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Trans-synaptic transmission of vesicular Wnt signals through Evi/Wntless
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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-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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(5Z)-(15S)-11alpha-Hydroxy-9,15-dioxoprostanoate [ChEBI:244]
Cloning and molecular analysis of the human citrate synthase gene
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(15S)-15-Hydroxy-5,8,11-cis-13-trans-eicosatetraenoate [ChEBI:147]
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abacavir 5'-carboxylic acid [ChEBI:64192]
Isolation, sequencing, and expression of a cDNA for the HXM-A form of xenobiotic/medium-chain fatty acid:CoA ligase from human liver mitochondria
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6-methoxy-3-methyl-2-decaprenyl-1,4-benzoquinol [ChEBI:64181]
2-methoxy-6-decaprenyl-1,4-benzoquinol [ChEBI:64180]
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The yeast mitochondrial carrier Leu5p and its human homologue Graves' disease protein are required for accumulation of coenzyme A in the matrix
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Novel molecular defects of the delta-aminolevulinate dehydratase gene in a patient with inherited acute hepatic porphyria
Hemostasis and Thrombosis: Basic Principles and Clinical Practice
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Platelets in thrombotic and non-thrombotic disorders.
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'Ac-CoA [mitochondrial matrix]' positively regulates 'Pyruvate + CO2 + ATP => ADP + Orthophosphate + Oxaloacetate'
'IMP [cytosol]' positively regulates 'Formation of phosphoribosyl pyrophosphate amidotransferase tetramer'
'Ac-CoA [cytosol]' negatively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'PRPP [cytosol]' positively regulates 'Dissociation of phosphoribosyl pyrophosphate amidotransferase tetramer'
'Formation of phosphoribosyl pyrophosphate amidotransferase tetramer' negatively regulates '5-phospho-alpha-D-ribose 1-diphosphate (PRPP) + H2O + L-glutamine <=> 5-phosphoribosylamine + L-glutamate +pyrophosphate'
'AMP [cytosol]' positively regulates 'Formation of phosphoribosyl pyrophosphate amidotransferase tetramer'
'GMP [cytosol]' positively regulates 'Formation of phosphoribosyl pyrophosphate amidotransferase tetramer'
'GDP [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
'Dissociation of phosphoribosyl pyrophosphate amidotransferase tetramer' positively regulates '5-phospho-alpha-D-ribose 1-diphosphate (PRPP) + H2O + L-glutamine <=> 5-phosphoribosylamine + L-glutamate +pyrophosphate'
'XMP [cytosol]' negatively regulates 'IMP + H2O + NAD+ => XMP + NADH + H+ [IMPDH1,2]'
Astrocytic Glutamate-Glutamine Uptake And Metabolism
Pyrimidine nucleotide biosynthesis in animals: genes, enzymes, and regulation of UMP biosynthesis.
A three-dimensional working model of the multienzyme complex of aminoacyl-tRNA synthetases based on electron microscopic placements of tRNA and proteins
Chapter 3 Activation of TRP Channels in Mammalian Systems
2-Deoxy-D-ribose 1-phosphate [ChEBI:28542]
Purification and characterization of a new alcohol dehydrogenase from human stomach.
Subcellular localization and regulation of coenzyme A synthase
Comparison of messenger RNA distribution for 60 proteins in fat cells vs the nonfat cells of human omental adipose tissue
Targeting purine and pyrimidine metabolism in human apicomplexan parasites
'Mg2+ [cytosol]' is required for 'ITPA hydrolyses dITP to dIMP'
'Mg2+ [cytosol]' is required for 'ITPA hydrolyses XTP to XMP'
'Mg2+ [cytosol]' is required for 'A phosphoribosyl group is added to nicotinate to form nicotinate mononucleotide (NaMN)'
'NAcGlu [mitochondrial matrix]' positively regulates '2 ATP + NH4+ + HCO3- => 2 ADP + orthophosphate + carbamoyl phosphate [mitochondrial]'
'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]'
'ADS [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
'Mg2+ [cytosol]' is required for 'ITPA hydrolyses ITP to IMP'
'Pb2+ [mitochondrial matrix]' negatively regulates 'FECH binds Fe2+ to PRIN9 to form heme'
The high-resolution structure of the NADP(H)-binding component (dIII) of proton-translocating transhydrogenase from human heart mitochondria
Biochemistry of mammalian peroxisomes revisited
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Negative regulation of dE2F1 by cyclin-dependent kinases controls cell cycle timing
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The renal plumbing system: aquaporin water channels
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The Drosophila tweety family: molecular candidates for large-conductance Ca2+-activated Cl- channels
D-Fructose 2,6-bisphosphate [ChEBI:28602]
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Human aquaporin adipose (AQPap) gene. Genomic structure, promoter analysis and functional mutation
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Prog Nucleic Acid Res Mol Biol 42:259-287
Human Na+ -coupled citrate transporter: primary structure, genomic organization, and transport function
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XBP1 induces WFS1 through an endoplasmic reticulum stress response element-like motif in SH-SY5Y cells
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Phosphorylation of uridine and cytidine nucleoside analogs by two human uridine-cytidine kinases
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Cloning and expression of a human neutral amino acid transporter with structural similarity to the glutamate transporter gene family
Characterization and tRNA recognition of mammalian mitochondrial seryl-tRNA synthetase
'Pi [cytosol]' is required for 'ribose phosphate diphosphokinase activity of phosphoribosyl pyrophosphate synthetase 1 holoenzyme (name copied from entity in Homo sapiens) [intracellular]'
'Mg2+ [cytosol]' is required for 'ribose phosphate diphosphokinase activity of phosphoribosyl pyrophosphate synthetase 1 holoenzyme (name copied from entity in Homo sapiens) [intracellular]'
'NAcGlu [mitochondrial matrix]' positively regulates 'carbamoyl-phosphate synthase (ammonia) activity of Homologues of CPS1 [intracellular]'
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Human HRD1 promoter carries a functional unfolded protein response element to which XBP1 but not ATF6 directly binds
Separate nuclear genes encode sarcomere-specific and ubiquitous human mitochondrial creatine kinase isoenzymes
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Molecular cloning of a human cDNA encoding a trifunctional enzyme of carbamoyl-phosphate synthetase-aspartate transcarbamoylase-dihydroorotase in de Novo pyrimidine synthesis
Isolation and characterization of the gene and cDNA encoding human mitochondrial creatine kinase
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New regulatory mechanisms of TGF-beta receptor function
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Localization and trafficking of aquaporin 2 in the kidney
Aquaporins in the hepatobiliary tract. Which, where and what they do in health and disease
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A new gene, encoding an anion transporter, is mutated in sialic acid storage diseases
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The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans
Cdk2-dependent and -independent pathways in E2F-mediated S phase induction
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Limiting role of 6-phosphogluconolactonase in erythrocyte hexose monophosphate pathway metabolism
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Structural relationships and the classification of aminoacyl-tRNA synthetases
Active and inhibited human catalase structures: ligand and NADPH binding and catalytic mechanism.
(5Z,8Z,10E,14Z)-(12S)-12-Hydroperoxyeicosa-5,8,10,14-tetraenoate [ChEBI:250]
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Identification of a vesicular glutamate transporter that defines a glutamatergic phenotype in neurons
Desaturation and chain elongation of n - 3 and n - 6 polyunsaturated fatty acids in the human CaCo-2 cell line
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5-Hydroperoxy-6-trans-8,11,14-cis-eicosatetraenoate [ChEBI:2061]
Wnt family proteins are secreted and associated with the cell surface
Excitatory amino acid transporter 5, a retinal glutamate transporter coupled to a chloride conductance
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Identification, purification, and partial characterization of a novel Mr 28,000 integral membrane protein from erythrocytes and renal tubules
How synaptotagmin promotes membrane fusion
Integrating signals from RTKs to ERK/MAPK
xanthosine 5'-monophosphate [ChEBI:15652]
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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Octameric structure of the human bifunctional enzyme PAICS in purine biosynthesis
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Point mutations in the aromatic/arginine region in aquaporin 1 allow passage of urea, glycerol, ammonia, and protons
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Distribution of aquaporin water channels AQP1 and AQP5 in the ductal system of the human pancreas
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(S)-3-Hydroxy-3-methylglutaryl-CoA [ChEBI:15467]
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Biochemical genetics of the pentose phosphate cycle: human ribose 5-phosphate isomerase (RPI) and ribulose 5-phosphate 3-epimerase (RPE)
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The way Wnt works: Components and mechanism
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Phosphorylation of acyclovir (acycloguanosine) monophosphate by GMP kinase
Isolation and characterization of a full-length expressible cDNA for human hypoxanthine phosphoribosyl transferase
Pentose phosphate pathway (hexose monophosphate shunt)
Lipid digestion, mobilization, and transport
Synthesis and recycling of tetrahydrobiopterin in endothelial function and vascular disease
Aquaporins in complex tissues. II. Subcellular distribution in respiratory and glandular tissues of rat
Identification and characterization of a putative human iodide transporter located at the apical membrane of thyrocytes
Expression, characterization, and tissue distribution of a new cellular selenium-dependent glutathione peroxidase, GSHPx-GI
Aquaporins in complex tissues. I. Developmental patterns in respiratory and glandular tissues of rat
2'-deoxyadenosine 5'-monophosphate [ChEBI:17713]
The functional human dihydrofolate reductase gene
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Aquaporin expression in normal human kidney and in renal disease
Role of glutathione peroxidase and hexose monophosphate shunt in the platelet lipoxygenase pathway
phosphofructokinase, P2L2 complex (name copied from entity in Homo sapiens)
Note: the coordinates are copied over from Homo sapiens.
phosphofructokinase, P3L complex (name copied from entity in Homo sapiens)
triosephosphate isomerase dimer (name copied from entity in Homo sapiens)
phosphofructokinase, PL3 complex (name copied from entity in Homo sapiens)
enolase 1 dimer, (alpha) (name copied from entity in Homo sapiens)
Thymidine phosphorylase precursor (EC 2.4.2.4) (TdRPase) (TP) (Platelet-derived endothelial cell growth factor) (PD-ECGF) (Gliostatin)
endothelial cell growth factor 1 (platelet-derived)
Platelet-derived endothelial cell growth factor
phosphoglycerate kinase 1 complex (name copied from entity in Homo sapiens)
pyruvate kinase M1 complex (name copied from entity in Homo sapiens)
Thymidine kinase, cytosolic (EC 2.7.1.21)
pyruvate carboxylase holoenzyme (name copied from entity in Homo sapiens)
Dihydroorotate dehydrogenase, mitochondrial precursor
Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdehase) (Fragment)
pyruvate kinase complex, liver and RBC (name copied from entity in Homo sapiens)
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))
In vivo disposal of phenylalanine in phenylketonuria: a study of two siblings
Characterization of the human gene encoding alpha-aminoadipate aminotransferase (AADAT).
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
HSD11B1 dimer (name copied from entity in Homo sapiens)
MVD dimer (name copied from entity in Homo sapiens)
ACHE dimer (name copied from entity in Homo sapiens)
PCYT2 dimer (name copied from entity in Homo sapiens)
MVK dimer (name copied from entity in Homo sapiens)
CEL:bile salt complex (name copied from entity in Homo sapiens)
Glutamine phosphoribosylpyrophosphate amidotransferase
Amidophosphoribosyltransferase precursor (EC 2.4.2.14) (Glutamine phosphoribosylpyrophosphate amidotransferase) (ATASE) (GPAT)
Amidophosphoribosyltransferase precursor
phosphoribosyl pyrophosphate 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
Phosphoribosylaminoimidazole carboxylase
Phosphoribosylaminoimidazole- succinocarboxamide synthase
phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthase
ACHE tetramer (name copied from entity in Homo sapiens)
PCYT1B dimer (name copied from entity in Homo sapiens)
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
PCYT1A dimer (name copied from entity in Homo sapiens)
Substrate specificity and phosphorylation of antiviral and anticancer nucleoside analogues by human deoxyribonucleoside kinases and ribonucleoside kinases
G6PD tetramer (name copied from entity in Homo sapiens)
G6PD dimer (name copied from entity in Homo sapiens)
GALE dimer (name copied from entity in Homo sapiens)
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
phosphoPFKFB1 dimer (name copied from entity in Homo sapiens)
Human arginase II: crystal structure and physiological role in male and female sexual arousal
AMP deaminase 3 (EC 3.5.4.6) (AMP deaminase isoform E) (Erythrocyte AMP deaminase)
Adenylosuccinate synthetase (EC 6.3.4.4) (IMP--aspartate ligase) (AdSS) (AMPSase)
dimerized CEL:bile salt complex (name copied from entity in Homo sapiens)
phosphoribosyl pyrophosphate synthetase holoenzyme
phosphoribosyl pyrophosphate synthetase 1 holoenzyme (name copied from entity in Homo sapiens)
RPE dimer (name copied from entity in Homo sapiens)
Hypoxanthine-guanine phosphoribosyltransferase
PGD dimer (name copied from entity in Homo sapiens)
Glycosylation and palmitoylation of Wnt-3a are coupled to produce an active form of Wnt-3a
The known unknowns of antigen processing and presentation
Peroxisome proliferator activated receptors and lipoprotein metabolism
2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial ecNumber2.1.1.201/ecNumber
Decaprenyl-diphosphate synthase subunit 1 ecNumber2.5.1.91/ecNumber
Decaprenyl-diphosphate synthase subunit 2 ecNumber2.5.1.91/ecNumber
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nicotinamide nucleotide transhydrogenase
Citrate synthase, mitochondrial precursor
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2-oxoglutarate dehydrogenase E1 component, mitochondrial precursor
alpha-ketoglutarate dehydrogenase E1 apoenzyme
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Dihydrolipoamide dehydrogenase, mitochondrial
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Human aldehyde dehydrogenase. Purification and characterization of a third isozyme with low Km for gamma-aminobutyraldehyde.
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Single eubacterial origin of eukaryotic sulfide:quinone oxidoreductase, a mitochondrial enzyme conserved from the early evolution of eukaryotes during anoxic and sulfidic times
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Constitutive and inducible expression and regulation of vascular endothelial growth factor
Ethanolamine-phosphate cytidylyltransferase
Corticosteroid 11-beta-dehydrogenase, isozyme 1
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Choline-phosphate cytidylyltransferase A
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Choline-phosphate cytidylyltransferase B
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Enzymatic, metabolic and secretory patterns in human islets of type 2 (non-insulin-dependent) diabetic patients
Studies on the subunit structure and molecular size of the human alcohol dehydrogenase isozymes determined by the different loci, ADH1, ADH2, and ADH3.
Mitochondrial localization of human PANK2 and hypotheses of secondary iron accumulation in pantothenate kinase-associated neurodegeneration
Purification, cDNA cloning and expression of 15-oxoprostaglandin 13-reductase from pig lung
Homologues of L-selenocysteine residue-GPX1
Phospholipid hydroperoxide glutathione peroxidase, mitochondrial
Interconversion of 2-oxoglutarate and 2-hydroxyglutarate
Regulation of Geminin and Cdt1 expression by E2F transcription factors
Expression, purification, and kinetic characterization of recombinant human adenylosuccinate lyase
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Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation
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Molecular mechanisms involved in the regulation of the endothelial nitric oxide synthase
Am J Physiol Regul Integr Comp Physiol 284:R1-12
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phosphoribosyl pyrophosphate synthetase 1
Phosphoribosyl pyrophosphate synthetase I
Ribose-phosphate pyrophosphokinase I (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase I) (PPRibP) (PRS-I)
Hydroxymethylglutaryl-CoA synthase, mitochondrial precursor
3-hydroxy-3-methylglutaryl coenzyme A synthase
Familial hyperlysinemias. Purification and characterization of the bifunctional aminoadipic semialdehyde synthase with lysine-ketoglutarate reductase and saccharopine dehydrogenase activities.
6-phosphogluconate dehydrogenase, decarboxylating
Biology, structure and mechanism of P-type ATPases
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Pyruvate carboxylase, mitochondrial precursor
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 4
6PF-2-K/Fru- 2,6-P2ASE testis-type isozyme
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Molecular characterization of human acetyl-CoA synthetase, an enzyme regulated by sterol regulatory element-binding proteins.
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Molecular cloning, cDNA sequence, and bacterial expression of human glutamine:fructose-6-phosphate amidotransferase
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Insulin signalling and the regulation of glucose and lipid metabolism
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Immunolocalization of the mercurial-insensitive water channel and glycerol intrinsic protein in epithelial cell plasma membranes
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Enzyme hyperspecificity. Rejection of threonine by the valyl-tRNA synthetase by misacylation and hydrolytic editing
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Nucleotide binding to nucleoside diphosphate kinases: X-ray structure of human NDPK-A in complex with ADP and comparison to protein kinases
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The canonical Notch signaling pathway: unfolding the activation mechanism
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Crystal structures of human glutaryl-CoA dehydrogenase with and without an alternate substrate: structural bases of dehydrogenation and decarboxylation reactions
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ER-mediated phagocytosis: a new membrane for new functions
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Kinetic analysis of peptide binding to the TAP transport complex: evidence for structural rearrangements induced by substrate binding
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Primary structure of human triosephosphate isomerase
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Characterization of the human mitochondrial methionyl-tRNA synthetase
Purification and properties of uroporphyrinogen I synthase from human erythrocytes. Identification of stable enzyme-substrate intermediates.
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Structure, function and regulation of pyruvate carboxylase
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Mechanism of porphobilinogen synthase. Requirement of Zn2+ for enzyme activity.
Phase 1 - Functionalization of compounds
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Molecular mechanisms and clinical pathophysiology of maturity-onset diabetes of the young
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Phagosomes are competent organelles for antigen cross-presentation
Lead-induced abnormalities of porphyrin metabolism. The relationship with iron deficiency.
ER-phagosome fusion defines an MHC class I cross-presentation compartment in dendritic cells
(5Z,13E)-11alpha-Hydroxy-9,15-dioxoprost-13-enoate [ChEBI:247]
Methylation pharmacogenetics: catechol O-methyltransferase, thiopurine methyltransferase, and histamine N-methyltransferase
alpha-D-Glucose 6-phosphate [ChEBI:17665]
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Amplification and kinetics of the activation steps in phototransduction
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An integrated genomic analysis of human glioblastoma multiforme
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Human and murine glycerol kinase: influence of exon 18 alternative splicing on function
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Reversible compartmentalization of de novo purine biosynthetic complexes in living cells
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Molecular mechanisms of MHC class I-antigen processing: redox considerations
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Isolation and characterization of the human pyruvate kinase M gene
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An overview of sphingolipid metabolism: from synthesis to breakdown
Stimulation of the human CTP:phosphoethanolamine cytidylyltransferase gene by early growth response protein 1
Distinct flippases translocate glycerophospholipids and oligosaccharide diphosphate dolichols across the endoplasmic reticulum
Molecular identification and characterization of two medium-chain acyl-CoA synthetases, MACS1 and the Sa gene product
Bone morphogenetic protein receptors and signal transduction
The retinoid cycle in cones (daylight vision)
Peroxisome proliferator-activated receptor alpha target genes
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Organic anion transport is the primary function of the SLC17/type I phosphate transporter family
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The human sugar-phosphate/phosphate exchanger family SLC37
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Novel variants in human Aquaporin-4 reduce cellular water permeability
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The porphobilinogen synthase catalyzed reaction mechanism
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Identification and expression of a cDNA encoding human alpha-amino-beta-carboxymuconate-epsilon-semialdehyde decarboxylase (ACMSD). A key enzyme for the tryptophan-niacine pathway and "quinolinate hypothesis".
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Water channel expression in human ADPKD kidneys
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Biotin uptake by human intestinal and liver epithelial cells: role of the SMVT system
Am. J. Physiol. Gastrointest. Liver Physiol. 285:G73-7
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Human cytidine deaminase: purification of enzyme, cloning, and expression of its complementary DNA
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Retinoids for treatment of retinal diseases
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Crystal structure of alanine:glyoxylate aminotransferase and the relationship between genotype and enzymatic phenotype in primary hyperoxaluria type 1
A general map of iron metabolism and tissue-specific subnetworks
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Na+-dependent purine nucleoside transporter from human kidney: cloning and functional characterization
Am J Physiol Renal Physiol 273:1058-1065
Human liver alcohol dehydrogenase: purification and kinetic characterization of the beta 2 beta 2, beta 2 beta 1, alpha beta 2, and beta 2 gamma 1 "Oriental" isoenzymes.
Acid-sensing ion channels (ASICs): pharmacology and implication in pain
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Antigen processing and presentation: TAPping into ABC transporters
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Isolation and characterization of argininosuccinate synthetase from human liver.
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D-Glucono-1,5-lactone 6-phosphate [ChEBI:16938]
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Leber congenital amaurosis: genes, proteins and disease mechanisms
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Purification and properties of phosphoribosyl pyrophosphate synthetase from rat liver
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Inborn errors of ketogenesis and ketone body utilization
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Depalmitoylation of endothelial nitric-oxide synthase by acyl-protein thioesterase 1 is potentiated by Ca(2+)-calmodulin
Molecular organization of the presynaptic active zone
The biochemistry and physiology of nucleotides
Ribose-5-phosphate isomerase deficiency: new inborn error in the pentose phosphate pathway associated with a slowly progressive leukoencephalopathy
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XBP-1 regulates a subset of endoplasmic reticulum resident chaperone genes in the unfolded protein response
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WNT secretion and signalling in human disease
Enzymes of the human erythrocyte. IV. Phosphoglucose isomerase, purification and properties.
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Enzymatic properties of the protein encoded by newly cloned human alcohol dehydrogenase ADH6 gene
SLC11 family of H+-coupled metal-ion transporters NRAMP1 and DMT1
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Human cationic amino acid transporter hCAT-3 is preferentially expressed in peripheral tissues
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Molecular machinations of the MHC-I peptide loading complex
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Purification and functional characterization of aquaporin-8
Two forms of Wilson disease protein produced by alternative splicing are localized in distinct cellular compartments
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Crystal structure of human thymidine phosphorylase in complex with a small molecule inhibitor
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Control of muscle ryanodine receptor calcium release channels by proteins in the sarcoplasmic reticulum lumen
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Purification and partial characterization of aldehyde dehydrogenase from human erythrocytes.
The unfolded protein response: a pathway that links insulin demand with beta-cell failure and diabetes
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Porcupine-mediated lipidation is required for Wnt recognition by Wls
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Regulation of human thymidine kinase during the cell cycle
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Transport of vitamins, nucleosides, and related molecules
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D-Fructose 1,6-bisphosphate [ChEBI:16905]
Double-strand DNA containing a 3-methyladenine
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Active Wnt proteins are secreted on exosomes
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Holocarboxylase synthetase: correlation of protein localisation with biological function
The Wilson disease gene is a putative copper transporting P-type ATPase similar to the Menkes gene
Human carbamylphosphate synthetase I. Stabilization, purification, and partial characterization of the enzyme from human liver.
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Bestrophin and TMEM16-Ca(2+) activated Cl(-) channels with different functions
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Alcohol dehydrogenases, aldehyde dehydrogenases, and related enzymes
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Purification and properties of human cytosolic folylpoly-gamma-glutamate synthetase and organization, localization, and differential splicing of its gene
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Isolation and characterization of human nuclear and cytosolic multisynthetase complexes and the intracellular distribution of p43/EMAPII
Rational design of a drug for Alzheimer's disease with cholinesterase inhibitory and neuroprotective activity
Synthesis and interconversion of nucleotide di- and triphosphates
(5Z,8Z,10E,14Z)-(12R)-12-Hydroperoxyeicosa-5,8,10,14-tetraenoic acid
(5Z,8Z,10E,14Z)-(12R)-12-Hydroperoxyicosa-5,8,10,14-tetraenoic acid
12(S)-hydroxy-5,8,14(Z),10(E)-eicosatetraenoic acid
(5Z,8Z,10E,14Z)-(12S)-12-Hydroxyicosa-5,8,10,14-tetraenoic acid
12(S)-hydroxy-5(Z),8(Z),10(E),14(Z)-eicosatetraenoic acid
(5Z,8Z,10E,14Z)-(12S)-12-Hydroxyeicosa-5,8,10,14-tetraenoic acid
(5Z,8Z,10E,12S,14Z)-12-hydroxyeicosa-5,8,10,14-tetraenoic acid
(12S)-12-hydroxy-5,8,14-cis-10-trans-eicosatetraenoic acid
(5Z,8Z,10E,12R,14Z)-12-hydroxy-5,8,10,14-eicosatetraenoic acid
12(R)-hydroxy-5(Z),8(Z),10(E),14(Z)-eicosatetraenoic acid
12(R)-hydroxy-5,8,14-cis-10-trans-eicosatetraenoic acid
(5Z,8Z,10E,14Z)-(12R)-12-Hydroxyeicosa-5,8,10,14-tetraenoic acid
(5Z,8Z,10E,14Z)-(12R)-12-Hydroxyicosa-5,8,10,14-tetraenoic acid
(5Z,8Z,10E,12R,14Z)-12-hydroxyeicosa-5,8,10,14-tetraenoic acid
Kinetic characterization of human hydroxyacid-oxoacid transhydrogenase: relevance to D-2-hydroxyglutaric and gamma-hydroxybutyric acidurias
Identification of covalently bound amino-terminal myristic acid in endothelial nitric oxide synthase
The formation of citric and alpha-ketoglutaric acids in the mammalian body
Regulation of the cyclin E gene by transcription factor E2F1
Bile salt and organic anion SLC transporters
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Ubiquinone. Biosynthesis of quinone ring and its isoprenoid side chain. Intracellular localization
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Heterotrimeric G protein activation by G-protein-coupled receptors
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The content of pentose-cycle intermediates in liver in starved, fed ad libitum and meal-fed rats.
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Concerted action of two cation filters in the aquaporin water channel
Adenylate kinases in man: evidence for a third locus
Cloning, expression and chromosomal localization of a human testis 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase gene
5'-Phosphoribosyl-5-amino-4-imidazolecarboxylate [ChEBI:28413]
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Purification and properties of an NADPH-dependent carbonyl reductase from human brain. Relationship to prostaglandin 9-ketoreductase and xenobiotic ketone reductase
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Expression of the AQP-1 water channel in normal human tissues: a semiquantitative study using tissue microarray technology
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Cloning and identification of a new member of water channel (AQP10) as an aquaglyceroporin
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Identification and expression of a cDNA for human hydroxypyruvate/glyoxylate reductase
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4-Imidazolone-5-propanoate [ChEBI:27384]
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Enzymic properties of different types of human erythrocyte glucose-6-phosphate dehydrogenase, with characterization of two new genetic variants
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Protein phosphatase 2Cepsilon is an endoplasmic reticulum integral membrane protein that dephosphorylates the ceramide transport protein CERT to enhance its association with organelle membranes
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Molecular cloning of human amidophosphoribosyltransferase
15-Keto-prostaglandin F2alpha [ChEBI:760]
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The copper transporter (Ctr) family of Cu+ uptake systems
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Porcupine homolog is required for canonical Wnt signaling and gastrulation in mouse embryos
(S)-alpha-amino-beta-(3-indolyl)-propionic acid
Congenital Disorders of Glycosylation Overview
The human renal sodium sulfate cotransporter (SLC13A1; hNaSi-1) cDNA and gene: organization, chromosomal localization, and functional characterization
beta-catenin destruction complex: insights and questions from a structural perspective
Enzymatic inactivation of leukotriene B4 by a novel enzyme found in the porcine kidney. Purification and properties of leukotriene B4 12-hydroxydehydrogenase
eNOS, COX-2, and prostacyclin production are impaired in endothelial cells from diabetics
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The human arginases and arginase deficiency
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1
Speed, sensitivity, and stability of the light response in rod and cone photoreceptors: facts and models
Human GMP synthetase. Protein purification, cloning, and functional expression of cDNA
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6PF-2-K/Fru- 2,6-P2ASE brain/placenta-type isozyme
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3
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6PF-2-K/Fru- 2,6-P2ASE heart-type isozyme
6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 2
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A role for the endoplasmic reticulum protein retrotranslocation machinery during crosspresentation by dendritic cells
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Magnesium transporters: properties, regulation and structure
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GlycoVis: visualizing glycan distribution in the protein N-glycosylation pathway in mammalian cells
Pyruvate metabolism and Citric Acid (TCA) cycle
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Docosahexaenoic acid synthesis in human skin fibroblasts involves peroxisomal retroconversion of tetracosahexaenoic acid
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Tuberculosis: what we don't know can, and does, hurt us
Regulation and dysregulation of aquaporins in water balance disorders
Cloning, characterization, and chromosomal mapping of human aquaporin of collecting duct
Nicotinate phosphoribosyltransferase of human erythrocytes. Purification and properties.
Functional expansion of aminoacyl-tRNA synthetases and their interacting factors: new perspectives on housekeepers
Cloning, characterization, and expression of cDNAs encoding human delta 1-pyrroline-5-carboxylate dehydrogenase
(S)-2-Amino-3-(p-hydroxyphenyl)propionic acid
Molecular cloning and functional characterization of human vesicular glutamate transporter 3
A novel pantothenate kinase gene (PANK2) is defective in Hallervorden-Spatz syndrome
Superoxide production and electron transport in mitochondrial oxidation of dihydroorotic acid.
Nicotinate D-ribonucleotide [ChEBI:7561]
(R)-4'-Phosphopantothenoyl-L-cysteine [ChEBI:328]
D-2-Hydroxyglutaric aciduria: unravelling the biochemical pathway and the genetic defect
The role of aminoacyl-tRNA synthetases in genetic diseases
Vesicle pools, docking, priming, and release
Cloning of a water channel homolog expressed in brain meningeal cells and kidney collecting duct that functions as a stilbene-sensitive glycerol transporter
Oligomeric structure of the multifunctional protein CAD that initiates pyrimidine biosynthesis in mammalian cells
Platelet-derived endothelial cell growth factor has thymidine phosphorylase activity.
2-Aminomuconate semialdehyde [ChEBI:15745]
Mutation of the fumarase gene in two siblings with progressive encephalopathy and fumarase deficiency
Functional properties of a Drosophila homolog of the E2F1 gene
taurolithocholic acid sulfate [ChEBI:17864]
Site-directed mutagenesis of recombinant human arylamine N-acetyltransferase expressed in Escherichia coli. Evidence for direct involvement of Cys68 in the catalytic mechanism of polymorphic human NAT2.
A complexin/synaptotagmin 1 switch controls fast synaptic vesicle exocytosis
(S)-Hydroperoxy-6-trans-8,11,14-cis-eicosatetraenoic acid
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Human arylamine N-acetyltransferase genes: isolation, chromosomal localization, and functional expression
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Mutations in the urocanase gene UROC1 are associated with urocanic aciduria
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Mechanistic studies on phosphopantothenoylcysteine decarboxylase: trapping of an enethiolate intermediate with a mechanism-based inactivating agent
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Developmental control of a G1-S transcriptional program in Drosophila
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Molecular mechanisms of conduction and selectivity in aquaporin water channels
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The cDNA and protein sequences of human lactate dehydrogenase B
Endonuclease III-like protein 1 (EC 4.2.99.18)
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)
DNA-3-methyladenine glycosylase (EC 3.2.2.21) (3-methyladenine DNA glycosidase) (ADPG) (3-alkyladenine DNA glycosylase) (N-methylpurine- DNA glycosirase)
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UDP-N-acetylhexosamine pyrophosphorylase
Ribonucleoside-diphosphate reductase M2 chain
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High-resolution x-ray structure of human aquaporin 5
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Biochemical characterization of human GMP synthetase
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Gephyrin, which stabilizes receptors on neuronal membranes, also catalyzes the transfer of a molybdenum ion onto the cofactor. The mechanism was elucidated in plants but, as the pathway is highly conserved, human gephyrin can complement missing plant proteins. Doubts remain about the actual molybdenum donor, probably molybdate, and whether a copper ion is possibly bound and removed (Stallmeyer et al, 1999).
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).
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GTP cyclizes in a reaction involving radicals of S-adenosylmethionine, catalyzed by the iron-sulfur cluster dimeric MOCS1. The intermediate result is called precursor Z (Hanzelmann et al, 2002; Hanzelmann et al, 2004).
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After the MOCS2A dimer is loaded with two sulfur atoms, their sequential deposition on the precursor Z molecule, with ring cleavage, is catalyzed by the MOCS2B half of the MOCS2 tetramer (Leimkuhler et al, 2003; Wuebbens & Rajagopalan, 2002).
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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).
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Mitochondrial ornithine aminotransferase (OAT) catalyzes the reversible reaction of glutamate semialdehyde and glutamate to form ornithine and alpha-ketoglutarate (Ohura et al. 1982). The active enzyme is a hexamer (Shen et al. 1998). Inherited OAT deficiency leads to ornithine accumulation in vivo and gyrate atrophy of the choroid and retina (Brody et al. 1992; Vallee and Simell 2001).
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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.
Cellular regulation of endothelial nitric oxide synthase
Serine biosynthesis starts from 3-phosphoglycerate, a glycolysis intermediate. Its dehydrogenation is catalysed by tetrameric phosphoglycerate dehydrogenase PHGDH. (Tabatabaie et al. 2009).
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).
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These reactions mediate the synthesis of aspartate, asparagine, glutamate, and glutamine from ammonia and intermediates of glycolysis, and allow the utilization of the carbon atoms from these four amino acids for glucose synthesis under fasting conditions. These reactions also provide a means to collect nitrogen, both as ammonia and as amino groups, and direct it towards urea synthesis. Transamination, the conversion of an amino acid to the corresponding alpha-keto acid coupled to the conversion of a molecule of alpha-ketoglutarate to glutamate, is the first step in the catabolism of most amino acids. Transamination reactions are freely reversible so they also provide a means to balance concentrations of various amino acids and alpha-keto (2-oxo) acids in the cytosol.
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Cancer-associated IDH1 mutations produce 2-hydroxyglutarate
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AADAT dimer localized in the mitochondrial matrix catalyzes the reaction of kynurenine and 2-oxoglutarate to form 4-(2-aminophenyl)-2,4-dioxobutanoate and glutamate (Han et al. 2008). Biochemical studies of kynurenine transamination in vitro invariably measure kynurenic acid, not 4-(2-aminophenyl)-2,4-dioxobutanoate, the expected transamination product. As noted by Miller et al. (1953), "The keto acid assumed to be formed prior to ring closure in the conversion of kynurenine to kynurenic acid has not yet been detected. In principle, such detection should be possible, since it is sufficiently stable to have been synthesized. It also remains to be established whether ring closure is spontaneous, enzymatic, or both. The formation of kynurenic acid from L-kynurenine by the L-amino acid oxidase of Neurospora suggests, however, that ring closure can be spontaneous, unless the somewhat improbable assumption is made that Neurospora filtrate contained the ring-closing enzyme."
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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).
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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).
At the beginning of this reaction, 1 molecule of '2-Amino-3-carboxymuconate semialdehyde' is present. At the end of this reaction, 1 molecule of 'CO2', and 1 molecule of '2-Aminomuconate semialdehyde' are present. This reaction takes place in the 'cytoplasm' and is mediated by the 'carboxy-lyase activity' of '2-amino-3-carboxymuconate-6-semialdehyde decarboxylase homodimer'.
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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.
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Mitochondrial delta-1-pyrroline-5-carboxylate dehydrogenase (ALDH4A1) catalyzes the reaction of L-glutamate gamma-semialdehyde and NAD+ to form glutamate and NADH + H+ (Hu et al. 1996). The enzyme is a dimer (Forte-McRobbie and Pietruszko 1986). ALDH4A1 mutations cause type II hyperprolinemia in vivo (Geraghty et al. 1998).
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Cytosolic tyrosine aminotransferase (TAT) catalyzes the reversible reaction of tyrosine and alpha-keto (2-oxo) glutarate to form 3-(4-hydroxyphenyl)pyruvate and glutamate (Mitchell et al. 2001). The enzymatic activity of the protein encoded by the cloned human TAT cDNA is inferred from the biochemical properties of its rat homologue. Unpublished crystallographic studies (PDB 3DYD) have shown TAT to be a homodimer with a pyridoxal phosphate moity attached to lysine-280 in each monomer.
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Cytosolic tyrosine aminotransferase (TAT) catalyzes the reversible reaction of 3-(4-hydroxyphenyl)pyruvate and glutamate to form tyrosine and alpha-keto (2-oxo) glutarate (Mitchell et al. 2001). The enzymatic activity of the protein encoded by the cloned human TAT cDNA is inferred from the biochemical properties of its rat homologue. Unpublished crystallographic studies (PDB 3DYD) have shown TAT to be a homodimer with a pyridoxal phosphate moity attached to lysine-280 in each monomer.
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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'.
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Human glutamine phosphoribosylpyrophosphate amidotransferase. Two molecular forms interconvertible by purine ribonucleotides and phosphoribosylpyrophosphate
Cytosolic imidazolonepropionase catalyzes the hydrolysis of 4-imidazolone-5-propanoate to form N-Formimino-L-glutamate. While evidence from many experimental systems indicates that this reaction occurs, existence of the human enzyme is inferred only from high-throughput screening studies (e.g., Yamada et al. 2004).
Molecular analysis of a series of alleles in humans with reduced activity at the triosephosphate isomerase locus
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The major pathway of histidine catabolism, annotated here, proceeds in four steps to yield glutamate and, in the process, convert one molecule of tetrahydrofolate to 5-formiminotetrahydrofolate (Morris et al. 1972). Histidine can also be decarboxylated to form histamine.
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Kynurenine/alpha-aminoadipate aminotransferase (AADAT) catalyzes the reversible reaction of alpha-aminoadipate and alpha-ketoglutarate to form alpha-ketoadipate and glutamate. Crystallographic studies have demonstrated that active AADAT enzyme is a homodimer with a pyridoxal phosphate moiety covalently attached to each monomer (Han et al. 2008; Rossi et al. 2008). The enzyme is inferred to be located within the mitochondrion because of a mitochondrial localization sequence motif at the aminoterminal end of the AADAT polypeptide (Goh et al. 2002).
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Kynurenine/alpha-aminoadipate aminotransferase (AADAT) catalyzes the reversible reaction of alpha-ketoadipate and glutamate to form alpha-aminoadipate and alpha-ketoglutarate. Crystallographic studies have demonstrated that active AADAT enzyme is a homodimer with a pyridoxal phosphate moiety covalently attached to each monomer (Han et al. 2008; Rossi et al. 2008). The enzyme is inferred to be located within the mitochondrion because of a mitochondrial localization sequence motif at the aminoterminal end of the AADAT polypeptide (Goh et al. 2002).
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The mitochondrial nranched-chain alpha-ketoacid dehydrogenase (BKCD) complex catalyzes the reactions of alpha-ketoisocaproate, alpha-keto beta-methylvalerate, or aalpha-ketoisovalerate with CoA and NAD+ to form isovaleryl-CoA, a-methylbutyryl-CoA, or isobuyryl-CoA, respectively, and CO2 and NADH (Chuang and Shih 2001). While bovine and microbial BCKD complexes have been characterized most extensively (Reed and Hackert 1990), structural studies of individual components and subcomplexes of human BKCD have confirmed their structures and roles in the overall oxidative carboxylation process, and have related these features to the disruptive effects of mutations on branched-chain amino acid metabolism in vivo: E1a and E1b components - AEvarsson et al. 2000; E2 - Chang et al. 2002; E3- Brautigam et al. 2005. In addition, structural studies have confirmed the lipoylation of lysine residue 44 in E2 protein (Chang et al. 2002) and the loss of an aminoterminal mitochondrial transport sequence from mature E3 protein (Bruatigam et al. 2005). Loss of mitochondrial transport sequences from proteins E1a, E1b, and E2 has been domstrated by sequence analysis (Wynn et al. 1999).
Fine-tuning of GPCR activity by receptor-interacting proteins
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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 histidine ammonia lyase (HAL) catalyzes the reaction of histidine to form urocanate and NH4+ (Kawai et al. 2005).
Cytosolic urocanate hydratase (UROC1) catalyzes the hydrolysis of urocanate to form 4-imidazolone-5-propanoate. Human UROC1 was first identified in surveys of genes differentially expressed in hepatoblastoma (Yamamda et al. 2004). Recent biochemical and molecular studies of UROC1 protein and cDNA from a patient with urocanic aciduria has confirmed the function of UROC1 in vivo (Espinos et al. 2009).
The mitochondrial alpha-ketoglutarate dehydrogenase complex catalyzes the reaction of alpha-ketoadipate, CoASH, and NAD+ to form glutaryl-CoA, CO2, and NADH. The enzyme complex contains multiple copies of three different proteins, E1 (OGDH), E2 (DLST), and E3 (DLD), each with distinct catalytic activities (Reed and Hackert 1990; Zhou et al 2001). The reaction starts with the oxidative decarboxylation of alpha-ketoadipate catalyzed by E1alpha and beta (alpha ketoglutarate dehydrogenase). Lipoamide cofactor associated with E1 is reduced at the same time. Next, the glutaryl group derived from alpha ketoglutarate is transferred to coenzyme A in two steps catalyzed E2 (dihydrolipolyl transacetylase). Finally, the oxidized form of lipoamide is regenerated and electrons are transferred to NAD+ in two steps catalyzed by E3 (dihydrolipoyl dehydrogenase). The biochemical details of this reaction have been worked out with alpha ketoglutarate dehydrogenase complex and subunits purified from bovine tissue (McCartney et al. 1998). While all of the human proteins are known as predicted protein products of cloned genes, direct experimental evidence for their functions is available only for E3 (DLD) (Brautigam et al. 2005).
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E2F-dependent accumulation of hEmi1 regulates S phase entry by inhibiting APC(Cdh1)
Glucagon and regulation of glucose metabolism
Am J Physiol Endocrinol Metab 284:E671-8
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).
Mitochondrial glutaryl-CoA dehydrogenase (GCDH) catalyzes the reaction of glutaryl-CoA and FAD to form crotonyl-CoA, FADH2, and CO2. The active enzyme is a tetramer of GCDH polypeptides lacking a 44-residue aminoterminal mitochondrial targeting sequence. Mutations in GCDH cause glutaric aciduria type 1 in vivo (Fu et al. 2004; Keyser et al. 2008).
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Mutations and polymorphisms in the human argininosuccinate synthetase (ASS1) gene
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DNA containing an apurinic/apyrimidinic (AP) site
Double-strand DNA containing an adenine opposite to an 8-oxo guanine
Double-strand DNA containing a hypoxanthine
Double-strand DNA containing an ethenoadenine
Double-strand DNA containing a thymine glycol
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Double-strand DNA containing a formamidopyrimidine
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Double-strand DNA containing a dihydrouracil
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Double-strand DNA containing a cytosine glycol
Diseases associated with visual transduction
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Expression of GFP-tagged neuronal glutamate transporters in cerebellar Purkinje neurons
Structure of human cytidine deaminase bound to a potent inhibitor
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Solution structure and dynamics of the lipoic acid-bearing domain of human mitochondrial branched-chain alpha-keto acid dehydrogenase complex
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Cytosolic nucleoside diphosphate kinases catalyze the reversible reaction of ribonucleoside and deoxyribonucleoside 5'-diphosphates with ATP to form the corresponding nucleoside 5'-triphosphates and ADP. These kinases are ubiquitously expressed enzymes with broad substrate specificities (Berg and Joklik 1954; Parks and Agarwal 1973). Three human cytosolic nucleoside diphosphate kinase proteins, NME1, 2, and 3, have been characterized biochemically (Gilles et al. 1991; Schaertl et al. 1998; Erent et al. 2001; Chen et al. 2003). All are catalytically active as hexamers: homohexamers of NME1, 2, and 3 have been described, as have heterohexamers containing all possible combinations of NME1 and 2 (Gilles et al. 1991; Erent et al. 2001). While cytosolic nucleoside diphosphate kinases can efficiently use several nucleotide triphosphates as a phosphate donor, the high concentrations of ATP relative to other nucleoside triphosphates in vivo makes it the likely major phosphate donor in these reactions and only reactions with ATP as the phosphate donor are annotated. All of these phosphorylation reactions are freely reversible in vitro (Parks and Agarwal 1973; Schaertl et al. 1998), but the high ratio of ATP to ADP concentrations in the cytosol should favor the conversion of (d)NDP and ATP to (d)NTP and ADP.
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).
Cytosolic guanylate kinase 1 (GUK1) catalyzes the reversible reactions of GMP and dGMP with ATP to form GDP and dGDP respectively and ADP. While native gel electrophoretic studies of whole cell extracts suggested the existence of multiple human enzymes with guanylate kinase activity (Jamil et al. 1975), only one has been purified and biochemically characterized (Agarwal et al. 1978; Brady et al. 1996). The enzyme is of clinical importance as it is a target of antitumor drugs and antiviral drugs such as acyclovir (Miller and Miller 1980).
The events of human pyrimidine metabolism are conveniently, if somewhat arbitrarily, grouped into four pathways: de novo synthesis of the pyrimidine ring and its conversion to uridine 5'-monophosphate (UMP), the biosynthesis of other pyrimidine ribo- and deoxyribonucleotides, pyrimidine salvage reactions, and pyrimidine catabolism (Loffler et al. 2005). De novo synthesis of the pyrimidine ring and its conversion to UMP. The pyrimidine base orotate is synthesized from glutamine, bicarbonate, and aspartate. Orotate reacts with 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) and is then decarboxylated to form the pyrimidine nucleotide UMP. Pyrimidine biosynthesis [interconversion]. Pyrimidine ribo- and deoxyribonucleotide di- and triphosphates are synthesized, both from UMP and from pyrimidine ribonucleotide monophosphates generated in salvage reactions. Pyrimidine salvage reactions. Pyrimidine nucleosides and free bases generated by DNA and RNA breakdown are converted to nucleotide monophosphates. Pyrimidine catabolism. The pyrimidine bases thymine and uracil are degraded to beta-aminoisobutyrate and beta-alanine, respectively, which are excreted from the body.
In parallel sequences of three reactions each, thymine is converted to beta-aminoisobutyrate and uracil is converted to beta-alanine. Both of these molecules are excreted in human urine and appear to be normal end products of pyrimidine catabolism (Griffith 1986; Webster et al. 2001). Mitochondrial AGXT2, however, can also catalyze the transamination of both molecules with pyruvate, yielding 2-oxoacids that can be metabolized further by reactions of branched-chain amino acid and short-chain fatty acid catabolism (Tamaki et al. 2000). The importance of these reactions in normal human pyrimidine catabolism has not been well worked out.
Cytosolic thymidine phosphorylase (TYMP) catalyzes the reversible reactions of thymidine or deoxyuridine with orthophosphate to form thymine or uracil and 2-deoxy-D-ribose 1-phosphate. The active form of the enzyme is a homodimer (Desgranges et al. 1981; Norman et al. 2004; Usuki et al. 1992).
5'-nucleotidase (NT5E) associated with the plasma membrane catalyzes the reactions of extracellular CMP, TMP, or UMP with H2O to yield the corresponding nucleoside and orthophosphate. The active enzyme is a glycolipid-anchored dimer (Misumi et al. 1990; Thompson et al. 1987; Zimmerman 1992)
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 uridine-cytidine kinase 2 (UCK2) catalyzes the reactions of cytidine or uridine with ATP to form CMP or UMP and ADP (Greenberg et al. 1977; Van Rompay et al. 2001). Crystallographic data show the enzyme to be a tetramer (Suzuki et al. 2004). When it is expressed as a fusion construct with green fluorescent protein, the protein localizes primarily to the cytosol of transfected CHO cells (Van Rompay et al. 2003).
Cytosolic thymidine kinase 1 (TK1) catalyzes the reaction of thymidine and ATP to form TMP (thymidine 5'-monophosphate) and ADP. TK1 has been purified from human spleen and from cultured cells. The enzyme is active as a homotetramer, and phosphorylates thymidine and deoxyuridine using ATP as a phosphate donor in vitro (Sherley and Kelly 1988a; Munch-Petersen et al. 1991; Birringer et al. 2005). Divalent cations are required for enzyme activity (Mg++ is preferred) (Lee and Cheng 1986), and ATP stabilizes the tetrameric form of the enzyme (Munch-Petersen et al. 1993). In cells, enzyme activity is high during S phase of the cell cycle and low otherwise, correlated with intracellular levels of thymidine kinase 1 protein (Sherley and Kelly 1988b), and consistent with a requirement for TMP synthesis in normal cells only as part of DNA replication.
Characterization of the enzymatic defect in late-onset muscle phosphofructokinase deficiency. New subtype of glycogen storage disease type VII.
Catabolism of thymidine in human blood platelets: purification and properties of thymidine phosphorylase
Crystal structure of human uroporphyrinogen decarboxylase
Lessons from photoreceptors: turning off G-protein signaling in living cells
Mechanism of selectivity in aquaporins and aquaglyceroporins
The plasma membrane-associated transport protein SLC5A6 (SMVT) mediates the uptake of one molecule of pantothenate (PanK) and two sodium ions from the extracellular space to the cytosol. Limited Northern blotting studies suggest that SLC5A6 is widely expressed, and abundant in placenta and small intestine. SLC5A6 may thus play a central role in pantothenate uptake. SLC5A6 also mediates the uptake of biotin and lipoate (Prasad et al. 1999; Wang et al. 1999).
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".
Cytosolic pantothenate kinases catalyze the reaction of ATP and pantothenate to form ADP and phosphopantothenate. This enzymatic activity has been demonstrated in crude cell extracts for two isoforms of mouse pantothenate kinase 1 (Rock et al. 2002) and for their human homologues (Ramaswamy and 2004). Two additional human genes, PANK3 and PANK4, encode closely related proteins but pantothenate kinase activity has not been demonstrated experimentally for them (Leonardi et al. 2005; Zhou et al. 2001).
Pantothenate kinase 2 catalyzes the reaction of ATP and pantothenate to form ADP and phosphopantothenate. While pantothenate kinase 2 co-purifies with mitocondria, its precise location within the mitochondrion has not been established (Hortnagel et al. 2003; Johnson et al. 2004). Recent work by Leonardi et al. (2007) supports a model in which the enzyme is located in the intermembrane space, hence freely accessible to small molecules from the cytosol.Pantothenate is phosphorylated by pantothenate kinase (PANK). Deficiencies in PANK2 cause a progressive neurodegenerative disorder associated with iron accumulation in the brain, but the relationship between disease symptoms and pantothenate metabolism remains unclear (Zhou et al. 2001; Zhang et al. 2006).
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).
An array of kinases catalyze the reversible phosphorylation of nucleotide monophosphates to form nucleotide diphosphates and triphosphates. Nucleoside monophosphate kinases catalyze the reversible phosphorylation of nucleoside and deoxynucleoside 5'-monophosphates to form the corresponding nucleoside 5'-diphosphates. Most appear to have restricted specificities for nucleoside monophosphates, and to use ATP preferentially (Van Rompay et al. 2000; Anderson 1973; Noda 1973). The total number of human enzymes that catalyze these reactions in vivo is not clear. In six cases, a well-defined biochemical activity has been associated with a purified protein, and these are annotated here. However, additional nucleoside monophosphate kinase-like human proteins have been identified in molecular cloning studies whose enzymatic activities are unknown, and several distinctive nucleoside monophosphate kinase activities detected in cell extracts, e.g., a GTP-requiring adenylate kinase activity (Wilson et al. 1976) and one or more guanylate kinase activities (Jamil et al. 1975) have not been unambiguously associated with specific human proteins. The nucleoside monophosphates against which each of the six well-characterized enzymes is active is shown in the table (Van Rompay et al. 2000). All six efficiently use ATP as a phosphate donor, but have some activity with other nucleoside triphosphates as well in vitro. The high concentrations of ATP relative to other nucleoside triphosphates in vivo makes it the likely major phosphate donor in these reactions under most conditions. All of these phosphorylation reactions are freely reversible in vitro when carried out with purified enzymes and substrates, having equilibrium constants near 1. In vivo, high ratios of ATP to ADP are likely to favor the forward direction of these reactions, i.e., the conversion of (d)NMP and ATP to (d)NDP and ADP. At the same time, the reversibility of the reactions and the overlapping substrate specificities of the enzymes raises the possibility that this group of reactions can buffer the intracellular nucleotide pool and regulate the relative concentrations of individual nucleotides in the pool: if any one molecule builds up to unusually high levels, multiple routes appear to be open not only to dispose of it but to use it to increase the supply of less abundant nucleotides. Ribonucleotide reductase catalyzes the synthesis of deoxyribonucleotide diphosphates from ribonucleotide diphosphates.
Cytosolic ITPA dimer catalyzes the reaction of XTP and water to form XMP and PPi (pyrophosphate). Mg++ is required for enzymatic activity. The hydrolysis of XTP is thought to prevent its incorporation into mRNA, which would lead to aberrant protein synthesis (Lin et al. 2001; Abolhassani et al. 2010).
Cytosolic 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).
Zinc fluxes and zinc transporter genes in chronic diseases
Cytosolic nucleoside diphosphate kinases catalyze the reversible reaction of ribonucleoside and deoxyribonucleoside 5'-diphosphates with ADP to form the corresponding nucleoside 5'-diphosphates and ATP. These kinases are ubiquitously expressed enzymes with broad substrate specificities (Berg and Joklik 1954; Parks and Agarwal 1973). Three human cytosolic nucleoside diphosphate kinase proteins, NME1, 2, and 3, have been characterized biochemically (Gilles et al. 1991; Schaertl et al. 1998; Erent et al. 2001; Chen et al. 2003). All are catalytically active as hexamers: homohexamers of NME1, 2, and 3 have been described, as have heterohexamers containing all possible combinations of NME1 and 2 (Gilles et al. 1991; Erent et al. 2001). While the high ratio of ATP to ADP concentrations in the cytosol normally favors the conversion of (d)NDP and ATP to (d)NTP and ADP, the reversibility of the reactions and the overlapping substrate specificities of the enzymes suggest that this group of reverse reactions can buffer the intracellular nucleotide pool and regulate the relative concentrations of individual nucleoside di- and tri-phosphates in the pool.
Nucleoside diphosphate kinase NME4 associated with the inner mitochondrial membrane (Tokarska-Schlattner et al. 2008) catalyzes the reversible reaction of ribonucleoside and deoxyribonucleoside 5'-diphosphates with ATP to form the corresponding nucleoside 5'-triphosphates and ADP. The active form of the enzyme is a hexamer of NME4 polypeptides whose amino-terminal 33 residues, a mitochondrial translocation signal, have been removed (Milon et al. 2000). The substrate specificity of NME4 has not been examined in detail but is inferred to be broad like that of the homologous NME1, 2, and 3 kinases (Schaertl et al. 1998).
Nucleoside diphosphate kinase NME4 associated with the inner mitochondrial membrane (Tokarska-Schlattner et al. 2008) catalyzes the reversible reaction of ribonucleoside and deoxyribonucleoside 5'-diphosphates with ADP to form the corresponding nucleoside 5'-diphosphates and ATP. The active form of the enzyme is a hexamer of NME4 polypeptides whose amino-terminal 33 residues, a mitochondrial translocation signal, have been removed (Milon et al. 2000). The substrate specificity of NME4 has not been examined in detail, but is inferred to be broad like that of the homologous NME1, 2, and 3 kinases (Schaertl et al. 1998).
Isolation of a candidate gene for Menkes disease and evidence that it encodes a copper-transporting ATPase
The kinase activity of CoA synthase (COASY) catalyzes the phosphorylation of dephospho-CoA to form Coenzyme A (CoA-SH). The enzyme is located in the mitochondrial outer membrane (Daugherty et al. 2002; Zhyvoloup et al. 2003).
The human gene for 11 beta-hydroxysteroid dehydrogenase. Structure, tissue distribution, and chromosomal localization.
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).
The plasma membrane-associated transport protein SLC5A6 (aka sodium-dependent multivitamin transporter, SMVT) mediates the uptake of one molecule of biotin (Btn) and two sodium ions from the extracellular space to the cytosol. Limited Northern blotting studies suggest that SLC5A6 is widely expressed and abundant in placenta, liver and small intestine. SLC5A6 may thus play a central role in Btn uptake from dietary sources. SLC5A6 also mediates the uptake of pantothenate and lipoate (Prasad et al. 1999; Wang et al. 1999, Balamurugan et al. 2003).
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.
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).
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.
Nicotinamide levels are modulated by the action of three enzymes involved in nicotinamide salvaging. They are nicotinamide deaminase, nicotinamide phosphoribosyltransferase and nicotinate phosphoribosyltransferase. These enzymes are poorly characterized in humans, depsite their importance in nicotinamide utilization.
Cytosolic nicotinate phosphoribosyltransferase (NaPRT) catalyzes the Mg++-dependent reaction of nicotinate and phosphoribosyl pyrophosphate to form nicotinate mononucleotide (NaMN, nicotinate D-ribonucleotide) and pyrophosphate. The active form of the enzyme is a homodimer (Preiss and Handler 1958; Niedel and Dietrich 1973; Hara et al. 2007).
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.
Glucosamine--fructose-6-phosphate aminotransferase (isomerizing) 1
Glucosamine--fructose-6-phosphate aminotransferase (isomerizing) 2
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.
The adenylyl transferase activity of bifunctional coenzyme A synthase (COASY) catalyzes the transfer of an adenylyl group from ATP to pantetheinephosphate (PPANT) to form dephospho-Coenzyme A (DP-CoA) (Daugherty et al. 2002). The enzyme is associated with the mitochondrial outer membrane (Zhyvoloup et al. 2003).
Sodium-dependent phosphate transport protein 4
Molecular cloning of human mitochondrial glycerophosphate dehydrogenase gene: genomic structure, chromosomal localization, and existence of a pseudogene
Cytosolic folylpolyglutamate synthase catalyzes the reaction of THF-glutamate(n), L-glutamate, and ATP to form THF-glutamate(n+1), ADP, and orthophosphate. (The first glutamate residue is attached to the glutamate moiety of THF itself; for convenience the process is annotated here as if it proceeded in a single concerted step.) The extent of conjugation is variable, but the commonest cytosolic form of THF has five added glutamate residues. Although its properties as a donor of one-carbon units are not affected by glutamate addition, THF that lacks added glutamate residues cannot be retained in the cytosol so this reaction is needed for normal THF function under physiological conditions (Garrow et al. 1992; Chen et al. 1996).
Cytosolic dihydrofolate reductase catalyzes the reaction of dihydrofolate, NADPH, and H+ to form tetrahydrofolate (THF) and NADP+ (Chen et al. 1984; Davies et al. 1990).
Mitochondrial folylpolyglutamate synthase catalyzes the reaction of THF-glutamate(n), L-glutamate, and ATP to form THF-glutamate(n+1), ADP, and orthophosphate. (The first glutamate residue is attached to the glutamate moiety of THF itself; for convenience the process is annotated here as if it proceeded in a single concerted step.) The extent of conjugation is variable, but the commonest mitochondrial form of THF has six added glutamate residues. Although its properties as a donor of one-carbon units are not affected by glutamate addition, THF that lacks added glutamate residues cannot be retained in the mitochondrial matrix so this reaction is needed for normal THF function under physiological conditions. The mitochondrial and cytosolic forms of folylpolyglutamate synthase are encoded by the same gene - alternative splicing generates mRNA with or without an initial exon encoding a mitochondrial targeting sequence (Garrow et al. 1992; Chen et al. 1996).
Cytosolic 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).
The methenyltetrahydrofolate cyclohydrolase activity of the trifunctional MTHFD1 enzyme catalyzes the reversible reaction of 10-formylTHF polyglutamate to form 5,10-methenylTHF polyglutamate and H2O. MTHFD1 is cytosolic and occurs as a dimer. The human enzyme has been identified and partially characterized biochemically (Hum et al. 1988); additional reaction details can be inferred from the properties of the well-studied homologous rabbit enzyme (Villar et al. 1985).
The 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).
Isolation of a candidate gene for Menkes disease that encodes a potential heavy metal binding protein
Peroxisome proliferator-activated receptors: nuclear control of metabolism
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).
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).
Folates are essential cofactors that provide one-carbon moieties in various states of reduction for biosynthetic reactions. Processes annotated here include transport reactions by which folates are taken up by cells and moved intracellularly, folate conjugation with glutamate (required for folate retention within a cell), and some of the key reactions in the generation of reduced folates and one-carbon derivatives of folate.
The methenyltetrahydrofolate cyclohydrolase activity of the trifunctional MTHFD1 enzyme catalyzes the reversible reaction of 5,10-methenylTHF polyglutamate and H2O to form 10-formylTHF polyglutamate. MTHFD1 is cytosolic and occurs as a dimer. The human enzyme has been identified and partially characterized biochemically (Hum et al. 1988); additional reaction details can be inferred from the properties of the well-studied homologous rabbit enzyme (Villar et al. 1985).
Cytosolic dihydrofolate reductase catalyzes the reaction of folate, NADPH, and H+ to form dihydrofolate and NADP+ (Chen et al. 1984; Davies et al. 1990).
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)
sodium-coupled nucleoside transporter, member 3
solute carrier family 28 (sodium-coupled nucleoside transporter), member 3
Neuron-specific human glutamate transporter: molecular cloning, characterization and expression in human brain
Sodium/purine nucleoside co- transporter
Sodium/nucleoside cotransporter 2 (Na(+)/nucleoside cotransporter 2) (Sodium-coupled nucleoside transporter 2) (Concentrative nucleoside transporter 2) (CNT 2) (hCNT2) (Sodium/purine nucleoside co- transporter) (SPNT)
solute carrier family 28 (sodium-coupled nucleoside transporter), member 2
PRPP stimulates the dissociation of phosphoribosyl pyrophosphate amidotransferase tetramers to form dimers (Holmes et al. 1973a,b).
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).
Cytosolic AMP, GMP, and IMP stimulate the association of phosphoribosyl pyrophosphate amidotransferase (PPAT) dimers to form tetramers (Holmes et al. 1973a,b).
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Cloning of a human cDNA for CTP-phosphoethanolamine cytidylyltransferase by complementation in vivo of a yeast mutant
Metabolism of water-soluble vitamins and cofactors
The metabolism of pyruvate provides one source of acetyl-CoA which enters the citric acid (TCA, tricarboxylic acid) cycle to generate energy and the reducing equivalent NADH. These reducing equivalents are re-oxidized back to NAD+ in the electron transport chain (ETC), coupling this process with the export of protons across the inner mitochondrial membrane. The chemiosmotic gradient created is used to drive ATP synthesis.
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Pyruvate metabolism and the citric acid (TCA) cycle together link the processes of energy metabolism in a human cell with one another and with key biosynthetic reactions. Pyruvate, derived from the reversible oxidation of lactate or transamination of alanine, can be converted to acetyl CoA. Other sources of acetyl CoA include breakdown of free fatty acids and ketone bodies in the fasting state. Acetyl CoA can enter the citric acid cycle, a major source of reducing equivalents used to synthesize ATP, or enter biosynthetic pathways. In addition to its role in energy generation, the citric acid cycle is a source of carbon skeletons for amino acid metabolism and other biosynthetic processes. One such process included here is the interconversion of 2-hydroxyglutarate, probably derived from porphyrin and amino acid metabolism, and 2-oxoglutarate (alpha-ketoglutarate), a citric acid cycle intermediate.
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The two stereoisomers of 2-hydroxyglutarate are normally converted to 2-oxoglutarate in the mitochondrial matrix, and can then be metabolized by the citric acid cycle. The physiological sources of 2-hydroxyglutarate have not been established although plausible hypotheses are that it is generated by lysine breakdown or as a byproduct of delta-aminolevulinate metabolism. The stereoisomers are oxidized to 2-oxoglutarate in FAD-dependent reactions catalyzed by the enzymes D2HGDH (specific for R(-)-2-hydroxyglutarate) and L2HGDH (specific for S(-)-2-hydroxyglutarate). An inherited deficiency in either enzyme is associated with accumulation of 2-hydroxyglutarate and variable neurological symptoms. R(-)-2-hydroxyglutarate also reacts reversibly with succinate semialdehyde to form 4-hydroxybutyrate and 2-oxoglutarate, catalyzed by ADHFE1. No deficiencies of this enzyme have been found in patients with elevated 2-hydroxyglutarate levels (Struys 2006).
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ADHFE1 catalyzes the reversible reaction of 2-oxoglutarate and 4-hydroxybutyrate to form (R)-2-hydroxyglutarate and succinate semialdehyde (Struys et al. 2005). The localization of human ADHFE1 to the mitochondrial matrix is inferred from the location determined experimentally for its rat homolog (Kaufman et al. 1988).
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ADHFE1 catalyzes the reversible reaction of (R)-2-hydroxyglutarate and succinate semialdehyde to form 2-oxoglutarate and 4-hydroxybutyrate (Struys et al. 2005). The localization of human ADHFE1 to the mitochondrial matrix is inferred from the location determined experimentally for its rat homolog (Kaufman et al. 1988).
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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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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 fumarate hydratase catalyzes the reversible reaction of fumarate and water to form malate, the seventh step of the TCA cycle (Bourgeron et al. 1994). Unpublished crystallographic data indicate that the protein is a tetramer (PDB 3E04).
The 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).
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).
Cytosolic GMP synthase (GMPS) catalyzes the reaction of xanthosine 5'-monophosphate (XMP), ATP, glutamine and water to form guanosine 5'-monophosphate (GMP), AMP, glutamate and pyrophosphate. GMPS is a monomer (Hirst et al. 1994; Nakamura and Lou 1995).
Two isoforms of adenylosuccinate synthetase, ADSS and ADSSL1, catalyze the reaction of IMP, aspartate, and GTP to form adenylosuccinate, GDP, and orthophosphate (Powell et al. 1992; Sun et al. 2005). ADSS is a homotetramer (unpublished crystallographic data - PDB 2V40) and ADSSL1 is inferred to be a tetramer likewise.
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Functionality of alternative splice forms of the first enzymes involved in human molybdenum cofactor biosynthesis
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
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 conversion of 5'-phosphoribosyl-5-aminoimidazole-4-carboxylate (CAIR) and aspartate to 5'-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide (SAICAR), accompanied by the conversion of ATP to ADP and orthophosphate, is catalyzed by the phosphoribosylaminoimidazole succinocarboxamide synthetase domain of the bifunctional protein "phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase" (PAICS) (Schild et al. 1990). The enzyme is an octamer (Li et al. 2007); it may associate in the cytosol with other enzymes of de novo IMP biosynthesis under some metabolic conditions (An et al. 2008).
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Octamer formation and coupling of cardiac sarcomeric mitochondrial creatine kinase are mediated by charged N-terminal residues
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).
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).
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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).
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Cellular signaling by fibroblast growth factor receptors
The reversible carboxylation of 5'-phosphoribosyl-5-aminoimidazole (AIR) to form 5'-phosphoribosyl-5-aminoimidazole-4-carboxylate (CAIR) is catalyzed by the phosphoribosylaminoimidazole carboxylase domain of the bifunctional protein "phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase" (PAICS) (Schild et al. 1990). The enzyme is an octamer (Li et al. 2007); it may associate in the cytosol with other enzymes of de novo IMP biosynthesis under some metabolic conditions (An et al. 2008).
The irreversible synthesis of cytosolic 5'-phosphoribosyl-5-aminoimidazole (AIR) from 5'-phosphoribosylformylglycinamidine (FGAM), accompanied by the conversion of ATP to ADP and orthophosphate, is catalyzed by the phosphoribosylaminoimidazole synthetase domain of the trifunctional protein, "phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase" (GART) (Aimi et al. 1990). The active form of the protein is cytosolic and may co-localize with other enzymes of de novo IMP biosynthesis under some metabolic conditions (Gooljarsingh et al. 2001; An et al. 2008).
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5'-nucleotidase (NT5E) associated with the plasma membrane catalyzes the reactions of extracellular AMP, dAMP, GMP, or IMP with H2O to yield the corresponding nucleoside and orthophosphate. The active enzyme is a glycolipid-anchored dimer (Misumi et al. 1990; Thompson et al. 1987; Zimmerman 1992)
The purine bases guanine and hypoxanthine (derived from adenine by events in the purine salvage pathways) are converted to xanthine and then to uric acid, which is excreted from the body (Watts 1974). The end-point of this pathway in humans and hominoid primates is unusual. Most other mammals metabolize uric acid further to yield more soluble end products, and much speculation has centered on possible roles for high uric acid levels in normal human physiology.
The events of human purine metabolism are conveniently, if somewhat arbitrarily, grouped into four pathways: de novo synthesis of inosine 5'-monophosphate (IMP), the biosynthesis of other purine ribo- and deoxyribonucleotides, purine salvage reactions, and purine catabolism (Watts 1974). De novo synthesis of inosine 5'-monophosphate (IMP). The purine ribonucleotide IMP is assembled on 5-phospho-alpha-D-ribose 1-diphosphate (PRPP). Purine biosynthesis [interconversion]. Purine ribo- and deoxyribonucleotide di- and triphosphates are synthesized, both from IMP and from guanosine and adenosine ribo- and deoxyribonucleotide monophosphates generated in salvage reactions. Purine salvage reactions. Purine nucleosides and free bases generated by DNA and RNA breakdown are converted to nucleotide monophosphates. Purine catabolism. The purine bases guanine and hypoxanthine are degraded to uric acid, which is excreted from the body.
Cytosolic glutathione peroxidase (GPX1) tetramer catalyzes the reaction of reduced glutathione and hydrogen peroxide to form reduced glutathione and water (Chu et al. 1993).
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.
Human sodium phosphate transporter 4 (hNPT4/SLC17A3) as a common renal secretory pathway for drugs and urate
Clinical, biochemical and molecular genetic correlations in adenylosuccinate lyase deficiency
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 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).
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 hypoxanthine-guanine phosphoribosyltransferase (HPRT1) tetramer catalyzes the reactions of guanine or hypoxanthine with PRPP to form GMP ir IMP and pyrophosphate (Holden and Kelley 1978; Jolly et al. 1983).
The decarboxylation of orotidine 5'-monophosphate (OMP) to form uridine 5'-monophosphate (UMP) is catalyzed by the orotidine 5'-phosphate decarboxylase activity of the bifunctional "uridine monophosphate synthetase (orotate phosphoribosyl transferase and orotidine 5'-decarboxylase)" protein. While purified human protein has not been characterized in detail, the close similarity of the human gene to that encoding the well-studied hamster protein, and the demonstration that mutations in the human gene are associated with failure to convert orotate to UMP in vivo, provide convincing evidence that the human uridine monophosphate synthetase protein indeed catalyzes these two reactions (McClard et al. 1980; Suchi et al. 1997). The active form of the human protein is a dimer (Yablonski et al. 1996; Wittmann et al. 2008).
Cytosolic deoxycytidylate deaminase (DCTD) catalyzes the hydrolysis of dCMP (2'-deoxyuridine 5'-monophosphate) to yield dUMP (2'-deoxyuridine 5'-monophosphate) and ammonia. The active enzyme is a homohexamer (Maley et al. 1993; Weiner et al. 1993; unpublished crystallography data - PDB 2W4L).
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 thymidine phosphorylase (TYMP) catalyzes the reversible reactions of thymine or uracil with 2-deoxy-D-ribose 1-phosphate to form thymidine or deoxyuridine and orthiophosphate. The active form of the enzyme is a homodimer (Desgranges et al. 1981; Norman et al. 2004; Usuki et al. 1992).
Cytosolic uridine-cytidine kinase 1 (UCK1) catalyzes the reactions of cytidine or uridine with ATP to form CMP or UMP and ADP (Greenberg et al. 1977; Van Rompay et al. 2001). Unpublished crystallographic data show the enzyme to be a tetramer (PDB - 2JEO).
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).
Dihydroorotate dehydrogenase catalyzes the oxidation of dihydroorotate to orotate (orotic acid). The enzyme is located in the inner mitochondrial membrane oriented so that cytosolic dihydroorotate molecules have access to it, and orotate is released into the cytosol. The reducing equivalents generated by the reaction are transferred by ubiquinone (Coenzyme Q) to the electron transport chain within the inner mitochondrial membrane. There is no evidence for the involvement of NAD+ as an acceptor of reducing equivalents in this reaction in mammalian cells (Jones 1980). In contrast, the reaction catalyzed by the enzyme isolated from the anaerobic bacterium Clostridium oroticum requires NAD+ as a cofactor but also proceeds strongly in the direction of dihydroorotate synthesis consistent with the greater electronegativity of NAD+ (Lieberman and Kornberg 1953). Early studies of purified rat liver enzyme by Forman and Kennedy suggested the presence of flavin mononucleotide and iron-sulfur complexes as cofactors. More recent work by Bader, Beuneu, and their colleagues with recombinant human protein expressed in insect cells has confirmed the presence of flavin mononucleotide, at a stoichiometry of one molecule per molecule of apoenzyme but suggests that iron-sulfur complexes, if indeed they are involved in the oxidation and electron transport process, are not an integral part of the dihydroorotate dehydrogenase holoenzyme.
The synthesis of 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).
Endoplasmic reticulum-mediated phagocytosis is a mechanism of entry into macrophages
The synthesis of orotidine 5'-monophosphate (OMP) from orotate and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) is catalyzed by the orotate phosphoribosyltransferase activity of the bifunctional "uridine monophosphate synthetase (orotate phosphoribosyl transferase and orotidine 5'-decarboxylase)" protein. The reaction itself is freely reversible, but is pulled in the forward direction in vivo by the irreversible hydrolysis of pyrophosphate. While purified human protein has not been characterized in detail, the close similarity of the human gene to that encoding the well-studied hamster protein, and the demonstration that mutations in the human gene are associated with failure to convert orotate to UMP in vivo, provide convincing evidence that the human uridine monophosphate synthetase protein indeed catalyzes these two reactions (McClard et al. 1980; Suchi et al. 1997). The active form of the human protein is a dimer (Yablonski et al. 1996; Wittmann et al. 2008).
The Menkes protein (ATP7A; MNK) cycles via the plasma membrane both in basal and elevated extracellular copper using a C-terminal di-leucine endocytic signal
The gene encoding hydroxypyruvate reductase (GRHPR) is mutated in patients with primary hyperoxaluria type II
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
Crystal structure of human aquaporin 4 at 1.8 A and its mechanism of conductance
Acetylcholine Neurotransmitter Release Cycle
adenosine, deoxyadenosine, guanosine, inosine
Metabolism of carotenoids and retinoids related to vision
Rod and cone visual pigments and phototransduction through pharmacological, genetic, and physiological approaches
3alpha,7alpha-Dihydroxy-5beta-cholanic acid
Molecular cloning, genomic organization, and functional expression of Na+/H+ exchanger isoform 5 (NHE5) from human brain
2-Hydroxy-1,2,3-propanetricarboxylic acid
Enzymatic phosphorylation of nucleoside diphosphates
5'-nucleotidase: molecular structure and functional aspects
Functional characterization and localization of AQP3 in the human colon
'D-Fructose 2,6-bisphosphate [cytosol]' positively regulates 'D-fructose 6-phosphate + ATP => D-fructose 2,6-bisphosphate + ADP'
Peroxisome proliferator-activated receptors, coactivators, and downstream targets
Indirect inhibition of mitochondrial dihydroorotate dehydrogenase activity by nitric oxide.
'ATP [nucleoplasm]' negatively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'CIT [cytosol]' negatively regulates 'D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP'
'3',5'-Cyclic AMP [cytosol]' negatively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'D-Fructose 1,6-bisphosphate [cytosol]' positively regulates 'phosphoenolpyruvate + ADP => pyruvate + ATP'
'D-Fructose 2,6-bisphosphate [cytosol]' positively regulates 'D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP'
'AMP [cytosol]' positively regulates 'D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP'
beta-Nicotinamide adenine dinucleotide phosphate
Nicotinamide adenine dinucleotide phosphate
'ATP [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'
Structure of human thymidylate synthase suggests advantages of chemotherapy with noncompetitive inhibitors
Nramp2 expression is associated with pH-dependent iron uptake across the apical membrane of human intestinal Caco-2 cells
Structure and expression of a complementary DNA for the nuclear coded precursor of human mitochondrial ornithine transcarbamylase.
Nucleoside diphosphate kinase from human erythrocytes. Structural characterization of the two polypeptide chains responsible for heterogeneity of the hexameric enzyme
Neurotransmitter Clearance In The Synaptic Cleft
ZnT-2, a mammalian protein that confers resistance to zinc by facilitating vesicular sequestration
Molecular cloning and expression of the cDNAs encoding human and yeast mevalonate pyrophosphate decarboxylase
Regulation of small GTPases at epithelial cell-cell junctions
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Enzymic synthesis and breakdown of a pyrimidine, orotic acid. I. Dihydro-orotic dehydrogenase
Antigen Presentation: Folding, assembly and peptide loading of class I MHC
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The biochemical and structural basis for trans-to-cis isomerization of retinoids in the chemistry of vision
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Cold Spring Harb Perspect Biol 4:a007864
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Transfer ribonucleic acid-induced hydrolysis of valyladenylate bound to isoleucyl ribonucleic acid synthetase
Purification and properties of isoleucyl ribonucleic acid synthetase from Escherichia coli
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Cloning and characterization of the cDNA encoding human adenylosuccinate synthetase
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Polyamines: metabolism and implications in human diseases
Purification to homogeneity of mitochondrial acyl coa:glycine n-acyltransferase from human liver
The solute carrier 26 family of proteins in epithelial ion transport
Tau-crystallin/alpha-enolase: one gene encodes both an enzyme and a lens structural protein
Disorders of cholesterol biosynthesis: prototypic metabolic malformation syndromes
Making heads or tails of phospholipids in mitochondria
The roles of anabolic and catabolic reactions in the synthesis and recycling of polyunsaturated fatty acids
Prostaglandins Leukot Essent Fatty Acids 67:79-83
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
5,10-methylenetetrahydrofolate polyglutamate
5,10-methylenetetrahydrofolate polyglutamate macromolecule
5,10-methylenetetrahydrofolate polyglutamate macromolecule [ChEBI:60473]
The lipoxin receptor ALX: potent ligand-specific and stereoselective actions in vivo
Diverging substrate specificity of pure human thymidine kinases 1 and 2 against antiviral dideoxynucleosides
The SLC34 family of type II Na+/Pi cotransporters consist of three members; NaPi-IIa (SLC34A1), NaPi-IIb (SLC34A2) and NaPi-IIc (SLC34A3) (Murer H et al, 2004). They are expressed mainly in the kidney and small intestine, located at the apical sites of epithelial cells although other areas of the body express them to a lesser extent. NaPi-IIa and b cotransports divalent Pi (HPO4[2-]) with three Na+ ions (electrogenic transport) whereas NaPi-IIc cotransports divalent Pi with two Na+ ions (electroneutral transport).
SLC34A1 encodes Na+/Pi cotransporter (NaPi-IIa) which is expressed in the kidney in the renal proximal tubule (Magagnin S et al, 1993). SLC34A2 encodes NaPi-IIb which is abundantly expressed in lung and to a lesser degree in tissues of epithelial origin including small intestine, pancreas, prostate, and kidney (Field JA et al, 1999). Both NaPi-IIa and NaPi-IIb cotransport divalent Pi (HPO4[2-]) with three Na+ ions (electrogenic transport). Defects in SLC34A1 are the cause of hypophosphatemic nephrolithiasis/osteoporosis type 1 (NPHLOP1) (Prie D et al, 2002). Defects in SLC34A2 are a cause of pulmonary alveolar microlithiasis (Corut A et al, 2006).
SLC34A3 is almost exclusively expressed in the kidney and encodes the Na+/Pi cotransporter NaPi-IIc (Segawa H et al, 2002). The protein is located at apical membranes of proximal tubules. It cotransports two Na+ ions with every Pi (electroneutral transport). Defects in SLC34A3 are the cause of hereditary hypophosphatemic rickets with hypercalciuria (HHRH) (Bergwitz C et al, 2006)
NHE9 (SLC9A9) (Nakamura N et al, 2005) is expressed ubiquitously and thought to play a housekeeping role in pH homeostasis in the late endosome membrane.
The 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.
NHE6 (SLC9A6) (Brett CL et al, 2002; Nakamura N et al, 2005) is expressed ubiquitously and thought to play a housekeeping role in pH homeostasis in early endosomes.
NHE7 and 8 (SLC9A7,8) (Nakamura N et al, 2005) are expressed ubiquitously and thought to play a housekeeping role in pH homeostasis in the trans-golgi network.
SLC1A4, associated with the plasma membrane, mediates the exchange of cysteine and an extracellular sodium ion for a cytosolic sodium ion and any one of the four amino acids alanine, serine, threonine, or cysteine (Zerangue and Kavanaugh 1996).
SLC1A4, associated with the plasma membrane, mediates the exchange of alanine and an extracellular sodium ion for a cytosolic sodium ion and any one of the four amino acids alanine, serine, threonine, or cysteine (Zerangue and Kavanaugh 1996).
Phosphorus is an essential element that is critical for structural and metabolic roles in all living organisms. Cells obtain phosphorus in the form of negatively-charged inorganic phosphate (Pi). Two SLC families transport phosphate in mammals; SLC34 (Murer H et al, 2004) and SLC20 (Collins JF et al, 2004). Both are secondary-active, Na+-coupled transporter systems which use the inward Na+ gradient (from the Na+-K+-ATPase) to drive phosphate influx into cells (Virkki LV et al, 2007).
There are two transporters of this type; The genes SLC20A1 and SLC20A2 encode for PiT1 (phosphate transporter 1) and PiT2 respectively. They both have a broad tissue distribution and may play a general housekeeping role in phosphate transport such as absorbing phosphate from interstitial fluid and in extracellular matrix and cartilage calcification as well as in vascular calcification. These proteins were originally described as retroviral receptors for the gibbin ape leukemia virus receptor 1 (GLVR1, now called PiT1) (O'Hara B et al, 1990) and GLVR2 (now called PiT2) (van Zeijl M et al, 1994). However, they were found to possess Na+-coupled phosphate cotransporter function (Fernandes I et al, 1999). The transport is electrogenic with a stoichiometry of 2:1 (Na+:Pi).
Human peroxisomal L-alanine: glyoxylate aminotransferase. Evolutionary loss of a mitochondrial targeting signal by point mutation of the initiation codon
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).
Functional characterization of the human high-affinity choline transporter
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).
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).
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.
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).
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.
NHE1 (SLC9A1) is present in most cells and is the most extensively characterized member of this family (Sardet C et al, 1989). NHE2-4 (SLC9A2-4) (Malakooti J et al, 1999; Brant SR et al, 1995) are expressed mainly in the kidney and GI tract. NHE5 (SLC9A5) (Baird NR et al, 1999) is highly expressed in neuronal-enriched areas of the CNS.
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.
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).
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.
GARS (cytosolic glycyl tRNA synthetase) catalyzes the reaction of glycine, tRNA(Gly), and ATP to form Gly tRNA(Gly), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a dimer. Cytosolic and mitochondrial glycyl tRNA synthetase enzymes are both encoded by the same gene; the cytosolic protein lacks an aminoterminal 54 residue sequence found in the mitochondrial protein. Mutations in GARS are associated with Charcot Marie Tooth disease and distal spinal muscular atrophy, two diseases characterized by axonal dysfunction (Antonellis et al. 2006)
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Neuotransmitter uptake by astrocytes is mediated by specific transporter located on the astrocytic membrane. The imported neurotransmitter in the astrocytes is metabolized and transported back to the neuron via specialized transporters.
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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.
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DARS2 (mitochondrial aspartyl tRNA synthetase) catalyzes the reaction of aspartate, mitochondrial tRNA(Asp), and ATP to form Asp tRNA(Asp), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a homodimer (Bonnefond et al. 2005). Homozygosity for DARS2 mutations is associated with leukoencephalopathy with brainstem and spinal cord involvement plus lactate elevation (Scheper et al 2007).
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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).
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Mechanisms of digestion and absorption of dietary vitamin A
Cytosolic tRNA synthetases catalyze the reactions of tRNAs encoded in the nuclear genome, their cognate amino acids, and ATP to form aminoacyl-tRNAs, AMP, and pyrophosphate. Eight of the tRNA synthetases, those specific for arginine, aspartate, glutamate and proline, glutamine, isoleucine, leucine, lysine, and methionine, associate to form a complex with three accessory proteins. Each of the component synthetases is active in vitro as a purified protein; complex formation is thought to channel aminoacylated tRNAs more efficiently to the site of protein synthesis in mRNA:ribosome complexes (Quevillon et al. 1999; Wolfe et al. 2003, 2005).
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NARS2 (mitochondrial asparaginyl tRNA synthetase) catalyzes the reaction of asparagine, mitochondrial tRNA(Asn), and ATP to form Asn-tRNA(Asn), AMP, and pyrophosphate. The NARS2 gene has been identified by computational analysis of the human genome sequence; its function has been inferred from those of the biochemically characterized mitochondrial aspartyl and tyrosyl tRNA synthetases (Bonnefond et al. 2005).
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LARS2 (mitochondrial leucyl tRNA synthetase) catalyzes the reaction of leucine, mitochondrial tRNA(Leu), and ATP to form Leu-tRNA(Leu), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is a monomer (Bullard et al. 2000).
IARS2 (mitochondrial isoleucyl tRNA synthetase) catalyzes the reaction of isoleucine, mitochondrial tRNA(Ile), and ATP to form Ile-tRNA(Ile), AMP, and pyrophosphate. The enzyme is a class I tRNA synthetase (Degoul et al. 1995).
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.
Excess L-Glutamate released by the pre-synaptic neuron in the synaptic cleft is cleared by high affinity transporters called the excitatory amino acid transporters (EAATs) to terminate synaptic actions of the neurotransmitter and to recycle these molecules. Five types of EAATs have been identified EAAT1-EAAT5 in the mammalian CNS. EAAT1 and EAAT2 are mainly expressed by astrocytes whereas EAAT3 and EAAT4 are predominantly neuronal. EAAT3 are expressed throughout the CNS however, EAAT4 is predominantly localized to purkinje cells. EAAT5 are expressed rod photoreceptor and bipolar cells of retina. Astrocytic EAATs are expressed in astrocytes in close apposition to the synapses and neuronal EAATs are expressed in the extra-synaptic or peri-synaptic locations on the neurons. Astrocytic EAATs are responsible for majority of the glutamate uptake, neuronal transporters are responsible for glutamate clearance in specialized synapses in cerebellum where the spatial relationship between the glutamate receptors and EAATs is altered and glutamate receptors are expressed in the peri-synaptic region.
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.
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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).
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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.
Sodium-dependent phosphate transport protein 2B
Communication at the synapse involves the release of glutamate from the presynaptic neuron and its binding to glutamate receptors on the postsynaptic cell to generate a series of events that lead to propagation of the synaptic transmission. This process begins with the formation of synaptic vesicles in the presynaptic neuron, proceeds to the loading of glutamate into the vesicles, and concludes with the release of glutamate into the synaptic cleft. The glutamate life cycle in the neuron begins with the loading of the nascent synaptic vesicles with cytosolic glutamate with the help the transporter protein, VGLUT1, located in the synaptic vesicular membrane. Glutamate loaded vesicles are formed in the cytoplasm and then transported to a site close to the plasma membrane where the vesicle is docked with the help of several proteins. One of the key players in the docking process in Munc 18, which interacts with syntaxin (in the plasma membrane), MINT (Munc18 interacting molecule), and DOC2. These interactions along with the secondary interactions are needed for docking the synaptic vesicle to the plasma membrane. The docked synaptic vesicle is not ready for release until it undergoes molecular changes to prime it for fusion with the plasma membrane. Munc13 is one of the main players in the priming process. Munc 13 interacts with RIM (Rab3A interacting molecule) located in the synaptic vesicle. Munc 13 also interacts with DOC2. The precise molecular mechanisms of the interactions that result in docking versus priming are not clear and the docking and priming process have been combined in this annotation of this pathway. Once primed the synaptic vesicle is ready for release. Synaptic transmission involves an action potential that is generated in the presynaptic cell which induces the opening of voltage gated Ca2+ channels (VGCC) located in the plasma membrane of the presynaptic neuron. Typically N, P/Q and R type of VGCCs are involved in the neurotransmitter release. Ca2+ influx through these channels results in the rise of intracellular Ca2+ concentration. In the microdomain of glutamatergic synapses, the Ca2+ concentration could rise between 10-25 micro molar. Synaptotagmin, a Ca2+-binding protein located in the synaptic vesicular membrane, responds to the rise in the Ca2+ levels in the microdomain and induces a synaptic vesicle membrane curvature that favors vesicle fusion. Fusion of the synaptic vesicle with the plasma membrane is characterized by the formation of a trimeric trans-SNARE complex that involves VAMP2 from the synaptic vesicle membrane, and syntaxin and SNAP-25 from plasma membrane. Vesicle fusion incorporates the synaptic vesicle membrane into the plasma membrane, releasing the vesicle contents (glutamate) into the synaptic cleft. Postfusion the synaptic vesicle membrane proteins (VAMP2, Rab3A, VGLUT1, and synaptotagmin) are also found in the plasma membrane.
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Sodium-dependent phosphate transport protein 2C
Choline transporter symports Na ion and Choline from the extracellular region into the cytosol. The choline transporters are located in the nerve terminals of cholinergic neurons.
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CHIP28 water channels are localized in constitutively water-permeable segments of the nephron
Acetylcholine neurotransmitter release cycle involves syntheis of choline, loading of clathrin scultpted synaptic vesicles, docking and priming of the acetyl choline loaded synaptic vesicles and then release of acetylcholine. This cycle occurs in neurons of central nervous system (CNS), peripheral, autonomic and somatic nervous system. In the CNS, the acetylcholine is released by the presynaptic neurons into the synaptic cleft where the released acetylcholine is accessible to acetylcholine receptors located on the postsynaptic neurons.
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Sodium-dependent phosphate transport protein 2A
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.
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Expression, purification, and characterization of histidine-tagged rat and human flavoenzyme dihydroorotate dehydrogenase.
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.
Bidirectional water fluxes and specificity for small hydrophilic molecules in aquaporins 0-5
Natural resistance-associated macrophage proteins (NRAMPs) regulates macrophage activation for antimicrobial activity against intracellular pathogens. They do this by mediating metal ion transport across macrophage membranes and the subsequent use of these ions in the control of free radical formation. The human gene SLC11A1 encodes NRAMP1 (Kishi F, 2004; Kishi F and Nobumoto M, 1995) which can utilize the protonmotive force to mediate divalent iron (Fe2+), zinc (Zn2+) and manganese (Mn2+) influx to or efflux from phagosomes.
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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Visual phototransduction is the process by which photon absorption by visual pigment molecules in photoreceptor cells is converted to an electrical cellular response. The events in this process are photochemical, biochemical and electrophysiological and are highly conserved across many species. This process occurs in two types of photoreceptors in the retina, rods and cones. Each type consists of two parts, the outer segment which detects a photon signal and the inner segment which contains the necessary machinery for cell metabolism. Each type of cell functions differently. Rods are very light sensitive but their flash response is slow so they work best in twilight conditions but are not good at detecting objects moving quickly. Cones are less light-sensitive and have a fast flash response so they work best in daylight conditions and are better at detecting fast moving objects than rods. The visual pigment consists of a chromophore (11-cis-retinal, 11cRAL, A1) covalently attached to a GPCR opsin family member. The linkage is via a Schiff base forming retinylidene protein. Upon photon absorption, 11cRAL isomerises to all-trans retinal (atRAL), changing the conformation of opsin to an activated form which can activate the regulatory G protein transducin (Gt). The alpha subunit of Gt activates phosphodiesterase which hydrolyses cGMP to 5'-GMP. As high level of cGMP keep cGMP-gated sodium channels open, the lowering of cGMP levels closes these channels which causes hyperpolarization of the cell and subsequently, closure of voltage-gated calcium channels. As calcium levels drop, the level of the neurotransmitter glutamate also drops causing depolarization of the cell. This effectively relays the light signal to postsynaptic neurons as electrical signal (Burns & Pugh 2010, Korenbrot 2012, Pugh & Lamb 1993). 11cRAL cannot be synthesised in vertebrates. Vitamin A from many dietary sources is the precursor for 11cRAL. It is taken from food in the form of esters such as retinyl acetate or palmitate or one of four caretenoids (alpha-carotene, beta-carotene, gamma-carotene and beta-cryptoxanthin). Retinoids are transported from the gut to be stored in liver, until required by target organs such as the eye (Harrison & Hussain 2001, Harrison 2005). In the eye, in the form 11cRAL, it is used in the retinoid (visual) cycle to initiate phototransduction and for visual pigment regeneration to ready the photoreceptor for the next phototransduction event (von Lintig 2012, Blomhoff & Blomhoff 2006, von Lintig et al. 2010, D'Ambrosio et al. 2011, Wang & Kefalov 2011, Kefalov 2012, Wolf 2004).
Rods and cones share the same mechanism for the phototransduction process but perform functionally different roles. Although cone photoreceptors make up around 5% of all photoreceptor cells and are outnumbered 20 to 1 by rod photoreceptors, they mediate daylight vision in the human eye whereas rods mediate twilight vision. Also, cones are around 100-times less light-sensitive than rods thereby depriving us of colour vision in dark conditions in which cones cannot function. Rod function saturates in even moderate amounts of light whereas cones can adjust to even very bright light conditions, a process called light adaptation. In bright conditions, rods can take up to one hour to regain their sensitivity whereas cones can recover in a few minutes, a process called dark adaptation and which allows us to retain visual perception in changing light conditions. Cone cells express three types of opsin which allow colour discrimination. Long Wavelength Sensitive Opsin (OPN1LW) detects red , Short Wavelength Sensitive Opsin (OPN1SW) detects blue, and Short Wavelength Sensitive Opsin (OPN1SW) detects green regions of the light spectrum. In the canonical retinoid (visual) cycle, the visual chromophore is regenerated in reactions involving the rod outer segments (ROS) and the retinal pigment epithelium (RPE). For cones, chromophore recycling is independent of the RPE and instead involves Muller cells in the retina which supply the chromophore selectively to cones. The molecular steps of the cone retinoid (visual) cycle are outlined in this section. The ability of cones to react to bright and differing light conditions means it has to regenerate the chromophore much quicker than rods. All-trans-retinol (atROL) released from cone outer segments is taken up by Muller cells where it is directly isomerized back to 11-cis-retinol (11cROL) then esterified by LRAT. When required, these 11-cis-retinyl esters can be hydrolysed by 11-cis-RE hydrolases back to 11cROL then oxidised in the cone photoreceptor cell to regenerate 11-cis-retinal (11cRAL), the visual chromophore (see reviews von Lintig 2012, Wang & Kefalov 2011, Kefalov 2012, Wolf 2004).
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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).
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).
Low affinity cationic amino acid transporter 2, isoform B
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).
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High affinity cationic amino acid transporter 1
Sodium-dependent phosphate transporter 2
Sodium-dependent phosphate transporter 1
The ability of human lactate dehydrogenase to catalyze the reaction of phenylalanine with NADH + H+ to form phenyllactate and NAD+ is inferred from the properties of bovine heart lactate dehydrogenase (Meister 1951). As these studies were carried out only on the one bovine isoform, the reaction is inferred only for the corresponding human isoform. The reaction rate measured for bovine LDHB acting on phenylpyruvate is approximately 2% of its rate on pyruvate, but could yield appreciable amounts of phenyllactate under conditions of high phenylpyruvate concentration.
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).
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Sodium-coupled monocarboxylate transporter 1
Sodium-dependent phosphate transport protein 1
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Natural resistance-associated macrophage protein 2
Overexpression of human alanine:glyoxylate aminotransferase in Escherichia coli: renaturation from guanidine-HCl and affinity for pyridoxal phosphate co-factor
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Dealing with methionine/homocysteine sulfur: cysteine metabolism to taurine and inorganic sulfur
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Sodium/nucleoside cotransporter 1 (Na(+)/nucleoside cotransporter 1) (Sodium-coupled nucleoside transporter 1) (Concentrative nucleoside transporter 1) (CNT 1) (hCNT1)
solute carrier family 28 (sodium-coupled nucleoside transporter), member 1
Xylulose 5-phosphate mediates glucose-induced lipogenesis by xylulose 5-phosphate-activated protein phosphatase in rat liver
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Latent infection of Homo sapiens with Mycobacterium tuberculosis
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Protoheme IX farnesyltransferase, mitochondrial ecNumber2.5.1.-/ecNumber
alcohol dehydrogenase 1A (class I), alpha polypeptide
alcohol dehydrogenase 4 (class II), pi polypeptide
Alcohol dehydrogenase class II pi chain precursor
alcohol dehydrogenase 7 (class IV), mu or sigma polypeptide
Alcohol dehydrogenase class IV mu/sigma chain
Acetyl-coenzyme A synthetase 2-like, mitochondrial
acyl-CoA synthetase short-chain family member 1
Acetyl-coenzyme A synthetase, cytoplasmic
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".
Interaction between citrate synthase and malate dehydrogenase. Substrate channeling of oxaloacetate
Glyoxylate reductase/hydroxypyruvate reductase
Identification and characterization of human mitochondrial tryptophanyl-tRNA synthetase
Phenylacetate metabolism is of clinical importance because its conjugation with glutamine to form phenylacetylglutamine, which can be excreted in the urine, provides an alternative pathway for nitrogen excretion in patients with urea cycle defects (James et al. 1972; Batshaw et al. 2001; Brusilow and Horwich 2001). This conjugation proceeds in two steps. First, phenylacetate and ATP react with coenzyme A to form phenylacetyl CoA, AMP, and pyrophosphate (Vessey et al. 1999). Two human CoA ligases have been characterized that catalyze this reaction efficiently in vitro: acyl-CoA synthetase medium-chain family member 1 (BUCS1) (Fujino et al. 2001) and xenobiotic/medium-chain fatty acid:CoA ligase (Vessey et al. 2003). Their relative contributions to phenylacetate metabolism in vivo are unknown. Second, phenylacetyl CoA and glutamine react to form phenyacetyl glutamine and Coenzyme A. The enzyme that catalyzes this reaction has been purified from human liver mitochondria and shown to be a distinct polypeptide species from glycine-N-acyltransferase (Webster et al. 1976). This human glutamine-N-acyltransferase activity has not been characterized by sequence analysis at the protein or DNA level, however, and thus cannot be associated with a known human protein in the annotation of phenylacetate conjugation.
ChEBI:32643 5-acetamido-6-formamido-3-methyluracil
Phenylacetate and ATP react with coenzyme A to form phenylacetyl CoA, AMP, and pyrophosphate (Vessey et al. 1999). Two human CoA ligases have been characterized that catalyze this reaction efficiently in vitro: acyl-CoA synthetase medium-chain family member 1 (BUCS1) (Fujino et al. 2001) and xenobiotic/medium-chain fatty acid:CoA ligase (Vessey et al. 2003). Their relative contributions to phenylacetate metabolism in vivo are unknown.
Benzoic acid, widely used as a food preservative, is converted to hippuric acid by activation and conjugation with glycine. This was one of the first detoxification pathways discovered, and was formerly exploited clinically as an alternative means of nitrogen excretion in patients with urea cycle defects (Brusilow and Horwich 2001).
Benzoate and ATP react with coenzyme A to form benzoyl CoA, AMP, and pyrophosphate (Vessey et al. 1999, 2003). Two human CoA ligases have been characterized that catalyze this reaction efficiently in vitro: acyl-CoA synthetase medium-chain family member 1 (BUCS1) (Fujino et al. 2001) and xenobiotic/medium-chain fatty acid:CoA ligase (Vessey et al. 2003). Their relative contributions to benzoate metabolism in vivo are unknown.
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.
N-acetyltransferases (NATs; EC 2.3.1.5) utilize acetyl Co-A in acetylation conjugation reactions. This is the preferred route of conjugating aromatic amines (R-NH2, converted to aromatic amides R-NH-COCH3) and hydrazines (R-NH-NH2, converted to R-NH-NH-COCH3). Aliphatic amines are not substrates for NAT. The basic reaction is Acetyl-CoA + an arylamine = CoA + an N- acetylarylamine NATs are cytosolic and in humans, 2 isoforms are expressed, NAT1 and NAT2. A third isoform, NATP, is a pseudogene and is not expressed. The NAT2 gene contains mutations that decrease NAT2 activity. This mutations was first seen as slow acetylation compared to the normal, fast acetylation of the antituberculosis drug isoniazid. Incidence of the slow acetylator phenotype is high in Middle Eastern populations (70%), average (50%) in Europeans, Americans and Australians and low in Asians (<25% in Chinese, Japanese and Koreans). N-acetylation and methylation pathways differ from other conjugation pathways in that they mask an amine with a nonionizable group so that the conjugates are less water soluble than the parent compound. However, certain N-acetlylations facilitate urinary excretion. N-acetylation occurs in two sequential steps via a ping-pong Bi-Bi mechanism. In the first step, the acetyl group from acetyl-CoA is transferred to a cysteine residue in NAT, with consequent release of coenzyme-A. In the second step, the acetyl group is released from the acetylated NAT to the substrate, subsequently regenerating the enzyme.
Typical NAT 2 substrates were chosen as examples. They are paraxanthine, isoniazid and N-hydroxy 4-aminobiphenyl.
Typical NAT 1 substrates were chosen as examples. They are sulfanilamide, 4-aminosalicylate, 4-aminobenzoate and N-hydroxy 4-aminobiphenyl.
Expression cloning of human and rat renal cortex Na/Pi cotransport
N-acetylation occurs in two sequential steps via a ping-pong Bi-Bi mechanism. In the first step, the acetyl group from acetyl-CoA is transferred to a conserved cysteine residue (position 68) in the active site of NAT, with consequent release of coenzyme-A. In the second step, the acetyl group is transferred to the acceptor substrate and the enzyme returns to its initial state.
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.
Abacavir activation proceeds steps of phosphorylation, deamination to yield carbovir monophosphate, and phosphorylation of the latter compound to yield the triphosphate. In addition, abacavir can be conjugated with glucuronide or oxidized to its 5'-carboxylate derivative, the two major forms in which it is excreted from the body (Yuen et al. 2008).
Cytosolic 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).
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.
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.
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.
Xenobiotics that contain either a carboxylic group or an aromatic hydroxylamine group are possible substrates for amino acid conjugation. Xenobiotics with a carboxylic group conjugate with an amino group of amino acids such as glycine, taurine and glutamine. The hydroxylamine group conjugates with the carboxylic group of amino acids such as proline and serine. The amino acid is first activated by an aminoacyl-tRNA-synthetase which then reacts with the hydroxylamine group to form a reactive N-ester. N-esters can degrade to form electrophilic nitrenium (R-N+-R') and carbonium (R-C+H2) ions. The pyrolysis product of tryptophan, an N-hydroxy intermediate, can potentially form these reactive electrophilic ions.
Cytosolic ADH alpha dimer catalyzes the reaction of abacavir and NAD to form abacavir 5'-carboxylate and NADH + H+. Abacavir 5'-carboxylate is one of the major forms in which abacavir is excreted from the body. Studies with purified enzymes in vitro indicate that only the alpha isoform of ADH has this activity. These studies also suggest that the reaction proceeds in two steps via an unstable aldehyde intermediate (Walsh et al. 2002). Whether conversion of the aldehyde to the carboxylate is spontaneous or also catalyzed by ADH has not been established.
Phagosomal maturation (early endosomal stage)
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.
Recent progress in structure-function analyses of Nramp proton-dependent metal-ion transporters
Xenobiotics and endogenous compounds containing carboxylate groups can be activated with coenzyme A to produce acyl-CoA thioesters and then conjugated with the amino groups of glycine or glutamine to form amide-linked conjugates. Clinically important substrates include benzoic acid, phenylacetic acid, and salicylic acid.
Natural resistance-associated macrophage protein 1
Short-chain dehydrogenase/reductase 3 ecNumber1.1.1.300/ecNumber
The Wnt/Ca2+ pathway: a new vertebrate Wnt signaling pathway takes shape
xenobiotic/medium-chain fatty acid:CoA ligases
Xenobiotic/medium-chain fatty acid:CoA ligase
Salicylate and ATP react with coenzyme A to form salicylate CoA, AMP, and pyrophosphate in a reaction catalyzed by xenobiotic/medium-chain fatty acid:CoA ligase (Vessey et al. 2003).
In the body, aspirin (acetylsalicylic acid) is hydrolyzed to salicylic acid. Salicylic acid (2-hydroxybenzoic acid) can then be hydroxylated to yield gentisic acid, conjugated with glucuronate, or conjugated with glycine to yield molecules that are excreted by the kidneys. The third of these conjugation processes is annotated here, and proceeds in two steps. First, salicylate and ATP react with coenzyme A to form salicylate CoA, AMP, and pyrophosphate in a reaction catalyzed by xenobiotic/medium-chain fatty acid:CoA ligase (Vessey et al. 2003). Second, salicylate CoA and glycine react to form salicyluric acid and Coenzyme A (Mawal and Qureshi 1994).
Lead binds to ALAD enzyme displacing half the zinc ions essential for its catalytic activity and inactivating it. Lead is a major environmental toxin and this enzyme is one of its principal molecular targets (Jaffe et al. 2001).
5-Aminolevulinic acid dehydratase (ALAD aka porphobilinogen synthase, PBGS), catalyzes the asymmetric condensation of two molecules of ALA to form porphobilinogen (PBG). The substrate that becomes the acetyl side chain-containing half of PBG is called A-side ALA; the half that becomes the propionyl side chains and the pyrrole nitrogen is called P-ALA (Jaffe 2004). PBG is the first pyrrole formed, the precursor to all tetrapyrrole pigments such as heme and chlorophyll. There are at least eight bonds that are made or broken during this reaction. The active form of the ALAD enzyme is an octamer complexed with eight Zn2+ ions, four that are strongly bound and four that are weakly bound. The four weakly bound ones are dispensible for enzyme activity in vitro (Bevan et al. 1980; Mitchell et al. 2001). Deficiencies of ALAD enzyme in vivo are associated with 5-aminolevulinate dehydratase-deficient porphyria (e.g., Akagi et al. 2000).
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).
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.
Cytosolic porphobilinogen deaminase catalyzes the polymerization of four molecules of porphobilinogen (PBG) to generate hydroxymethylbilane (HMB), an unstable tetrapyrrole. This reaction is the first step in the formation of the tetrapyrrole macrocycle. Two isoforms of porphobilinogen deaminase are generated by alternative splicing, one expresssed in erythroid tissues and one ubiquitously expressed in the body. Deficiencies of both forms of PBG deaminase are associated with acute intermittent porphyria.
Cytosolic uroporphyrinogen 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).
The main sulfur amino acids are methionine, cysteine, homocysteine and taurine. Of these, the first two are proteinogenic. This group of reactions contains all processes that 1) break down sulfur amino acids, 2) interconvert between them, and 3) synthesize them from solved sulfide which comes from sulfate assimilation and reduction. Only plants and microorganisms employ all processes. Humans cannot de novo synthesize any sulfur amino acid, nor convert cysteine to methionine (Brosnan & Brosnan, 2006).
While in humans excess methionine is converted to homocysteine, homocysteine and its transsulfuration product cysteine can be degraded to several end products, two of which, taurine and hydrogen sulfide, have uses in other biological processes (Stipanuk & Ueki 2011).
While the human body is very economical with sulfur amino acids (SAA), superfluous SAA are degraded via cysteine to toxic hydrogen sulfide which must be dealt with. The pathway to oxidize this gas is localized to mitochondria and is highly conserved, pointing back to a time when life was immersed in sulfide-rich waters. The pathway for sulfide oxidation consists of five reactions, one of which, the sulfur transfer from thiosulfate to glutathione, is still to be characterized fully. A mutation in one enzyme has been identified that is associated with ethylmalonyl encephalopathy and where tissue sulfide is elevated (Stipanuk & Ueki 2011).
When SQR is in the oxidized state, it can bind hydrogen sulfide as persulfide to one of its own cysteine residue, the electrons being transferred to ubiquinone. After that the additional sulfur is dioxygenated by another enzyme (ETHE1). The activity of human SQR was deduced from the orthologue in Arenicola marina (Theissen et al. 2003, Hildebrandt & Grieshaber 2008).
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".
Peroxisome proliferator-activated receptor alpha (PPARalpha) and athero-sclerosis
Curr Drug Targets Cardiovasc Haematol Disord 5:513-23
Cytosolic alcohol dehydrogenase catalyzes the reaction of ethanol and NAD+ to form acetaldehyde and NADH + H+. The active form of the enzyme is a dimer with one zinc ion bound to each protein subunit. In the body, alcohol dehydrogenase is present in the liver, kidney, lung and gastric mucosa. Six genes encode proteins active in ethanol oxidation: ADH1A, ADH1B, ADH1C, ADH4, ADH6, and ADH7 (Lange et al. 1976; Yin et al. 1985; Li et al. 1978; Bosron et al. 1979; Moreno and Pares 1991; Yokoyama et al. 1994; Chen and Yoshida 1991). ADH1A, B and C proteins can associate to form homodimers or heterodimers; ADH4, 6, and 7 proteins each form homodimers. Expression of ADH1A, B and C is developmentally regulated: ADH1A protein is abundant in the fetus, but expressed only at low levels in adulthood, when ADH1B and C proteins are abundant (Edenberg 2000). The various dimers differ substantially in the efficiency with which they oxidize ethanol. The ADH1B homodimer and heterodimers containing at least one 1B monomer are the most active towards ethanol (Yin et al. 1985). In addition, common polymorphic variants of ADH1B and C proteins differ substantially in this respect (Murray and Price 1972).
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).
Cytosolic ACSS2 (acetyl-coenzyme A synthetase) catalyzes the reaction of acetate, coenzyme A, and ATP to form acetyl-CoA, AMP, and pyrophosphate (Luong et al. 2000).
Human betaine-homocysteine methyltransferase (BHMT) and BHMT2: common gene sequence variation and functional characterization
Ethanol and related alcohols can be ingested as part of the diet and are formed by microorganisms in the intestinal tract. Ethanol oxidation to acetate occurs primarily in liver cells in a multistep process first described by Racker (1949). First, in the cytosol, ethanol is oxidized to acetaldehyde, with the formation of NADH. Second, in the mitochondrion, acetaldehyde is oxidized to acetate with the formation of NADH. Finally, acetate in the mitochondrion can be condensed with coenzyme A to form acetyl CoA. Polymorphisms in the enzymes catalyzing the first two steps are associated with variation in the efficiency of alcohol catabolism in human populations (Chen et al. 1999; Lange et al. 1976; Jornvall 1985). The molecular mechanism by which cytosolic acetaldehyde enters the mitochondrial matrix is not known (Lemasters 2007). Cytosolic enzymes capable of oxidizing acetaldehyde to acetate have also been identified and characterized in vitro (Inoue et al. 1979) so a purely cytosolic pathway for ethanol oxidation to acetate and conversion to acetyl-CoA can be annotated. The role of this pathway in vivo is unclear, though limited attempts to correlate deficiencies in the cytosolic enzyme with alcohol intolerance have yielded suggestive data (Yoshida et al. 1989). Additional peroxisomal and microsomal pathways for the oxidation of ethanol to acetaldehyde have been described; their physiological significance is unclear and they are not annotated here.
Phase 1 of metabolism is concerned with functionalization, that is the introduction or exposure of functional groups on the chemical structure of a compound. This provides a 'handle' for phase 2 conjugating species with which to react with. Many xenobiotics are lipophilic and almost chemically inert (e.g. PAHs) so would not necessarily undergo a phase 2 reaction. Making them more chemically reactive would facilitate their excretion but also increases their chance of reacting with cellular macromolecules (e.g. proteins, DNA). There is a fine balance between producing a more reactive metabolite and conjugation reactions. There are two groups of enzymes in phase 1 - oxidoreductases and hydrolases. Oxidoreductases introduce an oxygen atom into or remove electrons from their substrates. The major oxidoreductase enzyme system is called the P450 monooxygenases. Other systems include flavin-containing monooxygenases (FMO), cyclooxygenases (COX) and monoamine oxidases (MAO). Hydrolases hydrolyse esters, amides, epoxides and glucuronides.
UDP-glucose dehydrogenase (UGDH) catalyzes the conversion of UDP-glucose to UDP-glucuronic acid. The cytosolic enzyme is active as a hexamer and performs two successive oxidations to convert the 6'-hydroxyl of UDP-glucose to a carboxylate with concurrent reduction of 2 mol of NAD+ to NADH.
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.
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).
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).
Porphyrins are heterocyclic macrocycles, consisting of four pyrrole subunits (tetrapyrrole) linked by four methine (=CH-) bridges. The extensive conjugated porphyrin macrocycle is chromatic and the name itself, porphyrin, is derived from the Greek word for purple. The aromatic character of porphyrins can be seen by NMR spectroscopy. Porphyrins readily combine with metals by coordinating them in the central cavity. Iron (heme) and magnesium (chlorophyll) are two well known examples although zinc, copper, nickel and cobalt form other known metal-containing phorphyrins. A porphyrin which has no metal in the cavity is called a free base. Some iron-containing porphyrins are called hemes (heme-containing proteins or hemoproteins) and these are found extensively in nature ie. hemoglobin. Hemoglobin is quantitatively the most important hemoprotein. The hemoglobin iron is the transfer site of oxygen and carries it in the blood all round the body for cell respiration. Other examples are cytochromes present in mitochondria and endoplasmic reticulum which takes part in electron transfer events, catalase and peroxidase whic protect the body against the oxidant hydrogen peroxide and tryptophan oxygenase which is present in intermediary metabolism. Hemoproteins are synthesized in all mammalian cells and the major sites are erythropoietic tissue and the liver. The processes by which heme is synthesized, transported, and metabolized are a critical part of human iron metabolism (Severance and Hamze 2009); here the core processes of heme biosynthesis and catabolism have been annotated.
Eight enzymes are involved in heme biosynthesis, four each in the mitochondria and the cytosol. The process starts in the mitochondria with the condensation of succinyl CoA (from the TCA cycle) and glycine to form 5-aminolevulinate (ALA). The next four steps take place in the cytosol. Two molecules of ALA are condensed to form the monopyrrole porphobilinogen (PBG). The next two steps convert four molecules of PBG into the cyclic tetrapyrrole uroporphyringen III, which is then decarboxylated into coproporphyrinogen III. The last three steps occur in the mitochondria and involve modifications to the tetrapyrrole side chains and finally, insertion of iron. In addition to these synthetic steps, a spontaneous cytosolic reaction allows the formation of uroporphyringen I which is then enzymatically decarboxylated to coproporphyrinogen I, which cannot be metabolized further in humans. Also, lead can inactivate ALAD, the enzyme that catalyzes PBG synthesis, and ferrochelatase, the enzyme that catalyzes heme synthesis. The porphyrias are disorders that arise from defects in the enzymes of heme biosynthesis. Defective pathway enzymes after ALA synthase result in accumulated substrates which can cause either skin problems, neurological complications, or both due to their toxicity in higher concentrations. They are broadly classified as hepatic porphyrias or erythropoietic porphyrias, based on the site of the overproduction of the substrate. Each defect is described together with the reaction it affects.
The triglyceride lipases of the pancreas
Molecular cloning, primary structure, and expression of the human growth factor-activatable Na+/H+ antiporter
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.
As it hydrolyzes a guanidino group within agmatine and also contains signature amino acid residues that act as ligand binding sites for the potential Mn(++) cofactor, agmatinase is classified as a member of the arginase superfamily (Morris, 2003).
Creatine kinase octamers associated with the inner mitochondrial membrane catalyze the reaction of creatine and ATP to form phosphocreatine and ADP. Two mitochondrial creatine kinase proteins have been identified, one encoded by CKMT1A and B that is found in many tissues and one encoded by CKMT2 that is found in sarcomeres (Haas et al. 1988; Haas and Straus 1990). Studies of sarcomeric creatine kinase octamers suggest that their organization and association with phospholipids in the inner mitochondrial membrane may facilitate energy transfer from ATP generated in the mitochondrial matrix to cytosolic phosphocreatine (Khuchua et al. 1998; Schlattner et al. 2004).
In humans, creatine is synthesized primarily in the liver and kidney, from glycine, arginine, and S-adenosylmethionine, in a sequence of two reactions. From the liver, creatine is exported to tissues such as skeletal muscle and brain, where it undergoes phosphorylation and serves as a short-term energy store. The mechanism by which creatine leaves producer tissues is unclear, but its uptake by consumer tissues is mediated by the SLC6A8 transporter. Once formed, phosphocreatine undergoes a slow spontaneous reaction to form creatinine, which is excreted from the body.
Cytosolic creatine kinase catalyzes the reaction of creatine and ATP to form phosphocreatine and ADP. The active form of the enzyme is a dimer. Monomers of the cytosolic enzyme occur in two isoforms, B and M, so called because of their abundance in brain and muscle respectively. The enzyme is widely expressed in the body and many tissues express both isoforms. Both homo- (BB, MM) and heterodimers (BM) are catalytically active.
Carnitine is synthesized in four steps from trimethyllysine (generated in turn by the S-adenosyl-methionine-mediated methylation of lysine residues in proteins, followed by protein hydrolysis). The enzymes that catalyze the first three steps of carnitine synthesis, converting trimethyllysine to gamma-butyrobetaine, are widely distributed in human tissues. The enzyme that catalyzes the last reaction, converting gamma-butyrobetaine to carnitine, is found only in liver and kidney cells, and at very low levels in brain tissues. Other tissues that require carnitine, such as muscle, are dependent on transport systems that mediate its export from the liver and uptake by other tissues (Kerner and Hoppel 1998).
Cytosolic 4-trimethylaminobutyraldehyde dehydrogenase tetramer (ALDH9A1) catalyzes the reaction of NAD+', and 4-trimethylammoniobutanal to form 4-Trimethylammoniobutanoate and NADH + H+ (Kurys et al. 1989; Vaz et al. 2000).
The urea cycle yields urea, the major form in which excess nitrogen is excreted from the human body, and the amino acid arginine (Brusilow and Horwich 2001). It consists of four reactions: that of ornithine and carbamoyl phosphate to form citrulline, of citrulline and aspartate to form argininosuccinate, the cleavage of argininosuccinate to yield fumarate and arginine, and the cleavage of arginine to yield urea and re-form ornithine. The carbamoyl phosphate consumed in this cycle is synthesized in the mitochondria from bicarbonate and ammonia, and this synthesis in turn is dependent on the presence of N-acetylglutamate, which allosterically activates carbamoyl synthetase I enzyme. The synthesis of N-acetylglutamate is stimulated by high levels of arginine. Increased levels of free amino acids, indicated by elevated arginine levels, thus stimulate urea synthesis. Two enzymes catalyze the hydrolysis of arginine to yield ornithine and urea. Cytosolic ARG1 is the canonical urea cycle enzyme. Mitochondrial ARG2 likewise catalyzes urea production from arginine and may have a substantial sparing effect in patients lacking ARG1 enzyme, so its reaction is annotated here although the role of ARG2 under normal physiological conditions remains unclear.
Arginase 2 (ARG2) trimer catalyzes the hydrolysis of arginine to form urea and ornithine (Cama et al. 2003). ARG2 is localized to the mitochondrion (Gotoh ea 1996). The enzyme is expressed in many tissues in addition to liver and while its function appears to mitigate the effects of ARG1 deficiency on urea synthesis, its normal physiological roles have not been fully defined (Iyer et al. 1998).
Cytosolic Arginase 1 (ARG1) trimer catalyzes the hydrolysis of arginine to yield ornithine and urea (DiCostanzo et al. 2005). Patients expressing mutated forms of the enzyme with diminished in vitro arginase activity can accumulate arginine to pathogenic levels in the blood (e.g., Uchino et al. 1995).
Cytosolic argininosuccinate lyase (ASL) catalyzes the reversible reaction of argininosuccinate to form fumarate and arginine. The enzyme is a homotetramer (Turner et al. 1997). The function of the human enzyme in vivo is inferred from the defective argininosuccinate lyase enzyme activity observed in patients with mutant forms of the ASL gene (e.g., Walker et al. 1990).
Identification and characterization of the gene encoding the human phosphopantetheine adenylyltransferase and dephospho-CoA kinase bifunctional enzyme (CoA synthase)
Peroxisomal GRHPR catalyzes the reaction of glyoxylate and NADPH + H+ to form glycolate and NADP+. The active form of the enzyme is a monomer (Rumsby and Cregeen 1999); mutations in it are associated with primary hyperoxaluria type II (Cramer et al. 1999).
Glyoxylate is generated in the course of glycine and hydroxyproline catabolism and can be converted to oxalate. In humans, this process takes place in the liver. Defects in two enzymes of glyoxylate metabolism, alanine:glyoxylate aminotransferase (AGXT) and glycerate dehydrogenase/glyoxylate reductase (GRHPR), are associated with pathogenic overproduction of oxalate (Danpure 2005). The reactions that interconvert glycine, glycolate, and glyoxylate and convert glyoxylate to oxalate have been characterized in molecular detail in humans. A reaction sequence for the conversion of hydroxyproline to glyoxylate has been inferred from studies of partially purified extracts of rat and bovine liver but the enzymes involved in the corresponding human reactions have not been identified.
S-adenosylmethionine (SAM) is an essential metabolite in all cells. SAM is a precursor in the synthesis of polyamines. Methionine adenosyltransferase (MAT; EC 2.5.1.6) catalyzes the only known SAM biosynthetic reaction from methionine and ATP. In mammalian tissues, three different forms of MAT (MAT I, MAT III and MAT II) have been identified that are the product of two different genes (MAT1A and MAT2A). A third gene MAT2B has been identified and is known to be a part of MAT II heterotetramer complex.
Remethylation of homocysteine to methionine can also happen using betaine as a methyl donor. This reaction is also part of choline catabolism (Li et al. 2008).
Mechanisms for the role of tetrahydrobiopterin in endothelial function and vascular disease
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).
Catecholamines and thyroxine are synthesized from tyrosine, and serotonin and melatonin from tryptophan.
Thyroxine (3,5,3',5'-tetraiodothyronine, T4) promotes normal growth and development. It also regulates heat and energy production. T4 is released from the thyroid gland, the largest endocrine organ in the human body. The primary hormone released is T4 although T3 (3,5,3'-triiodothyronine) is also released in small quantities. Tyrosine residues in thyroglobulin (a glycoprotein scaffold containing many tyrosine residues) are iodinated to form mono- or diiodo-tyrosine which can then couple to form either T3 or T4.
L-ornithine is converted into putrescine by ODC holoenzyme complex.Putrescine is subsequent used for polyamine synthesis.
Agmatine is an amine that is formed by decarboxylation of L-arginine by the enzyme arginine decarboxylase (ADC) and hydrolyzed by the enzyme agmatinase to putrescine. Agmatine binds to several target receptors in the brain and has been proposed as a novel neuromodulator (Reghunathan 2006). Agmatine has the potential to serve in the coordination of the early and repair phase pathways of arginine in inflammation (Satriano, 2003).
Iodide (I-) is transported from blood serum into the thyroid cell by the Na+/I- symporter (sodium/iodide). This intrinsic membrane protein uses energy from the inward movement of Na+ to drive the process and accumulate I- in the cell, maintaining a cellular concentration 30-40 times that of the serum concentration. This process, also called the iodide trap, is stimulated by TSH (thyroid stimulating hormone) and is saturable by large amounts of I-.
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:
Macromolecular assemblage of aminoacyl-tRNA synthetases: identification of protein-protein interactions and characterization of a core protein
Enzymatic synthesis and properties of 5-phosphoribosylpyrophosphate
Ornithine delta-aminotransferase mutations in gyrate atrophy. Allelic heterogeneity and functional consequences.
Characterization of the COQ5 gene from Saccharomyces cerevisiae. Evidence for a C-methyltransferase in ubiquinone biosynthesis
Glutamate transporter expression and function in human glial progenitors
A humble hexose monophosphate pathway metabolite regulates short- and long-term control of lipogenesis
Molecular cloning of human mevalonate kinase and identification of a missense mutation in the genetic disease mevalonic aciduria
The remarkable structural and functional organization of the eukaryotic pyruvate dehydrogenase complexes.
Exploring the role of the active site cysteine in human muscle creatine kinase
Cloning and characterization of a second human CTP:phosphocholine cytidylyltransferase
Zinc efflux and compartmentalization by the SLC30 family
AKT/PKB signaling: navigating downstream
The human Aquaporin-5 gene. Molecular characterization and chromosomal localization
Molecular cloning and functional expression of cDNAs encoding a human Na+-nucleoside cotransporter (hCNT1)
Expression and characterization of the human mitochondrial leucyl-tRNA synthetase
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
Molybdenum cofactors, enzymes and pathways
The glucose-lactic acid cycle and gluconeogenesis
Isozymes of human phosphofructokinase in blood cells and cultured cell lines: molecular and genetic evidence for a trigenic system
Molecular and biochemical characterization of rat gamma-trimethylaminobutyraldehyde dehydrogenase and evidence for the involvement of human aldehyde dehydrogenase 9 in carnitine biosynthesis.
Glucuronidation and the UDP-glucuronosyltransferases in health and disease
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
Substrate specificity of human nucleoside-diphosphate kinase revealed by transient kinetic analysis
Primary structure of human deoxycytidylate deaminase and overexpression of its functional protein in Escherichia coli
Synthesis of substrates in N-glycan biosythesis
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
Cloning and functional expression of human aquaporin8 cDNA and analysis of its gene
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Studies on the substrate specificity of a carboxyl ester hydrolase from human pancreatic juice. II. Action on cholesterol esters and lipid-soluble vitamin esters.
Studies on the substrate specificity of a carboxyl ester hydrolase from human pancreatic juice. I. Action on carboxyl esters, glycerides and phospholipids.
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Phospholipid synthesis in a membrane fraction associated with mitochondria
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Isoleucylation properties of native human mitochondrial tRNAIle and tRNAIle transcripts. Implications for cardiomyopathy-related point mutations (4269, 4317) in the tRNAIle gene
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_136127.5
Structural determinants of water permeation through aquaporin-1
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Human phosphoribosylpyrophosphate synthetase
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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=76194
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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_2732.2
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Control of pyrimidine biosynthesis in human lymphocytes. Simultaneous increase in activities of glutamine-utilizing carbamyl phosphate synthetase and aspartate transcarbamylase in phytohemagglutinin-stimulated human peripheral lymphocytes and their enzyme co-purification
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Nitric oxide, tetrahydrobiopterin, oxidative stress, and endothelial dysfunction in hypertension
Identification of three cationic amino acid transporters in placental trophoblast: cloning, expression, and characterization of hCAT-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_157604.3
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Evidence for the presence of phospholipid hydroperoxide glutathione peroxidase in human platelets: implications for its involvement in the regulatory network of the 12-lipoxygenase pathway of arachidonic acid metabolism
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Intracellular mechanisms of antigen cross presentation in dendritic cells
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Cloning and expression of a novel Na(+)-dependent neutral amino acid transporter structurally related to mammalian Na+/glutamate cotransporters
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2-Amino-3-carboxymuconate semialdehyde [ChEBI:29044]
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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_7394.2
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=171126
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_154250.3
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Cloning of a complete protein-coding sequence of human platelet-type phosphofructokinase isozyme from pancreatic islet.
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Structure of a high-resolution crystal form of human triosephosphate isomerase: improvement of crystals using the gel-tube method
Acta Crystallogr Sect F Struct Biol Cryst Commun 61:346-9
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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_7775.3
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(2R)-2-Hydroxy-3-(phosphonooxy)-propanal [ChEBI:29052]
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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_154782.3
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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_3756.1
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=76116
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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_4327.2
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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=4229807
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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_149967.4
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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_148763.4
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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_2705.2
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=73871
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29374
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4229756
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4230227
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_97151.9
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=4231288
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_80882.9
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=73917
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3208.2
Identification of mutations associated with peroxisome-to-mitochondrion mistargeting of alanine/glyoxylate aminotransferase in primary hyperoxaluria type 1
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Aquaporin-3 water channel localization and regulation in rat kidney
Alteration of decreased plasma NO metabolites and platelet NO synthase activity by paroxetine in depressed patients
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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=31649
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=188458
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_18103.2
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=113596
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5229.1
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_95478.9
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=4231289
Reversible lysine acetylation controls the activity of the mitochondrial enzyme acetyl-CoA synthetase 2
Regulation of nitric oxide-sensitive guanylyl cyclase
Reversible ATP-dependent transition between two forms of human cytosolic thymidine kinase with different enzymatic properties
HGPRT homotetramer (name copied from entity in Homo sapiens)
APRT homodimer (name copied from entity in Homo sapiens)
AMPD3 tetramer (name copied from entity in Homo sapiens)
adenylosuccinate synthetase 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)
CAT tetramer (name copied from entity in Homo sapiens)
5'-nucleotidase, ecto (CD73) holoenzyme (name copied from entity in Homo sapiens)
2'-Deoxyinosine 5'-phosphate [ChEBI:28806]
Structural basis of Wnt recognition by Frizzled
adenylosuccinate synthetase like 1 holoenzyme (name copied from entity in Homo sapiens)
adenylosuccinate synthetase holoenzyme dimer (name copied from entity in Homo sapiens)
cDNA cloning of carboxyl ester lipase from human pancreas reveals a unique proline-rich repeat unit
PPAT dimer (name copied from entity in Homo sapiens)
fumarate hydratase tetramer (name copied from entity in Homo sapiens)
PAICS octamer (name copied from entity in Homo sapiens)
PPAT tetramer (name copied from entity in Homo sapiens)
ATIC dimer (name copied from entity in Homo sapiens)
adenylosuccinate lyase tetramer (name copied from entity in Homo sapiens)
IMP (inosine monophosphate) dehydrogenase 1 tetramer (name copied from entity in Homo sapiens)
adenylosuccinate synthetase like 1 holoenzyme dimer (name copied from entity in Homo sapiens)
Role of platelet-derived growth factors in physiology and medicine
Metabolism of highly unsaturated n-3 and n-6 fatty acids
alpha-ketoglutarate dehydrogenase E1 holoenzyme (name copied from entity in Homo sapiens)
alpha-keto acid dehydrogenase E3 holoenzyme (name copied from entity in Homo sapiens)
Bile salt-dependent lipase: its pathophysiological implications
alpha-keto acid dehydrogenase E3 homodimer (name copied from entity in Homo sapiens)
alpha-ketoglutarate dehydrogenase complex (name copied from entity in Homo sapiens)
NNT dimer (name copied from entity in Homo sapiens)
Citrate Synthase Holoenzyme (name copied from entity in Homo sapiens)
lactate dehydrogenase B4 complex (name copied from entity in Homo sapiens)
lactate dehydrogenase AB3 complex (name copied from entity in Homo sapiens)
lactate dehydrogenase A4 complex (name copied from entity in Homo sapiens)
MHC class I endosomal and lysosomal trafficking coincides with exogenous antigen loading in dendritic cells
alpha-ketoglutarate dehydrogenase E1 homodimer (name copied from entity in Homo sapiens)
alpha-ketoglutarate dehydrogenase E2 holoenzyme (name copied from entity in Homo sapiens)
palmitoylated, myristoylated eNOS dimer (name copied from entity in Homo sapiens)
PDSS1:Mg2+ (name copied from entity in Homo sapiens)
DHFR dimer (name copied from entity in Homo sapiens)
myristoylated eNOS dimer (name copied from entity in Homo sapiens)
Cloning of a new aquaporin (AQP10) abundantly expressed in duodenum and jejunum
GPX1 tetramer (name copied from entity in Homo sapiens)
PDSS1/2 tetramer (name copied from entity in Homo sapiens)
GPX2 tetramer (name copied from entity in Homo sapiens)
Functional characterization and genomic organization of the human Na(+)-sulfate cotransporter hNaS2 gene (SLC13A4)
lactate dehydrogenase A2B2 complex (name copied from entity in Homo sapiens)
lactate dehydrogenase A3B complex (name copied from entity in Homo sapiens)
Cross-talk between the endocytic pathway and the endoplasmic reticulum in cross-presentation by MHC class I molecules
5'-Phosphoribosyl-5-aminoimidazole [ChEBI:28843]
The human purH gene product, 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase
Distribution of AQP2 and AQP3 water channels in human tissue microarrays
2xMOCS2-CO-S(1-):2xMOCS2B (name copied from entity in Homo sapiens)
2xMOCS2A:2xMOCS2B (name copied from entity in Homo sapiens)
2xMTHFD1 (name copied from entity in Homo sapiens)
holo-MOCS1 (name copied from entity in Homo sapiens)
4x(Btn-PC:Mn2+) (name copied from entity in Homo sapiens)
2xNAPRT1 (name copied from entity in Homo sapiens)
3xPPCDC:3xFMN (name copied from entity in Homo sapiens)
ITPA dimer (name copied from entity in Homo sapiens)
NME4 hexamer (name copied from entity in Homo sapiens)
Tetrahydrobiopterin biosynthesis, regeneration and functions
Functional characterization of human aquaporin 9 as a facilitative glycerol carrier
Assembly and export of MHC class I peptide ligands
TK1 tetramer (name copied from entity in Homo sapiens)
CDA tetramer (name copied from entity in Homo sapiens)
nucleoside diphosphate kinase 1A:5B heterohexamer (name copied from entity in Homo sapiens)
TS dimer (name copied from entity in Homo sapiens)
TYMP dimer (name copied from entity in Homo sapiens)
UCK1 tetramer (name copied from entity in Homo sapiens)
UCK2 tetramer (name copied from entity in Homo sapiens)
dihydroorotate dehydrogenase holoenzyme (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)
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Tryptophan nutrition and metabolism: an overview
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Involvement of enzymes other than CYPs in the oxidative metabolism of xenobiotics
Expert Opin Drug Metab Toxicol 2:895-921
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Beta-amino acids: mammalian metabolism and utility as alpha-amino acid analogues
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Purification and properties of human erythrocyte glutathione peroxidase
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Structure, function, and genomic organization of human Na(+)-dependent high-affinity dicarboxylate transporter
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Human cytoplasmic 3-hydroxy-3-methylglutaryl coenzyme A synthase: expression, purification, and characterization of recombinant wild-type and Cys129 mutant enzymes
3alpha,7alpha,12alpha-Trihydroxy-5beta-cholanic acid
Thematic Review Series: Proteomics. An integrated omics analysis of eicosanoid biology
Mutation in the glutamate transporter EAAT1 causes episodic ataxia, hemiplegia, and seizures
Glucose and cAMP regulate the L-type pyruvate kinase gene by phosphorylation/dephosphorylation of the carbohydrate response element binding protein
Three enzymatic activities catalyze the oxidation of sulfide to thiosulfate in mammalian and invertebrate mitochondria
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Baillieres Clin Endocrinol Metab 7:551-86
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alpha-linolenic (omega3) and linoleic (omega6) acid metabolism
Folic acid: nutritional biochemistry, molecular biology, and role in disease processes
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N-hydroxy-4-aminobiphenyl O-acetylated conjugate
N-hydroxy-4-aminobiphenyl O-acetylated conjugate [ChEBI:16395]
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Identification of differentiation-associated brain-specific phosphate transporter as a second vesicular glutamate transporter (VGLUT2)
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Molecular characterization of histidinemia: identification of four missense mutations in the histidase gene
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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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NNT (nicotinamide nucleotide transhydrogenase) associated with the inner mitochondrial membrane catalyzes the reaction of mitochondrial NADPH and NAD+ to form NADP+ and NADH. The reaction is coupled to the translocation of a proton across the inner mitochondrial membrane into the mitochondrial matrix (White et al, 2000). The active form of NNT is inferred to be a homodimer based on the known structure of its bovine homolog (Yamaguchi and Hatefi 1991).
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Mitochondrial citrate synthase dimer catalyzes the irreversible reaction of acetyl-CoA, water, and oxaloacetate to form citrate and coenzyme A. This reaction is the entry point of two-carbon units into the citric acid cycle. The reaction is subject to allosteric regulation. The gene encoding the human enzyme has been cloned (Goldenthal et al. 1998), but the enzyme has not been characterized in detail - its properties are inferred from those of the well-studied homologous pig enzyme (e.g., Morgunov and Srere 1998).
Cytosolic lactate dehydrogenase catalyzes the freely reversible reaction of lactate and NAD+ to form pyruvate and NADH + H+. In liver parenchymal cells, this reaction allows lactate from red blood cells and exercising muscle to be converted to pyruvate which in turn is typically used for gluconeogenesis which also consumes the NADH from the reaction. Lactate dehydrogenase is active as a tetramer. Two isoforms of lactate dehydrogenase, A and B, are widely expressed in human tissues, and all five tetramers - A4, A3B, A2B2, AB3, and B4 - are found. A third isoform, C, and its tetramer, C4, are found in testis.
Pyruvate sits at an intersection of key pathways of energy metabolism. It is the end product of glycolysis and the starting point for gluconeogenesis, and can be generated by transamination of alanine. It can be converted by the pyruvate dehydrogenase complex to acetyl CoA (Reed and Hackert 1990) which can enter the TCA cycle or serve as the starting point for the syntheses of long chain fatty acids, steroids, and ketone bodies depending on the tissue and metabolic state in which it is formed. It also plays a central role in balancing the energy needs of various tissues in the body. Under conditions in which oxygen supply is limiting, e.g., in exercising muscle, or in the absence of mitochondria, e.g., in red blood cells, re-oxidation of NADH produced by glycolysis cannot be coupled to generation of ATP. Instead, re-oxidation is coupled to the reduction of pyruvate to lactate. This lactate is released into the blood, and is taken up primarily by the liver, where it is oxidized to pyruvate and can be used for gluconeogenesis (Cori 1981).
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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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Cytosolic lactate dehydrogenase catalyzes the reversible reaction of pyruvate and NADH + H+ to form lactate and NAD+. In the body under anaerobic conditions such as are found in red blood cells or rapidly exercising skeletal muscle, this reaction regenerates NAD+, allowing the continuation of glycolysis. Lactate dehydrogenase is active as a tetramer. Two isoforms of lactate dehydrogenase, A and B, are widely expressed in human tissues, and all five tetramers - A4, A3B, A2B2, AB3, and B4 - are found. A third isoform, C, and its tetramer, C4, are found in testis.
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Tetrahydrobiopterin (BH4) is an essential co-factor for the aromatic amino acid hydroxylases and glycerol ether monooxygenase and it regulates nitric oxide synthase (NOS) activity. Inherited BH4 deficiency leads to hyperphenylalaninemia, and dopamine and neurotransmitter deficiency in the brain. BH4 maintains enzymatic coupling to L-arginine oxidation to produce NO. Oxidation of BH4 to BH2 results in NOS uncoupling, resulting in superoxide (O2.-) formation rather than NO. Superoxide rapidly reacts with NO to produce peroxynitrite which can further uncouple NOS. These reactive oxygen species (superoxide and peroxynitrite) can contribute to increased oxidative stress in the endothelium leading to atherosclerosis and hypertension (Thöny et al. 2000, Crabtree & Channon 2011, Schulz et al. 2008, Schmidt & Alp 2007). The synthesis, recycling and effects of BH4 are shown here. Three enzymes are required for the de novo biosynthesis of BH4 and two enzymes for the recycling of BH4.
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Originally identified as endothelium-derived relaxing factor, eNOS derived NO is a critical signaling molecule in vascular homeostasis. It regulates blood pressure and vascular tone, and is involved in vascular smooth muscle cell proliferation, platelet aggregation, and leukocyte adhesion. Loss of the bioavailability of endothelium derived NO is a key feature of endothelial dysfunction and is implicated in the pathogenesis of cardiovascular disease such as hypertension and atherosclerosis. The endothelial isoform eNOS is unique among the nitric oxide synthase (NOS) family in that it is co-translationally modified at its amino terminus by myristoylation and is further acylated by palmitoylation (two residues next to the myristoylation site). These modifications target eNOS to the plasma membrane caveolae and lipid rafts. eNOS activation and subsequent nitric oxide (NO) production is stimulated by a variety of stimuli, such as fluid shear stress generated by blood flow, vascular endothelial growth factor (VEGF), bradykinin, estrogen, insulin, and angiopoietin. The activity of eNOS is further regulated by numerous post-translational modifications, including protein-protein interactions, phosphorylation, and subcellular localization. Following activation, eNOS shuttles between caveolae and other subcellular compartments such as the noncaveolar plasma membrane portions, Golgi apparatus, and perinuclear structures. This subcellular distribution is variable depending upon cell type and mode of activation. Subcellular localization of eNOS has a profound effect on its ability to produce NO as the availability of its substrates and cofactors will vary with location. eNOS is primarily particulate, and depending on the cell type, eNOS can be found in several membrane compartments: plasma membrane caveolae, lipid rafts, and intracellular membranes such as the Golgi complex. In addition, it has been reported that eNOS can also be detected in the nucleus, however, the conditions associated with nuclear localization of eNOS and its precise role in this cell compartment remains to be determined. Several stimuli can trigger a transient displacement of eNOS from the plasma membrane to other subcellular locations. This process can be mediated through various protein-protein interactions and/or changes in post-translational modifications. Knowledge of the precise molecular mechanisms governing the intracellular redistribution process is still rather limited.
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eNOS activity is regulated by numerous post-translational modifications including phosphorylation and acylation, which also modulate its interactions with other proteins and its subcellular localization. In general, following myristoylation and palmitoylation, eNOS localizes to caveolae in the plasma membrane, where in resting cells, it is bound to caveolin and remains inactive. Several agonists that raise intracellular calcium concentrations promote calmodulin binding to eNOS and the dissociation of caveolin from the enzyme, leading to an activated eNOS-calmodulin complex. Phosphorylation plays a significant role in regulating eNOS activity, especially the phosphorylation of Ser1177, located within the reductase domain, which increases enzyme activity by enhancing reductase activity and calcium sensitivity. In unstimulated, cultured endothelial cells, Ser1177 is rapidly phosphorylated following a variety of stimuli: fluid shear stress, insulin, estrogen, VEGF, or bradykinin. The kinases involved in this process depend upon the stimuli applied. For instance, shear stress phosphorylates Ser1177 by activating Akt and PKA; insulin activates both Akt and the AMP-activated protein kinase (AMPK); estrogen and VEGF mainly phosphorylate eNOS via Akt; whereas the bradykinin-induced phosphorylation of Ser1177 is mediated by CaMKII. When Ser1177 is phosphorylated, NO production is increased several-fold above basal levels. The phosphorylation of a threonine residue (Thr 495), located in the CaM binding domain, is associated with a decrease in eNOS activity. When this residue is dephosphorylated, substantially more CaM binds to eNOS and elevates enzyme activity. Stimuli associated with dephosphorylation of Thr495 (e.g., bradykinin, histamine, and Ca2+ ionophores) also increase Ca2+ levels resulting in the phosphorylation of Ser1177. Additional phosphorylation sites, such as Ser114 and Ser633, and tyrosine phosphorylation have all been detected, but their functional relevance remains unclear. It is speculated that the tyrosine phosphorylation of eNOS is unlikely to affect enzyme activity directly, but more likely to impact the protein-protein interactions with associated scaffolding and regulatory proteins.
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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).
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Once depalmitoylated, it's proposed that eNOS is displaced from the plasma membrane and redistributed to other intracellular membranes, including the Golgi, where re-palmitoylation occurs. The mechanism of transport from the plasma membrane is still unknown.
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D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP
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dihydroxyacetone phosphate <=> D-glyceraldehyde 3-phosphate
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1,3-Bisphosphoglycerate and ADP react to form 3-phosphoglycerate and ATP
1,3-bisphospho-D-glycerate + ADP <=> 3-phospho-D-glycerate + ADP
2-Phospho-D-glycerate <=> Phosphoenolpyruvate + H2O
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Nitric Oxide Synthase (NOS) produces Nitric Oxide (NO)
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Glucose 6-phosphate is isomerized to form fructose-6-phosphate
alpha-D-glucose 6-phosphate <=> D-fructose 6-phosphate
Fructose 6-phosphate and ATP react to form fructose 2,6-bisphosphate and ADP
D-fructose 6-phosphate + ATP => D-fructose 2,6-bisphosphate + ADP
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Pyruvate, CO2, and ATP react to form oxaloacetate, ADP, and orthophosphate
Pyruvate + CO2 + ATP => ADP + Orthophosphate + Oxaloacetate
phosphoenolpyruvate + ADP => pyruvate + ATP
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A human amphotropic retrovirus receptor is a second member of the gibbon ape leukemia virus receptor family
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Folding of glycoproteins: toward understanding the biophysics of the glycosylation code
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Human glucose-6-phosphate dehydrogenase: the crystal structure reveals a structural NADP(+) molecule and provides insights into enzyme deficiency
The citric acid (TCA) cycle and respiratory electron transport
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Na+/Ca2+-K+ exchangers (NCKX): functional properties and physiological roles
A revised picture of the E2F transcriptional network and RB function.
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Molecular physiology of bestrophins: multifunctional membrane proteins linked to best disease and other retinopathies
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Site-directed mutagenesis of the distal basic cluster of pancreatic bile salt-dependent lipase
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Investigation of coenzyme Q biosynthesis in human fibroblast and HepG2 cells
5-Hydroxy-12-oxo-delta5,8,11,14-eicosapolyenoic acid
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Expression of aquaporin 8 in colonic epithelium with diarrhoea-predominant irritable bowel syndrome
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The neurotransmitter receptor-anchoring protein gephyrin reconstitutes molybdenum cofactor biosynthesis in bacteria, plants, and mammalian cells
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beta-Hydroxy-beta-methylglutaryl coenzyme A
Complete amino acid sequence of human phosphoglycerate kinase. Cyanogen bromide peptides and complete amino acid sequence.
Neutral amino acid transporter ASCT2 displays substrate-induced Na+ exchange and a substrate-gated anion conductance
Isolation and characterization of a hydroxyacid-oxoacid transhydrogenase from rat kidney mitochondria
Genomic structure and expression of the human heme A:farnesyltransferase (COX10) gene
(R)-2-Hydroxy-3-(phosphonooxy)-1-monoanhydridewith phosphoric propanoic acid
An updated overview on Wnt signaling pathways: a prelude for more
Nitric oxide stimulates guanylate cyclase
The dynamic phagosomal proteome and the contribution of the endoplasmic reticulum
The energy-less red blood cell is lost: erythrocyte enzyme abnormalities of glycolysis
The sequence of a human mitochondrial glycerol-3-phosphate dehydrogenase-encoding cDNA
The 2.0 A structure of human ferrochelatase, the terminal enzyme of heme biosynthesis.
Crystal structure of human branched-chain alpha-ketoacid dehydrogenase and the molecular basis of multienzyme complex deficiency in maple syrup urine disease.
Cdc6 is regulated by E2F and is essential for DNA replication in mammalian cells.
ER-mediated phagocytosis: myth or reality?
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Cloning and characterization of human agmatinase
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The metabolic activation of abacavir by human liver cytosol and expressed human alcohol dehydrogenase isozymes
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Cytochrome P450s and other enzymes in drug metabolism and toxicity
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Human 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/inosine 5'-monophosphate cyclohydrolase. A bifunctional protein requiring dimerization for transformylase activity but not for cyclohydrolase activity
Molecular cloning and characterization of a novel (Na+,K+)/H+ exchanger localized to the trans-Golgi network
Phosphorylation of nucleosides and nucleoside analogs by mammalian nucleoside monophosphate kinases
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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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Interaction of Munc-18-2 with syntaxin 3 controls the association of apical SNAREs in epithelial cells
E2F mediated regulation of DNA replication
Pyrimidine pathways in health and disease
Cloning, expression, and characterization of a human inosine triphosphate pyrophosphatase encoded by the itpa gene
6-Phosphofructo-2-kinase/fructose-2,6-bisphosphatase: a metabolic signaling enzyme.
GPHN:Mg2+ (name copied from entity in Homo sapiens)
The equilibrative nucleoside transporter family, SLC29
3xGPHN:3xMg2+ (name copied from entity in Homo sapiens)
PHGHD tetramer (name copied from entity in Homo sapiens)
OAT hexamer (name copied from entity in Homo sapiens)
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ACMSD dimer (name copied from entity in Homo sapiens)
OTC trimer (name copied from entity in Homo sapiens)
ASS1 tetramer (name copied from entity in Homo sapiens)
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ASL tetramer (name copied from entity in Homo sapiens)
ALDH4A1 dimer (name copied from entity in Homo sapiens)
TAT dimer (name copied from entity in Homo sapiens)
GCDH tetramer (name copied from entity in Homo sapiens)
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branched-chain alpha-ketoacid dehydrogenase E1 complex (name copied from entity in Homo sapiens)
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branched-chain alpha-ketoacid dehydrogenase complex (name copied from entity in Homo sapiens)
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AADAT dimer (name copied from entity in Homo sapiens)
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urocanate hydratase (name copied from entity in Homo sapiens)
Lysine uptake by cloned hCAT-2B: comparison with hCAT-1 and with trophoblast surface membranes
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MAT I homotetramer (name copied from entity in Homo sapiens)
1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole [ChEBI:18319]
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MAT I/III (Mg, K cofactors) (name copied from entity in Homo sapiens)
AGXT dimer (name copied from entity in Homo sapiens)
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creatine kinase, sarcomeric, octamer (name copied from entity in Homo sapiens)
creatine kinase, ubiquitous, octamer (name copied from entity in Homo sapiens)
XBP1 controls diverse cell type- and condition-specific transcriptional regulatory networks
creatine kinase BB dimer (name copied from entity in Homo sapiens)
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ALDH9A1 tetramer (name copied from entity in Homo sapiens)
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ARG2 trimer (name copied from entity in Homo sapiens)
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ARG1 trimer (name copied from entity in Homo sapiens)
8xALAD:Pb2+:Zn2+ (name copied from entity in Homo sapiens)
HMBS:DIPY (name copied from entity in Homo sapiens)
2xUROD (name copied from entity in Homo sapiens)
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2xPPO:FAD (name copied from entity in Homo sapiens)
Quantitative and dynamic assessment of the contribution of the ER to phagosome formation
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2x(FECH:2Fe-2S cluster) (name copied from entity in Homo sapiens)
The ABCs of solute carriers: physiological, pathological and therapeutic implications of human membrane transport proteinsIntroduction
ADH1A dimer (name copied from entity in Homo sapiens)
BHMT tetramer (name copied from entity in Homo sapiens)
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MAT III homodimer (name copied from entity in Homo sapiens)
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8x(ALAD:Zn2+) (name copied from entity in Homo sapiens)
SQR:FAD (name copied from entity in Homo sapiens)
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DARS2 dimer (name copied from entity in Homo sapiens)
GARS dimer (name copied from entity in Homo sapiens)
6xUGDH (name copied from entity in Homo sapiens)
YARS2 dimer (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
KARS dimer (name copied from entity in Homo sapiens)
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Human amidophosphoribosyltransferase. An oxygen-sensitive iron-sulfur protein
SARS2 dimer (name copied from entity in Homo sapiens)
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alcohol dehydrogenase 7 (class IV), mu or sigma dimer (name copied from entity in Homo sapiens)
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alcohol dehydrogenase 6 (class V) complex (name copied from entity in Homo sapiens)
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alcohol dehydrogenase 4 (class II), pi dimer (name copied from entity in Homo sapiens)
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MPG glycosylase:3-methyladenine complex (name copied from entity in Homo sapiens)
Purification of 5'-nucleotidase from human placenta after release from plasma membranes by phosphatidylinositol-specific phospholipase C
TAP (name copied from entity in Homo sapiens)
MPG glycosylase:hypoxanthine complex (name copied from entity in Homo sapiens)
MPG glycosylase:ethenoadenine complex (name copied from entity in Homo sapiens)
AQP10 tetramer (name copied from entity in Homo sapiens)
2xUAP1 (name copied from entity in Homo sapiens)
2xUAP1-2 (name copied from entity in Homo sapiens)
AQP9 tetramer (name copied from entity in Homo sapiens)
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The molecular mechanism of lead inhibition of human porphobilinogen synthase
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5-phosphoribosylglycinamide [ChEBI:18349]
AQP3 tetramer (name copied from entity in Homo sapiens)
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AQP7 tetramer (name copied from entity in Homo sapiens)
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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)
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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_93209.9
DNA containing a hNTH1-bound apurinic/apyrimidinic site (name copied from entity in Homo sapiens)
hNTH1 glycosylase:thymine glycol complex (name copied from entity in Homo sapiens)
hNTH1 glycosylase: foramidopyrimidine 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)
DNA containing an MPG-bound apurinic/apyrimidinic site (name copied from entity in Homo sapiens)
DNA containing an MYH-bound apurinic/apyrimidinic site (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_3046.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=29790
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_103331.9
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=4230014
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4230012
MYH glycosylase:adenine 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_2628.2
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=73566
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4230111
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4230113
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_105917.9
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=4230365
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4230112
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4230366
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4230364
Mechanistic implications of mutations to the active site lysine of porphobilinogen synthase
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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_33224.10
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_3275.2
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=109386
Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
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Human lysyl-tRNA synthetase accepts nucleotide 73 variants and rescues Escherichia coli double-defective mutant
A second canon. Functions and mechanisms of beta-catenin-independent Wnt signaling
Structure-function analysis of the bestrophin family of anion channels
ChEBI:18381 5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide
Aquaporin-11: a channel protein lacking apparent transport function expressed in brain
Aquaporins in the kidney: from molecules to medicine
The human AQP4 gene: definition of the locus encoding two water channel polypeptides in brain
High-affinity glutamate transporter ligands
Mitochondrial iron trafficking and the integration of iron metabolism between the mitochondrion and cytosol
Primary hyperoxaluria: from gene defects to designer drugs?
2'-deoxyadenosine 5'-diphosphate [ChEBI:16174]
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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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NPT4, a new microsomal phosphate transporter: mutation analysis in glycogen storage disease type Ic
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Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design
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A quantitative model of human DNA base excision repair. I. Mechanistic insights
Identification of the peroxisomal beta-oxidation enzymes involved in the biosynthesis of docosahexaenoic acid
Antigen presentation and the ubiquitin-proteasome system in host-pathogen interactions
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
Differential lysosomal proteolysis in antigen-presenting cells determines antigen fate
The role for endoplasmic reticulum stress in diabetes mellitus
Overview of steroidogenic enzymes in the pathway from cholesterol to active steroid hormones
Regulation of repair of alkylation damage in mammalian genomes.
Prog Nucleic Acid Res Mol Biol 44:109-42
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Genetic disorders of carnitine metabolism and their nutritional management.
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From molecular action to physiological outputs: peroxisome proliferator-activated receptors are nuclear receptors at the crossroads of key cellular functions
Selective and ATP-dependent translocation of peptides by the MHC-encoded transporter
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Molecular cloning and expression of a novel human aquaporin from adipose tissue with glycerol permeability
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Dihydroxyacetone phosphate [ChEBI:16108]
The effect of elimination of intersubunit disulfide bonds on the activity, assembly, and secretion of recombinant human acetylcholinesterase. Expression of acetylcholinesterase Cys-580----Ala mutant
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Molecular cloning and characterization of an aquaporin cDNA from salivary, lacrimal, and respiratory tissues
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Tissue-differential expression of two distinct genes for phosphoribosyl pyrophosphate synthetase and existence of the testic-specific transcript
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Cloning of the sodium-dependent, broad-scope, neutral amino acid transporter Bo from a human placental choriocarcinoma cell line
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The complex route to MHC class I-peptide complexes
Crystal structures of human GAR Tfase at low and high pH and with substrate beta-GAR
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Interaction between the functional polymorphisms of the alcohol-metabolism genes in protection against alcoholism.
1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide [ChEBI:18406]
5'-Phospho-ribosyl-5-amino-4-imidazole carboxamide
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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_16107.1
5'-Phosphoribosylformylglycinamidine [ChEBI:18413]
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Identification of a novel aquaporin, AQP12, expressed in pancreatic acinar cells
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Phosphate transporters: a tale of two solute carrier families
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Overview of retinoid metabolism and function
Structural basis for the specificity, catalysis, and regulation of human uridine-cytidine kinase
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Mitochondrial aspartyl-tRNA synthetase deficiency causes leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation
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Chromosomal localization of the human genes for alpha 1A, alpha 1B, and alpha 1E voltage-dependent Ca2+ channel subunits
The sodium phosphate cotransporter family SLC34
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Cloning of the human sodium lodide symporter
In vivo expression and functional characterization of the zinc transporter ZnT8 in glucose-induced insulin secretion
Isozymes of human phosphofructokinase: identification and subunit structural characterization of a new system
Understanding specificity in metabolic pathways--structural biology of human nucleotide metabolism
Transcription factors direct the development and function of pancreatic beta cells
Modulation of mitochondrial membrane permeability in pathogenesis, autophagy and control of metabolism
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The SLC2 family of facilitated hexose and polyol transporters
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Human liver pi-alcohol dehydrogenase: kinetic and molecular properties.
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cDNA cloning, expression, and mutagenesis study of leukotriene B4 12-hydroxydehydrogenase
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Biosynthesis and bioproduction of coenzyme Q10 by yeasts and other organisms
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Regulation of Lipid Metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
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The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Scriver CR, et al., editors) 1:1553-1587
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Hormonal regulation of hepatic gluconeogenesis and glycolysis
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Purification, properties, and sequencing of aminoisobutyrate aminotransferases from rat liver
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Compartmentalization of aquaporins in the human intestine
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Synthesis of 15-eicosatetraenoic acid derivatives
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Purification and properties of uroporphyrinogen decarboxylase from human erythrocytes. A single enzyme catalyzing the four sequential decarboxylations of uroporphyrinogens I and III.
Synthesis of 12-eicosatetraenoic acid derivatives
Regulation of gene expression in beta cells
The murine pantothenate kinase (Pank1) gene encodes two differentially regulated pantothenate kinase isozymes
Human lung enolase: cloning and sequencing of cDNA and its inducibility with dexamethasone
Decarboxylases involved in polyamine biosynthesis and their inactivation by nitric oxide
UDP-N-acetyl-D-glucosamine [ChEBI:16264]
Structural basis for altered activity of M- and H-isozyme forms of human lactate dehydrogenase
Reduction of alpha gamma-diketo and alpha-keto acids catalyzed by muscle preparations and by crystalline lactic dehydrogenase
4-Trimethylammoniobutanoate [ChEBI:16244]
ASCT-1 is a neutral amino acid exchanger with chloride channel activity
Sodium-coupled monocarboxylate transporters in normal tissues and in cancer
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Expression cloning of a human cDNA encoding folylpoly(gamma-glutamate) synthetase and determination of its primary structure
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Enolase isoenzymes in rat tissues. Electrophoretic, chromatographic, immunological and kinetic properties
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Transcriptional activation of pyruvate kinase gene by ChREBP:MLX
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Cloning and functional characterization of human sodium-dependent organic anion transporter (SLC10A6)
Agmatine: biological role and therapeutic potentials in morphine analgesia and dependence
Regulation of purine synthesis de novo in human fibroblasts by purine nucleotides and phosphoribosylpyrophosphate
Amino acid transport across mammalian intestinal and renal epithelia
Proximal tubular handling of phosphate: A molecular perspective
Structure-function relationships in dihydrolipoamide acyltransferases.
Functional impairment of lens aquaporin in two families with dominantly inherited cataracts
The kinase activity of human brain 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase is regulated via inhibition by phosphoenolpyruvate
Regulation of the mammalian alcohol dehydrogenase genes.
Prog Nucleic Acid Res Mol Biol 64:295-341
Intact AQP0 performs cell-to-cell adhesion
Human UDP-glucuronosyltransferases: metabolism, expression, and disease
Activation of human mitochondrial pantothenate kinase 2 by palmitoylcarnitine
The SLC31 (Ctr) copper transporter family
Molecular characterization of a new urea transporter in the human kidney
Nephrolithiasis and osteoporosis associated with hypophosphatemia caused by mutations in the type 2a sodium-phosphate cotransporter
Receptor-mediated phagocytosis elicits cross-presentation in nonprofessional antigen-presenting cells
Subunit interactions in the mammalian alpha-ketoglutarate dehydrogenase complex. Evidence for direct association of the alpha-ketoglutarate dehydrogenase and dihydrolipoamide dehydrogenase components.
Different functions between human monomeric carbonyl reductase 3 and carbonyl reductase 1
Biochemical and genetic aspects of mevalonate kinase and its deficiency
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The subcellular localization of an aquaporin-2 tetramer depends on the stoichiometry of phosphorylated and nonphosphorylated monomers
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E2F mediates developmental and cell cycle regulation of ORC1 in Drosophila
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Defective copper-induced trafficking and localization of the Menkes protein in patients with mild and copper-treated classical Menkes disease
Aldehyde dehydrogenase, a diphosphopyridine nucleotide-linked enzyme
Cloning, expression, and characterization of a human 4'-phosphopantetheinyl transferase with broad substrate specificity
The spectrum of SLC17A5-gene mutations resulting in free sialic acid-storage diseases indicates some genotype-phenotype correlation
Growth-related renal type II Na/Pi cotransporter
The AMP-activated protein kinase pathway--new players upstream and downstream
Molecular cloning, tissue distribution, and functional expression of the human Na(+)/H(+) exchanger NHE2
Appearance of water channels in Xenopus oocytes expressing red cell CHIP28 protein
Primary structure of a human trifunctional enzyme. Isolation of a cDNA encoding methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase-formyltetrahydrofolate synthetase.
S-adenosylmethionine: nothing goes to waste
Nitric oxide and peroxynitrite in health and disease
Hexosamine biosynthetic pathway mutations cause neuromuscular transmission defect
Biochemical properties of human pantothenate kinase 2 isoforms and mutations linked to pantothenate kinase-associated neurodegeneration
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Molecular basis of phenotypic variation in patients with argininemia
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S-adenosylmethionine synthesis: molecular mechanisms and clinical implications
Biosynthesis of diphosphopyridine nucleotide. II. Enzymatic aspects.
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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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The oxidation of pyruvate in pigeon breast muscle
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Post-translational palmitoylation and glycosylation of Wnt-5a are necessary for its signalling
Metabolism of steroid hormones and vitamin D
Crystal structure of human arginase I at 1.29-A resolution and exploration of inhibition in the immune response
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).
Eight SLC gene families are involved in the transport of amino acids and oligopeptides.
A refined structure of human aquaporin-1
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)
leucine + tRNA(Leu) + ATP => Leu-tRNA(Leu) + AMP + pyrophosphate
isoleucine + tRNA(Ile) + ATP => Ile-tRNA(Ile) + AMP + pyrophosphate
glycine + tRNA(Gly) + ATP => Gly-tRNA(Gly) + AMP + pyrophosphate
glutamate + tRNA(Glu) + ATP => Glu-tRNA(Glu) + AMP + pyrophosphate
aspartate + tRNA(Asp) + ATP => Asp-tRNA(Asp) + AMP + pyrophosphate
asparagine + tRNA(Asn) + ATP => Asn-tRNA(Asn) + AMP + pyrophosphate
Molecular cloning of the human UMP synthase gene and characterization of point mutations in two hereditary orotic aciduria families
methionine + tRNA(Met) + ATP => Met-tRNA(Met) + AMP + pyrophosphate
Munc13-1 is essential for fusion competence of glutamatergic synaptic vesicles
lysine + tRNA(Lys) + ATP => Lys-tRNA(Lys) + AMP + pyrophosphate
Formation of the active cofactor, UDP-glucuronate
Disruption of aquaporin-11 produces polycystic kidneys following vacuolization of the proximal tubule
Identification of amino acid residues responsible for the pyrimidine and purine nucleoside specificities of human concentrative Na+ nucleoside cotransporters hCNT1 and hCNT2
Expression of human placental-type 6-phosphofructo-2-kinase/fructose 2,6-bisphosphatase in various cells and cell lines
The neurotransmitter cycle and quantal size
The acetyl group from acetyl-CoA is transferred to the NAT2
benzoate + Coenzyme A + ATP => benzoyl-CoA + AMP + pyrophosphate
Benzoate and Coenzyme A react to form benzoyl-CoA thioester
Ethanol is oxidized by NAD+ to form acetaldehyde, NADH, and H+
ethanol + NAD+ => acetaldehyde + NADH + H+
acetate + CoA + ATP => acetyl-CoA + AMP + pyrophosphate [mitochondrial]
acetate + CoA + ATP => acetyl-CoA + AMP + pyrophosphate [cytosolic]
UDP-glucose is oxidised to UDP-glucuronate
Ferrous iron is inserted into protoporphyrin IX to form heme
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phenylpyruvate + NADH + H+ => phenyllactate + NAD+
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NRAMP1 transports divalent metal ions across phagosomal membranes of macrophages
carbovir monophosphate + ATP => carbovir diphosphate + ADP
Phosphorylation of carbovir monophosphate
salicylic acid + Coenzyme A + ATP => salicylate-CoA + AMP + pyrophosphate
Salicylic acid and Coenzyme A react to form salicylate-CoA thioester
abacavir + 2 NAD+ => abacavir 5'-carboxylate + 2 NADH + 2 H+
Oxidation of abacavir to abacavir 5'-carboxylate
phenylacetate + Coenzyme A + ATP => phenylacetyl-CoA + AMP + pyrophosphate
Synthesis of phenylacetyl CoA from phenylacetate and Coenzyme A
Role of multiple phosphorylation sites in the COOH-terminal tail of aquaporin-2 for water transport: evidence against channel gating
Early phagosomes in dendritic cells form a cellular compartment sufficient for cross presentation of exogenous antigens
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phosphofructokinase, P4 complex (name copied from entity in Homo sapiens)
creatine + ATP => phosphocreatine + ADP [CK octamer]
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PFKFB3 dimer (name copied from entity in Homo sapiens)
Iodide is taken up by thyroid epithelial cells
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PFKFB4 dimer (name copied from entity in Homo sapiens)
glyoxylate + alanine => glycine + pyruvate [peroxisome]
phosphofructokinase, L4 complex (name copied from entity in Homo sapiens)
arginine + H2O => ornithine + urea [ARG1]
arginine + H2O => ornithine + urea [ARG2]
gamma-butyrobetaine semialdehyde + NAD+ => gamma-butyrobetaine + NADH + H+
creatine + ATP => phosphocreatine + ADP [CKB,CKM]
Post-proteasomal antigen processing for major histocompatibility complex class I presentation
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Uroporphyrinogen III is decarboxylated to form coproporphyrinogen III
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Uroporphyrinogen I is decarboxylated to form coproporphyrinogen I
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Two molecules of ALA condense to form porphobilinogen (PBG)
Four PBGs combine through deamination to form hydroxymethylbilane (HMB)
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Oxidation of protoporphyrinogen IX to protoporphyrin IX
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glyoxylate + NADPH + H+ => glycolate + NADP+
SQR oxidizes sulfide to bound persulfide
ALAD octamer associates with Pb++, forming a catalytically inactive complex
SAM is sythesized from methionine's reaction with ATP
Remethylation of homocysteine via betaine degradation
Mutations in the Delta1-pyrroline 5-carboxylate dehydrogenase gene cause type II hyperprolinemia.
Selectivity in post-translational biotin addition to five human carboxylases
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glutamate + L-glutamate gamma-semialdehyde <=> ornithine + alpha-ketoglutarate [OAT]
ornithine + alpha-ketoglutarate <=> glutamate + L-glutamate gamma-semialdehyde [OAT]
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alpha-aminoadipate + alpha-ketoglutarate <=> alpha-ketoadipate + glutamate
4-imidazolone-5-propionate + H2O => N-formiminoglutamate + 2H+
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Oxidative decarboxylation of alpha-ketoadipate to glutaryl CoA by alpha-ketoglutarate dehydrogenase
alpha-ketoadipate + CoASH + NAD+ => glutaryl-CoA + CO2 + NADH + H+
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alpha-ketoadipate + glutamate <=> alpha-aminoadipate + alpha-ketoglutarate
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a-ketoisocaproate, a-keto b-methylvalerate, or a-ketoisovalerate + CoA + NAD+ => isovaleryl-CoA, a-methylbutyryl-CoA, or isobuyryl-CoA + CO2 + NADH + H+
Oxidative decarboxylation of branched-chain alpha-keto acids
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urocanate + H2O => 4-imidazolone-5-propionate
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Structure and function of human erythrocyte pyruvate kinase. Molecular basis of nonspherocytic hemolytic anemia
p-hydroxyphenylpyruvate + glutamate <=> tyrosine + alpha-ketoglutarate
tyrosine + alpha-ketoglutarate <=> p-hydroxyphenylpyruvate + glutamate
glutaryl-CoA + FAD => crotonyl-CoA + FADH2 + CO2
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
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argininosuccinate <=> fumarate + arginine
Glutathione peroxidase protein. Absence in selenium deficiency states and correlation with enzymatic activity
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ATP + aspartate + citrulline <=> argininosuccinate + AMP + pyrophosphate
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carbamoyl phosphate + ornithine => citrulline + orthophosphate
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2 ATP + NH4+ + HCO3- => 2 ADP + orthophosphate + carbamoyl phosphate [mitochondrial]
2 ATP + NH4+ + HCO3- => 2 ADP + orthophosphate + carbamoyl phosphate
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kynurenine + 2-oxoglutarate => 4-(2-aminophenyl)-2,4-dioxobutanoic acid + glutamate
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2-amino-3-carboxymuconate semialdehyde => 2-aminomuconate semialdehyde + CO2
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L-glutamate gamma-semialdehyde + NAD+ => glutamate + NADH + H+
DHF is reduced to tetrahydrofolate (THF)
Conversion of cytosolic THF to THF-polyglutamate
Altered aquaporin 9 expression and localization in human hepatocellular carcinoma
Role of aquaporin-7 and aquaporin-9 in glycerol metabolism; involvement in obesity
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Phosphopantothenoylcysteine is decarboxylated
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pantothenate + ATP => phosphopanthothenate + ADP
Pantothenate is phosphorylated [PANK1;3;4]
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Phosphorylation of dephospho-CoA to produce CoA
COASY transfers an adenylyl group from ATP to PPANT
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Cytoslic carboxylases translocate to mitochondrial matrix
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biotin [extracellular] + 2 Na+ [extracellular] => biotin [cytosol] + 2 Na+ [cytosol]
SLC5A6 cotransports extracellular Btn and 2xNa+ to cytosol
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Folate is reduced to dihydrofolate (DHF)
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A phosphoribosyl group is added to nicotinate to form nicotinate mononucleotide (NaMN)
Molybdenum ion transfer onto molybdopterin
Characterization of solanesyl and decaprenyl diphosphate synthases in mice and humans
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Conversion of cytosolic 5-methyltetrahydrofolate (5-methylTHF) to 5-methylTHF-polyglutamate
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5,10-methenylTHF polyglutamate + NADPH + H+ <=> 5,10-methyleneTHF polyglutamate + NADP+
10-formylTHF polyglutamate <=> 5,10-methenylTHF polyglutamate + H2O
THF polyglutamate + formate + ATP => 10-formylTHF polyglutamate + ADP + orthophosphate
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Conversion of mitochondrial THF to THF-polyglutamate
Sulfhydrylation and ring cleavage of precursor Z
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5,10-methenylTHF polyglutamate + H2O <=> 10-formylTHF polyglutamate
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5,10-methyleneTHF polyglutamate + NADP+ <=> 5,10-methenylTHF polyglutamate + NADPH + H+
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pH dependence, substrate specificity and inhibition of human kynurenine aminotransferase I
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a-ketoisocaproate, a-keto b-methylvalerate, a-ketoisovalerate
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ZnT-3, a putative transporter of zinc into synaptic vesicles
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(d)NDP + ATP <=> (d)NTP + ADP [NME1,2,3]
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(d)NTP + ADP <=> (d)NDP + ATP [NME1,2,3]
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Discovery of the aquaporins and development of the field
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(S)-alpha-Amino-1H-imidazole-4-propionic acid
pantothenate [extracellular] + 2 Na+ [extracellular] => pantothenate [cytosol] + 2 Na+ [cytosol]
SLC5A6 cotransports extracellular PanK and 2Na+ to cytosol
isovaleryl-CoA, a-methylbutyryl-CoA, isobutyryl-CoA
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The ontogeny of human drug-metabolizing enzymes: phase II conjugation enzymes and regulatory mechanisms
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Expression profiling and differential screening between hepatoblastomas and the corresponding normal livers: identification of high expression of the PLK1 oncogene as a poor-prognostic indicator of hepatoblastomas
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5,10-methenyltetrahydrofolate polyglutamate
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Molecular cloning, expression, and chromosomal localization of a human brain-specific Na(+)-dependent inorganic phosphate cotransporter
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Changes in methionine adenosyltransferase and S-adenosylmethionine homeostasis in alcoholic rat liver
Am J Physiol Gastrointest Liver Physiol 279:G178-85
The NRAMP family of metal-ion transporters
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4-(2-aminophenyl)-2,4-dioxobutanoic acid
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Binding to Rab3A-interacting molecule RIM regulates the presynaptic recruitment of Munc13-1 and ubMunc13-2
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Water permeability and characterization of aquaporin-11
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5-phospho-alpha-D-ribose 1-diphosphate [ChEBI:17111]
Molecular cloning of a human, hemicholinium-3-sensitive choline transporter
Biochemistry of Lipids, Lipoproteins and Membranes, 5th Edition (Book): 213-244
Four Na+/H+ exchanger isoforms are distributed to Golgi and post-Golgi compartments and are involved in organelle pH regulation
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
The eicosanoids: cyclooxygenase, lipoxygenase, and epoxygenase pathways
Biochemistry of Lipids, Lipoproteins and Membranes, 5th Edition (Book): 331-362
Immunolocalization of AQP9 in liver, epididymis, testis, spleen, and brain
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Intracellular zinc homeostasis and zinc signaling
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Feedback regulation of EGFR signalling: decision making by early and delayed loops
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Genetic Analysis of Coenzyme Q Biosynthesis
Coenzyme Q: Molecular Mechanisms in Health and Disease (Book): 185-208
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Characterization of the CoA ligases of human liver mitochondria catalyzing the activation of short- and medium-chain fatty acids and xenobiotic carboxylic acids
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Molecular cloning of the cDNA encoding a human renal sodium phosphate transport protein and its assignment to chromosome 6p21.3-p23
Catecholamine biosynthesis and physiological regulation in neuroendocrine cells
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Uridine kinase activities and pyrimidine nucleoside phosphorylation in fluoropyrimidine-sensitive and -resistant cell lines of the Novikoff hepatoma
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A synopsis of the unconjugated acidic transamination metabolites of phenylalanine in phenylketonuria
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Neurotransmitter uptake and Metabolism In Glial Cells
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Human porphobilinogen deaminase mutations in the investigation of the mechanism of dipyrromethane cofactor assembly and tetrapyrrole formation
Determinants of function and substrate specificity in human UDP-galactose 4'-epimerase
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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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Biotin (vitamin H or B7) is a water-soluble B-complex vitamin. Biotin is a cofactor in the metabolism of fatty acids and leucine, and it plays a role in gluconeogenesis. D-Pantothoate (vitamin B5), is a water-soluble vitamin needed to form coenzyme-A (CoA), and is critical in the metabolism and synthesis of carbohydrates, proteins, and fats. Lipoic acid is an organosulfur compound, the R-enantiomer of which is an essential cofactor for many enzyme complexes. The human SLC5A6 encodes the Na+-dependent multivitamin transporter SMVT (Prasad PD et al, 1999; Wang H et al, 1999). SMVT co-transports these vitamins/cofactors into cells with Na+ ions electrogenically.
Arylamine N-acetyltransferases and drug response
Mechanism of aminoacylation of tRNA. Proof of the aminoacyl adenylate pathway for the isoleucyl- and tyrosyl-tRNA synthetases from Escherichia coli K12
Carrier-mediated urea transport allows rapid urea movement across the cell membrane, which is particularly important in the process of urinary concentration and for rapid urea equilibrium in non-renal tissues. Two carriers exist in humans, HUT2 which is renal-specific (Olives B et al, 1996) and HUT11, which is erythrocyte-specific (Olives B et al, 1994).
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.
Direct role of ChREBP.Mlx in regulating hepatic glucose-responsive genes.
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.
Carbohydrate response element binding protein directly promotes lipogenic enzyme gene transcription
Proteins with transporting functions can be roughly classified into 3 categories: ATP-powered pumps, ion channels, and transporters. Pumps utilize the energy released by ATP hydrolysis to power the movement of the substrates across the membrane, against their electrochemical gradient. Channels at the open state can transfer the substrates (ions or water) down their electrochemical gradient, at an extremely high efficiency (up to 108 s-1). Transporters facilitate the movement of a specific substrate âeither against or following their concentration gradient, at a lower speed (about 102 -104 s-1); as generally believed, conformational change of the transporter protein is involved in the transfer process. According to the Human Genome Organization (HUGO) Gene Nomenclature Committee, all human transporters can be grouped into the solute-carrier (SLC) superfamily. Currently, there are 55 SLC families in the superfamily, with a total of at least 362 putatively functional protein-coding genes (Hediger et al, 2004; He et al., 2009). At least 20-25% amino-acid sequence identity is shared by members belonging to the same SLC family. No homology is shared between different SLC families. While the HUGO nomenclature system by definition only includes human genes, the nomenclature system has been informally extended to include rodent species through the use of lower cases letters (e.g., Slc1a1 denotes the rodent ortholog of the human SLC1A1 gene). And it's worthwhile to mention that pumps, channels and aquporins are not included in SLC superfamily.
This pathway groups the processes mediated by SLC transporters, by which vitamins and cofactors, as well as nucleosides, nucleotides, nucleobases, and related molecules cross lipid bilayer membranes.
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 plasma membrane-associated protein SLC28A2 mediates the transport of one molecule of adenosine, guanosine, inosine, or uridine, and one sodium ion, from the extracellular space to the cytosol.
The plasma membrane-associated protein SLC28A3 mediates the transport of one molecule of adenosine, cytidine, guanosine, inosine, thymidine, or uridine, and two sodium ions, from the extracellular space to the cytosol.
The plasma membrane-associated protein SLC28A1 mediates the transport of one molecule of 2'-deoxyadenosine, adenosine, cytidine, thymidine, or uridine, and one sodium ion, from the extracellular space to the cytosol.
Mammalian sodium/dicarboxylate cotransporters (transport succinate and other Krebs cycle intermediates) fall into two categories based on their substrate affinity. The human gene SLC13A3 encodes a high-affinity sodium/dicarboxlate co-transporter, NaDC3. NaDC3 is expressed in the basolateral membrane of renal proximal tubular epithelial cells, sinusoidal membrane of hepatocytes, and brain synaptosomes. Kinetic studies in human retinal pigment epithelial (HRPE) cells suggest three sodium ions co-transported with every divalent succinate (Wang H et al, 2000).
The human SLC13A5 gene encodes a sodium-coupled citrate transporter, NACT. This gene is expressed mainly in the liver, with lower levels in brain and testis. NACT has a preference for trivalent citrate (Inoue K et al, 2002).
Five human SLC13 genes encode sodium-coupled sulphate, di- and tri-carboxylate transporters located on the plasma membrane. Two transporters (NaS1 and NaS2) co-transport sulphate with sodium. The other members (NaDC1, NaDC3, and NaCT) co-transport sodium with di- and tri-carboxylates such as succinate, citrate and alpha-ketoglutarate (Pajor AM, 2006).
The primary site for absorption of dietary iron is the duodenum. Ferrous iron (Fe2+) is taken up from the gut lumen across the apical membranes of enterocytes and released into the portal vein circulation across basolateral membranes. The human gene SLC11A2 encodes the divalent cation transporter DCT1 (NRAMP2, Natural resistance-associated macrophage protein 2). NRAMP2 resides on the apical membrane of enterocytes and mediates the uptake of ferrous iron into these cells (Tandy S et al, 2000). DCT1 can also accept a broad range of transition metal ions.
Zinc is an essential element for all organisms because it serves as a catalytic or structural cofactor for many different proteins. Cellular zinc homoeostasis is co-ordinated through Zn2+-specific transporters which are members of two distinct gene families. Members of the SLC39 gene family (ZRTL-like import proteins1â14, ZIP1-14) are responsible for Zn2+ import into the cytoplasm, either across the plasma membrane or out of intracellular organelles. In contrast, members of the SLC30 gene family (zinc transporters 1â10, ZnT1-10) export Zn2+ from the cytoplasm, either across the plasma membrane into the extracellular space or into intracellular organelles (Murakami M and Hirano T, 2008; Devirgiliis C et al, 2007; Eide DJ, 2006)
The human 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).
The human SLC5A7 gene encodes a sodium- and chloride-dependent, high affinity choline transporter, CHT (Apparsundaram S et al, 2000). CHT transports choline from the extracellular space into neuronal cells and is dependent on Na+ and Cl- ions for transport (Okuda T and Haga T, 2000). Choline uptake is the rate-limiting step in acetylcholine synthesis.
Six SLC gene families encode proteins which mediate transport of metals. The families are SLC11, SLC30, SLC31, SLC39, SLC40 and SLC41 (He L et al, 2009; Bressler JP et al, 2007).
The human gene SLC30A2 encodes zinc transporter ZnT2. Its function is inferred from experiments using rat Znt2 (Palmiter RD et al, 1996).
The human SLC30A8 gene encodes the zinc transporter ZnT8 which is specifically expressed in pancreatic beta cells. Zinc is required for zinc-insulin crystallization within secretory vesicles of these cells. After glucose stimulation, large amounts of zinc are secreted locally in the extracellular matrix together with insulin. It has been suggested that this co-secreted zinc plays a role in islet cell paracrine and/or autocrine communication (Chimienti F et al, 2006).
The human gene SLC30A3 encodes zinc transporter ZnT3. Through experiments on the mouse homologue Znt3, it is thought this transporter is expressed mainly in brain and testis and mediated the accumulation of zinc into synaptic vesicles (Palmiter et al, 1996).
Human SLC5A5 encodes a Na+/I- symporter, NIS (Smanik PA et al, 1996). NIS is localized in the basolateral membrane facing the bloodstream and mediates iodide accumulation into thyrocytes.Defects in SLC5A5 cause congenital hypothyroidism due to dyshormonogenesis type 1 (CHDH1) (Fujiwara H et al, 1997). NIS, together with AIT (see next reaction), mediates iodide transfer from blood to the colloid lumen of thyrocytes.
SLC5A8 encodes for the apical iodide transporter, AIT (also known as SMCT1). As well as functioning as a Na+-dependent monocarboxylate co-transporter, AIT also mediates iodide transport from the thyrocyte into the colloid lumen through the apical membrane (Rodriguez AM et al, 2002). AIT, together with NIS (see previous reaction), mediates iodide transfer from blood to the colloid lumen of thyrocytes.
SLC17A5 encodes a lysosomal sialic acid transporter, Sialin (AST, membrane glycoprotein HP59) (Verheijen FW et al, 1999; Fu C et al, 2001). Lysosomes export sialic acid which is derived from the degradation of glycosylated membrane proteins. This export is dependent in the proton electrochemical gradient across the lysosomal membrane. It is present in the pathological tumor vasculature of the lung, breast, colon, and ovary, but not in the normal vasculature, suggesting that the protein may be critical to pathological angiogenesis. Sialin is not expressed in a variety of normal tissues, but is significantly expressed in human fetal lung. Defects in SLC17A5 cause Salla disease (SD) and infantile sialic acid storage disorder (ISSD, also called N-acetylneuraminic acid storage disease (NSD)). Both are sialic acid storage diseases (SASDs) which are autosomal recessive neurodegenerative disorders characterized by hypotonia, cerebellar ataxia and mental retardation in very young infants (Verheijen FW et al, 1999; Aula N et al, 2000).
Four SLC17 genes are thought to encode type I Na+-dependent phosphate co-transporters in humans. SLC17A1 (NPT1) encodes Na+-dependent phosphate co-transporter 1 (Na/Pi-4). It is abundant in human kidney cortex, liver and brain and is important for the resorption of phosphate by the kidney. It does this by actively transporting phosphate into cells via Na+ cotransport in the renal brush border membrane (Chong SS et al, 1993). Three close relatives of NPT1 have been identified through genomic analysis and designated NPT3 (SLC17A2), NPT4 (SLC17A3) and a putative small intestine sodium-dependent phosphate co-transporter (SLC17A4). None of these three proteins have been functionally characterized yet.
The human tumour suppressor gene SLC5A8 encodes for a sodium-coupled monocarboxylate transporter 1, SMCT1 (also called AIT) and is abundantly expressed in the colon (Coady MJ et al, 2004; Myauchi S et al, 2004). When the human protein is expressed in Xenopus oocytes, it was found to transport small monocarboxylates, co-transporting Na+ ions electrogenically (3 Na+ ions co-transported with 1 carboxylate).
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 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).
Molybdenum cofactor biosynthesis and deficiency
Mammalian sodium/dicarboxylate cotransporters (transport succinate and other Krebs cycle intermediates) fall into two categories based on their substrate affinity. The human gene SLC13A2 encodes a low-affinity sodium/dicarboxlate co-transporter, NaDC1. NaDC1 is highly expressed in the brush-border membranes of kidney and intestinal cells and reabsorbs Krebs cycle intermediates, such as succinate and citrate, from the glomerular filtrate (Pajor AM, 1996).
The human gene SLC13A4 encodes a sodium/sulphate co-transporter NaS2 (Girard JP et al, 1999). NaS2 is highly expressed in placenta and testis, mainly in high endothelial venules. Kinetic experiments suggest two sodium ions co-transported for every sulphate ion (Markovich D et al, 2005).
The human gene SLC13A1 encodes a sodium/sulphate co-transporter NaS1 (Lee A et al, 2000). NaS1 is almost exclusively expressed in the kidney and mediates sulphate reabsorption there.
The human SLC10A6 gene encodes a sodium-dependant organic anion transporter, SOAT. Highest expressions of the gene are in testis, placenta and pancreas. Unlike the other SLC10A gene products, SOAT shows no affinity for binding bile acids. However, SOAT is able to transport sulpho-conjugated bile acids such as taurolithocholate 3-sulphate (Geyer J et al, 2007). It can also transport the structurally similar sulphated steroids (not shown here), thus SOAT may play a role in delivery of these prohormones to testis, pancreas and placenta.
C1-Tetrahydrofolate synthase from rabbit liver. Structural and kinetic properties of the enzyme and its two domains.
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SLC1A4, associated with the plasma membrane, mediates the exchange of serine and an extracellular sodium ion for a cytosolic sodium ion and any one of the four amino acids alanine, serine, threonine, or cysteine (Zerangue and Kavanaugh 1996).
SLC1A4, associated with the plasma membrane, mediates the exchange of threonine and an extracellular sodium ion for a cytosolic sodium ion and any one of the four amino acids alanine, serine, threonine, or cysteine (Zerangue and Kavanaugh 1996).
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SLC1A5, associated with the plasma membrane, mediates the exchange of extracellular alanine for cytosolic glutamine (Broer et al. 2000).
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SLC1A5, associated with the plasma membrane, mediates the exchange of extracellular glutamine for cytosolic alanine (Broer et al. 2000).
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SLC7A1 mediates the uptake of cationic amino acids across the plasma membranes of non-epithelial cells (Broer 2008; Closs et al. 1997; Furesz et al. 2002; Kamath et al. 1999).
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SLC7A2, isoform A, mediates the uptake of cationic amino acids across the plasma membranes of non-epithelial cells (Broer 2008; Closs et al. 1997).
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SLC7A2, isoform B, mediates the uptake of cationic amino acids across the plasma membranes of non-epithelial cells (Broer 2008; Closs et al. 1997; Furesz et al. 2002).
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).
Expression of human arginine decarboxylase, the biosynthetic enzyme for agmatine
SLC7A3 mediates the uptake of cationic amino acids across the plasma membranes of non-epithelial cells (Vekony et al. 2001).
There are two classes of glutamate transporters; the excitatory amino acid transporters (EAATs) which depend on an electrochemical gradient of Na+ ions and vesicular glutamate transporters (VGLUTs) which don't. Together, these transporters uptake and release glutamate to mediate this neurotransmitter's excitatory signal and are part of the glutamate-gluatamine cycle. Three members of the SLC17A gene family (7, 6 and 8) encode VGLUTs 1-3 respectively (Ni B et al, 1996; Takamori S et al, 2001; Takamori S et al, 2002 respectively). VGLUT1 (brain-specific Na+-dependent phopshate transporter, BNPI) and VGLUT2 (differentiation-associated Na+-dependent phosphate transporter, DNPI) were identified first and originally characterized as phosphate transporters. However, they are localized to synaptic vesicles, not the plasma membrane (like EAATs) and transport the organic anion glutamate into synaptic vesicles. This uptake is thought to be coupled to the proton electrochemical gradient generated by a vacuolar type H+-ATPase. They are all expressed in the CNS in neuron-rich areas but VGLUT3 is also expressed on astrocytes and in liver and kidney.
There are two classes of glutamate transporters; the excitatory amino acid transporters (EAATs) which depend on an electrochemical gradient of Na+ ions and vesicular glutamate transporters (VGLUTs) which don't. Together, these transporters uptake and release glutamate to mediate this neurotransmitter's excitatory signal and are part of the glutamate-gluatamine cycle. The SLC1 gene family includes five high-affinity glutamate transporters encoded by SLC1, 2, 3, 6 and 7. These transporters can mediate transport of L-Glutamate, L-Aspartate and D-Aspartate with cotransport of 3 Na+ ions and H+ and antiport of a K+ ion. This mechanism allows glutamate into cells against a concentration gradient. This is a crucial factor in the protection of neurons against glutamate excitotoxicity in the CNS. SLC1A1 encodes an excitatory amino-acid carrier 1 (EAAC1, also called EAAT3) (Shashidharan P et al, 1994; Arriza JL et al, 1994) and is abundant particularly in brain but also in liver, muscle, ovary, testis and in retinoblastoma cell lines. In the kidney, EAAC1 is present at apical membranes of proximal tubes. Defects in SLC1A1 may be a cause of dicarboxylicamino aciduria (glutamate-aspartate transport defect in the kidney and intestine). SLC1A2 encodes the glial-type high affinity glutamate transporter (GLT1, EAAT2) (Arriza JL et al, 1994). GLT1 is expressed mainly in the brain and is essential for terminating the postsynaptic action of glutamate by rapidly removing released glutamate from the synaptic cleft. SLC1A3 encodes a sodium-dependent glutamate/aspartate transporter 1 (GLAST1, EAAT1). It is particularly abundant in the cerebellum and, like GLT1, plays a role in terminating the postsynaptic action of glutamate (Arriza JL et al, 1994). Defects in SLC1A3 are the cause of episodic ataxia type 6 (EA6), characterized by episodic ataxia, seizures, migraine and alternating hemiplegia (Jen JC et al, 2005). SLC1A6 encodes an excitatory amino-acid transporter 4 (EAAT4) (Fairman WA et al, 1995) and is predominantly expressed in cerebellar Purkinje cells. SLC1A7 encodes an excitatory amino acid transporter 5 (EAAT5, retinal glutamate transporter) (Arriza JL et al, 1997) which is highly expressed in the retina.
triphopsphoric acid 1-xanthosin-5'-yl ester
Characterization of a human gene conferring sensitivity to infection by gibbon ape leukemia virus
At the beginning of this reaction, 1 molecule of 'hNTH1', and 1 molecule of 'Double-strand DNA containing a thymine glycol ' are present. At the end of this reaction, 1 molecule of 'hNTH1 glycosylase:thymine glycol' is present. This reaction takes place in the 'nucleus'.
Base excision repair is initiated by a DNA glycosylase which first recognizes and removes a damaged or incorrect (e.g. mismatched) base.
At the beginning of this reaction, 1 molecule of '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 'MPG glycosylase:hypoxanthine complex' is present. At the end of this reaction, 1 molecule of 'Hypoxanthine', and 1 molecule of 'DNA containing an MPG-bound apurinic/apyrimidinic site' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA N-glycosylase activity' of 'MPG glycosylase'.
At the beginning of this reaction, 1 molecule of 'MPG glycosylase:ethenoadenine complex' is present. At the end of this reaction, 1 molecule of 'DNA containing an MPG-bound apurinic/apyrimidinic site', and 1 molecule of 'ethenoadenine' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA N-glycosylase activity' of 'MPG glycosylase'.
At the beginning of this reaction, 1 molecule of 'MPG glycosylase:3-methyladenine complex' is present. At the end of this reaction, 1 molecule of 'DNA containing an MPG-bound apurinic/apyrimidinic site', and 1 molecule of '3-Methyladenine' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA N-glycosylase activity' of 'MPG glycosylase'.
Transmembrane transport of small molecules
hNTH1 glycosylase mediated recognition and binding of cytosine glycol
At the beginning of this reaction, 1 molecule of 'MYH glycosylase:adenine complex' is present. At the end of this reaction, 1 molecule of 'DNA containing an MYH-bound apurinic/apyrimidinic site', and 1 molecule of '8-oxoguanine' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA N-glycosylase activity' of 'MYH glycosylase'.
hNTH1 glycosylase mediated recognition and binding of dihydrouracil
hNTH1 glycosylase mediated recognition and binding of formamidopyrimidine
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'.
hNTH1 glycosylase mediated recognition and binding of thymine glycol
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.
Cleavage of thymine glycol by hNTH1 glycosylase
Damaged purines are first cleaved by purine-specific glycosylases (see Lindahl and Wood 1999).
Oxidoreductases in lipoxin A4 metabolic inactivation: a novel role for 15-oxoprostaglandin 13-reductase/leukotriene B4 12-hydroxydehydrogenase in inflammation
Cleavage of cytosine glycol by hNTH1 glycosylase
Cleavage of dihydrouracil by hNTH1 glycosylase
Cleavage of formamidopyrimidine by hNTH1 glycosylase
Molecular cloning of AMP deaminase isoform L. Sequence and bacterial expression of human AMPD2 cDNA
Vertebrate agmatinases: what role do they play in agmatine catabolism?
Molecular properties of the SLC13 family of dicarboxylate and sulfate transporters
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).
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.
Agmatine: at the crossroads of the arginine pathways
Reactive cellular catabolites can cause DNA damage by 6-O-methylation of guanine. 6-O-methylguanine can pair ambiguously with both C and T, and can cause transition mutations. Active reversal of such damage can be facilitated by proteins having 6-O-methylguanine-DNA methyltransferase (MGMT) activity. MGMT removes the methyl group from the guanine and transfers it to the cysteine residue at position 145 on the protein itself. MGMT thus methylated is not regenerated, as the S-methylcysteine is very stable. This is an energetically expensive approach to DNA repair as one entire protein molecule is sacrificed per lesion that is corrected in this manner (Yang et al. 2011).
DNA damage can be directly reversed by dealkylation.
Molecular variation in relation to purine metabolism
J Clin Pathol Suppl (R Coll Pathol) 8:48-63
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.
At the beginning of this reaction, 1 molecule of 'hNTH1 glycosylase:cytosine glycol complex' is present. At the end of this reaction, 1 molecule of 'cytosine glycol', and 1 molecule of 'DNA containing a hNTH1-bound apurinic/apyrimidinic site' are present. This reaction takes place in the 'nucleus' and is mediated by the 'pyrimidine-specific oxidized base lesion DNA N-glycosylase activity' of 'hNTH1'.
At the beginning of this reaction, 1 molecule of 'hNTH1 glycosylase:thymine glycol' is present. At the end of this reaction, 1 molecule of 'Thymine glycol', and 1 molecule of 'DNA containing a hNTH1-bound apurinic/apyrimidinic site' are present. This reaction takes place in the 'nucleus' and is mediated by the 'pyrimidine-specific oxidized base lesion DNA N-glycosylase activity' of 'hNTH1'.
At the beginning of this reaction, 1 molecule of 'hNTH1 glycosylase: foramidopyrimidine complex' is present. At the end of this reaction, 1 molecule of 'formamidopyrimidine', and 1 molecule of 'DNA containing a hNTH1-bound apurinic/apyrimidinic site' are present. This reaction takes place in the 'nucleus' and is mediated by the 'pyrimidine-specific oxidized base lesion DNA N-glycosylase activity' of 'hNTH1'.
At the beginning of this reaction, 1 molecule of 'hNTH1 glycosylase:dihydrouracil complex' is present. At the end of this reaction, 1 molecule of 'DNA containing a hNTH1-bound apurinic/apyrimidinic site', and 1 molecule of '5,6-Dihydrouracil' are present. This reaction takes place in the 'nucleus' and is mediated by the 'pyrimidine-specific oxidized base lesion DNA N-glycosylase activity' of 'hNTH1'.
Depyrimidination of a damaged nucleotide is mediated by a pyrimidine-specific DNA glycosylase. The glycosylase cleaves the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar generating a free base and an apyrimidinic (AP) site.
Damaged pyrimidines are first cleaved by pyrimide-specific glycosylases (see Lindahl and Wood 1999).
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Mitochondrial tRNA import: are there distinct mechanisms?
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E2F1 binds to E2F binding sites on the genome activating the synthesis of the target proteins. For annotation purposes, the reactions regulated by E2F1 are grouped under this pathway and information about the target genes alone are displayed for annotation purposes. Cellular targets for activation by E2F1 include thymidylate synthetase, Rir2, Dihydrofolate reductase, Cdc2, Cyclin A1, Cdc6 (DeGregori et al., 1995), Cdt1 (Yoshida and Inoue, 2004), CDC45 (Arata et al., 2000), CDC6 (Yan et al., 1998; Ohtani et al., 1998), Cyclin E (Ohtani et al., 1996), Emi1 (Hsu et al., 2002), and Orc1 (Ohtani et al., 1997). The activation of TK2 (Dnk1) and Cdc25A by E2F1 have been inferred from similar events in Drosophila (Duronio and O'Farrell, 1994;Reis and Edgar, 2004). Rir2 protein is involved in dNTP level regulation and activation of this enzyme results in higher levels of dNTPs in anticipation of S-phase. E2F activation of Rir2 has been shown also in Drosophila by Duronio and O'Farrell (1994). E2F1 activation of CDC45 is shown in mouse cells by using human E2F1 construct (Arata et al., 2000). Cyclin E is also transcriptionally regulated by E2F1. Cyclin E protein plays important role in the transition of G1 in S-phase by associating with Cdk2 (Ohtani et al., 1996). E2F activation of PCNA has been demonstrated in Drosophila (DeGregori et al., 1995) and in some human cells by using recombinant adenovirus constructs. E2F activation of Polymerase A (Pol A) has been demonstrated in some human cells. It has also been demonstrated in Drosophila by Ohtani and Nevins (1994). It has been observed in Drosophila that E2F1 regulated expression of Orc1 stimulates ORC1-6 complex formation and binding to the origin of replication (Asano and Wharton, 1999). Orc1-6 recruit Cdc6 and Cdt1 that are required to recruit the MCM2-7 replication helicases. E2F1 regulation incorporates a feedback mechanism where in Geminin can inhibit MCM2-7 recruitment of ORC1-6 complex by interacting with Cdc6/Cdt1. The activation of Cdc25A and TK2 (Dnk1) by E2F1 has been inferred from similar events in Drosophila (Duronio RJ, O'Farrell 1994; Reis and Edgar, 2004). E2F1 activates string (Cdc25) that in turn activates Cyclin B/Cdk1. A similar phenomenon has been observed in mouse NIH 3T3 cells and in Rat1 cells.
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.
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.
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).
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).
Unlike other glycoproteins, correct folding of MHC class I molecules is not sufficient to trigger their exit from the ER, they exit only after peptide loading. Described here is the process of antigen presentation which consists of the folding, assembly, and peptide loading of MHC class I molecules. The newly synthesized MHC class I Heavy Chain (HC) is initially folded with the help of several chaperones (calnexin, BiP, ERp57) and then binds with Beta-2-microglobulin (B2M). This MHC:B2M heterodimer enters the peptide loading complex (PLC), a multiprotein complex that includes calreticulin, endoplasmic reticulum resident protein 57 (ERp57), transporter associated with antigen processing (TAP) and tapasin. Peptides generated from Ub-proteolysis are transported into the ER through TAP. These peptides are further trimmed by ER-associated aminopeptidase (ERAP) and loaded on to MHC class I molecules. Stable MHC class I trimers with high-affinity peptide are transported from the ER to the cell surface by the Golgi apparatus.
After processing by the proteasome, some of the oligopeptides could be reinternalized to the phagosome lumen of the same phagosome through the TAP complex probably acquired during ER-phagosome fusion. Guermonprez et al. (2003) tested this model and observed abundant TAP complex in early phagosomes and its reduction over time. Electron microscopy analysis of purified phagosomes also showed the insertion of TAP2 into the phagosomal membrane.
Ttransporter associated with antigen processing (TAP) is a heterodimeric complex, composed of TAP1 and TAP2 proteins, members of the ATP-binding cassette (ABC) superfamily. TAP consists of two transmembrane domains (TMDs) and two cytosolic nucleotide-binding domains. Peptide binding to the cytosolic-facing cavity formed by the TMDs causes it to undergo a conformational change that induces ATP hydrolysis, forcing the opening of a pore and translocation of the peptide into the ER lumen. TAP transports peptides in the range of 8-16 amino acids into the ER, which is the peptide length typically generated by the immunoproteasome.
Five SLC gene families encode proteins that mediate transport of amines (neurotransmitters, biogenic amines, ammonium and choline). They are SLC6, SLC14, SLC18, SLC42. The fifth family, SLC22, will appear in a later release (He L et al, 2009).
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
Irreversible inactivation of glutathione peroxidase 1 and reversible inactivation of peroxiredoxin II by H2O2 in red blood cells
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.
Frizzled/PCP signalling: a conserved mechanism regulating cell polarity and directed motility
At the beginning of this reaction, 1 molecule of 'MPG glycosylase', and 1 molecule of 'Double-strand DNA containing a hypoxanthine' are present. At the end of this reaction, 1 molecule of 'MPG glycosylase:hypoxanthine complex' is present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'Double-strand DNA containing an adenine opposite to an 8-oxo guanine', and 1 molecule of 'MYH glycosylase' are present. At the end of this reaction, 1 molecule of 'MYH glycosylase:adenine complex' is present. This reaction takes place in the 'nucleus'.
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).
Phosphopantothenoylcysteine decarboxylase
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.
At the beginning of this reaction, 1 molecule of 'Double-strand DNA containing an ethenoadenine ', and 1 molecule of 'MPG glycosylase' are present. At the end of this reaction, 1 molecule of 'MPG glycosylase:ethenoadenine complex' is present. This reaction takes place in the 'nucleus'.
sodium-dependent multivitamin transporter
Cloning, tissue distribution, and functional analysis of the human Na+/N+ exchanger isoform, NHE3
At the beginning of this reaction, 1 molecule of 'Double-strand DNA containing a 3-methyladenine', and 1 molecule of 'MPG glycosylase' are present. At the end of this reaction, 1 molecule of 'MPG glycosylase:3-methyladenine complex' is present. This reaction takes place in the 'nucleus'.
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.
Nucleoside diphosphate kinase, mitochondrial
non-metastatic cells 4, protein expressed in
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.
non-metastatic cells 1, protein (NM23A) expressed in
Tumor metastatic process-associated protein
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.
Guanylate kinase (EC 2.7.4.8) (GMP kinase)
Sodium- and chloride-dependent choline transport by CHT
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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).
NaDC1 co-transports dicarboxylic acids and a sodium ion
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NaS2 co-transports sulphate and two sodium ions
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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).
NACT co-transports trivalent citrate and a sodium ion
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NaDC3 co-transports the dicarboxylic acid succinate and three sodium ion
ZnT2 facilitates zinc vesicular sequestration
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DCT1 (NRAMP2) mediates divalent iron uptake across the apical membrane of enterocytes
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ZnT8 transports zinc into the secretory vesicles of pancreatic beta cells specifically
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branched chain keto acid dehydrogenase E1, beta polypeptide
ZnT3 transports zinc into synaptic vesicles
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The human gene ATP7B encodes the copper-transporting ATPase 2 (ATP7B, ATPase2, Wilson's protein) which is expressed mainly in the liver, brain and kidneys (Bull et al, 1993). ATP7B resides on the trans-Golgi membrane where it it thought to sequester copper from the cytosol into the golgi (Yang et al, 1997). Defects in ATP7B are the cause of Wilson disease (WD), an autosomal recessive disorder of copper metabolism characterized by the toxic accumulation of copper in a number of organs, particularly the liver and brain (Thomas et al, 1995).
branched chain keto acid dehydrogenase E1, alpha polypeptide
The P-type ATPases (E1-E2 ATPases) are a large group of evolutionarily related ion pumps that are found in bacteria, archaea and eukaryotes. They are referred to as P-type ATPases because they catalyze auto-phosphorylation of a key conserved aspartate residue within the pump. They all appear to interconvert between at least two different conformations, E1 and E2. Most members of this transporter family pump a large variety of cations (Kuhlbrandt W, 2004).
The Wilson disease gene: spectrum of mutations and their consequences
The human gene ATP7A (MNK) encodes the copper-transporting ATPase 1 (ATP7A, ATPase1, Menkes protein) which is expressed in most tissues except the liver (Vulpe et al, 1993; Chelly et al, 1993). Normally, ATP7A resides on the trans-Golgi membrane (Dierick et al, 1997). When cells are exposed to excessive copper levels, it is rapidly relocalized to the plasma membrane where it functions in copper efflux (Petris and Mercer, 1999). Defects in ATP7A are the cause of Menkes disease (MNKD), an X-linked recessive disorder of copper metabolism characterized by generalized copper deficiency (Ambrosini and Mercer, 1999).
Mevalonate kinase is a cytosolic enzyme in humans
Influence of differential induction of histidine catabolic enzymes on histidine degradation in vivo
The sperm-specific Na+/H+ exchanger SLC9C1 (aka sodium/hydrogen exchanger 10, NHE10) is localized to the flagellar membrane and is involved in pH regulation of spermatozoa required for sperm motility and fertility. The activity of human SLC9C1 is inferred from experiments using mouse Slc9c1 (Wang et al. 2003).
Ion channels that mediate sensations such as pain, warmth, cold, taste pressure and vision. Channels that mediate these sensations include acid-sensing ion channels (ASICs) (Wang & Xu 2011, Qadri et al. 2012, Deval et al. 2010) and the transient receptor potential channels (TRPCs) (Takahashi et al. 2012, Numata et al. 2011 in "TRP Channels" Zhu, MX editor, CRC Press, 2011, Ramsey et al. 2006, Montell 2005). Many channels are sensitive to changes in calcium (Ca2+) levels, both inside and outside the cell. Examples are protein tweety homologs 2 and 3 (TTYH2, 3) (Suzuki 2006), bestrophins 1-4 (BEST1-4) (Sun et al. 2002, Tsunenari et al. 2003, Kunzelmann et al. 2009, Hartzell et al. 2008) and ryanodine receptor tetramers (RYRs) (Beard et al. 2009).
L-kynurenine/alpha-aminoadipate aminotransferase
The microsomal Na+/(PO4)3- transporter isoform 1 (SLC17A3, NPT4 isoform 1) is a member of the anion-cation symporter family. It is expressed in liver, kidney and intestine and may function as a cotransporter of sodium (Na+) and phosphate ((PO4)3- or Pi) across the ER membrane (Melis et al. 2004).
NaS1 co-transports sulphate and a sodium ion
Glutaryl-CoA dehydrogenase, mitochondrial
Human serum urate levels are largely maintained by its reabsorption and secretion in the kidney. Loss of this maintenance can elevate urate levels leading to gout, hypertension, and various cardiovascular diseases. Renal urate reabsorption is controlled via two proximal tubular urate transporters; apical SLC22A12 (URAT1) and basolateral SLC2A9 (URATv1, GLUT9). On the other hand, urate secretion is mediated by the orphan sodium phosphate transporter 4 isoform 2 (SLC17A3, NPT4 isoform 2). It is mainly expressed at the apical side of renal tubules and functions as a voltage-driven urate transporter (Jutabha et al. 2010). Genetic variations in SLC17A3 influence the variance in serum uric acid concentrations and define the serum uric acid concentration quantitative trait locus 4 (UAQTL4; MIM:612671). Excess serum urate (hyperuricemia) can lead to the development of gout, characterized by tissue deposition of monosodium urate crystals.
L-tyrosine:2-oxoglutarate aminotransferase
Protein metabolism comprises the pathways of translation, post-translational modification and protein folding.
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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.
Passive Transport of Water into Cells by Aquaporins
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The Unfolded Protein Response (UPR) is a regulatory system that protects the Endoplasmic Reticulum (ER) from overload. The UPR is provoked by the accumulation of improperly folded protein in the ER during times of unusually high secretion activity. Analysis of mutants with altered UPR, however, shows that the UPR is also required for normal development and function of secretory cells. One level at which the URP operates is transcriptional and translational regulation: mobilization of ATF6 and IRE1 leads to increased transcription of genes encoding chaperones, and mobilization of PERK (pancreatic eIF2alpha kinase) leads to phosphorylation of the translation initiation factor eIF2alpha and global down-regulation of protein synthesis. These three regulatory pathways are annotated here.
Concentrative transport (import) of nucleosides plus sodium ions by solute carrier family 28 (sodium-coupled nucleoside transporter), member 2
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Concentrative transport (import) of a nucleoside and two sodium ions by solute carrier family 28 (sodium-coupled nucleoside transporter), member 3
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Concentrative transport (import) of a nucleoside and a sodium ions by solute carrier family 28 (sodium-coupled nucleoside transporter), member 1
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Passive Transport of Urea into Cells by Aquaporins
Passive Transport of Glycerol out of Cells by Aquaporins
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Passive Transport of Glycerol into Cells by Aquaporins
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Passive Transport of Water out of Cells by Aquaporins
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Cytosolic UAP1 catalyzes the reaction of N-acetyl-D-glucosamine 1-phosphate (GlcNAc1P) and UTP to UDP-N-acetyl-D-glucosamine and pyrophosphate. Structural studies indicate that the active form of the enzyme is a dimer (Peneff C et al, 2001).
ornithine aminotransferase, mitochondrial
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.
adenosine 5'-monophosphate [ChEBI:16027]
Identification of natural resistance-associated macrophage protein in peripheral blood lymphocytes
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.
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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.
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.
dihydrolipoamide branched chain transacylase E2
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.
HUT2 and HUT11 mediate urea transport in kidney and erythrocytes respectively
The GFPT1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
Xbp-1 (S) binds the sequence CCACG in ER Stress Responsive Elements (ERSE, consensus sequence CCAAT (N)9 CCACG) located upstream from many genes. The ubiquitous transcription factor NF-Y, a heterotrimer, binds the CCAAT portion of the ERSE and together the IRE1-alpha: NF-Y complex activates transcription of a set of chaperone genes including DNAJB9, EDEM, RAMP4, p58IPK, and others. This results in an increase in protein folding activity in the ER.
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SLC17A3-2 transports cytosolic urate to extracellular region
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4-trimethylaminobutyraldehyde dehydrogenase
aldehyde dehydrogenase 9 family, member A1
Formation of glucosamine 6-phosphate from fructose 6-phosphate and glutamine
5'-Phosphoribosyl-N-formylglycinamide [ChEBI:18272]
Copper export from cells by copper-transporting ATPase1
ATP7A transports cytosolic Cu2+ to extracellular region
Passive Transport of Glycerol into Cell by Aquaporin-9
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SLC17A3-1 cotransports extracellular Na+ and Pi to cytosol
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Copper sequestration by copper-transporting ATPase 2
ATP7B transports cytosolic Cu2+ to Golgi lumen
Passive Transport of Urea out of Cells by Aquaporins
Passive Transport of Glycerol out of Cell by Aquaporin-7
Passive Transport of Water out of Cell by Aquaporin-3
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Cloning and expression of AQP3, a water channel from the medullary collecting duct of rat kidney
2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
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Cleavage of hypoxanthine by MPG glycosylase
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Cleavage of ethenoadenine by MPG glycosylase
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delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor
Cleavage of 3-methyladenine by MPG glycosylase
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.
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Cleavage 8-oxo guanine by MYH glycosylase
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.
MYH glycosylase mediated recognition and binding of an adenine opposite to an 8-oxo guanine
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.
MPG glycosylase mediated recognition and binding of hypoxanthine
The transport of iron between cells is mediated by transferrin. However, iron can also enter and leave cells not only by itself, but also in the form of heme and siderophores. When entering the cell via the main path (by transferrin endocytosis), its goal is not the (still elusive) chelated iron pool in the cytosol nor the lysosomes but the mitochondria, where heme is synthesized and iron-sulfur clusters are assembled (Kurz et al,2008, Hower et al 2009, Richardson et al 2010).
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MPG glycosylase mediated recognition and binding of ethenoadenine
MPG glycosylase mediated recognition and binding of 3-methyladenine
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..
3-Phospho-D-glyceroyl phosphate [ChEBI:16001]
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.
ornithine carbamoyltransferase, mitochondrial
GlcNAc1P is dephosphorylated to UDP-N-acetyl-glucosamine
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) and AQP10 are 6-pass transmembrane proteins that passively transport urea across the plasma membrane through a pore in each subunit of a homotetramer.
carbamoyl-phosphate synthase (ammonia), mitochondrial
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Human cytosolic thymidine kinase. Purification and physical characterization of the enzyme from HeLa cells
Molecular physiology of cation-coupled Cl- cotransport: the SLC12 family
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Cloning, characterization, and modeling of mouse and human guanylate kinases
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phenylalanine + tRNA(Phe) + ATP => Phe-tRNA(Phe) + AMP + pyrophosphate
proline + tRNA(Pro) + ATP => Pro-tRNA(Pro) + AMP + pyrophosphate
serine + tRNA(Ser) + ATP => Ser-tRNA(Ser) + AMP + pyrophosphate
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tryptophan + tRNA(Trp) + ATP => Trp-tRNA(Trp) + AMP + pyrophosphate
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tyrosine + tRNA(Tyr) + ATP => Tyr-tRNA(Tyr) + AMP + pyrophosphate
Na+/H+ exchanger transport (at cell membrane)
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Na+/H+ exchanger transport (at trans-golgi membrane)
Na+/H+ exchanger transport (at early endosome membrane)
Na+/H+ exchanger transport (at late endosome membrane)
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
Targeting and translocation of endothelial nitric oxide synthase
SLC1A4-mediated exchange of extracellular threonine for cytosolic alanine, serine, or cysteine
Molecular cloning of human class IV alcohol dehydrogenase cDNA.
SLC1A5-mediated exchange of alanine and glutamine across the plasma membrane
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SLC1A4-mediated exchange of extracellular cysteine for cytosolic alanine, serine, or threonine
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SLC1A4-mediated exchange of extracellular serine for cytosolic alanine, threonine, or cysteine
Role of glutathione and glutathione peroxidase in human platelet arachidonic acid metabolism
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SLC1A4-mediated exchange of extracellular alanine for cytosolic serine, threonine, or cysteine
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Primary structure of human placental 5'-nucleotidase and identification of the glycolipid anchor in the mature form
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SLC7A2, isoform A (CAT-2A)-mediated uptake of cationic amino acids
SLC7A1 (CAT-1)-mediated uptake of cationic amino acids
Beta-enolase deficiency, a new metabolic myopathy of distal glycolysis
SLC1A5-mediated exchange of glutamine and alanine across the plasma membrane
Class I MHC mediated antigen processing & presentation
Structure of human argininosuccinate synthetase
Acta Crystallogr D Biol Crystallogr 64:279-86
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Type I Na+-coupled phosphate co-transport
Na+/I- cotransport (influx) by the Na+/I- symporter
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SLC7A2, isoform B (CAT-2B)-mediated uptake of cationic amino acids
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Localization of human equilibrative nucleoside transporters, hENT1 and hENT2, in renal epithelial cells
SLC7A3 (CAT-3)-mediated uptake of cationic amino acids
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SOAT can transport taurolithocholate-3-sulphate
Na+-dependent monocarboxylate transport by SMCT
Structure of a type II thymidine kinase with bound dTTP
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Old and new generation lipid mediators in acute inflammation and resolution
(S)-alpha-amino-beta-phenylpropionic acid
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NaPO(4) cotransport type III (PiT1) expression in human embryonic kidney cells and regulation by PTH
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Emerging roles for E2F: beyond the G1/S transition and DNA replication.
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5-methyltetrahydrofolyl polyglutamate macromolecule
5-methyltetrahydrofolyl polyglutamate macromolecule [ChEBI:63907]
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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
Exosomes mediate stromal mobilization of autocrine Wnt-PCP signaling in breast cancer cell migration
Crystal structure of human kynurenine aminotransferase II, a drug target for the treatment of schizophrenia
The complete digestion of human milk triacylglycerol in vitro requires gastric lipase, pancreatic colipase-dependent lipase, and bile salt-stimulated lipase
Crystal structure of human kynurenine aminotransferase II
Recognition and association of DNA glycosylase with site containing an affected pyrimidine
Degradation of cysteine and homocysteine
Aminoacyl tRNA synthetases and their connections to disease
Expression and characterization of a human mitochondrial phenylalanyl-tRNA synthetase
Cloning of three human multifunctional de novo purine biosynthetic genes by functional complementation of yeast mutations
Human phosphoglycerate kinase. I. Crystallization and characterization of normal enzyme
PPARalpha controls the intracellular coenzyme A concentration via regulation of PANK1alpha gene expression
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Am. J. Physiol., Cell Physiol. 302:C943-65
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Isolation of pi-alcohol dehydrogenase of human liver: is it a determinant of alcoholism?
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Biosynthesis and metabolism of leukotrienes
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Cytosolic aldehyde dehydrogenase (ALDH1) variants found in alcohol flushers
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Glycoprotein folding, quality control and ER-associated degradation
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Human protoporphyrinogen oxidase: expression, purification, and characterization of the cloned enzyme
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Crystal structures of recombinant human dihydrofolate reductase complexed with folate and 5-deazafolate
Neurotrophin-regulated signalling pathways
Philos Trans R Soc Lond B Biol Sci 361:1545-64
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Mitochondrial energy-linked nicotinamide nucleotide transhydrogenase. Membrane topography of the bovine enzyme
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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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Characterization of MOCS1A, an oxygen-sensitive iron-sulfur protein involved in human molybdenum cofactor biosynthesis
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ChREBP activates metabolic gene expression
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Mercury-sensitive residues and pore site in AQP3 water channel
13,14-dihydro-15-keto-PGF2a [ChEBI:63976]
Synthesis of Prostaglandins (PG) and Thromboxanes (TX)
Characterization of the gene encoding human peroxisomal 3-oxoacyl-CoA thiolase (ACAA). No large DNA rearrangement in a thiolase-deficient patient
Efflux and compartmentalization of zinc by members of the SLC30 family of solute carriers
The sodium/glucose cotransport family SLC5
The SLC39 family of metal ion transporters
13,14-dihydro-15-keto-Lipoxin A4 [ChEBI:63993]
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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
Molecular cloning and characterization of a novel muscle adenylosuccinate synthetase, AdSSL1, from human bone marrow stromal cells
Metabolism, function and mass spectrometric analysis of bis(monoacylglycero)phosphate and cardiolipin
Endogenous synthesis of coenzyme Q in eukaryotes
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Human IL4I1 is a secreted L-phenylalanine oxidase expressed by mature dendritic cells that inhibits T-lymphocyte proliferation
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Recognition and association of DNA glycosylase with site containing an affected purine
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L-Glutamate 5-semialdehyde [ChEBI:17232]
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Functional characterization of a human aquaporin 0 mutation that leads to a congenital dominant lens cataract
The vitelliform macular dystrophy protein defines a new family of chloride channels
Proc. Natl. Acad. Sci. U.S.A. 99:4008-13
Human liver alcohol dehydrogenase: purification, composition, and catalytic features.
Human liver type pyruvate kinase: complete amino acid sequence and the expression in mammalian cells
Wnt/Fz signaling and the cytoskeleton: potential roles in tumorigenesis
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1857-1895
Proximal events in Wnt signal transduction
Phosphorylation of carbovir enantiomers by cellular enzymes determines the stereoselectivity of antiviral activity
Principles of bioactive lipid signalling: lessons from sphingolipids
Wnt/beta-catenin signaling: components, mechanisms, and diseases
A glycine residue (Gly2) at the N-terminus of eNOS is myristoylated, providing membrane localization.
Many hormones that affect individual physiological processes including the regulation of appetite, absorption, transport, and oxidation of foodstuffs influence energy metabolism pathways. While insulin mediates the storage of excess nutrients, glucagon is involved in the mobilization of energy resources in response to low blood glucose levels, principally by stimulating hepatic glucose output. Small doses of glucagon are sufficient to induce significant glucose elevations. These hormone-driven regulatory pathways enable the body to sense and respond to changed amounts of nutrients in the blood and demands for energy. Glucagon and Insulin act through various metabolites and enzymes that target specific steps in metabolic pathways for sugar and fatty acids. The processes responsible for the long-term control of fat synthesis and short term control of glycolysis by key metabolic products and enzymes are annotated in this module as six specific pathways: Pathway 1. Glucagon signalling in metabolic pathways: In response to low blood glucose, pancreatic alpha-cells release glucagon. The binding of glucagon to its receptor results in increased cAMP synthesis, and Protein Kinase A (PKA) activation. Pathway 2. PKA mediated phosphorylation:PKA phosphorylates key enzymes, e.g., 6-Phosphofructo-2-kinase /Fructose-2,6-bisphosphatase (PF2K-Pase) at serine 36, and regulatory proteins, e.g., Carbohydrate Response Element Binding Protein (ChREBP) at serine 196 and threonine 666. Insulin mediated responses to high blood glucose will be annotated in future versions of Reactome. In brief, the binding of insulin to its receptor leads to increased protein phosphatase activity and to hydrolysis of cAMP by cAMP phosphodiesterase. These events counteract the regulatory effects of glucagon. Pathway 3: Insulin stimulates increased synthesis of Xylulose-5-phosphate (Xy-5-P). Activation of the insulin receptor results indirectly in increased Xy-5-P synthesis from Glyceraldehyde-3-phosphate and Fructose-6-phosphate. Xy-5-P, a metabolite of the pentose phosphate pathway, stimulates protein phosphatase PP2A. Pathway 4: AMP Kinase (AMPK) mediated response to high AMP:ATP ratio: In response to diet with high fat content or low energy levels, the cytosolic AMP:ATP ratio is increased. AMP triggers a complicated cascade of events. In this module we have annotated only the phosphorylation of ChREBP by AMPK at serine 568, which inactivates this transcription factor. Pathway 5: Dephosphorylation of key metabolic factors by PP2A: Xy-5-P activated PP2A efficiently dephosphorylates phosphorylated PF2K-Pase resulting in the higher output of F-2,6-P2 that enhances PFK activity in the glycolytic pathway. PP2A also dephosphorylates (and thus activates) cytosolic and nuclear ChREBP. Pathway 6: Transcriptional activation of metabolic genes by ChREBP: Dephosphorylated ChREBP activates the transcription of genes involved in glucose metabolism such as pyruvate kinase, and lipogenic genes such as acetyl-CoA carboxylase, fatty acid synthetase, acyl CoA synthase and glycerol phosphate acyl transferase. The illustration below summarizes this network of events. Black lines are metabolic reactions, red lines are negative regulatory events, and green lines are positive regulatory events (figure reused with permission from Veech (2003) - Copyright (2003) National Academy of Sciences, U.S.A.).
Palymitoylated, myristoylated eNOS forms a dimer and is transported from the Golgi to the plasma membrane. Transport is thought to be mediated by intracellular vesicles, but the details remain unknown.
2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial (COQ5) catalyses the C-methyltransferase conversion of 2-methoxy-6-decaprenyl-1,4-benzoquinol (MDMQ10H2) to 6-methoxy-3-methyl-2-decaprenyl-1,4-benzoquinol (DMQ10H2). This reaction is inferred from the equivalent reaction in yeast (Barkovich et al. 1997).
The length of the polyisoprenoid chain of ubiquinone aka coenzyme Q (Q), varies depending on the species involved: it is 6 in budding yeast, Saccharomyces cerevisiae, (Q6) and 10 in humans (Q10). Most ubiquinone is naturally reduced to ubiquinol (Q10H2 in humans) and it is this form which dominates in most human tissues. It functions as an ubiquitous coenzyme in redox reactions and its ability both to associate with complexes I and III of the electron transport chain and to move freely in the inner mitochondrial membrane are central to its role in electron transport. In eukaryotes ubiquinones/ubiquinols are also found in other membranes such as the endoplasmic reticulum, Golgi vesicles, lysosomes and peroxisomes. Ubiquinol/ubiquinone is synthesized in the following way. Initially, the polyisoprenoid tail is assembled by a polyprenyl diphosphate synthase. Next, 4 hydroxybenzoate polyprenyltransferase (COQ2) catalyses the formation of the covalent linkage between the benzoquinone head group and the tail to produce 4 hydroxy 3 polyprenyl benzoic acid intermediate (DHB, 3 decaprenyl 4 hydroxybenzoic acid in humans). There follows modifications of the aromatic ring starting with hydroxylation, followed by O methylation, and decarboxylation to form the 2 methoxy 6 polyprenyl phenol intermediate (DMPhOH ; 2 methoxy 6 decaprenylphenol in humans). Following this, two additional methylations, one C methylation, and one O methylation step, finally generate the fully substituted hydroquinone, ubiquinol (Szkopinska 2000, Kagan & Quinn 2000, Tran & Clarke 2007, Kawamukai 2009).
Lipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphingolipids, eicosanoids, cholesterol, bile salts, steroid hormones, and fat-soluble vitamins. They function as a major source of energy (fatty acids, triacylglycerols, and ketone bodies), are major constituents of cell membranes (cholesterol and phospholipids), play a major role in their own digestion and uptake (bile salts), and participate in numerous signaling and regulatory processes (steroid hormones, eicosanoids, phosphatidylinositols, and sphingolipids). Because of their poor solubility in water, most lipids in extracellular spaces in the human body are found as complexes with specific carrier proteins. Regulation of the formation and movement of these lipoprotein complexes is a critical aspect of human lipid metabolism, and lipoprotein abnormalities are associated with major human disease processes including atherosclerosis and diabetes. The central steroid in human biology is cholesterol, obtained from animal fats consumed in the diet or synthesized de novo from acetyl-coenzyme A. (Vegetable fats contain various sterols but no cholesterol.) Cholesterol is an essential constituent of lipid bilayer membranes and is the starting point for the biosyntheses of bile acids and salts, steroid hormones, and vitamin D. Bile acids and salts are mostly synthesized in the liver. They are released into the intestine and function as detergents to solubilize dietary fats. Steroid hormones are mostly synthesized in the adrenal gland and gonads. They regulate energy metabolism and stress responses (glucocorticoids), salt balance (mineralocorticoids), and sexual development and function (androgens and estrogens). At the same time, chronically elevated cholesterol levels in the body are associated with the formation of atherosclerotic lesions and hence increased risk of heart attacks and strokes. The human body lacks a mechanism for degrading excess cholesterol, although an appreciable amount is lost daily in the form of bile salts and acids that escape recycling. Aspects of lipid metabolism currently annotated in Reactome include lipid digestion, mobilization, and transport; fatty acid, triacylglycerol, and ketone body metabolism; peroxisomal lipid metabolism; phospholipid and sphingolipid metabolism; cholesterol biosynthesis; bile acid and bile salt metabolism; and steroid hormone biosynthesis.
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.).
The main steps involved in de novo sphingolipid synthesis are annotated here (Merrill 2002, 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).
The polyprenyl diphosphate synthase consists of a tetramer comprising two units of decaprenyl-diphosphate synthase subunit 1 (PDSS1) and two units of decaprenyl-diphosphate synthase subunit 2 (PDSS2). It catalyses the combination of 2-trans,6-trans-farnesyl diphosphate (FPP) with isopentenyl diphosphate (IPPP) to form the polyisoprenoid tail all-trans-decaprenyl diphosphate (all-E-10PrP2) (Saiki et al. 2005, Tekle et al. 2008).
Molecular cloning, sequence analysis, and expression of a human liver cDNA coding for fructose-6-P,2-kinase:fructose-2,6-bisphosphatase
KDSR (3-ketodihydrosphingosine reductase) enzyme associated with the cytosolic face of the endoplasmic reticulum membrane catalyzes the reduction of 3-ketosphinganine by NADPH to form sphinganine (dihydrosphingosine) (Kihara and Igarashi 2004).
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.
Lipoxins A4 (LXA4) and B4 (LXB4), structurally characterized from human neutrophils incubated with 15-hydroperoxy-eicosatetraenoic acid (15-HpETE), each contain three hydroxyl moieties and a conjugated tetraene. The third hydroxyl of LXA4 is positioned at C-6, and of LXB4 at C-14. The action of arachidonate 5-lipoxygenase (ALOX5), in concert with an arachidonate 12-lipoxygenase (ALOX12) or arachidonate 15-lipoxygenase (ALOX15) activity, has been shown to produce lipoxins by three distinct pathways. Neutrophil ALOX5 can produce and secrete leukotriene A4 (LTA4) that is taken up by platelets, where it is acted upon by ALOX12 to form lipoxins. Likewise, ALOX15s can generate either 15-hydroperoxy-eicosatetraenoic acid (15-HpETE) or 15-hydro-eicosatetraenoic acid (15-HETE) that can be taken up by monocytes and neutrophils, where highly expressed ALOX5 uses it to generate lipoxins. Finally, aspirin acetylated prostaglandin G/H synthase 2 (PTGS2), rendered unable to synthesize prostaglandins, can act as a 15-lipoxygenase. This leads to the formation of 15R-HETE and culminates in creation of epi-lipoxins, which have altered stereochemistry at the C-15 hydroxyl but similar biological potency (Chiang et al. 2006, Buczynski et al. 2009, Vance & Vance 2008).
Prostaglandin reductase 1 (PTGR1) aka LTB4DH, a 15-oxoprostaglandin 13-reductase (Yokomizo et al. 1996), metabolises 15-oxo lipoxin A4 aka 15-keto-LXA4 (15k-LXA4) to produce 13,14-dihydro-15-keto-Lipoxin A4 (dhk-LXA4). This reaction has been inferred from a reaction in pig (Clish et al. 2000).
Glutathione peroxidase 1 (GPX1) (Bryant et al. 1982, Sutherland et al. 2001), 2 (GPX2) (Chu et al. 1993), and 4 (Bryant et al. 1982, Sutherland et al. 2001) are involved in converting 12S-hydroperoxy-eicosatetraenoic acid (12S-HpETE) to 12S-hydro-eicosatetraenoic acid (12S-HETE). GPXs are selenoenzymes that are responsible for reducing the cellular peroxide. Cellular GPXs compete with hepoxilins A3 (HXA3) synthase for 12S-HpETE as substrate either to produce 12S-HETE or to convert to HXA3, respectively.
The 12-eicosatetraenoic acids: 12-hydroperoxy-eicosatetraenoic acid (12-HpETE), 12-hydroxyeicosatetraenoic acid (12-HETE) and 12-oxo-eicosatetraenoic acid (12-oxoETE) are formed after the initial step of arachidonic acid oxidation by the arachidonate 12 and 15 lipoxygenases (ALOX12, ALOX12B and ALOX15 respectively). This part of the pathway is bifurcated at the level of 12S-hydroperoxy-eicosatetraenoic acid (12S-HpETE), which can either be reduced to 12S-hydro-eicosatetraenoic acid (12S-HETE) or converted to hepoxilins (Buczynski et al. 2009, Vance & Vance 2008).
The 15-eicosatetraenoic acids: 15-hydroperoxy-eicosatetraenoic acid (15-HpETE), 15-hydroxyeicosatetraenoic acid (15-HETE) and 15-oxo-eicosatetraenoic acid (15-oxoETE) are formed after the initial step of arachidonic acid oxidation by the arachidonate 15-lipoxygenases (ALOX15 and ALOX15B) (Buczynski et al. 2009, Vance & Vance 2008).
Glutathione peroxidase 1 (GPX1) (Bryant et al. 1982, Sutherland et al. 2001), 2 (GPX2) (Chu et al. 1993), and 4 (Bryant et al. 1982, Sutherland et al. 2001) are involved in converting 12R-hydroperoxy-eicosatetraenoic acid (12R-HpETE) to 12R-hydro-eicosatetraenoic acid (12R-HETE).
5-hydroperoxy-eicosatetraenoic acid (5-HpETE), 5-hydroxyeicosatetraenoic acid (5S-HETE) and 5-oxo-eicosatetraenoic acid (5-oxoETE) are formed after the initial step of arachidonic acid oxidation by arachidonate 5-lipoxygenase (ALOX5) (Buczynski et al. 2009, Vance & Vance 2008).
Glutathione peroxidases (GPXs) in human platelets (either GPX1, GPX2, or GPX4 are present in the cytosol) are involved in reducing 15S-hydroperoxyeicosatetraenoic acid (15S-HpETE) to 15S-hydroxyeicosatetraenoic acid (15S-HETE) (Hill et al. 1989).
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
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).
Prostaglandin reductase 1 (PTGR1) aka LTB4DH is a 13-prostaglandin reductase which metabolises eicosanoids by catalysing NADH/NADPH-dependant double bond reduction in 15-keto-prostaglandin E2 (15k-PGE2) and F2alpha (15k-PGF2a) to produce 13,14-dihydro-15-keto-prostaglandin E2 (dhk-PGE2) and F2alpha (dhk-PGF2a) respectively (Yokomizo 1996). This has been inferred from the reaction event in mice involving prostaglandin reductase 2 (Ptgr2) (Chou et al. 2007).
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
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).
Prostaglandin reductase 1 (PTGR1) aka LTB4DH metabolizes eicosanoids by catalysing the oxidation of leukotriene B4 (LTB4) to form 12-oxo-Leukotriene B4 (12-oxoLTB4) aka 12-Keto-LTB4. The gene was originally cloned as leukotriene B4 12-hydroxydehydrogenase (LTB4DH) but was later discovered to have dual functionality as a prostaglandin reductase (Yokomizo et al. 1996). This reaction has been inferred from a reaction in pigs (Yokomizo et al. 1993, Ensor et al. 1998).
Glutathione peroxidase 1 (GPX1) (Bryant et al. 1982, Sutherland et al. 2001), 2 (GPX2) (Chu et al. 1993), and 4 (Bryant et al. 1982, Sutherland et al. 2001) reduce 5-hydroperoxyeicosatetraenoic acid (5-HpETE) to 5-hydroxyeicosatetraenoic acid (5-HETE) in the presence of glutathione (GSH). This reaction is inferred from the event in rabbit involving the protein GPX1 (Chiba et al. 1999).
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.
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).
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).
Expression and characterization of a human pyruvate carboxylase variant by retroviral gene transfer
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).
Carbonyl reductase (CBR1) aka prostaglandin 9-keto reductase inactivates prostaglandin E2 (PGE2) by converting it to prostaglandin F2alpha (PGF2a) (Wermuth 1981, Miura et al. 2008).
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).
Acetylcholinesterase (ACHE) oligomers (comprising monomers, dimers and tetramers), anchored to the extracellular side of the plasma membrane, hydrolyze acetylcholine (AcCho) to form choline (Cho) and acetate (Weinstock & Groner 2008, Velan et al. 1991, Kryger et al. 2000). Acetylcholine from the synaptic cleft is degraded into inactive molecules, Cho and acetate by ACHE, which is located in the synaptic cleft (Weinstock & Groner 2008).
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).
The conjugation of phenylacetic acid in man, sub-human primates and some non-primate species
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).
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).
Cortisol, the major human glucocorticoid, is synthesized in the zona fasciculata of the adrenal cortex from pregnenolone. Pregnenolone is converted to 17alpha-hydoxyprogesterone in two reactions, both catalyzed by 3-beta-hydroxysteroid dehydrogenase/isomerase. 17Alpha-hydroxyprogesterone is hydroxylated by CYP21A2 to form 11-deoxycortisol, which in turn is converted to cortisol by CYP11B1. The conversion of the active steroid hormone, cortisol, to inactive cortisone occurs in many tissues, notably the liver (Payne and Hales 2004).
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.
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).
Cortisol and NADP+ react to form cortisone, NADPH, and H+. This reaction is catalyzed by 11beta-hydroxysteroid dehydrogenase (11beta-HSD), associated with the endoplasmic reticulum membrane. The conversion of cortisol, an active hormone, into inactive cortisone occurs in many tissues in the body, notably in the liver, and appears to play a role in regulating cortison activity.
Peroxisome proliferator-activated receptor alpha (PPAR-alpha) is the major regulator of fatty acid oxidation in the liver. PPARalpha is also the target of fibrate drugs used to treat abnormal plasma lipid levels. PPAR-alpha is a type II nuclear receptor (its subcellular location does not depend on ligand binding). PPAR-alpha forms heterodimers with Retinoid X receptor alpha (RXR-alpha), another type II nuclear receptor. PPAR-alpha is activated by binding fatty acid ligands, especially polyunsaturated fatty acids having 18-22 carbon groups and 2-6 double bonds. The PPAR-alpha:RXR-alpha heterodimer binds peroxisome proliferator receptor elements (PPREs) in and around target genes. Binding of fatty acids and synthetic ligands causes a conformational change in PPAR-alpha such that it releases the corepressors and binds coactivators (CBP-SRC-HAT complex, ASC complex, and TRAP-Mediator complex) which initiate transcription of the target genes. Target genes of PPAR-alpha participate in fatty acid transport, fatty acid oxidation, triglyceride clearance, lipoprotein production, and cholesterol homeostasis.
The set of genes regulated by PPAR-alpha is not fully known in humans, however many examples have been found in mice. Genes directly activated by PPAR-alpha contain peroxisome proliferator receptor elements (PPREs) in their promoters and include: 1) genes involved in fatty acid oxidation and ketogenesis (Acox1, Cyp4a, Acadm, Hmgcs2); 2) genes involved in fatty acid transport (Cd36, , Slc27a1, Fabp1, Cpt1a, Cpt2); 3) genes involved in producing fatty acids and very low density lipoproteins (Me1, Scd1); 4) genes encoding apolipoproteins (Apoa1, Apoa2, Apoa5); 5) genes involved in triglyceride clearance ( Angptl4); 6) genes involved in glycerol metabolism (Gpd1 in mouse); 7) genes involved in glucose metabolism (Pdk4); 8) genes involved in peroxisome proliferation (Pex11a); 9) genes involved in lipid storage (Plin, Adfp). Many other genes are known to be regulated by PPAR-alpha but whether their regulation is direct or indirect remains to be found. These genes include: ACACA, FAS, SREBP1, FADS1, DGAT1, ABCA1, PLTP, ABCB4, UGT2B4, SULT2A1, Pnpla2, Acsl1, Slc27a4, many Acot genes, and others (reviewed in Rakhshandehroo et al. 2010).
The HMGCS2 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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Mevalonate pyrophosphate decarboxylase (MPD) decarboxylates mevalonate-5-pyrophosphate into isopentenyl pyrophosphate while hydrolysing ATP to ADP and orthophosphate.
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.
Sodium-coupled sulphate, di- and tri-carboxylate transporters
Mevalonate kinase (MK) catalyzes the phosphorylation of mevalonate to mevalonate-5-phosphate.
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).
Human placental Na+-dependent multivitamin transporter. Cloning, functional expression, gene structure, and chromosomal localization.
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).
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.
Peroxisomal ACAA1 catalyzes the reaction of 3-ketohexacosanoyl-CoA and CoASH to form tetracosanoyl-CoA + acetyl-CoA (Bout et al. 1991).
CEL (bile salt-dependent lipase) catalyzes the hydrolysis of extracellular monoacylglycerols to yield glycerol and a long-chain fatty acid. This reaction, in the lumen of the small intestine, is essential for the complete digestion of milk-derived triacylglycerols in the nursing infant (Bernback et al. 1990). Its importance in adult fat digestion is unclear. While alternative splicing gives rise to two CEL isoforms, only the longer one encodes all of the residues that form the active site of the enzyme (Reue et al. 1991). In vitro, monomeric CEL protein is active even in the absence of bile salts. its activity is greatly increased when it is complexed with two molecules of cholate, chenodeoxycholate, or their glycine or taurine conjugates (Lombardo and Guy 1980), and the predominant form of the enzyme active on lipid micelles in the gut is a dimer of two such complexes (Aubert-Jousset et al. 2004). CEL is synthesized in pancreatic acinar cells and released into the small intestine. It is also synthesized in the mammary gland and is a constituent of breast milk (Lombardo 2001; Bernback et al. 1990).
The major sites of cellular phospholipid synthesis and molecular determinants of Fatty Acid and lipid head group specificity
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).
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).
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).
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.
Dietary lipids such as long-chain triacylglycerols and cholesterol esters are digested in the stomach and small intestine to yield long-chain fatty acids, monoacylglycerols, glycerol and cholesterol through the action of a variety of lipases, and are then absorbed into enterocytes.
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.
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.
The overall process of triglyceride (triacylglycerol) biosynthesis consists of four biochemical pathways: fatty acyl-CoA biosynthesis, conversion of fatty acyl-CoA to phosphatidic acid, conversion of phosphatidic acid to diacylglycerol, and conversion fo diacylglycerol to triacylglycerol.
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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).
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
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CEL (bile salt-dependent lipase) catalyzes the hydrolysis of extracellular cholesterol esters to yield cholesterol and a long-chain fatty acid. This reaction, in the lumen of the small intestine, is part of the process of digestion of dietary fats. While alternative splicing gives rise to two CEL isoforms, only the longer one encodes all of the residues that form the active site of the enzyme (Reue et al. 1991). In vitro, monomeric CEL protein is active even in the absence of bile salts. Its activity is greatly increased when it is complexed with two molecules of cholate, chenodeoxycholate, or their glycine or taurine conjugates (Lombardo and Guy 1980), and the predominant form of the enzyme active on lipid micelles in the gut is a dimer of two such complexes (Aubert-Jousset et al. 2004). CEL is synthesized in pancreatic acinar cells and released into the small intestine. It is also synthesized in the mammary gland and is a constituent of breast milk. The milk CEL is thought to play a role in digestion of milk fat in newborn infants, whose own pancreatic synthesis of the enzyme is low (Lombardo 2001; Bernback et al. 1990).
Renal physiology of SLC26 anion exchangers
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The reversible interconversion of ribose 5-phosphate and ribulose 5-phosphate is catalyzed by cytosolic ribose 5-phosphate isomerase (Huck et al. 2004).
Human Na(+)/H(+) exchanger isoform 6 is found in recycling endosomes of cells, not in mitochondria
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).
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).
The reversible interconversion of ribulose 5-phosphate and ribose 5-phosphate is catalyzed by cytosolic ribose 5-phosphate isomerase (Huck et al. 2004).
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.
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.
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).
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.
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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 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).
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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).
The fructose 2,6-bisphosphatase activity of cytosolic phosphofructokinase 2/fructose-2,6-bisphosphatase catalyzes the hydrolysis of fructose 2,6 bisphosphate to form fructose 6-phosphate. Fructose 2,6 bisphosphate is a key allosteric regulator of PFK1. In its absence the activity of PFK1 is reduced while fructose 1,6-bisphosphatase is activated, thus inhibiting glycolysis and favoring gluconeogenesis (Pilkis et al. 1995).
The reversible 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.
Glucose is the major form in which dietary sugars are made available to cells of the human body. Its breakdown is a major source of energy for all cells, and is essential for the brain and red blood cells. Glucose utilization begins with its uptake by cells and conversion to glucose 6-phosphate, which cannot traverse the cell membrane. Fates open to cytosolic glucose 6-phosphate include glycolysis to yield pyruvate, glycogen synthesis, and the pentose phosphate pathway. In some tissues, notably the liver and kidney, glucose 6-phosphate can be synthesized from pyruvate by the pathway of gluconeogenesis.
Cytosolic UDP-galactose 4-epimerase catalyzes the interconversion of UDP-D-galactose and UDPglucose (Schulz et al. 2004). The active form of the enzyme is a homodimer with one molecule of bound NAD per monomer (Thoden et al. 2000).
The main sources of galactose in the human diet are milk and milk products. The disaccharide lactose from these sources is hydrolyzed in the intestine to its constituent monosaccharides, glucose and galactose. Galactose is metabolized primarily in the liver in a sequence of three reactions that yield one molecule of glucose 1-phosphate per molecule of galactose. First, it is phosphorylated to yield galactose 1-phosphate. Then, galactose 1-phosphate and UDP-glucose react to form UDP-galactose and glucose 1-phosphate, and UDP-galactose undergoes epimerization to form UDP-glucose. In a reaction shared with other pathways, glucose 1-phosphate can be converted into glucose 6-phosphate (Holton et al. 2001; Elsas and Lai 2001).
Functional identification of SLC5A8, a tumor suppressor down-regulated in colon cancer, as a Na(+)-coupled transporter for short-chain fatty acids
Cytosolic pyruvate kinase catalyzes the transfer of a high-energy phosphate from phosphoenolpyruvate to ADP, forming pyruvate and ATP. This reaction, an instance of substrate-level phosphorylation, is essentially irreversible under physiological conditions. Four isozymes of human pyruvate kinase have been described, L, R, M1 and M2. Isozymes L and R are encoded by alternatively spliced transcripts of the PKLR gene; isozymes M1 and M2 are encoded by alternatively spliced transcripts of PKM2. In the body, L pyruvate kinase is found in liver (Tani et al. 1988), R in red blood cells (Kanno et al. 1991), M1 in muscle, heart and brain (Takenaka et al. 1991), and M2 in early fetal tissues and tumors (e.g., Lee et al. 2008). In all cases, the active form of the enzyme is a homotetramer, activated by fructose 1,6-bisphosphate (Valentini et al. 2002; Dombrauckas et al. 2005). Mutations in PKLR have been associated with hemolytic anemias (e.g., Zanella et al. 2005).
Cytosolic 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).
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 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).
Cytosolic phosphofructokinase 1 catalyzes the reaction of fructose 6-phosphate and ATP to form fructose 1,6-bisphosphate and ADP. This reaction, irreversible under physiological conditions, is the rate limiting step of glycolysis. Phosphofructokinase 1 activity is allosterically regulated by ATP, citrate, and fructose 2,6-bisphosphate. Phosphofructokinase 1 is active as a tetramer (although higher order multimers, not annotated here, may form in vivo). Two isoforms of phosphofructokinase 1 monomer, L and M, are widely expressed in human tissues. Different tissues can contain different homotetramers or heterotetramers: L4 in liver, M4 in muscle, and all possible heterotetramers, L4, L3M, L2M2, LM3, and M4, in red blood cells, for example (Raben et al. 1995; Vora et al. 1980, 1987; Vora 1981). A third isoform, P, is abundant in platelets, where it is found in P4, P3L, P2L2, and PL3 tetramers (Eto et al. 1994; Vora et al. 1987).
The 6-phosphofructo-2-kinase activity of cytosolic PFKFB (6-phosphofructo-2-kinase/fructose-2,6-biphosphatase) homodimer catalyzes the reaction of fructose 6-phosphate and ATP to form fructose 2,6-bisphosphate and ADP (Pilkis et al. 1988). Fructose 2,6-bisphosphate is not itself on the pathway of glycolysis. Rather, it acts as a positive allosteric effector of phosphofructokinase 1, greatly increasing the rate of synthesis of fructose 1,6-bisphosphate and hence the overall rate of glycolysis. The conversion of PFKFB between its dephosphorylated form, which catalyzes the synthesis of fructose 2,6-bisphosphate as described here, and its phosphorylated form, which catalyzes the hydrolysis of fructose 2,6-bisphosphate to fructose 6-phosphate and orthophosphate plays a central role in the short-term regulation of glycolysis (Pilkis et al. 1995). Four isoforms of PFKFB protein encoded by four different genes exhibit tissue-specific expression patterns. PFKFB1 is expressed in the liver (Algaier and Uyeda 1988), PFKFB2 is expressed in the heart (Hirata et al. 1998), PFKFB3 is ubiquitously expressed (Manes and el-Maghrabi 2005), and PFKFB4, originally described as a testis-specific gene product (Manzano et al. 1999), may also be expressed in several kinds of tumors.
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).
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.
The carboxylation of pyruvate to form oxaloacetate, catalyzed by mitochondrial pyruvate carboxylase, is an irreversible and allosterically regulated reaction (Jitrapakdee and Wallace 1999).
The reactions of glycolysis (e.g., van Wijk and van Solinge 2005) convert glucose 6-phosphate to pyruvate. The entire process is cytosolic. Glucose 6-phosphate is reversibly isomerized to form fructose 6-phosphate. Phosphofructokinase 1 catalyzes the physiologically irreversible phosphorylation of fructose 6-phosphate to form fructose 1,6-bisphosphate. In six reversible reactions, fructose 1,6-bisphosphate is converted to two molecules of phosphoenolpyruvate and two molecules of NAD+ are reduced to NADH + H+. Each molecule of phosphoenolpyruvate reacts with ADP to form ATP and pyruvate in a physiologically irreversible reaction. Under aerobic conditions the NADH +H+ can be reoxidized to NAD+ via electron transport to yield additional ATP, while under anaerobic conditions or in cells lacking mitochondria NAD+ can be regenerated via the reduction of pyruvate to lactate.
Platelet hyperaggregability: impaired responsiveness to nitric oxide ("platelet NO resistance") as a therapeutic target
De novo sphingolipid biosynthesis: a necessary, but dangerous, pathway
Structures of recombinant native and E202Q mutant human acetylcholinesterase complexed with the snake-venom toxin fasciculin-II
Acta Crystallogr D Biol Crystallogr 56:1385-94
Alternative pathway therapy for urea cycle disorders: twenty years later
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Regulation of mammalian liver methionine adenosyltransferase
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Cellular glutathione peroxidase as a predominant scavenger of hydroperoxyeicosatetraenoic acids in rabbit alveolar macrophages
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Biochemistry of soluble guanylate cyclase
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Transport of Glycerol from Adipocytes to the Liver by Aquaporins
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase isoform homodimers
glucose 6-phosphate isomerase dimer (name copied from entity in Homo sapiens)
PFKFB2 dimer (name copied from entity in Homo sapiens)
Identification of separate acyl- CoA:glycine and acyl-CoA:L-glutamine N-acyltransferase activities in mitochondrial fractions from liver of rhesus monkey and man
Pharmacokinetics of salicylate elimination in man
PFKFB1 dimer (name copied from entity in Homo sapiens)
Human adenine phosphoribosyltransferase. Affinity purification, subunit structure, amino acid composition, and peptide mapping.
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Pyruvate kinase isozyme type M2 (PKM2) interacts and cooperates with Oct-4 in regulating transcription
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3-(4-Hydroxyphenyl)pyruvate [ChEBI:1431]
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Monounsaturated fatty acid modification of Wnt protein: its role in Wnt secretion
Functional expression of human mutant phosphofructokinase in yeast: genetic defects in French Canadian and Swiss patients with phosphofructokinase deficiency
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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_8051.1
Cori Cycle (interconversion of glucose and lactate)
Studies on the properties and tissue distribution of the isozymes of guanylate kinase in man
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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_22848.2
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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_22578.2
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Immunocytochemical localization of the Menkes copper transport protein (ATP7A) to the trans-Golgi network
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Activation of Chaperone Genes by XBP1(S)
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6-Phosphogluconate dehydrogenase: the mechanism of action investigated by a comparison of the enzyme from different species
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The nature of the phagosomal membrane: endoplasmic reticulum versus plasmalemma
Molecular and functional characterization of the intestinal Na+-dependent multivitamin transporter
Knockdown of hepatocyte aquaporin-8 by RNA interference induces defective bile canalicular water transport
Am J Physiol Gastrointest Liver Physiol 296:G93-100
A new sperm-specific Na+/H+ exchanger required for sperm motility and fertility
SLC34A3 mutations in patients with hereditary hypophosphatemic rickets with hypercalciuria predict a key role for the sodium-phosphate cotransporter NaPi-IIc in maintaining phosphate homeostasis
Molecular basis for membrane phospholipid diversity: why are there so many lipids?
C-terminal lysines determine phospholipid interaction of sarcomeric mitochondrial creatine kinase
On the mechanism of sensing unfolded protein in the endoplasmic reticulum
Subcellular targeting and trafficking of nitric oxide synthases
Requirement of human renal water channel aquaporin-2 for vasopressin-dependent concentration of urine
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Organic acidemias due to defects in lysine oxidation: 2-ketoadipic acidemia and glutaric acidemia
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 2195-2204
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The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1777-1805
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Characterization of human UDP-glucose dehydrogenase. CYS-276 is required for the second of two successive oxidations
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The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1965-1970
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Disorders of tetrahydrobiopterin and related biogenic amines
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1725-1776
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Human glutamine phosphoribosylpyrophosphate amidotransferase. Kinetic and regulatory properties
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Beta-oxidation of very long chain fatty acids
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Maple syrup urine disease (branched-chain ketoaciduria)
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1971-2005
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The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 2125-2163
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Mycobacterium tuberculosis and the intimate discourse of a chronic infection
Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics
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The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1909-1963
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Disorders of proline and hydroxyproline metabolism
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1821-1838
Mutations in SLC34A2 cause pulmonary alveolar microlithiasis and are possibly associated with testicular microlithiasis
G(1) to S transition: more than a cell cycle engine switch.
Structural basis for tumor pyruvate kinase M2 allosteric regulation and catalysis
Functional and molecular characterization of the human neutral solute channel aquaporin-9
Half-site reactivity in 6-phosphogluconate dehydrogenase from human erythrocytes
Genetic basis of mitochondrial HMG-CoA synthase deficiency
all-trans-decaprenyl diphosphate [ChEBI:61011]
The structure and function of G-protein-coupled receptors
The characterization of gene mutations for human glucose phosphate isomerase deficiency associated with chronic hemolytic anemia
Protein interactions with nitric oxide synthases: controlling the right time, the right place, and the right amount of nitric oxide
The biochemistry, metabolism and inherited defects of the pentose phosphate pathway: a review
Amino acid transport across the plasma membrane
Amino acid synthesis and interconversion (transamination)
Transcriptional networks controlling pancreatic development and beta cell function
From structure to disease: the evolving tale of aquaporin biology
The quality control of MHC class I peptide loading
Mechanisms of glycerophospholipid homeostasis in mammalian cells
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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
The ABC-transporter signature motif is required for peptide translocation but not peptide binding by TAP
Disease-causing missense mutations affect enzymatic activity, stability and oligomerization of glutaryl-CoA dehydrogenase (GCDH)
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
Specificty of human and rat orthologs of the concentrative nucleoside transporter, SPNT
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Tryptophan metabolism in the central nervous system: medical implications
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Aquaporin-1, nothing but a water channel
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Molecular cloning and functional analysis of SUT-1, a sulfate transporter from human high endothelial venules
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Regulation of cell growth-dependent expression of mammalian CDC6 gene by the cell cycle transcription factor E2F.
Differential expression of aquaporin 7 in adipose tissue of lean and obese high fat consumers
The role of a group III AQP, AQP11 in intracellular organelle homeostasis
Isolation and characterization of human Nramp cDNA
Wnt proteins are lipid-modified and can act as stem cell growth factors
Mechanistic studies of human molybdopterin synthase reaction and characterization of mutants identified in group B patients of molybdenum cofactor deficiency
Purine ribonucleoside monophosphate biosynthesis
TRP channels: sensors and transducers of gasotransmitter signals
(S)-Lactate + NAD+ <=> Pyruvate + NADH + H+
Acetyl-CoA + H2O + Oxaloacetate => Citrate + CoA
NADPH + NAD+ + H+ [cytosol] => NADP+ + NADH + H+ [mitochondrial matrix]
Oxidative decarboxylation of alpha-ketoglutarate to succinyl CoA by alpha-ketoglutarate dehydrogenase
alpha-ketoglutarate + CoASH + NAD+ => succinyl-CoA + CO2 + NADH + H+
The concentrative nucleoside transporter family, SLC28
eNOS translocation from Golgi to Caveolae
depalmitoylated eNOS translocates from plasma membrane
Pyruvate + NADH + H+ <=> (S)-Lactate + NAD+
15k-LXA4 is reduced to dhk-LXA4 by PTGR1
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3-ketosphinganine + NADPH + H+ => sphinganine + NADP+
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12R-HpETE is reduced to 12R-HETE by GPX1/2/4
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12S-HpETE is reduced to 12S-HETE by GPX1/2/4
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FPP and IPPP are combined into all-E-10PrP2 by PDSS1/2 tetramer
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MDMQ10H2 is methylated to DMQ10H2 by COQ5
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5S-HpETE is reduced to 5S-HETE by GPX1/2/4
15S-HpETE is reduced to 15S-HETE by GPX1/2/4
15k-PGE2/F2a is reduced to dhk-PGE2/F2a by PTGR1
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adenylosuccinate => adenosine 5'-monophosphate + fumarate
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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]
5'-phosphoribosyl-5-aminoimidazole-4-carboxylate (CAIR) + L-aspartate + ATP => 5'-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide (SAICAR) + ADP + orthophosphate
CAIR + Aspartate + ATP => SAICAR + ADP + Pi
5'-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide (SAICAR) <=> 5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR) + fumarate
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5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR) + 10-formyltetrahydrofolate => 5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide (FAICAR) + tetrahydrofolate
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trans,trans-Farnesyl diphosphate [ChEBI:10700]
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Aquaporins: translating bench research to human disease
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5'-phosphoribosylformylglycinamidine (FGAM) + ATP => 5'-phosphoribosyl-5-aminoimidazole (AIR) + ADP + orthophosphate
5'-phosphoribosyl-5-aminoimidazole (AIR) + CO2 <=> 5'-phosphoribosyl-5-aminoimidazole-4-carboxylate (CAIR)
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5-phosphoribosylamine + glycine + ATP => 5-phosphoribosylglycinamide (GAR) + ADP + orthophosphate
5-Phosphoribosylamine + Glycine + ATP => GAR + ADP + Pi
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5-phosphoribosylglycinamide (GAR) + 10-formyl-tetrahydrofolate => 5'-phosphoribosylformylglycinamide (FGAR) + tetrahydrofolate
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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
2-oxoglutarate + 4-hydroxybutyrate <=> (R)-2-hydroxyglutarate + succinate semialdehyde
Formation of phosphoribosyl pyrophosphate amidotransferase tetramer
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(R)-2-hydroxyglutarate + succinate semialdehyde <=> 2-oxoglutarate + 4-hydroxybutyrate
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Toward the full set of human mitochondrial aminoacyl-tRNA synthetases: characterization of AspRS and TyrRS
Identification of a novel prostaglandin reductase reveals the involvement of prostaglandin E2 catabolism in regulation of peroxisome proliferator-activated receptor gamma activation
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Aquaporins: highways for cells to recycle water with the outside world
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Phosphoenolpyruvate + H2O <=> 2-Phospho-D-glycerate
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D-glyceraldehyde 3-phosphate <=> dihydroxyacetone phosphate
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ATP + 3-Phospho-D-glycerate <=> ADP + 1,3-bisphospho-D-glycerate
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D-fructose 6-phosphate <=> alpha-D-Glucose 6-phosphate
Fructose 2,6-bisphosphate is hydrolyzed to form fructose-6-phosphate and orthophosphate
alpha-D-glucose 6-phosphate + NADP+ => D-glucono-1,5-lactone 6-phosphate + NADPH + H+
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D-ribulose 5-phosphate <=> xylulose 5-phosphate
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6-phospho-D-gluconate + NADP+ => D-ribulose 5-phosphate + CO2 + NADPH + H+
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xylulose 5-phosphate <=> D-ribulose 5-phosphate
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3-ketohexacosanoyl-CoA + CoASH => tetracosanoyl-CoA + acetyl-CoA
Mevalonate is phosphorylated to mevalonate-5-phosphate
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Condensation of acetyl CoA with acetoacetyl CoA to form HMG-CoA
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ChEBI:17442 4-(2-aminophenyl)-2,4-dioxobutanoic acid
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Formation of DHA-CoA catalysed by 3-ketoacyl-CoA thiolase
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PCho and CTP are condensed to CDP-Cho by PCYT1 dimer
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cortisol + NADP+ => cortisone + NADPH + H+
Oxidation of cortisol to yield cortisone
Mevalonate-5-pyrophosphate is decarboxylated
AcCho is hydrolyzed to Cho and acetate by ACHE
Acetylcholine clearance from synaptic cleft
PETA and CTP are condensed to CDP-ETA by PCY2
Selective active site inhibitors of human lactate dehydrogenases A4, B4, and C4
Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA
ribose 5-phosphate <=> D-ribulose 5-phosphate
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D-ribulose 5-phosphate <=> ribose 5-phosphate
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Gly-3-P+FAD->DHAP+FADH2 (catalyzed by mitochondrial Gly-Phos dehydrogenase)
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acetoacetyl-CoA+acetyl-CoA => HMG-CoA + CoASH
Conversion of Glycerol to Glycerol-3-phosphate
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Digestion of triacylglycerols by extracellular CEL (bile salt-dependent lipase)
Digestion of monoacylglycerols by extracellular CEL (bile salt-dependent lipase)
Digestion of cholesterol esters by extracellular CEL (bile salt-dependent lipase)
addition of diphosphate (PP) to ribose 5-phosphate to form 5'-Phospho-alpha-D-ribose 1-diphosphate (PRPP)
D-ribose 5-phosphate + ATP => 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) + adenosine 5'-monophosphate
D-ribose 5-phosphate + 2'-deoxyadenosine 5'-triphosphate (dATP) => 5-Phospho-alpha-D-ribose 1-diphosphate (PRPP) + 2'-deoxyadenosine 5'-monophosphate
Molecular characterization of a novel short-chain dehydrogenase/reductase that reduces all-trans-retinal
Human X-linked phosphoribosylpyrophosphate synthetase superactivity is associated with distinct point mutations in the PRPS1 gene
An isoform of hPANK2, deficient in pantothenate kinase-associated neurodegeneration, localizes to mitochondria
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Elevation of cellular NAD levels by nicotinic acid and involvement of nicotinic acid phosphoribosyltransferase in human cells
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Human deoxythymidine kinase. I. Purification and general properties of the cytoplasmic and mitochondrial isozymes derived from blast cells of acute myelocytic leukemia
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Expression of human thymidylate synthase in Escherichia coli
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cytidine or uridine + ATP => CMP or UMP + ADP [UCK2]
cytidine or uridine + ATP => CMP or UMP + ADP [UCK1]
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thymine or uracil + 2-deoxy-D-ribose 1-phosphate <=> thymidine or deoxyuridine + orthophosphate [TYMP]
dUMP + N5,N10-methylene tetrahydrofolate => TMP + dihydrofolate
thymidine or deoxyuridine + orthophosphate <=> thymine or uracil + 2-deoxy-D-ribose 1-phosphate [TYMP]
CMP or TMP or UMP + H2O => cytidine, thymidine, or uridine + orthophosphate [NT5E]
(deoxy)cytidine + H2O => (deoxy)uridine + NH4+ [CDA]
deamination of 2'-Deoxycytidine to 2'-Deoxyuridine
thymidine + ATP => TMP (deoxythymidine 5'-monophosphate) + ADP [TK1]
phosphorylation of 2'-Deoxythymidine to dTMP
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Identification of a novel membrane protein, HP59, with therapeutic potential as a target of tumor angiogenesis
Tuberculosis - metabolism and respiration in the absence of growth
Structural and catalytic properties and homology modelling of the human nucleoside diphosphate kinase C, product of the DRnm23 gene
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AMP, dAMP, GMP, or IMP + H2O => adenosine, deoxyadenosine, guanosine, or inosine + orthophosphate [NT5E]
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guanine or hypoxanthine + PRPP => GMP or IMP + PPi [HPRT1]
2 glutathione, reduced + H2O2 => glutathione, oxidized + 2 H2O
carbamoyl phosphate + L-aspartate <=> N-carbamoyl L-aspartate + orthophosphate
carbamoyl phosphate and L-aspartate combine to form N-Carbamoyl-L-aspartate
L-glutamine + 2 ATP + HCO3- + H2O => carbamoyl phosphate + L-glutamate + 2 ADP + orthophosphate
bicarbonate and glutamine combine to form carbamoyl phosphate
The nucleoside diphosphate kinase D (NM23-H4) binds the inner mitochondrial membrane with high affinity to cardiolipin and couples nucleotide transfer with respiration
(S)-dihydroorotate + ubiquinone => orotate + ubiquinol
oxidation of (S)-Dihydroorotate to form Orotate
condensation of N-Carbamoyl-L-aspartate to form (S)-Dihydroorotate (ring closure)
N-carbamoyl L-aspartate + H+ <=> (S)-dihydroorotate + H2O
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decarboxylation of Orotidine 5'-phosphate to form Uridine 5'-phosphate
orotidine 5'-monophosphate => uridine 5'-monophosphate + CO2
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orotate + 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) <=> orotidine 5'-monophosphate (OMP) + pyrophosphate
phosphoribosylation of orotate to form oritidine 5'-phosphate (OMP)
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The sulfur-containing amino acids: an overview
Signalling via integrins: implications for cell survival and anticancer strategies
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Red cell pyruvate kinase deficiency: molecular and clinical aspects
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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
Molecular cloning and nucleotide sequence of a full-length cDNA for human alpha enolase
Newly made phosphatidylserine and phosphatidylethanolamine are preferentially translocated between rat liver mitochondria and endoplasmic reticulum
N-Acetyl-D-glucosamine 1-phosphate [ChEBI:7125]
Molecular cloning and functional expression of a sodium-dicarboxylate cotransporter from human kidney
Sinauer Associates, Inc., P.O. Box 407 23 Plumtree Road, Sunderland, MA 01375 U.S.A.
Insig-mediated degradation of HMG CoA reductase stimulated by lanosterol, an intermediate in the synthesis of cholesterol
Ontogenetic, polymorphic, and interethnic variation in the isoenzymes of human alcohol dehydrogenase.
Zinc transporters and the cellular trafficking of zinc
Transport of nucleosides and free purine and pyrimidine bases across the plasma membrane
Phosphoribosylpyrophosphate synthesis from glucose decreases during amino acid starvation of human lymphoblasts
Regulation of Water Balance by Renal Aquaporins
The sodium/calcium exchanger family-SLC8
Antimicrobial mechanisms of phagocytes and bacterial evasion strategies
Fatty acid, triacylglycerol, and ketone body metabolism
Human ornithine transcarbamylase: crystallographic insights into substrate recognition and conformational changes
Wnt and calcium signaling: beta-catenin-independent pathways
The visual cycle of the cone photoreceptors of the retina
Non-vesicular lipid transport by lipid-transfer proteins and beyond
10-formyltetrahydrofolyl polyglutamate macromolecule [ChEBI:28010]
10-formyltetrahydrofolyl polyglutamate macromolecule
The SLC40 basolateral iron transporter family (IREG1/ferroportin/MTP1)
Mechanisms involved in the intestinal digestion and absorption of dietary vitamin A
Molecular analysis of human argininosuccinate lyase: mutant characterization and alternative splicing of the coding region
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Cloning and functional characterization of a sodium-dependent phosphate transporter expressed in human lung and small intestine
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Roles of aquaporin-3 water channels in volume-regulatory water flow in a human epithelial cell line
Differential processing of human and rat E1 alpha precursors of the branched-chain alpha-keto acid dehydrogenase complex caused by an N-terminal proline in the rat sequence
Acidosis, acid-sensing ion channels, and neuronal cell death
Reconstitution of functional water channels in liposomes containing purified red cell CHIP28 protein
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Molecular mechanism of phase I and phase II drug-metabolizing enzymes: implications for detoxification
Characterization of human type I and type II IMP dehydrogenases
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Cellular targets for activation by the E2F1 transcription factor include DNA synthesis- and G1/S-regulatory genes
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Phospholipase C-gamma: diverse roles in receptor-mediated calcium signaling
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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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Isolation of a human cDNA for heme A:farnesyltransferase by functional complementation of a yeast cox10 mutant
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Crystal structure of human recombinant ornithine aminotransferase.
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Nitric oxide synthase (NOS) produces NO from L-arginine. There are three isoforms of NOS, endothelial, neuronal and inducible (eNOS, nNOS, and iNOS). eNOS and nNOS are constitutively expressed while iNOS is induced by immunostimulatory signals. The constitutive isoforms are regulated in vivo by the binding of calcium and calmodulin. NO produced by NOS acts as a signalling molecule by diffusing across cell membranes to activate soluble guanylate cyclase (sGC).
Human cationic amino acid transporters hCAT-1, hCAT-2A, and hCAT-2B: three related carriers with distinct transport properties
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Functional comparisons of three glutamate transporter subtypes cloned from human motor cortex
Novel mutations in 3-phosphoglycerate dehydrogenase (PHGDH) are distributed throughout the protein and result in altered enzyme kinetics
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Sprinter: a novel transmembrane protein required for Wg secretion and signaling
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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.
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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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.
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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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.
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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.
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Hemostasis is a physiological response that culminates in the arrest of bleeding from an injured vessel. Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhesion and activation, suppresses coagulation, enhances fibrin cleavage and is anti-inflammatory in character. Under acute vascular trauma, vasoconstrictor mechanisms predominate and the endothelium becomes prothrombotic, procoagulatory and proinflammatory in nature. This is achieved by a reduction of endothelial dilating agents: adenosine, NO and prostacyclin; and by the direct action of ADP, serotonin and thromboxane on vascular smooth muscle cells to elicit their contraction (Becker et al. 2000). The chief trigger for the change in endothelial function that leads to the formation of a haemostatic thrombus is the loss of the endothelial cell barrier between blood and extracellular matrix components (Ruggeri 2002). Circulating platelets identify and discriminate areas of endothelial lesions; here, they adhere to the exposed sub endothelium. Their interaction with the various thrombogenic substrates and locally generated or released agonists results in platelet activation. This process is described as possessing two stages, firstly, adhesion - the initial tethering to a surface, and secondly aggregation - the platelet-platelet cohesion (Savage & Cattaneo et al. 2001). Three mechansism contribute to the loss of blood following vessel injury. The vessel constricts, reducing the loss of blood. Platelets adhere to the site of injury, become activated and aggregate with fibrinogen into a soft plug that limits blood loss, a process termed primary hemostasis. Proteins and small molecules are released from granules by activated platelets, stimulating the plug formation process. Fibrinogen from plasma forms bridges between activated platelets. These events initiate the clotting cascade (secondary hemostasis). Negatively-charged phospholipids exposed at the site of injury and on activated platelets interact with tissue factor, leading to a cascade of reactions that culminates with the formation of an insoluble fibrin clot.
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At the end of this reaction, 1 molecule of 'pyruvate kinase, liver and RBC' is present. This reaction takes place in the 'nucleus'.
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Global gene expression profiling and histochemical analysis of the developing human fetal pancreas
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Cloning of human agmatinase. An alternate path for polyamine synthesis induced in liver by hepatitis B virus
Am J Physiol Gastrointest Liver Physiol 282:G375-81
A current view of the mammalian aquaglyceroporins
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FVT-1 is a mammalian 3-ketodihydrosphingosine reductase with an active site that faces the cytosolic side of the endoplasmic reticulum membrane
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Diversity of the mammalian sodium/proton exchanger SLC9 gene family
Plasma concentrations of phenyllactic acid in phenylketonuria
Cloning and functional expression of a urea transporter from human bone marrow cells
Analysis and update of the human solute carrier (SLC) gene superfamily
Transport of inorganic cations/anions and amino acids/oligopeptides
Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds
Oxidized LDL-induced endolysosomal phospholipidosis and enzymatically modified LDL-induced foam cell formation determine specific lipid species modulation in human macrophages
5-Phosphoribose 1-diphosphate biosynthesis
Synthesis of cytosolic 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) from D-ribose 5-phosphate
Amino acid and oligopeptide SLC transporters
A review of the pharmacokinetics of abacavir
Deficiency of carbohydrate response element-binding protein (ChREBP) reduces lipogenesis as well as glycolysis
On the frequency of protein glycosylation, as deduced from analysis of the SWISS-PROT database
Carbohydrate responsive element-binding protein (ChREBP): a key regulator of glucose metabolism and fat storage
Membrane-bound enzymes of cholesterol synthesis from lanosterol
5,10-methenyltetrahydrofolate polyglutamate [ChEBI:65049]
Complete amino acid sequence of human phosphoglycerate kinase. Isolation and amino acid sequence of tryptic peptides.
Metabolism of amino acids and derivatives
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
Human argininosuccinate lyase: a structural basis for intragenic complementation
Planar cell polarity signaling: from fly development to human disease
Interactions between the endoplasmic reticulum, mitochondria, plasma membrane and other subcellular organelles
The SLC20 family of proteins: dual functions as sodium-phosphate cotransporters and viral receptors
Conjugation of phenylacetate with glutamine
The human tumour suppressor gene SLC5A8 expresses a Na+-monocarboxylate cotransporter
Human cataract lens membrane at subnanometer resolution
Synthesis of Leukotrienes (LT) and Eoxins (EX)
Congenital hypothyroidism caused by a mutation in the Na+/I- symporter
Identification of arylsulfonamides as Aquaporin 4 inhibitors
Antigen processing and presentation by the class I major histocompatibility complex
An excitatory amino-acid transporter with properties of a ligand-gated chloride channel
Mechanistic and mutational studies of Escherichia coli molybdopterin synthase clarify the final step of molybdopterin biosynthesis
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
Comparative analysis of gene regulation by the transcription factor PPARalpha between mouse and human
The human nm23-H4 gene product is a mitochondrial nucleoside diphosphate kinase
Glutamate Neurotransmitter Release Cycle
Guanylate kinases from human erythrocytes, hog brain, and rat liver
Crystallization and properties of human liver ornithine aminotransferase