Note: the coordinates are copied over from Homo sapiens.
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.
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation
Cloning and molecular analysis of the human citrate synthase gene
Structure of the Rho family GTP-binding protein Cdc42 in complex with the multifunctional regulator RhoGDI
Signal transduction pathways used by NLR-type innate immune receptors
A tandemly repeated sequence at the termini of the extrachromosomal ribosomal RNA genes in Tetrahymena
Eukaryotic peptide chain release factor subunit 1
Multicatalytic endopeptidase complex chain Z
Proteasome subunit beta type 7 precursor
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Constitutive activation of fibroblast growth factor receptor 3 by mutations responsible for the lethal skeletal dysplasia thanatophoric dysplasia type I
Enzyme-substrate intermediate formation at lysine 329 of human deoxyhypusine synthase
The molecular dissection of Fc gamma receptor mediated phagocytosis
Cloning and expression of a human ATP-citrate lyase cDNA
Sequence differences between human muscle and liver cDNAs for UDPglucose pyrophosphorylase and kinetic properties of the recombinant enzymes expressed in Escherichia coli.
Conformational transition associated with E1-E2 interaction in small ubiquitin-like modifications
Removal of DNA patch containing abasic residue
The SUMO-specific protease SENP5 is required for cell division
Crystal structure of the human monoacylglycerol lipase, a key actor in endocannabinoid signaling
Isolation and functional expression of human COQ2, a gene encoding a polyprenyl transferase involved in the synthesis of CoQ
2-Deoxy-D-ribose 1-phosphate [ChEBI:28542]
Comparison of messenger RNA distribution for 60 proteins in fat cells vs the nonfat cells of human omental adipose tissue
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
Cellular signalling mechanisms of neural cell adhesion molecules
Multidrug resistance- associated protein MGr1-Ag
The ARE-dependent mRNA-destabilizing activity of BRF1 is regulated by protein kinase B
Receptor-mediated endocytosis of cobalamin (vitamin B12)
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
The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere
D-2-hydroxyglutaric acidaemia: identification of a new enzyme, D-2-hydroxyglutarate dehydrogenase, localized in mitochondria
Formation of Processive Complex on the C-strand of the telomere
Paused RNA Polymerase III Transcription Complex (name copied from entity in Homo sapiens)
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
RFC binding displaces Pol Alpha on the C-strand of the telomere
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Activated PKC alpha (name copied from entity in Homo sapiens)
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Recruitment of Dna2 endonuclease to the C strand
VAV3 Rho/Rac effectors:GDP (name copied from entity in Homo sapiens)
Removal of remaining Flap from the C-strand
VAV3 Rho/Rac effectors:GTP (name copied from entity in Homo sapiens)
VAV2 Rho/Rac effectors:GDP (name copied from entity in Homo sapiens)
Formation of the Flap Intermediate on the C-strand
VAV2 Rho/Rac effectors:GTP (name copied from entity in Homo sapiens)
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Protein kinase C, novel isoforms:DAG (name copied from entity in Homo sapiens)
Joining of adjacent Okazaki fragments of the C-strand
VAV family:PIP3 (name copied from entity in Homo sapiens)
Conservation of the Caenorhabditis elegans timing gene clk-1 from yeast to human: a gene required for ubiquinone biosynthesis with potential implications for aging
VAV family:PIP2 (name copied from entity in Homo sapiens)
ADP is exchanged for ATP in the (ADP:CCT/TriC):tubulin complex
Disassociation of Processive Complex and Completed Telomere End
EIF5A + spermidine <=> EIF5A(Dhp) + 1,3-diaminopropane
Exchange of ADP for ATP in CCT/TriC:actin complex
Regulation of origin recognition complex conformation and ATPase activity: differential effects of single-stranded and double-stranded DNA binding.
EIF5A(Dhp) + 1,3-diaminopropane <=> EIF5A + spermidine
Mechanism of the eukaryotic chaperonin: protein folding in the chamber of secrets
D-Fructose 2,6-bisphosphate [ChEBI:28602]
Identification of two mammalian reductases involved in the two-carbon fatty acyl elongation cascade
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phosphatidylinositol + UDP-N-acetyl-D-glucosamine -> N-acetylglucosaminyl-PI + UDP
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Molecular cloning of a novel member of the eukaryotic polypeptide chain-releasing factors (eRF). Its identification as eRF3 interacting with eRF1.
N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate
glucosaminyl-PI + fatty acyl-CoA -> glucosaminyl-acyl-PI + CoA-SH
mannose(a1-4)glucosaminyl-acyl-PI + phosphatidylethanolamine -> (ethanolamineP) mannose(al1-4)glucosaminyl-acyl-PI + diacylglycerol
GlcNAc1P is dephosphorylated to UDP-N-acetyl-glucosamine
Acetylation of glucosamine 6-phosphate to GlcNAc6P
Formation of glucosamine 6-phosphate from fructose 6-phosphate and glutamine
Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
The ERBB4/HER4 receptor tyrosine kinase regulates gene expression by functioning as a STAT5A nuclear chaperone
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
(ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI + dolichol phosphate D-mannose -> mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI + dolichol phosphate
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Mannose-1-phosphate converted to GDP-Mannose
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Fructose 6-phosphate isomerizes to Mannose 6-phosphate
Mannose 6-phosphate isomerizes to Mannose 1-phosphate
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Addition of a third mannose to the N-glycan precursor by ALG2
Addition of a second mannose to the N-glycan precursor by ALG2
Flipping of the N-glycan precursor to inside the ER
Addition of a fourth and fifth mannose to the N-glycan precursor by ALG11
Addition of N-acetyl-D-glucosamine to Dolichyl phosphate
Addition of the first mannose to the N-glycan precursor by ALG13/14
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Addition of the second N-acetyl-glucosamine to the N-glycan precursor
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Addition of the sixth mannose to the N-glycan precursor by ALG3.
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Addition of the seventh mannose to the N-glycan precursor by ALG9, inside the ER lumen
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Association of the human SUMO-1 protease SENP2 with the nuclear pore
Addition of the eighth mannose to the N-glycan precursor by ALG12, inside the ER lumen
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Addition of a second glucose to the N-glycan precursor by ALG8
Addition of a third glucose to the N-glycan precursor by an ALG10 homologue
Addition of the last mannose to the N-glycan precursor by ALG3, inside the ER lumen.
Addition of the first glucose to the N-glycan precursor by ALG6
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
Trimming of the second mannose on the A branch
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Re-addition of a glucose on the alpha 1,3 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
MIA40:ERV1 (CHCHD4:GFER) Catalyzes Formation of Disulfide Bonds
MPP Cleaves Presequence of Inner Membrane Precursors
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TIMM23 PAM Imports Proteins to Mitochondrial Matrix
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MPP Cleaves Presequence of Matrix Precursors
ADP Binding by Phosphorylated IRE1 Homodimer
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Mutations in COX15 produce a defect in the mitochondrial heme biosynthetic pathway, causing early-onset fatal hypertrophic cardiomyopathy
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Transfer of SUMO3 from E1 to UBE2I (UBC9)
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GAP Recruitment to the Coatomer:Arf1-GTP Complex
Coatomer:Arf1-GTP:GAP lattice formation on golgi membrane
Sculpting and pinching-off of Golgi vessicle
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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)
REV1: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)
Pol eta:damaged DNA template complex (name copied from entity in Homo sapiens)
Pol eta:lesioned DNA template inserted with correct base complement (name copied from entity in Homo sapiens)
Pol zeta complex (name copied from entity in Homo sapiens)
Pol zeta:damaged DNA template complex (name copied from entity in Homo sapiens)
Aquaporins in the hepatobiliary tract. Which, where and what they do in health and disease
DNA containing a TDG-bound apurinic/apyrimidinic site (name copied from entity in Homo sapiens)
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RAD51:resected ends of DNA double-strand break (name copied from entity in Homo sapiens)
Ku70:Ku80 heterodimer (name copied from entity in Homo sapiens)
RAD52: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)
XPC:HR23B:damaged DNA complex (name copied from entity in Homo sapiens)
pre-incision complex in GG-NER (name copied from entity in Homo sapiens)
Ku:DNA double-strand break ends (name copied from entity in Homo sapiens)
XPC:HR23B complex (name copied from entity in Homo sapiens)
dimeric phospho-ATM complex (name copied from entity in Homo sapiens)
RAD50:MRE11 complex (name copied from entity in Homo sapiens)
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dimeric ATM kinase (name copied from entity in Homo sapiens)
RNA Polymerase II holoenzyme complex (hyperphosphorylated) (name copied from entity in Homo sapiens)
Active Pol II transcription complex with damaged DNA hybrid (name copied from entity in Homo sapiens)
Transcription-coupled (TC) repair complex (name copied from entity in Homo sapiens)
pre-incision complex with open DNA bubble (name copied from entity in Homo sapiens)
ERCC1:XPF complex (name copied from entity in Homo sapiens)
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incision complex for GG-NER (name copied from entity in Homo sapiens)
Incision complex with 3'-incised damaged DNA (name copied from entity in Homo sapiens)
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RPA heterotrimer (name copied from entity in Homo sapiens)
TFIIH (name copied from entity in Homo sapiens)
CAK (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
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RNA Polymerase II holoenzyme complex (hypophosphorylated):TFIIF complex (name copied from entity in Homo sapiens)
Structural relationships and the classification of aminoacyl-tRNA synthetases
TFIIF (name copied from entity in Homo sapiens)
RNA Pol II (hypophosphorylated):capped pre-mRNA complex (name copied from entity in Homo sapiens)
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Cap Binding Complex (CBC) (name copied from entity in Homo sapiens)
NELF complex (name copied from entity in Homo sapiens)
RNA Pol II (hypophosphorylated) complex bound to DSIF protein (name copied from entity in Homo sapiens)
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DSIF complex (name copied from entity in Homo sapiens)
DSIF:NELF:early elongation complex (name copied from entity in Homo sapiens)
Stalled Pol II in TC-NER (name copied from entity in Homo sapiens)
Active Pol II complex with repaired DNA template:mRNA hybrid (name copied from entity in Homo sapiens)
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pol II open pre-initiation complex (name copied from entity in Homo sapiens)
Enzymatic activities of the human AGPAT isoform 3 and isoform 5: localization of AGPAT5 to mitochondria
TFIIA (name copied from entity in Homo sapiens)
TFIID (name copied from entity in Homo sapiens)
RNA Polymerase II (unphosphorylated):TFIIF complex (name copied from entity in Homo sapiens)
TFIIE (name copied from entity in Homo sapiens)
pol II closed pre-initiation complex (name copied from entity in Homo sapiens)
RNA Polymerase II holoenzyme complex (unphosphorylated) (name copied from entity in Homo sapiens)
pol II promoter:TFIID:TFIIA:TFIIB complex (name copied from entity in Homo sapiens)
pol II promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF complex (name copied from entity in Homo sapiens)
pol II promoter:TFIID complex (name copied from entity in Homo sapiens)
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Pol II initiation complex (name copied from entity in Homo sapiens)
pol II promoter:TFIID:TFIIA:TFIIB:Pol II:TFIIF:TFIIE complex (name copied from entity in Homo sapiens)
pol II transcription complex containing 3 Nucleotide long transcript (name copied from entity in Homo sapiens)
pol II transcription complex (name copied from entity in Homo sapiens)
Pol II Initiation complex with phosphodiester-PPi intermediate (name copied from entity in Homo sapiens)
Wnt family proteins are secreted and associated with the cell surface
RNA Polymearse II:NTP:TFIIF complex (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 transcription complex containing 11 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 4 nucleotide long transcript (name copied from entity in Homo sapiens)
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Localization of MCM2-7, Cdc45, and GINS to the site of DNA unwinding during eukaryotic DNA replication
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Reverse transcriptase motifs in the catalytic subunit of telomerase
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CE:Pol II CTD:Spt5 complex (name copied from entity in Homo sapiens)
Identification, purification, and partial characterization of a novel Mr 28,000 integral membrane protein from erythrocytes and renal tubules
RNA Pol II with phosphorylated CTD: CE complex (name copied from entity in Homo sapiens)
RNA Polymerase II (phosphorylated):TFIIF:capped pre-mRNA (name copied from entity in Homo sapiens)
capped pre-mRNA:CBC:RNA Pol II (phosphorylated) complex (name copied from entity in Homo sapiens)
Pol II transcription complex with (ser5) phosphorylated CTD containing extruded transcript to +30 (name copied from entity in Homo sapiens)
RNA Polymerase II holoenzyme complex (phosphorylated) (name copied from entity in Homo sapiens)
RNA polymerase II (phosphorylated):TFIIF complex (name copied from entity in Homo sapiens)
Cell cycle-regulated trafficking of human telomerase to telomeres
Active RNA Polymerase I (name copied from entity in Homo sapiens)
RNA Polymerase I Holoenzyme (name copied from entity in Homo sapiens)
RNA Polymerase I Transcription Initiation complex (name copied from entity in Homo sapiens)
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HsRPC4:HsRPC5 (name copied from entity in Homo sapiens)
RNA Polymerase III Holoenzyme (name copied from entity in Homo sapiens)
Elongating RNA Polymerase III Transcription Complex (name copied from entity in Homo sapiens)
RNA Polymerase I promoter escape complex (name copied from entity in Homo sapiens)
SL1 (name copied from entity in Homo sapiens)
Acetylated SL1 (name copied from entity in Homo sapiens)
A novel PtdIns3P and PtdIns(3,5)P2 phosphatase with an inactivating variant in centronuclear myopathy
Phosphorylated UBF-1:rDNA promoter (name copied from entity in Homo sapiens)
Acetylayed SL1:PhosUBF-1:rDNA promoter (name copied from entity in Homo sapiens)
Structure/function studies of human beta-cell glucokinase. Enzymatic properties of a sequence polymorphism, mutations associated with diabetes, and other site-directed mutants.
HsRPC6:HsRPC3:HsRPC7 (name copied from entity in Homo sapiens)
HsRPC8:HsRPC9 (name copied from entity in Homo sapiens)
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Molecular basis of signaling specificity of insulin and IGF receptors: neglected corners and recent advances
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Biosynthesis of delta-aminolevulinic acid and the regulation of heme formation by immature erythroid cells in man
Many cuts to ruin: a comprehensive update of caspase substrates
Reviews in molecular biology and biotechnology: transmembrane signaling by G protein-coupled receptors
Glucose-sensing mechanisms in pancreatic beta-cells
Philos Trans R Soc Lond B Biol Sci 360:2211-25
Aggregation states of mitochondrial malate dehydrogenase
Purification, characterization, and cDNA cloning of an AU-rich element RNA-binding protein, AUF1
Targeting, import, and dimerization of a mammalian mitochondrial ATP binding cassette (ABC) transporter, ABCB10 (ABC-me)
26S proteasome non-ATPase regulatory subunit 7
26S proteasome non-ATPase regulatory subunit 11
26S proteasome non-ATPase regulatory subunit 12
Multicatalytic endopeptidase complex subunit C9
26S proteasome non-ATPase regulatory subunit 8
Multicatalytic endopeptidase complex subunit C8
Argonaute proteins: mediators of RNA silencing
Multicatalytic endopeptidase complex subunit C5
26S proteasome non-ATPase regulatory subunit 3
Deletion of steroid 5 alpha-reductase 2 gene in male pseudohermaphroditism
Multicatalytic endopeptidase complex iota chain
26S proteasome non-ATPase regulatory subunit 9
Heterogeneous nuclear ribonucleoprotein D0
In vivo disposal of phenylalanine in phenylketonuria: a study of two siblings
Tumor necrosis factor type 1 receptor associated protein 2
26S proteasome non-ATPase regulatory subunit 2
Multicatalytic endopeptidase complex subunit C3
Multicatalytic endopeptidase complex subunit C13
Proteasome subunit beta type 8 precursor
Regulation of actin dynamics for phagocytic cup formation
Multicatalytic endopeptidase complex delta chain
Proteasome subunit beta type 6 precursor
26S proteasome non-ATPase regulatory subunit 13
Multicatalytic endopeptidase complex subunit C7-I
Probable 26S protease regulatory subunit 8
Multicatalytic endopeptidase complex subunit MECl-1
Proteasome subunit beta type 10 precursor
Multicatalytic endopeptidase complex epsilon chain
Proteasome subunit beta type 5 precursor
hCTR1: a human gene for copper uptake identified by complementation in yeast
Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.
Multicatalytic endopeptidase complex beta chain
Proteasome subunit beta type 4 precursor
Multicatalytic endopeptidase complex subunit C2
26S proteasome non-ATPase regulatory subunit 10
26S proteasome non-ATPase regulatory subunit 1
26S proteasome non-ATPase regulatory subunit 4
Multicatalytic endopeptidase complex chain 7
Proteasome subunit beta type 9 precursor
Profiling of promoter occupancy by PPAR{alpha} in human hepatoma cells via ChIP-chip analysis
Multicatalytic endopeptidase complex zeta chain
MD-2: the Toll 'gatekeeper' in endotoxin signalling
Retinol dehydrogenase 8 ecNumber1.1.1.300/ecNumber
Short-chain dehydrogenase/reductase 3 ecNumber1.1.1.300/ecNumber
Cell division control protein 42 homolog
U6 snRNA-associated Sm-like protein LSm6
U6 snRNA-associated Sm-like protein LSm3
U6 snRNA-associated Sm-like protein LSm1
U6 snRNA-associated Sm-like protein LSm5
U6 snRNA-associated Sm-like protein LSm7
U6 snRNA-associated Sm-like protein LSm2
U6 snRNA-associated Sm-like protein LSm4
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
Inorganic pyrophosphatase 2, mitochondrial
Familial hyperlysinemias. Purification and characterization of the bifunctional aminoadipic semialdehyde synthase with lysine-ketoglutarate reductase and saccharopine dehydrogenase activities.
E2F-enabled inhibition of pre-replication complex formation
Saccharomyces cerevisiae Ybr004c and its human homologue are required for addition of the second mannose during glycosylphosphatidylinositol precursor assembly
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Neuroepithelial cell-transforming gene 1 protein
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Rho guanine nucleotide exchange factor 12
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Insulin signalling and the regulation of glucose and lipid metabolism
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ER-mediated phagocytosis: a new membrane for new functions
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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.
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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.
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Formation of the Early Elongation Complex
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The human LSm1-7 proteins colocalize with the mRNA-degrading enzymes Dcp1/2 and Xrnl in distinct cytoplasmic foci
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Homologous DNA pairing and strand exchange
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Euplotes telomerase: evidence for limited base-pairing during primer elongation and dGTP as an effector of translocation
Requirement of the DEAD-Box protein ded1p for messenger RNA translation.
malate dehydrogenase 2, NAD (mitochondrial)
Malate dehydrogenase, mitochondrial precursor
Aspartate aminotransferase, mitochondrial precursor
aspartate aminotransferase, mitochondrial, apoenzyme monomer
D-fructose-1,6-bisphosphate 1-phosphohydrolase
D-fructose-1,6- bisphosphate 1-phosphohydrolase
UTP-glucose-1-phosphate uridylyltransferase
Activation of DNA-binding activity in an apparently cytoplasmic precursor of the NF-kappa B transcription factor
RNA Polymerase II Transcription Initiation
glyceraldehyde-3-phosphate dehydrogenase, testis-specific, monomer
Pyruvate carboxylase, mitochondrial precursor
An integrated genomic analysis of human glioblastoma multiforme
Phosphoinositides in cell regulation and membrane dynamics
Glyceraldehyde 3-phosphate dehydrogenase, liver
glyceraldehyde-3-phosphate dehydrogenase monomer
glyceraldehyde 3-phosphate dehydrogenase, muscle
Isolation and characterization of the human pyruvate kinase M gene
1-acylglycerol-3-phosphate O-acyltransferase 8
Hydroxymethylglutaryl-CoA synthase, mitochondrial precursor
3-hydroxy-3-methylglutaryl coenzyme A synthase
Acetyl-CoA acetyltransferase, mitochondrial
Lysophosphatidic acid acyltransferase-beta
1-acylglycerol-3-phosphate O- acyltransferase 2
1-acyl-sn-glycerol-3-phosphate acyltransferase beta
The catalytic mechanism of guanine nucleotide exchange factor action and competitive inhibition by phosphorylated eukaryotic initiation factor 2.
Lysophosphatidic acid acyltransferase-alpha
1-acylglycerol-3-phosphate O- acyltransferase 1
1-acyl-sn-glycerol-3-phosphate acyltransferase alpha
Initial-rate kinetics of human NMN-adenylyltransferases: substrate and metal ion specificity, inhibition by products and multisubstrate analogues, and isozyme contributions to NAD+ biosynthesis
Human spermidine synthase gene: structure and chromosomal localization
Trk receptors: roles in neuronal signal transduction
Cloning and characterization of DPPL1 and DPPL2, representatives of a novel type of mammalian phosphatidate phosphatase
phosphoribosyl pyrophosphate synthetase 1
Phosphoribosyl pyrophosphate synthetase I
Ribose-phosphate pyrophosphokinase I (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase I) (PPRibP) (PRS-I)
6-phosphogluconate dehydrogenase, decarboxylating
Galactose-1-phosphate uridylyltransferase
Regulation of PKC-? function by phosphorylation in T cell receptor signaling
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
Crystal structure of human tryptophanyl-tRNA synthetase catalytic fragment: insights into substrate recognition, tRNA binding, and angiogenesis activity
Isopentenyl-diphosphate delta-isomerase 1
The porphobilinogen synthase catalyzed reaction mechanism
Production of phosphatidylinositol 5-phosphate by the phosphoinositide 3-phosphatase myotubularin in mammalian cells
Farnesyl-diphosphate farnesyltransferase
3-hydroxy-3-methylglutaryl-coenzyme A reductase-1
Nuclear transcription factor Y subunit gamma
Ral guanine nucleotide dissociation stimulator-like 1
FUNCTION Protein kinase that acts both on serines and on tyrosines. It acts as a dosage-dependent negative regulator of entry into mitosis (G2 to M transition). Phosphorylates and inhibits cdc2.CATALYTIC ACTIVITY ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate.ENZYME REGULATION Negatively regulated by phosphorylation in the M-phase.PTM Phosphorylated in the C-terminal by NIM1/CDR1.SIMILARITY Belongs to the protein kinase superfamily. Ser/Thr protein kinase family. WEE1 subfamily.SIMILARITY Contains 1 protein kinase domain.
Cellular transformation and guanine nucleotide exchange activity are catalyzed by a common domain on the dbl oncogene product
The product of the MLD gene is a member of the membrane fatty acid desaturase family: overexpression of MLD inhibits EGF receptor biosynthesis
Human cytidine deaminase: purification of enzyme, cloning, and expression of its complementary DNA
Retinoids for treatment of retinal diseases
Mechanisms, regulation and consequences of protein SUMOylation
CDK-mediated phosphorylation and removal of Cdc6
Tetrahymena telomerase catalyzes nucleolytic cleavage and nonprocessive elongation
Human adenylate kinase deficiency associated with hemolytic anemia. A single base substitution affecting solubility and catalytic activity of the cytosolic adenylate kinase.
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
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Purification and properties of phosphoribosyl pyrophosphate synthetase from rat liver
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A GDP dissociation inhibitor that serves as a GTPase inhibitor for the Ras-like protein CDC42Hs
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Beta-arrestin-mediated activation of MAPK by inverse agonists reveals distinct active conformations for G protein-coupled receptors
The characterization of a mammalian DNA structure-specific endonuclease.
Ribose-5-phosphate isomerase deficiency: new inborn error in the pentose phosphate pathway associated with a slowly progressive leukoencephalopathy
Identification of a human mitochondrial ABC transporter, the functional orthologue of yeast Atm1p
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
Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal
Vertebrates have conserved capping protein alpha isoforms with specific expression patterns
Current knowledge of the large RhoGAP family of proteins
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Anomalous megakaryocytopoiesis in mice with mutations in the c-Myb gene
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Purification and partial characterization of aldehyde dehydrogenase from human erythrocytes.
The unfolded protein response: a pathway that links insulin demand with beta-cell failure and diabetes
Porcupine-mediated lipidation is required for Wnt recognition by Wls
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A direct role for sterol regulatory element binding protein in activation of 3-hydroxy-3-methylglutaryl coenzyme A reductase gene
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Active Wnt proteins are secreted on exosomes
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DNA primase from KB cells. Characterization of a primase activity tightly associated with immunoaffinity-purified DNA polymerase-alpha.
DNA polymerase zeta: new insight into eukaryotic mutagenesis and mammalian embryonic development.
Isolation and partial characterization of SAA-an amyloid-related protein from human serum
Accurate cleavage and polyadenylation of exogenous RNA substrate.
Advanced glycosylation endproduct receptor signaling
Alcohol dehydrogenases, aldehyde dehydrogenases, and related enzymes
TAX-responsive enhancer element binding protein 107
Purification and properties of human cytosolic folylpoly-gamma-glutamate synthetase and organization, localization, and differential splicing of its gene
Cell surface heparin binding protein HIP
TIRAP/Mal, TRIF and TRAM. Differential utilization of these TIR
Toll-like receptor 3: a link between toll-like receptor, interferon and viruses
Regulation of the cyclin E gene by transcription factor E2F1
Identification of the human sphingolipid C4-hydroxylase, hDES2, and its up-regulation during keratinocyte differentiation
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
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)
Interaction of proliferating cell nuclear antigen with yeast DNA polymerase delta.
Heterotrimeric G protein activation by G-protein-coupled receptors
20 kDa nuclear cap binding protein (NCBP 20 kDa subunit) (CBP20) (NCBP interacting protein 1) (NIP1)
Epstein-Barr virus small RNA associated protein
Constitutive receptor activation by Crouzon syndrome mutations in fibroblast growth factor receptor (FGFR)2 and FGFR2/Neu chimeras
Platelets in thrombotic and non-thrombotic disorders.
Homologues of K48poluUb-phospho-PAK-2p34(Thr402)
Biochemistry of signal transduction and regulation
Coenzyme Q biosynthesis: Coq6 is required for the C5-hydroxylation reaction and substrate analogs rescue Coq6 deficiency
Opposing motor activities are required for the organization of the mammalian mitotic spindle pole
Human TLR9 confers responsiveness to bacterial DNA via species-specific CpG motif recognition
Enzymic properties of different types of human erythrocyte glucose-6-phosphate dehydrogenase, with characterization of two new genetic variants
Hemostasis and Thrombosis: Basic Principles and Clinical Practice
GABA synthesis, release, reuptake and degradation
Porcupine homolog is required for canonical Wnt signaling and gastrulation in mouse embryos
Execution of nonsense-mediated mRNA decay: what defines a substrate?
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Role of gastrin peptides in carcinogenesis
Purification of deoxyribonucleic acid polymerase delta from calf thymus: partial characterization of physical properties.
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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
From hematopoietic stem cells to platelets
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
Cloning, sequencing and expression of a cDNA encoding mammalian valyl-tRNA synthetase
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
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Regulation and dysregulation of aquaporins in water balance disorders
ChEBI:53020 (Glc)2 (GlcNAc)2 (Man)9 (PP-Dol)1
ChEBI:53019 (Glc)3 (GlcNAc)2 (Man)9 (PP-Dol)1
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Vitamin C: biosynthesis, recycling and degradation in mammals
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The structure of human mitochondrial branched-chain aminotransferase.
Acta Crystallogr D Biol Crystallogr 57:506-15
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Mutation in cystatin C gene causes hereditary brain haemorrhage
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The role of aminoacyl-tRNA synthetases in genetic diseases
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Oligomeric structure of the multifunctional protein CAD that initiates pyrimidine biosynthesis in mammalian cells
Purification and some properties of inorganic pyrophosphatase from human erythrocytes
Mechanism of elongation of primed DNA by DNA polymerase delta, proliferating cell nuclear antigen, and activator 1.
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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]
(GlcN)1 (Ino(acyl)-P)1 (Man)2 (EtN)1 (P)1
6-O-[alpha-D-mannosyl-(1->4)-alpha-D-glucosaminyl]-O-acyl-1-phosphatidyl-1D-myo-inositol [ChEBI:53056]
Receptor-to-effector signaling through G proteins: roles for beta gamma dimers as well as alpha subunits
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A DNA helicase activity is associated with an MCM4, -6, and -7 protein complex.
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 'G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.-)' are present. At the end of this reaction, 1 molecule of 'TDG 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 a thymine opposite to a guanine', and 1 molecule of 'G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.-)' are present. At the end of this reaction, 1 molecule of 'TDG glycosylase:thymine complex' is present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA N-glycosylase activity' of 'G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.-)'.
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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 'Double-strand DNA containing an adenine opposite to an 8-oxo guanine', and 1 molecule of 'MYH glycosylase' are present. At the end of this reaction, 1 molecule of 'MYH glycosylase:adenine complex' is present. This reaction takes place in the 'nucleus'.
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At the beginning of this reaction, 1 molecule of 'Double-strand DNA containing an ethenocytosine', and 1 molecule of 'G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.-)' are present. At the end of this reaction, 1 molecule of 'TDG glycosylase:ethenocytosine complex' is present. This reaction takes place in the 'nucleus'.
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.
Damaged purines are first cleaved by purine-specific glycosylases (see Lindahl and Wood 1999).
Functional properties of a Drosophila homolog of the E2F1 gene
At the beginning of this reaction, 1 molecule of 'MYH glycosylase:adenine complex' is present. At the end of this reaction, 1 molecule of 'DNA containing an MYH-bound apurinic/apyrimidinic site', and 1 molecule of '8-oxoguanine' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA N-glycosylase activity' of 'MYH glycosylase'.
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Regulation of Rheb GTPase activity by AMPK
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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.
Tyrosine kinase inhibitors of FGFR1 fusion mutants
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Enzymatic hydration of leukotriene A4. Purification and characterization of a novel epoxide hydrolase from human erythrocytes
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The mechanism of PAK activation. Autophosphorylation events in both regulatory and kinase domains control activity
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Sensing and repairing DNA double-strand breaks
Raf and akt mediate distinct aspects of sensory axon growth
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
Cancer-associated IDH1 mutations produce 2-hydroxyglutarate
Fine-tuning of GPCR activity by receptor-interacting proteins
E2F-dependent accumulation of hEmi1 regulates S phase entry by inhibiting APC(Cdh1)
G-strand Chromosome end with an additional single strand repeat - Telomeric
NNNNNNNNNNNTTAGGGTTATTAGGGTTA - 3' (in human)
G-strand Chromosome end with two additional single strand repeats - Telomeric
NNNNNNNNNNNTTAGGGTTATTAGGGTTATTAGGGTTA - 3' (in human)
Mutations and polymorphisms in the human argininosuccinate synthetase (ASS1) gene
(S)-2-Amino-3-(p-hydroxyphenyl)propionic acid
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.
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).
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).
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.
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).
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).
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.
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.
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).
(S)-alpha-amino-beta-(3-indolyl)-propionic acid
Regulation of Lipid Metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
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).
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).
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).
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).
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).
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.
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".
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).
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.
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.
(S)-alpha-amino-beta-phenylpropionic acid
Fcgamma receptors: old friends and new family members
In the second step in the formation of glutathione, gamma-glutamylcysteine ligates with glycine to form glutathione (Gali and Board, 1995; ).
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).
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).
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.
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.
RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription
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.
Dihydroxybenzoate is a typical substrate for Catechol O-methyltransferase
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.
Nuclear organization of DNA replication initiation proteins in mammalian cells.
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).
Homologous DNA pairing by human recombination factors Rad51 and Rad54
Crystal structure of human uroporphyrinogen decarboxylase
A highly conserved repetitive DNA sequence, (TTAGGG)n, present at the telomeres of human chromosomes
A Toll-like receptor recognizes bacterial DNA
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.
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.
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.
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.
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).
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 and Mitoferrin-2. (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.
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.
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).
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).
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.
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.
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 Mühlenhoff 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.
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).
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).
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.
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)
At the beginning of this reaction, 1 molecule of 'dsRNA duplex', and 1 molecule of 'ADAR2 homodimer' are present. At the end of this reaction, 1 molecule of 'Editosome (ADAR2) complex' is present. This reaction takes place in the 'nucleus'.
It is still unclear how ADAR 1 and ADAR 2 proteins form the editosomes with the target RNA. Other components of these editosomes for A to I editing are unknown.
At the beginning of this reaction, 1 molecule of 'dsRNA duplex', and 1 molecule of 'ADAR1 homodimer ' are present. At the end of this reaction, 1 molecule of 'Editosome (ADAR1) complex' is present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 2 molecules of 'ADAR2 protein' is present. At the end of this reaction, 1 molecule of 'ADAR2 homodimer' is present. This reaction takes place in the 'nucleus'.
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.
At the beginning of this reaction, 2 molecules of 'ADAR1 protein' is present. At the end of this reaction, 1 molecule of 'ADAR1 homodimer ' is present. This reaction takes place in the 'nucleus'.
The cap binding complex binds to the methylated GMP cap on the nascent mRNA transcript.
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'.
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
GMP capped mRNA transcript dissociates from GT for further modification.
Oncogenic signaling from the hematopoietic growth factor receptors c-Kit and Flt3
Cloning of a human cDNA for CTP-phosphoethanolamine cytidylyltransferase by complementation in vivo of a yeast mutant
At the beginning of this reaction, 1 molecule of 'Editosome (ADAR1) complex', and 1 molecule of 'H2O' are present. At the end of this reaction, 1 molecule of 'A to I edited RNA:Editosome (ADAR1) complex', and 1 molecule of 'NH3' are present. This reaction takes place in the 'nucleus' and is mediated by the 'double-stranded RNA adenosine deaminase activity' of 'ADAR1 homodimer '.
Hydrolytic deamination of adenosine leads to inosine. Ammonia is presumed to be released during this reaction.
At the beginning of this reaction, 1 molecule of 'H2O', and 1 molecule of 'Editosome (ADAR2) complex' are present. At the end of this reaction, 1 molecule of 'NH3', and 1 molecule of 'A to I edited RNA:Editosome (ADAR2) complex' are present. This reaction takes place in the 'nucleus' and is mediated by the 'double-stranded RNA adenosine deaminase activity' of 'ADAR2 homodimer'.
After transcription, some RNA molecules are altered to contain bases not encoded in the genome. Most often this involves the editing or modification of one base to another, but in some organisms can involve the insertion or deletion of a base. Such editing events alter the coding properties of mRNA. RNA editing can be generally defined as the co- or post transcriptional modification of the primary sequence of RNA from that encoded in the genome through nucleotide deletion, insertion, or base modification mechanisms. There are two pathways of RNA editing: the substitution/conversion pathway and the insertion/deletion pathway. The insertion/deletion editing occurs in protozoans like Trypanosoma, Leishmania; in slime molds like Physarum spp., and in some viral categories like paramyxoviruses, Ebola virus etc. To date, the substitution/conversion pathway has been observed in human along with other mammals, Drosophila, and some plants. The RNA editing processes are known to create diversity in proteins involved in various pathways like lipid transport, metabolism etc. and may act as potential targets for therapeutic intervention (Smith et al., 1997). The reaction mechanisms of cytidine and adenosine deaminases is represented below. In both these reactions, NH3 is presumed to be released:
In humans the deamination of adenosines to inosines is the most common editing event. It is particularly prevalent in the brain, where it leads to amino acid changes that affect the conductance of several ion channels. Inosines are recognized by the translation machinery as if they were guanosines. ADARs (Adenosine Deaminases Acting on RNA) modify pre-mRNA, acting as single peptides and recognize structural determinants in the RNA. To date 3 members of this deaminase family are known: ADAR 1, ADAR 2, and ADAR 3 that share a common modular domain structure. ADAR 1 and 2 contain a catalytic deaminase domain, a double-stranded RNA binding domain and exhibit RNA editing activity. ADAR1 activity is found in various mammalian tissues with the highest concentration in brain. An increasing number of mammalian genes have been found to undergo deamination by ADARs. Deamination by editing in pre-mRNAs encoding subunits of ionotropic glutamate receptors (GluRs) is another well studied example. An editing event at the Q/R site of the GluR2 (GluRB) subunit of AMPA ââ¬âreceptors converts a Gln codon CAG to an Arg codon CIG rendering the heteromeric receptor impermeable to Ca 2+ ions. Another example is the editing of 5-HT2C subtype serotonin receptor mRNA resulting in receptor isoforms with reduced G-protein coupling efficiency (reviewed by Gerber and Keller, 2001). In mice, the editosomes with ADAR proteins require some cis-acting elements like an intronic 'editing-site complementary sequence (ECS)'. Although evolutionarily conserved, the actual role of ECS is not yet elucidated in humans. The editing complex can be generally represented as:
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'.
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.
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'.
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.
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.
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.
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).
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.
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).
Processing of mRNA encompasses the capping of mRNA, processing of mRNAs with and without introns, and also modification of mRNA, as in mRNA editing.
Activator protein-1 (AP-1) is a collective term referring to a group of transcription factors that bind to promoters of target genes in a sequence-specific manner. AP-1 family consists of hetero- and homodimers of bZIP (basic region leucine zipper) proteins, mainly of Jun-Jun, Jun-Fos or Jun-ATF. AP-1 members are involved in the regulation of a number of cellular processes including cell growth, proliferation, survival, apoptosis, differentiation, cell migration. The ability of a single transcription factor to determine a cell fate critically depends on the relative abundance of AP-1 subunits, the composition of AP-1 dimers, the quality of stimulus, the cell type, the co-factor assembly. AP-1 activity is regulated on multiple levels; transcriptional, translational and post-translational control mechanisms contribute to the balanced production of AP-1 proteins and their functions. Briefly, regulation occurs through: effects on jun, fos, atf gene transcription and mRNA turnover. AP-1 protein members turnover. post-translational modifications of AP-1 proteins that modulate their transactivation potential (effect of protein kinases or phosphatases). interactions with other transcription factors that can either induce or interfere with AP-1 activity.
At the beginning of this reaction, 1 molecule of 'ATP', and 1 molecule of 'ATF-2' are present. At the end of this reaction, 1 molecule of 'ADP', and 1 molecule of 'ATF-2-P' are present. This reaction is mediated by the 'protein kinase activity' of 'MAPK1-P'.
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.
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.
GABA is converted to succinate semialdehyde by 4-aminobutyrate aminotransferase
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.
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.
GABA is metabolized to succinated by the serial action of two enzymes, 4-aminobutyrate aminotransferase and suucinate semialdehyde dehydrogenase.
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.
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).
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.
Clinical, biochemical and molecular genetic correlations in adenylosuccinate lyase deficiency
Dopamine in the cytosol is metabolized to 3-methoxytyramine by catecholamine o-methyltransferase (COMT), which uses s-adenosylmethionine as a methyl group donor.
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.
Dopamine once taken up by the dopamine transporter from the extracellular space into the cytosol is metabolized in a two step reaction to homovanillic acid.The first reaction is catalyzed by catecholamine o-methyl transferase and the subsequent reaction is catalyzed by monoamine oxidase A.
Phosphoproteomics reveals new ERK MAP kinase targets and links ERK to nucleoporin-mediated nuclear transport
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.
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.
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.
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.
5-hydroxyindole acetaldehyde is then catalyzed by aldehyde dehydrogenase to form 5-hydroxyindole acetic acid
The human gene SLC6A3 encodes the sodium-dependent dopamine transporter, DAT which mediates the re-uptake of dopamine from the synaptic cleft (Vandenbergh DJ et al, 2000). Dopamine can then be degraded by either COMT or monoamine oxidase.
Alternately dopamine is metabolized to homovanillic acid in a two-step reaction in which dopamine is first oxidized to 3,4-dihydroxypheylacetic acid (DOPAC) and then converted to homovanillic acid by catecholamine o-methyltransferase.
3,4-dihydroxyphenylacetic acid, generated after oxidation of dopamine by monoamineoxidase, is methylated by catecholamine o-methyltransferase to homovanillic acid.
Endoplasmic reticulum-mediated phagocytosis is a mechanism of entry into macrophages
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.
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.
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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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[Receptors for cholecystokinin and gastrin]
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Mutations in phosphoinositide metabolizing enzymes and human disease
Nuclear mitotic apparatus protein (NuMA): spindle association, nuclear targeting and differential subcellular localization of various NuMA isoforms
Fibroblast Growth Factor Receptor (FGFR) signaling
Regulation of gene expression in beta cells
Coordinating TLR-activated signaling pathways in cells of the immune system
Upf1 senses 3'UTR length to potentiate mRNA decay
Structure of human thymidylate synthase suggests advantages of chemotherapy with noncompetitive inhibitors
Transport of vitamins, nucleosides, and related molecules
Succinate dehydrogenase deficiency in human
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The human REV1 gene codes for a DNA template-dependent dCMP transferase.
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Regulation and mechanisms of mammalian double-strand break repair.
Stem cell factor and its receptor c-Kit as targets for inflammatory diseases
Enzymic synthesis and breakdown of a pyrimidine, orotic acid. I. Dihydro-orotic dehydrogenase
1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate
The biochemical and structural basis for trans-to-cis isomerization of retinoids in the chemistry of vision
Cold Spring Harb Perspect Biol 4:a007864
Transfer ribonucleic acid-induced hydrolysis of valyladenylate bound to isoleucyl ribonucleic acid synthetase
Purification and properties of isoleucyl ribonucleic acid synthetase from Escherichia coli
Signal transduction via the stem cell factor receptor/c-Kit
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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
ATM mediated phosphorylation of repair proteins
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Tau-crystallin/alpha-enolase: one gene encodes both an enzyme and a lens structural protein
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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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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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Human geranylgeranyl diphosphate synthase: isolation of the cDNA, chromosomal mapping and tissue expression
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guanosine 5'-(3-(alpha-D-mannopyranosyl) dihydrogen diphosphate)
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Human L-3-phosphoserine phosphatase: sequence, expression and evidence for a phosphoenzyme intermediate
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Recruitment of repair and signaling proteins to double-strand breaks
Functional expression and characterisation of a new human phosphatidylinositol 4-kinase PI4K230
Mutations in ATP2C1, encoding a calcium pump, cause Hailey-Hailey disease
PAK and other Rho-associated kinases--effectors with surprisingly diverse mechanisms of regulation
CHIP28 water channels are localized in constitutively water-permeable segments of the nephron
SRP-dependent cotranslational protein targeting to membrane
ATP bound to the origin recognition complex is important for preRC formation.
Neural recognition molecules of the immunoglobulin superfamily: signaling transducers of axon guidance and neuronal migration
Cloning and characterisation of hAps1 and hAps2, human diadenosine polyphosphate-metabolising Nudix hydrolases
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).
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).
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.
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.
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).
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.
Activation of ErbB4 by the bifunctional epidermal growth factor family hormone epiregulin is regulated by ErbB2
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.
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.
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).
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.
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.
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).
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).
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).
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)
Dephosphorylation of O-phospho-L-serine to L-serine proceeds through a phospho-enzyme intermediate of the catalysing phosphatase PSP (Collet et al. 1997).
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).
Serine biosynthesis starts from 3-phosphoglycerate, a glycolysis intermediate. Its dehydrogenation is catalysed by tetrameric phosphoglycerate dehydrogenase PHGDH. (Tabatabaie et al. 2009).
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).
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).
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).
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).
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). 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). Acetyl-CoA carboxylases 1 and 2 (ACACA and ACACB) bind 2 Mn2+ and 1 Btn per subunit (Colbert et al. 2010). They can exist as either monomers, homodimers or homotetramers (latter two not shown in this reaction) (Magnard et al. 2002, Moreau et al. 2006). Unlike the other carboxylases acted upon by HCLS, ACACA and B are located in the cytosol (shown here) as well as the mitochondrial membrane. The exact order in which this complex is constructed is unknown.
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.
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 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.
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).
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).
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).
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).
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).
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).
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).
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.
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).
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).
Selectivity of docking sites in MAPK kinases
ERK6, a mitogen-activated protein kinase involved in C2C12 myoblast differentiation
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).
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.
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).
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'.
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).
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).
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).
Regulators of neurite outgrowth: role of cell adhesion molecules
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).
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.
Folding of A+U-rich RNA elements modulates AUF1 binding. Potential roles in regulation of mRNA turnover
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)
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).
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.
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.
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).
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).
Cytosolic 4-trimethylaminobutyraldehyde dehydrogenase tetramer (ALDH9A1) catalyzes the reaction of NAD+', and 4-trimethylammoniobutanal to form 4-Trimethylammoniobutanoate and NADH + H+ (Kurys et al. 1989; Vaz et al. 2000).
The role of transient receptor potential cation channels in Ca2+ signaling
Cold Spring Harb Perspect Biol 2:a003962
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).
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.
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).
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).
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).
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).
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.
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).
Mechanisms for the role of tetrahydrobiopterin in endothelial function and vascular disease
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).
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).
beta-Nicotinamide adenine dinucleotide phosphate
Nicotinamide adenine dinucleotide phosphate
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.
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."
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).
Cytosolic pterin-4-alpha-carbinolamine dehydratase (PCDB1) catalyzes the reaction of 4a-hydroxytetrahydrobiopterin to form q-dihydrobiopterin and water (Hauer et al. 1993. The active enzyme is a homotetramer (Ficner et al. 1995); mutations in the PCDB1 gene are associated with mild hyperphenylalanemia in vivo (Citron et al. 1993).
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 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).
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Characterization of the COQ5 gene from Saccharomyces cerevisiae. Evidence for a C-methyltransferase in ubiquinone biosynthesis
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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)
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)
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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.
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)
Peroxisomal D-amino-acid oxidase catalyzes the reaction of glycine, water, and O2 to form glyoxylate, H2O2, and NH4+. The active form of the enzyme is a homodimer and has FAD as a cofactor (Kawazoe et al. 2006; Molla et al. 2006).
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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.
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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)
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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:
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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.
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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'.
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The Xenopus Xmus101 protein is required for the recruitment of Cdc45 to origins of DNA replication.
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).
The first step in the formation of glutathione is the ligation of glutamate with cysteine, catalyzed by the dimeric protein glutamate-cysteine ligase (Gipp et al, 1995; Misra and Griffith, 1998).
A cytosolic, non-specific peptidase can hydrolyze cysteinylglycine to release cysteine and glycine (Tuefel et al, 2003).
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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)
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).
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When SQR is in the oxidized state, it can bind hydrogen sulfide as persulfide to one of its own cysteine residue, the electrons being transferred to ubiquinone. After that the additional sulfur is dioxygenated by another enzyme (ETHE1). The activity of human SQR was deduced from the orthologue in Arenicola marina (Theissen et al. 2003, Hildebrandt & Grieshaber 2008).
The main reaction catalyzed by rhodanase is not the name-giving detoxification of cyanide to thiocyanate, but the transfer of a sulfur atom from SQR-S-SH onto sulfite yielding thiosulfate during sulfide oxidation. The activity of human rhodanase was inferred from the rat orthologue by Hildebrandt & Grieshaber, 2008.
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Import of palmitoyl-CoA into the mitochondrial matrix
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
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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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Maintaining copper homeostasis: regulation of copper-trafficking proteins in response to copper deficiency or overload
Electrostatics of aquaporin and aquaglyceroporin channels correlates with their transport selectivity
Deoxyhypusine hydroxylase is a Fe(II)-dependent, HEAT-repeat enzyme. Identification of amino acid residues critical for Fe(II) binding and catalysis [corrected].
Control of mRNA decay by phosphorylation of tristetraprolin
Kinetics and inhibition of recombinant human cystathionine gamma-lyase. Toward the rational control of transsulfuration
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Crystal structure of Spot 14, a modulator of fatty acid synthesis
Proc. Natl. Acad. Sci. U.S.A. 107:18820-5
Eukaryotic translation initiation factor 4B
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Structures and mechanisms of Nudix hydrolases
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Megakaryocyte development and platelet production
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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
Fc receptor-mediated phagocytosis requires CDC42 and Rac1
NMD: multitasking between mRNA surveillance and modulation of gene expression
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Rho guanine nucleotide exchange factor 4
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Primary structure of human deoxycytidylate deaminase and overexpression of its functional protein in Escherichia coli
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Rho guanine nucleotide exchange factor 3
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Active breakpoint cluster region-related protein
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Rho guanine nucleotide exchange factor 1
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Rho guanine nucleotide exchange factor 9
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T-lymphoma invasion and metastasis-inducing protein 2
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Evaluation of the "scanning model" for initiation of protein synthesis in eucaryotes.
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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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1,2-Dihydroxy-3-oxo-methylthiopentene (1-)
Chaperonins: The hunt for the Group II mechanism
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Molecular cloning of human Syk. A B cell protein-tyrosine kinase associated with the surface immunoglobulin M-B cell receptor complex
Immunodeficiency in protein kinase cbeta-deficient mice
(S)-alpha-Amino-1H-imidazole-4-propionic acid
Lysophospholipid acyltransferases: 1-acylglycerol-3-phosphate O-acyltransferases (AGPATs) From discovery to disease
G alpha 12 and G alpha 13 stimulate Rho-dependent stress fiber formation and focal adhesion assembly
4-(2-aminophenyl)-2,4-dioxobutanoic acid
Gap-filling DNA repair synthesis and ligation in GG-NER
cDNA cloning, genomic structure, chromosomal mapping, and functional expression of a novel human alanine aminotransferase
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Scriver CR, et al., editors) 1:1553-1587
Genetic analysis of chromosome pairing, recombination, and cell cycle control during first meiotic prophase in mammals
Assembly of the RAD50-MRE11-NBS1 complex at DNA double-strand breaks
Internalization of the epidermal growth factor receptor: role in signalling
2'-Deoxyinosine 5'-phosphate [ChEBI:28806]
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
3-phosphoinositide dependent protein kinase-1
RNA interference suggests a primary role for monoacylglycerol lipase in the degradation of the endocannabinoid 2-arachidonoylglycerol
cAMP-dependent protein kinase, alpha-catalytic subunit
cAMP-dependent protein kinase type II-beta regulatory chain
cAMP-dependent protein kinase type II-alpha regulatory chain
MHC class I endosomal and lysosomal trafficking coincides with exogenous antigen loading in dendritic cells
Epidermal growth factor receptor activation in glioblastoma through novel missense mutations in the extracellular domain
Structural insight into the inhibition of human kynurenine aminotransferase I/glutamine transaminase K
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
Homologues of p-T507,S645,S664-PRKCD(1-676)
A common mutation in the fibroblast growth factor receptor 1 gene in Pfeiffer syndrome
Prolactin and ErbB4/HER4 signaling interact via Janus kinase 2 to induce mammary epithelial cell gene expression differentiation
The amino acid sequence of cytosolic aspartate aminotransferase from human liver
The E3 ligase Aip4/Itch ubiquitinates and targets ErbB-4 for degradation
5'-Phosphoribosyl-5-aminoimidazole [ChEBI:28843]
Molecular identification of microsomal acyl-CoA:glycerol-3-phosphate acyltransferase, a key enzyme in de novo triacylglycerol synthesis
The human purH gene product, 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase
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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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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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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Common structure of soluble amyloid oligomers implies common mechanism of pathogenesis
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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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Thematic Review Series: Proteomics. An integrated omics analysis of eicosanoid biology
Quantitating protein synthesis, degradation, and endogenous antigen processing
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Bromodomain and PHD finger-containing protein 3
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Intracellular hyaluronan-binding protein 4
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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
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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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Vacuolar protein sorting-associated protein 45
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Glucose and cAMP regulate the L-type pyruvate kinase gene by phosphorylation/dephosphorylation of the carbohydrate response element binding protein
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.
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 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".
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.
The loading of proliferating cell nuclear antigen (PCNA) leads to recruitment of pol delta. Human PCNA is a homotrimer of 36 kDa subunits that form a toroidal structure. The loading of PCNA by RFC is a key event in the transition from the priming mode to the extension mode of DNA synthesis. The processive complex is composed of the pol delta holoenzyme and PCNA.
Replication factor C is proposed to dissociate from PCNA following sliding clamp formation, and the DNA toroid alone tethers pol delta to the DNA.
Polymerase switching is a key event that allows the processive synthesis of DNA by the pol delta and PCNA complex. Polymerase delta possesses polymerization and proofreading activities, which increases the overall fidelity of DNA replication. The pol delta holoenzyme is a heterotetrameric complex that contains p125, p66, p50, and p12 subunits, in human cells.
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.
Mitochondrial ATP-binding cassette proteins
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.
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1623-1650
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.
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'.
In this reaction, 1 molecule of 'ubiquitinated Orc1' is translocated from nucleoplasm to cytosol. This movement of the molecule occurs through the 'nuclear pore'.
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'.
As cells enter S phase, HsCdc6p is phosphorylated by CDK promoting its export from the nucleus (see Bell and Dutta 2002).
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 beginning of this reaction, 1 molecule of 'CDC6', and 1 molecule of 'ATP' are present. At the end of this reaction, 1 molecule of 'ADP', and 1 molecule of 'phosphorylated Cdc6' are present. This reaction takes place in the 'nucleus' and is mediated by the 'kinase activity' of 'CDK'.
AU binding proteins recruit the exosome to degrade ARE-containing mRNAs
Insights into the structure, mechanism, and regulation of scavenger mRNA decapping activity
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'.
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'.
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).
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.
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.
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.
Once the Mcm2-7 complex has been assembled onto the origin of replication, the next step is the assembly of Cdc45, an essential replication protein, in late G1. The assembly of Cdc45 onto origins of replication forms a complex distinct from the pre-replicative complex, sometimes called the pre-initiation complex. The assembly of Cdc45 onto origins correlates with the time of initiation. Like the Mcm2-7 proteins, Cdc45 binds specifically to origins in the G1 phase of the cell cycle and then to non-origin DNA during S phase and is therefore thought to travel with the replication fork. Indeed, S. cerevisiae Cdc45 is required for DNA replication elongation as well as replication initiation. Cdc45 is required for the association of alpha DNA polymerase:primase with chromatin. Based on this observation and the observation that in S. cerevisiae, cCdc45 has been found in large complexes with some components of Mcm2-7 complex, it has been suggested that Cdc45 plays a scaffolding role at the replication fork, coupling Pol-alpha:primase to the replication fork through the helicase. Association of Cdc45 with origin DNA is regulated in the cell cycle and its association is dependent on the activity of cyclin-dependent kinases but not the Cdc7/Dbf4 kinase. In Xenopus egg extracts, association of Cdc45 with chromatin is dependent on Xmus101. TopBP1, the human homolog of Xmus1, is essential for DNA replication and interacts with DNA polymerase epsilon, one of the polymerases involved in replicating the genome. TopBP1 homologs have been found in S. cerevisiae and S. pombe. Sld3, an additional protein required for Cdc45 association with chromatin in S. cerevisiae and S. pombe, has no known human homolog.
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.
After pre-RC assembly and Cdc45 association with the origin of replication, Replication Protein A (RPA) also associates with chromatin. RPA is a heterotrimeric complex containing p70, p34, and p11 subunits, and also is required for DNA recombination and DNA repair. The p70 subunit of RPA binds to the primase subunits of Pol alpha:primase. The p70 and p34 subunits of RPA are phosphorylated in a cell cycle-dependent manner. RPA is a single-strand DNA (ssDNA) binding protein and its association with chromatin at this stage suggests that DNA is partially unwound. This suggestion has been confirmed by detection of ssDNA in budding yeast origins of replication using chemical methods.
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.
MCM10 is required for human DNA replication. In S. cerevisiae, Mcm10, like Mcm2-7, is required for minichromosome maintenance, but Mcm10 has no sequence homology with these other proteins (Merchant et al., 1997). Genetic studies have demonstrated that Mcm10 is required for DNA replication in S. pombe (Aves et al., 1998) and S. cerevisiae cells (Homesley et al., 2000) and immunodepletion of XlMcm10 interferes with DNA replication in Xenopus egg extracts (Wohlschlegel et al., 2002). Human Mcm10 interacts with chromatin in G1 phase and then dissociates during G2 phase. In S. cerevisiae, Mcm10 has been shown to localize to origins during G1 (Ricke and Bielinsky, 2004), and it may stabilize the association of Mcm2-7 with the pre-replicative complex (Sawyer et al., 2004). This timing of association is consistent with studies that demonstrate that, in Xenopus egg extracts, Mcm10 is required for association of Cdc45, but not Mcm2-7 with chromatin. Biochemical evidence that Mcm10 plays a direct role in the activation of the pre-replicative complex includes the requirement for SpMcm10 in the phosphorylation of the Mcm2-7 complex by DDK (Lee et al., 2004) and the fact that SpMcm10 binds and stimulates DNA polymerase alpha activity (Fien et al., 2004).
At the end of this reaction, 1 molecule of 'Cdc6' is present.
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.
Exon-intron organization and chromosomal localization of the mouse monoglyceride lipase gene
In Saccharomyces cerevisiae, the entire ORC complex is constitutively bound to the origin of replication. However, in mammalian cells, Orc1, and possibly other Orc subunits, dissociate from origins of replication, while Orc2 remains stably associated with chromatin across the cell cycle. The first step in formation of the pre-RC is assembly of the hexameric Origin Recognition Complex (ORC) at the origin of replication. Recent work on human (Hs) ORC has suggested that the heterohexamer assembles in an ordered manner. HsOrc2 appears to be constitutively bound to origins of replication. HsOrc2 and HsOrc3 form a complex that interacts with HsOrc4 and HsOrc5. Recruitment of HsOrc5 into the complex is important for the association of HsOrc1. HsOrc6 is also capable of interacting with the core HsOrc2:3:4:5 complex, but not smaller complexes. Interestingly, HsOrc1 and a subunit of the Mcm2-7 complex (HsMcm2) interact with a histone acetyltransferase, HsHBO1 (Bell & Stillman 1992; Diffley et al. 1994; Lee & Bell 1997; Wenger et al. 1975; Li & DePamphili;s 2001; Dhar et al. 2001; Vashee et al, 2001; Iizuka & Stillman 1999 Burke et al. 2001).
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
At the beginning of this reaction, 1 molecule of 'Orc4:Orc5:Orc3:Orc2:origin', and 1 molecule of 'Orc1' are present. At the end of this reaction, 1 molecule of 'Orc1:Orc4:Orc5:Orc3:Orc2:origin' is present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'Orc4', and 1 molecule of 'Orc5:Orc3:Orc2:origin' are present. At the end of this reaction, 1 molecule of 'Orc4:Orc5:Orc3:Orc2:origin' is present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'Orc3:Orc2:origin', and 1 molecule of 'Orc5' are present. At the end of this reaction, 1 molecule of 'Orc5:Orc3:Orc2:origin' is present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'Orc2:origin', and 1 molecule of 'Orc3' are present. At the end of this reaction, 1 molecule of 'Orc3:Orc2:origin' is present. This reaction takes place in the 'nucleus'.
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.
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
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1-phosphatidyl-1D-myo-inositol 3,4-bisphosphates
Activity of TKI258 against primary cells and cell lines with FGFR1 fusion genes associated with the 8p11 myeloproliferative syndrome
Crystalline D-glyceraldehyde-3-phosphate dehydrogenase from rabbit muscle
The NLRP3 inflammasome: a sensor of immune danger signals
The prosthetic group of crystalline D-glyceraldehyde-3-phosphate dehydrogenase
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
Regulated release of L13a from the 60S ribosomal subunit as a mechanism of transcript-specific translational control
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
Presynaptic phase of homologous DNA pairing and strand exchange
LASS5 is a bona fide dihydroceramide synthase that selectively utilizes palmitoyl-CoA as acyl donor
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.
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.
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).
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).
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).
The human gene SLC35C1 encodes the GDP-fucose transporter FUCT1. It resides on the Golgi membrane and mediates the transport of UDP-fucose into the Golgi lumen. Defects in SLC35C1 causes the congenital disorder of glycosylation type 2C, also known as leukocyte adhesion deficiency type II (LAD2) (Lubke T et al, 2001).
Na+/Ca2+-K+ exchangers (NCKX): functional properties and physiological roles
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.
FUNCTION Serine/threonine-protein kinase which is required for checkpoint-mediated cell cycle arrest and activation of DNA repair in response to the presence of DNA damage or unreplicated DNA. May also negatively regulate cell cycle progression during unperturbed cell cycles. Binds to and phosphorylates CDC25. This leads to negative regulation of CDC25 and prevents mitotic entry.CATALYTIC ACTIVITY ATP + a protein = ADP + a phosphoprotein.SUBUNIT Interacts with rfp1.PTM Phosphorylated.SIMILARITY Belongs to the protein kinase superfamily. CAMK Ser/Thr protein kinase family. NIM1 subfamily.SIMILARITY Contains 1 protein kinase domain.
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).
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.
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.
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.
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.
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..
Calcium ions are used by cells as ubiquitous signalling molecules that control diverse physiological events. Three mammalian gene families control Ca2+ transport across plasma membranes and intracellular compartments (Lytton J, 2007). They are the Na+/Ca2+ exchanger family designated NCX (SLC8) (three members NCX1-3) (Quednau BD et al, 2004), the Na+/Ca2+-K+ exchanger family designated NCKX (SLC24) (five members NCKX1-5) (Schnetkamp PP, 2004) and a Ca2+/cation exchanger (NCKX6, NCLX) whose physiological function remains unclear.
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.
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.
Molecular mechanisms regulating hormone-sensitive lipase and lipolysis
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 Clâ-dependent transport of basic anions [e.g. HCO3â, (CO3)2â] 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 Clâ ion electroneutral symporters (Hebert SC et al, 2004); SLC26 is the trans-epithelial multifunctional anion (e.g. sulfate, oxalate, HCO3â, Clâ) 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)2â 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)â 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 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).
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 prototypical transporters of the SLC15 gene family are PEPT1 and PEPT2, which mediate the uptake of every possible di- and tri-peptide. PEPT1 (PTR1) is expressed mainly in the intestine (Liang R et al, 1995; Saito H et al, 1997) while PEPT2 (PTR2) is expressed in the kidney (Liu W et al, 1995).
A bioinformatics approach identified two further human transporters, PHT1 and PHT2 (Botka CW et al, 2000). These two transporters may be located on the lysosomal membrane for the proton-coupled export of histidine and di-peptides from lysosomal protein degradation.
The human SLC15 gene family encode four proton-coupled oligopeptide transporters; PEPT1 (SLC15A1), PEPT2 (SLC15A2), PHT2 (SLC15A3) and PHT1 (SLC15A4). These cotransporters are part of the Proton-coupled Oligopeptide Transporter (POT) superfamily (also called Peptide Transporter (PTR) family) (Daniel H and Kottra G, 2004).
Cytoplasmic chaperonin containing TCP-1: structural and functional characterization
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 proteins1â14, 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 1â10, 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 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.
The human gene SLC30A7 encodes the zinc transporter ZnT7. It is thought to be present in the small intestine and lung in humans (Kirschke CP and Huang L, 2003). Functional properties assigned to ZnT7 are based on studies conducted with mouse experiments.
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 SLC35A1 encodes the CMP-sialic acid transporter which mediates the antiport of CMP-sialic acid into the Golgi lumen in exchange for CMP (Ishida N et al, 1996). Defects in SLC35A1 are the cause of congenital disorder of glycosylation type 2F (CDG2F). CDGs are a family of severe inherited diseases caused by a defect in protein N-glycosylation (Martinez-Duncker I et al, 2005).
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.
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).
Copper (Cu2+) is essential for many important biological processes such as mitochondrial oxidative phosphorylation, detoxification of free radicals, iron metabolism and neurotransmiter synthesis. Too much influx results in cell poisoning. In humans, there are two member of the SLC31 gene family that are implicated in copper transport. The human gene SLC31A1 encodes human copper transporter 1, hCTR1 and is ubiquitiously expressed, with highest levels seen in the liver.. It was first identified by functional complementation in ctr1-deficient yeast (Zhou B and Gitschier J, 1997). hCTR1 exists as a homotrimer at the plasma membrane of cells (De Feo CJ et al, 2007) and is responsible for high-affinity copper uptake (Lee J et al, 2002). The second gene product, hCTR2, has not be characterized yet.
AMP-activated/SNF1 protein kinases: conserved guardians of cellular energy
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).
After RFC initiates the assembly of the primer recognition complex, the complex of pol delta and PCNA is responsible for incorporating the additional nucleotides prior to the position of the next downstream initiator RNA primer. On the lagging strand, short discontinuous segments of DNA, called Okazaki fragments, are synthesized on RNA primers. The average length of the Okazaki fragments is 100 nucleotides. Polymerase switching is a key event that allows the processive synthesis of DNA by the pol delta and PCNA complex.
When the polymerase delta:PCNA complex reaches a downstream Okazaki fragment, strand displacement synthesis occurs. The primer containing 5'-terminus of the downstream Okazaki fragment is folded into a single-stranded flap.
After RPA binds the long flap, it recruits the Dna2 endonuclease. Dna2 endonuclease removes most of the flap, but the job of complete removal of the flap is then completed by FEN-1.
The remaining flap, which is too short to support RPA binding, is then processed by FEN-1. There is evidence that binding of RPA to the displaced end of the RNA-containing Okazaki fragment prevents FEN-1 from accessing the substrate. FEN-1 is a structure-specific endonuclease that cleaves near the base of the flap at a position one nucleotide into the annealed region. Biochemical studies have shown that the preferred substrate for FEN-1 consists of a one-nucleotide 3'-tail on the upstream primer in addition to the 5'-flap of the downstream primer.
Two endonucleases, Dna2 and flap endonuclease 1 (FEN-1), are responsible for resolving the nascent flap structure (Tsurimoto and Stillman 1991). The Dna2 endonuclease/helicase in yeast is a monomer of approximately 172 kDa. Human FEN-1 is a single polypeptide of approximately 42 kDa. Replication Protein A regulates the switching of endonucleases during the removal of the displaced flap.
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 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.
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.
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 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.
All three IkappaB isoforms and most Rel family members are stably associated with the IkappaB kinase 1/2 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.
DNA replication is regulated at various levels via ORC proteins. This pathway includes annotation of individual events that lead to the regulation of replication.
The eukaryotic six-subunit origin recognition complex (ORC) governs the initiation site of DNA replication and formation of the prereplication complex.
The human gene ABCB6 encodes a mitochondrial half-type ATP-binding cassette (ABC) protein MTABC3 which is uniquely located on the outer mitochondrial membrane and is functional as a homodimer (Krishnamurthy et al. 2006). It plays a crucial role in heme synthesis by mediating porphyrin uptake into mitochondria (Mitsuhashi et al. 2000, Krishnamurthy et al. 2006).
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).
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).
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.
SLC24A6 (NCKX6, NCLX) (Palty R et al, 2004) encodes a protein which can transport Li+ or Na+ in exchange for Ca2+ in an K+-independent manner (Cai X and Lytton J, 2004). Lithium exchange with calcium is shown here.
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).
Human pyridoxal kinase: overexpression and properties of the recombinant enzyme
1-acyl-sn-glycero-3-phospho-D-myo-inositol [ChEBI:28914]
Roles of glial p75NTR in axonal regeneration
N (epsilon)-(carboxymethyl)lysine protein adduct is a major immunological epitope in proteins modified with advanced glycation end products of the Maillard reaction
An updated overview on Wnt signaling pathways: a prelude for more
2-acyl-sn-glycero-3-phosphoethanolamine [ChEBI:28936]
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Destabilization of mRNA by Tristetraprolin (TTP)
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Structure of the human sulfhydryl oxidase augmenter of liver regeneration and characterization of a human mutation causing an autosomal recessive myopathy
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The 2.0 A structure of human ferrochelatase, the terminal enzyme of heme biosynthesis.
1-chloro-2,4-dinitrobenzene [ChEBI:34718]
Neurotrophins and their receptors: a convergence point for many signalling pathways
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L1 and NCAM adhesion molecules as signaling coreceptors in neuronal migration and process outgrowth
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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-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).
4,4-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).
4,4-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),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.
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).
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).
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.
In the second step, FDFT catalyzes the reduction of presqualene diphosphate to squalene (Pandit et al. 2000).
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).
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).
Regulation of telomerase by telomeric proteins
A structural model for the membrane-integral domain of succinate: quinone
Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways
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).
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.
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)
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).
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.
Mevalonate pyrophosphate decarboxylase (MPD) decarboxylates mevalonate-5-pyrophosphate into isopentenyl pyrophosphate while hydrolysing ATP to ADP and orthophosphate.
A critical review of the origin and control of adrenal androgens
Baillieres Clin Obstet Gynaecol 11:229-48
Mevalonate kinase (MK) catalyzes the phosphorylation of mevalonate to mevalonate-5-phosphate.
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).
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).
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).
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.
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 TIAM2 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.
The RGL1 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.
The HMGCS2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The molecular mechanics of eukaryotic translation
The HMGCS1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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).
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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 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).
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).
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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).
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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.
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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.
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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 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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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).
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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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).
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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).
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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, 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).
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Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform
WD repeat domain phosphoinositide-interacting protein 1
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).
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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).
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Iron-sulfur proteins in health and disease
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).
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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).
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).
Sentrin-specific protease 1 ecNumber3.4.22.68/ecNumber
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).
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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).
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Sentrin-specific protease 2 ecNumber3.4.22.68/ecNumber
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, 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, 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, phosphatidylethanolamine N-methyltransferase (PEMT) methylates phosphatidylethanolamine (PE) and produces phosphatidylcholine (PC) (Vance & Ridgway 1998, Shields et al. 2001, Guan et al. 1999).
The conversion of testosterone to the most potent androgen, 5-alpha-dihydrotestosterone (DHT), is catalyzed by the microsomal 5alpha-steroid reductase enzymes, of which there are three reported types in humans to date (SRD5A1-3) (Andersson S and Russell DW, 1990; Andersson S et al, 1991; Uemura M et al, 2008 respectively). These enzymes are expressed in the prostate and other androgen target sites. Defects in SRD5A2 are the cause of pseudovaginal perineoscrotal hypospadias, also known as male pseudohermaphroditism (Anwar R et al, 1997). 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).
Androgens are the determining factors for male development and behaviour in vertebrates (Miller 2002).
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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).
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).
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.
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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).
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Phosphorylation regulates the assembly of NuMA in a mammalian mitotic extract
Expression of HSD17B1 which is the main enzyme that catalyzes the hydrogenation of estrone is strongly restricted to placenta, ovaries, endometrium and breast tissue (Moeller and Adamski, 2009).
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In female vertebrates, estrogens control reproductive system development and reproductive functions (Payne AH and Hales DB, 2004).
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The human ATP-binding cassette (ABC) transporter superfamily
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).
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).
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).
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).
Isozymes of glyceraldehyde-3-phosphate dehydrogenase in man and other mammals.
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).
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).
Adaptor protein complex 2 (AP-2) large adaptins
The FDPS gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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Plasma membrane adapto AP-2 17 kDa protein
Adaptor protein complex AP-2 subunit sigma
The SC5D gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The SQLE gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The TM7SF2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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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).
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The control of glycogen metabolism in the liver
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AU-rich element-mediated translational control: complexity and multiple activities of trans-activating factors
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.
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.
Mitochondrial intermembrane space import and assembly protein 40
Mitochondrial import inner membrane translocase subunit Tim9
Mitochondrial import inner membrane translocase subunit Tim17-B
Mitochondrial import inner membrane translocase subunit Tim17-A
Mitochondrial import inner membrane translocase subunit TIM50
Mitochondrial import inner membrane translocase subunit Tim23
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Tumor necrosis factor-alpha-converting enzyme is required for cleavage of erbB4/HER4
Mitochondrial import inner membrane translocase subunit Tim8 A
Mitochondrial import inner membrane translocase subunit Tim8 B
Mitochondrial-processing peptidase subunit beta
Mitochondrial import inner membrane translocase subunit TIM16
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1777-1805
Disorders of tetrahydrobiopterin and related biogenic amines
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1725-1776
Precursors Imported to the Matrix by TIMM23 PAM
Mitochondrial-processing peptidase subunit alpha
1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole [ChEBI:18319]
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Mitochondrial import inner membrane translocase subunit TIM44
60 kDa heat shock protein, mitochondrial
Iron-sulfur cluster co-chaperone protein HscB, mitochondrial
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 2125-2163
Proteins Imported to the Matrix by TIMM23 PAM
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The ABCs of solute carriers: physiological, pathological and therapeutic implications of human membrane transport proteinsIntroduction
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pyruvate kinase M1 complex (name copied from entity in Homo sapiens)
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phosphoglycerate kinase 1 complex (name copied from entity in Homo sapiens)
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enolase 1 dimer, (alpha) (name copied from entity in Homo sapiens)
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glyceraldehyde-3-phosphate dehydrogenase tetramer (name copied from entity in Homo sapiens)
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glyceraldehyde-3-phosphate dehydrogenase, testis-specific, tetramer (name copied from entity in Homo sapiens)
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triosephosphate isomerase dimer (name copied from entity in Homo sapiens)
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glyceraldehyde-3-phosphate dehydrogenase tetramer
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1965-1970
pyruvate kinase complex, liver and RBC (name copied from entity in Homo sapiens)
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pyruvate carboxylase holoenzyme (name copied from entity in Homo sapiens)
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
Probable ATP-dependent RNA helicase DDX11
Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
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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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Targeting the phosphoinositide 3-kinase pathway in cancer
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.
SLC25A1, in the inner mitochondrial membrane, mediates the exchange of mitochondrial citrate for cytosolic malate.
1-phosphatidyl-1D-myo-inositol 4-phosphate
While fatty acid synthesis from acetyl CoA proceeds in the cytosol, most acetyl CoA in the cell is generated within the mitochondria, by oxidative decarboxylation of the pyruvate derived from glycolysis, as well as from a number of reactions of amino acid catabolism. Mitochondrial Acetyl-CoA is transported to cytoplasm as citrate to participate in fatty acid biosynthesis. Mitochondrial citrate synthase, a tricarboxylic acid transporter in the inner mitochondrial membrane, and cytosolic citrate lyase are involved in this transport.
N,N'-Diacetylchitobiosyldiphosphodolichol [ChEBI:7069]
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.
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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).
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5-phosphoribosylglycinamide [ChEBI:18349]
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).
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).
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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).
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1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate
ChEBI:18348 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate
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.
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Diphosphoinositol polyphosphate phosphohydrolases (DIPP), also known as nucleoside diphosphate-linked moiety X motif (NUDT) proteins, dephosphorylate inositol bisdiphospho-tetrakisphosphate ((PP)2-IP4) to inositol 5-diphospho-1,2,3,4,6-pentakisphosphate (5-PP-IP5). The NUDT proteins involved are: nucleoside diphosphate-linked moiety X motif 3 (NUDT3), 4 (NUDT4), 10 (NUDT10), and 11 (NUDT11). The reactants consumed are: inositol 1,5-bisdiphospho-2,3,4,6-tetrakisphosphate (1,5-(PP)2-IP4) and inositol 3,5-bisdiphospho-1,2,4,6-tetrakisphosphate (3,5-(PP)2-IP4). The following lists the above proteins with their corresponding literature references: NUDT3 (Safrany et al. 1999, Safrany et al. 1998, Yang et al. 1999, Caffrey et al. 2000), NUDT4 (Caffrey et al. 2000), NUDT10 (Leslie et al. 2002, Hidaka et al. 2002) and NUDT11 (Leslie et al. 2002, Hidaka 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 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).
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.
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).
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.
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 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).
Diphosphoinositol polyphosphate phosphohydrolases (DIPP), also known as nucleoside diphosphate-linked moiety X motif (NUDT) proteins, dephosphorylate inositol bisdiphospho-tetrakisphosphate ((PP)2-IP4) to inositol diphospho-pentakisphosphate (PP-IP5). The NUDT proteins involved are: nucleoside diphosphate-linked moiety X motif 3 (NUDT3), 4 (NUDT4), 10 (NUDT10), and 11 (NUDT11). The reactants consumed are: inositol 1,5-bisdiphospho-2,3,4,6-tetrakisphosphate (1,5-(PP)2-IP4) and inositol 3,5-bisdiphospho-1,2,4,6-tetrakisphosphate (3,5-(PP)2-IP4). The products made are: inositol 1-diphospho-2,3,4,5,6-pentakisphosphate (1-PP-IP5) and 3-diphospho-1,2,4,5,6-pentakisphosphate (3-PP-IP5). The following lists the above proteins with their corresponding literature references: NUDT3 (Safrany et al. 1999, Safrany et al. 1998, Yang et al. 1999, Caffrey et al. 2000), NUDT4 (Caffrey et al. 2000), NUDT10 (Leslie et al. 2002, Hidaka et al. 2002) and NUDT11 (Leslie et al. 2002, Hidaka et al. 2002).
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).
A novel skeletal dysplasia with developmental delay and acanthosis nigricans is caused by a Lys650Met mutation in the fibroblast growth factor receptor 3 gene
1-phosphatidyl-1D-myo-inositol 4-phosphates
Stable association of mitotic cyclin B/Cdc2 to replication origins prevents endoreduplication.
1-phosphatidyl-1D-myo-inositol 5-phosphate
Molecular enzymology of carnitine transfer and transport
1-phosphatidyl-1D-myo-inositol 3-phosphate
1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate
Mitochondrial import inner membrane translocase subunit Tim13
Mitochondrial import inner membrane translocase subunit Tim10
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
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1909-1963
The expanding role of mitochondria in apoptosis.
PIKFYVE:VAC14:FIG4 (name copied from entity in Homo sapiens)
LTA4H:Zn2+ (name copied from entity in Homo sapiens)
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beta-D-Mannosyldiacetylchitobiosyldiphosphodolichol [ChEBI:10408]
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SPTLC1:SPTLC2 (name copied from entity in Homo sapiens)
Human lysyl-tRNA synthetase accepts nucleotide 73 variants and rescues Escherichia coli double-defective mutant
SPTLC1:SPTLC3 (name copied from entity in Homo sapiens)
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GGT5 dimer (name copied from entity in Homo sapiens)
1-Hydroxypropane-1,2,3-tricarboxylic acid
GGT1 dimer (name copied from entity in Homo sapiens)
Enterohepatic bile salt transporters in normal physiology and liver disease
Human isopentenyl diphosphate: dimethylallyl diphosphate isomerase: overproduction, purification, and characterization
Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs
LPIN2:Mg2+ (name copied from entity in Homo sapiens)
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LPIN3:Mg2+ (name copied from entity in Homo sapiens)
PISD:Pyruvoyl (name copied from entity in Homo sapiens)
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PIK3C3:Mn2+:PIK3R4:Mn2+ (name copied from entity in Homo sapiens)
PIK3R4:Mn2+ (name copied from entity in Homo sapiens)
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PIK3C3:Mn2+ (name copied from entity in Homo sapiens)
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PCYT1A dimer (name copied from entity in Homo sapiens)
PCYT1B dimer (name copied from entity in Homo sapiens)
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Expression patterns of two human genes coding for different rab GDP-dissociation inhibitors (GDIs), extremely conserved proteins involved in cellular transport
ChEBI:18381 5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide
CDIPT:Mg2+/Mn2+ (name copied from entity in Homo sapiens)
Aquaporin-11: a channel protein lacking apparent transport function expressed in brain
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SREBP1A/1C/2:NF-Y:FDPS gene (name copied from entity in Homo sapiens)
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SREBP1A/2:NF-Y:SC5DL gene (name copied from entity in Homo sapiens)
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CH25H (Fe2+ cofactor) (name copied from entity in Homo sapiens)
HSD17B1 dimer (name copied from entity in Homo sapiens)
SREBP1A/2:SQLE gene (name copied from entity in Homo sapiens)
ChEBI:16152 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphates
ChEBI:16152 ChEBI:16152 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphates
SREBP1A/1C/2:NF-Y:TM7SF2 gene (name copied from entity in Homo sapiens)
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LPIN1:Mg2+ (name copied from entity in Homo sapiens)
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MGLL dimer (name copied from entity in Homo sapiens)
PCYT2 dimer (name copied from entity in Homo sapiens)
SQLE:FAD (name copied from entity in Homo sapiens)
Structure of the FGF receptor tyrosine kinase domain reveals a novel autoinhibitory mechanism
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HACL1 tetramer (name copied from entity in Homo sapiens)
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HACL1 holoenzyme monomer (name copied from entity in Homo sapiens)
HMGCR dimer (name copied from entity in Homo sapiens)
MVK dimer (name copied from entity in Homo sapiens)
MVD dimer (name copied from entity in Homo sapiens)
IDI1 or 2 (name copied from entity in Homo sapiens)
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holo-FDPS dimer (name copied from entity in Homo sapiens)
Stimulation of the cell death response by PAK-2p34
FDPS:3Mg++ (name copied from entity in Homo sapiens)
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FDFT (Mg2+ cofactor) (name copied from entity in Homo sapiens)
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SREBP1A/1C/2 Dimer (name copied from entity in Homo sapiens)
SREBP1A/1C/2:NF-Y:HMGCS1 gene (name copied from entity in Homo sapiens)
The human AQP4 gene: definition of the locus encoding two water channel polypeptides in brain
2'-deoxyadenosine 5'-diphosphate [ChEBI:16174]
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Succinate dehydrogenase flavoprotein (subunit A), oxidised (name copied from entity in Homo sapiens)
Succinate dehydrogenase complex (oxidised) (name copied from entity in Homo sapiens)
Succinate dehydrogenase Iron Sulphur (subunit B) (name copied from entity in Homo sapiens)
alpha-ketoglutarate dehydrogenase E1 homodimer (name copied from entity in Homo sapiens)
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alpha-ketoglutarate dehydrogenase E2 holoenzyme (name copied from entity in Homo sapiens)
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Succinyl-CoA synthetase heterodimer (ADP-forming) (name copied from entity in Homo sapiens)
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alpha-ketoglutarate dehydrogenase E1 holoenzyme (name copied from entity in Homo sapiens)
Citrate Synthase Holoenzyme (name copied from entity in Homo sapiens)
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alpha-ketoglutarate dehydrogenase complex (name copied from entity in Homo sapiens)
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IDH3 complex (name copied from entity in Homo sapiens)
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A protein interaction framework for human mRNA degradation
phosphorylated pyruvate dehydrogenase E1 complex (name copied from entity in Homo sapiens)
phosphorylated pyruvate dehydrogenase complex (name copied from entity in Homo sapiens)
pyruvate dehydrogenase E1 complex (name copied from entity in Homo sapiens)
pyruvate dehydrogenase E2 trimer (name copied from entity in Homo sapiens)
lactate dehydrogenase B4 complex (name copied from entity in Homo sapiens)
lactate dehydrogenase AB3 complex (name copied from entity in Homo sapiens)
alpha-keto acid dehydrogenase E3 holoenzyme (name copied from entity in Homo sapiens)
alpha-keto acid dehydrogenase E3 homodimer (name copied from entity in Homo sapiens)
pyruvate dehydrogenase complex (name copied from entity in Homo sapiens)
MPC1:MPC2 (name copied from entity in Homo sapiens)
A mannosyltransferase gene at 11q23 is disrupted by a translocation breakpoint that co-segregates with bipolar affective disorder in a small family
GCH1 dimer (name copied from entity in Homo sapiens)
lactate dehydrogenase A3B complex (name copied from entity in Homo sapiens)
lactate dehydrogenase A2B2 complex (name copied from entity in Homo sapiens)
lactate dehydrogenase A4 complex (name copied from entity in Homo sapiens)
PDSS1/2 tetramer (name copied from entity in Homo sapiens)
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COQ6:FAD (name copied from entity in Homo sapiens)
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PDSS1:Mg2+ (name copied from entity in Homo sapiens)
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GCH1 decamer (name copied from entity in Homo sapiens)
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COQ7:Fe2+ (name copied from entity in Homo sapiens)
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SAC1-like domains of yeast SAC1, INP52, and INP53 and of human synaptojanin encode polyphosphoinositide phosphatases
Human GTP cyclohydrolase I: only one out of three cDNA isoforms gives rise to the active enzyme
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).
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).
Differential lysosomal proteolysis in antigen-presenting cells determines antigen fate
The role for endoplasmic reticulum stress in diabetes mellitus
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 1,3,4,5,6-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).
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).
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).
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.
Signaling through PI3Kgamma: a common platform for leukocyte, platelet and cardiovascular stress sensing
Diphosphoinositol polyphosphate phosphohydrolases, also known as nucleoside diphosphate-linked moiety X motif (NUDT) proteins, dephosphorylate inositol diphospho-pentakisphosphate (PP-IP5) to inositol 1,2,3,4,5,6-hexakisphosphate (IP6). The NUDT proteins involved are: nucleoside diphosphate-linked moiety X motif 3 (NUDT3), 4 (NUDT4), 10 (NUDT10), and 11 (NUDT11). The reactants consumed are: inositol 1-diphospho-2,3,4,5,6-pentakisphosphate (1-PP-IP5) and 3-diphospho-1,2,4,5,6-pentakisphosphate (3-PP-IP5). The following lists the above proteins with their corresponding literature references: NUDT3 (Safrany et al. 1999, Safrany et al. 1998, Yang et al. 1999, Caffrey et al. 2000), NUDT4 (Caffrey et al. 2000), NUDT10 (Leslie et al. 2002, Hidaka et al. 2002) and NUDT11 (Leslie et al. 2002, Hidaka et al. 2002).
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).
Diphosphoinositol polyphosphate phosphohydrolase 2, also known as nucleoside diphosphate-linked moiety X motif 4 (NUDT4), dephosphorylates diphospho- tetrakisphosphate (PP-IP4) to inositol 1,3,4,5,6-pentakisphosphate (I(1,3,4,5,6)P5). The products made are: inositol 5-diphospho-1,3,4,6-tetrakisphosphate (5-PP-IP4); inositol 1-diphospho-3,4,5,6-tetrakisphosphate (1-PP-IP4); and inositol 3-diphospho-1,4,5,6-tetrakisphosphate (3-PP-IP4). The following lists the above protein with its corresponding literature references: NUDT4 (Saiardi et al. 2001, Saiardi et al. 2000).
Diphosphoinositol polyphosphate phosphohydrolases (DIPP), also known as nucleoside diphosphate-linked moiety X motif (NUDT) proteins, dephosphorylate inositol 5-diphospho-1,2,3,4,6-pentakisphosphate (5-PP-IP5) to inositol 1,2,3,4,5,6-hexakisphosphate (IP6). The NUDT proteins involved are: nucleoside diphosphate-linked moiety X motif 3 (NUDT3), 4 (NUDT4), 10 (NUDT10), and 11 (NUDT11). The following lists the above proteins with their corresponding literature references: NUDT3 (Safrany et al. 1999, Safrany et al. 1998, Yang et al. 1999, Caffrey et al. 2000), NUDT4 (Caffrey et al. 2000), NUDT10 (Leslie et al. 2002, Hidaka et al. 2002) and NUDT11 (Leslie et al. 2002, Hidaka et al. 2002).
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).
Differential stimulation of cholesterol and unsaturated fatty acid biosynthesis in cells expressing individual nuclear sterol regulatory element-binding proteins
phosphoribosyl pyrophosphate synthetase holoenzyme
NUDT4:Mg2+/Mn2+ (name copied from entity in Homo sapiens)
SREBP1A/2:NF-Y:HMGCR gene (name copied from entity in Homo sapiens)
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ACAT1 tetramer (name copied from entity in Homo sapiens)
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SREBP1A/2 Dimer (name copied from entity in Homo sapiens)
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NF-Y (name copied from entity in Homo sapiens)
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NUDT10:Mg2+/Mn2+ (name copied from entity in Homo sapiens)
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NUDT3:Mg2+ (name copied from entity in Homo sapiens)
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Btn-ACACA:2Mn2+ (name copied from entity in Homo sapiens)
Citrate lyase homotetramer (name copied from entity in Homo sapiens)
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Genetic disorders of carnitine metabolism and their nutritional management.
PGM2:Mg++ (name copied from entity in Homo sapiens)
8xUGP2 (name copied from entity in Homo sapiens)
PGM1:Mg++ (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)
PGD dimer (name copied from entity in Homo sapiens)
G6PD tetramer (name copied from entity in Homo sapiens)
G6PD dimer (name copied from entity in Homo sapiens)
GALE dimer (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)
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GOT1 dimer (name copied from entity in Homo sapiens)
FBP2 tetramer (name copied from entity in Homo sapiens)
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FBP1 tetramer (name copied from entity in Homo sapiens)
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1,2-diacyl-sn-glycero-3-phosphocholine [ChEBI:16110]
Dihydroxyacetone phosphate [ChEBI:16108]
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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.
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.
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.
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.
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).
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.
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).
Once synthesized mRNA can be utilized until degraded. Degradation itself is the final mode of gene expression regulation.
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.
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.
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 XRN1 exoribonuclease hydrolyzes decapped mRNA from 5' to 3' and yields ribonucleotides having 5'-monophosphates. In yeast Xrn1 associates with the Lsm1-7 complex.
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.
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.
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. 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).
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.
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.
Butyrate response factor 1 (BRF1) binds AU-rich elements in the 3' untranslated region of mRNAs.
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.
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.
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.
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.
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).
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.
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.
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).
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 .
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).
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).
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).
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).
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.
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.
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.
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.
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).
Activation of PAK-2p34 coincides with autophosphorylation of Thr 402 in the the catalytic domain (Walter et al., 1998).
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).
Inactive PAK-2 can be partially autophosphorylated in the regulatory region without being activated (Gatti et al. 1999).
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
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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).
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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.
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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).
The carboxylation of pyruvate to form oxaloacetate, catalyzed by mitochondrial pyruvate carboxylase, is an irreversible and allosterically regulated reaction (Jitrapakdee and Wallace 1999).
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).
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).
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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).
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NODs: intracellular proteins involved in inflammation and apoptosis
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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Interaction between the functional polymorphisms of the alcohol-metabolism genes in protection against alcoholism.
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 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).
1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide [ChEBI:18406]
5'-Phospho-ribosyl-5-amino-4-imidazole carboxamide
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).
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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).
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5'-Phosphoribosylformylglycinamidine [ChEBI:18413]
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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).
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.
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.
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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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).
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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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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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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.
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Identification of a novel aquaporin, AQP12, expressed in pancreatic acinar cells
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.
The reversible interconversion of ribulose 5-phosphate and ribose 5-phosphate is catalyzed by cytosolic ribose 5-phosphate isomerase (Huck et al. 2004).
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 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 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 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 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 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 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.
The MIA system for protein import into the mitochondrial intermembrane space
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 reversible interconversion of ribose 5-phosphate and ribulose 5-phosphate is catalyzed by cytosolic ribose 5-phosphate isomerase (Huck et al. 2004).
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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.
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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).
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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.
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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).
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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.
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.
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).
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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 (Hers 1976; Lomako et al. 2004; Villar-Palasi and Larner 1970). 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. These reactions are shown in the figure. Repetition of the last two reactions generates large, extensively branched glycogen polymers. The catalysis of several of these reactions by distinct isozymes in liver and muscle allows them to be regulated independently in the two tissues.
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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).
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).
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).
System-wide investigation of ErbB4 reveals 19 sites of Tyr phosphorylation that are unusually selective in their recruitment properties
Endosomal proteolysis of internalized proteins.
Understanding specificity in metabolic pathways--structural biology of human nucleotide metabolism
Modulation of mitochondrial membrane permeability in pathogenesis, autophagy and control of metabolism
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Biochemical characterization of DNA damage checkpoint complexes: clamp loader and clamp complexes with specificity for 5' recessed DNA
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The rate of bulk flow from the endoplasmic reticulum to the cell surface
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Biosynthesis and bioproduction of coenzyme Q10 by yeasts and other organisms
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57 varieties: the human cytochromes P450
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Structural determinants for branched-chain aminotransferase isozyme-specific inhibition by the anticonvulsant drug gabapentin
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Physiological functions of the pentose phosphate pathway
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Neurotrophin signal transduction in the nervous system
Iron-sulfur protein maturation in human cells: evidence for a function of frataxin
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Compartmentalization of aquaporins in the human intestine
Vacuolar protein-sorting-associated protein 25
Vacuolar protein-sorting-associated protein 36
ribose 1-phosphate, deoxyribose 1-phosphate
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ATP6V0 (name copied from entity in Homo sapiens)
a-ketoisocaproate, a-keto b-methylvalerate, a-ketoisovalerate
ATP6V0C hexamer (name copied from entity in Homo sapiens)
PIP3:PDK1 complex (name copied from entity in Homo sapiens)
V-ATPase (name copied from entity in Homo sapiens)
ATP6V1A trimer (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=3661746
ATP6V1G dimer (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_11368.2
ATP6V1 (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=200493
ATP6V1B trimer (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_11294.1
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=197220
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_96395.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661748
TSC1:p-S1387-TSC2 (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=3661614
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_11409.2
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=197256
Activated mTORC1 (name copied from entity in Homo sapiens)
Rheb:GTP (name copied from entity in Homo sapiens)
phospho-ERK-1 dimer (name copied from entity in Homo sapiens)
phospho-ERK-2 dimer (name copied from entity in Homo sapiens)
PDPK1:PIP3 (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_11509.2
PDPK1:PIP2 (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=200503
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661617
Rheb:GDP (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=3661615
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661741
Structure, function and evolution of the signal recognition particle
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_114560.8
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661744
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661742
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_80724.9
Decarboxylases involved in polyamine biosynthesis and their inactivation by nitric oxide
UDP-N-acetyl-D-glucosamine [ChEBI:16264]
PKA tetramer (name copied from entity in Homo sapiens)
cAMP:PKA regulatory subunit (name copied from entity in Homo sapiens)
Lsm1-7 Complex (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=3665392
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_98272.9
Exosome Complex (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=3661624
Exosome Ring Hexamer (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=3661622
SPO11 Dimer (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=3661621
SPO11 Covalently Attached to Double-strand Break (name copied from entity in Homo sapiens)
PPA1 dimer (name copied from entity in Homo sapiens)
PPA2 dimer (name copied from entity in Homo sapiens)
VPS35:VPS29:VPS26 (name copied from entity in Homo sapiens)
WLS:retromer (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_11817.2
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=197969
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_29368.10
RhoGTPase:GDP (name copied from entity in Homo sapiens)
RhoA,B,C:GDP (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_82018.9
RhoA/B/C:GTP (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_11451.2
Protein Kinase C, alpha type: DAG (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=200665
PIP3:RhoA (name copied from entity in Homo sapiens)
RhoGTPase:GTP (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=3661630
Activation of the FGF receptor underlies neurite outgrowth stimulated by L1, N-CAM, and N-cadherin
Inactivated RhoGTPase:GDP:GDI complex (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=3661628
4-Trimethylammoniobutanoate [ChEBI:16244]
RhoA (Mg cofactor):GDP (name copied from entity in Homo sapiens)
RhoA (Mg cofactor):GTP (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=174404
Cell cycle-dependent recruitment of telomerase RNA and Cajal bodies to human telomeres
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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_7545.3
5,10-methenyltetrahydrofolate polyglutamate
Active N-SMase:Mg2+ (name copied from entity in Homo sapiens)
5,10-methylenetetrahydrofolate polyglutamate
Ubiquitinated AUF1 Tetramer (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=3000125
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_165600.1
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_164390.1
SMG1:UPF1:EJC:Translated mRNP (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=3665628
TTP:mRNA 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_166159.1
BRF1:mRNA Complex (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=3665010
26S proteasome (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_168678.1
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)
Translated mRNA Complex with Premature Termination Codon Preceding Exon Junction (name copied from entity in Homo sapiens)
Structure of human nicotinamide/nicotinic acid mononucleotide adenylyltransferase. Basis for the dual substrate specificity and activation of the oncolytic agent tiazofurin.
SMG1:SMG8:SMG9 Complex (name copied from entity in Homo sapiens)
Magoh-Y14 complex (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=199207
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664972
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664971
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_11360.3
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=3664974
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664975
Decapped mRNA:LSM1-7 Complex (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=3664979
Deadenylated mRNA:Lsm1-7 Complex (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=3664981
AUF1 p37 Dimer (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_168964.1
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=3665007
AUF1 Tetramer: Destabilized mRNA Complex (name copied from entity in Homo sapiens)
Phosphorylated AUF1 p40 Dimer (name copied from entity in Homo sapiens)
AUF1 p37 Tetramer (name copied from entity in Homo sapiens)
Ubiquitinated AUF1 Tetramer: Destabilized mRNA Complex (name copied from entity in Homo sapiens)
Phosphorylated AUF1 p40 Tetramer (name copied from entity in Homo sapiens)
The general transcription factors of RNA polymerase II.
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665034
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665008
phosphofructokinase, P4 complex (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=3664989
phosphofructokinase, L4 complex (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=3664990
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664987
glucose 6-phosphate isomerase dimer (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=3664988
CPSF:capped intronless pre-mRNA:CBC complex (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=3664984
CPSF (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=3664985
capped intronless pre-mRNA:CBC complex (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=3664982
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664983
PKC-beta controls I kappa B kinase lipid raft recruitment and activation in response to BCR signaling
ChEBI:16290 5alpha-cholesta-7,24-dien-3beta-ol
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_165706.1
phosphofructokinase, PL3 complex (name copied from entity in Homo sapiens)
phosphofructokinase, P2L2 complex (name copied from entity in Homo sapiens)
phosphofructokinase, P3L complex (name copied from entity in Homo sapiens)
Caspase-activated PAK-2 is regulated by subcellular targeting and proteasomal degradation
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_167884.1
Total enzymic synthesis of cholesterol from lanosterol. Cytochrome b5-dependence of 4-methyl sterol oxidase.
60S ribosomal complex (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=200499
40S ribosomal 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_11729.2
mRNA Complex with a Premature Termination Codon Preceding an Exon Junction (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=3661745
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=200492
80S ribosome (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_11276.1
GDP bound eRF3 (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=3665626
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_168707.1
Translated mRNA Complex with Premature Termination Codon Not Preceding Exon Junction (name copied from entity in Homo sapiens)
Assembly of the ORC complex at the origin of replication
SMG1:Phosphorylated UPF1:EJC:Translated mRNP (name copied from entity in Homo sapiens)
UPF1:eRF3 Complex on Translated mRNA (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)
Structure-function relationships in dihydrolipoamide acyltransferases.
Functional impairment of lens aquaporin in two families with dominantly inherited cataracts
Phosphorylation of threonine 210 and the role of serine 137 in the regulation of mammalian polo-like kinase
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)
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).
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.
Processing of N-linked carbohydrate chains in a patient with glucosidase I deficiency (CDG type IIb)
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.
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.
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.
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.
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 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.
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.
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.
Activation of human mitochondrial pantothenate kinase 2 by palmitoylcarnitine
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 reversible, NADP(H)-dependent reduction of all-trans-retinal (atRAL) to all-trans-retinol (atROL) occurs in both rod and cone photoreceptor cells where multiple retinol dehydrogenases (RHDs) are located. RHDs belong to the short-chain dehydrogenase/reductase (SDR) superfamily. RDH8 (located in photoreceptor outer segments) is partially responsible, together with other RDHs, for mediating this reaction. The activity for human RDH8 is inferred from a bovine experiment (Rattner et al. 2000).
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.
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).
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 (Bänziger 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).
All WNT ligands are predicted to be highly glycosylated. By similarity with WNT ligands in mouse, human WNTs are believed to undergo N-linked glycosylation at multiple asparagine residues and this glycosylation is critical for their secretion (Smolich et al, 1993; Willert et al, 2003, Komekado et al, 2006; Kurayoshi et al, 2007). The mechanism of N-linked glycosylation is not shown here. For a more detailed description, please refer to pathway "Asparagine N-linked glycosylation".
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 ).
This black box event represents the non-WNT-specific ER-to-Golgi trafficking step of protein secretion (reviewed in Dancourt and Barlowe, 2010; Lippincott Schwatz et al, 2000; for more details, please refer to the pathway "ER to Golgi transport"). Two recent screens in Drosophila have identified members of the p24 family as WNT-specific regulators of ER-to-Golgi transport, although the details have not been elucidated (Port et al, 2011; Buechling et al, 2011; reviewed in Strating and Martens, 2009). Depletion of the Drosophila p24 protein Opossum causes accumulation of WNT ligand in the ER, suggesting a role for Opm in ER-to-Golgi transport of WNTs. WNT-dependent reporter activity was reduced in HEK293 cells that were depleted for the human p24 homologue TMED5, supporting a conserved role for these proteins in WNT signaling (Buechling et al, 2011; reviewed in Palmer et al, 2012).
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).
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.
Meiotic recombination exchanges segments of duplex DNA between chromosomal homologs, generating genetic diversity (reviewed in Handel and Schimenti 2010, Inagaki et al. 2010, Cohen et al. 2006). There are two forms of recombination: non-crossover (NCO) and crossover (CO). In mammals, the former is required for correct pairing and synapsis of homologous chromosomes, while CO intermediates called chiasmata are required for correct segregation of bivalents. Meiotic recombination is initiated by double-strand breaks created by SPO11, which remains covalently attached to the 5' ends after cleavage. SPO11 is removed by cleavage of single DNA strands adjacent to the covalent linkage. The resulting 5' ends are further resected to produce protruding 3' ends. The single-stranded 3' ends are bound by RAD51 and DMC1, homologs of RecA that catalyze a search for homology between the bound single strand and duplex DNA of the chromosomal homolog. RAD51 and DMC1 then catalyze the invasion of the single strand into the homologous duplex and the formation of a D-loop heteroduplex. Approximately 90% of heteroduplexes are resolved without crossovers (NCO), probably by synthesis-dependent strand annealing. The invasive strand is extended along the homolog and ligated back to its original duplex, creating a double Holliday junction. The mismatch repair proteins MSH4, MSH5 participate in this process, possibly by stabilizing the duplexes. The mismatch repair proteins MLH1 and MLH3 are then recruited to the double Holliday structure and an unidentified resolvase (Mus81? Gen1?) cleaves the junctions to yield a crossover. Crossovers are not randomly distributed: The histone methyltransferase PRDM9 recruits the recombination machinery to genetically determined hotspots in the genome and each incipient crossover somehow inhibits formation of crossovers nearby, a phenomenon called crossover interference. Each chromosome bivalent, including the X-Y body in males, has at least one crossover and this is required for meiosis to proceed correctly.
During meiosis the replicated chromosomes of a single diploid cell are segregated into 4 haploid daughter cells by two successive divisions, meiosis I and meiosis II. In meiosis I, the distinguishing event of meiosis, pairs (bivalents) of homologous chromosomes in the form of sister chromatids are paired, synapsed along their regions of homologous DNA (reviewed in Yang and Wang 2009), and then segregated, resulting in haploid daughters containing sister chromatids paired at their centromeres (reviewed in Cohen et al. 2006, Handel and Schimenti 2010). The sister chromatids are then separated and segregated during meiosis II. Recombination between chromosomal homologues but not between sister chromatids occurs during prophase of meiosis I (reviewed in Inagaki et al. 2010). Though hundreds of recombination events are initiated, most are resolved without crossovers and only tens proceed to become crossovers. In mammals recombination events are required between homologues for normal pairing, synapsis, and segregation.
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).
The gene encoding SPO11 shares sequence similarity to TopoVI, a type II topoisomerase. SPO11 dimers cleave both strands of DNA. Each subunit of the dimer remains covalently attached to the 5' end of one strand of DNA via a phosphodiester linkage to a conserved tyrosine residue of SPO11. In addition to SPO11, work from budding yeast has shown a total of 7 proteins essential for double strand break formation. The mammalian ortholog of Mei4 (S. cerevisiae) as well as a mammalian-specific gene called Mei1 are essential to formation of meiotic double strand breaks.
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).
Rods and cones share the same mechanism for the phototransduction process but perform functionally different roles. Although cone photoreceptors make up around 5% of all photoreceptor cells and are outnumbered 20 to 1 by rod photoreceptors, they mediate daylight vision in the human eye whereas rods mediate twilight vision. Also, cones are around 100-times less light-sensitive than rods thereby depriving us of colour vision in dark conditions in which cones cannot function. Rod function saturates in even moderate amounts of light whereas cones can adjust to even very bright light conditions, a process called light adaptation. In bright conditions, rods can take up to one hour to regain their sensitivity whereas cones can recover in a few minutes, a process called dark adaptation and which allows us to retain visual perception in changing light conditions. Cone cells express three types of opsin which allow colour discrimination. Long Wavelength Sensitive Opsin (OPN1LW) detects red , Short Wavelength Sensitive Opsin (OPN1SW) detects blue, and Short Wavelength Sensitive Opsin (OPN1SW) detects green regions of the light spectrum. In the canonical retinoid (visual) cycle, the visual chromophore is regenerated in reactions involving the rod outer segments (ROS) and the retinal pigment epithelium (RPE). For cones, chromophore recycling is independent of the RPE and instead involves Muller cells in the retina which supply the chromophore selectively to cones. The molecular steps of the cone retinoid (visual) cycle are outlined in this section. The ability of cones to react to bright and differing light conditions means it has to regenerate the chromophore much quicker than rods. All-trans-retinol (atROL) released from cone outer segments is taken up by Muller cells where it is directly isomerized back to 11-cis-retinol (11cROL) then esterified by LRAT. When required, these 11-cis-retinyl esters can be hydrolysed by 11-cis-RE hydrolases back to 11cROL then oxidised in the cone photoreceptor cell to regenerate 11-cis-retinal (11cRAL), the visual chromophore (see reviews von Lintig 2012, Wang & Kefalov 2011, Kefalov 2012, Wolf 2004).
All-trans-retinal (atRAL) can diffuse across membranes to the cytosol and is reduced to all-trans-retinol (atROL) by the action of a short-chain dehydrogenase/reductase 3 using NADP+/NADPH as cofactor (Haeseleer et al. 1998).
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.
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 SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition
Involvement of Rac/Cdc42/PAK pathway in cytoskeletal rearrangements
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.
The exosome complex hydrolyzes capped, deadenylated mRNA from 3' to 5' and yields ribonucleotides having 5'-monophosphates. In yeast the Ski2-Ski3-Ski8 complex assists degradation by the exosome complex, however little is known about the function of the homologous Ski complex in mammals. Although many exosomal components contain exonuclease signatures, only two components have been shown to degrade RNA. Rrp6/PMSCL-100 has been shown to be involved in the 3â-5â decay of nuclear mRNAs in yeast. Rrp6 may also function in the absence of the core exosomal components. The Rrp44/dDis3 component of the core exosome has been shown to possess both 3â-5â exonuclease activity along with endonuclease activity via its PIN domain.
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.
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.
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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Cross-presentation of soluble exogenous antigens (endosomes)
Complementation analysis in PtdInsP kinase-deficient yeast mutants demonstrates that Schizosaccharomyces pombe and murine Fab1p homologues are phosphatidylinositol 3-phosphate 5-kinases
Glutathione metabolism and its selective modification
An islet amyloid peptide is derived from an 89-amino acid precursor by proteolytic processing
Kinesin-5 homotetramer (name copied from entity in Homo sapiens)
Rabenosyn-5:VPS-45 (name copied from entity in Homo sapiens)
CENP-E dimer (name copied from entity in Homo sapiens)
Centralspindlin (name copied from entity in Homo sapiens)
Activated PKC beta (name copied from entity in Homo sapiens)
F-actin capping protein (name copied from entity in Homo sapiens)
Activated PKC gamma (name copied from entity in Homo sapiens)
Functional link between BLM defective in Bloom's syndrome and the ataxia-telangiectasia-mutated protein, ATM.
Identification and characterization of a major liver lysophosphatidylcholine acyltransferase
The faciogenital dysplasia gene product FGD1 functions as a Cdc42Hs-specific guanine-nucleotide exchange factor
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Editing-defective tRNA synthetase causes protein misfolding and neurodegeneration
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Primary structure of a human trifunctional enzyme. Isolation of a cDNA encoding methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase-formyltetrahydrofolate synthetase.
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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A comparison of eubacterial and archaeal structure-specific 5'-exonucleases.
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Disulphide bond formation in the intermembrane space of mitochondria
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Prolactin-derived amyloid in the aging pituitary gland
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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).
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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). 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.
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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.
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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).
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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).
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Pyridoxine-5'-phosphate oxidase (PNPO) is able to oxidize pyridoxine phosphate (PDXP) to pyridoxal 5'-phosphate (PXLP) (Kang et al. 2004).
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Pyridoxine-5'-phosphate oxidase (PNPO) is able to oxidize pyridoxamine phosphate (PXAP) to pyridoxal 5'-phosphate (PXLP) (Kang et al. 2004).
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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).
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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).
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).
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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.
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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).
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Molecular basis of phenotypic variation in patients with argininemia
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).
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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).
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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).
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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.
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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).
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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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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.
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Protease-activated receptors in hemostasis, thrombosis and vascular biology
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).
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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".
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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).
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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.
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Cytosolic glutathione reductase catalyzes the reaction of glutathione (oxidized) and NADPH + H+ to form two molecules of glutathione (reduced) and NADP+ (Loos et al. 1976).
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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.
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 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.
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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).
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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).
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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).
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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).
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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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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).
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Cytosolic adenylate kinase 1 (AK1) catalyzes the reversible reactions of AMP and dAMP with ATP to form ADP and dADP respectively, plus ADP (Tsuboi 1978; Matsuura et al. 1989).
GPVI and integrin alphaIIb beta3 signaling in platelets
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).
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Cytosolic adenylate kinase 1 (AK1) catalyzes the reversible reactions of ADP and dADP with ADP to form AMP and dAMP respectively, plus ATP (Tsuboi 1978; Matsuura et al. 1989).
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Cytosolic adenylate kinase 5 [AK5] catalyzes the reactions of (d)AMP and (d)CMP with ATP to form (d)ADP and (d)CDP, respectively, and ADP. In the body AK5 expression was observed only in brain of nine tissues tested by Northern blotting (Van Rompay et al. 1999). AK5 is inferred to occur as a dimer from unpublished crystallographic data obtained for the catalytically active carboxyterminal third of the protein (PDB 2BWJ).
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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).
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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).
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Cytosolic adenylate kinase 5 [AK5] catalyzes the reactions of (d)ADP and (d)CDP with ADP to form (d)AMP and (d)CMP, respectively, and ATP. In the body AK5 expression was observed only in brain of nine tissues tested by Northern blotting (Van Rompay et al. 1999). AK5 is inferred to occur as a dimer from unpublished crystallographic data obtained for the catalytically active carboxyterminal third of the protein (PDB 2BWJ).
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Formation of Double-strand Break in DNA by SPO11
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).
3' to 5' Exoribonuclease Digestion of mRNA by the Exosome Complex
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).
pyrophosphate + H2O => 2 orthophosphate [cytosolic]
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.
pyrophosphate + H2O => 2 orthophosphate [mitochondrial]
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).
Biochemistry - The Chemical Reactions of Living Cells 2nd Edn.
Biochemical Pathways - An Atlas of Biochemistry and Molecular Biology
Lehninger - Principles of Biochemistry 4th Edn.
Dihydroorotate dehydrogenase catalyzes the oxidation of dihydroorotate to orotate (orotic acid). The enzyme is located in the inner mitochondrial membrane oriented so that cytosolic dihydroorotate molecules have access to it, and orotate is released into the cytosol. The reducing equivalents generated by the reaction are transferred by ubiquinone (Coenzyme Q) to the electron transport chain within the inner mitochondrial membrane. There is no evidence for the involvement of NAD+ as an acceptor of reducing equivalents in this reaction in mammalian cells (Jones 1980). In contrast, the reaction catalyzed by the enzyme isolated from the anaerobic bacterium Clostridium oroticum requires NAD+ as a cofactor but also proceeds strongly in the direction of dihydroorotate synthesis consistent with the greater electronegativity of NAD+ (Lieberman and Kornberg 1953). Early studies of purified rat liver enzyme by Forman and Kennedy suggested the presence of flavin mononucleotide and iron-sulfur complexes as cofactors. More recent work by Bader, Beuneu, and their colleagues with recombinant human protein expressed in insect cells has confirmed the presence of flavin mononucleotide, at a stoichiometry of one molecule per molecule of apoenzyme but suggests that iron-sulfur complexes, if indeed they are involved in the oxidation and electron transport process, are not an integral part of the dihydroorotate dehydrogenase holoenzyme.
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).
5' to 3' Exoribonuclease Digestion of Decapped mRNA
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.
AUF1(hnRNP D0) Dimers Bind AU-rich Element in 3' UTR of Transcripts
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).
Scavenging of the 7-methylguanosine Cap by DCPS
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).
Binding of Lsm1-7 Complex to Deadenylated mRNA
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.
Cloning and characterization a novel human 1-acyl-sn-glycerol-3-phosphate acyltransferase gene AGPAT7
SMG1 Phosphorylates UPF1 (Enhanced by Exon Junction Complex)
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).
Formation of UPF1:eRF3 Complex on mRNA with a Premature Termination Codon and No Exon Junction Complex
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.
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).
Release of Cytochrome c from mitochondria
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).
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).
Butyrate Response Factor1 (BRF1) Binds AU-rich Element in 3' UTR of mRNA
The RNA polymerase II elongation complex.
Tristetraproline (TTP) Binds AU-rich Elements in 3' UTR of Target mRNAs
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).
Autophosphorylation of PAK-2p34 in the activation loop
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).
Proteolytic PAK-2p34 fragment translocates to the nucleus
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).
Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197
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.
Phosphorylation of Ribosomal protein S6 by activated S6K1
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).
Phosphorylation and activation of eIF4B by activated S6K1
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).
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.
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.
Active JNK moves to the nucleus and phosphorylates different transcription factors
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).
TSC2 activates intrinsic GTPase activity of Rheb
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).
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 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 APRT dimer catalyzes the reaction of adenine and 5-phospho-alpha-D-ribose 1-diphosphate to form AMP and pyrophosphate (Holden et al. 1979).
Production of ceramide which can activate JNK and other targets
RhoA is activated by nucleotide exchange and inhibits axonal growth
Diacylglycerol metabolism and arachidonic acid release in human fetal membranes and decidua vera
Purification and subunit structure studies of human placental threonyl-tRNA synthetase
PRPP stimulates the dissociation of phosphoribosyl pyrophosphate amidotransferase tetramers to form dimers (Holmes et al. 1973a,b).
GAPs inactivate Rho GTPase:GTP by hydrolysis
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).
Dissociation of Rho GTP:GDP from GDI complex
Cytosolic AMP, GMP, and IMP stimulate the association of phosphoribosyl pyrophosphate amidotransferase (PPAT) dimers to form tetramers (Holmes et al. 1973a,b).
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).
Activation of Protein kinase C, alpha type by Diacylglycerol
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 oxidation of pyruvate in pigeon breast muscle
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 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 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).
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).
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).
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.
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ETF-ubiquinone oxidoreductase (ETF-QO), catalyzes the re-oxidation of reduced ETF, with ubiquinone as the electron acceptor.
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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.
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Crystal structure of human arginase I at 1.29-A resolution and exploration of inhibition in the immune response
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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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.
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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).
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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.
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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.
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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).
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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).
Reconstitution of the transcription factor TFIIH: assignment of functions for the three enzymatic subunits, XPB, XPD, and cdk7
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Synthesis of Prostaglandins (PG) and Thromboxanes (TX)
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.
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).
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).
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).
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.
Nuclear translocation of phospho-ERK-1 dimer
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).
Nuclear translocation of phospho-ERK-2 dimer
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 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).
PKA catalytic subunit translocates to the nucleus
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)).
Step-size analyses of the mitochondrial Hsp70 import motor reveal the Brownian ratchet in operation
Mechanisms of caspase-1 activation by P2X7 receptor-mediated K+ release
Excision repair protein ERCC-6 (Cockayne syndrome protein CSB)
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DNA-directed RNA polymerase II 13.3 kDa polypeptide
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DNA-directed RNA polymerase II 33 kDa polypeptide
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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
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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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DNA-directed RNA polymerase II 16 kDa polypeptide
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DNA-directed RNA polymerase II 140 kDa polypeptide
DNA-directed RNA polymerase II 19 kDa polypeptide
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DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide
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
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An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor
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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
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DNA-directed RNA polymerases I, II, and III 7.0 kDa polypeptide
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DNA-directed RNA polymerase II 14.5 kDa polypeptide
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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
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La proteins from Drosophila melanogaster and Saccharomyces cerevisiae: a yeast homolog of the La autoantigen is dispensable for growth.
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)
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Xeroderma pigmentosum group E complementing protein
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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
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
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)
Transcription initiation factor TFIID 18 kDa subunit
Transcription initiation factor TFIID 250 kDa subunit
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Transcription initiation factor TFIID 20/15 kDa subunits
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Transcription initiation factor TFIID 100 kDa subunit
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Transcription initiation factor TFIID 70 kDa subunit
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Transcription initiation factor TFIID 28 kDa subunit
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Transcription initiation protein SPT4 homolog 1
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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
Transcription initiation factor IIF, beta subunit
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Transcription initiation factor IIF, alpha subunit
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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
IP6 is phosphorylated to 5-PP-IP5 by IP6K1/3 in the cytosol
5-PP-IP5 is dephosphorylated to IP6 by NUDT(1) in the cytosol
1/3 PP-IP5 is dephosphorylated to IP6 by NUDT(1) in the cytosol
1-PP-IP5 is phosphorylated to 1,5-(PP)2-IP4 by IP6K1/2 in the nucleus
I(1,3,4,5,6)P5 is phosphorylated to 5-PP-IP4 by IP6K1/3 in the cytosol
PP-IP4 is dephosphorylated to I(1,3,4,5,6)P5 by NUDT4 in the cytosol
1-PP-IP4 is phosphorylated to 1,5-(PP)2-IP3 by IP6K1/3 in the cytosol
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IP6 is phosphorylated to 5-PP-IP5 by IP6K1/2 in the nucleus
5-PP-IP5 is phosphorylated to 5-PPP-IP5 by IP6K1/2 in the nucleus
5-PP-IP4 is phosphorylated to 1,5-(PP)2-IP3 by IP6K1/2 in the nucleus
Serine-protein kinase ATM (EC 2.7.1.37) (Ataxia telangiectasia mutated) (A-T, mutated)
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Insulin degradation: mechanisms, products, and significance.
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Double-strand break repair protein MRE11A
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ribose 5-phosphate <=> D-ribulose 5-phosphate
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D-ribulose 5-phosphate <=> ribose 5-phosphate
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D-fructose 6-phosphate + D-erythrose 4-phosphate <=> sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate
sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate <=> D-erythrose 4-phosphate + D-fructose 6-phosphate
I(1,3,4,5,6)P5 is phosphorylated to 5-PP-IP4 by IP6K1/2 in the nucleus
I(1,3,4,5)P4 is dephosphorylated to I(1,3,4)P3 by INPP5[3]/ITPK1 in the cytosol
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
D-ribose 5-phosphate + 2'-deoxyadenosine 5'-triphosphate (dATP) => 5-Phospho-alpha-D-ribose 1-diphosphate (PRPP) + 2'-deoxyadenosine 5'-monophosphate
D-ribulose 5-phosphate <=> xylulose 5-phosphate
xylulose 5-phosphate <=> D-ribulose 5-phosphate
Cytochrome P450s and cholesterol homeostasis
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PCNA homotrimer (name copied from entity in Homo sapiens)
6-phospho-D-gluconate + NADP+ => D-ribulose 5-phosphate + CO2 + NADPH + H+
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RFC Heteropentamer:RNA primer-DNA primer:origin duplex:PCNA homotrimer (name copied from entity in Homo sapiens)
RNA primer-DNA primer:origin duplex:PCNA (name copied from entity in Homo sapiens)
DNA Polymerase delta tetramer (name copied from entity in Homo sapiens)
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RFC Heteropentamer:RNA primer-DNA primer:origin duplex (name copied from entity in Homo sapiens)
alpha-D-Glucose 6-phosphate <=> D-Glucose 1-phosphate
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Processive complex:Okazaki fragment:Flap:RPA heterotrimer:dna2 (name copied from entity in Homo sapiens)
D-fructose 6-phosphate <=> alpha-D-Glucose 6-phosphate
D-Glucose 1-phosphate <=> alpha-D-Glucose 6-phosphate
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UTP + D-glucose 1-phosphate <=> pyrophosphate + UDP-glucose
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659299
Processive complex (name copied from entity in Homo sapiens)
D-galactose 1-phosphate + UDP-glucose <=> D-glucose 1-phosphate + UDP-galactose
Processive complex:Okazaki fragment complex (name copied from entity in Homo sapiens)
D-glucono-1,5-lactone 6-phosphate + H2O => 6-phospho-D-gluconate
Processive complex:Okazaki fragment:Flap (name copied from entity in Homo sapiens)
alpha-D-glucose 6-phosphate + NADP+ => D-glucono-1,5-lactone 6-phosphate + NADPH + H+
Processive complex:Okazaki fragment:Flap:RPA heterotrimer (name copied from entity in Homo sapiens)
D-fructose 1,6-bisphosphate + H2O => D-fructose 6-phosphate + orthophosphate
DNA Replication factor A protein 2 (32kD)
DNA Replication factor A protein A1 (70kD)
Replication protein A 70 kDa DNA-binding subunit
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
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)
General transcription factor IIH polypeptide 1
TFIIH basal transcription factor complex p62 subunit
Basic transcription factor 62 kDa subunit
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
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
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)
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
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
RNA primer-DNA primer:origin duplex (name copied from entity in Homo sapiens)
ubiquitinated Orc1 (name copied from entity in Homo sapiens)
D-glyceraldehyde 3-phosphate <=> dihydroxyacetone phosphate
DNA polymerase alpha:primase:DNA polymerase alpha:origin complex (name copied from entity in Homo sapiens)
1,3-bisphospho-D-glycerate + NADH + H+ <=> D-glyceraldehyde 3-phosphate + Orthophosphate + NAD+
RNA primer:origin duplex:DNA polymerase alpha:primase complex (name copied from entity in Homo sapiens)
ATP + 3-Phospho-D-glycerate <=> ADP + 1,3-bisphospho-D-glycerate
2-Hydroxy-1,2,3-propanetricarboxylic acid
Mcm4,6,7 complex (name copied from entity in Homo sapiens)
Phosphoenolpyruvate + H2O <=> 2-Phospho-D-glycerate
GINS complex (name copied from entity in Homo sapiens)
phosphoenolpyruvate [mitochondrial matrix] + citrate [cytosol] => phosphoenolpyruvate [cytosol] + citrate [mitochondrial matrix]
Exchange of cytosolic citrate for mitochondrial phosphoenolpyruvate
aspartate + alpha-ketoglutarate <=> oxaloacetate + glutamate [GOT1]
ubiquitinated Cdc6 (name copied from entity in Homo sapiens)
oxaloacetate + glutamate <=> aspartate + alpha-ketoglutarate [GOT2]
Oxaloacetate + NADH + H+ <=> (S)-Malate + NAD+
Pyruvate, CO2, and ATP react to form oxaloacetate, ADP, and orthophosphate
Pyruvate + CO2 + ATP => ADP + Orthophosphate + Oxaloacetate
Unwinding complex at replication fork (name copied from entity in Homo sapiens)
phosphoenolpyruvate + ADP => pyruvate + ATP
RFC Heteropentamer (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=3659305
DNA repair protein RAD51 homolog 1 (hRAD51) (HsRAD51)
ATP-dependent DNA helicase II, 80 kDa subunit
ATP-dependent DNA helicase II, 70 kDa subunit
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)
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_100291.9
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_5211.1
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=76632
1,3-Bisphosphoglycerate and ADP react to form 3-phosphoglycerate and ATP
1,3-bisphospho-D-glycerate + ADP <=> 3-phospho-D-glycerate + ADP
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=76629
Structural basis of hereditary coproporphyria
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+
CDK (name copied from entity in Homo sapiens)
Mcm10:active pre-replicative complex (name copied from entity in Homo sapiens)
2-Phospho-D-glycerate <=> Phosphoenolpyruvate + H2O
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_4460.2
active pre-replicative complex (name copied from entity in Homo sapiens)
Glucose 6-phosphate is isomerized to form fructose-6-phosphate
alpha-D-glucose 6-phosphate <=> D-fructose 6-phosphate
DDK (name copied from entity in Homo sapiens)
glucokinase [nucleoplasm] => glucokinase [cytosol]
Cdc45:CDK:DDK:Mcm10:pre-replicative complex (name copied from entity in Homo sapiens)
dihydroxyacetone phosphate <=> D-glyceraldehyde 3-phosphate
DNA Replication Factor A (name copied from entity in Homo sapiens)
D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP
RPA:Cdc45:CDK:DDK:Mcm10:pre-replicative complex (name copied from entity in Homo sapiens)
Proteasome mediated degradation of PAK-2p34
DNA polymerase alpha:primase (name copied from entity in Homo sapiens)
DNA polymerase epsilon:origin complex (name copied from entity in Homo sapiens)
alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659315
DNA polymerase epsilon (name copied from entity in Homo sapiens)
Orc2 associated with MCM8 (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_158613.3
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=3659338
ORC:origin (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=3662946
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659339
CDK:DDK:Mcm10:pre-replicative 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_156219.3
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=3659341
Mcm10:pre-replicative complex (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=3665503
Mcm2-7 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_82029.9
pre-replicative complex (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=109366
CDC6:ORC:origin 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_152780.3
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=3660175
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_3334.2
CDT1:CDC6:ORC:origin complex (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=3665304
Orc1:Orc4:Orc5:Orc3:Orc2:origin (name copied from entity in Homo sapiens)
Orc4:Orc5:Orc3:Orc2:origin (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_106949.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665119
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_112502.8
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660171
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665200
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_97012.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660180
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_103042.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660178
Orc5:Orc3:Orc2:origin (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=3660179
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660172
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_97462.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=500829
Orc3:Orc2:origin (name copied from entity in Homo sapiens)
Recognition and association of DNA glycosylase with site containing an affected purine
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_21803.1
Orc2:origin (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=109379
Homodimer of 4 aminobutyrate aminotransferase (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_3054.2
post exon ligation 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_5143.2
ATAC C Complex (name copied from entity in Homo sapiens)
ATAC B Complex (name copied from entity in Homo sapiens)
SF3B (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=83949
U12 snRNP (name copied from entity in Homo sapiens)
capped, methylated pre-mRNA:CBC 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_3061.2
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=83929
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660176
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660177
Interconversion of 2-oxoglutarate and 2-hydroxyglutarate
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_108362.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665265
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_44470.10
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=3665201
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_102830.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660181
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660182
ATAC A Complex (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=3660183
U11 snRNP (name copied from entity in Homo sapiens)
A to I edited RNA:Editosome (ADAR2) complex (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=3663225
A to I edited RNA:Editosome (ADAR1) 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_155709.3
U4 ATAC snRNP:U6 ATAC snRNP (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=3663222
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
U4 ATAC:U5:U6 ATAC Complex (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=3663223
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659331
snRNP Sm core complex (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=3662807
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659332
U6 ATAC snRNP (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=3663221
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659334
U5 snRNP (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=3662811
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_31119.10
U4 ATAC snRNP (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=3662806
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=500739
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_22071.1
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=113518
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_3468.1
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=500742
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663228
Editosome (ADAR1) complex (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=192438
ADAR2 homodimer (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_153593.3
Editosome (ADAR2) complex (name copied from entity in Homo sapiens)
Pentose phosphate pathway (hexose monophosphate shunt)
Capping complex (intermediate) (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_153821.3
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_21695.1
Capping complex (hydrolyzed) (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=432019
Monoamine metabolism and behavioral responses to ethanol in mitochondrial aldehyde dehydrogenase knockout mice
Capping complex (initial) (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_21102.1
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=3663230
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659367
ADAR1 homodimer (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_9588.2
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=3659369
Capping complex (with freed 5'- GMP) (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=3663227
Interleukin 2 high-affinity receptor expression requires two distinct binding proteins
Capping complex (GpppN..) (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_159137.3
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=3659366
Covalent CE:GMP intermediate complex (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=3663229
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=73604
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_4329.2
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_135217.5
Latent infection of Homo sapiens with Mycobacterium tuberculosis
NUBP2:4Fe-4S:NUBP1 (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=3663233
ABC7 dimer (name copied from entity in Homo sapiens)
CIAPIN1:4Fe-4S:2Fe-2S reduced (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=3663232
NUBP1:4Fe-4S (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_156101.3
Variant apolipoprotein AI as a major constituent of a human hereditary amyloid
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660229
NDOR1:CIAPIN1 oxidized (name copied from entity in Homo sapiens)
NDOR1:FAD:FMN (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_97241.9
CIAPIN1:4Fe-4S:2Fe-2S oxidized (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=3660232
NDOR1:CIAPIN1 reduced (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_158368.3
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=3659641
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_155144.3
FDXR:FAD (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=3660225
FDXR:FADH2 (name copied from entity in Homo sapiens)
DNA-directed RNA polymerase III subunit RPC10
2 Iron:FXN (name copied from entity in Homo sapiens)
DNA-directed RNA polymerase III subunit 127.6 kDa polypeptide
DNA-directed RNA polymerase III largest subunit
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FXN:ISD11:NFS1:ISCU (name copied from entity in Homo sapiens)
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DNA-directed RNA polymerase I 135 kDa polypeptide
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2 Iron:FXN:NFS1:ISD11:ISCU (name copied from entity in Homo sapiens)
DNA-directed RNA polymerases I and III subunit RPAC1
DNA-directed RNA polymerase I and III 40 kDa polypeptide
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NFS1:pyridoxal phosphate (name copied from entity in Homo sapiens)
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DNA-directed RNA polymerase III subunit 22.9 kDa polypeptide
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DNA-directed RNA polymerase III subunit RPC3
DNA-directed RNA polymerase III subunit C
DNA-directed RNA polymerases III 39 kDa polypeptide
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
GSS (name copied from entity in Homo sapiens)
aldehyde dehydrogenase, mitochondrial, tetramer (name copied from entity in Homo sapiens)
aldehyde dehydrogenase 1A1 tetramer (name copied from entity in Homo sapiens)
2x(FECH:2Fe-2S cluster) (name copied from entity in Homo sapiens)
Transcription Factor IIA alpha chain - p35
Transcription initiation factor IIB (General transcription factor TFIIB) (S300-II)
Structural basis of guanine nucleotide exchange mediated by the T-cell essential Vav1
Transcription Factor IIA beta chain - p19
2xPPO:FAD (name copied from entity in Homo sapiens)
Transcription initiation factor IIA gamma chain
2xCPO (name copied from entity in Homo sapiens)
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2xUROD (name copied from entity in Homo sapiens)
Transcription initiation factor TFIID 30 kDa subunit
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HMBS:DIPY (name copied from entity in Homo sapiens)
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8xALAD:Pb2+:Zn2+ (name copied from entity in Homo sapiens)
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8x(ALAD:Zn2+) (name copied from entity in Homo sapiens)
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DNA-directed RNA polymerase I and III 16 kDa polypeptide
DNA-directed RNA polymerases I and III subunit RPAC2
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The NRAMP family of metal-ion transporters
DNA-directed RNA polymerase I largest subunit
Transcription initiation factor IIE, alpha subunit
General transcription factor IIE 56 kDa subunit
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RNA Pol II (unphosphorylated) largest subunit
DNA-directed RNA polymerase II largest subunit
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SQR:FAD (name copied from entity in Homo sapiens)
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ALAS1 homodimer (pyridoxal phosphate cofactor) (name copied from entity in Homo sapiens)
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ALAS2 homodimer (pyridoxal phosphate cofactor) (name copied from entity in Homo sapiens)
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Type II phosphoinositide 5-phosphatases have unique sensitivities towards fatty acid composition and head group phosphorylation
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Substrate preferences of a lysophosphatidylcholine acyltransferase highlight its role in phospholipid remodeling
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Amyloid fibril protein nomenclature: 2010 recommendations from the nomenclature committee of the International Society of Amyloidosis
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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).
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 (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).
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).
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).
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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).
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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).
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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.
Cytosolic lactate dehydrogenase catalyzes the freely reversible reaction of lactate and NAD+ to form pyruvate and NADH + H+. In liver parenchymal cells, this reaction allows lactate from red blood cells and exercising muscle to be converted to pyruvate which in turn is typically used for gluconeogenesis which also consumes the NADH from the reaction. Lactate dehydrogenase is active as a tetramer. Two isoforms of lactate dehydrogenase, A and B, are widely expressed in human tissues, and all five tetramers - A4, A3B, A2B2, AB3, and B4 - are found. A third isoform, C, and its tetramer, C4, are found in testis.
The methylation of phosphatidylethanolamine
Cytosolic lactate dehydrogenase catalyzes the reversible reaction of pyruvate and NADH + H+ to form lactate and NAD+. In the body under anaerobic conditions such as are found in red blood cells or rapidly exercising skeletal muscle, this reaction regenerates NAD+, allowing the continuation of glycolysis. Lactate dehydrogenase is active as a tetramer. Two isoforms of lactate dehydrogenase, A and B, are widely expressed in human tissues, and all five tetramers - A4, A3B, A2B2, AB3, and B4 - are found. A third isoform, C, and its tetramer, C4, are found in testis.
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At the end of this reaction, 1 molecule of 'citrate lyase monomer' 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'.
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'.
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.).
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.).
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).
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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 (Thöny et al. 2000, Crabtree & Channon 2011, Schulz et al. 2008, Schmidt & 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.
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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.
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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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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).
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Another outer surface membrane-bound, homodimeric enzyme, dipeptidase, existing in two forms DPEP1 (Adachi et al. 1989) and DPEP2 (Lee et al. 1983, Raulf et al. 1987), further hydrolyses leukotriene D4 (LTD4) to leukotriene E4 (LTE4), cleaving a glycine residue in the process.
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Post-Elongation Processing of the Transcript
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).
DEGS2 (sphingolipid C4-hydroxylase 2 / âdegenerative spermatocyte homolog 2â) enzyme associated with the cytosolic face of the endoplasmic reticulum catalyzes the hydroxylation of dihydroceramide to form phytoceramide (Mizutani et al. 2004). Sequence similarity to the bifunctional mouse DEGS2 enzyme suggests that human DEGS2 protein might also catalyze the C4-dehydrogenation of dihydroceramide, but this hypothesis has not been tested experimentally.
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DEGS1 (sphingolipid delta(4)-desaturase 1 / âdegenerative spermatocyte homolog 1â) enzyme associated with the cytosolic face of the endoplasmic reticulum catalyzes the desaturation of dihydroceramide to form ceramide (Cadena et al. 1997; Ternes et al. 2002). The stoichiometry and cofactor requirements of the reaction are inferred from those observed in studies of ceramide synthesis in vitro catalyzed by rat liver microsomes (Michel et al. 1997). DEGS1 may also catalyze the 4-hydroxylation of dihydroceramide to form 4-hydroxysphinganine, but with low efficiency.
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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).
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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.
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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).
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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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).
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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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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).
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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.
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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).
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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).
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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.
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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).
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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).
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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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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.
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).
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At the end of this reaction, 1 molecule of 'pyruvate kinase, liver and RBC' is present. This reaction takes place in the 'nucleus'.
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.
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).
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.
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.
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.
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).
Mitochondrial COQ3 is an O-methyltransferase required in the reaction to convert 3-demethylubiquinol-10 (DeMQ10H2) to ubiquinol-10 (Q10H2) (Jonassen & Clarke 2000).
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).
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.
Synaptojanin 2, a novel Rac1 effector that regulates clathrin-mediated endocytosis
Chaperonin-mediated folding of vertebrate actin-related protein and gamma-tubulin
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).
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).
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The steps involved in the synthesis of glycosphingolipids (sphingolipids with one or more sugars attached) are annotated here (Gault et al. 2010).
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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.
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The polyprenyl diphosphate synthase consists of a tetramer comprising two units of decaprenyl-diphosphate synthase subunit 1 (PDSS1) and two units of decaprenyl-diphosphate synthase subunit 2 (PDSS2). It catalyses the combination of 2-trans,6-trans-farnesyl diphosphate (FPP) with isopentenyl diphosphate (IPPP) to form the polyisoprenoid tail all-trans-decaprenyl diphosphate (all-E-10PrP2) (Saiki et al. 2005, Tekle et al. 2008).
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The main steps involved in de novo sphingolipid synthesis are annotated here (Merrill 2002, Gault et al. 2010).
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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).
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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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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.
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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).
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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).
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
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).
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+
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).
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]
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).
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]
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).
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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 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).
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
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
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4-(2-Aminoethyl)-1,2-benzenediol [ChEBI:18243]
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Identification of genetic mutations in Japanese patients with fructose-1,6-bisphosphatase deficiency
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Squalene 2,3-epoxide cyclizes, forming lanosterol
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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).
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
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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).
Reduction of presqualene diphosphate to form squalene
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At the endoplasmic reticulum (ER) membrane, lysocardiolipin acyltransferase 1 (LCLAT1) aka ALCAT1 acylates dilysocardiolipin (DLCL) to produce monolysocardiolipin (MLCL) (Zhao et al. 2009).
Fibroblast growth factor receptors: lessons from the genes
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).
Expression of Squalene Monooxygenase (SQLE)
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).
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).
Cholesterol is hydroxylated to 25-hydroxycholesterol
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).
Testosterone is converted to 5-alpha-dihydroxytestosterone
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).
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).
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).
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).
Determinants of function and substrate specificity in human UDP-galactose 4'-epimerase
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+
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).
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)
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).
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
Expression of Farnesyl Diphosphate Synthase (FDPS)
Expression of Lathosterol Oxidase (SC5D, SC5DL)
phosphatidylinositol 1,4,5-trisphosphate
The Mechanism of Hsp90 regulation by the protein kinase-specific cochaperone p50(cdc37)
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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).
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1D-myo-Inositol 1,3,4-trisphosphate [ChEBI:810]
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).
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).
PCho and CTP are condensed to CDP-Cho by PCYT1 dimer
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 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).
GPETA is hydrolyzed to ETA and G3P by GPCPD1
CD14 controls the LPS-induced endocytosis of Toll-like receptor 4
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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).
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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).
PETA and CTP are condensed to CDP-ETA by PCY2
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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).
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PC is hydrolyzed to PA and choline by PLD1/2
Role of phosphatidylinositol 3,4,5-trisphosphate in regulating the activity and localization of 3-phosphoinositide-dependent protein kinase-1
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2-MAG is hydrolyzed to fatty acid and glycerol by MGLL
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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.
1D-myo-Inositol 1,3,4,5,6-pentakisphosphate
myo-inositol 1,3,4,5,6-pentakisphosphate
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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, 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, 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, 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).
PC is transphosphatidylated to PG by PLD1-4/6
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 (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).
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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).
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).
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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).
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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).
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GPCho is hydrolyzed to Cho and G3P by GPCPD1
1D-myo-inositol 1,3,4,5-tetrakisphosphate
phosphatidylinositol 1,3,4,5-tetrakisphosphate
Intracellular signaling by the neural cell adhesion molecule
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Histone acetyltransferase HBO1 interacts with the ORC1 subunit of the human initiator protein.
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5-PP-IP5 is phosphorylated to 5-PPP-IP5 by IP6K1/3 in the cytosol
1-PP-IP5 is phosphorylated to 1,5-(PP)2-IP4 by IP6K1/3 in the cytosol
(PP)2-IP4 is dephosphorylated to 5-PP-IP5 by NUDT(1) in the cytosol
Cutting edge: Role of Toll-like receptor 9 in CpG DNA-induced activation of human cells
I(1,4,5)P3 is dephosphorylated to I(1,4)P2 by INPP5(4) in the cytosol
(PP)2-IP4 is dephosphorylated to 1/3-PP-IP5 by NUDT(1) in the cytosol
Transport of Citrate from Mitochondrial Matrix to cytosol
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2-acylglycerol + H2O -> glycerol + fatty acid
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acetyl-CoA + bicarbonate + ATP => malonyl-CoA + H2O + ADP + orthophosphate
Formation of Malonyl-CoA from Acetyl-CoA (liver)
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Generation of Cytoplasmic Acetyl CoA from Citrate
palmitate + CoASH + ATP => palmitoyl-CoA + AMP + pyrophosphate + H2O [ACSL3]
trans-octadec-2-enoyl-CoA + NADPH + H+ => stearoyl-CoA + NADP+
arachidonate + CoASH + ATP => arachidonoyl-CoA + AMP + pyrophosphate + H2O [ACSL4]
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Expression of 3-Hydroxy-3-methylglutaryl-coenzyme A Reductase (HMGCR)
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Gly-3-P+FAD->DHAP+FADH2 (catalyzed by mitochondrial Gly-Phos dehydrogenase)
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acetoacetyl-CoA+acetyl-CoA => HMG-CoA + CoASH
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Formation of Malonyl-CoA from Acetyl-CoA (muscle)
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1,2-diacyl-glycerol 3-phosphate + H2O => 1,2-diacyl-glycerol + orthophosphate
Conversion of Phosphatidic Acid to Diacylglycerol
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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)
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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)
Expression of Hydroxymethylglutaryl coenzyme A synthase (HMGCS1)
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Condensation of acetyl CoA with acetoacetyl CoA to form HMG-CoA
2-hydroxyphytanoyl-CoA => pristanal + formyl-CoA
beta-Hydroxy-beta-methylglutaryl coenzyme A
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The nonsense-mediated decay RNA surveillance pathway
Another isopentenyl pyrophosphate is added to geranyl pyrophosphate
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Addition of isopentenyl pyrophosphate to DMAPP
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Two FPP molecules dimerize to form presqualene diphosphate
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Mevalonate is phosphorylated to mevalonate-5-phosphate
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Reduction of HMG-CoA produces mevalonate
Isopentenyl pyrophosphate rearranges to dimethylallyl pyrophosphate
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Mevalonate-5-pyrophosphate is decarboxylated
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Primary structure and tissue distribution of human 4-aminobutyrate aminotransferase
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The Src, Syk, and Tec family kinases: distinct types of molecular switches
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Molecular cloning of AMP deaminase isoform L. Sequence and bacterial expression of human AMPD2 cDNA
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Gbetagammas and the Ras binding domain of p110gamma are both important regulators of PI(3)Kgamma signalling in neutrophils
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D-amino-acid oxidase:FAD complex (name copied from entity in Homo sapiens)
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MAT I/III (Mg, K cofactors) (name copied from entity in Homo sapiens)
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MAT I homotetramer (name copied from entity in Homo sapiens)
4x(AHCY:NAD+) (name copied from entity in Homo sapiens)
ChEBI:60125 N-epsilon-(1-(1-carboxy)ethyl)lysine
MAT III homodimer (name copied from entity in Homo sapiens)
CTH tetramer:PXLP (name copied from entity in Homo sapiens)
AHCY:NAD+ (name copied from entity in Homo sapiens)
CNDP2 (name copied from entity in Homo sapiens)
GCL (name copied from entity in Homo sapiens)
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Frizzled/PCP signalling: a conserved mechanism regulating cell polarity and directed motility
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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 early endosome membrane
P5CS short isoform, dimer (name copied from entity in Homo sapiens)
PI(3,5)P2 is dephosphorylated to PI3P by FIG4 at the early endosome membrane
PYCR1 decamer (name copied from entity in Homo sapiens)
PI3P is phosphorylated to PI(3,5)P2 by PIKFYVE at the early endosome membrane
delta-1-pyrroline-5-carboxylate synthetase dimers
PI4P is dephosphorylated to PI by SYNJ at the plasma membrane
P5CS long isoform, dimer (name copied from entity in Homo sapiens)
PI is phosphorylated to PI4P by PI4K2A/B at the plasma membrane
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CCBL1 dimer (name copied from entity in Homo sapiens)
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
ASNS dimer (name copied from entity in Homo sapiens)
PI3P is dephosphorylated to PI by SYNJ/MTM[1] at the plasma membrane
GLUL decamer (name copied from entity in Homo sapiens)
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Biochemical analysis of the intrinsic Mcm4-Mcm6-mcm7 DNA helicase activity.
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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_32304.10
GPT2 dimer (name copied from entity in Homo sapiens)
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OAT hexamer (name copied from entity in Homo sapiens)
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PI is phosphorylated to PI4P by PI4K2A/B at the early endosome membrane
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GPT dimer (name copied from entity in Homo sapiens)
PI(4,5)P2 is dephosphorylated to PI4P by SYNJ/INPP5[1] at the plasma membrane
Amino acid synthesis and interconversion (transamination)
PI4P is dephosphorylated to PI by SACM1L at the Golgi membrane
NMNAT2 (Mg2+) (name copied from entity in Homo sapiens)
PI is phosphorylated to PI4P by PI4KA/2A/2B at the Golgi membrane
4xNMNAT3:4xMg2+ (name copied from entity in Homo sapiens)
PI3P is dephosphorylated to PI by SACM1L at the Golgi membrane
NADSYN1 homohexamer (name copied from entity in Homo sapiens)
PI is phosphorylated to PI3P by PIK3C2A/3 at the Golgi membrane
2xMTHFD1 (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)
PI4P is dephosphorylated to PI by SACM1L at the ER membrane
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MOCS3-S-S(1-):Zn2+ (name copied from entity in Homo sapiens)
PI is phosphorylated to PI4P by PI4KA/2B at the ER membrane
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2xNFS1:2xPXLP (name copied from entity in Homo sapiens)
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adenosine 5'-monophosphate [ChEBI:16027]
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PI(3,5)P2 is dephosphorylated to PI3P by FIG4 at the Golgi membrane
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PI3P is phosphorylated to PI(3,5)P2 by PIKFYVE at the Golgi membrane
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Btn-ACACB:2Mn2+ (name copied from entity in Homo sapiens)
6xNMNAT1:6xZn2+ (name copied from entity in Homo sapiens)
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1857-1895
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DAO dimer (name copied from entity in Homo sapiens)
5'-Phosphoribosyl-N-formylglycinamide [ChEBI:18272]
E1:Mg++ (name copied from entity in Homo sapiens)
ARD:Fe++ (name copied from entity in Homo sapiens)
MTAP trimer (name copied from entity in Homo sapiens)
APIP:Zn++ (name copied from entity in Homo sapiens)
ARG2 trimer (name copied from entity in Homo sapiens)
ALDH9A1 tetramer (name copied from entity in Homo sapiens)
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ASL tetramer (name copied from entity in Homo sapiens)
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ARG1 trimer (name copied from entity in Homo sapiens)
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ASS1 tetramer (name copied from entity in Homo sapiens)
ChEBI:18278 N-acetyl-D-glucosaminyldiphosphodolichol
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Disorders of proline and hydroxyproline metabolism
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1821-1838
PI is phosphorylated to PI5P by PIKFYVE at the late endosome membrane
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CCBL2 dimer (name copied from entity in Homo sapiens)
PI(3,5)P2 is dephosphorylated to PI5P by MTM[3] at the late endosome membrane
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OTC trimer (name copied from entity in Homo sapiens)
PI3P is dephosphorylated to PI by MTM[3] at the late endosome membrane
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PI is phosphorylated to PI3P by PIK3C2A/3 at the late endosome membrane
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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
BCAT2 dimer (name copied from entity in Homo sapiens)
Prostaglandin E synthase isomerizes PGH2 to PGE2
AASS tetramer (name copied from entity in Homo sapiens)
Cleavage of the gamma-glutamyl bond of LTC4 forms LTD4
PCBD1 tetramer (name copied from entity in Homo sapiens)
LTC4 is exported from the cytosol by ABCC1
ABCC1 mediates LTC4 export from the cell
ALDH4A1 dimer (name copied from entity in Homo sapiens)
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PHGHD tetramer (name copied from entity in Homo sapiens)
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PSAT1 dimer (name copied from entity in Homo sapiens)
3-Phospho-D-glyceroyl phosphate [ChEBI:16001]
(R)-2-Hydroxy-3-(phosphonooxy)-1-monoanhydridewith phosphoric propanoic acid
PSPH:Mg++ dimer (name copied from entity in Homo sapiens)
Two aldehyde dehydrogenases from human liver. Isolation via affinity chromatography and characterization of the isozymes.
BCAT1 dimer (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_79156.9
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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_114925.8
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
CAT tetramer (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=3665352
CAD hexamer (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_138507.5
catalase holoenzyme monomer (name copied from entity in Homo sapiens)
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UMPS dimer (name copied from entity in Homo sapiens)
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dihydroorotate dehydrogenase holoenzyme (name copied from entity in Homo sapiens)
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DUT trimer (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=3662484
DCTD hexamer (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=3659362
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3662485
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660798
AMPD3 tetramer (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=3660799
NP trimer (name copied from entity in Homo sapiens)
APRT homodimer (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=3658917
Guanine deaminase homodimer (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_79088.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665351
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_113121.8
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665353
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658505
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658507
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658504
adenylosuccinate synthetase like 1 holoenzyme dimer (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_154194.3
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=111745
adenosine kinase holoenzyme (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=29450
adenylosuccinate synthetase holoenzyme (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_3050.2
adenylosuccinate synthetase holoenzyme dimer (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_3495.2
adenylosuccinate synthetase like 1 holoenzyme (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=29372
adenylosuccinate lyase tetramer (name copied from entity in Homo sapiens)
Cloning, expression and characterization of the pig liver GDP-mannose pyrophosphorylase. Evidence that GDP-mannose and GDP-Glc pyrophosphorylases are different proteins
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
ATIC dimer (name copied from entity in Homo sapiens)
PPAT dimer (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=3660740
PPAT tetramer (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=3662439
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3662440
IMP (inosine monophosphate) dehydrogenase 1 tetramer (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=3662442
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
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_103164.9
2xPPCS (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=3664825
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664826
The protein deficient in Lowe syndrome is a phosphatidylinositol-4,5-bisphosphate 5-phosphatase
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664828
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2509836
4x(Btn-PC:Mn2+) (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_151581.1
ACACB:2Mn2+ (name copied from entity in Homo sapiens)
ACACA:2Mn2+ (name copied from entity in Homo sapiens)
2xPNPO:2xFMN (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_80621.9
2xPDXK:2xZn2+ (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=3665101
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_115523.8
4x(PC:Mn2+) (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=38117
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665350
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_103732.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665349
RFK:Mg2+ (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_110168.9
2xENPP1 (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=3665443
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_79397.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665442
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_157545.3
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.
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664834
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_155297.3
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=109330
CYB5A:ferriheme (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_2753.2
CYB5A:heme (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_152050.1
NUDT5 dimer (name copied from entity in Homo sapiens)
ITPA dimer (name copied from entity in Homo sapiens)
glutathione reductase holoenzyme (name copied from entity in Homo sapiens)
CTPS2 tetramer (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=2509835
CTPS tetramer (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_157084.3
deoxythymidylate kinase (thymidylate kinase) holoenzyme (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=3664829
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_100541.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664835
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665206
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_143809.5
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_78235.9
AK5 dimer (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=3665192
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_143866.5
TS dimer (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=3665193
CDA tetramer (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_5133.3
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=3660160
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660161
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2509848
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664831
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_150529.1
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=3664832
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_159540.3
Coupling of rotation and catalysis in F(1)-ATPase revealed by single-molecule imaging and manipulation
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1131972
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_150475.1
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_86613.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665195
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_131318.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665194
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=74722
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_139937.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665196
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_5598.2
WW domain-containing proteins, WWOX and YAP, compete for interaction with ErbB-4 and modulate its transcriptional function
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659660
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659662
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659661
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659664
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659663
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659677
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659679
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659678
Succinate dehydrogenase complex (reduced) (name copied from entity in Homo sapiens)
Succinate dehydrogenase flavoprotein (subunit A) (name copied from entity in Homo sapiens)
ETF (name copied from entity in Homo sapiens)
ETF (reduced) (name copied from entity in Homo sapiens)
fumarate hydratase tetramer (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=3659681
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659680
Exosomes mediate stromal mobilization of autocrine Wnt-PCP signaling in breast cancer cell migration
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659673
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659672
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659668
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659697
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659713
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
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659691
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659690
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659693
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659692
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659698
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659699
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659707
Expression and characterization of a human mitochondrial phenylalanyl-tRNA synthetase
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659708
ARFGAP1 promotes the formation of COPI vesicles, suggesting function as a component of the coat
Human phosphoglycerate kinase. I. Crystallization and characterization of normal enzyme
5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide (FAICAR) <=> inosine 5'-monophosphate + H2O
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664931
inosine 5'-monophosphate (IMP) + NAD+ + H2O => xanthosine 5'-monophosphate (XMP) + NADH + H+
IMP + H2O + NAD+ => XMP + NADH + H+ [IMPDH1,2]
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=3664936
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'-phosphoribosylformylglycinamidine (FGAM) + ATP => 5'-phosphoribosyl-5-aminoimidazole (AIR) + ADP + orthophosphate
5'-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide (SAICAR) <=> 5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR) + fumarate
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664935
5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR) + 10-formyltetrahydrofolate => 5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide (FAICAR) + tetrahydrofolate
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664945
Dissociation of phosphoribosyl pyrophosphate amidotransferase tetramer
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
5-phosphoribosylamine + glycine + ATP => 5-phosphoribosylglycinamide (GAR) + ADP + orthophosphate
5-Phosphoribosylamine + Glycine + ATP => GAR + ADP + Pi
5-phosphoribosylglycinamide (GAR) + 10-formyl-tetrahydrofolate => 5'-phosphoribosylformylglycinamide (FGAR) + tetrahydrofolate
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664942
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664943
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=164121
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_2883.1
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_166294.1
Formation of phosphoribosyl pyrophosphate amidotransferase tetramer
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665621
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_168783.1
Reducing equivalents from beta-oxidation of fatty acids transfer to ETF
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664969
Transfer of electrons from ETF to ubiquinone by ETF-QO
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_165935.1
2-oxoglutarate + 4-hydroxybutyrate <=> (R)-2-hydroxyglutarate + succinate semialdehyde
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664970
Transfer of electrons through the succinate dehydrogenase complex
(R)-2-hydroxyglutarate + FAD => 2-oxoglutarate + FADH2
(R)-2-hydroxyglutarate + succinate semialdehyde <=> 2-oxoglutarate + 4-hydroxybutyrate
(S)-Malate + NAD+ <=> Oxaloacetate + NADH + H+
Cytosolic aldehyde dehydrogenase (ALDH1) variants found in alcohol flushers
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664964
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664966
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_168454.1
PDK-catalyzed phosphorylation (inactivation) of PDC E1 alpha subunit
Inactivation of PDC by phosphorylation of PDC E1 alpha component
Acetyl-CoA + H2O + Oxaloacetate => Citrate + CoA
isocitrate + NAD+ => alpha-ketoglutarate + CO2 + NADH + H+ [IDH3]
Oxidative decarboxylation of alpha-ketoglutarate to succinyl CoA by alpha-ketoglutarate dehydrogenase
alpha-ketoglutarate + CoASH + NAD+ => succinyl-CoA + CO2 + NADH + H+
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664946
ADP + Orthophosphate + Succinyl-CoA <=> ATP + Succinate + CoA
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Succinate <=> Fumarate (with FAD redox reaction on enzyme)
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Cytosolic PYR is transported to the mitochondrial matrix by MPC1:MPC2
PYR + H+ (cytosol) => PYR + H+ (mitochondrial matrix)
Oxidative decarboxylation of pyruvate to acetyl CoA by pyruvate dehydrogenase
pyruvate + CoASH + NAD+ => acetylCoA + CO2 + NADH + H+
(S)-Lactate + NAD+ <=> Pyruvate + NADH + H+
MDMQ10H2 is methylated to DMQ10H2 by COQ5
PHB and all-E-10PrP2 are combined into DHB by COQ2
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GCH1 reduces GTP to dihydroneopterin triphosphate
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Pyruvate + NADH + H+ <=> (S)-Lactate + NAD+
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DMQ10H2 is hydroxylated to DeMQ10H2 by COQ7
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FPP and IPPP are combined into all-E-10PrP2 by PDSS1/2 tetramer
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glutathione (oxidized) + NADPH + H+ => 2 glutathione (reduced) + NADP+
dUDP or TDP + ADP <=> dUMP or TMP + ATP [DTYMK]
dUMP or TMP + ATP <=> dUDP or TDP + ADP [DTYMK]
phosphorylation of dUMP or TMP to dUDP or TDP
amination of uridine 5'-triphosphate (UTP) to form cytidine 5'-triphosphate (CTP)
UTP + glutamine + ATP + H2O => CTP + glutamate + ADP + orthophosphate [CTPS2]
UTP + glutamine + ATP + H2O => CTP + glutamate + ADP + orthophosphate [CTPS]
Reduction of semidehydroascorbate to ascorbate
ADP-ribose + H2O => AMP + D-ribose 5-phosphate (cytosolic)
Cytosolic NUDT5 hydrolyses ADP-ribose to R5P and AMP
A new human hereditary amyloidosis: the result of a stop-codon mutation in the apolipoprotein AII gene
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(d)AMP or (d)CMP + ATP <=> (d)ADP or (d)CDP + ADP [AK5]
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(deoxy)cytidine + H2O => (deoxy)uridine + NH4+ [CDA]
deamination of 2'-Deoxycytidine to 2'-Deoxyuridine
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dUMP + N5,N10-methylene tetrahydrofolate => TMP + dihydrofolate
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(d)ADP or (d)CDP + ADP <=> (d)AMP or (d)CMP + ATP [AK5]
EJC-independent degradation of nonsense immunoglobulin-mu mRNA depends on 3' UTR length
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
(S)-dihydroorotate + ubiquinone => orotate + ubiquinol
oxidation of (S)-Dihydroorotate to form Orotate
condensation of N-Carbamoyl-L-aspartate to form (S)-Dihydroorotate (ring closure)
N-carbamoyl L-aspartate + H+ <=> (S)-dihydroorotate + H2O
decarboxylation of Orotidine 5'-phosphate to form Uridine 5'-phosphate
orotidine 5'-monophosphate => uridine 5'-monophosphate + CO2
orotate + 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) <=> orotidine 5'-monophosphate (OMP) + pyrophosphate
phosphoribosylation of orotate to form oritidine 5'-phosphate (OMP)
hydrolysis of 2'-deoxyuridine 5'-triphosphate to form 2'-deoxyuridine 5'-phosphate
Pathways of DNA double-strand break repair during the mammalian cell cycle.
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
(2'-deoxy)adenosine + ATP => (d)AMP + ADP [ADK]
adenylosuccinate => adenosine 5'-monophosphate + fumarate
inosine 5'-monophosphate + L-aspartate + GTP => adenylosuccinate + guanosine 5'-diphosphate + orthophosphate
IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]
(deoxy)guanosine + orthophosphate <=> guanine + (deoxy)ribose 1-phosphate [NP]
hypoxanthine + (deoxy)ribose 1-phosphate <=> (deoxy)inosine + orthophosphate [NP]
guanine + (deoxy)ribose 1-phosphate <=> (deoxy)guanosine + orthophosphate [NP]
(deoxy)inosine + orthophosphate <=> hypoxanthine + (deoxy)ribose 1-phosphate [NP]
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ChEBI:11805 3-hydroxy-2-methylpropanoate
Multidrug resistance-associated protein 3
ATP-binding cassette sub-family C member 3
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Multidrug resistance-associated protein 6
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UDP-xylose and UDP-N-acetylglucosamine transporter
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Calcium-transporting ATPase type 2C member 2
Calcium-transporting ATPase type 2C member 1
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Probable phospholipid-transporting ATPase IA
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sphingosine 1-phosphate + H2O => sphingosine + orthophosphate [cytosolic - SGPP]
sphinganine 1-phosphate + H2O => sphinganine + orthophosphate
sphinganine + stearyl-CoA => dihydroceramide + CoASH
palmitoyl-CoA + serine => 3-ketosphinganine + CoASH + CO2
dihydroceramide + NADPH + H+ + O2 => phytoceramide + NADP+ + H2O
dihydroceramide + NAD(P)H + H+ + O2 => ceramide + NAD(P)+ + H2O
3-ketosphinganine + NADPH + H+ => sphinganine + NADP+
The role of NuMA in the interphase nucleus
Sphingomyelin phosphodiesterase 2 and 3 (SMPD2 and 3) hydrolyse sphingomyelin to ceramide (plasma membrane)
Ectonucleotide pyrophosphatase/phosphodiesterase 7 (ENPP7) hydrolyses sphingomyelin
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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)
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ATP-binding cassette sub-family B member 6, mitochondrial
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Kinetic evaluation of human cloned coproporphyrinogen oxidase using a ring isomer of the natural substrate
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Apical GLUT2: a major pathway of intestinal sugar absorption
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Wnt/Fz signaling and the cytoskeleton: potential roles in tumorigenesis
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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_101211.9
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Endoplasmic reticulum (ER) chaperone regulation and survival of cells compensating for deficiency in the ER stress response kinase, PERK
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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=111584
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_3823.2
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_79659.9
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_140636.5
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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_103869.9
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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=3665213
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_127441.5
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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_134566.5
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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_4103.2
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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=3659467
Conversion of leukotriene D4 to leukotriene E4 by a dipeptidase released from the specific granule of human polymorphonuclear leucocytes
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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_85458.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=111427
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_155947.3
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Determinants for activation of the atypical AGC kinase Greatwall during M phase entry
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The TREM receptor family and signal integration
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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_30798.10
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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=29586
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_3661.2
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=111399
Probable phospholipid-transporting ATPase VA
Probable phospholipid-transporting ATPase VD
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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_5412.3
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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=3661377
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_155295.3
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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_153786.3
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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=3661386
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661385
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_2513.2
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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_99755.9
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Homologues of p-Y90,T538,S676,S695-PRKCQ
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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_4927.2
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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=3661366
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=114549
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661371
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661372
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_4514.1
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_3646.1
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=113572
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661373
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_3395.2
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=111354
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659492
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_3964.3
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Telomeres shorten during ageing of human fibroblasts
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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_82004.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=140344
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661356
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661355
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_2939.2
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_90409.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665380
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_89955.9
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Oligosaccharyl transferase 48 kDa subunit
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
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Rad51 recombinase and recombination mediators.
Protein kinase C substrate 60.1 kDa protein heavy chain
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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_133200.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664436
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_159530.3
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=3665444
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_102628.9
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_145344.5
5-triphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate
5-triphospho-1D-myo-inositol (1,2,3,4,6)pentakisphosphate [ChEBI:62985]
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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_139416.5
PLP from oxidation of pyridoxine phosphate
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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=3664446
Secretion of Wnt ligands requires Evi, a conserved transmembrane protein
PLP results from phosphorylation of pyridoxal
Wntless, a conserved membrane protein dedicated to the secretion of Wnt proteins from signaling cells
PLP from oxidation of pyridoxamine phosphate
Two novel rat liver membrane proteins that bind advanced glycosylation endproducts: relationship to macrophage receptor for glucose-modified proteins
Condensation of phosphopantothenate with cysteine
SLC25A16 transports cytosolic CoA-SH to mitichondrial matrix
CoA transport across the inner mitochondrial membrane
Renal physiology of SLC26 anion exchangers
Human alanyl-tRNA synthetase: conservation in evolution of catalytic core and microhelix recognition
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_137538.5
Human Na(+)/H(+) exchanger isoform 6 is found in recycling endosomes of cells, not in mitochondria
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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=3664384
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664368
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_144556.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664418
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_130402.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664396
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_126729.5
The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs
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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_147319.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664385
1,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6)tetrakisphosphate
1,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6)tetrakisphosphate [ChEBI:62923]
3-diphospho-1D-myo-inositol (1,2,4,5,6)pentakisphosphate
3-diphospho-1D-myo-inositol (1,2,4,5,6)pentakisphosphate [ChEBI:62922]
3-diphospho-1D-myo-inositol (1,4,5,6)tetrakisphosphate
3-diphospho-1D-myo-inositol (1,4,5,6)tetrakisphosphate [ChEBI:62927]
1-diphospho-1D-myo-inositol (3,4,5,6)tetrakisphosphate
1-diphospho-1D-myo-inositol (3,4,5,6)tetrakisphosphate [ChEBI:62926]
3,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6)tetrakisphosphate
3,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6)tetrakisphosphate [ChEBI:62924]
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_133853.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664374
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664406
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_128391.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664407
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664390
Recruitment of mitotic centrosome proteins and complexes
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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=3664395
1-diphospho-1D-myo-inositol (2,3,4,5,6)pentakisphosphate [ChEBI:62919]
1-diphospho-1D-myo-inositol (2,3,4,5,6)pentakisphosphate
1,5-bisdiphosphoinositol-1D-myo-inositol (3,4,6)trisphosphate
1,5-bisdiphosphoinositol-1D-myo-inositol (3,4,6)trisphosphate [ChEBI:62931]
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_132421.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664430
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664429
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_144342.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664363
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661663
Precise binding of single-stranded DNA termini by human RAD52 protein.
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_136768.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664373
5-diphospho-1D-myo-inositol (1,3,4,6)tetrakisphosphate
5-diphospho-1D-myo-inositol (1,3,4,6)tetrakisphosphate [ChEBI:62928]
Heteroduplex formation by human Rad51 protein: effects of DNA end-structure, hRP-A and hRad52.
Human frataxin is an allosteric switch that activates the Fe-S cluster biosynthetic complex
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_153343.3
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=3664369
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Replication protein A (RPA): the eukaryotic SSB.
Ribosomal scanning and start codon recognition
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NUDT16 is a (deoxy)inosine diphosphatase, and its deficiency induces accumulation of single-strand breaks in nuclear DNA and growth arrest
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Silica crystals and aluminum salts activate the NALP3 inflammasome through phagosomal destabilization
Identification of mammalian microRNA host genes and transcription units
Crystal structure of human kynurenine aminotransferase I
alpha-methyl-acetoacetyl-CoA + CoA => propionyl-CoA + acetyl-CoA
beta-hydroxyisobutyryl-CoA + H2O => beta-hydroxyisobutyrate + CoA
lysine + alpha-ketoglutarate +NADPH + H+ => saccharopine + NADP+ + H2O
saccharopine + NAD+ + H2O => alpha-aminoadipic semialdehyde + glutamate + NADH + H+
2-oxoglutarate [mitochondrial matrix] + 2-oxoadipate [cytosol] <=> 2-oxoglutarate [cytosol] + 2-oxoadipate [mitochondrial matrix]
Exchange of cytosolic 2-oxoadipate for mitochondrial 2-oxoglutarate
Oxidative decarboxylation of alpha-ketoadipate to glutaryl CoA by alpha-ketoglutarate dehydrogenase
alpha-ketoadipate + CoASH + NAD+ => glutaryl-CoA + CO2 + NADH + H+
phenylalanine + pyruvate => 3-(indol-3-yl)pyruvate + alanine
4a-hydroxytetrahydrobiopterin => q-dihydrobiopterin + H2O
L-glutamate gamma-semialdehyde + NAD+ => glutamate + NADH + H+
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aspartate + glutamine + ATP <=> asparagine + glutamate + AMP + pyrophosphate [ASNS]
glutamate + NH4+ + ATP => glutamine + ADP + orthophosphate [GLUL]
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3-phosphonooxypyruvic acid + L-glutamate = O-phospho-L-serine + 2-oxoglutarate
glutamine + pyruvate => 2-oxoglutaramate + alanine
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leu, ile, or val + alpha-ketoglutarate <=> a-ketoisocaproate, a-keto-b-methylvalerate, or a-ketoisovalerate + glutamate [BCAT2]
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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 [BCAT1]
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a-ketoisocaproate, a-keto-b-methylvalerate, or a-ketoisovalerate + glutamate <=> leu, ile, or val + alpha-ketoglutarate [BCAT1]
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S-Adenosyl methionine <=> Decarboxylated-Adenosyl methionine + CO2
Putrescine + dc-Adenosyl methionine => Spermidine + 5'-methylthioadenosine
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Identification, cloning, expression, and purification of three novel human calcium-independent phospholipase A2 family members possessing triacylglycerol lipase and acylglycerol transacylase activities
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Methylthio-ribose-P = Methylthio-ribulose-P
Methylthio-ribulose-P = Methylthio-ribose-P
glutamate + acetyl CoA => N-acetyl glutamate + CoA
2 ATP + NH4+ + HCO3- => 2 ADP + orthophosphate + carbamoyl phosphate [mitochondrial]
2 ATP + NH4+ + HCO3- => 2 ADP + orthophosphate + carbamoyl phosphate
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kynurenine + pyruvate => 4-(2-aminophenyl)-2,4-dioxobutanoic acid + alanine [CCBL1]
kynurenine + pyruvate => 4-(2-aminophenyl)-2,4-dioxobutanoic acid + alanine [CCBL2]
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arginine + H2O => ornithine + urea [ARG2]
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gamma-butyrobetaine semialdehyde + NAD+ => gamma-butyrobetaine + NADH + H+
argininosuccinate <=> fumarate + arginine
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arginine + H2O => ornithine + urea [ARG1]
carbamoyl phosphate + ornithine => citrulline + orthophosphate
ATP + aspartate + citrulline <=> argininosuccinate + AMP + pyrophosphate
Human platelets contain SNARE proteins and a Sec1p homologue that interacts with syntaxin 4 and is phosphorylated after thrombin activation: implications for platelet secretion
Uroporphyrinogen III is decarboxylated to form coproporphyrinogen III
Conversion of HMB to uroporphyrinogen III
Uroporphyrinogen I is decarboxylated to form coproporphyrinogen I
Excess cysteine yields lanthionine and H2S
Persulfide sulfur is transferred onto sulfite
SQR oxidizes sulfide to bound persulfide
ALAD octamer associates with Pb++, forming a catalytically inactive complex
Succinyl CoA and glycine condense to form 5-aminolevulinate (ALA)
ALAS condenses SUCC-CoA and Gly to form dALA
Four PBGs combine through deamination to form hydroxymethylbilane (HMB)
Two molecules of ALA condense to form porphobilinogen (PBG)
Excess homocysteine yields homolanthionine and H2S
Homocysteine is degraded to oxobutanoate and H2S
glycine + O2 => glyoxylate + H2O2 + NH4+
SAM is sythesized from methionine's reaction with ATP
Purification and partial amino acid sequence of human aconitase
Crystal structure of an Hsp90-geldanamycin complex: targeting of a protein chaperone by an antitumor agent
gamma-glutamylcysteine combines with glycine to form glutathione
3,4-dihydroxybenzoate can be O-methylated
acetaldehyde + NAD+ => acetate + NADH + H+ [cytosolic]
acetate + CoA + ATP => acetyl-CoA + AMP + pyrophosphate [mitochondrial]
acetaldehyde + NAD+ => acetate + NADH + H+ [mitochondrial]
Ferrous iron is inserted into protoporphyrin IX to form heme
Oxidation of protoporphyrinogen IX to protoporphyrin IX
Conversion of coproporphyrinogen III to protoporphyrinogen IX
eukaryotic translation initiation factor 3 subunit 6
Eukaryotic translation initiation factor 3 subunit 2
eukaryotic translation initiation factor 3 subunit 9
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
eukaryotic translation initiation factor 3 subunit 8
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Eukaryotic translation initiation factor 3 subunit 3
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Eukaryotic translation initiation factor 1A, X-chromosomal
eukaryotic translation initiation factor 1A
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Structural analysis and detection of biological inositol pyrophosphates reveal that the family of VIP/diphosphoinositol pentakisphosphate kinases are 1/3-kinases
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Inositol polyphosphates: a new frontier for regulating gene expression
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Phospholipases D1 and D2 coordinately regulate macrophage phagocytosis
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Mast cell signal transduction from the high-affinity IgE receptor
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Phenylalanyl-tRNA synthetase alpha chain
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Cytoslic carboxylases translocate to mitochondrial matrix
ABCC1 transports cytosolic Cbl to extracellular region
Ligand-independent dimerization activates the stress response kinases IRE1 and PERK in the lumen of the endoplasmic reticulum
Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT3]
Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2]
Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT1]
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Human glutamine phosphoribosylpyrophosphate amidotransferase. Kinetic and regulatory properties
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Conversion of cytosolic 5-methyltetrahydrofolate (5-methylTHF) to 5-methylTHF-polyglutamate
Human thymidylate kinase. Purification, characterization, and kinetic behavior of the thymidylate kinase derived from chronic myelocytic leukemia
Conversion of cytosolic THF to THF-polyglutamate
Rich, a rho GTPase-activating protein domain-containing protein involved in signaling by Cdc42 and Rac1
Homologues of p-Y90,T219,T538,S676,S695-PRKCQ
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Dynamics of transitional endoplasmic reticulum sites in vertebrate cells
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glutamate + ATP + NADPH + H+ => L-glutamate gamma-semialdehyde + NADP+ + ADP + orthophosphate [P5CS]
glutamate + L-glutamate gamma-semialdehyde <=> ornithine + alpha-ketoglutarate [OAT]
ornithine + alpha-ketoglutarate <=> glutamate + L-glutamate gamma-semialdehyde [OAT]
aspartate + alpha-ketoglutarate <=> oxaloacetate + glutamate [GOT2]
oxaloacetate + glutamate <=> aspartate + alpha-ketoglutarate [GOT1]
pyruvate + glutamate <=> alanine + alpha-ketoglutarate [GPT2]
alanine + alpha-ketoglutarate <=> pyruvate + glutamate [GPT2]
pyruvate + glutamate <=> alanine + alpha-ketoglutarate [GPT]
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alanine + alpha-ketoglutarate <=> pyruvate + glutamate [GPT]
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Sequence survey of receptor tyrosine kinases reveals mutations in glioblastomas
L-1-pyrroline-5-carboxylate + NADPH + H+ => proline + NADP+
5,10-methenylTHF polyglutamate + NADPH + H+ <=> 5,10-methyleneTHF polyglutamate + NADP+
10-formylTHF polyglutamate <=> 5,10-methenylTHF polyglutamate + H2O
5,10-methyleneTHF polyglutamate + NADP+ <=> 5,10-methenylTHF polyglutamate + NADPH + H+
5,10-methyleneTHF polyglutamate + NADPH + H+ => 5-methylTHF polyglutamate + NADP+
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
Conversion of mitochondrial THF to THF-polyglutamate
Synthesis of IP2, IP, and Ins in the cytosol
5,10-methenylTHF polyglutamate + H2O <=> 10-formylTHF polyglutamate
NFS1 transfers sulfur from cysteine onto MOCS3
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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=3661461
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661462
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_5821.1
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=113575
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659656
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_87653.9
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_3341.1
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=113535
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_2530.1
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=141343
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_5022.2
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=113602
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661555
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661556
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661559
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661560
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661557
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661558
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661442
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661562
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_29936.10
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_90043.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29382
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_3820.1
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=30064
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_3957.2
Structural basis for tumor pyruvate kinase M2 allosteric regulation and catalysis
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659653
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659654
Phosphoinositides as regulators of membrane trafficking in health and disease
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_30926.10
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=3659319
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659312
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659313
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_2904.2
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=111647
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665130
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_87357.9
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_146149.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665142
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660032
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660033
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660034
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660036
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113569
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_4475.1
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_79757.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661518
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661523
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661522
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661525
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661524
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661526
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_100721.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661514
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_4733.3
Recycling of the cell adhesion molecule L1 in axonal growth cones
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113599
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_3272.2
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=83927
Signal recognition particle 68 kDa protein
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_31724.10
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=3660364
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659646
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659645
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661508
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661507
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661506
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661505
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661513
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661511
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661510
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661509
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661504
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661503
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_129651.5
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_3489.2
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_3479.2
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=109328
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663878
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_21463.1
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=3663876
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=500245
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665550
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_140259.5
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_3095.2
The characterization of gene mutations for human glucose phosphate isomerase deficiency associated with chronic hemolytic anemia
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=83926
Tumor necrosis factor alpha-induced phosphorylation of I kappa B alpha is a signal for its degradation but not dissociation from NF-kappa B
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661554
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661551
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661550
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661553
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661552
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661547
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661546
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661549
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661548
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661545
eukaryotic translation initiation factor 3 subunit 5
eukaryotic translation initiation factor 3 subunit 7
eukaryotic translation initiation factor 3 subunit 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=3659648
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_110833.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659649
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_101336.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665141
From structure to disease: the evolving tale of aquaporin biology
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_32872.10
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=3659634
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659632
Eukaryotic translation initiation factor 3 subunit 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=3659631
eukaryotic translation initiation factor 2, subunit 2
Eukaryotic translation initiation factor 2 subunit 2
eukaryotic translation initiation factor 2 beta subunit
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
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661544
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661543
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661542
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661541
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661540
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661535
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661534
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661530
eukaryotic translation initiation factor 4H
Williams-Beuren syndrome chromosome region 1 protein
Tristetraprolin recruits functional mRNA decay complexes to ARE sequences
eukaryotic translation initiation factor 5
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_2585.2
Eukaryotic translation initiation factor 4E
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_92775.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660363
Signal transduction by immunoglobulin is mediated through Ig alpha and Ig beta
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=83951
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_4959.2
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=109331
translation initiation factor 2B alpha subunit
Translation initiation factor eIF-2B alpha subunit
eIF-2B GDP-GTP exchange factor, alpha 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_21661.1
Translation initiation factor eIF-2B gamma subunit
eIF-2B GDP-GTP exchange factor, gamma subunit
translation initiation factor 2B gamma 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=500172
translation initiation factor 2B beta subunit
eIF-2B GDP-GTP exchange factor, beta subunit
Translation initiation factor eIF-2B beta subunit
eIF-2B GDP-GTP exchange factor, epsilon subunit
Translation initiation factor eIF-2B epsilon subunit
translation initiation factor 2B epsilon subunit
DNA structural elements required for FEN-1 binding.
translation initiation factor 2B delta subunit
eIF-2B GDP-GTP exchange factor, delta subunit
Translation initiation factor eIF-2B delta 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=3663905
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663901
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663906
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663892
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663896
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663897
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663908
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663915
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_131444.5
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
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663870
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
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663855
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663868
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663869
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663867
Evidence that negative elongation factor represses transcription elongation through binding to a DRB sensitivity-inducing factor/RNA polymerase II complex and RNA.
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663859
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663871
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663850
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112016
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_128560.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=500244
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663826
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_21637.1
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=3663830
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663834
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=83956
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663835
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_4062.2
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=3663872
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112032
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Aquaporin-1, nothing but a water channel
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A novel disorder caused by defective biosynthesis of N-linked oligosaccharides due to glucosidase I deficiency
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Regulation of cell growth-dependent expression of mammalian CDC6 gene by the cell cycle transcription factor E2F.
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Differential expression of aquaporin 7 in adipose tissue of lean and obese high fat consumers
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Coupling RNA polymerase II transcription with pre-mRNA processing.
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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
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Translocation of cyclin B1 to the nucleus at prophase requires a phosphorylation-dependent nuclear import signal
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Metabolism of water-soluble vitamins and cofactors
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Comprehensive genomic characterization defines human glioblastoma genes and core pathways
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Diseases associated with visual transduction
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Multiple pathways for mitochondrial protein traffic
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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_88843.9
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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
Calcium is sequestered to the golgi by secretory pathway calcium-ATPases (SPCAs)
ATP2C1/2:Mg2+ transport cytosolic Ca2+ to Golgi lumen
Aquaporins: translating bench research to human disease
Acidification of Tf:TfR1 containing endosome
Translocation of PKC theta to plasma membrane
Translocation of PDK1 to Plasma membrane
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
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Activation of Protein Kinase C beta (PKC-beta)
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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_17687.1
Passive Transport of Urea out of Cells by Aquaporins
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Passive Transport of Water out of Cell by Aquaporin-3
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Passive Transport of Glycerol out of Cell by Aquaporin-7
Passive Transport of Glycerol into Cell by Aquaporin-9
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Passive Transport of Water out of Cells by Aquaporins
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Passive Transport of Glycerol into Cells by Aquaporins
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Passive Transport of Glycerol out of Cells by Aquaporins
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Passive Transport of Urea into Cells by Aquaporins
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SLC35C1 mediates the transport of UDP-fucose into the Golgi lumen
Passive Transport of Water into Cells by Aquaporins
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SLC35B4 mediates the transport of UDP-N-acetylglucosamine into the Golgi lumen
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SLC35A1 mediates the antiport of CMP-sialic acid in exchange for CMP
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SLC35B4 mediates the transport of UDP-xylose into the Golgi lumen
Cellular copper transport is mediated by human copper transporter 1 hCTR1
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AT1 transports acetyl-CoA into the Golgi lumen
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ZnT5 transports zinc into secretory granules in pancreatic beta cells
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ZnT7 transports zinc into the golgi apparatus
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ZnT1 mediates the efflux of zinc from the cell
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Proton-coupled histidine and di-peptide cotransport
Characterization of FIM-FGFR1, the fusion product of the myeloproliferative disorder-associated t(8;13) translocation
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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
The ABCC family mediates organic anion transport
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K+-independent Li+/Ca2+ exchanger transport
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Na+/H+ exchanger transport (at early endosome membrane)
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Na+/H+ exchanger transport (at trans-golgi membrane)
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Intracellular transport and kinesin superfamily proteins, KIFs: structure, function, and dynamics
Na+/H+ exchanger transport (at late endosome membrane)
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Proton-coupled di- and tri-peptide cotransport
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Serine/threonine-protein kinase Chk1 (EC 2.7.1.-)
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ABC7, mABC1 and mABC2 mediate heme transport
MTABC3 transports porphyrin into mitochondria
Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA
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Processive synthesis on the leading strand
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Loading of PCNA - Sliding Clamp Formation
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RFC dissociates after sliding clamp formation
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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_162893.2
Multiple proteins are localized at replication fork
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Ribonucleoside-diphosphate reductase M2 chain
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.
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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).
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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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The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer at the origin
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, Rönnstrand 2004, Lennartsson and Rönnstrand 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 (Rönnstrand 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, Rönnstrand 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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DNA polymerase epsilon binds at the origin
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.
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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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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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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.
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.
Mitotic spindle assembly checkpoint protein MAD2A (MAD2-like 1) (HsMAD2)
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.
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
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).
Phosphorylated Orc1 is ubiquitinated while still associated with chromatin
The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer at the origin
DNA polymerase alpha:primase binds at the origin
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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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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.
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 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.
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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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Methylation of 3,4-dihydroxyphenylacetic acid to homovanillic acid
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.
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).
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).
Mcm10 associates with the pre-replicative complex, stabilizing Mcm2-7
Orc1 associates with Orc4:Orc5:Orc3:Orc2:origin complexes
DNA Replication Factor A (RPA) associates with the pre-replicative complex at the origin
The mitochondrial electron transport and oxidative phosphorylation system
Cdc45 associates with the pre-replicative complex at the origin
Orc3 associates with Orc2 constitutively bound at origins of replication
5-hydroxyindole acetaldehyde to 5-hydroxyindole acetic acid
Orc4 associates with Orc5:Orc3:Orc2:origin complexes
PIKfyve, a mammalian ortholog of yeast Fab1p lipid kinase, synthesizes 5-phosphoinositides. Effect of insulin
Orc5 associates with Orc3:Orc2:origin complexes
Conversion of GABA to Succinate Semialdehyde
methylation of Dopamine to form 3-Methoxytyramine
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
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).
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 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.
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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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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.
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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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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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.
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RhoA is activated by guanine nucleotide exchange factors (RhoGEF), exchanging GDP for GTP. RHOA, activated following binding of MDGIs to the NgR:p75NTR complex, rigidifies the actin cytoskeleton, thereby inhibiting axonal elongation and causing growth cone collapse.
ATAC spliceosome mediated 3' splice site cleavage, exon ligation
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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.
ATAC spliceosome mediated Lariat formation,5' splice site cleavage
p75NTR can also form a receptor complex with the Nogo receptor (NgR). Such complexes mediates axonal outgrowth inhibitory signals of MDGIs (myelin-derived growth-inhibitors), such as Nogo66, myelin-associated glycoprotein (MAG), and oligodendrocyte myelin glycoprotein (OMGP).
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Phosphorylated MAPKs phosphorylate ATF-2
phosphorylated MKK3/MKK6 migrates to nucleus
Activated human JNKs migrate to nucleoplasm
Phosphorylation of human JNKs by activated MKK4/MKK7
Binding of ADAR2 homodimer to dsRNA duplex
Deamination at C6 position of adenosine in Editosome (ADAR1)
Expression of human thymidylate synthase in Escherichia coli
Deamination at C6 position of adenosine in Editosome (ADAR2)
Reconstitution of the strand invasion step of double-strand break repair using human Rad51 Rad52 and RPA proteins
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.
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.
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.
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.
p75NTR modulates axonal growth by regulating the activity of small GTPases like RHOA and RHOB, that control the state of actin polymerization. The best studied is RHOA. In its active, GTP-bound form, RHOA rigidifies the actin cytoskeleton, thereby inhibiting axonal elongation and causing growth cone collapse. Depending on the ligand that binds to it, p75NTR can either promote or inhibit axonal growth, Neurotrophin binding leads to inhibition of RHOA activity and axonal growth. Axonal growth inhibition is caused by myelin molecules named MDGIs (myelin-derived growth inhibitors), such as NOGO, MAG, OMGP. MDGIs bind to a complex made up of p75NTR and the NOGO receptor, causing RHOA activation and axonal growth inhibition.
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.
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.
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.
The adaptor protein Frs2 (Fibroblast growth factor receptor substrate 2) can mediate the prolonged activation of the MAPK (ERK) cascade.
Transfer of GMP from the capping enzyme GT site to 5'-end of mRNA
Critical role for the docking-protein FRS2 alpha in FGF receptor-mediated signal transduction pathways
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.
Recognition and binding of the mRNA cap by the cap-binding complex
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.
Dissociation of transcript with 5'-GMP from GT
Binding of ADAR1 homodimer to dsRNA duplex
Functional characterization of human 1-acylglycerol-3-phosphate acyltransferase isoform 8: cloning, tissue distribution, gene structure, and enzymatic activity
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The primary structure of mitochondrial aspartate aminotransferase from human heart
Formation of the CE:GMP intermediate complex
Hydrolysis of the 5'-end of the nascent transcript by the capping enzyme
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4Fe-4S Cluster Forms on NUBP2:NUBP1 Scaffold
Activated AMPK phosphorylates TSC2 and activates the TSC complex. TSC2 functions as a GTPase-activating protein and stimulates the intrinsic GTPase activity of a small G-protein Rheb. This results in conversion of Rheb-GTP into Rheb-GDP, and in inhibition of the mTOR activation by GTP-bound Rheb.
carbovir monophosphate + ATP => carbovir diphosphate + ADP
Phosphorylation of carbovir monophosphate
Transfer of Electrons from NADPH to FDXR
Mitoferrin Transports Iron Across the Mitochondrial Inner Membrane
TSC2 (in the TSC complex) functions as a GTPase-activating protein and stimulates the intrinsic GTPase activity of a small G-protein Rheb. This results in the conversion of Rheb-GTP into Rheb-GDP and in the inhibition of the mTOR activation by GTP-bound Rheb (Inoki K et al, 2003; Tee AR et al, 2003).
mTOR forms a functional protein complex with at least two proteins: Raptor (Regulated Associated Protein of mTOR) and mLst8. This complex is called mammalian TOR complex 1 (mTORC1). Raptor serves as a scaffolding protein to bridge the interaction between mTOR and its substrates. mLst8 enhances the association of mTOR with Raptor. [Rheb:GTP] binds and activates mTORC1. Besides binding directly to mTOR, Rheb can also bind to Raptor and mLst8 (PMIDs 15854902, 15755954 and 12150926).
S6K1 contains a TOS motif. mTORC1 requires an intact TOS motif to bind and phosphorylate S6K1 (PMID 15809305).
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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).
eIF4B is a physiologically relevant target of S6K1. Once phosphorylated and activated by S6K1, eIF4B specifically stimulates the ATPase and RNA helicase activities of eIF4A.
Serine/threonine-protein kinase greatwall
Rheb is a GTP binding protein that exhibits GTPase activity. GDP is exchanged for GTP in the [Rheb:GDP] complex to form [Rheb:GTP], which binds and activates the mTORC1 complex. This exchange is catalysed by an as yet unidentified guanine exchange factor (GEF) (PMIDs 15951850 and 15755954).
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Phospholipases and phagocytosis: the role of phospholipid-derived second messengers in phagocytosis
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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.
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'.
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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The sulfur-containing amino acids: an overview
Signalling via integrins: implications for cell survival and anticancer strategies
Each conserved active site tyr in the three subunits of human isocitrate dehydrogenase has a different function
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Running with RNA polymerase: eukaryotic transcript elongation.
Structural maintenance of chromosomes protein 4
The AU-rich element mRNA decay-promoting activity of BRF1 is regulated by mitogen-activated protein kinase-activated protein kinase 2
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
Chromosome condensation-related SMC-associated protein 1
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Structural maintenance of chromosomes protein 2
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T-complex protein 1 subunit epsilon (TCP-1-epsilon)
T-complex protein 1 subunit alpha (TCP-1-alpha)
T-complex protein 1 subunit eta (TCP-1-eta)
Overexpression of the normal phosphoribosylpyrophosphate synthetase 1 isoform undelies catalytic superactivity of human phosphoribosylpyrophosphate synthetase
T-complex protein 1 subunit beta (TCP-1-beta)
T-complex protein 1 subunit delta (TCP-1-delta)
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A cell-based reglucosylation assay demonstrates the role of GT1 in the quality control of a maturing glycoprotein
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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.
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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The ATM-Chk2-Cdc25A checkpoint pathway guards against radioresistant DNA synthesis.
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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.
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).
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).
GRB2 can bind EGFR directly or through another SH2-containing protein, SHC1. This association leads to RAS activation.
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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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After being phosphorylated, p-ERK1/2 dissociate from MEK1/2 and dimerize.
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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.
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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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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.
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.
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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.
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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.
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.
Two phospho-ERK1 molecules dimerise and enter the nucleus, where they may phosphorylate downstream targets.
Phospho-ERK-1 dimer is translocated from cytosol to nucleoplasm.
Activated MEK1 phosphorylates and activates ERK1.
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.
Activated MEK phosphorylates and activates ERK.
Activated MEK2 phosphorylates and activates ERK2.
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 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.
Human and murine serine-palmitoyl-CoA transferase--cloning, expression and characterization of the key enzyme in sphingolipid synthesis
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).
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.
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).
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.).
Structures of lung cancer-derived EGFR mutants and inhibitor complexes: mechanism of activation and insights into differential inhibitor sensitivity
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.
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.
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.
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 EâF-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).
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).
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.
Epidermal growth factor receptor: elements of intracellular communication
G beta:gamma signalling through PI3Kgamma
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.
The diadenosine hexaphosphate hydrolases from Schizosaccharomyces pombe and Saccharomyces cerevisiae are homologues of the human diphosphoinositol polyphosphate phosphohydrolase. Overlapping substrate specificities in a MutT-type protein
Regulation of actin filament assembly by Arp2/3 complex and formins
Annu Rev Biophys Biomol Struct 36:451-77
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.
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).
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).
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.
After Platelet activation '78 kDa glucose-regulated protein' from the endoplasmic reticulum lumen is released in to the extracellular platelet releasate.
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.
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.
Cytokinesis requires the central spindle, which forms during anaphase by the bundling of antiparallel nonkinetochore microtubules. Microtubule bundling and completion of cytokinesis require MKLP1, a kinesin-6 family member, and RACGAP1 (MgcRacGap), which contains a RhoGAP domain. These form a heterotetrameric complex known as centralspindlin. Centralspindlin, but not its individual components, strongly promotes microtubule bundling in vitro.
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).
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.
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.
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.
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.
Vav interacts directly with PIP2 and PIP3, with a fivefold selectivity for PIP3 over PIP2. PIP3 gives a twofold stimulation of Vav1 GEF activity while PIP2 leads to 90% inhibition. Binding probably occurs through the PH domain, known to bind phosphoinositides.
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.
Vav3 is a guanine nucleotide exchange factors (GEF) for RhoA, RhoB and to a lesser extent Rac1.
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'.
1,2-Diacyl-sn-glycerol 3-phospho-L-serine
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'.
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.
1-phosphatidyl-1D-myo-inositol 4,5- bisphosphate
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Regulation of pyruvate dehydrogenase (PDH) complex
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Human ornithine transcarbamylase: crystallographic insights into substrate recognition and conformational changes
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Signal-induced degradation of I kappa B alpha requires site-specific ubiquitination
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Non-vesicular lipid transport by lipid-transfer proteins and beyond
The LKB1 tumor suppressor kinase in human disease
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The SLC40 basolateral iron transporter family (IREG1/ferroportin/MTP1)
Complex genomic rearrangements lead to novel primate gene function
Why calcium-stimulated adenylyl cyclases?
Mechanisms involved in the intestinal digestion and absorption of dietary vitamin A
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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
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2-acyl-sn-glycero-3-phospho-D-myo-inositol [ChEBI:62746]
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Absorption of chlorophyll phytol in normal man and in patients with Refsum's disease
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AUF1, the regulator of tumor necrosis factor alpha messenger RNA decay, is targeted by autoantibodies of patients with systemic rheumatic diseases
dolichyl D-mannosyl phosphate [ChEBI:15809]
Eukaryotic translation initiation factor 5A
Recruitment of the Rad9-Hus1-Rad1 complex to DNA
MAD2 associates with the Mad1 kinetochore complex
MAD2 converted to an inhibitory state via interaction with Mad1
Release of activated MAD2 from kinetochores
Detection of damage during initiation of DNA synthesis in S-phase
Association of Cdc13/Cdk1 with replicative origin
At the beginning of this reaction, 1 molecule of 'ORC:origin complex', and 1 molecule of 'Cdc13 (Cyclin B) protein ' are present. At the end of this reaction, 1 molecule of 'ORC:origin:Cdc13 (cyclin B) complex' is present. This reaction takes place in the 'nucleus'.
Translocation of Cyclin B1:phospho-Cdc2 complexes to the nucleus
CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes
Phosphorylation of CAP-G is required for its chromosomal DNA localization during mitosis
Biochem. Biophys. Res. Commun. 377:1007-11
Translocation of Cyclin B1:phospho-Cdc2 to the cytoplasm
The Bcl10-Malt1 complex segregates Fc epsilon RI-mediated nuclear factor kappa B activation and cytokine production from mast cell degranulation
N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase
dolichyl-phosphate mannosyltransferase polypeptide 2
Eukaryotic translation initiation factor 5A-1
Frequent activating mutations of FGFR3 in human bladder and cervix carcinomas
Peptide transfer from P-site tRNA to the A-site tRNA
Synthesis of nascent polypeptide containing signal sequence
The SRP receptor binds the SRP:nascent peptide:ribosome complex
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex
Phosphorylation and activation of Chk1 by ATM
GTP bound eRF3:eRF1 complex binds the peptidyl tRNA:mRNA:80S Ribosome complex
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex
At the beginning of this reaction, 1 molecule of 'ATP', and 1 molecule of 'Wee1 POMBE' are present. At the end of this reaction, 1 molecule of 'phospho-Wee1 Pombe', and 1 molecule of 'ADP' are present. This reaction takes place in the 'nucleoplasm' and is mediated by the 'kinase activity' of 'CHK1 (POMBE)'.
Myt-1 mediated phosphorylation of Cyclin B:Cdc2 complexes
Eukaryotic tranlation initiation factor 5A2
T-complex protein 1 subunit theta (TCP-1-theta)
T-complex protein 1 subunit zeta (TCP-1-zeta)
T-complex protein 1 subunit gamma (TCP-1-gamma)
Cyclin B/Cdk1 mediate phosphorylation of NuMA
Phosphorylation of M phase proteins by active Cyclin B1:Cdc2 complexes
Cytosolic PLK1 translocates to the nucleus
Phosphorylation of Cyclin B1 in the CRS domain
Translocation of CRS phosphorylated Cyclin B1:Cdc2 complexes
Dephosphorylation of CK2-modified condensin I
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tryptophan + tRNA(Trp) + ATP => Trp-tRNA(Trp) + AMP + pyrophosphate
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.
methionine + tRNA(Met) + ATP => Met-tRNA(Met) + AMP + pyrophosphate
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.
lysine + tRNA(Lys) + ATP => Lys-tRNA(Lys) + AMP + pyrophosphate
leucine + tRNA(Leu) + ATP => Leu-tRNA(Leu) + AMP + pyrophosphate
RNA Polymerase II promoter escape occurs after the first phosphodiester bond has been created.
isoleucine + tRNA(Ile) + ATP => Ile-tRNA(Ile) + AMP + pyrophosphate
threonine + tRNA(Thr) + ATP => Thr-tRNA(Thr) + AMP + pyrophosphate
serine + tRNA(Ser) + ATP => Ser-tRNA(Ser) + AMP + pyrophosphate
The control of mammalian DNA replication: a brief history of space and timing.
proline + tRNA(Pro) + ATP => Pro-tRNA(Pro) + AMP + pyrophosphate
phenylalanine + tRNA(Phe) + ATP => Phe-tRNA(Phe) + AMP + pyrophosphate
UDP-glucose:glycoprotein glucosyltransferase 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'.
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'.
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 ââ¬Åfullââ¬Â open complex formation. This reaction is sensitive to inhibition by single-stranded oligonucleotides.
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glycine + tRNA(Gly) + ATP => Gly-tRNA(Gly) + AMP + pyrophosphate
Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
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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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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UDP-glucose:glycoprotein glucosyltransferase 1
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.
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Probable dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3-glucosyltransferase
Dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase
glutamate + tRNA(Glu) + ATP => Glu-tRNA(Glu) + AMP + pyrophosphate
glutamine + tRNA(Glu) + ATP => Glu-tRNA(Glu) + AMP + pyrophosphate
Activation of Gene Expression by SREBP (SREBF)
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]
valine + tRNA(Val) + ATP => Val-tRNA(Val) + AMP + pyrophosphate
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.
arginine + tRNA(Arg) + ATP => Arg-tRNA(Arg) + AMP + pyrophosphate
alanine + tRNA(Ala) + ATP => Ala-tRNA(Ala) + AMP + pyrophosphate
aspartate + tRNA(Asp) + ATP => Asp-tRNA(Asp) + AMP + pyrophosphate
asparagine + tRNA(Asn) + ATP => Asn-tRNA(Asn) + AMP + pyrophosphate
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'.
CpG motifs in bacterial DNA trigger direct B-cell activation
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.
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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Dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichyl mannosyltransferase
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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Asparagine-linked glycosylation protein 11 homolog
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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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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GDP-Man:GlcNAc2-PP-dolichol mannosyltransferase
Chitobiosyldiphosphodolichol beta-mannosyltransferase
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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Dolichyl-phosphate beta-glucosyltransferase
Mannose-1-phosphate guanyltransferase beta
UDP-N-acetylglucosamine transferase subunit ALG14 homolog
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UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
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. This event is inferred from an event in Saccharomyces cerevisiae.
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Association of phospho-L13a with GAIT element of Ceruloplasmin mRNA
Dissociation of L13a from the 60s ribosomal subunit
Formation of eIF2:GDP:eIF2B intermediate
The principal cleavage products are dinucleotides, and they are produced in large stoichiometric excess over complete transcripts. Overall productive RNA chain elongation proceeds quite rapidly. This event is inferred from an event in Saccharomyces cerevisiae.
The 60S subunit joins the translation initiation complex
The rRNA genes are transcribed by RNA polymerase I, one of three eukaryotic nuclear RNA polymerases. The polymerase is a multisubunit complex, composed of two large subunits (the most conserved portions include the catalytic site that shares similarity with other eukaryotic and bacterial multisubunit RNA polymerases) and a number of smaller subunits. Under a number of experimental conditions the core is competent to mediate ribonucleic acid synthesis, in vivo however, it requires additional factors to select the appropriate template. In humans the RNA transcript (45S) is approximately 13,000 nucleotides long. Before leaving the nucleus as assembled ribosomal particles, the 45S rRNA is cleaved to give one copy each of the 28S rRNA, the 18S rRNA, and the 5.8S rRNA. Equal quantities of the three rRNAs are produced by initially transcribing them as one transcript.
Promoter clearance is one of the rate-limiting steps in Polymerase I transcription. This step is composed of three phases, promoter opening, transcription initiation and promoter escape.
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Formation of translation initiation complexes containing mRNA that does not circularize
As the active RNA Polymerase I complex leaves the promoter Rrn3 dissociates from the complex. RNA polymerase I Promoter Clearance is complete and Chain Elongation begins.
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Cap-bound mRNA is activated by helicases
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At the beginning of this reaction, 1 molecule of 'elongating pre-rRNA transcript', and 1 molecule of 'NTP' are present. At the end of this reaction, 1 molecule of 'elongating pre-rRNA transcript' is present. This reaction takes place in the 'nucleolus' and is mediated by the 'DNA-directed RNA polymerase activity' of 'RNA Polymerase I promoter escape complex'.
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After the assembly of the RNA Polymerase I Holoenzyme, Rrn3 binding occurs.
At the beginning of this reaction, 1 molecule of 'DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide ', 1 molecule of 'DNA-directed RNA polymerase I 135 kDa polypeptide ', 1 molecule of 'DNA-directed RNA polymerases I, II, and III 7.0 kDa polypeptide ', 1 molecule of 'DNA-directed RNA polymerase I 16 kDa polypeptide ', 1 molecule of 'DNA-directed RNA polymerase I 40 kDa polypeptide ', and 1 molecule of 'DNA-directed RNA polymerase I largest subunit ' are present. At the end of this reaction, 1 molecule of 'RNA Polymerase I Holoenzyme (Human)' is present. This reaction takes place in the 'nucleolus'.
Upon transcription initiation it is thought that RRN3 is inactivated and dissociates from the Loss of Rrn3 from the RNA Polymerase I promoter escape complex. SL1 and UBF are thought to remain bound to the promoter for multiple rounds of transcription initiation
Mannose-1-phosphate guanyltransferase alpha
During initiation the double-stranded DNA must be melted and transcription begins. SL1 forms and interacts with UBF-1 and the rDNA promoter. It is this platform that will recruit active RNA polymerase I to the SL1:phosphorlated UBF-1:rDNA promoter complex. Mammalian rRNA genes are preceded by a terminator element that is recognized by the SL1 complex. This SL1 modulated acetylation of the basal Pol I transcription machinery has functional consequences suggesting that the reversible acetylation may be one way to regulate rDNA transcription.
Transcription by RNA Polymerase I, RNA Polymerase III and transcription from mitochondrial promoters.
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Glucosamine 6-phosphate N-acetyltransferase
Members of the Vav family are guanine nucleotide exchange factors (GEFs) for Rho-family GTPases. Vav2 is a GEF for RhoA, RhoB and RhoG, and possibly Rac1 and Cdc42
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Glucosamine--fructose-6-phosphate aminotransferase (isomerizing) 2
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Glucosamine--fructose-6-phosphate aminotransferase (isomerizing) 1
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UDP-N-acetylhexosamine pyrophosphorylase
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Met-tRNAi binds to eIF2:GTP to form the ternary complex
Formation of the 43S pre-initiation complex
Exportin complex translocates pre-miRNA to cytosol
Exportin-5 recognizes 3' overhang of pre-miRNA
Release of 40S and 60S subunits from the 80S ribosome
RNA polymerase III is one of three types of nuclear RNA polymerases present in eucaryotic cells. About 10% of the total transcription in dividing cells can be attributed to its activity. It synthesizes an eclectic collection of catalytic or structural RNA molecules, some of which are involved in protein synthesis, pre-mRNA splicing, tRNA processing, and the control of RNA polymerase II elongation, whereas some others have still unknown functions. Like other RNA polymerases, RNA polymerase III cannot recognize its target promoters directly. Instead it is recruited to specific promoter sequences through the help of transcription factors. There are three basic types of RNA polymerase III promoters, called types 1, 2, and 3(Geiduschek and Kassavetis, 1992). Although in vivo, RNA polymerase III may be recruited to these promoters as part of a large complex (holo RNA polymerase III) containing the polymerase and its initiation factors (Wang et al., 1997), in vitro the reaction can be divided into several steps. First, the promoter elements are recognized by DNA binding factors, which then recruit a factor known as TFIIIB. TFIIIB itself then directly contacts RNA polymerase III. In human cells but not in S. cerevisiae, there are at least two versions of TFIIIB. One contains TBP, Bdp1, and Brf1 (Brf1-TFIIIB), and the other TBP, Bdp1, and Brf2 (Brf2-TFIIIB) (Schramm et al., 2000; Teichmann et al., 2000).
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Pol III initiation complexes open the promoter spontaneously similar to the mechanism employed in archaeal and bacterial transcription.
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tyrosine + tRNA(Tyr) + ATP => Tyr-tRNA(Tyr) + AMP + pyrophosphate
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 5s RNA 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. This event is inferred from an event in Saccharomyces cerevisiae.
Abortive initiation, the repetitive formation of short oligonucleotides, is a ubiquitous feature of transcriptional initiation. This Pathway contains events inferred from events in Saccharomyces cerevisiae.
RNA Polymerase III terminates transcription at extremely simple sites, consistent with its role in producing small transcripts. These sites are essentially "Tn" (in the non-transcribed strand).
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. 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, and are hence described as positive regulators of termination.
RNA polymerase III transcribes microbial dsDNA to dsRNA
Activation of CDC42 by unknown mechanism
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Proteasomal clevage of exogenous antigen
Trimming of N-ter extended precursor fragments by cytosolic aminopeptidases
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cysteine + tRNA(Cys) + ATP => Cys-tRNA(Cys) + AMP + pyrophosphate
Signaling by target of rapamycin proteins in cell growth control
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Inositol hexakisphosphate kinase products contain diphosphate and triphosphate groups
phenylalanine + oxaloacetate => phenylpyruvate + aspartate [CCBL1]
phenylpyruvate + NADH + H+ => phenyllactate + NAD+
Tyrosine kinase inhibitors bind and inhibit FGFR1 fusion dimer phosphorylation
Phosphorylation of BCR moiety of BCR-FGFR1
HSP90 is inactivated by binding to benzaquinoid ansamycins
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Intraphagosomal pH is lowered to 5 by V-ATPase
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Amyloid precursor proteins form ordered fibrils
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Rad52 and Ku bind to different DNA structures produced early in double-strand break repair.
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Cell death signalling via NRAGE, NRIF and NADE
Analysis and update of the human solute carrier (SLC) gene superfamily
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Deficiency of carbohydrate response element-binding protein (ChREBP) reduces lipogenesis as well as glycolysis
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Regulation of KIF23 (MKLP1) by phosphorylation
Recruitment of Telomerase RNP to the Telomeric Chromosome End
Alignment Of The RNA Template On The Telomeric Chromosome End
Elongation Of The Telomeric Chromosome End
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Translocation Of Telomerase RNP And Alignment Of RNA Template (TERC) To Extended Single Stranded Telomeric Chromosome-End
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Elongation of Extended Telomeric Chromosome End
Disassociation of Telomerase RNP and the Chromosome End
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The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer on the G strand of the telomere
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Substrate specificity of MATE1 and MATE2-K, human multidrug and toxin extrusions/H(+)-organic cation antiporters
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Proteomic analysis of proteins associated with lipid droplets of basal and lipolytically stimulated 3T3-L1 adipocytes
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The glutamate/GABA-glutamine cycle: aspects of transport, neurotransmitter homeostasis and ammonia transfer
Molecular identity and cellular distribution of advanced glycation endproduct receptors: relationship of p60 to OST-48 and p90 to 80K-H membrane proteins
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A cytoplasmic chaperonin that catalyzes beta-actin folding
Architecture of the yeast origin recognition complex bound to origins of DNA replication.
Update on interconversions of vitamin B-6 with its coenzyme
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Endoplasmic reticulum stress induction of insulin-like growth factor-binding protein-1 involves ATF4
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Comparative analysis of gene regulation by the transcription factor PPARalpha between mouse and human
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Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib
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Discovery of a lysophospholipid acyltransferase family essential for membrane asymmetry and diversity
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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
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Partial purification of a microsomal sterol 4 -carboxylic acid decarboxylase
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Crystallization and properties of human liver ornithine aminotransferase
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Cetuximab monotherapy and cetuximab plus irinotecan in irinotecan-refractory metastatic colorectal cancer
Structural and biochemical properties of cloned and expressed human and rat steroid 5 alpha-reductases
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
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Identification of an autonomously initiating RNA polymerase III holoenzyme containing a novel factor that is selectively inactivated during protein synthesis inhibition
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The docking protein Gab1 is the primary mediator of EGF-stimulated activation of the PI-3K/Akt cell survival pathway
BRCA1 interacts with acetyl-CoA carboxylase through its tandem of BRCT domains
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A mediator of Rho-dependent invasion moonlights as a methionine salvage enzyme
Retrovirally mediated complementation of the glyB phenotype. Cloning of a human gene encoding the carrier for entry of folates into mitochondria.
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Wnts need a p(assport)24 to leave the ER
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poly(deoxyadenylic-deoxythymidylic) acid
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The substrate of Greatwall kinase, Arpp19, controls mitosis by inhibiting protein phosphatase 2A
Greatwall phosphorylates an inhibitor of protein phosphatase 2A that is essential for mitosis
K48-polyubiquitinated partially digested Ag
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Probable phospholipid-transporting ATPases
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Ghost homologue of E3 ligases in proteasomal degradation
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Rabenosyn-5, a novel Rab5 effector, is complexed with hVPS45 and recruited to endosomes through a FYVE finger domain
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p24 proteins are required for secretion of Wnt ligands
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'NAcGlu [mitochondrial matrix]' positively regulates 'carbamoyl-phosphate synthase (ammonia) activity of CPS1 [mitochondrial matrix]'
The renal plumbing system: aquaporin water channels
Nascent pre-mRNA with 5'-GMP dissociated from CE
Nascent pre-mRNA with 5'-GMP associated with CE
mRNA with premature termination codon not preceding exon junction
mRNA with premature termination codon preceding exon junction
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Ghost homologue of SREBF1A,1C,2 cleaved by S2P
Human lysozyme gene mutations cause hereditary systemic amyloidosis
Lsm1-7-Pat1 complex: A link between 3' and 5'-ends in mRNA decay?
Mammalian Orc1 protein is selectively released from chromatin and ubiquitinated during the S-to-M transition in the cell division cycle.
'NF-Y (name copied from entity in Homo sapiens) [nucleoplasm]' positively regulates 'Expression of BIP (78 kDa Glucose-regulated protein, GRP78, HSPA5)'
mRNA Transcript Targeted by Tristetraproline
'Mg2+ [cytosol]' is required for 'ribose phosphate diphosphokinase activity of phosphoribosyl pyrophosphate synthetase 1 holoenzyme (name copied from entity in Homo sapiens) [cytosol]'
'Pi [cytosol]' is required for 'ribose phosphate diphosphokinase activity of phosphoribosyl pyrophosphate synthetase 1 holoenzyme (name copied from entity in Homo sapiens) [cytosol]'
'L-Arg [cytosol]' positively regulates 'acetyl-CoA:L-glutamate N-acetyltransferase activity of NAGS(19-534) [mitochondrial matrix]'
Essential role for IKK? in production of type 1 interferons by plasmacytoid dendritic cells
New regulatory mechanisms of TGF-beta receptor function
Studies on the activator 1 protein complex, an accessory factor for proliferating cell nuclear antigen-dependent DNA polymerase delta.
Localization and trafficking of aquaporin 2 in the kidney
The secretory pathway Ca2+/Mn2+-ATPase 2 is a Golgi-localized pump with high affinity for Ca2+ ions
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
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
Genomic organization of the human phosphomannose isomerase (MPI) gene and mutation analysis in patients with congenital disorders of glycosylation type Ib (CDG-Ib)
Integrating signals from RTKs to ERK/MAPK
Point mutations in the aromatic/arginine region in aquaporin 1 allow passage of urea, glycerol, ammonia, and protons
The way Wnt works: Components and mechanism
Cdc42, Rac1, and Rac2 display distinct patterns of activation during phagocytosis
Association of licensing factors with the pre-replicative complex
The post-translational synthesis of a polyamine-derived amino acid, hypusine, in the eukaryotic translation initiation factor 5A (eIF5A)
Amyloid beta-protein: monomer structure and early aggregation states of Abeta42 and its Pro19 alloform
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Aquaporins in complex tissues. II. Subcellular distribution in respiratory and glandular tissues of rat
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Lathosterolosis: an inborn error of human and murine cholesterol synthesis due to lathosterol 5-desaturase deficiency
Aquaporins in complex tissues. I. Developmental patterns in respiratory and glandular tissues of rat
Molecular modeling-based analysis of interactions in the RFC-dependent clamp-loading process
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Mechanisms of human DNA repair: an update.
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The mechanism of adenosine to inosine conversion by the double-stranded RNA unwinding/modifying activity: a high-performance liquid chromatography-mass spectrometry analysis.
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The 7 TM G-protein-coupled receptor target family
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Dual role of the tyrosine activation motif of the Ig-alpha protein during signal transduction via the B cell antigen receptor
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RNA polymerase III Transcription Complexes
Transcriptional Regulation, eds. McKnight, S.L., Yamamoto, K.R. 22:247-280
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Evidence of functional modulation of the MEKK/JNK/cJun signaling cascade by the low density lipoprotein receptor-related protein (LRP)
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Conserved initiator proteins in eukaryotes.
Role of importin-beta in coupling Ran to downstream targets in microtubule assembly
The known unknowns of antigen processing and presentation
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Relationship between structures and biological activities of mycoplasmal diacylated lipopeptides and their recognition by toll-like receptors 2 and 6
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Different human TFIIIB activities direct RNA polymerase III transcription from TATA-containing and TATA-less promoters
Glycogen metabolism and glycolytic enzymes
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Single eubacterial origin of eukaryotic sulfide:quinone oxidoreductase, a mitochondrial enzyme conserved from the early evolution of eukaryotes during anoxic and sulfidic times
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Understanding RAGE, the receptor for advanced glycation end products
Constitutive and inducible expression and regulation of vascular endothelial growth factor
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Transmembrane transport of small molecules
EDEM3, a soluble EDEM homolog, enhances glycoprotein endoplasmic reticulum-associated degradation and mannose trimming
ATP-dependent positive supercoiling of DNA by 13S condensin: a biochemical implication for chromosome condensation
Biology, structure and mechanism of P-type ATPases
Three-dimensional structure of the bifunctional protein PCD/DCoH, a cytoplasmic enzyme interacting with transcription factor HNF1.
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
Enzyme hyperspecificity. Rejection of threonine by the valyl-tRNA synthetase by misacylation and hydrolytic editing
A human purine nucleoside phosphorylase deficiency caused by a single base change
Essential function for the kinase TAK1 in innate and adaptive immune responses
Kinetics of B cell receptor signaling in human B cell subsets mapped by phosphospecific flow cytometry
Diabetes-associated sustained activation of the transcription factor nuclear factor-kappaB
Molecular mechanisms and clinical pathophysiology of maturity-onset diabetes of the young
A genome-wide RNA interference screen uncovers two p24 proteins as regulators of Wingless secretion
Tripeptidyl peptidase II is the major peptidase needed to trim long antigenic precursors, but is not required for most MHC class I antigen presentation
3' -UTR-mediated translational regulation
Glucagon signaling in metabolic regulation
Mammalian nuclei become licensed for DNA replication during late telophase.
Lead-induced abnormalities of porphyrin metabolism. The relationship with iron deficiency.
Methylation pharmacogenetics: catechol O-methyltransferase, thiopurine methyltransferase, and histamine N-methyltransferase
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
Translesion synthesis by DNA polymerases bypassing lesion on DNA template
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
The Ras branch of small GTPases: Ras family members don't fall far from the tree
LSm proteins form heptameric rings that bind to RNA via repeating motifs
Structure of the dual enzyme Ire1 reveals the basis for catalysis and regulation in nonconventional RNA splicing
An overview of sphingolipid metabolism: from synthesis to breakdown
Differential activation of recombinant human acetyl-CoA carboxylases 1 and 2 by citrate
Identification of a novel human adenylate kinase. cDNA cloning, expression analysis, chromosome localization and characterization of the recombinant protein
Initial enzyme for glycosylphosphatidylinositol biosynthesis requires PIG-P and is regulated by DPM2
Bone morphogenetic protein receptors and signal transduction
DNA polymerase epsilon, catalytic subunit A
Cell division protein kinase 2 (EC 2.7.1.-)(p33 protein kinase)(CDK2)
Cell division cycle 7-related protein kinase
Cell division cycle 7-related protein kinase (EC 2.7.1.-) (CDC7- related kinase) (HsCdc7) (huCdc7)
Interleukin-2 receptor signaling in regulatory T cell development and homeostasis
DNA Replication factor A protein 4 (30kD)
Characterization of type II phosphatidylinositol 4-kinase isoforms reveals association of the enzymes with endosomal vesicular compartments
DNA polymerase alpha holoenzyme-associated protein P1
Water channel expression in human ADPKD kidneys
Phosphorylated JNKs: MAPK8, MAPK9, MAPK10
Hypothetical protein CGI-110 (Protein HSPC175)
Splicing factor, arginine/serine-rich 6 (Pre-mRNA splicing factor SRP55)
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
DNA polymerase delta holoenzyme: action on single-stranded DNA and on double-stranded DNA in the presence of replicative DNA helicases.
4-aminobutyrate aminotransferase, mitochondrial
Fractionation and properties of glutamic oxalacetic transaminase
Origin recognition complex subunit Latheo
Aspects on human amyloid forms and their fibril polypeptides
Maintaining cholesterol homeostasis: sterol regulatory element-binding proteins
Endoplasmic reticulum-associated degradation of mammalian glycoproteins involves sugar chain trimming to Man6-5GlcNAc2
Cyclic AMP-dependent transcription factor ATF-2
Enzymatic degradation of Dopamine by monoamine oxidase
Distinct phosphotyrosines on a growth factor receptor bind to specific molecules that mediate different signaling pathways
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N6-(L-1,3-Dicarboxypropyl)-L-lysine [ChEBI:16927]
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Isolation and characterization of argininosuccinate synthetase from human liver.
sn-Glycero-3-phosphoethanolamine [ChEBI:10647]
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D-Glucono-1,5-lactone 6-phosphate [ChEBI:16938]
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136 kDa double-stranded RNA binding protein
Double-stranded RNA-specific adenosine deaminase
ATP-binding cassette sub-family B member 7, mitochondrial
Cytosolic Fe-S cluster assembly factor NUBP1
Cytosolic Fe-S cluster assembly factor NUBP2
NADPH-dependent diflavin oxidoreductase 1 ecNumber1.6.-.-/ecNumber
NADPH:adrenodoxin oxidoreductase, mitochondrial
Leber congenital amaurosis: genes, proteins and disease mechanisms
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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
The stem cell factor receptor/c-Kit as a drug target in cancer
Small nuclear ribonucleoprotein associated proteins B and B'
Spliceosomal U5 snRNP-specific 15 kDa protein
Thioredoxin-like U5 snRNP protein U5-15kD
Critical role of novel Thr-219 autophosphorylation for the cellular function of PKCtheta in T lymphocytes
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
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)
Small nuclear ribonuclear protein D homolog
High mobility group-like nuclear protein 2 homolog 1
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)
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
Pre-mRNA splicing factor SF3b 10 kDa subunit
The biochemistry and physiology of nucleotides
Detection of the mitochondrial and catalytically active alanine aminotransferase in human tissues and plasma
Origin, Recognition, Signaling and Repair of DNA Double-Strand Breaks in Mammalian Cells
Damage Surveillance and Repair (Keith Caldecott, editor)1-40
ChEBI:16975 1-acyl-sn-glycerol 3-phosphate
Nonhomologous end joining: repair of DNA double strand breaks after ionizing radiation
Activation by Cdc42 and PIP(2) of Wiskott-Aldrich syndrome protein (WASp) stimulates actin nucleation by Arp2/3 complex
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
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Characterization of a family of nucleolar SUMO-specific proteases with preference for SUMO-2 or SUMO-3
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On the specificity of the tricarboxylate carrier system in rat liver mitochondria
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Dynamic binding of PKA regulatory subunit RI alpha
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Characterization of a leukotriene C4 export mechanism in human platelets: possible involvement of multidrug resistance-associated protein 1
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Tyrosine phosphorylation of MB-1, B29, and HS1 proteins in human B cells following receptor crosslinking
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D-Fructose 1,6-bisphosphate [ChEBI:16905]
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Post-transcriptional regulation of gene expression by degradation of messenger RNAs
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'ADS [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
'D-Fructose 1,6-bisphosphate [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
'Mg2+ [cytosol]' is required for 'ITPA hydrolyses ITP to IMP'
'Mg2+ [cytosol]' is required for 'ITPA hydrolyses dITP to dIMP'
'XMP [cytosol]' negatively regulates 'IMP + H2O + NAD+ => XMP + NADH + H+ [IMPDH1,2]'
'GDP [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
'GMP [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
'Mg2+ [cytosol]' is required for 'ITPA hydrolyses XTP to XMP'
'L-Phe [cytosol]' negatively regulates 'kynurenine + pyruvate => 4-(2-aminophenyl)-2,4-dioxobutanoic acid + alanine [CCBL1]'
'L-Arg [mitochondrial matrix]' positively regulates 'glutamate + acetyl CoA => N-acetyl glutamate + CoA'
Human carbamylphosphate synthetase I. Stabilization, purification, and partial characterization of the enzyme from human liver.
'GMP [cytosol]' positively regulates 'Formation of phosphoribosyl pyrophosphate amidotransferase tetramer'
'AMP [cytosol]' positively regulates 'Formation 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'
'ADP [mitochondrial matrix]' positively regulates 'isocitrate + NAD+ => alpha-ketoglutarate + CO2 + NADH + H+ [IDH3]'
'Mn2+ [mitochondrial matrix]' positively regulates '(R)-2-hydroxyglutarate + FAD => 2-oxoglutarate + FADH2'
Frequent and focal FGFR1 amplification associates with therapeutically tractable FGFR1 dependency in squamous cell lung cancer
'Formation of phosphoribosyl pyrophosphate amidotransferase tetramer' negatively regulates '5-phospho-alpha-D-ribose 1-diphosphate (PRPP) + H2O + L-glutamine <=> 5-phosphoribosylamine + L-glutamate +pyrophosphate'
'Dissociation of phosphoribosyl pyrophosphate amidotransferase tetramer' positively regulates '5-phospho-alpha-D-ribose 1-diphosphate (PRPP) + H2O + L-glutamine <=> 5-phosphoribosylamine + L-glutamate +pyrophosphate'
'IMP [cytosol]' positively regulates 'Formation of phosphoribosyl pyrophosphate amidotransferase tetramer'
'PRPP [cytosol]' positively regulates 'Dissociation of phosphoribosyl pyrophosphate amidotransferase tetramer'
Mechanisms of accurate translesion synthesis by human DNA polymerase eta.
'SREBP1A/1C/2:NF-Y:HMGCS1 gene (name copied from entity in Homo sapiens) [nucleoplasm]' positively regulates 'Expression of Hydroxymethylglutaryl coenzyme A synthase (HMGCS1)'
'SREBP1A/1C/2:NF-Y:FDPS gene (name copied from entity in Homo sapiens) [nucleoplasm]' positively regulates 'Expression of Farnesyl Diphosphate Synthase (FDPS)'
'SREBP1A/2:NF-Y:SC5DL gene (name copied from entity in Homo sapiens) [nucleoplasm]' positively regulates 'Expression of Lathosterol Oxidase (SC5D, SC5DL)'
'SREBP1A/2:SQLE gene (name copied from entity in Homo sapiens) [nucleoplasm]' positively regulates 'Expression of Squalene Monooxygenase (SQLE)'
'SREBP1A/1C/2:NF-Y:TM7SF2 gene (name copied from entity in Homo sapiens) [nucleoplasm]' positively regulates 'Expression of TM7SF2'
'BH4 [cytosol]' negatively regulates 'GCH1 reduces GTP to dihydroneopterin triphosphate'
'L-Phe [cytosol]' positively regulates 'GCH1 reduces GTP to dihydroneopterin triphosphate'
'Ac-CoA [mitochondrial matrix]' positively regulates 'PDK-catalyzed phosphorylation (inactivation) of PDC E1 alpha subunit'
'NADH [mitochondrial matrix]' positively regulates 'PDK-catalyzed phosphorylation (inactivation) of PDC E1 alpha subunit'
'PYR [mitochondrial matrix]' negatively regulates 'PDK-catalyzed phosphorylation (inactivation) of PDC E1 alpha subunit'
'D-Fructose 1,6-bisphosphate [cytosol]' positively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'Ac-CoA [cytosol]' negatively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'AMP [cytosol]' positively regulates 'D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP'
'ADP [cytosol]' positively regulates 'D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP'
'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'
'ATP [nucleoplasm]' negatively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'3',5'-Cyclic AMP [cytosol]' negatively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'CIT [cytosol]' positively regulates 'acetyl-CoA + bicarbonate + ATP => malonyl-CoA + H2O + ADP + orthophosphate'
'SREBP1A/2:NF-Y:HMGCR gene (name copied from entity in Homo sapiens) [nucleoplasm]' positively regulates 'Expression of 3-Hydroxy-3-methylglutaryl-coenzyme A Reductase (HMGCR)'
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The DNA-dependent protein kinase interacts with DNA to form a protein-DNA complex that is disrupted by phosphorylation.
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Phosphotyrosine-dependent activation of Rac-1 GDP/GTP exchange by the vav proto-oncogene product
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Congenital disorder of glycosylation type Ik (CDG-Ik): a defect of mannosyltransferase I
Rrn3 becomes inactivated in the process of ribosomal DNA transcription.
Deficiency of GDP-Man:GlcNAc2-PP-dolichol mannosyltransferase causes congenital disorder of glycosylation type Ik
1D-myo-Inositol 1,3,4,5-tetrakisphosphate [ChEBI:808]
D-myo-Inositol 1,3,4,5-tetrakisphosphate
Formation of the active cofactor, UDP-glucuronate
Concerted action of two cation filters in the aquaporin water channel
Expression of the AQP-1 water channel in normal human tissues: a semiquantitative study using tissue microarray technology
A yeast chromosomal origin of DNA replication defined by multiple functional elements.
Mechanisms of transcription-coupled DNA repair.
Congenital Disorders of Glycosylation Overview
Cell cycle- and cell growth-regulated proteolysis of mammalian CDC6 is dependent on APC-CDH1.
Systemic amyloid fibril main peptide chains
beta-catenin destruction complex: insights and questions from a structural perspective
Transthyretin fibril (name copied from entity in Homo sapiens)
Variant apolipoprotein AII fibril (name copied from entity in Homo sapiens)
RNA-binding protein in RNP (ribonucleoprotein) complexes
nascent polypeptide with signal sequence
Ghost homologue of Telomerase RNA Component (TERC)
phosphorylated nuclear Cyclin B1:Cdc2 substrates
RNA primer:origin duplex with DNA damage
(ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI
The kinesin-like protein CENP-E is kinetochore-associated throughout poleward chromosome segregation during anaphase-A
Ghost homologue of Unfolded alpha/beta tubulin
Coatomer:Arf1-GTP:GAP Lattice (name copied from entity in Homo sapiens)
Coatomer:GAP Lattice (name copied from entity in Homo sapiens)
Coatomer:ARFGAP1 lattice (name copied from entity in Homo sapiens)
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.
Ghost homologue of Precursor Cargo of TIMM23 SORT
sn-Glycero-3-phosphocholine [ChEBI:10646]
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
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
Coatomer:Arf1-GDP:GAP Lattice (name copied from entity in Homo sapiens)
1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate [ChEBI:16851]
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Cloning, characterization, and chromosomal mapping of human aquaporin of collecting duct
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Functional expansion of aminoacyl-tRNA synthetases and their interacting factors: new perspectives on housekeepers
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Superoxide production and electron transport in mitochondrial oxidation of dihydroorotic acid.
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Bile salt transporters: molecular characterization, function, and regulation
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Vesicle pools, docking, priming, and release
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Structure-function analysis of human Spt4: evidence that hSpt4 and hSpt5 exert their roles in transcriptional elongation as parts of the DSIF complex.
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Protein sorting receptors in the early secretory pathway
'XPO1 [nucleoplasm]' positively regulates 'Translocation of Cyclin B1:phospho-Cdc2 to the cytoplasm'
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Translocation after synthesis of a four-nucleotide RNA commits RNA polymerase II to promoter escape.
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'ATP [cytosol]' is required for 'Ribosomal scanning '
'GTP [cytosol]' is required for 'Met-tRNAi binds to eIF2:GTP to form the ternary complex'
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'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'
'RPA:Cdc45:CDK:DDK:Mcm10:pre-replicative complex (name copied from entity in Homo sapiens) [nucleoplasm]' positively regulates 'DNA polymerase epsilon binds at the origin'
'RPA:Cdc45:CDK:DDK:Mcm10:pre-replicative complex (name copied from entity in Homo sapiens) [nucleoplasm]' positively regulates 'DNA polymerase alpha:primase binds at the origin'
'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]'
'heme [mitochondrial matrix]' negatively regulates 'ALAS condenses SUCC-CoA and Gly to form dALA'
'Cys [cytosol]' positively regulates 'Excess cysteine yields lanthionine and H2S'
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The spindle checkpoint: structural insights into dynamic signalling
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High incidence of translocations t(11;14)(q13;q32) and t(4;14)(p16;q32) in patients with plasma cell malignancies
Developmental control of a G1-S transcriptional program in Drosophila
FGFR3-related dwarfism and cell signaling
Synthesis and interconversion of nucleotide di- and triphosphates
TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation
Activation of ATF6 and an ATF6 DNA binding site by the endoplasmic reticulum stress response
Protein kinase C phosphorylation of syntaxin 4 in thrombin-activated human platelets
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Central spindle assembly and cytokinesis require a kinesin-like protein/RhoGAP complex with microtubule bundling activity
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Human glutamine phosphoribosylpyrophosphate amidotransferase. Two molecular forms interconvertible by purine ribonucleotides and phosphoribosylpyrophosphate
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Class I MHC mediated antigen processing & presentation
Identification of human intestinal alkaline sphingomyelinase as a novel ecto-enzyme related to the nucleotide phosphodiesterase family
Dynamics and function of phospholipase D and phosphatidic acid during phagocytosis
Characterization of human PLD2 and the analysis of PLD isoform splice variants
Structure-function analysis of Friedreich's ataxia mutants reveals determinants of frataxin binding and activation of the Fe-S assembly complex
Purification and properties of uroporphyrinogen III synthase from human erythrocytes
Novel inositol polyphosphate 5-phosphatase localizes at membrane ruffles
Polymeric chains of SUMO-2 and SUMO-3 are conjugated to protein substrates by SAE1/SAE2 and Ubc9
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DNA end-joining catalyzed by human cell-free extracts.
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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
Neurotransmitter uptake and Metabolism In Glial Cells
Molecular cloning of human mitochondrial glycerophosphate dehydrogenase gene: genomic structure, chromosomal localization, and existence of a pseudogene
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Common and distinct elements in cellular signaling via EGF and FGF receptors
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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
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Role of cysteine-82 in the catalytic mechanism of human S-adenosylmethionine decarboxylase
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Delivery of yeast telomerase to a DNA break depends on the recruitment functions of Cdc13 and Est1
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Mutations in the X-linked pyruvate dehydrogenase (E1) alpha subunit gene (PDHA1) in patients with a pyruvate dehydrogenase complex deficiency
Neural cell adhesion molecule L1: signaling pathways and growth cone motility
ChEBI:16723 4-methylthio-2-oxobutanoate (1-)
ChEBI:16728 2-acyl-sn-glycero-3-phosphocholine
Topology of acyltransferase motifs and substrate specificity and accessibility in 1-acyl-sn-glycero-3-phosphate acyltransferase 1
Loading of the human 9-1-1 checkpoint complex onto DNA by the checkpoint clamp loader hRad17-replication factor C complex in vitro
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
1-phosphatidyl-1D-myo-inositol [ChEBI:16749]
Functional characterization and localization of AQP3 in the human colon
The ins and outs of IgE-dependent mast-cell exocytosis
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
A conserved region in the amino terminus of DNA polymerase delta is involved in proliferating cell nuclear antigen binding.
Tau oligomers and aggregation in Alzheimer's disease
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.
Getting in and out from calnexin/calreticulin cycles
A novel quality control compartment derived from the endoplasmic reticulum
Closing the gap: identification of human 3-ketosteroid reductase, the last unknown enzyme of mammalian cholesterol biosynthesis
Polyamines: metabolism and implications in human diseases
Frataxin and mitochondrial FeS cluster biogenesis
Translocation of lipid-linked oligosaccharides across the ER membrane requires Rft1 protein
Cytosolic iron-sulfur cluster assembly (CIA) system: factors, mechanism, and relevance to cellular iron regulation
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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
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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RNA editing: complexity and complications.
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On the mechanism of preprotein import by the mitochondrial presequence translocase
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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
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A regulatory role for 1-acylglycerol-3-phosphate-O-acyltransferase 2 in adipocyte differentiation
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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.
Dealing with methionine/homocysteine sulfur: cysteine metabolism to taurine and inorganic sulfur
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.
RNA editing by base deamination: more enzymes, more targets, new mysteries.
MDC1 is a mediator of the mammalian DNA damage checkpoint.
Identification and characterization of human mitochondrial tryptophanyl-tRNA synthetase
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Regulation of growth factor signaling by FRS2 family docking/scaffold adaptor proteins
Recent progress in structure-function analyses of Nramp proton-dependent metal-ion transporters
The Wnt/Ca2+ pathway: a new vertebrate Wnt signaling pathway takes shape
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Induction of CHOP expression by amino acid limitation requires both ATF4 expression and ATF2 phosphorylation
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Peroxisome proliferator-activated receptor alpha (PPARalpha) and athero-sclerosis
Curr Drug Targets Cardiovasc Haematol Disord 5:513-23
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Identification of a binding region for human origin recognition complex proteins 1 and 2 that coincides with an origin of DNA replication.
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Analysis of GPIIb/IIIa receptor number by quantification of 7E3 binding to human platelets
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In vivo demonstration that {alpha}-synuclein oligomers are toxic
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Enzymatic synthesis and properties of 5-phosphoribosylpyrophosphate
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Ornithine delta-aminotransferase mutations in gyrate atrophy. Allelic heterogeneity and functional consequences.
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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
Localization, regulation and function of type II phosphatidylinositol 5-phosphate 4-kinases
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ChEBI:16618 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate
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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
MicroRNAs: genomics, biogenesis, mechanism, and function
Phenylalanine hydroxylase-stimulating protein/pterin-4 alpha-carbinolamine dehydratase from rat and human liver. Purification, characterization, and complete amino acid sequence.
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Cardiolipin hydrolysis by human phospholipases A2. The multiple enzymatic activities of human cytosolic phospholipase A2
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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
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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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B cell lymphoma 10 is essential for FcepsilonR-mediated degranulation and IL-6 production in mast cells
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Isoleucylation properties of native human mitochondrial tRNAIle and tRNAIle transcripts. Implications for cardiomyopathy-related point mutations (4269, 4317) in the tRNAIle gene
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The enzymic chain elongation of fatty acids by rat-liver microsomes
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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
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Human phosphoribosylpyrophosphate synthetase
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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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Molecular cloning of cDNA encoding human lanosterol synthase
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Molecular cloning and mapping of a human cDNA (SC5DL) encoding a protein homologous to fungal sterol-C5-desaturase
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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
Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding
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Dopamine clearance from the synaptic cleft
Kerato-epithelin mutations in four 5q31-linked corneal dystrophies
A single enzyme catalyzes both platelet-activating factor production and membrane biogenesis of inflammatory cells. Cloning and characterization of acetyl-CoA:LYSO-PAF acetyltransferase
Synthesis of glycosylphosphatidylinositol (GPI)
Mitochondrial Iron-Sulfur Cluster Biogenesis
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
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
Human acetyl-CoA carboxylase: characterization, molecular cloning, and evidence for two isoforms
Loss of human Greatwall results in G2 arrest and multiple mitotic defects due to deregulation of the cyclin B-Cdc2/PP2A balance
Proc. Natl. Acad. Sci. U.S.A. 107:12564-9
Oxcarbazepine does not interact with cimetidine in healthy volunteers
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
Error-prone DNA polymerases: novel structures and the benefits of infidelity.
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
ChEBI:16500 1-phosphatidyl-1D-myo-inositol 5-phosphate
NMD: RNA biology meets human genetic medicine
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
Structural biology of shared cytokine receptors
Functional cloning of BRF1, a regulator of ARE-dependent mRNA turnover
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Characterization of the proteins released from activated platelets leads to localization of novel platelet proteins in human atherosclerotic lesions
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Indirubin-3'-monoxime inhibits autophosphorylation of FGFR1 and stimulates ERK1/2 activity via p38 MAPK
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The DNA replication fork in eukaryotic cells.
D-myo-Inositol 1,3,4,5,6-pentakisphosphate
1D-myo-Inositol 1,3,4,5,6-pentakisphosphate [ChEBI:807]
Phosphate bond hydrolysis by NUDT proteins
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
17beta-Hydroxyandrostan-3-one [ChEBI:793]
Three enzymatic activities catalyze the oxidation of sulfide to thiosulfate in mammalian and invertebrate mitochondria
Baillieres Clin Endocrinol Metab 7:551-86
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Mitotic checkpoint proteins HsMAD1 and HsMAD2 are associated with nuclear pore complexes in interphase
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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MyD88 cascade initiated on plasma membrane
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Pathogen recognition and innate immunity
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Characterization of the mechanisms controlling Greatwall activity
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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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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)
NOD-LRR proteins: role in host-microbial interactions and inflammatory disease
Transaldolase deficiency: liver cirrhosis associated with a new inborn error in the pentose phosphate pathway.
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
The stem-loop binding protein is required for efficient translation of histone mRNA in vivo and in vitro
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
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.
Structure and function of a protein folding machine: the eukaryotic cytosolic chaperonin CCT
Mechanism of the nucleotide exchange reaction in eukaryotic polypeptide chain initiation. Characterization of the guanine nucleotide exchange factor as a GTP-binding protein.
A double-hexamer archaeal minichromosome maintenance protein is an ATP-dependent DNA helicase.
Molecular cloning of PEPT 2, a new member of the H+/peptide cotransporter family, from human kidney
Regulation of phagocytosis by Rho GTPases
Murine p38-delta mitogen-activated protein kinase, a developmentally regulated protein kinase that is activated by stress and proinflammatory cytokines
Cytochrome P450s and other enzymes in drug metabolism and toxicity
The subcellular localization of acetyl-CoA carboxylase 2
Human 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/inosine 5'-monophosphate cyclohydrolase. A bifunctional protein requiring dimerization for transformylase activity but not for cyclohydrolase activity
Phosphatidylethanolamine is the donor of the phosphorylethanolamine linked to the alpha1,4-linked mannose of yeast GPI structures
Mutation of the predicted p34cdc2 phosphorylation sites in NuMA impair the assembly of the mitotic spindle and block mitosis
Cloning, expression, and characterization of a human inosine triphosphate pyrophosphatase encoded by the itpa gene
Characterization of the advanced glycation end-product receptor complex in human vascular endothelial cells
Biochemical characterization of human PC-1, an enzyme possessing alkaline phosphodiesterase I and nucleotide pyrophosphatase activities
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Human amidophosphoribosyltransferase. An oxygen-sensitive iron-sulfur protein
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The molecular mechanism of lead inhibition of human porphobilinogen synthase
Fibroblast growth factor receptor 1 is fused to FIM in stem-cell myeloproliferative disorder with t(8;13)
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Mechanistic implications of mutations to the active site lysine of porphobilinogen synthase
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26S proteasomes and immunoproteasomes produce mainly N-extended versions of an antigenic peptide
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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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Nuclear export of the stress-activated protein kinase p38 mediated by its substrate MAPKAP kinase-2
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Processive synthesis on the C-strand of the telomere
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cDNA cloning and mapping of a novel subtype of glutamine:fructose-6-phosphate amidotransferase (GFAT2) in human and mouse
Cobalamin (Cbl, vitamin B12) transport and metabolism
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Guanine nucleotide exchange factors for Rho GTPases: turning on the switch
A quantitative model of human DNA base excision repair. I. Mechanistic insights
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
Endogenous retroviral sequence is fused to FGFR1 kinase in the 8p12 stem-cell myeloproliferative disorder with t(8;19)(p12;q13.3)
Complementation cloning identifies CDG-IIc, a new type of congenital disorders of glycosylation, as a GDP-fucose transporter deficiency
Antigen presentation and the ubiquitin-proteasome system in host-pathogen interactions
Regulation of nuclear processes by inositol polyphosphates
KARAP/DAP12/TYROBP: three names and a multiplicity of biological functions
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
A human homolog of the vaccinia virus HindIII K4L gene is a member of the phospholipase D superfamily
Resolution of AP sites via the multiple-nucleotide patch replacement pathway
Cloning and characterization of murine 1-acyl-sn-glycerol 3-phosphate acyltransferases and their regulation by PPARalpha in murine heart
Molecular cloning and characterization of an aquaporin cDNA from salivary, lacrimal, and respiratory tissues
Formation of a preinitiation complex by S-phase cyclin CDK-dependent loading of Cdc45p onto chromatin.
In situ visualization of DNA double-strand break repair in human fibroblasts.
Comparative mechanistic and substrate specificity study of inositol polyphosphate 5-phosphatase Schizosaccharomyces pombe Synaptojanin and SHIP2
Platelet-collagen interaction: is GPVI the central receptor?
TIN2 binds TRF1 and TRF2 simultaneously and stabilizes the TRF2 complex on telomeres
Transcriptional control of megakaryocyte development
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
DNA synthesis at individual replication forks requires the essential initiation factor Cdc45p.
Over-expression in Escherichia coli and characterization of two recombinant isoforms of human FAD synthetase
Isozymes of human phosphofructokinase: identification and subunit structural characterization of a new system
RNA Polymerase II Pre-transcription Events
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
Replication factors MCM2 and ORC1 interact with the histone acetyltransferase HBO1.
Destabilization of mRNA by Butyrate Response Factor 1 (BRF1)
Expression and function of the human androgen-responsive gene ADI1 in prostate cancer
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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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Activation of purified human protein kinase C alpha and beta I isoenzymes in vitro by Ca2+, phosphatidylinositol and phosphatidylinositol 4,5-bisphosphate
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Myotubularin and MTMR2, phosphatidylinositol 3-phosphatases mutated in myotubular myopathy and type 4B Charcot-Marie-Tooth disease
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A structural perspective on copper uptake in eukaryotes
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
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The protein kinase/endoribonuclease IRE1alpha that signals the unfolded protein response has a luminal N-terminal ligand-independent dimerization domain
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Structural basis for altered activity of M- and H-isozyme forms of human lactate dehydrogenase
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IAP proteins: blocking the road to death's door
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The identification of a distinct export step following the biosynthesis of leukotriene C4 by human eosinophils
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Cleavage specificity of Saccharomyces cerevisiae flap endonuclease 1 suggests a double-flap structure as the cellular substrate.
Serum levels of beta 2-microglobulin as a new form of amyloid protein in patients undergoing long-term hemodialysis
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Cellular functions of TC10, a Rho family GTPase: regulation of morphology, signal transduction and cell growth
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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
Forearm blood flow during body temperature transients produced by leg exercise.
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Intact AQP0 performs cell-to-cell adhesion
Interfacial kinetic and binding properties of mammalian group IVB phospholipase A2 (cPLA2beta) and comparison with the other cPLA2 isoforms
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The SLC31 (Ctr) copper transporter family
'phospho-p-S722,S792-RPTOR-1 [cytosol]' negatively regulates 'Activation of S6K1'
'DAGs [plasma membrane]' positively regulates 'DAG stimulates protein kinase C-delta'
'DAG [plasma membrane]' positively regulates 'Activation of conventional Protein Kinase C'
'SSB [nucleoplasm]' positively regulates 'RNA Polymerase III Termination and release of transcribed mRNA'
'CIT [cytosol]' negatively 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'
'Mg2+ [cytosol]' is required for 'pyrophosphate + H2O => 2 orthophosphate [cytosolic]'
'Mg2+ [mitochondrial matrix]' is required for 'pyrophosphate + H2O => 2 orthophosphate [mitochondrial]'
'D-Fructose 2,6-bisphosphate [cytosol]' positively regulates 'D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP'
Identification and characterization of a sphingolipid delta 4-desaturase family
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.
Characterization of human D-amino acid oxidase
Roles of Tom70 in import of presequence-containing mitochondrial proteins
The subcellular localization of an aquaporin-2 tetramer depends on the stoichiometry of phosphorylated and nonphosphorylated monomers
Formation of a pool of free 40S subunits
Autoinhibition and activation mechanisms of the Wiskott-Aldrich syndrome protein
Aldehyde dehydrogenase, a diphosphopyridine nucleotide-linked enzyme
Expression of Human CTP synthetase in Saccharomyces cerevisiae reveals phosphorylation by protein kinase A
ATP-binding cassette (ABC) transporters in human metabolism and diseases
Peroxisome proliferator-activated receptor alpha target genes
MAPK targets/ Nuclear events mediated by MAP kinases
Pig-n, a mammalian homologue of yeast Mcd4p, is involved in transferring phosphoethanolamine to the first mannose of the glycosylphosphatidylinositol
A heterodimeric coiled-coil protein required for mitotic chromosome condensation in vitro
Iron-sulfur cluster biosynthesis. Characterization of frataxin as an iron donor for assembly of [2Fe-2S] clusters in ISU-type proteins
Subcellular localization and lysophospholipase/transacylation activities of human group IVC phospholipase A2 (cPLA2gamma)
The juxtamembrane region of the EGF receptor functions as an activation domain
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
The structural basis for substrate specificity and inhibition of human S-adenosylmethionine decarboxylase
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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Ubiquitin-dependent mechanism regulates rapid turnover of AU-rich cytokine mRNAs
MicroRNAs: small RNAs with a big role in gene regulation
Post-translational palmitoylation and glycosylation of Wnt-5a are necessary for its signalling
Identification of a specific telomere terminal transferase activity in Tetrahymena extracts
Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embryos.
Intrinsic activity and stability of bifunctional human UMP synthase and its two separate catalytic domains, orotate phosphoribosyltransferase and orotidine-5'-phosphate decarboxylase
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
Bile salt and organic anion SLC transporters
Disruption of aquaporin-11 produces polycystic kidneys following vacuolization of the proximal tubule
Mcm10 regulates the stability and chromatin association of DNA polymerase-alpha
Essential role for Gab2 in the allergic response
Myeloproliferative disorder FOP-FGFR1 fusion kinase recruits phosphoinositide-3 kinase and phospholipase Cgamma at the centrosome
Myelin-associated inhibitors of axonal regeneration in the adult mammalian CNS
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
Congenital disorder of glycosylation id presenting with hyperinsulinemic hypoglycemia and islet cell hyperplasia
The p75 receptor acts as a displacement factor that releases Rho from Rho-GDI
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
Role of aquaporin-7 and aquaporin-9 in glycerol metabolism; involvement in obesity
The human phosphatidylinositol phosphatase SAC1 interacts with the coatomer I complex
Discovery of the aquaporins and development of the field
The ontogeny of human drug-metabolizing enzymes: phase II conjugation enzymes and regulatory mechanisms
Immunological and inflammatory functions of the interleukin-1 family
Horror autoinflammaticus: the molecular pathophysiology of autoinflammatory disease (*)
Completion of mammalian lagging strand DNA replication using purified proteins.
Site specificity of four pyruvate dehydrogenase kinase isoenzymes toward the three phosphorylation sites of human pyruvate dehydrogenase
Expression and purification of human gamma-glutamylcysteine synthetase
Promoter clearance by RNA polymerase II is an extended, multistep process strongly affected by sequence.
The SLC24 Na+/Ca2+-K+ exchanger family: vision and beyond
PKC412 inhibits the zinc finger 198-fibroblast growth factor receptor 1 fusion tyrosine kinase and is active in treatment of stem cell myeloproliferative disorder
Cloning and initial characterization of a new subunit for mammalian serine-palmitoyltransferase
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
Effects of phosphorylation by CAK on cyclin binding by CDC2 and CDK2.
Odontogenic ameloblast-associated protein nature of the amyloid found in calcifying epithelial odontogenic tumors and unerupted tooth follicles
Regulation of PLK1 Activity at G2/M Transition
A synopsis of the unconjugated acidic transamination metabolites of phenylalanine in phenylketonuria
CENP-E, a novel human centromere-associated protein required for progression from metaphase to anaphase
Interaction of DNA polymerase alpha-primase with cellular replication protein A and SV40 T antigen.
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
Molybdenum cofactor biosynthesis and deficiency
Active site remodelling accompanies thioester bond formation in the SUMO E1
Ran-independent nuclear import of cyclin B1-Cdc2 by importin beta
The enzymes and control of eukaryotic mRNA turnover
Subcellular localization and targeting of N-acetylglucosaminyl phosphatidylinositol de-N-acetylase, the second enzyme in the glycosylphosphatidylinositol biosynthetic pathway
Mammalian translation initiation factor eIF1 functions with eIF1A and eIF3 in the formation of a stable 40 S preinitiation complex.
Anti-apoptotic signaling by the interleukin-2 receptor reveals a function for cytoplasmic tyrosine residues within the common gamma (gamma c) receptor subunit
Vertebrate agmatinases: what role do they play in agmatine catabolism?
Agmatine: at the crossroads of the arginine pathways
MTABC3, a novel mitochondrial ATP-binding cassette protein involved in iron homeostasis
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
Enzymes and reactions at the eukaryotic DNA replication fork.
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
Mechanistic and kinetic analysis of the DcpS scavenger decapping enzyme
Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs
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
Analysis of phosphoinositide binding domain properties within the myotubularin-related protein MTMR3
The extended protein kinase C superfamily
Subcellular locations of phosphatidylinositol 4-kinase isoforms
Old and new generation lipid mediators in acute inflammation and resolution
Transcriptional signaling by double-stranded RNA: role of TLR3
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
Novel mutant-selective EGFR kinase inhibitors against EGFR T790M
Deleterious mutation in the mitochondrial arginyl-transfer RNA synthetase gene is associated with pontocerebellar hypoplasia
Phase 1 - Functionalization of compounds
ZNF198-FGFR1 transforms Ba/F3 cells to growth factor independence and results in high level tyrosine phosphorylation of STATS 1 and 5
Biosynthesis and metabolism of leukotrienes
Gamma-glutamyl compounds: substrate specificity of gamma-glutamyl transpeptidase enzymes
Cdc13 delivers separate complexes to the telomere for end protection and replication
Identification of a mammalian mitochondrial porphyrin transporter
2-acyl-sn-glycero-3-phosphoserine [ChEBI:37646]
Humans possess two mitochondrial ferredoxins, Fdx1 and Fdx2, with distinct roles in steroidogenesis, heme, and Fe/S cluster biosynthesis
Ethanolamine-phosphate cytidylyltransferase
Isolation and complete sequence of a functional human glyceraldehyde-3-phosphate dehydrogenase gene
FUNCTION Has a role in establishing metaphase during mitosis. Required for chromosome segregation where it generates tension during kinetochore capturing.SUBUNIT Heterodimer with klp6.SIMILARITY Belongs to the kinesin-like protein family. Kinesin II subfamily.SIMILARITY Contains 1 kinesin-motor domain.
sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating
Degradation of cysteine and homocysteine
Transient receptor potential 1 regulates capacitative Ca(2+) entry and Ca(2+) release from endoplasmic reticulum in B lymphocytes
ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex.
Lck regulates Vav activation of members of the Rho family of GTPases
Phosphoinositide signalling in cancer: beyond PI3K and PTEN
Neurotrophin signaling: many exciting surprises!
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
An adjacent pair of human NUDT genes on chromosome X are preferentially expressed in testis and encode two new isoforms of diphosphoinositol polyphosphate phosphohydrolase
Nonsense Mediated Decay Independent of the Exon Junction Complex
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.
Human liver type pyruvate kinase: complete amino acid sequence and the expression in mammalian cells
Amyloid fibrils in human insulinoma and islets of Langerhans of the diabetic cat are derived from a neuropeptide-like protein also present in normal islet cells
Antigenic analysis of the major human phosphoglucomutase isozymes: PGM1, PGM2, PGM3 and PGM4
Predominant expression and activation-induced tyrosine phosphorylation of phospholipase C-gamma 2 in B lymphocytes
ZnT7, a novel mammalian zinc transporter, accumulates zinc in the Golgi apparatus
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
U-box proteins as a new family of ubiquitin ligases
Activation of ATR in response to replication stress
Methionine regeneration and aspartate aminotransferase in parasitic protozoa
Molecular interactions of Polo-like-kinase 1 with the mitotic kinesin-like protein CHO1/MKLP-1
(S)-3-Hydroxyisobutyryl-CoA [ChEBI:28259]
Identification of a fourth subunit of mammalian DNA polymerase delta.
The major sites of cellular phospholipid synthesis and molecular determinants of Fatty Acid and lipid head group specificity
1-phosphatidylinositol-3-phosphate 5-kinase
GAPs galore! A survey of putative Ras superfamily GTPase activating proteins in man and Drosophila
Phosphatidylserine decarboxylase proenzyme Chain B
Phosphatidylserine decarboxylase proenzyme Chain A
The p24 family and selective transport processes at the ER-Golgi interface
Lysophosphatidylinositol acyltransferase
Membrane-bound O-acyltransferase domain-containing protein 7
CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial
Putative glycerophosphocholine phosphodiesterase GPCPD1
Glycerophosphodiester phosphodiesterase 5
Choline-phosphate cytidylyltransferase A
Phosphatidylethanolamine N-methyltransferase
Choline-phosphate cytidylyltransferase B
CDP-diacylglycerol--inositol 3-phosphatidyltransferase
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
Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics
Regulation of Ca2+ signaling in mast cells by tyrosine-phosphorylated and unphosphorylated non-T cell activation linker
Multidrug resistance-associated protein 1
Diverse mechanisms and machineries for import of mitochondrial proteins
Pathways of chaperone-mediated protein folding in the cytosol
Molecular mechanisms of translational control
Human adenine phosphoribosyltransferase. Affinity purification, subunit structure, amino acid composition, and peptide mapping.
Ectonucleotide pyrophosphatase/phosphodiesterase family member 7
2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial ecNumber2.1.1.201/ecNumber
Hexaprenyldihydroxybenzoate methyltransferase, mitochondrial ecNumber2.1.1.114/ecNumber
Ubiquinone biosynthesis monooxygenase COQ6 ecNumber1.14.13.-/ecNumber
Para-hydroxybenzoate--polyprenyltransferase, mitochondrial
Decaprenyl-diphosphate synthase subunit 2 ecNumber2.5.1.91/ecNumber
Decaprenyl-diphosphate synthase subunit 1 ecNumber2.5.1.91/ecNumber
Thrombopoietin: a tool for understanding thrombopoiesis
Functional expression of human mutant phosphofructokinase in yeast: genetic defects in French Canadian and Swiss patients with phosphofructokinase deficiency
Three-step model for condensin activation during mitotic chromosome condensation
Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex
Dihydrolipoamide acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial precursor
70 kDa mitochondrial autoantigen of primary biliary cirrhosis
pyruvate dehydrogenase E1 alpha apoprotein
Pyruvate dehydrogenase E1 component alpha subunit, somatic form, mitochondrial precursor
Mapping residues of SUMO precursors essential in differential maturation by SUMO-specific protease, SENP1
Pyruvate dehydrogenase E1 component beta subunit, mitochondrial precursor
pyruvate dehydrogenase E1 beta apoprotein
Activation and signaling of the p38 MAP kinase pathway
Aconitate hydratase, mitochondrial precursor
Citrate synthase, mitochondrial precursor
Assembly of simian virus 40 Okazaki pieces from DNA primers is reversibly arrested by ATP depletion.
Ubiquinone biosynthesis protein COQ7 homolog
Cloning, characterization, and chromosomal localization of a gene frequently deleted in human liver cancer (DLC-1) homologous to rat RhoGAP
Dihydrolipoamide dehydrogenase, mitochondrial
Human liver glucokinase gene: cloning and sequence determination of two alternatively spliced cDNAs
Pyruvate dehydrogenase protein X component, mitochondrial precursor
Dihydrolipoamide dehydrogenase-binding protein of pyruvate dehydrogenase complex
pyruvate dehydrogenase complex X component (E3 binding protein)
Synthesis of pyrophosphates in the cytosol
Identification of human phosphoglucomutase 3 (PGM3) as N-acetylglucosamine-phosphate mutase (AGM1)
Subcellular targeting and trafficking of nitric oxide synthases
The human Myt1 kinase preferentially phosphorylates Cdc2 on threonine 14 and localizes to the endoplasmic reticulum and Golgi complex.
A yeast gene required for DNA replication encodes a protein with homology to DNA helicases.
Purification and characterization of human microsomal dipeptidase
Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics
A missense mutation in SLC33A1, which encodes the acetyl-CoA transporter, causes autosomal-dominant spastic paraplegia (SPG42)
Induction of ceruloplasmin synthesis by IFN-gamma in human monocytic cells
Phosphoinositide 3-kinase: the key switch mechanism in insulin signalling.
G(1) to S transition: more than a cell cycle engine switch.
Mcm10 and Cdc45 cooperate in origin activation in Saccharomyces cerevisiae
Functional and molecular characterization of the human neutral solute channel aquaporin-9
Genetic basis of mitochondrial HMG-CoA synthase deficiency
Human airway epithelial cells sense Pseudomonas aeruginosa infection via recognition of flagellin by Toll-like receptor 5
NGF signalling via TRKA from the plasma membrane
Characterization of the structure and function of a new mitogen-activated protein kinase (p38beta)
In vitro SUMO-1 modification requires two enzymatic steps, E1 and E2
Biochem. Biophys. Res. Commun. 254:693-8
A complex of NuMA and cytoplasmic dynein is essential for mitotic spindle assembly
Regulation of Ras in lymphocytes: get a GRP
The retinoid cycle in cones (daylight vision)
The quality control of MHC class I peptide loading
Succinate Dehydrogenase complex subunit C
Succinate-ubiquinone oxidoreductase cytochrome B large subunit
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor
Succinate Dehydrogenase complex subunit A
Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial
Succinate dehydrogenase (ubiquinone) iron-sulfur protein, mitochondrial
Succinate Dehydrogenase complex subunit B
Negative regulation of condensin I by CK2-mediated phosphorylation
Molecular cloning and expression of a cDNA for human kidney cysteine conjugate beta-lyase
Isocitrate dehydrogenase (NAD) subunit beta, mitochondrial precursor
Isocitrate dehydrogenase (NAD) subunit alpha, mitochondrial precursor
Isocitrate dehydrogenase (NAD) subunit gamma, mitochondrial precursor
2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor
alpha-ketoglutarate dehydrogenase E1 apoenzyme
Phosphoribosylformylglycinamidine synthase
Formylglycinamide ribotide amidotransferase
Electron Transfer Flavoprotein beta subunit
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
Glutamine phosphoribosylpyrophosphate amidotransferase
Amidophosphoribosyltransferase precursor (EC 2.4.2.14) (Glutamine phosphoribosylpyrophosphate amidotransferase) (ATASE) (GPAT)
Amidophosphoribosyltransferase precursor
phosphoribosyl pyrophosphate amidotransferase
C-to-U RNA editing: mechanisms leading to genetic diversity.
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
AMP deaminase 3 (EC 3.5.4.6) (AMP deaminase isoform E) (Erythrocyte AMP deaminase)
Adenylosuccinate synthetase (EC 6.3.4.4) (IMP--aspartate ligase) (AdSS) (AMPSase)
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
Multiple mechanisms regulate NuMA dynamics at spindle poles
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
Adenylate kinase isoenzyme 1 (EC 2.7.4.3) (ATP-AMP transphosphorylase) (AK1) (Myokinase)
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))
Dihydroorotate dehydrogenase, mitochondrial precursor
Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdehase) (Fragment)
Changes in serotonin metabolism during treatment with the aldehyde dehydrogenase inhibitors disulfiram and cyanamide
Glutathione reductase, mitochondrial precursor
deoxythymidylate kinase (thymidylate kinase)
Adenylate kinase isoenzyme 5 (EC 2.7.4.3) (ATP-AMP transphosphorylase)
Guanylate kinase (EC 2.7.4.8) (GMP kinase)
Adenylate kinase isoenzyme 2, mitochondrial
Adenylate kinase isoenzyme 2, mitochondrial (EC 2.7.4.3) (ATP-AMP transphosphorylase)
FAD1 flavin adenine dinucleotide synthetase homolog
Ectonucleotide pyrophosphatase/phosphodiesterase 1
Transcriptional activation of pyruvate kinase gene by ChREBP:MLX
Transcriptional activation of Citrate lyase monomer gene by ChREBP:MLX
CDC6 protein is synthesized under the control of E2F transcription factors
Transcriptional activation of Acetyl-CoA carboxylase by ChREBP:MLX
Transcriptional activation of GP-acyl transferase gene by ChREBP:MLX
Coiled bodies contain U7 small nuclear RNA and associate with specific DNA sequences in interphase human cells.
Ded1p, a DEAD-box protein required for translation initiation in Saccharomyces cerevisiae, is an RNA helicase.
Three-dimensional structure of human erythrocytic purine nucleoside phosphorylase at 3.2 A resolution
Kinesin-8 from fission yeast: a heterodimeric, plus-end-directed motor that can couple microtubule depolymerization to cargo movement
4-trimethylaminobutyraldehyde dehydrogenase
aldehyde dehydrogenase 9 family, member A1
delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor
carbamoyl-phosphate synthase (ammonia), mitochondrial
ornithine carbamoyltransferase, mitochondrial
A stop-codon mutation in the BRI gene associated with familial British dementia
4-alpha- hydroxy-tetrahydropterin dehydratase
Phenylalanine hydroxylase- stimulating protein
pterin-4-alpha-carbinolamine dehydratase
Dimerization cofactor of hepatocyte nuclear factor 1-alpha
4-alpha-hydroxy-tetrahydropterin dehydratase
Mitochondrial 2-oxodicarboxylate carrier
lysine-ketoglutarate reductase /saccharopine dehydrogenase monomer
3-hydroxyisobutyryl-coenzyme A hydrolase
Branched-chain amino acid aminotransferase, cytosolic
branched-chain amino acid aminotransferase, mitochondrial, apoenzyme
ErbB-3 and ErbB-4 function as the respective low and high affinity receptors of all Neu differentiation factor/heregulin isoforms
Delta-1-pyrroline-5-carboxylate synthetase short
Delta-1-pyrroline-5-carboxylate synthetase long
Glutamine- dependent asparagine synthetase
Asparagine synthetase (glutamine-hydrolyzing)
Toward the full set of human mitochondrial aminoacyl-tRNA synthetases: characterization of AspRS and TyrRS
Common origin and evolution of glycosyltransferases using Dol-P-monosaccharides as donor substrate
ornithine aminotransferase, mitochondrial
Aquaporins: highways for cells to recycle water with the outside world
Analysis of nucleocytoplasmic shuttling of NF kappa B proteins in human leukocytes
Nicotinamide mononucleotide adenylyltransferase 1
Nicotinamide mononucleotide adenylyltransferase 2
Nicotinamide mononucleotide adenylyltransferase 3
PIG-W is critical for inositol acylation but not for flipping of glycosylphosphatidylinositol-anchor
Biotin--protein ligase ecNumber6.3.4.-/ecNumber
The chromosomal association of condensin II is regulated by a noncatalytic function of PP2A
Selective active site inhibitors of human lactate dehydrogenases A4, B4, and C4
Signal transduction by the neurotrophin receptors
Post-translational modification: synthesis of GPI-anchored proteins
Diversification of Neu differentiation factor and epidermal growth factor signaling by combinatorial receptor interactions
Tuberculosis - metabolism and respiration in the absence of growth
A microRNA polycistron as a potential human oncogene
Regulation of deoxyadenosine and nucleoside analog phosphorylation by human placental adenosine kinase
Steroidogenic electron transport in adrenal cortex mitochondria
Acyl-CoA:lysophospholipid acyltransferases
Tyrosine-phosphorylated Vav1 as a point of integration for T-cell receptor- and CD28-mediated activation of JNK, p38, and interleukin-2 transcription
Molecular cloning and nucleotide sequence of a full-length cDNA for human alpha enolase
Cdc25A stability is controlled by the ubiquitin-proteasome pathway during cell cycle progression and terminal differentiation
Newly made phosphatidylserine and phosphatidylethanolamine are preferentially translocated between rat liver mitochondria and endoplasmic reticulum
Cleavage of oxidized guanine nucleotide and ADP sugar by human NUDT5 protein
Tuberous sclerosis complex gene products, Tuberin and Hamartin, control mTOR signaling by acting as a GTPase-activating protein complex toward Rheb
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
Employment of the epidermal growth factor receptor in growth factor-independent signaling pathways
Glycogenin: the primer for mammalian and yeast glycogen synthesis
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
Antimicrobial mechanisms of phagocytes and bacterial evasion strategies
A novel family of membrane-bound E3 ubiquitin ligases
RhoGDIgamma: a GDP-dissociation inhibitor for Rho proteins with preferential expression in brain and pancreas
P110delta, a novel phosphoinositide 3-kinase in leukocytes
Polymerase switching on the C-strand of the telomere
Wnt and calcium signaling: beta-catenin-independent pathways
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
Acetyl-coenzyme A synthetase 2-like, mitochondrial
acyl-CoA synthetase short-chain family member 1
Aldehyde dehydrogenase, mitochondrial precursor
Cytochrome c oxidase assembly protein COX15 homolog
Protoheme IX farnesyltransferase, mitochondrial ecNumber2.5.1.-/ecNumber
Coproporphyrinogen III oxidase, mitochondrial
10-formyltetrahydrofolyl polyglutamate macromolecule [ChEBI:28010]
10-formyltetrahydrofolyl polyglutamate macromolecule
Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
Vitamins B6 activation to pyridoxal phosphate
Advanced glycation endproduct (AGE) receptor 1 is a negative regulator of the inflammatory response to AGE in mesangial cells
5-aminolevulinate synthase, non-specific (pyridoxal phosphate cofactor)
5-aminolevulinate synthase, non-specific, mitochondrial
5-aminolevulinate synthase, erythroid (pyridoxal phosphate cofactor)
5-aminolevulinate synthase, erythroid-specific, mitochondrial precursor
Roles of aquaporin-3 water channels in volume-regulatory water flow in a human epithelial cell line
Reconstitution of functional water channels in liposomes containing purified red cell CHIP28 protein
Purification of, generation of monoclonal antibodies to, and mapping of phosphoribosyl N-formylglycinamide amidotransferase
Characterization of human type I and type II IMP dehydrogenases
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.
C-terminal binding domain of Rho GDP-dissociation inhibitor directs N-terminal inhibitory peptide to GTPases
Cell-cycle-regulated phosphorylation of DNA replication factor A from human and yeast cells.
Cellular targets for activation by the E2F1 transcription factor include DNA synthesis- and G1/S-regulatory genes
Crystal structure of 5-aminolevulinate synthase, the first enzyme of heme biosynthesis, and its link to XLSA in humans
The mitochondrial ABC transporter Atm1p functions as a homodimer
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.
Energy dependent regulation of mTOR by LKB1-AMPK
Fibroblast growth factors and their receptors in cancer
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
LAB/NTAL/Lat2: a force to be reckoned with in all leukocytes?
Lysine acetylation targets protein complexes and co-regulates major cellular functions
Sprinter: a novel transmembrane protein required for Wg secretion and signaling
Differential expression and regulation of toll-like receptors (TLR) in human leukocytes: selective expression of TLR3 in dendritic cells
Global gene expression profiling and histochemical analysis of the developing human fetal pancreas
The yeast Pif1p helicase removes telomerase from telomeric DNA
Structure of human phosphopantothenoylcysteine synthetase at 2.3 A resolution.
Bora and the kinase Aurora a cooperatively activate the kinase Plk1 and control mitotic entry
Glyceraldehyde-3-phosphate dehydrogenase from human tissues.
The endoribonuclease activity of mammalian IRE1 autoregulates its mRNA and is required for the unfolded protein response
Sequencing and expression of a cDNA for human glutathione synthetase
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
5,10-methenyltetrahydrofolate polyglutamate [ChEBI:65049]
SREBP transcription factors: master regulators of lipid homeostasis
miRNAs on the move: miRNA biogenesis and the RNAi machinery
Human MTH3 (NUDT18) Protein Hydrolyzes Oxidized Forms of Guanosine and Deoxyguanosine Diphosphates: COMPARISON WITH MTH1 AND MTH2
Transcriptional regulation of HMG-CoA synthase and HMG-CoA reductase genes by human ACBP
Interactions between the endoplasmic reticulum, mitochondria, plasma membrane and other subcellular organelles
Planar cell polarity signaling: from fly development to human disease
Eukaryotic ribosomes require initiation factors 1 and 1A to locate initiation codons.
Phosphatidylinositol-5-phosphate activation and conserved substrate specificity of the myotubularin phosphatidylinositol 3-phosphatases
Identification and characterization of PS-GAP as a novel regulator of caspase-activated PAK-2
Human CDC6/Cdc18 associates with Orc1 and cyclin-cdk and is selectively eliminated from the nucleus at the onset of S phase.
The molecular mechanisms that control thrombopoiesis
Novel 5 alpha-steroid reductase (SRD5A3, type-3) is overexpressed in hormone-refractory prostate cancer
Multisite autophosphorylation of p21-activated protein kinase gamma-PAK as a function of activation
6-methoxy-3-methyl-2-decaprenyl-1,4-benzoquinol [ChEBI:64181]
2-methoxy-6-decaprenyl-1,4-benzoquinol [ChEBI:64180]
The yeast mitochondrial carrier Leu5p and its human homologue Graves' disease protein are required for accumulation of coenzyme A in the matrix
IP3 receptor/Ca2+ channel: from discovery to new signaling concepts
Cloning and characterization of human guanine deaminase. Purification and partial amino acid sequence of the mouse protein.
Identification and characterization of a novel inositol polyphosphate 5-phosphatase
Apert syndrome results from localized mutations of FGFR2 and is allelic with Crouzon syndrome
Architecture of the human origin recognition complex.
NRAGE, a p75 neurotrophin receptor-interacting protein, induces caspase activation and cell death through a JNK-dependent mitochondrial pathway
Fibroblast growth factor signalling: from development to cancer
Pyrimidine nucleotide biosynthesis in animals: genes, enzymes, and regulation of UMP biosynthesis.
A three-dimensional working model of the multienzyme complex of aminoacyl-tRNA synthetases based on electron microscopic placements of tRNA and proteins
Synthesis of Leukotrienes (LT) and Eoxins (EX)
Translational regulation mechanisms of AP-1 proteins
Proximal signaling events in Fc epsilon RI-mediated mast cell activation
J. Allergy Clin. Immunol. 119:544-52; quiz 553-4
Transgenic mice as a model of pre-clinical Alzheimer's disease
The role of mast cells in allergic inflammation
Biochemistry of mammalian peroxisomes revisited
Protein misfolding, functional amyloid, and human disease
Members of the human glyceraldehyde-3-phosphate dehydrogenase-related gene family map to dispersed chromosomal locations.
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mRNA quality control: an ancient machinery recognizes and degrades mRNAs with nonsense codons
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
Saccharomyces cerevisiae replication factor C. II. Formation and activity of complexes with the proliferating cell nuclear antigen and with DNA polymerases delta and epsilon.
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Human aquaporin adipose (AQPap) gene. Genomic structure, promoter analysis and functional mutation
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Roles of C-terminal processing, and involvement in transacylation reaction of human group IVC phospholipase A2 (cPLA2gamma)
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XBP1 induces WFS1 through an endoplasmic reticulum stress response element-like motif in SH-SY5Y cells
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Uninterrupted MCM2-7 function required for DNA replication fork progression.
A lesion in the DNA replication initiation factor Mcm10 induces pausing of elongation forks through chromosomal replication origins in Saccharomyces cerevisiae
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Src-family kinases in B-cell development and signaling
Phosphoglucomutase 1: a gene with two promoters and a duplicated first exon
A stable complex of a novel transcription factor IIB- related factor, human TFIIIB50, and associated proteins mediate selective transcription by RNA polymerase III of genes with upstream promoter elements
5-Phosphoribose 1-diphosphate biosynthesis
Synthesis of cytosolic 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) from D-ribose 5-phosphate
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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3-decaprenyl-4-hydroxybenzoic acid [ChEBI:64136]
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Neuregulin-1 only induces trans-phosphorylation between ErbB receptor heterodimer partners
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The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans
Cdk2-dependent and -independent pathways in E2F-mediated S phase induction
Limiting role of 6-phosphogluconolactonase in erythrocyte hexose monophosphate pathway metabolism
Triggering and augmentation mechanisms, granule pools, and biphasic insulin secretion
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The role of the Rho GTPases in neuronal development
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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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GPI7 is the second partner of PIG-F and involved in modification of glycosylphosphatidylinositol
Lathosterolosis, a novel multiple-malformation/mental retardation syndrome due to deficiency of 3beta-hydroxysteroid-delta5-desaturase
Transfer of SUMO from E1 to E2 (UBE2I, UBC9)
Protein folding: versatility of the cytosolic chaperonin TRiC/CCT
Removal of licensing factors from origins
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
Enzymatic degradation of dopamine by COMT
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
Aurora-A and an interacting activator, the LIM protein Ajuba, are required for mitotic commitment in human cells
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Gastrin-CREB signalling pathway via PKC and MAPK
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
Rapid association of cytoskeletal remodeling proteins with the developing phagosomes of human neutrophils
Characterization of the human gene encoding alpha-aminoadipate aminotransferase (AADAT).
NLR functions beyond pathogen recognition
Expression of SRPR (SRP Receptor subunit alpha)
Expression of SRPRB (SRP Receptor subunit beta)
Gap-filling DNA repair synthesis and ligation in TC-NER
NEUROD1- and PDX1-dependent synthesis of glucokinase (GCK) protein
Peroxisome proliferator activated receptors and lipoprotein metabolism
Deficiency of the ADP-forming succinyl-CoA synthase activity is associated with encephalomyopathy and mitochondrial DNA depletion
Regulation of Ins(3,4,5,6)P(4) signaling by a reversible kinase/phosphatase
Crystal structures of human NUDT5 reveal insights into the structural basis of the substrate specificity
The distribution and function of phosphatidylserine in cellular membranes
The PI-3 kinase/Akt pathway and T cell activation: pleiotropic pathways downstream of PIP3
Vav1: a key signal transducer downstream of the TCR
RNA polymerase III detects cytosolic DNA and induces type I interferons through the RIG-I pathway
Phosphorylation of mammalian CDC6 by cyclin A/CDK2 regulates its subcellular localization.
Regulation of Geminin and Cdt1 expression by E2F transcription factors
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Control of cyclin B1 localization through regulated binding of the nuclear export factor CRM1
Inhibition of Mcm4,6,7 helicase activity by phosphorylation with cyclin A/Cdk2.
Binding of MET-TRNAf and GTP to homogeneous initiation factor MP.
Synthesis of PIPs at the early endosome membrane
Immunoreceptor DAP12 bearing a tyrosine-based activation motif is involved in activating NK cells
Pol II mediated transcription of microRNA genes
Expression of BIP (78 kDa Glucose-regulated protein, GRP78, HSPA5)
Interconversion of leukotrienes catalyzed by purified gamma-glutamyl transpeptidase: concomitant formation of leukotriene D4 and gamma-glutamyl amino acids
The kinase activity of IL-1 receptor-associated kinase 4 is required for interleukin-1 receptor/toll-like receptor-induced TAK1-dependent NFkappaB activation
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Structure, function and regulation of pyruvate carboxylase
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Mammalian G proteins and their cell type specific functions
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Importin beta is a mitotic target of the small GTPase Ran in spindle assembly
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Genetics of mammalian meiosis: regulation, dynamics and impact on fertility
Phagosomes are competent organelles for antigen cross-presentation
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ER-phagosome fusion defines an MHC class I cross-presentation compartment in dendritic cells
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(1R,2S)-1-Hydroxypropane-1,2,3-tricarboxylate [ChEBI:151]
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Control of translation and mRNA degradation by miRNAs and siRNAs
Condensins, chromosome condensation protein complexes containing XCAP-C, XCAP-E and a Xenopus homolog of the Drosophila Barren protein
Reversible compartmentalization of de novo purine biosynthetic complexes in living cells
Nuclear translocation of plk1 mediated by its bipartite nuclear localization signal
Stimulation of the human CTP:phosphoethanolamine cytidylyltransferase gene by early growth response protein 1
NSDHL, an enzyme involved in cholesterol biosynthesis, traffics through the Golgi and accumulates on ER membranes and on the surface of lipid droplets
Chk1 and Chk2 kinases in checkpoint control and cancer
Human Sgt1 binds HSP90 through the CHORD-Sgt1 domain and not the tetratricopeptide repeat domain
Identification and characterization of novel spliced variants of neuregulin 4 in prostate cancer
Apoptosis induced by the toll-like receptor adaptor TRIF is dependent on its receptor interacting protein homotypic interaction motif
Novel variants in human Aquaporin-4 reduce cellular water permeability
Polymorphism in the intermediates and products of amyloid assembly
A general map of iron metabolism and tissue-specific subnetworks
The Mad2 spindle checkpoint protein undergoes similar major conformational changes upon binding to either Mad1 or Cdc20
Pak1 kinase homodimers are autoinhibited in trans and dissociated upon activation by Cdc42 and Rac1
Kinesin-5 regulates the growth of the axon by acting as a brake on its microtubule array
Phosphorylation and activation of 13S condensin by Cdc2 in vitro
Identification of ARAP3, a novel PI3K effector regulating both Arf and Rho GTPases, by selective capture on phosphoinositide affinity matrices
De novo telomere addition by Tetrahymena telomerase in vitro
Inborn errors of ketogenesis and ketone body utilization
Crystal structure of the tetrameric Mad1-Mad2 core complex: implications of a 'safety belt' binding mechanism for the spindle checkpoint
Molecular organization of the presynaptic active zone
Transmembrane transport of endo- and xenobiotics by mammalian ATP-binding cassette multidrug resistance proteins
Alternate exon insertion controls selective ubiquitination and degradation of different AUF1 protein isoforms
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
A role for Plk1 phosphorylation of NudC in cytokinesis
Unresponsiveness of MyD88-deficient mice to endotoxin
Purification and characterization of 5'-deoxy-5'-methylthioadenosine phosphorylase from human placenta
Multiple pathways for sorting mitochondrial precursor proteins
Molecular machinations of the MHC-I peptide loading complex
Chk1 is a wee1 kinase in the G2 DNA damage checkpoint inhibiting cdc2 by Y15 phosphorylation.
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
Human cell growth requires a functional cytoplasmic exosome, which is involved in various mRNA decay pathways
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
COPI-coated ER-to-Golgi transport complexes segregate from COPII in close proximity to ER exit sites
EGF receptor activation by GPCRs: an universal pathway reveals different versions
Biological & physiological aspects of action of insulin-like growth factor peptide family
Holocarboxylase synthetase: correlation of protein localisation with biological function
Amino acid and oligopeptide SLC transporters
Crystal structure of human E1 enzyme and its complex with a substrate analog reveals the mechanism of its phosphatase/enolase activity
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
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
Human intestinal H+/peptide cotransporter. Cloning, functional expression, and chromosomal localization
TRAF6 Mediated Induction of proinflammatory cytokines
Ubiquinone. Biosynthesis of quinone ring and its isoprenoid side chain. Intracellular localization
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
Inflammasome adaptors and sensors: intracellular regulators of infection and inflammation
Molecular cloning of human amidophosphoribosyltransferase
Back in the water: the return of the inositol phosphates
PI3Kgamma is a key regulator of inflammatory responses and cardiovascular homeostasis
Regulation of WASP/WAVE proteins: making a long story short
Endotoxin signaling in human macrophages: signaling via an alternate mechanism
Cutting edge: bacterial flagellin activates basolaterally expressed TLR5 to induce epithelial proinflammatory gene expression
Purification and properties of human placental adenosine kinase
Sensing of viral infection and activation of innate immunity by toll-like receptor 3
Mutation in the 4a-carbinolamine dehydratase gene leads to mild hyperphenylalaninemia with defective cofactor metabolism.
Nuclear organization of DNA replication in primary mammalian cells
GlycoVis: visualizing glycan distribution in the protein N-glycosylation pathway in mammalian cells
Expression and regulation by interferon of a double-stranded-RNA-specific adenosine deaminase from human cells: evidence for two forms of the deaminase.
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
Homologous recombination repair of replication-independent double-strand breaks
The citric acid (TCA) cycle and respiratory electron transport
Investigation of the ABC transporter MRP1 in selected patients with presumed defects in vitamin B12 absorption
Cloning of a water channel homolog expressed in brain meningeal cells and kidney collecting duct that functions as a stilbene-sensitive glycerol transporter
Functional analysis of mRNA scavenger decapping enzymes
Codeposition of apolipoprotein A-IV and transthyretin in senile systemic (ATTR) amyloidosis
GRB2: a pivotal protein in signal transduction
The ubiquitin-editing enzyme A20 restricts nucleotide-binding oligomerization domain containing 2-triggered signals
GTP hydrolysis by eRF3 facilitates stop codon decoding during eukaryotic translation termination
Mutation of the fumarase gene in two siblings with progressive encephalopathy and fumarase deficiency
Characterization of human lysophospholipid acyltransferase 3
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Similar idiotypic specificity for the membrane IgD and IgM of human B lymphocytes
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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
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The cDNA and protein sequences of human lactate dehydrogenase B
Phagosomal maturation (early endosomal stage)
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RIG-I-dependent sensing of poly(dA:dT) through the induction of an RNA polymerase III-transcribed RNA intermediate
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DNA polymerase delta, an essential enzyme for DNA transactions.
High-resolution x-ray structure of human aquaporin 5
Purification and characterization of kynurenine aminotransferase I from human brain
Biochemical characterization of human GMP synthetase
Two distinct proteolytic processes in the generation of a major histocompatibility complex class I-presented peptide
Glucagon and regulation of glucose metabolism
Am J Physiol Endocrinol Metab 284:E671-8
Succinic semialdehyde dehydrogenase deficiency: lessons from mice and men
MicroRNAs: biogenesis, function and applications
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
Identification of the alpha-aminoadipic semialdehyde synthase gene, which is defective in familial hyperlysinemia.
A full-length cDNA of hREV3 is predicted to encode DNA polymerase zeta for damage-induced mutagenesis in humans.
Purine ribonucleoside monophosphate biosynthesis
Mutations in SPTLC1, encoding serine palmitoyltransferase, long chain base subunit-1, cause hereditary sensory neuropathy type I
Mitotic spindle assembly checkpoint protein MAD2B
Mitotic spindle assembly checkpoint protein MAD2B (MAD2-like 2) (hREV7)
DNA repair protein REV1 ecNumber2.7.7.-/ecNumber
Endonuclease III-like protein 1 (EC 4.2.99.18)
G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.-)
DNA double-strand breaks: signaling, repair and the cancer connection.
ArfGAP1 dynamics and its role in COPI coat assembly on Golgi membranes of living cells
The crystal structure and mutational analysis of human NUDT9
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.
Activation of Chaperone Genes by ATF6-alpha
When do Lasses (longevity assurance genes) become CerS (ceramide synthases)?: Insights into the regulation of ceramide synthesis
Mechanism of selectivity in aquaporins and aquaglyceroporins
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
Mammalian MAP kinase signalling cascades
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Replication of UV-damaged DNA: new insights into links between DNA polymerases, mutagenesis and human disease.
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Human proton/oligopeptide transporter (POT) genes: identification of putative human genes using bioinformatics
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Metabolic characteristics and importance of the universal methionine salvage pathway recycling methionine from 5'-methylthioadenosine
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Crystal structure of human aquaporin 4 at 1.8 A and its mechanism of conductance
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Differential induction of the toll-like receptor 4-MyD88-dependent and -independent signaling pathways by endotoxins
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Acceptor substrate binding revealed by crystal structure of human glucosamine-6-phosphate N-acetyltransferase 1
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Selective killing of human malignant cell lines deficient in methylthioadenosine phosphorylase, a purine metabolic enzyme
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Prefoldin, a chaperone that delivers unfolded proteins to cytosolic chaperonin
Transcriptional regulation of squalene epoxidase by sterols and inhibitors in HeLa cells
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Molecular cloning and expression of the cDNAs encoding human and yeast mevalonate pyrophosphate decarboxylase
Regulation of small GTPases at epithelial cell-cell junctions
AU-rich elements and associated factors: are there unifying principles?
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
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Defective T cell differentiation in the absence of Jnk1
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Cloning and characterization of the cDNA encoding human adenylosuccinate synthetase
FUNCTION Has a role in establishing metaphase during mitosis. Required for chromosome segregation where it generates tension during kinetochore capturing.SUBUNIT Heterodimer with klp5.SIMILARITY Belongs to the kinesin-like protein family. Kinesin II subfamily.SIMILARITY Contains 1 kinesin-motor domain.
Cell cycle-regulated nuclear import and export of Cdc47, a protein essential for initiation of DNA replication in budding yeast.
Direct activation of protein kinases by unanchored polyubiquitin chains
Identification and characterization of a novel inositol hexakisphosphate kinase
The solute carrier 26 family of proteins in epithelial ion transport
Activity of phosphatidylethanolamine-N-methyltransferase in brain affected by Alzheimer's disease
ChREBP activates metabolic gene expression
Structural basis for human monoglyceride lipase inhibition
Signaling mechanisms utilized by antigen receptors and integrins: common intermediates, different outcomes?
Identification of the human mitochondrial oxodicarboxylate carrier. Bacterial expression, reconstitution, functional characterization, tissue distribution, and chromosomal location
JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1
Identification and characterization of a mammalian mitochondrial ATP-binding cassette membrane protein
Phosphorylation of the CARMA1 linker controls NF-kappaB activation
Activation of p75NTR by proBDNF facilitates hippocampal long-term depression
NuMA is required for the organization of microtubules into aster-like mitotic arrays
DNA double strand break repair, chromosome synapsis and transcriptional silencing in meiosis
Mechanisms of digestion and absorption of dietary vitamin A
Identification of autophosphorylation sites of HER2/neu
PERK in the life and death of the pancreatic beta-cell
The human telomere terminal transferase enzyme is a ribonucleoprotein that synthesizes TTAGGG repeats
Expression, purification, and characterization of histidine-tagged rat and human flavoenzyme dihydroorotate dehydrogenase.
Phosphoinositide phosphatases in cell biology and disease
The proteasome and MHC class I antigen processing
Immunoglobulin E receptor signaling and asthma
Fcgamma receptor signaling in phagocytes
The PDGF family: four gene products form five dimeric isoforms
Interference footprinting analysis of telomerase elongation complexes
Mitogen-activated protein kinase pathways mediated by ERK, JNK, and p38 protein kinases
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Three tRNA binding sites in rabbit liver ribosomes and role of the intrinsic ATPase in 80S ribosomes from higher eukaryotes
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Transformation and Stat activation by derivatives of FGFR1, FGFR3, and FGFR4
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Tubulin subunits exist in an activated conformational state generated and maintained by protein cofactors
Condensation of Prometaphase Chromosomes
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Macromolecular assemblage of aminoacyl-tRNA synthetases: identification of protein-protein interactions and characterization of a core protein
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Molecular cloning of human mevalonate kinase and identification of a missense mutation in the genetic disease mevalonic aciduria
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Characterization of recombinant human nicotinamide mononucleotide adenylyl transferase (NMNAT), a nuclear enzyme essential for NAD synthesis
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Both human ferredoxins 1 and 2 and ferredoxin reductase are important for iron-sulfur cluster biogenesis
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Xenopus Mcm10 binds to origins of DNA replication after Mcm2-7 and stimulates origin binding of Cdc45.
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Molybdenum cofactors, enzymes and pathways
Function and biogenesis of iron-sulphur proteins
Molecular and biochemical characterization of rat gamma-trimethylaminobutyraldehyde dehydrogenase and evidence for the involvement of human aldehyde dehydrogenase 9 in carnitine biosynthesis.
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.
The crystal structure of the human toll-like receptor 10 cytoplasmic domain reveals a putative signaling dimer
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Cloning and functional expression of human aquaporin8 cDNA and analysis of its gene
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
Primer utilization by DNA polymerase alpha-primase is influenced by its interaction with Mcm10p
Pathogen recognition with Toll-like receptors
Comparison of human B cell activation by TLR7 and TLR9 agonists
Nitric oxide, tetrahydrobiopterin, oxidative stress, and endothelial dysfunction in hypertension
Signal transduction during Fc receptor-mediated phagocytosis
Selective function of PKC-theta in T cells
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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)
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Intracellular mechanisms of antigen cross presentation in dendritic cells
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In vitro evidence for the dual function of Alg2 and Alg11: essential mannosyltransferases in N-linked glycoprotein biosynthesis
hNTH1 glycosylase:thymine glycol complex (name copied from entity in Homo sapiens)
hNTH1 glycosylase: foramidopyrimidine complex (name copied from entity in Homo sapiens)
NLRs join TLRs as innate sensors of pathogens
Reversible lysine acetylation controls the activity of the mitochondrial enzyme acetyl-CoA synthetase 2
Targeting the oncogene and kinome chaperone CDC37
TDG glycosylase:thymine complex (name copied from entity in Homo sapiens)
TDG 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)
MYH glycosylase:adenine complex (name copied from entity in Homo sapiens)
DNA containing an MYH-bound apurinic/apyrimidinic site (name copied from entity in Homo sapiens)
TDG glycosylase:ethenocytosine complex (name copied from entity in Homo sapiens)
CD28/CTLA-4 and CD80/CD86 families: signaling and function
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
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
Structural basis of Wnt recognition by Frizzled
G proteins and opioid receptor-mediated signalling
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Cloning of a new aquaporin (AQP10) abundantly expressed in duodenum and jejunum
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Recycling of the general transcription factors during RNA polymerase II transcription.
Release and functional characterization of the leukotriene D4-metabolizing enzyme (dipeptidase) from human polymorphonuclear leucocytes
Resolution of D-loop structures through Holliday junction intermediates
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Processing of Capped Intron-Containing Pre-mRNA
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
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Novel fibroblast growth factor receptor 3 (FGFR3) mutations in bladder cancer previously identified in non-lethal skeletal disorders
Assembly and export of MHC class I peptide ligands
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High-throughput mass spectrometry screening for inhibitors of phosphatidylserine decarboxylase
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Male pseudohermaphroditism resulting from a novel mutation in the human steroid 5 alpha-reductase type 2 gene (SRD5A2)
Chemokine-mediated interaction of hematopoietic progenitors with the bone marrow vascular niche is required for thrombopoiesis
SUMOylation and deSUMOylation at a glance
Tryptophan nutrition and metabolism: an overview
Involvement of enzymes other than CYPs in the oxidative metabolism of xenobiotics
Expert Opin Drug Metab Toxicol 2:895-921
tetra-mu3-sulfido-tetrairon [ChEBI:49883]
Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex
The mechanism of action of protein synthesis initiation factors from rabbit reticulocytes.
Protein kinase C theta is expressed in mast cells and is functionally involved in Fcepsilon receptor I signaling
Small ubiquitin-related modifier (SUMO)-specific proteases: profiling the specificities and activities of human SENPs
Structural basis for inhibition of the epidermal growth factor receptor by cetuximab
Involvement of ACSL in local synthesis of neutral lipids in cytoplasmic lipid droplets in human hepatocyte HuH7
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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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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Damaged pyrimidines are first cleaved by pyrimide-specific glycosylases (see Lindahl and Wood 1999).
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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.
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At the beginning of this reaction, 1 molecule of 'TDG glycosylase:ethenocytosine complex' is present. At the end of this reaction, 1 molecule of 'DNA containing a TDG-bound apurinic/apyrimidinic site', and 1 molecule of 'ethenocytosine' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA N-glycosylase activity' of 'G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.-)'.
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Human glucose-6-phosphate dehydrogenase: the crystal structure reveals a structural NADP(+) molecule and provides insights into enzyme deficiency
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'.
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.
Resolution of AP sites can occur through the single-nucleotide replacement pathway or through the multiple-nucleotide patch replacement pathway.
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 3ââ¬â¢ 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).
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.
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'.
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).
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Two homologues encoding human UDP-glucose:glycoprotein glucosyltransferase differ in mRNA expression and enzymatic activity
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'.
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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.
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Identification and characterization of all-trans-retinol dehydrogenase from photoreceptor outer segments, the visual cycle enzyme that reduces all-trans-retinal to all-trans-retinol.
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'.
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At the beginning of this reaction, 1 molecule of 'dNTP', and 1 molecule of 'Pol zeta:damaged DNA template complex' are present. At the end of this reaction, 1 molecule of 'Pol zeta complex', 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 'Pol zeta:damaged DNA template complex'.
At the beginning of this reaction, 1 molecule of 'HREV7', and 1 molecule of 'HREV3' are present. At the end of this reaction, 1 molecule of 'Pol zeta complex' is present. This reaction takes place in the 'nucleus'.
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'.
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'.
At the beginning of this reaction, 1 molecule of 'damaged DNA substrate ', and 1 molecule of 'Pol zeta complex' are present. At the end of this reaction, 1 molecule of 'Pol zeta:damaged DNA template complex' is present. This reaction takes place in the 'nucleus'.
Pol eta consists of 713 amino acids and can bypass thymidine-thymidine dimers adding two AÃ¢â¬â¢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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Pol zeta consists of two proteins: HREV3 with polymerase activity and HREV7, an accessory factor with unidentified activity. It has the ability to bypass pyrimidine dimers and other adducts in DNA.
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ATM is present in unirradiated cells as a dimer or higher-order multimer. Following irradiation, ATM undergoes rapid intermolecular autophosphorylation of serine 1981.
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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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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).
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 3ââ¬â¢->5ââ¬â¢ 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.
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A revised picture of the E2F transcriptional network and RB function.
MRE11 has both manganese dependent ss DNA 3'-5' exonuclease and endonuclease activities. MRE11 associates with RAD50 resulting in increased 3'-5' exonuclease activity.
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.
Expression of mammalian paralogues of HRAD9 and Mrad9 checkpoint control genes in normal and cancerous testicular tissue
Following the detection of DSBs, ATM mediates the phosphorylation of proteins involved in DNA repair (Thompson and Schild, 2002).
H2AX phosphorylation (producing the gamma-H2AX protein form) occurs within 1-3 minutes of DNA damage (Rogakou et al,1998) and is promoted by MDC1/NFBD1 (Stewart et al., 2003). gamma H2AX is one of the first proteins to appear at the site of damage, localizing to a region of about 2 Mbp surrounding the site of the double-strand break (Rogakou et al,1998). gamma-H2AX appears to play an essential role in recruiting other repair proteins including Rad50, Rad51 and BRCA1(Paull et al., 2000) (Stewart et al., 2003).
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.
N-glycan trimming in the ER and Calnexin/Calreticulin cycle
A "slow" homotetrameric kinesin-related motor protein purified from Drosophila embryos
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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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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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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'.
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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).
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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'.
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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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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).
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.
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.
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.
Still a puzzle: why is haem covalently attached in c-type cytochromes?
Investigation of coenzyme Q biosynthesis in human fibroblast and HepG2 cells
Formation of the ternary complex, and subsequently, the 43S complex
Dissociation of GDP dissociation inhibitor and membrane translocation are required for efficient activation of Rac by the Dbl homology-pleckstrin homology region of Tiam
(5-hydroxyindol-3-yl)acetic acid [ChEBI:27823]
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BRCA1 affects lipid synthesis through its interaction with acetyl-CoA carboxylase
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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 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 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'.
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 'TDG glycosylase:uracil complex' is present. At the end of this reaction, 1 molecule of 'DNA containing a TDG-bound apurinic/apyrimidinic site', and 1 molecule of 'Uracil' are present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'TDG glycosylase:thymine complex' is present. At the end of this reaction, 1 molecule of 'DNA containing a TDG-bound apurinic/apyrimidinic site', and 1 molecule of 'Thymine' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA N-glycosylase activity' of 'G/T mismatch-specific thymine DNA glycosylase (EC 3.2.2.-)'.
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'.
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: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'.
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'.
The classical human phosphoglucomutase (PGM1) isozyme polymorphism is generated by intragenic recombination
Genomic structure and expression of the human heme A:farnesyltransferase (COX10) gene
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Ins and outs of cellular cobalamin transport
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Interaction of Hsp90 with the nascent form of the mutant epidermal growth factor receptor EGFRvIII
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.
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.
The NHEJ pathway is initiated in response to the formation of a DNA double-strand break (DSB) induced by a DNA-damaging agent such as ionizing radiation. First, the Ku70/80 heterodimer binds to the ends of the DSB. The catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs) is then recruited to DNA-bound Ku to form the DNA-PK holoenzyme. The ends of the break are brought together as two molecules of DNA-PK (one at each end of the break) are joined in a synaptic complex. Other factors, such as polynucleotide kinase (PNK), Artemis, the MRE complex, hTdp1 or the Werner Syndrome protein (WRN) may be required for processing of the DNA ends prior to end rejoining, but exactly when processing takes place is not known. Following the formation of the synaptic complex, the XRCC4/DNA ligase IV complex is recruited. Prior to end rejoining, protein factors must be removed from the DNA. This may involve DNA-PK autophosphorylation (Chan and Lees-Miller, 1996; Douglas et al., 2001; 2002; Merkle et al., 2002). After removal of the repair factors, the DNA ends are ligated and the DNA is repaired. Both Mg-ATP and the protein kinase activity of DNA-PKcs are required for NHEJ (Kurimasa et al.,1999; Kienker et al, 2000; Baumann and West, 1998), probably through phosphorylation of DNA-PKcs and/or other proteins. In addition, inositol hexaphosphate (IP6) stimulates end joining in vitro (Hanakahi et al., 2000) and binds to Ku, but its precise role in NHEJ is unknown.
Ionizing radiation (IR) induces single-strand breaks i.e. cleavage of the phosphodiester backbone. When two single-strand breaks occur within approximately 10 base pairs, a DNA double-strand break results. IR-induced DSBs are complex DNA damage lesions, containing base damage and frequently containing 5'-OH groups and 3'-hydroxy or phosphoglycolate groups that must be removed prior to ligation in the final step of NHEJ (Friedberg et al, 1995; Nikjoo et al, 2001; Valerie and Povirk, 2003). The Ku70/80 heterodimer (Walker et al., 2001) binds to the ends of the double-strand break. Ku can translocate inwards from the site of the break in an ATP-independent manner (reviewed in Dynan and Yoo, 1998).
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
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.
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 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.
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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Identification of a consensus motif for Plk (Polo-like kinase) phosphorylation reveals Myt1 as a Plk1 substrate
An active Pol II complex consisting mainly of the Pol II holoenzyme transcribes the damaged DNA template.
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.
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.
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.
ChEBI:59084 (Glc)3 (GlcNAc)2 (Man)9 (Asn)1
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.
ChEBI:59081 (Glc)1 (GlcNAc)2 (Man)9 (PP-Dol)1
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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.
ChEBI:59082 (Glc)2 (GlcNAc)2 (Man)9 (Asn)1
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.
ERCC1-XPF complex with 5ââ¬â¢ endonuclease activity binds to this pre-incision complex around the bubble structure to form an active incision complex.
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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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 Cockayneââ¬â¢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.
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'.
Ligand discrimination in signaling through an ErbB4 receptor homodimer
The ââ¬Åroad blockââ¬Â 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 ââ¬Ërepair-transcription uncoupling factorââ¬â¢ 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 3ââ¬â¢ end of the nascent RNA product leading to the enhanced access to damage site on the corresponding template DNA.
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'.
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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'.
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 '.
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 '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'.
Human liver mitochondrial aldehyde dehydrogenase: three-dimensional structure and the restoration of solubility and activity of chimeric forms
Polymerization is carried out by DNA polymerases, delta and epsilon.
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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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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 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'.
In the early elongation phase, shorter transcripts typically of ~30 nt in length are generated due to random termination of elongating nascent transcripts. This abortive cessation of elongation has been observed mainly in the presence of DSIF-NELF bound to Pol II complex. (Reviewed in Conaway et al.,2000; Shilatifard et al., 2003 ).
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'.
The PI3K-PDK1 connection: more than just a road to PKB
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
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
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.
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.
Binding of inositol phosphate to DNA-PK and stimulation of double-strand break repair.
ER-mediated phagocytosis: myth or reality?
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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.
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 Cockayneââ¬â¢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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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
Molecular cloning and characterization of a novel (Na+,K+)/H+ exchanger localized to the trans-Golgi network
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Purification and characterization of human liver "high Km" aldehyde dehydrogenase and its identification as glutamic gamma-semialdehyde dehydrogenase.
Lectin-deficient calreticulin retains full functionality as a chaperone for class I histocompatibility molecules
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Processing of Capped Intronless Pre-mRNA
Human kidney gamma-glutamyl transpeptidase. Catalytic properties, subunit structure, and localization of the gamma-glutamyl binding site on the light subunit
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Pyrimidine pathways in health and disease
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Hormone-sensitive lipase and monoacylglycerol lipase are both required for complete degradation of adipocyte triacylglycerol
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Nuclear import of hepatic glucokinase depends upon glucokinase regulatory protein, whereas export is due to a nuclear export signal sequence in glucokinase
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Quantitative and dynamic assessment of the contribution of the ER to phagosome formation
Molecular tinkering of G protein-coupled receptors: an evolutionary success
MyD88:Mal cascade initiated on plasma membrane
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Insulin degradation: progress and potential.
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Endoplasmic reticulum (ER) mannosidase I is compartmentalized and required for N-glycan trimming to Man5-6GlcNAc2 in glycoprotein ER-associated degradation
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Endocytosis of beta1 integrins is an early event in migration promoted by the cell adhesion molecule L1
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Microsomal enzymes of cholesterol biosynthesis from lanosterol. Purification and characterization of delta 7-sterol 5-desaturase of rat liver microsomes.
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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=3663756
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665271
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_7480.3
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_84085.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660251
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_114460.8
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_3196.1
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=3660250
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_110402.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110176
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661411
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=194668
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_10513.1
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=194704
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665548
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_10787.1
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_98180.9
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_10528.1
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=3665095
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_90774.9
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_10169.1
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=193446
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=194688
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_10649.2
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=389843
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660255
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_108882.9
Lipid digestion, mobilization, and transport
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110182
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_17198.1
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_2338.1
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_17634.1
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=3660254
Database identifier. Use 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
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
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110180
A plus-end-directed motor enzyme that moves antiparallel microtubules in vitro localizes to the interzone of mitotic spindles
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_5125.1
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=3660252
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660253
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_93354.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661273
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29386
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_4227.1
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=3661274
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661276
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_3731.1
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_90286.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1237155
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663777
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_131014.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663774
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663775
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_76332.1
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=191309
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_9761.1
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=1237176
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_76704.2
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=30140
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660261
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_105967.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110223
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_3342.1
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=3660262
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_110948.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110225
The extracellular signal-regulated kinase: multiple substrates regulate diverse cellular functions
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_4879.1
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=29460
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661307
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_29522.10
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_4966.2
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_130218.5
Aquaporins in the kidney: from molecules to medicine
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1237122
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_76120.1
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=3661305
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663767
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=194634
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663768
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_10504.2
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=3663770
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660258
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_108980.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660259
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663761
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663760
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_4654.2
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=3660256
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660257
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_97157.9
Primary hyperoxaluria: from gene defects to designer drugs?
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29692
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_4549.2
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=3661420
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661392
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_82599.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=194723
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_10930.1
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=194657
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660274
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110189
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660236
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_10167.1
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=3661407
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_77487.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665277
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_101209.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665278
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_109568.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=194691
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_112854.8
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661424
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_10977.1
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=3660272
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=194661
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_84870.9
Inhibition of replication initiation of damaged DNA by RB1/E2F1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661394
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_4681.2
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_101014.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110242
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.
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_2655.1
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_10642.2
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=110187
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_103632.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665276
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661413
The isoform-specific functions of the c-Jun N-terminal Kinases (JNKs): differences revealed by gene targeting
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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=3662494
Graded activation of fibroblast growth factor receptor 3 by mutations causing achondroplasia and thanatophoric dysplasia
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_128337.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3662493
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661421
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_5013.1
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_10958.1
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=141335
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_84647.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3662492
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661423
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=194735
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_10298.1
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_105734.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660241
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660240
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_2780.1
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_2927.1
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_115415.8
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110178
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660245
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_157976.3
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=3665453
Metabolism of steroid hormones and vitamin D
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3662496
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660247
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660246
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_79112.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661400
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661024
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661398
Concurrent versus individual binding of HuR and AUF1 to common labile target mRNAs
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Expression of two succinyl-CoA synthetases with different nucleotide specificities in mammalian tissues
Phosphorylation of Mnk1 by caspase-activated Pak2/gamma-PAK inhibits phosphorylation and interaction of eIF4G with Mnk
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Amyloid fibril protein related to prealbumin in familial amyloidotic polyneuropathy
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Role for NudC, a dynein-associated nuclear movement protein, in mitosis and cytokinesis
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CATERPILLERs, pyrin and hereditary immunological disorders
Purification and characterization of kidney and intestinal brush-border membrane trehalases from the rabbit
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RPA governs endonuclease switching during processing of Okazaki fragments in eukaryotes.
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Crystallographic evidence for Tyr 157 functioning as the active site base in human UDP-galactose 4-epimerase
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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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
Myotubularin phosphatases: policing 3-phosphoinositides
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
Hypophosphorylation of residue Y1045 leads to defective downregulation of EGFRvIII
T cell growth factor receptors. Quantitation, specificity, and biological relevance
ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage
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Atomic structures of amyloid cross-beta spines reveal varied steric zippers
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The FGF family: biology, pathophysiology and therapy
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Amyloid Oligomer Structures and Toxicity
Overview of retinoid metabolism and function
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Structures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1
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Polo kinase regulates mitotic chromosome condensation by hyperactivation of condensin DNA supercoiling activity
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=189407
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_9722.2
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_109251.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661199
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661253
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_81186.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661251
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_108366.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=189449
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_9601.2
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_9774.2
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=3661197
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661196
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=189447
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_9897.3
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=189411
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_9818.3
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=190128
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_9648.2
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=189461
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_104300.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661256
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_78935.9
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_9880.2
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=190157
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_9699.3
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=189455
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661217
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661220
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661218
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_29970.10
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=189487
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661213
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661211
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661210
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_9839.1
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=189484
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_9585.2
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=189463
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_93659.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661206
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661204
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_9751.1
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=189481
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661203
Long G tails at both ends of human chromosomes suggest a C strand degradation mechanism for telomere shortening
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_9886.2
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=189478
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_9640.1
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=189480
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664192
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664194
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_117647.1
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=3664178
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665572
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664191
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_149086.4
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=1614597
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=176478
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_7756.3
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=192148
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_10566.1
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=71067
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_140395.5
microRNA Biogenesis and Function : An overview
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1614538
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_116383.2
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_3428.2
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=3664184
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664186
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661348
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_117098.1
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=3661350
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664179
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661347
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1614595
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_82087.9
Human lung enolase: cloning and sequencing of cDNA and its inducibility with dexamethasone
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665376
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_87074.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665375
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_92109.9
Molecular cloning and expression of ribosome releasing factor
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_136681.5
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_105568.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665570
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_10360.2
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=3665363
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_143025.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=469662
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665568
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_23239.2
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_136304.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=159549
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665088
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=193057
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_99241.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663188
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663190
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_127706.5
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_9638.2
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=189466
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_7329.2
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=193132
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661232
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=193066
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661233
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_10667.2
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=3661234
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_32074.10
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=3661235
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661236
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665500
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663334
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_10500.2
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=3663330
Functional consequences of PRODH missense mutations
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=426925
Class II phosphoinositide 3-kinases are downstream targets of activated polypeptide growth factor receptors
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663336
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663335
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_129308.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663338
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_144575.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665510
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_100535.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665501
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_19536.2
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_139214.5
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_15646.2
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=264618
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664130
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664121
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664120
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664119
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665177
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_147681.5
Abortive initiation by RNA polymerase II in vitro at the adenovirus 2 major late promoter.
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664061
Agmatine: biological role and therapeutic potentials in morphine analgesia and dependence
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_121744.1
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=3664064
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664062
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_124200.1
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=1498728
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1500593
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_134545.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665556
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_139525.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1500603
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_5335.1
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=110614
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_20211.2
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=428686
Role of LAT2/NTAL/LAB on calcium mobilization
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658895
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659289
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_110616.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658938
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658894
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658937
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=72393
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_4829.1
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=3658936
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_104264.9
p38 MAPK signalling cascades: ancient roles and new functions
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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=3658902
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Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S
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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=72595
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Receptor-mediated phagocytosis elicits cross-presentation in nonprofessional antigen-presenting cells
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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=3660260
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660273
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660238
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=72617
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_155224.3
IMMPORT:Bioinformatics for the future of immunology
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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=3660616
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_155647.3
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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_157421.3
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_113676.8
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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_93372.9
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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=3658923
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658927
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_106049.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658926
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_3030.1
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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=3659285
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_95053.9
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Phosphorylation relieves autoinhibition of the kinetochore motor Cenp-E
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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_101670.9
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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=3659279
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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=3659281
The interaction between N-WASP and the Arp2/3 complex links Cdc42-dependent signals to actin assembly
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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=3664240
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658950
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664239
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664250
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_76965.9
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_149561.4
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=3664249
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664248
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664247
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658946
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664216
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_148798.4
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=3664215
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658925
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665571
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658959
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664226
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658961
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658960
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_149290.4
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=3664224
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_133491.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664223
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_103196.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664225
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664241
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664242
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_149349.4
Cloning, expression, and characterization of a human 4'-phosphopantetheinyl transferase with broad substrate specificity
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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=3660567
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660564
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_104355.9
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_158860.3
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_2336.2
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=3665616
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113532
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_159955.3
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=3665383
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665615
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_140799.5
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_155735.3
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=3665384
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665614
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_102967.9
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_158592.3
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=3665372
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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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664819
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664818
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_168928.1
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=3664815
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665002
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664816
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665000
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664817
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665618
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_164643.1
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_137070.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2995348
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_159387.3
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_168755.1
S-adenosylmethionine: nothing goes to waste
Nitric oxide and peroxynitrite in health and disease
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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_153651.3
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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=3664865
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_154419.3
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=3664879
3-hydroxy-4-methoxybenzoate [ChEBI:63797]
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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=3664866
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664860
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664863
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_154713.3
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=3664891
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_150933.1
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=2529006
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664887
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664888
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664889
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664883
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664839
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664856
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664847
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664878
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664877
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664873
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664875
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664871
Occurrence of surface IgM, IgD, and free light chains of human lymphocytes
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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_152925.3
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=3665609
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_96277.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664851
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664843
Sequence identification and characterization of human carnosinase and a closely related non-specific dipeptidase
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Characterization of rhoGAP. A GTPase-activating protein for rho-related small GTPases.
S-adenosylmethionine synthesis: molecular mechanisms and clinical implications
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The essential schizosaccharomyces pombe cdc23 DNA replication gene shares structural and functional homology with the Saccharomyces cerevisiae DNA43 (MCM10) gene
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Localization of GAR transformylase in Escherichia coli and mammalian cells
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Serotonin clearance from the synaptic cleft
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Identification of galectin-3 as a high-affinity binding protein for advanced glycation end products (AGE): a new member of the AGE-receptor complex
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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.
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Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R)
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A refined structure of human aquaporin-1
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Common variations in ALG9 are not associated with bipolar I disorder: a family-based study
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latheo encodes a subunit of the origin recognition complex and disrupts neuronal proliferation and adult olfactory memory when mutant.
Binding and release of radiolabeled eukaryotic initiation factors 2 and 3 during 80 S initiation complex formation.
The role of calcium signaling in phagocytosis
Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates
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
Augmenter of liver regeneration: a flavin-dependent sulfhydryl oxidase with cytochrome c reductase activity
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pXBP1(U) encoded in XBP1 pre-mRNA negatively regulates unfolded protein response activator pXBP1(S) in mammalian ER stress response
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Phosphoinositide-metabolizing enzymes at the interface between membrane traffic and cell signalling
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Altered aquaporin 9 expression and localization in human hepatocellular carcinoma
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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_4623.2
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=1500581
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=189408
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_124951.1
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_9665.2
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=113531
Regulation of Cholesterol Biosynthesis by SREBP (SREBF)
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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_133785.5
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_165517.1
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=3664994
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664078
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=391232
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_115421.8
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_17066.2
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=1498729
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_122811.1
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=2995328
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_124336.1
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=1524083
pH dependence, substrate specificity and inhibition of human kynurenine aminotransferase I
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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=3664148
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Antigen processing: Ubiquitination & Proteasome degradation
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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=3665566
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_143013.5
Performing in vitro sumoylation reactions using recombinant enzymes
Myotubularin regulates the function of the late endosome through the gram domain-phosphatidylinositol 3,5-bisphosphate interaction
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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=3664134
4-carboxy-4-methylzymosterol [ChEBI:63842]
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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_14559.2
Crystal structures of human mitochondrial branched chain aminotransferase reaction intermediates: ketimine and pyridoxamine phosphate forms
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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=3664144
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664142
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_146741.5
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_123472.1
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=1500644
Formation of editosomes by ADAR proteins
MCD4 encodes a conserved endoplasmic reticulum membrane protein essential for glycosylphosphatidylinositol anchor synthesis in yeast
Cooperation of translocase complexes in mitochondrial protein import
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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_113445.8
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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_113022.8
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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=3660968
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=182620
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660972
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_8297.1
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_127559.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665004
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665005
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665006
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660973
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660975
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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_75984.2
Cori Cycle (interconversion of glucose and lactate)
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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_19825.1
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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=428009
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1247930
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660474
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1247917
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660470
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_76476.1
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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=1247934
5-phospho-alpha-D-ribose 1-diphosphate [ChEBI:17111]
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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=3660934
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660933
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660475
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_13949.2
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_14096.2
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=352002
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=352030
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660903
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_14642.2
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=352006
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660907
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=352016
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660906
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_13874.2
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=3660913
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=351992
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660908
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_13893.2
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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=3660918
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660929
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660928
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660930
Four Na+/H+ exchanger isoforms are distributed to Golgi and post-Golgi compartments and are involved in organelle pH 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_109895.9
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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_131354.5
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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=3660965
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660957
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664010
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660956
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3664009
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_78121.9
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_151452.1
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
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660966
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660961
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660940
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665074
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660939
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_106111.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660942
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665073
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660941
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_147300.5
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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=3665362
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_133499.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660938
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665361
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660937
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_137774.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663794
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663792
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660944
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660943
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_114705.8
SUMO protease SENP1 induces isomerization of the scissile peptide bond
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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=113499
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_3748.1
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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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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
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TRAM couples endocytosis of Toll-like receptor 4 to the induction of interferon-beta
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Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction
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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
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Reconstitution of the B cell antigen receptor signaling components in COS cells
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Human porphobilinogen deaminase mutations in the investigation of the mechanism of dipyrromethane cofactor assembly and tetrapyrrole formation
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NUDT9, a member of the Nudix hydrolase family, is an evolutionarily conserved mitochondrial ADP-ribose pyrophosphatase
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Downstream Signaling Events Of B Cell Receptor (BCR)
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Ligand-independent activation of fibroblast growth factor receptors by point mutations in the extracellular, transmembrane, and kinase domains
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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
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Purified human erythrocyte pyrroline-5-carboxylate reductase. Preferential oxidation of NADPH.
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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
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Mechanisms of COPII vesicle formation and protein sorting
triphopsphoric acid 1-xanthosin-5'-yl ester
Molecular variation in relation to purine metabolism
J Clin Pathol Suppl (R Coll Pathol) 8:48-63
RED2, a brain-specific member of the RNA-specific adenosine deaminase family.
The monotopic membrane protein human oxidosqualene cyclase is active as monomer
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Metabolism of amino acids and derivatives
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Regulation of Endoplasmic Reticulum Stress-induced Cell Death by ATF4 in Neuroectodermal Tumor Cells
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Messenger RNA decay in mammalian cells: the exonuclease perspective
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The canonical retinoid cycle in rods (twilight vision)
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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
Lithium-calcium exchange is mediated by a distinct potassium-independent sodium-calcium exchanger
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Pathway and mechanism of initiation of protein synthesis.
Translational Control of Gene Expression. (Sonenberg, Hershey and Mathews, eds.)33-88
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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
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Protein quality control in the ER: the recognition of misfolded proteins
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
ATPase switches controlling DNA replication initiation.
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Emerging roles for E2F: beyond the G1/S transition and DNA replication.
5-methyltetrahydrofolyl polyglutamate macromolecule
5-methyltetrahydrofolyl polyglutamate macromolecule [ChEBI:63907]
Access of soluble antigens to the endoplasmic reticulum can explain cross-presentation by dendritic cells
The Protein Biosynthesis Elongation Cycle
Translational Control of Gene Expression89-127
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A telomeric sequence in the RNA of Tetrahymena telomerase required for telomere repeat synthesis
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Mechanisms of disease: molecular and metabolic mechanisms of insulin resistance and beta-cell failure in type 2 diabetes
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(R,R)-3,3'-thiobis-(2-aminopropanoic acid)
(R,R)-2,6-diamino-4-thiaheptanedioic acid
Tyrosine-phosphorylated forms of Ig beta, CD22, TCR zeta and HOSS are major ligands for tandem SH2 domains of Syk
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Glycoprotein folding, quality control and ER-associated degradation
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Vav regulates activation of Rac but not Cdc42 during FcgammaR-mediated phagocytosis
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Neurotrophin-regulated signalling pathways
Philos Trans R Soc Lond B Biol Sci 361:1545-64
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Novel aspects of tetramer assembly and N-terminal domain structure and function are revealed by recombinant expression of human AMP deaminase isoforms
Interaction of Ku protein and DNA-dependent protein kinase catalytic subunit with nucleic acids.
Pathogenic potential of human monoclonal immunoglobulin light chains: relationship of in vitro aggregation to in vivo organ deposition
Cloning and characterization of GEF-H1, a microtubule-associated guanine nucleotide exchange factor for Rac and Rho GTPases
Isolation and characterization of a human cDNA for mRNA 5'-capping enzyme.
Purification of the serine palmitoyltransferase complex responsible for sphingoid base synthesis by using affinity peptide chromatography techniques
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The Cdc23 (Mcm10) protein is required for the phosphorylation of minichromosome maintenance complex by the Dfp1-Hsk1 kinase
Human cytosolic asparaginyl-tRNA synthetase: cDNA sequence, functional expression in Escherichia coli and characterization as human autoantigen
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Na+/Ca2+ exchangers: three mammalian gene families control Ca2+ transport
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1-phosphatidyl-1D-myo-inositol 3-phosphate [ChEBI:17283]
Islet amyloid polypeptide: pinpointing amino acid residues linked to amyloid fibril formation
Structure of human adenosine kinase at 1.5 A resolution.
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Cloning and expression of the human gene for transaldolase. A novel highly repetitive element constitutes an integral part of the coding sequence
Endogenous synthesis of coenzyme Q in eukaryotes
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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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L-Glutamate 5-semialdehyde [ChEBI:17232]
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Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids
p21-activated protein kinase: a crucial component of morphological signaling?
Regulation of 5' template usage and incorporation of noncognate nucleotides by human telomerase
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
Proximal events in Wnt signal transduction
Cytochrome P450 - arranged by substrate type
Identification and functional characterization of a new human kidney-specific H+/organic cation antiporter, kidney-specific multidrug and toxin extrusion 2
Coregulation of estrogen receptor by ERBB4/HER4 establishes a growth-promoting autocrine signal in breast tumor cells
Principles of bioactive lipid signalling: lessons from sphingolipids
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Reconstitution of complete SV40 DNA replication with purified replication factors.
Membrane lipids: where they are and how they behave
Membrane recognition by phospholipid-binding domains
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Atomic structure of GTP cyclohydrolase I
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Regulation of Water Balance by Renal Aquaporins
Alteration of enzyme specificity by computational loop remodeling and design
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Activation of the AP-1 family of transcription factors
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Proximity of the poly(A)-binding protein to a premature termination codon inhibits mammalian nonsense-mediated mRNA decay
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Importance of extra- and intracellular domains of TLR1 and TLR2 in NFkappa B signaling
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Human Mcm proteins at a replication origin during the G1 to S phase transition.
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Regulation and physiological functions of G12/13-mediated signaling pathways
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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
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Which DNA polymerases are used for DNA-repair in eukaryotes?
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Functions and regulatory mechanisms of Gq-signaling pathways
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The crystal structure of human IRE1 luminal domain reveals a conserved dimerization interface required for activation of the unfolded protein response
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Regulation of mammalian liver methionine adenosyltransferase
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A novel cardiolipin-remodeling pathway revealed by a gene encoding an endoplasmic reticulum-associated acyl-CoA:lysocardiolipin acyltransferase (ALCAT1) in mouse
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Cloning and initial characterization of a human phospholipase D2 (hPLD2). ADP-ribosylation factor regulates hPLD2
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
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
Editing of glutamate receptor B subunit ion channel RNAs by four alternatively spliced DRADA2 double-stranded RNA adenosine deaminases.
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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(S)-1-Pyrroline-5-carboxylate [ChEBI:17388]
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Mediator function of the human Rad51B-Rad51C complex in Rad51/RPA-catalyzed DNA strand exchange.
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Greatwall kinase participates in the Cdc2 autoregulatory loop in Xenopus egg extracts
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Mycobacterium tuberculosis and the intimate discourse of a chronic infection
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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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c-Kit--a hematopoietic cell essential receptor tyrosine kinase
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PIG-A and PIG-H, which participate in glycosylphosphatidylinositol anchor biosynthesis, form a protein complex in the endoplasmic reticulum
G protein-independent activation of an inward Na(+) current by muscarinic receptors in mouse pancreatic beta-cells
Clinical and molecular characterization of the first adult congenital disorder of glycosylation (CDG) type Ic patient
NOD-like receptors (NLRs): bona fide intracellular microbial sensors
Half-site reactivity in 6-phosphogluconate dehydrogenase from human erythrocytes
Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds
ESCRTing proteins in the endocytic pathway
all-trans-decaprenyl diphosphate [ChEBI:61011]
Plk1-dependent phosphorylation of optineurin provides a negative feedback mechanism for mitotic progression
The structure and function of G-protein-coupled receptors
Mechanisms of glycerophospholipid homeostasis in mammalian cells
The transport of pyruvate in rat liver mitochondria
Dissecting and manipulating the pathway for glycosylphosphatidylinositol-anchor biosynthesis
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
Regulation of Insulin Secretion by Acetylcholine
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
The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5
FGFR1 is fused with a novel zinc-finger gene, ZNF198, in the t(8;13) leukaemia/lymphoma syndrome
Transport of inorganic cations/anions and amino acids/oligopeptides
DNA damage activates ATM through intermolecular autophosphorylation and dimer dissociation
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
trans,trans-Farnesyl diphosphate [ChEBI:10700]
Role of alpha-Asp181, beta-Asp192, and gamma-Asp190 in the distinctive subunits of human NAD-specific isocitrate dehydrogenase
Functional domains within FEN-1 and RAD2 define a family of structure-specific endonucleases: implications for nucleotide excision repair.
Synthesis of substrates in N-glycan biosythesis
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
ChEBI:17442 4-(2-aminophenyl)-2,4-dioxobutanoic acid
Regulation of activated PAK-2p34 by proteasome mediated degradation
Mammalian frataxin: an essential function for cellular viability through an interaction with a preformed ISCU/NFS1/ISD11 iron-sulfur assembly complex
The human homolog of Saccharomyces cerevisiae Mcm10 interacts with replication factors and dissociates from nuclease-resistant nuclear structures in G(2) phase.
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
Molecular characterization of a novel short-chain dehydrogenase/reductase that reduces all-trans-retinal
Human X-linked phosphoribosylpyrophosphate synthetase superactivity is associated with distinct point mutations in the PRPS1 gene
Computational approach for determining the spectrum of DNA damage induced by ionizing radiation.
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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
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A novel context for the 'MutT' module, a guardian of cell integrity, in a diphosphoinositol polyphosphate phosphohydrolase
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Human hexokinase II gene: exon-intron organization, mutation screening in NIDDM, and its relationship to muscle hexokinase activity
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Functional and mutational characterization of human MIA40 acting during import into the mitochondrial intermembrane space
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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
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Three transitions in the RNA polymerase II transcription complex during initiation.
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Advances in the understanding of cobalamin assimilation and metabolism
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Receptor-mediated endocytosis: the intracellular journey of transferrin and its receptor
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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
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Inflammasome components NALP 1 and 3 show distinct but separate expression profiles in human tissues suggesting a site-specific role in the inflammatory response
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Molecular cloning of a sixth member of the K+-dependent Na+/Ca2+ exchanger gene family, NCKX6
Evidence that tristetraprolin binds to AU-rich elements and promotes the deadenylation and destabilization of tumor necrosis factor alpha mRNA
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N-Acetyl-D-glucosamine 1-phosphate [ChEBI:7125]
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Lipid packing sensed by ArfGAP1 couples COPI coat disassembly to membrane bilayer curvature
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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
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Neurotransmitter Clearance In The Synaptic Cleft
A human transporter protein that mediates the final excretion step for toxic organic cations
Identification of the enzyme required for activation of the small ubiquitin-like protein SUMO-1
Molecular mechanisms involved in the regulation of cytokine production by muramyl dipeptide
The visual cycle of the cone photoreceptors of the retina
Physical interactions among human checkpoint control proteins HUS1p, RAD1p, and RAD9p, and implications for the regulation of cell cycle progression
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.
Neuronal phosphoproteins. Mediators of signal transduction
Oncogenic transformation by inhibitor-sensitive and -resistant EGFR mutants
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
Functions of replication factor C and proliferating-cell nuclear antigen: functional similarity of DNA polymerase accessory proteins from human cells and bacteriophage T4.
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Activation of TM7SF2 promoter by SREBP-2 depends on a new sterol regulatory element, a GC-box, and an inverted CCAAT-box
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ChEBI:17526 1-phosphatidyl-1D-myo-inositol 4-phosphates
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.
gamma-L-Glutamyl-L-cysteine [ChEBI:17515]
Pro-inflammatory cytokines and environmental stress cause p38 mitogen-activated protein kinase activation by dual phosphorylation on tyrosine and threonine
Identification of a novel gene, FGFR1OP2, fused to FGFR1 in 8p11 myeloproliferative syndrome
Similar regulation of human inducible nitric-oxide synthase expression by different isoforms of the RNA-binding protein AUF1
SLC4 base (HCO3 -, CO3 2-) transporters: classification, function, structure, genetic diseases, and knockout models
Metal transporters in intestine and brain: their involvement in metal-associated neurotoxicities
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
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Transport of phosphoenolpyruvate by the tricarboxylate transporting system in mammalian mitochondria
Both V(D)J recombination and radioresistance require DNA-PK kinase activity, though minimal levels suffice for V(D)J recombination.
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Role of the Zn(2+) motif of E1 in SUMO adenylation
The Bcl2 family: regulators of the cellular life-or-death switch
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Evidence for existence of tissue-specific regulation of the mammalian pyruvate dehydrogenase complex
Novel mutations in 3-phosphoglycerate dehydrogenase (PHGDH) are distributed throughout the protein and result in altered enzyme kinetics
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SUMO-specific proteases: a twist in the tail
Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs
Activation of the pre-replicative complex
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1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate [ChEBI:16618]
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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
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Positive and negative regulation of FcepsilonRI-mediated signaling by the adaptor protein LAB/NTAL
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Structural characterization of a human cytosolic NMN/NaMN adenylyltransferase and implication in human NAD biosynthesis
Cloning and characterization of a novel mammalian zinc transporter, zinc transporter 5, abundantly expressed in pancreatic beta cells
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Oxidized LDL-induced endolysosomal phospholipidosis and enzymatically modified LDL-induced foam cell formation determine specific lipid species modulation in human macrophages
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Characterization of purine nucleoside phosphorylase from human granulocytes and its metabolism of deoxyribonucleosides
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PTEN loss in the continuum of common cancers, rare syndromes and mouse models
Mammalian ABC transporters in health and disease
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Mechanism and regulation of human non-homologous DNA end-joining.
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Phosphatidylinositol 3-phosphate-interacting domains in PIKfyve. Binding specificity and role in PIKfyve. Endomenbrane localization
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Membrane-bound enzymes of cholesterol synthesis from lanosterol
Cholesterol, hydroxycholesterols, and bile acids
Familial deficiency of glutathione reductase in human blood cells
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Complete amino acid sequence of human phosphoglycerate kinase. Isolation and amino acid sequence of tryptic peptides.
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STIM1 clusters and activates CRAC channels via direct binding of a cytosolic domain to Orai1
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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
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)
Evolution of the Glx-tRNA synthetase family: the glutaminyl enzyme as a case of horizontal gene transfer
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
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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
Pannexin-1 mediates large pore formation and interleukin-1beta release by the ATP-gated P2X7 receptor
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.
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Regulation of mRNA Stability by Proteins that Bind AU-rich Elements
The proline-rich region of Vav binds to Grb2 and Grb3-3
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Pyruvate metabolism and Citric Acid (TCA) cycle
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Human Pat1b connects deadenylation with mRNA decapping and controls the assembly of processing bodies
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RNA editing by adenosine deaminases that act on RNA.
Structural requirements for PAK activation by Rac GTPases
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Cloning of the human cDNA which can complement the defect of the yeast mannosyltransferase I-deficient mutant alg 1
Control of elongation by RNA polymerase II.
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AMP (dAMP) kinase from human erythrocytes
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Guanylate kinases from human erythrocytes, hog brain, and rat liver
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Receptor specificity of the fibroblast growth factor family. The complete mammalian FGF family.
Trans-synaptic transmission of vesicular Wnt signals through Evi/Wntless
Formation of spindle poles by dynein/dynactin-dependent transport of NuMA
Distinct membrane domains on endosomes in the recycling pathway visualized by multicolor imaging of Rab4, Rab5, and Rab11
Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7
Dynamic changes of NuMA during the cell cycle and possible appearance of a truncated form of NuMA during apoptosis
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
The microsomal cardiolipin remodeling enzyme acyl-CoA lysocardiolipin acyltransferase is an acyltransferase of multiple anionic lysophospholipids
Gelsolin-related amyloidosis. Identification of the amyloid protein in Finnish hereditary amyloidosis as a fragment of variant gelsolin
ATM mediated response to DNA double-strand break
The regulation of AP-1 activity by mitogen-activated protein kinases
ChEBI:17825 7-methylguanosine 5'-phosphate
RNA Polymerase III Abortive And Retractive Initiation
4,4-Dimethyl-5alpha-cholesta-8,14,24-trien-3beta-ol [ChEBI:1743]
1D-myo-Inositol 1,4-bisphosphate [ChEBI:812]
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.
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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
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Human Rad51 protein can form homologous joints in the absence of net strand exchange.
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Seven novel mutations in the methylenetetrahydrofolate reductase gene and genotype/phenotype correlations in severe methylenetetrahydrofolate reductase deficiency
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Characterization of ceramide synthesis. A dihydroceramide desaturase introduces the 4,5-trans-double bond of sphingosine at the level of dihydroceramide
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Sequence-specific DNA primer effects on telomerase polymerization activity
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Coordination between the polymerase and 5'-nuclease components of DNA polymerase I of Escherichia coli.
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Negative regulation of dE2F1 by cyclin-dependent kinases controls cell cycle timing
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Expression, purification, and kinetic constants for human and Escherichia coli pyridoxal kinases
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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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endoplasmic reticulum quality control compartment
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Characterization and tRNA recognition of mammalian mitochondrial seryl-tRNA synthetase
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MyD88 dependent cascade initiated on endosome
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Compartmentation of hexokinase in human blood cells. Characterization of soluble and particulate enzymes.
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Stoichiometry of 4-methyl sterol oxidase of rat liver microsomes
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Human HRD1 promoter carries a functional unfolded protein response element to which XBP1 but not ATF6 directly binds
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RAGE and amyloid-beta peptide neurotoxicity in Alzheimer's disease
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The narrow substrate specificity of human tyrosine aminotransferase--the enzyme deficient in tyrosinemia type II
RNA Polymerase III Transcription Termination
G protein betagamma subunits: central mediators of G protein-coupled receptor signaling
Switching of origins to a post-replicative state
Identification of a dehydrogenase acting on D-2-hydroxyglutarate
Rabbit small intestinal trehalase. Purification, cDNA cloning, expression, and verification of glycosylphosphatidylinositol anchoring.
NF-kappaB p52, RelB and c-Rel are transported into the nucleus via a subset of importin alpha molecules
(5-Deoxy-5-adenosyl)(3-aminopropyl)methylsulfonium salt
Phosphorylation inhibits guanine nucleotide exchange on eukaryotic initiation factor 2.
xanthosine 5'-monophosphate [ChEBI:15652]
Electron microscopic observation and single-stranded DNA binding activity of the Mcm4,6,7 complex.
Cdc42 regulates Fc gamma receptor-mediated phagocytosis through the activation and phosphorylation of Wiskott-Aldrich syndrome protein (WASP) and neural-WASP
Distribution of aquaporin water channels AQP1 and AQP5 in the ductal system of the human pancreas
(S)-3-Hydroxy-3-methylglutaryl-CoA [ChEBI:15467]
Core exosome-independent roles for Rrp6 in cell cycle progression
Signaling by distinct classes of phosphoinositide 3-kinases
Mechanisms of p75-mediated death of hippocampal neurons. Role of caspases
Receptor for advanced glycation end products (RAGE) regulates sepsis but not the adaptive immune response
Biochemical genetics of the pentose phosphate cycle: human ribose 5-phosphate isomerase (RPI) and ribulose 5-phosphate 3-epimerase (RPE)
Transport to the Golgi and subsequent modification
Phospholipase C-gamma as a signal-transducing element
Phosphorylation of acyclovir (acycloguanosine) monophosphate by GMP kinase
Synthesis and recycling of tetrahydrobiopterin in endothelial function and vascular disease
Electron Transport from NADPH to Ferredoxin
2'-deoxyadenosine 5'-monophosphate [ChEBI:17713]
Sinauer Associates, Inc., P.O. Box 407 23 Plumtree Road, Sunderland, MA 01375 U.S.A.
Novel mutations in COX15 in a long surviving Leigh syndrome patient with cytochrome c oxidase deficiency
Human geranylgeranyl diphosphate synthase. cDNA cloning and expression.
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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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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Human CDC45 protein binds to minichromosome maintenance 7 protein and the p70 subunit of DNA polymerase alpha.
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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
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Human arginase II: crystal structure and physiological role in male and female sexual arousal
Glycosylation and palmitoylation of Wnt-3a are coupled to produce an active form of Wnt-3a
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E2F mediated regulation of DNA replication
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The DNA damage response: sensing and signaling
Human aldehyde dehydrogenase. Purification and characterization of a third isozyme with low Km for gamma-aminobutyraldehyde.
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ExoS Rho GTPase-activating protein activity stimulates reorganization of the actin cytoskeleton through Rho GTPase guanine nucleotide disassociation inhibitor
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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
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_154387.3
Expression, purification, and kinetic characterization of recombinant human adenylosuccinate lyase
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2023901
Phosphoinositide 3-kinase in T cell activation and survival
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665594
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_159696.3
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_3509.2
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=31339
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_2690.2
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=3661686
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663685
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663687
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_31729.10
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=3663686
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658270
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_5523.1
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_95126.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29882
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_126694.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658262
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29878
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_25633.1
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=3658260
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=984724
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658259
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_2886.2
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=3658459
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663681
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_158360.3
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_130644.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663220
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_134533.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663680
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663219
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_109572.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113585
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658442
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_126696.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663677
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663676
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661539
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_88032.9
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_3046.2
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=3658230
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29790
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663679
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_67549.10
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=3663678
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658239
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658449
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_97858.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658446
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658447
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663675
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_87468.9
Uses for JNK: the many and varied substrates of the c-Jun N-terminal kinases
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_147516.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110644
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663708
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663714
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_5673.1
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=3663713
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_78002.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663704
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661166
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_99803.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663712
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665076
Cloning of the rat and human mitochondrial branched chain aminotransferases (BCATm)
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109386
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_40426.10
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=3663238
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663237
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_140069.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663240
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663367
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663239
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663366
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663243
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_4214.2
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=3663365
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663241
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=73578
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663361
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_146273.5
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_77261.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660725
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_127368.5
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_81998.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665319
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658461
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658453
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658455
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660359
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_3437.2
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=3660351
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660360
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29432
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663571
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663572
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663569
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663568
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=30389
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_3751.1
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=3660358
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660357
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663576
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_91334.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112275
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661797
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_113684.8
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_32652.10
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=3661659
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665393
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661780
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661782
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_12312.3
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_158982.3
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=3661768
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661650
Immunolocalization of the mercurial-insensitive water channel and glycerol intrinsic protein in epithelial cell plasma membranes
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661658
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661656
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_107303.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661655
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661654
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_138017.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661645
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_93831.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113528
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661646
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=379697
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_2373.1
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_83615.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658169
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_94085.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663217
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661637
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_16024.2
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=3658435
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3661641
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3663216
The canonical Notch signaling pathway: unfolding the activation mechanism
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658166
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658168
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658165
Transcriptional activities of nuclear SREBP-1a, -1c, and -2 to different target promoters of lipogenic and cholesterogenic genes
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665515
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658440
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_141187.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665320
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_130489.5
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_3483.2
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=29732
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658439
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665538
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_126157.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665532
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=984665
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_128858.5
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_25388.1
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=3665389
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Factors involved in megakaryocyte development and platelet production
G(12)/G(13)-mediated signalling in mammalian physiology and disease
A novel mechanism of JNK1 activation. Nuclear translocation and activation of JNK1 during ischemia and reperfusion.
Studies on the initiation and elongation reactions in the simian virus 40 DNA replication system.
Regulation of pyruvate dehydrogenase activity through phosphorylation at multiple sites
NCAM-induced intracellular signaling revisited
alpha-D-Glucose 6-phosphate [ChEBI:17665]
Amplification and kinetics of the activation steps in phototransduction
RAGE mediates a novel proinflammatory axis: a central cell surface receptor for S100/calgranulin polypeptides
PIG-V involved in transferring the second mannose in glycosylphosphatidylinositol
Expression of human asparagine synthetase in Escherichia coli
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
The human sugar-phosphate/phosphate exchanger family SLC37
Subcellular compartmentation and differential catalytic properties of the three human nicotinamide mononucleotide adenylyltransferase isoforms
A human homolog of the Saccharomyces cerevisiae REV3 gene, which encodes the catalytic subunit of DNA polymerase zeta.
Targeted deletion of the mitogen-activated protein kinase kinase 4 gene in the nervous system causes severe brain developmental defects and premature death
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
Axonal growth inhibition (RHOA activation)
DNA replication control through interaction of E2F-RB and the origin recognition complex.
Recruitment of NuMA to mitotic centrosomes
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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Dolichyl phosphate D-mannose [ChEBI:4694]
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Dolichyl beta-D-glucosyl phosphate [ChEBI:4689]
The role of calcium-independent phospholipase A2 in cardiolipin remodeling in the spontaneously hypertensive heart failure rat heart
Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
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Cloning and characterization of a pH-sensing regulatory factor that modulates transport activity of the human H+/peptide cotransporter, PEPT1
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WNT secretion and signalling in human disease
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Leukocyte chemotactic factor 2: A novel renal amyloid protein
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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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M-ABC2, a new human mitochondrial ATP-binding cassette membrane protein
GTP hydrolysis and joining of the 60S ribosomal subunit
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
Purification and functional characterization of aquaporin-8
Regulation of human separase by securin binding and autocleavage
3-dehydro-4-methylzymosterol [ChEBI:50593]
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alpha-D-Galactose 1-phosphate [ChEBI:17973]
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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
Surprising versatility of Na+-glucose cotransporters: SLC5
Direct phosphorylation of IkappaB by IKKalpha and IKKbeta: discrimination between free and NF-kappaB-bound substrate
RNA Polymerase II Transcription Elongation
Purification and properties of guanosine diphosphate hexose pyrophosphorylase from mammalian tissues
Fcgamma receptor (FCGR) dependent phagocytosis
Proteases in MHC class I presentation and cross-presentation
Phosphotyrosine profiling identifies the KG-1 cell line as a model for the study of FGFR1 fusions in acute myeloid leukemia
Molecular identification of cytosolic prostaglandin E2 synthase that is functionally coupled with cyclooxygenase-1 in immediate prostaglandin E2 biosynthesis
L-2-Aminoadipate 6-semialdehyde [ChEBI:17917]
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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Preferential DNA repair of an active gene in human cells.
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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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Assembly of the RAD51-ssDNA nucleoprotein complex
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Cloning, heterologous expression, and enzymological characterization of human squalene monooxygenase
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Molecular identification of human glutamine- and ammonia-dependent NAD synthetases. Carbon-nitrogen hydrolase domain confers glutamine dependency.
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Glycoprotein folding and the role of EDEM1, EDEM2 and EDEM3 in degradation of folding-defective glycoproteins
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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
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The neural cell adhesion molecule L1 interacts with the AP-2 adaptor and is endocytosed via the clathrin-mediated pathway
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
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The Rac-RhoGDI complex and the structural basis for the regulation of Rho proteins by RhoGDI
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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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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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Response to elevated platelet cytosolic Ca2+
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Structural and kinetic features of amyloid beta-protein fibrillogenesis
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Activating and inhibitory functions of DAP12
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Plk1- and beta-TrCP-dependent degradation of Bora controls mitotic progression
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Tuberculosis: what we don't know can, and does, hurt us
Toxic proteins released from mitochondria in cell death
N-Acetyl-D-glucosamine 6-phosphate [ChEBI:7127]
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
Nicotinate D-ribonucleotide [ChEBI:7561]
(R)-4'-Phosphopantothenoyl-L-cysteine [ChEBI:328]
D-2-Hydroxyglutaric aciduria: unravelling the biochemical pathway and the genetic defect
The function of the human homolog of Saccharomyces cerevisiae REV1 is required for mutagenesis induced by UV light.
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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The role of endocytic l1 trafficking in polarized adhesion and migration of nerve growth cones
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Insertion of residues 429 to 822 at 585 from UniProt:P11362 FGFR1 (in Homo sapiens)
Insertion of residues 429 to 822 at 340 from UniProt:P11362 FGFR1 (in Homo sapiens)
Synaptojanin 1: localization on coated endocytic intermediates in nerve terminals and interaction of its 170 kDa isoform with Eps15
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Okazaki fragment processing: modulation of the strand displacement activity of DNA polymerase delta by the concerted action of replication protein A, proliferating cell nuclear antigen, and flap endonuclease-1.
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Astrocytic Glutamate-Glutamine Uptake And Metabolism
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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_95368.9
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
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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=3665269
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_139264.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658099
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658092
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658094
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665267
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_113405.8
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660211
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_91820.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658089
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660214
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658090
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_103155.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658091
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658085
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660212
Molecular mechanisms of conduction and selectivity in aquaporin water channels
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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_93932.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658087
Database identifier. Use 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
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658088
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
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=30014
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_3740.1
A human homolog of the Schizosaccharomyces pombe rad9+ checkpoint control gene
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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_103962.9
The enzymes, regulation, and genetics of bile acid synthesis
damaged DNA substrate inserted with correct base complement
Elongated DNA template with bypassed lesion
damaged DNA substrate with misinserted bases
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Heteroduplex DNA with D-loop structure with extended pairing between invading strand and complementary heteroduplex strand and containing newly synthesized ends
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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=3660410
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_2663.2
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=3660382
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29512
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660058
HEDJ, an Hsp40 co-chaperone localized to the endoplasmic reticulum of human cells
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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=3658104
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665078
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660216
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_104198.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665270
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_106670.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660217
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660218
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660979
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660981
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665268
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660980
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_80051.9
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_156855.3
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=3665137
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660982
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_134865.5
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_155408.3
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=3665360
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_156834.3
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=3665077
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658602
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658548
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658601
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658597
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658056
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=72085
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_153371.3
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_3987.1
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=3658543
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658054
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658053
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658052
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658051
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658050
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658049
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658048
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658047
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660388
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660373
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660377
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658538
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_86374.9
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660376
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660375
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660374
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658542
template DNA:11 nucleotide transcript hybrid
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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=3659587
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659586
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659597
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659601
gamma -Secretase cleavage and nuclear localization of ErbB-4 receptor tyrosine kinase
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template DNA opened from -10 to +2, with first nucleotide base-paired at 5'-end
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Template DNA hybrid with phosphodiester-PPi intermediate
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Open DNA -10 to +2 containing RNA Polymerase II promoter
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DNA containing RNA Polymerase II promoter
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template DNA:4 nucleotide transcript hybrid
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template DNA:9 nucleotide transcript hybrid
template DNA with first transcript dinucleotide, opened to +8 position
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template DNA:3 nucleotide transcript hybrid
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_126634.5
damaged DNA substrate:nascent mRNA hybrid with dual incisions
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.
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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=3659568
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659573
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659574
repaired DNA template:nascent mRNA hybrid
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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=3659578
Molecular analysis of a series of alleles in humans with reduced activity at the triosephosphate isomerase locus
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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=3659589
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659593
damaged DNA substrate:nascent mRNA hybrid
damaged DNA substrate:nascent mRNA hybrid with 3' incision
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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=3659609
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659613
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659588
mRNA Transcript Targeted by AUF1(hnRNP D0)
Normal human chromosomes have long G-rich telomeric overhangs at one end
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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=3658534
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658125
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658124
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_3473.2
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=30485
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29492
Promoter escape by RNA polymerase II. Formation of an escape-competent transcriptional intermediate is a prerequisite for exit of polymerase from the promoter.
mature mRNA (eukaryotic, capped and deadenylated)
oligoribonucleotide with a 5'-diphosphate
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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=3658072
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_127466.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658069
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658068
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658071
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658070
Protein Kinase C, unconventional isoforms
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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=29728
elongating pre-mRNA Pol III oligonucleotide
Structure of human cytidine deaminase bound to a potent inhibitor
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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_3116.2
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=29800
The PtdIns3P phosphatase myotubularin is a cytoplasmic protein that also localizes to Rac1-inducible plasma membrane ruffles
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_5115.1
Polymerase III gene DNA with transcription bubble (single-stranded region)
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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=3658066
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658065
Polymerase III gene DNA with a termination site
elongating pre-mRNA Pol III transcript plus 1 nucleotide
Recombinational DNA repair and human disease.
Cohesin cleavage by separase required for anaphase and cytokinesis in human cells
From birth to death: the complex lives of eukaryotic mRNAs
UBA2:SAE1 (name copied from entity in Homo sapiens)
Lessons from photoreceptors: turning off G-protein signaling in living cells
Zinc fluxes and zinc transporter genes in chronic diseases
Mechanisms underlying differential responses to FGF signaling
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
The DNA-dependent protein kinase is inactivated by autophosphorylation of the catalytic subunit.
The mitotic checkpoint: a signaling pathway that allows a single unattached kinetochore to inhibit mitotic exit
Cellular signaling by fibroblast growth factor receptors
ESCRT-II (name copied from entity in Homo sapiens)
ESCRT-II/Cargo Complex (name copied from entity in Homo sapiens)
ESCRT-III/Cargo Complex (name copied from entity in Homo sapiens)
Ubiquinated and PIP3 Endosmal Membrane Bound Cargo (name copied from entity in Homo sapiens)
cAMP-dependent protein kinase: framework for a diverse family of regulatory enzymes
Coatomer (name copied from entity in Homo sapiens)
Clathrin (name copied from entity in Homo sapiens)
Clathrin-coated vesicle (name copied from entity in Homo sapiens)
L1:AP-2 Clathrin complex (name copied from entity in Homo sapiens)
SUMO1 S-glycyl-cys173 UBA2:SAE1 (name copied from entity in Homo sapiens)
Arf1-GTP (name copied from entity in Homo sapiens)
Coatomer:Arf1-GTP Complex (name copied from entity in Homo sapiens)
pL1 (S1204, 1248):ERK2:clathrin-dynamin complex (name copied from entity in Homo sapiens)
AP-2 complex (name copied from entity in Homo sapiens)
Coatomer:Arf1-GTP:GAP Complex (name copied from entity in Homo sapiens)
Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternative-splice variants
ESCRT-III (name copied from entity in Homo sapiens)
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
Aquaporin-7 and glycerol permeability as novel obesity drug-target pathways
Uroporphyrinogen decarboxylase: complete human gene sequence and molecular study of three families with hepatoerythropoietic porphyria
Peeling by binding or twisting by cranking: models for promoter opening and transcription initiation by RNA polymerase II.
Metabolism of carotenoids and retinoids related to vision
Rod and cone visual pigments and phototransduction through pharmacological, genetic, and physiological approaches
Atrial amyloid deposits in the failing human heart display both atrial and brain natriuretic peptide-like immunoreactivity
Biogenesis of iron-sulfur clusters in mammalian cells: new insights and relevance to human disease
The type 1 insulin-like growth factor receptor pathway
CDC6 association with the ORC:origin complex
A novel role for human Nfs1 in the cytoplasm: Nfs1 acts as a sulfur donor for MOCS3, a protein involved in molybdenum cofactor biosynthesis
Indirect inhibition of mitochondrial dihydroorotate dehydrogenase activity by nitric oxide.
Peroxisome proliferator-activated receptors, coactivators, and downstream targets
M-phase kinases induce phospho-dependent ubiquitination of somatic Wee1 by SCFbeta-TrCP
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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Sld3, which interacts with Cdc45 (Sld4), functions for chromosomal DNA replication in Saccharomyces cerevisiae.
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The mechanism of axon growth: what we have learned from the cell adhesion molecule L1
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T cell receptor signaling: beyond complex complexes
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Amplification of signal from the kinetochores
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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)
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
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Disorders of cholesterol biosynthesis: prototypic metabolic malformation syndromes
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Making heads or tails of phospholipids in mitochondria
Structure of the Ku heterodimer bound to DNA and its implications for double-strand break repair.
Rheb GTPase is a direct target of TSC2 GAP activity and regulates mTOR signaling
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Differential expression of aquaporin 8 in human colonic epithelial cells and colorectal tumors
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Activation of the MAPK signal cascade by the neural cell adhesion molecule L1 requires L1 internalization
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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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5,10-methylenetetrahydrofolate polyglutamate macromolecule
5,10-methylenetetrahydrofolate polyglutamate macromolecule [ChEBI:60473]
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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
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
A new type of congenital disorders of glycosylation (CDG-Ii) provides new insights into the early steps of dolichol-linked oligosaccharide biosynthesis
3-decaprenyl-4,5-dihydroxybenzoic acid [ChEBI:50775]
all-trans-3-decaprenyl-4,5-dihydroxybenzoic acid
all-trans-3,4-dihydroxy-5-decaprenylbenzoic acid
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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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.
Fundamental Immunology (Book): 1077-1104
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Bidirectional water fluxes and specificity for small hydrophilic molecules in aquaporins 0-5
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Xylulose 5-phosphate mediates glucose-induced lipogenesis by xylulose 5-phosphate-activated protein phosphatase in rat liver
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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
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Sequential initiation of lagging and leading strand synthesis by two different polymerase complexes at the SV40 DNA replication origin.
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Crystal structure of human D-amino acid oxidase: context-dependent variability of the backbone conformation of the VAAGL hydrophobic stretch located at the si-face of the flavin ring
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8p11 myeloproliferative syndrome: a review
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
PKC beta regulates BCR-mediated IKK activation by facilitating the interaction between TAK1 and CARMA1
Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure
Calmodulin: a prototypical calcium sensor
Molecular Mechanisms of Phagocytosis (Book): 97-116
Translation initiation complex formation
Localized amyloidosis of the seminal vesicle: identification of lactoferrin immunoreactivity in the amyloid material
Stable dimeric assembly of the second membrane-spanning domain of CFTR (cystic fibrosis transmembrane conductance regulator) reconstitutes a chloride-selective pore
Eukaryotic mRNA cap binding protein: purification by affinity chromatography on sepharose-coupled m7GDP.
Insulin/IGF-I and related signaling pathways regulate aging in nondividing cells: from yeast to the mammalian brain
Characterization of kynurenine aminotransferase III, a novel member of a phylogenetically conserved KAT family
A humble hexose monophosphate pathway metabolite regulates short- and long-term control of lipogenesis
Zippers make signals: NCAM-mediated molecular interactions and signal transduction
The Cdc4/34/53 pathway targets Cdc6p for proteolysis in budding yeast.
The Saccharomyces cerevisiae COQ6 gene encodes a mitochondrial flavin-dependent monooxygenase required for coenzyme Q biosynthesis
Destabilization of mRNA by AUF1 (hnRNP D0)
AKT/PKB signaling: navigating downstream
A DNA damage-regulated BRCT-containing protein, TopBP1, is required for cell survival.
Purification and kinetic properties of human erythrocyte Mg2+-dependent inorganic pyrophosphatase
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.
The human Aquaporin-5 gene. Molecular characterization and chromosomal localization
Human RFT1 deficiency leads to a disorder of N-linked glycosylation
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Expression and characterization of the human mitochondrial leucyl-tRNA synthetase
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The glucose-lactic acid cycle and gluconeogenesis
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AP-1 subunits: quarrel and harmony among siblings
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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eIF2:GDP: eIF2B (name copied from entity in Homo sapiens)
eIF2:GDP (name copied from entity in Homo sapiens)
eIF2B subunits complex (name copied from entity in Homo sapiens)
40S:Met-tRNAi:mRNA (name copied from entity in Homo sapiens)
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Signal Recognition Particle (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_115332.8
SRP:polypeptide+signal:ribosome (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=3665075
ribosome:mRNA:polypeptide+signal (name copied from entity in Homo sapiens)
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phospho-L13a associated wth the 3' UTR GAIT element of ceruloplasmin mRNA within the translation initiation complex (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=3658029
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)
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_155365.3
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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_152617.3
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=3659442
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659441
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659440
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659439
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658026
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659393
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658021
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659396
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659397
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658025
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659400
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658015
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658017
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_105956.9
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_5012.2
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_3947.2
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=113560
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659394
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659395
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3659399
Ran:GTP:Exportin-5 (name copied from entity in Homo sapiens)
Ran:GTP (name copied from entity in Homo sapiens)
eIF3 subunits complex (name copied from entity in Homo sapiens)
40S:eIF3:eIF1A (name copied from entity in Homo sapiens)
eIF2 subunit complex (name copied from entity in Homo sapiens)
eIF2:GTP (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)
Ran-GTP (name copied from entity in Homo sapiens)
pre-miRNA:Ran:GTP:Exportin-5 (name copied from entity in Homo sapiens)
48S complex (name copied from entity in Homo sapiens)
80S:Met-tRNAi:mRNA:eIF5B:GTP (name copied from entity in Homo sapiens)
eIF4F:mRNP (name copied from entity in Homo sapiens)
mRNA:eIF4F:eIF4B:eIF4H (name copied from entity in Homo sapiens)
80S:Met-tRNAi:mRNA (name copied from entity in Homo sapiens)
eIF5B:GTP (name copied from entity in Homo sapiens)
eIF5B:GDP (name copied from entity in Homo sapiens)
eIF4A subunits complex (name copied from entity in Homo sapiens)
mRNP (name copied from entity in Homo sapiens)
eIF4F (name copied from entity in Homo sapiens)
HSP90 (name copied from entity in Homo sapiens)
Site-directed mutagenesis of diphosphoinositol polyphosphate phosphohydrolase, a dual specificity NUDT enzyme that attacks diadenosine polyphosphates and diphosphoinositol polyphosphates
ATP6V0A (name copied from entity in Homo sapiens)
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
HSP90:Benzoquinoid ansamycins (name copied from entity in Homo sapiens)
BCR-p-FGFR1 fusion mutant dimer (name copied from entity in Homo sapiens)
CUX1-p-FGFR1 fusion mutant dimer (name copied from entity in Homo sapiens)
FGFR1 fusion mutant dimers:TKIs (name copied from entity in Homo sapiens)
pY177-BCR-p-FGFR1 fusion mutant dimer (name copied from entity in Homo sapiens)
BCR-FGFR1 fusion mutant dimer (name copied from entity in Homo sapiens)
CUX1-FGFR1 fusion mutant dimer (name copied from entity in Homo sapiens)
4a-hydroxytetrahydrobiopterin [ChEBI:15374]
integral to lumenal side of endoplasmic reticulum membrane
GARS dimer (name copied from entity in Homo sapiens)
CARS dimer (name copied from entity in Homo sapiens)
SARS2 dimer (name copied from entity in Homo sapiens)
YARS2 dimer (name copied from entity in Homo sapiens)
KARS dimer (name copied from entity in Homo sapiens)
WARS 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)
TARS dimer (name copied from entity in Homo sapiens)
FARS A2B2 tetramer (name copied from entity in Homo sapiens)
p53-Independent G1/S DNA damage checkpoint
Ubiquitin:E2 conjugating enzymes (name copied from entity in Homo sapiens)
E3:Ub:substrate (name copied from entity in Homo sapiens)
Ub:substrate (name copied from entity in Homo sapiens)
E3:K48-polyubiquitinated substrate (name copied from entity in Homo sapiens)
SUGT1:HSP90 (name copied from entity in Homo sapiens)
AGE adducts:Peptide:AGER-1,2,3 (name copied from entity in Homo sapiens)
PAK1 dimer (name copied from entity in Homo sapiens)
RAC1/CDC42:PAK dimer (name copied from entity in Homo sapiens)
CDC42-GDP (name copied from entity in Homo sapiens)
CDC42-GTP:WASP/N-WASP (name copied from entity in Homo sapiens)
Recruitment and activation of mRNA decay enzymes by two ARE-mediated decay activation domains in the proteins TTP and BRF-1
p-5Y-PKC-theta:DAG (name copied from entity in Homo sapiens)
RAC1/CDC42:p-S144,T423-PAK (name copied from entity in Homo sapiens)
ATP6V0D (name copied from entity in Homo sapiens)
ATP6V0E (name copied from entity in Homo sapiens)
MTABC3 dimer (name copied from entity in Homo sapiens)
FYVE-DSP2, a FYVE domain-containing dual specificity protein phosphatase that dephosphorylates phosphotidylinositol 3-phosphate
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
AQP7 tetramer (name copied from entity in Homo sapiens)
AQP3 tetramer (name copied from entity in Homo sapiens)
PDK1:PIP2,PIP3 (name copied from entity in Homo sapiens)
PKC-theta (open): DAG (name copied from entity in Homo sapiens)
ATP2C1/2:Mg2+ (name copied from entity in Homo sapiens)
AQP9 tetramer (name copied from entity in Homo sapiens)
AQP10 tetramer (name copied from entity in Homo sapiens)
1-acyl-sn-glycero-3-phosphoethanolamine [ChEBI:29017]
PAK bound to Rac1 and Cdc42 (name copied from entity in Homo sapiens)
CDC42:GTP (name copied from entity in Homo sapiens)
PAK homodimer (name copied from entity in Homo sapiens)
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)
Processive complex:Okazaki fragments:Remaining Flap (name copied from entity in Homo sapiens)
Processive complex:nicked DNA from adjacent Okazaki fragments (name copied from entity in Homo sapiens)
RNA Pol II CTD phosphorylation and interaction with CE
Cloning of a complete protein-coding sequence of human platelet-type phosphofructokinase isozyme from pancreatic islet.
(2R)-2-Hydroxy-3-(phosphonooxy)-propanal [ChEBI:29052]
Platelet activation, signaling and aggregation
Aquaporin-3 water channel localization and regulation in rat kidney
Epidermal Growth Factor Receptor (EGFR) signaling
ChEBI:29089 1,2-diacyl-sn-glycerol 3-phosphate
Requirement for the kinase activity of human DNA-dependent protein kinase catalytic subunit in DNA strand break rejoining.
Two steps in the assembly of complexes at yeast replication origins in vivo.
ZNF198-FGFR1 transforming activity depends on a novel proline-rich ZNF198 oligomerization domain
Human Nbp35 is essential for both cytosolic iron-sulfur protein assembly and iron homeostasis
glucosaminylphosphatidylinositol [ChEBI:24275]
Role of platelet-derived growth factors in physiology and medicine
DNA double-stranded breaks induce histone H2AX phosphorylation on serine 139.
Mutations in the holocarboxylase synthetase gene HLCS
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3660053
The GAPs, GEFs, and GDIs of heterotrimeric G-protein alpha subunits
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
The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction
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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_109772.9
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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=3660393
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658605
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658604
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_133423.5
Selective activation of p38 mitogen-activated protein (MAP) kinase isoforms by the MAP kinase kinases MKK3 and MKK6
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Activation of Chaperone Genes by XBP1(S)
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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_131836.5
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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_34720.10
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Specific inhibition of pyruvate transport in rat liver mitochondria and human erythrocytes by alpha-cyano-4-hydroxycinnamate
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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_95562.9
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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_114276.8
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_90394.9
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_139921.5
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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=3658115
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658117
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_91418.9
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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=3658112
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658113
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Tetrahydrobiopterin biosynthesis, regeneration and functions
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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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_105965.9
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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_14919.2
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=29654
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_4667.2
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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_2630.2
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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=29804
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3658491
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_2842.2
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_3219.2
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Synthesis of PIPs at the late endosome membrane
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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_4478.1
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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_5253.2
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The inositol hexakisphosphate kinase family. Catalytic flexibility and function in yeast vacuole biogenesis
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Interactions of CD80 and CD86 with CD28 and CTLA4
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Structure of S6 kinase 1 determines whether raptor-mTOR or rictor-mTOR
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Signal-induced site-specific phosphorylation targets I kappa B alpha to the ubiquitin-proteasome pathway
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Structure, function and evolution of seryl-tRNA synthetases: implications for the evolution of aminoacyl-tRNA synthetases and the genetic code
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Three mammalian lipins act as phosphatidate phosphatases with distinct tissue expression patterns
Senile seminal vesicle amyloid is derived from semenogelin I
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unfolded protein:(Glc)3 (GlcNAc)2 (Man)9 (Asn)1 (name copied from entity in Homo sapiens)
2xUAP1 (name copied from entity in Homo sapiens)
Reconstitution, activities, and structure of the eukaryotic RNA exosome
unfolded protein:(Glc)2 (GlcNAc)2 (Man)9 (Asn)1 (name copied from entity in Homo sapiens)
unfolded protein:(GlcNAc)2 (Man)7aa (name copied from entity in Homo sapiens)
unfolded protein:(Glc)1 (GlcNAc)2 (Man)9 (name copied from entity in Homo sapiens)
(un)folded protein:(GlcNAc)2 (Man)9 (name copied from entity in Homo sapiens)
unfolded protein:(GlcNAc)2 (Man)8b (name copied from entity in Homo sapiens)
unfolded protein:(GlcNAc)2 (Man)8c (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)
Sec23p:Sec24p Complex (name copied from entity in Homo sapiens)
Sar1b:GTP:Sec23p:Sec24p (name copied from entity in Homo sapiens)
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MIA40:ERV1 (name copied from entity in Homo sapiens)
Sar1b:Sec23p:Sec24p:Sec13p:Sec31p Complex (name copied from entity in Homo sapiens)
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Sec13p:Sec31p Complex (name copied from entity in Homo sapiens)
Sar1b:GTP:Sec23p:Sec24p:Sec13p:Sec31p 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=76213
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Sar1b:GDP Complex (name copied from entity in Homo sapiens)
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TIMM23 SORT:Precursor Cargo (name copied from entity in Homo sapiens)
TIMM23 Complex (name copied from entity in Homo sapiens)
PAM Complex (name copied from entity in Homo sapiens)
TIMM23 SORT:Cargo (name copied from entity in Homo sapiens)
Mitochondrial processing peptidase (name copied from entity in Homo sapiens)
TIMM23 PAM:Precursor Cargo (name copied from entity in Homo sapiens)
TIMM23 PAM:Cargo (name copied from entity in Homo sapiens)
IRE1 homodimer (name copied from entity in Homo sapiens)
IRE1 homodimer (phosphorylated) (name copied from entity in Homo sapiens)
Double-strand DNA containing an adenine opposite to an 8-oxo guanine
IRE1 homodimer (phosphorylated):ADP (name copied from entity in Homo sapiens)
Deficiency of the first mannosylation step in the N-glycosylation pathway causes congenital disorder of glycosylation type Ik
Double-strand DNA containing an ethenocytosine
DNA containing an apurinic/apyrimidinic (AP) site
Double-strand DNA containing an uracil opposite to a guanine
Double-strand DNA containing a thymine opposite to a guanine
Double-strand DNA containing a dihydrouracil
Double-strand DNA containing a cytosine glycol
Double-strand DNA containing a thymine glycol
Double-strand DNA containing a formamidopyrimidine
Roles of AUF1 isoforms, HuR and BRF1 in ARE-dependent mRNA turnover studied by RNA interference
Cyclin B1:phospho-Cdc2(Thr 161) (name copied from entity in Homo sapiens)
Porphobilinogen deaminase and uroporphyrinogen III synthase: structure, molecular biology, and mechanism
nuclear Cyclin B1:phospho-Cdc2 ( Thr 14) complexes (name copied from entity in Homo sapiens)
Cyclin B1:phospho-Cdc2(Thr 161, Thr 14, Tyr 15) (name copied from entity in Homo sapiens)
phospho-Cyclin B1:phospho-Cdc2(Thr 161) (name copied from entity in Homo sapiens)
Cyclin B1:phospho-Cdc2 (Thr 14, Thr 161) (name copied from entity in Homo sapiens)
CK2 Phosphorylated Condensin I (name copied from entity in Homo sapiens)
Condensin I (name copied from entity in Homo sapiens)
CDK1 Phosphorylated Condensin I (name copied from entity in Homo sapiens)
Casein kinase II (name copied from entity in Homo sapiens)
Congenital glutamine deficiency with glutamine synthetase mutations
p-T161-CDK1:CCNB1 (name copied from entity in Homo sapiens)
Endotoxin induces rapid protein tyrosine phosphorylation in 70Z/3 cells expressing CD14
Telomerase RNP:Telomeric Chromosome End with an Additional single Stranded Telomere repeat (name copied from entity in Homo sapiens)
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)
CCNB:p-T161-CDK1 (name copied from entity in Homo sapiens)
ESPL1 Autocleaved (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)
RNA primer-DNA primer:G-strand extended telomere (name copied from entity in Homo sapiens)
RNA primer:G-strand extended telomere end:DNA polymerase alpha:primase complex (name copied from entity in Homo sapiens)
DNA polymerase epsilon:G-strand extended telomere end (name copied from entity in Homo sapiens)
DNA polymerase alpha:primase:DNA polymerase alpha:G-strand extended telomere end (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)
Mechanism of action and in vivo role of platelet-derived growth factor
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)
Processive complex loaded on telomere (name copied from entity in Homo sapiens)
Processive complex loaded on telomere:Okazaki fragment complex (name copied from entity in Homo sapiens)
Processive complex loaded on telomere:Okazaki fragment:Flap (name copied from entity in Homo sapiens)
Processive complex loaded on telomere:Okazaki fragment:Flap:RPA heterotrimer:dna2 (name copied from entity in Homo sapiens)
Processive complex loaded on telomere:Okazaki fragment:Flap:RPA heterotrimer (name copied from entity in Homo sapiens)
Processive complex loaded on telomere:nicked DNA from adjacent Okazaki fragments (name copied from entity in Homo sapiens)
Processive complex loaded on telomere:Okazaki fragments:Remaining Flap (name copied from entity in Homo sapiens)
Processive complex loaded on telomere:ligated C-strand Okazaki fragments (name copied from entity in Homo sapiens)
integral to cytosolic side of endoplasmic reticulum membrane
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)
deoxyhypusine synthase tetramer (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)
2xUAP1-2 (name copied from entity in Homo sapiens)
2xGNPNAT1 (name copied from entity in Homo sapiens)
GPI-N-acetylglucosaminyltransferase (name copied from entity in Homo sapiens)
DOHH:Fe++ (name copied from entity in Homo sapiens)
SRP receptor (name copied from entity in Homo sapiens)
SRP receptor:SRP:ribosome:polypeptide+signal (name copied from entity in Homo sapiens)
Comparison of human B cell antigen receptor complexes: membrane-expressed forms of immunoglobulin (Ig)M, IgD, and IgG are associated with structurally related heterodimers
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
Cyclin B1:phospho-Cdc2 ( Thr 14) (name copied from entity in Homo sapiens)
phospho-cyclin B1(CRS):phosph-Cdc2(Thr 161) (name copied from entity in Homo sapiens)
RNA primer-DNA primer:origin duplex with DNA damage
Kinetochore:Mad1:MAD2 Complex (name copied from entity in Homo sapiens)
Rad9-Hus1-Rad1 complex (name copied from entity in Homo sapiens)
RPA complexed to ssDNA (name copied from entity in Homo sapiens)
Mad1:kinetochore complex (name copied from entity in Homo sapiens)
Rad9-Hus1-Rad1 bound to DNA (name copied from entity in Homo sapiens)
Igf-I signaling and effects on longevity
Nestle Nutr Workshop Ser Pediatr Program 68:237-45; discussion 246-9
Rad17-RFC complex bound to DNA (name copied from entity in Homo sapiens)
Rad17-RFC complex (name copied from entity in Homo sapiens)
Differences between the trypanosomal and human GlcNAc-PI de-N-acetylases of glycosylphosphatidylinositol membrane anchor biosynthesis
Cyclin B:phospho-Cdc2(Thr 14) (name copied from entity in Homo sapiens)
Cyclin B:Cdc2 complex (name copied from entity in Homo sapiens)
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)
eRF3-GTP:eRF1:80S Ribosome:mRNA:peptidyl-tRNA Complex (name copied from entity in Homo sapiens)
GTP bound eRF3 (name copied from entity in Homo sapiens)
eEF2:GTP (name copied from entity in Homo sapiens)
80S Ribosome:mRNA:peptidyl-tRNA with elongating peptide (name copied from entity in Homo sapiens)
80S:Met-tRNAi:mRNA:aminoacyl-tRNA (name copied from entity in Homo sapiens)
Amyloid beta-protein assembly and Alzheimer disease
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
Neuregulin-3 (NRG3): a novel neural tissue-enriched protein that binds and activates ErbB4
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Tyrosine phosphorylation of phospholipase C induced by membrane immunoglobulin in B lymphocytes
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Identification of eukaryotic DNA replication proteins using simian virus 40 in vitro replication system.
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The sequence of a human mitochondrial glycerol-3-phosphate dehydrogenase-encoding cDNA
Eukaryotic protein synthesis: still a mystery
A monoclonal antibody that appears to recognize the receptor for human T-cell growth factor; partial characterization of the receptor
AT-AC pre-mRNA splicing mechanisms and conservation of minor introns in voltage-gated ion channel genes.
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TRAF6 autoubiquitination-independent activation of the NFkappaB and MAPK pathways in response to IL-1 and RANKL
Genetic Analysis of Coenzyme Q Biosynthesis
Coenzyme Q: Molecular Mechanisms in Health and Disease (Book): 185-208
Basic Medical Biochemistry: A Clinical Approach, 2nd ed (Book): 527
Fatty acid, triacylglycerol, and ketone body metabolism
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
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
The human and mouse replication-dependent histone genes
Syndromic craniosynostosis: from history to hydrogen bonds
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
Characterization of the localization and proteolytic activity of the SUMO-specific protease, SENP1
XBP1 controls diverse cell type- and condition-specific transcriptional regulatory networks
Inactivation of NF-kappa B inhibitor I kappa B alpha: ubiquitin-dependent proteolysis and its degradation product
The eicosanoids: cyclooxygenase, lipoxygenase, and epoxygenase pathways
Biochemistry of Lipids, Lipoproteins and Membranes, 5th Edition (Book): 331-362
Extracellular-signal-regulated kinase signalling in neurons
Characterization of MTMR3. an inositol lipid 3-phosphatase with novel substrate specificity
Complete sequencing and characterization of 21,243 full-length human cDNAs
Identical mutations in three different fibroblast growth factor receptor genes in autosomal dominant craniosynostosis syndromes
Release of arachidonate from diglyceride in human platelets requires the sequential action of a diglyceride lipase and a monoglyceride lipase
Origins and Mechanisms of miRNAs and siRNAs
A second canon. Functions and mechanisms of beta-catenin-independent Wnt signaling
Differential assembly of Cdc45p and DNA polymerases at early and late origins of DNA replication.
Protein phosphatases regulate DNA-dependent protein kinase activity.
Selective degradation of AU-rich mRNAs promoted by the p37 AUF1 protein isoform
ARF mediates recruitment of PtdIns-4-OH kinase-beta and stimulates synthesis of PtdIns(4,5)P2 on the Golgi complex
Phosphatidylinositol-3-OH kinases are Rab5 effectors
Mitochondrial iron trafficking and the integration of iron metabolism between the mitochondrion and cytosol
Identification of a novel guanine nucleotide exchange factor for the Rho GTPase
Disassembly of exon junction complexes by PYM
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
Insights into COPI coat assembly and function in living cells
RNA binding properties of the AU-rich element-binding recombinant Nup475/TIS11/tristetraprolin protein
Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design
The role of assembly in insulin's biosynthesis
Post-Elongation Processing of Intronless pre-mRNA
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
A conserved family of enzymes that phosphorylate inositol hexakisphosphate
Primate Genome Gain and Loss: A Bone Dysplasia, Muscular Dystrophy, and Bone Cancer Syndrome Resulting from Mutated Retroviral-Derived MTAP Transcripts
Identification of Mn2+-binding aspartates from alpha, beta, and gamma subunits of human NAD-dependent isocitrate dehydrogenase
Biochemical characterization of the human copper transporter Ctr1
Overview of steroidogenic enzymes in the pathway from cholesterol to active steroid hormones
The human Pif1 helicase, a potential Escherichia coli RecD homologue, inhibits telomerase activity
Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation
Guanosine triphosphate, the primary product of phosphorylation coupled to the breakdown of succinyl coenzyme A
Zinc efflux and compartmentalization by the SLC30 family
acylglucosaminylphosphatidylinositol [ChEBI:52572]
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).
Primary megakaryocytes reveal a role for transcription factor NF-E2 in integrin alpha IIb beta 3 signaling
LAT and NTAL mediate immunoglobulin E-induced sustained extracellular signal-regulated kinase activation critical for mast cell survival
The complex route to MHC class I-peptide complexes
Assignment of the human and mouse prion protein genes to homologous chromosomes
COPII (Coat Protein 2) Mediated Vesicle Transport
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)
Roles for LPS-dependent interaction and relocation of TLR4 and TRAM in TRIF-signaling
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
Endonucleolytic RNA cleavage by a eukaryotic exosome
Common themes in siRNA-mediated epigenetic silencing pathways
RNA Polymerase I Transcription Initiation
Organization and sequence of the human gene for the mitochondrial citrate transport protein
Replication protein A-mediated recruitment and activation of Rad17 complexes
EGFR interacts with phospholipase C-gamma
Crystal structure of human squalene synthase. A key enzyme in cholesterol biosynthesis.
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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L13a-mediated translational silencing of Ceruloplasmin expression
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Localization of the human mitochondrial citrate transporter protein gene to chromosome 22Q11 in the DiGeorge syndrome critical region
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Structural models of amyloid-like fibrils
Reduction of alpha gamma-diketo and alpha-keto acids catalyzed by muscle preparations and by crystalline lactic dehydrogenase
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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
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Ways of dying: multiple pathways to apoptosis.
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ChEBI:58548 S-methyl-5-thio-D-ribulose 1-phosphate(2?)
S-methyl-5-thio-D-ribulose 1-phosphate(2?)
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Enolase isoenzymes in rat tissues. Electrophoretic, chromatographic, immunological and kinetic properties
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Molecular mechanisms of megakaryocyte differentiation
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Consistent fusion of ZNF198 to the fibroblast growth factor receptor-1 in the t(8;13)(p11;q12) myeloproliferative syndrome
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Temporal differences in the activation of three classes of non-transmembrane protein tyrosine kinases following B-cell antigen receptor surface engagement
Human UDP-glucuronosyltransferases: metabolism, expression, and disease
Polymerase II promoter activation: closed complex formation and ATP-driven start site opening.
Human minichromosome maintenance proteins and human origin recognition complex 2 protein on chromatin.
S-methyl-5-thio-?-D-ribose 1-phosphate(2?)
ChEBI:58533 S-methyl-5-thio-?-D-ribose 1-phosphate(2?)
Formation of transcription-coupled NER (TC-NER) repair complex
E2F mediates developmental and cell cycle regulation of ORC1 in Drosophila
A human phosphatidylinositol 3-kinase complex related to the yeast Vps34p-Vps15p protein sorting system
Hormone-sensitive lipase (HSL)-mediated triacylglycerol hydrolysis
The AMP-activated protein kinase pathway--new players upstream and downstream
Appearance of water channels in Xenopus oocytes expressing red cell CHIP28 protein
Dre2, a conserved eukaryotic Fe/S cluster protein, functions in cytosolic Fe/S protein biogenesis
Characterization of human brain nicotinamide 5'-mononucleotide adenylyltransferase-2 and expression in human pancreas
Sequential actions of myotubularin lipid phosphatases regulate endosomal PI(3)P and growth factor receptor trafficking
Crystal structures of mammalian glutamine synthetases illustrate substrate-induced conformational changes and provide opportunities for drug and herbicide design
Phosphorylation of I kappa B alpha precedes but is not sufficient for its dissociation from NF-kappa B
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
Clamping down on clamps and clamp loaders--the eukaryotic replication factor C.
Gene duplication and the evolution of group II chaperonins: implications for structure and function
Human securin proteolysis is controlled by the spindle checkpoint and reveals when the APC/C switches from activation by Cdc20 to Cdh1
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
Medin: an integral fragment of aortic smooth muscle cell-produced lactadherin forms the most common human amyloid
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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
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Identification and characterization of a lysophosphatidylcholine acyltransferase in alveolar type II cells
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The neurotransmitter cycle and quantal size
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Cloning, expression, and cellular localization of the oncogenic 58-kDa inhibitor of the RNA-activated human and mouse protein kinase
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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
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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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How nucleotide excision repair protects against cancer.
Mutations in the gene for the E1beta subunit: a novel cause of pyruvate dehydrogenase deficiency
Generation of major histocompatibility complex class I antigens: functional interplay between proteasomes and TPPII
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Post-proteasomal antigen processing for major histocompatibility complex class I presentation
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Recognition and association of DNA glycosylase with site containing an affected pyrimidine
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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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RhoGDIs revisited: novel roles in Rho regulation
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Characterization of solanesyl and decaprenyl diphosphate synthases in mice and humans
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Human 1-D-myo-inositol-3-phosphate synthase is functional in yeast
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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
MyD88: an adapter that recruits IRAK to the IL-1 receptor complex
Lanosterol 14 alpha-methyl demethylase. Isolation and characterization of the third metabolically generated oxidative demethylation intermediate.
Replication protein A stimulates proliferating cell nuclear antigen-dependent repair of abasic sites in DNA by human cell extracts.
ARE-mRNA degradation requires the 5'-3' decay pathway
Changes in methionine adenosyltransferase and S-adenosylmethionine homeostasis in alcoholic rat liver
Am J Physiol Gastrointest Liver Physiol 279:G178-85
Identification and functional analysis of a defect in the human ALG9 gene: definition of congenital disorder of glycosylation type IL
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.
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).
The hydrolysis of Arf1-bound GTP is induced by the recruited ArfGAP.
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.
Water permeability and characterization of aquaporin-11
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.
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.
CD28 costimulation: a source of Vav-1 for TCR signaling with the help of SLP-76?
Formation of tubulin folding intermediates by CCT/TriC
Persistent initiation of DNA replication and chromatin-bound MCM proteins during the cell cycle in cdc6 mutants.
ORC5L, a new member of the human origin recognition complex, is deleted in uterine leiomyomas and malignant myeloid diseases.
Conversion of Phosphatidylcholine to Phosphatidylglycerol with Phospholipase D and glycerol
hNTH1 glycosylase mediated recognition and binding of dihydrouracil
hNTH1 glycosylase mediated recognition and binding of formamidopyrimidine
hNTH1 glycosylase mediated recognition and binding of thymine glycol
TDG glycosylase mediated recognition and binding of an ethenocytosine
TDG glycosylase mediated recognition and binding of an thymine opposite to a guanine
TDG glycosylase mediated recognition and binding of an uracil opposite to a guanine
hNTH1 glycosylase mediated recognition and binding of cytosine glycol
The mitochondrial disulfide relay system protein GFER is mutated in autosomal-recessive myopathy with cataract and combined respiratory-chain deficiency
MYH glycosylase mediated recognition and binding of an adenine opposite to an 8-oxo guanine
Cleavage 8-oxo guanine by MYH glycosylase
Cyclin A/B1 associated events during G2/M transition
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
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).
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.
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.
Once both coatomer and the active form of Arf1 have been recruited to the Golgi membrane surface, ArfGAP joins the complex.
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 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.
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).
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.
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 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.
Intracellular zinc homeostasis and zinc signaling
The role of eIF-4C in protein synthesis initiation complex formation.
Mcm10 and the MCM2-7 complex interact to initiate DNA synthesis and to release replication factors from origins.
Biochemistry of Lipids, Lipoproteins and Membranes, 5th Edition (Book): 213-244
Endosomal Sorting Complex Required For Transport (ESCRT)
Cloning and expression of the human N-acetylglutamate synthase gene.
T cell antigen-receptor signal transduction
Genetic evidence for the expression of ATP- and GTP-specific succinyl-CoA synthetases in multicellular eucaryotes
Characterization of the ATP- and GTP-specific succinyl-CoA synthetases in pigeon. The enzymes incorporate the same alpha-subunit.
Mechanism of diacylglycerol-induced membrane targeting and activation of protein kinase Ctheta
Expression of human arginine decarboxylase, the biosynthetic enzyme for agmatine
MicroRNA genes are transcribed by RNA polymerase II
Targeting mutant fibroblast growth factor receptors in cancer
Quality control of eukaryotic mRNA: safeguarding cells from abnormal mRNA function
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1-acyl-sn-glycero-3-phosphoserine [ChEBI:52603]
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The mammalian centrosome and its functional significance
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Mitochondrial tRNA import: are there distinct mechanisms?
Molecular identification of a novel mammalian brain isoform of acyl-CoA:lysophospholipid acyltransferase with prominent ethanolamine lysophospholipid acylating activity, LPEAT2
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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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).
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).
Protein metabolism comprises the pathways of translation, post-translational modification and protein folding.
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.
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.
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).
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).
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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).
Direct interaction between survivin and Smac/DIABLO is essential for the anti-apoptotic activity of survivin during taxol-induced apoptosis.
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 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 Sec31A gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The WIPI1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The YIF1A gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The p58IPK (DNAJC3) 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.
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.
ATF4 is a transcription factor and activates expression of IL-8, MCP1, IGFBP-1, CHOP, HERP1 and ATF3.
The Aspariagine Synthetase (ASNS) gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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) leads to phosphorylation of the translation initiation factor eIF2alpha and global down-regulation of protein synthesis. These three regulatory pathways are annotated here.
PERK 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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The Mammalian synaptonemal complex: a scaffold and beyond
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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.
Eight SLC gene families are involved in the transport of amino acids and oligopeptides.
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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.
Membrane bound L1 is internalized through clathrin coated vesicles and is endocytosed into recycling endosomes. Moreover, L1 promotes co-endocytosis of beta1 integrins with which it is associated into early endosomes.
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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),
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).
Cloning and expression of AQP3, a water channel from the medullary collecting duct of rat kidney
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.
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).
L1 functions in many aspects of neuronal development including axon outgrowth and neuronal migration. These functions require coordination between L1 and the actin cytoskeleton. F-actin continuously moves in a retrograde direction from the P-(peripheral) domain of the growth cone towards the growth coneâs C-(central) domain. L1, attached to the actin cytoskeleton via membrane cytoskeletal linkers (MCKs) such as ankyrins (Ankyrin-G, -B and -R) and members of the ERMs (ezrin, radixin, and moesin) family, link this retrograde F-actin flow with extracellular immobile ligands. Forward translocation of growth cone requires not only the CAM-actin linkage but also a gradient of cell substrate adhesion (strong adhesion at the front and weak adhesion at the rear) so that the cytoskeletal machinery is able to pull the cell forward as attachments at the rear are released. This asymmetry is achieved in part by internalizing L1 molecules as they are moved to the rear of the growth cone coupled to retrograde F-actin flow and recycling them to the leading edge plasma membrane. L1 internalization is mediated by phosphorylation and dephosphorylation. The L1 cytoplasmic domain (L1CD) carries an endocytic or sorting motif, YRSLE, that is recognized by the clathrin associated adaptor protein-2 (AP-2). AP-2 binds the YRSLE motif only when its tyrosine is not phosphorylated and triggers L1 endocytosis. SRC kinase associated with lipid rafts in the P-domain membrane phosphorylates L1 molecules on tyrosine-1176, stabilizing them in the plasma membrane. L1 endocytosis is triggered by the dephosphorylation of Y1176 within the C domain. Some of these internalized L1 molecules are transported in an anterograde direction along microtubules for reuse in the leading edge.
L1 cross linking can activate MAPK cascade components MEK1/2, ERK1/2, as well as Src, Raf-1,and p90rsk. MAP kinase signaling requires endocytosis mediated by Src. ERK2 can phos-phorylate internalized L1 at serine residues 1204 and 1248. This phosphorylation may increase the neurite growth.
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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 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.
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.
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
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.
The BIP (HSPA5) gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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.
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.
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.
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.
Release of apoptotic factors from the mitochondria
As inferred from the yeast MIA40:ERV1 complex, human CHCHD4 (MIA40 homolog) catalyzes the oxidation of cysteine residues in precursor proteins in the intermembrane space to form cystine bonds. The electrons from the cysteine residues are transferred to CHCHD4, then to GFER (ERV1 homolog), and eventually to the respiratory chain. The interaction between yeast MIA40 and ERV1 is transitory. In yeast, experimentally verified substrates of MIA40:ERV1 include COX17, COX19, CMC2, CMC3, CMC4, TIM13 (TIMM13 in human), TIM9 (TIMM9 in human), TIM10 (TIMM10 in human), CCS1 (CCS in human), TIM8 (TIMM8 in human), and ERV1 (GFER in human). Many other mitochondrial proteins are anticipated to be substrates of the MIA40:ERV1 complex.
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Once loaded the vesicles become fully sculpted, pinch off from the ER and bud into the cytosol.
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.
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.
Cytosolic Sec13p-Sec31p complexes bind to pre-bound Sec23p-Sec24p complexes.
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; Martínez-Menárguez et al, 1999). The other is mediated by LMAN1/MCFD2, mannose-binding lectins that recognize a glycan signal (Zhang B et al, 2003).
N-linked glycosylation is the most important form of post-translational modification for proteins synthesized and folded in the Endoplasmic Reticulum (Stanley P 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 R 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 D and Levy Y, 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 GZ, 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 P 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 SE et al, 2003), and classified as CDG type I for the genes in the LLO synthesis pathway, and CDG type II for the others.
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.
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.
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.
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).
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Transport of Glycerol from Adipocytes to the Liver by Aquaporins
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The SYVN1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The KDELR3 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.
The SRPR gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The SRPRB gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The GOSR2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The GFPT1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The HYOU1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The GSK3A gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The GAP gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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
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Human TLR10 is a functional receptor, expressed by B cells and plasmacytoid dendritic cells, which activates gene transcription through MyD88
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.
The CXXC1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The DDX11 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The ATP6VOD1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The CTDSP2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The ADD1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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.
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.
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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Phosphomannomutase 1 and 2 (PMM1 and PMM2) catalyze the isomerization of Mannose 6-phosphate to Mannose 1-phosphate (Wada Y and Sakamoto M et al, 1997; Matthijs G et al, February 1997). Mutations in the PMM2 gene are one of the causes of Jaeken syndrome. a disease of glycosylation, type CDGIa. (Matthijs G et al, May 1997).
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.
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).
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.
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).
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 V et al, 1998). This reaction is catalyzed by DPAGT1 (ALG7 in yeast), mutations in which are associated with CDG disorder type I-J (Wu X et al, 2003). The dolichyl phosphate acts as an anchor for the LLO, so the following sugar-addition reactions take place on a sugar anchored in the ER membrane.
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 S 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.
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 M et al, 2004; Kranz C et al, 2004; Grubenmann CE et al, 2004).
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).
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 C et al, 2003). Defects in ALG2 are the cause of CDG1I (Thiel C et al, 2003).
Interferon induces tryptophanyl-tRNA synthetase expression in human fibroblasts
Molecular mechanism of the Syk activation switch
Structural determinants in AUF1 required for high affinity binding to A + U-rich elements
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).
Removal of the second mannose on the alpha 1,3 branch (Frenzel Z et al, 2003).
Proteins that are released from the CNX or CRT complex with folding defects accumulate in a compartment of the ER called ERQC (Kamhi-Nesher S 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 the 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 V 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 GZ, 2009 and Määttänen P et al, 2010.
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 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).
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 CM et al, 2000; Völker C 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 A position (Hirao et al, 2006; Frenkel 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 C position (Hirao et al, 2006).
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).
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 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 PCNA-RFC families of DNA clamps and clamp loaders
Prog Nucleic Acid Res Mol Biol 78:227-60
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 sixth mannose is added to the N-glycan precursor. This reaction occurs in the ER lumen and uses a different mannose donor (dolichyl phosphate D-mannose) than the previous steps. It has been proposed that ALG3, along with all the mannosyl- and glucosyl transferases in the N-glycan biosynthesis pathway that use dolichyl phosphate D-mannose or dolichyl phosphate D-glucose as donor, derive from duplications of a common ancestral enzyme (Oriol R et al, 2002). Defects in ALG3 are associated with Congenital Disorder of Glycosylation 1D (CDG1D) (Sun L et al, 2005).
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 MA et al, 2008).
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. There are no known associations between ALG11 and CDG disorders to date.
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).
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.
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 proton oligopeptide cotransporter family SLC15 in physiology and pharmacology
DNA damage recognition during nucleotide excision repair in mammalian cells.
Human protoporphyrinogen oxidase: expression, purification, and characterization of the cloned enzyme
Evidence that the coproporphyrinogen oxidase activity of rat liver is situated in the intermembrane space of mitochondria
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
Effects of the mutations Ala30 to Pro and Ala53 to Thr on the physical and morphological properties of alpha-synuclein protein implicated in Parkinson's disease
Development of free-energy-based models for chaperonin containing TCP-1 mediated folding of actin
Integrated view on 17beta-hydroxysteroid dehydrogenases
Nonsense Mediated Decay Enhanced by the Exon Junction Complex
The intracellular interactions of the L1 family of cell adhesion molecules
Mercury-sensitive residues and pore site in AQP3 water channel
Processive synthesis on the lagging strand
Syk protein-tyrosine kinase is regulated by tyrosine-phosphorylated Ig alpha/Ig beta immunoreceptor tyrosine activation motif binding and autophosphorylation
Efflux and compartmentalization of zinc by members of the SLC30 family of solute carriers
The sodium/glucose cotransport family SLC5
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
The human homologue of yeast ArgRIII protein is an inositol phosphate multikinase with predominantly nuclear localization
Human IL4I1 is a secreted L-phenylalanine oxidase expressed by mature dendritic cells that inhibits T-lymphocyte proliferation
The FEN-1 family of structure-specific nucleases in eukaryotic DNA replication, recombination and repair.
ATP activates transcription initiation from promoters by RNA polymerase II in a reversible step prior to RNA synthesis.
VAV3 is a GEF for Rho/Rac family kinases
Activation of Protein Kinase C novel isoforms
The Nod-like receptor (NLR) family: a tale of similarities and differences
VAV2 is a GEF for Rho/Rac family kinases
Release of platelet cytosolic components
Synoviocyte innate immune responses: I. Differential regulation of interferon responses and the JNK pathway by MAPK kinases
Activation of conventional Protein Kinase C
Human liver alcohol dehydrogenase: purification, composition, and catalytic features.
Loss of Rrn3 from RNA Polymerase I promoter escape complex
Assembly of RNA Polymerase I Holoenzyme (human)
Initiation of RNA Polymerase III Productive Transcription
Resumption of RNA Polymerase III Productive Transcription
RNA Polymerase III Termination and release of transcribed mRNA
RNA Polymerase III Transcriptional Pause at Terminator Sequence
RNA Polymerase III Productive Transcription
RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites
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.
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.
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.
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.
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.
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.
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.
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'.
Addition of the third nucleotide on the nascent transcript
Addition of the fourth nucleotide on the Nascent Transcript: Second Transition
Addition of nucleotides 10 and 11 on the growing transcript: Third Transition
Addition of nucleotides between position +11 and +30
Extrusion of 5'-end of 30 nt long transcript through the pore in Pol II complex
Phosphorylation (Ser5) of RNA pol II CTD
SPT5 subunit of Pol II binds the RNA triphosphatase (RTP)
Hypophosphorylation of RNA Pol II CTD by FCP1P protein
DSIF complex binds to RNA Pol II (hypophosphorylated)
Phosphorylation by p34cdc2 regulates spindle association of human Eg5, a kinesin-related motor essential for bipolar spindle formation in vivo
Resumption of transcription after TC-NER
Recruitment of RNA Polymerase II Holoenzyme by TFIIF to the pol II promoter:TFIID:TFIIA:TFIIB complex
Formation of the closed pre-initiation complex
Abortive termination of early transcription elongation by DSIF:NELF
Fall Back to Closed Pre-initiation Complex
Nucleophillic Attack by 3'-hydroxyl Oxygen of nascent transcript on the Alpha Phosphate of NTP
Newly Formed Phosphodiester Bond Stabilized and PPi Released
RNA Polymerase II Promoter Opening: First Transition
NTP Binds Active Site of RNA Polymerase II
Phosphorylation of carbovir enantiomers by cellular enzymes determines the stereoselectivity of antiviral activity
Displacement of stalled Pol II from the lesion site
Assembly of repair proteins at the site of Pol II blockage
5' incision leading to excision of DNA fragment with lesion in TC-NER
Wnt/beta-catenin signaling: components, mechanisms, and diseases
3' incision of the lesioned strand of DNA in TC-NER
Ligation of newly synthesized repair patch to incised DNA in GG-NER
RNA Pol II is blocked by the lesion leading to reduced transcription
Formation of active Pol II complex with lesioned DNA template
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.
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).
Binding of ERCC1-XPF to preincision complex
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.
The polo-like kinase PLK1 phosphorylates KIF23 (also known as MKLP1 i.e. mitotic kinesin-like protein 1) on serine residues S904 and S905.
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.
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.
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).
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.
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).
Ligation of newly synthesized repair patch to incised DNA in TC-NER
XPC:HR23B complex binds to damaged DNA site with lesion
XPC binds to HR23B forming a heterodimeric complex
Association of Ku heterodimer with ends of DNA double-strand break
Ligation of DNA and formation of Holliday structures following repair synthesis
Association of RAD51 with the resected ends of the DNA double-strand break
Association of RAD51 with RAD52:DNA double-strand break ends
Association of RAD52 with ssDNA at resected ends of double-strand break
The polo-like kinase PLK1 phosphorylates NUDC on serine residues S274 and S326.
In this final phase of mitosis, new membranes are formed around two sets of chromatids and two daughter cells are formed. The chromosomes and the spindle fibers disperse, and the fiber ring around the center of the cell, composed of actin, contracts, pinching the cell into two daughter cells.
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.
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.
Resistance to thromboembolism in PI3Kgamma-deficient mice
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).
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).
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.
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.
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.
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).
Formation of open bubble structure in DNA by helicases
Formation of ERCC1-XPF heterodimeric complex
Insertion of correct bases opposite to the lesion by Pol eta
Binding of Pol eta to lesioned DNA template
Binding of Pol zeta to lesioned DNA template
BRF1 protein turnover and mRNA decay activity are regulated by protein kinase B at the same phosphorylation sites
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).
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).
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).
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).
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).
Cell cycle progression is regulated by cyclin-dependent protein kinases at both the G1/S and the G2/M transitions by cyclin-dependent protein kinases. The G2/M transition is regulated through the phosphorylation of nuclear lamins and histones (reviewed in Sefton, 2001).
A description of the mitotic proteins targeted by the mitotic cyclin:CDK complexes will be covered in a later release.
Intermolecular autophosphorylation of ATM within dimeric ATM complexes
Dissociation of dimeric phospho-ATM complexes
Phosphorylation of histone H2AX at Serine-139 by ATM at the site of DSB
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.
Expression and characterization of a human pyruvate carboxylase variant by retroviral gene transfer
Cleavage of formamidopyrimidine by hNTH1 glycosylase
Cleavage of dihydrouracil by hNTH1 glycosylase
Cleavage of cytosine glycol by hNTH1 glycosylase
Cleavage of thymine glycol by hNTH1 glycosylase
ChEBI:58828 5-(methylsulfanyl)-2,3-dioxopentyl phosphate(2?)
5-(methylsulfanyl)-2,3-dioxopentyl phosphate(2?)
At mitotic entry, Plk1 phosphorylates and activates Cdc25C phosphatase, whereas it phosphorylates and down-regulates Wee1A. Plk1 also phosphorylates and inhibits Myt1 activity. 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.
After the initiation of DNA condensation during mitosis, NuMA is phosphorylated by Cdc2 kinase and transported rapidly to the centrosomal region (Hsu and Yeh, 1996). Another phosphorylation event occurs when NuMA associates with the mitotic spindle (Gaglio et al., 1995; Hsu and Yeh, 1996). While p34cdc2/cyclin B-dependent phosphorylation appears to plays an essential role in the targeting of NuMA to the spindle apparatus (Compton and Luo, 1995)(Hsu and Yeh, 1996), there may be additional protein kinases that promote the release of NuMA from the nuclear compartment at nuclear envelope breakdown (Saredi et al., 1997).
The mitotic spindle becomes established once centrosomes have migrated to opposite poles and the nuclear envelope has broken down. During this stage, interphase centrosomes mature into mitotic centrosomes recruiting additional gamma TuRC complexes and acquiring mitosis-associated centrosomal proteins including NuMA, Plk1 and CDK11p58 (reviewed in Schatten 2008; Raynaud-Messina and Merdes 2007).
The NuMA protein, which functions as a nuclear matrix protein in interphase (Merdes and Cleveland 1998), redistributes to the cytoplasm following nuclear envelope breakdown where it plays an essential role in formation and maintenance of the spindle poles (Gaglio, et al., 1995; Gaglio, et al., 1996; Merdes et al, 1996). The mitotic activation of NuMA involves Ran-GTP-dependent dissociation from importin (Nachury et al, 2001, Wiese et al, 2001). NuMA is transported to the mitotic poles where it forms an insoluble crescent around centrosomes tethering microtubules into the bipolar configuration of the mitotic apparatus (Merdes et al., 2000; Kisurina-Evgenieva et al, 2004). Although NuMA is not a bona fide constituent of the mitotic centrosome but rather a protein associated with microtubules at the spindle pole, specific splice variants of NuMA have been identified that associate with the centrosome during interphase (Tang et al, 1994).
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.
The centrosome is the primary microtubule organizing center (MTOC) in vertebrate cells and plays an important role in orchestrating the formation of the mitotic spindle. Centrosome maturation is an early event in this process and involves a major reorganization of centrosomal material at the G2/M transition. During maturation, centrosomes undergo a dramatic increase in size and microtubule nucleating capacity. As part of this process, a number of proteins and complexes, including some that are required for microtubule nucleation and anchoring, are recruited to the centrosome while others that are required for organization of interphase microtubules and centrosome cohesion are lost (reviewed in Schatten, 2008; Raynaud-Messina and Merdes 2007).
At the beginning of mitosis, MASTL (GWL, Greatwall kinase) is activated by phosphorylation at several key sites. Many of these sites, including functionally important threonine residues T194, T207 and T741 (corresponding to Xenopus residues T193, T206 and T748), are proline directed, matching CDK1 consensus sequence, and thus probably phosphorylated by CDK1, as shown by in vitro studies (Yu et al. 2006. Blake-Hodek et al. 2012). Phosphorylation of the serine residue S875 (S883 in Xenopus) is implicated as critical for the mitotic function of MASTL (Vigneron et al. 2011) and likely occurs through autophosphorylation (Blake-Hodek et al. 2012). Other kinases, such as PLK1 (Vigneron et al. 2011) and other MASTL phosphorylation sites may also be involved in mitotic activation of MASTL (Yu et al. 2006, Vigneron et al. 2011, Blake-Hodek et al. 2012). Phosphorylation of the serine residue S102 (S101 in Xenopus) is functionally important but the responsible kinase has not been identified (Blake-Hodek et al. 2012).
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.
Cloning and expression of two human lysophosphatidic acid acyltransferase cDNAs that enhance cytokine-induced signaling responses in cells
The activity of MASTL, also known as the Greatwall kinase (GWL), is necessary for the entry and progression of mitosis. MASTL is activated by phosphorylation of several key residues during mitotic entry. Phosphorylation on the serine residue S875 (S883 in Xenopus), likely through autophosphorylation (Blake-Hodek et al. 2012) appears to be critical (Vigneron et al. 2011). Several other sites, including putative CDK1 targets T194, T207 and T741, contribute to the full activation of MASTL (Yu et al. 2006, Blake-Hodek et al. 2012). Other kinases, such as PLK1 (Vigneron et al. 2011) and other MASTL phosphorylation sites may also be functionally important (Yu et al. 2006, Blake-Hodek et al. 2012). Activated MASTL phosphorylates ARPP19 and ENSA on serines S62 and S67, respectively, enabling them to bind to and inhibit the phosphatase activity of PP2A complexed with the regulatory subunit PPP2R2D (B55-delta). Inhibition of PP2A-PPP2R2D activity by ARPP19 or ENSA prevents dephosphorylation of CDK1 targets, hence allowing entry and maintenance of mitosis (Mochida et al. 2010, Gharbi-Ayachi et al. 2010, Burgess et al. 2010).
Binding of REV1 to lesioned DNA template
Misinsertion of bases opposite to the lesion by HREV1
Cleavage of ethenocytosine by TDG glycosylase
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
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%â20% 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).
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).
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).
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.
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).
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).
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.
Chromosome maintenance is critical for stable chromosome function in mammalian and other eukaryotic cells. Aspects of telomere maintenance and nucleosome assembly are covered here.
In the seventh reaction of GPI synthesis, a second mannose residue is added to the glycolipid on the lumenal face of the endoplasmic reticulum membrane. PIG-V was identified as the catylyst, or a component of the catalyst, of this reaction, on the basis of its ability to correct the metabolic defects of yeast and mammalian mutant cells arrested at this stage of the GPI synthetic process (Fabre et al. 2005; Kang et al. 2005).
In the eighth reaction of GPI synthesis, a third mannose residue is added, catalyzed by PIG-B (Takahashi et al. 1996).
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).
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).
The first step of GPI synthesis is the transfer of N-acetylglucosamine from cytosolic UDP-N-acetylglucosamine to phosphatidyl inositol (PI) in the endoplasmic reticulum membrane. The reaction is catalyzed by a multimeric enzyme, also localized to the endoplasmic reticulum membrane, six components of which have been identified to date by mutagenesis studies in cultured cells and by co-recipitation studies in vitro (Watanabe et al. 1996, 1998, 2000).
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.
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).
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).
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).
Diversity of the pyruvate dehydrogenase kinase gene family in humans
The human gamma-glutamyltransferase gene family
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.
Rapid destruction of human Cdc25A in response to DNA damage.
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.
The complementary strand is synthesized by the polymerase primase complex using conventional RNA priming.
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.
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.
Telomerase acts as reverse transcriptase in the elongation of telomeres (Smogorzewska and de Lange 2004).
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.
At some point in the extension process a sufficient number of regulatory factors that repress telomere extension become bound to the extending telomere. These factors include the TRF1 complexes, TRF2 complexes, telomerase, other factors, and the telomere itself. As repeats are added to the G-rich strand, and once lagging strand synthesis completes the duplex, new binding sites become available for these repressive factors. Once a balance is reached between telomere extension and the telomere repression factors, extension ceases. In this state extension machinery disassociates, leaving the telomere to be folded into a stable conformation. This module details a single transit through the telomere extension process, detailing the addition of two repeats, and the corresponding synthesis of a section of lagging strand. An actual round of in vivo telomere extension would require thousands of telomere repeat additions, and it is the repressive effect of the factors bound to these repeats that turns off telomere extension.
The first step of glycosylphosphatidylinositol biosynthesis is mediated by a complex of PIG-A, PIG-H, PIG-C and GPI1
Once polymerase switching from pol alpha to pol delta is complete the processive synthesis of a short run of DNA called an Okazaki fragment begins. DNA synthesis is discontinuous and as the extending Okazaki fragment reaches the RNA primer, this primer is folded into a single-stranded flap, which is removed by endonucleases. The process of extension is completed 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 at the telomere.
Review of epidermal growth factor receptor biology
Isolation and characterization of an allelic cDNA for human muscle fructose-1,6-bisphosphatase
Characterization of human phosphoserine aminotransferase involved in the phosphorylated pathway of L-serine biosynthesis
Protein kinase C beta controls nuclear factor kappaB activation in B cells through selective regulation of the IkappaB kinase alpha
Mannose-6-phosphate isomerase (MPI) converts Fructose 6-phosphate to Mannose 6-phosphate (Proudfoot AE 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 E et al, 2000).
De novo sphingolipid biosynthesis: a necessary, but dangerous, pathway
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.
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.
The phosphorylation of a dolichol residue of the ER membrane is a starting step in the N-glycan biosynthesis pathway (Fernandez F et al, 2002). Defects in DOLK are the cause of congenital disorder of glycosylation type 1M (CDG1M), also known as dolichol kinase deficiency (Kranz C et al, 2007).
Dolichol is a polyisoprenol lipid comprised of five-carbon isoprene units linked linearly in a head-to-tail fashion. In the N-glycan biosynthesis pathway, dolichyl phosphate is used as an anchor for the N-glycan sugar to the ER membrane, and as an initiation point for the synthesis. Dolichyl phosphate can be obtained either from direct phosphorylation of dolichol or from de-phosphorylation of dolichyl diphosphate, released at the end of the N-glycan biosynthesis pathway.
Glucosamine-fructose 6-phosphate aminotransferase (GFAT) is the first and rate-limiting enzyme in the hexosamine synthesis pathway, and thus formation of hexosamines like N-acetylglucosamine (GlcNAc). This enzyme probably plays a role in limiting the availability of substrates for the N- and O- linked glycosylation of proteins. Two isoforms, GFAT 1 and 2, have been identified (McKnight GL et al, 1992; Oki T et al, 1999). GFAT is required normal functioning of neuromuscular synaptic transmission. Defects in the gene expressing this protein leads to altered muscle fiber morphology and impaired neuromuscular junction development (Senderek et al, 2011).
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).
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).
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).
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.
Fission yeast expresses two kinesin-8s. These polypeptides colocalize throughout the vegetative cell cycle as they bind cytoplasmic microtubules during interphase, spindle microtubules, and/or kinetochores during early mitosis, and the interpolar spindle as it elongates in anaphase. Homo- and hetero-dimers can be produced in vitro.
cAMP induces dissociation of inactive PKA tetramers
Telomeric protein distributions and remodeling through the cell cycle in Saccharomyces cerevisiae
Release of 78 kDa glucose-regulated protein
Release of (inferred) platelet cytosolic components
F-actin capping protein is a heterodimer
Kinesin-6 and RACGAP1 form the heterotetrameric complex centralspindlin
The single minichromosome maintenance protein of Methanobacterium thermoautotrophicum DeltaH contains DNA helicase activity.
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Identification and characterization of eukaryotic initiation factor 5A-2
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Phytanic acid alpha-oxidation, new insights into an old problem: a review
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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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Studies on the properties and tissue distribution of the isozymes of guanylate kinase in man
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
Knockdown of hepatocyte aquaporin-8 by RNA interference induces defective bile canalicular water transport
Am J Physiol Gastrointest Liver Physiol 296:G93-100
Aurora B controls the association of condensin I but not condensin II with mitotic chromosomes
TAK1 is a ubiquitin-dependent kinase of MKK and IKK
Molecular basis for membrane phospholipid diversity: why are there so many lipids?
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On the mechanism of sensing unfolded protein in the endoplasmic reticulum
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Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism.
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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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Requirement of human renal water channel aquaporin-2 for vasopressin-dependent concentration of urine
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Functions and mechanisms of RNA editing.
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The Bcl-2 family: roles in cell survival and oncogenesis.
Role of immunoproteasomes in cross-presentation
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Structural and functional modules in RNA interference
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N-acetyl-D-glucosaminylphosphatidylinositol [ChEBI:15935]
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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
ArPIKfyve homomeric and heteromeric interactions scaffold PIKfyve and Sac3 in a complex to promote PIKfyve activity and functionality
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
NLR proteins: integral members of innate immunity and mediators of inflammatory diseases
The human homolog of Saccharomyces cerevisiae CDC45.
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
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.
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)
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.
The ability of human lactate dehydrogenase to catalyze the reaction of phenylalanine with NADH + H+ to form phenyllactate and NAD+ is inferred from the properties of bovine heart lactate dehydrogenase (Meister 1951). As these studies were carried out only on the one bovine isoform, the reaction is inferred only for the corresponding human isoform. The reaction rate measured for bovine LDHB acting on phenylpyruvate is approximately 2% of its rate on pyruvate, but could yield appreciable amounts of phenyllactate under conditions of high phenylpyruvate concentration.
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.
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).
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).
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.
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).
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).
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).
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).
Protein interactions with nitric oxide synthases: controlling the right time, the right place, and the right amount of nitric oxide
The biochemistry, metabolism and inherited defects of the pentose phosphate pathway: a review
Transcriptional networks controlling pancreatic development and beta cell function
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
Extracellular transsulfuration generates hydrogen sulfide from homocysteine and protects endothelium from redox stress
Am J Physiol Heart Circ Physiol 299:H1568-76
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).
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).
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).
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).
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).
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).
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).
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.
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.
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.
Exportin-5 binds pre-microRNAs having 2-nucleotide overhangs at the 3' end. Binding is independent of sequence and depends on GTP.
Nuclear Export by Exportin-5. The pre-microRNA is bound by the Exportin-5:RanGTP complex in the nucleus and the complex is translocated through the nuclear pore into the cytoplasm. In the process GTP is hydrolyzed to GDP.
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, however only Argonaute2 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 Argonaute2, 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.
Cell cycle-dependent phosphorylation, nuclear localization, and activation of human condensin
New roles for cysteine and transsulfuration enzymes: production of H2S, a neuromodulator and smooth muscle relaxant
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).
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).
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).
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).
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.
Conversion of palmitic acid to very long chain fatty acyl-CoAs
Synthesis of very long-chain fatty acyl-CoAs
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.
The ternary complex forms upon binding of the initiator methionyl-tRNA to the active eIF2:GTP complex.
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.
The DEAD-box RNA helicase eIF4A, together with the RNA-binding proteins eIF4B or eIF4H, is thought to unwind RNA secondary structures near the 5'-end of the mRNA and in the presence of ATP.
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.
Activation of eIF2 through direct binding of GTP.
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.
eIF3 and eIF1A bind to the 40S ribosomal subunit.
80S monosomes dissociate into 40S and 60S ribosomal subunits. eIF1A promotes this dissociation.
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.
Joining of the 60S subunit to form the 80S ribosome is catalyzed by the presence of GTP-bound eIF5B.
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.
Molecular characterization of two galactosemia mutations: correlation of mutations with highly conserved domains in galactose-1-phosphate uridyl transferase
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.
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.
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.
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.
The translation initiation complex forms when the 43S complex binds the mRNA that is associated with eIF4F, eIF4B and eIF4H. eIF4G in the eIF4F complex can directly contact eIF3 in the 43S complex. eIF1A is necessary for the formation of this complex.
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.
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.
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.
Cytosolic sensors of pathogen-associated DNA
Hereditary renal amyloidosis associated with a mutant fibrinogen alpha-chain
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.
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.
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.
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.
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.
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.
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.
Signal transduction via platelet-derived growth factor receptors
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.
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.
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.
Bleeding due to disruption of a cargo-specific ER-to-Golgi transport complex
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'.
Inflammasomes: guardians of cytosolic sanctity
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.
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.
Please note that this reaction was inferred from experiments performed using Saccharomyces cerevisiae.
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
Adrenodoxin: structure, stability, and electron transfer properties
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
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.
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 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.
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)'.
cdc25A protein is degraded by the ubiquitin-proteasome machinery in both terminally differentiating and cycling cells (Bernardi et al. 2000).
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.
Myt1, which localizes preferentially to the endoplasmic reticulum and Golgi complex, phosphorylates Cdc2 on threonine 14 ( Liu et al., 1997).
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.
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.
DAP10- and DAP12-associated receptors in innate immunity
Function of Nod-like receptors in microbial recognition and host defense
Mechanisms of ubiquitin transfer by the anaphase-promoting complex
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.
Gamma-tubulin complexes and microtubule organization
Traffic control: regulation of kinesin motors
The signal from unattached kinetochores is amplified through a Mad2 inhibitory signal that is propagated by the binding of Mad1 to the kinetochore, the association of Mad2 with Mad1, the conversion of Mad2 conformation to an inhibitory form through its association with Mad1 and finally the release of the inhibitory form of Mad2 from the kinetochore.
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.
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.
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.
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).
Mad2 is recruited to the kinetochore through an interaction with Mad1.
In vitro structural studies have shown that Mad2 undergoes a major conformational change upon binding to Mad1. This conformational change is postulated to activate Mad2 into a high affinity state which can bind and sequester Cdc20 from the APC.
The mechanism by which the conformationally altered inhibitory form of Mad2 is released from its association with Mad1 at the kinetochore is not known. Mad1 and Cdc20 have a common 10 residue Mad2 binding motif. Therefore, one possibility is that Mad2 is transferred competitively from Mad1 to Cdc20 (Luo et al., 2002; Sironi et al., 2002).
The 9-1-1 complex is a heterotrimeric ring-shaped structure that is loaded onto DNA by the Rad17-RFC complex. In vitro studies indicate that loading is preferred onto DNA substrates containing ssDNA gaps that presumably resemble structures found upon replication fork stalling and DNA polymerase/helicase uncoupling. The Rad17-RFC and 9-1-1 complexes are structurally similar to the RFC (replication factor C) clamp loader and PCNA sliding clamp, respectively, and similar mechanisms are thought to be used during loading of the 9-1-1 complex and PCNA. Upon loading, the 9-1-1 complex can recruit Chk1 onto sites of replication fork uncoupling or DNA damage. The purified Rad17 and Rad9-Hus1-Rad1 (9-1-1) complexes can form a stable co-complex in the presence of ATP, using Rad17-Rad9 interactions. From computer modeling studies, the Rad17 subunit of the complex is also proposed to interact with the C-terminus of Rad1, p36 with the C-terminus of Hus1, and p38 with the C-terminus of Rad9. A major known function of the 9-1-1 complex is to recruit Chk1 to stalled replication forks for activation by ATR. However, the presence of the 9-1-1 complex also alters the ability of Rad17 to become phosphorylated, perhaps suggesting that 9-1-1 may regulate the recruiment of additional ATR substrates. The 9-1-1 complex has also been found to interact with base excision repair factors human DNA polymerase beta, flap endonuclease FEN1, and the S. pombe MutY homolog (SpMYH), indicating that 9-1-1 also plays a direct role in DNA repair.
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 Rad17ââ¬âRfc2-5 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.
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
Wnt proteins are lipid-modified and can act as stem cell growth factors
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
Comparison of the intracellular signaling responses by three chimeric fibroblast growth factor receptors in PC12 cells
Removal of the Flap Intermediate from the C-strand
Synthesis of PIPs at the plasma membrane
Identification of a cDNA encoding an isoform of human CTP synthetase
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'.
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).
Identification and characterization of a novel human sphingosine-1-phosphate phosphohydrolase, hSPP2
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.
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(Lelièvre, 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).
Unique among FGFR1 fusion proteins, which generally give rise to an atypical myeloproliferative syndrome (EMS) (reviewed in Jackson, 2010), the BCR-FGFR1 fusion results in a more typical chronic myeloid leukemia (CML). Although both EMS and CML activate PLCgamma signaling, and mutation of the FGFR1 Y766 PLCgamma binding site attenuates both diseases, CML-specific signaling also appears to be mediated through the BCR portion of the fusion protein. BCR Y177 binds GRB2-GAB1 and induces CML-like leukemia in mice, while expression of a Y177F BCR-FGFR1 fusion induces EMS-like disease (Roumiantsev, 2004).
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).
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).
Amyloid is a term used to describe typically extracellular deposits of aggregated proteins, sometimes known as plaques. Abnormal accumulation of amyloid is amyloidosis, a term associated with diseased organs and tissues, particularly neurodegenerative diseases such as Alzheimer's, Parkinson's and Huntingdon's. Amyloid deposits consist predominantly of amyloid fibrils, rigid, non-branching structures that form ordered assemblies, characteristically with a cross beta-sheet structure where the sheets run parallel to the direction of the fibril (Sawaya et al. 2007). Often the fibril has a left-handed twist (Nelson & Eisenberg 2006). At least 27 human proteins form amyloid fibrils (Sipe et al. 2010). Many of these proteins have non-pathological functions; the trigger that leads to abnormal aggregations differs between proteins and is not well understood but in many cases the peptides are abnormal fragments or mutant forms arising from polymorphisms, suggesting that the initial event may be aggregation of misfolded or unfolded peptides. Early studies of Amyloid-Beta assembly led to a widely accepted model that assembly was a nucleation-dependent polymerization reaction (Teplow 1998) but it is now understood to be more complex, with multiple 'off-pathway' events leading to a variety of oligomeric structures in addition to fibrils (Roychaudhuri et al. 2008). An increasing body of evidence suggests that these oligomeric forms are primarily responsible for the neurotoxic effects of Amyloid-beta (Roychaudhuri et al. 2008), alpha-synuclein (Winner et al. 2011) and tau (Dance & Strobel 2009, Meraz-Rios et al. 2010). Amyloid oligomers are believed to have a common structural motif that is independent of the protein involved and not present in fibrils (Kayed et al. 2003). Conformation dependent, aggregation specific antibodies suggest that there are 3 general classes of amyloid oligomer structures (Glabe 2009) including annular structures which may be responsible for the widely reported membrane permeabilization effect of amyloid oligomers. Toxicity of amyloid oligomers preceeds the appearance of plaques in mouse models (Ferretti et al. 2011). Fibrils are often associated with other molecules, notably heparan sulfate proteoglycans and Serum Amyloid P-component, which are universally associated and seem to stabilize fibrils, possibly by protecting them from degradation.
Amyloid fibril formation is associated with a wide range of diseases (Chiti & Dobson 2006), thoughthe accumulation and deposition of fibrillar material does not correlate well with disease pathogenesis and it is now widely believed that oligomeric amyloid forms are largely responsible for the cytotoxic effects of amyloid (Glabe 2009). Fibrils have been described as more like crystalline polymer structures than the protein monomers they are derived from (Wetzel et al. 2007). Fibril formation is usually preceded by the association of monomers into oligomeric structures (Kodali & Wetzel 2007). For Beta-amyloid, these are spherical structures with around 12 units (Bernstein et al. 2005). Larger structures called protofibrils are also observed, non-spherical filamentous structures lacking a periodic substructure (Goldsbury 2005).
Proteasome and peptidase function in MHC-class-I-mediated antigen presentation
Assembly of AUF1 oligomers on U-rich RNA targets by sequential dimer association
5-Hydroxyindoleacetaldehyde [ChEBI:2070]
Identification and characterization of hPEM-2, a guanine nucleotide exchange factor specific for Cdc42
Nucleotide receptor signaling in platelets
Genetic alterations in the tyrosine kinase transcriptome of human cancer cell lines
Reconstitution of proliferating cell nuclear antigen-dependent repair of apurinic/apyrimidinic sites with purified human proteins.
Red cell pyruvate kinase deficiency: molecular and clinical aspects
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).
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).
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).
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).
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 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).
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).
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).
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).
Cloning and expression of human deoxyhypusine synthase cDNA. Structure-function studies with the recombinant enzyme and mutant proteins.
Characterization of SMG-9, an essential component of the nonsense-mediated mRNA decay SMG1C complex
Oxidative protein folding in the mitochondrial intermembrane space
Shelterin: the protein complex that shapes and safeguards human telomeres
Adhesion molecule L1 stimulates neuronal migration through Vav2-Pak1 signaling
MPF localization is controlled by nuclear export
Comprehensive proteomic analysis of the human spliceosome.
Insig-mediated degradation of HMG CoA reductase stimulated by lanosterol, an intermediate in the synthesis of cholesterol
The ERBB4/HER4 intracellular domain 4ICD is a BH3-only protein promoting apoptosis of breast cancer cells
Zinc transporters and the cellular trafficking of zinc
Phosphoribosylpyrophosphate synthesis from glucose decreases during amino acid starvation of human lymphoblasts
Immunoglobulin heavy-chain-associated amyloidosis
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.
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.
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.
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
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).
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).
The dual phosphatase activity of synaptojanin1 is required for both efficient synaptic vesicle endocytosis and reavailability at nerve terminals
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).
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).
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 GDPGTP 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).
Innate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
Enzymic conversion of squalene 2,3-oxide to lanosterol and cholesterol
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.
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.
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).
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.
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).
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.
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).
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.
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.
RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
Translation of the phosphoinositide code by PI effectors
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).
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.
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).
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.
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.
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).
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).
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.
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.
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.
Regulation of Glucokinase by Glucokinase Regulatory Protein
Presence of pathogen-associated DNA in cytosol induces type I IFN production. Several intracellular receptors have been implicated to some degree. These include DNA-dependent activator of interferon (IFN)-regulatory factors (DAI) (also called Z-DNA-binding protein 1, ZBP1), absent in melanoma 2 (AIM2), RNA polymerase III (Pol III), IFN-inducible protein IFI16, leucine-rich repeat flightless interacting protein-1 (LRRFIP1), DEAH-box helicases (DHX9 and DHX36), DEAD-box helicase DDX41, meiotic recombination 11 homolog A (MRE11), DNA-dependent protein kinase (DNA-PK), cyclic GMP-AMP synthase (cGAS) and stimulator of interferon genes (STING). Detection of cytosolic DNA requires multiple and possibly redundant sensors leading to activation of the transcription factor NF-kappaB and TBK1-mediated phosphorylation of the transcription factor IRF3. Cytosolic DNA also activates caspase-1-dependent maturation of the pro-inflammatory cytokines interleukin IL-1beta and IL-18. This pathway is mediated by AIM2.
Uridine diphosphate glucose pyrophosphorylase. II
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).
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).
RNA polymerase III (POL III) was reported to sense and transcribe cytosolic AT-rich dsDNA into 5'-triphosphate poly(A-U) RNA in human and mouse cells. This dsRNA ligand in turn activated retinoic acid-inducible gene I (RIG-I) leading to production of type I interferon and activation of the transcription factor NF-kappaB (Chiu YH et al. 2009, Ablasser A et al. 2009). Knockdown of POL III expression by siRNA or inhibition of its enzymatic activity by specific chemical inhibitor ML-60218 prevented IFN beta induction in HEK293 cells stimulated with DNA viruses or poly(dA-dT) (Chiu YH et al. 2009, Ablasser A et al. 2009). Moreover, Pol-III inhibition blocked interferon induction by intracellular Legionella pneumophila bacteria [Chiu YH et al 2009]. This project represents cytosolic RNA polymerase III as a complex comprising 17 subunits, although the precise biochemical composition of the cytosolic holoenzyme complex which specifically recognizes AT-rich DNA is not yet known.
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).
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.
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).
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).
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.
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).
Calf RTH-1 nuclease can remove the initiator RNAs of Okazaki fragments by endonuclease activity.
Isolation of the human phosphomannomutase gene (PMM1) and assignment to chromosome 22q13
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).
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.
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.
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.
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.
Human glutamate pyruvate transaminase (GPT): localization to 8q24.3, cDNA and genomic sequences, and polymorphic sites.
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.
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 â 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.
Adaptors and molecular scaffolds in immune cell signaling
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.
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.
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].
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.
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).
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.
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).
Molecular analysis of human argininosuccinate lyase: mutant characterization and alternative splicing of the coding region
The carboxy terminus of the beta amyloid protein is critical for the seeding of amyloid formation: implications for the pathogenesis of Alzheimer's disease
The ends of the affair: capping and polyadenylation.
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.
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).
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.
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].
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.
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.
Cloning and sequencing of the cDNA for the light subunit of human liver gamma-glutamylcysteine synthetase and relative mRNA levels for heavy and light subunits in human normal tissues
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).
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
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).
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.
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.
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.
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.
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.
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.
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).
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).
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).
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).
Distinct missense mutations of the FGFR3 lys650 codon modulate receptor kinase activation and the severity of the skeletal dysplasia phenotype
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).
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).
Monoubiquitinated substrate acquires additional ubiquitin modifications in the form of multiple single attachments or a ubiquitin chain. Polyubiquitin chains added through K48 residue of ubiquitin typically targets the substrate for degradation (Raymond et al. 2009).
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.
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.
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).
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