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113564
UNG glycosylase mediated recognition and binding of a 5-hydroxyuracil opposite to a guanine
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_124125.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613306
Cleavage of formamidopyrimidine by hOGG1 glycosylase
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29428
Cleavage of 8-oxo guanine by hOGG1 glycosylase
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3913.3
hNTH1 glycosylase mediated recognition and binding of thymine glycol
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617216
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_188674.3
hNTH1 glycosylase mediated recognition and binding of formamidopyrimidine
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_210852.2
hNTH1 glycosylase mediated recognition and binding of dihydrouracil
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_188673.3
hNTH1 glycosylase mediated recognition and binding of cytosine glycol
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2334.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618263
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2731020
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_187809.3
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_160470.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618262
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617214
hOGG1 glycosylase mediated recognition and binding of a formamidopyrimidine
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617196
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3979.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617198
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159751
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_251447.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3165.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617199
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113519
DNA mismatch repair and mutation avoidance pathways
N-glycosylase/DNA lyase (Includes: 8-oxoguanine DNA glycosylase (EC 3.2.2.-); DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) (AP lyase))
DNA-(apurinic or apyrimidinic site) lyase
FATP1, 4 and 6 can mediate the influx of long chain fatty acids into cells
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Aquaporins passively transport water into cells
Aquaporins passively transport water out of cells
Aquaporins passively transport glycerol into cells
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615469
AT1 transports acetyl-CoA into the Golgi lumen
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613310
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615470
Equilibrative transport (import) of adenosine and biogenic amines by solute carrier family 29 (nucleoside transporters), member 4
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_188956.3
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_249921.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615465
SLC35B4 mediates the transport of UDP-N-acetylglucosamine into the Golgi lumen
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618453
SLC35B4 mediates the transport of UDP-xylose into the Golgi lumen
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_191567.3
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_238512.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618612
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618454
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_181502.3
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_251784.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615471
Equilibrative transport (export) of adenosine and biogenic amines by solute carrier family 29 (nucleoside transporters), member 4
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618611
Equilibrative transport (import) of nucleosides and adenine by solute carrier family 29 (nucleoside transporters), member 3
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_188958.3
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_25925.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5616352
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615461
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613307
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615457
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613308
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613309
Fine-tuning of GPCR activity by receptor-interacting proteins
COPII (Coat Protein 2) Mediated Vesicle Transport
Calcium is sequestered to the golgi by secretory pathway calcium-ATPases (SPCAs)
ATP2C1/2:Mg2+ transport cytosolic Ca2+ to Golgi lumen
Acidification of Tf:TfR1 containing endosome
Copper sequestration by copper-transporting ATPase 2
ATP7B transports cytosolic Cu2+ to Golgi lumen
DNA repair protein REV1 ecNumber2.7.7.-/ecNumber
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_182172.3
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_122430.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613165
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615496
Aquaporin-9 passively transports glycerol into cell
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2046049
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613167
Endonuclease III-like protein 1 (EC 4.2.99.18)
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_182160.3
Aquaporin-7 passively transports glycerol out of cell
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_121476.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613162
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618494
Aquaporin-3 passively transports water out of cell
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2046062
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613163
Serine-protein kinase ATM (EC 2.7.1.37) (Ataxia telangiectasia mutated) (A-T, mutated)
Aquaporins passively transport urea out of cells
E2F-dependent accumulation of hEmi1 regulates S phase entry by inhibiting APC(Cdh1)
6-O- methylguanine-DNA methyltransferase
Methylated-DNA--protein-cysteine methyltransferase
Aquaporins passively transport urea into cells
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_122294.1
Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) (6-O- methylguanine-DNA methyltransferase)
Aquaporins passively transport glycerol out of cells
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2046064
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613169
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119727.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613170
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=211579
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_121509.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615472
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615473
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613161
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615477
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615478
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613160
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615480
Equilibrative NBMPR-sensitive nucleoside transporter
Equilibrative nitrobenzylmercaptopurine riboside-sensitive nucleoside transporter
solute carrier family 29 (nucleoside transporters), member 1
Equilibrative nucleoside transporter 1 (Equilibrative nitrobenzylmercaptopurine riboside-sensitive nucleoside transporter) (Equilibrative NBMPR-sensitive nucleoside transporter) (Nucleoside transporter, es-type)
HMIT co-transports myo-inositol with a proton
GLUT9 transports glucose, fructose and urate
Equilibrative nucleoside transporter 2 (Equilibrative nitrobenzylmercaptopurine riboside-insensitive nucleoside transporter) (Equilibrative NBMPR-insensitive nucleoside transporter) (Nucleoside transporter, ei-type) (36 kDa nucleolar protein HNP36) (Hydrophobic nucleolar protein, 36 kDa) (Delayed-early response protein 12)
solute carrier family 29 (nucleoside transporters), member 2
Equilibrative nitrobenzylmercaptopurine riboside-insensitive nucleoside transporter
Equilibrative NBMPR-insensitive nucleoside transporter
NaS2 co-transports sulphate and two sodium ions
NaS1 co-transports sulphate and a sodium ion
NaDC3 co-transports the dicarboxylic acid succinate and three sodium ion
NaDC1 co-transports dicarboxylic acids and a sodium ion
In human, ten members of the Toll-like receptor (TLR) family (TLR1-TLR10) have been identified (TLR11 has been found in mouse, but not in human). All TLRs have a similar Toll/IL-1 receptor (TIR) domain in their cytoplasmic region and an Ig-like domain in the extracellular region, where each is enriched with a varying number of leucine-rich repeats (LRRs). Each TLR can recognize specific microbial pathogen components. The binding pathogenic component to TLR initializes signaling pathways that lead to induction of Interferon alpha/beta and inflammatory cytokines. There are two main signaling pathways. The first is a MyD88-dependent pathway that is common to all TLRs, except TLR3; the second is a TRIF(TICAM1)-dependent pathway that is peculiar to TLR3 and TLR4. TLR4-mediated signaling pathway via TRIF requires adapter molecule TRAM (TRIF-related adapter molecule or TICAM2). TRAM is thought to bridge between the activated TLR4 complex and TRIF.(Takeda & Akira 2004; Akira 2003; Takeda & Akira 2005; Kawai 2005; Heine & Ulmer 2005).
RNA Polymerase II Transcription Initiation And Promoter Clearance
CpG DNA is an unusual Pathogen-Associated Molecular Pattern (PAMP). Cytosine methylation exists in mammalian but not bacterial cells, and most (but not all) CpG in the mammalian genome is methylated. Therefore, unmethylated CpG DNA may signal the presence of microbial infection. Evidence of CpG recognition by TLR9 was demonstrated both in human and mouse, and this type of signaling requires its internalization into late endosomal/lysosomal compartments. TLR9 has been reported to be able to discern different types of CpG motifs, and therefore that it presumably recognizes CpG DNA directly. It appears that over evolutionary periods, TLR9 molecules expressed by different species have diverged. This has led to differences in the precise sequence motif (CpG dinucleotide plus flanking regions) that optimally stimulate the innate immune system of different animals.
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TRIF-related adapter molecule (TRAM or also known as TICAM2) is a sorting adapter which recruits TRIF to activated TLR4. Like TLR4, TRAM was detected both at the plasma membrane and in the endosomal compartment. TRAM was reported to recruit TRIF to the plasma membrane [Tanimuro N et al 2008]. However, TRAM did not induce TRIF-mediated signaling from the cell surface, instead, TRAM endocytosis was required for activation of IRF3 and induction of IFN-beta [Tanimuro N et al 2008; Kagan JC et al 2008]. Although, endocytosis of both TLR4 and TRAM and their association are required to trigger TRIF-mediated signaling, TRAM can target endosomes independently on its interaction with TLR4. TRAM cellular localization is controlled by myristoylation and phosphorylation of its N-terminal bipartite sorting signal motif [Kagan JC et al 2008]. TRAM has been shown to undergo phosphorylation on Ser-16 by protein kinase C epsilon in LPS-treated human THP1 and murine embryonic fibroblasts (MEF) cells [McGettrick AF et al 2006].
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The first known downstream component of TLR4 and TLR2 signaling is the adaptor MyD88. Another adapter MyD88-adaptor-like (Mal; also known as TIR-domain-containing adaptor protein or TIRAP) has also been described for TLR4 and TLR2 signaling. MyD88 comprises an N-terminal Death Domain (DD) and a C-terminal TIR, whereas Mal lacks the DD. The TIR homotypic interactions bring adapters into contact with the activated TLRs, whereas the DD modules recruit serine/threonine kinases such as interleukin-1-receptor-associated kinase (IRAK). Recruitment of these protein kinases is accompanied by phosphorylation, which in turn results in the interaction of IRAKs with TNF-receptor-associated factor 6 (TRAF6). The oligomerization of TRAF6 activates TAK1, a member of the MAP3-kinase family, and this leads to the activation of the IkB kinases. These kinases, in turn, phosphorylate IkB, leading to its proteolytic degradation and the translocation of NF-kB to the nucleus. Concomitantly, members of the activator protein-1 (AP-1) transcription factor family, Jun and Fos, are activated, and both AP-1 transcription factors and NF-kB are required for cytokine production, which in turn produces downstream inflammatory effects.
Cloning, sequencing, expression, and Gq-independent activation of phospholipase C-beta 2
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TLR4 is unique among the TLR family in its ability to recruit four adapters to activate two distinct signaling pathways. One pathway is activated by the pair of the adapters Mal or TIRAP (Toll/interleukin-1-receptor (TIR)-domain-containing adapter protein) and MyD88, which leads to the NFkB activation and the induction of pro-inflammatory cytokines. The second pathway is activated by the adapters TRIF (TIR-domain-containing adapter protein inducing interferon-beta) and TRAM (TRIF-related adapter molecule). The combined use of TRIF and TRAM adapters is specific for TLR4 signaling pathway and leads to the induction of type I interferons and delayed activation of NFkB. The previous model of TLR4 signaling pathway described the simultaneous activation of these two signaling pathways at the plasma membrane, however the later studies suggested that upon activation TLR4 first induces TIRAP-MyD88 signaling at the plasma membrane and is then endocytosed and activates TRAM-TRIF signaling from the early endosome [Kagan JC et al 2008; Tanimura N et al 2008; Zanoni I et al 2011].
Toll-like Receptor 4 is a Microbe Associated Molecular Pattern receptor well known for it's sensitivity to Bacterial Lipopolysaccharides (LPS). LPS is assembled within diverse Gram-negative bacteria, many of which are human or plant pathogens. It is a component of the outer membrane of Gram-negative bacteria and consists of lipid A, a core polysaccharide and an O-polysaccharide of variable length (often more than 50 monosaccharide units). LPS is a potent activator of the innate immune response in humans, causing reactions including fever, headache, nausea, diarrhoea, changes in leukocyte and platelet counts, disseminated intravascular coagulation, multiorgan failure, shock and death. All these reactions are induced by cytokines and other endogenous mediators which are produced after interaction of LPS with the humoral and cellular targets of the host. In macrophages and dendritic cells, LPS-mediated activation of TLR4 triggers the biosynthesis of diverse mediators of inflammation, such as TNF-alpha and IL6, and activates the production of co-stimulatory molecules required for the adaptive immune response. In mononuclear and endothelial cells, LPS also stimulates tissue factor production. These events are desirable for clearing local infections, but when these various mediators and clotting factors are overproduced, they can damage small blood vessels and precipitate shock accompanied by disseminated intravascular coagulation and multiple organ failure.
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TLR1 is expressed by monocytes. TLR1 and TLR2 cotranslationally form heterodimeric complexes on the cell surface and in the cytosol. The TLR2:TLR1 complex recognizes Neisserial PorB and Mycobacterial triacylated lipoproteins and peptides, amongst others, triggering up-regulation of nuclear factor-kappaB production and apoptotic cascades. Such cooperation between TLR1 and TLR2 on the cell surface of normal human peripheral blood mononuclear cells, for instance, leads to the activation of pro-inflammatory cytokine secretion (Sandor et al. 2003).
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TLR2 and TLR4 recognize different bacterial cell wall components. While TLR4 is trained onto Gram-negative lipopolysaccharide components, TLR2 - in combination with TLR6 - plays a major role in recognizing peptidoglycan wall products from Gram-positive bacteria, as well as Mycobacterial diacylated lipopeptides. In particular, TLR6 appears to participate in discriminating the subtle differences between dipalmitoyl and tripalmitoyl cysteinyl residues (Okusawa et al. 2004).
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TLR2 is involved in recognition of peptidoglycan from gram-positive bacteria, bacterial lipoproteins, mycoplasma lipoprotein and mycobacterial products. It is quite possible that recognition of at least some other TLR2 ligands may be assisted by additional accessory proteins, particularly in association with TLR1 or TLR6. TLR2 is expressed constitutively on macrophages, dendritic cells, and B cells, and can be induced in some other cell types, including epithelial cells. TLR1 and TLR6, on the other hand, are expressed almost ubiquitously (Muzio et al. 2000). TLR2 may be a sensor and inductor of specific defense processes, including oxidative stress and cellular necrosis initially spurred by microbial compounds.
Natural resistance-associated macrophage protein 2
SLC7A9-mediated exchange of extracellular arginine, lysine, or cystine for cytosolic leucine
Vesicular inhibitory amino acid transport
GLUT7 and GLUT11 transport glucose and fructose
RNA can serve as a danger signal, both in its double-stranded form (that is associated with viral infection), as well as single-stranded RNA (ssRNA). Specifically, guanosine (G)- and uridine (U)-rich ssRNA oligonucleotides derived from human immunodeficiency virus-1 (HIV-1), for example, stimulate dendritic cells (DC) and macrophages to secrete interferon-alpha and proinflammatory, as well as regulatory, cytokines. This has been found to be mediated by TLR7, as well as TLR8. Separate studies showed that imidazoquinoline compounds (e.g. imiquimod and R-848, low-molecular-weight immune response modifiers that can induce the synthesis of interferon-alpha) also exert their effects in a MyD88-dependent fashion independently through TLR7 and 8 (Heil et al. 2004).
Equilibrative transport (import) of nucleosides and free bases by solute carrier family 29 (nucleoside transporters), member 2
Equilibrative transport (import) of nucleosides and free bases by solute carrier family 29 (nucleoside transporters), member 1
Equilibrative transport (export) of nucleosides and free bases by solute carrier family 29 (nucleoside transporters), member 2
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Long-chain fatty acid transport protein 4
Equilibrative transport (export) of nucleosides and free bases by solute carrier family 29 (nucleoside transporters), member 1
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UDP-xylose and UDP-N-acetylglucosamine transporter
Equilibrative transport (export) of nucleosides and adenine by solute carrier family 29 (nucleoside transporters), member 3
Upon binding of their ligands, TLR7/8 and TLR9 recruit a cytoplasmic adaptor MyD88 and IRAKs, downstream of which the signaling pathways are divided to induce either inflammatory cytokines or type I IFNs.
TRAF6 mediates NFkB activation via canonical phosphorylation of IKK complex by TAK1. TRAF6 and TAK1 also regulate MAPK cascades leading to the activation of AP-1.
Mutations and polymorphisms in the human argininosuccinate synthetase (ASS1) gene
Mammalian myeloid differentiation factor 88 (MyD88) is Toll/interleukin (IL)-1 (TIR)-domain containing adapter protein which plays crucial role in TLR signaling. All TLRs, with only one exception of TLR3, can initiate downstream signaling trough MyD88. In the MyD88 - dependent pathway, once the adaptor is bound to TLR it leads to recruitment of IL1 receptor associated kinase family IRAK which is followed by activation of tumour necrosis factor receptor-associated factor 6 (TRAF6) . TRAF6 is an ubiquitin E3 ligase which in turn induces TGF-beta activating kinase 1 (TAK1) auto phosphorylation. Once activated TAK1 can ultimately mediate the induction of the transcription factor NF-kB or the mitogen-activated protein kinases (MAPK), such as JNK, p38 and ERK. This results in the translocation of the activated NF-kB and MAPKs to the nucleus and the initiation of appropriate gene transcription leading to the production of many proinflammatory cytokines and antimicrobial peptides.
Little is known about TLR10 ligands. It has been established that the receptor homodimerizes upon binding and signals in an MyD88-dependent manner (Hasan U et al 2005; Nyman T et al 2008). It may also heterodimerize with TLRs 1 and 2. It is expressed in a restricted fashion as a highly N-glycosylated protein detectable in B cells and dendritic cells.
Antigen presenting cells (APCs) such as B cells, dendritic cells (DCs) and monocytes/macrophages express major histocompatibility complex class II molecules (MHC II) at their surface and present exogenous antigenic peptides to CD4+ T helper cells. CD4+ T cells play a central role in immune protection. On their activation they stimulate differentiation of B cells into antibody-producing B-cell blasts and initiate adaptive immune responses. MHC class II molecules are transmembrane glycoprotein heterodimers of alpha and beta subunits. Newly synthesized MHC II molecules present in the endoplasmic reticulum bind to a chaperone protein called invariant (Ii) chain. The binding of Ii prevents the premature binding of self antigens to the nascent MHC molecules in the ER and also guides MHC molecules to endocytic compartments. In the acidic endosomal environment, Ii is degraded in a stepwise manner, ultimately to free the class II peptide-binding groove for loading of antigenic peptides. Exogenous antigens are internalized by the APC by receptor mediated endocytosis, phagocytosis or pinocytosis into endocytic compartments of MHC class II positive cells, where engulfed antigens are degraded in a low pH environment by multiple acidic proteases, generating MHC class II epitopes. Antigenic peptides are then loaded into the class II ligand-binding groove. The resulting class II peptide complexes then move to the cell surface, where they are scanned by CD4+ T cells for specific recognition (Berger & Roche 2009, Zhou & Blum 2004, Watts 2004, Landsverk et al. 2009).
Adaptive immunity refers to antigen-specific immune response efficiently involved in clearing the pathogens. The adaptive immune system is comprised of B and T lymphocytes that express receptors with remarkable diversity tailored to recognize aspects of particular pathogens or antigens. During infection, dendritic cells (DC) which act as sentinels in the peripheral tissues recognize and pick up the pathogen in the form of antigenic determinants and then process these antigens and present them to T cells. These T cells of appropriate specificity respond to the antigen, and either kill the pathogen directly or secrete cytokines that will stimulate B lymphocyte response. B cells provide humoral immunity by secreting antibodies specific for the pathogen or antigen.
Toll-like receptor 3 (TLR3) as was shown for mammals is expressed on myeloid dendritic cells, respiratory epithelium, macrophages, and appears to play a central role in mediating the antiviral and inflammatory responses of the innate immunity in combating viral infections. Mammalian TLR3 recognizes dsRNA, and that triggers the receptor to induce the activation of NF-kappaB and the production of type I interferons (IFNs). dsRNA-stimulated phosphorylation of two specific TLR3 tyrosine residues (Tyr759 and Tyr858) is essential for initiating TLR3 signaling pathways.
TLR5 is the receptor for flagellin, the protein that forms bacterial flagella. Unlike most other Pathogen-Associated Molecular Patterns (PAMPs), flagellin does not undergo any posttranslational modifications that would distinguish it from cellular proteins. However, flagellin is extremely conserved at its amino- and carboxyl-termini, which presumably explains why it was selected as a ligand for innate immune recognition. TLR5 is expressed on epithelial cells as well as on macrophages and dendritic cells. Expression of TLR5 on intestinal epithelium is polarized such that TLR5 is expressed only on the basolateral side of the cell, as pathogenic but not commensal microbes cross the epithelial barrier. This ensures that innate immune responses are confined to pathogenic but not commensal microbes (Paul 2004; Hayashi et al. 2001; Gewirtz et al. 2001).
TRIF(TICAM1) was shown to induce IRF3/7 and NF-?B activation and apoptosis through distinct intracellular signaling pathways [Han KJ et al 2004; Kaiser WJ and Offermann MK et al 2005]. TRIF consists of an N-terminal region (1-234), a TIR domain (235-500), and a C-terminal region (501-680). The N-terminal region of TRIF harbors TRAF (TNF receptor associated factor) family proteins and forms complexes containing IRF-3 and/or NFkB -activating kinases. The C-terminal region of TRIF can recruit receptor-interacting protein-1 (RIP-1), and this event is followed by the activation of IKK complex.
MyD88-independent signaling pathway is shared by TLR3 and TLR4 cascades. TIR-domain-containing adapter-inducing interferon-beta (TRIF or TICAM1) is a key adapter molecule in transducing signals from TLR3 and TLR4 in a MyD88-independent manner (Yamamoto M et al. 2003a). TRIF is recruited to ligand-stimulated TLR3 or 4 complex via its TIR domain. TLR3 directly binds TRIF (Oshiumi H et al 2003). In contrast, TLR4-mediated signaling pathway requires two adapter molecules, TRAM (TRIF-related adapter molecule or TICAM2) and TRIF. TRAM(TICAM2) is thought to bridge between the activated TLR4 complex and TRIF (Yamamoto M et al. 2003b, Tanimura N et al. 2008, Kagan LC et al. 2008). TRIF recruitment to TLR complex stimulates distinct pathways leading to production of type 1 interferons (IFNs), pro-inflammatory cytokines and induction of programmed cell death.
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NACT co-transports trivalent citrate and a sodium ion
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ZnT1 mediates the efflux of zinc from the cell
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ZIP7 mediates zinc efflux from the endoplasmic reticulum
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DCT1 (NRAMP2) mediates divalent iron uptake across the apical membrane of enterocytes
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ABCD1/D2/D3 mediate long chain fatty acid transport in to peroxisomes
CIA Targeting Complex transfers 4Fe-4S cluster to apoproteins
The ABCC family mediates organic anion transport
ABC7, mABC1 and mABC2 mediate heme transport
carbovir monophosphate + ATP => carbovir diphosphate + ADP
Phosphorylation of carbovir monophosphate
abacavir monophosphate + H2O => carbovir monophosphate + cyclopropylamine
Deamination of abacavir monophosphate to form carbovir monophosphate
4Fe-4S cluster assembles on NUBP2:NUBP1 scaffold
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Phospholipases play an integral role in phagocytosis by generating essential second messengers. An early step in phagocytic signaling is the association of PIP2 and IP3 with the phagocytic cup. These are formed by the activity of phosphoinositol kinases and phospholipases. PI3K is has been shown to accumulate at phagocytic cups and converts PI (4,5)P2 to PI (3,4,5)P3. These phosphoinositides are capable of binding and increasing the activity of proteins that regulate the actin cytoskeleton. Phospholipases are lipid modifying enzymes that produce lipid mediators such as diacylglycerol (DAG), arachidonic acid (AA) and IP3. Phopsholipases PLA, PLC and PLD have been shown to be involved in antibody (IgG) mediated phagocytosis. The PLC product IP3 stimulates release of calcium from the endoplasmic reticulum. This Ca+2 concentration increase is greatest in the cytoplasm surrounding the phagocytic cup. Calcium is involved in the various stages of phagosome formation, including phagocytic ingestion and phagosome maturation.
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Phagocytosis is one of the important innate immune responses that function to eliminate invading infectious agents. Monocytes, macrophages, and neutrophils are the professional phagocytic cells. Phagocytosis is a complex process involving the recognition of invading foreign particles by specific types of phagocytic receptors and the subsequent internalization of the particles. Fc gamma receptors (FCGRs) are among the best studied phagocytic receptors that bind to Fc portion of immunoglobulin G (IgG). Through their antigen binding F(ab) end, antibodies bind to specific antigen while their constant (Fc) region binds to FCGRs on phagocytes. The clustering of FCGRs by IgG antibodies on the phagocyte initiates a variety of signals, which lead, through the reorganisation of actin cytoskeleton and membrane remodelling, to the formation of pseudopod and phagosome. Fc gamma receptors are classified into three classes: FCGRI, FCGRII and FCGRIII. Each class of these FCGRs consists of several individual isoforms. Among all these isoforms FCGRI, FCGRIIA and FCGRIIIA, are able to mediate phagocytosis (Joshi et al. 2006, Garcia Garcia & Rosales 2002, Nimmerjahn & Ravetch 2006).
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The four protein kinase A (PKA) regulatory subunit isoforms differ in their tissue specificity and functional characteristics. The specific isoform activated in response to glucagon signalling is not known. The PKA kinase is a tetramer of two regulatory and two catalytic. The regulatory subunits block the catalytic subunits. Binding of cAMP to the regulatory subunit leads to the dissociation of the tetramer into two active dimers made up of a regulatory and a catalytic subunit.
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The actin cytoskeleton is fundamental for phagocytosis and members of the Rho family GTPases RAC and CDC42 are involved in actin cytoskeletal regulation leading to pseudopod extension. Active RAC and CDC42 exert their action through the members of WASP family proteins (WASP/N-WASP/WAVE) and ARP2/3 complex. Actin filaments move from the bottom toward the top of the phagocytic cup during pseudopod extension.
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Diacylglycerol (DAG) positively regulates the autophosphorylation of protein kinase C-delta (PKC-delta), which stimulates ERK1/2 and triggers neurite outgrowth. DAG also stimulates the translocation of PKC from the cytosol to the plasma membrane. PKC-delta contributes to growth factor specificity and response to neuronal cells by promoting cell-type-specific differences in growth factor signalling. DAG can also activate PKC-epsilon in the same manner.
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Phospholipase D (PLD) catalyses the hydrolysis of the membrane phospholipid, phosphatidylcholine (PC) to generate choline and metabolically active phosphatidic acid (PA) (Lennartz 1999). Pharmacological inhibition studies show that PLD participates in FCGR-mediated phagocytosis (Kusner et al. 1996). There is an increase in the activity of PLD following the activation of phagocytosis via FCGR (Kusner et al. 1999). Following activation of FCGR, PLD translocates to the plasma membrane at the phagocytic cup and generate PA. This PA can be converted to DAG through the action of phosphatidic acid phosphatase-1 (PAP-1). Thus activation of PLD may be an additional pathway leading to PKC activation. The two isoforms PLD1 and PLD2 are both shown to be essential for the formation of phagosome at different stages. PLD1 is localized on the endosomal/lysosomal compartment and PLD2 is localized at the plasma membrane. PLD2 may be linked to phagosome formation whereas PLD1 may be involved in the focal exocytosis at the plasma membrane and also in the maturation process (Carrotte et al. 2006).
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Phosphatidic acid phosphatase (PAP) bound to the plasma membrane catalyzes the dephosphorylation of phosphatidic acid (PA), yielding diacylglycerol (DAG) and inorganic phosphate. In humans, Diacylglycerol pyrophosphate (DPPL1 and DPPL2) perform this reaction.
Wiskott-Aldrich syndrome protein (WASP) and Neural-WASP (N-WASP) proteins are scaffolds that transduce signals from cell surface receptors to the activation of the ARP2/3 complex and actin polymerization. WASP and N-WASP possess a central GTPase binding domain (GBD) and an NH2-terminal WASP homology domain 1 (WH1), adjacent to this is a basic region (B) and a C-terminal containing VCA region that contains: a V domain (verprolin homology/WASP homology 2), a C domain (connecting), and an A motif (acidic). The VCA region is responsible for binding to and activating the ARP2/3 complex (Bompard & Caron 2004, Callebaut et al 1998). Under resting conditions, WASP and N-WASP are maintained in an autoinhibition state via interaction of the N-terminal GBD and the C-terminal VCA domains. This prevents access of the ARP2/3 complex to the VCA region. Activated CDC42 binds to the GBD region in N-WASP and this interaction releases the VCA region from autoinhibition enabling binding of the ARP2/3 complex stimulating actin polymerization (Kim et al 2000, Park & Cox 2009). Phosphoinositides (PtdIns(4,5)P2) interact with the basic (B) region in WASP and this interaction is important for activation of the WASP and ARP2/3 complex.(Higgs & Pollard 2000).
Band 3 Anion Exchanger (AE1, SLC4A1) exchanges cytosolic chloride for extracellular bicarbonate
PAK1, a downstream effector of CDC42 and RAC1, is found localized in phagosomes. Upon activation, PAK1 phosphorylates LIMK, which directly phosphorylates and inactivates cofilin, a protein that mediates depolymerization of actin filaments. Thus, RAC and CDC42 coordinate actin dynamics by inducing actin polymerization via ARP2/3 on one hand, and inhibiting actin depolyerization via LIMK and cofilin on the other (Garcia-Garcia & Rosales 2002). PAK1 exists as homodimer in a trans-inhibited conformation. The kinase inhibitory (KI) domain of one PAK1 molecule binds to the C-terminal catalytic domain of the other and inhibits catalytic activity. GTPases RAC1/CDC42 bind the GBD domain of PAK1 thereby altering the conformation of the KI domain, relieving inhibition of its catalytic domain, and allowing PAK1 autophosphorylation that is required for full kinase activity (Parrini et al. 2002, Zhao & Manser 2005).
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abacavir [cytosol] + ATP + H2O => abacavir[extracellular] + ADP + phosphate
PAK1 needs autophosphorylation for complete activation. PAK1 is autophosphorylated at several sites, but S144 flanking the kinase inhibitor region and T423 within the catalytic domain are the two conserved sites that regulate the catalytic activity (Chong et al. 2001, Parrini et al. 2001).
Probable phospholipid-transporting ATPase IA
Calcium-transporting ATPase type 2C member 2
SLC36A2-mediated uptake of glycine and proline
Calcium-transporting ATPase type 2C member 1
SLC36A1-mediated uptake of glycine, proline, and alanine
Na+/H+ exchanger transport (at late endosome membrane)
Na+/H+ exchanger transport (at trans-golgi membrane)
Na+/H+ exchanger transport (at early endosome membrane)
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Visualization of eukaryotic DNA mismatch repair reveals distinct recognition and repair intermediates
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Advanced Glycosylation End- product-specific Receptor (AGER) also known as Receptor for Advanced Glycation End-products (RAGE) is a multi-ligand membrane receptor belonging to the immunoglobulin superfamily. It is considered to be a Pattern Recognition Receptor (Liliensiek et al. 2004). It recognizes a large variety of modified proteins known as advanced glycation/glycosylation endproducts (AGEs), a heterogenous group of structures that are generated by the Maillard reaction, a consequence of long-term incubation of proteins with glucose (Ikeda et al. 1996). Their accumulation is associated with diabetes, atherosclerosis, renal failure and ageing (Schmidt et al. 1999). The most prevalent class of AGE in vivo are N(6)-carboxymethyllysine (NECML) adducts (Kislinger et al. 1991). In addition to AGEs, AGER is a signal transduction receptor for amyloid-beta peptide (Ab) (Yan et al. 1996), mediating Ab neurotoxicity and promoting Ab influx into the brain. AGER also responds to the proinflammatory S100/calgranulins (Hofmann et al. 1999) and High mobility group protein B1 (HMGB1/Amphoterin/DEF), a protein linked to neurite outgrowth and cellular motility (Hori et al. 1995). The major inflammatory pathway stimulated by AGER activation is NFkappaB. Though the signaling cascade is unclear, several pieces of experimental data suggest that activation of AGER leads to sustained activation and upregulation of NFkappaB, measured as NFkappaB translocation to the nucleus, and increased levels of de novo synthesized NFkappaB (Bierhaus et al. 2001). As this is clearly an indirect effect it is represented here as positive regulation of NFkappaB translocation to the nucleus. AGER can bind ERK1/2 and thereby activate the MAPK and JNK cascades (Bierhaus et al. 2005).
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FCGR mediated phagocytosis requires CDC42 to stimulate actin polymerization, generating the force for phagocytic cup protrusion or pseudopod extension. CDC42 activation is restricted at the advancing edge of the phagocytic cup, where actin is concentrated, and is deactivated at the base of the phagocytic cup (Beemiller et al 2010). The mechanism behind the recruitment and activation of CDC42 during FCGR phagocytosis is unknown. VAV regulates the activation of RAC1 but not CDC42 and the GEF responsible for CDC42 activation during FCGR-mediated phagocytosis remains unidentified (Adam et al 2004, Patel et al 2002).
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The innate immune system is the first line of defense against invading microorganisms, a broad specificity response characterized by the recruitment and activation of phagocytes and the release of anti-bacterial peptides. The receptors involved recognize conserved molecules present in microbes called pathogen-associated molecular patterns (PAMPs), and/or molecules that are produced as a result of tissue injury, the damage associated molecular pattern molecules (DAMPs). PAMPs are essential to the pathogen and therefore unlikely to vary. Examples are lipopolysaccharide (LPS), peptidoglycans (PGNs) and viral RNA. DAMPs include intracellular proteins, such as heat-shock proteins and extracellular matrix proteins released by tissue injury, such as hyaluronan fragments. Non-protein DAMPs include ATP, uric acid, heparin sulfate and dsDNA. The receptors for these factors are referred to collectively as pathogen- or pattern-recognition receptors (PRRs). The best studied of these are the membrane-associated Toll-like receptor family. Less well studied but more numerous are the intracellular nucleotide-binding domain, leucine rich repeat containing receptors (NLRs) also called nucleotide binding oligomerization domain (NOD)-like receptors, a family with over 20 members in humans and over 30 in mice. These recognise PAMPs/DAMPs from phagocytosed microorganisms or from intracellular infections (Kobayashi et al. 2003, Proell et al. 2008, Wilmanski et al. 2008). Some NLRs are involved in process unrelated to pathogen detection such as tissue homeostasis, apoptosis, graft-versus-host disease and early development (Kufer & Sansonetti 2011). Structurally NLRs can be subdivided into the caspase-recruitment domain (CARD)-containing NLRCs (NODs) and the pyrin domain (PYD)-containing NLRPs (NALPs), plus outliers including ice protease (caspase-1) activating factor (IPAF) (Martinon & Tschopp, 2005). In practical terms, NLRs can be divided into the relatively well characterized NOD1/2 which signal via RIP2 primarily to NFkappaB, and the remainder, some of which participate in macromolecular structures called Inflammasomes that activate caspases. Mutations in several members of the NLR protein family have been linked to inflammatory diseases, suggesting these molecules play important roles in maintaining host-pathogen interactions and inflammatory responses. Most NLRs have a tripartite structure consisting of a variable amino-terminal domain, a central nucleotide-binding oligomerization domain (NOD or NACHT) that is believed to mediate the formation of self oligomers, and a carboxy-terminal leucine-rich repeat (LRR) that detects PAMPs/DAMPs. In most cases the amino-terminal domain includes protein-interaction modules, such as CARD or PYD, some harbour baculovirus inhibitor repeat (BIR) or other domains. For most characterised NLRs these domains have been attributed to downstream signaling Under resting conditions, NLRs are thought to be present in an autorepressed form, with the LRR folded back onto the NACHT domain preventing oligomerization. Accessory proteins may help maintain the inactive state. PAMP/DAMP exposure is thought to triggers conformational changes that expose the NACHT domain enabling oligomerization and recruitment of effectors, though it should be noted that due to the lack of availability of structural data, the mechanistic details of NLR activation remain largely elusive. New terminology for NOD-like receptors was adopted by the Human Genome Organization (HUGO) in 2008 to standardize the nomenclature of NLRs. The acronym NLR, once standing for NOD-like receptor, now is an abbreviation of 'nucleotide-binding domain, leucine-rich repeat containing' protein. The term NOD-like receptor is officially outdated and replaced by NLRC where the C refers to the CARD domain. However the official gene symbols for NOD1 and NOD2 still contain NOD and this general term is still widely used.
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In addition to AGER/RAGE, several other proteins have been identified as AGE-binding proteins. AGE binding proteins p60 and p90 (Yang et al. 1991) were subsequently identified as the Oligosaccharyl transferase 48 kDa subunit (Ost-48) and Glucosidease-2 subunit beta (Li et al. 1996). A third member was identified as Galectin-3 (Vlassara et al. 1995). These 3 proteins have been shown to be present on the plasma membrane of many cell types including vascular endothelium (Stitt et al. 1999). They have been designated AGE-R1, -R2 and -R3. Their suggested function is the removal and degradation of AGEs, but AGER-1 was found to negatively regulate AGER/RAGE (Lu et al. 2004), with kinetics that suggested a more complex interaction than simple competition for the same ligand.
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The NLRP3 (Cryopyrin) inflammasome is currently the best characterized. It consists of NLRP3, ASC (PYCARD) and procaspase-1; CARD8 (Cardinal) is also suggested to be a component. It is activated by a number of pathogens and bacterial toxins as well as diverse PAMPs, danger-associated molecular patterns (DAMPS) such as hyaluronan and uric acid, and exogenous irritants such as silica and asbestos (see Table S1 Schroder & Tschopp, 2010). Mutations in NLRP3 which lead to constitutive activation are linked to the human diseases Muckle-Wells syndrome, familial cold autoinflammatory syndrome and NOMID (Ting et al. 2006), characterized by skin rashes and other symptoms associated with generalized inflammation. The cause of these symptoms is uncontrolled IL-1 beta production. Multiple studies have shown that activation of the NLRP3 inflammasome by particulate activators (e.g. Hornung et al. 2008) requires phagocytosis, but this is not required for the response to ATP, which is mediated by the P2X7 receptor (Kahlenberg & Dubyak, 2004) and appears to involve the pannexin membrane channel (Pellegrin & Suprenenant 2006). Direct binding of activators to NLRP3 has not been demonstrated and the exact process of activation is unclear, though it is speculated to involve changes in conformation that free the NACHT domain for oligomerization (Inohara & Nunez 2001, 2003).
In contrast to NOD1/2 some NLRPs function as large macromolecular complexes called 'Inflammasomes'. These multiprotein platforms control activation of the cysteinyl aspartate protease caspase-1 and thereby the subsequent cleavage of pro-interleukin 1B (pro-IL1B) into the active proinflammatory cytokine IL1B. Activation of caspase-1 is essential for production of IL1B and IL18, which respectively bind and activate the IL1 receptor (IL1R) and IL18 receptor (IL18R) complexes. IL1R and IL18R activate NFkappaB and other signaling cascades. As the activation of inflammasomes leads to caspase-1 activation, inflammasomes can be considered an upstream step of the IL1R and IL18R signaling cascades, linking intracellular pathogen sensing to immune response pathways mediated by Toll-Like Receptors (TLRs). Monocytes and macrophages do not express pro-IL1B until stimulated, typically by TLRs (Franchi et al. 2009). The resulting pro-IL1B is not converted to IL1B unless a second stimulus activates an inflammasome. This requirement for two distinct stimuli allows tight regulation of IL1B/IL18 production, necessary because excessive IL-1B production is associated with numerous inflammatory diseases such as gout and rheumatoid arthritis (Masters et al. 2009). There are at least four subtypes of the inflammasome, characterized by the NLRP. In addition the protein AIM2 can form an inflammasome. All activate caspase-1. NLRP1 (NALP1), NLRP3 (Cryopyrin, NALP3), IPAF (CARD12, NLRC4) and AIM2 inflammasomes all have clear physiological roles in vivo. NLRP2, NLRP6, NLRP7, NLRP10 and NLRP12 have been demonstrated to modulate caspase-1 activity in vitro but the significance of this is unclear (Mariathasan and Monack, 2007). NLRP3 and AIM2 bind the protein 'apoptosis-associated speck-like protein containing a CARD' (ASC, also called PYCARD), via a PYD-PYD domain interaction. This in turn recruits procaspase-1 through a CARD-CARD interaction. NLRP1 and IPAF contain CARD domains and can bind procaspase-1 directly, though both are stimulated by ASC. Oligomerization of NLRPs is believed to bring procaspases into close proximity, leading to 'induced proximity' auto-activation (Boatright et al. 2003). This leads to formation of the active caspase tetramer. NLRPs are generally considered to be cytoplasmic proteins, but there is evidence for cytoplasmic-nuclear shuttling of the family member CIITA (LeibundGut-Landmann et al. 2004) and tissue/cell dependent NALP1 expression in the nucleus of neurons and lymphocytes (Kummer et al. 2007); the significance of this remains unclear.
The ubiquitin ligaseâassociated protein SGT1 (SUGT1) has two putative HSP90 binding domains, a tetratricopeptide repeat and a p23-like CHORD and Sgt1 (CS) domain. The CS domain of human SGT1 physically interacts with HSP90. SGT1 and related proteins are believed to recruit heat shock proteins to multiprotein assemblies (Lee et al. 2004).
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The presence of reactive oxygen species (ROS) leads to the oxidation of thioredoxin and consequent release of TXNIP (Zhou et al. 2010). The source of the ROS is unclear but they are known to be essential for caspase-1 activation (Cruz et al. 2007) and are produced in response to all known NLRP3 activators (Dostert et al. 2008, Zhou et al. 2010). The freed TXNIP binds NLRP3 and is proposed to activate the NLRP3 inflammasome, explaining how ROS can bring about NLRP3 activation.
p38 MAPK has 4 representative isoforms in humans, p38 alpha (Han et al. 1993), p38-beta (Jiang et al. 1996), p38-gamma (Lechner et al. 1996) and p38-delta (Hu et al. 1999). All are activated by phosphorylation on a canonical TxY motif by the dual-specificity kinase MKK6, which displays minimal substrate selectivity amongst the p38 isoforms (Zarubin & Han, 2005). p38 alpha and gamma are also activated by MKK3.
Na+-driven Cl-/HCO3- exchanger transport
NOD1 is ubiquitously expressed, while NOD2 expression is restricted to monocytes, macrophages, dendritic cells, and intestinal Paneth cells (Inohara et al. 2005). NOD1 and NOD2 activation induces transcription of immune response genes, predominantly mediated by the proinflammatory transcriptional factor NFkappaB but also by AP-1 and Elk-1 (Inohara et al. 2005). NFkappaB translocates to the nucleus following release from IkappaB proteins. NOD1 and NOD2 signaling involves an interaction between their caspase-recruitment domain (CARD) and the CARD of the kinase RIPK2 (RIP2/RICK). This leads to the activation of the NFkappaB pathway and MAPK pathways (Windheim et al. 2007). Activated NODs oligomerize via their NACHT domains, inducing physical proximity of RIP2 proteins that is believed to trigger their K63-linked polyubiquitination, facilitating recruitment of the TAK1 complex. RIP2 also recruits NEMO, bringing the TAK1 and IKK complexes into proximity, leading to NF-kappaB activation and activation of MAPK signaling. Recent studies have demonstrated that K63-linked regulatory ubiquitination of RIP2 is essential for the recruitment of TAK1 (Hasegawa et al. 2008, Hitosumatsu et al. 2008). As observed for toll-like receptor (TLR) signaling, ubiquitination can be removed by the deubiquitinating enzyme A20, thereby dampening NOD1/NOD2-induced NF-kappaB activation. NOD1 and NOD2 both induce K63-linked ubiquitination of RIP2, but NOD2-signaling appears to preferentially utilize the E3 ligase TRAF6, while TRAF2 and TRAF5 were shown to be important for NOD1-mediated signaling. In both cases, activation of NF-kappaB results in the upregulated transcription and production of inflammatory mediators.
When cAMP level rises, the PKA catalytic subunit (C subunit) released from the holoenzyme enters the nucleus by passive diffusion whereas termination of signaling to the nucleus involves an active mechanism. In the nucleus, the C subunit binds to the heat-stable protein kinase inhibitor (PKI), and this binding not only inactivates the C subunit but also by conformational change unveils a nuclear export signal in PKI which leads to export of the C-PKI complex from the nucleus.
A number of inactive tetrameric PKA holoenzymes are produced by the combination of homo- or heterodimers of the different regulatory subunits associated with two catalytic subunits. When cAMP binds to two specific binding sites on the regulatory subunits, these undergo a conformational change that causes the dissociation of a dimer of regulatory subunits bound to four cAMP from two monomeric, catalytically active PKA subunits.
3' incision of the lesioned strand of DNA in TC-NER
GRK2 is phosphorylated at serine 29 in vitro and in vivo by the alpha, gamma and delta isoforms of PKC. PKC-mediated phosphorylation at Ser29 increases GRK2 kinase activity towards GPCR substrates, contributing to GPCR desensitization. Phosphorylation at Ser29, which falls within the calmodulin-binding region of GRK2, abolishes the inhibitory effect of calmodulin on GRK2 kinase activity.
Displacement of stalled Pol II from the lesion site
Cyclic adenosine 3',5'-monophosphate (cAMP) induces gene transcription through activation of cAMP-dependent protein kinase (PKA), and subsequent phosphorylation of the transcription factor cAMP response element-binding protein, CREB, at serine-133.
Fcgamma receptors: old friends and new family members
Formation of the LAT signaling complex leads to activation of MAPK and production of cytokines. The sequence of events that leads from LAT to cytokine production has not been as clearly defined as the sequence that leads to degranulation. However, the pathways that lead to cytokine production require the guanine-nucleotide-exchange factors SOS and VAV that regulate GDP-GTP exchange of RAS. After its activation, RAS positively regulates the RAF-dependent pathway that leads to phosphorylation and, in part, activation of the mitogen-activated protein kinases (MAPKs) extracellular-signal-regulated kinase 1 (ERK1) and ERK2 (Gilfillan & Tkaczyk 2006).
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DNAX activation protein of 12kDa (DAP12) is an immunoreceptor tyrosine-based activation motif (ITAM)-bearing adapter molecule that transduces activating signals in natural killer (NK) and myeloid cells. It mediates signalling for multiple cell-surface receptors expressed by these cells, associating with receptor chains through complementary charged transmembrane amino acids that form a salt-bridge in the context of the hydrophobic lipid bilayer (Lanier et al. 1998). DAP12 homodimers associate with a variety of receptors expressed by macrophages, monocytes and myeloid cells including TREM2, Siglec H and SIRP-beta, as well as activating KIR, LY49 and the NKG2C proteins expressed by NK cells. DAP12 is expressed at the cell surface, with most of the protein lying on the cytoplasmic side of the membrane (Turnbull & Colonna 2007, Tessarz & Cerwenka 2008).
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Calmodulin (CaM) is a small acidic protein that contains four EF-hand motifs, each of which can bind a calcium ion, therefore it can bind up to four calcium ions. The protein has two approximately symmetrical domains, separated by a flexible hinge region. Calmodulin is the prototypical example of the EF-hand family of Ca2+-sensing proteins. Changes in intracellular Ca2+ concentration regulate calmodulin in three distinct ways. First, by directing its subcellular distribution. Second, by promoting association with different target proteins. Third, by directing a variety of conformational states in calmodulin that result in target-specific activation. Calmodulin binds and activates several effector protein (e.g. the CaM-dependent adenylyl cyclases, phosphodiesterases, protein kinases and the protein phosphatase calcineurin).
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One important physiological role for Calmodulin is the regulation of adenylylcyclases. Four of the nine known adenylylcyclases are calcium sensitive, in particular type 8 (AC8).
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In response to receptor ligation, the tyrosine residues in DAP12's immunoreceptor tyrosine-based activation motif (ITAM) are phosphorylated by Src family kinases. These phosphotyrosines form the docking site for the protein tyrosine kinase SYK in myeloid cells and SYK and ZAP70 in NK cells. DAP12-bound SYK autophosphorylates and phosphorylates the scaffolding molecule LAT, recruiting the proximal signaling molecules phosphatidylinositol-3-OH kinase (PI3K), phospholipase-C gamma (PLC-gamma), GADS (GRB2-related adapter downstream of SHC), SLP76 (SH2 domain-containing leukocyte protein of 76 kDa), GRB2:SOS (Growth factor receptor-bound protein 2:Son of sevenless homolog 1) and VAV. All of these intermediate signalling molecules result in the recruitment and activation of kinases AKT, CBL (Casitas B-lineage lymphoma) and ERK (extracellular signal-regulated kinase), and rearrangement of the actin cytoskeleton (actin polymerization) finally leading to cellular activation. PLC-gamma generates the secondary messengers diacylglycerol (DAG) and inositol-1,4,5-trisphosphate (InsP3), leading to activation of protein kinase C (PKC) and calcium mobilization, respectively (Turnbull & Colonna 2007, Klesney-Tait et al. 2006).
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This pathway describes the generation of DAG and IP3 by the PLCgamma-mediated hydrolysis of PIP2 and the subsequent downstream signaling events.
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Mismatch repair endonuclease PMS2 ecNumber3.1.-.-/ecNumber
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DNA-repair protein complementing XP-F cell
DNA-repair protein complementing XP-F cell (Xeroderma pigmentosum group F complementing protein) (DNA excision repair protein ERCC-4)
Xeroderma pigmentosum group F complementing protein
MSH2:MSH6 recruits MLH1:PMS2 to mismatch and interacts with PCNA
MutSalpha binds ATP and recruits MutLalpha to mismatch
MLH1:PMS2 makes single strand incision near 1-2 base mismatch
EXO1 interacts with MSH2:MSH6 (MutSalpha) and MLH1:PMS2 (MutLalpha)
Excision repair protein ERCC-6 (Cockayne syndrome protein CSB)
5' incision leading to excision of DNA fragment with lesion in TC-NER
Transcription elongation factor A protein 1 (Transcription elongation factor S-II protein 1) (Transcription elongation factor TFIIS.o)
Transcription elongation factor A protein 1
Transcription elongation factor S-II protein 1
Nuclear organization of DNA replication initiation proteins in mammalian cells.
Ligation of newly synthesized repair patch to incised DNA in TC-NER
Resumption of transcription after TC-NER
MSH2:MSH6 binds 1 base mismatch or 1-2 base insertion/deletion loop
MutSalpha binds mismatch or 1-2 base insertion/deletion loop
Homologous DNA pairing by human recombination factors Rad51 and Rad54
XPC binds to HR23B forming a heterodimeric complex
Innate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
Mast cells (MC) are distributed in tissues throughout the human body and have long been recognized as key cells of type I hypersensitivity reactions. They also play important roles in inflammatory and immediate allergic reactions. Activation through FCERI-bound antigen-specific IgE causes release of potent inflammatory mediators, such as histamine, proteases, chemotactic factors, cytokines and metabolites of arachidonic acid that act on the vasculature, smooth muscle, connective tissue, mucous glands and inflammatory cells (Borish & Joseph 1992, Amin 2012, Metcalfe et al. 1993). FCERI is a multimeric cell-surface receptor that binds the Fc fragment of IgE with high affinity. On mast cells and basophils FCERI exists as a tetrameric complex consisting of one alpha-chain, one beta-chain, and two disulfide-bonded gamma-chains, and on dendritic cells, Langerhans cells, macrophages, and eosinophils it exists as a trimeric complex with one alpha-chain and two disulfide-bonded gamma-chains (Wu 2011, Kraft & Kinet 2007). FCERI signaling in mast cells includes a network of signaling molecules and adaptor proteins. These molecules coordinate ultimately leading to effects on degranulation, eicosanoid production, and cytokine and chemokine production and cell migration and adhesion, growth and survival. The first step in FCERI signaling is the phosphorylation of the tyrosine residues in the ITAM of both the beta and the gamma subunits of the FCERI by LYN, which is bound to the FCERI beta-chain. The phosphorylated ITAM then recruits the protein tyrosine kinase SYK (spleen tyrosine kinase) which then phosphorylates the adaptor protein LAT. Phosphorylated LAT (linker for activation of T cells) acts as a scaffolding protein and recruits other cytosolic adaptor molecules GRB2 (growth-factor-receptor-bound protein 2), GADS (GRB2-related adaptor protein), SHC (SRC homology 2 (SH2)-domain-containing transforming protein C) and SLP76 (SH2-domain-containing leukocyte protein of 76 kDa), as well as the exchange factors and adaptor molecules VAV and SOS (son of sevenless homologue), and the signalling enzyme phospholipase C gamma1 (PLC-gamma1). Tyrosoine phosphorylation of enzymes and adaptors, including VAV, SHC GRB2 and SOS stimulate small GTPases such as RAC, RAS and RAF. These pathways lead to activation of the ERK, JNK and p38 MAP kinases, histamine release and cytokine production. FCERI activation also triggers the phosphorylation of PLC-gamma which upon membrane localisation hydrolyse PIP2 to form IP3 and 1,2-diacylglycerol (DAG) - second messengers that release Ca2+ from internal stores and activate PKC, respectively. Degranulation or histamine release follows the activation of PLC-gamma and protein kinase C (PKC) and the increased mobilization of calcium (Ca2+). Receptor aggregation also results in the phosphorylation of adaptor protein NTAL/LAT2 which then recruits GAB2. PI3K associates with phosphorylated GAB2 and catalyses the formation of PIP3 in the membrane, which attracts many PH domain proteins like BTK, PLC-gamma, AKT and PDK. PI3K mediated activation of AKT then regulate the mast cell proliferation, development and survival (Gu et al. 2001).
The lipid raft resident adaptor molecules LAT1 and Non-T cell activation linker (NTAL), also known as linker for activation of B cells (LAB)/LAT2 are known participants in the regulation of mast cell calcium responses. Both LAT and NTAL are expressed and phosphorylated following engagement of FCERI on mast cells. NTAL is functionally and topographically different from LAT. There is a considerable debate on the role of NTAL in mast cell. Depending on the circumstances, NTAL appears to have a dual role as positive and negative regulator of MC responses elicited via FCERI. Studies conducted in bone marrow-derived mast cells (BMMCs) of mice lacking NTAL displayed enhanced FCERI-mediated tyrosine phosphorylation of several substrates, calcium response, degranulation, and cytokine production. This indicated that NTAL negatively regulates FCERI-mediated degranulation. However, in mice lacking both LAT and NTAL showed severe block in FCERI-mediated signaling than BMMCs deficient in LAT alone, suggesting that NTAL also shares a redundant function with LAT to play a positive role (Draberova et al. 2007, Orr & McVicar. 2011, Zhu et al. 2004, Volna et al. 2004). The major steps in NTAL mediated Ca+2 influx involves NTAL--> GAB2--> PI3K
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The increase in intracellular Ca+2 in conjunction with DAG also activates PKC and RasGRP, which inturn contributes to cytokine production by mast cells (Kambayashi et al. 2007). Activation of the FCERI engages CARMA1, BCL10 and MALT1 complex to activate NF-kB through PKC-theta (Klemm et al. 2006, Chen et al. 2007). FCERI stimulation leads to phosphorylation, and degradation of IkB which allows the release and nuclear translocation of the NF-kB proteins. Activation of the NF-kB transcription factors then results in the synthesis of several cytokines. NF-kB activation by FCERI is critical for proinflammatory cytokine production during mast cell activation and is crucial for allergic inflammatory diseases (Klemm et al. 2006).
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Crystal structure of human uroporphyrinogen decarboxylase
A highly conserved repetitive DNA sequence, (TTAGGG)n, present at the telomeres of human chromosomes
T219, T538 at the activation loop, S676 at the turn motif and S695 at the hydrophobic motif are autophosphorylated in cis-maanner. Posphorylation of T538 is critical for kinase activation and it stabilises the open active conformation. Some studies suggest the involvement of PDK1 (3-phosphoinositide-dependent protein kinase 1) and GLK kinases in the phosphorylation T538.
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Phosphorylation and activation of human cdc25-C by cdc2--cyclin B and its involvement in the self-amplification of MPF at mitosis
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Morquio's syndrome: deficiency of a chondroitin sulfate N-acetylhexosamine sulfate sulfatase
A Toll-like receptor recognizes bacterial DNA
Activated epidermal growth factor receptors (EGFR) can stimulate phosphatidylinositol (PI) turnover. Activated EGFR can activate phospholipase C-gamma1 (PLC-gamma1, i.e. PLCG1) which hydrolyses phosphatidylinositol 4,5-bisphosphate (PIP2) to inositol 1,4,5-triphosphate (IP3) and diacylglycerol (DAG). IP3 is instrumental in the release of calcium from intracellular stores and DAG is involved in protein kinase C activation.
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Humans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first critical hours and days of exposure to a new pathogen, our innate immune system.
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Cytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concentrations. Cytokines bind to specific membrane receptors, which then signal the cell via second messengers, to regulate cellular activity.
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Interleukins are low molecular weight proteins that bind to cell surface receptors and act in an autocrine and/or paracrine fashion. They were first identified as factors produced by leukocytes but are now known to be produced by many other cells throughout the body. They have pleiotropic effects on cells which bind them, impacting processes such as tissue growth and repair, hematopoietic homeostasis, and multiple levels of the host defense against pathogens where they are an essential part of the immune system.
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Interleukin-2 (IL-2) is a cytokine that is produced by T cells in response to antigen stimulation. Originally, IL-2 was discovered because of its potent growth factor activity on activated T cells in vitro and was therefore named 'T cell growth factor' (TCGF). However, the generation of IL-2- and IL-2 receptor-deficient mice revealed that IL-2 also plays a regulatory role in the immune system by suppressing autoimmune responses. Two main mechanisms have been identified that explain this suppressive function: (1) IL-2 sensitizes activated T cells for activation-induced cell death (AICD) and (2) IL-2 is critical for the survival and function of regulatory T cells (Tregs), which possess potent immunosuppressive properties. IL-2 signaling occurs when IL-2 binds to the heterotrimeric high-affinity IL-2 receptor (IL-2R), which consists of alpha, beta and gamma chains. The IL-2R was identified in 1981 via radiolabeled ligand binding (Robb et al. 1981). The IL-2R alpha chain was identified in 1982 (Leonard et al.), the beta chain in 1986/7 (Sharon et al. 1986, Teshigawara et al. 1987) and the IL-2R gamma chain in 1992 (Takeshita et al.). The high affinity of IL-2 binding to the IL-2R is created by a very rapid association rate to the IL-2R alpha chain, combined with a much slower dissociation rate contributed by the combination of the IL-2R beta and gamma chains (Wang & Smith 1987). After antigen stimulation, T cells upregulate the high-affinity IL-2R alpha chain; IL-2R alpha captures IL-2 and this complex then associates with the constitutively expressed IL-2R beta and gamma chains. The IL-2R gamma chain is shared by several other members of the cytokine receptor superfamily including IL-4, IL-7, IL-9, IL-15 and IL-21 receptors, and consequently is often referred to as the Common gamma chain (Gamma-c). The tyrosine kinases Jak1 and Jak3, which are constitutively associated with IL-2R beta and Gamma-c respectively, are activated resulting in phosphorylation of three critical tyrosine residues in the IL-2R beta cytoplasmic tail. These phosphorylated residues enable recruitment of the adaptor molecule Shc, activating the MAPK and PI3K pathways, and the transcription factor STAT5. After phosphorylation, STAT5 forms dimers that translocate to the nucleus and initiate gene expression. While STAT5 activation is critical for IL-2 function in most cell types, the contribution of the PI3K/Akt pathway differs between distinct T cell subsets. In Tregs for example, PI3K/Akt is not involved in IL-2 signaling and this may explain some of the different functional outcomes of IL-2 signaling in Tregs vs. effector T cells.
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DNA Replication factor A protein 2 (32kD)
DNA-repair protein complementing XP-G cells (Xeroderma pigmentosum group G complementing protein) (DNA excision repair protein ERCC-5)
Xeroderma pigmentosum group G complementing protein
DNA-repair protein complementing XP-G cells
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Assembly of repair proteins at the site of Pol II blockage
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Formation of active Pol II complex with lesioned DNA template
RNA Pol II is blocked by the lesion leading to reduced transcription
DNA repair protein RAD51 homolog 1 (hRAD51) (HsRAD51)
Ligation of newly synthesized repair patch to incised DNA in GG-NER
Double-strand break repair protein MRE11A
Formation of ERCC1-XPF heterodimeric complex
DNA-repair protein complementing XP-A cells
xeroderma pigmentosum, complementation group A
Xeroderma pigmentosum group A complementing protein
DNA-repair protein complementing XP-A cells (Xeroderma pigmentosum group A complementing protein)
Binding of ERCC1-XPF to preincision complex
DNA Replication factor A protein A1 (70kD)
Replication protein A 70 kDa DNA-binding subunit
XPC:HR23B complex binds to damaged DNA site with lesion
xeroderma pigmentosum, complementation group C
Xeroderma pigmentosum group C complementing protein
DNA-repair protein complementing XP-C cells (Xeroderma pigmentosum group C complementing protein) (P125)
DNA-repair protein complementing XP-C cells
Formation of open bubble structure in DNA by helicases
UV excision repair protein RAD23 homolog B
XP-C repair complementing complex 58 kDa protein
UV excision repair protein RAD23 homolog B (HHR23B) (XP-C repair complementing complex 58 kDa protein) (P58)
Isocitrate dehydrogenase (NAD) subunit 1, mitochondrial
GRB2 can bind EGFR directly or through another SH2-containing protein, SHC1. This association leads to RAS activation.
Autophosphorylated EGFR tyrosine residues are docking sites for many downstream effectors in EGFR signaling. The adaptor protein GRB2 binds to phosphotyrosine residues in the C-tail of EGFR through its SH2 domain. GRB2 is constitutively associated with SOS, a guanine nucleotide exchange factor of RAS. GRB2 binding to phosphorylated EGFR results in the recruitment of SOS to the plasma membrane where it comes in proximity to RAS. This mechanism has been seen to be the model for RAS activation.
The epidermal growth factor receptor (EGFR) is one member of the ERBB family of transmembrane glycoprotein tyrosine receptor kinases (RTK). Binding of EGFR to its ligands induces conformational change that unmasks the dimerization interface in the extracellular domain of EGFR, leading to receptor homo- or heterodimerization at the cell surface. Dimerization of the extracellular regions of EGFR triggers additional conformational change of the cytoplasmic EGFR regions, enabling the kinase domains of two EGFR molecules to achieve the catalytically active conformation. Ligand activated EGFR dimers trans-autophosphorylate on tyrosine residues in the cytoplasmic tail of the receptor. Phosphorylated tyrosines serve as binding sites for the recruitment of signal transducers and activators of intracellular substrates, which then stimulate intracellular signal transduction cascades that are involved in regulating cellular proliferation, differentiation, and survival. Recruitment of complexes containing GRB2 and SOS1 to phosphorylated EGFR dimers either directly, through phosphotyrosine residues that serve as GRB2 docking sites, or indirectly, through SHC1 recruitment, promotes GDP to GTP exchange on RAS, resulting in the activation of RAF/MAP kinase cascade. Binding of complexes of GRB2 and GAB1 to phosphorylated EGFR dimers leads to formation of the active PI3K complex, conversion of PIP2 into PIP3, and activation of AKT signaling. Phospholipase C-gamma1 (PLCG1) can also be recruited directly, through EGFR phosphotyrosine residues that serve as PLCG1 docking sites, which leads to PLCG1 phosphorylation by EGFR and activation of DAG and IP3 signaling. EGFR signaling is downregulated by the action of ubiquitin ligase CBL. CBL binds directly to the phosphorylated EGFR dimer through the phosphotyrosine Y1045 in the C-tail of EGFR, and after CBL is phosphorylated by EGFR, it becomes active and ubiquitinates phosphorylated EGFR dimers, targeting them for degradation. For a recent review of EGFR signaling, please refer to Avraham and Yarden, 2011.
GAB1 is recruited to the activated EGFR indirectly, through GRB2. GAB1 acts as an adaptor protein that enables formation of an active PIK3, through recruitment of PIK3 regulatory subunit PIK3R1 (also known as PI3Kp85), which subsequently recruits PIK3 catalytic subunit PIK3CA (also known as PI3Kp110). PIK3, in complex with EGFR, GRB2 and GAB1, catalyzes phosphorylation of PIP2 and its conversion to PIP3, which leads to the activation of the AKT signaling.
Phospholipase C-gamma (PLC-gamma) is a substrate of the fibroblast growth factor receptor (FGFR) and other receptors with tyrosine kinase activity. It is known that the src homology region 2 (SH2 domain) of PLC-gamma and of other signaling molecules (such as GTPase-activating protein and phosphatidylinositol 3-kinase-associated p85) direct their binding toward autophosphorylated tyrosine residues of the FGFR. Recruitment of PLC-gamma results in its phosphorylation and activation by the receptor. Activated PLC-gamma hydrolyzes phosphatidyl inositol[4,5] P2 to form the second messengers diacylglycerol (DAG) and Ins [1,4,5]P3, which stimulate calcium release and activation of calcium/calmodulin dependent kinases.
The FRS family of scaffolding adaptor proteins has two members, FRS2alpha and FRS2beta (also known as FRS3 or SNT-2). Activation of FGFR tyrosine kinase allows FRS2 proteins to become phosphorylated on tyrosine residues and then bind to the adaptor GRB2 and the tyrosine phosphatase SHP2. Subsequently, SHP2 activates the RAS-MAP kinase pathway and GRB2 activates the RAS-MAP kinase , PI-3-kinase and ubiquitinations/degradation pathways by binding to SOS, GAB1 and CBL, respectively, via the SH3 domains of GRB2. FRS2alpha acts as a central mediator in FGF signaling mainly because it induces sustained levels of activation of ERK with ubiquitous expression.
Signaling via FGFRs is mediated via direct recruitment of signaling proteins that bind to tyrosine auto-phosphorylation sites on the activated receptor and via closely linked docking proteins that become tyrosine phosphorylated in response to FGF-stimulation and form a complex with additional complement of signaling proteins. The activation loop in the catalytic domain of FGFR maintains the PTK domain in an inactive or low activity state. The activation-loop of FGFR1, for instance, contains two tyrosine residues that must be autophosphorylated for maintaining the catalytic domain in an active state. In the autoinhibited configuration, a kinase invariant proline residue at the C-terminal end of the activation loop interferes with substrate binding while allowing access to ATP in the nucleotide binding site. In addition to the catalytic PTK core, the cytoplasmic domain of FGFR contains several regulatory sequences. The juxtamembrane domain of FGFRs is considerably longer than that of other receptor tyrosine kinases. This region contains a highly conserved sequence that serves as a binding site for the phosphotyrosine binding (PTB) domain of FRS2. A variety of signaling proteins are phosphorylated in response to FGF stimulation, including Shc, phospholipase-C gamma and FRS2 leading to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape.
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The ability of growth factors to protect from apoptosis is primarily due to the activation of the AKT survival pathway. P-I-3-kinase dependent activation of PDK leads to the activation of AKT which in turn affects the activity or expression of pro-apoptotic factors, which contribute to protection from apoptosis. AKT activation also blocks the activity of GSK-3b which could lead to additional antiapoptotic signals.
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p-ERK1/2 dissociates from p-MEK1/2, allowing dimerization of the activated MAPKs and translocation to the nucleus. In FGFR signaling, there is evidence that this dissociation event is negatively regulated by the golgi membrane form of IL17RD, preventing the nuclear localization of activated ERK1/2.
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MEK1/2 phosphorylate critical tyrosine and threonine residues on ERK1/2, activating the kinase activity of the MAPKs. In FGFR signaling, this reaction appears to be negatively regulated by IL17RD through an unknown mechanism, limiting the extent of MAPK signaling after FGF stimulation.
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Proteins Imported by TOM40:TOM70 Complex
Innate immune activation through Nalp3 inflammasome sensing of asbestos and silica
Mitochondrial import inner membrane translocase subunit TIM22
Mitochondrial import inner membrane translocase subunit TIM54
Mitochondrial import receptor subunit TOM40
Release of phospho-SHC from the insulin receptor triggers a cascade of signalling events via SOS, RAF and the MAP kinases.
The 22 members of the fibroblast growth factor (FGF) family of growth factors mediate their cellular responses by binding to and activating the different isoforms encoded by the four receptor tyrosine kinases (RTKs) designated FGFR1, FGFR2, FGFR3 and FGFR4. These receptors are key regulators of several developmental processes in which cell fate and differentiation to various tissue lineages are determined. Unlike other growth factors, FGFs act in concert with heparin or heparan sulfate proteoglycan (HSPG) to activate FGFRs and to induce the pleiotropic responses that lead to the variety of cellular responses induced by this large family of growth factors. An alternative, FGF-independent, source of FGFR activation originates from the interaction with cell adhesion molecules, typically in the context of interactions on neural cell membranes and is crucial for neuronal survival and development. Upon ligand binding, receptor dimers are formed and their intrinsic tyrosine kinase is activated causing phosphorylation of multiple tyrosine residues on the receptors. These then serve as docking sites for the recruitment of SH2 (src homology-2) or PTB (phosphotyrosine binding) domains of adaptors, docking proteins or signaling enzymes. Signaling complexes are assembled and recruited to the active receptors resulting in a cascade of phosphorylation events. This leads to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape, depending on the cell type or stage of maturation.
After being phosphorylated, p-ERK1/2 dissociate from MEK1/2 and dimerize.
At the beginning of this reaction, 3 molecules of 'ATP', and 1 molecule of 'eIF4G' are present. At the end of this reaction, 3 molecules of 'ADP', and 1 molecule of 'eIF4G-P' are present. This reaction takes place in the 'cytosol' and is mediated by the 'kinase activity' of 'S6K1-P'.
Once phosphorylated, S6K1-P phosphorylates and activates ribosomal protein S6 (rpS6), which in turn selectively increases the translation of 5ââ¬â¢TOP mRNAs. These mRNAs encode exclusively for components of the translation machinery (PMID 15809305).
S6K1 contains a TOS motif. mTORC1 requires an intact TOS motif to bind and phosphorylate S6K1 (PMID 15809305).
SHC is one of the mediators of insulin signalling events. It is activated by phosphorylation and triggers a cascade of events involving SOS, RAF and the MAP kinases.
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Mammalian thioredoxin is a direct inhibitor of apoptosis signal-regulating kinase (ASK) 1
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Complete amino acid sequence of the neurone-specific gamma isozyme of enolase (NSE) from human brain and comparison with the non-neuronal alpha form (NNE)
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Cytochrome c1, heme protein, mitochondrial
ATP synthase subunit alpha, mitochondrial
ATP synthase subunit beta, mitochondrial
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At the beginning of this reaction, 2 molecules of 'ATP', and 1 molecule of 'PIP3:PKB complex ' are present. At the end of this reaction, 1 molecule of 'PIP3:Phosphorylated PKB complex', and 2 molecules of 'ADP' are present. This reaction takes place on the 'plasma membrane' and is mediated by the 'kinase activity' of 'PIP3:PDK complex [plasma membrane]'.
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Oncogenic signaling from the hematopoietic growth factor receptors c-Kit and Flt3
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Upon formation of a trimeric LKB1:STRAD:MO25 complex, LKB1 phosphorylates and activates AMPK. If the AMP:ATP ratio rises, this activation is maintained and AMPK activates the TSC complex by phosphorylating TSC2. Active TSC activates the intrinsic GTPase activity of Rheb, resulting in GDP-loaded Rheb and inhibition of mTOR pathway.
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Cloning of a human cDNA for CTP-phosphoethanolamine cytidylyltransferase by complementation in vivo of a yeast mutant
PKB and PDK1 are activated via membrane-bound PIP3. Activated PDK1 phosphorylates PKB, which in turn phosphorylates PDE3B. The latter hydrolyses cAMP to 5'AMP, depleting cAMP pools.
At the beginning of this reaction, 1 molecule of '3-phosphoinositide dependent protein kinase-1 ', and 1 molecule of 'Phosphatidylinositol-3,4,5-trisphosphate' are present. At the end of this reaction, 1 molecule of 'PIP3:PDK complex [plasma membrane]' is present. This reaction takes place in the 'cell'.
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Normally under low AMP:ATP conditions, the active AMPK is dephosphorylated (possibly by PP2C), and thus inactivated.
If AMP:ATP ratio rises, AMP (instead of ATP) is bound by the AMPK-gamma subunit, which inhibits the dephosphorylation of the AMPK-alpha subunit resulting in activation of AMPK. It is not clear, as of yet, whether AMP binds to unphosphorylated AMPK.
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Activated AMPK (phosphorylated on Thr172/Thr174 and AMP bound) phosphorylates Raptor on Ser 722 and Ser 792. These phosphorylations are required for inhibition of mTORC1 activity in response to energy stress (Gwinn DM et al, 2008).
LKB1 forms a complex with STRAD and MO25 thereby attaining a higher activity towards its substrates belonging to the subfamily of AMPK like kinases. LKB1:STRAD:MO25 complex phosphorylates AMPK constantly. This phosphorylation is immediately removed in basal conditions by PP2C, but if the cellular AMP:ATP ratio rises, binding of AMP by AMPK inhibits the dephosphorylation, and the maintained phosphorylation results in activation of the AMPK.
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Once bound by either NGF or proNGF, p75NTR interacts with NRAGE, thus leading to phosphorylation and activation of JUN Kinase (JNK). JNK controls apoptosis in two ways: it induces transcription of pro-apoptotic genes, and directly activates the cell death machinery. Only NGF-bound p75NTR is shown here.
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Insulin binding to its receptor results in receptor autophosphorylation on tyrosine residues and the tyrosine phosphorylation of insulin receptor substrates (e.g. IRS and Shc) by the insulin receptor tyrosine kinase. This allows association of IRSs with downstream effectors such as PI-3K via its Src homology 2 (SH2) domains leading to end point events such as Glut4 (Slc2a4) translocation. Shc when tyrosine phosphorylated associates with Grb2 and can thus activate the Ras/MAPK pathway independent of the IRSs. Signal transduction by the insulin receptor is not limited to its activation at the cell surface. The activated ligand-receptor complex initially at the cell surface, is internalised into endosomes itself a process which is dependent on tyrosine autophosphorylation. Endocytosis of activated receptors has the dual effect of concentrating receptors within endosomes and allows the insulin receptor tyrosine kinase to phosphorylate substrates that are spatially distinct from those accessible at the plasma membrane. Acidification of the endosomal lumen, due to the presence of proton pumps, results in dissociation of insulin from its receptor. (The endosome constitutes the major site of insulin degradation). This loss of the ligand-receptor complex attenuates any further insulin-driven receptor re-phosphorylation events and leads to receptor dephosphorylation by extra-lumenal endosomally-associated protein tyrosine phosphatases (PTPs). The identity of these PTPs is not clearly established yet. A discussion of candidates will be added in the near future.
The different molecules listed (NRAGE, NRIF, NADE, TRAF6) mediate, through unclear mechanisms, JNK activation by threonine and tyrosine phosphorylation. While active JNK does move to the nucleus and phosphorylates and activate transcription factors such as c-JUN and ATF2, these have not been implicated in p75-mediated cell death, but rather the direct activation of the cell death machinery by JNK has been implicated. p75 activates the intrinsic caspase pathway (involving mitochondrial release of cytochrome c, Apaf-1, and caspases-9) rather than the extrinsic (caspase-8) pathway activated by most other death receptors.
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The effect of the proton pump is to allow entry of [H+] ions into the lumen of the endosome. The net effect of this is to lower the pH of the lumen from pH 7.4 (the pH at the plasma membrane) to pH 6.0 (documented with studies using FITC-labeled insulin - a pH dependent fluorescence marker).
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Triggered by acidification of the endosome, insulin dissociates from the receptor and is degraded. The receptor is dephosphorylated and re-integrated into the plasma membrane, ready to be activated again by the binding of insulin molecules.
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IRS is one of the mediators of insulin signalling events. It is activated by phosphorylation and triggers a cascade of events involving PI3K, SOS, RAF and the MAP kinases. The proteins mentioned under IRS are examples of IRS family members acting as indicated. More family members are to be confirmed and added in the future.
Autophosphorylation of the insulin receptor triggers a series of signalling events, mediated by SHC or IRS, and resulting in activation of the Ras/RAF and MAP kinase cascades. A second effect of the autophosphorylation of the insulin receptor is its internalisation into an endosome, which downregulates its signalling activity.
SOS is recruited to the plasma membrane and mediates activation of Ras.
Release of phospho-IRS from the insulin receptor triggers a cascade of signalling events via PI3K, SOS, RAF and the MAP kinases.
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Crystal structure of the nucleosome core particle at 2.8 A resolution
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Clinical, biochemical and molecular genetic correlations in adenylosuccinate lyase deficiency
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Phosphoproteomics reveals new ERK MAP kinase targets and links ERK to nucleoporin-mediated nuclear transport
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GEF what? Dock180 and related proteins help Rac to polarize cells in new ways
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Endoplasmic reticulum-mediated phagocytosis is a mechanism of entry into macrophages
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Human cyclins A and B1 are differentially located in the cell and undergo cell cycle-dependent nuclear transport
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Isolation of two cDNAs encoding functional human cytoplasmic cysteinyl-tRNA synthetase
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Stress-induced transcription of satellite III repeats
[Receptors for cholecystokinin and gastrin]
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Mutations in phosphoinositide metabolizing enzymes and human disease
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SIMILARITY Belongs to the Tim17/Tim22/Tim23 family.
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Coordinating TLR-activated signaling pathways in cells of the immune system
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Upf1 senses 3'UTR length to potentiate mRNA decay
Structure of human thymidylate synthase suggests advantages of chemotherapy with noncompetitive inhibitors
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Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.
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Interconversion of 2-oxoglutarate and 2-hydroxyglutarate
Nramp2 expression is associated with pH-dependent iron uptake across the apical membrane of human intestinal Caco-2 cells
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Succinate dehydrogenase deficiency in human
Deciphering human heat shock transcription factor 1 regulation via post-translational modification in yeast
QLS motif in transmembrane helix VII of the glucose transporter family interacts with the C-1 position of D-glucose and is involved in substrate selection at the exofacial binding site.
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The human REV1 gene codes for a DNA template-dependent dCMP transferase.
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Novel functions of acyl-CoA thioesterases and acyltransferases as auxiliary enzymes in peroxisomal lipid metabolism
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Stem cell factor and its receptor c-Kit as targets for inflammatory diseases
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The mitogen activated protein kinase (MAPK) cascade, one of the most ancient and evolutionarily conserved signaling pathways, is involved in many processes of immune responses. The MAP kinases cascade transduces signals from the cell membrane to the nucleus in response to a wide range of stimuli (Chang and Karin, 2001; Johnson et al, 2002). There are three major groups of MAP kinases the extracellular signal-regulated protein kinases ERK1/2, the p38 MAP kinase and the c-Jun NH-terminal kinases JNK. ERK1 and ERK2 are activated in response to growth stimuli. Both JNKs and p38-MAPK are activated in response to a variety of cellular and environmental stresses. The MAP kinases are activated by dual phosphorylation of Thr and Tyr within the tripeptide motif Thr-Xaa-Tyr. The sequence of this tripeptide motif is different in each group of MAP kinases: ERK (Thr-Glu-Tyr); p38 (Thr-Gly-Tyr); and JNK (Thr-Pro-Tyr). MAPK activation is mediated by signal transduction in the conserved three-tiered kinase cascade: MAPKKKK (MAP4K or MKKKK or MAPKKK Kinase) activates the MAPKKK. The MAPKKKs then phosphorylates a dual-specificity protein kinase MAPKK, which in turn phosphorylates the MAPK. The dual specificity MAP kinase kinases (MAPKK or MKK) differ for each group of MAPK. The ERK MAP kinases are activated by the MKK1 and MKK2; the p38 MAP kinases are activated by MKK3, MKK4, and MKK6; and the JNK pathway is activated by MKK4 and MKK7. The ability of MAP kinase kinases (MKKs, or MEKs) to recognize their cognate MAPKs is facilitated by a short docking motif (the D-site) in the MKK N-terminus, which binds to a complementary region on the MAPK. MAPKs then recognize many of their targets using the same strategy, because many MAPK substrates also contain D-sites. The upstream signaling events in the TLR cascade that initiate and mediate the ERK signaling pathway remain unclear.
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MAPKs are protein kinases that, once activated, phosphorylate their specific cytosolic or nuclear substrates at serine and/or threonine residues. Such phosphorylation events can either positively or negatively regulate substrate, and thus entire signaling cascade activity. The major cytosolic target of activated ERKs are RSKs (90 kDa Ribosomal protein S6 Kinase). Active RSKs translocates to the nucleus and phosphorylates such factors as c-Fos(on Ser362), SRF (Serum Response Factor) at Ser103, and CREB (Cyclic AMP Response Element-Binding protein) at Ser133. In the nucleus activated ERKs phosphorylate many other targets such as MSKs (Mitogen- and Stress-activated protein kinases), MNK (MAP interacting kinase) and Elk1 (on Serine383 and Serine389). ERK can directly phosphorylate CREB and also AP-1 components c-Jun and c-Fos. Another important target of ERK is NF-KappaB. Recent studies reveals that nuclear pore proteins are direct substrates for ERK (Kosako H et al, 2009). Other ERK nuclear targets include c-Myc, HSF1 (Heat-Shock Factor-1), STAT1/3 (Signal Transducer and Activator of Transcription-1/3), and many more transcription factors. Activated p38 MAPK is able to phosphorylate a variety of substrates, including transcription factors STAT1, p53, ATF2 (Activating transcription factor 2), MEF2 (Myocyte enhancer factor-2), protein kinases MSK1, MNK, MAPKAPK2/3, death/survival molecules (Bcl2, caspases), and cell cycle control factors (cyclin D1). JNK, once activated, phosphorylates a range of nuclear substrates, including transcription factors Jun, ATF, Elk1, p53, STAT1/3 and many other factors. JNK has also been shown to directly phosphorylate many nuclear hormone receptors. For example, peroxisome proliferator-activated receptor 1 (PPAR-1) and retinoic acid receptors RXR and RAR are substrates for JNK. Other JNK targets are heterogeneous nuclear ribonucleoprotein K (hnRNP-K) and the Pol I-specific transcription factor TIF-IA, which regulates ribosome synthesis. Other adaptor and scaffold proteins have also been characterized as nonnuclear substrates of JNK.
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CDK1-mediated phosphorylation of GORASP1 (GRASP65) enables GORASP1 to recruit PLK1 (Preisinger et al. 2005). PLK1 phosphorylates GORASP1 on serine residue S189 (Sengupta and Linstedt 2010). This serine residue is near the GORASP1 region involved in GORASP1 dimerization and oligomerization, a process underlying the stacking of cis-Golgi cisternae (Wang et al. 2003). The phosphorylation of S189 by PLK1 impairs Golgi cisternae stacking (tethering), contributing to Golgi unlinking and fragmentation in mitosis, probably by preventing formation of GORASP1 dimers and oligomers (Sutterlin et al. 2001, Sengupta and Linstedt, 2010). Two other potential phosphorylation sites that match PLK1 substrate consensus sequence exist in GORASP1, but their functional significance has not yet been examined (Sengupta and Linstedt, 2010).
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In human, together with ubiquitin-conjugating E2-type enzymes UBC13 and UEV1A (also known as UBE2V1), TRAF6 catalyses Lys63-linked ubiquitination. It is believed that auto polyubiquitination and oligomerization of TRAF6 is followed by binding the ubiquitin receptors of TAB2 or TAB3 (TAK1 binding protein 2 and 3), which stimulates phosphorylation and activation of TGF beta-activated kinase 1(TAK1). TAK1 phosphorylates IKK alpha and IKK beta, which in turn phosphorylate NF-kB inhibitors - IkB and eventually results in IkB degradation and NF-kB translocation to the nucleus. Also TAK1 mediates JNK and p38 MAP kinases activation by phosphorylating MKK4/7 and MKK3/6 respectivly resulting in the activation of many transcription factors. The role of TRAF6 is somewhat controversial and probably cell type specific. TRAF6 autoubiquitination was found to be dispensable for TRAF6 function to activate TAK1 pathway. These findings are consistent with the new mechanism of TRAF6-mediated NF-kB activation that was suggested by Xia et al. (2009). TRAF6 generates unanchored Lys63-linked polyubiquitin chains that bind to the regulatory subunits of TAK1 (TAB2 or TAB3) and IKK(NEMO), leading to the activation of the kinases. Xia et al. (2009) demonstrated in vitro that unlike polyubiquitin chains covalently attached to TRAF6 or IRAK, TAB2 and NEMO-associated ubiquitin chains were found to be unanchored and susceptible to N-terminal ubiquitin cleavage. Only K63-linked polyubiquitin chains, but not monomeric ubiquitin, activated TAK1 in a dose-dependent manner. Optimal activation of the IKK complex was achieved using ubiquitin polymers containing both K48 and K63 linkages. Furthermore, the authors proposed that the TAK1 complexes might be brougt in close proximity by binding several TAB2/3 to a single polyubiquitin chain to facilitate TAK1 kinase trans-phosphorylation. Alternativly, the possibility that polyUb binding promotes allosteric activation of TAK1 complex should be considered (Walsh et al 2008).
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The pericentriolar stacks of Golgi cisternae undergo extensive fragmentation and reorganization in mitosis. In mammalian cells, Golgi apparatus consists of stacked cisternae that are connected by tubules to form a ribbon-like structure in the perinuclear region, in vicinity of the centrosome. Reorganization of the Golgi apparatus during cell division allows both daughter cells to inherit this organelle, and may play additional roles in the organization of the mitotic spindle. First changes in the structure of the Golgi apparatus likely start in G2 and are subtle, involving unlinking of the Golgi ribbon into separate stacks. These changes are required for the entry of mammalian cells into mitosis (Sutterlin et al. 2002). This initial unlinking of the Golgi ribbon depends on GRASP proteins and on CTBP1 (BARS) protein, which induces the cleavage of the tubular membranes connecting the stacks (Hidalgo Carcedo et al. 2004, Colanzi et al. 2007), but the exact mechanism is not known. Activation of MEK1/2 also contributes to unlinking of the Golgi ribbon in G2 (Feinstein and Linstedt 2007). From prophase to metaphase, Golgi cisternae undergo extensive fragmentation that is a consequence of unstacking of Golgi cisternae and cessation of transport through Golgi. At least three mitotic kinases, CDK1, PLK1 and MEK1, regulate these changes. CDK1 in complex with cyclin B phosphorylates GOLGA2 (GM130) and GORASP1 (GRASP65), constituents of a cis-Golgi membrane complex (Lowe et al. 1998, Preisinger et al. 2005). Phosphorylation of GOLGA2 prevents binding of USO1 (p115), a protein localizing to the membrane of ER (endoplasmic reticulum) to Golgi transport vesicles and cis-Golgi, thereby impairing fusion of these vesicles with cis-Golgi cisternae and stopping ER to Golgi transport (Lowe et al. 1998, Seeman et al. 2000, Moyer et al. 2001). Phosphorylation of GORASP1 by CDK1 enables further phosphorylation of GORASP1 by PLK1 (Sutterlin et al. 2001, Preisinger et al. 2005). Phosphorylation of GORASP1 by CDK1 and PLK1 impairs stacking of Golgi cisternae by interfering with formation of GORASP1 trans-oligomers that would normally link the Golgi cisternae together (Wang et al. 2003, Wang et al. 2005, Sengupta and Linstedt 2010). In the median Golgi, GORASP2 (GRASP55), a protein that forms a complex with BLFZ1 (Golgin-45) and RAB2A GTPase and contributes to cisternae stacking and Golgi trafficking (Short et al. 2001), is also phosphorylated in mitosis. Phosphorylation of GORASP2 by MEK1/2-activated MAPK1 (ERK2) and/or MAPK3-3 (ERK1b in human, Erk1c in rat) contributes to Golgi unlinking in G2 and fragmentation of Golgi cisternae in mitotic prophase (Acharya et al. 1998, Jesch et al. 2001, Colanzi et al. 2003, Shaul and Seger 2006, Duran et al. 2008, Feinstein and Linstedt 2007, Feinstein and Linstedt 2008, Xiang and Wang 2010).
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Activated MEK phosphorylates and activates ERK.
ERKs are inactivated by the protein phosphatase 2A (PP2A). The PP2A holoenzyme is a heterotrimer that consists of a core dimer, composed of a scaffold (A) and a catalytic (C) subunit that associates with a variety of regulatory (B) subunits. The B subunits have been divided into gene families named B (or PR55), B0 (or B56 or PR61) and B00 (or PR72). Each family comprises several members. B56 family members of PP2A in particular, increase ERK dephosphorylation, without affecting its activation by MEK. Induction of PP2A is involved in the extracellular signal-regulated kinase (ERK) signalling pathway, in which it provides a feedback control, as well as in a broad range of other cellular processes, including transcriptional regulation and control of the cell cycle.This diversity of functions is conferred by a diversity of regulatory subunits, the combination of which can give rise to over 50 different forms of PP2A. For example, five distinct mammalian genes encode members of the B56 family, called B56a, b, g, d and e, generating at least eight isoforms. Whether a specific holoenzyme dephosphorylates ERK and whether this activity is controlled during mitogenic stimulation is unknown.
The MEF2 (Myocyte-specific enhancer factor 2) proteins constitute a family of transcription factors: MEF2A, MEF2B, MEF2C, and MEF2D. MEF2A and MEF2C are known substrates of ERK5, and their transactivating activity can be stimulated by ERK5 via direct phosphorylation. MEF2A and MEF2C are expressed in developing and adult brain including cortex and cerebellum.
Apocytochrome c requires the TOM complex for translocation across the mitochondrial outer membrane
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ERK/MAPK kinases have a number of targets within the nucleus, usually transcription factors or other kinases. The best known targets, ELK1, ETS1, ATF2, MITF, MAPKAPK2, MSK1, RSK1/2/3 and MEF2 are annotated here.
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MAP Kinases are inactivated by a family of protein named MAP Kinase Phosphatases (MKPs). They act through dephosphorylation of threonine and/or tyrosine residues within the signature sequence -pTXpY- located in the activation loop of MAP kinases (pT=phosphothreonine and pY=phosphotyrosine). MKPs are divided into three major categories depending on their preference for dephosphorylating; tyrosine, serine/threonine and both the tyrosine and threonine (dual specificity phoshatases or DUSPs). The tyrosine-specific MKPs include PTP-SL, STEP and HePTP, serine/threonine-specific MKPs are PP2A and PP2C, and many DUSPs acting on MAPKs are known. Activated MAP kinases trigger activation of transcription of MKP genes. Therefore, MKPs provide a negative feedback regulatory mechanism on MAPK signaling, by inactivating MAPKs via dephosphorylation, in the cytoplasm and the nucleus. Some MKPs are more specific for ERKs, others for JNK or p38MAPK.
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Specific recognition of mitochondrial preproteins by the cytosolic domain of the import receptor MOM72
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The biochemical and structural basis for trans-to-cis isomerization of retinoids in the chemistry of vision
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The condensin I complex is evolutionarily conserved and consists of five subunits: two SMC (structural maintenance of chromosomes) family subunits, SMC2 and SMC4, and three non-SMC subunits, NCAPD2, NCAPH and NCAPG. The stoichiometry of the complex is 1:1:1:1:1 (Hirano and Mitchinson 1994, Hirano et al. 1997, Kimura et al. 2001). SMC2 and SMC4 subunits, shared between condensin I and condensin II, are DNA-dependent ATPases, and condensins are able to introduce positive supercoils into DNA in an ATP-dependent manner (Kimura and Hirano 1997). Protein levels of condensin subunits are constant during the cell cycle, however condensins are enriched on mitotic chromosomes. Four of the five subunits, SMC4, NCAPD2, NCAPG and NCAPH, are phosphorylated in both mitotic and interphase HeLa cells, but on different sites (Takemoto et al. 2004). CDK1 (CDC2) in complex with CCNB (cyclin B) phosphorylates NCAPD2, NCAPG and NCAPH in mitosis (Kimura et al. 1998, Kimura et al. 2001, Takemoto et al. 2006, Murphy et al. 2008), but other mitotic kinases, such as PLK1 (St-Pierre et al. 2009), and other post-translational modifications, such as acetylation, may also be involved (reviewed by Bazile et al. 2010). Global proteomic analysis of human cell lines has identified N6-acetylation of lysine residues in condensin subunits SMC2, SMC4 and NCAPH (Choudhary et al. 2009). Another high throughput proteomic study showed that condensin I subunits NCAPD2 and NCAPH are phosphorylated upon DNA damage, probably by ATM or ATR kinase (Matsuoka et al. 2007). As condensin I is cytosolic, it gains access to chromosomes only after the nuclear envelope breakdown at the start of prometaphase (Ono et al. 2004). Condensin I, activated by CDK1-mediated phosphorylation, promotes hypercondensation of chromosomes that were condensed in prophase through the action of condensin II (Hirota et al. 2004). AURKB may also regulate association of condensin I complex with chromatin (Lipp et al. 2007). Protein phosphatase PP2A acts independently of its catalytic activity to target condensin II complex to chromatin, but does not interact with condensin I (Takemoto et al. 2009). Full activation of condensin I requires dephosphorylation of sites modified by CK2 during interphase (Takemoto et al. 2006). Besides being essential for chromosome condensation in mitosis, condensin I may also contribute to cohesin removal from chromosome arms in prometaphase, but the exact mechanism is not known (Hirota et al. 2004).
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CDK1 (CDC2) in complex with CCNB (cyclin B) phosphorylates condensin I subunits NCAPD2, NCAPG and NCAPH in mitosis (Kimura et al. 2001, Takemoto et al. 2006), but other mitotic kinases may also be involved. CDK1 phosphorylation sites in NCAPH have not been established. NCAPD2 threonine residues T1339, T1384 and T1389 are inferred to be phosphorylated by CDK1 based on homologues sites in Xenopus laevis Ncapd2 (Kimura et al. 1998). NCAPG threonine residues T308 and T332 are phosphorylated by CDK1 in vitro and functionally important. The functional importance of threonine T931, also phosphorylated by CDK1 in vitro, has not been demonstrated (Murphy et al. 2008). Phosphorylation by CDK1 is required for mitotic activation of condensin I and promotes chromosomal binding, introduction of positive supercoils into DNA, and chromatin condensation (Kimura et al. 1998, Kimura et al. 2001, Takemoto et al. 2006).
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Inhibitory phosphate groups that were added to condensin I subunits by CK2 during interphase have to be removed for full mitotic activation of condensin I (Takemoto et al. 2006). The responsible phosphatase has not been identified.
Glycogenin-1 deficiency and inactivated priming of glycogen synthesis
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Protein levels of condensin subunits are constant during the cell cycle. Four subunits, SMC4, NCAPD2, NCAPG and NCAPH, are phosphorylated in interphase cells (Takemoto et al. 2004) by CK2 i.e. casein kinase II (Takemoto et al. 2006). Except for the phosphorylation of NCAPH subunit on serine residue S570, CK2 phosphorylation sites in condensin I subunits have not been identified. Phosphorylation by CK2 inhibits condensin I-mediated introduction of positive supercoils into DNA and chromatin condensation. Mitotic activation of condensin I involves removal of phosphate groups added by CK2 (Takemoto et al. 2006), but the responsible phosphatase has not been identified.
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Lipin proteins LPIN1, 2, and 3, associated with the nuclear envelope, can each catalyze the hydrolysis of phosphatidate to yield 1,2-diacyl-glycerol and orthophosphate. The activities of LPIN1 and LPIN2 have been established experimentally (Grimsey et al. 2008); that of LPIN3 is inferred from its structural similarities both to its human paralogues and to its mouse ortholog (Donkor et al. 2007).
Lipins (LPIN1, LPIN2, LPIN3) possess several proline-directed phosphorylation sites that can be phosphorylated by CDK1 (Grimsey et al. 2008), including S106. Serine S106 in lipins is a preferred target for dephosphorylation by the evolutionarilly conserved CTDNEP1:CNEP1R1 complex (ortholog of yeast NEM1:SPO7 complex). Lipin phosphorylation regulates lipin localization, with phosphorylated lipins being soluble and dephosphorylated lipins being membrane-bound. The yeast ortholog of CDK1, CDC28, as well as human CDK1 can phosphorylate yeast lipin PAH1, inducing its dissociation from the nuclear envelope and endoplasmic reticulum membrane (Choi et al. 2011).
During prophase, the chromatin in the nucleus condenses, and the nucleolus disappears. Centrioles begin moving to the opposite poles or sides of the cell. Some of the fibers that extend from the centromeres cross the cell to form the mitotic spindle.
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The nuclear envelope breakdown (NEBD) happens in late prophase of mitosis and involves disassembly of the nuclear pore complex, depolymerization of the nuclear lamina, and clearance of nuclear envelope from chromatin. NEBD allows mitotic spindle microtubules to access condensed chromosomes at kinetochores and enables nuclear division and segregation of genetic material to two daughter cells. For a recent review, please refer to Guttinger et al. 2009.
Cold Spring Harb Perspect Biol 4:a007864
The nuclear envelope breakdown in mitotic prophase involves depolymerisation of lamin filaments, the main constituents of the nuclear lamina. The nuclear lamina is located at the nuclear face of the inner nuclear membrane and plays and important role in the structure and function of the nuclear envelope (reviewed by Burke and Stewart 2012). Depolymerisation of lamin filaments, which consist of lamin homodimers associated through electrostatic interactions in head-to-tail molecular strings, is triggered by phosphorylation of lamins. While CDK1 phosphorylates the N-termini of lamins (Heald and McKeon 1990, Peter et al. 1990, Ward and Kirschner 1990, Mall et al. 2012), PKCs (PRKCA and PRKCB) phosphorylate the C-termini of lamins (Hocevar et al. 1993, Goss et al. 1994, Mall et al. 2012). PKCs are activated by lipid-mediated signaling, where lipins, activated by CTDNEP1:CNEP1R1 serine/threonine protein phosphatase complex, catalyze the formation of DAG (Gorjanacz et al. 2009, Golden et al. 2009, Wu et al. 2011, Han et al. 2012, Mall et al. 2012).
PKC contains an N-terminal C2 like domain, a pseudosubstrate (PS), DAG binding (C1) domain and a C-terminal kinase domain. The PS sequence resembles an ideal substrate with the exception that it contains an alanine residue instead of a substrate serine residue, is bound to the kinase domain in the resting state. As a result, PKC is maintained in a closed inactive state, which is inaccessible to cellular substrates (Colon-Gonzalez & Kazanietz 2006). Diacylglycerol (DAG) produced by activated lipins (LPIN1, LPIN2, LPIN3) leads to the activation of PKC (PRKCA and PRKCB) and their translocation from the nucleoplasm to the nuclear envelope where they can phosphorylate lamins (Mall et al. 2012). PKCs are tethered to the membrane through DAG binding to the C1 domain and this confers a high-affinity interaction between PKC and the membrane. This leads to a massive conformational change that releases the PS domain from the catalytic site and the system becomes both competent and accessible (Colon-Gonzalez & Kazanietz 2006).
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In the cytoplasm activated MEK1 (Serine phosphorylated) may encounter monomeric, inactive ERK1. ERK1 in its inactive form is not phosphorylated on a critical Threonine (T) and a critical Tyrosine (Y).
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At the beginning of this reaction, 2 molecules of 'ATP', and 1 molecule of 'MEK1' are present. At the end of this reaction, 1 molecule of 'phospho_MEK1', and 2 molecules of 'ADP' are present. This reaction takes place in the 'cytosol' and is mediated by the 'protein serine/threonine kinase activity' of 'phospho-Cdc2 (Thr 161)'.
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MEK1 phosphorylates the critical Tyrosine and Threonine on ERK1, converting two ATP to ADP. Phosphorylation of ERK-1 activates its kinase activity.
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C-Jun NH2 terminal kinases (JNKs) are an evolutionarily conserved family of serine/threonine protein kinases, that belong to mitogen activated protein kinase family (MAPKs - also known as stress-activated protein kinases, SAPKs). The JNK pathway is activated by heat shock, or inflammatory cytokines, or UV radiation. The JNKs are encoded by at least three genes: JNK1/SAPK-gamma, JNK2/SAPK-alpha and JNK3/ SAPK-beta. The first two are ubiquitously expressed, whereas the JNK3 protein is found mainly in brain and to a lesser extent in heart and testes. As a result of alternative gene splicing all cells express distinct active forms of JNK from 46 to 55 kDa in size. Sequence alignment of these different products shows homologies of >80%. In spite of this similarity, the multiple JNK isoforms differ in their ability to bind and phosphorylate different target proteins, thus leading to the distinctive cellular processes: induction of apoptosis, or enhancment of cell survival, or proliferation. Activation of JNKs is mediated by activated TAK1 which phosphorylates two dual specificity enzymes MKK4 (MAPK kinase 4) and MKK7(MAPK kinase 7).
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c-Jun NH2 terminal kinase (JNK) plays a role in conveying signals from the cytosol to the nucleus, where they associate and activate their target transcription factors.
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p38 mitogen-activated protein kinase (MAPK) belongs to a highly conserved family of serine/threonine protein kinases. The p38 MAPK-dependent signaling cascade is activated by pro-inflammatory or stressful stimuli such as ultraviolet radiation, oxidative injury, heat shock, cytokines, and other pro-inflammatory stimuli. p38 MAPK exists as four isoforms (alpha, beta, gamma, and delta). Of these, p38alpha and p38beta are ubiquitously expressed while p38gamma and p38delta are differentially expressed depending on tissue type. Each isoform is activated by upstream kinases including MAP kinase kinases (MKK) 3, 4, and 6, which in turn are phosphorylated by activated TAK1 at the typical Ser-Xaa-Ala-Xaa-Thr motif in their activation loops. Once p38 MAPK is phosphorylated it activates numerous downstream substrates, including MAPK-activated protein kinase-2 and 3 (MAPKAPK-2 or 3) and mitogen and stress-activated kinase-1/2 (MSK1/2). MAPKAPK-2/3 and MSK1/2 function to phosphorylate heat shock protein 27 (HSP27) and cAMP-response element binding protein transcriptional factor, respectively. Other transcription factors, including activating transcription factor 2, Elk, CHOP/GADD153, and myocyte enhancer factor 2, are known to be regulated by these kinases.
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The p38 activators MKK3 and MKK6 were present in both the nucleus and the cytoplasm, consistent with a role in activating p38 in the nucleus.
While circularization of mRNA during translation initiation is thought to contribute to an increase in the efficiency of translation, it also appears to provide a mechanism for translational silencing. This might be achieved by bringing inhibitory 3' UTR-binding proteins into a position in which they interfere either with the function of the translation initiation complex or with the assembly of the ribosome (Mazumder et al 2001). Translational silencing of Ceruloplasmin (Cp) occurs 16 hrs after its induction by INF-gamma (Mazumder et al., 1997). Although the mechanism by which silencing occurs has not yet been determined, this process is mediated by the L13a subunit of the 60s ribosome and thought to require circularization of the Cp mRNA (Sampath et al., 2003; Mazumder et al., 2001; Mazumder et al., 2003). Between 14 and 16 hrs after INF gamma induction, the L13a subunit of the 60s ribosome is phosphorylated and released from the 60s subunit. Phosphorylated L13a then associates with the GAIT element in the 3' UTR of the Cp mRNA inhibiting its translation.
Activated human JNK kinases (MKK4 and MKK7) phosphorylate Thr183 and Tyr185 residues in the characteristic Thr-Pro-Tyr phosphoacceptor loop of each JNK. JNK is differentially regulated by MKK4 and MKK7 depending on the stimulus. MKK7 is the primary activator of JNK in TNF, LPS, and PGN responses. However, TLR3 cascade requires both MKK4 and MKK7. Some studies reported that in three JNK isoforms tested MKK4 shows a striking preference for the tyrosine residue (Tyr-185), and MKK7 a striking preference for the threonine residue (Thr-183).
Translational control mechanisms often involve interactions between the 3' - or 5' -untranslated regions (UTRs) of mRNA and RNA-binding proteins. One such mechanism requires circularization of the mRNA molecule involving protein-protein interactions between the mRNA termini (Mazumder et al., 2001). While the circularization of mRNA during translation initiation is thought to contribute to an increase in the efficiency of translation, it also appears to provide a mechanism for translational silencing. This might be achieved by bringing inhibitory 3' UTR-binding proteins into a position in which they interfere either with the function of the translation initiation complex or with the assembly of the ribosome.
Transfer ribonucleic acid-induced hydrolysis of valyladenylate bound to isoleucyl ribonucleic acid synthetase
Purification and properties of isoleucyl ribonucleic acid synthetase from Escherichia coli
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The genetics of mammalian circadian order and disorder: implications for physiology and disease
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Activated MEK2 phosphorylates and activates ERK2.
Phospho-ERK-2 dimer is translocated from cytosol to nucleoplasm.
Two phospho-ERK2 molecules dimerise and enter the nucleus, where they may phosphorylate downstream targets.
MEK2 dissociates from phospho-ERK2, allowing phospho-ERK2 to dimerise with another phospho-ERK2.
MEK2 phosphorylates the critical Tyrosine and Threonine on ERK2, converting two ATP to ADP. Phosphorylation of ERK-2 activates its kinase activity.
In the cytoplasm activated MEK2 (Serine phosphorylated) may encounter monomeric, inactive ERK2. ERK2 in its inactive form is not phosphorylated on a critical Threonine (T183) and a critical Tyrosine (Y185).
Activated MEK1 phosphorylates and activates ERK1.
Phospho-ERK-1 dimer is translocated from cytosol to nucleoplasm.
Signal transduction via the stem cell factor receptor/c-Kit
Two phospho-ERK1 molecules dimerise and enter the nucleus, where they may phosphorylate downstream targets.
MEK1 dissociates from phospho-ERK1, allowing phospho-ERK1 to dimerise with another phospho-ERK1.
Mechanism underlying replication protein a stimulation of DNA ligase I
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Transcriptional activation domains stimulate initiation and elongation at different times and via different residues
The role of mismatched nucleotides in activating the hMSH2-hMSH6 molecular switch
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Tau-crystallin/alpha-enolase: one gene encodes both an enzyme and a lens structural protein
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3229.3
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The human sef-a isoform utilizes different mechanisms to regulate receptor tyrosine kinase signaling pathways and subsequent cell fate
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Localization of p21-activated kinase 1 (PAK1) to pseudopodia, membrane ruffles, and phagocytic cups in activated human neutrophils
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The roles of anabolic and catabolic reactions in the synthesis and recycling of polyunsaturated fatty acids
Prostaglandins Leukot Essent Fatty Acids 67:79-83
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The disulfide relay system of mitochondria is required for the biogenesis of mitochondrial Ccs1 and Sod1
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_123499.1
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Translational silencing of ceruloplasmin requires the essential elements of mRNA circularization: poly(A) tail, poly(A)-binding protein, and eukaryotic translation initiation factor 4G
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_21673.2
Human geranylgeranyl diphosphate synthase: isolation of the cDNA, chromosomal mapping and tissue expression
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_124477.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=742353
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_175362.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615148
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615146
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615145
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615141
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_181516.3
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Human L-3-phosphoserine phosphatase: sequence, expression and evidence for a phosphoenzyme intermediate
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_257934.1
High-level expression of enzymatically active human Cu/Zn superoxide dismutase in Escherichia coli
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_124533.1
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608633
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608645
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608647
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608643
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608644
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2814.1
Functional expression and characterisation of a new human phosphatidylinositol 4-kinase PI4K230
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=914003
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5614929
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26828.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_211568.2
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Mutations in ATP2C1, encoding a calcium pump, cause Hailey-Hailey disease
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5616408
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618550
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_189254.3
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5614938
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=400431
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19561.2
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615214
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5616399
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3632879
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_164213.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_125341.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_230311.1
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1806290
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_223495.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_180608.3
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_181452.3
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2728.2
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_239854.1
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PAK and other Rho-associated kinases--effectors with surprisingly diverse mechanisms of regulation
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_189233.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618137
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_175077.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618556
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615221
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617103
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615223
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5616398
Mitochondrial FAD-linked sulfhydryl oxidase ERV1
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Mitochondrial intermembrane space import and assembly protein 40
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5616397
Mitochondrial import inner membrane translocase subunit TIM23
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_181448.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5616402
Mitochondrial import inner membrane translocase subunit TIM8
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_247852.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_180343.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5616417
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_246275.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_188955.3
Mitochondrial import inner membrane translocase subunit TIM9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618036
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618614
SnapShot: motor proteins in spindle assembly
Sorting assembly machinery 37 kDa subunit
Sorting assembly machinery 50 kDa subunit
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611735
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611736
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611737
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611738
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611739
CHIP28 water channels are localized in constitutively water-permeable segments of the nephron
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611821
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5614529
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5614530
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5614341
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5614342
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5616373
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5614527
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_122466.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=392417
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617066
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5614528
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617063
Mitochondrial outer membrane protein porin 1
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Mitochondrial distribution and morphology protein 10
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5616376
Proteins Inserted into Outer Membrane by SAM50 Complex
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5616374
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5614343
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5614344
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1806276
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5614967
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_237673.1
Mitochondrial import inner membrane translocase subunit TIM17
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The Tim54p-Tim22p complex mediates insertion of proteins into the mitochondrial inner membrane
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TIM8:TIM13 chaperones hydrophobic proteins
The TIM8:TIM13 complex chaperones hydrophobic membrane proteins in the intermembrane space until their insertion into the inner or outer membrane (Leuenberger et al. 1999, Davis et al. 2000, Paschen et al. 2000, Curran et al. 2002, Wiedemann et al. 2004, Davis et al. 2007, Beverly et al. 2008, Hasson et al. 2010). Substrates of the TIM8:TIM13 complex include TIM23 (Leuenberger et al. 1999, Davis et al. 2000, Paschen et al. 2000, Curran et al. 2002, Davis et al. 2007, Beverly et al. 2008, Hasson et al. 2010) and TOM40 (Wiedemann et al. 2004).
Mitochondrial intermembrane space cysteine motif-containing protein MIC17
Mitochondrial intermembrane space cysteine motif-containing protein MIC14
MIA40:ERV1 oxidizes cysteine residues to cystine disulfide bonds
MIA40 catalyzes the oxidation of cysteine residues in precursor proteins in the intermembrane space to form cystine bonds (Chacinska et al. 2004, Terziyska et al. 2005, Milenkovic 2007, Sideris and Tokatlidis 2007, Terziyska et al. 2007, Misecke et al. 2008, Muller et al. 2008, Milenkovic et al. 2009, Stojanovski et al. 2008, Longen et al. 2009, Milenkovic et al. 2009, Reddehase et al. 2009, Sideris et al. 2009, Terziyska et al. 2009, Tienson et al. 2009, Bien et al. 2010). The electrons from the cysteine residues are transferred to MIA40, then to ERV1, and eventually to the respiratory chain (Allen et al. 2005, Bihlmaier et al. 2007). The interaction between MIA40 and ERV1 appears to be transitory (Stojanovski et al. 2008). Substrates of MIA40:ERV1 include COX17 (Mesecke et al. 2008, Sideris et al. 2009), COX19 (Bien et al. 2010), CMC2 (Longen et al. 2009), CMC3 (Longen et al. 2009), CMC4 (Longen et al. 2009), TIM13 (Terziyska et al. 2005, Muller et al. 2008, Stojanovski et al. 2008), TIM9 (Chacinska et al. 2004, Milenkovic et al. 2007, Stojanovski et al. 2008, Milenkovic et al. 2009), TIM10 (Chacinska et al. 2004, Milenkovic et al. 2007, Sideris and Tokatlidis 2007, Stojanovski et al. 2008, Terziyska et al. 2009, Milenkovic et al. 2009), CCS1 (Stojanovski et al. 2008, Reddehase et al. 2009), TIM8 (Muller et al. 2008, Stojanovski et al. 2008), and ERV1 (Terziyska et al. 2007).
Mitochondrial import inner membrane translocase subunit TIM13
The TIM9:TIM10 complex chaperones hydrophobic membrane proteins in the intermembrane space until their insertion into the inner or outer membrane (Koehler et al. 1998, Leuenberger et al. 1999, Luciano et al. 2001, Truscott et al. 2002, Vasiljev et al. 2004, Wiedemann et al. 2004, Davis et al. 2007, Baker et al. 2009, Hasson et al. 2010). Substrates of the TIM9:TIM10 complex include AAC (Koehler et al. 1998, Leuenberger et al. 1999, Luciano et al. 2001, Truscott et al. 2002, Vasiljev et al. 2004, Baker et al. 2009, Hasson et al. 2010), TIM17 (Leuenberger et al. 1999), TOM40 (Wiedemann et al. 2004), TIM23 (Davis et al. 2007), TIM22 (Hasson et al. 2010), and Tafazzin (Hasson et al. 2010).
Mitochondrial import inner membrane translocase subunit TIM10
MLH1:PMS2 makes single strand incision near insertion/deletion loop of 2 bases or more
MSH2:MSH3 recruits MLH1:PMS2 to mismatch and interacts with PCNA
MutSbeta recruits MutLalpha to mismatch and interacts with PCNA
TOM40:TOM70 complex translocates proteins from the cytosol to the mitochondrial intermembrane space
The TOM40:TOM70 Complex transports precursor proteins from the cytosol, across the outer membrane of the mitochondrion, and into the intermembrane space from where they may be targeted to all locations within the mitochondrion. TOM40, TOM22, TOM5, TOM6, and TOM7 form the general import pore across the membrane (Dekker et al. 1998). TOM20 and TOM22 interact with presequences on mitochondrial precursors (Haucke et al. 1995, Brix et al. 1997, Meisinger et al. 2001, Yamano et al. 2008). TOM70 interacts with hydrophobic sequences in mature internal regions of mitochondrial proteins (Schlossman et al. 1994, Brix et al. 1997, Yamamoto et al. 2009). Substrates of the TOM40:TOM70 complex include ATP1 (Yamamoto et al. 2009), ATP2 (Yamamoto et al. 2009), ATP9 (Hines et al. 1990), TOM40 (Yamamoto et al. 2009), SSC1 (Yamamoto et al. 2009), CIT1 (Yamamoto et al. 2009), ACO1 (Yamamoto et al. 2009), IDH1 (Yamamoto et al. 2009), BCS1 (Stan et al. 2003), CYT1 (Diekert et al. 2001), TIM54 (Kurz et al. 1999), TIM22 (Kurz et al. 1999), AAC (Sollner et al. 1990, Kurz et al. 1990, Kubrich et al. 1998, Endres et al. 1999, Truscott et al. 2002, Vasiljev et al. 2004), HSP60 (Yamano et al. 2008), CYB2 (Krayl et al. 2007). Some proteins such as Aco1, Atp1, Cit1, Idh1, and Atp2 contain both presequences that interact with TOM20 and mature regions that interact with TOM70 (Yamamoto et al. 2009).
EXO1 interacts with MSH2:MSH3 (MutSbeta) and MLH1:PMS2 (MutLalpha)
DNA ligase I ligates single stranded nick in double stranded DNA
MSH2:MSH3 binds insertion/deletion loop of 2 bases or more
MutSbeta binds insertion/deletion loop of 2 bases or more
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The replication of the genome and the subsequent segregation of chromosomes into daughter cells are controlled by a series of events collectively known as the cell cycle. DNA replication is carried out during a discrete temporal period known as the S (synthesis)-phase, and chromosome segregation occurs during a massive reorganization to cellular architecture at mitosis. Two gap-phases separate these major cell cycle events: G1 between mitosis and S-phase, and G2 between S-phase and mitosis. In the development of the human body, cells can exit the cell cycle for a period and enter a quiescent state known as G0, or terminally differentiate into cells that will not divide again, but undergo morphological development to carry out the wide variety of specialized functions of individual tissues. A family of protein serine/threonine kinases known as the cyclin-dependent kinases (CDKs) controls progression through the cell cycle. As the name suggests, the activity of the catalytic subunit is dependent on binding to a cyclin partner. The human genome encodes several cyclins and several CDKs, with their names largely derived from the order in which they were identified. The oscillation of cyclin abundance is one important mechanism by which these enzymes phosphorylate key substrates to promote events at the relevant time and place. Additional regulatory proteins and post-translational modifications ensure that CDK activity is precisely regulated, frequently confined to a narrow window of activity.
Cytochrome c oxidase assembly protein COX19
Mitochondrial distribution and morphology protein 35
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The elongation reaction proceeds as follows: The template of hTERC directs the sequential addition of nucleotides to the 3' telomeric DNA end. Following addition of a nucleotide, the template and catalytic site must move relative to one another within the telomerase RNP to place the appropriate template residue in the active site. As base-pairing and nucleotide addition occur at one end of the template, base pair melting occurs at the other (Collins and Greider 1993; Wang and Blackburn, 1997; Hammond and Cech 1998; Benjamin et al. 2000; Forstemann and Lingner 2005). This un-pairing is thought to reduce the energy used for mediating the subsequent translocation step. Nucleotide addition can occur up until the template boundary which in hTERC is defined by a helix called P1b (Chen and Greider 2003).
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In vitro, telomerase can disassociate from the primer following addition of each nucleotide or during the translocation step. The regulation of telomerase disassociation from the telomere in vivo is not well-characterized. One factor that may be involved is a helicase termed hPIF1, which can unanneal the telomerase RNA/telomeric DNA hybrid (Boule et al., 2005; Zhang et al., 2006).
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Humans, like most eukaryotic organisms, add direct repeats to the telomere using a specialized DNA polymerase called telomerase. Telomerase is a ribonucleoprotein (RNP) complex minimally composed of a conserved protein subunit containing a reverse transcriptase domain (human telomerase reverse transcriptase, hTERT) and a template-containing RNA (human telomerase RNA component, hTERC, or hTR, hTER). The primer for telomerase is the G-rich single-strand overhang at the chromosome end. Telomerase can perform multiple rounds of repeat synthesis. The reaction cycle has been inferred from in vitro studies of telomerase from multiple organisms and can be described as having four events: 1) DNA primer recognition, 2) RNA template alignment, 3) elongation, and 4) translocation. Telomeric DNA is recognized in part by a presumed "anchor site" in hTERT, which preferentially binds G-rich DNA, and this interaction can affect elongation and translocation steps. This interaction occurs 5' of the alignment of the RNA template with the end nucleotides of the chromosome. RNA alignment positions the template adjacent to the chromosome terminus. During elongation, the template directs sequential addition of nucleotides to the telomere end. After synthesis of a repeat is completed, relative movement of telomerase and the primer, termed translocation, repositions telomerase at the end of the newly added sequence to allow initiation of another round of repeat addition.
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The complementary strand is synthesized by the polymerase primase complex using conventional RNA priming.
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Studies in yeast and humans indicate that recruitment of telomerase to a telomere may be influenced by multiple variables, including regulatory protein factors, hTERT domains, telomere length, and the cell cycle. First, in yeast, the telomerase associated factor Est1 and the single-strand DNA binding protein Cdc13 play roles in telomerase recruitment (Pennock et al. 2001; Bianchi et al. 2004). Analogous proteins exist in human cells (Est1A, Est1B, Est1C, and POT1, respectively); however, how or whether these proteins are directly involved in telomerase recruitment remains to be elucidated. Second, N-terminal residues of hTERT within the DAT (dissociate the activities of telomerase) domain may have a role in binding single stranded telomeric DNA as the "anchor site" (Lee et al. 1993; Moriarty et al. 2005). Third, a cis-acting mechanism in yeast and humans that regulates telomere length maintenance may modulate telomerase access to the telomere (reviewed in Blackburn 2001; Smogorzewska and de Lange, 2004). Long telomeres, which have more associated protein factors, are in a state that is acted on by telomerase less frequently than that of short telomeres, which have fewer associated factors. Whether short telomeres actively recruit telomerase remains to be determined. Last, the recruitment of telomerase to telomeres shows cell-cycle regulation (Taggart et al. 2002; Smith et al. 2003; Fisher et al. 2004; Jady et al. 2006; Tomlinson et al. 2006). Further studies will be needed to determine the details of how human telomerase is recruited to a telomere.
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In vitro studies of telomerase complexes derived from multiple organisms indicate that at least two types of interactions are important for telomerase RNP catalytic site alignment at the 3' G-rich single-strand telomere end. In one interaction, an alignment region in hTERC base-pairs with the 3' G-rich single-strand telomeric DNA end to form an RNA-DNA hybrid, which positions the template adjacent to the 3' end of the telomere. In a second interaction, a portion of hTERT is proposed to interact with the DNA 5' of the telomerase RNA/DNA primer hybrid (Harrington and Greider 1991; Morin 1991; Moriarty et al. 2005), which is important for the catalytic rate (Lee and Blackburn, 1993) and presumably allows telomerase to maintain contact with the chromosome during the translocation step. How the anchor site binding and template hybridization are coordinated is not known.
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The template of hTERC directs the sequential addition of nucleotides to the 3' telomeric DNA end. Following addition of a nucleotide, the template and catalytic site must move relative to one another within the telomerase RNP to place the appropriate template residue in the active site. As base-pairing and nucleotide addition occur at one end of the template, base pair melting occurs at the other (Collins and Greider 1993; Wang and Blackburn, 1997; Hammond and Cech 1998; Benjamin et al. 2000; Forstemann and Lingner 2005). This un-pairing is thought to reduce the energy used for mediating the subsequent translocation step. Nucleotide addition can occur up until the template boundary which in hTERC is defined by a helix called P1b (Chen and Greider 2003).
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The human telomerase RNP can catalyze multiple rounds of repeat addition on the same telomeric substrate in vitro. Before initiating synthesis of another repeat, telomerase undergoes a translocation step to reposition itself on the telomere. Base pairs in the DNA/RNA hybrid are unannealed, the RNA template is repositioned relative to the active site, and the template base-pairs at the 3' end of the newly synthesized DNA. The anchor site interaction with DNA 5' of the RNA-DNA duplex is thought to maintain the interaction of telomerase with DNA during the translocation step.
Crystal structure of human indoleamine 2,3-dioxygenase: catalytic mechanism of O2 incorporation by a heme-containing dioxygenase
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The Anaphase Promoting Complex or Cyclosome (APC/C) functions during mitosis to promote sister chromatid separation and mitotic exit through the degradation of mitotic cyclins and securin. This complex is also active in interphase insuring the appropriate length of the G1 phase (reviewed in Peters, 2002). The APC/C contains at least 12 subunits and functions as an ubiquitin-protein ligase (E3) promoting the multiubiquitination of its target proteins (see Gieffers et al., 2001). In the ubiquitination reaction, ubiquitin is activated by the formation of a thioester bond with the (E1) ubiquitin activating enzyme then transferred to a cysteine residue within the ubiquitin conjugating enzyme (E2) and ultimately to a lysine residue within the target protein, with the aid of ubiquitin-protein ligase activity of the APC/C. The ubiquitin chains generated are believed to target proteins for destruction by the 26S proteasome (Reviewed in Peters, 1994 ) The activity of the APC/C is highly periodic during the cell cycle and is controlled by a combination of regulatory events. The APC/C is activated by phosphorylation and the regulated recruitment of activating subunits and is negatively regulated by sequestration by kinetochore-associated checkpoint proteins. The Emi1 protein associates with Cdh1 and Cdc20, inhibiting the APC/C between G1/S and prophase. RSSA1 may play a similar role in ihibiting the APC during early mitosis. Following phosphorylation of the APC/C core subunits by mitotic kinases, the activating subunit, Cdc20 is recruited to the APC/C and is responsible for mitotic activities, including the initiation of sister chromatid separation and the timing of exit from mitosis (See Zachariae and Nasmyth, 1999). Substrates of the Cdc20:APC/C complex, which are recognized by a motif known as the destruction box (D box) include Cyclin A, Nek2, Securin and Cyclin B. Degradation of Securin and Cyclin B does not occur until the mitotic spindle checkpoint has been satisfied (see Castro et al. 2005). Cdc20 is degraded late in mitosis (Reviewed in Owens and Hoyt, 2005). At this time the activating subunit, Cdh1, previously maintained in an inactive phosphorylated state by mitotic kinases, is dephosphorylated and associates with and activates the APC/C. The APC/C:Cdh1 complex recognizes substrates containing a D box, a KEN box (Pfleger and Kirschner, 2000) or a D box activated (DAD) domain (Castro et al., 2002) sequence and promotes the ordered degration of mitotic cyclins and other mitotic proteins culminating with its own ubiquitin-conjugating enzyme (E2) subunit UbcH10 (Rape et al., 2006). This ordered degradation promotes the stability of Cyclin A at the end of G1. This stabilization, in turn, promotes the phosphorylation of Cdh1 and its abrupt dissociation from the APC/C, allowing accumulation of cyclins for the next G1/S transition (Sorensen et al., 2001).
Coatomer:Arf1-GTP:GAP lattice formation on golgi membrane
GAP Recruitment to the Coatomer:Arf1-GTP Complex
TIM23 PAM complex translocates proteins from the mitochondrial intermembrane space to the mitochondrial matrix
The TIM23 complex transports precursor proteins across the inner membrane and into the matrix (Voisine et al. 2000, Mokranjac et al. 2003, Chacinska et al. 2005,Wiedemann et al. 2007, Hutu et al. 2008, Popov-Celeketic et al. 2008, Chacinska et al. 2010). Subunits TIM50, TIM17, and TIM23 are necessary for initiating translocation (Mokranjac et al.2003, Milisav et al. 2001) while the PAM complex with mtHSP70 (SSC1) provides the motive force that drives the transport (Milisav et al. 2001, Truscott et al. 2003, Frazier et al. 2004, D'Silva et al. 2005, van der Laan et al. 2005, Yamano et al. 2008). Hsp70 (mtHsp70, Ssc1) binding to the precursor pulls the protein into the matrix in a reaction requiring ATP hydrolysis (Gambill et al. 1993, Schneider et al. 1994, Kronidou et al. 1994, Ungermann et al. 1994, Voos et al. 1996, Voisine et al. 1999, Voisine et al. 2000, Krayl et al. 2007). The reaction appears to use a Brownian ratchet mechanism (Yamano et al. 2008). Substrates of TIM23:PAM include Hsp60 (Gallas et al. 2006) and Yfh1 (Voisine et al. 2000).
MPP hydrolyzes presequence of matrix precursors
The alpha subunit (MAS2, Alpha-MPP) of the mitochondrial processing peptidase (MPP) binds presequences of mitochondrial precursors and the beta subunit (MAS1, Beta-MPP) cleaves the presequence (Yang et al. 1991, Geli 1993, Luciano et al. 1997, Luciano et al. 1998, Taylor et al. 2001, Dvorakova-Hola et al. 2010). After cleavage, proteins destined for the matrix are drawn into the matrix by ATP-dependent interaction with mtHSP70 (SSC1) of the PAM complex.
Precursor proteins enter TIM23 PAM complex
The TIM23 Complex resides in the inner membrane of the mitochondrion and transfers precursor proteins to the matrix. The TIM23 complex appears to adopt different configurations (and perhaps different subunit compositions) depending on whether the substrate is destined for the inner membrane or the matrix. Here we refer to the TIM23 PAM complex as the configuration that delivers inner membrane proteins. The PAM17 subunit is required for this activity. The N-terminal presequence of precursors first interacts with TIM50 and TIM23 (Mokranjac et al. 2003, Martinez-Caballero et al. 2007, Tamura et al. 2009). The TIM17 and TIM23 subunits form a channel and are required to initiate translocation of precursors (Milislav et al. 2001). Substrates of TIM23 PAM include Hsp60 (Gallas et al. 2006) and Yfh1 (Voisine et al. 2000).
TIM23 SORT complex inserts proteins into inner membrane
The TIM23 Complex resides in the inner membrane of the mitochondrion and transfers precursor proteins to the inner membrane. The presequence of proteins targeted to the inner membrane is transferred to the matrix where it is cleaved. Sequences in the mature region of the protein then interact with the TIM23 complex to halt transfer across the inner membrane and the protein is released laterally into the inner membrane (Glick et al. 1992, Popov-Celeketic et al. 2008). TIM21 is required. Substrates of the TIM23 complex targeted to the inner membrane include CYB2 (Krayl et al. 2007, Hutu et al. 2008, Popov-Celeketic et al. 2008, Tamura et al. 2009, Mokranjac et al. 2009), DLD (Mokranjac et al. 2009), ATP9 (Leuenberger et al. 1999, Milisav et al. 2001, Tamura et al. 2009), COQ2 (Leuenberger et al. 1999), TIM54 (Leuenberger et al. 1999, Kurz et al. 1999), COX4 (Martinez-Caballero et al. 2007), COX5A (Mokranjac et al. 2003), and ATP2 (Dekker et al. 1997, Mokranjac et al. 2003).
Precursor proteins enter TIM23 SORT complex
The TIM23 Complex resides in the inner membrane of the mitochondrion and transfers precursor proteins to the inner membrane. The TIM23 complex appears to adopt different configurations (and perhaps different subunit compositions) depending on whether the substrate is destined for the inner membrane or the matrix. Here we refer to the TIM23 SORT complex as the configuration that delivers inner membrane proteins. The TIM21 subunit is required for this activity.The N-terminal presequence of precursors first interacts with TIM50 and TIM23 (Mokranjac et al. 2003, Martinez-Caballero et al. 2007, Tamura et al. 2009). The TIM17 and TIM23 subunits form a channel and are required to initiate translocation of precursors (Milislav et al. 2001). Substrates of the TIM23 SORT complex targeted to the inner membrane include CYB2 (Krayl et al. 2007, Hutu et al. 2008, Popov-Celeketic et al. 2008, Tamura et al. 2009, Mokranjac et al. 2009), DLD (Mokranjac et al. 2009), ATP9 (Leuenberger et al. 1999, Milisav et al. 2001, Tamura et al. 2009), COQ2 (Leuenberger et al. 1999), TIM54 (Leuenberger et al. 1999, Kurz et al. 1999), COX4 (Martinez-Caballero et al. 2007), COX5A (Mokranjac et al. 2003), and ATP2 (Dekker et al. 1997, Mokranjac et al. 2003).
MPP hydrolyzes presequence of inner membrane precursors
The alpha subunit (MAS2, Alpha-MPP) of the mitochondrial processing peptidase (MPP) binds presequences of mitochondrial precursors and the beta subunit (MAS1, Beta-MPP) cleaves the presequence (Yang et al. 1991, Geli 1993, Luciano et al. 1997, Luciano et al. 1998, Taylor et al. 2001, Dvorakova-Hola et al. 2010). After cleavage, proteins destined for the inner membrane are released laterally from TIM23 SORT into the membrane.
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Cyclin A can also form complexes with Cdc2 (Cdk1). Together with three B-type cyclins, Cdc2 (Cdk1) regulates the transition from G2 into mitosis. These complexes are activated by dephosphorylation of T14 and Y15. Cyclin A, B - Cdc2 complexes phosphorylate several proteins involved in mitotic spindle structure and function, the breakdown of the nuclear envelope, and topological changes in chromosomes allowing resolution of their entanglement and condensation that is necessary for the ~2 meters of DNA to be segregated at mitosis.
SAM50 complex inserts proteins into outer membrane
The SAM50 Complex (TOB55 Complex) inserts mainly beta-barrel proteins into the outer membrane after they have passed from the cytosol, through the TOM70:TOM40 complex, and into the intermembrane space (Kozjak et al. 2003, Ishikawa et al. 2004, Milenkovic et al. 2004, Waizenegger et al. 2004, Habib et al. 2007,Stojanovski et al. 2007, Kutik et al. 2008, Chan and Lithgow 2008). Substrates of the SAM50 complex include TOM40 (Kozjak et al. 2003, Ishikawa et al. 2004, Milenkovic et al. 2004, Waizenegger et al. 2004, Habib et al. 2007, Kutik et al. 2008, Chan and Lithgow 2008), MDM10 (Waizenegger et al. 2004, Habib et al. 2007, Kutik et al. 2008), Porin1 (Kozjak et al. 2003, Ishikawa et al. 2004, Milenkovic et al. 2004, Waizenegger et al. 2004, Habib et al. 2007, Kutik et al. 2008), and TOM22 (Stojanovski et al. 2007).
TIM22 complex inserts proteins into inner membrane
The TIM22 complex inserts precursor proteins into the inner membrane of the mitochondrion (Sirrenberg et al. 1996, Kaldi et al. 1998, Kerscher et al. 1997, Leuenberger et al. 1999, Endres et al. 1999, Kovermann et al. 2002, Rehling et al. 2003, Vergnolle et al. 2005, Yamano et al. 2005). The precursors are hydrophobic and are usually chaperoned to the TIM22 complex by the small TIM proteins (TIM10, TIM12) of the intermembrane space (Koehler et al. 1998, Sirrenberg et al. 1998). Substrates of the TIM22 complex include AAC (Sirrenberg et al. 1996, Kerscher et al. 1997, Leuenberger et al. 1999, Endres et al. 1999, Vergnolle et al. 2005), PIC (Kovermann et al. 2002, Rehling et al. 2003, Yamano et al. 2005), TIM22 (Leuenberger et al. 1999), and TIM23 (Kerscher et al. 1997, Kaldi 1998, Leuenberger et al. 1999).
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Phosphorylation by mitotic kinases is believed to alter the conformation of Cdh1 preventing it from associating with the APC/C. Cdc14 is thought to contribute to the dephosphorylation of Cdh1 in late mitosis. Dephosphorylated Cdh1 then associates with and activates the APC/C.
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The activity of the APC/C must be appropriately regulated during the cell cycle to ensure the timely degradation of its substrates. Of particular importance is the conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase. Phosphorylation of both the APC/C complex and Cdh1 regulate this conversion. During mitosis, several APC/C subunits are phosphorylated increasing the activity of APC/C:Cdc20. However, phosphorylation of Cdh1 by mitotic Cyclin:Cdk complexes prevents it from activating the APC/C. Dephosphorylation of Cdh1 in late anaphase by Cdc14a results in the activation of APC/C:Cdh1 (reviewed in Castro et al, 2005).
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At the onset of mitosis, Cdh1 is phosphorylated by Cyclin B-Cdc2 resulting in a conformational change that prevents Cdh1 from activating the APC/C.
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The APC/C is activated by either Cdc20 or Cdh1. While both activators associate with the APC/C, they do so at different points in the cell cycle and their binding is regulated differently (see Zachariae and Nasmyth, 1999). Cdc20, whose protein levels increase as cells enter into mitosis and decrease upon mitotic exit, only associates with the APC/C during M phase. Cdh1 associates with the APC/C in G1. This interaction is inhibited at other times by Cdk1 phosphorylation.
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Multiubiquitinated Emi1 is degraded by the 26S proteasome.
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Emi1 destruction in early mitosis requires the SCF beta-TrCP ubiquitin ligase complex. Binding of beta-TrCP to Emi1 occurs in late prophase and requires phosphorylation at the DSGxxS consensus motif as well as Cdk mediated phosphorylation. A two-step mechanism has been proposed in which the phosphorylation of Emi1 by Cdc2 occurs after the G2-M transition followed soon after by binding of beta-TrCP to the DSGxxS phosphorylation sites. Emi1 is then poly-ubiquitinated and degraded by the 26S proteasome.
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Following its association with SCF-ÃÂ²TrCP, phospho-Emi1 is poly-ubiquitinated.
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ATP bound to the origin recognition complex is important for preRC formation.
Addition of a third mannose to the N-glycan precursor by Alg2
A third mannose is added to the N-glycan precursor skeleton by alg2 using its alpha1,6-mannosyltransferase activity. This has been demonstrated in yeast (O'Reilly MK et al, 2006; Kämpf M et al, 2009).
Flipping of the N-glycan precursor into the ER lumen
The precursor of the N-glycan sugar, now in the form of (GlcNAc)2 (Man)5 (PP-Dol), is flipped through the ER membrane, moving it from the cytosolic side into the ER lumen. The exact mechanism of this translocation is not well understood but the protein RFT1 is known to be involved (Helenius J et al, 2002), along with an unknown flippase.
Addition of a third glucose to the N-glycan skeleton by Alg10
The last glucose is added to the N-glycan precursor. This reaction occurs inside the ER lumen and uses Dol-P-Glc as the glucose donor. In yeast, this reaction is catalyzed by ALG10 (Burda P and Aebi M,1998).
Characterization of Mmp37p, a Saccharomyces cerevisiae mitochondrial matrix protein with a role in mitochondrial protein import
Sculpting and pinching-off of Golgi vessicle
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Characterization of protein kinase C beta isoform's action on retinoblastoma protein phosphorylation, vascular endothelial growth factor-induced endothelial cell proliferation, and retinal neovascularization
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Neural recognition molecules of the immunoglobulin superfamily: signaling transducers of axon guidance and neuronal migration
Mitochondrial import receptor subunit TOM7
Mitochondrial import receptor subunit TOM70
Mitochondrial import receptor subunit TOM20
Mitochondrial import receptor subunit TOM6
Mitochondrial import receptor subunit TOM22
Mitochondrial import receptor subunit TOM5
A newly identified essential complex, Dre2-Tah18, controls mitochondria integrity and cell death after oxidative stress in yeast
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CDO/Cdon (cell-adhesion-molecule-related/downregulated by oncogenes) is a type I transmembrane multifunctional co-receptor consisting of five immunoglobulin and three fibronectin type III (FNIII) repeats in the extracellular domain, and an intracellular domain with no identifiable motifs. It has been implicated in enhancing muscle differentiation in promyogenic cells. CDO exert its promyogenic effects as a component of multiprotein complexes that include the closely related factor Boc, the Ig superfamily receptor neogenin and its ligand netrin-3, and the adhesion molecules N- and M-cadherin. CDO modulates the Cdc42 and p38 mitogen-activated protein kinase (MAPK) pathways via a direct association with two scaffold-type proteins, JLP and Bnip-2, to regulate activities of myogenic bHLH factors and myogenic differentiation. CDO activates myogenic bHLH factors via enhanced heterodimer formation, most likely by inducing hyper-phosphorylation of E proteins. Myogenic basic helix-loop-helix (bHLH) proteins are master regulatory proteins that activate the transcription of many muscle-specific genes during myogenesis. These myogenic bHLH proteins also referred to as MyoD family includes four members, MyoD, myogenin, myf5 and MRF4. These myogenic factors dimerize with E-proteins such as E12/E47, ITF-2 and HEB to form heterodimeric complexes that bind to a conserved DNA sequence known as the E box, which is present in the promoters and enhancers of most muscle-specific genes. Myocyte enhancer binding factor 2 (MEF2), which is a member of the MADS box family, also plays an important role in muscle differentiation. MEF2 activates transcription by binding to the consensus sequence, called the MEF2-binding site, which is also found in the control regions of numerous muscle-specific genes. MEF2 and myogenic bHLH proteins synergistically activate expression of muscle-specific genes via protein-protein interactions between DNA-binding domains of these heterologous classes of transcription factors. Members of the MyoD and MEF2 family of transcription factors associate combinatorially to control myoblast specification, differentiation and proliferation.
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The family of transcription factors myocyte enhancer factor-2 (MEF2) regulate myogenesis through combinatorial interactions with other transcription factors to the MEF2 site found in the promoter regions of numerous muscle specific genes. There are four members of the MEF2 family, MEF2A to D. p38 MAPK plays a role in the regulation of the MEF2 family members and this is mediated by the phosphorylation of two or three (Thr312 and 319 in MEF2A and Thr 293, 300 and ser387 in MEF2C) amino acids in the C-terminal activation domain of MEF2 factors. MEF2A and MEF2C are preferred substrates for p38 compared with MEF2B and MEF2D. The phosphorylation of MEF2 members results in their increased transcriptional activity.
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The glucokinase (GCK) gene is transcribed and its mRNA is translated. GCK transcription is positively regulated by the activity of the NEUROD1 and PDX1 transcription factors. These events and interactions are inferred from corresponding ones studied in molecular detail in the mouse.
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Cloning and characterisation of hAps1 and hAps2, human diadenosine polyphosphate-metabolising Nudix hydrolases
Myogenesis, the formation of muscle tissue, is a complex process involving steps of cell proliferation mediated by growth factor signaling, cell differentiation, reorganization of cells to form myotubes, and cell fusion. Here, one regulatory feature of this process has been annotated, the signaling cascade initiated by CDO (cell-adhesion-molecule-related/downregulated by oncogenes) and associated co-receptors.
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The GLUT2 gene is transcribed, its mRNA is translated, and the protein product is localized to the plasma membrane. GLUT2 expression is positively regulated by HNF1A. In vivo, pancreatic GLUT2 expression is positively regulated by HNF1A. Mutations in HNF1A are associated with a form of MODY (maturity onset diabetes of the young) (Fanjans et al. 2001) and interactions between the HNF1A protein product and the GLUT2 promoter have been demomstrated in vitro (Ban et al. 2002). However, the molecular details of GLUT2 expression in intact pancreatic beta cells have not been studied in humans, but are inferred from corresponding ones worked out in the mouse.
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Proteins Imported to the Matrix by TIM23 PAM Complex
The MAP kinase cascade describes a sequence of phosphorylation events involving serine/threonine-specific protein kinases. Used by various signal transduction pathways, this cascade constitutes a common 'module' in the transmission of an extracellular signal into the nucleus.
Frataxin homolog, mitochondrial component recommendedName: Frataxin homolog intermediate form /component
Besides adhesive roles in cell cell interaction, L1 functions as a signal transducing receptor providing neurons with cues from their environment for axonal growth and guidance. L1 associates with beta1 integrins on the cell surface to induce a signaling pathway involving sequential activation of pp60csrc, Vav2 -GEF, Rac1, PAK1, MEK and ERK1/2. L1 stimulates cell migration and neurite outgrowth through the MAP kinases ERK1/2. CHL1 also associates with integrins and activates a MAPK signaling pathway via pp60c-src, MEK and ERK1/2. L1 also binds the Sema3A receptor neuropilin1 and acts as an obligate coreceptor to mediate Sema3A induced growth cone collapse and axon repulsion. This repulsion can be converted to attraction by homophilic binding of L1 on an apposing cell in trans with L1 complexed with Neuropilin1 (NP1) in the responding neuron. L1 also interacts with FGF receptor and activates PLC gamma and DAG, resulting in the production of arachidonic acid and subsequent opening of voltage-gated channels.
The neural cell adhesion molecule, NCAM, is a member of the immunoglobulin (Ig) superfamily and is involved in a variety of cellular processes of importance for the formation and maintenance of the nervous system. The role of NCAM in neural differentiation and synaptic plasticity is presumed to depend on the modulation of intracellular signal transduction cascades. NCAM based signaling complexes can initiate downstream intracellular signals by at least two mechanisms: (1) activation of FGFR and (2) formation of intracellular signaling complexes by direct interaction with cytoplasmic interaction partners such as Fyn and FAK. Tyrosine kinases Fyn and FAK interact with NCAM and undergo phosphorylation and this transiently activates the MAPK, ERK 1 and 2, cAMP response element binding protein (CREB) and transcription factors ELK and NFkB. CREB activates transcription of genes which are important for axonal growth, survival, and synaptic plasticity in neurons. NCAM1 mediated intracellular signal transduction is represented in the figure below. The Ig domains in NCAM1 are represented in orange ovals and Fn domains in green squares. The tyrosine residues susceptible to phosphorylation are represented in red circles and their positions are numbered. Phosphorylation is represented by red arrows and dephosphorylation by yellow. Ig, Immunoglobulin domain; Fn, Fibronectin domain; Fyn, Proto-oncogene tyrosine-protein kinase Fyn; FAK, focal adhesion kinase; RPTPalpha, Receptor-type tyrosine-protein phosphatase; Grb2, Growth factor receptor-bound protein 2; SOS, Son of sevenless homolog; Raf, RAF proto-oncogene serine/threonine-protein kinase; MEK, MAPK and ERK kinase; ERK, Extracellular signal-regulated kinase; MSK1, Mitogen and stress activated protein kinase 1; CREB, Cyclic AMP-responsive element-binding protein; CRE, cAMP response elements.
Axon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, which senses the guidance cues in the environment through guidance cue receptors and responds by undergoing cytoskeletal changes that determine the direction of axon growth. Guidance cues present in the surrounding environment provide the necessary directional information for the trip. These extrinsic cues have been divided into attractive or repulsive signals that tell the growth cone where and where not to grow. Genetic and biochemical studies have led to the identification of highly conserved families of guidance molecules and their receptors that guide axons. These include netrins, Slits, semaphorins, and ephrins, and their cognate receptors, DCC and or uncoordinated-5 (UNC5), roundabouts (Robo), neuropilin and Eph. In addition, many other classes of adhesion molecules are also used by growth cones to navigate properly which include NCAM and L1CAM.
The L1 family of cell adhesion molecules (L1CAMs) are a subfamily of the immunoglobulin superfamily of transmembrane receptors, comprised of four structurally related proteins: L1, Close Homolog of L1 (CHL1), NrCAM, and Neurofascin. These CAMs contain six Ig like domains, five or six fibronectin like repeats, a transmembrane region and a cytoplasmic domain. The L1CAM family has been implicated in processes integral to nervous system development, including neurite outgrowth, neurite fasciculation and inter neuronal adhesion. L1CAM members are predominately expressed by neuronal, as well as some nonneuronal cells, during development. Except CHL1 all the other members of L1 family contain an alternatively spliced 12-nclueotide exon, encoding the amino acid residues RSLE in the neuronal splice forms but missing in the non-neuronal cells. The extracellular regions of L1CAM members are divergent and differ in their abilities to interact with extracellular, heterophilic ligands. The L1 ligands include other Ig-domain CAMs (such as NCAM, TAG-1/axonin and F11), proteoglycans type molecules (neurocan), beta1 integrins, and extra cellular matrix protein laminin, Neuropilin-1, FGF and EGF receptors. Some of these L1-interacting proteins also bind to other L1CAM members. For example TAG-1/axonin interact with L1 and NrCAM; L1, neurofascin and CHL1 binds to contactin family members. The cytoplasmic domains of L1CAM members are most highly conserved. Nevertheless, they have different cytoplasmic binding partners, and even those with similar binding partners may be involved in different signaling complexes and mechanisms. The most conserved feature of L1CAMs is their ability to interact with the actin cytoskeletal adapter protein ankyrin. The cytoplasmic ankyrin-binding domain, exhibits the highest degree of amino acid conservation throughout the L1 family.
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Activation of ErbB4 by the bifunctional epidermal growth factor family hormone epiregulin is regulated by ErbB2
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PKC theta is a member of the Ca++ independent and DAG dependent, novel PKC subfamily expressed mainly in T cells. It contains, N-term C2 like domain, a pseudosubstrate (PS), DAG binding (C1) domain and a C-term kinase domain. The PS sequence resembles an ideal substrate with the exception that it contains an alanine residue instead of a substrate serine residue, is bound to the kinase domain in the resting state. As a result, PKC theta is maintained in a closed inactive state, which is inaccessible to cellular substrates.
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PI3K activation results in recruitment of the serine/threonine kinase PDK1, (3-phosphoinositide-dependent kinase 1) to the plasma membrane where PDK1 subsequently phosphorylates and activates AKT. PDK1 with its PH domain binds to either PIP3 or PIP2 and is translocated to the plasma membrane. PDK1 seems to exist in an active, phosphorylated configuration under basal conditions (Vanhaesebroeck & Alessi 2000).
As a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are aspects of the roles of cell adhesion molecules in axonal guidance and myogenesis, of transcriptional regulation in hematopoiesis (specifically, B lymphopoiesis), pancreatic beta cell and white adipocyte differentiation, and molecular events of "nodal" signaling.
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Interaction between citrate synthase and malate dehydrogenase. Substrate channeling of oxaloacetate
The architecture of the human Rad54-DNA complex provides evidence for protein translocation along DNA.
Adipogenesis is the process of cell differentiation by which preadipocytes become adipocytes. During this process the preadipocytes cease to proliferate, begin to accumulate lipid droplets and develop morphologic and biochemical characteristics of mature adipocytes such as hormone responsive lipogenenic and lipolytic programs. The most intensively studied model system for adipogenesis is differentiation of the mouse 3T3-L1 preadipocyte cell line by an induction cocktail of containing mitogens (insulin/IGF1), glucocorticoid (dexamethasone), an inducer of cAMP (IBMX), and fetal serum (Cao et al. 1991, reviewed in Farmer 2006). More recently additional cellular models have become available to study adipogenesis that involve almost all stages of development (reviewed in Rosen and MacDougald 2006). In vivo knockout mice lacking putative adipogenic factors have also been extensively studied. Human pathways are traditionally inferred from those discovered in mouse but are now beginning to be validated in cellular models derived from human adipose progenitors (Fischer-Posovszky et al. 2008, Wdziekonski et al. 2011). Adipogenesis is controlled by a cascade of transcription factors (Yeh et al. 1995, reviewed in Farmer 2006, Gesta et al. 2007). One of the first observable events during adipocyte differentiation is a transient increase in expression of the CEBPB (CCAAT/Enhancer Binding Protein Beta, C/EBPB) and CEBPD (C/EBPD) transcription factors (Cao et al. 1991, reviewed in Lane et al. 1999). This occurs prior to the accumulation of lipid droplets. However, it is the subsequent inductions of CEBPA and PPARG that are critical for morphological, biochemical and functional adipocytes. Ectopic expression of CEBPB alone is capable of inducing substantial adipocyte differentiation in fibroblasts while CEBPD has a minimal effect. CEBPB is upregulated in response to intracellular cAMP (possibly via pCREB) and serum mitogens (possibly via Krox20). CEBPD is upregulated in response to glucocorticoids. The exact mechanisms that upregulate the CEBPs are not fully known. CEBPB and CEBPD act directly on the Peroxisome Proliferator-activated Receptor Gamma (PPARG) gene by binding its promoter and activating transcription. CEBPB and CEBPD also directly activate the EBF1 gene (and possibly other EBFs) and KLF5 (Jimenez et al. 2007, Oishi 2005). The EBF1 and KLF5 proteins, in turn bind, and activate the PPARG promoter. Other hormones, such as insulin, affect PPARG expression and other transcription factors, such as ADD1/SREBP1c, bind the PPARG promoter. This is an area of ongoing research. During adipogenesis the PPARG gene is transcribed to yield 2 variants. The adipogenic variant 2 mRNA encodes 30 additional amino acids at the N-terminus compared to the widely expressed variant 1 mRNA. PPARG encodes a type II nuclear hormone receptor (remains in the nucleus in the absence of ligand) that forms a heterodimer with the Retinoid X Receptor Alpha (RXRA). The heterodimer was initially identified as a complex regulating the aP2/FABP4 gene and named ARF6 (Tontonoz et al. 1994). The PPARG:RXRA heterodimer binds a recognition sequence that consists of two hexanucleotide motifs (DR1 motifs) separated by 1 nucleotide. Binding occurs even in the absence of ligands, such as fatty acids, that activate PPARG. In the absence of activating ligands, the PPARG:RXRA complex recruits repressors of transcription such as SMRT/NCoR2, NCoR1, and HDAC3 (Tontonoz and Spiegelman 2008). Each molecule of PPARG can bind 2 molecules of activating ligands. Although, the identity of the endogenous ligands of PPARG is unknown, exogenous activators include fatty acids and the thiazolidinedione class of antidiabetic drugs (reviewed in Berger et al. 2005, Heikkinen et al. 2007, Lemberger et al. 1996). The most potent activators of PPARG in vitro are oxidized derivatives of unsaturated fatty acids.. Upon binding activating ligands PPARG causes a rearrangement of adjacent factors: Corepressors such as SMRT/NCoR2 are lost and coactivators such as TIF2, PRIP, CBP, and p300 are recruited (Tontonoz and Spiegelman). PPARG also binds directly to the TRAP220 subunit of the TRAP/Mediator complex that recruits RNA polymerase II. Thus binding of activating ligand by PPARG causes transcription of PPARG target genes. Targets of PPARG include genes involved in differentiation (PGAR/HFARP, Perilipin, aP2/FABP4, CEBPA), fatty acid transport (LPL, FAT/CD36), carbohydrate metabolism (PEPCK-C, AQP7, GK, GLUT4 (SLC2A4)), and energy homeostasis (LEPTIN and ADIPONECTIN) (Perera et al. 2006). Within 10 days of differentiation CEBPB and CEBPD are no longer located at the PPARG promoter. Instead CEBPA is present. EBF1 and PPARG bind the CEBPA promoter and activate transcription of CEBPA, one of the key transcription factors in adipogenesis. A current hypothesis posits a self-reinforcing loop that maintains PPARG expression and the differentiated state: PPARG activates CEBPA and CEBPA activates PPARG. Additionally EBF1 (and possibly other EBFs) activates CEBPA, CEBPA activates EBF1, and EBF1 activates PPARG.
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Mitochondrial-processing peptidase subunit beta
The PKLR gene is transcribed, its mRNA is translated, spliced, and translated to yield the L isoform of PKLR protein. PKLR expression is positively regulated by HNF1A. Mutations in HNF1A are associated with a form of MODY (maturity onset diabetes of the young) (Fanjans et al. 2001) but the molecular details of PKLR expression in intact pancreatic beta cells have not been studied in humans, and are inferred from corresponding ones worked out in the mouse.
D-lactate dehydrogenase (cytochrome) 1, mitochondrial
At the end of this reaction, 1 molecule of 'pyruvate kinase, liver and RBC' is present. This reaction takes place in the 'nucleus'.
The GLUT4 (SLC2A4) gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
Increased expression of KLF5 occurs after activation of the transcription factors CEBPB and CEBPD during differentiation and activation of KLF5 depends on CEBPB and CEBPD. Both CEBPB and CEBPD bind the promoter of the KLF5 gene upstream of the site of transcription initiation and activate transcription of KLF5.
The normal development of the pancreas during gestation has been intensively investigated over the past decade especially in the mouse (Servitja and Ferrer 2004; Chakrabarti and Mirmira 2003). Studies of genetic defects associated with maturity onset diabetes of the young (MODY) has provided direct insight into these processes as they take place in humans (Fajans et al. 2001). During embryogenesis, committed epithelial cells from the early pancreatic buds differentiate into mature endocrine and exocrine cells. It is helpful to schematize this process into four consecutive cellular stages, to begin to describe the complex interplay of signal transduction pathways and transcriptional networks. The annotations here are by no means complete - factors in addition to the ones described here must be active, and even for the ones that are described, only key examples of their regulatory effects and interactions have been annotated. It is also important to realize that in the human, unlike the mouse, cells of the different stages can be present simultaneously in the developing pancreas and the linear representation of these developmental events shown here is an over-simplification of the actual developmental process (e.g., Sarkar et al. 2008). The first stage of this process involves the predifferentiated epithelial cells of the two pancreatic anlagen that arise from the definitive endoderm at approximately somite stages 11-15 and undergo budding from somite stages 20-22. This period corresponds to gestational days 8.75-9.5 in the mouse, and 26 in the human. Pancreatic buds subsequently coalesce to form a single primitive gland, while concomitantly a ductal tree lined by highly proliferative epithelial cells is formed. A subset of such epithelial cells is thought to differentiate into either endocrine or acinar exocrine cells. A third cellular stage is defined by the endocrine-committed progenitors that selectively express the basic helix-loop-helix transcription factor NEUROG3. NEUROG3 is known to activate a complex transcriptional network that is essential for the specification of endocrine cells. Many transcription factors that are activated by NEUROG3 are also involved in islet-subtype cellular specification and in subsequent stages of differentiation of endocrine cells. This transient cellular stage thus leads to the generation of all known pancreatic endocrine cells, including insulin-producing beta-cells, and glucagon-producing alpha cells, the final stage of this schematic developmental process. The diagram below summarizes interactions that take place between transcription factors and transcription factor target genes during these cellular stages, and shows cases where there is both functional evidence that a transcription factor is required for the target gene to be expressed, and biochemical evidence that this interaction is direct. We also describe instances where a signaling pathway is known to regulate a transcription factor gene in this process, even if the intervening signaling pathway is not fully understood.
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Two transcription factors, PDX1 and HNF1A, play key roles in maintaining the gene expression pattern characteristic of mature beta cells in the endocrine pancreas. Targets of these regulatory molecules include genes encoding insulin, the GLUT2 glucose transporter, the liver- (and pancreas) specific form of pyruvate kinase and other transcription factors including HNF4A, HNF4G, and FOXA3. PDX1 expression in turn is controlled by the activities of MAFA, FOXA2, and PAX6, and negatively regulated via AKT (Chakrabarti and Mirmira 2003; Servitja and Ferrer 2004).
Precursors Imported to the Matrix by TIM23 PAM Complex
Mutations of phosphorylation sites in lamin A that prevent nuclear lamina disassembly in mitosis
Mitochondrial-processing peptidase subunit alpha
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Anion exchanger 1 in human kidney and oncocytoma differs from erythroid AE1 in its NH2 terminus
Telomeres are protein-DNA complexes at the ends of linear chromosomes that are important for genome stability. Telomeric DNA in humans, as in many eukaryotic organisms, consists of tandem repeats (Blackburn and Gall 1978; Moyzis et al. 1988; Meyne et al. 1989). The repeats at human telomeres are composed of TTAGGG sequences and stretch for several kilobase pairs. Another feature of telomeric DNA in many eukaryotes is a G-rich 3' single strand overhang, which in humans is estimated to be approximately 50-300 bases long (Makarov et al. 1997; Wright et al. 1997; Huffman et al. 2000). Telomeric DNA isolated from humans and several other organisms can form a lasso-type structure called a t-loop in which the 3' single-strand end is presumed to invade the double stranded telomeric DNA repeat tract (Griffith et al. 1999). Telomeric DNA is bound by multiple protein factors that play important roles in regulating telomere length and in protecting the chromosome end from recombination, non-homologous end-joining, DNA damage signaling, and unregulated nucleolytic attack (reviewed in de Lange 2005). DNA attrition can occur at telomeres, which can impact cell viability. Attrition can occur owing to the "end-replication problem", a consequence of the mechanism of lagging-strand synthesis (Watson 1972; Olovnikov 1973). Besides incomplete replication, nucleolytic processing also likely contributes to telomere attrition (Huffman et al. 2000). If telomeres become critically shortened, replicative senescence can result (Harley et al. 1990). Thus, in order to undergo multiple divisions, cells need a mechanism to replenish the sequence at their chromosome ends. The primary means for maintaining the sequence at chromosome ends in many eukaryotic organisms, including humans, is based on telomerase (Greider and Blackburn, 1985; Morin 1989). Telomerase is a ribonucleoprotein complex minimally composed of a conserved protein subunit containing a reverse transcriptase domain (telomerase reverse transcriptase, TERT) (Lingner et al. 1997; Nakamura et al. 1997) and a template-containing RNA (telomerase RNA component, TERC, TR, TER) (Greider and Blackburn, 1987; Feng et al 1995). Telomerase uses the RNA template to direct addition of multiple tandem repeats to the 3' G-rich single strand overhang. Besides extension by telomerase, maintenance of telomeric DNA involves additional activities, including C-strand synthesis, which fills in the opposing strand, and nucleolytic processing, which likely contributes to the generation of the 3' overhang.
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Telomerase acts as reverse transcriptase in the elongation of telomeres (Smogorzewska and de Lange 2004).
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Chromosome maintenance is critical for stable chromosome function in mammalian and other eukaryotic cells. Aspects of telomere maintenance and nucleosome assembly are covered here.
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Replication factor C is proposed to dissociate from PCNA following sliding clamp formation, and the DNA toroid alone tethers pol delta to the DNA.
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The binding of the primer recognition complex involves the loading of proliferating cell nuclear antigen (PCNA). Replication Factor C transiently opens the PCNA toroid in an ATP-dependent reaction, and then allows PCNA to re-close around the double helix adjacent to the primer terminus. This leads to the formation of the "sliding clamp".
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Due to the antiparallel nature of DNA, DNA polymerization is unidirectional, and one strand is synthesized discontinuously. This strand is called the lagging strand. Although the polymerase switching on the lagging strand is very similar to that on the leading strand, the processive synthesis on the two strands proceeds quite differently. Short DNA fragments, about 100 bases long, called Okazaki fragments are synthesized on the RNA-DNA primers first. Strand-displacement synthesis occurs, whereby the primer-containing 5'-terminus of the adjacent Okazaki fragment is folded into a single-stranded flap structure. This flap structure is removed by endonucleases, and the adjacent Okazaki fragments are joined by DNA ligase.
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After the primers are synthesized on the G-Rich strand, Replication Factor C binds to the 3'-end of the initiator DNA to trigger polymerase switching. The non-processive nature of pol alpha catalytic activity and the tight binding of Replication Factor C to the primer-template junction presumably lead to the turnover of the pol alpha:primase complex. After the Pol alpha-primase primase complex is displaced from the primer, the proliferating cell nuclear antigen (PCNA) binds to form a "sliding clamp" structure. Replication Factor C then dissociates, and DNA polymerase delta binds and catalyzes the processive synthesis of DNA.
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TC II deficiency: avoidance of false-negative molecular genetics by RNA-based investigations
Once the RNA-DNA primer is synthesized, replication factor C (RFC) initiates a reaction called "polymerase switching"; pol delta, the processive enzyme replaces pol alpha, the priming enzyme. RFC binds to the 3'-end of the RNA-DNA primer on the Primosome, to displace the pol alpha primase complex. The binding of RFC triggers the binding of the primer recognition complex.
DNA polymerases are not capable of de novo DNA synthesis and require synthesis of a primer, usually by a DNA-dependent RNA polymerase (primase) to begin DNA synthesis. In eukaryotic cells, the primer is synthesized by DNA polymerase alpha:primase. First, the DNA primase portion of this complex synthesizes approximately 6-10 nucleotides of RNA primer and then the DNA polymerase portion synthesizes an additional 20 nucleotides of DNA. There have been reports that TRF1 inhibits this activity at telomeres, though the mechanism and physiological relevance of this inhibition remain to be elucidated.
Cytochrome c oxidase polypeptide 5A, mitochondrial
Proteins Imported to the Inner Membrane by TIM23 SORT Complex
Para-hydroxybenzoate--polyprenyltransferase, mitochondrial
Cytochrome c oxidase subunit 4, mitochondrial
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Post-transcriptional splicing of introns is affected neither by the elongating properties of RNA polymerase II, nor by the binding of splicing regulatory factors to the enzyme. It is only affected by the relative abundance of constitutive and/or regulatory splicing factors at the sites where splicing takes place. Nevertheless it is important to point out that cytological evidence indicates that unspliced or partially spliced pre-mRNAs do not diffuse in the nucleoplasm far from the transcription sites. Therefore, recruitment of splicing factors to transcription sites would still favor the post-transcriptional splicing of introns.
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Co-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per gene, which cannot serve as splicing substrates until both 5' and 3' ends of each intron are synthesized. Thus the time that it takes for pol II to synthesize each intron defines a minimal time and distance along the gene in which splicing factors can be recruited. The time that it takes for pol II to reach the end of the gene defines the maximal time in which splicing could occur co-transcriptionally. Thus, the kinetics of transcription can affect the kinetics of splicing. There are two classes of intronless pre-mRNAs (mRNAs expressed from genes that lack introns). The first class encodes the replication dependent histone mRNAs. These mRNAs have unique 3' ends that do not have a polyA tail. The replication dependent histone mRNAs in all metazoans, as well as Chlamydomonas and Volvox fall into this class. The second class of mRNAs end in polyA tails, which are formed by a mechanism similar to that which poly-adenylate pre-mRNAs containing introns. In the intronless genes there is a different method of replacing the 3' splice site that activates polyadenylation.
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The 3' ends of eukaryotic mRNAs are generated by posttranscriptional processing of an extended primary transcript. For almost all RNAs, 3' processing consists of two steps: The mRNA is first cleaved at a particular phosphodiester bond downstream of the coding sequence. The upstream fragment then receives a poly(A) tail of approximately 250 adenylate residues whereas the downstream fragment is degraded. The two partial reactions are coupled so that reaction intermediates are usually undetectable. While 3' processing can be studied as an isolated event in vitro, it appears to be connected to transcription, splicing and transcription termination in vivo.
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Poly(A) polymerase has no specificity for any particular RNA sequence, as well as a very low affinity for the RNA. Under physiological conditions, the activity of poly(A) polymerase depends on two auxiliary factors, both of which bind to specific RNA sequences and recruit the poly(A) polymerase by a direct contact. One of these proteins is the heterotetrameric CPSF, which binds the AAUAAA sequence and is also essential for 3' cleavage.
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At the center of the mammalian circadian clock is a negative transcription/translation-based feedback loop: The BMAL1:CLOCK/NPAS2 (ARNTL:CLOCK/NPAS2) heterodimer transactivates CRY and PER genes by binding E-box elements in their promoters; the CRY and PER proteins then inhibit transactivation by BMAL1:CLOCK/NPAS2. BMAL1:CLOCK/NPAS2 activates transcription of CRY, PER, and several other genes in the morning. Levels of PER and CRY proteins rise during the day and inhibit expression of CRY, PER, and other BMAL1:CLOCK/NPAS2-activated genes in the afternoon and evening. During the night CRY and PER proteins are targeted for degradation by phosphorylation and polyubiquitination, allowing the cycle to commence again in the morning. Transcription of the BMAL1 (ARNTL) gene is controlled by ROR-alpha and REV-ERBA (NR1D1), both of which are targets of BMAL1:CLOCK/NPAS2 in mice and both of which compete for the same element (RORE) in the BMAL1 promoter. ROR-alpha (RORA) activates transcription of BMAL1; REV-ERBA represses transcription of BMAL1. This mutual control forms a secondary, reinforcing loop of the circadian clock. REV-ERBA shows strong circadian rhythmicity and confers circadian expression on BMAL1. BMAL1 can form heterodimers with either CLOCK or NPAS2, which act redundantly but show different tissue specificity. The BMAL1:CLOCK and BMAL1:NPAS2 heterodimers activate a set of genes that possess E-box elements (consensus CACGTG) in their promoters. This confers circadian expression on the genes. The PER genes (PER1, PER2, PER3) and CRY genes (CRY1, CRY2) are among those activated by BMAL1:CLOCK and BMAL1:NPAS2. PER and CRY mRNA accumulates during the morning and the proteins accumulate during the afternoon. PER and CRY proteins form complexes in the cytosol and these are bound by either CSNK1D or CSNK1E kinases which phosphorylate PER and CRY. The phosphorylated PER:CRY:kinase complex is translocated into the nucleus due to the nuclear localization signal of PER and CRY. Within the nucleus the PER:CRY complexes bind BMAL1:CLOCK and BMAL1:NPAS2, inhibiting their transactivation activity and their phosphorylation. This reduces expression of the target genes of BMAL1:CLOCK and BMAL1:NPAS2 during the afternoon and evening. PER:CRY complexes also traffic out of the nucleus into the cytosol due to the nuclear export signal of PER. During the night PER:CRY complexes are polyubiquitinated and degraded, allowing the cycle to begin again. Phosphorylated PER is bound by Beta-TrCP1, a cytosolic F-box type component of some SCF E3 ubiquitin ligases. CRY is bound by FBXL3, a nucleoplasmic F-box type component of some SCF E3 ubiquitin ligases. Phosphorylation of CRY1 by Adenosine monophosphate-activated kinase (AMPK) enhances degradation of CRY1. PER and CRY are subsequently polyubiquitinated and proteolyzed by the 26S proteasome. The circadian clock is cell-autonomous and some, but not all cells of the body exhibit circadian rhythms in metabolism, cell division, and gene transcription. The suprachiasmatic nucleus (SCN) in the hypothalamus is the major clock in the body and receives its major input from light (via retinal neurons) and a minor input from nutrient intake. The SCN and other brain tissues determine waking and feeding cycles and influence the clocks in other tissues by hormone secretion and nervous stimulation. Independently of the SCN, other tissues such as liver receive inputs from signals from the brain and from nutrients.
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As inferred from mouse, BMAL1:CLOCK (ARNTL:CLOCK) and BMAL1:NPAS2 (ARNTL:NPAS2) heterodimers bind to sequence elements (E boxes) in the promoters of target genes and enhance transcription (Gekakis et al. 1998, reviewed in Munoz and Baler 2003).
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The CRYPTOCHROME-2 (CRY2) gene is transcribed to yield mRNA and the mRNA is translated to yield protein. As inferred from mouse, the CRY2 protein shows circadian rhythm in the suprachiasmatic nucleus (SCN) and in peripheral tissues. The mRNA shows circadian rhythm in muscle but not in the SCN. Expression is dependent on CLOCK.
The CRYPTOCHROME-1 (CRY1) gene is transcribed to yield mRNA and the mRNA is translated to yield protein. CRY1 mRNA and protein show circadian expression. The promoter of the CRY1 gene contains an E-box which is bound by the BMAL1:CLOCK (ARNTL:CLOCK) heterodimer (and probably also the BMAL1:NPAS2 heterodimer), which activates transcription of CRY1.
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Mitochondrial import inner membrane translocase subunit TIM50
Mitochondrial import inner membrane translocase subunit TIM44
Mitochondrial import inner membrane translocase subunit TIM21
Precursors Imported to the Inner Membrane by TIM23 SORT Complex
Biogenesis of Tim proteins of the mitochondrial carrier import pathway: differential targeting mechanisms and crossing over with the main import pathway
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Ribosomal protein S6 kinase beta-2 (RSK) activation is a highly conserved mitogenic response, and the activities of RSK are stimulated by multiple serine/threonine phosphorylations by different upstream kinases, one of which is AKT.
After translocation into the nucleus, AKT can phosphorylate a number of targets there such as CREB, forkhead transcription factors, SRK and NUR77.
PDPK1 (PDK1) possesses low affinity for PIP2, so small amounts of PDPK1 are always present at the membrane, in the absence of PI3K activity (Currie et al. 1999).
Signaling by AKT is one of the key outcomes of receptor tyrosine kinase (RTK) activation. AKT is activated by the cellular second messenger PIP3, a phospholipid that is generated by PI3K. In ustimulated cells, PI3K class IA enzymes reside in the cytosol as inactive heterodimers composed of p85 regulatory subunit and p110 catalytic subunit. In this complex, p85 stabilizes p110 while inhibiting its catalytic activity. Upon binding of extracellular ligands to RTKs, receptors dimerize and undergo autophosphorylation. The regulatory subunit of PI3K, p85, is recruited to phosphorylated cytosolic RTK domains either directly or indirectly, through adaptor proteins, leading to a conformational change in the PI3K IA heterodimer that relieves inhibition of the p110 catalytic subunit. Activated PI3K IA phosphorylates PIP2, converting it to PIP3; this reaction is negatively regulated by PTEN phosphatase. PIP3 recruits AKT to the plasma membrane, allowing TORC2 to phosphorylate a conserved serine residue of AKT. Phosphorylation of this serine induces a conformation change in AKT, exposing a conserved threonine residue that is then phosphorylated by PDPK1 (PDK1). Phosphorylation of both the threonine and the serine residue is required to fully activate AKT. The active AKT then dissociates from PIP3 and phosphorylates a number of cytosolic and nuclear proteins that play important roles in cell survival and metabolism. For a recent review of AKT signaling, please refer to Manning and Cantley, 2007.
Second messengers (calcium, diacylglycerol, inositol 1,4,5-trisphosphate, and phosphatidyinositol 3,4,5-trisphosphate) trigger signaling pathways: NF-kappaB is activated via protein kinase C beta, RAS via RasGRP proteins, NF-AT via calcineurin, and AKT via PDK1 (reviewed in Shinohara and Kurosaki 2009, Stone 2006).
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Mature B cells express IgM and IgD immunoglobulins which are complexed at the plasma membrane with Ig-alpha (CD79A, MB-1) and Ig-beta (CD79B, B29) to form the B cell receptor (BCR) (Fu et al. 1974, Fu et al. 1975, Kunkel et al. 1975, Van Noesel et al. 1992, Sanchez et al. 1993, reviewed in Brezski and Monroe 2008). Binding of antigen to the immunoglobulin activates phosphorylation of immunoreceptor tyrosine-based activation motifs (ITAMs) in the cytoplasmic tails of Ig-alpha and Ig-beta by Src family tyrosine kinases, including LYN, FYN, and BLK (Nel et al. 1984, Yamanashi et al. 1991, Flaswinkel and Reth 1994, Saouaf et al. 1994, Hata et al. 1994, Saouaf et al. 1995, reviewed in Gauld and Cambier 2004, reviewed in Harwood and Batista 2010). The protein kinase SYK binds the phosphorylated immunoreceptor tyrosine-activated motifs (ITAMs) on the cytoplasmic tails of Ig-alpha (CD79A, MB-1) and Ig-beta (CD79B, B29) (Wienands et al. 1995, Rowley et al. 1995, Tsang et al. 2008). The binding causes the activation and autophosphorylation of SYK (Law et al. 1994, Baldock et al. 2000, Irish et al. 2006, Tsang et al. 2008, reviewed in Bradshaw 2010). Activated SYK and other kinases phosphorylate BLNK (SLP-65), BCAP, and CD19 which serve as scaffolds for the assembly of large complexes, the signalosomes, by recruiting phosphoinositol 3-kinase (PI3K), phospholipase C gamma (predominantly PLC-gamma2 in B cells, Coggeshall et al. 1992), NCK, BAM32, BTK, VAV1, and SHC. The effectors are phosphorylated by SYK and other kinases. PLC-gamma associated with BLNK hydrolyzes phosphatidylinositol-4,5-bisphosphate to yield inositol-1,4,5-trisphosphate (IP3) and diacylglycerol (Carter et al. 1991, Kim et al. 2004). IP3 binds receptors on the endoplasmic reticulum and causes release of calcium ions from the ER into the cytosol. The depletion of calcium from the ER in turn activates STIM1 to interact with ORAI and TRPC1 channels in the plasma membrane, resulting in an influx of extracellular calcium ions (Muik et al. 2008, Luik et al. 2008, Park et al. 2009, Mori et al. 2002). PI3K associated with BCAP and CD19 phosphorylates phosphatidylinositol 4,5-bisphosphate to yield phosphatidyinositol 3,4,5-trisphosphate. Second messengers (calcium, diacylglycerol, inositol 1,4,5-trisphosphate, and phosphatidylinositol 3,4,5-trisphosphate) trigger signaling pathways: NF-kappaB is activated via protein kinase C beta, RAS is activated via RasGRP proteins, NF-AT is activated via calcineurin, and AKT (PKB) is activated via PDK1 (reviewed in Shinohara and Kurosaki 2009, Stone 2006).
The 26S proteasome complex consists of the 20S catalytic core particle which harbours the proteolytically active sites and the regulatory 19S particle which is responsible for substrate interaction. This process generates a vast number (perhaps hundreds) of different peptides, depending on the length and sequence of the substrate protein. Only a small fraction of these peptides (nearly 10%) form the exact length to be presented by class I MHC; most (approximately 70%) are too short to bind. The remaining proteasome products (10-20%) are N-terminally extended precursors that require additional cleavage by cytosolic aminopeptidases for presentation by MHC class I molecules.
Selectivity of docking sites in MAPK kinases
Some peptides generated by the 26S proteasome are too long to bind to MHC class I molecules. These N-terminal extended precursor peptides may be trimmed by cytosolic aminopeptidases, such as Tripeptidyl peptidase II (TPP2), puromycin-sensitive aminopeptidase (PSA), bleomycin hydrolase (BH), and leucine aminopeptidase (LAP).
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Intracellular foreign or aberrant host proteins are cleaved into peptide fragments of a precise size, such that they can be loaded on to class I MHC molecules and presented externally to cytotoxic T cells. The ubiquitin-26S proteasome system plays a central role in the generation of these class I MHC antigens. Ubiquitination is the mechanism of adding ubiquitin to lysine residues on substrate protein leading to the formation of a polyubiquitinated substrate. This process involves three classes of enzyme, an E1 ubiquitin-activating enzyme, an E2 ubiquitin-conjugating enzyme, and an E3 ubiquitin ligase. Polyubiquitination through lysine-48 (K48) generally targets the substrate protein for proteasomal destruction. The protease responsible for the degradation of K48-polyubiquitinated proteins is the 26S proteasome. This proteasome is a two subunit protein complex composed of the 20S (catalytic core) and 19S (regulatory) proteasome complexes. The proteasome eliminates most of the foreign and non-functional proteins from the cell by degrading them into short peptides; only a small fraction of the peptides generated are of the correct length to be presented by the MHC class I system. It has been calculated that between 994 and 3122 protein molecules have to be degraded for the formation of a single, stable MHC class I complex at the cell surface, with an average effciency of 1 in 2000 (Kloetzel et al. 2004, Princiotta et al. 2003).
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ERK6, a mitogen-activated protein kinase involved in C2C12 myoblast differentiation
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Presequence translocated-associated motor subunit PAM17, mitochondrial
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Mitochondrial import inner membrane translocase subunit TIM16
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Mitochondrial import inner membrane translocase subunit TIM14
Regulators of neurite outgrowth: role of cell adhesion molecules
Mitochondrial import inner membrane translocase subunit TIM12
Unlike other glycoproteins, correct folding of MHC class I molecules is not sufficient to trigger their exit from the ER, they exit only after peptide loading. Described here is the process of antigen presentation which consists of the folding, assembly, and peptide loading of MHC class I molecules. The newly synthesized MHC class I Heavy Chain (HC) is initially folded with the help of several chaperones (calnexin, BiP, ERp57) and then binds with Beta-2-microglobulin (B2M). This MHC:B2M heterodimer enters the peptide loading complex (PLC), a multiprotein complex that includes calreticulin, endoplasmic reticulum resident protein 57 (ERp57), transporter associated with antigen processing (TAP) and tapasin. Peptides generated from Ub-proteolysis are transported into the ER through TAP. These peptides are further trimmed by ER-associated aminopeptidase (ERAP) and loaded on to MHC class I molecules. Stable MHC class I trimers with high-affinity peptide are transported from the ER to the cell surface by the Golgi apparatus.
Ttransporter associated with antigen processing (TAP) is a heterodimeric complex, composed of TAP1 and TAP2 proteins, members of the ATP-binding cassette (ABC) superfamily. TAP consists of two transmembrane domains (TMDs) and two cytosolic nucleotide-binding domains. Peptide binding to the cytosolic-facing cavity formed by the TMDs causes it to undergo a conformational change that induces ATP hydrolysis, forcing the opening of a pore and translocation of the peptide into the ER lumen. TAP transports peptides in the range of 8-16 amino acids into the ER, which is the peptide length typically generated by the immunoproteasome.
The other TAP-dependent cross-presentation mechanism in phagocytes is the endoplasmic reticulum (ER)-phagosome model. Desjardins proposed that ER is recruited to the cell surface, where it fuses with the plasma membrane, underneath phagocytic cups, to supply membrane for the formation of nascent phagosomes (Gagnon et al. 2002). Three independent studies simultaneously showed that ER contributes to the vast majority of phagosome membrane (Guermonprez et al. 2003, Houde et al. 2003, Ackerman et al. 2003). The composition of early phagosome membrane contains ER-resident proteins, the components required for cross-presentation. This model is similar to the phagosome-to-cytosol model in that Ag is translocated to cytosol for proteasomal degradation, but differs in that antigenic peptides are translocated back into the phagosome (instead of ER) for peptide:MHC-I complexes. ER fusion with phagosome introduces molecules that are involved in Ag transport to cytosol (Sec61) and proteasome-generated peptides back into the phagosome (TAP) for loading onto MHC-I. Through extensive biochemical assays, fluorescent imaging and electron microscopy-based experiments, most of the evidence in favor of ER-phagocytosis has been challenged (Touret et al. 2005a/b). Using quantitative proteomics Roger and Foster have shown that the percentage of PM and ER membranes on phagosomes 10 min after internalization was approximately 10% and 0.2% (Rogers et al. 2007). They concluded that ER contributes only a small part of phagosomal membranes. Although the ER-phagosome pathway is controversial, the concept remains attractive as it explains how peptide-receptive MHC-I molecules could intersect with a relatively high concentration of exogenous antigens, presumably a crucial prerequisite for efficient cross-presentation (Basha et al. 2008).
Exogenous antigens are thought to be processed for cross-presentation in much the same manner as endogenous proteins once they enter the cytosolic pathway (Rock et al. 2010). Immunoproteasome components are the major proteases involved in generating the antigenic fragments. The precurssor peptides are further trimmed by cytosolic aminopeptidases and shuttled to ER through TAP for MHC class I loading.
Proteasomes are usually localized to the cytoplasm but are also present in the nucleus and ER. Houde et al. (2003) investigated the distribution of proteasomes in J774 macrophages and observed them on phagosomes. The proteasomes present on phagosomes may not come directly from ER, but instead assemble on phagosomes to play a function at a precise point during phagolysosomal biogenesis. Houde et al. also observed polyubiquitinated proteins on the cytoplasmic side of phagosomes and highlighted the link between the ubiquitination process and proteasomal degradation; translocated peptides are ubiquitinated and processed by the proteasome complex assembled on the cytoplasmic side of phagosomes, leading to the generation of MHC class I binding peptides.
After processing by the proteasome, some of the oligopeptides could be reinternalized to the phagosome lumen of the same phagosome through the TAP complex probably acquired during ER-phagosome fusion. Guermonprez et al. (2003) tested this model and observed abundant TAP complex in early phagosomes and its reduction over time. Electron microscopy analysis of purified phagosomes also showed the insertion of TAP2 into the phagosomal membrane.
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Major histocompatibility complex (MHC) class I molecules play an important role in cell mediated immunity by reporting on intracellular events such as viral infection, the presence of intracellular bacteria or tumor-associated antigens. They bind peptide fragments of these proteins and presenting them to CD8+ T cells at the cell surface. This enables cytotoxic T cells to identify and eliminate cells that are synthesizing abnormal or foreign proteins. MHC class I is a trimeric complex composed of a polymorphic heavy chain (HC or alpha chain) and an invariable light chain, known as beta2-microglobulin (B2M) plus an 8-10 residue peptide ligand. Represented here are the events in the biosynthesis of MHC class I molecules, including generation of antigenic peptides by the ubiquitin/26S-proteasome system, delivery of these peptides to the endoplasmic reticulum (ER), loading of peptides to MHC class I molecules and display of MHC class I complexes on the cell surface.
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Antigen processing and loading on to MHC class II molecules occurs in late endocytic/lysosomal vesicles, where epitopes which require extensive proteolytic processing are generated (Bryant & Ploegh 2003). These late endosome/lysosomal-like compartments are enriched in MHC II and are referred to as MIICs (MHC class II compartments) (Peters et al. 1991). A variety of lysosomal proteases like cathepsins S, D, B etc. and Asparaginyl endopeptidase (AEP) are suggested to be involved in the processing of antigens to generate CD4+ T cell epitopes (Deusing et al. 1998, Shi et al. 1999, Pluger et al. 2002, Watts et al. 2005). An initial cleavage by endopeptidases (AEP) would be necessary to unlock the antigen and allow further trimming of the ends by exopeptidases (Cathepsins). In the acidic environment of the lysosome, cathepsins are generally activated by autocatalytic cleavage of a propeptide which otherwise blocks the active site.
Exogenous soluble antigens are cross-presented by dendritic cells, albeit with lower efficiency than for particulate substrates. Soluble antigens destined for cross-presentation are taken up by distinct endocytosis mechanisms which route them into stable early endosomes and then to the cytoplasm for proteasomal degradation and peptide loading.
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MHC class I molecules generally present peptide antigens derived from proteins synthesized by the cell itself to CD8+ T cells. However, in some circumstances, antigens from extracellular environment can be presented on MHC class I to stimulate CD8+ T cell immunity, a process termed cross-presentation (Rock & Shen. 2005). Cross-presentation/cross-priming is the ability of antigen presenting cells (APCs) to present exogenous antigens on MHC class I molecules to CD8+ T lymphocytes. Among all the APCs, Dendritic cells (DC) are the dominant antigen cross presenting cell types in vivo, although macrophages and B cells appear to cross present model antigens in vitro with a low degree of efficiency (Amigorena & Savina. 2010, Ackermann & Peter Cresswell. 2004). Compared to macrophages, DCs have low levels of lysosomal proteases and exhibit limited lysosomal degradation (Delamarre et al. 2005). This limited proteolysis of internalized antigens by DCs might contribute to their high efficiency for cross presentation (Monua & Trombetta. 2007). APCs acquire the exogenous antigens through endocytic mechanisms, especially phagosomes for particulate/cell-associated antigens and endosomes for soluble protein antigens. There does not seem to be a unique pathway for cross-presentation but rather different potential mechanisms of cross-presentation have been proposed. These proposed pathways can be classified according to the location where two key events occur: 1) processing of the antigenic protein and 2) loading of the processed peptide on to MHC I molecule (Blanchard & Shastri. 2010). Based on the requirement for TAP and cytosolic proteases two mechanisms have been described, a cytosolic pathway (TAP-dependent and proteasome-dependent) or a vacuolar pathway (TAP- and proteasome-independent) (Blanchard & Shastri. 2010, Amigorena & Savina. 2010). Regarding peptide-loading, MHC I could be loaded in the ER or in the phagosome and recycled to cell surface (Blanchard & Shastri. 2010). Exogenous soluble antigens are cross-presented by dendritic cells, albeit with lower efficiency than for particulate substrates. Soluble antigens destined for cross-presentation are taken up by distinct endocytosis mechanisms which route them into stable early endosomes and then to the cytoplasm for proteasomal degradation and peptide loading. The outcome of the cross presentation can be either tolerance or immunity (Rock & Shen. 2005).
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Folding of A+U-rich RNA elements modulates AUF1 binding. Potential roles in regulation of mRNA turnover
Mitochondrial import inner membrane translocase subunit TIM18
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Proteins Inserted into Inner Membrane by TIM22 Complex
Sorting assembly machinery 35 kDa subunit
The TCR is a multisubunit complex that consists of clonotypic alpha/beta chains noncovalently associated with the invariant CD3 delta/epsilon/gamma and TCR zeta chains. T cell activation by antigen presenting cells (APCs) results in the activation of protein tyrosine kinases (PTKs) that associate with CD3 and TCR zeta subunits and the co-receptor CD4. Members of the Src kinases (Lck), Syk kinases (ZAP-70), Tec (Itk) and Csk families of nonreceptor PTKs play a crucial role in T cell activation. Activation of PTKs following TCR engagement results in the recruitment and tyrosine phosphorylation of enzymes such as phospholipase C gamma1 and Vav as well as critical adaptor proteins such as LAT, SLP-76 and Gads. These proximal activation leads to reorganization of the cytoskeleton as well as transcription activation of multiple genes leading to T lymphocyte proliferation, differentiation and/or effector function.
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The role of transient receptor potential cation channels in Ca2+ signaling
Cold Spring Harb Perspect Biol 2:a003962
PIP3 generated by PI3K recruits phosphatidylinositide-dependent protein kinase 1 (PDPK1 i.e. PDK1) to the membrane, through its PH (pleckstrin-homology) domain. PDPK1 binds PIP3 with high affinity, and also shows low affinity for PIP2 (Currie et al. 1999).
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PIP3 generated by PI3K recruits AKT (also known as protein kinase B) to the membrane, through its PH (pleckstrin-homology) domains. The binding of PIP3 to the PH domain of AKT is the rate-limiting step in AKT activation (Scheid et al. 2002). In mammals there are three AKT isoforms (AKT1-3) encoded by three separate genes. The three isoforms share a high degree of amino acid identity and have indistinguishable substrate specificity in vitro. However, isoform-preferred substrates in vivo cannot be ruled out. The relative expression of the three isoforms differs in different mammalian tissues: AKT1 is the predominant isoform in the majority of tissues, AKT2 is the predominant isoform in insulin-responsive tissues, and AKT3 is the predominant isoform in brain and testes. All 3 isoforms are expressed in human and mouse platelets (Yin et al. 2008; O'Brien et al. 2008). Note: all data in the pathway refer to AKT1, which is the most studied.
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Under conditions of growth and mitogen stimulation S473 phosphorylation of AKT is carried out by mTOR (mammalian Target of Rapamycin). This kinase is found in two structurally and functionally distinct protein complexes, named TOR complex 1 (TORC1) and TOR complex 2 (TORC2). It is TORC2 complex, which is composed of mTOR, RICTOR, SIN1 (also named MAPKAP1) and LST8, that phosphorylates AKT at S473 (Sarbassov et al., 2005). This complex also regulates actin cytoskeletal reorganization (Jacinto et al., 2004; Sarbassov et al., 2004). TORC1, on the other hand, is a major regulator of ribosomal biogenesis and protein synthesis (Hay and Sonenberg, 2004). TORC1 regulates these processes largely by the phosphorylation/inactivation of the repressors of mRNA translation 4E binding proteins (4E BPs) and by the phosphorylation/activation of ribosomal S6 kinase (S6K1). TORC1 is also the principal regulator of autophagy. In other physiological conditions, other kinases may be responsible for AKT S473 phosphorylation. Phosphorylation of AKT on S473 by TORC2 complex is a prerequisite for AKT phosphorylation on T308 by PDPK1 (Scheid et al. 2002, Sarabassov et al. 2005).
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DAG along with intracellular calcium signals cooperatively to activate PKCs, which then trigger other pathways such as the NF-kB pathway, ultimately leading to mast cell degranulation and cytokine production (Wu 2011). MCs express several Protein kinase C (PKC) isozymes and these kinases are involved in both the activation and termination of the degranulation process. PKC-delta is a negative regulator of FCERI mediated mast cell degranulation, whereas PKC-theta facilitates in degranulation (Leitges et al. 2002, Liu et al. 2001). In response to FCERI activation PKC-theta translocates to membrane by binding to DAG with its C1 domain. PKC-theta exists in two conformations closed/inactive and open/active state. In resting state, PKC-theta is autoinhibited where the pseudosubstrate sequence in the N-terminal regulatory region of PKC-theta forms intramolecular interaction with the substrate-binding region in the catalytic domain. This prevents the catalytic domain gaining access to substrates. The allosteric change of PKC-theta from closed to open state involves two important mechanisms: DAG binding to the C1 domains and autophosphorylation of T538 on the activation loop. Interaction with DAG induces conformational change resulting in the exposure of the activation loop of PKC-theta (Wang et al. 2012, Melowic et al. 2007).
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Raft localized PKC theta is further phosphorylated and activated by PDK1. The threonine residue (T538) in the kinase domain is the potential target of PDK1. Phosphorylation of this site is critical for the PKC theta kinase activity, and its ability to activate NF-kB pathway. PKC theta is later trans-autophopshorylated on putative phosphorylation sites (S676, S695) for the fine-tuning of its kinase activity.
Changes in gene expression are required for the T cell to gain full proliferative competence and to produce effector cytokines. Three transcription factors in particular have been found to play a key role in TCR-stimulated changes in gene expression, namely NF-kB, NFAT and AP-1. A key step in NF-kB activation is the stimulation and translocation of PKC theta. The critical element that effects PKC theta activation is PI3K. This enzyme complex translocates to the plasma membrane by interacting with phospho-tyrosines on CD28 via its two SH2 domains located in p85 subunit. The p110 subunit of PI3K phosphorylates the inositol ring of PIP2 to generate PIP3 (steps 17-18). PIP3 may also be dephosphorylated by the phosphatase SHIP to generate PI-3,4-P2. PIP3 and PI-3,4-P2 acts as binding sites to the PH domain of PKB/Akt and PDK1 (steps 19, 21 and 22). PKB is activated in response to PI3K stimulation by PDK1 (step 23). PDK1 has an essential role in regulating the activation of PKC theta and recruitment of CBM complex to the immune synapse. PKC theta is a member of novel class (DAG dependent, Ca++ independent) of PKC and the only member known to translocate to this synapse. Prior to TCR stimulation PKC theta exists in an inactive closed conformation. Upon release of DAG, it binds to PKC theta via the C1 domain and undergoes phosphorylation on tyrosine 90 by Lck to attain an open conformation. PKC theta is further phosphorylated by PDK1 on threonine 538. This step is critical for PKC activity (steps 24-26). CARMA1 translocates to the plasma membrane following the interaction of its SH3 domain with the 'PxxP' motif on PDK1. CARMA1 is phosphorylated by PKC-theta on residue S552, leading to the oligomerization of CARMA1. This complex acts as a scaffold, recruiting Bcl10 to the synapse by interacting with their CARD domains. Bcl10 undergoes phosphorylation mediated by the enzyme RIP2. Activated Bcl10 then mediates the ubiquitination of NEMO by recruiting MALT1 and TRAF6. MALT1 binds to Bcl10 with its Ig-like domains and undergoes oligomerization. TRAF6 binds to the oligomerized MALT1 and also undergoes oligomerization. Oligomerized TRAF6 acts as a ubiquitin-protein ligase, catalyzing auto-K63-linked polyubiquitination (steps 27-33). This K-63 ubiquitinated TRAF6 activates TAK1 kinase bound to TAB2 and also ubiquitinates NEMO/IKK-gamma in the IKK complex. TAK1 undergoes autophosphorylation on residues T184 and T187 and gets activated. Activated TAK1 kinase phosphorylates IKK-beta on residues S177 and S181 in the activation loop and activates the IKK kinase activity. IKK-beta phosphorylates the IkB-alpha bound to the NF-kB heterodimer, on residues S19 and S23 and directs IkB-beta to 26S proteasome degradation (step 34-38 & 40). The NF-kB heterodimer with a free NTS sequence finally migrates to the nucleus to regulate gene transcription (step 39).
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Homologous DNA pairing and strand exchange
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FUNCTION Copper chaperone for cytochrome c oxidase (COX). Binds two copper ions and deliver them to the Cu(A) site of COX.SIMILARITY Belongs to the COX17 family.
Once phosphorylated on serine residue S473, AKT bound to PIP3 forms a complex with PIP3-bound PDPK1 i.e. PDK1 (Scheid et al. 2002, Sarabassov et al. 2005)
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Once AKT is localized at the plasma membrane, it is phosphorylated at two critical residues for its full activation. These residues are a threonine (T308 in AKT1) in the activation loop within the catalytic domain, and a serine (S473 in AKT1), in a hydrophobic motif (HM) within the carboxy terminal, non-catalytic region. PDPK1 (PDK1) is the activation loop kinase; this kinase can also directly phosphorylate p70S6K. The HM kinase, previously termed PDK2, has been identified as the mammalian TOR (Target Of Rapamycin; Sarbassov et al., 2005) but several other kinases are also able to phosphorylate AKT at S473. Phosphorylation of AKT at S473 by TORC2 complex is a prerequisite for PDPK1-mediated phosphorylation of AKT threonine T308 (Scheid et al. 2002, Sarabassov et al. 2005).
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PI3Ks can be activated by a number of different receptors, including the TcR (T cell receptor), co-stimulatory receptors (CD28), cytokine receptors and chemokine receptors. However, the specific roles of PI3Ks downstream of these receptors vary. CD28 contains the YMNM consensus PI3K-binding motif, and PI3K recruitment by CD28 contributes to or complements TCR-dependent PI3K signaling. Activation of PI3K promotes PIP3 production at the plasma membrane and several potential target molecules for this phospholipid have been implicated in PI3K pathways downstream of the TcR and CD28. Of these targets, at least Vav and Akt have been implicated in CD28 costimulation of T cell activation. AKT/PKB connects PI3K to signaling pathways that promote cytokine transcription, survival, cell-cycle entry and growth.
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Human Protein kinase C beta (PKC-beta) is activated by calcium ions, diacylglycerol, and binds phosphatidylserine (Kochs et al. 1991). Experiments in mice have shown that knocking out PKC-beta causes severe defects in B cells, leading to the conclusion that PKC-beta is the predominant signaling PKC in these cells (Leitges et al. 1996, Su et al. 2002, Saijo et al. 2002).
DAG and calcium activate protein kinase C beta (PKC-beta, Kochs et al. 1991) which phosphorylates CARMA1 and other proteins (Sommer et al. 2005). Phosphorylated CARMA1 recruits BCL10 and MALT1 to form the CBM complex (Sommer et al. 2005, Tanner et al. 2007) which, in turn, recruits the kinase TAK1 and the IKK complex (Sommer et al. 2005, Shinohara et al. 2005 using chicken cells). TAK1 phosphorylates the IKK-beta subunit, activating it (Wang et al. 2001). The IKK complex then phosphorylates IkB complexed with NF-kappaB dimers in the cytosol (Zandi et al. 1998, Burke et al. 1999, Heilker et al. 1999), resulting in the degradation of IkB (Miyamoto et al. 1994, Traenckner et al. 1994, Alkalay et al. 1995, DiDonato et al. 1995, Li et al. 1995, Lin et al. 1995, Scherer et al. 1995, Chen et al. 1995). NF-kappaB dimers are thereby released and are translocated to the nucleus where they activate transcription (Baeuerle and Baltimore 1988, Blank et al. 1991, Ghosh et al. 2008, Fagerlund et al. 2008).
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CTLA4 is one of the best studied inhibitory receptors of the CD28 superfamily. CTLA4 inhibits Tcell activation by reducing IL2 production and IL2 expression, and by arresting T cells at the G1 phase of the cell cycle. CTLA-4 expressed by a T cell subpopulation exerts a dominant control on the proliferation of other T cells, which limits autoreactivity. CTLA4 also blocks CD28 signals by competing for the ligands B71 and B72 in the limited space between T cells and antigenpresenting cells. Though the mechanism is obscure, CTLA4 may also propagate inhibitory signals that actively counter those produced by CD28. CTLA4 can also function in a ligand-independent manner.? CTLA-4 regulates the activation of pathogenic T cells by directly modulating T cell receptor signaling (i.e. TCR-zeta chain phosphorylation) as well as downstream biochemical signals (i.e. ERK activation). The cytoplasmic region of CTLA4 contains a tyrosine motif YVKM and a proline rich region. After TCR stimulation, it undergoes tyrosine phosphorylation by src kinases, inducing surface retention.
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Optimal activation of T-lymphocytes requires at least two signals. A primary one is delivered by the T-cell receptor (TCR) complex after antigen recognition and additional costimulatory signals are delivered by the engagement of costimulatory receptors such as CD28. The best-characterized costimulatory pathways are mediated by a set of cosignaling molecules belonging to the CD28 superfamily, including CD28, CTLA4, ICOS, PD1 and BTLA receptors. These proteins deliver both positive and negative second signals to T-cells by interacting with B7 family ligands expressed on antigen presenting cells. Different subsets of T-cells have very different requirements for costimulation. CD28 family mediated costimulation is not required for all T-cell responses in vivo, and alternative costimulatory pathways also exist. Different receptors of the CD28 family and their ligands have different regulation of expression. CD28 is constitutively expressed on naive T cells whereas CTLA4 expression is dependent on CD28/B7 engagement and the other receptor members ICOS, PD1 and BTLA are induced after initial T-cell stimulation. The positive signals induced by CD28 and ICOS molecules are counterbalanced by other members of the CD28 family, including cytotoxic T-lymphocyte associated antigen (CTLA)4, programmed cell death (PD)1, and B and T lymphocyte attenuator (BTLA), which dampen immune responses. The balance of stimulatory and inhibitory signals is crucial to maximize protective immune responses while maintaining immunological tolerance and preventing autoimmunity. The costimulatory receptors CD28, CTLA4, ICOS and PD1 are composed of single extracellular IgV-like domains, whereas BTLA has one IgC-like domain. Receptors CTLA4, CD28 and ICOS are covalent homodimers, due to an interchain disulphide linkage. The costimulatory ligands B71, B72, B7H2, B7H1 and B7DC, have a membrane proximal IgC-like domain and a membrane distal IgV-like domain that is responsible for receptor binding and dimerization. CD28 and CTLA4 have no known intrinsic enzymatic activity. Instead, engagement by their physiologic ligands B71 and B72 leads to the physical recruitment and activation of downstream T-cell effector molecules.
In naive T cells, CD28 costimulation enhances cell cycle entry, potently stimulates expression of both the mitogenic lymphokine interleukin-2 (IL-2) and its receptor, and stimulates the activation of an antiapoptotic program. CD28 engages with one or both members of the B7 receptor family, B7.1 and B7.2. Upon ligand binding the tyrosines and proline-rich motifs present in the cytoplasmic tail of CD28 are phosphorylated by Lck or Fyn. Upon phosphorylation CD28 recruits and induces phosphorylation and activation of a more restricted set of intracellular signaling components that, together with those mobilized by the TCR, contribute to convert membrane-based biochemical and biophysical changes into gene activation events. Proteins like PI3K, Vav-1, Tec and Itk kinases, AKT, and the Dok-1 adaptor have been identified as elements of the CD28 signaling pathway by biochemical or genetic approaches or both.
When CTLA4 is engaged by B7 molecules, PP2A disassociates from CTLA4 in a phosphorylation dependent manner. Released PP2A acts downstream of early TCR and CD28 signaling, by inhibition of the PKB/Akt pathway.
In its unbound state PAK is maintained in an inactive conformation through intra domain interactions. On stimulation PAK is translocated to the plasma membrane where it specifically interacts with Rho family GTP-binding proteins Rac1-GTP and Cdc42-GTP. All PAK isoforms are direct effectors of the Rac and Cdc42. Rac and Cdc42 bind to a highly conserved motif in the amino terminus of PAK known as p21-binding domain (PBD) or Cdc42/Rac interactive binding (CRIB) domain. This binding is thought to induce a conformational change in PAK that relieves autoinhibition of the catalytic carboxy terminal domain, thereby inducing autophosphorylation at several sites and enabling the phosphorylation of exogenous substrates.
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CD28 binds to several intracellular proteins including PI3 kinase, Grb-2, Gads and ITK. Grb-2 specifically co-operates with Vav-1 in the up-regulation of NFAT/AP-1 transcription. CD28 costimulation resulted in a prolonged and sustained phosphorylation and membrane localization of Vav1 in comparison to T-cell receptor activation alone. Tyrosine-phosphorylated Vav1 is an early point of integration between the signaling routes triggered by the T-cell receptor and CD28. Vav1 transduces TCR and co-stimulatory signals to multiple biochemical pathways and several cytoskeleton-dependent processes. The products of Vav1 activation, Rac1 and Cdc42, in turn activate the mitogen-activated protein kinases JNK and p38. Vav1 is also required for TCR-induced calcium flux, activation of the ERK MAP kinase pathway, activation of the NF-kB transcription factor, inside-out activation of the integrin LFA-1, TCR clustering, and polarisation of the T cell.
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Mechanisms for the role of tetrahydrobiopterin in endothelial function and vascular disease
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GSK3 (glycogen synthase kinase-3) participates in the Wnt signaling pathway. It is implicated in the hormonal control of several regulatory proteins including glycogen synthase, and the transcription factors MYB and JUN. GSK3 phosphorylates JUN at sites proximal to its DNA-binding domain, thereby reducing its affinity for DNA. GSK3 is inhibited when phosphorylated by AKT1.
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Following activation, AKT can phosphorylate an array of target proteins in the cytoplasm, many of which are involved in cell survival control. Phosphorylation of TSC2 feeds positively to the TOR kinase, which, in turn, contributes to AKT activation (positive feedback loop).
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AKT, phosphorylated at threonine (AKT1 308; AKT2 309; AKT3 305) and serine (AKT1 473; AKT2 474; AKT3 472) translocates to the nucleus, reaching a maximum after 15 min and returning to a basal level after 45 min of NGF stimulation. Control of the amount of nuclear AKT is achieved through the action of the phosphatase PP2A.
Aflatoxin B1-induced hepatocellular carcinoma in developing countries: Geographical distribution, mechanism of action and prevention
Structural basis of GLUT1 inhibition by cytoplasmic ATP
Characterization of the COQ5 gene from Saccharomyces cerevisiae. Evidence for a C-methyltransferase in ubiquinone biosynthesis
Failure of blood-island formation and vasculogenesis in Flk-1-deficient mice
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A novel mechanism for GABA synthesis and packaging into synaptic vesicles
The remarkable structural and functional organization of the eukaryotic pyruvate dehydrogenase complexes.
Expression, purification, and characterization of human and rat acetyl coenzyme A carboxylase (ACC) isozymes
Identification of a vertebrate sister-chromatid separation inhibitor involved in transformation and tumorigenesis
Cloning and characterization of a second human CTP:phosphocholine cytidylyltransferase
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Crucial role of conserved cysteine residues in the assembly of two iron-sulfur clusters on the CIA protein Nar1
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Molecular cloning and functional expression of cDNAs encoding a human Na+-nucleoside cotransporter (hCNT1)
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JmjC: cupin metalloenzyme-like domains in jumonji, hairless and phospholipase A2beta
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carbamoyl-phosphate synthase (ammonia), mitochondrial
A novel interleukin-17 receptor-like protein identified in human umbilical vein endothelial cells antagonizes basic fibroblast growth factor-induced signaling
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Maintaining copper homeostasis: regulation of copper-trafficking proteins in response to copper deficiency or overload
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delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor
Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity
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ornithine carbamoyltransferase, mitochondrial
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International Union of Basic and Clinical Pharmacology. LXXXV: calcium-activated chloride channels
Deoxyhypusine hydroxylase is a Fe(II)-dependent, HEAT-repeat enzyme. Identification of amino acid residues critical for Fe(II) binding and catalysis [corrected].
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Control of mRNA decay by phosphorylation of tristetraprolin
gamma-butyrobetaine,2-oxoglutarate dioxygenase
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Kinetics and inhibition of recombinant human cystathionine gamma-lyase. Toward the rational control of transsulfuration
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Does cellular hydrogen peroxide diffuse or act locally?
The mitochondrial ornithine transporter. Bacterial expression, reconstitution, functional characterization, and tissue distribution of two human isoforms
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Structures and mechanisms of Nudix hydrolases
Mia40-dependent oxidation of cysteines in domain I of Ccs1 controls its distribution between mitochondria and the cytosol
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Megakaryocyte development and platelet production
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Glyoxylate reductase/hydroxypyruvate reductase
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MISCELLANEOUS Present with 5750 molecules/cell in log phase SD medium.SIMILARITY Belongs to the COX19 family.SIMILARITY Contains 1 CHCH domain.
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Sorting switch of mitochondrial presequence translocase involves coupling of motor module to respiratory chain
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Low levels of glucose transporters and K+ATP channels in human pancreatic beta cells early in development
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CpG-DNA-specific activation of antigen-presenting cells requires stress kinase activity and is preceded by non-specific endocytosis and endosomal maturation
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Fc receptor-mediated phagocytosis requires CDC42 and Rac1
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NMD: multitasking between mRNA surveillance and modulation of gene expression
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Primary structure of human deoxycytidylate deaminase and overexpression of its functional protein in Escherichia coli
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Relationship between interferon-gamma, indoleamine 2,3-dioxygenase, and tryptophan catabolism
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_191570.3
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Evaluation of the "scanning model" for initiation of protein synthesis in eucaryotes.
Characterization of human UMP/CMP kinase and its phosphorylation of D- and L-form deoxycytidine analogue monophosphates.
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Phospholipid synthesis in a membrane fraction associated with mitochondria
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Expression of the SNT-1/FRS2 phosphotyrosine binding domain inhibits activation of MAP kinase and PI3-kinase pathways and antiestrogen resistant growth induced by FGF-1 in human breast carcinoma cells
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Adenylate kinase isoenzyme 2, mitochondrial
Adenylate kinase isoenzyme 2, mitochondrial (EC 2.7.4.3) (ATP-AMP transphosphorylase)
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Guanylate kinase (EC 2.7.4.8) (GMP kinase)
deoxythymidylate kinase (thymidylate kinase)
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Ribonucleoside-diphosphate reductase M2 chain (EC 1.17.4.1) (Ribonucleotide reductase small chain)
Ribonucleoside-diphosphate reductase M2 chain
Chaperonins: The hunt for the Group II mechanism
glutaredoxin (thioltransferase), oxidized
Ribonucleoside-diphosphate reductase M1 chain (EC 1.17.4.1) (Ribonucleotide reductase large chain)
Ribonucleoside-diphosphate reductase M1 chain
Biogenesis of Tim23 and Tim17, integral components of the TIM machinery for matrix-targeted preproteins
Calcium/calmodulin kinase IV pathway is involved in the transcriptional regulation of the corticotropin-releasing hormone gene promoter in neuronal cells
The ratio between tetrahydrobiopterin and oxidized tetrahydrobiopterin analogues controls superoxide release from endothelial nitric oxide synthase: an EPR spin trapping study
Molecular cloning of human Syk. A B cell protein-tyrosine kinase associated with the surface immunoglobulin M-B cell receptor complex
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_226464.2
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Transcriptional regulation and binding of heat shock factor 1 and heat shock factor 2 to 32 human heat shock genes during thermal stress and differentiation
Structure of human holocarboxylase synthetase gene and mutation spectrum of holocarboxylase synthetase deficiency
The MuvB complex sequentially recruits B-Myb and FoxM1 to promote mitotic gene expression
non-metastatic cells 1, protein (NM23A) expressed in
Tumor metastatic process-associated protein
Nucleoside diphosphate kinase, mitochondrial
non-metastatic cells 4, protein expressed in
ribonucleotide reductase M2B (TP53 inducible)
Immunodeficiency in protein kinase cbeta-deficient mice
ornithine aminotransferase, mitochondrial
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CATALYTIC ACTIVITY 4 ferrocytochrome c + O(2) + 4 H(+) = 4 ferricytochrome c + 2 H(2)O.SUBUNIT Cytochrome c oxidase is composed of 11 subunits: one copy each of COX1, COX2, COX3, COX4, COX5A or COX5B, COX6, COX7, COX9, COX12, COX13 and two copies of COX8.MISCELLANEOUS Present with 3670 molecules/cell in log phase SD medium.SIMILARITY Belongs to the cytochrome c oxidase IV family.
Glutamate dehydrogenase 1, mitochondrial precursor
Delta-1-pyrroline-5-carboxylate synthetase long
Delta-1-pyrroline-5-carboxylate synthetase short
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Activation of ATR in response to replication stress
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5609676
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611009
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5609677
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110289
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5776.2
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Branched-chain amino acid aminotransferase, cytosolic
branched-chain amino acid aminotransferase, mitochondrial, apoenzyme
G alpha 12 and G alpha 13 stimulate Rho-dependent stress fiber formation and focal adhesion assembly
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lysine-ketoglutarate reductase /saccharopine dehydrogenase monomer
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4587.1
3-hydroxyisobutyryl-coenzyme A hydrolase
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5609774
L-kynurenine/alpha-aminoadipate aminotransferase
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618232
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Chromatin modifications and their function
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Mitochondrial 2-oxodicarboxylate carrier
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At the beginning of this reaction, 1 molecule of 'Ubiquitinated Phospho-Cdc25A' is present. At the end of this reaction, 1 molecule of 'Amino Acid' is present. This reaction takes place in the 'cytosol' and is mediated by the 'endopeptidase activity' of '26S proteasome'.
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At the beginning of this reaction, 1 molecule of 'ATP', and 1 molecule of 'Chk1' are present. At the end of this reaction, 1 molecule of 'phospho-Chk1', and 1 molecule of 'ADP' are present. This reaction takes place in the 'nucleus' and is mediated by the 'kinase activity' of 'phospho-ATM (Ser 1981)'.
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Detection of DNA damage caused by ionizing radiation results in the phosphorylation of Cdc25A at Ser-123 by Chk1, inhibiting Cdc25A.
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cdc25A protein is degraded by the ubiquitin-proteasome machinery in both terminally differentiating and cycling cells (Bernardi et al. 2000).
DNA replication is regulated at various levels via ORC proteins. This pathway includes annotation of individual events that lead to the regulation of replication.
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Studies in the past decade have suggested that the basic mechanism of DNA replication initiation is conserved in all kingdoms of life. Initiation in unicellular eukaryotes, in particular Saccharomyces cerevisiae (budding yeast), is well understood, and has served as a model for studies of DNA replication initiation in multicellular eukaryotes, including humans. In general terms, the first step of initiation is the binding of the replication initiator to the origin of replication. The replicative helicase is then assembled onto the origin, usually by a helicase assembly factor. Either shortly before or shortly after helicase assembly, some local unwinding of the origin of replication occurs in a region rich in adenine and thymine bases (often termed a DNA unwinding element, DUE). The unwound region provides the substrate for primer synthesis and initiation of DNA replication. The best-defined eukaryotic origins are those of S. cerevisiae, which have well-conserved sequence elements for initiator binding, DNA unwinding and binding of accessory proteins. In multicellular eukaryotes, unlike S. cerevisiae, these loci appear not to be defined by the presence of a DNA sequence motif. Indeed, choice of replication origins in a multicellular eukaryote may vary with developmental stage and tissue type. In cell-free models of metazoan DNA replication, such as the one provided by Xenopus egg extracts, there are only limited DNA sequence specificity requirements for replication initiation (Kelly & Brown 2000; Bell & Dutta 2002; Marahrens & Stillman 1992; Cimbora & Groudine 2001; Mahbubani et al 1992, Hyrien & Mechali 1993).
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Chk1 directly phosphorylates Cdc25A at Ser-123. Chk1 phosphorylation is required for cells to delay cell cycle progression in response to double-strand DNA breaks (Zhao et al., 2002).
Detection of DNA damage caused by ionizing radiation results in the phosphorylation of Cdc25A at Ser-123 by Chk2.
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The eukaryotic six-subunit origin recognition complex (ORC) governs the initiation site of DNA replication and formation of the prereplication complex.
Licensing factors are removed from the origin by various means like biochemical modification (phosphorylation) or by physical association with other proteins. This pathway includes the annotations of events in which the fates of different proteins at the origin are outlined.
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The Tim8-Tim13 complex has multiple substrate binding sites and binds cooperatively to Tim23
The G2/M DNA replication checkpoint ensures that mitosis is not initiated until DNA replication is complete. If replication is blocked, the DNA replication checkpoint signals to maintain Cyclin B - Cdc2 complexes in their T14Y15 phosphorylated and inactive state. This prevents the phosphorylation of proteins involved in G2/M transition, and prevents mitotic entry. Failure of these checkpoints results in changes of ploidy: in the case of mitosis without completion of DNA replication, aneuploidy of <2C will result, and the opposite is true if DNA replication is completed more than once in a single cell cycle with an overall increase in ploidy. The mechanism by which unreplicated DNA is first detected by the cell is unknown.
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Throughout the cell cycle, the genome is constantly monitored for damage, resulting either from errors of replication, by-products of metabolism or through extrinsic sources such as ultra-violet or ionizing radiation. The different DNA damage checkpoints act to inhibit or maintain the inhibition of the relevant CDK that will control the next cell cycle transition. The G2 DNA damage checkpoint prevents mitotic entry solely through T14Y15 phosphorylation of Cdc2 (Cdk1). Failure of the G2 DNA damage checkpoint leads to catastrophic attempts to segregate unrepaired chromosomes.
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Myt1, which localizes preferentially to the endoplasmic reticulum and Golgi complex, phosphorylates Cdc2 on threonine 14 ( Liu et al., 1997).
Cdc25C is phosphorylated by Chk1 at ser-216 (Blasina et al.,1999 ) resulting in both inhibition of the Cdc25 phosphatase activity and creation of a 14-3-3 docking site (Peng et al., 1997). Association of 14-3-3 protein is believed to exclude Cdc25C from the nucleus via cytoplasmic retention of the Cdc25C:14-3-3 complex.
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DNA damage induced activation of the checkpoint kinases Chk1/Chk2(Cds1) results in the conversion and/or maintenance of CyclinB:Cdc2 complex in its Tyrosine 15 phosphorylated (inactive) state. Cdc2 activity is regulated by a balance between the phosphorylation and dephosphorylation by the Wee1/Myt1 kinase and Cdc25 phosphatase. Inactivation of the Cyclin B:Cdc2 complex likely involves both inactivation of Cdc25 and/or stimulation of Wee1/Myt1 kinase activity.
At the beginning of this reaction, 1 molecule of 'ATP', and 1 molecule of 'Chk2' are present. At the end of this reaction, 1 molecule of 'phospho-Chk2', and 1 molecule of 'ADP' are present. This reaction takes place in the 'nucleus' and is mediated by the 'kinase activity' of 'phospho-ATM (Ser 1981)'.
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Cdc25C is negatively regulated by phosphorylation on Ser 216, the 14-3-3-binding site. This is an important regulatory mechanism used by cells to block mitotic entry under normal conditions and after DNA damage (Bulavin et al., 2003).
The G1 arrest induced by DNA damage has been ascribed to the transcription factor and tumor suppressor protein p53. To be effective within minutes after DNA damage, induction of the G1 block should exploit transcription and protein synthesis independent mechanisms. Upon exposure to ultraviolet light (UV) or ionizing radiation (IR), the abundance and activity of a protein, Cdc25A, rapidly decreases; this DNA damage response is not dependent on p53. The rapid destruction of Cdc25A phosphatase prevents entry of a cell into S-phase, by maintaining the CyclinE:Cdk2 complexes in their T14Y15 phosphorylated form.
In the G1 phase there are two types of DNA damage responses, the p53-dependent and the p53-independent pathways. The p53-dependent responses inhibit CDKs through the up-regulation of genes encoding CKIs mediated by the p53 protein, whereas the p53-independent mechanisms inhibit CDKs through the inhibitory T14Y15 phosphorylation of Cdk2. Failure of DNA damage checkpoints in G1 leads to mutagenic replication of damaged templates and other replication defects.
In response to DNA damage due to exposure to ultraviolet light or to ionizing radiation, Cdc25A is phosphorylated by Chk1 or Chk2. The phosphorylation of Cdc25A at ser-123, in response to DNA damage from ionizing radiation is a signal for ubiquitination and subsequent degradation of Cdc25A. The destruction of Cdc25A prevents the normal G1/S transition. Cdc25A is required for the activation of the Cyclin E:Cdk2 complexes via dephosphorylation. Chk1 is activated in response to DNA damage due to uv light. However, the phosphorylation occurs at a different site.
The E2F family of transcription factors regulate the transition from the G1 to the S phase in the cell cycle. E2F activity is regulated by members of the retinoblastoma protein (pRb) family, resulting in the tight control of the expression of E2F-responsive genes. Phosphorylation of pRb by cyclin D:CDK complexes releases pRb from E2F, inducing E2F-targeted genes such as cyclin E.
MISCELLANEOUS Present with 125 molecules/cell in log phase SD medium.
The transition from the G1 to S phase is controlled by the Cyclin E:Cdk2 complexes. As the Cyclin E:Cdk2 complexes are formed, the Cdk2 is phosphorylated by the Wee1 and Myt1 kinases. This phosphorylation keeps the Cdk2 inactive. In yeast this control is called the cell size checkpoint control. The dephosphorylation of the Cdk2 by Cdc25A activates the Cdk2, and is coordinated with the cells reaching the proper size, and with the DNA synthesis machinery being ready. The Cdk2 then phosphorylates G1/S specific proteins, including proteins required for DNA replication initiation. The beginning of S-phase is marked by the first nucleotide being laid down on the primer during DNA replication at the early-firing origins.Failure to appropriately regulate cyclin E accumulation can lead to accelerated S phase entry, genetic instability, and tumorigenesis. The amount of cyclin E protein in the cell is controlled by ubiquitin-mediated proteolysis (see Woo, 2003).This pathway has not yet been annotated in Reactome.
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E2F1 binds to E2F binding sites on the genome activating the synthesis of the target proteins. For annotation purposes, the reactions regulated by E2F1 are grouped under this pathway and information about the target genes alone are displayed for annotation purposes. Cellular targets for activation by E2F1 include thymidylate synthetase, Rir2, Dihydrofolate reductase, Cdc2, Cyclin A1, Cdc6 (DeGregori et al., 1995), Cdt1 (Yoshida and Inoue, 2004), CDC45 (Arata et al., 2000), CDC6 (Yan et al., 1998; Ohtani et al., 1998), Cyclin E (Ohtani et al., 1996), Emi1 (Hsu et al., 2002), and Orc1 (Ohtani et al., 1997). The activation of TK2 (Dnk1) and Cdc25A by E2F1 have been inferred from similar events in Drosophila (Duronio and O'Farrell, 1994;Reis and Edgar, 2004). Rir2 protein is involved in dNTP level regulation and activation of this enzyme results in higher levels of dNTPs in anticipation of S-phase. E2F activation of Rir2 has been shown also in Drosophila by Duronio and O'Farrell (1994). E2F1 activation of CDC45 is shown in mouse cells by using human E2F1 construct (Arata et al., 2000). Cyclin E is also transcriptionally regulated by E2F1. Cyclin E protein plays important role in the transition of G1 in S-phase by associating with Cdk2 (Ohtani et al., 1996). E2F activation of PCNA has been demonstrated in Drosophila (DeGregori et al., 1995) and in some human cells by using recombinant adenovirus constructs. E2F activation of Polymerase A (Pol A) has been demonstrated in some human cells. It has also been demonstrated in Drosophila by Ohtani and Nevins (1994). It has been observed in Drosophila that E2F1 regulated expression of Orc1 stimulates ORC1-6 complex formation and binding to the origin of replication (Asano and Wharton, 1999). Orc1-6 recruit Cdc6 and Cdt1 that are required to recruit the MCM2-7 replication helicases. E2F1 regulation incorporates a feedback mechanism where in Geminin can inhibit MCM2-7 recruitment of ORC1-6 complex by interacting with Cdc6/Cdt1. The activation of Cdc25A and TK2 (Dnk1) by E2F1 has been inferred from similar events in Drosophila (Duronio RJ, O'Farrell 1994; Reis and Edgar, 2004). E2F1 activates string (Cdc25) that in turn activates Cyclin B/Cdk1. A similar phenomenon has been observed in mouse NIH 3T3 cells and in Rat1 cells.
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Phosphorylation of Cdc25C at Ser 216 results in both the inhibition of Cdc25C phosphatase activity and the creation of a 14-3-3 docking site (Peng et al. 1997).
Genotoxic stress caused by DNA damage or stalled replication forks can lead to genomic instability. To guard against such instability, genotoxically-stressed cells activate checkpoint factors that halt or slow cell cycle progression. Among the pathways affected are DNA replication by reduction of replication origin firing, and mitosis by inhibiting activation of cyclin-dependent kinases (Cdks). A key factor involved in the response to stalled replication forks is the ATM- and rad3-related (ATR) kinase, a member of the phosphoinositide-3-kinase-related kinase (PIKK) family. Rather than responding to particular lesions in DNA, ATR and its binding partner ATRIP (ATR-interacting protein) sense replication fork stalling indirectly by associating with persistent ssDNA bound by RPA. These structures would be formed, for example, by dissociation of the replicative helicase from the leading or lagging strand DNA polymerase when the polymerase encounters a DNA lesion that blocks DNA synthesis. Along with phosphorylating the downstream transducer kinase Chk1 and the tumor suppressor p53, activated ATR modifies numerous factors that regulate cell cycle progression or the repair of DNA damage. The persistent ssDNA also stimulates recruitment of the RFC-like Rad17-Rfc2-5 alternative clamp-loading complex, which subsequently loads the Rad9-Hus1-Rad1 complex onto the DNA. The latter '9-1-1' complex serves to facilitate Chk1 binding to the stalled replication fork, where Chk1 is phosphorylated by ATR and thereby activated. Upon activation, Chk1 can phosphorylate additional substrates including the Cdc25 family of phosphatases (Cdc25A, Cdc25B, and Cdc25C). These enzymes catalyze the removal of inhibitory phosphate residues from cyclin-dependent kinases (Cdks), allowing their activation. In particular, Cdc25A primarily functions at the G1/S transition to dephosphorylate Cdk2 at Thr 14 and Tyr 15, thus positively regulating the Cdk2-cyclin E complex for S-phase entry. Cdc25A also has mitotic functions. Phosphorylation of Cdc25A at Ser125 by Chk1 leads to Cdc25A ubiquitination and degradation, thus inhibiting DNA replication origin firing. In contrast, Cdc25B and Cdc25C regulate the onset of mitosis through dephosphorylation and activation of Cdk1-cyclin B complexes. In response to replication stress, Chk1 phosphorylates Cdc25B and Cdc25C leading to Cdc25B/C complex formation with 14-3-3 proteins. As these complexes are sequestered in the cytoplasm, they are unable to activate the nuclear Cdk1-cyclin B complex for mitotic entry. These events are outlined in the figure. Persistent single-stranded DNA associated with RPA binds claspin (A) and ATR:ATRIP (B), leading to claspin phosphorylation (C). In parallel, the same single-stranded DNA:RPA complex binds RAD17:RFC (D), enabling the loading of RAD9:HUS1:RAD1 (9-1-1) complex onto the DNA (E). The resulting complex of proteins can then repeatedly bind (F) and phosphorylate (G) CHK1, activating multiple copies of CHK1.
G2/M checkpoints include the checks for damaged DNA, unreplicated DNA, and checks that ensure that the genome is replicated once and only once per cell cycle. If cells pass these checkpoints, they follow normal transition to the M phase. However, if any of these checkpoints fail, mitotic entry is prevented by specific G2/M checkpoint events. The G2/M checkpoints can fail due to the presence of unreplicated DNA or damaged DNA. In such instances, the cyclin-dependent kinase, Cdc2(Cdk1), is maintained in its inactive, phosphorylated state, and mitotic entry is prevented. Events that ensure that origins of DNA replication fire once and only once per cell cycle are also an example of a G2/M checkpoint. In the event of high levels of DNA damage, the cells may also be directed to undergo apopotosis (not covered).
In the sequestration model, the Mad2 molecules that dissociate from unattached kinetochores are perceived to bind to Cdc20, a protein that recruits specific substrates to the APC/C. Consequently, Mad2 indirectly inhibits the APC/C by sequestering its activator, Cdc20. This requires interaction between Mad1 and Mad2. Cdc20 and Mad1 bind to the same site on Mad2.
The target of the mitotic checkpoint is the Anaphase Promoting Complex/Cyclosome (APC/C) an E3 ubiquitin ligase that targets proteins whose destruction is essential for mitotic exit. Currently, there are two proposed mechanism by which inhibition of the APC/C is achieved. These mechanisms differ depending on the mechanism of signal transduction. The APC/C may be inhibited directly by association with the Mitotic Checkpoint Complex (MCC) or through the sequestration of its activator, Cdc20.
The mitotic checkpoint or spindle assembly checkpoint is an evolutionarily conserved mechanism that ensures that cells with misaligned chromosomes do not exit mitosis and divide to form aneuploid cells. As chromosome attachment to the spindle microtubules is a stochastic process, not all chromosomes achieve alignment at the spindle equator at the same time. It is therefore essential that even a single unaligned chromosome can prevent the onset of anaphase. The ability of the checkpoint to monitor the status of chromosome alignment is achieved by assigning checkpoint proteins to the kinetochore, a macromolecular complex that resides at centromeres of chromosomes that establishes connections with spindle microtubules. The checkpoint proteins monitor, in an unknown way, the mechanical activities between kinetochore-associated proteins and microtubules. Defects in mechanical activities at kinetochores activate the resident checkpoint proteins to initiate a signal that is amplified throughout the cell that ultimately prevents the activation of the proteolytic process that is required for sister chromatid separation and the onset of anaphase. Kinetochores of unaligned chromosomes differ from those of aligned chromosomes in two ways. Kinetochores of aligned chromosomes are saturated with between 20 to 30 microtubules. In addition, poleward directed forces exerted at each sister kinetochore generates tension between them. Unaligned kinetochores on the other hand, are not saturated with microtubules and are not under tension. The mitotic checkpoint detects the presence of unattached kinetochores rather than monitoring for the presence of attached kinetochores. Consequently, unattached kinetochores emit an inhibitory signal that inhibits the biochemical events that are required to initiate the onset of anaphase. The mechanism by which this inhibitory signal is generated at unattached kinetochores has not precisely been determined but the signal is generated as a result of the lack of microtubule occupancy and kinetochore tension. A single unattached kinetochore is capable of preventing cells from exiting mitosis. The mitotic checkpoint provides a way for a localized defect to affect the global biochemical status of the cell. In principle, the signal that is generated at an unattached kinetochore diffuses throughout the cell to affect its target. There are currently two models for how this is achieved. One model is based on the observation that the Mad2 checkpoint protein binds and is rapidly released from unattached kinetochores. The kinetochore is believed to act as a catalyst that converts Mad2 into an inhibitory state that diffuses throughout the cell upon its release from the kinetochore. A second model proposes that the signal is amplified by a kinase cascade much like a conventional signal transduction pathway. This kinase cascade is believed to be comprised of the checkpoint kinases, hBUBR1, hBUB1, hMPS1.
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A hallmark of the human cell cycle in normal somatic cells is its precision. This remarkable fidelity is achieved by a number of signal transduction pathways, known as checkpoints, which monitor cell cycle progression ensuring an interdependency of S-phase and mitosis, the integrity of the genome and the fidelity of chromosome segregation. Checkpoints are layers of control that act to delay CDK activation when defects in the division program occur. As the CDKs functioning at different points in the cell cycle are regulated by different means, the various checkpoints differ in the biochemical mechanisms by which they elicit their effect. However, all checkpoints share a common hierarchy of a sensor, signal transducers, and effectors that interact with the CDKs. The stability of the genome in somatic cells contrasts to the almost universal genomic instability of tumor cells. There are a number of documented genetic lesions in checkpoint genes, or in cell cycle genes themselves, which result either directly in cancer or in a predisposition to certain cancer types. Indeed, restraint over cell cycle progression and failure to monitor genome integrity are likely prerequisites for the molecular evolution required for the development of a tumor. Perhaps most notable amongst these is the p53 tumor suppressor gene, which is mutated in >50% of human tumors. Thus, the importance of the checkpoint pathways to human biology is clear.
The Myc/Max heterodimer binds to elements in the cdc25A gene and activates transcription in mid to late G1.
Cyclin dependent kinases are themselves catalytically inactive due to the fact that their active site is blocked by a portion of the Cdk molecule itself. Binding to their corresponding cyclin partner results in conformational change that partially exposes the active site.
During interphase, phopshorylated Cdc25C is associated with 14-3-3 proteins preventing nuclear import. At the onset of mitosis, dephosphorylation of Cdc25C and dissociation of 14-3-3 increases the rate of import (see Takizawa and Morgan, 2000)
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DNA synthesis occurs in the S phase, or the synthesis phase, of the cell cycle. The cell duplicates its hereditary material, and two copies of the chromosome are formed. As DNA replication continues, the E type cyclins shared by the G1 and S phases, are destroyed and the levels of the mitotic cyclins rise.
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At the end of this reaction, 1 molecule of 'Cyclin B:Cdk1 complex', and 1 molecule of 'Cdc25A' are present. This reaction takes place in the 'nucleus'.
Under specific conditions, Cyclin B, a mitotic cyclin, can inhibit the functions of pre-replicative complex. E2F1 activates Cdc25A protein which regulates Cyclin B in a positive manner. Cyclin B/Cdk1 function is restored which leads to the disruption of pre-replicative complex. This phenomenon has been demonstrated by Bosco et al (2001) in Drosophila.
At the beginning of this reaction, 1 molecule of 'RNA primer-DNA primer:origin duplex' is present. At the end of this reaction, 1 molecule of 'DNA polymerase alpha:primase', and 1 molecule of 'RNA primer-DNA primer:origin duplex with DNA damage' are present. This reaction takes place in the 'nucleus'.
Cyclin A:Cdk2 plays a key role in S phase entry by phosphorylation of proteins including Cdh1, Rb, p21 and p27. During G1 phase of the cell cycle, cyclin A is synthesized and associates with Cdk2. After forming in the cytoplasm, the Cyclin A:Cdk2 complexes are translocated to the nucleus (Jackman et al.,2002). Prior to S phase entry, the activity of Cyclin A:Cdk2 complexes is negatively regulated through Tyr 15 phosphorylation of Cdk2 (Gu et al., 1995) and also by the association of the cyclin kinase inhibitors (CKIs), p27 and p21. Phosphorylation of cyclin-dependent kinases (CDKs) by the CDK-activating kinase (CAK) is required for the activation of the CDK2 kinase activity (Aprelikova et al., 1995). The entry into S phase is promoted by the removal of inhibitory Tyr 15 phosphates from the Cdk2 subunit of Cyclin A:Cdk2 complex by the Cdc25 phosphatases (Blomberg and Hoffmann, 1999) and by SCF(Skp2)-mediated degradation of p27/p21 (see Ganoth et al., 2001). While Cdk2 is thought to play a primary role in regulating entry into S phase, recent evidence indicates that Cdk1 is equally capable of promoting entry into S phase and the initiation of DNA replication (see Bashir and Pagano, 2005). Thus, Cdk1 complexes may also play a significant role at this point in the cell cycle.
Progression through G1 and G1 to S-phase transition that initiates DNA synthesis involve many complexes that are regulated by RB1:E2F pathway. RB1:E2F pathway plays a key role in gene expression regulation in proliferating and differentiated cells. As a repressor, E2F remains bound to RB1; it can activate the expression of S-phase genes involved in DNA replication after the phosphorylation of RB1. E2F proteins regulate expression of genes involved in various processes thereby forming interlinks between cell cycle, DNA synthesis, DNA damage recognition etc. In this module, activation of replication related genes by E2F1 and two ways by which E2F1 regulates DNA replication initiation are annotated. Detailed connection between the E2F protein function and various pathways will be covered in future releases of Reactome.
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Cyclin E - Cdk2 complexes control the transition from G1 into S-phase. In this case, the binding of p21Cip1/Waf1 or p27kip1 is inhibitory. Important substrates for Cyclin E - Cdk2 complexes include proteins involved in the initiation of DNA replication. The two Cyclin E proteins are subjected to ubiquitin-dependent proteolysis, under the control of an E3 ubiquitin ligase known as the SCF. Cyclin A - Cdk2 complexes, which are also regulated by p21Cip1/Waf1 and p27kip1, are likely to be important for continued DNA synthesis, and progression into G2. An additional level of control of Cdk2 is reversible phosphorylation of Threonine-14 (T14) and Tyrosine-15 (Y15), catalyzed by the Wee1 and Myt1 kinases, and dephosphorylation by the three Cdc25 phosphatases, Cdc25A, B and C.
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Identification of mutations associated with peroxisome-to-mitochondrion mistargeting of alanine/glyoxylate aminotransferase in primary hyperoxaluria type 1
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cDNA cloning, genomic structure, chromosomal mapping, and functional expression of a novel human alanine aminotransferase
After APC/C-mediated degradation of PTTG1 (securin), ESPL1 (separin i.e. separase) is rapidly autocatalytically cleaved after arginine residues at positions 1506 and 1535. The N-terminal and C-terminal fragments remain bound to each other after cleavage. It has not been examined what happens with the short middle fragment of ESPL1, so it is annotated as a part of the autocleaved ESPL1 complex. The autocatalytic cleavage of ESPL1 is not a prerequisite for the subsequent cleavage of the cohesin subunit RAD21 (Waizenegger et al. 2002).
The dissolution of the nuclear membrane marks the beginning of the prometaphase. Kinetochores are created when proteins attach to the centromeres. Microtubules then attach at the kinetochores, and the chromosomes begin to move to the metaphase plate.
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Cdc6 is a regulator of DNA replication initiation in both yeasts and human cells, but its mechanism of action differs between the two systems. Genetic studies in budding yeast (S. cerevisiae) and fission yeast (S. pombe) indicate that the normal function of Cdc6 protein is required to restrict DNA replication to once per cell cycle. Specifically, Cdc6 may function as an ATPase switch linked to Mcm2-7 association with the Cdt1:Cdc6:ORC:origin complex. In S. cerevisiae, Cdc6 protein is expressed late in the M phase of the cell cycle and, in cells with a prolonged G1 phase, late in G1. This protein has a short half-life, and is destroyed by ubiquitin-mediated proteolysis, mediated by the SCF complex. Human Cdc6 protein levels are reduced early in G1 but otherwise are constant throughout the cell cycle. Some reports have suggested that after cells enter S phase, Cdc6 is phosphorylated, excluded from the nucleus and subject to ubiquitination and degradation. Replenishing Cdc6 protein levels during G1 appears to be regulated by E2F transcription factors.
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At the end of this reaction, 1 molecule of 'Cdc6' is present.
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DNA polymerase alpha:primase is comprised of four subunits, p180, p70, p58, and p49. The two primase subunits, p58 and p49, form a tight complex. The p49 subunit contains the DNA primase activity and one role of p58 appears to be tethering p49 to p180, the DNA polymerase catalytic subunit. The fourth subunit, p70, binds p180 and may tether the DNA polymerase alpha:primase complex to Cdc45.
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DNA replication pre-initiation in eukaryotic cells begins with the formation of the pre-replicative complex (pre-RC) during the late M phase and continues in the G1 phase of the mitotic cell cycle, a process also called DNA replication origin licensing. The association of initiation proteins (ORC, Cdc6, Cdt1, Mcm2-7) with the origin of replication in both S. cerevisiae and humans has been demonstrated by chromatin immunoprecipitation experiments. In S. cerevisiae, pre-replicative complexes are assembled from late M to G1. In mammalian cells as well, pre-replicative complexes are assembled from late M to G1, as shown by biochemical fractionation and immunostaining. There are significant sequence similarities among some of the proteins in the pre-replicative complex. The ORC subunits Orc1, Orc4 and Orc5 are homologous to one another and to Cdc6. The six subunits of the Mcm2-7 complex are homologous to one another. In addition, Orc1, Orc4, Orc5, Cdc6, and the Mcm2-7 subunits, are members of the AAA+ superfamily of ATPases. Since the initial identification of these pre-RC components other factors that participate in this complex have been found, including Cdt1 in human, Xenopus, S. pombe, and S. cerevisiae cells.
Alteration of decreased plasma NO metabolites and platelet NO synthase activity by paroxetine in depressed patients
In anaphase, the paired chromosomes separate at the centromeres, and move to the opposite sides of the cell. The movement of the chromosomes is facilitated by a combination of kinetochore movement along the spindle microtubules and through the physical interaction of polar microtubules.
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While sister chromatids resolve in prometaphase, separating along chromosomal arms, the cohesion of sister centromeres persists until anaphase. At the anaphase onset, the anaphase promoting complex/cyclosome (APC/C) ubiquitinates PTTG1 (securin), targeting it for degradation (Hagting et al. 2002). PTTG1 acts as an inhibitor of ESPL1 (known as separin i.e. separase). Hence, PTTG1 removal initiated by APC/C, enables ESPL1 to become catalytically active (Zou et al. 1999, Waizenegger et al. 2002). ESPL1 undergoes autoleavage (Waizenegger et al. 2002) and also cleaves RAD21 subunit of centromeric cohesin (Hauf et al. 2001). RAD21 cleavage promotes dissociation of cohesin complexes from sister centromeres, leading to separation of sister chromatids. Subsequent movement of sister chromatids to opposite poles of the mitotic spindle segregates replicated chromosomes to two daughter cells (Waizenegger et al. 2000, Hauf et al. 2001, Waizenegger et al. 2002).
Mitosis, or the M phase, involves nuclear division and cytokinesis, where two identical daughter cells are produced. Mitosis involves prophase, prometaphase, metaphase, anaphase, and telophase. Finally, cytokinesis leads to cell division. The phase between two M phases is called the interphase; it encompasses the G1, S, and G2 phases of the cell cycle.
Metaphase is marked by the formation of the metaphase plate. The metaphase plate is formed when the spindle fibers align the chromosomes along the middle of the cell. Such an organization helps to ensure that later, when the chromosomes are separated, each new nucleus that is formed receives one copy of each chromosome. This pathway has not yet been annotated in Reactome. The metaphase to anaphase transition during mitosis is triggered by the destruction of mitotic cyclins. In anaphase, the paired chromosomes separate at the centromeres, and move to the opposite sides of the cell. The movement of the chromosomes is facilitated by a combination of kinetochore movement along the spindle microtubules and through the physical interaction of polar microtubules.
Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences
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Although, DNA replication occurs in the S phase of the cell cycle, the formation of the DNA replication pre-initiation complex begins during G1 phase.
In S. cerevisiae, two ORC subunits, Orc1 and Orc5, both bind ATP, and Orc1 in addition has ATPase activity. Both ATP binding and ATP hydrolysis appear to be essential functions in vivo. ATP binding by Orc1 is unaffected by the association of ORC with origin DNA (ARS) sequences, but ATP hydrolysis is ARS-dependent, being suppressed by associated double-stranded DNA and stimulated by associated single-stranded DNA. These data are consistent with the hypothesis that ORC functions as an ATPase switch, hydrolyzing bound ATP and changing state as DNA unwinds at the origin immediately before replication. It is attractive to speculate that ORC likewise functions as a switch as human pre-replicative complexes are activated, but human Orc proteins are not well enough characterized to allow the model to be critically tested. mRNAs encoding human orthologs of all six Orc proteins have been cloned, and ATP-binding amino acid sequence motifs have been identified in Orc1, Orc4, and Orc5. Interactions among proteins expressed from the cloned genes have been characterized, but the ATP-binding and hydrolyzing properties of these proteins and complexes of them have not been determined.
At the beginning of this reaction, 1 molecule of 'origin of replication', and 1 molecule of 'DNA polymerase epsilon' are present. At the end of this reaction, 1 molecule of 'DNA polymerase epsilon:origin complex' is present.
The mitochondrial ADP/ATP carrier: structural, physiological and
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In this reaction, 1 molecule of 'ubiquitinated Orc1' is translocated from nucleoplasm to cytosol. This movement of the molecule occurs through the 'nuclear pore'.
Regulation of nitric oxide-sensitive guanylyl cyclase
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At the beginning of this reaction, 1 molecule of 'ubiquitin', and 1 molecule of 'phosphorylated Orc1' are present. At the end of this reaction, 1 molecule of 'ubiquitinated Orc1' is present. This reaction takes place in the 'nucleus'.
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DNA polymerases are not capable of de novo DNA synthesis and require synthesis of a primer, usually by a DNA-dependent RNA polymerase (primase) to begin DNA synthesis. In eukaryotic cells, the primer is synthesized by DNA polymerase alpha:primase. First, the DNA primase portion of this complex synthesizes approximately 6-10 nucleotides of RNA primer and then the DNA polymerase portion synthesizes an additional 20 nucleotides of DNA (Frick & Richardson 2002; Wang et al 1984).
At the beginning of this reaction, 1 molecule of 'dTTP', 1 molecule of 'dGTP', 1 molecule of 'dATP', 1 molecule of 'RNA primer:origin duplex:DNA polymerase alpha:primase complex', and 1 molecule of 'dCTP' are present. At the end of this reaction, 1 molecule of 'RNA primer-DNA primer:origin duplex' is present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA-directed DNA polymerase activity' of 'DNA polymerase alpha:primase'.
At the beginning of this reaction, 1 molecule of 'DNA polymerase alpha:primase:DNA polymerase alpha:origin complex', and 1 molecule of 'NTP' are present. At the end of this reaction, 1 molecule of 'DNA polymerase epsilon', and 1 molecule of 'RNA primer:origin duplex:DNA polymerase alpha:primase complex' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA-directed RNA polymerase activity' of 'DNA polymerase alpha:primase'.
E2F mediated regulation of DNA replication
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Finally, progression out of mitosis and division of the cell into two daughters (cytokinesis) requires the inactivation of Cyclin B - Cdc2 by ubiquitin-dependent proteolysis of Cyclin A and B, which is regulated by a large E3 ubiquitin ligase complex known as the Anaphase Promoting Complex (APC). The detailed annotation of the M/G1 transition will be completed in a later version of GK.
Glycosaminoglycan storage disorders: a review
The crystal structure of yeast thiamin pyrophosphokinase
At the beginning of this reaction, 1 molecule of 'ubiquitinated Orc1' is present. At the end of this reaction, 1 molecule of 'ubiquitin' is present. This reaction takes place in the 'cytosol' and is mediated by the 'endopeptidase activity' of '26S proteasome'.
At the beginning of this reaction, 1 molecule of 'ubiquitinated Cdc6' is present. At the end of this reaction, 1 molecule of 'ubiquitin' is present. This reaction takes place in the 'cytosol' and is mediated by the 'endopeptidase activity' of '26S proteasome'.
In this reaction, 1 molecule of 'phosphorylated Cdc6' is translocated from nucleoplasm to cytosol. This movement of the molecule occurs through the 'nuclear pore'.
At the start of the elongation phase of DNA replication, the Mcm2-7 complex may re-arrange to function as the replicative helicase associated with the replication fork. In general, a replicative helicase is associated with the replication fork and unwinds DNA ahead of the polymerase. In yeast, the Mcm proteins associate with origin DNA in G1 phase and then exit the origin upon replication initiation, consistent with moving out of the origin with the replication fork. The Mcm2-7 complex is a ring-shaped hexamer. Complexes of Mcm4, Mcm6 and Mcm7 proteins from humans or S. pombe display a modest ATP-dependent helicase activity in vitro. Consistent with the hypothesis that eukaryotic Mcm complexes function as helicases, an archaeal Mcm homolog is a ring-shaped double hexamer that has a processive DNA unwinding activity. Mcm proteins may have additional functions during elongation, as uninterrupted function of all six is required for replication fork progression in budding yeast. Mcm4,6,7 helicase activity may be negatively regulated in two ways. Mcm2, Mcm4, Mcm6, and Mcm7 also form a stable complex which, however, has no helicase activity, suggesting that Mcm2 inhibits DNA unwinding by Mcm4,6,7. In addition, phosphorylation of human Mcm4,6,7 complex by CDK inhibits its helicase activity.
As cells enter S phase, HsCdc6p is phosphorylated by CDK promoting its export from the nucleus (see Bell and Dutta 2002).
In budding yeast, all MCM proteins have been proved to be essential for elongation. The active form of this protein complex may be a heterohexamer. A subcomplex of MCM proteins consisting fo MCM4,6, and -7 has a weak helicase activity that may contribute to DNA unwinding.
DNA Replication is regulated accurately and precisely by various protein complexes. Many members of the MCM protein family are assembled into the pre-Replication Complexes (pre-RC) at the end of M phase of the cell cycle. DNA helicase activity of some of the MCM family proteins are important for the unwinding of DNA and initiation of replication processes. This section contains four events which have been proved in different eukaryotic experimental systems to involve various proteins for this essential step during DNA Replication.
By applying the chromatin immunoprecipitation technique to paused forks, certain proteins like DNA pol alpha, DNA pol delta, DNA pol epsilon, MCM2-7, CDC45, GINS and MCM10 were identified. By uncoupling a helicase at the site using a polymerase inhibitor, MCM2-7, GINS complex and CDC45 alone were found to be enriched at the paused fork suggesting these proteins may form a part of an "unwindosome" at the replicating fork.
The processive complex is responsible for synthesizing at least 5-10 kb of DNA in a continuous manner during leading strand synthesis. The incorporation of nucleotides by pol delta is quite accurate. However, incorporation of an incorrect nucleotide does occur occasionally. Misincorporated nucleotides are removed by the 3' to 5' exonucleolytic proofreading capability of pol delta.
After the primers are synthesized, Replication Factor C binds to the 3'-end of the initiator DNA to trigger polymerase switching. The non-processive nature of pol alpha catalytic activity and the tight binding of Replication Factor C to the primer-template junction presumably lead to the turnover of the pol alpha:primase complex. After the Pol alpha-primase primase complex is displaced from the primer, the proliferating cell nuclear antigen (PCNA) binds to form a "sliding clamp" structure. Replication Factor C then dissociates, and DNA polymerase delta binds and catalyzes the processive synthesis of DNA.
Accurate and efficient genome duplication requires coordinated processes to replicate two template strands at eucaryotic replication forks. Knowledge of the fundamental reactions involved in replication fork progression is derived largely from biochemical studies of the replication of simian virus and from yeast genetic studies. Since duplex DNA forms an anti-parallel structure, and DNA polymerases are unidirectional, one of the new strands is synthesized continuously in the direction of fork movement. This strand is designated as the leading strand. The other strand grows in the direction away from fork movement, and is called the lagging strand. Several specific interactions among the various proteins involved in DNA replication underlie the mechanism of DNA synthesis, on both the leading and lagging strands, at a DNA replication fork. These interactions allow the replication enzymes to cooperate in the replication process (Hurwitz et al 1990; Brush et al 1996; Ayyagari et al 1995; Budd & Campbell 1997; Bambara et al 1997).
The key event that allows the processive synthesis on the lagging strand, is polymerase switching from pol alpha to pol delta, as on the leading strand. However, the processive synthesis on the lagging strand proceeds very differently. DNA synthesis is discontinuous, and involves the formation of short fragments called the Okazaki fragments. During the synthesis of Okazaki fragments, the RNA primer is folded into a single-stranded flap, which is removed by endonucleases. This is followed by the ligation of adjacent Okazaki fragments.
Removal of the flap by FEN-1 leads to the generation of a nick between the 3'-end of the upstream Okazaki fragment and the 5'-end of the downstream Okazaki fragment. DNA ligase I then seals the nicks between adjacent processed Okazaki fragments to generate intact double-stranded DNA.
The actual synthesis of DNA occurs in the S phase of the cell cycle. This includes the initiation of DNA replication, when the first nucleotide of the new strand is laid down during the synthesis of the primer. The DNA replication preinitiation events begin in late M or early G1 phase.
Members of the Dedicator of cytokinesis (DOCK) family, also known as the Dock180 superfamily, are Rho GTPase guanine nucleotide exchange factors (GEFs), modulating Rho GTPase activity (Cote & Vuori 2002). All eleven human members share the presence of two evolutionarily conserved protein domains, termed DHR-1 and DHR-2 (Cote & Vuori 2007). The DHR-2 domains of several DOCKs interact with the nucleotide-free forms of Rho GTPases, intermediates in the catalytic reaction leading to the exchange of GDP for GTP. DHR-2 domains have been shown necessary and sufficient to promote specific guanine nucleotide exchange on various Rho GTPases, both in vitro and in vivo. Inactivation of the DHR-2 domain in DOCK1 (Dock180) has been shown to block Rac activation, cell migration and phagocytosis (Brugnera et al. 2002, Grimsley et al. 2004, Cote & Vuori 2002). The DHR-1 domain of DOCK1 was shown to mediate a specific interaction with PIP2 and PIP3 signaling lipids in vitro and in cells (Cote et al. 2005). Mutations of the DOCK1 DHR-1 domain blocked Rac-dependent cell elongation and cell migration suggesting that the role of DHR-1 is to position DOCK1 at sites of PIP3 production by PI3-kinase, coupling this to Rac signaling (Cote & Vuori 2007).
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Kinesin-5 motors are bipolar homotetramers with two motor domains at each end, separated by a stalk/tail region (Cole et al. 1994). During mitosis, Kinesin-5 motors function near the spindle midzone to maintain pole to pole distance. Motor domains attach to microtubules from opposite poles and translocate towards the plus ends, thereby pushing the spindle poles apart (Kapitein et al. 2005). Kinesin-5 is also involved in axon growth (Myers & Baas 2007).
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Human kinesin-7, or CENP-E was one of the first kinesins to be discovered (Yen et al. 1991). It is essential for mammalian development, having a role in stabilizing kinetochore-microtubule capture (Putkey et al. 2002), CENP-E is an integral component of kinetochore corona fibers that link centromeres to spindle microtubules and localizes to kinetochores throughout all phases of mitotic chromosome movement (early premetaphase through anaphase A). Though originally reported to be minus-end-directed it is now believed to be a plus-end-directed dimeric kinesin (Espeut et al. 2008). It is sequestered in the cytoplasm until nuclear envelope breakdown and then localizes to its chromosomal cargo at the kinetochores (Brown et al. 1996).
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Kinesin-8 is a plus-end-directed dimeric kinesin with an internal motor domain (Loughlin et al. 2008) that can depolymerize stable microtubuless specifically at their plus-ends (Pereira et al. 1997) in a length-dependent manner (Varga et al. 2006). Human kinesin-8 KIF18A is believed to promote chromosome congression by attenuating chromosome oscillation magnitudes (Stumpff et al. 2008).
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KIF9 has the coiled-coil domain typical of the dimeric kinesins and is believed to function as a dimer.
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Kinesins are a superfamily of microtubule-based motor proteins that have diverse functions in transport of vesicles, organelles and chromosomes, and regulate microtubule dynamics. There are 14 families of kinesins, all reprsented in humans. A standardized nomenclature was published in 2004 (Lawrence et al.).
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Megakaryocytes (MKs) give rise to circulating platelets (thrombocytes) through terminal differentiation of MKs which release cytoplasmic fragments as circulating platelets. As MKs mature they undergo endoreduplication (polyploidisation) and expansion of cytoplasmic mass to cell sizes larger than 50-100 microns, and ploidy ranges up to 128 N. As MK's mature, the polyploid nucleus becomes horseshoe-shaped, the cytoplasm expands, and platelet organelles and the demarcation membrane system are amplified. Proplatelet projections form which give rise to de novo circulating platelets (Deutsch & Tomer 2006). The processes of megakaryocytopoiesis and platelet production occur within a complex microenvironment where chemokines, cytokines and adhesive interactions play major roles (Avecilla et al. 2004). Megakaryocytopoiesis is regulated at several levels including proliferation, differentiation and platelet release (Kaushansky 2003). Thrombopoietin (TPO/c-Mpl ligand) is the most potent cytokine stimulating proliferation and maturation of MK progenitors (Kaushansky 2005) but many other growth factors are involved. MK development is controlled by the action of multiple Transcriptin Factors, many MK-specific genes are co-regulated by GATA and friend of GATA (FOG), RUNX1 and ETS proteins. Nuclear factor erythroid 2 (NF-E2) which has an MK-erythroid specific 45-kDa subunit controls terminal MK maturation, proplatelet formation and platelet release (Schulze & Shivdasani 2004). NF-E2 deficient mice have profound thrombocytopenia (Shiraga et al. 1999). c-myb functions with p300 as a negative regulator of thrombopoiesis (Metcalf et al. 2005). During MK maturation, internal membrane systems, granules and organelles are assembled. Cytoplasmic fragmentation requires changes in the MK cytoskeleton and formation of organelles and channels. Individual organelles migrate from the cell body to the proplatelet ends, with approximately 30 percent of organelles/granules in motion at any given time (Richardson et al. 2005).
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Hemostasis is a physiological response that culminates in the arrest of bleeding from an injured vessel. Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhesion and activation, suppresses coagulation, enhances fibrin cleavage and is anti-inflammatory in character. Under acute vascular trauma, vasoconstrictor mechanisms predominate and the endothelium becomes prothrombotic, procoagulatory and proinflammatory in nature. This is achieved by a reduction of endothelial dilating agents: adenosine, NO and prostacyclin; and by the direct action of ADP, serotonin and thromboxane on vascular smooth muscle cells to elicit their contraction (Becker et al. 2000). The chief trigger for the change in endothelial function that leads to the formation of a haemostatic thrombus is the loss of the endothelial cell barrier between blood and extracellular matrix components (Ruggeri 2002). Circulating platelets identify and discriminate areas of endothelial lesions; here, they adhere to the exposed sub endothelium. Their interaction with the various thrombogenic substrates and locally generated or released agonists results in platelet activation. This process is described as possessing two stages, firstly, adhesion - the initial tethering to a surface, and secondly aggregation - the platelet-platelet cohesion (Savage & Cattaneo et al. 2001). Three mechansism contribute to the loss of blood following vessel injury. The vessel constricts, reducing the loss of blood. Platelets adhere to the site of injury, become activated and aggregate with fibrinogen into a soft plug that limits blood loss, a process termed primary hemostasis. Proteins and small molecules are released from granules by activated platelets, stimulating the plug formation process. Fibrinogen from plasma forms bridges between activated platelets. These events initiate the clotting cascade (secondary hemostasis). Negatively-charged phospholipids exposed at the site of injury and on activated platelets interact with tissue factor, leading to a cascade of reactions that culminates with the formation of an insoluble fibrin clot.
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Internalization of the epidermal growth factor receptor: role in signalling
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The yeast ALG11 gene specifies addition of the terminal alpha 1,2-Man to the Man5GlcNAc2-PP-dolichol N-glycosylation intermediate formed on the cytosolic side of the endoplasmic reticulum
Apoptotic factors released from the mitochondria promote apoptosis through several different mechanisms. Cytochrome C participates in Apoptosome driven effector caspase activation while SMAC relieves IAP mediated caspase inhibition.
Permeabilization of the outer mitochondrial membrane by pro-apoptotic BCL2 family proteins, such as BAK and BAX, allows cytochrome c eflux from the mitochondrial intermembrane space into the cytosol (Arnoult et al. 2003).
Platelet releasate contains a range of proteins that do not originate in specialized storage granules. In some cases platelet lysis may contribute to the presence of these proteins in the platelet relesate.
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Activation of phospholipase C enzymes results in the generation of second messengers of the phosphatidylinositol pathway. The events resulting from this pathway are a rise in intracellular calcium and activation of Protein Kinase C (PKC). Phospholipase C cleaves the phosphodiester bond in PIP2 to form 1,2 Diacylglycerol (DAG) and 1,4,5-inositol trisphosphate (IP3). IP3 opens Ca2+ channels in the platelet dense tubular system, raising intracellular Ca2+ levels. DAG is a second messenger that regulates a family of Ser/Thr kinases consisting of PKC isozymes (Nishizuka 1995). DAG achieves activation of PKC isozymes by increasing their affinity for phospholipid. Most PKC enzymes are also calcium-dependent, so their activation is in synergy with the rise in intracellular Ca2+. Platelets contain several PKC isoforms that can be activated by DAG and/or Ca2+ (Chang 1997).
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Platelet activation begins with the initial binding of adhesive ligands and of the excitatory platelet agonists (released or generated at the sites of vascular trauma) to cognate receptors on the platelet membrane (Ruggeri 2002). Intracellular signaling reactions then enhance the adhesive and procoagulant properties of tethered platelets or of platelets circulating in the proximity. Once platelets have adhered they degranulate, releasing stored secondary agents such as ADP, ATP, and synthesize thromboxane A2. These amplify the response, activating and recruiting further platelets to the area and promoting platelet aggregation. These amplify the response, activating and recruiting further platelets to the area and promoting platelet aggregation. Adenosine nucleotides signal through P2 purinergic receptors on the platelet membrane. ADP activates P2Y1 and P2Y12, which signal via both the alpha and gamma:beta components of the heterotrimeric G-protein (Hirsch et al. 2001, 2006), while ATP activates the ionotropic P2X1 receptor (Kunapuli et al. 2003). Activation of these receptors initiates a complex signaling cascade that ultimately results in platelet activation, aggregation and thrombus formation (Kahner et al. 2006). Integrin AlphaIIbBeta3 is the most abundant platelet receptor, with 40 000 to 80 000 copies per resting platelet, acting as a major receptor for fibrinogen and other adhesive molecules (Wagner et al. 1996). Activation of AlphaIIbBeta3 enhances adhesion and leads to platelet-platelet interactions, and thus aggregation (Philips et al. 1991). GP VI is the most potent collagen receptor initiating signal generation, an ability derived from its interaction with the FcRI gamma chain. This results in the phosphorylation of the gamma-chain by non-receptor tyrosine kinases of the Src family (1). The phosphotyrosine motif is recognized by the SH2 domains of Syk, a tyrosine kinase. This association activates the Syk enzyme, leading to activation (by tyrosine phosphorylation) of PLC gamma2 (2). Thrombin is an important platelet agonist generated on the membrane of stimulated platelets. Thrombin acts via cell surface Protease Activated Receptors (PARs). PARs are G-protein coupled receptors activated by a proteolytic cleavage in an extracellular loop (Vu, 1991) (3). Activated PARs signal via G alpha q (4) and via the beta:gamma component of the G-protein (5). Both stimulate PLC giving rise to PIP2 hydrolysis and consequent activation of PI3K (6). PLCgamma2 activation also gives rise to IP3 (7) which stimulates the IP3 receptor (8) leading to increased intracellular calcium. Platelet activation further results in the scramblase-mediated transport of negatively-charged phospholipids to the platelet surface. These phospholipids provide a catalytic surface (with the charge provided by phosphatidylserine and phosphatidylethanolamine) for the tenase complex (formed by the activated forms of the blood coagulation factors factor VIII and factor I).
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After Platelet activation '78 kDa glucose-regulated protein' from the endoplasmic reticulum lumen is released in to the extracellular platelet releasate.
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Platelets function as exocytotic cells, secreting a plethora of effector molecules at sites of vascular injury. Platelets contain a number of distinguishable storage granules including alpha granules, dense granules and lysosomes. On activation platelets release a variety of proteins, largely from storage granules but also as the result of apparent cell lysis. These act in an autocrine or paracrine fashion to modulate cell signaling. Alpha granules contain mainly polypeptides such as fibrinogen, von Willebrand factor, growth factors and protease inhibitors that that supplement thrombin generation at the site of injury. Dense granules contain small molecules, particularly adenosine diphosphate (ADP), adenosine triphosphate (ATP), serotonin and calcium, all recruit platelets to the site of injury.
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RNA interference suggests a primary role for monoacylglycerol lipase in the degradation of the endocannabinoid 2-arachidonoylglycerol
The small GTPase Rab5 regulates membrane traffic into and between early endosomes by specifically recruiting cytosolic effector proteins to their site of action on early endosomal membranes. Rab5 occupies a restricted membrane subdomain on endosomes that has distinct biochemical features when compared with neighboring subcompartments (Sonnichsen et al. 2000). Rab5 is believed to form this subdomain by recruiting the specific PI3 kinase VPS-45, causing localized production of PI-3-phosphate (PI-3P) (Christoforidis et al. 1999). Rabenosyn-5 is a Rab5 effector, recruited in a phosphatidylinositol-3-kinase dependent fashion to early endosomes where it serves as a molecular link between VPS-45 and Rab5.
GTP-AMP phosphotransferase, also called Adenylate kinase 3 catalyzes phosphate transfer from GTP to AMP (EC 2.7.4.10). A crystal structure is available (Choe et al. 2005).
F-actin-capping protein binds in a Ca2+-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits. Unlike other capping proteins (such as gelsolin and severin), they do not sever actin filaments.
Metabolism of highly unsaturated n-3 and n-6 fatty acids
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A regulated balance between cell survival and apoptosis is essential for normal development and homeostasis of multicellular organisms (see Matsuzawa, 2001). Defects in control of this balance may contribute to autoimmune disease, neurodegeneration and cancer. Protein ubiquitination and degradation is one of the major mechanisms that regulate apoptotic cell death (reviewed in Yang and Yu 2003).
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Apoptosis is a distinct form of cell death that is functionally and morphologically different from necrosis. Nuclear chromatin condensation, cytoplasmic shrinking, dilated endoplasmic reticulum, and membrane blebbing characterize apoptosis in general. Mitochondria remain morphologically unchanged. In 1972 Kerr et al introduced the concept of apoptosis as a distinct form of "cell-death", and the mechanisms of various apoptotic pathways are still being revealed today. The two principal pathways of apoptosis are (1) the Bcl-2 inhibitable or intrinsic pathway induced by various forms of stress like intracellular damage, developmental cues, and external stimuli and (2) the caspase 8/10 dependent or extrinsic pathway initiated by the engagement of death receptors The caspase 8/10 dependent or extrinsic pathway is a death receptor mediated mechanism that results in the activation of caspase-8 and caspase-10. Activation of death receptors like Fas/CD95, TNFR1, and the TRAIL receptor is promoted by the TNF family of ligands including FASL (APO1L OR CD95L), TNF, LT-alpha, LT-beta, CD40L, LIGHT, RANKL, BLYS/BAFF, and APO2L/TRAIL. These ligands are released in response to microbial infection, or as part of the cellular, humoral immunity responses during the formation of lymphoid organs, activation of dendritic cells, stimulation or survival of T, B, and natural killer (NK) cells, cytotoxic response to viral infection or oncogenic transformation. The Bcl-2 inhibitable or intrinsic pathway of apoptosis is a stress-inducible process, and acts through the activation of caspase-9 via Apaf-1 and cytochrome c. The rupture of the mitochondrial membrane, a rapid process involving some of the Bcl-2 family proteins, releases these molecules into the cytoplasm. Examples of cellular processes that may induce the intrinsic pathway in response to various damage signals include: auto reactivity in lymphocytes, cytokine deprivation, calcium flux or cellular damage by cytotoxic drugs like taxol, deprivation of nutrients like glucose and growth factors like EGF, anoikis, transactivation of target genes by tumor suppressors including p53. In many non-immune cells, death signals initiated by the extrinsic pathway are amplified by connections to the intrinsic pathway. The connecting link appears to be the truncated BID (tBID) protein a proteolytic cleavage product mediated by caspase-8 or other enzymes.
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The L13a subunit of the 60s ribosome is phosphorylated about 16 hours after INF gamma induction by an unknown kinase. At this time, L13a is also released from the 60s subunit (Mazumder et al.,2003). It is unclear, however, whether phosphorylation occurs before or after the release of L13a. Here, phosphorylation is shown as occurring after release.
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Although the mechanism through which L13a prevents translation initiation has not been determined, Mazumder et al. (2003) have described four alternatives. L13a could (1) inhibit the function of eIF4F, (2) block the recruitment of the 43S preinitiation complex, (3) prevent scanning of the 43S complex to the initiation codon, or 4) interfere with joining of the 60S ribosomal subunit.
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Stimulation of cell death by PAK-2 requires the generation and stabilization of the caspase-activated form, PAK-2p34 (Walter et al., 1998;Jakobi et al., 2003). Levels of proteolytically activated PAK-2p34 protein are controlled by ubiquitin-mediated proteolysis. PAK-2p34 but not full-length PAK-2 is degraded by the 26 S proteasome (Jakobi et al., 2003). It is not known whether ubiquitination and degradation of PAK-2p34 occurs in the cytoplasm or in the nucleus.
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Murine PS-GAP interacts specifically with caspase-activated PAK-2p34, but not active or inactive full-length PAK-2, through a region between the GAP and SH3 domains (Koeppel et al.,2004). Evidence for this reaction comes from experiments using both mouse and rabbit proteins.
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Following caspase mediated cleavage, PAK-2p34 translocates to the nucleus (Jakobi et al., 2003). The interaction with PS-GAP changes the localization of PAK-2p34 from the nucleus to the perinuclear region (Koeppel et al.,2004).
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PS-GAP (RGH10) interacts specifically with caspase-activated PAK-2p34 reducing the ability of PAK-2p34 to induce cell death. This interaction inhibits the kinase activity of PAK-2p34 and changes the localization of PAK-2p34 from the nucleus to the perinuclear region (Koeppel et al., 2004).
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MHC class I endosomal and lysosomal trafficking coincides with exogenous antigen loading in dendritic cells
In the execution phase of apoptosis, effector caspases cleave vital cellular proteins leading to the morphological changes that characterize apoptosis. These changes include destruction of the nucleus and other organelles, DNA fragmentation, chromatin condensation, cell shrinkage and cell detachment and membrane blebbing (reviewed in Fischer et al., 2003).
Proteolytically activated PAK-2p34, but not full-length PAK-2, is degraded rapidly by the proteasome (Jakobi et al., 2003). Here, degradation of PAK-2p34 is described as occurring in the cytosol. However, to date it is not known whether this occurs in the nucleus or in the cytoplasm.
Epidermal growth factor receptor activation in glioblastoma through novel missense mutations in the extracellular domain
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Structural insight into the inhibition of human kynurenine aminotransferase I/glutamine transaminase K
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In response to stress signals, the p21-activated protein kinase PAK-2 stimulates a cell death response characterized by increased cell rounding and apoptotic chromatin condensation (see Jakobi et al., 2003). PAK-2 is proteolytically cleaved by caspase-3 producing a constitutively active fragment, PAK-2p34. Following cleavage, PAK-2p34 is autophosphorylated at Thr 402 and transported to the nucleus where it accumulates due to the loss of its nuclear export signal motif (Jakobi et al., 2003). The activity of PAK-2p34 appears to be regulated both by proteosomal degradation (Jakobi et al., 2003) and by association with the GTPase-activating protein PS-GAP/ RHG-10. This interaction inhibits the kinase activity of PAK-2p34 and changes the localization of PAK-2p34 from the nucleus to the perinuclear region (Koeppel et al., 2004). PAK-2p34 may function in the down-regulation of translation initiation in apoptosis through phosphorylation of Mnk1 (Orton et al.,2004).
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Adenoviral expression of the BAP31 cleavage product, p20 causes early release of Ca2+ from the ER, concomitant uptake of Ca2+ into mitochondria, and recruitment of Drp1 to the mitochondria (Breckenridge et al., 2003) . Drp1 mediates scission of the outer mitochondrial membrane, resulting in dramatic fragmentation and fission of the mitochondrial network .
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The subcellular localization of PAK-2 is controlled by nuclear localization and nuclear export signal motifs (Jakobi et al.,2003). The regulatory domain contains a nuclear export signal motif that prevents the nuclear accumulation of full-length PAK-2. The activating proteolytic cleavage disrupts the nuclear export signal in PAK-2 and removes most its regulatory domain. The resulting activated PAK-2p34 fragment contains a nuclear localization signal and translocates to and is retained in the nucleus (Jakobi et al.,2003).
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Inactive PAK-2 can be partially autophosphorylated in the regulatory region without being activated (Gatti et al. 1999).
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DNA fragmentation in response to apoptotic signals is achieved through the activity of two apoptotic nucleases, termed DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) and endonuclease G (Endo G) (reviewed in Widlak and Garrard, 2005). These endonucleases cleave chromatin producing 3'-hydroxyl groups and 5'-phosphate residues. 50-300 kb cleavage products are produced followed by internucleosomal DNA fragmentation. Although the activities of DFF and Endo G are similar, they reside in different locations within the cell and are regulated in different ways.
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Isolation and sequence of the human farnesyl pyrophosphate synthetase cDNA. Coordinate regulation of the mRNAs for farnesyl pyrophosphate synthetase, 3-hydroxy-3-methylglutaryl coenzyme A reductase, and 3-hydroxy-3-methylglutaryl coenzyme A synthase by phorbol ester
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Activation of PAK-2p34 coincides with autophosphorylation of Thr 402 in the the catalytic domain (Walter et al., 1998).
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The major HMG-box-containing chromatin proteins HMGB1 and HMGB2 stimulate DNA cleavage by DFF40/CAD (Liu et al., 1998; Toh et al., 1998; Widlak et al., 2000). Changes in DNA conformation following HMG-box binding makes the substrate more accessible to cleavage by DFF40/CAD nuclease and thus may contribute to preferential linker DNA cleavage during apoptosis (Kalinowska-Herok and Widlak., 2008).
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DNA fragmentation in response to apoptotic signals is achieved, in part, through the activity of apoptotic nucleases, termed DNA fragmentation factor (DFF) or caspase-activated DNase (CAD) (reviewed in Widlak and Garrard, 2005). In non-apoptotic cells, DFF is a nuclear heterodimer consisting of a 45 kD chaperone and inhibitor subunit (DFF45)/inhibitor of CAD (ICAD-L)] and a 40 kD nuclease subunit (DFF40/CAD)( Liu et al. 1997, 1998; Enari et al. 1998). During apoptosis, activated caspase-3 or -7 cleave DFF45/ICAD releasing active DFF40/CAD nuclease. The activity of DFF is tightly controlled at multiple stages. During translation, DFF45/ICAD, Hsp70, and Hsp40 proteins play a role in insuring the appropriate folding of DFF40 during translation(Sakahira and Nagata, 2002). The nuclease activity of DFF40 is enhanced by the chromosomal proteins histone H1, Topoisomerase II and HMGB1/2(Widlak et al., 2000). In addition, the inhibitors (DFF45/35; ICAD-S/L) are produced in stoichiometric excess (Widlak et al., 2003).
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The intrinsic (Bcl-2 inhibitable or mitochondrial) pathway of apoptosis functions in response to various types of intracellular stress including growth factor withdrawal, DNA damage, unfolding stresses in the endoplasmic reticulum and death receptor stimulation. Following the reception of stress signals, proapoptotic BCL-2 family proteins are activated and subsequently interact with and inactivate antiapoptotic BCL-2 proteins. This interaction leads to the destabilization of the mitochondrial membrane and release of apoptotic factors. These factors induce the caspase proteolytic cascade, chromatin condensation, and DNA fragmentation, ultimately leading to cell death. The key players in the Intrinsic pathway are the Bcl-2 family of proteins that are critical death regulators residing immediately upstream of mitochondria. The Bcl-2 family consists of both anti- and proapoptotic members that possess conserved alpha-helices with sequence conservation clustered in BCL-2 Homology (BH) domains. Proapoptotic members are organized as follows: 1. "Multidomain" BAX family proteins such as BAX, BAK etc. that display sequence conservation in their BH1-3 regions. These proteins act downstream in mitochondrial disruption. 2. "BH3-only" proteins such as BID,BAD, NOXA, PUMA,BIM, and BMF have only the short BH3 motif. These act upstream in the pathway, detecting developmental death cues or intracellular damage. Anti-apoptotic members like Bcl-2, Bcl-XL and their relatives exhibit homology in all segments BH1-4. One of the critical functions of BCL-2/BCL-XL proteins is to maintain the integrity of the mitochondrial outer membrane.
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A common mutation in the fibroblast growth factor receptor 1 gene in Pfeiffer syndrome
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Prolactin and ErbB4/HER4 signaling interact via Janus kinase 2 to induce mammary epithelial cell gene expression differentiation
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Proteolytic cleavage of the COOH-terminal domain of Mst3 by caspases promotes nuclear translocation of the catalytic domain (Huang et al., 2002).
The amino acid sequence of cytosolic aspartate aminotransferase from human liver
The localization of the Cdc25A, B and C proteins is dynamic involving the shuttling of these proteins between the nucleus and the cytoplasm. Sequences in these proteins mediate both nuclear export and import (Kallstrom et al., 2005; Lindqvist et al., 2004; Graves et al, 2001; Takizawa and Morgan, 2000).
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The rapid translocation of cyclin B1:Cdc2 from the cytoplasm to the nucleus at the onset of mitosis is a result of an increase in the rate of import and, likely, a decreased rate of export. The increased rate of nuclear import is dependent upon phosphorylation of the CRS which creates a nuclear import signal in the amino terminus of cyclin B1 (Hagting et al, 1999).
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At the onset of mitosis, cyclin B is phosphorylated in the CRS sequence which creates a nuclear import signal in the amino terminus. The kinase(s) responsible for this phosphorylation are not yet known (Hagting et al., 1999).
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Activation of the mitotic cyclin:Cdc2 complexes at mitosis requires the removal of the inhibitory phosphate groups on Cdc2. This dephosphorylation is achieved by the activity of the Cdc25 family of phosphatases. The Cdc25 members, Cdc25A, Cdc25B, and Cdc25C are kept inactive during interphase and are activated at the G2/M transition. Cyclin B1:Cdc2 itself appears to participate in the full activation of Cdc25 in a process that involves an amplication loop (see Wolfe and Gould, 2004). The initial activation of the cyclin B1-Cdc2 complex occurs in the cytoplasm in prophase (Jackman et al., 2003). Cdc25B, which is present at highest concentrations in the cytoplasm at this time, is thought to trigger the activation of cyclin B1-Cdc2 (Lindqvist et al. 2004; Honda et al., 1993). Active cyclin B:Cdc2 then phosphorylates and activates Cdc25C and stabilizes Cdc25A (Strausfeld et al., 1994; Hoffman et al.,1993; Mailand et al, 2002). This creates positive feedback loops that allows Cdc25A and Cdc25C to dephosphorylate and further activate Cdc2.
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Cdc25B shuttles between the nucleus and the cytoplasm. Translocation out of the nucleus involves a nuclear export sequence in the N-terminus of Cdc25B (Lindqvist et al., 2004).
During interphase, cyclin B1 shuttles continuously in and out of the nucleus. The cyclin B cytoplasmic retention sequence (CRS), which is responsible for its interphase cytoplasmic localization, functions as a nuclear export sequence (Yang et al., 1998).
Full activity of most CDKs is dependent on CAK mediated phosphorylation at a conserved residue (Thr 161 in Cdc2). This modification is thought to improve substrate binding. Cyclin B:Cdc2 complexes have considerably low activity in the absence of CAK mediated phosphorylation (Desai et al 1995).
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During interphase, cyclin B1:Cdc2 shuttles continuously in and out of the nucleus. Cyclin B1:Cdc2 is transported into the nucleus by an unusual mechanism that requires importin b but not importin a or Ran. Dissociation of the cyclin-B1:Cdc2:importin complex in the nucleus requires ATP and involves other yet unidentified nuclear factors (Takizawa et al.,1991).
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PHF8 activates transcription of rRNA genes through H3K4me3 binding and H3K9me1/2 demethylation
The E3 ligase Aip4/Itch ubiquitinates and targets ErbB-4 for degradation
A description of the mitotic proteins targeted by the mitotic cyclin:CDK complexes will be covered in a later release.
Cell cycle progression is regulated by cyclin-dependent protein kinases at both the G1/S and the G2/M transitions. The G2/M transition is regulated through the phosphorylation of nuclear lamins and histones (reviewed in Sefton, 2001).
Following its translocation to the nucleus, Cdc25 dephosphorylates and activates nuclear cyclin B1:Cdc2 complexes (Strausfeld et al., 1991).
At mitotic entry Plk1 phosphorylates and inhibits Myt1 activity. Cyclin B1-bound Cdc2, which is the target of Myt1, functions in a feedback loop and phosphorylates and further inhibits Myt1.
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Molecular identification of microsomal acyl-CoA:glycerol-3-phosphate acyltransferase, a key enzyme in de novo triacylglycerol synthesis
It has been shown that Xenopus polo homolog, Plx1, directly phosphorylates and activates Cdc25C, which in turn dephosphorylates and activates Cdc2. This step is critical for the onset of mitosis. Since Plx1-dependent Cdc25C phosphorylation occurs in the absence of Cdc2 activity, it is likely that Plx1 is a triggering kinase, which leads to the activation of Cdc2 and therefore the normal onset of mitosis. In addition to catalytically activating CDC25C, PLK1-mediated phosphorylation also results in the nuclear accumulation of CDC25C (Toyoshima-Morimoto et al. 2002).
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At mitotic entry, Plk1 phosphorylates and activates Cdc25C phosphatase, whereas it phosphorylates and down-regulates Wee1A (Watanabe et al. 2004). Plk1 also phosphorylates and inhibits Myt1 activity (Sagata 2005). Cyclin B1-bound Cdc2, which is the target of Cdc25C, Wee1A, and Myt1, functions in a feedback loop and phosphorylates the latter components (Cdc25C, Wee1A, Myt1). The Cdc2- dependent phosphorylation provides docking sites for the polo-box domain of Plk1, thus promoting the Plk1-dependent regulation of these components and, as a result, activation of Cdc2-Cyclin B1. PLK1 phosphorylates and activates the transcription factor FOXM1 which stimulates the expression of a number of genes needed for G2/M transition, including PLK1, thereby creating a positive feedback loop (Laoukili et al. 2005, Fu et al. 2008, Sadasivam et al. 2012, Chen et al. 2013).
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The two B-type cyclins localize to different regions within the cell and and are thought to have specific roles as CDK1-activating subunits (see Bellanger et al., 2007). Cyclin B1 is primarily cytoplasmic during interphase and translocates into the nucleus at the onset of mitosis (Jackman et al., 1995; Hagting et al., 1999). Cyclin B2 colocalizes with the Golgi apparatus and contributes to its fragmentation during mitosis (Jackman et al., 1995; Draviam et al., 2001).
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At the beginning of this reaction, 1 molecule of 'Cyclin B2:phospho-Cdc2(Thr 14, Thr 161)', and 1 molecule of 'H2O' are present. At the end of this reaction, 1 molecule of 'Cyclin B2:phospho-Cdc2(Thr 161)', and 1 molecule of 'Orthophosphate' are present. This reaction takes place in the 'cytosol' and is mediated by the 'phosphoprotein phosphatase activity' of 'Cdc25'.
The kinase activity of PLK1 is required for cell cycle progression as PLK1 phosphorylates and regulates a number of cellular proteins during mitosis. Centrosomic AURKA (Aurora A kinase), catalytically activated through AJUBA facilitated autophosphorylation on threonine residue T288 at G2/M transition (Hirota et al. 2003), activates PLK1 on centrosomes by phosphorylating threonine residue T210 of PLK1, critical for PLK1 activity (Jang et al. 2002), in the presence of BORA (Macurek et al. 2008, Seki et al. 2008). Once activated, PLK1 phosphorylates BORA and targets it for ubiquitination mediated degradation by SCF-beta-TrCP ubiquitin ligases. Degradation of BORA is thought to allow PLK1 to interact with other substrates (Seki, Coppinger, Du et al. 2008, Seki et al. 2008). The interaction of PLK1 with OPTN (optineurin) provides a negative-feedback mechanism for regulation of PLK1 activity. Phosphorylated PLK1 binds and phosphorylates OPTN associated with the Golgi membrane GTPase RAB8, promoting dissociation of OPTN from Golgi and translocation of OPTN to the nucleus. Phosphorylated OPTN facilitates the mitotic phosphorylation of the myosin phosphatase subunit PPP1R12A (MYPT1) and myosin phosphatase activation (Kachaner et al. 2012). The myosin phosphatase complex dephosphorylates threonine residue T210 of PLK1 and inactivates PLK1 (Yamashiro et al. 2008).
PLK1 is induced in S phase and can be find in both cytosol and nucleus in S and G2 phases of the cell cycle. PLK1 possesses a bipartite nuclear localization signal (NLS) that enables it to enter the nucleus (Taniguchi et al. 2002).
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The human purH gene product, 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase
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Crystal structures that suggest late development of genetic code components for differentiating aromatic side chains
Activation of the novel Protein Kinase C (nPKC) isoforms (delta, epsilon, eta and theta) requires binding to the membrane lipid diacylglycerol (DAG). nPKC activation is sensitive to DAG concentration.
The GPVI receptor is a complex of the GPVI protein with Fc epsilon R1 gamma (FcR). The Src family kinases Fyn and Lyn constitutively associate with the GPVI-FcR complex in platelets and initiate platelet activation through phosphorylation of the immunoreceptor tyrosine-based activation motif (ITAM) in the FcR gamma chain, leading to binding and activation of the tyrosine kinase Syk. Downstream of Syk, a series of adapter molecules and effectors lead to platelet activation. The GPVI receptor signaling cascade is similar to that of T- and B-cell immune receptors, involving the formation of a signalosome composed of adapter and effector proteins. At the core of the T-cell receptor signalosome is the transmembrane adapter LAT and two cytosolic adapters SLP-76 and Gads. While LAT is essential for signalling to PLCgamma1 downstream of the T-cell receptor, the absence of LAT in platelets only impairs the activation of PLCgamma2, the response to collagen and GPVI receptor ligands remains sufficient to elicit a full aggregation response. In contrast, GPVI signalling is almost entirely abolished in the absence of SLP-76.
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Diacylglycerol (DAG) is an important source of arachidonic acid, a signalling molecule and the precursor of the prostaglandins. In human platelet almost all the DAG produced from phosphatidylinositol degradation contains arachidonate (Takamura et al. 1987). DAG is hydrolysed by DAG lipase to 2-arachidonylglycerol (2-AG) which is further hydrolysed by monoacylglycerol lipase. 2-AG is an agonist of cannabinoid receptor 1.
Monoacylglycerol lipase (MAGL) is a key enzyme in the hydrolysis of the endocannabinoid 2-arachidonoylglycerol to arachidonate and glycerol. In adipocytes MAGL and hormone-sensitive lipase (LIPE) hydrolyze intracellular triglyceride stores. MAGL may also complement lipoprotein lipase (LPL) in completing hydrolysis of monoglycerides resulting from degradation of lipoprotein triglycerides.
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3-phosphoinositide dependent protein kinase-1 (PDK1, also known as PKB kinase because of its activity at Protein kinase B) phosphorylates T410 of Protein kinase C zeta type (PKC zeta), leading to activation. The motif surrounding T410 is highly conserved in other PKC family members suggesting that PDK1 might activate other PKCs.
3-phosphoinositide dependent protein kinase-1 (PDK1) and Protein kinase C zeta type (PKC zeta) are associated in fibroblasts. PDK1, also known as Protein kinase B kinase (PKBK), is known to co-localise with Protein kinase B (PKB) in transfected fibroblasts and platelets, suggesting a complex of PDK1, PKB and PKC zeta.
Hydrolysis of phosphatidyl inositol-bisphosphate (PIP2) by phospholipase C (PLC) produces diacylglycerol (DAG) and inositol triphosphate (IP3). Both are potent second messengers. IP3 diffuses into the cytosol, but as DAG is a hydrophobic lipid it remains within the plasma membrane. IP3 stimulates the release of calcium ions from the smooth endoplasmic reticulum, while DAG activates the conventional and unconventional protein kinase C (PKC) isoforms, facilitating the translocation of PKC from the cytosol to the plasma membrane. The effects of DAG are mimicked by tumor-promoting phorbol esters. DAG is also a precursor for the biosynthesis of prostaglandins, the endocannabinoid 2-arachidonoylglycerol and an activator of a subfamily of TRP-C (Transient Receptor Potential Canonical) cation channels 3, 6, and 7.
The conventional Protein Kinase C (cPKC) isoforms have two membrane-targetting domains, a C1 domain which binds to the membrane lipid diacylglycerol (DAG) and a C2 domain which binds membrane phospholipids such as phosphatidylserine, in a calcium-dependent manner. Association of both domains with the plasma membrane produces a conformational change that releases an autoinhibitory pseudosubstrate segment from the substrate-binding cavity, allowing substrate binding and downstream signaling.
At the beginning of this reaction, 1 molecule of 'ATP', and 1 molecule of 'Platelet SEC1 protein' are present. At the end of this reaction, 1 molecule of 'Phosphorylated platelet SEC1 protein', and 1 molecule of 'ADP' are present. This reaction is mediated by the 'calcium-dependent protein kinase C activity' of 'Activated Ca++ and DAG dependent PKC'.
At the beginning of this reaction, 1 molecule of 'ATP', and 1 molecule of 'Syntaxin 4' are present. At the end of this reaction, 1 molecule of 'Phosphorylated syntaxin 4', and 1 molecule of 'ADP' are present. This reaction is mediated by the 'calcium-dependent protein kinase C activity' of 'Activated Ca++ and DAG dependent PKC'.
Functional characterization of human aquaporin 9 as a facilitative glycerol carrier
COQ6 mutations in human patients produce nephrotic syndrome with sensorineural deafness
Role of adaptor TRIF in the MyD88-independent toll-like receptor signaling pathway
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Chromosomal localization of the gene for human glucosamine-6-sulphatase to 12q14
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Mitochondrial Ccs1 contains a structural disulfide bond crucial for the import of this unconventional substrate by the disulfide relay system
Cdc6 is an unstable protein whose de novo synthesis in G1 is important for the onset of S phase and for preventing a 'reductional' anaphase in the budding yeast Saccharomyces cerevisiae.
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ERK1c regulates Golgi fragmentation during mitosis
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MISCELLANEOUS Present with 6210 molecules/cell in log phase SD medium.SIMILARITY Belongs to the eukaryotic RPB8 RNA polymerase subunit family.
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Deregulated FGFR3 mutants in multiple myeloma cell lines with t(4;14): comparative analysis of Y373C, K650E and the novel G384D mutations
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Intracellular signaling pathways activated by neurotrophic factors
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Sodium-dependent phosphate transporter 1
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Sodium-dependent phosphate transporter 2
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Beta-amino acids: mammalian metabolism and utility as alpha-amino acid analogues
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Leptin receptor signaling: pathways to leptin resistance
Neutral and basic amino acid transport protein rBAT
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Vesicular inhibitory amino acid transporter
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Cloning of a human cDNA encoding a novel enzyme involved in the elongation of long-chain polyunsaturated fatty acids
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The in vitro replication of DNA containing the SV40 origin.
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Human cytoplasmic 3-hydroxy-3-methylglutaryl coenzyme A synthase: expression, purification, and characterization of recombinant wild-type and Cys129 mutant enzymes
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SIMILARITY Belongs to the archaeal RpoH/eukaryotic RPB5 RNA polymerase subunit family.
Erythrocytes take up carbon dioxide and release oxygen
MISCELLANEOUS Present with 6090 molecules/cell in log phase SD medium.SIMILARITY Belongs to the archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit family.
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Thematic Review Series: Proteomics. An integrated omics analysis of eicosanoid biology
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Quantitating protein synthesis, degradation, and endogenous antigen processing
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Crystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA thiolase: the importance of potassium and chloride ions for its structure and function
Recognition of nascent RNA by the human La antigen: conserved and divergent features of structure and function.
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cDNA cloning of mouse and human cholesterol 25-hydroxylases, polytopic membrane proteins that synthesize a potent oxysterol regulator of lipid metabolism
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ATP binding/hydrolysis by and phosphorylation of peroxisomal ATP-binding cassette proteins PMP70 (ABCD3) and adrenoleukodystrophy protein (ABCD1)
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MHC molecules and microbial antigen processing in phagosomes
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Glucose and cAMP regulate the L-type pyruvate kinase gene by phosphorylation/dephosphorylation of the carbohydrate response element binding protein
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Crystal structure of the heterodimeric bZIP transcription factor c-Fos-c-Jun bound to DNA
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Mitochondrial ATP-binding cassette proteins
Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
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NADPH:adrenodoxin oxidoreductase, mitochondrial
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MutLalpha and proliferating cell nuclear antigen share binding sites on MutSbeta
AU binding proteins recruit the exosome to degrade ARE-containing mRNAs
NADPH-dependent diflavin oxidoreductase 1 ecNumber1.6.-.-/ecNumber
5-aminolevulinate synthase, non-specific (pyridoxal phosphate cofactor)
5-aminolevulinate synthase, non-specific, mitochondrial
Insights into the structure, mechanism, and regulation of scavenger mRNA decapping activity
Protoheme IX farnesyltransferase, mitochondrial ecNumber2.5.1.-/ecNumber
Coproporphyrinogen III oxidase, mitochondrial
5-aminolevulinate synthase, erythroid (pyridoxal phosphate cofactor)
5-aminolevulinate synthase, erythroid-specific, mitochondrial precursor
Cytochrome c oxidase assembly protein COX15 homolog
hMSH3 and hMSH6 interact with PCNA and colocalize with it to replication foci
Exon-intron organization and chromosomal localization of the mouse monoglyceride lipase gene
Frequent translocation t(4;14)(p16.3;q32.3) in multiple myeloma is associated with increased expression and activating mutations of fibroblast growth factor receptor 3
Acetyl-coenzyme A synthetase 2-like, mitochondrial
acyl-CoA synthetase short-chain family member 1
WW domain-containing protein YAP associates with ErbB-4 and acts as a co-transcriptional activator for the carboxyl-terminal fragment of ErbB-4 that translocates to the nucleus
Hepatic flavin-containing monooxygenase 3
Dimethylaniline monooxygenase (N-oxide forming) 3
Dimethylaniline monooxygenase (N-oxide-forming) 2
Dimethylaniline monooxygenase (N-oxide-forming) 1
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The copper chaperone CCS directly interacts with copper/zinc superoxide dismutase
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The role of adipokines in beta-cell failure of type 2 diabetes
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Multidrug resistance-associated protein 6
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ATP-binding cassette sub-family C member 9
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ATP-binding cassette transporter sub-family C member 8
ATP-binding cassette transporter sub-family C member 11
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Activity of TKI258 against primary cells and cell lines with FGFR1 fusion genes associated with the 8p11 myeloproliferative syndrome
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Genetic disorders of vitamin B12 metabolism: eight complementation groups--eight genes
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Electrogenic sodium bicarbonate cotransporter 4
Electrogenic sodium bicarbonate cotransporter 1
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Mitochondrial GPx1 decreases induced but not basal oxidative damage to mtDNA in T47D cells
Biochem. Biophys. Res. Commun. 272:416-22
Sodium-driven chloride bicarbonate exchanger
Electroneutral sodium bicarbonate exchanger 1
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2459.1
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ATP-binding cassette sub-family B member 7, mitochondrial
Cytosolic Fe-S cluster assembly factor NUBP2
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Mitotic spindle-associated MMXD complex subunit MIP18
MMS19 nucleotide excision repair protein homolog
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Cytosolic Fe-S cluster assembly factor NUBP1
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TFIIH basal transcription factor complex helicase XPD subunit ecNumber3.6.4.12/ecNumber
Probable cytosolic iron-sulfur protein assembly protein CIAO1
Cytosolic Fe-S cluster assembly factor NARFL
DNA polymerase delta catalytic subunit ecNumber2.7.7.7/ecNumber
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Multidrug resistance-associated protein 2
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ATP-binding cassette sub-family D member 3
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ATP-binding cassette sub-family D member 2
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The NLRP3 inflammasome: a sensor of immune danger signals
Multidrug resistance-associated protein 3
ATP-binding cassette sub-family C member 3
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Aromatic-participant interactions are essential for disulfide-bond-based trimerization in human heat shock transcription factor 1
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Alg14 recruits Alg13 to the cytoplasmic face of the endoplasmic reticulum to form a novel bipartite UDP-N-acetylglucosamine transferase required for the second step of N-linked glycosylation
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Regulated release of L13a from the 60S ribosomal subunit as a mechanism of transcript-specific translational control
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The Polo-like kinase Plx1 interacts with and inhibits Myt1 after fertilization of Xenopus eggs
Chromosome condensation by a human condensin complex in Xenopus egg extracts
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LASS5 is a bona fide dihydroceramide synthase that selectively utilizes palmitoyl-CoA as acyl donor
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In vitro analysis of elongation and termination by mutant RNA polymerases with altered termination behavior.
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Na+/Ca2+-K+ exchangers (NCKX): functional properties and physiological roles
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Heat shock factors: integrators of cell stress, development and lifespan
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Molecular mechanisms regulating hormone-sensitive lipase and lipolysis
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Heat shock factor-1 protein in heat shock factor-1 gene-transfected human epidermoid A431 cells requires phosphorylation before inducing heat shock protein-70 production
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Structure of human carnitine acetyltransferase. Molecular basis for fatty acyl transfer.
Cytoplasmic chaperonin containing TCP-1: structural and functional characterization
Solute carrier family 2, facilitated glucose transporter member 7
Solute carrier family 2, facilitated glucose transporter member 9
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AMP-activated/SNF1 protein kinases: conserved guardians of cellular energy
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Characterization of human and murine PMP20 peroxisomal proteins that exhibit antioxidant activity in vitro
The import route of ADP/ATP carrier into mitochondria separates from the general import pathway of cleavable preproteins at the trans side of the outer membrane
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All three IkappaB isoforms and most Rel family members are stably associated with the IkappaB kinase 1/2 complex
A novel diacylglycerol acyltransferase (DGAT2) is decreased in human psoriatic skin and increased in diabetic mice
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The hydrophobic phosphorylation motif of conventional protein kinase C is regulated by autophosphorylation
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Human pyridoxal kinase: overexpression and properties of the recombinant enzyme
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Identification of peroxisomal acyl-CoA thioesterases in yeast and humans
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N (epsilon)-(carboxymethyl)lysine protein adduct is a major immunological epitope in proteins modified with advanced glycation end products of the Maillard reaction
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An updated overview on Wnt signaling pathways: a prelude for more
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Identification of novel PPARgamma target genes in primary human adipocytes
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Identification of the gene responsible for the cblA complementation group of vitamin B12-responsive methylmalonic acidemia based on analysis of prokaryotic gene arrangements
Proc. Natl. Acad. Sci. U.S.A. 99:15554-9
The 2.0 A structure of human ferrochelatase, the terminal enzyme of heme biosynthesis.
Role of subunit diversity in signaling by heterotrimeric G proteins
Neurotrophins and their receptors: a convergence point for many signalling pathways
L1 and NCAM adhesion molecules as signaling coreceptors in neuronal migration and process outgrowth
A structural model for the membrane-integral domain of succinate: quinone
Regulation of telomerase by telomeric proteins
A critical review of the origin and control of adrenal androgens
Baillieres Clin Obstet Gynaecol 11:229-48
AMPK-alpha2:AMPK-beta:AMPK-gamma:AMP (name copied from entity in Homo sapiens)
ESCRT-III/Cargo Complex (name copied from entity in Homo sapiens)
p-S237-TBC1D1:14-3-3 (name copied from entity in Homo sapiens)
AMPK gamma:AMP (name copied from entity in Homo sapiens)
ESCRT-III (name copied from entity in Homo sapiens)
The molecular mechanics of eukaryotic translation
ESCRT-II (name copied from entity in Homo sapiens)
Ubiquinated and PIP3 Endosmal Membrane Bound Cargo (name copied from entity in Homo sapiens)
ESCRT-II/Cargo Complex (name copied from entity in Homo sapiens)
Coatomer:Arf1-GTP:GAP Complex (name copied from entity in Homo sapiens)
Coatomer (name copied from entity in Homo sapiens)
Arf1-GTP (name copied from entity in Homo sapiens)
Modulation of human heat shock factor trimerization by the linker domain
Coatomer:Arf1-GTP Complex (name copied from entity in Homo sapiens)
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617952
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_238711.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617951
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_229232.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5358527
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_228934.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5358521
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617956
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617954
EXO1:MLH1:PMS2:MSH2:MSH3:ATP:PCNA:DNA containing IDL of 2 or more bases and single strand incision (name copied from entity in Homo sapiens)
MLH1:PMS2:MSH2:MSH3:ATP:PCNA:DNA containing IDL of 2 or more bases and single strand incision (name copied from entity in Homo sapiens)
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_236532.1
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MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool
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Stereospecific targeting of MTH1 by (S)-crizotinib as an anticancer strategy
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Iron-sulfur proteins in health and disease
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EXO1:MLH1:PMS2:MSH2:MSH6:ATP:PCNA:DNA containing 1-2 base mismatch and single strand incision (name copied from entity in Homo sapiens)
MSH2:MSH3:ADP (name copied from entity in Homo sapiens)
MSH2:MSH3:ATP (name copied from entity in Homo sapiens)
MLH1:PMS2:MSH2:MSH3:ATP:PCNA:DNA containing IDL of 2 bases or more (name copied from entity in Homo sapiens)
MSH2:MSH3:ADP:DNA containing IDL of 2 bases or more (name copied from entity in Homo sapiens)
MSH2:MSH3:ATP:DNA containing IDL of 2 bases or more (name copied from entity in Homo sapiens)
MLH1:PMS2:MSH2:MSH6:ATP:PCNA:DNA containing 1-2 base mismatch (name copied from entity in Homo sapiens)
MLH1:PMS2 (name copied from entity in Homo sapiens)
MSH2:MSH6:ATP (name copied from entity in Homo sapiens)
MSH2:MSH6:ATP:DNA containing 1-2 base mismatch (name copied from entity in Homo sapiens)
MLH1:PMS2:MSH2:MSH6:ATP:PCNA:DNA containing 1-2 base mismatch and single strand incision (name copied from entity in Homo sapiens)
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_239457.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618689
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_229822.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618690
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617972
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617973
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_242657.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118891.1
Stalled Pol II in TC-NER (name copied from entity in Homo sapiens)
FUNCTION Interacts with the internal control region (ICR) of approximately 50 bases within the 5S RNA genes, is required for correct transcription of these genes by RNA polymerase III. Also binds the transcribed 5S RNA's.MISCELLANEOUS Present with 1380 molecules/cell in log phase SD medium.SIMILARITY Contains 9 C2H2-type zinc fingers.
Active Pol II complex with repaired DNA template:mRNA hybrid (name copied from entity in Homo sapiens)
MSH2:MSH6:ADP (name copied from entity in Homo sapiens)
MSH2:MSH6:ADP:DNA containing 1-2 base mismatch (name copied from entity in Homo sapiens)
Transcription-coupled (TC) repair complex (name copied from entity in Homo sapiens)
Active Pol II transcription complex with damaged DNA hybrid (name copied from entity in Homo sapiens)
RNA Polymerase II holoenzyme complex (hyperphosphorylated) (name copied from entity in Homo sapiens)
ERCC1:XPF complex (name copied from entity in Homo sapiens)
pre-incision complex with open DNA bubble (name copied from entity in Homo sapiens)
Incision complex with 3'-incised damaged DNA (name copied from entity in Homo sapiens)
incision complex for GG-NER (name copied from entity in Homo sapiens)
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1252151
The human ATP-binding cassette (ABC) transporter superfamily
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1252172
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119473.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1252120
Isozymes of glyceraldehyde-3-phosphate dehydrogenase in man and other mammals.
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pre-incision complex in GG-NER (name copied from entity in Homo sapiens)
RPA heterotrimer (name copied from entity in Homo sapiens)
XPC:HR23B complex (name copied from entity in Homo sapiens)
XPC:HR23B:damaged DNA complex (name copied from entity in Homo sapiens)
The control of glycogen metabolism in the liver
RAD51:resected ends of DNA double-strand break (name copied from entity in Homo sapiens)
RAD51:RAD52:DNA double strand break end complex (name copied from entity in Homo sapiens)
RAD52:DNA double-strand break (name copied from entity in Homo sapiens)
RAD50:MRE11 complex (name copied from entity in Homo sapiens)
The equilibrative nucleoside transporter family, SLC29
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1252203
dimeric phospho-ATM complex (name copied from entity in Homo sapiens)
dimeric ATM kinase (name copied from entity in Homo sapiens)
Pol eta:lesioned DNA template inserted with correct base complement (name copied from entity in Homo sapiens)
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1252111
AU-rich element-mediated translational control: complexity and multiple activities of trans-activating factors
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119595.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118880.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1252092
Glucokinase and molecular aspects of liver glycogen metabolism
Tumor necrosis factor-alpha-converting enzyme is required for cleavage of erbB4/HER4
The ABCs of solute carriers: physiological, pathological and therapeutic implications of human membrane transport proteinsIntroduction
Phosphoinositide-3-OH kinase-dependent regulation of glycogen synthase kinase 3 and protein kinase B/AKT by the integrin-linked kinase
VEGF activates protein kinase C-dependent, but Ras-independent Raf-MEK-MAP kinase pathway for DNA synthesis in primary endothelial cells
Targeting the phosphoinositide 3-kinase pathway in cancer
Characterization of photolyase/blue-light receptor homologs in mouse and human cells
Orchestrating nuclear envelope disassembly and reassembly during mitosis
A novel skeletal dysplasia with developmental delay and acanthosis nigricans is caused by a Lys650Met mutation in the fibroblast growth factor receptor 3 gene
Molecular enzymology of carnitine transfer and transport
CREB phosphorylation through the activation of CaMKK
The expanding role of mitochondria in apoptosis.
Human lysyl-tRNA synthetase accepts nucleotide 73 variants and rescues Escherichia coli double-defective mutant
Substrate specificity of the RNase activity of yeast RNA polymerase III.
Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)
Enterohepatic bile salt transporters in normal physiology and liver disease
Human isopentenyl diphosphate: dimethylallyl diphosphate isomerase: overproduction, purification, and characterization
ATM mediated response to DNA double-strand break
Expression patterns of two human genes coding for different rab GDP-dissociation inhibitors (GDIs), extremely conserved proteins involved in cellular transport
Aquaporin-11: a channel protein lacking apparent transport function expressed in brain
Structure of the FGF receptor tyrosine kinase domain reveals a novel autoinhibitory mechanism
The human AQP4 gene: definition of the locus encoding two water channel polypeptides in brain
MISCELLANEOUS Present with 5640 molecules/cell in log phase SD medium.SIMILARITY Belongs to the WD repeat CIA1 family.SIMILARITY Contains 7 WD repeats.
A protein interaction framework for human mRNA degradation
Oxygen and carbon dioxide transport in vertebrate erythrocytes: an evolutionary change in the role of membrane transport
A mannosyltransferase gene at 11q23 is disrupted by a translocation breakpoint that co-segregates with bipolar affective disorder in a small family
A proposed nomenclature system for the cytosolic sulfotransferase (SULT) superfamily
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5428.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110303
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2556.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109960
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_220757.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5610928
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_235070.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618221
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_205262.2
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SAC1-like domains of yeast SAC1, INP52, and INP53 and of human synaptojanin encode polyphosphoinositide phosphatases
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_202535.2
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110298
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_214905.2
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Pol eta:damaged DNA template complex (name copied from entity in Homo sapiens)
REV1:lesioned DNA template with misinserted bases (name copied from entity in Homo sapiens)
REV1:damaged DNA template complex (name copied from entity in Homo sapiens)
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2845.1
Human GTP cyclohydrolase I: only one out of three cDNA isoforms gives rise to the active enzyme
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Protein kinase C alpha-dependent phosphorylation of the mRNA-stabilizing factor HuR: implications for posttranscriptional regulation of cyclooxygenase-2
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618094
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_232590.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5358514
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_230859.1
Differential lysosomal proteolysis in antigen-presenting cells determines antigen fate
The role for endoplasmic reticulum stress in diabetes mellitus
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_222535.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5610931
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5610930
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_246336.1
Signaling through PI3Kgamma: a common platform for leukocyte, platelet and cardiovascular stress sensing
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5610929
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110295
MISCELLANEOUS Present with 1800 molecules/cell in log phase SD medium.SIMILARITY Belongs to the MIP18 family.
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617935
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617946
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617947
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_230818.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5358526
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_228484.1
Thioredoxin-interacting protein links oxidative stress to inflammasome activation
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Differential stimulation of cholesterol and unsaturated fatty acid biosynthesis in cells expressing individual nuclear sterol regulatory element-binding proteins
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_230894.1
Reconstitution of the Mcm2-7p heterohexamer, subunit arrangement, and ATP site architecture
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617944
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617945
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617967
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_234857.1
Genetic disorders of carnitine metabolism and their nutritional management.
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Insulin vesicle release: walk, kiss, pause ... then run
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Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases
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ChREBP activates metabolic gene expression
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_236776.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617971
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617975
Molecular cloning and identification of 3'-phosphoadenosine 5'-phosphosulfate transporter
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617974
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_241763.1
2 Iron:FXN (name copied from entity in Homo sapiens)
2 Iron:FXN:NFS1:ISD11:ISCU (name copied from entity in Homo sapiens)
FDXR:FADH2 (name copied from entity in Homo sapiens)
FDXR:FAD (name copied from entity in Homo sapiens)
gamma-glutamyl-AA (name copied from entity in Homo sapiens)
NFS1:pyridoxal phosphate (name copied from entity in Homo sapiens)
FXN:ISD11:NFS1:ISCU (name copied from entity in Homo sapiens)
ALDH1A1 tetramer (name copied from entity in Homo sapiens)
OPLAH (name copied from entity in Homo sapiens)
GSS (name copied from entity in Homo sapiens)
Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage.
FMO3 (FAD cofactor) (name copied from entity in Homo sapiens)
FMO2 (FAD, Mg2+ cofactors) (name copied from entity in Homo sapiens)
FMO1 (FAD cofactor) (name copied from entity in Homo sapiens)
Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase.
2x(FECH:2Fe-2S cluster) (name copied from entity in Homo sapiens)
2xPPOX:FAD (name copied from entity in Homo sapiens)
2xCPO (name copied from entity in Homo sapiens)
2xUROD (name copied from entity in Homo sapiens)
8xALAD:Pb2+:Zn2+ (name copied from entity in Homo sapiens)
HMBS:DIPY (name copied from entity in Homo sapiens)
ALAS2 homodimer (pyridoxal phosphate cofactor) (name copied from entity in Homo sapiens)
8x(ALAD:Zn2+) (name copied from entity in Homo sapiens)
CIAPIN1:4Fe-4S:2Fe-2S reduced (name copied from entity in Homo sapiens)
NDOR1:CIAPIN1 reduced (name copied from entity in Homo sapiens)
NUBP2:4Fe-4S:NUBP1 (name copied from entity in Homo sapiens)
NUBP1:4Fe-4S (name copied from entity in Homo sapiens)
NARFL:CIAO1:FAM96B:MMS19 (name copied from entity in Homo sapiens)
ABC7 dimer (name copied from entity in Homo sapiens)
NARFL:4Fe-4S (name copied from entity in Homo sapiens)
holo-XPD (name copied from entity in Homo sapiens)
holo-POLD1 (name copied from entity in Homo sapiens)
CIAPIN1:4Fe-4S:2Fe-2S oxidized (name copied from entity in Homo sapiens)
FDX1L (oxidized) (name copied from entity in Homo sapiens)
FXN:NFS1:ISD11:ISCU:2Fe-2S Cluster (name copied from entity in Homo sapiens)
FDX1L (reduced) (name copied from entity in Homo sapiens)
FDX1 (reduced) (name copied from entity in Homo sapiens)
NDOR1:FAD:FMN (name copied from entity in Homo sapiens)
NDOR1:CIAPIN1 oxidized (name copied from entity in Homo sapiens)
ABCG2 dimer (name copied from entity in Homo sapiens)
SLC4A1 dimer (name copied from entity in Homo sapiens)
FDX1 (oxidized) (name copied from entity in Homo sapiens)
Crystal structures of human GAR Tfase at low and high pH and with substrate beta-GAR
Conservation of the human telomere sequence (TTAGGG)n among vertebrates
Close homolog of L1 is an enhancer of integrin-mediated cell migration
KYNU dimer (name copied from entity in Homo sapiens)
AMPK inhibits chREBP transcriptional activation activity
HAAO (name copied from entity in Homo sapiens)
OTC trimer (name copied from entity in Homo sapiens)
ASS1 tetramer (name copied from entity in Homo sapiens)
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NODs: intracellular proteins involved in inflammation and apoptosis
Interaction between the functional polymorphisms of the alcohol-metabolism genes in protection against alcoholism.
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PIKKing on PKB: regulation of PKB activity by phosphorylation
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Identification of a novel aquaporin, AQP12, expressed in pancreatic acinar cells
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Dual phosphorylation controls Cdc25 phosphatases and mitotic entry
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AHCY:NAD+ (name copied from entity in Homo sapiens)
CBS tetramer (name copied from entity in Homo sapiens)
CTH tetramer:PXLP (name copied from entity in Homo sapiens)
CNDP2 (name copied from entity in Homo sapiens)
mTOR is essential for the proteotoxic stress response, HSF1 activation and heat shock protein synthesis
ALAS1 homodimer (pyridoxal phosphate cofactor) (name copied from entity in Homo sapiens)
The MIA system for protein import into the mitochondrial intermembrane space
Presentation of antigens by MHC class II molecules: getting the most out of them
MAT I homotetramer (name copied from entity in Homo sapiens)
MAT III homodimer (name copied from entity in Homo sapiens)
MAT I/III (Mg, K cofactors) (name copied from entity in Homo sapiens)
4x(AHCY:NAD+) (name copied from entity in Homo sapiens)
E1:Mg++ (name copied from entity in Homo sapiens)
HAO1 tetramer (name copied from entity in Homo sapiens)
Hydroxyacid oxidase 1:Flavin mononucleotide complex (name copied from entity in Homo sapiens)
ARD:Fe++ (name copied from entity in Homo sapiens)
AGXT dimer (name copied from entity in Homo sapiens)
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Zizimin2: a novel, DOCK180-related Cdc42 guanine nucleotide exchange factor expressed predominantly in lymphocytes
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BBOX1 dimer (name copied from entity in Homo sapiens)
ARG2 trimer (name copied from entity in Homo sapiens)
System-wide investigation of ErbB4 reveals 19 sites of Tyr phosphorylation that are unusually selective in their recruitment properties
ARG1 trimer (name copied from entity in Homo sapiens)
ASL tetramer (name copied from entity in Homo sapiens)
APIP:Zn++ (name copied from entity in Homo sapiens)
MTAP trimer (name copied from entity in Homo sapiens)
Understanding specificity in metabolic pathways--structural biology of human nucleotide metabolism
Endosomal proteolysis of internalized proteins.
Differential mechanism of G-protein activation induced by endogenous mu-opioid peptides, endomorphin and beta-endorphin
Modulation of mitochondrial membrane permeability in pathogenesis, autophagy and control of metabolism
ARF promotes MDM2 degradation and stabilizes p53: ARF-INK4a locus deletion impairs both the Rb and p53 tumor suppression pathways
5-phospho-alpha-D-ribose 1-diphosphate [ChEBI:17111]
The rate of bulk flow from the endoplasmic reticulum to the cell surface
Biosynthesis and bioproduction of coenzyme Q10 by yeasts and other organisms
57 varieties: the human cytochromes P450
Sequential phosphorylation by mitogen-activated protein kinase and glycogen synthase kinase 3 represses transcriptional activation by heat shock factor-1
Structural determinants for branched-chain aminotransferase isozyme-specific inhibition by the anticonvulsant drug gabapentin
Physiological functions of the pentose phosphate pathway
hOGG1 glycosylase:8-oxo guanine complex (name copied from entity in Homo sapiens)
hOGG1 glycosylase: formamidopyrimidine complex (name copied from entity in Homo sapiens)
ATP2C1/2:Mg2+ (name copied from entity in Homo sapiens)
Aqauporins that transport glycerol across the plasma membrane.
Aquaporin-3, Aquaporin-7, Aquaporin-9, Aquaporin-10
AQP9 tetramer (name copied from entity in Homo sapiens)
AQP10 tetramer (name copied from entity in Homo sapiens)
AQP3 tetramer (name copied from entity in Homo sapiens)
AQP7 tetramer (name copied from entity in Homo sapiens)
Aquaporin-8 tetramer (name copied from entity in Homo sapiens)
ABCD2:ABCD3 (name copied from entity in Homo sapiens)
SLC7A9:SLC3A1 heterodimer (name copied from entity in Homo sapiens)
Aquaporins that transport water across the plasma membrane.
AQP0 (MIP), AQP1, p-AQP2, AQP3, AQP4, AQP5, AQP7, AQP8, AQP9, AQP10, AQP11
Aquaporin-0, Aquaporin-1, Phospho-Aquaporin-2, Aquaporin-3, Aquaporin-4, Aquaporin-5, Aquaporin-7, Aquaporin-8, Aquaporin-9, Aquaporin-10, Aquaporin-11
Neurotrophin signal transduction in the nervous system
ABCD1:ABCD2 (name copied from entity in Homo sapiens)
ABCD1:ABCD3 (name copied from entity in Homo sapiens)
Purification, properties, and sequencing of aminoisobutyrate aminotransferases from rat liver
Rictor, a novel binding partner of mTOR, defines a rapamycin-insensitive and raptor-independent pathway that regulates the cytoskeleton
Iron-sulfur protein maturation in human cells: evidence for a function of frataxin
Compartmentalization of aquaporins in the human intestine
hNTH1 glycosylase: foramidopyrimidine complex (name copied from entity in Homo sapiens)
hNTH1 glycosylase:thymine glycol complex (name copied from entity in Homo sapiens)
DNA containing UNG2-bound apurinic/apyrimidinic site (name copied from entity in Homo sapiens)
DNA containing a hNTH1-bound apurinic/apyrimidinic site (name copied from entity in Homo sapiens)
FEN1:PCNA complex (name copied from entity in Homo sapiens)
DNA containing an hOGG1-bound apurinic/apyrimidinic site (name copied from entity in Homo sapiens)
UNG2 glycosylase:5-hydroxyuracil complex (name copied from entity in Homo sapiens)
UNG2 glycosylase:uracil complex (name copied from entity in Homo sapiens)
hNTH1 glycosylase:cytosine glycol complex (name copied from entity in Homo sapiens)
hNTH1 glycosylase:dihydrouracil complex (name copied from entity in Homo sapiens)
Formation of a pool of free 40S subunits
Structure of D-3-hydroxyacyl-CoA dehydratase/D-3-hydroxyacyl-CoA dehydrogenase bifunctional protein
Mammalian flavin-containing monooxygenases: structure/function, genetic polymorphisms and role in drug metabolism
Identification of the major intestinal fatty acid transport protein
Structure, function and evolution of the signal recognition particle
Decarboxylases involved in polyamine biosynthesis and their inactivation by nitric oxide
Cathepsin S required for normal MHC class II peptide loading and germinal center development
Structural organization and complete nucleotide sequence of the gene encoding human acid sphingomyelinase (SMPD1)
Activation of the FGF receptor underlies neurite outgrowth stimulated by L1, N-CAM, and N-cadherin
FUNCTION Performs an essential role in the oxidative function of the citric acid cycle. Also binds RNA; specifically to the 5'-untranslated leaders of mitochondrial mRNAs.CATALYTIC ACTIVITY Isocitrate + NAD(+) = 2-oxoglutarate + CO(2) + NADH.ENZYME REGULATION Allosterically regulated by several compounds including AMP, NAD(+), and citrate.SUBUNIT Octamer of two non-identical subunits IDH1 and IDH2.MISCELLANEOUS Present with 10500 molecules/cell in log phase SD medium.SIMILARITY Belongs to the isocitrate and isopropylmalate dehydrogenases family.
Cell cycle-dependent recruitment of telomerase RNA and Cajal bodies to human telomeres
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2-acyl-sn-glycero-3-phosphoglycerol [ChEBI:27923]
Structure of human nicotinamide/nicotinic acid mononucleotide adenylyltransferase. Basis for the dual substrate specificity and activation of the oncolytic agent tiazofurin.
Mitochondrial frataxin interacts with ISD11 of the NFS1/ISCU complex and multiple mitochondrial chaperones
Repression of human heat shock factor 1 activity at control temperature by phosphorylation
The general transcription factors of RNA polymerase II.
PKC-beta controls I kappa B kinase lipid raft recruitment and activation in response to BCR signaling
Amino acid transport across mammalian intestinal and renal epithelia
Caspase-activated PAK-2 is regulated by subcellular targeting and proteasomal degradation
Acyl-coenzyme A synthetases in metabolic control
Total enzymic synthesis of cholesterol from lanosterol. Cytochrome b5-dependence of 4-methyl sterol oxidase.
Structure-function relationships in dihydrolipoamide acyltransferases.
Substrate specificity of the TIM22 mitochondrial import pathway revealed with small molecule inhibitor of protein translocation
Functional impairment of lens aquaporin in two families with dominantly inherited cataracts
Lipin is required for efficient breakdown of the nuclear envelope in Caenorhabditis elegans
Inactivation of the C. elegans lipin homolog leads to ER disorganization and to defects in the breakdown and reassembly of the nuclear envelope
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Phosphorylation of threonine 210 and the role of serine 137 in the regulation of mammalian polo-like kinase
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Processing of N-linked carbohydrate chains in a patient with glucosidase I deficiency (CDG type IIb)
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The eukaryotic polypeptide chain releasing factor (eRF3/GSPT) carrying the translation termination signal to the 3'-Poly(A) tail of mRNA. Direct association of erf3/GSPT with polyadenylate-binding protein.
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Activation of human mitochondrial pantothenate kinase 2 by palmitoylcarnitine
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The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition
Involvement of Rac/Cdc42/PAK pathway in cytoskeletal rearrangements
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Crystal structure of porcine mitochondrial NADP+-dependent isocitrate dehydrogenase complexed with Mn2+ and isocitrate. Insights into the enzyme mechanism
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TRAM is specifically involved in the Toll-like receptor 4-mediated
CDG-IL: an infant with a novel mutation in the ALG9 gene and additional phenotypic features
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Biochemical and genetic aspects of mevalonate kinase and its deficiency
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Complementation analysis in PtdInsP kinase-deficient yeast mutants demonstrates that Schizosaccharomyces pombe and murine Fab1p homologues are phosphatidylinositol 3-phosphate 5-kinases
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Glutathione metabolism and its selective modification
PTEN1 is frequently mutated in primary endometrial carcinomas
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Functional link between BLM defective in Bloom's syndrome and the ataxia-telangiectasia-mutated protein, ATM.
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Identification and characterization of a major liver lysophosphatidylcholine acyltransferase
Identification of a colon mucosa gene that is down-regulated in colon adenomas and adenocarcinomas
The faciogenital dysplasia gene product FGD1 functions as a Cdc42Hs-specific guanine-nucleotide exchange factor
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Haplotype analysis suggests that the two predominant mutations in Japanese patients with holocarboxylase synthetase deficiency are founder mutations
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Editing-defective tRNA synthetase causes protein misfolding and neurodegeneration
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Yeast kinesin-8 depolymerizes microtubules in a length-dependent manner
Primary structure of a human trifunctional enzyme. Isolation of a cDNA encoding methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase-formyltetrahydrofolate synthetase.
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Regulation of activated PAK-2p34 by proteasome mediated degradation
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Biochemistry, physiology, and genetics of GPAT, AGPAT, and lipin enzymes in triglyceride synthesis
Am J Physiol Endocrinol Metab 296:E1195-209
Hexosamine biosynthetic pathway mutations cause neuromuscular transmission defect
The cAMP signalling pathway activates CREB through PKA, p38 and MSK1 in NIH 3T3 cells
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Characterization of myotubularin-related protein 7 and its binding partner, myotubularin-related protein 9
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Disulphide bond formation in the intermembrane space of mitochondria
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Phosphoglycerate mutase isozyme marker for tissue differentiation in man
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Functional characterization of NBC4: a new electrogenic sodium-bicarbonate cotransporter
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Mitochondrial GTP-AMP phosphotransferase. 2. Kinetic and equilibrium dialysis studies
Molecular basis of phenotypic variation in patients with argininemia
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Protease-activated receptors in hemostasis, thrombosis and vascular biology
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GPVI and integrin alphaIIb beta3 signaling in platelets
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Cloning and functional characterization of the human GLUT7 isoform SLC2A7 from the small intestine
Am J Physiol Gastrointest Liver Physiol 287:G236-42
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Beta-oxidation of very long chain fatty acids
Cloning and characterization a novel human 1-acyl-sn-glycerol-3-phosphate acyltransferase gene AGPAT7
Trk receptors: roles in neuronal signal transduction
The RNA polymerase II elongation complex.
Use of chromatin immunoprecipitation to clone novel E2F target promoters
Plk1 regulates activation of the anaphase promoting complex by phosphorylating and triggering SCFbetaTrCP-dependent destruction of the APC Inhibitor Emi1
Diacylglycerol metabolism and arachidonic acid release in human fetal membranes and decidua vera
Purification and subunit structure studies of human placental threonyl-tRNA synthetase
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The oxidation of pyruvate in pigeon breast muscle
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Mammalian TOR complex 2 controls the actin cytoskeleton and is rapamycin insensitive
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Crystal structure of human arginase I at 1.29-A resolution and exploration of inhibition in the immune response
Serotonin clearance from the synaptic cleft
Human heat shock factor 1 is predominantly a nuclear protein before and after heat stress
Reconstitution of the transcription factor TFIIH: assignment of functions for the three enzymatic subunits, XPB, XPD, and cdk7
SIMILARITY In the C-terminal section; belongs to the flavoprotein pyridine nucleotide cytochrome reductase family.SIMILARITY Belongs to the NADPH-dependent diflavin oxidoreductase NDOR1 family.SIMILARITY Contains 1 FAD-binding FR-type domain.SIMILARITY Contains 1 flavodoxin-like domain.
Step-size analyses of the mitochondrial Hsp70 import motor reveal the Brownian ratchet in operation
Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate
Mechanisms of caspase-1 activation by P2X7 receptor-mediated K+ release
Characterization of protein synthesis factors from rabbit reticulocytes
(R,R)-3,3'-thiobis-(2-aminopropanoic acid)
(R,R)-2,6-diamino-4-thiaheptanedioic acid
Elongation factor 1 beta of artemia: localization of functional sites and homology to elongation factor 1 delta
Extrahelical (CAG)/(CTG) triplet repeat elements support proliferating cell nuclear antigen loading and MutL? endonuclease activation
Complementation of Saccharomyces cerevisiae coq7 mutants by mitochondrial targeting of the Escherichia coli UbiF polypeptide: two functions of yeast Coq7 polypeptide in coenzyme Q biosynthesis
An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor
La proteins from Drosophila melanogaster and Saccharomyces cerevisiae: a yeast homolog of the La autoantigen is dispensable for growth.
Phosphorylation of the protein kinase C-theta activation loop and hydrophobic motif regulates its kinase activity, but only activation loop phosphorylation is critical to in vivo nuclear-factor-kappaB induction
Pendred syndrome is caused by mutations in a putative sulphate transporter gene (PDS)
Pol II mediated transcription of microRNA genes
Expression of BIP (78 kDa Glucose-regulated protein, GRP78, HSPA5)
Expression of PDIA6 (Protein disulfide-isomerase A6)
Expression of SRPR (SRP Receptor subunit alpha)
Expression of SRPRB (SRP Receptor subunit beta)
Hyaluronan: from extracellular glue to pericellular cue
Insulin degradation: mechanisms, products, and significance.
Cytochrome P450s and cholesterol homeostasis
CATALYTIC ACTIVITY ATP + a protein = ADP + a phosphoprotein.COFACTOR Magnesium.MISCELLANEOUS Present with 259 molecules/cell in log phase SD medium.SIMILARITY Belongs to the protein kinase superfamily. Ser/Thr protein kinase family.SIMILARITY Contains 1 KEN domain.SIMILARITY Contains 1 protein kinase domain.
MISCELLANEOUS Present with 15800 molecules/cell in log phase SD medium.SIMILARITY Belongs to the TFIIIC subunit 5 family.
FUNCTION DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs.SUBUNIT Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits.MISCELLANEOUS Present with 2520 molecules/cell in log phase SD medium.SIMILARITY Belongs to the eukaryotic RPC3/POLR3C RNA polymerase subunit family.
Structural basis of hereditary coproporphyria
A cluster of proton/amino acid transporter genes in the human and mouse genomes
Cell signaling by receptor tyrosine kinases
Evolutionary conservation and adaptation in the mechanism that regulates SREBP action: what a long, strange tRIP it's been
Monoamine metabolism and behavioral responses to ethanol in mitochondrial aldehyde dehydrogenase knockout mice
Interleukin 2 high-affinity receptor expression requires two distinct binding proteins
Sequence, tissue distribution, and chromosomal localization of mRNA encoding a human glucose transporter-like protein
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Cloning and characterization of mouse lung-type acyl-CoA:lysophosphatidylcholine acyltransferase 1 (LPCAT1). Expression in alveolar type II cells and possible involvement in surfactant production
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Protein kinase B (c-Akt) in phosphatidylinositol-3-OH kinase signal transduction
Transcriptional activation of GP-acyl transferase gene by ChREBP:MLX
Transcriptional activation of Acetyl-CoA carboxylase by ChREBP:MLX
Structure-function analysis of liver-type (GLUT2) and brain-type (GLUT3) glucose transporters: expression of chimeric transporters in Xenopus oocytes suggests an important role for putative transmembrane helix 7 in determining substrate selectivity
Molecular components of the mammalian circadian clock
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Regulation of the anaphase-promoting complex by the dual specificity phosphatase human Cdc14a
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The NRAMP family of metal-ion transporters
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Type II phosphoinositide 5-phosphatases have unique sensitivities towards fatty acid composition and head group phosphorylation
Role of Stargardt-3 macular dystrophy protein (ELOVL4) in the biosynthesis of very long chain fatty acids
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Assignment of the gene for human arylsulfatase B, ARSB, to chromosome region 5p11----5qter
Biogenesis of the essential Tim9-Tim10 chaperone complex of mitochondria: site-specific recognition of cysteine residues by the intermembrane space receptor Mia40
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Substrate preferences of a lysophosphatidylcholine acyltransferase highlight its role in phospholipid remodeling
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The methylation of phosphatidylethanolamine
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ATP-dependent Ca++-extrusion from human red cells
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Immunolocalization of AQP9 in liver, epididymis, testis, spleen, and brain
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Myotubularin lipid phosphatase binds the hVPS15/hVPS34 lipid kinase complex on endosomes
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Temporal and spatial regulation of the phosphatidate phosphatases lipin 1 and 2
Recent advances in mechanisms regulating glucose oxidation at the level of the pyruvate dehydrogenase complex by PDKs
Am J Physiol Endocrinol Metab 284:E855-62
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CATALYTIC ACTIVITY ATP + H(2)O = ADP + phosphate.SIMILARITY Belongs to the DNA2/NAM7 helicase family.
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Synaptojanin 2, a novel Rac1 effector that regulates clathrin-mediated endocytosis
Chaperonin-mediated folding of vertebrate actin-related protein and gamma-tubulin
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Identification of genetic mutations in Japanese patients with fructose-1,6-bisphosphatase deficiency
Fibroblast growth factor receptors: lessons from the genes
Determinants of function and substrate specificity in human UDP-galactose 4'-epimerase
The Mechanism of Hsp90 regulation by the protein kinase-specific cochaperone p50(cdc37)
CD14 controls the LPS-induced endocytosis of Toll-like receptor 4
Role of phosphatidylinositol 3,4,5-trisphosphate in regulating the activity and localization of 3-phosphoinositide-dependent protein kinase-1
An interaction between frataxin and Isu1/Nfs1 that is crucial for Fe/S cluster synthesis on Isu1
Intracellular signaling by the neural cell adhesion molecule
Insertion of residues 429 to 822 at 340 from UniProt:P11362 FGFR1 (in Homo sapiens)
Beta glucuronidase deficiency: report of clinical, radiologic, and biochemical features of a new mucopolysaccharidosis
Cutting edge: Role of Toll-like receptor 9 in CpG DNA-induced activation of human cells
A caspase-activated DNase that degrades DNA during apoptosis, and its inhibitor ICAD
C1-Tetrahydrofolate synthase from rabbit liver. Structural and kinetic properties of the enzyme and its two domains.
Identification of the cDNA encoding human 6-phosphogluconolactonase, the enzyme catalyzing the second step of the pentose phosphate pathway(1)
The nonsense-mediated decay RNA surveillance pathway
Primary structure and tissue distribution of human 4-aminobutyrate aminotransferase
Activation of the DNA-binding ability of human heat shock transcription factor 1 may involve the transition from an intramolecular to an intermolecular triple-stranded coiled-coil structure
Protein arginine methyltransferases and cancer
The Src, Syk, and Tec family kinases: distinct types of molecular switches
Molecular cloning of AMP deaminase isoform L. Sequence and bacterial expression of human AMPD2 cDNA
Gbetagammas and the Ras binding domain of p110gamma are both important regulators of PI(3)Kgamma signalling in neutrophils
Glutathione peroxidase 3 mediates the antioxidant effect of peroxisome proliferator-activated receptor gamma in human skeletal muscle cells
Identification of cell cycle-regulated phosphorylation sites on nuclear lamin C
In vitro disassembly of the nuclear lamina and M phase-specific phosphorylation of lamins by cdc2 kinase
Structures of human cytosolic NADP-dependent isocitrate dehydrogenase reveal a novel self-regulatory mechanism of activity
Frizzled/PCP signalling: a conserved mechanism regulating cell polarity and directed motility
Mitotic and G2 checkpoint control: regulation of 14-3-3 protein binding by phosphorylation of Cdc25C on serine-216.
Biochemical analysis of the intrinsic Mcm4-Mcm6-mcm7 DNA helicase activity.
MMS19 assembles iron-sulfur proteins required for DNA metabolism and genomic integrity
MMS19 links cytoplasmic iron-sulfur cluster assembly to DNA metabolism
Identification of natural resistance-associated macrophage protein in peripheral blood lymphocytes
Identification of distinct classes and functional domains of Wnts through expression of wild-type and chimeric proteins in Xenopus embryos
Conserved docking site is essential for activation of mammalian MAP kinase kinases by specific MAP kinase kinase kinases
Biotinidase deficiency: "if you have to have an inherited metabolic disease, this is the one to have"
Purification from placenta, amino acid sequence, structure comparisons and cDNA cloning of human glutaredoxin
Xenobiotic, bile acid, and cholesterol transporters: function and regulation
Identification, expression, and characterization of a cDNA encoding human endoplasmic reticulum mannosidase I, the enzyme that catalyzes the first mannose trimming step in mammalian Asn-linked oligosaccharide biosynthesis
Two aldehyde dehydrogenases from human liver. Isolation via affinity chromatography and characterization of the isozymes.
Specificity of the deoxyhypusine hydroxylase-eukaryotic translation initiation factor (eIF5A) interaction: identification of amino acid residues of the enzyme required for binding of its substrate, deoxyhypusine-containing eIF5A
Cloning, expression and characterization of the pig liver GDP-mannose pyrophosphorylase. Evidence that GDP-mannose and GDP-Glc pyrophosphorylases are different proteins
Isolation and initial characterization of the single polypeptide that synthesizes uridine 5'-monophosphate from orotate in Ehrlich ascites carcinoma. Purification by tandem affinity chromatography of uridine-5'-monophosphate synthase
The protein deficient in Lowe syndrome is a phosphatidylinositol-4,5-bisphosphate 5-phosphatase
Replication factors required for SV40 DNA replication in vitro. II. Switching of DNA polymerase alpha and delta during initiation of leading and lagging strand synthesis.
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Heat shock factor 2 (HSF2) contributes to inducible expression of hsp genes through interplay with HSF1
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Coupling of rotation and catalysis in F(1)-ATPase revealed by single-molecule imaging and manipulation
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Enzymatic activities in cultured human lymphocytes that dephosphorylate dolichyl pyrophosphate and dolichyl phosphate
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WW domain-containing proteins, WWOX and YAP, compete for interaction with ErbB-4 and modulate its transcriptional function
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Activation of human heat shock genes is accompanied by oligomerization, modification, and rapid translocation of heat shock transcription factor HSF1
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NaPO(4) cotransport type III (PiT1) expression in human embryonic kidney cells and regulation by PTH
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Exosomes mediate stromal mobilization of autocrine Wnt-PCP signaling in breast cancer cell migration
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Fibroblast Growth Factor Receptor (FGFR) signaling
Aminoacyl tRNA synthetases and their connections to disease
Interactions between UPF1, eRFs, PABP and the exon junction complex suggest an integrated model for mammalian NMD pathways
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Expression and characterization of a human mitochondrial phenylalanyl-tRNA synthetase
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ARFGAP1 promotes the formation of COPI vesicles, suggesting function as a component of the coat
Mechanism of biotin responsiveness in biotin-responsive multiple carboxylase deficiency
Human phosphoglycerate kinase. I. Crystallization and characterization of normal enzyme
((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)GYG2 dimer (name copied from entity in Homo sapiens)
poly((1,4)-alpha-glucosyl) glycogenin dimer
poly((1,4)-alpha-glucosyl)GYG1 dimer (name copied from entity in Homo sapiens)
poly((1,4)-alpha-glucosyl)GYG2 dimer (name copied from entity in Homo sapiens)
glycogen-glycogenin-2 dimer (name copied from entity in Homo sapiens)
limit dextrin-glycogenin-2 dimer (name copied from entity in Homo sapiens)
PGYL dimer a form (name copied from entity in Homo sapiens)
((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl) glycogenin dimer
((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)GYG dimer
((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)GYG1 dimer (name copied from entity in Homo sapiens)
phosphoribosyl pyrophosphate synthetase 1 holoenzyme (name copied from entity in Homo sapiens)
RPE dimer (name copied from entity in Homo sapiens)
transketolase dimer (name copied from entity in Homo sapiens)
GYG2 dimer (name copied from entity in Homo sapiens)
GALE dimer (name copied from entity in Homo sapiens)
GYG1 dimer (name copied from entity in Homo sapiens)
Cytosolic aldehyde dehydrogenase (ALDH1) variants found in alcohol flushers
G6PD tetramer (name copied from entity in Homo sapiens)
PGD dimer (name copied from entity in Homo sapiens)
G6PD dimer (name copied from entity in Homo sapiens)
polyGlc-GYG2:GYS2-a tetramer (name copied from entity in Homo sapiens)
glycogen-GYG1:GYS1-a tetramer (name copied from entity in Homo sapiens)
GYG2:GYS2-b tetramer (name copied from entity in Homo sapiens)
oligoGlc-GYG2:GYS2-b tetramer (name copied from entity in Homo sapiens)
polyGlc-GYG1:GYS1-a tetramer (name copied from entity in Homo sapiens)
polyGlc-GYG1:GYS1-b tetramer (name copied from entity in Homo sapiens)
GYG1:GYS1-b tetramer (name copied from entity in Homo sapiens)
oligoGlc-GYG1:GYS1-b tetramer (name copied from entity in Homo sapiens)
GYG2:GYS2-a tetramer (name copied from entity in Homo sapiens)
oligoGlc-GYG2:GYS2-a tetramer (name copied from entity in Homo sapiens)
PGYM dimer a form (name copied from entity in Homo sapiens)
limit dextrin-glycogenin-1 dimer (name copied from entity in Homo sapiens)
PGYM b dimer:AMP (name copied from entity in Homo sapiens)
glycogen-glycogenin-1 dimer (name copied from entity in Homo sapiens)
PGYB b dimer:AMP (name copied from entity in Homo sapiens)
PGYM dimer, b form (name copied from entity in Homo sapiens)
Crystal structures of recombinant human dihydrofolate reductase complexed with folate and 5-deazafolate
glycogen-GYG2:GYS2-a tetramer (name copied from entity in Homo sapiens)
PGYB dimer b form (name copied from entity in Homo sapiens)
glycogen-GYG1:GYS1-b tetramer (name copied from entity in Homo sapiens)
phosphoglycerate mutase 2 dimer (name copied from entity in Homo sapiens)
enolase 1 dimer, (alpha) (name copied from entity in Homo sapiens)
enolase 3 dimer, (beta, muscle) (name copied from entity in Homo sapiens)
enolase 2 dimer, (gamma, neuronal) (name copied from entity in Homo sapiens)
pyruvate kinase M1 complex (name copied from entity in Homo sapiens)
pyruvate carboxylase holoenzyme (name copied from entity in Homo sapiens)
pyruvate kinase complex, liver and RBC (name copied from entity in Homo sapiens)
GOT2 dimer (name copied from entity in Homo sapiens)
malate dehydrogenase 2 dimer (name copied from entity in Homo sapiens)
FBP1 tetramer (name copied from entity in Homo sapiens)
GOT1 dimer (name copied from entity in Homo sapiens)
Mismatch repair deficiency associated with overexpression of the MSH3 gene
Proc. Natl. Acad. Sci. U.S.A. 95:8568-73
PGM2:Mg++ (name copied from entity in Homo sapiens)
PGM1:Mg++ (name copied from entity in Homo sapiens)
FBP2 tetramer (name copied from entity in Homo sapiens)
oligoGlc-GYG1:GYS1-a tetramer (name copied from entity in Homo sapiens)
GYG1:GYS1-a tetramer (name copied from entity in Homo sapiens)
8xUGP2 (name copied from entity in Homo sapiens)
Purification, molecular cloning, and sequencing of phospholipase C-beta 4
GLUT1:ATP (name copied from entity in Homo sapiens)
EJC-independent degradation of nonsense immunoglobulin-mu mRNA depends on 3' UTR length
glucose 6-phosphate isomerase dimer (name copied from entity in Homo sapiens)
phosphoPFKFB1 dimer (name copied from entity in Homo sapiens)
The 40-kDa subunit of DNA fragmentation factor induces DNA fragmentation and chromatin condensation during apoptosis
PFKFB4 dimer (name copied from entity in Homo sapiens)
PFKFB3 dimer (name copied from entity in Homo sapiens)
phosphofructokinase, L4 complex (name copied from entity in Homo sapiens)
PP2A-ABdeltaC complex (name copied from entity in Homo sapiens)
PFKFB1 dimer (name copied from entity in Homo sapiens)
Pathways of DNA double-strand break repair during the mammalian cell cycle.
PFKFB2 dimer (name copied from entity in Homo sapiens)
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase isoform homodimers
phosphofructokinase, P4 complex (name copied from entity in Homo sapiens)
phosphofructokinase, P3L complex (name copied from entity in Homo sapiens)
phosphofructokinase, P2L2 complex (name copied from entity in Homo sapiens)
phosphoglycerate mutase 1 dimer (name copied from entity in Homo sapiens)
phosphoglycerate kinase 1 complex (name copied from entity in Homo sapiens)
glyceraldehyde-3-phosphate dehydrogenase, testis-specific, tetramer (name copied from entity in Homo sapiens)
glyceraldehyde-3-phosphate dehydrogenase tetramer (name copied from entity in Homo sapiens)
glyceraldehyde-3-phosphate dehydrogenase tetramer
triosephosphate isomerase dimer (name copied from entity in Homo sapiens)
phosphofructokinase, PL3 complex (name copied from entity in Homo sapiens)
AKT inhibitors:AKT (name copied from entity in Homo sapiens)
IDH1 R132H dimer (name copied from entity in Homo sapiens)
GLUT2 tetramer (name copied from entity in Homo sapiens)
GLUT1 tetramer (name copied from entity in Homo sapiens)
GLUT3 tetramer (name copied from entity in Homo sapiens)
Characterization of the gene encoding human peroxisomal 3-oxoacyl-CoA thiolase (ACAA). No large DNA rearrangement in a thiolase-deficient patient
Mutations and polymorphisms in GUSB gene in mucopolysaccharidosis VII (Sly Syndrome)
Studies on the metabolic fate of n-3 polyunsaturated fatty acids
Condensation of Prometaphase Chromosomes
Kinetic evaluation of human cloned coproporphyrinogen oxidase using a ring isomer of the natural substrate
Trimethylamine N-oxide synthesis: a human variant
Histone demethylase JMJD3 contributes to epigenetic control of INK4a/ARF by oncogenic RAS
Apical GLUT2: a major pathway of intestinal sugar absorption
The H3K27me3 demethylase JMJD3 contributes to the activation of the INK4A-ARF locus in response to oncogene- and stress-induced senescence
Wnt/Fz signaling and the cytoskeleton: potential roles in tumorigenesis
Characterization of a 3-phosphoinositide-dependent protein kinase which phosphorylates and activates protein kinase Balpha
Endoplasmic reticulum (ER) chaperone regulation and survival of cells compensating for deficiency in the ER stress response kinase, PERK
Mutations in exon 3 of the glycogen debranching enzyme gene are associated with glycogen storage disease type III that is differentially expressed in liver and muscle.
Mismatch recognition and DNA-dependent stimulation of the ATPase activity of hMutSalpha is abolished by a single mutation in the hMSH6 subunit
ABC transporters and cholesterol metabolism
The TREM receptor family and signal integration
Telomeres shorten during ageing of human fibroblasts
Rad51 recombinase and recombination mediators.
The zinc-binding protein Hot13 promotes oxidation of the mitochondrial import receptor Mia40
MISCELLANEOUS Present with 3000 molecules/cell in log phase SD medium.SIMILARITY Belongs to the PAM17 family.
Secretion of Wnt ligands requires Evi, a conserved transmembrane protein
Wntless, a conserved membrane protein dedicated to the secretion of Wnt proteins from signaling cells
Two novel rat liver membrane proteins that bind advanced glycosylation endproducts: relationship to macrophage receptor for glucose-modified proteins
Human alanyl-tRNA synthetase: conservation in evolution of catalytic core and microhelix recognition
Renal physiology of SLC26 anion exchangers
Human Na(+)/H(+) exchanger isoform 6 is found in recycling endosomes of cells, not in mitochondria
Regulation of the MEF2 family of transcription factors by p38
2-acyl-sn-glycero-3-phospho-D-myo-inositol [ChEBI:62746]
1-acyl-sn-glycero-3-phosphoglycerol [ChEBI:62747]
MISCELLANEOUS Present with 1050 molecules/cell in log phase SD medium.SIMILARITY Belongs to the anamorsin family.
The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs
Cholesterol biosynthesis from lanosterol. Molecular cloning, tissue distribution, expression, chromosomal localization, and regulation of rat 7-dehydrocholesterol reductase, a Smith-Lemli-Opitz syndrome-related protein.
PP2A-mediated dephosphorylation of key metabolic factors
Sequence of the human iduronate 2-sulfatase (IDS) gene
p-S473-AKT1 E17K mutant:PIP2 (name copied from entity in Homo sapiens)
AKT1 E17K mutant:PIP2 (name copied from entity in Homo sapiens)
CCBL1 dimer (name copied from entity in Homo sapiens)
FGFR1 fusion mutant dimers:TKIs (name copied from entity in Homo sapiens)
CUX1-p-FGFR1 fusion mutant dimer (name copied from entity in Homo sapiens)
CUX1-FGFR1 fusion mutant dimer (name copied from entity in Homo sapiens)
Precise binding of single-stranded DNA termini by human RAD52 protein.
PDPK1:p-S473-AKT1 E17K mutant:PIP2 (name copied from entity in Homo sapiens)
The nuclease activity of Mre11 is required for meiosis but not for mating type switching, end joining, or telomere maintenance
Heteroduplex formation by human Rad51 protein: effects of DNA end-structure, hRP-A and hRad52.
HSP90:Benzoquinoid ansamycins (name copied from entity in Homo sapiens)
p-S230-HSF1 trimer (name copied from entity in Homo sapiens)
MLST8:MTOR:RPTOR:AKT1S1 (name copied from entity in Homo sapiens)
p-S303,307-HSF1:YWHAE (name copied from entity in Homo sapiens)
Human frataxin is an allosteric switch that activates the Fe-S cluster biosynthetic complex
HSF1 trimer:target gene (name copied from entity in Homo sapiens)
V-ATPase (name copied from entity in Homo sapiens)
ATP6V0D (name copied from entity in Homo sapiens)
ATP6V0E (name copied from entity in Homo sapiens)
ATP6V0A (name copied from entity in Homo sapiens)
Activation of Protein Kinase C novel isoforms
HSF1 trimer (name copied from entity in Homo sapiens)
Activation of conventional Protein Kinase C
HDAC6:VCP:protein aggregates (name copied from entity in Homo sapiens)
Post-Elongation Processing of Intronless pre-mRNA
HSP90 (name copied from entity in Homo sapiens)
HSF1:HSP90:PTGES3 (name copied from entity in Homo sapiens)
NUDT16 is a (deoxy)inosine diphosphatase, and its deficiency induces accumulation of single-strand breaks in nuclear DNA and growth arrest
YWHAE dimer (name copied from entity in Homo sapiens)
mTORC1 dimer (name copied from entity in Homo sapiens)
Nitric Oxide Synthase (NOS) produces Nitric Oxide (NO)
p-S326-HSF1 trimer (name copied from entity in Homo sapiens)
HSP90-beta dimer (name copied from entity in Homo sapiens)
ATP2B1-4 transport cytosolic Ca2+ to extracellular region
PIP3 recruits PDK1 and AKT to the membrane
Silica crystals and aluminum salts activate the NALP3 inflammasome through phagosomal destabilization
Phosphorylation and regulation of Akt/PKB by the rictor-mTOR complex
Identification of mammalian microRNA host genes and transcription units
Crystal structure of human kynurenine aminotransferase I
GLUL decamer (name copied from entity in Homo sapiens)
CaMKII (name copied from entity in Homo sapiens)
SOD1 dimer (name copied from entity in Homo sapiens)
SOD1:Zn2+:Cu2+ (name copied from entity in Homo sapiens)
CCS dimer (name copied from entity in Homo sapiens)
Characterization of phospholipase D activity in bovine photoreceptor membranes
CCS:Cu1+ dimer (name copied from entity in Homo sapiens)
CCS:Zn2+:2Cu1+ (name copied from entity in Homo sapiens)
CCS:SOD1 (name copied from entity in Homo sapiens)
SOD1:Zn2+ (name copied from entity in Homo sapiens)
Tim23-Tim50 pair coordinates functions of translocators and motor proteins in mitochondrial protein import
CCS:Zn2+:Cu1+ (name copied from entity in Homo sapiens)
Functional characterization of human sphingosine kinase-1
SOD2 tetramer (name copied from entity in Homo sapiens)
CCS:SOD1 dimer (name copied from entity in Homo sapiens)
Interactions between extracellular signal-regulated protein kinase 1, 14-3-3epsilon, and heat shock factor 1 during stress
SOD2:Mn2+ (name copied from entity in Homo sapiens)
AQP8 tetramer (name copied from entity in Homo sapiens)
Identification, cloning, expression, and purification of three novel human calcium-independent phospholipase A2 family members possessing triacylglycerol lipase and acylglycerol transacylase activities
CAT tetramer (name copied from entity in Homo sapiens)
catalase holoenzyme monomer (name copied from entity in Homo sapiens)
GPX1 tetramer (name copied from entity in Homo sapiens)
GSR dimer (name copied from entity in Homo sapiens)
GSR holoenzyme (name copied from entity in Homo sapiens)
Elongation factor 1 beta gamma from Artemia. Purification and properties of its subunits.
Hepatocyte nuclear factor-1alpha recruits the transcriptional co-activator p300 on the GLUT2 gene promoter
2xGSR-2:2xFAD (name copied from entity in Homo sapiens)
GPX2 tetramer (name copied from entity in Homo sapiens)
Hepatic and neuromuscular forms of glycogen storage disease type IV caused by mutations in the same glycogen-branching enzyme gene.
GPX3 tetramer (name copied from entity in Homo sapiens)
Cytochrome c (oxidized) (name copied from entity in Homo sapiens)
PRDX2 dimer (name copied from entity in Homo sapiens)
Cytochrome c (reduced) (name copied from entity in Homo sapiens)
PRDX1 dimer (name copied from entity in Homo sapiens)
HSF1:HSP90:HDAC6:VCP:PTGES3 (name copied from entity in Homo sapiens)
Human platelets contain SNARE proteins and a Sec1p homologue that interacts with syntaxin 4 and is phosphorylated after thrombin activation: implications for platelet secretion
UBA2:SAE1 (name copied from entity in Homo sapiens)
Sec13p:Sec31p Complex (name copied from entity in Homo sapiens)
Sec23p:Sec24p Complex (name copied from entity in Homo sapiens)
Sar1b:Sec23p:Sec24p:Sec13p:Sec31p Complex (name copied from entity in Homo sapiens)
Sar1b:GTP:Sec23p:Sec24p:Sec13p:Sec31p Complex (name copied from entity in Homo sapiens)
Sar1b:GDP Complex (name copied from entity in Homo sapiens)
Purification and partial amino acid sequence of human aconitase
SUMO1:UBA2:SAE1 (name copied from entity in Homo sapiens)
SUMO1:UBA2 (name copied from entity in Homo sapiens)
SUMO3:UBA2:SAE1 (name copied from entity in Homo sapiens)
SUMO2:UBA2 (name copied from entity in Homo sapiens)
SUMO1:C93-UBE2I (name copied from entity in Homo sapiens)
SUMO3:UBA2 (name copied from entity in Homo sapiens)
SUMO3:UBE2I (name copied from entity in Homo sapiens)
SUMO2:UBE2I (name copied from entity in Homo sapiens)
PAM Complex (name copied from entity in Homo sapiens)
TIMM23 Complex (name copied from entity in Homo sapiens)
3alpha,7alpha,12alpha-Trihydroxy-5beta-cholest-24-enoyl-CoA [ChEBI:1695]
SUMO2:UBA2:SAE1 (name copied from entity in Homo sapiens)
Crystal structure of an Hsp90-geldanamycin complex: targeting of a protein chaperone by an antitumor agent
TIMM23 SORT:Precursor Cargo (name copied from entity in Homo sapiens)
IRE1 dimer (name copied from entity in Homo sapiens)
NF-Y (name copied from entity in Homo sapiens)
TIMM23 PAM:Cargo (name copied from entity in Homo sapiens)
TIMM23 PAM:Precursor Cargo (name copied from entity in Homo sapiens)
aldehyde dehydrogenase, mitochondrial, tetramer (name copied from entity in Homo sapiens)
4 aminobutyrate aminotransferase homodimer (name copied from entity in Homo sapiens)
p-S724-IRE1 dimer:ADP (name copied from entity in Homo sapiens)
p-S724-IRE1 dimer (name copied from entity in Homo sapiens)
Mitochondrial processing peptidase (name copied from entity in Homo sapiens)
TIMM23 SORT:Cargo (name copied from entity in Homo sapiens)
Molecular cloning, expression, and chromosomal localization of two isoforms of the AE3 anion exchanger from human heart
Poly(I-C)-induced Toll-like receptor 3 (TLR3)-mediated activation of NFkappa B and MAP kinase is through an interleukin-1 receptor-associated kinase (IRAK)-independent pathway employing the signaling components TLR3-TRAF6-TAK1-TAB2-PKR
Structural analysis and detection of biological inositol pyrophosphates reveal that the family of VIP/diphosphoinositol pentakisphosphate kinases are 1/3-kinases
Inositol polyphosphates: a new frontier for regulating gene expression
Phospholipases D1 and D2 coordinately regulate macrophage phagocytosis
Mast cell signal transduction from the high-affinity IgE receptor
The stem cell marker Bcrp/ABCG2 enhances hypoxic cell survival through interactions with heme
Movement of tRNA but not the nascent peptide during peptide bond formation on ribosomes
CATALYTIC ACTIVITY Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).SUBUNIT Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits.MISCELLANEOUS Present with 1950 molecules/cell in log phase SD medium.SIMILARITY Belongs to the RNA polymerase beta chain family.
Ligand-independent dimerization activates the stress response kinases IRE1 and PERK in the lumen of the endoplasmic reticulum
GRASP55 and GRASP65 play complementary and essential roles in Golgi cisternal stacking
The LZT proteins; the LIV-1 subfamily of zinc transporters
Human glutamine phosphoribosylpyrophosphate amidotransferase. Kinetic and regulatory properties
Cori Cycle (interconversion of glucose and lactate)
Human thymidylate kinase. Purification, characterization, and kinetic behavior of the thymidylate kinase derived from chronic myelocytic leukemia
JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1
Rich, a rho GTPase-activating protein domain-containing protein involved in signaling by Cdc42 and Rac1
Dynamics of transitional endoplasmic reticulum sites in vertebrate cells
Sequence survey of receptor tyrosine kinases reveals mutations in glioblastomas
Dynamic interaction between Isp45 and mitochondrial hsp70 in the protein import system of the yeast mitochondrial inner membrane
Structural basis for tumor pyruvate kinase M2 allosteric regulation and catalysis
Phosphoinositides as regulators of membrane trafficking in health and disease
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1252214
PHF8 mediates histone H4 lysine 20 demethylation events involved in cell cycle progression
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120035.1
Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1252167
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119347.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_119708.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1252176
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1252063
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120056.1
Post-Elongation Processing of the Transcript
Fructose transporter in human spermatozoa and small intestine is GLUT5
The characterization of gene mutations for human glucose phosphate isomerase deficiency associated with chronic hemolytic anemia
Tumor necrosis factor alpha-induced phosphorylation of I kappa B alpha is a signal for its degradation but not dissociation from NF-kappa B
From structure to disease: the evolving tale of aquaporin biology
Tristetraprolin recruits functional mRNA decay complexes to ARE sequences
Signal transduction by immunoglobulin is mediated through Ig alpha and Ig beta
De novo purine nucleotide biosynthesis: cloning of human and avian cDNAs encoding the trifunctional glycinamide ribonucleotide synthetase-aminoimidazole ribonucleotide synthetase-glycinamide ribonucleotide transformylase by functional complementation in E. coli
unfolded protein:(Glc)1 (GlcNAc)2 (Man)9 (name copied from entity in Homo sapiens)
unfolded protein:(GlcNAc)2 (Man)7aa (name copied from entity in Homo sapiens)
unfolded protein:(GlcNAc)2 (Man)8a (name copied from entity in Homo sapiens)
Sar1b:GTP Complex (name copied from entity in Homo sapiens)
Sar1b:GTP:Sec23p:Sec24p (name copied from entity in Homo sapiens)
Crystal structures of two human pyrophosphorylase isoforms in complexes with UDPGlc(Gal)NAc: role of the alternatively spliced insert in the enzyme oligomeric assembly and active site architecture
Loss of signaling through the G protein, Gz, results in abnormal platelet activation and altered responses to psychoactive drugs
D box and KEN box motifs in budding yeast Hsl1p are required for APC-mediated degradation and direct binding to Cdc20p and Cdh1p
Evidence that negative elongation factor represses transcription elongation through binding to a DRB sensitivity-inducing factor/RNA polymerase II complex and RNA.
unfolded protein:(GlcNAc)2 (Man)8c (name copied from entity in Homo sapiens)
unfolded protein:(GlcNAc)2 (Man)8b (name copied from entity in Homo sapiens)
COFACTOR Copper or zinc.MISCELLANEOUS Present with 5040 molecules/cell in log phase SD medium.SIMILARITY Contains 1 CHCH domain.
Overexpression and characterization of the human peroxisomal acyl-CoA oxidase in insect cells
Purification and characterization of membrane-bound phospholipase C specific for phosphoinositides from human platelets
Aquaporin-1, nothing but a water channel
A novel disorder caused by defective biosynthesis of N-linked oligosaccharides due to glucosidase I deficiency
eRF3-GDP:eRF1:80S Ribosome:mRNA:tRNA Complex (name copied from entity in Homo sapiens)
eRF3-GDP:eRF1:80S Ribosome:mRNA:peptidyl-tRNA Complex (name copied from entity in Homo sapiens)
Regulation of cell growth-dependent expression of mammalian CDC6 gene by the cell cycle transcription factor E2F.
Prefoldin (name copied from entity in Homo sapiens)
80S Ribosome:mRNA:peptidyl-tRNA with elongating peptide (name copied from entity in Homo sapiens)
eEF2:GDP (name copied from entity in Homo sapiens)
eEF2:GTP (name copied from entity in Homo sapiens)
eEF1B:GDP exchange complex (name copied from entity in Homo sapiens)
eEF1B complex (name copied from entity in Homo sapiens)
eRF3-GTP:eRF1:80S Ribosome:mRNA:peptidyl-tRNA Complex (name copied from entity in Homo sapiens)
Differential expression of aquaporin 7 in adipose tissue of lean and obese high fat consumers
GTP bound eRF3 (name copied from entity in Homo sapiens)
Identification and characterization of human cardiolipin synthase
Coupling RNA polymerase II transcription with pre-mRNA processing.
80S:Met-tRNAi:mRNA:aminoacyl-tRNA (name copied from entity in Homo sapiens)
Protein kinase C is differentially stimulated by Wnt and Frizzled homologs in a G-protein-dependent manner
eEF1A:GDP (name copied from entity in Homo sapiens)
80S:aminoacyl tRNA:mRNA:eEF1A:GTP (name copied from entity in Homo sapiens)
eEF1A:GTP:aminoacyl-tRNA complex (name copied from entity in Homo sapiens)
SRP receptor (name copied from entity in Homo sapiens)
ribosome:mRNA:polypeptide+signal (name copied from entity in Homo sapiens)
eEF1A:GTP (name copied from entity in Homo sapiens)
SRP receptor:SRP:ribosome:polypeptide+signal (name copied from entity in Homo sapiens)
Signal Recognition Particle (name copied from entity in Homo sapiens)
SRP:polypeptide+signal:ribosome (name copied from entity in Homo sapiens)
Stimulation-dependent I kappa B alpha phosphorylation marks the NF-kappa B inhibitor for degradation via the ubiquitin-proteasome pathway
The role of a group III AQP, AQP11 in intracellular organelle homeostasis
(un)folded protein:(GlcNAc)2 (Man)9 (name copied from entity in Homo sapiens)
2xUAP1 (name copied from entity in Homo sapiens)
2xUAP1-2 (name copied from entity in Homo sapiens)
unfolded protein:(Glc)2 (GlcNAc)2 (Man)9 (Asn)1 (name copied from entity in Homo sapiens)
ChEBI:58828 5-(methylsulfanyl)-2,3-dioxopentyl phosphate(2?)
5-(methylsulfanyl)-2,3-dioxopentyl phosphate(2?)
unfolded protein:(Glc)3 (GlcNAc)2 (Man)9 (Asn)1 (name copied from entity in Homo sapiens)
PIG-F:GPI7 complex (name copied from entity in Homo sapiens)
PIG-F:PIG-O complex (name copied from entity in Homo sapiens)
2xGNPNAT1 (name copied from entity in Homo sapiens)
Translocation of cyclin B1 to the nucleus at prophase requires a phosphorylation-dependent nuclear import signal
MVD dimer (name copied from entity in Homo sapiens)
A conserved cyclin-binding domain determines functional interplay between anaphase-promoting complex-Cdh1 and cyclin A-Cdk2 during cell cycle progression
DOHH:Fe++ (name copied from entity in Homo sapiens)
Mitochondrial Cu,Zn-superoxide dismutase mediates pulmonary fibrosis by augmenting H2O2 generation
deoxyhypusine synthase tetramer (name copied from entity in Homo sapiens)
CCT/TriC(ADP):Sphingosine kinase 1 (name copied from entity in Homo sapiens)
CCT/TriC(ATP) (name copied from entity in Homo sapiens)
CCT/TriC(ATP)-associated actin (name copied from entity in Homo sapiens)
CCT/TriC (ADP) associated actin (name copied from entity in Homo sapiens)
tubulin-GTP folding intermediate (name copied from entity in Homo sapiens)
CCT/TriC(ATP):unfolded tubulin complex (name copied from entity in Homo sapiens)
CCT/TriC(ADP)-associated non-native tubulin (name copied from entity in Homo sapiens)
CCT/TriC(ADP) (name copied from entity in Homo sapiens)
Prefoldin-associated actin/tubulin (name copied from entity in Homo sapiens)
TRP channels: sensors and transducers of gasotransmitter signals
ribonucleotide reductase M2 polypeptide dimer (name copied from entity in Homo sapiens)
ribonucleotide reductase (name copied from entity in Homo sapiens)
ribonucleotide reductase M2B (TP53 inducible) variant (name copied from entity in Homo sapiens)
ribonucleotide reductase M1 polypeptide dimer (name copied from entity in Homo sapiens)
ribonucleotide reductase M2B (TP53 inducible) dimer (name copied from entity in Homo sapiens)
NME4 hexamer (name copied from entity in Homo sapiens)
nucleoside diphosphate kinase 1A:5B heterohexamer (name copied from entity in Homo sapiens)
NUDT5 dimer (name copied from entity in Homo sapiens)
ITPA dimer (name copied from entity in Homo sapiens)
1-hydroxy-5-(methylthio)-3-oxopent-1-en-2-olate (1-)
ChEBI:58795 1-hydroxy-5-(methylthio)-3-oxopent-1-en-2-olate (1-)
GPT dimer (name copied from entity in Homo sapiens)
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
P5CS long isoform, dimer (name copied from entity in Homo sapiens)
delta-1-pyrroline-5-carboxylate synthetase dimers
OAT hexamer (name copied from entity in Homo sapiens)
GPT2 dimer (name copied from entity in Homo sapiens)
GLUD1 hexamer (name copied from entity in Homo sapiens)
ASNS dimer (name copied from entity in Homo sapiens)
PYCR1 decamer (name copied from entity in Homo sapiens)
P5CS short isoform, dimer (name copied from entity in Homo sapiens)
Multiple pathways for mitochondrial protein traffic
PHGHD tetramer (name copied from entity in Homo sapiens)
adenosine kinase holoenzyme (name copied from entity in Homo sapiens)
adenylosuccinate synthetase holoenzyme (name copied from entity in Homo sapiens)
NP trimer (name copied from entity in Homo sapiens)
ADAL:Zn (name copied from entity in Homo sapiens)
Guanine deaminase homodimer (name copied from entity in Homo sapiens)
APRT homodimer (name copied from entity in Homo sapiens)
Termination sequence requirements vary among genes transcribed by RNA polymerase III
AMPD1 tetramer (name copied from entity in Homo sapiens)
AMPD3 tetramer (name copied from entity in Homo sapiens)
AMPD2 tetramer (name copied from entity in Homo sapiens)
adenylosuccinate synthetase holoenzyme dimer (name copied from entity in Homo sapiens)
Abortive initiation by Saccharomyces cerevisiae RNA polymerase III.
DCTD hexamer (name copied from entity in Homo sapiens)
UMPS dimer (name copied from entity in Homo sapiens)
Aquaporins: translating bench research to human disease
CAD hexamer (name copied from entity in Homo sapiens)
CTPS2 tetramer (name copied from entity in Homo sapiens)
CTPS tetramer (name copied from entity in Homo sapiens)
deoxythymidylate kinase (thymidylate kinase) holoenzyme (name copied from entity in Homo sapiens)
DPYD dimer (name copied from entity in Homo sapiens)
CDA tetramer (name copied from entity in Homo sapiens)
TS dimer (name copied from entity in Homo sapiens)
Inactivation, recovery and regulation of the phototransduction cascade
DUT trimer (name copied from entity in Homo sapiens)
(5-hydroxyindol-3-yl)acetic acid [ChEBI:27823]
Characterization of FIM-FGFR1, the fusion product of the myeloproliferative disorder-associated t(8;13) translocation
Glycosylation-induced conformational modification positively regulates receptor-receptor association: a study with an aberrant epidermal growth factor receptor (EGFRvIII/DeltaEGFR) expressed in cancer cells
A Cdc42 activation cycle coordinated by PI 3-kinase during Fc receptor-mediated phagocytosis
Intracellular transport and kinesin superfamily proteins, KIFs: structure, function, and dynamics
ALDH4A1 dimer (name copied from entity in Homo sapiens)
IDO1 (name copied from entity in Homo sapiens)
IDO2 (name copied from entity in Homo sapiens)
CCBL2 dimer (name copied from entity in Homo sapiens)
BCAT1 dimer (name copied from entity in Homo sapiens)
BCAT2 dimer (name copied from entity in Homo sapiens)
AASS tetramer (name copied from entity in Homo sapiens)
AADAT dimer (name copied from entity in Homo sapiens)
PSAT1 dimer (name copied from entity in Homo sapiens)
PSPH:Mg++ dimer (name copied from entity in Homo sapiens)
Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA
Distinct forms of mitochondrial TOM-TIM supercomplexes define signal-dependent states of preprotein sorting
Genetic alterations associated with hepatocellular carcinomas define distinct pathways of hepatocarcinogenesis
1-diphospho-1D-myo-inositol (2,3,4,5,6)pentakisphosphate [ChEBI:62919]
1-diphospho-1D-myo-inositol (2,3,4,5,6)pentakisphosphate
DAG and Ca+2 bind to PKC and tether it to membrane
Dephosphorylation of CK2-modified condensin I
Activation of the Anaphase Promoting Complex (APC) by PLK1
1,2-diacyl-glycerol 3-phosphate + H2O => 1,2-diacyl-glycerol + orthophosphate
LPIN catalyzes conversion of phosphatidic acid to diacylglycerol
Human mismatch repair: reconstitution of a nick-directed bidirectional reaction
DNA polymerase alpha:primase binds at the origin
DNA polymerase epsilon binds at the origin
ERKs are inactivated by protein phosphatase 2A
ERK5 activates the transcription factor MEF2
Nuclear translocation of phospho-ERK-2 dimer
COQ7:Fe2+ (name copied from entity in Homo sapiens)
The mitochondrial electron transport and oxidative phosphorylation system
Adenine nucleotide translocator homodimer
4Fe-4S cluster assembles on CFD1:NBP35 scaffold
A [4Fe-4S] cluster is assembled on a scaffold composed of the P-loop NTPases Cfd1 (human NUBP2) and Nbp35 (human NUBP1) in a nucleotide-dependent fashion. The two proteins form a heterotetramer which transiently binds the [4Fe-4S] cluster in a bridged form between two subunits of the complex. The Fe/S cluster is bound to two highly conserved Cys residues in the C-termini of each of these proteins. Nbp35 contains an additional, stably associated [4Fe-4S] cluster at its N-terminus which is essential for function. Mitochondria play a crucial role in cytosolic and nuclear Fe/S protein biogenesis. They export via a mitochondrial ABC transporter (yeast ATM1, human ABCB7) a still unknown, sulfur-containing compound which is essential for Fe/S cluster assembly in the cytosol. The general cytosolic iron donor, the multi-domain monothiol glutaredoxin (yeast Grx3-Grx4, human GRX3 or PICOT) plays a crucial role in cytosolic-nuclear Fe/S protein biogenesis. The precise molecular function of the glutaredoxin is still unclear.
CIA Targeting Complex transfers 4Fe-4S clusters to apoproteins
A complex of four proteins termed CIA targeting complex is involved in the delivery of the Cfd1-Nbp35-bound Fe/S cluster to specific target apoproteins. Nar1 (human IOP1) is similar in sequence to iron-only hydrogenases and binds two [4Fe-4S] clusters. These cofactors are essential for biogenesis but their molecular function is unknown. The WD40 domain protein Cia1 (human CIAO1) forms a propeller-like structure which may serve as a docking site for the other members of the CIA targeting complex. The role of Cia2 (human FAM96B) and Mms19 (human MMS19) is still unclear, but they show some specificity for the delivery of Fe/S clusters into certain target apoproteins. They directly interact with numerous Fe/S target proteins including many proteins involved in nuclear DNA integrity and maintenance such as DNA polymerases (Pol3), helicases of the DNA repair pathway (Rad3) or of telomere maintenance, and primases. Many of these target proteins are relevant to various cancer-related diseases or aging.
ADP/ATP translocase 2 homodimer (name copied from entity in Homo sapiens)
RNA Polymerase III Transcriptional Pause at Terminator Sequence
All RNA polymerases III terminate transcription at extremely simple sites, consistent with their role in producing small transcripts. These sites are essentially "Tn" (in the non-transcribed strand). Termination signals are recognized directly by polymerase III (Bogenhagen and Brown, 1981; Cozzarelli et al., 1983; Hamada et al., 2000). In vitro, hs sp and scpol III terminate transcription with comparable efficiency at T4, T4-5, and T5-6, respectively (Allison and Hall, 1985; Hamada et al., 2000; Huang and Maraia, 2001). At T runs that are sufficiently short to yield incomplete termination, nearby sequence influences the efficiency of termination (Bogenhagen and Brown, 1981; Gunnery et al., 1999; Mazabraud et al., 1987). The pol III termination site is a strong pause site; elongating transcription complexes that eventually read through a terminator do so with a significant time delay. This is in keeping with readily detectible slowing of RNA chain elongation by scpol III that is generated by even short runs of U incorporation into RNA (such as sequence found in U3) (Matsuzaki et al., 1994). Termination of transcription by scpol III is associated with repetitive hydrolytic resection of the nascent RNA chain's 3' end and resynthesis, an activity that requires the C11 subunit of pol III. In the absence of C11, pausing during transcript elongation is greatly reduced and RNA chain termination is severely but not absolutely defective. In such a case accurate termination (and RNA chain release) is restored at extremely low concentrations of UTP (1 and 3 ÃÂ¼M). C11 is proposed to exert its effect on termination indirectly by increasing RNA pausing. By increasing the time spent at the terminator the probability of read-through is decreased. This is different from the C11 subunit's direct RNase activity during hydrolytic RNA chain retraction (ChÃÂ©din et al., 1998).
PIKfyve, a mammalian ortholog of yeast Fab1p lipid kinase, synthesizes 5-phosphoinositides. Effect of insulin
ADP/ATP translocase 1 homodimer (name copied from entity in Homo sapiens)
Cytosolic Fe/S protein biogenesis depends on the electron transfer chain from NAD(P)H to the Fe/S protein Dre2 (human CIAPIN) via the flavoprotein Tah18 (human NDOR1). The precise role of electrons in the assembly process is unclear but in the absence of the electron chain the stable [4Fe-4S] cluster of Nbp35 is not assembled. Dre2 binds two Fe/S clusters of the [2Fe-2S] and the [4Fe-4S] type. The [2Fe-2S] cluster is reduced by Tah18-NADPH.
RFC dissociates after sliding clamp formation
Loading of PCNA - Sliding Clamp Formation
Phosphorylation of Cdc25A at Ser-123 in response to DNA damage
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
Regulation of actin dynamics for phagocytic cup formation
Proteolytic degradation of ubiquitinated-Cdc25A
Phosphorylation of Cdc25A at Ser-123 by Chk2
Phosphorylation of Cdc25A at Ser-123 by Chk1
Phosphorylation and activation of Chk1 by ATM
Polo-like kinase is required for the fragmentation of pericentriolar Golgi stacks during mitosis
Phosphorylation and activation of CHK2 by ATM
Model for the exceptional reactivity of peroxiredoxins 2 and 3 with hydrogen peroxide: a kinetic and computational study
Phosphorylated Orc1 is ubiquitinated while still associated with chromatin
Expression of human thymidylate synthase in Escherichia coli
The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer at the origin
The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer at the origin
Mcm4,6,7 trimer forms and associates with the replication fork
Rearrangement and mobilization of Mcm2-7
Ubiquitinated Cdc6 is degraded by the proteasome
Phosphorylated Cdc6 is exported from the nucleus
Ubiquitinated Orc1 is degraded by the proteasome
Reconstitution of the strand invasion step of double-strand break repair using human Rad51 Rad52 and RPA proteins
Protein kinase C alpha activates RAF-1 by direct phosphorylation
Phospholipase C-beta 1 is a GTPase-activating protein for Gq/11, its physiologic regulator
Critical role for the docking-protein FRS2 alpha in FGF receptor-mediated signal transduction pathways
Multiple proteins are localized at replication fork
Functional characterization of human 1-acylglycerol-3-phosphate acyltransferase isoform 8: cloning, tissue distribution, gene structure, and enzymatic activity
Zinc efflux and compartmentalization by the SLC30 family
Hyaluronan export by the ABC transporter MRP5 and its modulation by intracellular cGMP
The primary structure of mitochondrial aspartate aminotransferase from human heart
alpha-ketoglutarate dehydrogenase E2 holoenzyme (name copied from entity in Homo sapiens)
alpha-ketoglutarate dehydrogenase complex (name copied from entity in Homo sapiens)
IDH2 dimer (name copied from entity in Homo sapiens)
hMSH2-hMSH6 forms a hydrolysis-independent sliding clamp on mismatched DNA
Succinyl-CoA synthetase heterodimer (ADP-forming) (name copied from entity in Homo sapiens)
Succinate dehydrogenase complex (oxidised) (name copied from entity in Homo sapiens)
alpha-ketoglutarate dehydrogenase E1 homodimer (name copied from entity in Homo sapiens)
alpha-ketoglutarate dehydrogenase E1 holoenzyme (name copied from entity in Homo sapiens)
fumarate hydratase tetramer (name copied from entity in Homo sapiens)
Succinate dehydrogenase complex (reduced) (name copied from entity in Homo sapiens)
Succinate dehydrogenase flavoprotein (subunit A), oxidised (name copied from entity in Homo sapiens)
Succinate dehydrogenase Iron Sulphur (subunit B) (name copied from entity in Homo sapiens)
The role of the TIM8-13 complex in the import of Tim23 into mitochondria
Retention of phospho-Cdc25C:14-3-3 complexes within the cytoplasm
Phospholipases and phagocytosis: the role of phospholipid-derived second messengers in phagocytosis
ETF (name copied from entity in Homo sapiens)
Succinate dehydrogenase flavoprotein (subunit A) (name copied from entity in Homo sapiens)
Translocation of Cyclin B1:phospho-Cdc2 complexes to the nucleus
Activation of Cyclin B/Cdk1 by Cdc25a (string) protein
Translocation of active Cdc25C to the nucleus
Inactivation of APC/C via CDC20 sequestration
Detection of damage during initiation of DNA synthesis in S-phase
Myt-1 mediated phosphorylation of Cyclin B:Cdc2 complexes
Phosphorylation of Cdc25C at Ser 216 by Chk1
PPAT dimer (name copied from entity in Homo sapiens)
PPAT tetramer (name copied from entity in Homo sapiens)
adenylosuccinate lyase tetramer (name copied from entity in Homo sapiens)
ATIC dimer (name copied from entity in Homo sapiens)
IMP (inosine monophosphate) dehydrogenase 1 tetramer (name copied from entity in Homo sapiens)
The nucleoside diphosphate kinase D (NM23-H4) binds the inner mitochondrial membrane with high affinity to cardiolipin and couples nucleotide transfer with respiration
adenylosuccinate synthetase like 1 holoenzyme dimer (name copied from entity in Homo sapiens)
adenylosuccinate synthetase like 1 holoenzyme (name copied from entity in Homo sapiens)
ETF (reduced) (name copied from entity in Homo sapiens)
The sulfur-containing amino acids: an overview
Activated AMPK heterotrimer (name copied from entity in Homo sapiens)
AMPK gamma2:AMP (name copied from entity in Homo sapiens)
AMPK heterotrimer:AMP (name copied from entity in Homo sapiens)
AMPK heterotrimer (inactive) (name copied from entity in Homo sapiens)
Signalling via integrins: implications for cell survival and anticancer strategies
ADP/ATP translocase 3 homodimer (name copied from entity in Homo sapiens)
GCH1 decamer (name copied from entity in Homo sapiens)
GCH1 dimer (name copied from entity in Homo sapiens)
APT1 homodimer (name copied from entity in Homo sapiens)
Ceramide kinase, a novel lipid kinase. Molecular cloning and functional characterization
myristoylated eNOS dimer (name copied from entity in Homo sapiens)
p-S1177-eNOS:CaM:HSP90:p-AKT1:BH2 (name copied from entity in Homo sapiens)
Each conserved active site tyr in the three subunits of human isocitrate dehydrogenase has a different function
MPC1:MPC2 (name copied from entity in Homo sapiens)
Running with RNA polymerase: eukaryotic transcript elongation.
DHFR dimer (name copied from entity in Homo sapiens)
pyruvate dehydrogenase E1 complex (name copied from entity in Homo sapiens)
pyruvate dehydrogenase complex (name copied from entity in Homo sapiens)
phosphorylated pyruvate dehydrogenase complex (name copied from entity in Homo sapiens)
phosphorylated pyruvate dehydrogenase E1 complex (name copied from entity in Homo sapiens)
Citrate Synthase Holoenzyme (name copied from entity in Homo sapiens)
IDH3 complex (name copied from entity in Homo sapiens)
alpha-keto acid dehydrogenase E3 homodimer (name copied from entity in Homo sapiens)
alpha-keto acid dehydrogenase E3 holoenzyme (name copied from entity in Homo sapiens)
pyruvate dehydrogenase E2 trimer (name copied from entity in Homo sapiens)
Intracellular calcium release from human platelets: different messengers for multiple stores
Mutational spectrum of D-bifunctional protein deficiency and structure-based genotype-phenotype analysis
NUDT16 and ITPA play a dual protective role in maintaining chromosome stability and cell growth by eliminating dIDP/IDP and dITP/ITP from nucleotide pools in mammals
The AU-rich element mRNA decay-promoting activity of BRF1 is regulated by mitogen-activated protein kinase-activated protein kinase 2
Overexpression of the normal phosphoribosylpyrophosphate synthetase 1 isoform undelies catalytic superactivity of human phosphoribosylpyrophosphate synthetase
Cytosolic phosphogluconate dehydrogenase (PGD) catalyzes the reaction of 6-phospho-D-gluconate and NADP+ to form D-ribulose 5-phosphate, CO2, and NADPH + H+ (Beutler and Kuhl 1985; Rippa et al. 1998). The PGD enzyme is dimeric (Dallocchio et al. 1985).
Cytosolic UDP-galactose 4-epimerase catalyzes the interconversion of UDP-D-galactose and UDPglucose (Schulz et al. 2004). The active form of the enzyme is a homodimer with one molecule of bound NAD per monomer (Thoden et al. 2000).
The main sources of galactose in the human diet are milk and milk products. The disaccharide lactose from these sources is hydrolyzed in the intestine to its constituent monosaccharides, glucose and galactose. Galactose is metabolized primarily in the liver in a sequence of three reactions that yield one molecule of glucose 1-phosphate per molecule of galactose. First, it is phosphorylated to yield galactose 1-phosphate. Then, galactose 1-phosphate and UDP-glucose react to form UDP-galactose and glucose 1-phosphate, and UDP-galactose undergoes epimerization to form UDP-glucose. In a reaction shared with other pathways, glucose 1-phosphate can be converted into glucose 6-phosphate (Holton et al. 2001; Elsas and Lai 2001).
Cytosolic glucose-6-phosphate dehydrogenase (G6PD) catalyzes the reaction of glucose 6-phosphate and NADP+ to form D-glucono-1,5-lactone 6-phosphate and , and NADPH + H+. Biochemical studies indicate that both G6PD dimers and tetramers are catalytically active and capable or forming under physiological conditions in vivo (Au et al. 2000). Mutations that reduce the catalytic efficientcy of G6PD are remarkably common in human populations; these appear to have a protective effect against malaria (e.g., Luzzatto and Afolayan 1968).
Cytosolic 6-phosphogluconolactonase (PGLS) catalyzes the hydrolysis of D-glucono-1,5-lactone 6-phosphate to form 6-phospho-D-gluconate (Beutler and Kuhl 1985; Collard et al. 1999).
Cytosolic phosphoglucomutase (PGM) catalyzes the reversible conversion of glucose 1-phosphate to glucose 6-phosphate. Two PGM isoenzymes, both monomers, have been identified. PGM1 is the major form found in most tissues except erythrocytes, where PGM2 is abundant (March et al. 1993; Parrington et al. 1968; Putt et al. 1993). PGM2 also has substantial phosphopentomutase activity and its primary physiological in normal tissues in vivo is not clear.
Cytosolic glycogen breakdown occurs via the same chemical steps in all tissues but is separately regulated via tissue specific isozymes and signaling pathways that enable distinct physiological fates for liver glycogen and that in other tissues. Glycogen phosphorylase, which can be activated by phosphorylase kinase, catalyzes the removal of glucose residues as glucose 1-phosphate from the ends of glycogen branches. The final four residues of each branch are removed in two steps catalyzed by debranching enzyme, and further glycogen phosphorylase activity completes the process of glycogen breakdown. The figure shows the actions of phosphorylase and debranching enzyme. The first glucose residue in each branch is released as free glucose; all other residues are released as glucose 1-phosphate. The latter molecule can be converted to glucose 6-phosphate in a step shared with other pathways (Villar-Palasi and Larner 1970; Hers 1976). Glycogen can also be taken up into lysosomes, where it is normally broken done by the action of a single enzyme, lysosomal alpha-glucosidase (GAA).
Glucose is the major form in which dietary sugars are made available to cells of the human body. Its breakdown is a major source of energy for all cells, and is essential for the brain and red blood cells. Glucose utilization begins with its uptake by cells and conversion to glucose 6-phosphate, which cannot traverse the cell membrane. Fates open to cytosolic glucose 6-phosphate include glycolysis to yield pyruvate, glycogen synthesis, and the pentose phosphate pathway. In some tissues, notably the liver and kidney, glucose 6-phosphate can be synthesized from pyruvate by the pathway of gluconeogenesis.
Cytosolic galactose-1-phosphate uridylyltransferase (GALT) catalyzes the reaction of alpha-D-galactose 1-phosphate and UDP glucose to form D-glucose 1-phosphate and UDP galactose (Reichardt et al. 1991).
A cell-based reglucosylation assay demonstrates the role of GT1 in the quality control of a maturing glycoprotein
The phosphorylated PYGL dimer (a form) of glycogen phosphorylase catalyzes the reaction of orthophosphate and poly((1,4)-alpha-glucosyl) glycogenin-2 to form D-glucose 1-phosphate and glycogenin-2. This reaction occurs on the surfaces of cytosolic glycogen granules. Non-phosphorylated PYGL dimers (b form) are catalytically inactive even in the presence of AMP. In the body, this reaction takes place in the liver where its dependence on hormonally stimulated PYGL phosphorylation (and lack of sensitivity to AMP) allow glucose mobilization in response to a demand for glucose from the rest of the body (Newgard et al. 1989; Rath et al. 2000).
The PYGM and PYGB forms of glycogen phosphorylase catalyze the reaction of orthophosphate and poly((1,4) alpha glucosyl) glycogenin-1 to form D-glucose 1-phosphate and glycogenin-1. This reaction occurs on the surfaces of cytosolic glycogen granules. The phosphorylated forms of PYGM and PYGB dimers (a form) are catalytically active; the non-phosphorylated dimers (b form) become active when complexed with AMP. In the body, this reaction takes place in tissues other than the liver where its sensitivity to AMP allows glucose mobilization in response to acute energy needs of the individual cell, and hormonally mediated phosphorylation can stimulate increased glucose production, still for use by the individual producing cell, in response to stress signals. These reactions have not been characterized in detail but are inferred to occur from the very close similarity among PGYM, PGYB, and PGYL (Newgard et al. 1989; Rath et al. 2000).
At the beginning of this reaction, 1 molecule of '{(1,6)-alpha-glucosyl}poly{(1,4)-alpha-glucosyl}glycogenin-2' is present. At the end of this reaction, 1 molecule of 'alpha-D-glucose', and 1 molecule of 'poly{(1,4)-alpha-glucosyl}glycogenin-2' are present. This reaction takes place in the 'cytoplasm' and is mediated by the 'amylo-alpha-1,6-glucosidase activity' of 'glycogen debranching enzyme'.
The phosphorylated PYGL dimer (a form) of glycogen phosphorylase catalyzes the reaction of orthophosphate and glycogen-glycogenin 1 to form D-glucose 1-phosphate and limit dextrin-glycogenin 1. This reaction occurs on the surfaces of cytosolic glycogen granules. Non-phosphorylated PYGL dimers (b form) are catalytically inactive even in the presence of AMP. In the body, this reaction takes place in the liver where its dependence on hormonally stimulated PYGL phosphorylation (and lack of sensitivity to AMP) allow glucose mobilization in response to a demand for glucose from the rest of the body (Newgard et al. 1989; Rath et al. 2000).
Cytosolic debranching enzyme associated with glycogen granules transfers 3-glucose blocks from branches to the main linear polyglucose chain of limit dextrin formed on glycogenin 1 or glycogenin 2 (Chen et al. 1988; Shen et al. 1996).
Cytosolic, non-phosphorylated PGYM dimers (b form) complexed with AMP can reversibly dissociate (Rath et al. 2000).
The PYGM and PYGB forms of glycogen phosphorylase catalyze the reaction of orthophosphate and glycogen-glycogenin 1 to form D-glucose 1-phosphate and limit dextrin-glycogenin 1. This reaction occurs on the surfaces of cytosolic glycogen granules. The phosphorylated forms of PYGM and PYGB dimers (a form) are catalytically active; the non-phosphorylated dimers (b form) become active when complexed with AMP. In the body, this reaction takes place in tissues other than the liver where its sensitivity to AMP allows glucose mobilization in response to acute energy needs of the individual cell, and hormonally mediated phosphorylation can stimulate increased glucose production, still for use by the individual producing cell, in response to stress signals. These reactions have not been characterized in detail but are inferred to occur from the very close similarity among PGYM, PGYB, and PGYL (Newgard et al. 1989; Rath et al. 2000).
Cytosolic, non-phosphorylated PGYB dimers (b form) complexed with AMP can reversibly dissociate. This reaction is inferred from the AMP-binding properties of the closely homologous PGYM complex (Rath et al. 2000).
Cytosolic, non-phosphorylated PGYM dimers (b form) can reversibly bind AMP. This reaction is negatively regulated by ATP and glucose 6-phosphate and is the means by which high levels of these molecules repress PGYM activity (Rath et al. 2000).
Glycogen, a highly branched glucose polymer, is formed and broken down in most human tissues, but is most abundant in liver and muscle, where it serves as a major stored fuel. Glycogen metabolism has been studied in most detail in muscle, although considerable experimental data are available concerning these reactions in liver as well. Glycogen metabolism in other tissues has not been studied as extensively, and is thought to resemble the muscle process. Glycogen synthesis involves five reactions. The first two, conversion of glucose 6-phosphate to glucose 1-phosphate and synthesis of UDP-glucose from glucose 1-phosphate and UTP, are shared with several other pathways. The next three reactions, the auto-catalyzed synthesis of a glucose oligomer on glycogenin, the linear extension of the glucose oligomer catalyzed by glycogen synthase, and the formation of branches catalyzed by glycogen branching enzyme, are unique to glycogen synthesis. Repetition of the last two reactions generates large, extensively branched glycogen polymers. The catalysis of glycogenin glucosylation and oligoglucose chain extension by distinct isozymes in liver and nonhepatic tissues allows them to be regulated independently (Agius 2008; Bollen et al. 1998; Roach et al. 2012).
Cytosolic, non-phosphorylated PGYB dimers (b form) can reversibly bind AMP. This reaction is inferred from the AMP-binding properties of human PGYL and closely homologous PGYM proteins from other species (Newgard et al. 1989; Rath et al. 2000).
Constitutive PI3K/AKT Signaling in Cancer
Cytosolic glycogen branching enzyme (GBE1) associated with glycogen granules transfers terminal alpha(1,4) glucose blocks to form alpha(1,6) branches on growing glycogen molecules formed on glycogenin 1 (GYG1) complexed with phosphorylated glycogen synthase 1 (GYS1-b) (Bao et al. 1996; Roach et al. 2012).
Cytosolic glycogen branching enzyme (GBE1) associated with glycogen granules transfers terminal alpha(1,4) glucose blocks to form alpha(1,6) branches on growing glycogen molecules formed on glycogenin 1 (GYG1) complexed with unphosphorylated glycogen synthase 1 (GYS1-a) (Bao et al. 1996; Roach et al. 2012).
Cytosolic glycogen branching enzyme (GBE1) associated with glycogen granules transfers terminal alpha(1,4) glucose blocks to form alpha(1,6) branches on growing glycogen molecules formed on glycogenin 2 (GYG2) complexed with unphosphorylated glycogen synthase 2 (GYS2-a) (Bao et al. 1996; Roach et al. 2012).
The ATM-Chk2-Cdc25A checkpoint pathway guards against radioresistant DNA synthesis.
Glycogenin 1 (GYG1) catalyzes its autoglycosylation reaction with UDP-glucose to form oligo (1,4)-alpha-D-glucosyl GYG1 (Moslemi et al. 2010). The oligosaccharide is annotated here as containing four glucose residues. Glycogenin occurs as a homodimer complexed with two molecules of glycogen synthase 1 (GYS1), here in an unphosphorylated (a) form (Roach et al. 2012).
Glycogenin 1 (GYG1) catalyzes its autoglycosylation reaction with UDP-glucose to form oligo (1,4)-alpha-D-glucosyl GYG1 (Moslemi et al. 2010). The oligosaccharide is annotated here as containing four glucose residues. Glycogenin occurs as a homodimer complexed with two molecules of glycogen synthase 1 (GYS1), here in a phosphorylated (b) form (Roach et al. 2012).
Glycogenin 2 (GYG2) catalyzes its autoglycosylation reaction with UDP-glucose to form oligo (1,4)-alpha-D-glucosyl GYG2 (Mu et al. 1997). The oligosaccharide is annotated here as containing four glucose residues. Glycogenin occurs as a homodimer complexed with two molecules of glycogen synthase 1 (GYS2), here in a unphosphorylated (a) form (Roach et al. 2012).
Glycogenin 2 (GYG2) catalyzes its autoglycosylation reaction with UDP-glucose to form oligo (1,4)-alpha-D-glucosyl GYG2 (Mu et al. 1997). The oligosaccharide is annotated here as containing four glucose residues. Glycogenin occurs as a homodimer complexed with two molecules of glycogen synthase 1 (GYS2), here in a phosphorylated (b) form (Roach et al. 2012).
Unphosphorylated glycogen synthase 1 (GYS1-a) complexed with oligo-D-glucose-GYG1 catalyzes the polyglucosylation of the latter. (Here the addition of four glucose residues is annotated.) (Cameron et al. 2009; Roach et al. 2012).
Phosphorylated glycogen synthase 1 (GYS1-b) complexed with oligo-D-glucose-GYG1 catalyzes the polyglucosylation of the latter. (Here the addition of four glucose residues is annotated.) This reaction is allosterically activated by glucose-6-phosphate (G6P) (Cameron et al. 2009; Roach et al. 2012).
Unphosphorylated glycogen synthase 2 (GYS2-a) complexed with oligo-D-glucose-GYG2 catalyzes the polyglucosylation of the latter. (Here the addition of four glucose residues is annotated.) (Orho et al. 1998; Roach et al. 2012).
Cytosolic UDP-glucose pyrophosphorylase 2 (UGP2) catalyzes the reaction of UTP and glucose 1-phosphate to form UDP glucose and pyrophosphate (Knop and Hansen 1970; Duggleby et al. 1996). UGP2 is inferred to occur in the cell as a homooctamer from studies of its bovine homologue (Levine et al. 1969).
Cytosolic phosphoglucomutase (PGM) catalyzes the reversible conversion of glucose 6-phosphate to glucose 1-phosphate (Drago et al. 1991). Two PGM isoenzymes, both monomers, have been identified. PGM1 is the major form found in most tissues except erythrocytes, where PGM2 is abundant (March et al. 1993; Parrington et al. 1968; Putt et al. 1993). PGM2 also has substantial phosphopentomutase activity and its primary physiological in normal tissues in vivo is not clear.
The reactions of gluconeogenesis convert mitochondrial pyruvate to cytosolic glucose 6-phosphate which in turn can be hydrolyzed to glucose and exported from the cell. Gluconeogenesis is confined to cells of the liver and kidney and enables glucose synthesis from molecules such as lactate and alanine and other amino acids when exogenous glucose is not available (reviewed, e.g., by Gerich 1993). The process of gluconeogenesis as diagrammed below occurs in two parts: a network of reactions converts mitochondrial pyruvate to cytosolic phosphoenolpyruvate; then phosphoenolpyruvate is converted to glucose 6-phosphate in a single sequence of cytosolic reactions. Three variants of the first part of the process are physiologically important. 1) A series of transport and transamination reactions convert mitochondrial oxaloacetate to cytosolic oxaloacetate which is converted to phosphoenolpyruvate by a hormonally regulated, cytosolic isoform of phosphoenolpyruvate carboxykinase. This variant allows regulated glucose synthesis from lactate. 2) Mitochondrial oxaloacetate is reduced to malate, which is exported to the cytosol and re-oxidized to oxaloacetate. This variant provides reducing equivalents to the cytosol, needed for glucose synthesis from amino acids such as alanine and glutamine. 3) Constitutively expressed mitochondrial phosphoenolpyruvate carboxykinase catalyzes the conversion of mitochondrial oxaloacetate to phosphoenolpyruvate which is then transported to the cytosol. The exact path followed by any one molecule of pyruvate through this reaction network is determined by the tissue in which the reactions are occurring, the source of the pyruvate, and the physiological stress that triggered gluconeogenesis. In all cases, the synthesis of glucose from two molecules of pyruvate requires the generation and consumption of two reducing equivalents as cytosolic NADH + H+. For pyruvate derived from lactate (variants 1 and 3), NADH + H+ is generated with the oxidation of lactate to pyruvate in the cytosol (a reaction of pyruvate metabolism not shown in the diagram). For pyruvate derived from amino acids (variant 2), mitochondrial NADH + H+ generated by glutamate dehydrogenase (a reaction of amino acid metabolism, not shown) is used to reduce oxaloacetate to malate, which is transported to the cytosol and re-oxidized, generating cytosolic NADH + H+. The synthesis of glucose from pyruvate also requires the consumption of six high-energy phosphates, four from ATP and two from GTP. In the second part of gluconeogenesis, cytosolic phosphoenolpyruvate, however derived, is converted to fructose 1,6-bisphosphate by reactions that are the reverse of steps of glycolysis. Hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate is catalyzed by fructose 1,6-bisphosphatase, and fructose 6-phosphate is reversibly isomerized to glucose 6-phosphate.
The reversible isomerization of fructose-6-phosphate to form glucose-6-phosphate is catalyzed by cytosolic phosphoglucose isomerase (Noltman 1972; Xu and Beutler 1994; Tsuboi et al. 1958).
Cytosolic phosphoglycerate kinase complexed with magnesium catalyzes the reversible phosphorylation of 3-phosphoglycerate to form 1,3-bisphosphoglycerate (Huang et al. 1980a, 1980b).
The reversible reduction of 1,3-bisphosphoglycerate to form glyceraldehyde-3-phosphate is catalyzed by cytosolic glyceraldehyde-3-phosphate dehydrogenase tetramer. There are multiple human glyceraldehyde 3-phosphate dehydrogenase-like pseudogenes, but only one glyceraldehyde 3-phosphate dehydrogenase gene expressed in somatic tissue (Benham and Povey 1989). Consistent with this conclusion, the homogeneous enzymes purified from various human tissues had indistinguishable physical and immunochemical properties (Heinz and Freimuller 1982), and studies of human erythrocytes of various ages suggested that variant forms of the enzyme arise as a result of post-translational modifications (Edwards et al. 1976). There is, however, an authentic second isoform of glyceraldehyde 3-phosphate dehydrogenase whose expression is confined to spermatogenic cells of the testis (Welch et al. 2000).
Activated PKA (protein kinase A) phosphorylates serine 36 of the bifunctional 6-Phosphofructo-2-kinase /Fructose-2,6-bisphosphatase (PFKFB1) enzyme. This phosphorylation inhibits the enzyme's phosphofructokinase (PFK-2) activity while activating its phosphatase activity. As a result, cytosolic levels of Fructose-2,6-bisphosphate (F-2,6-P2) are reduced. F-2,6-P2 in turn is a key positive regulator of the committed step of glycolysis, so the net effect of this phosphorylation event is a reduced rate of glycolysis.
The fructose 2,6-bisphosphatase activity of cytosolic phosphofructokinase 2/fructose-2,6-bisphosphatase catalyzes the hydrolysis of fructose 2,6 bisphosphate to form fructose 6-phosphate. Fructose 2,6 bisphosphate is a key allosteric regulator of PFK1. In its absence the activity of PFK1 is reduced while fructose 1,6-bisphosphatase is activated, thus inhibiting glycolysis and favoring gluconeogenesis (Pilkis et al. 1995).
The reversible conversion of glyceraldehyde-3-phosphate to dihydroxyacetone phosphate is catalyzed by cytosolic triose phosphate isomerase (Watanabe et al. 1996; Lu et al. 1984).
Cytosolic fructose-1,6-bisphosphatase catalyzes the physiologically irreversible hydrolysis of fructose-1,6-bisphosphate to form fructose-6-phosphate and orthophosphate. In the body, two isoforms of the enzyme are expressed, one ubiquitous and one muscle-specific (Kikawa et al. 1997; Tillmann and Eschrich 1998).
Release of (inferred) platelet cytosolic components
Cytosolic phosphoglycerate mutase dimer catalyzes the reversible isomerisation of 2- and 3-phosphoglycerate. There are two isoforms of this enzyme, PGAM1 (isoform B) and PGAM2 (isoform M). In the body, erythrocytes express only PGAM1, while skeletal muscle expresses only PGAM2. Other tissues express both isoforms (Repiso et al. 2005; Tsujino et al. 1993).
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=163089
Release of platelet cytosolic components
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F-actin capping protein is a heterodimer
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Release of 78 kDa glucose-regulated protein
SLC25A12 and SLC25A13, located in the inner mitochondrial membrane, each mediate the exchange of cytosolic aspartate and mitochondrial glutamate. The exchange is physiologically irreversible because of the potential across the inner mitochondrial membrane (positive outside, negative inside). In the body, SLC25A12 (ARALAR1) is found mainly in heart, skeletal muscle, and brain, while SCL25A13 (CITRIN) is widely expressed but most abundant in liver (del Arco et al. 2000; Palmieri et al. 2001). Defects in SLC25A13 are associated with type II citrullinemia (Kobayashi et al. 1999).
Adenylate Kinase 3 is a GTP-AMP phosphotransferase
Cytosolic aspartate aminotransferase (glutamate oxaloacetate transaminase 1 - GOT1) catalyzes the reversible reaction of aspartate and 2-oxoglutarate (alpha-ketoglutarate) to form oxaloacetate and glutamate (Doyle et al. 1990). Unpublished crystallographic data (PBD 3IIO) suggest the enzyme is a homodimer).
SLC25A1, in the inner mitochondrial membrane, mediates the exchange of cytosolic citrate for mitochondrial phosphoenolpyruvate. The exchange is physiologically irreversible because of the potential of the inner mitochondrial membrane. The gene encoding human SLC25A1 has been cloned and its expression pattern has been characterized (Heisterkamp et al. 1995; Iacobazzi et al. 1997), but the biochemical details of the transport process are inferred from those worked out for the well-characterized rat system (Robinson 1971; Soling et al. 1971; Kleineke et al. 1973).
Cytosolic enolase dimer catalyzes the reversible reaction of phosphoenolpyruvate and water to form 2-phosphoglycerate. Three enolase isozymes have been purified and biochemically characterized. The alpha isoform is widely expressed (Giallongo et al. 1986). The beta isoform is expressed in muscle. Evidence for its function in vivo in humans comes from studies of a patient in whom a point mutation in the gene encoding the enzyme was associated specifically with reduced enolase activity in muscle extracts, and with other symptoms consistent with a defect in glycolysis (Comi et al. 2001). The gamma isoform of human enolase is normally expressed in neural tissue. It is not known to have distinctive biochemical functions, but is of possible clinical interest as a marker of some types of neuroendocrine and lung tumors (McAleese et al. 1988). Verma and Kurl (1993) identifed a possible fourth isoform, a "lung-specific" enolase whose expression is increased in response to dexamethasone treatment. The protein has not been biochemically characterized, however, nor have the levels of mRNA and protein in other tissues been examined. Thus, the observation that this protein is particularly similar in its predicted amino acid sequence to a duck crystallin (Wistow et al. 1988) raises the possibility that its normal function is unrelated to glycolysis.
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Mitochondrial malate dehydrogenase catalyzes the reversible reaction of oxaloacetate and NADH + H+ to form malate and NAD+ (Luo et al. 2006). Unpublished crystallographic data indicate that the protein is a dimer (PDB 3E04).
The carboxylation of pyruvate to form oxaloacetate, catalyzed by mitochondrial pyruvate carboxylase, is an irreversible and allosterically regulated reaction (Jitrapakdee and Wallace 1999).
Mitochondrial aspartate aminotransferase catalyzes the reversible reaction of oxaloacetate and glutamate to form aspartate and 2-oxoglutarate (alpha-ketoglutarate) (Martini et al. 1985). The active form of the enzyme is inferred to be a dimer with one molecule of pyridoxal phosphate associated with each monomer.
SLC25A10, the mitochondrial dicarboxylate carrier protein in the inner mitochondrial membrane, mediates the reversible exchange of mitochondrial malate for cytosolic phosphate (Fiermonte et al. 1999).
The reactions of glycolysis (e.g., van Wijk and van Solinge 2005) convert glucose 6-phosphate to pyruvate. The entire process is cytosolic. Glucose 6-phosphate is reversibly isomerized to form fructose 6-phosphate. Phosphofructokinase 1 catalyzes the physiologically irreversible phosphorylation of fructose 6-phosphate to form fructose 1,6-bisphosphate. In six reversible reactions, fructose 1,6-bisphosphate is converted to two molecules of phosphoenolpyruvate and two molecules of NAD+ are reduced to NADH + H+. Each molecule of phosphoenolpyruvate reacts with ADP to form ATP and pyruvate in a physiologically irreversible reaction. Under aerobic conditions the NADH +H+ can be reoxidized to NAD+ via electron transport to yield additional ATP, while under anaerobic conditions or in cells lacking mitochondria NAD+ can be regenerated via the reduction of pyruvate to lactate.
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Proteolytic PAK-2p34 fragment translocates to the nucleus
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Autophosphorylation of PAK-2p34 in the activation loop
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Association of HMGB1/HMGB2 with chromatin
Cytosolic enolase catalyzes the reversible reaction of 2 phosphoglycerate to form phosphoenolpyruvate and water, elevating the transfer potential of the phosphoryl group. Enolase is a homodimer and requires Mg++ for activity. Three isozymes have been purified and biochemically characterized. The alpha isoform is expressed in many normal human tissues (Giallongo et al. 1986). The beta isoform is expressed in muscle. Evidence for its function in vivo in humans comes from studies of a patient in whom a point mutation in the gene encoding the enzyme was associated specifically with reduced enolase activity in muscle extracts and with other symptoms consistent with a defect in glycolysis (Comi et al. 2001). The gamma isoform of human enolase is normally expressed in neural tissue and is of possible clinical interest as a marker of some types of neuroendocrine and lung tumors (McAleese et al. 1988). Biochemical studies of the homologous rat proteins indicate that both homo- and heterodimers of enolase form and are enzymatically active (Rider and Taylor 1974).
Human and murine serine-palmitoyl-CoA transferase--cloning, expression and characterization of the key enzyme in sphingolipid synthesis
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Release of Cytochrome c from mitochondria
Cytosolic pyruvate kinase catalyzes the transfer of a high-energy phosphate from phosphoenolpyruvate to ADP, forming pyruvate and ATP. This reaction, an instance of substrate-level phosphorylation, is essentially irreversible under physiological conditions. Four isozymes of human pyruvate kinase have been described, L, R, M1 and M2. Isozymes L and R are encoded by alternatively spliced transcripts of the PKLR gene; isozymes M1 and M2 are encoded by alternatively spliced transcripts of PKM2. In the body, L pyruvate kinase is found in liver (Tani et al. 1988), R in red blood cells (Kanno et al. 1991), M1 in muscle, heart and brain (Takenaka et al. 1991), and M2 in early fetal tissues and tumors (e.g., Lee et al. 2008). In all cases, the active form of the enzyme is a homotetramer, activated by fructose 1,6-bisphosphate (Valentini et al. 2002; Dombrauckas et al. 2005). Mutations in PKLR have been associated with hemolytic anemias (e.g., Zanella et al. 2005).
Cytosolic phosphoglycerate kinase catalyzes the reaction of ADP and 1,3-bisphosphoglycerate to form D glyceraldehyde 3-phosphate and ATP. The active form of the enzyme is a monomer and requires Mg++ (Yoshida and Watanabe 1972; Huang et al. 1980a,b). This is the first substrate level phosphorylation reaction in glycolysis.
Nuclear translocation of catalytic domain of Mst3
Cytosolic phosphoglycerate mutase catalyzes the reversible isomerisation of 3- and 2-phosphoglycerate. The active form of the enzyme is a dimer. There are two isoforms of this enzyme, PGAM1 (isoform B, widely expressed in non-muscle tissue) and PGAM2 (isoform M, expressed in muscle) (Blouquit et al. 1988; Omenn and Cheung 1974; Repiso et al. 2005; Tsujino et al. 1993).
Cytosolic triose phosphate isomerase catalyzes the freely reversible interconversion of dihydroxyacetone phosphate and glyceraldehyde 3-phosphate (Lu et al. 1984). The active form of the enzyme is a homodimer (Kinoshita et al. 2005).
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Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197
Cytosolic glyceraldehyde 3-phosphate dehydrogenase catalyzes the reversible reaction of glyceraldehyde 3-phosphate, orthophosphate, and NAD+ to form NADH + H+ and 1,3-bisphosphoglycerate, the first energy rich intermediate of glycolysis. The biochemical details of this reaction were worked out by C and G Cori and their colleagues (Taylor et al. 1948; Cori et al. 1948). While there are multiple human glyceraldehyde 3-phosphate dehydrogenase-like pseudogenes, there is only one glyceraldehyde 3-phosphate dehydrogenase gene expressed in somatic tissue (Benham and Povey 1989; Heinz and Freimuller 1982; Ercolani et al. 1988), and studies of aged human erythrocytes suggest that variant forms of the enzyme arise as a result of post-translational modifications (Edwards et al. 1976). There is, however, an authentic second isoform of glyceraldehyde 3-phosphate dehydrogenase whose expression is confined to spermatogenic cells of the testis (Welch et al. 2000).
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Structures of lung cancer-derived EGFR mutants and inhibitor complexes: mechanism of activation and insights into differential inhibitor sensitivity
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Epidermal growth factor receptor: elements of intracellular communication
Cytosolic phosphofructokinase 1 catalyzes the reaction of fructose 6-phosphate and ATP to form fructose 1,6-bisphosphate and ADP. This reaction, irreversible under physiological conditions, is the rate limiting step of glycolysis. Phosphofructokinase 1 activity is allosterically regulated by ATP, citrate, and fructose 2,6-bisphosphate. Phosphofructokinase 1 is active as a tetramer (although higher order multimers, not annotated here, may form in vivo). Two isoforms of phosphofructokinase 1 monomer, L and M, are widely expressed in human tissues. Different tissues can contain different homotetramers or heterotetramers: L4 in liver, M4 in muscle, and all possible heterotetramers, L4, L3M, L2M2, LM3, and M4, in red blood cells, for example (Raben et al. 1995; Vora et al. 1980, 1987; Vora 1981). A third isoform, P, is abundant in platelets, where it is found in P4, P3L, P2L2, and PL3 tetramers (Eto et al. 1994; Vora et al. 1987).
The 6-phosphofructo-2-kinase activity of cytosolic PFKFB (6-phosphofructo-2-kinase/fructose-2,6-biphosphatase) homodimer catalyzes the reaction of fructose 6-phosphate and ATP to form fructose 2,6-bisphosphate and ADP (Pilkis et al. 1988). Fructose 2,6-bisphosphate is not itself on the pathway of glycolysis. Rather, it acts as a positive allosteric effector of phosphofructokinase 1, greatly increasing the rate of synthesis of fructose 1,6-bisphosphate and hence the overall rate of glycolysis. The conversion of PFKFB between its dephosphorylated form, which catalyzes the synthesis of fructose 2,6-bisphosphate as described here, and its phosphorylated form, which catalyzes the hydrolysis of fructose 2,6-bisphosphate to fructose 6-phosphate and orthophosphate plays a central role in the short-term regulation of glycolysis (Pilkis et al. 1995). Four isoforms of PFKFB protein encoded by four different genes exhibit tissue-specific expression patterns. PFKFB1 is expressed in the liver (Algaier and Uyeda 1988), PFKFB2 is expressed in the heart (Hirata et al. 1998), PFKFB3 is ubiquitously expressed (Manes and el-Maghrabi 2005), and PFKFB4, originally described as a testis-specific gene product (Manzano et al. 1999), may also be expressed in several kinds of tumors.
At the beginning of this reaction, 1 molecule of 'pPF2K-Pase complex' is present. At the end of this reaction, 1 molecule of 'Orthophosphate', and 1 molecule of 'PF2K-Pase1 homodimer' are present. This reaction takes place in the 'cytosol' and is mediated by the 'phosphatidate phosphatase activity' of 'PP2A-ABdeltaC complex'.
Cytosolic phosphoglucose isomerase catalyzes the reversible interconversion of glucose 6-phosphate and fructose 6-phosphate (Tsuboi et al. 1958; Noltmann 1972; Bloxham and Lardy 1973). The active form of the enzyme is a homodimer (Read et al. 2001). Mutations in the enzyme are associated with hemolytic anemia (Xu and Beutler 1994).
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RNA Polymerase III Termination and release of transcribed mRNA
Efficient transcript production requires efficient release of RNA polymerase at the terminator; slow release at the terminator of a short transcription unit quickly becomes rate limiting for transcription at steady state. Although pol III autonomously recognizes sequence terminators, proteins that help to rapidly detach pol III from the terminator can affect the productivity of transcription if they eliminate termination as the rate-limiting step. Conceivably, efficiency of transcription can also be increased by the chaperone-like device of directly conveying pol III from the terminator to the promoter; the small size of pol III transcription units appears to make them especially suitable for the operation of such mechanisms and for continuous recycling of a molecule of pol III on the same transcription unit (Dieci and Sentenac, 1996; Dieci and Sentenac, 2003). The operation of both types of facilitation in multi-cycle transcription by pol III has been proposed. In all instances, the case for physiologically significant effect has not yet been proven despite the existence of intriguing observations. La, NF1 family proteins, PC4 and topoisomerase I have been proposed as accessory pol III transcription factors that facilitate multi-cycle transcription by hspol III. hsLa is an RNA-binding protein, with an N-terminal segment that binds to the short 3' terminal U tracts of primary pol III transcripts and a C-proximal site that recognizes primary transcript 5' ends. Phosphorylation of C-proximal Ser366 is required for La's participation in tRNA maturation (Maraia and Intine, 2001). In a Human Polymerase III in vitro system for transcriptional recycling that uses arrested transcription elongation complexes on immobilized DNA templates, further rounds of transcription require La (Maraia, 1996) and the just referred-to C-proximal Ser phosphorylation is required for this function (Fan et al., 1997). In contrast, highly efficient (>99%) immunodepletion of La from a frog oocyte extract that executes very efficiently recycling transcription in vitro has no effect on transcript yield (LinMarq and Clarkson, 1998). Although La is detected as a component of human holoPolymerase III, the gene encoding the yeast homologue of La is not essential (Yoo and Wolin, 1994). Thus, La is unlikely to be an essential and general transcription-recycling factor of pol III. Whether it is a significant factor in human pol III transcription remains unresolved (Maraia and Intine, 2001). Three other components that co-purify hsholoTFIIIC (Schramm and Hernandez, 2002) have been implicated in transcriptional termination and recycling: PC4, topoisomerase I and NF1. Topoisomerase I and PC4 were shown to promote multi-cycle transcription selectively and separately (Wang and Roeder, 1998), but the physiological significance of their activity has been discounted subsequently on account of the very great molecular excess of protein required for this action (Wang et al., 2000). Purification of a DNA-binding component of a TFIIIC-containing fraction (Wang and Roeder, 1998) to apparent homogeneity yields NF1 family proteins that bind to the adenovirus VAI gene's terminator. A recombinant NF1 protein also interacts with two subunits of hs TFIIIC2. The biochemically purified NF1 family proteins exert strong effects on transcriptional termination and increase the number of rounds of transcription in vitro. Detailed analysis of this effect has been confined to the VAI gene, which harbors consensus NF1 binding sites that overlap its two terminators and are essential for the transcription termination activity of NF1. However, terminator-overlapping NF1 sites are not a general feature of hspol III-transcribed genes. Involvement of NF1 proteins in transcription of genes lacking NF1-binding sites, conceivably through interaction with TFIIIC2, has been referred to (Wang et al., 2000) but not presented in concrete detail. [Nor has the implicit conflict with the proposed essential character of NF1-binding sites at the VAI gene terminator been resolved.] Biochemically purified NF1 has been reported to exert no effect on transcription in a highly purified system consisting only of recombinant TFIIIB, immunopurified TFIIIC and pol III (Wang et al., 2000). Because pol III transcription units are small, the transcribing polymerase never leaves the general vicinity of its promoter; DNA bending by transcription factors further compacts these transcription units. As a consequence, repeated utilization of an (isolated) pol III gene by the same molecule of polymerase could be based on purely stochastic principles. In addition, evidence for the operation of a specific handing-off mechanism that repetitively returns pol III from its termination site to the (same gene's) promoter has been presented (Dieci and Sentenac, 1996). However, the task of discriminating between purely stochastic recycling and handing-off mechanisms involving specific protein-protein interactions presents difficult technical challenges that have not yet been met. (Some of these difficulties are briefly discussed in (Geiduschek and Kassavetis, 2001).) Thus, the existence of a mechanism for directly guiding transcription-terminating pol III back to the same promoter (i.e. in cis), and the nature of the protein-protein interactions that might generate such a chaperone-like mediation remain to be established.
Cytosolic ATP reversibly associates with GLUT1. This association inhibits GLUT1 glucose transport (Blodgett et al. 2007).
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Removal of SPO11 and Resection of 5' Ends of DNA (yeast)
SPO11 forms a dimer and each subunit cleaves a single strand of DNA, thus creating a double-strand break. After cleaving DNA, a SPO11 subunit remains covalently attached to each 5' end via a tyrosine residue. SPO11 is removed from the DNA by cleavage of single strands 3' to the attached SPO11. The products are a resected 5' end (protruding 3' overhang) and a covalent complex of SPO11 with an oligonucleotide.
GLUT1:ATP complexes reversibly dissociate, restoring the glucose transport activity of GLUT1 glucose transport, with the result that depletion of cellular ATP leads to increased glucose uptake (Blodgett et al. 2007).
Cytosolic glucokinase and the three isoforms of hexokinase catalyze the irreversible reaction of glucose and ATP to form glucose 6 phosphate and ADP. In the body glucokinase is found only in hepatocytes and pancreatic beta cells. Glucokinase and the hexokinase enzymes differ in that glucokinase has a higher Km than the hexokinases and is less readily inhibited by the reaction product. As a result, glucokinase should be inactive in the fasting state when glucose concentrations are low but in the fed state should have an activity proportional to glucose concentration. These features are thought to enable efficient glucose uptake and retention in the liver, and to function as a sensor of glucose concentration coupled to insulin release in pancreatic beta cells (Thorens 2001). Glucokinase mutations are associated with MODY2, a heritable early onset form of type II diabetes (Tanizawa et al. 1991; Takeda et al. 1993). Three human hexokinase enzymes have been characterized, HK1 (Aleshin et al. 1998), HK2 (Lehto et al. 1995), and HK3 (Rijksen at al. 1982).
Free glucokinase (GCK1) leaves the nucleus via the nuclear pore. While the GCK1 protein contains a nuclear export sequence motif, the molecular details of the GCK1 export process remain to be worked out (Shiota et al. 1999).
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HMPhOH is hydroxylated to MDMQ6H2 by HMPhOH monooxygenase
2-hexaprenyl-6-methoxyphenol (HMPhOH) aka 2-methoxy-6-hexaprenylphenol is enzymatically converted to 2-hexaprenyl-6-methoxy-1,4-benzoquinol (MDMQ6H2) (Gin et al. 2003, Ozeir et al. 2011). It was thought at one time that the flavin-dependent monooxygenase, Coq6, was the enzyme that catalysed this reaction, however, it has been subsequently shown that Coq6 is not essential for this reaction (Ozeir et al. 2011). However, it is still believed that another member of the Coq family catalyses this event.
Glucokinase (GCK1) is negatively regulated by glucokinase regulatory protein (GKRP), which reversibly binds the enzyme to form an inactive complex. Binding is stimulated by fructose 6-phosphate and sorbitol 6-phosphate (hence high concentrations of these molecules tend to reduce GCK1 activity) and inhibited by fructose 1-phosphate (hence a high concentration of this molecule tends to increase GCK1 activity). Once formed, the complex is translocated to the nucleus. In the presence of high glucose concentrations, the nuclear GCK1:GKRP complex dissociates, freeing GCK1 to return to the cytosol. The free GKRP is thought also to return to the cytosol under these conditions, but this return has not been confirmed experimentally. Possible physiological roles for this sequestration process are to decrease futile cycling between glucose and glucose 6 phosphate in hepatocytes under low-glucose conditions, and to decrease the lag between a rise in intracellular glucose levels and the onset of glucose phosphorylation in both hepatocytes and pancreatic beta cells (Brocklehurst et al. 2004; Shiota et al. 1999).
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Association of phospho-L13a with GAIT element of Ceruloplasmin mRNA
Cells take up glucose by facilitated diffusion, via glucose transporters (GLUTs) associated with the plasma membrane, a reversible reaction (Joost and Thorens 2001). Four tissue-specific GLUT isoforms are known. Glucose in the cytosol is phosphorylated by tissue-specific kinases to yield glucose 6-phosphate, which cannot cross the plasma membrane because of its negative charge. In the liver, this reaction is catalyzed by glucokinase which has a low affinity for glucose (Km about 10 mM) but is not inhibited by glucose 6-phosphate. In other tissues, this reaction is catalyzed by isoforms of hexokinase. Hexokinases are feedback-inhibited by glucose 6-phosphate and have a high affinity for glucose (Km about 0.1 mM). Liver cells can thus accumulate large amounts of glucose 6-phosphate but only when blood glucose concentrations are high, while most other tissues can take up glucose even when blood glucose concentrations are low but cannot accumulate much intracellular glucose 6-phosphate. These differences are consistent with the view that that the liver functions to buffer blood glucose concentrations, while most other tissues take up glucose to meet immediate metabolic needs. Glucose 6-phosphatase, expressed in liver and kidney, allows glucose 6-phosphate generated by gluconeogenesis (both tissues) and glycogen breakdown (liver) to leave the cell. The absence of glucose 6-phosphatase from other tissues makes glucose uptake by these tissues essentially irreversible, consistent with the view that cells in these tissues take up glucose for local metabolic use.
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Pol III initiation complexes open the promoter spontaneously. Indeed, this is the general case for DNA-dependent RNA polymerases. Only pol II, with its requirement for TFIIH-directed and ATP-dependent promoter opening is exceptional. TFIIH introduces a layer of mechanism that is not in the repertoire of any other transcriptase. Thus, it is pol III-mediated transcription that is, from a mechanistic perspective, most directly comparable with archaeal and also bacterial transcription. Promoter opening has been analyzed only in the S. cerevisiae (sc) in vitro system. At the sc SUP4 tRNATyr promoter, a DNA segment extending from bp ââ¬â10 to +7 (relative to the transcriptional start site at +1) opens thermoreversibly between 0 and 40C, the upstream segment, bp ââ¬â9 to ââ¬â5, opening at slightly lower temperature than the downstream segment, bp ââ¬â2 to +7 (Kassavetis et al., 1992). The specification of 17 bp of DNA strand separation at the open promoter could be a slight overestimate. Even under the constraint of attachment to uniquely positioned TFIIIB, pol III can explore a short DNA segment for its initiation site (Fruscoloni et al., 1995). As a consequence, permanganate footprinting, which is used to analyze promoter opening, may provide a snapshot of a frequency-weighted superposition of multiple, closely spaced open promoter complexes that are in dynamic equilibrium instead of the unique complex that is precisely poised to form the first nucleotide linkage. Promoter opening (in linear DNA) naturally involves RNA polymerase, including the initiation-specific C34 subunit (sc gene RPC10) (Brun et al., 1997) and requires the participation of the Brf1 and Bdp1 subunits of sc TFIIIB (Hahn and Roberts, 2000; Kassavetis et al., 1998; Kassavetis et al., 2001). Thus, TFIIIB plays a role in transcriptional initiation that extends beyond recruiting pol III to the promoter.
Hexoses, notably fructose, glucose, and galactose, generated in the lumen of the small intestine by breakdown of dietary carbohydrate are taken up by enterocytes lining the microvilli of the small intestine and released from them into the blood. Uptake into enterocytes is mediated by two transporters localized on the lumenal surfaces of the cells, SGLT1 (glucose and galactose, together with sodium ions) and GLUT5 (fructose). GLUT2, localized on the basolateral surfaces of enterocytes, mediates the release of these hexoses into the blood (Wright et al. 2004). GLUT2 may also play a role in hexose uptake from the gut lumen into enterocytes when the lumenal content of monosaccharides is very high (e.g., Kellet and Brot-Laroche, 2005) and GLUT5 mediates fructose uptake from the blood into cells of the body, notably hepatocytes. Cells take up glucose by facilitated diffusion, via glucose transporters (GLUTs) associated with the plasma membrane, a reversible reaction. Four tissue-specific GLUT isoforms are known. Glucose in the cytosol is phosphorylated by tissue-specific kinases to yield glucose 6-phosphate, which cannot cross the plasma membrane because of its negative charge. In the liver, this reaction is catalyzed by glucokinase which has a low affinity for glucose (Km about 10 mM) but is not inhibited by glucose 6-phosphate. In other tissues, this reaction is catalyzed by isoforms of hexokinase. Hexokinases are feedback-inhibited by glucose 6-phosphate and have a high affinity for glucose (Km about 0.1 mM). Liver cells can thus accumulate large amounts of glucose 6-phosphate but only when blood glucose concentrations are high, while most other tissues can take up glucose even when blood glucose concentrations are low but cannot accumulate much intracellular glucose 6-phosphate. These differences are consistent with the view that that the liver functions to buffer blood glucose concentrations, while most other tissues take up glucose to meet immediate metabolic needs. Glucose 6-phosphatase, expressed in liver and kidney, allows glucose 6-phosphate generated by gluconeogenesis (both tissues) and glycogen breakdown (liver) to leave the cell. The absence of glucose 6-phosphatase from other tissues makes glucose uptake by these tissues essentially irreversible, consistent with the view that cells in these tissues take up glucose for local metabolic use.
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MHHB is decarboxylated to HMPhOH by MHHB decarboxylase
3-hexaprenyl-4-hydroxy-5-methoxybenzoic acid aka 3-methoxy-4-hydroxy-5-hexaprenylbenzoic acid (MHHB) is enzymatically decarboxylated to form 2-hexaprenyl-6-methoxyphenol (HMPhOH) (Casey & Threlfall 1978, Goewert et al. 1981). At the present time the enzyme identity is unknown but is thought to be a member of the COQ family.
Regulation of actin filament assembly by Arp2/3 complex and formins
Annu Rev Biophys Biomol Struct 36:451-77
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Proteasome mediated degradation of PAK-2p34
Rho GTPase-activating protein 10 (RHG10) interacts with caspase-activated PAK-2p34
Interaction of PAK-2p34 with RGH10/ PS-GAP results in accumulation of PAK-2p34 in the perinuclear region
Dissociation of L13a from the 60s ribosomal subunit
The reversible facilitated diffusion of fructose, galactose, and glucose from the cytosol to the extracellular space is mediated by the GLUT2 transporter in the plasma membrane. In the epithelial cells of the small intestine, the basolateral localization of GLUT2 (Thorens et al. 1990) enables hexose sugars derived from the diet and taken up by the action of the SGLT1 and GLUT5 transporters to be released into the circulation. The specificity of the GLUT2 transporter has been established directly through biochemical assays of purified recombinant proteins (Colville et al. 1993; Wu et al. 1998) and indirectly through studies of patients deficient in GLUT2 transporter protein (Santer et al. 1997).
GLUT2 (glucose transporter) homotetramers associated with the plasma membrane mediate the facilitated diffusion of glucose between the cytosol and the extracellular space, so glucose will leave cells when its intracellular concentration exceeds the extracellular one (Colville et al. 1993; Santer et al. 1997; Wu et al. 1998). In the body, such glucose export is a normal feature of liver cells when gluconeogenesis or glycogen breakdown is underway.
GLUT (glucose transporter) homotetramers associated with the plasma membrane mediate the facilitated diffusion of glucose between the extracellular space and the cytosol. Four human GLUT isoforms have been identified, members of a larger family of transporter proteins (Joost et al. 2002), encoded by the SCLC2A1, 2, 3, and 4 genes. Conserved sequence motifs in the GLUT proteins suggest the existence of shared structural features confirmed by in situ labeling and mutagenesis studies. Each GLUT protein has twelve membrane spanning domains organized to form an aqueous channel. While monomeric protein can form such a channel and transport glucose, kinetic studies suggest that the functional form of the protein is a homotetramer. Different GLUT proteins are expressed in different tissues. GLUT1 is expressed by many cell types, notably endothelial cells, red blood cells and cells of the brain. Its low Km for glucose (~1 mM) relative to normal blood glucose concentration (~5 mM) allows these cells to take up glucose independent of changes in blood glucose levels. Its abundance in red blood cells has allowed it to be purified and biochemically characterized (Hruz and Mueckler 2001; Liu et al. 2001). Cytosolic ATP associates with GLUT1 and inhibits its glucose transporter activity. GLUT2 is expressed on hepatocytes and pancreatic beta cells. Because of its high Km for glucose (~15-20 mM), GLUT2-mediated glucose uptake normally occurs only in the fed state, when its rate is proportional to blood glucose concentration. This feature of the transporter is thought to enable efficient uptake of large amounts of glucose by the liver in the fed state, and to allow it to function as part of a glucose sensor coupled to insulin release in pancreatic beta cells (Thorens 2001). GLUT2 also mediates glucose export from liver cells when gluconeogenesis is underway (Colville et al. 1993; Santer et al. 1997; Wu et al. 1998). GLUT3 is expressed by cells of the brain and possibly other cell types with a high constitutive requirement for glucose. Its low Km for glucose (~1.5 mM) allows these cells to import glucose independent of fluctuations in blood glucose levels (Colville et al. 1993). GLUT4, like GLUT1 and 3, has a high affinity for glucose. GLUT4 is abundant in cells of skeletal muscle and adipose tissue. GLUT4 molecules are translocated from an intracellular store to the cell surface in response to increased insulin levels (Bryant et al. 2002; Fukumoto et al. 1989).
This pathway describes how normal signaling by PI3K/AKT, presented in the contained module 'PIP3 Activates AKT Signaling' and recently reviewed by Manning and Cantley in 2007, is perturbed in cancer, as described in the contained module 'Constitutive Signaling by PI3K/AKT'. Please refer to Liu et al. 2009 and Hollander et al. 2011 for recent reviews.
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Mutant forms of IDH1 in which the arginine residue at position 132 has been replaced by histidine, cystine, leucine, or serine catalyze the reaction of 2-oxoglutarate and NADPH + H+ to form (R)-2-hydroxyglutarate and NADP+. Like normal IDH1, the mutant enzyme forms a dimer located in the cytosol (Dang et al. 2009). Such mutations occur frequently as a somatic event in human glioblastomas (Parsons et al. 2008). Cells expressing the mutant protein accumulate elevated levels of 2-hydroxyglutarate, probably in the cytosol as IDH1 is a cytosolic enzyme. The fate of the 2-hydroxyglutarate is unclear, but the high frequency with which the mutation is found in surveys of primary tumors is consistent with the possibility that it is advantageous to the tumor cells (Dang et al. 2009).
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AKT inhibitors bind AKT and prevent its association with the membrane, thereby blocking AKT activation (Kondapaka et al. 2003, Yap et al. 2011, Berndt et al. 2010). AKT inhibitors annotated here target all AKT isoforms (AKT1, AKT2 and AKT3). None of the annotated inhibitors are AKT E17K mutant specific and none of them have been approved for clinical use. For a recent review, please refer to Liu et al. 2009.
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Class IA PI3K is a heterodimer of a p85 regulatory subunit (encoded by PIK3R1, PIK3R2 or PIK3R3) and a p110 catalytic subunit (encoded by PIK3CA, PIK3CB or PIK3CD). In the absence of activating signals, the regulatory subunit stabilizes the catalytic subunit while inhibiting its activity. The complex becomes activated when extracellular signals stimulate the phosphorylation of the cytoplasmic domains of transmembrane receptors or receptor-associated proteins. The p85 regulatory subunit binds phosphorylated motifs of activator proteins, which induces a conformational change that relieves p85-mediated inhibition of the p110 catalytic subunit and enables PI3K to phosphorylate PIP2 to form PIP3. The phosphoinositide kinase activity of PI3K is opposed by the phosphoinositide phosphatase activity of PTEN. PIP3 acts as a messenger that recruits PDPK1 (PDK1) and AKT (AKT1, AKT2 or AKT3) to the plasma membrane. PDPK1 also possesses a low affinity for PIP2, so small amounts of PDPK1 are always present at the membrane. Binding of AKT to PIP3 induces a conformational change that enables TORC2 complex to phosphorylate AKT at a conserved serine residue (S473 in AKT1). Phosphorylation at the serine residue enables AKT to bind to PDPK1 and exposes a conserved threonine residue (T308) that is phosphorylated by PDPK1. AKT phosphorylated at both serine and threonine residues dissociates from the plasma membrane and acts as a serine/threonine kinase that phosphorylates a number of cytosolic and nuclear targets involved in regulation of cell metabolism, survival and gene expression. For a recent review, please refer to Manning and Cantley, 2007. Signaling by PI3K/AKT is frequently constitutively activated in cancer. This activation can be via gain-of-function mutations in PI3KCA (encoding catalytic subunit p110alpha), PIK3R1 (encoding regulatory subunit p85alpha) and AKT1. The PI3K/AKT pathway can also be constitutively activated by loss-of-function mutations in tumor suppressor genes such as PTEN. Gain-of-function mutations activate PI3K signaling by diverse mechanisms. Mutations affecting the helical domain of PIK3CA and mutations affecting nSH2 and iSH2 domains of PIK3R1 impair inhibitory interactions between these two subunits while preserving their association. Mutations in the catalytic domain of PIK3CA enable the kinase to achieve an active conformation. PI3K complexes with gain-of-function mutations therefore produce PIP3 and activate downstream AKT in the absence of growth factors (Huang et al. 2007, Zhao et al. 2005, Miled et al. 2007, Horn et al. 2008, Sun et al. 2010, Jaiswal et al. 2009, Zhao and Vogt 2010, Urick et al. 2011). While AKT1 gene copy number, expression level and phosphorylation are often increased in cancer, only one low frequency point mutation has been repeatedly reported in cancer and functionally studied. This mutation represents a substitution of a glutamic acid residue with lysine at position 17 of AKT1, and acts by enabling AKT1 to bind PIP2. PIP2-bound AKT1 is phosphorylated by TORC2 complex and by PDPK1 that is always present at the plasma membrane, due to low affinity for PIP2. Therefore, E17K substitution abrogates the need for PI3K in AKT1 activation (Carpten et al. 2007, Landgraf et al. 2008). Loss-of-function mutations affecting the phosphatase domain of PTEN are frequently found in sporadic cancers (Kong et al. 1997, Lee et al. 1999, Han et al. 2000), as well as in PTEN hamartoma tumor syndromes (PHTS) (Marsh et al. 1998). PTEN can also be inactivated by gene deletion or epigenetic silencing, or indirectly by overexpression of microRNAs that target PTEN mRNA (Huse et al. 2009). Cells with deficient PTEN function have increased levels of PIP3, and therefore increased AKT activity. For a recent review, please refer to Hollander et al. 2011. Because of their clear involvement in human cancers, PI3K and AKT are targets of considerable interest in the development of small molecule inhibitors. Although none of the currently available inhibitors display preference for mutant variants of PIK3CA or AKT, several inhibitors targeting the wild-type kinases are undergoing clinical trials. These include dual PI3K/mTOR inhibitors, class I PI3K inhibitors, pan-PI3K inhibitors, and pan-AKT inhibitors. While none have yet been approved for clinical use, these agents show promise for future therapeutics. In addition, isoform-specific PI3K and AKT inhibitors are currently being developed, and may provide more specific treatments along with reduced side-effects. For a recent review, please refer to Liu et al. 2009.
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Nuclear translocation of phospho-ERK-1 dimer
Carbohydrate is a major component of the human diet, and includes starch (amylose and amylopectin) and disaccharides such as sucrose, lactose, maltose and, in small amounts, trehalose. The digestion of starch begins with the action of amylase enzymes secreted in the saliva and small intestine, which convert it to maltotriose, maltose, limit dextrins, and some glucose. Digestion of the limit dextrins and disaccharides, both dietary and starch-derived, to monosaccharides - glucose, galactose, and fructose - is accomplished by enzymes located on the luminal surfaces of enterocytes lining the microvilli of the small intestine (Semenza et al. 2001).
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The reversible transport of extracellular fructose into the cytosol is mediated by GLUT5. In the small intestine, GLUT5 is localized on the lumenal surfaces of enterocytes (Davidson et al. 1992) and thus mediates the uptake of dietary fructose, which can be released into the circulation in a separate transport step mediated by basolaterally localized GLUT2. The specificity of GLUT5 has been worked out by studying sugar transport in Xenopus oocytes expressing recombinant human GLUT5 protein (Burant et al. 1992).
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Somatic mutations affecting arginine residue 132 of IDH1 (isocitrate dehydrogenase 1, a cytosolic enzyme that normally catalyzes the NADP+-dependent conversion of isocitrate to 2-oxoglutarate), are very commonly found in human glioblastomas (Parsons et al. 2008). These mutant proteins efficiently catalyze the NADPH-dependent reduction of 2-oxoglutarate to form 2-hydroxyglutarate. Cells expressing the mutant protein accumulate elevated levels of 2-hydroxyglutarate, probably in the cytosol as IDH1 is a cytosolic enzyme. The fate of the 2-hydroxyglutarate is unclear, but the high frequency with which the mutation is found in surveys of primary tumors is consistent with the possibility that it is advantageous to the tumor cells (Dang et al 2009).
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Extracellular trehalose, a disaccharide, is cleaved by trehalase associated with the plasma membrane to yield two molecules of glucose. Trehalase has been purified to homogeneity from rabbit intestine and shown to be a monomer attached to the plasma membrane by a GPI anchor (Galand 1984; Ruf et al. 1990). A human cDNA encoding a closely homologous protein has been cloned and the protein product of the clone has been shown to have trehalase activity in vitro (Ishihara et al. 1997). The human enzyme has not been characterized further, and so both the posttranslational modifications of the human enzyme and its activity in vivo have been inferred from the properties of the well studied rabbit enzyme.
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Activated human JNKs migrate to nucleoplasm
Phosphorylated MKK3/MKK6 migrates to nucleus
AKT1 E17K gain-of-function mutant is expected to phosphorylate ribosomal protein S6 kinase beta-2, like the wild-type AKT (Koh et al. 1999), but this has not been experimentally tested.
Phosphorylation of human JNKs by activated MKK4/MKK7
AKT1 E17K gain-of-function mutant is expected to translocate to the nucleus, like the wild-type AKT (Borgatti et al. 2003), but this has not been directly experimentally tested.
1,5-bisdiphosphoinositol-1D-myo-inositol (3,4,6)trisphosphate
1,5-bisdiphosphoinositol-1D-myo-inositol (3,4,6)trisphosphate [ChEBI:62931]
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Human ornithine transcarbamylase: crystallographic insights into substrate recognition and conformational changes
1,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6)tetrakisphosphate
1,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6)tetrakisphosphate [ChEBI:62923]
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1-diphospho-1D-myo-inositol (3,4,5,6)tetrakisphosphate
1-diphospho-1D-myo-inositol (3,4,5,6)tetrakisphosphate [ChEBI:62926]
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5-diphospho-1D-myo-inositol (1,3,4,6)tetrakisphosphate
5-diphospho-1D-myo-inositol (1,3,4,6)tetrakisphosphate [ChEBI:62928]
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Signal-induced degradation of I kappa B alpha requires site-specific ubiquitination
Fat and beyond: the diverse biology of PPARgamma
Regulation of HSF1-mediated heat shock response
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Non-vesicular lipid transport by lipid-transfer proteins and beyond
Fate of linoleic, arachidonic, and docosa-7,10,13,16-tetraenoic acids in rat testicles
Structural and mechanistic aspects of flavoproteins: electron transfer through the nitric oxide synthase flavoprotein domain
The LKB1 tumor suppressor kinase in human disease
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The SLC40 basolateral iron transporter family (IREG1/ferroportin/MTP1)
Why calcium-stimulated adenylyl cyclases?
Complex genomic rearrangements lead to novel primate gene function
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Mechanisms involved in the intestinal digestion and absorption of dietary vitamin A
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PCGF homologs, CBX proteins, and RYBP define functionally distinct PRC1 family complexes
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The intrinsic affinity between E2 and the Cys domain of E1 in ubiquitin-like modifications
Myosin phosphatase-targeting subunit 1 regulates mitosis by antagonizing polo-like kinase 1
Cytosolic phophoribosyl pyrophosphate synthetase catalyzes the reaction of D-ribose 5-phosphate and ATP to form 5-phospho-alpha-D-ribose and AMP. Three isoforms of the enzyme have been described. The first has been purified and characterized biochemically (Fox and Kelley 1971). The others are known only as inferred protein products of cloned genes; their catalytic properties have not been determined.
Cytosolic phosphoribosyl pyrophosphate synthetase 1 catalyzes the reaction of D-ribose 5-phosphate and dATP to form 5-phospho-alpha-D-ribose 1-diphosphate and 2'-deoxyadenosine 5'-monophosphate. While phosphoribosyl pyrophosphate synthetase 1 works well with either ATP or dATP as a substrate in vitro, the extent of the dATP reaction in vivo is unclear, as cellular dATP concentrations are normally very low (Fox and Kelley 1971).
The pentose phosphate pathway is responsible for the generation of a substantial fraction of the cytoplasmic NADPH required for biosynthetic reactions, and for the generation of ribose 5-phosphate for nucleotide synthesis. Although the pentose phosphate pathway and glycolysis are distinct, they involve three common intermediates, glucose 6-phosphate, glyceraldehyde 3-phosphate, and fructose 6-phosphate, so the two pathways are interconnected. The pentose phosphate pathway consists of eight reactions:1. Conversion glucose 6-phosphate to D-glucono-1,5-lactone 6-phosphate, with the formation of NADPH; 2. Conversion of D-glucono-1,5-lactone 6-phosphate to 6-phospho-D-gluconate; 3. Conversion of 6-phospho-D-gluconate to ribulose 5-phosphate, with the formation of NADPH; 4. Conversion of ribulose 5-phosphate to xylulose 5-phosphate; 5. Conversion of ribulose 5-phosphate to ribose 5-phosphate; 6. Rearrangement of ribose 5-phosphate and xylulose 5-phosphate to form sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; 7. Rearrangement of sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate to form erythrose 4-phosphate and fructose 6-phosphate; and 8. Rearrangement of xylulose 5-phosphate and erythrose 4-phosphate to form glyceraldehyde 3-phosphate and fructose-6-phosphate. The oxidative branch of the pentose phosphate pathway, reactions 1-3, generates NADPH and pentose 5-phosphate. The non-oxidative branch of the pathway, reactions 4-8, converts pentose 5-phosphate to other sugars. The overall pathway can operate to generate only NADPH (glucose 6-phosphate is converted to pentose 5-phosphates, which are directed to the synthesis of fructose 6-phosphate and glyceraldehyde 3-phosphate, which in turn are converted back to glucose 6-phosphate). The reactions of the non-oxidative branch can operate to generate net amounts of ribose 5-phosphate with no production of NADPH. Net flux through this network of reactions appears to depend on the metabolic state of the cell and the nature of the biosynthetic reactions underway (Casazza and Veech 1987). G6PD, the enzyme that catalyzes the first reaction of the pathway, is more extensively mutated in human populations than any other enzyme, pehaps because these mutant alleles confer malaria resistance (Luzzatto and Afolayan 1968). Mutations affecting other parts of the pathway are rare, though several have been described and studies of their effects have contributed to our understanding of the normal flux of metabolites through this network of reactions (Wamelink et al. 2008).
The regulated turnover of glycogen plays a central, tissue-specific role in the maintenance of blood glucose levels and in the provision of glucose to tissues such as muscle and brain in response to stress. Defects in the enzymes involved in glycogen turnover are associated with abnormal responses to fasting and exercise that can differ widely in their presentation and severity. Additional symptoms can be the result of accumulation of abnormal products of glycogen metabolism (www.ommbid.com). In this initial release, we have annotated two forms of myoclonic epilepsy of Lafora that are due to defects in proteins required for the turnover of the low levels of phosphoglycogen that accumulate in many tissues of the body. This module will be extended in future releases to cover diseases due to deficiencies in GYG1, the ubiquitously expressed form of glycogenin (GSD type XV), GYS2 and GYS1, the liver-specific and ubiquitously expressed forms of glycogen synthase (GSD type 0), GBE1, the single form of branching enzyme (GSD type IV), and in the endoplasmic reticulum-associated phosphatase (G6PC) and transporter (SLC37A4) required for export of glucose geneated by glycogen breakdown in liver (GSD type 1a and 1b, respectively). Severe congenital neutropenia type 4 (SCN4) is included in this group because its molecular basis is loss of glucose 6-phosphatase 3 (G6PC3) activity (Boztug et al. 2009). G6PC3 is a ubiquitously expressed isozyme of G6PC, the enzyme whose deficiency is the cause of glycogen storage disease type 1a (GSD 1a).
Lafora disease is a progressive neurodegenerative disorder with onset typically late in childhood, characterized by seizures and progressive neurological deterioration and death within ten years of onset. Recessive mutations in EPM2A (laforin) and NHLRC1 (malin) have been identified as causes of the disease. The disease is classified here as one of glycogen storage as EPM2A (laforin) and NHLRC1 (malin) regulate normal glycogen turnover and defects in either protein are associated with the formation of Lafora bodies, accumulations of abnormal, insoluble glycogen molecules in tissues including brain, muscle, liver, and heart (Ramachandran et al. 2009; Roach et al. 2012). Consistent with a central role for glycogen accumulation in the disease, reduced (Turnbull et al. 2011) or absent (Pederson et al. 2013) glycogen synthase activity prevents Lafora Disease in mouse models. Type 2A disease. EPM2A (laforin) associated with cytosolic glycogen granules, normally catalyzes the removal of the phosphate groups added rarely but consistently to growing glycogen molecules (Tagliabracci et al. 2011). Defects in this catalytic activity lead to the formation of phosphorylated glycogen molecules that are insoluble and that show abnormal branching patterns (Minassian et al. 1998, Serratosa et al. 1999, Tagliabracci et al. 2011). Type 2B disease. NHLRC1 (malin) normally mediates polyubiquitination of EPM2A (laforin) and PPP1R3C (PTG). The two polyubiquitinated proteins are targeted for proteasome-mediated degradation, leaving a glycogen-glycogenin particle associated with glycogen synthase. In the absence of NHLRC1 activity, EPM2A and PPP1R3C proteins appear to persist, associated with the formation of abnormal, stable glycogen granules (Lafora bodies) (Chan et al. 2003; Gentry et al. 2005). In NHLRC1 knockout mice PPP1R3C levels are unchanged rather than increased, suggesting that NHLRC1 does not target PPP1R3C for degradation. However, EPM2A protein levels are increased in this knockout consistent with NHLRC1's proposed role (DePaoli-Roach et al. 2010).
These pathways together are responsible for: 1) the extraction of energy and carbon skeletons for biosyntheses from dietary sugars and related molecules; 2) the short-term storage of glucose in the body (as glycogen) and its mobilization during a short fast; and 3) the synthesis of glucose from pyruvate during extended fasts.
5-Phospho-alpha-D-ribose 1-diphosphate (PRPP) is a key intermediate in both the de novo and salvage pathways of purine and pyrimidine synthesis. PRPP and the enzymatic activity responsible for its synthesis were first described by Kornberg et al. (1955). The enzyme, phosphoribosyl pyrophosphate synthetase 1, has been purified from human erythrocytes and characterized biochemically. The purified enzyme readily forms multimers; its smallest active form appears to be a dimer and for simplicity it is annotated as a dimer here. It specifically catalyzes the transfer of pyrophosphate from ATP or dATP to D-ribose 5-phosphate, and has an absolute requirement for Mg++ and orthophosphate (Fox and Kelley 1971; Roth et al. 1974). The significance of the reaction with dATP in vivo is unclear, as the concentration of cytosolic dATP is normally much lower than that of ATP. The importance of this enzyme for purine synthesis in vivo has been established by demonstrating excess phosphoribosyl pyrophosphate synthetase activity, correlated with elevated enzyme levels or altered enzyme properties, in individuals whose rates of uric acid production are constitutively abnormally high (Becker and Kim 1987; Roessler et al. 1993). Molecular cloning studies have revealed the existence of two additional genes that encode phosphoribosyl pyrophosphate synthetase-like proteins, one widely expressed (phosphoribosyl pyrophosphate synthetase 2) and one whose expression appears to be confined to the testis (phosphoribosyl pyrophosphate synthetase 1-like 1) (Taira et al. 1989; 1991). Neither of these proteins has been purified and characterized enzymatically, nor have variations in the abundance or sequence of either protein been associated with alterations in human nucleotide metabolism (Roessler et al. 1993; Becker et al. 1996), so their dimerization and ability to catalyze the synthesis of PRPP from D-ribose 5-phosphate are inferred here on the basis of their predicted amino acid sequence similarity to phosphoribosyl pyrophosphate synthetase 1.
Cytochrome b5 reductase (CYB5R3) catalyzes the reduction of cytosolic ferric CYB5A (CYB5A:ferriheme) to ferrous CYPB5A (CYB5A:heme), coupled to the conversion of NADH to NAD+ (Shirabe et al. 1995). CYB5R3 is associated with the outer mitochondrial membrane via a myristoyl group added post-translationally to glycine residue 2 of the protein (Borgese et al. 1993).
The reduction of cytosolic semidehydroascorbate (SDA) to ascorbate (vitC) is catalyzed by cytochrome B5 (CYB5A) associated with the mitochondrial outer membrane. In the course of the reaction, the heme iron of the cytochrome is oxidized (Linster & Van Schaftingen 2007, Shirabe et al. 1995).
The uptake of extracellular dehydroascorbate into the cytosol is mediated by GLUT1 and GLUT3 associated with the plasma membrane (Rumsey et al. 1997, 2000). This process may play a significant role in ascorbate utilization in the central nervous system (Agus et al. 1997). The process is efficiently competitively inhibited by glucose, leading to the suggestion that inhibited dehydroascorbate uptake may contribute to the pathology of diabetes (Liang et al. 2001; Rumsey et al. 2000).
G protein activation by G protein coupled receptors: ternary complex formation or catalyzed reaction?
Cytosolic ribulose-5-phosphate-3-epimerase (RPE) catalyzes the reversible interconversion of D-xylulose 5-phosphate and D-ribulose 5-phosphate (Bose and 1985). The electrophoretic properties of RPE activity detected in extracts of mouse-human somatic cell hybrids suggest that the active form of the enzyme is a homodimer (Spencer and Hopkinson 1980).
Cytosolic ribulose-5-phosphate-3-epimerase (RPE) catalyzes the reversible interconversion of D-ribulose 5-phosphate and D-xylulose 5-phosphate (Bose and 1985). The electrophoretic properties of RPE activity detected in extracts of mouse-human somatic cell hybrids suggest that the active form of the enzyme is a homodimer (Spencer and Hopkinson 1980).
Cytosolic transketolase catalyzes the reversible reaction of D-glyceraldehyde 3-phosphate and sedoheptulose 7-phosphate to form D-xylulose 5-phosphate and D-ribose 5-phosphate. The active transketolase enzyme is a homodimer with one molecule of thiamine pyrophosphate and magnesium bound to each monomer (Wang et al. 1997).
Cytosolic transketolase catalyzes the reversible reaction of D-xylulose 5-phosphate and D-ribose 5-phosphate to form D-glyceraldehyde 3-phosphate and sedoheptulose 7-phosphate. The active transketolase enzyme is a homodimer with one molecule of thiamine pyrophosphate and magnesium bound to each monomer (Wang et al. 1997).
Cytosolic transaldolase (TALDO1) catalyzes the reversible reaction of D-erythrose 4-phosphate and D-fructose 6-phosphate to form D-glyceraldehyde 3-phosphate and sedoheptulose 7-phosphate. Protein expressed from the cloned gene has been characterized biochemically (Banki et al. 1994) and transaldolase deficiency in a patient has been correlated with a mutation in the TALDO1 gene (Verhoeven et al. 2001).
Cytosolic transaldolase (TALDO1) catalyzes the reversible reaction of D-glyceraldehyde 3-phosphate and sedoheptulose 7-phosphate to form D-erythrose 4-phosphate and D-fructose 6-phosphate. Protein expressed from the cloned gene has been characterized biochemically (Banki et al. 1994) and transaldolase deficiency in a patient has been correlated with a mutation in the TALDO1 gene (Verhoeven et al. 2001).
Cytosolic transketolase catalyzes the reaction of D-glyceraldehyde 3-phosphate and D-fructose 6-phosphate to form D-erythrose 4-phosphate and D-xylulose 5-phosphate. The active transketolase enzyme is a homodimer with one molecule of thiamine pyrophosphate and magnesium bound to each monomer (Wang et al. 1997).
Cytosolic transketolase catalyzes the reaction of D-erythrose 4-phosphate and D-xylulose 5-phosphate to form D-glyceraldehyde 3-phosphate and D-fructose 6-phosphate. The active transketolase enzyme is a homodimer with one molecule of thiamine pyrophosphate and magnesium bound to each monomer (Wang et al. 1997).
The reversible interconversion of ribose 5-phosphate and ribulose 5-phosphate is catalyzed by cytosolic ribose 5-phosphate isomerase (Huck et al. 2004).
The reversible interconversion of ribulose 5-phosphate and ribose 5-phosphate is catalyzed by cytosolic ribose 5-phosphate isomerase (Huck et al. 2004).
5-triphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate
5-triphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate [ChEBI:62985]
Absorption of chlorophyll phytol in normal man and in patients with Refsum's disease
GPD1L dimer (name copied from entity in Homo sapiens)
GPD1 dimer (name copied from entity in Homo sapiens)
ACAT1 tetramer (name copied from entity in Homo sapiens)
AMPK heterotrimer (active) (name copied from entity in Homo sapiens)
SUP4 tRNATyr gene DNA with transcription bubble (single-stranded)
NPC1L1:ezetimibe complex (name copied from entity in Homo sapiens)
ISYNA1:NAD+ (name copied from entity in Homo sapiens)
AUF1, the regulator of tumor necrosis factor alpha messenger RNA decay, is targeted by autoantibodies of patients with systemic rheumatic diseases
ABCG5:ABCG8 heterodimer (name copied from entity in Homo sapiens)
IMPA2:Mg2+ (name copied from entity in Homo sapiens)
Identification of active flavin-containing monooxygenase isoform 2 in human lung and characterization of expressed protein
Hereditary juvenile cobalamin deficiency caused by mutations in the intrinsic factor gene
Proc. Natl. Acad. Sci. U.S.A. 102:4130-3
IMPA1:Mg2+ (name copied from entity in Homo sapiens)
IMPA2 dimer (name copied from entity in Homo sapiens)
IDH1 dimer (name copied from entity in Homo sapiens)
ACOX1:FAD complex (name copied from entity in Homo sapiens)
ACOX1 dimer (name copied from entity in Homo sapiens)
ABCD1 homodimer (name copied from entity in Homo sapiens)
HSD17B4 dimer (name copied from entity in Homo sapiens)
ACOX2:FAD (name copied from entity in Homo sapiens)
HACL1 holoenzyme monomer (name copied from entity in Homo sapiens)
HACL1 tetramer (name copied from entity in Homo sapiens)
SREBP1A,1C,2 dimer (name copied from entity in Homo sapiens)
Expression of the blue-light receptor cryptochrome in the human retina
SREBP1A,1C,2:NF-Y:FDPS gene (name copied from entity in Homo sapiens)
2(FDPS:3Mg2+) (name copied from entity in Homo sapiens)
6(GGPS1:3Mg2+) (name copied from entity in Homo sapiens)
SUMO is transferred from E1 to E2 (UBE2I, UBC9)
FDPS:3Mg2+ (name copied from entity in Homo sapiens)
FDFT:Mg2+ (name copied from entity in Homo sapiens)
GGPS1:3Mg2+ (name copied from entity in Homo sapiens)
SQLE:FAD (name copied from entity in Homo sapiens)
HMGCR dimer (name copied from entity in Homo sapiens)
IDI1 or 2 (name copied from entity in Homo sapiens)
MVK dimer (name copied from entity in Homo sapiens)
phosphorylated nuclear Cyclin B1:Cdc2 substrates
RNA primer:origin duplex with DNA damage
PCYT2 dimer (name copied from entity in Homo sapiens)
CHKA:CHKB (name copied from entity in Homo sapiens)
CHKB:CHKB (name copied from entity in Homo sapiens)
LPIN2:Mg2+ (name copied from entity in Homo sapiens)
LPIN1:Mg2+ (name copied from entity in Homo sapiens)
CHKA:CHKA (name copied from entity in Homo sapiens)
MGLL dimer (name copied from entity in Homo sapiens)
CH25H (Fe2+ cofactor) (name copied from entity in Homo sapiens)
PTG depletion removes Lafora bodies and rescues the fatal epilepsy of Lafora disease
CEPT1:Mg2+/Mn2+ (name copied from entity in Homo sapiens)
EPT1:Mg2+/Mn2+ (name copied from entity in Homo sapiens)
PISD:Pyruvoyl (name copied from entity in Homo sapiens)
LPIN3:Mg2+ (name copied from entity in Homo sapiens)
CDS1:Mg2+ (name copied from entity in Homo sapiens)
Phosphorylation of CAP-G is required for its chromosomal DNA localization during mitosis
Biochem. Biophys. Res. Commun. 377:1007-11
PCYT1A dimer (name copied from entity in Homo sapiens)
PCYT1B dimer (name copied from entity in Homo sapiens)
The Bcl10-Malt1 complex segregates Fc epsilon RI-mediated nuclear factor kappa B activation and cytokine production from mast cell degranulation
CHPT1:Mg2+/Mn2+ (name copied from entity in Homo sapiens)
K48-polyubiquitinated partially digested Ag
released pre-mRNA Pol III oligonucleotide
elongating pre-mRNA Pol III oligonucleotide
PIKFYVE:VAC14:FIG4 (name copied from entity in Homo sapiens)
PIK3R4:Mn2+ (name copied from entity in Homo sapiens)
PIK3C3:Mn2+ (name copied from entity in Homo sapiens)
Frequent activating mutations of FGFR3 in human bladder and cervix carcinomas
CDIPT:Mg2+/Mn2+ (name copied from entity in Homo sapiens)
PIK3C3:Mn2+:PIK3R4:Mn2+ (name copied from entity in Homo sapiens)
The trithorax-group protein Lid is a histone H3 trimethyl-Lys4 demethylase
template DNA with first transcript dinucleotide, opened to +8 position
PIP4K2B:PIP4K2B (name copied from entity in Homo sapiens)
PIP4K2A:PIP4K2A (name copied from entity in Homo sapiens)
PIP4K2A:PIP4K2B (name copied from entity in Homo sapiens)
Protein kinase C conventional and novel isoforms
DNA containing RNA Polymerase II promoter
Open DNA -10 to +2 containing RNA Polymerase II promoter
Template DNA hybrid with phosphodiester-PPi intermediate
template DNA opened from -10 to +2, with first nucleotide base-paired at 5'-end
Cyclin A:Cdk2-associated events at S phase entry
Tim17p regulates the twin pore structure and voltage gating of the mitochondrial protein import complex TIM23
ACSL1 (name copied from entity in Homo sapiens)
LTA4H:Zn2+ (name copied from entity in Homo sapiens)
Kinetic mechanism of human DNA ligase I reveals magnesium-dependent changes in the rate-limiting step that compromise ligation efficiency
GGT1 (name copied from entity in Homo sapiens)
GGT5 (name copied from entity in Homo sapiens)
SPTLC1:SPTLC2 (name copied from entity in Homo sapiens)
SPTLC1:SPTLC3 (name copied from entity in Homo sapiens)
COQ6:FAD (name copied from entity in Homo sapiens)
template DNA:11 nucleotide transcript hybrid
template DNA:9 nucleotide transcript hybrid
template DNA:4 nucleotide transcript hybrid
template DNA:3 nucleotide transcript hybrid
oligoribonucleotide with a 5'-diphosphate
Phosphoglycerate mutase BB isoenzyme deficiency in a patient with non-spherocytic anemia: familial and metabolic studies
Nascent pre-mRNA with 5'-GMP associated with CE
Nascent pre-mRNA with 5'-GMP dissociated from CE
The control of mammalian DNA replication: a brief history of space and timing.
Hot-spot mutations in p110alpha of phosphatidylinositol 3-kinase (pI3K): differential interactions with the regulatory subunit p85 and with RAS
Catalytic pathway of manganese superoxide dismutase by direct observation of superoxide
Molecular characterization of heat shock-like factor encoded on the human Y chromosome, and implications for male infertility
CpG motifs in bacterial DNA trigger direct B-cell activation
Whole-exome sequencing links a variant in DHDDS to retinitis pigmentosa
Mitochondrial Hsp70/MIM44 complex facilitates protein import
Crystal structure of the PTEN tumor suppressor: implications for its phosphoinositide phosphatase activity and membrane association
4x(Btn-PC:Mn2+) (name copied from entity in Homo sapiens)
ACACA:2Mn2+ (name copied from entity in Homo sapiens)
Btn-ACACA:2Mn2+ (name copied from entity in Homo sapiens)
2xPNPO:2xFMN (name copied from entity in Homo sapiens)
4x(PC:Mn2+) (name copied from entity in Homo sapiens)
NMNAT2 (Mg2+) (name copied from entity in Homo sapiens)
6xNMNAT1:6xZn2+ (name copied from entity in Homo sapiens)
Btn-ACACB:2Mn2+ (name copied from entity in Homo sapiens)
Phagosomal maturation (early endosomal stage)
ACACB:2Mn2+ (name copied from entity in Homo sapiens)
NADSYN1 hexamer (name copied from entity in Homo sapiens)
Inositol hexakisphosphate kinase products contain diphosphate and triphosphate groups
4xNADK:Zn2+ (name copied from entity in Homo sapiens)
4xNMNAT3:4xMg2+ (name copied from entity in Homo sapiens)
2xMTHFR (name copied from entity in Homo sapiens)
MOCS3:Zn2+ (red.) (name copied from entity in Homo sapiens)
2xMTHFD1 (name copied from entity in Homo sapiens)
4xSHMT1 (name copied from entity in Homo sapiens)
2xNFS1:2xPXLP (name copied from entity in Homo sapiens)
SUP4 tRNATyr gene DNA with Open promoter (single-stranded)
MOCS3-S-S(1-):Zn2+ (name copied from entity in Homo sapiens)
SUP4 tRNATyr gene DNA with Closed promoter (duplex)
Effector role reversal during evolution: the case of frataxin in Fe-S cluster biosynthesis
Superoxide dismutases: role in redox signaling, vascular function, and diseases
PLCB1:Ca2+ (name copied from entity in Homo sapiens)
PLCB2:Ca2+ (name copied from entity in Homo sapiens)
SUP4 tRNATyr gene DNA with a termination site
PLCB3:Ca2+ (name copied from entity in Homo sapiens)
PLCB4:Ca2+ (name copied from entity in Homo sapiens)
PLCE1:Ca2+ (name copied from entity in Homo sapiens)
IMPA1 dimer (name copied from entity in Homo sapiens)
Single-Stranded Oligodeoxyribonucleotide (12 to 34 nucleotides)
In the absence of stress HSF1 is predominantly monomeric and is thought to be repressed in its inactive monomeric state by the following mechanisms: interaction with chaperone proteins such as HSP90 (Zou J et al.1998; Guo Y et al. 2001) intramolecular coiled-coil interactions between a hydrophobic leucine zipper domain in the carboxyl-terminus of the protein and three amino-terminal leucine zippers, which are required for homotrimerization and transcriptional activation (Rabindran SK et al. 1993; Zuo J et al. 1995) post-translation modifications that include protein acetylation, sumoylation and phosphorylation may also contribute to HSF1 repression (Knauf U et al. 1996; Hietakangas V et al. 2003; Batista-Nascimento L et al. 2011) The accumulation of misfolded proteins upon proteotoxic stresses leads to the release of HSF1 from the HSP90-containing multichaperone complex and results in HSF1 self-association to form homotrimers (Baler R et al. 1993). There is also evidence showing that HDAC6 senses the accumulation of misfolded, ubiquitinated protein aggregates in cells and induces dissociation of a repressive HDAC6:HSF1:HSP90 complex and subsequent HSF1 activation (Boyault C et al. 2007).
Reactive oxygen species such as superoxide (O2.-), peroxides (ROOR), singlet oxygen, peroxynitrite (ONOO-), and hydroxyl radical (OH.) are generated by cellular processes such as respiration (reviewed in Murphy 2009, Brand 2010) and redox enzymes and are required for signaling yet they are damaging due to their high reactivity (reviewed in Imlay 2008, Buettner 2011, Kavdia 2011, Birben et al. 2012, Ray et al. 2012). Aerobic cells have defenses that detoxify reactive oxygen species by converting them to less reactive products. Superoxide dismutases convert superoxide to hydrogen peroxide and oxygen (reviewed in Fukai and Ushio-Fukai 2011). Catalase and peroxidases then convert hydrogen peroxide to water. Humans contain 3 superoxide dismutases: SOD1 is located in the cytosol and mitochondrial intermembrane space, SOD2 is located in the mitochondrial matrix, and SOD3 is located in the extracellular region. Superoxide, a negative ion, is unable to easily cross membranes and tends to remain in the compartment where it was produced. Hydrogen peroxide, one of the products of superoxide dismutase, is able to diffuse across membranes and pass through aquaporin channels. In most cells the primary source of hydrogen peroxide is mitochondria and, once in the cytosol, hydrogen peroxide serves as a signaling molecule to regulate redox-sensitive proteins such as transcription factors, kinases, phosphatases, ion channels, and others (reviewed in Veal and Day 2011, Ray et al. 2012). Hydrogen peroxide is decomposed to water by catalase, decomposed to water plus oxidized thioredoxin by peroxiredoxins, and decomposed to water plus oxidized glutathione by glutathione peroxidases (Presnell et al. 2013).
Rad52 and Ku bind to different DNA structures produced early in double-strand break repair.
Accumulation of non-native or misfolded proteins upon cellular stress is believed to release monomeric HSF1 from chaperon regulatory proteins (Guo Y et al. 2001). The released HSF1 monomer is rapidly converted to a homotrimer (Baler R et al. 1993; Herbomel G et al 2013). Upon trimerization HSF1 undergoes significant conformational changes resulting in an assembly of a stable triple-stranded alpha-helical coiled-coil structure with the amino-terminal hydrophobic domains from individual monomeric units (Rabindran SK et al. 1993; Zuo J et al. 1994, 1995; Neef DW et al. 2013). Biochemical and structural analysis strongly suggest that the monomer-to-trimer transition is tightly regulated at several interdependent levels. Thus, HSPs and cofactors bind HSF1 monomers preventing trimerization (Zou J et al.1998; Guo Y et al. 2001). In addition, leucine zippers (LZ) in the trimerization domain (LZ1-LZ3) are thought to retain HSF1 in its inactive monomeric form by intramolecular coiled-coil interactions with LZ4 in the carboxyl-terminus of HSF1, while LZ interactions between trimerization domains of individual monomeric units facilitate homotrimerization (Rabindran SK et al. 1993; Zuo J et al. 1994, 1995; Neef DW et al. 2013). HSF1 flexible linker region between DNA binding domain and first LZ of the trimerization domain was also found to modulate the monomer-trimer equilibrium (Liu PCC and Thiele DJ 1999). Furthermore, intermolecular disulfide bonds between cysteine residues 36 and 103 were reported to stabilize HSF1 trimer, while intramolecular disulfide crosslink inhibited HSF1 oligomerization (Lu M et al. 2008, 2009). Moreover, redox regulatory mechanisms were shown to regulate thiol-disulfide exchange and the conformation and activity of mammalian HSF1 in response to stress (Manalo DJ et al. 2002; Ahn SG and Thiele DJ 2003). A ribonucleoprotein complex containing translation elongation factor EEF1A1 (eEF1A) and a long non-coding RNA, HSR1 (heat shock RNA-1) was shown to mediate trimerization of HSF1 (Shamovsky I et al. 2006).
Proteotoxic stress results in an accumulation of misfolded proteins which tend to form insoluble protein aggregates. Histone deacetylase 6 (HDAC6) binds to ubiquitinated protein aggregates to regulate their degradation (Boyault C et al. 2006). HDAC6 was also found to interact with HSP90 and to regulate HSP90 chaperone complex activity via deacetylation of HSP90 (Kovacs JJ et al. 2005; Boyault C et al. 2007). Binding of HDAC6 to polyubiquitinted proteins triggers the dissociation of the HDAC6:HSP90:HSF1 complex resulting in the activation of HSF1 (Boyault C et al. 2007). In the absence of stress HSF1 is predominantly monomeric and is thought to be repressed in its inactive monomeric state by the following mechanisms: interaction with chaperone proteins such as HSP90 (Zou J et al.1998; Guo Y et al. 2001) intramolecular coiled-coil interactions between a hydrophobic leucine zipper domain in the carboxyl-terminus of the protein and three amino-terminal leucine zippers, which are required for homotrimerization and transcriptional activation (Rabindran SK et al. 1993; Zuo J et al. 1995) post-translation modifications that include protein acetylation, sumoylation and phosphorylation may also contribute to HSF1 repression (Knauf U et al. 1996; Hietakangas V et al. 2003; Batista-Nascimento L et al. 2011)
Analysis and update of the human solute carrier (SLC) gene superfamily
Cytosolic glutathione reductase catalyzes the reaction of glutathione (oxidized) and NADPH + H+ to form two molecules of glutathione (reduced) and NADP+ (Scott et al. 1963, Loos et al. 1976). Deficiency of glutathione reductase can cause hemolytic anemia.
First-in-man clinical trial of the oral pan-AKT inhibitor MK-2206 in patients with advanced solid tumors
GPX2 (located in the gastrointestinal tract, also called GPX-GI), like glutathione peroxidase 1 (GPX1, ubiquitous), reduces hydrogen peroxide (H2O2) with glutathione to yield oxidized glutathione and water (Chu et al. 1998, Faucher et al. 2003).
Glutathione peroxidase 3 (GPX3) in plasma reduces hydrogen peroxide (H2O2) with glutathione to yield oxidized glutathione and water (Maddipati and Marnett 1987, Takahashi et al. 1987, Chung et al. 2009, Ottaviano et al. 2009). Glutathione is synthesized in the liver and exported into the plasma.
Superoxide can reduce cytochrome c in the intermembrane space (Wegerich et al. 2013, and inferred from other mammals in Butler et al. 1975, Koppenol et al. 1976, Butler et al. 1982). Superoxide has been shown in rat and mouse mitochondria to be released into the intermembrane space by the complex III of the respiratory chain (Han et al. 2001, Muller et al. 2004).
Peroxiredoxin 1 (PRDX1), PRDX2, and PRDX5 in the cytosol reduce hydrogen peroxide (H2O2) with thioredoxin yielding oxidized thioredoxin and water (Yamashita et al. 1999, Lee et al. 2007, Nagy et al. 2011).
Peroxiredoxin 5 (PRDX5) very efficiently reduces peroxynitrite using thioredoxin to yield nitrite (NO2-), water, and oxidized thioredoxin (Dubuisson et al. 2004). The N-terminal cysteine (Cys 47) of PRDX5 attacks the O-O peroxide bond of peroxynitrite.
Glutathione reductase (GSR) in the mitochondrial matrix regenerates reduced glutathione from oxidized glutathione and NADPH (Berkholz et al. 2008).
Glutathione peroxidase 1 (GPX1) located in the mitochondrial matrix uses glutathione to reduce hydrogen peroxide (H2O2) to yield oxidized glutathione and water (Legault et al. 2000, Li et al. 2000, Faucher et al. 2003). As inferred from rat mitochondria, GPX1 is the major determinant of steady-state hydrogen peroxide levels (Antunes et al. 2002).
Hydrogen peroxide is generated in the course of peroxisomal fatty acid oxidation and purine catabolism, and is rapidly converted to water and molecular oxygen by the enzyme catalase. This enzyme is widely distributed in the body, but is especially abundant in liver, kidney, and red blood cells.
As inferred from rat heart mitochondria, hydrogen peroxide is released from mitochondria at a rate that is dependent on the membrane potential. Knockdown of Aquaporin-8 (AQP8) in human cells indicates that hydrogen peroxide is able to transit through the water channel of AQP8 located in the inner mitochodrial membrane (Marchissio et al. 2012). The resulting level of cytosolic hydrogen peroxide is hypothesized to signal the state of the mitochondria to regulatory molecules in the cytosol and nucleus (reviewed in Antico Arciuch et al. 2012).
Cytosolic glutathione peroxidase (GPX1) tetramer catalyzes the reaction of reduced glutathione and hydrogen peroxide to form reduced glutathione and water (Chu et al. 1993).
As inferred from the cytosolic reaction and from the mouse mitochondrial reaction, Copper chaperone of superoxide dismutase (CCS) transfers a copper(I) atom to a SOD1 monomer that already contains a Zn atom. The reaction proceeds by a two step mechanism in which SOD1 first forms heterodimers with CCS. The amounts of CCS and SOD1 in the intermembrane space appear to be regulated by the concentration of oxygen. Mutations in SOD1 are responsible for familial amyotrophic lateral sclerosis (fALS) and cause unregulated localization and aggregation of SOD1 in the intermembrane space (reviewed in Kawamata and Manfredi 2010).
Deficiency of carbohydrate response element-binding protein (ChREBP) reduces lipogenesis as well as glycolysis
A portion of SOD1 is located in the mitochondrial intermembrane space (IMS) where it catalyzes the formation of oxygen (O2) and hydrogen peroxide (H2O2) from superoxide (O2.-) (He et al. 2011, Higgins et al. 2002, inferred from rat in Okado-Matsumoto and Fridovich 2001).
Mn superoxide dismutase (SOD2) is located in the mitochondrial matrix where it catalyzes the reaction of two molecules of superoxide (O2-.) to form one molecule of oxygen (O2) and one molecule of hydrogen peroxide (H2O2). Data from mouse liver indicate that respiratory complex I leaks superoxide into the matrix and respiratory complex III leaks superoxide into both the matrix and the intermembrane space (Muller et al. 2004). Because of its negative charge superoxide is unable to cross membranes, however hydrogen peroxide, a product of SOD2, is released from mitochondria to the cytosol in proportion to the proton potential (inferred from rat heart mitochondria in Boveris et al. 2006, Korshunov et al. 1997).
As inferred from the cytosolic reaction and from the mitochondrial reaction in mouse, Copper chaperone of superoxide dismutase (CCS) transfers a copper(I) atom to a SOD1 monomer that already contains a Zn atom. After initial heterodimerization between SOD1 and CCS, the copper atom is transferred, intramolecular cysteine disulfide bonds are formed in SOD1, and SOD1 dimerizes.
Cu-Zn superoxide dismutase (SOD1), originally known as erythrocuprein, catalyzes the reaction of two molecules of superoxide (O2.-) to yield one molecule of hydrogen peroxide (H2O2) and one molecule of oxygen (O2) (McCord and Fridovich 1969 assayed both bovine and human Cu-Zn superoxide dismutase, the human sample provided by Carrico and Deutsch). Diffusion of hydrogen peroxide, the product of SOD1, across the cytosol is limited (Mishina et al. 2011)
Infection by Mycobacterium tuberculosis (Mtb) is soon countered by the host's immune system, the organism is however almost never eradicated; ten per cent of infections will develop into "open tuberculosis", while the other ninety per cent become "latent", a state that can persist for decades until loss of immune control. A third of the world's population is estimated to harbour latent tuberculosis. Latent infection involves the bacterium being internalized by macrophages where it stops and counters the innate immune answer (Russell 2011, Russell et al. 2010). When a status-quo is reached, Mtb enters a non-replicating persistent state (Barry et al. 2009, Boshoff & Barry 2005).
Alveolar macrophages normally develop their phagosome along the endolysosomal pathway. However, after having internalized Mtb, this development is arrested at an early stage and only includes acidification, nitric oxide and superoxide production, as well as the use of a few other proteins that can be gained from other endosomes which still can interact with the phagosome (Flannagan et al. 2009).
Cellular senescence involves irreversible growth arrest accompanied by phenotypic changes such as enlarged morphology, reorganization of chromatin through formation of senescence-associated heterochromatic foci (SAHF), and changes in gene expression that result in secretion of a number of proteins that alter local tissue environment, known as senescence-associated secretory phenotype (SASP). Senescence is considered to be a cancer protective mechanism and is also involved in aging. Senescent cells accumulate in aged tissues (reviewed by Campisi 1997 and Lopez-Otin 2013), which may be due to an increased senescence rate and/or decrease in the rate of clearance of senescent cells. In a mouse model of accelerated aging, clearance of senescent cells delays the onset of age-related phenotypes (Baker et al. 2011). Cellular senescence can be triggered by the aberrant activation of oncogenes or loss-of-function of tumor suppressor genes, and this type of senescence is known as the oncogene-induced senescence, with RAS signaling-induced senescence being the best studied. Oxidative stress, which may or may not be caused by oncogenic RAS signaling, can also trigger senescence. Finally, the cellular senescence program can be initiated by DNA damage, which may be caused by reactive oxygen species (ROS) during oxidative stress, and by telomere shortening caused by replicative exhaustion which may be due to oncogenic signaling. The senescent phenotype was first reported by Hayflick and Moorhead in 1961, when they proposed replicative senescence as a mechanism responsible for the cessation of mitotic activity and morphological changes that occur in human somatic diploid cell strains as a consequence of serial passaging, preventing the continuous culture of untransformed cells-the Hayflick limit (Hayflick and Moorhead 1961). Senescent cells may remain viable for years, such as senescent melanocytes of moles and nevi, or they can be removed by phagocytic cells. The standard marker for immunohistochemical detection of senescent cells is senescence-associated beta-galactosidase (SA-beta-Gal), a lysosomal enzyme that is not required for senescence. For a recent review, please refer to Collado et al. 2007, Adams 2009, Kuilman et al. 2010. For a review of differential gene expression between senescent and immortalized cells, please refer to Fridman and Tainsky 2008.
Cells are subject to external molecular and physical stresses such as foreign molecules that perturb metabolic or signaling processes, and changes in temperature or pH. The ability of cells and tissues to modulate molecular processes in response to such external stresses is essential to the maintenance of tissue homeostasis (Kultz 2005).
The function of V-type proton pumping ATPases is basically the same as that of F-type ATPases, except that V-ATPases cannot synthesize ATP from the proton motive force, the reverse reaction of pumping. When pumping, ATP hydrolysis drives a 120 degree rotation of the rotor which leads to movement of three protons into the phagosome (Adachi et al. 2007).
Cytosolic iron-sulfur cluster assembly (yeast)
Iron-sulfur clusters containing 4 atoms of iron and 4 atoms of sulfur (4Fe-4S clusters) are assembled in the cytosol on a heterotetrameric scaffold composed of CFD1 and NBP35 subunits (reviewed in Lill et al. 2012, Rouault et al. 2012, Sharma et al. 2010, Lill and Muhlenhoff 2006). The sources of iron and sulfur are uncertain but the process requires a sulfur-containing compound exported from mitochondria via Atm1. Newly synthesized 4Fe-4S are transferred to apoproteins such as RAD3 and POL3 via the CIA targeting complex, composed of NAR1, CIA1, YHR122W (CIA2), and MMS19.
Natural resistance-associated macrophage proteins (NRAMPs) regulates macrophage activation for antimicrobial activity against intracellular pathogens. They do this by mediating metal ion transport across macrophage membranes and the subsequent use of these ions in the control of free radical formation. The human gene SLC11A1 encodes NRAMP1 (Kishi F, 2004; Kishi F and Nobumoto M, 1995) which can utilize the protonmotive force to mediate divalent iron (Fe2+), zinc (Zn2+) and manganese (Mn2+) influx to or efflux from phagosomes.
YWHAE (14-3-3epsilon) was found to bind directly to HSF1 and that binding required serine phosphorylation at Ser303 and Ser307 and, moreover, the strongest binding was detected when both residues were phosphorylated.
The ability of HSF1 to respond to cellular stresses is under negative regulation by chaperones, modulation of nucleocytoplasmic shuttling, post-translational modifications and transition from monomeric to trimeric state.
In response to exposure to elevated temperature and certain other proteotoxic stimuli (e.g., hypoxia, free radicals) cells activate a number of cytoprotective mechanisms known collectively as "heat shock response". Major aspects of the heat shock response (HSR) are evolutionarily conserved events that allow cells to recover from protein damage induced by stress (Liu XD et al. 1997; Voellmy R & Boellmann F 2007; Shamovsky I & Nudler E 2008; Anckar J & Sistonen L 2011). The main hallmark of HSR is the dramatic alteration of the gene expression pattern. A diverse group of protein genes is induced by the exposure to temperatures 3-5 degrees higher than physiological. Functionally, most of these genes are molecular chaperones that ensure proper protein folding and quality control to maintain cell proteostasis. At the same time, heat shock-induced phosphorylation of translation initiation factor eIF2alpha leads to the shutdown of the nascent polypeptide synthesis reducing the burden on the chaperone system that has to deal with the increased amount of misfolded and thermally denatured proteins (Duncan RF & Hershey JWB 1989; Sarkar A et al. 2002; Spriggs KA et al. 2010). The induction of HS gene expression primarily occurs at the level of transcription and is mediated by heat shock transcription factor HSF1(Sarge KD et al. 1993; Baler R et al. 1993). Human cells express five members of HSF protein family: HSF1, HSF2, HSF4, HSFX and HSFY. HSF1 is the master regulator of the heat inducible gene expression (Zuo J et al. 1995; Akerfelt M et al. 2010). HSF2 is activated in response to certain developmental stimuli in addition to being co-activated with HSF1 to provide promoter-specific fine-tuning of the HS response by forming heterotrimers with HSF1 (Ostling P et al. 2007; Sandqvist A et al. 2009). HSF4 lacks the transcription activation domain and acts as a repressor of certain genes during HS (Nakai A et al. 1997; Tanabe M et al. 1999; Kim SA et al. 2012). Two additional family members HSFX and HSFY, which are located on the X and Y chromosomes respectively, remain to be characterized (Bhowmick BK et al. 2006; Shinka T et al. 2004; Kichine E et al. 2012). Under normal conditions HSF1 is present in both cytoplasm and nucleus in the form of an inactive monomer. The monomeric state of HSF1 is maintained by an intricate network of protein-protein interactions that include the association with HSP90 multichaperone complex, HSP70/HSP40 chaperone machinery, as well as intramolecular interaction of two conserved hydrophobic repeat regions. Monomeric HSF1 is constitutively phosphorylated on Ser303 and Ser 307 by (Zou J et al. 1998; Knauf U et al. 1996; Kline MP & Moromoto RI 1997; Guettouche T et al. 2005). This phosphorylation plays an essential role in ensuring cytoplasmic localization of at least a subpopulation of HSF1 molecules under normal conditions (Wang X et al. 2004). Exposure to heat and other proteotoxic stimuli results in the release of HSF1 from the inhibitory complex with chaperones and its subsequent trimerization, which is promoted by its interaction with translation elongation factor eEF1A1 (Baler R et al. 1993; Shamovsky I et al. 2006; Herbomel G et al 2013). The trimerization is believed to involve intermolecular interaction between hydrophobic repeats 1-3 leading to the formation of a triple coil structure. Additional stabilization of the HSF1 trimer is provided by the formation of intermolecular S-S bonds between Cys residues in the DNA binding domain (Lu M et al.2008). Trimeric HSF1 is predominantly localized in the nucleus where it binds the specific sequence in the promoter of hsp genes (Sarge KD et al. 1993; Wang Y and Morgan WD 1994). The binding sequence for HSF1 (HSE, heat shock element) contains series of inverted repeats nGAAn in head-to-tail orientation, with at least three elements being required for the high affinity binding. Binding of the HSF1 trimer to the promoter is not sufficient to induce transcription of the gene (Cotto J et al. 1996). In order to do so, HSF1 needs to undergo inducible phosphorylation on specific Ser residues such as Ser230, Ser326. This phosphorylated form of HSF1 trimer is capable of increasing the promoter initiation rate. HSF1 bound to DNA promotes recruiting components of the transcription mediator complex and relieving promoter-proximal pause of RNA polymerase II through its interaction with TFIIH transcription factor (Yuan CX & Gurley WB 2000). HSF1 activation is regulated in a precise and tight manner at multiple levels (Zuo J et al. 1995; Cotto J et al. 1996). This allows fast and robust activation of HS response to minimize proteotoxic effects of the stress. The exact set of HSF1 inducible genes is probably cell type specific. Moreover, cells in different pathophysiological states will display different but overlapping profile of HS inducible genes.
Oxidative stress, caused by increased concentration of reactive oxygen species (ROS) in the cell, can happen as a consequence of mitochondrial dysfunction induced by the oncogenic RAS (Moiseeva et al. 2009) or independent of oncogenic signaling. Prolonged exposure to interferon-beta (IFNB, IFN-beta) also results in ROS increase (Moiseeva et al. 2006). ROS oxidize thioredoxin (TXN), which causes TXN to dissociate from the N-terminus of MAP3K5 (ASK1), enabling MAP3K5 to become catalytically active (Saitoh et al. 1998). ROS also stimulate expression of Ste20 family kinases MINK1 (MINK) and TNIK through an unknown mechanism, and MINK1 and TNIK positively regulate MAP3K5 activation (Nicke et al. 2005). MAP3K5 phosphorylates and activates MAP2K3 (MKK3) and MAP2K6 (MKK6) (Ichijo et al. 1997, Takekawa et al. 2005), which act as p38 MAPK kinases, as well as MAP2K4 (SEK1) (Ichijo et al. 1997, Matsuura et al. 2002), which, together with MAP2K7 (MKK7), acts as a JNK kinase. MKK3 and MKK6 phosphorylate and activate p38 MAPK alpha (MAPK14) and beta (MAPK11) (Raingeaud et al. 1996), enabling p38 MAPKs to phosphorylate and activate MAPKAPK2 (MK2) and MAPKAPK3 (MK3) (Ben-Levy et al. 1995, Clifton et al. 1996, McLaughlin et al. 1996, Sithanandam et al. 1996, Meng et al. 2002, Lukas et al. 2004, White et al. 2007), as well as MAPKAPK5 (PRAK) (New et al. 1998 and 2003, Sun et al. 2007). Phosphorylation of JNKs (MAPK8, MAPK9 and MAPK10) by MAP3K5-activated MAP2K4 (Deacon and Blank 1997, Fleming et al. 2000) allows JNKs to migrate to the nucleus (Mizukami et al. 1997) where they phosphorylate JUN. Phosphorylated JUN binds FOS phosphorylated by ERK1 or ERK2, downstream of activated RAS (Okazaki and Sagata 1995, Murphy et al. 2002), forming the activated protein 1 (AP-1) complex (FOS:JUN heterodimer) (Glover and Harrison 1995, Ainbinder et al. 1997). Activation of p38 MAPKs and JNKs downstream of MAP3K5 (ASK1) ultimately converges on transcriptional regulation of CDKN2A locus. In dividing cells, nucleosomes bound to the CDKN2A locus are trimethylated on lysine residue 28 of histone H3 (HIST1H3A) by the Polycomb repressor complex 2 (PRC2), creating the H3K27Me3 (Me3K-28-HIST1H3A) mark (Bracken et al. 2007, Kotake et al. 2007). The expression of Polycomb constituents of PRC2 (Kuzmichev et al. 2002) - EZH2, EED and SUZ12 - and thereby formation of the PRC2, is positively regulated in growing cells by E2F1, E2F2 and E2F3 (Weinmann et al. 2001, Bracken et al. 2003). H3K27Me3 mark serves as a docking site for the Polycomb repressor complex 1 (PRC1) that contains BMI1 (PCGF4) and is therefore named PRC1.4, leading to the repression of transcription of p16-INK4A and p14-ARF from the CDKN2A locus, where PCR1.4 mediated repression of p14-ARF transcription in humans may be context dependent (Voncken et al. 2005, Dietrich et al. 2007, Agherbi et al. 2009, Gao et al. 2012). MAPKAPK2 and MAPKAPK3, activated downstream of the MAP3K5-p38 MAPK cascade, phosphorylate BMI1 of the PRC1.4 complex, leading to dissociation of PRC1.4 complex from the CDKN2A locus and upregulation of p14-ARF transcription (Voncken et al. 2005). AP-1 transcription factor, formed as a result of MAP3K5-JNK signaling, as well as RAS signaling, binds the promoter of KDM6B (JMJD3) gene and stimulates KDM6B expression. KDM6B is a histone demethylase that removes H3K27Me3 mark i.e. demethylates lysine K28 of HIST1H3A, thereby preventing PRC1.4 binding to the CDKN2A locus and allowing transcription of p16-INK4A (Agger et al. 2009, Barradas et al. 2009, Lin et al. 2012). p16-INK4A inhibits phosphorylation-mediated inactivation of RB family members by CDK4 and CDK6, leading to cell cycle arrest (Serrano et al. 1993). p14-ARF inhibits MDM2-mediated degradation of TP53 (p53) (Zhang et al. 1998), which also contributes to cell cycle arrest in cells undergoing oxidative stress. In addition, phosphorylation of TP53 by MAPKAPK5 (PRAK) activated downstream of MAP3K5-p38 MAPK signaling, activates TP53 and contributes to cellular senescence (Sun et al. 2007).
Constitutive phosphorylation at Ser303 within the regulatory domain of HSF1 was shown to inhibit its transcriptional activity under normal temperatures. Substitution of Ser303 with alanine derepresses the transactivation domain such that the S303A mutant showed increased transcriptional activity in human and mouse cells (Knauf U et al. 1996; Kline MP & Morimoto RI 1997). Phosphorylation of HSF1 at Ser303 was mediated by glycogen synthase kinase 3 (GSK3) activity in human acute monocytic leukemia THP1 cells and mouse embryonic fibroblast NIH 3T3 cells (Chu B et al. 1996, 1998). However, the other group showed that GSK3 inhibits HSF1 activity in HeLa cells through a mechanism that is independent of Ser303 phosphorylation, thus suggesting that Ser303 may be phosphorylated by multiple MAPKs (Batista?Nascimento L et al. 2011). The phosphorylation at Ser303 in turn promoted HSF1 association with YWHAE (14-3-3 epsilon), which may be involved in the attenuation of HSF1 activity during recovery leading to accelerated cytoplasmic localization of HSF1 (Wang X et al. 2003, 2004).In addition, stress stimulated human K562 erythroleukemia cells showed enhanced level of sumoylation in the HSF1 regulatory domain at Lys298, which was positively regulated by Ser303 phosphorylation (Hietakangas V et al. 2003).
Constitutive phosphorylation at Ser307 was shown to inhibit HSF1 transcriptional activity under normal temperatures. Substitution of Ser307 with alanine derepresses the transactivation domain such that the S307A mutant showed increased transcriptional activity in human and mouse cells (Knauf U et al. 1996; Kline MP & Morimoto RI 1997). HSF1-ERK association was shown to promote ERK activity in human HeLa, acute monocytic leukemia THP1 and metastatic cutaneous SCC7 cells resulting in phosphorylation of HSF1 on Ser307 (Chu B et al. 1996; Wang X et al. 2004). This phosphorylation in turn promoted HSF1 association with YWHAE (14-3-3 epsilon), which may be involved in the attenuation of HSF1 activity during recovery and leads to accelerated cytoplasmic localization of HSF1 (Wang X et al. 2003, 2004).
Acquisition of DNA binding activity by HSF1 is necessary but insufficient for transcriptional activation (Cotto JJ et al. 1996; Trinklein ND et al. 2004). In addition to having a sequence-specific DNA binding domain, HSF1 contains a C-terminal region which is involved in activating the transcription of the target genes (Green M et al. 1995). However, the transactivating ability of the transactivation domain itself is not stress sensitive. Rather, it's controled by a regulatory domain of HSF1 (amino acids 221-310), which represses the transactivating ability under normal physiological conditions (Green M et al. 1995; Zuo J et al. 1995; Newton EM et al. 1996). The HSF1 transactivation domain can be divided into two distinct regions, activation domain 1 (AD1) and activation domain 2 (AD2) (Brown SA et al. 1998). AD1 and AD2 each contain residues that are important for both transcriptional initiation and elongation. Mutations in acidic residues in both AD1 and AD2 preferentially affect the ability of HSF1 to stimulate transcriptional initiation, while mutations in phenylalanine residues preferentially affect stimulation of elongation (Brown SA et al. 1998). Activation of the DNA-bound but transcriptionally incompetent HSF1 is thought to occur upon stress induced HSF1 phosphorylation at several serine residues (Ding XZ et al. 1997; Holmberg CI et al. 2001; Guettouche T et al. 2005). In cells exposed to heat, acquisition of HSE DNA-binding activity was observed to precede phosphorylation of HSF1 (Cotto JJ et al. 1996; Kline MP & Morimoto RI 1997). While there is a sufficient evidence to suggest that phosphorylation of HSF1 is essential to modulate HSF1 transactiviting capacity, mechanisms behind stress stimuli and kinases/phosphatases involved have not been clearly established.
The RNA cleavage activity of RNA polymerase III is mediated by an essential TFIIS-like subunit and is important for transcription termination.
Different functional domains of GLUT2 glucose transporter are required for glucose affinity and substrate specificity
The transcriptional activity of HSF1 has been shown to be controlled by the regulatory domain composed of amino acids 221-310 (Green M et al. 1995; Zuo J et al. 1995; Newton EM et al., 1996). Ser230 is located in this regulatory domain of HSF1 and is constitutively and stress-inducibly phosphorylated (Holmberg CI et al. 2001). Analyses with phosphopeptide-specific antibody and site-directed mutagenesis revealed that phosphorylation at Ser230 enhanced the inducible HSF1 transcriptional activity in heat-shocked human K562 erythroleukemia and HeLa cells (Holmberg CI et al 2001). Active calcium/calmodulin-dependent protein kinase II (CaMKII) was shown to phosphorylate HSF1 at Ser230 in vitro. Moreover, CaMKII enhanced heat-induced tranactivating capacity of HSF1 and the level of endogenous Ser230 phosphorylation in K562 cells transfected with active CaMKII together with a CAT reporter plasmid containing the proximal HSE of human hsp70 promoter. Thus, CaMKII signaling may be involved in the positive regulation of HSF1-mediated transactivation. However, the possibility that other protein kinases might also phosphorylate Ser230 in vivo should not be excluded (Holmberg CI et al 2001).
Combination of chromatin immunoprecipitation (ChIP) microarray analysis and time course gene expression microarray analysis with and without siRNA-mediated inhibition of HSF1 showed that human HSF1 can induce the expression of different sets of target genes to maintain a wide range of biological processes (e.g., anti-apoptosis, RNA splicing, ubiquitination)(Page TG et al. 2006; Vihervaara A. et al. 2013). However, HSF1 is best known for rapid stress-induced upregulation of certain genes related to protein folding, such as HSPA1A/HSP70, HSPC/HSP90, HSPB1/HSP27, and DNAJB1/HSP40 (Mosser DD et al. 1988; Trinklein ND et al. 2004a,b; Page TG et al. 2006; Vihervaara A. et al. 2013).
Heat shock factor 1 (HSF1) is a transcription factor that activates gene expression in response to a variety of stresses, including heat shock, oxidative stress, as well as inflammation and infection (Shamovsky I and Nudler E 2008; Akerfelt et al. 2010; Bjork and Sistonen 2010; Anckar and Sistonen 2011). HSF1 is constitutively present in the cell. In the absence of stress HSF1 is found in both the cytoplasm and the nucleus as an inactive monomer (Sarge KD et al. 1993; Mercier PA et al. 1999; Vujanac M et al. 2005). A physical or chemical proteotoxic stress rapidly induces HSF1 activation, which occurs through a multi?step process, involving HSF1 monomer-to-homotrimer transition, nuclear accumulation, and binding to a promoter element, called the heat shock element (HSE), which leads to the increase in the stress-inducible gene expression (Sarge KD et al. 1993; Baler R et al. 1998; Sonna LA et al. 2002; Shamovsky I and Nudler E 2008; Sakurai H and Enoki Y 2010; Herbomel G et al. 2013). Depending on the type of stress stimulus, the multiple events associated with HSF1 activation might be affected differently (Holmberg CI et al 2000; Bjork and Sistonen 2010).
Mutagenesis experiments and functional studies suggest that phosphorylation of HSF1 residue Ser326 promotes induction of the HSF1 transcriptional competence in response to heat and other cell stressors including proteasome inhibitors and sodium arsenite (Guettouche T et al. 2005; Chou SD et al. 2012). The mammalian target of rapamycin complex 1 (mTORC1) has been implicated in sensing intracellular protein misfolding (Qian SB et al. 2010; Chou SD et al. 2012). RNA interference?mediated repression of mTOR kinase activity in human HeLa cells was found to increase sensitivity to heat shock. Moreover, inhibition of HSF1 phosphorylation on Ser326 by rapamycin suggests that this site in HSF1 is a target for the mTORC1complex (Chou SD et al. 2012).
The inactive HSF1 was reported to constitutively shuttle between the nucleus and the cytoplasm in mammalian cells (Vujanac M et al. 2005). There is no consensus on whether inactive HSF1 monomers localize in the nucleus or in the cytosol (Sarge KD et al. 1993; Zuo J et al. 1995; Mercier PA et al. 1999; Vujanac M et al. 2005). This event shows stress-induced activation of HSF1 in the nucleus. In the absence of stress HSF1 is predominantly monomeric and is thought to be repressed in its inactive monomeric state by the following mechanisms: interaction with chaperone proteins such as HSP90 (Zou J et al.1998; Guo Y et al. 2001) intramolecular coiled-coil interactions between a hydrophobic leucine zipper domain in the carboxyl-terminus of the protein and three amino-terminal leucine zippers, which are required for homotrimerization and transcriptional activation (Rabindran SK et al. 1993; Zuo J et al. 1995) post-translation modifications that include protein acetylation, sumoylation and phosphorylation may also contribute to HSF1 repression (Knauf U et al. 1996; Hietakangas V et al. 2003; Batista-Nascimento L et al. 2011) The accumulation of misfolded proteins upon proteotoxic stresses leads to the release of HSF1 from the HSP90-containing multichaperone complex and results in HSF1 self-association to form homotrimers (Baler R et al. 1993).
There is no consensus on whether inactive HSF1 monomers localize in the nucleus or in the cytosol (Sarge KD et al. 1993; Zuo J et al. 1995; Mercier PA et al. 1999; Vujanac M et al. 2005). Moreover, inactive HSF1 was reported to constitutively shuttle between the nucleus and the cytoplasm in mammalian cells (Vujanac M et al. 2005). However, active HSF1 trimers were shown to rapidly accumulate in the nucleus where they bind to heat shock elements (HSE) present within promoters of hsp genes (Wang Y and Morgan WD 1994; Herbomel G et al. 2013). Heat shock response in human and monkey cells (but not rodent cells) is also associated with the stress-induced relocalization of HSF1 within the nucleus not only on hsp gene promoters but also into specific subnuclear organelles termed nuclear stress bodies (nSBs, also known as HSF1 granules) (Sarge KD et a. 1993; Cotto JJ et al. 1997; Jolly C et al. 1999). nSBs are rarely detectable in unstressed cells but their number drastically increases after heat shock. Formation of nSBs is initiated by the interaction between HSF1 and pericentric tandem repeats of satellite III sequences on chromosome 9, where sat III repeats are transcribed by RNA polymerase II in an HSF1-dependent manner. (Jolly C et al. 2002, 2004). HSF1 can also bind to DNA regions enriched in sat II and sat III repeated sequences detected on other human chromosomes (Eymery A et al. 2010). The functional relevance of HSF1 granules and their transcripts remains an open question.
Cloning and characterization of the major insulin-responsive glucose transporter expressed in human skeletal muscle and other insulin-responsive tissues.
Substrate specificity of MATE1 and MATE2-K, human multidrug and toxin extrusions/H(+)-organic cation antiporters
Proteomic analysis of proteins associated with lipid droplets of basal and lipolytically stimulated 3T3-L1 adipocytes
Copper chaperone of superoxide dismutase (CCS) transfers a copper(I) atom to a SOD1 monomer that already contains a Zn atom (Culotta et al. 1997, Casareno et al. 1998, Rae et al. 2001, Brown et al. 2004, Banci et al. 2012). The reaction proceeds by a two step mechanism in which SOD1 first forms heterodimers with CCS (Rae et al. 2001, Banci et al. 2012).
Copper chaperone of superoxide dismutase (CCS) transfers a copper(I) atom to a SOD1 monomer that already contains a Zn atom. After initial heterodimerization between SOD1 and CCS, the copper atom is transferred, intramolecular cysteine disulfide bonds are formed in SOD1, and SOD1 dimerizes (Banci et al. 2012, Casareno et al. 1998, Culotta et al. 1997, Rae et al. 2001, Brown et al. 2004, Carroll et al. 2006, Kawamata and Manfredi 2008). The transfer of copper to SOD1 requires oxygen but it is unknown at which step the oxygen acts (Brown et al. 2004). There is also a CCS-independent, oxygen-independent pathway of maturation of SOD1 (Leitch et al. 2009) whose molecular details and physiological role are not well characterized.
The glutamate/GABA-glutamine cycle: aspects of transport, neurotransmitter homeostasis and ammonia transfer
NMDA receptors are a subtype of ionotropic glutamate receptors that are specifically activated by a glutamate agonist N-methyl-D-aspartate (NMDA). Activation of NMDA receptor involves opening of the ion channel that allows the influx of Ca2+. NMDA receptors are central to activity dependent changes in synaptic strength and are predominantly involved in the synaptic plasticity that pertain to learning and memory. A unique feature of NMDA receptor unlike other glutamate receptors is the requirement of dual activation of the NMDA receptor, which require both voltage dependent and ligand dependent activation. At resting membrane potential the NMDA receptors are blocked by Mg2+. The voltage dependent Mg2+ block is relieved upon depolarization of the post-synpatic membrane . The ligand dependent activation of the NMDA receptor requires co-activation by two ligands, namely glutamate and glycine. NMDA receptors are coincidence detector, and are activated only if there is simultaneous activation of both pre and post-synaptic cell. Upon activation NMDA receptors allow the influx of Ca2+ that initiates various molecular signaling cascades that are involved in the process of learning and memory.
The neurotransmitter in the synaptic cleft released by the pre-synaptic neuron binds specific receptors located on the post-synaptic terminal. These receptors are either ion channels or G protein coupled receptors that function to transmit the signals from the post-synaptic membrane to the cell body.
Molecular identity and cellular distribution of advanced glycation endproduct receptors: relationship of p60 to OST-48 and p90 to 80K-H membrane proteins
Chemical synapses are specialized junctions that are used for communication between neurons, neurons and muscle or gland cells. The synapse involves a pre-synaptic neuron and a post-synaptic neuron, muscle cell or glad cell. The pre and the post-synaptic cell are separated by a gap of 20nm called the synaptic cleft. The signals pass in a unidirection from pre-synaptic to post-synaptic. The pre-synaptic neuron communicates via the release of neurotransmitter which bind the receptors on the post-synaptic cell.
The human brain contains at least 100 billion neurons, each with the ability to influence many other cells. Clearly, highly sophisticated and efficient mechanisms are needed to enable communication among this astronomical number of elements. This communication occurs across synapses, the functional connection between neurons. Synapses can be divided into two general classes: electrical synapses and chemical synapses. Electrical synapses permit direct, passive flow of electrical current from one neuron to another. The current flows through gap junctions, specialized membrane channels that connect the two cells. Chemical synapses enable cell-to-cell communication using neurotransmitter release. Neurotransmitters are chemical agents released by presynaptic neurons that trigger a secondary current flow in postsynaptic neurons by activating specific receptor molecules. Neurotransmitter secretion is triggered by the influx of Ca2+ through voltage-gated channels, which gives rise to a transient increase in Ca2+ concentration within the presynaptic terminal. The rise in Ca2+ concentration causes synaptic vesicles (the presynaptic organelles that store neurotransmitters) to fuse with the presynaptic plasma membrane and release their contents into the space between the pre- and postsynaptic cells.
CaMKK is fully activated upon binding Ca2+/Calmodulin after intracellular Ca2+ levels increase. Once CaMKK binds Ca2+/Calmodulin it autophosphorylates, resulting in activation. CaMKK is negatively regulated by phosphorylation of S74 and T108 by PKA. Once activated CaMKK phosphorylates CaMKIV in a Ca2+/Calmodulin dependent manner.
Ca2+ signal generated through NMDA receptor in the post-synaptic neuron activates adenylate cyclase signal transduction, leading to the activation of PKA and phosphorylation and activation of CREB-induced transcription. The isoforms of adenylate cyclase that are activated by Ca2+ in the brain are I, III and IX.
Ca2+ influx through the NMDA receptor initiates subsequent molecular pathways that have a defined role in establishing long-lasting synaptic changes. The molecular signaling initiated by a rise in Ca2+ within the spine leads to phosphorylation of Cyclic AMP Response Element binding protein (CREB) at serine 133 which is involved in the transcription of genes that results in long lasting changes in the synapse. The phosphorylation of CREB by increased Ca2+ can be brought about by distinct molecular pathways that may involve MAP kinase, activation of adenylate cyclase, activation of CaMKII and/or the activation of CaMKIV.
Transient increase in intracellular Ca2+ concentration after NMDA receptor activation leads to the activation of the CaMKIV via the activation of CaM-kinase kinase. CaM-kinase kinase and CaMKIV are both activated upon binding Ca2+/Calmodulin after Ca2+ influx through activated NMDA receptor.
Nuclear targeting of CaMKII depends on several factors including the phosphorylation in the regulatory domain of CaMKII and induction of other signal transduction pathways.
In astrocytic glutamate-glutamine cycle, the excess glutamate released by the pre-synaptic neuron in the synaptic cleft is transported into the astrocyte by a family glutamate transporters called the excitatory amino acid transporters 1 and 2, EAAT1 and EAAT2. Astrocytes carrying these transporters exist in close apposition to the synapse to clear excess glutamate to prevent excessive activation of neurons and hence neuronal death. Glutamate in astrocytes is converted to glutamine by glutamine synthetase. Glutamine is then transported into the extracellular space by system N transporters. The glutamate in the extracellular space is available for neuronal uptake.
Neuotransmitter uptake by astrocytes is mediated by specific transporter located on the astrocytic membrane. The imported neurotransmitter in the astrocytes is metabolized and transported back to the neuron via specialized transporters.
Neurotransmitter released in the synaptic cleft binds to specific receptors on the post-synaptic cell and the excess of the neurotransmitter is cleared to prevent over activation of the post-synaptic cell. The neurotransmitter is cleared by either re-uptake by the pre-synaptic neuron, diffusion in the perisynaptic area, uptake by astrocytes surrounding the synaptic cleft or enzymatic degradation of the neurotransmitter. This topic will be annotated in a future release.
Cytosolic glutamine synthetase (glutamate-ammonia ligase - GLUL) catalyzes the reaction of glutamate, ammonia, and ATP to form glutamine, ADP, and orthophosphate. The enzyme is a decamer (Krajewski et al. 2008). Mutations in the gene encoding GLUL cause glutamine deficiency in vivo (Haberle et al. 2005).
Serotonin is first metabolized to 5-hydroxyindole acetaldehyde by monoamine oxidase. 5-hydroxyindole acetaldehyde is then catalyzed by aldehyde dehydrogenase to form 5-hydroxyindole acetic acid.
Serotonergic neurotransmission affects a wide range of behaviors, from food intake and reproductive activity, to sensory processing and motor activity, to cognition and emotion. One such key regulator is the serotonin transporter (5-HTT), which is observed to remove serotonin released into the synaptic cleft.
5-hydroxyindole acetaldehyde is then catalyzed by aldehyde dehydrogenase to form 5-hydroxyindole acetic acid
Neurotransmitter is stored in the synaptic vesicle in the pre-synaptic terminal prior to its release in the synaptic cleft upon depolarization of the pre-synaptic membrane. The release of the neurotransmitter is a multi-step process that is controlled by electrical signals passing through the axons in form of action potential. Neurotransmitters include glutamate, acetylcholine, nor-epinephrine, dopamine and seratonin. Each of the neurotransmitter cycle is independently described.
GABA is a major inhibitory neurotransmitter in the mammalian central nervous system. GABA modulates neuronal excitability throughout the nervous system. Disruption of GABA neurotransmission leads to many neurological diseases including epilepsy and a general anxiety disorder. GABA is synthesized by two distinct enzymes GAD67 and GAD65 that differ in their cellular localization, functional properties and co-factor requirements. GABA synthesized by GAD65 is used for neurotransmission whereas GABA synthesized by GAD67 is used for processes other than neurotransmission such as synaptogenesis and protection against neuronal injury. GABA is loaded into synaptic vesicle with the help of vesicular inhibitory amino acid transporter or VGAT. GAD65 and VGAT are functionally linked at the synaptic vesicle membrane and GABA synthesized by GAD65 is preferentially loaded into the synaptic vesicle over GABA synthesized in cytoplasm by GAD67.The GABA loaded synaptic vesicles are docked at the plasma membrane with the help of the SNARE complexes and primed by interplay between various proteins including Munc18, complexin etc. Release of GABA loaded synaptic vesicle is initiated by the arrival of action potential at the presynaptic bouton and opening of N or P/Q voltage gated Ca2+ channels. Ca2+ influx results in Ca2+ binding by synaptobrevin, which is a part of the SNARE complex that also includes SNAP25 and syntaxin, leading to synaptic vesicle fusion. Release of GABA in the synaptic cleft leads to binding of GABA by the GABA receptors and post ligand binding events.
A cytoplasmic chaperonin that catalyzes beta-actin folding
2xPDXK:2xZn2+ (name copied from entity in Homo sapiens)
3xPPCDC:3xFMN (name copied from entity in Homo sapiens)
CYB5R3:FAD (name copied from entity in Homo sapiens)
CYB5A:ferriheme (name copied from entity in Homo sapiens)
CYB5A:heme (name copied from entity in Homo sapiens)
phosphoribosyl pyrophosphate synthetase holoenzyme
Update on interconversions of vitamin B-6 with its coenzyme
2xPPCS (name copied from entity in Homo sapiens)
2xENPP1 (name copied from entity in Homo sapiens)
RFK:Mg2+ (name copied from entity in Homo sapiens)
2xTPK1:Mg2+ (name copied from entity in Homo sapiens)
Inhibition of replication initiation of damaged DNA by RB1/E2F1
Processing of Capped Intronless Pre-mRNA
Hyaluronan (hyaluronic acid, hyaluronate or HA) is an anionic glycosaminoglycan (GAG) distributed widely throughout connective, epithelial, and neural tissues and most abundant in the extracellular matrix and skin. HA is unique among the GAGs in that it is not sulfated and is not found covalently attached to proteins as a proteoglycan. HA polymers are very large (they can reach molecular weights of 10 million Da) and can displace a large volume of water making them excellent lubricators and shock absorbers. Another unique feature of HA is that it is synthesized at the plasma membrane unlike other GAGs which are formed in the Golgi. HA is a polymer of the disaccharide unit D-glucuronic acid and D-N-acetylglucosamine, linked via alternating beta-1,4 and beta-1,3 glycosidic bonds (Toole 2000, 2004, Volpi et al. 2009).
Hyaluronan (hyaluronic acid, HA) is composed of repeating disaccharide units of glucuronic acid and N-acetylglucosamine [-4GlcAb1-3GlcNAcb1-]. It is synthesized in the cell membrane by adding monosaccharides to the reducing end of the chain using the precursors UDP-glucuronic acid and UDP-N-acetylglucosamine in the presence of Mg2+. The integral membrane dual-action glycosyltransferase proteins hyaluronan synthases, of which vertebrates have three types (HAS1-3), catalyze these monosaccharide additions. Unlike other GAGs, HA is synthesized as a free glycan, not attached to a protein (Laurent 1987, Weigel & DeAngelis, 2007). As HA is synthesised it is extruded from the cell by an ABC-type transporter into the extracellular medium.
As hyaluronan (HA) is synthesised, it is continually extruded from the cell by the ABC transporter C5 (ABCC5), also called multidrug resistance-associated protein 5 (MRP5) (Schulz et al. 2007).
Phenylalanine hydroxylase (PAH) catalyzes the conversion of phenylalanine to tyrosine. In the absence of functional PAH, phenylalanine accumulates to high levels in the blood (Mitchell and Scriver 2010) and is converted to phenylpyruvate and phenyllactate (Clemens et al. 1990; Langenbeck et al. 1992). The extent of these conversions is modulated by genetic factors distinct from PAH, as siblings with the identical PAH defect can produce different amounts of them (Treacy et al. 1996). Both L-amino acid oxidase (Boulland et al. 2004) and Kynurenine--oxoglutarate transaminase 3 (Han et al. 2004) can catalyze the conversion of phenylalanine to phenylpyruvate and lactate dehydrogenase can catalyze the conversion of the latter molecule to phenyllactate (Meister 1951). Elevated levels of phenylalanine, phenylpyruvate, and phenyllactate are all thought to contribute to the symptoms of phenylketonuria. One possible target is the metabolism of kynurenine.
PAPS (3'-phosphoadenosine-5'-phosphosulfate), which functions as a sulfate donor in the cell, is synthesized from sulfate and two molecules of ATP in a two-step process (Robbins & Lipmann 1958) catalyzed in vertebrates by a bifunctional enzyme (Venkatachalam et al. 1998). PAPS synthesis takes place in the cytosol, and it is either consumed there in the sulfonation of a variety of hormones and xenobiotics, or it is transported to the Golgi apparatus and consumed in the synthesis of proteoglycans like chondroitin sulfate. Two isoforms of the human bifunctional enzyme are known, mutations in one of which are associated with defects in proteoglycan biosynthesis (Girard et al. 1998, ul Haque et al. 1998).
The human gene SLC35B2 encodes the adenosine 3'-phospho 5'-phosphosulfate transporter 1 (PAPST1) (Ozeran et al. 1996, Kamiyama et al. 2003). In human tissues, PAPST1 is highly expressed in the placenta and pancreas and present at lower levels in the colon and heart. The human gene SLC35B3 encodes a human PAPS transporter gene that is closely related to PAPST1. Called PAPST2, it is predominantly expressed in the colon (Kamiyama et al. 2006).
In the second step of PAPS biosynthesis, adenylyl sulfate (APS) is phosphorylated to 3'-phosphoadenylyl sulfate (PAPS), catalysed by the bifunctional enzymes PAPS synthases 1 and 2 (PAPSS1 and 2). PAPSS2 is essential for the sulfation of proteoglycans, a necessary post-translational modification. Defective PAPSS2 results in undersulfation of proteoglycans which causes spondyloepimetaphyseal dysplasia Pakistani type (SEMD-PA; MIM:612847), a bone disease characterized by epiphyseal dysplasia with mild metaphyseal abnormalities. Mutations resulting in SEMD-PA include S438*, T48R and R329* (Ahmad et al. 1998, ul Haque et al. 1998, Noordam et al. 2009).
In the first step of PAPS biosynthesis, ATP and sulfate react to form adenylyl sulfate (APS) and pyrophosphate (PPi), catalysed by the bifunctional enzymes PAPS synthases 1 and 2 (PAPSS1 and 2). PAPSS2 is essential for the sulfation of proteoglycans, a necessary post-translational modification. Defective PAPSS2 results in undersulfation of proteoglycans which causes spondyloepimetaphyseal dysplasia Pakistani type (SEMD-PA; MIM:612847), a bone disease characterized by epiphyseal dysplasia with mild metaphyseal abnormalities. Mutations resulting in SEMD-PA include S438*, T48R and R329* (Ahmad et al. 1998, ul Haque et al. 1998, Noordam et al. 2009).
Purification of superoxide dismutases from human placenta using immunoadsorbent columns
CCBL1 (KAT 1) catalyzes the reaction of kynurenine and pyruvate to form 4-(2-aminophenyl)-2,4-dioxobutanoate and alanine. The active form of CCBL1 is a homodimer with one molecule of pyridoxal phosphate bound to each monomer (Baran et al. 1994; Han et al. 2009; Rossi et al. 2004). The enzyme's cytosolic localization is inferred from that of recombinant protein overexpressed in transfected cells (Perry et al. 1995). The pH optimum observed for CCBL1 in vitro is 9.5 - 10.0, so its role in kynurenine metabolism in vivo is not clear (Baran et al. 1994). Biochemical studies of CCBL1 activity in vitro (e.g., Baren et al. 1994) invariably measure kynurenic acid as the reaction product, not 4-(2-aminophenyl)-2,4-dioxobutanoate, the product to be expected from transamination of kynurenine. The condensation of 4-(2-aminophenyl)-2,4-dioxobutanoate and elimination of a water molecule to form kynurenic acid has not been demonstrated directly. As noted by Miller et al. (1953), discussing their characterization of a bacterial form of the enzyme, "The keto acid assumed to be formed prior to ring closure in the conversion of kynurenine to kynurenic acid has not yet been detected. In principle, such detection should be possible, since it is sufficiently stable to have been synthesized. It also remains to be established whether ring closure is spontaneous, enzymatic, or both. The formation of kynurenic acid from L-kynurenine by the L-amino acid oxidase of Neurospora suggests, however, that ring closure can be spontaneous, unless the somewhat improbable assumption is made that Neurospora filtrate contained the ring-closing enzyme."
CCBL1 (KAT1) catalyzes the reaction of phenylalanine and oxaloacetate to form keto-phenylpyruvate and aspartate. The active form of CCBL1 is a homodimer with one molecule of pyridoxal phosphate bound to each monomer (Rossi et al. 2004). CCBL1 (KAT1) acts on phenylalanine and kynurenine with comparable efficiencies (Han et al. 2004), consistent with the idea that when phenylalanine levels are elevated CCBL1 (KAT1) activity could be a major source of phenylpyruvate. Oxaloacetate is one of several 2-oxoacids that function efficiently in CCBL1-mediated transamination (Han et al. 2004). Notably, neither tyrosine aminotransferase (Sivaraman and Kirsch 2006) nor glutamate-oxaloacetate aminotransferase (Cammarata and Cohen 1951) acts on phenylalanine.
Obesity, leptin, and Alzheimer's disease
Endoplasmic reticulum stress induction of insulin-like growth factor-binding protein-1 involves ATF4
The pathway "Signaling by EGFR in Cancer" shows "Signaling by constitutively active EGFR" in parallel with "Signaling by EGFR". This allows users to compare signaling by constitutively active EGFR cancer mutants with the wild-type EGFR protein. Red lines emphasize cancer related events and physical entities, while wild-type entities and events are shaded. Please refer to "Signaling by constitutively active EGFR" and "Signaling by EGFR" for detailed pathway summations.
Signaling by EGFR is frequently activated in cancer through either genomic amplification of the EGFR locus, resulting in over-expression of the wild-type protein, or through activating mutations in the coding sequence of the EGFR gene, resulting in expression of a constitutively active mutant protein. Epidermal growth factor receptor kinase domain mutants are present in ~16% of non-small-cell lung cancers (NSCLCs), but are also found in other cancer types, such as breast cancer, colorectal cancer, ovarian cancer and thyroid cancer. EGFR kinase domain mutants harbor activating mutations in exons 18-21 which code for the kinase domain (amino acids 712-979) . Small deletions, insertions or substitutions of amino acids within the kinase domain lock EGFR in its active conformation in which the enzyme can dimerize and undergo autophosphorylation spontaneously, without ligand binding (although ligand binding ability is preserved), and activate downstream signaling pathways that promote cell survival (Greulich et al. 2005, Zhang et al. 2006, Yun et al. 2007, Red Brewer et al. 2009). In glioblastoma, the most prevalent EGFR mutation, present in ~25% of tumors, is the deletion of the ligand binding domain of EGFR, accompanied with amplification of the mutated allele, which results in over-expression of the mutant protein known as EGFRvIII. EGFRvIII mutant is not able to bind a ligand, but dimerizes and autophosphorylates spontaneously and is therefore constitutively active (Fernandes et al. 2001). Point mutations in the extracellular domain of EGFR are also frequently found in glioblastoma. Similar to kinase domain mutations, point mutations in the extracellular domain result in constitutively active EGFR proteins that signal in the absence of ligands, but ligand binding ability and responsiveness are preserved (Lee et al. 2006). Both EGFR kinase domain mutants and EGFRvIII mutant need to maintain association with the chaperone heat shock protein 90 (HSP90) for proper functioning (Shimamura et al. 2005, Lavictoire et al. 2003). CDC37 is a co-chaperone of HSP90 that acts as a scaffold and regulator of interaction between HSP90 and its protein kinase clients. CDC37 is frequently over-expressed in cancers involving mutant kinases and acts as an oncogene (Roe et al. 2004, reviewed by Gray Jr. et al. 2008). Over-expression of the wild-type EGFR or EGFR cancer mutants results in aberrant activation of downstream signaling cascades, namely RAS/RAF/MAP kinase signaling and PI3K/AKT signaling, and possibly signaling by PLCG1, which leads to increased cell proliferation and survival, providing selective advantage to cancer cells that harbor activating mutations in the EGFR gene (Sordella et al. 2004, Huang et al. 2007). While growth factor activated wild-type EGFR is promptly down-regulated by internalization and degradation, cancer mutants of EGFR demonstrate prolonged activation (Lynch et al. 2004). Association of HSP90 with EGFR kinase domain mutants negatively affects CBL-mediated ubiquitination, possibly through decreasing the affinity of EGFR kinase domain mutants for phosphorylated CBL, so that CBL dissociates from the complex upon phosphorylation and cannot perform ubiquitination (Yang et al. 2006, Padron et al. 2007). EGFRvIII mutant does not autophosorylate on the tyrosine residue Y1045, a docking site for CBL, and is therefore unable to recruit CBL ubiquitin ligase, which enables it to escape degradation (Han et al. 2006). Various molecular therapeutics are being developed to target aberrantly activated EGFR in cancer. Non-covalent (reversible) small tyrosine kinase inhibitors (TKIs), such as gefitinib and erlotinib, selectively bind kinase domain of EGFR, competitively inhibiting ATP binding and subsequent autophosphorylation of EGFR dimers. EGFR kinase domain mutants sensitive to non-covalent TKIs exhibit greater affinity for TKIs than ATP compared with the wild-type EGFR protein, and are therefore preferential targets of non-covalent TKI therapeutics (Yun et al. 2007). EGFR proteins that harbor point mutations in the extracellular domain also show sensitivity to non-covalent tyrosine kinase inhibitors (Lee et al. 2006). EGFR kinase domain mutants harboring small insertions in exon 20 or a secondary T790M mutation are resistant to reversible TKIs (Balak et al. 2006) due to increased affinity for ATP (Yun et al. 2008), and are targets of covalent (irreversible) TKIs that form a covalent bond with EGFR cysteine residue C397. However, effective concentrations of covalent TKIs also inhibit wild-type EGFR, causing severe side effects (Zhou et al. 2009). Hence, covalent TKIs have not shown much promise in clinical trials (Reviewed by Pao and Chmielecki in 2010). Recombinant monoclonal antibody Cetuximab acts as an antagonist of EGFR ligand binding, and is approved for the treatment of tumors that over-express wild-type EGFR receptor (Cunningham et al. 2004, Li et al. 2005, Burtness et al. 2005).
After ligand-independent dimerization, FGFR1 fusions are trans-autophosphorylated on tyrosine residues (see for instance Popovici, 1998; Ollendorff, 1999; Guasch, 2000). Although the sites of tyrosine phosphorylation have not been mapped in the context of the fusion proteins, at least some of the same residues appear to be phosphorylated as in full length FGFR1. For instance, phospho-specific antibodies have demonstrated that TRIM24 is phosphorylated on Y653 and Y654, the activation loop tyrosines of FGFR1 (Belloni, 2005). Likewise, FGFR1 fusions with ZMYM2, BCR, FGFR1OP and TRIM24 all result in recruitment and phosphorylation of PLCgamma, and where mutational studies have been performed, mutation of the PLCgamma binding site Y766 has been shown to abrogate this signaling (Roumiantsev, 2004, Lelievre, 2008, Chase, 2007). In the case of BCR-FGFR1, the BCR moiety of the fusion protein has also been shown to be phosphorylated on at least one tyrosine residue, Y177, which results in the recruitment of GRB2 (Roumiantsev, 2004).
8p11 myeloproliferative syndrome (EMS) is a myeloproliferative disorder that rapidly progresses to acute myeloid leukemia if not treated (reviewed in Jackson, 2010, Knights and Cook, 2010). A characteristic feature of EMS is the presence of fusion proteins that contain the kinase domain of FGFR1 and the oligomerization domain of an unrelated protein. This is believed to promote the ligand independent dimerization and activation of the kinase domain. To date, there are 11 identified partners that form fusion proteins with FGFR1 in EMS: ZMYM2 (Xiao, 1998; Popovici, 1998; Reiter, 1998; Ollendorff, 1999; Xiao, 2000), FGFR1OP1 (Popovici, 1999), CNTRL (Guasch, 2000), BCR (Demiroglu, 2001), FGFR1OP2 (Grand, 2004), TRIM24 (Belloni, 2005), CUX1 (Wasag, 2011), MYO18A (Walz, 2005), CPSF6 (Hidalgo-Curtis, 2008), HERV-K (Guasch, 2003) and LRRFIP1 (Soler, 2009).
8p11 myeloproliferative syndrome (EMS) is an aggressive disorder that is associated with a translocation event at the FGFR1 gene on chromosome 8p11. Typical symptoms upon diagnosis include eosinophilia and associated T-cell lymphoblastic lymphoma; the disease rapidly advances to acute leukemia, usually of myeloid lineage. At present the only effective treatment is allogenic stem cell transplantation (reviewed in Jackson, 2010). At the molecular level, EMS appears to be caused by translocation events on chromosome 8 that create gene fusions between the intracellular domain of FGFR1 and an N-terminal partner gene that encodes a dimerization domain. The resulting fusion protein dimerizes in a ligand-independent fashion based the N-terminal domain provided by the partner protein and stimulates constititutive downstream FGFR1 signaling without altering the intrisic kinase activity of the receptor. To date, 11 partner genes have been identified: ZMYM2, FGFR1OP, FGFR1OP2, HERVK, TRIM24, CUX1, BCR, CEP110, LRRFIP1, MYO18A and CPSF6, although not all have been functionally characterized (reviewed in Jackson, 2010, Turner and Grose, 2010; Wesche, 2011). Where examined, cell lines carrying FGFR1 fusion genes have been shown to be transforming and to support IL3-independent proliferation through anti-apoptotic, prosurvival pathways(Lelievre, 2008; Ollendorff, 1999; Chase, 2007; Guasch, 2001; Wasag 2011; Roumiantsev, 2004; Demiroglu, 2001; Smedley, 1999). Signaling appears to occur predominantly through PLCgamma, PI3K and STAT signaling, with a more minor contribution from MAPK activation. Because the fusion proteins lack the FRS2-binding site, the mechanism of MAPK activation is unclear. Recruitment of GRB2:SOS1 through recruitment of SHC is one possibility (Guasch, 2001).
In a murine mouse model of ZNF198-FGFR1-induced EMS, treatment with the FGFR-inhibitor Midostaurin (PKC412) resulted in prolonged survival (Chen, 2004). Similarly, growth of ZNF-198-FGFR1-, FGFR1OP2-FGFR1-, and BCR-FGFR1-expressing lines is blocked by treatment with FGFR-inhibitors (Demiroglu, 2001; Gu, 2006; Chase, 2007; Zhen, 2007; Wasag, 2011).
A number of skeletal and developmental diseases have been shown to arise as a result of mutations in the FGFR1, 2 and 3 genes. These include dwarfism syndromes (achondroplasia, hypochondroplasia and the neonatal lethal disorders thanatophoric dysplasia I and II), as well as craniosynostosis disorders such as Pfeiffer, Apert, Crouzon, Jackson-Weiss and Muenke syndromes (reviewed in Webster and Donoghue 1997; Burke, 1998, Cunningham, 2009; Harada, 2009). These mutations fall into four general regions of the receptor: a) the immunoglobulin (Ig)-like domain II-III linker region, b) the alternatively spliced second half of the Ig III domain, c) the transmembrane domain and d) the tyrosine kinase domain (reviewed in Webster and Donoghue, 1997). With the exception of mutations in class b), which affect only the relevant splice variant, these mutations may be present in either the 'b' or 'c' isoforms. These activating mutations affect FGFR function by altering or expanding the ligand-binding range of the receptors (see for instance Ibrahimi, 2004a), by promoting ligand-independent dimerization (for instance, Galvin,1996; Neilson and Friesel, 1996; d'Avis,1998) or by increasing the activity of the kinase domain (for instance, Webster, 1996; Naski, 1996; Tavormina, 1999; Bellus, 2000). Thus, a number of the point mutations found in FGFR receptors alter their activity without altering their intrinsic kinase activity. Many of the mutations that promote constitutive dimerization do so by creating or removing cysteine residues; the presence of an unpaired cysteine in the receptor is believed to promote dimerization through the formation of intramolecular disulphide bonds (Galvin, 1996; Robertson, 1998). Paralogous mutations at equivalent positions have been identified in more than one FGF receptor, sometimes giving rise to different diseases. For instance, mutation of the highly conserved FGFR2 Ser252-Pro253 dipeptide in the region between the second and third Ig domain is responsible for virtually all cases of Apert Syndrome (Wilkie, 1995), while paralogous mutations in FGFR1 (S252R) and FGFR3 (P250R) are associated with Pfeiffer and Crouzon syndromes, respectively (Bellus, 1996). FGFR4 is unique in that mutations of this gene are not known to be associated with any developmental disorders. Recently, many of the same activating mutations in the FGFR genes that have been characterized in skeletal and developmental disorders have begun to be identified in a range of cancers (reviewed in Turner and Gross, 2010; Greulich and Pollock, 2011; Wesche, 2011). The best established link between a somatic mutation of an FGFR and the development of cancer is in the case of FGFR3, where 50% of bladder cancers have mutations in the FGFR3 coding sequence. Of these mutations, which largely match the activating mutations seen in thanatophoric dysplasias, over half occur at a single residue (S249C) (Cappellen, 1999; van Rhijn, 2002). Activating mutations have also been identified in the coding sequences of FGFR1, 2 and 4 (for review, see Wesche, 2011) In addition to activating point mutations, the FGFR1, 2 and 3 genes are subject to misregulation in cancer through gene amplification and translocation events, which are thought to lead to overexpression and ligand-independent dimerization (Weiss, 2010; Turner, 2010; Kunii, 2008; Takeda, 2007; Chesi, 1997; Avet-Loiseau, 1998; Ronchetti, 2001). It is important to note, however, that in each of these cases, the amplification or translocation involve large genomic regions encompassing additional genes, and the definitive roles of the FGFR genes in promoting oncogenesis has not been totally established. In the case of FGFR1, translocation events also give rise to FGFR1 fusion proteins that contain the intracellular kinase domain of the receptor fused to a dimerization domain from the partner gene. These fusions, which are expressed in a pre-leukemic myeloproliferative syndrome, dimerize constitutively based on the dimerization domain provided by the fusion partner and are constitutively active (reviewed in Jackson, 2010).
The FGFR1 gene has been shown to be subject to activating mutations, chromosomal rearrangements and gene amplification leading to a variety of proliferative and developmental disorders depending on whether these events occur in the germline or arise somatically (reviewed in Webster and Donoghue, 1997; Burke, 1998; Cunningham, 2007; Wesche, 2011; Greulich and Pollock, 2011). Activating mutation P252R in FGFR1 is associated with the development of Pfeiffer syndrome, characterized by craniosynostosis (premature fusion of several sutures in the skull) and broadened thumbs and toes (Muenke, 1994; reviewed in Cunningham, 2007). This residue falls in a highly conserved Pro-Ser dipeptide between the second and third Ig domains of the extracellular region of the receptor. The mutation is thought to increase the number of hydrogen bonds formed with the ligand and to thereby increase ligand-binding affinity (Ibrahimi, 2004a). Unlike other FGF receptors, few activating point mutations in the FGFR1 coding sequence have been identified in cancer. Point mutations in the Ig II-III linker analagous to the P252R Pfeiffer syndrome mutation have been identified in lung cancer and melanoma (Ruhe, 2007; Davies, 2005), and two kinase-domain mutations in FGFR1 have been identified in glioblastoma (Rand, 2005, Network TCGA, 2008). In contrast, FGFR1 is a target of chromosomal rearrangements in a number of cancers. FGFR1 has been shown to be recurrently translocated in the 8p11 myeloproliferative syndrome (EMS), a pre-leukemic condition also known as stem cell leukemia/lymphoma (SCLL) that rapidly progresses to leukemia. This translocation fuses the kinase domain of FGFR1 with the dimerization domain of one of 10 identified fusion partners, resulting in the constitutive dimerization and activation of the kinase (reviewed in Jackson, 2010). Amplification of the FGFR1 gene has been implicated as a oncogenic factor in a range of cancers, including breast, ovarian, bladder, lung, oral squamous carcinomas, and rhabdomyosarcoma (reviewed in Turner and Grose, 2010; Wesche, 2011; Greulich and Pollock, 2011), although there are other candidate genes in the amplified region and the definitive role of FGFR1 has not been fully established.
Comparative analysis of gene regulation by the transcription factor PPARalpha between mouse and human
Benzoquinoid ansamycins (geldanamycin, herbimycin, and geldanamycin derivatives 17-AAG, 17-DMAG and IPI-504) are antitumor antibiotics that inactivate HSP90 by binding to its substrate-binding pocket.
The pathway 'Signaling by FGFR in disease' shows 'Signaling by FGFR mutants' in parallel with the wild-type pathway 'Signaling by FGFR', allowing users to compare disease and normal events. FGFR mutants and events associated with germline diseases and cancer are highlighted in red. The wild-type pathway is shaded in the background. For detailed pathway summations, please see 'Signaling by FGFR mutants' and 'Signaling by FGFR'.
L13a-mediated translational silencing of Ceruloplasmin expression
Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib
AKT1 E17K gain-of-function mutant preserves the ability to phosphorylate GSK3 (Malanga et al. 2008). AKT-mediated phosphorylation inactivates GSK3 and enables WNT-independent stabilization of beta-catenin (CTNNB1) (Haq et al. 2003). AKT-mediated inactivation of GSK3 also triggers changes in glucose metabolism (Ueki et al. 1997).
PIP2-bound AKT1 E17K mutant is constitutively phosphorylated on threonine residue T308 (Carpten et al. 2007, Landgraf et al. 2008), presumably by PIP2-bound PDPK1 (Currie et al. 1999).
A portion of PDPK1 (PDK1) is anchored to the plasma membrane in the absence of PI3K activity through PIP2 binding (Currie et al. 1999). This PIP2-bound PDPK1 is able to bind and phosphorylate PIP2-bound AKT E17K mutants (Carpten et al. 2007, Landgraf et al. 2008) phosphorylated on serine residue S473.
PIP2-binding AKT1 E17K mutants are anchored to the plasma membrane in the absence of PI3K activity and are constitutively phosphorylated on serine S473, presumably by the TORC2 complex (Carpten et al. 2007, Landgraf et al. 2008).
Substitution of glutamic acid with lysine at position 17 of AKT1 results in constitutive plasma membrane localization of AKT1, independent of PI3K activity and PIP3 generation (Carpten et al. 2007). This constitutive plasma membrane targeting of AKT1 E17K mutant is due to an increased affinity for PIP2 (Landgraf et al. 2008).
The process of vision involves two stages; the retinoid cycle which supplies and regenerates the visual chromophore required for vision and phototransduction which propagates the light signal. Defects in the genes involved in the retinoid cycle cause degenerative retinal diseases. These defective genes are described here (for reviews see Travis et al. 2007, Palczewski 2010, Fletcher et al. 2011, den Hollander et al. 2008).
The gene defects which cause diseases related to the retinoid cycle are described here (Travis et al. 2007, Palczewski 2010, Fletcher et al. 2011, den Hollander et al. 2008).
The mucopolysaccharidoses (MPS) are a group of rare, inherited lysosomal storage disorders caused by deficiencies of enzymes catalyzing the stepwise degradation of glycosaminoglycans (GAGs, originally called mucopolysaccharides) (Neufeld & Muenzer in Scriver et al. 2001). Catabolism of the GAGs dermatan sulfate, heparan sulfate, heparin, keratan sulfate, chondroitin sulfate or hyaluronan may be blocked at one or more steps, resulting in lysosomal accumulation of GAG fragments of varying size. Over time these collect in the cells, blood and connective tissues ultimately resulting in progressive irreversible cellular damage which affects appearance, physical abilities, organ and system function, vision, and usually mental development (Lehman et al. 2011, Ashworth et al. 2006). Life expectancy is also reduced. There are 11 known enzyme deficiencies that give rise to 7 distinct MPS. These disorders are biochemically characterized by elevated levels of partially or undegraded GAGs in lysosomes, blood, urine and cerebro-spinal fluid (Muenzer 2011, Coutinho et al. 2012). The MPS are part of the lysosomal storage disease family, a group of about 50 genetic disorders caused by deficient lysosomal proteins (Ballabio & Gieselmann 2009).
Mucopolysaccharidosis type IX (MPS IX, Natowicz syndrome, Hyaluronidase deficiency, MIM:601492) is a rare lysosomal storage disease characterized by high hyaluronan (HA) concentration in the serum resulting from deficiency in hyaluronidase 1 (HYAL1, MIM:607071) which normally hydrolyses 1-4 linkages between N-acetylglucosamine (GlcNAc) and D-glucuronate (GlcA) residues. Symptoms of MPS IX are periodically painful soft tissue masses around the joints, acquired short stature and erosion of the hip joint, although joint movement and intelligence are normal (Natowicz et al. 1996, Triggs-Raine et al. 1999).
Mucopolysaccharidosis type VII (MPS VII, Sly syndrome, beta-glucuronidase deficiency; MIM:253220) is an autosomal recessive lysosomal storage disease characterized by a deficiency of the enzyme beta-glucuronidase (GUSB; MIM:611499) which would normally cleave glucuronide residues from dematan sulphate, keratan sulphate and chondroitin sulphate, resulting in build up of these GAGs in cells and tissues (Sly et al. 1973). The gene encoding GUSB is 21 kb long, contains 12 exons and gives rise to two different types of cDNAs, through an alternate splicing mechanism (Miller et al. 1990). It maps to 7q11.21-q11.22 (Speleman et al. 1996). The phenotype is highly variable, ranging from severe causing death, non-immune hydrops fetalis (Vervoort et al. 1996) to mild forms with survival into adulthood (Storch et al. 2003). Most patients with the intermediate phenotype show hepatomegaly, skeletal anomalies, coarse facies, and variable degrees of mental impairment (Shipley et al. 1993, Tomatsu et al. 2009).
Discovery of a lysophospholipid acyltransferase family essential for membrane asymmetry and diversity
Defects in beta-galactosidase (GLB1; MIM:611458) can result in GM1 gangliosidosis (GM1; MIM:230500) (Nishimoto et al. 1991) (not described here), with several phenotypes indicating mental deterioration, as well as in mucopolysaccharidosis IVB, a characteristic mucopolysaccharidosis with no neurological symptoms (Callahan 1999). Mucopolysaccharidosis IVB (MPS IVB, Morquio's syndrome B; MIM:253010) is a rare, autosomal recessive mucopolysaccharide storage disease characterized by intracellular accumulation of keratan sulfate (KS), skeletal dysplasia and corneal clouding. There is no central nervous system involvement, intelligence is normal and there is increased KS excretion in urine (Suzuki et al. "Beta-galactosidase deficiency (beta-galactosidosis): GM1 gangliosidosis and Morquio B disease", p3775-3809 in Stryer et al. 2001). MPSIVB is caused by a defect in betagalactosidase (GLB1), which normally cleaves terminal galactosyl residues from glycosaminoglycans, gangliosides and glycoproteins. The GLB1 gene spans 62.5 kb and contains 16 exons (Oshima et al.1988, Santamaria et al. 2007) and maps to chromosome 3p21.33 (Takano & Yamanouchi 1993).
Mucopolysaccharidosis IV A (MPS IVA, MPS4A, Morquio's syndrome, Morquio's; MIM:253000) is a rare, autosomal recessive mucopolysaccharide storage disease, first described simultaneously in 1929 by L Morquio (Morquio L, Sur une forme de distrophie familiale, Bull Soc Pediat, Paris, 27, 1929, 145-152) and JF Brailsford (Brailsford, JF, Chondro-osteo-dystrophy: roentgenographic and clinical features of child with dislocation of vertebrae, Am j Surg, 7, 1929, 404-410). MPSIVA is caused by a deficiency in N-acetylgalactosamine 6-sulfatase (GALNS; MIM:612222) which normally hydrolyses 6-sulfate groups of N-acetylgalactosamine 6-sulfate units of chondroitin sulfate (CS) and of galactose 6-sulfate units of keratan sulfate (KS) (Matalon et al. 1974). The result is accumulation of KS/DS in cells and overexcretion in urine. Severe osteochondrodysplasia is a commonly seen phenotype for this disease. The severity of the disease is variable but severe cases limits lifespan to their 20's or 30's (Prat et al. 2008, Tomatsu et al. 2011). The gene coding for human GALNS was mapped to chromosome 16q24.3 (Masuno et al. 1993) and its structure described at the same time by two independent groups as comprising 14 exons and spanning approximately 40-50 kb (Nakashima et al.1994, Morris et al.1994).
Mucopolysaccharidosis type VI (MPS VI, Maroteaux-Lamy syndrome, polydystrophic dwarfism; MIM:253200) is an autosomal recessive lysosomal storage disorder caused by a deficiency in arylsulfatase B (ARSB, N-acetyl-galactosamine 4-sulfatase; MIM:611542). It is named after two French physicians, Pierre Maroteaux and Maurice Emil Joseph Lamy. Maroteaux first described this disorder as a novel dysostosis associated with increased urinary excretion of chondroitin sulfate (CS; Maroteaux et al. 1963). The gene encoding ARSB is mapped to chromosome 5q11-q13 (Fidzianska et al. 1984) and contains 8 exons spanning about 206 kb (Karangeorgos et al. 2007). Defective ARSB results in build up of dermatan sulfate (DS) and chondroitin sulfate (CS) in soft tissues causing compression and blockages in blood vessels, nerves, trachea, corneal clouding and disrupting normal bone development. Symptoms are similar to MPS I but with normal intelligence generally (Rapini et al. 2007, Valayannopoulos et al. 2010).
Mucopolysaccharidosis III (Sanfilippo syndrome) was described in 1963 by a pediatrician named Sylvester Sanfilippo (J. Pediat. 63: 837838, 1963, no reference). MPS IIIB (Mucopolysaccharidosis type IIIB, MPS IIIB, Sanfilippo syndrome type B; MIM:252920) is an autosomal recessive genetic disorder due to loss of function of alpha-N-acetylglucosaminidase (NAGLU; MIM:609701), involved in the hydrolysis of terminal non-reducing N-acetylglucosamine residues in heparan sulfate (HS) The gene encoding NAGLU was cloned in 1996 by Zhao and colleagues. It contains 6 exons and spans 8.3 kb on chromosome 17q21 (Zhao et al. 1996). MPSIIIB is characterized by severe CNS retardation but only mild somatic disease and death usually occurs in the second or third decade of life (Zhao et al. 1996, Yogalingam & Hopwood 2001, de Ruijter et al. 2011). MPS IIIB shows extensive molecular heterogeneity (Schmidtchen et al. 1998).
Mucopolysaccharidosis III (MPS III, Sanfilippo syndrome) was described in 1963 by a pediatrician named Sylvester Sanfilippo (J. Pediat. 63: 837-838, 1963, no reference). Mucopolysaccharidosis IIIA (MPS IIIA, Sanfilippo syndrome A, MIM:252900) is a rare, autosomal recessive lysosomal storage disease characterised by severe CNS degeneration in early childhood leading to death between 10 and 20 years of age. A deficiency of the enzyme N-sulphoglucosamine sulphohydrolase (SGSH, MIM:605270), which normally hydrolyses the sulfate group from the terminal N-sulphoglucosamine residue of heparan sulfate (HS), leads to the build-up of HS in cells and tissues and its presence in urine (van de Kamp et al. 1981, Yogalingam & Hopwood 2001, de Ruijter et al. 2011). The gene encoding N-sulfoglucosamine sulfohydrolase, SGSH, was cloned in 1995 (Scott et al.1995) and, later, shown to contain 8 exons spanning approximately 11 kb (Karageorgos et al. 1996).
Mucopolysaccharidosis III (Sanfilippo syndrome) was described in 1963 by a pediatrician named Sylvester Sanfilippo (J. Pediat. 63: 837-838, 1963, no reference). Mucopolysaccharidosis type IIID (MPS IIID, Sanfilippo syndrome D, MIM:252940) is an autosomal recessive genetic disorder due to the loss of N-acetyl-D-glucosamine 6-sulfatase (GNS; MIM:607664), that hydrolyses the 6-sulfate groups of the N-acetyl-D-glucosamine 6-sulfate units of the glycosaminoglycans (GAGs) heparan sulfate and keratan sulfate. GNS is localized to chromosome 12q14 and has 14 exons spanning 46 kb (Robertson et al. 1988, Mok et al. 2003). Loss of enzyme activity leads to lysosomal accumulation and urinary excretion of heparan sulfate and N-acetylglucosamine 6-sulfate residues (Mok et al. 2003). Keratan sulphate does not accumulate in MPS IIID, as beta-linked N-acetyl-D-glucosamine 6-sulphate can be cleaved by beta-hexosaminidase A (Kresse et al. 1980). This disorder is characterized by progressive mental deterioration but only moderate physical abnormalities and death duing the second or third decade of life, presenting a phenotype similar to MPSIIIA (Jones et al. 1997, de Ruijter et al. 2011).
Mucopolysaccharidosis III (Sanfilippo syndrome) was described in 1963 by a pediatrician named Sylvester Sanfilippo (J. Pediat. 63: 837838, 1963, no reference). Mucopolysaccharidosis type IIIC (MPS IIIC, Sanfilippo syndrome C; MIM:252930) is an autosomal recessive genetic disorder due to the loss of heparan alpha-glucosaminide N-acetyltransferase (HGSNAT; MIM:610453) that normally acetylates the non-reducing terminal alpha-glucosamine residue of heparan sulfate. The molecular defects underlying MPS IIIC remained unknown for almost three decades due to the low tissue content and instability of HGSNAT. But, during the last decade, the gene was cloned in parallel by two different groups and shown to contain 18 exons and span approximately 62Kb (Fan et al. 2006, Hrebicek et al. 2006). Loss of HGSNAT results in build up of this glycosaminglycan (GAG) in cells and tissues and is characterized by severe central nervous system degeneration but only with mild somatic disease and death occurs typically during the second or third decade of life (Kresse et al. 1978, Klein et al. 1978, Feldhammer et al. 2009, de Ruijter et al. 2011).
Glycosaminoglycans (GAGs) are long, unbranched polysaccharides containing a repeating disaccharide unit composed of a hexosamine (either N-acetylgalactosamine (GalNAc) or N-acetylglucosamine (GlcNAc)) and a uronic acid (glucuronate or iduronate). They can be heavily sulfated. GAGs are located primarily in the extracellular matrix (ECM) and on cell membranes, acting as a lubricating fluid for joints and as part of signalling processes. They have structural roles in connective tissue, cartilage, bone and blood vessels (Esko et al. 2009). GAGs are degraded in the lysosome as part of their natural turnover. Defects in the lysosomal enzymes responsible for the metabolism of membrane-associated GAGs lead to lysosomal storage diseases called mucopolysaccharidoses (MPS). MPSs are characterised by the accumulation of GAGs in lysosomes resulting in chronic, progressively debilitating disorders that in many instances lead to severe psychomotor retardation and premature death (Cantz & Gehler 1976, Clarke 2008). The biosynthesis and breakdown of the main GAGs (hyaluronate, keratan sulfate, chondroitin sulfate, dermatan sulfate and heparan sulfate) is described here.
Mucopolysaccharidosis II (MPS II, Hunter syndrome, MIM:309900) is an X-linked, recessive genetic disorder which therefore primarily affects males. MPS II was first described in 1917, by Major Charles Hunter (Hunter 1917) and is caused by a deficiency (or absence) of iduronate-2-sulfatase (IDS, MIM:300823), which would normally hydrolyse the 2-sulfate groups of the L-iduronate 2-sulfate units of dermatan sulfate, heparan sulfate and heparin. Without IDS, these GAGs accumulate in the body and are excessively excreted in urine. Although the disease was known since the early 1970s, being the first MPS to be defined clinically in humans, it wasn't until the 1990s that IDS was cloned. It is now known to be localized to Xq28 (Wilson et al. 1991) and contain 9 exons (Flomen et al. 1993) spanning approximately 24 kb (Wilson et al. 1993). Build up can occur in the liver and spleen as well as in the walls and valves of the heart (reduced hepatic and cardiac function, liver/spleen hepatosplenomegaly), airways (leading to obstructive airway disease), all major joints and bones (joint stiffness and skeletal deformities) and in brain (severe mental retardation). The rate of progression and degree of severity of the disorder can be different for each person with MPS II. Severe forms of the disorder can result in death in childhood whereas those with a "milder" form can expect to live to their 20's or 30's. Some patients even survive into their fifth and sixth decades of life (Wraith et al. 2008, Beck 2011).
Mucopolysaccharidosis type I (MPS I, Hurler syndrome, Hurler's disease, gargoylism, Scheie, Hirler-Scheie syndrome; MIM:607014, 607015 and 607016) is an autosomal recessive genetic disorder where there is a deficiency of alpha-L iduronidase (IDUA, MIM:252800), a glycosidase that removes non-reducing terminal alpha-L-iduronide residues during the lysosomal degradation of the glycosaminoglycans heparan sulphate and dermatan sulphate (McKusick 1959). In 1992, Scott and colleagues were able to clone and purify the gene that encodes this enzyme, IDUA, demonstrating that it spans approximately 19 kb and contains 14 exons (Scott et al. 1992). Hurler syndrome is named after a German paediatrician Gertrud Hurler (1919, no reference available). The result is build up of heparan sulfate and dermatan sulfate in the body and increased urinary excretion of these GAGs. Symptoms and signs include hepatosplenomegaly, dwarfism, unique facial features, corneal clouding, retinopathy, progressive mental retardation appears during childhood and early death can occur due to organ damage (Campos & Monaga 2012). MPS I is divided into three subtypes, ranging from severe to mild phenotypes; Mucopolysaccharidosis type IH (MPSIH, Hurler syndrome, MIM:607014), mucopolysaccharidosis type IH/S (MPSIH/S, HurlerScheie syndrome, MIM: 607015) and mucopolysaccharidosis type IS (MPSIS, Scheie syndrome, MIM: 607016) respectively (McKusick 1972).
Expression of isoforms of the human receptor tyrosine kinase c-kit in leukemic cell lines and acute myeloid leukemia
Uridine diphosphate glucose pyrophosphorylase. IV. Crystallization and properties of the enzyme from human liver
Partial purification of a microsomal sterol 4 -carboxylic acid decarboxylase
Crystallization and properties of human liver ornithine aminotransferase
MISCELLANEOUS Present with 3250 molecules/cell in log phase SD medium.SIMILARITY Belongs to the ABC transporter superfamily. ABCB family. Heavy Metal importer (TC 3.A.1.210) subfamily.SIMILARITY Contains 1 ABC transmembrane type-1 domain.SIMILARITY Contains 1 ABC transporter domain.
High mobility group proteins stimulate DNA cleavage by apoptotic endonuclease DFF40/CAD due to HMG-box interactions with DNA
PTM The N-terminus is blocked.MISCELLANEOUS Present with 907 molecules/cell in log phase SD medium.SIMILARITY Belongs to the archaeal RpoP/eukaryotic RPC10 RNA polymerase subunit family.
Cetuximab monotherapy and cetuximab plus irinotecan in irinotecan-refractory metastatic colorectal cancer
Ligand-regulated association of ErbB-4 to the transcriptional co-activator YAP65 controls transcription at the nuclear level
Phosphoinositides in constitutive membrane traffic
Nerve growth factor signaling, neuroprotection, and neural repair
MISCELLANEOUS Present with 3150 molecules/cell in log phase SD medium.SIMILARITY Belongs to the MET18/MMS19 family.SIMILARITY Contains 13 HEAT repeats.
The docking protein Gab1 is the primary mediator of EGF-stimulated activation of the PI-3K/Akt cell survival pathway
A yeast mitochondrion contains about 1000 proteins, more than 99% of which are encoded in the nucleus, synthesized in the cytosol and imported into the mitochondrion. Proteins are targeted to four locations (outer membrane, intermembrane space, inner membrane, and matrix) and must be sorted accordingly (reviewed in Kutik et al. 2007, Milenkovic et al. 2007, Bolender et al. 2008, Endo and Yamano 2009). Newly synthesized proteins are transported from the cytosol across the outer membrane by the TOM40:TOM70 complex. Proteins that contain presequences first interact with the TOM20 subunit of the complex while proteins that contain internal targeting elements first interact with the TOM70 subunit. Some proteins such as Aco1, Atp1, Cit1, Idh1, and Atp2 contain presequences that interact with TOM20 and mature regions that interact with TOM70 (Yamamoto et al. 2009). After initial interaction the protein is conducted across the outer membrane by TOM40 subunits. After passage across the outer membrane, proteins may be targeted to the outer membrane via the SAM50 complex, to the inner membrane via the TIM22 or TIM23 complexes (reviewed in van der Laan et al. 2010), to the matrix via the TIM23 complex (reviewed in van der Laan et al. 2010), or proteins may fold and remain in the intermembrane space (reviewed in Stojanovski et al. 2008, Deponte and Hell 2009, Sideris and Tokatlidis 2010). Presequences on matrix and inner membrane proteins cause interaction with TIM23 complexes; internal targeting sequences cause outer membrane proteins to interact with the SAM50 complex and inner membrane proteins to interact with the TIM22 complex. While in the intermembrane space hydrophobic proteins are chaperoned by the TIM8:TIM13 complex and/or the TIM9:TIM10 complex.
1D-myo-Inositol 1,3,4,5-tetrakisphosphate
1D-myo-Inositol 1,3,4,5-tetrakisphosphate [ChEBI:808]
D-myo-Inositol 1,3,4,5-tetrakisphosphate
Characterization of the major hydroperoxide-reducing activity of human plasma. Purification and properties of a selenium-dependent glutathione peroxidase
PLP results from phosphorylation of pyridoxal
COASY transfers an adenylyl group from ATP to PPANT
Phosphopantothenoylcysteine is decarboxylated
SLC25A16 transports cytosolic CoA-SH to mitichondrial matrix
CoA transport across the inner mitochondrial membrane
Phosphorylation of dephospho-CoA to produce CoA
ChEBI:16728 2-acyl-sn-glycero-3-phosphocholine
Condensation of phosphopantothenate with cysteine
ChEBI:16723 4-methylthio-2-oxobutanoate (1-)
Clinical issues and frequent questions about biotinidase deficiency
Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2]
Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT1]
A phospho-ribosyl group is added to quinolinate
Cytoslic carboxylases translocate to mitochondrial matrix
ABCC1 transports cytosolic Cbl to extracellular region
PLP from oxidation of pyridoxine phosphate
PLP from oxidation of pyridoxamine phosphate
Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT3]
A mediator of Rho-dependent invasion moonlights as a methionine salvage enzyme
Conversion of mitochondrial THF to THF-polyglutamate
DHF is reduced to tetrahydrofolate (THF)
Folate is reduced to dihydrofolate (DHF)
Retrovirally mediated complementation of the glyB phenotype. Cloning of a human gene encoding the carrier for entry of folates into mitochondria.
Conversion of cytosolic 5-methyltetrahydrofolate (5-methylTHF) to 5-methylTHF-polyglutamate
Conversion of cytosolic THF to THF-polyglutamate
Mitochondrial tetrahydrofolate export across the inner mitochondrial membrane
Cytosolic tetrahydrofolate import across the inner mitochondrial membrane
THF polyglutamate + formate + ATP => 10-formylTHF polyglutamate + ADP + orthophosphate
10-formylTHF polyglutamate <=> 5,10-methenylTHF polyglutamate + H2O
Formation of transcription-coupled NER (TC-NER) repair complex
5,10-methyleneTHF polyglutamate + glycine <=> tetrahydrofolate polyglutamate (THF polyglutamate) + serine
5,10-methyleneTHF polyglutamate + NADPH + H+ => 5-methylTHF polyglutamate + NADP+
Tetrahydrofolate polyglutamate (THF polyglutamate) + serine <=> 5,10-methyleneTHF polyglutamate + glycine
5,10-methenylTHF polyglutamate + NADPH + H+ <=> 5,10-methyleneTHF polyglutamate + NADP+
Defective HLCS does not biotinylate apo-CBXs
NFS1 transfers sulfur from cysteine onto MOCS3
5,10-methenylTHF polyglutamate + H2O <=> 10-formylTHF polyglutamate
5,10-methyleneTHF polyglutamate + NADP+ <=> 5,10-methenylTHF polyglutamate + NADPH + H+
PI(4,5)P2 is hydrolysed to I(1,4,5)P3 and DAG by tethered PLC[1] at the plasma membrane
I(1,3,4,5)P4 is dephosphorylated to I(1,3,4)P3 by INPP5[3]/ITPK1 in the cytosol
PI(4,5)P2 is hydrolysed to I(1,4,5)P3 and DAG by cytosolic PLC[2] at the plasma membrane
I(1,3,4,5,6)P5 is phosphorylated to 5-PP-IP4 by IP6K1/2 in the nucleus
5-PP-IP4 is phosphorylated to 1,5-(PP)2-IP3 by IP6K1/2 in the nucleus
IP6 is phosphorylated to 5-PP-IP5 by IP6K1/2 in the nucleus
I(1,4,5)P3 is phosphorylated to I(1,3,4,5)P4 by IPMK in the nucleus
I(1,3,4,5)P4 is phosphorylated to I(1,3,4,5,6)P5 by IPMK in the nucleus
I(1,3,4,6)P4 is phosphorylated to I(1,3,4,5,6)P5 by IPMK in the nucleus
I(1,4,5,6)P4 is phosphorylated to I(1,3,4,5,6)P5 by IPMK in the nucleus
Rabenosyn-5, a novel Rab5 effector, is complexed with hVPS45 and recruited to endosomes through a FYVE finger domain
The autosomal recessively inherited progressive myoclonus epilepsies and their genes
A dual role for mitochondrial heat shock protein 70 in membrane translocation of preproteins
Processing of meiotic DNA double strand breaks requires cyclin-dependent kinase and multiple nucleases
Neurotransmitter Receptor Binding And Downstream Transmission In The Postsynaptic Cell
DNA-directed RNA polymerases III 12.5 kDa polypeptide
DNA-directed RNA polymerase III largest subunit
DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
Wnt5a signaling directly affects cell motility and invasion of metastatic melanoma
DNA-directed RNA polymerase III 130 kDa polypeptide
Hypothetical 18.6 kDa protein in CCT3-CCT8 intergenic region
DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide
DNA-directed RNA polymerases I and III 16 kDa polypeptide
Transcription factor tau 131 kDa subunit
DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
Transcription factor tau 138 kDa subunit
Physiology and pathophysiology of vascular signaling controlled by guanosine 3',5'-cyclic monophosphate-dependent protein kinase [corrected]
Transcription factor TFIIIB B\" component
Transcription factor IIIB 70 kDa subunit
Transcription initiation factor TFIID TBP subunit
I(1,4,5)P3 is dephosphorylated to I(1,4)P2 by INPP5(4) in the cytosol
I(1,3,4,5,6)P5 is phosphorylated to 5-PP-IP4 by IP6K1/3 in the cytosol
1-PP-IP5 is phosphorylated to 1,5-(PP)2-IP4 by IP6K1/2 in the nucleus
IP6 is phosphorylated to 5-PP-IP5 by IP6K1/3 in the cytosol
1-PP-IP4 is phosphorylated to 1,5-(PP)2-IP3 by IP6K1/3 in the cytosol
5-PP-IP5 is phosphorylated to 5-PPP-IP5 by IP6K1/3 in the cytosol
IP6 is phosphorylated to 1-PP-IP5 by PPIP5K1/2 in the cytosol
1-PP-IP5 is phosphorylated to 1,5-(PP)2-IP4 by IP6K1/3 in the cytosol
5-PP-IP5 is phosphorylated to 1,5-(PP)2-IP4 by PPIP5K1/2 in the cytosol
5-PP-IP5 is phosphorylated to 5-PPP-IP5 by IP6K1/2 in the nucleus
Defective BTD causes biotidinase deficiency
The renal plumbing system: aquaporin water channels
The Drosophila tweety family: molecular candidates for large-conductance Ca2+-activated Cl- channels
Chromatin higher-order structures and gene regulation
The solution structure of the guanine nucleotide exchange domain of human elongation factor 1beta reveals a striking resemblance to that of EF-Ts from Escherichia coli
lignoceroyl-CoA + malonyl-CoA => 3-oxocerotoyl-CoA + CO2 + CoASH [ELOVL4]
palmitoyl-CoA + malonyl-CoA => 3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA) + CO2 + CoASH [ELOVL2]
arachidonoyl-CoA + malonyl-CoA => 3-oxo-(7,10,13,16)-docosatetraenoyl-CoA + CO2 + CoASH [ELOVL5]
palmitate + CoASH + ATP => palmitoyl-CoA + AMP + pyrophosphate + H2O [ACSL5]
arachidonate + CoASH + ATP => arachidonoyl-CoA + AMP + pyrophosphate + H2O [ACSL4]
palmitoyl-CoA + malonyl-CoA => 3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA) + CO2 + CoASH [ELOVL1]
palmitate + CoASH + ATP => palmitoyl-CoA + AMP + pyrophosphate + H2O [ACSL6]
acetyl-CoA + bicarbonate + ATP => malonyl-CoA + H2O + ADP + orthophosphate
Formation of Malonyl-CoA from Acetyl-CoA (liver)
palmitate + CoASH + ATP => palmitoyl-CoA + AMP + pyrophosphate + H2O [ACSL3]
palmitate + CoASH + ATP => palmitoyl-CoA + AMP + pyrophosphate + H2O [ACSL1]
Conversion of palmitic acid to palmitoyl-CoA
Transport of Citrate from Mitochondrial Matrix to cytosol
2-acylglycerol + H2O -> glycerol + fatty acid
sterols[cytosol] + ATP => sterols[extracellular] + ADP + Pi
ABCG5:ABCG8-mediated export of cholesterol and phytosterols
NPC1L1 + ezetimibe => NPC1L1:ezetimibe complex
I3P is dephosphorylated to Ins by IMPA1/2 in the cytosol
Glc6P is isomerised to I3P by ISYNA1 in the cytosol
I1P is dephosphorylated to Ins by IMPA1/2 in the cytosol
I4P is dephosphorylated to Ins by IMPA1/2 in the cytosol
DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
DNA-directed RNA polymerase III 36 kDa polypeptide
DNA-directed RNA polymerase III 31 kDa polypeptide
DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide
DNA-directed RNA polymerase III 25 kDa polypeptide
DNA-directed RNA polymerase III 47 kDa polypeptide
DNA-directed RNA polymerases I and III 40 kDa polypeptide
DNA-directed RNA polymerase III 74 kDa polypeptide
Formation of Malonyl-CoA from Acetyl-CoA (muscle)
pAMPK inactivates ACC2 inhibiting malonyl-CoA synthesis
acetoacetyl-CoA+acetyl-CoA => HMG-CoA + CoASH
Gly-3-P+FAD->DHAP+FADH2 (catalyzed by mitochondrial Gly-Phos dehydrogenase)
Lsm1-7-Pat1 complex: A link between 3' and 5'-ends in mRNA decay?
Expression of 3-Hydroxy-3-methylglutaryl-coenzyme A Reductase (HMGCR)
Mammalian Orc1 protein is selectively released from chromatin and ubiquitinated during the S-to-M transition in the cell division cycle.
Expression of Hydroxymethylglutaryl coenzyme A synthase (HMGCS1)
PMP34-mediated exchange of cytosolic ATP for peroxisomal AMP
2-hydroxyphytanoyl-CoA => pristanal + formyl-CoA
Double-strand break repair protein MRE11
trans-octadec-2-enoyl-CoA + NADPH + H+ => stearoyl-CoA + NADP+
Conversion of Dihydroxyacetone Phosphate to Glycerol -3- phosphate
arachidoyl-CoA + malonyl-CoA => 3-oxobehenoyl-CoA + CO2 + CoASH [ELOVL7]
3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA) + NADPH + H+ => 3-hydroxyoctadecanoyl-CoA + NADP+
Conversion of Phosphatidic Acid to Diacylglycerol
1,2-diacyl-glycerol + acyl-CoA => triacylglycerol + CoASH [DGAT2]
Conversion of Diacylglycerol to Triacylglycerol [DGAT2]
Conversion of Glycerol to Glycerol-3-phosphate
lysophosphatidic acid + fatty acyl CoA => phosphatidic acid + CoA (1)
1-acyl-glycerol 3-phosphate + acyl-CoA => 1,2-diacyl-glycerol 3-phosphate + CoASH
1-acyl LPA is acylated to PA by AGPAT (LPAAT)
Exchange of palmitoylcarnitine and carnitine across the inner mitochondrial membrane
palmitoylcarnitine + CoASH => palmitoyl-CoA + carnitine
CPT2 converts palmitoyl carnitine to palmitoyl-CoA
Phosphorylated JNKs: MAPK8, MAPK9, MAPK10
Transport of inorganic cations/anions and amino acids/oligopeptides
Condensation of acetyl CoA with acetoacetyl CoA to form HMG-CoA
Reduction of HMG-CoA produces mevalonate
Mevalonate is phosphorylated to mevalonate-5-phosphate
The Wnt5A/protein kinase C pathway mediates motility in melanoma cells via the inhibition of metastasis suppressors and initiation of an epithelial to mesenchymal transition
Isopentenyl pyrophosphate rearranges to dimethylallyl pyrophosphate
Essential role for IKK? in production of type 1 interferons by plasmacytoid dendritic cells
3-ketohexacosanoyl-CoA + CoASH => tetracosanoyl-CoA + acetyl-CoA
isocitrate + NADP+ => 2-oxoglutarate + CO2 + NADPH + H+
Addition of isopentenyl pyrophosphate to DMAPP
Another isopentenyl pyrophosphate is added to geranyl pyrophosphate
Two FPP molecules dimerize to form presqualene diphosphate
New regulatory mechanisms of TGF-beta receptor function
Dual specificity mitogen-activated protein kinase kinase 1 (EC 2.7.1.-) (MAP kinase kinase 1) (MAPKK 1) (ERK activator kinase 1) (MAPK/ERK kinase 1) (MEK1)
Dual specificity mitogen-activated protein kinase kinase 1
(24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA
propionyl-CoA + carnitine => propionylcarnitine + CoASH
Studies on the activator 1 protein complex, an accessory factor for proliferating cell nuclear antigen-dependent DNA polymerase delta.
(24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA
3-hydroxypristanoyl-CoA + NAD+ => 3-ketoxypristanoyl-CoA + NADH + H+
25(S) 3alpha,7alpha-dihydroxy-5beta-cholest-24-enoyl-CoA
acetyl-CoA + carnitine => acetylcarnitine + CoASH
25(S) 3alpha,7alpha-dihydroxy-5beta-cholestanoyl-CoA
(2S)-pristanoyl-CoA + O2 => trans-2,3-dehydropristanoyl-CoA + H2O2 (ACOX2)
trans-2,3-dehydropristanoyl-CoA + H2O => 3-hydroxypristanoyl-CoA
25(S) 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA
trans-2,3-dehydrohexacosanoyl-CoA + H2O => 3-hydroxyhexacosanoyl-CoA
3-hydroxyhexacosanoyl-CoA + NAD+ => 3-ketohexacosanoyl-CoA + NADH + H+
Peroxisomal uptake of very long-chain fatty acyl CoA
hexacosanoyl-CoA + O2 => trans-2,3-dehydrohexacosanoyl-CoA + H2O2
Localization and trafficking of aquaporin 2 in the kidney
Structure-function analysis of HKE4, a member of the new LIV-1 subfamily of zinc transporters
1-phosphatidyl-1D-myo-inositol 4-phosphate
1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate
1-phosphatidyl-1D-myo-inositol 3-phosphate
1-phosphatidyl-1D-myo-inositol 4-phosphates
The secretory pathway Ca2+/Mn2+-ATPase 2 is a Golgi-localized pump with high affinity for Ca2+ ions
Two distinct disulfide bonds formed in human heat shock transcription factor 1 act in opposition to regulate its DNA binding activity
Active and inhibited human catalase structures: ligand and NADPH binding and catalytic mechanism.
The NOD: a signaling module that regulates apoptosis and host defense against pathogens
PPARs: therapeutic targets for metabolic disease
Nuclear factor 1 (NF1) affects accurate termination and multiple-round transcription by human RNA polymerase III.
Crystal structures of human DcpS in ligand-free and m7GDP-bound forms suggest a dynamic mechanism for scavenger mRNA decapping
Binding of a novel SMG-1-Upf1-eRF1-eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay
Endotoxin recognition and signal transduction by the TLR4/MD2-complex
Dock6, a Dock-C subfamily guanine nucleotide exchanger, has the dual specificity for Rac1 and Cdc42 and regulates neurite outgrowth
Genomic organization of the human phosphomannose isomerase (MPI) gene and mutation analysis in patients with congenital disorders of glycosylation type Ib (CDG-Ib)
Structure and sequence of the human alpha-L-iduronidase gene
1-phosphatidyl-1D-myo-inositol 5-phosphate
Integrating signals from RTKs to ERK/MAPK
Proteoglycans and Sulfated Glycosaminoglycans
Characteristics of human types 1, 2 and 3 17 beta-hydroxysteroid dehydrogenase activities: oxidation/reduction and inhibition
Role of the CCAAT enhancer binding proteins (C/EBPs) in adipocyte differentiation
Point mutations in the aromatic/arginine region in aquaporin 1 allow passage of urea, glycerol, ammonia, and protons
1D-myo-Inositol 1,3,4,5,6-pentakisphosphate
myo-inositol 1,3,4,5,6-pentakisphosphate
Synthesis of glycosylphosphatidylinositol (GPI)
The anaphase-promoting complex: a key factor in the regulation of cell cycle
Coexpression of glucose transporters and glucokinase in Xenopus oocytes indicates that both glucose transport and phosphorylation determine glucose utilization
The way Wnt works: Components and mechanism
Cdc42, Rac1, and Rac2 display distinct patterns of activation during phagocytosis
The post-translational synthesis of a polyamine-derived amino acid, hypusine, in the eukaryotic translation initiation factor 5A (eIF5A)
Human sphingosine-1-phosphate lyase: cDNA cloning, functional expression studies and mapping to chromosome 10q22(1)
'Pi [cytosol]' is required for 'ribose phosphate diphosphokinase activity of phosphoribosyl pyrophosphate synthetase 1 holoenzyme (name copied from entity in Homo sapiens) [cytosol]'
'GTP [cytosol]' positively regulates 'glutamate dehydrogenase [NAD(P)+] activity of GLUD1 hexamer (name copied from entity in Homo sapiens) [mitochondrial matrix]'
'Mg2+ [cytosol]' is required for 'ribose phosphate diphosphokinase activity of phosphoribosyl pyrophosphate synthetase 1 holoenzyme (name copied from entity in Homo sapiens) [cytosol]'
'GDP [cytosol]' positively regulates 'glutamate dehydrogenase [NAD(P)+] activity of GLUD1 hexamer (name copied from entity in Homo sapiens) [mitochondrial matrix]'
'ADP [cytosol]' positively regulates 'glutamate dehydrogenase [NAD(P)+] activity of GLUD1 hexamer (name copied from entity in Homo sapiens) [mitochondrial matrix]'
'ATP [nucleoplasm]' positively regulates 'glutamate dehydrogenase [NAD(P)+] activity of GLUD1 hexamer (name copied from entity in Homo sapiens) [mitochondrial matrix]'
Cloning and expression of a human choline/ethanolaminephosphotransferase: synthesis of phosphatidylcholine and phosphatidylethanolamine
Aquaporins in complex tissues. II. Subcellular distribution in respiratory and glandular tissues of rat
Regulation of endothelium-derived nitric oxide production by the protein kinase Akt
Activation of nitric oxide synthase in endothelial cells by Akt-dependent phosphorylation
Lathosterolosis: an inborn error of human and murine cholesterol synthesis due to lathosterol 5-desaturase deficiency
TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation
Sequence of the human erythrocyte phosphoglycerate mutase by microsequencer and mass spectrometry
Aquaporins in complex tissues. I. Developmental patterns in respiratory and glandular tissues of rat
Mechanisms of human DNA repair: an update.
The 7 TM G-protein-coupled receptor target family
Dual role of the tyrosine activation motif of the Ig-alpha protein during signal transduction via the B cell antigen receptor
HSP90 is inactivated by binding to benzaquinoid ansamycins
NRAMP1 transports divalent metal ions across phagosomal membranes of macrophages
Role of glutathione peroxidase and hexose monophosphate shunt in the platelet lipoxygenase pathway
phenylalanine + oxaloacetate => phenylpyruvate + aspartate [CCBL1]
Tyrosine kinase inhibitors bind and inhibit FGFR1 fusion dimer phosphorylation
Growing HA is extruded from the cell by ABCC5
kynurenine + pyruvate => 4-(2-aminophenyl)-2,4-dioxobutanoic acid + alanine [CCBL1]
APS reacts with another ATP molecule to form PAPS
PAPSS1,2 transfer PO4(2-) group from ATP to APS to form PAPS
adenylyl sulfate (APS) + ATP => PAPS + ADP
Calmodulin-kinases: modulators of neuronal development and plasticity
PAPSS1,2 transfer PO4(2-) group from ATP to form APS
ATP + sulfate => adenylyl sulfate (APS) + pyrophosphate
Activation of inorganic sulfate forms APS
Mitogen-activated protein kinase 1 (EC 2.7.1.-) (Extracellular signal- regulated kinase 2) (ERK-2) (Mitogen-activated protein kinase 2) (MAP kinase 2) (MAPK 2) (p42-MAPK) (ERT1)
Nitric Oxide as a Unique Bioactive Signaling Messenger in Physiology and Pathophysiology
Microtubule- associated protein-2 kinase
SLC35B2,3 transport cytosolic PAPS to Golgi lumen
PIP2-bound p-S473-AKT1 mutant binds PIP2-bound PDPK1
AKT1 E17K mutant is phosphorylated by TORC2 complex
AKT inhibitors block AKT membrane recruitment
AKT1 E17K mutant translocates to the nucleus
2-oxoglutarate + NADPH + H+ => (R)-2-hydroxyglutarate + NADP+ [mutant IDH1]
extracellular fructose => cytosolic fructose
Systematic analysis of the twin cx(9)c protein family
GPX3 catalyzes 2 glutathione, reduced + H2O2 => glutathione, oxidized + 2 H2O
GPX2 catalyzes 2 glutathione, reduced + H2O2 => glutathione, oxidized + 2 H2O
PRDX1,2,5 catalyze TXN reduced + H2O2 => TXN oxidized + 2H2O
glutathione (oxidized) + NADPH + H+ => 2 glutathione (reduced) + NADP+
2 glutathione, reduced + H2O2 => glutathione, oxidized + 2 H2O
Dissociation of cytosolic HSF1:HSP90 complex
PRDX5 reduces peroxynitrite to nitrite using TXN
Dissociation of cytosolic HSF1:HSP90:HDAC6:PTGES3 upon sensing protein aggregates
Evidence of functional modulation of the MEKK/JNK/cJun signaling cascade by the low density lipoprotein receptor-related protein (LRP)
Recognition of histone H3K4 trimethylation by the plant homeodomain of PHF2 modulates histone demethylation
Phosphorylation of HSF1 at Ser230 induces transactivation
Phosphorylation of HSF1 at Ser326 induces transactivation
Dissociation of HSF1:HSP90 complex in the nucleus
1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate [ChEBI:16618]
1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate
Intraphagosomal pH is lowered to 5 by V-ATPase
Conserved initiator proteins in eukaryotes.
The known unknowns of antigen processing and presentation
Mitogen-activated protein kinase 3 (EC 2.7.1.-) (Extracellular signal- regulated kinase 1) (ERK-1) (Insulin-stimulated MAP2 kinase) (MAP kinase 1) (MAPK 1) (p44-ERK1) (ERT2) (p44-MAPK) (Microtubule- associated protein-2 kinase)
aspartate + alpha-ketoglutarate <=> oxaloacetate + glutamate [GOT1]
phosphoenolpyruvate [mitochondrial matrix] + citrate [cytosol] => phosphoenolpyruvate [cytosol] + citrate [mitochondrial matrix]
Exchange of cytosolic citrate for mitochondrial phosphoenolpyruvate
Phosphoenolpyruvate + H2O <=> 2-Phospho-D-glycerate
2-Phospho-D-glycerate <=> 3-Phospho-D-glycerate
ATP + 3-Phospho-D-glycerate <=> ADP + 1,3-bisphospho-D-glycerate
1,3-bisphospho-D-glycerate + NADH + H+ <=> D-glyceraldehyde 3-phosphate + Orthophosphate + NAD+
Relationship between structures and biological activities of mycoplasmal diacylated lipopeptides and their recognition by toll-like receptors 2 and 6
Homodimerization of Nemo-like kinase is essential for activation and nuclear localization
Glycogen metabolism and glycolytic enzymes
Understanding RAGE, the receptor for advanced glycation end products
Constitutive and inducible expression and regulation of vascular endothelial growth factor
alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP
glucokinase [nucleoplasm] => glucokinase [cytosol]
Glucose 6-phosphate is isomerized to form fructose-6-phosphate
alpha-D-glucose 6-phosphate <=> D-fructose 6-phosphate
cytosolic fructose, galactose, or glucose => extracellular fructose, galactose, or glucose
Transport (efflux) of fructose, galactose, and glucose by GLUT2
GLUT tetramers transport Glc from extracellular region to cytosol
Glucose is taken up across the plasma membrane by a glucose transport protein (GLUT)
alpha-D-glucose (extracellular) <=> alpha-D-glucose (cytosol)
alpha-D-glucose (cytosol) <=> alpha-D-glucose (extracellular)
Glucose is secreted across the plasma membrane
DNA replication ATP-dependent helicase DNA2 ecNumber3.6.4.12/ecNumber
Dephosphorylation of phosphoPFKFB1 by PP2A complex
DNA repair helicase RAD3 ecNumber3.6.4.12/ecNumber
DNA repair/transcription protein MET18/MMS19
D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP
Cytosolic iron-sulfur protein assembly protein 1
Fructose 6-phosphate and ATP react to form fructose 2,6-bisphosphate and ADP
D-fructose 6-phosphate + ATP => D-fructose 2,6-bisphosphate + ADP
Cytosolic Fe-S cluster assembly factor NAR1
Mutations in GLUT2, the gene for the liver-type glucose transporter, in patients with Fanconi-Bickel syndrome
FATP1 channels exogenous FA into 1,2,3-triacyl-sn-glycerol and down-regulates sphingomyelin and cholesterol metabolism in growing 293 cells
Pyruvate, CO2, and ATP react to form oxaloacetate, ADP, and orthophosphate
Pyruvate + CO2 + ATP => ADP + Orthophosphate + Oxaloacetate
2-Phospho-D-glycerate <=> Phosphoenolpyruvate + H2O
phosphoenolpyruvate + ADP => pyruvate + ATP
1,3-Bisphosphoglycerate and ADP react to form 3-phosphoglycerate and ATP
1,3-bisphospho-D-glycerate + ADP <=> 3-phospho-D-glycerate + ADP
3-Phospho-D-glycerate <=> 2-Phospho-D-glycerate
Cytosolic Fe-S cluster assembly factor NBP35
dihydroxyacetone phosphate <=> D-glyceraldehyde 3-phosphate
Iron-sulfur clusters transporter ATM1, mitochondrial
Glyceraldehyde 3 phosphate, NAD+, and orthophosphate react to form 1,3 bisphosphoglycerate and NADH + H+
D-glyceraldehyde 3-phosphate + orthophosphate + NAD+ <=> 1,3-bisphospho-D-glycerate + NADH + H+
aspartate [mitochondrial matrix] + glutamate [cytosol] => aspartate [cytosol] + glutamate [mitochondrial matrix]
Exchange of cytosolic glutamate and mitochondrial aspartate
TMEM16A confers receptor-activated calcium-dependent chloride conductance
oxaloacetate + glutamate <=> aspartate + alpha-ketoglutarate [GOT2]
malate [mitochondrial matrix] + orthophosphate [cytosol] <=> malate [cytosol] + orthophosphate [mitochondrial matrix]
Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform
Oxaloacetate + NADH + H+ <=> (S)-Malate + NAD+
Cytosolic Fe-S cluster assembly factor CFD1
Probable NADPH reductase TAH18 ecNumber1.-.-.-/ecNumber
EDEM3, a soluble EDEM homolog, enhances glycoprotein endoplasmic reticulum-associated degradation and mannose trimming
D-fructose 1,6-bisphosphate + H2O => D-fructose 6-phosphate + orthophosphate
D-glyceraldehyde 3-phosphate <=> dihydroxyacetone phosphate
ATP-dependent positive supercoiling of DNA by 13S condensin: a biochemical implication for chromosome condensation
Nuclear envelope phosphatase 1-regulatory subunit 1 (formerly TMEM188) is the metazoan Spo7p ortholog and functions in the lipin activation pathway
8 UDP-glucose + GYG1 => 8 UDP + oligoGlc-GYG1 (GYS1-a)
Autoglucosylation of GYG1 complexed with GYS1-a
UTP + D-glucose 1-phosphate <=> pyrophosphate + UDP-glucose
8 UDP-glucose + GYG2 => 8 UDP + oligoGlc-GYG2 (GYS2-a)
Autoglucosylation of GYG2 complexed with GYS2-a
8 UDP-glucose + GYG1 => 8 UDP + oligoGlc-GYG1 (GYS1-b)
Autoglucosylation of GYG1 complexed with GYS1-b
Fructose 2,6-bisphosphate is hydrolyzed to form fructose-6-phosphate and orthophosphate
Phosphorylation of PF2K-Pase by PKA catalytic subunit
alpha-D-Glucose 6-phosphate <=> D-Glucose 1-phosphate
D-fructose 6-phosphate <=> alpha-D-Glucose 6-phosphate
Biology, structure and mechanism of P-type ATPases
Degradation of cysteine and homocysteine
Mitochondrial association of a plus end-directed microtubule motor expressed during mitosis in Drosophila
Nucleotide sequences in Xenopus 5S DNA required for transcription termination.
Loading of an Mcm protein onto DNA replication origins is regulated by Cdc6p and CDKs.
Vav-family proteins in T-cell signalling
Purification, molecular cloning, and expression of 2-hydroxyphytanoyl-CoA lyase, a peroxisomal thiamine pyrophosphate-dependent enzyme that catalyzes the carbon-carbon bond cleavage during alpha-oxidation of 3-methyl-branched fatty acids
Molecular cloning, cDNA sequence, and bacterial expression of human glutamine:fructose-6-phosphate amidotransferase
Reduction of semidehydroascorbate to ascorbate
ferric CYB5A + NADH + H+ => ferrous CYPB5A + NAD+
CYB5R3:FAD reduces CYB5A:ferriheme to CYB5A:heme
ribose 5-phosphate <=> D-ribulose 5-phosphate
D-ribose 5-phosphate + 2'-deoxyadenosine 5'-triphosphate (dATP) => 5-Phospho-alpha-D-ribose 1-diphosphate (PRPP) + 2'-deoxyadenosine 5'-monophosphate
addition of diphosphate (PP) to ribose 5-phosphate to form 5'-Phospho-alpha-D-ribose 1-diphosphate (PRPP)
D-ribose 5-phosphate + ATP => 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) + adenosine 5'-monophosphate
dehydroascorbate [extracellular] => dehydroascorbate [cytosol]
Dehydroascorbate transport across the plasma membrane
GLUT1/3 transports extracellular DHvitC to cytosol
D-glyceraldehyde 3-phosphate + D-fructose 6-phosphate <=> xylulose 5-phosphate + D-erythrose 4-phosphate
D-ribulose 5-phosphate <=> ribose 5-phosphate
DNA polymerase epsilon, catalytic subunit A
xylulose 5-phosphate + D-erythrose 4-phosphate <=> D-glyceraldehyde 3-phosphate + D-fructose 6-phosphate
sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate <=> D-erythrose 4-phosphate + D-fructose 6-phosphate
D-fructose 6-phosphate + D-erythrose 4-phosphate <=> sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate
ribose 5-phosphate + xylulose 5-phosphate <=> sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate
D-glyceraldehyde 3-phosphate + sedoheptulose 7-phosphate<=> xylulose 5-phosphate+ribose 5-phosphate
D-ribulose 5-phosphate <=> xylulose 5-phosphate
xylulose 5-phosphate <=> D-ribulose 5-phosphate
D-glucono-1,5-lactone 6-phosphate + H2O => 6-phospho-D-gluconate
6-phospho-D-gluconate + NADP+ => D-ribulose 5-phosphate + CO2 + NADPH + H+
alpha-D-glucose 6-phosphate + NADP+ => D-glucono-1,5-lactone 6-phosphate + NADPH + H+
Nuclear localization of human DNA mismatch repair protein exonuclease 1 (hEXO1)
Chromosome condensation-related SMC-associated protein 1
Structural maintenance of chromosomes protein 2
Structural maintenance of chromosomes protein 4
Enzyme hyperspecificity. Rejection of threonine by the valyl-tRNA synthetase by misacylation and hydrolytic editing
((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin => poly{(1,4)-alpha-glucosyl} glycogenin + alpha-D-glucose
SIMILARITY Belongs to the eukaryotic RPC34/RPC39 RNA polymerase subunit family.
poly((1,4)-alpha-glycosyl) glycogenin-1 + n orthophosphate => glycogenin-1 + n D-glucose 1-phosphate [PYGM,PYGB]
poly((1,4)-alpha-glucosyl) glycogenin-2 + n orthophosphate => glycogenin-2 + n D-glucose 1-phosphate [PYGL]
D-Glucose 1-phosphate <=> alpha-D-Glucose 6-phosphate
D-galactose 1-phosphate + UDP-glucose <=> D-glucose 1-phosphate + UDP-galactose
Crystal structures of human glycerol 3-phosphate dehydrogenase 1 (GPD1)
A human purine nucleoside phosphorylase deficiency caused by a single base change
PGYM b dimer:AMP complex <=> PGYM dimer, b form + 2 AMP
glycogen-glycogenin-1 + n orthophosphate => limit dextrin-glycogenin-1 + n D-glucose 1-phosphate [PYGM,PYGB]
glycogen-glycogenin-2 + n orthophosphate => limit dextrin-glycogenin-2 + n D-glucose 1-phosphate [PYGL]
limit dextrin-glycogenin => ((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl) glycogenin
poly((1,4)-alpha-D-glucosyl) glycogenin1 => glycogen-glycogenin 1 (GYS1-b)
GBE1 catalyzes branch formation in polyGlc-GYG1 complexed with GYS1-b
Kinetic analysis of peptide binding to the TAP transport complex: evidence for structural rearrangements induced by substrate binding
poly((1,4)-alpha-D-glucosyl) glycogenin2 => glycogen-glycogenin 2 (GYS2-a)
GBE1 catalyzes branch formation in polyGlc-GYG2 complexed with GYS2-a
Mitotic Golgi partitioning is driven by the membrane-fissioning protein CtBP3/BARS
8 UDP-glucose + ((1,4)-alpha-D-glucosyl)4 glycogenin2 => 8 UDP + ((1,4)-alpha-D-glucosyl)8 glycogenin2 (GYS2-a)
GYS2 catalyzes the polyglucosylation of oligoGlc-GYG2
poly((1,4)-alpha-D-glucosyl) glycogenin1 => glycogen-glycogenin 1 (GYS1-a)
GBE1 catalyzes branch formation in polyGlc-GYG1 complexed with GYS1-a
Essential function for the kinase TAK1 in innate and adaptive immune responses
PGYM dimer, b form + 2 AMP <=> PGYM b dimer:AMP complex
PGYB dimer, b form + 2 AMP <=> PGYB b dimer:AMP complex
PGYB b dimer:AMP complex <=> PGYB dimer, b form + 2 AMP
8 UDP-glucose + ((1,4)-alpha-D-glucosyl)4 glycogenin2 => 8 UDP + ((1,4)-alpha-D-glucosyl)8 glycogenin2 (GYS1-a)
GYS1 catalyzes the polyglucosylation of oligoGlc-GYG1
8 UDP-glucose + ((1,4)-alpha-D-glucosyl)4 glycogenin => 8 UDP + ((1,4)-alpha-D-glucosyl)8 glycogenin (GYS1-b)
Phosphorylated GYS1 catalyzes the polyglucosylation of oligoGlc-GYG1
8 UDP-glucose + GYG2 => 8 UDP + oligoGlc-GYG2 (GYS2-b)
Autoglucosylation of GYG2 complexed with GYS2-b
Aspartate 155 of human transketolase is essential for thiamine diphosphate-magnesium binding, and cofactor binding is required for dimer formation
Kinetics of B cell receptor signaling in human B cell subsets mapped by phosphospecific flow cytometry
The histone mark H3K36me3 regulates human DNA mismatch repair through its interaction with MutS?
Diabetes-associated sustained activation of the transcription factor nuclear factor-kappaB
Molecular mechanisms and clinical pathophysiology of maturity-onset diabetes of the young
Protein arginine methylation in mammals: who, what, and why
beta-Hydroxy-beta-methylglutaryl coenzyme A
Cellular transformation and guanine nucleotide exchange activity are catalyzed by a common domain on the dbl oncogene product
Sanfilippo disease type D: deficiency of N-acetylglucosamine-6-sulfate sulfatase required for heparan sulfate degradation
Tripeptidyl peptidase II is the major peptidase needed to trim long antigenic precursors, but is not required for most MHC class I antigen presentation
Mammalian nuclei become licensed for DNA replication during late telophase.
Lead-induced abnormalities of porphyrin metabolism. The relationship with iron deficiency.
1-Hydroxypropane-1,2,3-tricarboxylic acid
Methylation pharmacogenetics: catechol O-methyltransferase, thiopurine methyltransferase, and histamine N-methyltransferase
beta-Nicotinamide adenine dinucleotide phosphate
Nicotinamide adenine dinucleotide phosphate
Protein kinase C as a molecular machine for decoding calcium and diacylglycerol signals
The mechanism of regulation of hexokinase: new insights from the crystal structure of recombinant human brain hexokinase complexed with glucose and glucose-6-phosphate
MISCELLANEOUS Present with 998 molecules/cell in log phase SD medium.SIMILARITY Belongs to the eukaryotic RPC4/POLR3D RNA polymerase subunit family.
Neurotransmitter Clearance In The Synaptic Cleft
The cyclin-dependent kinase Cdc28p regulates distinct modes of Cdc6p proteolysis during the budding yeast cell cycle.
Rho guanine dissociation inhibitors: pivotal molecules in cellular signalling
COFACTOR Binds 2 copper ions per subunit.MISCELLANEOUS Present with 12000 molecules/cell in log phase SD medium.SIMILARITY Belongs to the CCS1 family.SIMILARITY Contains 1 HMA domain.
The Ras branch of small GTPases: Ras family members don't fall far from the tree
Identification and expression of a cDNA for human glycolate oxidase
LSm proteins form heptameric rings that bind to RNA via repeating motifs
Molecular genetics of mucopolysaccharidosis type IIIA and IIIB: Diagnostic, clinical, and biological implications
Cloning and characterization of a cDNA encoding human cardiolipin synthase (hCLS1)
Molecular mechanisms of MHC class I-antigen processing: redox considerations
Structure of the dual enzyme Ire1 reveals the basis for catalysis and regulation in nonconventional RNA splicing
MISCELLANEOUS Present with 1030 molecules/cell in log phase SD medium.SIMILARITY Belongs to the COM1/SAE2/CtIP family.
Cloning, characterization and chromosomal assignment of NBC4, a new member of the sodium bicarbonate cotransporter family
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An overview of sphingolipid metabolism: from synthesis to breakdown
Cell surface heparin binding protein HIP
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Differential activation of recombinant human acetyl-CoA carboxylases 1 and 2 by citrate
Tumor necrosis factor type 1 receptor associated protein 2
26S proteasome non-ATPase regulatory subunit 2
Multicatalytic endopeptidase complex subunit C5
Multicatalytic endopeptidase complex subunit C2
Multicatalytic endopeptidase complex subunit C13
Proteasome subunit beta type 8 precursor
26S proteasome non-ATPase regulatory subunit 11
Multicatalytic endopeptidase complex chain 7
Proteasome subunit beta type 9 precursor
26S proteasome non-ATPase regulatory subunit 1
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4-(2-aminophenyl)-2,4-dioxobutanoic acid
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Bone morphogenetic protein receptors and signal transduction
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Tyrosine kinase inhibitors of FGFR1 fusion mutants
26S proteasome non-ATPase regulatory subunit 13
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Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R)
26S proteasome non-ATPase regulatory subunit 7
26S proteasome non-ATPase regulatory subunit 8
Mutations in HYAL1, a member of a tandemly distributed multigene family encoding disparate hyaluronidase activities, cause a newly described lysosomal disorder, mucopolysaccharidosis IX
Proc. Natl. Acad. Sci. U.S.A. 96:6296-300
Interleukin-2 receptor signaling in regulatory T cell development and homeostasis
Multicatalytic endopeptidase complex subunit C9
Multicatalytic endopeptidase complex zeta chain
Multicatalytic endopeptidase complex epsilon chain
Proteasome subunit beta type 5 precursor
Defective CD320 causes methylmalonic aciduria
Multicatalytic endopeptidase complex beta chain
Proteasome subunit beta type 4 precursor
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Characterization of type II phosphatidylinositol 4-kinase isoforms reveals association of the enzymes with endosomal vesicular compartments
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26S proteasome non-ATPase regulatory subunit 4
Multicatalytic endopeptidase complex subunit C3
Multicatalytic endopeptidase complex delta chain
Proteasome subunit beta type 6 precursor
Proteasome regulatory particle subunit p44S10
26S proteasome non-ATPase regulatory subunit 6
Multicatalytic endopeptidase complex iota chain
26S proteasome non-ATPase regulatory subunit 10
Multicatalytic endopeptidase complex subunit C7-I
26S proteasome non-ATPase regulatory subunit 3
Multicatalytic endopeptidase complex chain Z
Proteasome subunit beta type 7 precursor
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26S proteasome non-ATPase regulatory subunit 12
Multicatalytic endopeptidase complex subunit C8
Probable 26S protease regulatory subunit 8
26S proteasome non-ATPase regulatory subunit 9
Water channel expression in human ADPKD kidneys
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DNA chain length dependence of formation and dynamics of hMutSalpha.hMutLalpha.heteroduplex complexes
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Ectonucleotide pyrophosphatase/phosphodiesterase 7 (ENPP7) hydrolyses sphingomyelin
Sphingomyelin phosphodiesterase 2 and 3 (SMPD2 and 3) hydrolyse sphingomyelin to ceramide (plasma membrane)
PHB and all-E-10PrP2 are combined into DHB by COQ2
Ceramide kinase (CERK) mediates the phosphorylation of ceramide
sphingosine 1-phosphate + H2O => sphingosine + orthophosphate [cytosolic - SGPP]
sphingosine +ATP => sphingosine 1-phosphate + ADP
Sphingomyelin phosphodiesterase (SMPD1) hydrolyses sphingomyelin to ceramide (lysosome)
sphingosine 1-phosphate => phosphoethanolamine + hexadec-2-enal
Synergistic activation of stress-activated protein kinase 1/c-Jun N-terminal kinase (SAPK1/JNK) isoforms by mitogen-activated protein kinase kinase 4 (MKK4) and MKK7
ChEBI:16500 1-phosphatidyl-1D-myo-inositol 5-phosphate
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Fractionation and properties of glutamic oxalacetic transaminase
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Crystal structure of alanine:glyoxylate aminotransferase and the relationship between genotype and enzymatic phenotype in primary hyperoxaluria type 1
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Maintaining cholesterol homeostasis: sterol regulatory element-binding proteins
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Crystal structures of human TBC1D1 and TBC1D4 (AS160) RabGTPase-activating protein (RabGAP) domains reveal critical elements for GLUT4 translocation
Endoplasmic reticulum-associated degradation of mammalian glycoproteins involves sugar chain trimming to Man6-5GlcNAc2
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Na+-dependent purine nucleoside transporter from human kidney: cloning and functional characterization
Am J Physiol Renal Physiol 273:1058-1065
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Distinct phosphotyrosines on a growth factor receptor bind to specific molecules that mediate different signaling pathways
amination of uridine 5'-triphosphate (UTP) to form cytidine 5'-triphosphate (CTP)
UTP + glutamine + ATP + H2O => CTP + glutamate + ADP + orthophosphate [CTPS]
UTP + glutamine + ATP + H2O => CTP + glutamate + ADP + orthophosphate [CTPS2]
Reduction of cytosolic ribonucleoside 5'-diphosphates to deoxyribonucleoside 5'-diphosphates (glutaredoxin)
NDP + reduced glutaredoxin => dNDP + oxidized glutaredoxin + H2O
Reduction of cytosolic ribonucleoside 5'-diphosphates to deoxyribonucleoside 5'-diphosphates (thioredoxin)
NDP + reduced thioredoxin => dNDP + oxidized thioredoxin + H2O
Reduction of nuclear ribonucleoside 5'-diphosphates to deoxyribonucleoside 5'-diphosphates (thioredoxin)
glutaredoxin (oxidized) + glutathione (reduced) => glutaredoxin (reduced) + glutathione (oxidized)
thioredoxin, oxidized (nucleus) <=> thioredoxin, oxidized (cytosol)
Isolation and characterization of argininosuccinate synthetase from human liver.
thioredoxin, reduced (cytosol) <=> thioredoxin, reduced (nucleus)
(d)NDP + ATP <=> (d)NTP + ADP [NME1,2,3]
(d)NTP + ADP <=> (d)NDP + ATP [NME1,2,3]
uracil + NADPH + H+ => 5,6-dihydrouracil + NADP+
reduction of uracil to form dihydrouracil
thymine + NADPH + H+ => 5,6-dihydrothymine + NADP+
reduction of thymine to form 5,6-Dihydrothymine
dUMP or TMP + ATP <=> dUDP or TDP + ADP [DTYMK]
phosphorylation of dUMP or TMP to dUDP or TDP
dUDP or TDP + ADP <=> dUMP or TMP + ATP [DTYMK]
(d)CMP or UMP + ATP <=> (d)CDP or UDP + ADP [CMPK1]
(d)CDP or UDP + ADP <=> (d)CMP or UMP + ATP [CMPK1]
Leber congenital amaurosis: genes, proteins and disease mechanisms
The stem cell factor receptor/c-Kit as a drug target in cancer
Critical role of novel Thr-219 autophosphorylation for the cellular function of PKCtheta in T lymphocytes
alanine + alpha-ketoglutarate <=> pyruvate + glutamate [GPT]
pyruvate + glutamate <=> alanine + alpha-ketoglutarate [GPT]
ADP-ribose + H2O => AMP + D-ribose 5-phosphate (cytosolic)
Cytosolic NUDT5 hydrolyses ADP-ribose to R5P and AMP
triphopsphoric acid 1-xanthosin-5'-yl ester
alanine + alpha-ketoglutarate <=> pyruvate + glutamate [GPT2]
pyruvate + glutamate <=> alanine + alpha-ketoglutarate [GPT2]
5'-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide (SAICAR) <=> 5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR) + fumarate
The biochemistry and physiology of nucleotides
5'-phosphoribosylformylglycinamidine (FGAM) + ATP => 5'-phosphoribosyl-5-aminoimidazole (AIR) + ADP + orthophosphate
Two intermembrane space TIM complexes interact with different domains of Tim23p during its import into mitochondria
5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide (FAICAR) <=> inosine 5'-monophosphate + H2O
5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR) + 10-formyltetrahydrofolate => 5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide (FAICAR) + tetrahydrofolate
xanthosine 5'-monophosphate (XMP) + L-glutamine + ATP + H2O => guanosine 5'-monophosphate (GMP) + L-glutamate + adenosine 5'-monophosphate (AMP) + pyrophosphate
XMP + L-Glutamine + ATP + H2O => GMP + L-Glutamate + AMP + pyrophosphate
Detection of the mitochondrial and catalytically active alanine aminotransferase in human tissues and plasma
inosine 5'-monophosphate (IMP) + NAD+ + H2O => xanthosine 5'-monophosphate (XMP) + NADH + H+
IMP + H2O + NAD+ => XMP + NADH + H+ [IMPDH1,2]
inosine 5'-monophosphate + L-aspartate + GTP => adenylosuccinate + guanosine 5'-diphosphate + orthophosphate
IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]
5-phosphoribosylamine + glycine + ATP => 5-phosphoribosylglycinamide (GAR) + ADP + orthophosphate
5-Phosphoribosylamine + Glycine + ATP => GAR + ADP + Pi
5'-phosphoribosylformylglycinamide (FGAR) + L-glutamine + ATP + H2O => 5'-phosphoribosylformylglycinamidine (FGAM) + L-glutamate + adenosine 5'-diphosphate + orthophosphate
FGAR + L-Glutamine + ATP + H2O => FGAM + L-Glutamate + ADP + Pi
5-phosphoribosylglycinamide (GAR) + 10-formyl-tetrahydrofolate => 5'-phosphoribosylformylglycinamide (FGAR) + tetrahydrofolate
Reducing equivalents from beta-oxidation of fatty acids transfer to ETF
Transfer of electrons through the succinate dehydrogenase complex
2-oxoglutarate + 4-hydroxybutyrate <=> (R)-2-hydroxyglutarate + succinate semialdehyde
(R)-2-hydroxyglutarate + succinate semialdehyde <=> 2-oxoglutarate + 4-hydroxybutyrate
5-phospho-alpha-D-ribose 1-diphosphate (PRPP) + H2O + L-glutamine <=> 5-phosphoribosylamine + L-glutamate +pyrophosphate
PRPP + H2O + L-Glutamine => 5-Phosphoribosylamine + L-Glutamate + PPi
Dissociation of phosphoribosyl pyrophosphate amidotransferase tetramer
Formation of phosphoribosyl pyrophosphate amidotransferase tetramer
Transfer of electrons from ETF to ubiquinone by ETF-QO
(R)-2-hydroxyglutarate + FAD => 2-oxoglutarate + FADH2
(S)-Malate + NAD+ <=> Oxaloacetate + NADH + H+
Activation by Cdc42 and PIP(2) of Wiskott-Aldrich syndrome protein (WASp) stimulates actin nucleation by Arp2/3 complex
(deoxy)cytidine + H2O => (deoxy)uridine + NH4+ [CDA]
deamination of 2'-Deoxycytidine to 2'-Deoxyuridine
decarboxylation of Orotidine 5'-phosphate to form Uridine 5'-phosphate
orotidine 5'-monophosphate => uridine 5'-monophosphate + CO2
dUMP + N5,N10-methylene tetrahydrofolate => TMP + dihydrofolate
hydrolysis of 2'-deoxyuridine 5'-triphosphate to form 2'-deoxyuridine 5'-phosphate
carbamoyl phosphate + L-aspartate <=> N-carbamoyl L-aspartate + orthophosphate
carbamoyl phosphate and L-aspartate combine to form N-Carbamoyl-L-aspartate
L-glutamine + 2 ATP + HCO3- + H2O => carbamoyl phosphate + L-glutamate + 2 ADP + orthophosphate
bicarbonate and glutamine combine to form carbamoyl phosphate
orotate + 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) <=> orotidine 5'-monophosphate (OMP) + pyrophosphate
phosphoribosylation of orotate to form oritidine 5'-phosphate (OMP)
condensation of N-Carbamoyl-L-aspartate to form (S)-Dihydroorotate (ring closure)
N-carbamoyl L-aspartate + H+ <=> (S)-dihydroorotate + H2O
Comparison of the RNA polymerase III transcription machinery in Schizosaccharomyces pombe, Saccharomyces cerevisiae and human.
Characterization of two human genes encoding acyl coenzyme A:cholesterol acyltransferase-related enzymes
Analysis of the open region of RNA polymerase II transcription complexes in the early phase of elongation.
Apoptosis and disease: a life or death decision
Hereditary disorders of connective tissue
(deoxy)inosine + orthophosphate <=> hypoxanthine + (deoxy)ribose 1-phosphate [NP]
(deoxy)guanosine + orthophosphate <=> guanine + (deoxy)ribose 1-phosphate [NP]
Abcg2/Bcrp1 mediates the polarized transport of antiretroviral nucleosides abacavir and zidovudine
hypoxanthine + (deoxy)ribose 1-phosphate <=> (deoxy)inosine + orthophosphate [NP]
guanine + (deoxy)ribose 1-phosphate <=> (deoxy)guanosine + orthophosphate [NP]
Deamination of N6-methyl-AMP to form IMP
N6-methyl-AMP + H2O => IMP + methylamine
(2'-deoxy)adenosine + ATP => (d)AMP + ADP [ADK]
(2'-deoxy)adenosine + H2O => (2'-deoxy)inosine + NH3 [ADA]
adenylosuccinate => adenosine 5'-monophosphate + fumarate
LKB1 phosphorylates the alpha subunit of AMPK heterotrimer
AMP binds to gamma subunit of AMP kinase heterotrimer
5,10-methenyltetrahydrofolate polyglutamate
Characterization of a family of nucleolar SUMO-specific proteases with preference for SUMO-2 or SUMO-3
MDMQ10H2 is methylated to DMQ10H2 by COQ5
DMQ10H2 is hydroxylated to DeMQ10H2 by COQ7
ADP-ATP translocase maintains a high ADP:ATP ratio in the matrix
Activation of PP2A by Xylulose-5-phosphate
Transport of Extracellular Glucose to the Cytosol by GLUT1 and GLUT2
PRMT6-mediated methylation of R2 in histone H3 antagonizes H3 K4 trimethylation
phosphatidylinositol 1,3,4,5-tetrakisphosphate
1D-myo-inositol 1,3,4,6-tetrakisphosphate
PTIP associates with MLL3- and MLL4-containing histone H3 lysine 4 methyltransferase complex
How mitochondria produce reactive oxygen species
On the specificity of the tricarboxylate carrier system in rat liver mitochondria
Acetyl-CoA + H2O + Oxaloacetate => Citrate + CoA
Aflatoxin B1 endo glutathione conjugate [ChEBI:78581]
Succinate <=> Fumarate (with FAD redox reaction on enzyme)
Aflatoxin B1 exo-cysteinylglycine conjugate
Aflatoxin B1 exo-cysteinylglycine conjugate [ChEBI:78584]
Aflatoxin B1 exo glutathione conjugate [ChEBI:78587]
Oxidative decarboxylation of alpha-ketoglutarate to succinyl CoA by alpha-ketoglutarate dehydrogenase
alpha-ketoglutarate + CoASH + NAD+ => succinyl-CoA + CO2 + NADH + H+
ADP + Orthophosphate + Succinyl-CoA <=> ATP + Succinate + CoA
isocitrate + NAD+ => alpha-ketoglutarate + CO2 + NADH + H+ [IDH3]
isocitrate + NADP+ => alpha-ketoglutarate + CO2 + NADPH + H+ [IDH2]
Dynamic binding of PKA regulatory subunit RI alpha
PDK-catalyzed phosphorylation (inactivation) of PDC E1 alpha subunit
Inactivation of PDC by phosphorylation of PDC E1 alpha component
Oxidative decarboxylation of pyruvate to acetyl CoA by pyruvate dehydrogenase
pyruvate + CoASH + NAD+ => acetylCoA + CO2 + NADH + H+
Plk1 docking to GRASP65 phosphorylated by Cdk1 suggests a mechanism for Golgi checkpoint signalling
Characterization of a leukotriene C4 export mechanism in human platelets: possible involvement of multidrug resistance-associated protein 1
GCH1 reduces GTP to dihydroneopterin triphosphate
Cytosolic PYR is transported to the mitochondrial matrix by MPC1:MPC2
PYR + H+ (cytosol) => PYR + H+ (mitochondrial matrix)
eNOS translocation from Golgi to Caveolae
Uncoupled eNOS favours the formation of superoxide
depalmitoylated eNOS translocates from plasma membrane
MyD88 dependent cascade initiated on endosome
Tyrosine phosphorylation of MB-1, B29, and HS1 proteins in human B cells following receptor crosslinking
Aflatoxin B1 endo-cysteinylglycine conjugate
Aflatoxin B1 endo-cysteinylglycine conjugate [ChEBI:78579]
(R)-2-Hydroxy-3-(phosphonooxy)-1-monoanhydridewith phosphoric propanoic acid
2-Hydroxy-1,2,3-propanetricarboxylic acid
Post-transcriptional regulation of gene expression by degradation of messenger RNAs
Functional interaction of proliferating cell nuclear antigen with MSH2-MSH6 and MSH2-MSH3 complexes
Dephosphorylation and activation of a p34cdc2/cyclin B complex in vitro by human CDC25 protein
Human carbamylphosphate synthetase I. Stabilization, purification, and partial characterization of the enzyme from human liver.
Frequent and focal FGFR1 amplification associates with therapeutically tractable FGFR1 dependency in squamous cell lung cancer
Mechanisms of accurate translesion synthesis by human DNA polymerase eta.
B56-containing PP2A dephosphorylate ERK and their activity is controlled by the early gene IEX-1 and ERK
Evidence for a mechanism of repression of heat shock factor 1 transcriptional activity by a multichaperone complex
(ethanolamineP) mannose (a1-2) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI
mannose (a1-2) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI
(ethanolamineP) mannose (a1-2) (ethanolamineP) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI
ditrans, polycis-polyprenol pyrophosphate
Identification of covalently bound amino-terminal myristic acid in endothelial nitric oxide synthase
mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI
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eukaryotic translation initiation factor 2, subunit 2
Eukaryotic translation initiation factor 2 subunit 2
eukaryotic translation initiation factor 2 beta subunit
Eukaryotic translation initiation factor 3 subunit 2
translation initiation factor 2 alpha subunit
Eukaryotic translation initiation factor 2 subunit 1
translation initiation factor 2, subunit 1
Eukaryotic translation initiation factor 2 alpha subunit
Eukaryotic translation initiation factor 2 gamma subunit
eukaryotic translation initiation factor 2, subunit 3
Eukaryotic translation initiation factor 2 subunit 3
Eukaryotic translation initiation factor 4 gamma
Eukaryotic translation initiation factor 1A, X-chromosomal
eukaryotic translation initiation factor 1A
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New insights into the mechanism of heat shock response activation
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Eukaryotic translation initiation factor 4E
Congenital disorder of glycosylation type Ik (CDG-Ik): a defect of mannosyltransferase I
TAX-responsive enhancer element binding protein 107
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Activation of gene expression by SREBF (SREBP)
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RNA Pol II CTD phosphorylation and interaction with CE
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Deficiency of GDP-Man:GlcNAc2-PP-dolichol mannosyltransferase causes congenital disorder of glycosylation type Ik
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Critical role for Ebf1 and Ebf2 in the adipogenic transcriptional cascade
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Rat1p and Xrn1p are functionally interchangeable exoribonucleases that are restricted to and required in the nucleus and cytoplasm, respectively
Epstein-Barr virus small RNA associated protein
Concerted action of two cation filters in the aquaporin water channel
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Expression of the AQP-1 water channel in normal human tissues: a semiquantitative study using tissue microarray technology
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A yeast chromosomal origin of DNA replication defined by multiple functional elements.
(24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA + NAD+ => 3alpha,7alpha-dihydroxy-5beta-cholest-24-one-CoA + NADH + H+
(24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA is oxidized to 3alpha,7alpha-dihydroxy-5beta-cholest-24-one-CoA
(24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA + NAD+ => 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-one-CoA + NADH + H+
(24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA is oxidized to 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-one-CoA
Cholesterol is hydroxylated to 25-hydroxycholesterol
Hydrolysis of choloyl-CoA to cholate and CoASH
1-acyl LPA is acylated to PA by AGPAT5 (OM)
Reduction of androstenedione to testosterone
Defective MUT causes methylmalonic aciduria mut type
PC is hydrolyzed to PA and choline by PLD1/2
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Heat shock factor 4a (HSF4a) represses HSF2 expression and HSF2-mediated transcriptional activity
Communication between the synapse and the nucleus in neuronal development, plasticity, and disease
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The Akt activation inhibitor TCN-P inhibits Akt phosphorylation by binding to the PH domain of Akt and blocking its recruitment to the plasma membrane
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4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form cholesta-8(9),24-dien-3-one (zymosterone)
4-carboxycholesta-8(9),24-dien-3beta-ol + NAD+ => cholesta-8(9),24-dien-3-one (zymosterone) + CO2 + NADH + H+
Mechanisms of transcription-coupled DNA repair.
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4,4-dimethylcholesta-8(9),14,24-trien-3beta-ol + NADPH + H+ => 4,4-dimethylcholesta-8(9),24-dien-3beta-ol + NADP+ [TM7SF2]
4,4-dimethylcholesta-8(9),14,24-trien-3beta-ol is reduced to 4,4-dimethylcholesta-8(9),24-dien-3beta-ol [TM7SF2]
4,4-dimethylcholesta-8(9),14,24-trien-3beta-ol + NADPH + H+ => 4,4-dimethylcholesta-8(9),24-dien-3beta-ol + NADP+ [LBR]
4,4-dimethylcholesta-8(9),14,24-trien-3beta-ol is reduced to 4,4-dimethylcholesta-8(9),24-dien-3beta-ol [LBR]
4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one
4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol + NAD+ => 4-methylcholesta-8(9),24-dien-3-one + CO2 + NADH + H+
4,4-dimethylcholesta-8(9),24-dien-3beta-ol + 3 NADPH + 3 H+ + 3 O2 => 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol + 3 NADP+ + 4 H2O
4,4-dimethylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol
Reduction of presqualene diphosphate to form squalene
lanosterol + 3 NADPH + 3 H+ + 3 O2 => 4,4-dimethylcholesta-8(9),14,24-trien-3beta-ol + 3 NADP+ + 4 H2O + formate
Lanosterol is oxidatively demethylated to 4,4-dimethylcholesta-8(9),14,24-trien-3beta-ol
Squalene 2,3-epoxide cyclizes, forming lanosterol
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4-methylcholesta-8(9),24-dien-3beta-ol + 3 NADPH + 3 H+ + 3 O2 => 4-carboxycholesta-8(9),24-dien-3beta-ol + 3 NADP+ + 4 H2O
4-methylcholesta-8(9),24-dien-3beta-ol is oxidized to 4-carboxycholesta-8(9),24-dien-3beta-ol
4-methylcholesta-8(9),24-dien-3-one + NADPH + H+ => 4-methylcholesta-8(9),24-dien-3beta-ol + NADP+
4-methylcholesta-8(9),24-dien-3-one is reduced to 4-methylcholesta-8(9),24-dien-3beta-ol
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3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA (THCA-CoA) is hydrated to (24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA
3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA + H2O => (24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA
25(S) 3alpha,7alpha-dihydroxy-5beta-cholest-24-enoyl-CoA is hydrated to (24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA
25(S) 3alpha,7alpha-dihydroxy-5beta-cholest-24-enoyl-CoA + H2O => (24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA
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Insulin action on glucose transporters through molecular switches, tracks and tethers
25(S) THCA-CoA is dehydrogenated to 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA (THCA-CoA)
Expression of Squalene Monooxygenase (SQLE)
Expression of Lathosterol Oxidase (SC5D, SC5DL)
Expression of Farnesyl Diphosphate Synthase (FDPS)
cholesta-5,7,24-trien-3beta-ol + NADPH + H+ => desmosterol + NADP+
Cholesta-5,7,24-trien-3beta-ol is reduced to desmosterol
cholesta-7,24-dien-3beta-ol + NADPH + H+ + O2 => cholesta-5,7,24-trien-3beta-ol + NADP+ + 2 H2O
Cholesta-7,24-dien-3beta-ol is desaturated to form cholesta-5,7,24-trien-3beta-ol
zymosterone (cholesta-8(9),24-dien-3-one) + NADPH + H+ => zymosterol (cholesta-8(9),24-dien-3beta-ol) + NADP+
Zymosterone (cholesta-8(9),24-dien-3-one) is reduced to zymosterol (cholesta-8(9),24-dien-3beta-ol)
25(S) DHCA-CoA is dehydrogenated to 25(S) 3alpha,7alpha-dihydroxy-5beta-cholest-24-enoyl-CoA
25(S) DHCA-CoA + O2 => 25(S) 3alpha,7alpha-dihydroxy-5beta-cholest-24-enoyl-CoA + H2O2
A functional link between the histone demethylase PHF8 and the transcription factor ZNF711 in X-linked mental retardation
sphinganine + stearyl-CoA => dihydroceramide + CoASH
sphinganine 1-phosphate + H2O => sphinganine + orthophosphate
3-ketosphinganine + NADPH + H+ => sphinganine + NADP+
palmitoyl-CoA + serine => 3-ketosphinganine + CoASH + CO2
phytoceramide + H2O => stearate + phytosphingosine
sphinganine (dihydrosphingosine) +ATP => sphinganine 1-phosphate + ADP
Congenital Disorders of Glycosylation Overview
5S-HpETE is reduced to 5S-HETE by GPX1/2/4
15S-HpETE is reduced to 15S-HETE by GPX1/2/4
12R-HpETE is reduced to 12R-HETE by GPX1/2/4
12S-HpETE is reduced to 12S-HETE by GPX1/2/4
sphinganine 1-phosphate => phosphoethanolamine + hexadecanal
The human renal sodium sulfate cotransporter (SLC13A1; hNaSi-1) cDNA and gene: organization, chromosomal localization, and functional characterization
eukaryotic translation initiation factor 3 subunit 10
eukaryotic translation initiation factor 3 subunit 9
Eukaryotic translation initiation factor 3 subunit 4
eukaryotic translation initiation factor 3 subunit 8
In vivo binding of active heat shock transcription factor 1 to human chromosome 9 heterochromatin during stress
The Mammalian Proteins MMS19, MIP18, and ANT2 Are Involved in Cytoplasmic Iron-Sulfur Cluster Protein Assembly
Cleavage of the gamma-glutamyl bond of LTC4 forms LTD4
Cell cycle- and cell growth-regulated proteolysis of mammalian CDC6 is dependent on APC-CDH1.
LTC4 is exported from the cytosol by ABCC1
ABCC1 mediates LTC4 export from the cell
Translocation of tetracosapentaenoyl-CoA to peroxisomes
Prostaglandin E synthase isomerizes PGH2 to PGE2
Elongation of arachidonyl-CoA to docosatetraenoyl-CoA
Elongation of docosatetraenoyl-CoA to tetracosatetraenoyl-CoA
tetra-mu3-sulfido-tetrairon [ChEBI:49883]
Activation of linoleic acid to linoleoyl-CoA
Elongation of gamma-lenolenoyl-CoA to dihomo-gamma-lenolenoyl-CoA
Conversion of DHA-CoA to docosahexaenoic acid (DHA)
Activated PKC gamma (name copied from entity in Homo sapiens)
beta-catenin destruction complex: insights and questions from a structural perspective
F-actin capping protein (name copied from entity in Homo sapiens)
Colorectal cancer and genetic alterations in the Wnt pathway
Protein kinase C, novel isoforms:DAG (name copied from entity in Homo sapiens)
Activated PKC beta (name copied from entity in Homo sapiens)
PDK1:AKT:PIP3 (name copied from entity in Homo sapiens)
Multidrug resistance- associated protein MGr1-Ag
PIP3:PDK1:AKT:PKC zeta (name copied from entity in Homo sapiens)
PIP3:PDK1:AKT:p(T410)-PKC zeta (name copied from entity in Homo sapiens)
Oxidation of tetracosapentaenoyl-CoA to delta2-tetracosaheptaenoyl-CoA
Hydration of delta2-tetracosaheptaenoyl-CoA to 3-hydroxy tetracosahexaenoyl-CoA
Dehydrogenation of 3-hydroxy tetracosahexaenoyl-CoA
Formation of DHA-CoA catalysed by 3-ketoacyl-CoA thiolase
PI3P is dephosphorylated to PI by MTM[3] at the late endosome membrane
Activation of alpha-linolenic acid to alpha-linolenoyl-CoA
Elongation of stearidonoyl-CoA to eicosatetraenoyl-CoA
Elongation of eicosapentaenoyl-CoA to docosapentaenoyl-CoA
Elongation of docosapentaenoyl-CoA to tetracosapentaenoyl-CoA
Translocation of tetracosahexaenoyl-CoA to peroxisomes
PI(3,5)P2 is dephosphorylated to PI5P by MTM[3] at the late endosome membrane
PI is phosphorylated to PI5P by PIKFYVE at the late endosome membrane
PI3P is phosphorylated to PI(3,5)P2 by PIKFYVE at the late endosome membrane
PI(3,5)P2 is dephosphorylated to PI3P by FIG4 at the late endosome membrane
PI is phosphorylated to PI3P by PIK3C2A/3 at the late endosome membrane
PI4P is dephosphorylated to PI by SYNJ at the plasma membrane
PI is phosphorylated to PI3P by PIK3C2A/3 at the early endosome membrane
PI is phosphorylated to PI4P by PI4K2A/B at the early endosome membrane
PI3P is phosphorylated to PI(3,5)P2 by PIKFYVE at the early endosome membrane
PI(3,5)P2 is dephosphorylated to PI3P by FIG4 at the early endosome membrane
Structures of active conformations of Gi alpha 1 and the mechanism of GTP hydrolysis
PI3P is phosphorylated to PI(3,5)P2 by PIKFYVE at the Golgi membrane
PI3P is dephosphorylated to PI by SACM1L at the Golgi membrane
PI(4,5)P2 is dephosphorylated to PI4P by SYNJ/INPP5[1] at the plasma membrane
PI(3,5)P2 is dephosphorylated to PI3P by FIG4 at the Golgi membrane
PI is phosphorylated to PI4P by PI4K2A/B at the plasma membrane
PI5P is phosphorylated to PI(4,5)P2 by PIP4K2A/B at the plasma membrane
The kinesin-like protein CENP-E is kinetochore-associated throughout poleward chromosome segregation during anaphase-A
PI3P is dephosphorylated to PI by SYNJ/MTM[1] at the plasma membrane
PI3P is phosphorylated to PI(3,4)P2 by PIP4K2/5K1 at the plasma membrane
PI(3,5)P2 is dephosphorylated to PI5P by SYNJ/MTM[1] at the plasma membrane
PI(3,5)P2 is dephosphorylated to PI3P by SYNJ at the plasma membrane
CL and 1-acyl LPE are converted to MLCL and PE by TAZ (IM) (Reversible)
MLCL and PE are converted to CL and 1-acyl LPE by TAZ (IM) (Reversible)
CL and 1-acyl LPC are converted to MLCL and PC by TAZ (IM) (Reversible)
PI is phosphorylated to PI3P by PIK3C2A/3 at the Golgi membrane
PI4P is dephosphorylated to PI by SACM1L at the Golgi membrane
PI is phosphorylated to PI4P by PI4KA/2A/2B at the Golgi membrane
PI4P is dephosphorylated to PI by SACM1L at the ER membrane
PI is phosphorylated to PI4P by PI4KA/2B at the ER membrane
Systematic analysis of myotubularins: heteromeric interactions, subcellular localisation and endosome related functions
A role for the endoplasmic reticulum protein retrotranslocation machinery during crosspresentation by dendritic cells
Multistep regulation of DNA replication by Cdk phosphorylation of HsCdc6.
An essential role of Sam50 in the protein sorting and assembly machinery of the mitochondrial outer membrane
Expression cloning and characterization of a cDNA encoding a novel membrane protein required for the formation of O-acetylated ganglioside: a putative acetyl-CoA transporter
PC is transphosphatidylated to PG by PLD1-4/6
2-acyl LPG is acylated to PG by CRLS1 (IM)
1-acyl LPG is acylated to PG by CRLS1 (IM)
MLCL and PC are converted to CL and 1-acyl LPC by TAZ (IM) (Reversible)
PG and CDP-DAG are converted to CL by CRLS1
Magnesium transporters: properties, regulation and structure
The human homolog of the rat inositol phosphate multikinase is an inositol 1,3,4,6-tetrakisphosphate 5-kinase
Cho is phosphorylated to PCho by CHK dimer
CDP-Cho and DAG are converted to PC by CHPT1 at the Golgi membrane
CDP-Cho and DAG are converted to PC by CEPT1 at the ER membrane
PCho and CTP are condensed to CDP-Cho by PCYT1 dimer
GPCho is hydrolyzed to Cho and G3P by GPCPD1
Vitamins B6 activation to pyridoxal phosphate
GPETA is hydrolyzed to ETA and G3P by GPCPD1
CDP-ETA and DAG are converted to PE by CEPT1/EPT1
The hexameric eukaryotic MCM helicase: building symmetry from nonidentical parts
PETA and CTP are condensed to CDP-ETA by PCY2
2-MAG is hydrolyzed to fatty acid and glycerol by MGLL
ETA is phosphorylated to PETA by CHK/ETNK
Cloning, characterization, and chromosomal mapping of human aquaporin of collecting duct
Metabolism of water-soluble vitamins and cofactors
Glycine-rich loop of mitochondrial processing peptidase alpha-subunit is responsible for substrate recognition by a mechanism analogous to mitochondrial receptor Tom20
Functional expansion of aminoacyl-tRNA synthetases and their interacting factors: new perspectives on housekeepers
Transcription termination factor La is also an initiation factor for RNA polymerase III.
Lysosomal disorders: from storage to cellular damage
The Golgi mitotic checkpoint is controlled by BARS-dependent fission of the Golgi ribbon into separate stacks in G2
Bile salt transporters: molecular characterization, function, and regulation
Vesicle pools, docking, priming, and release
Purification and characterization of human plasma glutathione peroxidase: a selenoglycoprotein distinct from the known cellular enzyme
NAGLU mutations underlying Sanfilippo syndrome type B
Structure-function analysis of human Spt4: evidence that hSpt4 and hSpt5 exert their roles in transcriptional elongation as parts of the DSIF complex.
Bi-directional routing of DNA mismatch repair protein human exonuclease 1 to replication foci and DNA double strand breaks
Translocation after synthesis of a four-nucleotide RNA commits RNA polymerase II to promoter escape.
The spindle checkpoint: structural insights into dynamic signalling
Signal transduction via vascular endothelial growth factor (VEGF) receptors and their roles in atherogenesis
Cobalamin (Cbl, vitamin B12) transport and metabolism
High incidence of translocations t(11;14)(q13;q32) and t(4;14)(p16;q32) in patients with plasma cell malignancies
Isolation and characterization of a human thiamine pyrophosphokinase cDNA
Diseases associated with visual transduction
Developmental control of a G1-S transcriptional program in Drosophila
FGFR3-related dwarfism and cell signaling
Molecular cloning of human thiamin pyrophosphokinase
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Oxidation of tamoxifen by human flavin-containing monooxygenase (FMO) 1 and FMO3 to tamoxifen-N-oxide and its novel reduction back to tamoxifen by human cytochromes P450 and hemoglobin
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Activation of ATF6 and an ATF6 DNA binding site by the endoplasmic reticulum stress response
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Protein kinase C phosphorylation of syntaxin 4 in thrombin-activated human platelets
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D-myo-Inositol 1,3,4,5,6-pentakisphosphate
1D-myo-Inositol 1,3,4,5,6-pentakisphosphate [ChEBI:807]
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3alpha,7alpha,12alpha-Trihydroxy-5beta-cholanic acid
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phosphatidylinositol 1,4,5-trisphosphate
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Human glutamine phosphoribosylpyrophosphate amidotransferase. Two molecular forms interconvertible by purine ribonucleotides and phosphoribosylpyrophosphate
Endocytosis, recycling, and regulated exocytosis of glucose transporter 4
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Identification of human intestinal alkaline sphingomyelinase as a novel ecto-enzyme related to the nucleotide phosphodiesterase family
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Dynamics and function of phospholipase D and phosphatidic acid during phagocytosis
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Characterization of human PLD2 and the analysis of PLD isoform splice variants
(S)-alpha-Amino-1H-imidazole-4-propionic acid
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Structure-function analysis of Friedreich's ataxia mutants reveals determinants of frataxin binding and activation of the Fe-S assembly complex
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Purification and properties of uroporphyrinogen III synthase from human erythrocytes
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Novel inositol polyphosphate 5-phosphatase localizes at membrane ruffles
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Cloning and characterization of the human phosphoinositide-specific phospholipase C-beta 1 (PLC beta 1)
Polycomb mediated epigenetic silencing and replication timing at the INK4a/ARF locus during senescence
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ChEBI:16290 5alpha-cholesta-7,24-dien-3beta-ol
Analysis of dolichol in human tissues by high pressure liquid chromatography
Polymeric chains of SUMO-2 and SUMO-3 are conjugated to protein substrates by SAE1/SAE2 and Ubc9
A transforming mutation in the pleckstrin homology domain of AKT1 in cancer
Mitogen-activated protein kinase kinase 1-dependent Golgi unlinking occurs in G2 phase and promotes the G2/M cell cycle transition
Phosphatidylinositol-4-phosphate 5-kinase isozymes catalyze the synthesis of 3-phosphate-containing phosphatidylinositol signaling molecules
Clinical and genetic spectrum of pyruvate dehydrogenase deficiency: dihydrolipoamide acetyltransferase (E2) deficiency
Molecular cloning of human mitochondrial glycerophosphate dehydrogenase gene: genomic structure, chromosomal localization, and existence of a pseudogene
hMutSalpha forms an ATP-dependent complex with hMutLalpha and hMutLbeta on DNA
Presentation of cytosolic antigens via MHC class II molecules
Common and distinct elements in cellular signaling via EGF and FGF receptors
4-Trimethylammoniobutanoate [ChEBI:16244]
Proinflammatory activities of leptin in non-autoimmune conditions
Glycyl tRNA synthetase mutations in Charcot-Marie-Tooth disease type 2D and distal spinal muscular atrophy type V
Ror-family receptor tyrosine kinases in noncanonical Wnt signaling: their implications in developmental morphogenesis and human diseases
The structure of a human p110alpha/p85alpha complex elucidates the effects of oncogenic PI3Kalpha mutations
Role of cysteine-82 in the catalytic mechanism of human S-adenosylmethionine decarboxylase
UDP-N-acetyl-D-glucosamine [ChEBI:16264]
(S)-alpha-amino-beta-(3-indolyl)-propionic acid
(S)-2-Amino-3-(p-hydroxyphenyl)propionic acid
Delivery of yeast telomerase to a DNA break depends on the recruitment functions of Cdc13 and Est1
(S)-alpha-amino-beta-phenylpropionic acid
Mutations in the X-linked pyruvate dehydrogenase (E1) alpha subunit gene (PDHA1) in patients with a pyruvate dehydrogenase complex deficiency
Activation and detoxication of aflatoxin B1
Neural cell adhesion molecule L1: signaling pathways and growth cone motility
Mutations in TMEM76* cause mucopolysaccharidosis IIIC (Sanfilippo C syndrome)
Topology of acyltransferase motifs and substrate specificity and accessibility in 1-acyl-sn-glycero-3-phosphate acyltransferase 1
(IscS-IscU)2 complex structures provide insights into Fe2S2 biogenesis and transfer
Mini-review: Specificity and expression of CIITA, the master regulator of MHC class II genes
Molecular cloning, sequencing and expression of cDNA encoding human trehalase
Functional characterization and localization of AQP3 in the human colon
The ins and outs of IgE-dependent mast-cell exocytosis
Synthesis of IP2, IP, and Ins in the cytosol
cis-Delta(9,12)-octadecadienoyl-coenzyme A
Identification of a member of the MAPKKK family as a potential mediator of TGF-beta signal transduction
The ARF1 GTPase-activating protein: zinc finger motif and Golgi complex localization
New initiation factor activity required for globin mRNA translation.
Structure and expression of a complementary DNA for the nuclear coded precursor of human mitochondrial ornithine transcarbamylase.
Protein kinase G mediates vascular endothelial growth factor-induced Raf-1 activation and proliferation in human endothelial cells
Getting in and out from calnexin/calreticulin cycles
The polo-like kinase Plx1 is required for activation of the phosphatase Cdc25C and cyclin B-Cdc2 in Xenopus oocytes
Mitotic phosphorylation of Golgi reassembly stacking protein 55 by mitogen-activated protein kinase ERK2
A new biochemical subtype of the Sanfilippo syndrome: characterization of the storage material in cultured fibroblasts of Sanfilippo C patients
A novel quality control compartment derived from the endoplasmic reticulum
Mutational analysis of the transcription start site of the yeast tRNA(Leu3) gene.
Closing the gap: identification of human 3-ketosteroid reductase, the last unknown enzyme of mammalian cholesterol biosynthesis
Biotransformation of Aflatoxin B1 and Its Relationship with the Differential Toxicological Response to Aflatoxin in Commercial Poultry Species,
Aflatoxins - Biochemistry and Molecular Biology (Book)
Polyamines: metabolism and implications in human diseases
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Frataxin and mitochondrial FeS cluster biogenesis
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Activating E17K mutation in the gene encoding the protein kinase AKT1 in a subset of squamous cell carcinoma of the lung
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Translocation of lipid-linked oligosaccharides across the ER membrane requires Rft1 protein
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MHC II and the endocytic pathway: regulation by invariant chain
Biosynthesis of A2E, implicated in retinal degradation
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Cytosolic iron-sulfur cluster assembly (CIA) system: factors, mechanism, and relevance to cellular iron regulation
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Motor-free mitochondrial presequence translocase drives membrane integration of preproteins
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The t(1;9)(p34;q34) and t(8;12)(p11;q15) fuse pre-mRNA processing proteins SFPQ (PSF) and CPSF6 to ABL and FGFR1
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Peptides corresponding to the N and C termini of IkappaB-alpha, -beta, and -epsilon as probes of the two catalytic subunits of IkappaB kinase, IKK-1 and IKK-2
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Regulation of PAK-2p34 activity by PS-GAP/RHG10
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Kinetics and mechanism of the reduction of ferricytochrome c by the superoxide anion
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Dissecting the role of 5'-AMP for allosteric stimulation, activation, and deactivation of AMP-activated protein kinase
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Three-dimensional structure of the anaphase-promoting complex
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On the mechanism of preprotein import by the mitochondrial presequence translocase
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Purification, cloning, complementary DNA structure, and predicted amino acid sequence of human estradiol 17 beta-dehydrogenase
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Signal transduction pathways mediated by the interaction of CpG DNA with Toll-like receptor 9
Template boundary definition in mammalian telomerase
TIR domains, which are conserved among all TLRs. Recent accumulating
The role of Hsp70 in conferring unidirectionality on protein translocation into mitochondria
A regulatory role for 1-acylglycerol-3-phosphate-O-acyltransferase 2 in adipocyte differentiation
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Mechanism of Cu,Zn-superoxide dismutase activation by the human metallochaperone hCCS
Protein ligands to HuR modulate its interaction with target mRNAs in vivo
Opposing roles for ATF6alpha and ATF6beta in endoplasmic reticulum stress response gene induction
A multifactor complex of eukaryotic initiation factors, eIF1, eIF2, eIF3, eIF5, and initiator tRNA(Met) is an important translation initiation intermediate in vivo.
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Dealing with methionine/homocysteine sulfur: cysteine metabolism to taurine and inorganic sulfur
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Mutation of a putative mitochondrial iron transporter gene (ABC7) in X-linked sideroblastic anemia and ataxia (XLSA/A)
Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription.
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Dephosphorylation of human p34cdc2 kinase on both Thr-14 and Tyr-15 by human cdc25B phosphatase
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Carnitine palmitoyltransferase II deficiency: structure of the gene and characterization of two novel disease-causing mutations
Jmjd6 catalyses lysyl-hydroxylation of U2AF65, a protein associated with RNA splicing
Docosapentaenoic acid (22:5, n-3), an elongation metabolite of eicosapentaenoic acid (20:5, n-3), is a potent stimulator of endothelial cell migration on pretreatment in vitro
Prostaglandins Leukot Essent Fatty Acids 54:319-25
Central insulin and leptin-mediated autonomic control of glucose homeostasis
The metabolism of 7,10,13,16,19-docosapentaenoic acid to 4,7,10,13,16,19-docosahexaenoic acid in rat liver is independent of a 4-desaturase
glutamate + ATP + NADPH + H+ => L-glutamate gamma-semialdehyde + NADP+ + ADP + orthophosphate [P5CS]
L-1-pyrroline-5-carboxylate + NADPH + H+ => proline + NADP+
ornithine + alpha-ketoglutarate <=> glutamate + L-glutamate gamma-semialdehyde [OAT]
glutamate + L-glutamate gamma-semialdehyde <=> ornithine + alpha-ketoglutarate [OAT]
oxaloacetate + glutamate <=> aspartate + alpha-ketoglutarate [GOT1]
aspartate + alpha-ketoglutarate <=> oxaloacetate + glutamate [GOT2]
glutamine + pyruvate => 2-oxoglutaramate + alanine
glutamate + NAD(P)+ => alpha-ketoglutarate + NH4+ + NAD(P)H + H+ [GLUD1]
alpha-ketoglutarate + NH4+ + NAD(P)H + H+ <=> glutamate + NAD(P)+ [GLUD1]
aspartate + glutamine + ATP <=> asparagine + glutamate + AMP + pyrophosphate [ASNS]
Identification and characterization of human mitochondrial tryptophanyl-tRNA synthetase
Regulation of growth factor signaling by FRS2 family docking/scaffold adaptor proteins
A GRASP55-rab2 effector complex linking Golgi structure to membrane traffic
Recent progress in structure-function analyses of Nramp proton-dependent metal-ion transporters
2'-deoxyadenosine 5'-diphosphate [ChEBI:16174]
The Wnt/Ca2+ pathway: a new vertebrate Wnt signaling pathway takes shape
2 ATP + NH4+ + HCO3- => 2 ADP + orthophosphate + carbamoyl phosphate [mitochondrial]
2 ATP + NH4+ + HCO3- => 2 ADP + orthophosphate + carbamoyl phosphate
glutamate + acetyl CoA => N-acetyl glutamate + CoA
ATP + aspartate + citrulline <=> argininosuccinate + AMP + pyrophosphate
carbamoyl phosphate + ornithine => citrulline + orthophosphate
3-hydroxykynurenine + H2O => 3-hydroxyanthranilate + alanine
kynurenine + O2 + NADPH + H+ => 3-hydroxykynurenine + NADP+ + H2O
kynurenine + 2-oxoglutarate => 4-(2-aminophenyl)-2,4-dioxobutanoic acid + glutamate
3-hydroxyanthranilate + O2 => 2-amino-3-carboxymuconate semialdehyde
kynurenine + pyruvate => 4-(2-aminophenyl)-2,4-dioxobutanoic acid + alanine [CCBL2]
Induction of CHOP expression by amino acid limitation requires both ATF4 expression and ATF2 phosphorylation
argininosuccinate <=> fumarate + arginine
The sites and topology of mitochondrial superoxide production
Putrescine + dc-Adenosyl methionine => Spermidine + 5'-methylthioadenosine
S-Adenosyl methionine <=> Decarboxylated-Adenosyl methionine + CO2
Peroxisome proliferator-activated receptor alpha (PPARalpha) and athero-sclerosis
Curr Drug Targets Cardiovasc Haematol Disord 5:513-23
A mitogen-activated protein kinase-dependent signaling pathway in the activation of platelet integrin alpha IIbbeta3
gamma-butyrobetaine + alpha-ketoglutarate + O2 => carnitine + succinate + CO2
beta-hydroxy-trimethyllysine => gamma-butyrobetaine aldehyde + glycine
ornithine (cytosolic) + citrulline (mitochondrial) => ornithine (mitochondrial) + citrulline (cytosolic)
arginine + H2O => ornithine + urea [ARG2]
arginine + H2O => ornithine + urea [ARG1]
Vitamin B12 transport from food to the body's cells--a sophisticated, multistep pathway
Synthesis of PIPs at the late endosome membrane
D-myo-Inositol 1,3,4,6-tetrakisphosphate
1D-myo-Inositol 1,3,4,6-tetrakisphosphate [ChEBI:809]
ChEBI:16152 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphates
ChEBI:16152 ChEBI:16152 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphates
3-phosphonooxypyruvic acid + L-glutamate = O-phospho-L-serine + 2-oxoglutarate
a-ketoisocaproate, a-keto-b-methylvalerate, or a-ketoisovalerate + glutamate <=> leu, ile, or val + alpha-ketoglutarate [BCAT1]
leu, ile, or val + alpha-ketoglutarate <=> a-ketoisocaproate, a-keto-b-methylvalerate, or a-ketoisovalerate + glutamate [BCAT1]
a-ketoisocaproate, a-keto-b-methylvalerate, or a-ketoisovalerate + glutamate <=> leu, ile, or val + alpha-ketoglutarate [BCAT2]
leu, ile, or val + alpha-ketoglutarate <=> a-ketoisocaproate, a-keto-b-methylvalerate, or a-ketoisovalerate + glutamate [BCAT2]
Identification of a binding region for human origin recognition complex proteins 1 and 2 that coincides with an origin of DNA replication.
alpha-methyl-acetoacetyl-CoA + CoA => propionyl-CoA + acetyl-CoA
beta-hydroxyisobutyryl-CoA + H2O => beta-hydroxyisobutyrate + CoA
lysine + alpha-ketoglutarate +NADPH + H+ => saccharopine + NADP+ + H2O
Identification and characterization of the gene encoding the human phosphopantetheine adenylyltransferase and dephospho-CoA kinase bifunctional enzyme (CoA synthase)
2-oxoglutarate [mitochondrial matrix] + 2-oxoadipate [cytosol] <=> 2-oxoglutarate [cytosol] + 2-oxoadipate [mitochondrial matrix]
Exchange of cytosolic 2-oxoadipate for mitochondrial 2-oxoglutarate
alpha-ketoadipate + glutamate <=> alpha-aminoadipate + alpha-ketoglutarate
alpha-aminoadipate + alpha-ketoglutarate <=> alpha-ketoadipate + glutamate
saccharopine + NAD+ + H2O => alpha-aminoadipic semialdehyde + glutamate + NADH + H+
L-glutamate gamma-semialdehyde + NAD+ => glutamate + NADH + H+
phenylalanine + pyruvate => 3-(indol-3-yl)pyruvate + alanine
Oxidative decarboxylation of alpha-ketoadipate to glutaryl CoA by alpha-ketoglutarate dehydrogenase
alpha-ketoadipate + CoASH + NAD+ => glutaryl-CoA + CO2 + NADH + H+
Analysis of GPIIb/IIIa receptor number by quantification of 7E3 binding to human platelets
Formation of open and elongating transcription complexes by RNA polymerase III.
tryptophan + O2 => N-formylkynurenine [IDO]
tryptophan + O2 => N-formylkynurenine [IDO2]
Enzymatic synthesis and properties of 5-phosphoribosylpyrophosphate
Two molecules of ALA condense to form porphobilinogen (PBG)
Ornithine delta-aminotransferase mutations in gyrate atrophy. Allelic heterogeneity and functional consequences.
Four PBGs combine through deamination to form hydroxymethylbilane (HMB)
Succinyl CoA and glycine condense to form 5-aminolevulinate (ALA)
ALAS condenses SUCC-CoA and Gly to form dALA
ALAD octamer associates with Pb++, forming a catalytically inactive complex
Sulfate is exported to the cytosol in exchange for dicarboxylate
Oxidation of protoporphyrinogen IX to protoporphyrin IX
Uroporphyrinogen I is decarboxylated to form coproporphyrinogen I
Conversion of coproporphyrinogen III to protoporphyrinogen IX
Conversion of HMB to uroporphyrinogen III
Uroporphyrinogen III is decarboxylated to form coproporphyrinogen III
FMO1 N-oxidizes the anti-cancer drug tamoxifen
FMO2 S-oxidizes the antithyroid drug methimazole
Ferrous iron is inserted into protoporphyrin IX to form heme
A tyrosine-phosphorylated carboxy-terminal peptide of the fibroblast growth factor receptor (Flg) is a binding site for the SH2 domain of phospholipase C-gamma 1
Trimethylamine N-oxidised to Trimethylamine-N-oxide
FMO3 N-oxidizes the tertiary amine trimethylamine
Localization, regulation and function of type II phosphatidylinositol 5-phosphate 4-kinases
acetaldehyde + NAD+ => acetate + NADH + H+ [mitochondrial]
acetate + CoA + ATP => acetyl-CoA + AMP + pyrophosphate [mitochondrial]
acetaldehyde + NAD+ => acetate + NADH + H+ [cytosolic]
Methylthio-ribose-P = Methylthio-ribulose-P
The bisretinoids of retinal pigment epithelium
Methylthio-ribulose-P = Methylthio-ribose-P
glyoxylate + alanine => glycine + pyruvate [peroxisome]
glyoxylate + NADPH + H+ => glycolate + NADP+
From glycosylation disorders to dolichol biosynthesis defects: a new class of metabolic diseases
SAM is sythesized from methionine's reaction with ATP
Cystathionine is formed from homocysteine and serine
A proteasome inhibitor prevents activation of NF-kappa B and stabilizes a newly phosphorylated form of I kappa B-alpha that is still bound to NF-kappa B
Homocysteine is degraded to oxobutanoate and H2S
Excess homocysteine yields homolanthionine and H2S
Excess cysteine yields lanthionine and H2S
MicroRNAs: genomics, biogenesis, mechanism, and function
Redox regulation of mammalian heat shock factor 1 is essential for Hsp gene activation and protection from stress
Band 3 Anion Exchanger (AE1, SLC4A1) exchanges cytosolic bicarbonate for extracellular chloride
FXN:NFS1:ISD11:ISCU assembles iron-sulfur cluster
gamma-glutamylcysteine combines with glycine to form glutathione
Cleavage of 5-oxoproline to form glutamate
Mitoferrin translocates iron from the mitochondrial intermembrane space to the mitochondrial matrix
GGTs hydrolyse glutamate from AFXBO-SG, AFNBO-SG
Identification and molecular characterization of acyl-CoA synthetase in human erythrocytes and erythroid precursors
The proliferative effect of vascular endothelial growth factor requires protein kinase C-alpha and protein kinase C-zeta
Arterioscler. Thromb. Vasc. Biol. 19:178-85
FUNCTION Essential component of the TIM23 complex, a complex that mediates the translocation of transit peptide-containing proteins across the mitochondrial inner membrane.MISCELLANEOUS Present with 1440 molecules/cell in log phase SD medium.SIMILARITY Belongs to the Tim17/Tim22/Tim23 family.
Cardiolipin hydrolysis by human phospholipases A2. The multiple enzymatic activities of human cytosolic phospholipase A2
TTP and BRF proteins nucleate processing body formation to silence mRNAs with AU-rich elements
Assembly and iron-binding properties of human frataxin, the protein deficient in Friedreich ataxia
Glucuronidation and the UDP-glucuronosyltransferases in health and disease
MAPKAP kinase 3pK phosphorylates and regulates chromatin association of the polycomb group protein Bmi1
Triggering and amplifying pathways of regulation of insulin secretion by glucose
A human testis-specific mRNA for phosphoribosylpyrophosphate synthetase that initiates from a non-AUG codon
cDNA cloning of human R-type pyruvate kinase and identification of a single amino acid substitution (Thr384----Met) affecting enzymatic stability in a pyruvate kinase variant (PK Tokyo) associated with hereditary hemolytic anemia
Diacylglycerol, when simplicity becomes complex
New insights into the regulation of T cells by gamma(c) family cytokines
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Characterization of bovine endothelial nitric oxide synthase as a homodimer with down-regulated uncoupled NADPH oxidase activity: tetrahydrobiopterin binding kinetics and role of haem in dimerization
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B cell lymphoma 10 is essential for FcepsilonR-mediated degranulation and IL-6 production in mast cells
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The Rad50 hook domain is a critical determinant of Mre11 complex functions
Isoleucylation properties of native human mitochondrial tRNAIle and tRNAIle transcripts. Implications for cardiomyopathy-related point mutations (4269, 4317) in the tRNAIle gene
Zinc influx into cells by the SLC39 gene family
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The enzymic chain elongation of fatty acids by rat-liver microsomes
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Cyclic nucleotides and phosphodiesterases in platelets
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Structural determinants of water permeation through aquaporin-1
Mutations in the NSDHL gene, encoding a 3beta-hydroxysteroid dehydrogenase, cause CHILD syndrome
Human phosphoribosylpyrophosphate synthetase
Translational regulation of gene expression during conditions of cell stress
Control of pyrimidine biosynthesis in human lymphocytes. Simultaneous increase in activities of glutamine-utilizing carbamyl phosphate synthetase and aspartate transcarbamylase in phytohemagglutinin-stimulated human peripheral lymphocytes and their enzyme co-purification
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Protein kinase C-delta is a negative regulator of antigen-induced mast cell degranulation
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1,2-diacyl-sn-glycero-3-phosphocholine [ChEBI:16110]
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A fatal mitochondrial disease is associated with defective NFU1 function in the maturation of a subset of mitochondrial Fe-S proteins
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Molecular cloning of cDNA encoding human lanosterol synthase
Dihydroxyacetone phosphate [ChEBI:16108]
Molecular cloning and mapping of a human cDNA (SC5DL) encoding a protein homologous to fungal sterol-C5-desaturase
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Prefoldin mediated transfer of substrate to CCT/TriC
3-Phospho-D-glyceroyl phosphate [ChEBI:16001]
Structure of a high-resolution crystal form of human triosephosphate isomerase: improvement of crystals using the gel-tube method
Acta Crystallogr Sect F Struct Biol Cryst Commun 61:346-9
adenosine 5'-monophosphate [ChEBI:16027]
Molecular aspects of the adenine nucleotide carrier from mitochondria
A single enzyme catalyzes both platelet-activating factor production and membrane biogenesis of inflammatory cells. Cloning and characterization of acetyl-CoA:LYSO-PAF acetyltransferase
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Heat shock factor 1 binds to and transcribes satellite II and III sequences at several pericentromeric regions in heat-shocked cells
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The forkhead transcription factor FOXM1 controls cell cycle-dependent gene expression through an atypical chromatin binding mechanism
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1D-myo-Inositol 1,4,5,6-tetrakisphosphate
1D-myo-Inositol 1,4,5,6-tetrakisphosphate [ChEBI:811]
D-myo-Inositol 1,4,5,6-tetrakisphosphate
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Insulin effects increased synthesis of Xylulose-5-Phosphate
Human SMG-1, a novel phosphatidylinositol 3-kinase-related protein kinase, associates with components of the mRNA surveillance complex and is involved in the regulation of nonsense-mediated mRNA decay
Determination of nitric oxide synthase cofactors: heme, FAD, FMN, and tetrahydrobiopterin
Genomic organization, cDNA sequence, bacterial expression, and purification of human seryl-tRNA synthase
MKK3- and MKK6-regulated gene expression is mediated by the p38 mitogen-activated protein kinase signal transduction pathway
Cell cycle regulation of CDK2 activity by phosphorylation of Thr160 and Tyr15
Human acetyl-CoA carboxylase: characterization, molecular cloning, and evidence for two isoforms
The regulatory domain of human heat shock factor 1 is sufficient to sense heat stress
3pK, a new mitogen-activated protein kinase-activated protein kinase located in the small cell lung cancer tumor suppressor gene region
Oxcarbazepine does not interact with cimetidine in healthy volunteers
The mechanism of mismatch repair and the functional analysis of mismatch repair defects in Lynch syndrome
Cross-talk between the endocytic pathway and the endoplasmic reticulum in cross-presentation by MHC class I molecules
Full mass spectrometric characterization of human monoacylglycerol lipase generated by large-scale expression and single-step purification
N-acylphosphatidylethanolamine-hydrolyzing phospholipase D: a novel enzyme of the beta-lactamase fold family releasing anandamide and other N-acylethanolamines
FUNCTION Essential for the expression of the Rieske iron-sulfur protein.MISCELLANEOUS Present with 1990 molecules/cell in log phase SD medium.SIMILARITY Belongs to the AAA ATPase family. BCS1 subfamily.
Error-prone DNA polymerases: novel structures and the benefits of infidelity.
SUBUNIT Forms a complex with RAD50 and XRS2.MISCELLANEOUS Present with 432 molecules/cell in log phase SD medium.SIMILARITY Belongs to the MRE11/RAD32 family.
Distribution of AQP2 and AQP3 water channels in human tissue microarrays
Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits
SIMILARITY Belongs to the small Tim family.
NMD: RNA biology meets human genetic medicine
FUNCTION General activator of RNA polymerase III transcription.SIMILARITY Belongs to the TFC5 family.SIMILARITY Contains 1 SANT domain.
Mutant human adenosine deaminase alleles and their expression by transfection into fibroblasts
Characterization of an acyl-coA thioesterase that functions as a major regulator of peroxisomal lipid metabolism
Spatial expression patterns and biochemical properties distinguish a second myo-inositol monophosphatase IMPA2 from IMPA1
An NADH-tetrazolium-coupled sensitive assay for malate dehydrogenase in mitochondria and crude tissue homogenates
Metabolism of stearidonic acid in human subjects: comparison with the metabolism of other n-3 fatty acids
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1857-1895
Structural biology of shared cytokine receptors
Functional cloning of BRF1, a regulator of ARE-dependent mRNA turnover
Cyclin B2 suppresses mitotic failure and DNA re-replication in human somatic cells knocked down for both cyclins B1 and B2
Characterization of the proteins released from activated platelets leads to localization of novel platelet proteins in human atherosclerotic lesions
Indirubin-3'-monoxime inhibits autophosphorylation of FGFR1 and stimulates ERK1/2 activity via p38 MAPK
The DNA replication fork in eukaryotic cells.
Isolation and chromosomal localization of a novel FMS-like tyrosine kinase gene
Proline to arginine mutations in FGF receptors 1 and 3 result in Pfeiffer and Muenke craniosynostosis syndromes through enhancement of FGF binding affinity
Nitric oxide synthase lies downstream from vascular endothelial growth factor-induced but not basic fibroblast growth factor-induced angiogenesis
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Baillieres Clin Endocrinol Metab 7:551-86
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NOD-like receptors: role in innate immunity and inflammatory disease
Folic acid: nutritional biochemistry, molecular biology, and role in disease processes
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COFACTOR Binds 4 4Fe-4S clusters per heterotetramer. Contains two stable clusters in the N-termini of NBP35 and two labile, bridging clusters between subunits of the NBP35-CFD1 heterotetramer.SIMILARITY Belongs to the Mrp/NBP35 ATP-binding proteins family. NUBP2/CFD1 subfamily.
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Functional characterization of novel human and mouse equilibrative nucleoside transporters (hENT3 and mENT3) located in intracellular membranes
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The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1909-1963
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The MutSalpha-proliferating cell nuclear antigen interaction in human DNA mismatch repair
Pathogen recognition and innate immunity
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Disorders of proline and hydroxyproline metabolism
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1821-1838
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ERCC1/XPF removes the 3' overhang from uncapped telomeres and represses formation of telomeric DNA-containing double minute chromosomes
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A human amphotropic retrovirus receptor is a second member of the gibbon ape leukemia virus receptor family
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Disorders of tetrahydrobiopterin and related biogenic amines
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1725-1776
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1777-1805
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Organic acidemias due to defects in lysine oxidation: 2-ketoadipic acidemia and glutaric acidemia
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 2195-2204
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The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1965-1970
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Maple syrup urine disease (branched-chain ketoaciduria)
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1971-2005
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The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 2125-2163
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The generation and the manipulation of human multipotent adipose-derived stem cells
Cloned mammalian neutral sphingomyelinase: functions in sphingolipid signaling?
Mutations in PMM2, a phosphomannomutase gene on chromosome 16p13, in carbohydrate-deficient glycoprotein type I syndrome (Jaeken syndrome)
Structure, function, and formation of biological iron-sulfur clusters
NOD-LRR proteins: role in host-microbial interactions and inflammatory disease
Molecular physiology of bestrophins: multifunctional membrane proteins linked to best disease and other retinopathies
Human mucopolysaccharidosis IIID: clinical, biochemical, morphological and immunohistochemical characteristics
Characterization of human SLC4A10 as an electroneutral Na/HCO3 cotransporter (NBCn2) with Cl- self-exchange activity
Binding of yeast frataxin to the scaffold for Fe-S cluster biogenesis, Isu
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Transaldolase deficiency: liver cirrhosis associated with a new inborn error in the pentose phosphate pathway.
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Complete amino acid sequence of human phosphoglycerate kinase. Cyanogen bromide peptides and complete amino acid sequence.
Two new proteases in the MHC class I processing pathway
Evaluating the role of carbonic anhydrases in the transport of HCO3--related species
The stem-loop binding protein is required for efficient translation of histone mRNA in vivo and in vitro
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In vitro assays of 5' to 3'-exoribonuclease activity
Cloning of a novel phosphatidylinositol kinase-related kinase: characterization of the human SMG-1 RNA surveillance protein
Isolation and characterization of a hydroxyacid-oxoacid transhydrogenase from rat kidney mitochondria
Differential hydrolysis of phospholipid molecular species during activation of human platelets with thrombin and collagen
A critical role of RICK/RIP2 polyubiquitination in Nod-induced NF-kappaB activation
Participation of the microsomal CDP-diglycerides in the mitochondrial biosynthesis of phosphatidylglycerol
Ectopic expression of Cdc25A accelerates the G(1)/S transition and leads to premature activation of cyclin E- and cyclin A-dependent kinases
DNA polymerase switching: II. Replication factor C abrogates primer synthesis by DNA polymerase alpha at a critical length.
DNA polymerase switching: I. Replication factor C displaces DNA polymerase alpha prior to PCNA loading.
The dynamic phagosomal proteome and the contribution of the endoplasmic reticulum
The energy-less red blood cell is lost: erythrocyte enzyme abnormalities of glycolysis
DARPP-32: an integrator of neurotransmission
Cdc6 is regulated by E2F and is essential for DNA replication in mammalian cells.
The anaphase-promoting complex: it's not just for mitosis any more.
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'GDP [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
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'GMP [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
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Structure and function of a protein folding machine: the eukaryotic cytosolic chaperonin CCT
'ADS [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
'XMP [cytosol]' negatively regulates 'IMP + H2O + NAD+ => XMP + NADH + H+ [IMPDH1,2]'
'dATP [cytosol]' negatively regulates 'NDP + reduced thioredoxin => dNDP + oxidized thioredoxin + H2O'
'ATP [cytosol]' positively regulates 'NDP + reduced glutaredoxin => dNDP + oxidized glutaredoxin + H2O'
'dATP [cytosol]' negatively regulates 'NDP + reduced glutaredoxin => dNDP + oxidized glutaredoxin + H2O'
'D-Fructose 1,6-bisphosphate [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
Cloning and characterization of human agmatinase
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'Mg2+ [cytosol]' is required for 'ITPA hydrolyses ITP to IMP'
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'ATP [cytosol]' positively regulates 'NDP + reduced thioredoxin => dNDP + oxidized thioredoxin + H2O'
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The circadian E-box: when perfect is not good enough
Expression of Gs alpha in Escherichia coli. Purification and properties of two forms of the protein
Mechanism of the nucleotide exchange reaction in eukaryotic polypeptide chain initiation. Characterization of the guanine nucleotide exchange factor as a GTP-binding protein.
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'Mg2+ [cytosol]' is required for 'ITPA hydrolyses dITP to dIMP'
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'GTP [mitochondrial matrix]' negatively regulates 'alpha-ketoglutarate + NH4+ + NAD(P)H + H+ <=> glutamate + NAD(P)+ [GLUD1]'
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'Mg2+ [cytosol]' is required for 'ITPA hydrolyses XTP to XMP'
'ADP [mitochondrial matrix]' positively regulates 'glutamate + NAD(P)+ => alpha-ketoglutarate + NH4+ + NAD(P)H + H+ [GLUD1]'
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'ADP [mitochondrial matrix]' positively regulates 'alpha-ketoglutarate + NH4+ + NAD(P)H + H+ <=> glutamate + NAD(P)+ [GLUD1]'
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'L-Arg [mitochondrial matrix]' positively regulates 'glutamate + acetyl CoA => N-acetyl glutamate + CoA'
'GTP [mitochondrial matrix]' negatively regulates 'glutamate + NAD(P)+ => alpha-ketoglutarate + NH4+ + NAD(P)H + H+ [GLUD1]'
'HCYS [cytosol]' positively regulates 'Excess homocysteine yields homolanthionine and H2S'
'NAcGlu [mitochondrial matrix]' positively regulates '2 ATP + NH4+ + HCO3- => 2 ADP + orthophosphate + carbamoyl phosphate [mitochondrial]'
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'L-Cys [cytosol]' positively regulates 'Excess cysteine yields lanthionine and H2S'
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A double-hexamer archaeal minichromosome maintenance protein is an ATP-dependent DNA helicase.
'Ca2+ [cytosol]' positively regulates 'ANOs transport cytosolic Cl- to extracellular region'
'GSH [cytosol]' negatively regulates 'gamma-glutamylcysteine combines with glycine to form glutathione'
'Pb2+ [mitochondrial matrix]' negatively regulates 'FECH binds Fe2+ to PRIN9 to form heme'
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'heme [mitochondrial matrix]' negatively regulates 'ALAS condenses SUCC-CoA and Gly to form dALA'
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_246186.1
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Regulation of phagocytosis by Rho GTPases
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Murine p38-delta mitogen-activated protein kinase, a developmentally regulated protein kinase that is activated by stress and proinflammatory cytokines
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Cytochrome P450s and other enzymes in drug metabolism and toxicity
The subcellular localization of acetyl-CoA carboxylase 2
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Human 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/inosine 5'-monophosphate cyclohydrolase. A bifunctional protein requiring dimerization for transformylase activity but not for cyclohydrolase activity
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APC/C-mediated degradation of cell cycle proteins
'D-Fructose 2,6-bisphosphate [cytosol]' positively regulates 'D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP'
'ATP [cytosol]' negatively regulates 'D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP'
'YWHAE dimer (name copied from entity in Homo sapiens) [cytosol]' negatively regulates 'HSF1 trimer translocates to the nucleus'
'p-S230-HSF1 trimer (name copied from entity in Homo sapiens) [nucleoplasm]' positively regulates 'HSF1-mediated gene expression'
Acetylcholine regulates insulin secretion
Phosphatidylethanolamine is the donor of the phosphorylethanolamine linked to the alpha1,4-linked mannose of yeast GPI structures
'ATP [cytosol]' is required for 'Ribosomal scanning '
'EEF1A1 [cytosol]' positively regulates 'Trimerization of cytosolic HSF1'
'D-Fructose 2,6-bisphosphate [cytosol]' positively regulates 'D-fructose 6-phosphate + ATP => D-fructose 2,6-bisphosphate + ADP'
'CIT [cytosol]' negatively regulates 'D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP'
'p-S326-HSF1 trimer (name copied from entity in Homo sapiens) [nucleoplasm]' positively regulates 'HSF1-mediated gene expression'
'L-Phe [cytosol]' negatively regulates 'kynurenine + pyruvate => 4-(2-aminophenyl)-2,4-dioxobutanoic acid + alanine [CCBL1]'
Regulation of molecular chaperone gene transcription involves the serine phosphorylation, 14-3-3 epsilon binding, and cytoplasmic sequestration of heat shock factor 1
'G6P [cytosol]' negatively regulates 'PGYM dimer, b form + 2 AMP <=> PGYM b dimer:AMP complex'
Distribution of NG, NG,-dimethylarginine in nuclear protein fractions
Biochem. Biophys. Res. Commun. 74:969-76
'ADP [cytosol]' positively regulates 'D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP'
'ATP [nucleoplasm]' negatively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'D-Fructose 1,6-bisphosphate [cytosol]' positively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'Ac-CoA [cytosol]' negatively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'cAMP [cytosol]' negatively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'Ac-CoA [mitochondrial matrix]' positively regulates 'Pyruvate + CO2 + ATP => ADP + Orthophosphate + Oxaloacetate'
'AMP [cytosol]' negatively regulates 'D-fructose 1,6-bisphosphate + H2O => D-fructose 6-phosphate + orthophosphate'
'G6P [cytosol]' is required for 'Phosphorylated GYS1 catalyzes the polyglucosylation of oligoGlc-GYG1'
'AMP [cytosol]' positively regulates 'D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP'
'BH4 [cytosol]' negatively regulates 'GCH1 reduces GTP to dihydroneopterin triphosphate'
'PYR [mitochondrial matrix]' negatively regulates 'PDK-catalyzed phosphorylation (inactivation) of PDC E1 alpha subunit'
'XY5P [cytosol]' positively regulates 'Activation of PP2A by Xylulose-5-phosphate'
'L-Phe [cytosol]' positively regulates 'GCH1 reduces GTP to dihydroneopterin triphosphate'
'SREBP1A,1C,2:NF-Y:FDPS gene (name copied from entity in Homo sapiens) [nucleoplasm]' positively regulates 'Expression of Squalene Monooxygenase (SQLE)'
'SREBP1A,1C,2:NF-Y:FDPS gene (name copied from entity in Homo sapiens) [nucleoplasm]' positively regulates 'Expression of TM7SF2'
'SREBP1A,1C,2:NF-Y:FDPS gene (name copied from entity in Homo sapiens) [nucleoplasm]' positively regulates 'Expression of Farnesyl Diphosphate Synthase (FDPS)'
'SREBP1A,1C,2:NF-Y:FDPS gene (name copied from entity in Homo sapiens) [nucleoplasm]' positively regulates 'Expression of Lathosterol Oxidase (SC5D, SC5DL)'
'ATP [cytosol]' negatively regulates 'PGYM dimer, b form + 2 AMP <=> PGYM b dimer:AMP complex'
'CIT [cytosol]' positively regulates 'acetyl-CoA + bicarbonate + ATP => malonyl-CoA + H2O + ADP + orthophosphate'
Carbon dioxide transport and carbonic anhydrase in blood and muscle
Cloning, expression, and characterization of a human inosine triphosphate pyrophosphatase encoded by the itpa gene
6-Phosphofructo-2-kinase/fructose-2,6-bisphosphatase: a metabolic signaling enzyme.
'IMP [cytosol]' positively regulates 'Formation of phosphoribosyl pyrophosphate amidotransferase tetramer'
'AMP [cytosol]' positively regulates 'Formation of phosphoribosyl pyrophosphate amidotransferase tetramer'
'PRPP [cytosol]' positively regulates 'Dissociation of phosphoribosyl pyrophosphate amidotransferase tetramer'
'Co2+ [mitochondrial matrix]' positively regulates '(R)-2-hydroxyglutarate + FAD => 2-oxoglutarate + FADH2'
'Zn2+ [mitochondrial matrix]' positively regulates '(R)-2-hydroxyglutarate + FAD => 2-oxoglutarate + FADH2'
'Mn2+ [mitochondrial matrix]' positively regulates '(R)-2-hydroxyglutarate + FAD => 2-oxoglutarate + FADH2'
'GMP [cytosol]' positively regulates 'Formation of phosphoribosyl pyrophosphate amidotransferase tetramer'
'NADH [mitochondrial matrix]' positively regulates 'PDK-catalyzed phosphorylation (inactivation) of PDC E1 alpha subunit'
'Ac-CoA [mitochondrial matrix]' positively regulates 'PDK-catalyzed phosphorylation (inactivation) of PDC E1 alpha subunit'
'ADP [mitochondrial matrix]' positively regulates 'isocitrate + NAD+ => alpha-ketoglutarate + CO2 + NADH + H+ [IDH3]'
Characterization of the advanced glycation end-product receptor complex in human vascular endothelial cells
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Alternative splicing generates an isoform of the human Sef gene with altered subcellular localization and specificity
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Biochemical characterization of human PC-1, an enzyme possessing alkaline phosphodiesterase I and nucleotide pyrophosphatase activities
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Glycogen and its metabolism: some new developments and old themes
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Human amidophosphoribosyltransferase. An oxygen-sensitive iron-sulfur protein
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Reduced half-life of holocarboxylase synthetase from patients with severe multiple carboxylase deficiency
integral component of cytoplasmic side of endoplasmic reticulum membrane
At the beginning of this reaction, 1 molecule of 'Pol eta:lesioned DNA template inserted with correct base complement' is present. At the end of this reaction, 1 molecule of 'Pol eta protein', and 1 molecule of 'Elongated DNA template with bypassed lesion' are present. This reaction takes place in the 'nucleus' and is mediated by the 'eta DNA polymerase activity' of 'Pol eta:lesioned DNA template inserted with correct base complement'.
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At the beginning of this reaction, 1 molecule of 'Pol eta:damaged DNA template complex' is present. At the end of this reaction, 1 molecule of 'Pol eta:lesioned DNA template inserted with correct base complement' is present. This reaction takes place in the 'nucleus' and is mediated by the 'eta DNA polymerase activity' of 'Pol eta:damaged DNA template complex'.
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Ubiquitous environmental and endogenous genotoxic agents cause lesions that can interfere with normal DNA metabolism including DNA replication, eventually resulting in mutations that lead to carcinogenesis and/or cell death. While cells posses repair mechanisms like nucleotide excision and base excision repair pathways to maintain the integrity of the genome, not all lesions on the genome can be repaired efficiently by these processes in time for DNA replication, and some types of lesion are repaired very inefficiently. To prevent acute cell death through arrested DNA replication at unrepaired lesions, cells have a mechanism, referred to as translesion synthesis, which allows DNA synthesis to proceed past lesions (Masutani et al., 2000).
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Pol eta consists of 713 amino acids and can bypass thymidine-thymidine dimers adding two A's correctly opposite to the lesion. Mutations in Pol eta gene result in the loss of this bypass activity in accounting for the XP variant phenotype (XPV) among human xeroderma pigmentosum disorder patients. Pol eta can carry out TLS past various UV and chemical induced lesions via two steps: a. preferential incorporation of correct bases opposite to the lesion b. conditional elongation only at the sites where such correct bases are inserted.
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The molecular mechanism of lead inhibition of human porphobilinogen synthase
Of the three major pathways involved in the repair of nucleotide damage in DNA, base excision repair (BER) involves the greatest number of individual enzymatic activities. This is the consequence of the numerous individual glycosylases, each of which recognizes and removes a specific modified base(s) from DNA. BER is responsible for the repair of the most prevalent types of DNA lesions, alterations, which arise intracellularly as a consequence of normal mitochondrial metabolism or by oxidative free radicals resulting from ionizing radiation, lipid peroxidation or activated phagocytic cells. BER is a two-step process initiated by one of the DNA glycosylases that recognizes a specific modified base(s) and removes that base through the catalytic cleavage of the glycosylic bond, leaving an abasic site without disruption of the phosphate-sugar DNA backbone. Subsequently, abasic sites are resolved by a series of enzymes that cleave the backbone, synthesize the replacement residue(s), and ligate the DNA strand. BER may occur by either a single-nucleotide replacement pathway or a multiple-nucleotide patch replacement pathway, depending on the structure of the terminal sugar phosphate residue. The glycosylases found in human cells recognize "foreign adducts" and not standard functional modifications such as DNA methylation.
Fibroblast growth factor receptor 1 is fused to FIM in stem-cell myeloproliferative disorder with t(8;13)
At the beginning of this reaction, 1 molecule of 'damaged DNA substrate ', and 1 molecule of 'HREV1 protein' are present. At the end of this reaction, 1 molecule of 'HREV1:damaged DNA template complex' is present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'HREV1:damaged DNA template complex' is present. At the end of this reaction, 1 molecule of 'HREV1:lesioned DNA template with misinserted bases' is present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA-directed DNA polymerase activity' of 'HREV1:damaged DNA template complex'.
At the beginning of this reaction, 1 molecule of 'HREV1:lesioned DNA template with misinserted bases' is present. At the end of this reaction, 1 molecule of 'HREV1 protein', and 1 molecule of 'Elongated DNA template with bypassed lesion' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA-directed DNA polymerase activity' of 'HREV1:lesioned DNA template with misinserted bases'.
HREV1 encodes a template dependent dCMP transferase activity that can insert a C residue opposite an abasic site.
Molecular identification and characterization of novel human and mouse concentrative Na+-nucleoside cotransporter proteins (hCNT3 and mCNT3) broadly selective for purine and pyrimidine nucleosides (system cib)
At the beginning of this reaction, 1 molecule of 'damaged DNA substrate ', and 1 molecule of 'Pol eta protein' are present. At the end of this reaction, 1 molecule of 'Pol eta:damaged DNA template complex' is present. This reaction takes place in the 'nucleus'.
Following exposure to ionizing radiation, a number of recombination/repair proteins and complexes relocalize to nuclear foci that are believed to correspond to the sites of double-strand breaks. These proteins include gamma-H2AX, ATM, RAD51, BRCA1, BRCA2, NBS1, RPA, and MDC1/NFBD1 and the MRE11-RAD50-NBS1. Gamma-H2AX, the phosphorylated form of H2AX, is one of the first proteins to appear within nuclear foci and plays an essential role in recruiting other repair proteins (Paull et al., 2000). One model illustrating the organization of the recruited repair proteins (Van den Bosch et al., 2003) is shown here. (A) Undamaged section of a chromosome, showing two chromatin loops and an inactive ATM dimer. (B,C) Induction of a DNA double-stranded break (DSB), modification of chromatin, activation of ATM and recruitment of both ATM and MRE11/RAD50/NBS1(MRN). The possibility that MRN binds before ATM is shown, but the activation of ATM appears to require the MDC1 and the MRN complex (Uziel, et al 2003; Mochan et al. 2003). The thin black line indicates modified chromatin. (D,E) Following DNA damage, a wave of H2AX phosphorylation occurs and the mediator proteins (mediator of DNA damage checkpoint protein 1 (MDC1), p53-binding protein 1(53BP1), and breast-cancer-associated protein 1(BRCA1)) are recruited to the growing focus where they are phosphorylated in an ATM-dependent manner. The molecular architecture of the focus is unknown. (F) Disassembly of the focus, ATM inactivation and chromatin remodeling. The model suggests at least two distinct forms of soluble ATM: an inactive oligomer and an active monomer, and at least two distinct active, insoluble forms: one directly at the lesion and another integral to the growing focus. Note that the MRN complex is also a component of the growing focus, but for clarity, has been omitted here. Complex persistent lesions are thought to be more difficult to repair, and this is reflected in the size attained by the growing focus.
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MRN complexes localize to nuclear foci in response to double-strand breaks and have been implicated in DNA end-processing during homologous recombination repair (Trujillo et al., 1998). The MRN complex may function as a bridge between double-strand break ends through interactions between the coiled-coil domains of RAD50 (Hoptner et al., 2002).
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Assembly of the RAD50-MRE11-NBS1 complex at DNA double-strand breaks involves the formation of RAD50:MRE11 complex, association of RAD50:MRE11 complex with NBS1 through MRE11 and association of the MRN with sites of DSB.
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Recruitment and regulation of phosphatidylinositol phosphate kinase type 1 gamma by the FERM domain of talin
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Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane
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Reactive cellular catabolites can cause DNA damage by 6-O-methylation of guanine. 6-O-methylguanine can pair ambiguously with both C and T, and can cause transition mutations. Active reversal of such damage can be facilitated by proteins having 6-O-methylguanine-DNA methyltransferase (MGMT) activity. MGMT removes the methyl group from the guanine and transfers it to the cysteine residue at position 145 on the protein itself. MGMT thus methylated is not regenerated, as the S-methylcysteine is very stable. This is an energetically expensive approach to DNA repair as one entire protein molecule is sacrificed per lesion that is corrected in this manner (Yang et al. 2011).
DNA damage can be directly reversed by dealkylation.
In addition to various processes for removing damaging lesions from the DNA, cells have developed specific mechanisms for tolerating unexcised damages during the replication of the genome. Such processes are collectively called DNA damage bypass pathways. Several proteins including novel Y-family polymerases that have been recently identified in multitude of organisms are involved in this process. Translesion synthesis (TLS) or replicative bypass of damaged bases that are known to arrest high fidelity, highly processive polymerases involved in DNA replication is carried out by error-prone polymerases Pol zeta, Pol eta and Rev3 protein among others. TLS is implicated in UV and chemical induced mutagenesis of normal human cells where lesions in the replicating genome are carried over to the newly formed daughter cells. All these 3 enzymes are found to lack 3'->5' exonuclease activity, while exhibiting low fidelity, weak processivity and sufficient polymerase activities. An outline of the bypass synthesis by these 3 enzymes is annotated here. Complete details of damage recognition and discrimination, initiation of specific polymerase activity and the finer mechanisms are yet to be elucidated.
clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane
Detection of DNA double-strand breaks involves sensor proteins that become activated setting off of signaling cascades. This signaling leads to the recruitment of repair proteins and subsequent repair of the damaged DNA. ATM is one of the primary candidate sensors in double-strand break repair.
MRE11 has both manganese dependent ss DNA 3'-5' exonuclease and endonuclease activities. MRE11 associates with RAD50 resulting in increased 3'-5' exonuclease activity.
ATM is present in unirradiated cells as a dimer or higher-order multimer. Following irradiation, ATM undergoes rapid intermolecular autophosphorylation of serine 1981.
clathrin-sculpted gamma-aminobutyric acid transport vesicle lumen
Autophosphorylation of ATM results in the dissociation of the dimeric/multimeric ATM complex and initiation of ATM kinase activity. Autophosphorylation does not directly regulate ATM kinase activity. Instead, it is the resulting dissociation of ATM oligomers that allows substrates access to the ATM kinase domain.
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Homologous recombination repair of replication-independent double-strand breaks requires the activation of ATM followed by ATM mediated phosphorylation of DNA repair proteins. DNA repair and signaling proteins are then recruited to double-strand breaks. The ends of the DNA double strand breaks must be resectioned and RPA complexes associate with the resulting ssDNA. Homologous DNA pairing and strand exchange then occurs followed by DNA repair synthesis and resolution of D-loop structures.
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Once repair synthesis has occurred, the D-loop structure may be resolved either through Holliday junction intermediates of through synthesis-dependent strand-annealing.
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The presynaptic phase of homologous DNA pairing and strand exchange begins with the displacement of RPA from ssDNA, followed by the association of RAD51 with BRCA2, formation of RAD52 heptameric ring structure complexes on ssDNA, association of RAD52 with the RPA complex, association of RAD52 with ssDNA at resected ends of double-strand break and assembly of the RAD51-ssDNA nucleoprotein complex.
The presynaptic phase of homologous DNA pairing and strand exchange begins with the displacement of RPA from ssDNA, followed by the association of RAD51 with BRCA2, formation of RAD52 heptameric ring structure complexes on ssDNA, association of RAD52 with the RPA complex, association of RAD52 with ssDNA at resected ends of double-strand break and assembly of the RAD51-ssDNA nucleoprotein complex. Stable synaptic pairing between recombining DNA molecules involves the invasion of homologous duplex DNA by the processed single-stranded ends of the double-strand break, followed by displacement of the non-complimentary strand of the duplex. This results in the formation of a D-loop structure. Invasion of the heteroduplex DNA by RAD51 nucleoprotein filament involves the identification of a region of homology between these two molecules. The mechanism by which this occurs is not yet known. RAD51 catalyses the invasion of the nucleoprotein filament into homologous double-stranded DNA. Watson-Crick hydrogen bonding between the ssDNA within the nucleoprotein filament and the homologous strand of the invaded DNA duplex result in the displacement of the non-pairing strand (strand displacement) and formation of the D-loop structure (Sung et al., 2003). The RAD51 nucleoprotein filament has independent binding sites for the ssDNA strand upon which it assembles and the recombining homologous duplex DNA. The repair proteins RPA, RAD52, and RAD54 appear to promote RAD51 mediated invasion and homologous DNA pairing reaction (McIlwraith et al, 2000 and Sigurdsson et al., 2002). The conformation of the RAD52-ssDNA complex is thought to place the ssDNA on an exposed surface of the protein, in a configuration that may promote the DNA-DNA annealing of complementary DNA strands. RAD54 may function in the transient separation of the duplex DNA strands via its ATP hydrolysis-mediated DNA supercoiling function (Sigurdsson et al., 2002). Branch migration or strand exchange occurs as the complimentary duplex DNA strand is progressively taken up into the nucleoprotein filament to base pair with the invading single-strand sequence (Sung et al., 2003).
Ligation of the crossed-strand intermediate results in the formation of Holliday structures with two crossovers. In humans, the identity of this ligase activity involved in this process is not known.
Following the synthesis of new DNA at resected 5' ends of the DSB, the heterologous DNA molecules may be ligated resulting in the formation of Holliday junctions. The Holliday structures are then cleaved resulting in reciprocal exchange of sequence between sister chromatids.
At the beginning of this reaction, 1 molecule of '3' overhanging DNA at resected DSB ends', and 1 molecule of 'RAD52' are present. At the end of this reaction, 1 molecule of 'RAD52:DNA double-strand break' is present. This reaction takes place in the 'nucleus'.
Binding of the RAD51:RAD52 complex to ssDNA may provide nucleation sites promoting the association of free RAD51 with the growing nucleoprotein filament. This interaction may also play a role in stimulating the strand transfer reactions mediated by RAD51 (Baumann, 1999).
At the beginning of this reaction, 1 molecule of 'RAD51', and 1 molecule of '3' overhanging DNA at resected DSB ends' are present. At the end of this reaction, 1 molecule of 'RAD51:resected ends of DNA double-strand break' is present. This reaction takes place in the 'nucleus'.
The RAD51-ssDNA nucleoprotein filament is a right-hand helical nucleoprotein filament referred to as the presynaptic filament. This nucleoprotein complex contains a binding site for the double-stranded homologous DNA molecule with which it interacts during strand exchange. Loading of RAD51 onto ssDNA is thought to be facilitated by recombination mediator RAD52 (McIlwraith et al., 2000), RAD51 paralogs: RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3 (Sigurdsson et al., 2001), by the association of RAD52 with ssDNA (Parsons et al., 2000) and by the association of RAD51 with BRCA2 (Tarsounas et al., 2003).
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Wnt regulation of planar cell polarity (PCP)
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The H syndrome is caused by mutations in the nucleoside transporter hENT3
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Import of carrier proteins into the mitochondrial inner membrane mediated by Tim22
Mechanistic implications of mutations to the active site lysine of porphobilinogen synthase
Ion channels mediate the flow of ions across the plasma membrane of cells. They are integral membrane proteins, typically a multimer of proteins, which, when arranged in the membrane, create a pore for the flow of ions. There are different types of ion channels. P-type ATPases undergo conformational changes to translocate ions. Ligand-gated ion channels operate like a gate, opened or closed by a chemical signal. Voltage-gated ion channels are activated by changes in electrical potential difference at the membrane (Purves, 2001; Kuhlbrandt, 2004).
Plk1 promotes nuclear translocation of human Cdc25C during prophase
Active steroid hormones are produced from the precursor cholesterol.The steps involved in the biosynthesis of the adrenal steroid hormones, corticosterone, cortisol, and aldosterone; and the gonadal steroid hormones, progesterone, estradiol, and testosterone are annotated here. The enzymes that catalyze these reactions fall into two major classes of proteins: the cytochrome P450 heme-containing proteins and the hydroxysteroid dehydrogenases.
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At the beginning of this reaction, 1 molecule of 'hOGG1 glycosylase: formamidopyrimidine complex' is present. At the end of this reaction, 1 molecule of 'DNA containing an hOGG1-bound apurinic/apyrimidinic site', and 1 molecule of 'formamidopyrimidine' are present. This reaction takes place in the 'nucleus' and is mediated by the 'purine-specific oxidized base lesion DNA N-glycosylase activity' of 'hOGG1 glycosylase'.
Damaged purines are first cleaved by purine-specific glycosylases (see Lindahl and Wood 1999).
Depurination of a damaged nucleotide is mediated by a purine-specific DNA glycosylase. The glycosylase cleaves the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar generating a free base and an apurinic (AP) site.
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At the beginning of this reaction, 1 molecule of 'Double-strand DNA containing an 8-oxo guanine opposite to a cytosine', and 1 molecule of 'hOGG1 glycosylase' are present. At the end of this reaction, 1 molecule of 'hOGG1 glycosylase:8-oxo guanine complex' is present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'Double-strand DNA containing a formamidopyrimidine ', and 1 molecule of 'hOGG1 glycosylase' are present. At the end of this reaction, 1 molecule of 'hOGG1 glycosylase: formamidopyrimidine complex' is present. This reaction takes place in the 'nucleus'.
The recognition and cleavage of an altered base by a DNA glycosylase is thought to involve the diffusion of the enzyme along the minor grove of the DNA molecule. The enzyme presumably compresses the backbone of the affected DNA strand at the site of damage. This compression is thought to result in an outward rotation of the damaged residue into a "pocket" of the enzyme that recognizes and cleaves the altered base (Parikh et al., 1998).
At the beginning of this reaction, 1 molecule of 'hOGG1 glycosylase:8-oxo guanine complex' is present. At the end of this reaction, 1 molecule of '8-oxoguanine', and 1 molecule of 'DNA containing an hOGG1-bound apurinic/apyrimidinic site' are present. This reaction takes place in the 'nucleus' and is mediated by the 'purine-specific oxidized base lesion DNA N-glycosylase activity' of 'hOGG1 glycosylase'.
The human gene ATP7B encodes the copper-transporting ATPase 2 (ATP7B, ATPase2, Wilson's protein) which is expressed mainly in the liver, brain and kidneys (Bull et al, 1993). ATP7B resides on the trans-Golgi membrane where it it thought to sequester copper from the cytosol into the golgi (Yang et al, 1997). Defects in ATP7B are the cause of Wilson disease (WD), an autosomal recessive disorder of copper metabolism characterized by the toxic accumulation of copper in a number of organs, particularly the liver and brain (Thomas et al, 1995).
The transport of iron between cells is mediated by transferrin. However, iron can also enter and leave cells not only by itself, but also in the form of heme and siderophores. When entering the cell via the main path (by transferrin endocytosis), its goal is not the (still elusive) chelated iron pool in the cytosol nor the lysosomes but the mitochondria, where heme is synthesized and iron-sulfur clusters are assembled (Kurz et al,2008, Hower et al 2009, Richardson et al 2010).
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26S proteasomes and immunoproteasomes produce mainly N-extended versions of an antigenic peptide
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The H+/Cl- exchange transporters CLCN4 (Kawasaki et al. 1999, Zdebik et al. 2008), CLCN5 (Zdebik et al. 2008) and CLCN6 (Neagoe et al. 2010) mediate the exchange of endosomal Cl- for cytosolic H+ across endosomal membranes, contributing to the acidification of endosomes.
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Ion channels that mediate sensations such as pain, warmth, cold, taste pressure and vision. Channels that mediate these sensations include acid-sensing ion channels (ASICs) (Wang & Xu 2011, Qadri et al. 2012, Deval et al. 2010) and the transient receptor potential channels (TRPCs) (Takahashi et al. 2012, Numata et al. 2011 in "TRP Channels" Zhu, MX editor, CRC Press, 2011, Ramsey et al. 2006, Montell 2005). Many channels are sensitive to changes in calcium (Ca2+) levels, both inside and outside the cell. Examples are protein tweety homologs 2 and 3 (TTYH2, 3) (Suzuki 2006), bestrophins 1-4 (BEST1-4) (Sun et al. 2002, Tsunenari et al. 2003, Kunzelmann et al. 2009, Hartzell et al. 2008) and ryanodine receptor tetramers (RYRs) (Beard et al. 2009).
Calcium-activated chloride channels (CaCCs) are ubiquitously expressed and implicated in physiological processes such as sensory transduction, fertilization, epithelial secretion, and smooth muscle contraction. The anoctamin family of transmembrane proteins (ANO, TMEM16) belong to CaCCs and have been shown to transport Cl- ions when activated by intracellular Ca2+ (Galietta 2009, Huang et al. 2012). There are currently 10 members, ANO1-10, all having a similar structure, with eight putative transmembrane domains and cytosolic amino- and carboxy-termini. ANO1 and 2 possess Ca2+ activated Cl- transport activity (Yang et al. 2008, Scudieri et al. 2012) while the remaining members also show some demonstrable activity (Tian et al. 2012).
The H+/Cl- exchange transporter CLCN3 (Borsani et al. 1995) mediates the exchange of endosomal Cl- for cytosolic H+ across late endosomal membranes, contributing to the acidification of endosomes. The activity of CLCN3 is inferred from experiments in mice (Stobrawa et al. 2001, Hara-Chikuma et al. 2005).
The plasma membrane contains a broad range of lipids making up the bilayer. Aminophospholipids (APLs) such as phosphatidylserine (PS) and phosphatidylethanolamine (PE) are distributed in this bilayer and their arrangement is mediated by the P-type ATPases type IV family (Paulusma and Oude Elferink, 2005).
The P-type ATPases (E1-E2 ATPases) are a large group of evolutionarily related ion pumps that are found in bacteria, archaea and eukaryotes. They are referred to as P-type ATPases because they catalyze auto-phosphorylation of a key conserved aspartate residue within the pump. They all appear to interconvert between at least two different conformations, E1 and E2. Most members of this transporter family pump a large variety of cations (Kuhlbrandt W, 2004).
Accumulation of calcium into the Golgi apparatus is mediated by sarco(endo)plasmic reticulum calcium-ATPases (SERCAs) and by secretory pathway calcium-ATPases (SPCAs). There are two human genes which encode SPCAs; ATP2C1 and ATP2C2 which encode magnesium-dependent calcium-transporting ATPase type 2C members 1 and 2 (ATP2C1 and 2) respectively (Sudbrak et al, 2000; Vanoevelen et al, 2005). Defects in ATP2C1 are the cause of Hailey-Hailey disease (HHD), an autosomal dominant disease characterized by persistent blisters and erosions of the skin (Hu et al, 2000).
The plasma membrane contains a broad range of lipids making up the bilayer. Aminophospholipids such as phosphatidylserine (PS) and phosphatidylethanolamine (PE) are distributed in this bilayer and their arrangement is mediated by the P-type ATPases type IV family (Paulusma and Oude Elferink, 2005).
At the beginning of this reaction, 1 molecule of 'hNTH1 glycosylase:cytosine glycol complex' is present. At the end of this reaction, 1 molecule of 'cytosine glycol', and 1 molecule of 'DNA containing a hNTH1-bound apurinic/apyrimidinic site' are present. This reaction takes place in the 'nucleus' and is mediated by the 'pyrimidine-specific oxidized base lesion DNA N-glycosylase activity' of 'hNTH1'.
At the beginning of this reaction, 1 molecule of 'hNTH1 glycosylase: foramidopyrimidine complex' is present. At the end of this reaction, 1 molecule of 'formamidopyrimidine', and 1 molecule of 'DNA containing a hNTH1-bound apurinic/apyrimidinic site' are present. This reaction takes place in the 'nucleus' and is mediated by the 'pyrimidine-specific oxidized base lesion DNA N-glycosylase activity' of 'hNTH1'.
At the beginning of this reaction, 1 molecule of 'hNTH1 glycosylase:dihydrouracil complex' is present. At the end of this reaction, 1 molecule of 'DNA containing a hNTH1-bound apurinic/apyrimidinic site', and 1 molecule of '5,6-Dihydrouracil' are present. This reaction takes place in the 'nucleus' and is mediated by the 'pyrimidine-specific oxidized base lesion DNA N-glycosylase activity' of 'hNTH1'.
Depyrimidination of a damaged nucleotide is mediated by a pyrimidine-specific DNA glycosylase. The glycosylase cleaves the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar generating a free base and an apyrimidinic (AP) site.
Damaged pyrimidines are first cleaved by pyrimide-specific glycosylases (see Lindahl and Wood 1999).
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AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes.
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DOMAIN The prion domain (PrD) is a Gln/Asn (Q/N)-rich domain, which is unstructured in its native, soluble form, and which forms a parallel in-register beta-sheet in its amyloid form.MISCELLANEOUS [PSI+] is the prion form of SUP35 (PubMed:8978027). [PSI+] is the result of a conformational change of the cellular SUP35 protein that becomes self-propagating and infectious. This conformational change generates a form of SUP35 that assembles into amyloid fibrils. [PSI+] aggregates sequester soluble SUP35, resulting in defects in faithful translation termination by read-through of translation termination codons (PubMed:8670813). [PSI+] can be cured by GdnHCl and by deletion of the molecular chaperone HSP104, which is required for [PSI+] propagation (PubMed:9335589). It is speculated that the prion form would be at least mildly deleterious in most environments, but it might sometimes increases evolvability in certain harsh environments (PubMed:19917766).MISCELLANEOUS Present with 78900 molecules/cell in log phase SD medium.SIMILARITY Belongs to the GTP-binding elongation factor family. ERF3 subfamily.
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SIMILARITY Belongs to the chaperonin (HSP60) family.
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Base excision repair is initiated by DNA glycosylases that hydrolytically cleave of the base-deoxyribose glycosyl bond of a damaged nucleotide residue releasing the damaged base (Lindahl and Wood, 1999).
SUBUNIT F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c.MISCELLANEOUS Present with 164000 molecules/cell in log phase SD medium.SIMILARITY Belongs to the ATPase alpha/beta chains family.
At the beginning of this reaction, 1 molecule of 'PCNA', and 1 molecule of 'Flap endonuclease-1 ' are present. At the end of this reaction, 1 molecule of 'FEN1:PCNA complex' is present. This reaction takes place in the 'nucleus'.
During removal of DNA patch containing abasic residue, DNA glycosylase is displaced by APE1 which endonucleolytically cleaves the 5' side of the base-free deoxyribose residue. POL Beta is recruited to the AP site where it mediates incorporation of the first replacement nucleotide. Association of POL delta with the AP site displaces POL Beta. DNA strand displacement synthesis then follows and flap structures are cleaved.
SUBUNIT F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. In yeast, the dimeric form of ATP synthase consists of 17 polypeptides: alpha, beta, gamma, delta, epsilon, 4 (B), 5 (OSCP), 6 (A), 8, 9 (C), d, E (Tim11), f, g, h, i/j and k.SIMILARITY Belongs to the ATPase C chain family.
While the single-nucleotide replacement pathway appears to facilitate the repair of most damaged bases, an alternative BER pathway is evoked when the structure of the terminal sugar phosphate is such that it can not be cleaved through the AP lyase activity of DNA polymerase, POL Beta. Under these circumstances, a short stretch of residues containing the abasic site is excised and replaced (Dianov et al., 1999). Following DNA glycosylase mediated cleavage of the damaged base, the endonuclease APE1 is recruited to the site of damage where it cleaves the 5' side of the base-free deoxyribose residue. POL Beta then displaces the DNA glycosylase and synthesizes the first replacement residue. DNA polymerase, POL Delta replaces POL Beta and mediates the synthesis of several additional residues resulting in the displacement of a DNA flap containing the abasic sugar phosphate and 3' flanking residues. The flap structure is recognized and cleaved by the flap endonuclease, FEN1 and the replacement residues are then ligated by the DNA ligase, LIG1 (Klungland and Lindahl, 1997; Matsumoto et al., 1999).
Resolution of AP sites can occur through the single-nucleotide replacement pathway or through the multiple-nucleotide patch replacement pathway.
Nuclear export of the stress-activated protein kinase p38 mediated by its substrate MAPKAP kinase-2
At the beginning of this reaction, 1 molecule of 'hNTH1', and 1 molecule of 'Double-strand DNA containing a dihydrouracil' are present. At the end of this reaction, 1 molecule of 'hNTH1 glycosylase:dihydrouracil complex' is present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'hNTH1', and 1 molecule of 'Double-strand DNA containing a cytosine glycol' are present. At the end of this reaction, 1 molecule of 'hNTH1 glycosylase:cytosine glycol complex' is present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'Double-strand DNA containing an uracil opposite to a guanine', and 1 molecule of 'UNG2' are present. At the end of this reaction, 1 molecule of 'UNG2 glycosylase:uracil complex' is present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'Double-strand DNA containing 5-hydroxyuracil opposite to a guanine', and 1 molecule of 'UNG2' are present. At the end of this reaction, 1 molecule of 'UNG2 glycosylase:5-hydroxyuracil complex' is present. This reaction takes place in the 'nucleus'.
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CATALYTIC ACTIVITY (S)-lactate + 2 ferricytochrome c = pyruvate + 2 ferrocytochrome c + 2 H(+).COFACTOR FMN (PubMed:11914072).COFACTOR Binds 1 heme B (iron-protoporphyrin IX) group non-covalently per subunit (PubMed:11914072).SUBUNIT Homotetramer.INDUCTION By L-lactate. Induced during respiratory adaptation.MISCELLANEOUS Present with 4590 molecules/cell in log phase SD medium.SIMILARITY Contains 1 cytochrome b5 heme-binding domain.SIMILARITY Contains 1 FMN hydroxy acid dehydrogenase domain.
Base excision repair is initiated by a DNA glycosylase which first recognizes and removes a damaged or incorrect (e.g. mismatched) base.
At the beginning of this reaction, 1 molecule of 'UNG2 glycosylase:uracil complex' is present. At the end of this reaction, 1 molecule of 'DNA containing UNG2-bound apurinic/apyrimidinic site', and 1 molecule of 'Uracil' are present. This reaction takes place in the 'nucleus' and is mediated by the 'uracil DNA N-glycosylase activity' of 'UNG2'.
At the beginning of this reaction, 1 molecule of 'hNTH1', and 1 molecule of 'Double-strand DNA containing a formamidopyrimidine ' are present. At the end of this reaction, 1 molecule of 'hNTH1 glycosylase: foramidopyrimidine complex' is present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'hNTH1', and 1 molecule of 'Double-strand DNA containing a thymine glycol ' are present. At the end of this reaction, 1 molecule of 'hNTH1 glycosylase:thymine glycol' is present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'UNG2 glycosylase:5-hydroxyuracil complex' is present. At the end of this reaction, 1 molecule of 'DNA containing UNG2-bound apurinic/apyrimidinic site', and 1 molecule of '5-hydroxyuracil' are present. This reaction takes place in the 'nucleus' and is mediated by the 'uracil DNA N-glycosylase activity' of 'UNG2'.
At the beginning of this reaction, 1 molecule of 'hNTH1 glycosylase:thymine glycol' is present. At the end of this reaction, 1 molecule of 'Thymine glycol', and 1 molecule of 'DNA containing a hNTH1-bound apurinic/apyrimidinic site' are present. This reaction takes place in the 'nucleus' and is mediated by the 'pyrimidine-specific oxidized base lesion DNA N-glycosylase activity' of 'hNTH1'.
Energy dependent regulation of mTOR by LKB1-AMPK
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Endothelium-derived relaxing and contracting factors
The human gene SLC29A4 encodes the equilibrative nucleoside transporter 4 (ENT4). It is ubiquitously expressed and mediates the reversible transport of the nucleoside adenosine at acidic pH (this transport is absent at pH 7.4) (Barnes K et al, 2006). ENT4 has also been shown to mediate the transport of biogenic amines such as serotonin, dopamine, norepinephrine and epinephrine. For this reason, ENT4 is also known as the plasma membrane monoamine transporter (PMAT) (Engel K et al, 2004).
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The human gene SLC33A1 encodes acetyl-CoA transporter AT1 (Kanamori A et al, 1997).Acetyl-CoA is transported to the lumen of the Golgi apparatus, where it serves as the substrate of acetyltransferases that modify the sialyl residues of gangliosides and glycoproteins. Defects in SLC33A1 are the cause of spastic paraplegia autosomal dominant type 42 (SPG42) which is a neurodegenerative disorder (Lin P et al, 2008).
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Two families of transport proteins mediate the movement of nucleosides and free purine and pyrimidine bases across the plasma membrane. Equilibrative nucleoside transporters allow the movement of these molecules along concentration gradients into or out of cells (Baldwin et al. 2003); concentrative nucleoside transporters actively transport nucleosides into cells by coupling their transport to the inward movement of sodium ions (Gray et al. 2003). Of the four human equilibrative nucleoside transporters, two are well characterized. SLC29A1 (solute carrier family 29 (nucleoside transporters), member 1) mediates the transport of nucleosides across the plasma membrane. SLC29A2 (solute carrier family 29 (nucleoside transporters), member 2) mediates the transport of both nucleosides and free bases. Transporter specificities were determined by expressing cloned human genes in Xenopus oocytes or in mammalian cultured cell lines whose own nucleotide transporters had been disrupted by mutation. These studies establish that the transport processes are specific and saturable, and that the multiple nucleotides and bases compete for a single binding site on each transporter. Some features of SLC29A2 specificity are complex. For example, in the Xenopus oocyte system, radiolabeled uracil and adenine are taken up, and an excess of either molecule inhibits uptake of radiolabeled hypoxanthine, while in the cultured mammalian cell system, neither adenine nor uracil can inhibit uptake of radiolabeled uridine. If these results reflect ENT2 function in vivo, they indicate that the net movement of a nucleoside or base across the cell membrane is determined not only by its own concentrations in the extracellular space and the cytosol, but also by the concentrations of the other nucleosides and bases competing for access to the transporter. The human genome encodes three concentrative transporters, SLC28A1, 2, and 3 (solute carrier family 28 (sodium-coupled nucleoside transporter), member 1, 2, and 3). All three genes have been cloned, and expression of the human proteins in Xenopus oocytes has allowed their transport properties to be determined. SLC28A1 mediates the uptake of pyrimidine nucleosides and adenosine (Ritzel et al. 1997); SLC28A2 the uptake of purine nucleosides and uridine (Wang et al. 1997); and SLC28A3 the uptake of purine and pyrimidine nucleosides (Ritzel et al. 2001). Amino acid sequence motifs that determine the specificities of these transporters have been identified in studies of chimeric and mutant proteins (Loewen et al. 1999). SLC28A3 protein co-transports two sodium ions per nucleoside; SLC28A1 and 2 transport one sodium per nucleoside (Ritzel et al. 2001). Physiological roles for nucleoside and base transport include provision of nucleosides to cells with little capacity to synthesize these molecules de novo, and regulation of extracellular levels of adenosine, which is released from muscle during intense exercise and has signaling properties. In kidney and intestinal epithelia, the combination of apically localized CNT transporters and basolaterally localized ENT transporters provides a mechanism for net transport of nucleosides (Mangravite et al. 2003). These transporters also mediate the uptake of nucleoside analogs used clinically as anti-viral and anti-tumor drugs. Orthologs of human concentrative and equilibrative transporter proteins have been identified in many eukaryotes, but functional studies of transporters even from organisms closely related to humans (e.g. rat, Gerstin et al. 2002) have revealed differences in substrate specificities. Prediction of drug uptake and other functions of these molecules by human - model organism orthology is thus risky.
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The plasma membrane-associated protein SLC29A2 mediates the reversible transport of one molecule of adenine, adenosine, cytidine, cytosine, guanine, guanosine, hypoxanthine, inosine, thymidine, thymine, uracil, or uridine from the extracellular space to the cytosol.
The human gene SLC29A3 encodes the equilibrative nucleoside transporter 3 (ENT3). It is abundant in many tissues, especially the placenta and is localized intracellularly on the lysosomal membrane. ENT3 mediates the reversible transport of nucleosides and the nucleobase adenine (Baldwin SA et al, 2005). Defects in SLC29A3 are the cause of H syndrome, an autosomal recessive disorder(Molho-Pessach V et al, 2008).
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The human gene SLC35B4 encodes the bifunctional UDP-xylose and UDP-N-acetylglucosamine transporter YEA4. YEA4 resides on the Golgi membrane and mediates the influx of UDP-N-acetylglucosamine into the lumen (Ashikov A et al, 2005).
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The human gene SLC35B4 encodes the bifunctional UDP-xylose and UDP-N-acetylglucosamine transporter YEA4. YEA4 resides on the Golgi membrane and mediates the influx of UDP-xylose into the lumen (Ashikov A et al, 2005).
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Nucleotide sugars are used as sugar donors by glycosyltransferases to create the sugar chains for glycoconjugates such as glycoproteins, polysaccharides and glycolipids. Glycosyltransferases reside mainly in the lumen of the Golgi apparatus and endoplasmic reticulum (ER) whereas nucleotide sugars are synthesized in the cytosol. The human solute carrier family SLC35 encode nucleotide sugar transporters (NSTs) which can mediate the antiport of nucleotide sugars in exchange for the corresponding nucleoside monophosphates (eg. UMP for UDP-sugars). Owing to their function, NSTs are primarily located on Golgi and ER membranes (He L et al, 2009; Handford M et al, 2006; Ishida N and Kawakita M, 2004).
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cDNA cloning and mapping of a novel subtype of glutamine:fructose-6-phosphate amidotransferase (GFAT2) in human and mouse
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Aquaporins (AQP's) are six-pass transmembrane proteins that form channels in membranes. Each monomer contains a central channel formed in part by two asparagine-proline-alanine motifs (NPA boxes) that confer selectivity for water and/or solutes. The monomers assemble into tetramers. Most aquaporins (i.e. AQP0/MIP, AQP1, AQP2, AQP3, AQP4, AQP5, AQP7, AQP8, AQP9, AQP10) passively transport water into and out of cells according to the osmotic gradient across the membrane. Four aquaporins (the aquaglyceroporins AQP3, AQP7, AQP9, AQP10) conduct glycerol, three aquaporins (AQP7, AQP9, AQP10) conduct urea, and one aquaporin (AQP6) conducts anions, especially nitrate. AQP8 also conducts ammonia in addition to water. AQP11 and AQP12, classified as group III aquaporins, were identified as a result of the genome sequencing project and are characterized by having variations in the first NPA box when compared to more traditional aquaporins. Additionally, a conserved cysteine residue is present about 9 amino acids downstream from the second NPA box and this cysteine is considered indicative of group III aquaporins. Purified AQP11 incorporated into liposomes showed water transport. Knockout mice lacking AQP11 had fatal cyst formation in the proximal tubule of the kidney. Exogenously expressed AQP12 showed intracellular localization. AQP12 is expressed exclusively in pancreatic acinar cells. Aquaporins are important in fluid and solute transport in various tissues. In adipocytes, glycerol generated by triglyceride hydrolysis is exported by AQP7 and is imported by liver cells via AQP9. AQP1 plays a role in forming cerebrospinal fluid and AQP1, AQP4, and AQP9 appear to be important in maintaining fluid balance in the brain. AQP0, AQP1, AQP3, AQP4, AQP8, AQP9, and AQP11 play roles in the physiology of the hepatobiliary tract. In the kidney, water and solutes are passed out of the bloodstream and into the proximal tubule via the slit-like structure formed by nephrin in the glomerulus. Water is reabsorbed from the filtrate during its transit through the proximal tubule, the descending loop of Henle, the distal convoluted tubule, and the collecting duct. Aquaporin-1 (AQP1) in the proximal tubule and the descending thin limb of Henle is responsible for about 90% of reabsorption (as estimated from mouse knockouts of AQP1). AQP1 is located on both the apical and basolateral surface of epithelial cells and thus transports water through the epithelium and back into the bloodstream. In the collecting duct epithelial cells have AQP2 on their apical surfaces and AQP3 and AQP4 on their basolateral surfaces to transport water across the epithelium. The permeability of the epithelium is regulated by vasopressin, which activates a signaling cascade leading to the phosphorylation of AQP2 and its translocation from intracellular vesicles to the apical membrane of collecting duct cells. Here, three views of aquaporin-mediated transport have been annotated: a generic view of transport mediated by the various families of aquaporins independent of tissue type, a view of the role of specific aquaporins in maintenance of renal water balance, and a view of the role of specific aquaporins in glycerol transport from adipocytes to the liver.
In the kidney water and solutes are passed out of the bloodstream and into the proximal tubule via the slit-like structure formed by nephrin in the glomerulus. Water is reabsorbed from the filtrate during its transit through the proximal tubule, the descending loop of Henle, the distal convoluted tubule, and the collecting duct. Aquaporin-1 (AQP1) in the proximal tubule and the descending thin limb of Henle is responsible for about 90% of reabsorption (as estimated from mouse knockouts of AQP1). AQP1 is located on both the apical and basolateral surface of epithelial cells and thus transports water through the epithelium and back into the bloodstream. In the collecting duct epithelial cells have AQP2 on their apical surface and AQP3 and AQP4 on their basolateral surface to transport water across the epithelium. The permeability of the epithelium is regulated by vasopressin, which activates the phosphorylation and subsequent translocation of AQP2 from intracellular vesicles to the plasma membrane.
Aquaporin-3 (AQP3) passively transports water and glycerol across the plasma membrane according to the osmotic gradient. AQP3 is expressed in airway epithelia, secretory glands, skin, the collecting ducts of the kidney, and the basolateral surface of intestinal epithelium..
Aquaporin-9 (AQP9) passively transports water, glycerol, urea, and some other small neutral solutes across the plasma membrane according to the osmotic gradient. AQP9 is expressed in the sinusoidal plasma membrane in the liver facing the portal vein where it is believed to be responsible for glycerol uptake as part of gluconeogenesis. AQP9 is also expressed in glia, neurons, and peripheral leukocytes.
Aquaporin-7 (AQP7) passively transports glycerol and water across the plasma membrane according to the osmotic gradient. AQP7 is expressed in adipocytes under the direct control of the PPARG and RXRA nuclear receptors. Expression of AQP7 correlates with release of glycerol from adipocytes. AQP7 is seen to translocate from the nuclear periphery to the plasma membrane during adrenaline-stimulated lipolysis. In rat AQP7 also transports urea.
Triglycerides stored in adipocytes are hydrolyzed to yield fatty acids and glycerol. The glycerol is passively transported out of the adipocyte and into the bloodstream by Aquaporin-7 (AQP7) located in the plasma membrane of adipocytes. Glycerol in the bloodstream is passively transported into liver cells by AQP9 located in the plasma membrane of hepatocytes. Once inside the liver cell the glycerol is a substrate for gluconeogenesis.
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The efflux pump ABCG2 can relieve cells from toxic heme concentrations even against a concentration gradient. It is expressed in placenta, liver, and small intestine (Krishnamurthy et al, 2004; Doyle & Ross, 2003; Zhang et al, 2003).
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CATALYTIC ACTIVITY ATP + H(2)O = ADP + phosphate.MISCELLANEOUS Present with 35100 molecules/cell in log phase SD medium.MISCELLANEOUS Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY Belongs to the MCM family.SIMILARITY Contains 1 MCM domain.
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CATALYTIC ACTIVITY ATP + H(2)O = ADP + phosphate.MISCELLANEOUS Present with 13400 molecules/cell in log phase SD medium.MISCELLANEOUS Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. Specifically a MCM467 subcomplex is shown to have in vitro helicase activity which is inhibited by the MCM2 subunit. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY Belongs to the MCM family.SIMILARITY Contains 1 MCM domain.
Endocytosis of iron loaded transferrin/receptor complex leads, after acidification of the endosome, to the separation of iron and its diffusion out of the vesicle. The endosome is not fused with a lysosome but recycles its content back to the cell surface where soon transferrin dissociates from its receptor (Dautry-Varsat, 1986).
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CATALYTIC ACTIVITY ATP + H(2)O = ADP + phosphate.MISCELLANEOUS Present with 8800 molecules/cell in log phase SD medium.MISCELLANEOUS Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. Specifically a MCM467 subcomplex is shown to have in vitro helicase activity which is inhibited by the MCM2 subunit. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY Belongs to the MCM family.SIMILARITY Contains 1 MCM domain.
CATALYTIC ACTIVITY ATP + H(2)O = ADP + phosphate.MISCELLANEOUS Present with 166 molecules/cell in log phase SD medium.MISCELLANEOUS Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. Specifically a MCM467 subcomplex is shown to have in vitro helicase activity which is inhibited by the MCM2 subunit. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY Belongs to the MCM family.SIMILARITY Contains 1 MCM domain.
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CATALYTIC ACTIVITY ATP + H(2)O = ADP + phosphate.MISCELLANEOUS Present with 1690 molecules/cell in log phase SD medium.MISCELLANEOUS Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. Specifically a MCM467 subcomplex is shown to have in vitro helicase activity which is inhibited by the MCM2 subunit. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY Belongs to the MCM family.SIMILARITY Contains 1 MCM domain.
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CATALYTIC ACTIVITY ATP + H(2)O = ADP + phosphate.MISCELLANEOUS Present with 10300 molecules/cell in log phase SD medium.MISCELLANEOUS Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY Belongs to the MCM family.SIMILARITY Contains 1 MCM domain.
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PATHWAY Cofactor biosynthesis; ubiquinone biosynthesis.SIMILARITY Belongs to the COQ7 family.
FUNCTION Methyltransferase required for the conversion of 2-polyprenyl-6-methoxy-1,4-benzoquinol (DDMQH2) to 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQH2).PATHWAY Cofactor biosynthesis; ubiquinone biosynthesis.MISCELLANEOUS Present with 8100 molecules/cell in log phase SD medium.SIMILARITY Belongs to the class I-like SAM-binding methyltransferase superfamily. UbiE family.
PATHWAY Cofactor biosynthesis; ubiquinone biosynthesis.MISCELLANEOUS Present with 2940 molecules/cell in log phase SD medium.SIMILARITY Belongs to the UbiH/COQ6 family.
Proteins with transporting functions can be roughly classified into 3 categories: ATP-powered pumps, ion channels, and transporters. Pumps utilize the energy released by ATP hydrolysis to power the movement of the substrates across the membrane, against their electrochemical gradient. Channels at the open state can transfer the substrates (ions or water) down their electrochemical gradient, at an extremely high efficiency (up to 108 s-1). Transporters facilitate the movement of a specific substrate âeither against or following their concentration gradient, at a lower speed (about 102 -104 s-1); as generally believed, conformational change of the transporter protein is involved in the transfer process. According to the Human Genome Organization (HUGO) Gene Nomenclature Committee, all human transporters can be grouped into the solute-carrier (SLC) superfamily. Currently, there are 55 SLC families in the superfamily, with a total of at least 362 putatively functional protein-coding genes (Hediger et al, 2004; He et al., 2009). At least 20-25% amino-acid sequence identity is shared by members belonging to the same SLC family. No homology is shared between different SLC families. While the HUGO nomenclature system by definition only includes human genes, the nomenclature system has been informally extended to include rodent species through the use of lower cases letters (e.g., Slc1a1 denotes the rodent ortholog of the human SLC1A1 gene). And it's worthwhile to mention that pumps, channels and aquporins are not included in SLC superfamily.
This pathway groups the processes mediated by SLC transporters, by which vitamins and cofactors, as well as nucleosides, nucleotides, nucleobases, and related molecules cross lipid bilayer membranes.
Long chain fatty acids (LCFAs) are involved in many cellular functions. They can be used as an important source of energy by skeletal muscle and heart tissues. Also, they are used in the production of hormones which can regulate inflammation, blood pressure, the clotting process, blood lipid levels and the immune response. Fatty acid transporter proteins (FATPs) are a family of proteins which mediate fatty acid uptake into cells when overexpressed. FATPs also possess enzymatic activity, the details of which are captured elsewhere. There are 6 human genes of the SLC27A family which encode for FATP1-6 (Stahl A, 2004; Gimeno RE, 2007). To date, only FATP1, 4 and 6 have demonstrable transporter function. Fatty acids with carbon chain lengths of more than 10 are the most likely substrates for these transporters.
Of the six fatty acid transporter proteins (FATP) characterized, only three have been shown to mediate the influx into cells of long chain fatty acids (LCFAs); FATP1, 4 and 6. They have been shown to transport the prototypical LCFA oleic acid (OLEA) but are believed to be able to transport LCFAs with chain lengths longer than 10 carbons. FATP1 is highly expressed in adipose tissue and muscle (Hatch GM et al, 2002). FATP4 is the major intestinal LCFA transporter (Fitscher BA et al, 1998; Stahl A et al, 1999). FATP6 is localized to cardiac myocytes (Gimeno RE et al, 2003).
Aquaporin-3 (AQP3), AQP7, AQP9, and AQP10 are 6-pass transmembrane proteins that passively transport glycerol across the plasma membrane through a pore in each subunit of a homotetramer.
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Cloning and characterization of band 3, the human erythrocyte anion-exchange protein (AE1)
Aquaporin-0 (AQP0, also known as MIP), AQP1, AQP2, AQP3, AQP4, AQP5, AQP7, AQP8, AQP9, and AQP10 are 6-pass transmembrane proteins that passively transport water across the plasma membrane according to the concentration gradient. Each molecule contains a water channel and subunits assemble into homotetramers. In principle water can move in either direction through an aquaporin, however in vivo flow may occur in only one direction. Conductance of water by AQP0 and AQP11 are low relative to other aquaporins.
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Aquaporin-9 (AQP9) and AQP10 are 6-pass transmembrane proteins that passively transport urea across the plasma membrane through a pore in each subunit of a homotetramer.
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Guanine nucleotide exchange factors for Rho GTPases: turning on the switch
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A quantitative model of human DNA base excision repair. I. Mechanistic insights
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Functional characterization of three novel tissue-specific anion exchangers SLC26A7, -A8, and -A9
Phosphorylation of p40AUF1 regulates binding to A + U-rich mRNA-destabilizing elements and protein-induced changes in ribonucleoprotein structure
Regulation of A + U-rich element-directed mRNA turnover involving reversible phosphorylation of AUF1
Enhanced tyrosine phosphorylation in B lymphocytes upon complexing of membrane immunoglobulin
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Endogenous retroviral sequence is fused to FGFR1 kinase in the 8p12 stem-cell myeloproliferative disorder with t(8;19)(p12;q13.3)
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A 40-bp RNA element that mediates stabilization of vascular endothelial growth factor mRNA by HuR
Antigen presentation and the ubiquitin-proteasome system in host-pathogen interactions
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Regulation of nuclear processes by inositol polyphosphates
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KARAP/DAP12/TYROBP: three names and a multiplicity of biological functions
A cooperative action of the ATP-dependent import motor complex and the inner membrane potential drives mitochondrial preprotein import
Clearance of p16Ink4a-positive senescent cells delays ageing-associated disorders
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The processivity of multiubiquitination by the APC determines the order of substrate degradation
A third MRX family (MRX68) is the result of mutation in the long chain fatty acid-CoA ligase 4 (FACL4) gene: proposal of a rapid enzymatic assay for screening mentally retarded patients
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A human homolog of the vaccinia virus HindIII K4L gene is a member of the phospholipase D superfamily
Selective and ATP-dependent translocation of peptides by the MHC-encoded transporter
HDAC6-p97/VCP controlled polyubiquitin chain turnover
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Cloning and characterization of murine 1-acyl-sn-glycerol 3-phosphate acyltransferases and their regulation by PPARalpha in murine heart
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Molecular cloning and characterization of an aquaporin cDNA from salivary, lacrimal, and respiratory tissues
In situ visualization of DNA double-strand break repair in human fibroblasts.
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Comparative mechanistic and substrate specificity study of inositol polyphosphate 5-phosphatase Schizosaccharomyces pombe Synaptojanin and SHIP2
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'NAcGlu [mitochondrial matrix]' positively regulates 'carbamoyl-phosphate synthase (ammonia) activity of CPS1 [mitochondrial matrix]'
'L-Arg [cytosol]' positively regulates 'acetyl-CoA:L-glutamate N-acetyltransferase activity of NAGS(19-534) [mitochondrial matrix]'
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Platelet-collagen interaction: is GPVI the central receptor?
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Glycogen debranching enzyme: purification, antibody characterization, and immunoblot analyses of type III glycogen storage disease.
Mitochondrial respiratory chain-dependent generation of superoxide anion and its release into the intermembrane space
Liver glucose transporter: a basolateral protein in hepatocytes and intestine and kidney cells
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p38 mitogen-activated protein kinase pathway promotes skeletal muscle differentiation. Participation of the Mef2c transcription factor
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Both p16 and p21 families of cyclin-dependent kinase (CDK) inhibitors block the phosphorylation of cyclin-dependent kinases by the CDK-activating kinase
The role of flavin-containing monooxygenases in drug metabolism and development
TIN2 binds TRF1 and TRF2 simultaneously and stabilizes the TRF2 complex on telomeres
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Transcriptional control of megakaryocyte development
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Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation
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2-acyl-sn-glycero-3-phosphoserine [ChEBI:37646]
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ChEBI:37643 (25S)-3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA
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Small is beautiful: insulin-like growth factors and their role in growth, development, and cancer
Phosphate transporters: a tale of two solute carrier families
Two cofactors and cytoplasmic chaperonin are required for the folding of alpha- and beta-tubulin
Ligand-induced, receptor-mediated dimerization and activation of EGF receptor
The path to perdition is paved with protons
Mitochondrial aspartyl-tRNA synthetase deficiency causes leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation
Regulation of the biosynthesis of 4,7,10,13,16,19-docosahexaenoic acid
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Over-expression in Escherichia coli and characterization of two recombinant isoforms of human FAD synthetase
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Isozymes of human phosphofructokinase: identification and subunit structural characterization of a new system
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Iron-sulfur protein biogenesis in eukaryotes: components and mechanisms
Autosomal recessive HEM/Greenberg skeletal dysplasia is caused by 3 beta-hydroxysterol delta 14-reductase deficiency due to mutations in the lamin B receptor gene
The plasma membrane-associated protein SLC29A1 mediates the reversible transport of one molecule of adenosine, guanosine, inosine, or uridine from the cytosol to the extracellular space.
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The human gene SLC30A1 encodes the zinc transporter ZnT1. It is widely expressed throughout the body and it's expression is regulated by zinc. ZnT1 is the only member of the SLC30 gene family that is located on the plasma membrane and mediates the transport of zinc out of the cell (Devergnas S et al, 2004).
The human gene SLC39A7 encodes the zinc transporter ZIP7 (HKE4, Histidine-rich membrane protein Ke4). It is expressed in many tissues but especially in liver, kidney and the hormonal tissues apart from brain. Unlike the other members of the LZT subfamily, ZIP7 is localized to intracellular membranes of the ER rather than the plasma membrane and mediates zinc efflux into the cytoplasm (Taylor KM et al, 2004).
The human SLC30 gene family of solute carriers is thought to participate in the homeostasis of zinc ions and facilitate zinc transport into specialized compartments of the cell such as endosomes, golgi network and synaptic vesicles. There are 10 members of this family, named ZnT1-10. ZnT4, ZnT9 and ZnT10 have no function determined as of yet (Palmiter RD and Huang L, 2004).
Zinc is an essential element for all organisms because it serves as a catalytic or structural cofactor for many different proteins. Cellular zinc homoeostasis is co-ordinated through Zn2+-specific transporters which are members of two distinct gene families. Members of the SLC39 gene family (ZRTL-like import proteins1-14, ZIP1-14) are responsible for Zn2+ import into the cytoplasm, either across the plasma membrane or out of intracellular organelles. In contrast, members of the SLC30 gene family (zinc transporters 1-10, ZnT1-10) export Zn2+ from the cytoplasm, either across the plasma membrane into the extracellular space or into intracellular organelles (Murakami M and Hirano T, 2008; Devirgiliis C et al, 2007; Eide DJ, 2006).
The SLC39 gene family encode zinc transporters belonging to the ZIP (Zrt-, Irt-like proteins) family of metal ion transporters. All ZIPs transport metal ions into the cytoplasm of cells, be it across cellular membranes or from intracellular compartments. To date, there are 14 human SLC39 genes that encode the zinc transporters hZIP1-14. There are 9 members which belong to a subfamily of the ZIPs called the LZTs (LIV-1 subfamily of ZIP zinc transporters) (Taylor KM and Nicholson RI, 2003). Of these 14 proteins, four (hZIP9, 11, 12 and 13) have no function determined yet (Eide DJ, 2004).
Hexoses like glucose, galactose and fructose serve as basic fuel molecules for eukaryotic cells. Indeed, glucose is the main energy source for mammalian cells. These sugars are unable to diffuse across cellular membranes, and require transporter proteins for entry into and exit out of cells. Four gene families encode hexose transporter proteins (He et al, 2009). SLC2 family contains 14 genes and encode facilitative glucose transporters (GLUTs) (Uldry M and Thorens B, 2004). SLC5 family contains 12 genes and encode Na+/glucose symporters (Wright EM and Turk E, 2004). SLC37 family contains 4 members and encode sugar-phosphate/phosphate exchangers (Bartoloni L and Antonarakis SE, 2004). SLC45 family has 4 members and encode putative sugar/H+ symporters.
Six SLC gene families encode proteins which mediate transport of metals. The families are SLC11, SLC30, SLC31, SLC39, SLC40 and SLC41 (He L et al, 2009; Bressler JP et al, 2007).
The plasma membrane-associated protein SLC29A2 mediates the reversible transport of one molecule of adenine, adenosine, cytidine, cytosine, guanine, guanosine, hypoxanthine, inosine, thymidine, thymine, uracil, or uridine from the cytosol to the extracellular space.
The plasma membrane-associated protein SLC29A1 mediates the reversible transport of one molecule of adenosine, cytosine, guanosine, inosine, thymidine, or uridine from the extracellular space to the cytosol.
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DNA mismatch repair: functions and mechanisms
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Class II facilitative transporters consist of GLUT5, 7, 9 and 11 (Zhao FQ and Keating AF, 2007; Wood IS and Trayhurn P, 2003).
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The human SLC2A9 gene encodes two isoforms of class II facilitative glucose transporter 9; GLUT9 (Phay JE et al, 2000) and GLUT9DeltaN (Augustin R et al, 2004). GLUT9 is expressed mainly in kidney (proximal tubules of epithelial cells) and liver while GLUT9DeltaN is expressed mainly in kidney and placenta. As well as mediating the uptake of fructose and glucose (at a low rate), GLUT9 can also mediate the tranpsort of urate (uric acid), the end product of purine metabolism in humans and great apes (Vitart V et al, 2008). Mutations in SLC2A9 influence serum urate concentrations with excess serum accumulation of urate leading to the development of gout (Vitart V et al, 2008).
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Two gene families are responsible for glucose transport in humans. SLC2 (encoding GLUTs) and SLC5 (encoding SGLTs) families mediate glucose absorption in the small intestine, glucose reabsorption in the kidney, glucose uptake by the brain across the blood-brain barrier and glucose release by all cells in the body. Glucose is the main energy source used by cells to make energy. Im mammals, blood glucose levels are tightly controlled and glucose is taken up from interstitial fluid by a passive, facilitative transport driven by the diffusion gradient of glucose (and other sugars) across the plasma membrane. This process is mediated by a family of Na+-independent, facilitative glucose transporters (GLUTs) encoded by the SLC2A gene family (Zhao FQ and Keating AF, 2007; Wood IS and Trayhurn P, 2003). There are 14 members belonging to this family (GLUT1-12, 14 and HMIT (H+/myo-inositol symporter)). The GLUT family can be subdivided into three subclasses (I-III) based on sequence similarity and characteristic sequence motifs (Joost HG and Thorens B, 2001).
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Gamma-Aminobutyric acid (GABA) is the major inhibitory transmitter of the vertebrate retina. The gene SLC32A1 encodes the vesicular inhibitory amino acid transporter (VIAAT, also called vesicular GABA transporter VGAT) (Jellali A et al, 2002). VIAAT is a proton-coupled amino acid antiporter, uptaking the inhibitory neurotransmitters GABA and glycine into synaptic vesicles in exchange for protons. This process is driven by the H+-ATPase, providing the driving force for uptake of these neurotransmitters. The protein is expressed throughout the terminal ends of horizontal cells of the retina.
Teleologically, one might argue that inorganic cation and anion transport would be evolutionarily among the oldest transport functions. Eight families comprise the group that transports exclusively inorganic cations and anions across membranes : SLC4 plays a pivotal role in mediating Na+ - and/or Cl- -dependent transport of basic anions [e.g. HCO3-, (CO3)2-] in various tissues and cell types (in addition to pH regulation, specific members of this family also contribute to vectorial trans-epithelial base transport in several organ systems including the kidney, pancreas, and eye) (Pushkin A and Kurtz I, 2006); SLC8 is a group of Na+/Ca2+ exchangers (SLC8A1 is involved in cardiac contractility) (Quednau BD et al, 2004); SLC24 is a group of Na+/Ca2+ or Na+/K+ exchangers (Altimimi HF and Schnetkamp PP, 2007); SLC9 comprises Na+/H+ exchanger proteins involved in the electroneutral exchange of sodium ion and protons (Orlowski J and Grinstein S, 2004); SLC12 functions as Na+, K+ and Cl- ion electroneutral symporters (Hebert SC et al, 2004); SLC26 is the trans-epithelial multifunctional anion (e.g. sulfate, oxalate, HCO-, Cl-) exchanger family, important in cartilage development, production of thyroid hormone, sound amplification in the cochlea etc (Sindic A et al, 2007; Dorwart MR et al, 2008; Ashmore J, 2008). SLC34 is an important Type II Na+/(HPO4)2- symporter (Forster IC et al, 2006; Virkki LV et al, 2007); SLC20 was originally identified as a viral receptor, and functions as a Type III Na+/(H2PO4)- symporter (Collins JF et al, 2004; Virkki LV et al, 2007). Eight SLC gene families are involved in the transport of amino acids and oligopeptides.
The class I facilitative glucose transporters contain GLUT1-4. As well as glucose, these proteins can transport other hexoses such as fructose, galactose and glucosamine. GLUT2 is expressed by SLC2A2 and is a low affinity glucose transporter (Fukumoto H et al, 1988). It is expressed mainly in the kidney, liver and pancreatic beta-cells. In beta-cells, it functions as a glucose-sensor for insulin secretion and in the liver, it allows for bi-directional glucose transport. In this reaction, it is shown to mediate the influx of glucose. In the next reaction, it is shown to be mediating efflux of glucose. Defects in SLC2A2 are the cause of Fanconi-Bickel syndrome (FBS). It is characterized by hepatorenal glycogen accumulation, proximal renal tubular dysfunction, and impaired utilization of glucose and galactose (Burwinkel B et al, 1999). SLC2A3 encodes GLUT3 which is mainly expressed in the brain but also in a wide range of tissues. If has a high affinity for glucose and can also transport other sugars (Kayano T et al, 1988). GLUT4, encoded by SLC2A4, is an insulin-responsive glucose transporter found in heart, skeletal muscle, brain and adipose tissue. Due to its sensitivity to insulin, it may play a role in diabetes. In a non-insulin condition, GLUT4 is localized in intracellular GLUT4-containing vesicles. On insulin stimulation, GLUT4 translocates to the plasma membrane where it can increase glucose transport 10-20-fold (Fukumoto H et al, 1989). Defects in SLC2A4 may be a cause of non-insulin-dependent diabetes mellitus (NIDDM) (Kusari J et al, 1991; Choi WH et al, 1991). GLUT1 is curated in its own reaction in this section.
SLC2A7 encodes GLUT7, a class II facilitative glucose transporter which was cloned from a human intestinal cDNA library (Li Q et al, 2004). It has a high affinity for glucose and fructose uptake. GLUT7 is found predominantly in the small intestine, colon, testis and prostate. SLC2A11 encodes GLUT11 (Doege H et al, 2001), another member of the class II facilitative glucose transporters. It has the highest similarity with GLUT5 and in humans, three isoforms are expressed (GLUT11A-C) (Sasaki T et al, 2001). Human GLUT11 has been shown to transport glucose and fructose but not galactose when expressed in Xenopus oocytes ( Scheepers A et al, 2005).
Amino acid transport across plasma membranes is critical to the uptake of these molecules from the gut, to their reabsortion in the kidney proximal tubulues, and to their distribution to cells in which they are required for the synthesis of proteins and of amino acid derived small molecules such as neurotransmitters. Physiological studies have defined 18 "systems" that mediate amino acid transport, each characterized by its amino acid substrates, as well as its pH sensitivity and its association (or not) with ion transport. More recently, molecular cloning studies have allowed the identification of the plasma membrane transport proteins that mediate these reactions. Amino acid uptake mediated by 17 of these transporters is annotated here (Broer 2008).
The SLC17 gene family encode proteins which are organic anion transporters. There are three distinct subfamilies within SLC17; vesicular glutamate transporters (VGLUT1-3 encoded by SLC17A7,6 and 8), type I Na+-coupled phosphate co-transporters (encoded by SLC17A1-4) and a proton-coupled sialic acid co-transporter (encoded by SLC17A5) (Reimer RJ and Edwards RH, 2004). Two members of the SLC5 gene family encode carboxylate transporters, SMCT1 and SMCT2 (Ganapathy V et al, 2008).
The human SLC36A gene family encodes four proton-coupled neutral amino acid transporters, PAT1-4. PAT1 and 2 mediate electroneutral symport of protons and small neutral amino acids like glycine, alanine and proline. PAT3 and 4 are orphans with unknown function (Boll M et al, 2004).
Expression and function of the human androgen-responsive gene ADI1 in prostate cancer
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The primary site for absorption of dietary iron is the duodenum. Ferrous iron (Fe2+) is taken up from the gut lumen across the apical membranes of enterocytes and released into the portal vein circulation across basolateral membranes. The human gene SLC11A2 encodes the divalent cation transporter DCT1 (NRAMP2, Natural resistance-associated macrophage protein 2). NRAMP2 resides on the apical membrane of enterocytes and mediates the uptake of ferrous iron into these cells (Tandy S et al, 2000). DCT1 can also accept a broad range of transition metal ions.
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The human gene family SLC47 encodes 2 multidrug and toxin extrusion (MATE) proteins. Mammalian MATE-type transporters are responsible for the final step in the excretion of metabolic waste and xenobiotic organic cations in the kidney and liver through electroneutral exchange of H(+). MATE1 is primarily expressed in the kidney and liver, where it is localized to the luminal membranes of the urinary tubules and bile canaliculi. When expressed in HEK293 cells, MATE1 mediates H(+)-coupled electroneutral exchange of various drugs (Otsuka M et al, 2005). MATE2 is a human kidney-specific H+/organic cation antiporter that is responsible for the tubular secretion of cationic drugs across the brush border membranes (Masuda S et al, 2006). Substrates for both MATEs include tetraethylammonium, 1-methyl-4-phenylpyridinium, cimetidine, metformin, creatinine, guanidine and procainamide (Tanihara Y et al, 2007).
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The human SLC13A5 gene encodes a sodium-coupled citrate transporter, NACT. This gene is expressed mainly in the liver, with lower levels in brain and testis. NACT has a preference for trivalent citrate (Inoue K et al, 2002).
Five human SLC13 genes encode sodium-coupled sulphate, di- and tri-carboxylate transporters located on the plasma membrane. Two transporters (NaS1 and NaS2) co-transport sulphate with sodium. The other members (NaDC1, NaDC3, and NaCT) co-transport sodium with di- and tri-carboxylates such as succinate, citrate and alpha-ketoglutarate (Pajor AM, 2006).
Mammalian sodium/dicarboxylate cotransporters (transport succinate and other Krebs cycle intermediates) fall into two categories based on their substrate affinity. The human gene SLC13A2 encodes a low-affinity sodium/dicarboxlate co-transporter, NaDC1. NaDC1 is highly expressed in the brush-border membranes of kidney and intestinal cells and reabsorbs Krebs cycle intermediates, such as succinate and citrate, from the glomerular filtrate (Pajor AM, 1996).
Mammalian sodium/dicarboxylate cotransporters (transport succinate and other Krebs cycle intermediates) fall into two categories based on their substrate affinity. The human gene SLC13A3 encodes a high-affinity sodium/dicarboxlate co-transporter, NaDC3. NaDC3 is expressed in the basolateral membrane of renal proximal tubular epithelial cells, sinusoidal membrane of hepatocytes, and brain synaptosomes. Kinetic studies in human retinal pigment epithelial (HRPE) cells suggest three sodium ions co-transported with every divalent succinate (Wang H et al, 2000).
DNA ligases: structure, reaction mechanism, and function
The human gene SLC13A1 encodes a sodium/sulphate co-transporter NaS1 (Lee A et al, 2000). NaS1 is almost exclusively expressed in the kidney and mediates sulphate reabsorption there.
The human gene SLC13A4 encodes a sodium/sulphate co-transporter NaS2 (Girard JP et al, 1999). NaS2 is highly expressed in placenta and testis, mainly in high endothelial venules. Kinetic experiments suggest two sodium ions co-transported for every sulphate ion (Markovich D et al, 2005).
SLC2A13 encodes a H+/myo-inositol co-transporter, HMIT (Uldry M et al, 2001) which is abundantly expressed in the brain. A proton is co-transported with myo-inositol uptake into cells. No glucose transport function has been detected to date.
Myo-Inositol is a neutral cyclic polyol, abundant in mammalian tissues. It plays important roles; it is a precursor to phosphatidylinositols (PtdIns) and to the inositol phosphates (IP), which serve as second messengers and as key regulators of many cell functions. It can also serve as a compatible osmolyte during volume regulation in many tissues where cells are exposed to hyperosmotic conditions. Three members of the glucose transporter families are inositol transporters. Two (SMIT1 and SMIT2) couple myo-inositol transport with two Na+ ions. Unlike SMIT1, SMIT2 also transports D-chiro_inositol. The third transporter (HMIT), couples myo-inositol transport with a proton.
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Nonsense-mediated mRNA decay in human cells: mechanistic insights, functions beyond quality control and the double-life of NMD factors
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Some members of the SLC4A family couple the transport of bicarbonate (HCO3-) to the movement of sodium ions (Na+), they being members 4, 5, 7 and 9. SLC4A4 (NBCe1) is an electrogenic sodium/bicarbonate cotransporter with a Na+:HCO3- stoichiometry of 1:3, although it can also be 1:2 (Burnham CE et al, 1997). SLC4A4 encodes a protein which is expressed in the kidney and pancreas, with lesser expression in many other tissues (Abuladze N et al, 1998). Mutations in SLC4A4 cause permanent isolated proximal renal tubular acidosis (pRTA) (results in accumulation of acid in the body due to a failure of the kidneys to effectively acidify urine) with ocular abnormalities (Igarashi T et al, 1999). SLC4A5 encodes a protein which is expressed in liver, spleen and testes, with lower levels expressed in parts of the brain and kidney (Sassani P et al, 2002). It may have a housekeeping function in regulating the pH of these tissues (Pushkin A et al, 2000). SLC4A7 (NBC3, NBCn1) encodes a protein which performs electroneutral cotransport of Na+ and HCO3- with a 1:1 stoichiometry. It is highly expressed in testes and spleen and, to a lesser extent, in many other tissues including heart, muscle, kidney and GI tract (Pushkin A et al, 1999). SLC4A9 (AE4) was originally thought to exchange Cl- with HCO3- (hence the name AE4) but this has not been reported. Consensus has emerged that it is indeed a Na+/HCO3- co-transporter (Lipovich L et al, 2001). It is predominantly expressed in the kidney, salivary glands, testes, thyroid glands and trachea (Parker MD et al, 2001).
The proteins responsible for the exchange of Cl- with HCO3- are members of the SLC4 (1-3) and SLC26 (3, 4, 6, 7 and 9) transporter families. The SLC26 members are discussed under the section "Multifunctional anion exchangers". SLC4A1 (Band 3, AE1, anion exchanger 1) was the first bicarbonate transporter gene to be cloned and sequenced (Lux SE et al, 1989). It is ubiquitous throughout vertebrates and in humans, is present on erythrocytes and the basolateral surfaces of kidney cells. The erythrocyte and kidney forms are different isoforms of the same protein (Kollert-Jons A et al, 1993). Mutations of erythroid AE1 determine the Diego blood group system (Bruce LJ et al, 1994). A more serious consequence of mutated erythroid AE1 is Hereditary spherocytosis (a disorder leading to haemolytic anaemia) (Jarolim P et al, 1995). Defects in the kidney form of AE1 cause distal (type1) renal tubular acidosis (an inability to acidify urine) (Bruce LJ et al, 1997). SLC4A2 (Non-erythroid band 3-like protein, AE2, anion exchanger 2) is widely expressed and is considered to be the 'housekeeping' isoform of the bicarbonate transporters (Demuth DR et al, 1986). SLC4A3 (Cardiac/brain band 3-like protein, AE3) is expressed in heart and brain (Yannoukakos D et al, 1994).
Respiratory oxidation in the mitochondria produces carbon dioxide (CO2) as a waste product. CO2 is in equilibrium with bicarbonate (HCO3-) and is the body's central pH buffering system. HCO3- is charged so cannot move across membranes unaided. The bicarbonate transport proteins move bicarbonate across the membrane. There are 14 genes which encode these transport proteins in mammals. Applying the Human Genome Organization's sytematic nomenclature to human genes, the bicarbonate transporters belong to the SLC4A and SLC26A families. Within SLC4A, there are two distinct subfamilies, functionally corresponding to the electroneutral Cl-/HCO3- exchangers and Na+-coupled HCO3- co-transporters (Romero MF et al, 2004; Cordat E and Casey JR, 2009).
Two genes encode Na+-dependent Cl-/HCO3- exchangers; SLC4A8 (NDCBE1) and 10 (NCBE). SLC4A8 (NDCBE1) encodes a exchanger protein which mediates Na+:HCO3- transport with a stoichiometry of 1:2:1 (Na+/HCO3-/Cl-). This protein is highly expressed in brain and spine and moderately expressed in trachea, thyroid, and kidney (Amlal H et al, 1999). SLC4A10 (NCBE, NBCn2) encodes a Na+-driven Cl-/HCO3- exchanger protein (Parker MD et al, 2008). It transports extracellular Na+ and HCO3- into cells in exchange for intracellular Cl- and H+, thus raising the intracellular pH.
NHE6 (SLC9A6) (Brett CL et al, 2002; Nakamura N et al, 2005) is expressed ubiquitously and thought to play a housekeeping role in pH homeostasis in early endosomes.
A defined subset of the ABC transporter superfamily, the ABCA transporters, are highly expressed in monocytes and macrophages and are regulated by cholesterol flux which may indicate their role in in chronic inflammatory diseases (Schmitz and Kaminski 2001, Schmitz et al. 2000).
Mitochondrial ABC transporters are thought to play a key role in iron metabolism and heme biosynthesis. All mitochondrial ABC transporters described to date are of the half-transporter type and would probably function as dimers (Ramjeesingh et al. 2003) but their dimerization partners have not yet been identified. ABC7 is the functional human orthologue of yeast Atm1p (Csere et al. 1998), is predicted to dimerize in the same way as Atm1p (Chloupková et al. 2004) and is probably involved in iron homeostasis. Defects in ABCB7 are the cause of X-linked sideroblastic anemia with ataxia (ASAT) [MIM:301310] (Allikmets et al. 1999). Human genes ABCB8 and ABCB10 encode mABC1 and mABC2 respectively (Hogue et al. 1999, Zhang et al 2000 respectively). They would be expected to dimerize, as demonstrated for mABC2 (Graf et al. 2004). Both are believed to have similar functionality to ABC7 although this has not been demonstrated yet.
Mammalian ABC transporters are usually found on the plasma membrane and on organelles such as the ER and peroxisome but a small number are also located on the mitochondria. Here they are thought to play roles in heme biosynthesis and iron-sulphur cluster synthesis (Burke & Ardehali 2007).
The multidrug resistance associated protein (MRPs) subfamily of the ABC transporter family can transport a wide and diverse range of organic anions that can be endogenous compounds and xenobiotics and their metabolites. All human MRPs (except MRP9) can mediate these transport reactions (Deeley et al. 2006). Separately, specific reactions have also been annotated to describe the roles of ABCC4 in platelet dense granule assembly, of ABCC1 in LTC4 export (an aspect of leukotriene synthesis), and of ABCC3 in bile salt efflux.
The ATP-binding cassette (ABC) superfamily of active transporters involves a large number of functionally diverse transmembrane proteins. They transport a variety of compounds through membranes against steep concentration gradients at the cost of ATP hydrolysis. These substrates include amino acids, lipids, inorganic ions, peptides, saccharides, peptides for antigen presentation, metals, drugs, and proteins. The ABC transporters not only move a variety of substrates into and out of the cell, but are also involved in intracellular compartmental transport. Energy derived from the hydrolysis of ATP is used to transport the substrate across the membrane against a concentration gradient. Human genome contains 48 ABC genes; 16 of these have a known function and 14 are associated with a defined human disease (Dean et al. 2001, Borst and Elferink 2002, Rees et al. 2009).
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SLC7A9 as a heterodimer with SLC3A1 in the plasma membrane mediates the exchange of arginine, lysine, or cystine for leucine. The physiological concentrations of these amino acids favor leucine export and arginine / lysine / cystine import. Defects in SLC7A9 and SLC3A1 are associated with cystinuria. In the body, this transport process is prominent in the kidney (Mizoguchi et al. 2001).
SLC36A2 (PAT2), associated with the plasma membrane, has been shown in a limited set of tests in vitro to mediate the uptake of glycine and proline coupled to the uptake of a proton (Boll et al. 2003). PAT2 is most abundantly expressed in kidney and muscle.
SLC36A1 (PAT1), associated with the plasma membrane, mediates the uptake of glycine, alanine, and proline coupled to the uptake of a proton. Northern blotting experiments indicate gene expression principally in the intestine (Chen et al. 2003).
Phosphorus is an essential element that is critical for structural and metabolic roles in all living organisms. Cells obtain phosphorus in the form of negatively-charged inorganic phosphate (Pi). Two SLC families transport phosphate in mammals; SLC34 (Murer H et al, 2004) and SLC20 (Collins JF et al, 2004). Both are secondary-active, Na+-coupled transporter systems which use the inward Na+ gradient (from the Na+-K+-ATPase) to drive phosphate influx into cells (Virkki LV et al, 2007).
NHE7 and 8 (SLC9A7,8) (Nakamura N et al, 2005) are expressed ubiquitously and thought to play a housekeeping role in pH homeostasis in the trans-golgi network.
NHE9 (SLC9A9) (Nakamura N et al, 2005) is expressed ubiquitously and thought to play a housekeeping role in pH homeostasis in the late endosome membrane.
The human SLC26 gene family consists of eleven members which encode multifunctional anion exchangers.These exchangers are capable of transporting a variety of anions such as sulphate, bicarbonate, oxalate, hydroxyl, formate, iodide and chloride. SLC26 members can be grouped according to functional similiarities and three groups can be classified this way. Group 1 are selective sulphate transporters and include SLC26A1 and 2. Group 2 are Cl-/HCO3- exchangers and include SLC26A3, 4 and 6. Group 3 function as ion channels and include SLC26A7 and 9.
There are two transporters of this type; The genes SLC20A1 and SLC20A2 encode for PiT1 (phosphate transporter 1) and PiT2 respectively. They both have a broad tissue distribution and may play a general housekeeping role in phosphate transport such as absorbing phosphate from interstitial fluid and in extracellular matrix and cartilage calcification as well as in vascular calcification. These proteins were originally described as retroviral receptors for the gibbin ape leukemia virus receptor 1 (GLVR1, now called PiT1) (O'Hara B et al, 1990) and GLVR2 (now called PiT2) (van Zeijl M et al, 1994). However, they were found to possess Na+-coupled phosphate cotransporter function (Fernandes I et al, 1999). The transport is electrogenic with a stoichiometry of 2:1 (Na+:Pi).
The SLC9 gene family encode proteins (sodium/proton exchangers, NHE or NHX) which exchange sodium (influx) for protons (efflux) electroneutrally. This mechanism is important because many metabolic processes generate acids which need to be removed to maintain pH. This is the major proton extruding system in cells, driven by the inward sodium ion chemical gradient. To date, there are eleven NHE genes, NHE1-11. NHE1-5 exchange cations at the cell membrane. NHE6-9 exchange cations at endosomal membranes or the trans-golgi network membranes.
The proteins responsible for the exchange of Cl- with HCO3- are members of the SLC4 (1-3) and SLC26 (3, 4 and 6) transporter families. SLC4 members are discussed in the section "Bicarbonate transporters". SLC26A3 (Chloride anion exchanger, Down-regulated in adenoma, DRA) is expressed in the mucosa of the colon and helps mediate electrolyte and fluid absorption (Schweinfest CW et al, 1993). Defects in SLC26A3 cause congenital chloride diarrhea (CLD), a disease characterized by watery stools containing an excess of chloride (Hoeglund P et al, 1996). SLC26A4 (Pendrin) is highly expressed in the adult thyroid and its activity is necessary for production of thyroid hormone. (Everett et al, 1997). Mutations in this gene are associated with Pendred syndrome, an autosomal-recessive disease. It is the most common form of syndromic deafness (Everett et al, 1997). Pendred syndrome is also characterized by hypothyroidism. SLC26A6 encodes a protein involved in transporting chloride, oxalate, sulfate and bicarbonate (Waldegger S et al, 2001). It is ubiquitously expressed, the highest levels present in kidney and pancreas.
Protein kinase B is regulated in platelets by the collagen receptor glycoprotein VI
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Activation of purified human protein kinase C alpha and beta I isoenzymes in vitro by Ca2+, phosphatidylinositol and phosphatidylinositol 4,5-bisphosphate
Cytosolic GUK1 (guanylate kinase 1) catalyzes the reaction of carbovir monophosphate and ATP to form carbovir diphosphate and ADP. The activity of human GUK1 is inferred from that of the corresponding pig protein (Miller et al. 1992).
Cytosolic ADAL (Adenosine DeAminase-Like) catalyzes the reaction of abacavir monophosphate and water to form carbovir monophosphate and cyclopropylamine. The active form of the enzyme is a protein monomer complexed with a zinc ion (Murakami et al. 2011).
Abacavir is a nucleoside analogue reverse transcriptase inhibitor with antiretroviral activity, widely used in combination with other drugs to treat HIV-1 infection (Yuen et al. 2008). Its uptake across the plasma membrane is mediated by organic cation transporters SLC22A1, 2, and 3; the transport proteins ABCB1 and ABCG2 mediate its efflux. Abacavir itself is a prodrug. Activation requires phosphorylation by a cytosolic adenosine phosphotransferase and deamination by ADAL deaminase to yield carbovir monophosphate. Cytosolic nucleotide kinases convert carbovir monophosphate to carbovir triphosphate, the active HIV reverse transcriptase inhibitor. Abacavir can be glucuronidated or oxidized to a 5'-carboxylate; these are the major forms in which it is excreted from the body.
Abacavir activation proceeds steps of phosphorylation, deamination to yield carbovir monophosphate, and phosphorylation of the latter compound to yield the triphosphate. In addition, abacavir can be conjugated with glucuronide or oxidized to its 5'-carboxylate derivative, the two major forms in which it is excreted from the body (Yuen et al. 2008).
Cytosolic Fe/S protein biogenesis depends on the electron transfer chain from NAD(P)H to the Fe/S protein (CIAPIN1 in humans, DRE2 in yeast) via the flavoprotein NDOR1 (TAH18 in yeast). The precise role of electrons in the assembly process is unclear but in the absence of the electron chain the stable [4Fe-4S] cluster of NUBP1 is not assembled. CIAPIN1 binds two Fe/S clusters of the [2Fe-2S] and the [4Fe-4S] type. The [2Fe-2S] cluster is reduced by NDOR1-NADPH.
A [4Fe-4S] cluster is assembled on a scaffold composed of the P-loop NTPases NUBP2 (CFD1 in yeast) and NUBP1 (Nbp35 in yeast) in a nucleotide-dependent fashion. The two proteins form a heterotetramer which transiently binds the [4Fe-4S] cluster in a bridged form between two subunits of the complex. The Fe/S cluster is bound to two highly conserved Cys residues in the C-termini of each of these proteins. NUBP1 contains an additional, stably associated [4Fe-4S] cluster at its N-terminus which is essential for function. Mitochondria play a crucial role in cytosolic and nuclear Fe/S protein biogenesis. They export via a mitochondrial ABC transporter (yeast ATM1, human ABCB7) a still unknown, sulfur-containing compound which is essential for Fe/S cluster assembly in the cytosol. The general cytosolic iron donor, the multi-domain monothiol glutaredoxin (human GRX3 or PICOT, yeast Grx3-Grx4) plays a crucial role in cytosolic-nuclear Fe/S protein biogenesis. The precise molecular function of the glutaredoxin is still unclear.
A complex of four proteins termed CIA targeting complex is involved in the delivery of the NUBP1-NUBP2-bound Fe/S cluster to specific target apoproteins. NARFL (IOP1, Nar1 in yeast) is similar in sequence to iron-only hydrogenases and binds two [4Fe-4S] clusters. These cofactors are essential for biogenesis but their molecular function is unknown. The WD40 domain protein CIAO1 (Cia1 in yeast) forms a propeller-like structure which may serve as a docking site for the other members of the CIA targeting complex. The role of FAM96B (YHR122W, CIA2 in yeast) and MMS19 is still unclear, but they show some specificity for the delivery of Fe/S clusters into certain target apoproteins. They directly interact with numerous Fe/S target proteins including many proteins involved in nuclear DNA integrity and maintenance such as DNA polymerases (POLD1), helicases of the DNA repair pathway (XPD or FANCJ) or of telomere maintenance (RTEL1), and primases. Cells with mutated MMS19 are hypersensitive to DNA damage and have elongated telomeres therefore these target proteins are relevant to various cancer-related diseases and aging.
Iron-sulfur clusters containing 4 atoms of iron and 4 atoms of sulfur (4Fe-4S clusters) are assembled in the cytosol on a heterotetrameric scaffold composed of NUBP2 and NUBP1 subunits (reviewed in Lill et al. 2012, Rouault et al. 2012, Sharma et al. 2010, Lill and Muhlenhoff 2006). The sources of iron and sulfur are uncertain but the process requires a sulfur-containing compound exported from mitochondria via ABCB7 (ABC7). Newly synthesized 4Fe-4S are transferred to apoproteins such as XPD and POLD1 via the CIA targeting complex, composed of NARFL, CIAO1, FAM96B, and MMS19.
Metabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as the inactivation and elimination of toxic ones generated endogenously or present in the extracellular environment. The processes of energy metabolism can be classified into two groups according to whether they involve carbohydrate-derived or lipid-derived molecules, and within each group it is useful to distinguish processes that mediate the breakdown and oxidation of these molecules to yield energy from ones that mediate their synthesis and storage as internal energy reserves. Synthetic reactions are conveniently grouped by the chemical nature of the end products, such as nucleotides, amino acids and related molecules, and porphyrins. Detoxification reactions (biological oxidations) are likewise conveniently classified by the chemical nature of the toxin. At the same time, all of these processes are tightly integrated. Intermediates in reactions of energy generation are starting materials for biosyntheses of amino acids and other compounds, broad-specificity oxidoreductase enzymes can be involved in both detoxification reactions and biosyntheses, and hormone-mediated signaling processes function to coordinate the operation of energy-generating and energy-storing reactions and to couple these to other biosynthetic processes.
The 70-kDa peroxisomal membrane protein (PMP70) and the adrenoleukodystrophy protein (ALDP) are half ATP binding cassette (ABC) transporters in the peroxisome membrane. Mutations in the ALD gene encoding ALDP result in the X-linked neurodegenerative disorder adrenoleukodystrophy (Roerig et al. 2001). They are involved in metabolic transport of long and very long chain fatty acids into peroxisomes. ATP binding/hydrolysis by and phosphorylation of PMP70 and ALDP are involved in the regulation of fatty acid transport into peroxisomes (Tanaka et al. 2002).
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Myotubularin and MTMR2, phosphatidylinositol 3-phosphatases mutated in myotubular myopathy and type 4B Charcot-Marie-Tooth disease
Iron-sulfur (Fe-S) proteins are localized in the cytosol, nucleus, and mitochondria of mammalian cells (reviewed in Stemmler et al. 2010, Rouault 2012, Bandyopadhyay et al. 2008, Lill 2009, Lill et al. 2012). Fe-S protein biogenesis in the mitochondrial matrix involves the iron-sulfur cluster (ISC) assembly machinery. Ferrous iron is transported across the inner mitochondrial membrane into the mitochondrial matrix by Mitoferrin-1 (SLC25A37) and Mitoferrin-2 (SLC25A28). (Mitoferrin-1 is enriched in erythroid cells while Mitoferrin-2 is ubiquitous.) Frataxin binds ferrous iron in the mitochondrial matrix. The cysteine desulfurase NFS1 in a subcomplex with ISD11 provides the sulfur by converting cyteine into alanine and forming a persulfide which is used for cluster formation on ISCU, the scaffold protein. Interaction between NFS1 and ISD11 is necessary for desulfurase activity. Frataxin binds to a complex containing NFS1, ISD11, and ISCU and is proposed to function as an iron donor to ISCU or as an allosteric switch that activates sulfur transfer and Fe-S cluster assembly (Tsai and Barondeau 2010). Cluster formation also involves the electron transfer chain ferredoxin reductase and ferredoxin. ISCU initially forms clusters containing 2 iron atoms and 2 sulfur atoms ([2Fe-2S] clusters). They are released by the function of HSP70-HSC20 chaperones and the monothiol glutaredoxin GLRX5 and used for assembly of [2Fe-2S] proteins. Assembly of larger clusters such as [4Fe-4S] clusters may involve the function of ISCA1, ISCA2, and IBA57. The clusters are transferred to apo-enzymes such as the respiratory complexes, aconitase, and lipoate synthase through dedicated targeting factors such as IND1, NFU1, and BOLA3.
Transcriptional induction of the human asparagine synthetase gene during the unfolded protein response does not require the ATF6 and IRE1/XBP1 arms of the pathway
Iron-sulfur clusters are assembled on the scaffold, ISCU. Based on homology with bacterial IscU:IscS complexes (reviewed in Johnson et al. 2005), one molecule of ISCU is bound to each subunit of a NFS1 dimer (Marinoni et al. 2012). A single complex may thus be capable of assembling two 2Fe-2S clusters. Sulfide is provided by desulfuration of cysteine by NFS1:ISD11 (Biederbick et al. 2006, Shi et al. 2009, Tsai and Barondeau 2010). It has been proposed that ferrous iron is delivered by FXN (Gerber et al. 2003, Yoon and Cowan 2003, Schmucker et al. 2011) bound to ISCU (inferred from yeast, Wang and Craig 2008), although more recent studies suggested that FXN functions as an allosteric effector to stimulate sulfide transfer (Tsai et al. 2010). Holo-ISCU (ISCU bound to a newly synthesized 2Fe-2S cluster) transiently interacts with a dedicated HSP70 chaperone system including Mortalin (GRP75) and HSP20 and GLRX5 (GRX5). Electrons supplied by FDXL1 (FDX2) are required and may reduce the sulfur from S0 to S2-. NFU1 binds an Fe-S cluster (Tong et al. 2003, inferred from bacteria Yuvaniyama et al. 2000) and, from biochemical studies of bacterial NFU1 homologues, is proposed to be an intermediate Fe-S cluster carrier (Bandyopadhy et al. 2008). Mutations in human NFU1 affect only a subset of Fe-S proteins (Navarro-Sastre et al. 2011).
NADPH, ferredoxin reductase (FDXR, Adrenodoxin reductase), and ferredoxins (FDX1, FDX1L) comprise a short electron transport chain that provides electrons for biosynthesis of iron-sulfur clusters and steroid hormones (Sheftel et al. 2010, Shi et al. 2012, reviewed in Grinberg et al. 2000, Lambeth et al. 1982).
The molecular genetic basis of muscle phosphoglycerate mutase (PGAM) deficiency
The band 3 anion exchange protein (AE1, SLC4A1) exchanges chloride (Cl-) for bicarbonate (HCO3-) across the plasma membrane according to the concentration gradients of the anions (Knauf et al. 1996, Dahl et al. 2003). SLC4A1 may be part of a complex ("metabolon") with carbonic anhydrase II (CA2) which would facilitate the transport of HCO3- (Sterling et al. 2001).
Erythrocytes circulating through the capillaries of the lung must exchange carbon dioxide (CO2) for oxygen (O2) during their short (0.5-1 sec.) transit time in pulmonary tissue (Reviewed in Jensen 2004, Esbaugh and Tufts 2006, Boron 2010). CO2 bound as carbamate to the N-terminus of hemoglobin and protons (H+) bound to histidine residues in hemoglobin are released as hemoglobin (HbA) binds O2. Bicarbonate (HCO3-) present in plasma is taken up by erythrocytes via the band3 anion exchanger (AE1, SLC4A1) and combined with H+ by carbonic anhydrases I and II (CA1/CA2) to yield water and CO2 (Reviewed by Esbaugh and Tufts 2006). CO2 is passively transported out of the erythrocyte by AQP1 and RhAG. HCO3- in plasma is also directly dehydrated by extracellular carbonic anhydrase IV (CA4) present on endothelial cells lining the capillaries in the lung.
Carbon dioxide (CO2) in plasma is hydrated to yield protons (H+) and bicarbonate (HCO3-) by carbonic anhydrase IV (CA4) located on the apical plasma membranes of endothelial cells. Plasma CO2 is also taken up by erythrocytes via AQP1 and RhAG. Within erythrocytes CA1 and, predominantly, CA2 hydrate CO2 to HCO3- and protons (reviewed in Geers & Gros 2000, Jensen 2004, Boron 2010). The HCO3- is transferred out of the erythrocyte by the band 3 anion exchange protein (AE1, SLC4A1) which cotransports a chloride ion (Cl-) into the erythrocyte. Also within the erythrocyte, CO2 combines with the N-terminal alpha amino groups of HbA to form carbamates while protons bind histidine residues in HbA. The net result is the Bohr effect, a conformational change in HbA that reduces its affinity for O2 and hence assists the delivery of O2 to tissues.
Cytosolic levels of abacavir are determined by the balance of its facilitated diffusion into the cell mediated by organic cation transporters SLC22A1, 2, and 3, and its ATP-dependent efflux from cells mediated by ABCG2 and ABCB1 (Klaasen and Aleksunes 2010; Pan et al. 2007; Shaik et al. 2007).
In capillaries of the lungs erythrocytes release carbon dioxide (CO2) and acquire oxygen (O2). In other tissues of the body the reverse reaction occurs (reviewed in Nikinmaa 1997, Jensen 2004). In the lungs, CO2 bound as carbamate to the N-terminus of hemoglobin (HbA) and protons bound to histidine residues in HbA are released as HbA binds oxygen. Bicarbonate (HCO3-) present in plasma is taken up by erythrocytes via the band3 anion exchanger (AE1, SLC4A1) and combined with protons by carbonic anhydrases I and II (CA1, CA2) to yield water and CO2 (reviewed by Esbaugh & Tufts 2006, De Rosa et al. 2007). The CO2 is passively transported out of the erythrocyte by AQP1 and RhAG. HCO3- in plasma is also directly dehydrated by extracellular carbonic anhydrase IV (CA4) present on endothelial cells lining the capillaries in the lung. In non-pulmonary tissues CO2 in plasma is hydrated to yield protons and HCO3- by CA4 located on the apical plasma membranes of endothelial cells. Plasma CO2 is also taken up by erythrocytes via AQP1 and RhAG. Within erythrocytes CA1 and, predominantly, CA2 hydrate CO2 to yield HCO3- and protons (reviewed in Geers & Gros 2000, Jensen 2004, Boron 2010). HCO3- is transferred out of the erythrocyte by the band 3 anion exchange protein (AE1, SLC4A1) which cotransports a chloride ion into the erythrocyte. Also within the erythrocyte, CO2 combines with the N-terminal alpha amino groups of HbA to form carbamates while protons bind histidine residues in HbA. The net result is the Bohr effect, a conformational change in HbA that reduces its affinity for O2 and hence assists the delivery of O2 to tissues.
ATP-binding cassette sub-family G member 2 (ABCG2), associated with the plasma membrane, mediates the ATP-dependent efflux of abacavir (Doyle et al. 1998). The active form of ABCG2 is a homodimer stabilized by an interchain disulfide bond (Wakabayashi et al. 2007). The abacavir specificity of the human ABCG2 transporter is inferred from studies of the corresponding mouse protein (Pan et al. 2007).
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Mucopolysaccharidosis type IVA (Morquio A disease): clinical review and current treatment
The protein kinase/endoribonuclease IRE1alpha that signals the unfolded protein response has a luminal N-terminal ligand-independent dimerization domain
Glutathione S-Transferases (GSTs; EC 2.5.1.18) are another major set of phase II conjugation enzymes. They can be found in the cytosol as well as being microsomal membrane-bound. Cytosolic GSTs are encoded by at least 5 gene families (alpha, mu, pi, theta and zeta GST) whereas membrane-bound enzymes are encoded by single genes. Soluble GSTs are homo- or hetero-dimeric enzymes (approximately 25KDa subunits) which can act on a wide range of endogenous and exogenous electrophiles. GSTs mediate conjugation using glutathione (GSH), a tripeptide synthesized from its precursor amino acids gamma-glutamate, cysteine and glycine. A generalized reaction is RX + GSH -> HX + GSR Glutathione conjugates are excreted in bile and converted to cysteine and mercapturic acid conjugates in the intestine and kidneys. GSH is the major, low molecular weight, non-protein thiol synthesized de novo in mammalian cells. As well as taking part in conjugation reactions, GSH also has antioxidant ability and can metabolize endogenous and exogenous compounds. The nucleophilic GSH attacks the electrophilic substrate forming a thioether bond between the cysteine residue of GSH and the electrophile. The result is generally a less reactive and more water-soluble conjugate that can be easily excreted. In some cases, GSTs can activate compounds to reactive species such as certain haloalkanes and haloalkenes. Substrates for GSTs include epoxides, alkenes and compounds with electrophilic carbon, sulfur or nitrogen centres. There are two types of conjugation reaction with glutathione: displacement reactions where glutathione displaces an electron-withdrawing group and addition reactions where glutathione is added to activated double bond structures or strained ring systems.
The combination of glutamate, cysteine and ATP is required to form glutathione. The steps involved in the synthesis and recycling of glutathione are outlined (Meister, 1988).
As inferred from biochemical studies in yeast and phenotypic studies in mouse, Mitoferrin-1 (SLC25A37) and Mitoferrin-2 (SLC25A28) transport ferrous iron across the inner mitochondrial membrane. Mitoferrin-1 is essential for maintaining mitochondrial iron uptake in developing erythroid cells; mitoferrin-2 is ubiquitously expressed. Defects in Mitoferrin-1 and Mitoferrin-2 cause a reduction in mitochondrial iron acquisition and biogenesis of iron-sulfur clusters and heme.
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Frataxin (FXN) specifically binds 2 atoms of ferrous iron per monomer (reviewed in Stemmler et al. 2010). Iron bound to Frataxin may (Yoon and Cowan 2003, Gerber et al. 2003) or may not (Schmucker et al. 2011) enhance the interaction of Frataxin with NFS1, ICSU, and ISD11. Frataxin was shown to stimulate the cysteine desulfurase activity of NFS1 and was proposed to be a regulator of sulfur production (Tsai et al. 2010). The formation of sulfide by NFS1 is most efficiently observed when NFS1 is in complex with ISD11, ISCU, and FXN in the presence of cysteine and iron. This means that only the complete system of NFS1, ISD11, ISCU, FXN, cysteine, and iron is fully active as a desulfurase. FXN therefore seems to be a regulator of the cysteine desulfurase permitting sulfide production only when all components needed for Fe-S cluster synthesis are present and the ISCU-bound Fe-S cluster can be formed.
Two electrons and one proton are transferred from NADPH to the FAD moiety of ferredoxin reductase. A proton from the medium is also taken up by ferredoxin reductase.
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Two electrons are transferred from reduced ferredoxin reductase (FDXR, adrenodoxin reductase) to two ferredoxin-1 or ferredoxin-1L (FDX1, FDX1L) molecules, each of which binds one electron. Two protons are released during the reaction.
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Phase II of biotransformation is concerned with conjugation, that is using groups from cofactors to react with functional groups present or introduced from phase I on the compound. The enzymes involved are a set of transferases which perform the transfer of the cofactor group to the substrate. The resultant conjugation results in greatly increasing the excretory potential of compounds. Although most conjugations result in pharmacological inactivation or detoxification, some can result in bioactivation. Most of the phase II enzymes are located in the cytosol except UDP-glucuronosyltransferases (UGT), which are microsomal. Phase II reactions are typically much faster than phase I reactions therefore the rate-limiting step for biotransformation of a compound is usually the phase I reaction. Phase II metabolism can deal with all the products of phase I metabolism, be they reactive (Type I substrate) or unreactive/poorly active (Type II substrate) compounds. With the exception of glutathione, the conjugating species needs to be made chemically reactive after synthesis. The availability of the cofactor in the synthesis may be a rate-limiting factor in some phase II pathways as it may prevent the formation of enough conjugating species to deal with the substrate or it's metabolite. As many substrates and/or their metabolites are chemically reactive, their continued presence may lead to toxicity.
To be excreted in urine, glutathione conjugates undergo several hydrolysis steps to form mercapturic acids which are readily excreted. The first step is the hydrolysis of a gamma-glutamyl residue from the conjugate catalysed by gamma-glutamyltransferases (GGTs). These are membrane-bound, heterodimeric enzymes composed of light and heavy peptide chains. GGT1 and 2 are well characterised while GGT3P, 5, 6 and 7 are putative transferases. Extracellular glutathione or its conjugates can be hydrolysed to give cysteinylglycine (CG, or CG conjugates) and free glutamate (L-Glu) (Heisterkamp et al. 2008, Tate & Ross 1977, Pawlak et al. 1989).
Aflatoxins are among the principal mycotoxins produced as secondary metabolites by the molds Aspergillus flavus and Aspergillus parasiticus that contaminate economically important food and feed crops (Wild & Turner 2002). Aflatoxin B1 (AFB1) is the most potent naturally occurring carcinogen known and is also an immunosuppressant. It is a potent hepatocarcinogenic agent in many species, and has been implicated in the etiology of human hepatocellular carcinoma. Poultry, especially turkeys, are extremely sensitive to the toxic and carcinogenic action of AFB1 present in animal feed, resulting in multi-million dollar losses to the industry. Discerning the biochemical and molecular mechanisms of this extreme sensitivity of poultry to AFB1 will help with the development of new strategies to increase aflatoxin resistance (Rawal et al. 2010, Diaz & Murcia 2011). AFB1 has one major genotoxic metabolic fate, conversion to AFXBO, and several others that are less mutagenic but that can still be quite toxic, causing [X, Y, and Z]. AFB1 can be oxidised to the toxic AFB1 exo 8,9 epoxide (AFXBO) product by several cytochrome P450 enzymes, especially P450 3A4 in the liver. This 8,9 epoxide can react with the N7 atom of a guanyl base of DNA to produce adducts by intercalating between DNA base pairs. The exo epoxide is unstable in solution, however, and can react spontaneously to form a diol that is no longer reactive with DNA. The diol product in turn undergoes base-catalysed rearrangement to a dialdehyde that can react with protein lysine residues. AFB1 can also be metabolised to products (AFQ1, AFM1, AFM1E) which have far less genotoxic consequences than AFB1. The main route of detoxification of AFB1 is conjugation of its reactive 8,9-epoxide form with glutathione (GSH). This reaction is carried out by trimeric glutathione transferases (GSTs), providing a chemoprotective mechanism against toxicity. Glutathione conjugates are usually excreted as mercapturic acids in urine (Guengerich et al. 1998, Hamid et al. 2013). The main metabolic routes of aflatoxin in humans are described here.
All organisms are constantly exposed to foreign chemicals every day. These can be man-made (drugs, industrial chemicals) or natural (alkaloids, toxins from plants and animals). Uptake is usually via ingestion but inhalation and transdermal routes are also common. The very nature of many chemicals that make them suitable for uptake by these routes, in other words their lipophilicty (favours fat solubility) is also the main reason organisms have developed mechanisms that convert them to hydrophilic (favours water solubility) compounds which are readily excreted via bile and urine. Otherwise, lipophilic chemicals would accumulate in the body and overwhelm defense mechanisms. This process is called biotransformation and is catalyzed by enzymes mainly in the liver of higher organisms but a number of other organs have considerable ability to process xenobiotica such as kidneys, gut and lungs. As well as xenobiotics, many endogenous compounds are commonly eliminated by this process. This mechanism is of ancient origin and a major factor for its development in animals is plants. Most animals are plant eaters and thus are subject to a huge variety of chemical compounds which plants produce to stop themselves being eaten. This complex set of enzymes have several features which make them ideal for biotransformation; (1) metabolites of the parent chemical are usually made more water soluble so it favours rapid excretion via bile and urine (2) the enzymes possess broad and overlapping specificity to be able to deal with newly exposed chemicals (3) metabolites of the parent generally don't have adverse biological effects. In the real world however, all these criteria have exceptions. Many chemicals are transformed into reactive metabolites. In pharmacology, the metabolites of some parent drugs exert the desired pharmacological effect but in the case of polycyclic aromatic hydrocarbons (PAHs), which can undergo epoxidation, it results in the formation of an electrophile which can attack proteins and DNA. Metabolism of xenobiotica occurs in several steps called Phase 1 (functionalization) and Phase 2 (conjugation). To improve water solubility, a functional group is added to or exposed on the chemical in one or more steps (Phase 1) to which hydrophilic conjugating species can be added (Phase 2). Functional groups can either be electrophilic (epoxides, carbonyl groups) or nucleophilic (hydroxyls, amino and sulfhydryl groups, carboxylic groups) (see picture). Once chemicals undergo functionalization, the electrophilic or nucleophilic species can be detrimental to biological systems. Electrophiles can react with electron-rich macromolecules such as proteins, DNA and RNA by covalent interaction whilst nucleophiles have the potential to interact with biological receptors. That's why conjugation is so important as it mops up these potentially reactive species. Many chemicals, when exposed to certain metabolizing enzymes can induce those enzymes, a process called enzyme induction. The effect of this is that these chemicals accelerate their own biotransformation and excretion. The reverse is also true where some chemicals cause enzyme inhibition. Some other factors that alter enzyme levels are sex, age and genetic predisposition. Between species, there can be considerable differences in biotransformation ability which is a problem faced by drug researchers interpreting toxicological results to humans.
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IAP proteins: blocking the road to death's door
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ALDH1A1 (aldehyde dehydrogenase) in the cytosol catalyzes the reaction of acetaldehyde and NAD+ to form acetate and NADH + H+ (Inoue et al. 1979). The active form of the enzyme is a tetramer (Ni et al. 1999).
5-oxoprolinase catalyzes the cleavage of 5-oxoproline to form L-glutamate, coupled to the hydrolysis of ATP to ADP and inorganic phosphate (Chen et al, 1998).
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In the second step in the formation of glutathione, gamma-glutamylcysteine ligates with glycine to form glutathione (Gali and Board, 1995; ).
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Two groups of sulfotransferease (SULT) enzymes catalyze the transfer of a sulfate group from 3-phosphoadenosine 5-phosphosulfate (PAPS) to a hydroxyl group on an acceptor molecule, yielding a sulfonated acceptor and 3-phosphoadenosine 5-phosphate (PAP). One is localized to the Golgi apparatus and mediates the sulfonation of proteoglycans. The second, annotated here, is cytosolic and mediates the sulfonation of a diverse array of small molecules, increasing their solubilities in water and modifying their physiological functions. There are probably thirteen or more human cytosolic SULT enzymes; eleven of these have been purified and characterized enzymatically, and are annotated here (Blanchard et al. 2004; Gamage et al. 2005). These enzymes appear to be active as dimers. Their substrate specificities are typically broad, and not related in an obvious way to their structures; indeed, apparently orthologous human and rodent SULT enzymes can have different substrate specificities (Glatt 2000), and none has been exhaustively characterized. The substrates listed in the table and annotated here are a sample of the known ones, chosen to indicate the range of activity of these enzymes and to capture some of their known physiologically important targets. Absence of a small molecule - enzyme pair from the table, however, may only mean that it has not yet been studied.
Methylation is a common but minor pathway of Phase II conjugation compared to glucuronidation or sulfonation. The cofactor used in methylation conjugation is S-adenosylmethionine (SAM). SAM is the second most widely used enzyme substrate after ATP and is involved in a wide range of important biological processes. SAM is sythesized from methionine's reaction with ATP, catalyzed by methionine adenosyltransferase (MAT). There are two genes, MAT1A and MAT2A, which encode for two homologous MAT catalytic subunits, 1 and 2. During conjugation with nucleophilic substrates, the methyl group attached to the sulfonium ion of SAM is transferred to the substrate forming the conjugate. SAM, having lost the methyl moiety, is converted to S-adenosylhomocysteine (SAH). SAH can be hydrolyzed to form adenosine and homocysteine. Homocysteine can either be converted to glutathione or methylated to form methionine, thus forming the starting point for SAM synthesis and completing the cycle. Fuctional groups attacked are phenols, catechols, aliphatic and aromatic amines and sulfhydryl-containing groups. The enzymes that catalyze the transfer of the methyl group to these functional groups are the methyltransferases (MT). MTs are small, cytosolic, monomeric enzymes that utilize SAM as a methyl donor. There are many MTs but the best studied ones are named on the basis of their prototypical substrates: COMT (catechol O-methyltransferase), TPMT (thiopurine methyltransferase), TMT (thiol methyltransferase), HNMT (histamine N-methyltransferase) and NNMT (nicotinamide N-methyltransferase). An example of each enzyme mentioned is given. In each case, a typical substrate for the enzyme is shown.
Glucose 1-phosphate and UTP are the precursors to UDP-glucuronate formation. After oxidation of the resultant complex, UDP-glucuronate is transported to the ER lumen.
Glucuronidation conjugation utilizes UDP-glucuronosyltransferases (UGTs; EC 2.4.1.17) to catalyze a wide range of diverse endogenous and xenobiotic compounds. Glucuronidation is the major pathway in phase II metabolism and accounts for approximately 35% of drug conjugation. UGTs are microsomal membrane-bound and catalyze the transfer of a glucuronate group of uridine diphosphoglucuronate (UDPGA, a co-substrate) to the functional group of specific substrates. UDPGA is synthesized from glucose-1-phosphate (G1P). G1P is required for glycolysis and is present in high concentrations in the cell, making it is unlikely to be a limiting factor in UDPGA synthesis. UDP is added to G1P to form UDP-glucose which is then dehydrogenated to form UDPGA. The basic reaction is UDP-Glucuronate + acceptor -> UDP + acceptor-beta-D-glucuronide The effect of this conjugation is to confer polarity to the substrate which can then be easily excreted in urine or bile. Functional groups acted on include hydroxyl, carboxylate, amino and sulfate groups. There are 2 families of UGTs, UGT1 and UGT2 which are further sub-divided into 3 subfamilies, UGT1A, UGT2A and UGT2B. There are more than 26 different isozymes in humans, of which 18 are functional proteins. They are composed of 527-530 residues and have a molecular weight of 50-57KDa. The UGT1 family comprises of 9 proteins (UGT1A1, 1A3-1A10) but only 5 have been isolated in humans. Example substrates which are glucuronidated are acetaminophen by UGT1A6 and bilirubin by UGT1A1. Members of the UGT2 subfamily are each encoded by their own genes, in contrast to UGT1As which are encoded at the UGT1 locus. Example substrates are morphine conjugation by UGT2B7 and androgenic steroid conjugation by UGT2B17. Xenobiotics conjugated with glucuronic acid can be substrates for beta-glucuronidase, an enzyme common in gut microflora. This enzyme can release the parent or phase I metabolite which can be reabsorbed. It can then either re-exert it's original effects or be conjugated by glucuronic acid again. This cycle is called enterohepatic circulation and can delay the elimination of the xenobiotic.
Ethanol and related alcohols can be ingested as part of the diet and are formed by microorganisms in the intestinal tract. Ethanol oxidation to acetate occurs primarily in liver cells in a multistep process first described by Racker (1949). First, in the cytosol, ethanol is oxidized to acetaldehyde, with the formation of NADH. Second, in the mitochondrion, acetaldehyde is oxidized to acetate with the formation of NADH. Finally, acetate in the mitochondrion can be condensed with coenzyme A to form acetyl CoA. Polymorphisms in the enzymes catalyzing the first two steps are associated with variation in the efficiency of alcohol catabolism in human populations (Chen et al. 1999; Lange et al. 1976; Jornvall 1985). The molecular mechanism by which cytosolic acetaldehyde enters the mitochondrial matrix is not known (Lemasters 2007). Cytosolic enzymes capable of oxidizing acetaldehyde to acetate have also been identified and characterized in vitro (Inoue et al. 1979) so a purely cytosolic pathway for ethanol oxidation to acetate and conversion to acetyl-CoA can be annotated. The role of this pathway in vivo is unclear, though limited attempts to correlate deficiencies in the cytosolic enzyme with alcohol intolerance have yielded suggestive data (Yoshida et al. 1989). Additional peroxisomal and microsomal pathways for the oxidation of ethanol to acetaldehyde have been described; their physiological significance is unclear and they are not annotated here.
Phase 1 of metabolism is concerned with functionalization, that is the introduction or exposure of functional groups on the chemical structure of a compound. This provides a 'handle' for phase 2 conjugating species with which to react with. Many xenobiotics are lipophilic and almost chemically inert (e.g. PAHs) so would not necessarily undergo a phase 2 reaction. Making them more chemically reactive would facilitate their excretion but also increases their chance of reacting with cellular macromolecules (e.g. proteins, DNA). There is a fine balance between producing a more reactive metabolite and conjugation reactions. There are two groups of enzymes in phase 1 - oxidoreductases and hydrolases. Oxidoreductases introduce an oxygen atom into or remove electrons from their substrates. The major oxidoreductase enzyme system is called the P450 monooxygenases. Other systems include flavin-containing monooxygenases (FMO), cyclooxygenases (COX) and monoamine oxidases (MAO). Hydrolases hydrolyse esters, amides, epoxides and glucuronides.
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Extracellular glutathione can be hydrolyzed to give cysteinylglycine (Cys-Gly) and gamma glutamate, which, in the presence of amino acids, can form a gamma-glutamate:AA product (Heisterkamp et al, 2008). This hydrolysis provides cells with a cysteine supply and contributes to the maintainance of intracellular glutathione levels (Tate and Ross, 1977; Pawlak et al, 1989).
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The identification of a distinct export step following the biosynthesis of leukotriene C4 by human eosinophils
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ACSS1 (acyl-CoA synthetase short-chain family member 1) in the mitochondrial matrix catalyzes the reaction of acetate, coenzyme A, and ATP to form acetyl-CoA, AMP, and pyrophosphate (Schwer et al. 2006).
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ALDH2 (aldehyde dehydrogenase) in the mitochondrial matrix catalyzes the reaction of acetaldehyde and NAD+ to form acetate and NADH + H+ (Greenfield and Pietruszko 1977; Hempel et al. 1985). The active form of the enzyme is a tetramer (Ni et al. 1999).
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Retinoic acid (RA) is a biologically active analogue of vitamin A (retinol). RA plays an important role in regulating cell growth and differentiation.CYP26A1 is involved in the metabolic breakdown of RA by 4-hydroxylation. CYP26A1-mediated 4-hydroxylation is specific for all-trans-RA but not for the isomers 13-cis-RA and 9-cis-RA (Sonneveld et al. 1998). CYP26B1 can also deactivate all-trans-retinoic acid by 4-hydroxylation. High expression levels in the cerebellum and pons of human brain suggests a protective role of specific tissues against retinoid damage (White et al. 2000).
A number of CYPs take part in cholesterol biosynthesis and elimination, thus playing an important role in maintaining cholesterol homeostasis. Under normal physiological conditions, cholesterol intake (diet or synthesized de novo from acetyl CoA) equals cholesterol elimination (degraded to bile salts, secreted in bile and used in steroid hormone synthesis). These processes are under tight regulatory control and any disruption leads to increased cholesterol levels resulting in cardiovacular disease. The CYPs involved in cholesterol homeostasis could serve as potential targets for cholesterol-lowering drugs.
The P450 isozyme system is the major phase 1 biotransforming system in man, accounting for more than 90% of drug biotransformations. This system has huge catalytic versatility and a broad substrate specificity, acting upon xenobiotica and endogenous compounds. It is also called the mixed-function oxidase system, the P450 monooxygenases and the heme-thiolate protein system. All P450 enzymes are a group of heme-containing isozymes which are located on the membrane of the smooth endoplasmic reticulum. They can be found in all tissues of the human body but are most concentrated in the liver. The name "cytochrome P450" (CYP) is derived from the spectral absorbance maximum at 450nm when carbon monoxide binds to CYP in its reduced (ferrous, Fe2+) state. The basic reaction catalyzed by CYP is mono-oxygenation, that is the transfer of one oxygen atom from molecular oxygen to a substrate. The other oxygen atom is reduced to water during the reaction with the equivalents coming from the cofactor NADPH. The basic reaction is; RH (substrate) + O2 + NADPH + H+ = ROH (product) + H2O + NADP+ The end results of this reaction can be (N-)hydroxylation, epoxidation, heteroatom (N-, S-) oxygenation, heteroatom (N-, S-, O-) dealkylation, ester cleavage, isomerization, dehydrogenation, replacement by oxygen or even reduction under anaerobic conditions. The metabolites produced from these reactions can either be mere intermediates which have relatively little reactivity towards cellular sysytems and are readily conjugated, or, they can be disruptive to cellular systems. Indeed, inert compounds need to be prepared for conjugation and thus the formation of potentially reactive metabolites is in most cases unavoidable. There are 57 human CYPs (in 18 families and 42 subfamilies), mostly concentrated in the endoplasmic reticulum of liver cells although many tissues have them to some extent (Nelson DR et al, 2004). CYPs are grouped into 14 families according to their sequence similarity. Generally, enzymes in the same family share 40% sequence similarity and 55% within a subfamily. Nomenclature of P450s is as follows. CYP (to represent cytochrome P450 superfamily), followed by an arabic number for the family, a capital letter for the subfamily and finally a second arabic number to denote the isoenzyme. An example is CYP1A1 which is the first enzyme in subfamily A of cytochrome P450 family 1. The majority of the enzymes are present in the CYP1-4 families. CYP1-3 are primarily concerned with xenobiotic biotransformation whereas the other CYPs deal primarily with endogenous compounds. The CYP section is structured by the typical substrate they act upon. Of the 57 human CYPs, 7 encode mitochondrial enzymes, all involved in sterol biosynthesis. Of the remaining 50 microsomal enzymes, 20 act upon endogenous compounds, 15 on xenobiotics and 15 are the so-called "orphan enzymes" with no substrate identified. The P450 catalytic cycle (picture) shows the steps involved when a substrate binds to the enzyme. (1) The normal state of a P450 with the iron in its ferric [Fe3+] state. (2) The substrate binds to the enzyme. (3) The enzyme is reduced to the ferrous [Fe2+] state by the addition of an electron from NADPH cytochrome P450 reductase. The bound substrate facilitates this process. (4,5) Molecular oxygen binds and forms an Fe2+OOH complex with the addition of a proton and a second donation of an electron from either NADPH cytochrome P450 reductase or cytochrome b5. A second proton cleaves the Fe2+OOH complex to form water. (6) An unstable [FeO]3+ complex donates its oxygen to the substrate (7). The oxidised substrate is released and the enzyme returns to its initial state (1).
Methimazole is a drug used to treat hyperthyroidism, a condition arising when the thyroid gland is producing too much thyroid hormone. FMO2 is able to the S-oxidized form of methimazole.
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Tamoxifen (TAM) is an antiestrogen and currently used extensively for breast cancer therapy. FMOs, especially FMO1 can N-oxidze TAM to tamoxifen N-oxide (TNO). TNO can be reduced back to TAM by the P450 system. TNO appears to be just as potent as TAM but with fewer side-effects so this metabolic cycling could play a part in the use of TNO in the treatment of breast cancer.
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Flavin-containing monooxygenases (FMOs) are the second family of microsomal oxidative enzymes with broad and overlapping specificity. The major reactions FMOs catalyze are nucleophilic hetero-atom compounds such as nitrogen, sulfur or phosphorus as the hetero-atom to form N-oxides, S-oxides or P-oxides respectively. Despite the functional overlap with cytochrome P450s, the mechanism of action differs. FMOs bind and activate molecular oxygen before the substrate binds to the enzyme (picture). They also require flavin adenosine dinucleotide (FAD) as a cofactor. Unlike cytochrome P450 enzymes, FMOs are heat-labile, a useful way to distinguish which enzyme system is at work for researchers studying metabolism. Also, FMOs are not inducible by substrates, unlike the P450 enzymes.\n(1) NADPH binds to the enzyme and reduces the prosthetic group FAD to FADH2. NADP+ remains bound to the enzyme.\n(2) Incorporation of molecular oxygen to form a hydroperoxide.\n(3) A peroxide oxygen is transferred to the substrate.\n(4) Water is released.\n(5) NADP+ dissociates returning the enzyme to its initial state.\n\nTo date, there are 6 isozymes of FMO (FMO1-6) in humans, the most prominent and active one being FMO3. The FMO6 gene does not encode for a functional enzyme although it has the greatest sequence similarity with FMO3 (71%), whilst the others range from 50-58% sequence similarity with FMO3. FMO1-3 are the ones that exhibit activity towards nucleophiles, the others are insignificant in this respect.
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Trimethylamine (TMA) is present in the diet (in fish) but primarily formed in vivo from the breakdown of choline. It is N-oxidized by FMO3 in the liver, the major isoform active towards TMA Trimethylaminuria (âfish-odour syndromeâ) is a human genetic disorder characterized by an impaired ability to convert the malodourous TMA to its odourless N-oxide.
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Cellular functions of TC10, a Rho family GTPase: regulation of morphology, signal transduction and cell growth
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Structure, function and immunolocalization of a proton-coupled amino acid transporter (hPAT1) in the human intestinal cell line Caco-2
Regulation of purine synthesis de novo in human fibroblasts by purine nucleotides and phosphoribosylpyrophosphate
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Mutations in PYCR1 cause cutis laxa with progeroid features
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Proximal tubular handling of phosphate: A molecular perspective
Biosynthesis of tricarboxylic acids by carbon dioxide fixation; enzymatic mechanisms
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Forearm blood flow during body temperature transients produced by leg exercise.
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Endonucleolytic processing of covalent protein-linked DNA double-strand breaks
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Intact AQP0 performs cell-to-cell adhesion
Processing of Capped Intron-Containing Pre-mRNA
Interfacial kinetic and binding properties of mammalian group IVB phospholipase A2 (cPLA2beta) and comparison with the other cPLA2 isoforms
The SLC31 (Ctr) copper transporter family
Importance of dietary gamma-linolenic acid in human health and nutrition
A unified model for apical caspase activation
Subunit interactions in the mammalian alpha-ketoglutarate dehydrogenase complex. Evidence for direct association of the alpha-ketoglutarate dehydrogenase and dihydrolipoamide dehydrogenase components.
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Roles of Tom70 in import of presequence-containing mitochondrial proteins
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The subcellular localization of an aquaporin-2 tetramer depends on the stoichiometry of phosphorylated and nonphosphorylated monomers
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A novel function of the human CLS1 in phosphatidylglycerol synthesis and remodeling
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Autoinhibition and activation mechanisms of the Wiskott-Aldrich syndrome protein
Aldehyde dehydrogenase, a diphosphopyridine nucleotide-linked enzyme
Identification of a putative lysosomal cobalamin exporter altered in the cblF defect of vitamin B12 metabolism
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Expression of Human CTP synthetase in Saccharomyces cerevisiae reveals phosphorylation by protein kinase A
ATP-binding cassette (ABC) transporters in human metabolism and diseases
Human Sulfotransferases and Their Role in Chemical Metabolism
Peroxisome proliferator-activated receptor alpha target genes
Pig-n, a mammalian homologue of yeast Mcd4p, is involved in transferring phosphoethanolamine to the first mannose of the glycosylphosphatidylinositol
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Closing the folding chamber of the eukaryotic chaperonin requires the transition state of ATP hydrolysis
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A heterodimeric coiled-coil protein required for mitotic chromosome condensation in vitro
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Site of mitochondrial reactive oxygen species production in skeletal muscle of chronic obstructive pulmonary disease and its relationship with exercise oxidative stress
Am. J. Respir. Cell Mol. Biol. 47:358-62
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Identification and characterization of a novel monoamine transporter in the human brain
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Molecular basis of acid sphingomyelinase deficiency in a patient with Niemann-Pick disease type A
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Iron-sulfur cluster biosynthesis. Characterization of frataxin as an iron donor for assembly of [2Fe-2S] clusters in ISU-type proteins
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The juxtamembrane region of the EGF receptor functions as an activation domain
Subcellular localization and lysophospholipase/transacylation activities of human group IVC phospholipase A2 (cPLA2gamma)
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Competitive binding of AUF1 and TIAR to MYC mRNA controls its translation
The E3 ubiquitin ligase WWP1 selectively targets HER4 and its proteolytically derived signaling isoforms for degradation
Characterization of distinct nuclear and mitochondrial forms of human deoxyuridine triphosphate nucleotidohydrolase
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The structural basis for substrate specificity and inhibition of human S-adenosylmethionine decarboxylase
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The diverse functions of histone lysine methylation
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The role of cellular glutathione peroxidase redox regulation in the suppression of tumor cell growth by manganese superoxide dismutase
The noncatalytic portion of human UDP-glucose: glycoprotein glucosyltransferase I confers UDP-glucose binding and transferase function to the catalytic domain
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The NMR solution structure of human glutaredoxin in the fully reduced form
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Ubiquitin-dependent mechanism regulates rapid turnover of AU-rich cytokine mRNAs
MyD88:Mal cascade initiated on plasma membrane
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Wilms tumor suppressor WTX negatively regulates WNT/beta-catenin signaling
MicroRNAs: small RNAs with a big role in gene regulation
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Identification of a specific telomere terminal transferase activity in Tetrahymena extracts
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Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embryos.
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Intrinsic activity and stability of bifunctional human UMP synthase and its two separate catalytic domains, orotate phosphoribosyltransferase and orotidine-5'-phosphate decarboxylase
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PC and PE synthesis: mixed micellar analysis of the cholinephosphotransferase and ethanolaminephosphotransferase activities of human choline/ethanolamine phosphotransferase 1 (CEPT1)
A competition between stimulators and antagonists of Upf complex recruitment governs human nonsense-mediated mRNA decay
Posttranscriptional gene regulation by spatial rearrangement of the 3' untranslated region
Molecular cloning of the human UMP synthase gene and characterization of point mutations in two hereditary orotic aciduria families
3-(3-sn-phosphatidyl)-sn-glycerol 1-phosphate [ChEBI:37393]
1,2-Diacyl-sn-glycero-3-phospho-sn-glycerol 3'-phosphate
3-(3-sn-phosphatidyl)-sn-glycerol 1-phosphates
3(3-Phosphatidyl-)L-glycerol 1-phosphate
3(3-sn-Phosphatidyl)-sn-glycerol 1-phosphate
3-(3-sn-phosphatidyl)-sn-glycerol 1-phosphate
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Disruption of aquaporin-11 produces polycystic kidneys following vacuolization of the proximal tubule
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Essential role for Gab2 in the allergic response
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Expression of human placental-type 6-phosphofructo-2-kinase/fructose 2,6-bisphosphatase in various cells and cell lines
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Idiopathic chronic megaloblastic anemia in children
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Myeloproliferative disorder FOP-FGFR1 fusion kinase recruits phosphoinositide-3 kinase and phospholipase Cgamma at the centrosome
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CARMA1 coiled-coil domain is involved in the oligomerization and subcellular localization of CARMA1 and is required for T cell receptor-induced NF-kappaB activation
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Effect of acute heat shock on gene expression by human peripheral blood mononuclear cells
Formation of tubulin folding intermediates by CCT/TriC
Synthesis of Prostaglandins (PG) and Thromboxanes (TX)
Congenital disorder of glycosylation id presenting with hyperinsulinemic hypoglycemia and islet cell hyperplasia
Structure and function of human erythrocyte pyruvate kinase. Molecular basis of nonspherocytic hemolytic anemia
FCP1, a phosphatase specific for the heptapeptide repeat of the largest subunit of RNA polymerase II, stimulates transcription elongation.
Recognition of a chromosome truncation site associated with alpha-thalassaemia by human telomerase
Telomerase primer specificity and chromosome healing
TICAM-1, an adaptor molecule that participates in Toll-like receptor 3-mediated interferon-beta induction
Glutathione peroxidase protein. Absence in selenium deficiency states and correlation with enzymatic activity
Role of aquaporin-7 and aquaporin-9 in glycerol metabolism; involvement in obesity
Genetic depletion of the malin E3 ubiquitin ligase in mice leads to lafora bodies and the accumulation of insoluble laforin
Arginine methylation at histone H3R2 controls deposition of H3K4 trimethylation
Methylation of histone H3R2 by PRMT6 and H3K4 by an MLL complex are mutually exclusive
The human phosphatidylinositol phosphatase SAC1 interacts with the coatomer I complex
The nuclear lamins: flexibility in function
5'-AMP inhibits dephosphorylation, as well as promoting phosphorylation, of the AMP-activated protein kinase. Studies using bacterially expressed human protein phosphatase-2C alpha and native bovine protein phosphatase-2AC
VEGF receptor expression and signaling in human bladder tumors
Discovery of the aquaporins and development of the field
The ontogeny of human drug-metabolizing enzymes: phase II conjugation enzymes and regulatory mechanisms
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Immunological and inflammatory functions of the interleukin-1 family
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Horror autoinflammaticus: the molecular pathophysiology of autoinflammatory disease (*)
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Completion of mammalian lagging strand DNA replication using purified proteins.
CDC6 protein is synthesized under the control of E2F transcription factors
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NEUROD1- and PDX1-dependent synthesis of glucokinase (GCK) protein
A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31
Site specificity of four pyruvate dehydrogenase kinase isoenzymes toward the three phosphorylation sites of human pyruvate dehydrogenase
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Dissecting membrane insertion of mitochondrial beta-barrel proteins
Origin, Recognition, Signaling and Repair of DNA Double-Strand Breaks in Mammalian Cells
Damage Surveillance and Repair (Keith Caldecott, editor)1-40
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Transcriptional activation of pyruvate kinase gene by ChREBP:MLX
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HNF1A-dependent synthesis of GLUT2 protein
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Promoter clearance by RNA polymerase II is an extended, multistep process strongly affected by sequence.
Localization of phosphatidylinositol phosphate kinase IIgamma in kidney to a membrane trafficking compartment within specialized cells of the nephron
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PRAK is essential for ras-induced senescence and tumor suppression
PKC412 inhibits the zinc finger 198-fibroblast growth factor receptor 1 fusion tyrosine kinase and is active in treatment of stem cell myeloproliferative disorder
Chapter 3 Activation of TRP Channels in Mammalian Systems
Cloning and initial characterization of a new subunit for mammalian serine-palmitoyltransferase
Control of the SCF(Skp2-Cks1) ubiquitin ligase by the APC/C(Cdh1) ubiquitin ligase
Mutations of conserved arginines in the membrane domain of erythroid band 3 lead to a decrease in membrane-associated band 3 and to the phenotype of hereditary spherocytosis
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Characterization of yeast methyl sterol oxidase (ERG25) and identification of a human homologue
Feedback regulation of EGFR signalling: decision making by early and delayed loops
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Phospholipase Czeta causes Ca2+ oscillations and parthenogenetic activation of human oocytes
Effects of phosphorylation by CAK on cyclin binding by CDC2 and CDK2.
Deficient HCO3- transport in an AE1 mutant with normal Cl- transport can be rescued by carbonic anhydrase II presented on an adjacent AE1 protomer
A synopsis of the unconjugated acidic transamination metabolites of phenylalanine in phenylketonuria
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Activation of heat shock factor 1 DNA binding precedes stress-induced serine phosphorylation. Evidence for a multistep pathway of regulation
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CENP-E, a novel human centromere-associated protein required for progression from metaphase to anaphase
Regulation of protein kinase C zeta by PI 3-kinase and PDK-1
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Mutations in iron-sulfur cluster scaffold genes NFU1 and BOLA3 cause a fatal deficiency of multiple respiratory chain and 2-oxoacid dehydrogenase enzymes
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Ribosomal scanning and start codon recognition
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Mechanism of aminoacylation of tRNA. Proof of the aminoacyl adenylate pathway for the isoleucyl- and tyrosyl-tRNA synthetases from Escherichia coli K12
Carbohydrate response element binding protein directly promotes lipogenic enzyme gene transcription
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Structural, molecular and cellular functions of MSH2 and MSH6 during DNA mismatch repair, damage signaling and other noncanonical activities
Neurotransmitter uptake and Metabolism In Glial Cells
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The anaphase-promoting complex: proteolysis in mitosis and beyond
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Molybdenum cofactor biosynthesis and deficiency
Active site remodelling accompanies thioester bond formation in the SUMO E1
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Ran-independent nuclear import of cyclin B1-Cdc2 by importin beta
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The enzymes and control of eukaryotic mRNA turnover
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Once synthesized mRNA can be utilized until degraded. Degradation itself is the final mode of gene expression regulation.
Characterization of a human gene conferring sensitivity to infection by gibbon ape leukemia virus
Gastrin-CREB signalling pathway via PKC and MAPK
Four SLC gene families encode proteins that mediate the transport of bile salts and organic anions; SLC10, SLC13, SLC16 and SLC47 (He L et al, 2009).
Once both coatomer and the active form of Arf1 have been recruited to the Golgi membrane surface, ArfGAP joins the complex.
RNA metabolism consists of both mRNA degradative pathways and non-coding RNA metabolism. Non-coding RNA metabolism includes the processing and packaging of the small nuclear ribonucleoproteins (snRNPs).
Subcellular localization and targeting of N-acetylglucosaminyl phosphatidylinositol de-N-acetylase, the second enzyme in the glycosylphosphatidylinositol biosynthetic pathway
All of the key components and regulators of the COPI coat (GBF1, Arf1, ArfGAP1 and coatomer) cycle on and off the Golgi membrane. This cycle is required for vesicle formation, but is uncoupled from the actual vesicle release. Continuous membrane binding and release of these molecules enables the COPI lattice to be dynamically modulated. Once the vesicle is released from the Golgi apparatus, this lattice is completely disassociated from the vesicle.
How MHC class II molecules acquire peptide cargo: biosynthesis and trafficking through the endocytic pathway
Together, the complex of coatomer, Arf1, and ArfGAP assembles into a lattice that concentrates cargo proteins and deforms the membrane. Eventually this membrane pocket forms into a bud that pinches off the membrane, and is released into the cytoplasm (Lippincott-Schwartz and Liu 2006).
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Ultimately the hydrolysis of Arf1-bound GTP, induced by the recruited ArfGAP, allows the inactive Arf1-GDP to diffuse away from the membrane, initiating disassembly of the lattice from the vesicle (Lippincott-Schwartz and Liu 2006).
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The hydrolysis of Arf1-bound GTP is induced by the recruited ArfGAP.
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The mismatch repair (MMR) system corrects single base mismatches and small insertion and deletion loops (IDLs) of unpaired bases. MMR is primarily associated with DNA replication and is highly conserved across prokaryotes and eukaryotes. MMR consists of the following basic steps: a sensor (MutS homologue) detects a mismatch or IDL, the sensor activates a set of proteins (a MutL homologue and an exonuclease) that select the nascent DNA strand to be repaired, nick the strand, exonucleolytically remove a region of nucleotides containing the mismatch, and finally a DNA polymerase resynthesizes the strand and a ligase seals the remaining nick (reviewed in Kolodner and Marsischkny 1999, Iyer et al. 2006, Li 2008, Fukui 2010, Jiricny 2013). Humans have 2 different MutS complexes. The MSH2:MSH6 heterodimer (MutSalpha) recognizes single base mismatches and small loops of one or two unpaired bases. The MSH2:MSH3 heterodimer (MutSbeta) recognizes loops of two or more unpaired bases. Upon binding a mismatch, the MutS complex becomes activated in an ATP-dependent manner allowing for subsequent downstream interactions and movement on the DNA substrate. (There are two mechanisms proposed: a sliding clamp and a switch diffusion model.) Though the order of steps and structural details are not fully known, the activated MutS complex interacts with MLH1:PMS2 (MutLalpha) and PCNA, the sliding clamp present at replication foci. The role of PCNA is multifaceted as it may act as a processivity factor in recruiting MMR proteins to replicating DNA, interact with MLH1:PMS2 and Exonuclease 1 (EXO1) to initiate excision of the recently replicated strand and direct DNA polymerase delta to initiate replacement of bases. MLH1:PMS2 makes an incision in the strand to be repaired and EXO1 extends the incision to make a single-stranded gap of up to 1 kb that removes the mismatched base(s). (Based on assays of purified human proteins, there is also a variant of the mismatch repair pathway that does not require EXO1, however the mechanism is not clear. EXO1 is almost always required, it is possible that the exonuclease activity of DNA polymerase delta may compensate in some situations and it has been proposed that other endonucleases may perform redundant functions in the absence of EXO1.) RPA binds the single-stranded region and a new strand is synthesized across the gap by DNA polymerase delta. The remaining nick is sealed by DNA ligase I (LIG1). Concentrations of MMR proteins MSH2:MSH6 and MLH1:PMS2 increase in human cells during S phase and are at their highest level and activity during this phase of the cell cycle (Edelbrock et al. 2009). Defects in MSH2, MSH6, MLH1, and PMS2 cause hereditary nonpolyposis colorectal cancer (HNPCC, also known as Lynch syndrome) (reviewed in Martin-Lopez and Fishel 2013).
DNA repair is a phenomenal multi-enzyme, multi-pathway system required to ensure the integrity of the cellular genome. These cellular mechanisms that must cope with the plethora of DNA base pair adducts that arise. DNA damage can arise spontaneously in the cellular milieu through chemical alteration of base nucleotides or as a consequence of errors during DNA replication. For example, it is well known that normal cellular pH and temperature offer an environment, which is hostile to the integrity of DNA and its nucleotide components. Additionally, DNA damage may be induced in response to environmental exposures, including exposure to physical agents such as ionizing or ultraviolet (UV) radiation. Finally, specific chemical agents are known to alkylate or cross-link DNA bases, produce bulky adducts on DNA bases, or break DNA phosphate-sugar backbone. The pioneering work from a number of laboratories have elucidated the basic mechanisms underlying distinct DNA repair pathways that include nucleotide excision repair (NER), base excision repair (BER), DNA strand break repair (DSBR), direct reversal of DNA damage, and the replication past DNA lesions by specialized DNA bypass polymerases (bypass replication). Defects in most of these repair pathways have been associated with one or more specific human diseases. Additionally, the repair of damaged DNA is intimately associated with a number of other distinct cellular processes such as DNA replication, DNA recombination, cell cycle checkpoint arrest, and other basic cellular mechanisms as outlined herein.
Anti-apoptotic signaling by the interleukin-2 receptor reveals a function for cytoplasmic tyrosine residues within the common gamma (gamma c) receptor subunit
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MSH2:MSH3 (MutSbeta) binds unpaired loops of 2 or more nucleotides (Palombo et al. 1996, Genschel et al. 1998). Human cells contain about 6-fold more MSH2:MSH6 than MSH2:MSH3 (MutSbeta) and an imbalance in the ratio can cause a mutator phenotype (Drummond et al. 1997, Marra et al. 1998). Binding of the mismatch activates MSH2:MSH3 to exchange ADP for ATP, adopt the conformation to allow movement along the DNA, and interact with downstream effectors PCNA, MLH1:PMS2 and EXO1. The interaction with PCNA initiates excision of the recently replicated strand. MLH1:PMS2 makes a nick that is enlarged to a gap of hundreds of nucleotides by EXO1. DNA is polymerized across the gap by DNA polymerase delta and the remaining nick is sealed by DNA ligase I.
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MSH2:MSH3 (MutSbeta) binds preferentially to insertions and deletion loops (IDLs) of 2 bases or more (Palombo et al. 1996, Drummond et al. 1997, Genschel et al. 1998, Tian et al. 2009, Panigrahi et al. 2010, Kantelinen et al. 2010, Gupta et al. 2012). Unlike MSH2:MSH6 (MutSalpha), which binds the base of a mismatched nucleotide, MSH2:MSH3 binds 3 phosphates in the loop of unpaired nucleotides (Gupta et al. 2012). MSH2:MSH3 is localized at replication foci during S phase via an interaction between MSH3 and PCNA (Kleczkowska et al. 2001).
MSH2:MSH6 (MutSalpha) binds single base mismatches and unpaired loops of 1-2 nucleotides (reviewed in Edelbrock et al. 2013). Human cells contain about 6-fold more MSH2:MSH6 than MSH2:MSH3 (MutSbeta), which mediates repair of larger mismatches, and an imbalance in the ratio can cause a mutator phenotype (Drummond et al. 1997, Marra et al. 1998). The MSH6 subunit is responsible for binding the mismatch, which activates MSH2:MSH6 to exchange ADP for ATP, adopt the conformation to allow movement on the DNA, and interact with downstream effectors PCNA, MLH1:PMS2 and EXO1. The interaction with PCNA initiates excision of the recently replicated strand. MLH1:PMS2 has endonucleolytic activity and makes a nick that is enlarged to a gap of hundreds of nucleotides by EXO1. DNA is polymerized across the gap by DNA polymerase delta and the remaining nick is sealed by DNA ligase I.
Vertebrate agmatinases: what role do they play in agmatine catabolism?
LIG1 (DNA ligase I) catalyzes the formation of a phosphodiester bond between a 3' hydroxyl group and a 5' phosphate group to form an intact DNA strand (Bhat and Grossman 1986). ATP is hydrolyzed to AMP and pyrophosphate in a reaction mechanism that involves adenylylation of a lysine residue of the enzyme, transfer of the adenylyl group to the 5' phosphate of DNA, and nick sealing by nucleophilic attack of the 3' hydroxyl group on the adenylylated 5' phosphate (Taylor et al. 2011, reviewed in Tomkinson et al. 2006). RPA stimulates the activity of LIG1 about 15-fold (Ranalli et al. 2002). LIG1 is recruited to repair sites by interaction with PCNA (Mortusewicz et al. 2006). Ligation is the final step in mismatch repair (Zhang et al. 2005, Constantin et al. 2005).
EXO1 interacts with MSH2 and MLH1 (and therefore is presumed to interact with their respective heterodimers MSH2:MSH6 and MLH1:PMS2), forming a ternary complex with MLH1:PMS2 (Nielsen et al. 2004). EXO1 also interacts with PCNA in S phase (Nielsen et al. 2004, Zhang et al. 2005, Constantin et al. 2005, Knudsen et al. 2007, Liberti et al. 2011)
EXO1 interacts with MSH2 and MLH1 (and therefore is presumed to interact with their respective heterodimers MSH2:MSH3 and MLH1:PMS2), forming a ternary complex with MLH1:PMS2 (Nielsen et al. 2004). EXO1 also interacts with PCNA in S phase (Nielsen et al. 2004, Zhang et al. 2005, Constantin et al. 2005, Knudsen et al. 2007, Liberti et al. 2011)
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Agmatine: at the crossroads of the arginine pathways
The latent endonuclease activity of MLH1:PMS2 (MutLalpha) is activated by interaction with MSH2:MSH3 (MutSbeta) (Zhang et al. 2005, and inferred from activation of MLH1:PMS2 by MSH2:MSH6). MLH1:PMS2 makes a nick in the strand of DNA that will be repaired (Kadyrov et al. 2006).
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After being activated by an insertion/deletion loop (IDL), MSH2:MSH3 (MutSbeta) recruits MLH1:PMS2 (MutLalpha) (Iyer et al. 2010, Pluciennik et al. 2013) and interacts with PCNA (Iyer et al. 2010). As inferred from yeast, more than one molecule of MLH1:PMS2 may bind per molecule of MSH2:MSH3 (Hombauer et al. 2011). MLH1:PMS2 and PCNA compete for the same binding site on MSH2:MSH3 (Iyer et al. 2010). The interaction with PCNA determines which strand of DNA will serve as template and which strand will be repaired (Zhang et al. 2005, and inferred from MSH2:MSH6).
After binding a mismatch, the MSH2:MSH3 (MutSbeta) heterodimer exchanges ADP for ATP, which changes the conformation of MSH2:MSH3 to a sliding clamp or molecular switch able to diffuse in one direction along duplex DNA (Gu et al. 1998, Zhang et al. 2005, and inferred from MSH2:MSH6).
The latent endonuclease activity of MLH1:PMS2 (MutLalpha) is activated by interaction with MSH2:MSH6 and PCNA (Kadyrov et al 2006). MLH1:PMS2 makes a nick in the replicated strand of DNA. As inferred from yeast, more than one MLH1:PMS2 may bind per MSH2:MSH6 (Hombauer et al. 2011). Strand selection of the nick is determined by interaction with PCNA, though the exact mechanism is unknown (Pluciennik et al 2010).
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After being activated by a mismatch, MSH2:MSH6 (MutSalpha) recruits MLH1:PMS2 (MutLalpha) to form a ternary complex with mismatched DNA (Gu et al. 1998, Blackwell et al. 2001, Plotz et al. 2002). As inferred from yeast, multiple MLH1:PMS2 complexes may be loaded at each mismatch (Hombauer et al. 2011). MSH2:MSH6 and MLH1:PMS2 interact with PCNA (Gu et al. 1998, Clark et al. 2000, Kleczkowska et al. 2001, Zhang et al. 2005, Constantin et al. 2005, Iyer et al. 2008, Masih et al. 2008, Iyer et al. 2010). The binding sites for MLH1:PMS2 and PCNA are distinct on MSH2:MSH6 so it is possible that both can bind simultaneously (Iyer et al. 2010). The interaction with PCNA appears to direct the orientation of the repair complex so as to determine which strand will be used as template and which strand will be repaired. In vivo, the recently replicated strand is repaired. In vitro, the strand containing a nick is repaired (Zhang et al. 2005, Constantin et al. 2005), possibly due to the ability of the nick to orient the loading of PCNA onto DNA by RFC (Pluciennik et al. 2010).
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After binding a mismatch, the MSH2:MSH6 (MutSalpha) heterodimer exchanges ADP for ATP, which alters its conformation to a sliding clamp or molecular switch able to diffuse in one direction along duplex DNA (Gradia et al. 1997, Blackwell et al. 1998, Gradia et al. 1999, Gradia et al. 2000). Each heterodimer can bind 2 molecules of ATP or ADP or a combination of ADP and ATP. The affinities and hydrolysis rates of the binding sites differ (Tian et al. 2009, Heinen et al. 2011). However, the exact location of a given adenosine at a given binding location and the conferred function is unclear but believed to control downstream events. Hydrolysis of the ATP by MSH2:MSH6 is not required for mismatch binding but is required for subsequent mismatch repair (Gu et al. 1998, Tian et al. 2009, Geng et al. 2012).
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The preferential repair of UV-induced damage in transcribed strands of active genes is known as Transcription-coupled NER (TC-NER). Impairment of the ability for TC-NER results in the onset of a severe hereditary disorder called Cockayne's syndrome, an autosomal recessive disease characterized by hypersensitivity to UV light . Many types of helix distorting lesions can block the movement of elongating RNA Pol II leading to its stalling and subsequent triggering of repair mechanisms. The repair of DNA damage in active genes occurs much faster compared to the repair in non-transcribed genomic regions (via GG-NER). Also, the non-transcribed strand of the same gene is repaired at a similar rate as that of non-transcribed genomic regions. The transcriptional responses to DNA damage in terms of stalling of Pol II, its displacement from the lesion site etc. are not well elucidated. The following annotation in GK provides an overall picture of TC-NER and will be updated as and when new insights are obtained about these crucial steps.
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At the beginning of this reaction, 1 molecule of 'Stalled Pol II in TC-NER', and 1 molecule of 'repaired DNA template:nascent mRNA hybrid' are present. At the end of this reaction, 1 molecule of 'Active Pol II complex with repaired DNA template:mRNA hybrid' is present. This reaction takes place in the 'nucleus'.
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The MSH2:MSH6 (MutSalpha) heterodimer binds single base mismatches and insertion or deletion loops (IDLs) of 1-2 bases (Drummond et al. 1997, Genschel et al. 1998, Gradia et al. 2000, Zhang et al. 2005, Constantin et al. 2005, Tian et al. 2009, reviewed in Edelbrock et al. 2013). The MSH6 subunit contains a Phe-X-Glu motif that binds the mismatched base (Dufner et al 2000, Warren et al. 2007). During replication most nuclear MSH2:MSH6 is observed to colocalize with PCNA via an interaction between PCNA and MSH6 at replication forks during S phase (Kleczkowska et al. 2001), presumably coupling mismatch repair to DNA replication. The MSH6 subunit of MSH2:MSH6 also binds histone H3 methylated at lysine-36, which is enriched in chromatin during G1 and early S phase (Li et al. 2013).
NER was first described in the model organism E. coli in the early 1960s as a process whereby bulky base damage is enzymatically removed from DNA, facilitating the recovery of DNA synthesis and cell survival. Deficient NER processes have been identified from the cells of cancer-prone patients with different variants of xeroderma pigmentosum (XP), trichothiodystrophy (TTD), and Cockayne's syndrome. These XP cells exhibited an ultraviolet radiation hypersensitivity leading to a hypermutability response to UV, offering a direct connection between deficient NER, increased mutations, and cancer. While the NER pathway in prokaryotes is unique, the pathway utilized in yeast and higher eukaryotes is highly conserved and includes a variety of proteins that interact to form complexes. NER is involved in the repair of bulky adducts in DNA, such as UV-induced photo lesions [of both 6-4 photoproducts (6-4 pps) and cyclobutane pyrimidine dimer (CPDs)], intrastrand cross-links, large chemical adducts formed from exposure to aflatoxin, benzopyrene and other genotoxic agents. Specific proteins have been identified that participate in base damage recognition, cleavage of the damaged strand on both sides of the lesion, excision of the oligonucleotide bearing the lesion, and accessory proteins necessary for efficient function. Polymerization and ligation restore the strand to its original state. NER consists of two related pathways called global genomic repair (GG-NER) and transcription-coupled NER (TC-NER). The pathways differ in the way in which DNA damage is initially recognized, but the majority of the participating molecules are shared between these two branches of NER. GG-NER is considered to be transcription-independent, removing lesions from non-transcribed regions of genome in addition to non-transcribed strands of transcribed regions. The preferential repair of UV-induced damage in transcribed strands of active genes is known as Transcription-coupled NER (TC-NER). Several of the proteins involved in NER are key components of the basal transcription complex TFIIH. NER proteins have also been shown to interact with the 19S regulatory subunit of the proteasome, suggesting a role in cellular regulation signal pathways. The establishment of mutant mouse models for NER genes and other DNA repair-related genes have been useful in demonstrating the associations between NER defects and cancer.
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Dual incisions are carried out by XPG, and ERCC1-XPF complex as seen in GG-NER.
At the beginning of this reaction, 1 molecule of 'Transcription-coupled (TC) repair complex', and 1 molecule of 'damaged DNA substrate:nascent mRNA hybrid with 3' incision' are present. At the end of this reaction, 1 molecule of 'Transcription-coupled (TC) repair complex', 1 molecule of 'excised DNA fragment with lesion', and 1 molecule of 'damaged DNA substrate:nascent mRNA hybrid with dual incisions' are present. This reaction takes place in the 'nucleus' and is mediated by the 'endodeoxyribonuclease activity' of 'Transcription-coupled (TC) repair complex'.
Polymerization is carried out by DNA polymerases, delta and epsilon.
At the beginning of this reaction, 1 molecule of 'newly synthesized DNA fragment ', 1 molecule of 'DNA ligase I ', and 1 molecule of 'damaged DNA substrate:nascent mRNA hybrid with dual incisions' are present. At the end of this reaction, 1 molecule of 'repaired DNA template:nascent mRNA hybrid', and 1 molecule of 'DNA ligase I ' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA ligase activity' of 'DNA ligase I '.
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Characterization of a second member of the subfamily of calcium-binding mitochondrial carriers expressed in human non-excitable tissues
MISCELLANEOUS Present with 2010 molecules/cell in log phase SD medium.SIMILARITY Belongs to the HscB family.SIMILARITY Contains 1 J domain.
PTM Processed in two steps by mitochondrial processing peptidase (MPP). MPP first cleaves the precursor to intermediate form and subsequently converts the intermediate to mature size protein.MISCELLANEOUS Present with 1560 molecules/cell in log phase SD medium.SIMILARITY Belongs to the frataxin family.
Irreversible inactivation of glutathione peroxidase 1 and reversible inactivation of peroxiredoxin II by H2O2 in red blood cells
Herp is dually regulated by both the endoplasmic reticulum stress-specific branch of the unfolded protein response and a branch that is shared with other cellular stress pathways
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PATHWAY Protein modification; protein glycosylation.MISCELLANEOUS Present with 1840 molecules/cell in log phase SD medium.SIMILARITY Belongs to the glycosyltransferase group 1 family. Glycosyltransferase 4 subfamily.
PATHWAY Protein modification; protein glycosylation.SIMILARITY Belongs to the ALG10 glucosyltransferase family.
At the beginning of this reaction, 1 molecule of 'Transcription-coupled (TC) repair complex', and 1 molecule of 'damaged DNA substrate:nascent mRNA hybrid' are present. At the end of this reaction, 1 molecule of 'Transcription-coupled (TC) repair complex', and 1 molecule of 'damaged DNA substrate:nascent mRNA hybrid with 3' incision' are present. This reaction takes place in the 'nucleus' and is mediated by the 'endodeoxyribonuclease activity' of 'Transcription-coupled (TC) repair complex'.
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At the beginning of this reaction, 1 molecule of 'Transcription-coupled (TC) repair complex', and 1 molecule of 'Stalled Pol II complex with damaged DNA hybrid' are present. At the end of this reaction, 1 molecule of 'Transcription-coupled (TC) repair complex', 1 molecule of 'Stalled Pol II in TC-NER', and 1 molecule of 'damaged DNA substrate:nascent mRNA hybrid' are present. This reaction takes place in the 'nucleus'.
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The 'road block' induced by the DNA damage to the transcription machinery triggers assembly of a transcription couple repair complex, whose composition and function are yet to fully understood. Damage recognition is achieved by the arrest of Pol II active complex. Subsequently various factors like CSA, CSB, TFIIH, XPG, XPF-ERCC1 complexes are recruited. The importance of active CSA and CSB are known from the mutation profile of the patients bearing the corresponding disease phenotypes. CSB can act as a 'repair-transcription uncoupling factor' that may use its DNA translocase activity to remove the Pol II activity from the lesion site. TFIIS may cleave up to 35 nucleotides from the 3' end of the nascent RNA product leading to the enhanced access to damage site on the corresponding template DNA.
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A proper assembly of repair complex may require displacement of Pol II from the damage site exposing a significant length of the corresponding template DNA with the lesions. Speculations on the mode of this displacement of Pol II are available from experimental evidences: a. CSB mediated dissociation of Pol II b. degradation of Pol II c. CSB mediated remodeling of damaged DNA-RNA PII interface etc. The TC-repair complex now consists of damaged DNA template: nascent mRNA hybrid. The damage site needs to be exposed to subsequent endonuclease activities.
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At the site of damage, the Pol II complex is arrested resulting in reduced levels of transcription. Several models have been proposed to explain the mechanism of this transcriptional downregulation. These include a. hyperphosphorylation of Pol II resulting in aborted entry to new pre-initiation complexes b. sequestration of TATA-binding proteins (TBP) c. enhanced use of TFIIH complexes for repair purposes precluding their use in transcription.
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An active Pol II complex consisting mainly of the Pol II holoenzyme transcribes the damaged DNA template.
GG-NER is considered to be transcription-independent, removing lesions from non-transcribed regions of genome in addition to non-transcribed strands of transcribed regions. The three events that characterize NER are well characterized in GG-NER: damage recognition, bimodal incision of DNA via repair protein complex, resulting excision of DNA fragment with the lesion. Post-excision polymerization and ligation restore back the native chemistry and configuration to the damaged DNA.
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The resultant gap is filled by polymerase activities of Pol delta and Pol epsilon. Accessory replication protein complexes of RPA, PCNA and RFC play a role in this synthesis. DNA Ligase 1 seals the gap restoring the covalent integrity of the repaired strand.
DNA Ligase 1 ligates the newly synthesized fragment to the gap in the template DNA.
Dual incision at defined positions flanking the DNA damage is carried out by XPG (3' -incision) and ERCC1-XPF (5'-incision) complex. The resulting excised fragment is ~27-30 bp long and contains the lesion.
Enzymes and reactions at the eukaryotic DNA replication fork.
A direct role for GRASP65 as a mitotically regulated Golgi stacking factor
Identification of an acid-activated Cl(-) channel from human skeletal muscles
Oligosaccharide translocation protein RFT1
Mevalonate kinase is a cytosolic enzyme in humans
Characteristics of the interaction of a synthetic human tristetraprolin tandem zinc finger peptide with AU-rich element-containing RNA substrates
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Mechanistic and kinetic analysis of the DcpS scavenger decapping enzyme
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The secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is made up of distinct organelles, including the endoplasmic reticulum (ER), Golgi complex, plasma membrane, and tubulovesicular transport intermediates. These organelles mediate intracellular membrane transport between themselves and the cell surface. Membrane traffic within this system flows along highly organized directional routes. Secretory cargo is synthesized and assembled in the ER and then transported to the Golgi complex for further processing and maturation. Upon arrival at the trans Golgi network (TGN), the cargo is sorted and packaged into post-Golgi carriers that move through the cytoplasm to fuse with the cell surface. This directional membrane flow is balanced by retrieval pathways that bring membrane and selected proteins back to the compartment of origin.
Eight SLC gene families are involved in the transport of amino acids and oligopeptides.
TBC1D1 phosphorylated on serine-237 binds 14-3-3 proteins in assays with yeast 14-3-3 proteins BMH1 and BMH2 (Chen et al. 2008, Frosig et al. 2010). Binding with human 14-3-3 proteins is inferred.
In adipocytes and myocytes insulin signaling causes intracellular vesicles carrying the GLUT4 (SLC2A4) glucose transporter to translocate to the plasma membrane, allowing the cells to take up glucose from the bloodstream (reviewed in Zaid et al. 2008, Leney and Tavare 2009, Bogan and Kandror 2010, Foley et al. 2011, Hoffman and Elmendorf 2011, Kandror and Pilch 2011). In myocytes muscle contraction alone can also cause translocation of GLUT4. Though the entire pathway leading to GLUT4 translocation has not been elucidated, several steps are known. Insulin activates the kinases AKT1 and AKT2. Muscle contraction activates the kinase AMPK-alpha2 and possibly also AKT. AKT2 and, to a lesser extent, AKT1 phosphorylate the RAB GTPase activators TBC1D1 and TBC1D4, causing them to bind 14-3-3 proteins and lose GTPase activation activity. As a result RAB proteins (probably RAB8A, RAB10, RAB14 and possibly RAB13) accumulate GTP. The connection between RAB:GTP and vesicle translocation is unknown but may involve recruitment and activation of myosins. Myosins 1C, 2A, 2B, 5A, 5B have all been shown to play a role in translocating GLUT4 vesicles near the periphery of the cell. Following docking at the plasma membrane the vesicles fuse with the plasma membrane in a process that depends on interaction between VAMP2 on the vesicle and SNAP23 and SYNTAXIN-4 at the plasma membrane.
Many plasma membrane proteins are in a constant flux throughout the internal trafficking pathways of the cell. Some receptors are continuously internalized into recycling endosomes and returned to the cell surface. Others are sorted into intralumenal vesicles of morphologically distinctive endosomes that are known as multivesicular bodies (MVBs). These MVBs fuse with lysosomes, resulting in degradation of their cargo by lysosomal acidic hydrolases. Endosomes can be operationally defined as being either early or late, referring to the relative time it takes for endocytosed material to reach either stage. Ultrastructural studies indicate that early endosomes are predominantly tubulovesicular structures, which constitute a major sorting platform in the cell, whereas late endosomes show the characteristics of typical MVBs and are capable of fusing with lysosomes. A well characterized signal for shunting membrane proteins into the degradative MVB pathway is the ubiquitylation of these cargoes. At the center of a vast protein:protein and protein:lipid interaction network that underpins ubiquitin mediated sorting to the lysosome are the endosomal sorting complexes required for transport (ESCRTs), which are conserved throughout all major eukaryotic taxa.
In response to muscle contraction and insulin signaling, AMPK-alpha2 phosphorylates TBC1D1 on serine 237 and probably other residues (Frosig et al. 2010, Vichaiwong et al. 2010). As inferred from rat L6 muscle cells TBC1D1 colocalizes with perinuclear vesicles bearing GLUT4 (SLC2A4) and may be involved in an early step that mobilizes them (Chen et al. 2008). Human TBC1D1 appears cytosolic and is believed to be concentrated near vesicle membranes (Park et al. 2011).
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Vacuolar protein-sorting-associated protein 36
Vacuolar protein-sorting-associated protein 25
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ESCRT-III assembles into a highly ordered filament-like hetero-oligomer. Vps20 nucleates the homo-oligomerization of Snf7 that is capped by Vps24. Vps24 recruits Vps2 and initiates Vps4-dependent ESCRT-III disassembly. ESCRT-III is required for the last steps of MVB sorting, cargo sequestration, and MVB vesicle formation.
The anterograde membrane flow from the ER to the Golgi is compensated for by a retrograde pathway. This pathway's functions include the recycling of membrane and proteins to the ER.
Secretory transport depends on membrane-bounded carriers to move protein and lipid between intracellular compartments. The COPI coat has a central role in this process, creating a sorting domain on the membrane into which cargo proteins, destined to return to the endoplasmic reticulum (ER), concentrate. The membrane domain deforms into a coated bud, pinches off the membrane as a coated carrier, and then uncoats. Successful operation of the COPI coat system is necessary for selective retrieval of protein and lipid components back to the ER.
Subcellular localization and properties of alkaline inorganic pyrophosphatase in human polymorphonuclear leucocytes
Molecular physiology of cation-coupled Cl- cotransport: the SLC12 family
Cloning, characterization, and modeling of mouse and human guanylate kinases
Isolation and characterization of the faciogenital dysplasia (Aarskog-Scott syndrome) gene: a putative Rho/Rac guanine nucleotide exchange factor
Mutations in the catalytic subunit of class IA PI3K confer leukemogenic potential to hematopoietic cells
Analysis of phosphoinositide binding domain properties within the myotubularin-related protein MTMR3
Pam17 is required for architecture and translocation activity of the mitochondrial protein import motor
The extended protein kinase C superfamily
Role of glutathione and glutathione peroxidase in human platelet arachidonic acid metabolism
Trimethylaminuria: the fish-odour syndrome
Localization of human equilibrative nucleoside transporters, hENT1 and hENT2, in renal epithelial cells
Subcellular locations of phosphatidylinositol 4-kinase isoforms
Docosapentaenoic acid (22:5n-3): a review of its biological effects
The HRR pathway is an "error free" DNA repair mechanism that utilizes information encoded by homologous sequence to repair double-strand breaks (DSBs). HRR acts on DSBs occurring within replicated DNA (replication-independent DSBs) or on DSBs that are generated at broken replication forks (replication-dependent DSBs). Repair by homologous recombination involves processing of the ends of the DNA double-strand break, homologous DNA pairing and strand exchange, repair DNA synthesis, and resolution of the heteroduplex molecules.
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Old and new generation lipid mediators in acute inflammation and resolution
Numerous types of DNA damage can occur within a cell due to the endogenous production of oxygen free radicals, normal alkylation reactions, or exposure to exogenous radiations and chemicals. Double-strand breaks (DSBs), one of the most dangerous type of DNA damage along with interstrand crosslinks, are caused by ionizing radiation or certain chemicals such as bleomycin, and occur normally during the processes of DNA replication, meiotic exchange, and V(D)J recombination. Two distinct mechanisms for DSB repair are the error-free homologous recombination repair (HRR) pathway and the error-prone nonhomologous end-joining (NHEJ) pathway. The choice of pathway may be determined by whether the DNA region has already replicated and the precise nature of the break. NHEJ functions at all stages of the cell cycle, but plays the predominant role in both the G1 phase and in S-phase regions of DNA that have not yet replicated (Rothkamm et al. 2003). HRR functions primarily in repairing both one-sided DSBs that arise at DNA replication forks and two-sided DSBs arising in S or G2-phase chromatid regions that have replicated.
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Several subunits of the NER multiprotein repair machinery are required for the recognition of damage in DNA. Mainly, XPC, HR23B, XPA and RPA are implicated in this process. XPA and RPA are thought to be binding to the damage site after the binding of XPC-HR23B complex.
Two DNA helicases XPG and XPD, which are part of TFIIH, unwind DNA duplex around this lesion to form an open bubble structure that exposes the damaged site.
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XPC is mutated in individuals with xeroderma pigmentosum from genetic Complementation Group C (XP-C). It forms a tight heterodimeric complex with human Rad 23B homolog, HR23B and is thought to bind to the damaged site with lesion first triggering subsequent reactions
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Disruption of normal Watson-Crick base pairing and altered chemistry in the damaged strand involving bases may act as signals of damage that are recognized by XPC:HR23B complex.
Binding of XPC complex to the damaged site on the DNA substrate is followed by XPA and RPA recruitment. XPA is a metalloprotein that binds to different types of DNA damage. Binding of RPA, or Replicative protein A, a heterotrimer, initiates the formation of incision complex. This includes a serial assembly of the rest of the NER machinery consisting of TFIIH, XPG etc. Action of helicases in TFIIH complex opens up a bubble structure in the DNA template, exposing a fragment of DNA with lesion for endonuclease activity.
The cleavage of the damaged strand of DNA 3' to the site of damage occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision is carried out by XPG.
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At the beginning of this reaction, 1 molecule of 'ERCC1, DNA excision repair protein', and 1 molecule of 'XPF protein' are present. At the end of this reaction, 1 molecule of 'ERCC1:XPF complex' is present. This reaction takes place in the 'nucleus'.
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CATALYTIC ACTIVITY A polyprenyl diphosphate + 4-hydroxybenzoate = diphosphate + a 4-hydroxy-3-polyprenylbenzoate.PATHWAY Cofactor biosynthesis; ubiquinone biosynthesis.SIMILARITY Belongs to the UbiA prenyltransferase family.
ERCC1-XPF complex with 5ââ¬â¢ endonuclease activity binds to this pre-incision complex around the bubble structure to form an active incision complex.
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MISCELLANEOUS Present with 3180 molecules/cell in log phase SD medium.SIMILARITY Belongs to the TIM16/PAM16 family.
SIMILARITY Belongs to the TIM14 family.SIMILARITY Contains 1 J domain.
FUNCTION Catalyzes the stereospecific oxidation of D-lactate to pyruvate.CATALYTIC ACTIVITY (R)-lactate + 2 ferricytochrome c = pyruvate + 2 ferrocytochrome c + 2 H(+).COFACTOR Binds 2 FAD.COFACTOR Binds 4-6 zinc ions.INDUCTION By D-lactate. Induced during respiratory adaptation.MISCELLANEOUS Present with 10800 molecules/cell in log phase SD medium.SIMILARITY Belongs to the FAD-binding oxidoreductase/transferase type 4 family.SIMILARITY Contains 1 FAD-binding PCMH-type domain.
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FUNCTION Cleaves presequences (transit peptides) from mitochondrial protein precursors. The cleavage sites typically contain an arginine at position -2 (in the N-terminal portion) from the scissible peptide bond in addition to other distal basic residues, and an aromatic residue at position +1.CATALYTIC ACTIVITY Release of N-terminal transit peptides from precursor proteins imported into the mitochondrion, typically with Arg in position P2.SUBUNIT Heterodimer of alpha and beta subunits.MISCELLANEOUS Present with 31400 molecules/cell in log phase SD medium.SIMILARITY Belongs to the peptidase M16 family.CAUTION Does not seem to have a protease activity as it lack the zinc-binding site.
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FUNCTION Cleaves presequences (transit peptides) from mitochondrial protein precursors.CATALYTIC ACTIVITY Release of N-terminal transit peptides from precursor proteins imported into the mitochondrion, typically with Arg in position P2.COFACTOR Binds 1 zinc ion per subunit.SUBUNIT Heterodimer of alpha and beta subunits.MISCELLANEOUS Present with 1360 molecules/cell in log phase SD medium.SIMILARITY Belongs to the peptidase M16 family.
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MISCELLANEOUS Present with 2400 molecules/cell in log phase SD medium.SIMILARITY Belongs to the TIM50 family.SIMILARITY Contains 1 FCP1 homology domain.
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FUNCTION Essential component of the PAM complex, a complex required for the translocation of transit peptide-containing proteins from the inner membrane into the mitochondrial matrix in an ATP-dependent manner. Recruits mitochondrial HSP70 and its co-chaperone (MGE1) to drive protein translocation into the matrix using ATP as an energy source.SIMILARITY Belongs to the Tim44 family.
Transcriptional signaling by double-stranded RNA: role of TLR3
A unique fold of phospholipase C-beta mediates dimerization and interaction with G alpha q
Distribution of the AQP4 water channel in normal human tissues: protein and tissue microarrays reveal expression in several new anatomical locations, including the prostate gland and seminal vesicles
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Novel mutant-selective EGFR kinase inhibitors against EGFR T790M
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Deleterious mutation in the mitochondrial arginyl-transfer RNA synthetase gene is associated with pontocerebellar hypoplasia
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The CoA esters of 2-methyl-branched chain fatty acids and of the bile acid intermediates di- and trihydroxycoprostanic acids are oxidized by one single peroxisomal branched chain acyl-CoA oxidase in human liver and kidney
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FUNCTION Essential component of the TIM23 complex, a complex that mediates the translocation of transit peptide-containing proteins across the mitochondrial inner membrane.MISCELLANEOUS Present with 1210 molecules/cell in log phase SD medium.SIMILARITY Belongs to the Tim17/Tim22/Tim23 family.
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ZNF198-FGFR1 transforms Ba/F3 cells to growth factor independence and results in high level tyrosine phosphorylation of STATS 1 and 5
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SGPL1 (sphingosine-1-phosphate lyase 1), associated with the endoplasmic reticulum membrane, catalyzes the cleavage of cytosolic sphingosine 1-phosphate to form phosphoethanolamine and hexadec-2-enal (Van Veldhoven et al. 2000; Fyrst and Saba 2008).
SGPP1 and 2 (sphingosine-1-phosphate phosphatase 1 and 2) enzymes associated with the endoplasmic reticulum membrane catalyze the hydrolysis of cytosolic sphingosine 1-phosphate to form sphingosine and orthophosphate (Johnson et al. 2003; Ogawa et al. 2003).
SPHK1 and 2 (sphingosine kinases 1 and 2) catalyze the reaction of sphingosine and ATP to form sphingosine 1-phosphate and ADP. Both enzymes are found in the cytosol (although they are also present in membrane-associated forms). Both enzymes also catalyze the phosphorylation of sphinganine (dihydrosphingosine) (Liu et al. 2000; Nava et al. 2000; Pitson et al. 2000).
SPTLC (serine palmitoyltransferase) enzyme complexes associated with the endoplasmic reticulum membrane catalyze the reaction of palmitoyl-CoA and serine to form 3-ketosphinganine. SPTLC2 and SPTLC3 polypeptides exhibit enzyme activity when either is complexed with SPTLC1. SPTLC1 and 2 are abundant and widely expressed in human tissues, while SPTLC3 is expressed only in a smaller group of tissues and at variable levels. Results of studies in which siRNA was used to reduce levels of the three endogenous mRNAs differentially suggest that SPTLC2 and 3 both encode active serine palmitoyltransferases (Hornemann et al. 2006). Neither human nor mouse SPTLC1 has detectable enzyme activity, but the protein has an essential function, as mutations that disrupt it are associated with hereditary neuropathy (Dawkins et al. 2001). Studies of mouse and hamster proteins support the hypothesis that heterodimerization with SPTLC1 stabilizes SPTLC2 (or 3) and mediates its localization to the endoplasmic reticulum membrane (Hanada et al. 2000; Weiss and Stoffel 1997). Analyses of complexes extracted from human placenta, and of cultured human cells over-expressing various SPTLC constructs, suggest that these heterodimers may associate into larger complexes (Hanada et al. 2000; Weiss and Stoffel 1997; Hornemann et al. 2006, 2007).
ACER3 (alkaline ceramidase 3) catalyzes the hydrolysis of phytoceramide to yield a free fatty acid (annotated here as stearate) and phytosphingosine. ACER3 mRNA is widely expressed in the body, although most abundant in placenta. Immunofluoresence studies of cultured cells over-expressing GFP-tagged protein suggest its localization to membranes of the endoplasmic reticulum (annotated here) and also the Golgi apparatus (Mao et al. 2001).
KDSR (3-ketodihydrosphingosine reductase) enzyme associated with the cytosolic face of the endoplasmic reticulum membrane catalyzes the reduction of 3-ketosphinganine by NADPH to form sphinganine (dihydrosphingosine) (Kihara and Igarashi 2004).
Human SWI/SNF-associated PRMT5 methylates histone H3 arginine 8 and negatively regulates expression of ST7 and NM23 tumor suppressor genes
SGPP1 and 2 (sphingosine-1-phosphate phosphatase 1 and 2) enzymes associated with the endoplasmic reticulum membrane catalyze the hydrolysis of cytosolic sphinganine 1-phosphate to form sphinganine (dihydrosphingosine) and orthophosphate (Johnson et al. 2003; Ogawa et al. 2003).
SGPL1 (sphingosine-1-phosphate lyase 1), associated with the endoplasmic reticulum membrane, catalyzes the cleavage of cytosolic sphinganine (dihydrosphingosine) 1-phosphate to form phosphoethanolamine and hexadecanal (Van Veldhoven et al. 2000; Fyrst and Saba 2008).
SPHK1 and 2 (sphingosine kinases 1 and 2) each catalyze the reaction of sphinganine (dihydrosphingosine) and ATP to form dihydrosphingosine 1-phosphate and ADP. Both enzymes are found in the cytosol (although they are also present in membrane-associated forms). Both enzymes also catalyze the phosphorylation of sphingosine (Liu et al. 2000; Nava et al. 2000; Pitson et al. 2000).
LASS (âlongevity assurance homologâ, also known as ceramide synthase, CerS) enzymes associated with the endoplasmic reticulum membrane catalyze the reaction of sphinganine (dihydrosphingosine) and a long-chain fatty acyl CoA such as stearyl-CoA to form a dihydroceramide and CoASH (Pewzner-Jung et al. 2006). Six human LASS genes have been identified; they differ in the identities of the fatty acyl CoAs that they use most efficiently as substrates (Lahiri and Futerman 2005; Laviad et al. 2008).
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Biosynthesis and metabolism of leukotrienes
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Yin and Yang of hypothalamic insulin and leptin signaling in regulating white adipose tissue metabolism
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Glutathione peroxidase 1 (GPX1) (Bryant et al. 1982, Sutherland et al. 2001), 2 (GPX2) (Chu et al. 1993), and 4 (Bryant et al. 1982, Sutherland et al. 2001) are involved in converting 12S-hydroperoxy-eicosatetraenoic acid (12S-HpETE) to 12S-hydro-eicosatetraenoic acid (12S-HETE). GPXs are selenoenzymes that are responsible for reducing the cellular peroxide. Cellular GPXs compete with hepoxilins A3 (HXA3) synthase for 12S-HpETE as substrate either to produce 12S-HETE or to convert to HXA3, respectively.
Glutathione peroxidase 1 (GPX1) (Bryant et al. 1982, Sutherland et al. 2001), 2 (GPX2) (Chu et al. 1993), and 4 (Bryant et al. 1982, Sutherland et al. 2001) are involved in converting 12R-hydroperoxy-eicosatetraenoic acid (12R-HpETE) to 12R-hydro-eicosatetraenoic acid (12R-HETE).
Eicosanoids, oxygenated, 20-carbon fatty acids, are autocrine and paracrine signaling molecules that modulate physiological processes including pain, fever, inflammation, blood clot formation, smooth muscle contraction and relaxation, and the release of gastric acid. Eicosanoids are synthesized in humans primarily from arachidonic acid (all-cis 5,8,11,14-eicosatetraenoic acid) that is released from membrane phospholipids. Once released, arachidonic acid is acted on by prostaglandin G/H synthases (PTGS, also known as cyclooxygenases (COX)) to form prostaglandins and thromboxanes, by arachidonate lipoxygenases (ALOX) to form leukotrienes, epoxygenases (cytochrome P450s and epoxide hydrolase) to form epoxides such as 15-eicosatetraenoic acids, and omega-hydrolases (cytochrome P450s) to form hydroxyeicosatetraenoic acids (Buczynski et al. 2009, Vance & Vance 2008). Levels of free arachidonic acid in the cell are normally very low so the rate of synthesis of eicosanoids is determined primarily by the activity of phospholipase A2, which mediates phospholipid cleavage to generate free arachidonic acid. The enzymes involved in arachidonic acid metabolism are typically constitutively expressed so the subset of these enzymes expressed by a cell determines the range of eicosanoids it can synthesize. Eicosanoids are unstable, undergoing conversion to inactive forms with half-times under physiological conditions of seconds or minutes. Many of these reactions appear to be spontaneous.
The 12-eicosatetraenoic acids: 12-hydroperoxy-eicosatetraenoic acid (12-HpETE), 12-hydroxyeicosatetraenoic acid (12-HETE) and 12-oxo-eicosatetraenoic acid (12-oxoETE) are formed after the initial step of arachidonic acid oxidation by the arachidonate 12 and 15 lipoxygenases (ALOX12, ALOX12B and ALOX15 respectively). This part of the pathway is bifurcated at the level of 12S-hydroperoxy-eicosatetraenoic acid (12S-HpETE), which can either be reduced to 12S-hydro-eicosatetraenoic acid (12S-HETE) or converted to hepoxilins (Buczynski et al. 2009, Vance & Vance 2008).
The reversible conversion of leukotriene C4 (LTC4) to leukotriene D4 (LTD4) is catalysed by gamma-glutamyl transferases 1 (GGT1) and 5 (GGT5). GGTs are present on the outer surface of plasma membranes and are a heterodimer of a heavy and a light chain. Its action involves the cleavage of the gamma-glutamyl peptide bond of glutathione conjugates, releasing glutamate (Anderson et al. 1982, Wickham et al. 2011).
Gamma-glutamyl compounds: substrate specificity of gamma-glutamyl transpeptidase enzymes
Leukotrienes (LTs) are biologically active molecules formed in response to inflammatory stimuli. They cause contraction of bronchial smooth muscles, stimulation of vascular permeability, and attraction and activation of leukocytes. LTs were discovered in 1938 and were termed the "slow release substance" (SRS) until their structures were determined in 1979 and they were then renamed to leukotrienes. LTs are derived from arachidonic acid through action by arachidonate 5-lipoxygenase (ALOX5). Cysteinyl leukotrienes (LTC4, LTD4, and LTE4) are generated as products derived from leukotriene A4 (LTA4). Eoxins are generated from leukotrienes (LTs) and resemble cysteinyl leukotrienes but have a different three-dimensional structure (Murphy & Gijon 2007, Hammarstrom 1983, MA.Claesson 2009, Vance & Vance 2008, Buczynski et al. 2009).
Glutathione peroxidase 1 (GPX1) (Bryant et al. 1982, Sutherland et al. 2001), 2 (GPX2) (Chu et al. 1993), and 4 (Bryant et al. 1982, Sutherland et al. 2001) reduce 5-hydroperoxyeicosatetraenoic acid (5-HpETE) to 5-hydroxyeicosatetraenoic acid (5-HETE) in the presence of glutathione (GSH). This reaction is inferred from the event in rabbit involving the protein GPX1 (Chiba et al. 1999).
5-hydroperoxy-eicosatetraenoic acid (5-HpETE), 5-hydroxyeicosatetraenoic acid (5S-HETE) and 5-oxo-eicosatetraenoic acid (5-oxoETE) are formed after the initial step of arachidonic acid oxidation by arachidonate 5-lipoxygenase (ALOX5) (Buczynski et al. 2009, Vance & Vance 2008).
Glutathione peroxidases (GPXs) in human platelets (either GPX1, GPX2, or GPX4 are present in the cytosol) are involved in reducing 15S-hydroperoxyeicosatetraenoic acid (15S-HpETE) to 15S-hydroxyeicosatetraenoic acid (15S-HETE) (Hill et al. 1989).
The 15-eicosatetraenoic acids: 15-hydroperoxy-eicosatetraenoic acid (15-HpETE), 15-hydroxyeicosatetraenoic acid (15-HETE) and 15-oxo-eicosatetraenoic acid (15-oxoETE) are formed after the initial step of arachidonic acid oxidation by the arachidonate 15-lipoxygenases (ALOX15 and ALOX15B) (Buczynski et al. 2009, Vance & Vance 2008).
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Cdc13 delivers separate complexes to the telomere for end protection and replication
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Nuclear Events (kinase and transcription factor activation)
Adenylate cyclase catalyses the synthesis of cyclic AMP (cAMP) from ATP. In the absence of cAMP, protein kinase A (PKA) exists as inactive tetramers of two catalytic subunits and two regulatory subunits. cAMP binding to PKA tetramers causes them to dissociate and release their catalytic subunits as active monomers. Four isoforms of the regulatory subunit are known, that differ in their tissue specificity and functional characteristics, but the specific isoform activated in response to glucagon signaling has not yet been identified.
A family of antiport, ATP-ADP translocases, preferentially export ATP from the matrix while importing ADP from the cytosol, thereby maintaining a high ADP:ATP ratio in the matrix. When there are increased energy demands on the body, such as under heavy exercise, cytosolic ADP rises and is exchanged with mitochondrial matrix ATP via the transmembrane ADP:ATP translocase. Increased ADP causes the proton-motive force to be discharged and protons enter via ATPase, thereby regenerating the ATP pool. There are 3 isoforms of translocases in humans; isoform 1 is the heart/skeletal muscle form, isoform 2 is the fibroblast form and isoform 3 is the liver form. All isoforms exist as homodimers. The translocase can adopt 2 different conformations, called the CATR (carboxyatractyloside) and BA (bongkrekic acid) conformations. Amongst the endogenous nucleotides, only ADP and ATP can trigger the rapid conversion between the CATR and BA conformations. The reaction can be summed as below: ADPout + ATPin <-> ADPin + ATPout
Pancreatic beta cells integrate signals from several metabolites and hormones to control the secretion of insulin. In general, glucose triggers insulin secretion while other factors can amplify or inhibit the amount of insulin secreted in response to glucose. Factors which increase insulin secretion include the incretin hormones Glucose-dependent insulinotropic polypeptide (GIP and glucagon-like peptide-1 (GLP-1), acetylcholine, and fatty acids. Factors which inhibit insulin secretion include adrenaline and noradrenaline. Increased blood glucose levels from dietary carbohydrate play a dominant role in insulin release from the beta cells of the pancreas. Glucose catabolism in the beta cell is the transducer that links increased glucose levels to insulin release. Glucose uptake and glycolysis generate cytosolic pyruvate; pyruvate is transported to mitochondria and converted both to oxaloacetate which increases levels of TCA cycle intermediates, and to acetyl-CoA which is oxidized to CO2 via the TCA cycle. The rates of ATP synthesis and transport to the cytosol increase, plasma membrane ATP-sensitive inward rectifying potassium channels (KATP channels) close, the membrane depolarizes, and voltage-gated calcium channels in the membrane open (Muoio and Newgard 2008; Wiederkehr and Wollheim 2006). Elevated calcium concentrations near the plasma membrane cause insulin secretion in two phases: an initial high rate within minutes of glucose stimulation and a slow, sustained release lasting longer than 30 minutes. In the initial phase, 50-100 insulin granules already docked at the membrane are exocytosed. Exocytosis is rendered calcium-dependent by Synaptotagmin V/IX, a calcium-binding membrane protein located in the membrane of the docked granule, although the exact action of Synapototagmin in response to calcium is unknown. Calcium also causes a translocation of reserve granules within the cell towards the plasma membrane for release in the second, sustained phase of secretion. Human cells contain L-type (continually reopening), P/Q-type (long burst), R-type (long burst), and T-type (short burst) calcium channels and these partly account for differences between the two phases of secretion. Other factors that distinguish the two phases are not yet fully known (Bratanova-Tochkova et al. 2002; Henquin 2000; MacDonald et al. 2005).
Acetylcholine released by parasympathetic nerve endings in the pancreas causes a potentiation of insulin release when glucose is present at concentrations greater than about 7 mM. Acetylcholine binds the Muscarinic Acetylcholine Receptor M3 on pancreatic beta cells. The binding has two effects: an increase in permeability of the cell to Na+ ions through an unknown mechanism, and the activation of Phospholipase C beta-1 through a heterotrimeric G protein, G(q). After acetylcholine binds the Muscarinic Acetycholine Receptor M3, the receptor activates the G protein Gq by causing the alpha subunit of Gq to exchange GDP for GTP. Activation of Gq in turn activates Phospholipase C beta-1. Phospholipase C beta-1 hydrolyzes the phosphodiester bond at the third position of phosphoinositol 4,5-bisphosphate, producing diacylglycerols (DAG) and inositol 1,4,5-trisphosphate. DAG remains in the cell membrane and causes Protein Kinase C alpha (PKC alpha) to translocate from the cytosol to the membrane. This results in the activation of PKC alpha which then phosphorylates target proteins on serine and threonine residues. One known target of PKC alpha is Myristoylated Alanine-rich C Kinase Substrate (MARCKS), which is believed to affect vesicle transport and may be responsible for the increased traffic of insulin granules seen in response to acetylcholine. Inositol trisphophate binds a receptor, the IP3 receptor, on calcium stores in the cell (probably the endoplasmic reticulum). The release of calcium into the cytosol stimulates the exocytosis of insulin granules.
Human pancreatic beta cells express glucose transporters 1 and (GLUT1, GLUT2), which are responsible for uptake of glucose from the extracellular medium into the cytosol. (Rodent pancreatic beta cells express only Glut2.)
The length of the polyisoprenoid chain of ubiquinone aka coenzyme Q (Q), varies depending on the species involved: it is 6 in budding yeast, Saccharomyces cerevisiae, (Q6) and 10 in humans (Q10). Most ubiquinone is naturally reduced to ubiquinol (Q10H2 in humans) and it is this form which dominates in most human tissues. It functions as an ubiquitous coenzyme in redox reactions and its ability both to associate with complexes I and III of the electron transport chain and to move freely in the inner mitochondrial membrane are central to its role in electron transport. In eukaryotes ubiquinones/ubiquinols are also found in other membranes such as the endoplasmic reticulum, Golgi vesicles, lysosomes and peroxisomes. Ubiquinol/ubiquinone is synthesized in the following way. Initially, the polyisoprenoid tail is assembled by a polyprenyl diphosphate synthase. Next, 4 hydroxybenzoate polyprenyltransferase (COQ2) catalyses the formation of the covalent linkage between the benzoquinone head group and the tail to produce 4 hydroxy 3 polyprenyl benzoic acid intermediate (DHB, 3 decaprenyl 4 hydroxybenzoic acid in humans). There follows modifications of the aromatic ring starting with hydroxylation, followed by O methylation, and decarboxylation to form the 2 methoxy 6 polyprenyl phenol intermediate (DMPhOH ; 2 methoxy 6 decaprenylphenol in humans). Following this, two additional methylations, one C methylation, and one O methylation step, finally generate the fully substituted hydroquinone, ubiquinol (Szkopinska 2000, Kagan & Quinn 2000, Tran & Clarke 2007, Kawamukai 2009).
Lipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphingolipids, eicosanoids, cholesterol, bile salts, steroid hormones, and fat-soluble vitamins. They function as a major source of energy (fatty acids, triacylglycerols, and ketone bodies), are major constituents of cell membranes (cholesterol and phospholipids), play a major role in their own digestion and uptake (bile salts), and participate in numerous signaling and regulatory processes (steroid hormones, eicosanoids, phosphatidylinositols, and sphingolipids). Because of their poor solubility in water, most lipids in extracellular spaces in the human body are found as complexes with specific carrier proteins. Regulation of the formation and movement of these lipoprotein complexes is a critical aspect of human lipid metabolism, and lipoprotein abnormalities are associated with major human disease processes including atherosclerosis and diabetes. The central steroid in human biology is cholesterol, obtained from animal fats consumed in the diet or synthesized de novo from acetyl-coenzyme A. (Vegetable fats contain various sterols but no cholesterol.) Cholesterol is an essential constituent of lipid bilayer membranes and is the starting point for the biosyntheses of bile acids and salts, steroid hormones, and vitamin D. Bile acids and salts are mostly synthesized in the liver. They are released into the intestine and function as detergents to solubilize dietary fats. Steroid hormones are mostly synthesized in the adrenal gland and gonads. They regulate energy metabolism and stress responses (glucocorticoids), salt balance (mineralocorticoids), and sexual development and function (androgens and estrogens). At the same time, chronically elevated cholesterol levels in the body are associated with the formation of atherosclerotic lesions and hence increased risk of heart attacks and strokes. The human body lacks a mechanism for degrading excess cholesterol, although an appreciable amount is lost daily in the form of bile salts and acids that escape recycling. Aspects of lipid metabolism currently annotated in Reactome include lipid digestion, mobilization, and transport; fatty acid, triacylglycerol, and ketone body metabolism; peroxisomal lipid metabolism; phospholipid and sphingolipid metabolism; cholesterol biosynthesis; bile acid and bile salt metabolism; and steroid hormone biosynthesis.
Ubiquinone biosynthesis protein COQ7 homolog (COQ7) (Vajo et al. 1999) catalyses the hydroxylation of 6-methoxy-3-methyl-2-decaprenyl-1,4-benzoquinol (DMQ10H2) to 3-demethylubiquinol-10 (DeMQ10H2). This reaction is inferred from the equivalent reaction in yeast (Marbois & Clarke 1996, Tran et al. 2006).
Mitochondrial COQ3 is an O-methyltransferase required in the reaction to convert 3-demethylubiquinol-10 (DeMQ10H2) to ubiquinol-10 (Q10H2) (Jonassen & Clarke 2000).
2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial (COQ5) catalyses the C-methyltransferase conversion of 2-methoxy-6-decaprenyl-1,4-benzoquinol (MDMQ10H2) to 6-methoxy-3-methyl-2-decaprenyl-1,4-benzoquinol (DMQ10H2). This reaction is inferred from the equivalent reaction in yeast (Barkovich et al. 1997).
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The role of the Tim8p-Tim13p complex in a conserved import pathway for mitochondrial polytopic inner membrane proteins
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Humans possess two mitochondrial ferredoxins, Fdx1 and Fdx2, with distinct roles in steroidogenesis, heme, and Fe/S cluster biosynthesis
Mitochondrial COQ3 is an O-methyltransferase required in the reaction to convert 3,4-dihydroxy-5-decaprenylbenzoic acid (DHDB) to 3-methoxy-4-hydroxy-5-decaprenylbenzoic acid (MHDB) (Jonassen & Clarke 2000).
A flavin-dependent monooxygenase involved in ubiquinone/ubiquinol biosynthesis, COQ6 (Heeringa et al. 2011) catalyses the C5-hydroxylation of 3-decaprenyl-4-hydroxybenzoic acid (DHB) to 3,4-dihydroxy-5-decaprenylbenzoic acid (DHDB). COQ6 is a peripheral membrane protein that localizes to the matrix side of the inner mitochondrial membrane (Gin et al. 2003). This reaction involving COQ6 is inferred from the equivalent reaction in yeast (Ozeir et al. 2011, Gin et al. 2003).
Ceramide kinase (CERK) mediates the phosphorylation of ceramide (CERA) to the lipid second messenger, ceramide 1-phosphate (C1P) (Sugiura et al. 2002).
The steps involved in the synthesis of glycosphingolipids (sphingolipids with one or more sugars attached) are annotated here (Gault et al. 2010).
Sphingolipids are derivatives of long chain sphingoid bases such as sphingosine (trans-1,3-dihydroxy 2-amino-4-octadecene), an 18-carbon unsaturated amino alcohol which is the most abundant sphingoid base in mammals. Amide linkage of a fatty acid to sphingosine yields ceramides. Esterification of phosphocholine to ceramides yields sphingomyelin, and ceramide glycosylation yields glycosylceramides. Introduction of sialic acid residues yields gangliosides. These molecules appear to be essential components of cell membranes, and intermediates in the pathways of sphingolipid synthesis and breakdown modulate processes including apoptosis and T cell trafficking. While sphingolipids are abundant in a wide variety of foodstuffs, these dietary molecules are mostly degraded by the intestinal flora and intestinal enzymes. The body primarily depends on de novo synthesis for its sphingolipid supply (Hannun and Obeid 2008; Merrill 2002). De novo synthesis proceeds in four steps: the condensation of palmitoyl-CoA and serine to form 3-ketosphinganine, the reduction of 3-ketosphinganine to sphinganine, the acylation of sphinganine with a long-chain fatty acyl CoA to form dihydroceramide, and the desaturation of dihydroceramide to form ceramide. Other sphingolipids involved in signaling are derived from ceramide and its biosynthetic intermediates. These include sphinganine (dihydrosphingosine) 1-phosphate, phytoceramide, sphingosine, and sphingosine 1-phosphate. Sphingomyelin is synthesized in a single step in the membrane of the Golgi apparatus from ceramides generated in the endoplasmic reticulum (ER) membrane and transferred to the Golgi by CERT (ceramide transfer protein), an isoform of COL4A3BP that is associated with the ER membrane as a complex with PPM1L (protein phosphatase 1-like) and VAPA or VAPB (VAMP-associated proteins A or B). Sphingomyelin synthesis appears to be regulated primarily at the level of this transport process through the reversible phosphorylation of CERT (Saito et al. 2008).
4-hydroxybenzoate polyprenyltransferase, mitochondrial (COQ2) catalyses the combination of 4-hydroxybenzoic acid, aka para-hydroxybenzoic acid (PHB) with the polyisoprenoid tail all-trans-decaprenyl diphosphate (all-E-10PrP2) to form 3-decaprenyl-4-hydroxybenzoic acid (DHB) (Forsgren et a l. 2004, Tekle et al. 2008). This reaction is irreversible and occurs in the mitochondria.
The main steps involved in de novo sphingolipid synthesis are annotated here (Merrill 2002, Gault et al. 2010).
Sphingomyelin phosphodiesterase (SMPD1), also called acid sphingomyelinase (ASM), is a lysosomal phosphodiesterase that hydrolyses sphingomyelin to ceramide and phosphocholine (Schuchman et al. 1991, Schuchman et al. 1992). Defects in SMPD1 are the cause of two types of Niemann-Pick disease. Type A (NPDA, Niemann-Pick disease classical infantile form) (MIM:257200) (Ferlinz et al. 1991) and type B (NPDB, Niemann-Pick disease visceral form) (MIM:607616) (Rodriguez-Pascau et al. 2009).
The mammalian brain-specific, Mg2+-dependent, neutral sphingomyelin phosphodiesterases 2 (Tomiuk et al. 1998, Hofmann et al. 2000) and 3 (Marchesini et al. 2003) (SMPD2 and 3) hydrolyse sphingomyelin (SPHM) to ceramide (CERA) at the plasma membrane.
Membrane-bound ectonucleotide pyrophosphatase/phosphodiesterase 7 (ENPP7) mediates the hydrolysis of sphingomyelin to ceramide and choline phosphate (Duan et al. 2003, Wu et al. 2005).
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TRAF6 Mediated Induction of proinflammatory cytokines
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At the late endosome membrane, the primary event is the dephosphorylation of the phosphoinositide phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) to phosphatidylinositol 3-phosphate (PI3P) and phosphatidylinositol 5-phosphate (PI5P) (Sbrissa et al. 2007, Sbrissa et al. 2008, Cao et al. 2007, Cao et al. 2008, Arcaro et al. 2000, Kim et al. 2002).
Phosphatidylinositol (PI), a membrane phospholipid, can be reversibly phosphorylated at the 3, 4, and 5 positions of the inositol ring to generate seven phosphoinositides: phosphatidylinositol 3-phosphate (PI3P), phosphatidylinositol 4-phosphate (PI4P), phosphatidylinositol 5-phosphate (PI5P), phosphatidylinositol 3,4-bisphosphate PI(3,4)P2, phosphatidylinositol 4,5-bisphosphate PI(4,5)P2, phosphatidylinositol 3,5-bisphosphate PI(3,5)P2, and phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3). These seven phosphoinositides, which are heterogeneously distributed within cells, can serve as signature components of different intracellular compartment membranes and so help to mediate specificity of membrane interactions. Phosphoinositide levels are tightly regulated spatially and temporally by the action of various kinases and phosphatases whilst PI(4,5)P2 is also a substrate for phospholipase C. The differential localisation of each of these enzymes on specific compartment membranes ensures maintenance of the heterogeneous distribution of phosphoinositides despite the continuous membrane flow from one compartment to another. PI is primarily synthesised in the endoplasmic reticulum from where the phospholipid is exported to other compartments via membrane traffic or via cytosolic phospholipid transfer proteins. Phosphorylation of PI to PI4P primarily occurs in the Golgi, where PI4P plays an important role in the biogenesis of transport vesicles such as the secretory vesicle involved in its transport to the plasma membrane. At this place, PI4P has a major function acting as a precursor of PI(4,5)P2, which is located predominantly at this membrane. PI(4,5)P2 binds and regulates a wide range of proteins that function on the cell surface and serves as a precursor for second messengers. Additionally, it helps define this membrane as a target for secretory vesicles, functions as a coreceptor in endocytic processes, and functions as a cofactor for actin nucleation. At the plasma membrane, PI(4,5)P2 is further phosphorylated to PI(3,4,5)P3, another phosphoinositide with important signalling functions including stimulating cell survival and proliferation. The inositol 3-phosphatase, phosphatase and tensin homolog (PTEN) regenerates PI (4,5)P2, while the 5-phosphatases convert PI(3,4,5)P3 into the phosphoinositide, PI(3,4)P2, propagating the signal initiated by PI(3,4,5)P3. PI(3,4)P2 is further dephosphorylated in the endocytic pathway by inositol 4-phosphatases to PI3P, the signature phosphoinositide of the early endosomal compartment and a ligand for numerous endosomal proteins. However, the bulk of PI3P is generated directly in the endosomes by phosphorylation of PI. The subsequent endosomal phosphorylation of PI3P to PI(3,5)P2 is believed to generate docking sites for recruitment of cytosolic factors responsible for the control of outgoing traffic from the endosomes. The main localisation and function of the low abundance phosphoinositide PI5P, that can be generated by several pathways, remains to be determined (Krauss & Haucke 2007, Leventis & Grinstein 2010, Roth 2004, Gees et al. 2010, De Matteis & Godi 2004, van Meer et al. 2008, Vicinanza et al. 2008, Lemmon 2008, Kutaleladze 2010, Robinson & Dixon 2006, Blero et al. 2007, Liu & Bankaitis 2010, McCrea & De Camilli 2009, Vicinanza et al. 2008, Di Paolo & De Camilli, 2006).
At the late endosome membrane, phosphatidylinositol 3-kinase catalytic subunit type 3 (PIK3C3) aka VPS34 binds to phosphoinositide 3-kinase regulatory subunit 4 (PIK3R4). The PIK3C3:PIK3R4 complex and phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing subunit alpha (PIK3C2A) phosphorylate phosphatidylinositol (PI) to phosphatidylinositol 3-phosphate (PI3P). The following lists the above proteins with their corresponding literature references: PIK3C3:PIK3R4 (Panaretou et al. 1997, Volinia et al. 1995, Cao et al. 2007) and PIK3C2A (Arcaro et al. 2000, Domin et al. 2000).
At the late endosome membrane, myotubularin (MTM1), myotubularin-related protein 2 (MTMR2), myotubularin-related protein 4 (MTMR4), and myotubularin-related protein 7 (MTMR7) dephosphorylate phosphatidylinositol 3-phosphate (PI3P) to phosphatidylinositol (PI). The following lists the above proteins with their corresponding literature references: MTM1 (Cao et al. 2007, Cao et al. 2008, Tsujita et al. 2004, Tronchere et al. 2004, Kim et al. 2002); MTMR2 (Cao et al. 2008, Kim et al. 2002); MTMR4 (Lorenzo et al. 2006); and MTMR7 (Mochizuki & Majerus 2003, Lorenzo et al. 2006).
SDA-CoA (6,9,12,15-18:4(n-3)) is rapidly elongated by two carbon atoms to 8,11,14,17-eicosatetraenoyl-CoA (8,11,14,17-20:4(n-3), ETA-CoA). The NADPH-consuming enzyme long-chain fatty acyl elongase (ELOVL5) mediates this reaction which and adds malonyl-CoA to the SDA-CoA and releases carbon dioxide and free CoA (Leonard et al. 2004).
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Phospholipids contain a polar head group and two long-chain fatty acyl moieties, one of which is generally unsaturated. The head group is a glycerol or serine phosphate attached to a polar group such as choline. These molecules are a major constituent of cellular membranes, where their diverse structures and asymmetric distributions play major roles in determining membrane properties (Dowhan 1997). The four major classes of phospholipids in human plasma membranes are phosphatidylethanolamine, phosphatidylserine, phosphatidylcholine, and sphingomyelin. The first three are derivatives of glycerol while sphingomyelin is a derivative of serine. Here, pathways for the metabolism of glycerophospholipids, phosphphatidylinositol (PI), and sphingolipids are annotated.
In the first step the precursor apha-linolenic (9,12,15-18:3(n-3)) acid is activated to a high energy form known as alpha-linolenoyl-CoA (9Z,12Z,15Z-octadecatrienoyl-CoA) by the iron enzyme long-chain-fatty-acid-CoA-ligase (acyl-CoA synthetase 1, ACSL1) and coenzyme A.
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Human choline acetyltransferase (CHAT): partial gene sequence and potential control regions
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Evidence for a family of human glucose transporter-like proteins. Sequence and gene localization of a protein expressed in fetal skeletal muscle and other tissues
5'-AMP-activated protein kinase subunit gamma-3
5'-AMP-activated protein kinase subunit gamma-1
5'-AMP-activated protein kinase catalytic subunit alpha-1
5'-AMP-activated protein kinase subunit beta-1
Isolation and complete sequence of a functional human glyceraldehyde-3-phosphate dehydrogenase gene
At the late endosome membrane, the PAS complex, consisting of FYVE finger-containing phosphoinositide kinase (PIKFYVE), yeast VAC14 homologue (VAC14), and polyphosphoinositide phosphatase aka SAC3 (FIG4), binds to the membrane via PIKFYVE's FYVE finger. The PIKFYVE kinase component phosphorylates phosphatidylinositol (PI) to phosphatidylinositol 5-phosphate (PI5P) (Sbrissa et al. 1999, Sbrissa et al. 2002). The PAS complex is present in the cytosol and is recruited to the membrane.
At the late endosome membrane, myotubularin (MTM1), myotubularin-related protein 2 (MTMR2), myotubularin-related protein 4 (MTMR4), and myotubularin-related protein 7 (MTMR7) dephosphorylate phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) to phosphatidylinositol 5-phosphate (PI5P). The following lists the above proteins with their corresponding literature references: MTM1 (Cao et al. 2007, Cao et al. 2008, Tsujita et al. 2004, Tronchere et al. 2004), MTMR2 (Cao et al. 2008), MTMR4 (Lorenzo et al. 2006), and MTMR7 (Mochizuki & Majerus 2003, Lorenzo et al. 2006).
At the late endosome membrane, the PAS complex, consisting of FYVE finger-containing phosphoinositide kinase (PIKFYVE), yeast VAC14 homologue (VAC14), and polyphosphoinositide phosphatase aka SAC3 (FIG4), binds to the membrane via PIKFYVE's FYVE finger. The FIG4 phosphatase component dephosphorylates phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) to phosphatidylinositol 3-phosphate (PI3P) (Sbrissa et al. 2007, Sbrissa et al. 2008).
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Homologues of p-S1108,S1148,S1192-EIF4G1
On formation, leukotriene C4 (LTC4) is exported to the extracellular region by the ABCC1 transporter (Sjolinder et al. 1999, Lam et al. 1989) and processed further by cleavage reactions.
The bioactive prostaglandin (PG) signalling molecules, including PGA2, PGE2, PGF2a, and PGI2 (prostacyclin) are synthesised from arachidonic acid and its products by various prostaglandin synthase type enzymes. Prostaglandin H2 (PGH2) is the starting point for the synthesis of Thromboxanes (TXs) (Buczynski et al. 2009, Vance & Vance 2008). PGs and TXs are collectively known as the prostanoids. Two enzymes, PTGS1 and 2 (COX1 and 2) both catalyze the two-step conversion of arachidonic acid to PGH2. PTGS1 is constitutively expressed in many cell types while PTGS2 is induced in response to stress and mediates the syntheses of prostaglandins associated with pain, fever, and inflammation. Aspirin irreversibly inactivates both enzymes (though it acts more efficiently on PTGS1), explaining both its antiinflammatory effects and side effects like perturbed gastic acid secretion. Drugs like celecoxib, by specifically inhibiting PTGS2, have a strong anti-inflammatory effect with fewer side effects. These PTGS2-specific drugs, however, probably because of their effects on the balance of prostaglandin synthesis in platelets and endothelial cells, can also promote blood clot formation (Buczynski et al. 2009; Stables & Gilroy 2011).
Leukotriene A4 hydrolase (LTA4H) is a monomeric, soluble enzyme that catalyzes the hydrolysis of the allylic epoxide leukotriene A4 (LTA4) to the dihydroxy acid leukotriene B4 (LTB4) (Radmark et al. 1984, McGee & Fitzpatrick 1985).
There are two major classes of polyunsaturated fatty acids (PUFAs): the omega-3 (n-3) and the omega-6 (n-6) fatty acids, where the number corresponds to the position of the first double bond proximate to the methyl end of the fatty acid. Omega-3 and omega-6 fatty acids are considered essential fatty acids. Humans cannot synthesize them, instead they are supplied through diet. Linoleic acid (LA, 18:2(n-6)), a major component of omega-6 fatty acids and alpha-linolenic acid (ALA, 18:2(n-3)) a major component of omega-3 fatty acids are the two main dietary essential fatty acids (EFAs) in humans. ALA and LA obtained from diet are converted in the body into their longer chain and more unsaturated omega-3 and omega-6 products by a series of desaturation and elongation steps. Metabolism of ALA and LA to their corresponding products is mediated via common enzyme systems. In humans ALA is finally converted to docosahexaenoic acid (DHA, C22:6(n-3)), and LA is converted to docosapentaenoic acid (DPA, C22:5(n-6)). The intermediary omega-3 and omega-6 series fatty acids play a significant role in health and disease by generating potent modulatory molecules for inflammatory responses, including eicosanoids (prostaglandins, and leukotrienes), and cytokines (interleukins) and affecting the gene expression of various bioactive molecules (Kapoor & Huang 2006, Sprecher 2002, Burdge 2006).
Prostaglandin E2 (PGE2) is the most abundant prostanoid in the body and is a major mediator of inflammation in diseases such as osteoarthritis and rheumatoid arthritis. The product of arachidonic acid, prostaglandin H2 (PGH2) serves as the substrate for the isomerization to PGE2. The conversion is carried out by prostaglandin E synthase (PGES), of which there are three forms. Two are membrane-bound enzymes and are designated as mPGES-1 (functionally linked with COX-2) and mPGES-2 (golgi membrane-associated, functionally coupled with both COX-1 and COX-2). The other is cytosolic (cPGES, PTGES3) and functionally linked to COX-1 to produce PGE2 immediately. In this reaction, cPGES is used for conversion of PGH2 to PGE2.
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cAMP-dependent protein kinase, alpha-catalytic subunit
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Linoleic acid (LA, 18:2(n-6)) is an omega-6 fatty acid obtained through diet, mainly from vegetable oils. Omega-6 fatty acids helps stimulate skin and hair growth, maintain bone health, regulate metabolism, and maintain the reproductive system. All the desaturation and elongation steps occur in the endoplasmic reticulum (ER) except for the final step which requires translocation to peroxisomes for partial beta-oxidation. The linoleic acid pathway involves the following steps: 18:2(n-6)-->18:3(n-6)--> 20:3(n-6)-->20:4(n-6)-->22:4(n-6)-->24:4(n-6)-->24:5(n-6)-->22:5(n-6). Two desaturation enzymes are involved in this process: delta-6 desaturase which converts 18:2(n-6) to 18:3 (n-6) and 24:4(n-6) to 24:5(n-6) respectively, and delta-5 desaturase which converts 20:3(n-6) to 20:4(n-6). (Sprecher 2002).
Prior to this reaction all the enzymes involved in the desaturation and elongation of linoleic acid are located in the ER, but for this last step tetracosapentaenoyl-CoA must be transferred to the peroxisomes for partial beta-oxidation to docosapentaenoyl-CoA (DPA-CoA, 4,7,10,13,16-22:5(n-6)) (Su et al. 2001).
Docosatetraenoyl-CoA is elongated to tetracosatetraenoyl-CoA (TTA-CoA, 9,12,15,18-tetracosatetraenoic acid, 9,12,15,18-24:4(n-6)) by the elongase enzyme ELOVL2.
Arachidonyl-CoA undergoes a two-carbon chain elongation on the carboxyl end to form docosatetraenoyl-CoA (DTA-CoA/Adrenic acid/7,10,13,16-docosatetraenoic acid (7,10,13,16-22:4(n-6)). This reaction is catalyzed by the enzymes ELOVL5 or ELOVL2. Malanoyl-CoA provides the additional two carbons required for elongation. Docosatetraenoyl-CoA is further metabolized by cyclooxygenases (COX), lipoxygenases (LO) and cytochrome P450s (CYP450s) to dihomo (DH) eicosanoids (Kopf et al. 2010, Leonard et al. 2004).
Gamma-linolenoyl-CoA (6,9,12-20:3(n-6)) is rapidly elongated to dihomo-gamma-linolenoyl-CoA (DGL-CoA; 8,11,14-20:3(n-6)) by the action of C18-PUFA-specific elongase 5 (ELOVL5). Two carbon atoms are added during this reaction. DGL-CoA later undergoes desaturation to form arachidonic acid (AA, 5,8,11,14-20:4(n-6)). Depending on the cell type, DGL-CoA can also be metabolized by cyclooxygenases and lipoxygenases to produce anti-inflammatory eicosanoids (prostaglandins of series 1 (PGE1) and 15-hydroxyeico- satrienoic acid (15-HETrE)). GLA and these two oxidative metabolites exert clinical effects in a variety of diseases, including suppression of chronic inflammation, vasodilation and lowering of blood pressure, inhibition of platelet aggregation and thrombosis. (Fan et al. 2001, Fan & Chapkin 1998, Kapoor & Huang. 2006)
Alpha-linolenic acid (ALA, 18:3(n-3)) is an omega-3 fatty acid, supplied through diet as it cannot be synthesized by humans. ALA has an important role in human health. It is converted to long chain more unsaturated n-3 fatty acids by a series of alternating desaturation and elongation reactions. Omega-3 products of ALA such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) reduce inflammation and may help lower risk of chronic diseases, such as heart disease and arthritis. All the desaturation and elongation steps occur in the endoplasmic reticulum (ER) except for the final step which requires translocation to peroxisomes for partial beta-oxidation. The alpha-linolenic acid pathway involves the following steps: 18:3(n-3)--> 18:4(n-3)-->20:4(n-3)-->20:5(n-3)-->22:5(n-3)-->24:5(n-3)-->24:6(n-3)-->22:6(n-3). Two desaturation enzymes are involved in this process: delta-6 desaturase that converts 18:3(n-3) to 18:4(n-3) and 24:5(n-3) to 24:6(n-3) respectively, delta-5 desaturase 20:4(n-3) to 20:5(n-3). (Sprecher 2002).
The dietary essential fatty acid (EFA) linoleic acid (LA) is activated to a high energy form known as linoleoyl-CoA by the action of long-chain acyl-CoA synthetases (ACSLs). Thioesterification of long-chain fatty acids into their acyl-CoA derivatives is considered to be the first committed step in fatty acid metabolism. Formation of acyl-CoA allows an otherwise non-reactive fatty acid to participate in biosynthetic or catabolic pathways. This acyl CoA form is converted to its longer-chain polyunsaturated products by a series of desaturation and elongation reactions (Ellis et al. 2010, Watkins 2008).
Delta2-THA-CoA is hydrated to 3-hydroxyacyl-CoA intermediate 1-(3-hydroxy-6Z,9Z,12Z,15Z,18Z,21Z-tetracosahexaenoyl)-CoA by HSD17B4/DBP (d-bifunctional protein) dimer.
3-hydroxy tetracosahexaenoyl-CoA undergoes dehydrogenation to form 1-(3-oxo-6Z,9Z,12Z,15Z,18Z,21Z-tetracosahexaenoyl)-CoA, catalysed by DBP. DBP is a bifunctional enzyme, involved in the hydration of a variety of trans-2,3-dehydroacyl-CoA's but also mediating dehydrogenation of a variety of 3-hydroxyacyl-CoA's (Jiang et al. 1997).
The final step in the beta-oxidation process is the thiolytic cleavage of 1-(3-oxo-6Z,9Z,12Z,15Z,18Z,21Z-tetracosahexaenoyl)-CoA to form docosahexaenoyl-CoA (DHA-CoA). This step is catalysed by both sterol carrier protein X (SCPx) and the classic 3-ketoacyl-CoA thiolase (this reaction) (Ferdinandusse et al. 2001).
DHA-CoA preferentially moves back to the ER, perhaps as a free fatty acid. This conversion is usually catalysed by acyl-CoA thioesterases (ACOTs). No specific acyl-CoA thioesterase enzyme has been identified for the peroxisomal metabolism of DHA-CoA, but the peroxisomal ACOT8 has a wide substrate specificity and is likely to be responsible (Ferdinandusse et al. 2003, Hunt & Alexson. 2008).
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Reactive oxygen species (ROS) homeostasis and redox regulation in cellular signaling
cAMP-dependent protein kinase type II-alpha regulatory chain
cAMP-dependent protein kinase type II-beta regulatory chain
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Docosapentaenoyl-CoA is elongated to tetracosapentaenoyl-CoA (9,12,15,18,21-24:5(n-3)) by the enzyme ELOVL2.
Eicosapentaenoyl-CoA (EPA-CoA) is transformed to docosapentaenoyl-CoA (DPA-CoA/clupanodonic acid; 7,10,13,16,19-22:5(n-3)) by addition of two carbon atoms from malanoyl-CoA. This reaction is catalyzed by the enzymes ELOVL5/2 (Leonard et al. 2004). DPA is quite high in seal oil and may act as an anti-atherogenic factor. DPA has 10-fold greater endothelial cell migration ability than EPA, which is important in wound-healing processes. DPA may act as a precursor for production of the DPA-related D-series of resolvins or neuroprotectins (Kaur et al. 2011).
Retroconversion of C24:6(n-3) to docosahexaenoic acid (22:6(n-3) involves the initial oxidation of tetracosahexaenoyl-CoA to an intermediate 1-(2E,6Z,9Z,12Z,15Z,18Z,21Z-tetracosaheptaenoyl)-CoA (delta2-THA-CoA). This step is catalysed by the peroxisomal enzyme Straight-chain acyl-CoA oxidase (SCOX) (Ferdinandusse et al. 2001).
The 24-carbon tetracosahexaenoyl-CoA (6,9,12,15,18,21-24:6(n-3) is transported to peroxisomes to undergo a putative single cycle of peroxisomal beta-oxidation, producing Docosahexaenoic Acid (DHA) (Sprecher 2002, Luthria et al. 1996).
Transient receptor potential 1 regulates capacitative Ca(2+) entry and Ca(2+) release from endoplasmic reticulum in B lymphocytes
Catalytic properties of human manganese superoxide dismutase
Phosphoinositide signalling in cancer: beyond PI3K and PTEN
Neurotrophin signaling: many exciting surprises!
RAC-beta serine/threonine protein kinase
ChREBP (Carbohydrate Response Element Binding Protein) is a large multidomain protein containing a nuclear localization signal near its amino terminus, polyproline domains, a basic helix-loop-helix-leucine zipper domain, and a leucine-zipper-like domain (Uyeda et al., 2002). Its dephosphorylation in response to molecular signals associated with the well-fed state allows it to enter the nucleus, interact with MLX protein, and bind to ChRE DNA sequence motifs near Acetyl-CoA carboxylase, Fatty acid synthase, and Pyruvate kinase (L isoform) genes (Ishi et al.2004). This sequence of events is outlined schematically in the picture below (adapted from Kawaguchi et al. (2001) - copyright (2001) National Academy of Sciences, U.S.A.).
Hormone-sensitive lipase (HSL)-mediated triacylglycerol hydrolysis
A glycine residue (Gly2) at the N-terminus of eNOS is myristoylated, providing membrane localization.
Many hormones that affect individual physiological processes including the regulation of appetite, absorption, transport, and oxidation of foodstuffs influence energy metabolism pathways. While insulin mediates the storage of excess nutrients, glucagon is involved in the mobilization of energy resources in response to low blood glucose levels, principally by stimulating hepatic glucose output. Small doses of glucagon are sufficient to induce significant glucose elevations. These hormone-driven regulatory pathways enable the body to sense and respond to changed amounts of nutrients in the blood and demands for energy. Glucagon and Insulin act through various metabolites and enzymes that target specific steps in metabolic pathways for sugar and fatty acids. The processes responsible for the long-term control of fat synthesis and short term control of glycolysis by key metabolic products and enzymes are annotated in this module as six specific pathways: Pathway 1. Glucagon signalling in metabolic pathways: In response to low blood glucose, pancreatic alpha-cells release glucagon. The binding of glucagon to its receptor results in increased cAMP synthesis, and Protein Kinase A (PKA) activation. Pathway 2. PKA mediated phosphorylation:PKA phosphorylates key enzymes, e.g., 6-Phosphofructo-2-kinase /Fructose-2,6-bisphosphatase (PF2K-Pase) at serine 36, and regulatory proteins, e.g., Carbohydrate Response Element Binding Protein (ChREBP) at serine 196 and threonine 666. Insulin mediated responses to high blood glucose will be annotated in future versions of Reactome. In brief, the binding of insulin to its receptor leads to increased protein phosphatase activity and to hydrolysis of cAMP by cAMP phosphodiesterase. These events counteract the regulatory effects of glucagon. Pathway 3: Insulin stimulates increased synthesis of Xylulose-5-phosphate (Xy-5-P). Activation of the insulin receptor results indirectly in increased Xy-5-P synthesis from Glyceraldehyde-3-phosphate and Fructose-6-phosphate. Xy-5-P, a metabolite of the pentose phosphate pathway, stimulates protein phosphatase PP2A. Pathway 4: AMP Kinase (AMPK) mediated response to high AMP:ATP ratio: In response to diet with high fat content or low energy levels, the cytosolic AMP:ATP ratio is increased. AMP triggers a complicated cascade of events. In this module we have annotated only the phosphorylation of ChREBP by AMPK at serine 568, which inactivates this transcription factor. Pathway 5: Dephosphorylation of key metabolic factors by PP2A: Xy-5-P activated PP2A efficiently dephosphorylates phosphorylated PF2K-Pase resulting in the higher output of F-2,6-P2 that enhances PFK activity in the glycolytic pathway. PP2A also dephosphorylates (and thus activates) cytosolic and nuclear ChREBP. Pathway 6: Transcriptional activation of metabolic genes by ChREBP: Dephosphorylated ChREBP activates the transcription of genes involved in glucose metabolism such as pyruvate kinase, and lipogenic genes such as acetyl-CoA carboxylase, fatty acid synthetase, acyl CoA synthase and glycerol phosphate acyl transferase. The illustration below summarizes this network of events. Black lines are metabolic reactions, red lines are negative regulatory events, and green lines are positive regulatory events (figure reused with permission from Veech (2003) - Copyright (2003) National Academy of Sciences, U.S.A.).
BH2 may compete with BH4 to bind eNOS, uncoupling eNOS leading to the formation of superoxide rather than nitric oxide. BH2, the oxidised form of BH4, cannot contribute electrons to heme in the reductase domain of eNOS, thereby uncoupling it from arginine oxidation and producing superoxide from oxygen instead (Vasquez-Vivar et al. 2002).
Palymitoylated, myristoylated eNOS forms a dimer and is transported from the Golgi to the plasma membrane. Transport is thought to be mediated by intracellular vesicles, but the details remain unknown.
Once depalmitoylated, it's proposed that eNOS is displaced from the plasma membrane and redistributed to other intracellular membranes, including the Golgi, where re-palmitoylation occurs. The mechanism of transport from the plasma membrane is still unknown.
Increases in intracellular calcium and calmodulin stimulate depalmitoylation of eNOS by acyl protein thioesterase 1, which displaces eNOS from the membrane. This might be a mechanism to downregulate NO production following intense stimuli.
The first and rate-limiting enzyme in tetrahydrobiopterin de novo biosynthesis is GTP cyclohydrolase I (GCH1, GTPCHI). Three different isoforms are produced but only isoform 1 is functionally active (Gütlich et al. 1994). GCH1 is functional as a homodecamer. First, a monomer of GCH1 forms a dimer. Then five dimers arrange into a ring-like structure to form the homodecamer (Nar et al. 1995).
eNOS activity is regulated by numerous post-translational modifications including phosphorylation and acylation, which also modulate its interactions with other proteins and its subcellular localization. In general, following myristoylation and palmitoylation, eNOS localizes to caveolae in the plasma membrane, where in resting cells, it is bound to caveolin and remains inactive. Several agonists that raise intracellular calcium concentrations promote calmodulin binding to eNOS and the dissociation of caveolin from the enzyme, leading to an activated eNOS-calmodulin complex. Phosphorylation plays a significant role in regulating eNOS activity, especially the phosphorylation of Ser1177, located within the reductase domain, which increases enzyme activity by enhancing reductase activity and calcium sensitivity. In unstimulated, cultured endothelial cells, Ser1177 is rapidly phosphorylated following a variety of stimuli: fluid shear stress, insulin, estrogen, VEGF, or bradykinin. The kinases involved in this process depend upon the stimuli applied. For instance, shear stress phosphorylates Ser1177 by activating Akt and PKA; insulin activates both Akt and the AMP-activated protein kinase (AMPK); estrogen and VEGF mainly phosphorylate eNOS via Akt; whereas the bradykinin-induced phosphorylation of Ser1177 is mediated by CaMKII. When Ser1177 is phosphorylated, NO production is increased several-fold above basal levels. The phosphorylation of a threonine residue (Thr 495), located in the CaM binding domain, is associated with a decrease in eNOS activity. When this residue is dephosphorylated, substantially more CaM binds to eNOS and elevates enzyme activity. Stimuli associated with dephosphorylation of Thr495 (e.g., bradykinin, histamine, and Ca2+ ionophores) also increase Ca2+ levels resulting in the phosphorylation of Ser1177. Additional phosphorylation sites, such as Ser114 and Ser633, and tyrosine phosphorylation have all been detected, but their functional relevance remains unclear. It is speculated that the tyrosine phosphorylation of eNOS is unlikely to affect enzyme activity directly, but more likely to impact the protein-protein interactions with associated scaffolding and regulatory proteins.
The oxidation product of BH4, 7,8-dihydrobiopterin (BH2), can compete with BH4 for binding to eNOS. This can lead to the uncoupling of eNOS and can result in the formation of reactive oxygen species (Vasquez-Vivar et al. 2002).
Molecular cloning and characterization of a novel muscle adenylosuccinate synthetase, AdSSL1, from human bone marrow stromal cells
FGFR1 is fused to the centrosome-associated protein CEP110 in the 8p12 stem cell myeloproliferative disorder with t(8;9)(p12;q33)
Metabolism, function and mass spectrometric analysis of bis(monoacylglycero)phosphate and cardiolipin
Oligomerization of STIM1 couples ER calcium depletion to CRAC channel activation
Upon dissociation of protein kinase A (PKA) tetramers in the presence of cAMP, the released PKA catalytic monomers phosphorylate specific serine and threonine residues of several metabolic enzymes. These target enzymes include glycogen phosphorylase kinase, glycogen synthase and PF2K-Pase. PKA also phosphorylates ChREBP (Carbohydrate Response Element Binding Protein), preventing its movement into the nucleus and thus its function as a positive transcription factor for genes involved in glycolytic and lipogenic reactions.
Glucagon and insulin are peptide hormones released from the pancreas into the blood, that normally act in complementary fashion to stabilize blood glucose concentration. When blood glucose levels rise, insulin release stimulates glucose uptake from the blood, glucose breakdown (glycolysis), and glucose storage as glycogen. When blood glucose levels fall, glucagon release stimulates glycogen breakdown and de novo glucose synthesis (gluconeogenesis), while inhibiting glycolysis and glycogen synthesis. At a molecular level, the binding of glucagon to the extracellular face of its receptor causes conformational changes in the receptor that allow the dissociation and activation of subunits Gs and Gq. The activation of Gq leads to the activation of phospholipase C, production of inositol 1,4,5-triphosphate, and subsequent release of intracellular calcium. The activation of Gs leads to activation of adenylate cyclase, an increase in intracellular cAMP levels, and activation of protein kinase A (PKA). Active PKA phosphorylates key enzymes of glycogenolysis, glycogenesis, gluconeogenesis, and glycolysis, modifying their activities. These signal transduction events, and some of their downstream consequences, are illustrated below (adapted from Jiang and Zhang, 2003).
LKB1 phosphorylates threonine residue 172 of the alpha subunit of the AMPK heterotrimer, activating it. LKB1, a serine/threonine kinase, was first identified as the gene whose mutation is associated with the Peutz-Jeghers familial cancer syndrome. This disease phenotype is consistent with the hypothesis that the interaction between LKB1 and AMPK normally plays a key role in the negative regulation of cell growth (Hardie 2004).
At the beginning of this reaction, 1 molecule of 'AMPK heterotrimer (inactive)', and 1 molecule of 'AMP' are present. At the end of this reaction, 1 molecule of 'AMPK heterotrimer:AMP' is present. This reaction takes place in the 'nucleus'.
Xylulose-5-phosphate binds to Protein phosphatase 2A (PP2A), activating it. This regulatory step may be the crucial physiological link explaining the coordinately increased rates of glycolysis and lipogenesis generally observed in individuals consuming high-carbohydrate diets.
One of the downstream effects of insulin, mediated via protein phosphatase 2A (PP2A), is increased synthesis of Fructose-2,6-bisphosphate, an allosteric activator of phosphofructokinase 1 (PFK1). PFK1 in turn catalyzes the committed step of glycolysis so the net effect of this whole sequence of events set off by insulin is to increase cytosolic concentrations of the small molecules formed in the course of glycolysis. This in turn drives the increased synthesis of Xylulose-5-phosphate, itself a positive regulator of PP2A.
At the end of this reaction, 1 molecule of '1-acyl-sn-glycerol-3-phosphate acyltransferase alpha ' is present. This reaction takes place in the 'nucleus'.
At the end of this reaction, 1 molecule of 'Acetyl-CoA carboxylase 2 ' is present. This reaction takes place in the 'nucleus'.
A member of the PP2A family of phosphatases dephosphorylates both cytosolic and nuclear forms of ChREBP (Carbohydrate Response Elemant Binding Protein). In the nucleus, dephosphorylated ChREBP complexes with MLX protein and binds to ChRE sequence elements in chromosomal DNA, activating transcription of genes involved in glycolysis and lipogenesis. The phosphatase is activated by Xylulose-5-phosphate, an intermediate of the pentose phosphate pathway (Kabashima et al. 2003). The rat enzyme has been purified to homogeneity and shown by partial amino acid sequence analysis to differ from previously described PP2A phosphatases (Nishimura and Uyeda 1995) - the human enzyme has not been characterized.
AMP-activated protein kinase (AMPK) is a sensor of cellular energy levels. A high cellular ratio of AMP:ATP triggers the phosphorylation and activation of AMPK. Activated AMPK in turn phosphorylates a wide array of target proteins, as shown in the figure below (reproduced from (Hardie et al. 2003), with the permission of D.G. Hardie). These targets include ChREBP (Carbohydrate Response Element Binding Protein), whose inactivation by phosphorylation reduces transcription of key enzymes of the glycolytic and lipogenic pathways.
Biochemical and stability properties of recombinant human MnSOD
Characterization of the XRN1 gene encoding a 5'-->3' exoribonuclease: sequence data and analysis of disparate protein and mRNA levels of gene-disrupted yeast cells
Nitric oxide (NO), a multifunctional second messenger, is implicated in physiological functions in mammals that range from immune response and potentiation of synaptic transmission to dilation of blood vessels and muscle relaxation. NO is a highly active molecule that diffuses across cell membranes and cannot be stored inside the producing cell. Its signaling capacity must be controlled at the levels of biosynthesis and local availability. Indeed, NO production by NO synthases is under complex and tight control, being regulated at transcriptional and translational levels, through co- and posttranslational modifications, and by subcellular localization. NO is synthesized from L-arginine by a family of nitric oxide synthases (NOS). Three NOS isoforms have been characterized: neuronal NOS (nNOS, NOS1) primarily found in neuronal tissue and skeletal muscle; inducible NOS (iNOS, NOS2) originally isolated from macrophages and later discovered in many other cells types; and endothelial NOS (eNOS, NOS3) present in vascular endothelial cells, cardiac myocytes, and in blood platelets. The enzymatic activity of all three isoforms is dependent on calmodulin, which binds to nNOS and eNOS at elevated intracellular calcium levels, while it is tightly associated with iNOS even at basal calcium levels. As a result, the enzymatic activity of nNOS and eNOS is modulated by changes in intracellular calcium levels, leading to transient NO production, while iNOS continuously releases NO independent of fluctuations in intracellular calcium levels and is mainly regulated at the gene expression level (Pacher et al. 2007). The NOS enzymes share a common basic structural organization and requirement for substrate cofactors for enzymatic activity. A central calmodulin-binding motif separates an oxygenase (NH2-terminal) domain from a reductase (COOH-terminal) domain. Binding sites for cofactors NADPH, FAD, and FMN are located within the reductase domain, while binding sites for tetrahydrobiopterin (BH4) and heme are located within the oxygenase domain. Once calmodulin binds, it facilitates electron transfer from the cofactors in the reductase domain to heme enabling nitric oxide production. Both nNOS and eNOS contain an additional insert (40-50 amino acids) in the middle of the FMN-binding subdomain that serves as autoinhibitory loop, destabilizing calmodulin binding at low calcium levels and inhibiting electron transfer from FMN to the heme in the absence of calmodulin. iNOS does not contain this insert. Because NOS enzymatic activity is modulated by the presence of its substrates and cofactors within the cell, under certain conditions, NOS may generate superoxide instead of NO, a process referred to as uncoupling (uncoupling of NADPH oxidation and NO synthesis). The molecular details of eNOS function are annotated here.
Originally identified as endothelium-derived relaxing factor, eNOS derived NO is a critical signaling molecule in vascular homeostasis. It regulates blood pressure and vascular tone, and is involved in vascular smooth muscle cell proliferation, platelet aggregation, and leukocyte adhesion. Loss of the bioavailability of endothelium derived NO is a key feature of endothelial dysfunction and is implicated in the pathogenesis of cardiovascular disease such as hypertension and atherosclerosis. The endothelial isoform eNOS is unique among the nitric oxide synthase (NOS) family in that it is co-translationally modified at its amino terminus by myristoylation and is further acylated by palmitoylation (two residues next to the myristoylation site). These modifications target eNOS to the plasma membrane caveolae and lipid rafts. eNOS activation and subsequent nitric oxide (NO) production is stimulated by a variety of stimuli, such as fluid shear stress generated by blood flow, vascular endothelial growth factor (VEGF), bradykinin, estrogen, insulin, and angiopoietin. The activity of eNOS is further regulated by numerous post-translational modifications, including protein-protein interactions, phosphorylation, and subcellular localization. Following activation, eNOS shuttles between caveolae and other subcellular compartments such as the noncaveolar plasma membrane portions, Golgi apparatus, and perinuclear structures. This subcellular distribution is variable depending upon cell type and mode of activation. Subcellular localization of eNOS has a profound effect on its ability to produce NO as the availability of its substrates and cofactors will vary with location. eNOS is primarily particulate, and depending on the cell type, eNOS can be found in several membrane compartments: plasma membrane caveolae, lipid rafts, and intracellular membranes such as the Golgi complex. In addition, it has been reported that eNOS can also be detected in the nucleus, however, the conditions associated with nuclear localization of eNOS and its precise role in this cell compartment remains to be determined. Several stimuli can trigger a transient displacement of eNOS from the plasma membrane to other subcellular locations. This process can be mediated through various protein-protein interactions and/or changes in post-translational modifications. Knowledge of the precise molecular mechanisms governing the intracellular redistribution process is still rather limited.
Tetrahydrobiopterin (BH4) is an essential co-factor for the aromatic amino acid hydroxylases and glycerol ether monooxygenase and it regulates nitric oxide synthase (NOS) activity. Inherited BH4 deficiency leads to hyperphenylalaninemia, and dopamine and neurotransmitter deficiency in the brain. BH4 maintains enzymatic coupling to L-arginine oxidation to produce NO. Oxidation of BH4 to BH2 results in NOS uncoupling, resulting in superoxide (O2.-) formation rather than NO. Superoxide rapidly reacts with NO to produce peroxynitrite which can further uncouple NOS. These reactive oxygen species (superoxide and peroxynitrite) can contribute to increased oxidative stress in the endothelium leading to atherosclerosis and hypertension (Thony et al. 2000, Crabtree and Channon 2011,Schulz et al. 2008, Schmidt and Alp 2007). The synthesis, recycling and effects of BH4 are shown here. Three enzymes are required for the de novo biosynthesis of BH4 and two enzymes for the recycling of BH4.
In the second salvage step, dihydrofolate reductase (DHFR) can regenerate BH4 from BH2, a process which increases the BH4:BH2 ratio providing BH4 for coupled eNOS production of NO. In mice cell lines, DHFR inhibition or knockdown diminishes the BH4:BH2 ratio and exacerbates eNOS uncoupling (Crabtree et al. 2009).
Mitochondrial citrate synthase dimer catalyzes the irreversible reaction of acetyl-CoA, water, and oxaloacetate to form citrate and coenzyme A. This reaction is the entry point of two-carbon units into the citric acid cycle. The reaction is subject to allosteric regulation. The gene encoding the human enzyme has been cloned (Goldenthal et al. 1998), but the enzyme has not been characterized in detail - its properties are inferred from those of the well-studied homologous pig enzyme (e.g., Morgunov and Srere 1998).
Pyruvate sits at an intersection of key pathways of energy metabolism. It is the end product of glycolysis and the starting point for gluconeogenesis, and can be generated by transamination of alanine. It can be converted by the pyruvate dehydrogenase complex to acetyl CoA (Reed and Hackert 1990) which can enter the TCA cycle or serve as the starting point for the syntheses of long chain fatty acids, steroids, and ketone bodies depending on the tissue and metabolic state in which it is formed. It also plays a central role in balancing the energy needs of various tissues in the body. Under conditions in which oxygen supply is limiting, e.g., in exercising muscle, or in the absence of mitochondria, e.g., in red blood cells, re-oxidation of NADH produced by glycolysis cannot be coupled to generation of ATP. Instead, re-oxidation is coupled to the reduction of pyruvate to lactate. This lactate is released into the blood, and is taken up primarily by the liver, where it is oxidized to pyruvate and can be used for gluconeogenesis (Cori 1981).
The mitochondrial pyruvate dehydrogenase (PDH) complex catalyzes the oxidative decarboxylation of pyruvate, linking glycolysis to the tricarboxylic acid cycle and fatty acid synthesis. PDH inactivation is crucial for glucose conservation when glucose is scarce, while adequate PDH activity is required to allow both ATP and fatty acid production from glucose. The mechanisms that control human PDH activity include its phosphorylation (inactivation) by pyruvate dehydrogenase kinases (PDK 1-4) and its dephosphorylation (activation, reactivation) by pyruvate dehydrogenase phosphate phosphatases (PDP 1 and 2). Isoform-specific differences in kinetic parameters, regulation, and phosphorylation site specificity of the PDKs introduce variations in the regulation of PDC activity in differing endocrine and metabolic states (Sugden and Holness 2003).
Pyruvate Dehydrogenase Kinase (PDK) in the mitochondrial matrix catalyzes the phosphorylation of serine residues of the E1 alpha subunit of the pyruvate dehydrogenase complex, inactivating it. Pyruvate negatively regulates this reaction, and NADH and acetyl CoA positively regulate it (Bao et al. 2004). Four PDK isoforms have been identified and shown to catalyze the phosphorylation of E1 alpha in vitro (Gudi et al. 1995; Kolobova et al. 2001; Rowles et al. 1996). They differ in their expression patterns and quantitative responses to regulatory small molecules. All four isoforms catalyze the phosphorylation of serine residues 293 ("site 1") and 300 ("site 2"); PDK1 also catalyzes the phosphorylation of serine 232 ("site 3"). Phosphorylation of a single site in a single E1 alpha subunit is sufficient for enzyme inactivation (Bowker-Kinley et al. 1998; Gudi et al. 1995; Kolobova et al. 2001; Korotchkina and Patel, 2001). In the nucleus, cellular retinoic acid-binding protein 1 or 2 (CRABP1 or 2), bound to all-trans-retinoic acid (atRA), directly binds to the heterodimeric complex of retinoic acid receptor alpha RXRA) and peroxisome proliferator-activated receptor delta (PPARD). When bound to PPARD, atRA can significantly increase the expression of proteins involved in energy metabolism such as PDK via its induction of PPARD (Wolf 2010).
The mitochondrial pyruvate dehydrogenase complex catalyzes the reaction of pyruvate, CoASH, and NAD+ to form acetylCoA, CO2, and NADH. The enzyme complex contains multiple copies of three different proteins, E1 alpha, E1 beta, E2, and E3, each with distinct catalytic activities (Reed and Hackert 1990; Zhou et al 2001). The reaction starts with the oxidative decarboxylation of pyruvate catalyzed by E1 alpha and beta (pyruvate dehydrogenase). Lipoamide cofactor associated with E1 is reduced at the same time. Next, the acetyl group derived from pyruvate is transferred to coenzyme A in two steps catalyzed by E2 (dihydrolipolyl transacetylase). Finally, the oxidized form of lipoamide is regenerated and electrons are transferred to NAD+ in two steps catalyzed by E3 (dihydrolipoyl dehydrogenase). The biochemical details of this reaction have been worked out with pyruvate dehydrogenase complex and subunits purified from bovine tissue and other non-human sources. Direct evidence for the roles of the corresponding human proteins comes from studies of patients expressing mutant forms of E1 alpha (Lissens et al. 2000), E1 beta (Brown et al. 2004), E2 (Head et al. 2005), and E3 (Brautigam et al. 2005).
Pyruvate (PYR) and a proton are transported from the cytosol into the mitochondrial matrix, mediated by a complex of MCP1 and MCP2 in the inner mitochondrial membrane. Studies of pyruvate uptake in rat indicate that it is specific, saturable, and competitively inhibitable, indicating a specific role for a membrane transport protein (Papa et al. 1971; Halestrap and Denton 1974), and the stoichiometry of the human reaction is inferred from this work. MCP1 and MCP2 have been identified as essential components of the transporter based on the observation that expression of both proteins (but not either one alone) restored mitochondrial pyruvate uptake in mutant budding yeast. The proteins form a multimeric complex; its stoichiometry is unknown (Bricker et al. 2012).
Functional characterization of a human aquaporin 0 mutation that leads to a congenital dominant lens cataract
Microsomal enzymes of cholesterol biosynthesis. Purification of lanosterol 14 alpha-methyl demethylase cytochrome P-450 from hepatic microsomes.
Dephosphorylation of nuclear Cyclin B1:phospho-Cdc2 (Thr 14, Tyr15) complexes by Cdc25 phosphatases
Phosphorylation of M phase proteins by active Cyclin B1:Cdc2 complexes
Dephosphorylation of cyclin B2:phospho-Cdc2 (Thr 14) by Cdc25
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CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes
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Translocation of Cyclin B1:phospho-Cdc2 to the cytoplasm
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Translocation of Cdc25B to the cytoplasm
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Dephosphorylation of cytoplasmic Cyclin B1:phospho-Cdc2 (Thr 14, Tyr 15) complexes by Cdc25 phosphatases
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Phosphorylation of Cyclin B1 in the CRS domain
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Translocation of CRS phosphorylated Cyclin B1:Cdc2 complexes
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Human liver type pyruvate kinase: complete amino acid sequence and the expression in mammalian cells
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Isolation of MutSbeta from human cells and comparison of the mismatch repair specificities of MutSbeta and MutSalpha
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HSF1 granules: a novel stress-induced nuclear compartment of human cells
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Antigenic analysis of the major human phosphoglucomutase isozymes: PGM1, PGM2, PGM3 and PGM4
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Predominant expression and activation-induced tyrosine phosphorylation of phospholipase C-gamma 2 in B lymphocytes
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Regulation of cholesterol biosynthesis by SREBP (SREBF)
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Defective MMAA causes methylmalonic aciduria type cblA
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PRKCB (Protein kinase C beta, PKC-beta) binds diacylglycerol and phosphatidylserine
Protein Kinase C beta (PKC-beta, PRKCB) is activated
3-decaprenyl-4-hydroxybenzoic acid [ChEBI:64136]
Trimming of N-ter extended precursor fragments by cytosolic aminopeptidases
Ire1 phosphorylated in the activation domain preferentially binds ADP (rather than ATP).
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex
At the beginning of this reaction, 1 molecule of 'eRF3-GDP:eRF1:peptidyl-tRNA:mRNA:80S Ribosome Complex' is present. At the end of this reaction, 1 molecule of 'polypeptide', and 1 molecule of 'eRF3-GDP:eRF1:tRNA:mRNA:80S Ribosome Complex' are present. This reaction takes place in the 'cytosol'.
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex
At the beginning of this reaction, 1 molecule of 'eRF3-GTP:eRF1:peptidyl-tRNA:mRNA:80S Ribosome Complex' is present. At the end of this reaction, 1 molecule of 'eRF3-GDP:eRF1:peptidyl-tRNA:mRNA:80S Ribosome Complex', and 1 molecule of 'Orthophosphate' are present. This reaction takes place in the 'cytosol'.
Translocation of PKC theta to plasma membrane
Translocation of PDK1 to Plasma membrane
RFC binding displaces Pol Alpha on the C-strand of the telomere
The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere
Molecular cloning of cDNA for nonhepatic mitochondrial arginase (arginase II) and comparison of its induction with nitric oxide synthase in a murine macrophage-like cell line
RFC dissociates after sliding clamp formation on the C-strand of the telomere
Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere
Elongation of Extended Telomeric Chromosome End
Translocation Of Telomerase RNP And Alignment Of RNA Template (TERC) To Extended Single Stranded Telomeric Chromosome-End
The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere
Disassociation of Telomerase RNP and the Chromosome End
5' to 3' Exoribonuclease Digestion of Decapped mRNA (yeast)
Addition of the fourth and fifth mannose to the N-glycan precursor skeleton by Alg11
A fourth and fifth mannose is added to the N-glycan precursor skeleton by Alg11, characterized from yeast (Cipollo JF et al, 2001).
GTP bound eRF3:eRF1 complex binds the peptidyl-tRNA:mRNA:Ribosome complex
At the beginning of this reaction, 1 molecule of 'peptidyl-tRNA:mRNA:80S Ribosome Complex', 1 molecule of 'GTP bound eRF3', and 1 molecule of 'Erf-1' are present. At the end of this reaction, 1 molecule of 'eRF3-GTP:eRF1:peptidyl-tRNA:mRNA:80S Ribosome Complex' is present. This reaction takes place in the 'cytosol'.
Phosphorylation of Cdh1 by Cyclin B1:Cdc2
Sulfation in high endothelial venules: cloning and expression of the human PAPS synthetase
Cytosolic PLK1 translocates to the nucleus
Elongation Of The Telomeric Chromosome End
Alignment Of The RNA Template On The Telomeric Chromosome End
Recruitment of Telomerase RNP to the Telomeric Chromosome End
Methionine regeneration and aspartate aminotransferase in parasitic protozoa
Production of ceramide which can activate JNK and other targets
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Active JNK moves to the nucleus and phosphorylates different transcription factors
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Identification of a target RNA motif for RNA-binding protein HuR
Identification and characterization of a gene encoding human LPGAT1, an endoplasmic reticulum-associated lysophosphatidylglycerol acyltransferase
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Phosphorylation of Ribosomal protein S6 by activated S6K1
Phosphorylation and activation of eIF4G by activated S6K1
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The major sites of cellular phospholipid synthesis and molecular determinants of Fatty Acid and lipid head group specificity
RNA Polymerase III Initiation At a Simple Start Sequence
Transcription by pol III initiates at characteristic, simple start sequences. The universal core of these start sites is a pyrimidine-purine step, transcription initiating most frequently with ATP or GTP (Fruscoloni et al., 1995)
Abortive initiation, the repetitive formation of short oligonucleotides, is a ubiquitous feature of transcriptional initiation. For pol III, it has been analyzed only in S. cerevisiae (Bhargava and Kassavetis, 1999). The released products of abortive initiation, principally di- and tri-nucleotides, indicate the participation of retractive endonucleolytic cleavage of these initially forming abortive products. The transition from abortive to productive transcription may occur at bp +5.
Beginning of RNA Polymerase III Productive Transcription
The transition from abortive to productive transcription may occur at bp +5. The primary transcripts of pol III-transcribed genes are short, ~90 to 120 nt for tRNA and 5 sRNA genes (which constitute the great majority of products) and even the longest transcripts (e.g. the RNA of the signal recognition particles) are only ~500 nt. The special feature of this transcription is the presence of initiation factors bound within the transcription unit ââ¬â TFIIIA within class 1 genes (NH section) and TFIIIC in class 1 and class 2 genes. Transcript elongation, which has been analyzed at single-step resolution on a single sc tRNA gene, is rapid with highly purified components (TFIIIC, TFIIIB and pol III), and also in crude extracts (Matsuzaki et al., 1994; Shaaban et al., 1996). In particular, TFIIIC does not present a barrier to transcript elongation, generating a delay at only a single site of only 0.15-0.2 s duration at 20C. In other words, the requirement to displace TFIIIC during transcript elongation is not rate-limiting for tRNA gene activity. On the other hand, transcript elongation slows down when short U-tracts, e.g. UUU, are laid down, even at high concentrations of NTPs. These pauses exceed the TFIIIC-imposed delay on transcription of the sc SUP4 gene by a factor of ~3 or greater. Sc TFIIIC is entirely displaced from a tRNA gene during multiple cycles of transcription in vitro (Bardeleben et al., 1994) and its occupancy of pol III genes in vivo during active cell growth is also low (Roberts et al., 2003).
RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites
Productive transcription is accompanied by retractive RNase activity at U-tract pause sites and at the terminator. The principal cleavage products are dinucleotides, and they are produced in large stoichiometric excess over complete transcripts, despite the rapid overall rate of productive RNA chain elongation (Bobkova and Hall, 1997). This RNase activity is intrinsic to pol III, and is mediated by its C11 subunit (gene RPC10), a paralog of pol II Rpb9 with a C-terminal 26 amino acid domain that is highly similar to the extrinsic pol II transcription factor TFIIS (ChÃÂ©din et al., 1998). Two acidic amino acids in this segment (D91/E92 in scC11; D88/E89 in hC11), which are universally conserved in bacterial, archaeal and eukaryotic transcript cleavage factors, play a critical role in the activation of transcript cleavage by donating catalytic residues to the active centers of RNA polymerases for hydrolytic RNA chain retraction (ChÃÂ©din et al., 1998; Kettenberger et al., 2003; Opalka et al., 2003; Sosunova et al., 2003). However, the extrinsic transcript cleavage factors, as well as the C11 subunit of pol III, are devoid of separate RNase activity.
GAPs galore! A survey of putative Ras superfamily GTPase activating proteins in man and Drosophila
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In S. cerevisiae the dehydratation of 5'-methylthio ribulose-1-phosphate with the help of Mde1p is a one-way reaction. (Pirkov et al, 2008)
PKA catalytic subunit translocates to the nucleus
cAMP induces dissociation of inactive PKA tetramers
Male pseudohermaphroditism caused by mutations of testicular 17 beta-hydroxysteroid dehydrogenase 3
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The role of the tethering proteins p115 and GM130 in transport through the Golgi apparatus in vivo
Activation of CDC42 by unknown mechanism
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Translocation of antigenic peptides back to phagosomes via TAP
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Proteasomal clevage of exogenous antigen
Expression and purification of recombinant tristetraprolin that can bind to tumor necrosis factor-alpha mRNA and serve as a substrate for mitogen-activated protein kinases
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Histone variants--ancient wrap artists of the epigenome
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Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics
Recognition and association of DNA glycosylase with site containing an affected purine
Regulation of Ca2+ signaling in mast cells by tyrosine-phosphorylated and unphosphorylated non-T cell activation linker
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2-methoxy-6-decaprenyl-1,4-benzoquinol [ChEBI:64180]
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The cofactor BH4 is required for electron transfer in the eNOS catalytic cycle
6-methoxy-3-methyl-2-decaprenyl-1,4-benzoquinol [ChEBI:64181]
VEGF induces CDC42 activation by unknown mechanism
Diverse mechanisms and machineries for import of mitochondrial proteins
At the endoplasmic reticulum (ER) membrane, lysophospholipid acyltransferases acylate 1-acyl lysophosphatidylserine (LPS) to form phosphatidylserine (PS). The lysophospholipid acyltransferases involved are: lysophospholipid acyltransferase 5 (LPCAT3) (Gijon et al. 2008, Hishikawa et al. 2008); lysophospholipid acyltransferase LPCAT4 (LPCAT4) aka LPEAT2 (Cao et al. 2008); or lysophospholipid acyltransferase 1 (MBOAT1) aka LPEAT1 (Hishikawa et al. 2008, Gijon et al. 2008).
Lysophosphatidylcholine (LPC) is hydrolyzed by phospholipases to produce glycerophosphocholine (GPCho) which is in turn hydrolyzed by glycerophosphocholine phosphodiesterase to produce choline (Cho) and glycerol-3-phosphate (G3P) (Yamashita et al. 2009, Yamashita et al. 2005, Ghomashchi et al. 2010).
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In the acyl chain remodelling pathway (Lands cycle), phosphatidylcholine (PC) is hydrolysed by phopholipases and subsequently reacylated by acyltransferases. These cycles modify the fatty acid composition of glycerophospholipids to generate diverse molecules asymmetrically distributed in the cell membrane (Ghomashchi et al. 2010, Singer et al. 2002, Cao et al. 2008, Zhao et al. 2008).
The effects of glutaredoxin and copper activation pathways on the disulfide and stability of Cu,Zn superoxide dismutase
In the cytosol, glycerophosphocholine phosphodiesterase (GPCPD1, also known as GDE5) hydrolyzes glycerophosphocholine (GPCho) to produce choline (Cho) and glycerol-3-phosphate (G3P). This event has been inferred from mice. GPCPD1 has also been characterized in humans (Ota et al. 2004).
At the endoplasmic reticulum (ER) membrane, lysophospholipid acyltransferases acylate 1-acyl lysophosphatidylcholine (LPC) to form phosphatidylcholine (PC). The lysophospholipid acyltransferases involved are: lysophosphatidylcholine acyltransferase 1 (LPCAT1) (Nakanishi et al. 2006, Chen et al. 2006); lysophosphatidylcholine acyltransferase 2 (LPCAT2) (Shindou et al. 2006); lysophospholipid acyltransferase 5 (LPCAT3) (Hishikawa et al. 2008, Zhao et al. 2008, Gijon et al. 2008, Jain et al. 2009, Kazachkov et al. 2008); lysophospholipid acyltransferase LPCAT4 (LPCAT4) aka LPEAT2 (Cao et al. 2008, Ye et al. 2005); or lysophospholipid acyltransferase 2 (MBOAT2) aka LPCAT4 (Hishikawa et al. 2008, Gijon et al. 2008).
At the endoplasmic reticulum (ER) membrane, lysophospholipid acyltransferases acylate 2-acyl lysophosphatidylcholine (LPC) to form phosphatidylcholine (PC). The lysophospholipid acyltransferases involved are: lysophosphatidylcholine acyltransferase 1 (LPCAT1) (Nakanishi et al. 2006, Chen et al. 2006); lysophosphatidylcholine acyltransferase 2 (LPCAT2) (Shindou et al. 2006); lysophospholipid acyltransferase 5 (LPCAT3) (Hishikawa et al. 2008, Zhao et al. 2008, Gijon et al. 2008, Jain et al. 2009, Kazachkov et al. 2008); lysophospholipid acyltransferase LPCAT4 (LPCAT4) aka LPEAT2 (Cao et al. 2008, Ye et al. 2005); or lysophospholipid acyltransferase 2 (MBOAT2) aka LPCAT4 (Hishikawa et al. 2008, Gijon et al. 2008).
At the Golgi membrane, cholinephosphotransferase 1 (CHPT1) converts CDP-choline (CDP-Cho) and diacylglycerol (DAG) to phosphatidylcholine (PC) and cytidine monophosphate (CMP) (Wright et al. 2002, Henneberry et al. 1999, Henneberry et al. 2002, Henneberry et al. 2000).
De novo (Kennedy pathway) synthesis of phosphatidylcholine (PC) involves phosphorylation of choline (Cho) to phosphocholine (PCho) followed by condensing with cytidine triphosphate (CTP) to form CDP-choline (CDP-Cho). Diacylglycerol (DAG) and CDP-ETA together then form PC. Alternatively, PC is formed when phosphatidylethanolamine (PE) is methylated by phosphatidylethanolamine N-methyltransferase (PEMT) (Henneberry et al. 2002; Wright & McMaster 2002).
At the endoplasmic reticulum (ER) membrane, active membrane-bound choline-phosphate cytidylyltransferase A (PCYT1A) or B (PCYT1B) homodimer condenses phosphocholine (PCho) and cytidine triphosphate (CTP) to produce CDP-choline (CDP-Cho) (Lykidis et al. 1998).
At the endoplasmic reticulum (ER) membrane, choline/ethanolaminephosphotransferase (CEPT1) converts CDP-choline (CDP-Cho) and diacylglycerol (DAG) to phosphatidylcholine (PC) and cytidine monophosphate (CMP) (Wright et al. 2002, Henneberry et al. 1999, Henneberry et al. 2002, Henneberry et al. 2000).
At the endoplasmic reticulum (ER) membrane, phosphatidylethanolamine N-methyltransferase (PEMT) methylates phosphatidylethanolamine (PE) and produces phosphatidylcholine (PC) (Vance & Ridgway 1998, Shields et al. 2001, Guan et al. 1999).
Lysophosphatidylethanolamine (LPE) is hydrolyzed by phospholipases to produce glycerophosphoethanolamine (GPETA) which is in turn hydrolyzed by glycerophosphocholine phosphodiesterase to produce ethanolamine (ETA) and glycerol-3-phosphate (G3P) (Yamashita et al. 2009, Yamashita et al. 2005).
In the cytosol, choline kinase alpha subunit (CHKA) homodimer, choline kinase beta subunit (CHKB) dimer, or CHKA:CHKB heterodimer phosphorylates choline (Cho) to produce phosphocholine (PCho) (Malito et al. 2006, Gallego-Ortega et al. 2009).
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Synthesis of substrates in N-glycan biosythesis
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Pathways of chaperone-mediated protein folding in the cytosol
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Molecular mechanisms of translational control
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At the endoplasmic reticulum (ER) membrane, lysophospholipid acyltransferases acylate 1-acyl lysophosphatidylethanolamine (LPE) to form phosphatidylethanolamine (PE). The lysophospholipid acyltransferases involved are: lysophospholipid acyltransferase 1 (MBOAT1) aka LPEAT1 (Gijon et al. 2008, Hishikawa et al. 2008); lysophospholipid acyltransferase LPCAT4 (LPCAT4) aka LPEAT2 (Cao et al. 2008, Ye et al., 2005); lysophospholipid acyltransferase 2 (MBOAT2) aka LPCAT4 (Hishikawa et al. 2008, Gijon et al. 2008); lysophospholipid acyltransferase 5 (LPCAT3) (Hishikawa et al. 2008, Zhao et al. 2008, Gijon et al. 2008, Jain et al. 2009, Kazachkov et al. 2008).
At the endoplasmic reticulum (ER) membrane, lysophospholipid acyltransferases acylate 2-acyl lysophosphatidylethanolamine (LPE) to form phosphatidylethanolamine (PE). The lysophospholipid acyltransferases involved are: lysophospholipid acyltransferase 1 (MBOAT1) aka LPEAT1 (Gijon et al. 2008, Hishikawa et al. 2008); lysophospholipid acyltransferase LPCAT4 (LPCAT4) aka LPEAT2 (Cao et al. 2008, Ye et al. 2005); lysophospholipid acyltransferase 2 (MBOAT2) aka LPCAT4 (Hishikawa et al. 2008, Gijon et al. 2008); lysophospholipid acyltransferase 5 (LPCAT3) (Hishikawa et al. 2008, Zhao et al. 2008, Gijon et al. 2008, Jain et al. 2009, Kazachkov et al. 2008).
In the acyl chain remodelling pathway (Lands cycle), phosphatidylethanolamine (PE) is hydrolyzed by phopholipases and subsequently reacylated by acyltransferases. These cycles modify the fatty acid composition of glycerophospholipids to generate diverse molecules asymmetrically distributed in the cell membrane (Ghomashchi et al. 2010, Singer et al. 2002, Cao et al. 2008, Zhao et al. 2008, Hishikawa et al. 2008).
In the cytosol, glycerophosphocholine phosphodiesterase (GPCPD1, also known as GDE5) hydrolyzes glycerophosphoethanolamine (GPETA) to produce ethanolamine (ETA) and glycerol-3-phosphate (G3P). This event has been inferred from mice. GPCPD1 has also been characterized in humans (Ota et al. 2004).
At the endoplasmic reticulum (ER) membrane, choline/ethanolaminephosphotransferase 1 (CEPT1) or ethanolaminephosphotransferase 1 (EPT1) converts CDP- ethanolamine (CDP-ETA) and diacylglycerol (DAG) to phosphatidylethanolamine (PE) and cytidine monophosphate (CMP) (Horibata et al. 2007, Wright et al. 2002, Henneberry et al. 1999, Henneberry et al. 2002, Henneberry et al. 2000).
At the inner mitochondrial (IM) membrane, phosphatidylserine decarboxylase proenzyme (heterodimer of two chains from the same protein) (PISD) decarboxylates phosphatidylserine (PS) to phosphatidylethanolamine (PE). This event has been inferred from rats and limited data for a human PISD (Forbes et al. 2007).
De novo (Kennedy pathway) synthesis of phosphatidylethanolamine (PE) involves phosphorylation of ethanolamine (ETA) to phosphoethanolamine (PETA) followed by condensing with cytidine triphosphate (CTP) to form CDP-ethanolamine (CDP-ETA). Diacylglycerol (DAG) and CDP-ETA together then form PE. Alternatively, PE is formed when phosphatidylserine (PS) is decarboxylated by phosphatidylserine decarboxylase proenzyme (PISD) (Henneberry et al. 2002, Vance 1991, Vance 1990).
At the endoplasmic reticulum (ER) membrane, phosphatidate phosphatase 1-3 (LPIN) dephosphorylates phosphatidic acid (PA) to form diacylglycerol (DAG) (Grimsey et al. 2008, Donkor et al. 2007).
At the endoplasmic reticulum (ER) membrane, active membrane-bound ethanolamine-phosphate cytidylyltransferase (PCY2) dimer condenses phosphoethanolamine (PETA) and cytidine triphosphate (CTP) to produce CDP-ethanolamine (CDP-ETA) (Zhu et al. 2008, Nakashima et al. 1997).
Regulation of Glucokinase by Glucokinase Regulatory Protein
In the cytosol, ethanolamine (ETA) is phosphorylated to phosphoethanolamine (PETA) by choline kinase (CHK) dimer or by ethanolamine kinase 1/2 (ETNK1/2) (Lykidis et al. 2001, Gallego-Ortega et al. 2009). CHK dimer consists of either choline kinase alpha subunit (CHKA) or beta subunit (CHKB) homodimer, or of CHKA:CHKB heterodimer.
Acyl chain remodeling of triacylglycerol (TAG) and diacylglycerol (DAG) progresses through their hydrolysis by patatin-like phospholipase domain-containing proteins 2/3 (PNPLA2/3). DAG is reacylated back to TAG by acylglycerol O-acyltransferase 1/2 (DGAT1/2), while DAG and its hydrolysis product 2-monoacylglycerol (2-MAG) are transacylated back to TAG by PNPLA2/3. In addition, the DAG hydrolysis product 2-MAG is subsequently hydrolyzed to fatty acid and glycerol by monoglyceride lipase (MGLL) (Jenkins et al. 2004).
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The mucopolysaccharidoses: inborn errors of glycosaminoglycan catabolism
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Steroid hormones are synthesized primarily in the adrenal gland and gonads. They regulate energy metabolism and stress responses (glucocorticoids), salt balance (mineralocorticoids), and sexual development and function (androgens and estrogens). All steroids are synthesized from cholesterol. Steroid hormone synthesis is largely regulated at the initial steps of cholesterol mobilization and transport into the mitochondrial matrix for conversion to pregnenolone. In the body, the fate of pregnenolone is tissue-specific: in the zona fasciculata of the adrenal cortex it is converted to cortisol, in the zona glomerulosa to aldosterone, and in the gonads to testosterone and then to estrone and estradiol. These pathways are outlined in the figure below, which also details the sites on the cholesterol molecule that undergo modification in the course of these reactions. Vitamin D3 (cholecalciferol) is a steroid hormone that plays a role in regulating calcium and bone metabolism. The processes by which it is synthesized, modified, and transported in the body are annotated here.
At the outer mitochondrial (OM) membrane, 1-acyl lysophosphatidic acid (LPA) is acylated to phosphatidic acid (PA) by the enzyme 1-acyl-sn-glycerol-3-phosphate acyltransferases epsilon (AGPAT5) (Prasad et al. 2011).
At the endoplasmic reticulum (ER) membrane, diacylglycerol (DAG) is acylated and forms triacylglycerol (TAG) by the action of diacylglycerol O-acyltransferase 1 (DGAT1) tetramer or by diacylglycerol O-acyltransferase 2 (DGAT2) (Wakimoto et al. 2003, Oelkers et al. 1998, Cases et al. 2001).
At the endoplasmic reticulum (ER) membrane, monoglyceride lipase (MGLL) hydrolyzes 2-monoacylglycerol (2-MAG) to form a fatty acid and glycerol (Dinh et al. 2004, Zvonok et al. 2008, Bertrand et al. 2010, Labar et al. 2010).
Phosphatidylcholine (PC) is hydrolyzed to phosphatidic acid (PA) and choline (Cho) by the enzymes phospholipase D1/2 (PLD1/2), at the endoplasmic reticulum (ER) membrane (Lopez et al. 1998, Hammond et al. 1995).
In the de novo synthesis of phosphatidic acid (PA), lysophosphatidic acid (LPA) is initially formed by the esterification of sn-1 by glycerol 3-phosphate acyltransferase (GPAT) from glycerol 3-phosphate (G3P). Next, LPA is converted to PA by a LPA acyltransferase (AGPAT, also known as LPAAT). In addition to this, PA is also formed when phosphatidylcholine (PC) is hydrolyzed by phospholipase D1/2 (PLD1/2). PA is involved in acyl chain remodeling via cleavage by phospholipases followed by reacylation by acyltransferases (Ghomashchi et al. 2010, Singer et al. 2002, Prasad et al. 2011, Shindou & Shimizu 2009, Cao et al. 2006).
In a healthy adult human, about 500 mg of cholesterol is converted to bile salts daily (Russell 2003). The major pathway for bile salt synthesis in the liver begins with the conversion of cholesterol to 7alpha-hydroxycholesterol. Bile salt synthesis can also begin with the synthesis of an oxysterol - 24-hydroxycholesterol or 27-hydroxycholesterol. In the body, the initial steps of these two pathways occur in extrahepatic tissues, generating intermediates that are transported to the liver and converted to bile salts via the 7alpha-hydroxycholesterol pathway. These extrahepatic pathways contribute little to the total synthesis of bile salts, but are thought to play important roles in cholesterol homeostasis (Javitt 2002).
The microsomal enzyme cholesterol 25-hydroxylase is a member of a lipid metabolizing enzyme family that utilizes oxygen and diiron-oxygen cofactor to hydroxylate, desaturate, epoxidate and acetylate substrates.
The 17HSD family of enzymes catalyze the final step in the synthesis of estradiol and testosterone. They convert inactive 17-ketosteroids to their active 17beta-hydroxy forms. Androstenedione, a ketosteroid, is reduced to testosterone, a highly potent androgen, by the enzyme 17beta-hydroxysteroid dehydrogenase isoform III (17HSD3). The other human isoforms of 17HSDs to take part in the final steps of active steroid biosynthesis are types 1 and VII, which reduce estrone to estradiol. Corticotropin (Adrenocorticotropic hormone, ACTH) acts through the ACTH receptor called melanocortin receptor type 2 (MC2R) to stimulate steroidogenesis, increasing the production of androgens (McKenna et al, 1997). In males, Lutropin (LH) stimulates testosterone production.
In a healthy adult human, about 500 mg of cholesterol is converted to bile salts daily. Newly synthesized bile salts are secreted into the bile and released into the small intestine where they emulsify dietary fats (Russell 2003). About 95% of the bile salts in the intestine are recovered and returned to the liver (Kullak-Ublick et al. 2004; Trauner and Boyer 2002). The major pathway for bile salt synthesis in the liver begins with the conversion of cholesterol to 7alpha-hydroxycholesterol. Bile salt synthesis can also begin with the synthesis of an oxysterol - 24-hydroxycholesterol or 27-hydroxycholesterol. In the body, the initial steps of these two pathways occur in extrahepatic tissues, generating intermediates that are transported to the liver and converted to bile salts via the 7alpha-hydroxycholesterol pathway. These extrahepatic pathways contribute little to the total synthesis of bile salts, but are thought to play important roles in extrahepatic cholesterol homeostasis (Javitt 2002).
Androgens are the determining factors for male development and behaviour in vertebrates (Miller 2002).
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Human adenine phosphoribosyltransferase. Affinity purification, subunit structure, amino acid composition, and peptide mapping.
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25(S) 3alpha,7alpha-dihydroxy-5beta-cholest-24-enoyl-CoA is hydrated to form (24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA. This reaction, catalyzed by the peroxisomal D-bifunctional enzyme (Huyghe et al. 2006), occurs in the peroxisomal matrix.
(24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA and NAD+ react to form 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-one-CoA, NADH, and H+. This oxidation reaction, catalyzed by the peroxisomal D-bifunctional enzyme (Huyghe et al. 2006), occurs in the peroxisomal matrix.
(24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA and NAD+ react to form 3alpha,7alpha-dihydroxy-5beta-cholest-24-one-CoA, NADH, and H+. This oxidation reaction, catalyzed by the peroxisomal D-bifunctional enzyme (Huyghe et al. 2006), occurs in the peroxisomal matrix.
Choloyl-CoA and water react to form cholate and CoASH. This reaction, catalyzed by acyl-coenzyme A thioesterase 8, occurs in the peroxisomal matrix (Jones et al. 1999; Hunt et al. 2002). While bile salts are the major product of the de novo biosynthetic pathway in the normal human liver, bile acids are major feedback regulators of this pathway and this hydrolysis reaction is thought to play a role in generating them (Russell 2003).
In the liver, synthesis of bile acids and bile salts is initiated with the conversion of cholesterol to 7alpha-hydroxycholesterol and of 7alpha-hydroxycholesterol to 4-cholesten-7alpha-ol-3-one. The pathway then branches: hydroxylation of 4-cholesten-7alpha-ol-3-one to 4-cholesten-7alpha, 12alpha-diol-3-one leads ultimately to the formation of cholate, while its reduction to 5beta-cholestan-7alpha-ol-3-one leads to chenodeoxycholate formation. The amounts of substrate following each branch appear to be determined by abundance of the hydroxylase enzyme: in human liver, cholate synthesis predominates. In both branches, reactions in the cytosol, the mitochondrial matrix, and the peroxisomal matrix result in modifications to the ring structure, shortening and oxidation of the side chain, conversion to a Coenzyme A derivative, and conjugation with the amino acids glycine or taurine. In the body, glycocholate, taurocholate, glycochenodeoxycholate, and taurochenodeoxycholate are released from hepatocytes into the bile and ultimately into the lumen of the small intestine, where they function as detergents to solubilize dietary fats. The liver synthetic pathway also yields small amounts of bile acids, cholate and deoxycholate, which may play a feedback role in regulating the bile acid synthetic pathway (Russell 2003). These reactions are outlined in the figure below.
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Differential role of human choline kinase alpha and beta enzymes in lipid metabolism: implications in cancer onset and treatment
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25(S) DHCA-CoA and O2 react to form 25(S) 3alpha,7alpha-dihydroxy-5beta-cholest-24-enoyl-CoA and H2O2. This dehydrogenation reaction occurs in the peroxisomal matrix. It is catalyzed by the FAD-containing peroxisomal enzyme branched chain acyl-CoA oxidase (ACOX2). The enzyme transfers electrons to molecular oxygen and hydrogen peroxide is produced as a byproduct.
3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA (THCA-CoA) is hydrated to form (24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA. This reaction, catalyzed by the peroxisomal D-bifunctional enzyme (Huyghe et al. 2006), occurs in the peroxisomal matrix.
Sterol regulatory element binding proteins (SREBPs, SREBFs) respond to low cholesterol concentrations by transiting to the nucleus and activating genes involved in cholesterol and lipid biosynthesis (reviewed in Brown and Goldstein 2009, Osborne and Espenshade 2009, Weber et al. 2004). Newly synthesized SREBPs are transmembrane proteins that bind SCAP in the endoplasmic reticulum (ER) membrane. SCAP binds cholesterol which causes a conformational change that allows SCAP to interact with INSIG, retaining the SCAP:SREBP complex in the ER. INSIG binds oxysterols, which cause INSIG to bind SCAP and retain SCAP:SREBP in the endoplasmic reticulum. In low cholesterol (below about 5 mol%) SCAP no longer interacts with cholesterol or INSIG and binds Sec24 of the CopII coat complex instead. Thus SCAP:SREBP transits with the CopII complex from the ER to the Golgi. In the Golgi SREBP is cleaved by S1P and then by S2P, releasing the N-terminal fragment of SREBP into the cytosol. The N-terminal fragment is imported to the nucleus by importin-beta and then acts with other factors, such as SP1 and NF-Y, to activate transcription of target genes. Targets of SREBP include the genes encoding all enzymes of cholesterol biosynthesis and several genes involved in lipogenesis. SREBP2 most strongly activates cholesterol biosynthesis while SREBP1C most strongly activates lipogenesis.
25(S) THCA-CoA and O2 react to form 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA (THCA-CoA) and H2O2. This dehydrogenation reaction occurs in the peroxisomal matrix. It is catalyzed by the FAD-containing peroxisomal enzyme branched chain acyl-CoA oxidase (ACOX2). The enzyme transfers electrons to molecular oxygen and hydrogen peroxide is produced as a byproduct.
The p46 subunit of eukaryotic initiation factor (eIF)-4F exchanges with eIF-4A.
The TM7SF2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
After transiting to the nucleus SREBPs (SREBP1A/1C/2, SREBFs) bind short sequences, sterol regulatory elements (SREs), in the promoters of target genes (reviewed in Eberle et al. 2004, Weber et al. 2004). SREBPs alone are relatively weak activators of transcription, with SREBP1C being significantly weaker than SREBP1A or SREBP2. In combination with other transcription factors such as SP1 and NF-Y the SREBPs are much stronger activators. SREBP1C seems to more specifically target genes involved in fatty acid synthesis while SREBP2 seems to target genes involved in cholesterol synthesis (Pai et al. 1998).
The SQLE gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The SC5D gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
Rho guanine nucleotide exchange factor 3
The FDPS gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
Cholesterol is synthesized de novo from from acetyl CoA. The overall synthetic process is outlined in the figure below. Enzymes whose regulation plays a major role in determining the rate of cholesterol synthesis in the body are highlighted in red, and connections to other metabolic processes are indicated. The transformation of lanosterol into cholesterol requires multiple steps, including the removal of three methyl groups, the reduction of one double bond and the migration of another. These reactions may not occur in a single fixed order in the body, so the linear pathway laid out here following the work of Gaylor and colleagues (Gaylor 2002) is an oversimplification of the process that occurs in vivo. Defects in several of the enzymes involved in this process are associated with human disease and have provided useful insights into the regulatory roles of cholesterol and its synthetic intermediates in human development (Herman 2003; Song et al. 2005).
Neuroepithelial cell-transforming gene 1 protein
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Thrombopoietin: a tool for understanding thrombopoiesis
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T-lymphoma invasion and metastasis-inducing protein 2
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Functional expression of human mutant phosphofructokinase in yeast: genetic defects in French Canadian and Swiss patients with phosphofructokinase deficiency
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Three-step model for condensin activation during mitotic chromosome condensation
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High affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A
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Mapping residues of SUMO precursors essential in differential maturation by SUMO-specific protease, SENP1
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Activation and signaling of the p38 MAP kinase pathway
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Plasma membrane calcium-transporting ATPase 3
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Plasma membrane calcium-transporting ATPase 1
Plasma membrane calcium-transporting ATPase 2
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SLIT-ROBO Rho GTPase-activating protein 1
Cloning, characterization, and chromosomal localization of a gene frequently deleted in human liver cancer (DLC-1) homologous to rat RhoGAP
SLIT-ROBO Rho GTPase-activating protein 3
Human liver glucokinase gene: cloning and sequence determination of two alternatively spliced cDNAs
1,2-Dihydroxy-3-oxo-methylthiopentene (1-)
Cloning and characterization of a novel human alkaline ceramidase. A mammalian enzyme that hydrolyzes phytoceramide
Identification of human phosphoglucomutase 3 (PGM3) as N-acetylglucosamine-phosphate mutase (AGM1)
Identification of an evolutionarily conserved superfamily of DOCK180-related proteins with guanine nucleotide exchange activity
N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 3
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 4
Subcellular targeting and trafficking of nitric oxide synthases
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 2
At the plasma membrane, phosphatidylinositol-5-phosphate 4-kinase type-2 alpha (PIP4K2A) and beta (PIP4K2B) homodimers and heterodimers (Clarke et al. 2010) phosphorylate phosphatidylinositol 5-phosphate (PI5P) to phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). The following lists the above proteins with their corresponding literature references: PIP4K2A (Rameh et al. 1997, Clarke et al. 2008) and PIP4K2B (Rameh et al. 1997).
1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 1
The human Myt1 kinase preferentially phosphorylates Cdc2 on threonine 14 and localizes to the endoplasmic reticulum and Golgi complex.
At the plasma membrane, subsequent phosphorylation of phosphatidylinositol 4-phosphate (PI4P) produces phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and phosphatidylinositol 3,4,5-trisphosphate (PI(3,4,5)P3) while the actions of various other kinases and phosphatases produces phosphatidylinositol 3-phosphate (PI3P), phosphatidylinositol 5-phosphate (PI5P), phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2), and phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) (Zhang et al. 1997, Gurung et al. 2003, Guo et al. 1999, Vanhaesebroeck et al. 1997, Tolias et al. 1998, Schaletzky et al. 2003, Kim et al. 2002, Clarke et al. 2010).
At the early endosome membrane, the PAS complex, consisting of FYVE finger-containing phosphoinositide kinase (PIKFYVE), yeast VAC14 homologue (VAC14), and polyphosphoinositide phosphatase aka SAC3 (FIG4), binds to the membrane via PIKFYVE's FYVE finger (Sbrissa et al. 2002, Cao et al. 2007). The PIKFYVE kinase component phosphorylates phosphatidylinositol 3-phosphate (PI3P) to phosphatidylinositol 3,5-bisphosphate PI(3,5)P2 (Sbrissa et al. 1999). The PAS complex is present in the cytosol and is recruited to the membrane (Sbrissa et al. 2007).
At the plasma membrane, phosphatidylinositol 4-kinase type 2-alpha (PI4K2A) (Balla et al. 2002, Minogue et al. 2001) and beta (PI4K2B) (Balla et al. 2002, Wei et al. 2002) phosphorylate phosphatidylinositol (PI) to phosphatidylinositol 4-phosphate (PI4P).
At the plasma membrane, synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1 aka Synaptojanin-1 (SYNJ1) (Guo et al. 1999, Mani et al. 2007, Johenning et al. 2004) and -2 (SYNJ2) (Malecz et al. 2000) dephosphorylate phosphatidylinositol 4-phosphate (PI4P) phosphatidylinositol (PI). The SAC1 domains of SYNJ1 and SYNJ2 demonstrate 4-phosphatase activity.
At the early endosome membrane, phosphatidylinositol 4-kinase type 2-alpha/beta (PI4K2A/B) (Balla et al. 2002) phosphorylates phosphatidylinositol (PI) to produce phosphatidylinositol 4-phosphate (PI4P).
Guanine nucleotide-binding protein G(i), alpha-2 subunit
Adenylate cyclase-inhibiting G alpha protein
At the early endosome membrane, phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) is generated in two steps from phosphatidylinositol 3,4-bisphosphate PI(3,4)P2 by the action of various kinases and phosphatases (Sbrissa et al. 2007, Sbrissa et al. 2008, Cao et al. 2007, Cao et al. 2008, Arcaro et al. 2000, Kim et al. 2002).
Guanine nucleotide-binding protein G(k), alpha subunit
At the early endosome membrane, the PAS complex, consisting of FYVE finger-containing phosphoinositide kinase (PIKFYVE), yeast VAC14 homologue (VAC14), and polyphosphoinositide phosphatase aka SAC3 (FIG4), binds to the membrane via PIKFYVE's FYVE finger. The FIG4 phosphatase component dephosphorylates phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) to phosphatidylinositol 3-phosphate (PI3P) (Sbrissa et al. 2007, Sbrissa et al. 2008).
At the early endosome membrane, phosphatidylinositol 3-kinase catalytic subunit type 3 (PIK3C3) aka VPS34 binds to phosphoinositide 3-kinase regulatory subunit 4 (PIK3R4). The PIK3C3:PIK3R4 complex and phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing subunit alpha (PIK3C2A) phosphorylate phosphatidylinositol (PI) to phosphatidylinositol 3-phosphate (PI3P). The following lists the above proteins with their corresponding literature references: PIK3C3:PIK3R4 complex (Panaretou et al. 1997, Volinia et al. 1995, Cao et al. 2007) and PIK3C2A (Arcaro et al. 2000, Domin et al. 2000).
At the late endosome membrane, the PAS complex, consisting of FYVE finger-containing phosphoinositide kinase (PIKFYVE), yeast VAC14 homologue (VAC14), and polyphosphoinositide phosphatase aka SAC3 (FIG4), binds to the membrane via PIKFYVE's FYVE finger (Sbrissa et al. 2002, Cao et al. 2007). The PIKFYVE kinase component phosphorylates phosphatidylinositol 3-phosphate (PI3P) to phosphatidylinositol 3,5-bisphosphate PI(3,5)P2 (Sbrissa et al. 1999). The PAS complex is present in the cytosol and is recruited to the membrane (Sbrissa et al. 2007).
At the plasma membrane, synaptojanin-1 aka Synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1 (SYNJ1) (Guo et al. 1999), -2 (SYNJ2) and some myotubularins (MTMs) dephosphorylate phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) to phosphatidylinositol 5-phosphate (PI5P). The MTMs involved are: myotubularin (MTM1) (Cao et al. 2007, Tronchere et al. 2004, Schaletzky et al. 2003, Laporte et al. 2002) and myotubularin-related proteins 1 (MTMR1) (Tronchere et al. 2004), 3 (MTMR3) (Walker et al. 2001, Lorenzo et al. 2005), 6 (MTMR6) (Schaletzky et al. 2003, Choudhury et al. 2006), and 14 (MTMR14) (Tosch et al. 2006).
At the plasma membrane, synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1 aka synaptojanin-1 (SYNJ1) (Guo et al. 1999, Mani et al. 2007) and -2 (SYNJ2) (Malecz et al. 2000) dephosphorylate phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) to phosphatidylinositol 3-phosphate (PI3P).
At the plasma membrane, Synaptojanin-1 (SYNJ1) and -2 (SYNJ2), inositol polyphosphate 5-phosphatase K (INPP5K) aka SKIP, phosphatidylinositol 4,5-bisphosphate 5-phosphatase A (INPP5J) aka PIPP dephosphorylate phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) to form phosphatidylinositol 4-phosphate (PI4P). SYNJ1/2 both have an N-terminal Sac1-like domain, a central 5-phosphatase domain and a C-terminal proline-rich segment, with this latter part being the most divergent part of the protein sequence. The following lists the above proteins with their corresponding literature references: SYNJ1 (Johenning et al. 2004, Haffner et al. 1997, Guo et al. 1999, Mani et al. 2007), SYNJ2 (Malecz et al. 2000), INPP5K (Injuin et al. 2000, Gurung et al. 2003), and INPP5J (Gurung et al. 2003, Mochizuki & Takenawa 1999).
At the Golgi membrane, phosphatidylinositol 4-phosphate (PI4P) is primarily generated from phosphorylation of phosphatidylinositol (PI). Other phosphoinositides are also generated by the action of various kinases and phosphatases such as: phosphatidylinositol 3-phosphate (PI3P), phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2), phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) (Godi et al. 1999, Minogue et al. 2001, Rohde et al. 2003, Sbrissa et al. 2007, Sbrissa et al. 2008, Domin et al. 2000, Arcaro et al. 2000).
At the plasma membrane, synaptojanin-1 aka Synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1 (SYNJ1) (Guo et al. 1999), -2 (SYNJ2) and some myotubularins (MTMs) dephosphorylate phosphatidylinositol 3-phosphate (PI3P) to phosphatidylinositol (PI). The MTMs involved are: myotubularin (MTM1) (Cao et al. 2007, Tronchere et al. 2004, Schaletzky et al. 2003, Laporte et al. 2002, Kim et al. 2002) and myotubularin-related proteins 1 (MTMR1) (Kim et al. 2002, Tronchere et al. 2004), 3 (MTMR3) (Kim et al. 2002, Zhao et al. 2001, Walker et al. 2001, Lorenzo et al. 2005), 6 (MTMR6) (Schaletzky et al. 2003, Kim et al. 2002, Choudhury et al. 2006), and 14 (MTMR14) (Tosch et al. 2006).
At the plasma membrane, phosphatidylinositol-5-phosphate 4-kinase type-2 alpha (PIP4K2A) and beta (PIP4K2B) homodimers and heterodimers (Clarke et al. 2010), along with phosphatidylinositol-4-phosphate 5-kinase type-1 alpha (PIP5K1A), beta (PIP5K1B), and gamma (PIP5K1C) phosphorylate phosphatidylinositol 3-phosphate (PI3P) to phosphatidylinositol 3,4-bisphosphate (PI(3,4)P2). The following lists the above proteins with their corresponding literature references: PIP4K2A (Zhang et al. 1997, Rameh et al. 1997, Clarke et al. 2008), PIP4K2B (Zhang et al. 1997, Rameh et al. 1997), PIP5K1A (Zhang et al. 1997, Tolias et al. 1998), PIP5K1B (Zhang et al. 1997, Tolias et al. 1998), and PIP5K1C (Wenk et al. 2001, Di Paolo et al. 2002).
Leptin in human physiology and therapeutics
At the Golgi membrane, phosphatidylinositide phosphatase SAC1 (SACM1L) dephosphorylates phosphatidylinositol 3-phosphate (PI3P) to phosphatidylinositol (PI) but not as efficiently as phosphatidylinositol 4-phosphate (PI4P) dephosphorylation. No significant activity of this enzyme towards phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) was detected (Rohde et al. 2003).
At the Golgi membrane, phosphatidylinositol 3-kinase catalytic subunit type 3 (PIK3C3) aka VPS34 is bound to phosphoinositide 3-kinase regulatory subunit 4 (PIK3R4). This PIK3C3:PIK2R4 complex and phosphatidylinositol-4-phosphate 3-kinase C2 domain-containing subunit alpha (PIK3C2A) phosphorylate phosphatidylinositol (PI) to phosphatidylinositol 3-phosphate (PI3P). The following lists the above proteins with their corresponding literature references: PIK3C3:PIK2R4 (Panaretou et al. 1997, Volinia et al. 1995) and PIK3C2A (Arcaro et al. 2000, Domin et al. 2000).
At the Golgi membrane, the PAS complex, consisting of FYVE finger-containing phosphoinositide kinase (PIKFYVE), yeast VAC14 homologue (VAC14), and polyphosphoinositide phosphatase aka SAC3 (FIG4), binds to the membrane via PIKFYVE's FYVE finger. The FIG4 phosphatase component dephosphorylates phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) to phosphatidylinositol 3-phosphate (PI3P) (Sbrissa et al. 2007, Sbrissa et al. 2008).
At the Golgi membrane, the PAS complex, consisting of FYVE finger-containing phosphoinositide kinase (PIKFYVE), yeast VAC14 homologue (VAC14), and polyphosphoinositide phosphatase aka SAC3 (FIG4), binds to the membrane via PIKFYVE's FYVE finger (Sbrissa et al. 2002). The PIKFYVE kinase component phosphorylates phosphatidylinositol 3-phosphate (PI3P) to phosphatidylinositol 3,5-bisphosphate PI(3,5)P2 (Sbrissa et al. 1999, McEwen et al. 1999). The PAS complex is present in the cytosol and is recruited to the membrane (Sbrissa et al. 2007). VAC14 acts as a scaffolding protein via its C-terminal domain (Sbrissa et al. 2008).
A dityrosyl-diiron radical cofactor center is essential for human ribonucleotide reductases
At the Golgi membrane, phosphatidylinositide phosphatase SAC1 (SACM1L) efficiently dephosphorylates phosphatidylinositol 4-phosphate (PI4P), and to a lesser extent phosphatidylinositol 3-phosphate (PI3P), to phosphatidylinositol (PI). No significant activity of this enzyme towards phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) was detected (Rohde et al. 2003).
At the Golgi membrane, phosphatidylinositol 4-kinase alpha (PI4KA) (Gehrmann et al. 1999, Godi et al. 1999), or phosphatidylinositol 4-kinase type 2-alpha/beta (PI4K2A/B) (Balla et al. 2002, Minogue et al. 2001, Wei et al. 2002) phosphorylate phosphatidylinositol (PI) to produce phosphatidylinositol 4-phosphate (PI4P).
At the endoplasmic reticulum (ER) membrane, phosphatidylinositol (PI) and phosphatidylinositol 4-phosphate (PI4P) are interconverted (Wong et al. 1997, Gehrmann et al. 1999, Wei et al. 2002, Rohde et al. 2003).
At the endoplasmic reticulum (ER) membrane, transmembrane protein phosphatidylinositide phosphatase SAC1 (SACM1L) efficiently dephosphorylates phosphatidylinositol 4-phosphate (PI4P), and to a lesser extent phosphatidylinositol 3-phosphate (PI3P), to phosphatidylinositol (PI). No significant activity of this enzyme towards phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) was detected (Rohde et al. 2003).
At the endoplasmic reticulum (ER) membrane, phosphatidylinositol 4-kinase alpha (PI4KA) (Wong et al. 1997, Gehrmann et al. 1999) or phosphatidylinositol 4-kinase type 2-beta (PI4K2B) (Wei et al. 2002) phosphorylate phosphatidylinositol (PI) to produce phosphatidylinositol 4-phosphate (PI4P).
Glycerophospholipids are important structural and functional components of biological membranes and constituents of serum lipoproteins and the pulmonary surfactant. In addition, glycerophospholipids act as precursors of lipid mediators such as platelet-activating factor and eicosanoids. Cellular membranes contains a distinct composition of various glycerophospholipids such as phosphatidic acid (PA), phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), phosphatidylglycerol (PG), phosphatidylinositol (PI), cardiolipin (CL), lysophosphatidic acid (LPA) and lysobisphosphatidic acid (also known as bis(monoacylglycerol) hydrogen phosphate - BMP). Glycerophospholipids are first formed by the de novo (Kennedy) pathway using fatty acids activated as acyl-CoA donors. However, the acyl groups of glycerophospholipids are highly diverse and distributed in an asymmetric manner. Saturated and monounsaturated fatty acids are usually esterified at the sn-1 position, whereas polyunsaturated acyl groups are esterified at the sn-2 position. Subsequent acyl chain remodeling (Lands cycle) generates the diverse glycerophospholipid composition and asymmetry characteristic of cell membranes. In the de novo pathway of glycerophospholipid biosynthesis, lysophosphatidic acid (LPA) is initially formed from glycerol 3-phosphate (G3P). Next, LPA is converted to PA by a LPA acyltransferase (AGPAT, also known as LPAAT), then PA is metabolized into two types of glycerol derivatives. The first is diacylglycerol (DAG) which is converted to triacylglycerol (TAG), PC, and PE. Subsequently, PS is synthesized from PC or PE. The second is cytidine diphosphate-diacylglycerol (CDP-DAG), which is processed into PI, PG, CL, and BMP. Each glycerophospholipid is involved in acyl chain remodeling via cleavage by phospholipases followed by reacylation by an acyltransferase. Most of the glycerophospholipids are synthesized at the endoplasmic reticulum (ER), however, some, most notably cardiolipin, and BMP are synthesized in the mitochondrial and endosomal membranes respectively. Since the most of the glycerophospholipids are found in all membrane compartments, there must be extensive network of transport of glycerophospholipids from one membrane compartment to another via various mechanisms including diffusion through the cytosol, formation of transportation complexes, and diffusion via membrane contact sites (MCS) (Osman et al. 2011, Lebiedzinska et al. 2009, Lev 2010, Scherer & Schmitz 2011, Orso et al. 2011, Hermansson et al. 2011, Vance & Vance 2008).
Repression of heat shock transcription factor HSF1 activation by HSP90 (HSP90 complex) that forms a stress-sensitive complex with HSF1
Acyl chain remodeling of cardiolipin (CL) occurs in the inner mitochondria membranes (IM) via hydrolysis by phopholipases and subsequent reacylation by acyltransferases. At the endoplasmic reticulum (ER) membrane the situation is more complicated with monolysocardiolipin (MLCL) involved in hydrolysis and subsequent reacylation back to CL (Zachman et al. 2010, Malhotra et al. 2009, Xu et al. 2003, Taylor & Hatch 2009, Cao et al. 2004, Zhao et al. 2009, Buckland et al. 1998).
At the endoplasmic reticulum (ER) membrane, lysocardiolipin acyltransferase 1 (LCLAT1) aka ALCAT1 acylates dilysocardiolipin (DLCL) to produce monolysocardiolipin (MLCL) (Zhao et al. 2009).
Eukaryotic methionyl aminopeptidases: two classes of cobalt-dependent enzymes
At the endoplasmic reticulum (ER) membrane, lysocardiolipin acyltransferase 1 (LCLAT1) aka ALCAT1 acylates monolysocardiolipin (MLCL) to cardiolipin (CL) (Cao et al. 2004, Zhao et al. 2009).
At the inner mitochondrial membrane (IM), tafazzin (TAZ) converts cardiolipin (CL) and 1-acyl lysophosphatidylethanolamine (LPE) to monolysocardiolipin (MLCL) and phosphatidylethanolamine (PE) (Xu et al. 2003, Xu et al. 2006, Malhotra et al. 2009).
Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics
The Mos/MAP kinase pathway stabilizes c-Fos by phosphorylation and augments its transforming activity in NIH 3T3 cells
At the inner mitochondrial membrane (IM), cardiolipin synthase (CRLS1) acylates 2-acyl lysophosphatidylglycerol (LPG) to form phosphatidylglycerol (PG) (Nie et al. 2010).
At the inner mitochondrial (IR) membrane, cardiolipin synthase (CRLS1) acylates 1-acyl lysophosphatidylglycerol (LPG) to form phosphatidylglycerol (PG) (Nie et al. 2010).
At the inner mitochondrial membrane (IM), cardiolipin synthase (CRLS1) converts phosphatidylglycerol (PG) and cytidine diphosphate-diacylglycerol (CDP-DAG) into cardiolipin (CL) (Lu et al. 2006, Houtkooper et al. 2006).
In the acyl chain remodelling pathway (Lands cycle), phosphatidylglycerol (PG) is hydrolyzed by phopholipases and subsequently reacylated by acyltransferases. These cycles modify the fatty acid composition of glycerophospholipids to generate diverse molecules asymmetrically distributed in the cell membrane. The events occur additionally in the inner mitochondria membranes (IM) as well as in the endoplasmic reticulum (ER) membrane (Ghomashchi et al. 2010, Singer et al. 2002, Cao et al. 2008, Yang et al. 2004, Nie et al. 2010).
At the inner mitochondrial membrane (IM), tafazzin (TAZ) converts monolysocardiolipin (MLCL) and phosphatidylcholine (PC) to cardiolipin (CL) and 1-acyl lysophosphatidylcholine (LPC) (Xu et al. 2003, Xu et al. 2006, Malhotra et al. 2009). Although this reaction is reversible, the net effect of the phospholipase A and acyltransferase reactions drives it towards the formation of LPC and CL.
Cardiolipin(CL) is synthesized in the inner mitochondrial membrane (IM), when phosphatidylglycerol (PG) and cytidine diphosphate-diacylglycerol (CDP-DAG) are converted into CL (Lu et al. 2006, Houtkooper et al. 2006).
At the inner mitochondrial membrane (IM), tafazzin (TAZ) converts monolysocardiolipin (MLCL) and phosphatidylethanolamine (PE) to cardiolipin (CL) and 1-acyl lysophosphatidylethanolamine (LPE) (Xu et al. 2003, Xu et al. 2006, Malhotra et al. 2009). Although this reaction is reversible, the net effect of the phospholipase A and acyltransferase reactions drives it towards the formation of LPE and CL.
At the inner mitochondrial membrane (IM), tafazzin (TAZ) converts cardiolipin (CL) and 1-acyl lysophosphatidylcholine (LPC) to monolysocardiolipin (MLCL) and phosphatidylcholine (PC) (Xu et al. 2003, Xu et al. 2006, Malhotra et al. 2009).
A missense mutation in SLC33A1, which encodes the acetyl-CoA transporter, causes autosomal-dominant spastic paraplegia (SPG42)
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The role of GRASP55 in Golgi fragmentation and entry of cells into mitosis
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Phosphatidylglycerol (PG) is synthesised at the inner mitochondrial (IM) membrane, phosphatidic acid (PA) and cytidine triphosphate (CTP) are converted into cytidine diphosphate-diacylglycerol (CDP-DAG), which in turn is converted with glycerol-3-phosphate (G3P) into phosphatidylglycerophosphate (PGP) and cytidine monophosphate (CMP). Finally, PGP is dephosphorylated to PG. In addition, PG can be synthesised at the endoplamic reticulum (ER) membrane when phospholipase D transphosphatidylates phosphatidylcholine (PC) with glycerol to displace choline (Cho) and form PG (Piazza & Marmer 2007, Stuhne-Sekalec et al. 1986, Lykidis et al. 1997, Cao & Hatch 1994).
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At the inner mitochondrial (IM) membrane, CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (PGS1) converts cytidine diphosphate-diacylglycerol (CDP-DAG) and glycerol-3-phosphate (G3P) to phosphatidylglycerophosphate (PGP) and cytidine monophosphate (CMP). This event is inferred from rats. The enzyme PGS1 has been characterized in humans (Ota et al. 2004).
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Induction of ceruloplasmin synthesis by IFN-gamma in human monocytic cells
Phosphatidylinositol (PI) is synthesized when phosphatidic acid (PA) and cytidine triphosphate (CTP) are converted into cytidine diphosphate-diacylglycerol (CDP-DAG) followed by conversion into PI and cytidine monophosphate (CMP) (Stuhne-Sekalec et al 1986, Lykidis et al. 1997).
At the endoplasmic reticulum (ER) membrane, CDP-diacylglycerol-inositol 3-phosphatidyltransferase (CDIPT) converts cytidine diphosphate-diacylglycerol (CDP-DAG) and inositol (Ins) into phosphatidylinositol (PI) and cytidine monophosphate (CMP) (Lykidis et al. 1997).
At the endoplasmic reticulum (ER) membrane, phosphatidate cytidylyltransferase 1 (CDS1) converts phosphatidic acid (PA) and cytidine triphosphate (CTP) into cytidine diphosphate-diacylglycerol (CDP-DAG). Both ER and mitochondrial membranes have the capability to synthesize cytidine diphosphate-diacylglycerol (CDP-DAG) with phosphatidate cytidylyltransferase 1 and 2 (CDS1 and CDS2) (Lykidis et al. 1997). However, transport of CDP-DAG between organelles cannot be ruled out (Stuhne-Sekalec et al. 1986).
In the acyl chain remodelling pathway (Lands cycle), phosphatidylserine (PS) is hydrolysed by phopholipases and subsequently reacylated by acyltransferases. These cycles modify the fatty acid composition of glycerophospholipids to generate diverse molecules asymmetrically distributed in the cell membrane (Ghomashchi et al. 2010, Singer et al. 2002, Cao et al. 2008; Hishikawa et al. 2008).
In the endoplasmic reticulum (ER) membrane, phospholipase D1-4,6 (PLD1-4,6) transphosphatidylates phosphatidylcholine (PC) with glycerol to displace choline (Cho) and form phosphatidylglycerol (PG). This reaction is inferred from rats, but PLD enzymes are present in humans (Hammond et al. 1995, Steed et al. 1998, Cao et al. 1997).
In the acyl chain remodelling pathway (Lands cycle), phosphatidylinositol (PI) is hydrolyzed by phospholipases and subsequently reacylated by acyltransferases. These cycles modify the fatty acid composition of glycerophospholipids to generate diverse molecules asymmetrically distributed in the cell membrane (Ghomashchi et al. 2010, Singer et al. 2002, Gijon et al. 2008, Lee et al. 2008).
At the endoplasmic reticulum (ER) membrane, lysophospholipid acyltransferase 7 (MBOAT7) aka LPIAT acylates 2-acyl lysophosphatidylinositol (LPI) to form phosphatidylinositol (PI) (Gijon et al. 2008, Lee et al. 2008).
At the endoplasmic reticulum (ER) membrane, lysophospholipid acyltransferase 7 (MBOAT7) aka LPIAT acylates 1-acyl lysophosphatidylinositol (LPI) to form phosphatidylinositol (PI) (Gijon et al. 2008, Lee et al. 2008).
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At the endoplasmic reticulum (ER) membrane, lysophospholipid acyltransferases acylate 2-acyl lysophosphatidylserine (LPS) to form phosphatidylserine (PS). The lysophospholipid acyltransferases involved are: lysophospholipid acyltransferase 5 (LPCAT3) (Gijon et al. 2008, Hishikawa et al. 2008); lysophospholipid acyltransferase LPCAT4 (LPCAT4) aka LPEAT2 (Cao et al. 2008); or lysophospholipid acyltransferase 1 (MBOAT1) aka LPEAT1 (Hishikawa et al. 2008, Gijon et al. 2008).
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At the inner mitochondrial (IM) membrane, phosphatidate cytidylyltransferase 2 (CDS2) converts phosphatidic acid (PA) and cytidine triphosphate (CTP) into cytidine diphosphate-diacylglycerol (CDP-DAG). Both ER and mitochondrial membranes have the capability to synthesise cytidine diphosphate-diacylglycerol (CDP-DAG) with phosphatidate cytidylyltransferase 1 and 2 (CDS1 and CDS2) (Lykidis et al. 1997, Schlame & Haldar 1993). However, transport of CDP-DAG between organelles cannot be ruled out (Stuhne-Sekalec et al. 1986).
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Phosphoinositide 3-kinase: the key switch mechanism in insulin signalling.
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A roller coaster ride with the mitotic cyclins
G(1) to S transition: more than a cell cycle engine switch.
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Unspecific permeation and specific exchange of adenine nucleotides in
Functional and molecular characterization of the human neutral solute channel aquaporin-9
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Genetic basis of mitochondrial HMG-CoA synthase deficiency
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Human airway epithelial cells sense Pseudomonas aeruginosa infection via recognition of flagellin by Toll-like receptor 5
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Characterization of the structure and function of a new mitogen-activated protein kinase (p38beta)
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In vitro SUMO-1 modification requires two enzymatic steps, E1 and E2
Biochem. Biophys. Res. Commun. 254:693-8
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Purine ribonucleoside monophosphate biosynthesis
DNA damage signaling and p53-dependent senescence after prolonged beta-interferon stimulation
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Regulation of Ras in lymphocytes: get a GRP
a-ketoisocaproate, a-keto b-methylvalerate, a-ketoisovalerate
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The quality control of MHC class I peptide loading
(2S)-2,6,10,14-tetramethylpentadecanoyl-coenzyme A
Negative regulation of condensin I by CK2-mediated phosphorylation
Molecular cloning and functional characterization of a novel mammalian sphingosine kinase type 2 isoform
Molecular cloning and expression of a cDNA for human kidney cysteine conjugate beta-lyase
Specificty of human and rat orthologs of the concentrative nucleoside transporter, SPNT
Cloning, genomic organization, and characterization of a human cholinephosphotransferase
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Biochemistry of signal transduction and regulation
Novel lipogenic enzyme ELOVL7 is involved in prostate cancer growth through saturated long-chain fatty acid metabolism
Changes in serotonin metabolism during treatment with the aldehyde dehydrogenase inhibitors disulfiram and cyanamide
RAF1-activated MEK1 is found on the Golgi apparatus in late prophase and is required for Golgi complex fragmentation in mitosis
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Morquio A syndrome: cloning, sequence, and structure of the human N-acetylgalactosamine 6-sulfatase (GALNS) gene
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Arteriosclerosis, Thrombosis, and Vascular Biology 28:e162
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Platelets in thrombotic and non-thrombotic disorders.
Identification of the gene encoding the enzyme deficient in mucopolysaccharidosis IIIC (Sanfilippo disease type C)
Purification and characterization of recombinant human liver glycolate oxidase
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Defective MMACHC causes methylmalonic aciduria and homocystinuria type cblC
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Coiled bodies contain U7 small nuclear RNA and associate with specific DNA sequences in interphase human cells.
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Ded1p, a DEAD-box protein required for translation initiation in Saccharomyces cerevisiae, is an RNA helicase.
The concentrative nucleoside transporter family, SLC28
At the beginning of this reaction, 1 molecule of 'NH4+', 1 molecule of 'HCO3-', and 1 molecule of 'ATP' are present. At the end of this reaction, 1 molecule of 'Carbamoyl phosphate', 1 molecule of 'ADP', and 1 molecule of 'Orthophosphate' are present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'carbamoyl-phosphate synthase (ammonia) activity' of 'carbamoyl-phosphate synthetase I dimer'.
A current review of fatty acid transport proteins (SLC27)
Three-dimensional structure of human erythrocytic purine nucleoside phosphorylase at 3.2 A resolution
Cytosolic Arginase 1 (ARG1) trimer catalyzes the hydrolysis of arginine to yield ornithine and urea (DiCostanzo et al. 2005). Patients expressing mutated forms of the enzyme with diminished in vitro arginase activity can accumulate arginine to pathogenic levels in the blood (e.g., Uchino et al. 1995).
Cytosolic argininosuccinate lyase (ASL) catalyzes the reversible reaction of argininosuccinate to form fumarate and arginine. The enzyme is a homotetramer (Turner et al. 1997). The function of the human enzyme in vivo is inferred from the defective argininosuccinate lyase enzyme activity observed in patients with mutant forms of the ASL gene (e.g., Walker et al. 1990).
Cytosolic argininosuccinate synthase catalyzes the reaction of aspartate, citrulline, and ATP to form argininosuccinate, AMP, and pyrophosphate. The function of the human enzyme in vivo is inferred from the hypercitrullinemia observed in patients with defective forms of the enzyme (e.g., Engel et al. 2009). The enzyme is active as a homotetramer (OâBrien 1980; Karlberg et al. 2008).
Structural and functional requirements for activity of the Tim9-Tim10 complex in mitochondrial protein import
Mitochondrial ornithine transcarbamoylase (OTC) catalyzes the reaction of ornithine and carbamoyl phosphate to form citrulline (Horwich et al. 1984). The enzyme is a homotrimer (Shi et al. 2001).
Demethylation of trimethylated histone H3 Lys4 in vivo by JARID1 JmjC proteins
The urea cycle yields urea, the major form in which excess nitrogen is excreted from the human body, and the amino acid arginine (Brusilow and Horwich 2001). It consists of four reactions: that of ornithine and carbamoyl phosphate to form citrulline, of citrulline and aspartate to form argininosuccinate, the cleavage of argininosuccinate to yield fumarate and arginine, and the cleavage of arginine to yield urea and re-form ornithine. The carbamoyl phosphate consumed in this cycle is synthesized in the mitochondria from bicarbonate and ammonia, and this synthesis in turn is dependent on the presence of N-acetylglutamate, which allosterically activates carbamoyl synthetase I enzyme. The synthesis of N-acetylglutamate is stimulated by high levels of arginine. Increased levels of free amino acids, indicated by elevated arginine levels, thus stimulate urea synthesis. Two enzymes catalyze the hydrolysis of arginine to yield ornithine and urea. Cytosolic ARG1 is the canonical urea cycle enzyme. Mitochondrial ARG2 likewise catalyzes urea production from arginine and may have a substantial sparing effect in patients lacking ARG1 enzyme, so its reaction is annotated here although the role of ARG2 under normal physiological conditions remains unclear.
Cytosolic serine hydroxymethyltransferase tetramer (SHMT1) catalyzes the reaction of 3-Hydroxy-N6,N6,N6-trimethyl-L-lysine to form glycine and 4-trimethylammoniobutanal (Hulse et al. 1978).
Arginase 2 (ARG2) trimer catalyzes the hydrolysis of arginine to form urea and ornithine (Cama et al. 2003). ARG2 is localized to the mitochondrion (Gotoh ea 1996). The enzyme is expressed in many tissues in addition to liver and while its function appears to mitigate the effects of ARG1 deficiency on urea synthesis, its normal physiological roles have not been fully defined (Iyer et al. 1998).
The mitochondrial ornithine transporters SLC25A15 and SLC25A2 mediate the exchange of cytosolic ornithine for citrulline from the mitochondrial matrix. SLC25A15 was the first protein shown to have this function, identified because mutations in the protein are associated with elevated levels of ammonia, ornithine, and citrulline in affected individuals (Camacho et al. 1999). The second transporter, SLC25A2, identified later, is also expressed in normal cells and their apparently partly redundant function may explain the relatively mild symptoms associated with SLC25A15 deficiency compared to other defects of the urea cycle (Fiermonte et al. 2003).
Cytosolic gamma-butyrobetaine hydroxylase dimer (BBOX1) catalyzes the reaction of oxygen, 4-trimethylammoniobutanoate, and 2-oxoglutarate to form C)2, succinate, and carnitine (Lindstedt and Nordin 1984; Vaz et al. 1998).
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Cytosolic indoleamine 2,3-dioxygenase (IDO) catalyzes the conversion of L-tryptophan and oxygen to formylkynurenine. The structure and catalytic properties of the human enzyme have been analyzed directly (Sugimoto et al. 2006); the subcellular location and monomeric state of the active form of the enzyme are inferred from the properties of its rabbit ortholog (Shimizu et al. 1976). In the body, IDO is ubiquitously expressed and is induced by interferon. These properties, together with IDO's broad substrate specificity, are consistent with the hypothesis that the enzyme functions functions in anti bacterial and inflammatory processes (Taylor and Feng 1991).
Proline is catabolized in two steps to yield L-glutamate gamma-semialdehyde, which can react further with glutamate to yield ornithine and alpha-ketoglutarate (annotated as a reaction of amino acid synthesis and interconversion) or with NAD+ to yield glutamate and NADH + H+ (Phang et al. 2001).
CCBL2 (KAT 3) catalyzes the reaction of kynurenine and pyruvate to form 4-(2-aminophenyl)-2,4-dioxobutanoate and alanine. CCBL2 is known only as the predicted protein product of a cloned human gene closely homologous to CCBL1 (Yu et al. 2006) and all of the structural and catalytic properties annotated here are inferred from those of CCBL1.
Cytosolic indoleamine 2,3-dioxygenase 2 (IDO2) catalyzes the conversion of L-tryptophan and oxygen to formylkynurenine. The catalytic properties of the human enzyme have been analyzed directly; the subcellular location and monomeric state of the active form of the enzyme are inferred from the properties of its rabbit ortholog. In the body, IDO2 mRNA can be detected in a variety of cells, including dendritic cells, consistent with a normal role in immune function and a pathological one in tumor progression. Two IDO2 variants common in human populations encode enzymatically inactive protiens, suggesting that absence of IDO2 activity may be common in humans (Metz et al. 2007).
Cytosolic kynurenine 3-monooxygenase catalyzes the reaction of L-kynurenine, NADPH + H+, and O2 to form 3-hydroxy-L-kynurenine, NADP+, and H2O.
Cytosolic kynureninase catalyzes the hydrolysis of 3-hydroxy-L-kynurenine to form L-alanine and 3-hydroxyanthranilate.
Cytosolic 3-hydroxyanthranilate oxygenase catalyzes the reaction of 3-hydroxyanthranilate and O2 to form 2-amino-3-carboxymuconate semialdehyde.
AADAT dimer localized in the mitochondrial matrix catalyzes the reaction of kynurenine and 2-oxoglutarate to form 4-(2-aminophenyl)-2,4-dioxobutanoate and glutamate (Han et al. 2008). Biochemical studies of kynurenine transamination in vitro invariably measure kynurenic acid, not 4-(2-aminophenyl)-2,4-dioxobutanoate, the expected transamination product. As noted by Miller et al. (1953), "The keto acid assumed to be formed prior to ring closure in the conversion of kynurenine to kynurenic acid has not yet been detected. In principle, such detection should be possible, since it is sufficiently stable to have been synthesized. It also remains to be established whether ring closure is spontaneous, enzymatic, or both. The formation of kynurenic acid from L-kynurenine by the L-amino acid oxidase of Neurospora suggests, however, that ring closure can be spontaneous, unless the somewhat improbable assumption is made that Neurospora filtrate contained the ring-closing enzyme."
Tryptophan is catabolized in seven steps to yield aminomuconate. Intermedistes in this process are used as well for the synthesis of serotonin and kynurenine (Peters 1991).
Mitochondrial N acetylglutamate synthetase (NAGS) catalyzes the reaction of glutamate and acetyl-CoA to form N-acetylglutamate and CoA. NAGS is activated by arginine and the N-acetylglutamate produced in the reaction in turn is required to activate carbamoyl synthetase I. Consistent with this regulatory role in urea synthesis, NAGS mutations in humans are associated with hyperammonemia (Caldovic et al. 2002; Morizono et al. 2004).
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Alanine-glyoxylate transaminase (AGXT) catalyzes the irreversible reaction of glyoxylate and alanine to form glycine and pyruvate (Danpure and Jennings 1988). The active form of the enzyme is a homodimer (Zhang et al. 2003) with one molecule of pyridoxal phosphate bound to each subunit (Coulter-Mackie et al. 2005). Mutations in this enzyme are associated with primary hyperoxaluria type I. Mutant alleles encode both catalytically inactive proteins and active ones that are mis-localized to mitochondria (Purdue et al. 1990; Takada et al. 1990).
Polyamines is a family of molecules (i.e. putrescine, spermine, spermidine) derived from ornithine according to a decarboxylation/condensative process. More recently, it has been demonstrated that arginine can be metabolised according to the same pathway leading to agmatine formation. Polyamines are essential for the growth, the maintenance and the function of normal cells. The complexity of their metabolism and the fact that polyamines homeostasis is tightly regulated support the idea that polyamines are essential to cell survival. Multiple abnormalities in the control of polyamines metabolism might be implicated in several pathological processes (Moinard et al., 2005). Legend for the following figure:
Methionine salvage is a sequential pathway of six reactions that create methionine from 5'-methylthioadenosine (MTA) which is a byproduct of polyamine biosynthesis in nearly all organisms. The process happens completely in the cytosol. It is important in humans for recycling of sulphur that has to be assimilated using energy. (Pirkov et al, 2008; Albers, 2009)
In the last step MOB gets transaminated to methionine. The reaction was confirmed in yeast, where several transaminases catalyze it, which appears to be also the case in rat. At the moment, the human enzymes involved are unknown but due to homology to the respective enzyme in the parasite Crithidia fasciculata we feel supported to state that human GOT is probably one of the involved transaminases. (Berger et al, 2001)
Acireducone (1,2-Dihydroxy-3-oxo-5'-methylthiopentene) is oxidized using acireductone dioxygenase and dioxygen. There are two reactions possible, dependent on the metal cofactor: the alternative product 3-methylthiopropionate using nickel was confirmed in Klebsiella. In eukaryotes using iron(II) the result is 4-methylthio-2-oxobutanoate (MOB). (Ju et al, 2006)
Acireductone synthase (also: enolase-phosphatase E1) catalyzes the dephosphorylation and conversion to enolate of 2,3-dioxo-5'-methylthiopentane-1-phosphate, yielding acireductone. (Wang et al, 2005)
The human enzyme with 5'-methylthio ribulose-1-phosphate isomerase activity is probably produced from the APIP gene, according to its orthology with the yeast Mde1p enzyme.
Gap-filling DNA repair synthesis and ligation in TC-NER
Peroxisomal hydroxyacid oxidase 1 catalyzes the reaction of glyoxylate to form oxalate. The active form of the enzyme is associated with FMN and is a tetramer (Jones et al. 2000; Murray et al. 2008; Vignaud et al. 2007; Williams et al. 2000).
Peroxisomal GRHPR catalyzes the reaction of glyoxylate and NADPH + H+ to form glycolate and NADP+. The active form of the enzyme is a monomer (Rumsby and Cregeen 1999); mutations in it are associated with primary hyperoxaluria type II (Cramer et al. 1999).
Peroxisomal hydroxyacid oxidase 1 catalyzes the reaction of glycolate and O2 to form glyoxylate and H2O2. The active form of the enzyme is associated with FMN and is a tetramer (Jones et al. 2000; Murray et al. 2008; Vignaud et al. 2007; Williams et al. 2000).
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ErbB-3 and ErbB-4 function as the respective low and high affinity receptors of all Neu differentiation factor/heregulin isoforms
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Agmatine is an amine that is formed by decarboxylation of L-arginine by the enzyme arginine decarboxylase (ADC) and hydrolyzed by the enzyme agmatinase to putrescine. Agmatine binds to several target receptors in the brain and has been proposed as a novel neuromodulator (Reghunathan 2006). Agmatine has the potential to serve in the coordination of the early and repair phase pathways of arginine in inflammation (Satriano, 2003).
As it hydrolyzes a guanidino group within agmatine and also contains signature amino acid residues that act as ligand binding sites for the potential Mn(++) cofactor, agmatinase is classified as a member of the arginase superfamily (Morris, 2003).
S-Adenosylmethionine decarboxylase belongs to a small class of amino acid decarboxylases that use a covalently bound pyruvate as a prosthetic group. It is an essential enzyme for polyamine biosynthesis and provides an important target for the design of anti-parasitic and cancer chemotherapeutic agents. It catalyzes the formation of the aminopropyl group donor in the biosynthesis of the polyamines spermidine and spermine. These pyruvoyl-dependent decarboxylases also form amines such as histamine, decarboxylated S-adenosylmethionine, phosphatidylethanolamine (a component of membrane phospholipids), and -alanine (a precursor of coenzyme A), which are all of critical importance in cellular physiology and provide important targets for drug design.
L-ornithine is converted into putrescine by ODC holoenzyme complex.Putrescine is subsequent used for polyamine synthesis.
Toward the full set of human mitochondrial aminoacyl-tRNA synthetases: characterization of AspRS and TyrRS
Agmatine is polyamine formed by decarboxylation of L-arginine by arginine decarboxylase (ADC). Human ADC is a 460-amino acid protein that shows about 48% identity to mammalian ornithine decarboxylase (ODC) but has no ODC activity.
Carnitine is synthesized in four steps from trimethyllysine (generated in turn by the S-adenosyl-methionine-mediated methylation of lysine residues in proteins, followed by protein hydrolysis). The enzymes that catalyze the first three steps of carnitine synthesis, converting trimethyllysine to gamma-butyrobetaine, are widely distributed in human tissues. The enzyme that catalyzes the last reaction, converting gamma-butyrobetaine to carnitine, is found only in liver and kidney cells, and at very low levels in brain tissues. Other tissues that require carnitine, such as muscle, are dependent on transport systems that mediate its export from the liver and uptake by other tissues (Kerner and Hoppel 1998).
Common origin and evolution of glycosyltransferases using Dol-P-monosaccharides as donor substrate
Spermidine synthase is one of four enzymes in the polyamine-biosynthetic pathway and carries out the final step of spermidine biosynthesis. This enzyme catalyzes the conversion of putrescine to spermidine using decarboxylated S-adenosylmethionine as the cofactor.
MTA phosphorylase catalyzes the cleavage of adenine from S-methylthioadenosine (MTA) and subsequent phosphorylation of the product, yielding 5'-methylthio ribose-1-phosphate (Kamatani et al. 1981). The active form of the enzyme is a homotrimer (Della Ragione et al. 1985). Mutations in the gene are associated with a rare bone dysplasia and cancer syndrome, DMS-MFH (Camacho-Vanegas et al. 2012).
Equilibrium between 5'-methylthio ribose-1-phosphate and 5'-methylthio ribulose-1-phosphate is catalyzed by 5'-methylthio ribose-1-phosphate isomerase. (Kabuyama et al, 2009)
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While in humans excess methionine is converted to homocysteine, homocysteine and its transsulfuration product cysteine can be degraded to several end products, two of which, taurine and hydrogen sulfide, have uses in other biological processes (Stipanuk & Ueki 2011).
The main sulfur amino acids are methionine, cysteine, homocysteine and taurine. Of these, the first two are proteinogenic. This group of reactions contains all processes that 1) break down sulfur amino acids, 2) interconvert between them, and 3) synthesize them from solved sulfide which comes from sulfate assimilation and reduction. Only plants and microorganisms employ all processes. Humans cannot de novo synthesize any sulfur amino acid, nor convert cysteine to methionine (Brosnan & Brosnan, 2006).
Aquaporins: highways for cells to recycle water with the outside world
Sulfate leaves the mitochondrion with the help of the dicarboxylate carrier, via antiport with malate (Crompton et al. 1974, Fiemont et al. 1999)
While the human body is very economical with sulfur amino acids (SAA), superfluous SAA are degraded via cysteine to toxic hydrogen sulfide which must be dealt with. The pathway to oxidize this gas is localized to mitochondria and is highly conserved, pointing back to a time when life was immersed in sulfide-rich waters. The pathway for sulfide oxidation consists of five reactions, one of which, the sulfur transfer from thiosulfate to glutathione, is still to be characterized fully. A mutation in one enzyme has been identified that is associated with ethylmalonyl encephalopathy and where tissue sulfide is elevated (Stipanuk & Ueki 2011).
Lead binds to ALAD enzyme displacing half the zinc ions essential for its catalytic activity and inactivating it. Lead is a major environmental toxin and this enzyme is one of its principal molecular targets (Jaffe et al. 2001).
5-Aminolevulinic acid dehydratase (ALAD aka porphobilinogen synthase, PBGS), catalyzes the asymmetric condensation of two molecules of ALA to form porphobilinogen (PBG). The substrate that becomes the acetyl side chain-containing half of PBG is called A-side ALA; the half that becomes the propionyl side chains and the pyrrole nitrogen is called P-ALA (Jaffe 2004). PBG is the first pyrrole formed, the precursor to all tetrapyrrole pigments such as heme and chlorophyll. There are at least eight bonds that are made or broken during this reaction. The active form of the ALAD enzyme is an octamer complexed with eight Zn2+ ions, four that are strongly bound and four that are weakly bound. The four weakly bound ones are dispensible for enzyme activity in vitro (Bevan et al. 1980; Mitchell et al. 2001). Deficiencies of ALAD enzyme in vivo are associated with 5-aminolevulinate dehydratase-deficient porphyria (e.g., Akagi et al. 2000).
This group of reactions is responsible for: 1) the breakdown of amino acids; 2) the synthesis of urea from ammonia and amino groups generated by amino acid breakdown; 3) the synthesis of the ten amino acids that are not essential components of the human diet; and 4) the synthesis of related nitrogen-containing molecules including carnitine and creatine. Transport of these molecuels across lipid bilayer membranes is annotated separately as part of the module on "transmembrane transport of small molecules".
Analysis of nucleocytoplasmic shuttling of NF kappa B proteins in human leukocytes
The committed step for porphyrin synthesis is the formation of 5-aminolevulinate (ALA) by condensation of glycine (from the general amino acid pool) and succinyl-CoA (from the TCA cycle), in the mitochondrial matrix. The reaction is catalyzed by two different ALA synthases, one expressed ubiquitously (ALAS1) and the other only expressed in erythroid precursors (ALAS2). Both enzymes are expressed as homodimers and require pyridoxal 5-phosphate as a cofactor. No disease-causing mutations of ALAS1 have been recognised in humans. Mutations in ALAS2 cause X-linked sideroblastic anaemia (XLSA), characterised by a microcytic hypochromic anaemia.
Excess homocysteine will change the enzymatic activity of CBS such that other reactions than transsulfuration take place. In these reactions, oxobutanoate, lanthionine, and homolanthionine are produced by cystathionine gamma-lyase (CTH) (Chiku et al. 2009, Steegborn et al. 1999)
Cytosolic porphobilinogen deaminase catalyzes the polymerization of four molecules of porphobilinogen (PBG) to generate hydroxymethylbilane (HMB), an unstable tetrapyrrole. This reaction is the first step in the formation of the tetrapyrrole macrocycle. Two isoforms of porphobilinogen deaminase are generated by alternative splicing, one expresssed in erythroid tissues and one ubiquitously expressed in the body. Deficiencies of both forms of PBG deaminase are associated with acute intermittent porphyria.
Functional analysis of the purified anandamide-generating phospholipase D as a member of the metallo-beta-lactamase family
Glyoxylate is generated in the course of glycine and hydroxyproline catabolism and can be converted to oxalate. In humans, this process takes place in the liver. Defects in two enzymes of glyoxylate metabolism, alanine:glyoxylate aminotransferase (AGXT) and glycerate dehydrogenase/glyoxylate reductase (GRHPR), are associated with pathogenic overproduction of oxalate (Danpure 2005). The reactions that interconvert glycine, glycolate, and glyoxylate and convert glyoxylate to oxalate have been characterized in molecular detail in humans. A reaction sequence for the conversion of hydroxyproline to glyoxylate has been inferred from studies of partially purified extracts of rat and bovine liver but the enzymes involved in the corresponding human reactions have not been identified.
S-adenosylmethionine (SAM) is an essential metabolite in all cells. SAM is a precursor in the synthesis of polyamines. Methionine adenosyltransferase (MAT; EC 2.5.1.6) catalyzes the only known SAM biosynthetic reaction from methionine and ATP. In mammalian tissues, three different forms of MAT (MAT I, MAT III and MAT II) have been identified that are the product of two different genes (MAT1A and MAT2A). A third gene MAT2B has been identified and is known to be a part of MAT II heterotetramer complex.
At the beginning of this reaction, 1 molecule of 'S-adenosylhomocysteine', and 1 molecule of 'H2O' are present. At the end of this reaction, 1 molecule of 'adenosine', and 1 molecule of 'Homocysteine' are present. This reaction takes place in the 'cytosol' and is mediated by the 'adenosylhomocysteinase activity' of 'SAH hydrolase homotetramer'.
The first step of homocysteine conversion to cysteine is catalyzed by cystathionine beta-lyase, which adds a serine molecule to the substrate. The enzyme is a tetramer with two heme molecules as cofactor (Janosik et al. 2001).
Cystathionine is cleaved to cysteine, oxobutanoate, and ammonia by the alpha,gamma-elimination activity of cystathionine gamma-lyase (CTH) (Chiku et al. 2009, Steegborn et al. 1999).
Transsulfuration is the interconversion of homocysteine and cysteine, and it fully takes place in bacteria and some plants and fungi. Animals however have only one direction of this bidirectional path, the synthesis of cysteine from homocysteine via cystathionine. Because excess cysteine is degraded to hydrogen sulfide, which is now known as a neuromodulator and smooth muscle relaxant, this pathway is also the main source of its production, which takes place in the cytosol, as well as in extracellular space (Dominy & Stipanuk 2004, Bearden et al. 2010).
A cytosolic, non-specific peptidase can hydrolyze cysteinylglycine to release cysteine and glycine (Tuefel et al, 2003).
Characterization of human glucose transporter (GLUT) 11 (encoded by SLC2A11), a novel sugar-transport facilitator specifically expressed in heart and skeletal muscle
Role of human mitochondrial Nfs1 in cytosolic iron-sulfur protein biogenesis and iron regulation
PIG-W is critical for inositol acylation but not for flipping of glycosylphosphatidylinositol-anchor
alpha,beta-elimination activity of cystathionine-gamma-lyase (CTH) replaces the sulfur in cysteine with oxygen from water, resulting in serine and toxic hydrogen sulfide, which is further oxidized in mitochondria (Chiku et al. 2009, Steegborn et al. 1999).
The chromosomal association of condensin II is regulated by a noncatalytic function of PP2A
Heme O and heme A are specifically synthesised for the heme-copper respiratory oxidases. Mitochondrial protoheme IX farnesyltransferase (COX10) mediates the transformation of protoheme IX (heme) and farnesyl diphosphate (FAPP) to heme O (Glerum & Tzagoloff 1994). COX10 is highly expressed in muscle, heart and brain (Murakami et al. 1997).
Heme A is the prosthetic group of cytochrome c oxidase, the terminal enzyme in the respiratory chain. It is formed by the action of cytochrome c oxidase assembly protein COX15 homolog (COX15) on heme O (Petruzzella et al. 1998, Antonicka et al. 2003). Defects in COX15 cause of mitochondrial complex IV deficiency (MT-C4D; MIM:220110), also called cytochrome c oxidase deficiency resulting in a disorder of the mitochondrial respiratory chain seen as heterogeneous clinical manifestations, ranging from isolated myopathy to severe multisystem disease affecting several tissues and organs (Antonicka et al. 2003). Defects in COX15 also cause Leigh syndrome (LS; MIM:256000), an early-onset progressive neurodegenerative disorder characterised by the presence of focal, bilateral lesions in one or more areas of the central nervous system (Oquendo et al. 2004, Bugiani et al. 2005).
Eight enzymes are involved in heme biosynthesis, four each in the mitochondria and the cytosol. The process starts in the mitochondria with the condensation of succinyl CoA (from the TCA cycle) and glycine to form 5-aminolevulinate (ALA). The next four steps take place in the cytosol. Two molecules of ALA are condensed to form the monopyrrole porphobilinogen (PBG). The next two steps convert four molecules of PBG into the cyclic tetrapyrrole uroporphyringen III, which is then decarboxylated into coproporphyrinogen III. The last three steps occur in the mitochondria and involve modifications to the tetrapyrrole side chains and finally, insertion of iron. In addition to these synthetic steps, a spontaneous cytosolic reaction allows the formation of uroporphyringen I which is then enzymatically decarboxylated to coproporphyrinogen I, which cannot be metabolized further in humans. Also, lead can inactivate ALAD, the enzyme that catalyzes PBG synthesis, and ferrochelatase, the enzyme that catalyzes heme synthesis. The porphyrias are disorders that arise from defects in the enzymes of heme biosynthesis. Defective pathway enzymes after ALA synthase result in accumulated substrates which can cause either skin problems, neurological complications, or both due to their toxicity in higher concentrations. They are broadly classified as hepatic porphyrias or erythropoietic porphyrias, based on the site of the overproduction of the substrate. Each defect is described together with the reaction it affects.
Porphyrins are heterocyclic macrocycles, consisting of four pyrrole subunits (tetrapyrrole) linked by four methine (=CH-) bridges. The extensive conjugated porphyrin macrocycle is chromatic and the name itself, porphyrin, is derived from the Greek word for purple. The aromatic character of porphyrins can be seen by NMR spectroscopy. Porphyrins readily combine with metals by coordinating them in the central cavity. Iron (heme) and magnesium (chlorophyll) are two well known examples although zinc, copper, nickel and cobalt form other known metal-containing phorphyrins. A porphyrin which has no metal in the cavity is called a free base. Some iron-containing porphyrins are called hemes (heme-containing proteins or hemoproteins) and these are found extensively in nature ie. hemoglobin. Hemoglobin is quantitatively the most important hemoprotein. The hemoglobin iron is the transfer site of oxygen and carries it in the blood all round the body for cell respiration. Other examples are cytochromes present in mitochondria and endoplasmic reticulum which takes part in electron transfer events, catalase and peroxidase whic protect the body against the oxidant hydrogen peroxide and tryptophan oxygenase which is present in intermediary metabolism. Hemoproteins are synthesized in all mammalian cells and the major sites are erythropoietic tissue and the liver. The processes by which heme is synthesized, transported, and metabolized are a critical part of human iron metabolism (Severance and Hamze 2009); here the core processes of heme biosynthesis and catabolism have been annotated.
Cytosolic uroporphyrinogen decarboxylase (UROD) catalyzes the sequential removal of four carboxylic groups from the acetic acid side chains of uroporphyrinogen I (URO1) to form coproporphyrinogen I (COPRO1). UROD catalyzes this reaction less efficiently than the decarboxylation of uroporphyrinogen III (de Verneuil et al. 1983).
O2-dependent coproporpyrinogen oxidase (CPO) catalyzes the conversion of coproporphyrinogen III (COPRO3) to protoporphyrinogen IX (PPGEN9). The localization of the human enzyme to the mitochondrial intermembrane space is inferred from studies of the homologous rat enzyme (Elder and Evans 1978). The human enzyme functions as a homodimer (Lee et al. 2005). Enzyme deficiency is associated with hereditary coproporphyria in vivo.
Six electrons are oxidized in protophorphyrinogen IX (PPGEN9) to form the planar macrocycle protoporphyrin IX (PRIN9). This reaction is performed by the enzyme protoporphyrinogen oxidase (PPO). PPO functions as a homodimer containing one non-covalently-bound FAD. The protein resides on the outer surface of the inner mitochondrial membrane. PPO deficiency is associated with variegate porphyria in vivo.
Ferrochelatase (FECH) catalyzes the insertion of ferrous iron into protoporphyrin IX (PRIN9) to form heme. FECH is localized on the matrix surface of the inner mitochondrial membrane and this reaction takes place within the mitochondrial matrix. The enzyme functions as a homodimer with each monomer containing a nitric oxide-sensitive 2Fe-2S cluster. Enzyme deficiency is associated with erythropoietic protoporphyria in vivo, and inhibition of ferrochelatase activity is a clinically important consequence of lead poisoning (Piomelli et al. 1987).
Signalling functions and biochemical properties of pertussis toxin-resistant G-proteins
Cytosolic uroporphyrinogen III synthase (URO3S) catalyzes the conversion of HMB (hydroxymethylbilane) to uroporphyrinogen III, a reaction involving ring closure and intramolecular rearrangement. Uroporphyrinogen III represents a branch point for the pathways leading to formation of heme, chlorophyll and corrins. HMB is rapidly converted from a linear tetrapyrrole to the cyclic form. Deficiencies of URO3S in vivo are associated with congenital erythropoietic porphyria.
Cytosolic uroporphyrinogen decarboxylase (UROD) catalyzes the sequntial removal of four carboxylic groups from the acetic acid side chains of uroporphyrinogen III (URO3) to form coproporphyrinogen III (COPRO3) (de Verneuil et al. 1983). Human UROD is a dimer (Whitby et al. 1998). Heterogenous and homogenous deficiencies of UROD are associated with porphyria cutanea tarda and hepatoerythropoietic porphyria respectively in vivo (Moran-Jiminez et al. 1996).
Conversion of GABA to Succinate Semialdehyde
Loading of GABA into clathrin sculpted GABA transport vesicle lumen
MISCELLANEOUS Present with 45300 molecules/cell in log phase SD medium.SIMILARITY Belongs to the Tom70 family.SIMILARITY Contains 9 TPR repeats.
5-hydroxyindole acetaldehyde to 5-hydroxyindole acetic acid
Conversion of succinate semialdehyde to succinate
glutamate + NH4+ + ATP => glutamine + ADP + orthophosphate [GLUL]
20 kDa nuclear cap binding protein (NCBP 20 kDa subunit) (CBP20) (NCBP interacting protein 1) (NIP1)
Serine/threonine-protein kinase/endoribonuclease IRE1 (phosphorylated)
Eukaryotic peptide chain release factor subunit 1
Cleavage and polyadenylation specificity factor, 160 kDa subunit
Cleavage and polyadenylation specificity factor, 73 kDa subunit
Cleavage and polyadenylation specificity factor, 100 kDa subunit
80 kDa nuclear cap binding protein (NCBP 80 kDa subunit) (CBP80)
SOD1 catalyzes 2H+ + O2.- => O2 + H2O2 (mitochondrial intermembrane space)
SOD1 catalyzes 2H+ + 2O2.- => O2 + H2O2 (cytosol)
CCS transfers Cu to SOD1 (mitochondrial)
SOD1 apoenzyme binds CCS:Cu1+ (mitochondrial)
Signal transduction by the neurotrophin receptors
GSR catalyzes glutathione (oxidized) + NADPH + H+ => 2 glutathione (reduced) + NADP+
GPX1 catalyzes 2 glutathione, reduced + H2O2 => glutathione, oxidized + 2 H2O
H2O2 diffuses from the mitochondrial matrix to the cytosol
SOD2 catalyzes 2H+ + 2O2.- => O2 + H2O2 (mitochondrial matrix)
The mitochondrial processing peptidase behaves as a zinc-metallopeptidase
Mitochondrial import of the ADP/ATP carrier: the essential TIM complex of the intermembrane space is required for precursor release from the TOM complex
Sphingosine kinase mediates vascular endothelial growth factor-induced activation of ras and mitogen-activated protein kinases
(GlcN)1 (Ino(acyl)-P)1 (Man)2 (EtN)1 (P)1
6-O-{alpha-D-mannosyl-(1->2)-alpha-D-mannosyl-(1->6)-2-O-[(2-aminoethyl)phosphoryl]-alpha-D-mannosyl-(1->4)-alpha-D-glucosaminyl}-O-acyl-1-phosphatidyl-1D-myo-inositol [ChEBI:53059]
Transfer of SUMO3 from E1 to UBE2I (UBC9)
6-O-[alpha-D-mannosyl-(1->4)-alpha-D-glucosaminyl]-O-acyl-1-phosphatidyl-1D-myo-inositol [ChEBI:53056]
TIMM23 PAM translocates proteins from the mitochndrial intermebrane space to the mitochondrial matrix
TIMM23 SORT inserts proteins into inner membrane
ZnT5 transports zinc into secretory granules in pancreatic beta cells
Phagocytosis of retinal rod and cone photoreceptors
M-phase inducer phosphatase 2 (EC 3.1.3.48) (Dual specificity phosphatase Cdc25B)
Diversification of Neu differentiation factor and epidermal growth factor signaling by combinatorial receptor interactions
Cell division protein kinase 7 (EC 2.7.1.-) (CDK-activating kinase) (CAK)(TFIIH) (basal transcription factor complex kinase subunit) (39 kDa protein kinase) (P39 Mo15)(STK1)(CAK1)
TFIIH basal transcription factor complex kinase subunit
CDK-activating kinase assembly factor MAT1
CDK-activating kinase assembly factor MAT1 (RING finger protein MAT1) (Menage a trois) (CDK7/cyclin H assembly factor) (p36) (p35) (Cyclin G1 interacting protein)
D-Fructose 1,6-bisphosphate [ChEBI:16905]
SUBUNIT F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c.MISCELLANEOUS Present with 41500 molecules/cell in log phase SD medium.SIMILARITY Belongs to the ATPase alpha/beta chains family.
Tuberculosis - metabolism and respiration in the absence of growth
M-phase inducer phosphatase 3 (EC 3.1.3.48) (Dual specificity phosphatase Cdc25C)
A microRNA polycistron as a potential human oncogene
Regulation of deoxyadenosine and nucleoside analog phosphorylation by human placental adenosine kinase
Activation of the transcription factor MEF2C by the MAP kinase p38 in inflammation
ChEBI:53020 (Glc)2 (GlcNAc)2 (Man)9 (PP-Dol)1
Recruitment of RNA polymerase III to its target promoters.
Catalysis and function of the p38 alpha.MK2a signaling complex
Steroidogenic electron transport in adrenal cortex mitochondria
ribose 1-phosphate, deoxyribose 1-phosphate
Serine/threonine-protein kinase Chk2 (EC 2.7.1.-) (Cds1)
Acyl-CoA:lysophospholipid acyltransferases
ChEBI:53019 (Glc)3 (GlcNAc)2 (Man)9 (PP-Dol)1
Tyrosine-phosphorylated Vav1 as a point of integration for T-cell receptor- and CD28-mediated activation of JNK, p38, and interleukin-2 transcription
Serine/threonine-protein kinase Chk1 (EC 2.7.1.-)
Re-addition of a glucose on the alpha 1,3 branch
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Trimming of the second mannose on the A branch
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Glycoproteins with major folding defects are sent to degradation by EDEMs
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Cargo, Sec31p:Sec13p, and v-SNARE recruitment
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Molecular cloning and nucleotide sequence of a full-length cDNA for human alpha enolase
Trimming of the terminal mannose on the C branch
Trimming of the first mannose on the A branch
Trimming of the first glucose by glucosidase I
Trimming of the terminal mannose on the B branch
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Addition of the last mannose to the N-glycan precursor by ALG9
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Addition of the eighth mannose to the N-glycan precursor by ALG12
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Addition of the seventh mannose to the N-glycan precursor by ALG9
Addition of the sixth mannose to the N-glycan precursor by ALG3.
Addition of a third glucose to the N-glycan precursor by an ALG10 homologue
Addition of a second glucose to the N-glycan precursor by ALG8
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Addition of the first glucose to the N-glycan precursor by ALG6
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Addition of a fourth and fifth mannose to the N-glycan precursor by ALG11
ALG11 transfers the fourth and fifth Man to the N-glycan precursor
Flipping of the N-glycan precursor to inside the ER
Cdc25A stability is controlled by the ubiquitin-proteasome pathway during cell cycle progression and terminal differentiation
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Addition of the second N-acetyl-glucosamine to the N-glycan precursor
Newly made phosphatidylserine and phosphatidylethanolamine are preferentially translocated between rat liver mitochondria and endoplasmic reticulum
Addition of N-acetyl-D-glucosamine to Dolichyl phosphate
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Addition of a second mannose to the N-glycan precursor by ALG2
Addition of the first mannose to the N-glycan precursor by ALG1
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Mannose 6-phosphate isomerizes to Mannose 1-phosphate
D-Glucono-1,5-lactone 6-phosphate [ChEBI:16938]
Fructose 6-phosphate isomerizes to Mannose 6-phosphate
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Mannose-1-phosphate converted to GDP-Mannose
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GlcNAc1P is dephosphorylated to UDP-N-acetyl-glucosamine
Formation of glucosamine 6-phosphate from fructose 6-phosphate and glutamine
GFPT1,2 transfer an amino group from L-Gln to F6P to form GlcN6P
Cleavage of oxidized guanine nucleotide and ADP sugar by human NUDT5 protein
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DHDDS elongates E,E-FPP with (n)IPPP to form pPPP
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Mevalonate-5-pyrophosphate is decarboxylated
sn-Glycero-3-phosphoethanolamine [ChEBI:10647]
(ethanolamineP) mannose (a1-2) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI -> (ethanolamineP) mannose (a1-2) (ethanolamineP) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI
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mannose (a1-2) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI + phosphatidylethanolamine -> (ethanolamineP) mannose (a1-2) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI (acyl-GPI) + diacylglycerol
N6-(L-1,3-Dicarboxypropyl)-L-lysine [ChEBI:16927]
mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI + dolichol phosphate D-mannose -> mannose (a1-2) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI + dolichol phosphate
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Acetylation of glucosamine 6-phosphate to GlcNAc6P
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DNA polymerase alpha holoenzyme-associated protein P1
mannose(a1-4)glucosaminyl-acyl-PI + phosphatidylethanolamine -> (ethanolamineP) mannose(al1-4)glucosaminyl-acyl-PI + diacylglycerol
N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate
glucosaminyl-PI + fatty acyl-CoA -> glucosaminyl-acyl-PI + CoA-SH
Nitric oxide synthase (NOS) produces NO from L-arginine. There are three isoforms of NOS, endothelial, neuronal and inducible (eNOS, nNOS, and iNOS). eNOS and nNOS are constitutively expressed while iNOS is induced by immunostimulatory signals. The constitutive isoforms are regulated in vivo by the binding of calcium and calmodulin. NO produced by NOS acts as a signalling molecule by diffusing across cell membranes to activate soluble guanylate cyclase (sGC).
Cyclic GMP phosphodiesterase are hydrolases selective for cAMP (PDE4, 7 and 8), cGMP (PDE5, 6 and 9) or able to hydrolyse both cAMP and cGMP (PDE1, 2, 3, 10 and 11). Â The dual-specificity PDEs allow for cross-regulation of the cAMP and cGMP pathways, e.g. PDE2 can hydrolyse both, but binding of cGMP to the regulatory GAF-B domain increases cAMP affinity and hydrolysis. PDE2, 3 and 5 are expressed in platelets.
Cyclic guanosine monophosphate (cGMP) is an important secondary messenger synthesized by guanylate cyclases. cGMP has effects on phosphodiesterases (PDE), ion-gated channels, and the cGMP-dependent protein kinases (cGK, Protein Kinase G or PKG). It is involved in regulation of several physiological functions including vasodilation, platelet aggregation and neurotransmission. Elevation of intracellular cGMP activates PKG (Haslam et al. 1999) which regulates several intracellular molecules and pathways including the vasodilator-stimulated phosphoprotein (VASP) (Halbrugge et al. 1990) and the ERK pathway (Hood and Granger 1998, Li et al. 2001). cGMP mediates nitric oxide (NO)-induced vascular smooth muscle relaxation (Furchgott and Vanhoutte 1989). Phosphodiesterase 5 (PDE5) hydrolyzes cGMP; the PDE5 inhibitor sildenafil (Viagra) increases intracellular cGMP and thereby can be used as a treatment for erectile dysfunction (Corbin and Francis 1999). The role of the cGMP and PKG in platelet activation was controversial as increases in platelet cGMP levels were observed in response to both platelet agonists (thrombin, ADP or collagen) and inhibitors (NO donors such as sodium nitroprusside), but it is currently accepted that PKG inhibits platelet activation (Haslam et al. 1999). Consistent with this, nitric oxide (NO) donors that inhibit platelet activation enhance intracellular cGMP (Haslam et al. 1999). cGMP also plays an important stimulatory role in GPIb-IX-mediated platelet activation. Platelet responses to cGMP have been proposed to be biphasic, consisting of an early stimulatory response that promotes platelet activation followed by a delayed platelet inhibition that serves to limit the size of platelet aggregates (Li et al 2003).
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Actin/tubulin:prefoldin complex associates with CCT/TriC
Nitric Oxide (NO) inhibits smooth muscle cell proliferation and migration, oxidation of low-density lipoproteins, and platelet aggregation and adhesion. It can stimulate vasodilatation of the endothelium, disaggregation of preformed platelet aggregates and inhibits activated platelet recruitment to the aggregate. NO is synthesized from L-arginine by a family of isoformic enzymes known as nitric oxide synthase (NOS). Three isoforms, namely endothelial, neuronal, and inducible NOS (eNOS, nNOS, and iNOS, respectively), have been identified. The eNOS isoform is found in the endothelium and platelets. NO regulation of cyclic guanosine-3,5-monophosphate (cGMP), via activation of soluble guanylate cyclase, is the principal mechanism of negative control over platelet activity. Defects in this control mechanism have been associated with platelet hyperaggregability and associated thrombosis.
ADP is exchanged for ATP in the (ADP:CCT/TriC):tubulin complex
The plasma membrane Ca-ATPases 1-4 (ATP2B1-4, PMCAs) are P-type Ca2+-ATPases regulated by calmodulin. The PMCA also counter-transports a proton. PMCA is important for Ca2+ homeostasis and function.
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Hydrolysis of ATP and release of tubulin folding intermediate from CCT/TriC
During steady state conditions, cytoplasmic [Ca2+] is reduced by the accumulation of Ca2+ in intracellular stores and Ca2+ extrusion.
Exchange of ADP for ATP in CCT/TriC:actin complex
Ca2+ homeostasis is controlled by processes that elevate or counter the elevation of cytosolic Ca2+. During steady state conditions, cytoplasmic Ca2+ is reduced by the accumulation of Ca2+ in intracellular stores and by Ca2+ extrusion. The primary intracellular calcium store in platelets is the dense tubular system, the equivalent of the ER system in other cell types. Ca2+ is extruded by Ca2+-ATPases including plasma membrane Ca2+ ATPases (PMCAs) and sarco/endoplasmic reticulum Ca2+ -ATPase isoforms (SERCAs). Activation of non- excitable cells involves the agonist-induced elevation of cytosolic Ca2+, an essential process for platelet activation. It occurs through Ca2+ release from intracellular stores and Ca2+ entry through the plasma membrane. Ca2+ store release involves phospholipase C (PLC)-mediated production of inositol-1,4,5-trisphosphate (IP3), which in turn stimulates IP3 receptor channels to release Ca2+ from intracellular stores. This is followed by Ca2+ entry into the cell through plasma membrane calcium channels, a process referred to as store-operated calcium entry (SOCE). Stromal interaction molecule 1 (STIM1), a Ca2+ sensor molecule in intracellular stores, and the four transmembrane channel protein Orai1 are the key players in platelet SOCE. Other major Ca2+ entry mechanisms are mediated by the direct receptor-operated calcium (ROC) channel, P2X1 and transient receptor potential channels (TRPCs).
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Association of CCT/TriC with sphingosine kinase 1
Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhesion and activation, suppresses coagulation, enhances fibrin cleavage and is anti-inflammatory in character. Under acute vascular trauma, vasoconstrictor mechanisms predominate and the endothelium becomes prothrombotic, procoagulatory and proinflammatory in nature. This is achieved by a reduction of endothelial dilating agents: adenosine, NO and prostacyclin; and by the direct action of ADP, serotonin and thromboxane on vascular smooth muscle cells to elicit their contraction (Becker et al. 2000). Cyclooxygenase-2 (COX-2) and endothelial nitric oxide synthase (eNOS) are primarily expressed in endothelial cells. Both are important regulators of vascular function. Under normal conditions, laminar flow induces vascular endothelial COX-2 expression and synthesis of Prostacyclin (PGI2) which in turn stimulates endothelial Nitric Oxide Synthase (eNOS) activity. PGI2 and NO both oppose platelet activation and aggregation, as does the CD39 ecto-ADPase, which decreases platelet activation and recruitment by metabolizing platelet-released ADP.
EIF5A + spermidine <=> EIF5A(Dhp) + 1,3-diaminopropane
Phosphatidylinositides generated by PI3K recruit phosphatidylinositide-dependent protein kinase 1 (PDK1) and AKT (also known as protein kinase B) to the membrane, through their PH (pleckstrin-homology) domains. The binding of PIP3 to the PH domain of AKT is the rate-limiting step in AKT activation. In mammals there are three AKT isoforms (AKT1-3) encoded by three separate genes. The three isoforms share a high degree of amino acid identity and have indistinguishable substrate specificity in vitro. However, isoform-preferred substrates in vivo cannot be ruled out. The relative expression of the three isoforms differs in different mammalian tissues: AKT1 is the predominant isoform in the majority of tissues, AKT2 is the predominant isoform in insulin-responsive tissues, and AKT3 is the predominant isoform in brain and testes. All 3 isoforms are expressed in human and mouse platelets (Yin et al. 2008; O'Brien et al. 2008). Note: all data in the pathway refer to AKT1, which is the most studied.
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EIF5A(Dhp) + 1,3-diaminopropane <=> EIF5A + spermidine
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Molecular cloning and functional expression of a sodium-dicarboxylate cotransporter from human kidney
M-phase inducer phosphatase 1 (EC 3.1.3.48) (Dual specificity phosphatase Cdc25A)
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Activator 1 36 kDa subunit (Replication factor C 36 kDa subunit) (A1 36 kDa subunit) (RF-C 36 kDa subunit) (RFC36)
unfolded actin/tubulin associates with prefoldin
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Peptide transfer from P-site tRNA to the A-site tRNA
Translocation of ribosome by 3 bases in the 3' direction
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GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex
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Regeneration of eEF1A:GTP by eEF1B activity
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ChEBI:16975 1-acyl-sn-glycerol 3-phosphate
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FACL4, encoding fatty acid-CoA ligase 4, is mutated in nonspecific X-linked mental retardation
Novel interleukin-2 receptor subunit detected by cross-linking under high-affinity conditions
The SRP receptor binds the SRP:nascent peptide:ribosome complex
eEF1A:GTP:aminoacyl tRNA ternary complex formation.
Aminoacyl-tRNA binds to the ribosome at the A-site
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The 60S subunit joins the translation initiation complex
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Formation of eIF2:GDP:eIF2B intermediate
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Synthesis of nascent polypeptide containing signal sequence
Employment of the epidermal growth factor receptor in growth factor-independent signaling pathways
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Gene identification for the cblD defect of vitamin B12 metabolism
Formation of the cap-binding eIF4F complex
Met-tRNAi binds to eIF2:GTP to form the ternary complex
Formation of the 43S pre-initiation complex
Release of 40S and 60S subunits from the 80S ribosome
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Association with HSP90 inhibits Cbl-mediated down-regulation of mutant epidermal growth factor receptors
LRRFIP1, a new FGFR1 partner gene associated with 8p11 myeloproliferative syndrome
The sodium/calcium exchanger family-SLC8
Genomic organization, tissue distribution and deletion mutation of human pyridoxine 5'-phosphate oxidase
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Antimicrobial mechanisms of phagocytes and bacterial evasion strategies
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The D-Box-activating domain (DAD) is a new proteolysis signal that stimulates the silent D-Box sequence of Aurora-A
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RhoGDIgamma: a GDP-dissociation inhibitor for Rho proteins with preferential expression in brain and pancreas
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P110delta, a novel phosphoinositide 3-kinase in leukocytes
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Wnt and calcium signaling: beta-catenin-independent pathways
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Regulation of lipid metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
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Dephosphorylation of O-phospho-L-serine to L-serine proceeds through a phospho-enzyme intermediate of the catalysing phosphatase PSP (Collet et al. 1997).
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Advanced glycation endproduct (AGE) receptor 1 is a negative regulator of the inflammatory response to AGE in mesangial cells
CCBL1 (KAT 1) catalyzes the reaction of glutamine and pyruvate to form 2-oxoglutaramate and alanine. The active form of CCBL1 is a homodimer with one molecule of pyridoxal phosphate bound to each monomer (Baran et al. 1994; Han et al. 2009; Rossi et al. 2004). The enzyme's cytosolic localization is inferred from that of recombinant protein overexpressed in transfected cells (Perry et al. 1995).
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Mitochondrial glutamate dehydrogenase 1 (GLUD1) catalyzes the reversible reaction of glutamate and NAD(P)+ to form 2-oxoglutarate, NAD(P)H + H+, and ammonia (Fang et al. 2002). Mature GLUD1 protein lacks the 53 aminoterminal residues of the nascent protein (Julliard and Smith 1979), which function as a mitochondrial import signal. The active form of the enzyme is a hexamer, allosterically activated by ADP and inhibited by GTP (Fang et al. 2002; Smith et al. 2002).
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The amino group needed for serine biosynthesis comes from glutamate. Its transfer onto 3-phosphonooxpyruvate is catalysed by the PSAT1 dimer which needs pyridoxal phosphate as cofactor. (Baek et al. 2003)
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Serine biosynthesis starts from 3-phosphoglycerate, a glycolysis intermediate. Its dehydrogenation is catalysed by tetrameric phosphoglycerate dehydrogenase PHGDH. (Tabatabaie et al. 2009).
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Pyrroline-5-carboxylate reductase 1 (PYCR1) catalyzes the reaction of (S)-1-pyrroline-5-carboxylate with NADPH + H+ to form proline and NADP+ (Merrill et al. 1989). The active enzyme is a homodecamer (Meng et al. 2006). Recent immunofluoresence studies show that PYCR1 colocalizes with mitochondrial markers including pyrroline 5-carboxylate synthase in cultured human fibroblasts (Reversade et al. 2009).
Delta-1-pyrroline-5-carboxylate synthetase associated with the inner mitochondrial membrane catalyzes the two-step reaction that converts glutamate, ATP, and NADPH + H+ to L-glutamate gamma-semialdehyde, NADP+, ADP, and orthophosphate. Two P5CS isoforms have been identified; both are active when expressed in enzyme-deficient cells in culture (Hu et al. 1999). Unpublished crystallographic data (PDB 2H5G) indicate that the enzyme is a dimer.
Mitochondrial glutamate dehydrogenase 1 (GLUD1) catalyzes the reversible reaction of 2-oxoglutarate, NAD(P)H + H+, and ammonia to form glutamate and NAD(P)+ (Fang et al. 2002). Mature GLUD1 protein lacks the 53 aminoterminal residues of the nascent protein (Julliard and Smith 1979), which function as a mitochondrial import signal. The active form of the enzyme is a hexamer, allosterically activated by ADP and inhibited by GTP (Fang et al. 2002; Smith et al. 2002).
Cytosolic asparagine synthase (ASNS) catalyzes the reaction of aspartate, glutamine, and ATP to form asparagine, glutamate, AMP, and pyrophosphate. Studies of the recombinant protein expressed in E. coli suggest that the active form of the enzyme is a dimer (Van Heeke and Schuster 1989).
Mitochondrial ornithine aminotransferase (OAT) catalyzes the reversible reaction of glutamate semialdehyde and glutamate to form ornithine and alpha-ketoglutarate (Ohura et al. 1982). The active enzyme is a hexamer (Shen et al. 1998). Inherited OAT deficiency leads to ornithine accumulation in vivo and gyrate atrophy of the choroid and retina (Brody et al. 1992; Vallee and Simell 2001).
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Mitochondrial branched-chain-amino-acid aminotransferase (BCAT2) catalyzes the reversible reactions of alpha-ketoisocaproate, alpha-keto-beta-methylvalerate, or a-ketoisovalerate with glutamate to form leucine, isoleucine, or valine, respectively, and alpha-ketoglutarate (Bledsoe et al. 1997). The active enzyme is a homodimer (Yennawar et al. 2001, 2002). In the body, this enzyme is widely expressed but is especially abundant in muscle tissue.
Mitochondrial branched-chain-amino-acid aminotransferase (BCAT2) catalyzes the reversible reactions of leucine, isoleucine, or valine with alpha-ketoglutarate (2-oxoglutarate) to form alpha-ketoisocaproate, alpha-keto-beta-methylvalerate, or a-ketoisovalerate, respectively, and glutamate (Bledsoe et al. 1997). The active enzyme is a homodimer (Yennawar et al. 2001, 2002). In the body, this enzyme is widely expressed but is especially abundant in muscle tissue.
Cytosolic branched-chain-amino-acid aminotransferase (BCAT1) catalyzes the reversible reactions of alpha-ketoisocaproate, alpha-keto-beta-methylvalerate, or a-ketoisovalerate with glutamate to form leucine, isoleucine, or valine, respectively, and alpha-ketoglutarate (2-oxoglutarate). The active enzyme is a homodimer (Goto et al. 2005).
Cytosolic branched-chain-amino-acid aminotransferase (BCAT1) catalyzes the reversible reactions of leucine, isoleucine, or valine with alpha-ketoglutarate (2-oxoglutarate) to form alpha-ketoisocaproate, alpha-keto-beta-methylvalerate, or a-ketoisovalerate, respectively, and glutamate. The active enzyme is a homodimer. Hutson and colleagues have argues that cytosolic BCAT1 plays a major role in the generation of glutamate involved in synaptic transmission in neural tissue (Goto et al. 2005).
The saccharopine dehydrogenase activity of lysine-ketoglutarate reductase / saccharopine dehydrogenase homotetramer in the mitochondrial matrix catalyzes the reaction of lysine, alpha-ketoglutarate, and NADPH + H+ to form saccharopine, NADP+, and H2O (Markovitz et al. 1984; Sacksteder et al. 2001).
The branched-chain amino acids, leucine, isoleucine, and valine, are all essential amino acids (i.e., ones required in the diet). They are major constituents of muscle protein. The breakdown of these amino acids starts with two common steps catalyzed by enzymes that act on all three amino acids: reversible transamination by branched-chain amino acid aminotransferase, and irreversible oxidative decarboxylation by the branched-chain ketoacid dehydrogenase complex. Isovaleryl-CoA is produced from leucine by these two reactions, alpha-methylbutyryl-CoA from isoleucine, and isobutyryl-CoA from valine. These acyl-CoA's undergo dehydrogenation, catalyzed by three different but related enzymes, and the breakdown pathways then diverge. Leucine is ultimately converted to acetyl-CoA and acetoacetate; isoleucine to acetyl-CoA and succinyl-CoA; and valine to succinyl-CoA. Under fasting conditions, substantial amounts of all three amino acids are generated by protein breakdown. In muscle, the final products of leucine, isoleucine, and valine catabolism can be fully oxidized via the citric acid cycle; in liver they can be directed toward the synthesis of ketone bodies (acetoacetate and acetyl-CoA) and glucose (succinyl-CoA) (Chuang & Shih 2001, Sweetman & Williams 2001).
Mitochondrial 3-hydroxyisobutyryl-CoA hydrolase (HIBCH) catalyzes the hydrolysis of beta-hydroxyisobutyryl-CoA to form beta-hydroxyisobutyrate (3-hydroxy-2-methylpropanoate) and CoA (Hawes et al. 1996).
Mitochondrial acetyl-CoA acetyltransferase (ACAT1) catalyzes the reaction of alpha-methyl-acetoacetyl-CoA and CoA to form propionyl-CoA and acetyl-CoA. Structural studies have shown the active enzyme to be a tetramer of ACAT1 polypeptides whose aminoterminal 34 residues, a mitochondrial targeting sequence, have been removed (Haapalainen et al. 2007).
L-Serine is needed in human brain in large amounts as precursor to important biomolecules such as nucleotides, phospholipids and the neurotransmitters glycine and D-serine. The pathway for its synthesis starts with 3-phosphoglycerate and it later needs glutamate as an amination agent. Deficiencies in the participating enzymes lead to severe neurological symptoms that are treatable with serine if treatment starts early (de Koning & Klomp 2004).
These reactions mediate the synthesis of aspartate, asparagine, glutamate, and glutamine from ammonia and intermediates of glycolysis, and allow the utilization of the carbon atoms from these four amino acids for glucose synthesis under fasting conditions. These reactions also provide a means to collect nitrogen, both as ammonia and as amino groups, and direct it towards urea synthesis. Transamination, the conversion of an amino acid to the corresponding alpha-keto acid coupled to the conversion of a molecule of alpha-ketoglutarate to glutamate, is the first step in the catabolism of most amino acids. Transamination reactions are freely reversible so they also provide a means to balance concentrations of various amino acids and alpha-keto (2-oxo) acids in the cytosol.
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The mitochondrial alpha-ketoglutarate dehydrogenase complex catalyzes the reaction of alpha-ketoadipate, CoASH, and NAD+ to form glutaryl-CoA, CO2, and NADH. The enzyme complex contains multiple copies of three different proteins, E1 (OGDH), E2 (DLST), and E3 (DLD), each with distinct catalytic activities (Reed and Hackert 1990; Zhou et al 2001). The reaction starts with the oxidative decarboxylation of alpha-ketoadipate catalyzed by E1alpha and beta (alpha ketoglutarate dehydrogenase). Lipoamide cofactor associated with E1 is reduced at the same time. Next, the glutaryl group derived from alpha ketoglutarate is transferred to coenzyme A in two steps catalyzed E2 (dihydrolipolyl transacetylase). Finally, the oxidized form of lipoamide is regenerated and electrons are transferred to NAD+ in two steps catalyzed by E3 (dihydrolipoyl dehydrogenase). The biochemical details of this reaction have been worked out with alpha ketoglutarate dehydrogenase complex and subunits purified from bovine tissue (McCartney et al. 1998). While all of the human proteins are known as predicted protein products of cloned genes, direct experimental evidence for their functions is available only for E3 (DLD) (Brautigam et al. 2005).
Transfer of SUMO2 from E1 to UBE2I (UBC9)
SLC25A21, the mitochondrial 2-oxodicarboxylate carrier, mediates the exchange of 2-oxoadipate and 2-oxoglutarate across the inner mitochondrial membrane. While the exchange is reversible, under physiological conditions it proceeds in the direction of 2-oxoadipate import into the mitochondrial matrix and 2-oxoglutarate export (Fiermonte et al. 2001).
CCBL1 (KAT 1) catalyzes the reaction of phenylalanine and pyruvate to form 3-(indol-3-yl)pyruvate and alanine. The active form of CCBL1 is a homodimer with one molecule of pyridoxal phosphate bound to each monomer (Baran et al. 1994; Han et al. 2009; Rossi et al. 2004). The enzyme's cytosolic localization is inferred from that of recombinant protein overexpressed in transfected cells (Perry et al. 1995).
In humans, most catabolism of L-lysine normally proceeds via a sequence of seven reactions which feeds into the pathway for fatty acid catabolism. In the first two reactions, catalyzed by a single enzyme complex, lysine is combined with alpha-ketoglutarate to form saccharopine, which in turn is cleaved and oxidized to yield glutamate and alpha-ketoadipic semialdehyde. The latter molecule is further oxidized to alpha-ketoadipate. Alpha-ketoadipate is oxidatively decarboxylated by the alpha-ketoglutarate dehydrogenase complex (the same enzyme complex responsible for the conversion of alpha-ketoglutarate to succinyl-CoA in the citric acid cycle), yielding glutaryl-CoA. Glutaryl-CoA is converted to crotonyl-CoA, crotonyl-CoA is converted to beta-hydroxybutyryl-CoA, and beta-hydroxybutyryl-CoA is converted to acetoacetyl-CoA. The products of lysine catabolism are thus exclusively ketogenic; i.e., under starvation conditions they can be used for the synthesis of ketone bodies, beta-hydroxybutyrate and acetoacetate, but not for the net synthesis of glucose (Cox 2001; Goodman and Freeman 2001).
The dehydrogenation of proline to L-1-pyrroline-5-carboxylate coupled to the conversion of FAD to FADH2 is the first step in proline breakdown (Bender et al. 2005). Proline dehydrogenase (PRODH), the enzyme that catalyzes this reaction, is found in liver, kidney, and brain cells, where it is tightly bound to the inner mitochondrial membrane.
The first reaction in this pathway converts phenylalanine to tyrosine, coupled to the conversion of tetrahydrobiopterin to 4a-hydroxytetrahydrobiopterin, catalyzed by phenylalanine hydroxylase. (Deficiencies in this enzyme are responsible for the commonest form of phenylketonuria (PKU) in humans.) This reaction functions both as the first step in the pathway by which the body disposes of excess phenylalanine, and as a source of the amino acid tyrosine. The next two reactions are responsible for the regeneration of tetrahydrobiopterin from 4a-hydroxytetrahydrobiopterin. The following five reactions convert tyrosine to fumarate, an intermediate in the citric acid cycle, and acetoacetate, a ketone body.
Mitochondrial delta-1-pyrroline-5-carboxylate dehydrogenase (ALDH4A1) catalyzes the reaction of L-glutamate gamma-semialdehyde and NAD+ to form glutamate and NADH + H+ (Hu et al. 1996). The enzyme is a dimer (Forte-McRobbie and Pietruszko 1986). ALDH4A1 mutations cause type II hyperprolinemia in vivo (Geraghty et al. 1998).
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Transfer of SUMO1 from E1 to UBE2I (UBC9)
The saccharopine dehydrogenase activity of lysine-ketoglutarate reductase / saccharopine dehydrogenase homotetramer in the mitochondrial matrix catalyzes the reaction of saccharopine (N6-(L-1,3-Dicarboxypropyl)-L-lysine), H2O, and NAD+ to form 'L-2-Aminoadipate 6-semialdehyde, glutamate, and NADH + H+ (Markovitz et al. 1984; Sacksteder et al. 2001).
Kynurenine/alpha-aminoadipate aminotransferase (AADAT) catalyzes the reversible reaction of alpha-aminoadipate and alpha-ketoglutarate to form alpha-ketoadipate and glutamate. Crystallographic studies have demonstrated that active AADAT enzyme is a homodimer with a pyridoxal phosphate moiety covalently attached to each monomer (Han et al. 2008; Rossi et al. 2008). The enzyme is inferred to be located within the mitochondrion because of a mitochondrial localization sequence motif at the aminoterminal end of the AADAT polypeptide (Goh et al. 2002).
Kynurenine/alpha-aminoadipate aminotransferase (AADAT) catalyzes the reversible reaction of alpha-ketoadipate and glutamate to form alpha-aminoadipate and alpha-ketoglutarate. Crystallographic studies have demonstrated that active AADAT enzyme is a homodimer with a pyridoxal phosphate moiety covalently attached to each monomer (Han et al. 2008; Rossi et al. 2008). The enzyme is inferred to be located within the mitochondrion because of a mitochondrial localization sequence motif at the aminoterminal end of the AADAT polypeptide (Goh et al. 2002).
Roles of aquaporin-3 water channels in volume-regulatory water flow in a human epithelial cell line
Cytosolic nucleoside phosphorylase (NP) trimer catalyzes the reversible reaction of guanosine or deoxyguanosine with orthophosphate to form guanine and ribose 1-phosphate or deoxyribose 1-phosphate (Ealick et al. 1990; Wiginton et al. 1980). While NP is active with either nuckeotide in vitro, levels of deoxyguanosine are normally low in vivo, limiting the extent of this reaction. NP deficiency in vivo is associated with defects in purine nucleotide salvage and leads to immunodeficiency (Williams et al. 1987).
Nucleosides and free bases generated by DNA and RNA breakdown are converted back to nucleotide monophosphates, allowing them to re-enter the pathway of purine biosynthesis. Nucleosides and free bases generated by DNA breakdown are converted back to nucleotide monophosphates, allowing them to re-enter the pathway of purine biosynthesis. Nucleosides and free bases generated by RNA breakdown are converted back to nucleotide monophosphates, allowing them to re-enter the pathways of purine biosynthesis. Under normal conditions, DNA turnover is limited and deoxyribonucleotide salvage operates at a correspondingly low level (Watts 1974).
Ordered cooperative functions of PRMT1, p300, and CARM1 in transcriptional activation by p53
Cytosolic APRT dimer catalyzes the reaction of adenine and 5-phospho-alpha-D-ribose 1-diphosphate to form AMP and pyrophosphate (Holden et al. 1979).
Cytosolic nucleoside phosphorylase (NP) trimer catalyzes the reversible reaction of hypoxanthine with ribose 1-phosphate or deoxyribose 1-phosphate to form inosine or deoxyinosine and orthophosphate (Ealick et al. 1990; Wiginton et al. 1980). While NP is active with either ribose 1-phosphate or deoxyribose 1-phosphate in vitro, levels of deoxyribose 1-phosphate are normally low in vivo, limiting the extent of this reaction. NP deficiency in vivo is associated with defects in purine nucleotide salvage and leads to immunodeficiency (Williams et al. 1987).
Cytosolic nucleoside phosphorylase (NP) trimer catalyzes the reversible reaction of guanine with ribose 1-phosphate or deoxyribose 1-phosphate to form guanosine or deoxyguanosine and orthophosphate (Ealick et al. 1990; Wiginton et al. 1980). While NP is active with either ribose 1-phosphate or deoxyribose 1-phosphate in vitro, levels of deoxyribose 1-phosphate are normally low in vivo, limiting the extent of this reaction. NP deficiency in vivo is associated with defects in purine nucleotide salvage and leads to immunodeficiency (Williams et al. 1987).
Cytosolic ADAL (Adenosine DeAminase-Like) catalyzes the reaction of N6-methyl-AMP and water to form IMP and methylamine. The active form of the enzyme is a protein monomer complexed with a zinc ion (Murakami et al. 2011).
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The purine bases guanine and hypoxanthine (derived from adenine by events in the purine salvage pathways) are converted to xanthine and then to uric acid, which is excreted from the body (Watts 1974). The end-point of this pathway in humans and hominoid primates is unusual. Most other mammals metabolize uric acid further to yield more soluble end products, and much speculation has centered on possible roles for high uric acid levels in normal human physiology.
The events of human purine metabolism are conveniently, if somewhat arbitrarily, grouped into four pathways: de novo synthesis of inosine 5'-monophosphate (IMP), the biosynthesis of other purine ribo- and deoxyribonucleotides, purine salvage reactions, and purine catabolism (Watts 1974). De novo synthesis of inosine 5'-monophosphate (IMP). The purine ribonucleotide IMP is assembled on 5-phospho-alpha-D-ribose 1-diphosphate (PRPP). Purine biosynthesis [interconversion]. Purine ribo- and deoxyribonucleotide di- and triphosphates are synthesized, both from IMP and from guanosine and adenosine ribo- and deoxyribonucleotide monophosphates generated in salvage reactions. Purine salvage reactions. Purine nucleosides and free bases generated by DNA and RNA breakdown are converted to nucleotide monophosphates. Purine catabolism. The purine bases guanine and hypoxanthine are degraded to uric acid, which is excreted from the body.
Cytosolic nucleoside phosphorylase (NP) trimer catalyzes the reversible reaction of inosine or deoxyinosine with orthophosphate to form hypoxanthine and ribose 1-phosphate or deoxyribose 1-phosphate (Ealick et al. 1990; Wiginton et al. 1980). While NP is active with either nuckeotide in vitro, levels of deoxyinosine are normally low in vivo, limiting the extent of this reaction. NP deficiency in vivo is associated with defects in purine nucleotide salvage and leads to immunodeficiency (Williams et al. 1987).
Cytosolic guanine deaminase (GDA) catalyzes the reaction of guanine and water to form xanthine and ammonia (Yuan et al. 1999). The active enzyme is a homodimer (Murphy et al. 2009).
Two human isoenzymes, IMP dehydrogenase 1 and 2 (IMPDH1,2) catalyze the irreversible dehydrogenation of inosine 5'-monophosphate (IMP) to form xanthosine 5'-monophosphate (XMP). The active forms of both isoenzymes are homotetramers, and they are nearly identical in their catalytic efficiencies and their susceptibility to inhibition by XMP (Carr et al. 1993; Colby et al. 1999; Hager et al. 1995). Both enzymes occur as homotetramers (Colby et al. 1999 - IMPDH2; unpubliched data in PDB 1JCN IMPDH1). A variety of experiments suggest that IMPDH1 and 2 have distinct functions in vivo. While IMPDH1 is expressed at constant levels, IMPDH2 is expressed at elevated levels in tumor cells and in mitotic normal cells. In humans, heterozygosity for mutant forms of IMPDH1 is associated with a form of retinitis pigmentosa (Bowne et al. 2002). In laboratory mice, mutations that disrupt the homologue of IMPDH1 have no obvious effect at the level of the whole organism, while ones that disrupt IMPDH2 are lethal (Gu et al. 2003). This reaction is the rate limiting step in the synthesis of guanosine 5'-monophosphate (GMP) from IMP, and GMP competitively inhibits the well-characterized bacterial IMP dehydrogenase enzyme. Evidence for an inhibitory effect of GMP on the human isoenzymes has not been reported. Rather, they appear to be inhibited by XMP; in addition, transcription of one or both IMP dehydrogenase mRNAs may be inhibited by high cellular GMP concentrations (Glesne et al. 1991).
The reversible synthesis of inosine 5'-monophosphate from 5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide (FAICAR) is catalyzed by the IMP cyclohydrolase activity of the bifunctional 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase enzyme. This cytosolic protein occurs primarily as a dimer (Rayl et al. 1996; Vergis et al. 2001) and may further associate with other enzymes of de novo IMP biosynthesis under some metabolic conditions (An et al. 2008).
Reconstitution of functional water channels in liposomes containing purified red cell CHIP28 protein
Two isoforms of adenylosuccinate synthetase, ADSS and ADSSL1, catalyze the reaction of IMP, aspartate, and GTP to form adenylosuccinate, GDP, and orthophosphate (Powell et al. 1992; Sun et al. 2005). ADSS is a homotetramer (unpublished crystallographic data - PDB 2V40) and ADSSL1 is inferred to be a tetramer likewise.
Purification of, generation of monoclonal antibodies to, and mapping of phosphoribosyl N-formylglycinamide amidotransferase
Cytosolic GMP synthase (GMPS) catalyzes the reaction of xanthosine 5'-monophosphate (XMP), ATP, glutamine and water to form guanosine 5'-monophosphate (GMP), AMP, glutamate and pyrophosphate. GMPS is a monomer (Hirst et al. 1994; Nakamura and Lou 1995).
The irreversible transfer of a formyl group to 5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR), to yield 5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide (FAICAR), is catalyzed by the phosphoribosylaminoimidazolecarboxamide formyltransferase activity of the bifunctional 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase enzyme. This cytosolic protein occurs primarily as a dimer (Rayl et al. 1996; Vergis et al. 2001) and may further associate with other enzymes of de novo IMP biosynthesis under some metabolic conditions (An et al. 2008).
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Cytosolic AMP deaminase (AMPD) catalyzes the hydrolysis of AMP to yield IMP and ammonia. Three isoforms of AMPD, E, L, and M, have been identified that differ in their expression patterns in the body. All occur as tetramers and all have qualitatively the same catalytic activity, however (Bausch-Jurken et al. 1992; Mahnke-Zizelman et al. 1998).
Coordinate changes in heat shock element-binding activity and HSP70 gene transcription rates in human cells
The irreversible conversion of adenylosuccinate to adenosine 5'-monophosphate and fumarate is catalyzed by adenylosuccinate lyase. The active form of this enzyme is a cytosolic tetramer (Stone et al. 1993). The enzyme also catalyzes the conversion of 5'-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide (SAICAR) to 5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR) and fumarate. Humans lacking the enzyme accumulate dephosphorylated forms of both substrates, indicating that the enzyme mediates both reactions in vivo as well (Race et al. 2000).
The purine ribonucleotide inosine 5'-monophosphate (IMP) is assembled on 5-phospho-alpha-D-ribose 1-diphosphate (PRPP), with atoms derived from aspartate, glutamine, glycine, N10-formyl-tetrahydrofolate, and carbon dioxide. Although several of the individual reactions in this sequence are reversible, as indicated by the double-headed arrows in the diagram, other irreversible steps drive the pathway in the direction of IMP synthesis in the normal cell. All of these reactions are thus annotated here only in the direction of IMP synthesis. Guanosine 5'-monophosphate (GMP) and adenosine 5'-monophosphate (AMP) are synthesized from IMP.
Characterization of human type I and type II IMP dehydrogenases
Cytosolic adenosine deaminase (ADA) catalyzes the hydrolysis of 2'deoxyadenosine and adenosine to yield deoxyinosine and inosine, respectively, plus ammonia (Akeson et al. 1988). Unpublished crystallographic data (PDB 3IAR) indicate that the human enzyme is a monomer.
Cytosolic adenosine linase (ADK) catalyzes the reactions of adenosine and deoxyadenosine with ATP to yield the corresponding nucleotide monophosphates and ADP (Andres and Fox 1979). The enzyme is substantially more active on adenosine than deoxyadenosine in vitro (Hurley at al. 1985) though studies of cultured cells suggest that both reactions may be physiologically relevant (Hershfield et al. 1982). The enzyme is a monomer complexed with magnesium (Mathews et al. 1998).
PRPP stimulates the dissociation of phosphoribosyl pyrophosphate amidotransferase tetramers to form dimers (Holmes et al. 1973a,b).
Cytosolic AMP, GMP, and IMP stimulate the association of phosphoribosyl pyrophosphate amidotransferase (PPAT) dimers to form tetramers (Holmes et al. 1973a,b).
The metabolism of pyruvate provides one source of acetyl-CoA which enters the citric acid (TCA, tricarboxylic acid) cycle to generate energy and the reducing equivalent NADH. These reducing equivalents are re-oxidized back to NAD+ in the electron transport chain (ETC), coupling this process with the export of protons across the inner mitochondrial membrane. The chemiosmotic gradient created is used to drive ATP synthesis.
Oxidation of fatty acids and pyruvate in the mitochondrial matrix yield large amounts of NADH. The respiratory electron transport chain couples the re-oxidation of this NADH to NAD+ to the export of protons from the mitochonrial matrix, generating a chemiosmotic gradient across the inner mitochondrial membrane. This gradient is used to drive the synthesis of ATP; it can also be bypassed by uncoupling proteins to generate heat, a reaction in brown fat that may be important in regulation of body temperature in newborn children.
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Characterization of the mitogen-activated protein kinase kinase 4 (MKK4)/c-Jun NH2-terminal kinase 1 and MKK3/p38 pathways regulated by MEK kinases 2 and 3. MEK kinase 3 activates MKK3 but does not cause activation of p38 kinase in vivo.
The irreversible transfer of a formyl group to cytosolic 5-phosphoribosylglycinamide (GAR) to form 5'-phosphoribosylformylglycinamide (FGAR) is catalyzed by the phosphoribosylglycinamide formyltransferase domain of the trifunctional protein, "phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase" (GART) (Aimi et al. 1990; Zhang et al. 2002). Fluoresence microscopy studies of cultured human cells have shown that GART is cytosolic and suggest that it may co-localize with other enzymes of de novo IMP biosynthesis under some metabolic conditions (Gooljarsingh et al. 2001; An et al. 2008).
The irreversible transfer of an amino group from L-glutamine to 5'-phosphoribosylformylglycinamide (FGAR), forming 5'-phosphoribosylformylglycinamidine (FGAM) and glutamate, accompanied by the conversion of ATP to ADP and orthophosphate, is catalyzed by phosphoribosylformylglycinamidine synthetase. The human enzyme has been purified and characterized biochemically (Barnes et al. 1994). Fluoresence microscopy studies of cultured human cells have shown that the enzyme is cytosolic and suggest that it may co-localize with other enzymes of de novo IMP biosynthesis under some metabolic conditions (An et al. 2008).
Cytosolic PPAT (phosphoribosyl pyrophosphate amidotransferase) catalyzes the reaction of 5-phospho-alpha-D-ribose 1-diphosphate (PRPP), water, and L-glutamine to form 5-phosphoribosylamine, L-glutamate, and pyrophosphate. This event is the committed step in de novo purine synthesis. The reaction itself is reversible, but it is pulled strongly in the direction of 5'-phosphoribosylamine synthesis by the irreversible hydrolysis of the pyrophosphate that is also formed in the reaction. Fluoresence microscopy studies of cultured human cells have shown that PPAT is cytosolic and suggest that it may co-localize with other enzymes of de novo IMP biosynthesis under some metabolic conditions (An et al. 2008). The PPAT enzyme is inferred to be an iron-sulfur protein, like its well-characterized B. subtilis homologue, because incubation of purified enzyme with molecular oxygen or chelating agents inactivates it, and activity can be restored by incubation with ferrous iron and inorganic sulfide. The stoichiometry of the iron-sulfur moiety and its role in enzyme activity remain unknown (Itakura and Holmes 1979). The fully active form of the enzyme is a dimer, which can associate further to form a tetramer with sharply reduced activity (Holmes et al. 1973b; Iwahana et al. 1993). Interaction of the enzyme with inosine 5'-monophosphate (IMP), guanosine 5'-monophosphate (GMP), and adenosine 5'-monophosphate (AMP), end products of de novo purine biosynthesis, favors tetramer formation, while interaction with 5-phospho-alpha-D-ribose 1-diphosphate (PRPP), a required substrate, favors formation of the active dimer. Kinetic studies suggest that the enzyme's binding site for GMP and IMP is separate from its AMP binding site (Holmes et al. 1973a).
The synthesis of cytosolic 5-phosphoribosylglycinamide from 5-phosphoribosylamine and glycine, accompanied by the conversion of ATP to ADP and orthophosphate, is catalyzed by the phosphoribosylglycinamide synthetase domain of the trifunctional protein, "phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase" (GART) (Aimi et al. 1990). The active form of the protein is cytosolic (Gooljarsingh et al. 2001; An et al. 2008).
The irreversible synthesis of cytosolic 5'-phosphoribosyl-5-aminoimidazole (AIR) from 5'-phosphoribosylformylglycinamidine (FGAM), accompanied by the conversion of ATP to ADP and orthophosphate, is catalyzed by the phosphoribosylaminoimidazole synthetase domain of the trifunctional protein, "phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase" (GART) (Aimi et al. 1990). The active form of the protein is cytosolic and may co-localize with other enzymes of de novo IMP biosynthesis under some metabolic conditions (Gooljarsingh et al. 2001; An et al. 2008).
The reversible conversion of 5'-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide (SAICAR) to 5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR) and fumarate is catalyzed by adenylosuccinate lyase. The active form of this enzyme is a cytosolic tetramer (Stone et al. 1993), and fluoresence microscopy of cultured human cells suggests that it may associate with other enzymes of de novo IMP biosynthesis under some metabolic conditions (An et al. 2008). The enzyme also catalyzes the conversion of adenylosuccinate to adenosine 5'-monophosphate and fumarate. Humans lacking the enzyme accumulate dephosphorylated forms of both substrates, indicating that the enzyme mediates both reactions in vivo as well (Race et al. 2000).
In the citric acid or tricarboxylic acid (TCA) cycle, the acetyl group of acetyl CoA (derived primarily from oxidative decarboxylation of pyruvate, beta-oxidation of long-chain fatty acids, and catabolism of ketone bodies and several amino acids) can be completely oxidized to CO2 in reactions that also yield one high-energy phosphate bond (as GTP or ATP) and four reducing equivalents (three NADH + H+, and one FADH2). The NADH and FADH2 are then oxidized by the electron transport chain to yield nine more high-energy phosphate bonds (as ATP). All reactions of the citric acid cycle take place in the mitochondrion. Eight canonical reactions mediate the synthesis of citrate from acetyl-CoA and oxaloacetate and the metabolism of citrate to re-form oxaloacetate. Six additional reactions are included here. Three reversible reactions, the interconversions of citrate and isocitrate, of fumarate and malate, and of malate and oxaloacetate are annotated in both their canonical (forward) and reverse directions. The synthesis of succinate from succinyl-CoA can be coupled to the phosphorylation of either GDP (the canonical reaction) or ADP; both reactions are annotated. Two mitochondrial isocitrate dehydrogenase isozymes catalyze the oxidative decarboxylation of isocitrate to form alpha-ketoglutarate (2-oxoglutarate): IDH3 catalyzes the canonical reaction coupled to the reduction of NAD+, while IDH2 catalyzes the same reaction coupled to reduction of NADP+, a reaction whose normal physiological function is unclear. Both reactions are annotated. Finally, a reaction is annotated in which reducing equivalents are transferred from NADPH to NAD+ coupled to proton import across the inner mitochondrial membrane. The cyclical nature of the reactions responsible for the oxidation of acetate was first suggested by Hans Krebs, from biochemical studies of pigeon breast muscle (Krebs et al. 1938; Krebs and Eggleston 1940). Many of the molecular details of individual reactions were worked out by Ochoa and colleagues, largely through studies of enzymes purified from pig heart (Ochoa 1980). While the human homologues of these enzymes have all been identified, their biochemical characterization has in general been limited and many molecular details of the human reactions are inferred from those worked out in studies of the model systems.
ADHFE1 catalyzes the reversible reaction of (R)-2-hydroxyglutarate and succinate semialdehyde to form 2-oxoglutarate and 4-hydroxybutyrate (Struys et al. 2005). The localization of human ADHFE1 to the mitochondrial matrix is inferred from the location determined experimentally for its rat homolog (Kaufman et al. 1988).
D2HDGH associated with the mitochondrial inner membrane catalyzes the FAD-dependent reaction of (R)-2-hydroxyglutarate to form 2-oxoglutarate (Achouri et al. 2004). D2HDGH mutations are associated with high levels of (R)-2-hydroxyglutarate in vivo and variable neurological symptoms (Struys et al. 2005; Wanders and Mooyer 1995)).
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C-terminal binding domain of Rho GDP-dissociation inhibitor directs N-terminal inhibitory peptide to GTPases
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ADHFE1 catalyzes the reversible reaction of 2-oxoglutarate and 4-hydroxybutyrate to form (R)-2-hydroxyglutarate and succinate semialdehyde (Struys et al. 2005). The localization of human ADHFE1 to the mitochondrial matrix is inferred from the location determined experimentally for its rat homolog (Kaufman et al. 1988).
The two stereoisomers of 2-hydroxyglutarate are normally converted to 2-oxoglutarate in the mitochondrial matrix, and can then be metabolized by the citric acid cycle. The physiological sources of 2-hydroxyglutarate have not been established although plausible hypotheses are that it is generated by lysine breakdown or as a byproduct of delta-aminolevulinate metabolism. The stereoisomers are oxidized to 2-oxoglutarate in FAD-dependent reactions catalyzed by the enzymes D2HGDH (specific for R(-)-2-hydroxyglutarate) and L2HGDH (specific for S(-)-2-hydroxyglutarate). An inherited deficiency in either enzyme is associated with accumulation of 2-hydroxyglutarate and variable neurological symptoms. R(-)-2-hydroxyglutarate also reacts reversibly with succinate semialdehyde to form 4-hydroxybutyrate and 2-oxoglutarate, catalyzed by ADHFE1. No deficiencies of this enzyme have been found in patients with elevated 2-hydroxyglutarate levels (Struys 2006).
Pyruvate metabolism and the citric acid (TCA) cycle together link the processes of energy metabolism in a human cell with one another and with key biosynthetic reactions. Pyruvate, derived from the reversible oxidation of lactate or transamination of alanine, can be converted to acetyl CoA. Other sources of acetyl CoA include breakdown of free fatty acids and ketone bodies in the fasting state. Acetyl CoA can enter the citric acid cycle, a major source of reducing equivalents used to synthesize ATP, or enter biosynthetic pathways. In addition to its role in energy generation, the citric acid cycle is a source of carbon skeletons for amino acid metabolism and other biosynthetic processes. One such process included here is the interconversion of 2-hydroxyglutarate, probably derived from porphyrin and amino acid metabolism, and 2-oxoglutarate (alpha-ketoglutarate), a citric acid cycle intermediate.
This event is deduced on the basis of bovine experimental data. Complex II (succinate dehydrogenase) transfers electrons from the TCA cycle to ubiquinone. The 6th step in the TCA cycle is where succinate is dehydrogenated to fumarate with subsequent reduction of FAD to FADH2. FADH2 provides the electrons for the transport chain. Succinate dehydrogenase belongs to subclass 1 of the SQR family (succinate:quinone reductase) (classified by Hagerhall, C and Hederstedt, L [1996]). It consists of 4 subunits (referred to as A, B, C and D), all nuclear-encoded and is located on the matrix side of the inner mitochondrial membrane. Subunits A and B are hydrophilic whereas subunits C and D are integral proteins of the inner membrane. SQRs usually contain 3 Fe-S clusters bound by the B subunit. Succinate dehydrogenase contains one [2Fe-2S] cluster, one [4Fe-4S] cluster and one [3Fe-4S] cluster. Additionally, the A subunit has a covalently-bound FAD group. Reduced complex II has this FAD converted to FADH2. The electrons from complex II are transferred to ubiquinone (also called Q, Coenzyme Q or CoQ), a small mobile carrier of electrons located within the inner membrane. Ubiquinone is reduced to ubiquinol during this process.
Electron transfer flavoprotein, ETF, a 63kDa heterodimer composed of alpha and beta subunit, binds one FAD and one AMP per dimer. ETF resides on the matrix face of the mitochondrial inner membrane. Reducing equivalents from the beta-oxidation of fatty acyl CoAs are transferred to ETF, reducing the ETF-bound FAD to FADH2.
ETF-ubiquinone oxidoreductase (ETF-QO), catalyzes the re-oxidation of reduced ETF, with ubiquinone as the electron acceptor.
Mitochondria are often described as the "powerhouse" of a cell as it is here that energy is largely released from the oxidation of food. Reducing equivalents generated from beta-oxidation of fatty acids and from the Krebs cycle enter the electron transport chain (also called the respiratory chain). During a series of redox reactions, electrons travel down the chain releasing their energy in controlled steps. These reactions drive the active transport of H+ ions from the mitochondrial matrix , through the inner membrane to the intermembrane space. The respiratory chain consists of five main types of carrier; flavins, iron-sulfur centres, quinones, cytochromes (heme proteins) and copper. The two main reducing equivalents entering the respiratory chain are NADH and FADH2. NADH is linked through the NADH-specific dehydrogenase whereas FADH2 is reoxidised within succinate dehydrogenase and a ubiquinone reductase of the fatty acid oxidation pathway. Oxygen is the final acceptor of electrons and with H+ ions, is converted to form water, the end product of aerobic cellular respiration. A proton electrochemical gradient (often called protonmotive force) is established across the inner membrane, with positive charge in the intermembrane space relative to the matrix. Protons driven by the proton-motive force, can enter ATP synthase thus returning to the mitochondrial matrix. ATP synthases use this exergonic flow to form ATP in the matrix, a process called chemiosmotic coupling. A by-product of this process is heat generation. An antiport, ATP-ADP translocase, preferentially exports ATP from the matrix thereby maintaining a high ADP:ATP ratio in the matrix. The tight coupling of electron flow to ATP synthesis means oxygen consumption is dependent on ADP availability (termed respiratory control). High ADP (low ATP) increases electron flow thereby increasing oxygen consumption and low ADP (high ATP) decreases electron flow and thereby decreases oxygen consumption. There are many inhibitors of mitochondrial ATP synthesis. Most act by either blocking the flow of electrons (eg cyanide, carbon monoxide, rotenone) or uncoupling electron flow from ATP synthesis (eg dinitrophenol). Thermogenin is a natural protein found in brown fat. Newborn babies have a large amount of brown fat and the heat generated by thermogenin is an alternative to ATP synthesis (and thus electron flow only produces heat) and allows the maintenance of body temperature in newborns. The electron transport chain is located in the inner mitochondrial membrane and comprises some 80 proteins organized in four enzymatic complexes (I-IV). Complex V generates ATP but has no electron transfer activity. In addition to these 5 complexes, there are also two electron shuttle molecules; Coenzyme Q (also known as ubiquinone, CoQ) and Cytochrome c (Cytc). These two molecules shuttle electrons between the large complexes in the chain. How many ATPs are generated by this process? Theoretically, for each glucose molecule, 32 ATPs can be produced. As electrons drop from NADH to oxygen in the chain, the number of protons pumped out and returning through ATP synthase can produce 2.5 ATPs per electron pair. For each pair donated by FADH2, only 1.5 ATPs can be formed. Twelve pairs of electrons are removed from each glucose molecule; 10 by NAD+ = 25 ATPs 2 by FADH2 = 3 ATPs. Making a total of 28 ATPs. However, 2 ATPs are formed during the Krebs' cycle and 2 ATPs formed during glycolysis for each glucose molecule therefore making a total ATP yield of 32 ATPs. In reality, the energy from the respiratory chain is used for other processes (such as active transport of important ions and molecules) so under conditions of normal respiration, the actual ATP yield probably does not reach 32 ATPs. The reducing equivalents that fuel the electron transport chain, namely NADH and FADH2, are produced by the Krebs cycle (TCA cycle) and the beta-oxidation of fatty acids. At three steps in the Krebs cycle (isocitrate conversion to oxoglutarate; oxoglutarate conversion to succinyl-CoA; Malate conversion to oxaloacetate), a pair of electrons (2e-) are removed and transferred to NAD+, forming NADH and H+. At a single step, a pair of electrons are removed from succinate, reducing FAD to FADH2. From the beta-oxidation of fatty acids, one step in the process forms NADH and H+ and another step forms FADH2. Cytoplasmic NADH, generated from glycolysis, has to be oxidized to reform NAD+, essential for glycolysis, otherwise glycolysis would cease to function. There is no carrier that transports NADH directly into the mitochondrial matrix and the inner mitochondrial membrane is impermeable to NADH so the cell uses two shuttle systems to move reducing equivalents into the mitochondrion and regenerate cytosolic NAD+. The first is the glycerol phosphate shuttle, which uses electrons from cytosolic NADH to produce FADH2 within the inner membrane. These electrons then flow to Coenzyme Q. Complex I is bypassed so only 1.5 ATPs can be formed per NADH via this route. The overall balanced equation, summing all the reactions in this system, is NADHcytosol + H+cytosol + NAD+mito -> NAD+cytosol + NADHmito + H+mito The malate-aspartate shuttle uses the oxidation of malate to generate NADH in the mitochondrial matrix. This NADH can then be fed directly to complex I and thus can form 3 ATPs via the respiratory chain. The overall balanced equation is NADHcytosol + H+cytosol + FADinner memb -> NAD+cytosol + FADH2 inner memb Both of these shuttle systems regenerate cytosolic NAD+. The entry point for NADH is complex I (NADH dehydrogenase) and the entry point for FADH2 is Coenzyme Q. The input of electrons from fatty acid oxidation via ubiquinone is complicated and not shown in the diagram.
In this reaction, 1 molecule of 'Thioredoxin' is translocated from cytosol to nucleoplasm. This movement of the molecule occurs through the 'nuclear pore'.
Cytosolic nucleoside diphosphate kinases catalyze the reversible reaction of ribonucleoside and deoxyribonucleoside 5'-diphosphates with ATP to form the corresponding nucleoside 5'-triphosphates and ADP. These kinases are ubiquitously expressed enzymes with broad substrate specificities (Berg and Joklik 1954; Parks and Agarwal 1973). Three human cytosolic nucleoside diphosphate kinase proteins, NME1, 2, and 3, have been characterized biochemically (Gilles et al. 1991; Schaertl et al. 1998; Erent et al. 2001; Chen et al. 2003). All are catalytically active as hexamers: homohexamers of NME1, 2, and 3 have been described, as have heterohexamers containing all possible combinations of NME1 and 2 (Gilles et al. 1991; Erent et al. 2001). While cytosolic nucleoside diphosphate kinases can efficiently use several nucleotide triphosphates as a phosphate donor, the high concentrations of ATP relative to other nucleoside triphosphates in vivo makes it the likely major phosphate donor in these reactions and only reactions with ATP as the phosphate donor are annotated. All of these phosphorylation reactions are freely reversible in vitro (Parks and Agarwal 1973; Schaertl et al. 1998), but the high ratio of ATP to ADP concentrations in the cytosol should favor the conversion of (d)NDP and ATP to (d)NTP and ADP.
Cellular targets for activation by the E2F1 transcription factor include DNA synthesis- and G1/S-regulatory genes
Cytosolic ITPA dimer catalyzes the reaction of XTP and water to form XMP and PPi (pyrophosphate). Mg++ is required for enzymatic activity. The hydrolysis of XTP is thought to prevent its incorporation into mRNA, which would lead to aberrant protein synthesis (Lin et al. 2001; Abolhassani et al. 2010).
Cytosolic NUDT5 dimer (ADP-ribose pyrophosphatase) catalyzes the hydrolysis of ADP-ribose to form AMP and D-ribose 5-phosphate. Each NUDT5 subunit is associated with three magnesium ions (Zha et al. 2006, 2008). NUDT5 also catalyzes the hydrolysis of 8-oxo-dGTP but with a strongly alkaline pH optimum (Ito et al. 2011) so the physiological relevance of this reaction is unclear and it is not annotated here.
Cytosolic ITPA dimer catalyzes the reaction of ITP and water to form IMP and PPi (pyrophosphate). Mg++ is required for enzymatic activity. The hydrolysis of ITP is thought to prevent its incorporation into mRNA, which would lead to aberrant protein synthesis (Lin et al. 2001; Abolhassani et al. 2010).
Cytosolic ITPA dimer catalyzes the reaction of dITP and water to form dIMP and PPi (pyrophosphate). Mg++ is required for enzymatic activity. The hydrolysis of dITP is thought to prevent its incorporation into DNA, which would be mutagenic (Lin et al. 2001; Abolhassani et al. 2010).
Nucleoside diphosphate kinase NME4 associated with the inner mitochondrial membrane (Tokarska-Schlattner et al. 2008) catalyzes the reversible reaction of ribonucleoside and deoxyribonucleoside 5'-diphosphates with ADP to form the corresponding nucleoside 5'-diphosphates and ATP. The active form of the enzyme is a hexamer of NME4 polypeptides whose amino-terminal 33 residues, a mitochondrial translocation signal, have been removed (Milon et al. 2000). The substrate specificity of NME4 has not been examined in detail, but is inferred to be broad like that of the homologous NME1, 2, and 3 kinases (Schaertl et al. 1998).
An array of kinases catalyze the reversible phosphorylation of nucleotide monophosphates to form nucleotide diphosphates and triphosphates. Nucleoside monophosphate kinases catalyze the reversible phosphorylation of nucleoside and deoxynucleoside 5'-monophosphates to form the corresponding nucleoside 5'-diphosphates. Most appear to have restricted specificities for nucleoside monophosphates, and to use ATP preferentially (Van Rompay et al. 2000; Anderson 1973; Noda 1973). The total number of human enzymes that catalyze these reactions in vivo is not clear. In six cases, a well-defined biochemical activity has been associated with a purified protein, and these are annotated here. However, additional nucleoside monophosphate kinase-like human proteins have been identified in molecular cloning studies whose enzymatic activities are unknown, and several distinctive nucleoside monophosphate kinase activities detected in cell extracts, e.g., a GTP-requiring adenylate kinase activity (Wilson et al. 1976) and one or more guanylate kinase activities (Jamil et al. 1975) have not been unambiguously associated with specific human proteins. The nucleoside monophosphates against which each of the six well-characterized enzymes is active is shown in the table (Van Rompay et al. 2000). All six efficiently use ATP as a phosphate donor, but have some activity with other nucleoside triphosphates as well in vitro. The high concentrations of ATP relative to other nucleoside triphosphates in vivo makes it the likely major phosphate donor in these reactions under most conditions. All of these phosphorylation reactions are freely reversible in vitro when carried out with purified enzymes and substrates, having equilibrium constants near 1. In vivo, high ratios of ATP to ADP are likely to favor the forward direction of these reactions, i.e., the conversion of (d)NMP and ATP to (d)NDP and ADP. At the same time, the reversibility of the reactions and the overlapping substrate specificities of the enzymes raises the possibility that this group of reactions can buffer the intracellular nucleotide pool and regulate the relative concentrations of individual nucleotides in the pool: if any one molecule builds up to unusually high levels, multiple routes appear to be open not only to dispose of it but to use it to increase the supply of less abundant nucleotides. Ribonucleotide reductase catalyzes the synthesis of deoxyribonucleotide diphosphates from ribonucleotide diphosphates.
Cytosolic nucleoside diphosphate kinases catalyze the reversible reaction of ribonucleoside and deoxyribonucleoside 5'-diphosphates with ADP to form the corresponding nucleoside 5'-diphosphates and ATP. These kinases are ubiquitously expressed enzymes with broad substrate specificities (Berg and Joklik 1954; Parks and Agarwal 1973). Three human cytosolic nucleoside diphosphate kinase proteins, NME1, 2, and 3, have been characterized biochemically (Gilles et al. 1991; Schaertl et al. 1998; Erent et al. 2001; Chen et al. 2003). All are catalytically active as hexamers: homohexamers of NME1, 2, and 3 have been described, as have heterohexamers containing all possible combinations of NME1 and 2 (Gilles et al. 1991; Erent et al. 2001). While the high ratio of ATP to ADP concentrations in the cytosol normally favors the conversion of (d)NDP and ATP to (d)NTP and ADP, the reversibility of the reactions and the overlapping substrate specificities of the enzymes suggest that this group of reverse reactions can buffer the intracellular nucleotide pool and regulate the relative concentrations of individual nucleoside di- and tri-phosphates in the pool.
Nucleoside diphosphate kinase NME4 associated with the inner mitochondrial membrane (Tokarska-Schlattner et al. 2008) catalyzes the reversible reaction of ribonucleoside and deoxyribonucleoside 5'-diphosphates with ATP to form the corresponding nucleoside 5'-triphosphates and ADP. The active form of the enzyme is a hexamer of NME4 polypeptides whose amino-terminal 33 residues, a mitochondrial translocation signal, have been removed (Milon et al. 2000). The substrate specificity of NME4 has not been examined in detail but is inferred to be broad like that of the homologous NME1, 2, and 3 kinases (Schaertl et al. 1998).
Crystal structure of 5-aminolevulinate synthase, the first enzyme of heme biosynthesis, and its link to XLSA in humans
Cytosolic UMP-CMP kinase (CMPK1) catalyzes the reversible reaction of CDP, dCDP, or UDP and ADP to form CMP, dCMP, or UMP and ATP (Liou et al. 2002; Scott and Wright 1979).
The mitochondrial ABC transporter Atm1p functions as a homodimer
Cytosolic ribonucleotide reductase catalyzes the reduction of adenine, guanine, cytidine, and uridine ribonucleoside 5'-diphosphates to form the corresponding deoxyribonucleoside 5'-diphosphates, coupled to the oxidation of glutaredoxin (Eklund et al. 2001). Ribonucleotide reductase is a tetramer of two large and two small subunits (Shao et al. 2004; Zhou et al. 2005). The overall activity of the enzyme is regulated allosterically: ATP binding is stimulatory while dATP binding is inhibitory (Reichard et al. 2000). The reducing equivalents needed for ribonucleotide reductase activity can be provided by either of two small proteins, glutaredoxin and thioredoxin (Holmgren 1989; Sun et al. 1998). Both are re-reduced with NADPH as the donor of reducing equivalents, and so are active in catalytic amounts. The relative contributions of glutaredoxin and thioredoxin in vivo are unknown.
Cytosolic ribonucleotide reductase catalyzes the reduction of adenine, guanine, cytidine, and uridine ribonucleoside 5'-diphosphates to form the corresponding deoxyribonucleoside 5'-diphosphates, coupled to the oxidation of thioredoxin (Holmgren 1989; Eklund et al. 2001). Ribonucleotide reductase is a tetramer of two large and two small subunits (Shao et al. 2004; Zhou et al. 2005). The overall activity of the enzyme is regulated allosterically: ATP binding is stimulatory while dATP binding is inhibitory (Reichard et al. 2000). The reducing equivalents needed for ribonucleotide reductase activity can be provided by either of two small proteins, glutaredoxin and thioredoxin (Holmgren 1989; Sun et al. 1998). Both are re-reduced with NADPH as the donor of reducing equivalents, and so are active in catalytic amounts. The relative contributions of glutaredoxin and thioredoxin in vivo are unknown.
Deoxyribonucleotides needed for DNA repair are synthesized de novo by the reduction of ribonucleoside 5'-diphosphates. This reaction is catalyzed by a nuclear form of ribonucleotide reductase active throughout the cell cycle. The reducing equivalents needed for these reactions can be provided directly by thioredoxin.
Cytosolic glutaredoxin (oxidized) and glutathione (reduced) react to form glutaredoxin (reduced) and glutathione (oxidized) (Padilla et al. 1995).
Cytosolic deoxythymidylate kinase (DTYMK) catalyzes the reversible reaction of either dUMP or TMP with ATP to form dUDP or TDP. The active form of the enzyme is a homodimer (Lee and Cheng 1977).
Vascular endothelial growth factor signaling to endothelial nitric oxide synthase: more than a FLeeTing moment
Cytosolic deoxythymidylate kinase (DTYMK) catalyzes the reversible reaction of either dUDP or TDP with ADP to form dUMP or TMP. The active form of the enzyme is a homodimer (Lee and Cheng 1977).
Regulation of HSF1 function in the heat stress response: implications in aging and disease
Cytosolic CTP synthase 1 (CTPS) catalyzes the reaction of UTP, glutamine, ATP and water to form CTP, glutamate, ADP, and orthophosphate (Han et al. 2005). The active form of the enzyme is a tetramer (Kursala et al. 2006). Both CTPS and a second human gene product, CPTS2, have CTP synthase activity in various test systems; their relative contributions to CTP metabolism in the body is not clear.
Cytosolic CTP synthase 2 (CTPS) catalyzes the reaction of UTP, glutamine, ATP and water to form CTP, glutamate, ADP, and orthophosphate (Han et al. 2005; van Kuilenberg et al. 2000). Unpublished X-ray crystallographic data suggest that the enzyme is a tetramer (PDB 3IHL). Both CTPS2 and a second human gene product, CPTS, have CTP synthase activity in various test systems; their relative contributions to CTP metabolism in the body is not clear.
In this reaction, 1 molecule of 'thioredoxin, oxidized' is translocated from nucleoplasm to cytosol. This movement of the molecule occurs through the 'nuclear pore'.
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Citrin and aralar1 are Ca(2+)-stimulated aspartate/glutamate transporters in mitochondria
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A mutational analysis of the yeast proliferating cell nuclear antigen indicates distinct roles in DNA replication and DNA repair.
DNA replication initiates at multiple sites on plasmid DNA in Xenopus egg extracts.
Cytosolic dihydropyrimidine dehydrogenase catalyzes the reaction of thymine and NADPH + H+ to form 5,6-dihydrothymine and NADP+. The mechanism of the human reaction is inferred from that of the well-characterized pig enzyme (Yokota et al. 1994).
In parallel sequences of three reactions each, thymine is converted to beta-aminoisobutyrate and uracil is converted to beta-alanine. Both of these molecules are excreted in human urine and appear to be normal end products of pyrimidine catabolism (Griffith 1986; Webster et al. 2001). Mitochondrial AGXT2, however, can also catalyze the transamination of both molecules with pyruvate, yielding 2-oxoacids that can be metabolized further by reactions of branched-chain amino acid and short-chain fatty acid catabolism (Tamaki et al. 2000). The importance of these reactions in normal human pyrimidine catabolism has not been well worked out.
In pyrimidine salvage reactions, nucleosides and free bases generated by DNA and RNA breakdown are converted back to nucleotide monophosphates, allowing them to re-enter the pathways of pyrimidine biosynthesis (interconversion).
integral component of lumenal side of endoplasmic reticulum membrane
Cytosolic dihydropyrimidine dehydrogenase catalyzes the reaction of uracil and NADPH + H+ to form 5,6-dihydrouracil and NADP+. The mechanism of the human reaction is inferred from that of the well-characterized pig enzyme (Yokota et al. 1994).
Mitochondrial adenylate kinase 2 (AK2) catalyzes the reaction of two molecules of ADP to form AMP and ATP (Hamade et al. 1982). Localization of AK2 specifically to the mitochondrial intermembrane space is inferred from studies of the homologous rat enzyme (Criss 1970).
Cytosolic guanylate kinase 1 (GUK1) catalyzes the reversible reactions of GMP and dGMP with ATP to form GDP and dGDP respectively and ADP. While native gel electrophoretic studies of whole cell extracts suggested the existence of multiple human enzymes with guanylate kinase activity (Jamil et al. 1975), only one has been purified and biochemically characterized (Agarwal et al. 1978; Brady et al. 1996). The enzyme is of clinical importance as it is a target of antitumor drugs and antiviral drugs such as acyclovir (Miller and Miller 1980).
The events of human pyrimidine metabolism are conveniently, if somewhat arbitrarily, grouped into four pathways: de novo synthesis of the pyrimidine ring and its conversion to uridine 5'-monophosphate (UMP), the biosynthesis of other pyrimidine ribo- and deoxyribonucleotides, pyrimidine salvage reactions, and pyrimidine catabolism (Loffler et al. 2005). De novo synthesis of the pyrimidine ring and its conversion to UMP. The pyrimidine base orotate is synthesized from glutamine, bicarbonate, and aspartate. Orotate reacts with 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) and is then decarboxylated to form the pyrimidine nucleotide UMP. Pyrimidine biosynthesis [interconversion]. Pyrimidine ribo- and deoxyribonucleotide di- and triphosphates are synthesized, both from UMP and from pyrimidine ribonucleotide monophosphates generated in salvage reactions. Pyrimidine salvage reactions. Pyrimidine nucleosides and free bases generated by DNA and RNA breakdown are converted to nucleotide monophosphates. Pyrimidine catabolism. The pyrimidine bases thymine and uracil are degraded to beta-aminoisobutyrate and beta-alanine, respectively, which are excreted from the body.
Mitochondrial adenylate kinase 2 (AK2) catalyzes the reaction of AMP and ATP to form two molecules of ADP (Hamade et al. 1982). Localization of AK2 specifically to the mitochondrial intermembrane space is inferred from studies of the homologous rat enzyme (Criss 1970).
Cytosolic UMP-CMP kinase (CMPK1) catalyzes the reversible reaction of CMP, dCMP, or UMP and ATP to form CDP, dCDP, or UDP and ADP (Liou et al. 2002; Scott and Wright 1979).
Cytosolic guanylate kinase 1 (GUK1) catalyzes the reversible reactions of GDP and dGDP with ADP to form GMP and dGMP respectively and ATP. While native gel electrophoretic studies of whole cell extracts suggested the existence of multiple human enzymes with guanylate kinase activity (Jamil et al. 1975), only one has been purified and biochemically characterized (Agarwal et al. 1978; Brady et al. 1996). The enzyme is of clinical importance as it is a target of antitumor drugs and antiviral drugs such as acyclovir (Miller and Miller 1980).
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Multiple layers of regulation of human heat shock transcription factor 1
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The synthesis of carbamoyl phosphate from glutamine, bicarbonate, and ATP is catalyzed by the carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity of cytosolic trifunctional CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase) protein (Ito and Uchino 1973; Iwahana et al. 1996). The purified human protein is active in several different oligomerization states, as is its Syrian hamster homologue. The most abundant form of the latter is a hexamer, and the active human protein is annotated as a hexamer by inference (Ito and Uchino 1973; Lee et al. 1985).
The synthesis of N-carbamoyl L-aspartate from carbamoyl phosphate and L-aspartate is catalyzed by the aspartate carbamoyltansferase activity of cytosolic trifunctional CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase) protein (Ito and Uchino 1973; Iwahana et al. 1996). The purified human protein is active in several different oligomerization states as is its Syrian hamster homologue. The most abundant form of the latter is a hexamer, and the active human protein is annotated as a hexamer by inference (Ito and Uchino 1973; Lee et al. 1985).
The synthesis of dihydroorotate from N-carbamoyl L-aspartate is catalyzed by the dihydroorotase activity of cytosolic trifunctional CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase) protein. This activity has not been directly demonstrated in experimental studies of the purified human protein, but has been inferred from the behavior of the purified hamster protein and the high degree of sequence similarity between the cloned hamster and human genes (Iwahana et al. 1996). Also on the basis of this similarity, the active human protein is annotated as a hexamer (Lee et al. 1985).
The synthesis of orotidine 5'-monophosphate (OMP) from orotate and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) is catalyzed by the orotate phosphoribosyltransferase activity of the bifunctional "uridine monophosphate synthetase (orotate phosphoribosyl transferase and orotidine 5'-decarboxylase)" protein. The reaction itself is freely reversible, but is pulled in the forward direction in vivo by the irreversible hydrolysis of pyrophosphate. While purified human protein has not been characterized in detail, the close similarity of the human gene to that encoding the well-studied hamster protein, and the demonstration that mutations in the human gene are associated with failure to convert orotate to UMP in vivo, provide convincing evidence that the human uridine monophosphate synthetase protein indeed catalyzes these two reactions (McClard et al. 1980; Suchi et al. 1997). The active form of the human protein is a dimer (Yablonski et al. 1996; Wittmann et al. 2008).
The decarboxylation of orotidine 5'-monophosphate (OMP) to form uridine 5'-monophosphate (UMP) is catalyzed by the orotidine 5'-phosphate decarboxylase activity of the bifunctional "uridine monophosphate synthetase (orotate phosphoribosyl transferase and orotidine 5'-decarboxylase)" protein. While purified human protein has not been characterized in detail, the close similarity of the human gene to that encoding the well-studied hamster protein, and the demonstration that mutations in the human gene are associated with failure to convert orotate to UMP in vivo, provide convincing evidence that the human uridine monophosphate synthetase protein indeed catalyzes these two reactions (McClard et al. 1980; Suchi et al. 1997). The active form of the human protein is a dimer (Yablonski et al. 1996; Wittmann et al. 2008).
Cytosolic deoxycytidylate deaminase (DCTD) catalyzes the hydrolysis of dCMP (2'-deoxyuridine 5'-monophosphate) to yield dUMP (2'-deoxyuridine 5'-monophosphate) and ammonia. The active enzyme is a homohexamer (Maley et al. 1993; Weiner et al. 1993; unpublished crystallography data - PDB 2W4L).
Deoxyuridine triphosphatase (DUT) catalyzes the hydrolysis of dUTP to form dUMP and pyrophosphate. Two isoforms of DUT are expressed, generated by alternative splicing. The major one, annotated here, is localized to the nucleoplasm (Ladner et al. 1996). The enzyme is a homotrimer (Mol et al. 1996). In the cell, this reaction depletes the supply of dUTP, preventing its incorporation into DNA, while generating dUMP, the immediate precursor of thymidine nucleotides.
The pyrimidine orotate (orotic acid) is synthesized in a sequence of four reactions, deriving its atoms from glutamine, bicarbonate, and aspartate. A single multifunctional cytosolic enzyme catalyzes the first three of these reactions, while the last one is catalyzed by an enzyme associated with the inner mitochondrial membrane. In two further reactions, catalyzed by a bifunctional cytosolic enzyme, orotate reacts with 1-phosphoribosyl 5-pyrophosphate (PRPP) to yield orotidine 5'-monophosphate, which is decarboxylated to yield uridine 5'-monophosphate (UMP). While several individual reactions in this pathway are reversible, other irreversible reactions drive the pathway in the direction of UMP biosynthesis in the normal cell. All reactions are thus annotated here only in the forward direction. This pathway has been most extensively analyzed at the genetic and biochemical level in hamster cell lines. All three enzymes have also been purified from human sources, however, and the key features of these reactions have been confirmed from studies of this human material (Jones 1980; Webster et al. 2001). All other pyrimidines are synthesized from UMP. The reactions annotaed here, catalyzed by dCMP deaminase and dUTP diphosphatase yield dUMP, which in turn is converted to TMP by thymidylate synthase.
Cytosolic thymidylate synthase catalyzes the reaction of dUMP and N5,N10-methylene tetrahydrofolate to form TMP and dihydrofolate (Davisson et al. 1989). The enzyme is a homodimer (Phan et al. 2001).
Fibroblast growth factors and their receptors in cancer
Cytosolic cytidine deaminase catalyzes the hydrolysis of cytidine or dexoycytidine to form uridine or deoxyuridine and ammonia (Laliberte and Momparler 1994). The active form of the enzyme is a tetramer (Chung et al. 2005).
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Human acid sphingomyelinase. Isolation, nucleotide sequence and expression of the full-length and alternatively spliced cDNAs
The Hsp70 and TRiC/CCT chaperone systems cooperate in vivo to assemble the von Hippel-Lindau tumor suppressor complex
Different gamma-glutamyl transpeptidase mRNAs are expressed in human liver and kidney
(S)-Hydroperoxy-6-trans-8,11,14-cis-eicosatetraenoic acid
LAB/NTAL/Lat2: a force to be reckoned with in all leukocytes?
Lysine acetylation targets protein complexes and co-regulates major cellular functions
ZFP36 (Tristetraproline, TTP) binds AU-rich elements in 3' UTR of target mRNAs
Protein Kinase B/Akt phosphorylates BRF1
Butyrate Response Factor1 (BRF1) binds AU-rich element in 3' UTR of mRNA
9Z,12Z,15Z,18Z-Tetracosatetraenoyl-CoA (TTA-CoA)
AUF1(hnRNP D0) dimers bind AU-rich element in 3' UTR of mRNA
Formation of UPF1:eRF3 complex on mRNA with a premature termination codon and no Exon Junction Complex
7Z,10Z,13Z,16Z-docosatetraenoyl-CoA (DTA-CoA)
SMG1 phosphorylates UPF1 (enhanced by Exon Junction Complex)
Glutamic-pyruvate transaminase 2 (alanine aminotransferase 2) (GPT2) catalyzes the reversible reaction of pyruvate and glutamate to form alanine and 2-oxoglutarate (alpha-ketoglutarate) (Yang et al. 2002). Unpublished crystallographic data are consistent with a homodimeric structure for the enzyme with one molecule of pyridoxal phosphate associated with each monomer (PDB 3IHJ). Recent studies of organelles purified from cultured human muscle cells suggest that GPT2 is localized to mitochondria (Glinghammar et al. 2009).
Glutamic-pyruvate transaminase 2 (alanine aminotransferase 2) (GPT2) catalyzes the reversible reaction of alanine and 2-oxoglutarate (alpha-ketoglutarate) to form pyruvate and glutamate (Yang et al. 2002). Unpublished crystallographic data are consistent with a homodimeric structure for the enzyme with one molecule of pyridoxal phosphate associated with each monomer (PDB 3IHJ). Recent studies of organelles purified from cultured human muscle cells suggest that GPT2 is localized to mitochondria (Glinghammar et al. 2009).
Oligosaccharyl transferase 48 kDa subunit
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
Cytosolic glutamic-pyruvate transaminase (alanine aminotransferase) (GPT) catalyzes the reversible reaction of pyruvate and glutamate to form alanine and 2-oxoglutarate (alpha-ketoglutarate) (Sohocki et al. 1997; Yang et al. 2002). The active form of the enzyme is a dimer (Ishiguro et al. 1991) and is inferred to have a molecule of pyridoxal phosphate associated with each monomer. This reaction allows the synthesis of alanine from intermediates of glucose metabolism in a well-fed person. Under fasting conditions, alanine, derived from protein breakdown, can be converted to pyruvate and used to synthesize glucose via the gluconeogenic pathway in liver, or fully oxidized via the TCA cycle in other tissues.
6Z,9Z,12Z,15Z,18Z-tetracosapentaenoyl-CoA (TPA-CoA)
Cytosolic glutamic-pyruvate transaminase (alanine aminotransferase) (GPT) catalyzes the reversible reaction of alanine and 2-oxoglutarate (alpha-ketoglutarate) to form pyruvate and glutamate (Sohocki et al. 1997; Yang et al. 2002). The active form of the enzyme is a dimer (Ishiguro et al. 1991) and is inferred to have a molecule of pyridoxal phosphate associated with each monomer. This reaction allows the synthesis of alanine from intermediates of glucose metabolism in a well-fed person. Under fasting conditions, alanine, derived from protein breakdown, can be converted to pyruvate and used to synthesize glucose via the gluconeogenic pathway in liver, or fully oxidized via the TCA cycle in other tissues.
Sprinter: a novel transmembrane protein required for Wg secretion and signaling
Mitochondrial ornithine aminotransferase (OAT) catalyzes the reversible reaction of ornithine and alpha-ketoglutarate to form glutamate semialdehyde and glutamate (Ohura et al. 1982). The active enzyme is a hexamer (Shen et al. 1998). Inherited OAT deficiency leads to ornithine accumulation in vivo and gyrate atrophy of the choroid and retina (Brody et al. 1992; Valle and Simell 2001).
Mitochondrial glutamate oxaloacetate transaminase 2 (aspartate aminotransferase 2 - GOT2) catalyzes the reversible reaction of aspartate and 2-oxoglutarate (alpha-ketoglutarate) to form oxaloacetate and glutamate (Martini et al. 1985). The active form of the enzyme is inferred to be a dimer with one molecule of pyridoxal phosphate associated with each monomer.
Protein kinase C substrate 60.1 kDa protein heavy chain
Mucopolysaccharidosis type II (Hunter syndrome): a clinical review and recommendations for treatment in the era of enzyme replacement therapy
Cytosolic aspartate aminotransferase (glutamate oxaloacetate transaminase 1 - GOT1) catalyzes the reversible reaction of oxaloacetate and glutamate to form aspartate and 2-oxoglutarate (alpha-ketoglutarate) (Doyle et al. 1990). Unpublished crystallographic data (PBD 3IIO) suggest the enzyme is a homodimer.
Vitamins are a diverse group of organic compounds, required in small amounts in the diet. They have distinct biochemical roles, often as coenzymes, and are either not synthesized or synthesized only in limited amounts by human cells. Vitamins are classified according to their solubility, either fat-soluble or water-soluble. The physiological processes dependent on vitamin-requiring reactions include many aspects of intermediary metabolism, vision, bone formation, and blood coagulation, and vitamin deficiencies are associated with a correspondingly diverse and severe group of diseases. The metabolism of water-soluble vitamins and of vitamin D are annotated in Reactome.
Nucleotides and their derivatives are used for short-term energy storage (ATP, GTP), for intra- and extra-cellular signaling (cAMP; adenosine), as enzyme cofactors (NAD, FAD), and for the synthesis of DNA and RNA. Most dietary nucleotides are consumed by gut flora; the human body's own supply of these molecules is synthesized de novo. Additional metabolic pathways allow the interconversion of nucleotides, the salvage and reutilization of nucleotides released by degradation of DNA and RNA, and the catabolism of excess nucleotides (Rudolph 1994). These pathways are regulated to control the total size of the intracellular nucleotide pool, to balance the relative amounts of individual nucleotides, and to couple the synthesis of deoxyribonucleotides to the onset of DNA replication (S phase of the cell cycle). These pathways are also of major clinical interest as they are the means by which nucleotide analogues used as anti-viral and anti-tumor drugs are taken up by cells, activated, and catabolized (Weilin and Nordlund 2010). As well, differences in nuclotide metabolic pathways between humans and aplicomplexan parasites like Plasmodium have been exploited to design drugs to attack the latter (Hyde 2007). The movement of nucleotides and purine and pyrimidine bases across lipid bilayer membranes, mediated by SLC transporters, is annotated as part of the module "transmembrane transport of small molecules".
Enzymes that belong to the NUDT (Nudix) superfamily catalyze the hydrolysis of phosphodiester bonds in molecules including nucleoside triphosphates and diphosphates and nucleotide sugars. Family members are defined by the presence of an amino acid sequence motif shared with the E. coli MutT gene product, and are involved in diverse physiological processes (Mildvan et al. 2005; McLennan 2006). The hydrolysis of nucleoside di and triphosphates whose purine bases have been oxidized or deaminated may protect the cell from the mutational damage that would occur if modified deoxyribonucleotides were incorporated into DNA and from the aberrant protein synthesis that would occur if modified ribonucleotides were incorporated into mRNA (Iyama et al. 2010; Takagi et al. 2012). The hydrolysis of ADP ribose may prevent the aberrant spontaneous ADP ribosylation of cellular proteins that could occur were this molecule to accumulate to high levels in the cell (Perraud et al. 2003; Shen et al. 2003). This hypothesis is further supported by the demonstration that mice lacking NUDT1 show an increased lifetime incidence of liver and other tumors compared to normal controls, and that rapidly metabolizing tumor cells in culture are killed under conditions where synthesis of NUDT1 protein is suppressed or its catalytic activity is inhibited (Gad et al. 2014; Huber et al. 2014).
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9Z,12Z,15Z,18Z,21Z-tetracosapentaenoyl-CoA (TPA-CoA)
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7Z,10Z,13Z,16Z,19Z-docosapentaenoyl-CoA (DPA-CoA)
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6Z,9Z,12Z,15Z,18Z,21Z-tetracosahexaenoyl-CoA (THA-CoA)
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PP2A -56 kDa regulatory subunit B epsilon isoform
Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
(4Z,7Z,10Z,13Z,16Z,19Z)-Docosahexaenoic acid
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Differential expression and regulation of toll-like receptors (TLR) in human leukocytes: selective expression of TLR3 in dendritic cells
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Multidrug resistance mediated by the breast cancer resistance protein BCRP (ABCG2)
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Global gene expression profiling and histochemical analysis of the developing human fetal pancreas
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Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform
PP2A- 56 kDa regulatory subunit, alpha isoform
8Z,11Z,14Z,17Z-Eicosatetraenoyl-CoA (ETA-CoA)
The yeast Pif1p helicase removes telomerase from telomeric DNA
SCF-beta-TrCP mediated degradation of Emi1
Cathepsin D component recommendedName: Cathepsin D light chain /component component recommendedName: Cathepsin D heavy chain /component
FUNCTION Heme-containing component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex), which is part of the mitochondrial respiratory chain that generates an electrochemical potential coupled to ATP synthesis. The complex couples electron transfer from ubiquinol to cytochrome c.SUBUNIT Fungal cytochrome b-c1 complex contains 10 subunits; 3 respiratory subunits, 2 core proteins and 5 low-molecular weight proteins. Cytochrome b-c1 complex is a homodimer.PTM Binds 1 heme group per subunit.MISCELLANEOUS Present with 39900 molecules/cell in log phase SD medium.SIMILARITY Belongs to the cytochrome c family.SIMILARITY Contains 1 cytochrome c domain.
Cloning, tissue distribution, genomic organization, and functional characterization of NBC3, a new member of the sodium bicarbonate cotransporter family
On the discovery of precursor processing
Structure of human phosphopantothenoylcysteine synthetase at 2.3 A resolution.
RBBP7 binds histone H3 arginine-3 (H3R2).
MRS3/4 Transports Iron Across the Mitochondrial Inner Membrane
MRS3/4 transports ferrous iron across the mitochondrial inner membrane (Foury et al. 2002, Muhlenhoff et al. 2003).
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KDM6A, KDM6B, KDM7A demethylate Me2K28/Me3K28 histone H3
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KDM3A, KDM3B, KDM7A, PHF2:ARID5B, PHF8 demethylate MeK10/Me2K10 histone H3
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KDM2A, KDM2B, KDM4A demethylate MeK37/Me2K37 histone H3
Regulated expression of three C/EBP isoforms during adipose conversion of 3T3-L1 cells
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KDM5A-D demethylate Me2K5/Me3K5 histone H3
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KDM4A, KDM4B, KDM4C, KDM4D demethylate Me2K10/Me3K10 histone H3
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SPT5 subunit of Pol II binds the RNA triphosphatase (RTP)
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DSIF complex binds to RNA Pol II (hypophosphorylated)
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Hypophosphorylation of RNA Pol II CTD by FCP1P protein
RNA Polymerase II CTD (phosphorylated) binds to CE
Phosphorylation (Ser5) of RNA pol II CTD
Extrusion of 5'-end of 30 nt long transcript through the pore in Pol II complex
Addition of nucleotides between position +11 and +30
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Addition of nucleotides 10 and 11 on the growing transcript: Third Transition
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Addition of the fourth nucleotide on the Nascent Transcript: Second Transition
Addition of the third nucleotide on the nascent transcript
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Newly Formed Phosphodiester Bond Stabilized and PPi Released
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Nucleophillic Attack by 3'-hydroxyl Oxygen of nascent transcript on the Alpha Phosphate of NTP
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NTP Binds Active Site of RNA Polymerase II
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RNA Polymerase II Promoter Opening: First Transition
3-Hexaprenyl-4-hydroxy-5-methoxybenzoate [ChEBI:1510]
phenylalanine + tRNA(Phe) + ATP => Phe-tRNA(Phe) + AMP + pyrophosphate
serine + tRNA(Ser) + ATP => Ser-tRNA(Ser) + AMP + pyrophosphate
threonine + tRNA(Thr) + ATP => Thr-tRNA(Thr) + AMP + pyrophosphate
tryptophan + tRNA(Trp) + ATP => Trp-tRNA(Trp) + AMP + pyrophosphate
The transcriptional repressor JHDM3A demethylates trimethyl histone H3 lysine 9 and lysine 36
The putative oncogene GASC1 demethylates tri- and dimethylated lysine 9 on histone H3
Bora and the kinase Aurora a cooperatively activate the kinase Plk1 and control mitotic entry
Glyceraldehyde-3-phosphate dehydrogenase from human tissues.
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ATAC spliceosome mediated 3' splice site cleavage, exon ligation
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ATAC spliceosome mediated Lariat formation,5' splice site cleavage
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asparagine + tRNA(Asn) + ATP => Asn-tRNA(Asn) + AMP + pyrophosphate
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alanine + tRNA(Ala) + ATP => Ala-tRNA(Ala) + AMP + pyrophosphate
glycine + tRNA(Gly) + ATP => Gly-tRNA(Gly) + AMP + pyrophosphate
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cysteine + tRNA(Cys) + ATP => Cys-tRNA(Cys) + AMP + pyrophosphate
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histidine + tRNA(His) + ATP => His-tRNA(His) + AMP + pyrophosphate
The endoribonuclease activity of mammalian IRE1 autoregulates its mRNA and is required for the unfolded protein response
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Transfer of GMP from the capping enzyme GT site to 5'-end of mRNA
Formation of the CE:GMP intermediate complex
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Hydrolysis of the 5'-end of the nascent transcript by the capping enzyme
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Recognition and binding of the mRNA cap by the cap-binding complex
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Methylation of GMP-cap by RNA Methyltransferase
Molecular cloning and characterization of PLC-eta2
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Dissociation of transcript with 5'-GMP from GT
1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate [ChEBI:16851]
Sequencing and expression of a cDNA for human glutathione synthetase
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Carbohydrate responsive element-binding protein (ChREBP): a key regulator of glucose metabolism and fat storage
The unfolded protein response is an important regulator of inflammatory genes in endothelial cells
Solute carrier family 2, facilitated glucose transporter, member 2
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GAPs inactivate Rho GTPase:GTP by hydrolysis
Dissociation of Rho GTP:GDP from GDI complex
G alpha (i) auto-inactivates by hydrolysing GTP to GDP
Glucose transporter type 4, insulin-responsive
Solute carrier family 2, facilitated glucose transporter, member 4
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Pam16 has an essential role in the mitochondrial protein import motor
Cloning and functional expression of a human kidney Na+:HCO3- cotransporter
SREBP transcription factors: master regulators of lipid homeostasis
sn-Glycero-3-phosphocholine [ChEBI:10646]
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Mutational analysis of a patient with mucopolysaccharidosis type VII, and identification of pseudogenes
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Fall Back to Closed Pre-initiation Complex
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Recognition and Binding of Core Promoter Elements by TFIID
Binding of TFIIA and TFIIB to the pol II promoter:TFIID complex
Recruitment of RNA Polymerase II Holoenzyme by TFIIF to the pol II promoter:TFIID:TFIIA:TFIIB complex
miRNAs on the move: miRNA biogenesis and the RNAi machinery
Formation of the closed pre-initiation complex
Human MTH3 (NUDT18) Protein Hydrolyzes Oxidized Forms of Guanosine and Deoxyguanosine Diphosphates: COMPARISON WITH MTH1 AND MTH2
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G alpha (z) auto-inactivates by hydrolysing GTP to GDP
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Transcriptional regulation of HMG-CoA synthase and HMG-CoA reductase genes by human ACBP
translocation and activation of PKC alpha in response to WNT signaling
Diacylgycerol activates Protein kinase C, alpha type
Phytanic acid and pristanic acid are oxidized by sequential peroxisomal and mitochondrial reactions in cultured fibroblasts
Planar cell polarity signaling: from fly development to human disease
Interactions between the endoplasmic reticulum, mitochondria, plasma membrane and other subcellular organelles
Sodium-coupled sulphate, di- and tri-carboxylate transporters
The oncogenic properties of mutant p110alpha and p110beta phosphatidylinositol 3-kinases in human mammary epithelial cells
Proc. Natl. Acad. Sci. U.S.A. 102:18443-8
Platelet activation, signaling and aggregation
Eukaryotic ribosomes require initiation factors 1 and 1A to locate initiation codons.
Synthesis of PIPs at the plasma membrane
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lysine + tRNA(Lys) + ATP => Lys-tRNA(Lys) + AMP + pyrophosphate
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methionine + tRNA(Met) + ATP => Met-tRNA(Met) + AMP + pyrophosphate
isoleucine + tRNA(Ile) + ATP => Ile-tRNA(Ile) + AMP + pyrophosphate
leucine + tRNA(Leu) + ATP => Leu-tRNA(Leu) + AMP + pyrophosphate
ABC transporters in cellular lipid trafficking
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valine + tRNA(Val) + ATP => Val-tRNA(Val) + AMP + pyrophosphate
tyrosine + tRNA(Tyr) + ATP => Tyr-tRNA(Tyr) + AMP + pyrophosphate
Phosphatidylinositol-5-phosphate activation and conserved substrate specificity of the myotubularin phosphatidylinositol 3-phosphatases
proline + tRNA(Pro) + ATP => Pro-tRNA(Pro) + AMP + pyrophosphate
Mitochondrial isocitrate dehydrogenase IDH2 catalyzes the irreversible reaction of isocitrate and NADP+ to form alpha ketoglutarate, CO2, and NADPH + H+ (Hartong et al. 2008). The structure of the active human enzyme has not been determined experimentally, but is inferred to be a homodimer with one Mn++ bound to each subunit based on detailed studies of the homologous pig enzyme (Ceccarelli et al. 2002). NADP-specific IDH2 was the first isocitrate dehydrogenase isoenzyme to be characterized in biochemical studies of the mammalian TCA cycle (Ochoa 1948). Later work with yeast revealed the existence of both NADP-specific (IDH2-homologous) and NAD-specific (IDH3-homologous) enzymes and demonstrated the ADP-dependence of the latter (Kornberg and Pricer 1951), consistent with the now widely accepted view that IDH3 mediates the conversion of isocitrate to alpha-ketoglutarate in the TCA cycle. The physiological function of IDH2 is thus unclear. The recent observation that individuals homozygous for IDH3 mutations that sharply reduce its activity do not show symptoms of deficient energy metabolism in most tissues raises the possibility that the IDH2 reaction may play an accessory role in the TCA cycle (Hartong et al. 2008).
arginine + tRNA(Arg) + ATP => Arg-tRNA(Arg) + AMP + pyrophosphate
Central leptin and ghrelin signalling: comparing and contrasting their mechanisms of action in the brain
Mitochondrial isocitrate dehydrogenase IDH3 catalyzes the irreversible reaction of isocitrate and NAD+ to form alpha ketoglutarate, CO2, and NADH + H+. The enzyme is a heteromer containing four polypeptide chains, two IDH3A, one IDH3B, and one IDH3G, and two Mn++ (Dange and Colman 2010). It is activated by ADP (Soundar et al. 2003, 2006; Bzymek and Colman 2007). This is the first of four oxidation reactions in the citric acid cycle, and the first decarboxylation.
Mitochondrial succinate CoA ligase (ADP-forming) catalyzes the reversible conversion of succinyl CoA to succinate plus Coenzyme A, coupled to the conversion of ADP and orthophosphate to ATP. The enzyme is a heterodimer containing SUCLG1 and SUCLA2 monomers. The enzyme catalyzing the reaction in vertebrates is a heterodimer that occurs in two isoforms. The enzymes have been purified from pigeon and rat tissue and characterized in detail. Both isoforms, an alpha:betaA heterodimer and an alpha:betaG heterodimer, catalyze the reversible conversion of succinyl CoA to succinate plus Coenzyme A. The alpha:betaA heterodimer couples this conversion to the synthesis of ATP from ADP and orthophosphate, while the alpha:betaG heterodimer couples it to the synthesis of GTP from GDP and orthophosphate (Johnson et al. 1998a,b; Lambeth et al. 2004). Consistent with these results in model systems, patients homozygous for a mutant allele of the gene encoding the ADP enzyme beta subunit, SUCLA2, are deficient in succinyl CoA ligase activity (Elpeleg et al. 2005). Both isoforms are found in vivo, and appear to be expressed at different levels in various tissues. Their relative contributions to the flux of carbon atoms through the TCA cycle are unknown. Genetic and biochemical data suggest that the alpha:betaA isoform may be required to catalyze the reverse reaction, conversion of succinate, Coenzyme A, and ATP to succinyl CoA, ADP, and orthophosphate for heme biosynthesis (Furuyama and Sassa 2000).
The mitochondrial alpha-ketoglutarate dehydrogenase complex catalyzes the reaction of alpha-ketoglutarate, CoASH, and NAD+ to form succinyl-CoA, CO2, and NADH. The enzyme complex contains multiple copies of three different proteins, E1 (OGDH), E2 (DLST), and E3 (DLD), each with distinct catalytic activities (Reed and Hackert 1990; Zhou et al 2001). The reaction starts with the oxidative decarboxylation of alpha ketoglutarate catalyzed by E1alpha and beta (alpha ketoglutarate dehydrogenase). Lipoamide cofactor associated with E1 is reduced at the same time. Next, the succinyl group derived from alpha ketoglutarate is transferred to coenzyme A in two steps catalyzed E2 (dihydrolipolyl transacetylase). Finally, the oxidized form of lipoamide is regenerated and electrons are transferred to NAD+ in two steps catalyzed by E3 (dihydrolipoyl dehydrogenase). The biochemical details of this reaction have been worked out with alpha ketoglutarate dehydrogenase complex and subunits purified from bovine tissue (McCartney et al. 1998). While all of the human proteins are known as predicted protein products of cloned genes, direct experimental evidence for their functions is available only for E3 (DLD) (Brautigam et al. 2005).
Mitochondrial fumarate hydratase catalyzes the reversible reaction of fumarate and water to form malate, the seventh step of the TCA cycle (Bourgeron et al. 1994). Unpublished crystallographic data indicate that the protein is a tetramer (PDB 3E04).
tyrosine + tRNA(Tyr) + ATP =>Tyr-tRNA(Tyr) + AMP + pyrophosphate
The succinate dehydrogenase complex, associated with the inner mitochondrial membrane, catalyzes the dehydrogenation of succinate to fumarate, reducing the FAD cofactor bound to the enzyme. This redox potential is then used in the electron transfer chain to drive a proton motive force to generate ATP.
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Mitochondrial malate dehydrogenase catalyzes the reversible reaction of malate and NAD+ to form oxaloacetate and NADH + H+ (Luo et al. 2006). This reaction is highly endergonic but is pulled in the direction annotated here when the TCA cycle is operating. Unpublished crystallographic data indicate that the protein is a dimer (PDB 3E04).
pyrophosphate + H2O => 2 orthophosphate [cytosolic]
Mitochondrial fumarate hydratase catalyzes the reversible reaction of malate to form fumarate and water (Bourgeron et al. 1994). Unpublished crystallographic data indicate that the protein is a tetramer (PDB 3E04).
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Erythrocytes take up oxygen and release carbon dioxide
glutamine + tRNA(Glu) + ATP => Glu-tRNA(Glu) + AMP + pyrophosphate
glutamate + tRNA(Glu) + ATP => Glu-tRNA(Glu) + AMP + pyrophosphate
Mitochondrial aconitase reversibly converts citrate to isocitrate via a cis-aconitate intermediate. Mitochondrial aconitase activity has been demonstrated in diverse human tissue extracts (Slaughter et al. 1975) and a protein homologous to the well-characterized porcine enzyme has been purified from human tissues (Baldwin et al. 1991).
aspartate + tRNA(Asp) + ATP => Asp-tRNA(Asp) + AMP + pyrophosphate
Mitochondrial aconitase reversibly converts isocitrate to citrate via a cis-aconitate intermediate. Mitochondrial aconitase activity has been demonstrated in diverse human tissue extracts (Slaughter et al. 1975) and a protein homologous to the well-characterized porcine enzyme has been purified from human tissues (Baldwin et al. 1991).
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pyrophosphate + H2O => 2 orthophosphate [mitochondrial]
Identification and characterization of PS-GAP as a novel regulator of caspase-activated PAK-2
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DCPS scavenges the 7-methylguanosine cap of mRNA
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5' to 3' exoribonuclease hydrolyzes decapped mRNA
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Human CDC6/Cdc18 associates with Orc1 and cyclin-cdk and is selectively eliminated from the nucleus at the onset of S phase.
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Potential role of protein kinase B in insulin-induced glucose transport, glycogen synthesis, and protein synthesis
The molecular mechanisms that control thrombopoiesis
Multisite autophosphorylation of p21-activated protein kinase gamma-PAK as a function of activation
Cellular circadian pacemaking and the role of cytosolic rhythms
Regulation of conventional protein kinase C isozymes by phosphoinositide-dependent kinase 1 (PDK-1)
The yeast mitochondrial carrier Leu5p and its human homologue Graves' disease protein are required for accumulation of coenzyme A in the matrix
Cloning and characterization of a nuclear S6 kinase, S6 kinase-related kinase (SRK); a novel nuclear target of Akt
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IP3 receptor/Ca2+ channel: from discovery to new signaling concepts
Acetylcholine Neurotransmitter Release Cycle
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Cloning and characterization of human guanine deaminase. Purification and partial amino acid sequence of the mouse protein.
Molecular determinants of regulated exocytosis
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Amino acid and oligopeptide SLC transporters
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Somatic mutations in p85alpha promote tumorigenesis through class IA PI3K activation
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Cloning of the human equilibrative, nitrobenzylmercaptopurine riboside (NBMPR)-insensitive nucleoside transporter ei by functional expression in a transport-deficient cell line
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Identification and characterization of a novel inositol polyphosphate 5-phosphatase
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Apert syndrome results from localized mutations of FGFR2 and is allelic with Crouzon syndrome
Architecture of the human origin recognition complex.
Caspase activation of mammalian sterile 20-like kinase 3 (Mst3). Nuclear translocation and induction of apoptosis
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NRAGE, a p75 neurotrophin receptor-interacting protein, induces caspase activation and cell death through a JNK-dependent mitochondrial pathway
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Human MSH2 (hMSH2) protein controls ATP processing by hMSH2-hMSH6
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Fibroblast growth factor signalling: from development to cancer
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MyD88 cascade initiated on plasma membrane
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Pyrimidine nucleotide biosynthesis in animals: genes, enzymes, and regulation of UMP biosynthesis.
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A three-dimensional working model of the multienzyme complex of aminoacyl-tRNA synthetases based on electron microscopic placements of tRNA and proteins
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Protein import into yeast mitochondria is accelerated by the outer membrane protein MAS70
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Subcellular localization and regulation of coenzyme A synthase
Proximal signaling events in Fc epsilon RI-mediated mast cell activation
J. Allergy Clin. Immunol. 119:544-52; quiz 553-4
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Distinct nucleotide binding/hydrolysis properties and molar ratio of MutSalpha and MutSbeta determine their differential mismatch binding activities
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The role of mast cells in allergic inflammation
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Biochemistry of mammalian peroxisomes revisited
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Role, metabolism, chemical modifications and applications of hyaluronan
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Analysis of phosphorylation of human heat shock factor 1 in cells experiencing a stress
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Members of the human glyceraldehyde-3-phosphate dehydrogenase-related gene family map to dispersed chromosomal locations.
Alternative function for the mitochondrial SAM complex in biogenesis of alpha-helical TOM proteins
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mRNA quality control: an ancient machinery recognizes and degrades mRNAs with nonsense codons
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Integrating mRNA processing with transcription.
Caenorhabditis elegans mboa-7, a member of the MBOAT family, is required for selective incorporation of polyunsaturated fatty acids into phosphatidylinositol
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Human aquaporin adipose (AQPap) gene. Genomic structure, promoter analysis and functional mutation
Roles of C-terminal processing, and involvement in transacylation reaction of human group IVC phospholipase A2 (cPLA2gamma)
XBP1 induces WFS1 through an endoplasmic reticulum stress response element-like motif in SH-SY5Y cells
Fcgamma receptor (FCGR) dependent phagocytosis
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Uninterrupted MCM2-7 function required for DNA replication fork progression.
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Src-family kinases in B-cell development and signaling
Redox-switch modulation of human SSADH by dynamic catalytic loop
Transport of glycerol from adipocytes to the liver by Aquaporins
Phosphoglucomutase 1: a gene with two promoters and a duplicated first exon
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SLC2A9 is a newly identified urate transporter influencing serum urate concentration, urate excretion and gout
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Molecular cloning of a human cDNA encoding a trifunctional enzyme of carbamoyl-phosphate synthetase-aspartate transcarbamoylase-dihydroorotase in de Novo pyrimidine synthesis
Facilitated folding of actins and tubulins occurs via a nucleotide-dependent interaction between cytoplasmic chaperonin and distinctive folding intermediates
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DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs.
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Neuregulin-1 only induces trans-phosphorylation between ErbB receptor heterodimer partners
COFACTOR Binds 4 4Fe-4S clusters per heterotetramer. Contains two stable clusters in the N-termini of NBP35 and two labile, bridging clusters between subunits of the NBP35-CFD1 heterotetramer.SIMILARITY Belongs to the Mrp/NBP35 ATP-binding proteins family. NUBP1/NBP35 subfamily.
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The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans
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Overexpression of cytosolic glutathione peroxidase (GPX1) delays endothelial cell growth and increases resistance to toxic challenges
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Cdk2-dependent and -independent pathways in E2F-mediated S phase induction
Limiting role of 6-phosphogluconolactonase in erythrocyte hexose monophosphate pathway metabolism
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Adipocyte differentiation from the inside out
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Triggering and augmentation mechanisms, granule pools, and biphasic insulin secretion
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Mia40, a novel factor for protein import into the intermembrane space of mitochondria is able to bind metal ions
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Cloning, sequencing, and expression of cDNA for human beta-galactosidase
Biochem. Biophys. Res. Commun. 157:238-44
The role of the Rho GTPases in neuronal development
(S)-3-Hydroxyisobutyryl-CoA [ChEBI:28259]
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Defective CUBN causes hereditary megaloblastic anemia 1
Identification of holocarboxylase synthetase (HCS) proteins in human placenta
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The spectrum of latent tuberculosis: rethinking the biology and intervention strategies
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Mismatch Repair proteins are recruited to replicating DNA through interaction with Proliferating Cell Nuclear Antigen (PCNA)
GPI7 is the second partner of PIG-F and involved in modification of glycosylphosphatidylinositol
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Lathosterolosis, a novel multiple-malformation/mental retardation syndrome due to deficiency of 3beta-hydroxysteroid-delta5-desaturase
Identification of Gz alpha as a pertussis toxin-insensitive G protein in human platelets and megakaryocytes
Protein folding: versatility of the cytosolic chaperonin TRiC/CCT
Effects of mutational loss of adenosine kinase and deoxycytidine kinase on deoxyATP accumulation and deoxyadenosine toxicity in cultured CEM human T-lymphoblastoid cells
Somatic mutations of the protein kinase gene family in human lung cancer
Mitochondrial aldehyde dehydrogenase from human liver. Primary structure, differences in relation to the cytosolic enzyme, and functional correlations.
The role of phosphatidylinositol 3-kinase in neural cell adhesion molecule-mediated neuronal differentiation and survival
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Aurora-A and an interacting activator, the LIM protein Ajuba, are required for mitotic commitment in human cells
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A role for transportin in deposition of TTP to cytoplasmic RNA granules and mRNA decay
Tah18 transfers electrons to Dre2 in cytosolic iron-sulfur protein biogenesis
Aquaporin expression in normal human kidney and in renal disease
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A human homologue of the checkpoint kinase Cds1 directly inhibits Cdc25 phosphatase
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Rapid association of cytoskeletal remodeling proteins with the developing phagosomes of human neutrophils
Mucopolysaccharidosis type I: current knowledge on its pathophysiological mechanisms
Characterization of the human gene encoding alpha-aminoadipate aminotransferase (AADAT).
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NLR functions beyond pathogen recognition
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Sef is a spatial regulator for Ras/MAP kinase signaling
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Peroxisome proliferator activated receptors and lipoprotein metabolism
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ATP activates a reactive oxygen species-dependent oxidative stress response and secretion of proinflammatory cytokines in macrophages
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Deficiency of the ADP-forming succinyl-CoA synthase activity is associated with encephalomyopathy and mitochondrial DNA depletion
Crystal structures of human NUDT5 reveal insights into the structural basis of the substrate specificity
Regulation of Ins(3,4,5,6)P(4) signaling by a reversible kinase/phosphatase
The distribution and function of phosphatidylserine in cellular membranes
Structure and activation of the visual pigment rhodopsin
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The PI-3 kinase/Akt pathway and T cell activation: pleiotropic pathways downstream of PIP3
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Vav1: a key signal transducer downstream of the TCR
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Phosphorylation of mammalian CDC6 by cyclin A/CDK2 regulates its subcellular localization.
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Regulation of Geminin and Cdt1 expression by E2F transcription factors
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Phosphorylation of tyrosine 1214 on VEGFR2 is required for VEGF-induced activation of Cdc42 upstream of SAPK2/p38
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Synthesis of 5-demethoxyubiquinone-6 and ubiquinone-6 from 3-hexaprenyl-4-hydroxybenzoate in yeast mitochondria
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Multiple forms of gamma-butyrobetaine hydroxylase (EC 1.14.11.1).
Control of cyclin B1 localization through regulated binding of the nuclear export factor CRM1
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Lipid digestion, mobilization, and transport
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Inhibition of Mcm4,6,7 helicase activity by phosphorylation with cyclin A/Cdk2.
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N-glycan trimming in the ER and Calnexin/Calreticulin cycle
Binding of MET-TRNAf and GTP to homogeneous initiation factor MP.
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Immunoreceptor DAP12 bearing a tyrosine-based activation motif is involved in activating NK cells
Phosphorylation of Tyr1214 within VEGFR-2 triggers the recruitment of Nck and activation of Fyn leading to SAPK2/p38 activation and endothelial cell migration in response to VEGF
Structural basis for an inositol pyrophosphate kinase surmounting phosphate crowding
Cloning and characterization of two human VIP1-like inositol hexakisphosphate and diphosphoinositol pentakisphosphate kinases
Interconversion of leukotrienes catalyzed by purified gamma-glutamyl transpeptidase: concomitant formation of leukotriene D4 and gamma-glutamyl amino acids
Role of Pam16's degenerate J domain in protein import across the mitochondrial inner membrane
The kinase activity of IL-1 receptor-associated kinase 4 is required for interleukin-1 receptor/toll-like receptor-induced TAK1-dependent NFkappaB activation
Structure, function and regulation of pyruvate carboxylase
HIstome--a relational knowledgebase of human histone proteins and histone modifying enzymes
Management of cellular energy by the AMP-activated protein kinase system
Mammalian G proteins and their cell type specific functions
Defective AMN causes hereditary megaloblastic anemia 1
Mapping the functional domains of the Golgi stacking factor GRASP65
Overexpression of a mammalian ethanolamine-specific kinase accelerates the CDP-ethanolamine pathway
Purification and properties of human D-3-hydroxyacyl-CoA dehydratase: medium-chain enoyl-CoA hydratase is D-3-hydroxyacyl-CoA dehydratase
Phagosomes are competent organelles for antigen cross-presentation
ER-phagosome fusion defines an MHC class I cross-presentation compartment in dendritic cells
Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S
Endonucleolytic function of MutLalpha in human mismatch repair
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Control of translation and mRNA degradation by miRNAs and siRNAs
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Condensins, chromosome condensation protein complexes containing XCAP-C, XCAP-E and a Xenopus homolog of the Drosophila Barren protein
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Human and murine glycerol kinase: influence of exon 18 alternative splicing on function
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Identification and characterization of an enzyme involved in the elongation of n-6 and n-3 polyunsaturated fatty acids
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Cellular localization of the vesicular inhibitory amino acid transporter in the mouse and human retina
Reversible compartmentalization of de novo purine biosynthetic complexes in living cells
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Nuclear translocation of plk1 mediated by its bipartite nuclear localization signal
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RNA Polymerase II Pre-transcription Events
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Stimulation of the human CTP:phosphoethanolamine cytidylyltransferase gene by early growth response protein 1
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MISCELLANEOUS Present with 1580 molecules/cell in log phase SD medium.
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NSDHL, an enzyme involved in cholesterol biosynthesis, traffics through the Golgi and accumulates on ER membranes and on the surface of lipid droplets
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Conversion of alpha-linolenic acid to eicosapentaenoic, docosapentaenoic and docosahexaenoic acids in young women
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Chk1 and Chk2 kinases in checkpoint control and cancer
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Eicosapentaenoic and docosapentaenoic acids are the principal products of alpha-linolenic acid metabolism in young men*
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Human Sgt1 binds HSP90 through the CHORD-Sgt1 domain and not the tetratricopeptide repeat domain
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Identification and characterization of novel spliced variants of neuregulin 4 in prostate cancer
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Fundamental Immunology (Book): 1077-1104
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Apoptosis induced by the toll-like receptor adaptor TRIF is dependent on its receptor interacting protein homotypic interaction motif
Structure of the human MutSalpha DNA lesion recognition complex
Novel variants in human Aquaporin-4 reduce cellular water permeability
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Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)
A general map of iron metabolism and tissue-specific subnetworks
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Pak1 kinase homodimers are autoinhibited in trans and dissociated upon activation by Cdc42 and Rac1
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Kinesin-5 regulates the growth of the axon by acting as a brake on its microtubule array
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Phosphorylation and activation of 13S condensin by Cdc2 in vitro
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Identification of ARAP3, a novel PI3K effector regulating both Arf and Rho GTPases, by selective capture on phosphoinositide affinity matrices
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Acid-sensing ion channels (ASICs): pharmacology and implication in pain
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De novo telomere addition by Tetrahymena telomerase in vitro
[A NEW DYSOSTOSIS WITH URINARY ELIMINATION OF CHONDROITIN SULFATE B]
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Inborn errors of ketogenesis and ketone body utilization
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Regulation of mRNA stability by proteins that bind AU-rich elements
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Molecular organization of the presynaptic active zone
Transmembrane transport of endo- and xenobiotics by mammalian ATP-binding cassette multidrug resistance proteins
Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)
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Alternate exon insertion controls selective ubiquitination and degradation of different AUF1 protein isoforms
Mitochondrial protein import: precursor oxidation in a ternary complex with disulfide carrier and sulfhydryl oxidase
XBP-1 regulates a subset of endoplasmic reticulum resident chaperone genes in the unfolded protein response
Enzymes of the human erythrocyte. IV. Phosphoglucose isomerase, purification and properties.
A comprehensive profile of brain enzymes that hydrolyze the endocannabinoid 2-arachidonoylglycerol
Unresponsiveness of MyD88-deficient mice to endotoxin
Purification and characterization of 5'-deoxy-5'-methylthioadenosine phosphorylase from human placenta
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Multiple pathways for sorting mitochondrial precursor proteins
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Selective vitamin B12 malabsorption and proteinuria in young people. A syndrome
Molecular machinations of the MHC-I peptide loading complex
The target of ezetimibe is Niemann-Pick C1-Like 1 (NPC1L1)
Deletion of the mitochondrial carrier genes MRS3 and MRS4 suppresses mitochondrial iron accumulation in a yeast frataxin-deficient strain
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VEGFs and receptors involved in angiogenesis versus lymphangiogenesis
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Phase III randomized trial of cisplatin plus placebo compared with cisplatin plus cetuximab in metastatic/recurrent head and neck cancer: an Eastern Cooperative Oncology Group study
10-formyltetrahydrofolyl polyglutamate macromolecule [ChEBI:28010]
10-formyltetrahydrofolyl polyglutamate macromolecule
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ChEBI:16618 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate
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Structural basis for the functional differences between type I and type II human methionine aminopeptidases
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Developmental origin of fat: tracking obesity to its source
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The human peroxisomal ABC half transporter ALDP functions as a homodimer and accepts acyl-CoA esters
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Defective platelet activation in G alpha(q)-deficient mice
Expression of the MAPK kinases MKK-4 and MKK-7 in rheumatoid arthritis and their role as key regulators of JNK
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Peroxisomal multifunctional protein-2: the enzyme, the patients and the knockout mouse model
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COPI-coated ER-to-Golgi transport complexes segregate from COPII in close proximity to ER exit sites
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EGF receptor activation by GPCRs: an universal pathway reveals different versions
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Biological & physiological aspects of action of insulin-like growth factor peptide family
Holocarboxylase synthetase: correlation of protein localisation with biological function
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CREB phosphorylation through the activation of CaMKII
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The transport of sulphate and sulphite in rat liver mitochondria
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Crystal structure of human E1 enzyme and its complex with a substrate analog reveals the mechanism of its phosphatase/enolase activity
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Isolation and characterization of human nuclear and cytosolic multisynthetase complexes and the intracellular distribution of p43/EMAPII
Mitochondrial release of AIF and EndoG requires caspase activation downstream of Bax/Bak-mediated permeabilization.
Association of B cell antigen receptor with protein tyrosine kinase Lyn
DHFR/MSH3 amplification in methotrexate-resistant cells alters the hMutSalpha/hMutSbeta ratio and reduces the efficiency of base-base mismatch repair
Proc. Natl. Acad. Sci. U.S.A. 94:10144-9
Kinetic characterization of human hydroxyacid-oxoacid transhydrogenase: relevance to D-2-hydroxyglutaric and gamma-hydroxybutyric acidurias
A stress response pathway from the endoplasmic reticulum to the nucleus requires a novel bifunctional protein kinase/endoribonuclease (Ire1p) in mammalian cells
The formation of citric and alpha-ketoglutaric acids in the mammalian body
Defective LMBRD1 causes methylmalonic aciduria and homocystinuria type cblF
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IMMPORT:Bioinformatics for the future of immunology
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Fatty acid, triacylglycerol, and ketone body metabolism
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Cloning of DGAT2, a second mammalian diacylglycerol acyltransferase, and related family members
Ubiquinone. Biosynthesis of quinone ring and its isoprenoid side chain. Intracellular localization
Molecular Mechanisms of Phagocytosis (Book): 97-116
HER4-mediated biological and biochemical properties in NIH 3T3 cells. Evidence for HER1-HER4 heterodimers
Adenylate kinases in man: evidence for a third locus
Core protein machinery for mammalian phosphatidylinositol 3,5-bisphosphate synthesis and turnover that regulates the progression of endosomal transport. Novel Sac phosphatase joins the ArPIKfyve-PIKfyve complex
Cloning and identification of a new member of water channel (AQP10) as an aquaglyceroporin
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Inflammasome adaptors and sensors: intracellular regulators of infection and inflammation
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Molecular cloning of human amidophosphoribosyltransferase
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Back in the water: the return of the inositol phosphates
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PI3Kgamma is a key regulator of inflammatory responses and cardiovascular homeostasis
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Regulation of WASP/WAVE proteins: making a long story short
Endotoxin signaling in human macrophages: signaling via an alternate mechanism
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Cutting edge: bacterial flagellin activates basolaterally expressed TLR5 to induce epithelial proinflammatory gene expression
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Defining the TRiC/CCT interactome links chaperonin function to stabilization of newly made proteins with complex topologies
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Characterization of Na+/HCO-3 cotransporter isoform NBC-3
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Butyrate Response Factor 1 (BRF1) destabilizes mRNA
Phosphorylation at conserved carboxyl-terminal hydrophobic motif regulates the catalytic and regulatory domains of protein kinase C
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Role of leptin in the pancreatic ?-cell: effects and signaling pathways
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Purification and properties of human placental adenosine kinase
Sensing of viral infection and activation of innate immunity by toll-like receptor 3
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Nuclear organization of DNA replication in primary mammalian cells
Structure-Function analysis of the CTLA-4 interaction with PP2A
In vitro characterization of enzymatic properties and inhibition of the p53R2 subunit of human ribonucleotide reductase
Identification and partial purification of PAPS translocase
GlycoVis: visualizing glycan distribution in the protein N-glycosylation pathway in mammalian cells
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Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)
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Evaluation by mutagenesis of the importance of 3 arginines in alpha, beta, and gamma subunits of human NAD-dependent isocitrate dehydrogenase
Role of two residues proximal to the active site of Ubc9 in substrate recognition by the Ubc9.SUMO-1 thiolester complex
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Defective GIF causes intrinsic factor deficiency
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Sulfotransferase catalyzing sulfation of heterocyclic amines
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The essential WD40 protein Cia1 is involved in a late step of cytosolic and nuclear iron-sulfur protein assembly
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Homologous recombination repair of replication-independent double-strand breaks
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Investigation of the ABC transporter MRP1 in selected patients with presumed defects in vitamin B12 absorption
Functional analysis of mRNA scavenger decapping enzymes
Cytochrome P450 - arranged by substrate type
Cloning of a water channel homolog expressed in brain meningeal cells and kidney collecting duct that functions as a stilbene-sensitive glycerol transporter
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GRB2: a pivotal protein in signal transduction
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Relative contributions of heart mitochondria glutathione peroxidase and catalase to H(2)O(2) detoxification in in vivo conditions
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The ubiquitin-editing enzyme A20 restricts nucleotide-binding oligomerization domain containing 2-triggered signals
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Red blood cell pH, the Bohr effect, and other oxygenation-linked phenomena in blood O2 and CO2 transport
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GTP hydrolysis by eRF3 facilitates stop codon decoding during eukaryotic translation termination
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Mutation of the fumarase gene in two siblings with progressive encephalopathy and fumarase deficiency
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Characterization of human lysophospholipid acyltransferase 3
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Contraction regulates site-specific phosphorylation of TBC1D1 in skeletal muscle
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Methylation of histone H4 by arginine methyltransferase PRMT1 is essential in vivo for many subsequent histone modifications
Similar idiotypic specificity for the membrane IgD and IgM of human B lymphocytes
The conjugation of cysteine (Cys) and 4'- phosphopantothenate (PPanK) to form 4-phosphopantothenoylcysteine (PPC) , coupled to the conversion of ATP to AMP and pyrophosphate, is catalyzed by cytosolic phosphopantothenate-cysteine ligase (PPCS aka Phosphopantothenoylcysteine synthase or PPC synthase). Mammalian PPCS prefers ATP to CTP, unlike the E. coli ortholog (Daughtery et al. 2002; Manoj et al. 2003).
Riboflavin (vitamin B2, E101) is an essential component for the cofactors FAD (flavin-adenine dinucleotide) and FMN (flavin mononucleotide). Together with NAD+ and NADP+, FAD and FMN are important hydrogen carriers and take part in more than 100 redox reactions involved in energy metabolism. Riboflavin is present in many vegetables and meat and during digestion, various flavoproteins from food are degraded and riboflavin is resorbed. The major degradation and excretion product in humans is riboflavin (Rivlin 1970).
The adenylyl transferase activity of bifunctional coenzyme A synthase (COASY) catalyzes the transfer of an adenylyl group from ATP to pantetheinephosphate (PPANT) to form dephospho-Coenzyme A (DP-CoA) (Daugherty et al. 2002). The enzyme is associated with the mitochondrial outer membrane (Zhyvoloup et al. 2003).
The decarboxylation of phosphopantothenoylcysteine (PPC) to 4'-phosphopantetheine (PPANT) is carried out by phosphopantothenoylcysteine decarboxylase (PPCDC). PPCDC is cytosolic and exists as a homotrimer, binding one FMN cofactor per subunit. While a second isoform has been inferred from large-scale sequnceing studies, it lacks the protein's FMN-binding domain and would thus appear to be nonfunctional if it is expressed.
Crystal structure of the catalytic portion of human HMG-CoA reductase: insights into regulation of activity and catalysis
Molecular enzymology of mammalian Delta1-pyrroline-5-carboxylate synthase. Alternative splice donor utilization generates isoforms with different sensitivity to ornithine inhibition
Vitamin C (ascorbate) is an antioxidant and a cofactor in reactions catalyzed by Cu+-dependent monooxygenases and Fe++-dependent dioxygenases. Many mammals can synthesize ascorbate de novo; humans and other primates cannot due to an evolutionarily recent mutation in the gene catalyzing the last step of the biosynthetic pathway. Reactions annotated here mediate the uptake of ascorbate and its fully oxidized form, dehydroascorbate (DHA) by cells, and the reduction of DHA and monodehydroascorbate to regenerate ascorbate (Linster and Van Schaftingen 2007).
Cytosolic thiamin pyrophosphokinase (TPK1) catalyzes the reaction of thiamin (THMN) and ATP to form thiamin diphosphate (ThDP aka thiamin pyrophosphate) and ADP. ThDP is an active cofactor for transketolase, pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase, enzymes involved in glycolysis and energy production. The gene encoding the human enzyme has been cloned and its protein product has been shown to have TPK1 activity (Nosaka et al. 2001; Zhao et al. 2001). Its homodomeric structure and association with Mg2+ are inferred from properties of the homologous yeast enzyme (Baker et al. 2001).
Vitamin B1 (thiamin) is found naturally in certain foodstuffs such as green peas, spinach, liver, bananas, whole grains and legumes. Human diseases associated with thiamin deficiency include beriberi, due to a thiamin-deficient diet, TMRA, due to defects in the SLC19A2 transport protein, and Wernicke-Korsakoff Syndrome, associated with thiamin deficiency in alcoholism (Haas 1988). Thiamin is water-soluble so is not stored in the body. When pyrophosphorylated, thiamin is converted into the coenzyme thiamin pyrophosphate (ThPP, codecarboxylase) which plays an essential role in oxidative decarboxylation and group transfer reactions.
Phosphorylation of riboflavin (RIB) results in the formation of the first cofactor, flavin mononucleotide (FMN). This reaction is catalyzed by riboflavin kinase (RFK), a cytosolic enzyme existing as a monomer. It utilizes either zinc or magnesium ions in the reaction.
FMN can be phosphorylated and adenylated to produce the second cofactor from riboflavin origins, flavin adenine dinucleotide (FAD). The enzyme responsible , FMN adenylyltransferase (FLAD1 aka FAD synthase), is cytosolic and transfers a phosphate and an adenyl group from ATP to form FAD.
Phosphatase action on flavin adenine dinucleotide (FAD) can reform flavin mononucleotide (FMN). The enzyme performing the reaction is nucleotide pyrophosphatase (ENPP1) and it exists as a homodimer on the plasma membrane.
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DNA polymerase delta, an essential enzyme for DNA transactions.
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High-resolution x-ray structure of human aquaporin 5
A subset of ATM- and ATR-dependent phosphorylation events requires the BRCA1 protein.
Purification and characterization of kynurenine aminotransferase I from human brain
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Biochemical characterization of human GMP synthetase
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Separation of the two enzymatic phases in active sulfate synthesis
The peripheral membrane subunits of the SAM complex function codependently in mitochondrial outer membrane biogenesis
Defects in GIF cause hereditary intrinsic factor deficiency (IFD, aka congenital pernicious anemia; MIM:261000). IFD is an autosomal recessive disorder characterized by megaloblastic anemia (Tanner et al. 2005).
Precursor oxidation by Mia40 and Erv1 promotes vectorial transport of proteins into the mitochondrial intermembrane space
Defects in MMACHC cause methylmalonic aciduria and homocystinuria type cblC (MMAHCC; MIM:277400). MMAHCC is the most common disorder of cobalamin metabolism and is characterized by decreased levels of the coenzymes adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl). Affected individuals may have developmental, haematologic, neurologic, metabolic, ophthalmologic, and dermatologic clinical findings (Lerner-Ellis et al. 2006).
Defects in MMADHC cause methylmalonic aciduria and homocystinuria type cblD (MMAHCD; MIM:277410), a disorder of cobalamin metabolism characterized by decreased levels of the coenzymes adenosylcobalamin (AdoCbl) and methylcobalamin (MeCbl) (Coelho et al. 2008).
Defects in AMN cause recessive hereditary megaloblastic anemia 1 (RH-MGA1 aka MGA1 Norwegian type or Imerslund-Grasbeck syndrome, I-GS; MIM:261100). The Norwegian cases described by Imerslund were due to defects in AMN (Imerslund 1960). The resultant malabsorption of Cbl (vitamin B12) leads to impaired B12-dependent folate metabolism and ultimately impaired thymine synthesis and DNA replication.
Defects in the CUBN gene cause recessive hereditary megaloblastic anemia 1 (RH-MGA1 aka MGA1 Finnish type or Imerslund-Grasbeck syndrome, I-GS; MIM:261100). The Finnish cases described by Grasbeck et al. were caused by defects in CUBN (Grasbeck et al. 1960). The resultant malabsorption of Cbl (cobalamin, vitamin B12) leads to impaired B12-dependent folate metabolism and ultimately impaired thymine synthesis and DNA replication.
Defective transcobalamin II (produced by the TCN2 gene) results in TCN2 deficiency (MIM:275350), an autosomal recessive disorder with early-onset in infancy characterized by failure to thrive, megaloblastic anemia, and pancytopenia. If left untreated, the disorder can result in mental retardation and neurologic abnormalities (Haberle et al. 2009).
Defects in LMBRD1 cause methylmalonic aciduria and homocystinuria type cblF (MMAHCF; MIM:277380), characterised biochemically by decreased levels of the coenzymes adenosylcobalamin (AdoCbl) and methylcobalamin (MetCbl) (Rutsch et al. 2009, Gailus et al. 2010).
In order to get a sulfur atom for subsequent sulfuration reactions, cysteine is first desulfurated by NFS1 which transfers it onto a cysteine of MOCS3, yielding a protein persulfide (Marelja et al, 2008).
Proteasomes: protein degradation machines of the cell
Molybdenum cofactor (MoCo) is needed by three enzymes in humans: sulfite oxidase, xanthine oxidase and aldehyde oxidase. The pathway of its synthesis is so conserved that plants and bacteria can readily use human enzymes. Bacteria, however, diverge after the first three steps from this path and their final MoCo differs from that of the eukaryotes. Plants and animals have also developed a refinement of their MoCo which is needed for the function of their xanthine and aldehyde oxidases. This means, in humans we find sulfurated instead of desulfurated molybdenum cofactor on these two enzymes (Schwarz 2005; Schwarz, Mendel, Ribbe 2009).
Vitamins are a diverse group of organic compounds, required in small amounts in the diet. They have distinct biochemical roles, often as coenzymes, and are either not synthesized or synthesized only in limited amounts by human cells. Vitamins are classified according to their solubility, either fat-soluble or water-soluble. The physiological processes dependent on vitamin-requiring reactions include many aspects of intermediary metabolism, vision, bone formation, and blood coagulation, and vitamin deficiencies are associated with a correspondingly diverse and severe group of diseases. Water-soluble vitamins include ascorbate (vitamin C) and the members of the B group: thiamin (vitamin B1), riboflavin (B2), niacin (B3), pantothenate (B5), pyridoxine (B6), biotin (B7), folate (B9), and cobalamin (B12). Metabolic processes annotated here include the synthesis of thiamin pyrophosphate (TPP) from thiamin (B1), the synthesis of FMN and FAD from riboflavin (B2), the synthesis of nicotinic acid (niacin - B3) from tryptophan, the synthesis of Coenzyme A from pantothenate (B5), and features of the metabolism of folate (B9).
Latent infection of Homo sapiens with Mycobacterium tuberculosis
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Defects in HLCS causes holocarboxylase synthetase deficiency (HLCS deficiency aka early onset multiple carboxylase deficiency; MIM:253270). HLCS deficiency is an autosomal recessive disorder whereby deficient HLCS activity results in reduced activity of all five biotin-dependent carboxylases. Symptoms include metabolic acidosis, organic aciduria, lethargy, hypotonia, convulsions and dermatitis (Suzuki et al. 2005). Patients can present symptoms shortly after birth to up to early childhood and will be prescribed oral biotin supplements, typically 10-20 mg daily. Two classes of HLCS deficiency have been reported depending on whether patients respond to biotin therapy. Most patients respond favourably to treatment and show complete reversal of biochemical and clinical symptoms (Morrone et al. 2002, Dupuis et al. 1999). Here mutations in the HLCS active site cause a reduced affinity for biotin that can be overcome by pharmacological doses of the vitamin (Pendini et al. 2008). Patients who display incomplete responsiveness to biotin therapy have a poor long-term prognosis (Bailey et al. 2008). Here mutations that reside outside of the enzyme's active site have no effect on biotin binding but do compromise the protein-protein interaction between the HLCS and its substrates, resulting in reduced biotinylation of all five carboxylases thus reducing their enzymatic activity (Mayende et al. 2012).
BTD deficiency is an autosomal recessive disorder in which the body is unable to recycle and reuse biotin (Btn). This results in a secondary Btn deficiency that leads to juvenile-onset multiple carboxylase deficiency (MIM:253260) (Wolf 2012, Wolf et al. 1983). Patients present with neurological and cutaneous symptoms, including seizures, hypotonia, skin rash, and alopecia, usually between the second and fifth months of life (Wolf 2010). Children with profound BTD deficiency are treated with pharmacological doses of biotin (5-20 mg daily). Neonatal screening for BTD deficiency is performed in most states of the United States and many other countries.
Cobalamin (Cbl, vitamin B12) is a nutrient essential for normal functioning of the brain and nervous system and for the formation of blood. Cbl-dependent methionine synthase (MTR) is required for conversion of 5-methyltetrahydrofolate (metTHF) to tetrahydrofolate (THF), in addition to its role in conversion of homocysteine to methionine. In Cbl deficiency, and in inborn errors of Cbl metabolism that affect function of methionine synthase, inability to regenerate THF from metTHF results in decreased function of folate-dependent reactions that are involved in 2 steps of purine biosynthesis and thymidylate synthesis. Cbl deficiency results in hyperhomocysteinemia (due to defects in the conversion of homocysteine to methionine which requires Cbl as a cofactor) and increased levels of methylmalonic acid (MMA). Methionine is used in myelin production, protein, neurotransmitter, fatty acid and phospholipid production and DNA methylation. Symptoms of Cbl deficiency are bone marrow promegaloblastosis (megaloblastic anemia) due to the inhibition of DNA synthesis (specifically purines and thymidine) and neurological symptoms. The defective genes involved in Cbl deficiencies are described below (Froese & Gravel 2010, Nielsen et al. 2012, Whitehead 2006, Watkins & Rosenblatt 2011, Fowler 1998).
Biotin (Btn) acts as a coenzyme for 5 carboxylases that exist in their inactive apo forms. In the cytosol and mitochondrion, these apo carboxylases (apo-CBXs) are biotinylated to their active holo forms by the activity of biotin protein ligase (HCLS) (Ingaramo & Beckett 2012, Bailey et al. 2010, Hiratsuka et al. 1998). Defects in HLCS causes holocarboxylase synthetase deficiency (HLCS deficiency aka early-onset multiple carboxylase deficiency; MIM:253270). HLCS deficiency is an autosomal recessive disorder whereby deficient HLCS activity results in reduced activity of all 5 carboxylases. Symptoms include metabolic acidosis, organic aciduria, lethargy, hypotonia, convulsions and dermatitis. Mutations in HCLS associated with HLCS deficiency include the compound heterozygote G261Vfs*20/L237P, D571N, R508W, G581S, V550M and L216R (Suzuki et al. 1994, Yang et al. 2000, Dupuis et al. 1996, Aoki et al, 1999, Yang et al. 2001, Morrone et al. 2002).
Defects in MUT cause methylmalonic aciduria, mut type (MMAM; MIM:251000), an often fatal disorder of organic acid metabolism (Worgan et al. 2006).
Defects in CD320 cause methylmalonic aciduria type TCblR (MMATC aka methylmalonic aciduria; MIM:613646) resulting in elevated methylmalonic acid (MMA) and homocysteine (HCYS) in newborns (Quadros et al. 2010).
Defects in MMAB cause methylmalonic aciduria type cblB (cblB aka methylmalonic aciduria type B or vitamin B12 responsive methylmalonicaciduria of cblB complementation type; MIM:251110). Affected individuals have methylmalonic aciduria and episodes of metabolic ketoacidosis, despite a functional methylmalonyl CoA mutase. In severe cases, newborns become severely acidotic and may die if acidosis is not treated promptly (Dobson et al. 2002).
Defects in MMAA cause methylmalonic aciduria type cblA (cblA aka methylmalonic aciduria type A or vitamin B12-responsive methylmalonic aciduria of cblA complementation type; MIM:251100). Affected individuals accumulate methylmalonic acid in the blood and urine and are prone to potentially life threatening acidotic crises in infancy or early childhood (Dobson et al. 2002, Lerner-Ellis et al. 2004).
Defects in MTRR cause methylcobalamin deficiency type E (cblE; methionine synthase reductase deficiency; MIM:236270) (Wilson et al. 1999). Patients with cblE exhibit megaloblastic anemia and hyperhomocysteinemia. SAM is used as a methyl donor in many biological reactions and demethylation of SAM produces S-adenosylhomocysteine, which is deadenosylated to form homocysteine. Homocysteine remethylation is carried out by MTR, which requires MTRR to maintain enzyme-bound cobalamin (Cbl) in its active form; but in cblE patients, MTR becomes inactivated and thus homocysteine accumulates.
Defects in MTR cause methylcobalamin deficiency type G (cblG; MIM:250940), an autosomal recessive inherited disease that causes mental retardation, macrocytic anemia, and homocystinuria (Leclerc et al. 1996, Gulati et al. 1996, Watkins et al. 2002).
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Histone H4 acetylation differentially modulates arginine methylation by an in Cis mechanism
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At the plasma membrane, a group of phospholipase C (PLC(bz)) proteins hydrolyse phosphatidylinositol 4,5 bisphosphate (PI(4,5)P2) to inositol 1,4,5 trisphosphate (I(1,4,5)P3) and diacylglycerol (DAG). This group of phospholipase C proteins lack a PH domain and so are is cytosolic. Their C2 domains bind to PI(4,5)P2 at the membrane. The PLC-beta proteins are thought to be responsible for the majority of PI(4,5)P2 hydrolysis. The phospholipase C isoforms involved and their corresponding literature references are: phosphoinositide phospholipase C beta-1 (PLCB1) (Caricasole et al. 2000, Jhon et al. 1993, Park et al. 1992); beta-2 (PLCB2) (Jhon et al. 1993, Park et al. 1992); beta-3 (PLCB3) (Carozzi et al. 1992, Jhon et al. 1993); beta-4 (PLCB4) (Alvarez et al. 1995, Lee et al. 1993); and zeta-1 (PLCZ1) (Kouchi et al. 2005, Rogers et al. 2004).
A group of phospholipase C proteins (PLC(degh)) bind to the plasma membrane via their PH domains. These phospholipases hydrolyse phosphatidylinositol 4,5 bisphosphate (PI(4,5)P2) to inositol 1,4,5 trisphosphate (I(1,4,5)P3) and diacylglycerol (DAG). The C2 domains of the enzymes bind to PI(4,5)P2 at the membrane. The phospholipase C isoforms involved and their corresponding literature references are: phosphoinositide phospholipase C delta-1(PLCD1) (Cheng et al. 1995); epsilon-1 (PLCE1) (Song et al. 2001, Lopez et al. 2001); delta-3 (PLCD3) (Pawelczyk & Matecki 1997); gamma-1 (PLCG1) (Harita et al. 2009, Baldassare et al. 1989); gamma-2 (PLCG2) (Banno et al. 1988); eta-1 (PLCH1) (Hwang et al. 2005); and eta-2 (PLCH2) (Zhou et al 2005).
Two distinct proteolytic processes in the generation of a major histocompatibility complex class I-presented peptide
A group of inositol phosphatases and the broad specificity enzyme inositol-tetrakisphosphate 1-kinase (ITPK1) dephosphorylate inositol 1,3,4,5-tetrakisphosphate (I(1,3,4,5)P4) to inositol 1,3,4-trisphosphate (I(1,3,4)P3). The group of inositol phosphatases involved are: inositol polyphosphate 5-phosphatase OCRL-1 (OCRL), phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 1 (INPP5D) aka SHIP1, phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase 2 (INPPL1) aka SHIP2, phosphatidylinositol 4,5-bisphosphate 5-phosphatase A (INPP5J) aka PIPP, and synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1 (SYNJ1). The following lists the above proteins with their corresponding literature references: OCRL (Chang et al. 2002, Zhang et al. 1995, Zhang et al. 1998, Schmid et al. 2004); INPP5D (Drayer et al. 1996, Kavanaugh et al. 1996); INPPL1 (Chi et al. 2004); INPP5J (Mochizuki & Thompson 1999); SYNJ1 (Schmid et al. 2004); ITPK1 (Ho et al. 2002).
An array of inositol trisphosphate (IP3) and tetrakisphosphate (IP4) molecules are synthesised by the action of various kinases and phosphatases in the cytosol (Irvine & Schell 2001, Bunney & Katan 2010).
In the nucleus, inositol polyphosphate multikinase (IPMK) phosphorylates inositol 1,4,5-trisphosphate (I(1,4,5)P3) to inositol 1,3,4,5-tetrakisphosphate (I(1,3,4,5)P4) (Nalaskowski et al. 2002, Chang et al. 2002, Chang & Majerus 2006).
Biotin (Btn, vitamin B7, vitamin H, coenzyme R) is an essential cofactor for five biotin-dependent carboxylase enzymes, involved in the synthesis of fatty acids, isoleucine, valine and in gluconeogenesis. Thus, Btn is necessary for cell growth, fatty acid synthesis and the metabolism of fats and amino acids. Inherited metabolic disorders characterized by deficient activities of all five biotin dependent carboxylases are termed multiple carboxylase deficiencies. Two congenital defects in biotin metabolism leading to multiple carboxylase deficiency are known, holocarboxylase synthetase deficiency (MIM 609018) and biotinidase deficiency (MIM 253260). In both scenarios symptoms include ketolactic acidosis, organic aciduria, hyperammonemia, skin rashes, hypotonia, seizures, developmental delay, alopecia, and coma. As humans are auxotrophic for Btn, the micronutrient must be obtained from external soures such as intestinal microflora and dietary forms. Accordingly, severe malnutrition can also give rise to biotin deficiency and multiple carboxylase deficiency. Biotin deficiency can also be induced by the excessive consumption of raw egg white that contains the biotin-binding protein avidin. Holocarboxylase synthetase deficiency arises when all five biotin-dependent enzymes are not biotinylated leading to their reduced activities. The defective genes causing these conditions are described here (Pendini et al. 2008, Suzuki et al. 2005). Biotinidase deficiency is caused by defects in the recycling of Btn. General symptoms include decreased appetite and growth, dermatitis and perosis. The defective genes causing these conditions are described here (Procter et al. 2013).
Vitamins are essential nutrients, required in small amounts from the diet for the normal growth and development of a multicellular organism. Where there is vitamin deficiency, either by poor diet or a defect in metabolic conversion, diseases called Avitaminoses occur. Currently, cobalamin (Cbl, vitamin B12) metabolic defects are described below (Chapter 155 in The Metabolic and Molecular Bases of Inherited Disease, 8th ed, Scriver et al. 2001)
Aberrant WNT signaling is associated with the development of numerous cancers, and strategies for targeting this pathway are under intense investigation (reviewed in Polakis, 2012; Polakis, 2000; Yao et al, 2011). Secretion of WNT ligand depends on its PORCN-dependent palmitoleoylation in the ER, making PORCN a attractive therapeutic target in cases where WNT is aberrantly over-expressed (reviewed in MacDonald et al, 2009). LGK974 is a PORCN-inhibitor that was identified in a screen for compounds that abrogate the secretion of WNT ligands, and is in Phase I clinical trials for the treatment of WNT-dependent cancers (Liu et al, 2013)
The WNT signaling pathway has been linked with cancer ever since the identification of the first WNT as a gene activated by integration of mouse mammary tumor virus proviral DNA in virally-induced breast tumors (Nusse et al, 1984). The most well known example of aberrant WNT signaling in cancer is in colorectal cancer, where an activating mutation in a WNT pathway component is seen in 90% of sporadic cases. Inappropriate WNT pathway activation has also been implicated in most other solid human cancers but is not always associated with mutations in WNT pathway components (reviewed in Polakis, 2012). Both tumor suppressors and oncogenes have been identified in the so-called canonical WNT pathway, which regulates WNT-dependent transcription by promoting the degradation of beta-catenin in the absence of ligand (reviewed in Polakis, 2012). Loss-of-function mutations in the destruction complex components APC, Axin and AMER1 and gain-of-function mutations in beta-catenin itself cause constitutive signaling and are found in cancers of the intestine, kidney, liver and stomach, among others (Polakis, 1995; Segiditsas and Tomlinson, 2006; Peifer and Polakis, 2000; Laurent-Puig et al, 2001; Liu et al, 2000; Satoh et al, 2000; Major et al, 2007; Ruteshouser et al, 2008). WNTs and WNT pathway components are also frequently over- or under-expressed in various cancers, and these changes are correlated with epigenetic regulation of promoter activity. In some contexts, both the canonical and non-canonical WNT signaling, which governs processes such as cell polarity and morphogenesis, may also contribute to tumor formation by promoting cell migration, invasiveness and metastasis.
Biological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular viewpoint, human disease pathways have three mechanistic causes: the inclusion of microbially-expressed proteins, altered functions of human proteins, or changed expression levels of otherwise functionally normal human proteins. The first group encompasses the infectious diseases such as influenza, tuberculosis and HIV infection. The second group involves human proteins modified either by a mutation or by an abnormal post-translational event that produces an aberrant protein with a novel function. Examples include somatic mutations of EGFR and FGFR (epidermal and fibroblast growth factor receptor) genes, which encode constitutively active receptors that signal even in the absence of their ligands, or the somatic mutation of IDH1 (isocitrate dehydrogenase 1) that leads to an enzyme active on 2-oxoglutarate rather than isocitrate, or the abnormal protein aggregations of amyloidosis which lead to diseases such as Alzheimer's. Infectious diseases are represented in Reactome as microbial-human protein interactions and the consequent events. The existence of variant proteins and their association with disease-specific biological processes is represented by inclusion of the modified protein in a new or variant reaction, an extension to the 'normal' pathway. Diseases which result from proteins performing their normal functions but at abnormal rates can also be captured, though less directly. Many mutant alleles encode proteins that retain their normal functions but have abnormal stabilities or catalytic efficiencies, leading to normal reactions that proceed to abnormal extents. The phenotypes of such diseases can be revealed when pathway annotations are combined with expression or rate data from other sources.
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Within the nucleus, inositol polyphosphate multikinase (IPMK), inositol-pentakisphosphate 2-kinase (IPPK), inositol hexakisphosphate kinase 1 (IP6K1) and 2 (IP6K2) produce IP5, IP6, IP7, and IP8 inositol phosphate molecules (Irvine & Schell 2001, Alcazar-Romain & Wente 2008, York 2006, Monserrate and York 2010, Nalaskowski et al. 2002, Chang et al. 2002, Chang & Majerus 2006, Saiardi et al. 2001, Saiardi et al. 2000, Draskovic et al. 2008, Mulugu et al. 2007).
Inositol hexakisphosphate kinase 1 (IP6K1) and 3 (IP6K3) phosphorylate inositol 1,3,4,5,6-pentakisphosphate (I(1,3,4,5,6)P5) to inositol 5-diphospho-(1,3,4,6)-tetrakisphosphate (5-PP-IP4) (Saiardi et al. 2001, Saiardi et al. 2000, Draskovic et al. 2008).
In the nucleus, inositol hexakisphosphate kinase 1 (IP6K1) and 2 (IP6K2) phosphorylate inositol 5-diphospho-1,2,3,4,6-pentakisphosphate (5-PP-IP5) to inositol 5-triphospho- 1,2,3,4,6-pentakisphosphate (5-PPP-IP5) (Saiardi et al. 2001, Draskovic et al. 2008) and IP6K2 (Saiardi et al. 2001, Draskovic et al. 2008). While this reaction has been demonstrated to occur in vitro, the extent to which it occurs in vivo is less clear.
In the nucleus, inositol hexakisphosphate kinase 1 (IP6K1) and 2 (IP6K2) phosphorylate 1-diphospho-2,3,4,5,6-pentakisphosphate (1-PP-IP5) to make inositol 1,5-bisdiphospho-2,3,4,6-tetrakisphosphate (1,5-(PP)2-IP4) (Saiardi et al. 2001, Mulugu et al. 2007).
3-(2-Aminoethyl)-1H-indol-5-ol [ChEBI:28790]
In the nucleus, inositol polyphosphate multikinase (IPMK) phosphorylates inositol 1,3,4,5-tetrakisphosphate (I(1,3,4,5)P4) to inositol 1,3,4,5,6-pentakisphosphate (I(1,3,4,5,6)P5) (Nalaskowski et al. 2002, Chang & Majerus 2006).
In the nucleus, inositol polyphosphate multikinase (IPMK) phosphorylates inositol 1,3,4,6-tetrakisphosphate (I(1,3,4,6)P4) to inositol 1,3,4,5,6-pentakisphosphate (I(1,3,4,5,6)P5) (Chang et al. 2002, Chang & Majerus 2006).
In the nucleus, inositol hexakisphosphate kinase 1 (IP6K1) and 2 (IP6K2) phosphorylate5-diphospho-1,3,4,6-tetrakisphosphate (5-PP-IP4) to inositol 1,5-bisdiphospho-3,4,6-trisphosphate (1,5-(PP)2-IP3) (Saiardi et al. 2001, Saiardi et al. 2000, Draskovic et al. 2008).
In the nucleus, inositol hexakisphosphate kinase 1 (IP6K1) and 2 (IP6K2) phosphorylate inositol 1,2,3,4,5,6-hexakisphosphate (IP6) to inositol 5-diphospho-1,2,3,4,6-pentakisphosphate (5-PP-IP5). The following lists the above proteins with their corresponding literature references: IP6K1 (Saiardi et al. 2001, Mulugu et al. 2007, Draskovic et al. 2008) and IP6K2 (Saiardi et al. 2001, Mulugu et al. 2007, Draskovic et al. 2008).
In the nucleus, inositol polyphosphate multikinase (IPMK) phosphorylates inositol 1,4,5,6-tetrakisphosphate (I(1,4,5,6)P4) to inositol 1,3,4,5,6-pentakisphosphate (I(1,3,4,5,6)P5) (Nalaskowski et al. 2002, Chang & Majerus 2006).
In the nucleus, inositol hexakisphosphate kinase 1 (IP6K1) and 2 (IP6K2) phosphorylate inositol 1,3,4,5,6-pentakisphosphate (I(1,3,4,5,6)P5) to inositol 5-diphospho-(1,3,4,6)-tetrakisphosphate (5-PP-IP4) (Saiardi et al. 2001, Saiardi et al. 2000, Draskovic et al. 2008).
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Glucagon and regulation of glucose metabolism
Am J Physiol Endocrinol Metab 284:E671-8
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Chromatin organization in the mammalian nucleus
Succinic semialdehyde dehydrogenase deficiency: lessons from mice and men
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MicroRNAs: biogenesis, function and applications
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Expression, purification, and characterization of human acetyl-CoA carboxylase 2
The cellular response to neuregulins is governed by complex interactions of the erbB receptor family
Stimulation of phosphatidylglycerolphosphate phosphatase activity by unsaturated fatty acids in rat heart
Pyridoxal kinase (PDXK) catalyzes the ATP-dependent phosphorylation of pyridoxal (PXL) to form pyridoxal 5'-phosphate (PXLP) (Lee et al. 2000, di Salvo et al. 2004).
The human PICD gene encodes a cytoplasmic and peroxisomal NADP(+)-dependent isocitrate dehydrogenase
Panthothenate (vitamin B5) is the precursor of coenzyme A (Robishaw and Neely 1985) and is the prosthetic group of acyl carrier protein (ACP) (Joshi et al. 2003). Its name is derived from the Greek pantothen meaning "from everywhere" and small quantities of pantothenic acid are found in nearly every foodstuff.
Pyridoxal kinase (PDXK) catalyzes the ATP-dependent phosphorylation of pyridoxine (PDX) to form pyridoxine phosphate (PDXP) (Lee et al. 2000, di Salvo et al. 2004).
Pyridoxal kinase (PDXK) catalyzes the ATP-dependent phosphorylation of pyridoxamine (PXA) to form pyridoxamine phosphate (PXAP) (Lee et al. 2000, di Salvo et al. 2004).
The kinase activity of CoA synthase (COASY) catalyzes the phosphorylation of dephospho-CoA to form Coenzyme A (CoA-SH). The enzyme is located in the mitochondrial outer membrane (Daugherty et al. 2002; Zhyvoloup et al. 2003).
Coenzyme A (CoA) is a ubiquitous cofactor that functions as an acyl group carrier in diverse processes including fatty acid metabolism and the TCA cycle (Lipmann 1953). It is synthesized from the vitamin pantothenate in a sequence of five reactions (Daugherty et al. 2002; Leonardi et al. 2005; Robishaw and Neely 1985). These reactions all occur in the cytosol or the mitochondrial intermembrane space (Leonardi et al. 2005). A recently described transport protein appears to mediate the uptake of Coenzyme A into the mitochondrial matrix (Prohl et al. 2001).
Graves disease carrier protein (SLC25A16), associated with the inner mitochondrial membrane, mediates the transport of cytosolic coenzyme A (CoA-SH) into the mitochondrial matrix. Evidence for this event is indirect. The protein has the sequence motifs expected for a transport protein, and yeast cells deficient in its homologue, Leu5p, fail to accumulate mitochondrial CoA-SH and can be rescued by expression of SLC25A16. At the same time, neither the yeast nor the human protein has been shown directly to function as a transporter (Prohl et al. 2001, Leonardi et al. 2007).
Pyridoxine-5'-phosphate oxidase (PNPO) is able to oxidize pyridoxamine phosphate (PXAP) to pyridoxal 5'-phosphate (PXLP) (Kang et al. 2004).
A phosphorylation-regulated amphipathic helix controls the membrane translocation and function of the yeast phosphatidate phosphatase
Pyridoxine-5'-phosphate oxidase (PNPO) is able to oxidize pyridoxine phosphate (PDXP) to pyridoxal 5'-phosphate (PXLP) (Kang et al. 2004).
Animals cannot synthesize pyridoxal 5'-phosphate (PLP) which is a ligand in aminotransferases and other enzymes. PLP's accessible derivatives pyridoxine, pyridoxal, and pyridoxamine are traditionally called vitamins B6. They are taken up nutritionally from bacteria and plants, but also created from PLP in the body. The pathways used to recycle PLP from these three compounds can therefore be called vitamin B6 activation as well as PLP salvage. Because of the close similarity of the molecules, only two enzymes are needed for the task (McCormick & Chen, 1999).
Identification of the alpha-aminoadipic semialdehyde synthase gene, which is defective in familial hyperlysinemia.
The enzyme, nicotinate nucleotide pyrophosphorylase, is specific for quinolinate. Its activity is strictly dependent on Mg2+ ions being present. A phosphoribosyl group is transferred to quinolinate to form nicotinate D-ribonucleotide. This reaction represents another rate-limiting step of the pathway from tryptophan to NAD+.
Biotin (Btn) is an essential cofactor in a variety of carboxylation reactions (Zempleni et al. 2009). Humans cannot synthesize Btn but it is abundant in the human diet and can be taken up from the intestinal lumen by the SLC5A6 transporter. Its uptake, intracellular translocation, covalent conjugation to apoenzymes, and salvage are described here.
Biotin (Btn) acts as a coenzyme for 5 carboxylases that exist in their inactive apo forms. In the cytosol and mitochondrion, these apo-carboxylases are biotinylated to their active holo forms by the activity of biotin protein ligase (HCLS) (Ingaramo & Beckett 2012, Bailey et al. 2010, Hiratsuka et al. 1998). Defects in HLCS causes holocarboxylase synthetase deficiency (HLCS deficiency aka early-onset multiple carboxylase deficiency; MIM:253270). HLCS deficiency is an autosomal recessive disorder whereby deficient HLCS activity results in reduced activity of all five carboxylases. Symptoms include metabolic acidosis, organic aciduria, lethargy, hypotonia, convulsions and dermatitis (Suzuki et al. 2005). The first committed step in the synthesis of fatty acids is performed by the biotin-dependent enzyme acetyl CoA carboxylase [EC 6.4.1.2]. Acetyl CoA carboxylases 1 and 2 (ACACA and ACACB) have one Btn moiety covalently attached to each subunit (Abu-Elheiga et al. 1995). Eukaryotic acetyl-CoA carboxylases are heterodimers that can form catalytically active extended oligomers (Weatherly et al. 2004). Unlike the other biotin-dependent carboxylases that reside inside the mitochondrion, ACACA and B are located in the cytosol and outer mitochondrial membrane (shown here) respectively (Abu-Elheiga et al. 2000).
Biotin (Btn) acts as a coenzyme for 5 carboxylases that exist in their inactive apo forms. In the cytosol and mitochondrion, these apo-carboxylases are biotinylated to their active holo forms by the activity of biotin protein ligase (HCLS) (Ingaramo & Beckett 2012, Bailey et al. 2010, Hiratsuka et al. 1998). Defects in HLCS causes holocarboxylase synthetase deficiency (HLCS deficiency aka early-onset multiple carboxylase deficiency; MIM:253270). HLCS deficiency is an autosomal recessive disorder whereby deficient HLCS activity results in reduced activity of all five carboxylases. Symptoms include metabolic acidosis, organic aciduria, lethargy, hypotonia, convulsions and dermatitis (Suzuki et al. 2005). The first committed step in the synthesis of fatty acids is performed by the biotin-dependent enzyme acetyl CoA carboxylase [EC 6.4.1.2]. Acetyl CoA carboxylases 1 and 2 (ACACA and ACACB) have one Btn moiety covalently attached to each subunit (Abu-Elheiga et al. 1995). Eukaryotic acetyl-CoA carboxylases are heterodimers that can form catalytically active extended oligomers (Weatherly et al. 2004). Unlike the other biotin-dependent carboxylases that reside inside the mitochondrion, ACACA and B are located in the cytosol (shown here) and outer mitochondrial membrane respectively (Abu-Elheiga et al. 2000).
Once biotinylated, three halocarboxylases (hCBXs) are localised to the mitochondrial matrix. The mechanism of transfer is still unclear. Pyruvate carboxylase (PC) is required for gluconeogenesis, lipogenesis, neurotransmitter synthesis and insulin secretion; Methylcrotonyl-CoA carboxylase (MCC) is required for amino acid metabolism; propionyl-CoA carboxylase (PCC) is required for odd-chain fatty acid oxidation (Ingaramo & Beckett 2012, Hiratsuka et al. 1998, Bailey et al. 2010).
Biotin (Btn) acts as a coenzyme to 4 carboxylases which exist in their inactive apo forms. In the cytosol, these apo-carboxylases are biotinylated to their active halo forms by the activity of biotin-protein ligase (HCLS) (Ingaramo & Beckett 2012, Hiratsuka et al. 1998, Bailey et al. 2010). HCLS is localised to the cytosol and mitochondrion so can perform this activity in either of these locations. Defects in HLCS causes holocarboxylase synthetase deficiency (HLCS deficiency aka biotin-responsive multiple carboxylase deficiency; MIM:253270). HLCS deficiency is an autosomal recessive disorder whereby deficient HLCS activity results in reduced activity of multiple carboxylases. Symptoms include metabolic acidosis, organic aciduria, lethargy, hypotonia, convulsions and dermatitis (Suzuki et al. 2005). Pyruvate carboxylase (PC) is homotetrameric, binds 1 Mn2+ and 1 Btn per PC subunit (Xiang & Tong 2008). The exact order in which this complex is constructed is unknown.
Vitamin B12 (cobalamin, Cbl) is a water-soluble vitamin with a key role in blood formation and normal functioning of the brain and nervous system. Cbl consists of a planar corrin ring coordinating with a cobalt atom through four nitrogen atoms. A 5,6-dimethylbenzamidizole base coordinates with the cobalt atom in the lower axial position while a number of different species can coordinate with the cobalt atom in the upper axial position. It is the cobalt-corrin ring complex that gives all Cbls a deep red colour. Only bacteria and archaea are able to synthesize Cbl thus humans need a dietary intake to prevent deficiency (Green 2010, Quadros 2010, Watkins & Rosenblatt 2011). A common semi-synthetic form of the vitamin, cyanocobalamin (CNCbl, where a cyanide group is in the upper axial position), is produced from bacterial hydroxocobalamin and used in many pharmaceuticals, supplements and as a food additive. In mammalian cells, Cbl or CNCbl is converted to two active coenzyme derivatives; methylcobalamin (MetCbl) and adenosylcobalamin (AdoCbl). MetCbl is required for activity of the cytoplasmic enzyme methionine synthase, which converts homocysteine to methionine. AdoCbl is required for activity of the mitochondrial enzyme methylmalonyl CoA mutase, which converts L-methylmalonyl-CoA to succinyl-CoA (Seetharam 1999). This pathway outlines the intake, transport and metabolism of Cbl and is assumed to be equally applicable to CNCbl.
Multidrug resistance-associated protein 1 (ABCC1, MRP1) can specifically mediate the ATP-dependant export of free cobalamin (Cbl aka vitamin B12) from small intestine cells to the portal vein (Shah et al. 2011).
NMNAT1 catalyzes the reaction of nicotinate D-ribonucleotide and ATP to form deamino-NAD+ (nicotinate adenine dinucleotide) and pyrophosphate (Schweiger et al. 2001). The active form of the enzyme in vitro is a hexamer (Zhou et al. 2002), and its activity is substantially greater in the presence of Zn++ than of Mg++ (Sorci et al. 2007). The predicted amino acid sequence of the enzyme contains a nuclear localization domain and the protein is observed to localize to the nucleus (Schweiger et al. 2001; Berger et al. 2005).
NMNAT2 catalyzes the reaction of nicotinate D-ribonucleotide and ATP to form deamino-NAD+ (nicotinate adenine dinucleotide) and pyrophosphate (Sorci et al. 2007). The active form of the enzyme is a monomer in vitro (Raffaelli et al. 2002). Although the predicted amino acid sequence of the enzyme lacks an obvious signal sequence or transmembrane domain (Yalowitz et al. 2004), recombinant FLAG-tagged protein expressed in HeLa cells localizes predominantly to the Golgi apparatus (Berger et al. 2005). Its localization within the Golgi apparatus is unknown and the annotation here is based on the plausible but speculative assumption that the enzyme is associated with the Gogi membrane and accessible from the cytosol. Immunostaining studies indicate that the protein is abundant in Islets of Langerhans and in several regions of the brain (Yalowitz et al. 2004).
NMNAT3 catalyzes the reaction of nicotinate D-ribonucleotide and ATP to form deamino-NAD+ (nicotinate adenine dinucleotide) and pyrophosphate (Sorci et al. 2007). The active form of the enzyme is a tetramer in vitro (Zhang et al. 2003). Recombinant FLAG-tagged protein expressed in HeLa cells localizes both to the cytosol and to mitochondria (Berger et al. 2005). The cytosolic protein is annotated here.
NAD+ kinase catalyzes the transfer of a phosphate group from ATP to NAD+, forming NADP+. This is the only way to generate NADP+ in all living organisms. The enzyme requires a divalent metal to be effective. Zn2+ is the best metal for this purpose.
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NAD synthase catalyzes the final step in the biosynthesis of NAD+, both in the de novo synthesis and in the salvage pathways. The enzyme makes use of glutamine as an amide donor in the reaction. NAD synthase exists as a homohexamer in the cytosol. There are two forms of NAD synthase in humans, NADsyn1 and NADsyn2. The major difference between the two forms is that NADsyn1 appears to be glutamine-dependent whereas NADsyn2 is strictly ammonia-dependent.
Cytosolic dihydrofolate reductase catalyzes the reaction of folate, NADPH, and H+ to form dihydrofolate and NADP+ (Chen et al. 1984; Davies et al. 1990).
Nicotinate (niacin) and nicotinamide are precursors of the coenzymes nicotinamide-adenine dinucleotide (NAD+) and nicotinamide-adenine dinucleotide phosphate (NADP+). When NAD+ and NADP+ are interchanged in a reaction with their reduced forms, NADH and NADPH respectively, they are important cofactors in several hundred redox reactions. Nicotinate is synthesized from 2-amino-3-carboxymuconate semialdehyde, an intermediate in the catabolism of the essential amino acid tryptophan.
Cytosolic folylpolyglutamate synthase catalyzes the reaction of THF-glutamate(n), L-glutamate, and ATP to form THF-glutamate(n+1), ADP, and orthophosphate. (The first glutamate residue is attached to the glutamate moiety of THF itself; for convenience the process is annotated here as if it proceeded in a single concerted step.) The extent of conjugation is variable, but the commonest cytosolic form of THF has five added glutamate residues. Although its properties as a donor of one-carbon units are not affected by glutamate addition, THF that lacks added glutamate residues cannot be retained in the cytosol so this reaction is needed for normal THF function under physiological conditions (Garrow et al. 1992; Chen et al. 1996).
Cytosolic dihydrofolate reductase catalyzes the reaction of dihydrofolate, NADPH, and H+ to form tetrahydrofolate (THF) and NADP+ (Chen et al. 1984; Davies et al. 1990).
SLC25A32 protein in the inner mitochondrial membrane mediates the reversible transport of tetrahydrofolate between the cytosol and the mitochondrial matrix. Retention of tetrahydrofolate within the mitochondrial matrix is dependent on mitochondrial polyglutamate addition (Titus and Moran 2000; Chen et al. 1996).
Mutations in SPTLC1, encoding serine palmitoyltransferase, long chain base subunit-1, cause hereditary sensory neuropathy type I
Cytosolic folylpolyglutamate synthase catalyzes the reaction of 5-methylTHF-glutamate(n), L-glutamate, and ATP to form 5-methylTHF-glutamate(n+1), ADP, and orthophosphate. (The first glutamate residue is attached to the glutamate moiety of 5-methylTHF itself; for convenience the process is annotated here as if it proceeded in a single concerted step.) The extent of conjugation is variable, but the commonest cytosolic form of 5-methylTHF has five added glutamate residues. Although its properties as a donor of one-carbon units are not affected by glutamate addition, 5-methylTHF that lacks added glutamate residues cannot be retained in the cytosol so this reaction is needed for normal 5-methylTHF function under physiological conditions (Garrow et al. 1992; Chen et al. 1996).
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The formate-tetrahydrofolate ligase activity of the trifunctional MTHFD1 enzyme catalyzes the reaction of THF polyglutamate, formate, and ATP to form 10-formylTHF polyglutamate, ADP, and orthophosphate. MTHFD1 is cytosolic and occurs as a dimer. The human enzyme has been identified and partially characterized biochemically (Hum et al. 1988); additional reaction details can be inferred from the properties of the well-studied homologous rabbit enzyme (Villar et al. 1985).
Mitochondrial folylpolyglutamate synthase catalyzes the reaction of THF-glutamate(n), L-glutamate, and ATP to form THF-glutamate(n+1), ADP, and orthophosphate. (The first glutamate residue is attached to the glutamate moiety of THF itself; for convenience the process is annotated here as if it proceeded in a single concerted step.) The extent of conjugation is variable, but the commonest mitochondrial form of THF has six added glutamate residues. Although its properties as a donor of one-carbon units are not affected by glutamate addition, THF that lacks added glutamate residues cannot be retained in the mitochondrial matrix so this reaction is needed for normal THF function under physiological conditions. The mitochondrial and cytosolic forms of folylpolyglutamate synthase are encoded by the same gene - alternative splicing generates mRNA with or without an initial exon encoding a mitochondrial targeting sequence (Garrow et al. 1992; Chen et al. 1996).
Cytosolic MTHFR dimer catalyzes the reaction of 5,10-methyleneTHF polyglutamate, NADPH, and H+ to form 5-methylTHF polyglutamate and NADP+. The specificity and importance of this reaction in vivo have been established through the study of patients deficient in the enzyme (Goyette et al. 1995).
Cytosolic serine hydroxymethyltransferase catalyzes the reversible reaction of tetrahydrofolate polyglutamate (THF polyglutamate) and serine to form 5,10-methyleneTHF polyglutamate and glycine. The active form of the enzyme is a tetramer (Renwick et al. 1998). In the body, this reaction is a major source of 5,10-methyleneTHF, which in turn is a critical precursor in the synthesis of dTMP.
The methylenetetrahydrofolate dehydrogenase activity of the trifunctional MTHFD1 enzyme catalyzes the reversible reaction of 5,10-methenylTHF polyglutamate, NADPH, and H+ to form 5,10-methyleneTHF polyglutamate and NADP+. MTHFD1 is cytosolic and occurs as a dimer. The human enzyme has been identified and partially characterized biochemically (Hum et al. 1988); additional reaction details can be inferred from the properties of the well-studied homologous rabbit enzyme (Villar et al. 1985).
The methenyltetrahydrofolate cyclohydrolase activity of the trifunctional MTHFD1 enzyme catalyzes the reversible reaction of 10-formylTHF polyglutamate to form 5,10-methenylTHF polyglutamate and H2O. MTHFD1 is cytosolic and occurs as a dimer. The human enzyme has been identified and partially characterized biochemically (Hum et al. 1988); additional reaction details can be inferred from the properties of the well-studied homologous rabbit enzyme (Villar et al. 1985).
DNA double-strand breaks: signaling, repair and the cancer connection.
Folates are essential cofactors that provide one-carbon moieties in various states of reduction for biosynthetic reactions. Processes annotated here include transport reactions by which folates are taken up by cells and moved intracellularly, folate conjugation with glutamate (required for folate retention within a cell), and some of the key reactions in the generation of reduced folates and one-carbon derivatives of folate.
The methenyltetrahydrofolate cyclohydrolase activity of the trifunctional MTHFD1 enzyme catalyzes the reversible reaction of 5,10-methenylTHF polyglutamate and H2O to form 10-formylTHF polyglutamate. MTHFD1 is cytosolic and occurs as a dimer. The human enzyme has been identified and partially characterized biochemically (Hum et al. 1988); additional reaction details can be inferred from the properties of the well-studied homologous rabbit enzyme (Villar et al. 1985).
The methylenetetrahydrofolate dehydrogenase activity of the trifunctional MTHFD1 enzyme catalyzes the reversible reaction of 5,10-methyleneTHF polyglutamate and NADP+ to form 5,10-methenylTHF polyglutamate, NADPH, and H+. MTHFD1 is cytosolic and occurs as a dimer. The human enzyme has been identified and partially characterized biochemically (Hum et al. 1988); additional reaction details can be inferred from the properties of the well-studied homologous rabbit enzyme (Villar et al. 1985).
Cytosolic serine hydroxymethyltransferase catalyzes the reversible reaction of 5,10-methyleneTHF polyglutamate and glycine to form tetrahydrofolate polyglutamate (THF polyglutamate) and serine. The active form of the enzyme is a tetramer (Renwick et al. 1998).
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ArfGAP1 dynamics and its role in COPI coat assembly on Golgi membranes of living cells
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The crystal structure and mutational analysis of human NUDT9
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Ca2+/calmodulin-dependent protein kinase IIdelta and protein kinase D overexpression reinforce the histone deacetylase 5 redistribution in heart failure
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Leukotriene A4 hydrolase in human leukocytes. Purification and properties
Characterization of the enzymatic defect in late-onset muscle phosphofructokinase deficiency. New subtype of glycogen storage disease type VII.
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Inactivation of NPC1L1 causes multiple lipid transport defects and protects against diet-induced hypercholesterolemia
When do Lasses (longevity assurance genes) become CerS (ceramide synthases)?: Insights into the regulation of ceramide synthesis
Mechanism of selectivity in aquaporins and aquaglyceroporins
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A highly conserved eukaryotic protein family possessing properties of polypeptide chain release factor
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Peroxisome proliferator-activated receptors: nuclear control of metabolism
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Mammalian MAP kinase signalling cascades
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Tim22, the essential core of the mitochondrial protein insertion complex, forms a voltage-activated and signal-gated channel
Cancer-derived mutations in the regulatory subunit p85alpha of phosphoinositide 3-kinase function through the catalytic subunit p110alpha
Replication of UV-damaged DNA: new insights into links between DNA polymerases, mutagenesis and human disease.
di-retinoid-pyridinium-ethanolamine [ChEBI:71980]
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Metabolic characteristics and importance of the universal methionine salvage pathway recycling methionine from 5'-methylthioadenosine
Two novel proteins in the mitochondrial outer membrane mediate beta-barrel protein assembly
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Specific protein domains mediate cooperative assembly of HuR oligomers on AU-rich mRNA-destabilizing sequences
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The gene encoding hydroxypyruvate reductase (GRHPR) is mutated in patients with primary hyperoxaluria type II
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Crystal structure of human aquaporin 4 at 1.8 A and its mechanism of conductance
FUNCTION MRS4 suppresses a mitochondrial splice defect in the first intron of the COB gene. It may act as a carrier, exerting its suppressor activity via modulation of solute concentrations in the mitochondrion (possibly of cations). Not essential.MISCELLANEOUS Present with 1340 molecules/cell in log phase SD medium.SIMILARITY Belongs to the mitochondrial carrier (TC 2.A.29) family.SIMILARITY Contains 3 Solcar repeats.
CATALYTIC ACTIVITY Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).DOMAIN The CysA-type zinc finger is required for PCNA-binding (PubMed:22119860).DOMAIN The CysB motif binds 1 4Fe-4S cluster and is required for the formation of polymerase complexes (PubMed:22119860).MISCELLANEOUS In eukaryotes there are five DNA polymerases: alpha, beta, gamma, delta, and epsilon which are responsible for different reactions of DNA synthesis.SIMILARITY Belongs to the DNA polymerase type-B family.SIMILARITY Contains 1 CysA-type zinc finger.
Molecular basis for methionine synthase reductase deficiency in patients belonging to the cblE complementation group of disorders in folate/cobalamin metabolism
Mitochondrial dysfunction contributes to oncogene-induced senescence
PCNA function in the activation and strand direction of MutL? endonuclease in mismatch repair
Differential induction of the toll-like receptor 4-MyD88-dependent and -independent signaling pathways by endotoxins
Acceptor substrate binding revealed by crystal structure of human glucosamine-6-phosphate N-acetyltransferase 1
Selective killing of human malignant cell lines deficient in methylthioadenosine phosphorylase, a purine metabolic enzyme
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Enzymatic phosphorylation of nucleoside diphosphates
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Prefoldin, a chaperone that delivers unfolded proteins to cytosolic chaperonin
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Transcriptional regulation of squalene epoxidase by sterols and inhibitors in HeLa cells
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Cloning of the sulphamidase gene and identification of mutations in Sanfilippo A syndrome
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Tob38, a novel essential component in the biogenesis of beta-barrel proteins of mitochondria
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Molecular cloning and expression of the cDNAs encoding human and yeast mevalonate pyrophosphate decarboxylase
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Regulation of small GTPases at epithelial cell-cell junctions
Elongation of very long chain fatty acids protein 1 (ELOVL1) catalyzes the reaction of palmitoyl-CoA and malonyl-CoA to form 3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA), CO2, and CoASH. Limited data are available for human ELOVL1 protein. Its localization to the endoplasmic reticulum membrane and catalytic activity are inferred from the properties of better-studied human ELOVL proteins (Jakobsson et al. 2006; Shimamura et al. 2009).
AU-rich elements and associated factors: are there unifying principles?
Acyl-CoA synthetase long-chain family member 6 (ACSL6) associated with the plasma membrane catalyzes the reaction of palmitate, CoASH, and ATP to form palmitoyl-CoA, AMP, pyrophosphate, and water. In the body, ACSL6 is found in red blood cells. It is active on oleic acid as well as palmitic acid (Malhotra et al. 1999).
Acyl-CoA synthetase long-chain family member 5 (ACSL5) associated with the endoplasmic reticulum membrane catalyzes the reaction of palmitate, CoASH, and ATP to form palmitoyl-CoA, AMP, pyrophosphate, and water (Gassler et al. 2007).
Acyl-CoA synthetase long-chain family member 4 (ACSL4) associated with the endoplasmic reticulum membrane catalyzes the reaction of arachidonate, CoASH, and ATP to form arachidonyl-CoA, AMP, pyrophosphate, and water (Longo et al. 2003; Meloni et al. 2003).
Defective HLCS causes multiple carboxylase deficiency
FGFR2-amplified gastric cancer cell lines require FGFR2 and Erbb3 signaling for growth and survival
The joining of ribosomal subunits in eukaryotes requires eIF5B.
Fatty acid elongases in mammals: their regulation and roles in metabolism
Functional analysis of human P5, a protein disulfide isomerase homologue
Triacylglycerol is a major energy store in the body and its hydrolysis to yield fatty acids and glycerol is a tightly regulated part of energy metabolism. A central part in this regulation is played by hormone-sensitive lipase (HSL), a neutral lipase abundant in adipocytes and skeletal and cardiac muscle, but also abundant in ovarian and adrenal tissue, where it mediates cholesterol ester hydrolysis, yielding cholesterol for steroid biosynthesis. The hormones to which it is sensitive include catecholamines (e.g., epinephrine), ACTH, and glucagon, all of which trigger signaling cascades that lead to its phosphorylation and activation, and insulin, which sets off events leading to its dephosphorylation and inactivation (Holm et al. 2000; Kraemer and Shen 2002). The processes of triacylglycerol and cholesterol ester hydrolysis are also regulated by subcellular compartmentalization: these lipids are packaged in cytosolic particles and the enzymes responsible for their hydrolysis, and perhaps for additional steps in their metabolism, are organized at the surfaces of these particles (e.g., Brasaemle et al. 2004). This organization is dynamic: the inactive form of HSL is not associated with the particles, but is translocated there after being phosphorylated. Conversely, perilipin, a major constituent of the particle surface, appears to block access of enzymes to the lipids within the particle; its phosphorylation allows greater access. Here, HSL-mediated triacylglycerol hydrolysis is described as a pathway containing twelve reactions. The first six of these involve activation: phosphorylation of HSL, dimerization of HSL, disruption of CGI-58:perilipin complexes at the surfaces of cytosolic lipid particles, phosphorylation of perilipin, association of phosphorylated HSL with FABP, and translocation of HSL from the cytosol to the surfaces of lipid particles. The next four reactions are the hydrolysis reactions themselves: the hydrolysis of cholesterol esters, and the successive removal of three fatty acids from triacylglycerol. The last two reactions, dephosphorylation of perilipin and HSL, negatively regulate the pathway. These events are outlined in the figure below. Inputs (substrates) and outputs (products) of individual reactions are connected by black arrows; blue lines connect output activated enzymes to the other reactions that they catalyze. Despite the undoubted importance of these reactions in normal human energy metabolism and in the pathology of diseases such as type II diabetes, they have been studied only to a limited extent in human cells and tissues. Most experimental data are derived instead from two rodent model systems: primary adipocytes from rats, and mouse 3T3-L1 cells induced to differentiate into adipocytes.
Processes annotated here include the digestion of dietary lipids, sterol uptake, the formation and turnover of lipoproteins (chylomicrons, VLDL, LDL, and HDL), and the mobilization of fatty acids through the action of hormone-sensitive lipase.
Detours and shortcuts to transcription reinitiation.
Membrane-associated acyl-CoA synthetase long-chain family member 1 (ACSL1) catalyzes the reaction of palmitate, CoASH, and ATP to form palmitoyl-CoA, AMP, pyrophosphate, and water. Human ACSL1 has not been characterized in detail, but available data suggest that it is associated specifically with the membrane of the endoplasmic reticulum and that it can act on oleic acid as well as on palmitic acid (Malhotra et al. 1999).
Membrane-associated acyl-CoA synthetase long-chain family member 3 (ACSL3) catalyzes the reaction of palmitate, CoASH, and ATP to form palmitoyl-CoA, AMP, pyrophosphate, and water. The enzyme is probably associated specifically with the endoplasmic reticulum membrane, and can also associate with lipid droplets. It is active on oleic acid as well as on palmitic acid (Fujimoto ea 2007).
SLC25A1, in the inner mitochondrial membrane, mediates the exchange of mitochondrial citrate for cytosolic malate.
Cytosolic acetyl-CoA carboxylase 1 (ACACA) catalyzes the reaction of bicarbonate, ATP, and acetyl-CoA to form malonyl-CoA, ADP, and orthophosphate. The reaction is positively regulated by citrate. The human ACACA cDNA has been cloned (Abu-Elheiga et al. 1995) and the biochemical properties of the human enzyme have recently been described (Cheng et al. 2007; Locke et al. 2008). Four ACACA isoforms generated by alternative splicing have been identified as mRNAs - the protein product of the first has been characterized experimentally.
Dihydroxyacetone phosphate (DHAP) is converted to glycerol-3-phosphate (G3P) by glycerol-3-phosphate dehydrogenase (GPD1) or by glycerol-3-phosphate dehydrogenase-like (GPD1L) enzymes (Ou et al. 2006, Valdivia et al. 2009). The active forms of both enzymes are homodimers. This reaction may be found in white adipose tissues where glycerol-3-kinase activity is not observed in sufficient levels. GPD1/GPD1L reduces dihydroxyacetone phosphate with NADH donating electrons to this reduction.
Fatty acyl-CoA biosynthesis involves following steps: -Palmitate synthesis catalyzed by Acetyl-CoA carboxylase and Fatty acid synthase -Conversion of palmitic acid to long chain fatty acids and -Conversion of long chain fatty acids to fatty acyl-CoA by acyl-CoA synthases.
Glycerol can be a source for glycerol-3-phosphate, in which case, a phosphate form ATP is transferred to glycerol by glycerol kinase forming glycerol-3-phosphate and ADP.
Threonine 308 phosphorylated form of Akt translocates to the nucleus of PC12 cells under nerve growth factor stimulation and associates with the nuclear matrix protein nucleolin
Elongation of very long chain fatty acids protein 2 (ELOVL2) catalyzes the reaction of palmitoyl-CoA and malonyl-CoA to form 3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA), CO2, and CoASH. Indirect data from studies of transfected cells expressing ELOVL2 are consistent with its localization to the endoplasmic reticulum and activity on palmitoyl-CoA. It may also catalyze the condensation of arachidonyl-CoA with malonyl-CoA (Kobayashi et al. 2007).
Elongation of very long chain fatty acids protein 4 (ELOVL4) catalyzes the reaction of lignoceroyl-CoA and malonyl-CoA to form 3-oxocerotoyl-CoA, CO2, and CoASH. ELOVL4 is abundant in retinal cells, where it is localized to the endoplasmic reticulum membrane (Grayson and Molday 2005). The catalytic activity of ELOVL4 has not been examined directly but is inferred from that of the homologous mouse protein, which is also active on polyunsaturated fatty acids (PUFAs) (Agbada et al. 2008).
Elongation of very long chain fatty acids protein 5 (ELOVL5) catalyzes the reaction of arachidonyl-CoA and malonyl-CoA to form 3-oxo-(7,10,13,16)-docosatetraenoyl-CoA, CO2, and CoASH. Localization of ELOVL5 to the endoplasmic reticulum membrane is inferred from that of other human ELOVL proteins; its catalytic activity has been studied in ELO- yeast cells expressing human ELOVL5 protein (Leonard et al. 2000).
Elongation of very long chain fatty acids protein 7 (ELOVL7) catalyzes the reaction of arachidoyl-CoA (C20:0) and malonyl-CoA to form 3-oxobehenoyl-CoA, CO2, and CoASH. ELOVL7 is localized to the endoplasmic reticulum in transfected cells expressing the cloned cDNA (Tamura et al. 2009).
Hydroxysteroid (17-beta) dehydrogenase 12 (HSD17B12) catalyzes the reaction of 3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA) and NADPH + H+ to form 3-hydroxyoctadecanoyl-CoA and NADP+. This activity of HSD17B12 protein and its localization to the endoplasmic reticulum membrane was established in studies of transfected cells expressing the protein (Moon and Horton 2003).
Trans-2,3-enoyl-CoA reductase (TECR) catalyzes the reaction of trans-octadec-2-enoyl-CoA and NADPH + H+ to form stearoyl-CoA and NADP+. This activity of TECR protein and its localization to the endoplasmic reticulum membrane was established in studies of transfected cells expressing the protein (Moon and Horton 2003).
Very long-chain fatty acyl-CoA molecules are synthesized from palmitic acid (C16) or other fatty acids that are synthesized de novo or obtained from the diet. Before they can be elongated, these fatty acids are activated by conversion to fatty acyl-CoAs in reactions catalyzed by the five members of the ACSL (acyl-CoA synthetase long-chain) enzyme family. Elongation proceeds by a four-step reaction sequence parallel to that responsible for the synthesis of palmitate (C16) from acetyl-CoA and malonyl-CoA: a molecule of malonyl-CoA condenses with the long chain fatty acyl-CoA forming a 3-oxoacyl-CoA containing two more carbon atoms than the starting long chain fatty acyl-CoA and CO2. This reaction is catalyzed by one of the seven members of the ELOVL (Elongation of very long chain fatty acids protein) enzyme family. The 3-oxoacyl-CoA is reduced to a 3-hydroxyacyl-CoA by HSD17B12 (hydroxysteroid (17-beta) dehydrogenase 12), 3-hydroxyacyl-CoA is dehydrated to a trans-2,3-enoyl-CoA, and the trans-2,3-enoyl-CoA is reduced to a fatty acid two carbon atoms longer than the input one by TECR (trans-2,3-enoyl-CoA reductase) enzyme. All of these enzyme activities are associated with separate polypeptides associated with the endoplasmic reticulum membrane, unlike the multifunctional and cytosolic FAS complex responsible for synthesis of palmitic acid (Jakobsson ea 2006; Nugteren 1965). The specific reactions annotated here mediate the synthesis of stearoyl-CoA (3-hydroxyoctadecanoyl-CoA) from palmitate, as well as the activation and condensation with malonyl-CoA of arachidonic acid, a 20-carbon unsaturated fatty acid that plays a central role in the synthesis of prostaglandins and related hormones. Human cells contain a wide range of very long chain fatty acids, and the enzymes involved in these reactions are believed to have broader substrate specificities than are shown in these annotations, but few direct experimental data are available to support more extensive annotations.
Structure and regulation of MAPK phosphatases
D-Fructose 2,6-bisphosphate [ChEBI:28602]
Defective T cell differentiation in the absence of Jnk1
Rat monoacylglycerol lipase (MGLL) catalyzes the hydrolysis of 2-acylglycerol to yield glycerol + fatty acid (Tornqvist and Belfrage 1976; Fredrikson et al. 1986). Localization of the enzyme to lipid particles is plausible, given its low solubility and its involvement in acylglycerol metabolism, but this localization has not been directly experimentally verified. The human reaction is inferred from the well-studied rat one.
Human NPC1L1, associated with the plasma membrane, binds ezetimibe and becomes incapable of mediating cholesterol uptake. The molecular mechanisms of cholesterol transport and ezetimibe inhibition, however, remain unclear (Garcia-Calvo et al. 2005; Weinglass et al. 2008).
Dietary phytosterols (sterols derived from plants) are taken up into enterocytes from the gut lumen. The reaction is thought to be mediated by plasma membrane-associated NPC1L1 protein. Detailed studies in Maden-Darby canine kidney cells, both mediated by endogenous (canine) NPC1L1 and by overexpressed human protein, indicate a major role for NPC1L1 in the uptake of extracellular sterol. These studies have also shown that ezetimibe binds both human and canine proteins and renders them incapable of mediating sterol uptake. The molecular mechanisms of cholesterol transport and ezetimibe inhibition, however, remain unclear (Weinglass et al. 2008).
NPC1L1 protein mediates the uptake of dietary sterols from the gut lumen. These include cholesterol and plant sterols (phytosterols). Half to two-thirds of the 250-500 milligrams of cholesterol consumed daily from a typical western diet is taken up by this route and exported from enterocytes into the lymph in chylomicrons. Of the 200-400 milligrams of dietary phytosterol, only about 5% is absorbed.The drug ezetimibe interferes with NPC1L1-mediated sterol uptake (Oram and Vaughan 2006). Both cholesterol and phytosterols are secreted from the liver into the bile (Salen et al. 1970). Mutations affecting the ABCG5/8 transporter complex inhibit this process (e.g., Berge et al. 2000), while the molecular details of sterol export in human cells have not been worked out, they can be inferred from the properties of the homologous mouse proteins (Graf et al. 2003; Wang et al. 2006).
ABCG5/8 in the plasma membrane mediates the ATP-dependent export of cytosolic sterols (cholesterol and phytosterols). Mutations affecting the ABCG5/8 proteins are associated with the accumulation of high levels of cholesterol and phytosterols in the body, demonstrating the specificity and physiological importance of this process (Berge et al. 2000). Human ABCG5/8 has not been studied in detail, but the homologous mouse protein complex mediate ATP-dependent sterol export (Wang et al. 2006). The mouse proteins localize to the apical plasma membranes of enterocytes and hepatocytes, consistent with the hypothesis that in vivo ABCG5/8 mediates sterol export into the gut lumen and from hepatocytes into the bile (Graf et al. 2003).
Cloning and characterization of the cDNA encoding human adenylosuccinate synthetase
Inositol monophosphatase 1 (IMPA1) and 2 (IMPA2) homodimers dephosphorylate inositol 3-phosphate (I3P) to inositol (Ins). In vitro, IMPA1 and 2 differ in their pH optima and IMPA1 has a significantly greater activity on IP4 than does IMPA2 (Ohnishi et al. 2007).
Direct activation of protein kinases by unanchored polyubiquitin chains
Inositol phosphates IP2, IP and the six-carbon cyclic alcohol inositol (Ins) are produced by various phosphatases and the inositol-3-phosphate synthase 1 (ISYNA1) (Ju et al. 2004, Ohnishi et al. 2007, Irvine & Schell 2001, Bunney & Katan 2010).
Inositol phosphates (IPs) are molecules involves in signalling processes in eukaryotes. myo-Inositol consists of a six-carbon cyclic alcohol with an axial 2-hydroxy and five equatorial hydroxyls. Mono-, di-, and triphosphorylation of the inositol ring generates a wide variety of stereochemically distinct signalling entities. Inositol 1,4,5-trisphosphate (I(1,4,5)P3), is formed when the phosphoinositide phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is hydrolysed by a phospholipase C isozyme. An array of inositol trisphosphate (IP3) and tetrakisphosphate (IP4) molecules are synthesised by the action of various kinases and phosphatases in the cytosol. These species then transport between the cytosol and the nucleus where they are acted on by inositol polyphosphate multikinase (IPMK), inositol-pentakisphosphate 2-kinase (IPPK), inositol hexakisphosphate kinase 1 (IP6K1) and 2 (IP6K2), to produce IP5, IP6, IP7, and IP8 molecules. Some of these nuclear produced IPs transport back to the cytosol where they are converted to an even wider variety of IPs, by kinases and phosphatases, including the di- and triphospho inositol phosphates aka pyrophosphates (Irvine & Schell 2001, Bunney & Katan 2010, Alcazar-Romain & Wente 2008, York 2006, Monserrate and York 2010).
Dietary cholesterol is taken up into enterocytes from the gut lumen in a reaction mediated by plasma membrane-associated NPC1L1 protein. This role for NPC1L1 was first observed in studies of a mouse model system (Altman et al. 2004). Subsequent studies of human cultured cells confirmed the participation of NPC1L1 in cholesterol transport across membranes but suggested that this transport process might not be a major factor in dietary cholesterol uptake (Davies et al. 2005). Detailed studies in Maden-Darby canine kidney cells, both mediated by endogenous (canine) NPC1L1 and by overexpressed human protein, indicate a major role for NPC1L1 in the uptake of extracellular cholesterol. These studies have also shown that ezetimibe binds both human and canine proteins and renders them incapable of mediating cholesterol uptake. The molecular mechanisms of cholesterol transport and ezetimibe inhibition, however, remain unclear (Weinglass et al. 2008).
Inositol-3-phosphate synthase 1 (ISYNA1) aka hIPS isomerises glucose 6-phosphate (Glc6P) to inositol 3-phosphate (I3P) (Ju et al. 2004).
The solute carrier 26 family of proteins in epithelial ion transport
Identification and characterization of a novel inositol hexakisphosphate kinase
Activity of phosphatidylethanolamine-N-methyltransferase in brain affected by Alzheimer's disease
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Structural basis for human monoglyceride lipase inhibition
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Signaling mechanisms utilized by antigen receptors and integrins: common intermediates, different outcomes?
CDC6 association with the ORC:origin complex
ATP-Binding cassette cholesterol transporters and cardiovascular disease
Recruitment of repair and signaling proteins to double-strand breaks
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Identification of the human mitochondrial oxodicarboxylate carrier. Bacterial expression, reconstitution, functional characterization, tissue distribution, and chromosomal location
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Identification and characterization of a mammalian mitochondrial ATP-binding cassette membrane protein
4,4-dimethylcholesta-8(9),14,24-trien-3beta-ol and NADPH + H+ react to form 4,4-dimethylcholesta-8(9),24-dien-3beta-ol and NADP+, catalyzed by LBR in the nuclear envelope. LBR protein spans the inner nuclear envelope, has an aminoterminal region with properties of a laminin receptor and a carboxyterminal domain with sequence similarity to sterol delta14-reductases (Holmer et al. 1998). Studies of material from an individual with HEM/Greenberg skeletal dysplasia indicate that LBR catalyzes the sterol delta14-reductase step of cholesterol biosynthesis in vivo. DNA sequencing revealed homozygosity for a mutant LBR allele encoding a truncated protein in the affected individual, and cells from the individual accumulated cholesta-8,14-dien-3beta-ol in culture. Transfection of wild-type LBR into the cultured cells reversed the accumulation of cholesta-8,14-dien-3beta-ol (Waterham et al. 2003). This observation is surprising because a second gene, TM7SF2, encodes an efficient sterol delta14-reductase that is localized to the endoplasmic reticulum whose expression is up-regulated in response to sterol depletion (Bennati et al. 2006). The physiological roles of LBR and TM7SF2 in vivo remain to be determined.
4,4-dimethylcholesta-8(9),14,24-trien-3beta-ol and NADPH + H+ react to form 4,4-dimethylcholesta-8(9),24-dien-3beta-ol and NADP+, catalyzed by TM7SF2 in the endoplasmic reticulum. TM7SF2 protein has sterol delta14-reductase activity in vitro, and expression of the gene is induced by sterol starvation in human cells, as expected for a gene involved in sterol biosynthesis (Bennati et al. 2006). However, molecular studies of material from an individual with HEM/Greenberg skeletal dysplasia indicate that LBR, a protein that spans the inner nuclear membrane and has both laminin receptor and sterol delta14-reductase activities, is required for normal sterol 14delta-reductase activity in human cells. It remains to be determined whether both LBR and TM7SF2 catalyze this reaction in vivo, and whether the role of TM7SF2 is essential (Waterham et al. 2003).
4,4-dimethylcholesta-8(9),24-dien-3beta-ol, NADPH + H+, and O2 react to form 4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol, NADP+, and H2O. This reaction, in the endoplasmic reticulum, is catalyzed by SC4MOL (C-4 methylsterol oxidase). The human enzyme has been identified based on its sequence similarity to yeast methyl sterol oxidase (ERG25) and the ability of the cloned human gene to rescue ERG25-deficient yeast cells (Li and Kaplan 1996). The mechanism and stoichiometry of the reaction have been inferred from studies of partially purified rat enzyme (Gaylor et al. 1975; Fukushima et al. 1981).
4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol and NAD+ react to form 4-methylcholesta-8(9),24-dien-3-one, CO2, and NADH + H+. This reaction occurs in the endoplasmic reticulum, catalyzed by NSDHL (Caldas and Herman 2003). Defects in this enzyme are associated with CHILD syndrome (Congenital Hemidysplasia with Ichthyosiform nevus and Limb Defects) (Konig et al. 2000), but cholesterol biosynthesis in cells and tissues from affected individuals has not been characterized. Instead, the mechanism and stoichiometry of the reaction are inferred from biochemical studies of partially purified rat enzyme (Rahimtula and Gaylor 1972).
4-methylcholesta-8(9),24-dien-3-one and NADPH + H+ react to form 4-methylcholesta-8(9),24-dien-3beta-ol and NADP+. This reaction takes place in the endoplasmic reticulum, catalyzed by HSD17B7. Two isoforms of the enzyme due to alternative splicing have been identified but only the first has been tested for enzymatic activity (Marijanovic et al. 2003). The human enzyme has not been studied extensively; molecular details of the reaction are inferred from those worked out in studies of material from rat liver (Gaylor 2002).
4-methylcholesta-8(9),24-dien-3beta-ol, NADPH + H+, and O2 react to form 4-carboxycholesta-8(9),24-dien-3beta-ol, NADP+, and H2O. This reaction, in the endoplasmic reticulum, is catalyzed by SC4MOL (C-4 methylsterol oxidase). The human enzyme has been identified based on its sequence similarity to yeast methyl sterol oxidase (ERG25) and the ability of the cloned human gene to rescue ERG25-deficient yeast cells (Li and Kaplan 1996). The mechanism and stoichiometry of the reaction have been inferred from studies of partially purified rat enzyme (Gaylor et al. 1975; Fukushima et al. 1981).
4-carboxycholesta-8(9),24-dien-3beta-ol and NAD+ react to form zymosterone (cholesta-8(9),24-dien-3-one), CO2, and NADH + H+. This reaction occurs in the endoplasmic reticulum, catalyzed by NSDHL (Caldas and Herman 2003). Defects in this enzyme are associated with CHILD syndrome (Congenital Hemidysplasia with Ichthyosiform nevus and Limb Defects) (Konig et al. 2000), but cholesterol biosynthesis in cells and tissues from affceted individuals has not been characterized. Instead, the mechanism and stoichiometry of the reaction are inferred from biochemical studies of partially purified rat enzyme (Rahimtula and Gaylor 1972).
Zymosterone (cholesta-8(9),24-dien-3-one) and NADPH + H+ react to form zymosterol (cholesta-8(9),24-dien-3beta-ol) and NADP+. This reaction takes place in the endoplasmic reticulum, catalyzed by HSD17B7. Two isoforms of the enzyme due to alternative splicing have been identified but only the first has been tested for enzymatic activity (Marijanovic et al. 2003). The human enzyme has not been studied extensively; molecular details of the reaction are inferred from those worked out in studies of material from rat liver (Gaylor 2002).
Cholesta-7,24-dien-3beta-ol, NADPH + H+, and O2 react to form cholesta-5,7,24-trien-3beta-ol, NADP+, and 2 H2O, catalyzed by SC5D. This reaction takes place in the endoplasmic reticulum. Its biochemical details are inferred from those of the reaction catalyzed by the purified rat protein (Kawata et al. 1985). The role of human SC5D in catalyzing this reaction in vivo is established from studies of patients in whom the enzyme is defective (Brunetti-Pierri et al. 2002; Krakowiak et al. 2003).
Cholesta-5,7,24-trien-3beta-ol and NADPH + H+ react to form desmosterol and NADP+. This reaction is catalyzed by DHCR7, associated with the endoplasmic reticulum membrane. The biochemical details of the reaction are inferred from those of the reaction catalyzed by the well-studied rat enzyme (Bae et al. 1999).
ChEBI:59081 (Glc)1 (GlcNAc)2 (Man)9 (PP-Dol)1
ChEBI:59082 (Glc)2 (GlcNAc)2 (Man)9 (Asn)1
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Phosphorylation of the CARMA1 linker controls NF-kappaB activation
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Human superoxide dismutase 1 (hSOD1) maturation through interaction with human copper chaperone for SOD1 (hCCS)
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SIMILARITY Belongs to the heat shock protein 70 family.CAUTION S.cerevisiae displays strain polymorphism with regard to Endo.SceI endouclease activity. This is due to the mitochondrion-encoded, catalytic subunit ENS2, which exhibits strain polymorphism. It can be either present as continuous ORF in the mitochondrial genome (e.g. strain IAM 4274), present but disrupted by the insertion of GC clusters (e.g. strain D273-10B/A), or completely absent in the mitochondrial genome (e.g. strain S288c).
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Activation of p75NTR by proBDNF facilitates hippocampal long-term depression
A novel and evolutionarily conserved PtdIns(3,4,5)P3-binding domain is necessary for DOCK180 signalling
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ChEBI:59084 (Glc)3 (GlcNAc)2 (Man)9 (Asn)1
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Peroxisomal ACOX1 catalyzes the reaction of hexacosanoyl-CoA and O2 to form trans-2,3-dehydrohexacosanoyl-CoA and H2O2. The active form of the enzyme is a homodimer with FAD as a cofactor (Chu et al. 1995). Mutations in the ACOX1 gene are asociated with accumulation of very long chain fatty acids. Two isoforms of ACOX1, generated by alternative splicing are known; a mutation affecting specifically the second isoform blocks the oxidation of very long chain fatty acids (Ferdinandusse et al. 2007).
Peroxisomal HSD17B4 dimer catalyzes the reaction of trans-2,3-dehydrohexacosanoyl-CoA and H2O to form 3-hydroxyhexacosanoyl-CoA. The enzyme is bifunctional - an aminoterminal domain catalyzes the dehydrogenation of a variety of 3-hydroxyacyl-CoA's and a carboxyterminal domain catalyzes the hydration of a variety of trans-2,3-dehydroacyl-CoA's, the reaction annotated here (Jiang et al. 1996, 1997). Defects in the enzyme are associated with a severe disorder of peroxisomal fatty acid metabolism in humans (Ferdinandusse et al. 2006).
Peroxisomal HSD17B4 dimer catalyzes the reaction of 3-hydroxyhexacosanoyl-CoA and NAD+ to form 3-ketohexacosanoyl-CoA and NADH + H+. The enzyme is bifunctional - an aminoterminal domain catalyzes the dehydrogenation of a variety of 3-hydroxyacyl-CoA's, the reaction annotated here, and a carboxyterminal domain catalyzes the hydration of a variety of trans-2,3-dehydroacyl-CoA's (Jiang et al. 1996, 1997). Defects in the enzyme are associated with a severe disorder of peroxisomal fatty acid metabolism in humans (Ferdinandusse et al. 2006).
Peroxisomal ACAA1 catalyzes the reaction of 3-ketohexacosanoyl-CoA and CoASH to form tetracosanoyl-CoA + acetyl-CoA (Bout et al. 1991).
Processive synthesis on the lagging strand
In humans, the catabolism of phytanate, pristanate, and very long chain fatty acids as well as the first four steps of the biosynthesis of plasmalogens are catalyzed by peroxisomal enzymes. Defects in any of these enzymes or in the assembly of peroxisomes are associated with severe developmental disorders (Wanders and Watherham 2006).
3-hydroxy-3-methylglutaryl Coenzyme A synthase (HMG-CoA synthase) catalyzes the condensation of acetyl CoA with acetoacetyl CoA to produce HMG-CoA. There are two forms of this enzyme, cytosolic and mitochondrial. The cytosolic form is ubiquitous in the body and is involved in cholesterol biosynthesis and synthesis of other isoprenoid products. The mitochondrial form, found solely in the liver and kidney, is involved in the ketogenic pathway.
Linear fatty acids containing more than 18 carbons are broken down by beta-oxidation in peroxisomes to yield acetyl-CoA and medium chain-length fatty acyl CoA's such as octanoyl-CoA (Wanders and Waterham 2006).
Peroxisomal IDH1 (isocitrate dehydrogenase 1) homodimer catalyzes the reaction of isocitrate and NADP+ to form 2-oxoglutarate, CO2, and NADPH + H+. The same enzyme can also localize to the cytosol in at least some cell types (Geisbrecht and Gould 1999; Xu et al. 2004).
Mechanisms of digestion and absorption of dietary vitamin A
Cytosolic IDH1 (isocitrate dehydrogenase 1) homodimer catalyzes the reaction of isocitrate and NADP+ to form 2-oxoglutarate, CO2, and NADPH + H+. The same enzyme can also localize to peroxisomes (Geisbrecht and Gould 1999; Xu et al. 2004).
The conversion of isocitrate to 2-oxoglutarate (alpha-ketoglutarate) with the concomitant synthesis of NADPH from NADP+ is thought to play a significant role in supplying NADPH for other reactions in both the cytosol and the peroxisome (Geisbrecht and Gould 1999).
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Identification of autophosphorylation sites of HER2/neu
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The family of enzymes called prenyltransferases is involved in the biosynthesis of isoprenoids. Two members of this family are known to catalyse the sequential condensation of isopentenyl pyrophosphate to DMAPP: farnesyl pyrophosphate synthase (FPPS) and geranylgeranyl pyrophosphate synthetase (GGPPS) (Kavanaugh et al, 2006).
Further condensation of an isopentenyl pyrophosphate with geranyl pyrophosphate to form farnesyl pyrophosphate is catalyzed by the prenyltransferases FPP synthase and GGPP synthase. (Kavanagh et al, 2006)
Mevalonate kinase (MK) catalyzes the phosphorylation of mevalonate to mevalonate-5-phosphate.
PERK in the life and death of the pancreatic beta-cell
Cytosolic isopentenyl diphosphate isomerase (IPP isomerase) catalyzes an essential activation step in the isoprenoid biosynthetic pathway. It rearranges isopentenyl pyrophosphate into its highly electrophilic isomer, dimethylallyl pyrophosphate (DMAPP). IPP isomerase may also be located in human peroxisomes but it's function there is not clear.
3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) catalyzes the four-electron reduction of HMG-CoA to mevalonate. Mevalonate concentrations in the cell are tightly controlled through the activity of HMGR, which is one of the most highly regulated enzymes known (Goldstein and Brown 1990).
Lanosterol, NADPH + H+, and O2 react to form 4,4-dimethylcholesta-8(9),14,24-trien-3beta-ol, NADP+, H2O and formate. This oxidative demethylation reaction, in the endoplasmic reticulum, is catalyzed by lanosterol 14alpha-demethylase (CYP51A1). Although the reaction is annotated here as a single concerted event, studies with purified rat enzyme indicate that the methyl group is converted successively to an alcohol and an aldehyde before being released as formate (Trzaskos et al. 1986; Fischer et al. 1991; Gaylor 2002).
Squalene monooxygenase (squalene epoxidase, SE) is located on the endoplamic reticulum. It catalyzes the oxidation of squalene to squalene 2,3-epoxide. SE seems to be an important rate-limiting enzyme in cholesterol biosynthesis.
Lanosterol synthase (LS) catalyzes the cyclization of squalene 2,3-epoxide to lanosterol, a reaction that forms the sterol nucleus.LS is located on the ER membrane and is active as the monomer (Ruf et al, 2004).
Farnesyl diphosphate farnesyltransferase (FDFT; squalene synthase) catalyzes the reductive dimerization of two farnesyl diphosphate (FPP) molecules to form squalene. This happens in two distinct steps. The first step of dimerization forms presqualene diphosphate (Pandit et al. 2000).
In the second step, FDFT catalyzes the reduction of presqualene diphosphate to squalene (Pandit et al. 2000).
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The human telomere terminal transferase enzyme is a ribonucleoprotein that synthesizes TTAGGG repeats
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The ME1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
5,10-methenyltetrahydrofolate polyglutamate [ChEBI:65049]
The HMGCS2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The TIAM2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The PEX11A gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
Peroxisome proliferator-activated receptor alpha (PPAR-alpha) is the major regulator of fatty acid oxidation in the liver. PPARalpha is also the target of fibrate drugs used to treat abnormal plasma lipid levels. PPAR-alpha is a type II nuclear receptor (its subcellular location does not depend on ligand binding). PPAR-alpha forms heterodimers with Retinoid X receptor alpha (RXR-alpha), another type II nuclear receptor. PPAR-alpha is activated by binding fatty acid ligands, especially polyunsaturated fatty acids having 18-22 carbon groups and 2-6 double bonds. The PPAR-alpha:RXR-alpha heterodimer binds peroxisome proliferator receptor elements (PPREs) in and around target genes. Binding of fatty acids and synthetic ligands causes a conformational change in PPAR-alpha such that it releases the corepressors and binds coactivators (CBP-SRC-HAT complex, ASC complex, and TRAP-Mediator complex) which initiate transcription of the target genes. Target genes of PPAR-alpha participate in fatty acid transport, fatty acid oxidation, triglyceride clearance, lipoprotein production, and cholesterol homeostasis.
The set of genes regulated by PPAR-alpha is not fully known in humans, however many examples have been found in mice. Genes directly activated by PPAR-alpha contain peroxisome proliferator receptor elements (PPREs) in their promoters and include: 1) genes involved in fatty acid oxidation and ketogenesis (Acox1, Cyp4a, Acadm, Hmgcs2); 2) genes involved in fatty acid transport (Cd36, , Slc27a1, Fabp1, Cpt1a, Cpt2); 3) genes involved in producing fatty acids and very low density lipoproteins (Me1, Scd1); 4) genes encoding apolipoproteins (Apoa1, Apoa2, Apoa5); 5) genes involved in triglyceride clearance ( Angptl4); 6) genes involved in glycerol metabolism (Gpd1 in mouse); 7) genes involved in glucose metabolism (Pdk4); 8) genes involved in peroxisome proliferation (Pex11a); 9) genes involved in lipid storage (Plin, Adfp). Many other genes are known to be regulated by PPAR-alpha but whether their regulation is direct or indirect remains to be found. These genes include: ACACA, FAS, SREBP1, FADS1, DGAT1, ABCA1, PLTP, ABCB4, UGT2B4, SULT2A1, Pnpla2, Acsl1, Slc27a4, many Acot genes, and others (reviewed in Rakhshandehroo et al. 2010).
The peroxisomal membrane transport protein PMP34 mediates the exchange of adenine nucleotides between the cytosol and the peroxisomal matrix. The localization of PMP34 has been established by immunofluoresence studies (Wylin et al. 1998). The cloned human protein restores adenine nucleotide transport in yeast whose endogenous peroxisomal transporter has been disrupted, and has adenine nucleotide transport activity in reconstituted lipid vesicles in vitro (Visser et al. 2002), consistent with its hypothesized role in vivo (Wanders and Waterham 2006).
The reactions involved in the metabolism of fatty acids and of the triacylglycerols and ketone bodies derived from them form a closely interrelated, coordinately regulated module that plays a central role in human energy metabolism.
The HMGCS1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The FATP1 (SLC27A1) gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
Phosphoinositide phosphatases in cell biology and disease
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Peroxisomal ACOT8 catalyzes the hydrolysis of acetyl-CoA to form acetate and CoASH (Jones et al. 1999; Wanders and Waterham 2006).
Peroxisomal carnitineacetyltransferase (CRAT) catalyzes the reaction of acetyl-CoA and carnitine to form acetylcarnitine and CoASH. The active form of the enzyme is a monomer (Bloisi et al. 1990; Wu et al. 2003).
Peroxisomal HSD17B4 dimer catalyzes the reaction of 3-hydroxypristanoyl-CoA and NAD+ to form 3-ketoxypristanoyl-CoA and NADH + H+. The enzyme is bifunctional - an aminoterminal domain catalyzes the dehydrogenation of a variety of 3-hydroxyacyl-CoA's, the reaction annotated here, and a carboxyterminal domain catalyzes the hydration of a variety of trans-2,3-dehydroacyl-CoA's (Jiang et al. 1996, 1997). Defects in the enzyme are associated with a severe disorder of peroxisomal fatty acid metabolism in humans (Ferdinandusse et al. 2006).
Peroxisomal HSD17B4 dimer catalyzes the reaction of trans-2,3-dehydropristanoyl-CoA and H2O to form 3-hydroxypristanoyl-CoA. The enzyme is bifunctional - an aminoterminal domain catalyzes the dehydrogenation of a variety of 3-hydroxyacyl-CoA's and a carboxyterminal domain catalyzes the hydration of a variety of trans-2,3-dehydroacyl-CoA's, the reaction annotated here (Jiang et al. 1996, 1997). Defects in the enzyme are associated with a severe disorder of peroxisomal fatty acid metabolism in humans (Ferdinandusse et al. 2006).
Homodimeric ABCD1 associated with the peroxisomal membrane mediates the uptake of cytosolic very long chain fatty acyl CoAs such as hexacosanoyl-CoA into the peroxisomal matrix. While the requirement for this uptake step in the catabolism of very long chain fatty acids is well-established, direct evidence for the function of ABCD1 as a transporter comes only from studies of its ability to restore peroxisomal long chain fatty acid catabolism in yeast strains whose endogenous transporters have been disrupted by mutation. ABCD1 is inferred to function as a dimer like other members of the ABCD transporter family. The energy requirements of peroxisomal fatty acid uptake (other ABCD transporter-mediated reactions are coupled to ATP hydrolysis) have not been established (van Roermund et al. 2008).
Pristanoyl-CoA, generated in the peroxisome by alpha-oxidation of dietary phytanic acid, is further catabolized by three cycles of peroxisomal beta-oxidation to yield 4,8-dimethylnonanoyl-CoA, acetyl-CoA and two molecules of propionyl-CoA. These molecules in turn are converted to carnitine conjugates, which can be transported to mitochondria (Wanders and Waterham 2006, Verhoeven et al. 1998, Ferdinandusse et al. 1999).
Peroxisomal carnitineacetyltransferase (CRAT) catalyzes the reaction of propionyl-CoA and carnitine to form propionylcarnitine and CoASH. The active form of the enzyme is a monomer (Bloisi et al. 1990; Wu et al. 2003).
In human liver and kidney tissue, monomeric peroxisomal ACOX2 catalyzes the reaction of (2S)-pristanoyl-CoA and O2 to form trans-2,3-dehydropristanoyl-CoA and H2O2 (Vanhove et al. 1993; Baumgart et al. 1996).
Phytanic acid arises through ruminant metabolism of chlorophyll and enters the human diet as a constituent of dairy products (Baxter 1968). It can act as an agonist for PPAR and other nuclear hormone receptors, but its normal role in human physiology, if any, is unclear. It is catabolized via a five-step alpha-oxidation reaction sequence that yields pristanoyl-CoA, which is turn is a substrate for beta-oxidation. These reactions take place in the peroxisomal matrix and their failure is associated with Refsum disease (Wanders et al. 2003).
Peroxisomal HACL1 catalyzes the reaction of 2-hydroxyphytanoyl-CoA to form pristanal and formyl-CoA. The active form of the enzyme is a homotetramer, with one Mg++ and one molecule of thiamin pyrophosphate bound to each monomer (Croes et al. 1997; Foulon et al. 1999).
The proteasome and MHC class I antigen processing
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CPT2, associated with the inner mitochondrial membrane, catalyzes the reaction of palmitoylcarnitine and CoASH to form palmitoyl-CoA and carnitine (Verderio et al. 1995).
The carnitine-acylcarnitine transporter (SLC25A20 / CACT), embedded in the inner mitochondrial membrane, mediates the exchange of palmitoyl-carnitine (and other acylcarnitine esters) and carnitine across the inner mitochondrial membrane (Huizing et al., 1997).
The phosphorylated AMPK inactivates ACC2 in muscle cells by phophorylation. This results in decreased levels of malonyl CoA.
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Lipin proteins LPIN1, 2, and 3, associated with the endoplasmic reticulum membrane, can each catalyze the hydrolysis of phosphatidate to yield 1,2-diacyl-glycerol and orthophosphate. The activities of LPIN1 and LPIN2 have been established experimentally (Grimsey et al. 2008); that of LPIN3 is inferred from its structural similarities both to its human paralogues and to its mouse ortholog (Donkor et al. 2007). Only LPIN1 has been shown to be stably associated with the endoplasmic reticulum, but all three enzymes appear to be catalytically active at that location (Grimsey et al. 2008; Donkor et al. 2007).
At the endoplasmic reticulum (ER) membrane, 1-acyl-lysophosphatidic acid (LPA) is acylated to phosphatidic acid (PA) by the enzymes 1-acyl-sn-glycerol-3-phosphate acyltransferases (AGPAT1 through 11), and lysophosphatidylcholine acyltransferase (LPCAT1) (Aguado and Campbell 1998). See recent review by Agarwal (2012, in press). AGPAT1, 2, 3 and LPCAT1 have been characterized biochemically (AGPAT1, 2: Yamashita et al. 2007, West et al. 1997, Aguado and Campbell 1998, Gale et al. 2006; AGPAT3: Agarwal et al. 2006; LPCAT1: Nakanishi et al. 2006, Chen et al. 2006). Two additional proteins, AGPAT4 and AGPAT5, are inferred to have such activity based on studies of homologous mouse enzymes (Lu et al. 2005). These enzymes differ in their tissue specific patterns of expression in the body and in their preferences for specific acyl CoA molecules (Shindou and Shimizu 2009; Takeuchi and Reue 2009).
The overall process of triglyceride (triacylglycerol) biosynthesis consists of four biochemical pathways: fatty acyl-CoA biosynthesis, conversion of fatty acyl-CoA to phosphatidic acid, conversion of phosphatidic acid to diacylglycerol, and conversion fo diacylglycerol to triacylglycerol.
Immunoglobulin E receptor signaling and asthma
Diacylglycerol O-acyltransferase 1 (DGAT2) associated with the endoplasmic reticulum membrane catalyzes the reaction of 1,2-diacyl-glycerol and acyl-CoA to form triacylglycerol + CoASH (Cases et al. 2001, Wakimoto et al. 2003).
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The sulfhydryl oxidase Erv1 is a substrate of the Mia40-dependent protein translocation pathway
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The mitochondrial carnitine system catalyzes the transport of long-chain fatty acids into the mitochondrial matrix where they undergo beta oxidation. This transport system consists of the malonyl-CoA sensitive carnitine palmitoyltransferase I (CPT-I) localized in the mitochondrial outer membrane, the carnitine:acylcarnitine translocase, an integral inner membrane protein, and carnitine palmitoyltransferase II localized on the matrix side of the inner membrane. (Kerner and Hoppel, 2000).
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Acetyl-CoA acetyltransferase tetramer (ACAT1) in the mitochondrial matrix catalyzes the reversible reaction of two molecules of acetyl-CoA to form acetoacetyl-CoA and CoA (Middleton et al. 1986).
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The ACSL1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The ACOX1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The HMGCR gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
FAD-linked mitochondrial glycerol 3-phosphate dehydrogenase (GPD2, alias: mGPDH) and its NAD-linked cytosolic isoform (GPD1, alias:cGPDH) constitute glycerol phosphate shuttle. GPD2 catalyzes the unidirectional conversion of glycerol-3-phosphate (G-3-P) to dihydroxyacetone phosphate (DHAP) with concomitant reduction of the enzyme-bound FAD. Impaired activity of GPD2 has been suggested to be one of the primary causes of insulin secretory defects in beta-cells and thus it is a candidate gene for type 2 diabetes.
Acetoacetate, beta-hydroxybutyrate, and acetone collectively are called ketone bodies. The first two are synthesized from acetyl-CoA, in the mitochondria of liver cells; acetone is formed by spontaneous decarboxylation of acetoacetate. Ketone body synthesis in liver is effectively irreversible because the enzyme that catalyzes the conversion of acetoacetate to acetoacetyl-CoA is not present in liver cells. Ketone bodies, unlike fatty acids and triglycerides, are water-soluble. They are exported from the liver, and are taken up by other tissues, notably brain and skeletal and cardiac muscle. There, they are broken down to acetyl-CoA which is oxidized via the TCA cycle to yield energy. In a normal person, this pathway of ketone body synthesis and utilization is most active during extended periods of fasting. Under these conditions, mobilization and breakdown of stored fatty acids generates abundant acetyl-CoA acetyl-CoA in liver cells for synthesis of ketone bodies, and their utilization in other tissues minimizes the demand of these tissues for glucose (Sass 2011).
The levels of acetone in ketone bodies are much lower than those of acetoacetic acid and beta-hydroxybutyric acid. Acetone cannot be converted back to acetyl-CoA, and is excreted in urine, or breathed out through the lungs. Extrahepatic tissues utilize ketone bodies by converting the beta-hydroxybutyrate successively to acetoacetate, acetoacetatyl-CoA, finally to acetyl-CoA (Sass 2011).
Acetyl-CoA acetyltransferase tetramer (ACAT1) in the mitochondrial matrix catalyzes the reversible reaction of acetoacetyl-CoA and CoA to form two molecules of acetyl-CoA (Middleton et al. 1986).
In a healthy, well-nourished individual, the production of ketone bodies occurs at a relatively low rate. During periods of normal physiological responses to carbohydrate shortages, the liver increases the production of ketone bodies from acetyl-CoA generated from fatty acid oxidation. This allows heart and skeletal muscle to use ketone bodies as the primary source of energy, thereby preserving the limited glucose supply for use in brain tissue. In untreated diabetes mellitus, a huge buildup of ketone bodies occurs due to an increase in fatty acid oxidation. The production of ketone bodies exceeds the ability of peripheral tissues to oxidize them, and results in lowering the pH of blood. Blood acidification is dangerous, chiefly as it impairs the ability of hemoglobin to bind oxygen. Ketone body synthesis proceeds via the synthesis of ccetoacetic acid in three steps from acetyl CoA, followed by the reduction of acetoacetic acid to beta-hydroxybutyrate. In the body, these reactions occur in the mitochondria of liver cells (Sass 2011).
Hydroxymethylglutaryl-CoA synthase tetramer (HMGCS2) in the mitochondrial matrix catalyzes the reaction of acetoacetyl-CoA and acetyl-CoA to form beta-hydroxy-beta-methylglutaryl coenzyme A (HMG CoA) and CoA (Aledo et al. 2001).
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The CPT2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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Fcgamma receptor signaling in phagocytes
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GRASP55 regulates Golgi ribbon formation
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The asymmetry of chloride transport at 38 degrees C in human red blood cell membranes
Molecular cloning of a member of the facilitative glucose transporter gene family GLUT11 (SLC2A11) and identification of transcription variants
Regulation of the insulin gene by glucose and fatty acids
The PDGF family: four gene products form five dimeric isoforms
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Mutation spectrum and genotype-phenotype analyses in Cowden disease and Bannayan-Zonana syndrome, two hamartoma syndromes with germline PTEN mutation
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A role for the thiol isomerase protein ERP5 in platelet function
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Interference footprinting analysis of telomerase elongation complexes
Oxidative folding of small Tims is mediated by site-specific docking onto Mia40 in the mitochondrial intermembrane space
Identification of mitogen-activated protein (MAP) kinase-activated protein kinase-3, a novel substrate of CSBP p38 MAP kinase
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GABA synthesis, release, reuptake and degradation
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DOMAIN The twin CX3C motif contains 4 conserved Cys residues that form 2 disulfide bonds in the mitochondrial intermembrane space. However, during the transit of TIM10 from cytoplasm into mitochondrion, the Cys residues probably coordinate zinc, thereby preventing folding and allowing its transfer across mitochondrial outer membrane.SIMILARITY Belongs to the small Tim family.
Mitogen-activated protein kinase pathways mediated by ERK, JNK, and p38 protein kinases
Healing and hurting: molecular mechanisms, functions, and pathologies of cellular senescence
Three tRNA binding sites in rabbit liver ribosomes and role of the intrinsic ATPase in 80S ribosomes from higher eukaryotes
Transformation and Stat activation by derivatives of FGFR1, FGFR3, and FGFR4
Tubulin subunits exist in an activated conformational state generated and maintained by protein cofactors
Inositol monophosphatase 1 (IMPA1) and 2 (IMPA2) homodimers dephosphorylate inositol 1-phosphate (I1P) to inositol (Ins). In vitro, IMPA1 and 2 differ in their pH optima and IMPA1 has a significantly greater activity on IP4 than does IMPA2 (McAllister et al. 1992, Ohnishi et al. 2007).
Inositol monophosphatase 1 (IMPA1) and 2 (IMPA2) homodimers dephosphorylate inositol 4-phosphate (I4P) to inositol (Ins). In vitro, IMPA1 and 2 differ in their pH optima and IMPA1 has a significantly greater activity on IP4 than does IMPA2 (Ohnishi et al. 2007).
A group of inositol phosphatases dephosphorylate inositol 1,4,5-trisphosphate (I(1,4,5)P3) to inositol 1,4-bisphosphate (I(1,4)P2). The group of inositol phosphatases involved are: inositol polyphosphate 5-phosphatase OCRL-1 (OCRL), phosphatidylinositol 4,5-bisphosphate 5-phosphatase A (INPP5J), and synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1 (SYNJ1). The following lists the above proteins with their corresponding literature references: OCRL (Zhang et al. 1995, Zhang et al. 1998, Schmid et al. 2004); INPP5J (Mochizuki & Thompson 1999); SYNJ1 (Schmid et al. 2004).
Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 1/2 (PPIP5K1) and 2 (PPIP5K2) phosphorylate inositol 1,2,3,4,5,6-hexakisphosphate (IP6) to inositol 1-diphospho-2,3,4,5,6-pentakisphosphate (1-PP-IP5)) (Fridy et al. 2007, Mulugu et al. 2007, Choi et al. 2007, Lin et al. 2009; Wang et al. 2011).
Inositol hexakisphosphate kinase 1 (IP6K1) and 3 (IP6K3) phosphorylate inositol 1,2,3,4,5,6-hexakisphosphate (IP6) to inositol 5-diphospho-1,2,3,4,6-pentakisphosphate (5-PP-IP5). The following lists the above proteins with their corresponding literature references: IP6K1 (Saiardi et al. 2001, Mulugu et al. 2007, Draskovic et al. 2008; Lin et al. 2009) and IP6K3 (Saiardi et al. 2001, Draskovic et al. 2008).
Inositol hexakisphosphate kinase 1 (IP6K1) and 3 (IP6K3) phosphorylate inositol 1-diphospho-3,4,5,6-tetrakisphosphate (1-PP-IP4) to form inositol 1,5-bisdiphospho-3,4,6-trisphosphate (1,5-(PP)2-IP3) (Saiardi et al. 2001, Saiardi et al. 2000, Draskovic et al. 2008).
Inositol phosphates such as IP4, IP5 and IP6 are converted to an even wider variety of IPs including the di- and triphospho inositol phosphates, also known as pyrophosphates (Irvine & Schell 2001, Alcazar-Romain & Wente 2008, York 2006, Monserrate and York 2010, Ho et al. 2002, Saiardi et al. 2001, Draskovic et al. 2008, Choi et al. 2007, Caffrey et al. 2000, Leslie et al. 2002).
Inositol hexakisphosphate kinase 1 (IP6K1) and 3 (IP6K3) phosphorylate 1-diphospho-2,3,4,5,6-pentakisphosphate (1-PP-IP5) to form inositol 1,5-bisdiphospho-2,3,4,6-tetrakisphosphate (1,5-(PP)2-IP4) (Saiardi et al. 2001, Mulugu et al. 2007).
Inositol hexakisphosphate and diphosphoinositol-pentakisphosphate kinase 1/2 (PPIP5K1) and 2 (PPIP5K2) phosphorylate inositol 5-diphospho-1,2,3,4,6-pentakisphosphate (5-PP-IP5) to inositol 1,5-bisdiphospho-2,3,4,6-tetrakisphosphate (1,5-(PP)2-IP4) (Fridy et al. 2007, Mulugu et al. 2007, Choi et al. 2007, Lin et al. 2009).
Inositol hexakisphosphate kinase 1 (IP6K1) and 3 (IP6K3) phosphorylate inositol 5-diphospho-1,2,3,4,6-pentakisphosphate (5-PP-IP5) to inositol 5-triphospho- 1,2,3,4,6-pentakisphosphate (5-PPP-IP5). The following lists the above proteins with their corresponding literature references: IP6K1 (Saiardi et al. 2001, Draskovic et al. 2008) and IP6K3 (Saiardi et al. 2001, Draskovic et al. 2008).
Macromolecular assemblage of aminoacyl-tRNA synthetases: identification of protein-protein interactions and characterization of a core protein
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Peroxisomal straight-chain Acyl-CoA oxidase and D-bifunctional protein are essential for the retroconversion step in docosahexaenoic acid synthesis
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Repression of the heat shock factor 1 transcriptional activation domain is modulated by constitutive phosphorylation
Novel tryptophan catabolic enzyme IDO2 is the preferred biochemical target of the antitumor indoleamine 2,3-dioxygenase inhibitory compound D-1-methyl-tryptophan
Molecular cloning of human mevalonate kinase and identification of a missense mutation in the genetic disease mevalonic aciduria
Characterization and functional analysis of the nucleotide binding fold in human peroxisomal ATP binding cassette transporters
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Genetic selection for constitutively trimerized human HSF1 mutants identifies a role for coiled-coil motifs in DNA binding
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Characterization of recombinant human nicotinamide mononucleotide adenylyl transferase (NMNAT), a nuclear enzyme essential for NAD synthesis
Functional interactions between Sae2 and the Mre11 complex
Defects in vitamin and cofactor metabolism
The family of glycogen phosphorylases: structure and function
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Thrombin and phorbol esters cause the selective phosphorylation of a G protein other than Gi in human platelets
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Both human ferredoxins 1 and 2 and ferredoxin reductase are important for iron-sulfur cluster biogenesis
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Cyclin E associated events during G1/S transition
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The TMEM16 protein family: a new class of chloride channels?
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5616897
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618210
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_243121.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5616895
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_237622.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_247121.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618209
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_233996.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618211
Mitotic inhibition of GRASP65 organelle tethering involves Polo-like kinase 1 (PLK1) phosphorylation proximate to an internal PDZ ligand
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611851
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615788
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611850
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611849
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611848
Adenosine deaminase-like protein 1 (ADAL1): characterization and substrate specificity in the hydrolysis of N(6)- or O(6)-substituted purine or 2-aminopurine nucleoside monophosphates
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_238176.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618200
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_262965.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618202
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_254076.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618201
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_251879.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618203
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_256610.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618198
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_254714.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618199
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_187567.3
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_241071.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618197
Transcription initiation factor TFIID 70 kDa subunit
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618187
TATA box binding protein (Transcription initiation factor TFIID) (TATA-box factor) (TATA sequence-binding protein) (TBP)
Transcription initiation factor TFIID 28 kDa subunit
Transcription initiation factor TFIID 18 kDa subunit
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618242
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_238853.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611172
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_234468.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618245
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_188664.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618243
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_262648.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27529.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611170
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=936706
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615538
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615541
TFIIH basal transcription factor complex helicase XPB subunit (EC 3.6.1.-) (Basic transcription factor 2 89 kDa subunit) (BTF2-p89) (TFIIH 89 kDa subunit) (DNA-repair protein complementing XP-B cells) (Xeroderma pigmentosum group B complementing protein) (DNA excision repair protein ERCC-3)
Xeroderma pigmentosum group B complementing protein
Basic transcription factor 2 89 kDa subunit
DNA-repair protein complementing XP-B cells
TFIIH basal transcription factor complex helicase XPB subunit
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615539
Basic transcription factor 52 kDa subunit
General transcription factor IIH polypeptide 4
TFIIH basal transcription factor complex p52 subunit (Basic transcription factor 52 kDa subunit) (BTF2-p52) (General transcription factor IIH polypeptide 4)
TFIIH basal transcription factor complex p52 subunit
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_182439.3
Xeroderma pigmentosum group D complementing protein
TFIIH basal transcription factor complex helicase subunit
TFIIH basal transcription factor complex helicase subunit (EC 3.6.1.-) (DNA-repair protein complementing XP-D cells) (Xeroderma pigmentosum group D complementing protein) (CXPD) (DNA excision repair protein ERCC-2)
DNA-repair protein complementing XP-D cells
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615532
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615531
General transcription factor IIH polypeptide 3
TFIIH basal transcription factor complex p34 subunit
TFIIH basal transcription factor complex p34 subunit (Basic transcription factor 2 34 kDa subunit) (BTF2-p34) (General transcription factor IIH polypeptide 3)
Basic transcription factor 2 34 kDa subunit
(HCE) (HCAP1) (Includes: Polynucleotide 5'- triphosphatase (EC 3.1.3.33) (mRNA 5'-triphosphatase) (TPase); mRNA guanylyltransferase (EC 2.7.7.50) (GTP--RNA guanylyltransferase) (GTase))
Transcription initiation factor IIB (General transcription factor TFIIB) (S300-II)
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_191490.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618191
Molybdenum cofactors, enzymes and pathways
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_191493.3
Function and biogenesis of iron-sulphur proteins
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617209
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617210
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5617211
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_187986.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618663
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615534
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618040
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_189053.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618570
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618188
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_182432.3
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_191489.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=70701
Transcription initiation factor TFIID 250 kDa subunit
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608582
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_245457.1
Transcription initiation factor TFIID 30 kDa subunit
Transcription initiation factor TFIID 100 kDa subunit
Transcription initiation factor TFIID 20/15 kDa subunits
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3652.2
Lysine-specific demethylase 2A ecNumber1.14.11.27/ecNumber
Lysine-specific demethylase 2B ecNumber1.14.11.27/ecNumber
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608529
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=977329
Me2K37-replicative histone H3, MeK5-replicative histone H3
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117597.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26092.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=893598
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_259397.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615283
MeK37-replicative histone H3, Replicative histone H3
Me3K10 replicative histone H3, Me2K10-replicative histone H3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611162
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611169
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5618241
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_257022.1
A multidrug resistance transporter from human MCF-7 breast cancer cells
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611160
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611145
Specific features of glycogen metabolism in the liver
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611146
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5611147
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_262994.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615547
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615545
Histone H3.1 with dimethylated lysine9 (H3K9)
Me2K10 replicative histone H3, MeK10-replicative histone H3
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_230735.1
JmjC domain-containing histone demethylation protein 3A
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615553
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615551
Lysine-specific demethylase 7A ecNumber1.14.11.-/ecNumber
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615550
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615549
MeK10-replicative histone H3, Replicative histone H3
Histone H3.1 with methylated lysine9 (H3K9)
Perifosine, a novel alkylphospholipid, inhibits protein kinase B activation
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608502
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608497
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613836
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608526
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_243718.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613832
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608491
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113561
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3412.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608492
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613840
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613841
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608496
Characterization of human exonuclease 1 in complex with mismatch repair proteins, subcellular localization and association with PCNA
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17366.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=389822
Initiation of mammalian protein synthesis. II. The assembly of the initiation complex with purified initiation factors.
Initiation of mammalian protein synthesis. I. Purification and characterization of seven initiation factors.
Transcription initiation protein SPT4 homolog 1
Glycylpeptide N-tetradecanoyltransferase 2 ecNumber2.3.1.97/ecNumber
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608528
Glycylpeptide N-tetradecanoyltransferase 1 ecNumber2.3.1.97/ecNumber
Pathway and mechanism of initiation of protein synthesis.
Translational Control of Gene Expression. (Sonenberg, Hershey and Mathews, eds.)33-88
Guanine nucleotide-binding protein G(T), alpha-1 subunit
The crystal structure of the human toll-like receptor 10 cytoplasmic domain reveals a putative signaling dimer
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17855.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608503
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613848
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_242402.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613849
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608501
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613851
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608500
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_230064.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608527
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_257821.1
New insights into an old problem: ternary complex (Met-tRNAf.eIF.GTP) formation in animal cells.
Post-transcriptional control of gene expression. J.E. McCarty and M.F.Tuite (eds).521-526
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608505
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608504
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613843
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_222311.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608499
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5613847
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=389864
DNA-directed RNA polymerase II 33 kDa polypeptide
DNA-directed RNA polymerase II 140 kDa polypeptide
DNA-directed RNA polymerase II 16 kDa polypeptide
DNA-directed RNA polymerase II 13.3 kDa polypeptide
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5614998
DNA-directed RNA polymerase II 19 kDa polypeptide
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5614997
DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5615001
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5614999
DNA-directed RNA polymerase II 14.4 kDa polypeptide (EC 2.7.7.6) (RPB6) (RPB14.4)
DNA-directed RNA polymerase II 14.4 kDa polypeptide
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_259847.1
CATALYTIC ACTIVITY ATP + H(2)O = ADP + phosphate.MISCELLANEOUS Present with 14400 molecules/cell in log phase SD medium.SIMILARITY Belongs to the helicase family. RAD3/XPD subfamily.SIMILARITY Contains 1 helicase ATP-binding domain.
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=389678
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=389664
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Identification of the global transcriptomic response of the hypothalamic arcuate nucleus to fasting and leptin
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Chromatin-specific transcription elongation factor 80 kDa subunit
Recombination signal sequence recognition protein
Structure-specific recognition protein 1 (SSRP1) (Recombination signal sequence recognition protein) (T160) (Chromatin-specific transcription elongation factor 80 KDA subunit
Structure-specific recognition protein 1
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Transcription initiation factor IIE, alpha subunit
General transcription factor IIE 56 kDa subunit
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Transcription Factor IIA alpha chain - p35
G beta:gamma signalling through PI3Kgamma
Transcription Factor IIA beta chain - p19
Transcription initiation factor IIA gamma chain
Transcription initiation factor IIF, beta subunit
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General transcription factor IIH polypeptide 1
TFIIH basal transcription factor complex p62 subunit
Basic transcription factor 62 kDa subunit
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TFIIH basal transcription factor complex p44 subunit
General transcription factor IIH polypeptide 2
Basic transcription factor 2 44 kDa subunit
TFIIH basal transcription factor complex p44 subunit (Basic transcription factor 2 44 kDa subunit) (BTF2-p44) (General transcription factor IIH polypeptide 2)
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RNA Pol II (unphosphorylated) largest subunit
DNA-directed RNA polymerase II largest subunit
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DNA-directed RNA polymerase II 14.5 kDa polypeptide
DNA-directed RNA polymerase II 7.6 kDa polypeptide
DNA-directed RNA polymerase II 7.6 kDa polypeptide (EC 2.7.7.6) (RPB10) (RPB7.6)
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DNA-directed RNA polymerase II 23 kDa polypeptide (EC 2.7.7.6) (RPB25) (XAP4) (RPB5)
DNA-directed RNA polymerase II 23 kDa polypeptide
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Cloning and functional expression of human aquaporin8 cDNA and analysis of its gene
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cDNA cloning and chromosome mapping of human dihydropyrimidine dehydrogenase, an enzyme associated with 5-fluorouracil toxicity and congenital thymine uraciluria
Role of LAT2/NTAL/LAB on calcium mobilization
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Protein kinase C-theta (PKC theta): a key enzyme in T cell life and death
Vesicular tubular clusters between the ER and Golgi mediate concentration of soluble secretory proteins by exclusion from COPI-coated vesicles
ABCG5 and ABCG8 are obligate heterodimers for protein trafficking and biliary cholesterol excretion
Leptin-cytokine crosstalk in breast cancer
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ChEBI:28533 3alpha,7alpha-dihydroxy-24-oxo-5beta-cholestanoyl-CoA
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The Trithorax group protein Lid is a trimethyl histone H3K4 demethylase required for dMyc-induced cell growth
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Pathogen recognition with Toll-like receptors
Lysine-specific demethylase 4D ecNumber1.14.11.-/ecNumber
The serial cultivation of human diploid cell strains
Me3K28 replicative histone H3, Me2K28-replicative histone H3
Me2K28 replicative histone H3, MeK28-replicative histone H3
Histone H3.1 with trimethylated lysine-4
Me2K5 replicative histone H3, MeK5-replicative histone H3
Retinoblastoma-binding protein 2 homolog 1
Jumonji/ARID domain-containing protein 1B
Identification of a novel mutation in GYS1 (muscle-specific glycogen synthase) resulting in sudden cardiac death, that is diagnosable from skin fibroblasts
Me3K5 replicative histone H3, Me2K5-replicative histone H3
Comparison of human B cell activation by TLR7 and TLR9 agonists
Nitric oxide, tetrahydrobiopterin, oxidative stress, and endothelial dysfunction in hypertension
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Biological characterization of various forms of elongation factor 1 from rabbit reticulocytes
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Signal transduction during Fc receptor-mediated phagocytosis
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Lysine-specific demethylase 6A ecNumber1.14.11.-/ecNumber
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2-Deoxy-D-ribose 1-phosphate [ChEBI:28542]
Mutational analysis in longest known survivor of mucopolysaccharidosis type VII
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Elongation factor Tu, a GTPase triggered by codon recognition on the ribosome: mechanism and GTP consumption
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Selective function of PKC-theta in T cells
GLUT2 in pancreatic and extra-pancreatic gluco-detection (review)
The extended GLUT-family of sugar/polyol transport facilitators: nomenclature, sequence characteristics, and potential function of its novel members (review)
Intracellular mechanisms of antigen cross presentation in dendritic cells
HSF4, a new member of the human heat shock factor family which lacks properties of a transcriptional activator
Genetic approaches to translation initiation in Saccharomyces cerevisiae.
Translational Control of Gene Expression. N. Sonenberg, J.W. Hershey and M.B. Mathews (eds.)487-502
In vitro evidence for the dual function of Alg2 and Alg11: essential mannosyltransferases in N-linked glycoprotein biosynthesis
NLRs join TLRs as innate sensors of pathogens
Reversible lysine acetylation controls the activity of the mitochondrial enzyme acetyl-CoA synthetase 2
Superoxide dismutase. An enzymic function for erythrocuprein (hemocuprein)
Targeting the oncogene and kinome chaperone CDC37
Defective TCN2 causes hereditary megaloblastic anemia
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CD28/CTLA-4 and CD80/CD86 families: signaling and function
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Simultaneous blockade of NFkappaB, JNK, and p38 MAPK by a kinase-inactive mutant of the protein kinase TAK1 sensitizes cells to apoptosis and affects a distinct spectrum of tumor necrosis factor [corrected] target genes
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The human lamin B receptor/sterol reductase multigene family
Pyruvate dehydrogenase kinase isoform 2 activity limited and further inhibited by slowing down the rate of dissociation of ADP
Identification and characterization of human cDNAs specific to BCS1, PET112, SCO1, COX15, and COX11, five genes involved in the formation and function of the mitochondrial respiratory chain
FUNCTION General activator of RNA polymerase III transcription. Interacts with TBP. Binds to Pol III subunit C34 and to the TAU135 component of TFIIIC.SUBUNIT TFIIIB comprises the TATA-binding protein (TBP), the B-related factor (BRF) and the B" component (TFC5).MISCELLANEOUS Present with 4330 molecules/cell in log phase SD medium.SIMILARITY Belongs to the TFIIB family.SIMILARITY Contains 1 TFIIB-type zinc finger.
Structural basis of Wnt recognition by Frizzled
G proteins and opioid receptor-mediated signalling
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N6-adenosine-methyltransferase 70 kDa subunit
Small nuclear ribonucleoprotein associated proteins B and B'
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Cloning of a new aquaporin (AQP10) abundantly expressed in duodenum and jejunum
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EGFR interacts with phospholipase C-gamma
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Recycling of the general transcription factors during RNA polymerase II transcription.
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The Protein Biosynthesis Elongation Cycle
Translational Control of Gene Expression89-127
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Differences in regulatory properties between human and rat glucokinase regulatory protein
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A mutation in the human ortholog of the Saccharomyces cerevisiae ALG6 gene causes carbohydrate-deficient glycoprotein syndrome type-Ic
FUNCTION DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNA. The RPC25/RPC8-RPC17/RPC9 subcomplex may bind Pol III transcripts emerging from the adjacent exit pore during elongation.SUBUNIT Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits. RPC25/RPC8 and RPC17/RPC9 form a Pol III subcomplex.MISCELLANEOUS Present with 752 molecules/cell in log phase SD medium.SIMILARITY Belongs to the eukaryotic RPB7/RPC8 RNA polymerase subunit family.
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Novel fibroblast growth factor receptor 3 (FGFR3) mutations in bladder cancer previously identified in non-lethal skeletal disorders
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Assembly and export of MHC class I peptide ligands
Preprotein translocase of the outer mitochondrial membrane: molecular dissection and assembly of the general import pore complex
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Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds
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High-throughput mass spectrometry screening for inhibitors of phosphatidylserine decarboxylase
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Identification and characterization of human ethanolaminephosphotransferase1
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Chemokine-mediated interaction of hematopoietic progenitors with the bone marrow vascular niche is required for thrombopoiesis
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U6 snRNA-associated Sm-like protein LSm1
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U6 snRNA-associated Sm-like protein LSm7
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U6 snRNA-associated Sm-like protein LSm6
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U6 snRNA-associated Sm-like protein LSm2
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Heterogeneous nuclear ribonucleoprotein D0
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SUMOylation and deSUMOylation at a glance
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Tryptophan nutrition and metabolism: an overview
Mechanism of mismatch recognition revealed by human MutS? bound to unpaired DNA loops
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Involvement of enzymes other than CYPs in the oxidative metabolism of xenobiotics
Expert Opin Drug Metab Toxicol 2:895-921
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U6 snRNA-associated Sm-like protein LSm3
U6 snRNA-associated Sm-like protein LSm5
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Inorganic pyrophosphatase 2, mitochondrial
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Characterization and functional expression of the cDNA encoding human brain quinolinate phosphoribosyltransferase
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The mechanism of action of protein synthesis initiation factors from rabbit reticulocytes.
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Identification of novel phosphorylation sites required for activation of MAPKAP kinase-2
Complete primary structure of a human plasma membrane Ca2+ pump
Protein kinase C theta is expressed in mast cells and is functionally involved in Fcepsilon receptor I signaling
Phenylalanyl-tRNA synthetase alpha chain
Small ubiquitin-related modifier (SUMO)-specific proteases: profiling the specificities and activities of human SENPs
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Splicing factor 3B subunit 1 (Spliceosome associated protein 155) (SAP 155) (SF3b155) (Pre-mRNA splicing factor SF3b 155 kDa subunit)
Pre-mRNA splicing factor SF3b 155 kDa subunit
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Spliceosomal U5 snRNP-specific 15 kDa protein
Thioredoxin-like U5 snRNP protein U5-15kD
Pre-mRNA splicing factor SF3b 145 kDa subunit
Splicing factor 3B subunit 2 (Spliceosome associated protein 145) (SAP 145) (SF3b150) (Pre-mRNA splicing factor SF3b 145 kDa subunit)
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Splicing factor 3B subunit 4 (Spliceosome associated protein 49) (SAP 49) (SF3b50) (Pre-mRNA splicing factor SF3b 49 kDa subunit)
Pre-mRNA splicing factor SF3b 49 kDa subunit
Rapid and reversible relocalization of heat shock factor 1 within seconds to nuclear stress granules
Proc. Natl. Acad. Sci. U.S.A. 96:6769-74
116 kDa U5 small nuclear ribonucleoprotein component (U5 snRNP- specific protein, 116 kDa) (U5-116 kDa)
116 kDa U5 small nuclear ribonucleoprotein component
U5 small nuclear ribonucleoprotein 200 kDa helicase
Small nuclear ribonuclear protein D homolog
Structural basis for inhibition of the epidermal growth factor receptor by cetuximab
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High mobility group-like nuclear protein 2 homolog 1
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Involvement of ACSL in local synthesis of neutral lipids in cytoplasmic lipid droplets in human hepatocyte HuH7
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Splicing factor, arginine/serine-rich 6 (Pre-mRNA splicing factor SRP55)
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Pre-mRNA splicing factor SF3b 130 kDa subunit
Splicing factor 3B subunit 3 (Spliceosome associated protein 130) (SAP 130) (SF3b130) (Pre-mRNA splicing factor SF3b 130 kDa subunit)
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Remodeling of cardiolipin by phospholipid transacylation
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Human glyceraldehyde 3-phosphate dehydrogenase-2 gene is expressed specifically in spermatogenic cells.
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AKT phosphorylates targets in the nucleus
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The kinesin-8 motor Kif18A suppresses kinetochore movements to control mitotic chromosome alignment
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The tyrosine kinase network regulating mast cell activation
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Golgi Cisternae Pericentriolar Stack Reorganization
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Unifying concepts in CD28, ICOS and CTLA4 co-receptor signalling
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Folding of glycoproteins: toward understanding the biophysics of the glycosylation code
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DEVELOPMENTAL STAGE Meiosis-specific.SIMILARITY Belongs to the TOP6A family.
Human glucose-6-phosphate dehydrogenase: the crystal structure reveals a structural NADP(+) molecule and provides insights into enzyme deficiency
Two homologues encoding human UDP-glucose:glycoprotein glucosyltransferase differ in mRNA expression and enzymatic activity
Activation of NMDA receptor upon glutamate binding and postsynaptic events
A revised picture of the E2F transcriptional network and RB function.
Mutations in the liver glycogen synthase gene in children with hypoglycemia due to glycogen storage disease type 0
Clinical and molecular characterization of the first adult congenital disorder of glycosylation (CDG) type Ic patient
A "slow" homotetrameric kinesin-related motor protein purified from Drosophila embryos
Still a puzzle: why is haem covalently attached in c-type cytochromes?
Investigation of coenzyme Q biosynthesis in human fibroblast and HepG2 cells
Dissociation of GDP dissociation inhibitor and membrane translocation are required for efficient activation of Rac by the Dbl homology-pleckstrin homology region of Tiam
The biosynthesis of delta-9,12,15,18-tetracosatetraenoic and of delta-6,9,12,15,18-tetracosapentaenoic acids by rat testes
Identification of a mammalian H(+)-myo-inositol symporter expressed predominantly in the brain
Inhibiting glycogen synthesis prevents lafora disease in a mouse model
Regulation of gene expression in beta cells
Analysis of the gene sequences of the insulin receptor and the insulin-sensitive glucose transporter (GLUT-4) in patients with common-type non-insulin-dependent diabetes mellitus
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The classical human phosphoglucomutase (PGM1) isozyme polymorphism is generated by intragenic recombination
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Identification of the gene responsible for the cblB complementation group of vitamin B12-dependent methylmalonic aciduria
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Characterization of AMP-activated protein kinase gamma-subunit isoforms and their role in AMP binding
Genomic structure and expression of the human heme A:farnesyltransferase (COX10) gene
eIF-2B GDP-GTP exchange factor, epsilon subunit
Translation initiation factor eIF-2B epsilon subunit
translation initiation factor 2B epsilon subunit
RNA Polymerase II Transcription Elongation
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Cloning and recombinant expression of rat and human kynureninase.
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Characterization of the human SLC2A11 (GLUT11) gene: alternative promoter usage, function, expression, and subcellular distribution of three isoforms, and lack of mouse orthologue
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Ins and outs of cellular cobalamin transport
translation initiation factor 2B alpha subunit
Translation initiation factor eIF-2B alpha subunit
eIF-2B GDP-GTP exchange factor, alpha subunit
translation initiation factor 2B beta subunit
eIF-2B GDP-GTP exchange factor, beta subunit
Translation initiation factor eIF-2B beta subunit
Translation initiation factor eIF-2B gamma subunit
eIF-2B GDP-GTP exchange factor, gamma subunit
translation initiation factor 2B gamma subunit
Mitochondrial protein import motor: differential role of Tim44 in the recruitment of Pam17 and J-complex to the presequence translocase
translation initiation factor 2B delta subunit
eIF-2B GDP-GTP exchange factor, delta subunit
Translation initiation factor eIF-2B delta subunit
UTX and JMJD3 are histone H3K27 demethylases involved in HOX gene regulation and development
Interaction of Hsp90 with the nascent form of the mutant epidermal growth factor receptor EGFRvIII
eukaryotic translation initiation factor 5
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Identification of a consensus motif for Plk (Polo-like kinase) phosphorylation reveals Myt1 as a Plk1 substrate
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Ligand discrimination in signaling through an ErbB4 receptor homodimer
Human liver mitochondrial aldehyde dehydrogenase: three-dimensional structure and the restoration of solubility and activity of chimeric forms
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Cloning and characterization of PDK4 on 7q21.3 encoding a fourth pyruvate dehydrogenase kinase isoenzyme in human
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Molecular basis of MAPK-activated protein kinase 2:p38 assembly
The PI3K-PDK1 connection: more than just a road to PKB
A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage.
Interaction between PCNA and DNA ligase I is critical for joining of Okazaki fragments and long-patch base-excision repair.
Purification, cDNA cloning and heterologous expression of human phosphomannose isomerase
ER-mediated phagocytosis: myth or reality?
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Insights into Lafora disease: malin is an E3 ubiquitin ligase that ubiquitinates and promotes the degradation of laforin
Proc. Natl. Acad. Sci. U.S.A. 102:8501-6
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Defective MTR causes methylmalonic aciduria and homocystinuria type cblG
Vascular endothelial growth factor family of ligands and receptors: review
Cloning of a human type II phosphatidylinositol 4-kinase reveals a novel lipid kinase family
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Reconstitution of two recombinant LSm protein complexes reveals aspects of their architecture, assembly, and function
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Molecular cloning and characterization of a novel (Na+,K+)/H+ exchanger localized to the trans-Golgi network
Biogenesis and regulation of insulin-responsive vesicles containing GLUT4
Purification and characterization of human liver "high Km" aldehyde dehydrogenase and its identification as glutamic gamma-semialdehyde dehydrogenase.
Band 3 Memphis variant II. Altered stilbene disulfonate binding and the Diego (Dia) blood group antigen are associated with the human erythrocyte band 3 mutation Pro854-->Leu
Lectin-deficient calreticulin retains full functionality as a chaperone for class I histocompatibility molecules
Human kidney gamma-glutamyl transpeptidase. Catalytic properties, subunit structure, and localization of the gamma-glutamyl binding site on the light subunit
Pyrimidine pathways in health and disease
Central leptin receptor action and resistance in obesity
Hormone-sensitive lipase and monoacylglycerol lipase are both required for complete degradation of adipocyte triacylglycerol
FoxM1 is required for execution of the mitotic programme and chromosome stability
Nuclear import of hepatic glucokinase depends upon glucokinase regulatory protein, whereas export is due to a nuclear export signal sequence in glucokinase
Quantitative and dynamic assessment of the contribution of the ER to phagosome formation
Molecular tinkering of G protein-coupled receptors: an evolutionary success
Insulin degradation: progress and potential.
3-dehydro-4-methylzymosterol [ChEBI:50593]
Endoplasmic reticulum (ER) mannosidase I is compartmentalized and required for N-glycan trimming to Man5-6GlcNAc2 in glycoprotein ER-associated degradation
Identification of the nuclear factor HMG2 as an activator for DFF nuclease activity
Microsomal enzymes of cholesterol biosynthesis from lanosterol. Purification and characterization of delta 7-sterol 5-desaturase of rat liver microsomes.
PIG-B, a membrane protein of the endoplasmic reticulum with a large lumenal domain, is involved in transferring the third mannose of the GPI anchor
The extracellular signal-regulated kinase: multiple substrates regulate diverse cellular functions
Aquaporins in the kidney: from molecules to medicine
Primary hyperoxaluria: from gene defects to designer drugs?
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Active remodelling of the TIM23 complex during translocation of preproteins into mitochondria
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Dynamics of the full length and mutated heat shock factor 1 in human cells
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Functional dissection of eukaryotic initiation factor 4F: the 4A subunit and the central domain of the 4G subunit are sufficient to mediate internal entry of 43S preinitiation complexes.
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The isoform-specific functions of the c-Jun N-terminal Kinases (JNKs): differences revealed by gene targeting
Graded activation of fibroblast growth factor receptor 3 by mutations causing achondroplasia and thanatophoric dysplasia
'GTP [cytosol]' is required for 'Met-tRNAi binds to eIF2:GTP to form the ternary complex'
Phosphorylation of serine 303 is a prerequisite for the stress-inducible SUMO modification of heat shock factor 1
Transcriptional control of adipocyte formation
Plk1-dependent phosphorylation of FoxM1 regulates a transcriptional programme required for mitotic progression
'XPO1 [nucleoplasm]' positively regulates 'Translocation of Cyclin B1:phospho-Cdc2 to the cytoplasm'
'DAGs [plasma membrane]' positively regulates 'DAG stimulates protein kinase C-delta'
'DAG [plasma membrane]' positively regulates 'Activation of conventional Protein Kinase C'
'p-MEK1 [cytosol]' negatively regulates 'MEK1 phosphorylates ERK-1'
'Mg2+ [cytosol]' is required for 'pyrophosphate + H2O => 2 orthophosphate [cytosolic]'
'Mg2+ [mitochondrial matrix]' is required for 'pyrophosphate + H2O => 2 orthophosphate [mitochondrial]'
'phospho-p-S722,S792-RPTOR [cytosol]' negatively regulates 'Activation of S6K1'
'Me2sR3-replicative histone H3 [nucleoplasm]' negatively regulates 'RBBP7 binds histone H3 arginine-3 (H3R2).'
Concurrent versus individual binding of HuR and AUF1 to common labile target mRNAs
Mechanisms of leptin action and leptin resistance
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Expression of two succinyl-CoA synthetases with different nucleotide specificities in mammalian tissues
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Role of Tim50 in the transfer of precursor proteins from the outer to the inner membrane of mitochondria
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Phosphorylation of Mnk1 by caspase-activated Pak2/gamma-PAK inhibits phosphorylation and interaction of eIF4G with Mnk
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CATERPILLERs, pyrin and hereditary immunological disorders
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Purification and characterization of kidney and intestinal brush-border membrane trehalases from the rabbit
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A proposed role for the Azotobacter vinelandii NfuA protein as an intermediate iron-sulfur cluster carrier
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E2F-enabled inhibition of pre-replication complex formation
A novel bifunctional phospholipase c that is regulated by Galpha 12 and stimulates the Ras/mitogen-activated protein kinase pathway
Regulation of a novel human phospholipase C, PLCepsilon, through membrane targeting by Ras
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Crystallographic evidence for Tyr 157 functioning as the active site base in human UDP-galactose 4-epimerase
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Expression of the HsOrc1 gene, a human ORC1 homolog, is regulated by cell proliferation via the E2F transcription factor
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Heregulin-dependent delay in mitotic progression requires HER4 and BRCA1
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Clinical findings and biochemical and molecular analysis of four patients with holocarboxylase synthetase deficiency
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Transcript-selective translational silencing by gamma interferon is directed by a novel structural element in the ceruloplasmin mRNA 3' untranslated region
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From molecular action to physiological outputs: peroxisome proliferator-activated receptors are nuclear receptors at the crossroads of key cellular functions
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Rescue of an hTERT mutant defective in telomere elongation by fusion with hPot1
Molecular cloning and expression of a novel human aquaporin from adipose tissue with glycerol permeability
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Synergy between Ca2+ and protein kinase C is the major factor in determining the level of secretion from human platelets
Defective MMAB causes methylmalonic aciduria type cblB
Myotubularin phosphatases: policing 3-phosphoinositides
4-(2-Aminoethyl)-1,2-benzenediol [ChEBI:18243]
Inhibitory and stimulatory regulation of Rac and cell motility by the G12/13-Rho and Gi pathways integrated downstream of a single G protein-coupled sphingosine-1-phosphate receptor isoform
Biochemical characterization and membrane topology of Alg2 from Saccharomyces cerevisiae as a bifunctional alpha1,3- and 1,6-mannosyltransferase involved in lipid-linked oligosaccharide biosynthesis
Human and rat beta cells differ in glucose transporter but not in glucokinase gene expression
Hypophosphorylation of residue Y1045 leads to defective downregulation of EGFRvIII
T cell growth factor receptors. Quantitation, specificity, and biological relevance
1D-myo-Inositol 1,3,4-trisphosphate [ChEBI:810]
Cloning and characterization of human ORNT2: a second mitochondrial ornithine transporter that can rescue a defective ORNT1 in patients with the hyperornithinemia-hyperammonemia-homocitrullinuria syndrome, a urea cycle disorder
ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage
Sam35 of the mitochondrial protein sorting and assembly machinery is a peripheral outer membrane protein essential for cell viability
The FGF family: biology, pathophysiology and therapy
Modular structure of the TIM23 preprotein translocase of mitochondria
Molecular cloning and functional expression of human 3-hydroxyanthranilic-acid dioxygenase.
Overview of retinoid metabolism and function
Activation of human liver glycogen phosphorylase by alteration of the secondary structure and packing of the catalytic core
MISCELLANEOUS Present with 876 molecules/cell in log phase SD medium.SIMILARITY Contains 11 TPR repeats.
Structures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1
VEGF receptor signalling - in control of vascular function
The histone H3 lysine-27 demethylase Jmjd3 links inflammation to inhibition of polycomb-mediated gene silencing
Regulation of human cystathionine beta-synthase by S-adenosyl-L-methionine: evidence for two catalytically active conformations involving an autoinhibitory domain in the C-terminal region
Polo kinase regulates mitotic chromosome condensation by hyperactivation of condensin DNA supercoiling activity
FUNCTION During meiosis is involved in homologous recombination and during vegetative growth it is necessary for DNA repair. It probably regulates the 5'-3' exonuclease degradation of double strand breaks either at the initiation stage or a later stage.MISCELLANEOUS Present with 358 molecules/cell in log phase SD medium.
Hormonal regulation of hepatic gluconeogenesis and glycolysis
Regulation of PLK1 Activity at G2/M Transition
The disulfide relay system of mitochondria is connected to the respiratory chain
ChEBI:18278 N-acetyl-D-glucosaminyldiphosphodolichol
5'-Phosphoribosyl-N-formylglycinamide [ChEBI:18272]
Phosphorylation of the human La antigen on serine 366 can regulate recycling of RNA polymerase III transcription complexes.
Cold Spring Harb Perspect Biol 5:a012633
Long G tails at both ends of human chromosomes suggest a C strand degradation mechanism for telomere shortening
Transcriptional response to stress in the dynamic chromatin environment of cycling and mitotic cells
Proc. Natl. Acad. Sci. U.S.A. 110:E3388-97
microRNA Biogenesis and Function : An overview
Human lung enolase: cloning and sequencing of cDNA and its inducibility with dexamethasone
Molecular cloning and expression of ribosome releasing factor
Specific role for cathepsin S in the generation of antigenic peptides in vivo
Localization of human Cdc25C is regulated both by nuclear export and 14-3-3 protein binding.
Functional consequences of PRODH missense mutations
Class II phosphoinositide 3-kinases are downstream targets of activated polypeptide growth factor receptors
G(z) signaling: emerging divergence from G(i) signaling
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p38 and extracellular signal-regulated kinases regulate the myogenic program at multiple steps
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Computational insights into the role of glutathione in oxidative stress
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Abortive initiation by RNA polymerase II in vitro at the adenovirus 2 major late promoter.
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Agmatine: biological role and therapeutic potentials in morphine analgesia and dependence
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Potential targets for HSF1 within the preinitiation complex
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The kinase activity of human brain 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase is regulated via inhibition by phosphoenolpyruvate
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Identification and characterization of a selective radioligand for ELOVL6
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p38 MAPK signalling cascades: ancient roles and new functions
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Receptor-mediated phagocytosis elicits cross-presentation in nonprofessional antigen-presenting cells
Differential recruitment of DNA Ligase I and III to DNA repair sites
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A specific role of the yeast mitochondrial carriers MRS3/4p in mitochondrial iron acquisition under iron-limiting conditions
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Regulation of APC/C activators between G1/S and early anaphase
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Expression and characterization of recombinant fungal acetyl-CoA carboxylase and isolation of a soraphen-binding domain
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Phosphorylation relieves autoinhibition of the kinetochore motor Cenp-E
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Disrupted function and axonal distribution of mutant tyrosyl-tRNA synthetase in dominant intermediate Charcot-Marie-Tooth neuropathy
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Subcellular compartmentalization of human Nfu, an iron-sulfur cluster scaffold protein, and its ability to assemble a [4Fe-4S] cluster
Proc. Natl. Acad. Sci. U.S.A. 100:9762-7
The interaction between N-WASP and the Arp2/3 complex links Cdc42-dependent signals to actin assembly
Protein insertion into the mitochondrial inner membrane by a twin-pore translocase
Mucopolysaccharidosis type III (Sanfilippo Syndrome): emerging treatment strategies
Mucopolysaccharidosis Type II (Hunter Syndrome): clinical picture and treatment
DNA mismatch repair efficiency and fidelity are elevated during DNA synthesis in human cells
Cloning, expression, and characterization of a human 4'-phosphopantetheinyl transferase with broad substrate specificity
1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole [ChEBI:18319]
Defective MMADHC causes methylmalonic aciduria and homocystinuria type cblD
Role of human sphingosine-1-phosphate phosphatase 1 in the regulation of intra- and extracellular sphingosine-1-phosphate levels and cell viability
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S-adenosylmethionine: nothing goes to waste
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Nitric oxide and peroxynitrite in health and disease
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Human sphingosine kinase: purification, molecular cloning and characterization of the native and recombinant enzymes
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Clustering of mutations in the biotin-binding region of holocarboxylase synthetase in biotin-responsive multiple carboxylase deficiency
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4-[(1R)-2-Amino-1-hydroxyethyl]-1,2-benzenediol [ChEBI:1]
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PRAK, a novel protein kinase regulated by the p38 MAP kinase
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Occurrence of surface IgM, IgD, and free light chains of human lymphocytes
5-phosphoribosylglycinamide [ChEBI:18349]
1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate
ChEBI:18348 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate
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N,N'-Diacetylchitobiosyldiphosphodolichol [ChEBI:7069]
Sequence identification and characterization of human carnosinase and a closely related non-specific dipeptidase
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ChEBI:18381 5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide
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6-(L-erythro-1,2-Dihydroxypropyl 3-triphosphate)-7,8-dihydropterin
7,8-dihydroneopterin 3'-triphosphate [ChEBI:18372]
2-Amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)dihydropteridine triphosphate
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Characterization of rhoGAP. A GTPase-activating protein for rho-related small GTPases.
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S-adenosylmethionine synthesis: molecular mechanisms and clinical implications
beta-D-Mannosyldiacetylchitobiosyldiphosphodolichol [ChEBI:10408]
Localization of GAR transformylase in Escherichia coli and mammalian cells
Metabolism of alpha-linolenic acid in humans
Prostaglandins Leukot Essent Fatty Acids 75:161-8
Identification of galectin-3 as a high-affinity binding protein for advanced glycation end products (AGE): a new member of the AGE-receptor complex
Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
The type 4 subfamily of P-type ATPases, putative aminophospholipid translocases with a role in human disease
Function of eukaryotic initiation factor 5 in the formation of an 80 S ribosomal polypeptide chain initiation complex.
Vasopressin regulates renal water homeostasis via Aquaporins
Cellular senescence: when bad things happen to good cells
Cytochromes c1 and b2 are sorted to the intermembrane space of yeast mitochondria by a stop-transfer mechanism
Phase 1 - Functionalization of compounds
A refined structure of human aquaporin-1
MISCELLANEOUS Present with 4440 molecules/cell in log phase SD medium.SIMILARITY Belongs to the CybS family.
Histone modifying enzymes: structures, mechanisms, and specificities
Common variations in ALG9 are not associated with bipolar I disorder: a family-based study
latheo encodes a subunit of the origin recognition complex and disrupts neuronal proliferation and adult olfactory memory when mutant.
Molecular cloning and expression of human carnitine octanoyltransferase: evidence for its role in the peroxisomal beta-oxidation of branched-chain fatty acids
Binding and release of radiolabeled eukaryotic initiation factors 2 and 3 during 80 S initiation complex formation.
Heteroduplex DNA with D-loop structure with extended pairing between invading strand and complementary heteroduplex strand and containing newly synthesized ends
The role of calcium signaling in phagocytosis
damaged DNA substrate:nascent mRNA hybrid with 3' incision
damaged DNA substrate:nascent mRNA hybrid
Double-strand DNA containing a thymine glycol
Double-strand DNA containing a cytosine glycol
Double-strand DNA containing a dihydrouracil
Double-strand DNA containing 5-hydroxyuracil opposite to a guanine
Double-strand DNA containing an uracil opposite to a guanine
damaged DNA substrate inserted with correct base complement
Elongated DNA template with bypassed lesion
damaged DNA substrate with misinserted bases
Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates
Coatomer:Arf1-GDP:GAP Lattice (name copied from entity in Homo sapiens)
RNA polymerase III transcribes human microRNAs
Role of multiple phosphorylation sites in the COOH-terminal tail of aquaporin-2 for water transport: evidence against channel gating
Synthesis of 12-eicosatetraenoic acid derivatives
repaired DNA template:nascent mRNA hybrid
damaged DNA substrate:nascent mRNA hybrid with dual incisions
DNA containing 1-2 base mismatch and single-strand incision
DNA containing single strand nick (5' phosphate, 3' hydroxyl)
Coatomer:ARFGAP1 lattice (name copied from entity in Homo sapiens)
Coatomer:GAP Lattice (name copied from entity in Homo sapiens)
Coatomer:Arf1-GTP:GAP Lattice (name copied from entity in Homo sapiens)
DNA containing IDL greater than 1 base and single strand incision
Resolution of AP sites via the multiple-nucleotide patch replacement pathway
(ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI
nascent polypeptide with signal sequence
RNA-binding protein in RNP (ribonucleoprotein) complexes
pXBP1(U) encoded in XBP1 pre-mRNA negatively regulates unfolded protein response activator pXBP1(S) in mammalian ER stress response
Further studies on the activity and subcellular distribution of alanine:glyoxylate aminotransferase in the livers of patients with primary hyperoxaluria type 1
Phosphoinositide-metabolizing enzymes at the interface between membrane traffic and cell signalling
Double-strand DNA containing an 8-oxo guanine opposite to a cytosine
Altered aquaporin 9 expression and localization in human hepatocellular carcinoma
Probable phospholipid-transporting ATPases
Double-strand DNA containing a formamidopyrimidine
DNA containing an apurinic/apyrimidinic (AP) site
HA polymer (name copied from entity in Homo sapiens)
1-acyl-sn-glycero-3-phospho-D-myo-inositol [ChEBI:28914]
pH dependence, substrate specificity and inhibition of human kynurenine aminotransferase I
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4-[(1R)-1-Hydroxy-2-(methylamino)ethyl]-1,2-benzenediol [ChEBI:1942]
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Performing in vitro sumoylation reactions using recombinant enzymes
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Myotubularin regulates the function of the late endosome through the gram domain-phosphatidylinositol 3,5-bisphosphate interaction
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2-acyl-sn-glycero-3-phosphoethanolamine [ChEBI:28936]
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mature mRNA (eukaryotic, capped and deadenylated)
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mRNA Transcript Targeted by AUF1(hnRNP D0)
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mRNA with premature termination codon preceding exon junction
Crystal structures of human mitochondrial branched chain aminotransferase reaction intermediates: ketimine and pyridoxamine phosphate forms
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mRNA with premature termination codon not preceding exon junction
mRNA Transcript Targeted by HuR Phosphorylated on Ser158 and Ser318.
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mRNA Transcript Targeted by HuR Phosphorylated on Ser221 and Ser318
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mRNA Transcript Targeted by Tristetraproline
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mRNA Transcript Targeted by HuR with Unknown Phosphorylation
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Distribution and functional characterization of equilibrative nucleoside transporter-4, a novel cardiac adenosine transporter activated at acidic pH
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MCD4 encodes a conserved endoplasmic reticulum membrane protein essential for glycosylphosphatidylinositol anchor synthesis in yeast
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Cooperation of translocase complexes in mitochondrial protein import
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1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide [ChEBI:18406]
5'-Phospho-ribosyl-5-amino-4-imidazole carboxamide
Human cyclins B1 and B2 are localized to strikingly different structures: B1 to microtubules, B2 primarily to the Golgi apparatus
5'-Phosphoribosylformylglycinamidine [ChEBI:18413]
Phosphorylation of GRK2 by protein kinase C abolishes its inhibition by calmodulin.
FUNCTION DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. C31 is involved in the formation of the initiation complex.SUBUNIT Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits.MISCELLANEOUS The acidic domain is essential for its function.SIMILARITY Belongs to the eukaryotic RPC7 RNA polymerase subunit family.
Four Na+/H+ exchanger isoforms are distributed to Golgi and post-Golgi compartments and are involved in organelle pH regulation
SUMO protease SENP1 induces isomerization of the scissile peptide bond
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Molecular identification of mammalian phosphopentomutase and glucose-1,6-bisphosphate synthase, two members of the alpha-D-phosphohexomutase family
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(5Z,8Z,10E,14Z)-(12R)-12-Hydroperoxyeicosa-5,8,10,14-tetraenoic acid
(5Z,8Z,10E,14Z)-(12R)-12-Hydroperoxyicosa-5,8,10,14-tetraenoic acid
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(5Z,8Z,10E,12R,14Z)-12-hydroxy-5,8,10,14-eicosatetraenoic acid
12(R)-hydroxy-5(Z),8(Z),10(E),14(Z)-eicosatetraenoic acid
12(R)-hydroxy-5,8,14-cis-10-trans-eicosatetraenoic acid
(5Z,8Z,10E,14Z)-(12R)-12-Hydroxyeicosa-5,8,10,14-tetraenoic acid
(5Z,8Z,10E,14Z)-(12R)-12-Hydroxyicosa-5,8,10,14-tetraenoic acid
(5Z,8Z,10E,12R,14Z)-12-hydroxyeicosa-5,8,10,14-tetraenoic acid
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12(S)-hydroxy-5,8,14(Z),10(E)-eicosatetraenoic acid
(5Z,8Z,10E,14Z)-(12S)-12-Hydroxyicosa-5,8,10,14-tetraenoic acid
12(S)-hydroxy-5(Z),8(Z),10(E),14(Z)-eicosatetraenoic acid
(5Z,8Z,10E,14Z)-(12S)-12-Hydroxyeicosa-5,8,10,14-tetraenoic acid
(5Z,8Z,10E,12S,14Z)-12-hydroxyeicosa-5,8,10,14-tetraenoic acid
(12S)-12-hydroxy-5,8,14-cis-10-trans-eicosatetraenoic acid
Activating mutations in the extracellular domain of the fibroblast growth factor receptor 2 function by disruption of the disulfide bond in the third immunoglobulin-like domain
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Signal transduction induced by opioids in immune cells: a review
Partial amino acid sequence of the glutamate dehydrogenase of human liver and a revision of the sequence of the bovine enzyme
TRAM couples endocytosis of Toll-like receptor 4 to the induction of interferon-beta
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Cathepsins B and D are dispensable for major histocompatibility complex class II-mediated antigen presentation
SUBUNIT Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits.SIMILARITY Belongs to the archaeal RpoM/eukaryotic RPA12/RPB9/RPC11 RNA polymerase family.SIMILARITY Contains 1 TFIIS-type zinc finger.
Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction
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Removal of licensing factors from origins
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Control of cross-over by single-strand DNA resection.
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Profound ligand-independent kinase activation of fibroblast growth factor receptor 3 by the activation loop mutation responsible for a lethal skeletal dysplasia, thanatophoric dysplasia type II
Reconstitution of the B cell antigen receptor signaling components in COS cells
Human porphobilinogen deaminase mutations in the investigation of the mechanism of dipyrromethane cofactor assembly and tetrapyrrole formation
Regulated transport of the glucose transporter GLUT4.
NUDT9, a member of the Nudix hydrolase family, is an evolutionarily conserved mitochondrial ADP-ribose pyrophosphatase
FUNCTION Transport of phosphate groups from the cytosol to the mitochondrial matrix.SIMILARITY Belongs to the mitochondrial carrier (TC 2.A.29) family.SIMILARITY Contains 3 Solcar repeats.
Lysosomal cathepsin B plays an important role in antigen processing, while cathepsin D is involved in degradation of the invariant chain inovalbumin-immunized mice
Characterization of a heart-specific fatty acid transport protein
Ligand-independent activation of fibroblast growth factor receptors by point mutations in the extracellular, transmembrane, and kinase domains
Direct role of ChREBP.Mlx in regulating hepatic glucose-responsive genes.
Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma
Purified human erythrocyte pyrroline-5-carboxylate reductase. Preferential oxidation of NADPH.
A lipid-anchored Grb2-binding protein that links FGF-receptor activation to the Ras/MAPK signaling pathway
AU-rich elements and the control of gene expression through regulated mRNA stability
Mechanisms of COPII vesicle formation and protein sorting
MISCELLANEOUS Present with 3870 molecules/cell in log phase SD medium.SIMILARITY Belongs to the TRIAP1/MDM35 family.
Cloning of the human carnitine-acylcarnitine carrier cDNA and identification of the molecular defect in a patient
The human kinesin Kif18A is a motile microtubule depolymerase essential for chromosome congression
Molecular properties of the SLC13 family of dicarboxylate and sulfate transporters
Molecular variation in relation to purine metabolism
J Clin Pathol Suppl (R Coll Pathol) 8:48-63
Mathematical and computational models of oxidative and nitrosative stress
P-glycoprotein-mediated active efflux of the anti-HIV1 nucleoside abacavir limits cellular accumulation and brain distribution
Organization and sequence of the gene for the human mitochondrial dicarboxylate carrier: evolution of the carrier family
The monotopic membrane protein human oxidosqualene cyclase is active as monomer
The Wilson disease gene: spectrum of mutations and their consequences
Cloning, sequencing, purification, and Gq-dependent activation of phospholipase C-beta 3
Regulation of Endoplasmic Reticulum Stress-induced Cell Death by ATF4 in Neuroectodermal Tumor Cells
The structure and function of carbonic anhydrase isozymes in the respiratory system of vertebrates
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FUNCTION Central component of the TOM (translocase of outer membrane) receptor complex responsible for the recognition and translocation of cytosolically synthesized mitochondrial preproteins. Together with TOM22 functions as the transit peptide receptor at the surface of the mitochondrion outer membrane and facilitates the movement of preproteins into the TOM40 translocation pore.MISCELLANEOUS Present with 5680 molecules/cell in log phase SD medium.SIMILARITY Belongs to the Tom20 family.
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Messenger RNA decay in mammalian cells: the exonuclease perspective
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2'-Deoxyinosine 5'-phosphate [ChEBI:28806]
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Molecular mechanisms of the decision between life and death: regulation of apoptosis by apoptosis signal-regulating kinase 1
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GDIs: central regulatory molecules in Rho GTPase activation
Gap-filling DNA repair synthesis and ligation in GG-NER
CATALYTIC ACTIVITY Acyl-CoA + 1-acyl-sn-glycero-3-phosphocholine = CoA + 1,2-diacyl-sn-glycero-3-phosphocholine.MISCELLANEOUS Present with 1340 molecules/cell in log phase SD medium.SIMILARITY Belongs to the taffazin family.
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Protein quality control in the ER: the recognition of misfolded proteins
5'-Phosphoribosyl-5-aminoimidazole [ChEBI:28843]
ATPase switches controlling DNA replication initiation.
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Emerging roles for E2F: beyond the G1/S transition and DNA replication.
Access of soluble antigens to the endoplasmic reticulum can explain cross-presentation by dendritic cells
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A telomeric sequence in the RNA of Tetrahymena telomerase required for telomere repeat synthesis
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Signal transduction by VEGF receptors in regulation of angiogenesis and lymphangiogenesis
Glucose transporter isoforms GLUT1 and GLUT3 transport dehydroascorbic acid
Mechanisms of disease: molecular and metabolic mechanisms of insulin resistance and beta-cell failure in type 2 diabetes
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Tyrosine-phosphorylated forms of Ig beta, CD22, TCR zeta and HOSS are major ligands for tandem SH2 domains of Syk
Glycoprotein folding, quality control and ER-associated degradation
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Vav regulates activation of Rac but not Cdc42 during FcgammaR-mediated phagocytosis
Acquired and inherited disorders of cobalamin and folate in children
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Neurotrophin-regulated signalling pathways
Philos Trans R Soc Lond B Biol Sci 361:1545-64
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Rab1 interaction with a GM130 effector complex regulates COPII vesicle cis--Golgi tethering
Novel aspects of tetramer assembly and N-terminal domain structure and function are revealed by recombinant expression of human AMP deaminase isoforms
Cloning and characterization of GEF-H1, a microtubule-associated guanine nucleotide exchange factor for Rac and Rho GTPases
The Cfd1-Nbp35 complex acts as a scaffold for iron-sulfur protein assembly in the yeast cytosol
Isolation and characterization of a human cDNA for mRNA 5'-capping enzyme.
The Polycomb group proteins bind throughout the INK4A-ARF locus and are disassociated in senescent cells
Purification of the serine palmitoyltransferase complex responsible for sphingoid base synthesis by using affinity peptide chromatography techniques
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Human cytosolic asparaginyl-tRNA synthetase: cDNA sequence, functional expression in Escherichia coli and characterization as human autoantigen
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Dual role of phosphatidylinositol-3,4,5-trisphosphate in the activation of protein kinase B
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Hyaluronan synthases: a decade-plus of novel glycosyltransferases
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Role of the jelly-roll fold in substrate binding by 2-oxoglutarate oxygenases
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PTM: gamma carboxylation, hypusine formation and arylsulfatase activation
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CATALYTIC ACTIVITY 2 R'C(R)SH + O(2) = R'C(R)S-S(R)CR' + H(2)O(2).COFACTOR FAD.SIMILARITY Contains 1 ERV/ALR sulfhydryl oxidase domain.
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Structure of human adenosine kinase at 1.5 A resolution.
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AMP kinase and malonyl-CoA: targets for therapy of the metabolic syndrome
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The prosthetic group of crystalline d-glyceraldehyde-3-phosphate dehydrogenase
Cloning and expression of the human gene for transaldolase. A novel highly repetitive element constitutes an integral part of the coding sequence
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Efficient synthesis, termination and release of RNA polymerase III transcripts in Xenopus extracts depleted of La protein
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The reaction between the superoxide anion radical and cytochrome c
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Endogenous synthesis of coenzyme Q in eukaryotes
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Class I MHC mediated antigen processing & presentation
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Opening of an RNA polymerase II promoter occurs in two distinct steps and requires the basal transcription factors IIE and IIH.
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Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids
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p21-activated protein kinase: a crucial component of morphological signaling?
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The vitelliform macular dystrophy protein defines a new family of chloride channels
Proc. Natl. Acad. Sci. U.S.A. 99:4008-13
Hormone-sensitive lipase: control of intracellular tri-(di-)acylglycerol and cholesteryl ester hydrolysis
Production of formyl-CoA during peroxisomal alpha-oxidation of 3-methyl-branched fatty acids
Hyperhomocysteinemia due to methionine synthase deficiency, cblG: structure of the MTR gene, genotype diversity, and recognition of a common mutation, P1173L
Proximal events in Wnt signal transduction
Identification and functional characterization of a new human kidney-specific H+/organic cation antiporter, kidney-specific multidrug and toxin extrusion 2
Principles of bioactive lipid signalling: lessons from sphingolipids
Coregulation of estrogen receptor by ERBB4/HER4 establishes a growth-promoting autocrine signal in breast tumor cells
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Membrane lipids: where they are and how they behave
Membrane recognition by phospholipid-binding domains
Atomic structure of GTP cyclohydrolase I
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Critical role for tetrahydrobiopterin recycling by dihydrofolate reductase in regulation of endothelial nitric-oxide synthase coupling: relative importance of the de novo biopterin synthesis versus salvage pathways
Alteration of enzyme specificity by computational loop remodeling and design
Proximity of the poly(A)-binding protein to a premature termination codon inhibits mammalian nonsense-mediated mRNA decay
Importance of extra- and intracellular domains of TLR1 and TLR2 in NFkappa B signaling
endoplasmic reticulum quality control compartment
Human Mcm proteins at a replication origin during the G1 to S phase transition.
Frequent deletions at Xq28 indicate genetic heterogeneity in Hunter syndrome
Regulation and physiological functions of G12/13-mediated signaling pathways
A natural ErbB4 isoform that does not activate phosphoinositide 3-kinase mediates proliferation but not survival or chemotaxis
A MAP kinase-signaling pathway mediates neurite outgrowth on L1 and requires Src-dependent endocytosis
Which DNA polymerases are used for DNA-repair in eukaryotes?
Hemostasis and Thrombosis: Basic Principles and Clinical Practice
Functions and regulatory mechanisms of Gq-signaling pathways
The crystal structure of human IRE1 luminal domain reveals a conserved dimerization interface required for activation of the unfolded protein response
MISCELLANEOUS Present with 6960 molecules/cell in log phase SD medium.SIMILARITY Contains 1 CHCH domain.
The role of Akt in the signaling pathway of the glycoprotein Ib-IX induced platelet activation
Regulation of mammalian liver methionine adenosyltransferase
Cellular glutathione peroxidase as a predominant scavenger of hydroperoxyeicosatetraenoic acids in rabbit alveolar macrophages
A novel cardiolipin-remodeling pathway revealed by a gene encoding an endoplasmic reticulum-associated acyl-CoA:lysocardiolipin acyltransferase (ALCAT1) in mouse
Cloning and initial characterization of a human phospholipase D2 (hPLD2). ADP-ribosylation factor regulates hPLD2
C1 domains exposed: from diacylglycerol binding to protein-protein interactions
Pyruvate kinase isozyme type M2 (PKM2) interacts and cooperates with Oct-4 in regulating transcription
Chromatin association of human origin recognition complex, cdc6, and minichromosome maintenance proteins during the cell cycle: assembly of prereplication complexes in late mitosis.
Two distinct pathways remove mammalian cohesin from chromosome arms in prophase and from centromeres in anaphase
Monounsaturated fatty acid modification of Wnt protein: its role in Wnt secretion
NADH-cytochrome b5 reductase and cytochrome b5 isoforms as models for the study of post-translational targeting to the endoplasmic reticulum
Signaling by Vascular Epithelial Growth Factors (VEGF)
CD28-mediated co-stimulation: a quantitative support for TCR signalling
Novel D761Y and common secondary T790M mutations in epidermal growth factor receptor-mutant lung adenocarcinomas with acquired resistance to kinase inhibitors
The sugar is sIRVed: sorting Glut4 and its fellow travelers
BRCA2-dependent and independent formation of RAD51 nuclear foci.
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Separate SCF(CDC4) recognition elements target Cdc6 for proteolysis in S phase and mitosis.
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Direct interaction of mitochondrial targeting presequences with purified components of the TIM23 protein complex
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A mutation in the Glut2 glucose transporter gene of a diabetic patient abolishes transport activity
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Mediator function of the human Rad51B-Rad51C complex in Rad51/RPA-catalyzed DNA strand exchange.
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Mycobacterium tuberculosis and the intimate discourse of a chronic infection
Antigen processing: Ubiquitination & Proteasome degradation
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The t(8;22) in chronic myeloid leukemia fuses BCR to FGFR1: transforming activity and specific inhibition of FGFR1 fusion proteins
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The anoctamin family: TMEM16A and TMEM16B as calcium-activated chloride channels
Isolation and characterization of mutations in the human holocarboxylase synthetase cDNA
c-Kit--a hematopoietic cell essential receptor tyrosine kinase
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G protein-independent activation of an inward Na(+) current by muscarinic receptors in mouse pancreatic beta-cells
NOD-like receptors (NLRs): bona fide intracellular microbial sensors
Half-site reactivity in 6-phosphogluconate dehydrogenase from human erythrocytes
Adrenoleukodystrophy gene: unexpected homology to a protein involved in peroxisome biogenesis
Regulation of PRAK subcellular location by p38 MAP kinases
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ESCRTing proteins in the endocytic pathway
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Plk1-dependent phosphorylation of optineurin provides a negative feedback mechanism for mitotic progression
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The structure and function of G-protein-coupled receptors
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Cloning and structural characterization of a human non-erythroid band 3-like protein
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Mechanisms of glycerophospholipid homeostasis in mammalian cells
The transport of pyruvate in rat liver mitochondria
Sanfilippo syndrome type C: deficiency of acetyl-CoA:alpha-glucosaminide N-acetyltransferase in skin fibroblasts
The ABC-transporter signature motif is required for peptide translocation but not peptide binding by TAP
Phosphorylation-dependent scaffolding role of JSAP1/JIP3 in the ASK1-JNK signaling pathway. A new mode of regulation of the MAP kinase cascade
Dissecting and manipulating the pathway for glycosylphosphatidylinositol-anchor biosynthesis
Expression of CD83 is regulated by HuR via a novel cis-active coding region RNA element
Cleavage and activation of p21-activated protein kinase gamma-PAK by CPP32 (caspase 3). Effects of autophosphorylation on activity
Phosphoinositide phosphatases in a network of signalling reactions
A mitochondrial pyruvate carrier required for pyruvate uptake in yeast, Drosophila, and humans
MCM8 is an MCM2-7-related protein that functions as a DNA helicase during replication elongation and not initiation
5-Hydroxyindoleacetaldehyde [ChEBI:2070]
The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5
Dock4 is regulated by RhoG and promotes Rac-dependent cell migration
FGFR1 is fused with a novel zinc-finger gene, ZNF198, in the t(8;13) leukaemia/lymphoma syndrome
The relative role of PLCbeta and PI3Kgamma in platelet activation
Regulatory mechanisms involved in activator-protein-1 (AP-1)-mediated activation of glutathione-S-transferase gene expression by chemical agents
Analysis of Gz alpha by site-directed mutagenesis. Sites and specificity of protein kinase C-dependent phosphorylation
DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation
Nucleotide-promoted release of hMutSalpha from heteroduplex DNA is consistent with an ATP-dependent translocation mechanism
Role of alpha-Asp181, beta-Asp192, and gamma-Asp190 in the distinctive subunits of human NAD-specific isocitrate dehydrogenase
Positive newborn screen for methylmalonic aciduria identifies the first mutation in TCblR/CD320, the gene for cellular uptake of transcobalamin-bound vitamin B(12)
Replication factor C disengages from proliferating cell nuclear antigen (PCNA) upon sliding clamp formation, and PCNA itself tethers DNA polymerase delta to DNA.
Degradation of endocytosed epidermal growth factor and virally ubiquitinated major histocompatibility complex class I is independent of mammalian ESCRTII
Mammalian frataxin: an essential function for cellular viability through an interaction with a preformed ISCU/NFS1/ISD11 iron-sulfur assembly complex
Purification, sequencing, and molecular identification of a mammalian PP-InsP5 kinase that is activated when cells are exposed to hyperosmotic stress
Calcium signalling: past, present and future
Cholesterol feedback: from Schoenheimer's bottle to Scap's MELADL
Rich tapestry of G protein-coupled receptor signaling and regulatory mechanisms
A three-step purification of manganese superoxide dismutase from human liver on both large and small scales
Close encounters: regulation of vertebrate skeletal myogenesis by cell-cell contact
Human X-linked phosphoribosylpyrophosphate synthetase superactivity is associated with distinct point mutations in the PRPS1 gene
Regulation of apoptosis: the ubiquitous way
Kit- and Fc epsilonRI-induced differential phosphorylation of the transmembrane adaptor molecule NTAL/LAB/LAT2 allows flexibility in its scaffolding function in mast cells
Association of Fyn and Lyn with the proline-rich domain of glycoprotein VI regulates intracellular signaling
Human hexokinase II gene: exon-intron organization, mutation screening in NIDDM, and its relationship to muscle hexokinase activity
Phospholipid meets all-trans-retinal: the making of RPE bisretinoids
Erv1 mediates the Mia40-dependent protein import pathway and provides a functional link to the respiratory chain by shuttling electrons to cytochrome c
Enzymatic characterization of the individual mammalian primase subunits reveals a biphasic mechanism for initiation of DNA replication.
Specificity of the myotubularin family of phosphatidylinositol-3-phosphatase is determined by the PH/GRAM domain
Whose end is destruction: cell division and the anaphase-promoting complex.
Three transitions in the RNA polymerase II transcription complex during initiation.
The protein import motor of mitochondria: unfolding and trapping of preproteins are distinct and separable functions of matrix Hsp70
AXIN1 mutations in hepatocellular carcinomas, and growth suppression in cancer cells by virus-mediated transfer of AXIN1
Advances in the understanding of cobalamin assimilation and metabolism
Receptor-mediated endocytosis: the intracellular journey of transferrin and its receptor
RNA sequence elements required for high affinity binding by the zinc finger domain of tristetraprolin: conformational changes coupled to the bipartite nature of Au-rich MRNA-destabilizing motifs
Inflammasome components NALP 1 and 3 show distinct but separate expression profiles in human tissues suggesting a site-specific role in the inflammatory response
Targeting of p38 mitogen-activated protein kinases to MEF2 transcription factors
Mitochondrial presequence translocase: switching between TOM tethering and motor recruitment involves Tim21 and Tim17
Evidence that tristetraprolin binds to AU-rich elements and promotes the deadenylation and destabilization of tumor necrosis factor alpha mRNA
Regulation of fructose-6-phosphate 2-kinase by phosphorylation and dephosphorylation: possible mechanism for coordinated control of glycolysis and glycogenolysis
Oxidative stress and antioxidant defense
Lipid packing sensed by ArfGAP1 couples COPI coat disassembly to membrane bilayer curvature
Cloning and expression of human phenylalanyl-tRNA synthetase in Escherichia coli: comparative study of purified recombinant enzymes
Epidermal growth factor receptors with tyrosine kinase domain mutations exhibit reduced Cbl association, poor ubiquitylation, and down-regulation but are efficiently internalized
Cytoplasmic localization of human cdc25C during interphase requires an intact 14-3-3 binding site.
Interaction network of human aminoacyl-tRNA synthetases and subunits of elongation factor 1 complex
Electron transport from NADPH to Ferredoxin
A human transporter protein that mediates the final excretion step for toxic organic cations
Mucopolysaccharidosis IV A: molecular cloning of the human N-acetylgalactosamine-6-sulfatase gene (GALNS) and analysis of the 5'-flanking region
Identification of the enzyme required for activation of the small ubiquitin-like protein SUMO-1
all-trans-5-methoxy-2-methyl-3-hexaprenylhydroquinone [ChEBI:61473]
Human adrenoleukodystrophy protein and related peroxisomal ABC transporters interact with the peroxisomal assembly protein PEX19p
all-trans-6-methoxy-2-hexaprenylhydroquinone [ChEBI:61472]
Molecular mechanisms involved in the regulation of cytokine production by muramyl dipeptide
Bypass of senescence by the polycomb group protein CBX8 through direct binding to the INK4A-ARF locus
The visual cycle of the cone photoreceptors of the retina
Integrated signalling pathways for mast-cell activation
Molecular cloning of a functional thrombin receptor reveals a novel proteolytic mechanism of receptor activation
Mechanism of RNA polymerase II--specific initiation of transcription in vitro: ATP requirement and uncapped runoff transcripts.
Noncanonical Wnt signaling in vertebrate development, stem cells, and diseases
Birth Defects Res. C Embryo Today 90:243-56
Neuronal phosphoproteins. Mediators of signal transduction
Oncogenic transformation by inhibitor-sensitive and -resistant EGFR mutants
Discovery, regulation, and action of the major apoptotic nucleases DFF40/CAD and endonuclease G
Human ESCRT-II complex and its role in human immunodeficiency virus type 1 release
History of the events leading to the formulation of the apoptosis concept
Tim9p, an essential partner subunit of Tim10p for the import of mitochondrial carrier proteins
Functions of replication factor C and proliferating-cell nuclear antigen: functional similarity of DNA polymerase accessory proteins from human cells and bacteriophage T4.
A novel protein tyrosine phosphatase gene is mutated in progressive myoclonus epilepsy of the Lafora type (EPM2)
Translesion synthesis by DNA polymerases bypassing lesion on DNA template
Activation of TM7SF2 promoter by SREBP-2 depends on a new sterol regulatory element, a GC-box, and an inverted CCAAT-box
Sterol transfer by ABCG5 and ABCG8: in vitro assay and reconstitution
PHF8, a gene associated with cleft lip/palate and mental retardation, encodes for an Nepsilon-dimethyl lysine demethylase
RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
Molecular mechanism of phase I and phase II drug-metabolizing enzymes: implications for detoxification
The Rad50 zinc-hook is a structure joining Mre11 complexes in DNA recombination and repair.
Pro-inflammatory cytokines and environmental stress cause p38 mitogen-activated protein kinase activation by dual phosphorylation on tyrosine and threonine
Complementary regulation of TBC1D1 and AS160 by growth factors, insulin and AMPK activators
Identification of a novel gene, FGFR1OP2, fused to FGFR1 in 8p11 myeloproliferative syndrome
Structural and functional roles of the conserved cysteine residues of the redox-regulated import receptor Mia40 in the intermembrane space of mitochondria
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Characterisation of Cdc25B localisation and nuclear export during the cell cycle and in response to stress
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Similar regulation of human inducible nitric-oxide synthase expression by different isoforms of the RNA-binding protein AUF1
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SLC4 base (HCO3 -, CO3 2-) transporters: classification, function, structure, genetic diseases, and knockout models
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Metal transporters in intestine and brain: their involvement in metal-associated neurotoxicities
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Expression and characterization of human mitochondrial ferredoxin reductase in Escherichia coli
Molecular mechanism of ADP-ribose hydrolysis by human NUDT5 from structural and kinetic studies
Isolation of a human cDNA for heme A:farnesyltransferase by functional complementation of a yeast cox10 mutant
3-Hexaprenyl-4,5-dihydroxybenzoate [ChEBI:1509]
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GPD1L links redox state to cardiac excitability by PKC-dependent phosphorylation of the sodium channel SCN5A
Am J Physiol Heart Circ Physiol 297:H1446-52
Transport of phosphoenolpyruvate by the tricarboxylate transporting system in mammalian mitochondria
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Role of the Zn(2+) motif of E1 in SUMO adenylation
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The Bcl2 family: regulators of the cellular life-or-death switch
Kinetics and equilibria of pyrimidine nucleoside monophosphate kinase from human erythrocytes
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Evidence for existence of tissue-specific regulation of the mammalian pyruvate dehydrogenase complex
Allelism, non-allelism, and genetic compounds among the mucopolysaccharidoses
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Novel mutations in 3-phosphoglycerate dehydrogenase (PHGDH) are distributed throughout the protein and result in altered enzyme kinetics
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Induction of apoptosis by ASK1, a mammalian MAPKKK that activates SAPK/JNK and p38 signaling pathways
SUMO-specific proteases: a twist in the tail
Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs
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Cloning of human agmatinase. An alternate path for polyamine synthesis induced in liver by hepatitis B virus
Am J Physiol Gastrointest Liver Physiol 282:G375-81
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Negative regulation of mast cell signaling and function by the adaptor LAB/NTAL
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Human mitochondrial pyrophosphatase: cDNA cloning and analysis of the gene in patients with mtDNA depletion syndromes
Positive and negative regulation of FcepsilonRI-mediated signaling by the adaptor protein LAB/NTAL
Structural characterization of a human cytosolic NMN/NaMN adenylyltransferase and implication in human NAD biosynthesis
Involvement of the ERK signaling cascade in protein kinase C-mediated cell cycle arrest in intestinal epithelial cells
Cloning and characterization of a novel mammalian zinc transporter, zinc transporter 5, abundantly expressed in pancreatic beta cells
PIP kinase Igamma is the major PI(4,5)P(2) synthesizing enzyme at the synapse
Oxidized LDL-induced endolysosomal phospholipidosis and enzymatically modified LDL-induced foam cell formation determine specific lipid species modulation in human macrophages
Characterization of purine nucleoside phosphorylase from human granulocytes and its metabolism of deoxyribonucleosides
Mitochondrial metabolic states regulate nitric oxide and hydrogen peroxide diffusion to the cytosol
PTEN loss in the continuum of common cancers, rare syndromes and mouse models
Mammalian ABC transporters in health and disease
Identification of nuclear beta II protein kinase C as a mitotic lamin kinase
Phosphatidylinositol 3-phosphate-interacting domains in PIKfyve. Binding specificity and role in PIKfyve. Endomenbrane localization
Tim50, a novel component of the TIM23 preprotein translocase of mitochondria
The second messenger system of mouse epidermis. IV. Cyclic AMP and cyclic GMP phosphodiesterase.
Membrane-bound enzymes of cholesterol synthesis from lanosterol
Cholesterol, hydroxycholesterols, and bile acids
Familial deficiency of glutathione reductase in human blood cells
MAPK targets/ Nuclear events mediated by MAP kinases
Complete amino acid sequence of human phosphoglycerate kinase. Isolation and amino acid sequence of tryptic peptides.
Asparaginyl endopeptidase: case history of a class II MHC compartment protease
STIM1 clusters and activates CRAC channels via direct binding of a cytosolic domain to Orai1
Mechanisms of MHC class I-restricted antigen processing and cross-presentation
Lysosomes in iron metabolism, ageing and apoptosis
Cross-presentation: underlying mechanisms and role in immune surveillance
Discovery of molecular and catalytic diversity among human diphosphoinositol-polyphosphate phosphohydrolases. An expanding Nudt family
Regulation of 5' template usage and incorporation of noncognate nucleotides by human telomerase
The SLC20 family of proteins: dual functions as sodium-phosphate cotransporters and viral receptors
Molecular physiology and pathology of the nucleotide sugar transporter family (SLC35)
The SLC26 gene family of multifunctional anion exchangers
Evolution of the Glx-tRNA synthetase family: the glutaminyl enzyme as a case of horizontal gene transfer
Cloning of a human nucleoside transporter implicated in the cellular uptake of adenosine and chemotherapeutic drugs
Identification and characterization of HAOX1, HAOX2, and HAOX3, three human peroxisomal 2-hydroxy acid oxidases
Stoichiometric and reversible phosphorylation of a 46-kDa protein in human platelets in response to cGMP- and cAMP-elevating vasodilators
Resolution of D-loop structures through Holliday junction intermediates
A new fused transcript in Philadelphia chromosome positive acute lymphocytic leukaemia
Assembly of the human origin recognition complex.
Human cataract lens membrane at subnanometer resolution
Antigen processing and presentation by the class I major histocompatibility complex
Amino acid synthesis and interconversion (transamination)
Mapping iron binding sites on human frataxin: implications for cluster assembly on the ISU Fe-S cluster scaffold protein
Isolation and functional expression of human COQ3, a gene encoding a methyltransferase required for ubiquinone biosynthesis
Catalytic cycle of human glutathione reductase near 1 A resolution
Pannexin-1 mediates large pore formation and interleukin-1beta release by the ATP-gated P2X7 receptor
Phosphate bond hydrolysis by NUDT proteins
Targeting death and decoy receptors of the tumour-necrosis factor superfamily
Nuclease activities in a complex of human recombination and DNA repair factors Rad50, Mre11, and p95.
The proline-rich region of Vav binds to Grb2 and Grb3-3
MutSbeta exceeds MutSalpha in dinucleotide loop repair
Human Pat1b connects deadenylation with mRNA decapping and controls the assembly of processing bodies
The human nm23-H4 gene product is a mitochondrial nucleoside diphosphate kinase
Structural requirements for PAK activation by Rac GTPases
Cloning and sequencing of the cDNA encoding human P5
Cloning of the human cDNA which can complement the defect of the yeast mannosyltransferase I-deficient mutant alg 1
hMutSbeta, a heterodimer of hMSH2 and hMSH3, binds to insertion/deletion loops in DNA
Control of elongation by RNA polymerase II.
Guanylate kinases from human erythrocytes, hog brain, and rat liver
Receptor specificity of the fibroblast growth factor family. The complete mammalian FGF family.
Superoxide dismutase in redox biology: the roles of superoxide and hydrogen peroxide
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Trans-synaptic transmission of vesicular Wnt signals through Evi/Wntless
(15S)-15-Hydroxy-5,8,11-cis-13-trans-eicosatetraenoate [ChEBI:147]
Distinct membrane domains on endosomes in the recycling pathway visualized by multicolor imaging of Rab4, Rab5, and Rab11
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Phosphorylation of phosphatidate phosphatase regulates its membrane association and physiological functions in Saccharomyces cerevisiae: identification of SER(602), THR(723), AND SER(744) as the sites phosphorylated by CDC28 (CDK1)-encoded cyclin-dependent kinase
Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7
Removal of DNA patch containing abasic residue
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Mechanistic insights into the superoxide-cytochrome c reaction by lysine surface scanning
Activation of NF-kappa B requires proteolysis of the inhibitor I kappa B-alpha: signal-induced phosphorylation of I kappa B-alpha alone does not release active NF-kappa B
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The microsomal cardiolipin remodeling enzyme acyl-CoA lysocardiolipin acyltransferase is an acyltransferase of multiple anionic lysophospholipids
4,4-Dimethyl-5alpha-cholesta-8,14,24-trien-3beta-ol [ChEBI:1743]
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1D-myo-Inositol 1,4-bisphosphate [ChEBI:812]
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ChEBI:17825 7-methylguanosine 5'-phosphate
Molecular cloning, chromosomal localization, tissue distribution, and functional expression of the human pancreatic sodium bicarbonate cotransporter
Novel molecular defects of the delta-aminolevulinate dehydratase gene in a patient with inherited acute hepatic porphyria
Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II.
MAP kinase pathway-dependent phosphorylation of the L1-CAM ankyrin binding site regulates neuronal growth
Functional studies of human intestinal alkaline sphingomyelinase by deglycosylation and mutagenesis
PKA-mediated phosphorylation of key metabolic factors
Human Rad51 protein can form homologous joints in the absence of net strand exchange.
Seven novel mutations in the methylenetetrahydrofolate reductase gene and genotype/phenotype correlations in severe methylenetetrahydrofolate reductase deficiency
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(1R,2S)-1-Hydroxypropane-1,2,3-tricarboxylate [ChEBI:151]
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Sequence-specific DNA primer effects on telomerase polymerization activity
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Human peroxiredoxin 1 and 2 are not duplicate proteins: the unique presence of CYS83 in Prx1 underscores the structural and functional differences between Prx1 and Prx2
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acylglucosaminylphosphatidylinositol [ChEBI:52572]
Signaling, cytoskeletal and membrane mechanisms regulating GLUT4 exocytosis
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Multiple phosphoinositide 3-kinase-dependent steps in activation of protein kinase B
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N-retinylidene-N-retinylphosphatidylethanolamine [ChEBI:52592]
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3' -UTR-mediated translational regulation
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Negative regulation of dE2F1 by cyclin-dependent kinases controls cell cycle timing
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Mechanisms and functions of DNA mismatch repair
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Expression, purification, and kinetic constants for human and Escherichia coli pyridoxal kinases
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A cryptic matrix targeting signal of the yeast ADP/ATP carrier normally inserted by the TIM22 complex is recognized by the TIM23 machinery
Unstable kinetochore-microtubule capture and chromosomal instability following deletion of CENP-E
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Prog Nucleic Acid Res Mol Biol 42:259-287
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Characterization and tRNA recognition of mammalian mitochondrial seryl-tRNA synthetase
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1-acyl-sn-glycero-3-phosphoserine [ChEBI:52603]
Cross-talk between the allosteric effector-binding sites in mouse ribonucleotide reductase
Compartmentation of hexokinase in human blood cells. Characterization of soluble and particulate enzymes.
Stoichiometry of 4-methyl sterol oxidase of rat liver microsomes
RNA-mediated response to heat shock in mammalian cells
Human HRD1 promoter carries a functional unfolded protein response element to which XBP1 but not ATF6 directly binds
Antigen processing and presentation in human muscle: cathepsin S is critical for MHC class II expression and upregulated in inflammatory myopathies
RAGE and amyloid-beta peptide neurotoxicity in Alzheimer's disease
Expression, purification and kinetic properties of human recombinant phospholipase C delta 3
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FUNCTION MRS3 suppresses a mitochondrial splice defect in the first intron of the COB gene. It may act as a carrier, exerting its suppressor activity via modulation of solute concentrations in the mitochondrion (possibly of cations).MISCELLANEOUS Present with 1360 molecules/cell in log phase SD medium.SIMILARITY Belongs to the mitochondrial carrier (TC 2.A.29) family.SIMILARITY Contains 3 Solcar repeats.
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The narrow substrate specificity of human tyrosine aminotransferase--the enzyme deficient in tyrosinemia type II
G protein betagamma subunits: central mediators of G protein-coupled receptor signaling
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Identification of a dehydrogenase acting on D-2-hydroxyglutarate
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Rabbit small intestinal trehalase. Purification, cDNA cloning, expression, and verification of glycosylphosphatidylinositol anchoring.
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NF-kappaB p52, RelB and c-Rel are transported into the nucleus via a subset of importin alpha molecules
Phosphorylation inhibits guanine nucleotide exchange on eukaryotic initiation factor 2.
Dehydroascorbic acid transport by GLUT4 in Xenopus oocytes and isolated rat adipocytes
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Oncogenic role and therapeutic target of leptin signaling in breast cancer and cancer stem cells
Desaturation and chain elongation of n - 3 and n - 6 polyunsaturated fatty acids in the human CaCo-2 cell line
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Mutations in the APC gene and their implications for protein structure and function
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Electron microscopic observation and single-stranded DNA binding activity of the Mcm4,6,7 complex.
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Cdc42 regulates Fc gamma receptor-mediated phagocytosis through the activation and phosphorylation of Wiskott-Aldrich syndrome protein (WASP) and neural-WASP
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Distribution of aquaporin water channels AQP1 and AQP5 in the ductal system of the human pancreas
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Signaling by distinct classes of phosphoinositide 3-kinases
Mechanisms of p75-mediated death of hippocampal neurons. Role of caspases
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Receptor for advanced glycation end products (RAGE) regulates sepsis but not the adaptive immune response
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Biochemical genetics of the pentose phosphate cycle: human ribose 5-phosphate isomerase (RPI) and ribulose 5-phosphate 3-epimerase (RPE)
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Phospholipase C-gamma as a signal-transducing element
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Phosphorylation of acyclovir (acycloguanosine) monophosphate by GMP kinase
2'-deoxyadenosine 5'-monophosphate [ChEBI:17713]
Cloning and characterization of three human cDNAs encoding mRNA (guanine-7-)-methyltransferase, an mRNA cap methylase.
AMPK phosphorylation of raptor mediates a metabolic checkpoint
Synthesis and recycling of tetrahydrobiopterin in endothelial function and vascular disease
Sphingosine-1-phosphate lyase in development and disease: sphingolipid metabolism takes flight
Ca2+ entry, efflux and release in smooth muscle
Genetic heterogeneity and clinical variability in the Sanfilippo syndrome (types A, B, and C)
Novel mutations in COX15 in a long surviving Leigh syndrome patient with cytochrome c oxidase deficiency
Structural and functional characterization of human NAD kinase
Human geranylgeranyl diphosphate synthase. cDNA cloning and expression.
A novel intermembrane space-targeting signal docks cysteines onto Mia40 during mitochondrial oxidative folding
Cloning, tissue expression, and mapping of a human photolyase homolog with similarity to plant blue-light receptors
Symmetric dimethylation of H3R2 is a newly identified histone mark that supports euchromatin maintenance
Formation of the 3' end of histone mRNA.
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Ten years on: mediation of cell death by the common neurotrophin receptor p75(NTR)
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Molecular basis of GM1 gangliosidosis and Morquio disease, type B. Structure-function studies of lysosomal beta-galactosidase and the non-lysosomal beta-galactosidase-like protein
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(5Z,8Z,10E,14Z)-(12S)-12-Hydroperoxyeicosa-5,8,10,14-tetraenoate [ChEBI:250]
(5-Deoxy-5-adenosyl)(3-aminopropyl)methylsulfonium salt
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The bipolar mitotic kinesin Eg5 moves on both microtubules that it crosslinks
Initiating DNA synthesis: from recruiting to activating the MCM complex.
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Cloning and expression of a human placenta inositol 1,3,4,5-tetrakisphosphate and phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase
Human arginase II: crystal structure and physiological role in male and female sexual arousal
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xanthosine 5'-monophosphate [ChEBI:15652]
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The DNA damage response: sensing and signaling
ExoS Rho GTPase-activating protein activity stimulates reorganization of the actin cytoskeleton through Rho GTPase guanine nucleotide disassociation inhibitor
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5-Hydroperoxy-6-trans-8,11,14-cis-eicosatetraenoate [ChEBI:2061]
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Initiation of eukaryotic DNA replication: origin unwinding and sequential chromatin association of Cdc45, RPA, and DNA polymerase alpha.
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Distinct stem cell myeloproliferative/T lymphoma syndromes induced by ZNF198-FGFR1 and BCR-FGFR1 fusion genes from 8p11 translocations
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Expression, purification, and kinetic characterization of recombinant human adenylosuccinate lyase
Phosphoinositide 3-kinase in T cell activation and survival
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A heat shock-responsive domain of human HSF1 that regulates transcription activation domain function
1-phosphatidyl-1D-myo-inositol 4,5- bisphosphate
1-phosphatidyl-1D-myo-inositol 3,4-bisphosphates
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Uses for JNK: the many and varied substrates of the c-Jun N-terminal kinases
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Cloning of the rat and human mitochondrial branched chain aminotransferases (BCATm)
Structure and transcription termination of a lysine tRNA gene from Xenopus laevis.
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The role of EF-hand domains and C2 domain in regulation of enzymatic activity of phospholipase Czeta
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Cyclin A/B1 associated events during G2/M transition
Epidermal Growth Factor Receptor (EGFR) signaling
Immunolocalization of the mercurial-insensitive water channel and glycerol intrinsic protein in epithelial cell plasma membranes
Nucleotide binding to nucleoside diphosphate kinases: X-ray structure of human NDPK-A in complex with ADP and comparison to protein kinases
The canonical Notch signaling pathway: unfolding the activation mechanism
Transcriptional activities of nuclear SREBP-1a, -1c, and -2 to different target promoters of lipogenic and cholesterogenic genes
Cloning of a human gene, PIG-F, a component of glycosylphosphatidylinositol anchor biosynthesis, by a novel expression cloning strategy
Isolated short CTG/CAG DNA slip-outs are repaired efficiently by hMutSbeta, but clustered slip-outs are poorly repaired
Proc. Natl. Acad. Sci. U.S.A. 107:12593-8
A novel molecular mechanism to explain biotin-unresponsive holocarboxylase synthetase deficiency
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The CCT/TRiC chaperonin is required for maturation of sphingosine kinase 1
The late endosomal ClC-6 mediates proton/chloride countertransport in heterologous plasma membrane expression
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G(12)/G(13)-mediated signalling in mammalian physiology and disease
Cooperative interaction of human HSF1 heat shock transcription factor with promoter DNA
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Fragmentation and dispersal of the pericentriolar Golgi complex is required for entry into mitosis in mammalian cells
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Tandem phosphorylation of serine 221 and 318 by PKC{delta} coordinates mRNA binding and nucleo-cytoplasmic shuttling of HuR
Protein import channel of the outer mitochondrial membrane: a highly stable Tom40-Tom22 core structure differentially interacts with preproteins, small tom proteins, and import receptors
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The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships.
Insights into lysosomal cobalamin trafficking: lessons learned from cblF disease
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A novel mechanism of JNK1 activation. Nuclear translocation and activation of JNK1 during ischemia and reperfusion.
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A second mammalian N-myristoyltransferase
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Studies on the initiation and elongation reactions in the simian virus 40 DNA replication system.
Identification of protein kinase C (PKC) phosphorylation sites on human lamin B. Potential role of PKC in nuclear lamina structural dynamics
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A novel eukaryotic factor for cytosolic Fe-S cluster assembly
Components involved in assembly and dislocation of iron-sulfur clusters on the scaffold protein Isu1p
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The toxicology of aflatoxins as a basis for public health decisions
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Regulation of pyruvate dehydrogenase activity through phosphorylation at multiple sites
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NCAM-induced intracellular signaling revisited
Purification and properties of two DNA ligases from human placenta
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Functional cooperation of the mitochondrial processing peptidase subunits
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Amplification and kinetics of the activation steps in phototransduction
RAGE mediates a novel proinflammatory axis: a central cell surface receptor for S100/calgranulin polypeptides
Expression of human asparagine synthetase in Escherichia coli
Activation of p34cdc2 protein kinase by microinjection of human cdc25C into mammalian cells. Requirement for prior phosphorylation of cdc25C by p34cdc2 on sites phosphorylated at mitosis.
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A theory of marginotomy. The incomplete copying of template margin in enzymic synthesis of polynucleotides and biological significance of the phenomenon.
Human origin recognition complex large subunit is degraded by ubiquitin-mediated proteolysis after initiation of DNA replication.
Distinct flippases translocate glycerophospholipids and oligosaccharide diphosphate dolichols across the endoplasmic reticulum
The human solute carrier gene SLC35B4 encodes a bifunctional nucleotide sugar transporter with specificity for UDP-xylose and UDP-N-acetylglucosamine
Nucleotide-sugar transporters: structure, function and roles in vivo
Cytokines and chemokines in autoimmune disease: an overview
N-Acetyl-D-glucosamine 1-phosphate [ChEBI:7125]
Regulation of enterocyte apoptosis by acyl-CoA synthetase 5 splicing
Evolution of leptin structure and function
(R)-4'-Phosphopantothenoyl-L-cysteine [ChEBI:328]
Nicotinate D-ribonucleotide [ChEBI:7561]
Organic anion transport is the primary function of the SLC17/type I phosphate transporter family
The human sugar-phosphate/phosphate exchanger family SLC37
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Subcellular compartmentation and differential catalytic properties of the three human nicotinamide mononucleotide adenylyltransferase isoforms
3-Hydroxy-N6,N6,N6-trimethyl-L-lysine [ChEBI:15786]
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N-Acetyl-D-glucosamine 6-phosphate [ChEBI:7127]
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Targeted deletion of the mitogen-activated protein kinase kinase 4 gene in the nervous system causes severe brain developmental defects and premature death
PIK3R1 (p85?) is somatically mutated at high frequency in primary endometrial cancer
Requirement of the MRN complex for ATM activation by DNA damage.
Crystal structure of human riboflavin kinase reveals a beta barrel fold and a novel active site arch
Activation of sphingosine kinase 1 by ERK1/2-mediated phosphorylation
DNA replication control through interaction of E2F-RB and the origin recognition complex.
[Exchange between extra- and intramitochondrial adenine nucleotides]
The cell-cycle regulatory protein Cks1 is required for SCF(Skp2)-mediated ubiquitinylation of p27
Congenital disorders of glycosylation type Ig is defined by a deficiency in dolichyl-P-mannose:Man7GlcNAc2-PP-dolichyl mannosyltransferase
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Recent insights into the structure of Toll-like receptors and post-translational modifications of their associated signalling proteins
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Triggering of TLR7 and TLR8 expressed by human lung cancer cells induces cell survival and chemoresistance
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The role of calcium-independent phospholipase A2 in cardiolipin remodeling in the spontaneously hypertensive heart failure rat heart
Transmembrane transport of small molecules
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Depalmitoylation of endothelial nitric-oxide synthase by acyl-protein thioesterase 1 is potentiated by Ca(2+)-calmodulin
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Recent advances in understanding leptin signaling and leptin resistance
Am. J. Physiol. Endocrinol. Metab. 297:E1247-59
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WNT secretion and signalling in human disease
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The class II phosphoinositide 3-kinase PI3K-C2alpha is concentrated in the trans-Golgi network and present in clathrin-coated vesicles
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Glucagon signaling in metabolic regulation
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M-ABC2, a new human mitochondrial ATP-binding cassette membrane protein
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26S proteasome (name copied from entity in Homo sapiens)
PAK-2p34:RHG10 complex (name copied from entity in Homo sapiens)
KIF9 dimer (name copied from entity in Homo sapiens)
HMGB1/HMGB2- bound chromatin (name copied from entity in Homo sapiens)
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60S ribosomal complex (name copied from entity in Homo sapiens)
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43S: Ceruloplasmin mRNA:eIF4F:eIF4B:eIF4H:PABP (name copied from entity in Homo sapiens)
60s ribosomal complex lacking L13a subunit (name copied from entity in Homo sapiens)
ternary complex (name copied from entity in Homo sapiens)
43S complex (name copied from entity in Homo sapiens)
eIF4A subunits complex (name copied from entity in Homo sapiens)
eIF4F (name copied from entity in Homo sapiens)
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Cloning and characterization of the mammalian brain-specific, Mg2+-dependent neutral sphingomyelinase
Orc6 involved in DNA replication, chromosome segregation, and cytokinesis.
Est1p as a cell cycle-regulated activator of telomere-bound telomerase
Rabenosyn-5:VPS-45 (name copied from entity in Homo sapiens)
Kinesin-5 homotetramer (name copied from entity in Homo sapiens)
DOCK-GEFs:RAC1, CDC42 (name copied from entity in Homo sapiens)
KIF18A dimer (name copied from entity in Homo sapiens)
CENP-E dimer (name copied from entity in Homo sapiens)
Purification and functional characterization of aquaporin-8
A mutation in GLUT2, not in phosphorylase kinase subunits, in hepato-renal glycogenosis with Fanconi syndrome and low phosphorylase kinase activity
Two forms of Wilson disease protein produced by alternative splicing are localized in distinct cellular compartments
SPO11 Covalently Attached to Oligonucleotide
phospho-ERK-2:MEK2 (name copied from entity in Homo sapiens)
MEK2:ERK-2 (name copied from entity in Homo sapiens)
Regulation of human separase by securin binding and autocleavage
phospho-ERK-1 dimer (name copied from entity in Homo sapiens)
phospho-ERK-1:MEK1 (name copied from entity in Homo sapiens)
MEK1:ERK-1 (name copied from entity in Homo sapiens)
RNA Polymerase III Terminator Paused Complex
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eIF2:GTP (name copied from entity in Homo sapiens)
EIF2S1:EIF2S2:EIF2S3 (name copied from entity in Homo sapiens)
eIF3 subunits complex (name copied from entity in Homo sapiens)
40S ribosomal complex (name copied from entity in Homo sapiens)
SPO11 Covalently Attached to Double-strand Break
RNA Polymerase III Open SUP4 tRNATyr Promoter Complex
phospho-L13a associated wth the 3' UTR GAIT element of ceruloplasmin mRNA within the translation initiation complex (name copied from entity in Homo sapiens)
RNA Polymerase III Closed SUP4 tRNATyr Promoter Complex
Control of muscle ryanodine receptor calcium release channels by proteins in the sarcoplasmic reticulum lumen
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Bile salt and organic anion SLC transporters
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Differential recognition by CD28 of its cognate counter receptors CD80 (B7.1) and B70 (B7.2): analysis by site directed mutagenesis
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Dynamic coupling of the putative coiled-coil domain of ORAI1 with STIM1 mediates ORAI1 channel activation
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Surprising versatility of Na+-glucose cotransporters: SLC5
A mitochondrial import receptor for the ADP/ATP carrier
The Wilson disease gene is a putative copper transporting P-type ATPase similar to the Menkes gene
Direct phosphorylation of IkappaB by IKKalpha and IKKbeta: discrimination between free and NF-kappaB-bound substrate
Clinical and biochemical manifestations of hyaluronidase deficiency
GINS complex (name copied from entity in Homo sapiens)
Mcm4,6,7 complex (name copied from entity in Homo sapiens)
Mcm2-7 complex (name copied from entity in Homo sapiens)
ubiquitinated Cdc6 (name copied from entity in Homo sapiens)
ubiquitinated Orc1 (name copied from entity in Homo sapiens)
RFC Heteropentamer:RNA primer-DNA primer:origin duplex:PCNA homotrimer (name copied from entity in Homo sapiens)
PCNA homotrimer (name copied from entity in Homo sapiens)
RFC Heteropentamer:RNA primer-DNA primer:origin duplex (name copied from entity in Homo sapiens)
RFC Heteropentamer (name copied from entity in Homo sapiens)
Unwinding complex at replication fork (name copied from entity in Homo sapiens)
The molecular basis of Sanfilippo syndrome type B
Purification and properties of guanosine diphosphate hexose pyrophosphorylase from mammalian tissues
JHDM2A, a JmjC-containing H3K9 demethylase, facilitates transcription activation by androgen receptor
Reversal of histone lysine trimethylation by the JMJD2 family of histone demethylases
Functional characterization and mechanism of action of recombinant human kynurenine 3-hydroxylase
Proteases in MHC class I presentation and cross-presentation
L-2-Aminoadipate 6-semialdehyde [ChEBI:17917]
CSNK2A1 dimer (name copied from entity in Homo sapiens)
CSNK2A2 dimer (name copied from entity in Homo sapiens)
Casein kinase II (name copied from entity in Homo sapiens)
Phosphotyrosine profiling identifies the KG-1 cell line as a model for the study of FGFR1 fusions in acute myeloid leukemia
CSNK2A1:CSNK2A2 (name copied from entity in Homo sapiens)
CDK1 Phosphorylated Condensin I (name copied from entity in Homo sapiens)
Condensin I (name copied from entity in Homo sapiens)
all-trans-decaprenyl diphosphate [ChEBI:61011]
CK2 Phosphorylated Condensin I (name copied from entity in Homo sapiens)
Molecular identification of cytosolic prostaglandin E2 synthase that is functionally coupled with cyclooxygenase-1 in immediate prostaglandin E2 biosynthesis
Identification of the human cytochrome P450, P450RAI-2, which is predominantly expressed in the adult cerebellum and is responsible for all-trans-retinoic acid metabolism
DNA polymerase epsilon (name copied from entity in Homo sapiens)
DNA polymerase alpha:primase (name copied from entity in Homo sapiens)
DNA polymerase alpha:primase:DNA polymerase alpha:origin complex (name copied from entity in Homo sapiens)
RNA primer:origin duplex:DNA polymerase alpha:primase complex (name copied from entity in Homo sapiens)
RNA primer-DNA primer:origin duplex (name copied from entity in Homo sapiens)
CCNB1:p-T161-CDK1 (name copied from entity in Homo sapiens)
CCNB2:p-T161-CDK1 (name copied from entity in Homo sapiens)
ESPL1 Autocleaved (name copied from entity in Homo sapiens)
DNA polymerase epsilon:origin complex (name copied from entity in Homo sapiens)
RNA Polymerase III SUP4 tRNATyr gene Transcription Complex
Role of the mitochondrial Hsp70s, Ssc1 and Ssq1, in the maturation of Yfh1
DOMAIN Consists mainly of membrane-spanning sided beta-sheets. 19 strands distributed along the entire VDAC protein, have the potential to adopt transmembrane beta pleated sheet structures, which rolled together may form a "beta-barrel" type structure, possessing pore dimensions.SIMILARITY Belongs to the eukaryotic mitochondrial porin family.
phospho-ERK-2 dimer (name copied from entity in Homo sapiens)
p-T216,S274,S373-GORASP1:p-S37-GOLGA2:p-RAB1:GTP (name copied from entity in Homo sapiens)
p-RAB1:GTP (name copied from entity in Homo sapiens)
p-T216,S189,S274,S373-GORASP1:p-S37-GOLGA2:p-RAB1:GTP:PLK1 (name copied from entity in Homo sapiens)
p-T216,S274,S373-GORASP1:p-S37-GOLGA2:p-RAB1:GTP:PLK1 (name copied from entity in Homo sapiens)
Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase
DNA topoisomerase I and PC4 can interact with human TFIIIC to promote both accurate termination and transcription reinitiation by RNA polymerase III.
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Carnitine biosynthesis: identification of the cDNA encoding human gamma-butyrobetaine hydroxylase.
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Pyruvate metabolism and Citric Acid (TCA) cycle
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Preferential DNA repair of an active gene in human cells.
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Functional reconstitution of the import of the yeast ADP/ATP carrier mediated by the TIM10 complex
The content of pentose-cycle intermediates in liver in starved, fed ad libitum and meal-fed rats.
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Hailey-Hailey disease is caused by mutations in ATP2C1 encoding a novel Ca(2+) pump
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Cloning, expression and chromosomal localization of a human testis 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase gene
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex
Cloning, heterologous expression, and enzymological characterization of human squalene monooxygenase
Molecular identification of human glutamine- and ammonia-dependent NAD synthetases. Carbon-nitrogen hydrolase domain confers glutamine dependency.
Glycoprotein folding and the role of EDEM1, EDEM2 and EDEM3 in degradation of folding-defective glycoproteins
Protein phosphatase 2Cepsilon is an endoplasmic reticulum integral membrane protein that dephosphorylates the ceramide transport protein CERT to enhance its association with organelle membranes
Characterization of ceramide synthase 2: tissue distribution, substrate specificity, and inhibition by sphingosine 1-phosphate
alpha-D-Galactose 1-phosphate [ChEBI:17973]
The copper transporter (Ctr) family of Cu+ uptake systems
Complete amino acid sequence of human liver cytosolic alanine aminotransferase (GPT) determined by a combination of conventional and mass spectral methods
3'-Phosphoadenylyl sulfate [ChEBI:17980]
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EZH2 is downstream of the pRB-E2F pathway, essential for proliferation and amplified in cancer
The Rac-RhoGDI complex and the structural basis for the regulation of Rho proteins by RhoGDI
Transport of the ADP/ATP carrier of mitochondria from the TOM complex to the TIM22.54 complex
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Dolichyl beta-D-glucosyl phosphate [ChEBI:4689]
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dolichyl D-mannosyl phosphate [ChEBI:15809]
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eNOS, COX-2, and prostacyclin production are impaired in endothelial cells from diabetics
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Xeroderma pigmentosum variant (XP-V) correcting protein from HeLa cells has a thymine dimer bypass DNA polymerase activity.
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The human arginases and arginase deficiency
Speed, sensitivity, and stability of the light response in rod and cone photoreceptors: facts and models
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A molecular perspective of CTLA-4 function
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The novel Cdc42 guanine nucleotide exchange factor, zizimin1, dimerizes via the Cdc42-binding CZH2 domain
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The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy
HSFY genes and the P4 palindrome in the AZFb interval of the human Y chromosome are not required for spermatocyte maturation
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The COQ7 gene encodes a protein in Saccharomyces cerevisiae necessary for ubiquinone biosynthesis
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Comprehending the complex connection between PKCbeta, TAK1, and IKK in BCR signaling
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Docosahexaenoic acid synthesis in human skin fibroblasts involves peroxisomal retroconversion of tetracosahexaenoic acid
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Activating and inhibitory functions of DAP12
Plk1- and beta-TrCP-dependent degradation of Bora controls mitotic progression
Tuberculosis: what we don't know can, and does, hurt us
Toxic proteins released from mitochondria in cell death
Adapters in the organization of mast cell signaling
A defect in dolichol phosphate biosynthesis causes a new inherited disorder with death in early infancy
Cloning, characterization, and expression of cDNAs encoding human delta 1-pyrroline-5-carboxylate dehydrogenase
Subcellular distribution of superoxide dismutases (SOD) in rat liver: Cu,Zn-SOD in mitochondria
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Molecular and evolutionary basis of the cellular stress response
D-2-Hydroxyglutaric aciduria: unravelling the biochemical pathway and the genetic defect
Prefoldin-nascent chain complexes in the folding of cytoskeletal proteins
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The function of the human homolog of Saccharomyces cerevisiae REV1 is required for mutagenesis induced by UV light.
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FGF signaling pathways in endochondral and intramembranous bone development and human genetic disease
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Characterization of the proteins of isolated human platelet alpha-granules. Evidence for a separate alpha-granule-pool of the glycoproteins IIb and IIIa.
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pRB family proteins are required for H3K27 trimethylation and Polycomb repression complexes binding to and silencing p16INK4alpha tumor suppressor gene
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Synaptojanin 1: localization on coated endocytic intermediates in nerve terminals and interaction of its 170 kDa isoform with Eps15
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trans,trans-Farnesyl diphosphate [ChEBI:10700]
Expression and characterization of a human cDNA that complements the temperature-sensitive defect in dolichol kinase activity in the yeast sec59-1 mutant: the enzymatic phosphorylation of dolichol and diacylglycerol are catalyzed by separate CTP-mediated kinase activities in Saccharomyces cerevisiae
myo-Inositol hexakisphosphate [ChEBI:10603]
D-myo-Inositol 1,2,3,4,5,6-hexakisphosphate
myo-Inositol 1,2,3,4,5,6-hexakisphosphate
1D-myo-Inositol 1,2,3,4,5,6-hexakisphosphate
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Molecular mechanisms of conduction and selectivity in aquaporin water channels
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Molecular analysis of patients with beta-glucuronidase deficiency presenting as hydrops fetalis or as early mucopolysaccharidosis VII
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The enzymes, regulation, and genetics of bile acid synthesis
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HEDJ, an Hsp40 co-chaperone localized to the endoplasmic reticulum of human cells
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Wilms tumor genetics: mutations in WT1, WTX, and CTNNB1 account for only about one-third of tumors
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Synthesis and interconversion of nucleotide di- and triphosphates
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Peroxisome proliferator-activated receptor alpha (PPARalpha ) turnover by the ubiquitin-proteasome system controls the ligand-induced expression level of its target genes
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Involvement of MINK, a Ste20 family kinase, in Ras oncogene-induced growth arrest in human ovarian surface epithelial cells
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Molecular characterization of the human peroxisomal branched-chain acyl-CoA oxidase: cDNA cloning, chromosomal assignment, tissue distribution, and evidence for the absence of the protein in Zellweger syndrome
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ChEBI:17442 4-(2-aminophenyl)-2,4-dioxobutanoic acid
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A stimulatory role for cGMP-dependent protein kinase in platelet activation
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Conservation of a stress response: human heat shock transcription factors functionally substitute for yeast HSF
Response to elevated platelet cytosolic Ca2+
5-Phosphoribose 1-diphosphate biosynthesis
Synthesis of cytosolic 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) from D-ribose 5-phosphate
gamma -Secretase cleavage and nuclear localization of ErbB-4 receptor tyrosine kinase
A syndrome with congenital neutropenia and mutations in G6PC3
Wnt signaling in oncogenesis and embryogenesis--a look outside the nucleus
Changes in histones H2A and H3 variant composition in differentiating and mature rat brain cortical neurons
FGFR1 amplification drives endocrine therapy resistance and is a therapeutic target in breast cancer
Identification of HsORC4, a member of the human origin of replication recognition complex.
A new regulatory motif in cell-cycle control causing specific inhibition of cyclin D/CDK4
Molecular analysis of a series of alleles in humans with reduced activity at the triosephosphate isomerase locus
Activation of the pre-replicative complex
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Normal human chromosomes have long G-rich telomeric overhangs at one end
Sae2p phosphorylation is crucial for cooperation with Mre11p for resection of DNA double-strand break ends during meiotic recombination in Saccharomyces cerevisiae
Promoter escape by RNA polymerase II. Formation of an escape-competent transcriptional intermediate is a prerequisite for exit of polymerase from the promoter.
Structure of human cytidine deaminase bound to a potent inhibitor
Synthesis of PIPs at the early endosome membrane
The PtdIns3P phosphatase myotubularin is a cytoplasmic protein that also localizes to Rac1-inducible plasma membrane ruffles
Recombinational DNA repair and human disease.
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Cohesin cleavage by separase required for anaphase and cytokinesis in human cells
From birth to death: the complex lives of eukaryotic mRNAs
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Lessons from photoreceptors: turning off G-protein signaling in living cells
Human SGBS cells - a unique tool for studies of human fat cell biology
Zinc fluxes and zinc transporter genes in chronic diseases
Human N-myristoyltransferase amino-terminal domain involved in targeting the enzyme to the ribosomal subcellular fraction
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Mechanisms underlying differential responses to FGF signaling
Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components
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Role of the CLOCK protein in the mammalian circadian mechanism
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Telomerase limits the extent of base pairing between template RNA and telomeric DNA
An interferon-induced protein with release factor activity is a tryptophanyl-tRNA synthetase
Fc gamma receptor-mediated activation of phospholipase D regulates macrophage phagocytosis of IgG-opsonized particles
Desumoylation of homeodomain-interacting protein kinase 2 (HIPK2) through the cytoplasmic-nuclear shuttling of the SUMO-specific protease SENP1
Determination of the organisation of coding sequences within the iduronate sulphate sulphatase (IDS) gene
The KEN box: an APC recognition signal distinct from the D box targeted by Cdh1
The mitotic checkpoint: a signaling pathway that allows a single unattached kinetochore to inhibit mitotic exit
The zinc ribbon domains of the general transcription factors TFIIB and Brf: conserved functional surfaces but different roles in transcription initiation.
Cellular signaling by fibroblast growth factor receptors
cAMP-dependent protein kinase: framework for a diverse family of regulatory enzymes
Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternative-splice variants
The receptor for advanced glycation end products (RAGE) is a cellular binding site for amphoterin. Mediation of neurite outgrowth and co-expression of rage and amphoterin in the developing nervous system
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Cdc2 kinase directly phosphorylates the cis-Golgi matrix protein GM130 and is required for Golgi fragmentation in mitosis
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Aquaporin-7 and glycerol permeability as novel obesity drug-target pathways
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Uroporphyrinogen decarboxylase: complete human gene sequence and molecular study of three families with hepatoerythropoietic porphyria
Familial distal renal tubular acidosis is associated with mutations in the red cell anion exchanger (Band 3, AE1) gene
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Peeling by binding or twisting by cranking: models for promoter opening and transcription initiation by RNA polymerase II.
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Metabolism of carotenoids and retinoids related to vision
Rod and cone visual pigments and phototransduction through pharmacological, genetic, and physiological approaches
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Mitochondrial protein import: biochemical and genetic evidence for interaction of matrix hsp70 and the inner membrane protein MIM44
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G proteins: transducers of receptor-generated signals
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Biogenesis of iron-sulfur clusters in mammalian cells: new insights and relevance to human disease
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Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination
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The type 1 insulin-like growth factor receptor pathway
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Functional reconstitution in Escherichia coli of the yeast mitochondrial matrix peptidase from its two inactive subunits
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Structure of mitogen-activated protein kinase-activated protein (MAPKAP) kinase 2 suggests a bifunctional switch that couples kinase activation with nuclear export
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A novel role for human Nfs1 in the cytoplasm: Nfs1 acts as a sulfur donor for MOCS3, a protein involved in molybdenum cofactor biosynthesis
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Synthesis of Leukotrienes (LT) and Eoxins (EX)
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(S)-1-Pyrroline-5-carboxylate [ChEBI:17388]
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5-methyltetrahydrofolyl polyglutamate macromolecule
5-methyltetrahydrofolyl polyglutamate macromolecule [ChEBI:63907]
Peroxisome proliferator-activated receptors, coactivators, and downstream targets
Stabilization of beta-catenin by a Wnt-independent mechanism regulates cardiomyocyte growth
Proc. Natl. Acad. Sci. U.S.A. 100:4610-5
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M-phase kinases induce phospho-dependent ubiquitination of somatic Wee1 by SCFbeta-TrCP
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N-acetyl-D-glucosaminylphosphatidylinositol [ChEBI:15935]
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3-hydroxy-2,6,10,14-tetramethylpentadecanoyl-coenzyme A
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The Akt kinase signals directly to endothelial nitric oxide synthase
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Nucleoside diphosphate kinase from human erythrocytes. Structural characterization of the two polypeptide chains responsible for heterogeneity of the hexameric enzyme
Messenger RNA capping enzymes from eukaryotic cells.
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The interleukin 2 receptor. Functional consequences of its bimolecular structure
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Constitutive nuclear import and stress-regulated nucleocytoplasmic shuttling of mammalian heat-shock factor 1
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Rous sarcoma virus transforming protein lacking myristic acid phosphorylates known polypeptide substrates without inducing transformation
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Loss of the candidate tumor suppressor BTG3 triggers acute cellular senescence via the ERK-JMJD3-p16(INK4a) signaling axis
The mechanism of axon growth: what we have learned from the cell adhesion molecule L1
A new pathway for synthesis of phosphatidylinositol-4,5-bisphosphate
T cell receptor signaling: beyond complex complexes
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Molecular cloning and characterization of a novel phospholipase C, PLC-eta
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ChEBI:11805 3-hydroxy-2-methylpropanoate
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Identification of a novel domain in two mammalian inositol-polyphosphate 5-phosphatases that mediates membrane ruffle localization. The inositol 5-phosphatase skip localizes to the endoplasmic reticulum and translocates to membrane ruffles following epidermal growth factor stimulation
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Purification and characterization of homogeneous initiation factor M2A from rabbit reticulocytes.
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Mechanisms of organelle transport and capture along proplatelets during platelet production
Identification of the human mitochondrial linoleoyl-coenzyme A monolysocardiolipin acyltransferase (MLCL AT-1)
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Post-translational modification: synthesis of GPI-anchored proteins
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8p11 myeloproliferative syndrome with a novel t(7;8) translocation leading to fusion of the FGFR1 and TIF1 genes
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Mechanism and regulation of eukaryotic protein synthesis
Disorders of cholesterol biosynthesis: prototypic metabolic malformation syndromes
Making heads or tails of phospholipids in mitochondria
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Differential expression of aquaporin 8 in human colonic epithelial cells and colorectal tumors
Activation of the MAPK signal cascade by the neural cell adhesion molecule L1 requires L1 internalization
The crystal structure of human phosphoglucose isomerase at 1.6 A resolution: implications for catalytic mechanism, cytokine activity and haemolytic anaemia
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The Tim core complex defines the number of mitochondrial translocation contact sites and can hold arrested preproteins in the absence of matrix Hsp70-Tim44
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Ectodomain cleavage of ErbB-4: characterization of the cleavage site and m80 fragment
Getting to the end: telomerase access in yeast and humans
Disruption of ClC-3, a chloride channel expressed on synaptic vesicles, leads to a loss of the hippocampus
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A new type of congenital disorders of glycosylation (CDG-Ii) provides new insights into the early steps of dolichol-linked oligosaccharide biosynthesis
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Neuregulin-2, a new ligand of ErbB3/ErbB4-receptor tyrosine kinases
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A complete inventory of all enzymes in the eukaryotic methionine salvage pathway
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Human peroxisomal L-alanine: glyoxylate aminotransferase. Evolutionary loss of a mitochondrial targeting signal by point mutation of the initiation codon
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Effects of synthetic analogues of phosphoenolpyruvate on muscle and liver pyruvate kinase, muscle enolase, liver phosphoenolpyruvate carboxykinase and on the intra-/extra-mitochondrial tricarboxylic acid carrier transport system
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The Orc4p and Orc5p subunits of the Xenopus and human origin recognition complex are related to Orc1p and Cdc6p.
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Overexpression of endothelial NO synthase induces angiogenesis in a co-culture model
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Bidirectional water fluxes and specificity for small hydrophilic molecules in aquaporins 0-5
Differential requirement for the mitochondrial Hsp70-Tim44 complex in unfolding and translocation of preproteins
Overexpression of human alanine:glyoxylate aminotransferase in Escherichia coli: renaturation from guanidine-HCl and affinity for pyridoxal phosphate co-factor
Xylulose 5-phosphate mediates glucose-induced lipogenesis by xylulose 5-phosphate-activated protein phosphatase in rat liver
The stress-activated protein kinase subfamily of c-Jun kinases
Activation of HER4 by heparin-binding EGF-like growth factor stimulates chemotaxis but not proliferation
Sequential initiation of lagging and leading strand synthesis by two different polymerase complexes at the SV40 DNA replication origin.
8p11 myeloproliferative syndrome: a review
Cloning and characterization of the human beta-glucuronidase gene
Exercise-induced TBC1D1 Ser237 phosphorylation and 14-3-3 protein binding capacity in human skeletal muscle
Purification and characterization of a novel xylulose 5-phosphate-activated protein phosphatase catalyzing dephosphorylation of fructose-6-phosphate,2-kinase:fructose-2,6-bisphosphatase
Encounters of Saccharomyces cerevisiae RNA polymerase III with its transcription factors during RNA chain elongation.
Analysis of RNA chain elongation and termination by Saccharomyces cerevisiae RNA polymerase III.
Interaction between succinyl CoA synthetase and the heme-biosynthetic enzyme ALAS-E is disrupted in sideroblastic anemia
Recognition of bacterial products by toll-like receptors
Identification of 14 novel GLB1 mutations, including five deletions, in 19 patients with GM1 gangliosidosis from South America
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Different import pathways through the mitochondrial intermembrane space for inner membrane proteins
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PKC beta regulates BCR-mediated IKK activation by facilitating the interaction between TAK1 and CARMA1
Mutations in the MMAA gene in patients with the cblA disorder of vitamin B12 metabolism
Normal transitions in synthesis of replacement histones H2A.Z and H3.3 during differentiation of dystrophic myotube cells. A brief note
FUNCTION Catalyzes the exchange of ADP and ATP across the mitochondrial inner membrane.SUBUNIT Homodimer.SIMILARITY Belongs to the mitochondrial carrier (TC 2.A.29) family.SIMILARITY Contains 3 Solcar repeats.
Proton-coupled neutral amino acid transporters
Calmodulin: a prototypical calcium sensor
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Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
L-Glutamate 5-semialdehyde [ChEBI:17232]
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Stable dimeric assembly of the second membrane-spanning domain of CFTR (cystic fibrosis transmembrane conductance regulator) reconstitutes a chloride-selective pore
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4-carboxy-4-methylzymosterol [ChEBI:63842]
Eukaryotic mRNA cap binding protein: purification by affinity chromatography on sepharose-coupled m7GDP.
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Insulin/IGF-I and related signaling pathways regulate aging in nondividing cells: from yeast to the mammalian brain
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Characterization of kynurenine aminotransferase III, a novel member of a phylogenetically conserved KAT family
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A humble hexose monophosphate pathway metabolite regulates short- and long-term control of lipogenesis
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Regulation of heat shock factor trimer formation: role of a conserved leucine zipper
Formation of the ternary complex, and subsequently, the 43S complex
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(7Z,10Z,13Z,16Z)-3-oxodocosatetraenoyl-CoA [ChEBI:63821]
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The Cdc4/34/53 pathway targets Cdc6p for proteolysis in budding yeast.
Zippers make signals: NCAM-mediated molecular interactions and signal transduction
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The Saccharomyces cerevisiae COQ6 gene encodes a mitochondrial flavin-dependent monooxygenase required for coenzyme Q biosynthesis
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1-phosphatidyl-1D-myo-inositol 3-phosphate [ChEBI:17283]
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CDK-mediated phosphorylation and removal of Cdc6
Carrier protein import into mitochondria mediated by the intermembrane proteins Tim10/Mrs11 and Tim12/Mrs5
AKT/PKB signaling: navigating downstream
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(E)-2,3-didehydropristanoyl-CoA [ChEBI:63803]
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Purification and kinetic properties of human erythrocyte Mg2+-dependent inorganic pyrophosphatase
Association of licensing factors with the pre-replicative complex
Caspase cleavage product of BAP31 induces mitochondrial fission through endoplasmic reticulum calcium signals, enhancing cytochrome c release to the cytosol
Structural basis of transcription: an RNA polymerase II elongation complex at 3.3 A resolution.
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Kinetic analysis of the liver-type (GLUT2) and brain-type (GLUT3) glucose transporters in Xenopus oocytes: substrate specificities and effects of transport inhibitors
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The human Aquaporin-5 gene. Molecular characterization and chromosomal localization
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Assembly of the RAD50-MRE11-NBS1 complex at DNA double-strand breaks
Mitotic lamin disassembly is triggered by lipid-mediated signaling
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Cloning and characterization of two distinct human extracellular signal-regulated kinase activator kinases, MEK1 and MEK2.
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Human RFT1 deficiency leads to a disorder of N-linked glycosylation
alpha-D-Glucose 6-phosphate [ChEBI:17665]
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Expression and characterization of the human mitochondrial leucyl-tRNA synthetase
Bicarbonate transport in cell physiology and disease
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The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book)
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The glucose-lactic acid cycle and gluconeogenesis
Cell lines from kidney proximal tubules of a patient with Lowe syndrome lack OCRL inositol polyphosphate 5-phosphatase and accumulate phosphatidylinositol 4,5-bisphosphate
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Isozymes of human phosphofructokinase in blood cells and cultured cell lines: molecular and genetic evidence for a trigenic system
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Deletion of mouse Porcn blocks Wnt ligand secretion and reveals an ectodermal etiology of human focal dermal hypoplasia/Goltz syndrome
Proc. Natl. Acad. Sci. U.S.A. 108:12752-7
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Beta-galactosidase deficiency (beta-galactosidosis): GM1 gangliosidosis and Morquio B disease
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 3775-3809
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Substrate specificity of human nucleoside-diphosphate kinase revealed by transient kinetic analysis
Adipocyte-specific transcription factor ARF6 is a heterodimeric complex of two nuclear hormone receptors, PPAR gamma and RXR alpha
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Dolichyl phosphate D-mannose [ChEBI:4694]
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A transport metabolon. Functional interaction of carbonic anhydrase II and chloride/bicarbonate exchangers
Ataxia telangiectasia-mutated phosphorylates Chk2 in vivo and in vitro
Homologous recombinational repair of DNA ensures mammalian chromosome stability
Inborn errors of cobalamin absorption and metabolism
Am J Med Genet C Semin Med Genet 157:33-44
Metabolism of gammalinolenic acid in human neutrophils
Structure of the yeast WD40 domain protein Cia1, a component acting late in iron-sulfur protein biogenesis
Niemann-Pick C1 Like 1 protein is critical for intestinal cholesterol absorption
Mechanism of two classes of cancer mutations in the phosphoinositide 3-kinase catalytic subunit
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Different regulation of wild-type and mutant Cu,Zn superoxide dismutase localization in mammalian mitochondria
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Recruitment and activation of mRNA decay enzymes by two ARE-mediated decay activation domains in the proteins TTP and BRF-1
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Subunit structures and stoichiometries of human DNA fragmentation factor proteins before and after induction of apoptosis
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The RNA polymerase III transcription initiation factor TFIIIB participates in two steps of promoter opening.
FYVE-DSP2, a FYVE domain-containing dual specificity protein phosphatase that dephosphorylates phosphotidylinositol 3-phosphate
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Molecular mechanism of an oncogenic mutation that alters membrane targeting: Glu17Lys modifies the PIP lipid specificity of the AKT1 PH domain
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SRP-dependent cotranslational protein targeting to membrane
Evidence for the presence of phospholipid hydroperoxide glutathione peroxidase in human platelets: implications for its involvement in the regulatory network of the 12-lipoxygenase pathway of arachidonic acid metabolism
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GM1-gangliosidosis (genetic beta-galactosidase deficiency): identification of four mutations in different clinical phenotypes among Japanese patients
Cloning of a complete protein-coding sequence of human platelet-type phosphofructokinase isozyme from pancreatic islet.
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Mode of proviral activation of a putative mammary oncogene (int-1) on mouse chromosome 15
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Mutations in SLC4A4 cause permanent isolated proximal renal tubular acidosis with ocular abnormalities
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Synthesis of pyrophosphates in the cytosol
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Aquaporin-3 water channel localization and regulation in rat kidney
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Metabolism of amino acids and derivatives
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Structure and function of the radical enzyme ribonucleotide reductase
(2E,4E,6E,8E)-9-(3-hydroxy-2,6,6-trimethyl-1-cyclohexenyl)-3,7-dimethyl-nona-2,4,6,8-tetraenoic acid
(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethyl-3-hydroxy-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acid
all-trans-4-hydroxyretinoic acid [ChEBI:63795]
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ZNF198-FGFR1 transforming activity depends on a novel proline-rich ZNF198 oligomerization domain
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Human Nbp35 is essential for both cytosolic iron-sulfur protein assembly and iron homeostasis
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Purification and molecular cloning of Plx1, a Cdc25-regulatory kinase from Xenopus egg extracts
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Role of platelet-derived growth factors in physiology and medicine
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Assignment of human beta-galactosidase-A gene to 3p21.33 by fluorescence in situ hybridization
Mutations in the holocarboxylase synthetase gene HLCS
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Structure of the synthetase domain of human CTP synthetase, a target for anticancer therapy
Acta Crystallogr Sect F Struct Biol Cryst Commun 62:613-7
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The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction
Selective activation of p38 mitogen-activated protein (MAP) kinase isoforms by the MAP kinase kinases MKK3 and MKK6
Functional characterization and genomic organization of the human Na(+)-sulfate cotransporter hNaS2 gene (SLC13A4)
Activation of Cu,Zn-superoxide dismutase in the absence of oxygen and the copper chaperone CCS
Specific inhibition of pyruvate transport in rat liver mitochondria and human erythrocytes by alpha-cyano-4-hydroxycinnamate
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glucosaminylphosphatidylinositol [ChEBI:24275]
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Control of mitosis by changes in the subcellular location of cyclin-B1-Cdk1 and Cdc25C
Peroxisome proliferator-activated receptors: a nuclear receptor signaling pathway in lipid physiology
Biosynthetic studies of A2E, a major fluorophore of retinal pigment epithelial lipofuscin
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Molecular mechanism of neuronal plasticity: induction and maintenance of long-term potentiation in the hippocampus
Posttranslational modification of the AU-rich element binding protein HuR by protein kinase Cdelta elicits angiotensin II-induced stabilization and nuclear export of cyclooxygenase 2 mRNA
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Tetrahydrobiopterin biosynthesis, regeneration and functions
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Selective RNA binding by a single CCCH zinc-binding domain from Nup475 (Tristetraprolin)
Chaperone Hsp27, a novel subunit of AUF1 protein complexes, functions in AU-rich element-mediated mRNA decay
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Peptide binding and antigen presentation by class II histocompatibility glycoproteins
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MISCELLANEOUS Present with 3770 molecules/cell in log phase SD medium.SIMILARITY Belongs to the TIM21 family.
The plasma membrane of erythrocytes plays a fundamental role in the transport of oxygen, carbon dioxide and nitric oxide and in the maintenance of the reduced state of the heme iron
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Purification and properties of human erythrocyte glutathione peroxidase
The inositol hexakisphosphate kinase family. Catalytic flexibility and function in yeast vacuole biogenesis
Analysis of the putative role of 24-carbon polyunsaturated fatty acids in the biosynthesis of docosapentaenoic (22:5n-6) and docosahexaenoic (22:6n-3) acids
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Interactions of CD80 and CD86 with CD28 and CTLA4
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Structure, function, and genomic organization of human Na(+)-dependent high-affinity dicarboxylate transporter
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The molecular basis of insulin-stimulated glucose uptake: signalling, trafficking and potential drug targets
ChEBI:17526 1-phosphatidyl-1D-myo-inositol 4-phosphates
Structure of S6 kinase 1 determines whether raptor-mTOR or rictor-mTOR
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A novel gene oriented in a head-to-head configuration with the human histidyl-tRNA synthetase (HRS) gene encodes an mRNA that predicts a polypeptide homologous to HRS
gamma-L-Glutamyl-L-cysteine [ChEBI:17515]
Signal-induced site-specific phosphorylation targets I kappa B alpha to the ubiquitin-proteasome pathway
Wnt5A activates the calpain-mediated cleavage of filamin A
Structure, function and evolution of seryl-tRNA synthetases: implications for the evolution of aminoacyl-tRNA synthetases and the genetic code
Three mammalian lipins act as phosphatidate phosphatases with distinct tissue expression patterns
Differential transformation of mammary epithelial cells by Wnt genes
Nitric oxide: a physiologic messenger molecule
Nucleosome structure(s) and stability: variations on a theme
WNT ligand secretion is abrogated by the PORCN inhibitor LGK974
The human mismatch recognition complex hMSH2-hMSH6 functions as a novel molecular switch
DOMAIN Its cytoplasmic domain associates with the cytoplasmic domains of TOM20 and TOM70. Its intermembrane space domain provides a trans binding site for presequences and the single membrane anchor is required for a stable interaction between the GIP complex proteins.MISCELLANEOUS Present with 6610 molecules/cell in log phase SD medium.SIMILARITY Belongs to the Tom22 family.
Import of palmitoyl-CoA into the mitochondrial matrix
Deficiency of the first mannosylation step in the N-glycosylation pathway causes congenital disorder of glycosylation type Ik
Roles of AUF1 isoforms, HuR and BRF1 in ARE-dependent mRNA turnover studied by RNA interference
Porphobilinogen deaminase and uroporphyrinogen III synthase: structure, molecular biology, and mechanism
Congenital glutamine deficiency with glutamine synthetase mutations
Endotoxin induces rapid protein tyrosine phosphorylation in 70Z/3 cells expressing CD14
The canonical retinoid cycle in rods (twilight vision)
Mechanism of action and in vivo role of platelet-derived growth factor
Regulation of the extracellular antioxidant selenoprotein plasma glutathione peroxidase (GPx-3) in mammalian cells
Identification and characterization of a cDNA encoding a long-chain cis-isoprenyltranferase involved in dolichyl monophosphate biosynthesis in the ER of brain cells
Biochem. Biophys. Res. Commun. 312:1349-56
Comparison of human B cell antigen receptor complexes: membrane-expressed forms of immunoglobulin (Ig)M, IgD, and IgG are associated with structurally related heterodimers
The gene mutated in adult-onset type II citrullinaemia encodes a putative mitochondrial carrier protein
Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein
Hyperornithinaemia-hyperammonaemia-homocitrullinuria syndrome is caused by mutations in a gene encoding a mitochondrial ornithine transporter.
Mechanism for fatty acid sparing effect on glucose-induced transcription: regulation of carbohydrate-responsive element-binding protein by AMP-activated protein kinase
DNA topology and a minimal set of basal factors for transcription by RNA polymerase II.
Nedd4 mediates ErbB4 JM-a/CYT-1 ICD ubiquitination and degradation in MDCK II cells
Carnitine biosynthesis. beta-Hydroxylation of trimethyllysine by an alpha-ketoglutarate-dependent mitochondrial dioxygenase.
AKT phosphorylates targets in the cytosol
Igf-I signaling and effects on longevity
Nestle Nutr Workshop Ser Pediatr Program 68:237-45; discussion 246-9
Differences between the trypanosomal and human GlcNAc-PI de-N-acetylases of glycosylphosphatidylinositol membrane anchor biosynthesis
Molecular characterization of a phospholipase D generating anandamide and its congeners
Expression of aquaporin 8 in colonic epithelium with diarrhoea-predominant irritable bowel syndrome
Characterization of p150, an adaptor protein for the human phosphatidylinositol (PtdIns) 3-kinase. Substrate presentation by phosphatidylinositol transfer protein to the p150.Ptdins 3-kinase complex
Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8
Spatial and temporal regulation of Condensins I and II in mitotic chromosome assembly in human cells
Defective MTRR causes methylmalonic aciduria and homocystinuria type cblE
Neuregulin-3 (NRG3): a novel neural tissue-enriched protein that binds and activates ErbB4
Cdc25 cell-cycle phosphatase as a target of c-myc
Tyrosine phosphorylation of phospholipase C induced by membrane immunoglobulin in B lymphocytes
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(ethanolamineP) mannose (a1-2) (ethanolamineP) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI [ChEBI:77364]
Identification of eukaryotic DNA replication proteins using simian virus 40 in vitro replication system.
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3-decaprenyl-4-hydroxy-5-methoxybenzoic acid
4-hydroxy-3-methoxy-5-decaprenylbenzoic acid
all-trans-4-hydroxy-3-methoxy-5-decaprenylbenzoic acid
3-decaprenyl-4-hydroxy-5-methoxybenzoic acid [ChEBI:50776]
all-trans-3-decaprenyl-4-hydroxy-5-methoxybenzoic acid
3-decaprenyl-4,5-dihydroxybenzoic acid [ChEBI:50775]
all-trans-3-decaprenyl-4,5-dihydroxybenzoic acid
all-trans-3,4-dihydroxy-5-decaprenylbenzoic acid
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GTP hydrolysis and joining of the 60S ribosomal subunit
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The sequence of a human mitochondrial glycerol-3-phosphate dehydrogenase-encoding cDNA
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Eukaryotic protein synthesis: still a mystery
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A monoclonal antibody that appears to recognize the receptor for human T-cell growth factor; partial characterization of the receptor
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AT-AC pre-mRNA splicing mechanisms and conservation of minor introns in voltage-gated ion channel genes.
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In vivo protein-interaction mapping of a mitochondrial translocator protein Tom22 at work
Glutamine- dependent asparagine synthetase
Asparagine synthetase (glutamine-hydrolyzing)
WD repeat domain phosphoinositide-interacting protein 1
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TRAF6 autoubiquitination-independent activation of the NFkappaB and MAPK pathways in response to IL-1 and RANKL
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Aldehyde dehydrogenase, mitochondrial precursor
4-aminobutyrate aminotransferase, mitochondrial
Succinate-semialdehyde dehydrogenase, mitochondrial
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CATALYTIC ACTIVITY Citrate = isocitrate.ENZYME REGULATION Subject to catabolite regulation.PATHWAY Carbohydrate metabolism; tricarboxylic acid cycle; isocitrate from oxaloacetate: step 2/2.MISCELLANEOUS The fermenting yeast S.cerevisiae has 2 aconitases, ACO1 essential for the citric acid cycle, and ACO2 specifically and exclusively contributing to lysine biosynthesis. In contrast, in respiring filamentous fungi the ACO2 homologs (acoB) seem enzymatically inactive and the ACO1 homolog (acoA) is solely responsible for these functions.MISCELLANEOUS Present with 96700 molecules/cell in log phase SD medium.SIMILARITY Belongs to the aconitase/IPM isomerase family.
MISCELLANEOUS Present with 3250 molecules/cell in log phase SD medium.SIMILARITY Belongs to the Tom7 family.
Calcium/calmodulin-dependent protein kinase kinase 1
Copper chaperone for superoxide dismutase
Superoxide dismutase [Cu-Zn] ecNumber1.15.1.1/ecNumber
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Superoxide dismutase [Mn], mitochondrial ecNumber1.15.1.1/ecNumber
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Phosphorylation of nucleosides and nucleoside analogs by mammalian nucleoside monophosphate kinases
Interfacial kinetic and binding properties of the complete set of human and mouse groups I, II, V, X, and XII secreted phospholipases A2
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60 kDa heat shock protein, mitochondrial
Proteins Imported to the Matrix by TIMM23 PAM
Iron-sulfur cluster co-chaperone protein HscB, mitochondrial
Adenosine triphosphate-adenosine-5'-monophosphate phosphotransferase from normal human liver mitochondria. Isolation, chemical properties, and immunochemical comparison with Duchenne muscular dystrophic serum aberrant adenylate kinase
Precursors Imported to the Matrix by TIMM23 PAM
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The human and mouse replication-dependent histone genes
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Syndromic craniosynostosis: from history to hydrogen bonds
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Nuclear transcription factor Y subunit gamma
Metabolism of steroid hormones and vitamin D
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Probable ATP-dependent RNA helicase DDX11
Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
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A novel point mutation in a 3' splice site of the NADH-cytochrome b5 reductase gene results in immunologically undetectable enzyme and impaired NADH-dependent ascorbate regeneration in cultured fibroblasts of a patient with type II hereditary methemoglobinemia
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Functional evaluation of PTEN missense mutations using in vitro phosphoinositide phosphatase assay
Identification, purification and characterization of a novel phosphatidylinositol-specific phospholipase C, a third member of the beta subfamily
Oxygen and the copper chaperone CCS regulate posttranslational activation of Cu,Zn superoxide dismutase
Proc. Natl. Acad. Sci. U.S.A. 101:5518-23
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Characterization of the localization and proteolytic activity of the SUMO-specific protease, SENP1
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XBP1 controls diverse cell type- and condition-specific transcriptional regulatory networks
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Accumulation of dietary cholesterol in sitosterolemia caused by mutations in adjacent ABC transporters
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Inactivation of NF-kappa B inhibitor I kappa B alpha: ubiquitin-dependent proteolysis and its degradation product
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Prophase destruction of Emi1 by the SCF(betaTrCP/Slimb) ubiquitin ligase activates the anaphase promoting complex to allow progression beyond prometaphase
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Extracellular-signal-regulated kinase signalling in neurons
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Characterization of MTMR3. an inositol lipid 3-phosphatase with novel substrate specificity
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Complete sequencing and characterization of 21,243 full-length human cDNAs
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Histone H3 lysine 9 methylation is an epigenetic imprint of facultative heterochromatin
Identical mutations in three different fibroblast growth factor receptor genes in autosomal dominant craniosynostosis syndromes
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Release of arachidonate from diglyceride in human platelets requires the sequential action of a diglyceride lipase and a monoglyceride lipase
Translocation of GLUT4 to the plasma membrane
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Origins and Mechanisms of miRNAs and siRNAs
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Sanfilippo syndrome type C: mutation spectrum in the heparan sulfate acetyl-CoA: alpha-glucosaminide N-acetyltransferase (HGSNAT) gene
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A second canon. Functions and mechanisms of beta-catenin-independent Wnt signaling
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Structure-function analysis of the bestrophin family of anion channels
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Association of TriC/CCT with target proteins during biosynthesis
The expression and functional characterization of ABCG2 in brain endothelial cells and vessels
Selective degradation of AU-rich mRNAs promoted by the p37 AUF1 protein isoform
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OMMBID Chapter 71: Glycogen Storage Diseases
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ARF mediates recruitment of PtdIns-4-OH kinase-beta and stimulates synthesis of PtdIns(4,5)P2 on the Golgi complex
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Phosphatidylinositol-3-OH kinases are Rab5 effectors
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Mitochondrial iron trafficking and the integration of iron metabolism between the mitochondrion and cytosol
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Identification of a novel guanine nucleotide exchange factor for the Rho GTPase
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The N-terminal domain of Tob55 has a receptor-like function in the biogenesis of mitochondrial beta-barrel proteins
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Disassembly of exon junction complexes by PYM
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Type II phosphatidylinositol 4-kinase beta is a cytosolic and peripheral membrane protein that is recruited to the plasma membrane and activated by Rac-GTP
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Insights into COPI coat assembly and function in living cells
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RNA binding properties of the AU-rich element-binding recombinant Nup475/TIS11/tristetraprolin protein
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Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design
Mutant Cu, Zn superoxide dismutase that causes motoneuron degeneration is present in mitochondria in the CNS
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Tissue distribution and cDNA cloning of a human fatty acid transport protein (hsFATP4)
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The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Scriver CR, et al., editors) 1:1553-1587
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The role of assembly in insulin's biosynthesis
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The N-terminal shuttle domain of Erv1 determines the affinity for Mia40 and mediates electron transfer to the catalytic Erv1 core in yeast mitochondria
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Sulfotransferases in the bioactivation of xenobiotics
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Proteins Inserted into Inner Membrane by TIMM23 SORT
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Probable D-lactate dehydrogenase, mitochondrial
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Identification of the peroxisomal beta-oxidation enzymes involved in the biosynthesis of docosahexaenoic acid
Synthesis of 15-eicosatetraenoic acid derivatives
The phosphatidylinositol 3-kinase/Akt signaling pathway modulates the endocrine differentiation of trophoblast cells
Deficiency of UDP-GlcNAc:Dolichol Phosphate N-Acetylglucosamine-1 Phosphate Transferase (DPAGT1) causes a novel congenital disorder of Glycosylation Type Ij
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Import, maturation, and function of SOD1 and its copper chaperone CCS in the mitochondrial intermembrane space
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A conserved family of enzymes that phosphorylate inositol hexakisphosphate
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Molecular cloning and characterization of a novel 3'-phosphoadenosine 5'-phosphosulfate transporter, PAPST2
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Primate Genome Gain and Loss: A Bone Dysplasia, Muscular Dystrophy, and Bone Cancer Syndrome Resulting from Mutated Retroviral-Derived MTAP Transcripts
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Identification of Mn2+-binding aspartates from alpha, beta, and gamma subunits of human NAD-dependent isocitrate dehydrogenase
mTORC1 links protein quality and quantity control by sensing chaperone availability
Overview of steroidogenic enzymes in the pathway from cholesterol to active steroid hormones
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The human Pif1 helicase, a potential Escherichia coli RecD homologue, inhibits telomerase activity
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Mitochondrial import inner membrane translocase subunit Tim17-A
Regulation of repair of alkylation damage in mammalian genomes.
Prog Nucleic Acid Res Mol Biol 44:109-42
Mitochondrial import inner membrane translocase subunit Tim17-B
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Sentrin-specific protease 2 ecNumber3.4.22.68/ecNumber
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Guanosine triphosphate, the primary product of phosphorylation coupled to the breakdown of succinyl coenzyme A
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Precursors Inserted into Mitochondrial Inner Membrane by TIMM23 SORT
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ATP synthase lipid-binding protein precursor
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Targeting the Wnt/?-catenin signaling pathway in human cancers
Gamma linolenic acid: an antiinflammatory omega-6 fatty acid
Tissue-differential expression of two distinct genes for phosphoribosyl pyrophosphate synthetase and existence of the testic-specific transcript
Second pathway for completion of human DNA base excision-repair: reconstitution with purified proteins and requirement for DNase IV (FEN1).
Spectrum of mutations in mut methylmalonic acidemia and identification of a common Hispanic mutation and haplotype
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Primary megakaryocytes reveal a role for transcription factor NF-E2 in integrin alpha IIb beta 3 signaling
Sentrin-specific protease 1 ecNumber3.4.22.68/ecNumber
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Nitric oxide stimulates guanylate cyclase
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LAT and NTAL mediate immunoglobulin E-induced sustained extracellular signal-regulated kinase activation critical for mast cell survival
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The complex route to MHC class I-peptide complexes
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PURIFICATION AND PROPERTIES OF GLUTATHIONE REDUCTASE OF HUMAN ERYTHROCYTES
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UDP-glucose:glycoprotein glucosyltransferase 1
UDP-glucose:glycoprotein glucosyltransferase 2
Dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase
Probable dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3-glucosyltransferase
Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
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The kinase inhibitor TKI258 is active against the novel CUX1-FGFR1 fusion detected in a patient with T-lymphoblastic leukemia/lymphoma and t(7;8)(q22;p11)
Cardiolipin is synthesized on the matrix side of the inner membrane in rat liver mitochondria
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Sinauer Associates, Inc., P.O. Box 407 23 Plumtree Road, Sunderland, MA 01375 U.S.A.
The sodium phosphate cotransporter family SLC34
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Roles for LPS-dependent interaction and relocation of TLR4 and TRAM in TRIF-signaling
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Transcription factors direct the development and function of pancreatic beta cells
The SLC2 family of facilitated hexose and polyol transporters
PMM (PMM1), the human homologue of SEC53 or yeast phosphomannomutase, is localized on chromosome 22q13
The SLC32 transporter, a key protein for the synaptic release of inhibitory amino acids
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(all-E)-3-(3,7,11,15,19,23-hexamethyl-2,6,10,14,18,22-tetracosahexaenyl)-4-hydroxybenzoic acid
all-trans-3-(3,7,11,15,19,23-hexamethyl-2,6,10,14,18,22-tetracosahexaenyl)-4-hydroxybenzoic acid
3-hexaprenyl-4-hydroxybenzoic acid [ChEBI:31116]
Common themes in siRNA-mediated epigenetic silencing pathways
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Protein synthesis and protein phosphorylation during heat stress, recovery, and adaptation
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Organization and sequence of the human gene for the mitochondrial citrate transport protein
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ClC-3 chloride channels facilitate endosomal acidification and chloride accumulation
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Crystal structure of human squalene synthase. A key enzyme in cholesterol biosynthesis.
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The kinetics of the reduction of cytochrome c by the superoxide anion radical
Purification and properties of uroporphyrinogen decarboxylase from human erythrocytes. A single enzyme catalyzing the four sequential decarboxylations of uroporphyrinogens I and III.
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Endosomal Sorting Complex Required For Transport (ESCRT)
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_219926.2
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Signaling via mitogen-activated protein kinase kinase (MEK1) is required for Golgi fragmentation during mitosis
Localization of the human mitochondrial citrate transporter protein gene to chromosome 22Q11 in the DiGeorge syndrome critical region
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Sodium-coupled monocarboxylate transporters in normal tissues and in cancer
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FGFR activation in skeletal disorders: too much of a good thing
The Role of Gbetagamma Subunits in the Organization, Assembly, and Function of GPCR Signaling Complexes
Expression cloning of a human cDNA encoding folylpoly(gamma-glutamate) synthetase and determination of its primary structure
The eukaryotic P loop NTPase Nbp35: an essential component of the cytosolic and nuclear iron-sulfur protein assembly machinery
Proc. Natl. Acad. Sci. U.S.A. 102:3266-71
Ways of dying: multiple pathways to apoptosis.
Dominant negative mechanism underlies autosomal dominant Stargardt-like macular dystrophy linked to mutations in ELOVL4
Enolase isoenzymes in rat tissues. Electrophoretic, chromatographic, immunological and kinetic properties
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The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1623-1650
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20116.2
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Molecular mechanisms of megakaryocyte differentiation
Consistent fusion of ZNF198 to the fibroblast growth factor receptor-1 in the t(8;13)(p11;q12) myeloproliferative syndrome
Formation of the Early Elongation Complex
Temporal differences in the activation of three classes of non-transmembrane protein tyrosine kinases following B-cell antigen receptor surface engagement
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_243849.1
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FUNCTION: Catalyzes the dehydration of methylthioribulose-1- phosphate (MTRu-1-P) into 2,3-diketo-5-methylthiopentyl-1- phosphate (DK-MTP-1-P).
Human UDP-glucuronosyltransferases: metabolism, expression, and disease
Mannose-1-phosphate guanyltransferase beta
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Polymerase II promoter activation: closed complex formation and ATP-driven start site opening.
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Dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichyl mannosyltransferase
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Asparagine-linked glycosylation protein 11 homolog
UDP-N-acetylglucosamine transferase subunit ALG14 homolog
GDP-Man:GlcNAc2-PP-dolichol mannosyltransferase
Chitobiosyldiphosphodolichol beta-mannosyltransferase
Dolichyl-phosphate beta-glucosyltransferase
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UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20195.2
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Glucosamine--fructose-6-phosphate aminotransferase (isomerizing) 2
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Glucosamine 6-phosphate N-acetyltransferase
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UDP-N-acetylhexosamine pyrophosphorylase
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FUNCTION DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. The RPC25/RPC8-RPC17/RPC9 subcomplex may bind Pol III transcripts emerging from the adjacent exit pore during elongation.MISCELLANEOUS Present with 2930 molecules/cell in log phase SD medium.SIMILARITY Belongs to the eukaryotic RPC9 RNA polymerase subunit family.
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608990
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608992
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5608993
Glucosamine--fructose-6-phosphate aminotransferase (isomerizing) 1
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_150517.1
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N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_189325.3
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Eukaryotic translation initiation factor 5A
Mucopolysaccharidosis IV A: assignment of the human N-acetylgalactosamine-6-sulfate sulfatase (GALNS) gene to chromosome 16q24
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Eukaryotic tranlation initiation factor 5A2
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Activation of the apoptotic endonuclease DFF40 (caspase-activated DNase or nuclease). Oligomerization and direct interaction with histone H1
Eukaryotic translation initiation factor 5A-1
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Import of mitochondrial carriers mediated by essential proteins of the intermembrane space
Molecular cloning and expression of the human delta7-sterol reductase
MISCELLANEOUS Present with 13100 molecules/cell in log phase SD medium.SIMILARITY Belongs to the eukaryotic release factor 1 family.
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E2F mediates developmental and cell cycle regulation of ORC1 in Drosophila
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=428204
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=5614179
T-complex protein 1 subunit gamma (TCP-1-gamma)
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Cyclic GMP phosphodiesterase-5: target of sildenafil
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Amino acid transport across the plasma membrane
Crystalline D-glyceraldehyde-3-phosphate dehydrogenase from rabbit muscle
cDNA sequence and gene locus of the human retinal phosphoinositide-specific phospholipase-C beta 4 (PLCB4)
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A human phosphatidylinositol 3-kinase complex related to the yeast Vps34p-Vps15p protein sorting system
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T-complex protein 1 subunit theta (TCP-1-theta)
T-complex protein 1 subunit delta (TCP-1-delta)
T-complex protein 1 subunit zeta (TCP-1-zeta)
T-complex protein 1 subunit eta (TCP-1-eta)
T-complex protein 1 subunit beta (TCP-1-beta)
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T-complex protein 1 subunit epsilon (TCP-1-epsilon)
T-complex protein 1 subunit alpha (TCP-1-alpha)
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malate dehydrogenase 2, NAD (mitochondrial)
Malate dehydrogenase, mitochondrial precursor
Mitochondrial dicarboxylate carrier protein
Aspartate aminotransferase, mitochondrial precursor
aspartate aminotransferase, mitochondrial, apoenzyme monomer
mitochondrial aspartate glutamate carrier
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The AMP-activated protein kinase pathway--new players upstream and downstream
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Appearance of water channels in Xenopus oocytes expressing red cell CHIP28 protein
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Dre2, a conserved eukaryotic Fe/S cluster protein, functions in cytosolic Fe/S protein biogenesis
D-fructose-1,6- bisphosphate 1-phosphohydrolase
Unconventional Rac-GEF activity is mediated through the Dock180-ELMO complex
Molecular interpretation of ERK signal duration by immediate early gene products
D-fructose-1,6-bisphosphate 1-phosphohydrolase
UTP-glucose-1-phosphate uridylyltransferase
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Homologues of oligo((1,4)-alpha-glucosyl) GYG1
oligo((1,4)-alpha-glucosyl) glycogenin-1
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Characterization of human brain nicotinamide 5'-mononucleotide adenylyltransferase-2 and expression in human pancreas
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Homologues of oligo((1,4)-alpha-glycosyl) GYG2
oligo((1,4)-alpha-glycosyl) glycogenin-2
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Homologues of poly((1,4)-alpha-glucosyl)GYG2
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Homologues of poly((1,4)-alpha-glucosyl)GYG1
Targeting Wnt-driven cancer through the inhibition of Porcupine by LGK974
Proc. Natl. Acad. Sci. U.S.A. 110:20224-9
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Detoxification of Reactive Oxygen Species
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PDK-1 and protein kinase C phosphorylation
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Sequential actions of myotubularin lipid phosphatases regulate endosomal PI(3)P and growth factor receptor trafficking
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Homologues of limit dextrin-glycogenin-1
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Homologues of limit dextrin-glycogenin-2
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Homologues of ((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)GYG1
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alpha-linolenic (omega3) and linoleic (omega6) acid metabolism
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Crystal structures of mammalian glutamine synthetases illustrate substrate-induced conformational changes and provide opportunities for drug and herbicide design
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Phosphorylation of I kappa B alpha precedes but is not sufficient for its dissociation from NF-kappa B
Cleavage preferences of the apoptotic endonuclease DFF40 (caspase-activated DNase or nuclease) on naked DNA and chromatin substrates
The localization of human cyclins B1 and B2 determines CDK1 substrate specificity and neither enzyme requires MEK to disassemble the Golgi apparatus
The ALG10 locus of Saccharomyces cerevisiae encodes the alpha-1,2 glucosyltransferase of the endoplasmic reticulum: the terminal glucose of the lipid-linked oligosaccharide is required for efficient N-linked glycosylation
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Clamping down on clamps and clamp loaders--the eukaryotic replication factor C.
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The Ca2+-pumping ATPase of plasma membranes. Purification, reconstitution and properties
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Gene duplication and the evolution of group II chaperonins: implications for structure and function
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Point mutations in a hinge linking the small and large domains of beta-actin result in trapped folding intermediates bound to cytosolic chaperonin CCT
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Human securin proteolysis is controlled by the spindle checkpoint and reveals when the APC/C switches from activation by Cdc20 to Cdh1
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glyceraldehyde-3-phosphate dehydrogenase, testis-specific, monomer
Glyceraldehyde 3-phosphate dehydrogenase, liver
glyceraldehyde-3-phosphate dehydrogenase monomer
glyceraldehyde 3-phosphate dehydrogenase, muscle
The role of CDP-diacylglycerol synthetase and phosphatidylinositol synthase activity levels in the regulation of cellular phosphatidylinositol content
Distinct functions of condensin I and II in mitotic chromosome assembly
Translational control by the 3'-UTR: the ends specify the means
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53BP1 and NFBD1/MDC1-Nbs1 function in parallel interacting pathways activating ataxia-telangiectasia mutated (ATM) in response to DNA damage.
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Function in protein folding of TRiC, a cytosolic ring complex containing TCP-1 and structurally related subunits
Pyruvate carboxylase, mitochondrial precursor
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Identification and characterization of a lysophosphatidylcholine acyltransferase in alveolar type II cells
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Peptide hormone expression and precursor processing
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Identification of amino acid residues responsible for the pyrimidine and purine nucleoside specificities of human concentrative Na+ nucleoside cotransporters hCNT1 and hCNT2
The neurotransmitter cycle and quantal size
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Characterization of vascular endothelial growth factor's effect on the activation of protein kinase C, its isoforms, and endothelial cell growth
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Early phagosomes in dendritic cells form a cellular compartment sufficient for cross presentation of exogenous antigens
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GTPase signaling: bridging the GAP between ARF and Rho
Lysophospholipid acyltransferases: 1-acylglycerol-3-phosphate O-acyltransferases (AGPATs) From discovery to disease
An associated molecule, p64, with IL-2 receptor beta chain. Its possible involvement in the formation of the functional intermediate-affinity IL-2 receptor complex
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Presenilin-dependent ErbB4 nuclear signaling regulates the timing of astrogenesis in the developing brain
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Mutations in the gene for the E1beta subunit: a novel cause of pyruvate dehydrogenase deficiency
How nucleotide excision repair protects against cancer.
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Generation of major histocompatibility complex class I antigens: functional interplay between proteasomes and TPPII
Post-proteasomal antigen processing for major histocompatibility complex class I presentation
The exogenous pathway for antigen presentation on major histocompatibility complex class II and CD1 molecules
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Mutations in the Delta1-pyrroline 5-carboxylate dehydrogenase gene cause type II hyperprolinemia.
Selectivity in post-translational biotin addition to five human carboxylases
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Genetic Analysis of Complex Interactions Amongst Components of the Mitochondrial Import Motor and Translocon in Saccharomyces cerevisiae
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RhoGDIs revisited: novel roles in Rho regulation
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Nomenclature of the GLUT/SLC2A family of sugar/polyol transport facilitators.
Am J Physiol Endocrinol Metab 282:E974-6
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Human 1-D-myo-inositol-3-phosphate synthase is functional in yeast
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6PF-2-K/Fru- 2,6-P2ASE brain/placenta-type isozyme
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4
6PF-2-K/Fru- 2,6-P2ASE testis-type isozyme
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Mitochondrial regulation of cell cycle and proliferation
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6PF-2-K/Fru- 2,6-P2ASE heart-type isozyme
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2
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6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1
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Structure, expression profile and alternative processing of the human phosphatidylethanolamine N-methyltransferase (PEMT) gene
Mechanism of B-cell receptor-induced phosphorylation and activation of phospholipase C-gamma2
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Insights from retinitis pigmentosa into the roles of isocitrate dehydrogenases in the Krebs cycle
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MyD88: an adapter that recruits IRAK to the IL-1 receptor complex
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Lanosterol 14 alpha-methyl demethylase. Isolation and characterization of the third metabolically generated oxidative demethylation intermediate.
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Replication protein A stimulates proliferating cell nuclear antigen-dependent repair of abasic sites in DNA by human cell extracts.
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Changes in methionine adenosyltransferase and S-adenosylmethionine homeostasis in alcoholic rat liver
Am J Physiol Gastrointest Liver Physiol 279:G178-85
ARE-mRNA degradation requires the 5'-3' decay pathway
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Identification and functional analysis of a defect in the human ALG9 gene: definition of congenital disorder of glycosylation type IL
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hSef inhibits PC-12 cell differentiation by interfering with Ras-mitogen-activated protein kinase MAPK signaling
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The MAS-encoded processing protease of yeast mitochondria. Interaction of the purified enzyme with signal peptides and a purified precursor protein
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Water permeability and characterization of aquaporin-11
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CD28 costimulation: a source of Vav-1 for TCR signaling with the help of SLP-76?
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Persistent initiation of DNA replication and chromatin-bound MCM proteins during the cell cycle in cdc6 mutants.
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ORC5L, a new member of the human origin recognition complex, is deleted in uterine leiomyomas and malignant myeloid diseases.
Natural resistance-associated macrophage protein 1
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Adrenic acid metabolites as endogenous endothelium-derived and zona glomerulosa-derived hyperpolarizing factors
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On the biosynthesis and biological role of eoxins and 15-lipoxygenase-1 in airway inflammation and Hodgkin lymphoma
Prostaglandins Other Lipid Mediat 89:120-5
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CATALYTIC ACTIVITY Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).SUBUNIT Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits.MISCELLANEOUS Present with 6020 molecules/cell in log phase SD medium.SIMILARITY Belongs to the RNA polymerase beta' chain family.
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_161274.1
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Isocitrate dehydrogenase (NADP) cytoplasmic R132H
Intracellular zinc homeostasis and zinc signaling
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Solute carrier family 2, facilitated glucose transporter member 5
Homologues of N-seryl-glycosylphosphatidylinositolethanolamine-TREH
Solute carrier family 2, facilitated glucose transporter, member 3
Solute carrier family 2, facilitated glucose transporter, member 1
Glucose transporter type 1, erythrocyte/brain
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Glycogenin-2, a novel self-glucosylating protein involved in liver glycogen biosynthesis.
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Multidrug resistance-associated protein 5
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_189277.3
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Adenosine 3'-phospho 5'-phosphosulfate transporter 1
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Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase 2
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Cloning and expression analysis of a novel member of the facilitative glucose transporter family, SLC2A9 (GLUT9)
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Cloning and expression of the human N-acetylglutamate synthase gene.
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Dual-specificity histone demethylase KIAA1718 (KDM7A) regulates neural differentiation through FGF4
Biochemical analysis of the human mismatch repair proteins hMutS? MSH2(G674A)-MSH6 and MSH2-MSH6(T1219D)
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Purified RNA polymerase III accurately and efficiently terminates transcription of 5S RNA genes.
T cell antigen-receptor signal transduction
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Genetic evidence for the expression of ATP- and GTP-specific succinyl-CoA synthetases in multicellular eucaryotes
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Characterization of the ATP- and GTP-specific succinyl-CoA synthetases in pigeon. The enzymes incorporate the same alpha-subunit.
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Mcm4,6,7 uses a 'pump in ring' mechanism to unwind DNA by steric exclusion and actively translocate along a duplex
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Mechanism of diacylglycerol-induced membrane targeting and activation of protein kinase Ctheta
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Expression of human arginine decarboxylase, the biosynthetic enzyme for agmatine
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MicroRNA genes are transcribed by RNA polymerase II
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Targeting mutant fibroblast growth factor receptors in cancer
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Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function
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Lead exposure and heat shock inhibit cell proliferation in human HeLa and K562 cells by inducing expression and activity of the heme-regulated eIF-2alpha kinase
Histone demethylation by a family of JmjC domain-containing proteins
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Localization by fluorescence in situ hybridization of the human functional beta-glucuronidase gene (GUSB) to 7q11.21 --> q11.22 and two pseudogenes to 5p13 and 5q13
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Cascade regulation of terminal adipocyte differentiation by three members of the C/EBP family of leucine zipper proteins
Mitochondrial tRNA import: are there distinct mechanisms?
Mitochondrial iron-sulfur cluster biogenesis
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Molecular identification of a novel mammalian brain isoform of acyl-CoA:lysophospholipid acyltransferase with prominent ethanolamine lysophospholipid acylating activity, LPEAT2
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Properties of an affinity-column-purified human deoxycytidylate deaminase
Crystal structure of human dihydrolipoamide dehydrogenase: NAD+/NADH binding and the structural basis of disease-causing mutations
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BMAL1:CLOCK,NPAS2 activates circadian gene expression
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Direct interaction between survivin and Smac/DIABLO is essential for the anti-apoptotic activity of survivin during taxol-induced apoptosis.
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Chapter 155: Inherited Disorders of Folate and Cobalamin Transport and Metabolism
The Online Metabolic and Molecular Bases of Inherited Disease (Book)
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cDNA cloning of human and rat brain myo-inositol monophosphatase. Expression and characterization of the human recombinant enzyme
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Cloning and expression of AQP3, a water channel from the medullary collecting duct of rat kidney
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DNA mismatch repair in eukaryotes and bacteria
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The Tim9p/10p and Tim8p/13p complexes bind to specific sites on Tim23p during mitochondrial protein import
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Transitional endoplasmic reticulum ATPase
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Targeting and translocation of endothelial nitric oxide synthase
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Peroxiredoxin-5, mitochondrial ecNumber1.11.1.15/ecNumber
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Peroxiredoxin-1 ecNumber1.11.1.15/ecNumber
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Peroxiredoxin-2 ecNumber1.11.1.15/ecNumber
Beta-enolase deficiency, a new metabolic myopathy of distal glycolysis
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Structure of human argininosuccinate synthetase
Acta Crystallogr D Biol Crystallogr 64:279-86
Human TLR10 is a functional receptor, expressed by B cells and plasmacytoid dendritic cells, which activates gene transcription through MyD88
FUNCTION Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water.CATALYTIC ACTIVITY 4 ferrocytochrome c + O(2) + 4 H(+) = 4 ferricytochrome c + 2 H(2)O.PATHWAY Energy metabolism; oxidative phosphorylation.SUBUNIT Cytochrome c oxidase is composed of 11 subunits: one copy each of COX1, COX2, COX3, COX4, COX5A or COX5B, COX6, COX7, COX9, COX12, COX13 and two copies of COX8.MISCELLANEOUS Present with 9410 molecules/cell in log phase SD medium.SIMILARITY Belongs to the cytochrome c oxidase subunit 5B family.
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Glutathione reductase, mitochondrial precursor
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Elucidation of human choline kinase crystal structures in complex with the products ADP or phosphocholine
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Interferon induces tryptophanyl-tRNA synthetase expression in human fibroblasts
Disruption of the checkpoint kinase 1/cell division cycle 25A pathway abrogates ionizing radiation-induced S and G2 checkpoints.
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Molecular mechanism of the Syk activation switch
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The role of leptin in the control of insulin-glucose axis
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Structural determinants in AUF1 required for high affinity binding to A + U-rich elements
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Crystal structure of human kynurenine aminotransferase II, a drug target for the treatment of schizophrenia
Crystal structure of human kynurenine aminotransferase II
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Biogenesis of the protein import channel Tom40 of the mitochondrial outer membrane: intermembrane space components are involved in an early stage of the assembly pathway
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Comparative analysis of human masculinity
Am. J. Physiol., Cell Physiol. 302:C943-65
Lysophosphatidic acid acyltransferase-alpha
1-acylglycerol-3-phosphate O- acyltransferase 1
1-acyl-sn-glycerol-3-phosphate acyltransferase alpha
Lysophosphatidic acid acyltransferase-beta
1-acylglycerol-3-phosphate O- acyltransferase 2
1-acyl-sn-glycerol-3-phosphate acyltransferase beta
1-acyl-sn-glycerol-3-phosphate acyltransferase epsilon
1-acylglycerol-3-phosphate O-acyltransferase 5
Lysophosphatidic acid acyltransferase-epsilon
1-acylglycerol-3-phosphate O-acyltransferase 8
Glycerol-3-phosphate dehydrogenase 1-like protein
Pancreatic islet GLUT2 glucose transporter mRNA and protein expression in humans with and without NIDDM
Glycerol-3-phosphate dehydrogenase (NAD+), cytoplasmic
DNA damage recognition during nucleotide excision repair in mammalian cells.
Elongation of very long chain fatty acids protein 5
Elongation of very long chain fatty acids protein 7
Elongation of very long chain fatty acids protein 2
Elongation of very long chain fatty acids protein 4
Elongation of very long chain fatty acids protein 1
acyl-CoA synthetase long-chain family member 5
Pentose phosphate pathway (hexose monophosphate shunt)
Acetyl-CoA acetyltransferase, mitochondrial
Hydroxymethylglutaryl-CoA synthase, mitochondrial precursor
3-hydroxy-3-methylglutaryl coenzyme A synthase
The arginine methyltransferase CARM1 regulates the coupling of transcription and mRNA processing
Human protoporphyrinogen oxidase: expression, purification, and characterization of the cloned enzyme
3-hydroxy-3-methylglutaryl-coenzyme A reductase-1
Interaction of J-protein co-chaperone Jac1 with Fe-S scaffold Isu is indispensable in vivo and conserved in evolution
Evidence that the coproporphyrinogen oxidase activity of rat liver is situated in the intermembrane space of mitochondria
solute carrier family 25 (carnitine/acylcarnitine translocase), member 20
AZD2171 shows potent antitumor activity against gastric cancer over-expressing fibroblast growth factor receptor 2/keratinocyte growth factor receptor
Inositol polyphosphate multikinase regulates inositol 1,4,5,6-tetrakisphosphate
Development of free-energy-based models for chaperonin containing TCP-1 mediated folding of actin
Antiatherogenic Potential of gamma Linolenic Acid
Recognition and association of DNA glycosylase with site containing an affected pyrimidine
1-acyl-sn-glycero-3-phosphoethanolamine [ChEBI:29017]
Transport of vitamins, nucleosides, and related molecules
The eicosanoids: cyclooxygenase, lipoxygenase, and epoxygenase pathways
Biochemistry of Lipids, Lipoproteins and Membranes, 5th Edition (Book): 331-362
acyl-CoA synthetase long-chain family member 1
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The intracellular interactions of the L1 family of cell adhesion molecules
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Mercury-sensitive residues and pore site in AQP3 water channel
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Syk protein-tyrosine kinase is regulated by tyrosine-phosphorylated Ig alpha/Ig beta immunoreceptor tyrosine activation motif binding and autophosphorylation
Human retinoic acid (RA) 4-hydroxylase (CYP26) is highly specific for all-trans-RA and can be induced through RA receptors in human breast and colon carcinoma cells
FUNCTION Involved in DNA double-strand break repair (DSBR). The rad50/mre11 complex possesses single-strand endonuclease activity and ATP-dependent double-strand-specific exonuclease activity. Rad50 provides ATP-dependent control of mre11 by unwinding and/or repositioning DNA ends into the mre11 active site.SUBUNIT Homodimer (By similarity). Forms a complex with MRE11.MISCELLANEOUS Present with 830 molecules/cell in log phase SD medium.SIMILARITY Belongs to the SMC family. RAD50 subfamily.SIMILARITY Contains 1 zinc-hook domain.
Efflux and compartmentalization of zinc by members of the SLC30 family of solute carriers
2-Amino-3-carboxymuconate semialdehyde [ChEBI:29044]
The sodium/glucose cotransport family SLC5
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The SLC36 family: proton-coupled transporters for the absorption of selected amino acids from extracellular and intracellular proteolysis
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(2R)-2-Hydroxy-3-(phosphonooxy)-propanal [ChEBI:29052]
The SLC39 family of metal ion transporters
Cloning and functional expression of the human GlcNAc-1-P transferase, the enzyme for the committed step of the dolichol cycle, by heterologous complementation in Saccharomyces cerevisiae
Reconstitution of 5'-directed human mismatch repair in a purified system
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Isocitrate dehydrogenase (NADP) cytoplasmic
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The human homologue of yeast ArgRIII protein is an inositol phosphate multikinase with predominantly nuclear localization
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Peroxisomal multifunctional enzyme type 2
hydroxysteroid (17-beta) dehydrogenase 4
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DOMAIN Its C-terminal part seems to contain many membrane-spanning sided beta-sheets, that have the potential to adopt a transmembrane beta-barrel type structure.SIMILARITY Belongs to the SAM50/omp85 family.
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Long-chain fatty acid transport protein 1
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Human IL4I1 is a secreted L-phenylalanine oxidase expressed by mature dendritic cells that inhibits T-lymphocyte proliferation
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PATHWAY Protein modification; protein glycosylation.MISCELLANEOUS Present with 3140 molecules/cell in log phase SD medium.SIMILARITY Belongs to the glycosyltransferase group 1 family. Glycosyltransferase 4 subfamily.
ChEBI:29089 1,2-diacyl-sn-glycerol 3-phosphate
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ATP activates transcription initiation from promoters by RNA polymerase II in a reversible step prior to RNA synthesis.
Farnesyl-diphosphate farnesyltransferase
Isopentenyl-diphosphate delta-isomerase 1
The Nod-like receptor (NLR) family: a tale of similarities and differences
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Synoviocyte innate immune responses: I. Differential regulation of interferon responses and the JNK pathway by MAPK kinases
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Human liver alcohol dehydrogenase: purification, composition, and catalytic features.
Genome-wide analysis of human HSF1 signaling reveals a transcriptional program linked to cellular adaptation and survival
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Differential recognition of preproteins by the purified cytosolic domains of the mitochondrial import receptors Tom20, Tom22, and Tom70
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Phosphorylation by p34cdc2 regulates spindle association of human Eg5, a kinesin-related motor essential for bipolar spindle formation in vivo
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Phosphorylation of carbovir enantiomers by cellular enzymes determines the stereoselectivity of antiviral activity
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Wnt/beta-catenin signaling: components, mechanisms, and diseases
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Elucidation of the function of type 1 human methionine aminopeptidase during cell cycle progression
Molecular cloning, sequence analysis, and expression of a human liver cDNA coding for fructose-6-P,2-kinase:fructose-2,6-bisphosphatase
Sulfation and sulfotransferases 1: Sulfotransferase molecular biology: cDNAs and genes
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Resistance to thromboembolism in PI3Kgamma-deficient mice
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BRF1 protein turnover and mRNA decay activity are regulated by protein kinase B at the same phosphorylation sites
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Expression and characterization of a human pyruvate carboxylase variant by retroviral gene transfer
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Cloning and expression of two human lysophosphatidic acid acyltransferase cDNAs that enhance cytokine-induced signaling responses in cells
Function and dysfunction of the PI system in membrane trafficking
Rat liver adenosine triphosphate:adenosine monophosphate phosphotransferase activity. II. Subcellular localization of adenylate kinase isozymes
Telomerase catalytic subunit homologs from fission yeast and human
Diversity of the pyruvate dehydrogenase kinase gene family in humans
Transcriptional activity of heat shock factor 1 at 37 degrees C is repressed through phosphorylation on two distinct serine residues by glycogen synthase kinase 3 and protein kinases Calpha and Czeta
The human gamma-glutamyltransferase gene family
Rapid destruction of human Cdc25A in response to DNA damage.
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Assembly of a complex containing Cdc45p, replication protein A, and Mcm2p at replication origins controlled by S-phase cyclin-dependent kinases and Cdc7p-Dbf4p kinase.
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ELOVL2 overexpression enhances triacylglycerol synthesis in 3T3-L1 and F442A cells
Review of epidermal growth factor receptor biology
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Cross-presentation of soluble exogenous antigens (endosomes)
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Isolation and characterization of an allelic cDNA for human muscle fructose-1,6-bisphosphatase
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Isolation and characterization of cDNAs corresponding to two human calcium, calmodulin-regulated, 3',5'-cyclic nucleotide phosphodiesterases
Characterization of human phosphoserine aminotransferase involved in the phosphorylated pathway of L-serine biosynthesis
Formation of the active cofactor, UDP-glucuronate
Protein kinase C beta controls nuclear factor kappaB activation in B cells through selective regulation of the IkappaB kinase alpha
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Platelet hyperaggregability: impaired responsiveness to nitric oxide ("platelet NO resistance") as a therapeutic target
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De novo sphingolipid biosynthesis: a necessary, but dangerous, pathway
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Mutations in NHLRC1 cause progressive myoclonus epilepsy
Telomeric protein distributions and remodeling through the cell cycle in Saccharomyces cerevisiae
The single minichromosome maintenance protein of Methanobacterium thermoautotrophicum DeltaH contains DNA helicase activity.
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Multidrug resistance-associated protein 1
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FAD1 flavin adenine dinucleotide synthetase homolog
Ectonucleotide pyrophosphatase/phosphodiesterase 1
Phosphopantothenoylcysteine decarboxylase
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Biochemistry of Lipids, Lipoproteins and Membranes, 5th Edition (Book): 213-244
Identification and characterization of eukaryotic initiation factor 5A-2
Biochemistry of soluble guanylate cyclase
phosphoribosyl pyrophosphate synthetase 1
Phosphoribosyl pyrophosphate synthetase I
Ribose-phosphate pyrophosphokinase I (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase I) (PPRibP) (PRS-I)
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6-phosphogluconate dehydrogenase, decarboxylating
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Conversion of Phosphatidylcholine to Phosphatidylglycerol with Phospholipase D and glycerol
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Phytanic acid alpha-oxidation, new insights into an old problem: a review
RNA Polymerase II Transcription Initiation
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Galactose-1-phosphate uridylyltransferase
Homologues of ((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)GYG2
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Clinical and molecular features of three patients with congenital disorders of glycosylation type Ih (CDG-Ih) (ALG8 deficiency)
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Functional and genetic studies demonstrate that mutation in the COX15 gene can cause Leigh syndrome
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Regulation of G(2)/M events by Cdc25A through phosphorylation-dependent modulation of its stability
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Madin-Darby canine kidney II cells: a pharmacologically validated system for NPC1L1-mediated cholesterol uptake
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Studies on the properties and tissue distribution of the isozymes of guanylate kinase in man
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6-Phosphogluconate dehydrogenase: the mechanism of action investigated by a comparison of the enzyme from different species
Enzymes of the SUMO modification pathway localize to filaments of the nuclear pore complex
The nature of the phagosomal membrane: endoplasmic reticulum versus plasmalemma
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Knockdown of hepatocyte aquaporin-8 by RNA interference induces defective bile canalicular water transport
Am J Physiol Gastrointest Liver Physiol 296:G93-100
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Aurora B controls the association of condensin I but not condensin II with mitotic chromosomes
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TAK1 is a ubiquitin-dependent kinase of MKK and IKK
Molecular basis for membrane phospholipid diversity: why are there so many lipids?
Highly potent inhibitors of methionine aminopeptidase-2 based on a 1,2,4-triazole pharmacophore
On the mechanism of sensing unfolded protein in the endoplasmic reticulum
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Phosphorylation of Mcm4 at specific sites by cyclin-dependent kinase leads to loss of Mcm4,6,7 helicase activity.
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The phosphate carrier has an ability to be sorted to either the TIM22 pathway or the TIM23 pathway for its import into yeast mitochondria
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Requirement of human renal water channel aquaporin-2 for vasopressin-dependent concentration of urine
Putative inorganic polyphosphate/ATP-NAD kinase
Nicotinamide mononucleotide adenylyltransferase 1
The Bcl-2 family: roles in cell survival and oncogenesis.
Nicotinamide mononucleotide adenylyltransferase 2
Nicotinamide mononucleotide adenylyltransferase 3
Assembly of the RAD51-ssDNA nucleoprotein complex
Role of immunoproteasomes in cross-presentation
Nicotinate-nucleotide pyrophosphorylase (carboxylating)
The RNA polymerase III transcription apparatus.
Structural and functional modules in RNA interference
Biotin--protein ligase ecNumber6.3.4.-/ecNumber
Studies on human erythrocyte inorganic pyrophosphatase.
8p12 stem cell myeloproliferative disorder: the FOP-fibroblast growth factor receptor 1 fusion protein of the t(6;8) translocation induces cell survival mediated by mitogen-activated protein kinase and phosphatidylinositol 3-kinase/Akt/mTOR pathways
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ArPIKfyve homomeric and heteromeric interactions scaffold PIKfyve and Sac3 in a complex to promote PIKfyve activity and functionality
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Ras superfamily and interacting proteins database
Human methionine synthase: cDNA cloning and identification of mutations in patients of the cblG complementation group of folate/cobalamin disorders
Defects in human methionine synthase in cblG patients
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NLR proteins: integral members of innate immunity and mediators of inflammatory diseases
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Antigen Presentation: Folding, assembly and peptide loading of class I MHC
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Identification and characterization of SMPD1 mutations causing Niemann-Pick types A and B in Spanish patients
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Type I phosphatidylinositol-4-phosphate 5-kinases synthesize the novel lipids phosphatidylinositol 3,5-bisphosphate and phosphatidylinositol 5-phosphate
Polo-like kinase-1 is activated by aurora A to promote checkpoint recovery
Leptin and the central nervous system control of glucose metabolism
Protein interactions with nitric oxide synthases: controlling the right time, the right place, and the right amount of nitric oxide
Cloning and characterization of SLC26A6, a novel member of the solute carrier 26 gene family
Histone H2A variants in nucleosomes and chromatin: more or less stable?
The biochemistry, metabolism and inherited defects of the pentose phosphate pathway: a review
Transcriptional networks controlling pancreatic development and beta cell function
Extracellular transsulfuration generates hydrogen sulfide from homocysteine and protects endothelium from redox stress
Am J Physiol Heart Circ Physiol 299:H1568-76
The Biotinidase Gene Variants Registry: A Paradigm Public Database
Cell cycle-dependent phosphorylation, nuclear localization, and activation of human condensin
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New roles for cysteine and transsulfuration enzymes: production of H2S, a neuromodulator and smooth muscle relaxant
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Role of AMP-activated protein kinase in the metabolic syndrome and in heart disease
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Active cyclin B1-Cdk1 first appears on centrosomes in prophase
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Molecular characterization of two galactosemia mutations: correlation of mutations with highly conserved domains in galactose-1-phosphate uridyl transferase
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Clinical, biochemical, and mutational spectrum of peroxisomal acyl-coenzyme A oxidase deficiency
Mutational analysis of 105 mucopolysaccharidosis type VI patients
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Molecular cloning and functional analysis of SUT-1, a sulfate transporter from human high endothelial venules
Di- and triphosphopyridine nucleotide isocitric dehydrogenases in yeast
Signal transduction via platelet-derived growth factor receptors
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Bleeding due to disruption of a cargo-specific ER-to-Golgi transport complex
Inflammasomes: guardians of cytosolic sanctity
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Adrenodoxin: structure, stability, and electron transfer properties
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Control of mRNA decay by heat shock-ubiquitin-proteasome pathway
Sterol dependent regulation of human TM7SF2 gene expression: role of the encoded 3beta-hydroxysterol Delta14-reductase in human cholesterol biosynthesis
(24R,25R)-3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestan-26-oyl-CoA [ChEBI:52050]
DAP10- and DAP12-associated receptors in innate immunity
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Function of Nod-like receptors in microbial recognition and host defense
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Isolation and characterization of human Nramp cDNA
Traffic control: regulation of kinesin motors
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SMG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay
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Novel mitochondrial intermembrane space proteins as substrates of the MIA import pathway
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N(epsilon)-(carboxymethyl)lysine adducts of proteins are ligands for receptor for advanced glycation end products that activate cell signaling pathways and modulate gene expression
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Comparison of the intracellular signaling responses by three chimeric fibroblast growth factor receptors in PC12 cells
Polymerase switching on the C-strand of the telomere
Identification of a cDNA encoding an isoform of human CTP synthetase
Characterization of a human and murine gene (CLCN3) sharing similarities to voltage-gated chloride channels and to a yeast integral membrane protein
Identification and characterization of a novel human sphingosine-1-phosphate phosphohydrolase, hSPP2
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Proteasome and peptidase function in MHC-class-I-mediated antigen presentation
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Tom20 and Tom22 share the common signal recognition pathway in mitochondrial protein import
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Determinants of anion-proton coupling in mammalian endosomal CLC proteins
Cdc25A localisation and shuttling: characterisation of sequences mediating nuclear export and import
Biochemical Pathways - An Atlas of Biochemistry and Molecular Biology
Lehninger - Principles of Biochemistry 4th Edn.
MISCELLANEOUS Present with 1470 molecules/cell in log phase SD medium.
Biochemistry - The Chemical Reactions of Living Cells 2nd Edn.
Assembly of AUF1 oligomers on U-rich RNA targets by sequential dimer association
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Hydrogen peroxide as a signaling molecule
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Identification and characterization of hPEM-2, a guanine nucleotide exchange factor specific for Cdc42
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Nucleotide receptor signaling in platelets
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Genetic alterations in the tyrosine kinase transcriptome of human cancer cell lines
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Structural and catalytic properties and homology modelling of the human nucleoside diphosphate kinase C, product of the DRnm23 gene
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High protonic potential actuates a mechanism of production of reactive oxygen species in mitochondria
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Reconstitution of proliferating cell nuclear antigen-dependent repair of apurinic/apyrimidinic sites with purified human proteins.
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Red cell pyruvate kinase deficiency: molecular and clinical aspects
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Hereditary orotic aciduria and other disorders of pyrimidine metabolism
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 2663-2704
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Reconstitution of the mia40-erv1 oxidative folding pathway for the small tim proteins
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G-strand Chromosome end with two additional single strand repeats - Telomeric
NNNNNNNNNNNTTAGGGTTATTAGGGTTATTAGGGTTA - 3' (in human)
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guanosine 5'-(3-(alpha-D-mannopyranosyl) dihydrogen diphosphate)
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G-strand Chromosome end with an additional single strand repeat - Telomeric
NNNNNNNNNNNTTAGGGTTATTAGGGTTA - 3' (in human)
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Cloning and expression of human deoxyhypusine synthase cDNA. Structure-function studies with the recombinant enzyme and mutant proteins.
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Characterization of SMG-9, an essential component of the nonsense-mediated mRNA decay SMG1C complex
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Discovery of an arachidonoyl coenzyme A synthetase in human platelets
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Oxidative protein folding in the mitochondrial intermembrane space
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Donation of catalytic residues to RNA polymerase active center by transcription factor Gre.
The structure of apo human glutamate dehydrogenase details subunit communication and allostery
Shelterin: the protein complex that shapes and safeguards human telomeres
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Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding
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Switching of origins to a post-replicative state
1,2-Diacyl-sn-glycerol 3-phospho-L-serine
Adhesion molecule L1 stimulates neuronal migration through Vav2-Pak1 signaling
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Class II MHC peptide loading by the professionals
Leptin therapy, insulin sensitivity, and glucose homeostasis
MPF localization is controlled by nuclear export
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Comprehensive proteomic analysis of the human spliceosome.
The ERBB4/HER4 intracellular domain 4ICD is a BH3-only protein promoting apoptosis of breast cancer cells
Insig-mediated degradation of HMG CoA reductase stimulated by lanosterol, an intermediate in the synthesis of cholesterol
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Zinc transporters and the cellular trafficking of zinc
Phosphoribosylpyrophosphate synthesis from glucose decreases during amino acid starvation of human lymphoblasts
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Mechanism of GTP hydrolysis by G-protein alpha subunits
The dual phosphatase activity of synaptojanin1 is required for both efficient synaptic vesicle endocytosis and reavailability at nerve terminals
Enzymic conversion of squalene 2,3-oxide to lanosterol and cholesterol
The role of heat shock transcription factor 1 in the genome-wide regulation of the mammalian heat shock response
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Regulation of pyruvate dehydrogenase (PDH) complex
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Cytosolic sulfonation of small molecules
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Translation of the phosphoinositide code by PI effectors
Intracellular signaling pathways in IgE-dependent mast cell activation
Arch. Immunol. Ther. Exp. (Warsz.) 54:393-401
2,4,6,8-Nonatetraenoic acid, 3,7-dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-, (all-E)-
3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexene-1-yl)-2,4,6,8-nonatetraenoic acid (ECL)
(all-E)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acid
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Uridine diphosphate glucose pyrophosphorylase. II
Cell death signalling via NRAGE, NRIF and NADE
Isolation of the human phosphomannomutase gene (PMM1) and assignment to chromosome 22q13
Human glutamate pyruvate transaminase (GPT): localization to 8q24.3, cDNA and genomic sequences, and polymorphic sites.
Adaptors and molecular scaffolds in immune cell signaling
Molecular analysis of human argininosuccinate lyase: mutant characterization and alternative splicing of the coding region
The ends of the affair: capping and polyadenylation.
Molecular cloning, expression, and characterization of human bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase and its functional domains
Purification and some properties of a monoacylglycerol-hydrolyzing enzyme of rat adipose tissue
Regulation of the interaction of Pak2 with Cdc42 via autophosphorylation of serine 141
Phosphorylation of Nephrin Triggers Ca2+ Signaling by Recruitment and Activation of Phospholipase C-{gamma}1
Reconstituted TOM core complex and Tim9/Tim10 complex of mitochondria are sufficient for translocation of the ADP/ATP carrier across membranes
Distinct missense mutations of the FGFR3 lys650 codon modulate receptor kinase activation and the severity of the skeletal dysplasia phenotype
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Identification of a novel human nicotinamide mononucleotide adenylyltransferase
Acidosis, acid-sensing ion channels, and neuronal cell death
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CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial
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CDP-diacylglycerol--inositol 3-phosphatidyltransferase
Lysophosphatidylinositol acyltransferase
Membrane-bound O-acyltransferase domain-containing protein 7
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Human ISD11 is essential for both iron-sulfur cluster assembly and maintenance of normal cellular iron homeostasis
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Diacylglycerol cholinephosphotransferase 1
Choline-phosphate cytidylyltransferase B
Choline-phosphate cytidylyltransferase A
Phosphatidylethanolamine N-methyltransferase
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De-regulated FGF receptors as therapeutic targets in cancer
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Putative glycerophosphocholine phosphodiesterase GPCPD1
Glycerophosphodiester phosphodiesterase 5
Phosphatidylserine decarboxylase proenzyme Chain B
Phosphatidylserine decarboxylase proenzyme Chain A
Pre-mRNA splicing: the discovery of a new spliceosome doubles the challenge.
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Choline/ethanolaminephosphotransferase 1
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Ethanolamine-phosphate cytidylyltransferase
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NifS-directed assembly of a transient [2Fe-2S] cluster within the NifU protein
Proc. Natl. Acad. Sci. U.S.A. 97:599-604
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Apoptosis-inducing factor (AIF): a ubiquitous mitochondrial oxidoreductase involved in apoptosis.
Minireview: implication of mitochondria in insulin secretion and action
Phospholipase C-gamma: diverse roles in receptor-mediated calcium signaling
Coordinate binding of ATP and origin DNA regulates the ATPase activity of the origin recognition complex.
Phospholipid hydroperoxide glutathione peroxidase, mitochondrial
Isolation and characterization of one soluble and two membrane-associated forms of phosphoinositide-specific phospholipase C from human platelets
1-phosphatidylinositol-3-phosphate 5-kinase
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ATF6 as a transcription activator of the endoplasmic reticulum stress element: thapsigargin stress-induced changes and synergistic interactions with NF-Y and YY1
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Sensing DNA damage through ATRIP recognition of RPA-ssDNA complexes
PHF8 targets histone methylation and RNA polymerase II to activate transcription
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Phosphatidylinositol 5-phosphate biosynthesis is linked to PIKfyve and is involved in osmotic response pathway in mammalian cells
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Cytoplasmic retention, DNA binding and processing of the NF-kappa B p50 precursor are controlled by a small region in its C-terminus
Biotinidase deficiency: the enzymatic defect in late-onset multiple carboxylase deficiency
Crystal structure of human recombinant ornithine aminotransferase.
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Critical pathways in cellular senescence and immortalization revealed by gene expression profiling
Krüppel-like transcription factor KLF5 is a key regulator of adipocyte differentiation
The ubiquitously expressed human CYP51 encodes lanosterol 14 alpha-demethylase, a cytochrome P450 whose expression is regulated by oxysterols
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Molecular mechanisms of ligand binding, signaling, and regulation within the superfamily of G-protein-coupled receptors: molecular modeling and mutagenesis approaches to receptor structure and function
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Ectonucleotide pyrophosphatase/phosphodiesterase family member 7
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The citric acid (TCA) cycle and respiratory electron transport
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Inositol phosphate synthesis and the nuclear processes they affect
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Basic Medical Biochemistry: A Clinical Approach, 2nd ed (Book): 527
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Type II chaperonins, prefoldin, and the tubulin-specific chaperones
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Conversion of palmitic acid to very long chain fatty acyl-CoAs
Synthesis of very long-chain fatty acyl-CoAs
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Biochemical properties of mammalian neutral sphingomyelinase 2 and its role in sphingolipid metabolism
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A unique signal transduction from FLT tyrosine kinase, a receptor for vascular endothelial growth factor VEGF
A current view of the mammalian aquaglyceroporins
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FVT-1 is a mammalian 3-ketodihydrosphingosine reductase with an active site that faces the cytosolic side of the endoplasmic reticulum membrane
Genetic Analysis of Coenzyme Q Biosynthesis
Coenzyme Q: Molecular Mechanisms in Health and Disease (Book): 185-208
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Diversity of the mammalian sodium/proton exchanger SLC9 gene family
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Plasma concentrations of phenyllactic acid in phenylketonuria
Glucose transporters (GLUT and SGLT): expanded families of sugar transport proteins
Despite substantial degradation, 2-arachidonoylglycerol is a potent full efficacy agonist mediating CB(1) receptor-dependent G-protein activation in rat cerebellar membranes
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Gefitinib-sensitizing EGFR mutations in lung cancer activate anti-apoptotic pathways
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Effects of alterations in the 3' flanking sequence on in vivo and in vitro expression of the yeast SUP4-o tRNATyr gene.
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A review of the pharmacokinetics of abacavir
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Mechanisms and physiological significance of the cholinergic control of pancreatic beta-cell function
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Human ADP-ribosylation factor-activated phosphatidylcholine-specific phospholipase D defines a new and highly conserved gene family
On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database
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The emerging shape of the ESCRT machinery
Secretory protein trafficking and organelle dynamics in living cells
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Segregation of MHC class II molecules from MHC class I molecules in the Golgi complex for transport to lysosomal compartments
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Facilitative Na+-independent glucose transporters
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The role of mitochondria in cellular iron-sulfur protein biogenesis and iron metabolism
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The mammalian HSF4 gene generates both an activator and a repressor of heat shock genes by alternative splicing
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TRF1 inhibits telomere C-strand DNA synthesis in vitro
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Trif-related adapter molecule is phosphorylated by PKC{epsilon} during Toll-like receptor 4 signaling
Presynaptic phase of homologous DNA pairing and strand exchange
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Human argininosuccinate lyase: a structural basis for intragenic complementation
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Interferon-gamma can stimulate post-proteasomal trimming of the N terminus of an antigenic peptide by inducing leucine aminopeptidase
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Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA (N6-adenosine)-methyltransferase.
HDAC6 regulates Hsp90 acetylation and chaperone-dependent activation of glucocorticoid receptor
The t(8;17)(p11;q23) in the 8p11 myeloproliferative syndrome fuses MYO18A to FGFR1
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Activation of heat shock gene transcription by heat shock factor 1 involves oligomerization, acquisition of DNA-binding activity, and nuclear localization and can occur in the absence of stress
3alpha,7alpha-Dihydroxy-5beta-cholestanoyl-CoA [ChEBI:1709]
Identification of arylsulfonamides as Aquaporin 4 inhibitors
Characterizing the specificity and cooperation of aminopeptidases in the cytosol and endoplasmic reticulum during MHC class I antigen presentation
Characterization of 5-oxo-L-prolinase in normal and tumor tissues of humans and rats: a potential new target for biochemical modulation of glutathione
gene ontology term for cellular function
Diseases caused by defects in the visual cycle: retinoids as potential therapeutic agents
Annu. Rev. Pharmacol. Toxicol. 47:469-512
Human Smp3p adds a fourth mannose to yeast and human glycosylphosphatidylinositol precursors in vivo
Primary structure and tissue-specific expression of human beta-hydroxyisobutyryl-coenzyme A hydrolase.
sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating
(S)-3-Hydroxy-3-methylglutaryl-CoA [ChEBI:15467]
Identification and characterization of mutations in patients with holocarboxylase synthetase deficiency
Human acetyl-CoA carboxylase 2. Molecular cloning, characterization, chromosomal mapping, and evidence for two isoforms.