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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_16090.2
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_114105.8
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Note: the coordinates are copied over from Homo sapiens.
Acetyl-coenzyme A synthetase 2-like, mitochondrial
acyl-CoA synthetase short-chain family member 1
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Protoheme IX farnesyltransferase, mitochondrial ecNumber2.5.1.-/ecNumber
Cytochrome c oxidase assembly protein COX15 homolog
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Coproporphyrinogen III oxidase, mitochondrial
This event has been computationally inferred from an event that has been demonstrated in another species. The inference is based on the homology mapping in Ensembl Compara. Briefly, reactions for which all involved PhysicalEntities (in input, output and catalyst) have a mapped orthologue/paralogue (for complexes at least 75% of components must have a mapping) are inferred to the other species. High level events are also inferred for these events to allow for easier navigation. More details and caveats of the event inference in Reactome. For details on the Ensembl Compara system see also: Gene orthology/paralogy prediction method.
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5-aminolevulinate synthase, non-specific (pyridoxal phosphate cofactor)
5-aminolevulinate synthase, non-specific, mitochondrial
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5-aminolevulinate synthase, erythroid (pyridoxal phosphate cofactor)
5-aminolevulinate synthase, erythroid-specific, mitochondrial precursor
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Structure of the Rho family GTP-binding protein Cdc42 in complex with the multifunctional regulator RhoGDI
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Signal transduction pathways used by NLR-type innate immune receptors
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A tandemly repeated sequence at the termini of the extrachromosomal ribosomal RNA genes in Tetrahymena
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Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
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Constitutive activation of fibroblast growth factor receptor 3 by mutations responsible for the lethal skeletal dysplasia thanatophoric dysplasia type I
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Enzyme-substrate intermediate formation at lysine 329 of human deoxyhypusine synthase
SUBUNIT Component of the RNA polymerase I (Pol I) and RNA polymerase III (Pol III) complexes consisting of at least 13 and 17 subunits, respectively. Interacts with the RPC19/RPAC2 and RPC53/RPC4.MISCELLANEOUS Present with 13000 molecules/cell in log phase SD medium.SIMILARITY Belongs to the archaeal RpoD/eukaryotic RPB3 RNA polymerase subunit family.
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The molecular dissection of Fc gamma receptor mediated phagocytosis
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Sequence differences between human muscle and liver cDNAs for UDPglucose pyrophosphorylase and kinetic properties of the recombinant enzymes expressed in Escherichia coli.
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Aldose reductase is a major reductase for isocaproaldehyde, a product of side-chain cleavage of cholesterol, in human and animal adrenal glands
Nicotinamide mononucleotide adenylyltransferase 3
Nicotinamide mononucleotide adenylyltransferase 2
Conformational transition associated with E1-E2 interaction in small ubiquitin-like modifications
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
Delta-1-pyrroline-5-carboxylate synthetase long
Delta-1-pyrroline-5-carboxylate synthetase short
Structural analysis of the GLUT1 facilitative glucose transporter (review).
ornithine aminotransferase, mitochondrial
ChEBI:28540 5beta-cholestane-3alpha,7alpha,26-triol
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
Mitochondrial 2-oxodicarboxylate carrier
BMAL1:CLOCK/NPAS2 Activates Circadian Expression
delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor
ChEBI:28533 3alpha,7alpha-dihydroxy-24-oxo-5beta-cholestanoyl-CoA
branched-chain amino acid aminotransferase, mitochondrial, apoenzyme
lysine-ketoglutarate reductase /saccharopine dehydrogenase monomer
3-hydroxyisobutyryl-coenzyme A hydrolase
Branched-chain amino acid aminotransferase, cytosolic
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.
ornithine carbamoyltransferase, mitochondrial
carbamoyl-phosphate synthase (ammonia), mitochondrial
Nucleocytoplasmic shuttling modulates activity and ubiquitination-dependent turnover of SUMO-specific protease 2
gamma-butyrobetaine,2-oxoglutarate dioxygenase
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D-2-hydroxyglutaric acidaemia: identification of a new enzyme, D-2-hydroxyglutarate dehydrogenase, localized in mitochondria
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Regulation of origin recognition complex conformation and ATPase activity: differential effects of single-stranded and double-stranded DNA binding.
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Mechanism of the eukaryotic chaperonin: protein folding in the chamber of secrets
D-Fructose 2,6-bisphosphate [ChEBI:28602]
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Identification of two mammalian reductases involved in the two-carbon fatty acyl elongation cascade
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The ERBB4/HER4 receptor tyrosine kinase regulates gene expression by functioning as a STAT5A nuclear chaperone
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Identification of human PMP34 as a peroxisomal ATP transporter
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Hereditary orotic aciduria and other disorders of pyrimidine metabolism
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 2663-2704
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Association of the human SUMO-1 protease SENP2 with the nuclear pore
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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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NADPH:adrenodoxin oxidoreductase, mitochondrial
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Iron-sulfur clusters transporter ATM1, mitochondrial
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Astrocytic Glutamate-Glutamine Uptake And Metabolism
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Probable NADPH reductase TAH18 ecNumber1.-.-.-/ecNumber
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Cytosolic Fe-S cluster assembly factor NBP35
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Cytosolic Fe-S cluster assembly factor CFD1
Aquaporins in the hepatobiliary tract. Which, where and what they do in health and disease
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The retinoid cycle in cones (daylight vision)
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Multiple forms of an inositol polyphosphate 5-phosphatase form signaling complexes with Shc and Grb2
Structural relationships and the classification of aminoacyl-tRNA synthetases
Enzymatic activities of the human AGPAT isoform 3 and isoform 5: localization of AGPAT5 to mitochondria
Wnt family proteins are secreted and associated with the cell surface
Localization of MCM2-7, Cdc45, and GINS to the site of DNA unwinding during eukaryotic DNA replication
PMP70, the 70-kDa peroxisomal membrane protein: a member of the ATP-binding cassette transporters
Reverse transcriptase motifs in the catalytic subunit of telomerase
Identification, purification, and partial characterization of a novel Mr 28,000 integral membrane protein from erythrocytes and renal tubules
Cell cycle-regulated trafficking of human telomerase to telomeres
Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.
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A novel PtdIns3P and PtdIns(3,5)P2 phosphatase with an inactivating variant in centronuclear myopathy
Structure/function studies of human beta-cell glucokinase. Enzymatic properties of a sequence polymorphism, mutations associated with diabetes, and other site-directed mutants.
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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
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Many cuts to ruin: a comprehensive update of caspase substrates
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Reviews in molecular biology and biotechnology: transmembrane signaling by G protein-coupled receptors
Insulin-responsive human adipocytes express two glucose transporter isoforms and target them to different vesicles
Identification and characterization of human glucose transporter-like protein-9 (GLUT9): alternative splicing alters trafficking
Glucose-sensing mechanisms in pancreatic beta-cells
Philos Trans R Soc Lond B Biol Sci 360:2211-25
DNA-directed RNA polymerase III 36 kDa polypeptide
DNA-directed RNA polymerase III 130 kDa polypeptide
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DNA-directed RNA polymerase III 31 kDa polypeptide
DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptide
DNA-directed RNA polymerase III largest subunit
DNA-directed RNA polymerases I, II, and III 8.3 kDa polypeptide
DNA-directed RNA polymerases I and III 16 kDa polypeptide
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DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptide
DNA-directed RNA polymerases III 12.5 kDa polypeptide
DNA-directed RNA polymerase III 47 kDa polypeptide
A J-protein is an essential subunit of the presequence translocase-associated protein import motor of mitochondria
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Purification, characterization, and cDNA cloning of an AU-rich element RNA-binding protein, AUF1
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Targeting, import, and dimerization of a mammalian mitochondrial ATP binding cassette (ABC) transporter, ABCB10 (ABC-me)
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The functional human dihydrofolate reductase gene
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TRAF6 Mediated Induction of proinflammatory cytokines
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Argonaute proteins: mediators of RNA silencing
Deletion of steroid 5 alpha-reductase 2 gene in male pseudohermaphroditism
dolichyl D-mannosyl phosphate [ChEBI:15809]
Large neutral amino acids transporter small subunit 4
Large neutral amino acids transporter small subunit 3
In vivo disposal of phenylalanine in phenylketonuria: a study of two siblings
Vesicular inhibitory amino acid transporter
Large neutral amino acids transporter small subunit 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=3670796
hCTR1: a human gene for copper uptake identified by complementation in yeast
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Double-strand break repair protein MRE11
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DNA repair/transcription protein MET18/MMS19
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Cytosolic iron-sulfur protein assembly protein 1
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Eukaryotic peptide chain release factor subunit 1
DNA repair helicase RAD3 ecNumber3.6.4.12/ecNumber
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DNA replication ATP-dependent helicase DNA2 ecNumber3.6.4.12/ecNumber
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Cytosolic Fe-S cluster assembly factor NAR1
Profiling of promoter occupancy by PPAR{alpha} in human hepatoma cells via ChIP-chip analysis
MD-2: the Toll 'gatekeeper' in endotoxin signalling
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DNA polymerase delta catalytic subunit ecNumber2.7.7.7/ecNumber
DNA-directed RNA polymerases I, II, and III 23 kDa polypeptide
DNA-directed RNA polymerase III 25 kDa polypeptide
DNA-directed RNA polymerases I and III 40 kDa polypeptide
Hypothetical 18.6 kDa protein in CCT3-CCT8 intergenic region
DNA-directed RNA polymerase III 74 kDa polypeptide
Transcription factor tau 138 kDa subunit
Transcription factor IIIB 70 kDa subunit
Transcription initiation factor TFIID TBP subunit
DNA-directed RNA polymerases I and III subunit RPAC1
DNA-directed RNA polymerase I and III 40 kDa polypeptide
DNA-directed RNA polymerase I and III 16 kDa polypeptide
DNA-directed RNA polymerases I and III subunit RPAC2
DNA-directed RNA polymerase I 135 kDa polypeptide
DNA-directed RNA polymerase I largest subunit
Transcription factor TFIIIB B\" component
Transcription factor tau 131 kDa subunit
Homologues of K48poluUb-phospho-PAK-2p34(Thr402)
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
Essential role of Mia40 in import and assembly of mitochondrial intermembrane space proteins
1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate [ChEBI:16618]
1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate
Axonal growth inhibition (RHOA activation)
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Transcription termination by RNA polymerase III in fission yeast. A genetic and biochemically tractable model system.
Mitochondrial protein import: recognition of internal import signals of BCS1 by the TOM complex
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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_4966.2
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=194644
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Genetic Analysis of Coenzyme Q Biosynthesis
Coenzyme Q: Molecular Mechanisms in Health and Disease (Book): 185-208
Familial hyperlysinemias. Purification and characterization of the bifunctional aminoadipic semialdehyde synthase with lysine-ketoglutarate reductase and saccharopine dehydrogenase activities.
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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_86645.9
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_10513.1
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Saccharomyces cerevisiae Ybr004c and its human homologue are required for addition of the second mannose during glycosylphosphatidylinositol precursor assembly
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FUNCTION DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common core component of RNA polymerases I and III which synthesize ribosomal RNA precursors and small RNAs, such as 5S rRNA and tRNAs, respectively.SUBUNIT Component of the RNA polymerase I (Pol I) and RNA polymerase III (Pol III) complexes consisting of 14 and 17 subunits, respectively. Interacts with the AC40 subunit.MISCELLANEOUS Present with 8680 molecules/cell in log phase SD medium.SIMILARITY Belongs to the archaeal RpoL/eukaryotic RPB11/RPC19 RNA polymerase subunit family.
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_10169.1
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_10787.1
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Transcription Factor IIA beta chain - p19
Transcription Factor IIA alpha chain - p35
Transcription initiation factor IIA gamma chain
Transcription initiation factor TFIID 18 kDa subunit
Transcription initiation factor TFIID 70 kDa subunit
Transcription initiation factor IIB (General transcription factor TFIIB) (S300-II)
Phenylalanyl-tRNA synthetase alpha chain
Insulin signalling and the regulation of glucose and lipid metabolism
Functional properties and genomics of glucose transporters
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Basic Medical Biochemistry: A Clinical Approach, 2nd ed (Book): 527
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Transcription initiation protein SPT4 homolog 1
ER-mediated phagocytosis: a new membrane for new functions
DNA-directed RNA polymerases I, II, and III 27 kDa polypeptide
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Transcription initiation factor IIE, alpha subunit
General transcription factor IIE 56 kDa subunit
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Primary structure of human triosephosphate isomerase
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Transcription initiation factor TFIID 100 kDa subunit
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Transcription initiation factor TFIID 30 kDa subunit
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Transcription initiation factor TFIID 28 kDa subunit
Transcription initiation factor TFIID 20/15 kDa subunits
Transcription initiation factor TFIID 250 kDa subunit
Characterization of the human mitochondrial methionyl-tRNA synthetase
Purification and properties of uroporphyrinogen I synthase from human erythrocytes. Identification of stable enzyme-substrate intermediates.
Biochemical Pathways - An Atlas of Biochemistry and Molecular Biology
Biochemistry - The Chemical Reactions of Living Cells 2nd Edn.
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.
Lehninger - Principles of Biochemistry 4th Edn.
Transport of inorganic cations/anions and amino acids/oligopeptides
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Role of LAT2/NTAL/LAB on calcium mobilization
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Euplotes telomerase: evidence for limited base-pairing during primer elongation and dGTP as an effector of translocation
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Requirement of the DEAD-Box protein ded1p for messenger RNA translation.
Isocitrate dehydrogenase (NAD) subunit alpha, mitochondrial precursor
Aconitate hydratase, mitochondrial precursor
Isocitrate dehydrogenase (NAD) subunit gamma, mitochondrial precursor
Isocitrate dehydrogenase (NAD) subunit beta, mitochondrial precursor
Pyruvate dehydrogenase E1 component beta subunit, mitochondrial precursor
pyruvate dehydrogenase E1 beta apoprotein
pyruvate dehydrogenase E1 alpha apoprotein
Pyruvate dehydrogenase E1 component alpha subunit, somatic form, mitochondrial precursor
Activation of DNA-binding activity in an apparently cytoplasmic precursor of the NF-kappa B transcription factor
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 protein X component, mitochondrial precursor
Dihydrolipoamide dehydrogenase-binding protein of pyruvate dehydrogenase complex
pyruvate dehydrogenase complex X component (E3 binding protein)
2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor
alpha-ketoglutarate dehydrogenase E1 apoenzyme
An integrated genomic analysis of human glioblastoma multiforme
Phosphoinositides in cell regulation and membrane dynamics
Dihydrolipoamide dehydrogenase, mitochondrial
Facilitated recycling pathway for RNA polymerase III.
Isolation and characterization of the human pyruvate kinase M gene
Succinate Dehydrogenase complex subunit C
Succinate-ubiquinone oxidoreductase cytochrome B large subunit
Succinate dehydrogenase cytochrome b560 subunit, mitochondrial precursor
Succinate dehydrogenase (ubiquinone) iron-sulfur protein, mitochondrial
Succinate Dehydrogenase complex subunit B
Succinate Dehydrogenase complex subunit A
Succinate dehydrogenase (ubiquinone) flavoprotein subunit, mitochondrial
The catalytic mechanism of guanine nucleotide exchange factor action and competitive inhibition by phosphorylated eukaryotic initiation factor 2.
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
Cloning and characterization of DPPL1 and DPPL2, representatives of a novel type of mammalian phosphatidate phosphatase
2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial ecNumber2.1.1.201/ecNumber
Ectonucleotide pyrophosphatase/phosphodiesterase family member 7
Para-hydroxybenzoate--polyprenyltransferase, mitochondrial
Ubiquinone biosynthesis monooxygenase COQ6 ecNumber1.14.13.-/ecNumber
Hexaprenyldihydroxybenzoate methyltransferase, mitochondrial ecNumber2.1.1.114/ecNumber
CATALYTIC ACTIVITY Acetyl-CoA + H(2)O + oxaloacetate = citrate + CoA.PATHWAY Carbohydrate metabolism; tricarboxylic acid cycle; isocitrate from oxaloacetate: step 1/2.MISCELLANEOUS Citrate synthase is found in nearly all cells capable of oxidative metabolism.SIMILARITY Belongs to the citrate synthase family.
1-phosphatidylinositol-3-phosphate 5-kinase
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
Regulation of APC/C activators between G1/S and early anaphase
Multidrug resistance-associated protein 1
Crystal structure of human tryptophanyl-tRNA synthetase catalytic fragment: insights into substrate recognition, tRNA binding, and angiogenesis activity
The porphobilinogen synthase catalyzed reaction mechanism
Production of phosphatidylinositol 5-phosphate by the phosphoinositide 3-phosphatase myotubularin in mammalian cells
Effects of cyclic GMP on smooth muscle relaxation
Human cytidine deaminase: purification of enzyme, cloning, and expression of its complementary DNA
Retinoids for treatment of retinal diseases
FUNCTION Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core, and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Subunits alpha and beta form the catalytic core in F(1). Rotation of the central stalk against the surrounding alpha(3)beta(3) subunits leads to hydrolysis of ATP in three separate catalytic sites on the beta subunits.CATALYTIC ACTIVITY ATP + H(2)O + H(+)(In) = ADP + phosphate + H(+)(Out).SUBUNIT F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c.MISCELLANEOUS Present with 164000 molecules/cell in log phase SD medium.SIMILARITY Belongs to the ATPase alpha/beta chains family.
Mechanisms, regulation and consequences of protein SUMOylation
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
The t(6;8)(q27;p11) translocation in a stem cell myeloproliferative disorder fuses a novel gene, FOP, to fibroblast growth factor receptor 1
Purification and properties of phosphoribosyl pyrophosphate synthetase from rat liver
Identification and characterization of human PMP34, a protein closely related to the peroxisomal integral membrane protein PMP47 of Candida boidinii
A GDP dissociation inhibitor that serves as a GTPase inhibitor for the Ras-like protein CDC42Hs
p53-Independent G1/S DNA damage checkpoint
Beta-arrestin-mediated activation of MAPK by inverse agonists reveals distinct active conformations for G protein-coupled receptors
Ribose-5-phosphate isomerase deficiency: new inborn error in the pentose phosphate pathway associated with a slowly progressive leukoencephalopathy
Human intestinal glucose transporter expression and localization of GLUT5
Identification of a human mitochondrial ABC transporter, the functional orthologue of yeast Atm1p
RNA Polymerase I Transcription Initiation
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
FUNCTION Multifunctional protein that exhibits several independent functions at different levels of the cellular processes. 5'-3' exonuclease component of the nonsense-mediated mRNA decay (NMD) which is a highly conserved mRNA degradation pathway, an RNA surveillance system whose role is to identify and rid cells of mRNA with premature termination codons and thus prevents accumulation of potentially harmful truncated proteins. The NMD pathway has a second role regulating the decay of wild-type mRNAs, and especially mRNAs that are important for telomere functions. Participate in CTH2-mediated and VTS1-mediated mRNA turnover. Involved in the degradation of several hypomodified mature tRNA species and participates in the 5'-processing or the degradation of the snoRNA precursors and rRNA processing. Involved in defense against virus and suppresses viral RNA recombination by rapidly removing the 5'-truncated RNAs, the substrates of recombination, and thus reducing the chance for recombination to occur in the parental strain. Required for the assembly of the virus-like particles of the Ty3 retrotransposon and contributes to the efficient generation of narnavirus 20S RNA by playing a major role in the elimination of the non-viral upstream sequences from the primary transcripts. Degrades single-stranded DNA (ss-DNA) and can renature complementary ss-DNA as well as catalyzes the formation of heteroduplex DNA from circular ss-DNA and homologous linear ds-DNA in vitro. Acts as a microtubule-associated protein which interacts with cytoplasmic microtubules through beta-tubulin and promotes in vitro assembly of tubulin into microtubules. Associates with microtubule functions such as chromosome transmission, nuclear migration, and SPB duplication. Has also a role in G1 to S transition and is involved in nuclear fusion during karyogamy. Required for the expression of ROK1 at the post-transcriptional level and for the alpha-factor induction of the karyogamy genes KAR3 and KAR4. Plays a role in filamentous growth.COFACTOR Magnesium. Both strand exchange and nuclease activities require magnesium, for the strand exchange activity, calcium can replace magnesium when the linear ds-DNA has been first resected with an exogenous endonuclease.ENZYME REGULATION 3'-phosphoadenosine 5'-phosphate (pAp) is an inhibitor of KEM1. Sodium-induced GCN4 expression reduces pAp accumulation by activating HAL2 expression, and therefore maintains mRNA degradation capacity which is likely to be important for the accurate and rapid adaptation of gene expression to salt stress.DISRUPTION PHENOTYPE Mutations affect nuclear fusion, leed to reduced chromosome stability and defects in spindle pole body duplication and/or separation as well as loss of viability under conditions of nitrogen starvation. Homozygous diploids are unable to sporulate. Leads also to arrest in pachytene and deficiency in meiotic recombination and sensitivity to oleate.MISCELLANEOUS Present with 11700 molecules/cell in log phase SD medium.SIMILARITY Belongs to the 5'-3' exonuclease family.
Vertebrates have conserved capping protein alpha isoforms with specific expression patterns
Current knowledge of the large RhoGAP family of proteins
Anomalous megakaryocytopoiesis in mice with mutations in the c-Myb gene
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
A direct role for sterol regulatory element binding protein in activation of 3-hydroxy-3-methylglutaryl coenzyme A reductase gene
The eicosanoids: cyclooxygenase, lipoxygenase, and epoxygenase pathways
Biochemistry of Lipids, Lipoproteins and Membranes, 5th Edition (Book): 331-362
Active Wnt proteins are secreted on exosomes
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.
Accurate cleavage and polyadenylation of exogenous RNA substrate.
ChEBI:28477 7alpha,12alpha-dihydroxycholest-4-en-3-one
Alcohol dehydrogenases, aldehyde dehydrogenases, and related enzymes
Purification and properties of human cytosolic folylpoly-gamma-glutamate synthetase and organization, localization, and differential splicing of its gene
Nicotinamide mononucleotide adenylyltransferase 1
The yeast mitochondrial protein import receptor Mas20p binds precursor proteins through electrostatic interaction with the positively charged presequence
Nicotinate-nucleotide pyrophosphorylase (carboxylating)
Pyruvate carboxylase, mitochondrial precursor
TIRAP/Mal, TRIF and TRAM. Differential utilization of these TIR
Biotin--protein ligase ecNumber6.3.4.-/ecNumber
Phosphopantothenoylcysteine decarboxylase
Toll-like receptor 3: a link between toll-like receptor, interferon and viruses
Regulation of the cyclin E gene by transcription factor E2F1
Glutathione reductase, mitochondrial precursor
FAD1 flavin adenine dinucleotide synthetase homolog
Ectonucleotide pyrophosphatase/phosphodiesterase 1
Guanylate kinase (EC 2.7.4.8) (GMP kinase)
deoxythymidylate kinase (thymidylate kinase)
Adenylate kinase isoenzyme 2, mitochondrial
Adenylate kinase isoenzyme 2, mitochondrial (EC 2.7.4.3) (ATP-AMP transphosphorylase)
Adenylate kinase isoenzyme 5 (EC 2.7.4.3) (ATP-AMP transphosphorylase)
Molecular scanning of insulin-responsive glucose transporter (GLUT4) gene in NIDDM subjects
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
Assembly of the RAD51-ssDNA nucleoprotein complex
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))
Adenylate kinase isoenzyme 1 (EC 2.7.4.3) (ATP-AMP transphosphorylase) (AK1) (Myokinase)
Dihydroorotate dehydrogenase, mitochondrial precursor
Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdehase) (Fragment)
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
AMP deaminase 3 (EC 3.5.4.6) (AMP deaminase isoform E) (Erythrocyte AMP deaminase)
Heterotrimeric G protein activation by G-protein-coupled receptors
Constitutive receptor activation by Crouzon syndrome mutations in fibroblast growth factor receptor (FGFR)2 and FGFR2/Neu chimeras
AMP deaminase 2 (EC 3.5.4.6) (AMP deaminase isoform L)
AMP deaminase 1 (EC 3.5.4.6) (Myoadenylate deaminase) (AMP deaminase isoform M)
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
FUNCTION DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RBP10 is part of the core element with the central large cleft.SUBUNIT Component of the RNA polymerase I (Pol I), RNA polymerase II (Pol II) and RNA polymerase III (Pol III) complexes consisting of 14, 12 and 17 subunits, respectively.MISCELLANEOUS Present with 5300 molecules/cell in log phase SD medium.SIMILARITY Belongs to the archaeal RpoN/eukaryotic RPB10 RNA polymerase subunit family.
FUNCTION Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative helicase essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells. The active ATPase sites in the MCM2-7 ring are formed through the interaction surfaces of two neighboring subunits such that a critical structure of a conserved arginine finger motif is provided in trans relative to the ATP-binding site of the Walker A box of the adjacent subunit. The six ATPase active sites, however, are likely to contribute differentially to the complex helicase activity. Once loaded onto DNA, double hexamers can slide on dsDNA in the absence of ATPase activity. Necessary for cell growth.CATALYTIC ACTIVITY ATP + H(2)O = ADP + phosphate.SUBUNIT Component of the MCM2-7 complex. The complex forms a toroidal hexameric ring with the proposed subunit order MCM2-MCM6-MCM4-MCM7-MCM3-MCM5; loaded onto DNA, forms a head-head double hexamer. Interacts with CSM1.MISCELLANEOUS Present with 35100 molecules/cell in log phase SD medium.MISCELLANEOUS Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY Belongs to the MCM family.SIMILARITY Contains 1 MCM domain.
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
Phosphodiesterase: overview of protein structures, potential therapeutic applications and recent progress in drug development
Coenzyme Q biosynthesis: Coq6 is required for the C5-hydroxylation reaction and substrate analogs rescue Coq6 deficiency
Human TLR9 confers responsiveness to bacterial DNA via species-specific CpG motif recognition
Processive DNA helicase activity of the minichromosome maintenance proteins 4, 6, and 7 complex requires forked DNA structures
Electron Transfer Flavoprotein beta subunit
Phosphoribosylformylglycinamidine synthase
Formylglycinamide ribotide amidotransferase
phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase
Trifunctional purine biosynthetic protein adenosine-3 (Includes: Phosphoribosylamine--glycine ligase (EC 6.3.4.13) (GARS) (Glycinamide ribonucleotide synthetase) (Phosphoribosylglycinamide synthetase); Phosphoribosylformylglycinamidine cyclo-ligase (EC 6.3.3.1) (AIRS) (Phosphoribosyl-aminoimidazole synthetase) (AIR synthase); Phosphoribosylglycinamide formyltransferase (EC 2.1.2.2) (GART) (GAR transformylase) (5'-phosphoribosylglycinamide transformylase))
Trifunctional purine biosynthetic protein adenosine-3
5'-phosphoribosylglycinamide transformylase
Phosphoribosylformylglycinamidine cyclo-ligase
Phosphoribosylglycinamide formyltransferase
Phosphoribosyl-aminoimidazole synthetase
Glutamine phosphoribosylpyrophosphate amidotransferase
Amidophosphoribosyltransferase precursor (EC 2.4.2.14) (Glutamine phosphoribosylpyrophosphate amidotransferase) (ATASE) (GPAT)
Amidophosphoribosyltransferase precursor
phosphoribosyl pyrophosphate amidotransferase
Enzymic properties of different types of human erythrocyte glucose-6-phosphate dehydrogenase, with characterization of two new genetic variants
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Porcupine homolog is required for canonical Wnt signaling and gastrulation in mouse embryos
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Purification and properties of carnitine acetyltransferase from human liver
Execution of nonsense-mediated mRNA decay: what defines a substrate?
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Role of gastrin peptides in carcinogenesis
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Purification of deoxyribonucleic acid polymerase delta from calf thymus: partial characterization of physical properties.
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A bridging [4Fe-4S] cluster and nucleotide binding are essential for function of the Cfd1-Nbp35 complex as a scaffold in iron-sulfur protein maturation
Import of palmitoyl-CoA into the mitochondrial matrix
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Human GMP synthetase. Protein purification, cloning, and functional expression of cDNA
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The predicted ATP-binding domains in the hexose transporter GLUT1 critically affect transporter activity.
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From hematopoietic stem cells to platelets
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Rho GTPases have diverse effects on the organization of the actin filament system
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H2S biogenesis by human cystathionine gamma-lyase leads to the novel sulfur metabolites lanthionine and homolanthionine and is responsive to the grade of hyperhomocysteinemia
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Cloning, sequencing and expression of a cDNA encoding mammalian valyl-tRNA synthetase
Epidermal growth factor receptors harboring kinase domain mutations associate with the heat shock protein 90 chaperone and are destabilized following exposure to geldanamycins
Human Myt1 is a cell cycle-regulated kinase that inhibits Cdc2 but not Cdk2 activity
Regulation and dysregulation of aquaporins in water balance disorders
ChEBI:53020 (Glc)2 (GlcNAc)2 (Man)9 (PP-Dol)1
ChEBI:53019 (Glc)3 (GlcNAc)2 (Man)9 (PP-Dol)1
Activation of Chaperone Genes by XBP1(S)
Vitamin C: biosynthesis, recycling and degradation in mammals
The structure of human mitochondrial branched-chain aminotransferase.
Acta Crystallogr D Biol Crystallogr 57:506-15
The role of aminoacyl-tRNA synthetases in genetic diseases
Oligomeric structure of the multifunctional protein CAD that initiates pyrimidine biosynthesis in mammalian cells
Purification and some properties of inorganic pyrophosphatase from human erythrocytes
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
A DNA helicase activity is associated with an MCM4, -6, and -7 protein complex.
Dock180 and ELMO1 proteins cooperate to promote evolutionarily conserved Rac-dependent cell migration
Functional properties of a Drosophila homolog of the E2F1 gene
Mitochondrial disulfide bond formation is driven by intersubunit electron transfer in Erv1 and proofread by glutathione
ChEBI:27403 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA
Mechanistic studies on phosphopantothenoylcysteine decarboxylase: trapping of an enethiolate intermediate with a mechanism-based inactivating agent
Indoleamine 2,3-dioxygenase. Purification and some properties
Selective inhibition of 2-AG hydrolysis enhances endocannabinoid signaling in hippocampus
The MRN complex: coordinating and mediating the response to broken chromosomes.
RNA polymerase III Transcription Complexes
Transcriptional Regulation, eds. McKnight, S.L., Yamamoto, K.R. 22:247-280
Enzymatic hydration of leukotriene A4. Purification and characterization of a novel epoxide hydrolase from human erythrocytes
Identification of the signal directing Tim9 and Tim10 into the intermembrane space of mitochondria
Removal of licensing factors from origins
The mechanism of PAK activation. Autophosphorylation events in both regulatory and kinase domains control activity
Nitric oxide stimulates guanylate cyclase
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).
Raf and akt mediate distinct aspects of sensory axon growth
GTP-AMP phosphotransferase, also called Adenylate kinase 3 catalyzes phosphate transfer from GTP to AMP (EC 2.7.4.10). A crystal structure is available (Choe et al. 2005).
F-actin-capping protein binds in a Ca2+-independent manner to the fast growing ends of actin filaments (barbed end) thereby blocking the exchange of subunits. Unlike other capping proteins (such as gelsolin and severin), they do not sever actin filaments.
Members of the Dedicator of cytokinesis (DOCK) family, also known as the Dock180 superfamily, are Rho GTPase guanine nucleotide exchange factors (GEFs), modulating Rho GTPase activity (Cote & Vuori 2002). All eleven human members share the presence of two evolutionarily conserved protein domains, termed DHR-1 and DHR-2 (Cote & Vuori 2007). The DHR-2 domains of several DOCKs interact with the nucleotide-free forms of Rho GTPases, intermediates in the catalytic reaction leading to the exchange of GDP for GTP. DHR-2 domains have been shown necessary and sufficient to promote specific guanine nucleotide exchange on various Rho GTPases, both in vitro and in vivo. Inactivation of the DHR-2 domain in DOCK1 (Dock180) has been shown to block Rac activation, cell migration and phagocytosis (Brugnera et al. 2002, Grimsley et al. 2004, Cote & Vuori 2002). The DHR-1 domain of DOCK1 was shown to mediate a specific interaction with PIP2 and PIP3 signaling lipids in vitro and in cells (Cote et al. 2005). Mutations of the DOCK1 DHR-1 domain blocked Rac-dependent cell elongation and cell migration suggesting that the role of DHR-1 is to position DOCK1 at sites of PIP3 production by PI3-kinase, coupling this to Rac signaling (Cote & Vuori 2007).
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.
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).
Chromokinesins consist of the kinesin-4 and kinesin-10 families.They act in various steps of mitosis, including chromosome condensation, metaphase alignment, chromosome segregation and cytokinesis (Mazumdar & Misteli 2005). Both families consist of homodimeric microtubule-based plus-end directed motor proteins (Sekine et al. 1994, Yajima et al. 2003).
Identification of 3-methoxy-4-hydroxy-5-hexaprenylbenzoic acid as a new intermediate in ubiquinone biosynthesis by Saccharomyces cerevisiae
Kinesin-8 is a plus-end-directed dimeric kinesin with an internal motor domain (Loughlin et al. 2008) that can depolymerize stable microtubuless specifically at their plus-ends (Pereira et al. 1997) in a length-dependent manner (Varga et al. 2006). Human kinesin-8 KIF18A is believed to promote chromosome congression by attenuating chromosome oscillation magnitudes (Stumpff et al. 2008).
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).
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
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.
Cancer-associated IDH1 mutations produce 2-hydroxyglutarate
FUNCTION Methyltransferase required for the conversion of 2-polyprenyl-6-methoxy-1,4-benzoquinol (DDMQH2) to 2-polyprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQH2).CATALYTIC ACTIVITY S-adenosyl-L-methionine + 2-methoxy-6-all-trans-polyprenyl-1,4-benzoquinol = S-adenosyl-L-homocysteine + 6-methoxy-3-methyl-2-all-trans-polyprenyl-1,4-benzoquinol.PATHWAY Cofactor biosynthesis; ubiquinone biosynthesis.MISCELLANEOUS Present with 8100 molecules/cell in log phase SD medium.SIMILARITY Belongs to the methyltransferase superfamily. UbiE family.
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.
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'.
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.
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.
After Platelet activation '78 kDa glucose-regulated protein' from the endoplasmic reticulum lumen is released in to the extracellular platelet releasate.
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.
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.
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.
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.
Vav3 is a guanine nucleotide exchange factors (GEF) for RhoA, RhoB and to a lesser extent Rac1.
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.
Nitric Oxide (NO) inhibits smooth muscle cell proliferation and migration, oxidation of low-density lipoproteins, and platelet aggregation and adhesion. It can stimulate vasodilatation of the endothelium, disaggregation of Â preformed platelet aggregates and inhibits activated platelet recruitment to the aggregate. NO is synthesized from L-arginine by a family of isoformic enzymes known as nitric oxide synthase (NOS). Three isoforms, namely endothelial, neuronal, and inducible NOS (eNOS, nNOS, and iNOS, respectively), have been identified. The eNOS isoform is found in the endothelium and platelets. NO regulation of cyclic guanosine-3,5-monophosphate (cGMP), via activation of soluble guanylate cyclase, is the principal mechanism of negative control over platelet activity. Defects in this control mechanism have been associated with platelet hyperaggregability and associated thrombosis.
Cyclic guanosine monophosphate (cGMP) is an important secondary messenger synthesized by guanylate cyclases. cGMP has effects on phosphodiesterases (PDE), ion-gated channels, and the cGMP-dependent protein kinases (cGK, Protein Kinase G or PKG). It is involved in regulation of several physiological functions including vasodilation, platelet aggregation and neurotransmission. Elevation of intracellular cGMP activates PKG (Haslam et al. 1999) which regulates several intracellular molecules and pathways including the vasodilator-stimulated phosphoprotein (VASP) (Halbrugge et al. 1990) and the ERK pathway (Hood and Granger 1998, Li et al. 2001). cGMP mediates nitric oxide (NO)-induced vascular smooth muscle relaxation (Furchgott and Vanhoutte 1989). Phosphodiesterase 5 (PDE5) hydrolyzes cGMP; the PDE5 inhibitor sildenafil (Viagra) increases intracellular cGMP and thereby can be used as a treatment for erectile dysfunction (Corbin and Francis 1999). The role of the cGMP and PKG in platelet activation was controversial as increases in platelet cGMP levels were observed in response to both platelet agonists (thrombin, ADP or collagen) and inhibitors (NO donors such as sodium nitroprusside), but it is currently accepted that PKG inhibits platelet activation (Haslam et al. 1999). Consistent with this, nitric oxide (NO) donors that inhibit platelet activation enhance intracellular cGMP (Haslam et al. 1999). cGMP also plays an important stimulatory role in GPIb-IX-mediated platelet activation. Platelet responses to cGMP have been proposed to be biphasic, consisting of an early stimulatory response that promotes platelet activation followed by a delayed platelet inhibition that serves to limit the size of platelet aggregates (Li et al 2003).
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
Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhesion and activation, suppresses coagulation, enhances fibrin cleavage and is anti-inflammatory in character. Under acute vascular trauma, vasoconstrictor mechanisms predominate and the endothelium becomes prothrombotic, procoagulatory and proinflammatory in nature. This is achieved by a reduction of endothelial dilating agents: adenosine, NO and prostacyclin; and by the direct action of ADP, serotonin and thromboxane on vascular smooth muscle cells to elicit their contraction (Becker et al. 2000). Cyclooxygenase-2 (COX-2) and endothelial nitric oxide synthase (eNOS) are primarily expressed in endothelial cells. Both are important regulators of vascular function. Under normal conditions, laminar flow induces vascular endothelial COX-2 expression and synthesis of Prostacyclin (PGI2) which in turn stimulates endothelial Nitric Oxide Synthase (eNOS) activity. PGI2 and NO both oppose platelet activation and aggregation, as does the CD39 ecto-ADPase, which decreases platelet activation and recruitment by metabolizing platelet-released ADP.
RNA Polymerase II Transcription Elongation
Fine-tuning of GPCR activity by receptor-interacting proteins
E2F-dependent accumulation of hEmi1 regulates S phase entry by inhibiting APC(Cdh1)
Mutations and polymorphisms in the human argininosuccinate synthetase (ASS1) gene
Mutations in MCT1 cDNA in patients with symptomatic deficiency in lactate transport
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Fcgamma receptors: old friends and new family members
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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.
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Aquaporin-9 (AQP9) and AQP10 are 6-pass transmembrane proteins that passively transport urea across the plasma membrane through a pore in each subunit of a homotetramer.
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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.
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Aquaporin-3 (AQP3) passively transports water and glycerol across the plasma membrane according to the osmotic gradient. AQP3 is expressed in airway epithelia, secretory glands, skin, the collecting ducts of the kidney, and the basolateral surface of intestinal epithelium..
Aquaporin-0 (AQP0, also known as MIP), AQP1, AQP2, AQP3, AQP4, AQP5, AQP7, AQP8, AQP9, and AQP10 are 6-pass transmembrane proteins that passively transport water across the plasma membrane according to the concentration gradient. Each molecule contains a water channel and subunits assemble into homotetramers. In principle water can move in either direction through an aquaporin, however in vivo flow may occur in only one direction. Conductance of water by AQP0 and AQP11 are low relative to other aquaporins.
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Aquaporin-3 (AQP3), AQP7, AQP9, and AQP10 are 6-pass transmembrane proteins that passively transport glycerol across the plasma membrane through a pore in each subunit of a homotetramer.
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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.
Nuclear organization of DNA replication initiation proteins in mammalian cells.
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
The ubiquitous octamer-binding protein Oct-1 contains a POU domain with a homeo box subdomain
A Toll-like receptor recognizes bacterial DNA
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The plasma membrane-associated protein SLC29A1 mediates the reversible transport of one molecule of adenosine, guanosine, inosine, or uridine from the cytosol to the extracellular space.
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The plasma membrane-associated protein SLC29A2 mediates the reversible transport of one molecule of adenine, adenosine, cytidine, cytosine, guanine, guanosine, hypoxanthine, inosine, thymidine, thymine, uracil, or uridine from the cytosol to the extracellular space.
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The plasma membrane-associated protein SLC29A2 mediates the reversible transport of one molecule of adenine, adenosine, cytidine, cytosine, guanine, guanosine, hypoxanthine, inosine, thymidine, thymine, uracil, or uridine from the extracellular space to the cytosol.
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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 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)
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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.
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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).
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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.
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The plasma membrane-associated protein SLC29A1 mediates the reversible transport of one molecule of adenosine, cytosine, guanosine, inosine, thymidine, or uridine from the extracellular space to the cytosol.
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This pathway groups the processes mediated by SLC transporters, by which vitamins and cofactors, as well as nucleosides, nucleotides, nucleobases, and related molecules cross lipid bilayer membranes.
Long chain fatty acids (LCFAs) are involved in many cellular functions. They can be used as an important source of energy by skeletal muscle and heart tissues. Also, they are used in the production of hormones which can regulate inflammation, blood pressure, the clotting process, blood lipid levels and the immune response. Fatty acid transporter proteins (FATPs) are a family of proteins which mediate fatty acid uptake into cells when overexpressed. FATPs also possess enzymatic activity, the details of which are captured elsewhere. There are 6 human genes of the SLC27A family which encode for FATP1-6 (Stahl A, 2004; Gimeno RE, 2007). To date, only FATP1, 4 and 6 have demonstrable transporter function. Fatty acids with carbon chain lengths of more than 10 are the most likely substrates for these transporters.
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Two families of transport proteins mediate the movement of nucleosides and free purine and pyrimidine bases across the plasma membrane. Equilibrative nucleoside transporters allow the movement of these molecules along concentration gradients into or out of cells (Baldwin et al. 2003); concentrative nucleoside transporters actively transport nucleosides into cells by coupling their transport to the inward movement of sodium ions (Gray et al. 2003). Of the four human equilibrative nucleoside transporters, two are well characterized. SLC29A1 (solute carrier family 29 (nucleoside transporters), member 1) mediates the transport of nucleosides across the plasma membrane. SLC29A2 (solute carrier family 29 (nucleoside transporters), member 2) mediates the transport of both nucleosides and free bases. Transporter specificities were determined by expressing cloned human genes in Xenopus oocytes or in mammalian cultured cell lines whose own nucleotide transporters had been disrupted by mutation. These studies establish that the transport processes are specific and saturable, and that the multiple nucleotides and bases compete for a single binding site on each transporter. Some features of SLC29A2 specificity are complex. For example, in the Xenopus oocyte system, radiolabeled uracil and adenine are taken up, and an excess of either molecule inhibits uptake of radiolabeled hypoxanthine, while in the cultured mammalian cell system, neither adenine nor uracil can inhibit uptake of radiolabeled uridine. If these results reflect ENT2 function in vivo, they indicate that the net movement of a nucleoside or base across the cell membrane is determined not only by its own concentrations in the extracellular space and the cytosol, but also by the concentrations of the other nucleosides and bases competing for access to the transporter. The human genome encodes three concentrative transporters, SLC28A1, 2, and 3 (solute carrier family 28 (sodium-coupled nucleoside transporter), member 1, 2, and 3). All three genes have been cloned, and expression of the human proteins in Xenopus oocytes has allowed their transport properties to be determined. SLC28A1 mediates the uptake of pyrimidine nucleosides and adenosine (Ritzel et al. 1997); SLC28A2 the uptake of purine nucleosides and uridine (Wang et al. 1997); and SLC28A3 the uptake of purine and pyrimidine nucleosides (Ritzel et al. 2001). Amino acid sequence motifs that determine the specificities of these transporters have been identified in studies of chimeric and mutant proteins (Loewen et al. 1999). SLC28A3 protein co-transports two sodium ions per nucleoside; SLC28A1 and 2 transport one sodium per nucleoside (Ritzel et al. 2001). Physiological roles for nucleoside and base transport include provision of nucleosides to cells with little capacity to synthesize these molecules de novo, and regulation of extracellular levels of adenosine, which is released from muscle during intense exercise and has signaling properties. In kidney and intestinal epithelia, the combination of apically localized CNT transporters and basolaterally localized ENT transporters provides a mechanism for net transport of nucleosides (Mangravite et al. 2003). These transporters also mediate the uptake of nucleoside analogs used clinically as anti-viral and anti-tumor drugs. Orthologs of human concentrative and equilibrative transporter proteins have been identified in many eukaryotes, but functional studies of transporters even from organisms closely related to humans (e.g. rat, Gerstin et al. 2002) have revealed differences in substrate specificities. Prediction of drug uptake and other functions of these molecules by human - model organism orthology is thus risky.
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).
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)
The human gene SLC29A3 encodes the equilibrative nucleoside transporter 3 (ENT3). It is abundant in many tissues, especially the placenta and is localized intracellularly on the lysosomal membrane. ENT3 mediates the reversible transport of nucleosides and the nucleobase adenine (Baldwin SA et al, 2005). Defects in SLC29A3 are the cause of H syndrome, an autosomal recessive disorder(Molho-Pessach V et al, 2008).
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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).
Of the six fatty acid transporter proteins (FATP) characterized, only three have been shown to mediate the influx into cells of long chain fatty acids (LCFAs); FATP1, 4 and 6. They have been shown to transport the prototypical LCFA oleic acid (OLEA) but are believed to be able to transport LCFAs with chain lengths longer than 10 carbons. FATP1 is highly expressed in adipose tissue and muscle (Hatch GM et al, 2002). FATP4 is the major intestinal LCFA transporter (Fitscher BA et al, 1998; Stahl A et al, 1999). FATP6 is localized to cardiac myocytes (Gimeno RE et al, 2003).
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The human gene SLC35B4 encodes the bifunctional UDP-xylose and UDP-N-acetylglucosamine transporter YEA4. YEA4 resides on the Golgi membrane and mediates the influx of UDP-xylose into the lumen (Ashikov A et al, 2005).
The human gene SLC35B4 encodes the bifunctional UDP-xylose and UDP-N-acetylglucosamine transporter YEA4. YEA4 resides on the Golgi membrane and mediates the influx of UDP-N-acetylglucosamine into the lumen (Ashikov A et al, 2005).
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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.
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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).
Oncogenic signaling from the hematopoietic growth factor receptors c-Kit and Flt3
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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.
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The ATP-binding cassette (ABC) superfamily of active transporters involves a large number of functionally diverse transmembrane proteins. They transport a variety of compounds through membranes against steep concentration gradients at the cost of ATP hydrolysis. These substrates include amino acids, lipids, inorganic ions, peptides, saccharides, peptides for antigen presentation, metals, drugs, and proteins. The ABC transporters not only move a variety of substrates into and out of the cell, but are also involved in intracellular compartmental transport. Energy derived from the hydrolysis of ATP is used to transport the substrate across the membrane against a concentration gradient. Human genome contains 48 ABC genes; 16 of these have a known function and 14 are associated with a defined human disease (Dean et al. 2001, Borst and Elferink 2002, Rees et al. 2009).
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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.
Cloning of a human cDNA for CTP-phosphoethanolamine cytidylyltransferase by complementation in vivo of a yeast mutant
The 70-kDa peroxisomal membrane protein (PMP70) and the adrenoleukodystrophy protein (ALDP) are half ATP binding cassette (ABC) transporters in the peroxisome membrane. Mutations in the ALD gene encoding ALDP result in the X-linked neurodegenerative disorder adrenoleukodystrophy (Roerig et al. 2001). They are involved in metabolic transport of long and very long chain fatty acids into peroxisomes. ATP binding/hydrolysis by and phosphorylation of PMP70 and ALDP are involved in the regulation of fatty acid transport into peroxisomes (Tanaka et al. 2002).
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).
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.
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A defined subset of the ABC transporter superfamily, the ABCA transporters, are highly expressed in monocytes and macrophages and are regulated by cholesterol flux which may indicate their role in in chronic inflammatory diseases (Schmitz and Kaminski 2001, Schmitz et al. 2000).
Once synthesized mRNA can be utilized until degraded. Degradation itself is the final mode of gene expression regulation.
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The human gene SLC30A1 encodes the zinc transporter ZnT1. It is widely expressed throughout the body and it's expression is regulated by zinc. ZnT1 is the only member of the SLC30 gene family that is located on the plasma membrane and mediates the transport of zinc out of the cell (Devergnas S et al, 2004).
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The human gene SLC30A5 encodes the zinc transporter ZnT5. This protein is widely expressed but is most abundant in pancreatic beta cells (Kambe T et al, 2002). In these cells, ZnT5 mediates the transport of zinc into secretory granules that contain insulin.
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Class II facilitative transporters consist of GLUT5, 7, 9 and 11 (Zhao FQ and Keating AF, 2007; Wood IS and Trayhurn P, 2003).
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Two gene families are responsible for glucose transport in humans. SLC2 (encoding GLUTs) and SLC5 (encoding SGLTs) families mediate glucose absorption in the small intestine, glucose reabsorption in the kidney, glucose uptake by the brain across the blood-brain barrier and glucose release by all cells in the body. Glucose is the main energy source used by cells to make energy. Im mammals, blood glucose levels are tightly controlled and glucose is taken up from interstitial fluid by a passive, facilitative transport driven by the diffusion gradient of glucose (and other sugars) across the plasma membrane. This process is mediated by a family of Na+-independent, facilitative glucose transporters (GLUTs) encoded by the SLC2A gene family (Zhao FQ and Keating AF, 2007; Wood IS and Trayhurn P, 2003). There are 14 members belonging to this family (GLUT1-12, 14 and HMIT (H+/myo-inositol symporter)). The GLUT family can be subdivided into three subclasses (I-III) based on sequence similarity and characteristic sequence motifs (Joost HG and Thorens B, 2001).
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The human SLC2A9 gene encodes two isoforms of class II facilitative glucose transporter 9; GLUT9 (Phay JE et al, 2000) and GLUT9DeltaN (Augustin R et al, 2004). GLUT9 is expressed mainly in kidney (proximal tubules of epithelial cells) and liver while GLUT9DeltaN is expressed mainly in kidney and placenta. As well as mediating the uptake of fructose and glucose (at a low rate), GLUT9 can also mediate the tranpsort of urate (uric acid), the end product of purine metabolism in humans and great apes (Vitart V et al, 2008). Mutations in SLC2A9 influence serum urate concentrations with excess serum accumulation of urate leading to the development of gout (Vitart V et al, 2008).
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SLC2A7 encodes GLUT7, a class II facilitative glucose transporter which was cloned from a human intestinal cDNA library (Li Q et al, 2004). It has a high affinity for glucose and fructose uptake. GLUT7 is found predominantly in the small intestine, colon, testis and prostate. SLC2A11 encodes GLUT11 (Doege H et al, 2001), another member of the class II facilitative glucose transporters. It has the highest similarity with GLUT5 and in humans, three isoforms are expressed (GLUT11A-C) (Sasaki T et al, 2001). Human GLUT11 has been shown to transport glucose and fructose but not galactose when expressed in Xenopus oocytes ( Scheepers A et al, 2005).
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The class I facilitative glucose transporters contain GLUT1-4. As well as glucose, these proteins can transport other hexoses such as fructose, galactose and glucosamine. GLUT1 was cloned from a HepG2 cell line (Mueckler M et al, 1985). GLUT1 is expressed by SLC2A1 mainly in brain and erythrocytes but is also expressed at lower levels in many other tissues containing endothelial and epithelial barriers. Defects in SLC2A1 are the cause of autosomal dominant GLUT1 deficiency syndrome which results in impaired glucose transport across the brain tissue barrier and is characterized by infantile seizures, delayed development and acquired microcephaly (Klepper J et al, 1999). GLUT2 is expressed by SLC2A2 and is a low affinity glucose transporter (Fukumoto H et al, 1988). It is expressed mainly in the kidney, liver and pancreatic beta-cells. In beta-cells, it functions as a glucose-sensor for insulin secretion and in the liver, it allows for bi-directional glucose transport. In this reaction, it is shown to mediate the influx of glucose. In the next reaction, it is shown to be mediating efflux of glucose. Defects in SLC2A2 are the cause of Fanconi-Bickel syndrome (FBS). It is characterized by hepatorenal glycogen accumulation, proximal renal tubular dysfunction, and impaired utilization of glucose and galactose (Burwinkel B et al, 1999). SLC2A3 encodes GLUT3 which is mainly expressed in the brain but also in a wide range of tissues. If has a high affinity for glucose and can also transport other sugars (Kayano T et al, 1988). GLUT4, encoded by SLC2A4, is an insulin-responsive glucose transporter found in heart, skeletal muscle, brain and adipose tissue. Due to its sensitivity to insulin, it may play a role in diabetes. In a non-insulin condition, GLUT4 is localized in intracellular GLUT4-containing vesicles. On insulin stimulation, GLUT4 translocates to the plasma membrane where it can increase glucose transport 10-20-fold (Fukumoto H et al, 1989). Defects in SLC2A4 may be a cause of non-insulin-dependent diabetes mellitus (NIDDM) (Kusari J et al, 1991; Choi WH et al, 1991).
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 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.
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.
Hemostasis is a physiological response that culminates in the arrest of bleeding from an injured vessel. Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhesion and activation, suppresses coagulation, enhances fibrin cleavage and is anti-inflammatory in character. Under acute vascular trauma, vasoconstrictor mechanisms predominate and the endothelium becomes prothrombotic, procoagulatory and proinflammatory in nature. This is achieved by a reduction of endothelial dilating agents: adenosine, NO and prostacyclin; and by the direct action of ADP, serotonin and thromboxane on vascular smooth muscle cells to elicit their contraction (Becker et al. 2000). The chief trigger for the change in endothelial function that leads to the formation of a haemostatic thrombus is the loss of the endothelial cell barrier between blood and extracellular matrix components (Ruggeri 2002). Circulating platelets identify and discriminate areas of endothelial lesions; here, they adhere to the exposed sub endothelium. Their interaction with the various thrombogenic substrates and locally generated or released agonists results in platelet activation. This process is described as possessing two stages, firstly, adhesion - the initial tethering to a surface, and secondly aggregation - the platelet-platelet cohesion (Savage & Cattaneo et al. 2001). Three mechansism contribute to the loss of blood following vessel injury. The vessel constricts, reducing the loss of blood. Platelets adhere to the site of injury, become activated and aggregate with fibrinogen into a soft plug that limits blood loss, a process termed primary hemostasis. Proteins and small molecules are released from granules by activated platelets, stimulating the plug formation process. Fibrinogen from plasma forms bridges between activated platelets. These events initiate the clotting cascade (secondary hemostasis). Negatively-charged phospholipids exposed at the site of injury and on activated platelets interact with tissue factor, leading to a cascade of reactions that culminates with the formation of an insoluble fibrin clot.
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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).
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c-Jun NH2 terminal kinase (JNK) plays a role in conveying signals from the cytosol to the nucleus, where they associate and activate their target transcription factors.
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C-Jun NH2 terminal kinases (JNKs) are an evolutionarily conserved family of serine/threonine protein kinases, that belong to mitogen activated protein kinase family (MAPKs - also known as stress-activated protein kinases, SAPKs). The JNK pathway is activated by heat shock, or inflammatory cytokines, or UV radiation. The JNKs are encoded by at least three genes: JNK1/SAPK-gamma, JNK2/SAPK-alpha and JNK3/ SAPK-beta. The first two are ubiquitously expressed, whereas the JNK3 protein is found mainly in brain and to a lesser extent in heart and testes. As a result of alternative gene splicing all cells express distinct active forms of JNK from 46 to 55 kDa in size. Sequence alignment of these different products shows homologies of >80%. In spite of this similarity, the multiple JNK isoforms differ in their ability to bind and phosphorylate different target proteins, thus leading to the distinctive cellular processes: induction of apoptosis, or enhancment of cell survival, or proliferation. Activation of JNKs is mediated by activated TAK1 which phosphorylates two dual specificity enzymes MKK4 (MAPK kinase 4) and MKK7(MAPK kinase 7).
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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.
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p38 mitogen-activated protein kinase (MAPK) belongs to a highly conserved family of serine/threonine protein kinases. The p38 MAPK-dependent signaling cascade is activated by pro-inflammatory or stressful stimuli such as ultraviolet radiation, oxidative injury, heat shock, cytokines, and other pro-inflammatory stimuli. p38 MAPK exists as four isoforms (alpha, beta, gamma, and delta). Of these, p38alpha and p38beta are ubiquitously expressed while p38gamma and p38delta are differentially expressed depending on tissue type. Each isoform is activated by upstream kinases including MAP kinase kinases (MKK) 3, 4, and 6, which in turn are phosphorylated by activated TAK1 at the typical Ser-Xaa-Ala-Xaa-Thr motif in their activation loops. Once p38 MAPK is phosphorylated it activates numerous downstream substrates, including MAPK-activated protein kinase-2 and 3 (MAPKAPK-2 or 3) and mitogen and stress-activated kinase-1/2 (MSK1/2). MAPKAPK-2/3 and MSK1/2 function to phosphorylate heat shock protein 27 (HSP27) and cAMP-response element binding protein transcriptional factor, respectively. Other transcription factors, including activating transcription factor 2, Elk, CHOP/GADD153, and myocyte enhancer factor 2, are known to be regulated by these kinases.
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The mitogen activated protein kinase (MAPK) cascade, one of the most ancient and evolutionarily conserved signaling pathways, is involved in many processes of immune responses. The MAP kinases cascade transduces signals from the cell membrane to the nucleus in response to a wide range of stimuli (Chang and Karin, 2001; Johnson et al, 2002). There are three major groups of MAP kinases the extracellular signal-regulated protein kinases ERK1/2, the p38 MAP kinase and the c-Jun NH-terminal kinases JNK. ERK1 and ERK2 are activated in response to growth stimuli. Both JNKs and p38-MAPK are activated in response to a variety of cellular and environmental stresses. The MAP kinases are activated by dual phosphorylation of Thr and Tyr within the tripeptide motif Thr-Xaa-Tyr. The sequence of this tripeptide motif is different in each group of MAP kinases: ERK (Thr-Glu-Tyr); p38 (Thr-Gly-Tyr); and JNK (Thr-Pro-Tyr). MAPK activation is mediated by signal transduction in the conserved three-tiered kinase cascade: MAPKKKK (MAP4K or MKKKK or MAPKKK Kinase) activates the MAPKKK. The MAPKKKs then phosphorylates a dual-specificity protein kinase MAPKK, which in turn phosphorylates the MAPK. The dual specificity MAP kinase kinases (MAPKK or MKK) differ for each group of MAPK. The ERK MAP kinases are activated by the MKK1 and MKK2; the p38 MAP kinases are activated by MKK3, MKK4, and MKK6; and the JNK pathway is activated by MKK4 and MKK7. The ability of MAP kinase kinases (MKKs, or MEKs) to recognize their cognate MAPKs is facilitated by a short docking motif (the D-site) in the MKK N-terminus, which binds to a complementary region on the MAPK. MAPKs then recognize many of their targets using the same strategy, because many MAPK substrates also contain D-sites. The upstream signaling events in the TLR cascade that initiate and mediate the ERK signaling pathway remain unclear.
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Clinical, biochemical and molecular genetic correlations in adenylosuccinate lyase deficiency
Kinesin-14 proteins have a C-terminal motor domain. At least four members of the group (Dm Ncd, Sc KAR3, Cg CHO2, At KCBP) have been demonstrated to be minus-end directed motors (Walker et al. 1990), in contrast to the usual plus-end directed motility of other kinesin proteins. During spindle formation, Kinesin-14 cross-links antiparallel microtubules and slides them together (thereby generating inward forces) to balance the outward forces generated by plus-end-directed kinesins of the Kinesin-5 family. Kinesin-14 family members also gather microtubule minus-ends and focus them into spindle poles. Mutation or inhibition of Kinesin-14 family members often results in disordered or splayed meiotic spindle poles (Ambrose et al. 2005).
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).
Kinesins are a superfamily of microtubule-based motor proteins that have diverse functions in transport of vesicles, organelles and chromosomes, and regulate microtubule dynamics. There are 14 families of kinesins, all reprsented in humans. A standardized nomenclature was published in 2004 (Lawrence et al.).
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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.
The GLUT4 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The GLUT2 gene is transcribed, its mRNA is translated, and the protein product is localized to the plasma membrane. GLUT2 expression is positively regulated by HNF1A. In vivo, pancreatic GLUT2 expression is positively regulated by HNF1A. Mutations in HNF1A are associated with a form of MODY (maturity onset diabetes of the young) (Fanjans et al. 2001) and interactions between the HNF1A protein product and the GLUT2 promoter have been demomstrated in vitro (Ban et al. 2002). However, the molecular details of GLUT2 expression in intact pancreatic beta cells have not been studied in humans, but are inferred from corresponding ones worked out in the mouse.
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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).
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GEF what? Dock180 and related proteins help Rac to polarize cells in new ways
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Adipogenesis is the process of cell differentiation by which preadipocytes become adipocytes. During this process the preadipocytes cease to proliferate, begin to accumulate lipid droplets and develop morphologic and biochemical characteristics of mature adipocytes such as hormone responsive lipogenenic and lipolytic programs. The most intensively studied model system for adipogenesis is differentiation of the mouse 3T3-L1 preadipocyte cell line by an induction cocktail of containing mitogens (insulin/IGF1), glucocorticoid (dexamethasone), an inducer of cAMP (IBMX), and fetal serum (Cao et al. 1991, reviewed in Farmer 2006). More recently additional cellular models have become available to study adipogenesis that involve almost all stages of development (reviewed in Rosen and MacDougald 2006). In vivo knockout mice lacking putative adipogenic factors have also been extensively studied. Human pathways are traditionally inferred from those discovered in mouse but are now beginning to be validated in cellular models derived from human adipose progenitors (Fischer-Posovszky et al. 2008, Wdziekonski et al. 2011). Adipogenesis is controlled by a cascade of transcription factors (Yeh et al. 1995, reviewed in Farmer 2006, Gesta et al. 2007). One of the first observable events during adipocyte differentiation is a transient increase in expression of the CEBPB (CCAAT/Enhancer Binding Protein Beta, C/EBPB) and CEBPD (C/EBPD) transcription factors (Cao et al. 1991, reviewed in Lane et al. 1999). This occurs prior to the accumulation of lipid droplets. However, it is the subsequent inductions of CEBPA and PPARG that are critical for morphological, biochemical and functional adipocytes. Ectopic expression of CEBPB alone is capable of inducing substantial adipocyte differentiation in fibroblasts while CEBPD has a minimal effect. CEBPB is upregulated in response to intracellular cAMP (possibly via pCREB) and serum mitogens (possibly via Krox20). CEBPD is upregulated in response to glucocorticoids. The exact mechanisms that upregulate the CEBPs are not fully known. CEBPB and CEBPD act directly on the Peroxisome Proliferator-activated Receptor Gamma (PPARG) gene by binding its promoter and activating transcription. CEBPB and CEBPD also directly activate the EBF1 gene (and possibly other EBFs) and KLF5 (Jimenez et al. 2007, Oishi 2005). The EBF1 and KLF5 proteins, in turn bind, and activate the PPARG promoter. Other hormones, such as insulin, affect PPARG expression and other transcription factors, such as ADD1/SREBP1c, bind the PPARG promoter. This is an area of ongoing research. During adipogenesis the PPARG gene is transcribed to yield 2 variants. The adipogenic variant 2 mRNA encodes 30 additional amino acids at the N-terminus compared to the widely expressed variant 1 mRNA. PPARG encodes a type II nuclear hormone receptor (remains in the nucleus in the absence of ligand) that forms a heterodimer with the Retinoid X Receptor Alpha (RXRA). The heterodimer was initially identified as a complex regulating the aP2/FABP4 gene and named ARF6 (Tontonoz et al. 1994). The PPARG:RXRA heterodimer binds a recognition sequence that consists of two hexanucleotide motifs (DR1 motifs) separated by 1 nucleotide. Binding occurs even in the absence of ligands, such as fatty acids, that activate PPARG. In the absence of activating ligands, the PPARG:RXRA complex recruits repressors of transcription such as SMRT/NCoR2, NCoR1, and HDAC3 (Tontonoz and Spiegelman 2008). Each molecule of PPARG can bind 2 molecules of activating ligands. Although, the identity of the endogenous ligands of PPARG is unknown, exogenous activators include fatty acids and the thiazolidinedione class of antidiabetic drugs (reviewed in Berger et al. 2005, Heikkinen et al. 2007, Lemberger et al. 1996). The most potent activators of PPARG in vitro are oxidized derivatives of unsaturated fatty acids.. Upon binding activating ligands PPARG causes a rearrangement of adjacent factors: Corepressors such as SMRT/NCoR2 are lost and coactivators such as TIF2, PRIP, CBP, and p300 are recruited (Tontonoz and Spiegelman). PPARG also binds directly to the TRAP220 subunit of the TRAP/Mediator complex that recruits RNA polymerase II. Thus binding of activating ligand by PPARG causes transcription of PPARG target genes. Targets of PPARG include genes involved in differentiation (PGAR/HFARP, Perilipin, aP2/FABP4, CEBPA), fatty acid transport (LPL, FAT/CD36), carbohydrate metabolism (PEPCK-C, AQP7, GK, GLUT4), and energy homeostasis (LEPTIN and ADIPONECTIN) (Perera et al. 2006). Within 10 days of differentiation CEBPB and CEBPD are no longer located at the PPARG promoter. Instead CEBPA is present. EBF1 and PPARG bind the CEBPA promoter and activate transcription of CEBPA, one of the key transcription factors in adipogenesis. A current hypothesis posits a self-reinforcing loop that maintains PPARG expression and the differentiated state: PPARG activates CEBPA and CEBPA activates PPARG. Additionally EBF1 (and possibly other EBFs) activates CEBPA, CEBPA activates EBF1, and EBF1 activates PPARG.
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As a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are aspects of the roles of cell adhesion molecules in axonal guidance and myogenesis, of transcriptional regulation in hematopoiesis (specifically, B lymphopoiesis), pancreatic beta cell and white adipocyte differentiation, and molecular events of "nodal" signaling.
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CATALYTIC ACTIVITY (S)-lactate + 2 ferricytochrome c = pyruvate + 2 ferrocytochrome c + 2 H(+).COFACTOR FMN.COFACTOR Protoheme IX groups.SUBUNIT Homotetramer.INDUCTION By L-lactate. Induced during respiratory adaptation.MISCELLANEOUS Present with 4590 molecules/cell in log phase SD medium.SIMILARITY Contains 1 cytochrome b5 heme-binding domain.SIMILARITY Contains 1 FMN hydroxy acid dehydrogenase domain.
Endoplasmic reticulum-mediated phagocytosis is a mechanism of entry into macrophages
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.
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 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.
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).
Human cyclins A and B1 are differentially located in the cell and undergo cell cycle-dependent nuclear transport
Isolation of two cDNAs encoding functional human cytoplasmic cysteinyl-tRNA synthetase
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[Receptors for cholecystokinin and gastrin]
Mutations in phosphoinositide metabolizing enzymes and human disease
FUNCTION Essential core component of the TIM22 complex, a complex that mediates the import and insertion of multi-pass transmembrane proteins, such as mitochondrial carrier family members, into the mitochondrial inner membrane. In the TIM22 complex, it constitutes the voltage-activated and signal-gated channel. Forms a twin-pore translocase that uses the membrane potential as external driving force in 2 voltage-dependent steps. Mediates the insertion of precursor proteins in a 3 step process. After the precursor is tethered to the translocase without losing energy from the Delta(psi), 2 energy-requiring steps are needed. First, Delta(psi) acts on the precursor protein and promotes its docking in the translocase complex. Then, Delta(psi) and an internal signal peptide together induce rapid gating transitions in one pore and closing of the other pore and drive membrane insertion to completion.SUBUNIT Component of the TIM22 complex, whose core is composed of TIM18, TIM22 and TIM54, associated with the peripheral proteins MRS5/TIM12 and the 70 kDa heterohexamer composed of TIM9 and TIM10 (or TIM8 and TIM13).SIMILARITY Belongs to the Tim17/Tim22/Tim23 family.
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
Succinate dehydrogenase deficiency in human
QLS motif in transmembrane helix VII of the glucose transporter family interacts with the C-1 position of D-glucose and is involved in substrate selection at the exofacial binding site.
The human REV1 gene codes for a DNA template-dependent dCMP transferase.
Expression cloning of a Na+-independent aromatic amino acid transporter with structural similarity to H+/monocarboxylate transporters
Novel functions of acyl-CoA thioesterases and acyltransferases as auxiliary enzymes in peroxisomal lipid metabolism
Stem cell factor and its receptor c-Kit as targets for inflammatory diseases
Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding
Enzymic synthesis and breakdown of a pyrimidine, orotic acid. I. Dihydro-orotic dehydrogenase
Apocytochrome c requires the TOM complex for translocation across the mitochondrial outer membrane
Specific recognition of mitochondrial preproteins by the cytosolic domain of the import receptor MOM72
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
The genetics of mammalian circadian order and disorder: implications for physiology and disease
Signal transduction via the stem cell factor receptor/c-Kit
Tau-crystallin/alpha-enolase: one gene encodes both an enzyme and a lens structural protein
Localization of p21-activated kinase 1 (PAK1) to pseudopodia, membrane ruffles, and phagocytic cups in activated human neutrophils
Insertion of residues 429 to 822 at 340 from UniProt:P11362 FGFR1 (in Homo sapiens)
The roles of anabolic and catabolic reactions in the synthesis and recycling of polyunsaturated fatty acids
Prostaglandins Leukot Essent Fatty Acids 67:79-83
The disulfide relay system of mitochondria is required for the biogenesis of mitochondrial Ccs1 and Sod1
Translational silencing of ceruloplasmin requires the essential elements of mRNA circularization: poly(A) tail, poly(A)-binding protein, and eukaryotic translation initiation factor 4G
Human geranylgeranyl diphosphate synthase: isolation of the cDNA, chromosomal mapping and tissue expression
Human L-3-phosphoserine phosphatase: sequence, expression and evidence for a phosphoenzyme intermediate
Functional expression and characterisation of a new human phosphatidylinositol 4-kinase PI4K230
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'.
SOS is recruited to the plasma membrane and mediates activation of Ras.
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.
Mutations in ATP2C1, encoding a calcium pump, cause Hailey-Hailey disease
Release of phospho-IRS from the insulin receptor triggers a cascade of signalling events via PI3K, SOS, RAF and the MAP kinases.
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).
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).
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.
Release of phospho-SHC from the insulin receptor triggers a cascade of signalling events via SOS, RAF and the MAP kinases.
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).
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).
Once phosphorylated, S6K1-P phosphorylates and activates ribosomal protein S6 (rpS6), which in turn selectively increases the translation of 5ââ¬â¢TOP mRNAs. These mRNAs encode exclusively for components of the translation machinery (PMID 15809305).
S6K1 contains a TOS motif. mTORC1 requires an intact TOS motif to bind and phosphorylate S6K1 (PMID 15809305).
PAK and other Rho-associated kinases--effectors with surprisingly diverse mechanisms of regulation
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.
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).
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.
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.
The adaptor protein Frs2 (Fibroblast growth factor receptor substrate 2) can mediate the prolonged activation of the MAPK (ERK) cascade.
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.
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.
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.
SnapShot: motor proteins in spindle assembly
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.
CHIP28 water channels are localized in constitutively water-permeable segments of the nephron
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.
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.
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.
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).
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.
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.
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.
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.
L13a-mediated translational silencing of Ceruloplasmin expression
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The Tim54p-Tim22p complex mediates insertion of proteins into the mitochondrial inner membrane
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Crystal structure of human indoleamine 2,3-dioxygenase: catalytic mechanism of O2 incorporation by a heme-containing dioxygenase
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3-Hexaprenyl-4,5-dihydroxybenzoate [ChEBI:1509]
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ATP bound to the origin recognition complex is important for preRC formation.
Accumulation of calcium into the Golgi apparatus is mediated by sarco(endo)plasmic reticulum calcium-ATPases (SERCAs) and by secretory pathway calcium-ATPases (SPCAs). There are two human genes which encode SPCAs; ATP2C1 and ATP2C2 which encode magnesium-dependent calcium-transporting ATPase type 2C members 1 and 2 (ATP2C1 and 2) respectively (Sudbrak et al, 2000; Vanoevelen et al, 2005). Defects in ATP2C1 are the cause of Hailey-Hailey disease (HHD), an autosomal dominant disease characterized by persistent blisters and erosions of the skin (Hu et al, 2000).
The plasma membrane contains a broad range of lipids making up the bilayer. Aminophospholipids such as phosphatidylserine (PS) and phosphatidylethanolamine (PE) are distributed in this bilayer and their arrangement is mediated by the P-type ATPases type IV family (Paulusma and Oude Elferink, 2005).
Characterization of Mmp37p, a Saccharomyces cerevisiae mitochondrial matrix protein with a role in mitochondrial protein import
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).
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.
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.
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.
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).
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).
A newly identified essential complex, Dre2-Tah18, controls mitochondria integrity and cell death after oxidative stress in yeast
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At the beginning of this reaction, 1 molecule of 'Double-strand DNA containing a formamidopyrimidine ', and 1 molecule of 'hOGG1 glycosylase' are present. At the end of this reaction, 1 molecule of 'hOGG1 glycosylase: formamidopyrimidine complex' is present. This reaction takes place in the 'nucleus'.
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At the beginning of this reaction, 1 molecule of 'Double-strand DNA containing an 8-oxo guanine opposite to a cytosine', and 1 molecule of 'hOGG1 glycosylase' are present. At the end of this reaction, 1 molecule of 'hOGG1 glycosylase:8-oxo guanine complex' is present. This reaction takes place in the 'nucleus'.
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Cloning and characterisation of hAps1 and hAps2, human diadenosine polyphosphate-metabolising Nudix hydrolases
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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 ).
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).
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).
Phosphorylated IGF1R binds and phosphorylates SHC1 (reviewed in Pavelic et al. 2007, Chitnis et al. 2008, Maki et al. 2010, Parrella et al. 2010, Siddle et al. 2012). Phosphorylated SHC then binds GRB:SOS, which activates RAS-RAF-MAPK signaling.
The phosphorylated type 1 insulin-like growth factor receptor phosphorylates IR1, IRS2, IRS4 and possibly other IRS/DOK family members (reviewed in Pavelic et al. 2007, Chitnis et al. 2008, Maki et al. 2010, Parrella et al. 2010, Siddle et al. 2012). The phosphorylated IRS proteins serve as scaffolds that bind the effector molecules PI3K and GRB2:SOS. PI3K then activates PKB (AKT) signaling while GRB2:SOS activates RAS-RAF-MAPK signaling.
Activation of ErbB4 by the bifunctional epidermal growth factor family hormone epiregulin is regulated by ErbB2
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.
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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).
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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).
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The architecture of the human Rad54-DNA complex provides evidence for protein translocation along DNA.
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Biogenesis of Tim proteins of the mitochondrial carrier import pathway: differential targeting mechanisms and crossing over with the main import pathway
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Selectivity of docking sites in MAPK kinases
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.
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.
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.
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.
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.
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).
ERK6, a mitogen-activated protein kinase involved in C2C12 myoblast differentiation
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.
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.
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.
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.
Regulators of neurite outgrowth: role of cell adhesion molecules
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The human genome includes approximately 70 genes that are predicted to encode Rho-specific GTPase Activating Proteins (RhoGAPs). As in the case of GEFs, some RhoGAPs are believed to be highly specific, whereas others are more promiscuous with respect to their target GTPases. Increasing evidence suggests that GAPs are also regulated by external cues in addition to being signal terminators leading to Rho GTPase inactivation. These proteins play important role in many Rho mediated signaling pathways. Some known GAPs include p190 A, cdGAP, ARAP3, MgcRacGAP, Chimaerin, Nadrin, TCGAP, DLC 1, 2, ArhGAP6, Myosin IXA. These and other GAPs have been implicated in many processes, such as exocytosis, endocytosis, cytokinesis, cell differentiation, migration, neuronal morphogenesis, angiogenesis and tumor suppression. Detailed annotations of the biological role of GAPs in Rho mediated signaling will be available in future releases.
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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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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).
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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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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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.
Folding of A+U-rich RNA elements modulates AUF1 binding. Potential roles in regulation of mRNA turnover
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).
All splicing isoforms of ERBB4 possess two tyrosine residues in the C-tail that serve as docking sites for SHC1 (Kaushansky et al. 2008, Pinkas-Kramarski et al. 1996, Cohen et al. 1996). Once bound to ERBB4, SHC1 becomes phosphorylated on tyrosine residues by the tyrosine kinase activity of ERBB4, which enables it to recruit the complex of GRB2 and SOS1, resulting in the guanyl-nucleotide exchange on RAS and activation of RAF and MAP kinase cascade (Kainulainen et al. 2000).
ERBB2, also known as HER2 or NEU, is a receptor tyrosine kinase (RTK) belonging to the EGFR family. ERBB2 possesses an extracellular domain that does not bind any known ligand, contrary to other EGFR family members, a single transmembrane domain, and an intracellular domain consisting of an active kinase and a C-tail with multiple tyrosine phosphorylation sites. Inactive ERBB2 is associated with a chaperone heat shock protein 90 (HSP90) and its co-chaperone CDC37 (Xu et al. 2001, Citri et al. 2004, Xu et al. 2005). In addition, ERBB2 is associated with ERBB2IP (also known as ERBIN or LAP2), a protein responsible for proper localization of ERBB2. In epithelial cells, ERBB2IP restricts expression of ERBB2 to basolateral plasma membrane regions (Borg et al. 2000). ERBB2 becomes activated by forming a heterodimer with another ligand-activated EGFR family member, either EGFR, ERBB3 or ERBB4, which is accompanied by dissociation of chaperoning proteins HSP90 and CDC37 (Citri et al. 2004), as well as ERBB2IP (Borg et al. 2000) from ERBB2. ERBB2 heterodimers function to promote cell proliferation, cell survival and differentiation, depending on the cellular context. ERBB2 can also be activated by homodimerization when it is overexpressed, in cancer for example. In cells expressing both ERBB2 and EGFR, EGF stimulation of EGFR leads to formation of both ERBB2:EGFR heterodimers (Wada et al. 1990, Karunagaran et al. 1996) and EGFR homodimers. Heterodimers of ERBB2 and EGFR trans-autophosphorylate on twelve tyrosine residues, six in the C-tail of EGFR and six in the C-tail of ERBB2 - Y1023, Y1139, Y1196, Y1221, Y1222 and Y1248 (Margolis et al. 1989, Hazan et al. 1990,Walton et al. 1990, Helin et al. 1991, Ricci et al. 1995, Pinkas-Kramarski 1996). Phosphorylated tyrosine residues in the C-tail of EGFR and ERBB2 serve as docking sites for downstream signaling molecules. Three key signaling pathways activated by ERBB2:EGFR heterodimers are RAF/MAP kinase cascade, PI3K-induced AKT signaling, and signaling by phospholipase C gamma (PLCG1). Downregulation of EGFR signaling is mediated by ubiquitin ligase CBL, and is shown under Signaling by EGFR. In cells expressing ERBB2 and ERBB3, ERBB3 activated by neuregulin NRG1 or NRG2 binding (Tzahar et al. 1994) forms a heterodimer with ERBB2 (Pinkas-Kramarski et al. 1996, Citri et al. 2004). ERBB3 is the only EGFR family member with no kinase activity, and can only function in heterodimers, with ERBB2 being its preferred heterodimerization partner. After heterodimerization, ERBB2 phosphorylates ten tyrosine residues in the C-tail of ERBB3, Y1054, Y1197, Y1199, Y1222, Y1224, Y1260, Y1262, Y1276, Y1289 and Y1328 (Prigent et al. 1994, Pinkas-Kramarski et al. 1996, Vijapurkar et al. 2003, Li et al. 2007) that subsequently serve as docking sites for downstream signaling molecules, resulting in activation of PI3K-induced AKT signaling and RAF/MAP kinase cascade. Signaling by ERBB3 is downregulated by the action of RNF41 ubiquitin ligase, also known as NRDP1. In cells expressing ERBB2 and ERBB4, ligand stimulated ERBB4 can either homodimerize or form heterodimers with ERBB2 (Li et al. 2007), resulting in trans-autophosphorylation of ERBB2 and ERBB4 on C-tail tyrosine residues that will subsequently serve as docking sites for downstream signaling molecules, leading to activation of RAF/MAP kinase cascade and, in the case of ERBB4 CYT1 isoforms, PI3K-induced AKT signaling (Hazan et al. 1990, Cohen et al. 1996, Li et al. 2007, Kaushansky et al. 2008). Signaling by ERBB4 is downregulated by the action of WWP1 and ITCH ubiquitin ligases, and is shown under Signaling by ERBB4.
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).
The role of transient receptor potential cation channels in Ca2+ signaling
Cold Spring Harb Perspect Biol 2:a003962
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FUNCTION Copper chaperone for cytochrome c oxidase (COX). Binds two copper ions and deliver them to the Cu(A) site of COX.SIMILARITY Belongs to the COX17 family.
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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.
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PI3K gamma (PI3KG) is a heterodimer consisting of a p110 catalytic subunit associated with a regulatory p101 or p84 subunit. PI3KG is most highly expressed in neutrophils, where the p101 form predominates (approximately 95%). G beta:gamma recruits PI3KG to the plasma membrane, both activating PI3KG and providing access to its substrate PIP2, which is converted to PIP3.
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The classical role of the G-protein beta/gamma dimer was believed to be the inactivation of the alpha subunit, Gbeta/gamma was viewed as a negative regulator of Galpha signalling. It is now known that Gbeta/gamma subunits can directly modulate many effectors, including some also regulated by G alpha.
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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 general function of the G alpha (s) subunit (Gs) is to activate adenylate cyclase, which in turn produces cAMP, leading to the activation of cAMP-dependent protein kinases (often referred to collectively as Protein Kinase A). The signal from the ligand-stimulated GPCR is amplified because the receptor can activate several Gs heterotrimers before it is inactivated.
Cyclic nucleotide phosphodiesterases (PDEs) are a large family of enzymes that regulate signal transduction by the second messenger molecules cAMP and cGMP. Some PDEs are cAMP selective (PDE4, 7 and 8), some cGMP selective (PDE5, 6 and 9) while others can hydrolyse cAMP and cGMP (PDE1, 2, 3, 10 and 11). PDEs are important as drug targets: Sildenafil (Viagra) is an inhibitor of PDE5; Cilostazol (Pletal) inhibits PDE3, increasing the flexibility of erythrocytes.
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The classic signalling route for G alpha (q) is activation of phospholipase C beta thereby triggering phosphoinositide hydrolysis, calcium mobilization and protein kinase C activation. This provides a path to calcium-regulated kinases and phosphatases, GEFs, MAP kinase cassettes and other proteins that mediate cellular responses ranging from granule secretion, integrin activation, and aggregation in platelets. Gq participates in many other signalling events including direct interaction with RhoGEFs that stimulate RhoA activity and inhibition of PI3K. Both in vitro and in vivo, the G-protein Gq seems to be the predominant mediator of the activation of platelets.
The Rho family of small guanine nucleotide binding proteins is one of five generally recognized branches of the Ras superfamily. Like most Ras superfamily members, typical Rho proteins function as binary switches controlling a variety of biological processes. They perform this function by cycling between active GTP-bound and inactive GDP-bound conformations. Mammalian Rho GTPases include RhoA, RhoB and RhoC (Rho proteins), Rac1 3 (Rac proteins), Cdc42, TC10, TCL, Wrch1, Chp/Wrch2, RhoD and RhoG, to name some. The family also includes RhoH and Rnd1-3, which lack GTPase activity and are predicted to exist in a constitutively active state. Members of the Rho family have been identified in all eukaryotes. Including the atypical RHOBTB1-3 and RHOT1-2 proteins, 24 Rho family members have been identified in mammals (Jaffe and Hall, 2005; Bernards, 2005; Ridley, 2006). Among Rho GTPases, RhoA, Rac1 and Cdc42 have been most extensively studied. These proteins are best known for their ability to induce dynamic rearrangements of the plasma membrane-associated actin cytoskeleton (Aspenstrom et al, 2004; Murphy et al, 1999; Govek et al, 2005). Beyond this function, Rho GTPases also regulate actomyosin contractility and microtubule dynamics. Rho mediated effects on transcription and membrane trafficking are believed to be secondary to these functions. At the more macroscopic level, Rho GTPases have been implicated in many important cell biological processes, including cell growth control, cytokinesis, cell motility, cell cell and cell extracellular matrix adhesion, cell transformation and invasion, and development (Govek et al., 2005). The illustration below lists Rho GTPase effectors implicated in actin and microtubule dynamics (courtesy: Govek et al., 2005, Genes and Development, CSHL Press). Detailed annotations of various biological processes regulated by Rho GTPases will be available in future releases.
The cycling of Rho GTPases is tightly controlled by three classes of protein. These are (1) guanine nucleotide dissociation inhibitors or GDIs, which maintain Rho proteins in an inactive state in the cytoplasm, (2) guanine nucleotide exchange factors or GEFs, which destabilize the interaction between Rho proteins and their bound nucleotide, the net result of which is the exchange of bound GDP for the more abundant GTP, and (3) GTPase Activating Proteins or GAPs, which stimulate the low intrinsic GTP hydrolysis activity of Rho family members, thus promoting their inactivation. GDIs, GEFs, and GAPs are themselves subject to tight regulation, and the overall level of Rho activity reflects the balance of their activities. In their active GTP-bound state, Rho family members have the ability to interact with a large variety of so-called effector proteins. By changing the subcellular localization of effectors, by altering their enzymatic properties, or by directing the formation of specific effector complexes, members of the Rho family mediate their various effects. This Rho GTPase cycle is diagrammed in the figure below. External or internal cues promote the release of Rho GTPases from the inhibitory complex (1) which allows them to associate with the plasma membrane (2) where they are activated by GEFs (3) and can signal to effector proteins. Then, GAPs inactivate the GTPases by accelerating the intrinsic GTPase activity, leading to the GDP bound form (4). Once again, the GDI molecules stabilize the inactive GDP bound form in the cytoplasm, waiting for further instructions (5). (Figure and text from Tcherkezian and Lamarche Vane, 2007).
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Mechanisms for the role of tetrahydrobiopterin in endothelial function and vascular disease
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).
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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.
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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".
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)
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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).
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beta-Nicotinamide adenine dinucleotide phosphate
Nicotinamide adenine dinucleotide phosphate
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).
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.
Structural basis of GLUT1 inhibition by cytoplasmic ATP
Characterization of the COQ5 gene from Saccharomyces cerevisiae. Evidence for a C-methyltransferase in ubiquinone biosynthesis
GABA synthesis, release, reuptake and degradation
The Xenopus Xmus101 protein is required for the recruitment of Cdc45 to origins of DNA replication.
A novel mechanism for GABA synthesis and packaging into synaptic vesicles
The remarkable structural and functional organization of the eukaryotic pyruvate dehydrogenase complexes.
Expression, purification, and characterization of human and rat acetyl coenzyme A carboxylase (ACC) isozymes
Identification of a vertebrate sister-chromatid separation inhibitor involved in transformation and tumorigenesis
Cloning and characterization of a second human CTP:phosphocholine cytidylyltransferase
Crucial role of conserved cysteine residues in the assembly of two iron-sulfur clusters on the CIA protein Nar1
Molecular cloning and functional expression of cDNAs encoding a human Na+-nucleoside cotransporter (hCNT1)
di-retinoid-pyridinium-ethanolamine [ChEBI:71980]
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].
Kinetics and inhibition of recombinant human cystathionine gamma-lyase. Toward the rational control of transsulfuration
Crystal structure of Spot 14, a modulator of fatty acid synthesis
Proc. Natl. Acad. Sci. U.S.A. 107:18820-5
Structures and mechanisms of Nudix hydrolases
Mia40-dependent oxidation of cysteines in domain I of Ccs1 controls its distribution between mitochondria and the cytosol
Megakaryocyte development and platelet production
FUNCTION Required for the assembly of mitochondrial cytochrome c oxidase.MISCELLANEOUS Present with 5750 molecules/cell in log phase SD medium.SIMILARITY Belongs to the COX19 family.SIMILARITY Contains 1 CHCH domain.
Sorting switch of mitochondrial presequence translocase involves coupling of motor module to respiratory chain
Low levels of glucose transporters and K+ATP channels in human pancreatic beta cells early in development
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
Primary structure of human deoxycytidylate deaminase and overexpression of its functional protein in Escherichia coli
Relationship between interferon-gamma, indoleamine 2,3-dioxygenase, and tryptophan catabolism
Resolution of AP sites can occur through the single-nucleotide replacement pathway or through the multiple-nucleotide patch replacement pathway.
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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.
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At the beginning of this reaction, 1 molecule of 'damaged DNA substrate ', and 1 molecule of 'HREV1 protein' are present. At the end of this reaction, 1 molecule of 'HREV1:damaged DNA template complex' is present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'HREV1:damaged DNA template complex' is present. At the end of this reaction, 1 molecule of 'HREV1:lesioned DNA template with misinserted bases' is present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA-directed DNA polymerase activity' of 'HREV1:damaged DNA template complex'.
At the beginning of this reaction, 1 molecule of 'HREV1:lesioned DNA template with misinserted bases' is present. At the end of this reaction, 1 molecule of 'HREV1 protein', and 1 molecule of 'Elongated DNA template with bypassed lesion' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA-directed DNA polymerase activity' of 'HREV1:lesioned DNA template with misinserted bases'.
HREV1 encodes a template dependent dCMP transferase activity that can insert a C residue opposite an abasic site.
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'.
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 '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'.
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.
Evaluation of the "scanning model" for initiation of protein synthesis in eucaryotes.
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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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'.
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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'.
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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'.
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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.
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).
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'.
Damaged pyrimidines are first cleaved by pyrimide-specific glycosylases (see Lindahl and Wood 1999).
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).
At the beginning of this reaction, 1 molecule of 'PCNA', and 1 molecule of 'Flap endonuclease-1 ' are present. At the end of this reaction, 1 molecule of 'FEN1:PCNA complex' is present. This reaction takes place in the 'nucleus'.
During removal of DNA patch containing abasic residue, DNA glycosylase is displaced by APE1 which endonucleolytically cleaves the 5' side of the base-free deoxyribose residue. POL Beta is recruited to the AP site where it mediates incorporation of the first replacement nucleotide. Association of POL delta with the AP site displaces POL Beta. DNA strand displacement synthesis then follows and flap structures are cleaved.
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At the beginning of this reaction, 1 molecule of 'hOGG1 glycosylase: formamidopyrimidine complex' is present. At the end of this reaction, 1 molecule of 'DNA containing an hOGG1-bound apurinic/apyrimidinic site', and 1 molecule of 'formamidopyrimidine' are present. This reaction takes place in the 'nucleus' and is mediated by the 'purine-specific oxidized base lesion DNA N-glycosylase activity' of 'hOGG1 glycosylase'.
Damaged purines are first cleaved by purine-specific glycosylases (see Lindahl and Wood 1999).
Depurination of a damaged nucleotide is mediated by a purine-specific DNA glycosylase. The glycosylase cleaves the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar generating a free base and an apurinic (AP) site.
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'.
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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).
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At the beginning of this reaction, 1 molecule of 'hOGG1 glycosylase:8-oxo guanine complex' is present. At the end of this reaction, 1 molecule of '8-oxoguanine', and 1 molecule of 'DNA containing an hOGG1-bound apurinic/apyrimidinic site' are present. This reaction takes place in the 'nucleus' and is mediated by the 'purine-specific oxidized base lesion DNA N-glycosylase activity' of 'hOGG1 glycosylase'.
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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 formamidopyrimidine ' are present. At the end of this reaction, 1 molecule of 'hNTH1 glycosylase: foramidopyrimidine complex' is present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'hNTH1', and 1 molecule of 'Double-strand DNA containing a thymine glycol ' are present. At the end of this reaction, 1 molecule of 'hNTH1 glycosylase:thymine glycol' is present. This reaction takes place in the 'nucleus'.
Base excision repair is initiated by a DNA glycosylase which first recognizes and removes a damaged or incorrect (e.g. mismatched) base.
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Chaperonins: The hunt for the Group II mechanism
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Biogenesis of Tim23 and Tim17, integral components of the TIM machinery for matrix-targeted preproteins
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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
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.
An active Pol II complex consisting mainly of the Pol II holoenzyme transcribes the damaged DNA template.
GG-NER is considered to be transcription-independent, removing lesions from non-transcribed regions of genome in addition to non-transcribed strands of transcribed regions. The three events that characterize NER are well characterized in GG-NER: damage recognition, bimodal incision of DNA via repair protein complex, resulting excision of DNA fragment with the lesion. Post-excision polymerization and ligation restore back the native chemistry and configuration to the damaged DNA.
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.
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.
ERCC1-XPF complex with 5ââ¬â¢ endonuclease activity binds to this pre-incision complex around the bubble structure to form an active incision complex.
Binding of XPC complex to the damaged site on the DNA substrate is followed by XPA and RPA recruitment. XPA is a metalloprotein that binds to different types of DNA damage. Binding of RPA, or Replicative protein A, a heterotrimer, initiates the formation of incision complex. This includes a serial assembly of the rest of the NER machinery consisting of TFIIH, XPG etc. Action of helicases in TFIIH complex opens up a bubble structure in the DNA template, exposing a fragment of DNA with lesion for endonuclease activity.
The cleavage of the damaged strand of DNA 3' to the site of damage occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound. The incision is carried out by XPG.
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.
Immunodeficiency in protein kinase cbeta-deficient mice
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.
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.
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.
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'.
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.
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.
Once repair synthesis has occurred, the D-loop structure may be resolved either through Holliday junction intermediates of through synthesis-dependent strand-annealing.
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.
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.
CATALYTIC ACTIVITY 4 ferrocytochrome c + O(2) + 4 H(+) = 4 ferricytochrome c + 2 H(2)O.SUBUNIT Cytochrome c oxidase is composed of 11 subunits: one copy each of COX1, COX2, COX3, COX4, COX5A or COX5B, COX6, COX7, COX9, COX12, COX13 and two copies of COX8.MISCELLANEOUS Present with 3670 molecules/cell in log phase SD medium.SIMILARITY Belongs to the cytochrome c oxidase IV family.
The presynaptic phase of homologous DNA pairing and strand exchange begins with the displacement of RPA from ssDNA, followed by the association of RAD51 with BRCA2, formation of RAD52 heptameric ring structure complexes on ssDNA, association of RAD52 with the RPA complex, association of RAD52 with ssDNA at resected ends of double-strand break and assembly of the RAD51-ssDNA nucleoprotein complex.
The 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).
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.
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).
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'.
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.
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'.
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).
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.
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).
G alpha 12 and G alpha 13 stimulate Rho-dependent stress fiber formation and focal adhesion assembly
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.
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).
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.
ATM is present in unirradiated cells as a dimer or higher-order multimer. Following irradiation, ATM undergoes rapid intermolecular autophosphorylation of serine 1981.
DNA damage can be directly reversed by dealkylation.
Reactive cellular catabolites can cause DNA damage by 6-O-methylation of guanine. 6-O-methylguanine can pair ambiguously with both C and T, and can cause transition mutations. Active reversal of such damage can be facilitated by proteins having 6-O-methylguanine-DNA methyltransferase (MGMT) activity. MGMT removes the methyl group from the guanine and transfers it to the cysteine residue at position 145 on the protein itself. MGMT thus methylated is not regenerated, as the S-methylcysteine is very stable. This is an energetically expensive approach to DNA repair as one entire protein molecule is sacrificed per lesion that is corrected in this manner (Yang et al. 2011).
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.
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).
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).
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).
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).
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.
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).
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.
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.
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).
Specificity, promiscuity and localization of ARF protein interactions with NCS-1 and phosphatidylinositol-4 kinase-III beta
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The Tim8-Tim13 complex has multiple substrate binding sites and binds cooperatively to Tim23
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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' 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'.
FUNCTION TFIIIC mediates tRNA and 5S RNA gene activation by binding to intragenic promoter elements. Upstream of the transcription start site, TFIIIC assembles the initiation complex TFIIIB-TFIIIC-tDNA, which is sufficient for RNA polymerase III recruitment and function. Part of the tauB domain of TFIIIC that binds boxB DNA promoter sites of tRNA and similar genes. TFC3 is essential for cell viability. Cooperates with TFC6 in DNA binding.SUBUNIT Component of the TFIIIC complex composed of TFC1, TFC3, TFC4, TFC6, TFC7 and TFC8. The subunits are organized in two globular domains, tauA and tauB, connected by a proteolysis-sensitive and flexible linker. Interacts with TFC1, TFC4 and TFC6.MISCELLANEOUS Present with 125 molecules/cell in log phase SD medium.
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'.
Dual incisions are carried out by XPG, and ERCC1-XPF complex as seen in GG-NER.
At the beginning of this reaction, 1 molecule of 'Transcription-coupled (TC) repair complex', and 1 molecule of 'damaged DNA substrate:nascent mRNA hybrid with 3' incision' are present. At the end of this reaction, 1 molecule of 'Transcription-coupled (TC) repair complex', 1 molecule of 'excised DNA fragment with lesion', and 1 molecule of 'damaged DNA substrate:nascent mRNA hybrid with dual incisions' are present. This reaction takes place in the 'nucleus' and is mediated by the 'endodeoxyribonuclease activity' of 'Transcription-coupled (TC) repair complex'.
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 '.
Polymerization is carried out by DNA polymerases, delta and epsilon.
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'.
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.
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.
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).
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.
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).
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.
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).
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.
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.
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.
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Identification of mutations associated with peroxisome-to-mitochondrion mistargeting of alanine/glyoxylate aminotransferase in primary hyperoxaluria type 1
cDNA cloning, genomic structure, chromosomal mapping, and functional expression of a novel human alanine aminotransferase
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Alteration of decreased plasma NO metabolites and platelet NO synthase activity by paroxetine in depressed patients
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Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences
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FUNCTION Promotes the biosynthesis of heme as well as the assembly and repair of iron-sulfur clusters by delivering Fe(2+) to proteins involved in these pathways. Plays a role in the protection against iron-catalyzed oxidative stress through its ability to catalyze the oxidation of Fe(2+) to Fe(3+). Can store large amounts of the metal in the form of a ferrihydrite mineral by oligomerization. May be involved in regulation of the mitochondrial electron transport chain.CATALYTIC ACTIVITY 4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O.SUBUNIT Monomer; increments in mitochondrial iron uptake induce stepwise assembly of species ranging from trimers to 24-mers. Interacts with ISU1. Interacts with YHB1, SDH1, SDH2, AIM45 and CIR1.PTM Processed in two steps by mitochondrial processing peptidase (MPP). MPP first cleaves the precursor to intermediate form and subsequently converts the intermediate to mature size protein.MISCELLANEOUS Present with 1560 molecules/cell in log phase SD medium.SIMILARITY Belongs to the frataxin family.
Regulation of nitric oxide-sensitive guanylyl cyclase
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The crystal structure of yeast thiamin pyrophosphokinase
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Genetic analysis of chromosome pairing, recombination, and cell cycle control during first meiotic prophase in mammals
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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
RNA interference suggests a primary role for monoacylglycerol lipase in the degradation of the endocannabinoid 2-arachidonoylglycerol
Metabolism of highly unsaturated n-3 and n-6 fatty acids
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
A common mutation in the fibroblast growth factor receptor 1 gene in Pfeiffer syndrome
RNA Pol II CTD phosphorylation and interaction with CE
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
Lipid digestion, mobilization, and transport
The human purH gene product, 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase
Functional characterization of human aquaporin 9 as a facilitative glycerol carrier
Role of adaptor TRIF in the MyD88-independent toll-like receptor signaling pathway
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.
FUNCTION DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively.SUBUNIT Component of the RNA polymerase I (Pol I), RNA polymerase II (Pol II) and RNA polymerase III (Pol III) complexes consisting of 14, 12 and 17 subunits, respectively. Directly interacts with POLR2A.MISCELLANEOUS Present with 6210 molecules/cell in log phase SD medium.SIMILARITY Belongs to the eukaryotic RPB8 RNA polymerase subunit family.
Deregulated FGFR3 mutants in multiple myeloma cell lines with t(4;14): comparative analysis of Y373C, K650E and the novel G384D mutations
The in vitro replication of DNA containing the SV40 origin.
Human cytoplasmic 3-hydroxy-3-methylglutaryl coenzyme A synthase: expression, purification, and characterization of recombinant wild-type and Cys129 mutant enzymes
SUBUNIT Component of the RNA polymerase I (Pol I), RNA polymerase II (Pol II) and RNA polymerase III (Pol III) complexes consisting of at least 14, 12 and 17 subunits, respectively.SIMILARITY Belongs to the archaeal RpoH/eukaryotic RPB5 RNA polymerase subunit family.
MISCELLANEOUS Present with 6090 molecules/cell in log phase SD medium.SIMILARITY Belongs to the archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit family.
Thematic Review Series: Proteomics. An integrated omics analysis of eicosanoid biology
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.
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).
Quantitating protein synthesis, degradation, and endogenous antigen processing
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.
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.
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).
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.
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.
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.
Crystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA thiolase: the importance of potassium and chloride ions for its structure and function
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation
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.
Recognition of nascent RNA by the human La antigen: conserved and divergent features of structure and function.
cDNA cloning of mouse and human cholesterol 25-hydroxylases, polytopic membrane proteins that synthesize a potent oxysterol regulator of lipid metabolism
ATP binding/hydrolysis by and phosphorylation of peroxisomal ATP-binding cassette proteins PMP70 (ABCD3) and adrenoleukodystrophy protein (ABCD1)
Glucose and cAMP regulate the L-type pyruvate kinase gene by phosphorylation/dephosphorylation of the carbohydrate response element binding protein
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).
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.
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.
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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.
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Toll-like Receptor 4 is a Microbe Associated Molecular Pattern receptor well known for it's sensitivity to Bacterial Lipopolysaccharides (LPS). LPS is assembled within diverse Gram-negative bacteria, many of which are human or plant pathogens. It is a component of the outer membrane of Gram-negative bacteria and consists of lipid A, a core polysaccharide and an O-polysaccharide of variable length (often more than 50 monosaccharide units). LPS is a potent activator of the innate immune response in humans, causing reactions including fever, headache, nausea, diarrhoea, changes in leukocyte and platelet counts, disseminated intravascular coagulation, multiorgan failure, shock and death. All these reactions are induced by cytokines and other endogenous mediators which are produced after interaction of LPS with the humoral and cellular targets of the host. In macrophages and dendritic cells, LPS-mediated activation of TLR4 triggers the biosynthesis of diverse mediators of inflammation, such as TNF-alpha and IL6, and activates the production of co-stimulatory molecules required for the adaptive immune response. In mononuclear and endothelial cells, LPS also stimulates tissue factor production. These events are desirable for clearing local infections, but when these various mediators and clotting factors are overproduced, they can damage small blood vessels and precipitate shock accompanied by disseminated intravascular coagulation and multiple organ failure.
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TLR1 is expressed by monocytes. TLR1 and TLR2 cotranslationally form heterodimeric complexes on the cell surface and in the cytosol. The TLR2:TLR1 complex recognizes Neisserial PorB and Mycobacterial triacylated lipoproteins and peptides, amongst others, triggering up-regulation of nuclear factor-kappaB production and apoptotic cascades. Such cooperation between TLR1 and TLR2 on the cell surface of normal human peripheral blood mononuclear cells, for instance, leads to the activation of pro-inflammatory cytokine secretion (Sandor et al. 2003).
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TLR2 and TLR4 recognize different bacterial cell wall components. While TLR4 is trained onto Gram-negative lipopolysaccharide components, TLR2 - in combination with TLR6 - plays a major role in recognizing peptidoglycan wall products from Gram-positive bacteria, as well as Mycobacterial diacylated lipopeptides. In particular, TLR6 appears to participate in discriminating the subtle differences between dipalmitoyl and tripalmitoyl cysteinyl residues (Okusawa et al. 2004).
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Mitochondrial ATP-binding cassette proteins
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].
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.
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].
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.
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).
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).
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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.
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MyD88-independent signaling pathway is shared by TLR3 and TLR4 cascades. TIR-domain-containing adapter-inducing interferon-beta (TRIF or TICAM1) is a key adapter molecule in transducing signals from TLR3 and TLR4 in a MyD88-independent manner (Yamamoto M et al. 2003a). TRIF is recruited to ligand-stimulated TLR3 or 4 complex via its TIR domain. TLR3 directly binds TRIF (Oshiumi H et al 2003). In contrast, TLR4-mediated signaling pathway requires two adapter molecules, TRAM (TRIF-related adapter molecule or TICAM2) and TRIF. TRAM(TICAM2) is thought to bridge between the activated TLR4 complex and TRIF (Yamamoto M et al. 2003b, Tanimura N et al. 2008, Kagan LC et al. 2008). TRIF recruitment to TLR complex stimulates distinct pathways leading to production of type 1 interferons (IFNs), pro-inflammatory cytokines and induction of programmed cell death.
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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.
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Innate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
Insights into the structure, mechanism, and regulation of scavenger mRNA decapping activity
Phagocytosis is one of the important innate immune responses that function to eliminate invading infectious agents. Monocytes, macrophages, and neutrophils are the professional phagocytic cells. Phagocytosis is a complex process involving the recognition of invading foreign particles by specific types of phagocytic receptors and the subsequent internalization of the particles. Fc gamma receptors (FCGRs) are among the best studied phagocytic receptors that bind to Fc portion of immunoglobulin G (IgG). Through their antigen binding F(ab) end, antibodies bind to specific antigen while their constant (Fc) region binds to FCGRs on phagocytes. The clustering of FCGRs by IgG antibodies on the phagocyte initiates a variety of signals, which lead, through the reorganisation of actin cytoskeleton and membrane remodelling, to the formation of pseudopod and phagosome. Fc gamma receptors are classified into three classes: FCGRI, FCGRII and FCGRIII. Each class of these FCGRs consists of several individual isoforms. Among all these isoforms FCGRI, FCGRIIA and FCGRIIIA, are able to mediate phagocytosis (Joshi et al. 2006, Garcia Garcia & Rosales 2002, Nimmerjahn & Ravetch 2006).
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In response to receptor ligation, the tyrosine residues in DAP12's immunoreceptor tyrosine-based activation motif (ITAM) are phosphorylated by Src family kinases. These phosphotyrosines form the docking site for the protein tyrosine kinase SYK in myeloid cells and SYK and ZAP70 in NK cells. DAP12-bound SYK autophosphorylates and phosphorylates the scaffolding molecule LAT, recruiting the proximal signaling molecules phosphatidylinositol-3-OH kinase (PI3K), phospholipase-C gamma (PLC-gamma), GADS (GRB2-related adapter downstream of SHC), SLP76 (SH2 domain-containing leukocyte protein of 76 kDa), GRB2:SOS (Growth factor receptor-bound protein 2:Son of sevenless homolog 1) and VAV. All of these intermediate signalling molecules result in the recruitment and activation of kinases AKT, CBL (Casitas B-lineage lymphoma) and ERK (extracellular signal-regulated kinase), and rearrangement of the actin cytoskeleton (actin polymerization) finally leading to cellular activation. PLC-gamma generates the secondary messengers diacylglycerol (DAG) and inositol-1,4,5-trisphosphate (InsP3), leading to activation of protein kinase C (PKC) and calcium mobilization, respectively (Turnbull & Colonna 2007, Klesney-Tait et al. 2006).
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DNAX activation protein of 12kDa (DAP12) is an immunoreceptor tyrosine-based activation motif (ITAM)-bearing adapter molecule that transduces activating signals in natural killer (NK) and myeloid cells. It mediates signalling for multiple cell-surface receptors expressed by these cells, associating with receptor chains through complementary charged transmembrane amino acids that form a salt-bridge in the context of the hydrophobic lipid bilayer (Lanier et al. 1998). DAP12 homodimers associate with a variety of receptors expressed by macrophages, monocytes and myeloid cells including TREM2, Siglec H and SIRP-beta, as well as activating KIR, LY49 and the NKG2C proteins expressed by NK cells. DAP12 is expressed at the cell surface, with most of the protein lying on the cytoplasmic side of the membrane (Turnbull & Colonna 2007, Tessarz & Cerwenka 2008).
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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).
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).
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Phospholipases play an integral role in phagocytosis by generating essential second messengers. An early step in phagocytic signaling is the association of PIP2 and IP3 with the phagocytic cup. These are formed by the activity of phosphoinositol kinases and phospholipases. PI3K is has been shown to accumulate at phagocytic cups and converts PI (4,5)P2 to PI (3,4,5)P3. These phosphoinositides are capable of binding and increasing the activity of proteins that regulate the actin cytoskeleton. Phospholipases are lipid modifying enzymes that produce lipid mediators such as diacylglycerol (DAG), arachidonic acid (AA) and IP3. Phopsholipases PLA, PLC and PLD have been shown to be involved in antibody (IgG) mediated phagocytosis. The PLC product IP3 stimulates release of calcium from the endoplasmic reticulum. This Ca+2 concentration increase is greatest in the cytoplasm surrounding the phagocytic cup. Calcium is involved in the various stages of phagosome formation, including phagocytic ingestion and phagosome maturation.
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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).
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.
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).
FCGR mediated phagocytosis requires CDC42 to stimulate actin polymerization, generating the force for phagocytic cup protrusion or pseudopod extension. CDC42 activation is restricted at the advancing edge of the phagocytic cup, where actin is concentrated, and is deactivated at the base of the phagocytic cup (Beemiller et al 2010). The mechanism behind the recruitment and activation of CDC42 during FCGR phagocytosis is unknown. VAV regulates the activation of RAC1 but not CDC42 and the GEF responsible for CDC42 activation during FCGR-mediated phagocytosis remains unidentified (Adam et al 2004, Patel et al 2002).
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The innate immune system is the first line of defense against invading microorganisms, a broad specificity response characterized by the recruitment and activation of phagocytes and the release of anti-bacterial peptides. The receptors involved recognize conserved molecules present in microbes called pathogen-associated molecular patterns (PAMPs), and/or molecules that are produced as a result of tissue injury, the damage associated molecular pattern molecules (DAMPs). PAMPs are essential to the pathogen and therefore unlikely to vary. Examples are lipopolysaccharide (LPS), peptidoglycans (PGNs) and viral RNA. DAMPs include intracellular proteins, such as heat-shock proteins and extracellular matrix proteins released by tissue injury, such as hyaluronan fragments. Non-protein DAMPs include ATP, uric acid, heparin sulfate and dsDNA. The receptors for these factors are referred to collectively as pathogen- or pattern-recognition receptors (PRRs). The best studied of these are the membrane-associated Toll-like receptor family. Less well studied but more numerous are the intracellular nucleotide-binding domain, leucine rich repeat containing receptors (NLRs) also called nucleotide binding oligomerization domain (NOD)-like receptors, a family with over 20 members in humans and over 30 in mice. These recognise PAMPs/DAMPs from phagocytosed microorganisms or from intracellular infections (Kobayashi et al. 2003, Proell et al. 2008, Wilmanski et al. 2008). Some NLRs are involved in process unrelated to pathogen detection such as tissue homeostasis, apoptosis, graft-versus-host disease and early development (Kufer & Sansonetti 2011). Structurally NLRs can be subdivided into the caspase-recruitment domain (CARD)-containing NLRCs (NODs) and the pyrin domain (PYD)-containing NLRPs (NALPs), plus outliers including ice protease (caspase-1) activating factor (IPAF) (Martinon & Tschopp, 2005). In practical terms, NLRs can be divided into the relatively well characterized NOD1/2 which signal via RIP2 primarily to NFkappaB, and the remainder, some of which participate in macromolecular structures called Inflammasomes that activate caspases. Mutations in several members of the NLR protein family have been linked to inflammatory diseases, suggesting these molecules play important roles in maintaining host-pathogen interactions and inflammatory responses. Most NLRs have a tripartite structure consisting of a variable amino-terminal domain, a central nucleotide-binding oligomerization domain (NOD or NACHT) that is believed to mediate the formation of self oligomers, and a carboxy-terminal leucine-rich repeat (LRR) that detects PAMPs/DAMPs. In most cases the amino-terminal domain includes protein-interaction modules, such as CARD or PYD, some harbour baculovirus inhibitor repeat (BIR) or other domains. For most characterised NLRs these domains have been attributed to downstream signaling Under resting conditions, NLRs are thought to be present in an autorepressed form, with the LRR folded back onto the NACHT domain preventing oligomerization. Accessory proteins may help maintain the inactive state. PAMP/DAMP exposure is thought to triggers conformational changes that expose the NACHT domain enabling oligomerization and recruitment of effectors, though it should be noted that due to the lack of availability of structural data, the mechanistic details of NLR activation remain largely elusive. New terminology for NOD-like receptors was adopted by the Human Genome Organization (HUGO) in 2008 to standardize the nomenclature of NLRs. The acronym NLR, once standing for NOD-like receptor, now is an abbreviation of 'nucleotide-binding domain, leucine-rich repeat containing' protein. The term NOD-like receptor is officially outdated and replaced by NLRC where the C refers to the CARD domain. However the official gene symbols for NOD1 and NOD2 still contain NOD and this general term is still widely used.
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In addition to AGER/RAGE, several other proteins have been identified as AGE-binding proteins. AGE binding proteins p60 and p90 (Yang et al. 1991) were subsequently identified as the Oligosaccharyl transferase 48 kDa subunit (Ost-48) and Glucosidease-2 subunit beta (Li et al. 1996). A third member was identified as Galectin-3 (Vlassara et al. 1995). These 3 proteins have been shown to be present on the plasma membrane of many cell types including vascular endothelium (Stitt et al. 1999). They have been designated AGE-R1, -R2 and -R3. Their suggested function is the removal and degradation of AGEs, but AGER-1 was found to negatively regulate AGER/RAGE (Lu et al. 2004), with kinetics that suggested a more complex interaction than simple competition for the same ligand.
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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).
Exon-intron organization and chromosomal localization of the mouse monoglyceride lipase gene
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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
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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
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).
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).
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).
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).
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The eukaryotic chaperonin TCP-1 ring complex (TRiC/ CCT) plays an essential role in the folding of a subset of proteins prominent among which are the actins and tubulins (reviewed in Altschuler and Willison, 2008). CCT/TRiC is an example of a type II chaperonin, defined (in contrast to type I) as functioning in the absence of a cochaperonin. TriC/CCT is a multisubunit toroidal complex that forms a cylinder containing two back-to-back stacked rings enclosing a cavity where substrate folding occurs in an ATP dependent process (reviewed in Altschuler and Willison, 2008 ). CCT/TriC contains eight paralogous subunits that are conserved throughout eukaryotic organisms (Leroux and Hartl 2000; Archibald et al. 2001; Valpuesta et al. 2002). CCT-mediated folding of non-native substrate protein involves capture through hydrophobic contacts with multiple chaperonin subunits followed by transfer of the protein into the central ring cavity where it folds. Although folding is initiated within this central cavity, only 5%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).
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Due to the crowded envirnoment within the cell, many proteins must interact with molecular chaperones to attain their native conformation (reviewed in Young et al., 2004). Chaperones recognize and associate with proteins in their non-native state and facilitate their folding by stabilizing the conformation of productive folding intermediates. Chaperones that take part broadly in de novo protein folding, such as the Hsp70s and the chaperonins, facilitate the folding process through cycles of substrate binding and release regulated by their ATPase activity (see Young et al., 2004; Spiess et al., 2004; Bigotti and Clarke, 2008).
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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).
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In the case of actin and tubulin folding, and perhaps other substrates, the emerging polypeptide chain is transferred from the ribosome to TRiC via Prefoldin (Vainberg et al., 1998).
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.
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).
Polarized expression of monocarboxylate transporters in human retinal pigment epithelium and ARPE-19 cells
Activity of TKI258 against primary cells and cell lines with FGFR1 fusion genes associated with the 8p11 myeloproliferative syndrome
Transcription by RNA Polymerase I, RNA Polymerase III and transcription from mitochondrial promoters.
Humans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first critical hours and days of exposure to a new pathogen, our innate immune system.
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Cytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concentrations. Cytokines bind to specific membrane receptors, which then signal the cell via second messengers, to regulate cellular activity.
Interleukin-2 (IL-2) is a cytokine that is produced by T cells in response to antigen stimulation. Originally, IL-2 was discovered because of its potent growth factor activity on activated T cells in vitro and was therefore named 'T cell growth factor' (TCGF). However, the generation of IL-2- and IL-2 receptor-deficient mice revealed that IL-2 also plays a regulatory role in the immune system by suppressing autoimmune responses. Two main mechanisms have been identified that explain this suppressive function: (1) IL-2 sensitizes activated T cells for activation-induced cell death (AICD) and (2) IL-2 is critical for the survival and function of regulatory T cells (Tregs), which possess potent immunosuppressive properties. IL-2 signaling occurs when IL-2 binds to the heterotrimeric high-affinity IL-2 receptor (IL-2R), which consists of alpha, beta and gamma chains. The IL-2R was identified in 1981 via radiolabeled ligand binding (Robb et al. 1981). The IL-2R alpha chain was identified in 1982 (Leonard et al.), the beta chain in 1986/7 (Sharon et al. 1986, Teshigawara et al. 1987) and the IL-2R gamma chain in 1992 (Takeshita et al.). The high affinity of IL-2 binding to the IL-2R is created by a very rapid association rate to the IL-2R alpha chain, combined with a much slower dissociation rate contributed by the combination of the IL-2R beta and gamma chains (Wang & Smith 1987). After antigen stimulation, T cells upregulate the high-affinity IL-2R alpha chain; IL-2R alpha captures IL-2 and this complex then associates with the constitutively expressed IL-2R beta and gamma chains. The IL-2R gamma chain is shared by several other members of the cytokine receptor superfamily including IL-4, IL-7, IL-9, IL-15 and IL-21 receptors, and consequently is often referred to as the Common gamma chain (Gamma-c). The tyrosine kinases Jak1 and Jak3, which are constitutively associated with IL-2R beta and Gamma-c respectively, are activated resulting in phosphorylation of three critical tyrosine residues in the IL-2R beta cytoplasmic tail. These phosphorylated residues enable recruitment of the adaptor molecule Shc, activating the MAPK and PI3K pathways, and the transcription factor STAT5. After phosphorylation, STAT5 forms dimers that translocate to the nucleus and initiate gene expression. While STAT5 activation is critical for IL-2 function in most cell types, the contribution of the PI3K/Akt pathway differs between distinct T cell subsets. In Tregs for example, PI3K/Akt is not involved in IL-2 signaling and this may explain some of the different functional outcomes of IL-2 signaling in Tregs vs. effector T cells.
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Interleukins are low molecular weight proteins that bind to cell surface receptors and act in an autocrine and/or paracrine fashion. They were first identified as factors produced by leukocytes but are now known to be produced by many other cells throughout the body. They have pleiotropic effects on cells which bind them, impacting processes such as tissue growth and repair, hematopoietic homeostasis, and multiple levels of the host defense against pathogens where they are an essential part of the immune system.
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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).
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.
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.
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.
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.
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.
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).
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).
FUNCTION Mitochondrial membrane ATP synthase (F(1)F(0) ATP synthase or Complex V) produces ATP from ADP in the presence of a proton gradient across the membrane which is generated by electron transport complexes of the respiratory chain. F-type ATPases consist of two structural domains, F(1) - containing the extramembraneous catalytic core and F(0) - containing the membrane proton channel, linked together by a central stalk and a peripheral stalk. During catalysis, ATP synthesis in the catalytic domain of F(1) is coupled via a rotary mechanism of the central stalk subunits to proton translocation. Part of the complex F(0) domain. A homomeric c-ring of probably 10 subunits is part of the complex rotary element.SUBUNIT F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. In yeast, the dimeric form of ATP synthase consists of 17 polypeptides: alpha, beta, gamma, delta, epsilon, 4 (B), 5 (OSCP), 6 (A), 8, 9 (C), d, E (Tim11), f, g, h, i/j and k.SIMILARITY Belongs to the ATPase C chain family.
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).
Removal of DNA patch containing abasic residue
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).
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.
In the last step of the N-glycan precursor biosynthesis pathway, the mature N-glycan (Glc3Man9GlcNAc2) is removed from the dolichyl diphosphate molecule upon which it has been synthesized, and attached to a nascent protein. In this process, a dolichyl diphosphate molecule is released and once de-phosphorylated by dolichyl diphosphatase 1 (DOLPP1) to obtain dolichyl phosphate, it can be used as a substrate for the synthesis of another N-glycan oligosaccharide (Wedgwood JF and Strominger JL, 1980).
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).
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 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).
The NLRP3 inflammasome: a sensor of immune danger signals
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.
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).
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).
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).
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).
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 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).
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
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 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).
Regulated release of L13a from the 60S ribosomal subunit as a mechanism of transcript-specific translational control
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).
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 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
LASS5 is a bona fide dihydroceramide synthase that selectively utilizes palmitoyl-CoA as acyl donor
In vitro analysis of elongation and termination by mutant RNA polymerases with altered termination behavior.
Na+/Ca2+-K+ exchangers (NCKX): functional properties and physiological roles
Molecular mechanisms regulating hormone-sensitive lipase and lipolysis
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Structure of human carnitine acetyltransferase. Molecular basis for fatty acyl transfer.
Cytoplasmic chaperonin containing TCP-1: structural and functional characterization
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The import route of ADP/ATP carrier into mitochondria separates from the general import pathway of cleavable preproteins at the trans side of the outer membrane
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All three IkappaB isoforms and most Rel family members are stably associated with the IkappaB kinase 1/2 complex
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The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1909-1963
Human pyridoxal kinase: overexpression and properties of the recombinant enzyme
1-acyl-sn-glycero-3-phospho-D-myo-inositol [ChEBI:28914]
Identification of peroxisomal acyl-CoA thioesterases in yeast and humans
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
Monocarboxylate transporters: past, present, and future
An updated overview on Wnt signaling pathways: a prelude for more
2-acyl-sn-glycero-3-phosphoethanolamine [ChEBI:28936]
Disorders of tetrahydrobiopterin and related biogenic amines
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1725-1776
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1777-1805
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
The human liver-specific homolog of very long-chain acyl-CoA synthetase is cholate:CoA ligase
Maple syrup urine disease (branched-chain ketoaciduria)
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1971-2005
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 2125-2163
Identification of novel PPARgamma target genes in primary human adipocytes
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1965-1970
Disorders of proline and hydroxyproline metabolism
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1821-1838
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1857-1895
The 2.0 A structure of human ferrochelatase, the terminal enzyme of heme biosynthesis.
Neurotrophins and their receptors: a convergence point for many signalling pathways
L1 and NCAM adhesion molecules as signaling coreceptors in neuronal migration and process outgrowth
NUDT3:Mg2+ (name copied from entity in Homo sapiens)
IMPA2 dimer (name copied from entity in Homo sapiens)
IMPA2:Mg2+ (name copied from entity in Homo sapiens)
ISYNA1:NAD+ (name copied from entity in Homo sapiens)
NPC1L1:ezetimibe complex (name copied from entity in Homo sapiens)
NUDT10:Mg2+/Mn2+ (name copied from entity in Homo sapiens)
IMPA1 dimer (name copied from entity in Homo sapiens)
IMPA1:Mg2+ (name copied from entity in Homo sapiens)
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NUDT4:Mg2+/Mn2+ (name copied from entity in Homo sapiens)
Regulation of telomerase by telomeric proteins
A structural model for the membrane-integral domain of succinate: quinone
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((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin-2 dimer (name copied from entity in Homo sapiens)
phosphoribosyl pyrophosphate synthetase 1 holoenzyme (name copied from entity in Homo sapiens)
phosphoribosyl pyrophosphate synthetase holoenzyme
PGD dimer (name copied from entity in Homo sapiens)
A critical review of the origin and control of adrenal androgens
Baillieres Clin Obstet Gynaecol 11:229-48
RPE dimer (name copied from entity in Homo sapiens)
G6PD dimer (name copied from entity in Homo sapiens)
G6PD tetramer (name copied from entity in Homo sapiens)
GALE dimer (name copied from entity in Homo sapiens)
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((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin-1 dimer (name copied from entity in Homo sapiens)
((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin dimer
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673294
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_83441.9
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=109939
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2765.1
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=3668469
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668470
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4587.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109735
HSD17B4 dimer (name copied from entity in Homo sapiens)
ABCD1 homodimer (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)
Type III cGMP-inhibited cyclic nucleotide phosphodiesterases (PDE3 gene family)
holo-FDPS dimer (name copied from entity in Homo sapiens)
FDPS:3Mg++ (name copied from entity in Homo sapiens)
holo-GGPS1 hexamer (name copied from entity in Homo sapiens)
The molecular mechanics of eukaryotic translation
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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_32474.10
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=3673300
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_100450.9
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=3673302
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_79222.9
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_83674.9
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=3668487
Btn-ACACA:2Mn2+ (name copied from entity in Homo sapiens)
ACAT1 tetramer (name copied from entity in Homo sapiens)
ABCG5:ABCG8 heterodimer (name copied from entity in Homo sapiens)
NF-Y (name copied from entity in Homo sapiens)
SREBP1A/1C/2:NF-Y:HMGCS1 gene (name copied from entity in Homo sapiens)
SREBP1A/2:NF-Y:HMGCR gene (name copied from entity in Homo sapiens)
SREBP1A/2 Dimer (name copied from entity in Homo sapiens)
HACL1 holoenzyme monomer (name copied from entity in Homo sapiens)
SREBP1A/1C/2 Dimer (name copied from entity in Homo sapiens)
HACL1 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_105070.9
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=110289
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5776.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668483
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668485
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668480
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668481
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668482
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_78847.9
oligo((1,4)-alpha-glucosyl) glycogenin dimer
GYG2 dimer (name copied from entity in Homo sapiens)
oligo((1,4)-alpha-glucosyl) glycogenin 2 dimer (name copied from entity in Homo sapiens)
oligo((1,4)-alpha-glucosyl) glycogenin 1 dimer (name copied from entity in Homo sapiens)
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GYG1 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_2875.1
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=3667107
Database identifier. Use 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
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29438
Reactome stable identifier. Use this 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
Reactome stable identifier. Use this 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=110225
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_104266.9
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=3668449
Database identifier. Use 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
8xUGP2 (name copied from entity in Homo sapiens)
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FBP2 tetramer (name copied from entity in Homo sapiens)
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PGM1:Mg++ (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_3731.1
PGM2:Mg++ (name copied from entity in Homo sapiens)
FBP1 tetramer (name copied from entity in Homo sapiens)
Iron-sulfur proteins in health and disease
GOT1 dimer (name copied from entity in Homo sapiens)
pyruvate carboxylase holoenzyme (name copied from entity in Homo sapiens)
pyruvate kinase complex, liver and RBC (name copied from entity in Homo sapiens)
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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=3667128
Purine ribonucleoside monophosphate biosynthesis
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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=3668672
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_106653.9
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=3668682
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668681
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667478
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667447
Database identifier. Use 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=3668441
Reactome stable identifier. Use this 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
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_83237.9
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=3668442
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_81890.9
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=3673291
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)
phosphofructokinase, PL3 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_3342.1
triosephosphate isomerase dimer (name copied from entity in Homo sapiens)
PGYM b dimer:AMP (name copied from entity in Homo sapiens)
PGYM dimer, b form (name copied from entity in Homo sapiens)
limit dextrin-glycogenin-1 dimer (name copied from entity in Homo sapiens)
limit dextrin-glycogenin-2 dimer (name copied from entity in Homo sapiens)
PGYM dimer a form (name copied from entity in Homo sapiens)
PGYL dimer a form (name copied from entity in Homo sapiens)
FUNCTION Interacts with the internal control region (ICR) of approximately 50 bases within the 5S RNA genes, is required for correct transcription of these genes by RNA polymerase III. Also binds the transcribed 5S RNA's.MISCELLANEOUS Present with 1380 molecules/cell in log phase SD medium.SIMILARITY Contains 9 C2H2-type zinc fingers.
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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_105109.9
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=3668497
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668496
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668495
glycogen-glycogenin-2 dimer (name copied from entity in Homo sapiens)
PGYB dimer b form (name copied from entity in Homo sapiens)
The human ATP-binding cassette (ABC) transporter superfamily
PGYB b dimer:AMP (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_82921.9
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=3673305
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_93137.9
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=3673304
GYS2 tetramer, a form (name copied from entity in Homo sapiens)
GYS1 tetramer, a form (name copied from entity in Homo sapiens)
glycogen-glycogenin-1 dimer (name copied from entity in Homo sapiens)
GYS2 tetramer, b form (name copied from entity in Homo sapiens)
GYS1 tetramer, b form (name copied from entity in Homo sapiens)
The control of glycogen metabolism in the liver
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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_85151.9
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=3673295
The equilibrative nucleoside transporter family, SLC29
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_78298.9
poly((1,4)-alpha-glucosyl) glycogenin-2 dimer (name copied from entity in Homo sapiens)
AU-rich element-mediated translational control: complexity and multiple activities of trans-activating factors
poly((1,4)-alpha-glucosyl) glycogenin dimer
poly((1,4)-alpha-glucosyl) glycogenin-1 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_94342.9
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=3673292
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_93909.9
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=3673293
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667429
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667291
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667413
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667414
Tumor necrosis factor-alpha-converting enzyme is required for cleavage of erbB4/HER4
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1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole [ChEBI:18319]
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NGF signalling via TRKA from the plasma membrane
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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=3667239
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667240
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667212
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667213
The ABCs of solute carriers: physiological, pathological and therapeutic implications of human membrane transport proteinsIntroduction
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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=3667203
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667199
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667442
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667204
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667446
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667293
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667294
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667346
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667405
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667422
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667424
Targeting the phosphoinositide 3-kinase pathway in cancer
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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=3667341
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667177
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667332
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667415
N,N'-Diacetylchitobiosyldiphosphodolichol [ChEBI:7069]
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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=3667230
5-phosphoribosylglycinamide [ChEBI:18349]
1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate
ChEBI:18348 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate
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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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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).
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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).
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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 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).
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The UBA2:SAE1 complex catalyzes the formation of a thioester bond between SUMO3 and cysteine-173 of UBA2 (Tatham et al. 2001, Werner et al. 2009). ATP reacts with the C-terminal glycine residue of SUMO3 to yield pyrophosphate and a transient intermediate, SUMO3 adenylate, which then reacts with the thiol group of the cysteine residue on UBA2.
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The UBA2:SAE1 complex catalyzes the formation of a thioester bond between SUMO2 and cysteine-173 of UBA2 (Tatham et al. 2001, Werner et al. 2009). ATP reacts with the C-terminal glycine residue of SUMO2 to yield pyrophosphate and a transient intermediate, SUMO2 adenylate, which then reacts with the thiol group of the cysteine residue on UBA2.
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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.
SUMO3 is transferred from cysteine-173 of UBA2 to cysteine-93 of UBC9 (UBE2I) in a transthiolation reaction (Tatham et al. 2001, Werner et al. 2009).
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PCYT2 dimer (name copied from entity in Homo sapiens)
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SREBP1A/1C/2:NF-Y:TM7SF2 gene (name copied from entity in Homo sapiens)
SREBP1A/2:SQLE gene (name copied from entity in Homo sapiens)
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MGLL dimer (name copied from entity in Homo sapiens)
CH25H (Fe2+ cofactor) (name copied from entity in Homo sapiens)
SQLE:FAD (name copied from entity in Homo sapiens)
FDFT (Mg2+ cofactor) (name copied from entity in Homo sapiens)
SREBP1A/2:NF-Y:SC5DL gene (name copied from entity in Homo sapiens)
SREBP1A/1C/2:NF-Y:FDPS gene (name copied from entity in Homo sapiens)
GGPS1:3Mg++ (name copied from entity in Homo sapiens)
A novel skeletal dysplasia with developmental delay and acanthosis nigricans is caused by a Lys650Met mutation in the fibroblast growth factor receptor 3 gene
Regulation of 5' template usage and incorporation of noncognate nucleotides by human telomerase
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Molecular enzymology of carnitine transfer and transport
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6-(L-erythro-1,2-Dihydroxypropyl 3-triphosphate)-7,8-dihydropterin
7,8-dihydroneopterin 3'-triphosphate [ChEBI:18372]
2-Amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)dihydropteridine triphosphate
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The expanding role of mitochondria in apoptosis.
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beta-D-Mannosyldiacetylchitobiosyldiphosphodolichol [ChEBI:10408]
Human lysyl-tRNA synthetase accepts nucleotide 73 variants and rescues Escherichia coli double-defective mutant
Substrate specificity of the RNase activity of yeast RNA polymerase III.
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
ChEBI:18381 5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide
Expression patterns of two human genes coding for different rab GDP-dissociation inhibitors (GDIs), extremely conserved proteins involved in cellular transport
Aquaporin-11: a channel protein lacking apparent transport function expressed in brain
ChEBI:16152 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphates
ChEBI:16152 ChEBI:16152 1-phosphatidyl-1D-myo-inositol 3,4-bisphosphates
Structure of the FGF receptor tyrosine kinase domain reveals a novel autoinhibitory mechanism
The human AQP4 gene: definition of the locus encoding two water channel polypeptides in brain
2'-deoxyadenosine 5'-diphosphate [ChEBI:16174]
7alpha,12alpha-Dihydroxy-5beta-cholestan-3-one [ChEBI:2288]
The SRPR gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The PPP2R5B gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The SYVN1 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.
7alpha-Hydroxy-5beta-cholestan-3-one [ChEBI:2290]
The KDELR3 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 WIPI1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The Sec31A gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The YIF1A gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
At the center of the mammalian circadian clock is a negative transcription/translation-based feedback loop: The BMAL1:CLOCK/NPAS2 heterodimer transactivates CRY and PER genes by binding E-box elements in their promoters; the CRY and PER proteins then inhibit transactivation by BMAL1:CLOCK/NPAS2. BMAL1:CLOCK/NPAS2 activates transcription of CRY, PER, and several other genes in the morning. Levels of PER and CRY proteins rise during the day and inhibit expression of CRY, PER, and other BMAL1:CLOCK/NPAS2-activated genes in the afternoon and evening. During the night CRY and PER proteins are targeted for degradation by phosphorylation and polyubiquitination, allowing the cycle to commence again in the morning. Transcription of the BMAL1 (ARNTL) gene is controlled by ROR-alpha and REV-ERBA, both of which are targets of BMAL1:CLOCK/NPAS2 in mice and both of which compete for the same element (RORE) in the BMAL1 promoter. ROR-alpha activates transcription of BMAL1; REV-ERBA represses transcription of BMAL1. This mutual control forms a secondary, reinforcing loop of the circadian clock. REV-ERBA shows strong circadian rhythmicity and confers circadian expression on BMAL1. BMAL1 can form heterodimers with either CLOCK or NPAS2, which act redundantly but show different tissue specificity. The BMAL1:CLOCK and BMAL1:NPAS2 heterodimers activate a set of genes that possess E-box elements (consensus CACGTG) in their promoters. This confers circadian expression on the genes. The PER genes (PER1, PER2, PER3) and CRY genes (CRY1, CRY2) are among those activated by BMAL1:CLOCK and BMAL1:NPAS2. PER and CRY mRNA accumulates during the morning and the proteins accumulate during the afternoon. PER and CRY proteins form complexes in the cytosol and these are bound by either CSNK1D or CSNK1E kinases which phosphorylate PER and CRY. The phosphorylated PER:CRY:kinase complex is translocated into the nucleus due to the nuclear localization signal of PER and CRY. Within the nucleus the PER:CRY complexes bind BMAL1:CLOCK and BMAL1:NPAS2, inhibiting their transactivation activity and their phosphorylation. This reduces expression of the target genes of BMAL1:CLOCK and BMAL1:NPAS2 during the afternoon and evening. PER:CRY complexes also traffic out of the nucleus into the cytosol due to the nuclear export signal of PER. During the night PER:CRY complexes are polyubiquitinated and degraded, allowing the cycle to begin again. Phosphorylated PER is bound by Beta-TrCP1, a cytosolic F-box type component of some SCF E3 ubiquitin ligases. CRY is bound by FBXL3, a nucleoplasmic F-box type component of some SCF E3 ubiquitin ligases. Phosphorylation of CRY1 by Adenosine monophosphate-activated kinase (AMPK) enhances degradation of CRY1. PER and CRY are subsequently polyubiquitinated and proteolyzed by the 26S proteasome. The circadian clock is cell-autonomous and some, but not all cells of the body exhibit circadian rhythms in metabolism, cell division, and gene transcription. The suprachiasmatic nucleus (SCN) in the hypothalamus is the major clock in the body and receives its major input from light (via retinal neurons) and a minor input from nutrient intake. The SCN and other brain tissues determine waking and feeding cycles and influence the clocks in other tissues by hormone secretion and nervous stimulation. Independently of the SCN, other tissues such as liver receive inputs from signals from the brain and from nutrients.
As inferred from mouse, BMAL1:CLOCK and BMAL1:NPAS2 heterodimers bind to sequence elements (E boxes) in the promoters of target genes and enhance transcription (Gekakis et al. 1998, reviewed in Munoz and Baler 2003).
The NOCTURNIN gene is transcribed to yield mRNA and the mRNA is translated to yield protein. The NOCTURNIN gene shows circadian expression because the BMAL1:CLOCK heterodimer binds an E-box element in the NOCTURNIN promoter and activates transcription.
Protein metabolism comprises the pathways of translation, post-translational modification and protein folding.
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.
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.
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.
FUNCTION Essential component of the cytosolic iron-sulfur (Fe/S) protein assembly machinery. Required for the maturation of extramitochondrial Fe/S proteins.SUBUNIT Interacts with NAR1.MISCELLANEOUS Present with 5640 molecules/cell in log phase SD medium.SIMILARITY Belongs to the WD repeat CIA1 family.SIMILARITY Contains 7 WD repeats.
A protein interaction framework for human mRNA degradation
A mannosyltransferase gene at 11q23 is disrupted by a translocation breakpoint that co-segregates with bipolar affective disorder in a small family
SAC1-like domains of yeast SAC1, INP52, and INP53 and of human synaptojanin encode polyphosphoinositide phosphatases
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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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).
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Removal of the second mannose on the alpha 1,3 branch (Frenzel Z et al, 2003).
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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).
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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.
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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).
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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 B position (Gonzalez et al, 1999: Hirao et al, 2006).
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 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).
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LPIN1:Mg2+ (name copied from entity in Homo sapiens)
LPIN2:Mg2+ (name copied from entity in Homo sapiens)
Human GTP cyclohydrolase I: only one out of three cDNA isoforms gives rise to the active enzyme
A human mitochondrion contains about 1500 proteins, more than 99% of which are encoded in the nucleus, synthesized in the cytosol and imported into the mitochondrion. Proteins are targeted to four locations (outer membrane, intermembrane space, inner membrane, and matrix) and must be sorted accordingly (reviewed in Kutik et al. 2007, Milenkovic et al. 2007, Bolender et al. 2008, Endo and Yamano 2009). Newly synthesized proteins are transported from the cytosol across the outer membrane by the TOMM40:TOMM70 complex. Proteins that contain presequences first interact with the TOMM20 subunit of the complex while proteins that contain internal targeting elements first interact with the TOMM70 subunit. After initial interaction the protein is conducted across the outer membrane by TOMM40 subunits. In yeast some proteins such as Aco1, Atp1, Cit1, Idh1, and Atp2 have both presequences that interact with TOM20 and mature regions that interact with TOM70 (Yamamoto et al. 2009). After passage across the outer membrane, proteins may be targeted to the outer membrane via the SAMM50 complex, to the inner membrane via the TIMM22 or TIMM23 complexes (reviewed in van der Laan et al. 2010), to the matrix via the TIMM23 complex (reviewed in van der Laan et al. 2010), or proteins may fold and remain in the intermembrane space (reviewed in Stojanovski et al. 2008, Deponte and Hell 2009, Sideris and Tokatlidis 2010). Presequences on matrix and inner membrane proteins cause interaction with TIMM23 complexes; internal targeting sequences cause outer membrane proteins to interact with the SAMM50 complex and inner membrane proteins to interact with the TIMM22 complex. While in the intermembrane space hydrophobic proteins are chaperoned by the TIMM8:TIMM13 complex and/or the TIMM9:TIMM10:FXC1 complex.
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CDIPT:Mg2+/Mn2+ (name copied from entity in Homo sapiens)
The BIP (HSPA5) gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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PCYT1B dimer (name copied from entity in Homo sapiens)
Mucins are a family of high molecular weight, heavily glycosylated proteins (glycoconjugates) produced by epithelial tissues in most metazoa. Mucins' key characteristic is their ability to form gels; therefore they are a key component in most gel-like secretions, serving functions from lubrication to cell signalling to forming chemical barriers. To date, there are approximately 20 genes that express mucins. Mature mucins are composed of two distinct regions: (1) The amino- and carboxy-terminal regions are very lightly glycosylated, but rich in cysteines. The cysteine residues participate in establishing disulfide linkages within and among mucin monomers. (2) A large central region rich in serine, threonine and proline residues called the variable number of tandem repeat (VNTR) region which can become heavily O-glycosylated with hundreds of O-GalNAc glycans. N-acetyl-galactosamine (GalNAc) is the first glycan to be attached, forming the simplest mucin O-glycan. After this, several different pathways are possible generating "core" structures. Four core structures are commonly formed, several others are possible but infrequent. O-linked glycans are often capped by the addition of a sialic acid residue, terminating the addition of any more O-glycans (Brockhausen et al, 2009; Tarp and Clausen, 2008).
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After translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the body. These modifications include the internal peptide bond cleavages that activate proenzymes, the attachment of oligosaccharide moieties to membrane-bound and secreted proteins, the attachment of lipid or glycolipid moieties that serve to anchor proteins to cellular membranes, and the vitamin K-dependent attachment of carboxyl groups to glutamate residues.
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ARF1:GTP (name copied from entity in Homo sapiens)
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PISD:Pyruvoyl (name copied from entity in Homo sapiens)
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LPIN3:Mg2+ (name copied from entity in Homo sapiens)
The N-terminal fragment of ATF6-alpha contains a bZIP domain and binds the sequence CCACG in ER Stress Response Elements (ERSEs). ATF6-alpha binds ERSEs together with the heterotrimeric transcription factor NF-Y, which binds the sequence CCAAT in the ERSEs, and together the two factors activate transcription of ER stress-responsive genes. Evidence from overexpression and knockdowns indicates that ATF6-alpha is a potent activator but its homolog ATF6-beta is not and ATF6-beta may actually reduce expression of ER stress proteins.
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PCYT1A dimer (name copied from entity in Homo sapiens)
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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.
An unknown N-acetylgalactosaminyltransferase mediates the transfer of GalNAc is transferred to Tn antigens via an alpha-1,6 linkage to create Core 7 mucins (Brockhausen et al. 2009).
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Differential lysosomal proteolysis in antigen-presenting cells determines antigen fate
An unknown galactosyltransferase mediates the transfer of galactose is transferred to Tn antigens via an alpha-1,3 linkage to create Core 8 mucins (Brockhausen et al. 2009).
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An unknown N-acetylglucosaminyltransferase mediates the transfer of GlcNAc to Tn antigens via an alpha-1,3 linkage to create Core 5 mucins (Brockhausen et al. 2009).
An unknown N-acetylglucosaminyltransferase mediates the transfer of GlcNAc to Tn antigens via an beta-1,6 linkage to create Core 6 mucins (Brockhausen et al. 2009).
The role for endoplasmic reticulum stress in diabetes mellitus
ARF1/3:GTP:PI4KB (name copied from entity in Homo sapiens)
PIK3C3:Mn2+:PIK3R4:Mn2+ (name copied from entity in Homo sapiens)
PIK3R4:Mn2+ (name copied from entity in Homo sapiens)
PIK3C3:Mn2+ (name copied from entity in Homo sapiens)
The DDX11 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The DNAJB11 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The EDEM gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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GGT1 dimer (name copied from entity in Homo sapiens)
The GFPT1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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LTA4H:Zn2+ (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_28281.10
PIKFYVE:VAC14:FIG4 (name copied from entity in Homo sapiens)
Signaling through PI3Kgamma: a common platform for leukocyte, platelet and cardiovascular stress sensing
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ATF6-alpha is a transmembrane protein that normally resides in the Endoplasmic Reticulum (ER) membrane. Here its luminal C-terminal domain is associated with BiP, shielding 2 Golgi-targeting regions and thus keeping ATF6-alpha in the ER. Upon interaction of BiP with unfolded proteins in the ER, ATF6-alpha dissociates and transits to the Golgi where it is cleaved by the S1P and S2P proteases that reside in the Golgi, releasing the N-terminal domain of ATF6-alpha into the cytosol. After transiting to the nucleus, the N-terminal domain acts as a transcription factor to activate genes encoding chaperones.
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.
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 ATP6VOD1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The CTDSP2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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The CXXC1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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SPTLC1:SPTLC3 (name copied from entity in Homo sapiens)
Active N-SMase:Mg2+ (name copied from entity in Homo sapiens)
SPTLC1:SPTLC2 (name copied from entity in Homo sapiens)
GGT5 dimer (name copied from entity in Homo sapiens)
FUNCTION May play a role in chromosome segregation through establishment of sister chromatid cohesion.MISCELLANEOUS Present with 1800 molecules/cell in log phase SD medium.SIMILARITY Belongs to the MIP18 family.
Differential stimulation of cholesterol and unsaturated fatty acid biosynthesis in cells expressing individual nuclear sterol regulatory element-binding proteins
Reconstitution of the Mcm2-7p heterohexamer, subunit arrangement, and ATP site architecture
Genetic disorders of carnitine metabolism and their nutritional management.
1,2-diacyl-sn-glycero-3-phosphocholine [ChEBI:16110]
Dihydroxyacetone phosphate [ChEBI:16108]
Capping complex (GpppN..) (name copied from entity in Homo sapiens)
Capping complex (with freed 5'- GMP) (name copied from entity in Homo sapiens)
RNA Polymerase II (phosphorylated):TFIIF:capped pre-mRNA (name copied from entity in Homo sapiens)
Cap Binding Complex (CBC) (name copied from entity in Homo sapiens)
capped pre-mRNA:CBC:RNA Pol II (phosphorylated) complex (name copied from entity in Homo sapiens)
RNA Pol II with phosphorylated CTD: CE complex (name copied from entity in Homo sapiens)
ADAR1 homodimer (name copied from entity in Homo sapiens)
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Capping complex (hydrolyzed) (name copied from entity in Homo sapiens)
Capping complex (intermediate) (name copied from entity in Homo sapiens)
Covalent CE:GMP intermediate 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_81078.9
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=110182
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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=3668456
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110184
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2574.1
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
CE:Pol II CTD:Spt5 complex (name copied from entity in Homo sapiens)
TFIIH (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)
TFIIF (name copied from entity in Homo sapiens)
Capping complex (initial) (name copied from entity in Homo sapiens)
RNA polymerase II (phosphorylated):TFIIF complex (name copied from entity in Homo sapiens)
RNA Polymerase II holoenzyme complex (phosphorylated) (name copied from entity in Homo sapiens)
Architecture of the RNA polymerase II-TFIIS complex and implications for mRNA cleavage.
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Structure and function of the transcription elongation factor GreB bound to bacterial RNA polymerase.
FGFR1 fusion mutant dimers:TKIs (name copied from entity in Homo sapiens)
Formation of tubulin folding intermediates by CCT/TriC
CCBL1 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_154569.3
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=3673218
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_153507.3
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=3673219
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_166391.1
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=3673225
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_145300.5
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=3673217
CUX1-p-FGFR1 fusion mutant dimer (name copied from entity in Homo sapiens)
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CUX1-FGFR1 fusion mutant dimer (name copied from entity in Homo sapiens)
PDPK1:PIP3 (name copied from entity in Homo sapiens)
PDPK1:PIP2 (name copied from entity in Homo sapiens)
HSP90 (name copied from entity in Homo sapiens)
HSP90:Benzoquinoid ansamycins (name copied from entity in Homo sapiens)
phospho-ERK-2 dimer (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=3673051
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673036
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673054
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_167289.1
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=3673052
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673053
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673440
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673439
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_165989.1
phospho-ERK-1 dimer (name copied from entity in Homo sapiens)
cAMP:PKA regulatory subunit (name copied from entity in Homo sapiens)
ATP6V1B trimer (name copied from entity in Homo sapiens)
PKA tetramer (name copied from entity in Homo sapiens)
ATP6V1A trimer (name copied from entity in Homo sapiens)
ATP6V1G dimer (name copied from entity in Homo sapiens)
ATP6V0E (name copied from entity in Homo sapiens)
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=3673441
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_167112.1
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=3673050
Crystal structures of human GAR Tfase at low and high pH and with substrate beta-GAR
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Conservation of the human telomere sequence (TTAGGG)n among vertebrates
ATP6V0C hexamer (name copied from entity in Homo sapiens)
ATP6V0A (name copied from entity in Homo sapiens)
ATP6V0D (name copied from entity in Homo sapiens)
3alpha,7alpha,12alpha-Trihydroxy-5beta-cholestanoate [ChEBI:1698]
ESCRT-II (name copied from entity in Homo sapiens)
ESCRT-III/Cargo Complex (name copied from entity in Homo sapiens)
ESCRT-III (name copied from entity in Homo sapiens)
RAB8A/10/13/14:GTP (name copied from entity in Homo sapiens)
RAB8A/10/13/14:GDP (name copied from entity in Homo sapiens)
ATP6V0 (name copied from entity in Homo sapiens)
NODs: intracellular proteins involved in inflammation and apoptosis
V-ATPase (name copied from entity in Homo sapiens)
Arf1-GTP (name copied from entity in Homo sapiens)
Interaction between the functional polymorphisms of the alcohol-metabolism genes in protection against alcoholism.
Arf1-GDP (name copied from entity in Homo sapiens)
ESCRT-II/Cargo 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_166790.1
Ubiquinated and PIP3 Endosmal Membrane Bound Cargo (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_133429.5
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=3673254
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_130868.5
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=3673253
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_127474.5
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=3673489
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_106868.9
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1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide [ChEBI:18406]
5'-Phospho-ribosyl-5-amino-4-imidazole carboxamide
5'-Phosphoribosylformylglycinamidine [ChEBI:18413]
Sec13p:Sec31p Complex (name copied from entity in Homo sapiens)
Sar1b:GTP:Sec23p:Sec24p:Sec13p:Sec31p Complex (name copied from entity in Homo sapiens)
Sec23p:Sec24p Complex (name copied from entity in Homo sapiens)
Sar1b:Sec23p:Sec24p:Sec13p:Sec31p Complex (name copied from entity in Homo sapiens)
Identification of a novel aquaporin, AQP12, expressed in pancreatic acinar cells
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Sar1b:GTP:Sec23p:Sec24p (name copied from entity in Homo sapiens)
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Sar1b:GTP 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_31869.10
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=3673310
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_103798.9
Sar1b:GDP Complex (name copied from entity in Homo sapiens)
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_128839.5
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=3673431
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_91506.9
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=3673309
eIF4F (name copied from entity in Homo sapiens)
40S ribosomal complex (name copied from entity in Homo sapiens)
phospho-L13a associated wth the 3' UTR GAIT element of ceruloplasmin mRNA within the translation initiation complex (name copied from entity in Homo sapiens)
eIF4A subunits complex (name copied from entity in Homo sapiens)
eIF3 subunits complex (name copied from entity in Homo sapiens)
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The MIA system for protein import into the mitochondrial intermembrane space
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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_95084.9
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_105270.9
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=3673430
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_135936.5
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=3670668
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3670661
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3670660
Zizimin2: a novel, DOCK180-related Cdc42 guanine nucleotide exchange factor expressed predominantly in lymphocytes
System-wide investigation of ErbB4 reveals 19 sites of Tyr phosphorylation that are unusually selective in their recruitment properties
Understanding specificity in metabolic pathways--structural biology of human nucleotide metabolism
Endosomal proteolysis of internalized proteins.
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Modulation of mitochondrial membrane permeability in pathogenesis, autophagy and control of metabolism
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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=3666853
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3666851
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3666985
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3666967
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3666898
Facilitative Na+-independent glucose transporters
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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
Synthesis of PIPs at the plasma membrane
Regulation of Water Balance by Renal Aquaporins
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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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post exon ligation complex (name copied from entity in Homo sapiens)
ATAC C Complex (name copied from entity in Homo sapiens)
GLUT2 tetramer (name copied from entity in Homo sapiens)
GLUT3 tetramer (name copied from entity in Homo sapiens)
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GLUT1 tetramer (name copied from entity in Homo sapiens)
GLUT1:ATP (name copied from entity in Homo sapiens)
Neurotrophin signal transduction in the nervous system
GLUT4 tetramer (name copied from entity in Homo sapiens)
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glucose 6-phosphate isomerase dimer (name copied from entity in Homo sapiens)
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Iron-sulfur protein maturation in human cells: evidence for a function of frataxin
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U4 ATAC:U5:U6 ATAC Complex (name copied from entity in Homo sapiens)
U11 snRNP (name copied from entity in Homo sapiens)
SF3B (name copied from entity in Homo sapiens)
snRNP Sm core complex (name copied from entity in Homo sapiens)
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U12 snRNP (name copied from entity in Homo sapiens)
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Compartmentalization of aquaporins in the human intestine
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ATAC B Complex (name copied from entity in Homo sapiens)
U5 snRNP (name copied from entity in Homo sapiens)
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U4 ATAC snRNP (name copied from entity in Homo sapiens)
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U6 ATAC snRNP (name copied from entity in Homo sapiens)
U4 ATAC snRNP:U6 ATAC snRNP (name copied from entity in Homo sapiens)
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ADAR2 homodimer (name copied from entity in Homo sapiens)
Editosome (ADAR1) complex (name copied from entity in Homo sapiens)
A to I edited RNA:Editosome (ADAR1) complex (name copied from entity in Homo sapiens)
Editosome (ADAR2) complex (name copied from entity in Homo sapiens)
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ATAC A Complex (name copied from entity in Homo sapiens)
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mRNA (N6-adenosine)-methyltransferase (name copied from entity in Homo sapiens)
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capped, methylated pre-mRNA:CBC Complex (name copied from entity in Homo sapiens)
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A to I edited RNA:Editosome (ADAR2) complex (name copied from entity in Homo sapiens)
RNA Polymerase II holoenzyme complex (unphosphorylated) (name copied from entity in Homo sapiens)
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RNA Polymerase II (unphosphorylated):TFIIF complex (name copied from entity in Homo sapiens)
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Structure of D-3-hydroxyacyl-CoA dehydratase/D-3-hydroxyacyl-CoA dehydrogenase bifunctional protein
Identification of the major intestinal fatty acid transport protein
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Structure, function and evolution of the signal recognition particle
Decarboxylases involved in polyamine biosynthesis and their inactivation by nitric oxide
UDP-N-acetyl-D-glucosamine [ChEBI:16264]
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Activation of the FGF receptor underlies neurite outgrowth stimulated by L1, N-CAM, and N-cadherin
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4-Trimethylammoniobutanoate [ChEBI:16244]
FUNCTION Performs an essential role in the oxidative function of the citric acid cycle. Also binds RNA; specifically to the 5'-untranslated leaders of mitochondrial mRNAs.CATALYTIC ACTIVITY Isocitrate + NAD(+) = 2-oxoglutarate + CO(2) + NADH.ENZYME REGULATION Allosterically regulated by several compounds including AMP, NAD(+), and citrate.SUBUNIT Octamer of two non-identical subunits IDH1 and IDH2.MISCELLANEOUS Present with 10500 molecules/cell in log phase SD medium.SIMILARITY Belongs to the isocitrate and isopropylmalate dehydrogenases family.
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Cell cycle-dependent recruitment of telomerase RNA and Cajal bodies to human telomeres
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Structure of human nicotinamide/nicotinic acid mononucleotide adenylyltransferase. Basis for the dual substrate specificity and activation of the oncolytic agent tiazofurin.
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Hemostasis and Thrombosis: Basic Principles and Clinical Practice
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Mitochondrial frataxin interacts with ISD11 of the NFS1/ISCU complex and multiple mitochondrial chaperones
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The general transcription factors of RNA polymerase II.
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PKC-beta controls I kappa B kinase lipid raft recruitment and activation in response to BCR signaling
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ChEBI:16290 5alpha-cholesta-7,24-dien-3beta-ol
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Amino acid transport across mammalian intestinal and renal epithelia
Caspase-activated PAK-2 is regulated by subcellular targeting and proteasomal degradation
Total enzymic synthesis of cholesterol from lanosterol. Cytochrome b5-dependence of 4-methyl sterol oxidase.
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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_2558.2
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Structure-function relationships in dihydrolipoamide acyltransferases.
Substrate specificity of the TIM22 mitochondrial import pathway revealed with small molecule inhibitor of protein translocation
Functional impairment of lens aquaporin in two families with dominantly inherited cataracts
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Phosphorylation of threonine 210 and the role of serine 137 in the regulation of mammalian polo-like kinase
Processing of N-linked carbohydrate chains in a patient with glucosidase I deficiency (CDG type IIb)
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Activation of human mitochondrial pantothenate kinase 2 by palmitoylcarnitine
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phosphofructokinase, P3L complex (name copied from entity in Homo sapiens)
phosphofructokinase, P2L2 complex (name copied from entity in Homo sapiens)
phosphofructokinase, L4 complex (name copied from entity in Homo sapiens)
phosphofructokinase, P4 complex (name copied from entity in Homo sapiens)
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The SUMO pathway: emerging mechanisms that shape specificity, conjugation and recognition
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Involvement of Rac/Cdc42/PAK pathway in cytoskeletal rearrangements
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Pentose phosphate pathway (hexose monophosphate shunt)
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
Biochemical and genetic aspects of mevalonate kinase and its deficiency
Activation of Chaperone Genes by ATF6-alpha
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
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
Editing-defective tRNA synthetase causes protein misfolding and neurodegeneration
Conversion of palmitic acid to very long chain fatty acyl-CoAs
Synthesis of very long-chain fatty acyl-CoAs
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Yeast kinesin-8 depolymerizes microtubules in a length-dependent manner
Primary structure of a human trifunctional enzyme. Isolation of a cDNA encoding methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase-formyltetrahydrofolate synthetase.
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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
Characterization of myotubularin-related protein 7 and its binding partner, myotubularin-related protein 9
Cloning and expression of cDNA of human delta 4-3-oxosteroid 5 beta-reductase and substrate specificity of the expressed enzyme
Disulphide bond formation in the intermembrane space of mitochondria
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Synthesis of PIPs at the early endosome membrane
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Mitochondrial GTP-AMP phosphotransferase. 2. Kinetic and equilibrium dialysis studies
Molecular basis of phenotypic variation in patients with argininemia
Protease-activated receptors in hemostasis, thrombosis and vascular biology
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RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription
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GPVI and integrin alphaIIb beta3 signaling in platelets
Cloning and functional characterization of the human GLUT7 isoform SLC2A7 from the small intestine
Am J Physiol Gastrointest Liver Physiol 287:G236-42
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Cloning and characterization a novel human 1-acyl-sn-glycerol-3-phosphate acyltransferase gene AGPAT7
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Trk receptors: roles in neuronal signal transduction
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The RNA polymerase II elongation complex.
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Diacylglycerol metabolism and arachidonic acid release in human fetal membranes and decidua vera
Purification and subunit structure studies of human placental threonyl-tRNA synthetase
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The oxidation of pyruvate in pigeon breast muscle
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Crystal structure of human arginase I at 1.29-A resolution and exploration of inhibition in the immune response
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Reconstitution of the transcription factor TFIIH: assignment of functions for the three enzymatic subunits, XPB, XPD, and cdk7
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FUNCTION Probable oxidoreductase which may be involved in DNA replication.SIMILARITY In the C-terminal section; belongs to the flavoprotein pyridine nucleotide cytochrome reductase family.SIMILARITY Contains 1 FAD-binding FR-type domain.SIMILARITY Contains 1 flavodoxin-like domain.
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AS160, the Akt substrate regulating GLUT4 translocation, has a functional Rab GTPase-activating protein domain
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Step-size analyses of the mitochondrial Hsp70 import motor reveal the Brownian ratchet in operation
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Mechanisms of caspase-1 activation by P2X7 receptor-mediated K+ release
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Complementation of Saccharomyces cerevisiae coq7 mutants by mitochondrial targeting of the Escherichia coli UbiF polypeptide: two functions of yeast Coq7 polypeptide in coenzyme Q biosynthesis
An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor
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Platelets in thrombotic and non-thrombotic disorders.
La proteins from Drosophila melanogaster and Saccharomyces cerevisiae: a yeast homolog of the La autoantigen is dispensable for growth.
Phosphorylation of the protein kinase C-theta activation loop and hydrophobic motif regulates its kinase activity, but only activation loop phosphorylation is critical to in vivo nuclear-factor-kappaB induction
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The second messenger system of mouse epidermis. IV. Cyclic AMP and cyclic GMP phosphodiesterase.
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FUNCTION Essential component of the PAM complex, a complex required for the translocation of transit peptide-containing proteins from the inner membrane into the mitochondrial matrix in an ATP-dependent manner. In the complex, it is required to stimulate activity of mtHSP70 (SSC1).SUBUNIT Homodimer and heterodimer with PAM16/TIM16. Homodimerization may not be relevant in vivo, while heterodimerization is essential for activity regulation of mtHSP70. Component of the PAM complex, at least composed of mtHsp70, MGE1, TIM44, PAM16, PAM17 and PAM18/TIM14. Interacts directly with mtHsp70. Interacts directly with TIM17 subunit of the TIM23 complex.DOMAIN The J domain is essential for co-chaperone activity and mediates the heterodimerization with the J-like domain of PAM16.SIMILARITY Belongs to the TIM14 family.SIMILARITY Contains 1 J domain.
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The Protein Biosynthesis Elongation Cycle
Translational Control of Gene Expression89-127
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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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Insulin degradation: mechanisms, products, and significance.
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CATALYTIC ACTIVITY A polyprenyl diphosphate + 4-hydroxybenzoate = diphosphate + a 4-hydroxy-3-polyprenylbenzoate.PATHWAY Cofactor biosynthesis; ubiquinone biosynthesis.SIMILARITY Belongs to the UbiA prenyltransferase family.
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Cytochrome P450s and cholesterol homeostasis
FUNCTION Senses unfolded proteins in the lumen of the endoplasmic reticulum via its N-terminal domain which leads to enzyme auto-activation. The active endoribonuclease domain splices HAC1 precursor mRNA to produce the mature form which then induces transcription of UPR target genes.CATALYTIC ACTIVITY ATP + a protein = ADP + a phosphoprotein.COFACTOR Magnesium.ENZYME REGULATION The kinase domain is activated by trans-autophosphorylation. Kinase activity is required for activation of the endoribonuclease domain.SUBUNIT Homodimer; in response to the accumulation of unfolded proteins.PTM Autophosphorylated mainly on serine residues.MISCELLANEOUS Present with 259 molecules/cell in log phase SD medium.SIMILARITY Belongs to the protein kinase superfamily. Ser/Thr protein kinase family.SIMILARITY Contains 1 KEN domain.SIMILARITY Contains 1 protein kinase domain.
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FUNCTION TFIIIC mediates tRNA and 5S RNA gene activation by binding to intragenic promoter elements. Upstream of the transcription start site, TFIIIC assembles the initiation complex TFIIIB-TFIIIC-tDNA, which is sufficient for RNA polymerase III recruitment and function. Part of the tauA domain of TFIIIC that binds boxA DNA promoter sites of tRNA and similar genes. Participates in the interconnection of tauA with tauB via its contacts with TFC3 and TFC6. Serves as a scaffold critical for tauA-DNA spatial configuration and tauB-DNA stability.SUBUNIT Component of the TFIIIC complex composed of TFC1, TFC3, TFC4, TFC6, TFC7 and TFC8. The subunits are organized in two globular domains, tauA and tauB, connected by a proteolysis-sensitive and flexible linker. Interacts with TFC3, TFC4 and TFC6.MISCELLANEOUS Present with 15800 molecules/cell in log phase SD medium.SIMILARITY Belongs to the TFIIIC subunit 5 family.
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FUNCTION DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific core component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs.SUBUNIT Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits.MISCELLANEOUS Present with 2520 molecules/cell in log phase SD medium.SIMILARITY Belongs to the eukaryotic RPC3/POLR3C RNA polymerase subunit family.
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Structural basis of hereditary coproporphyria
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7alpha,26-dihydroxy-5beta-cholestan-3-one [ChEBI:48778]
Cell signaling by receptor tyrosine kinases
Evolutionary conservation and adaptation in the mechanism that regulates SREBP action: what a long, strange tRIP it's been
Monoamine metabolism and behavioral responses to ethanol in mitochondrial aldehyde dehydrogenase knockout mice
Class I MHC mediated antigen processing & presentation
Interleukin 2 high-affinity receptor expression requires two distinct binding proteins
Sequence, tissue distribution, and chromosomal localization of mRNA encoding a human glucose transporter-like protein
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
Structure-function analysis of liver-type (GLUT2) and brain-type (GLUT3) glucose transporters: expression of chimeric transporters in Xenopus oocytes suggests an important role for putative transmembrane helix 7 in determining substrate selectivity
Molecular components of the mammalian circadian clock
Structural basis of guanine nucleotide exchange mediated by the T-cell essential Vav1
Regulation of the anaphase-promoting complex by the dual specificity phosphatase human Cdc14a
The NRAMP family of metal-ion transporters
Biochemistry of signal transduction and regulation
Type II phosphoinositide 5-phosphatases have unique sensitivities towards fatty acid composition and head group phosphorylation
Biogenesis of the essential Tim9-Tim10 chaperone complex of mitochondria: site-specific recognition of cysteine residues by the intermembrane space receptor Mia40
Substrate preferences of a lysophosphatidylcholine acyltransferase highlight its role in phospholipid remodeling
Structure, localization, and regulation of cGMP-inhibited phosphodiesterase (PDE3)
The methylation of phosphatidylethanolamine
Immunolocalization of AQP9 in liver, epididymis, testis, spleen, and brain
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Myotubularin lipid phosphatase binds the hVPS15/hVPS34 lipid kinase complex on endosomes
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Temporal and spatial regulation of the phosphatidate phosphatases lipin 1 and 2
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Fibroblast Growth Factor Receptor (FGFR) signaling
FUNCTION Key enzyme involved in DNA replication and DNA repair. Involved in Okazaki fragments processing by cleaving long flaps that escape FEN1: flaps that are longer than 27 nucleotides are coated by replication protein A complex (RPA), leading to recruit DNA2 which cleaves the flap until it is too short to bind RPA and becomes a substrate for FEN1. Also involved in 5'-end resection of DNA during double-strand break (DSB) repair by mediating the cleavage of 5'-ssDNA. Possesses different enzymatic activities, such as single-stranded DNA (ssDNA)-dependent ATPase, 5'-3' helicase and endonuclease activities. While the ATPase and endonuclease activities are well-defined and play a key role in Okazaki fragments processing and DSB repair, the 5'-3' DNA helicase activity is atypical: it cannot load onto its tracking strand internally and has an absolute free 5'-end requirement. Helicase activity may promote the motion of DNA2 on the flap, helping the nuclease function.CATALYTIC ACTIVITY ATP + H(2)O = ADP + phosphate.COFACTOR Binds 1 4Fe-4S cluster.PTM Phosphorylated at Ser-17 and Ser-237 by CDK1 in response to DNA damage, leading to promote recruitment to double-strand break (DSB) sites and DNA resection.SIMILARITY Belongs to the DNA2/NAM7 helicase family.
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Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane
COPII (Coat Protein 2) Mediated Vesicle Transport
Chaperonin-mediated folding of vertebrate actin-related protein and gamma-tubulin
Synaptojanin 2, a novel Rac1 effector that regulates clathrin-mediated endocytosis
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Identification of genetic mutations in Japanese patients with fructose-1,6-bisphosphatase deficiency
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Fibroblast growth factor receptors: lessons from the genes
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Determinants of function and substrate specificity in human UDP-galactose 4'-epimerase
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The Mechanism of Hsp90 regulation by the protein kinase-specific cochaperone p50(cdc37)
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1D-myo-Inositol 1,3,4-trisphosphate [ChEBI:810]
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CD14 controls the LPS-induced endocytosis of Toll-like receptor 4
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Role of phosphatidylinositol 3,4,5-trisphosphate in regulating the activity and localization of 3-phosphoinositide-dependent protein kinase-1
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An interaction between frataxin and Isu1/Nfs1 that is crucial for Fe/S cluster synthesis on Isu1
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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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Cutting edge: Role of Toll-like receptor 9 in CpG DNA-induced activation of human cells
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FUNCTION Essential component of the TIM23 complex, a complex that mediates the translocation of transit peptide-containing proteins across the mitochondrial inner membrane. Required to direct preproteins in transit and direct them to the channel protein TIM23, and possibly facilitates transfer of the translocating proteins from the TOM complex to the TIM23 complex. Does not act as a structural subunit of the TIM23 complex but plays a dynamic role in protein import. Has no phosphatase activity.SUBUNIT Component of the TIM23 complex, at least composed of TIM23, TIM17, TIM50 and TIM21. Interacts directly with TIM23. Interacts with preproteins in transit.DOMAIN The mitochondrial intermembrane region is required for generation but not stabilization of the TIM23 complex.DOMAIN The FCP1 homology domain does not contain the canonical D-x-D-x-[TV] active site, suggesting that it probably does not display phosphatase activity.MISCELLANEOUS Present with 2400 molecules/cell in log phase SD medium.SIMILARITY Belongs to the TIM50 family.SIMILARITY Contains 1 FCP1 homology domain.
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Serotonin clearance from the synaptic cleft
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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)
The nonsense-mediated decay RNA surveillance pathway
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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
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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ChEBI:60125 N-epsilon-(1-(1-carboxy)ethyl)lysine
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Frizzled/PCP signalling: a conserved mechanism regulating cell polarity and directed motility
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Biochemical analysis of the intrinsic Mcm4-Mcm6-mcm7 DNA helicase activity.
MMS19 assembles iron-sulfur proteins required for DNA metabolism and genomic integrity
MMS19 links cytoplasmic iron-sulfur cluster assembly to DNA metabolism
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adenosine 5'-monophosphate [ChEBI:16027]
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5'-Phosphoribosyl-N-formylglycinamide [ChEBI:18272]
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ChEBI:18278 N-acetyl-D-glucosaminyldiphosphodolichol
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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
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3-Phospho-D-glyceroyl phosphate [ChEBI:16001]
(R)-2-Hydroxy-3-(phosphonooxy)-1-monoanhydridewith phosphoric propanoic acid
Two aldehyde dehydrogenases from human liver. Isolation via affinity chromatography and characterization of the isozymes.
Specificity of the deoxyhypusine hydroxylase-eukaryotic translation initiation factor (eIF5A) interaction: identification of amino acid residues of the enzyme required for binding of its substrate, deoxyhypusine-containing eIF5A
Cloning, expression and characterization of the pig liver GDP-mannose pyrophosphorylase. Evidence that GDP-mannose and GDP-Glc pyrophosphorylases are different proteins
Sentrin-specific protease 1 ecNumber3.4.22.68/ecNumber
Sentrin-specific protease 2 ecNumber3.4.22.68/ecNumber
Isolation and initial characterization of the single polypeptide that synthesizes uridine 5'-monophosphate from orotate in Ehrlich ascites carcinoma. Purification by tandem affinity chromatography of uridine-5'-monophosphate synthase
The protein deficient in Lowe syndrome is a phosphatidylinositol-4,5-bisphosphate 5-phosphatase
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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
Replication factors required for SV40 DNA replication in vitro. II. Switching of DNA polymerase alpha and delta during initiation of leading and lagging strand synthesis.
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Coupling of rotation and catalysis in F(1)-ATPase revealed by single-molecule imaging and manipulation
Enzymatic activities in cultured human lymphocytes that dephosphorylate dolichyl pyrophosphate and dolichyl phosphate
WW domain-containing proteins, WWOX and YAP, compete for interaction with ErbB-4 and modulate its transcriptional function
Exosomes mediate stromal mobilization of autocrine Wnt-PCP signaling in breast cancer cell migration
Interactions between UPF1, eRFs, PABP and the exon junction complex suggest an integrated model for mammalian NMD pathways
Aminoacyl tRNA synthetases and their connections to disease
Expression and characterization of a human mitochondrial phenylalanyl-tRNA synthetase
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Human phosphoglycerate kinase. I. Crystallization and characterization of normal enzyme
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Cytosolic aldehyde dehydrogenase (ALDH1) variants found in alcohol flushers
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Crystal structures of recombinant human dihydrofolate reductase complexed with folate and 5-deazafolate
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Synthesis of Leukotrienes (LT) and Eoxins (EX)
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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_32705.10
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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=965131
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Identification of two essential glutamic acid residues in glycogen synthase
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EJC-independent degradation of nonsense immunoglobulin-mu mRNA depends on 3' UTR length
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Pathways of DNA double-strand break repair during the mammalian cell cycle.
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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_79234.9
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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_136710.5
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ChEBI:11805 3-hydroxy-2-methylpropanoate
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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_84845.9
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_86490.9
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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=169509
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7812.1
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_7610.1
Amino acid transport across the plasma membrane
Characterization of the gene encoding human peroxisomal 3-oxoacyl-CoA thiolase (ACAA). No large DNA rearrangement in a thiolase-deficient patient
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Studies on the metabolic fate of n-3 polyunsaturated fatty acids
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CDC42-GTP:WASP/N-WASP (name copied from entity in Homo sapiens)
PAK1 dimer (name copied from entity in Homo sapiens)
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AGE adducts:Peptide:AGER-1,2,3 (name copied from entity in Homo sapiens)
CDC42-GDP (name copied from entity in Homo sapiens)
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SUGT1:HSP90 (name copied from entity in Homo sapiens)
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Ub:substrate (name copied from entity in Homo sapiens)
E3:K48-polyubiquitinated substrate (name copied from entity in Homo sapiens)
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E3:Ub:substrate (name copied from entity in Homo sapiens)
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Ubiquitin:E2 conjugating enzymes (name copied from entity in Homo sapiens)
PAK bound to Rac1 and Cdc42 (name copied from entity in Homo sapiens)
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RAC1/CDC42:PAK dimer (name copied from entity in Homo sapiens)
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CDC6 association with the ORC:origin complex
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_141960.5
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=3673073
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_146407.5
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Kinetic evaluation of human cloned coproporphyrinogen oxidase using a ring isomer of the natural substrate
Apical GLUT2: a major pathway of intestinal sugar absorption
Wnt/Fz signaling and the cytoskeleton: potential roles in tumorigenesis
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Scriver CR, et al., editors) 1:1553-1587
Mutations in exon 3 of the glycogen debranching enzyme gene are associated with glycogen storage disease type III that is differentially expressed in liver and muscle.
Determinants for activation of the atypical AGC kinase Greatwall during M phase entry
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ABC transporters and cholesterol metabolism
The TREM receptor family and signal integration
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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=3665781
IRE1 homodimer (name copied from entity in Homo sapiens)
IRE1 homodimer (phosphorylated) (name copied from entity in Homo sapiens)
Phosphorylated Ire1 Dimer:ADP Complex (yeast)
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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=3665844
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Telomeres shorten during ageing of human fibroblasts
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Prostaglandin F2alpha formation from prostaglandin H2 by prostaglandin F synthase (PGFS): crystal structure of PGFS containing bimatoprost
Rad51 recombinase and recombination mediators.
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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_11734.2
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_166582.1
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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=197238
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The zinc-binding protein Hot13 promotes oxidation of the mitochondrial import receptor Mia40
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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=3672999
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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=3672997
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672996
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_166821.1
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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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FUNCTION Component of the PAM complex, a complex required for the translocation of transit peptide-containing proteins from the inner membrane into the mitochondrial matrix in an ATP-dependent manner. In the complex, it is required to organize PAM16-PAM18 (TIM16-TIM14) heterodimer.SUBUNIT Component of the PAM complex, at least composed of mtHsp70, MGE1, TIM44, PAM16, PAM17 and PAM18/TIM14.MISCELLANEOUS Present with 3000 molecules/cell in log phase SD medium.SIMILARITY Belongs to the PAM17 family.
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Secretion of Wnt ligands requires Evi, a conserved transmembrane protein
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Wntless, a conserved membrane protein dedicated to the secretion of Wnt proteins from signaling cells
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_11729.2
Two novel rat liver membrane proteins that bind advanced glycosylation endproducts: relationship to macrophage receptor for glucose-modified proteins
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unfolded protein:(Glc)2 (GlcNAc)2 (Man)9 (Asn)1 (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)
Renal physiology of SLC26 anion exchangers
Human alanyl-tRNA synthetase: conservation in evolution of catalytic core and microhelix recognition
2xGNPNAT1 (name copied from entity in Homo sapiens)
2xUAP1-2 (name copied from entity in Homo sapiens)
Lysophospholipid acyltransferases: 1-acylglycerol-3-phosphate O-acyltransferases (AGPATs) From discovery to disease
2xUAP1 (name copied from entity in Homo sapiens)
unfolded protein:(Glc)3 (GlcNAc)2 (Man)9 (Asn)1 (name copied from entity in Homo sapiens)
Human Na(+)/H(+) exchanger isoform 6 is found in recycling endosomes of cells, not in mitochondria
unfolded protein:(GlcNAc)2 (Man)8a (name copied from entity in Homo sapiens)
unfolded protein:(GlcNAc)2 (Man)7aa (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
Database identifier. Use 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
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_90894.9
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=200499
Database identifier. Use 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
COFACTOR Binds 4Fe-4S.COFACTOR Binds 2Fe-2S.SUBUNIT Interacts with TAH18.PTM Ubiquitinated.MISCELLANEOUS Present with 1050 molecules/cell in log phase SD medium.SIMILARITY Belongs to the anamorsin family.
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669618
The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs
Reactome stable identifier. Use this 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
CCT/TriC (ADP) associated actin (name copied from entity in Homo sapiens)
CCT/TriC(ATP)-associated actin (name copied from entity in Homo sapiens)
CCT/TriC(ADP) (name copied from entity in Homo sapiens)
CCT/TriC(ATP):unfolded tubulin complex (name copied from entity in Homo sapiens)
p-5Y-PKC-theta:DAG (name copied from entity in Homo sapiens)
CCT/TriC(ADP)-associated non-native tubulin (name copied from entity in Homo sapiens)
RAC1/CDC42:p-S144,T423-PAK (name copied from entity in Homo sapiens)
DOHH:Fe++ (name copied from entity in Homo sapiens)
CCT/TriC(ATP) (name copied from entity in Homo sapiens)
deoxyhypusine synthase tetramer (name copied from entity in Homo sapiens)
1,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6)tetrakisphosphate
1,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6)tetrakisphosphate [ChEBI:62923]
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=426755
3-diphospho-1D-myo-inositol (1,2,4,5,6)pentakisphosphate
3-diphospho-1D-myo-inositol (1,2,4,5,6)pentakisphosphate [ChEBI:62922]
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120138.1
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=1500578
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118995.1
3-diphospho-1D-myo-inositol (1,4,5,6)tetrakisphosphate
3-diphospho-1D-myo-inositol (1,4,5,6)tetrakisphosphate [ChEBI:62927]
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668171
1-diphospho-1D-myo-inositol (3,4,5,6)tetrakisphosphate
1-diphospho-1D-myo-inositol (3,4,5,6)tetrakisphosphate [ChEBI:62926]
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3,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6)tetrakisphosphate
3,5-bisdiphosphoinositol-1D-myo-inositol (2,3,4,6)tetrakisphosphate [ChEBI:62924]
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1-diphospho-1D-myo-inositol (2,3,4,5,6)pentakisphosphate [ChEBI:62919]
1-diphospho-1D-myo-inositol (2,3,4,5,6)pentakisphosphate
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1,5-bisdiphosphoinositol-1D-myo-inositol (3,4,6)trisphosphate
1,5-bisdiphosphoinositol-1D-myo-inositol (3,4,6)trisphosphate [ChEBI:62931]
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Precise binding of single-stranded DNA termini by human RAD52 protein.
5-diphospho-1D-myo-inositol (1,3,4,6)tetrakisphosphate
5-diphospho-1D-myo-inositol (1,3,4,6)tetrakisphosphate [ChEBI:62928]
The nuclease activity of Mre11 is required for meiosis but not for mating type switching, end joining, or telomere maintenance
Heteroduplex formation by human Rad51 protein: effects of DNA end-structure, hRP-A and hRad52.
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Human frataxin is an allosteric switch that activates the Fe-S cluster biosynthetic complex
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Replication protein A (RPA): the eukaryotic SSB.
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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
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Identification of mammalian microRNA host genes and transcription units
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Crystal structure of human kynurenine aminotransferase I
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Characterization of phospholipase D activity in bovine photoreceptor membranes
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Tim23-Tim50 pair coordinates functions of translocators and motor proteins in mitochondrial protein import
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Inactivation of glycogen synthetase and activation of phosphorylase kinase by muscle adenosine 3',5'-monophosphate-dependent protein kinases
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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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Hepatocyte nuclear factor-1alpha recruits the transcriptional co-activator p300 on the GLUT2 gene promoter
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Hepatic and neuromuscular forms of glycogen storage disease type IV caused by mutations in the same glycogen-branching enzyme gene.
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Human platelets contain SNARE proteins and a Sec1p homologue that interacts with syntaxin 4 and is phosphorylated after thrombin activation: implications for platelet secretion
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The binding of a transcription factor to deletion mutants of a 5S ribosomal RNA gene
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Purification and partial amino acid sequence of human aconitase
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Crystal structure of an Hsp90-geldanamycin complex: targeting of a protein chaperone by an antitumor agent
Metabolism of steroid hormones and vitamin D
FUNCTION Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative helicase essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells. The active ATPase sites in the MCM2-7 ring are formed through the interaction surfaces of two neighboring subunits such that a critical structure of a conserved arginine finger motif is provided in trans relative to the ATP-binding site of the Walker A box of the adjacent subunit. The six ATPase active sites, however, are likely to contribute differentially to the complex helicase activity. Once loaded onto DNA, double hexamers can slide on dsDNA in the absence of ATPase activity. Required for S phase execution.CATALYTIC ACTIVITY ATP + H(2)O = ADP + phosphate.SUBUNIT Component of the MCM2-7 complex. The complex forms a toroidal hexameric ring with the proposed subunit order MCM2-MCM6-MCM4-MCM7-MCM3-MCM5; loaded onto DNA, forms a head-head double hexamer.MISCELLANEOUS Present with 8800 molecules/cell in log phase SD medium.MISCELLANEOUS Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. Specifically a MCM467 subcomplex is shown to have in vitro helicase activity which is inhibited by the MCM2 subunit. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY Belongs to the MCM family.SIMILARITY Contains 1 MCM domain.
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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
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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
Inositol polyphosphates: a new frontier for regulating gene expression
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Phospholipases D1 and D2 coordinately regulate macrophage phagocytosis
Mast cell signal transduction from the high-affinity IgE receptor
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CATALYTIC ACTIVITY Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).SUBUNIT Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits.MISCELLANEOUS Present with 1950 molecules/cell in log phase SD medium.SIMILARITY Belongs to the RNA polymerase beta chain family.
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Synthesis of prostaglandin F ethanolamide by prostaglandin F synthase and identification of Bimatoprost as a potent inhibitor of the enzyme: new enzyme assay method using LC/ESI/MS
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Ligand-independent dimerization activates the stress response kinases IRE1 and PERK in the lumen of the endoplasmic reticulum
eIF2B subunits complex (name copied from entity in Homo sapiens)
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eIF2:GDP (name copied from entity in Homo sapiens)
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SRP receptor (name copied from entity in Homo sapiens)
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SRP:polypeptide+signal:ribosome (name copied from entity in Homo sapiens)
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eIF2:GDP: eIF2B (name copied from entity in Homo sapiens)
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ribosome:mRNA:polypeptide+signal (name copied from entity in Homo sapiens)
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Human glutamine phosphoribosylpyrophosphate amidotransferase. Kinetic and regulatory properties
80S:Met-tRNAi:mRNA:aminoacyl-tRNA (name copied from entity in Homo sapiens)
Elongation complex with growing peptide chain (name copied from entity in Homo sapiens)
Signal Recognition Particle (name copied from entity in Homo sapiens)
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SRP receptor:SRP:ribosome:polypeptide+signal (name copied from entity in Homo sapiens)
40S:Met-tRNAi:mRNA (name copied from entity in Homo sapiens)
Human thymidylate kinase. Purification, characterization, and kinetic behavior of the thymidylate kinase derived from chronic myelocytic leukemia
Rich, a rho GTPase-activating protein domain-containing protein involved in signaling by Cdc42 and Rac1
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Dynamics of transitional endoplasmic reticulum sites in vertebrate cells
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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_29575.10
AUF1 p37 Tetramer (name copied from entity in Homo sapiens)
Phosphorylated AUF1 p40 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_107311.9
AUF1 Tetramer: Destabilized mRNA Complex (name copied from entity in Homo sapiens)
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_104953.9
AUF1 p37 Dimer (name copied from entity in Homo sapiens)
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Ran:GTP:Exportin-5 (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_107359.9
Ran:GTP (name copied from entity in Homo sapiens)
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Sequence survey of receptor tyrosine kinases reveals mutations in glioblastomas
pre-miRNA:Ran:GTP:Exportin-5 (name copied from entity in Homo sapiens)
Ran-GTP (name copied from entity in Homo sapiens)
StAR protein and the regulation of steroid hormone biosynthesis
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673069
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_81914.9
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Ubiquitinated AUF1 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_93304.9
80S:Met-tRNAi:mRNA:eIF5B:GTP (name copied from entity in Homo sapiens)
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eIF5B:GTP (name copied from entity in Homo sapiens)
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80S:Met-tRNAi:mRNA (name copied from entity in Homo sapiens)
eIF5B:GDP (name copied from entity in Homo sapiens)
40S:eIF3:eIF1A (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=3673075
mRNP (name copied from entity in Homo sapiens)
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eIF4F:mRNP (name copied from entity in Homo sapiens)
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48S complex (name copied from entity in Homo sapiens)
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Ubiquitinated AUF1 Tetramer: Destabilized mRNA Complex (name copied from entity in Homo sapiens)
Phosphorylated AUF1 p40 Tetramer (name copied from entity in Homo sapiens)
Transcription-coupled (TC) repair complex (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)
PAK homodimer (name copied from entity in Homo sapiens)
CDC42:GTP (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)
PKC-theta (open): DAG (name copied from entity in Homo sapiens)
PDK1:PIP2,PIP3 (name copied from entity in Homo sapiens)
Active Pol II complex with repaired DNA template:mRNA hybrid (name copied from entity in Homo sapiens)
Stalled Pol II in TC-NER (name copied from entity in Homo sapiens)
Dynamic interaction between Isp45 and mitochondrial hsp70 in the protein import system of the yeast mitochondrial inner membrane
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)
RAD51:resected ends of DNA double-strand break (name copied from entity in Homo sapiens)
XPC:HR23B complex (name copied from entity in Homo sapiens)
ERCC1:XPF complex (name copied from entity in Homo sapiens)
pre-incision complex with open DNA bubble (name copied from entity in Homo sapiens)
Incision complex with 3'-incised damaged DNA (name copied from entity in Homo sapiens)
incision complex for GG-NER (name copied from entity in Homo sapiens)
XPC:HR23B:damaged DNA complex (name copied from entity in Homo sapiens)
RPA heterotrimer (name copied from entity in Homo sapiens)
pre-incision complex in GG-NER (name copied from entity in Homo sapiens)
Structural basis for tumor pyruvate kinase M2 allosteric regulation and catalysis
Phosphoinositides as regulators of membrane trafficking in health and disease
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)
hNTH1 glycosylase: foramidopyrimidine complex (name copied from entity in Homo sapiens)
hNTH1 glycosylase:thymine glycol complex (name copied from entity in Homo sapiens)
REV1:damaged DNA template complex (name copied from entity in Homo sapiens)
Pol eta:damaged DNA template complex (name copied from entity in Homo sapiens)
REV1:lesioned DNA template with misinserted bases (name copied from entity in Homo sapiens)
RAD50:MRE11 complex (name copied from entity in Homo sapiens)
dimeric phospho-ATM complex (name copied from entity in Homo sapiens)
dimeric ATM kinase (name copied from entity in Homo sapiens)
Pol eta:lesioned DNA template inserted with correct base complement (name copied from entity in Homo sapiens)
RhoGTPase:GDP (name copied from entity in Homo sapiens)
RhoA,B,C:GDP (name copied from entity in Homo sapiens)
RhoA/B/C:GTP (name copied from entity in Homo sapiens)
WLS:retromer (name copied from entity in Homo sapiens)
VPS35:VPS29:VPS26 (name copied from entity in Homo sapiens)
hOGG1 glycosylase:8-oxo guanine complex (name copied from entity in Homo sapiens)
DNA containing an hOGG1-bound apurinic/apyrimidinic site (name copied from entity in Homo sapiens)
hOGG1 glycosylase: formamidopyrimidine complex (name copied from entity in Homo sapiens)
hNTH1 glycosylase:dihydrouracil complex (name copied from entity in Homo sapiens)
hNTH1 glycosylase:cytosine glycol complex (name copied from entity in Homo sapiens)
RhoA (Mg cofactor):GTP (name copied from entity in Homo sapiens)
RhoA (Mg cofactor):GDP (name copied from entity in Homo sapiens)
PIP3:PDK1 complex (name copied from entity in Homo sapiens)
Activated mTORC1 (name copied from entity in Homo sapiens)
Rheb:GTP (name copied from entity in Homo sapiens)
Rheb:GDP (name copied from entity in Homo sapiens)
ATP2C1/2:Mg2+ (name copied from entity in Homo sapiens)
RhoGTPase:GTP (name copied from entity in Homo sapiens)
Inactivated RhoGTPase:GDP:GDI complex (name copied from entity in Homo sapiens)
PIP3:RhoA (name copied from entity in Homo sapiens)
Fructose transporter in human spermatozoa and small intestine is GLUT5
AQP9 tetramer (name copied from entity in Homo sapiens)
AQP7 tetramer (name copied from entity in Homo sapiens)
AQP10 tetramer (name copied from entity in Homo sapiens)
ABC7 dimer (name copied from entity in Homo sapiens)
AQP3 tetramer (name copied from entity in Homo sapiens)
Aquaporins that transport water across the plasma membrane.
AQP0 (MIP), AQP1, p-AQP2, AQP3, AQP4, AQP5, AQP7, AQP8, AQP9, AQP10, AQP11
Aquaporin-0, Aquaporin-1, Phospho-Aquaporin-2, Aquaporin-3, Aquaporin-4, Aquaporin-5, Aquaporin-7, Aquaporin-8, Aquaporin-9, Aquaporin-10, Aquaporin-11
The characterization of gene mutations for human glucose phosphate isomerase deficiency associated with chronic hemolytic anemia
DOCK-GEFs:RAC1, CDC42 (name copied from entity in Homo sapiens)
Tumor necrosis factor alpha-induced phosphorylation of I kappa B alpha is a signal for its degradation but not dissociation from NF-kappa B
Rabenosyn-5:VPS-45 (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)
KIF18A dimer (name copied from entity in Homo sapiens)
CENP-E dimer (name copied from entity in Homo sapiens)
Kinesin-5 homotetramer (name copied from entity in Homo sapiens)
Kinesin-10 (name copied from entity in Homo sapiens)
Kinesin-14 (name copied from entity in Homo sapiens)
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From structure to disease: the evolving tale of aquaporin biology
ABCD1:ABCD2 (name copied from entity in Homo sapiens)
VAV2 Rho/Rac effectors:GDP (name copied from entity in Homo sapiens)
eEF2:GTP (name copied from entity in Homo sapiens)
VAV3 Rho/Rac effectors:GDP (name copied from entity in Homo sapiens)
VAV2 Rho/Rac effectors:GTP (name copied from entity in Homo sapiens)
VAV family:PIP3 (name copied from entity in Homo sapiens)
VAV3 Rho/Rac effectors:GTP (name copied from entity in Homo sapiens)
Protein kinase C, novel isoforms:DAG (name copied from entity in Homo sapiens)
VAV family:PIP2 (name copied from entity in Homo sapiens)
Activated PKC alpha (name copied from entity in Homo sapiens)
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Signal transduction by immunoglobulin is mediated through Ig alpha and Ig beta
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Activated PKC beta (name copied from entity in Homo sapiens)
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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
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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
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D box and KEN box motifs in budding yeast Hsl1p are required for APC-mediated degradation and direct binding to Cdc20p and Cdh1p
Evidence that negative elongation factor represses transcription elongation through binding to a DRB sensitivity-inducing factor/RNA polymerase II complex and RNA.
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FUNCTION Required for the import and folding of small cysteine-containing proteins (small Tim) in the mitochondrial intermembrane space (IMS). Forms a redox cycle with ERV1 that involves a disulfide relay system. Precursor proteins to be imported into the IMS are translocated in their reduced form into the mitochondria. The oxidized form of MIA40 forms a transient intermolecular disulfide bridge with the reduced precursor protein, resulting in oxidation of the precursor protein that now contains an intramolecular disulfide bond and is able to undergo folding in the IMS. Reduced MIA40 is reoxidized by FAD-linked sulfhydryl oxidase ERV1.COFACTOR Copper or zinc.SUBUNIT Monomer. Interacts with the FAD-linked sulfhydryl oxidase ERV1 and with the substrate proteins COX17, TIM9, and TIM13, forming transient intermolecular disulfide bridges. Interacts with FCJ1.MISCELLANEOUS Present with 5040 molecules/cell in log phase SD medium.SIMILARITY Contains 1 CHCH domain.
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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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Identification and characterization of human cardiolipin synthase
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
A conserved cyclin-binding domain determines functional interplay between anaphase-promoting complex-Cdh1 and cyclin A-Cdk2 during cell cycle progression
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Comprehensive genomic characterization defines human glioblastoma genes and core pathways
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Multiple pathways for mitochondrial protein traffic
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Termination sequence requirements vary among genes transcribed by RNA polymerase III
Abortive initiation by Saccharomyces cerevisiae RNA polymerase III.
Aquaporins: translating bench research to human 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_32272.10
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_96031.9
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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
Intracellular transport and kinesin superfamily proteins, KIFs: structure, function, and dynamics
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Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA
Distinct forms of mitochondrial TOM-TIM supercomplexes define signal-dependent states of preprotein sorting
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Signaling by Type 1 Insulin-like Growth Factor 1 Receptor (IGF1R)
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ALAS1 homodimer (pyridoxal phosphate cofactor) (name copied from entity in Homo sapiens)
CNDP2 (name copied from entity in Homo sapiens)
CTH tetramer:PXLP (name copied from entity in Homo sapiens)
2xCPO (name copied from entity in Homo sapiens)
2xPPO:FAD (name copied from entity in Homo sapiens)
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HMBS:DIPY (name copied from entity in Homo sapiens)
2xUROD (name copied from entity in Homo sapiens)
8x(ALAD:Zn2+) (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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ALAS2 homodimer (pyridoxal phosphate cofactor) (name copied from entity in Homo sapiens)
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aldehyde dehydrogenase 1A1 tetramer (name copied from entity in Homo sapiens)
2x(FECH:2Fe-2S cluster) (name copied from entity in Homo sapiens)
GSS (name copied from entity in Homo sapiens)
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2 Iron:FXN:NFS1:ISD11:ISCU (name copied from entity in Homo sapiens)
2 Iron:FXN (name copied from entity in Homo sapiens)
FDXR:FAD (name copied from entity in Homo sapiens)
FDXR:FADH2 (name copied from entity in Homo sapiens)
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FXN:ISD11:NFS1:ISCU (name copied from entity in Homo sapiens)
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NFS1:pyridoxal phosphate (name copied from entity in Homo sapiens)
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The mitochondrial electron transport and oxidative phosphorylation system
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PIKfyve, a mammalian ortholog of yeast Fab1p lipid kinase, synthesizes 5-phosphoinositides. Effect of insulin
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The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14
FDX1 (reduced) (name copied from entity in Homo sapiens)
FDX1 (oxidized) (name copied from entity in Homo sapiens)
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FXN:NFS1:ISD11:ISCU:2Fe-2S Cluster (name copied from entity in Homo sapiens)
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Expression of human thymidylate synthase in Escherichia coli
Reconstitution of the strand invasion step of double-strand break repair using human Rad51 Rad52 and RPA proteins
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eRF3-GTP:eRF1:peptidyl-tRNA:mRNA:80S Ribosome Complex
eRF3-GDP:eRF1:peptidyl-tRNA:mRNA:80S Ribosome Complex
eRF3-GDP:eRF1:tRNA:mRNA:80S Ribosome Complex
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Critical role for the docking-protein FRS2 alpha in FGF receptor-mediated signal transduction pathways
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Functional characterization of human 1-acylglycerol-3-phosphate acyltransferase isoform 8: cloning, tissue distribution, gene structure, and enzymatic activity
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SPO11 Covalently Attached to Double-strand Break (name copied from entity in Homo sapiens)
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SPO11 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_17364.2
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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=390394
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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=3670620
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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=3673484
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_79977.9
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_153567.3
The role of the TIM8-13 complex in the import of Tim23 into mitochondria
SPO11 Covalently Attached to Oligonucleotide
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SPO11 Covalently Attached to Double-strand Break
Phospholipases and phagocytosis: the role of phospholipid-derived second messengers in phagocytosis
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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_18221.1
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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_78552.9
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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_135631.5
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_80757.9
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The sulfur-containing amino acids: an overview
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Signalling via integrins: implications for cell survival and anticancer strategies
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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_17480.1
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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.
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Mutational spectrum of D-bifunctional protein deficiency and structure-based genotype-phenotype analysis
NUDT16 and ITPA play a dual protective role in maintaining chromosome stability and cell growth by eliminating dIDP/IDP and dITP/ITP from nucleotide pools in mammals
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Overexpression of the normal phosphoribosylpyrophosphate synthetase 1 isoform undelies catalytic superactivity of human phosphoribosylpyrophosphate synthetase
pol II open pre-initiation complex (name copied from entity in Homo sapiens)
TFIIE (name copied from entity in Homo sapiens)
RNA Polymerase II holoenzyme complex (hypophosphorylated):TFIIF complex (name copied from entity in Homo sapiens)
The ATM-Chk2-Cdc25A checkpoint pathway guards against radioresistant DNA synthesis.
RNA Pol II (hypophosphorylated):capped pre-mRNA complex (name copied from entity in Homo sapiens)
RNA Pol II (hypophosphorylated) complex bound to DSIF protein (name copied from entity in Homo sapiens)
NELF complex (name copied from entity in Homo sapiens)
DSIF:NELF:early elongation complex (name copied from entity in Homo sapiens)
DSIF complex (name copied from entity in Homo sapiens)
RNA Polymerase III Terminator Paused Complex
RNA Polymerase III Closed SUP4 tRNATyr Promoter Complex
RNA Polymerase III SUP4 tRNATyr gene Transcription Complex
Active RNA Polymerase I (name copied from entity in Homo sapiens)
RNA Polymerase I Holoenzyme (name copied from entity in Homo sapiens)
RNA Polymerase III Open SUP4 tRNATyr Promoter Complex
CARS dimer (name copied from entity in Homo sapiens)
TARS dimer (name copied from entity in Homo sapiens)
SARS dimer (name copied from entity in Homo sapiens)
FARS A2B2 tetramer (name copied from entity in Homo sapiens)
GARS dimer (name copied from entity in Homo sapiens)
pol II transcription complex containing 9 nucleotide long transcript (name copied from entity in Homo sapiens)
pol II transcription complex containing 11 nucleotide long transcript (name copied from entity in Homo sapiens)
pol II transcription complex containing 3 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)
Pol II transcription complex containing extruded transcript to +30 (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)
Human and murine serine-palmitoyl-CoA transferase--cloning, expression and characterization of the key enzyme in sphingolipid synthesis
RNA Polymearse II:NTP:TFIIF complex (name copied from entity in Homo sapiens)
Structures of lung cancer-derived EGFR mutants and inhibitor complexes: mechanism of activation and insights into differential inhibitor sensitivity
Pol II initiation complex (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)
TFIID (name copied from entity in Homo sapiens)
TFIIA (name copied from entity in Homo sapiens)
pol II closed pre-initiation 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:TFIIA:TFIIB complex (name copied from entity in Homo sapiens)
pol II promoter:TFIID 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)
Epidermal growth factor receptor: elements of intracellular communication
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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
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Regulation of actin filament assembly by Arp2/3 complex and formins
Annu Rev Biophys Biomol Struct 36:451-77
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)
Translated mRNA Complex with Premature Termination Codon Not Preceding Exon Junction (name copied from entity in Homo sapiens)
SMG1:Phosphorylated UPF1:EJC:Translated mRNP (name copied from entity in Homo sapiens)
SMG1:SMG8:SMG9 Complex (name copied from entity in Homo sapiens)
mRNA Complex with a Premature Termination Codon Preceding an Exon Junction (name copied from entity in Homo sapiens)
Core Exon Junction Complex (Core EJC) (name copied from entity in Homo sapiens)
Magoh-Y14 complex (name copied from entity in Homo sapiens)
GDP bound eRF3 (name copied from entity in Homo sapiens)
Exon Junction:UPF2:UPF3 Complex (name copied from entity in Homo sapiens)
Conversion of Phosphatidylcholine to Phosphatidylglycerol with Phospholipase D and glycerol
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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_32966.10
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SMG1:UPF1:EJC:Translated mRNP (name copied from entity in Homo sapiens)
Deadenylated mRNA:Lsm1-7 Complex (name copied from entity in Homo sapiens)
80S ribosome (name copied from entity in Homo sapiens)
Translated mRNA Complex with Premature Termination Codon Preceding Exon Junction (name copied from entity in Homo sapiens)
Lsm1-7 Complex (name copied from entity in Homo sapiens)
YARS2 dimer (name copied from entity in Homo sapiens)
SARS2 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)
KARS dimer (name copied from entity in Homo sapiens)
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Biochemistry of Lipids, Lipoproteins and Membranes, 5th Edition (Book): 213-244
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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
Fat and beyond: the diverse biology of PPARgamma
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Non-vesicular lipid transport by lipid-transfer proteins and beyond
Neurotransmitter Clearance In The Synaptic Cleft
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Insulin effects increased synthesis of Xylulose-5-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=508187
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The SLC40 basolateral iron transporter family (IREG1/ferroportin/MTP1)
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
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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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1-acyl-sn-glycero-3-phosphoglycerol [ChEBI:62747]
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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_2393.2
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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_4106.2
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Absorption of chlorophyll phytol in normal man and in patients with Refsum's 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_78748.9
AUF1, the regulator of tumor necrosis factor alpha messenger RNA decay, is targeted by autoantibodies of patients with systemic rheumatic diseases
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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_90690.9
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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_79421.9
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_94257.9
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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=3667276
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667275
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_105897.9
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=3669641
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=389894
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17125.1
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=389982
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667306
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_143739.5
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=3667307
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667302
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669631
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_113004.8
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=3669633
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667181
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673474
Reactome stable identifier. Use this 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
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_109097.9
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=3667172
Database identifier. Use 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_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=197969
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667186
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667185
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17536.2
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_11509.2
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=3669612
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669614
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=389578
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=389594
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17914.2
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_114248.8
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=3670538
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3670540
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_90006.9
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=197256
Reactome stable identifier. Use this 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=3669606
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669610
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669611
Database identifier. Use 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=191328
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17719.2
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=3670534
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669624
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669625
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=389589
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17089.2
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=3670533
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669744
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=389636
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669745
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17891.1
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_114828.8
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=3669743
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_70840.10
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=3669746
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669748
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669627
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17648.2
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=3667451
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=390287
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667456
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667455
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17437.2
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=3667337
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_140390.5
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=3670621
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667369
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3670618
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17568.2
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=390305
Phosphorylation of CAP-G is required for its chromosomal DNA localization during mitosis
Biochem. Biophys. Res. Commun. 377:1007-11
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667367
The Bcl10-Malt1 complex segregates Fc epsilon RI-mediated nuclear factor kappa B activation and cytokine production from mast cell degranulation
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667368
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667388
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3670623
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667476
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669339
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667195
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667194
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_139500.5
Frequent activating mutations of FGFR3 in human bladder and cervix carcinomas
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_10735.1
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=192314
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=390274
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667477
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17584.1
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=3667192
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667475
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667170
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_101938.9
Tim17p regulates the twin pore structure and voltage gating of the mitochondrial protein import complex TIM23
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3670608
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667469
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669333
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669332
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667317
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17101.1
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=3667319
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667318
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_10257.1
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=193465
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_10489.1
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=192307
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_10230.1
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=3667363
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=192305
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_94022.9
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=3667267
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3670609
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667266
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667264
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_18106.1
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=389996
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667474
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667473
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17174.2
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=390294
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=353123
Succinate dehydrogenase flavoprotein (subunit A) (name copied from entity in Homo sapiens)
Succinate dehydrogenase complex (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=3673180
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_101403.9
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=3673181
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_141940.5
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=75220
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5857.1
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=3668098
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_105041.9
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=83898
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2357.1
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=3667327
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667323
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667342
The control of mammalian DNA replication: a brief history of space and timing.
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667328
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667433
PPAT dimer (name copied from entity in Homo sapiens)
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=3667401
ETF (name copied from entity in Homo sapiens)
ETF (reduced) (name copied from entity in Homo sapiens)
IMP (inosine monophosphate) dehydrogenase 1 tetramer (name copied from entity in Homo sapiens)
adenylosuccinate lyase tetramer (name copied from entity in Homo sapiens)
ATIC dimer (name copied from entity in Homo sapiens)
adenylosuccinate synthetase like 1 holoenzyme (name copied from entity in Homo sapiens)
adenylosuccinate synthetase like 1 holoenzyme 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=3667761
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667765
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_84402.9
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_108237.9
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=3673176
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_32319.10
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=3673175
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673174
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667437
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667438
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667394
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667396
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667397
adenylosuccinate synthetase holoenzyme dimer (name copied from entity in Homo sapiens)
adenylosuccinate synthetase holoenzyme (name copied from entity in Homo sapiens)
CpG motifs in bacterial DNA trigger direct B-cell activation
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667373
adenosine kinase holoenzyme (name copied from entity in Homo sapiens)
AMPD1 tetramer (name copied from entity in Homo sapiens)
AMPD2 tetramer (name copied from entity in Homo sapiens)
AMPD3 tetramer (name copied from entity in Homo sapiens)
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=3668344
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_139646.5
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=3668303
GCH1 decamer (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=3668305
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668306
Protein Kinase C, alpha type: DAG (name copied from entity in Homo sapiens)
Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_100532.9
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=3668194
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668304
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667355
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667311
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667354
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667350
alpha-keto acid dehydrogenase E3 homodimer (name copied from entity in Homo sapiens)
alpha-keto acid dehydrogenase E3 holoenzyme (name copied from entity in Homo sapiens)
MPC1:MPC2 (name copied from entity in Homo sapiens)
pyruvate dehydrogenase complex (name copied from entity in Homo sapiens)
GCH1 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=3667298
DHFR 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=3667315
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667316
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_79053.9
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=3673208
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_28107.10
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=3673207
pyruvate dehydrogenase E2 trimer (name copied from entity in Homo sapiens)
pyruvate dehydrogenase E1 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_140292.5
alpha-ketoglutarate dehydrogenase complex (name copied from entity in Homo sapiens)
IDH3 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_109525.9
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_82523.9
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=3673206
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668345
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668346
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667284
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667285
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667462
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667280
Succinyl-CoA synthetase heterodimer (ADP-forming) (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)
Succinate dehydrogenase flavoprotein (subunit A), oxidised (name copied from entity in Homo sapiens)
MyD88 cascade initiated on plasma membrane
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667464
alpha-ketoglutarate dehydrogenase E2 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=3667465
alpha-ketoglutarate dehydrogenase E1 homodimer (name copied from entity in Homo sapiens)
alpha-ketoglutarate dehydrogenase E1 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=3668384
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3670548
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667794
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_90835.9
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=3667795
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_85828.9
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=3667789
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667793
Mitochondrial Hsp70/MIM44 complex facilitates protein import
ACACA:2Mn2+ (name copied from entity in Homo sapiens)
4x(Btn-PC:Mn2+) (name copied from entity in Homo sapiens)
ACACB:2Mn2+ (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_46117.10
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_17123.1
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=389620
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17192.1
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=389573
2xPNPO:2xFMN (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=3670546
2xPDXK:2xZn2+ (name copied from entity in Homo sapiens)
3xPPCDC:3xFMN (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_17533.1
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=193514
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17583.1
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=389596
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_10138.1
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=389615
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_18008.2
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=389593
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668381
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667766
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667767
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_86975.9
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_95985.9
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=3668382
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_95988.9
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=3673286
Signaling by target of rapamycin proteins in cell growth control
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667777
Guanine deaminase homodimer (name copied from entity in Homo sapiens)
AK5 dimer (name copied from entity in Homo sapiens)
CDA tetramer (name copied from entity in Homo sapiens)
TS dimer (name copied from entity in Homo sapiens)
DUT trimer (name copied from entity in Homo sapiens)
DCTD hexamer (name copied from entity in Homo sapiens)
UMPS dimer (name copied from entity in Homo sapiens)
dihydroorotate dehydrogenase holoenzyme (name copied from entity in Homo sapiens)
CAD hexamer (name copied from entity in Homo sapiens)
catalase holoenzyme monomer (name copied from entity in Homo sapiens)
Inositol hexakisphosphate kinase products contain diphosphate and triphosphate groups
CAT 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=3667781
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667775
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667771
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5682.1
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=109944
Effector role reversal during evolution: the case of frataxin in Fe-S cluster biosynthesis
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667782
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667776
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667783
2xENPP1 (name copied from entity in Homo sapiens)
RFK:Mg2+ (name copied from entity in Homo sapiens)
Cyclic nucleotide phosphodiesterase-mediated integration of cGMP and cAMP signaling in cells of the cardiovascular system
2xPPCS (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)
2xTPK1:Mg2+ (name copied from entity in Homo sapiens)
NUDT5 dimer (name copied from entity in Homo sapiens)
deoxythymidylate kinase (thymidylate kinase) holoenzyme (name copied from entity in Homo sapiens)
CTPS2 tetramer (name copied from entity in Homo sapiens)
CTPS tetramer (name copied from entity in Homo sapiens)
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667785
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_89030.9
Rad52 and Ku bind to different DNA structures produced early in double-strand break repair.
Btn-ACACB:2Mn2+ (name copied from entity in Homo sapiens)
6xNMNAT1:6xZn2+ (name copied from entity in Homo sapiens)
Analysis and update of the human solute carrier (SLC) gene superfamily
Deficiency of carbohydrate response element-binding protein (ChREBP) reduces lipogenesis as well as glycolysis
Cytosolic Iron-sulfur Cluster Assembly (yeast)
Iron-sulfur clusters containing 4 atoms of iron and 4 atoms of sulfur (4Fe-4S clusters) are assembled in the cytosol on a heterotetrameric scaffold composed of CFD1 and NBP35 subunits (reviewed in Lill et al. 2012, Rouault et al. 2012, Sharma et al. 2010, Lill and Mühlenhoff 2006). The sources of iron and sulfur are uncertain but the process requires a sulfur-containing compound exported from mitochondria via Atm1. Newly synthesized 4Fe-4S are transferred to apoproteins such as RAD3 and POL3 via the CIA targeting complex, composed of NAR1, CIA1, YHR122W (CIA2), and MMS19.
The RNA cleavage activity of RNA polymerase III is mediated by an essential TFIIS-like subunit and is important for transcription termination.
Different functional domains of GLUT2 glucose transporter are required for glucose affinity and substrate specificity
CBS tetramer (name copied from entity in Homo sapiens)
AHCY:NAD+ (name copied from entity in Homo sapiens)
4x(AHCY:NAD+) (name copied from entity in Homo sapiens)
MAT III homodimer (name copied from entity in Homo sapiens)
MAT I/III (Mg, K cofactors) (name copied from entity in Homo sapiens)
MAT I homotetramer (name copied from entity in Homo sapiens)
ARD:Fe++ (name copied from entity in Homo sapiens)
AGXT dimer (name copied from entity in Homo sapiens)
APIP:Zn++ (name copied from entity in Homo sapiens)
E1:Mg++ (name copied from entity in Homo sapiens)
ARG2 trimer (name copied from entity in Homo sapiens)
ARG1 trimer (name copied from entity in Homo sapiens)
MTAP trimer (name copied from entity in Homo sapiens)
BBOX1 dimer (name copied from entity in Homo sapiens)
ASL tetramer (name copied from entity in Homo sapiens)
Cloning and characterization of the major insulin-responsive glucose transporter expressed in human skeletal muscle and other insulin-responsive tissues.
Substrate specificity of MATE1 and MATE2-K, human multidrug and toxin extrusions/H(+)-organic cation antiporters
Proteomic analysis of proteins associated with lipid droplets of basal and lipolytically stimulated 3T3-L1 adipocytes
OTC trimer (name copied from entity in Homo sapiens)
ASS1 tetramer (name copied from entity in Homo sapiens)
IDO2 (name copied from entity in Homo sapiens)
CCBL2 dimer (name copied from entity in Homo sapiens)
KYNU dimer (name copied from entity in Homo sapiens)
HAAO (name copied from entity in Homo sapiens)
IDO1 (name copied from entity in Homo sapiens)
ALDH4A1 dimer (name copied from entity in Homo sapiens)
AASS tetramer (name copied from entity in Homo sapiens)
BCAT2 dimer (name copied from entity in Homo sapiens)
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
P5CS short isoform, dimer (name copied from entity in Homo sapiens)
PYCR1 decamer (name copied from entity in Homo sapiens)
delta-1-pyrroline-5-carboxylate synthetase dimers
P5CS long isoform, dimer (name copied from entity in Homo sapiens)
BCAT1 dimer (name copied from entity in Homo sapiens)
PSAT1 dimer (name copied from entity in Homo sapiens)
PSPH:Mg++ dimer (name copied from entity in Homo sapiens)
GPT dimer (name copied from entity in Homo sapiens)
OAT hexamer (name copied from entity in Homo sapiens)
GPT2 dimer (name copied from entity in Homo sapiens)
A cytoplasmic chaperonin that catalyzes beta-actin folding
NMNAT2 (Mg2+) (name copied from entity in Homo sapiens)
4xNMNAT3:4xMg2+ (name copied from entity in Homo sapiens)
NADSYN1 homohexamer (name copied from entity in Homo sapiens)
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)
MOCS3-S-S(1-):Zn2+ (name copied from entity in Homo sapiens)
2xNFS1:2xPXLP (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_11283.2
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=3669771
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_83916.9
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=200739
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_11343.2
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=3669796
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_91046.9
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=200640
Architecture of the yeast origin recognition complex bound to origins of DNA replication.
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669761
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4874.3
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=3669767
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669795
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669765
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669766
Update on interconversions of vitamin B-6 with its coenzyme
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=111353
Formation and stability of the 5 S RNA transcription 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_101002.9
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=200679
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_11336.2
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=3669791
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669793
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669789
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_128688.5
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=3669797
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_84854.9
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_144493.5
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=3673598
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669477
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672690
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669787
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_144491.5
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=3673155
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_141769.5
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=3673599
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_159692.3
Mitochondrial Iron-Sulfur Cluster Biogenesis
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_11639.2
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=3672688
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_34774.10
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=200671
Reactome stable identifier. Use this 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
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669790
Post-translational modification: synthesis of GPI-anchored proteins
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Comparative analysis of gene regulation by the transcription factor PPARalpha between mouse and human
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Regulation of actin dynamics for phagocytic cup formation
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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
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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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FUNCTION Performs an essential function in the generation of cytoplasmic iron-sulfur proteins by mediating export of Fe/S cluster precursors synthesized by NFS1 and other mitochondrial proteins.SUBUNIT Homodimer.MISCELLANEOUS Present with 3250 molecules/cell in log phase SD medium.SIMILARITY Belongs to the ABC transporter superfamily. ABCB family. Heavy Metal importer (TC 3.A.1.210) subfamily.SIMILARITY Contains 1 ABC transmembrane type-1 domain.SIMILARITY Contains 1 ABC transporter domain.
Condensation of Prometaphase Chromosomes
FUNCTION DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and a small RNAs, such as 5S rRNA and tRNAs, respectively. Pols are composed of mobile elements that move relative to each other. In Pol II, the core element with the central large cleft comprises RPB3, RBP10, RPB11, RPB12 and regions of RPB1 and RPB2 forming the active center.SUBUNIT Component of the RNA polymerase I (Pol I), RNA polymerase II (Pol II) and RNA polymerase III (Pol III) complexes consisting of 14, 12 and 17 subunits, respectively. Interacts, via its C-terminus, with TFIIIC subunit TFC4.PTM The N-terminus is blocked.MISCELLANEOUS Present with 907 molecules/cell in log phase SD medium.SIMILARITY Belongs to the archaeal RpoP/eukaryotic RPC10 RNA polymerase subunit family.
Activator 1 36 kDa subunit (Replication factor C 36 kDa subunit) (A1 36 kDa subunit) (RF-C 36 kDa subunit) (RFC36)
Cetuximab monotherapy and cetuximab plus irinotecan in irinotecan-refractory metastatic colorectal cancer
Multicatalytic endopeptidase complex subunit C5
Multicatalytic endopeptidase complex epsilon chain
Proteasome subunit beta type 5 precursor
Multicatalytic endopeptidase complex subunit C8
Multicatalytic endopeptidase complex chain 7
Proteasome subunit beta type 9 precursor
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
26S proteasome non-ATPase regulatory subunit 4
Multicatalytic endopeptidase complex subunit C7-I
26S proteasome non-ATPase regulatory subunit 13
Tumor necrosis factor type 1 receptor associated protein 2
26S proteasome non-ATPase regulatory subunit 2
26S proteasome non-ATPase regulatory subunit 10
Phosphoinositides in constitutive membrane traffic
Multicatalytic endopeptidase complex subunit MECl-1
Proteasome subunit beta type 10 precursor
Nerve growth factor signaling, neuroprotection, and neural repair
FUNCTION Key component of the cytosolic iron-sulfur protein assembly (CIA) machinery that mediates the incorporation of iron-sulfur cluster into apoproteins specifically involved in DNA metabolism and genomic integrity. Acts as an adapter between early-acting CIA components and a subset of cellular target iron-sulfur proteins such as RAD3/XPD and DNA2, thereby playing a key role in nucleotide excision repair (NER) and RNA polymerase II (POL II) transcription.MISCELLANEOUS Present with 3150 molecules/cell in log phase SD medium.SIMILARITY Belongs to the MET18/MMS19 family.SIMILARITY Contains 13 HEAT repeats.
Identification of an autonomously initiating RNA polymerase III holoenzyme containing a novel factor that is selectively inactivated during protein synthesis inhibition
The docking protein Gab1 is the primary mediator of EGF-stimulated activation of the PI-3K/Akt cell survival pathway
A yeast mitochondrion contains about 1000 proteins, more than 99% of which are encoded in the nucleus, synthesized in the cytosol and imported into the mitochondrion. Proteins are targeted to four locations (outer membrane, intermembrane space, inner membrane, and matrix) and must be sorted accordingly (reviewed in Kutik et al. 2007, Milenkovic et al. 2007, Bolender et al. 2008, Endo and Yamano 2009). Newly synthesized proteins are transported from the cytosol across the outer membrane by the TOM40:TOM70 complex. Proteins that contain presequences first interact with the TOM20 subunit of the complex while proteins that contain internal targeting elements first interact with the TOM70 subunit. Some proteins such as Aco1, Atp1, Cit1, Idh1, and Atp2 contain presequences that interact with TOM20 and mature regions that interact with TOM70 (Yamamoto et al. 2009). After initial interaction the protein is conducted across the outer membrane by TOM40 subunits. After passage across the outer membrane, proteins may be targeted to the outer membrane via the SAM50 complex, to the inner membrane via the TIM22 or TIM23 complexes (reviewed in van der Laan et al. 2010), to the matrix via the TIM23 complex (reviewed in van der Laan et al. 2010), or proteins may fold and remain in the intermembrane space (reviewed in Stojanovski et al. 2008, Deponte and Hell 2009, Sideris and Tokatlidis 2010). Presequences on matrix and inner membrane proteins cause interaction with TIM23 complexes; internal targeting sequences cause outer membrane proteins to interact with the SAM50 complex and inner membrane proteins to interact with the TIM22 complex. While in the intermembrane space hydrophobic proteins are chaperoned by the TIM8:TIM13 complex and/or the TIM9:TIM10 complex.
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)
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
BRCA1 interacts with acetyl-CoA carboxylase through its tandem of BRCT domains
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.
Cell surface heparin binding protein HIP
Wnts need a p(assport)24 to leave the ER
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
Rabenosyn-5, a novel Rab5 effector, is complexed with hVPS45 and recruited to endosomes through a FYVE finger domain
A dual role for mitochondrial heat shock protein 70 in membrane translocation of preproteins
p24 proteins are required for secretion of Wnt ligands
Processing of meiotic DNA double strand breaks requires cyclin-dependent kinase and multiple nucleases
Physiology and pathophysiology of vascular signaling controlled by guanosine 3',5'-cyclic monophosphate-dependent protein kinase [corrected]
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The renal plumbing system: aquaporin water channels
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The Drosophila claret segregation protein is a minus-end directed motor molecule
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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.
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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
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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
PPARs: therapeutic targets for metabolic disease
Epstein-Barr virus small RNA associated protein
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
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Binding of a novel SMG-1-Upf1-eRF1-eRF3 complex (SURF) to the exon junction complex triggers Upf1 phosphorylation and nonsense-mediated mRNA decay
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Endotoxin recognition and signal transduction by the TLR4/MD2-complex
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Dock6, a Dock-C subfamily guanine nucleotide exchanger, has the dual specificity for Rac1 and Cdc42 and regulates neurite outgrowth
TAX-responsive enhancer element binding protein 107
Genomic organization of the human phosphomannose isomerase (MPI) gene and mutation analysis in patients with congenital disorders of glycosylation type Ib (CDG-Ib)
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Integrating signals from RTKs to ERK/MAPK
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Differential clathrin binding and subcellular localization of OCRL1 splice isoforms
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Role of the CCAAT enhancer binding proteins (C/EBPs) in adipocyte differentiation
Point mutations in the aromatic/arginine region in aquaporin 1 allow passage of urea, glycerol, ammonia, and protons
The anaphase-promoting complex: a key factor in the regulation of cell cycle
Coexpression of glucose transporters and glucokinase in Xenopus oocytes indicates that both glucose transport and phosphorylation determine glucose utilization
The way Wnt works: Components and mechanism
Cdc42, Rac1, and Rac2 display distinct patterns of activation during phagocytosis
The post-translational synthesis of a polyamine-derived amino acid, hypusine, in the eukaryotic translation initiation factor 5A (eIF5A)
Human sphingosine-1-phosphate lyase: cDNA cloning, functional expression studies and mapping to chromosome 10q22(1)
Eukaryotic translation initiation factor 2 gamma subunit
eukaryotic translation initiation factor 2, subunit 3
Eukaryotic translation initiation factor 2 subunit 3
eukaryotic translation initiation factor 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 3 subunit 8
Eukaryotic translation initiation factor 3 subunit 1
eukaryotic translation initiation factor 3 subunit 9
Eukaryotic translation initiation factor 3 subunit 4
Eukaryotic translation initiation factor 3 subunit 2
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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
Mechanisms of human DNA repair: an update.
The mechanism of adenosine to inosine conversion by the double-stranded RNA unwinding/modifying activity: a high-performance liquid chromatography-mass spectrometry analysis.
The 7 TM G-protein-coupled receptor target family
Dual role of the tyrosine activation motif of the Ig-alpha protein during signal transduction via the B cell antigen receptor
Systematic analysis of the twin cx(9)c protein family
Evidence of functional modulation of the MEKK/JNK/cJun signaling cascade by the low density lipoprotein receptor-related protein (LRP)
Conserved initiator proteins in eukaryotes.
The known unknowns of antigen processing and presentation
Relationship between structures and biological activities of mycoplasmal diacylated lipopeptides and their recognition by toll-like receptors 2 and 6
Different human TFIIIB activities direct RNA polymerase III transcription from TATA-containing and TATA-less promoters
Glycogen metabolism and glycolytic enzymes
Understanding RAGE, the receptor for advanced glycation end products
Constitutive and inducible expression and regulation of vascular endothelial growth factor
Diseases associated with visual transduction
Mutations in GLUT2, the gene for the liver-type glucose transporter, in patients with Fanconi-Bickel syndrome
FATP1 channels exogenous FA into 1,2,3-triacyl-sn-glycerol and down-regulates sphingomyelin and cholesterol metabolism in growing 293 cells
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.
EDEM3, a soluble EDEM homolog, enhances glycoprotein endoplasmic reticulum-associated degradation and mannose trimming
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.
ATP-dependent positive supercoiling of DNA by 13S condensin: a biochemical implication for chromosome condensation
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.
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'.
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).
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.
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.
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.
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.
Biology, structure and mechanism of P-type ATPases
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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).
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While sister chromatids resolve in prometaphase, separating along chromosomal arms, the cohesion of sister centromeres persists until anaphase. At the anaphase onset, the anaphase promoting complex/cyclosome (APC/C) ubiquitinates PTTG1 (securin), targeting it for degradation (Hagting et al. 2002). PTTG1 acts as an inhibitor of ESPL1 (known as separin i.e. separase). Hence, PTTG1 removal initiated by APC/C, enables ESPL1 to become catalytically active (Zou et al. 1999, Waizenegger et al. 2002). ESPL1 undergoes autoleavage (Waizenegger et al. 2002) and also cleaves RAD21 subunit of centromeric cohesin (Hauf et al. 2001). RAD21 cleavage promotes dissociation of cohesin complexes from sister centromeres, leading to separation of sister chromatids. Subsequent movement of sister chromatids to opposite poles of the mitotic spindle segregates replicated chromosomes to two daughter cells (Waizenegger et al. 2000, Hauf et al. 2001, Waizenegger et al. 2002).
5-Phosphoribose 1-diphosphate biosynthesis
Synthesis of cytosolic 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) from D-ribose 5-phosphate
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.
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.
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).
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.
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.
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).
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).
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).
Mitochondrial association of a plus end-directed microtubule motor expressed during mitosis in Drosophila
Nucleotide sequences in Xenopus 5S DNA required for transcription termination.
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Androgens are the determining factors for male development and behaviour in vertebrates (Miller 2002).
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.
Small Ubiquitin-like MOdifiers (SUMOs) are a family of 3 proteins (SUMO1,2,3) that are reversibly conjugated to lysine residues of target proteins via a glycine-lysine isopeptide bond (reviewed in Hay 2013, Hannoun et al. 2010, Gareau and Lima 2010, Wilkinson and Henley 2010, Wang and Dasso 2009). Proteomic methods have yielded estimates of hundreds of target proteins. Targets are mostly located in the nucleus and therefore SUMOylation disproportionately affects gene expression. SUMOs are initially translated as proproteins possessing extra amino acid residues at the C-terminus which are removed by the SUMO processing endoproteases SENP1,2,5 (Hay 2007). Different SENPs have significantly different efficiencies with different SUMOs. The processing exposes a glycine residue at the C-terminus that is activated by ATP-dependent thiolation at cysteine-173 of UBA2 in a complex with SAE1, the E1 complex. The SUMO is transferred from E1 to cysteine-93 of a single E2 enzyme, UBC9 (UBE2I). UBC9 with or, in some cases, without an E3 ligase conjugates the glycine C-terminus of SUMO to an epsilon amino group of a lysine residue on the target protein. SUMO2 and SUMO3 may then be further polymerized, forming chains. SUMO1 is unable to form polymers. Conjugated SUMO can act as a biinding site for proteins possessing SUMO interaction motifs (SIMs) and can also directly affect the formation of complexes between the target protein and other proteins. Conjugated SUMOs are removed by cleavage of the isopeptide bond by processing enzymes SENP1,2,3,5. The processing enzymes SENP6 and SENP7 edit chains of SUMO2 and SUMO3.
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Isocaproaldehyde is reduced by NADPH + H+ to yield 4-methylpentan-1-ol and NADP+. This cytosolic reaction is catalyzed by AKR1B1 (aldose reductase). The purified human enzyme has been shown to catalyze this reaction efficiently in vitro; its abundance in adrenal tissue in humans and other mammals and its concordant expression with other enzymes of steroid hormone synthesis are consistent with it performing this role in vivo as well (Matsuura et al. 1996; Lefrancois-Martinez et al. 2004). The metabolic fate of 4-methylpentan-1-ol is unknown.
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The first process in the synthesis of all steroid hormones is the synthesis of pregnenolone from cholesterol. In this process, cholesterol mobilized from cytosolic lipid droplets or from lysosomes is transported to mitochondria and becomes localized to the inner mitochondrial membrane. Cholesterol transport appears to be rate-limiting for steroid hormone synthesis and its regulation, at the step of StAR-mediated traversal of the mitochondrial membrane, plays a central role in determining the amounts and identities of steroid hormones made in the body. In the inner mitochondrial membrane, cholesterol is converted to pregnenolone in a sequence of three reactions, all catalyzed by CYP11A (side chain cleavage enzyme). Finally, pregnenolone re-enters the cytosol (Payne and Hales 2004; Stocco 2001).
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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).
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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).
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.
Hormone-sensitive lipase (HSL)-mediated triacylglycerol hydrolysis
The initial translation products of SUMO1, SUMO2, and SUMO3 are precursors that have extra amino acid residues at the C-terminus (reviewed in Wang and Dasso 2009, Wilkinson and Henley 2010, Hannoun et al. 2010, Gareau and Lima 2010, Hay 2007). SUMO1 has 4 extra residues, SUMO2 has 2 extra residues, and SUMO3 has 11 extra residues. Proteolytic cleavage by SUMO peptidases (SENPs) removes the propeptide and leaves diglycine residues at the C-terminus. Each SENP has distinct preferences for certain SUMOs. SENP1 has highest activity on SUMO1; SENP2 and SENP5 have highest activity on SUMO2 (Shen et al. 2006, Reverter and Lima 2006, Mikolajczyk et al. 2007). SENP1 and SENP2 are predominantly nucleoplasmic (Bailey and O'Hare 2004, Kim et al. 2005, Zhang et al. 2002, Hang and Dasso 2002, Itahana et al. 2006) and SENP5 is predominantly nucleolar (Di Bacco et al. 2006, Gong and Yeh 2006), therefore the processing reactions are believed to occur in the nucleus. The processed SUMO is then activated by formation of a thioester bond with a cysteine residue of an E1 enzyme, UBA2 (SAE2) in a complex with SAE1. SUMO is then transferred from the E1 enzyme to an E2 enzyme, UBC9 (UBE2I).
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Loading of an Mcm protein onto DNA replication origins is regulated by Cdc6p and CDKs.
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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
FUNCTION DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Involved in recruitment of Pol III to the preinitiation complex. Involved in the configuration of an initiation-competent form of RNA polymerase.SUBUNIT Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits. Interacts with BRF1/TDS4.SIMILARITY Belongs to the eukaryotic RPC34/RPC39 RNA polymerase subunit family.
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
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Diabetes-associated sustained activation of the transcription factor nuclear factor-kappaB
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Molecular mechanisms and clinical pathophysiology of maturity-onset diabetes of the young
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A genome-wide RNA interference screen uncovers two p24 proteins as regulators of Wingless secretion
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Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol
Cellular transformation and guanine nucleotide exchange activity are catalyzed by a common domain on the dbl oncogene product
Tripeptidyl peptidase II is the major peptidase needed to trim long antigenic precursors, but is not required for most MHC class I antigen presentation
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Mammalian nuclei become licensed for DNA replication during late telophase.
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Lead-induced abnormalities of porphyrin metabolism. The relationship with iron deficiency.
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Methylation pharmacogenetics: catechol O-methyltransferase, thiopurine methyltransferase, and histamine N-methyltransferase
Multidrug resistance- associated protein MGr1-Ag
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Protein kinase C as a molecular machine for decoding calcium and diacylglycerol signals
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The mechanism of regulation of hexokinase: new insights from the crystal structure of recombinant human brain hexokinase complexed with glucose and glucose-6-phosphate
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FUNCTION DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Essential for tRNA synthesis. The RPC53/RPC4-RPC37/RPC5 subcomplex is required for terminator recognition and reinitiation.SUBUNIT Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits. Interacts with RPC37/RPC5. RPC53/RPC4, RPC37/RPC5 and RPC11/RPC10 probably form a Pol III subcomplex.MISCELLANEOUS Present with 998 molecules/cell in log phase SD medium.SIMILARITY Belongs to the eukaryotic RPC4/POLR3D RNA polymerase subunit family.
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The cyclin-dependent kinase Cdc28p regulates distinct modes of Cdc6p proteolysis during the budding yeast cell cycle.
Mitochondrial import inner membrane translocase subunit TIM22
Mitochondrial import inner membrane translocase subunit TIM54
Mitochondrial import receptor subunit TOM40
Proteins Imported by TOM40:TOM70 Complex
Isocitrate dehydrogenase (NAD) subunit 1, mitochondrial
ATP synthase subunit alpha, mitochondrial
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Cytochrome c1, heme protein, mitochondrial
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ATP synthase subunit beta, mitochondrial
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Rho guanine dissociation inhibitors: pivotal molecules in cellular signalling
Aldehyde dehydrogenase, mitochondrial precursor
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The Ras branch of small GTPases: Ras family members don't fall far from the tree
FUNCTION Copper chaperone for apo superoxide dismutase 1 (SOD1). Binds copper ions and delivers them specifically to apo-SOD1.COFACTOR Binds 2 copper ions per subunit.SUBUNIT Homodimer, and heterodimer with apo-SOD1. Zinc-binding at His-16 of CCS1 and 'Glu-43' of apo-SOD1 is required for this heterodimerization.MISCELLANEOUS Present with 12000 molecules/cell in log phase SD medium.SIMILARITY Belongs to the CCS1 family.SIMILARITY Contains 1 HMA domain.
LSm proteins form heptameric rings that bind to RNA via repeating motifs
4-aminobutyrate aminotransferase, mitochondrial
Succinate-semialdehyde dehydrogenase, mitochondrial
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Cloning and characterization of a cDNA encoding human cardiolipin synthase (hCLS1)
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Structure of the dual enzyme Ire1 reveals the basis for catalysis and regulation in nonconventional RNA splicing
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FUNCTION Endonuclease that cooperates with the MRX complex in processing meiotic and mitotic double-strand breaks by allowing the endonucleolytic removal of SPO11 from the break sites and ensuring both resection and intrachromosomal association of the broken ends. Required for proper recovery from checkpoint-mediated cell cycle arrest after DNA damage. MRX complex and SAE2 remove a small oligonucleotide(s) from the DNA ends to form an early intermediate which is rapidly processed by EXO1 and/or SGS1 to generate extensive tracts of single-stranded DNA that serve as substrate for RAD51. Plays a transitional role in the dissociation of MRE11 from, and the recruitment of RAD52 to, repair foci. Ensures that both ends of a DSB participate in a recombination event and impairs the formation of palindromic structures in the genome. With TEL1, promotes microhomology-mediated end joining (MMEJ) but inhibits non-homologous end joining (NHEJ), likely by regulating MRE11-dependent ssDNA accumulation at DNA break. SAE2 and MRX are particularly important for removal of hairpins, bulky adducts and other irregular end structures. Facilitates telomere length reequilibration and subsequent checkpoint switch off. Involved in homing efficiency of VMA1 intein VDE and in repair of transposon excision sites.SUBUNIT Dimer or multimer. Interacts with MRE11.PTM Phosphorylated forms accumulate periodically during the unperturbed cell cycle and in response to DNA damage in G2. Phosphorylated by MEC1 and TEL1. Mutagenesis experiments showed that several of the 5 residues located in canonical (S/T)Q motifs, which are favored for phosphorylation by ATM/ATR kinases (Ser-73, Thr-90, Ser-249, Thr-279 and Ser-289) may be phosphorylated. Phosphorylated at Ser-267 by CDC28 which is required to initiate meiotic DSB resection by allowing SPO11 removal from DSB ends.MISCELLANEOUS Present with 1030 molecules/cell in log phase SD medium.SIMILARITY Belongs to the COM1/SAE2/CtIP family.
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Transfer of SUMO from E1 to E2 (UBE2I, UBC9)
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
Bone morphogenetic protein receptors and signal transduction
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.
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.
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.
Interleukin-2 receptor signaling in regulatory T cell development and homeostasis
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.
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 SLC16A gene family encode proton-linked monocarboxylate transporters (MCT) which mediate the transport of monocarboxylates such as lactate and pyruvate. Monocarboxylates are a major energy source for all cells in the body so their transport in and out of cells is crucial for cellular function. To date, 14 SLC16A members have been identified through sequence homology. Of these 14 members, only seven isoforms have been functionally characterized and not all of these function as proton-coupled transporters. A number can transport diuretics, thyroid hormones and aromatic amino acids. The seven remaining SLC16A members are classed as orphan MCTs (Morris ME and Felmlee MA, 2008; Merezhinskaya N and Fishbein WN, 2009).
Four members of the SLC16A gene family encode classical monocarboxylate transporters, MCT1-4. They all function as proton-dependent transporters of monocarboxylic acids such as lactate and pyruvate and ketone bodies such as acetacetate and beta-hydroxybutyrate. These processes are crucial in the regulation of energy metabolism and acid-base homeostasis. SLC16A1 encodes MCT1, a ubiquitiously expressed protein (Garcia CK et al, 1994). Defects in SLC16A1 are the cause of symptomatic deficiency in lactate transport (SDLT), resulting in an acidic intracellular environment and muscle degeneration (Merezhinskaya N et al, 2000). Another defect in SLC16A1 causes exercise-induced hyperinsulinism (EIHI), a dominantly inherited hypoglycemic disorder characterized by inappropriate insulin secretion during anaerobic exercise or on pyruvate load (Otonkoski T et al, 2000). SLC16A7 encodes MCT2, a high affinity pyruvate transporter highly expressed in testis (Lin RY et al, 1998). SLC16A8 encodes MCT3 (Yoon H et al, 1999). Human RPE (retinal pigment epithelial) cells express two proton-coupled monocarboxylate transporters: MCT1 in the apical membrane and MCT3 in the basolateral membrane. This suggested that the coordinated activities of these two transporters could facilitate the transepithelial transport of lactate from the retina to the choroid. (Philip NJ et al, 2003).
Characterization of type II phosphatidylinositol 4-kinase isoforms reveals association of the enzymes with endosomal vesicular compartments
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).
GABA is converted to succinate semialdehyde by 4-aminobutyrate aminotransferase
Succinate semialdehyde dehydrogenase (SSADH) converts succinate semialdehyde, in a final step of GABA degradation, into succinate. SSADH uses one water molecule and one molecule of NAD+ per molecule of succinyate semialdehyde.
In the cytosol, choline O-acetyltransferase (CHAT) acetylates choline (Cho) to produce acetylcholine (AcCho) (Toussaint 1992). AcCho is synthesised in the cytoplasm of cholinergic neurons from acetyl-CoA and Cho by CHAT enzyme.
Acetylcholine neurotransmitter release cycle involves syntheis of choline, loading of clathrin scultpted synaptic vesicles, docking and priming of the acetyl choline loaded synaptic vesicles and then release of acetylcholine. This cycle occurs in neurons of central nervous system (CNS), peripheral, autonomic and somatic nervous system. In the CNS, the acetylcholine is released by the presynaptic neurons into the synaptic cleft where the released acetylcholine is accessible to acetylcholine receptors located on the postsynaptic neurons.
5-hydroxyindole acetaldehyde is then catalyzed by aldehyde dehydrogenase to form 5-hydroxyindole acetic acid
Neurotransmitter is stored in the synaptic vesicle in the pre-synaptic terminal prior to its release in the synaptic cleft upon depolarization of the pre-synaptic membrane. The release of the neurotransmitter is a multi-step process that is controlled by electrical signals passing through the axons in form of action potential. Neurotransmitters include glutamate, acetylcholine, nor-epinephrine, dopamine and seratonin. Each of the neurotransmitter cycle is independently described.
GABA is a major inhibitory neurotransmitter in the mammalian central nervous system. GABA modulates neuronal excitability throughout the nervous system. Disruption of GABA neurotransmission leads to many neurological diseases including epilepsy and a general anxiety disorder. GABA is synthesized by two distinct enzymes GAD67 and GAD65 that differ in their cellular localization, functional properties and co-factor requirements. GABA synthesized by GAD65 is used for neurotransmission whereas GABA synthesized by GAD67 is used for processes other than neurotransmission such as synaptogenesis and protection against neuronal injury. GABA is loaded into synaptic vesicle with the help of vesicular inhibitory amino acid transporter or VGAT. GAD65 and VGAT are functionally linked at the synaptic vesicle membrane and GABA synthesized by GAD65 is preferentially loaded into the synaptic vesicle over GABA synthesized in cytoplasm by GAD67.The GABA loaded synaptic vesicles are docked at the plasma membrane with the help of the SNARE complexes and primed by interplay between various proteins including Munc18, complexin etc. Release of GABA loaded synaptic vesicle is initiated by the arrival of action potential at the presynaptic bouton and opening of N or P/Q voltage gated Ca2+ channels. Ca2+ influx results in Ca2+ binding by synaptobrevin, which is a part of the SNARE complex that also includes SNAP25 and syntaxin, leading to synaptic vesicle fusion. Release of GABA in the synaptic cleft leads to binding of GABA by the GABA receptors and post ligand binding events.
GABA is metabolized to succinated by the serial action of two enzymes, 4-aminobutyrate aminotransferase and suucinate semialdehyde dehydrogenase.
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.
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).
In astrocytic glutamate-glutamine cycle, the excess glutamate released by the pre-synaptic neuron in the synaptic cleft is transported into the astrocyte by a family glutamate transporters called the excitatory amino acid transporters 1 and 2, EAAT1 and EAAT2. Astrocytes carrying these transporters exist in close apposition to the synapse to clear excess glutamate to prevent excessive activation of neurons and hence neuronal death. Glutamate in astrocytes is converted to glutamine by glutamine synthetase. Glutamine is then transported into the extracellular space by system N transporters. The glutamate in the extracellular space is available for neuronal uptake.
Neuotransmitter uptake by astrocytes is mediated by specific transporter located on the astrocytic membrane. The imported neurotransmitter in the astrocytes is metabolized and transported back to the neuron via specialized transporters.
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.
Sorting assembly machinery 37 kDa subunit
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.
Mitochondrial outer membrane protein porin 1
Sorting assembly machinery 50 kDa subunit
Proteins Inserted into Outer Membrane by SAM50 Complex
Mitochondrial distribution and morphology protein 10
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.
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.
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 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.
The G1 arrest induced by DNA damage has been ascribed to the transcription factor and tumor suppressor protein p53. To be effective within minutes after DNA damage, induction of the G1 block should exploit transcription and protein synthesis independent mechanisms. Upon exposure to ultraviolet light (UV) or ionizing radiation (IR), the abundance and activity of a protein, Cdc25A, rapidly decreases; this DNA damage response is not dependent on p53. The rapid destruction of Cdc25A phosphatase prevents entry of a cell into S-phase, by maintaining the CyclinE:Cdk2 complexes in their T14Y15 phosphorylated form.
In the G1 phase there are two types of DNA damage responses, the p53-dependent and the p53-independent pathways. The p53-dependent responses inhibit CDKs through the up-regulation of genes encoding CKIs mediated by the p53 protein, whereas the p53-independent mechanisms inhibit CDKs through the inhibitory T14Y15 phosphorylation of Cdk2. Failure of DNA damage checkpoints in G1 leads to mutagenic replication of damaged templates and other replication defects.
cdc25A protein is degraded by the ubiquitin-proteasome machinery in both terminally differentiating and cycling cells (Bernardi et al. 2000).
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.
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.
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)'.
Mitochondrial intermembrane space import and assembly protein 40
Mitochondrial import inner membrane translocase subunit TIM23
Mitochondrial import inner membrane translocase subunit TIM8
Mitochondrial import inner membrane translocase subunit TIM9
Mitochondrial FAD-linked sulfhydryl oxidase ERV1
Water channel expression in human ADPKD kidneys
Mitochondrial import inner membrane translocase subunit TIM17
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).
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.
Myt1, which localizes preferentially to the endoplasmic reticulum and Golgi complex, phosphorylates Cdc2 on threonine 14 ( Liu et al., 1997).
Mitochondrial intermembrane space cysteine motif-containing protein MIC14
Mitochondrial distribution and morphology protein 35
Cytochrome c oxidase assembly protein COX19
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.
Mitochondrial import inner membrane translocase subunit TIM13
Mitochondrial import inner membrane translocase subunit TIM10
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'.
Mitochondrial intermembrane space cysteine motif-containing protein MIC17
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.
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.
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).
Mitochondrial import receptor subunit TOM5
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'.
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.
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
Mitochondrial import receptor subunit TOM6
Fractionation and properties of glutamic oxalacetic transaminase
Mitochondrial import receptor subunit TOM7
Mitochondrial import receptor subunit TOM70
Mitochondrial import receptor subunit TOM22
Crystal structure of alanine:glyoxylate aminotransferase and the relationship between genotype and enzymatic phenotype in primary hyperoxaluria type 1
Mitochondrial import receptor subunit TOM20
Maintaining cholesterol homeostasis: sterol regulatory element-binding proteins
Endoplasmic reticulum-associated degradation of mammalian glycoproteins involves sugar chain trimming to Man6-5GlcNAc2
Na+-dependent purine nucleoside transporter from human kidney: cloning and functional characterization
Am J Physiol Renal Physiol 273:1058-1065
Distinct phosphotyrosines on a growth factor receptor bind to specific molecules that mediate different signaling pathways
N6-(L-1,3-Dicarboxypropyl)-L-lysine [ChEBI:16927]
Isolation and characterization of argininosuccinate synthetase from human liver.
sn-Glycero-3-phosphoethanolamine [ChEBI:10647]
D-Glucono-1,5-lactone 6-phosphate [ChEBI:16938]
Leber congenital amaurosis: genes, proteins and disease mechanisms
The stem cell factor receptor/c-Kit as a drug target in cancer
Critical role of novel Thr-219 autophosphorylation for the cellular function of PKCtheta in T lymphocytes
Advanced glycosylation endproduct receptor signaling
The biochemistry and physiology of nucleotides
Two intermembrane space TIM complexes interact with different domains of Tim23p during its import into mitochondria
Detection of the mitochondrial and catalytically active alanine aminotransferase in human tissues and plasma
ChEBI:16975 1-acyl-sn-glycerol 3-phosphate
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Transport of Glycerol from Adipocytes to the Liver by Aquaporins
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Activation by Cdc42 and PIP(2) of Wiskott-Aldrich syndrome protein (WASp) stimulates actin nucleation by Arp2/3 complex
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Comparison of the RNA polymerase III transcription machinery in Schizosaccharomyces pombe, Saccharomyces cerevisiae and human.
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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Formation of editosomes by ADAR proteins
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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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Cloning of the human monocarboxylate transporter MCT3 gene: localization to chromosome 22q12.3-q13.2
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Cytochrome c oxidase polypeptide 5A, mitochondrial
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Cytochrome c oxidase subunit 4, mitochondrial
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D-lactate dehydrogenase (cytochrome) 1, mitochondrial
Proteins Imported to the Inner Membrane by TIM23 SORT Complex
Human carbamylphosphate synthetase I. Stabilization, purification, and partial characterization of the enzyme from human liver.
Sequence and structure of a human glucose transporter
Frequent and focal FGFR1 amplification associates with therapeutically tractable FGFR1 dependency in squamous cell lung cancer
Precursors Imported to the Inner Membrane by TIM23 SORT Complex
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Mechanisms of accurate translesion synthesis by human DNA polymerase eta.
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Proteins Imported to the Matrix by TIM23 PAM Complex
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Frataxin homolog, mitochondrial component recommendedName: Frataxin homolog intermediate form /component
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20 kDa nuclear cap binding protein (NCBP 20 kDa subunit) (CBP20) (NCBP interacting protein 1) (NIP1)
80 kDa nuclear cap binding protein (NCBP 80 kDa subunit) (CBP80)
Cleavage and polyadenylation specificity factor, 100 kDa subunit
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Mitochondrial-processing peptidase subunit beta
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Mitochondrial-processing peptidase subunit alpha
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Precursors Imported to the Matrix by TIM23 PAM Complex
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Phosphotyrosine-dependent activation of Rac-1 GDP/GTP exchange by the vav proto-oncogene product
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G beta:gamma signalling through PI3Kgamma
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Presequence translocated-associated motor subunit PAM17, mitochondrial
Mitochondrial import inner membrane translocase subunit TIM50
Mitochondrial import inner membrane translocase subunit TIM12
Mitochondrial import inner membrane translocase subunit TIM44
Mitochondrial import inner membrane translocase subunit TIM21
Mitochondrial import inner membrane translocase subunit TIM16
Mitochondrial import inner membrane translocase subunit TIM14
Mitochondrial import inner membrane translocase subunit TIM18
Proteins Inserted into Inner Membrane by TIM22 Complex
Sorting assembly machinery 35 kDa subunit
Congenital disorder of glycosylation type Ik (CDG-Ik): a defect of mannosyltransferase I
Deficiency of GDP-Man:GlcNAc2-PP-dolichol mannosyltransferase causes congenital disorder of glycosylation type Ik
1D-myo-Inositol 1,3,4,5-tetrakisphosphate
1D-myo-Inositol 1,3,4,5-tetrakisphosphate [ChEBI:808]
D-myo-Inositol 1,3,4,5-tetrakisphosphate
Critical role for Ebf1 and Ebf2 in the adipogenic transcriptional cascade
Rat1p and Xrn1p are functionally interchangeable exoribonucleases that are restricted to and required in the nucleus and cytoplasm, respectively
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
26S proteasome non-ATPase regulatory subunit 8
26S proteasome non-ATPase regulatory subunit 1
A yeast chromosomal origin of DNA replication defined by multiple functional elements.
Ribonucleoside-diphosphate reductase M2 chain
FUNCTION Cleaves presequences (transit peptides) from mitochondrial protein precursors. The cleavage sites typically contain an arginine at position -2 (in the N-terminal portion) from the scissible peptide bond in addition to other distal basic residues, and an aromatic residue at position +1.CATALYTIC ACTIVITY Release of N-terminal transit peptides from precursor proteins imported into the mitochondrion, typically with Arg in position P2.SUBUNIT Heterodimer of alpha and beta subunits.MISCELLANEOUS Present with 31400 molecules/cell in log phase SD medium.SIMILARITY Belongs to the peptidase M16 family.CAUTION Does not seem to have a protease activity as it lack the zinc-binding site.
Serine/threonine-protein kinase Chk1 (EC 2.7.1.-)
Cleavage and polyadenylation specificity factor, 160 kDa subunit
Cleavage and polyadenylation specificity factor, 73 kDa subunit
Multicatalytic endopeptidase complex delta chain
Proteasome subunit beta type 6 precursor
26S proteasome non-ATPase regulatory subunit 9
Multicatalytic endopeptidase complex subunit C2
26S proteasome non-ATPase regulatory subunit 7
Probable 26S protease regulatory subunit 8
Mechanisms of transcription-coupled DNA repair.
Multicatalytic endopeptidase complex iota chain
Multicatalytic endopeptidase complex subunit C9
Multicatalytic endopeptidase complex subunit C13
Proteasome subunit beta type 8 precursor
Multicatalytic endopeptidase complex zeta chain
26S proteasome non-ATPase regulatory subunit 11
26S proteasome non-ATPase regulatory subunit 3
Multicatalytic endopeptidase complex subunit C3
Multicatalytic endopeptidase complex chain Z
Proteasome subunit beta type 7 precursor
Multicatalytic endopeptidase complex beta chain
Proteasome subunit beta type 4 precursor
Insulin action on glucose transporters through molecular switches, tracks and tethers
26S proteasome non-ATPase regulatory subunit 12
(S)-alpha-amino-beta-(3-indolyl)-propionic acid
Congenital Disorders of Glycosylation Overview
Cell cycle- and cell growth-regulated proteolysis of mammalian CDC6 is dependent on APC-CDH1.
3-Hexaprenyl-4-hydroxy-5-methoxybenzoate [ChEBI:1510]
beta-catenin destruction complex: insights and questions from a structural perspective
The kinesin-like protein CENP-E is kinetochore-associated throughout poleward chromosome segregation during anaphase-A
Systematic analysis of myotubularins: heteromeric interactions, subcellular localisation and endosome related functions
A role for the endoplasmic reticulum protein retrotranslocation machinery during crosspresentation by dendritic cells
Multistep regulation of DNA replication by Cdk phosphorylation of HsCdc6.
An essential role of Sam50 in the protein sorting and assembly machinery of the mitochondrial outer membrane
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
1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate [ChEBI:16851]
1-phosphatidyl-1D-myo-inositol 3,5-bisphosphate
The hexameric eukaryotic MCM helicase: building symmetry from nonidentical parts
A novel microtubule-based motor protein (KIF4) for organelle transports, whose expression is regulated developmentally
Cloning, characterization, and chromosomal mapping of human aquaporin of collecting duct
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Glycine-rich loop of mitochondrial processing peptidase alpha-subunit is responsible for substrate recognition by a mechanism analogous to mitochondrial receptor Tom20
Functional expansion of aminoacyl-tRNA synthetases and their interacting factors: new perspectives on housekeepers
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Transcription termination factor La is also an initiation factor for RNA polymerase III.
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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
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Translocation after synthesis of a four-nucleotide RNA commits RNA polymerase II to promoter escape.
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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
Isolation and characterization of a human thiamine pyrophosphokinase cDNA
Synthesis of pyrophosphates in the cytosol
Developmental control of a G1-S transcriptional program in Drosophila
FGFR3-related dwarfism and cell signaling
Serine/threonine-protein kinase greatwall
UDP-N-acetyl-D-galactosamine [ChEBI:9820]
Molecular cloning of human thiamin pyrophosphokinase
Structural maintenance of chromosomes protein 2
Structural maintenance of chromosomes protein 4
Chromosome condensation-related SMC-associated protein 1
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
Inhibition of replication initiation of damaged DNA by RB1/E2F1
Double-strand DNA containing a dihydrouracil
Double-strand DNA containing a thymine glycol
DNA containing an apurinic/apyrimidinic (AP) site
Double-strand DNA containing a cytosine glycol
Double-strand DNA containing an 8-oxo guanine opposite to a cytosine
Double-strand DNA containing a formamidopyrimidine
Probable phospholipid-transporting ATPases
nascent polypeptide with signal sequence
RNA-binding protein in RNP (ribonucleoprotein) complexes
mRNA Transcript Targeted by AUF1(hnRNP D0)
Human glutamine phosphoribosylpyrophosphate amidotransferase. Two molecular forms interconvertible by purine ribonucleotides and phosphoribosylpyrophosphate
Endocytosis, recycling, and regulated exocytosis of glucose transporter 4
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
mRNA with premature termination codon not preceding exon junction
Cell division cycle 7-related protein kinase
Cell division cycle 7-related protein kinase (EC 2.7.1.-) (CDC7- related kinase) (HsCdc7) (huCdc7)
mRNA with premature termination codon preceding exon junction
Cell division protein kinase 2 (EC 2.7.1.-)(p33 protein kinase)(CDK2)
Characterization of human PLD2 and the analysis of PLD isoform splice variants
DNA polymerase alpha holoenzyme-associated protein P1
template DNA:4 nucleotide transcript hybrid
template DNA with first transcript dinucleotide, opened to +8 position
template DNA:3 nucleotide transcript hybrid
DNA polymerase epsilon, catalytic subunit A
DNA Replication factor A protein A1 (70kD)
Replication protein A 70 kDa DNA-binding subunit
DNA Replication factor A protein 2 (32kD)
DNA Replication factor A protein 4 (30kD)
oligoribonucleotide with a 5'-diphosphate
template DNA:11 nucleotide transcript hybrid
template DNA:9 nucleotide transcript hybrid
mature mRNA (eukaryotic, capped and deadenylated)
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
Open DNA -10 to +2 containing RNA Polymerase II promoter
DNA containing RNA Polymerase II promoter
Template DNA hybrid with phosphodiester-PPi intermediate
template DNA opened from -10 to +2, with first nucleotide base-paired at 5'-end
elongating pre-mRNA Pol III oligonucleotide
released pre-mRNA Pol III oligonucleotide
SUP4 tRNATyr gene DNA with Open promoter (single-stranded)
SUP4 tRNATyr gene DNA with a termination site
SUP4 tRNATyr gene DNA with Closed promoter (duplex)
SUP4 tRNATyr gene DNA with transcription bubble (single-stranded)
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Single-Stranded Oligodeoxyribonucleotide (12 to 34 nucleotides)
Homologues of limit dextrin-glycogenin-1
Polymeric chains of SUMO-2 and SUMO-3 are conjugated to protein substrates by SAE1/SAE2 and Ubc9
Processing of Capped Intron-Containing Pre-mRNA
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
Homologues of poly((1,4)-alpha-glucosyl) GYG2
Homologues of poly((1,4)-alpha-glucosyl) GYG1
Homologues of oligo((1,4)-alpha-glucosyl) GYG1
oligo((1,4)-alpha-glucosyl) glycogenin-1
oligo((1,4)-alpha-glycosyl) glycogenin-2
Molecular cloning of human mitochondrial glycerophosphate dehydrogenase gene: genomic structure, chromosomal localization, and existence of a pseudogene
Homologues of oligo((1,4)-alpha-glycosyl) GYG2
Common and distinct elements in cellular signaling via EGF and FGF receptors
phosphoribosyl pyrophosphate synthetase 1
Phosphoribosyl pyrophosphate synthetase I
Ribose-phosphate pyrophosphokinase I (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase I) (PPRibP) (PRS-I)
Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
Ror-family receptor tyrosine kinases in noncanonical Wnt signaling: their implications in developmental morphogenesis and human diseases
Glycyl tRNA synthetase mutations in Charcot-Marie-Tooth disease type 2D and distal spinal muscular atrophy type V
6-phosphogluconate dehydrogenase, decarboxylating
Role of cysteine-82 in the catalytic mechanism of human S-adenosylmethionine decarboxylase
Galactose-1-phosphate uridylyltransferase
Homologues of ((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin-2
Delivery of yeast telomerase to a DNA break depends on the recruitment functions of Cdc13 and Est1
Homologues of limit dextrin-glycogenin-2
Homologues of ((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin-1
isocaproaldehyde + NADPH + H+ => 4-methylpentan-1-ol + NADP+
Reduction of isocaproaldehyde to 4-methylpentan-1-ol
Transfer of SUMO3 from E1 to UBE2I (UBC9)
Mutations in the X-linked pyruvate dehydrogenase (E1) alpha subunit gene (PDHA1) in patients with a pyruvate dehydrogenase complex deficiency
Testosterone is converted to 5-alpha-dihydroxytestosterone
FUNCTION Essential component of the TIM23 complex, a complex that mediates the translocation of transit peptide-containing proteins across the mitochondrial inner membrane.SUBUNIT Component of the TIM23 complex, at least composed of TIM23, TIM17, TIM50 and TIM21. The complex interacts with the TIM44 component of the PAM complex.MISCELLANEOUS Present with 1210 molecules/cell in log phase SD medium.SIMILARITY Belongs to the Tim17/Tim22/Tim23 family.
ChEBI:16723 4-methylthio-2-oxobutanoate (1-)
ChEBI:16728 2-acyl-sn-glycero-3-phosphocholine
3alpha,7alpha-Dihydroxy-5beta-cholanic acid
Topology of acyltransferase motifs and substrate specificity and accessibility in 1-acyl-sn-glycero-3-phosphate acyltransferase 1
(IscS-IscU)2 complex structures provide insights into Fe2S2 biogenesis and transfer
Mini-review: Specificity and expression of CIITA, the master regulator of MHC class II genes
D-fructose-1,6- bisphosphate 1-phosphohydrolase
UTP-glucose-1-phosphate uridylyltransferase
Functional characterization and localization of AQP3 in the human colon
The ins and outs of IgE-dependent mast-cell exocytosis
D-fructose-1,6-bisphosphate 1-phosphohydrolase
Mitochondrial dicarboxylate carrier protein
mitochondrial aspartate glutamate carrier
Identification of a member of the MAPKKK family as a potential mediator of TGF-beta signal transduction
New initiation factor activity required for globin mRNA translation.
Structure and expression of a complementary DNA for the nuclear coded precursor of human mitochondrial ornithine transcarbamylase.
Protein kinase G mediates vascular endothelial growth factor-induced Raf-1 activation and proliferation in human endothelial cells
Getting in and out from calnexin/calreticulin cycles
A novel quality control compartment derived from the endoplasmic reticulum
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Mutational analysis of the transcription start site of the yeast tRNA(Leu3) gene.
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Closing the gap: identification of human 3-ketosteroid reductase, the last unknown enzyme of mammalian cholesterol biosynthesis
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Polyamines: metabolism and implications in human diseases
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3alpha,7alpha-Dihydroxy-5beta-cholestanate [ChEBI:1707]
Frataxin and mitochondrial FeS cluster biogenesis
Translocation of lipid-linked oligosaccharides across the ER membrane requires Rft1 protein
Synthesis of IP2, IP, and Ins in the cytosol
Cytosolic iron-sulfur cluster assembly (CIA) system: factors, mechanism, and relevance to cellular iron regulation
Motor-free mitochondrial presequence translocase drives membrane integration of preproteins
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Regulation of activated PAK-2p34 by proteasome mediated degradation
The t(1;9)(p34;q34) and t(8;12)(p11;q15) fuse pre-mRNA processing proteins SFPQ (PSF) and CPSF6 to ABL and FGFR1
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Peptides corresponding to the N and C termini of IkappaB-alpha, -beta, and -epsilon as probes of the two catalytic subunits of IkappaB kinase, IKK-1 and IKK-2
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RNA editing: complexity and complications.
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Three-dimensional structure of the anaphase-promoting complex
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On the mechanism of preprotein import by the mitochondrial presequence translocase
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Signal transduction pathways mediated by the interaction of CpG DNA with Toll-like receptor 9
Template boundary definition in mammalian telomerase
TIR domains, which are conserved among all TLRs. Recent accumulating
The role of Hsp70 in conferring unidirectionality on protein translocation into mitochondria
A regulatory role for 1-acylglycerol-3-phosphate-O-acyltransferase 2 in adipocyte differentiation
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Opposing roles for ATF6alpha and ATF6beta in endoplasmic reticulum stress response gene induction
A multifactor complex of eukaryotic initiation factors, eIF1, eIF2, eIF3, eIF5, and initiator tRNA(Met) is an important translation initiation intermediate in vivo.
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Dealing with methionine/homocysteine sulfur: cysteine metabolism to taurine and inorganic sulfur
Mutation of a putative mitochondrial iron transporter gene (ABC7) in X-linked sideroblastic anemia and ataxia (XLSA/A)
Different phosphorylated forms of RNA polymerase II and associated mRNA processing factors during transcription.
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RNA editing by base deamination: more enzymes, more targets, new mysteries.
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Farnesyl-diphosphate farnesyltransferase
Isopentenyl-diphosphate delta-isomerase 1
damaged DNA substrate with misinserted bases
MDC1 is a mediator of the mammalian DNA damage checkpoint.
T-lymphoma invasion and metastasis-inducing protein 2
Peroxisomal multifunctional enzyme type 2
hydroxysteroid (17-beta) dehydrogenase 4
damaged DNA substrate inserted with correct base complement
Elongated DNA template with bypassed lesion
3-hydroxy-3-methylglutaryl-coenzyme A reductase-1
Heteroduplex DNA with D-loop structure with extended pairing between invading strand and complementary heteroduplex strand and containing newly synthesized ends
Long-chain fatty acid transport protein 1
Identification and characterization of human mitochondrial tryptophanyl-tRNA synthetase
Ghost homologue of E3 ligases in proteasomal degradation
Ethanolamine-phosphate cytidylyltransferase
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repaired DNA template:nascent mRNA hybrid
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damaged DNA substrate:nascent mRNA hybrid with dual incisions
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damaged DNA substrate:nascent mRNA hybrid with 3' incision
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damaged DNA substrate:nascent mRNA hybrid
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Regulation of growth factor signaling by FRS2 family docking/scaffold adaptor proteins
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Recent progress in structure-function analyses of Nramp proton-dependent metal-ion transporters
(ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI
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Ghost homologue of Unfolded alpha/beta tubulin
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sterol-4-alpha-carboxylate 3-dehydrogenase, decarboxylating
The Wnt/Ca2+ pathway: a new vertebrate Wnt signaling pathway takes shape
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K48-polyubiquitinated partially digested Ag
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Processive synthesis on the lagging strand
CDP-diacylglycerol-glycerol-3-phosphate 3-phosphatidyltransferase, mitochondrial
Lysophosphatidylinositol acyltransferase
Membrane-bound O-acyltransferase domain-containing protein 7
CDP-diacylglycerol--inositol 3-phosphatidyltransferase
Choline-phosphate cytidylyltransferase A
Choline-phosphate cytidylyltransferase B
Peroxisome proliferator-activated receptor alpha (PPARalpha) and athero-sclerosis
Curr Drug Targets Cardiovasc Haematol Disord 5:513-23
A mitogen-activated protein kinase-dependent signaling pathway in the activation of platelet integrin alpha IIbbeta3
Phosphatidylserine decarboxylase proenzyme Chain B
Phosphatidylserine decarboxylase proenzyme Chain A
Phosphatidylethanolamine N-methyltransferase
Putative glycerophosphocholine phosphodiesterase GPCPD1
Glycerophosphodiester phosphodiesterase 5
Identification of a binding region for human origin recognition complex proteins 1 and 2 that coincides with an origin of DNA replication.
Analysis of GPIIb/IIIa receptor number by quantification of 7E3 binding to human platelets
Formation of open and elongating transcription complexes by RNA polymerase III.
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Enzymatic synthesis and properties of 5-phosphoribosylpyrophosphate
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Tyrosine kinase inhibitors of FGFR1 fusion mutants
(S)-alpha-amino-beta-phenylpropionic acid
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
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Localization, regulation and function of type II phosphatidylinositol 5-phosphate 4-kinases
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The bisretinoids of retinal pigment epithelium
G-strand Chromosome end with two additional single strand repeats - Telomeric
NNNNNNNNNNNTTAGGGTTATTAGGGTTATTAGGGTTA - 3' (in human)
G-strand Chromosome end with an additional single strand repeat - Telomeric
NNNNNNNNNNNTTAGGGTTATTAGGGTTA - 3' (in human)
ChEBI:16618 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate
Glucagon signaling in metabolic regulation
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1-phosphatidyl-1D-myo-inositol 4,5- bisphosphate
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
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MicroRNAs: genomics, biogenesis, mechanism, and function
Degradation of cysteine and homocysteine
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Acetyl-CoA acetyltransferase, mitochondrial
solute carrier family 25 (carnitine/acylcarnitine translocase), member 20
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Hydroxymethylglutaryl-CoA synthase, mitochondrial precursor
3-hydroxy-3-methylglutaryl coenzyme A synthase
Nuclear transcription factor Y subunit gamma
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Lysophosphatidic acid acyltransferase-alpha
1-acylglycerol-3-phosphate O- acyltransferase 1
1-acyl-sn-glycerol-3-phosphate acyltransferase alpha
Lysophosphatidic acid acyltransferase-beta
1-acylglycerol-3-phosphate O- acyltransferase 2
1-acyl-sn-glycerol-3-phosphate acyltransferase beta
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FUNCTION Essential component of the TIM23 complex, a complex that mediates the translocation of transit peptide-containing proteins across the mitochondrial inner membrane.SUBUNIT Component of the TIM23 complex, at least composed of TIM23, TIM17, TIM50 and TIM21. The complex interacts with the TIM44 component of the PAM complex.MISCELLANEOUS Present with 1440 molecules/cell in log phase SD medium.SIMILARITY Belongs to the Tim17/Tim22/Tim23 family.
FUNCTION Catalyzes the stereospecific oxidation of D-lactate to pyruvate.CATALYTIC ACTIVITY (R)-lactate + 2 ferricytochrome c = pyruvate + 2 ferrocytochrome c + 2 H(+).COFACTOR Binds 2 FAD.COFACTOR Binds 4-6 zinc ions.INDUCTION By D-lactate. Induced during respiratory adaptation.MISCELLANEOUS Present with 10800 molecules/cell in log phase SD medium.SIMILARITY Belongs to the FAD-binding oxidoreductase/transferase type 4 family.SIMILARITY Contains 1 FAD-binding PCMH-type domain.
Cardiolipin hydrolysis by human phospholipases A2. The multiple enzymatic activities of human cytosolic phospholipase A2
Assembly and iron-binding properties of human frataxin, the protein deficient in Friedreich ataxia
Glucuronidation and the UDP-glucuronosyltransferases in health and disease
Triggering and amplifying pathways of regulation of insulin secretion by glucose
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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
B cell lymphoma 10 is essential for FcepsilonR-mediated degranulation and IL-6 production in mast cells
The Rad50 hook domain is a critical determinant of Mre11 complex functions
Isoleucylation properties of native human mitochondrial tRNAIle and tRNAIle transcripts. Implications for cardiomyopathy-related point mutations (4269, 4317) in the tRNAIle gene
ChEBI:16496 5beta-Cholestane-3alpha,7alpha,12alpha-triol
The enzymic chain elongation of fatty acids by rat-liver microsomes
Cyclic nucleotides and phosphodiesterases in platelets
Mutations in the NSDHL gene, encoding a 3beta-hydroxysteroid dehydrogenase, cause CHILD syndrome
Structural determinants of water permeation through aquaporin-1
Human phosphoribosylpyrophosphate synthetase
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
Protein kinase C-delta is a negative regulator of antigen-induced mast cell degranulation
A fatal mitochondrial disease is associated with defective NFU1 function in the maturation of a subset of mitochondrial Fe-S proteins
Molecular cloning of cDNA encoding human lanosterol synthase
Molecular cloning and mapping of a human cDNA (SC5DL) encoding a protein homologous to fungal sterol-C5-desaturase
Eukaryotic translation initiation factor 4E
cAMP-dependent protein kinase, alpha-catalytic subunit
cAMP-dependent protein kinase type II-alpha regulatory chain
cAMP-dependent protein kinase type II-beta regulatory chain
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
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A single enzyme catalyzes both platelet-activating factor production and membrane biogenesis of inflammatory cells. Cloning and characterization of acetyl-CoA:LYSO-PAF acetyltransferase
Vacuolar protein-sorting-associated protein 25
Vacuolar protein-sorting-associated protein 36
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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
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MKK3- and MKK6-regulated gene expression is mediated by the p38 mitogen-activated protein kinase signal transduction pathway
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Human acetyl-CoA carboxylase: characterization, molecular cloning, and evidence for two isoforms
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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
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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
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Full mass spectrometric characterization of human monoacylglycerol lipase generated by large-scale expression and single-step purification
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N-acylphosphatidylethanolamine-hydrolyzing phospholipase D: a novel enzyme of the beta-lactamase fold family releasing anandamide and other N-acylethanolamines
FUNCTION Essential for the expression of the Rieske iron-sulfur protein.MISCELLANEOUS Present with 1990 molecules/cell in log phase SD medium.SIMILARITY Belongs to the AAA ATPase family. BCS1 subfamily.
Error-prone DNA polymerases: novel structures and the benefits of infidelity.
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FUNCTION Involved in DNA double-strand break repair (DSBR). Possesses single-strand endonuclease activity and double-strand-specific 3'-5' exonuclease activity. Also involved in meiotic DSB processing.SUBUNIT Forms a complex with RAD50 and XRS2.MISCELLANEOUS Present with 432 molecules/cell in log phase SD medium.SIMILARITY Belongs to the MRE11/RAD32 family.
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Distribution of AQP2 and AQP3 water channels in human tissue microarrays
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Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits
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FUNCTION Essential component of the TIM22 complex, a complex that mediates the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. The TIM22 complex forms a twin-pore translocase that uses the membrane potential as external driving force. In the TIM22 complex, it acts as a docking point for the soluble TIM9-TIM10 heterohexamer that guides the target proteins in transit through the aqueous mitochondrial intermembrane space.SUBUNIT Component of the TIM22 complex, whose core is composed of TIM18, TIM22 and TIM54, associated with the peripheral proteins MRS5/TIM12 and the 70 kDa heterohexamer composed of TIM9 and TIM10 (or TIM8 and TIM13). Interacts directly with both the TIM22 protein and the TIM9-TIM10 heterohexamer. Interacts with multi-pass transmembrane proteins in transit.SIMILARITY Belongs to the small Tim family.
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ChEBI:16500 1-phosphatidyl-1D-myo-inositol 5-phosphate
1-phosphatidyl-1D-myo-inositol 5-phosphate
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NMD: RNA biology meets human genetic medicine
FUNCTION General activator of RNA polymerase III transcription.SUBUNIT TFIIIB comprises the TATA-binding protein (TBP), the B-related factor (BRF) and the B" component (BDP1). Interacts with TFC4.SIMILARITY Belongs to the TFC5 family.SIMILARITY Contains 1 SANT domain.
Characterization of an acyl-coA thioesterase that functions as a major regulator of peroxisomal lipid metabolism
Spatial expression patterns and biochemical properties distinguish a second myo-inositol monophosphatase IMPA2 from IMPA1
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Structural biology of shared cytokine receptors
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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
3alpha,7alpha,12alpha-Trihydroxy-5beta-cholanic acid
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The DNA replication fork in eukaryotic cells.
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1D-myo-Inositol 1,3,4,5,6-pentakisphosphate
D-myo-Inositol 1,3,4,5,6-pentakisphosphate
1D-myo-Inositol 1,3,4,5,6-pentakisphosphate [ChEBI:807]
Isolation and chromosomal localization of a novel FMS-like tyrosine kinase gene
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Proline to arginine mutations in FGF receptors 1 and 3 result in Pfeiffer and Muenke craniosynostosis syndromes through enhancement of FGF binding affinity
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17beta-Hydroxyandrostan-3-one [ChEBI:793]
Cross-presentation of soluble exogenous antigens (endosomes)
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Baillieres Clin Endocrinol Metab 7:551-86
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NOD-like receptors: role in innate immunity and inflammatory disease
Folic acid: nutritional biochemistry, molecular biology, and role in disease processes
Gap-filling DNA repair synthesis and ligation in GG-NER
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FUNCTION Component of the cytosolic iron-sulfur (Fe/S) protein assembly (CIA) machinery. Required for maturation of extramitochondrial Fe-S proteins. The NBP35-CFD1 heterotetramer forms a Fe-S scaffold complex, mediating the de novo assembly of an Fe-S cluster and its transfer to target apoproteins. Nucleotide binding/hydrolysis seems to be critcal for loading of Fe-S clusters onto CFD1 and NBP35. Required for biogenesis and export of both ribosomal subunits, which may reflect a role in assembly of the Fe/S clusters in RLI1, a protein which performs rRNA processing and ribosome export.COFACTOR Binds 4 4Fe-4S clusters per heterotetramer. Contains two stable clusters in the N-termini of NBP35 and two labile, bridging clusters between subunits of the NBP35-CFD1 heterotetramer.SUBUNIT Heterotetramer of 2 NBP35 and 2 CFD1 chains.SIMILARITY Belongs to the Mrp/NBP35 ATP-binding proteins family. NUBP2/CFD1 subfamily.
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Functional characterization of novel human and mouse equilibrative nucleoside transporters (hENT3 and mENT3) located in intracellular membranes
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Pathogen recognition and innate immunity
Characterization of the mechanisms controlling Greatwall activity
3-phosphoinositide dependent protein kinase-1
ERCC1/XPF removes the 3' overhang from uncapped telomeres and represses formation of telomeric DNA-containing double minute chromosomes
Short-chain dehydrogenase/reductase 3 ecNumber1.1.1.300/ecNumber
Inorganic pyrophosphatase 2, mitochondrial
The generation and the manipulation of human multipotent adipose-derived stem cells
N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
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Solute carrier family 2, facilitated glucose transporter, member 1
Glucose transporter type 1, erythrocyte/brain
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Cloned mammalian neutral sphingomyelinase: functions in sphingolipid signaling?
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Solute carrier family 2, facilitated glucose transporter, member 3
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Glucose transporter type 4, insulin-responsive
Solute carrier family 2, facilitated glucose transporter, member 4
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Mutations in PMM2, a phosphomannomutase gene on chromosome 16p13, in carbohydrate-deficient glycoprotein type I syndrome (Jaeken syndrome)
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High mobility group-like nuclear protein 2 homolog 1
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Spliceosomal U5 snRNP-specific 15 kDa protein
Thioredoxin-like U5 snRNP protein U5-15kD
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Solute carrier family 2, facilitated glucose transporter member 5
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Solute carrier family 2, facilitated glucose transporter, member 2
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Structure, function, and formation of biological iron-sulfur clusters
NOD-LRR proteins: role in host-microbial interactions and inflammatory disease
Sinauer Associates, Inc., P.O. Box 407 23 Plumtree Road, Sunderland, MA 01375 U.S.A.
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DNA-directed RNA polymerase II 13.3 kDa polypeptide
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
DNA-directed RNA polymerase II 14.5 kDa polypeptide
GLUL decamer (name copied from entity in Homo sapiens)
Homodimer of 4 aminobutyrate aminotransferase (name copied from entity in Homo sapiens)
aldehyde dehydrogenase, mitochondrial, tetramer (name copied from entity in Homo sapiens)
DNA polymerase alpha:primase:DNA polymerase alpha:origin complex (name copied from entity in Homo sapiens)
DNA-directed RNA polymerase II 19 kDa polypeptide
DNA-directed RNA polymerase II 23 kDa polypeptide (EC 2.7.7.6) (RPB25) (XAP4) (RPB5)
DNA-directed RNA polymerase II 23 kDa polypeptide
DNA-directed RNA polymerase II 140 kDa polypeptide
DNA-directed RNA polymerase II 33 kDa polypeptide
Transcription initiation factor IIF, alpha subunit
Transcription initiation factor IIF, beta subunit
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
Binding of yeast frataxin to the scaffold for Fe-S cluster biogenesis, Isu
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
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)
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
DNA-directed RNA polymerase II 16 kDa polypeptide
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
DNA-directed RNA polymerases I, II, and III 17.1 kDa polypeptide
DNA-directed RNA polymerase II 7.6 kDa polypeptide
DNA-directed RNA polymerase II 7.6 kDa polypeptide (EC 2.7.7.6) (RPB10) (RPB7.6)
capped intronless pre-mRNA:CBC complex (name copied from entity in Homo sapiens)
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
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
Small nuclear ribonucleoprotein associated proteins B and B'
Orc5:Orc3:Orc2:origin (name copied from entity in Homo sapiens)
Orc3:Orc2:origin (name copied from entity in Homo sapiens)
Orc4:Orc5:Orc3:Orc2:origin (name copied from entity in Homo sapiens)
CDK:DDK:Mcm10:pre-replicative complex (name copied from entity in Homo sapiens)
Transaldolase deficiency: liver cirrhosis associated with a new inborn error in the pentose phosphate pathway.
CDK (name copied from entity in Homo sapiens)
Orc2:origin (name copied from entity in Homo sapiens)
U5 small nuclear ribonucleoprotein 200 kDa helicase
Orc1:Orc4:Orc5:Orc3:Orc2:origin (name copied from entity in Homo sapiens)
Mcm2-7 complex (name copied from entity in Homo sapiens)
U6 snRNA-associated Sm-like protein LSm2
Small nuclear ribonuclear protein D homolog
116 kDa U5 small nuclear ribonucleoprotein component (U5 snRNP- specific protein, 116 kDa) (U5-116 kDa)
116 kDa U5 small nuclear ribonucleoprotein component
Mcm10:active pre-replicative complex (name copied from entity in Homo sapiens)
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)
active pre-replicative complex (name copied from entity in Homo sapiens)
136 kDa double-stranded RNA binding protein
Double-stranded RNA-specific adenosine deaminase
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
CDC6:ORC:origin complex (name copied from entity in Homo sapiens)
The stem-loop binding protein is required for efficient translation of histone mRNA in vivo and in vitro
ORC:origin (name copied from entity in Homo sapiens)
Orc2 associated with MCM8 (name copied from entity in Homo sapiens)
DDK (name copied from entity in Homo sapiens)
Cdc45:CDK:DDK:Mcm10:pre-replicative complex (name copied from entity in Homo sapiens)
DNA Replication Factor A (name copied from entity in Homo sapiens)
RPA:Cdc45:CDK:DDK:Mcm10:pre-replicative complex (name copied from entity in Homo sapiens)
DNA polymerase alpha:primase (name copied from entity in Homo sapiens)
N6-adenosine-methyltransferase 70 kDa subunit
DNA polymerase epsilon:origin complex (name copied from entity in Homo sapiens)
RNA Pol II (unphosphorylated) largest subunit
DNA-directed RNA polymerase II largest subunit
DNA polymerase epsilon (name copied from entity in Homo sapiens)
CAK (name copied from entity in Homo sapiens)
Cyclin B1:phospho-Cdc2(Thr 161, Thr 14, Tyr 15) (name copied from entity in Homo sapiens)
nuclear Cyclin B1:phospho-Cdc2 ( Thr 14) complexes (name copied from entity in Homo sapiens)
Cyclin B1:phospho-Cdc2 (Thr 14, Thr 161) (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) (name copied from entity in Homo sapiens)
In vitro assays of 5' to 3'-exoribonuclease activity
Cloning of a novel phosphatidylinositol kinase-related kinase: characterization of the human SMG-1 RNA surveillance protein
phospho-cyclin B1(CRS):phosph-Cdc2(Thr 161) (name copied from entity in Homo sapiens)
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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
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)
Telomerase RNP:Telomeric Chromosome End with an Additional single Stranded Telomere repeat (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)
Telomerase RNP (name copied from entity in Homo sapiens)
Cyclin B1:phospho-Cdc2(Thr 161) (name copied from entity in Homo sapiens)
ubiquitinated Orc1 (name copied from entity in Homo sapiens)
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A critical role of RICK/RIP2 polyubiquitination in Nod-induced NF-kappaB activation
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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_118388.7
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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_127503.5
CPSF (name copied from entity in Homo sapiens)
Cyclin B:Cdc2 complex (name copied from entity in Homo sapiens)
CPSF:capped intronless pre-mRNA:CBC complex (name copied from entity in Homo sapiens)
RNA primer-DNA primer:origin duplex (name copied from entity in Homo sapiens)
Cyclin B:phospho-Cdc2(Thr 14) (name copied from entity in Homo sapiens)
RNA primer-DNA primer:origin duplex with DNA damage
RNA primer:origin duplex:DNA polymerase alpha:primase complex (name copied from entity in Homo sapiens)
Participation of the microsomal CDP-diglycerides in the mitochondrial biosynthesis of phosphatidylglycerol
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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=174375
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117679.1
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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_7206.3
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RNA primer-DNA primer:origin duplex:PCNA (name copied from entity in Homo sapiens)
RFC Heteropentamer:RNA primer-DNA primer:origin duplex:PCNA homotrimer (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=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_9638.2
GINS complex (name copied from entity in Homo sapiens)
Mcm4,6,7 complex (name copied from entity in Homo sapiens)
ubiquitinated Cdc6 (name copied from entity in Homo sapiens)
Destabilization of mRNA by AUF1 (hnRNP D0)
PCNA homotrimer (name copied from entity in Homo sapiens)
RFC Heteropentamer:RNA primer-DNA primer:origin duplex (name copied from entity in Homo sapiens)
RFC Heteropentamer (name copied from entity in Homo sapiens)
Unwinding complex at replication fork (name copied from entity in Homo sapiens)
Reactome stable identifier. Use this 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=159549
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_98173.9
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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.
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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_117652.1
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=1614594
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_156447.3
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=1614532
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116358.1
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=3672254
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_130909.5
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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
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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=3672251
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_128546.5
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=3672246
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672245
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_144263.5
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=1614582
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117648.1
60S ribosomal complex (name copied from entity in Homo sapiens)
60s ribosomal complex lacking L13a subunit (name copied from entity in Homo sapiens)
43S: Ceruloplasmin mRNA:eIF4F:eIF4B:eIF4H:PABP (name copied from entity in Homo sapiens)
43S complex (name copied from entity in Homo sapiens)
ternary complex (name copied from entity in Homo sapiens)
eIF2:GTP (name copied from entity in Homo sapiens)
eIF2 subunit complex (name copied from entity in Homo sapiens)
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RFC Heteropentamer:RNA primer-DNA primer:G-strand extended telomere end (name copied from entity in Homo sapiens)
N-glycan trimming in the ER and Calnexin/Calreticulin cycle
RNA primer-DNA primer:G-strand extended telomere:PCNA (name copied from entity in Homo sapiens)
RFC Heteropentamer:RNA primer-DNA primer:G-strand extended telomere end duplex:PCNA homotrimer (name copied from entity in Homo sapiens)
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Cdc6 is regulated by E2F and is essential for DNA replication in mammalian cells.
The anaphase-promoting complex: it's not just for mitosis any more.
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Structure and function of a protein folding machine: the eukaryotic cytosolic chaperonin CCT
The circadian E-box: when perfect is not good enough
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
Synthesis of Prostaglandins (PG) and Thromboxanes (TX)
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
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
Human amidophosphoribosyltransferase. An oxygen-sensitive iron-sulfur protein
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)
Molecular identification and characterization of novel human and mouse concentrative Na+-nucleoside cotransporter proteins (hCNT3 and mCNT3) broadly selective for purine and pyrimidine nucleosides (system cib)
The H syndrome is caused by mutations in the nucleoside transporter hENT3
Import of carrier proteins into the mitochondrial inner membrane mediated by Tim22
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
AAA+: A class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes.
FUNCTION Involved in translation termination. Stimulates the activity of ERF1. Binds guanine nucleotides. Recruited by polyadenylate-binding protein PAB1 to poly(A)-tails of mRNAs. Interaction with PAB1 is also required for regulation of normal mRNA decay through translation termination-coupled poly(A) shortening.SUBUNIT Heterodimer of two subunits, one of which binds GTP. Interacts with polyadenylate-binding protein PAB1, and TPA1.DOMAIN The prion domain (PrD) is a Gln/Asn (Q/N)-rich domain, which is unstructured in its native, soluble form, and which forms a parallel in-register beta-sheet in its amyloid form.MISCELLANEOUS [PSI+] is the prion form of SUP35 (PubMed:8978027). [PSI+] is the result of a conformational change of the cellular SUP35 protein that becomes self-propagating and infectious. This conformational change generates a form of SUP35 that assembles into amyloid fibrils. [PSI+] aggregates sequester soluble SUP35, resulting in defects in faithful translation termination by read-through of translation termination codons (PubMed:8670813). [PSI+] can be cured by GdnHCl and by deletion of the molecular chaperone HSP104, which is required for [PSI+] propagation (PubMed:9335589). It is speculated that the prion form would be at least mildly deleterious in most environments, but it might sometimes increases evolvability in certain harsh environments (PubMed:19917766).MISCELLANEOUS Present with 78900 molecules/cell in log phase SD medium.SIMILARITY Belongs to the GTP-binding elongation factor family. ERF3 subfamily.
Nuclear export of the stress-activated protein kinase p38 mediated by its substrate MAPKAP kinase-2
Endothelium-derived relaxing and contracting factors
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cDNA cloning and mapping of a novel subtype of glutamine:fructose-6-phosphate amidotransferase (GFAT2) in human and mouse
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Guanine nucleotide exchange factors for Rho GTPases: turning on the switch
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A quantitative model of human DNA base excision repair. I. Mechanistic insights
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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
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Enhanced tyrosine phosphorylation in B lymphocytes upon complexing of membrane immunoglobulin
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Endogenous retroviral sequence is fused to FGFR1 kinase in the 8p12 stem-cell myeloproliferative disorder with t(8;19)(p12;q13.3)
Antigen presentation and the ubiquitin-proteasome system in host-pathogen interactions
Transformation of prostaglandin D2 to 9 alpha, 11 beta-(15S)-trihydroxyprosta-(5Z,13E)-dien-1-oic acid (9 alpha, 11 beta-prostaglandin F2): a unique biologically active prostaglandin produced enzymatically in vivo in humans
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Regulation of nuclear processes by inositol polyphosphates
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KARAP/DAP12/TYROBP: three names and a multiplicity of biological functions
A cooperative action of the ATP-dependent import motor complex and the inner membrane potential drives mitochondrial preprotein import
The processivity of multiubiquitination by the APC determines the order of substrate degradation
A third MRX family (MRX68) is the result of mutation in the long chain fatty acid-CoA ligase 4 (FACL4) gene: proposal of a rapid enzymatic assay for screening mentally retarded patients
A human homolog of the vaccinia virus HindIII K4L gene is a member of the phospholipase D superfamily
Cloning and characterization of murine 1-acyl-sn-glycerol 3-phosphate acyltransferases and their regulation by PPARalpha in murine heart
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Molecular cloning and characterization of an aquaporin cDNA from salivary, lacrimal, and respiratory tissues
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?
Glycogen debranching enzyme: purification, antibody characterization, and immunoblot analyses of type III glycogen storage disease.
Liver glucose transporter: a basolateral protein in hepatocytes and intestine and kidney cells
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
Cholesterol homeostasis in human brain: turnover of 24S-hydroxycholesterol and evidence for a cerebral origin of most of this oxysterol in the circulation
Phosphate transporters: a tale of two solute carrier families
Two cofactors and cytoplasmic chaperonin are required for the folding of alpha- and beta-tubulin
Ligand-induced, receptor-mediated dimerization and activation of EGF receptor
The path to perdition is paved with protons
Mitochondrial aspartyl-tRNA synthetase deficiency causes leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation
Regulation of the biosynthesis of 4,7,10,13,16,19-docosahexaenoic acid
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
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.
Expression and function of the human androgen-responsive gene ADI1 in prostate cancer
Nonsense-mediated mRNA decay in human cells: mechanistic insights, functions beyond quality control and the double-life of NMD factors
Activation of purified human protein kinase C alpha and beta I isoenzymes in vitro by Ca2+, phosphatidylinositol and phosphatidylinositol 4,5-bisphosphate
Myotubularin and MTMR2, phosphatidylinositol 3-phosphatases mutated in myotubular myopathy and type 4B Charcot-Marie-Tooth disease
A structural perspective on copper uptake in eukaryotes
The protein kinase/endoribonuclease IRE1alpha that signals the unfolded protein response has a luminal N-terminal ligand-independent dimerization domain
IAP proteins: blocking the road to death's door
The identification of a distinct export step following the biosynthesis of leukotriene C4 by human eosinophils
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Cellular functions of TC10, a Rho family GTPase: regulation of morphology, signal transduction and cell growth
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
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Forearm blood flow during body temperature transients produced by leg exercise.
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Endonucleolytic processing of covalent protein-linked DNA double-strand breaks
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Downstream Signaling Events Of B Cell Receptor (BCR)
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
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A unified model for apical caspase activation
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Subunit interactions in the mammalian alpha-ketoglutarate dehydrogenase complex. Evidence for direct association of the alpha-ketoglutarate dehydrogenase and dihydrolipoamide dehydrogenase components.
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CDK-mediated phosphorylation and removal of Cdc6
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Roles of Tom70 in import of presequence-containing mitochondrial proteins
Comparative characterization of human and rat liver glycogen synthase.
The subcellular localization of an aquaporin-2 tetramer depends on the stoichiometry of phosphorylated and nonphosphorylated monomers
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A novel function of the human CLS1 in phosphatidylglycerol synthesis and remodeling
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Autoinhibition and activation mechanisms of the Wiskott-Aldrich syndrome protein
Aldehyde dehydrogenase, a diphosphopyridine nucleotide-linked enzyme
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Cobalamin (Cbl, vitamin B12) transport and metabolism
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Expression of Human CTP synthetase in Saccharomyces cerevisiae reveals phosphorylation by protein kinase A
ATP-binding cassette (ABC) transporters in human metabolism and diseases
Peroxisome proliferator-activated receptor alpha target genes
alpha-linolenic (omega3) and linoleic (omega6) acid metabolism
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
Two conserved sequence blocks within eukaryotic tRNA genes are major promoter elements
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
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
Molecular characterization of a membrane transporter for lactate, pyruvate, and other monocarboxylates: implications for the Cori cycle
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
Disruption of aquaporin-11 produces polycystic kidneys following vacuolization of the proximal tubule
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Essential role for Gab2 in the allergic response
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Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S
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
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CARMA1 coiled-coil domain is involved in the oligomerization and subcellular localization of CARMA1 and is required for T cell receptor-induced NF-kappaB activation
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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
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Structure and function of human erythrocyte pyruvate kinase. Molecular basis of nonspherocytic hemolytic anemia
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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
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Role of aquaporin-7 and aquaporin-9 in glycerol metabolism; involvement in obesity
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Recognition and association of DNA glycosylase with site containing an affected pyrimidine
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The human phosphatidylinositol phosphatase SAC1 interacts with the coatomer I complex
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Discovery of the aquaporins and development of the field
The ontogeny of human drug-metabolizing enzymes: phase II conjugation enzymes and regulatory mechanisms
RNA Polymerase II Transcription Pre-Initiation And Promoter Opening
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.
Crystal structure of the autocatalytic initiator of glycogen biosynthesis, glycogenin.
Dissecting membrane insertion of mitochondrial beta-barrel proteins
Promoter clearance by RNA polymerase II is an extended, multistep process strongly affected by sequence.
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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.
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
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Mutations in iron-sulfur cluster scaffold genes NFU1 and BOLA3 cause a fatal deficiency of multiple respiratory chain and 2-oxoacid dehydrogenase enzymes
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
The anaphase-promoting complex: proteolysis in mitosis and beyond
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
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Subcellular localization and targeting of N-acetylglucosaminyl phosphatidylinositol de-N-acetylase, the second enzyme in the glycosylphosphatidylinositol biosynthetic pathway
Anti-apoptotic signaling by the interleukin-2 receptor reveals a function for cytoplasmic tyrosine residues within the common gamma (gamma c) receptor subunit
CDC6 protein is synthesized under the control of E2F transcription factors
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Vertebrate agmatinases: what role do they play in agmatine catabolism?
Transcriptional activation of GP-acyl transferase gene by ChREBP:MLX
Transcriptional activation of pyruvate kinase gene by ChREBP:MLX
Human very-long-chain acyl-CoA synthetase: cloning, topography, and relevance to branched-chain fatty acid metabolism
Agmatine: at the crossroads of the arginine pathways
Transcriptional activation of Acetyl-CoA carboxylase by ChREBP:MLX
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Characterization of a second member of the subfamily of calcium-binding mitochondrial carriers expressed in human non-excitable tissues
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Enzymes and reactions at the eukaryotic DNA replication fork.
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Cytochrome P450 - arranged by substrate type
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Mevalonate kinase is a cytosolic enzyme in humans
Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways
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Mechanistic and kinetic analysis of the DcpS scavenger decapping enzyme
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Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs
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Synthesis of substrates in N-glycan biosythesis
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Post-Elongation Processing of the Transcript
2-Hydroxy-1,2,3-propanetricarboxylic acid
Identification of LAT4, a novel amino acid transporter with system L activity
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
Pam17 is required for architecture and translocation activity of the mitochondrial protein import motor
The extended protein kinase C superfamily
Localization of human equilibrative nucleoside transporters, hENT1 and hENT2, in renal epithelial cells
Subcellular locations of phosphatidylinositol 4-kinase isoforms
Old and new generation lipid mediators in acute inflammation and resolution
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Regulation of mRNA Stability by Proteins that Bind AU-rich Elements
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Transcriptional signaling by double-stranded RNA: role of TLR3
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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
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ZNF198-FGFR1 transforms Ba/F3 cells to growth factor independence and results in high level tyrosine phosphorylation of STATS 1 and 5
Eukaryotic translation initiation factor 5A-1
Eukaryotic tranlation initiation factor 5A2
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
Glucosamine--fructose-6-phosphate aminotransferase (isomerizing) 1
N-acetylglucosaminyl-phosphatidylinositol de-N-acetylase
The role of the Tim8p-Tim13p complex in a conserved import pathway for mitochondrial polytopic inner membrane proteins
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
Eukaryotic translation initiation factor 5A
ChEBI:37642 (25R)-3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA
Human choline acetyltransferase (CHAT): partial gene sequence and potential control regions
Evidence for a family of human glucose transporter-like proteins. Sequence and gene localization of a protein expressed in fetal skeletal muscle and other tissues
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Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit beta isoform
Probable ATP-dependent RNA helicase DDX11
Carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 2
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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
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Serine/threonine-protein kinase/endoribonuclease IRE1 (phosphorylated)
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Phosphoinositide signalling in cancer: beyond PI3K and PTEN
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WD repeat domain phosphoinositide-interacting protein 1
Neurotrophin signaling: many exciting surprises!
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Dolichyl-phosphate beta-glucosyltransferase
Mannose-1-phosphate guanyltransferase beta
Molecular cloning and characterization of a novel muscle adenylosuccinate synthetase, AdSSL1, from human bone marrow stromal cells
GDP-Man:GlcNAc2-PP-dolichol mannosyltransferase
Chitobiosyldiphosphodolichol beta-mannosyltransferase
FGFR1 is fused to the centrosome-associated protein CEP110 in the 8p12 stem cell myeloproliferative disorder with t(8;9)(p12;q33)
UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase
UDP-N-acetylglucosamine transferase subunit ALG14 homolog
Metabolism, function and mass spectrometric analysis of bis(monoacylglycero)phosphate and cardiolipin
Oligomerization of STIM1 couples ER calcium depletion to CRAC channel activation
Glucosamine--fructose-6-phosphate aminotransferase (isomerizing) 2
UDP-N-acetylhexosamine pyrophosphorylase
An adjacent pair of human NUDT genes on chromosome X are preferentially expressed in testis and encode two new isoforms of diphosphoinositol polyphosphate phosphohydrolase
Glucosamine 6-phosphate N-acetyltransferase
Characterization of the XRN1 gene encoding a 5'-->3' exoribonuclease: sequence data and analysis of disparate protein and mRNA levels of gene-disrupted yeast cells
FUNCTION General transcription factor that functions at the core of the DNA-binding general transcription factor complex TFIID. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription.SUBUNIT Binds DNA as monomer. The 1.2 MDa TFIID complex is composed of TATA binding protein (TBP) and the 14 TBP-associated factors. One copy of each TAF1, TAF2, TAF3, TAF7, TAF8, TAF11, TAF13, two copies of each TAF4, TAF5, TAF6, TAF9, TAF10, TAF12, and three copies of TAF14. Interacts with TFC8.SIMILARITY Belongs to the TBP family.
Oligosaccharide translocation protein RFT1
Dolichyl-P-Man:Man(5)GlcNAc(2)-PP-dolichyl mannosyltransferase
Dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase
Probable dolichyl pyrophosphate Glc1Man9GlcNAc2 alpha-1,3-glucosyltransferase
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Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase
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Functional characterization of a human aquaporin 0 mutation that leads to a congenital dominant lens cataract
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Microsomal enzymes of cholesterol biosynthesis. Purification of lanosterol 14 alpha-methyl demethylase cytochrome P-450 from hepatic microsomes.
FUNCTION Essential component of the PAM complex, a complex required for the translocation of transit peptide-containing proteins from the inner membrane into the mitochondrial matrix in an ATP-dependent manner. In the complex, it is required to regulate activity of mtHSP70 (SSC1) via its interaction with PAM18/TIM14. May act by positioning PAM18/TIM14 in juxtaposition to mtHSP70 at the translocon to maximize ATPase stimulation.SUBUNIT Homodimer and heterodimer with PAM18. Homodimerization may not be relevant in vivo, while heterodimerization is essential for activity regulation of mtHSP70. Component of the PAM complex, at least composed of mtHsp70, MGE1, TIM44, PAM16, PAM17 and PAM18. Interacts with MDJ2.DOMAIN The J-like region, although related to the J domain does not stimulate ATPase activity of mtHSP70. It nevertheless mediates the heterodimerization with the J domain of PAM18 and is therefore essential for PAM complex function.MISCELLANEOUS Present with 3180 molecules/cell in log phase SD medium.SIMILARITY Belongs to the TIM16/PAM16 family.
Human liver type pyruvate kinase: complete amino acid sequence and the expression in mammalian cells
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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
Antigen processing: Ubiquitination & Proteasome degradation
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ZnT7, a novel mammalian zinc transporter, accumulates zinc in the Golgi apparatus
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T-complex protein 1 subunit zeta (TCP-1-zeta)
T-complex protein 1 subunit alpha (TCP-1-alpha)
T-complex protein 1 subunit gamma (TCP-1-gamma)
T-complex protein 1 subunit delta (TCP-1-delta)
T-complex protein 1 subunit beta (TCP-1-beta)
T-complex protein 1 subunit eta (TCP-1-eta)
T-complex protein 1 subunit epsilon (TCP-1-epsilon)
T-complex protein 1 subunit theta (TCP-1-theta)
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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
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U-box proteins as a new family of ubiquitin ligases
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Methionine regeneration and aspartate aminotransferase in parasitic protozoa
(S)-3-Hydroxyisobutyryl-CoA [ChEBI:28259]
Identification and characterization of a gene encoding human LPGAT1, an endoplasmic reticulum-associated lysophosphatidylglycerol acyltransferase
MyD88:Mal cascade initiated on plasma membrane
The major sites of cellular phospholipid synthesis and molecular determinants of Fatty Acid and lipid head group specificity
GAPs galore! A survey of putative Ras superfamily GTPase activating proteins in man and Drosophila
The p24 family and selective transport processes at the ER-Golgi interface
Phase 1 - Functionalization of compounds
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
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.
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
Mapping residues of SUMO precursors essential in differential maturation by SUMO-specific protease, SENP1
Activation and signaling of the p38 MAP kinase pathway
Interaction of retinitis pigmentosa GTPase regulator (RPGR) with RAB8A GTPase: implications for cilia dysfunction and photoreceptor degeneration
Overview of the proton-coupled MCT (SLC16A) family of transporters: characterization, function and role in the transport of the drug of abuse gamma-hydroxybutyric acid
Cloning, characterization, and chromosomal localization of a gene frequently deleted in human liver cancer (DLC-1) homologous to rat RhoGAP
Human liver glucokinase gene: cloning and sequence determination of two alternatively spliced cDNAs
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Protein kinase C substrate 60.1 kDa protein heavy chain
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Oligosaccharyl transferase 48 kDa subunit
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kDa subunit
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Identification of human phosphoglucomutase 3 (PGM3) as N-acetylglucosamine-phosphate mutase (AGM1)
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Identification of an evolutionarily conserved superfamily of DOCK180-related proteins with guanine nucleotide exchange activity
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Subcellular targeting and trafficking of nitric oxide synthases
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The human Myt1 kinase preferentially phosphorylates Cdc2 on threonine 14 and localizes to the endoplasmic reticulum and Golgi complex.
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Crystal structure of human prostaglandin F synthase (AKR1C3)
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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
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RNA Polymerase III Abortive And Retractive Initiation
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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)
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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)
Xeroderma pigmentosum group E complementing protein
Resolution of D-loop structures through Holliday junction intermediates
DNA-repair protein complementing XP-G cells (Xeroderma pigmentosum group G complementing protein) (DNA excision repair protein ERCC-5)
Xeroderma pigmentosum group G complementing protein
DNA-repair protein complementing XP-G cells
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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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Excision repair protein ERCC-6 (Cockayne syndrome protein CSB)
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Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics
Serine-protein kinase ATM (EC 2.7.1.37) (Ataxia telangiectasia mutated) (A-T, mutated)
A missense mutation in SLC33A1, which encodes the acetyl-CoA transporter, causes autosomal-dominant spastic paraplegia (SPG42)
DNA repair protein RAD51 homolog 1 (hRAD51) (HsRAD51)
Double-strand break repair protein MRE11A
Induction of ceruloplasmin synthesis by IFN-gamma in human monocytic cells
Synthesis and interconversion of nucleotide di- and triphosphates
N-glycosylase/DNA lyase (Includes: 8-oxoguanine DNA glycosylase (EC 3.2.2.-); DNA-(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) (AP lyase))
DNA-(apurinic or apyrimidinic site) lyase
DNA repair protein REV1 ecNumber2.7.7.-/ecNumber
6-O- methylguanine-DNA methyltransferase
Methylated-DNA--protein-cysteine methyltransferase
Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) (6-O- methylguanine-DNA methyltransferase)
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Endonuclease III-like protein 1 (EC 4.2.99.18)
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Phosphoinositide 3-kinase: the key switch mechanism in insulin signalling.
A roller coaster ride with the mitotic cyclins
G(1) to S transition: more than a cell cycle engine switch.
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
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
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Regulation of Ras in lymphocytes: get a GRP
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Rho guanine nucleotide exchange factor 4
Rho guanine nucleotide exchange factor 3
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The quality control of MHC class I peptide loading
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Neuroepithelial cell-transforming gene 1 protein
Rho guanine nucleotide exchange factor 12
Negative regulation of condensin I by CK2-mediated phosphorylation
Molecular cloning and expression of a cDNA for human kidney cysteine conjugate beta-lyase
'G6P [cytosol]' positively regulates 'glycogen (starch) synthase activity of GYS tetramers D form [cytosol]'
'Pi [cytosol]' is required for 'ribose phosphate diphosphokinase activity of phosphoribosyl pyrophosphate synthetase 1 holoenzyme (name copied from entity in Homo sapiens) [cytosol]'
'Mg2+ [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]'
'NAcGlu [mitochondrial matrix]' positively regulates 'carbamoyl-phosphate synthase (ammonia) activity of CPS1 [mitochondrial matrix]'
Epidermal Growth Factor Receptor (EGFR) signaling
Specificty of human and rat orthologs of the concentrative nucleoside transporter, SPNT
C-to-U RNA editing: mechanisms leading to genetic diversity.
Changes in serotonin metabolism during treatment with the aldehyde dehydrogenase inhibitors disulfiram and cyanamide
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.
The concentrative nucleoside transporter family, SLC28
A current review of fatty acid transport proteins (SLC27)
Three-dimensional structure of human erythrocytic purine nucleoside phosphorylase at 3.2 A resolution
Structural and functional requirements for activity of the Tim9-Tim10 complex in mitochondrial protein import
ErbB-3 and ErbB-4 function as the respective low and high affinity receptors of all Neu differentiation factor/heregulin isoforms
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
Aquaporins: highways for cells to recycle water with the outside world
Analysis of nucleocytoplasmic shuttling of NF kappa B proteins in human leukocytes
Functional analysis of the purified anandamide-generating phospholipase D as a member of the metallo-beta-lactamase family
Characterization of human glucose transporter (GLUT) 11 (encoded by SLC2A11), a novel sugar-transport facilitator specifically expressed in heart and skeletal muscle
Role of human mitochondrial Nfs1 in cytosolic iron-sulfur protein biogenesis and iron regulation
PIG-W is critical for inositol acylation but not for flipping of glycosylphosphatidylinositol-anchor
The chromosomal association of condensin II is regulated by a noncatalytic function of PP2A
Assembly of the RAD50-MRE11-NBS1 complex at DNA double-strand breaks
Long-chain fatty acid transport protein 6
FUNCTION Component of the TOM (translocase of outer membrane) receptor complex responsible for the recognition and translocation of cytosolically synthesized mitochondrial preproteins. Together with TOM20 and TOM22 functions as the transit peptide receptor at the surface of the mitochondrion outer membrane and facilitates the movement of preproteins into the TOM40 translocation pore.SUBUNIT Forms part of the TOM (translocase of outer membrane) complex that consists of at least 7 different proteins (TOM5, TOM6, TOM7, TOM20, TOM22, TOM40 and TOM70). In the complex interacts with TOM22. Interacts with TOM37.MISCELLANEOUS Present with 45300 molecules/cell in log phase SD medium.SIMILARITY Belongs to the Tom70 family.SIMILARITY Contains 9 TPR repeats.
Long-chain fatty acid transport protein 4
Transcription of class III genes: formation of preinitiation complexes
Signal transduction by the neurotrophin receptors
Calcium-transporting ATPase type 2C member 2
Probable phospholipid-transporting ATPase IA
Calcium-transporting ATPase type 2C member 1
Probable phospholipid-transporting ATPase VA
The mitochondrial processing peptidase behaves as a zinc-metallopeptidase
Mitochondrial import of the ADP/ATP carrier: the essential TIM complex of the intermembrane space is required for precursor release from the TOM complex
Phagocytosis of retinal rod and cone photoreceptors
Diversification of Neu differentiation factor and epidermal growth factor signaling by combinatorial receptor interactions
Gap-filling DNA repair synthesis and ligation in TC-NER
SUBUNIT F-type ATPases have 2 components, CF(1) - the catalytic core - and CF(0) - the membrane proton channel. CF(1) has five subunits: alpha(3), beta(3), gamma(1), delta(1), epsilon(1). CF(0) has three main subunits: a, b and c.MISCELLANEOUS Present with 41500 molecules/cell in log phase SD medium.SIMILARITY Belongs to the ATPase alpha/beta chains family.
Tuberculosis - metabolism and respiration in the absence of growth
Probable phospholipid-transporting ATPase VD
A microRNA polycistron as a potential human oncogene
Regulation of deoxyadenosine and nucleoside analog phosphorylation by human placental adenosine kinase
Recruitment of RNA polymerase III to its target promoters.
Rho guanine nucleotide exchange factor 9
Steroidogenic electron transport in adrenal cortex mitochondria
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Rho guanine nucleotide exchange factor 1
Acyl-CoA:lysophospholipid acyltransferases
Cell division control protein 42 homolog
Tyrosine-phosphorylated Vav1 as a point of integration for T-cell receptor- and CD28-mediated activation of JNK, p38, and interleukin-2 transcription
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Molecular cloning and nucleotide sequence of a full-length cDNA for human alpha enolase
Phosphorylated JNKs: MAPK8, MAPK9, MAPK10
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ATP-binding cassette sub-family B member 7, mitochondrial
ATP-binding cassette sub-family D member 2
Multidrug resistance-associated protein 6
Multidrug resistance-associated protein 3
ATP-binding cassette sub-family C member 3
Cdc25A stability is controlled by the ubiquitin-proteasome pathway during cell cycle progression and terminal differentiation
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Newly made phosphatidylserine and phosphatidylethanolamine are preferentially translocated between rat liver mitochondria and endoplasmic reticulum
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Solute carrier family 2, facilitated glucose transporter member 7
Solute carrier family 2, facilitated glucose transporter member 9
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Cleavage of oxidized guanine nucleotide and ADP sugar by human NUDT5 protein
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Equilibrative nucleoside transporter 2 (Equilibrative nitrobenzylmercaptopurine riboside-insensitive nucleoside transporter) (Equilibrative NBMPR-insensitive nucleoside transporter) (Nucleoside transporter, ei-type) (36 kDa nucleolar protein HNP36) (Hydrophobic nucleolar protein, 36 kDa) (Delayed-early response protein 12)
solute carrier family 29 (nucleoside transporters), member 2
Equilibrative nitrobenzylmercaptopurine riboside-insensitive nucleoside transporter
Equilibrative NBMPR-insensitive nucleoside transporter
UDP-xylose and UDP-N-acetylglucosamine transporter
Equilibrative NBMPR-sensitive nucleoside transporter
Equilibrative nitrobenzylmercaptopurine riboside-sensitive nucleoside transporter
solute carrier family 29 (nucleoside transporters), member 1
Equilibrative nucleoside transporter 1 (Equilibrative nitrobenzylmercaptopurine riboside-sensitive nucleoside transporter) (Equilibrative NBMPR-sensitive nucleoside transporter) (Nucleoside transporter, es-type)
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FACL4, encoding fatty acid-CoA ligase 4, is mutated in nonspecific X-linked mental retardation
Novel interleukin-2 receptor subunit detected by cross-linking under high-affinity conditions
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Employment of the epidermal growth factor receptor in growth factor-independent signaling pathways
Glycogenin: the primer for mammalian and yeast glycogen synthesis
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RNA Polymerase III Transcription Initiation From Type 2 Promoter
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Association with HSP90 inhibits Cbl-mediated down-regulation of mutant epidermal growth factor receptors
LRRFIP1, a new FGFR1 partner gene associated with 8p11 myeloproliferative syndrome
The sodium/calcium exchanger family-SLC8
Genomic organization, tissue distribution and deletion mutation of human pyridoxine 5'-phosphate oxidase
Antimicrobial mechanisms of phagocytes and bacterial evasion strategies
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The D-Box-activating domain (DAD) is a new proteolysis signal that stimulates the silent D-Box sequence of Aurora-A
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3alpha,7alpha-Dihydroxy-5beta-cholestane [ChEBI:1708]
A novel family of membrane-bound E3 ubiquitin ligases
RhoGDIgamma: a GDP-dissociation inhibitor for Rho proteins with preferential expression in brain and pancreas
A minus-end-directed kinesin with plus-end tracking protein activity is involved in spindle morphogenesis
P110delta, a novel phosphoinositide 3-kinase in leukocytes
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
Identification of a SPH element in the distal region of a human U6 small nuclear RNA gene promoter and characterization of the SPH binding factor in HeLa cell extracts
10-formyltetrahydrofolyl polyglutamate macromolecule [ChEBI:28010]
10-formyltetrahydrofolyl polyglutamate macromolecule
Advanced glycation endproduct (AGE) receptor 1 is a negative regulator of the inflammatory response to AGE in mesangial cells
Roles of aquaporin-3 water channels in volume-regulatory water flow in a human epithelial cell line
Transport to the Golgi and subsequent modification
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.
Internal control regions for transcription of eukaryotic tRNA genes
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
Resolution of AP sites via the multiple-nucleotide patch replacement pathway
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
Citrin and aralar1 are Ca(2+)-stimulated aspartate/glutamate transporters in mitochondria
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.
Fibroblast growth factors and their receptors in cancer
Protein Kinase C, unconventional isoforms
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
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Vacuolar protein sorting-associated protein 45
Differential expression and regulation of toll-like receptors (TLR) in human leukocytes: selective expression of TLR3 in dendritic cells
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Global gene expression profiling and histochemical analysis of the developing human fetal pancreas
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GTP:AMP phosphotransferase, mitochondrial
The yeast Pif1p helicase removes telomerase from telomeric DNA
Intracellular hyaluronan-binding protein 4
Bromodomain and PHD finger-containing protein 3
Metabolism of water-soluble vitamins and cofactors
FUNCTION Heme-containing component of the ubiquinol-cytochrome c reductase complex (complex III or cytochrome b-c1 complex), which is part of the mitochondrial respiratory chain that generates an electrochemical potential coupled to ATP synthesis. The complex couples electron transfer from ubiquinol to cytochrome c.SUBUNIT Fungal cytochrome b-c1 complex contains 10 subunits; 3 respiratory subunits, 2 core proteins and 5 low-molecular weight proteins. Cytochrome b-c1 complex is a homodimer.PTM Binds 1 heme group per subunit.MISCELLANEOUS Present with 39900 molecules/cell in log phase SD medium.SIMILARITY Belongs to the cytochrome c family.SIMILARITY Contains 1 cytochrome c domain.
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Structure of human phosphopantothenoylcysteine synthetase at 2.3 A resolution.
U6 snRNA-associated Sm-like protein LSm5
U6 snRNA-associated Sm-like protein LSm7
U6 snRNA-associated Sm-like protein LSm6
U6 snRNA-associated Sm-like protein LSm1
U6 snRNA-associated Sm-like protein LSm3
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Regulated expression of three C/EBP isoforms during adipose conversion of 3T3-L1 cells
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Bora and the kinase Aurora a cooperatively activate the kinase Plk1 and control mitotic entry
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The endoribonuclease activity of mammalian IRE1 autoregulates its mRNA and is required for the unfolded protein response
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Phosphodiesterases, dual (cAMP, cGMP) activity
Sequencing and expression of a cDNA for human glutathione synthetase
Signal recognition particle 68 kDa protein
cGMP-inhibited 3',5'-cyclic phosphodiesterase 3A
Carbohydrate responsive element-binding protein (ChREBP): a key regulator of glucose metabolism and fat storage
Neurotransmitter uptake and Metabolism In Glial Cells
5,10-methenyltetrahydrofolate polyglutamate [ChEBI:65049]
5,10-methenyltetrahydrofolate polyglutamate
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Pam16 has an essential role in the mitochondrial protein import motor
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SREBP transcription factors: master regulators of lipid homeostasis
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Heterogeneous nuclear ribonucleoprotein D0
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miRNAs on the move: miRNA biogenesis and the RNAi machinery
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Translation initiation factor eIF-2B gamma subunit
eIF-2B GDP-GTP exchange factor, gamma subunit
translation initiation factor 2B gamma subunit
Human MTH3 (NUDT18) Protein Hydrolyzes Oxidized Forms of Guanosine and Deoxyguanosine Diphosphates: COMPARISON WITH MTH1 AND MTH2
eIF-2B GDP-GTP exchange factor, epsilon subunit
Translation initiation factor eIF-2B epsilon subunit
translation initiation factor 2B epsilon subunit
translation initiation factor 2B delta subunit
eIF-2B GDP-GTP exchange factor, delta subunit
Translation initiation factor eIF-2B delta subunit
translation initiation factor 2B alpha subunit
Translation initiation factor eIF-2B alpha subunit
eIF-2B GDP-GTP exchange factor, alpha subunit
translation initiation factor 2B beta subunit
eIF-2B GDP-GTP exchange factor, beta subunit
Translation initiation factor eIF-2B beta subunit
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Transcriptional regulation of HMG-CoA synthase and HMG-CoA reductase genes by human ACBP
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Phytanic acid and pristanic acid are oxidized by sequential peroxisomal and mitochondrial reactions in cultured fibroblasts
Planar cell polarity signaling: from fly development to human disease
Interactions between the endoplasmic reticulum, mitochondria, plasma membrane and other subcellular organelles
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Eukaryotic ribosomes require initiation factors 1 and 1A to locate initiation codons.
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ABC transporters in cellular lipid trafficking
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Phosphatidylinositol-5-phosphate activation and conserved substrate specificity of the myotubularin phosphatidylinositol 3-phosphatases
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Identification and characterization of PS-GAP as a novel regulator of caspase-activated PAK-2
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Human CDC6/Cdc18 associates with Orc1 and cyclin-cdk and is selectively eliminated from the nucleus at the onset of S phase.
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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.
Activation of PAK-2p34 coincides with autophosphorylation of Thr 402 in the the catalytic domain (Walter et al., 1998).
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.
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).
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 .
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).
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).
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).
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).
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).
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.
Gamma-Aminobutyric acid (GABA) is the major inhibitory transmitter of the vertebrate retina. The gene SLC32A1 encodes the vesicular inhibitory amino acid transporter (VIAAT, also called vesicular GABA transporter VGAT) (Jellali A et al, 2002). VIAAT is a proton-coupled amino acid antiporter, uptaking the inhibitory neurotransmitters GABA and glycine into synaptic vesicles in exchange for protons. This process is driven by the H+-ATPase, providing the driving force for uptake of these neurotransmitters. The protein is expressed throughout the terminal ends of horizontal cells of the retina.
The SLC17 gene family encode proteins which are organic anion transporters. There are three distinct subfamilies within SLC17; vesicular glutamate transporters (VGLUT1-3 encoded by SLC17A7,6 and 8), type I Na+-coupled phosphate co-transporters (encoded by SLC17A1-4) and a proton-coupled sialic acid co-transporter (encoded by SLC17A5) (Reimer RJ and Edwards RH, 2004). Two members of the SLC5 gene family encode carboxylate transporters, SMCT1 and SMCT2 (Ganapathy V et al, 2008).
SLC43A1 (LAT3), associated with the plasma membrane, mediates the uptake of isoleucine, leucine, methionine, phenylalanine, and valine in a biphasic and sodium ion-independent transport process. Northern blotting experiments indicate gene expression in liver, pancreas, and skeletal muscle, and at lower levels in many tissues including kidney and intestine (Babu et al. 2003).
SLC16A10 mediates the reversible facilitated diffusion of phenylalanine, tyrosine, and tryptophan across the plasma membrane. The process is Na+-independent and not coupled to H+ transport. As measured by Northern blotting SLC16A10 is widely expressed in the body but especially abundant in kidney. In situ hybridization studies indicate that the gene product is abundant in kidney proximal tubules (Kim et al. 2001; Kim et al. 2002; Park et al. 2005).
Amino acid transport across plasma membranes is critical to the uptake of these molecules from the gut, to their reabsortion in the kidney proximal tubulues, and to their distribution to cells in which they are required for the synthesis of proteins and of amino acid derived small molecules such as neurotransmitters. Physiological studies have defined 18 "systems" that mediate amino acid transport, each characterized by its amino acid substrates, as well as its pH sensitivity and its association (or not) with ion transport. More recently, molecular cloning studies have allowed the identification of the plasma membrane transport proteins that mediate these reactions. Amino acid uptake mediated by 17 of these transporters is annotated here (Broer 2008).
SLC43A2 (LAT4), associated with the plasma membrane, mediates the uptake of isoleucine, leucine, methionine, phenylalanine, and valine in a biphasic and sodium ion-independent transport process. Northern blotting and in situ hybridization experiments indicate gene expression in kidney and intestine (Bodoy et al. 2005).
Eight SLC gene families are involved in the transport of amino acids and oligopeptides.
Nonsense Mediated Decay Independent of the Exon Junction Complex
The molecular mechanisms that control thrombopoiesis
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'.
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).
Pol III initiation complexes open the promoter spontaneously similar to the mechanism employed in archaeal and bacterial transcription.
There are three basic types of RNA polymerase III promoters. The three types of RNA polymerase III promoters are known as type 1, type 2, and type 3 promoters. Type 1 promoters are found in the 5S genes and consist of a gene-internal element called the internal control region (ICR), that is subdivided into A block, intermediate element, and C block (Bogenhagen, 1985; Sakonju et al., 1980). Type 2 promoters are found in tRNA genes, Adenovirus 2 VAI gene, and other genes (Galli et al., 1981; Sharp et al., 1981). These promoters consists of two gene-internal elements called the A and the B boxes. Type 3 promoters consist of a distal sequence element (DSE) that serves as an enhancer, a proximal sequence element (PSE), and a TATA box (Baer et al., 1989; Lobo and Hernandez, 1989). Some promoters combine elements from type 2 and 3 promoters. For example, the S. cerevisiae U6 promoter, also shown in the figure, contains the TATA box typical of type 3 promoters and the A and B boxes typical of type 2 promoters. Moreover, in S. pombe, nearly all tRNA and 5S genes contain a TATA box in addition to gene-internal elements, and the TATA box is required for transcription. ÃÂ
The metazoan-specific type 3 promoters, which are exemplified by the human U6 promoter, recruit a complex variously called the snRNA activating protein complex (SNAPc) (Sadowski et al., 1993), the PSE binding protein (PBP) (Waldschmidt et al., 1991), or the PSE transcription factor (PTF) (Murphy et al., 1992). The complex contains five types of subunits and binds to the PSE. Type 3 promoters also recruit Brf2-TFIIIB through a combination of protein-protein contacts with SNAPc and a direct association of the TBP component of Brf2-TFIIIB with the TATA box. This then allows RNA polymerase III to join the complex. The down stream element (DSE) of type 3 promoters, which enhances transcription from the core promoter, almost invariably contains an octamer sequence and an SPH element (also called NONOCT element)(Cheung et al., 1993; Danzeiser et al., 1993; Kunkel et al., 1996; Myslinski et al., 1992). The octamer sequence recruits the POU domain protein Oct-1 (Herr et al., 1988; Sturm et al., 1988), and the SPH element recruits a zinc finger protein known as Staf or SPH binding factor (SBF), which has been cloned from humans (Myslinski et al., 1998; Rincon et al., 1998).
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
Cellular circadian pacemaking and the role of cytosolic rhythms
The type 1 promoters recruit TFIIIA, the founding member of the C2H2 zinc finger family of DNA-binding proteins (Engelke et al., 1980; Sakonju et al., 1981). The binding of TFIIIA then allows the binding of TFIIC (Lassar et al., 1983), a complex consisting of five subunits (which differs from the six subunits in S. cerevisiae) in human cells and S. pombe. Once the DNA/TFIIIA/TFIIIC complex is formed, Brf1-TFIIIB joins the complex and this in turn allows the recruitment of RNA polymerase III (Bieker et al., 1985; Setzer and Brown, 1985).
The type 2 promoters can recruit TFIIIC without the help of TFIIIA because TFIIIC binds directly to the A and B boxes. As for the type 1 promoters, this then allows the binding of Brf1-TFIIIB and RNA polymerase III. Importantly, in the yeast system, once Brf1-TFIIIB has been recruited to type 1 or 2 promoters, TFIIIA and/or TFIIIC can be stripped from the DNA with high salt or heparin treatment. Brf1-TFIIIB remains bound to the DNA and is sufficient to direct multiple rounds of transcription .
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.
After the assembly of the RNA Polymerase I Holoenzyme, Rrn3 binding occurs.
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.
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).
At the beginning of this reaction, 1 molecule of '3',5'-Cyclic AMP' is present. At the end of this reaction, 1 molecule of 'AMP' is present. This reaction is mediated by the 'hydrolase activity' of 'Phosphorylated PDE3B'.
The yeast mitochondrial carrier Leu5p and its human homologue Graves' disease protein are required for accumulation of coenzyme A in the matrix
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.
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.
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.
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.
IP3 receptor/Ca2+ channel: from discovery to new signaling concepts
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.
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).
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).
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).
Cloning and characterization of human guanine deaminase. Purification and partial amino acid sequence of the mouse protein.
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O2-dependent coproporpyrinogen oxidase (CPO) catalyzes the conversion of coproporphyrinogen III (COPRO3) to protoporphyrinogen IX (PPGEN9). The localization of the human enzyme to the mitochondrial intermembrane space is inferred from studies of the homologous rat enzyme (Elder and Evans 1978). The human enzyme functions as a homodimer (Lee et al. 2005). Enzyme deficiency is associated with hereditary coproporphyria in vivo.
Six electrons are oxidized in protophorphyrinogen IX (PPGEN9) to form the planar macrocycle protoporphyrin IX (PRIN9). This reaction is performed by the enzyme protoporphyrinogen oxidase (PPO). PPO functions as a homodimer containing one non-covalently-bound FAD. The protein resides on the outer surface of the inner mitochondrial membrane. PPO deficiency is associated with variegate porphyria in vivo.
Ferrochelatase (FECH) catalyzes the insertion of ferrous iron into protoporphyrin IX (PRIN9) to form heme. FECH is localized on the matrix surface of the inner mitochondrial membrane and this reaction takes place within the mitochondrial matrix. The enzyme functions as a homodimer with each monomer containing a nitric oxide-sensitive 2Fe-2S cluster. Enzyme deficiency is associated with erythropoietic protoporphyria in vivo, and inhibition of ferrochelatase activity is a clinically important consequence of lead poisoning (Piomelli et al. 1987).
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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).
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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).
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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.
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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.
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Cytosolic uroporphyrinogen III synthase (URO3S) catalyzes the conversion of HMB (hydroxymethylbilane) to uroporphyrinogen III, a reaction involving ring closure and intramolecular rearrangement. Uroporphyrinogen III represents a branch point for the pathways leading to formation of heme, chlorophyll and corrins. HMB is rapidly converted from a linear tetrapyrrole to the cyclic form. Deficiencies of URO3S in vivo are associated with congenital erythropoietic porphyria.
Cytosolic uroporphyrinogen decarboxylase (UROD) catalyzes the sequntial removal of four carboxylic groups from the acetic acid side chains of uroporphyrinogen III (URO3) to form coproporphyrinogen III (COPRO3) (de Verneuil et al. 1983). Human UROD is a dimer (Whitby et al. 1998). Heterogenous and homogenous deficiencies of UROD are associated with porphyria cutanea tarda and hepatoerythropoietic porphyria respectively in vivo (Moran-Jiminez et al. 1996).
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).
Cloning of the human equilibrative, nitrobenzylmercaptopurine riboside (NBMPR)-insensitive nucleoside transporter ei by functional expression in a transport-deficient cell line
Identification and characterization of a novel inositol polyphosphate 5-phosphatase
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.
Metabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as the inactivation and elimination of toxic ones generated endogenously or present in the extracellular environment. The processes of energy metabolism can be classified into two groups according to whether they involve carbohydrate-derived or lipid-derived molecules, and within each group it is useful to distinguish processes that mediate the breakdown and oxidation of these molecules to yield energy from ones that mediate their synthesis and storage as internal energy reserves. Synthetic reactions are conveniently grouped by the chemical nature of the end products, such as nucleotides, amino acids and related molecules, and porphyrins. Detoxification reactions (biological oxidations) are likewise conveniently classified by the chemical nature of the toxin. At the same time, all of these processes are tightly integrated. Intermediates in reactions of energy generation are starting materials for biosyntheses of amino acids and other compounds, broad-specificity oxidoreductase enzymes can be involved in both detoxification reactions and biosyntheses, and hormone-mediated signaling processes function to coordinate the operation of energy-generating and energy-storing reactions and to couple these to other biosynthetic processes.
The 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.
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.
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.
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).
Iron-sulfur clusters are assembled on the scaffold, ISCU. Based on homology with bacterial IscU:IscS complexes (reviewed in Johnson et al. 2005), one molecule of ISCU is bound to each subunit of a NFS1 dimer (Marinoni et al. 2012). A single complex may thus be capable of assembling two 2Fe-2S clusters. Sulfide is provided by desulfuration of cysteine by NFS1:ISD11 (Biederbick et al. 2006, Shi et al. 2009, Tsai and Barondeau 2010). It has been proposed that ferrous iron is delivered by FXN (Gerber et al. 2003, Yoon and Cowan 2003, Schmucker et al. 2011) bound to ISCU (inferred from yeast, Wang and Craig 2008), although more recent studies suggested that FXN functions as an allosteric effector to stimulate sulfide transfer (Tsai et al. 2010). Holo-ISCU (ISCU bound to a newly synthesized 2Fe-2S cluster) transiently interacts with a dedicated HSP70 chaperone system including Mortalin (GRP75) and HSP20 and GLRX5 (GRX5). Electrons supplied by FDXL1 (FDX2) are required and may reduce the sulfur from S0 to S2-. NFU1 binds an Fe-S cluster (Tong et al. 2003, inferred from bacteria Yuvaniyama et al. 2000) and, from biochemical studies of bacterial NFU1 homologues, is proposed to be an intermediate Fe-S cluster carrier (Bandyopadhy et al. 2008). Mutations in human NFU1 affect only a subset of Fe-S proteins (Navarro-Sastre et al. 2011).
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.
Apert syndrome results from localized mutations of FGFR2 and is allelic with Crouzon syndrome
Architecture of the human origin recognition complex.
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).
NRAGE, a p75 neurotrophin receptor-interacting protein, induces caspase activation and cell death through a JNK-dependent mitochondrial pathway
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.
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.
Two electrons are transferred from reduced ferredoxin reductase (FDXR, adrenodoxin reductase) to two ferredoxin-1 or ferredoxin-1L (FDX1, FDX1L) molecules, each of which binds one electron. Two protons are released during the reaction.
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).
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.
In the second step in the formation of glutathione, gamma-glutamylcysteine ligates with glycine to form glutathione (Gali and Board, 1995; ).
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Fibroblast growth factor signalling: from development to cancer
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Pyrimidine nucleotide biosynthesis in animals: genes, enzymes, and regulation of UMP biosynthesis.
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A three-dimensional working model of the multienzyme complex of aminoacyl-tRNA synthetases based on electron microscopic placements of tRNA and proteins
Protein import into yeast mitochondria is accelerated by the outer membrane protein MAS70
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Sulfate leaves the mitochondrion with the help of the dicarboxylate carrier, via antiport with malate (Crompton et al. 1974, Fiemont et al. 1999)
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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)
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.
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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.
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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).
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While in humans excess methionine is converted to homocysteine, homocysteine and its transsulfuration product cysteine can be degraded to several end products, two of which, taurine and hydrogen sulfide, have uses in other biological processes (Stipanuk & Ueki 2011).
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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).
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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".
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).
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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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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A cytosolic, non-specific peptidase can hydrolyze cysteinylglycine to release cysteine and glycine (Tuefel et al, 2003).
Proximal signaling events in Fc epsilon RI-mediated mast cell activation
J. Allergy Clin. Immunol. 119:544-52; quiz 553-4
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).
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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).
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The first step of homocysteine conversion to cysteine is catalyzed by cystathionine beta-lyase, which adds a serine molecule to the substrate. The enzyme is a tetramer with two heme molecules as cofactor (Janosik et al. 2001).
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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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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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The role of mast cells in allergic inflammation
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Human liver-specific very-long-chain acyl-coenzyme A synthetase: cDNA cloning and characterization of a second enzymatically active protein
Biochemistry of mammalian peroxisomes revisited
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Electron Transport from NADPH to Ferredoxin
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Alternative function for the mitochondrial SAM complex in biogenesis of alpha-helical TOM proteins
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mRNA quality control: an ancient machinery recognizes and degrades mRNAs with nonsense codons
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
Human aquaporin adipose (AQPap) gene. Genomic structure, promoter analysis and functional mutation
Roles of C-terminal processing, and involvement in transacylation reaction of human group IVC phospholipase A2 (cPLA2gamma)
XBP1 induces WFS1 through an endoplasmic reticulum stress response element-like motif in SH-SY5Y cells
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Uninterrupted MCM2-7 function required for DNA replication fork progression.
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Src-family kinases in B-cell development and signaling
Redox-switch modulation of human SSADH by dynamic catalytic loop
Phosphoglucomutase 1: a gene with two promoters and a duplicated first exon
FUNCTION Essential component of the PAM complex, a complex required for the translocation of transit peptide-containing proteins from the inner membrane into the mitochondrial matrix in an ATP-dependent manner. Recruits mitochondrial HSP70 and its co-chaperone (MGE1) to drive protein translocation into the matrix using ATP as an energy source.SUBUNIT Component of the PAM complex, at least composed of SSC1 (mtHsp70), MGE1, TIM44, PAM16/TIM16, PAM17 and PAM18/TIM14. Forms part of the receptor complex that consists of at least 3 different proteins (TIM17, TIM23, TIM44).SIMILARITY Belongs to the Tim44 family.
Fcgamma receptor (FCGR) dependent phagocytosis
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
Origin, Recognition, Signaling and Repair of DNA Double-Strand Breaks in Mammalian Cells
Damage Surveillance and Repair (Keith Caldecott, editor)1-40
SLC2A9 is a newly identified urate transporter influencing serum urate concentration, urate excretion and gout
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
FUNCTION Component of the cytosolic iron-sulfur (Fe/S) protein assembly (CIA) machinery. Required for maturation of extramitochondrial Fe-S proteins. The NBP35-CFD1 heterotetramer forms a Fe-S scaffold complex, mediating the de novo assembly of an Fe-S cluster and its transfer to target apoproteins. Required for biogenesis and export of both ribosomal subunits, which may reflect a role in assembly of the Fe/S clusters in RLI1, a protein which performs rRNA processing and ribosome export.COFACTOR Binds 4 4Fe-4S clusters per heterotetramer. Contains two stable clusters in the N-termini of NBP35 and two labile, bridging clusters between subunits of the NBP35-CFD1 heterotetramer.SUBUNIT Heterotetramer of 2 NBP35 and 2 CFD1 chains.SIMILARITY Belongs to the Mrp/NBP35 ATP-binding proteins family. NUBP1/NBP35 subfamily.
The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans
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Cdk2-dependent and -independent pathways in E2F-mediated S phase induction
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Mutations in INPP5E, encoding inositol polyphosphate-5-phosphatase E, link phosphatidyl inositol signaling to the ciliopathies
Limiting role of 6-phosphogluconolactonase in erythrocyte hexose monophosphate pathway metabolism
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Adipocyte differentiation from the inside out
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Triggering and augmentation mechanisms, granule pools, and biphasic insulin secretion
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Mia40, a novel factor for protein import into the intermembrane space of mitochondria is able to bind metal ions
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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
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Lathosterolosis, a novel multiple-malformation/mental retardation syndrome due to deficiency of 3beta-hydroxysteroid-delta5-desaturase
Identification and characterization of a novel human phosphatidylinositol 4-kinase
Functional characterization of elements in a human U6 small nuclear RNA gene distal control region
Protein folding: versatility of the cytosolic chaperonin TRiC/CCT
Cyclic GMP phosphodiesterase are hydrolases selective for cAMP (PDE4, 7 and 8), cGMP (PDE5, 6 and 9) or able to hydrolyse both cAMP and cGMP (PDE1, 2, 3, 10 and 11). Â The dual-specificity PDEs allow for cross-regulation of the cAMP and cGMP pathways, e.g. PDE2 can hydrolyse both, but binding of cGMP to the regulatory GAF-B domain increases cAMP affinity and hydrolysis. PDE2, 3 and 5 are expressed in platelets.
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.
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'.
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.
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.
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 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
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.
Effects of mutational loss of adenosine kinase and deoxycytidine kinase on deoxyATP accumulation and deoxyadenosine toxicity in cultured CEM human T-lymphoblastoid cells
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.
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.
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.
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.
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.
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.
Joining of the 60S subunit to form the 80S ribosome is catalyzed by the presence of GTP-bound eIF5B.
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.
Inactive eIF2:GDP binds eIF2B to form an eIF2:GDP:eIF2B intermediate.
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.
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.
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.
Activation of eIF2 through direct binding of GTP.
The ternary complex forms upon binding of the initiator methionyl-tRNA to the active eIF2:GTP complex.
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).
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.
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.
Somatic mutations of the protein kinase gene family in human lung cancer
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 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 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.
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
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.
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.
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.
During normal translation termination eRF3 associates with the ribosome and then interacts with PABP bound to the polyadenylate tail of the mRNA to release the ribosome and allow a new round of translation to commence. Nonsense-mediated decay (NMD) is triggered if eRF3 at the ribosome interacts with UPF1, which may compete with PABP (reviewed in Isken and Maquat 2007, Chang et al. 2007, Behm-Ansmant et al. 2007, Rebbapragada and Lykke-Andersen 2009, Bhuvanagiri et al. 2010, Nicholson et al. 2010, Durand and Lykke-Andersen 2011). An exon junction located 50-55 nt downstream of a termination codon is observed to enhance NMD. Exon-junction complexes (EJCs) are deposited on the mRNA during splicing in the nucleus, remain on mRNAs after transport to the cytosol, and are dislodged by the ribosome as it progresses along the mRNA during the pioneer round of translation (Gehring et al. 2009). EJCs contain the core factors eIF4A-III, Magoh-Y14, and CASC3 as well as the peripheral factors RNPS1, UPF2, and UPF3. UPF2 and UPF3 recruit UPF1 to eRF3 at the terminating ribosome. Thus an EJC downstream of a termination codon will not have been dislodged during translation and will recruit UPF1, triggering NMD. UPF1 is believed to form a complex containing SMG1, SMG8, and SMG9. In the key regulatory step of NMD SMG1 phosphorylates UPF1. The phosphorylated UPF1 then recruits either SMG6 or SMG5 and SMG7. SMG6 is itself an endoribonuclease that cleaves the mRNA. SMG5 and SMG7 do not have endoribonuclease activty, but are thought to recruit ribonucleases. Nonsense-mediated decay has been observed to involve deadenlyation, decapping, and both 5' to 3' and 3' to 5' exonuclease activities, but the exact degradative pathways taken by a given mRNA are not yet known. UPF1 also plays roles in Staufen-mediated decay, histone mRNA decay, telomere maintenance, genome integrity, and may play a role in normal termination of translation.
Nonsense-mediated decay of an mRNA can be triggered even if the termination codon does not precede an exon junction (Buhler et al. 2006, Eberle et al. 2008, Silva et al. 2008, Singh et al. 2008, Ivanov et al. 2008). UPF1 and PABP seem to modulate the efficiency of translation termination and PABP in the proximity of a termination codon prevents NMD likely by outcompeting UPF1 for interaction with eRF3 (Singh et al. 2008, Ivanov et al. 2008, Silva et al. 2008). Factors in the competition may be the length and secondary structure of the 3' UTR (Buhler et al. 2006, Eberle et al. 2008). UPF1 preferentially binds some but not all longer UTRs (Hogg and Goff 2010). Interaction of eRF3 with PABP stimulates ribosome dissociation and initiation of a new round of translation on the mRNA. Interaction of eRF3 with UPF1 appears to promote nonsense-mediated decay. It is possible but not yet demonstrated that all components of the SURF complex (SMG1, UPF1, eRF1, eRF3) are assembled on an mRNA without an exon junction complex and that UPF1 is phosphorylated by SMG1.
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.
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.
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.
Aurora-A and an interacting activator, the LIM protein Ajuba, are required for mitotic commitment in human cells
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).
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tRNA synthetases catalyze the ligation of tRNAs to their cognate amino acids in an ATP-dependent manner. The reaction proceeds in two steps. First, amino acid and ATP form an aminoacyl adenylate molecule, releasing pyrophosphate. The aminoacyl adenylate remains associated with the synthetase enzyme where, in the second step it reacts with tRNA to form aminoacyl tRNA and AMP. The rapid hydrolysis of pyrophosphate makes these reactions essentially irreversible under physiological conditions (Fersht and Kaethner 1976a). Specificity of the tRNA charging reactions is achieved both by specific recognition of amino acid and tRNA substrates by the synthetase, and by an editing process in which incorrect aminoacyl adenylate molecules (e.g., valyl adenylate associated with isoleucyl tRNA synthetase) are hydrolyzed rather than conjugated to tRNAs in the second step of the reaction (Baldwin and Berg 1966a,b; Fersht and Kaethner 1976b). The tRNA synthetases can be divided into two structural classes based on conserved amino acid sequence features (Burnbaum and Schimmel 1991). A single synthetase mediates the charging of all of the tRNA species specific for any one amino acid but, with three exceptions, glycine, lysine, and glutamine, the synthetase that catalyzes aminoacylation of mitochondrial tRNAs is encoded by a different gene than the one that acts on mitochondrial tRNAs. Both mitochondrial and cytosolic tRNA synthetase enzymes are encoded by genes in the nuclear genome. A number of tRNA synthetases are known to have functions distinct from tRNA charging (reviewed by Park et al. 2005). Additionally, mutations in several of the tRNA synthetases, often affecting protein domains that are dispensable in vitro for aminoacyl tRNA synthesis, are associated with a diverse array of neurological and other diseases (Antonellis and Green 2008; Park et al. 2008). These findings raise interest into the role of these enzymes in human development and disease.
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.
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).
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Mitochondrial tRNA synthetases act in the mitochondrial matrix to catalyze the reactions of tRNAs encoded in the mitochondrial genome, their cognate amino acids, and ATP to form aminoacyl-tRNAs, AMP, and pyrophosphate (Schneider et al. 2000). The synthetase enzymes that catalyze these reactions are all encoded in the nuclear genome. In three cases, glycine, lysine, and glutamine, a single gene encodes two enzyme isoforms, one cytosolic and one mitochondrial. All other mitochondrial tRNA synthetases are encoded by genes different from the ones encoding the corresponding cytosolic enzymes.
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).
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.
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.
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.
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).
Tah18 transfers electrons to Dre2 in cytosolic iron-sulfur protein biogenesis
Aquaporin expression in normal human kidney and in renal disease
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).
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).
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).
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).
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).
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).
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).
SARS2 (mitochondrial seryl tRNA synthetase) catalyzes the reaction of serine, mitochondrial tRNA(Ser), and ATP to form Ser-tRNA(Ser), AMP, and pyrophosphate. SARS2 is a class II tRNA synthetase inferred from the biochemical properties of its bovine homologue to function as a dimer (Yokogawa et al. 2000).
TARS2 (mitochondrial threonyl tRNA synthetase) catalyzes the reaction of threonine, mitochondrial tRNA(Thr), and ATP to form Thr-tRNA(Thr), AMP, and pyrophosphate. The TARS2 gene has been identified by computational analysis of the human genome sequence; its function has been inferred from those of the biochemically characterized mitochondrial aspartyl and tyrosyl tRNA synthetases (Bonnefond et al. 2005).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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).
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)
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).
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).
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]
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.
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.
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
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Formation of phosphodiester bonds nine and ten creates RNA products, which do not dissociate from the RNA pol II initiation complex. The transcription complex has enter the productive elongation phase. TFIIH and ATP-hydrolysis are required for efficient promoter escape. The open region (ââ¬Åtranscription bubbleââ¬Â) expands concomitant with the site of RNA-extension. The region upstream from the transcription start site (-9 to -3) collapses to the double-stranded state. TFIIH remains associated to the RNA pol II initiation complex.
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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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RNA Polymerase II promoter escape occurs after the first phosphodiester bond has been created.
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RNA polymerase II transcription complexes are susceptible to transcriptional stalling and arrest, when extending nascent transcripts to 30-nt. This susceptibility depends on presence on down-stream DNA, the particular DNA-sequence of the template and presence of transcription factors. Transcription factor TFIIH remains associated to the RNA pol II elongation complex until position +30. At this stage transcription elongation factor TFIIS can rescue stalled transcription elongation complexes. The transcription bubble varies between 13- and 22-nt in size.
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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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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.
Phosphorylation of serine 5 residue at the CTD of pol II largest subunit is an important step signaling the end of initiation and escape into processive elongation processes. Cdk7 protein subunit of TFIIH phosphorylates RNA Pol II CTD serine 5 residues on its heptad repeats.
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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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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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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.
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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'.
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At the beginning of this reaction, 1 molecule of 'Pol II initiation complex' is present. At the end of this reaction, 1 molecule of 'Pol II Initiation complex with phosphodiester-PPi intermediate' is present. This reaction takes place in the 'nucleus'.
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At the beginning of this reaction, 1 molecule of 'pol II open pre-initiation complex', and 2 molecules of 'NTP' are present. At the end of this reaction, 1 molecule of 'Pol II initiation complex' is present. This reaction takes place in the 'nucleus'.
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After assembly of the complete RNA polymerase II-preinitiation complex, the next step is separation of the two DNA strands. This isomerization step is known as the closed-to-open complex transition and occurs prior to the initiation of mRNA synthesis. In the RNA polymerase II system this step requires the hydrolysis of ATP or dATP into Pi and ADP or dADP (in contrast to the other RNA polymerase systems) and is catalyzed by the XPB subunit of TFIIH. The region of the promoter, which becomes single-stranded , spans from ââ¬â10 to +2 relative to the transcription start site. Negative supercoiling in the promoter region probably induces transient opening events and can alleviate requirement of TFIIE, TFIIH and ATP-hydrolysis for open complex formation. ATP is also used in this step by the cdk7-subunit of TFIIH to phosphorylate the heptad repeats of the C-terminal domain of the largest subunit of RNA polymerase II (RPB1) on serine-2
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Peroxisome proliferator activated receptors and lipoprotein metabolism
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At the beginning of this reaction, 1 molecule of 'Pol II Initiation complex with phosphodiester-PPi intermediate' is present. At the end of this reaction, 1 molecule of 'pyrophosphate', and 1 molecule of 'pol II transcription complex' are present. This reaction takes place in the 'nucleus'.
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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Deficiency of the ADP-forming succinyl-CoA synthase activity is associated with encephalomyopathy and mitochondrial DNA depletion
Crystal structures of human NUDT5 reveal insights into the structural basis of the substrate specificity
Regulation of Ins(3,4,5,6)P(4) signaling by a reversible kinase/phosphatase
The distribution and function of phosphatidylserine in cellular membranes
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Homologous DNA pairing and strand exchange
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The PI-3 kinase/Akt pathway and T cell activation: pleiotropic pathways downstream of PIP3
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Vav1: a key signal transducer downstream of the TCR
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Phosphorylation of mammalian CDC6 by cyclin A/CDK2 regulates its subcellular localization.
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Regulation of Geminin and Cdt1 expression by E2F transcription factors
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Synthesis of 5-demethoxyubiquinone-6 and ubiquinone-6 from 3-hexaprenyl-4-hydroxybenzoate in yeast mitochondria
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Multiple forms of gamma-butyrobetaine hydroxylase (EC 1.14.11.1).
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Control of cyclin B1 localization through regulated binding of the nuclear export factor CRM1
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Inhibition of Mcm4,6,7 helicase activity by phosphorylation with cyclin A/Cdk2.
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Binding of MET-TRNAf and GTP to homogeneous initiation factor MP.
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(all-E)-3-(3,7,11,15,19,23-hexamethyl-2,6,10,14,18,22-tetracosahexaenyl)-4-hydroxybenzoic acid
all-trans-3-(3,7,11,15,19,23-hexamethyl-2,6,10,14,18,22-tetracosahexaenyl)-4-hydroxybenzoic acid
3-hexaprenyl-4-hydroxybenzoic acid [ChEBI:31116]
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Immunoreceptor DAP12 bearing a tyrosine-based activation motif is involved in activating NK cells
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Interconversion of leukotrienes catalyzed by purified gamma-glutamyl transpeptidase: concomitant formation of leukotriene D4 and gamma-glutamyl amino acids
Role of Pam16's degenerate J domain in protein import across the mitochondrial inner membrane
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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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FUNCTION Adds the third glucose residue to the lipid-linked oligosaccharide precursor for N-linked glycosylation. Transfers glucose from dolichyl phosphate glucose (Dol-P-Glc) onto the lipid-linked oligosaccharide Glc(2)Man(9)GlcNAc(2)-PP-Dol.CATALYTIC ACTIVITY Dolichyl beta-D-glucosyl phosphate + D-Glc-alpha-(1->3)-D-Glc-alpha-(1->3)-D-Man-alpha-(1->2)-D-Man-alpha-(1->2)-D-Man-alpha-(1->3)-[D-Man-alpha-(1->2)-D-Man-alpha-(1->3)-(D-Man-alpha-(1->2)-D-Man-alpha-(1->6))-D-Man-alpha-(1->6)]-D-Man-beta-(1->4)-D-GlcNAc-beta-(1->4)-D-GlcNAc-diphosphodolichol = D-Glc-alpha-(1->2)-D-Glc-alpha-(1->3)-D-Glc-alpha-(1->3)-D-Man-alpha-(1->2)-D-Man-alpha-(1->2)-D-Man-alpha-(1->3)-[D-Man-alpha-(1->2)-D-Man-alpha-(1->3)-(D-Man-alpha-(1->2)-D-Man-alpha-(1->6))-D-Man-alpha-(1->6)]-D-Man-beta-(1->4)-D-GlcNAc-beta-(1->4)-D-GlcNAc-diphosphodolichol + dolichyl phosphate.PATHWAY Protein modification; protein glycosylation.SIMILARITY Belongs to the ALG10 glucosyltransferase family.
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Purification and properties of human D-3-hydroxyacyl-CoA dehydratase: medium-chain enoyl-CoA hydratase is D-3-hydroxyacyl-CoA dehydratase
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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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Association of licensing factors with the pre-replicative complex
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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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Synthesis of bile acids and bile salts via 27-hydroxycholesterol
Beta-oxidation of very long chain fatty acids
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Control of translation and mRNA degradation by miRNAs and siRNAs
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phosphorylated nuclear Cyclin B1:Cdc2 substrates
Ghost homologue of Telomerase RNA Component (TERC)
Condensins, chromosome condensation protein complexes containing XCAP-C, XCAP-E and a Xenopus homolog of the Drosophila Barren protein
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Human and murine glycerol kinase: influence of exon 18 alternative splicing on function
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).
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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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.
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D2HDGH associated with the mitochondrial inner membrane catalyzes the FAD-dependent reaction of (R)-2-hydroxyglutarate to form 2-oxoglutarate (Achouri et al. 2004). D2HDGH mutations are associated with high levels of (R)-2-hydroxyglutarate in vivo and variable neurological symptoms (Struys et al. 2005; Wanders and Mooyer 1995)).
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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).
Mitochondrial fumarate hydratase catalyzes the reversible reaction of malate to form fumarate and water (Bourgeron et al. 1994). Unpublished crystallographic data indicate that the protein is a tetramer (PDB 3E04).
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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 succinate dehydrogenase complex, associated with the inner mitochondrial membrane, catalyzes the dehydrogenation of succinate to fumarate, reducing the FAD cofactor bound to the enzyme. This redox potential is then used in the electron transfer chain to drive a proton motive force to generate ATP.
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Mitochondrial 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.
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).
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Cellular localization of the vesicular inhibitory amino acid transporter in the mouse and human retina
Reversible compartmentalization of de novo purine biosynthetic complexes in living cells
RNA primer:origin duplex with DNA damage
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).
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).
Nuclear translocation of plk1 mediated by its bipartite nuclear localization signal
Mitochondrial aconitase reversibly converts isocitrate to citrate via a cis-aconitate intermediate. Mitochondrial aconitase activity has been demonstrated in diverse human tissue extracts (Slaughter et al. 1975) and a protein homologous to the well-characterized porcine enzyme has been purified from human tissues (Baldwin et al. 1991).
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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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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.
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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).
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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).
RNA Polymerase III Transcription Termination
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In the second salvage step, dihydrofolate reductase (DHFR) can regenerate BH4 from BH2, a process which increases the BH4:BH2 ratio providing BH4 for coupled eNOS production of NO. In mice cell lines, DHFR inhibition or knockdown diminishes the BH4:BH2 ratio and exacerbates eNOS uncoupling (Crabtree et al. 2009).
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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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).
Cytosolic PPAT (phosphoribosyl pyrophosphate amidotransferase) catalyzes the reaction of 5-phospho-alpha-D-ribose 1-diphosphate (PRPP), water, and L-glutamine to form 5-phosphoribosylamine, L-glutamate, and pyrophosphate. This event is the committed step in de novo purine synthesis. The reaction itself is reversible, but it is pulled strongly in the direction of 5'-phosphoribosylamine synthesis by the irreversible hydrolysis of the pyrophosphate that is also formed in the reaction. Fluoresence microscopy studies of cultured human cells have shown that PPAT is cytosolic and suggest that it may co-localize with other enzymes of de novo IMP biosynthesis under some metabolic conditions (An et al. 2008). The PPAT enzyme is inferred to be an iron-sulfur protein, like its well-characterized B. subtilis homologue, because incubation of purified enzyme with molecular oxygen or chelating agents inactivates it, and activity can be restored by incubation with ferrous iron and inorganic sulfide. The stoichiometry of the iron-sulfur moiety and its role in enzyme activity remain unknown (Itakura and Holmes 1979). The fully active form of the enzyme is a dimer, which can associate further to form a tetramer with sharply reduced activity (Holmes et al. 1973b; Iwahana et al. 1993). Interaction of the enzyme with inosine 5'-monophosphate (IMP), guanosine 5'-monophosphate (GMP), and adenosine 5'-monophosphate (AMP), end products of de novo purine biosynthesis, favors tetramer formation, while interaction with 5-phospho-alpha-D-ribose 1-diphosphate (PRPP), a required substrate, favors formation of the active dimer. Kinetic studies suggest that the enzyme's binding site for GMP and IMP is separate from its AMP binding site (Holmes et al. 1973a).
The 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 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 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).
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).
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 human isoenzymes, IMP dehydrogenase 1 and 2 (IMPDH1,2) catalyze the irreversible dehydrogenation of inosine 5'-monophosphate (IMP) to form xanthosine 5'-monophosphate (XMP). The active forms of both isoenzymes are homotetramers, and they are nearly identical in their catalytic efficiencies and their susceptibility to inhibition by XMP (Carr et al. 1993; Colby et al. 1999; Hager et al. 1995). Both enzymes occur as homotetramers (Colby et al. 1999 - IMPDH2; unpubliched data in PDB 1JCN IMPDH1). A variety of experiments suggest that IMPDH1 and 2 have distinct functions in vivo. While IMPDH1 is expressed at constant levels, IMPDH2 is expressed at elevated levels in tumor cells and in mitotic normal cells. In humans, heterozygosity for mutant forms of IMPDH1 is associated with a form of retinitis pigmentosa (Bowne et al. 2002). In laboratory mice, mutations that disrupt the homologue of IMPDH1 have no obvious effect at the level of the whole organism, while ones that disrupt IMPDH2 are lethal (Gu et al. 2003). This reaction is the rate limiting step in the synthesis of guanosine 5'-monophosphate (GMP) from IMP, and GMP competitively inhibits the well-characterized bacterial IMP dehydrogenase enzyme. Evidence for an inhibitory effect of GMP on the human isoenzymes has not been reported. Rather, they appear to be inhibited by XMP; in addition, transcription of one or both IMP dehydrogenase mRNAs may be inhibited by high cellular GMP concentrations (Glesne et al. 1991).
The reversible synthesis of inosine 5'-monophosphate from 5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide (FAICAR) is catalyzed by the IMP cyclohydrolase activity of the bifunctional 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase enzyme. This cytosolic protein occurs primarily as a dimer (Rayl et al. 1996; Vergis et al. 2001) and may further associate with other enzymes of de novo IMP biosynthesis under some metabolic conditions (An et al. 2008).
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).
Stimulation of the human CTP:phosphoethanolamine cytidylyltransferase gene by early growth response protein 1
FUNCTION Component of the mitochondrial outer membrane sorting assembly machinery (SAM or TOB) complex, which is required for the sorting of proteins with complicated topology, such as beta-barrel proteins, to the mitochondrial outer membrane after import by the TOM complex.SUBUNIT Component of the mitochondrial outer membrane sorting assembly machinery (SAM or TOB) complex, which at least consists of SAM35, SAM37 and SAM50. SAM37 interacts with TOM70.MISCELLANEOUS Present with 1580 molecules/cell in log phase SD medium.
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).
NSDHL, an enzyme involved in cholesterol biosynthesis, traffics through the Golgi and accumulates on ER membranes and on the surface of lipid droplets
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.
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.
ETF-ubiquinone oxidoreductase (ETF-QO), catalyzes the re-oxidation of reduced ETF, with ubiquinone as the electron acceptor.
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.
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.
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.
Cytosolic AMP, GMP, and IMP stimulate the association of phosphoribosyl pyrophosphate amidotransferase (PPAT) dimers to form tetramers (Holmes et al. 1973a,b).
The metabolism of pyruvate provides one source of acetyl-CoA which enters the citric acid (TCA, tricarboxylic acid) cycle to generate energy and the reducing equivalent NADH. These reducing equivalents are re-oxidized back to NAD+ in the electron transport chain (ETC), coupling this process with the export of protons across the inner mitochondrial membrane. The chemiosmotic gradient created is used to drive ATP synthesis.
PRPP stimulates the dissociation of phosphoribosyl pyrophosphate amidotransferase tetramers to form dimers (Holmes et al. 1973a,b).
The synthesis of dihydroorotate from N-carbamoyl L-aspartate is catalyzed by the dihydroorotase activity of cytosolic trifunctional CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase) protein. This activity has not been directly demonstrated in experimental studies of the purified human protein, but has been inferred from the behavior of the purified hamster protein and the high degree of sequence similarity between the cloned hamster and human genes (Iwahana et al. 1996). Also on the basis of this similarity, the active human protein is annotated as a hexamer (Lee et al. 1985).
The synthesis of N-carbamoyl L-aspartate from carbamoyl phosphate and L-aspartate is catalyzed by the aspartate carbamoyltansferase activity of cytosolic trifunctional CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase) protein (Ito and Uchino 1973; Iwahana et al. 1996). The purified human protein is active in several different oligomerization states as is its Syrian hamster homologue. The most abundant form of the latter is a hexamer, and the active human protein is annotated as a hexamer by inference (Ito and Uchino 1973; Lee et al. 1985).
The synthesis of carbamoyl phosphate from glutamine, bicarbonate, and ATP is catalyzed by the carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity of cytosolic trifunctional CAD (carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase) protein (Ito and Uchino 1973; Iwahana et al. 1996). The purified human protein is active in several different oligomerization states, as is its Syrian hamster homologue. The most abundant form of the latter is a hexamer, and the active human protein is annotated as a hexamer by inference (Ito and Uchino 1973; Lee et al. 1985).
The 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.
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.
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 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).
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).
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).
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 decarboxylation of orotidine 5'-monophosphate (OMP) to form uridine 5'-monophosphate (UMP) is catalyzed by the orotidine 5'-phosphate decarboxylase activity of the bifunctional "uridine monophosphate synthetase (orotate phosphoribosyl transferase and orotidine 5'-decarboxylase)" protein. While purified human protein has not been characterized in detail, the close similarity of the human gene to that encoding the well-studied hamster protein, and the demonstration that mutations in the human gene are associated with failure to convert orotate to UMP in vivo, provide convincing evidence that the human uridine monophosphate synthetase protein indeed catalyzes these two reactions (McClard et al. 1980; Suchi et al. 1997). The active form of the human protein is a dimer (Yablonski et al. 1996; Wittmann et al. 2008).
Cytosolic 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 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).
Cytosolic nucleoside phosphorylase (NP) trimer catalyzes the reversible reaction of hypoxanthine with ribose 1-phosphate or deoxyribose 1-phosphate to form inosine or deoxyinosine and orthophosphate (Ealick et al. 1990; Wiginton et al. 1980). While NP is active with either ribose 1-phosphate or deoxyribose 1-phosphate in vitro, levels of deoxyribose 1-phosphate are normally low in vivo, limiting the extent of this reaction. NP deficiency in vivo is associated with defects in purine nucleotide salvage and leads to immunodeficiency (Williams et al. 1987).
Cytosolic nucleoside phosphorylase (NP) trimer catalyzes the reversible reaction of guanine with ribose 1-phosphate or deoxyribose 1-phosphate to form guanosine or deoxyguanosine and orthophosphate (Ealick et al. 1990; Wiginton et al. 1980). While NP is active with either ribose 1-phosphate or deoxyribose 1-phosphate in vitro, levels of deoxyribose 1-phosphate are normally low in vivo, limiting the extent of this reaction. NP deficiency in vivo is associated with defects in purine nucleotide salvage and leads to immunodeficiency (Williams et al. 1987).
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 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.
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).
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).
Cytosolic APRT dimer catalyzes the reaction of adenine and 5-phospho-alpha-D-ribose 1-diphosphate to form AMP and pyrophosphate (Holden et al. 1979).
Cytosolic nucleoside phosphorylase (NP) trimer catalyzes the reversible reaction of 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).
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
Exchange of ADP for ATP in CCT/TriC:actin complex
Apoptosis induced by the toll-like receptor adaptor TRIF is dependent on its receptor interacting protein homotypic interaction motif
ADP is exchanged for ATP in the (ADP:CCT/TriC):tubulin complex
EIF5A(Dhp) + 1,3-diaminopropane <=> EIF5A + spermidine
EIF5A + spermidine <=> EIF5A(Dhp) + 1,3-diaminopropane
Ghost homologue of SREBF1A,1C,2 cleaved by S2P
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Novel variants in human Aquaporin-4 reduce cellular water permeability
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Nascent pre-mRNA with 5'-GMP dissociated from CE
Nascent pre-mRNA with 5'-GMP associated with CE
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Pyruvate metabolism and Citric Acid (TCA) cycle
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A general map of iron metabolism and tissue-specific subnetworks
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Pak1 kinase homodimers are autoinhibited in trans and dissociated upon activation by Cdc42 and Rac1
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Kinesin-5 regulates the growth of the axon by acting as a brake on its microtubule array
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Phosphorylation and activation of 13S condensin by Cdc2 in vitro
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Identification of ARAP3, a novel PI3K effector regulating both Arf and Rho GTPases, by selective capture on phosphoinositide affinity matrices
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De novo telomere addition by Tetrahymena telomerase in vitro
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Ire1 phosphorylated in the activation domain preferentially binds ADP (rather than ATP).
A control region in the center of the 5S RNA gene directs specific initiation of transcription: II. The 3' border of the region.
Inborn errors of ketogenesis and ketone body utilization
Molecular organization of the presynaptic active zone
Transmembrane transport of endo- and xenobiotics by mammalian ATP-binding cassette multidrug resistance proteins
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Alternate exon insertion controls selective ubiquitination and degradation of different AUF1 protein isoforms
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glucosaminyl-PI + fatty acyl-CoA -> glucosaminyl-acyl-PI + CoA-SH
N-acetylglucosaminyl-PI + H2O -> glucosaminyl-PI + acetate
Mitochondrial protein import: precursor oxidation in a ternary complex with disulfide carrier and sulfhydryl oxidase
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XBP-1 regulates a subset of endoplasmic reticulum resident chaperone genes in the unfolded protein response
Dephosphorylation of dolichyl diphosphate
Formation of glucosamine 6-phosphate from fructose 6-phosphate and glutamine
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Acetylation of glucosamine 6-phosphate to GlcNAc6P
mannose(a1-4)glucosaminyl-acyl-PI + phosphatidylethanolamine -> (ethanolamineP) mannose(al1-4)glucosaminyl-acyl-PI + diacylglycerol
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(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 (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI + dolichol phosphate D-mannose -> mannose (a1-2) mannose (a1-6) (ethanolamineP) mannose (a1-4) glucosaminyl-acyl-PI + dolichol phosphate
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Enzymes of the human erythrocyte. IV. Phosphoglucose isomerase, purification and properties.
Mannose 6-phosphate isomerizes to Mannose 1-phosphate
A comprehensive profile of brain enzymes that hydrolyze the endocannabinoid 2-arachidonoylglycerol
Fructose 6-phosphate isomerizes to Mannose 6-phosphate
GlcNAc1P is dephosphorylated to UDP-N-acetyl-glucosamine
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Addition of a third mannose to the N-glycan precursor by Alg2
A third mannose is added to the N-glycan precursor skeleton by alg2 using its alpha1,6-mannosyltransferase activity. This has been demonstrated in yeast (O'Reilly MK et al, 2006; Kämpf M et al, 2009).
Addition of the first mannose to the N-glycan precursor by ALG13/14
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Addition of a second mannose to the N-glycan precursor by ALG2
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Addition of N-acetyl-D-glucosamine to Dolichyl phosphate
Addition of the second N-acetyl-glucosamine to the N-glycan precursor
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Mannose-1-phosphate converted to GDP-Mannose
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Flipping of the N-glycan precursor into the ER lumen
The precursor of the N-glycan sugar, now in the form of (GlcNAc)2 (Man)5 (PP-Dol), is flipped through the ER membrane, moving it from the cytosolic side into the ER lumen. The exact mechanism of this translocation is not well understood but the protein RFT1 is known to be involved (Helenius J et al, 2002), along with an unknown flippase.
Addition of the fourth and fifth mannose to the N-glycan precursor skeleton by Alg11
A fourth and fifth mannose is added to the N-glycan precursor skeleton by Alg11, characterized from yeast (Cipollo JF et al, 2001).
Unresponsiveness of MyD88-deficient mice to endotoxin
Addition of the seventh mannose to the N-glycan precursor by ALG9, inside the ER lumen
Purification and characterization of 5'-deoxy-5'-methylthioadenosine phosphorylase from human placenta
Addition of the sixth mannose to the N-glycan precursor by ALG3.
Multiple pathways for sorting mitochondrial precursor proteins
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Addition of the eighth mannose to the N-glycan precursor by ALG12, inside the ER lumen
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Addition of the last mannose to the N-glycan precursor by ALG3, inside the ER lumen.
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Addition of the first glucose to the N-glycan precursor by ALG6
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Addition of a second glucose to the N-glycan precursor by ALG8
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Addition of a third glucose to the N-glycan skeleton by Alg10
The last glucose is added to the N-glycan precursor. This reaction occurs inside the ER lumen and uses Dol-P-Glc as the glucose donor. In yeast, this reaction is catalyzed by ALG10 (Burda P and Aebi M,1998).
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Trimming of the first glucose by glucosidase I
Trimming of the terminal mannose on the B branch
Glycoproteins with major folding defects are sent to degradation by EDEMs
Trimming of the second mannose on the A branch
Trimming of the first mannose on the A branch
Trimming of the terminal mannose on the C branch
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Molecular machinations of the MHC-I peptide loading complex
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Addition of GalNAc to the Tn antigen via an alpha-1,6 linkage forms a Core 7 glycoprotein
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Addition of galactose to the Tn antigen via an alpha-1,3 linkage forms a Core 8 glycoprotein
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Addition of GlcNAc to the Tn antigen via an alpha-1,3 linkage forms a Core 5 glycoprotein
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Addition of GlcNAc to the Tn antigen via a beta-1,6 linkage forms a Core 6 glycoprotein
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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).
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).
FUNCTION Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative helicase essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells. The active ATPase sites in the MCM2-7 ring are formed through the interaction surfaces of two neighboring subunits such that a critical structure of a conserved arginine finger motif is provided in trans relative to the ATP-binding site of the Walker A box of the adjacent subunit. The six ATPase active sites, however, are likely to contribute differentially to the complex helicase activity; specifically the MCM2-MCM5 association is proposed to be reversible and to mediate a open ring conformation which may facilitate DNA loading. Once loaded onto DNA, double hexamers can slide on dsDNA in the absence of ATPase activity. Necessary for cell growth.CATALYTIC ACTIVITY ATP + H(2)O = ADP + phosphate.SUBUNIT Component of the MCM2-7 complex. The complex forms a toroidal hexameric ring with the proposed subunit order MCM2-MCM6-MCM4-MCM7-MCM3-MCM5; loaded onto DNA, forms a head-head double hexamer.MISCELLANEOUS Present with 1690 molecules/cell in log phase SD medium.MISCELLANEOUS Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. Specifically a MCM467 subcomplex is shown to have in vitro helicase activity which is inhibited by the MCM2 subunit. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY Belongs to the MCM family.SIMILARITY Contains 1 MCM domain.
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The target of ezetimibe is Niemann-Pick C1-Like 1 (NPC1L1)
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Deletion of the mitochondrial carrier genes MRS3 and MRS4 suppresses mitochondrial iron accumulation in a yeast frataxin-deficient strain
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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).
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.
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).
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).
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).
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).
The pyrimidine orotate (orotic acid) is synthesized in a sequence of four reactions, deriving its atoms from glutamine, bicarbonate, and aspartate. A single multifunctional cytosolic enzyme catalyzes the first three of these reactions, while the last one is catalyzed by an enzyme associated with the inner mitochondrial membrane. In two further reactions, catalyzed by a bifunctional cytosolic enzyme, orotate reacts with 1-phosphoribosyl 5-pyrophosphate (PRPP) to yield orotidine 5'-monophosphate, which is decarboxylated to yield uridine 5'-monophosphate (UMP). While several individual reactions in this pathway are reversible, other irreversible reactions drive the pathway in the direction of UMP biosynthesis in the normal cell. All reactions are thus annotated here only in the forward direction. This pathway has been most extensively analyzed at the genetic and biochemical level in hamster cell lines. All three enzymes have also been purified from human sources, however, and the key features of these reactions have been confirmed from studies of this human material (Jones 1980; Webster et al. 2001). All other pyrimidines are synthesized from UMP. The reactions annotaed here, catalyzed by dCMP deaminase and dUTP diphosphatase yield dUMP, which in turn is converted to TMP by thymidylate synthase.
Cytosolic deoxycytidylate deaminase (DCTD) catalyzes the hydrolysis of dCMP (2'-deoxyuridine 5'-monophosphate) to yield dUMP (2'-deoxyuridine 5'-monophosphate) and ammonia. The active enzyme is a homohexamer (Maley et al. 1993; Weiner et al. 1993; unpublished crystallography data - PDB 2W4L).
Deoxyuridine triphosphatase (DUT) catalyzes the hydrolysis of dUTP to form dUMP and pyrophosphate. Two isoforms of DUT are expressed, generated by alternative splicing. The major one, annotated here, is localized to the nucleoplasm (Ladner et al. 1996). The enzyme is a homotrimer (Mol et al. 1996). In the cell, this reaction depletes the supply of dUTP, preventing its incorporation into DNA, while generating dUMP, the immediate precursor of thymidine nucleotides.
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).
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).
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
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 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).
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).
Cytosolic CTP synthase 1 (CTPS) catalyzes the reaction of UTP, glutamine, ATP and water to form CTP, glutamate, ADP, and orthophosphate (Han et al. 2005). The active form of the enzyme is a tetramer (Kursala et al. 2006). Both CTPS and a second human gene product, CPTS2, have CTP synthase activity in various test systems; their relative contributions to CTP metabolism in the body is not clear.
Cytosolic CTP synthase 2 (CTPS) catalyzes the reaction of UTP, glutamine, ATP and water to form CTP, glutamate, ADP, and orthophosphate (Han et al. 2005; van Kuilenberg et al. 2000). Unpublished X-ray crystallographic data suggest that the enzyme is a tetramer (PDB 3IHL). Both CTPS2 and a second human gene product, CPTS, have CTP synthase activity in various test systems; their relative contributions to CTP metabolism in the body is not clear.
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).
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).
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).
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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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.
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.
Vitamin B1 (thiamin) is found naturally in certain foodstuffs such as green peas, spinach, liver, bananas, whole grains and legumes. Human diseases associated with thiamin deficiency include beriberi, due to a thiamin-deficient diet, TMRA, due to defects in the SLC19A2 transport protein, and Wernicke-Korsakoff Syndrome, associated with thiamin deficiency in alcoholism (Haas 1988). Thiamin is water-soluble so is not stored in the body. When pyrophosphorylated, thiamin is converted into the coenzyme thiamin pyrophosphate (ThPP, codecarboxylase) which plays an essential role in oxidative decarboxylation and group transfer reactions.
Cytosolic thiamin pyrophosphokinase (TPK1) catalyzes the reaction of thiamin (THMN) and ATP to form thiamin diphosphate (ThDP aka thiamin pyrophosphate) and ADP. ThDP is an active cofactor for transketolase, pyruvate dehydrogenase and alpha-ketoglutarate dehydrogenase, enzymes involved in glycolysis and energy production. The gene encoding the human enzyme has been cloned and its protein product has been shown to have TPK1 activity (Nosaka et al. 2001; Zhao et al. 2001). Its homodomeric structure and association with Mg2+ are inferred from properties of the homologous yeast enzyme (Baker et al. 2001).
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Fundamental Immunology (Book): 1077-1104
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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.
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).
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).
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).
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).
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".
The uptake of extracellular dehydroascorbate into the cytosol is mediated by GLUT1 and GLUT3 associated with the plasma membrane (Rumsey et al. 1997, 2000). This process may play a significant role in ascorbate utilization in the central nervous system (Agus et al. 1997). The process is efficiently competitively inhibited by glucose, leading to the suggestion that inhibited dehydroascorbate uptake may contribute to the pathology of diabetes (Liang et al. 2001; Rumsey et al. 2000).
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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.
Riboflavin (vitamin B2, E101) is an essential component for the cofactors FAD (flavin-adenine dinucleotide) and FMN (flavin mononucleotide). Together with NAD+ and NADP+, FAD and FMN are important hydrogen carriers and take part in more than 100 redox reactions involved in energy metabolism. Riboflavin is present in many vegetables and meat and during digestion, various flavoproteins from food are degraded and riboflavin is resorbed. The major degradation and excretion product in humans is riboflavin (Rivlin 1970).
The 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).
The decarboxylation of phosphopantothenoylcysteine (PPC) to 4'-phosphopantetheine (PPANT) is carried out by phosphopantothenoylcysteine decarboxylase (PPCDC). PPCDC is cytosolic and exists as a homotrimer, binding one FMN cofactor per subunit. While a second isoform has been inferred from large-scale sequnceing studies, it lacks the protein's FMN-binding domain and would thus appear to be nonfunctional if it is expressed.
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).
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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Developmental origin of fat: tracking obesity to its source
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FUNCTION Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative helicase essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells. The active ATPase sites in the MCM2-7 ring are formed through the interaction surfaces of two neighboring subunits such that a critical structure of a conserved arginine finger motif is provided in trans relative to the ATP-binding site of the Walker A box of the adjacent subunit. The six ATPase active sites, however, are likely to contribute differentially to the complex helicase activity; specifically the MCM2-MCM5 association is proposed to be reversible and to mediate a open ring conformation which may facilitate DNA loading. Once loaded onto DNA, double hexamers can slide on dsDNA in the absence of ATPase activity.CATALYTIC ACTIVITY ATP + H(2)O = ADP + phosphate.SUBUNIT Component of the MCM2-7 complex. The complex forms a toroidal hexameric ring with the proposed subunit order MCM2-MCM6-MCM4-MCM7-MCM3-MCM5; loaded onto DNA, forms a head-head double hexamer. Interacts with CSM1.MISCELLANEOUS Present with 10300 molecules/cell in log phase SD medium.MISCELLANEOUS Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY Belongs to the MCM family.SIMILARITY Contains 1 MCM domain.
The human peroxisomal ABC half transporter ALDP functions as a homodimer and accepts acyl-CoA esters
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
Peroxisomal multifunctional protein-2: the enzyme, the patients and the knockout mouse model
COPI-coated ER-to-Golgi transport complexes segregate from COPII in close proximity to ER exit sites
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).
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).
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.
EGF receptor activation by GPCRs: an universal pathway reveals different versions
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).
Biological & physiological aspects of action of insulin-like growth factor peptide family
Holocarboxylase synthetase: correlation of protein localisation with biological function
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).
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.
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).
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.
Cytosolic dihydrofolate reductase catalyzes the reaction of dihydrofolate, NADPH, and H+ to form tetrahydrofolate (THF) and NADP+ (Chen et al. 1984; Davies et al. 1990).
Cytosolic folylpolyglutamate synthase catalyzes the reaction of THF-glutamate(n), L-glutamate, and ATP to form THF-glutamate(n+1), ADP, and orthophosphate. (The first glutamate residue is attached to the glutamate moiety of THF itself; for convenience the process is annotated here as if it proceeded in a single concerted step.) The extent of conjugation is variable, but the commonest cytosolic form of THF has five added glutamate residues. Although its properties as a donor of one-carbon units are not affected by glutamate addition, THF that lacks added glutamate residues cannot be retained in the cytosol so this reaction is needed for normal THF function under physiological conditions (Garrow et al. 1992; Chen et al. 1996).
Cytosolic 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).
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).
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).
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).
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 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).
E2F mediated regulation of DNA replication
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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). 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.
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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.
The transport of sulphate and sulphite in rat liver mitochondria
Activation of the pre-replicative complex
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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).
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).
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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.
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The enzyme, nicotinate nucleotide pyrophosphorylase, is specific for quinolinate. Its activity is strictly dependent on Mg2+ ions being present. A phosphoribosyl group is transferred to quinolinate to form nicotinate D-ribonucleotide. This reaction represents another rate-limiting step of the pathway from tryptophan to NAD+.
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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).
Cytosolic dihydrofolate reductase catalyzes the reaction of folate, NADPH, and H+ to form dihydrofolate and NADP+ (Chen et al. 1984; Davies et al. 1990).
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Crystal structure of human E1 enzyme and its complex with a substrate analog reveals the mechanism of its phosphatase/enolase activity
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.
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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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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).
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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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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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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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Pyridoxine-5'-phosphate oxidase (PNPO) is able to oxidize pyridoxine phosphate (PDXP) to pyridoxal 5'-phosphate (PXLP) (Kang et al. 2004).
Animals cannot synthesize pyridoxal 5'-phosphate (PLP) which is a ligand in aminotransferases and other enzymes. PLP's accessible derivatives pyridoxine, pyridoxal, and pyridoxamine are traditionally called vitamins B6. They are taken up nutritionally from bacteria and plants, but also created from PLP in the body. The pathways used to recycle PLP from these three compounds can therefore be called vitamin B6 activation as well as PLP salvage. Because of the close similarity of the molecules, only two enzymes are needed for the task (McCormick & Chen, 1999).
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).
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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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.
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
Cytosolic argininosuccinate lyase (ASL) catalyzes the reversible reaction of argininosuccinate to form fumarate and arginine. The enzyme is a homotetramer (Turner et al. 1997). The function of the human enzyme in vivo is inferred from the defective argininosuccinate lyase enzyme activity observed in patients with mutant forms of the ASL gene (e.g., Walker et al. 1990).
Cytosolic argininosuccinate synthase catalyzes the reaction of aspartate, citrulline, and ATP to form argininosuccinate, AMP, and pyrophosphate. The function of the human enzyme in vivo is inferred from the hypercitrullinemia observed in patients with defective forms of the enzyme (e.g., Engel et al. 2009). The enzyme is active as a homotetramer (OâBrien 1980; Karlberg et al. 2008).
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).
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).
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).
Cytosolic 3-hydroxyanthranilate oxygenase catalyzes the reaction of 3-hydroxyanthranilate and O2 to form 2-amino-3-carboxymuconate semialdehyde.
Cytosolic kynureninase catalyzes the hydrolysis of 3-hydroxy-L-kynurenine to form L-alanine and 3-hydroxyanthranilate.
Cytosolic kynurenine 3-monooxygenase catalyzes the reaction of L-kynurenine, NADPH + H+, and O2 to form 3-hydroxy-L-kynurenine, NADP+, and H2O.
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).
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).
Kinetic characterization of human hydroxyacid-oxoacid transhydrogenase: relevance to D-2-hydroxyglutaric and gamma-hydroxybutyric acidurias
Cytosolic indoleamine 2,3-dioxygenase 2 (IDO2) catalyzes the conversion of L-tryptophan and oxygen to formylkynurenine. The catalytic properties of the human enzyme have been analyzed directly; the subcellular location and monomeric state of the active form of the enzyme are inferred from the properties of its rabbit ortholog. In the body, IDO2 mRNA can be detected in a variety of cells, including dendritic cells, consistent with a normal role in immune function and a pathological one in tumor progression. Two IDO2 variants common in human populations encode enzymatically inactive protiens, suggesting that absence of IDO2 activity may be common in humans (Metz et al. 2007).
Cytosolic indoleamine 2,3-dioxygenase (IDO) catalyzes the conversion of L-tryptophan and oxygen to formylkynurenine. The structure and catalytic properties of the human enzyme have been analyzed directly (Sugimoto et al. 2006); the subcellular location and monomeric state of the active form of the enzyme are inferred from the properties of its rabbit ortholog (Shimizu et al. 1976). In the body, IDO is ubiquitously expressed and is induced by interferon. These properties, together with IDO's broad substrate specificity, are consistent with the hypothesis that the enzyme functions functions in anti bacterial and inflammatory processes (Taylor and Feng 1991).
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.
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).
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).
SLC25A21, the mitochondrial 2-oxodicarboxylate carrier, mediates the exchange of 2-oxoadipate and 2-oxoglutarate across the inner mitochondrial membrane. While the exchange is reversible, under physiological conditions it proceeds in the direction of 2-oxoadipate import into the mitochondrial matrix and 2-oxoglutarate export (Fiermonte et al. 2001).
CCBL1 (KAT 1) catalyzes the reaction of phenylalanine and pyruvate to form 3-(indol-3-yl)pyruvate and alanine. The active form of CCBL1 is a homodimer with one molecule of pyridoxal phosphate bound to each monomer (Baran et al. 1994; Han et al. 2009; Rossi et al. 2004). The enzyme's cytosolic localization is inferred from that of recombinant protein overexpressed in transfected cells (Perry et al. 1995).
In humans, most catabolism of L-lysine normally proceeds via a sequence of seven reactions which feeds into the pathway for fatty acid catabolism. In the first two reactions, catalyzed by a single enzyme complex, lysine is combined with alpha-ketoglutarate to form saccharopine, which in turn is cleaved and oxidized to yield glutamate and alpha-ketoadipic semialdehyde. The latter molecule is further oxidized to alpha-ketoadipate. Alpha-ketoadipate is oxidatively decarboxylated by the alpha-ketoglutarate dehydrogenase complex (the same enzyme complex responsible for the conversion of alpha-ketoglutarate to succinyl-CoA in the citric acid cycle), yielding glutaryl-CoA. Glutaryl-CoA is converted to crotonyl-CoA, crotonyl-CoA is converted to beta-hydroxybutyryl-CoA, and beta-hydroxybutyryl-CoA is converted to acetoacetyl-CoA. The products of lysine catabolism are thus exclusively ketogenic; i.e., under starvation conditions they can be used for the synthesis of ketone bodies, beta-hydroxybutyrate and acetoacetate, but not for the net synthesis of glucose (Cox 2001; Goodman and Freeman 2001).
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
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.
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).
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).
Cytosolic branched-chain-amino-acid aminotransferase (BCAT1) catalyzes the reversible reactions of alpha-ketoisocaproate, alpha-keto-beta-methylvalerate, or a-ketoisovalerate with glutamate to form leucine, isoleucine, or valine, respectively, and alpha-ketoglutarate (2-oxoglutarate). The active enzyme is a homodimer (Goto et al. 2005).
Cytosolic branched-chain-amino-acid aminotransferase (BCAT1) catalyzes the reversible reactions of leucine, isoleucine, or valine with alpha-ketoglutarate (2-oxoglutarate) to form alpha-ketoisocaproate, alpha-keto-beta-methylvalerate, or a-ketoisovalerate, respectively, and glutamate. The active enzyme is a homodimer. Hutson and colleagues have argues that cytosolic BCAT1 plays a major role in the generation of glutamate involved in synaptic transmission in neural tissue (Goto et al. 2005).
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 3-hydroxyisobutyryl-CoA hydrolase (HIBCH) catalyzes the hydrolysis of beta-hydroxyisobutyryl-CoA to form beta-hydroxyisobutyrate (3-hydroxy-2-methylpropanoate) and CoA (Hawes et al. 1996).
Mitochondrial acetyl-CoA acetyltransferase (ACAT1) catalyzes the reaction of alpha-methyl-acetoacetyl-CoA and CoA to form propionyl-CoA and acetyl-CoA. Structural studies have shown the active enzyme to be a tetramer of ACAT1 polypeptides whose aminoterminal 34 residues, a mitochondrial targeting sequence, have been removed (Haapalainen et al. 2007).
Mitochondrial branched-chain-amino-acid aminotransferase (BCAT2) catalyzes the reversible reactions of alpha-ketoisocaproate, alpha-keto-beta-methylvalerate, or a-ketoisovalerate with glutamate to form leucine, isoleucine, or valine, respectively, and alpha-ketoglutarate (Bledsoe et al. 1997). The active enzyme is a homodimer (Yennawar et al. 2001, 2002). In the body, this enzyme is widely expressed but is especially abundant in muscle tissue.
Mitochondrial branched-chain-amino-acid aminotransferase (BCAT2) catalyzes the reversible reactions of leucine, isoleucine, or valine with alpha-ketoglutarate (2-oxoglutarate) to form alpha-ketoisocaproate, alpha-keto-beta-methylvalerate, or a-ketoisovalerate, respectively, and glutamate (Bledsoe et al. 1997). The active enzyme is a homodimer (Yennawar et al. 2001, 2002). In the body, this enzyme is widely expressed but is especially abundant in muscle tissue.
Human intestinal H+/peptide cotransporter. Cloning, functional expression, and chromosomal localization
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)
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).
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).
Dephosphorylation of O-phospho-L-serine to L-serine proceeds through a phospho-enzyme intermediate of the catalysing phosphatase PSP (Collet et al. 1997).
A control region in the center of the 5S RNA gene directs specific initiation of transcription: I. The 5' border of the region.
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.
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).
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).
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).
Pyrroline-5-carboxylate reductase 1 (PYCR1) catalyzes the reaction of (S)-1-pyrroline-5-carboxylate with NADPH + H+ to form proline and NADP+ (Merrill et al. 1989). The active enzyme is a homodecamer (Meng et al. 2006). Recent immunofluoresence studies show that PYCR1 colocalizes with mitochondrial markers including pyrroline 5-carboxylate synthase in cultured human fibroblasts (Reversade et al. 2009).
Delta-1-pyrroline-5-carboxylate synthetase associated with the inner mitochondrial membrane catalyzes the two-step reaction that converts glutamate, ATP, and NADPH + H+ to L-glutamate gamma-semialdehyde, NADP+, ADP, and orthophosphate. Two P5CS isoforms have been identified; both are active when expressed in enzyme-deficient cells in culture (Hu et al. 1999). Unpublished crystallographic data (PDB 2H5G) indicate that the enzyme is a dimer.
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Ubiquinone. Biosynthesis of quinone ring and its isoprenoid side chain. Intracellular localization
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HER4-mediated biological and biochemical properties in NIH 3T3 cells. Evidence for HER1-HER4 heterodimers
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Decreased expression of cyclic adenosine monophosphate-regulated aldose reductase (AKR1B1) is associated with malignancy in human sporadic adrenocortical tumors
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Adenylate kinases in man: evidence for a third locus
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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
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ChEBI:27379 3alpha,7alpha,12alpha-trihydroxy-24-oxo-5beta-cholestanoyl-CoA
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Cloning and identification of a new member of water channel (AQP10) as an aquaglyceroporin
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Inflammasome adaptors and sensors: intracellular regulators of infection and inflammation
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Molecular cloning of human amidophosphoribosyltransferase
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ChEBI:27393 3alpha,7alpha-dihydroxy-5beta-cholest-24-enoyl-CoA
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Back in the water: the return of the inositol phosphates
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PI3Kgamma is a key regulator of inflammatory responses and cardiovascular homeostasis
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Regulation of WASP/WAVE proteins: making a long story short
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Endotoxin signaling in human macrophages: signaling via an alternate mechanism
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Cleavage of cytosine glycol by hNTH1 glycosylase
Cleavage of dihydrouracil by hNTH1 glycosylase
Cleavage of formamidopyrimidine by hNTH1 glycosylase
Binding of REV1 to lesioned DNA template
Misinsertion of bases opposite to the lesion by HREV1
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Insertion of correct bases opposite to the lesion by Pol eta
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Binding of Pol eta to lesioned DNA template
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Dissociation of dimeric phospho-ATM complexes
Phosphorylation of histone H2AX at Serine-139 by ATM at the site of DSB
Intermolecular autophosphorylation of ATM within dimeric ATM complexes
Association of RAD51 with RAD52:DNA double-strand break ends
Association of RAD51 with the resected ends of the DNA double-strand break
Association of RAD52 with ssDNA at resected ends of double-strand break
Cutting edge: bacterial flagellin activates basolaterally expressed TLR5 to induce epithelial proinflammatory gene expression
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XPC binds to HR23B forming a heterodimeric complex
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Latent infection of Homo sapiens with Mycobacterium tuberculosis
Ligation of DNA and formation of Holliday structures following repair synthesis
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GAPs inactivate Rho GTPase:GTP by hydrolysis
RhoA is activated by nucleotide exchange and inhibits axonal growth
Dissociation of Rho GTP:GDP from GDI complex
Cleavage of formamidopyrimidine by hOGG1 glycosylase
hNTH1 glycosylase mediated recognition and binding of cytosine glycol
hOGG1 glycosylase mediated recognition and binding of a formamidopyrimidine
Cleavage of 8-oxo guanine by hOGG1 glycosylase
hOGG1 glycosylase mediated recognition and binding of an 8-oxo guanine opposite to a cytosine
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Cleavage of thymine glycol by hNTH1 glycosylase
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hNTH1 glycosylase mediated recognition and binding of thymine glycol
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hNTH1 glycosylase mediated recognition and binding of formamidopyrimidine
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hNTH1 glycosylase mediated recognition and binding of dihydrouracil
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Passive Transport of Water out of Cells by Aquaporins
Passive Transport of Glycerol out of Cells by Aquaporins
Passive Transport of Glycerol into Cells by Aquaporins
Passive Transport of Urea into Cells by Aquaporins
Purification and properties of human placental adenosine kinase
Passive Transport of Urea out of Cells by Aquaporins
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Sensing of viral infection and activation of innate immunity by toll-like receptor 3
Passive Transport of Water out of Cell by Aquaporin-3
Passive Transport of Glycerol out of Cell by Aquaporin-7
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Passive Transport of Glycerol into Cell by Aquaporin-9
Acidification of Tf:TfR1 containing endosome
Calcium is sequestered to the golgi by secretory pathway calcium-ATPases (SPCAs)
ATP2C1/2:Mg2+ transport cytosolic Ca2+ to Golgi lumen
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Aminophospholipids are transported from in the internal to the external side of the plasma membrane
P-type ATPases type IV transport internal-facing APLs to external side of the plasma membrane
P-type ATPases type IV transport external-facing APLs to internal side of the plasma membrane
P-type ATPase type IV subfamily transporters may mediate phospholipid transfer
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Phosphorylation of Ribosomal protein S6 by activated S6K1
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Active JNK moves to the nucleus and phosphorylates different transcription factors
Production of ceramide which can activate JNK and other targets
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Equilibrative transport (import) of nucleosides and free bases by solute carrier family 29 (nucleoside transporters), member 1
Equilibrative transport (export) of nucleosides and free bases by solute carrier family 29 (nucleoside transporters), member 2
GlycoVis: visualizing glycan distribution in the protein N-glycosylation pathway in mammalian cells
FATP1, 4 and 6 can mediate the influx of long chain fatty acids into cells
Passive Transport of Water into Cells by Aquaporins
SLC35B4 mediates the transport of UDP-xylose into the Golgi lumen
SLC35B4 mediates the transport of UDP-N-acetylglucosamine into the Golgi lumen
Equilibrative transport (import) of nucleosides and adenine by solute carrier family 29 (nucleoside transporters), member 3
AT1 transports acetyl-CoA into the Golgi lumen
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Equilibrative transport (import) of nucleosides and free bases by solute carrier family 29 (nucleoside transporters), member 2
Equilibrative transport (export) of nucleosides and adenine by solute carrier family 29 (nucleoside transporters), member 3
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Defective glucose transport across brain tissue barriers: a newly recognized neurological syndrome
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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
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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).
3alpha,7alpha,24-Trihydroxy-5beta-cholestanoyl-CoA [ChEBI:1701]
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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.
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.
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).
L-ornithine is converted into putrescine by ODC holoenzyme complex.Putrescine is subsequent used for polyamine synthesis.
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).
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.
The urea cycle yields urea, the major form in which excess nitrogen is excreted from the human body, and the amino acid arginine (Brusilow and Horwich 2001). It consists of four reactions: that of ornithine and carbamoyl phosphate to form citrulline, of citrulline and aspartate to form argininosuccinate, the cleavage of argininosuccinate to yield fumarate and arginine, and the cleavage of arginine to yield urea and re-form ornithine. The carbamoyl phosphate consumed in this cycle is synthesized in the mitochondria from bicarbonate and ammonia, and this synthesis in turn is dependent on the presence of N-acetylglutamate, which allosterically activates carbamoyl synthetase I enzyme. The synthesis of N-acetylglutamate is stimulated by high levels of arginine. Increased levels of free amino acids, indicated by elevated arginine levels, thus stimulate urea synthesis. Two enzymes catalyze the hydrolysis of arginine to yield ornithine and urea. Cytosolic ARG1 is the canonical urea cycle enzyme. Mitochondrial ARG2 likewise catalyzes urea production from arginine and may have a substantial sparing effect in patients lacking ARG1 enzyme, so its reaction is annotated here although the role of ARG2 under normal physiological conditions remains unclear.
Cytosolic gamma-butyrobetaine hydroxylase dimer (BBOX1) catalyzes the reaction of oxygen, 4-trimethylammoniobutanoate, and 2-oxoglutarate to form C)2, succinate, and carnitine (Lindstedt and Nordin 1984; Vaz et al. 1998).
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The essential WD40 protein Cia1 is involved in a late step of cytosolic and nuclear iron-sulfur protein assembly
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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)
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:
Alanine-glyoxylate transaminase (AGXT) catalyzes the irreversible reaction of glyoxylate and alanine to form glycine and pyruvate (Danpure and Jennings 1988). The active form of the enzyme is a homodimer (Zhang et al. 2003) with one molecule of pyridoxal phosphate bound to each subunit (Coulter-Mackie et al. 2005). Mutations in this enzyme are associated with primary hyperoxaluria type I. Mutant alleles encode both catalytically inactive proteins and active ones that are mis-localized to mitochondria (Purdue et al. 1990; Takada et al. 1990).
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)
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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Investigation of the ABC transporter MRP1 in selected patients with presumed defects in vitamin B12 absorption
Functional analysis of mRNA scavenger decapping enzymes
Cloning of a water channel homolog expressed in brain meningeal cells and kidney collecting duct that functions as a stilbene-sensitive glycerol transporter
Trimming of N-ter extended precursor fragments by cytosolic aminopeptidases
Proteasomal clevage of exogenous antigen
Activation of CDC42 by unknown mechanism
GRB2: a pivotal protein in signal transduction
Displacement of stalled Pol II from the lesion site
The ubiquitin-editing enzyme A20 restricts nucleotide-binding oligomerization domain containing 2-triggered signals
XPC:HR23B complex binds to damaged DNA site with lesion
GTP hydrolysis by eRF3 facilitates stop codon decoding during eukaryotic translation termination
Assembly of repair proteins at the site of Pol II blockage
RNA Pol II is blocked by the lesion leading to reduced transcription
Formation of active Pol II complex with lesioned DNA template
Mutation of the fumarase gene in two siblings with progressive encephalopathy and fumarase deficiency
Ligation of newly synthesized repair patch to incised DNA in GG-NER
Binding of ERCC1-XPF to preincision complex
Formation of ERCC1-XPF heterodimeric complex
Formation of open bubble structure in DNA by helicases
Characterization of human lysophospholipid acyltransferase 3
5' incision leading to excision of DNA fragment with lesion in TC-NER
3' incision of the lesioned strand of DNA in TC-NER
Activation of Protein Kinase C beta (PKC-beta)
Resumption of transcription after TC-NER
Ligation of newly synthesized repair patch to incised DNA in TC-NER
Translocation of PKC theta to plasma membrane
Translocation of PDK1 to Plasma membrane
Similar idiotypic specificity for the membrane IgD and IgM of human B lymphocytes
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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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
The peripheral membrane subunits of the SAM complex function codependently in mitochondrial outer membrane biogenesis
Precursor oxidation by Mia40 and Erv1 promotes vectorial transport of proteins into the mitochondrial intermembrane space
Proteasomes: protein degradation machines of the cell
Two distinct proteolytic processes in the generation of a major histocompatibility complex class I-presented peptide
Phytanic acid arises through ruminant metabolism of chlorophyll and enters the human diet as a constituent of dairy products (Baxter 1968). It can act as an agonist for PPAR and other nuclear hormone receptors, but its normal role in human physiology, if any, is unclear. It is catabolized via a five-step alpha-oxidation reaction sequence that yields pristanoyl-CoA, which is turn is a substrate for beta-oxidation. These reactions take place in the peroxisomal matrix and their failure is associated with Refsum disease (Wanders et al. 2003).
Peroxisomal HSD17B4 dimer catalyzes the reaction of trans-2,3-dehydropristanoyl-CoA and H2O to form 3-hydroxypristanoyl-CoA. The enzyme is bifunctional - an aminoterminal domain catalyzes the dehydrogenation of a variety of 3-hydroxyacyl-CoA's and a carboxyterminal domain catalyzes the hydration of a variety of trans-2,3-dehydroacyl-CoA's, the reaction annotated here (Jiang et al. 1996, 1997). Defects in the enzyme are associated with a severe disorder of peroxisomal fatty acid metabolism in humans (Ferdinandusse et al. 2006).
Peroxisomal HSD17B4 dimer catalyzes the reaction of 3-hydroxypristanoyl-CoA and NAD+ to form 3-ketoxypristanoyl-CoA and NADH + H+. The enzyme is bifunctional - an aminoterminal domain catalyzes the dehydrogenation of a variety of 3-hydroxyacyl-CoA's, the reaction annotated here, and a carboxyterminal domain catalyzes the hydration of a variety of trans-2,3-dehydroacyl-CoA's (Jiang et al. 1996, 1997). Defects in the enzyme are associated with a severe disorder of peroxisomal fatty acid metabolism in humans (Ferdinandusse et al. 2006).
Peroxisomal carnitineacetyltransferase (CRAT) catalyzes the reaction of acetyl-CoA and carnitine to form acetylcarnitine and CoASH. The active form of the enzyme is a monomer (Bloisi et al. 1990; Wu et al. 2003).
VLCS (very long chain acyl-CoA synthetase), associated with the inner surface of the peroxisomal membrane, catalyzes the reaction of pristanate, CoA-SH and ATP to form pristanoyl-CoA, AMP and pyrophosphate (Steinberg et al. 1999).
Peroxisomal HSD17B4 dimer catalyzes the reaction of trans-2,3-dehydrohexacosanoyl-CoA and H2O to form 3-hydroxyhexacosanoyl-CoA. The enzyme is bifunctional - an aminoterminal domain catalyzes the dehydrogenation of a variety of 3-hydroxyacyl-CoA's and a carboxyterminal domain catalyzes the hydration of a variety of trans-2,3-dehydroacyl-CoA's, the reaction annotated here (Jiang et al. 1996, 1997). Defects in the enzyme are associated with a severe disorder of peroxisomal fatty acid metabolism in humans (Ferdinandusse et al. 2006).
Peroxisomal ACOT8 catalyzes the hydrolysis of acetyl-CoA to form acetate and CoASH (Jones et al. 1999; Wanders and Waterham 2006).
Peroxisomal carnitineacetyltransferase (CRAT) catalyzes the reaction of propionyl-CoA and carnitine to form propionylcarnitine and CoASH. The active form of the enzyme is a monomer (Bloisi et al. 1990; Wu et al. 2003).
Pristanoyl-CoA, generated in the peroxisome by alpha-oxidation of dietary phytanic acid, is further catabolized by three cycles of peroxisomal beta-oxidation to yield 4,8-dimethylnonanoyl-CoA, acetyl-CoA and two molecules of propionyl-CoA. These molecules in turn are converted to carnitine conjugates, which can be transported to mitochondria (Wanders and Waterham 2006, Verhoeven et al. 1998, Ferdinandusse et al. 1999).
Homodimeric ABCD1 associated with the peroxisomal membrane mediates the uptake of cytosolic very long chain fatty acyl CoAs such as hexacosanoyl-CoA into the peroxisomal matrix. While the requirement for this uptake step in the catabolism of very long chain fatty acids is well-established, direct evidence for the function of ABCD1 as a transporter comes only from studies of its ability to restore peroxisomal long chain fatty acid catabolism in yeast strains whose endogenous transporters have been disrupted by mutation. ABCD1 is inferred to function as a dimer like other members of the ABCD transporter family. The energy requirements of peroxisomal fatty acid uptake (other ABCD transporter-mediated reactions are coupled to ATP hydrolysis) have not been established (van Roermund et al. 2008).
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.
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).
Linear fatty acids containing more than 18 carbons are broken down by beta-oxidation in peroxisomes to yield acetyl-CoA and medium chain-length fatty acyl CoA's such as octanoyl-CoA (Wanders and Waterham 2006).
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).
Peroxisomal HSD17B4 dimer catalyzes the reaction of 3-hydroxyhexacosanoyl-CoA and NAD+ to form 3-ketohexacosanoyl-CoA and NADH + H+. The enzyme is bifunctional - an aminoterminal domain catalyzes the dehydrogenation of a variety of 3-hydroxyacyl-CoA's, the reaction annotated here, and a carboxyterminal domain catalyzes the hydration of a variety of trans-2,3-dehydroacyl-CoA's (Jiang et al. 1996, 1997). Defects in the enzyme are associated with a severe disorder of peroxisomal fatty acid metabolism in humans (Ferdinandusse et al. 2006).
Peroxisomal ACAA1 catalyzes the reaction of 3-ketohexacosanoyl-CoA and CoASH to form tetracosanoyl-CoA + acetyl-CoA (Bout et al. 1991).
Glucagon and regulation of glucose metabolism
Am J Physiol Endocrinol Metab 284:E671-8
Succinic semialdehyde dehydrogenase deficiency: lessons from mice and men
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.
Clinical and molecular characterization of the first adult congenital disorder of glycosylation (CDG) type Ic patient
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).
Mevalonate kinase (MK) catalyzes the phosphorylation of mevalonate to mevalonate-5-phosphate.
MicroRNAs: biogenesis, function and applications
Mevalonate pyrophosphate decarboxylase (MPD) decarboxylates mevalonate-5-pyrophosphate into isopentenyl pyrophosphate while hydrolysing ATP to ADP and orthophosphate.
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
Human chromokinesin KIF4A functions in chromosome condensation and segregation
Identification of the alpha-aminoadipic semialdehyde synthase gene, which is defective in familial hyperlysinemia.
Mutations in SPTLC1, encoding serine palmitoyltransferase, long chain base subunit-1, cause hereditary sensory neuropathy type I
ChEBI:27458 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA
DNA double-strand breaks: signaling, repair and the cancer connection.
Cardiomyopathy and exercise intolerance in muscle glycogen storage disease 0
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).
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).
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).
The crystal structure and mutational analysis of human NUDT9
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.
Phosphatidylcholine (PC) is hydrolyzed to phosphatidic acid (PA) and choline (Cho) by the enzymes phospholipase D1/2 (PLD1/2), at the endoplasmic reticulum (ER) membrane (Lopez et al. 1998, Hammond et al. 1995).
In the de novo synthesis of phosphatidic acid (PA), lysophosphatidic acid (LPA) is initially formed by the esterification of sn-1 by glycerol 3-phosphate acyltransferase (GPAT) from glycerol 3-phosphate (G3P). Next, LPA is converted to PA by a LPA acyltransferase (AGPAT, also known as LPAAT). In addition to this, PA is also formed when phosphatidylcholine (PC) is hydrolyzed by phospholipase D1/2 (PLD1/2). PA is involved in acyl chain remodeling via cleavage by phospholipases followed by reacylation by acyltransferases (Ghomashchi et al. 2010, Singer et al. 2002, Prasad et al. 2011, Shindou & Shimizu 2009, Cao et al. 2006).
Leukotriene A4 hydrolase in human leukocytes. Purification and properties
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).
At the endoplasmic reticulum (ER) membrane, phosphatidate phosphatase 1-3 (LPIN) dephosphorylates phosphatidic acid (PA) to form diacylglycerol (DAG) (Grimsey et al. 2008, Donkor et al. 2007).
At the endoplasmic reticulum (ER) membrane, 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).
Characterization of the enzymatic defect in late-onset muscle phosphofructokinase deficiency. New subtype of glycogen storage disease type VII.
De novo (Kennedy pathway) synthesis of phosphatidylethanolamine (PE) involves phosphorylation of ethanolamine (ETA) to phosphoethanolamine (PETA) followed by condensing with cytidine triphosphate (CTP) to form CDP-ethanolamine (CDP-ETA). Diacylglycerol (DAG) and CDP-ETA together then form PE. Alternatively, PE is formed when phosphatidylserine (PS) is decarboxylated by phosphatidylserine decarboxylase proenzyme (PISD) (Henneberry et al. 2002, Vance 1991, Vance 1990).
At the endoplasmic reticulum (ER) membrane, 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).
In the body, 27-hydroxycholesterol is synthesized in multiple tissues, exported to the liver, and converted there to bile acids and bile salts. This pathway is only a minor source of bile acids and bile salts, but may play a significant role particularly in the mobilization of cholesterol from lung phagocytes (Bjorkhem et al. 1994; Babiker et al. 1999; Javitt 2002). In the liver, conversion of 27-hydroxycholesterol to bile acids and bile salts is initiated with hydroxylation and oxidoreductase reactions to form 4-cholesten-7alpha,27-diol-3-one. The pathway then branches: hydroxylation of 4-cholesten-7alpha,27-diol-3-one to 4-cholesten-7alpha,12alpha,27-triol-3-one leads ultimately to the formation of cholate, while its reduction to 5beta-cholestan-7alpha,27-diol-3-one leads to chenodeoxycholate formation. In both branches, reactions in the cytosol, the mitochondrial matrix, and the peroxisomal matrix result in modifications to the ring structure, shortening and oxidation of the side chain, conversion to a Coenzyme A derivative, and conjugation with the amino acids glycine or taurine (Russell 2003). These reactions are outlined in the figure below. The final nine reactions are identical to ones of bile salt synthesis initiated by 7alpha-hydroxylation and are shown as arrows with no substrates.
5Beta-cholesten-7alpha,12a,27-triol-3-one and NADPH + H+ form 5beta-cholestan-3alpha,7alpha,12a,27-tetrol and NAPDP+. The reaction is catalyzed by 3alpha-hydroxysteroid dehydrogenase (AKR1C4), a cytosolic enzyme belonging to the aldo-keto reductase family (Dufort et al. 2001). Biochemical studies with rat proteins raise the possibility that other related enzymes may also carry out this reaction in vivo (Russell 2003).
5Beta-cholesten-7alpha,27-diol-3-one and NADPH + H+ form 5beta-cholestan-3alpha,7alpha,27-triol and NAPDP+. The reaction is catalyzed by 3alpha-hydroxysteroid dehydrogenase (AKR1C4), a cytosolic enzyme belonging to the aldo-keto reductase family (Dufort et al. 2001). Biochemical studies with rat proteins raise the possibility that other related enzymes may also carry out this reaction in vivo (Russell 2003).
4-Cholesten-7alpha,12alpha,27-triol-3-one and NADPH + H+ react to form 5beta-cholesten-7alpha,12alpha,27-triol-3-one + NADP+. This reaction is catalyzed by AKR1D1 (3-oxo-5-beta-steroid 4-dehydrogenase). AKR1D1 is localized to the cytosol, and in the course of the reaction its steroid substrate moves from the endoplasmic reticulum membrane to the cytosol. It is unclear whether this translocation results simply from its increased hydrophilicity or is mediated by the enzyme or another transport protein (Russell 2003).
4-Cholesten-7alpha,27-diol-3-one, NADPH, and H+ react to form 5beta-cholestan-7alpha,27-diol-3-one and NADP+. This reaction is catalyzed by AKR1D1 (3-oxo-5-beta-steroid 4-dehydrogenase). AKR1D1 is localized to the cytosol, and in the course of the reaction its steroid substrate moves from the endoplasmic reticulum membrane to the cytosol. It is unclear whether this translocation results simply from its increased hydrophilicity or is mediated by the enzyme or another transport protein (Russell 2003).
Inactivation of NPC1L1 causes multiple lipid transport defects and protects against diet-induced hypercholesterolemia
3,7,24THCA (25(R) 3alpha,7alpha,24(S)-trihydroxy-5beta-cholestanoate), coenzyme A, and ATP react to form the CoA conjugate of 3,7,24THCA, AMP, pyrophosphate and water. This cytosolic reaction is catalyzed by SLC27A2 (VLCS). SLC27A5 (BACS) also catalyzes this reaction; the relative contributions of the two enzymes to de novo bile acid synthesis in vivo are not certain (Mihalik et al. 2002).
In the body, 24-hydroxycholesterol is synthesized in the brain, exported to the liver, and converted there to bile acids and bile salts. This pathway is only a minor source of bile acids and bile salts, but appears to be critical for the disposal of excess cholesterol from the brain (Bjorkhem et al. 1998; Javitt 2002). In the liver, conversion of 24-hydroxycholesterol to bile acids and bile salts is initiated with hydroxylation and oxidoreductase reactions to form 4-cholesten-7alpha,24(S)-diol-3-one. The pathway then branches: hydroxylation of 4-cholesten-7alpha,24(S)-diol-3-one to 4-cholesten-7alpha,12alpha,24(S)-triol-3-one leads ultimately to the formation of cholate, while its reduction to 5beta-cholestan-7alpha,24(S)-diol-3-one leads to chenodeoxycholate formation. In both branches, reactions in the cytosol, the mitochondrial matrix, and the peroxisomal matrix result in modifications to the ring structure, shortening and oxidation of the side chain, conversion to a Coenzyme A derivative, and conjugation with the amino acids glycine or taurine (Russell 2003). These reactions are outlined in the figure below. The final three reactions are identical to ones of bile salt synthesis initiated by 7alpha-hydroxylation and are shown as arrows with no substrates.
Mechanism of selectivity in aquaporins and aquaglyceroporins
When do Lasses (longevity assurance genes) become CerS (ceramide synthases)?: Insights into the regulation of ceramide synthesis
Of the 20-40 grams of bile salts released daily by the liver, all but approximately 0.5 grams are reabsorbed from the intestine, returned to the liver, and re-used. This recycling involves a series of transport processes: uptake by enterocytes mediated by ASBT (SLC10A2), traversal of the enterocyte cytosol mediated by ileal bile acid binding protein (I-BABP - FABP6), efflux from enterocytes mediated by MRP3 (ABCC3), travel through the portal blood as a complex with albumin, and uptake by hepatocytes mediated by Na+-taurocholate transporting protein (NTPC - SLC10A1) and, to a lesser extent by organic anion transporting proteins A, C, and 8 (OATPA - SLCO1A2, OATPC - SLCO1B1, and OATP-8 - SLCO1B3). Once returned to the hepatocyte cytosol, bile acids (generated in the intestine by the action of bacteria on secreted bile salts) are activated by conjugation with coenzyme A, then coupled to glycine or taurine, regenerating bile salts for re-export into the bile, mediated by the bile salt export pump, ABCB11 (Kullak-Ublick et al. 2004; Mihalik et al. 2002; Trauner and Boyer 2003). Unmodified bile salts returned to the hepatocyte cytosol can be re-exported by ABCB11 without further modification.
Cholate or chenodeoxycholate, coenzyme A, and ATP react to form their CoA conjugates, AMP, pyrophosphate and water. This reaction is catalyzed by SLC27A5 (BACS) associated with the endoplasmic reticulum membrane, but the substrates and products are cytosolic (Mihalik et al. 2002).
In a healthy adult human, about 500 mg of cholesterol is converted to bile salts daily (Russell 2003). The major pathway for bile salt synthesis in the liver begins with the conversion of cholesterol to 7alpha-hydroxycholesterol. Bile salt synthesis can also begin with the synthesis of an oxysterol - 24-hydroxycholesterol or 27-hydroxycholesterol. In the body, the initial steps of these two pathways occur in extrahepatic tissues, generating intermediates that are transported to the liver and converted to bile salts via the 7alpha-hydroxycholesterol pathway. These extrahepatic pathways contribute little to the total synthesis of bile salts, but are thought to play important roles in cholesterol homeostasis (Javitt 2002).
The microsomal enzyme cholesterol 25-hydroxylase is a member of a lipid metabolizing enzyme family that utilizes oxygen and diiron-oxygen cofactor to hydroxylate, desaturate, epoxidate and acetylate substrates.
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).
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).
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).
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).
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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).
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).
At the endoplasmic reticulum (ER) membrane, lysophospholipid acyltransferases acylate 2-acyl lysophosphatidylethanolamine (LPE) to form phosphatidylethanolamine (PE). The lysophospholipid acyltransferases involved are: lysophospholipid acyltransferase 1 (MBOAT1) aka LPEAT1 (Gijon et al. 2008, Hishikawa et al. 2008); lysophospholipid acyltransferase LPCAT4 (LPCAT4) aka LPEAT2 (Cao et al. 2008, Ye et al. 2005); lysophospholipid acyltransferase 2 (MBOAT2) aka LPCAT4 (Hishikawa et al. 2008, Gijon et al. 2008); lysophospholipid acyltransferase 5 (LPCAT3) (Hishikawa et al. 2008, Zhao et al. 2008, Gijon et al. 2008, Jain et al. 2009, Kazachkov et al. 2008).
In the acyl chain remodelling pathway (Lands cycle), phosphatidylethanolamine (PE) is hydrolyzed by phopholipases and subsequently reacylated by acyltransferases. These cycles modify the fatty acid composition of glycerophospholipids to generate diverse molecules asymmetrically distributed in the cell membrane (Ghomashchi et al. 2010, Singer et al. 2002, Cao et al. 2008, Zhao et al. 2008, Hishikawa et al. 2008).
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).
Peroxisome proliferator-activated receptors: nuclear control of metabolism
Mammalian MAP kinase signalling cascades
De novo (Kennedy pathway) synthesis of phosphatidylcholine (PC) involves phosphorylation of choline (Cho) to phosphocholine (PCho) followed by condensing with cytidine triphosphate (CTP) to form CDP-choline (CDP-Cho). Diacylglycerol (DAG) and CDP-ETA together then form PC. Alternatively, PC is formed when phosphatidylethanolamine (PE) is methylated by phosphatidylethanolamine N-methyltransferase (PEMT) (Henneberry et al. 2002; Wright & McMaster 2002).
At the endoplasmic reticulum (ER) membrane, active membrane-bound choline-phosphate cytidylyltransferase A (PCYT1A) or B (PCYT1B) homodimer condenses phosphocholine (PCho) and cytidine triphosphate (CTP) to produce CDP-choline (CDP-Cho) (Lykidis et al. 1998).
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).
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).
At the endoplasmic reticulum (ER) membrane, lysophospholipid acyltransferases acylate 2-acyl lysophosphatidylcholine (LPC) to form phosphatidylcholine (PC). The lysophospholipid acyltransferases involved are: lysophosphatidylcholine acyltransferase 1 (LPCAT1) (Nakanishi et al. 2006, Chen et al. 2006); lysophosphatidylcholine acyltransferase 2 (LPCAT2) (Shindou et al. 2006); lysophospholipid acyltransferase 5 (LPCAT3) (Hishikawa et al. 2008, Zhao et al. 2008, Gijon et al. 2008, Jain et al. 2009, Kazachkov et al. 2008); lysophospholipid acyltransferase LPCAT4 (LPCAT4) aka LPEAT2 (Cao et al. 2008, Ye et al. 2005); or lysophospholipid acyltransferase 2 (MBOAT2) aka LPCAT4 (Hishikawa et al. 2008, Gijon et al. 2008).
At the 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).
The TM7SF2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The SQLE gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
Cholesterol is synthesized de novo from from acetyl CoA. The overall synthetic process is outlined in the figure below. Enzymes whose regulation plays a major role in determining the rate of cholesterol synthesis in the body are highlighted in red, and connections to other metabolic processes are indicated. The transformation of lanosterol into cholesterol requires multiple steps, including the removal of three methyl groups, the reduction of one double bond and the migration of another. These reactions may not occur in a single fixed order in the body, so the linear pathway laid out here following the work of Gaylor and colleagues (Gaylor 2002) is an oversimplification of the process that occurs in vivo. Defects in several of the enzymes involved in this process are associated with human disease and have provided useful insights into the regulatory roles of cholesterol and its synthetic intermediates in human development (Herman 2003; Song et al. 2005).
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).
The SC5D gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The FDPS gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
4-methylcholesta-8(9),24-dien-3beta-ol, NADPH + H+, and O2 react to form 4-carboxycholesta-8(9),24-dien-3beta-ol, NADP+, and H2O. This reaction, in the endoplasmic reticulum, is catalyzed by SC4MOL (C-4 methylsterol oxidase). The human enzyme has been identified based on its sequence similarity to yeast methyl sterol oxidase (ERG25) and the ability of the cloned human gene to rescue ERG25-deficient yeast cells (Li and Kaplan 1996). The mechanism and stoichiometry of the reaction have been inferred from studies of partially purified rat enzyme (Gaylor et al. 1975; Fukushima et al. 1981).
4-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).
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).
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).
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).
Essentials of Glycobiology, 2nd edition (Book)
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).
Tim22, the essential core of the mitochondrial protein insertion complex, forms a voltage-activated and signal-gated channel
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).
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)
Replication of UV-damaged DNA: new insights into links between DNA polymerases, mutagenesis and human disease.
(24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA and NAD+ react to form 3alpha,7alpha-dihydroxy-5beta-cholest-24-one-CoA, NADH, and H+. This oxidation reaction, catalyzed by the peroxisomal D-bifunctional enzyme (Huyghe et al. 2006), occurs in the peroxisomal matrix.
(24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA and NAD+ react to form 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-one-CoA, NADH, and H+. This oxidation reaction, catalyzed by the peroxisomal D-bifunctional enzyme (Huyghe et al. 2006), occurs in the peroxisomal matrix.
In the liver, synthesis of bile acids and bile salts is initiated with the conversion of cholesterol to 7alpha-hydroxycholesterol and of 7alpha-hydroxycholesterol to 4-cholesten-7alpha-ol-3-one. The pathway then branches: hydroxylation of 4-cholesten-7alpha-ol-3-one to 4-cholesten-7alpha, 12alpha-diol-3-one leads ultimately to the formation of cholate, while its reduction to 5beta-cholestan-7alpha-ol-3-one leads to chenodeoxycholate formation. The amounts of substrate following each branch appear to be determined by abundance of the hydroxylase enzyme: in human liver, cholate synthesis predominates. In both branches, reactions in the cytosol, the mitochondrial matrix, and the peroxisomal matrix result in modifications to the ring structure, shortening and oxidation of the side chain, conversion to a Coenzyme A derivative, and conjugation with the amino acids glycine or taurine. In the body, glycocholate, taurocholate, glycochenodeoxycholate, and taurochenodeoxycholate are released from hepatocytes into the bile and ultimately into the lumen of the small intestine, where they function as detergents to solubilize dietary fats. The liver synthetic pathway also yields small amounts of bile acids, cholate and deoxycholate, which may play a feedback role in regulating the bile acid synthetic pathway (Russell 2003). These reactions are outlined in the figure below.
Choloyl-CoA and water react to form cholate and CoASH. This reaction, catalyzed by acyl-coenzyme A thioesterase 8, occurs in the peroxisomal matrix (Jones et al. 1999; Hunt et al. 2002). While bile salts are the major product of the de novo biosynthetic pathway in the normal human liver, bile acids are major feedback regulators of this pathway and this hydrolysis reaction is thought to play a role in generating them (Russell 2003).
4-Cholesten-7alpha,24(S)-diol-3-one, NADPH, and H+ react to form 5beta-cholestan-7alpha,24(S)-diol-3-one and NADP+. This reaction is catalyzed by AKR1D1 (3-oxo-5-beta-steroid 4-dehydrogenase). AKR1D1 is localized to the cytosol, and in the course of the reaction its steroid substrate moves from the endoplasmic reticulum membrane to the cytosol. It is unclear whether this translocation results simply from its increased hydrophilicity or is mediated by the enzyme or another transport protein (Russell 2003).
4-cholesten-7alpha,12alpha,24(S)-triol-3-one and NADPH + H+ react to form 5beta-cholesten-7alpha,12alpha,24(S)-triol-3-one and NADP+. This reaction is catalyzed by AKR1D1 (3-oxo-5-beta-steroid 4-dehydrogenase). AKR1D1 is localized to the cytosol, and in the course of the reaction its steroid substrate moves from the endoplasmic reticulum membrane to the cytosol. It is unclear whether this translocation results simply from its increased hydrophilicity or is mediated by the enzyme or another transport protein (Russell 2003).
5Beta-cholesten-7alpha,24(S)-diol-3-one and NADPH + H+ form 5beta-cholestan-3alpha,7alpha,24(S)-triol and NAPDP+. The reaction is catalyzed by 3alpha-hydroxysteroid dehydrogenase (AKR1C4), a cytosolic enzyme belonging to the aldo-keto reductase family (Dufort et al. 2001). Biochemical studies with rat proteins raise the possibility that other related enzymes may also carry out this reaction in vivo (Russell 2003).
5Beta-cholesten-7alpha,12alpha,24(S)-triol-3-one and NADPH + H+ form 5beta-cholestan-3alpha,7alpha,12alpha,24(S)-tetrol and NAPDP+. The reaction is catalyzed by 3alpha-hydroxysteroid dehydrogenase (AKR1C4), a cytosolic enzyme belonging to the aldo-keto reductase family (Dufort et al. 2001). Biochemical studies with rat proteins raise the possibility that other related enzymes may also carry out this reaction in vivo (Russell 2003).
TetraHCA (25(R) 3alpha,7alpha,12alpha,24(S)-tetrahydroxy-5beta-cholestanoate), coenzyme A, and ATP react to form the CoA conjugate of 25(R) TetraHCA, AMP, pyrophosphate and water. This cytosolic reaction is catalyzed by SLC27A5 (BACS). SLC27A2 (VLCS) also catalyzes this reaction; the relative contributions of the two enzymes to de novo bile acid synthesis in vivo are not certain (Mihalik et al. 2002).
3,7,24THCA (25(R) 3alpha,7alpha,24(S)-trihydroxy-5beta-cholestanoate), coenzyme A, and ATP react to form the CoA conjugate of 3,7,24THCA, AMP, pyrophosphate and water. This cytosolic reaction is catalyzed by SLC27A5 (BACS). SLC27A2 (VLCS) also catalyzes this reaction; the relative contributions of the two enzymes to de novo bile acid synthesis in vivo are not certain (Mihalik et al. 2002).
TetraHCA (25(R) 3alpha,7alpha,12alpha,24(S)-tetrahydroxy-5beta-cholestanoate), coenzyme A, and ATP react to form the CoA conjugate of 25(R) TetraHCA, AMP, pyrophosphate and water. This cytosolic reaction is catalyzed by SLC27A2 (VLCS). SLC27A5 (BACS) also catalyzes this reaction; the relative contributions of the two enzymes to de novo bile acid synthesis in vivo are not certain (Mihalik et al. 2002).
DHCA (25(R) 3alpha,7alpha-dihydroxy-5beta-cholestanoate) , coenzyme A, and ATP react to form the CoA conjugate of 25(R) DHCA, AMP, and pyrophosphate. This cytosolic reaction is catalyzed by SLC27A5 (BACS). SLC27A2 (VLCS) also catalyzes this reaction; the relative contributions of the two enzymes to de novo bile acid synthesis in vivo are not certain (Mihalik et al. 2002).
5Beta-cholesten-7alpha,12alpha-diol-3-one and NADPH + H+ form 5beta-cholestan-3alpha,7alpha,12alpha-triol and NAPDP+. The reaction is catalyzed by 3alpha-hydroxysteroid dehydrogenase (AKR1C4), a cytosolic enzyme belonging to the aldo-keto reductase family (Dufort et al. 2001). Biochemical studies with rat proteins raise the possibility that other related enzymes may also carry out this reaction in vivo (Russell 2003).
4-Cholesten-7alpha-ol-3-one, NADPH, and H+ react to form 5beta-cholestan-7alpha-ol-3-one and NADP+. This reaction is catalyzed by AKR1D1 (3-oxo-5-beta-steroid 4-dehydrogenase). AKR1D1 is localized to the cytosol, and in the course of the reaction its steroid substrate moves from the endoplasmic reticulum membrane to the cytosol. It is unclear whether this translocation results simply from its increased hydrophilicity or is mediated by the enzyme or another transport protein (Russell 2003).
4-Cholesten-7alpha, 12alpha-diol-3-one and NADPH + H+ react to form 5beta-cholesten-7alpha,12alpha-diol-3-one + NADP+. This reaction is catalyzed by AKR1D1 (3-oxo-5-beta-steroid 4-dehydrogenase). AKR1D1 is localized to the cytosol, and in the course of the reaction its steroid substrate moves from the endoplasmic reticulum membrane to the cytosol. It is unclear whether this translocation results simply from its increased hydrophilicity or is mediated by the enzyme or another transport protein (Russell 2003).
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.
THCA (25(R) 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoate) , coenzyme A, and ATP react to form the CoA conjugate of 25(R) THCA, AMP, and pyrophosphate. This cytosolic reaction is catalyzed by SLC27A5 (BACS). SLC27A2 (VLCS) also catalyzes this reaction; the relative contributions of the two enzymes to de novo bile acid synthesis in vivo are not certain (Mihalik et al. 2002).
DHCA (25(R) 3alpha,7alpha-dihydroxy-5beta-cholestanoate), coenzyme A, and ATP react to form the CoA conjugate of 25(R) DHCA, AMP, and pyrophosphate. This cytosolic reaction is catalyzed by SLC27A2 (VLCS). SLC27A5 (BACS) also catalyzes this reaction; the relative contributions of the two enzymes to de novo bile acid synthesis in vivo are not certain (Mihalik et al. 2002).
THCA (25(R) 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoate), coenzyme A, and ATP react to form the CoA conjugate of 25(R) THCA, AMP, and pyrophosphate. This cytosolic reaction is catalyzed by SLC27A2 (VLCS). SLC27A5 (BACS) also catalyzes this reaction; the relative contributions of the two enzymes to de novo bile acid synthesis in vivo are not certain (Mihalik et al. 2002).
3alpha,7alpha,12alpha-Trihydroxy-5beta-cholest-24-enoyl-CoA [ChEBI:1695]
5Beta-cholesten-7alpha-ol-3-one and NADPH + H+ form 5beta-cholestan-3alpha,7alpha-diol and NAPDP+. The reaction is catalyzed by 3alpha-hydroxysteroid dehydrogenase (AKR1C4), a cytosolic enzyme belonging to the aldo-keto reductase family (Dufort et al. 2001). Biochemical studies with rat proteins raise the possibility that other related enzymes may also carry out this reaction in vivo (Russell 2003).
Human proton/oligopeptide transporter (POT) genes: identification of putative human genes using bioinformatics
Metabolic characteristics and importance of the universal methionine salvage pathway recycling methionine from 5'-methylthioadenosine
3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA (THCA-CoA) is hydrated to form (24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA. This reaction, catalyzed by the peroxisomal D-bifunctional enzyme (Huyghe et al. 2006), occurs in the peroxisomal matrix.
Two novel proteins in the mitochondrial outer membrane mediate beta-barrel protein assembly
25(S) 3alpha,7alpha-dihydroxy-5beta-cholest-24-enoyl-CoA is hydrated to form (24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA. This reaction, catalyzed by the peroxisomal D-bifunctional enzyme (Huyghe et al. 2006), occurs in the peroxisomal matrix.
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Crystal structure of human aquaporin 4 at 1.8 A and its mechanism of conductance
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FUNCTION MRS4 suppresses a mitochondrial splice defect in the first intron of the COB gene. It may act as a carrier, exerting its suppressor activity via modulation of solute concentrations in the mitochondrion (possibly of cations). Not essential.MISCELLANEOUS Present with 1340 molecules/cell in log phase SD medium.SIMILARITY Belongs to the mitochondrial carrier (TC 2.A.29) family.SIMILARITY Contains 3 Solcar repeats.
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FUNCTION DNA polymerase delta (DNA polymerase III) participates in chromosomal DNA replication. It is required during synthesis of the leading and lagging DNA strands at the replication fork and binds at/or near replication origins and moves along DNA with the replication fork. It has 3'-5' proofreading exonuclease activity that correct errors arising during DNA replication. It is also involved in DNA synthesis during DNA repair. POL3 contains the polymerase active site and most likely the active site for the 3'-5' exonuclease activity.CATALYTIC ACTIVITY Deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).COFACTOR Binds 1 4Fe-4S cluster.SUBUNIT DNA polymerase delta is a heterotrimer of POL3, POL32 and HYS2. Interacts with PCNA.DOMAIN The CysA-type zinc finger is required for PCNA-binding (PubMed:22119860).DOMAIN The CysB motif binds 1 4Fe-4S cluster and is required for the formation of polymerase complexes (PubMed:22119860).MISCELLANEOUS In eukaryotes there are five DNA polymerases: alpha, beta, gamma, delta, and epsilon which are responsible for different reactions of DNA synthesis.SIMILARITY Belongs to the DNA polymerase type-B family.SIMILARITY Contains 1 CysA-type zinc finger.
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FUNCTION Essential component of a cytosolic Fe/S protein assembly machinery. Required for maturation of extramitochondrial Fe/S proteins. May play a role in the transfer of pre-assembled Fe/S clusters to target apoproteins.SUBUNIT Interacts with CIA1.SIMILARITY Belongs to the NARF family.
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(S)-alpha-Amino-1H-imidazole-4-propionic acid
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(S)-2-Amino-3-(p-hydroxyphenyl)propionic acid
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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
Selective killing of human malignant cell lines deficient in methylthioadenosine phosphorylase, a purine metabolic enzyme
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Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors
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Prefoldin, a chaperone that delivers unfolded proteins to cytosolic chaperonin
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Transcriptional regulation of squalene epoxidase by sterols and inhibitors in HeLa cells
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Tob38, a novel essential component in the biogenesis of beta-barrel proteins of mitochondria
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Molecular cloning and expression of the cDNAs encoding human and yeast mevalonate pyrophosphate decarboxylase
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Regulation of small GTPases at epithelial cell-cell junctions
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
Detours and shortcuts to transcription reinitiation.
Defective T cell differentiation in the absence of Jnk1
Cloning and characterization of the cDNA encoding human adenylosuccinate synthetase
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
FUNCTION May participate in assembly and/or disassembly of proteins imported into the mitochondrion. HSP60 are ATPases and have affinity for unfolded proteins.SIMILARITY Belongs to the chaperonin (HSP60) family.
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
Structural basis for human monoglyceride lipase inhibition
Molecular cloning of a cDNA encoding human SPH-binding factor, a conserved protein that binds to the enhancer-like region of the U6 small nuclear RNA gene promoter
Signaling mechanisms utilized by antigen receptors and integrins: common intermediates, different outcomes?
ATP-Binding cassette cholesterol transporters and cardiovascular disease
Identification of the human mitochondrial oxodicarboxylate carrier. Bacterial expression, reconstitution, functional characterization, tissue distribution, and chromosomal location
'NF-Y (name copied from entity in Homo sapiens) [nucleoplasm]' positively regulates 'Expression of BIP (78 kDa Glucose-regulated protein, GRP78, HSPA5)'
Identification and characterization of a mammalian mitochondrial ATP-binding cassette membrane protein
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).
Phosphorylation of the CARMA1 linker controls NF-kappaB activation
At the Golgi membrane, phosphatidylinositide phosphatase SAC1 (SACM1L) dephosphorylates phosphatidylinositol 3-phosphate (PI3P) to phosphatidylinositol (PI) but not as efficiently as phosphatidylinositol 4-phosphate (PI4P) dephosphorylation. No significant activity of this enzyme towards phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) was detected (Rohde et al. 2003).
At the Golgi membrane, 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).
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, ADP-ribosylation factor 1 and 3 (ARF1 and ARF3) complexed to GTP bind to phosphatidylinositol 4-kinase beta (PI4KB) and activate it (Haynes et al. 2007, Wong et al. 1997, Godi et al. 1999).
At the Golgi membrane, activated phosphatidylinositol 4-kinase beta (PI4KB) complexed to ADP-ribosylation factor 1/3 (ARF1/3) phosphorylates phosphatidylinositol (PI) to phosphatidylinositol 4-phosphate (PI4P) (Suzuki et al. 1997).
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).
FUNCTION Acts as a non-catalytic component of endonuclease SceI (endo.SceI), which cleaves specifically at multiple sites on mitochondrial DNA and produces double-stranded breaks. SSC1 confers broader sequence specificity, greater stability, and higher activity on the catalytic subunit.SUBUNIT Component of the PAM complex, at least composed of SSC1 (mtHsp70), MGE1, TIM44, PAM16/TIM16, PAM17 and PAM18/TIM14. In the complex, SSC1 interacts directly with PAM18 and TIM44. Interacts with NAP1 (By similarity). Component of endonuclease SceI (endo.SceI), which is a heterodimer of ENS2 and SSC1.SIMILARITY Belongs to the heat shock protein 70 family.CAUTION S.cerevisiae displays strain polymorphism with regard to Endo.SceI endouclease activity. This is due to the mitochondrion-encoded, catalytic subunit ENS2, which exhibits strain polymorphism. It can be either present as continuous ORF in the mitochondrial genome (e.g. strain IAM 4274), present but disrupted by the insertion of GC clusters (e.g. strain D273-10B/A), or completely absent in the mitochondrial genome (e.g. strain S288c).
At the endoplasmic reticulum (ER) membrane, transmembrane protein phosphatidylinositide phosphatase SAC1 (SACM1L) efficiently dephosphorylates phosphatidylinositol 4-phosphate (PI4P), and to a lesser extent phosphatidylinositol 3-phosphate (PI3P), to phosphatidylinositol (PI). No significant activity of this enzyme towards phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) was detected (Rohde et al. 2003).
At the endoplasmic reticulum (ER) membrane, phosphatidylinositol (PI) and phosphatidylinositol 4-phosphate (PI4P) are interconverted (Wong et al. 1997, Gehrmann et al. 1999, Wei et al. 2002, Rohde et al. 2003).
Activation of p75NTR by proBDNF facilitates hippocampal long-term depression
Molecular Mechanisms of Phagocytosis (Book): 97-116
A novel and evolutionarily conserved PtdIns(3,4,5)P3-binding domain is necessary for DOCK180 signalling
At the early endosome membrane, the PAS complex, consisting of FYVE finger-containing phosphoinositide kinase (PIKFYVE), yeast VAC14 homologue (VAC14), and polyphosphoinositide phosphatase aka SAC3 (FIG4), binds to the membrane via PIKFYVE's FYVE finger (Sbrissa et al. 2002, Cao et al. 2007). The PIKFYVE kinase component phosphorylates phosphatidylinositol 3-phosphate (PI3P) to phosphatidylinositol 3,5-bisphosphate PI(3,5)P2 (Sbrissa et al. 1999). The PAS complex is present in the cytosol and is recruited to the membrane (Sbrissa et al. 2007).
At the plasma membrane, synaptic inositol-1,4,5-trisphosphate 5-phosphatase 1 aka Synaptojanin-1 (SYNJ1) (Guo et al. 1999, Mani et al. 2007, Johenning et al. 2004) and -2 (SYNJ2) (Malecz et al. 2000) dephosphorylate phosphatidylinositol 4-phosphate (PI4P) phosphatidylinositol (PI). The SAC1 domains of SYNJ1 and SYNJ2 demonstrate 4-phosphatase activity.
At the 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 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).
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).
At the Golgi membrane, phosphatidylinositol 4-phosphate (PI4P) inositol polyphosphate 5-phosphatase OCRL-1 (OCRL) (Choudhury et al. 2009, Suchy et al. 1995, Zhang et al. 1995) and 72 kDa inositol polyphosphate 5-phosphatase (INPP5E) (Bilas et al. 2009) dephosphorylate phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) to form phosphatidylinositol 4-phosphate (PI4P). INPP5E is located in the Golgi membrane, mediated by its N-terminal proline-rich domain (Kong et al. 2000).
DNA double strand break repair, chromosome synapsis and transcriptional silencing in meiosis
Mechanisms of digestion and absorption of dietary vitamin A
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).
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).
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).
At the inner mitochondrial (IR) membrane, cardiolipin synthase (CRLS1) acylates 1-acyl lysophosphatidylglycerol (LPG) to form phosphatidylglycerol (PG) (Nie et al. 2010).
At the inner mitochondrial membrane (IM), cardiolipin synthase (CRLS1) acylates 2-acyl lysophosphatidylglycerol (LPG) to form phosphatidylglycerol (PG) (Nie et al. 2010).
Identification of autophosphorylation sites of HER2/neu
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).
Phosphatidylinositol (PI) is synthesized when phosphatidic acid (PA) and cytidine triphosphate (CTP) are converted into cytidine diphosphate-diacylglycerol (CDP-DAG) followed by conversion into PI and cytidine monophosphate (CMP) (Stuhne-Sekalec et al 1986, Lykidis et al. 1997).
At the endoplasmic reticulum (ER) membrane, lysophospholipid acyltransferase 7 (MBOAT7) aka LPIAT acylates 1-acyl lysophosphatidylinositol (LPI) to form phosphatidylinositol (PI) (Gijon et al. 2008, Lee et al. 2008).
At the endoplasmic reticulum (ER) membrane, lysophospholipid acyltransferase 7 (MBOAT7) aka LPIAT acylates 2-acyl lysophosphatidylinositol (LPI) to form phosphatidylinositol (PI) (Gijon et al. 2008, Lee et al. 2008).
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).
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).
At the inner mitochondrial membrane (IM), tafazzin (TAZ) converts monolysocardiolipin (MLCL) and phosphatidylethanolamine (PE) to cardiolipin (CL) and 1-acyl lysophosphatidylethanolamine (LPE) (Xu et al. 2003, Xu et al. 2006, Malhotra et al. 2009). Although this reaction is reversible, the net effect of the phospholipase A and acyltransferase reactions drives it towards the formation of LPE and CL.
The human telomere terminal transferase enzyme is a ribonucleoprotein that synthesizes TTAGGG repeats
At the inner mitochondrial membrane (IM), tafazzin (TAZ) converts cardiolipin (CL) and 1-acyl lysophosphatidylethanolamine (LPE) to monolysocardiolipin (MLCL) and phosphatidylethanolamine (PE) (Xu et al. 2003, Xu et al. 2006, Malhotra et al. 2009).
Expression, purification, and characterization of histidine-tagged rat and human flavoenzyme dihydroorotate dehydrogenase.
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).
In the acyl chain remodelling pathway (Lands cycle), phosphatidylglycerol (PG) is hydrolyzed by phopholipases and subsequently reacylated by acyltransferases. These cycles modify the fatty acid composition of glycerophospholipids to generate diverse molecules asymmetrically distributed in the cell membrane. The events occur additionally in the inner mitochondria membranes (IM) as well as in the endoplasmic reticulum (ER) membrane (Ghomashchi et al. 2010, Singer et al. 2002, Cao et al. 2008, Yang et al. 2004, Nie et al. 2010).
At the inner mitochondrial membrane (IM), tafazzin (TAZ) converts monolysocardiolipin (MLCL) and phosphatidylcholine (PC) to cardiolipin (CL) and 1-acyl lysophosphatidylcholine (LPC) (Xu et al. 2003, Xu et al. 2006, Malhotra et al. 2009). Although this reaction is reversible, the net effect of the phospholipase A and acyltransferase reactions drives it towards the formation of LPC and CL.
At the inner mitochondrial membrane (IM), tafazzin (TAZ) converts cardiolipin (CL) and 1-acyl lysophosphatidylcholine (LPC) to monolysocardiolipin (MLCL) and phosphatidylcholine (PC) (Xu et al. 2003, Xu et al. 2006, Malhotra et al. 2009).
At the inner mitochondrial membrane (IM), cardiolipin synthase (CRLS1) converts phosphatidylglycerol (PG) and cytidine diphosphate-diacylglycerol (CDP-DAG) into cardiolipin (CL) (Lu et al. 2006, Houtkooper et al. 2006).
Cardiolipin(CL) is synthesized in the inner mitochondrial membrane (IM), when phosphatidylglycerol (PG) and cytidine diphosphate-diacylglycerol (CDP-DAG) are converted into CL (Lu et al. 2006, Houtkooper et al. 2006).
Phosphoinositide phosphatases in cell biology and disease
The proteasome and MHC class I antigen processing
Immunoglobulin E receptor signaling and asthma
The sulfhydryl oxidase Erv1 is a substrate of the Mia40-dependent protein translocation pathway
JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1
11-epi-Prostaglandin F2alpha [ChEBI:730]
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Fcgamma receptor signaling in phagocytes
Molecular cloning of a member of the facilitative glucose transporter gene family GLUT11 (SLC2A11) and identification of transcription variants
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The PDGF family: four gene products form five dimeric isoforms
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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.).
Interference footprinting analysis of telomerase elongation complexes
Oxidative folding of small Tims is mediated by site-specific docking onto Mia40 in the mitochondrial intermembrane space
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.
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.).
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Acetylcholine released by parasympathetic nerve endings in the pancreas causes a potentiation of insulin release when glucose is present at concentrations greater than about 7 mM. Acetylcholine binds the Muscarinic Acetylcholine Receptor M3 on pancreatic beta cells. The binding has two effects: an increase in permeability of the cell to Na+ ions through an unknown mechanism, and the activation of Phospholipase C beta-1 through a heterotrimeric G protein, G(q). After acetylcholine binds the Muscarinic Acetycholine Receptor M3, the receptor activates the G protein Gq by causing the alpha subunit of Gq to exchange GDP for GTP. Activation of Gq in turn activates Phospholipase C beta-1. Phospholipase C beta-1 hydrolyzes the phosphodiester bond at the third position of phosphoinositol 4,5-bisphosphate, producing diacylglycerols (DAG) and inositol 1,4,5-trisphosphate. DAG remains in the cell membrane and causes Protein Kinase C alpha (PKC alpha) to translocate from the cytosol to the membrane. This results in the activation of PKC alpha which then phosphorylates target proteins on serine and threonine residues. One known target of PKC alpha is Myristoylated Alanine-rich C Kinase Substrate (MARCKS), which is believed to affect vesicle transport and may be responsible for the increased traffic of insulin granules seen in response to acetylcholine. Inositol trisphophate binds a receptor, the IP3 receptor, on calcium stores in the cell (probably the endoplasmic reticulum). The release of calcium into the cytosol stimulates the exocytosis of insulin granules.
Human pancreatic beta cells express glucose transporters 1 and (GLUT1, GLUT2), which are responsible for uptake of glucose from the extracellular medium into the cytosol. (Rodent pancreatic beta cells express only Glut2.)
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.
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.
Mitochondrial COQ3 is an O-methyltransferase required in the reaction to convert 3-demethylubiquinol-10 (DeMQ10H2) to ubiquinol-10 (Q10H2) (Jonassen & Clarke 2000).
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).
At the end of this reaction, 1 molecule of 'pyruvate kinase, liver and RBC' is present. This reaction takes place in the 'nucleus'.
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.
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).
FUNCTION Mitochondrial intermembrane chaperone that participates in the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. Also required for the transfer of beta-barrel precursors from the TOM complex to the sorting and assembly machinery (SAM complex) of the outer membrane. Acts as a chaperone-like protein that protects the hydrophobic precursors from aggregation and guide them through the mitochondrial intermembrane space. Compared to TIM9, it may function as a substrate sensor.SUBUNIT Heterohexamer; composed of 3 copies of TIM9 and 3 copies of TIM10, named soluble 70 kDa complex. Associates directly with the TIM12 component of the TIM22 complex, whose core is composed of TIM18, TIM22 and TIM54. Interacts with the transmembrane regions of multi-pass transmembrane proteins in transit.DOMAIN The twin CX3C motif contains 4 conserved Cys residues that form 2 disulfide bonds in the mitochondrial intermembrane space. However, during the transit of TIM10 from cytoplasm into mitochondrion, the Cys residues probably coordinate zinc, thereby preventing folding and allowing its transfer across mitochondrial outer membrane.SIMILARITY Belongs to the small Tim family.
SGPL1 (sphingosine-1-phosphate lyase 1), associated with the endoplasmic reticulum membrane, catalyzes the cleavage of cytosolic sphinganine (dihydrosphingosine) 1-phosphate to form phosphoethanolamine and hexadecanal (Van Veldhoven et al. 2000; Fyrst and Saba 2008).
SGPP1 and 2 (sphingosine-1-phosphate phosphatase 1 and 2) enzymes associated with the endoplasmic reticulum membrane catalyze the hydrolysis of cytosolic sphinganine 1-phosphate to form sphinganine (dihydrosphingosine) and orthophosphate (Johnson et al. 2003; Ogawa et al. 2003).
SGPL1 (sphingosine-1-phosphate lyase 1), associated with the endoplasmic reticulum membrane, catalyzes the cleavage of cytosolic sphingosine 1-phosphate to form phosphoethanolamine and hexadec-2-enal (Van Veldhoven et al. 2000; Fyrst and Saba 2008).
SGPP1 and 2 (sphingosine-1-phosphate phosphatase 1 and 2) enzymes associated with the endoplasmic reticulum membrane catalyze the hydrolysis of cytosolic sphingosine 1-phosphate to form sphingosine and orthophosphate (Johnson et al. 2003; Ogawa et al. 2003).
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.
The main steps involved in de novo sphingolipid synthesis are annotated here (Merrill 2002, Gault et al. 2010).
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).
IMMPORT:Bioinformatics for the future of immunology
The steps involved in the synthesis of glycosphingolipids (sphingolipids with one or more sugars attached) are annotated here (Gault et al. 2010).
Sphingolipids are derivatives of long chain sphingoid bases such as sphingosine (trans-1,3-dihydroxy 2-amino-4-octadecene), an 18-carbon unsaturated amino alcohol which is the most abundant sphingoid base in mammals. Amide linkage of a fatty acid to sphingosine yields ceramides. Esterification of phosphocholine to ceramides yields sphingomyelin, and ceramide glycosylation yields glycosylceramides. Introduction of sialic acid residues yields gangliosides. These molecules appear to be essential components of cell membranes, and intermediates in the pathways of sphingolipid synthesis and breakdown modulate processes including apoptosis and T cell trafficking. While sphingolipids are abundant in a wide variety of foodstuffs, these dietary molecules are mostly degraded by the intestinal flora and intestinal enzymes. The body primarily depends on de novo synthesis for its sphingolipid supply (Hannun and Obeid 2008; Merrill 2002). De novo synthesis proceeds in four steps: the condensation of palmitoyl-CoA and serine to form 3-ketosphinganine, the reduction of 3-ketosphinganine to sphinganine, the acylation of sphinganine with a long-chain fatty acyl CoA to form dihydroceramide, and the desaturation of dihydroceramide to form ceramide. Other sphingolipids involved in signaling are derived from ceramide and its biosynthetic intermediates. These include sphinganine (dihydrosphingosine) 1-phosphate, phytoceramide, sphingosine, and sphingosine 1-phosphate. Sphingomyelin is synthesized in a single step in the membrane of the Golgi apparatus from ceramides generated in the endoplasmic reticulum (ER) membrane and transferred to the Golgi by CERT (ceramide transfer protein), an isoform of COL4A3BP that is associated with the ER membrane as a complex with PPM1L (protein phosphatase 1-like) and VAPA or VAPB (VAMP-associated proteins A or B). Sphingomyelin synthesis appears to be regulated primarily at the level of this transport process through the reversible phosphorylation of CERT (Saito et al. 2008).
4-hydroxybenzoate polyprenyltransferase, mitochondrial (COQ2) catalyses the combination of 4-hydroxybenzoic acid, aka para-hydroxybenzoic acid (PHB) with the polyisoprenoid tail all-trans-decaprenyl diphosphate (all-E-10PrP2) to form 3-decaprenyl-4-hydroxybenzoic acid (DHB) (Forsgren et a l. 2004, Tekle et al. 2008). This reaction is irreversible and occurs in the mitochondria.
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).
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).
Three tRNA binding sites in rabbit liver ribosomes and role of the intrinsic ATPase in 80S ribosomes from higher eukaryotes
Aldo-keto reductase family 1 member C3 (AKR1C3) aka PGFS is the enzyme involved in NADPH-dependent prostaglandin D2 11-keto reductase activity of reducing prostaglandin D2 (PGD2) to 11-epi-Prostaglandin F2alpha (11-epi-PGF2a) (Liston & Roberts 1985, Koda et al. 2004).
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.
Aldo-keto reductase family 1 member C3 (AKR1C3) aka PGFS is responsible for the reduction of prostaglandin H2 (PGH2) to prostaglandin F2alpha (PGF2a) (Suzuki-Yamamoto et al. 1999, Komoto et al. 2004, Komoto et al. 2006). There is an additional way of achieving this reaction involving the prostamide/prostaglandin F synthase, FAM213B and thioredoxin (TRX).
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).
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).
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).
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).
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).
Eicosanoids, oxygenated, 20-carbon fatty acids, are autocrine and paracrine signaling molecules that modulate physiological processes including pain, fever, inflammation, blood clot formation, smooth muscle contraction and relaxation, and the release of gastric acid. Eicosanoids are synthesized in humans primarily from arachidonic acid (all-cis 5,8,11,14-eicosatetraenoic acid) that is released from membrane phospholipids. Once released, arachidonic acid is acted on by prostaglandin G/H synthases (PTGS, also known as cyclooxygenases (COX)) to form prostaglandins and thromboxanes, by arachidonate lipoxygenases (ALOX) to form leukotrienes, epoxygenases (cytochrome P450s and epoxide hydrolase) to form epoxides such as 15-eicosatetraenoic acids, and omega-hydrolases (cytochrome P450s) to form hydroxyeicosatetraenoic acids (Buczynski et al. 2009, Vance & Vance 2008). Levels of free arachidonic acid in the cell are normally very low so the rate of synthesis of eicosanoids is determined primarily by the activity of phospholipase A2, which mediates phospholipid cleavage to generate free arachidonic acid. The enzymes involved in arachidonic acid metabolism are typically constitutively expressed so the subset of these enzymes expressed by a cell determines the range of eicosanoids it can synthesize. Eicosanoids are unstable, undergoing conversion to inactive forms with half-times under physiological conditions of seconds or minutes. Many of these reactions appear to be spontaneous.
The final step in the beta-oxidation process is the thiolytic cleavage of 1-(3-oxo-6Z,9Z,12Z,15Z,18Z,21Z-tetracosahexaenoyl)-CoA to form docosahexaenoyl-CoA (DHA-CoA). This step is catalysed by both sterol carrier protein X (SCPx) and the classic 3-ketoacyl-CoA thiolase (this reaction) (Ferdinandusse et al. 2001).
3-hydroxy tetracosahexaenoyl-CoA undergoes dehydrogenation to form 1-(3-oxo-6Z,9Z,12Z,15Z,18Z,21Z-tetracosahexaenoyl)-CoA, catalysed by DBP. DBP is a bifunctional enzyme, involved in the hydration of a variety of trans-2,3-dehydroacyl-CoA's but also mediating dehydrogenation of a variety of 3-hydroxyacyl-CoA's (Jiang et al. 1997).
Alpha-linolenic acid (ALA, 18:3(n-3)) is an omega-3 fatty acid, supplied through diet as it cannot be synthesized by humans. ALA has an important role in human health. It is converted to long chain more unsaturated n-3 fatty acids by a series of alternating desaturation and elongation reactions. Omega-3 products of ALA such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) reduce inflammation and may help lower risk of chronic diseases, such as heart disease and arthritis. All the desaturation and elongation steps occur in the endoplasmic reticulum (ER) except for the final step which requires translocation to peroxisomes for partial beta-oxidation. The alpha-linolenic acid pathway involves the following steps: 18:3(n-3)--> 18:4(n-3)-->20:4(n-3)-->20:5(n-3)-->22:5(n-3)-->24:5(n-3)-->24:6(n-3)-->22:6(n-3). Two desaturation enzymes are involved in this process: delta-6 desaturase that converts 18:3(n-3) to 18:4(n-3) and 24:5(n-3) to 24:6(n-3) respectively, delta-5 desaturase 20:4(n-3) to 20:5(n-3). (Sprecher 2002).
DHA-CoA preferentially moves back to the ER, perhaps as a free fatty acid. This conversion is usually catalysed by acyl-CoA thioesterases (ACOTs). No specific acyl-CoA thioesterase enzyme has been identified for the peroxisomal metabolism of DHA-CoA, but the peroxisomal ACOT8 has a wide substrate specificity and is likely to be responsible (Ferdinandusse et al. 2003, Hunt & Alexson. 2008).
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.
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).
Delta2-THA-CoA is hydrated to 3-hydroxyacyl-CoA intermediate 1-(3-hydroxy-6Z,9Z,12Z,15Z,18Z,21Z-tetracosahexaenoyl)-CoA by HSD17B4/DBP (d-bifunctional protein) dimer.
The 24-carbon tetracosahexaenoyl-CoA (6,9,12,15,18,21-24:6(n-3) is transported to peroxisomes to undergo a putative single cycle of peroxisomal beta-oxidation, producing Docosahexaenoic Acid (DHA) (Sprecher 2002, Luthria et al. 1996).
Prior to this reaction all the enzymes involved in the desaturation and elongation of linoleic acid are located in the ER, but for this last step tetracosapentaenoyl-CoA must be transferred to the peroxisomes for partial beta-oxidation to docosapentaenoyl-CoA (DPA-CoA, 4,7,10,13,16-22:5(n-6)) (Su et al. 2001).
Transformation and Stat activation by derivatives of FGFR1, FGFR3, and FGFR4
Linoleic acid (LA, 18:2(n-6)) is an omega-6 fatty acid obtained through diet, mainly from vegetable oils. Omega-6 fatty acids helps stimulate skin and hair growth, maintain bone health, regulate metabolism, and maintain the reproductive system. All the desaturation and elongation steps occur in the endoplasmic reticulum (ER) except for the final step which requires translocation to peroxisomes for partial beta-oxidation. The linoleic acid pathway involves the following steps: 18:2(n-6)-->18:3(n-6)--> 20:3(n-6)-->20:4(n-6)-->22:4(n-6)-->24:4(n-6)-->24:5(n-6)-->22:5(n-6). Two desaturation enzymes are involved in this process: delta-6 desaturase which converts 18:2(n-6) to 18:3 (n-6) and 24:4(n-6) to 24:5(n-6) respectively, and delta-5 desaturase which converts 20:3(n-6) to 20:4(n-6). (Sprecher 2002).
There are two major classes of polyunsaturated fatty acids (PUFAs): the omega-3 (n-3) and the omega-6 (n-6) fatty acids, where the number corresponds to the position of the first double bond proximate to the methyl end of the fatty acid. Omega-3 and omega-6 fatty acids are considered essential fatty acids. Humans cannot synthesize them, instead they are supplied through diet. Linoleic acid (LA, 18:2(n-6)), a major component of omega-6 fatty acids and alpha-linolenic acid (ALA, 18:2(n-3)) a major component of omega-3 fatty acids are the two main dietary essential fatty acids (EFAs) in humans. ALA and LA obtained from diet are converted in the body into their longer chain and more unsaturated omega-3 and omega-6 products by a series of desaturation and elongation steps. Metabolism of ALA and LA to their corresponding products is mediated via common enzyme systems. In humans ALA is finally converted to docosahexaenoic acid (DHA, C22:6(n-3)), and LA is converted to docosapentaenoic acid (DPA, C22:5(n-6)). The intermediary omega-3 and omega-6 series fatty acids play a significant role in health and disease by generating potent modulatory molecules for inflammatory responses, including eicosanoids (prostaglandins, and leukotrienes), and cytokines (interleukins) and affecting the gene expression of various bioactive molecules (Kapoor & Huang 2006, Sprecher 2002, Burdge 2006).
At the late endosome membrane, the PAS complex, consisting of FYVE finger-containing phosphoinositide kinase (PIKFYVE), yeast VAC14 homologue (VAC14), and polyphosphoinositide phosphatase aka SAC3 (FIG4), binds to the membrane via PIKFYVE's FYVE finger. The PIKFYVE kinase component phosphorylates phosphatidylinositol (PI) to phosphatidylinositol 5-phosphate (PI5P) (Sbrissa et al. 1999, Sbrissa et al. 2002). The PAS complex is present in the cytosol and is recruited to the membrane.
At the late endosome membrane, myotubularin (MTM1), myotubularin-related protein 2 (MTMR2), myotubularin-related protein 4 (MTMR4), and myotubularin-related protein 7 (MTMR7) dephosphorylate phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) to phosphatidylinositol 5-phosphate (PI5P). The following lists the above proteins with their corresponding literature references: MTM1 (Cao et al. 2007, Cao et al. 2008, Tsujita et al. 2004, Tronchere et al. 2004), MTMR2 (Cao et al. 2008), MTMR4 (Lorenzo et al. 2006), and MTMR7 (Mochizuki & Majerus 2003, Lorenzo et al. 2006).
At the late endosome membrane, the PAS complex, consisting of FYVE finger-containing phosphoinositide kinase (PIKFYVE), yeast VAC14 homologue (VAC14), and polyphosphoinositide phosphatase aka SAC3 (FIG4), binds to the membrane via PIKFYVE's FYVE finger. The FIG4 phosphatase component dephosphorylates phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) to phosphatidylinositol 3-phosphate (PI3P) (Sbrissa et al. 2007, Sbrissa et al. 2008).
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 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).
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-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).
Tubulin subunits exist in an activated conformational state generated and maintained by protein cofactors
At the early endosome membrane, the PAS complex, consisting of FYVE finger-containing phosphoinositide kinase (PIKFYVE), yeast VAC14 homologue (VAC14), and polyphosphoinositide phosphatase aka SAC3 (FIG4), binds to the membrane via PIKFYVE's FYVE finger. The FIG4 phosphatase component dephosphorylates phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) to phosphatidylinositol 3-phosphate (PI3P) (Sbrissa et al. 2007, Sbrissa et al. 2008).
At the 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).
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).
1,2-Dihydroxy-3-oxo-methylthiopentene (1-)
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).
Macromolecular assemblage of aminoacyl-tRNA synthetases: identification of protein-protein interactions and characterization of a core protein
Peroxisomal straight-chain Acyl-CoA oxidase and D-bifunctional protein are essential for the retroconversion step in docosahexaenoic acid synthesis
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Novel tryptophan catabolic enzyme IDO2 is the preferred biochemical target of the antitumor indoleamine 2,3-dioxygenase inhibitory compound D-1-methyl-tryptophan
Molecular cloning of human mevalonate kinase and identification of a missense mutation in the genetic disease mevalonic aciduria
Characterization and functional analysis of the nucleotide binding fold in human peroxisomal ATP binding cassette transporters
a-ketoisocaproate, a-keto b-methylvalerate, a-ketoisovalerate
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Characterization of recombinant human nicotinamide mononucleotide adenylyl transferase (NMNAT), a nuclear enzyme essential for NAD synthesis
Functional interactions between Sae2 and the Mre11 complex
The family of glycogen phosphorylases: structure and function
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Both human ferredoxins 1 and 2 and ferredoxin reductase are important for iron-sulfur cluster biogenesis
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5,10-methylenetetrahydrofolate polyglutamate
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Translocation of Cyclin B1:phospho-Cdc2 complexes to the nucleus
Loading of PCNA - Sliding Clamp Formation
RFC dissociates after sliding clamp formation
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Ubiquitinated Cdc6 is degraded by the proteasome
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Mcm4,6,7 trimer forms and associates with the replication fork
Rearrangement and mobilization of Mcm2-7
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The MCM2-7 complex is the putative replicative helicase that unwinds replication forks. While an S.erevisiae MCM hexameric complex consisting of one copy of each of the six subunits has been reconstituted in vitro from purified subunits (Davey et al. 2003), an active helicase can be assembled with three of the six MCM proteins, MCM4, MCM6 and MCM7, in human (Ishimi,1997), S. pombe (Lee and Hurwitz, 2001) and S. cerevisiae (Kaplan et al., 2003). However, this in vitro reaction may not represent the in vivo situation. In vivo experiments suggest that all six subunits are required at the replication fork (Labib et al., 2000; reviewed by Tye and Sawyer, 2000).
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Multiple proteins are localized at replication fork
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Recruitment of Telomerase RNP to the Telomeric Chromosome End
Phosphorylation of Cdh1 by Cyclin B1:Cdc2
Cytosolic PLK1 translocates to the nucleus
Translocation of CRS phosphorylated Cyclin B1:Cdc2 complexes
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Phosphorylation of M phase proteins by active Cyclin B1:Cdc2 complexes
Molybdenum cofactors, enzymes and pathways
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Translocation of Cyclin B1:phospho-Cdc2 to the cytoplasm
Function and biogenesis of iron-sulphur proteins
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Phosphorylation of Cyclin B1 in the CRS domain
CAK-mediated phosphorylation of Cyclin B1:Cdc2 complexes
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The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer on the G strand of the telomere
RFC binding displaces Pol Alpha on the C-strand of the telomere
Loading of PCNA - Sliding Clamp Formation on the C-strand of the telomere
RFC dissociates after sliding clamp formation on the C-strand of the telomere
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
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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Association of phospho-L13a with GAIT element of Ceruloplasmin mRNA
Dissociation of L13a from the 60s ribosomal subunit
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Cargo, Sec31p:Sec13p, and v-SNARE recruitment
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RNA Polymerase II Transcription Initiation And Promoter Clearance
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PKA catalytic subunit translocates to the nucleus
cAMP induces dissociation of inactive PKA tetramers
Nuclear translocation of phospho-ERK-1 dimer
Intraphagosomal pH is lowered to 5 by V-ATPase
Nuclear translocation of phospho-ERK-2 dimer
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Initiation of mammalian protein synthesis. II. The assembly of the initiation complex with purified initiation factors.
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Initiation of mammalian protein synthesis. I. Purification and characterization of seven initiation factors.
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Amino acid and oligopeptide SLC transporters
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The crystal structure of the human toll-like receptor 10 cytoplasmic domain reveals a putative signaling dimer
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FUNCTION ATP-dependent DNA helicase involved in excision repair of DNA damaged with UV light, bulky adducts, or cross-linking agents. Necessary for excision of pyrimidine dimers. Also unwinds DNA/RNA duplexes. Plays an essential role in the cell viability. Involved in the maintenance of the fidelity of DNA replication. Acts as component of the general transcription and DNA repair factor IIH (TFIIH) core, which is essential for both basal and activated transcription, and is involved in nucleotide excision repair (NER) of damaged DNA. TFIIH has CTD kinase and DNA-dependent ATPase activity, and is essential for polymerase II transcription in vitro.CATALYTIC ACTIVITY ATP + H(2)O = ADP + phosphate.SUBUNIT Component of the TFIIH core complex, which is composed of RAD3, SSL1, SSL2, TFB1, TFB2, TFB4 and TFB5.MISCELLANEOUS Present with 14400 molecules/cell in log phase SD medium.SIMILARITY Belongs to the helicase family. RAD3/XPD subfamily.SIMILARITY Contains 1 helicase ATP-binding domain.
Phosphate bond hydrolysis by NUDT proteins
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TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation
Cloning and functional expression of human aquaporin8 cDNA and analysis of its gene
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Vesicular tubular clusters between the ER and Golgi mediate concentration of soluble secretory proteins by exclusion from COPI-coated vesicles
Protein kinase C-theta (PKC theta): a key enzyme in T cell life and death
ABCG5 and ABCG8 are obligate heterodimers for protein trafficking and biliary cholesterol excretion
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Glycogenin protein and mRNA expression in response to changing glycogen concentration in exercise and recovery
Am J Physiol Endocrinol Metab 292:E1815-22
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Formation of a rate-limiting intermediate in 5S RNA gene transcription
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Pathogen recognition with Toll-like receptors
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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
GLUT2 in pancreatic and extra-pancreatic gluco-detection (review)
The extended GLUT-family of sugar/polyol transport facilitators: nomenclature, sequence characteristics, and potential function of its novel members (review)
Intracellular mechanisms of antigen cross presentation in dendritic cells
FUNCTION Mitochondrial intermembrane chaperone that participates in the import and insertion of some multi-pass transmembrane proteins into the mitochondrial inner membrane. Also required for the transfer of beta-barrel precursors from the TOM complex to the sorting and assembly machinery (SAM complex) of the outer membrane. Acts as a chaperone-like protein that protects the hydrophobic precursors from aggregation and guide them through the mitochondrial intermembrane space. The TIM8-TIM13 complex is non essential and only mediates the import of few proteins under precise conditions, while the predominant TIM9-TIM10 70 kDa complex is crucial and mediates the import of much more proteins. Strictly required for import of TIM23 in some conditions, when a low membrane potential exists in the mitochondria.SUBUNIT Heterohexamer; composed of 3 copies of TIM8 and 3 copies of TIM13, named soluble 70 kDa complex. Associates with the TIM22 complex, whose core is composed of TIM18, TIM22 and TIM54. Interacts with the transmembrane regions of multi-pass transmembrane proteins in transit.SIMILARITY Belongs to the small Tim family.
Factors involved in megakaryocyte development and platelet production
cDNA cloning, expression and characterization of human prostaglandin F synthase
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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).
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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).
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.
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.
After being phosphorylated, p-ERK1/2 dissociate from MEK1/2 and dimerize.
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.
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).
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.
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).
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.
The pathway "Signaling by EGFR in Cancer" shows "Signaling by constitutively active EGFR" in parallel with "Signaling by EGFR". This allows users to compare signaling by constitutively active EGFR cancer mutants with the wild-type EGFR protein. Red lines emphasize cancer related events and physical entities, while wild-type entities and events are shaded. Please refer to "Signaling by constitutively active EGFR" and "Signaling by EGFR" for detailed pathway summations.
Signaling by EGFR is frequently activated in cancer through either genomic amplification of the EGFR locus, resulting in over-expression of the wild-type protein, or through activating mutations in the coding sequence of the EGFR gene, resulting in expression of a constitutively active mutant protein. Epidermal growth factor receptor kinase domain mutants are present in ~16% of non-small-cell lung cancers (NSCLCs), but are also found in other cancer types, such as breast cancer, colorectal cancer, ovarian cancer and thyroid cancer. EGFR kinase domain mutants harbor activating mutations in exons 18-21 which code for the kinase domain (amino acids 712-979) . Small deletions, insertions or substitutions of amino acids within the kinase domain lock EGFR in its active conformation in which the enzyme can dimerize and undergo autophosphorylation spontaneously, without ligand binding (although ligand binding ability is preserved), and activate downstream signaling pathways that promote cell survival (Greulich et al. 2005, Zhang et al. 2006, Yun et al. 2007, Red Brewer et al. 2009). In glioblastoma, the most prevalent EGFR mutation, present in ~25% of tumors, is the deletion of the ligand binding domain of EGFR, accompanied with amplification of the mutated allele, which results in over-expression of the mutant protein known as EGFRvIII. EGFRvIII mutant is not able to bind a ligand, but dimerizes and autophosphorylates spontaneously and is therefore constitutively active (Fernandes et al. 2001). Point mutations in the extracellular domain of EGFR are also frequently found in glioblastoma. Similar to kinase domain mutations, point mutations in the extracellular domain result in constitutively active EGFR proteins that signal in the absence of ligands, but ligand binding ability and responsiveness are preserved (Lee et al. 2006). Both EGFR kinase domain mutants and EGFRvIII mutant need to maintain association with the chaperone heat shock protein 90 (HSP90) for proper functioning (Shimamura et al. 2005, Lavictoire et al. 2003). CDC37 is a co-chaperone of HSP90 that acts as a scaffold and regulator of interaction between HSP90 and its protein kinase clients. CDC37 is frequently over-expressed in cancers involving mutant kinases and acts as an oncogene (Roe et al. 2004, reviewed by Gray Jr. et al. 2008). Over-expression of the wild-type EGFR or EGFR cancer mutants results in aberrant activation of downstream signaling cascades, namely RAS/RAF/MAP kinase signaling and PI3K/AKT signaling, and possibly signaling by PLCG1, which leads to increased cell proliferation and survival, providing selective advantage to cancer cells that harbor activating mutations in the EGFR gene (Sordella et al. 2004, Huang et al. 2007). While growth factor activated wild-type EGFR is promptly down-regulated by internalization and degradation, cancer mutants of EGFR demonstrate prolonged activation (Lynch et al. 2004). Association of HSP90 with EGFR kinase domain mutants negatively affects CBL-mediated ubiquitination, possibly through decreasing the affinity of EGFR kinase domain mutants for phosphorylated CBL, so that CBL dissociates from the complex upon phosphorylation and cannot perform ubiquitination (Yang et al. 2006, Padron et al. 2007). EGFRvIII mutant does not autophosorylate on the tyrosine residue Y1045, a docking site for CBL, and is therefore unable to recruit CBL ubiquitin ligase, which enables it to escape degradation (Han et al. 2006). Various molecular therapeutics are being developed to target aberrantly activated EGFR in cancer. Non-covalent (reversible) small tyrosine kinase inhibitors (TKIs), such as gefitinib and erlotinib, selectively bind kinase domain of EGFR, competitively inhibiting ATP binding and subsequent autophosphorylation of EGFR dimers. EGFR kinase domain mutants sensitive to non-covalent TKIs exhibit greater affinity for TKIs than ATP compared with the wild-type EGFR protein, and are therefore preferential targets of non-covalent TKI therapeutics (Yun et al. 2007). EGFR proteins that harbor point mutations in the extracellular domain also show sensitivity to non-covalent tyrosine kinase inhibitors (Lee et al. 2006). EGFR kinase domain mutants harboring small insertions in exon 20 or a secondary T790M mutation are resistant to reversible TKIs (Balak et al. 2006) due to increased affinity for ATP (Yun et al. 2008), and are targets of covalent (irreversible) TKIs that form a covalent bond with EGFR cysteine residue C397. However, effective concentrations of covalent TKIs also inhibit wild-type EGFR, causing severe side effects (Zhou et al. 2009). Hence, covalent TKIs have not shown much promise in clinical trials (Reviewed by Pao and Chmielecki in 2010). Recombinant monoclonal antibody Cetuximab acts as an antagonist of EGFR ligand binding, and is approved for the treatment of tumors that over-express wild-type EGFR receptor (Cunningham et al. 2004, Li et al. 2005, Burtness et al. 2005).
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.
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.
SRP-dependent cotranslational protein targeting to membrane
The epidermal growth factor receptor (EGFR) is one member of the ERBB family of transmembrane glycoprotein tyrosine receptor kinases (RTK). Binding of EGFR to its ligands induces conformational change that unmasks the dimerization interface in the extracellular domain of EGFR, leading to receptor homo- or heterodimerization at the cell surface. Dimerization of the extracellular regions of EGFR triggers additional conformational change of the cytoplasmic EGFR regions, enabling the kinase domains of two EGFR molecules to achieve the catalytically active conformation. Ligand activated EGFR dimers trans-autophosphorylate on tyrosine residues in the cytoplasmic tail of the receptor. Phosphorylated tyrosines serve as binding sites for the recruitment of signal transducers and activators of intracellular substrates, which then stimulate intracellular signal transduction cascades that are involved in regulating cellular proliferation, differentiation, and survival. Recruitment of complexes containing GRB2 and SOS1 to phosphorylated EGFR dimers either directly, through phosphotyrosine residues that serve as GRB2 docking sites, or indirectly, through SHC1 recruitment, promotes GDP to GTP exchange on RAS, resulting in the activation of RAF/MAP kinase cascade. Binding of complexes of GRB2 and GAB1 to phosphorylated EGFR dimers leads to formation of the active PI3K complex, conversion of PIP2 into PIP3, and activation of AKT signaling. Phospholipase C-gamma1 (PLCG1) can also be recruited directly, through EGFR phosphotyrosine residues that serve as PLCG1 docking sites, which leads to PLCG1 phosphorylation by EGFR and activation of DAG and IP3 signaling. EGFR signaling is downregulated by the action of ubiquitin ligase CBL. CBL binds directly to the phosphorylated EGFR dimer through the phosphotyrosine Y1045 in the C-tail of EGFR, and after CBL is phosphorylated by EGFR, it becomes active and ubiquitinates phosphorylated EGFR dimers, targeting them for degradation. For a recent review of EGFR signaling, please refer to Avraham and Yarden, 2011.
GAB1 is recruited to the activated EGFR indirectly, through GRB2. GAB1 acts as an adaptor protein that enables formation of an active PIK3, through recruitment of PIK3 regulatory subunit PIK3R1 (also known as PI3Kp85), which subsequently recruits PIK3 catalytic subunit PIK3CA (also known as PI3Kp110). PIK3, in complex with EGFR, GRB2 and GAB1, catalyzes phosphorylation of PIP2 and its conversion to PIP3, which leads to the activation of the AKT signaling.
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.
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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.
In vitro evidence for the dual function of Alg2 and Alg11: essential mannosyltransferases in N-linked glycoprotein biosynthesis
GMP capped mRNA transcript dissociates from GT for further modification.
The diphosphate 5'-end of the mRNA is joined to the GMP, releasing it from the enzyme. At this time, it is unclear how the RNA diphosphate end is transferred from the active site of the triphosphatase to the guanylyltransferase site. The covalent enzyme-GMP complex can form in the absence of RNA. Guanylyltransferase (GT) catalyzed second reaction can be represented as:ppN(pN)n + GTP -> GpppN(pN)n + PPi
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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.
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 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)
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.
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.
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).
Cytosolic PPA1 (pyrophosphatase (inorganic) 1) catalyzes the hydrolysis of pyrophosphate to yield two molecules of orthophosphate. The enzyme, a homodimer, requires Mg++ for activity (Fisher et al. 1974; Pynes and Younathan 1967; Thuiller et al. 1978).
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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).
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).
NLRs join TLRs as innate sensors of pathogens
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The gene defects which cause diseases related to the retinoid cycle are described here (Travis et al. 2007, Palczewski 2010, Fletcher et al. 2011, den Hollander et al. 2008).
Reversible lysine acetylation controls the activity of the mitochondrial enzyme acetyl-CoA synthetase 2
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 outer segment of photoreceptor cells is shed every 10-14 days to be completely replaced. The shed material is phagocytosed and transferred to the retinal pigment epithelium (RPE). Diretinoid-pyridinium-phosphatidylethanolamine (A2PE) can be hydrolysed to diretinoid-pyridinium-ethanolamine (A2E), a prominent constituent of lipofuscin (the material deposited in retinal tissue which accumulates over time and is implicated in macular degeneration). Evidence suggests this happens before transfer to RPE cells as part of the phagocytosed outer segment. A2E has been detected in outer segments (Ben-Shabat et al. 2002) and an N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D (NAPEPLD) activity detected in rat, mouse and human proteins (Okamoto et al. 2004, Ueda et al. 2005, Wang et al. 2006). This activity has been shown to hydrolyse A2PE to A2E in bovine outer segments before phagocytosis and transfer to RPE cells, suggesting A2PE is hydrolysed to A2E in photoreceptor outer segment membranes (Sparrow et al. 2003, Salvador & Giusto 1998).
Lipofuscin is a yellow-brown pigment grain composed mainly of lipids but also sugars and certain metals. Accumulation of lipofuscin is associated with degenerative diseases such as Alzheimer's disease, Parkinson's disease, chronic obstructive pulmonary disease and retinal macular degeneration. A prominent component of lipofuscin in retinal pigment epithelial (RPE) cells is the bisretinoid A2E (di-retinoid-pyridinium-ethanolamine), the end-product of the condensation of 2 molecules of all-trans-retinal (atRAL) and phosphatidylethanolamine (PE) in photoreceptor outer disc membranes. Once formed, A2E is phagocytosed, together with outer segments (Kevany & Palczewski 2010), to RPE where it accumulates. There is no evidence as yet to indicate that A2E can be catabolised (Sparrow et al. 2012, Sparrow et al. 2010). A simplified biosynthetic pathway for A2E is described here.
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."
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 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'.
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.
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).
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At the beginning of this reaction, 1 molecule of 'ATAC B Complex' is present. At the end of this reaction, 1 molecule of 'U4 ATAC snRNP', and 1 molecule of 'ATAC C Complex' are present. This reaction takes place in the 'nucleus'.
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 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.
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.
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'.
Hydrolytic deamination of adenosine leads to inosine. Ammonia is presumed to be released during this reaction.
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:
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 addition to the methylation of the 5'-cap, there is methylation of internal nucleotides in the mRNA. This methylation can occur in translated and untranslated regions. One to three methyl groups have been seen per mRNA molecule, but methylation is non-stoichiometric. The most frequent methylation observed is at the N6 position of adenosine. The function of mRNA internal methylation, if any, is unknown.
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.
Targeting the oncogene and kinome chaperone CDC37
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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 '.
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 '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'.
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 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.
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'.
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'.
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'.
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'.
CD28/CTLA-4 and CD80/CD86 families: signaling and function
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Simultaneous blockade of NFkappaB, JNK, and p38 MAPK by a kinase-inactive mutant of the protein kinase TAK1 sensitizes cells to apoptosis and affects a distinct spectrum of tumor necrosis factor [corrected] target genes
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The human lamin B receptor/sterol reductase multigene family
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).
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).
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.
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.
The carboxylation of pyruvate to form oxaloacetate, catalyzed by mitochondrial pyruvate carboxylase, is an irreversible and allosterically regulated reaction (Jitrapakdee and Wallace 1999).
SLC25A10, the mitochondrial dicarboxylate carrier protein in the inner mitochondrial membrane, mediates the reversible exchange of mitochondrial malate for cytosolic phosphate (Fiermonte et al. 1999).
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
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).
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.
FUNCTION General activator of RNA polymerase III transcription. Interacts with TBP. Binds to Pol III subunit C34 and to the TAU135 component of TFIIIC.SUBUNIT TFIIIB comprises the TATA-binding protein (TBP), the B-related factor (BRF) and the B" component (TFC5).MISCELLANEOUS Present with 4330 molecules/cell in log phase SD medium.SIMILARITY Belongs to the TFIIB family.SIMILARITY Contains 1 TFIIB-type zinc finger.
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.
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).
Structural basis of Wnt recognition by Frizzled
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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G proteins and opioid receptor-mediated signalling
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GLUT (glucose transporter) homotetramers associated with the plasma membrane mediate the facilitated diffusion of glucose between the extracellular space and the cytosol. Four human GLUT isoforms have been identified, members of a larger family of transporter proteins (Joost et al. 2002), encoded by the SCLC2A1, 2, 3, and 4 genes. Conserved sequence motifs in the GLUT proteins suggest the existence of shared structural features confirmed by in situ labeling and mutagenesis studies. Each GLUT protein has twelve membrane spanning domains organized to form an aqueous channel. While monomeric protein can form such a channel and transport glucose, kinetic studies suggest that the functional form of the protein is a homotetramer. Different GLUT proteins are expressed in different tissues. GLUT1 is expressed by many cell types, notably endothelial cells, red blood cells and cells of the brain. Its low Km for glucose (~1 mM) relative to normal blood glucose concentration (~5 mM) allows these cells to take up glucose independent of changes in blood glucose levels. Its abundance in red blood cells has allowed it to be purified and biochemically characterized (Hruz and Mueckler 2001; Liu et al. 2001). Cytosolic ATP associates with GLUT1 and inhibits its glucose transporter activity. GLUT2 is expressed on hepatocytes and pancreatic beta cells. Because of its high Km for glucose (~15-20 mM), GLUT2-mediated glucose uptake normally occurs only in the fed state, when its rate is proportional to blood glucose concentration. This feature of the transporter is thought to enable efficient uptake of large amounts of glucose by the liver in the fed state, and to allow it to function as part of a glucose sensor coupled to insulin release in pancreatic beta cells (Thorens 2001). GLUT2 also mediates glucose export from liver cells when gluconeogenesis is underway (Colville et al. 1993; Santer et al. 1997; Wu et al. 1998). GLUT3 is expressed by cells of the brain and possibly other cell types with a high constitutive requirement for glucose. Its low Km for glucose (~1.5 mM) allows these cells to import glucose independent of fluctuations in blood glucose levels (Colville et al. 1993). GLUT4, like GLUT1 and 3, has a high affinity for glucose. GLUT4 is abundant in cells of skeletal muscle and adipose tissue. GLUT4 molecules are translocated from an intracellular store to the cell surface in response to increased insulin levels (Bryant et al. 2002; Fukumoto et al. 1989).
Processing of mRNA encompasses the capping of mRNA, processing of mRNAs with and without introns, and also modification of mRNA, as in mRNA editing.
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 reversible facilitated diffusion of fructose, galactose, and glucose from the cytosol to the extracellular space is mediated by the GLUT2 transporter in the plasma membrane. In the epithelial cells of the small intestine, the basolateral localization of GLUT2 (Thorens et al. 1990) enables hexose sugars derived from the diet and taken up by the action of the SGLT1 and GLUT5 transporters to be released into the circulation. The specificity of the GLUT2 transporter has been established directly through biochemical assays of purified recombinant proteins (Colville et al. 1993; Wu et al. 1998) and indirectly through studies of patients deficient in GLUT2 transporter protein (Santer et al. 1997).
The reversible transport of extracellular fructose into the cytosol is mediated by GLUT5. In the small intestine, GLUT5 is localized on the lumenal surfaces of enterocytes (Davidson et al. 1992) and thus mediates the uptake of dietary fructose, which can be released into the circulation in a separate transport step mediated by basolaterally localized GLUT2. The specificity of GLUT5 has been worked out by studying sugar transport in Xenopus oocytes expressing recombinant human GLUT5 protein (Burant et al. 1992).
GLUT1:ATP complexes reversibly dissociate, restoring the glucose transport activity of GLUT1 glucose transport, with the result that depletion of cellular ATP leads to increased glucose uptake (Blodgett et al. 2007).
Cytosolic glucokinase and the three isoforms of hexokinase catalyze the irreversible reaction of glucose and ATP to form glucose 6 phosphate and ADP. In the body glucokinase is found only in hepatocytes and pancreatic beta cells. Glucokinase and the hexokinase enzymes differ in that glucokinase has a higher Km than the hexokinases and is less readily inhibited by the reaction product. As a result, glucokinase should be inactive in the fasting state when glucose concentrations are low but in the fed state should have an activity proportional to glucose concentration. These features are thought to enable efficient glucose uptake and retention in the liver, and to function as a sensor of glucose concentration coupled to insulin release in pancreatic beta cells (Thorens 2001). Glucokinase mutations are associated with MODY2, a heritable early onset form of type II diabetes (Tanizawa et al. 1991; Takeda et al. 1993). Three human hexokinase enzymes have been characterized, HK1 (Aleshin et al. 1998), HK2 (Lehto et al. 1995), and HK3 (Rijksen at al. 1982).
Free glucokinase (GCK1) leaves the nucleus via the nuclear pore. While the GCK1 protein contains a nuclear export sequence motif, the molecular details of the GCK1 export process remain to be worked out (Shiota et al. 1999).
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).
GLUT2 (glucose transporter) homotetramers associated with the plasma membrane mediate the facilitated diffusion of glucose between the cytosol and the extracellular space, so glucose will leave cells when its intracellular concentration exceeds the extracellular one (Colville et al. 1993; Santer et al. 1997; Wu et al. 1998). In the body, such glucose export is a normal feature of liver cells when gluconeogenesis or glycogen breakdown is underway.
Cytosolic ATP reversibly associates with GLUT1. This association inhibits GLUT1 glucose transport (Blodgett et al. 2007).
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Glycogen synthase catalyzes the addition of glucose residues to the non-reducing end of a (1,4)-alpha-D-glucose multimer formed on glycogenin-1 or -2. (Here the addition of four glucose residues is annotated.) The enzyme is associated with glycogen granules in the cytosol. Glycogen synthase proteins are encoded by two human genes, GYS1 and GYS2. GYS1 protein is abundant in skeletal muscle while GYS2 is abundant in liver. The cytosolic location and glycogen synthase activity of GYS1 protein has been demonstrated in studies of wild-type and mutant proteins expressed in cultured cells in vitro (Cid et al. 2000). Defects in GYS1 protein in vivo are associated with deficient muscle glycogen synthesis and exercise intolerance in vivo (Kollberg et al. 2007). The enzymatic activity of purified GYS2 protein has been characterized experimentally (Westphal and Nuttall 1992). Defects in GYS2 protein in vivo are associated with fasting hypoglycemia and defective glycogen synthesis in the liver (Orho et al. 1998). Human GYS enzymes are inferred to be active as homotetramers, from detailed characterization of the homologous rabbit muscle enzyme (Soderling et al. 1970). GYS activity is regulated by phosphorylation. In its non-phosphorylated I form, annotated here, the enzyme is active with no added cofactor.
Glycogenin catalyzes its own reaction with UDP-glucose to synthesize an oligo (1,4)-alpha-D-glucosyl chain attached to itself (Mu et al. 1997; Mu and Roach 1998). The oligosaccharide is annotated here as containing four glucose residues. Glycogenin occurs as a homodimer associated with glycogen granules in the cytosol (Wilson et al. 2007). Glycogenin proteins are encoded by two human genes, GYG1 and GYG2. Multiple isoforms of each protein due to alternative splicing have been described, but none of these isoforms has yet been associated with a distinctive function. GYG1 protein is abundant in skeletal muscle while GYG2 is abundant in liver. Human GYG2 has been characterized biochemically (Mu et al. 1997; Mu and Roach 1998) but while the role of human GYG1 in muscle glycogen metabolism during exercise has been studied (Wilson et al. 2007), details of its structure and catalytic activities are inferred from those of its rabbit homologue (e.g., Gibbons et al. 2002).
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1-phosphatidyl-1D-myo-inositol 3,4-bisphosphates
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Cloning of a new aquaporin (AQP10) abundantly expressed in duodenum and jejunum
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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).
SLC25A12 and SLC25A13, located in the inner mitochondrial membrane, each mediate the exchange of cytosolic aspartate and mitochondrial glutamate. The exchange is physiologically irreversible because of the potential across the inner mitochondrial membrane (positive outside, negative inside). In the body, SLC25A12 (ARALAR1) is found mainly in heart, skeletal muscle, and brain, while SCL25A13 (CITRIN) is widely expressed but most abundant in liver (del Arco et al. 2000; Palmieri et al. 2001). Defects in SLC25A13 are associated with type II citrullinemia (Kobayashi et al. 1999).
SLC25A1, in the inner mitochondrial membrane, mediates the exchange of cytosolic citrate for mitochondrial phosphoenolpyruvate. The exchange is physiologically irreversible because of the potential of the inner mitochondrial membrane. The gene encoding human SLC25A1 has been cloned and its expression pattern has been characterized (Heisterkamp et al. 1995; Iacobazzi et al. 1997), but the biochemical details of the transport process are inferred from those worked out for the well-characterized rat system (Robinson 1971; Soling et al. 1971; Kleineke et al. 1973).
Cytosolic enolase dimer catalyzes the reversible reaction of phosphoenolpyruvate and water to form 2-phosphoglycerate. Three enolase isozymes have been purified and biochemically characterized. The alpha isoform is widely expressed (Giallongo et al. 1986). The beta isoform is expressed in muscle. Evidence for its function in vivo in humans comes from studies of a patient in whom a point mutation in the gene encoding the enzyme was associated specifically with reduced enolase activity in muscle extracts, and with other symptoms consistent with a defect in glycolysis (Comi et al. 2001). The gamma isoform of human enolase is normally expressed in neural tissue. It is not known to have distinctive biochemical functions, but is of possible clinical interest as a marker of some types of neuroendocrine and lung tumors (McAleese et al. 1988). Verma and Kurl (1993) identifed a possible fourth isoform, a "lung-specific" enolase whose expression is increased in response to dexamethasone treatment. The protein has not been biochemically characterized, however, nor have the levels of mRNA and protein in other tissues been examined. Thus, the observation that this protein is particularly similar in its predicted amino acid sequence to a duck crystallin (Wistow et al. 1988) raises the possibility that its normal function is unrelated to glycolysis.
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 conversion of glyceraldehyde-3-phosphate to dihydroxyacetone phosphate is catalyzed by cytosolic triose phosphate isomerase (Watanabe et al. 1996; Lu et al. 1984).
Cytosolic fructose-1,6-bisphosphatase catalyzes the physiologically irreversible hydrolysis of fructose-1,6-bisphosphate to form fructose-6-phosphate and orthophosphate. In the body, two isoforms of the enzyme are expressed, one ubiquitous and one muscle-specific (Kikawa et al. 1997; Tillmann and Eschrich 1998).
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).
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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TIM8:TIM13 Complex Chaperones Hydrophobic Proteins
The TIM8:TIM13 complex chaperones hydrophobic membrane proteins in the intermembrane space until their insertion into the inner or outer membrane (Leuenberger et al. 1999, Davis et al. 2000, Paschen et al. 2000, Curran et al. 2002, Wiedemann et al. 2004, Davis et al. 2007, Beverly et al. 2008, Hasson et al. 2010). Substrates of the TIM8:TIM13 complex include TIM23 (Leuenberger et al. 1999, Davis et al. 2000, Paschen et al. 2000, Curran et al. 2002, Davis et al. 2007, Beverly et al. 2008, Hasson et al. 2010) and TOM40 (Wiedemann et al. 2004).
Recycling of the general transcription factors during RNA polymerase II transcription.
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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
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MCTs mediate proton-coupled transport of monocarboxylates and ketone bodies
Conversion of succinate semialdehyde to succinate
Conversion of GABA to Succinate Semialdehyde
glutamate + NH4+ + ATP => glutamine + ADP + orthophosphate [GLUL]
5-hydroxyindole acetaldehyde to 5-hydroxyindole acetic acid
MIA40:ERV1 Catalyzes Formation of Disulfide Bonds
MIA40 catalyzes the oxidation of cysteine residues in precursor proteins in the intermembrane space to form cystine bonds (Chacinska et al. 2004, Terziyska et al. 2005, Milenkovic 2007, Sideris and Tokatlidis 2007, Terziyska et al. 2007, Misecke et al. 2008, Muller et al. 2008, Milenkovic et al. 2009, Stojanovski et al. 2008, Longen et al. 2009, Milenkovic et al. 2009, Reddehase et al. 2009, Sideris et al. 2009, Terziyska et al. 2009, Tienson et al. 2009, Bien et al. 2010). The electrons from the cysteine residues are transferred to MIA40, then to ERV1, and eventually to the respiratory chain (Allen et al. 2005, Bihlmaier et al. 2007). The interaction between MIA40 and ERV1 appears to be transitory (Stojanovski et al. 2008). Substrates of MIA40:ERV1 include COX17 (Mesecke et al. 2008, Sideris et al. 2009), COX19 (Bien et al. 2010), CMC2 (Longen et al. 2009), CMC3 (Longen et al. 2009), CMC4 (Longen et al. 2009), TIM13 (Terziyska et al. 2005, Muller et al. 2008, Stojanovski et al. 2008), TIM9 (Chacinska et al. 2004, Milenkovic et al. 2007, Stojanovski et al. 2008, Milenkovic et al. 2009), TIM10 (Chacinska et al. 2004, Milenkovic et al. 2007, Sideris and Tokatlidis 2007, Stojanovski et al. 2008, Terziyska et al. 2009, Milenkovic et al. 2009), CCS1 (Stojanovski et al. 2008, Reddehase et al. 2009), TIM8 (Muller et al. 2008, Stojanovski et al. 2008), and ERV1 (Terziyska et al. 2007).
TOM40:TOM70 Complex Imports Proteins Across Mitochondrial Outer Membrane
The TOM40:TOM70 Complex transports precursor proteins from the cytosol, across the outer membrane of the mitochondrion, and into the intermembrane space from where they may be targeted to all locations within the mitochondrion. TOM40, TOM22, TOM5, TOM6, and TOM7 form the general import pore across the membrane (Dekker et al. 1998). TOM20 and TOM22 interact with presequences on mitochondrial precursors (Haucke et al. 1995, Brix et al. 1997, Meisinger et al. 2001, Yamano et al. 2008). TOM70 interacts with hydrophobic sequences in mature internal regions of mitochondrial proteins (Schlossman et al. 1994, Brix et al. 1997, Yamamoto et al. 2009). Substrates of the TOM40:TOM70 complex include ATP1 (Yamamoto et al. 2009), ATP2 (Yamamoto et al. 2009), ATP9 (Hines et al. 1990), TOM40 (Yamamoto et al. 2009), SSC1 (Yamamoto et al. 2009), CIT1 (Yamamoto et al. 2009), ACO1 (Yamamoto et al. 2009), IDH1 (Yamamoto et al. 2009), BCS1 (Stan et al. 2003), CYT1 (Diekert et al. 2001), TIM54 (Kurz et al. 1999), TIM22 (Kurz et al. 1999), AAC (Sollner et al. 1990, Kurz et al. 1990, Kubrich et al. 1998, Endres et al. 1999, Truscott et al. 2002, Vasiljev et al. 2004), HSP60 (Yamano et al. 2008), CYB2 (Krayl et al. 2007). Some proteins such as Aco1, Atp1, Cit1, Idh1, and Atp2 contain both presequences that interact with TOM20 and mature regions that interact with TOM70 (Yamamoto et al. 2009).
DNA polymerase alpha:primase binds at the origin
DNA polymerase epsilon binds at the origin
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Differences in regulatory properties between human and rat glucokinase regulatory protein
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guanosine 5'-(3-(alpha-D-mannopyranosyl) dihydrogen diphosphate)
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Dephosphorylation of CK2-modified condensin I
DNA Replication Factor A (RPA) associates with the pre-replicative complex at the origin
Cdc45 associates with the pre-replicative complex at the origin
Orc1 associates with Orc4:Orc5:Orc3:Orc2:origin complexes
A mutation in the human ortholog of the Saccharomyces cerevisiae ALG6 gene causes carbohydrate-deficient glycoprotein syndrome type-Ic
FUNCTION DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNA. The RPC25/RPC8-RPC17/RPC9 subcomplex may bind Pol III transcripts emerging from the adjacent exit pore during elongation.SUBUNIT Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits. RPC25/RPC8 and RPC17/RPC9 form a Pol III subcomplex.MISCELLANEOUS Present with 752 molecules/cell in log phase SD medium.SIMILARITY Belongs to the eukaryotic RPB7/RPC8 RNA polymerase subunit family.
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Phosphorylation and activation of Chk1 by ATM
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Detection of damage during initiation of DNA synthesis in S-phase
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Myt-1 mediated phosphorylation of Cyclin B:Cdc2 complexes
Novel fibroblast growth factor receptor 3 (FGFR3) mutations in bladder cancer previously identified in non-lethal skeletal disorders
Ubiquitinated Orc1 is degraded by the proteasome
Assembly and export of MHC class I peptide ligands
Phosphorylated Cdc6 is exported from the nucleus
The polymerase component of DNA polymerase alpha:primase synthesizes a 20-nucleotide primer at the origin
The primase component of DNA polymerase:primase synthesizes a 6-10 nucleotide RNA primer at the origin
Phosphorylated Orc1 is ubiquitinated while still associated with chromatin
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Preprotein translocase of the outer mitochondrial membrane: molecular dissection and assembly of the general import pore complex
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SAM50 Complex Inserts Proteins into Outer Membrane
The SAM50 Complex (TOB55 Complex) inserts mainly beta-barrel proteins into the outer membrane after they have passed from the cytosol, through the TOM70:TOM40 complex, and into the intermembrane space (Kozjak et al. 2003, Ishikawa et al. 2004, Milenkovic et al. 2004, Waizenegger et al. 2004, Habib et al. 2007,Stojanovski et al. 2007, Kutik et al. 2008, Chan and Lithgow 2008). Substrates of the SAM50 complex include TOM40 (Kozjak et al. 2003, Ishikawa et al. 2004, Milenkovic et al. 2004, Waizenegger et al. 2004, Habib et al. 2007, Kutik et al. 2008, Chan and Lithgow 2008), MDM10 (Waizenegger et al. 2004, Habib et al. 2007, Kutik et al. 2008), Porin1 (Kozjak et al. 2003, Ishikawa et al. 2004, Milenkovic et al. 2004, Waizenegger et al. 2004, Habib et al. 2007, Kutik et al. 2008), and TOM22 (Stojanovski et al. 2007).
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TIM9:TIM10 Complex Chaperones Hydrophobic Proteins
The TIM9:TIM10 complex chaperones hydrophobic membrane proteins in the intermembrane space until their insertion into the inner or outer membrane (Koehler et al. 1998, Leuenberger et al. 1999, Luciano et al. 2001, Truscott et al. 2002, Vasiljev et al. 2004, Wiedemann et al. 2004, Davis et al. 2007, Baker et al. 2009, Hasson et al. 2010). Substrates of the TIM9:TIM10 complex include AAC (Koehler et al. 1998, Leuenberger et al. 1999, Luciano et al. 2001, Truscott et al. 2002, Vasiljev et al. 2004, Baker et al. 2009, Hasson et al. 2010), TIM17 (Leuenberger et al. 1999), TOM40 (Wiedemann et al. 2004), TIM23 (Davis et al. 2007), TIM22 (Hasson et al. 2010), and Tafazzin (Hasson et al. 2010).
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High-throughput mass spectrometry screening for inhibitors of phosphatidylserine decarboxylase
TIM23 PAM Complex Imports Proteins to Mitochondrial Matrix
The TIM23 complex transports precursor proteins across the inner membrane and into the matrix (Voisine et al. 2000, Mokranjac et al. 2003, Chacinska et al. 2005,Wiedemann et al. 2007, Hutu et al. 2008, Popov-Celeketic et al. 2008, Chacinska et al. 2010). Subunits TIM50, TIM17, and TIM23 are necessary for initiating translocation (Mokranjac et al.2003, Milisav et al. 2001) while the PAM complex with mtHSP70 (SSC1) provides the motive force that drives the transport (Milisav et al. 2001, Truscott et al. 2003, Frazier et al. 2004, D'Silva et al. 2005, van der Laan et al. 2005, Yamano et al. 2008). Hsp70 (mtHsp70, Ssc1) binding to the precursor pulls the protein into the matrix in a reaction requiring ATP hydrolysis (Gambill et al. 1993, Schneider et al. 1994, Kronidou et al. 1994, Ungermann et al. 1994, Voos et al. 1996, Voisine et al. 1999, Voisine et al. 2000, Krayl et al. 2007). The reaction appears to use a Brownian ratchet mechanism (Yamano et al. 2008). Substrates of TIM23:PAM include Hsp60 (Gallas et al. 2006) and Yfh1 (Voisine et al. 2000).
MPP Cleaves Presequence of Matrix Precursors
The alpha subunit (MAS2, Alpha-MPP) of the mitochondrial processing peptidase (MPP) binds presequences of mitochondrial precursors and the beta subunit (MAS1, Beta-MPP) cleaves the presequence (Yang et al. 1991, Geli 1993, Luciano et al. 1997, Luciano et al. 1998, Taylor et al. 2001, Dvorakova-Hola et al. 2010). After cleavage, proteins destined for the matrix are drawn into the matrix by ATP-dependent interaction with mtHSP70 (SSC1) of the PAM complex.
Precursor Proteins Enter TIM23 PAM Complex
The TIM23 Complex resides in the inner membrane of the mitochondrion and transfers precursor proteins to the matrix. The TIM23 complex appears to adopt different configurations (and perhaps different subunit compositions) depending on whether the substrate is destined for the inner membrane or the matrix. Here we refer to the TIM23 PAM complex as the configuration that delivers inner membrane proteins. The PAM17 subunit is required for this activity. The N-terminal presequence of precursors first interacts with TIM50 and TIM23 (Mokranjac et al. 2003, Martinez-Caballero et al. 2007, Tamura et al. 2009). The TIM17 and TIM23 subunits form a channel and are required to initiate translocation of precursors (Milislav et al. 2001). Substrates of TIM23 PAM include Hsp60 (Gallas et al. 2006) and Yfh1 (Voisine et al. 2000).
TIM23 SORT Complex Inserts Proteins into Inner Membrane
The TIM23 Complex resides in the inner membrane of the mitochondrion and transfers precursor proteins to the inner membrane. The presequence of proteins targeted to the inner membrane is transferred to the matrix where it is cleaved. Sequences in the mature region of the protein then interact with the TIM23 complex to halt transfer across the inner membrane and the protein is released laterally into the inner membrane (Glick et al. 1992, Popov-Celeketic et al. 2008). TIM21 is required. Substrates of the TIM23 complex targeted to the inner membrane include CYB2 (Krayl et al. 2007, Hutu et al. 2008, Popov-Celeketic et al. 2008, Tamura et al. 2009, Mokranjac et al. 2009), DLD (Mokranjac et al. 2009), ATP9 (Leuenberger et al. 1999, Milisav et al. 2001, Tamura et al. 2009), COQ2 (Leuenberger et al. 1999), TIM54 (Leuenberger et al. 1999, Kurz et al. 1999), COX4 (Martinez-Caballero et al. 2007), COX5A (Mokranjac et al. 2003), and ATP2 (Dekker et al. 1997, Mokranjac et al. 2003).
MPP Cleaves Presequence of Inner Membrane Precursors
The alpha subunit (MAS2, Alpha-MPP) of the mitochondrial processing peptidase (MPP) binds presequences of mitochondrial precursors and the beta subunit (MAS1, Beta-MPP) cleaves the presequence (Yang et al. 1991, Geli 1993, Luciano et al. 1997, Luciano et al. 1998, Taylor et al. 2001, Dvorakova-Hola et al. 2010). After cleavage, proteins destined for the inner membrane are released laterally from TIM23 SORT into the membrane.
Precursor Proteins Enter TIM23 SORT Complex
The TIM23 Complex resides in the inner membrane of the mitochondrion and transfers precursor proteins to the inner membrane. The TIM23 complex appears to adopt different configurations (and perhaps different subunit compositions) depending on whether the substrate is destined for the inner membrane or the matrix. Here we refer to the TIM23 SORT complex as the configuration that delivers inner membrane proteins. The TIM21 subunit is required for this activity.The N-terminal presequence of precursors first interacts with TIM50 and TIM23 (Mokranjac et al. 2003, Martinez-Caballero et al. 2007, Tamura et al. 2009). The TIM17 and TIM23 subunits form a channel and are required to initiate translocation of precursors (Milislav et al. 2001). Substrates of the TIM23 SORT complex targeted to the inner membrane include CYB2 (Krayl et al. 2007, Hutu et al. 2008, Popov-Celeketic et al. 2008, Tamura et al. 2009, Mokranjac et al. 2009), DLD (Mokranjac et al. 2009), ATP9 (Leuenberger et al. 1999, Milisav et al. 2001, Tamura et al. 2009), COQ2 (Leuenberger et al. 1999), TIM54 (Leuenberger et al. 1999, Kurz et al. 1999), COX4 (Martinez-Caballero et al. 2007), COX5A (Mokranjac et al. 2003), and ATP2 (Dekker et al. 1997, Mokranjac et al. 2003).
TIM22 Complex Inserts Proteins into Inner Membrane
The TIM22 complex inserts precursor proteins into the inner membrane of the mitochondrion (Sirrenberg et al. 1996, Kaldi et al. 1998, Kerscher et al. 1997, Leuenberger et al. 1999, Endres et al. 1999, Kovermann et al. 2002, Rehling et al. 2003, Vergnolle et al. 2005, Yamano et al. 2005). The precursors are hydrophobic and are usually chaperoned to the TIM22 complex by the small TIM proteins (TIM10, TIM12) of the intermembrane space (Koehler et al. 1998, Sirrenberg et al. 1998). Substrates of the TIM22 complex include AAC (Sirrenberg et al. 1996, Kerscher et al. 1997, Leuenberger et al. 1999, Endres et al. 1999, Vergnolle et al. 2005), PIC (Kovermann et al. 2002, Rehling et al. 2003, Yamano et al. 2005), TIM22 (Leuenberger et al. 1999), and TIM23 (Kerscher et al. 1997, Kaldi 1998, Leuenberger et al. 1999).
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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
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SUMOylation and deSUMOylation at a glance
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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
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tetra-mu3-sulfido-tetrairon [ChEBI:49883]
Characterization and functional expression of the cDNA encoding human brain quinolinate phosphoribosyltransferase
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The mechanism of action of protein synthesis initiation factors from rabbit reticulocytes.
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Protein kinase C theta is expressed in mast cells and is functionally involved in Fcepsilon receptor I signaling
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Small ubiquitin-related modifier (SUMO)-specific proteases: profiling the specificities and activities of human SENPs
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Structural basis for inhibition of the epidermal growth factor receptor by cetuximab
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Involvement of ACSL in local synthesis of neutral lipids in cytoplasmic lipid droplets in human hepatocyte HuH7
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Remodeling of cardiolipin by phospholipid transacylation
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The kinesin-8 motor Kif18A suppresses kinetochore movements to control mitotic chromosome alignment
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Unifying concepts in CD28, ICOS and CTLA4 co-receptor signalling
Folding of glycoproteins: toward understanding the biophysics of the glycosylation code
FUNCTION Required for meiotic recombination. Mediates DNA cleavage that forms the double-strand breaks (DSB) that initiate meiotic recombination. The action of SPO11 is important in setting off a regulatory chain of events encompassing 5' to 3' resection. When there are no SPO11-DSBs, resection of a site specific VDE-DSB takes place but it is faster than in wild-type meiosis and increases the risk of uncovering flanking homology.DEVELOPMENTAL STAGE Meiosis-specific.SIMILARITY Belongs to the TOP6A family.
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Within the nucleus, inositol polyphosphate multikinase (IPMK), inositol-pentakisphosphate 2-kinase (IPPK), inositol hexakisphosphate kinase 1 (IP6K1) and 2 (IP6K2) produce IP5, IP6, IP7, and IP8 inositol phosphate molecules (Irvine & Schell 2001, Alcazar-Romain & Wente 2008, York 2006, Monserrate and York 2010, Nalaskowski et al. 2002, Chang et al. 2002, Chang & Majerus 2006, Saiardi et al. 2001, Saiardi et al. 2000, Draskovic et al. 2008, Mulugu et al. 2007).
Inositol hexakisphosphate kinase 1 (IP6K1) and 3 (IP6K3) phosphorylate inositol 1,3,4,5,6-pentakisphosphate (I(1,3,4,5,6)P5) to inositol 5-diphospho-(1,3,4,6)-tetrakisphosphate (5-PP-IP4) (Saiardi et al. 2001, Saiardi et al. 2000, Draskovic et al. 2008).
Human glucose-6-phosphate dehydrogenase: the crystal structure reveals a structural NADP(+) molecule and provides insights into enzyme deficiency
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.
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).
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).
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.
Recruitment of repair and signaling proteins to double-strand breaks
In the nucleus, inositol hexakisphosphate kinase 1 (IP6K1) and 2 (IP6K2) phosphorylate inositol 1,2,3,4,5,6-hexakisphosphate (IP6) to inositol 5-diphospho-1,2,3,4,6-pentakisphosphate (5-PP-IP5). The following lists the above proteins with their corresponding literature references: IP6K1 (Saiardi et al. 2001, Mulugu et al. 2007, Draskovic et al. 2008) and IP6K2 (Saiardi et al. 2001, Mulugu et al. 2007, Draskovic et al. 2008).
In the nucleus, inositol 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).
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Cytosolic phophoribosyl pyrophosphate synthetase catalyzes the reaction of D-ribose 5-phosphate and ATP to form 5-phospho-alpha-D-ribose and AMP. Three isoforms of the enzyme have been described. The first has been purified and characterized biochemically (Fox and Kelley 1971). The others are known only as inferred protein products of cloned genes; their catalytic properties have not been determined.
Cytosolic ribulose-5-phosphate-3-epimerase (RPE) catalyzes the reversible interconversion of D-xylulose 5-phosphate and D-ribulose 5-phosphate (Bose and 1985). The electrophoretic properties of RPE activity detected in extracts of mouse-human somatic cell hybrids suggest that the active form of the enzyme is a homodimer (Spencer and Hopkinson 1980).
Cytosolic ribulose-5-phosphate-3-epimerase (RPE) catalyzes the reversible interconversion of D-ribulose 5-phosphate and D-xylulose 5-phosphate (Bose and 1985). The electrophoretic properties of RPE activity detected in extracts of mouse-human somatic cell hybrids suggest that the active form of the enzyme is a homodimer (Spencer and Hopkinson 1980).
Cytosolic 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 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).
The reversible interconversion of ribose 5-phosphate and ribulose 5-phosphate is catalyzed by cytosolic ribose 5-phosphate isomerase (Huck et al. 2004).
The reversible interconversion of ribulose 5-phosphate and ribose 5-phosphate is catalyzed by cytosolic ribose 5-phosphate isomerase (Huck et al. 2004).
Cytosolic transaldolase (TALDO1) catalyzes the reversible reaction of D-erythrose 4-phosphate and D-fructose 6-phosphate to form D-glyceraldehyde 3-phosphate and sedoheptulose 7-phosphate. Protein expressed from the cloned gene has been characterized biochemically (Banki et al. 1994) and transaldolase deficiency in a patient has been correlated with a mutation in the TALDO1 gene (Verhoeven et al. 2001).
Cytosolic transaldolase (TALDO1) catalyzes the reversible reaction of D-glyceraldehyde 3-phosphate and sedoheptulose 7-phosphate to form D-erythrose 4-phosphate and D-fructose 6-phosphate. Protein expressed from the cloned gene has been characterized biochemically (Banki et al. 1994) and transaldolase deficiency in a patient has been correlated with a mutation in the TALDO1 gene (Verhoeven et al. 2001).
Cytosolic 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).
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A revised picture of the E2F transcriptional network and RB function.
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).
Cytosolic phosphoglucomutase (PGM) catalyzes the reversible conversion of glucose 1-phosphate to glucose 6-phosphate. Two PGM isoenzymes, both monomers, have been identified. PGM1 is the major form found in most tissues except erythrocytes, where PGM2 is abundant (March et al. 1993; Parrington et al. 1968; Putt et al. 1993). PGM2 also has substantial phosphopentomutase activity and its primary physiological in normal tissues in vivo is not clear.
Cytosolic 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).
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.
At the beginning of this reaction, 1 molecule of '{(1,6)-alpha-glucosyl}poly{(1,4)-alpha-glucosyl}glycogenin-2' is present. At the end of this reaction, 1 molecule of 'alpha-D-glucose', and 1 molecule of 'poly{(1,4)-alpha-glucosyl}glycogenin-2' are present. This reaction takes place in the 'cytoplasm' and is mediated by the 'amylo-alpha-1,6-glucosidase activity' of 'glycogen debranching enzyme'.
The phosphorylated PYGL dimer (a form) of glycogen phosphorylase catalyzes the reaction of orthophosphate and poly((1,4)-alpha-glucosyl) glycogenin-2 to form D-glucose 1-phosphate and glycogenin-2. This reaction occurs on the surfaces of cytosolic glycogen granules. Non-phosphorylated PYGL dimers (b form) are catalytically inactive even in the presence of AMP. In the body, this reaction takes place in the liver where its dependence on hormonally stimulated PYGL phosphorylation (and lack of sensitivity to AMP) allow glucose mobilization in response to a demand for glucose from the rest of the body (Newgard et al. 1989; Rath et al. 2000).
The PYGM and PYGB forms of glycogen phosphorylase catalyze the reaction of orthophosphate and poly((1,4) alpha glucosyl) glycogenin-1 to form D-glucose 1-phosphate and glycogenin-1. This reaction occurs on the surfaces of cytosolic glycogen granules. The phosphorylated forms of PYGM and PYGB dimers (a form) are catalytically active; the non-phosphorylated dimers (b form) become active when complexed with AMP. In the body, this reaction takes place in tissues other than the liver where its sensitivity to AMP allows glucose mobilization in response to acute energy needs of the individual cell, and hormonally mediated phosphorylation can stimulate increased glucose production, still for use by the individual producing cell, in response to stress signals. These reactions have not been characterized in detail but are inferred to occur from the very close similarity among PGYM, PGYB, and PGYL (Newgard et al. 1989; Rath et al. 2000).
Mutations in the liver glycogen synthase gene in children with hypoglycemia due to glycogen storage disease type 0
The main sources of galactose in the human diet are milk and milk products. The disaccharide lactose from these sources is hydrolyzed in the intestine to its constituent monosaccharides, glucose and galactose. Galactose is metabolized primarily in the liver in a sequence of three reactions that yield one molecule of glucose 1-phosphate per molecule of galactose. First, it is phosphorylated to yield galactose 1-phosphate. Then, galactose 1-phosphate and UDP-glucose react to form UDP-galactose and glucose 1-phosphate, and UDP-galactose undergoes epimerization to form UDP-glucose. In a reaction shared with other pathways, glucose 1-phosphate can be converted into glucose 6-phosphate (Holton et al. 2001; Elsas and Lai 2001).
Cytosolic 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).
A "slow" homotetrameric kinesin-related motor protein purified from Drosophila embryos
Cytosolic glucose-6-phosphate dehydrogenase (G6PD) catalyzes the reaction of glucose 6-phosphate and NADP+ to form D-glucono-1,5-lactone 6-phosphate and , and NADPH + H+. Biochemical studies indicate that both G6PD dimers and tetramers are catalytically active and capable or forming under physiological conditions in vivo (Au et al. 2000). Mutations that reduce the catalytic efficientcy of G6PD are remarkably common in human populations; these appear to have a protective effect against malaria (e.g., Luzzatto and Afolayan 1968).
Cytosolic, non-phosphorylated PGYM dimers (b form) can reversibly bind AMP. This reaction is negatively regulated by ATP and glucose 6-phosphate and is the means by which high levels of these molecules repress PGYM activity (Rath et al. 2000).
Cytosolic, non-phosphorylated PGYB dimers (b form) complexed with AMP can reversibly dissociate. This reaction is inferred from the AMP-binding properties of the closely homologous PGYM complex (Rath et al. 2000).
Cytosolic, non-phosphorylated PGYB dimers (b form) can reversibly bind AMP. This reaction is inferred from the AMP-binding properties of human PGYL and closely homologous PGYM proteins from other species (Newgard et al. 1989; Rath et al. 2000).
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.
Cytosolic glycogen branching enzyme associated with glycogen granules transfers terminal alpha(1,4) glucose blocks to form alpha(1,6) branches on growing glycogen molecules formed on glycogenin (Bao et al. 1996).
Phosphorylated glycogen synthase catalyzes the addition of glucose residues to the non reducing end of a (1,4)-alpha-D-glucose multimer formed on glycogenin 1 or 2 when activated by glucose 6-phosphate. (Here the addition of four glucose residues is annotated.) The enzyme is associated with glycogen granules in the cytosol. Glycogen synthase proteins are encoded by two human genes, GYS1 and GYS2. GYS1 protein is abundant in skeletal muscle while GYS2 is abundant in liver. The cytosolic location and glycogen synthase activity of GYS1 protein has been demonstrated in studies of wild-type and mutant proteins expressed in cultured cells in vitro (Cid et al. 2000). Defects in GYS1 protein in vivo are associated with deficient muscle glycogen synthesis and exercise intolerance in vivo (Kollberg et al. 2007). The enzymatic activity of purified GYS2 protein has been characterized experimentally (Westphal and Nuttall 1992). Defects in GYS2 protein in vivo are associated with fasting hypoglycemia and defective glycogen synthesis in the liver (Orho et al. 1998). GYS activity is regulated by phosphorylation. In its phosphorylated D form, annotated here, enzyme activity requires the presence of glucose 6-phosphate. The structure and activity of phosphorylated human GYS protein tetramers are inferred from the properties of the rabbit GYS1 (skeletal muscle) protein which has been purified and characterized in detail (Soderling et al. 1970).
Cytosolic debranching enzyme associated with glycogen granules transfers 3-glucose blocks from branches to the main linear polyglucose chain of limit dextrin formed on glycogenin 1 or glycogenin 2 (Chen et al. 1988; Shen et al. 1996).
The phosphorylated PYGL dimer (a form) of glycogen phosphorylase catalyzes the reaction of orthophosphate and glycogen-glycogenin 1 to form D-glucose 1-phosphate and limit dextrin-glycogenin 1. This reaction occurs on the surfaces of cytosolic glycogen granules. Non-phosphorylated PYGL dimers (b form) are catalytically inactive even in the presence of AMP. In the body, this reaction takes place in the liver where its dependence on hormonally stimulated PYGL phosphorylation (and lack of sensitivity to AMP) allow glucose mobilization in response to a demand for glucose from the rest of the body (Newgard et al. 1989; Rath et al. 2000).
The PYGM and PYGB forms of glycogen phosphorylase catalyze the reaction of orthophosphate and glycogen-glycogenin 1 to form D-glucose 1-phosphate and limit dextrin-glycogenin 1. This reaction occurs on the surfaces of cytosolic glycogen granules. The phosphorylated forms of PYGM and PYGB dimers (a form) are catalytically active; the non-phosphorylated dimers (b form) become active when complexed with AMP. In the body, this reaction takes place in tissues other than the liver where its sensitivity to AMP allows glucose mobilization in response to acute energy needs of the individual cell, and hormonally mediated phosphorylation can stimulate increased glucose production, still for use by the individual producing cell, in response to stress signals. These reactions have not been characterized in detail but are inferred to occur from the very close similarity among PGYM, PGYB, and PGYL (Newgard et al. 1989; Rath et al. 2000).
Cytosolic, non-phosphorylated PGYM dimers (b form) complexed with AMP can reversibly dissociate (Rath et al. 2000).
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).
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).
In a healthy, well-nourished individual, the production of ketone bodies occurs at a relatively low rate. During periods of normal physiological responses to carbohydrate shortages, the liver increases the production of ketone bodies from acetyl-CoA generated from fatty acid oxidation. This allows heart and skeletal muscle to use ketone bodies as the primary source of energy, thereby preserving the limited glucose supply for use in brain tissue. In untreated diabetes mellitus, a huge buildup of ketone bodies occurs due to an increase in fatty acid oxidation. The production of ketone bodies exceeds the ability of peripheral tissues to oxidize them, and results in lowering the pH of blood. Blood acidification is dangerous, chiefly as it impairs the ability of hemoglobin to bind oxygen. Ketone body synthesis proceeds via the synthesis of ccetoacetic acid in three steps from acetyl CoA, followed by the reduction of acetoacetic acid to beta-hydroxybutyrate. In the body, these reactions occur in the mitochondria of liver cells (Sass 2011).
Hydroxymethylglutaryl-CoA synthase tetramer (HMGCS2) in the mitochondrial matrix catalyzes the reaction of acetoacetyl-CoA and acetyl-CoA to form beta-hydroxy-beta-methylglutaryl coenzyme A (HMG CoA) and CoA (Aledo et al. 2001).
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).
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Still a puzzle: why is haem covalently attached in c-type cytochromes?
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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).
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).
Investigation of coenzyme Q biosynthesis in human fibroblast and HepG2 cells
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.
The carnitine-acylcarnitine transporter (SLC25A20 / CACT), embedded in the inner mitochondrial membrane, mediates the exchange of palmitoyl-carnitine (and other acylcarnitine esters) and carnitine across the inner mitochondrial membrane (Huizing et al., 1997).
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.
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).
Dissociation of GDP dissociation inhibitor and membrane translocation are required for efficient activation of Rac by the Dbl homology-pleckstrin homology region of Tiam
Glycerol can be a source for glycerol-3-phosphate, in which case, a phosphate form ATP is transferred to glycerol by glycerol kinase forming glycerol-3-phosphate and ADP.
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.
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.
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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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.
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.
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.
(5-hydroxyindol-3-yl)acetic acid [ChEBI:27823]
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).
Human NPC1L1, associated with the plasma membrane, binds ezetimibe and becomes incapable of mediating cholesterol uptake. The molecular mechanisms of cholesterol transport and ezetimibe inhibition, however, remain unclear (Garcia-Calvo et al. 2005; Weinglass et al. 2008).
Dietary phytosterols (sterols derived from plants) are taken up into enterocytes from the gut lumen. The reaction is thought to be mediated by plasma membrane-associated NPC1L1 protein. Detailed studies in Maden-Darby canine kidney cells, both mediated by endogenous (canine) NPC1L1 and by overexpressed human protein, indicate a major role for NPC1L1 in the uptake of extracellular sterol. These studies have also shown that ezetimibe binds both human and canine proteins and renders them incapable of mediating sterol uptake. The molecular mechanisms of cholesterol transport and ezetimibe inhibition, however, remain unclear (Weinglass et al. 2008).
BRCA1 affects lipid synthesis through its interaction with acetyl-CoA carboxylase
NPC1L1 protein mediates the uptake of dietary sterols from the gut lumen. These include cholesterol and plant sterols (phytosterols). Half to two-thirds of the 250-500 milligrams of cholesterol consumed daily from a typical western diet is taken up by this route and exported from enterocytes into the lymph in chylomicrons. Of the 200-400 milligrams of dietary phytosterol, only about 5% is absorbed.The drug ezetimibe interferes with NPC1L1-mediated sterol uptake (Oram and Vaughan 2006). Both cholesterol and phytosterols are secreted from the liver into the bile (Salen et al. 1970). Mutations affecting the ABCG5/8 transporter complex inhibit this process (e.g., Berge et al. 2000), while the molecular details of sterol export in human cells have not been worked out, they can be inferred from the properties of the homologous mouse proteins (Graf et al. 2003; Wang et al. 2006).
ABCG5/8 in the plasma membrane mediates the ATP-dependent export of cytosolic sterols (cholesterol and phytosterols). Mutations affecting the ABCG5/8 proteins are associated with the accumulation of high levels of cholesterol and phytosterols in the body, demonstrating the specificity and physiological importance of this process (Berge et al. 2000). Human ABCG5/8 has not been studied in detail, but the homologous mouse protein complex mediate ATP-dependent sterol export (Wang et al. 2006). The mouse proteins localize to the apical plasma membranes of enterocytes and hepatocytes, consistent with the hypothesis that in vivo ABCG5/8 mediates sterol export into the gut lumen and from hepatocytes into the bile (Graf et al. 2003).
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Inositol phosphates IP2, IP and the six-carbon cyclic alcohol inositol (Ins) are produced by various phosphatases and the inositol-3-phosphate synthase 1 (ISYNA1) (Ju et al. 2004, Ohnishi et al. 2007, Irvine & Schell 2001, Bunney & Katan 2010).
Inositol phosphates (IPs) are molecules involves in signalling processes in eukaryotes. myo-Inositol consists of a six-carbon cyclic alcohol with an axial 2-hydroxy and five equatorial hydroxyls. Mono-, di-, and triphosphorylation of the inositol ring generates a wide variety of stereochemically distinct signalling entities. Inositol 1,4,5-trisphosphate (I(1,4,5)P3), is formed when the phosphoinositide phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is hydrolysed by a phospholipase C isozyme. An array of inositol trisphosphate (IP3) and tetrakisphosphate (IP4) molecules are synthesised by the action of various kinases and phosphatases in the cytosol. These species then transport between the cytosol and the nucleus where they are acted on by inositol polyphosphate multikinase (IPMK), inositol-pentakisphosphate 2-kinase (IPPK), inositol hexakisphosphate kinase 1 (IP6K1) and 2 (IP6K2), to produce IP5, IP6, IP7, and IP8 molecules. Some of these nuclear produced IPs transport back to the cytosol where they are converted to an even wider variety of IPs, by kinases and phosphatases, including the di- and triphospho inositol phosphates aka pyrophosphates (Irvine & Schell 2001, Bunney & Katan 2010, Alcazar-Romain & Wente 2008, York 2006, Monserrate and York 2010).
Dietary cholesterol is taken up into enterocytes from the gut lumen in a reaction mediated by plasma membrane-associated NPC1L1 protein. This role for NPC1L1 was first observed in studies of a mouse model system (Altman et al. 2004). Subsequent studies of human cultured cells confirmed the participation of NPC1L1 in cholesterol transport across membranes but suggested that this transport process might not be a major factor in dietary cholesterol uptake (Davies et al. 2005). Detailed studies in Maden-Darby canine kidney cells, both mediated by endogenous (canine) NPC1L1 and by overexpressed human protein, indicate a major role for NPC1L1 in the uptake of extracellular cholesterol. These studies have also shown that ezetimibe binds both human and canine proteins and renders them incapable of mediating cholesterol uptake. The molecular mechanisms of cholesterol transport and ezetimibe inhibition, however, remain unclear (Weinglass et al. 2008).
Inositol monophosphatase 1 (IMPA1) and 2 (IMPA2) homodimers dephosphorylate inositol 4-phosphate (I4P) to inositol (Ins). In vitro, IMPA1 and 2 differ in their pH optima and IMPA1 has a significantly greater activity on IP4 than does IMPA2 (Ohnishi et al. 2007).
Inositol monophosphatase 1 (IMPA1) and 2 (IMPA2) homodimers dephosphorylate inositol 1-phosphate (I1P) to inositol (Ins). In vitro, IMPA1 and 2 differ in their pH optima and IMPA1 has a significantly greater activity on IP4 than does IMPA2 (McAllister et al. 1992, Ohnishi et al. 2007).
Inositol-3-phosphate synthase 1 (ISYNA1) aka hIPS isomerises glucose 6-phosphate (Glc6P) to inositol 3-phosphate (I3P) (Ju et al. 2004).
Inositol monophosphatase 1 (IMPA1) and 2 (IMPA2) homodimers dephosphorylate inositol 3-phosphate (I3P) to inositol (Ins). In vitro, IMPA1 and 2 differ in their pH optima and IMPA1 has a significantly greater activity on IP4 than does IMPA2 (Ohnishi et al. 2007).
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 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).
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).
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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).
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).
Analysis of the gene sequences of the insulin receptor and the insulin-sensitive glucose transporter (GLUT-4) in patients with common-type non-insulin-dependent diabetes mellitus
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).
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).
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).
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).
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).
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The classical human phosphoglucomutase (PGM1) isozyme polymorphism is generated by intragenic recombination
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Genomic structure and expression of the human heme A:farnesyltransferase (COX10) gene
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Cloning and recombinant expression of rat and human kynureninase.
Characterization of the human SLC2A11 (GLUT11) gene: alternative promoter usage, function, expression, and subcellular distribution of three isoforms, and lack of mouse orthologue
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Ins and outs of cellular cobalamin transport
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Mitochondrial protein import motor: differential role of Tim44 in the recruitment of Pam17 and J-complex to the presequence translocase
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).
VLCS (very long chain acyl-CoA synthetase), associated with the inner surface of the peroxisomal membrane, cayalyzes the reaction of phytanate, CoA-SH, and ATP to form phytanoyl-CoA, AMP, and pyrophosphate (Steinberg et al. 1999).
The peroxisomal membrane transport protein PMP34 mediates the exchange of adenine nucleotides between the cytosol and the peroxisomal matrix. The localization of PMP34 has been established by immunofluoresence studies (Wylin et al. 1998). The cloned human protein restores adenine nucleotide transport in yeast whose endogenous peroxisomal transporter has been disrupted, and has adenine nucleotide transport activity in reconstituted lipid vesicles in vitro (Visser et al. 2002), consistent with its hypothesized role in vivo (Wanders and Waterham 2006).
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Interaction of Hsp90 with the nascent form of the mutant epidermal growth factor receptor EGFRvIII
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FAD-linked mitochondrial glycerol 3-phosphate dehydrogenase (GPD2, alias: mGPDH) and its NAD-linked cytosolic isoform (GPD1, alias:cGPDH) constitute glycerol phosphate shuttle. GPD2 catalyzes the unidirectional conversion of glycerol-3-phosphate (G-3-P) to dihydroxyacetone phosphate (DHAP) with concomitant reduction of the enzyme-bound FAD. Impaired activity of GPD2 has been suggested to be one of the primary causes of insulin secretory defects in beta-cells and thus it is a candidate gene for type 2 diabetes.
Acetoacetate, beta-hydroxybutyrate, and acetone collectively are called ketone bodies. The first two are synthesized from acetyl-CoA, in the mitochondria of liver cells; acetone is formed by spontaneous decarboxylation of acetoacetate. Ketone body synthesis in liver is effectively irreversible because the enzyme that catalyzes the conversion of acetoacetate to acetoacetyl-CoA is not present in liver cells. Ketone bodies, unlike fatty acids and triglycerides, are water-soluble. They are exported from the liver, and are taken up by other tissues, notably brain and skeletal and cardiac muscle. There, they are broken down to acetyl-CoA which is oxidized via the TCA cycle to yield energy. In a normal person, this pathway of ketone body synthesis and utilization is most active during extended periods of fasting. Under these conditions, mobilization and breakdown of stored fatty acids generates abundant acetyl-CoA acetyl-CoA in liver cells for synthesis of ketone bodies, and their utilization in other tissues minimizes the demand of these tissues for glucose (Sass 2011).
The FATP1 (SLC27A1) 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.
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The TIAM2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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).
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 reactions involved in the metabolism of fatty acids and of the triacylglycerols and ketone bodies derived from them form a closely interrelated, coordinately regulated module that plays a central role in human energy metabolism.
The HMGCS1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The HMGCS2 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.
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Identification of a consensus motif for Plk (Polo-like kinase) phosphorylation reveals Myt1 as a Plk1 substrate
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ChEBI:59084 (Glc)3 (GlcNAc)2 (Man)9 (Asn)1
ChEBI:59081 (Glc)1 (GlcNAc)2 (Man)9 (PP-Dol)1
ChEBI:59082 (Glc)2 (GlcNAc)2 (Man)9 (Asn)1
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Cori Cycle (interconversion of glucose and lactate)
Ligand discrimination in signaling through an ErbB4 receptor homodimer
Human liver mitochondrial aldehyde dehydrogenase: three-dimensional structure and the restoration of solubility and activity of chimeric forms
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Post-Elongation Processing of Intronless pre-mRNA
The PI3K-PDK1 connection: more than just a road to PKB
A critical role for histone H2AX in recruitment of repair factors to nuclear foci after DNA damage.
Interaction between PCNA and DNA ligase I is critical for joining of Okazaki fragments and long-patch base-excision repair.
Purification, cDNA cloning and heterologous expression of human phosphomannose isomerase
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1,2-Diacyl-sn-glycerol 3-phospho-L-serine
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ER-mediated phagocytosis: myth or reality?
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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
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Participation of two members of the very long-chain acyl-CoA synthetase family in bile acid synthesis and recycling
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Molecular cloning and characterization of a novel (Na+,K+)/H+ exchanger localized to the trans-Golgi network
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Biogenesis and regulation of insulin-responsive vesicles containing GLUT4
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Purification and characterization of human liver "high Km" aldehyde dehydrogenase and its identification as glutamic gamma-semialdehyde dehydrogenase.
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2-Hexaprenyl-6-methoxyphenol [ChEBI:1109]
Lectin-deficient calreticulin retains full functionality as a chaperone for class I histocompatibility molecules
Human kidney gamma-glutamyl transpeptidase. Catalytic properties, subunit structure, and localization of the gamma-glutamyl binding site on the light subunit
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2-acyl-sn-glycero-3-phosphoglycerol [ChEBI:27923]
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
Nuclear import of hepatic glucokinase depends upon glucokinase regulatory protein, whereas export is due to a nuclear export signal sequence in glucokinase
Quantitative and dynamic assessment of the contribution of the ER to phagosome formation
Nonsense Mediated Decay Enhanced by the Exon Junction Complex
Molecular tinkering of G protein-coupled receptors: an evolutionary success
25(R) 3alpha,7alpha,24(S)-trihydroxy-5beta-cholestanoyl-CoA
25(R) 3alpha,7alpha,12alpha,24(S)-tetrahydroxy-5beta-cholestanoyl-CoA
Insulin degradation: progress and potential.
25(R) 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA
Endoplasmic reticulum (ER) mannosidase I is compartmentalized and required for N-glycan trimming to Man5-6GlcNAc2 in glycoprotein ER-associated degradation
(24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA
25(S) 3alpha,7alpha-dihydroxy-5beta-cholest-24-enoyl-CoA
(24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA
3alpha, 7alpha, 12alpha-trihydroxy-5beta-cholestanoate
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Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds
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5beta-cholesten-7alpha, 12alpha-diol-3-one
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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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GBF1: A novel Golgi-associated BFA-resistant guanine nucleotide exchange factor that displays specificity for ADP-ribosylation factor 5
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
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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_88528.9
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Aquaporins in the kidney: from molecules to medicine
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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_110921.9
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Primary hyperoxaluria: from gene defects to designer drugs?
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Active remodelling of the TIM23 complex during translocation of preproteins into mitochondria
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Stimulation of the cell death response by PAK-2p34
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Functional dissection of eukaryotic initiation factor 4F: the 4A subunit and the central domain of the 4G subunit are sufficient to mediate internal entry of 43S preinitiation complexes.
The isoform-specific functions of the c-Jun N-terminal Kinases (JNKs): differences revealed by gene targeting
Graded activation of fibroblast growth factor receptor 3 by mutations causing achondroplasia and thanatophoric dysplasia
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Transcriptional control of adipocyte formation
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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
Role of Tim50 in the transfer of precursor proteins from the outer to the inner membrane of mitochondria
Phosphorylation of Mnk1 by caspase-activated Pak2/gamma-PAK inhibits phosphorylation and interaction of eIF4G with Mnk
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CATERPILLERs, pyrin and hereditary immunological disorders
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A proposed role for the Azotobacter vinelandii NfuA protein as an intermediate iron-sulfur cluster carrier
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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
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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
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Myotubularin phosphatases: policing 3-phosphoinositides
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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
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Human and rat beta cells differ in glucose transporter but not in glucokinase gene expression
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Hypophosphorylation of residue Y1045 leads to defective downregulation of EGFRvIII
T cell growth factor receptors. Quantitation, specificity, and biological relevance
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ATM and ATR substrate analysis reveals extensive protein networks responsive to DNA damage
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Identification of transcription factors required for the expression of mammalian U6 genes in vitro
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Sam35 of the mitochondrial protein sorting and assembly machinery is a peripheral outer membrane protein essential for cell viability
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'DAGs [plasma membrane]' positively regulates 'DAG stimulates protein kinase C-delta'
'XPO1 [nucleoplasm]' positively regulates 'Translocation of Cyclin B1:phospho-Cdc2 to the cytoplasm'
The FGF family: biology, pathophysiology and therapy
'Mg2+ [cytosol]' is required for 'pyrophosphate + H2O => 2 orthophosphate [cytosolic]'
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Modular structure of the TIM23 preprotein translocase of mitochondria
'L-Phe [cytosol]' negatively regulates 'kynurenine + pyruvate => 4-(2-aminophenyl)-2,4-dioxobutanoic acid + alanine [CCBL1]'
'D-Fructose 2,6-bisphosphate [cytosol]' positively regulates 'D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP'
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'Mg2+ [mitochondrial matrix]' is required for 'pyrophosphate + H2O => 2 orthophosphate [mitochondrial]'
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'AMP [cytosol]' positively regulates 'D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP'
Molecular cloning and functional expression of human 3-hydroxyanthranilic-acid dioxygenase.
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Overview of retinoid metabolism and function
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'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'
'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'
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Activation of human liver glycogen phosphorylase by alteration of the secondary structure and packing of the catalytic core
FUNCTION TFIIIC mediates tRNA and 5S RNA gene activation by binding to intragenic promoter elements. Upstream of the transcription start site, TFIIIC assembles the initiation complex TFIIIB-TFIIIC-tDNA, which is sufficient for RNA polymerase III recruitment and function. Part of the tauA domain of TFIIIC that binds boxA DNA promoter sites of tRNA and similar genes. TFC4 is the TFIIIB-assembling subunit of TFIIIC and essential for viability.SUBUNIT Component of the TFIIIC complex composed of TFC1, TFC3, TFC4, TFC6, TFC7 and TFC8. The subunits are organized in two globular domains, tauA and tauB, connected by a proteolysis-sensitive and flexible linker. Interacts with TFC1, TFC3, TFC6, TFIIIB subunits BRF1 and BDP1, and with RNA polymerase III subunit RPC10.PTM Phosphorylated.MISCELLANEOUS Present with 876 molecules/cell in log phase SD medium.SIMILARITY Contains 11 TPR repeats.
Structures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1
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Regulation of human cystathionine beta-synthase by S-adenosyl-L-methionine: evidence for two catalytically active conformations involving an autoinhibitory domain in the C-terminal region
Polo kinase regulates mitotic chromosome condensation by hyperactivation of condensin DNA supercoiling activity
FUNCTION During meiosis is involved in homologous recombination and during vegetative growth it is necessary for DNA repair. It probably regulates the 5'-3' exonuclease degradation of double strand breaks either at the initiation stage or a later stage.MISCELLANEOUS Present with 358 molecules/cell in log phase SD medium.
Interconversion of 2-oxoglutarate and 2-hydroxyglutarate
beta-Hydroxy-beta-methylglutaryl coenzyme A
The disulfide relay system of mitochondria is connected to the respiratory chain
Phosphorylation of the human La antigen on serine 366 can regulate recycling of RNA polymerase III transcription complexes.
Long G tails at both ends of human chromosomes suggest a C strand degradation mechanism for telomere shortening
microRNA Biogenesis and Function : An overview
myo-inositol 1,3,4,5,6-pentakisphosphate
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Human lung enolase: cloning and sequencing of cDNA and its inducibility with dexamethasone
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phosphatidylinositol 1,4,5-trisphosphate
Molecular cloning and expression of ribosome releasing factor
Functional consequences of PRODH missense mutations
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Class II phosphoinositide 3-kinases are downstream targets of activated polypeptide growth factor receptors
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Abortive initiation by RNA polymerase II in vitro at the adenovirus 2 major late promoter.
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Agmatine: biological role and therapeutic potentials in morphine analgesia and dependence
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phosphatidylinositol 1,3,4,5-tetrakisphosphate
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p38 MAPK signalling cascades: ancient roles and new functions
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Receptor-mediated phagocytosis elicits cross-presentation in nonprofessional antigen-presenting cells
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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=1252087
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120107.1
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_78738.9
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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_5798.3
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_118967.1
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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_137909.5
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A specific role of the yeast mitochondrial carriers MRS3/4p in mitochondrial iron acquisition under iron-limiting conditions
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Phosphorylation relieves autoinhibition of the kinetochore motor Cenp-E
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Subcellular compartmentalization of human Nfu, an iron-sulfur cluster scaffold protein, and its ability to assemble a [4Fe-4S] cluster
Proc. Natl. Acad. Sci. U.S.A. 100:9762-7
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The interaction between N-WASP and the Arp2/3 complex links Cdc42-dependent signals to actin assembly
Protein insertion into the mitochondrial inner membrane by a twin-pore translocase
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all-trans-6-methoxy-2-hexaprenylhydroquinone [ChEBI:61472]
all-trans-5-methoxy-2-methyl-3-hexaprenylhydroquinone [ChEBI:61473]
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Cloning, expression, and characterization of a human 4'-phosphopantetheinyl transferase with broad substrate specificity
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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_4026.2
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Role of human sphingosine-1-phosphate phosphatase 1 in the regulation of intra- and extracellular sphingosine-1-phosphate levels and cell viability
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S-adenosylmethionine: nothing goes to waste
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Nitric oxide and peroxynitrite in health and disease
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_21081.2
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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_20771.2
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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_13894.1
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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=3670862
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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=429875
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_92279.9
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_20726.1
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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_21171.2
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_21240.2
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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_20978.2
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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_20993.2
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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_20887.1
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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_160649.1
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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_5783.1
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Sequence identification and characterization of human carnosinase and a closely related non-specific dipeptidase
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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_21065.2
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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_21154.2
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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=446606
ribose 1-phosphate, deoxyribose 1-phosphate
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Characterization of rhoGAP. A GTPase-activating protein for rho-related small GTPases.
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S-adenosylmethionine synthesis: molecular mechanisms and clinical implications
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Localization of GAR transformylase in Escherichia coli and mammalian cells
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Metabolism of alpha-linolenic acid in humans
Prostaglandins Leukot Essent Fatty Acids 75:161-8
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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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Cytochromes c1 and b2 are sorted to the intermembrane space of yeast mitochondria by a stop-transfer mechanism
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A refined structure of human aquaporin-1
FUNCTION Component of the TIM22 complex, a complex that mediates the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. The TIM22 complex forms a twin-pore translocase that uses the membrane potential as external driving force. Its role in the complex is unclear but it may be involved in the assembly and stabilization of the TIM22 complex.SUBUNIT Component of the TIM22 complex, whose core is composed of TIM18, TIM22 and TIM54, associated with the peripheral proteins MRS5/TIM12 and the 70 kDa heterohexamer composed of TIM9 and TIM10 (or TIM8 and TIM13).DISRUPTION PHENOTYPE Although cells lacking TIM18 live well and do not display any strong phenotype, they do not survive in the absence of mitochondrial DNA.MISCELLANEOUS Present with 4440 molecules/cell in log phase SD medium.SIMILARITY Belongs to the CybS family.
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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.
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Molecular cloning and expression of human carnitine octanoyltransferase: evidence for its role in the peroxisomal beta-oxidation of branched-chain fatty acids
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Binding and release of radiolabeled eukaryotic initiation factors 2 and 3 during 80 S initiation complex formation.
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The role of calcium signaling in phagocytosis
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Structural basis for SENP2 protease interactions with SUMO precursors and conjugated substrates
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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
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The human chromokinesin Kid is a plus end-directed microtubule-based motor
pXBP1(U) encoded in XBP1 pre-mRNA negatively regulates unfolded protein response activator pXBP1(S) in mammalian ER stress response
Further studies on the activity and subcellular distribution of alanine:glyoxylate aminotransferase in the livers of patients with primary hyperoxaluria type 1
Phosphoinositide-metabolizing enzymes at the interface between membrane traffic and cell signalling
Altered aquaporin 9 expression and localization in human hepatocellular carcinoma
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(24S)-3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestan-26-oate [ChEBI:63824]
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pH dependence, substrate specificity and inhibition of human kynurenine aminotransferase I
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(24S)-7alpha,24-dihydroxy-5beta-cholestan-3-one [ChEBI:63829]
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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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4-carboxy-4-methylzymosterol [ChEBI:63842]
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Crystal structures of human mitochondrial branched chain aminotransferase reaction intermediates: ketimine and pyridoxamine phosphate forms
(24S)-7alpha,12alpha,24-trihydroxycholest-4-en-3-one [ChEBI:63839]
(24S)-7alpha,24-dihydroxycholest-4-en-3-one [ChEBI:63838]
(24S)-5beta-cholestane-3alpha,7alpha,24-triol [ChEBI:63831]
(24S)-7alpha,12alpha,24-trihydroxy-5beta-cholestan-3-one [ChEBI:63830]
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MCD4 encodes a conserved endoplasmic reticulum membrane protein essential for glycosylphosphatidylinositol anchor synthesis in yeast
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Cooperation of translocase complexes in mitochondrial protein import
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(E)-2,3-didehydropristanoyl-CoA [ChEBI:63803]
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5-phospho-alpha-D-ribose 1-diphosphate [ChEBI:17111]
FUNCTION DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. C31 is involved in the formation of the initiation complex.SUBUNIT Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits.MISCELLANEOUS The acidic domain is essential for its function.SIMILARITY Belongs to the eukaryotic RPC7 RNA polymerase subunit family.
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Four Na+/H+ exchanger isoforms are distributed to Golgi and post-Golgi compartments and are involved in organelle pH regulation
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SUMO protease SENP1 induces isomerization of the scissile peptide bond
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Molecular identification of mammalian phosphopentomutase and glucose-1,6-bisphosphate synthase, two members of the alpha-D-phosphohexomutase family
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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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Presynaptic phase of homologous DNA pairing and strand exchange
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1-phosphatidyl-1D-myo-inositol 3-phosphate
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1-phosphatidyl-1D-myo-inositol 4-phosphates
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Crystal structures of human and Staphylococcus aureus pyruvate carboxylase and molecular insights into the carboxyltransfer reaction
FUNCTION DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. Involved in Pol III transcription reinitiation and RNA cleavage during transcription termination.SUBUNIT Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits.SIMILARITY Belongs to the archaeal RpoM/eukaryotic RPA12/RPB9/RPC11 RNA polymerase family.SIMILARITY Contains 1 TFIIS-type zinc finger.
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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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6Z,9Z,12Z,15Z,18Z-tetracosapentaenoyl-CoA (TPA-CoA)
Reconstitution of the B cell antigen receptor signaling components in COS cells
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6Z,9Z,12Z,15Z,18Z,21Z-tetracosahexaenoyl-CoA (THA-CoA)
Human porphobilinogen deaminase mutations in the investigation of the mechanism of dipyrromethane cofactor assembly and tetrapyrrole formation
Regulated transport of the glucose transporter GLUT4.
NUDT9, a member of the Nudix hydrolase family, is an evolutionarily conserved mitochondrial ADP-ribose pyrophosphatase
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(4Z,7Z,10Z,13Z,16Z,19Z)-Docosahexaenoic acid
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FUNCTION Channel-forming protein essential for import of protein precursors into mitochondria.SUBUNIT Forms part of the preprotein translocase complex of the outer mitochondrial membrane (TOM complex) which consists of at least 7 different proteins (TOM5, TOM6, TOM7, TOM20, TOM22, TOM40 and TOM70). Interacts with mitochondrial targeting sequences. Interacts with FCJ1.SIMILARITY Belongs to the Tom40 family.
FUNCTION Transport of phosphate groups from the cytosol to the mitochondrial matrix.SIMILARITY Belongs to the mitochondrial carrier (TC 2.A.29) family.SIMILARITY Contains 3 Solcar repeats.
Regulation of PLK1 Activity at G2/M Transition
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Characterization of a heart-specific fatty acid transport protein
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Ligand-independent activation of fibroblast growth factor receptors by point mutations in the extracellular, transmembrane, and kinase domains
Direct role of ChREBP.Mlx in regulating hepatic glucose-responsive genes.
1-Hydroxypropane-1,2,3-tricarboxylic acid
Release of apoptotic factors from the mitochondria
Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma
Purified human erythrocyte pyrroline-5-carboxylate reductase. Preferential oxidation of NADPH.
A lipid-anchored Grb2-binding protein that links FGF-receptor activation to the Ras/MAPK signaling pathway
AU-rich elements and the control of gene expression through regulated mRNA stability
Mechanisms of COPII vesicle formation and protein sorting
FUNCTION Involved in mitochondrial distribution and morphology. Mediates the import of UPS1, UPS2 and UPS3, 3 atypical mitochondrial intermembrane space (IMS) proteins lacking the two major IMS-targeting signals, into the intermembrane space.SUBUNIT Interacts with UPS1, UPS2 and UPS3.MISCELLANEOUS Present with 3870 molecules/cell in log phase SD medium.SIMILARITY Belongs to the TRIAP1/MDM35 family.
triphopsphoric acid 1-xanthosin-5'-yl ester
Cloning of the human carnitine-acylcarnitine carrier cDNA and identification of the molecular defect in a patient
The human kinesin Kif18A is a motile microtubule depolymerase essential for chromosome congression
1-phosphatidyl-1D-myo-inositol 4-phosphate
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Molecular variation in relation to purine metabolism
J Clin Pathol Suppl (R Coll Pathol) 8:48-63
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RED2, a brain-specific member of the RNA-specific adenosine deaminase family.
Organization and sequence of the gene for the human mitochondrial dicarboxylate carrier: evolution of the carrier family
The monotopic membrane protein human oxidosqualene cyclase is active as monomer
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FUNCTION Central component of the TOM (translocase of outer membrane) receptor complex responsible for the recognition and translocation of cytosolically synthesized mitochondrial preproteins. Together with TOM22 functions as the transit peptide receptor at the surface of the mitochondrion outer membrane and facilitates the movement of preproteins into the TOM40 translocation pore.SUBUNIT Forms part of the preprotein translocase complex of the outer mitochondrial membrane (TOM complex) which consists of at least 7 different proteins (TOM5, TOM6, TOM7, TOM20, TOM22, TOM40 and TOM70). In the complex, interacts with TOM22.MISCELLANEOUS Present with 5680 molecules/cell in log phase SD medium.SIMILARITY Belongs to the Tom20 family.
Messenger RNA decay in mammalian cells: the exonuclease perspective
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Formation of the active cofactor, UDP-glucuronate
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Gastrin-CREB signalling pathway via PKC and MAPK
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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
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FUNCTION Acyltransferase which mediates the conversion of 1-acyl-sn-glycero-3-phosphocholine (LPC) into phosphatidylcholine (PC). Displays a broad LPC fatty acyl chain substrate specificity utilizing LPC molecules ranging in length from C-10 to C-20. Does not utilize other lysolipids than LPC as acceptor. Also shows acyl-CoA-independent acyltransferase activity. Required for normal phospholipid content of mitochondrial membranes. Involved in the remodeling of the acyl groups of cardiolipin in the mitochondrial inner membrane, which affects the assembly and stability of respiratory chain complex IV and its supercomplex forms.CATALYTIC ACTIVITY Acyl-CoA + 1-acyl-sn-glycero-3-phosphocholine = CoA + 1,2-diacyl-sn-glycero-3-phosphocholine.ENZYME REGULATION Inhibited by zinc and o-phenanthroline.MISCELLANEOUS Present with 1340 molecules/cell in log phase SD medium.SIMILARITY Belongs to the taffazin family.
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activated TAK1 mediates p38 MAPK activation
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Protein quality control in the ER: the recognition of misfolded proteins
3-hydroxy-2,6,10,14-tetramethylpentadecanoyl-coenzyme A
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]
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Access of soluble antigens to the endoplasmic reticulum can explain cross-presentation by dendritic 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=3670776
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_144715.5
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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=3670786
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3670783
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_86997.9
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=428663
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20116.2
A telomeric sequence in the RNA of Tetrahymena telomerase required for telomere repeat synthesis
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Regulation of Cholesterol Biosynthesis by SREBP (SREBF)
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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=3673645
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_158356.3
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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_156804.3
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=3672901
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_159000.3
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=3668945
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667483
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672899
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667484
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667485
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669001
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Glucose transporter isoforms GLUT1 and GLUT3 transport dehydroascorbic acid
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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=3668999
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669000
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668939
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_83133.9
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=3668994
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668995
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668996
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667163
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673139
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_110187.9
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Mechanisms of disease: molecular and metabolic mechanisms of insulin resistance and beta-cell failure in type 2 diabetes
The human T-type amino acid transporter-1: characterization, gene organization, and chromosomal location
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(R,R)-3,3'-thiobis-(2-aminopropanoic acid)
(R,R)-2,6-diamino-4-thiaheptanedioic acid
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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=3668936
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_83592.9
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Tyrosine-phosphorylated forms of Ig beta, CD22, TCR zeta and HOSS are major ligands for tandem SH2 domains of Syk
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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=3672895
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667147
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_156048.3
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Glycoprotein folding, quality control and ER-associated degradation
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2728.2
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Database identifier. Use 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
Reactome stable identifier. Use this 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
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_116459.1
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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=3672533
Vav regulates activation of Rac but not Cdc42 during FcgammaR-mediated phagocytosis
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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_100314.9
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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_98045.9
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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_155141.3
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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=29356
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
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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=3672532
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672513
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672525
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672535
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672564
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118312.7
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15677.1
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=379707
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15566.1
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=379772
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118486.7
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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_15727.1
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Cloning and characterization of GEF-H1, a microtubule-associated guanine nucleotide exchange factor for Rac and Rho GTPases
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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_16052.1
The Cfd1-Nbp35 complex acts as a scaffold for iron-sulfur protein assembly in the yeast cytosol
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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_17915.1
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=379757
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17273.1
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=379787
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_17784.1
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Isolation and characterization of a human cDNA for mRNA 5'-capping enzyme.
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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=3666777
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3666789
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3667650
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3666788
Purification of the serine palmitoyltransferase complex responsible for sphingoid base synthesis by using affinity peptide chromatography techniques
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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=3666773
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_144895.5
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=3666785
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2066767
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3666795
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3666765
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3666769
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2046054
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_123619.1
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=211606
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668614
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_23217.1
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=3668613
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2046047
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668990
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_124358.1
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=3672756
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668605
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668609
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3668601
Human cytosolic asparaginyl-tRNA synthetase: cDNA sequence, functional expression in Escherichia coli and characterization as human autoantigen
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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_124098.1
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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=3666761
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3666799
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2066766
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3666792
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_121859.1
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_123653.1
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=3666781
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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=2066762
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Characterization of human glycogenin-2, a self-glucosylating initiator of liver glycogen metabolism.
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1-phosphatidyl-1D-myo-inositol 3-phosphate [ChEBI:17283]
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ChEBI:17278 5beta-cholestane-3alpha,7alpha,12alpha,26-tetrol
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FUNCTION FAD-dependent sulfhydryl oxidase that catalyzes disulfide bond formation. Required for the import and folding of small cysteine-containing proteins in the mitochondrial intermembrane space (IMS). Forms a redox cycle with MIA40 that involves a disulfide relay system. Important for maintaining the cysteine residues in MIA40 in an oxidized state. Reduced ERV1 is reoxidized by cytochrome c. Required for the maturation of cytoplasmic, but not of mitochondrial Fe/S proteins.CATALYTIC ACTIVITY 2 R'C(R)SH + O(2) = R'C(R)S-S(R)CR' + H(2)O(2).COFACTOR FAD.SUBUNIT Homodimer. Interacts with MIA40, forming transient intermolecular disulfide bridges.SIMILARITY Contains 1 ERV/ALR sulfhydryl oxidase domain.
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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_3796.2
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Structure of human adenosine kinase at 1.5 A resolution.
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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_5617.1
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=265283
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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
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Efficient synthesis, termination and release of RNA polymerase III transcripts in Xenopus extracts depleted of La protein
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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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p21-activated protein kinase: a crucial component of morphological signaling?
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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=75086
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_154278.3
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_4119.1
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Expression of BIP (78 kDa Glucose-regulated protein, GRP78, HSPA5)
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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_155903.3
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=265287
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_15804.2
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_31593.10
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=72084
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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_3913.3
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_5393.1
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Human monocarboxylate transporter 2 (MCT2) is a high affinity pyruvate transporter
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Hormone-sensitive lipase: control of intracellular tri-(di-)acylglycerol and cholesteryl ester hydrolysis
Pol II mediated transcription of microRNA genes
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NEUROD1- and PDX1-dependent synthesis of glucokinase (GCK) protein
HNF1A-dependent synthesis of GLUT2 protein
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7747.2
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Production of formyl-CoA during peroxisomal alpha-oxidation of 3-methyl-branched fatty acids
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Expression of SRPR (SRP Receptor subunit alpha)
Expression of SRPRB (SRP Receptor subunit beta)
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Proximal events in Wnt signal transduction
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Identification and functional characterization of a new human kidney-specific H+/organic cation antiporter, kidney-specific multidrug and toxin extrusion 2
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Principles of bioactive lipid signalling: lessons from sphingolipids
Coregulation of estrogen receptor by ERBB4/HER4 establishes a growth-promoting autocrine signal in breast tumor cells
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Membrane lipids: where they are and how they behave
Membrane recognition by phospholipid-binding domains
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Atomic structure of GTP cyclohydrolase I
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Critical role for tetrahydrobiopterin recycling by dihydrofolate reductase in regulation of endothelial nitric-oxide synthase coupling: relative importance of the de novo biopterin synthesis versus salvage pathways
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Alteration of enzyme specificity by computational loop remodeling and design
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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
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
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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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Synthesis of glycosylphosphatidylinositol (GPI)
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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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MISCELLANEOUS Present with 6960 molecules/cell in log phase SD medium.SIMILARITY Contains 1 CHCH domain.
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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
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Pyruvate kinase isozyme type M2 (PKM2) interacts and cooperates with Oct-4 in regulating transcription
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Chromatin association of human origin recognition complex, cdc6, and minichromosome maintenance proteins during the cell cycle: assembly of prereplication complexes in late mitosis.
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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
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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
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The sugar is sIRVed: sorting Glut4 and its fellow travelers
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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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Direct interaction of mitochondrial targeting presequences with purified components of the TIM23 protein complex
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Lowe syndrome, a deficiency of phosphatidylinositol 4,5-bisphosphate 5-phosphatase in the Golgi apparatus
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Metabolism of amino acids and derivatives
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(S)-1-Pyrroline-5-carboxylate [ChEBI:17388]
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A mutation in the Glut2 glucose transporter gene of a diabetic patient abolishes transport activity
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Mediator function of the human Rad51B-Rad51C complex in Rad51/RPA-catalyzed DNA strand exchange.
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118468.7
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673638
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665738
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672419
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_162160.2
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=3672417
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673637
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673237
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_124477.1
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_133401.5
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=1806205
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673629
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672418
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_161988.2
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=3672416
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665725
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665731
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665734
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665728
Greatwall kinase participates in the Cdc2 autoregulatory loop in Xenopus egg extracts
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665737
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3666746
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3666737
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3666741
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665722
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3666743
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3666742
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_77713.9
Mycobacterium tuberculosis and the intimate discourse of a chronic infection
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3666745
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665708
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665704
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_92729.9
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=3673057
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665719
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29926
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665709
The t(8;22) in chronic myeloid leukemia fuses BCR to FGFR1: transforming activity and specific inhibition of FGFR1 fusion proteins
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2473607
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26419.2
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=975622
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_162438.2
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=3672395
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673640
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672393
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_162989.2
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=1806224
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673639
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_126193.5
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_120430.6
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672351
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_122144.1
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_140625.5
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=3665697
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665698
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665747
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665703
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1806240
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_113360.8
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_123499.1
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=3665752
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672430
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665715
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665746
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_162031.2
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=3672830
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_162104.2
c-Kit--a hematopoietic cell essential receptor tyrosine kinase
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673636
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_130729.5
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=3672823
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672312
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672828
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672310
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672827
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_142935.5
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=3673600
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_132036.5
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_160756.1
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=3672391
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665713
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665714
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665745
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665744
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1806200
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665743
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_124533.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665742
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_145110.5
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=3665739
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665741
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3665740
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3671367
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3671368
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_102268.9
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=3673135
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_85873.9
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_4653.3
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=29448
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4077.3
G protein-independent activation of an inward Na(+) current by muscarinic receptors in mouse pancreatic beta-cells
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29502
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5376.2
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=76213
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673245
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672421
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_145319.5
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_145942.5
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=3672423
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147199.5
NOD-like receptors (NLRs): bona fide intracellular microbial sensors
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1806199
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_123880.1
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=3672387
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_130845.5
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=1806180
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_122226.1
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=3673606
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672487
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_138249.5
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=3672486
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672510
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_136204.5
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_140609.5
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_132151.5
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=3673612
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_144619.5
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=3673610
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_145359.5
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=3673611
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2045079
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_123740.1
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=3672575
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672576
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3673472
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_82072.9
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=3673471
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_146654.5
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=3672449
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672450
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_130626.5
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=3672477
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_146341.5
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=3672504
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_121922.1
Half-site reactivity in 6-phosphogluconate dehydrogenase from human erythrocytes
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2054052
Adrenoleukodystrophy gene: unexpected homology to a protein involved in peroxisome biogenesis
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2038921
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1839035
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_125075.1
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=2038919
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_123273.1
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_124230.1
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=3672509
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672508
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_125882.5
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=3672465
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672466
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_134549.5
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=3672482
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672455
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672456
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_133717.5
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ESCRTing proteins in the endocytic pathway
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all-trans-decaprenyl diphosphate [ChEBI:61011]
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Plk1-dependent phosphorylation of optineurin provides a negative feedback mechanism for mitotic progression
The structure and function of G-protein-coupled receptors
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Mechanisms of glycerophospholipid homeostasis in mammalian cells
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The transport of pyruvate in rat liver mitochondria
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Dissecting and manipulating the pathway for glycosylphosphatidylinositol-anchor biosynthesis
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Cleavage and activation of p21-activated protein kinase gamma-PAK by CPP32 (caspase 3). Effects of autophosphorylation on activity
Phosphoinositide phosphatases in a network of signalling reactions
A mitochondrial pyruvate carrier required for pyruvate uptake in yeast, Drosophila, and humans
MCM8 is an MCM2-7-related protein that functions as a DNA helicase during replication elongation and not initiation
Polymerase switching on the C-strand of the telomere
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The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5
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Dock4 is regulated by RhoG and promotes Rac-dependent cell migration
FGFR1 is fused with a novel zinc-finger gene, ZNF198, in the t(8;13) leukaemia/lymphoma syndrome
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ZNF76 and ZNF143 are two human homologs of the transcriptional activator Staf
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
Switching of origins to a post-replicative state
Replication factor C disengages from proliferating cell nuclear antigen (PCNA) upon sliding clamp formation, and PCNA itself tethers DNA polymerase delta to DNA.
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Degradation of endocytosed epidermal growth factor and virally ubiquitinated major histocompatibility complex class I is independent of mammalian ESCRTII
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4-(2-aminophenyl)-2,4-dioxobutanoic acid
ChEBI:17442 4-(2-aminophenyl)-2,4-dioxobutanoic acid
Mammalian frataxin: an essential function for cellular viability through an interaction with a preformed ISCU/NFS1/ISD11 iron-sulfur assembly complex
Purification, sequencing, and molecular identification of a mammalian PP-InsP5 kinase that is activated when cells are exposed to hyperosmotic stress
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Calcium signalling: past, present and future
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Cholesterol feedback: from Schoenheimer's bottle to Scap's MELADL
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Rich tapestry of G protein-coupled receptor signaling and regulatory mechanisms
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Molecular characterization of a novel short-chain dehydrogenase/reductase that reduces all-trans-retinal
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Human X-linked phosphoribosylpyrophosphate synthetase superactivity is associated with distinct point mutations in the PRPS1 gene
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Regulation of apoptosis: the ubiquitous way
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Kit- and Fc epsilonRI-induced differential phosphorylation of the transmembrane adaptor molecule NTAL/LAB/LAT2 allows flexibility in its scaffolding function in mast cells
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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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FUNCTION Component of the TOM (translocase of outer membrane) receptor complex responsible for the recognition and translocation of cytosolically synthesized mitochondrial preproteins. TOM6 is involved in assembly and stability of the TOM complex.SUBUNIT Forms part of the TOM (translocase of outer membrane) complex that consists of at least 7 different proteins (TOM5, TOM6, TOM7, TOM20, TOM22, TOM40 and TOM70).SIMILARITY Belongs to the Tom6 family.
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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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Phospholipid meets all-trans-retinal: the making of RPE bisretinoids
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Erv1 mediates the Mia40-dependent protein import pathway and provides a functional link to the respiratory chain by shuttling electrons to cytochrome c
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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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Whose end is destruction: cell division and the anaphase-promoting complex.
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Three transitions in the RNA polymerase II transcription complex during initiation.
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The protein import motor of mitochondria: unfolding and trapping of preproteins are distinct and separable functions of matrix Hsp70
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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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Transcriptional Regulation of White Adipocyte Differentiation
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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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Mitochondrial presequence translocase: switching between TOM tethering and motor recruitment involves Tim21 and Tim17
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N-Acetyl-D-glucosamine 1-phosphate [ChEBI:7125]
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RNA Polymerase II Pre-transcription Events
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Cloning and expression of human phenylalanyl-tRNA synthetase in Escherichia coli: comparative study of purified recombinant enzymes
Mucin-type O-glycosylation and its potential use in drug and vaccine development
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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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
Human adrenoleukodystrophy protein and related peroxisomal ABC transporters interact with the peroxisomal assembly protein PEX19p
Molecular mechanisms involved in the regulation of cytokine production by muramyl dipeptide
Glycine and taurine conjugation of bile acids by a single enzyme. Molecular cloning and expression of human liver bile acid CoA:amino acid N-acyltransferase.
The visual cycle of the cone photoreceptors of the retina
Integrated signalling pathways for mast-cell activation
Molecular cloning of a functional thrombin receptor reveals a novel proteolytic mechanism of receptor activation
Human types 1 and 3 3 alpha-hydroxysteroid dehydrogenases: differential lability and tissue distribution
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
Tim9p, an essential partner subunit of Tim10p for the import of mitochondrial carrier proteins
Functions of replication factor C and proliferating-cell nuclear antigen: functional similarity of DNA polymerase accessory proteins from human cells and bacteriophage T4.
Activation of TM7SF2 promoter by SREBP-2 depends on a new sterol regulatory element, a GC-box, and an inverted CCAAT-box
Sterol transfer by ABCG5 and ABCG8: in vitro assay and reconstitution
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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]
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Pro-inflammatory cytokines and environmental stress cause p38 mitogen-activated protein kinase activation by dual phosphorylation on tyrosine and threonine
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Identification of a novel gene, FGFR1OP2, fused to FGFR1 in 8p11 myeloproliferative syndrome
Structural and functional roles of the conserved cysteine residues of the redox-regulated import receptor Mia40 in the intermembrane space of mitochondria
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MyD88 dependent cascade initiated on endosome
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Similar regulation of human inducible nitric-oxide synthase expression by different isoforms of the RNA-binding protein AUF1
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SLC4 base (HCO3 -, CO3 2-) transporters: classification, function, structure, genetic diseases, and knockout models
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Metal transporters in intestine and brain: their involvement in metal-associated neurotoxicities
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Expression and characterization of human mitochondrial ferredoxin reductase in Escherichia coli
Molecular mechanism of ADP-ribose hydrolysis by human NUDT5 from structural and kinetic studies
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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
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Role of the Zn(2+) motif of E1 in SUMO adenylation
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The Bcl2 family: regulators of the cellular life-or-death switch
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Proton-coupled monocarboxylate transport
SUMO-specific proteases: a twist in the tail
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Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs
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Formation of transcription-coupled NER (TC-NER) repair complex
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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
Oxidized LDL-induced endolysosomal phospholipidosis and enzymatically modified LDL-induced foam cell formation determine specific lipid species modulation in human macrophages
Characterization of purine nucleoside phosphorylase from human granulocytes and its metabolism of deoxyribonucleosides
PTEN loss in the continuum of common cancers, rare syndromes and mouse models
Mammalian ABC transporters in health and disease
Phosphatidylinositol 3-phosphate-interacting domains in PIKfyve. Binding specificity and role in PIKfyve. Endomenbrane localization
Tim50, a novel component of the TIM23 preprotein translocase of mitochondria
Membrane-bound enzymes of cholesterol synthesis from lanosterol
Cholesterol, hydroxycholesterols, and bile acids
Familial deficiency of glutathione reductase in human blood cells
Complete amino acid sequence of human phosphoglycerate kinase. Isolation and amino acid sequence of tryptic peptides.
STIM1 clusters and activates CRAC channels via direct binding of a cytosolic domain to Orai1
Mechanisms of MHC class I-restricted antigen processing and cross-presentation
Lysosomes in iron metabolism, ageing and apoptosis
Cross-presentation: underlying mechanisms and role in immune surveillance
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Discovery of molecular and catalytic diversity among human diphosphoinositol-polyphosphate phosphohydrolases. An expanding Nudt family
Atherosclerosis and sterol 27-hydroxylase: evidence for a role of this enzyme in elimination of cholesterol from human macrophages
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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_57045.10
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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)
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Evolution of the Glx-tRNA synthetase family: the glutaminyl enzyme as a case of horizontal gene transfer
Cloning of a human nucleoside transporter implicated in the cellular uptake of adenosine and chemotherapeutic drugs
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Stoichiometric and reversible phosphorylation of a 46-kDa protein in human platelets in response to cGMP- and cAMP-elevating vasodilators
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A new fused transcript in Philadelphia chromosome positive acute lymphocytic leukaemia
Assembly of the human origin recognition complex.
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Human cataract lens membrane at subnanometer resolution
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Antigen processing and presentation by the class I major histocompatibility complex
Mapping iron binding sites on human frataxin: implications for cluster assembly on the ISU Fe-S cluster scaffold protein
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Isolation and functional expression of human COQ3, a gene encoding a methyltransferase required for ubiquinone biosynthesis
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Formation of the ternary complex, and subsequently, the 43S complex
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Pannexin-1 mediates large pore formation and interleukin-1beta release by the ATP-gated P2X7 receptor
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Targeting death and decoy receptors of the tumour-necrosis factor superfamily
Nuclease activities in a complex of human recombination and DNA repair factors Rad50, Mre11, and p95.
The proline-rich region of Vav binds to Grb2 and Grb3-3
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.
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Structural requirements for PAK activation by Rac GTPases
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.
AMP (dAMP) kinase from human erythrocytes
Guanylate kinases from human erythrocytes, hog brain, and rat liver
Receptor specificity of the fibroblast growth factor family. The complete mammalian FGF family.
Trans-synaptic transmission of vesicular Wnt signals through Evi/Wntless
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Distinct membrane domains on endosomes in the recycling pathway visualized by multicolor imaging of Rab4, Rab5, and Rab11
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(5Z,13E)-(15S)-9alpha,15-Dihydroxy-11-oxoprosta-5,13-dienoate [ChEBI:246]
5-Heptenoic acid, 7-[3,5-dihydroxy-2-(3-hydroxy-1-octenyl)cyclopentyl]-
7-[3, 5-dihydroxy-2-(3-hydroxy-1-octenyl) cyclopentyl]-5-heptenoic acid
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Phosphorylation of hUPF1 induces formation of mRNA surveillance complexes containing hSMG-5 and hSMG-7
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Activation of NF-kappa B requires proteolysis of the inhibitor I kappa B-alpha: signal-induced phosphorylation of I kappa B-alpha alone does not release active NF-kappa B
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The microsomal cardiolipin remodeling enzyme acyl-CoA lysocardiolipin acyltransferase is an acyltransferase of multiple anionic lysophospholipids
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ChEBI:17825 7-methylguanosine 5'-phosphate
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4,4-Dimethyl-5alpha-cholesta-8,14,24-trien-3beta-ol [ChEBI:1743]
1D-myo-Inositol 1,4-bisphosphate [ChEBI:812]
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Novel molecular defects of the delta-aminolevulinate dehydratase gene in a patient with inherited acute hepatic porphyria
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Transcription factors IIE and IIH and ATP hydrolysis direct promoter clearance by RNA polymerase II.
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Functional studies of human intestinal alkaline sphingomyelinase by deglycosylation and mutagenesis
Human Rad51 protein can form homologous joints in the absence of net strand exchange.
Seven novel mutations in the methylenetetrahydrofolate reductase gene and genotype/phenotype correlations in severe methylenetetrahydrofolate reductase deficiency
Sequence-specific DNA primer effects on telomerase polymerization activity
Signaling, cytoskeletal and membrane mechanisms regulating GLUT4 exocytosis
Zinc efflux and compartmentalization by the SLC30 family
Negative regulation of dE2F1 by cyclin-dependent kinases controls cell cycle timing
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The isolation and characterization of a cDNA encoding phospholipid-specific inositol polyphosphate 5-phosphatase
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Expression, purification, and kinetic constants for human and Escherichia coli pyridoxal kinases
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A cryptic matrix targeting signal of the yeast ADP/ATP carrier normally inserted by the TIM22 complex is recognized by the TIM23 machinery
Unstable kinetochore-microtubule capture and chromosomal instability following deletion of CENP-E
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Prog Nucleic Acid Res Mol Biol 42:259-287
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endoplasmic reticulum quality control compartment
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Characterization and tRNA recognition of mammalian mitochondrial seryl-tRNA synthetase
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FUNCTION Cleaves presequences (transit peptides) from mitochondrial protein precursors.CATALYTIC ACTIVITY Release of N-terminal transit peptides from precursor proteins imported into the mitochondrion, typically with Arg in position P2.COFACTOR Binds 1 zinc ion per subunit.SUBUNIT Heterodimer of alpha and beta subunits.MISCELLANEOUS Present with 1360 molecules/cell in log phase SD medium.SIMILARITY Belongs to the peptidase M16 family.
Vitamins B6 activation to pyridoxal phosphate
Compartmentation of hexokinase in human blood cells. Characterization of soluble and particulate enzymes.
Stoichiometry of 4-methyl sterol oxidase of rat liver microsomes
Human HRD1 promoter carries a functional unfolded protein response element to which XBP1 but not ATF6 directly binds
Cloning and characterization of a 72-kDa inositol-polyphosphate 5-phosphatase localized to the Golgi network
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RAGE and amyloid-beta peptide neurotoxicity in Alzheimer's disease
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FUNCTION MRS3 suppresses a mitochondrial splice defect in the first intron of the COB gene. It may act as a carrier, exerting its suppressor activity via modulation of solute concentrations in the mitochondrion (possibly of cations).MISCELLANEOUS Present with 1360 molecules/cell in log phase SD medium.SIMILARITY Belongs to the mitochondrial carrier (TC 2.A.29) family.SIMILARITY Contains 3 Solcar repeats.
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The narrow substrate specificity of human tyrosine aminotransferase--the enzyme deficient in tyrosinemia type II
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G protein betagamma subunits: central mediators of G protein-coupled receptor signaling
Telomere C-strand (Lagging Strand) Synthesis
Identification of a dehydrogenase acting on D-2-hydroxyglutarate
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
Transmembrane transport of small molecules
Phosphorylation inhibits guanine nucleotide exchange on eukaryotic initiation factor 2.
Dehydroascorbic acid transport by GLUT4 in Xenopus oocytes and isolated rat adipocytes
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Desaturation and chain elongation of n - 3 and n - 6 polyunsaturated fatty acids in the human CaCo-2 cell line
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Structure and transcription of a human gene for H1 RNA, the RNA component of human RNase P
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xanthosine 5'-monophosphate [ChEBI:15652]
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Electron microscopic observation and single-stranded DNA binding activity of the Mcm4,6,7 complex.
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Cdc42 regulates Fc gamma receptor-mediated phagocytosis through the activation and phosphorylation of Wiskott-Aldrich syndrome protein (WASP) and neural-WASP
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Distribution of aquaporin water channels AQP1 and AQP5 in the ductal system of the human pancreas
(S)-3-Hydroxy-3-methylglutaryl-CoA [ChEBI:15467]
Fatty acid, triacylglycerol, and ketone body metabolism
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Signaling by distinct classes of phosphoinositide 3-kinases
Mechanisms of p75-mediated death of hippocampal neurons. Role of caspases
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Receptor for advanced glycation end products (RAGE) regulates sepsis but not the adaptive immune response
Biochemical genetics of the pentose phosphate cycle: human ribose 5-phosphate isomerase (RPI) and ribulose 5-phosphate 3-epimerase (RPE)
RNA Polymerase II Transcription Initiation
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Phospholipase C-gamma as a signal-transducing element
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Phosphorylation of acyclovir (acycloguanosine) monophosphate by GMP kinase
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Synthesis and recycling of tetrahydrobiopterin in endothelial function and vascular disease
Sphingosine-1-phosphate lyase in development and disease: sphingolipid metabolism takes flight
3alpha,7alpha-Dihydroxy-5beta-cholestanoyl-CoA [ChEBI:1709]
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Processing of Capped Intronless Pre-mRNA
2'-deoxyadenosine 5'-monophosphate [ChEBI:17713]
Novel mutations in COX15 in a long surviving Leigh syndrome patient with cytochrome c oxidase deficiency
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Human geranylgeranyl diphosphate synthase. cDNA cloning and expression.
A novel intermembrane space-targeting signal docks cysteines onto Mia40 during mitochondrial oxidative folding
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Formation of the 3' end of histone mRNA.
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'G6P [cytosol]' negatively regulates 'PGYM dimer, b form + 2 AMP <=> PGYM b dimer:AMP complex'
'ATP [cytosol]' negatively regulates 'PGYM dimer, b form + 2 AMP <=> PGYM b dimer:AMP complex'
'CIT [cytosol]' positively regulates 'acetyl-CoA + bicarbonate + ATP => malonyl-CoA + H2O + ADP + orthophosphate'
'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)'
'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'
'L-Phe [cytosol]' positively regulates 'GCH1 reduces GTP to dihydroneopterin triphosphate'
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Ten years on: mediation of cell death by the common neurotrophin receptor p75(NTR)
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'CIT [cytosol]' negatively 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'
'3',5'-Cyclic AMP [cytosol]' negatively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'Ac-CoA [cytosol]' negatively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'ATP [cytosol]' negatively regulates 'D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP'
'D-Fructose 1,6-bisphosphate [cytosol]' positively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'AMP [cytosol]' negatively regulates 'D-fructose 1,6-bisphosphate + H2O => D-fructose 6-phosphate + orthophosphate'
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'G6P [cytosol]' positively regulates '8 UDP-glucose + ((1,4)-alpha-D-glucosyl)4 glycogenin => 8 UDP + ((1,4)-alpha-D-glucosyl)8 glycogenin [GYS D form]'
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'ATP [nucleoplasm]' negatively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
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'Ac-CoA [mitochondrial matrix]' positively regulates 'Pyruvate + CO2 + ATP => ADP + Orthophosphate + Oxaloacetate'
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'GDP [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'
'Mg2+ [cytosol]' is required for 'ITPA hydrolyses XTP to XMP'
'XMP [cytosol]' negatively regulates 'IMP + H2O + NAD+ => XMP + NADH + H+ [IMPDH1,2]'
'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]'
'GMP [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
The bipolar mitotic kinesin Eg5 moves on both microtubules that it crosslinks
'L-Arg [mitochondrial matrix]' positively regulates 'glutamate + acetyl CoA => N-acetyl glutamate + CoA'
Initiating DNA synthesis: from recruiting to activating the MCM complex.
'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]'
'AMP [cytosol]' positively regulates 'Formation of phosphoribosyl pyrophosphate amidotransferase tetramer'
'GMP [cytosol]' positively regulates 'Formation of phosphoribosyl pyrophosphate amidotransferase tetramer'
'Mn2+ [mitochondrial matrix]' positively regulates '(R)-2-hydroxyglutarate + FAD => 2-oxoglutarate + FADH2'
'IMP [cytosol]' positively regulates 'Formation of phosphoribosyl pyrophosphate amidotransferase tetramer'
Human CDC45 protein binds to minichromosome maintenance 7 protein and the p70 subunit of DNA polymerase alpha.
'Zn2+ [mitochondrial matrix]' positively regulates '(R)-2-hydroxyglutarate + FAD => 2-oxoglutarate + FADH2'
'Co2+ [mitochondrial matrix]' positively regulates '(R)-2-hydroxyglutarate + FAD => 2-oxoglutarate + FADH2'
Cloning and expression of a human placenta inositol 1,3,4,5-tetrakisphosphate and phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase
'BH4 [cytosol]' negatively regulates 'GCH1 reduces GTP to dihydroneopterin triphosphate'
'ADP [mitochondrial matrix]' positively regulates 'isocitrate + NAD+ => alpha-ketoglutarate + CO2 + NADH + H+ [IDH3]'
Human arginase II: crystal structure and physiological role in male and female sexual arousal
'PRPP [cytosol]' positively regulates 'Dissociation of phosphoribosyl pyrophosphate amidotransferase tetramer'
'Dissociation of phosphoribosyl pyrophosphate amidotransferase tetramer' positively regulates '5-phospho-alpha-D-ribose 1-diphosphate (PRPP) + H2O + L-glutamine <=> 5-phosphoribosylamine + L-glutamate +pyrophosphate'
Glycosylation and palmitoylation of Wnt-3a are coupled to produce an active form of Wnt-3a
'Formation of phosphoribosyl pyrophosphate amidotransferase tetramer' negatively regulates '5-phospho-alpha-D-ribose 1-diphosphate (PRPP) + H2O + L-glutamine <=> 5-phosphoribosylamine + L-glutamate +pyrophosphate'
FUNCTION Mitochondrial intermembrane chaperone that participates in the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. Also required for the transfer of beta-barrel precursors from the TOM complex to the sorting and assembly machinery (SAM complex) of the outer membrane. Acts as a chaperone-like protein that protects the hydrophobic precursors from aggregation and guide them through the mitochondrial intermembrane space. Compared to TIM10, it may have a strong structural role.SUBUNIT Heterohexamer; composed of 3 copies of TIM9 and 3 copies of TIM10, named soluble 70 kDa complex. Associates with the TIM12 component of the TIM22 complex, whose core is composed of TIM18, TIM22 and TIM54. Interacts with the transmembrane regions of multi-pass transmembrane proteins in transit.SIMILARITY Belongs to the small Tim family.
'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'
'heme [mitochondrial matrix]' negatively regulates 'ALAS condenses SUCC-CoA and Gly to form dALA'
'Cys [cytosol]' positively regulates 'Excess cysteine yields lanthionine and H2S'
'phospho-p-S722,S792-RPTOR-1 [cytosol]' negatively regulates 'Activation of S6K1'
'DAG [plasma membrane]' positively regulates 'Activation of conventional Protein Kinase C'
'ATP [cytosol]' is required for 'Ribosomal scanning '
'GTP [cytosol]' is required for 'Met-tRNAi binds to eIF2:GTP to form the ternary complex'
Translocation of GLUT4 to the Plasma Membrane
ExoS Rho GTPase-activating protein activity stimulates reorganization of the actin cytoskeleton through Rho GTPase guanine nucleotide disassociation inhibitor
Initiation of eukaryotic DNA replication: origin unwinding and sequential chromatin association of Cdc45, RPA, and DNA polymerase alpha.
Distinct stem cell myeloproliferative/T lymphoma syndromes induced by ZNF198-FGFR1 and BCR-FGFR1 fusion genes from 8p11 translocations
Expression, purification, and kinetic characterization of recombinant human adenylosuccinate lyase
Phosphoinositide 3-kinase in T cell activation and survival
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Endosomal Sorting Complex Required For Transport (ESCRT)
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Cloning of the rat and human mitochondrial branched chain aminotransferases (BCATm)
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Structure and transcription termination of a lysine tRNA gene from Xenopus laevis.
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FUNCTION Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative helicase essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells. The active ATPase sites in the MCM2-7 ring are formed through the interaction surfaces of two neighboring subunits such that a critical structure of a conserved arginine finger motif is provided in trans relative to the ATP-binding site of the Walker A box of the adjacent subunit. The six ATPase active sites, however, are likely to contribute differentially to the complex helicase activity. Once loaded onto DNA, double hexamers can slide on dsDNA in the absence of ATPase activity.CATALYTIC ACTIVITY ATP + H(2)O = ADP + phosphate.SUBUNIT Component of the MCM2-7 complex. The complex forms a toroidal hexameric ring with the proposed subunit order MCM2-MCM6-MCM4-MCM7-MCM3-MCM5; loaded onto DNA, forms a head-head double hexamer. Interacts with CSM1 and MCM10.MISCELLANEOUS Present with 166 molecules/cell in log phase SD medium.MISCELLANEOUS Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. Specifically a MCM467 subcomplex is shown to have in vitro helicase activity which is inhibited by the MCM2 subunit. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY Belongs to the MCM family.SIMILARITY Contains 1 MCM domain.
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Immunolocalization of the mercurial-insensitive water channel and glycerol intrinsic protein in epithelial cell plasma membranes
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Reabsorption of neutral amino acids mediated by amino acid transporter LAT2 and TAT1 in the basolateral membrane of proximal tubule
The canonical Notch signaling pathway: unfolding the activation mechanism
Transcriptional activities of nuclear SREBP-1a, -1c, and -2 to different target promoters of lipogenic and cholesterogenic genes
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Regulation of Insulin Secretion by Acetylcholine
Transport of vitamins, nucleosides, and related molecules
G(12)/G(13)-mediated signalling in mammalian physiology and disease
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Protein import channel of the outer mitochondrial membrane: a highly stable Tom40-Tom22 core structure differentially interacts with preproteins, small tom proteins, and import receptors
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The RNA polymerase III transcriptome revealed by genome-wide localization and activity-occupancy relationships.
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A novel mechanism of JNK1 activation. Nuclear translocation and activation of JNK1 during ischemia and reperfusion.
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Studies on the initiation and elongation reactions in the simian virus 40 DNA replication system.
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A novel eukaryotic factor for cytosolic Fe-S cluster assembly
Components involved in assembly and dislocation of iron-sulfur clusters on the scaffold protein Isu1p
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NCAM-induced intracellular signaling revisited
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alpha-D-Glucose 6-phosphate [ChEBI:17665]
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Functional cooperation of the mitochondrial processing peptidase subunits
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Amplification and kinetics of the activation steps in phototransduction
RAGE mediates a novel proinflammatory axis: a central cell surface receptor for S100/calgranulin polypeptides
PIG-V involved in transferring the second mannose in glycosylphosphatidylinositol
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
Organic anion transport is the primary function of the SLC17/type I phosphate transporter family
The human sugar-phosphate/phosphate exchanger family SLC37
Subcellular compartmentation and differential catalytic properties of the three human nicotinamide mononucleotide adenylyltransferase isoforms
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
Congenital disorders of glycosylation type Ig is defined by a deficiency in dolichyl-P-mannose:Man7GlcNAc2-PP-dolichyl mannosyltransferase
Recent insights into the structure of Toll-like receptors and post-translational modifications of their associated signalling proteins
Triggering of TLR7 and TLR8 expressed by human lung cancer cells induces cell survival and chemoresistance
Dolichyl phosphate D-mannose [ChEBI:4694]
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
Cloning and characterization of a pH-sensing regulatory factor that modulates transport activity of the human H+/peptide cotransporter, PEPT1
WNT secretion and signalling in human disease
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The class II phosphoinositide 3-kinase PI3K-C2alpha is concentrated in the trans-Golgi network and present in clathrin-coated vesicles
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M-ABC2, a new human mitochondrial ATP-binding cassette membrane protein
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Orc6 involved in DNA replication, chromosome segregation, and cytokinesis.
Cloning and characterization of the mammalian brain-specific, Mg2+-dependent neutral sphingomyelinase
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Est1p as a cell cycle-regulated activator of telomere-bound telomerase
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Purification and functional characterization of aquaporin-8
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A mutation in GLUT2, not in phosphorylase kinase subunits, in hepato-renal glycogenosis with Fanconi syndrome and low phosphorylase kinase activity
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Regulation of human separase by securin binding and autocleavage
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Activation of the U2 snRNA promoter by the octamer motif defines a new class of RNA polymerase II enhancer elements
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3-dehydro-4-methylzymosterol [ChEBI:50593]
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
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Surprising versatility of Na+-glucose cotransporters: SLC5
A mitochondrial import receptor for the ADP/ATP carrier
Direct phosphorylation of IkappaB by IKKalpha and IKKbeta: discrimination between free and NF-kappaB-bound substrate
Purification and properties of guanosine diphosphate hexose pyrophosphorylase from mammalian tissues
Functional characterization and mechanism of action of recombinant human kynurenine 3-hydroxylase
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]
Role of the mitochondrial Hsp70s, Ssc1 and Ssq1, in the maturation of Yfh1
FUNCTION Forms a channel through the cell membrane that allows diffusion of small hydrophilic molecules. The channel adopts an open conformation at low or zero membrane potential and a closed conformation at potentials above 30-40 mV. The open state has a weak anion selectivity whereas the closed state is cation-selective. Is the major permeability fator of the mitochondrial outer membrane.SUBUNIT Interacts with AIM5, FCJ1 and MOS1.DOMAIN Consists mainly of membrane-spanning sided beta-sheets. 19 strands distributed along the entire VDAC protein, have the potential to adopt transmembrane beta pleated sheet structures, which rolled together may form a "beta-barrel" type structure, possessing pore dimensions.SIMILARITY Belongs to the eukaryotic mitochondrial porin family.
DNA topoisomerase I and PC4 can interact with human TFIIIC to promote both accurate termination and transcription reinitiation by RNA polymerase III.
Carnitine biosynthesis: identification of the cDNA encoding human gamma-butyrobetaine hydroxylase.
Preferential DNA repair of an active gene in human cells.
Functional reconstitution of the import of the yeast ADP/ATP carrier mediated by the TIM10 complex
The content of pentose-cycle intermediates in liver in starved, fed ad libitum and meal-fed rats.
Hailey-Hailey disease is caused by mutations in ATP2C1 encoding a novel Ca(2+) pump
Cloning, heterologous expression, and enzymological characterization of human squalene monooxygenase
Molecular identification of human glutamine- and ammonia-dependent NAD synthetases. Carbon-nitrogen hydrolase domain confers glutamine dependency.
Glycoprotein folding and the role of EDEM1, EDEM2 and EDEM3 in degradation of folding-defective glycoproteins
Protein phosphatase 2Cepsilon is an endoplasmic reticulum integral membrane protein that dephosphorylates the ceramide transport protein CERT to enhance its association with organelle membranes
Characterization of ceramide synthase 2: tissue distribution, substrate specificity, and inhibition by sphingosine 1-phosphate
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
The Rac-RhoGDI complex and the structural basis for the regulation of Rho proteins by RhoGDI
Transport of the ADP/ATP carrier of mitochondria from the TOM complex to the TIM22.54 complex
eNOS, COX-2, and prostacyclin production are impaired in endothelial cells from diabetics
3' -UTR-mediated translational regulation
Xeroderma pigmentosum variant (XP-V) correcting protein from HeLa cells has a thymine dimer bypass DNA polymerase activity.
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 novel Cdc42 guanine nucleotide exchange factor, zizimin1, dimerizes via the Cdc42-binding CZH2 domain
Amino acid synthesis and interconversion (transamination)
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ADP-ribosylation factor 1 transiently activates high-affinity adaptor protein complex AP-1 binding sites on Golgi membranes
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The COQ7 gene encodes a protein in Saccharomyces cerevisiae necessary for ubiquinone biosynthesis
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Comprehending the complex connection between PKCbeta, TAK1, and IKK in BCR signaling
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Docosahexaenoic acid synthesis in human skin fibroblasts involves peroxisomal retroconversion of tetracosahexaenoic acid
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Activating and inhibitory functions of DAP12
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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
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N-Acetyl-D-glucosamine 6-phosphate [ChEBI:7127]
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A defect in dolichol phosphate biosynthesis causes a new inherited disorder with death in early infancy
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Cloning, characterization, and expression of cDNAs encoding human delta 1-pyrroline-5-carboxylate dehydrogenase
ChEBI:17899 7alpha-hydroxycholest-4-en-3-one
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Nicotinate D-ribonucleotide [ChEBI:7561]
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(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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Physical exercise-induced hypoglycemia caused by failed silencing of monocarboxylate transporter 1 in pancreatic beta cells
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Synaptojanin 1: localization on coated endocytic intermediates in nerve terminals and interaction of its 170 kDa isoform with Eps15
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
Molecular mechanisms of conduction and selectivity in aquaporin water channels
The enzymes, regulation, and genetics of bile acid synthesis
HEDJ, an Hsp40 co-chaperone localized to the endoplasmic reticulum of human cells
Peroxisome proliferator-activated receptor alpha (PPARalpha ) turnover by the ubiquitin-proteasome system controls the ligand-induced expression level of its target genes
RNA Polymerase III Transcription Initiation From Type 1 Promoter
A stimulatory role for cGMP-dependent protein kinase in platelet activation
Ribosomal scanning and start codon recognition
FUNCTION Co-chaperone required for the assembly of iron-sulfur (Fe/S) clusters in mitochondria. Stimulates the ATPase activity of its specialized Hsp70 chaperone partner SSQ1. Binds to the substrate protein ISU1 and targets it to SSQ1. May function together with SSQ1 in the dislocation of the Fe/S cluster from ISU1 and its insertion into apoproteins.SUBUNIT Interacts with the Fe/S cluster assembly protein ISU1.MISCELLANEOUS Present with 2010 molecules/cell in log phase SD medium.SIMILARITY Belongs to the HscB family.SIMILARITY Contains 1 J domain.
gamma -Secretase cleavage and nuclear localization of ErbB-4 receptor tyrosine kinase
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.
Molecular analysis of a series of alleles in humans with reduced activity at the triosephosphate isomerase locus
Normal human chromosomes have long G-rich telomeric overhangs at one end
Sae2p phosphorylation is crucial for cooperation with Mre11p for resection of DNA double-strand break ends during meiotic recombination in Saccharomyces cerevisiae
Promoter escape by RNA polymerase II. Formation of an escape-competent transcriptional intermediate is a prerequisite for exit of polymerase from the promoter.
FUNCTION Mannosylates Man(2)GlcNAc(2)-dolichol diphosphate and Man(1)GlcNAc(2)-dolichol diphosphate to form Man(3)GlcNAc(2)-dolichol diphosphate.CATALYTIC ACTIVITY GDP-D-mannose + D-Man-beta-(1->4)-D-GlcNAc-beta-(1->4)-D-GlcNAc-diphosphodolichol = GDP + D-Man-alpha-(1->3)-D-Man-beta-(1->4)-D-GlcNAc-beta-(1->4)-GlcNAc-diphosphodolichol.CATALYTIC ACTIVITY GDP-D-mannose + D-Man-alpha-(1->3)-D-Man-beta-(1->4)-D-GlcNAc-beta-(1->4)-D-GlcNAc-diphosphodolichol = GDP + D-Man-alpha-(1->3)-(D-Man-alpha-(1->6))-D-Man-beta-(1->4)-D-GlcNAc-beta-(1->4)-D-GlcNAc-diphosphodolichol.PATHWAY Protein modification; protein glycosylation.SUBUNIT Interacts with ALG1.MISCELLANEOUS Present with 1840 molecules/cell in log phase SD medium.SIMILARITY Belongs to the glycosyltransferase group 1 family. Glycosyltransferase 4 subfamily.
Structure of human cytidine deaminase bound to a potent inhibitor
The PtdIns3P phosphatase myotubularin is a cytoplasmic protein that also localizes to Rac1-inducible plasma membrane ruffles
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
Lessons from photoreceptors: turning off G-protein signaling in living cells
Human SGBS cells - a unique tool for studies of human fat cell biology
Zinc fluxes and zinc transporter genes in chronic diseases
Mechanisms underlying differential responses to FGF signaling
Role of the CLOCK protein in the mammalian circadian mechanism
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 KEN box: an APC recognition signal distinct from the D box targeted by Cdh1
The zinc ribbon domains of the general transcription factors TFIIB and Brf: conserved functional surfaces but different roles in transcription initiation.
Cellular signaling by fibroblast growth factor receptors
cAMP-dependent protein kinase: framework for a diverse family of regulatory enzymes
Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternative-splice variants
The receptor for advanced glycation end products (RAGE) is a cellular binding site for amphoterin. Mediation of neurite outgrowth and co-expression of rage and amphoterin in the developing nervous system
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
Mitochondrial protein import: biochemical and genetic evidence for interaction of matrix hsp70 and the inner membrane protein MIM44
Biogenesis of iron-sulfur clusters in mammalian cells: new insights and relevance to human disease
The type 1 insulin-like growth factor receptor pathway
Functional reconstitution in Escherichia coli of the yeast mitochondrial matrix peptidase from its two inactive subunits
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.
Targeting TBP to a non-TATA box cis-regulatory element: a TBP-containing complex activates transcription from snRNA promoters through the PSE
The interleukin 2 receptor. Functional consequences of its bimolecular structure
Sld3, which interacts with Cdc45 (Sld4), functions for chromosomal DNA replication in Saccharomyces cerevisiae.
T cell receptor signaling: beyond complex complexes
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
Purification and characterization of homogeneous initiation factor M2A from rabbit reticulocytes.
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Mechanisms of organelle transport and capture along proplatelets during platelet production
Identification of the human mitochondrial linoleoyl-coenzyme A monolysocardiolipin acyltransferase (MLCL AT-1)
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8p11 myeloproliferative syndrome with a novel t(7;8) translocation leading to fusion of the FGFR1 and TIF1 genes
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Mechanism and regulation of eukaryotic protein synthesis
Disorders of cholesterol biosynthesis: prototypic metabolic malformation syndromes
Making heads or tails of phospholipids in mitochondria
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Differential expression of aquaporin 8 in human colonic epithelial cells and colorectal tumors
The crystal structure of human phosphoglucose isomerase at 1.6 A resolution: implications for catalytic mechanism, cytokine activity and haemolytic anaemia
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The Tim core complex defines the number of mitochondrial translocation contact sites and can hold arrested preproteins in the absence of matrix Hsp70-Tim44
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5,10-methylenetetrahydrofolate polyglutamate macromolecule
5,10-methylenetetrahydrofolate polyglutamate macromolecule [ChEBI:60473]
Ectodomain cleavage of ErbB-4: characterization of the cleavage site and m80 fragment
Getting to the end: telomerase access in yeast and humans
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3-decaprenyl-4-hydroxy-5-methoxybenzoic acid
4-hydroxy-3-methoxy-5-decaprenylbenzoic acid
all-trans-4-hydroxy-3-methoxy-5-decaprenylbenzoic acid
3-decaprenyl-4-hydroxy-5-methoxybenzoic acid [ChEBI:50776]
all-trans-3-decaprenyl-4-hydroxy-5-methoxybenzoic acid
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A new type of congenital disorders of glycosylation (CDG-Ii) provides new insights into the early steps of dolichol-linked oligosaccharide biosynthesis
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3-decaprenyl-4,5-dihydroxybenzoic acid [ChEBI:50775]
all-trans-3-decaprenyl-4,5-dihydroxybenzoic acid
all-trans-3,4-dihydroxy-5-decaprenylbenzoic acid
FUNCTION Acts as component of the MCM2-7 complex (MCM complex) which is the putative replicative helicase essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells. The active ATPase sites in the MCM2-7 ring are formed through the interaction surfaces of two neighboring subunits such that a critical structure of a conserved arginine finger motif is provided in trans relative to the ATP-binding site of the Walker A box of the adjacent subunit. The six ATPase active sites, however, are likely to contribute differentially to the complex helicase activity. Once loaded onto DNA, double hexamers can slide on dsDNA in the absence of ATPase activity. Required for the entry in S phase and for cell division.CATALYTIC ACTIVITY ATP + H(2)O = ADP + phosphate.SUBUNIT Component of the MCM2-7 complex. The complex forms a toroidal hexameric ring with the proposed subunit order MCM2-MCM6-MCM4-MCM7-MCM3-MCM5; loaded onto DNA, forms a head-head double hexamer. Interacts with MCM10.MISCELLANEOUS Present with 13400 molecules/cell in log phase SD medium.MISCELLANEOUS Early fractionation of eukaryotic MCM proteins yielded a variety of dimeric, trimeric and tetrameric complexes with unclear biological significance. Specifically a MCM467 subcomplex is shown to have in vitro helicase activity which is inhibited by the MCM2 subunit. The MCM2-7 hexamer is the proposed physiological active complex.SIMILARITY Belongs to the MCM family.SIMILARITY Contains 1 MCM domain.
Neuregulin-2, a new ligand of ErbB3/ErbB4-receptor tyrosine kinases
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A complete inventory of all enzymes in the eukaryotic methionine salvage pathway
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Human peroxisomal L-alanine: glyoxylate aminotransferase. Evolutionary loss of a mitochondrial targeting signal by point mutation of the initiation codon
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Effects of synthetic analogues of phosphoenolpyruvate on muscle and liver pyruvate kinase, muscle enolase, liver phosphoenolpyruvate carboxykinase and on the intra-/extra-mitochondrial tricarboxylic acid carrier transport system
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The Orc4p and Orc5p subunits of the Xenopus and human origin recognition complex are related to Orc1p and Cdc6p.
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Bidirectional water fluxes and specificity for small hydrophilic molecules in aquaporins 0-5
Differential requirement for the mitochondrial Hsp70-Tim44 complex in unfolding and translocation of preproteins
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Overexpression of human alanine:glyoxylate aminotransferase in Escherichia coli: renaturation from guanidine-HCl and affinity for pyridoxal phosphate co-factor
Xylulose 5-phosphate mediates glucose-induced lipogenesis by xylulose 5-phosphate-activated protein phosphatase in rat liver
The stress-activated protein kinase subfamily of c-Jun kinases
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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.
8p11 myeloproliferative syndrome: a review
Encounters of Saccharomyces cerevisiae RNA polymerase III with its transcription factors during RNA chain elongation.
Analysis of RNA chain elongation and termination by Saccharomyces cerevisiae RNA polymerase III.
Interaction between succinyl CoA synthetase and the heme-biosynthetic enzyme ALAS-E is disrupted in sideroblastic anemia
Recognition of bacterial products by toll-like receptors
Different import pathways through the mitochondrial intermembrane space for inner membrane proteins
PKC beta regulates BCR-mediated IKK activation by facilitating the interaction between TAK1 and CARMA1
FUNCTION Catalyzes the exchange of ADP and ATP across the mitochondrial inner membrane.SUBUNIT Homodimer.SIMILARITY Belongs to the mitochondrial carrier (TC 2.A.29) family.SIMILARITY Contains 3 Solcar repeats.
FUNCTION Essential component of the PAM complex, a complex required for the translocation of transit peptide-containing proteins from the inner membrane into the mitochondrial matrix in an ATP-dependent manner. Seems to control the nucleotide-dependent binding of SSC1 to substrate proteins and the association of SSC1 with TIM44.SUBUNIT Component of the PAM complex, at least composed of SSC1 (mtHsp70), MGE1, TIM44, PAM16/TIM16, PAM17 and PAM18/TIM14. Interacts with SSQ1.PTM The N-terminus is blocked.SIMILARITY Belongs to the GrpE family.
Calmodulin: a prototypical calcium sensor
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
RNA Polymerase III Transcription Initiation
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
Carrier protein import into mitochondria mediated by the intermembrane proteins Tim10/Mrs11 and Tim12/Mrs5
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.
Kinetic analysis of the liver-type (GLUT2) and brain-type (GLUT3) glucose transporters in Xenopus oocytes: substrate specificities and effects of transport inhibitors
The human Aquaporin-5 gene. Molecular characterization and chromosomal localization
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Expression and characterization of the human mitochondrial leucyl-tRNA synthetase
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PATHWAY Cofactor biosynthesis; ubiquinone biosynthesis.MISCELLANEOUS Present with 2940 molecules/cell in log phase SD medium.SIMILARITY Belongs to the UbiH/COQ6 family.
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The glucose-lactic acid cycle and gluconeogenesis
Cell lines from kidney proximal tubules of a patient with Lowe syndrome lack OCRL inositol polyphosphate 5-phosphatase and accumulate phosphatidylinositol 4,5-bisphosphate
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Isozymes of human phosphofructokinase in blood cells and cultured cell lines: molecular and genetic evidence for a trigenic system
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Deletion of mouse Porcn blocks Wnt ligand secretion and reveals an ectodermal etiology of human focal dermal hypoplasia/Goltz syndrome
Proc. Natl. Acad. Sci. U.S.A. 108:12752-7
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Adipocyte-specific transcription factor ARF6 is a heterodimeric complex of two nuclear hormone receptors, PPAR gamma and RXR alpha
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Selective inhibition of heterotrimeric Gs signaling. Targeting the receptor-G protein interface using a peptide minigene encoding the Galpha(s) carboxyl terminus
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CLOCK/BMAL1 regulates human nocturnin transcription through binding to the E-box of nocturnin promoter
Site-directed mutagenesis of diphosphoinositol polyphosphate phosphohydrolase, a dual specificity NUDT enzyme that attacks diadenosine polyphosphates and diphosphoinositol polyphosphates
Homologous recombinational repair of DNA ensures mammalian chromosome stability
Inborn errors of cobalamin absorption and metabolism
Am J Med Genet C Semin Med Genet 157:33-44
Metabolism of gammalinolenic acid in human neutrophils
Structure of the yeast WD40 domain protein Cia1, a component acting late in iron-sulfur protein biogenesis
Niemann-Pick C1 Like 1 protein is critical for intestinal cholesterol absorption
integral to lumenal side of endoplasmic reticulum membrane
Formation of the Early Elongation Complex
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The RNA polymerase III transcription initiation factor TFIIIB participates in two steps of promoter opening.
FYVE-DSP2, a FYVE domain-containing dual specificity protein phosphatase that dephosphorylates phosphotidylinositol 3-phosphate
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1-acyl-sn-glycero-3-phosphoethanolamine [ChEBI:29017]
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CCNB:p-T161-CDK1 (name copied from entity in Homo sapiens)
ESPL1 Autocleaved (name copied from entity in Homo sapiens)
Casein kinase II (name copied from entity in Homo sapiens)
CDK1 Phosphorylated Condensin I (name copied from entity in Homo sapiens)
2-Amino-3-carboxymuconate semialdehyde [ChEBI:29044]
Cloning of a complete protein-coding sequence of human platelet-type phosphofructokinase isozyme from pancreatic islet.
(2R)-2-Hydroxy-3-(phosphonooxy)-propanal [ChEBI:29052]
Aquaporin-3 water channel localization and regulation in rat kidney
Elimination of cholesterol as cholestenoic acid in human lung by sterol 27-hydroxylase: evidence that most of this steroid in the circulation is of pulmonary origin
ChEBI:29089 1,2-diacyl-sn-glycerol 3-phosphate
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
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
FUNCTION Component of the TOM (translocase of outer membrane) receptor complex responsible for the recognition and translocation of cytosolically synthesized mitochondrial preproteins. TOM5 is involved in insertion of preproteins into the TOM40 translocation pore.SUBUNIT Forms part of the TOM (translocase of outer membrane) complex that consists of at least 7 different proteins (TOM5, TOM6, TOM7, TOM20, TOM22, TOM40 and TOM70).SIMILARITY Belongs to the Tom5 family.
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
Cyclin A/B1 associated events during G2/M transition
The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction
Selective activation of p38 mitogen-activated protein (MAP) kinase isoforms by the MAP kinase kinases MKK3 and MKK6
Specific inhibition of pyruvate transport in rat liver mitochondria and human erythrocytes by alpha-cyano-4-hydroxycinnamate
Peroxisome proliferator-activated receptors: a nuclear receptor signaling pathway in lipid physiology
Biosynthetic studies of A2E, a major fluorophore of retinal pigment epithelial lipofuscin
Tetrahydrobiopterin biosynthesis, regeneration and functions
Chaperone Hsp27, a novel subunit of AUF1 protein complexes, functions in AU-rich element-mediated mRNA decay
Condensin I (name copied from entity in Homo sapiens)
CK2 Phosphorylated Condensin I (name copied from entity in Homo sapiens)
SUMO1 S-glycyl-cys173 UBA2:SAE1 (name copied from entity in Homo sapiens)
p-T161-CDK1:CCNB1 (name copied from entity in Homo sapiens)
UBA2:SAE1 (name copied from entity in Homo sapiens)
FUNCTION Involved in N-linked oligosaccharide assembly. Required for the translocation of Man(5)GlcNAc(2)-PP-dolichol from the cytoplasmic side to the lumenal side of the endoplasmic reticulum membrane.SIMILARITY Belongs to the RFT1 family.
APC/C-mediated degradation of cell cycle proteins
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A 7 bp mutation converts a human RNA polymerase II snRNA promoter into an RNA polymerase III promoter
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FUNCTION Essential component of the TIM23 complex, a complex that mediates the translocation of transit peptide-containing proteins across the mitochondrial inner membrane. Required to keep the TOM and the TIM23 complexes in close contact. At some point, it is released from the TOM23 complex to allow protein translocation into the mitochondrial matrix. In the complex, it acts as an antagonist of TIM50 by reducing preprotein accumulation at the TOM23 complex and promotes dissociation of the PAM complex from the TIM23 complex.SUBUNIT Component of the TIM23 complex, at least composed of TIM23, TIM17, TIM50 and TIM21. Interacts directly with TIM23. Interacts with TOM22 component of the TOM complex. Released from the TOM23 complex by the PAM complex, leading to protein translocation into the mitochondrial matrix.MISCELLANEOUS Present with 3770 molecules/cell in log phase SD medium.SIMILARITY Belongs to the TIM21 family.
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The inositol hexakisphosphate kinase family. Catalytic flexibility and function in yeast vacuole biogenesis
Analysis of the putative role of 24-carbon polyunsaturated fatty acids in the biosynthesis of docosapentaenoic (22:5n-6) and docosahexaenoic (22:6n-3) acids
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Interactions of CD80 and CD86 with CD28 and CTLA4
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The molecular basis of insulin-stimulated glucose uptake: signalling, trafficking and potential drug targets
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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
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FUNCTION Mitochondrial intermembrane chaperone that participates in the import and insertion of some multi-pass transmembrane proteins into the mitochondrial inner membrane. Also required for the transfer of beta-barrel precursors from the TOM complex to the sorting and assembly machinery (SAM complex) of the outer membrane. Acts as a chaperone-like protein that protects the hydrophobic precursors from aggregation and guide them through the mitochondrial intermembrane space. The TIM8-TIM13 complex is non essential and only mediates the import of few proteins under precise conditions while the predominant TIM9-TIM10 70 kDa complex is crucial and mediates the import of much more proteins. Strictly required for import of TIM23 in some conditions, when a low membrane potential exists in the mitochondria.SUBUNIT Heterohexamer; composed of 3 copies of TIM8 and 3 copies of TIM13, named soluble 70 kDa complex. Associates with the TIM22 complex, whose core is composed of TIM18, TIM22 and TIM54. Interacts with the transmembrane regions of multi-pass transmembrane proteins in transit.DOMAIN The twin CX3C motif contains 4 conserved Cys residues that form 2 disulfide bonds in the mitochondrial intermembrane space. However, during the transit of TIM13 from cytoplasm into mitochondrion, the Cys residues probably coordinate zinc, thereby preventing folding and allowing its transfer across mitochondrial outer membrane.SIMILARITY Belongs to the small Tim family.
FUNCTION Central component of the TOM (translocase of outer membrane) receptor complex responsible for the recognition and translocation of cytosolically synthesized mitochondrial preproteins. Together with TOM20 and TOM70 functions as the transit peptide receptor at the surface of the mitochondrion outer membrane and facilitates the movement of preproteins into the TOM40 translocation pore. Docks TOM20 and TOM70 for interaction with the general TOM40 import pore (GIP) complex. May regulate the TOM machinery organization, stability and channel gating.SUBUNIT Forms part of the preprotein translocase complex of the outer mitochondrial membrane (TOM complex) which consists of at least 7 different proteins (TOM5, TOM6, TOM7, TOM20, TOM22, TOM40 and TOM70). Interacts with TOM20 and TOM70. Interacts with FCJ1.DOMAIN Its cytoplasmic domain associates with the cytoplasmic domains of TOM20 and TOM70. Its intermembrane space domain provides a trans binding site for presequences and the single membrane anchor is required for a stable interaction between the GIP complex proteins.MISCELLANEOUS Present with 6610 molecules/cell in log phase SD medium.SIMILARITY Belongs to the Tom22 family.
Deficiency of the first mannosylation step in the N-glycosylation pathway causes congenital disorder of glycosylation type Ik
Roles of AUF1 isoforms, HuR and BRF1 in ARE-dependent mRNA turnover studied by RNA interference
Porphobilinogen deaminase and uroporphyrinogen III synthase: structure, molecular biology, and mechanism
Congenital glutamine deficiency with glutamine synthetase mutations
Endotoxin induces rapid protein tyrosine phosphorylation in 70Z/3 cells expressing CD14
Mechanism of action and in vivo role of platelet-derived growth factor
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integral to cytosolic side of endoplasmic reticulum membrane
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Comparison of human B cell antigen receptor complexes: membrane-expressed forms of immunoglobulin (Ig)M, IgD, and IgG are associated with structurally related heterodimers
The gene mutated in adult-onset type II citrullinaemia encodes a putative mitochondrial carrier protein
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
Igf-I signaling and effects on longevity
Nestle Nutr Workshop Ser Pediatr Program 68:237-45; discussion 246-9
Differences between the trypanosomal and human GlcNAc-PI de-N-acetylases of glycosylphosphatidylinositol membrane anchor biosynthesis
Molecular characterization of a phospholipase D generating anandamide and its congeners
Expression of aquaporin 8 in colonic epithelium with diarrhoea-predominant irritable bowel syndrome
Characterization of p150, an adaptor protein for the human phosphatidylinositol (PtdIns) 3-kinase. Substrate presentation by phosphatidylinositol transfer protein to the p150.Ptdins 3-kinase complex
Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8
Spatial and temporal regulation of Condensins I and II in mitotic chromosome assembly in human cells
Neuregulin-3 (NRG3): a novel neural tissue-enriched protein that binds and activates ErbB4
Tyrosine phosphorylation of phospholipase C induced by membrane immunoglobulin in B lymphocytes
Bile salt and organic anion SLC transporters
Identification of eukaryotic DNA replication proteins using simian virus 40 in vitro replication system.
EGFR interacts with phospholipase C-gamma
Regulation of Lipid Metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
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.
In vivo protein-interaction mapping of a mitochondrial translocator protein Tom22 at work
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.
Chromosome maintenance is critical for stable chromosome function in mammalian and other eukaryotic cells. Aspects of telomere maintenance and nucleosome assembly are covered here.
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.
Telomerase acts as reverse transcriptase in the elongation of telomeres (Smogorzewska and de Lange 2004).
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.
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.
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 complementary strand is synthesized by the polymerase primase complex using conventional RNA priming.
TRAF6 autoubiquitination-independent activation of the NFkappaB and MAPK pathways in response to IL-1 and RANKL
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".
Replication factor C is proposed to dissociate from PCNA following sliding clamp formation, and the DNA toroid alone tethers pol delta to the DNA.
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.
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.
Once loaded the vesicles become fully sculpted, pinch off from the ER and bud into the cytosol.
Cytosolic Sec13p-Sec31p complexes bind to pre-bound Sec23p-Sec24p complexes.
COPII components (known as Sec13p, Sec23p, Sec24p, Sec31p, and Sar1p in yeast) traffic cargo from the endoplasmic reticulum to the Golgi apparatus. COPII-coated vesicles were originally discovered in the yeast Saccharomyces cerevisiae using genetic approaches coupled with a cell-free assay. The mammalian counterpart of this pathway is represented here. Newly synthesized proteins destined for secretion are sorted into COPII-coated vesicles at specialized regions of the ER. These vesicles leave the ER, become uncoated and subsequently fuse with the Golgi apparatus membrane.
Vesicle uncoating is triggered by Sar1p-GTP hydrolysis leaving only the vesicle cargo and the v-SNARE to target the vesicle to the Golgi membrane.
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.
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.
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.
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.
FUNCTION Required for growth on nonfermentable carbon sources and for biosynthesis of glutamate.CATALYTIC ACTIVITY Citrate = isocitrate.ENZYME REGULATION Subject to catabolite regulation.PATHWAY Carbohydrate metabolism; tricarboxylic acid cycle; isocitrate from oxaloacetate: step 2/2.SUBUNIT Monomer.MISCELLANEOUS Present with 96700 molecules/cell in log phase SD medium.SIMILARITY Belongs to the aconitase/IPM isomerase family.
RAB proteins have intrinsic weak GTPase activity that is enhanced by RAB-GTPase activating proteins (RAB-GAPs, Sano et al. 2007). The GTPase activity of RAB13 is inferred from other RAB proteins. AS160 (TBC1D4) and TBC1D1 are GAPs that activate the GTPase activity of RAB8A/10/13. Insulin signaling activates AKT, which phosphorylates and inactivates AS160 and TBC1D1, allowing GTP-bound (active) RABs to accumulate.
FUNCTION Component of the TOM (translocase of outer membrane) receptor complex responsible for the recognition and translocation of cytosolically synthesized mitochondrial preproteins. TOM7 is involved in assembly and stability of the TOM complex.SUBUNIT Forms part of the preprotein translocase complex of the outer mitochondrial membrane (TOM complex) which consists of at least 7 different proteins (TOM5, TOM6, TOM7, TOM20, TOM22, TOM40 and TOM70).MISCELLANEOUS Present with 3250 molecules/cell in log phase SD medium.SIMILARITY Belongs to the Tom7 family.
RAB8A/10/13/14 release GDP and bind GTP to yield the active complex. Guanine nucleotide exchange factors (GEFs) stimulate the reaction. GTPase-activating proteins (GAPs) oppose the reaction by stimulating the intrinsic GTPase activity of the RAB proteins.
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.
After passing through the Golgi complex, secretory cargo is packaged into post-Golgi transport intermediates (post-Golgi), which translocate plus-end directed along microtubules to the plasma membrane.
There at least two classes of clathrin coated vesicles in cells, one predominantly Golgi-associated, involved in budding from the trans-Golgi network and the other at the plasma membrane. Here the clathrin-coated vesicles emerging from the Golgi apparatus are triggered by the heterotetrameric adaptor protein complex, AP-1 at the trans-Golgi network membrane. The cargo can be transmembrane, membrane associated or golgi luminal proteins. Each step in the vesicle sculpting pathway, gathers cargo and clathrin triskeletons, until a complete vesicular sphere is formed. With the scission of the membrane the vesicle is released and eventually losses its clathrin coat.
ARF1 helps to recruit AP-1 to Golgi membrane. AP-1 is not alone in this process of establishing a docking complex at the trans-Golgi Network. This section of the Golgi membrane will be where the new vesicle will be built and loaded.
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.
The anterograde membrane flow from the ER to the Golgi is compensated for by a retrograde pathway. This pathway's functions include the recycling of membrane and proteins to the ER.
Secretory 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.
The formation of the COPI coat requires membrane recruitment and activation of Arf1. Arf1 activation is normally mediated by guanine nucleotide exchange factors (GEFs) that convert Arf1 to its active GTP-bound state on the membrane. In this reaction that GEF is represented by GBF1.
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.
Cell death signalling via NRAGE, NRIF and NADE
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.
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.
Infection by Mycobacterium tuberculosis (Mtb) is soon countered by the host's immune system, the organism is however almost never eradicated; ten per cent of infections will develop into "open tuberculosis", while the other ninety per cent become "latent", a state that can persist for decades until loss of immune control. A third of the world's population is estimated to harbour latent tuberculosis. Latent infection involves the bacterium being internalized by macrophages where it stops and counters the innate immune answer (Russell 2011, Russell et al. 2010). When a status-quo is reached, Mtb enters a non-replicating persistent state (Barry et al. 2009, Boshoff & Barry 2005).
Alveolar macrophages normally develop their phagosome along the endolysosomal pathway. However, after having internalized Mtb, this development is arrested at an early stage and only includes acidification, nitric oxide and superoxide production, as well as the use of a few other proteins that can be gained from other endosomes which still can interact with the phagosome (Flannagan et al. 2009).
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.
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.
In adipocytes and myocytes insulin signaling causes intracellular vesicles carrying the GLUT4 glucose transporter to translocate to the plasma membrane, allowing the cells to take up glucose from the bloodstream (reviewed in Zaid et al. 2008, Leney and Tavare 2009, Bogan and Kandror 2010, Foley et al. 2011, Hoffman and Elmendorf 2011, Kandror and Pilch 2011). In myocytes muscle contraction alone can also cause translocation of GLUT4. Though the entire pathway leading to GLUT4 translocation has not been elucidated, several steps are known. Insulin activates the kinases AKT1 and AKT2. Muscle contraction activates the kinase AMPK-alpha2 and possibly also AKT. AKT2 and, to a lesser extent, AKT1 phosphorylate the RAB GTPase activators TBC1D1 and TBC1D4, causing them to bind 14-3-3 proteins and lose GTPase activation activity. As a result RAB proteins (probably RAB8A, RAB10, RAB14 and possibly RAB13) accumulate GTP. The connection between RAB:GTP and vesicle translocation is unknown but may involve recruitment and activation of myosins. Myosins 1C, 2A, 2B, 5A, 5B have all been shown to play a role in translocating GLUT4 vesicles near the periphery of the cell. Following docking at the plasma membrane the vesicles fuse with the plasma membrane in a process that depends on interaction between VAMP2 on the vesicle and SNAP23 and SYNTAXIN-4 at the plasma membrane.
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.
Activated MEK1 phosphorylates and activates ERK1.
Two phospho-ERK2 molecules dimerise and enter the nucleus, where they may phosphorylate downstream targets.
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 MEK phosphorylates and activates ERK.
Phosphorylation of nucleosides and nucleoside analogs by mammalian nucleoside monophosphate kinases
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.
Phospho-ERK-2 dimer is translocated from cytosol to nucleoplasm.
Activated MEK2 phosphorylates and activates ERK2.
Interfacial kinetic and binding properties of the complete set of human and mouse groups I, II, V, X, and XII secreted phospholipases A2
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.
This pathway describes the generation of DAG and IP3 by the PLCgamma-mediated hydrolysis of PIP2 and the subsequent downstream signaling events.
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).
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
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 human and mouse replication-dependent histone genes
Syndromic craniosynostosis: from history to hydrogen bonds
Regulation of gene expression in beta cells
HSP90 is inactivated by binding to benzaquinoid ansamycins
Tyrosine kinase inhibitors bind and inhibit FGFR1 fusion dimer phosphorylation
phenylalanine + oxaloacetate => phenylpyruvate + aspartate [CCBL1]
Characterization of the localization and proteolytic activity of the SUMO-specific protease, SENP1
XBP1 controls diverse cell type- and condition-specific transcriptional regulatory networks
kynurenine + pyruvate => 4-(2-aminophenyl)-2,4-dioxobutanoic acid + alanine [CCBL1]
Formation of the CE:GMP intermediate complex
Transfer of GMP from the capping enzyme GT site to 5'-end of mRNA
Dissociation of transcript with 5'-GMP from GT
Recognition and binding of the mRNA cap by the cap-binding complex
pyrophosphate + H2O => 2 orthophosphate [cytosolic]
pyrophosphate + H2O => 2 orthophosphate [mitochondrial]
Hydrolysis of the 5'-end of the nascent transcript by the capping enzyme
Accumulation of dietary cholesterol in sitosterolemia caused by mutations in adjacent ABC transporters
Inactivation of NF-kappa B inhibitor I kappa B alpha: ubiquitin-dependent proteolysis and its degradation product
Deamination at C6 position of adenosine in Editosome (ADAR1)
Deamination at C6 position of adenosine in Editosome (ADAR2)
Binding of ADAR2 homodimer to dsRNA duplex
Binding of ADAR1 homodimer to dsRNA duplex
SPT5 subunit of Pol II binds the RNA triphosphatase (RTP)
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.
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.
Extracellular-signal-regulated kinase signalling in neurons
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.
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 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.
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).
Characterization of MTMR3. an inositol lipid 3-phosphatase with novel substrate specificity
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).
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.
The eukaryotic six-subunit origin recognition complex (ORC) governs the initiation site of DNA replication and formation of the prereplication complex.
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.
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.
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).
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).
Complete sequencing and characterization of 21,243 full-length human cDNAs
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.
DNA replication is regulated at various levels via ORC proteins. This pathway includes annotation of individual events that lead to the regulation of replication.
Identical mutations in three different fibroblast growth factor receptor genes in autosomal dominant craniosynostosis syndromes
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).
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 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.
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.
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.
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.
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).
Release of arachidonate from diglyceride in human platelets requires the sequential action of a diglyceride lipase and a monoglyceride lipase
At the onset of mitosis, Cdh1 is phosphorylated by Cyclin B-Cdc2 resulting in a conformational change that prevents Cdh1 from activating the APC/C.
The APC/C is activated by either Cdc20 or Cdh1. While both activators associate with the APC/C, they do so at different points in the cell cycle and their binding is regulated differently (see Zachariae and Nasmyth, 1999). Cdc20, whose protein levels increase as cells enter into mitosis and decrease upon mitotic exit, only associates with the APC/C during M phase. Cdh1 associates with the APC/C in G1. This interaction is inhibited at other times by Cdk1 phosphorylation.
Phosphorylation by mitotic kinases is believed to alter the conformation of Cdh1 preventing it from associating with the APC/C. Cdc14 is thought to contribute to the dephosphorylation of Cdh1 in late mitosis. Dephosphorylated Cdh1 then associates with and activates the APC/C.
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 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.
Origins and Mechanisms of miRNAs and siRNAs
The Anaphase Promoting Complex or Cyclosome (APC/C) functions during mitosis to promote sister chromatid separation and mitotic exit through the degradation of mitotic cyclins and securin. This complex is also active in interphase insuring the appropriate length of the G1 phase (reviewed in Peters, 2002). The APC/C contains at least 12 subunits and functions as an ubiquitin-protein ligase (E3) promoting the multiubiquitination of its target proteins (see Gieffers et al., 2001). In the ubiquitination reaction, ubiquitin is activated by the formation of a thioester bond with the (E1) ubiquitin activating enzyme then transferred to a cysteine residue within the ubiquitin conjugating enzyme (E2) and ultimately to a lysine residue within the target protein, with the aid of ubiquitin-protein ligase activity of the APC/C. The ubiquitin chains generated are believed to target proteins for destruction by the 26S proteasome (Reviewed in Peters, 1994 ) The activity of the APC/C is highly periodic during the cell cycle and is controlled by a combination of regulatory events. The APC/C is activated by phosphorylation and the regulated recruitment of activating subunits and is negatively regulated by sequestration by kinetochore-associated checkpoint proteins. The Emi1 protein associates with Cdh1 and Cdc20, inhibiting the APC/C between G1/S and prophase. RSSA1 may play a similar role in ihibiting the APC during early mitosis. Following phosphorylation of the APC/C core subunits by mitotic kinases, the activating subunit, Cdc20 is recruited to the APC/C and is responsible for mitotic activities, including the initiation of sister chromatid separation and the timing of exit from mitosis (See Zachariae and Nasmyth, 1999). Substrates of the Cdc20:APC/C complex, which are recognized by a motif known as the destruction box (D box) include Cyclin A, Nek2, Securin and Cyclin B. Degradation of Securin and Cyclin B does not occur until the mitotic spindle checkpoint has been satisfied (see Castro et al. 2005). Cdc20 is degraded late in mitosis (Reviewed in Owens and Hoyt, 2005). At this time the activating subunit, Cdh1, previously maintained in an inactive phosphorylated state by mitotic kinases, is dephosphorylated and associates with and activates the APC/C. The APC/C:Cdh1 complex recognizes substrates containing a D box, a KEN box (Pfleger and Kirschner, 2000) or a D box activated (DAD) domain (Castro et al., 2002) sequence and promotes the ordered degration of mitotic cyclins and other mitotic proteins culminating with its own ubiquitin-conjugating enzyme (E2) subunit UbcH10 (Rape et al., 2006). This ordered degradation promotes the stability of Cyclin A at the end of G1. This stabilization, in turn, promotes the phosphorylation of Cdh1 and its abrupt dissociation from the APC/C, allowing accumulation of cyclins for the next G1/S transition (Sorensen et al., 2001).
The activity of the APC/C must be appropriately regulated during the cell cycle to ensure the timely degradation of its substrates. Of particular importance is the conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase. Phosphorylation of both the APC/C complex and Cdh1 regulate this conversion. During mitosis, several APC/C subunits are phosphorylated increasing the activity of APC/C:Cdc20. However, phosphorylation of Cdh1 by mitotic Cyclin:Cdk complexes prevents it from activating the APC/C. Dephosphorylation of Cdh1 in late anaphase by Cdc14a results in the activation of APC/C:Cdh1 (reviewed in Castro et al, 2005).
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).
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 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 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).
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.
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
The N-terminal domain of Tob55 has a receptor-like function in the biogenesis of mitochondrial beta-barrel proteins
Cytosolic and membrane-associated proteins involved in the recruitment of AP-1 adaptors onto the trans-Golgi network
ATM mediated response to DNA double-strand break
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
Kid, a novel kinesin-like DNA binding protein, is localized to chromosomes and the mitotic spindle
Insights into COPI coat assembly and function in living cells
Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design
Tissue distribution and cDNA cloning of a human fatty acid transport protein (hsFATP4)
The role of assembly in insulin's biosynthesis
The N-terminal shuttle domain of Erv1 determines the affinity for Mia40 and mediates electron transfer to the catalytic Erv1 core in yeast mitochondria
Identification of the peroxisomal beta-oxidation enzymes involved in the biosynthesis of docosahexaenoic acid
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
Synthesis of bile acids and bile salts via 24-hydroxycholesterol
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
Regulation of repair of alkylation damage in mammalian genomes.
Prog Nucleic Acid Res Mol Biol 44:109-42
N-retinylidene-N-retinylphosphatidylethanolamine [ChEBI:52592]
Guanosine triphosphate, the primary product of phosphorylation coupled to the breakdown of succinyl coenzyme A
Oct-1 and Oct-2 potentiate functional interactions of a transcription factor with the proximal sequence element of small nuclear RNA genes
RNA Polymerase III Transcription Initiation From Type 3 Promoter
acylglucosaminylphosphatidylinositol [ChEBI:52572]
Gamma linolenic acid: an antiinflammatory omega-6 fatty acid
Tissue-differential expression of two distinct genes for phosphoribosyl pyrophosphate synthetase and existence of the testic-specific transcript
Second pathway for completion of human DNA base excision-repair: reconstitution with purified proteins and requirement for DNase IV (FEN1).
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
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)
phytanate + CoA-SH + ATP => phytanoyl-CoA + AMP + pyrophosphate
2-hydroxyphytanoyl-CoA => pristanal + formyl-CoA
propionyl-CoA + carnitine => propionylcarnitine + CoASH
Peroxisomal uptake of very long-chain fatty acyl CoA
trans-2,3-dehydrohexacosanoyl-CoA + H2O => 3-hydroxyhexacosanoyl-CoA
pristanate + CoA-SH + ATP => pristanoyl-CoA + AMP + pyrophosphate
trans-2,3-dehydropristanoyl-CoA + H2O => 3-hydroxypristanoyl-CoA
3-hydroxypristanoyl-CoA + NAD+ => 3-ketoxypristanoyl-CoA + NADH + H+
Roles for LPS-dependent interaction and relocation of TLR4 and TRAM in TRIF-signaling
acetyl-CoA + carnitine => acetylcarnitine + CoASH
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
3-ketohexacosanoyl-CoA + CoASH => tetracosanoyl-CoA + acetyl-CoA
Condensation of acetyl CoA with acetoacetyl CoA to form HMG-CoA
3-hydroxyhexacosanoyl-CoA + NAD+ => 3-ketohexacosanoyl-CoA + NADH + H+
Two FPP molecules dimerize to form presqualene diphosphate
Addition of isopentenyl pyrophosphate to DMAPP
Another isopentenyl pyrophosphate is added to geranyl pyrophosphate
Mevalonate-5-pyrophosphate is decarboxylated
Isopentenyl pyrophosphate rearranges to dimethylallyl pyrophosphate
Reduction of HMG-CoA produces mevalonate
Mevalonate is phosphorylated to mevalonate-5-phosphate
NPC1L1 + ezetimibe => NPC1L1:ezetimibe complex
sterols[cytosol] + ATP => sterols[extracellular] + ADP + Pi
ABCG5:ABCG8-mediated export of cholesterol and phytosterols
2-acylglycerol + H2O -> glycerol + fatty acid
Transport of Citrate from Mitochondrial Matrix to cytosol
acetyl-CoA + bicarbonate + ATP => malonyl-CoA + H2O + ADP + orthophosphate
Formation of Malonyl-CoA from Acetyl-CoA (liver)
palmitate + CoASH + ATP => palmitoyl-CoA + AMP + pyrophosphate + H2O [ACSL3]
arachidonate + CoASH + ATP => arachidonoyl-CoA + AMP + pyrophosphate + H2O [ACSL4]
trans-octadec-2-enoyl-CoA + NADPH + H+ => stearoyl-CoA + NADP+
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)
Conversion of Glycerol to Glycerol-3-phosphate
1,2-diacyl-glycerol 3-phosphate + H2O => 1,2-diacyl-glycerol + orthophosphate
Conversion of Phosphatidic Acid to Diacylglycerol
Common themes in siRNA-mediated epigenetic silencing pathways
acetoacetyl-CoA+acetyl-CoA => HMG-CoA + CoASH
Exchange of palmitoylcarnitine and carnitine across the inner mitochondrial membrane
Formation of Malonyl-CoA from Acetyl-CoA (muscle)
Expression of 3-Hydroxy-3-methylglutaryl-coenzyme A Reductase (HMGCR)
Expression of Hydroxymethylglutaryl coenzyme A synthase (HMGCS1)
Gly-3-P+FAD->DHAP+FADH2 (catalyzed by mitochondrial Gly-Phos dehydrogenase)
PMP34-mediated exchange of cytosolic ATP for peroxisomal AMP
Organization and sequence of the human gene for the mitochondrial citrate transport protein
Glc6P is isomerised to I3P by ISYNA1 in the cytosol
I1P is dephosphorylated to Ins by IMPA1/2 in the cytosol
I4P is dephosphorylated to Ins by IMPA1/2 in the cytosol
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
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
I3P is dephosphorylated to Ins by IMPA1/2 in the cytosol
Chromokinesins: multitalented players in mitosis
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.
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
5-PP-IP5 is phosphorylated to 5-PPP-IP5 by IP6K1/2 in the nucleus
1-PP-IP5 is phosphorylated to 1,5-(PP)2-IP4 by IP6K1/2 in the nucleus
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-IP4 is phosphorylated to 1,5-(PP)2-IP3 by IP6K1/3 in the cytosol
IP6 is phosphorylated to 5-PP-IP5 by IP6K1/3 in the cytosol
5-PP-IP5 is phosphorylated to 5-PPP-IP5 by IP6K1/3 in the cytosol
Localization of the human mitochondrial citrate transporter protein gene to chromosome 22Q11 in the DiGeorge syndrome critical region
IP6 is phosphorylated to 5-PP-IP5 by IP6K1/2 in the nucleus
ribose 5-phosphate <=> D-ribulose 5-phosphate
D-ribose 5-phosphate + 2'-deoxyadenosine 5'-triphosphate (dATP) => 5-Phospho-alpha-D-ribose 1-diphosphate (PRPP) + 2'-deoxyadenosine 5'-monophosphate
addition of diphosphate (PP) to ribose 5-phosphate to form 5'-Phospho-alpha-D-ribose 1-diphosphate (PRPP)
D-ribose 5-phosphate + ATP => 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) + adenosine 5'-monophosphate
I(1,3,4,5)P4 is dephosphorylated to I(1,3,4)P3 by INPP5[3]/ITPK1 in the cytosol
xylulose 5-phosphate <=> D-ribulose 5-phosphate
sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate <=> D-erythrose 4-phosphate + D-fructose 6-phosphate
D-fructose 6-phosphate + D-erythrose 4-phosphate <=> sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate
D-ribulose 5-phosphate <=> ribose 5-phosphate
I(1,3,4,5,6)P5 is phosphorylated to 5-PP-IP4 by IP6K1/2 in the nucleus
5-PP-IP4 is phosphorylated to 1,5-(PP)2-IP3 by IP6K1/2 in the nucleus
alpha-D-glucose 6-phosphate + NADP+ => D-glucono-1,5-lactone 6-phosphate + NADPH + H+
D-Glucose 1-phosphate <=> alpha-D-Glucose 6-phosphate
D-galactose 1-phosphate + UDP-glucose <=> D-glucose 1-phosphate + UDP-galactose
poly((1,4)-alpha-glycosyl) glycogenin-1 + n orthophosphate => glycogenin-1 + n D-glucose 1-phosphate [PYGM,PYGB]
poly((1,4)-alpha-glucosyl) glycogenin-2 + n orthophosphate => glycogenin-2 + n D-glucose 1-phosphate [PYGL]
Sodium-coupled monocarboxylate transporters in normal tissues and in cancer
((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl)glycogenin => poly{(1,4)-alpha-glucosyl} glycogenin + alpha-D-glucose
FGFR activation in skeletal disorders: too much of a good thing
D-ribulose 5-phosphate <=> xylulose 5-phosphate
D-glucono-1,5-lactone 6-phosphate + H2O => 6-phospho-D-gluconate
The Role of Gbetagamma Subunits in the Organization, Assembly, and Function of GPCR Signaling Complexes
6-phospho-D-gluconate + NADP+ => D-ribulose 5-phosphate + CO2 + NADPH + H+
Expression cloning of a human cDNA encoding folylpoly(gamma-glutamate) synthetase and determination of its primary structure
glycogen-glycogenin-1 + n orthophosphate => limit dextrin-glycogenin-1 + n D-glucose 1-phosphate [PYGM,PYGB]
PGYM b dimer:AMP complex <=> PGYM dimer, b form + 2 AMP
limit dextrin-glycogenin => ((1,6)-alpha-glucosyl)poly((1,4)-alpha-glucosyl) glycogenin
glycogen-glycogenin-2 + n orthophosphate => limit dextrin-glycogenin-2 + n D-glucose 1-phosphate [PYGL]
The eukaryotic P loop NTPase Nbp35: an essential component of the cytosolic and nuclear iron-sulfur protein assembly machinery
Proc. Natl. Acad. Sci. U.S.A. 102:3266-71
Ways of dying: multiple pathways to apoptosis.
8 UDP-glucose + ((1,4)-alpha-D-glucosyl)4 glycogenin => 8 UDP + ((1,4)-alpha-D-glucosyl)8 glycogenin [GYS D form]
8 UDP-glucose + ((1,4)-alpha-D-glucosyl}4 glycogenin => 8 UDP + ((1,4)-alpha-D-glucosyl)8 glycogenin [GYS I form]
PGYB dimer, b form + 2 AMP <=> PGYB b dimer:AMP complex
ChEBI:58548 S-methyl-5-thio-D-ribulose 1-phosphate(2?)
S-methyl-5-thio-D-ribulose 1-phosphate(2?)
poly((1,4)-alpha-D-glucosyl) glycogenin => glycogen-glycogenin
PGYM dimer, b form + 2 AMP <=> PGYM b dimer:AMP complex
PGYB b dimer:AMP complex <=> PGYB dimer, b form + 2 AMP
Enolase isoenzymes in rat tissues. Electrophoretic, chromatographic, immunological and kinetic properties
UTP + D-glucose 1-phosphate <=> pyrophosphate + UDP-glucose
alpha-D-Glucose 6-phosphate <=> D-Glucose 1-phosphate
D-fructose 6-phosphate <=> alpha-D-Glucose 6-phosphate
D-fructose 1,6-bisphosphate + H2O => D-fructose 6-phosphate + orthophosphate
8 UDP-glucose + glycogenin dimer => 8 UDP + {(1,4)-alpha-D-glucosyl}4 glycogenin dimer
aspartate + alpha-ketoglutarate <=> oxaloacetate + glutamate [GOT1]
D-glyceraldehyde 3-phosphate <=> dihydroxyacetone phosphate
ATP + 3-Phospho-D-glycerate <=> ADP + 1,3-bisphospho-D-glycerate
Phosphoenolpyruvate + H2O <=> 2-Phospho-D-glycerate
phosphoenolpyruvate [mitochondrial matrix] + citrate [cytosol] => phosphoenolpyruvate [cytosol] + citrate [mitochondrial matrix]
Exchange of cytosolic citrate for mitochondrial phosphoenolpyruvate
Molecular mechanisms of megakaryocyte differentiation
aspartate [mitochondrial matrix] + glutamate [cytosol] => aspartate [cytosol] + glutamate [mitochondrial matrix]
Exchange of cytosolic glutamate and mitochondrial aspartate
malate [mitochondrial matrix] + orthophosphate [cytosol] <=> malate [cytosol] + orthophosphate [mitochondrial matrix]
Consistent fusion of ZNF198 to the fibroblast growth factor receptor-1 in the t(8;13)(p11;q12) myeloproliferative syndrome
2-Phospho-D-glycerate <=> Phosphoenolpyruvate + H2O
1,3-Bisphosphoglycerate and ADP react to form 3-phosphoglycerate and ATP
1,3-bisphospho-D-glycerate + ADP <=> 3-phospho-D-glycerate + ADP
Pyruvate, CO2, and ATP react to form oxaloacetate, ADP, and orthophosphate
Pyruvate + CO2 + ATP => ADP + Orthophosphate + Oxaloacetate
phosphoenolpyruvate + ADP => pyruvate + ATP
Glucose 6-phosphate is isomerized to form fructose-6-phosphate
alpha-D-glucose 6-phosphate <=> D-fructose 6-phosphate
glucokinase [nucleoplasm] => glucokinase [cytosol]
dihydroxyacetone phosphate <=> D-glyceraldehyde 3-phosphate
D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP
alpha-D-Glucose + ATP => alpha-D-glucose 6-phosphate + ADP
alpha-D-glucose (cytosol) <=> alpha-D-glucose (extracellular)
Glucose is secreted across the plasma membrane
Glucose is taken up across the plasma membrane by a glucose transport protein (GLUT)
alpha-D-glucose (extracellular) <=> alpha-D-glucose (cytosol)
cytosolic fructose, galactose, or glucose => extracellular fructose, galactose, or glucose
Transport (efflux) of fructose, galactose, and glucose by GLUT2
extracellular fructose => cytosolic fructose
ATAC spliceosome mediated 3' splice site cleavage, exon ligation
ATAC spliceosome mediated Lariat formation,5' splice site cleavage
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.
FUNCTION DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Specific peripheric component of RNA polymerase III which synthesizes small RNAs, such as 5S rRNA and tRNAs. The RPC25/RPC8-RPC17/RPC9 subcomplex may bind Pol III transcripts emerging from the adjacent exit pore during elongation.SUBUNIT Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits. Forms a Pol III subcomplex with RPC25/RPC8. Interacts with BURF1/TDS4.MISCELLANEOUS Present with 2930 molecules/cell in log phase SD medium.SIMILARITY Belongs to the eukaryotic RPC9 RNA polymerase subunit family.
S-methyl-5-thio-?-D-ribose 1-phosphate(2?)
ChEBI:58533 S-methyl-5-thio-?-D-ribose 1-phosphate(2?)
Import of mitochondrial carriers mediated by essential proteins of the intermembrane space
SUBUNIT Heterodimer of two subunits, one of which binds GTP. Interacts with TPA1.PTM N5-methylated on Gln-182 by MTQ2.MISCELLANEOUS Present with 13100 molecules/cell in log phase SD medium.SIMILARITY Belongs to the eukaryotic release factor 1 family.
E2F mediates developmental and cell cycle regulation of ORC1 in Drosophila
Cyclic GMP phosphodiesterase-5: target of sildenafil
A human phosphatidylinositol 3-kinase complex related to the yeast Vps34p-Vps15p protein sorting system
FUNCTION Essential component of the TIM22 complex, a complex that mediates the import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane. The TIM22 complex forms a twin-pore translocase that uses the membrane potential as external driving force. Its precise function within the TIM22 complex is unclear.SUBUNIT Component of the TIM22 complex, whose core is composed of TIM18, TIM22 and TIM54, associated with the peripheral proteins MRS5/TIM12 and the 70 kDa heterohexamer composed of TIM9 and TIM10 (or TIM8 and TIM13).SIMILARITY Belongs to the TIM54 family.
Recognition and association of DNA glycosylase with site containing an affected purine
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
Unconventional Rac-GEF activity is mediated through the Dock180-ELMO complex
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
Response to elevated platelet cytosolic Ca2+
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
53BP1 and NFBD1/MDC1-Nbs1 function in parallel interacting pathways activating ataxia-telangiectasia mutated (ATM) in response to DNA damage.
Function in protein folding of TRiC, a cytosolic ring complex containing TCP-1 and structurally related subunits
Identification and characterization of a lysophosphatidylcholine acyltransferase in alveolar type II cells
Identification of amino acid residues responsible for the pyrimidine and purine nucleoside specificities of human concentrative Na+ nucleoside cotransporters hCNT1 and hCNT2
The neurotransmitter cycle and quantal size
Early phagosomes in dendritic cells form a cellular compartment sufficient for cross presentation of exogenous antigens
GTPase signaling: bridging the GAP between ARF and Rho
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
Presenilin-dependent ErbB4 nuclear signaling regulates the timing of astrogenesis in the developing brain
How nucleotide excision repair protects against cancer.
Mutations in the gene for the E1beta subunit: a novel cause of pyruvate dehydrogenase deficiency
DOMAIN Lacks alpha-helical transmembrane segments, suggesting that it resides in the membrane via beta-sheet conformations similar to those predicted for other outer membrane proteins and porin.SIMILARITY Belongs to the MDM10 family.
Generation of major histocompatibility complex class I antigens: functional interplay between proteasomes and TPPII
Post-proteasomal antigen processing for major histocompatibility complex class I presentation
Mutations in the Delta1-pyrroline 5-carboxylate dehydrogenase gene cause type II hyperprolinemia.
Selectivity in post-translational biotin addition to five human carboxylases
Genetic Analysis of Complex Interactions Amongst Components of the Mitochondrial Import Motor and Translocon in Saccharomyces cerevisiae
RhoGDIs revisited: novel roles in Rho regulation
Nomenclature of the GLUT/SLC2A family of sugar/polyol transport facilitators.
Am J Physiol Endocrinol Metab 282:E974-6
Human 1-D-myo-inositol-3-phosphate synthase is functional in yeast
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.
Acetylcholine Neurotransmitter Release Cycle
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
The MAS-encoded processing protease of yeast mitochondria. Interaction of the purified enzyme with signal peptides and a purified precursor protein
Water permeability and characterization of aquaporin-11
CD28 costimulation: a source of Vav-1 for TCR signaling with the help of SLP-76?
Identification of a novel system L amino acid transporter structurally distinct from heterodimeric amino acid transporters
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.
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
CATALYTIC ACTIVITY Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1).SUBUNIT Component of the RNA polymerase III (Pol III) complex consisting of 17 subunits.MISCELLANEOUS Present with 6020 molecules/cell in log phase SD medium.SIMILARITY Belongs to the RNA polymerase beta' chain family.
Intracellular zinc homeostasis and zinc signaling
Glycogenin-2, a novel self-glucosylating protein involved in liver glycogen biosynthesis.
Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation
Cloning and expression analysis of a novel member of the facilitative glucose transporter family, SLC2A9 (GLUT9)
Cloning and expression of the human N-acetylglutamate synthase gene.
Purified RNA polymerase III accurately and efficiently terminates transcription of 5S RNA genes.
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.
Mcm4,6,7 uses a 'pump in ring' mechanism to unwind DNA by steric exclusion and actively translocate along a duplex
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
1-acyl-sn-glycero-3-phosphoserine [ChEBI:52603]
Cascade regulation of terminal adipocyte differentiation by three members of the C/EBP family of leucine zipper proteins
Mitochondrial tRNA import: are there distinct mechanisms?
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
Direct interaction between survivin and Smac/DIABLO is essential for the anti-apoptotic activity of survivin during taxol-induced apoptosis.
The Mammalian synaptonemal complex: a scaffold and beyond
7alpha,12alpha,26-trihydroxy-5beta-cholestan-3-one [ChEBI:48834]
cDNA cloning of human and rat brain myo-inositol monophosphatase. Expression and characterization of the human recombinant enzyme
7alpha,26-dihydroxycholest-4-en-3-one [ChEBI:48825]
Cloning and expression of AQP3, a water channel from the medullary collecting duct of rat kidney
The Tim9p/10p and Tim8p/13p complexes bind to specific sites on Tim23p during mitochondrial protein import
Beta-enolase deficiency, a new metabolic myopathy of distal glycolysis
Structure of human argininosuccinate synthetase
Acta Crystallogr D Biol Crystallogr 64:279-86
Human TLR10 is a functional receptor, expressed by B cells and plasmacytoid dendritic cells, which activates gene transcription through MyD88
SUBUNIT Cytochrome c oxidase is composed of 11 subunits: one copy each of COX1, COX2, COX3, COX4, COX5A or COX5B, COX6, COX7, COX9, COX12, COX13 and two copies of COX8.MISCELLANEOUS Present with 9410 molecules/cell in log phase SD medium.SIMILARITY Belongs to the cytochrome c oxidase subunit 5B family.
Interferon induces tryptophanyl-tRNA synthetase expression in human fibroblasts
Molecular mechanism of the Syk activation switch
Synthesis of PIPs at the late endosome membrane
Structural determinants in AUF1 required for high affinity binding to A + U-rich elements
Biogenesis of the protein import channel Tom40 of the mitochondrial outer membrane: intermembrane space components are involved in an early stage of the assembly pathway
Hydrolysis of cAMP to 5' AMP by Phosphorylated PDE3B
Proteasome mediated degradation of PAK-2p34
Beginning of RNA Polymerase III Productive Transcription
The transition from abortive to productive transcription may occur at bp +5. The primary transcripts of pol III-transcribed genes are short, ~90 to 120 nt for tRNA and 5 sRNA genes (which constitute the great majority of products) and even the longest transcripts (e.g. the RNA of the signal recognition particles) are only ~500 nt. The special feature of this transcription is the presence of initiation factors bound within the transcription unit ââ¬â TFIIIA within class 1 genes (NH section) and TFIIIC in class 1 and class 2 genes. Transcript elongation, which has been analyzed at single-step resolution on a single sc tRNA gene, is rapid with highly purified components (TFIIIC, TFIIIB and pol III), and also in crude extracts (Matsuzaki et al., 1994; Shaaban et al., 1996). In particular, TFIIIC does not present a barrier to transcript elongation, generating a delay at only a single site of only 0.15-0.2 s duration at 20C. In other words, the requirement to displace TFIIIC during transcript elongation is not rate-limiting for tRNA gene activity. On the other hand, transcript elongation slows down when short U-tracts, e.g. UUU, are laid down, even at high concentrations of NTPs. These pauses exceed the TFIIIC-imposed delay on transcription of the sc SUP4 gene by a factor of ~3 or greater. Sc TFIIIC is entirely displaced from a tRNA gene during multiple cycles of transcription in vitro (Bardeleben et al., 1994) and its occupancy of pol III genes in vivo during active cell growth is also low (Roberts et al., 2003).
Abortive initiation, the repetitive formation of short oligonucleotides, is a ubiquitous feature of transcriptional initiation. For pol III, it has been analyzed only in S. cerevisiae (Bhargava and Kassavetis, 1999). The released products of abortive initiation, principally di- and tri-nucleotides, indicate the participation of retractive endonucleolytic cleavage of these initially forming abortive products. The transition from abortive to productive transcription may occur at bp +5.
Partial autophosphorylation of PAK-2 at Ser-19, Ser-20, Ser-55, Ser-192, and Ser-197
Proteolytic PAK-2p34 fragment translocates to the nucleus
Autophosphorylation of PAK-2p34 in the activation loop
Release of Cytochrome c from mitochondria
The proton oligopeptide cotransporter family SLC15 in physiology and pharmacology
Pancreatic islet GLUT2 glucose transporter mRNA and protein expression in humans with and without NIDDM
Proton-coupled di- and tri-peptide cotransport
Removal of SPO11 and Resection of 5' Ends of DNA (yeast)
SPO11 forms a dimer and each subunit cleaves a single strand of DNA, thus creating a double-strand break. After cleaving DNA, a SPO11 subunit remains covalently attached to each 5' end via a tyrosine residue. SPO11 is removed from the DNA by cleavage of single strands 3' to the attached SPO11. The products are a resected 5' end (protruding 3' overhang) and a covalent complex of SPO11 with an oligonucleotide.
Vesicular inhibitory amino acid transport
Proton-coupled histidine and di-peptide cotransport
SLC43A1 (LAT3)-mediated uptake of large neutral amino acids
SLC16A10-mediated uptake of aromatic amino acids
SLC43A2 (LAT4)-mediated uptake of large neutral amino acids
DNA damage recognition during nucleotide excision repair in mammalian cells.
GTP Hydrolysis by eRF3 bound to the eRF1:mRNA:polypeptide:80S Ribosome complex
At the beginning of this reaction, 1 molecule of 'eRF3-GTP:eRF1:peptidyl-tRNA:mRNA:80S Ribosome Complex' is present. At the end of this reaction, 1 molecule of 'eRF3-GDP:eRF1:peptidyl-tRNA:mRNA:80S Ribosome Complex', and 1 molecule of 'Orthophosphate' are present. This reaction takes place in the 'cytosol'.
Formation of Double-strand Break in DNA by SPO11
Polypeptide release from the eRF3-GDP:eRF1:mRNA:80S Ribosome complex
At the beginning of this reaction, 1 molecule of 'eRF3-GDP:eRF1:peptidyl-tRNA:mRNA:80S Ribosome Complex' is present. At the end of this reaction, 1 molecule of 'polypeptide', and 1 molecule of 'eRF3-GDP:eRF1:tRNA:mRNA:80S Ribosome Complex' are present. This reaction takes place in the 'cytosol'.
Human protoporphyrinogen oxidase: expression, purification, and characterization of the cloned enzyme
Formation of the closed pre-initiation complex
Abortive termination of early transcription elongation by DSIF:NELF
Recruitment of RNA Polymerase II Holoenzyme by TFIIF to the pol II promoter:TFIID:TFIIA:TFIIB complex
Fall Back to Closed Pre-initiation Complex
RNA Polymerase III Initiation At a Simple Start Sequence
Transcription by pol III initiates at characteristic, simple start sequences. The universal core of these start sites is a pyrimidine-purine step, transcription initiating most frequently with ATP or GTP (Fruscoloni et al., 1995)
RNA Polymerase III Retractive RNase Activity at U-tract Pause Sites
Productive transcription is accompanied by retractive RNase activity at U-tract pause sites and at the terminator. The principal cleavage products are dinucleotides, and they are produced in large stoichiometric excess over complete transcripts, despite the rapid overall rate of productive RNA chain elongation (Bobkova and Hall, 1997). This RNase activity is intrinsic to pol III, and is mediated by its C11 subunit (gene RPC10), a paralog of pol II Rpb9 with a C-terminal 26 amino acid domain that is highly similar to the extrinsic pol II transcription factor TFIIS (ChÃÂ©din et al., 1998). Two acidic amino acids in this segment (D91/E92 in scC11; D88/E89 in hC11), which are universally conserved in bacterial, archaeal and eukaryotic transcript cleavage factors, play a critical role in the activation of transcript cleavage by donating catalytic residues to the active centers of RNA polymerases for hydrolytic RNA chain retraction (ChÃÂ©din et al., 1998; Kettenberger et al., 2003; Opalka et al., 2003; Sosunova et al., 2003). However, the extrinsic transcript cleavage factors, as well as the C11 subunit of pol III, are devoid of separate RNase activity.
RNA Polymerase III Transcriptional Pause at Terminator Sequence
All RNA polymerases III terminate transcription at extremely simple sites, consistent with their role in producing small transcripts. These sites are essentially "Tn" (in the non-transcribed strand). Termination signals are recognized directly by polymerase III (Bogenhagen and Brown, 1981; Cozzarelli et al., 1983; Hamada et al., 2000). In vitro, hs sp and scpol III terminate transcription with comparable efficiency at T4, T4-5, and T5-6, respectively (Allison and Hall, 1985; Hamada et al., 2000; Huang and Maraia, 2001). At T runs that are sufficiently short to yield incomplete termination, nearby sequence influences the efficiency of termination (Bogenhagen and Brown, 1981; Gunnery et al., 1999; Mazabraud et al., 1987). The pol III termination site is a strong pause site; elongating transcription complexes that eventually read through a terminator do so with a significant time delay. This is in keeping with readily detectible slowing of RNA chain elongation by scpol III that is generated by even short runs of U incorporation into RNA (such as sequence found in U3) (Matsuzaki et al., 1994). Termination of transcription by scpol III is associated with repetitive hydrolytic resection of the nascent RNA chain's 3' end and resynthesis, an activity that requires the C11 subunit of pol III. In the absence of C11, pausing during transcript elongation is greatly reduced and RNA chain termination is severely but not absolutely defective. In such a case accurate termination (and RNA chain release) is restored at extremely low concentrations of UTP (1 and 3 ÃÂ¼M). C11 is proposed to exert its effect on termination indirectly by increasing RNA pausing. By increasing the time spent at the terminator the probability of read-through is decreased. This is different from the C11 subunit's direct RNase activity during hydrolytic RNA chain retraction (ChÃÂ©din et al., 1998).
RNA Polymerase III Termination and release of transcribed mRNA
Efficient transcript production requires efficient release of RNA polymerase at the terminator; slow release at the terminator of a short transcription unit quickly becomes rate limiting for transcription at steady state. Although pol III autonomously recognizes sequence terminators, proteins that help to rapidly detach pol III from the terminator can affect the productivity of transcription if they eliminate termination as the rate-limiting step. Conceivably, efficiency of transcription can also be increased by the chaperone-like device of directly conveying pol III from the terminator to the promoter; the small size of pol III transcription units appears to make them especially suitable for the operation of such mechanisms and for continuous recycling of a molecule of pol III on the same transcription unit (Dieci and Sentenac, 1996; Dieci and Sentenac, 2003). The operation of both types of facilitation in multi-cycle transcription by pol III has been proposed. In all instances, the case for physiologically significant effect has not yet been proven despite the existence of intriguing observations. La, NF1 family proteins, PC4 and topoisomerase I have been proposed as accessory pol III transcription factors that facilitate multi-cycle transcription by hspol III. hsLa is an RNA-binding protein, with an N-terminal segment that binds to the short 3' terminal U tracts of primary pol III transcripts and a C-proximal site that recognizes primary transcript 5' ends. Phosphorylation of C-proximal Ser366 is required for La's participation in tRNA maturation (Maraia and Intine, 2001). In a Human Polymerase III in vitro system for transcriptional recycling that uses arrested transcription elongation complexes on immobilized DNA templates, further rounds of transcription require La (Maraia, 1996) and the just referred-to C-proximal Ser phosphorylation is required for this function (Fan et al., 1997). In contrast, highly efficient (>99%) immunodepletion of La from a frog oocyte extract that executes very efficiently recycling transcription in vitro has no effect on transcript yield (LinMarq and Clarkson, 1998). Although La is detected as a component of human holoPolymerase III, the gene encoding the yeast homologue of La is not essential (Yoo and Wolin, 1994). Thus, La is unlikely to be an essential and general transcription-recycling factor of pol III. Whether it is a significant factor in human pol III transcription remains unresolved (Maraia and Intine, 2001). Three other components that co-purify hsholoTFIIIC (Schramm and Hernandez, 2002) have been implicated in transcriptional termination and recycling: PC4, topoisomerase I and NF1. Topoisomerase I and PC4 were shown to promote multi-cycle transcription selectively and separately (Wang and Roeder, 1998), but the physiological significance of their activity has been discounted subsequently on account of the very great molecular excess of protein required for this action (Wang et al., 2000). Purification of a DNA-binding component of a TFIIIC-containing fraction (Wang and Roeder, 1998) to apparent homogeneity yields NF1 family proteins that bind to the adenovirus VAI gene's terminator. A recombinant NF1 protein also interacts with two subunits of hs TFIIIC2. The biochemically purified NF1 family proteins exert strong effects on transcriptional termination and increase the number of rounds of transcription in vitro. Detailed analysis of this effect has been confined to the VAI gene, which harbors consensus NF1 binding sites that overlap its two terminators and are essential for the transcription termination activity of NF1. However, terminator-overlapping NF1 sites are not a general feature of hspol III-transcribed genes. Involvement of NF1 proteins in transcription of genes lacking NF1-binding sites, conceivably through interaction with TFIIIC2, has been referred to (Wang et al., 2000) but not presented in concrete detail. [Nor has the implicit conflict with the proposed essential character of NF1-binding sites at the VAI gene terminator been resolved.] Biochemically purified NF1 has been reported to exert no effect on transcription in a highly purified system consisting only of recombinant TFIIIB, immunopurified TFIIIC and pol III (Wang et al., 2000). Because pol III transcription units are small, the transcribing polymerase never leaves the general vicinity of its promoter; DNA bending by transcription factors further compacts these transcription units. As a consequence, repeated utilization of an (isolated) pol III gene by the same molecule of polymerase could be based on purely stochastic principles. In addition, evidence for the operation of a specific handing-off mechanism that repetitively returns pol III from its termination site to the (same gene's) promoter has been presented (Dieci and Sentenac, 1996). However, the task of discriminating between purely stochastic recycling and handing-off mechanisms involving specific protein-protein interactions presents difficult technical challenges that have not yet been met. (Some of these difficulties are briefly discussed in (Geiduschek and Kassavetis, 2001).) Thus, the existence of a mechanism for directly guiding transcription-terminating pol III back to the same promoter (i.e. in cis), and the nature of the protein-protein interactions that might generate such a chaperone-like mediation remain to be established.
Interaction of J-protein co-chaperone Jac1 with Fe-S scaffold Isu is indispensable in vivo and conserved in evolution
Evidence that the coproporphyrinogen oxidase activity of rat liver is situated in the intermembrane space of mitochondria
Pol III initiation complexes open the promoter spontaneously. Indeed, this is the general case for DNA-dependent RNA polymerases. Only pol II, with its requirement for TFIIH-directed and ATP-dependent promoter opening is exceptional. TFIIH introduces a layer of mechanism that is not in the repertoire of any other transcriptase. Thus, it is pol III-mediated transcription that is, from a mechanistic perspective, most directly comparable with archaeal and also bacterial transcription. Promoter opening has been analyzed only in the S. cerevisiae (sc) in vitro system. At the sc SUP4 tRNATyr promoter, a DNA segment extending from bp ââ¬â10 to +7 (relative to the transcriptional start site at +1) opens thermoreversibly between 0 and 40C, the upstream segment, bp ââ¬â9 to ââ¬â5, opening at slightly lower temperature than the downstream segment, bp ââ¬â2 to +7 (Kassavetis et al., 1992). The specification of 17 bp of DNA strand separation at the open promoter could be a slight overestimate. Even under the constraint of attachment to uniquely positioned TFIIIB, pol III can explore a short DNA segment for its initiation site (Fruscoloni et al., 1995). As a consequence, permanganate footprinting, which is used to analyze promoter opening, may provide a snapshot of a frequency-weighted superposition of multiple, closely spaced open promoter complexes that are in dynamic equilibrium instead of the unique complex that is precisely poised to form the first nucleotide linkage. Promoter opening (in linear DNA) naturally involves RNA polymerase, including the initiation-specific C34 subunit (sc gene RPC10) (Brun et al., 1997) and requires the participation of the Brf1 and Bdp1 subunits of sc TFIIIB (Hahn and Roberts, 2000; Kassavetis et al., 1998; Kassavetis et al., 2001). Thus, TFIIIB plays a role in transcriptional initiation that extends beyond recruiting pol III to the promoter.
ChREBP activates metabolic gene expression
Sulfate is exported to the cytosol in exchange for dicarboxylate
Succinyl CoA and glycine condense to form 5-aminolevulinate (ALA)
ALAS condenses SUCC-CoA and Gly to form dALA
Excess homocysteine yields homolanthionine and H2S
Excess cysteine yields lanthionine and H2S
Four PBGs combine through deamination to form hydroxymethylbilane (HMB)
Conversion of HMB to uroporphyrinogen III
AZD2171 shows potent antitumor activity against gastric cancer over-expressing fibroblast growth factor receptor 2/keratinocyte growth factor receptor
ALAD octamer associates with Pb++, forming a catalytically inactive complex
Two molecules of ALA condense to form porphobilinogen (PBG)
Uroporphyrinogen I is decarboxylated to form coproporphyrinogen I
Uroporphyrinogen III is decarboxylated to form coproporphyrinogen III
Inositol polyphosphate multikinase regulates inositol 1,4,5,6-tetrakisphosphate
Development of free-energy-based models for chaperonin containing TCP-1 mediated folding of actin
glyoxylate + alanine => glycine + pyruvate [peroxisome]
SAM is sythesized from methionine's reaction with ATP
Cystathionine is formed from homocysteine and serine
Homocysteine is degraded to oxobutanoate and H2S
MRS3/4 Transports Iron Across the Mitochondrial Inner Membrane
MRS3/4 transports ferrous iron across the mitochondrial inner membrane (Foury et al. 2002, Muhlenhoff et al. 2003).
CIA Targeting Complex Transfers 4Fe-4S Clusters to Apoproteins
A complex of four proteins termed CIA targeting complex is involved in the delivery of the Cfd1-Nbp35-bound Fe/S cluster to specific target apoproteins. Nar1 (human IOP1) is similar in sequence to iron-only hydrogenases and binds two [4Fe-4S] clusters. These cofactors are essential for biogenesis but their molecular function is unknown. The WD40 domain protein Cia1 (human CIAO1) forms a propeller-like structure which may serve as a docking site for the other members of the CIA targeting complex. The role of Cia2 (human FAM96B) and Mms19 (human MMS19) is still unclear, but they show some specificity for the delivery of Fe/S clusters into certain target apoproteins. They directly interact with numerous Fe/S target proteins including many proteins involved in nuclear DNA integrity and maintenance such as DNA polymerases (Pol3), helicases of the DNA repair pathway (Rad3) or of telomere maintenance, and primases. Many of these target proteins are relevant to various cancer-related diseases or aging.
GTP bound eRF3:eRF1 complex binds the peptidyl-tRNA:mRNA:Ribosome complex
At the beginning of this reaction, 1 molecule of 'peptidyl-tRNA:mRNA:80S Ribosome Complex', 1 molecule of 'GTP bound eRF3', and 1 molecule of 'Erf-1' are present. At the end of this reaction, 1 molecule of 'eRF3-GTP:eRF1:peptidyl-tRNA:mRNA:80S Ribosome Complex' is present. This reaction takes place in the 'cytosol'.
Cytosolic Fe/S protein biogenesis depends on the electron transfer chain from NAD(P)H to the Fe/S protein Dre2 (human CIAPIN) via the flavoprotein Tah18 (human NDOR1). The precise role of electrons in the assembly process is unclear but in the absence of the electron chain the stable [4Fe-4S] cluster of Nbp35 is not assembled. Dre2 binds two Fe/S clusters of the [2Fe-2S] and the [4Fe-4S] type. The [2Fe-2S] cluster is reduced by Tah18-NADPH.
4Fe-4S Cluster Forms on CFD1:NBP35 Scaffold
A [4Fe-4S] cluster is assembled on a scaffold composed of the P-loop NTPases Cfd1 (human NUBP2) and Nbp35 (human NUBP1) in a nucleotide-dependent fashion. The two proteins form a heterotetramer which transiently binds the [4Fe-4S] cluster in a bridged form between two subunits of the complex. The Fe/S cluster is bound to two highly conserved Cys residues in the C-termini of each of these proteins. Nbp35 contains an additional, stably associated [4Fe-4S] cluster at its N-terminus which is essential for function. Mitochondria play a crucial role in cytosolic and nuclear Fe/S protein biogenesis. They export via a mitochondrial ABC transporter (yeast ATM1, human ABCB7) a still unknown, sulfur-containing compound which is essential for Fe/S cluster assembly in the cytosol. The general cytosolic iron donor, the multi-domain monothiol glutaredoxin (yeast Grx3-Grx4, human GRX3 or PICOT) plays a crucial role in cytosolic-nuclear Fe/S protein biogenesis. The precise molecular function of the glutaredoxin is still unclear.
FXN:NFS1:ISD11:ISCU Synthesizes Iron-Sulfur Cluster
carbovir monophosphate + ATP => carbovir diphosphate + ADP
Phosphorylation of carbovir monophosphate
Transfer of Electrons from NADPH to FDXR
Transfer of Electrons from FDXR to FDX1/1L
Conversion of coproporphyrinogen III to protoporphyrinogen IX
acetaldehyde + NAD+ => acetate + NADH + H+ [mitochondrial]
acetate + CoA + ATP => acetyl-CoA + AMP + pyrophosphate [mitochondrial]
acetaldehyde + NAD+ => acetate + NADH + H+ [cytosolic]
gamma-glutamylcysteine combines with glycine to form glutathione
Oxidation of protoporphyrinogen IX to protoporphyrin IX
Ferrous iron is inserted into protoporphyrin IX to form heme
Translesion synthesis by DNA polymerases bypassing lesion on DNA template
phenylalanine + pyruvate => 3-(indol-3-yl)pyruvate + alanine
L-glutamate gamma-semialdehyde + NAD+ => glutamate + NADH + H+
tryptophan + O2 => N-formylkynurenine [IDO]
tryptophan + O2 => N-formylkynurenine [IDO2]
kynurenine + pyruvate => 4-(2-aminophenyl)-2,4-dioxobutanoic acid + alanine [CCBL2]
saccharopine + NAD+ + H2O => alpha-aminoadipic semialdehyde + glutamate + NADH + H+
lysine + alpha-ketoglutarate +NADPH + H+ => saccharopine + NADP+ + H2O
Oxidative decarboxylation of alpha-ketoadipate to glutaryl CoA by alpha-ketoglutarate dehydrogenase
alpha-ketoadipate + CoASH + NAD+ => glutaryl-CoA + CO2 + 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
Mercury-sensitive residues and pore site in AQP3 water channel
Syk protein-tyrosine kinase is regulated by tyrosine-phosphorylated Ig alpha/Ig beta immunoreceptor tyrosine activation motif binding and autophosphorylation
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3670924
FUNCTION Involved in DNA double-strand break repair (DSBR). The rad50/mre11 complex possesses single-strand endonuclease activity and ATP-dependent double-strand-specific exonuclease activity. Rad50 provides ATP-dependent control of mre11 by unwinding and/or repositioning DNA ends into the mre11 active site.SUBUNIT Homodimer (By similarity). Forms a complex with MRE11.MISCELLANEOUS Present with 830 molecules/cell in log phase SD medium.SIMILARITY Belongs to the SMC family. RAD50 subfamily.SIMILARITY Contains 1 zinc-hook domain.
Efflux and compartmentalization of zinc by members of the SLC30 family of solute carriers
The sodium/glucose cotransport family SLC5
Methylthio-ribose-P = Methylthio-ribulose-P
Methylthio-ribulose-P = Methylthio-ribose-P
S-Adenosyl methionine <=> Decarboxylated-Adenosyl methionine + CO2
Putrescine + dc-Adenosyl methionine => Spermidine + 5'-methylthioadenosine
gamma-butyrobetaine + alpha-ketoglutarate + O2 => carnitine + succinate + CO2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2529016
The SLC39 family of metal ion transporters
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672845
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
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672900
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3669063
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3672929
arginine + H2O => ornithine + urea [ARG2]
argininosuccinate <=> fumarate + arginine
arginine + H2O => ornithine + urea [ARG1]
carbamoyl phosphate + ornithine => citrulline + orthophosphate
ATP + aspartate + citrulline <=> argininosuccinate + AMP + pyrophosphate
2 ATP + NH4+ + HCO3- => 2 ADP + orthophosphate + carbamoyl phosphate [mitochondrial]
2 ATP + NH4+ + HCO3- => 2 ADP + orthophosphate + carbamoyl phosphate
glutamate + acetyl CoA => N-acetyl glutamate + CoA
3-hydroxyanthranilate + O2 => 2-amino-3-carboxymuconate semialdehyde
3-hydroxykynurenine + H2O => 3-hydroxyanthranilate + alanine
kynurenine + O2 + NADPH + H+ => 3-hydroxykynurenine + NADP+ + 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=3671244
The human homologue of yeast ArgRIII protein is an inositol phosphate multikinase with predominantly nuclear localization
FUNCTION Component of the mitochondrial outer membrane sorting assembly machinery (SAM or TOB) complex, which is required for the sorting of proteins with complicated topology, such as beta-barrel proteins, to the mitochondrial outer membrane after import by the TOM complex.DOMAIN Its C-terminal part seems to contain many membrane-spanning sided beta-sheets, that have the potential to adopt a transmembrane beta-barrel type structure.SIMILARITY Belongs to the SAM50/omp85 family.
Human IL4I1 is a secreted L-phenylalanine oxidase expressed by mature dendritic cells that inhibits T-lymphocyte proliferation
FUNCTION Required for N-linked oligosaccharide assembly. Has a role in the last step of the synthesis of the Man(5)GlcNAc(2)-PP-dolichol core oligosaccharide on the cytoplasmic face of the endoplasmic reticulum.CATALYTIC ACTIVITY 2 GDP-alpha-D-mannose + D-Man-alpha-(1->3)-(D-Man-alpha-(1->6))-D-Man-beta-(1->4)-D-GlcNAc-beta-(1->4)-D-GlcNAc-diphosphodolichol = 2 GDP + D-Man-alpha-(1->2)-D-Man-alpha-(1->2)-D-Man-alpha-(1->3)-(D-Man-alpha-(1->6))-D-Man-beta-(1->4)-D-GlcNAc-beta-(1->4)-D-GlcNAc-diphosphodolichol.PATHWAY Protein modification; protein glycosylation.SUBUNIT Interacts with ALG1.MISCELLANEOUS Present with 3140 molecules/cell in log phase SD medium.SIMILARITY Belongs to the glycosyltransferase group 1 family. Glycosyltransferase 4 subfamily.
ATP activates transcription initiation from promoters by RNA polymerase II in a reversible step prior to RNA synthesis.
The Nod-like receptor (NLR) family: a tale of similarities and differences
Synoviocyte innate immune responses: I. Differential regulation of interferon responses and the JNK pathway by MAPK kinases
Human liver alcohol dehydrogenase: purification, composition, and catalytic features.
Differential recognition of preproteins by the purified cytosolic domains of the mitochondrial import receptors Tom20, Tom22, and Tom70
Phosphorylation by p34cdc2 regulates spindle association of human Eg5, a kinesin-related motor essential for bipolar spindle formation in vivo
Phosphorylation of carbovir enantiomers by cellular enzymes determines the stereoselectivity of antiviral activity
Wnt/beta-catenin signaling: components, mechanisms, and diseases
Resistance to thromboembolism in PI3Kgamma-deficient mice
Expression and characterization of a human pyruvate carboxylase variant by retroviral gene transfer
ChEBI:58828 5-(methylsulfanyl)-2,3-dioxopentyl phosphate(2?)
5-(methylsulfanyl)-2,3-dioxopentyl phosphate(2?)
Cloning and expression of two human lysophosphatidic acid acyltransferase cDNAs that enhance cytokine-induced signaling responses in cells
Function and dysfunction of the PI system in membrane trafficking
Rat liver adenosine triphosphate:adenosine monophosphate phosphotransferase activity. II. Subcellular localization of adenylate kinase isozymes
Telomerase catalytic subunit homologs from fission yeast and human
The human gamma-glutamyltransferase gene family
Rapid destruction of human Cdc25A in response to DNA damage.
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.
Review of epidermal growth factor receptor biology
leu, ile, or val + alpha-ketoglutarate <=> a-ketoisocaproate, a-keto-b-methylvalerate, or a-ketoisovalerate + glutamate [BCAT1]
a-ketoisocaproate, a-keto-b-methylvalerate, or a-ketoisovalerate + glutamate <=> leu, ile, or val + alpha-ketoglutarate [BCAT1]
3-phosphonooxypyruvic acid + L-glutamate = O-phospho-L-serine + 2-oxoglutarate
L-1-pyrroline-5-carboxylate + NADPH + H+ => proline + NADP+
glutamine + pyruvate => 2-oxoglutaramate + alanine
Isolation and characterization of an allelic cDNA for human muscle fructose-1,6-bisphosphatase
alpha-methyl-acetoacetyl-CoA + CoA => propionyl-CoA + acetyl-CoA
beta-hydroxyisobutyryl-CoA + H2O => beta-hydroxyisobutyrate + CoA
leu, ile, or val + alpha-ketoglutarate <=> a-ketoisocaproate, a-keto-b-methylvalerate, or a-ketoisovalerate + glutamate [BCAT2]
a-ketoisocaproate, a-keto-b-methylvalerate, or a-ketoisovalerate + glutamate <=> leu, ile, or val + alpha-ketoglutarate [BCAT2]
Isolation and characterization of cDNAs corresponding to two human calcium, calmodulin-regulated, 3',5'-cyclic nucleotide phosphodiesterases
Characterization of human phosphoserine aminotransferase involved in the phosphorylated pathway of L-serine biosynthesis
Protein kinase C beta controls nuclear factor kappaB activation in B cells through selective regulation of the IkappaB kinase alpha
Platelet hyperaggregability: impaired responsiveness to nitric oxide ("platelet NO resistance") as a therapeutic target
De novo sphingolipid biosynthesis: a necessary, but dangerous, pathway
Telomeric protein distributions and remodeling through the cell cycle in Saccharomyces cerevisiae
The single minichromosome maintenance protein of Methanobacterium thermoautotrophicum DeltaH contains DNA helicase activity.
Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase
Identification and characterization of eukaryotic initiation factor 5A-2
Na+/H+ exchanger transport (at late endosome membrane)
Na+/H+ exchanger transport (at trans-golgi membrane)
GLUT7 and GLUT11 transport glucose and fructose
ZnT1 mediates the efflux of zinc from the cell
GLUT9 transports glucose, fructose and urate
ZnT7 transports zinc into the golgi apparatus
ZnT5 transports zinc into secretory granules in pancreatic beta cells
Equilibrative transport (export) of nucleosides and free bases by solute carrier family 29 (nucleoside transporters), member 1
Cellular copper transport is mediated by human copper transporter 1 hCTR1
Na+/H+ exchanger transport (at early endosome membrane)
ABC7, mABC1 and mABC2 mediate heme transport
The ABCC family mediates organic anion transport
phosphorylated MKK3/MKK6 migrates to nucleus
ABCD1/D2/D3 mediate long chain fatty acid transport in to peroxisomes
Phosphorylation of human JNKs by activated MKK4/MKK7
Activated human JNKs migrate to nucleoplasm
Phytanic acid alpha-oxidation, new insights into an old problem: a review
Release of (inferred) platelet cytosolic components
Release of 78 kDa glucose-regulated protein
F-actin capping protein is a heterodimer
Adenylate Kinase 3 is a GTP-AMP phosphotransferase
Clinical and molecular features of three patients with congenital disorders of glycosylation type Ih (CDG-Ih) (ALG8 deficiency)
Release of platelet cytosolic components
Functional and genetic studies demonstrate that mutation in the COX15 gene can cause Leigh syndrome
VAV3 is a GEF for Rho/Rac family kinases
VAV2 is a GEF for Rho/Rac family kinases
Activation of conventional Protein Kinase C
Activation of Protein Kinase C novel isoforms
Madin-Darby canine kidney II cells: a pharmacologically validated system for NPC1L1-mediated cholesterol uptake
Studies on the properties and tissue distribution of the isozymes of guanylate kinase in man
Formation of the 43S pre-initiation complex
The 60S subunit joins the translation initiation complex
Formation of eIF2:GDP:eIF2B intermediate
Synthesis of nascent polypeptide containing signal sequence
Peptide transfer from P-site tRNA to the A-site tRNA
The SRP receptor binds the SRP:nascent peptide:ribosome complex
6-Phosphogluconate dehydrogenase: the mechanism of action investigated by a comparison of the enzyme from different species
Met-tRNAi binds to eIF2:GTP to form the ternary complex
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
Exportin-5 recognizes 3' overhang of pre-miRNA
Formation of UPF1:eRF3 Complex on mRNA with a Premature Termination Codon and No Exon Junction Complex
Aurora B controls the association of condensin I but not condensin II with mitotic chromosomes
AUF1(hnRNP D0) Dimers Bind AU-rich Element in 3' UTR of Transcripts
Exportin complex translocates pre-miRNA to cytosol
Binding of Lsm1-7 Complex to Deadenylated mRNA
SMG1 Phosphorylates UPF1 (Enhanced by Exon Junction Complex)
5' to 3' Exoribonuclease Digestion of Decapped mRNA (yeast)
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.
valine + tRNA(Val) + ATP => Val-tRNA(Val) + AMP + pyrophosphate
Scavenging of the 7-methylguanosine Cap by DCPS
tryptophan + tRNA(Trp) + ATP => Trp-tRNA(Trp) + AMP + pyrophosphate
tyrosine + tRNA(Tyr) + ATP => Tyr-tRNA(Tyr) + AMP + pyrophosphate
TAK1 is a ubiquitin-dependent kinase of MKK and IKK
Regulation of Glucokinase by Glucokinase Regulatory Protein
threonine + tRNA(Thr) + ATP => Thr-tRNA(Thr) + AMP + pyrophosphate
serine + tRNA(Ser) + ATP => Ser-tRNA(Ser) + AMP + pyrophosphate
proline + tRNA(Pro) + ATP => Pro-tRNA(Pro) + AMP + pyrophosphate
phenylalanine + tRNA(Phe) + ATP => Phe-tRNA(Phe) + AMP + pyrophosphate
methionine + tRNA(Met) + ATP => Met-tRNA(Met) + AMP + pyrophosphate
lysine + tRNA(Lys) + ATP => Lys-tRNA(Lys) + AMP + pyrophosphate
glutamate + tRNA(Glu) + ATP => Glu-tRNA(Glu) + AMP + pyrophosphate
glutamine + tRNA(Glu) + ATP => Glu-tRNA(Glu) + AMP + pyrophosphate
Molecular basis for membrane phospholipid diversity: why are there so many lipids?
glycine + tRNA(Gly) + ATP => Gly-tRNA(Gly) + AMP + pyrophosphate
isoleucine + tRNA(Ile) + ATP => Ile-tRNA(Ile) + AMP + pyrophosphate
leucine + tRNA(Leu) + ATP => Leu-tRNA(Leu) + AMP + pyrophosphate
On the mechanism of sensing unfolded protein in the endoplasmic reticulum
Replication protein A: a heterotrimeric, single-stranded DNA-binding protein required for eukaryotic DNA metabolism.
Activation of Gene Expression by SREBP (SREBF)
Phosphorylation of Mcm4 at specific sites by cyclin-dependent kinase leads to loss of Mcm4,6,7 helicase activity.
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
cysteine + tRNA(Cys) + ATP => Cys-tRNA(Cys) + AMP + pyrophosphate
The phosphate carrier has an ability to be sorted to either the TIM22 pathway or the TIM23 pathway for its import into yeast mitochondria
DSIF complex binds to RNA Pol II (hypophosphorylated)
Hypophosphorylation of RNA Pol II CTD by FCP1P protein
Requirement of human renal water channel aquaporin-2 for vasopressin-dependent concentration of urine
Extrusion of 5'-end of 30 nt long transcript through the pore in Pol II complex
Addition of nucleotides between position +11 and +30
Phosphorylation (Ser5) of RNA pol II CTD
Addition of the third nucleotide on the nascent transcript
Functions and mechanisms of RNA editing.
Newly Formed Phosphodiester Bond Stabilized and PPi Released
Addition of nucleotides 10 and 11 on the growing transcript: Third Transition
Addition of the fourth nucleotide on the Nascent Transcript: Second Transition
RNA Polymerase II Promoter Opening: First Transition
NTP Binds Active Site of RNA Polymerase II
Nucleophillic Attack by 3'-hydroxyl Oxygen of nascent transcript on the Alpha Phosphate of NTP
The Bcl-2 family: roles in cell survival and oncogenesis.
The citric acid (TCA) cycle and respiratory electron transport
Role of immunoproteasomes in cross-presentation
(24R,25R)-3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestan-26-oyl-CoA [ChEBI:52050]
The RNA polymerase III transcription apparatus.
Structural and functional modules in RNA interference
GTP hydrolysis and joining of the 60S ribosomal subunit
N-acetyl-D-glucosaminylphosphatidylinositol [ChEBI:15935]
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Studies on human erythrocyte inorganic pyrophosphatase.
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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
NLR proteins: integral members of innate immunity and mediators of inflammatory diseases
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The human homolog of Saccharomyces cerevisiae CDC45.
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Type I phosphatidylinositol-4-phosphate 5-kinases synthesize the novel lipids phosphatidylinositol 3,5-bisphosphate and phosphatidylinositol 5-phosphate
Polo-like kinase-1 is activated by aurora A to promote checkpoint recovery
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Protein interactions with nitric oxide synthases: controlling the right time, the right place, and the right amount of nitric oxide
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The biochemistry, metabolism and inherited defects of the pentose phosphate pathway: a review
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Transcriptional networks controlling pancreatic development and beta cell function
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Extracellular transsulfuration generates hydrogen sulfide from homocysteine and protects endothelium from redox stress
Am J Physiol Heart Circ Physiol 299:H1568-76
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
Molecular characterization of two galactosemia mutations: correlation of mutations with highly conserved domains in galactose-1-phosphate uridyl transferase
Signal transduction via platelet-derived growth factor receptors
Bleeding due to disruption of a cargo-specific ER-to-Golgi transport complex
Inflammasomes: guardians of cytosolic sanctity
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
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
Traffic control: regulation of kinesin motors
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
GPCho is hydrolyzed to Cho and G3P by GPCPD1
GPETA is hydrolyzed to ETA and G3P by GPCPD1
PCho and CTP are condensed to CDP-Cho by PCYT1 dimer
Novel mitochondrial intermembrane space proteins as substrates of the MIA import pathway
Specific interaction of a purified transcription factor with an internal control region of 5S RNA genes
PI3P is phosphorylated to PI(3,5)P2 by PIKFYVE at the Golgi membrane
PI3P is dephosphorylated to PI by SACM1L at the Golgi membrane
PI4P is dephosphorylated to PI by SACM1L at the Golgi membrane
PI is phosphorylated to PI3P by PIK3C2A/3 at the Golgi membrane
PI4KB binds to ARF1/3:GTP at the Golgi membrane
PI is phosphorylated to PI4P by PI4KB at the Golgi membrane
PI4P is dephosphorylated to PI by SACM1L at the ER membrane
PI is phosphorylated to PI4P by PI4KA/2A/2B at the Golgi membrane
CL and 1-acyl LPE are converted to MLCL and PE by TAZ (IM) (Reversible)
PI is phosphorylated to PI4P by PI4KA/2B at the ER membrane
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
CL and 1-acyl LPC are converted to MLCL and PC by TAZ (IM) (Reversible)
MLCL and PC are converted to CL and 1-acyl LPC by TAZ (IM) (Reversible)
MLCL and PE are converted to CL and 1-acyl LPE by TAZ (IM) (Reversible)
1-acyl LPG is acylated to PG by CRLS1 (IM)
2-acyl LPG is acylated to PG by CRLS1 (IM)
PG and CDP-DAG are converted to CL by CRLS1
PC is transphosphatidylated to PG by PLD1-4/6
Homologous recombination repair of replication-independent double-strand breaks
PI is phosphorylated to PI5P by PIKFYVE at the late endosome membrane
PI(3,5)P2 is dephosphorylated to PI5P by MTM[3] at the late endosome membrane
PI(3,5)P2 is dephosphorylated to PI3P by FIG4 at the late endosome membrane
PI3P is phosphorylated to PI(3,5)P2 by PIKFYVE at the late endosome membrane
Hydration of delta2-tetracosaheptaenoyl-CoA to 3-hydroxy tetracosahexaenoyl-CoA
Translocation of tetracosahexaenoyl-CoA to peroxisomes
PI3P is dephosphorylated to PI by MTM[3] at the late endosome membrane
PI is phosphorylated to PI3P by PIK3C2A/3 at the late endosome membrane
PI is phosphorylated to PI4P by PI4K2A/B at the early endosome membrane
PI is phosphorylated to PI3P by PIK3C2A/3 at the early endosome membrane
PI(3,5)P2 is dephosphorylated to PI3P by FIG4 at the early endosome membrane
Comparison of the intracellular signaling responses by three chimeric fibroblast growth factor receptors in PC12 cells
PI(4,5)P2 is dephosphorylated to PI4P by SYNJ/INPP5[1] at the plasma membrane
PI(4,5)P2 is dephosphorylated to PI4P by OCRL/INPP5E at the Golgi membrane
PI(3,5)P2 is dephosphorylated to PI3P by SYNJ at the plasma membrane
PI3P is dephosphorylated to PI by SYNJ/MTM[1] at the plasma membrane
PI is phosphorylated to PI4P by PI4K2A/B at the plasma membrane
PI(3,5)P2 is dephosphorylated to PI5P by SYNJ/MTM[1] at the plasma membrane
PI3P is phosphorylated to PI(3,5)P2 by PIKFYVE at the early endosome membrane
PI4P is dephosphorylated to PI by SYNJ at the plasma membrane
PI(3,5)P2 is dephosphorylated to PI3P by FIG4 at the Golgi membrane
A flavin-dependent monooxygenase involved in ubiquinone/ubiquinol biosynthesis, Coq6 (Heeringa et al. 2011) catalyses the C5-hydroxylation of 3-hexaprenyl-4-hydroxybenzoic acid (HHB) to 3,4-dihydroxy-5-hexaprenylbenzoic acid (DHHB) (Ozeir et al. 2011, Gin et al. 2003). Coq6 is a peripheral membrane protein that localizes to the matrix side of the inner mitochondrial membrane (Gin et al. 2003). Ferredoxin, Yah1 and the ferredoxin reductase, Arh1 may be the in vivo source of electrons for Coq6 and additionally required for this reaction (Ozeir et al. 2011).
PHB and all-E-10PrP2 are combined into DHB by COQ2
Ectonucleotide pyrophosphatase/phosphodiesterase 7 (ENPP7) hydrolyses sphingomyelin
Sphingomyelin phosphodiesterase 2 and 3 (SMPD2 and 3) hydrolyse sphingomyelin to ceramide (plasma membrane)
sphingosine 1-phosphate => phosphoethanolamine + hexadec-2-enal
sphingosine 1-phosphate + H2O => sphingosine + orthophosphate [cytosolic - SGPP]
sphinganine 1-phosphate => phosphoethanolamine + hexadecanal
Identification of a cDNA encoding an isoform of human CTP synthetase
sphinganine 1-phosphate + H2O => sphinganine + orthophosphate
sphinganine + stearyl-CoA => dihydroceramide + CoASH
palmitoyl-CoA + serine => 3-ketosphinganine + CoASH + CO2
LTC4 is exported from the cytosol by ABCC1
ABCC1 mediates LTC4 export from the cell
Identification and characterization of a novel human sphingosine-1-phosphate phosphohydrolase, hSPP2
Cleavage of the gamma-glutamyl bond of LTC4 forms LTD4
Translocation of tetracosapentaenoyl-CoA to peroxisomes
PGD2 is reduced to 11-epi-PGF2a by AKRIC3
Prostaglandin E synthase isomerizes PGH2 to PGE2
Dehydrogenation of 3-hydroxy tetracosahexaenoyl-CoA
Conversion of DHA-CoA to docosahexaenoic acid (DHA)
Formation of DHA-CoA catalysed by 3-ketoacyl-CoA thiolase
Proteasome and peptidase function in MHC-class-I-mediated antigen presentation
Tom20 and Tom22 share the common signal recognition pathway in mitochondrial protein import
FUNCTION Essential component of the mitochondrial outer membrane sorting assembly machinery (SAM or TOB) complex, which is required for the sorting of proteins with complicated topology, such as beta-barrel proteins, to the mitochondrial outer membrane after import by the TOM complex.SUBUNIT Component of the mitochondrial outer membrane sorting assembly machinery (SAM or TOB) complex, which at least consists of SAM35, SAM37 and SAM50.MISCELLANEOUS Present with 1470 molecules/cell in log phase SD medium.
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
Reconstitution of the mia40-erv1 oxidative folding pathway for the small tim proteins
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
Donation of catalytic residues to RNA polymerase active center by transcription factor Gre.
Shelterin: the protein complex that shapes and safeguards human telomeres
MPF localization is controlled by nuclear export
Comprehensive proteomic analysis of the human spliceosome.
The ERBB4/HER4 intracellular domain 4ICD is a BH3-only protein promoting apoptosis of breast cancer cells
Insig-mediated degradation of HMG CoA reductase stimulated by lanosterol, an intermediate in the synthesis of cholesterol
Zinc transporters and the cellular trafficking of zinc
Phosphoribosylpyrophosphate synthesis from glucose decreases during amino acid starvation of human lymphoblasts
Squalene 2,3-epoxide cyclizes, forming lanosterol
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
Reduction of presqualene diphosphate to form squalene
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
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
The dual phosphatase activity of synaptojanin1 is required for both efficient synaptic vesicle endocytosis and reavailability at nerve terminals
4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol is decarboxylated and oxidized to form 4-methylcholesta-8(9),24-dien-3-one
4-methyl,4-carboxycholesta-8(9),24-dien-3beta-ol + NAD+ => 4-methylcholesta-8(9),24-dien-3-one + CO2 + NADH + H+
4,4-dimethylcholesta-8(9),14,24-trien-3beta-ol + NADPH + H+ => 4,4-dimethylcholesta-8(9),24-dien-3beta-ol + NADP+ [LBR]
4,4-dimethylcholesta-8(9),14,24-trien-3beta-ol is reduced to 4,4-dimethylcholesta-8(9),24-dien-3beta-ol [LBR]
4,4-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]
Enzymic conversion of squalene 2,3-oxide to lanosterol and cholesterol
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)
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)
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+
5Beta-cholesten-7alpha, 12alpha-diol-3-one + NADPH + H+ => 5beta-cholestan-3alpha, 7alpha, 12alpha-triol + NAPDP+
5Beta-cholesten-7alpha, 12alpha-diol-3-one is reduced to 5beta-cholestan-3alpha, 7alpha, 12alpha-triol
Expression of Squalene Monooxygenase (SQLE)
4-cholesten-7alpha, 12alpha-diol-3-one + NADPH + H+ => 5beta-cholesten-7alpha,12alpha-diol-3-one + NADP+
4-cholesten-7alpha, 12alpha-diol-3-one is reduced to 5beta-cholesten-7alpha, 12alpha-diol-3-one
4-cholesten-7alpha-ol-3-one + NADPH + H+ => 5beta-cholestan-7alpha-ol-3-one + NADP+
4-cholesten-7alpha-ol-3-one is reduced to 5beta-cholestan-7alpha-ol-3-one
Measurement and subcellular distribution of choloyl-CoA synthetase and bile acid-CoA:amino acid N-acyltransferase activities in rat liver
5beta-cholestan-7alpha-ol-3-one+ NADPH + H+ => 5beta-cholestan-3alpha, 7alpha-diol + NADP+
5beta-cholestan-7alpha-ol-3-one is reduced to 5beta-cholestan-3alpha, 7alpha-diol
THCA + ATP + CoASH => 25(R) THCA-CoA + AMP + pyrophosphate (SLC27A2 "VLCS")
THCA is conjugated with Coenzyme A (SLC27A2 VLCS)
DHCA + ATP + CoASH => 25(R) DHCA-CoA + AMP + pyrophosphate (SCLS25A5 "BACS")
DHCA is conjugated with Coenzyme A (SLC27A5 BACS)
3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA (THCA-CoA) is hydrated to (24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA
3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA + H2O => (24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA
DHCA + ATP + CoASH => 25(R) DHCA-CoA + AMP + pyrophosphate (SLC27A2 "VLCS")
DHCA is conjugated with Coenzyme A (SLC27A2 VLCS)
THCA + ATP + CoASH => 25(R) THCA-CoA + AMP + pyrophosphate (SCLS25A5 "BACS")
THCA is conjugated with Coenzyme A (SLC27A5 BACS)
(24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA + NAD+ => 3alpha,7alpha-dihydroxy-5beta-cholest-24-one-CoA + NADH + H+
(24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA is oxidized to 3alpha,7alpha-dihydroxy-5beta-cholest-24-one-CoA
Translation of the phosphoinositide code by PI effectors
Hydrolysis of choloyl-CoA to cholate and CoASH
25(S) 3alpha,7alpha-dihydroxy-5beta-cholest-24-enoyl-CoA is hydrated to (24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA
25(S) 3alpha,7alpha-dihydroxy-5beta-cholest-24-enoyl-CoA + H2O => (24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA
(24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA + NAD+ => 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-one-CoA + NADH + H+
(24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA is oxidized to 3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-one-CoA
4-cholesten-7alpha,12alpha,24(S)-triol-3-one + NADPH + H+ => 5beta-cholestan-7alpha,12alpha,24(S)-triol-3-one + NADP+
4-cholesten-7alpha,12alpha,24(S)-triol-3-one is reduced to 5beta-cholestan-7alpha,12alpha,24(S)-triol-3-one
4-cholesten-7alpha,24(S)-diol-3-one + NADPH + H+ => 5beta-cholestan-7alpha,24(S)-diol-3-one + NADP+
4-cholesten-7alpha,24(S)-diol-3-one is reduced to 5beta-cholestan-7alpha,24(S)-diol-3-one
5Beta-cholestan-7alpha,12alpha,24(S)-triol-3-one + NADPH + H+ => 5beta-cholestan-3alpha,7alpha,12alpha,24(S)-tetrol + NAPDP+
5Beta-cholestan-7alpha,12alpha,24(S)-triol-3-one is reduced to 5beta-cholestan-3alpha,7alpha,12alpha,24(S)-tetrol
5beta-cholestan-7alpha,24(S)-diol-3-one+ NADPH + H+ => 5beta-cholestan-3alpha,7alpha,24(S)-triol + NADP+
5beta-cholestan-7alpha,24(S)-diol-3-one is reduced to 5beta-cholestan-3alpha,7alpha,24(S)-triol
TetraHCA + ATP + CoASH => 25(R) TetraHCA-CoA + AMP + pyrophosphate + H2O (SCLS25A5 "BACS")
TetraHCA is conjugated with Coenzyme A (SLC27A5 BACS)
3,7,24THCA + ATP + CoASH => 3,7,24THCA-CoA + AMP + pyrophosphate + H2O (SCLS25A5 "BACS")
3,7,24THCA is conjugated with Coenzyme A (SLC27A5 BACS)
TetraHCA + ATP + CoASH => 25(R) THCA-CoA + AMP + pyrophosphate + H2O (SLC27A2 "VLCS")
TetraHCA is conjugated with Coenzyme A (SLC27A2 VLCS)
3,7,24THCA + ATP + CoASH => 3,7,24THCA-CoA + AMP + pyrophosphate + H2O (SLC27A2 "VLCS")
3,7,24THCA is conjugated with Coenzyme A (SLC27A2 VLCS)
Uridine diphosphate glucose pyrophosphorylase. II
4-cholesten-7alpha,12alpha,27-triol-3-one + NADPH + H+ => 5beta-cholestan-7alpha,12alpha,27-triol-3-one + NADP+
4-cholesten-7alpha,12alpha,27-triol-3-one is reduced to 5beta-cholestan-7alpha,12alpha,27-triol-3-one
4-cholesten-7alpha,27-diol-3-one + NADPH + H+ => 5beta-cholestan-7alpha,27-diol-3-one + NADP+
4-cholesten-7alpha,27-diol-3-one is reduced to 5beta-cholestan-7alpha,27-diol-3-one
Isolation of the human phosphomannomutase gene (PMM1) and assignment to chromosome 22q13
PETA and CTP are condensed to CDP-ETA by PCY2
2-MAG is hydrolyzed to fatty acid and glycerol by MGLL
PC is hydrolyzed to PA and choline by PLD1/2
Human glutamate pyruvate transaminase (GPT): localization to 8q24.3, cDNA and genomic sequences, and polymorphic sites.
Cytosolic cholate and chenodeoxycholate are conjugated with Coenzyme A (SLC27A5 BACS)
Cholesterol is hydroxylated to 25-hydroxycholesterol
5beta-cholestan-7alpha,27-diol-3-one+ NADPH + H+ => 5beta-cholestan-3alpha,7alpha,27-triol + NADP+
5beta-cholestan-7alpha,27-diol-3-one is reduced to 5beta-cholestan-3alpha,7alpha,27-triol
5Beta-cholestan-7alpha,12alpha,27-triol-3-one + NADPH + H+ => 5beta-cholestan-3alpha,7alpha,12alpha,27-tetrol + NAPDP+
5Beta-cholestan-7alpha,12alpha,27-triol-3-one is reduced to 5beta-cholestan-3alpha,7alpha,12alpha,27-tetrol
Adaptors and molecular scaffolds in immune cell signaling
Molecular analysis of human argininosuccinate lyase: mutant characterization and alternative splicing of the coding region
The ends of the affair: capping and polyadenylation.
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
Assembly of the ORC complex at the origin of replication
Reconstituted TOM core complex and Tim9/Tim10 complex of mitochondria are sufficient for translocation of the ADP/ATP carrier across membranes
Distinct missense mutations of the FGFR3 lys650 codon modulate receptor kinase activation and the severity of the skeletal dysplasia phenotype
Identification of a novel human nicotinamide mononucleotide adenylyltransferase
ADP-ribose + H2O => AMP + D-ribose 5-phosphate (cytosolic)
Cytosolic NUDT5 hydrolyses ADP-ribose to R5P and AMP
dehydroascorbate [extracellular] => dehydroascorbate [cytosol]
Dehydroascorbate transport across the plasma membrane
GLUT1/3 transports extracellular DHvitC to cytosol
glutathione (oxidized) + NADPH + H+ => 2 glutathione (reduced) + NADP+
amination of uridine 5'-triphosphate (UTP) to form cytidine 5'-triphosphate (CTP)
UTP + glutamine + ATP + H2O => CTP + glutamate + ADP + orthophosphate [CTPS2]
Human ISD11 is essential for both iron-sulfur cluster assembly and maintenance of normal cellular iron homeostasis
UTP + glutamine + ATP + H2O => CTP + glutamate + ADP + orthophosphate [CTPS]
dUDP or TDP + ADP <=> dUMP or TMP + ATP [DTYMK]
(d)ADP or (d)CDP + ADP <=> (d)AMP or (d)CMP + ATP [AK5]
De-regulated FGF receptors as therapeutic targets in cancer
dUMP or TMP + ATP <=> dUDP or TDP + ADP [DTYMK]
phosphorylation of dUMP or TMP to dUDP or TDP
(d)AMP or (d)CMP + ATP <=> (d)ADP or (d)CDP + ADP [AK5]
Pre-mRNA splicing: the discovery of a new spliceosome doubles the challenge.
(deoxy)cytidine + H2O => (deoxy)uridine + NH4+ [CDA]
deamination of 2'-Deoxycytidine to 2'-Deoxyuridine
dUMP + N5,N10-methylene tetrahydrofolate => TMP + dihydrofolate
condensation of N-Carbamoyl-L-aspartate to form (S)-Dihydroorotate (ring closure)
N-carbamoyl L-aspartate + H+ <=> (S)-dihydroorotate + H2O
(S)-dihydroorotate + ubiquinone => orotate + ubiquinol
oxidation of (S)-Dihydroorotate to form Orotate
carbamoyl phosphate + L-aspartate <=> N-carbamoyl L-aspartate + orthophosphate
carbamoyl phosphate and L-aspartate combine to form N-Carbamoyl-L-aspartate
hydrolysis of 2'-deoxyuridine 5'-triphosphate to form 2'-deoxyuridine 5'-phosphate
orotate + 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) <=> orotidine 5'-monophosphate (OMP) + pyrophosphate
phosphoribosylation of orotate to form oritidine 5'-phosphate (OMP)
decarboxylation of Orotidine 5'-phosphate to form Uridine 5'-phosphate
orotidine 5'-monophosphate => uridine 5'-monophosphate + CO2
Role of substrates and products of PI 3-kinase in regulating activation of Rac-related guanosine triphosphatases by Vav
(deoxy)inosine + orthophosphate <=> hypoxanthine + (deoxy)ribose 1-phosphate [NP]
L-glutamine + 2 ATP + HCO3- + H2O => carbamoyl phosphate + L-glutamate + 2 ADP + orthophosphate
bicarbonate and glutamine combine to form carbamoyl phosphate
(2'-deoxy)adenosine + ATP => (d)AMP + ADP [ADK]
guanine + (deoxy)ribose 1-phosphate <=> (deoxy)guanosine + orthophosphate [NP]
hypoxanthine + (deoxy)ribose 1-phosphate <=> (deoxy)inosine + orthophosphate [NP]
(deoxy)guanosine + orthophosphate <=> guanine + (deoxy)ribose 1-phosphate [NP]
NifS-directed assembly of a transient [2Fe-2S] cluster within the NifU protein
Proc. Natl. Acad. Sci. U.S.A. 97:599-604
Apoptosis-inducing factor (AIF): a ubiquitous mitochondrial oxidoreductase involved in apoptosis.
Minireview: implication of mitochondria in insulin secretion and action
alanine + alpha-ketoglutarate <=> pyruvate + glutamate [GPT2]
pyruvate + glutamate <=> alanine + alpha-ketoglutarate [GPT]
alanine + alpha-ketoglutarate <=> pyruvate + glutamate [GPT]
NFS1 transfers sulfur from cysteine onto MOCS3
5,10-methenylTHF polyglutamate + H2O <=> 10-formylTHF polyglutamate
Phospholipase C-gamma: diverse roles in receptor-mediated calcium signaling
Coordinate binding of ATP and origin DNA regulates the ATPase activity of the origin recognition complex.
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]
oxaloacetate + glutamate <=> aspartate + alpha-ketoglutarate [GOT1]
pyruvate + glutamate <=> alanine + alpha-ketoglutarate [GPT2]
Conversion of cytosolic 5-methyltetrahydrofolate (5-methylTHF) to 5-methylTHF-polyglutamate
Conversion of cytosolic THF to THF-polyglutamate
Mitochondrial tetrahydrofolate export across the inner mitochondrial membrane
Cytosolic tetrahydrofolate import across the inner mitochondrial membrane
5,10-methyleneTHF polyglutamate + NADP+ <=> 5,10-methenylTHF polyglutamate + NADPH + H+
5,10-methyleneTHF polyglutamate + NADPH + H+ => 5-methylTHF polyglutamate + NADP+
THF polyglutamate + formate + ATP => 10-formylTHF polyglutamate + ADP + orthophosphate
Conversion of mitochondrial THF to THF-polyglutamate
5,10-methenylTHF polyglutamate + NADPH + H+ <=> 5,10-methyleneTHF polyglutamate + NADP+
10-formylTHF polyglutamate <=> 5,10-methenylTHF polyglutamate + H2O
Cytoslic carboxylases translocate to mitochondrial matrix
Biosynthesis of A2E, implicated in retinal degradation
Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT3]
Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT2]
Nicotinate D-ribonucleotide + ATP => deamino-NAD+ + pyrophosphate [NMNAT1]
A phospho-ribosyl group is added to quinolinate
DHF is reduced to tetrahydrofolate (THF)
Folate is reduced to dihydrofolate (DHF)
ATF6 as a transcription activator of the endoplasmic reticulum stress element: thapsigargin stress-induced changes and synergistic interactions with NF-Y and YY1
Condensation of phosphopantothenate with cysteine
SLC25A16 transports cytosolic CoA-SH to mitichondrial matrix
CoA transport across the inner mitochondrial membrane
Phosphopantothenoylcysteine is decarboxylated
PLP results from phosphorylation of pyridoxal
PLP from oxidation of pyridoxamine phosphate
ABCC1 transports cytosolic Cbl to extracellular region
PLP from oxidation of pyridoxine phosphate
Phosphatidylinositol 5-phosphate biosynthesis is linked to PIKfyve and is involved in osmotic response pathway in mammalian cells
Cytoplasmic retention, DNA binding and processing of the NF-kappa B p50 precursor are controlled by a small region in its C-terminus
Crystal structure of human recombinant ornithine aminotransferase.
Phagosomal maturation (early endosomal stage)
Krüppel-like transcription factor KLF5 is a key regulator of adipocyte differentiation
The ubiquitously expressed human CYP51 encodes lanosterol 14 alpha-demethylase, a cytochrome P450 whose expression is regulated by oxysterols
Molecular mechanisms of ligand binding, signaling, and regulation within the superfamily of G-protein-coupled receptors: molecular modeling and mutagenesis approaches to receptor structure and function
Inositol phosphate synthesis and the nuclear processes they affect
5'-phosphoribosylformylglycinamidine (FGAM) + ATP => 5'-phosphoribosyl-5-aminoimidazole (AIR) + ADP + orthophosphate
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'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR) + 10-formyltetrahydrofolate => 5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide (FAICAR) + tetrahydrofolate
5'-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide (SAICAR) <=> 5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR) + fumarate
5-phosphoribosylglycinamide (GAR) + 10-formyl-tetrahydrofolate => 5'-phosphoribosylformylglycinamide (FGAR) + tetrahydrofolate
adenylosuccinate => adenosine 5'-monophosphate + fumarate
Type II chaperonins, prefoldin, and the tubulin-specific chaperones
5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide (FAICAR) <=> inosine 5'-monophosphate + H2O
inosine 5'-monophosphate (IMP) + NAD+ + H2O => xanthosine 5'-monophosphate (XMP) + NADH + H+
IMP + H2O + NAD+ => XMP + NADH + H+ [IMPDH1,2]
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
inosine 5'-monophosphate + L-aspartate + GTP => adenylosuccinate + guanosine 5'-diphosphate + orthophosphate
IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]
ATM mediated phosphorylation of repair proteins
Biochemical properties of mammalian neutral sphingomyelinase 2 and its role in sphingolipid metabolism
A unique signal transduction from FLT tyrosine kinase, a receptor for vascular endothelial growth factor VEGF
A current view of the mammalian aquaglyceroporins
Diversity of the mammalian sodium/proton exchanger SLC9 gene family
Plasma concentrations of phenyllactic acid in phenylketonuria
Glucose transporters (GLUT and SGLT): expanded families of sugar transport proteins
Despite substantial degradation, 2-arachidonoylglycerol is a potent full efficacy agonist mediating CB(1) receptor-dependent G-protein activation in rat cerebellar membranes
Gefitinib-sensitizing EGFR mutations in lung cancer activate anti-apoptotic pathways
Effects of alterations in the 3' flanking sequence on in vivo and in vitro expression of the yeast SUP4-o tRNATyr gene.
A review of the pharmacokinetics of abacavir
Mechanisms and physiological significance of the cholinergic control of pancreatic beta-cell function
Human ADP-ribosylation factor-activated phosphatidylcholine-specific phospholipase D defines a new and highly conserved gene family
On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database
The emerging shape of the ESCRT machinery
Secretory protein trafficking and organelle dynamics in living cells
The role of mitochondria in cellular iron-sulfur protein biogenesis and iron metabolism
TRF1 inhibits telomere C-strand DNA synthesis in vitro
Trif-related adapter molecule is phosphorylated by PKC{epsilon} during Toll-like receptor 4 signaling
5-phosphoribosylamine + glycine + ATP => 5-phosphoribosylglycinamide (GAR) + ADP + orthophosphate
5-Phosphoribosylamine + Glycine + ATP => GAR + ADP + Pi
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
(R)-2-hydroxyglutarate + succinate semialdehyde <=> 2-oxoglutarate + 4-hydroxybutyrate
2-oxoglutarate + 4-hydroxybutyrate <=> (R)-2-hydroxyglutarate + succinate semialdehyde
(R)-2-hydroxyglutarate + FAD => 2-oxoglutarate + FADH2
Transfer of electrons from ETF to ubiquinone by ETF-QO
Human argininosuccinate lyase: a structural basis for intragenic complementation
Formation of phosphoribosyl pyrophosphate amidotransferase tetramer
Interferon-gamma can stimulate post-proteasomal trimming of the N terminus of an antigenic peptide by inducing leucine aminopeptidase
Transfer of electrons through the succinate dehydrogenase complex
Reducing equivalents from beta-oxidation of fatty acids transfer to ETF
1-hydroxy-5-(methylthio)-3-oxopent-1-en-2-olate (1-)
ChEBI:58795 1-hydroxy-5-(methylthio)-3-oxopent-1-en-2-olate (1-)
Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA (N6-adenosine)-methyltransferase.
Platelet activation, signaling and aggregation
The t(8;17)(p11;q23) in the 8p11 myeloproliferative syndrome fuses MYO18A to FGFR1
Transport of Extracellular Glucose to the Cytosol by GLUT1 and GLUT2
GCH1 reduces GTP to dihydroneopterin triphosphate
Activation of Protein kinase C, alpha type by Diacylglycerol
2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial (Coq5) catalyses the C-methyltransferase conversion of 2-hexaprenyl-6-methoxy-1,4-benzoquinol (MDMQ6H2) to 2-hexaprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQ6H2) (Barkovich et al. 1997).
DMQ6H2 is hydroxylated to DeMQ6H2 by Cat5
Catabolite repression protein Cat5 aka ubiquinone biosynthesis protein catalyses the hydroxylation of 2-hexaprenyl-3-methyl-6-methoxy-1,4-benzoquinol (DMQ6H2) to 3-demethylubiquinol-6 (DeMQ6H2) (Marbois & Clarke 1996, Tran et al. 2006).
MHHB is decarboxylated to HMPhOH by MHHB decarboxylase
3-hexaprenyl-4-hydroxy-5-methoxybenzoic acid aka 3-methoxy-4-hydroxy-5-hexaprenylbenzoic acid (MHHB) is enzymatically decarboxylated to form 2-hexaprenyl-6-methoxyphenol (HMPhOH) (Casey & Threlfall 1978, Goewert et al. 1981). At the present time the enzyme identity is unknown but is thought to be a member of the COQ family.
HMPhOH is hydroxylated to MDMQ6H2 by HMPhOH monooxygenase
2-hexaprenyl-6-methoxyphenol (HMPhOH) aka 2-methoxy-6-hexaprenylphenol is enzymatically converted to 2-hexaprenyl-6-methoxy-1,4-benzoquinol (MDMQ6H2) (Gin et al. 2003, Ozeir et al. 2011). It was thought at one time that the flavin-dependent monooxygenase, Coq6, was the enzyme that catalysed this reaction, however, it has been subsequently shown that Coq6 is not essential for this reaction (Ozeir et al. 2011). However, it is still believed that another member of the Coq family catalyses this event.
FUNCTION Central metabolic regulator required for the derepression of PCK1, and thereby gluconeogenesis. Necessary for transcriptional activation of the CAT8 gene. Also involved in the control of expression of other enzymes of gluconeogenesis and those of respiration and the glyoxylate cycle. Also involved in one or more monooxygenase steps of ubiquinone biosynthesis.PATHWAY Cofactor biosynthesis; ubiquinone biosynthesis.SIMILARITY Belongs to the COQ7 family.
ADP + Orthophosphate + Succinyl-CoA <=> ATP + Succinate + CoA
Succinate <=> Fumarate (with FAD redox reaction on enzyme)
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+
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+
Identification of arylsulfonamides as Aquaporin 4 inhibitors
Characterizing the specificity and cooperation of aminopeptidases in the cytosol and endoplasmic reticulum during MHC class I antigen presentation
gene ontology term for cellular function
Diseases caused by defects in the visual cycle: retinoids as potential therapeutic agents
Annu. Rev. Pharmacol. Toxicol. 47:469-512
Human Smp3p adds a fourth mannose to yeast and human glycosylphosphatidylinositol precursors in vivo
Primary structure and tissue-specific expression of human beta-hydroxyisobutyryl-coenzyme A hydrolase.
Human acetyl-CoA carboxylase 2. Molecular cloning, characterization, chromosomal mapping, and evidence for two isoforms.