The diastrophic dysplasia gene encodes a novel sulfate transporter: positional cloning by fine-structure linkage disequilibrium mapping
Calmodulin-binding sites on adenylyl cyclase type VIII
Drug targets in mycobacterial sulfur metabolism
6-methoxy-3-methyl-2-decaprenyl-1,4-benzoquinol [ChEBI:64181]
2-methoxy-6-decaprenyl-1,4-benzoquinol [ChEBI:64180]
Extracellular matrix dynamics in development and regenerative medicine
The yeast mitochondrial carrier Leu5p and its human homologue Graves' disease protein are required for accumulation of coenzyme A in the matrix
IP3 receptor/Ca2+ channel: from discovery to new signaling concepts
Iron storage proteins are essential for the survival and pathogenesis of Mycobacterium tuberculosis in THP-1 macrophages and the guinea pig model of infection
Cytochrome P450 - arranged by substrate type
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.
Subcellular localization of 3-methylcrotonyl-coenzyme A carboxylase in bovine kidney
Cloning and expression of a human ATP-citrate lyase cDNA
Mutations in orthologous genes in human spondyloepimetaphyseal dysplasia and the brachymorphic mouse
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
Crystal structure of the human monoacylglycerol lipase, a key actor in endocannabinoid signaling
2-Deoxy-D-ribose 1-phosphate [ChEBI:28542]
Targeting purine and pyrimidine metabolism in human apicomplexan parasites
Isolated isobutyryl-CoA dehydrogenase deficiency: an unrecognized defect in human valine metabolism.
Type I Collagen D-Spacing in Fibril Bundles of Dermis, Tendon, and Bone: Bridging between Nano- and Micro-Level Tissue Hierarchy
Phase 1 - Functionalization of compounds
ChEBI:28533 3alpha,7alpha-dihydroxy-24-oxo-5beta-cholestanoyl-CoA
Biochemistry of mammalian peroxisomes revisited
Human liver-specific very-long-chain acyl-coenzyme A synthetase: cDNA cloning and characterization of a second enzymatically active protein
Structures of the human GTPase MMAA and vitamin B12-dependent methylmalonyl-CoA mutase and insight into their complex formation
Receptor-mediated endocytosis of cobalamin (vitamin B12)
Metabolism of water-soluble vitamins and cofactors
D-2-hydroxyglutaric acidaemia: identification of a new enzyme, D-2-hydroxyglutarate dehydrogenase, localized in mitochondria
D-Fructose 2,6-bisphosphate [ChEBI:28602]
Identification of two mammalian reductases involved in the two-carbon fatty acyl elongation cascade
XBP1 induces WFS1 through an endoplasmic reticulum stress response element-like motif in SH-SY5Y cells
Human brain monoamine oxidase type B: mechanism of deamination as probed by steady-state methods
Serotonin clearance from the synaptic cleft
Redox-switch modulation of human SSADH by dynamic catalytic loop
Phosphoglucomutase 1: a gene with two promoters and a duplicated first exon
2-Methylbutyryl-coenzyme A dehydrogenase deficiency: a new inborn error of L-isoleucine metabolism.
Purification of peroxisomal acyl-CoA: dihydroxyacetonephosphate acyltransferase from human placenta
Dermatan sulphate-rich proteoglycan associates with rat tail-tendon collagen at the d band in the gap region
Molecular cloning of a human cDNA encoding a trifunctional enzyme of carbamoyl-phosphate synthetase-aspartate transcarbamoylase-dihydroorotase in de Novo pyrimidine synthesis
Mutations in antiquitin in individuals with pyridoxine-dependent seizures
Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET)
Phosphorylation of Munc18 by protein kinase C regulates the kinetics of exocytosis
The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans
Cdk2-dependent and -independent pathways in E2F-mediated S phase induction
Limiting role of 6-phosphogluconolactonase in erythrocyte hexose monophosphate pathway metabolism
Functional analysis of L-serine O-acetyltransferase from Corynebacterium glutamicum
Structural relationships and the classification of aminoacyl-tRNA synthetases
Adipocyte differentiation from the inside out
Alkyl-dihydroxyacetonephosphate synthase. Presence and role of flavin adenine dinucleotide
Enzymatic activities of the human AGPAT isoform 3 and isoform 5: localization of AGPAT5 to mitochondria
Thiol and sulfenic acid oxidation of AhpE, the one-cysteine peroxiredoxin from Mycobacterium tuberculosis: kinetics, acidity constants, and conformational dynamics
Wnt family proteins are secreted and associated with the cell surface
Cloning, sequencing, and expression of cDNA for human beta-galactosidase
Biochem. Biophys. Res. Commun. 157:238-44
Innate protection of Mycobacterium smegmatis against the antimicrobial activity of nitric oxide is provided by mycothiol
PMP70, the 70-kDa peroxisomal membrane protein: a member of the ATP-binding cassette transporters
How synaptotagmin promotes membrane fusion
Identification of holocarboxylase synthetase (HCS) proteins in human placenta
Fibulin-5 is an elastin-binding protein essential for elastic fibre development in vivo
Fibulin-5/DANCE is essential for elastogenesis in vivo
Functional and structural characterization of a thiol peroxidase from Mycobacterium tuberculosis
Mechanisms of collagen trimer formation. Construction and expression of a recombinant minigene in HeLa cells reveals a direct effect of prolyl hydroxylation on chain assembly of type XII collagen
Identification of Gz alpha as a pertussis toxin-insensitive G protein in human platelets and megakaryocytes
Reviews in molecular biology and biotechnology: transmembrane signaling by G protein-coupled receptors
Melatonin in the skin: synthesis, metabolism and functions
Comparative study on the thermostability of collagen I of skin and bone: influence of posttranslational hydroxylation of prolyl and lysyl residues
Isolation and characterization of a full-length expressible cDNA for human hypoxanthine phosphoribosyl transferase
(2S)-2,6,10,14-tetramethylpentadecanoyl-coenzyme A
Genomic basis of mucopolysaccharidosis type IIID (MIM 252940) revealed by sequencing of GNS encoding N-acetylglucosamine-6-sulfatase
Mucopolysaccharidosis type I: current knowledge on its pathophysiological mechanisms
Characterization of the human gene encoding alpha-aminoadipate aminotransferase (AADAT).
NLR functions beyond pathogen recognition
Peroxisome proliferator activated receptors and lipoprotein metabolism
ATP activates a reactive oxygen species-dependent oxidative stress response and secretion of proinflammatory cytokines in macrophages
Enzymatic, metabolic and secretory patterns in human islets of type 2 (non-insulin-dependent) diabetic patients
The many niches and strategies used by pathogenic mycobacteria for survival within host macrophages
The arrangement of intra- and intermolecular disulfide bonds in the carboxyterminal, non-collagenous aggregation and cross-linking domain of basement-membrane type IV collagen
The zipper-like folding of collagen triple helices and the effects of mutations that disrupt the zipper
Biosynthesis of A2E, implicated in retinal degradation
Regulation of Geminin and Cdt1 expression by E2F transcription factors
Familial hyperlysinemias. Purification and characterization of the bifunctional aminoadipic semialdehyde synthase with lysine-ketoglutarate reductase and saccharopine dehydrogenase activities.
Structure and sequence of the human sulphamidase gene
Cloning and expression of the trehalose-phosphate phosphatase of Mycobacterium tuberculosis: comparison to the enzyme from Mycobacterium smegmatis
Immunoreceptor DAP12 bearing a tyrosine-based activation motif is involved in activating NK cells
Molecular characterization of human acetyl-CoA synthetase, an enzyme regulated by sterol regulatory element-binding proteins.
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Insulin signalling and the regulation of glucose and lipid metabolism
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Functional properties and genomics of glucose transporters
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Differential unfolding of alpha1 and alpha2 chains in type I collagen and collagenolysis
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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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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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Mycothiol (MSH), a conjugate of glucosamine, cysteine and inositol, is the Actinobacteria equivalent of glutathione. It serves as a pool for both the unstable cysteine and reduction equivalents. Mycothiol takes part in enzymatic reactions including detoxification of electrophilic compounds, inactivation of reactive oxygen and nitrogen species, reductions, and isomerizations. M. smegmatis mutants devoid of MSH are sensitive to oxidative and nitrosative stress, and antibiotics. In M. tuberculosis, however, mycothiol synthesis is essential, no null mutants are known. Results from MshD mutants, which have about 1 per cent of MSH, show the importance of mycothiol in environments where antimicrobial factors, including reactive oxygen and reactive nitrogen intermediates, are formed, such as within macrophages (Newton et al, 2008; Rawat and Av-Gay, 2007)
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Mechanism of porphobilinogen synthase. Requirement of Zn2+ for enzyme activity.
The tissue form of type VII collagen is an antiparallel dimer
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Mammalian G proteins and their cell type specific functions
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Cytochrome P450 and arachidonic acid bioactivation. Molecular and functional properties of the arachidonate monooxygenase
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Variants in a novel epidermal collagen gene (COL29A1) are associated with atopic dermatitis
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Functional demonstration of reverse transsulfuration in the Mycobacterium tuberculosis complex reveals that methionine is the preferred sulfur source for pathogenic Mycobacteria
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The crucial role of trimerization domains in collagen folding
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Trehalose-phosphate synthase of Mycobacterium tuberculosis. Cloning, expression and properties of the recombinant enzyme
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(1R,2S)-1-Hydroxypropane-1,2,3-tricarboxylate [ChEBI:151]
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Synthesis of IP2, IP, and Ins in the cytosol
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Activation of Chaperone Genes by ATF6-alpha
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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
Hormone-sensitive lipase (HSL)-mediated triacylglycerol hydrolysis
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Reversible compartmentalization of de novo purine biosynthetic complexes in living cells
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Fibroblast Growth Factor Receptor (FGFR) signaling
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The crucial role of trehalose and structurally related oligosaccharides in the biosynthesis and transfer of mycolic acids in Corynebacterineae
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Peptide methionine sulfoxide reductase from Escherichia coli and Mycobacterium tuberculosis protects bacteria against oxidative damage from reactive nitrogen intermediates
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'Ac-CoA [mitochondrial matrix]' positively regulates 'Pyruvate + CO2 + ATP => ADP + Orthophosphate + Oxaloacetate'
'ATP [cytosol]' negatively regulates 'PGYM dimer, b form + 2 AMP <=> PGYM b dimer:AMP complex'
'D-Fructose 2,6-bisphosphate [cytosol]' positively regulates 'D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP'
'ADP [cytosol]' positively regulates 'D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP'
'ATP [cytosol]' negatively 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'
The most important response of Mtb to oxidative stress is provided by catalase and peroxiredoxins, both of which get their reducing equivalents through a network of disulfide proteins and, finally, from NAD(P)H. Multiple redundancies make choosing a good drug target difficult (Koul et al. 2011). Optimum efficacy can only be expected from inhibitors of the most upstream components of the redox cascades, i.e. the NAD(P)H-dependent reductases TrxB and Lpd (Jaeger & Flohe 2006).
'CIT [cytosol]' negatively regulates 'D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP'
'G6P [cytosol]' negatively regulates 'PGYM dimer, b form + 2 AMP <=> PGYM b dimer:AMP complex'
'BH4 [cytosol]' negatively regulates 'GCH1 reduces GTP to dihydroneopterin triphosphate'
trans,cis-Lauro-2,6-dienoyl-CoA [ChEBI:28387]
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Electron-microscopical approach to a structural model of intima collagen
ATP-dependent L-cysteine:1D-myo-inosityl 2-amino-2-deoxy-alpha-D-glucopyranoside ligase, mycothiol biosynthesis enzyme MshC, is related to class I cysteinyl-tRNA synthetases
Formation of molecular species of mitochondrial cardiolipin. 1. A novel transacylation mechanism to shuttle fatty acids between sn-1 and sn-2 positions of multiple phospholipid species
Amino acid transport across the plasma membrane
The porphobilinogen synthase catalyzed reaction mechanism
Distribution of myocilin and extracellular matrix components in the corneoscleral meshwork of human eyes
Human cytidine deaminase: purification of enzyme, cloning, and expression of its complementary DNA
Retinoids for treatment of retinal diseases
Activation of NMDA receptor upon glutamate binding and postsynaptic events
Acid-sensing ion channels (ASICs): pharmacology and implication in pain
Antigen processing and presentation: TAPping into ABC transporters
[A NEW DYSOSTOSIS WITH URINARY ELIMINATION OF CHONDROITIN SULFATE B]
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Purification and properties of phosphoribosyl pyrophosphate synthetase from rat liver
Active site and loop 4 movements within human glycolate oxidase: implications for substrate specificity and drug design
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Inborn errors of ketogenesis and ketone body utilization
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Molecular organization of the presynaptic active zone
Transmembrane transport of endo- and xenobiotics by mammalian ATP-binding cassette multidrug resistance proteins
Beta-arrestin-mediated activation of MAPK by inverse agonists reveals distinct active conformations for G protein-coupled receptors
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XBP-1 regulates a subset of endoplasmic reticulum resident chaperone genes in the unfolded protein response
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Enzymes of the human erythrocyte. IV. Phosphoglucose isomerase, purification and properties.
A comprehensive profile of brain enzymes that hydrolyze the endocannabinoid 2-arachidonoylglycerol
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Purification and characterization of 5'-deoxy-5'-methylthioadenosine phosphorylase from human placenta
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Molecular machinations of the MHC-I peptide loading complex
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Crystal structure of inositol 1-phosphate synthase from Mycobacterium tuberculosis, a key enzyme in phosphatidylinositol synthesis
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Phase III randomized trial of cisplatin plus placebo compared with cisplatin plus cetuximab in metastatic/recurrent head and neck cancer: an Eastern Cooperative Oncology Group study
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EGFR interacts with phospholipase C-gamma
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Crystal structure of human thymidine phosphorylase in complex with a small molecule inhibitor
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147490.5
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Developmental origin of fat: tracking obesity to its source
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Purification and partial characterization of aldehyde dehydrogenase from human erythrocytes.
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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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CATALYTIC ACTIVITY Acetyl-CoA + L-serine = CoA + O-acetyl-L-serine.PATHWAY Amino-acid biosynthesis; L-cysteine biosynthesis; L-cysteine from L-serine: step 1/2.DISRUPTION PHENOTYPE Strains lacking this gene are shown to be attenuated in a mouse tuberculosis model.MISCELLANEOUS Was identified as a high-confidence drug target.SIMILARITY Belongs to the transferase hexapeptide repeat family.
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The human peroxisomal ABC half transporter ALDP functions as a homodimer and accepts acyl-CoA esters
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Defective platelet activation in G alpha(q)-deficient mice
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Antigen processing: Ubiquitination & Proteasome degradation
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Subcellular localization of human neutral ceramidase expressed in HEK293 cells
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Active Wnt proteins are secreted on exosomes
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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_116259.1
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DNA polymerase zeta: new insight into eukaryotic mutagenesis and mammalian embryonic development.
Holocarboxylase synthetase: correlation of protein localisation with biological function
Structure and formation of a stable histidine-based trifunctional cross-link in skin collagen
Crystal structure of human cytosolic phosphoenolpyruvate carboxykinase reveals a new GTP-binding site
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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_139138.5
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_76013.2
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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_126788.5
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1247904
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ChEBI:28477 7alpha,12alpha-dihydroxycholest-4-en-3-one
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Processive synthesis on the lagging strand
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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_94714.9
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7424.3
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Bestrophin and TMEM16-Ca(2+) activated Cl(-) channels with different functions
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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_141843.5
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Alcohol dehydrogenases, aldehyde dehydrogenases, and related enzymes
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Virulence of Mycobacterium tuberculosis depends on lipoamide dehydrogenase, a member of three multienzyme complexes
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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
Antiangiogenic activity of restin, NC10 domain of human collagen XV: comparison to endostatin
Kinetic characterization of human hydroxyacid-oxoacid transhydrogenase: relevance to D-2-hydroxyglutaric and gamma-hydroxybutyric acidurias
Homologous recombination repair of replication-independent double-strand breaks
Metabolic functions of the two pathways of oleate beta-oxidation double bond metabolism during the beta-oxidation of oleic acid in rat heart mitochondria
The formation of citric and alpha-ketoglutaric acids in the mammalian body
Mutations of the Down-regulated in adenoma (DRA) gene cause congenital chloride diarrhoea
Regulation of the cyclin E gene by transcription factor E2F1
Identification of the human methylmalonyl-CoA racemase gene based on the analysis of prokaryotic gene arrangements. Implications for decoding the human genome.
Type VII collagen: the anchoring fibril protein at fault in dystrophic epidermolysis bullosa
Characterization of a human lysophosphatidic acid acyltransferase that is encoded by a gene located in the class III region of the human major histocompatibility complex
Ubiquinone. Biosynthesis of quinone ring and its isoprenoid side chain. Intracellular localization
Heterotrimeric G protein activation by G-protein-coupled receptors
Transport of inorganic cations/anions and amino acids/oligopeptides
Cell-type specific recognition of RGD- and non-RGD-containing cell binding domains in fibrillin-1
Adenylate kinases in man: evidence for a third locus
ChEBI:27379 3alpha,7alpha,12alpha-trihydroxy-24-oxo-5beta-cholestanoyl-CoA
Enzymic properties of different types of human erythrocyte glucose-6-phosphate dehydrogenase, with characterization of two new genetic variants
Inflammasome adaptors and sensors: intracellular regulators of infection and inflammation
Metabolism of propionic acid in animal tissues. IX. Methylmalonyl coenzyme A racemase
Molecular cloning of human amidophosphoribosyltransferase
Back in the water: the return of the inositol phosphates
Human sulfatases: a structural perspective to catalysis
Assembly of collagen fibrils and other multimeric structures
Porcupine homolog is required for canonical Wnt signaling and gastrulation in mouse embryos
Collagen type IX: evidence for covalent linkages to type II collagen in cartilage
Repair of methylation damage in DNA and RNA by mammalian AlkB homologues
Role of gastrin peptides in carcinogenesis
Human GMP synthetase. Protein purification, cloning, and functional expression of cDNA
In vitro characterization of enzymatic properties and inhibition of the p53R2 subunit of human ribonucleotide reductase
Structure and function of matrix metalloproteinases and TIMPs
GlycoVis: visualizing glycan distribution in the protein N-glycosylation pathway in mammalian cells
H2S biogenesis by human cystathionine gamma-lyase leads to the novel sulfur metabolites lanthionine and homolanthionine and is responsive to the grade of hyperhomocysteinemia
Cloning, sequencing and expression of a cDNA encoding mammalian valyl-tRNA synthetase
Epidermal growth factor receptors harboring kinase domain mutations associate with the heat shock protein 90 chaperone and are destabilized following exposure to geldanamycins
Interchain disulfide bonds in procollagen are located in a large nontriple-helical COOH-terminal domain
Microfibrillar structure of type I collagen in situ
ChEBI:27403 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA
(S)-3-Hydroxyhexadecanoyl-CoA [ChEBI:27402]
Sulfotransferase catalyzing sulfation of heterocyclic amines
Uptake of iron in Mtb, especially when the bacterium is in the host, strongly depends on siderophores. Humans, through secretion of lactoferrin, maintain an iron concentration of 10^(-18) M within macrophages, and the bacterium has evolved the siderophores mycobactin T and exomycobactin T (formerly exochelin) to cope with this shortage. While nonpolar mycobactin T stays in the cell wall and only moves around in liquid droplets, polar exochelin is abundantly secreted. As it can bind iron with higher affinity than lactoferrin, it frequently scavenges iron ions from this molecule (Miethke & Marahiel 2007).
3alpha,7alpha,24-Trihydroxy-5beta-cholestanoyl-CoA [ChEBI:1701]
The role of aminoacyl-tRNA synthetases in genetic diseases
Investigation of the ABC transporter MRP1 in selected patients with presumed defects in vitamin B12 absorption
Oligomeric structure of the multifunctional protein CAD that initiates pyrimidine biosynthesis in mammalian cells
The mucopolysaccharidoses: a success of molecular medicine
New insights on trehalose: a multifunctional molecule
Receptor-to-effector signaling through G proteins: roles for beta gamma dimers as well as alpha subunits
Platelet-derived endothelial cell growth factor has thymidine phosphorylase activity.
Mutation of the fumarase gene in two siblings with progressive encephalopathy and fumarase deficiency
Functional properties of a Drosophila homolog of the E2F1 gene
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.
FUNCTION: May perform analogous functions in iron detoxification and storage to that of animal ferritins (By similarity).
Molecular basis of mitochondrial fatty acid oxidation defects.
Mechanistic studies on phosphopantothenoylcysteine decarboxylase: trapping of an enethiolate intermediate with a mechanism-based inactivating agent
Molecular enzymology of mammalian Delta1-pyrroline-5-carboxylate synthase. Alternative splice donor utilization generates isoforms with different sensitivity to ornithine inhibition
Selective inhibition of 2-AG hydrolysis enhances endocannabinoid signaling in hippocampus
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SIMILARITY Belongs to the AhpC/TSA family. Tpx subfamily.SIMILARITY Contains 1 thioredoxin domain.
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Reconstitution of a new cysteine biosynthetic pathway in Mycobacterium tuberculosis
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Biochemical characterization of human GMP synthetase
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Separation of the two enzymatic phases in active sulfate synthesis
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ATF6 activated by proteolysis binds in the presence of NF-Y (CBF) directly to the cis-acting element responsible for the mammalian unfolded protein response
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Cancer-associated IDH1 mutations produce 2-hydroxyglutarate
CATALYTIC ACTIVITY 5-O-(1-carboxyvinyl)-3-phosphoshikimate = chorismate + phosphate.PATHWAY Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 7/7.MISCELLANEOUS Was identified as a high-confidence drug target.SIMILARITY Belongs to the chorismate synthase family.
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Fine-tuning of GPCR activity by receptor-interacting proteins
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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
Succinic semialdehyde dehydrogenase deficiency: lessons from mice and men
The human PICD gene encodes a cytoplasmic and peroxisomal NADP(+)-dependent isocitrate dehydrogenase
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Mutations and polymorphisms in the human argininosuccinate synthetase (ASS1) gene
Reversal of Alkylation Damage By DNA Dioxygenases
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(S)-3-Hydroxytetradecanoyl-CoA [ChEBI:27466]
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Unique features of the sodC-encoded superoxide dismutase from Mycobacterium tuberculosis, a fully functional copper-containing enzyme lacking zinc in the active site
ChEBI:27458 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA
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DNA double-strand breaks: signaling, repair and the cancer connection.
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Lysyl oxidase: an oxidative enzyme and effector of cell function
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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
Fibrillin immunoreactive fibers constitute a unique network in the human dermis: immunohistochemical comparison of the distributions of fibrillin, vitronectin, amyloid P component, and orcein stainable structures in normal skin and elastosis
Crystal structure of human uroporphyrinogen decarboxylase
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Morquio's syndrome: deficiency of a chondroitin sulfate N-acetylhexosamine sulfate sulfatase
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Innate immune activation through Nalp3 inflammasome sensing of asbestos and silica
Peroxisome proliferator-activated receptors: nuclear control of metabolism
Complete amino acid sequence of the neurone-specific gamma isozyme of enolase (NSE) from human brain and comparison with the non-neuronal alpha form (NNE)
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Replication of UV-damaged DNA: new insights into links between DNA polymerases, mutagenesis and human disease.
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Clinical, biochemical and molecular genetic correlations in adenylosuccinate lyase deficiency
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Metabolic characteristics and importance of the universal methionine salvage pathway recycling methionine from 5'-methylthioadenosine
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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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WNT signaling pathways control a wide range of developmental and adult process in metozoans including cell proliferation, cell fate decisions, cell polarity and stem cell maintenance (reviewed in Saito-Diaz et al, 2013; MacDonald et al, 2009). The pathway is named for the WNT ligands, a large family of secreted cysteine-rich glycoproteins. At least 19 WNT members have been identified in humans and mice with distinct expression patterns during development (reviewed in Willert and Nusse, 2012). These ligands can activate at least three different downstream signaling cascades depending on which receptors they engage. In the so-called 'canonical' WNT signaling pathway, WNT ligands bind one of the 10 human Frizzled (FZD) receptors in conjunction with the LRP5/6 co-receptors to activate a transcriptional cascade that controls processes such as cell fate, proliferation and self-renenwal of stem cells. Engagement of the FZD-LRP receptor by WNT ligand results in the stabilization and translocation of cytosolic beta-catenin to the nucleus where it is a co-activator for LEF (lymphoid enhancer-binding factor)- and TCF (T cell factor) -dependent transcription. In the absence of WNT ligand, cytosolic beta-catenin is phosphorylated by a degradation complex consisting of glycogen synthase kinase 3 (GSK3), casein kinase 1 (CK1), Axin and Adenomatous polyposis coli (APC), and subsequently ubiquitinated and degraded by the 26S proteasome (reviewed in Saito-Diaz et al, 2013; Kimmelman and Xu, 2006). In addition to the beta-catenin-dependent transcriptional response, WNT signaling can also activate distinct non-transcriptional pathways that regulate cell migration and polarity. These beta-catenin-independent 'non-canonical' pathways signal through Frizzled receptors independently of LRP5/6, or occur through the tyrosine kinase receptors ROR and RYK (reviewed in Veeman et al, 2003; James et al, 2009). Non-canonical WNT pathways are best studied in Drosophila where the planar cell polarity (PCP) pathway controls the orientation of wing hairs and eye facets, but are also involved in processes such as convergent extension, neural tube closure, inner ear development and hair orientation in vertebrates and mammals(reviewed in Seifert and Mlodzik, 2007; Simons and Mlodzik, 2008). In the PCP pathway, binding of WNT ligand to the FZD receptor leads to activation of small Rho GTPases and JNK, which regulate the cytoskeleton and coordinate cell migration and polarity (reviewed in Lai et al, 2009; Schlessinger et al, 2009). In some cases, a FZD-WNT interaction increases intracellular calcium concentration and activates CaMK II and PKC; this WNT calcium pathway promotes cell migration and inhibits the canonical beta-catenin dependent transcriptional pathway (reviewed in Kuhl et al, 2000; Kohn and Moon, 2005; Rao et al 2010). Binding of WNT to ROR or RYK receptors also regulates cell migration, apparently through activation of JNK or SRC kinases, respectively, however the details of these pathways remain to be worked out (reviewed in Minami et al, 2010). Although the WNT signaling pathways were originally viewed as discrete, linear pathways controlled by defined subsets of 'canonical' or 'non-canonical' ligands and receptors, the emerging evidence is challenging this notion. Instead, the specificity and the downstream response appear to depend on the particular cellular context and vary with species, tissue and stage of development (reviewed in van Amerongen and Nusse, 2009; Rao et al, 2010).
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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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Gastrin is a hormone whose main function is to stimulate secretion of hydrochloric acid by the gastric mucosa, which results in gastrin formation inhibition. This hormone also acts as a mitogenic factor for gastrointestinal epithelial cells. Gastrin has two biologically active peptide forms, G34 and G17.Gastrin gene expression is upregulated in both a number of pre-malignant conditions and in established cancer through a variety of mechanisms. Depending on the tissue where it is expressed and the level of expression, differential processing of the polypeptide product leads to the production of different biologically active peptides. In turn, acting through the classical gastrin cholecystokinin B receptor CCK-BR, its isoforms and alternative receptors, these peptides trigger signalling pathways which influence the expression of downstream genes that affect cell survival, angiogenesis and invasion (Wank 1995, de Weerth et al. 1999, Grabowska & Watson 2007)
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
G protein-coupled receptors (GPCRs; 7TM receptors; seven transmembrane domain receptors; heptahelical receptors; G protein-linked receptors [GPLR]) are the largest family of transmembrane receptors in humans, accounting for more than 1% of the protein-coding capacity of the human genome. All known GPCRs share a common architecture of seven membrane-spanning helices connected by intra- and extracellular loops. The extracellular loops contain two highly-conserved cysteine residues that form disulphide bonds to stabilize the structure of the receptor. They recognize diverse messengers such as light, odorants, small molecules, hormones and neurotransmitters. Most GPCRs act as guanine nucleotide exchange factors; activated by ligand binding, they promote GDP-GTP exchange on associated heterotrimeric guanine nucleotide-binding (G) proteins. There are two models for GPCR-G Protein interactions: 1) ligand-GPCR binding first, then binding to G Proteins; 2) "Pre-coupling" of GPCRs and G Proteins before ligand binding (review Oldham WM and Hamm HE, 2008). These in turn activate effector enzymes or ion channels. GPCRs are involved in a range of physiological roles which include the visual sense, smell, behavioural regulation, functions of the autonomic nervous system and regulation of the immune system and inflammation. GPCRs are divided into 6 classes based on sequence homology and functional similarity; the main mammalian families are classes A/1-C/3; Class A/1 (Rhodopsin-like) Class B/2 (Secretin receptor family) Class C/3 (Metabotropic glutamate/pheromones) Class D/4 (fungal mating pheromone receptors) Class E/5 (cAMP receptors) Class F/6 (Frizzled/Smoothened) Here, those Class A/1 (Rhodopsin-like) receptors that bind peptide ligands have been annotated. The binding events mediated by other classes of receptors, as well as the downstream events triggered by receptor-ligand interactions will be annotated in future releases of Reactome.
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All WNT ligands are predicted to be highly glycosylated. By similarity with WNT ligands in mouse, human WNTs are believed to undergo N-linked glycosylation at multiple asparagine residues and this glycosylation is critical for their secretion (Smolich et al, 1993; Willert et al, 2003, Komekado et al, 2006; Kurayoshi et al, 2007). The mechanism of N-linked glycosylation is not shown here. For a more detailed description, please refer to pathway "Asparagine N-linked glycosylation".
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[Receptors for cholecystokinin and gastrin]
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Selective killing of human malignant cell lines deficient in methylthioadenosine phosphorylase, a purine metabolic enzyme
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Enzymatic phosphorylation of nucleoside diphosphates
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Structure of human thymidylate synthase suggests advantages of chemotherapy with noncompetitive inhibitors
Cloning of the sulphamidase gene and identification of mutations in Sanfilippo A syndrome
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Procollagen trafficking, processing and fibrillogenesis
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The human REV1 gene codes for a DNA template-dependent dCMP transferase.
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Novel functions of acyl-CoA thioesterases and acyltransferases as auxiliary enzymes in peroxisomal lipid metabolism
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Location of type XV collagen in human tissues and its accumulation in the interstitial matrix of the fibrotic kidney
Regulation of small GTPases at epithelial cell-cell junctions
Enzymic synthesis and breakdown of a pyrimidine, orotic acid. I. Dihydro-orotic dehydrogenase
Fatty acid elongases in mammals: their regulation and roles in metabolism
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Identification of the human and bovine ATP:Cob(I)alamin adenosyltransferase cDNAs based on complementation of a bacterial mutant
Enzymes of fatty acid metabolism. II. Properties of crystalline crotonase.
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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
Cloning and characterization of the cDNA encoding human adenylosuccinate synthetase
Beta oxidation of decanoyl-CoA to octanoyl-CoA-CoA
The solute carrier 26 family of proteins in epithelial ion transport
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Tau-crystallin/alpha-enolase: one gene encodes both an enzyme and a lens structural protein
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The roles of anabolic and catabolic reactions in the synthesis and recycling of polyunsaturated fatty acids
Prostaglandins Leukot Essent Fatty Acids 67:79-83
The carboxyl terminus of type VII collagen mediates antiparallel dimer formation and constitutes a new antigenic epitope for epidermolysis Bullosa acquisita autoantibodies
Structural basis for human monoglyceride lipase inhibition
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ATP-Binding cassette cholesterol transporters and cardiovascular disease
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Covalent cross-linking of the NC1 domain of collagen type IX to collagen type II in cartilage
Human L-3-phosphoserine phosphatase: sequence, expression and evidence for a phosphoenzyme intermediate
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beta-Nicotinamide adenine dinucleotide phosphate
Nicotinamide adenine dinucleotide phosphate
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Functionally defective high-density lipoprotein: a new therapeutic target at the crossroads of dyslipidemia, inflammation, and atherosclerosis
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1-Hydroxypropane-1,2,3-tricarboxylic acid
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Lack of collagen XV impairs peripheral nerve maturation and, when combined with laminin-411 deficiency, leads to basement membrane abnormalities and sensorimotor dysfunction
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GABA synthesis, release, reuptake and degradation
PERK in the life and death of the pancreatic beta-cell
phosphofructokinase, L4 complex (name copied from entity in Homo sapiens)
phosphofructokinase, P3L complex (name copied from entity in Homo sapiens)
phosphofructokinase, P4 complex (name copied from entity in Homo sapiens)
phosphofructokinase, PL3 complex (name copied from entity in Homo sapiens)
phosphofructokinase, P2L2 complex (name copied from entity in Homo sapiens)
triosephosphate isomerase dimer (name copied from entity in Homo sapiens)
Expression, purification, and characterization of histidine-tagged rat and human flavoenzyme dihydroorotate dehydrogenase.
SUMF1:SUMF2 (name copied from entity in Homo sapiens)
glucose 6-phosphate isomerase dimer (name copied from entity in Homo sapiens)
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On the mechanism of dehydrogenation of fatty acyl derivatives of coenzyme A. II. The electron-transferring flavoprotein.
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Biosynthesis and functions of mycothiol, the unique protective thiol of Actinobacteria
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The PDGF family: four gene products form five dimeric isoforms
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Unique small sulfur compounds, as well as unique pathways to sulfur amino acids are known in Mycobacteria. Sulfoglycolipids and mycothiols are an important part of the hardy pathogen nature of these organisms. Their pathways make interesting targets for drug designers (Bhave et al, 2007).
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ChEBI:32643 5-acetamido-6-formamido-3-methyluracil
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Genetic disorders of mitochondrial fatty acid oxidation.
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Mechanisms for the role of tetrahydrobiopterin in endothelial function and vascular disease
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Macromolecular assemblage of aminoacyl-tRNA synthetases: identification of protein-protein interactions and characterization of a core protein
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'Small'-proteoglycan:collagen interactions: keratan sulphate proteoglycan associates with rabbit corneal collagen fibrils at the 'a' and 'c' bands
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Peroxisomal straight-chain Acyl-CoA oxidase and D-bifunctional protein are essential for the retroconversion step in docosahexaenoic acid synthesis
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Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways
Characterization of the COQ5 gene from Saccharomyces cerevisiae. Evidence for a C-methyltransferase in ubiquinone biosynthesis
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FUNCTION Destroys superoxide anion radicals which are normally produced within the cells and which are toxic to biological systems.CATALYTIC ACTIVITY 2 superoxide + 2 H(+) = O(2) + H(2)O(2).COFACTOR Binds 1 iron ion per subunit.SUBUNIT Homotetramer.SIMILARITY Belongs to the iron/manganese superoxide dismutase family.CAUTION Although found extracellularly, no signal sequence is present. An alternative secretory pathway may be used.
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Characterization and functional analysis of the nucleotide binding fold in human peroxisomal ATP binding cassette transporters
NADPH-dependent GMP reductase isoenzyme of human (GMPR2). Expression, purification, and kinetic properties
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Norepinephrine Neurotransmitter Release Cycle
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The family of glycogen phosphorylases: structure and function
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Both human ferredoxins 1 and 2 and ferredoxin reductase are important for iron-sulfur cluster biogenesis
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A novel mechanism for GABA synthesis and packaging into synaptic vesicles
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Expression and supramolecular assembly of recombinant alpha1(viii) and alpha2(viii) collagen homotrimers
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Adenosine deaminase-like protein 1 (ADAL1): characterization and substrate specificity in the hydrolysis of N(6)- or O(6)-substituted purine or 2-aminopurine nucleoside monophosphates
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di-retinoid-pyridinium-ethanolamine [ChEBI:71980]
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Molybdenum cofactors, enzymes and pathways
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Function and biogenesis of iron-sulphur proteins
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Kinetics and inhibition of recombinant human cystathionine gamma-lyase. Toward the rational control of transsulfuration
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RGS17, an overexpressed gene in human lung and prostate cancer, induces tumor cell proliferation through the cyclic AMP-PKA-CREB pathway
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FUNCTION Catalyzes the formation of a covalent CysO-cysteine adduct via a sulfur transfer, using the thiocarboxylated sulfur carrier protein CysO-COSH as sulfur donor and O-phospho-L-serine (OPS) as sulfur acceptor. Can also use sodium sulfide as sulfur donor in vitro, albeit with less efficiency, but not thiosulfate or thio-nitro-benzoate. O-acetylserine (OAS) is a very poor substrate in comparison with OPS. May be of particular importance for cysteine biosynthesis in the persistent phase of M.tuberculosis.CATALYTIC ACTIVITY O-phospho-L-serine + H(2)S = L-cysteine + phosphate.CATALYTIC ACTIVITY O-phospho-L-serine + [CysO]-SH = [CysO]-L-cysteine + phosphate.COFACTOR Pyridoxal phosphate.PATHWAY Amino-acid biosynthesis; L-cysteine biosynthesis.SUBUNIT Homodimer.INDUCTION Up-regulated under oxidative stress conditions.DOMAIN The five C-terminal amino acid residues are inserted into the active site cleft in the closed conformation, protect the aminoacrylate intermediate and are involved in sulfur donor selectivity.DISRUPTION PHENOTYPE Strains lacking this gene are shown to be attenuated in macrophages.SIMILARITY Belongs to the cysteine synthase/cystathionine beta-synthase family.
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Cell adhesion to fibrillin-1 molecules and microfibrils is mediated by alpha 5 beta 1 and alpha v beta 3 integrins
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The shikimate pathway leads to the biosynthesis of chorismate, which, in mycobacteria, is a precursor of aromatic amino acids, naphthoquinones, menaquinones and siderophores. The enzymes of this pathway are attractive pharmaceutical targets, as the pathway is absent from mammals, and there are no redundancies in it (Herrmann and Weaver, 1999).
Gap-filling DNA repair synthesis and ligation in GG-NER
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Structural basis of the matrix metalloproteinases and their physiological inhibitors, the tissue inhibitors of metalloproteinases
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Lysyl oxidases in mammalian development and certain pathological conditions
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Purification and characterization of recombinant human prostacyclin synthase
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Ferritin structure from Mycobacterium tuberculosis: comparative study with homologues identifies extended C-terminus involved in ferroxidase activity
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3-(2-Aminoethyl)-1H-indol-5-ol [ChEBI:28790]
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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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ABCG5 and ABCG8 are obligate heterodimers for protein trafficking and biliary cholesterol excretion
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Deposition of tropoelastin into the extracellular matrix requires a competent elastic fiber scaffold but not live cells
Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol
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SLC26A7 is a Cl- channel regulated by intracellular pH
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Assembly and protection of the radical enzyme, methylmalonyl-CoA mutase, by its chaperone
FUNCTION Component of the pyruvate dehydrogenase (PDH) complex, that catalyzes the overall conversion of pyruvate to acetyl-CoA and CO(2).FUNCTION Together with AhpC, AhpD and Lpd, constitutes an NADH-dependent peroxidase active against hydrogen and alkyl peroxides as well as serving as a peroxynitrite reductase, thus protecting the bacterium against reactive nitrogen intermediates and oxidative stress generated by the host immune system.FUNCTION Appears to be essential for Mtb pathogenesis.CATALYTIC ACTIVITY Acetyl-CoA + enzyme N(6)-(dihydrolipoyl)lysine = CoA + enzyme N(6)-(S-acetyldihydrolipoyl)lysine.COFACTOR Binds 2 lipoyl cofactors covalently.ENZYME REGULATION Inhibited by rhodanine compounds. Some of them almost exclusively kill non-replicating mycobacteria in synergy with products of host immunity, such as nitric oxide and hypoxia, and are effective on bacteria within macrophages.SUBUNIT Forms a 24-polypeptide structural core with octahedral symmetry (By similarity). Identified in a complex with AhpC, AhpD and Lpd. Also makes part of the PDH complex, consisting of multiple copies of AceE (E1), DlaT (E2) and Lpd (E3).DISRUPTION PHENOTYPE Cells lacking this gene show severely retarded growth in vitro, and display no PDH activity. They are also more sensitive to nitrosative stress caused by NaNO(2), and to macrophage-induced killing in vitro. They also show at least 20-fold reduction in survival in a mouse tuberculosis model, and are unable to cause disease in a guinea pig model of tuberculosis infection. Disruption of dlaT leads to high up-regulation of the expression of the bkdABC operon.MISCELLANEOUS Is the only lipoylated protein in strain H37Rv grown on a standard rich medium. However, in a DlaT-deficient strain, another protein, BkdC, becomes lipoylated.SIMILARITY Belongs to the 2-oxoacid dehydrogenase family.SIMILARITY Contains 1 E3-binding domain.SIMILARITY Contains 2 lipoyl-binding domains.
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Nitric oxide, tetrahydrobiopterin, oxidative stress, and endothelial dysfunction in hypertension
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Identification of three cationic amino acid transporters in placental trophoblast: cloning, expression, and characterization of hCAT-1
(S)-3-Hydroxydodecanoyl-CoA [ChEBI:27668]
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Mutational analysis in longest known survivor of mucopolysaccharidosis type VII
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CATALYTIC ACTIVITY Adenosine 3',5'-bisphosphate + sulfite + thioredoxin disulfide = 3'-phosphoadenylyl sulfate + thioredoxin.PATHWAY Sulfur metabolism; hydrogen sulfide biosynthesis; sulfite from sulfate: step 3/3.MISCELLANEOUS Was identified as a high-confidence drug target.SIMILARITY Belongs to the PAPS reductase family. CysH subfamily.
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The extended GLUT-family of sugar/polyol transport facilitators: nomenclature, sequence characteristics, and potential function of its novel members (review)
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CATALYTIC ACTIVITY ATP + sulfate = diphosphate + adenylyl sulfate.PATHWAY Sulfur metabolism; hydrogen sulfide biosynthesis; sulfite from sulfate: step 1/3.SUBUNIT Heterodimer composed of CysD, the smaller subunit, and CysNC.INDUCTION Induced by sulfur limitation and oxidative stress. Repressed by the presence of cysteine.MISCELLANEOUS Was identified as a high-confidence drug target.SIMILARITY Belongs to the PAPS reductase family. CysD subfamily.
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CATALYTIC ACTIVITY 2 R'-SH + ROOH = R'-S-S-R' + H(2)O + ROH.SIMILARITY Belongs to the AhpC/TSA family.SIMILARITY Contains 1 thioredoxin domain.
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NLRs join TLRs as innate sensors of pathogens
trans-Tetradec-2-enoyl-CoA [ChEBI:27721]
Reversible lysine acetylation controls the activity of the mitochondrial enzyme acetyl-CoA synthetase 2
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Glycosaminoglycan storage disorders: a review
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Targeting the oncogene and kinome chaperone CDC37
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Remodelling of high density lipoproteins by plasma factors
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2'-Deoxyinosine 5'-phosphate [ChEBI:28806]
Structural basis of Wnt recognition by Frizzled
The collagen substrate specificity of human neutrophil collagenase
G proteins and opioid receptor-mediated signalling
FUNCTION: Participates in various redox reactions through the reversible oxidation of its active center dithiol to a disulfide and catalyzes dithiol-disulfide exchange reactions (By similarity).
cDNA cloning of carboxyl ester lipase from human pancreas reveals a unique proline-rich repeat unit
RNA interference suggests a primary role for monoacylglycerol lipase in the degradation of the endocannabinoid 2-arachidonoylglycerol
Metabolism of highly unsaturated n-3 and n-6 fatty acids
Epidermal growth factor receptor activation in glioblastoma through novel missense mutations in the extracellular domain
Plasmalogens: biosynthesis and functions
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5'-Phosphoribosyl-5-aminoimidazole [ChEBI:28843]
Molecular identification of microsomal acyl-CoA:glycerol-3-phosphate acyltransferase, a key enzyme in de novo triacylglycerol synthesis
Epidermal Growth Factor Receptor (EGFR) signaling
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The human purH gene product, 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase
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Assembly and export of MHC class I peptide ligands
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Chromosomal localization of the gene for human glucosamine-6-sulphatase to 12q14
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Acyl-CoA:dihydroxyacetonephosphate acyltransferase: cloning of the human cDNA and resolution of the molecular basis in rhizomelic chondrodysplasia punctata type 2
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Involvement of enzymes other than CYPs in the oxidative metabolism of xenobiotics
Expert Opin Drug Metab Toxicol 2:895-921
Beta-amino acids: mammalian metabolism and utility as alpha-amino acid analogues
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Characterization of the human sulfate anion transporter (hsat-1) protein and gene (SAT1; SLC26A1)
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Characterization and functional expression of the cDNA encoding human brain quinolinate phosphoribosyltransferase
Activity and genomic organization of human glucose transporter 9 (GLUT9), a novel member of the family of sugar-transport facilitators predominantly expressed in brain and leucocytes
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Complete primary structure of a human plasma membrane Ca2+ pump
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The in vitro replication of DNA containing the SV40 origin.
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Cytosolic sulfonation of small molecules
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Thematic Review Series: Proteomics. An integrated omics analysis of eicosanoid biology
Structural basis for inhibition of the epidermal growth factor receptor by cetuximab
Quantitating protein synthesis, degradation, and endogenous antigen processing
Crystallographic and kinetic studies of human mitochondrial acetoacetyl-CoA thiolase: the importance of potassium and chloride ions for its structure and function
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Macromolecular organization of chicken type X collagen in vitro
ATP binding/hydrolysis by and phosphorylation of peroxisomal ATP-binding cassette proteins PMP70 (ABCD3) and adrenoleukodystrophy protein (ABCD1)
Glucose and cAMP regulate the L-type pyruvate kinase gene by phosphorylation/dephosphorylation of the carbohydrate response element binding protein
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Remodeling of cardiolipin by phospholipid transacylation
Purification and properties of beta-hydroxyisobutyric dehydrogenase
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Exon-intron organization and chromosomal localization of the mouse monoglyceride lipase gene
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Synaptotagmin activates membrane fusion through a Ca2+-dependent trans interaction with phospholipids
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Folding of glycoproteins: toward understanding the biophysics of the glycosylation code
The NLRP3 inflammasome: a sensor of immune danger signals
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Human glucose-6-phosphate dehydrogenase: the crystal structure reveals a structural NADP(+) molecule and provides insights into enzyme deficiency
Tissue-specific expression of the fibril-associated collagens XII and XIV
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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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Site-directed mutagenesis of the distal basic cluster of pancreatic bile salt-dependent lipase
Type XIV Collagen Regulates Fibrillogenesis: PREMATURE COLLAGEN FIBRIL GROWTH AND TISSUE DYSFUNCTION IN NULL MICE
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Molecular mechanisms regulating hormone-sensitive lipase and lipolysis
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Still a puzzle: why is haem covalently attached in c-type cytochromes?
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Investigation of coenzyme Q biosynthesis in human fibroblast and HepG2 cells
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Structure and function of the mammalian fibrillin gene family: Implications for human connective tissue diseases
Identification of a mammalian H(+)-myo-inositol symporter expressed predominantly in the brain
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Matrix metalloproteinases and tissue inhibitors of metalloproteinases: structure, function, and biochemistry
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The classical human phosphoglucomutase (PGM1) isozyme polymorphism is generated by intragenic recombination
Genomic structure and expression of the human heme A:farnesyltransferase (COX10) gene
Crystal structures of F420-dependent glucose-6-phosphate dehydrogenase FGD1 involved in the activation of the anti-tuberculosis drug candidate PA-824 reveal the basis of coenzyme and substrate binding
Identification of peroxisomal acyl-CoA thioesterases in yeast and humans
Ins and outs of cellular cobalamin transport
Subcellular localization and physiological role of alpha-methylacyl-CoA racemase
Interaction of Hsp90 with the nascent form of the mutant epidermal growth factor receptor EGFRvIII
An updated overview on Wnt signaling pathways: a prelude for more
Mitochondrial and peroxisomal targeting of 2-methylacyl-CoA racemase in humans
Cell adhesion and integrin binding to recombinant human fibrillin-1
The human liver-specific homolog of very long-chain acyl-CoA synthetase is cholate:CoA ligase
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Identification of novel PPARgamma target genes in primary human adipocytes
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CATALYTIC ACTIVITY: O(4)-succinyl-L-homoserine + L-cysteine = L- cystathionine + succinate.
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Identification of the gene responsible for the cblA complementation group of vitamin B12-responsive methylmalonic acidemia based on analysis of prokaryotic gene arrangements
Proc. Natl. Acad. Sci. U.S.A. 99:15554-9
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The 2.0 A structure of human ferrochelatase, the terminal enzyme of heme biosynthesis.
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1-chloro-2,4-dinitrobenzene [ChEBI:34718]
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Hydroxylation of (X-Pro-Gly)n by protocollagen proline hydroxylase. Effect of chain length, helical conformation and amino acid sequence in the substrate
Role of subunit diversity in signaling by heterotrimeric G proteins
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Crystal structure of human branched-chain alpha-ketoacid dehydrogenase and the molecular basis of multienzyme complex deficiency in maple syrup urine disease.
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Purification, cDNA cloning and heterologous expression of human phosphomannose isomerase
Interaction between PCNA and DNA ligase I is critical for joining of Okazaki fragments and long-patch base-excision repair.
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The precision of lateral size control in the assembly of corneal collagen fibrils
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Note: the coordinates are copied over from Homo sapiens.
carbamoyl-phosphate synthase (ammonia), mitochondrial
ornithine carbamoyltransferase, mitochondrial
L-tyrosine:2-oxoglutarate aminotransferase
delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial precursor
Glutaryl-CoA dehydrogenase, mitochondrial
Identification of a new inborn error in bile acid synthesis: mutation of the oxysterol 7alpha-hydroxylase gene causes severe neonatal liver disease
A critical review of the origin and control of adrenal androgens
Baillieres Clin Obstet Gynaecol 11:229-48
methylmalonate semialdehyde dehydrogenase, monomer
Methylmalonate-semialdehyde dehydrogenase (acylating) (EC 1.2.1.27) (MMSDH)
Alpha-aminoadipic semialdehyde dehydrogenase
ABCG1 redistributes cellular cholesterol to domains removable by high density lipoproteins but not by lipid-depleted lipoproteins
3-hydroxyisobutyryl-coenzyme A hydrolase
3-hydroxyisobutyrate dehydrogenase, monomer
3-hydroxyisobutyrate dehydrogenase, mitochondrial precursor
2-methyl-3-hydroxybutyryl-CoA dehydrogenase
Endoplasmic reticulum-associated amyloid beta-peptide binding protein
Acyl-CoA dehydrogenase family member 8, mitochondrial precursor
Activator- recruited cofactor 42 kDa component
Isovaleryl-CoA dehydrogenase, mitochondrial precursor
acyl-CoA dehydrogenase, short/branched chain specific
Acyl-CoA dehydrogenase, short/branched chain specific, mitochondrial precursor
2-methyl branched chain acyl-CoA dehydrogenase
2-methylbutyryl-coenzyme A dehydrogenase
Acyl-CoA dehydrogenase, short/branched chain specific, mitochondrial precursor (EC 1.3.99.-) (SBCAD) (2-methyl branched chain acyl-CoA dehydrogenase) (2-MEBCAD) (2-methylbutyryl-coenzyme A dehydrogenase) (2-methylbutyryl-CoA dehydrogenase)
branched chain keto acid dehydrogenase E1, beta polypeptide
Dihydrolipoamide dehydrogenase, mitochondrial
ornithine aminotransferase, mitochondrial
The 10+4 microfibril structure of thin cartilage fibrils
Delta-1-pyrroline-5-carboxylate synthetase long
Delta-1-pyrroline-5-carboxylate synthetase short
branched chain keto acid dehydrogenase E1, alpha polypeptide
Disorders of propionate and methylmalonate metabolism
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 2165-2193
Participation of two members of the very long-chain acyl-CoA synthetase family in bile acid synthesis and recycling
Molecular cloning and characterization of a novel (Na+,K+)/H+ exchanger localized to the trans-Golgi network
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).
Deoxyuridine triphosphatase (DUT) catalyzes the hydrolysis of dUTP to form dUMP and pyrophosphate. Two isoforms of DUT are expressed, generated by alternative splicing. The major one, annotated here, is localized to the nucleoplasm (Ladner et al. 1996). The enzyme is a homotrimer (Mol et al. 1996). In the cell, this reaction depletes the supply of dUTP, preventing its incorporation into DNA, while generating dUMP, the immediate precursor of thymidine nucleotides.
The human ABCG4 gene is regulated by oxysterols and retinoids in monocyte-derived macrophages
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.
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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).
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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).
Structural heterogeneity of type I collagen triple helix and its role in osteogenesis imperfecta
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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 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).
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The synthesis of orotidine 5'-monophosphate (OMP) from orotate and 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) is catalyzed by the orotate phosphoribosyltransferase activity of the bifunctional "uridine monophosphate synthetase (orotate phosphoribosyl transferase and orotidine 5'-decarboxylase)" protein. The reaction itself is freely reversible, but is pulled in the forward direction in vivo by the irreversible hydrolysis of pyrophosphate. While purified human protein has not been characterized in detail, the close similarity of the human gene to that encoding the well-studied hamster protein, and the demonstration that mutations in the human gene are associated with failure to convert orotate to UMP in vivo, provide convincing evidence that the human uridine monophosphate synthetase protein indeed catalyzes these two reactions (McClard et al. 1980; Suchi et al. 1997). The active form of the human protein is a dimer (Yablonski et al. 1996; Wittmann et al. 2008).
Dihydroorotate dehydrogenase catalyzes the oxidation of dihydroorotate to orotate (orotic acid). The enzyme is located in the inner mitochondrial membrane oriented so that cytosolic dihydroorotate molecules have access to it, and orotate is released into the cytosol. The reducing equivalents generated by the reaction are transferred by ubiquinone (Coenzyme Q) to the electron transport chain within the inner mitochondrial membrane. There is no evidence for the involvement of NAD+ as an acceptor of reducing equivalents in this reaction in mammalian cells (Jones 1980). In contrast, the reaction catalyzed by the enzyme isolated from the anaerobic bacterium Clostridium oroticum requires NAD+ as a cofactor but also proceeds strongly in the direction of dihydroorotate synthesis consistent with the greater electronegativity of NAD+ (Lieberman and Kornberg 1953). Early studies of purified rat liver enzyme by Forman and Kennedy suggested the presence of flavin mononucleotide and iron-sulfur complexes as cofactors. More recent work by Bader, Beuneu, and their colleagues with recombinant human protein expressed in insect cells has confirmed the presence of flavin mononucleotide, at a stoichiometry of one molecule per molecule of apoenzyme but suggests that iron-sulfur complexes, if indeed they are involved in the oxidation and electron transport process, are not an integral part of the dihydroorotate dehydrogenase holoenzyme.
Cytosolic nucleoside phosphorylase (NP) trimer catalyzes the reversible reaction of guanosine or deoxyguanosine with orthophosphate to form guanine and ribose 1-phosphate or deoxyribose 1-phosphate (Ealick et al. 1990; Wiginton et al. 1980). While NP is active with either nuckeotide in vitro, levels of deoxyguanosine are normally low in vivo, limiting the extent of this reaction. NP deficiency in vivo is associated with defects in purine nucleotide salvage and leads to immunodeficiency (Williams et al. 1987).
Cytosolic nucleoside phosphorylase (NP) trimer catalyzes the reversible reaction of inosine or deoxyinosine with orthophosphate to form hypoxanthine and ribose 1-phosphate or deoxyribose 1-phosphate (Ealick et al. 1990; Wiginton et al. 1980). While NP is active with either nuckeotide in vitro, levels of deoxyinosine are normally low in vivo, limiting the extent of this reaction. NP deficiency in vivo is associated with defects in purine nucleotide salvage and leads to immunodeficiency (Williams et al. 1987).
Iron-sulfur proteins in health and disease
Cytosolic GMP reductase (GMPR) catalyzes the reaction of GMP and NADPH + H+ to yield IMP and NADP+ + NH4+ (Spector et al. 1979; Deng et al. 2002). Two GMPR proteins have been identified, GMPR and GMPR2. Both proteins form homotetramers (GMPR - unpublished crstallographic data PDB 2BLE; GMPR2 - Li et al. 2006).
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).
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).
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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).
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The purine bases guanine and hypoxanthine (derived from adenine by events in the purine salvage pathways) are converted to xanthine and then to uric acid, which is excreted from the body (Watts 1974). The end-point of this pathway in humans and hominoid primates is unusual. Most other mammals metabolize uric acid further to yield more soluble end products, and much speculation has centered on possible roles for high uric acid levels in normal human physiology.
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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.
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Pyruvate carboxylase, mitochondrial precursor
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Mitochondrial fatty acid oxidation disorders
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 2297-2326
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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).
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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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Putative inorganic polyphosphate/ATP-NAD kinase
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).
Nicotinate-nucleotide pyrophosphorylase (carboxylating)
methylcrotonyl-CoA carboxylase beta chain
methylcrotonyl-CoA carboxylase alpha chain
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SIMILARITY Contains 1 FAD-binding FR-type domain.
ribonucleotide reductase M2B (TP53 inducible)
The human ATP-binding cassette (ABC) transporter superfamily
non-metastatic cells 1, protein (NM23A) expressed in
Tumor metastatic process-associated protein
Nucleoside diphosphate kinase, mitochondrial
non-metastatic cells 4, protein expressed in
Pyrimidine pathways in health and disease
Phosphopantothenoylcysteine decarboxylase
Adenylate kinase isoenzyme 2, mitochondrial
Adenylate kinase isoenzyme 2, mitochondrial (EC 2.7.4.3) (ATP-AMP transphosphorylase)
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
Conversion of palmitic acid to very long chain fatty acyl-CoAs
Synthesis of very long-chain fatty acyl-CoAs
Cysteine synthase (CysM) of Mycobacterium tuberculosis is an O-phosphoserine sulfhydrylase: evidence for an alternative cysteine biosynthesis pathway in mycobacteria
The control of glycogen metabolism in the liver
Ribonucleoside-diphosphate reductase M1 chain (EC 1.17.4.1) (Ribonucleotide reductase large chain)
Ribonucleoside-diphosphate reductase M1 chain
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The enzyme, nicotinate nucleotide pyrophosphorylase, is specific for quinolinate. Its activity is strictly dependent on Mg2+ ions being present. A phosphoribosyl group is transferred to quinolinate to form nicotinate D-ribonucleotide. This reaction represents another rate-limiting step of the pathway from tryptophan to NAD+.
NAD synthase catalyzes the final step in the biosynthesis of NAD+, both in the de novo synthesis and in the salvage pathways. The enzyme makes use of glutamine as an amide donor in the reaction. NAD synthase exists as a homohexamer in the cytosol. There are two forms of NAD synthase in humans, NADsyn1 and NADsyn2. The major difference between the two forms is that NADsyn1 appears to be glutamine-dependent whereas NADsyn2 is strictly ammonia-dependent.
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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.
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.
NAD+ kinase catalyzes the transfer of a phosphate group from ATP to NAD+, forming NADP+. This is the only way to generate NADP+ in all living organisms. The enzyme requires a divalent metal to be effective. Zn2+ is the best metal for this purpose.
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).
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Mutations in the 3beta-hydroxysterol Delta24-reductase gene cause desmosterolosis, an autosomal recessive disorder of cholesterol biosynthesis
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Hormone-sensitive lipase and monoacylglycerol lipase are both required for complete degradation of adipocyte triacylglycerol
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The formate-tetrahydrofolate ligase activity of the trifunctional MTHFD1 enzyme catalyzes the reaction of THF polyglutamate, formate, and ATP to form 10-formylTHF polyglutamate, ADP, and orthophosphate. MTHFD1 is cytosolic and occurs as a dimer. The human enzyme has been identified and partially characterized biochemically (Hum et al. 1988); additional reaction details can be inferred from the properties of the well-studied homologous rabbit enzyme (Villar et al. 1985).
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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).
Synthesis of bile acids and bile salts via 27-hydroxycholesterol
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Cytosolic folylpolyglutamate synthase catalyzes the reaction of 5-methylTHF-glutamate(n), L-glutamate, and ATP to form 5-methylTHF-glutamate(n+1), ADP, and orthophosphate. (The first glutamate residue is attached to the glutamate moiety of 5-methylTHF itself; for convenience the process is annotated here as if it proceeded in a single concerted step.) The extent of conjugation is variable, but the commonest cytosolic form of 5-methylTHF has five added glutamate residues. Although its properties as a donor of one-carbon units are not affected by glutamate addition, 5-methylTHF that lacks added glutamate residues cannot be retained in the cytosol so this reaction is needed for normal 5-methylTHF function under physiological conditions (Garrow et al. 1992; Chen et al. 1996).
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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).
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Pyridoxine-5'-phosphate oxidase (PNPO) is able to oxidize pyridoxamine phosphate (PXAP) to pyridoxal 5'-phosphate (PXLP) (Kang et al. 2004).
Pyridoxine-5'-phosphate oxidase (PNPO) is able to oxidize pyridoxine phosphate (PDXP) to pyridoxal 5'-phosphate (PXLP) (Kang et al. 2004).
Animals cannot synthesize pyridoxal 5'-phosphate (PLP) which is a ligand in aminotransferases and other enzymes. PLP's accessible derivatives pyridoxine, pyridoxal, and pyridoxamine are traditionally called vitamins B6. They are taken up nutritionally from bacteria and plants, but also created from PLP in the body. The pathways used to recycle PLP from these three compounds can therefore be called vitamin B6 activation as well as PLP salvage. Because of the close similarity of the molecules, only two enzymes are needed for the task (McCormick & Chen, 1999).
Mitochondrial cob(I)yrinic acid a,c-diamide adenosyltransferase (MMAB) is a dual purpose enzyme involved in the reduction and adenosylation of cobalamin. In the first step, MMAB reduces cob(II)alamin (B12r) to cob(I)alamin (B12s) (Fan & Bobik 2008, Leal et al. 2003). Defects in MMAB cause methylmalonic aciduria type cblB (MMAB aka methylmalonic aciduria type B or vitamin B12-responsive methylmalonicaciduria of cblB complementation type; MIM:251110). Affected individuals have methylmalonic aciduria and metabolic ketoacidosis, despite a functional methylmalonyl-CoA mutase. In severe cases, newborns are lethargic, prone to vomiting and fail to thrive (Dobson et al. 2002).
Mitochondrial cob(I)yrinic acid a,c-diamide adenosyltransferase (MMAB) is a dual purpose enzyme involved in the reduction and adenosylation of cobalamin. In the second step, MMAB transfers an adenosyl group from ATP to cob(I)alamin (B12s) to form adenosylcabalamin (AdoCbl) (Fan & Bobik 2008, Leal et al. 2003). Defects in MMAB cause methylmalonic aciduria type cblB (MMAB aka methylmalonic aciduria type B or vitamin B12-responsive methylmalonicaciduria of cblB complementation type; MIM:251110). Affected individuals have methylmalonic aciduria and metabolic ketoacidosis, despite a functional methylmalonyl-CoA mutase. In severe cases, newborns are lethargic, prone to vomiting and fail to thrive (Dobson et al. 2002).
1-(5'-Phosphoribosyl)-5-amino-4-(N-succinocarboxamide)-imidazole [ChEBI:18319]
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Biochemical characterization of human collagenase-3
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Multidrug resistance-associated protein 1 (ABCC1, MRP1) can specifically mediate the ATP-dependant export of free cobalamin (Cbl aka vitamin B12) from small intestine cells to the portal vein (Shah et al. 2011).
Methylmalonyl-CoA mutase (MUT aka MCM) (Jansen et al. 1989) utilises adenosylcobalamin (AdoCbl) as a cofactor and transfers an adenosyl group from AdoCbl to methymalonyl-CoA to form succinyl-CoA, a precursor for the citric acid cycle. MUT has a homodimeric structure and is located in the mitochondrial matrix. Defects in MUT cause methylmalonic aciduria type mut (MMAM; MIM:251000), an often fatal disorder of organic acid metabolism (Worgan et al. 2006). Methylmalonic aciduria type A protein (MMAA) (Dobson et al. 2002) is thought to act as a chaperone to MUT and is suggested to play a dual role with regards to MUT protection and reactivation. Defects in MMAA cause methylmalonic aciduria type cblA (MMAA aka methylmalonic aciduria type A or vitamin B12-responsive methylmalonicaciduria of cblA complementation type; MIM:251100). Affected individuals accumulate methylmalonic acid in the blood and urine and are prone to potentially life threatening acidotic crises in infancy or early childhood (Dobson et al. 2002, Lerner-Ellis et al. 2004).
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).
Vitamin B12 (cobalamin, Cbl) is a water-soluble vitamin with a key role in blood formation and normal functioning of the brain and nervous system. Cbl consists of a planar corrin ring coordinating with a cobalt atom through four nitrogen atoms. A 5,6-dimethylbenzamidizole base coordinates with the cobalt atom in the lower axial position while a number of different species can coordinate with the cobalt atom in the upper axial position. It is the cobalt-corrin ring complex that gives all Cbls a deep red colour. Only bacteria and archaea are able to synthesize Cbl thus humans need a dietary intake to prevent deficiency (Green 2010, Quadros 2010, Watkins & Rosenblatt 2011). A common semi-synthetic form of the vitamin, cyanocobalamin (CNCbl, where a cyanide group is in the upper axial position), is produced from bacterial hydroxocobalamin and used in many pharmaceuticals, supplements and as a food additive. In mammalian cells, Cbl or CNCbl is converted to two active coenzyme derivatives; methylcobalamin (MetCbl) and adenosylcobalamin (AdoCbl). MetCbl is required for activity of the cytoplasmic enzyme methionine synthase, which converts homocysteine to methionine. AdoCbl is required for activity of the mitochondrial enzyme methylmalonyl CoA mutase, which converts L-methylmalonyl-CoA to succinyl-CoA (Seetharam 1999). This pathway outlines the intake, transport and metabolism of Cbl and is assumed to be equally applicable to CNCbl.
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.
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 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).
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).
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The ABCs of solute carriers: physiological, pathological and therapeutic implications of human membrane transport proteinsIntroduction
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Cloning and expression of a cDNA encoding human sterol carrier protein 2
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Panthothenate (vitamin B5) is the precursor of coenzyme A (Robishaw and Neely 1985) and is the prosthetic group of acyl carrier protein (ACP) (Joshi et al. 2003). Its name is derived from the Greek pantothen meaning "from everywhere" and small quantities of pantothenic acid are found in nearly every foodstuff.
Coenzyme A (CoA) is a ubiquitous cofactor that functions as an acyl group carrier in diverse processes including fatty acid metabolism and the TCA cycle (Lipmann 1953). It is synthesized from the vitamin pantothenate in a sequence of five reactions (Daugherty et al. 2002; Leonardi et al. 2005; Robishaw and Neely 1985). These reactions all occur in the cytosol or the mitochondrial intermembrane space (Leonardi et al. 2005). A recently described transport protein appears to mediate the uptake of Coenzyme A into the mitochondrial matrix (Prohl et al. 2001).
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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.
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Nucleotides and their derivatives are used for short-term energy storage (ATP, GTP), for intra- and extra-cellular signaling (cAMP; adenosine), as enzyme cofactors (NAD, FAD), and for the synthesis of DNA and RNA. Most dietary nucleotides are consumed by gut flora; the human body's own supply of these molecules is synthesized de novo. Additional metabolic pathways allow the interconversion of nucleotides, the salvage and reutilization of nucleotides released by degradation of DNA and RNA, and the catabolism of excess nucleotides (Rudolph 1994). These pathways are regulated to control the total size of the intracellular nucleotide pool, to balance the relative amounts of individual nucleotides, and to couple the synthesis of deoxyribonucleotides to the onset of DNA replication (S phase of the cell cycle). These pathways are also of major clinical interest as they are the means by which nucleotide analogues used as anti-viral and anti-tumor drugs are taken up by cells, activated, and catabolized (Weilin and Nordlund 2010). As well, differences in nuclotide metabolic pathways between humans and aplicomplexan parasites like Plasmodium have been exploited to design drugs to attack the latter (Hyde 2007). The movement of nucleotides and purine and pyrimidine bases across lipid bilayer membranes, mediated by SLC transporters, is annotated as part of the module "transmembrane transport of small molecules".
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).
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.
The events of human pyrimidine metabolism are conveniently, if somewhat arbitrarily, grouped into four pathways: de novo synthesis of the pyrimidine ring and its conversion to uridine 5'-monophosphate (UMP), the biosynthesis of other pyrimidine ribo- and deoxyribonucleotides, pyrimidine salvage reactions, and pyrimidine catabolism (Loffler et al. 2005). De novo synthesis of the pyrimidine ring and its conversion to UMP. The pyrimidine base orotate is synthesized from glutamine, bicarbonate, and aspartate. Orotate reacts with 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) and is then decarboxylated to form the pyrimidine nucleotide UMP. Pyrimidine biosynthesis [interconversion]. Pyrimidine ribo- and deoxyribonucleotide di- and triphosphates are synthesized, both from UMP and from pyrimidine ribonucleotide monophosphates generated in salvage reactions. Pyrimidine salvage reactions. Pyrimidine nucleosides and free bases generated by DNA and RNA breakdown are converted to nucleotide monophosphates. Pyrimidine catabolism. The pyrimidine bases thymine and uracil are degraded to beta-aminoisobutyrate and beta-alanine, respectively, which are excreted from the body.
Mitochondrial adenylate kinase 2 (AK2) catalyzes the reaction of AMP and ATP to form two molecules of ADP (Hamade et al. 1982). Localization of AK2 specifically to the mitochondrial intermembrane space is inferred from studies of the homologous rat enzyme (Criss 1970).
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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.
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In this reaction, 1 molecule of 'Thioredoxin' is translocated from cytosol to nucleoplasm. This movement of the molecule occurs through the 'nuclear pore'.
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Molecular tinkering of G protein-coupled receptors: an evolutionary success
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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.
Cytosolic ribonucleotide reductase catalyzes the reduction of adenine, guanine, cytidine, and uridine ribonucleoside 5'-diphosphates to form the corresponding deoxyribonucleoside 5'-diphosphates, coupled to the oxidation of thioredoxin (Holmgren 1989; Eklund et al. 2001). Ribonucleotide reductase is a tetramer of two large and two small subunits (Shao et al. 2004; Zhou et al. 2005). The overall activity of the enzyme is regulated allosterically: ATP binding is stimulatory while dATP binding is inhibitory (Reichard et al. 2000). The reducing equivalents needed for ribonucleotide reductase activity can be provided by either of two small proteins, glutaredoxin and thioredoxin (Holmgren 1989; Sun et al. 1998). Both are re-reduced with NADPH as the donor of reducing equivalents, and so are active in catalytic amounts. The relative contributions of glutaredoxin and thioredoxin in vivo are unknown.
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Mitochondrial adenylate kinase 2 (AK2) catalyzes the reaction of two molecules of ADP to form AMP and ATP (Hamade et al. 1982). Localization of AK2 specifically to the mitochondrial intermembrane space is inferred from studies of the homologous rat enzyme (Criss 1970).
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In this reaction, 1 molecule of 'thioredoxin, oxidized' is translocated from nucleoplasm to cytosol. This movement of the molecule occurs through the 'nuclear pore'.
Deoxyribonucleotides needed for DNA repair are synthesized de novo by the reduction of ribonucleoside 5'-diphosphates. This reaction is catalyzed by a nuclear form of ribonucleotide reductase active throughout the cell cycle. The reducing equivalents needed for these reactions can be provided directly by thioredoxin.
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Mitochondrial 3-hydroxyisobutyrate dehydrogenase (HIBADH) catalyzes the reversible reaction of methylmalonyl semialdehyde and NADH + H+ to form beta-hydroxyisobutyrate and NAD+. The biochemical properties of human HIBADH are inferred from those of its better-studied porcine homologue (Robinson and Coon 1957). Unpublished crystallographic studies (PDB 2GF2) have shown the active enzyme to be a tetramer of HIBADH polypeptides whose aminoterminal 40 residues, a mitochondrial targeting sequence, have been removed.
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Mitochondrial 3-hydroxyisobutyrate dehydrogenase (HIBADH) catalyzes the reversible reaction of beta-hydroxyisobutyrate and NAD+ to form methylmalonyl semialdehyde and NADH + H+. The biochemical properties of human HIBADH are inferred from those of its better-studied porcine homologue (Robinson and Coon 1957). Unpublished crystallographic studies (PDB 2GF2) have shown the active enzyme to be a tetramer of HIBADH polypeptides whose aminoterminal 40 residues, a mitochondrial targeting sequence, have been removed.
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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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Alpha-aminoadipic semialdehyde dehydrogenase (ALDH7A1) catalyzes the reaction of alpha-aminoadipic semialdehyde and NAD+ to form alpha-aminoadipate and NADH + H+ (Mills et al. 2006). Unpublished crystallographic data (PDB 2J6L) indicate that the enzyme is a homodimer. Recent immunofluorescence studies of both endogenous and GFP-tagged ALDH7A1 proteins in cultured human embryonic kidney cells indicate that the protein is present in both mitochondria and the cytosol (Wong et al. 2010).
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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).
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Mitochondrial methylmalonate semialdehyde dehydrogenase (ALDH6A1) catalyzes the reaction of methylmalonate semialdehyde, NAD+, and CoA to form propionyl-CoA, CO2, and NADH + H+. A human ALDH6A1 gene has been cloned. Its sequence is closely homologous to that of the better-characterized rat enzyme (Kedishvili et al. 1992) and a missense mutation in a normally well-conserved codon has been found in the allele of the gene from a patient with a defect in methylmalonic semialdehyde dehydrogenase activity (Chambliss et al. 2000).
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.
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 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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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).
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5-phosphoribosylglycinamide [ChEBI:18349]
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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).
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Methylcrotonyl CoA carboxylase (MCCA) catalyzes the reversible reaction of beta-methylcrotonyl-CoA, ATP, and CO2 to form beta-methylglutaconyl-CoA, ADP, orthophosphate, and H2O. Active MCCA is composed of two polypeptides, MCCA1 and MCCA2 (Baumgartner et al. 2001; Holzinger et al. 2001). The enzyme has been purified from fibroblast mitochondria. By analogy to the more thoroughly studied bovine homologue, MCCA is thought to be a hexamer of six MCCA1:MCCA2 dimers, and the MCCA1 polypeptide is thought to have a biotin moiety covalently bound to lysine residue 681. Localization of the complex to the mitochondrial inner membrane is inferred from studies of the bovine homologue (Hector et al. 1980). Mitochondrial import of MCCA1 and 2 is associated with removal of aminoterminal mitochondrial targeting sequences (Stadler et al. 2005).
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Mitochondrial isovaleryl dehydrogenase (IVD) catalyzes the reaction of isovaleryl-CoA and FAD to form beta-methylcrotonyl-CoA and FADH2 (Finocchiaro et al. 1978; Rhead and Tanaka 1980). Crystallographic studies demonstrated the existene of a tetramer of IVD polypeptides lacking an aminoterminal mitochondrial targeting sequence (Tiffany et al. 1997).
Mitochondrial 2-methyl branched chain acyl-CoA dehydrogenase (ACADSB) catalyzes the reaction of alpha-methylbutyryl-CoA and FAD to form 'tiglyl-CoA and FADH2 (Andresen et al. 2000; Gibson et al. 2000). Unpublished crystallographic data (PDB 2JIF) indicate that the enzyme is a tetramer of ACADSB polypeptides whose aminoterminal 51 residues, a mitochondrial targeting sequence, have been removed.
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Methylcrotonyl CoA carboxylase (MCCA) catalyzes the reversible reaction of beta-methylglutaconyl-CoA, ADP, orthophosphate, and H2O to form beta-methylcrotonyl-CoA, ATP, and CO2. Active MCCA is composed of two polypeptides, MCCA1 and MCCA2 (Baumgartner et al. 2001; Holzinger et al. 2001). The enzyme has been purified from fibroblast mitochondria. By analogy to the more thoroughly studied bovine homologue, MCCA is thought to be a hexamer of six MCCA1:MCCA2 dimers, and the MCCA1 polypeptides are thought to have biotin moieties covalently bound to a lysine residue at position 681 in the polypeptide chain. Mitochondrial import of MCCA1 and 2 is associated with removal of aminoterminal mitochondrial targeting sequences but the exact lengths of these sequences have not been determined.
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Mitochondrial 3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10; HADH2) catalyzes the reversible reaction of alpha-methylacetoacetyl-CoA and NADH + H+ to form alpha-methyl-beta-hydroxybutyryl-CoA and NAD+ (Ofman et al. 2003). Crystallographic data indicate that the enzyme is a homotetramer (Kissinger et al. 2004).
Mitochondrial 3-hydroxyacyl-CoA dehydrogenase type-2 (HSD17B10; HADH2) catalyzes the reversible reaction of alpha-methyl-beta-hydroxybutyryl-CoA and NAD+ to form alpha-methylacetoacetyl-CoA and NADH + H+ (Ofman et al. 2003). Crystallographic data indicate that the enzyme is a homotetramer (Kissinger et al. 2004).
Studies on beta-phenylethylamine deamination by human placental monoamine oxidase
Mitochondrial isobutyryl-CoA dehydrogenase (ACAD8) catalyzes the reaction of isobutyryl-CoA and FAD to form methacrylyl-CoA and FADH2 (Roe et al. 1999; Nguyen et al. 2002). Crystallographic studies have shown the active enzyme to be a tetramer of ACAD8 polypeptides whose aminoterminal 23 residues, a mitochondrial targeting sequence, have been removed (Bataille et al. 2004).
Mitochondrial acetyl-CoA acetyltransferase (ACAT1) catalyzes the reaction of alpha-methyl-acetoacetyl-CoA and CoA to form propionyl-CoA and acetyl-CoA. Structural studies have shown the active enzyme to be a tetramer of ACAT1 polypeptides whose aminoterminal 34 residues, a mitochondrial targeting sequence, have been removed (Haapalainen et al. 2007).
Mitochondrial 3-hydroxyisobutyryl-CoA hydrolase (HIBCH) catalyzes the hydrolysis of beta-hydroxyisobutyryl-CoA to form beta-hydroxyisobutyrate (3-hydroxy-2-methylpropanoate) and CoA (Hawes et al. 1996).
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4-[(1R)-2-Amino-1-hydroxyethyl]-1,2-benzenediol [ChEBI:1]
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Dephosphorylation of O-phospho-L-serine to L-serine proceeds through a phospho-enzyme intermediate of the catalysing phosphatase PSP (Collet et al. 1997).
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Serine biosynthesis starts from 3-phosphoglycerate, a glycolysis intermediate. Its dehydrogenation is catalysed by tetrameric phosphoglycerate dehydrogenase PHGDH. (Tabatabaie et al. 2009).
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Cytosolic asparagine synthase (ASNS) catalyzes the reaction of aspartate, glutamine, and ATP to form asparagine, glutamate, AMP, and pyrophosphate. Studies of the recombinant protein expressed in E. coli suggest that the active form of the enzyme is a dimer (Van Heeke and Schuster 1989).
Gap-filling DNA repair synthesis and ligation in TC-NER
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Delta-1-pyrroline-5-carboxylate synthetase associated with the inner mitochondrial membrane catalyzes the two-step reaction that converts glutamate, ATP, and NADPH + H+ to L-glutamate gamma-semialdehyde, NADP+, ADP, and orthophosphate. Two P5CS isoforms have been identified; both are active when expressed in enzyme-deficient cells in culture (Hu et al. 1999). Unpublished crystallographic data (PDB 2H5G) indicate that the enzyme is a dimer.
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Mitochondrial ornithine aminotransferase (OAT) catalyzes the reversible reaction of glutamate semialdehyde and glutamate to form ornithine and alpha-ketoglutarate (Ohura et al. 1982). The active enzyme is a hexamer (Shen et al. 1998). Inherited OAT deficiency leads to ornithine accumulation in vivo and gyrate atrophy of the choroid and retina (Brody et al. 1992; Vallee and Simell 2001).
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Mitochondrial 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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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.
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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).
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L-Serine is needed in human brain in large amounts as precursor to important biomolecules such as nucleotides, phospholipids and the neurotransmitters glycine and D-serine. The pathway for its synthesis starts with 3-phosphoglycerate and it later needs glutamate as an amination agent. Deficiencies in the participating enzymes lead to severe neurological symptoms that are treatable with serine if treatment starts early (de Koning & Klomp 2004).
These reactions mediate the synthesis of aspartate, asparagine, glutamate, and glutamine from ammonia and intermediates of glycolysis, and allow the utilization of the carbon atoms from these four amino acids for glucose synthesis under fasting conditions. These reactions also provide a means to collect nitrogen, both as ammonia and as amino groups, and direct it towards urea synthesis. Transamination, the conversion of an amino acid to the corresponding alpha-keto acid coupled to the conversion of a molecule of alpha-ketoglutarate to glutamate, is the first step in the catabolism of most amino acids. Transamination reactions are freely reversible so they also provide a means to balance concentrations of various amino acids and alpha-keto (2-oxo) acids in the cytosol.
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Structure and expression of fibrillin-2, a novel microfibrillar component preferentially located in elastic matrices
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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).
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Cytosolic serine hydroxymethyltransferase catalyzes the reversible reaction of 5,10-methyleneTHF polyglutamate and glycine to form tetrahydrofolate polyglutamate (THF polyglutamate) and serine. The active form of the enzyme is a tetramer (Renwick et al. 1998).
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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).
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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).
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Cytosolic serine hydroxymethyltransferase catalyzes the reversible reaction of tetrahydrofolate polyglutamate (THF polyglutamate) and serine to form 5,10-methyleneTHF polyglutamate and glycine. The active form of the enzyme is a tetramer (Renwick et al. 1998). In the body, this reaction is a major source of 5,10-methyleneTHF, which in turn is a critical precursor in the synthesis of dTMP.
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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).
6-(L-erythro-1,2-Dihydroxypropyl 3-triphosphate)-7,8-dihydropterin
7,8-dihydroneopterin 3'-triphosphate [ChEBI:18372]
2-Amino-4-hydroxy-6-(erythro-1,2,3-trihydroxypropyl)dihydropteridine triphosphate
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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).
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).
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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Human lysyl-tRNA synthetase accepts nucleotide 73 variants and rescues Escherichia coli double-defective mutant
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Enterohepatic bile salt transporters in normal physiology and liver disease
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Human isopentenyl diphosphate: dimethylallyl diphosphate isomerase: overproduction, purification, and characterization
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Folding of carboxyl domain and assembly of procollagen I
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The Mycobacterium tuberculosis ino1 gene is essential for growth and virulence
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ChEBI:18381 5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide
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Structure of the FGF receptor tyrosine kinase domain reveals a novel autoinhibitory mechanism
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Primary hyperoxaluria: from gene defects to designer drugs?
2'-deoxyadenosine 5'-diphosphate [ChEBI:16174]
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Transcriptional control of adipocyte formation
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Heparan sulfate depletion within pulmonary fibroblasts: implications for elastogenesis and repair
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A proposed nomenclature system for the cytosolic sulfotransferase (SULT) superfamily
Collagenase unwinds triple-helical collagen prior to peptide bond hydrolysis
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Protoheme IX farnesyltransferase, mitochondrial ecNumber2.5.1.-/ecNumber
CATERPILLERs, pyrin and hereditary immunological disorders
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Human GTP cyclohydrolase I: only one out of three cDNA isoforms gives rise to the active enzyme
Acetylserotonin O-methyltransferase ecNumber2.1.1.4/ecNumber
Crystallographic evidence for Tyr 157 functioning as the active site base in human UDP-galactose 4-epimerase
Expression of the HsOrc1 gene, a human ORC1 homolog, is regulated by cell proliferation via the E2F transcription factor
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The role for endoplasmic reticulum stress in diabetes mellitus
Signaling through PI3Kgamma: a common platform for leukocyte, platelet and cardiovascular stress sensing
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Thioredoxin-interacting protein links oxidative stress to inflammasome activation
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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
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3,4,5-Trihydroxy-1-cyclohexenecarboxylic acid
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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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Siderophore-based iron acquisition and pathogen control
ATP-binding cassette sub-family B member 11
Acyl- CoA:dihydroxyacetonephosphateacyltransferase
Dihydroxyacetone phosphate acyltransferase
Isocitrate dehydrogenase (NADP) cytoplasmic
Isopentenyl-diphosphate delta-isomerase 1
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Scriver CR, et al., editors) 1:1553-1587
Multidrug resistance-associated protein 1
Decaprenyl-diphosphate synthase subunit 2 ecNumber2.5.1.91/ecNumber
Hypophosphorylation of residue Y1045 leads to defective downregulation of EGFRvIII
The OtsAB pathway is essential for trehalose biosynthesis in Mycobacterium tuberculosis
FUNCTION Transferrins are iron binding transport proteins which can bind two Fe(3+) ions in association with the binding of an anion, usually bicarbonate.FUNCTION Lactotransferrin has antimicrobial activity which depends on the extracellular cation concentration.FUNCTION Lactoferroxins A, B and C have opioid antagonist activity. Lactoferroxin A shows preference for mu-receptors, while lactoferroxin B and C have somewhat higher degrees of preference for kappa-receptors than for mu-receptors.FUNCTION The lactotransferrin transferrin-like domain 1 functions as a serine protease of the peptidase S60 family that cuts arginine rich regions. This function contributes to the antimicrobial activity.FUNCTION Isoform DeltaLf: transcription factor with antiproliferative properties and inducing cell cycle arrest. Binds to DeltaLf response element found in the SKP1, BAX, DCPS, and SELH promoters.CATALYTIC ACTIVITY Preferential at -Arg-Ser-Arg-Arg-|- and -Arg-Arg-Ser-Arg-|-, and of Z-Phe-Arg-|-aminomethylcoumarin.SUBUNIT Monomer. Found in a complex with LTF, CLU, EPPIN and SEMG1.PTM Isoform DeltaLf: Ubiquitinated at Lys-379 and Lys-391.SIMILARITY Belongs to the transferrin family.SIMILARITY Contains 2 transferrin-like domains.
Crystal structures of human GAR Tfase at low and high pH and with substrate beta-GAR
glycerol-3-phosphate acyltransferase 2, mitochondrial
3alpha,7alpha,12alpha-Trihydroxy-5beta-cholestanoate [ChEBI:1698]
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S-adenosylmethionine (SAM) is an essential metabolite in all cells. SAM is a precursor in the synthesis of polyamines. Methionine adenosyltransferase (MAT; EC 2.5.1.6) catalyzes the only known SAM biosynthetic reaction from methionine and ATP. In mammalian tissues, three different forms of MAT (MAT I, MAT III and MAT II) have been identified that are the product of two different genes (MAT1A and MAT2A). A third gene MAT2B has been identified and is known to be a part of MAT II heterotetramer complex.
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Acetyl-CoA acetyltransferase, mitochondrial
Peroxisomal D-amino-acid oxidase catalyzes the reaction of glycine, water, and O2 to form glyoxylate, H2O2, and NH4+. The active form of the enzyme is a homodimer and has FAD as a cofactor (Kawazoe et al. 2006; Molla et al. 2006).
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Peroxisomal hydroxyacid oxidase 1 catalyzes the reaction of glycolate and O2 to form glyoxylate and H2O2. The active form of the enzyme is associated with FMN and is a tetramer (Jones et al. 2000; Murray et al. 2008; Vignaud et al. 2007; Williams et al. 2000).
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Succinyl-CoA:3-ketoacid-coenzyme A transferase, mitochondrial precursor
Peroxisomal hydroxyacid oxidase 1 catalyzes the reaction of glyoxylate to form oxalate. The active form of the enzyme is associated with FMN and is a tetramer (Jones et al. 2000; Murray et al. 2008; Vignaud et al. 2007; Williams et al. 2000).
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.
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:
Hydroxyindole-O-methyltransferase (HIOMT) catalyzes the last step in the synthesis of melatonin. Melatonin is synthesized and released by the pineal gland and is thought to control circadian rhythms. HIOMT has 3 isoforms and utilizes S-adenosyl-L-methionine (SAM) as the methyl donor in the conversion of N-acetyl-5HT to melatonin.
Serotonin (5-HT) is a hormone and neurotransmitter used for regulatory purposes in animal CNS. In the human brain, serotonin is involved in many physiological functions such as sleep, pain, mood and is the precursor to melatonin, a hormone produced in the pineal gland.
NODs: intracellular proteins involved in inflammation and apoptosis
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Catecholamines and thyroxine are synthesized from tyrosine, and serotonin and melatonin from tryptophan.
Interaction between the functional polymorphisms of the alcohol-metabolism genes in protection against alcoholism.
Methionine salvage is a sequential pathway of six reactions that create methionine from 5'-methylthioadenosine (MTA) which is a byproduct of polyamine biosynthesis in nearly all organisms. The process happens completely in the cytosol. It is important in humans for recycling of sulphur that has to be assimilated using energy. (Pirkov et al, 2008; Albers, 2009)
FUNCTION Phosphatase with a broad specificity. Its primary physiological function is to dephosphorylate 3'-phosphoadenosine 5'-phosphate (PAP) and 3'-phosphoadenosine 5'-phosphosulfate (PAPS). Thus, plays a role in mycobacterial sulfur metabolism, since it can serve as a key regulator of the sulfate assimilation pathway by controlling the pools of PAP and PAPS in the cell. To a lesser extent, is also able to hydrolyze inositol 1-phosphate (I-1-P), fructose 1,6-bisphosphate (FBP) (to fructose 6-phosphate (F-6-P)) and AMP in vitro, but this might has no significance in vivo. Glucose-1-phosphate (G-1-P), p-nitrophenyl phosphate (pNPP), and beta-glycerol phosphate (beta-GP) are also good substrates, compared to I-1-P. With much lower efficiency, can also hydrolyze inositol 2-phosphate (I-2-P) and glucose-6-phosphate (G-6-P) in vitro, but not fructose-6-phosphate (F-6-P) and trehalose-6-phosphate (T-6-P).CATALYTIC ACTIVITY Adenosine 3',5'-bisphosphate + H(2)O = adenosine 5'-phosphate + phosphate.CATALYTIC ACTIVITY D-fructose 1,6-bisphosphate + H(2)O = D-fructose 6-phosphate + phosphate.CATALYTIC ACTIVITY Myo-inositol phosphate + H(2)O = myo-inositol + phosphate.COFACTOR Magnesium. Mn(2+) can substitute for Mg(2+) for PAP phosphatase and IMPase activities, but is less efficient (50%-60% of the activity observed with Mg(2+)).ENZYME REGULATION PAP phosphatase and IMPase activities are inhibited by Li(+). To a lesser extent, PAP hydrolysis is also inhibited by Na(+) and K(+), with IC50 values of 150 and 250 mM, respectively, so much higher than IC50 with Li(+) (0.5 mM). Exhibits about 50% residual IMPase activity at 5 mM Li(+) and about 10% at 30 mM Li(+). Na(+) and K(+) have no significant effect on IMPase activity between 0 and 200 mM.PATHWAY Sulfur metabolism; sulfate assimilation.SUBUNIT Homodimer.INDUCTION When comparing gene expression levels of the four IMPase family genes in exponential cultures of M.tuberculosis, the level of cysQ is the highest, almost equal to sigA; impA and impC are expressed at approximately 40% of this level, while suhB is lowest, at 12% of the cysQ level.DISRUPTION PHENOTYPE Strains lacking this gene show normal growth, do not require exogenous inositol for growth, and show no differences in levels of phosphatidylinosotol mannosides (PIMs), lipomannan (LM), lipoarabinomannan (LAM) or mycothiol (in the absence of exogenous inositol).SIMILARITY Belongs to the inositol monophosphatase family.
1-(5'-Phosphoribosyl)-5-amino-4-imidazolecarboxamide [ChEBI:18406]
5'-Phospho-ribosyl-5-amino-4-imidazole carboxamide
a-(5,6-Dimethylbenzimidazolyl)cobamide coenzyme
(5,6-dimethylbenzimidazolyl)cobamide coenzyme
The identification and structural characterization of C7orf24 as gamma-glutamyl cyclotransferase. An essential enzyme in the gamma-glutamyl cycle
5'-Phosphoribosylformylglycinamidine [ChEBI:18413]
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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).
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MTA phosphorylase catalyzes the cleavage of adenine from S-methylthioadenosine (MTA) and subsequent phosphorylation of the product, yielding 5'-methylthio ribose-1-phosphate (Kamatani et al. 1981). The active form of the enzyme is a homotrimer (Della Ragione et al. 1985). Mutations in the gene are associated with a rare bone dysplasia and cancer syndrome, DMS-MFH (Camacho-Vanegas et al. 2012).
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.
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Cytosolic serine hydroxymethyltransferase tetramer (SHMT1) catalyzes the reaction of 3-Hydroxy-N6,N6,N6-trimethyl-L-lysine to form glycine and 4-trimethylammoniobutanal (Hulse et al. 1978).
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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).
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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).
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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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).
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).
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).
2,4-dienoyl-CoA reductase, mitochondrial precursor
Methylmalonic aciduria type A protein, mitochondrial ecNumber3.6.-.-/ecNumber
Methylmalonyl-CoA mutase, mitochondrial precursor
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The FGF family: biology, pathophysiology and therapy
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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 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).
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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).
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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.
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Ferrochelatase (FECH) catalyzes the insertion of ferrous iron into protoporphyrin IX (PRIN9) to form heme. FECH is localized on the matrix surface of the inner mitochondrial membrane and this reaction takes place within the mitochondrial matrix. The enzyme functions as a homodimer with each monomer containing a nitric oxide-sensitive 2Fe-2S cluster. Enzyme deficiency is associated with erythropoietic protoporphyria in vivo, and inhibition of ferrochelatase activity is a clinically important consequence of lead poisoning (Piomelli et al. 1987).
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Alkyldihydroxyacetonephosphate synthase, peroxisomal precursor
Alkyldihydroxyacetonephosphate synthase precursor
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).
Structural enzymology of sulphur metabolism in Mycobacterium tuberculosis
This group of reactions is responsible for: 1) the breakdown of amino acids; 2) the synthesis of urea from ammonia and amino groups generated by amino acid breakdown; 3) the synthesis of the ten amino acids that are not essential components of the human diet; and 4) the synthesis of related nitrogen-containing molecules including carnitine and creatine. Transport of these molecuels across lipid bilayer membranes is annotated separately as part of the module on "transmembrane transport of small molecules".
The main sulfur amino acids are methionine, cysteine, homocysteine and taurine. Of these, the first two are proteinogenic. This group of reactions contains all processes that 1) break down sulfur amino acids, 2) interconvert between them, and 3) synthesize them from solved sulfide which comes from sulfate assimilation and reduction. Only plants and microorganisms employ all processes. Humans cannot de novo synthesize any sulfur amino acid, nor convert cysteine to methionine (Brosnan & Brosnan, 2006).
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Excess homocysteine will change the enzymatic activity of CBS such that other reactions than transsulfuration take place. In these reactions, oxobutanoate, lanthionine, and homolanthionine are produced by cystathionine gamma-lyase (CTH) (Chiku et al. 2009, Steegborn et al. 1999)
alpha,beta-elimination activity of cystathionine-gamma-lyase (CTH) replaces the sulfur in cysteine with oxygen from water, resulting in serine and toxic hydrogen sulfide, which is further oxidized in mitochondria (Chiku et al. 2009, Steegborn et al. 1999).
Activation of human liver glycogen phosphorylase by alteration of the secondary structure and packing of the catalytic core
Transsulfuration is the interconversion of homocysteine and cysteine, and it fully takes place in bacteria and some plants and fungi. Animals however have only one direction of this bidirectional path, the synthesis of cysteine from homocysteine via cystathionine. Because excess cysteine is degraded to hydrogen sulfide, which is now known as a neuromodulator and smooth muscle relaxant, this pathway is also the main source of its production, which takes place in the cytosol, as well as in extracellular space (Dominy & Stipanuk 2004, Bearden et al. 2010).
A cytosolic, non-specific peptidase can hydrolyze cysteinylglycine to release cysteine and glycine (Tuefel et al, 2003).
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Long-chain fatty acid transport protein 1
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).
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While the human body is very economical with sulfur amino acids (SAA), superfluous SAA are degraded via cysteine to toxic hydrogen sulfide which must be dealt with. The pathway to oxidize this gas is localized to mitochondria and is highly conserved, pointing back to a time when life was immersed in sulfide-rich waters. The pathway for sulfide oxidation consists of five reactions, one of which, the sulfur transfer from thiosulfate to glutathione, is still to be characterized fully. A mutation in one enzyme has been identified that is associated with ethylmalonyl encephalopathy and where tissue sulfide is elevated (Stipanuk & Ueki 2011).
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Cystathionine is cleaved to cysteine, oxobutanoate, and ammonia by the alpha,gamma-elimination activity of cystathionine gamma-lyase (CTH) (Chiku et al. 2009, Steegborn et al. 1999).
The first step of homocysteine conversion to cysteine is catalyzed by cystathionine beta-lyase, which adds a serine molecule to the substrate. The enzyme is a tetramer with two heme molecules as cofactor (Janosik et al. 2001).
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At the beginning of this reaction, 1 molecule of 'Oxygen', 1 molecule of 'H2O', and 1 molecule of '2-Phenylethylamine' are present. At the end of this reaction, 1 molecule of 'NH3', 1 molecule of 'H2O2', and 1 molecule of 'Phenylacetaldehyde' are present. This reaction takes place in the 'mitochondrial outer membrane' and is mediated by the 'amine oxidase activity' of 'MAOB-FAD complex'.
Human monoamine oxidases (MAOs) are flavin-containing enzymes that are present on the outer mitochondrial membrane and act on primary, secondary and tertiary amines. In contrast to the P450s which have a large number of isozymes, MAOs number only two isozymes, MAO-A and MAO-B. These gene products share over 70% sequence identity, are approximately 59KDa in size and have overlapping substrates (for example dopamine, tryamine and tryptamine) but each form also has distinct substrate specificities. MAO-A (primary type in fibroblasts) preferentially oxidises serotonin (5-Hydroxytryptamine) whereas MAO-B (primary type in platelets) prefers phenylethylamine. MAOs are of particular clinical interest because of the use of MAO inhibitors (MAOI) as antidepressants or in the treatment of neurodegenerative diseases.
Monoamine oxidases (MAO-A/B), present in the outer mitochondrial membrane, catalyze the oxidation of biogenic amines, releasing hydrogen peroxide (H2O2). H2O2 produced during the oxidative deamination of these amines appears to be involved in the progress of neurodegenerative disorders such as Parkinson disease, presumably via oxidative damage to the mitochondrial membrane.
At the beginning of this reaction, 1 molecule of 'Oxygen', 1 molecule of 'H2O', and 1 molecule of '5-Hydroxytryptamine' are present. At the end of this reaction, 1 molecule of 'NH3', 1 molecule of '5-Hydroxyindoleacetaldehyde', and 1 molecule of 'H2O2' are present. This reaction takes place in the 'mitochondrial outer membrane' and is mediated by the 'amine oxidase activity' of 'MAOA-FAD complex'.
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The P450 isozyme system is the major phase 1 biotransforming system in man, accounting for more than 90% of drug biotransformations. This system has huge catalytic versatility and a broad substrate specificity, acting upon xenobiotica and endogenous compounds. It is also called the mixed-function oxidase system, the P450 monooxygenases and the heme-thiolate protein system. All P450 enzymes are a group of heme-containing isozymes which are located on the membrane of the smooth endoplasmic reticulum. They can be found in all tissues of the human body but are most concentrated in the liver. The name "cytochrome P450" (CYP) is derived from the spectral absorbance maximum at 450nm when carbon monoxide binds to CYP in its reduced (ferrous, Fe2+) state. The basic reaction catalyzed by CYP is mono-oxygenation, that is the transfer of one oxygen atom from molecular oxygen to a substrate. The other oxygen atom is reduced to water during the reaction with the equivalents coming from the cofactor NADPH. The basic reaction is; RH (substrate) + O2 + NADPH + H+ = ROH (product) + H2O + NADP+ The end results of this reaction can be (N-)hydroxylation, epoxidation, heteroatom (N-, S-) oxygenation, heteroatom (N-, S-, O-) dealkylation, ester cleavage, isomerization, dehydrogenation, replacement by oxygen or even reduction under anaerobic conditions. The metabolites produced from these reactions can either be mere intermediates which have relatively little reactivity towards cellular sysytems and are readily conjugated, or, they can be disruptive to cellular systems. Indeed, inert compounds need to be prepared for conjugation and thus the formation of potentially reactive metabolites is in most cases unavoidable. There are 57 human CYPs (in 18 families and 42 subfamilies), mostly concentrated in the endoplasmic reticulum of liver cells although many tissues have them to some extent (Nelson DR et al, 2004). CYPs are grouped into 14 families according to their sequence similarity. Generally, enzymes in the same family share 40% sequence similarity and 55% within a subfamily. Nomenclature of P450s is as follows. CYP (to represent cytochrome P450 superfamily), followed by an arabic number for the family, a capital letter for the subfamily and finally a second arabic number to denote the isoenzyme. An example is CYP1A1 which is the first enzyme in subfamily A of cytochrome P450 family 1. The majority of the enzymes are present in the CYP1-4 families. CYP1-3 are primarily concerned with xenobiotic biotransformation whereas the other CYPs deal primarily with endogenous compounds. The CYP section is structured by the typical substrate they act upon. Of the 57 human CYPs, 7 encode mitochondrial enzymes, all involved in sterol biosynthesis. Of the remaining 50 microsomal enzymes, 20 act upon endogenous compounds, 15 on xenobiotics and 15 are the so-called "orphan enzymes" with no substrate identified. The P450 catalytic cycle (picture) shows the steps involved when a substrate binds to the enzyme. (1) The normal state of a P450 with the iron in its ferric [Fe3+] state. (2) The substrate binds to the enzyme. (3) The enzyme is reduced to the ferrous [Fe2+] state by the addition of an electron from NADPH cytochrome P450 reductase. The bound substrate facilitates this process. (4,5) Molecular oxygen binds and forms an Fe2+OOH complex with the addition of a proton and a second donation of an electron from either NADPH cytochrome P450 reductase or cytochrome b5. A second proton cleaves the Fe2+OOH complex to form water. (6) An unstable [FeO]3+ complex donates its oxygen to the substrate (7). The oxidised substrate is released and the enzyme returns to its initial state (1).
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Understanding specificity in metabolic pathways--structural biology of human nucleotide metabolism
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Phase 1 of metabolism is concerned with functionalization, that is the introduction or exposure of functional groups on the chemical structure of a compound. This provides a 'handle' for phase 2 conjugating species with which to react with. Many xenobiotics are lipophilic and almost chemically inert (e.g. PAHs) so would not necessarily undergo a phase 2 reaction. Making them more chemically reactive would facilitate their excretion but also increases their chance of reacting with cellular macromolecules (e.g. proteins, DNA). There is a fine balance between producing a more reactive metabolite and conjugation reactions. There are two groups of enzymes in phase 1 - oxidoreductases and hydrolases. Oxidoreductases introduce an oxygen atom into or remove electrons from their substrates. The major oxidoreductase enzyme system is called the P450 monooxygenases. Other systems include flavin-containing monooxygenases (FMO), cyclooxygenases (COX) and monoamine oxidases (MAO). Hydrolases hydrolyse esters, amides, epoxides and glucuronides.
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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.
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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).
Modulation of mitochondrial membrane permeability in pathogenesis, autophagy and control of metabolism
ACSS1 (acyl-CoA synthetase short-chain family member 1) in the mitochondrial matrix catalyzes the reaction of acetate, coenzyme A, and ATP to form acetyl-CoA, AMP, and pyrophosphate (Schwer et al. 2006).
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Human amine oxidases (AO) catalyze the oxidative deamination of biogenic amines (neurotransmitters such as serotonin, noradrenaline, the hormone adrenaline and polyamines such as the spermines) and xenobiotic amines (exogenous dietary tyramine and phenylethylamine). The basic reaction is the oxidative cleavage of the alpha-H to form an imine product with the concomitant reduction of a FAD cofactor. The imine product then hydrolyses to an aldehyde and ammonia (or amine for secondary and tertiary amine substrates). Reduced FAD is reoxidized to form hydrogen peroxide to complete the catalytic cycle. The reaction can be summarized as RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2 The resultant hydrogen peroxide is the source of the most toxic free radical, the hydroxyl radical (.OH). This free radical is produced in the Fenton reaction with the use of ferrous (Fe2+) iron.
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Type-III procollagen assembly in semi-intact cells: chain association, nucleation and triple-helix folding do not require formation of inter-chain disulphide bonds but triple-helix nucleation does require hydroxylation
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Heme O and heme A are specifically synthesised for the heme-copper respiratory oxidases. Mitochondrial protoheme IX farnesyltransferase (COX10) mediates the transformation of protoheme IX (heme) and farnesyl diphosphate (FAPP) to heme O (Glerum & Tzagoloff 1994). COX10 is highly expressed in muscle, heart and brain (Murakami et al. 1997).
Eight enzymes are involved in heme biosynthesis, four each in the mitochondria and the cytosol. The process starts in the mitochondria with the condensation of succinyl CoA (from the TCA cycle) and glycine to form 5-aminolevulinate (ALA). The next four steps take place in the cytosol. Two molecules of ALA are condensed to form the monopyrrole porphobilinogen (PBG). The next two steps convert four molecules of PBG into the cyclic tetrapyrrole uroporphyringen III, which is then decarboxylated into coproporphyrinogen III. The last three steps occur in the mitochondria and involve modifications to the tetrapyrrole side chains and finally, insertion of iron. In addition to these synthetic steps, a spontaneous cytosolic reaction allows the formation of uroporphyringen I which is then enzymatically decarboxylated to coproporphyrinogen I, which cannot be metabolized further in humans. Also, lead can inactivate ALAD, the enzyme that catalyzes PBG synthesis, and ferrochelatase, the enzyme that catalyzes heme synthesis. The porphyrias are disorders that arise from defects in the enzymes of heme biosynthesis. Defective pathway enzymes after ALA synthase result in accumulated substrates which can cause either skin problems, neurological complications, or both due to their toxicity in higher concentrations. They are broadly classified as hepatic porphyrias or erythropoietic porphyrias, based on the site of the overproduction of the substrate. Each defect is described together with the reaction it affects.
Porphyrins are heterocyclic macrocycles, consisting of four pyrrole subunits (tetrapyrrole) linked by four methine (=CH-) bridges. The extensive conjugated porphyrin macrocycle is chromatic and the name itself, porphyrin, is derived from the Greek word for purple. The aromatic character of porphyrins can be seen by NMR spectroscopy. Porphyrins readily combine with metals by coordinating them in the central cavity. Iron (heme) and magnesium (chlorophyll) are two well known examples although zinc, copper, nickel and cobalt form other known metal-containing phorphyrins. A porphyrin which has no metal in the cavity is called a free base. Some iron-containing porphyrins are called hemes (heme-containing proteins or hemoproteins) and these are found extensively in nature ie. hemoglobin. Hemoglobin is quantitatively the most important hemoprotein. The hemoglobin iron is the transfer site of oxygen and carries it in the blood all round the body for cell respiration. Other examples are cytochromes present in mitochondria and endoplasmic reticulum which takes part in electron transfer events, catalase and peroxidase whic protect the body against the oxidant hydrogen peroxide and tryptophan oxygenase which is present in intermediary metabolism. Hemoproteins are synthesized in all mammalian cells and the major sites are erythropoietic tissue and the liver. The processes by which heme is synthesized, transported, and metabolized are a critical part of human iron metabolism (Severance and Hamze 2009); here the core processes of heme biosynthesis and catabolism have been annotated.
Cytochrome P450 8B1 (CYP8B1, sterol 12-alpha- hydroxylase) has a broad substrate specificity including a number of 7-alpha- hydroxylated C27 steroids. It is also involved in bile acid synthesis and is responsible for the balance between the formation of cholic acid and chenodeoxycholic acid.
Endogenous retinoic acids (RA) which play a role in gene regulation exist as either cis or trans isomers. While CYP26C1 can also hydroxylate the trans form, it is unique in hydroxylating the 9-cis isomer of RA.
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Arachidonic acid is metabolized via three major enzymatic pathways: cyclooxygenase, lipoxygenase, and cytochrome P450. The cytochrome P450 pathway metabolites are oxygenated metabolites of arachidonic acid.
A number of CYPs take part in cholesterol biosynthesis and elimination, thus playing an important role in maintaining cholesterol homeostasis. Under normal physiological conditions, cholesterol intake (diet or synthesized de novo from acetyl CoA) equals cholesterol elimination (degraded to bile salts, secreted in bile and used in steroid hormone synthesis). These processes are under tight regulatory control and any disruption leads to increased cholesterol levels resulting in cardiovacular disease. The CYPs involved in cholesterol homeostasis could serve as potential targets for cholesterol-lowering drugs.
CYP26B1 can also deactivate all-trans-retinoic acid by 4-hydroxylation. High expression levels in the cerebellum and pons of human brain suggests a protective role of specific tissues against retinoid damage.
Regulation of human cystathionine beta-synthase by S-adenosyl-L-methionine: evidence for two catalytically active conformations involving an autoinhibitory domain in the C-terminal region
Retinoic acid (RA) is a biologically active analogue of vitamin A (retinol). RA plays an important role in regulating cell growth and differentiation.CYP26A1 is involved in the metabolic breakdown of RA by 4-hydroxylation. CYP26A1-mediated 4-hydroxylation is specific for all-trans-RA but not for the isomers 13-cis-RA and 9-cis-RA.
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Purification and characterization of recombinant catalase-peroxidase, which confers isoniazid sensitivity in Mycobacterium tuberculosis
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Gamma-glutamylcyclotransferase (GGCT) homodimer (Bae et al, 2008) catalyzes the formation of 5-oxoproline from gamma-glutamylcysteine and thus, may play a role in glutathione homeostasis (Oakley et al, 2008).
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Gamma-glutamylcyclotransferase (GGCT) homodimer (Bae et al, 2008) can catalyzes the formation of 5-oxoproline from gamma-glutamyl-amino acid products and thus can play a role in glutathione homeostasis (Oakley et al, 2008).
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.
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.
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.
The combination of glutamate, cysteine and ATP is required to form glutathione. The steps involved in the synthesis and recycling of glutathione are outlined (Meister, 1988).
Glutathione S-Transferases (GSTs; EC 2.5.1.18) are another major set of phase II conjugation enzymes. They can be found in the cytosol as well as being microsomal membrane-bound. Cytosolic GSTs are encoded by at least 5 gene families (alpha, mu, pi, theta and zeta GST) whereas membrane-bound enzymes are encoded by single genes. Soluble GSTs are homo- or hetero-dimeric enzymes (approximately 25KDa subunits) which can act on a wide range of endogenous and exogenous electrophiles. GSTs mediate conjugation using glutathione (GSH), a tripeptide synthesized from its precursor amino acids gamma-glutamate, cysteine and glycine. A generalized reaction is RX + GSH -> HX + GSR Glutathione conjugates are excreted in bile and converted to cysteine and mercapturic acid conjugates in the intestine and kidneys. GSH is the major, low molecular weight, non-protein thiol synthesized de novo in mammalian cells. As well as taking part in conjugation reactions, GSH also has antioxidant ability and can metabolize endogenous and exogenous compounds. The nucleophilic GSH attacks the electrophilic substrate forming a thioether bond between the cysteine residue of GSH and the electrophile. The result is generally a less reactive and more water-soluble conjugate that can be easily excreted. In some cases, GSTs can activate compounds to reactive species such as certain haloalkanes and haloalkenes. Substrates for GSTs include epoxides, alkenes and compounds with electrophilic carbon, sulfur or nitrogen centres. There are two types of conjugation reaction with glutathione: displacement reactions where glutathione displaces an electron-withdrawing group and addition reactions where glutathione is added to activated double bond structures or strained ring systems.
Iron-sulfur (Fe-S) proteins are localized in the cytosol, nucleus, and mitochondria of mammalian cells (reviewed in Stemmler et al. 2010, Rouault 2012, Bandyopadhyay et al. 2008, Lill 2009, Lill et al. 2012). Fe-S protein biogenesis in the mitochondrial matrix involves the iron-sulfur cluster (ISC) assembly machinery. Ferrous iron is transported across the inner mitochondrial membrane into the mitochondrial matrix by Mitoferrin-1 and Mitoferrin-2. (Mitoferrin-1 is enriched in erythroid cells while Mitoferrin-2 is ubiquitous.) Frataxin binds ferrous iron in the mitochondrial matrix. The cysteine desulfurase NFS1 in a subcomplex with ISD11 provides the sulfur by converting cyteine into alanine and forming a persulfide which is used for cluster formation on ISCU, the scaffold protein. Interaction between NFS1 and ISD11 is necessary for desulfurase activity. Frataxin binds to a complex containing NFS1, ISD11, and ISCU and is proposed to function as an iron donor to ISCU or as an allosteric switch that activates sulfur transfer and Fe-S cluster assembly (Tsai and Barondeau 2010). Cluster formation also involves the electron transfer chain ferredoxin reductase and ferredoxin. ISCU initially forms clusters containing 2 iron atoms and 2 sulfur atoms ([2Fe-2S] clusters). They are released by the function of HSP70-HSC20 chaperones and the monothiol glutaredoxin GLRX5 and used for assembly of [2Fe-2S] proteins. Assembly of larger clusters such as [4Fe-4S] clusters may involve the function of ISCA1, ISCA2, and IBA57. The clusters are transferred to apo-enzymes such as the respiratory complexes, aconitase, and lipoate synthase through dedicated targeting factors such as IND1, NFU1, and BOLA3.
Lysophospholipid acyltransferases: 1-acylglycerol-3-phosphate O-acyltransferases (AGPATs) From discovery to disease
NADPH, ferredoxin reductase (FDXR, Adrenodoxin reductase), and ferredoxins (FDX1, FDX1L) comprise a short electron transport chain that provides electrons for biosynthesis of iron-sulfur clusters and steroid hormones (Sheftel et al. 2010, Shi et al. 2012, reviewed in Grinberg et al. 2000, Lambeth et al. 1982).
Two electrons and one proton are transferred from NADPH to the FAD moiety of ferredoxin reductase. A proton from the medium is also taken up by ferredoxin reductase.
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Biosynthesis and bioproduction of coenzyme Q10 by yeasts and other organisms
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'NAcGlu [mitochondrial matrix]' positively regulates 'carbamoyl-phosphate synthase (ammonia) activity of Homologues of CPS1 [intracellular]'
'Fe2+ [nucleoplasm]' is required for 'damaged DNA binding activity of ALKBH2 [intracellular]'
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'Pi [cytosol]' is required for 'ribose phosphate diphosphokinase activity of phosphoribosyl pyrophosphate synthetase 1 holoenzyme (name copied from entity in Homo sapiens) [intracellular]'
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'Mg2+ [cytosol]' is required for 'ribose phosphate diphosphokinase activity of phosphoribosyl pyrophosphate synthetase 1 holoenzyme (name copied from entity in Homo sapiens) [intracellular]'
57 varieties: the human cytochromes P450
'Fe2+ [nucleoplasm]' is required for 'damaged DNA binding activity of ALKBH3 [intracellular]'
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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.
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.
Two groups of sulfotransferease (SULT) enzymes catalyze the transfer of a sulfate group from 3-phosphoadenosine 5-phosphosulfate (PAPS) to a hydroxyl group on an acceptor molecule, yielding a sulfonated acceptor and 3-phosphoadenosine 5-phosphate (PAP). One is localized to the Golgi apparatus and mediates the sulfonation of proteoglycans. The second, annotated here, is cytosolic and mediates the sulfonation of a diverse array of small molecules, increasing their solubilities in water and modifying their physiological functions. There are probably thirteen or more human cytosolic SULT enzymes; eleven of these have been purified and characterized enzymatically, and are annotated here (Blanchard et al. 2004; Gamage et al. 2005). These enzymes appear to be active as dimers. Their substrate specificities are typically broad, and not related in an obvious way to their structures; indeed, apparently orthologous human and rodent SULT enzymes can have different substrate specificities (Glatt 2000), and none has been exhaustively characterized. The substrates listed in the table and annotated here are a sample of the known ones, chosen to indicate the range of activity of these enzymes and to capture some of their known physiologically important targets. Absence of a small molecule - enzyme pair from the table, however, may only mean that it has not yet been studied.
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.
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.
Dihydroxybenzoate is a typical substrate for Catechol O-methyltransferase
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.
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ChEBI:18431 7alpha,26-dihydroxycholesterol
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Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds
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The pathway "Signaling by EGFR in Cancer" shows "Signaling by constitutively active EGFR" in parallel with "Signaling by EGFR". This allows users to compare signaling by constitutively active EGFR cancer mutants with the wild-type EGFR protein. Red lines emphasize cancer related events and physical entities, while wild-type entities and events are shaded. Please refer to "Signaling by constitutively active EGFR" and "Signaling by EGFR" for detailed pathway summations.
Adenylosuccinate synthetase (EC 6.3.4.4) (IMP--aspartate ligase) (AdSS) (AMPSase)
Signaling by EGFR is frequently activated in cancer through either genomic amplification of the EGFR locus, resulting in over-expression of the wild-type protein, or through activating mutations in the coding sequence of the EGFR gene, resulting in expression of a constitutively active mutant protein. Epidermal growth factor receptor kinase domain mutants are present in ~16% of non-small-cell lung cancers (NSCLCs), but are also found in other cancer types, such as breast cancer, colorectal cancer, ovarian cancer and thyroid cancer. EGFR kinase domain mutants harbor activating mutations in exons 18-21 which code for the kinase domain (amino acids 712-979) . Small deletions, insertions or substitutions of amino acids within the kinase domain lock EGFR in its active conformation in which the enzyme can dimerize and undergo autophosphorylation spontaneously, without ligand binding (although ligand binding ability is preserved), and activate downstream signaling pathways that promote cell survival (Greulich et al. 2005, Zhang et al. 2006, Yun et al. 2007, Red Brewer et al. 2009). In glioblastoma, the most prevalent EGFR mutation, present in ~25% of tumors, is the deletion of the ligand binding domain of EGFR, accompanied with amplification of the mutated allele, which results in over-expression of the mutant protein known as EGFRvIII. EGFRvIII mutant is not able to bind a ligand, but dimerizes and autophosphorylates spontaneously and is therefore constitutively active (Fernandes et al. 2001). Point mutations in the extracellular domain of EGFR are also frequently found in glioblastoma. Similar to kinase domain mutations, point mutations in the extracellular domain result in constitutively active EGFR proteins that signal in the absence of ligands, but ligand binding ability and responsiveness are preserved (Lee et al. 2006). Both EGFR kinase domain mutants and EGFRvIII mutant need to maintain association with the chaperone heat shock protein 90 (HSP90) for proper functioning (Shimamura et al. 2005, Lavictoire et al. 2003). CDC37 is a co-chaperone of HSP90 that acts as a scaffold and regulator of interaction between HSP90 and its protein kinase clients. CDC37 is frequently over-expressed in cancers involving mutant kinases and acts as an oncogene (Roe et al. 2004, reviewed by Gray Jr. et al. 2008). Over-expression of the wild-type EGFR or EGFR cancer mutants results in aberrant activation of downstream signaling cascades, namely RAS/RAF/MAP kinase signaling and PI3K/AKT signaling, and possibly signaling by PLCG1, which leads to increased cell proliferation and survival, providing selective advantage to cancer cells that harbor activating mutations in the EGFR gene (Sordella et al. 2004, Huang et al. 2007). While growth factor activated wild-type EGFR is promptly down-regulated by internalization and degradation, cancer mutants of EGFR demonstrate prolonged activation (Lynch et al. 2004). Association of HSP90 with EGFR kinase domain mutants negatively affects CBL-mediated ubiquitination, possibly through decreasing the affinity of EGFR kinase domain mutants for phosphorylated CBL, so that CBL dissociates from the complex upon phosphorylation and cannot perform ubiquitination (Yang et al. 2006, Padron et al. 2007). EGFRvIII mutant does not autophosorylate on the tyrosine residue Y1045, a docking site for CBL, and is therefore unable to recruit CBL ubiquitin ligase, which enables it to escape degradation (Han et al. 2006). Various molecular therapeutics are being developed to target aberrantly activated EGFR in cancer. Non-covalent (reversible) small tyrosine kinase inhibitors (TKIs), such as gefitinib and erlotinib, selectively bind kinase domain of EGFR, competitively inhibiting ATP binding and subsequent autophosphorylation of EGFR dimers. EGFR kinase domain mutants sensitive to non-covalent TKIs exhibit greater affinity for TKIs than ATP compared with the wild-type EGFR protein, and are therefore preferential targets of non-covalent TKI therapeutics (Yun et al. 2007). EGFR proteins that harbor point mutations in the extracellular domain also show sensitivity to non-covalent tyrosine kinase inhibitors (Lee et al. 2006). EGFR kinase domain mutants harboring small insertions in exon 20 or a secondary T790M mutation are resistant to reversible TKIs (Balak et al. 2006) due to increased affinity for ATP (Yun et al. 2008), and are targets of covalent (irreversible) TKIs that form a covalent bond with EGFR cysteine residue C397. However, effective concentrations of covalent TKIs also inhibit wild-type EGFR, causing severe side effects (Zhou et al. 2009). Hence, covalent TKIs have not shown much promise in clinical trials (Reviewed by Pao and Chmielecki in 2010). Recombinant monoclonal antibody Cetuximab acts as an antagonist of EGFR ligand binding, and is approved for the treatment of tumors that over-express wild-type EGFR receptor (Cunningham et al. 2004, Li et al. 2005, Burtness et al. 2005).
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Benzoquinoid ansamycins (geldanamycin, herbimycin, and geldanamycin derivatives 17-AAG, 17-DMAG and IPI-504) are antitumor antibiotics that inactivate HSP90 by binding to its substrate-binding pocket.
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The epidermal growth factor receptor (EGFR) is one member of the ERBB family of transmembrane glycoprotein tyrosine receptor kinases (RTK). Binding of EGFR to its ligands induces conformational change that unmasks the dimerization interface in the extracellular domain of EGFR, leading to receptor homo- or heterodimerization at the cell surface. Dimerization of the extracellular regions of EGFR triggers additional conformational change of the cytoplasmic EGFR regions, enabling the kinase domains of two EGFR molecules to achieve the catalytically active conformation. Ligand activated EGFR dimers trans-autophosphorylate on tyrosine residues in the cytoplasmic tail of the receptor. Phosphorylated tyrosines serve as binding sites for the recruitment of signal transducers and activators of intracellular substrates, which then stimulate intracellular signal transduction cascades that are involved in regulating cellular proliferation, differentiation, and survival. Recruitment of complexes containing GRB2 and SOS1 to phosphorylated EGFR dimers either directly, through phosphotyrosine residues that serve as GRB2 docking sites, or indirectly, through SHC1 recruitment, promotes GDP to GTP exchange on RAS, resulting in the activation of RAF/MAP kinase cascade. Binding of complexes of GRB2 and GAB1 to phosphorylated EGFR dimers leads to formation of the active PI3K complex, conversion of PIP2 into PIP3, and activation of AKT signaling. Phospholipase C-gamma1 (PLCG1) can also be recruited directly, through EGFR phosphotyrosine residues that serve as PLCG1 docking sites, which leads to PLCG1 phosphorylation by EGFR and activation of DAG and IP3 signaling. EGFR signaling is downregulated by the action of ubiquitin ligase CBL. CBL binds directly to the phosphorylated EGFR dimer through the phosphotyrosine Y1045 in the C-tail of EGFR, and after CBL is phosphorylated by EGFR, it becomes active and ubiquitinates phosphorylated EGFR dimers, targeting them for degradation. For a recent review of EGFR signaling, please refer to Avraham and Yarden, 2011.
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Activated epidermal growth factor receptors (EGFR) can stimulate phosphatidylinositol (PI) turnover. Activated EGFR can activate phospholipase C-gamma1 (PLC-gamma1, i.e. PLCG1) which hydrolyses phosphatidylinositol 4,5-bisphosphate (PIP2) to inositol 1,4,5-triphosphate (IP3) and diacylglycerol (DAG). IP3 is instrumental in the release of calcium from intracellular stores and DAG is involved in protein kinase C activation.
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This pathway describes the generation of DAG and IP3 by the PLCgamma-mediated hydrolysis of PIP2 and the subsequent downstream signaling events.
Calmodulin (CaM) is a small acidic protein that contains four EF-hand motifs, each of which can bind a calcium ion, therefore it can bind up to four calcium ions. The protein has two approximately symmetrical domains, separated by a flexible hinge region. Calmodulin is the prototypical example of the EâF-hand family of Ca2+-sensing proteins. Changes in intracellular Ca2+ concentration regulate calmodulin in three distinct ways. First, by directing its subcellular distribution. Second, by promoting association with different target proteins. Third, by directing a variety of conformational states in calmodulin that result in target-specific activation. Calmodulin binds and activates several effector protein (e.g. the CaM-dependent adenylyl cyclases, phosphodiesterases, protein kinases and the protein phosphatase calcineurin).
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One important physiological role for Calmodulin is the regulation of adenylylcyclases. Four of the nine known adenylylcyclases are calcium sensitive, in particular type 8 (AC8).
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
Cyclic adenosine 3',5'-monophosphate (cAMP) induces gene transcription through activation of cAMP-dependent protein kinase (PKA), and subsequent phosphorylation of the transcription factor cAMP response element-binding protein, CREB, at serine-133.
Glutamine phosphoribosylpyrophosphate amidotransferase
Amidophosphoribosyltransferase precursor (EC 2.4.2.14) (Glutamine phosphoribosylpyrophosphate amidotransferase) (ATASE) (GPAT)
Amidophosphoribosyltransferase precursor
phosphoribosyl pyrophosphate amidotransferase
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
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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
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Phosphoribosylformylglycinamidine synthase
Formylglycinamide ribotide amidotransferase
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Phospholipase C-gamma (PLC-gamma) is a substrate of the fibroblast growth factor receptor (FGFR) and other receptors with tyrosine kinase activity. It is known that the src homology region 2 (SH2 domain) of PLC-gamma and of other signaling molecules (such as GTPase-activating protein and phosphatidylinositol 3-kinase-associated p85) direct their binding toward autophosphorylated tyrosine residues of the FGFR. Recruitment of PLC-gamma results in its phosphorylation and activation by the receptor. Activated PLC-gamma hydrolyzes phosphatidyl inositol[4,5] P2 to form the second messengers diacylglycerol (DAG) and Ins [1,4,5]P3, which stimulate calcium release and activation of calcium/calmodulin dependent kinases.
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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.
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nicotinamide nucleotide transhydrogenase
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).
Electron Transfer Flavoprotein beta subunit
Studies in the past decade have suggested that the basic mechanism of DNA replication initiation is conserved in all kingdoms of life. Initiation in unicellular eukaryotes, in particular Saccharomyces cerevisiae (budding yeast), is well understood, and has served as a model for studies of DNA replication initiation in multicellular eukaryotes, including humans. In general terms, the first step of initiation is the binding of the replication initiator to the origin of replication. The replicative helicase is then assembled onto the origin, usually by a helicase assembly factor. Either shortly before or shortly after helicase assembly, some local unwinding of the origin of replication occurs in a region rich in adenine and thymine bases (often termed a DNA unwinding element, DUE). The unwound region provides the substrate for primer synthesis and initiation of DNA replication. The best-defined eukaryotic origins are those of S. cerevisiae, which have well-conserved sequence elements for initiator binding, DNA unwinding and binding of accessory proteins. In multicellular eukaryotes, unlike S. cerevisiae, these loci appear not to be defined by the presence of a DNA sequence motif. Indeed, choice of replication origins in a multicellular eukaryote may vary with developmental stage and tissue type. In cell-free models of metazoan DNA replication, such as the one provided by Xenopus egg extracts, there are only limited DNA sequence specificity requirements for replication initiation (Kelly & Brown 2000; Bell & Dutta 2002; Marahrens & Stillman 1992; Cimbora & Groudine 2001; Mahbubani et al 1992, Hyrien & Mechali 1993).
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.
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Cytosolic levels of abacavir are determined by the balance of its facilitated diffusion into the cell mediated by organic cation transporters SLC22A1, 2, and 3, and its ATP-dependent efflux from cells mediated by ABCG2 and ABCB1 (Klaasen and Aleksunes 2010; Pan et al. 2007; Shaik et al. 2007).
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The ABCB1 transporter associated with the plasma membrane mediates the ATP-dependent efflux of a variety of xenobiotic molecules. Its ability to transport abacavir is inferred from studies of the corresponding mouse protein (Shaik et al. 2007).
Cytosolic PCK1 (phosphoenolpyruvate carboxykinase 1) catalyzes the reaction of carbovir diphosphate and ATP to form carbovir triphosphate and ADP. The activity of human PCK1 and relative inactivity of human nucleoside diphosphate kinase are inferred from the properties of the purified rat and bovine enzymes in vitro (Miller et al. 1992).
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Cytosolic ADAL (Adenosine DeAminase-Like) catalyzes the reaction of abacavir monophosphate and water to form carbovir monophosphate and cyclopropylamine. The active form of the enzyme is a protein monomer complexed with a zinc ion (Murakami et al. 2011).
Decaprenyl-diphosphate synthase subunit 1 ecNumber2.5.1.91/ecNumber
2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial ecNumber2.1.1.201/ecNumber
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Isocitrate dehydrogenase 2 (NADP), mitochondrial
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Neurotrophin signal transduction in the nervous system
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Adenylate cyclase is responsive to calcium and calmodulin and produces cAMP. One important physiological role for Calmodulin is the regulation of adenylylcyclases. Four of the ten known adenylylcyclases are calcium sensitive, in particular type 8 (AC8).
A number of inactive tetrameric PKA holoenzymes are produced by the combination of homo- or heterodimers of the different regulatory subunits associated with two catalytic subunits. When cAMP binds to two specific binding sites on the regulatory subunits, these undergo a conformational change that causes the dissociation of a dimer of regulatory subunits bound to four cAMP from two monomeric, catalytically active PKA subunits.
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Purification, properties, and sequencing of aminoisobutyrate aminotransferases from rat liver
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Organization of fibrillar collagen in the human and bovine cornea: collagen types V and III
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Lipid digestion, mobilization, and transport
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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_2490.1
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_3751.1
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_2857.1
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_110608.9
Structure of human epoxide hydrolase reveals mechanistic inferences on bifunctional catalysis in epoxide and phosphate ester hydrolysis
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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_32896.10
Identification of the major intestinal fatty acid transport protein
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_90867.9
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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_85790.9
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=4236129
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_95309.9
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=4234250
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4230309
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236357
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_133275.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236358
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_138515.5
Human lung enolase: cloning and sequencing of cDNA and its inducibility with dexamethasone
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_123917.1
(R)-2-Hydroxy-3-(phosphonooxy)-1-monoanhydridewith phosphoric propanoic acid
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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_123712.1
Decarboxylases involved in polyamine biosynthesis and their inactivation by nitric oxide
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UDP-N-acetyl-D-glucosamine [ChEBI:16264]
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_126829.5
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_95407.9
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=4234042
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236101
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236107
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236108
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_87979.9
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=4230241
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_103570.9
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4230240
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234976
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234977
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3368.2
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=110668
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3541.2
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=4234399
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110720
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2983.2
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=4234397
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110652
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234398
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4429.2
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=4234395
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110680
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234396
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234393
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234394
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5595.2
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=4234391
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=110732
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234392
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234390
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235491
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235489
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235488
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_113806.8
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234982
Metabolism of amino acids and derivatives
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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=4234979
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234978
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_108373.9
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5419.2
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=110638
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234388
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_144680.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234389
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235171
Activation of the FGF receptor underlies neurite outgrowth stimulated by L1, N-CAM, and N-cadherin
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_147686.5
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234384
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235168
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234385
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235167
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234386
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234387
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_21786.1
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=4234379
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234382
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234383
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234975
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_16095.2
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=382577
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_16090.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=382571
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_98432.9
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=4236103
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_86513.9
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=4236095
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236146
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_95000.9
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=4236145
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_103354.9
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_90816.9
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=4236147
Tolerance by Mtb to nitric oxide produced by macrophages
Reactive nitrogen species (RNS), like reactive oxygen species, have numerous target molecules in the bacterial cell, and Mtb has developed remedies to the most important ones of them. This is a key reason for its ability to stay alive in the hostile environment of the late phagosome within human macrophages. Mtb repairs single-base DNA damage caused by DNA alkylation; it scavenges nitric oxide with large amounts of mycothiol and methionine-rich proteins (the nitroso compounds later being reduced). Nitric oxide and peroxynitrite are also directly reduced by a battery of hemoglobins and peroxiredoxins, supported by a network of thioredoxins and respective NADPH-dependent reductases (Fang. 2004).
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_92301.9
G(z) signaling: emerging divergence from G(i) signaling
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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_157095.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234856
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_156300.3
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_107461.9
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=4236225
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236144
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_159822.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236226
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234411
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234403
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234402
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234405
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234404
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234407
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234406
E2F mediated regulation of DNA replication
carboxymycobactin (loaded) [ChEBI:47333]
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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=4234408
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234853
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_7089.1
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=171095
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236220
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_156250.3
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_14189.1
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=216762
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234400
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_158098.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234401
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117054.2
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=1217510
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117645.1
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=1217505
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236104
Amino acid transport across mammalian intestinal and renal epithelia
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_83013.9
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=4234845
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234043
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_101302.9
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=4230245
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234842
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4230246
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234843
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234841
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_13826.1
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_116852.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=265546
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_14321.1
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=265781
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Can type VII collagen injections cure dystrophic epidermolysis bullosa?
Structure-function relationships in dihydrolipoamide acyltransferases.
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FUNCTION Iron-storage protein that displays ferroxidase activity, catalyzing the oxidation of Fe(2+) ions into Fe(3+) ions, that can then be deposited as a ferric-oxide mineral core within the central cavity of the protein complex.CATALYTIC ACTIVITY 4 Fe(2+) + 4 H(+) + O(2) = 4 Fe(3+) + 2 H(2)O.SUBUNIT Homooligomer of 24 subunits that are packed together to form an approximately spherical molecule with a central cavity, in which large amounts of iron can be stored.INDUCTION Induced by 1 mM reactive nitrogen intermediate sodium nitroprusside dihydrate (at protein level). Induced by exposure to 50 uM FeCl(3). A possible member of the dormancy regulon. Induced in response to reduced oxygen tension (hypoxia), repressed by carbon monoxide (CO). It is hoped that this regulon will give insight into the latent, or dormant phase of infection.SIMILARITY Belongs to the ferritin family. Prokaryotic subfamily.SIMILARITY Contains 1 ferritin-like diiron domain.
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Synthesis of Leukotrienes (LT) and Eoxins (EX)
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Etherphospholipid biosynthesis and dihydroxyactetone-phosphate acyltransferase: resolution of the genomic organization of the human gnpat gene and its use in the identification of novel mutations
FUNCTION Catalyzes the coenzyme F420-dependent oxidation of glucose 6-phosphate to 6-phosphogluconolactone. Is essential for the bioreductive activation of the prodrug PA-824 (nitroimidazo-oxazine) developed for anti-tuberculosis therapy against both replicating and persistent bacteria. It does not interact directly with PA-824 but, rather, provides reduced F420 to an accessory protein (Rv3547), which in turn activates PA-824. Also probably has a role in resistance to oxidative stress, via its consumption of G6P that serves as a source of reducing power to combat oxidative stress in mycobacteria.CATALYTIC ACTIVITY D-glucose 6-phosphate + oxidized coenzyme F420 = D-glucono-1,5-lactone 6-phosphate + reduced coenzyme F420.ENZYME REGULATION Inhibited by citrate.SUBUNIT Homodimer.DISRUPTION PHENOTYPE Cells lacking this gene display a strong resistance to PA-824 and CGI-17341 (nitroimidazo-oxazole).SIMILARITY Belongs to the F420-dependent glucose-6-phosphate dehydrogenase family.
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Hypoxanthine-guanine phosphoribosyltransferase
Demonstration of a specific mitochondrial isovaleryl-CoA dehydrogenase deficiency in fibroblasts from patients with isovaleric acidemia.
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Dihydroorotate dehydrogenase, mitochondrial precursor
Dihydroorotate dehydrogenase, mitochondrial precursor (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdehase) (Fragment)
Crystal structure of porcine mitochondrial NADP+-dependent isocitrate dehydrogenase complexed with Mn2+ and isocitrate. Insights into the enzyme mechanism
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))
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
Assembly of collagen fibrils de novo by cleavage of the type I pC-collagen with procollagen C-proteinase. Assay of critical concentration demonstrates that collagen self-assembly is a classical example of an entropy-driven process
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ABCG4: a novel human white family ABC-transporter expressed in the brain and eye
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Ribonucleoside-diphosphate reductase M2 chain (EC 1.17.4.1) (Ribonucleotide reductase small chain)
Ribonucleoside-diphosphate reductase M2 chain
Glucosamine--fructose-6-phosphate aminotransferase (isomerizing) 1
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Mucopolysaccharidosis type III (Sanfilippo Syndrome): emerging treatment strategies
Mucopolysaccharidosis Type II (Hunter Syndrome): clinical picture and treatment
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Defective copper-induced trafficking and localization of the Menkes protein in patients with mild and copper-treated classical Menkes disease
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Glutathione metabolism and its selective modification
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The deamination of dopamine by human brain monoamine oxidase. Specificity for the two enzyme forms in seven brain regions
Naunyn Schmiedebergs Arch Pharmacol 322:198-202
The metabolism of nitrosothiols in the Mycobacteria: identification and characterization of S-nitrosomycothiol reductase
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Identification of a colon mucosa gene that is down-regulated in colon adenomas and adenocarcinomas
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Cloning, expression, and characterization of a human 4'-phosphopantetheinyl transferase with broad substrate specificity
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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.
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.
During steady state conditions, cytoplasmic [Ca2+] is reduced by the accumulation of Ca2+ in intracellular stores and Ca2+ extrusion.
The plasma membrane Ca-ATPases 1-4 (ATP2B1-4, PMCAs) are P-type Ca2+-ATPases regulated by calmodulin. The PMCA also counter-transports a proton. PMCA is important for Ca2+ homeostasis and function.
Ca2+ homeostasis is controlled by processes that elevate or counter the elevation of cytosolic Ca2+. During steady state conditions, cytoplasmic Ca2+ is reduced by the accumulation of Ca2+ in intracellular stores and by Ca2+ extrusion. The primary intracellular calcium store in platelets is the dense tubular system, the equivalent of the ER system in other cell types. Ca2+ is extruded by Ca2+-ATPases including plasma membrane Ca2+ ATPases (PMCAs) and sarco/endoplasmic reticulum Ca2+ -ATPase isoforms (SERCAs). Activation of non- excitable cells involves the agonist-induced elevation of cytosolic Ca2+, an essential process for platelet activation. It occurs through Ca2+ release from intracellular stores and Ca2+ entry through the plasma membrane. Ca2+ store release involves phospholipase C (PLC)-mediated production of inositol-1,4,5-trisphosphate (IP3), which in turn stimulates IP3 receptor channels to release Ca2+ from intracellular stores. This is followed by Ca2+ entry into the cell through plasma membrane calcium channels, a process referred to as store-operated calcium entry (SOCE). Stromal interaction molecule 1 (STIM1), a Ca2+ sensor molecule in intracellular stores, and the four transmembrane channel protein Orai1 are the key players in platelet SOCE. Other major Ca2+ entry mechanisms are mediated by the direct receptor-operated calcium (ROC) channel, P2X1 and transient receptor potential channels (TRPCs).
Mechanistic insights into a novel exporter-importer system of Mycobacterium tuberculosis unravel its role in trafficking of iron
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.
Monoacylglycerol lipase (MAGL) is a key enzyme in the hydrolysis of the endocannabinoid 2-arachidonoylglycerol to arachidonate and glycerol. In adipocytes MAGL and hormone-sensitive lipase (LIPE) hydrolyze intracellular triglyceride stores. MAGL may also complement lipoprotein lipase (LPL) in completing hydrolysis of monoglycerides resulting from degradation of lipoprotein triglycerides.
Diacylglycerol (DAG) is an important source of arachidonic acid, a signalling molecule and the precursor of the prostaglandins. In human platelet almost all the DAG produced from phosphatidylinositol degradation contains arachidonate (Takamura et al. 1987). DAG is hydrolysed by DAG lipase to 2-arachidonylglycerol (2-AG) which is further hydrolysed by monoacylglycerol lipase. 2-AG is an agonist of cannabinoid receptor 1.
Hydrolysis of phosphatidyl inositol-bisphosphate (PIP2) by phospholipase C (PLC) produces diacylglycerol (DAG) and inositol triphosphate (IP3). Both are potent second messengers. IP3 diffuses into the cytosol, but as DAG is a hydrophobic lipid it remains within the plasma membrane. IP3 stimulates the release of calcium ions from the smooth endoplasmic reticulum, while DAG activates the conventional and unconventional protein kinase C (PKC) isoforms, facilitating the translocation of PKC from the cytosol to the plasma membrane. The effects of DAG are mimicked by tumor-promoting phorbol esters. DAG is also a precursor for the biosynthesis of prostaglandins, the endocannabinoid 2-arachidonoylglycerol and an activator of a subfamily of TRP-C (Transient Receptor Potential Canonical) cation channels 3, 6, and 7.
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Platelet activation begins with the initial binding of adhesive ligands and of the excitatory platelet agonists (released or generated at the sites of vascular trauma) to cognate receptors on the platelet membrane (Ruggeri 2002). Intracellular signaling reactions then enhance the adhesive and procoagulant properties of tethered platelets or of platelets circulating in the proximity. Once platelets have adhered they degranulate, releasing stored secondary agents such as ADP, ATP, and synthesize thromboxane A2. These amplify the response, activating and recruiting further platelets to the area and promoting platelet aggregation. These amplify the response, activating and recruiting further platelets to the area and promoting platelet aggregation. Adenosine nucleotides signal through P2 purinergic receptors on the platelet membrane. ADP activates P2Y1 and P2Y12, which signal via both the alpha and gamma:beta components of the heterotrimeric G-protein (Hirsch et al. 2001, 2006), while ATP activates the ionotropic P2X1 receptor (Kunapuli et al. 2003). Activation of these receptors initiates a complex signaling cascade that ultimately results in platelet activation, aggregation and thrombus formation (Kahner et al. 2006). Integrin AlphaIIbBeta3 is the most abundant platelet receptor, with 40 000 to 80 000 copies per resting platelet, acting as a major receptor for fibrinogen and other adhesive molecules (Wagner et al. 1996). Activation of AlphaIIbBeta3 enhances adhesion and leads to platelet-platelet interactions, and thus aggregation (Philips et al. 1991). GP VI is the most potent collagen receptor initiating signal generation, an ability derived from its interaction with the FcRI gamma chain. This results in the phosphorylation of the gamma-chain by non-receptor tyrosine kinases of the Src family (1). The phosphotyrosine motif is recognized by the SH2 domains of Syk, a tyrosine kinase. This association activates the Syk enzyme, leading to activation (by tyrosine phosphorylation) of PLC gamma2 (2). Thrombin is an important platelet agonist generated on the membrane of stimulated platelets. Thrombin acts via cell surface Protease Activated Receptors (PARs). PARs are G-protein coupled receptors activated by a proteolytic cleavage in an extracellular loop (Vu, 1991) (3). Activated PARs signal via G alpha q (4) and via the beta:gamma component of the G-protein (5). Both stimulate PLC giving rise to PIP2 hydrolysis and consequent activation of PI3K (6). PLCgamma2 activation also gives rise to IP3 (7) which stimulates the IP3 receptor (8) leading to increased intracellular calcium. Platelet activation further results in the scramblase-mediated transport of negatively-charged phospholipids to the platelet surface. These phospholipids provide a catalytic surface (with the charge provided by phosphatidylserine and phosphatidylethanolamine) for the tenase complex (formed by the activated forms of the blood coagulation factors factor VIII and factor I).
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Serotonin is first metabolized to 5-hydroxyindole acetaldehyde by monoamine oxidase. 5-hydroxyindole acetaldehyde is then catalyzed by aldehyde dehydrogenase to form 5-hydroxyindole acetic acid.
The human gene SLC6A3 encodes the sodium-dependent dopamine transporter, DAT which mediates the re-uptake of dopamine from the synaptic cleft (Vandenbergh DJ et al, 2000). Dopamine can then be degraded by either COMT or monoamine oxidase.
Alternately dopamine is metabolized to homovanillic acid in a two-step reaction in which dopamine is first oxidized to 3,4-dihydroxypheylacetic acid (DOPAC) and then converted to homovanillic acid by catecholamine o-methyltransferase.
Ca2+ fluxes through NMDA receptors in the post-synaptic neuron facilitate binding of Ca2+/Calmodulin to adenylate cyclase type 1, 3 or 8, resulting in its activation. Once activated, cAMP is produced which further activates PKA.
Ca2+ signal generated through NMDA receptor in the post-synaptic neuron activates adenylate cyclase signal transduction, leading to the activation of PKA and phosphorylation and activation of CREB-induced transcription. The isoforms of adenylate cyclase that are activated by Ca2+ in the brain are I, III and IX.
Serotonergic neurotransmission affects a wide range of behaviors, from food intake and reproductive activity, to sensory processing and motor activity, to cognition and emotion. One such key regulator is the serotonin transporter (5-HTT), which is observed to remove serotonin released into the synaptic cleft.
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.
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The neurotransmitter in the synaptic cleft released by the pre-synaptic neuron binds specific receptors located on the post-synaptic terminal. These receptors are either ion channels or G protein coupled receptors that function to transmit the signals from the post-synaptic membrane to the cell body.
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Ca2+ influx through the NMDA receptor initiates subsequent molecular pathways that have a defined role in establishing long-lasting synaptic changes. The molecular signaling initiated by a rise in Ca2+ within the spine leads to phosphorylation of Cyclic AMP Response Element binding protein (CREB) at serine 133 which is involved in the transcription of genes that results in long lasting changes in the synapse. The phosphorylation of CREB by increased Ca2+ can be brought about by distinct molecular pathways that may involve MAP kinase, activation of adenylate cyclase, activation of CaMKII and/or the activation of CaMKIV.
NMDA receptors are a subtype of ionotropic glutamate receptors that are specifically activated by a glutamate agonist N-methyl-D-aspartate (NMDA). Activation of NMDA receptor involves opening of the ion channel that allows the influx of Ca2+. NMDA receptors are central to activity dependent changes in synaptic strength and are predominantly involved in the synaptic plasticity that pertain to learning and memory. A unique feature of NMDA receptor unlike other glutamate receptors is the requirement of dual activation of the NMDA receptor, which require both voltage dependent and ligand dependent activation. At resting membrane potential the NMDA receptors are blocked by Mg2+. The voltage dependent Mg2+ block is relieved upon depolarization of the post-synpatic membrane . The ligand dependent activation of the NMDA receptor requires co-activation by two ligands, namely glutamate and glycine. NMDA receptors are coincidence detector, and are activated only if there is simultaneous activation of both pre and post-synaptic cell. Upon activation NMDA receptors allow the influx of Ca2+ that initiates various molecular signaling cascades that are involved in the process of learning and memory.
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Primary structure of a human trifunctional enzyme. Isolation of a cDNA encoding methylenetetrahydrofolate dehydrogenase-methenyltetrahydrofolate cyclohydrolase-formyltetrahydrofolate synthetase.
Succinate semialdehyde dehydrogenase (SSADH) converts succinate semialdehyde, in a final step of GABA degradation, into succinate. SSADH uses one water molecule and one molecule of NAD+ per molecule of succinyate semialdehyde.
GABA is converted to succinate semialdehyde by 4-aminobutyrate aminotransferase
S-adenosylmethionine: nothing goes to waste
Nitric oxide and peroxynitrite in health and disease
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3-methoxytyramine generated by COMT after methylation of dopamine is oxidized into homovanillic acid by monoamine oxidase A
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Dopamine once taken up by the dopamine transporter from the extracellular space into the cytosol is metabolized in a two step reaction to homovanillic acid.The first reaction is catalyzed by catecholamine o-methyl transferase and the subsequent reaction is catalyzed by monoamine oxidase A.
Biochemistry, physiology, and genetics of GPAT, AGPAT, and lipin enzymes in triglyceride synthesis
Am J Physiol Endocrinol Metab 296:E1195-209
Dopamine is oxidized to 3,4-dihydroxyphenylacetic acid by monoamine oxidase.
Hexosamine biosynthetic pathway mutations cause neuromuscular transmission defect
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3,4-dihydroxyphenylacetic acid, generated after oxidation of dopamine by monoamineoxidase, is methylated by catecholamine o-methyltransferase to homovanillic acid.
The cAMP signalling pathway activates CREB through PKA, p38 and MSK1 in NIH 3T3 cells
GABA is metabolized to succinated by the serial action of two enzymes, 4-aminobutyrate aminotransferase and suucinate semialdehyde dehydrogenase.
GABA is a major inhibitory neurotransmitter in the mammalian central nervous system. GABA modulates neuronal excitability throughout the nervous system. Disruption of GABA neurotransmission leads to many neurological diseases including epilepsy and a general anxiety disorder. GABA is synthesized by two distinct enzymes GAD67 and GAD65 that differ in their cellular localization, functional properties and co-factor requirements. GABA synthesized by GAD65 is used for neurotransmission whereas GABA synthesized by GAD67 is used for processes other than neurotransmission such as synaptogenesis and protection against neuronal injury. GABA is loaded into synaptic vesicle with the help of vesicular inhibitory amino acid transporter or VGAT. GAD65 and VGAT are functionally linked at the synaptic vesicle membrane and GABA synthesized by GAD65 is preferentially loaded into the synaptic vesicle over GABA synthesized in cytoplasm by GAD67.The GABA loaded synaptic vesicles are docked at the plasma membrane with the help of the SNARE complexes and primed by interplay between various proteins including Munc18, complexin etc. Release of GABA loaded synaptic vesicle is initiated by the arrival of action potential at the presynaptic bouton and opening of N or P/Q voltage gated Ca2+ channels. Ca2+ influx results in Ca2+ binding by synaptobrevin, which is a part of the SNARE complex that also includes SNAP25 and syntaxin, leading to synaptic vesicle fusion. Release of GABA in the synaptic cleft leads to binding of GABA by the GABA receptors and post ligand binding events.
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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Dopamine in the cytosol is metabolized to 3-methoxytyramine by catecholamine o-methyltransferase (COMT), which uses s-adenosylmethionine as a methyl group donor.
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Biochemistry - The Chemical Reactions of Living Cells 2nd Edn.
(2E,4E,6E,8E)-9-(3-hydroxy-2,6,6-trimethyl-1-cyclohexenyl)-3,7-dimethyl-nona-2,4,6,8-tetraenoic acid
(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethyl-3-hydroxy-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acid
all-trans-4-hydroxyretinoic acid [ChEBI:63795]
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3-hydroxy-4-methoxybenzoate [ChEBI:63797]
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Biochemical Pathways - An Atlas of Biochemistry and Molecular Biology
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Lehninger - Principles of Biochemistry 4th Edn.
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Fibrillin-1 and -2 contain heparin-binding sites important for matrix deposition and that support cell attachment
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Somatic mutations affecting arginine residue 132 of IDH1 (isocitrate dehydrogenase 1, a cytosolic enzyme that normally catalyzes the NADP+-dependent conversion of isocitrate to 2-oxoglutarate), are very commonly found in human glioblastomas (Parsons et al. 2008). These mutant proteins efficiently catalyze the NADPH-dependent reduction of 2-oxoglutarate to form 2-hydroxyglutarate. Cells expressing the mutant protein accumulate elevated levels of 2-hydroxyglutarate, probably in the cytosol as IDH1 is a cytosolic enzyme. The fate of the 2-hydroxyglutarate is unclear, but the high frequency with which the mutation is found in surveys of primary tumors is consistent with the possibility that it is advantageous to the tumor cells (Dang et al 2009).
Eight SLC gene families are involved in the transport of amino acids and oligopeptides.
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Noradrenaline is degraded by Monoamine oxidase A, which contains FAD as a cofactor. Monoamine oxidase is located in the outer mitochondrial membrane facing the cytoplasmic site. Monoamine xoidase functions as a monomer and is functional both is astrocyes and neurons.
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SLC7A3 mediates the uptake of cationic amino acids across the plasma membranes of non-epithelial cells (Vekony et al. 2001).
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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).
SLC7A2, isoform A, mediates the uptake of cationic amino acids across the plasma membranes of non-epithelial cells (Broer 2008; Closs et al. 1997).
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).
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.
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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Noradrenalin release cycle consists of reacidification of the empty clathrin sculpted monoamine transport vesicle, loading of dopamine into reacidified clathrin coated monamine transport vesicle, conversion of dopamine into Noradrenalin, docking and priming of the noradrenalin synaptic veiscle and then release of noradrenalin synaptic vesicle. In the peripheral nervous system in the peripheral nervous system noradrenalin is stored in large and small dense vesicles and is realesed from large vesicles.
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Mutant forms of IDH1 in which the arginine residue at position 132 has been replaced by histidine, cystine, leucine, or serine catalyze the reaction of 2-oxoglutarate and NADPH + H+ to form (R)-2-hydroxyglutarate and NADP+. Like normal IDH1, the mutant enzyme forms a dimer located in the cytosol (Dang et al. 2009). Such mutations occur frequently as a somatic event in human glioblastomas (Parsons et al. 2008). Cells expressing the mutant protein accumulate elevated levels of 2-hydroxyglutarate, probably in the cytosol as IDH1 is a cytosolic enzyme. The fate of the 2-hydroxyglutarate is unclear, but the high frequency with which the mutation is found in surveys of primary tumors is consistent with the possibility that it is advantageous to the tumor cells (Dang et al. 2009).
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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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Mucopolysaccharidosis type VI (MPS VI, Maroteaux-Lamy syndrome, polydystrophic dwarfism; MIM:253200) is an autosomal recessive lysosomal storage disorder caused by a deficiency in arylsulfatase B (ARSB, N-acetyl-galactosamine 4-sulfatase; MIM:611542). It is named after two French physicians, Pierre Maroteaux and Maurice Emil Joseph Lamy. Maroteaux first described this disorder as a novel dysostosis associated with increased urinary excretion of chondroitin sulfate (CS; Maroteaux et al. 1963). The gene encoding ARSB is mapped to chromosome 5q11-q13 (Fidzianska et al. 1984) and contains 8 exons spanning about 206 kb (Karangeorgos et al. 2007). Defective ARSB results in build up of dermatan sulfate (DS) and chondroitin sulfate (CS) in soft tissues causing compression and blockages in blood vessels, nerves, trachea, corneal clouding and disrupting normal bone development. Symptoms are similar to MPS I but with normal intelligence generally (Rapini et al. 2007, Valayannopoulos et al. 2010).
Defects in beta-galactosidase (GLB1; MIM:611458) can result in GM1 gangliosidosis (GM1; MIM:230500) (Nishimoto et al. 1991) (not described here), with several phenotypes indicating mental deterioration, as well as in mucopolysaccharidosis IVB, a characteristic mucopolysaccharidosis with no neurological symptoms (Callahan 1999). Mucopolysaccharidosis IVB (MPS IVB, Morquio's syndrome B; MIM:253010) is a rare, autosomal recessive mucopolysaccharide storage disease characterized by intracellular accumulation of keratan sulfate (KS), skeletal dysplasia and corneal clouding. There is no central nervous system involvement, intelligence is normal and there is increased KS excretion in urine (Suzuki et al. "Beta-galactosidase deficiency (beta-galactosidosis): GM1 gangliosidosis and Morquio B disease", p3775-3809 in Stryer et al. 2001). MPSIVB is caused by a defect in betagalactosidase (GLB1), which normally cleaves terminal galactosyl residues from glycosaminoglycans, gangliosides and glycoproteins. The GLB1 gene spans 62.5 kb and contains 16 exons (Oshima et al.1988, Santamaria et al. 2007) and maps to chromosome 3p21.33 (Takano & Yamanouchi 1993).
Mucopolysaccharidosis type IX (MPS IX, Natowicz syndrome, Hyaluronidase deficiency, MIM:601492) is a rare lysosomal storage disease characterized by high hyaluronan (HA) concentration in the serum resulting from deficiency in hyaluronidase 1 (HYAL1, MIM:607071) which normally hydrolyses 1-4 linkages between N-acetylglucosamine (GlcNAc) and D-glucuronate (GlcA) residues. Symptoms of MPS IX are periodically painful soft tissue masses around the joints, acquired short stature and erosion of the hip joint, although joint movement and intelligence are normal (Natowicz et al. 1996, Triggs-Raine et al. 1999).
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Mucopolysaccharidosis type VII (MPS VII, Sly syndrome, beta-glucuronidase deficiency; MIM:253220) is an autosomal recessive lysosomal storage disease characterized by a deficiency of the enzyme beta-glucuronidase (GUSB; MIM:611499) which would normally cleave glucuronide residues from dematan sulphate, keratan sulphate and chondroitin sulphate, resulting in build up of these GAGs in cells and tissues (Sly et al. 1973). The gene encoding GUSB is 21 kb long, contains 12 exons and gives rise to two different types of cDNAs, through an alternate splicing mechanism (Miller et al. 1990). It maps to 7q11.21-q11.22 (Speleman et al. 1996). The phenotype is highly variable, ranging from severe causing death, non-immune hydrops fetalis (Vervoort et al. 1996) to mild forms with survival into adulthood (Storch et al. 2003). Most patients with the intermediate phenotype show hepatomegaly, skeletal anomalies, coarse facies, and variable degrees of mental impairment (Shipley et al. 1993, Tomatsu et al. 2009).
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The outer segment of photoreceptor cells is shed every 10-14 days to be completely replaced. The shed material is phagocytosed and transferred to the retinal pigment epithelium (RPE). Diretinoid-pyridinium-phosphatidylethanolamine (A2PE) can be hydrolysed to diretinoid-pyridinium-ethanolamine (A2E), a prominent constituent of lipofuscin (the material deposited in retinal tissue which accumulates over time and is implicated in macular degeneration). Evidence suggests this happens before transfer to RPE cells as part of the phagocytosed outer segment. A2E has been detected in outer segments (Ben-Shabat et al. 2002) and an N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D (NAPEPLD) activity detected in rat, mouse and human proteins (Okamoto et al. 2004, Ueda et al. 2005, Wang et al. 2006). This activity has been shown to hydrolyse A2PE to A2E in bovine outer segments before phagocytosis and transfer to RPE cells, suggesting A2PE is hydrolysed to A2E in photoreceptor outer segment membranes (Sparrow et al. 2003, Salvador & Giusto 1998).
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The mucopolysaccharidoses (MPS) are a group of rare, inherited lysosomal storage disorders caused by deficiencies of enzymes catalyzing the stepwise degradation of glycosaminoglycans (GAGs, originally called mucopolysaccharides) (Neufeld & Muenzer in Scriver et al. 2001). Catabolism of the GAGs dermatan sulfate, heparan sulfate, heparin, keratan sulfate, chondroitin sulfate or hyaluronan may be blocked at one or more steps, resulting in lysosomal accumulation of GAG fragments of varying size. Over time these collect in the cells, blood and connective tissues ultimately resulting in progressive irreversible cellular damage which affects appearance, physical abilities, organ and system function, vision, and usually mental development (Lehman et al. 2011, Ashworth et al. 2006). Life expectancy is also reduced. There are 11 known enzyme deficiencies that give rise to 7 distinct MPS. These disorders are biochemically characterized by elevated levels of partially or undegraded GAGs in lysosomes, blood, urine and cerebro-spinal fluid (Muenzer 2011, Coutinho et al. 2012). The MPS are part of the lysosomal storage disease family, a group of about 50 genetic disorders caused by deficient lysosomal proteins (Ballabio & Gieselmann 2009).
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The gene defects which cause diseases related to the retinoid cycle are described here (Travis et al. 2007, Palczewski 2010, Fletcher et al. 2011, den Hollander et al. 2008).
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Lipofuscin is a yellow-brown pigment grain composed mainly of lipids but also sugars and certain metals. Accumulation of lipofuscin is associated with degenerative diseases such as Alzheimer's disease, Parkinson's disease, chronic obstructive pulmonary disease and retinal macular degeneration. A prominent component of lipofuscin in retinal pigment epithelial (RPE) cells is the bisretinoid A2E (di-retinoid-pyridinium-ethanolamine), the end-product of the condensation of 2 molecules of all-trans-retinal (atRAL) and phosphatidylethanolamine (PE) in photoreceptor outer disc membranes. Once formed, A2E is phagocytosed, together with outer segments (Kevany & Palczewski 2010), to RPE where it accumulates. There is no evidence as yet to indicate that A2E can be catabolised (Sparrow et al. 2012, Sparrow et al. 2010). A simplified biosynthetic pathway for A2E is described here.
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Mucopolysaccharidosis IV A (MPS IVA, MPS4A, Morquio's syndrome, Morquio's; MIM:253000) is a rare, autosomal recessive mucopolysaccharide storage disease, first described simultaneously in 1929 by L Morquio (Morquio L, Sur une forme de distrophie familiale, Bull Soc Pediat, Paris, 27, 1929, 145-152) and JF Brailsford (Brailsford, JF, Chondro-osteo-dystrophy: roentgenographic and clinical features of child with dislocation of vertebrae, Am j Surg, 7, 1929, 404-410). MPSIVA is caused by a deficiency in N-acetylgalactosamine 6-sulfatase (GALNS; MIM:612222) which normally hydrolyses 6-sulfate groups of N-acetylgalactosamine 6-sulfate units of chondroitin sulfate (CS) and of galactose 6-sulfate units of keratan sulfate (KS) (Matalon et al. 1974). The result is accumulation of KS/DS in cells and overexcretion in urine. Severe osteochondrodysplasia is a commonly seen phenotype for this disease. The severity of the disease is variable but severe cases limits lifespan to their 20's or 30's (Prat et al. 2008, Tomatsu et al. 2011). The gene coding for human GALNS was mapped to chromosome 16q24.3 (Masuno et al. 1993) and its structure described at the same time by two independent groups as comprising 14 exons and spanning approximately 40-50 kb (Nakashima et al.1994, Morris et al.1994).
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Mucopolysaccharidosis III (Sanfilippo syndrome) was described in 1963 by a pediatrician named Sylvester Sanfilippo (J. Pediat. 63: 837-838, 1963, no reference). Mucopolysaccharidosis type IIID (MPS IIID, Sanfilippo syndrome D, MIM:252940) is an autosomal recessive genetic disorder due to the loss of N-acetyl-D-glucosamine 6-sulfatase (GNS; MIM:607664), that hydrolyses the 6-sulfate groups of the N-acetyl-D-glucosamine 6-sulfate units of the glycosaminoglycans (GAGs) heparan sulfate and keratan sulfate. GNS is localized to chromosome 12q14 and has 14 exons spanning 46 kb (Robertson et al. 1988, Mok et al. 2003). Loss of enzyme activity leads to lysosomal accumulation and urinary excretion of heparan sulfate and N-acetylglucosamine 6-sulfate residues (Mok et al. 2003). Keratan sulphate does not accumulate in MPS IIID, as beta-linked N-acetyl-D-glucosamine 6-sulphate can be cleaved by beta-hexosaminidase A (Kresse et al. 1980). This disorder is characterized by progressive mental deterioration but only moderate physical abnormalities and death duing the second or third decade of life, presenting a phenotype similar to MPSIIIA (Jones et al. 1997, de Ruijter et al. 2011).
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Mucopolysaccharidosis III (Sanfilippo syndrome) was described in 1963 by a pediatrician named Sylvester Sanfilippo (J. Pediat. 63: 837838, 1963, no reference). Mucopolysaccharidosis type IIIC (MPS IIIC, Sanfilippo syndrome C; MIM:252930) is an autosomal recessive genetic disorder due to the loss of heparan alpha-glucosaminide N-acetyltransferase (HGSNAT; MIM:610453) that normally acetylates the non-reducing terminal alpha-glucosamine residue of heparan sulfate. The molecular defects underlying MPS IIIC remained unknown for almost three decades due to the low tissue content and instability of HGSNAT. But, during the last decade, the gene was cloned in parallel by two different groups and shown to contain 18 exons and span approximately 62Kb (Fan et al. 2006, Hrebicek et al. 2006). Loss of HGSNAT results in build up of this glycosaminglycan (GAG) in cells and tissues and is characterized by severe central nervous system degeneration but only with mild somatic disease and death occurs typically during the second or third decade of life (Kresse et al. 1978, Klein et al. 1978, Feldhammer et al. 2009, de Ruijter et al. 2011).
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The pathway 'Signaling by FGFR in disease' shows 'Signaling by FGFR mutants' in parallel with the wild-type pathway 'Signaling by FGFR', allowing users to compare disease and normal events. FGFR mutants and events associated with germline diseases and cancer are highlighted in red. The wild-type pathway is shaded in the background. For detailed pathway summations, please see 'Signaling by FGFR mutants' and 'Signaling by FGFR'.
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The 22 members of the fibroblast growth factor (FGF) family of growth factors mediate their cellular responses by binding to and activating the different isoforms encoded by the four receptor tyrosine kinases (RTKs) designated FGFR1, FGFR2, FGFR3 and FGFR4. These receptors are key regulators of several developmental processes in which cell fate and differentiation to various tissue lineages are determined. Unlike other growth factors, FGFs act in concert with heparin or heparan sulfate proteoglycan (HSPG) to activate FGFRs and to induce the pleiotropic responses that lead to the variety of cellular responses induced by this large family of growth factors. An alternative, FGF-independent, source of FGFR activation originates from the interaction with cell adhesion molecules, typically in the context of interactions on neural cell membranes and is crucial for neuronal survival and development. Upon ligand binding, receptor dimers are formed and their intrinsic tyrosine kinase is activated causing phosphorylation of multiple tyrosine residues on the receptors. These then serve as docking sites for the recruitment of SH2 (src homology-2) or PTB (phosphotyrosine binding) domains of adaptors, docking proteins or signaling enzymes. Signaling complexes are assembled and recruited to the active receptors resulting in a cascade of phosphorylation events. This leads to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape, depending on the cell type or stage of maturation.
Signaling via FGFRs is mediated via direct recruitment of signaling proteins that bind to tyrosine auto-phosphorylation sites on the activated receptor and via closely linked docking proteins that become tyrosine phosphorylated in response to FGF-stimulation and form a complex with additional complement of signaling proteins. The activation loop in the catalytic domain of FGFR maintains the PTK domain in an inactive or low activity state. The activation-loop of FGFR1, for instance, contains two tyrosine residues that must be autophosphorylated for maintaining the catalytic domain in an active state. In the autoinhibited configuration, a kinase invariant proline residue at the C-terminal end of the activation loop interferes with substrate binding while allowing access to ATP in the nucleotide binding site. In addition to the catalytic PTK core, the cytoplasmic domain of FGFR contains several regulatory sequences. The juxtamembrane domain of FGFRs is considerably longer than that of other receptor tyrosine kinases. This region contains a highly conserved sequence that serves as a binding site for the phosphotyrosine binding (PTB) domain of FRS2. A variety of signaling proteins are phosphorylated in response to FGF stimulation, including Shc, phospholipase-C gamma and FRS2 leading to stimulation of intracellular signaling pathways that control cell proliferation, cell differentiation, cell migration, cell survival and cell shape.
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Mucopolysaccharidosis III (Sanfilippo syndrome) was described in 1963 by a pediatrician named Sylvester Sanfilippo (J. Pediat. 63: 837838, 1963, no reference). MPS IIIB (Mucopolysaccharidosis type IIIB, MPS IIIB, Sanfilippo syndrome type B; MIM:252920) is an autosomal recessive genetic disorder due to loss of function of alpha-N-acetylglucosaminidase (NAGLU; MIM:609701), involved in the hydrolysis of terminal non-reducing N-acetylglucosamine residues in heparan sulfate (HS) The gene encoding NAGLU was cloned in 1996 by Zhao and colleagues. It contains 6 exons and spans 8.3 kb on chromosome 17q21 (Zhao et al. 1996). MPSIIIB is characterized by severe CNS retardation but only mild somatic disease and death usually occurs in the second or third decade of life (Zhao et al. 1996, Yogalingam & Hopwood 2001, de Ruijter et al. 2011). MPS IIIB shows extensive molecular heterogeneity (Schmidtchen et al. 1998).
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Mucopolysaccharidosis III (MPS III, Sanfilippo syndrome) was described in 1963 by a pediatrician named Sylvester Sanfilippo (J. Pediat. 63: 837-838, 1963, no reference). Mucopolysaccharidosis IIIA (MPS IIIA, Sanfilippo syndrome A, MIM:252900) is a rare, autosomal recessive lysosomal storage disease characterised by severe CNS degeneration in early childhood leading to death between 10 and 20 years of age. A deficiency of the enzyme N-sulphoglucosamine sulphohydrolase (SGSH, MIM:605270), which normally hydrolyses the sulfate group from the terminal N-sulphoglucosamine residue of heparan sulfate (HS), leads to the build-up of HS in cells and tissues and its presence in urine (van de Kamp et al. 1981, Yogalingam & Hopwood 2001, de Ruijter et al. 2011). The gene encoding N-sulfoglucosamine sulfohydrolase, SGSH, was cloned in 1995 (Scott et al.1995) and, later, shown to contain 8 exons spanning approximately 11 kb (Karageorgos et al. 1996).
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Mucopolysaccharidosis II (MPS II, Hunter syndrome, MIM:309900) is an X-linked, recessive genetic disorder which therefore primarily affects males. MPS II was first described in 1917, by Major Charles Hunter (Hunter 1917) and is caused by a deficiency (or absence) of iduronate-2-sulfatase (IDS, MIM:300823), which would normally hydrolyse the 2-sulfate groups of the L-iduronate 2-sulfate units of dermatan sulfate, heparan sulfate and heparin. Without IDS, these GAGs accumulate in the body and are excessively excreted in urine. Although the disease was known since the early 1970s, being the first MPS to be defined clinically in humans, it wasnt until the 1990s that IDS was cloned. It is now known to be localized to Xq28 (Wilson et al. 1991) and contain 9 exons (Flomen et al. 1993) spanning approximately 24 kb (Wilson et al. 1993). Build up can occur in the liver and spleen as well as in the walls and valves of the heart (reduced hepatic and cardiac function, liver/spleen hepatosplenomegaly), airways (leading to obstructive airway disease), all major joints and bones (joint stiffness and skeletal deformities) and in brain (severe mental retardation). The rate of progression and degree of severity of the disorder can be different for each person with MPS II. Severe forms of the disorder can result in death in childhood whereas those with a "milder" form can expect to live to their 20's or 30's. Some patients even survive into their fifth and sixth decades of life (Wraith et al. 2008, Beck 2011).
Sequence identification and characterization of human carnosinase and a closely related non-specific dipeptidase
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Mucopolysaccharidosis type I (MPS I, Hurler syndrome, Hurler's disease, gargoylism, Scheie, Hirler-Scheie syndrome; MIM:607014, 607015 and 607016) is an autosomal recessive genetic disorder where there is a deficiency of alpha-L iduronidase (IDUA, MIM:252800), a glycosidase that removes non-reducing terminal alpha-L-iduronide residues during the lysosomal degradation of the glycosaminoglycans heparan sulphate and dermatan sulphate (McKusick 1959). In 1992, Scott and colleagues were able to clone and purify the gene that encodes this enzyme, IDUA, demonstrating that it spans approximately 19 kb and contains 14 exons (Scott et al. 1992). Hurler syndrome is named after a German paediatrician Gertrud Hurler (1919, no reference available). The result is build up of heparan sulfate and dermatan sulfate in the body and increased urinary excretion of these GAGs. Symptoms and signs include hepatosplenomegaly, dwarfism, unique facial features, corneal clouding, retinopathy, progressive mental retardation appears during childhood and early death can occur due to organ damage (Campos & Monaga 2012). MPS I is divided into three subtypes, ranging from severe to mild phenotypes; Mucopolysaccharidosis type IH (MPSIH, Hurler syndrome, MIM:607014), mucopolysaccharidosis type IH/S (MPSIH/S, HurlerScheie syndrome, MIM: 607015) and mucopolysaccharidosis type IS (MPSIS, Scheie syndrome, MIM: 607016) respectively (McKusick 1972).
Protease-activated receptors in hemostasis, thrombosis and vascular biology
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Functional characterization and mutation analysis of human ATP:Cob(I)alamin adenosyltransferase
S-adenosylmethionine synthesis: molecular mechanisms and clinical implications
Hereditary orotic aciduria and other disorders of pyrimidine metabolism
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 2663-2704
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Localization of GAR transformylase in Escherichia coli and mammalian cells
Metabolism of alpha-linolenic acid in humans
Prostaglandins Leukot Essent Fatty Acids 75:161-8
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Trk receptors: roles in neuronal signal transduction
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Diacylglycerol metabolism and arachidonic acid release in human fetal membranes and decidua vera
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The oxidation of pyruvate in pigeon breast muscle
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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 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'.
Elastic fibres (EF) are a major structural constituent of dynamic connective tissues such as large arteries and lung parenchyma, where they provide essential properties of elastic recoil and resilience. EF are composed of a central cross-linked core of elastin, surrounded by a mesh of microfibrils, which are composed largely of fibrillin. In addition to elastin and fibrillin-1, over 30 ancillary proteins are involved in mediating important roles in elastic fibre assembly as well as interactions with the surrounding environment. These include fibulins, elastin microfibril interface located proteins (EMILINs), microfibril-associated glycoproteins (MAGPs) and Latent TGF-beta binding proteins (LTBPs). Fibulin-5 for example, is expressed by vascular smooth muscle cells and plays an essential role in the formation of elastic fibres through mediating interactions between elastin and fibrillin (Yanigasawa et al. 2002, Freeman et al. 2005). In addition, it plays a role in cell adhesion through integrin receptors and has been shown to influence smooth muscle cell proliferation (Yanigasawa et al. 2002, Nakamura et al. 2002). EMILINs are a family of homologous glycoproteins originally identified in extracts of aortas. Found at the elastin-fibrillin interface, early studies showed that antibodies to EMILIN can affect the process of elastic fibre formation (Bressan et al. 1993). EMILIN1 has been shown to bind elastin and fibulin-5 and appears to coordinate their common interaction (Zanetti et al. 2004). MAGPs are found to co-localize with microfibrils. MAGP-1, for example, binds strongly to an N-terminal sequence of fibrillin-1. Other proteins found associated with microfibrils include vitronectin (Dahlback et al. 1990). Fibrillin is most familiar as a component of elastic fibres but microfibrils with no elastin are found in the ciliary zonules of the eye and invertebrate circulatory systems. The addition of elastin to microfibrils is a vertebrate adaptation to high pulsatile pressures in their closed circulatory systems (Faury et al. 2003). Elastin appears to have emerged after the divergence of jawless vertebrates from other vertebrates (Sage 1982). Fibrillin-1 is the major structural component of microfibrils. Fibrillin-2 is expressed earlier in development than fibrillin-1 and may be important for elastic fiber formation (Zhang et al. 1994). Fibrillin-3 arose as a duplication of fibrillin-2 that did not occur in the rodent lineage. It was first isolated from human brain (Corson et al. 2004). Fibrillin assembly is not as well defined as elastin assembly. The primary structure of fibrillin is dominated by calcium binding epidermal growth factor like repeats (Kielty et al. 2002). Fibrillin may form dimers or trimers before secretion. However, multimerisation predominantly occurs outside the cell. Formation of fibrils appears to require cell surface structures suggesting an involvement of cell surface receptors. Fibrillin is assembled pericellularly (i.e. on or close to the cell surface) into microfibrillar arrays that undergo time dependent maturation into microfibrils with beaded-string appearance. Transglutaminase forms gamma glutamyl epsilon lysine isopeptide bonds within or between peptide chains. Additionally, intermolecular disulfide bond formation between fibrillins is an important contributor to fibril maturation (Reinhardt et al. 2000). Models of fibrillin-1 microfibril structure suggest that the N-terminal half of fibrillin-1 is asymmetrically exposed in outer filaments, while the C-terminal half is buried in the interior (Kuo et al. 2007). Fibrillinopathies include Marfan syndrome, familial ectopia lentis, familial thoracic aneurysm, all due to mutations in the fibrillin-1 gene FBN1, and congenital contractural arachnodactyly which is caused by mutation of FBN2 (Maslen & Glanville 1993, Davis & Summers 2012). In vivo assembly of fibrillin requires the presence of extracellular fibronectin fibres (Sabatier et al. 2009). Fibrillins have Arg-Gly-Asp (RGD) sequences that interact with integrins (Pfaff et al. 1996, Sakamoto et al. 1996, Bax et al., 2003, Jovanovic et al. 2008) and heparin-binding domains that interact with a cell-surface heparan sulfate proteoglycan (Tiedemann et al. 2001) possibly a syndecan (Ritty et al. 2003). Fibrillins also have a major role in binding and sequestering growth factors such as TGF beta into the ECM (Neptune et al. 2003). Proteoglycans such as versican (Isogai et al. 2002), biglycan, and decorin (Reinboth et al. 2002) can interact with the microfibrils. They confer specific properties including hydration, impact absorption, molecular sieving, regulation of cellular activities, mediation of growth factor association, and release and transport within the extracellular matrix (Buczek-Thomas et al. 2002). In addition, glycosaminoglycans have been shown to interact with tropoelastin through its lysine side chains (Wu et al. 1999), regulating tropoelastin assembly (Tu & Weiss 2008). Elastin is synthesized as a 70kDa monomer called tropoelastin, a highly hydrophobic protein composed largely of two types of domains that alternate along the polypeptide chain. Hydrophobic domains are rich in glycine, proline, alanine, leucine and valine. These amino acids occur in characteristic short (3-9 amino acids) tandem repeats, with a flexible and highly dynamic structure (Floquet et al. 2004). Unlike collagen, glycine in elastin is not rigorously positioned every 3 residues. However, glycine is distributed frequently throughout all hydrophobic domains of elastin, and displays a strong preference for inter-glycine spacing of 0-3 residues (Rauscher et al. 2006). Elastic fibre formation involves the deposition of tropoelastin onto a template of fibrillin rich microfibrils. Recent results suggest that the first step of elastic fiber formation is the organization of small globules of elastin on the cell surface followed by globule aggregation into microfibres (Kozel et al. 2006). An important contribution to the initial stages assembly is thought to be made by the intrinsic ability of the protein to direct its own polymeric organization in a process termed 'coacervation' (Bressan et al. 1986). This self-assembly process appears to be determined by interactions between hydrophobic domains (Bressan et al. 1986, Vrhovski et al. 1997, Bellingham et al. 2003, Cirulis & Keeley 2010) which result in alignment of the cross-linking domains, allowing the stabilization of elastin through the formation of cross-links generated through the oxidative deamination of lysine residues, catalyzed by members of the lysyl oxidase (LOX) family (Reiser et al. 1992, Mithieux & Weiss 2005). The first step in the cross-linking reaction is the oxidative formation of the delta aldehyde, known as alpha aminoadipic semialdehyde or allysine (Partridge 1963). Subsequent reactions that are probably spontaneous lead to the formation of cross-links through dehydrolysinonorleucine and allysine aldol, a trifunctional cross-link dehydromerodesmosine and two tetrafunctional cross-links desmosine and isodesmosine (Lucero & Kagan 2006), which are unique to elastin. These cross-links confer mechanical integrity and high durability. In addition to their role in self-assembly, hydrophobic domains provide elastin with its elastomeric properties, with initial studies suggesting that the elastomeric propereties of elastin are driven through changes in entropic interactions with surrounding water molecules (Hoeve & Flory 1974). A very specific set of proteases, broadly grouped under the name elastases, is responsible for elastin remodelling (Antonicelli et al. 2007). The matrix metalloproteinases (MMPs) are particularly important in elastin breakdown, with MMP2, 3, 9 and 12 explicitly shown to degrade elastin (Ra & Parks 2007). Nonetheless, elastin typically displays a low turnover rate under normal conditions over a lifetime (Davis 1993).
Collagens type XV and XVIII are closely related non-fibrillar collagens that define the multiplexin (multiple triple helix domains with interruptions) subfamily of collagens. Both are homotrimers characterized by highly interrupted collagenous domains flanked by large globular domains with attached glycosaminoglycan chains. Collagen XV is localized in the outermost layer of the basement membrane (BM) and in the fibrillar matrix. Collagen type XV is the only collagen able to self-assemble into higher-order cruciform structures with intermolecular binding sites (Myers et al. 2007). The interaction is mediated by interactions between triple helical regions (Hurskainen et al. 2010). It is predominantly located in the basement membranes of microvessels, and cardiac and skeletal myocytes (Hägg et al. 1997), where it binds basement membrane and microfibrillar components such as fibulin-2, nidogen-2, vitronectin, laminin, and fibronectin (Sasaki et al. 2000, Hurskainen et al. 2010). It may form a bridge between fibrillar collagens and the basement membrane (Amenta et al. 2005), acting as a molecular shock absorber to stabilize and enhance resilience to compressive and expansive forces (Myers et al. 2007). Lack of Collagen type XV in Col15a1-null mice resulted in increased permeability and impaired microvascular hemodynamics, distinct early-onset and age-dependent defects in heart structure and function, a poorly organized fibrillar collagen matrix with marked interstitial deposition of nonfibrillar protein aggregates, increased tissue stiffness, and irregularly organized cardiomyocytes (Rasi et al. 2010a). Col15a1 knockout also leads to loosely packed axons in C-fibers and polyaxonal myelination. Simultaneous knockout with laminin alpha-4 leads to severely impaired radial sorting and myelination (Rasi et al. 2010b). The C-terminal non-collagenous region of collagen type XV is known as restin because it resembles endostatin, having antiangiogenic effects (Ramchandran et al. 1999, Sasaki et al. 2000).
Collagen is a family of at least 29 structural proteins derived from over 40 human genes (Myllyharju & Kivirikko 2004). It is the main component of connective tissue, and the most abundant protein in mammals making up about 25% to 35% of whole-body protein content. A defining feature of collagens is the formation of trimeric left-handed polyproline II-type helical collagenous regions. The packing within these regions is made possible by the presence of the smallest amino acid, glycine, at every third residue, resulting in a repeating motif Gly-X-Y where X is often proline (Pro) and Y often 4-hydroxyproline (4Hyp). Gly-Pro-Hyp is the most common triplet in collagen (Ramshaw et al. 1998). Collagen peptide chains also have non-collagenous domains, with collagen subclasses having common chain structures. Collagen fibrils are mostly found in fibrous tissues such as tendon, ligament and skin. Other forms of collagen are abundant in cornea, cartilage, bone, blood vessels, the gut, and intervertebral disc. In muscle tissue, collagen is a major component of the endomysium, constituting up to 6% of muscle mass. Gelatin, used in food and industry, is collagen that has been irreversibly hydrolyzed. On the basis of their fibre architecture in tissues, the genetically distinct collagens have been divided into subgroups. Group 1 collagens have uninterrupted triple-helical domains of about 300 nm, forming large extracellular fibrils. They are referred to as the fibril-forming collagens, consisting of collagens types I, II, III, V, XI, XXIV and XXVII. Group 2 collagens are types IV and VII, which have extended triple helices (>350 nm) with imperfections in the Gly-X-Y repeat sequences. Group 3 are the short-chain collagens. These have two subgroups. Group 3A have continuous triple-helical domains (type VI, VIII and X). Group 3B have interrupted triple-helical domains, referred to as the fibril-associated collagens with interrupted triple helices (FACIT collagens, Shaw & Olsen 1991). FACITs include collagen IX, XII, XIV, XVI, XIX, XX, XXI, XXII and XXVI plus the transmembrane collagens (XIII, XVII, XXIII and XXV) and the multiple triple helix domains and interruptions (Multiplexin) collagens XV and XVIII (Myllyharju & Kivirikko 2004). The non-collagenous domains of collagens have regulatory functions; several are biologically active when cleaved from the main peptide chain. Fibrillar collagen peptides all have a large triple helical domain (COL1) bordered by N and C terminal extensions, called the N- and C-propeptides, which are cleaved prior to formation of the collagen fibril. The intact form is referred to as a collagen propeptide, not procollagen, which is used to refer to the trimeric triple-helical precursor of collagen before the propeptides are removed. The C-propeptide, also called the NC1 domain, directs chain association during assembly of the procollagen molecule from its three constituent alpha chains (Hulmes 2002). Fibril forming collagens are the most familiar and best studied subgroup. Collagen fibres are aggregates or bundles of collagen fibrils, which are themselves polymers of tropocollagen complexes, each consisting of three polypeptide chains known as alpha chains. Tropocollagens are considered the subunit of larger collagen structures. They are approximately 300 nm long and 1.5 nm in diameter, with a left-handed triple-helical structure, which becomes twisted into a right-handed coiled-coil 'super helix' in the collagen fibril. Tropocollagens in the extracellular space polymerize spontaneously with regularly staggered ends (Hulmes 2002). In fibrillar collagens the molecules are staggered by about 67 nm, a unit known as D that changes depending upon the hydration state. Each D-period contains slightly more than four collagen molecules so that every D-period repeat of the microfibril has a region containing five molecules in cross-section, called the 'overlap', and a region containing only four molecules, called the 'gap'. The triple-helices are arranged in a hexagonal or quasi-hexagonal array in cross-section, in both the gap and overlap regions (Orgel et al. 2006). Collagen molecules cross-link covalently to each other via lysine and hydroxylysine side chains. These cross-links are unusual, occuring only in collagen and elastin, a related protein. The macromolecular structures of collagen are diverse. Several group 3 collagens associate with larger collagen fibers, serving as molecular bridges which stabilize the organization of the extracellular matrix. Type IV collagen is arranged in an interlacing network within the dermal-epidermal junction and vascular basement membranes. Type VI collagen forms distinct microfibrils called beaded filaments. Type VII collagen forms anchoring fibrils. Type VIII and X collagens form hexagonal networks. Type XVII collagen is a component of hemidesmosomes where it is complexed wtih alpha6Beta4 integrin, plectin, and laminin-332 (de Pereda et al. 2009). Type XXIX collagen has been recently reported to be a putative epidermal collagen with highest expression in suprabasal layers (Soderhall et al. 2007). Collagen fibrils/aggregates arranged in varying combinations and concentrations in different tissues provide specific tissue properties. In bone, collagen triple helices lie in a parallel, staggered array with 40 nm gaps between the ends of the tropocollagen subunits, which probably serve as nucleation sites for the deposition of crystals of the mineral component, hydroxyapatite (Ca10(PO4)6(OH)2) with some phosphate. Collagen structure affects cell-cell and cell-matrix communication, tissue construction in growth and repair, and is changed in development and disease (Sweeney et al. 2006, Twardowski et al. 2007). A single collagen fibril can be heterogeneous along its axis, with significantly different mechanical properties in the gap and overlap regions, correlating with the different molecular organizations in these regions (Minary-Jolandan & Yu 2009).
The core protein representing ~90% of the mass of elastic fibres is elastin, a highly insoluble protein. It is secreted as soluble protein monomers referred to as tropoelastin, which have alternating hydrophobic and cross linking domains. The self-assembly of tropoelastin into a fibrillar elastin matrix is a multi step process. The first step is the self-association of secreted monomers via hydrophobic domains, in a process known as coacervation. This process concentrates monomers and may align residues in the correct register for subsequent cross linking (Yeo et al. 2011). Under physiological conditions the ~15 nm monomers phase-separate and coalesce into spherical packages 2-6 micrometers in diameter (Clarke et al. 2006, Kozel et al. 2004). This process is represented here by the association of an arbitrary 10 tropoelastin monomers. While they grow, coacervate packages are tethered to the cell surface (Wise & Weiss 2009). The binding interactions between tropoelastin and the cell surface are not fully understood but possible partners include integrins and glycosaminoglycans (Broekelmann et al. 2005). Extracellular fibrillin microfibrils act as a scaffold for the deposition of tropoelastin globules as part of elastic fibre formation (Kozel et al. 2004).
The extracellular matrix is a component of all mammalian tissues, a network consisting largely of the fibrous proteins collagen, elastin and associated-microfibrils, fibronectin and laminins embedded in a viscoelastic gel of anionic proteoglycan polymers. It performs many functions in addition to its structural role; as a major component of the cellular microenvironment it influences cell behaviours such as proliferation, adhesion and migration, and regulates cell differentiation and death (Hynes 2009). ECM composition is highly heterogeneous and dynamic, being constantly remodeled (Frantz et al. 2010) and modulated, largely by matrix metalloproteinases (MMPs) and growth factors that bind to the ECM influencing the synthesis, crosslinking and degradation of ECM components (Hynes 2009). ECM remodeling is involved in the regulation of cell differentiation processes such as the establishment and maintenance of stem cell niches, branching morphogenesis, angiogenesis, bone remodeling, and wound repair. Redundant mechanisms modulate the expression and function of ECM modifying enzymes. Abnormal ECM dynamics can lead to deregulated cell proliferation and invasion, failure of cell death, and loss of cell differentiation, resulting in congenital defects and pathological processes including tissue fibrosis and cancer. Collagen is the most abundant fibrous protein within the ECM constituting up to 30% of total protein in multicellular animals. Collagen provides tensile strength. It associates with elastic fibres, composed of elastin and fibrillin microfibrils, which give tissues the ability to recover after stretching. Other ECM proteins such as fibronectin, laminins, and matricellular proteins participate as connectors or linking proteins (Daley et al. 2008). Chondroitin sulfate, dermatan sulfate and keratan sulfate proteoglycans are structural components associated with collagen fibrils (Scott & Haigh 1985; Scott & Orford 1981), serving to tether the fibril to the surrounding matrix. Decorin belongs to the small leucine-rich repeat proteoglycan family (SLRPs) which also includes biglycan, fibromodulin, lumican and asporin. All appear to be involved in collagen fibril formation and matrix assembly (Ameye & Young 2002). ECM proteins such as osteonectin (SPARC), osteopontin and thrombospondins -1 and -2, collectively referred to as matricellular proteins (reviewed in Mosher & Adams 2012) appear to modulate cell-matrix interactions. In general they induce de-adhesion, characterized by disruption of focal adhesions and a reorganization of actin stress fibers (Bornstein 2009). Thrombospondin (TS)-1 and -2 bind MMP2. The resulting complex is endocytosed by the low-density lipoprotein receptor-related protein (LRP), clearing MMP2 from the ECM (Yang et al. 2001). Osteopontin (SPP1, bone sialoprotein-1) interacts with collagen and fibronectin (Mukherjee et al. 1995). It also contains several cell adhesive domains that interact with integrins and CD44. Aggrecan is the predominant ECM proteoglycan in cartilage (Hardingham & Fosang 1992). Its relatives include versican, neurocan and brevican (Iozzo 1998). In articular cartilage the major non-fibrous macromolecules are aggrecan, hyaluronan and hyaluronan and proteoglycan link protein 1 (HAPLN1). The high negative charge density of these molecules leads to the binding of large amounts of water (Bruckner 2006). Hyaluronan is bound by several large proteoglycans proteoglycans belonging to the hyalectan family that form high-molecular weight aggregates (Roughley 2006), accounting for the turgid nature of cartilage. The most significant enzymes in ECM remodeling are the Matrix Metalloproteinase (MMP) and A disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS) families (Cawston & Young 2010). Other notable ECM degrading enzymes include plasmin and cathepsin G. Many ECM proteinases are initially present as precursors, activated by proteolytic processing. MMP precursors include an amino prodomain which masks the catalytic Zn-binding motif (Page-McCawet al. 2007). This can be removed by other proteinases, often other MMPs. ECM proteinases can be inactivated by degradation, or blocked by inhibitors. Some of these inhibitors, including alpha2-macroglobulin, alpha1-proteinase inhibitor, and alpha1-chymotrypsin can inhibit a large variety of proteinases (Woessner & Nagase 2000). The tissue inhibitors of metalloproteinases (TIMPs) are potent MMP inhibitors (Brew & Nagase 2010).
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'.
Collagen fibril diameter and spatial organisation are dependent on the species, tissue type and stage of development (Parry 1988). The lengths of collagen fibrils in mature tissues are largely unknown but in tendon can be measured in millimetres (Craig et al. 1989). Collagen fibrils isolated from adult bovine corneal stroma had ~350 collagen molecules in transverse section, tapering down to three molecules at the growing tip (Holmes & Kadler 2005). The classical view of collagenases is that they actively unwind the triple helical chain, a process termed molecular tectonics (Overall 2002, Bode & Maskos 2003), before preferentially cleaving the alpha2 chain followed by the remaining chains (Chung et al. 2004). More recently it has been suggested that collagen fibrils exist in an equilibrium between protected and vulnerable states (Stultz 2002, Nerenberg & Stultz 2008). The prototypical triple-helical structure of collagen does not fit into the active site of collagenase MMPs. In addition the scissile bonds are not solvent-exposed and are therefore inaccessible to the collagenase active site (Chung et al. 2004, Stultz 2002). It was realized that collagen must locally unfold into non-triple helical regions to allow collagenolysis. Observations using circular dichroism and differential scanning calorimetry confirm that there is considerable heterogeneity along collagen fibres (Makareeva et al. 2008) allowing access for MMPs at physiological temperatures (Salsas-Escat et al. 2010). Collagen fibrils with cut chains are unstable and accessible to proteinases that cannot cleave intact collagen strands (Woessner & Nagase 2000, Somerville et al. 2003). Continued degradation leads to the formation of gelatin (Lovejoy et al. 1999). Degradation of collagen types other than I-III is less well characterized but believed to occur in a similar manner. Metalloproteinases (MMPs) play a major part in the degradation of several extracellular macromolecules including collagens. MMP1 (Welgus et al. 1981), MMP8 (Hasty et al. 1987), and MMP13 (Knauper et al. 1996), sometimes referred to as collagenases I, II and III respectively, are able to initiate the intrahelical cleavage of the major fibril forming collagens I, II and III at neutral pH, and thus thought to define the rate-limiting step in normal tissue remodeling events. All can cleave additional substrates including other collagen subtypes. Collagenases cut collagen alpha chains at a single conserved Gly-Ile/Leu site approximately 3/4 of the molecule's length from the N-terminus (Fields 1991, Chung et al. 2004). The cleavage site is characterised by the motif G(I/L)(A/L); the G-I/L bond is cleaved. In collagen type I this corresponds to G953-I954 in the Uniprot canonical alpha chain sequences (often given as G775-I776 in literature). It is not clear why only this bond is cleaved, as the motif occurs at several other places in the chain. MMP14, a membrane-associated MMP also known as Membrane-type matrix metalloproteinase 1 (MT-MMP1), is able to cleave collagen types I, II and III (Ohuchi et al. 1997).
Matrix metalloproteinases (MMPs), previously referred to as matrixins because of their role in degradation of the extracellular matrix (ECM), are zinc and calcium dependent proteases belonging to the metzincin family. They contain a characteristic zinc-binding motif HEXXHXXGXXH (Stocker & Bode 1995) and a conserved Methionine which forms a Met-turn. Humans have 24 MMP genes giving rise to 23 MMP proteins, as MMP23 is encoded by two identical genes. All MMPs contain an N-terminal secretory signal peptide and a prodomain with a conserved PRCGXPD motif that in the inactive enzyme is localized with the catalytic site, the cysteine acting as a fourth unpaired ligand for the catalytic zinc atom. Activation involves delocalization of the domain containing this cysteine by a conformational change or proteolytic cleavage, a mechanism referred to as the cysteine-switch (Van Wart & Birkedal-Hansen 1990). Most MMPs are secreted but the membrane type MT-MMPs are membrane anchored and some MMPs may act on intracellular proteins. Various domains determine substrate specificity, cell localization and activation (Hadler-Olsen et al. 2011). MMPs are regulated by transcription, cellular location (most are not activated until secreted), activating proteinases that can be other MMPs, and by metalloproteinase inhibitors such as the tissue inhibitors of metalloproteinases (TIMPs). MMPs are best known for their role in the degradation and removal of ECM molecules. In addition, cleavage of the ECM and other cell surface molecules can release ECM-bound growth factors, and a number of non-ECM proteins are substrates of MMPs (Nagase et al. 2006). MMPs can be divided into subgroups based on domain structure and substrate specificity but it is clear that these are somewhat artificial, many MMPs belong to more than one functional group (Vise & Nagase 2003, Somerville et al. 2003).
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Identification of cross-linking sites in bovine cartilage type IX collagen reveals an antiparallel type II-type IX molecular relationship and type IX to type IX bonding
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Collagen VII forms anchoring fibrils, composed of antiparallel dimers that connect the dermis to the epidermis (Bruckner-Tuderman 2009, Has & Kern 2010). During fibrillogenesis, the nascent type VII procollagen molecules dimerize in an antiparallel manner. The C-propeptide is then removed by Bone morphogenetic protein 1 (Rattenholl et al. 2002) and the processed antiparallel dimers laterally aggregate (Villone et al. 2008, Gordon & Hahn 2010).
Collagen VII forms anchoring fibrils, composed of antiparallel dimers that connect the dermis to the epidermis (Bruckner-Tuderman 2009). During fibrillogenesis, the nascent type VII procollagen molecules dimerize in an antiparallel manner. The C-propeptides are then removed by bone morphogenetic protein 1 (Rattenholl et al. 2002) and the processed antiparallel dimers laterally aggregate (Gordon & Hahn 2010).
Collagen trimers in triple-helical form, referred to as procollagen or collagen molecules, are exported from the ER and trafficked through the Golgi network before secretion into the extracellular space. For fibrillar collagens namely types I, II, III, V, XI, XXIV and XXVII (Gordon & Hahn 2010, Ricard-Blum 2011) secretion is concomitant with processing of the N and C terminal collagen propeptides. These processed molecules are known as tropocollagens, considered to be the units of higher order collagen structures. They form within the extracellular space via a process that can proceed spontaneously, but in the cellular environment is regulated by many collagen binding proteins such as the FACIT (Fibril Associated Collagens with Interrupted Triple helices) family collagens and Small Leucine-Rich Proteoglycans (SLRPs). The architecture formed ultimately depends on the collagen subtype and the cellular conditions. Structures include the well-known fibrils and fibres formed by the major structural collagens type I and II plus several different types of supramolecular assembly (Bruckner 2010). The mechanical and physical properties of tissues depend on the spatial arrangement and composition of these collagen-containing structures (Kadler et al. 1996, Shoulders & Raines 2009, Birk & Bruckner 2011). Fibrillar collagen structures are frequently heterotypic, composed of a major collagen type in association with smaller amounts of other types, e.g. type I collagen fibrils are associated with types III and V, while type II fibrils frequently contain types IX and XI (Wess 2005). Fibres composed exclusively of a single collagen type probably do not exist, as type I and II fibrils require collagens V and XI respectively as nucleators (Kadler et al. 2008, Wenstrup et al. 2011). Much of the structural understanding of collagen fibrils has been obtained with fibril-forming collagens, particularly type I, but some central features are believed to apply to at least the other fibrillar collagen subtypes (Wess 2005). Fibril diameter and length varies considerably, depending on the tissue and collagen types (Fang et al. 2012). The reasons for this are poorly understood (Wess 2005). Some tissues such as skin have fibres that are approximately the same diameter while others such as tendon or cartilage have a bimodal distribution of thick and thin fibrils. Mature type I collagen fibrils in tendon are up to 1 cm in length, with a diameter of approx. 500 nm. An individual fibrillar collagen triple helix is less than 1.5 nm in diameter and around 300 nm long; collagen molecules must assemble to give rise to the higher-order fibril structure, a process known as fibrillogenesis, prevented by the presence of C-terminal propeptides (Kadler et al. 1987). In electron micrographs, fibrils have a banded appearance, due to regular gaps where fewer collagen molecules overlap, which occur because the fibrils are aligned in a quarter-stagger arrangement (Hodge & Petruska 1963). Collagen microfibrils are believed to have a quasi-hexagonal unit cell, with tropocollagen arranged to form supertwisted, right-handed microfibrils that interdigitate with neighbouring microfibrils, leading to a spiral-like structure for the mature collagen fibril (Orgel et al. 2006, Holmes & Kadler 2006). Neighbouring tropocollagen monomers interact with each other and are cross-linked covalently by lysyl oxidase (Orgel et al. 2000, Mäki 2006). Mature collagen fibrils are stabilized by lysyl oxidase-mediated cross-links. Hydroxylysyl pyridinoline and lysyl pyridinoline cross-links form between (hydroxy) lysine and hydroxylysine residues in bone and cartilage (Eyre et al. 1984). Arginoline cross-links can form in cartilage (Eyre et al. 2010); mature bovine articular cartilage contains roughly equimolar amounts of arginoline and hydroxylysyl pyridinoline based on peptide yields. Mature collagen fibrils in skin are stabilized by the lysyl oxidase-mediated cross-link histidinohydroxylysinonorleucine (Yamauch et al. 1987). Due to the quarter-staggered arrangement of collagen molecules in a fibril, telopeptides most often interact with the triple helix of a neighbouring collagen molecule in the fibril, except for collagen molecules in register staggered by 4D from another collagen molecule. Fibril aggregation in vitro can be unipolar or bipolar, influenced by temperature and levels of C-proteinase, suggesting a role for the N- and C- propeptides in regulation of the aggregation process (Kadler et al. 1996). In vivo, collagen molecules at the fibril surface may retain their N-propeptides, suggesting that this may limit further accretion, or alternatively represents a transient stage in a model whereby fibrils grow in diameter through a cycle of deposition, cleavage and further deposition (Chapman 1989). In vivo, fibrils are often composed from more than one type of collagen. Type III collagen is found associated with type I collagen in dermal fibrils, with the collagen III on the periphery, suggesting a regulatory role (Fleischmajer et al. 1990). Type V collagen associates with type I collagen fibrils, where it may limit fibril diameter (Birk et al. 1990, White et al. 1997). Type IX associates with the surface of narrow diameter collagen II fibrils in cartilage and the cornea (Wu et al. 1992, Eyre et al. 2004). Highly specific patterns of crosslinking sites suggest that collagen IX functions in interfibrillar networking (Wess 2005). Type XII and XIV collagens are localized near the surface of banded collagen I fibrils (Nishiyama et al. 1994). Certain fibril-associated collagens with interrupted triple helices (FACITs) associate with the surface of collagen fibrils, where they may serve to limit fibril fusion and thereby regulate fibril diameter (Gordon & Hahn 2010). Collagen XV, a member of the multiplexin family, is almost exclusively associated with the fibrillar collagen network, in very close proximity to the basement membrane. In human tissues collagen XV is seen linking banded collagen fibers subjacent to the basement membrane (Amenta et al. 2005). Type XIV collagen, SLRPs and discoidin domain receptors also regulate fibrillogenesis (Ansorge et al. 2009, Kalamajski et al. 2010, Flynn et al. 2010). Collagen IX is cross-linked to the surface of collagen type II fibrils (Eyre et al. 1987). Type XII and XIV collagens are found in association with type I (Walchli et al. 1994) and type II (Watt et al. 1992, Eyre 2002) fibrils in cartilage. They are thought to associate non-covalently via their COL1/NC1 domains (Watt et al. 1992, Eyre 2002). Some non-fibrillar collagens form supramolecular assemblies that are distinct from typical fibrils. Collagen VII forms anchoring fibrils, composed of antiparallel dimers that connect the dermis to the epidermis (Bruckner-Tuderman 2009). During fibrillogenesis, the nascent type VII procollagen molecules dimerize in an antiparallel manner. The C-propeptides are then removed by Bone morphogenetic protein 1 (Rattenholl et al. 2002) and the processed antiparallel dimers aggregate laterally. Collagens VIII and X form hexagonal networks and collagen VI forms beaded filament (Gordon & Hahn 2010, Ricard-Blum et al. 2011).
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.
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.
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.
The C-propeptides are essential for the association of three alpha chains into a trimeric non-helical procollagen. Alignment determines the composition of the trimer, brings the individual chains into the correct register and initiates formation of the triple helix at the C-terminus, which then proceeds to the N-terminus in a zipper-like fashion (Engel & Prockop 1991). Most early refolding studies were performed with collagen type III which contains a disulfide linkage at the C-terminus of its triple helix (Bächinger et al. 1978, Bruckner et al. 1978) that acts as a permanent linker even after removal of the non-collagenous domains. Mutations within the C-propeptides further suggest that they are crucial for the correct interaction of the three polypeptide chains and for subsequent correct folding (refs. in Boudko et al. 2011).
Secretion of transmembrane collagens is presumably similar to the secretion of extracellular forms except that they are trafficked to the plasma membrane rather than the extracellular space.
The biosynthesis of collagen is a multistep process. Collagen propeptides are cotranslationally translocated into the ER lumen. Propeptides undergo a number of post-translational modifications. Proline and lysine residues may be hydroxylated by prolyl 3-, prolyl 4- and lysyl hydroxylases. 4-hydroxyproline is essential for intramolecular hydrogen bonding and stability of the triple helical collagenous domain. In fibril forming collagens approximately 50% of prolines are 4-hydroxylated; the extent of this and of 3-hydroxyproline and lysine hydroxylation varies between tissues and collagen types (Kivirikko et al. 1972, 1992). Hydroxylysine molecules can form cross-links between collagen molecules in fibrils, and are sites for glycosyl- and galactosylation. Collagen peptides all have non-collagenous domains; collagens within the subclasses have common chain structures. These non-collagenous domains have regulatory functions; some are biologically active when cleaved from the main peptide chain. Fibrillar collagens all have a large triple helical domain (COL1) bordered by N and C terminal extensions, called the N and C propeptides, which are cleaved prior to formation of the collagen fibril. The C propeptide, also called the NC1 domain, is highly conserved. It directs chain association during intracellular assembly of the procollagen molecule from three collagen propeptide alpha chains (Hulmes 2002). The N-propeptide has a short linker (NC2) connecting the main triple helix to a short minor one (COL2) and a globular N-terminal region NC3. NC3 domains are variable both in size and the domains they contain. Collagen propeptides typically undergo a number of post-translational modifications. Proline and lysine residues are hydroxylated by prolyl 3-, prolyl 4- and lysyl hydroxylases. 4-hydroxyproline is essential for intramolecular hydrogen bonding and stability of the triple helical collagenous domain. Prolyl 4-hydroxylase may also have a role in alpha chain association as no association of the C-propeptides of type XII collagen was seen in the presence of prolyl 4-hydroxylase inhibitors (Mazzorana et al. 1993, 1996). In fibril forming collagens approximately 50% of prolines are 4-hydroxylated; the extent of this is species dependent, lower hydroxylation correlating with lower ambient temperature and thermal stability (Cohen-Solal et al. 1986, Notbohm et al. 1992). Similarly the extent of 3-hydroxyproline and lysine hydroxylation varies between tissues and collagen types (Kivirikko et al. 1992). Hydroxylysine molecules can form cross-links between collagen molecules in fibrils, and are sites for glycosyl- and galactosylation. Collagen molecules fold and assemble through a series of distinct intermediates (Bulleid 1996). Individual collagen polypeptide chains are translocated co-translationally across the membrane of the endoplasmic reticulum (ER). Intra-chain disulfide bonds are formed within the N-propeptide, and hydroxylation of proline and lysine residues occurs within the triple helical domain (Kivirikko et al. 1992). When the peptide chain is fully translocated into the ER lumen the C-propeptide folds, the conformation being stabilized by intra-chain disulfide bonds (Doege and Fessler 1986). Pro alpha-chains associate via the C-propeptides (Byers et al. 1975, Bächinger et al. 1978), or NC2 domains for FACIT family collagens (Boudko et al. 2008) to form an initial trimer which can be stabilized by the formation of inter-chain disulfide bonds (Schofield et al. 1974, Olsen et al. 1976), though these are not a prerequisite for further folding (Bulleid et al. 1996). The triple helix then nucleates and folds in a C- to N- direction. The association of the individual chains and subsequent triple helix formation are distinct steps (Bächinger et al. 1980). The N-propeptides associate and in some cases form inter-chain disulfide bonds (Bruckner et al., 1978). Procollagen is released via carriers into the exracellular space (Canty & Kadler 2005). Fibrillar procollagens undergo removal of the C- and N-propeptides by procollagen C and N proteinases respectively, both Zn2+ dependent metalloproteinases. Propeptide processing is a required step for normal collagen I and III fibril formation, but collagens can retain some or all of their non-collagenous propeptides. Retained collagen type V and XI N-propeptides contribute to the control of fibril growth by sterically limiting lateral molecule addition (Fichard et al. 1995). Processed fibrillar procollagen is termed tropocollagen, which is considered to be the unit of higher order fibrils and fibres. Tropocollagens of the fibril forming collagens I, II, III, V and XI sponteneously aggregate in vitro in a manner that has been compared with crystallization, commencing with a nucleation event followed by subsequent organized aggregation (Silver et al. 1992, Prockop & Fertala 1998). Fibril formation is stabilized by lysyl oxidase catalyzed crosslinks between adjacent molecules (Siegel & Fu 1976).
Collagen VII triple-helices form an anti-parallel dimer, associating through disulfide bonds formed in a 60-nm overlap (NC2 domain) of the amino terminal triple helical ends. A portion of this region is proteolytically removed (Morris et al. 1986, Chen et al. 2001) prior to aggregation of dimers into anchoring fibrils (Lundstrum et al. 1986).
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Mitochondrial tRNA synthetases act in the mitochondrial matrix to catalyze the reactions of tRNAs encoded in the mitochondrial genome, their cognate amino acids, and ATP to form aminoacyl-tRNAs, AMP, and pyrophosphate (Schneider et al. 2000). The synthetase enzymes that catalyze these reactions are all encoded in the nuclear genome. In three cases, glycine, lysine, and glutamine, a single gene encodes two enzyme isoforms, one cytosolic and one mitochondrial. All other mitochondrial tRNA synthetases are encoded by genes different from the ones encoding the corresponding cytosolic enzymes.
VARS2 (mitochondrial valyl tRNA synthetase) catalyzes the reaction of valine, mitochondrial tRNA(val), and ATP to form Val-tRNA(Val), AMP, and pyrophosphate. The VARS2 gene has been identified by computational analysis of the human genome sequence; its function has been inferred from those of the biochemically characterized mitochondrial aspartyl and tyrosyl tRNA synthetases (Bonnefond et al. 2005).
YARS2 (mitochondrial tyrosyl tRNA synthetase) catalyzes the reaction of tyrosine, mitochondrial tRNA(Tyr), and ATP to form Tyr-tRNA(Tyr), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is a homodimer (Bonnefond et al. 2005).
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).
PARS2 (mitochondrial prolyl tRNA synthetase) catalyzes the reaction of proline, mitochondrial tRNA(Pro), and ATP to form Pro-tRNA(Pro), AMP, and pyrophosphate. The PARS2 gene has been identified by computational analysis of the human genome sequence; its function has been inferred from those of the biochemically characterized mitochondrial aspartyl and tyrosyl tRNA synthetases (Bonnefond et al. 2005).
SARS2 (mitochondrial seryl tRNA synthetase) catalyzes the reaction of serine, mitochondrial tRNA(Ser), and ATP to form Ser-tRNA(Ser), AMP, and pyrophosphate. SARS2 is a class II tRNA synthetase inferred from the biochemical properties of its bovine homologue to function as a dimer (Yokogawa et al. 2000).
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).
Structural insights into catalysis and inhibition of O-acetylserine sulfhydrylase from Mycobacterium tuberculosis. Crystal structures of the enzyme alpha-aminoacrylate intermediate and an enzyme-inhibitor complex
LARS2 (mitochondrial leucyl tRNA synthetase) catalyzes the reaction of leucine, mitochondrial tRNA(Leu), and ATP to form Leu-tRNA(Leu), AMP, and pyrophosphate. The enzyme, a class I tRNA synthetase, is a monomer (Bullard et al. 2000).
KARS (mitochondrial lysyl tRNA synthetase) catalyzes the reaction of lysine, tRNA(Lys), and ATP to form Lys-tRNA(Lys), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a homodimer. The same gene encodes both cytosolic and mitochondrial KARS enzymes (Shiba et al. 1997).
Collagens, modifying enzymes and their mutations in humans, flies and worms
Mechanisms of caspase-1 activation by P2X7 receptor-mediated K+ release
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GARS (mitochondrial glycyl tRNA synthetase) catalyzes the reaction of glycine, tRNA(Gly), and ATP to form Gly-tRNA(Gly), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a dimer. Cytosolic and mitochondrial glycyl tRNA synthetase enzymes are both encoded by the same gene; the cytosolic protein lacks an aminoterminal 54-residue sequence found in the mitochondrial protein. Mutations in GARS are associated with Charcot-Marie-Tooth disease (Antonellis et al. 2007).
Cytosolic tRNA synthetases catalyze the reactions of tRNAs encoded in the nuclear genome, their cognate amino acids, and ATP to form aminoacyl-tRNAs, AMP, and pyrophosphate. Eight of the tRNA synthetases, those specific for arginine, aspartate, glutamate and proline, glutamine, isoleucine, leucine, lysine, and methionine, associate to form a complex with three accessory proteins. Each of the component synthetases is active in vitro as a purified protein; complex formation is thought to channel aminoacylated tRNAs more efficiently to the site of protein synthesis in mRNA:ribosome complexes (Quevillon et al. 1999; Wolfe et al. 2003, 2005).
VARS (cytosolic valyl tRNA synthetase) catalyzes the reaction of valine, tRNA(Val), and ATP to form Val-tRNA(Val), AMP, and pyrophosphate. The enzyme is a class I tRNA synthetase (Vilalta et al. 1993).
EARS2 (mitochondrial glutamyl tRNA synthetase) catalyzes the reaction of glutamate, mitochondrial tRNA(Glu), and ATP to form Glu-tRNA(Glu), AMP, and pyrophosphate. The EARS2 gene has been identified by computational analysis of the human genome sequence; its function has been inferred from those of the biochemically characterized mitochondrial aspartyl and tyrosyl tRNA synthetases (Bonnefond et al. 2005).
DARS2 (mitochondrial aspartyl tRNA synthetase) catalyzes the reaction of aspartate, mitochondrial tRNA(Asp), and ATP to form Asp tRNA(Asp), AMP, and pyrophosphate. The enzyme, a class II tRNA synthetase, is a homodimer (Bonnefond et al. 2005). Homozygosity for DARS2 mutations is associated with leukoencephalopathy with brainstem and spinal cord involvement plus lactate elevation (Scheper et al 2007).
The PEPCK-C gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
Adipogenesis is the process of cell differentiation by which preadipocytes become adipocytes. During this process the preadipocytes cease to proliferate, begin to accumulate lipid droplets and develop morphologic and biochemical characteristics of mature adipocytes such as hormone responsive lipogenenic and lipolytic programs. The most intensively studied model system for adipogenesis is differentiation of the mouse 3T3-L1 preadipocyte cell line by an induction cocktail of containing mitogens (insulin/IGF1), glucocorticoid (dexamethasone), an inducer of cAMP (IBMX), and fetal serum (Cao et al. 1991, reviewed in Farmer 2006). More recently additional cellular models have become available to study adipogenesis that involve almost all stages of development (reviewed in Rosen and MacDougald 2006). In vivo knockout mice lacking putative adipogenic factors have also been extensively studied. Human pathways are traditionally inferred from those discovered in mouse but are now beginning to be validated in cellular models derived from human adipose progenitors (Fischer-Posovszky et al. 2008, Wdziekonski et al. 2011). Adipogenesis is controlled by a cascade of transcription factors (Yeh et al. 1995, reviewed in Farmer 2006, Gesta et al. 2007). One of the first observable events during adipocyte differentiation is a transient increase in expression of the CEBPB (CCAAT/Enhancer Binding Protein Beta, C/EBPB) and CEBPD (C/EBPD) transcription factors (Cao et al. 1991, reviewed in Lane et al. 1999). This occurs prior to the accumulation of lipid droplets. However, it is the subsequent inductions of CEBPA and PPARG that are critical for morphological, biochemical and functional adipocytes. Ectopic expression of CEBPB alone is capable of inducing substantial adipocyte differentiation in fibroblasts while CEBPD has a minimal effect. CEBPB is upregulated in response to intracellular cAMP (possibly via pCREB) and serum mitogens (possibly via Krox20). CEBPD is upregulated in response to glucocorticoids. The exact mechanisms that upregulate the CEBPs are not fully known. CEBPB and CEBPD act directly on the Peroxisome Proliferator-activated Receptor Gamma (PPARG) gene by binding its promoter and activating transcription. CEBPB and CEBPD also directly activate the EBF1 gene (and possibly other EBFs) and KLF5 (Jimenez et al. 2007, Oishi 2005). The EBF1 and KLF5 proteins, in turn bind, and activate the PPARG promoter. Other hormones, such as insulin, affect PPARG expression and other transcription factors, such as ADD1/SREBP1c, bind the PPARG promoter. This is an area of ongoing research. During adipogenesis the PPARG gene is transcribed to yield 2 variants. The adipogenic variant 2 mRNA encodes 30 additional amino acids at the N-terminus compared to the widely expressed variant 1 mRNA. PPARG encodes a type II nuclear hormone receptor (remains in the nucleus in the absence of ligand) that forms a heterodimer with the Retinoid X Receptor Alpha (RXRA). The heterodimer was initially identified as a complex regulating the aP2/FABP4 gene and named ARF6 (Tontonoz et al. 1994). The PPARG:RXRA heterodimer binds a recognition sequence that consists of two hexanucleotide motifs (DR1 motifs) separated by 1 nucleotide. Binding occurs even in the absence of ligands, such as fatty acids, that activate PPARG. In the absence of activating ligands, the PPARG:RXRA complex recruits repressors of transcription such as SMRT/NCoR2, NCoR1, and HDAC3 (Tontonoz and Spiegelman 2008). Each molecule of PPARG can bind 2 molecules of activating ligands. Although, the identity of the endogenous ligands of PPARG is unknown, exogenous activators include fatty acids and the thiazolidinedione class of antidiabetic drugs (reviewed in Berger et al. 2005, Heikkinen et al. 2007, Lemberger et al. 1996). The most potent activators of PPARG in vitro are oxidized derivatives of unsaturated fatty acids.. Upon binding activating ligands PPARG causes a rearrangement of adjacent factors: Corepressors such as SMRT/NCoR2 are lost and coactivators such as TIF2, PRIP, CBP, and p300 are recruited (Tontonoz and Spiegelman). PPARG also binds directly to the TRAP220 subunit of the TRAP/Mediator complex that recruits RNA polymerase II. Thus binding of activating ligand by PPARG causes transcription of PPARG target genes. Targets of PPARG include genes involved in differentiation (PGAR/HFARP, Perilipin, aP2/FABP4, CEBPA), fatty acid transport (LPL, FAT/CD36), carbohydrate metabolism (PEPCK-C, AQP7, GK, GLUT4), and energy homeostasis (LEPTIN and ADIPONECTIN) (Perera et al. 2006). Within 10 days of differentiation CEBPB and CEBPD are no longer located at the PPARG promoter. Instead CEBPA is present. EBF1 and PPARG bind the CEBPA promoter and activate transcription of CEBPA, one of the key transcription factors in adipogenesis. A current hypothesis posits a self-reinforcing loop that maintains PPARG expression and the differentiated state: PPARG activates CEBPA and CEBPA activates PPARG. Additionally EBF1 (and possibly other EBFs) activates CEBPA, CEBPA activates EBF1, and EBF1 activates PPARG.
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.
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)
Molecular cloning and expression of human carnitine octanoyltransferase: evidence for its role in the peroxisomal beta-oxidation of branched-chain fatty acids
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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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234246
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_13943.2
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=4234245
An allosteric mechanism for activation of the kinase domain of epidermal growth factor receptor
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234247
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_94076.9
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=4234239
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4645.1
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=109986
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235060
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_92386.9
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_87434.9
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=4236256
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234236
Abnormal behavior associated with a point mutation in the structural gene for monoamine oxidase A
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_97870.9
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_20336.1
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=425977
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19873.2
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=4235058
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3866.1
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=109990
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=425999
Pendred syndrome is caused by mutations in a putative sulphate transporter gene (PDS)
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235074
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235076
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5502.2
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=4235072
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4233814
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235073
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4233812
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234875
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_100697.9
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=4234888
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_77347.9
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=4234871
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4233803
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234874
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_86696.9
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=425958
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19769.2
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=425969
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_19508.1
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_14929.2
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=375800
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234877
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_112624.8
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3159297
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_161218.1
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_18523.1
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=4233804
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=420746
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_80377.9
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=4234252
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_129894.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234249
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=71019
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3645998
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_91623.9
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=4236128
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234883
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4910.2
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=4234884
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234887
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234885
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3646011
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=71009
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_114502.8
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=3646012
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=77251
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_97448.9
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4099.2
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=4236281
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_139574.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235124
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5111.1
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=4235122
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234216
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235121
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_153290.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235120
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236125
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236308
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_108441.9
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_138331.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=77313
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_14554.2
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=3645997
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_14453.2
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=351991
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118403.7
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=351977
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_161744.2
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=4236164
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2878.2
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=70113
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_93037.9
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_92903.9
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4078.3
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4131.2
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=70115
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234217
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236278
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_114838.8
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=77318
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236232
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=77320
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_112147.8
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4535.1
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_77721.9
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_162633.2
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=4234218
Cytochrome P450s and cholesterol homeostasis
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235250
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235251
pXBP1(U) encoded in XBP1 pre-mRNA negatively regulates unfolded protein response activator pXBP1(S) in mammalian ER stress response
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235252
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236371
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_162216.2
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=880042
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_26229.2
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=4235102
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235104
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235254
Amino acid and oligopeptide SLC transporters
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4665.1
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=4235094
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234233
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5727.2
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=4234234
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235100
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235099
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235098
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235097
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=77358
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235101
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3487.1
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=4234237
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_88762.9
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=77360
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_160703.1
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=2466848
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_163360.2
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=4236369
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235969
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235971
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_162589.2
Proteoglycans: many forms and many functions
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236370
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109277
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235110
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=77359
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235108
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3246.2
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=4235087
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_93798.9
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_105463.9
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=4235089
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235088
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_79095.9
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=4235091
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_80676.9
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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_110285.9
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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_148845.4
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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_161305.1
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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_160577.1
(24S)-3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestan-26-oate [ChEBI:63824]
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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_21637.1
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=112032
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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_2825.2
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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_4062.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_148816.4
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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=112016
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_149606.4
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_133390.5
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alpha-D-GlcN-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl-yl group
alpha-D-GlcN-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl-yl group [ChEBI:63811]
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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_149723.4
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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_149887.4
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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_149666.4
alpha-D-GlcNS3S-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl-yl group [ChEBI:63810]
alpha-D-GlcNS3S-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl-yl group
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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_112458.8
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_137838.5
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_118456.7
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2759.1
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=77324
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234219
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234214
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234213
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3348.1
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=77322
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_156509.3
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(24S)-7alpha,12alpha,24-trihydroxycholest-4-en-3-one [ChEBI:63839]
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235420
(24S)-7alpha,24-dihydroxycholest-4-en-3-one [ChEBI:63838]
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117275.1
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=1217511
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_146586.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236319
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_136905.5
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_117607.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1217514
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2447.1
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=31633
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_85512.9
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=4234028
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234026
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234025
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_21428.1
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Cloning and characterization of mouse lung-type acyl-CoA:lysophosphatidylcholine acyltransferase 1 (LPCAT1). Expression in alveolar type II cells and possible involvement in surfactant production
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_21911.1
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=500259
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2585.2
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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=4234019
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=83951
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_108434.9
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=4234413
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234037
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234036
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234412
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4733.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=113599
alpha-D-GlcNS6S-(1->4)-beta-D-IdoA2S-(1->4)-alpha-D-GlcNS3S-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl-yl group
alpha-D-GlcNS6S-(1->4)-beta-D-IdoA2S-(1->4)-alpha-D-GlcNS3S-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl-yl group [ChEBI:63805]
Candidate cell and matrix interaction domains on the collagen fibril, the predominant protein of vertebrates
alpha-D-GlcN-(1->4)-beta-D-IdoA2S-(1->4)-alpha-D-GlcNS3S-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl-yl group [ChEBI:63806]
alpha-D-GlcN-(1->4)-beta-D-IdoA2S-(1->4)-alpha-D-GlcNS3S-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl-yl group
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_77184.9
Recognition and association of DNA glycosylase with site containing an affected purine
9-cis-4-hydroxyretinoic acid [ChEBI:63802]
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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=83956
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=83926
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3489.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3479.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=109328
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_21463.1
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Initial steps in assembly of microfibrils. Formation of disulfide-cross-linked multimers containing fibrillin-1
Assignment of the gene for human arylsulfatase B, ARSB, to chromosome region 5p11----5qter
GG-NER is considered to be transcription-independent, removing lesions from non-transcribed regions of genome in addition to non-transcribed strands of transcribed regions. The three events that characterize NER are well characterized in GG-NER: damage recognition, bimodal incision of DNA via repair protein complex, resulting excision of DNA fragment with the lesion. Post-excision polymerization and ligation restore back the native chemistry and configuration to the damaged DNA.
Polymerization is carried out by DNA polymerases, delta and epsilon.
At the beginning of this reaction, 1 molecule of 'newly synthesized DNA fragment ', 1 molecule of 'DNA ligase I ', and 1 molecule of 'damaged DNA substrate:nascent mRNA hybrid with dual incisions' are present. At the end of this reaction, 1 molecule of 'repaired DNA template:nascent mRNA hybrid', and 1 molecule of 'DNA ligase I ' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA ligase activity' of 'DNA ligase I '.
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234430
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_21955.1
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Reaction mechanism and specificity of human GMP reductase. Substrates, inhibitors, activators, and inactivators
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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_5143.2
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=4234651
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_10863.1
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=83949
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=193813
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234434
5-phospho-alpha-D-ribose 1-diphosphate [ChEBI:17111]
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Human ABCG4 shows sequence homology to the Drosophila white gene, the product of which must dimerise to become functionally active. ABCG4 is closely related to ABCG1 with 74% identity and is thus thought to play a role in the efflux of excess cholesterol (Engel et al. 2001). Northern Blot analysis shows that ABCG4 is expressed specifically in brain and the eye (Oldfield et al. 2002).
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A defined subset of the ABC transporter superfamily, the ABCA transporters, are highly expressed in monocytes and macrophages and are regulated by cholesterol flux which may indicate their role in in chronic inflammatory diseases (Schmitz and Kaminski 2001, Schmitz et al. 2000).
The multidrug resistance associated protein (MRPs) subfamily of the ABC transporter family can transport a wide and diverse range of organic anions that can be endogenous compounds and xenobiotics and their metabolites. All human MRPs (except MRP9) can mediate these transport reactions (Deeley et al. 2006). Separately, specific reactions have also been annotated to describe the roles of ABCC4 in platelet dense granule assembly, of ABCC1 in LTC4 export (an aspect of leukotriene synthesis), and of ABCC3 in bile salt efflux.
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The preferential repair of UV-induced damage in transcribed strands of active genes is known as Transcription-coupled NER (TC-NER). Impairment of the ability for TC-NER results in the onset of a severe hereditary disorder called Cockayneââ¬â¢s syndrome, an autosomal recessive disease characterized by hypersensitivity to UV light . Many types of helix distorting lesions can block the movement of elongating RNA Pol II leading to its stalling and subsequent triggering of repair mechanisms. The repair of DNA damage in active genes occurs much faster compared to the repair in non-transcribed genomic regions (via GG-NER). Also, the non-transcribed strand of the same gene is repaired at a similar rate as that of non-transcribed genomic regions. The transcriptional responses to DNA damage in terms of stalling of Pol II, its displacement from the lesion site etc. are not well elucidated. The following annotation in GK provides an overall picture of TC-NER and will be updated as and when new insights are obtained about these crucial steps.
NER was first described in the model organism E. coli in the early 1960s as a process whereby bulky base damage is enzymatically removed from DNA, facilitating the recovery of DNA synthesis and cell survival. Deficient NER processes have been identified from the cells of cancer-prone patients with different variants of xeroderma pigmentosum (XP), trichothiodystrophy (TTD), and Cockayneââ¬â¢s syndrome. These XP cells exhibited an ultraviolet radiation hypersensitivity leading to a hypermutability response to UV, offering a direct connection between deficient NER, increased mutations, and cancer. While the NER pathway in prokaryotes is unique, the pathway utilized in yeast and higher eukaryotes is highly conserved and includes a variety of proteins that interact to form complexes. NER is involved in the repair of bulky adducts in DNA, such as UV-induced photo lesions [of both 6-4 photoproducts (6-4 pps) and cyclobutane pyrimidine dimer (CPDs)], intrastrand cross-links, large chemical adducts formed from exposure to aflatoxin, benzopyrene and other genotoxic agents. Specific proteins have been identified that participate in base damage recognition, cleavage of the damaged strand on both sides of the lesion, excision of the oligonucleotide bearing the lesion, and accessory proteins necessary for efficient function. Polymerization and ligation restore the strand to its original state. NER consists of two related pathways called global genomic repair (GG-NER) and transcription-coupled NER (TC-NER). The pathways differ in the way in which DNA damage is initially recognized, but the majority of the participating molecules are shared between these two branches of NER". GG-NER is considered to be transcription-independent, removing lesions from non-transcribed regions of genome in addition to non-transcribed strands of transcribed regions. The preferential repair of UV-induced damage in transcribed strands of active genes is known as Transcription-coupled NER (TC-NER). Several of the proteins involved in NER are key components of the basal transcription complex TFIIH. NER proteins have also been shown to interact with the 19S regulatory subunit of the proteasome, suggesting a role in cellular regulation signal pathways. The establishment of mutant mouse models for NER genes and other DNA repair-related genes have been useful in demonstrating the associations between NER defects and cancer.
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.
The 70-kDa peroxisomal membrane protein (PMP70) and the adrenoleukodystrophy protein (ALDP) are half ATP binding cassette (ABC) transporters in the peroxisome membrane. Mutations in the ALD gene encoding ALDP result in the X-linked neurodegenerative disorder adrenoleukodystrophy (Roerig et al. 2001). They are involved in metabolic transport of long and very long chain fatty acids into peroxisomes. ATP binding/hydrolysis by and phosphorylation of PMP70 and ALDP are involved in the regulation of fatty acid transport into peroxisomes (Tanaka et al. 2002).
DNA damage can be directly reversed by dealkylation.
DNA in cells is susceptible to different types of cytotoxic and mutagenic damages caused by alkylating agents. These genotoxic chemicals generate major lesions like 1-methyladenine and 3-methylcytosine in single-stranded DNA and 3-methyladenine and O6-methylguanine in double-stranded DNA . Cells have inbuilt repair mechanisms against such toxic molecules. For example, 3-methyladeninie-DNA glycosylases excise some methylated bases while MGMT/hAGT protein transfers alkyl groups from others lesions onto cysteine residues. E.coli AlkB protein has a unique function wherein 1-methyladenine and 3-methylcytosine are demethylated by a combination of oxidative decarboxylation and hydroxylation activities. AlkB and its human orthologs, ABH2 and ABH3 belong to alpha-ketoglutarate deoxygenase family of enzymes that oxidize chemically inert compounds in the presence of alpha-ketoglutarate, oxygen and ferrous ions. As a byproduct of these chemical reactions, formaldehyde is released in the case of methylated lesions and acetaldehyde in the case 1-ethyladenine in DNA. CO2 and succinate are also released in an intermediate step not shown in the following illustration.Unlike other mechanisms which involve some kind of nuclease activities, this type of repair mechanism leaves the repaired bases intact by just removing the reactive alkyl groups that get bound to the bases thereby effecting accurate restoration of damaged DNA sequences.
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ATP-dependent Ca++-extrusion from human red cells
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The collagen substrate specificity of human skin fibroblast collagenase
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DNA Ligase 1 ligates the newly synthesized fragment to the gap in the template DNA.
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The resultant gap is filled by polymerase activities of Pol delta and Pol epsilon. Accessory replication protein complexes of RPA, PCNA and RFC play a role in this synthesis. DNA Ligase 1 seals the gap restoring the covalent integrity of the repaired strand.
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The HRR pathway is an "error free" DNA repair mechanism that utilizes information encoded by homologous sequence to repair double-strand breaks (DSBs). HRR acts on DSBs occurring within replicated DNA (replication-independent DSBs) or on DSBs that are generated at broken replication forks (replication-dependent DSBs). Repair by homologous recombination involves processing of the ends of the DNA double-strand break, homologous DNA pairing and strand exchange, repair DNA synthesis, and resolution of the heteroduplex molecules.
Numerous types of DNA damage can occur within a cell due to the endogenous production of oxygen free radicals, normal alkylation reactions, or exposure to exogenous radiations and chemicals. Double-strand breaks (DSBs), one of the most dangerous type of DNA damage along with interstrand crosslinks, are caused by ionizing radiation or certain chemicals such as bleomycin, and occur normally during the processes of DNA replication, meiotic exchange, and V(D)J recombination. Two distinct mechanisms for DSB repair are the error-free homologous recombination repair (HRR) pathway and the error-prone nonhomologous end-joining (NHEJ) pathway. The choice of pathway may be determined by whether the DNA region has already replicated and the precise nature of the break. NHEJ functions at all stages of the cell cycle, but plays the predominant role in both the G1 phase and in S-phase regions of DNA that have not yet replicated (Rothkamm et al. 2003). HRR functions primarily in repairing both one-sided DSBs that arise at DNA replication forks and two-sided DSBs arising in S or G2-phase chromatid regions that have replicated.
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Once repair synthesis has occurred, the D-loop structure may be resolved either through Holliday junction intermediates of through synthesis-dependent strand-annealing.
Homologous recombination repair of replication-independent double-strand breaks requires the activation of ATM followed by ATM mediated phosphorylation of DNA repair proteins. DNA repair and signaling proteins are then recruited to double-strand breaks. The ends of the DNA double strand breaks must be resectioned and RPA complexes associate with the resulting ssDNA. Homologous DNA pairing and strand exchange then occurs followed by DNA repair synthesis and resolution of D-loop structures.
Ligation of the crossed-strand intermediate results in the formation of Holliday structures with two crossovers. In humans, the identity of this ligase activity involved in this process is not known.
Following the synthesis of new DNA at resected 5' ends of the DSB, the heterologous DNA molecules may be ligated resulting in the formation of Holliday junctions. The Holliday structures are then cleaved resulting in reciprocal exchange of sequence between sister chromatids.
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).
Four Na+/H+ exchanger isoforms are distributed to Golgi and post-Golgi compartments and are involved in organelle pH regulation
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.
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).
Two gene families are responsible for glucose transport in humans. SLC2 (encoding GLUTs) and SLC5 (encoding SGLTs) families mediate glucose absorption in the small intestine, glucose reabsorption in the kidney, glucose uptake by the brain across the blood-brain barrier and glucose release by all cells in the body. Glucose is the main energy source used by cells to make energy. Im mammals, blood glucose levels are tightly controlled and glucose is taken up from interstitial fluid by a passive, facilitative transport driven by the diffusion gradient of glucose (and other sugars) across the plasma membrane. This process is mediated by a family of Na+-independent, facilitative glucose transporters (GLUTs) encoded by the SLC2A gene family (Zhao FQ and Keating AF, 2007; Wood IS and Trayhurn P, 2003). There are 14 members belonging to this family (GLUT1-12, 14 and HMIT (H+/myo-inositol symporter)). The GLUT family can be subdivided into three subclasses (I-III) based on sequence similarity and characteristic sequence motifs (Joost HG and Thorens B, 2001).
Class III facilitative transporters consist of five members; GLUT6, 8, 10, 12 and HMIT (a H+/myo-inositol transporter). They possess a characteristic glycosylation site on loop 9 (found in loop 1 of classes I and II transporters). Four class III facilitative transporters can transport glucose. SLC2A6 encodes GLUT6, expressed mainly in brain, spleen and leucocytes (Doege H et al, 2000a). In literature, this protein is incorrectly described as GLUT9. SLC2A8 encodes GLUT8 and is expressed in brain, testis and adipose tissue (Doege H et al, 2000b). SLC2A10 (located in the Type 2 diabetes-linked region of human chromosome 20q12-13.1) encodes GLUT10, a transporter with high affinity for glucose (McVie-Wylie AJ et al, 2001) . GLUT10 is highly expressed in liver and pancreas but is present in most tissues in lower levels. Defects in SLC2A10 are the cause of arterial tortuosity syndrome (ATS), an autosomal recessive disorder characterized by tortuosity and elongation of major arteries, often resulting in death at a young age (Coucke PJ et al, 2006). SLC2A12 encodes GLUT12, which is highly expressed in skeletal muscle, heart and prostate, with lower levels in brain, placenta and kidney. It was originally cloned from the human breast cancer cell line MCF-7 (Rogers S et al, 2002).
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SLC2A13 encodes a H+/myo-inositol co-transporter, HMIT (Uldry M et al, 2001) which is abundantly expressed in the brain. A proton is co-transported with myo-inositol uptake into cells. No glucose transport function has been detected to date.
Myo-Inositol is a neutral cyclic polyol, abundant in mammalian tissues. It plays important roles; it is a precursor to phosphatidylinositols (PtdIns) and to the inositol phosphates (IP), which serve as second messengers and as key regulators of many cell functions. It can also serve as a compatible osmolyte during volume regulation in many tissues where cells are exposed to hyperosmotic conditions. Three members of the glucose transporter families are inositol transporters. Two (SMIT1 and SMIT2) couple myo-inositol transport with two Na+ ions. Unlike SMIT1, SMIT2 also transports D-chiro_inositol. The third transporter (HMIT), couples myo-inositol transport with a proton.
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.
Of the six fatty acid transporter proteins (FATP) characterized, only three have been shown to mediate the influx into cells of long chain fatty acids (LCFAs); FATP1, 4 and 6. They have been shown to transport the prototypical LCFA oleic acid (OLEA) but are believed to be able to transport LCFAs with chain lengths longer than 10 carbons. FATP1 is highly expressed in adipose tissue and muscle (Hatch GM et al, 2002). FATP4 is the major intestinal LCFA transporter (Fitscher BA et al, 1998; Stahl A et al, 1999). FATP6 is localized to cardiac myocytes (Gimeno RE et al, 2003).
Long chain fatty acids (LCFAs) are involved in many cellular functions. They can be used as an important source of energy by skeletal muscle and heart tissues. Also, they are used in the production of hormones which can regulate inflammation, blood pressure, the clotting process, blood lipid levels and the immune response. Fatty acid transporter proteins (FATPs) are a family of proteins which mediate fatty acid uptake into cells when overexpressed. FATPs also possess enzymatic activity, the details of which are captured elsewhere. There are 6 human genes of the SLC27A family which encode for FATP1-6 (Stahl A, 2004; Gimeno RE, 2007). To date, only FATP1, 4 and 6 have demonstrable transporter function. Fatty acids with carbon chain lengths of more than 10 are the most likely substrates for these transporters.
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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.
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.
The ATP-binding cassette (ABC) superfamily of active transporters involves a large number of functionally diverse transmembrane proteins. They transport a variety of compounds through membranes against steep concentration gradients at the cost of ATP hydrolysis. These substrates include amino acids, lipids, inorganic ions, peptides, saccharides, peptides for antigen presentation, metals, drugs, and proteins. The ABC transporters not only move a variety of substrates into and out of the cell, but are also involved in intracellular compartmental transport. Energy derived from the hydrolysis of ATP is used to transport the substrate across the membrane against a concentration gradient. Human genome contains 48 ABC genes; 16 of these have a known function and 14 are associated with a defined human disease (Dean et al. 2001, Borst and Elferink 2002, Rees et al. 2009).
Some members of the ABC transporter superfamily are able to mediate the efflux of a broad range of cytotoxic drugs from cells, leading to the name multidrug resistance (MDR) proteins (Seeger and van Veen 2009). The ABCB1 (P-glycoprotein 1[PGP], multidrug resistance protein 1 [MRP1]) is the most characterised MDR (Shen et al. 1986, Gottesman & Pastan 1988). ABCB5 (Frank et al. 2005) and ABCA8 (Tsuruoka et al. 2002) are newer members of MDRs.
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Type I collagen and collagen mimetics as angiogenesis promoting superpolymers
Biochemistry of Lipids, Lipoproteins and Membranes, 5th Edition (Book): 213-244
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The SLC9 gene family encode proteins (sodium/proton exchangers, NHE or NHX) which exchange sodium (influx) for protons (efflux) electroneutrally. This mechanism is important because many metabolic processes generate acids which need to be removed to maintain pH. This is the major proton extruding system in cells, driven by the inward sodium ion chemical gradient. To date, there are eleven NHE genes, NHE1-11. NHE1-5 exchange cations at the cell membrane. NHE6-9 exchange cations at endosomal membranes or the trans-golgi network membranes.
The proteins responsible for the exchange of Cl- with HCO3- are members of the SLC4 (1-3) and SLC26 (3, 4 and 6) transporter families. SLC4 members are discussed in the section "Bicarbonate transporters". SLC26A3 (Chloride anion exchanger, Down-regulated in adenoma, DRA) is expressed in the mucosa of the colon and helps mediate electrolyte and fluid absorption (Schweinfest CW et al, 1993). Defects in SLC26A3 cause congenital chloride diarrhea (CLD), a disease characterized by watery stools containing an excess of chloride (Hoeglund P et al, 1996). SLC26A4 (Pendrin) is highly expressed in the adult thyroid and its activity is necessary for production of thyroid hormone. (Everett et al, 1997). Mutations in this gene are associated with Pendred syndrome, an autosomal-recessive disease. It is the most common form of syndromic deafness (Everett et al, 1997). Pendred syndrome is also characterized by hypothyroidism. SLC26A6 encodes a protein involved in transporting chloride, oxalate, sulfate and bicarbonate (Waldegger S et al, 2001). It is ubiquitously expressed, the highest levels present in kidney and pancreas.
NHE7 and 8 (SLC9A7,8) (Nakamura N et al, 2005) are expressed ubiquitously and thought to play a housekeeping role in pH homeostasis in the trans-golgi network.
NHE9 (SLC9A9) (Nakamura N et al, 2005) is expressed ubiquitously and thought to play a housekeeping role in pH homeostasis in the late endosome membrane.
Group 3 members (SLC26A7 and 9) function as ion channels. SLC26A7 encodes an ion channel which is abundantly expressed in medullary collecting duct cells of the kidney, high endothelial venule enothelial cells (HEVEC) and gastric parietal cells (Vincourt JB et al, 2002; Lohi H et al, 2002). SLC26A9 encodes an ion channel which is predominantly expressed on the lumenal side of the bronchiolar and alveolar epithelium of lung (Lohi H et al, 2002). Both these ion channels appear to transport Cl- without cotransport of HCO3- (Kim KH et al, 2005; Dorwart MR et al, 2007).
The human SLC26 gene family consists of eleven members which encode multifunctional anion exchangers.These exchangers are capable of transporting a variety of anions such as sulphate, bicarbonate, oxalate, hydroxyl, formate, iodide and chloride. SLC26 members can be grouped according to functional similiarities and three groups can be classified this way. Group 1 are selective sulphate transporters and include SLC26A1 and 2. Group 2 are Cl-/HCO3- exchangers and include SLC26A3, 4 and 6. Group 3 function as ion channels and include SLC26A7 and 9.
At the beginning of this reaction, 1 molecule of 'hNTH1 glycosylase:cytosine glycol complex' is present. At the end of this reaction, 1 molecule of 'cytosine glycol', and 1 molecule of 'DNA containing a hNTH1-bound apurinic/apyrimidinic site' are present. This reaction takes place in the 'nucleus' and is mediated by the 'pyrimidine-specific oxidized base lesion DNA N-glycosylase activity' of 'hNTH1'.
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At the beginning of this reaction, 1 molecule of 'hNTH1 glycosylase:thymine glycol' is present. At the end of this reaction, 1 molecule of 'Thymine glycol', and 1 molecule of 'DNA containing a hNTH1-bound apurinic/apyrimidinic site' are present. This reaction takes place in the 'nucleus' and is mediated by the 'pyrimidine-specific oxidized base lesion DNA N-glycosylase activity' of 'hNTH1'.
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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'.
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=193778
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'.
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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=4234646
Base excision repair is initiated by a DNA glycosylase which first recognizes and removes a damaged or incorrect (e.g. mismatched) base.
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Heparan sulfate proteoglycans on the cell surface: versatile coordinators of cellular functions
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'.
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Depyrimidination of a damaged nucleotide is mediated by a pyrimidine-specific DNA glycosylase. The glycosylase cleaves the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar generating a free base and an apyrimidinic (AP) site.
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Damaged pyrimidines are first cleaved by pyrimide-specific glycosylases (see Lindahl and Wood 1999).
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Base excision repair is initiated by DNA glycosylases that hydrolytically cleave of the base-deoxyribose glycosyl bond of a damaged nucleotide residue releasing the damaged base (Lindahl and Wood, 1999).
Molecular identification of mammalian phosphopentomutase and glucose-1,6-bisphosphate synthase, two members of the alpha-D-phosphohexomutase family
Formation of the active cofactor, UDP-glucuronate
Monoamines are oxidized to aldehydes by MAOA and MAOB, producing NH3 and H2O2
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'.
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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'.
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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'.
Cobalamin (Cbl, vitamin B12) transport and metabolism
At the beginning of this reaction, 1 molecule of 'MYH glycosylase:adenine complex' is present. At the end of this reaction, 1 molecule of 'DNA containing an MYH-bound apurinic/apyrimidinic site', and 1 molecule of '8-oxoguanine' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA N-glycosylase activity' of 'MYH glycosylase'.
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The recognition and cleavage of an altered base by a DNA glycosylase is thought to involve the diffusion of the enzyme along the minor grove of the DNA molecule. The enzyme presumably compresses the backbone of the affected DNA strand at the site of damage. This compression is thought to result in an outward rotation of the damaged residue into a "pocket" of the enzyme that recognizes and cleaves the altered base (Parikh et al., 1998).
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At the beginning of this reaction, 1 molecule of 'Double-strand DNA containing an adenine opposite to an 8-oxo guanine', and 1 molecule of 'MYH glycosylase' are present. At the end of this reaction, 1 molecule of 'MYH glycosylase:adenine complex' is present. This reaction takes place in the 'nucleus'.
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_82358.9
The eicosanoids: cyclooxygenase, lipoxygenase, and epoxygenase pathways
Biochemistry of Lipids, Lipoproteins and Membranes, 5th Edition (Book): 331-362
Signal transduction induced by opioids in immune cells: a review
At the beginning of this reaction, 1 molecule of 'hNTH1', and 1 molecule of 'Double-strand DNA containing a dihydrouracil' are present. At the end of this reaction, 1 molecule of 'hNTH1 glycosylase:dihydrouracil complex' is present. This reaction takes place in the 'nucleus'.
At the beginning of this reaction, 1 molecule of 'hNTH1', and 1 molecule of 'Double-strand DNA containing a cytosine glycol' are present. At the end of this reaction, 1 molecule of 'hNTH1 glycosylase:cytosine glycol complex' is present. This reaction takes place in the 'nucleus'.
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Depurination of a damaged nucleotide is mediated by a purine-specific DNA glycosylase. The glycosylase cleaves the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar generating a free base and an apurinic (AP) site.
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Damaged purines are first cleaved by purine-specific glycosylases (see Lindahl and Wood 1999).
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In addition to various processes for removing damaging lesions from the DNA, cells have developed specific mechanisms for tolerating unexcised damages during the replication of the genome. Such processes are collectively called DNA damage bypass pathways. Several proteins including novel Y-family polymerases that have been recently identified in multitude of organisms are involved in this process. Translesion synthesis (TLS) or replicative bypass of damaged bases that are known to arrest high fidelity, highly processive polymerases involved in DNA replication is carried out by error-prone polymerases Pol zeta, Pol eta and Rev3 protein among others. TLS is implicated in UV and chemical induced mutagenesis of normal human cells where lesions in the replicating genome are carried over to the newly formed daughter cells. All these 3 enzymes are found to lack 3ââ¬â¢->5ââ¬â¢ exonuclease activity, while exhibiting low fidelity, weak processivity and sufficient polymerase activities. An outline of the bypass synthesis by these 3 enzymes is annotated here. Complete details of damage recognition and discrimination, initiation of specific polymerase activity and the finer mechanisms are yet to be elucidated.
At the beginning of this reaction, 1 molecule of 'Oxygen', 1 molecule of '2-Oxoglutarate', and 1 molecule of 'Alkylated DNA with 1-methyladenine' are present. At the end of this reaction, 1 molecule of 'Formaldehyde', 1 molecule of 'Repaired DNA after oxidative dealkylation', 1 molecule of 'CO2', and 1 molecule of 'Succinate' are present. This reaction takes place in the 'nucleus' and is mediated by the 'damaged DNA binding activity' of 'ABH2 protein'.
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).
At the beginning of this reaction, 1 molecule of 'Oxygen', 1 molecule of 'Alkylated DNA with 1-ethyladenine', and 1 molecule of '2-Oxoglutarate' are present. At the end of this reaction, 1 molecule of 'Repaired DNA after oxidative dealkylation', 1 molecule of 'CO2', 1 molecule of 'Succinate', and 1 molecule of 'Acetaldehyde' are present. This reaction takes place in the 'nucleus' and is mediated by the 'damaged DNA binding activity' of 'ABH2 protein'.
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At the beginning of this reaction, 1 molecule of 'Alkylated DNA with 3-methylcytosine', 1 molecule of 'Oxygen', and 1 molecule of '2-Oxoglutarate' are present. At the end of this reaction, 1 molecule of 'Formaldehyde', 1 molecule of 'Repaired DNA after oxidative dealkylation', 1 molecule of 'CO2', and 1 molecule of 'Succinate' are present. This reaction takes place in the 'nucleus' and is mediated by the 'damaged DNA binding activity' of 'ABH2 protein'.
At the beginning of this reaction, 1 molecule of 'Oxygen', 1 molecule of '2-Oxoglutarate', and 1 molecule of 'Alkylated DNA with 1-methyladenine' are present. At the end of this reaction, 1 molecule of 'Formaldehyde', 1 molecule of 'Repaired DNA after oxidative dealkylation', 1 molecule of 'CO2', and 1 molecule of 'Succinate' are present. This reaction takes place in the 'nucleus' and is mediated by the 'damaged DNA binding activity' of 'ABH3 protein'.
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AlkB is an alpha-ketoglutarate- and Fe(II)-dependent dioxygenase that oxidizes the relevant methyl groups and releases them as formaldehyde. The human homologs of both these enzymes remove 1-methyladenine and 3-methylcytosine from methylated polynucleotides in an alpha-ketoglutarate-dependent reaction. They act by direct damage reversal with the regeneration of the unsubstituted bases. E.coli AlkB, and human ABH2, and ABH3 can also repair 1-ethyladenine residues in DNA with the release of acetaldehyde (Duncan et al., 2002).
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At the beginning of this reaction, 1 molecule of 'Oxygen', 1 molecule of 'Alkylated DNA with 1-ethyladenine', and 1 molecule of '2-Oxoglutarate' are present. At the end of this reaction, 1 molecule of 'Repaired DNA after oxidative dealkylation', 1 molecule of 'CO2', 1 molecule of 'Succinate', and 1 molecule of 'Acetaldehyde' are present. This reaction takes place in the 'nucleus' and is mediated by the 'damaged DNA binding activity' of 'ABH3 protein'.
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_10857.1
At the beginning of this reaction, 1 molecule of 'Alkylated DNA with 3-methylcytosine', 1 molecule of 'Oxygen', and 1 molecule of '2-Oxoglutarate' are present. At the end of this reaction, 1 molecule of 'Formaldehyde', 1 molecule of 'Repaired DNA after oxidative dealkylation', 1 molecule of 'CO2', and 1 molecule of 'Succinate' are present. This reaction takes place in the 'nucleus' and is mediated by the 'damaged DNA binding activity' of 'ABH3 protein'.
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234647
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=193388
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=193732
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_10221.1
At the beginning of this reaction, 1 molecule of 'HREV1:lesioned DNA template with misinserted bases' is present. At the end of this reaction, 1 molecule of 'HREV1 protein', and 1 molecule of 'Elongated DNA template with bypassed lesion' are present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA-directed DNA polymerase activity' of 'HREV1:lesioned DNA template with misinserted bases'.
Control of cross-over by single-strand DNA resection.
At the beginning of this reaction, 1 molecule of 'HREV1:damaged DNA template complex' is present. At the end of this reaction, 1 molecule of 'HREV1:lesioned DNA template with misinserted bases' is present. This reaction takes place in the 'nucleus' and is mediated by the 'DNA-directed DNA polymerase activity' of 'HREV1:damaged DNA template complex'.
At the beginning of this reaction, 1 molecule of 'damaged DNA substrate ', and 1 molecule of 'HREV1 protein' are present. At the end of this reaction, 1 molecule of 'HREV1:damaged DNA template complex' is present. This reaction takes place in the 'nucleus'.
Of the three major pathways involved in the repair of nucleotide damage in DNA, base excision repair (BER) involves the greatest number of individual enzymatic activities. This is the consequence of the numerous individual glycosylases, each of which recognizes and removes a specific modified base(s) from DNA. BER is responsible for the repair of the most prevalent types of DNA lesions, alterations, which arise intracellularly as a consequence of normal mitochondrial metabolism or by oxidative free radicals resulting from ionizing radiation, lipid peroxidation or activated phagocytic cells. BER is a two-step process initiated by one of the DNA glycosylases that recognizes a specific modified base(s) and removes that base through the catalytic cleavage of the glycosylic bond, leaving an abasic site without disruption of the phosphate-sugar DNA backbone. Subsequently, abasic sites are resolved by a series of enzymes that cleave the backbone, synthesize the replacement residue(s), and ligate the DNA strand. BER may occur by either a single-nucleotide replacement pathway or a multiple-nucleotide patch replacement pathway, depending on the structure of the terminal sugar phosphate residue. The glycosylases found in human cells recognize "foreign adducts" and not standard functional modifications such as DNA methylation.
At the beginning of this reaction, 1 molecule of 'Pol eta:lesioned DNA template inserted with correct base complement' is present. At the end of this reaction, 1 molecule of 'Pol eta protein', and 1 molecule of 'Elongated DNA template with bypassed lesion' are present. This reaction takes place in the 'nucleus' and is mediated by the 'eta DNA polymerase activity' of 'Pol eta:lesioned DNA template inserted with correct base complement'.
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At the beginning of this reaction, 1 molecule of 'Pol eta:damaged DNA template complex' is present. At the end of this reaction, 1 molecule of 'Pol eta:lesioned DNA template inserted with correct base complement' is present. This reaction takes place in the 'nucleus' and is mediated by the 'eta DNA polymerase activity' of 'Pol eta:damaged DNA template complex'.
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At the beginning of this reaction, 1 molecule of 'damaged DNA substrate ', and 1 molecule of 'Pol eta protein' are present. At the end of this reaction, 1 molecule of 'Pol eta:damaged DNA template complex' is present. This reaction takes place in the 'nucleus'.
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HREV1 encodes a template dependent dCMP transferase activity that can insert a C residue opposite an abasic site.
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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_7516.4
Ubiquitous environmental and endogenous genotoxic agents cause lesions that can interfere with normal DNA metabolism including DNA replication, eventually resulting in mutations that lead to carcinogenesis and/or cell death. While cells posses repair mechanisms like nucleotide excision and base excision repair pathways to maintain the integrity of the genome, not all lesions on the genome can be repaired efficiently by these processes in time for DNA replication, and some types of lesion are repaired very inefficiently. To prevent acute cell death through arrested DNA replication at unrepaired lesions, cells have a mechanism, referred to as translesion synthesis, which allows DNA synthesis to proceed past lesions (Masutani et al., 2000).
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Pol eta consists of 713 amino acids and can bypass thymidine-thymidine dimers adding two AÃ¢â¬â¢s correctly opposite to the lesion. Mutations in Pol eta gene result in the loss of this bypass activity in accounting for the XP variant phenotype (XPV) among human xeroderma pigmentosum disorder patients. Pol eta can carry out TLS past various UV and chemical induced lesions via two steps: a. preferential incorporation of correct bases opposite to the lesion b. conditional elongation only at the sites where such correct bases are inserted.
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Catecholamine biosynthesis and physiological regulation in neuroendocrine cells
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4-(2-Aminoethyl)-1,2-benzenediol [ChEBI:18243]
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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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Fibroblast growth factor receptors: lessons from the genes
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Characterization and identification of cytochrome P450 metabolites of arachidonic acid released by human peritoneal macrophages obtained from the pouch of Douglas
Prostaglandins Leukot Essent Fatty Acids 67:397-404
Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
Determinants of function and substrate specificity in human UDP-galactose 4'-epimerase
Human porphobilinogen deaminase mutations in the investigation of the mechanism of dipyrromethane cofactor assembly and tetrapyrrole formation
The Mechanism of Hsp90 regulation by the protein kinase-specific cochaperone p50(cdc37)
Characterization of a heart-specific fatty acid transport protein
In response to receptor ligation, the tyrosine residues in DAP12's immunoreceptor tyrosine-based activation motif (ITAM) are phosphorylated by Src family kinases. These phosphotyrosines form the docking site for the protein tyrosine kinase SYK in myeloid cells and SYK and ZAP70 in NK cells. DAP12-bound SYK autophosphorylates and phosphorylates the scaffolding molecule LAT, recruiting the proximal signaling molecules phosphatidylinositol-3-OH kinase (PI3K), phospholipase-C gamma (PLC-gamma), GADS (GRB2-related adapter downstream of SHC), SLP76 (SH2 domain-containing leukocyte protein of 76 kDa), GRB2:SOS (Growth factor receptor-bound protein 2:Son of sevenless homolog 1) and VAV. All of these intermediate signalling molecules result in the recruitment and activation of kinases AKT, CBL (Casitas B-lineage lymphoma) and ERK (extracellular signal-regulated kinase), and rearrangement of the actin cytoskeleton (actin polymerization) finally leading to cellular activation. PLC-gamma generates the secondary messengers diacylglycerol (DAG) and inositol-1,4,5-trisphosphate (InsP3), leading to activation of protein kinase C (PKC) and calcium mobilization, respectively (Turnbull & Colonna 2007, Klesney-Tait et al. 2006).
The innate immune system is the first line of defense against invading microorganisms, a broad specificity response characterized by the recruitment and activation of phagocytes and the release of anti-bacterial peptides. The receptors involved recognize conserved molecules present in microbes called pathogen-associated molecular patterns (PAMPs), and/or molecules that are produced as a result of tissue injury, the damage associated molecular pattern molecules (DAMPs). PAMPs are essential to the pathogen and therefore unlikely to vary. Examples are lipopolysaccharide (LPS), peptidoglycans (PGNs) and viral RNA. DAMPs include intracellular proteins, such as heat-shock proteins and extracellular matrix proteins released by tissue injury, such as hyaluronan fragments. Non-protein DAMPs include ATP, uric acid, heparin sulfate and dsDNA. The receptors for these factors are referred to collectively as pathogen- or pattern-recognition receptors (PRRs). The best studied of these are the membrane-associated Toll-like receptor family. Less well studied but more numerous are the intracellular nucleotide-binding domain, leucine rich repeat containing receptors (NLRs) also called nucleotide binding oligomerization domain (NOD)-like receptors, a family with over 20 members in humans and over 30 in mice. These recognise PAMPs/DAMPs from phagocytosed microorganisms or from intracellular infections (Kobayashi et al. 2003, Proell et al. 2008, Wilmanski et al. 2008). Some NLRs are involved in process unrelated to pathogen detection such as tissue homeostasis, apoptosis, graft-versus-host disease and early development (Kufer & Sansonetti 2011). Structurally NLRs can be subdivided into the caspase-recruitment domain (CARD)-containing NLRCs (NODs) and the pyrin domain (PYD)-containing NLRPs (NALPs), plus outliers including ice protease (caspase-1) activating factor (IPAF) (Martinon & Tschopp, 2005). In practical terms, NLRs can be divided into the relatively well characterized NOD1/2 which signal via RIP2 primarily to NFkappaB, and the remainder, some of which participate in macromolecular structures called Inflammasomes that activate caspases. Mutations in several members of the NLR protein family have been linked to inflammatory diseases, suggesting these molecules play important roles in maintaining host-pathogen interactions and inflammatory responses. Most NLRs have a tripartite structure consisting of a variable amino-terminal domain, a central nucleotide-binding oligomerization domain (NOD or NACHT) that is believed to mediate the formation of self oligomers, and a carboxy-terminal leucine-rich repeat (LRR) that detects PAMPs/DAMPs. In most cases the amino-terminal domain includes protein-interaction modules, such as CARD or PYD, some harbour baculovirus inhibitor repeat (BIR) or other domains. For most characterised NLRs these domains have been attributed to downstream signaling Under resting conditions, NLRs are thought to be present in an autorepressed form, with the LRR folded back onto the NACHT domain preventing oligomerization. Accessory proteins may help maintain the inactive state. PAMP/DAMP exposure is thought to triggers conformational changes that expose the NACHT domain enabling oligomerization and recruitment of effectors, though it should be noted that due to the lack of availability of structural data, the mechanistic details of NLR activation remain largely elusive. New terminology for NOD-like receptors was adopted by the Human Genome Organization (HUGO) in 2008 to standardize the nomenclature of NLRs. The acronym NLR, once standing for NOD-like receptor, now is an abbreviation of 'nucleotide-binding domain, leucine-rich repeat containing' protein. The term NOD-like receptor is officially outdated and replaced by NLRC where the C refers to the CARD domain. However the official gene symbols for NOD1 and NOD2 still contain NOD and this general term is still widely used.
In contrast to NOD1/2 some NLRPs function as large macromolecular complexes called 'Inflammasomes'. These multiprotein platforms control activation of the cysteinyl aspartate protease caspase-1 and thereby the subsequent cleavage of pro-interleukin 1B (pro-IL1B) into the active proinflammatory cytokine IL1B. Activation of caspase-1 is essential for production of IL1B and IL18, which respectively bind and activate the IL1 receptor (IL1R) and IL18 receptor (IL18R) complexes. IL1R and IL18R activate NFkappaB and other signaling cascades. As the activation of inflammasomes leads to caspase-1 activation, inflammasomes can be considered an upstream step of the IL1R and IL18R signaling cascades, linking intracellular pathogen sensing to immune response pathways mediated by Toll-Like Receptors (TLRs). Monocytes and macrophages do not express pro-IL1B until stimulated, typically by TLRs (Franchi et al. 2009). The resulting pro-IL1B is not converted to IL1B unless a second stimulus activates an inflammasome. This requirement for two distinct stimuli allows tight regulation of IL1B/IL18 production, necessary because excessive IL-1B production is associated with numerous inflammatory diseases such as gout and rheumatoid arthritis (Masters et al. 2009). There are at least four subtypes of the inflammasome, characterized by the NLRP. In addition the protein AIM2 can form an inflammasome. All activate caspase-1. NLRP1 (NALP1), NLRP3 (Cryopyrin, NALP3), IPAF (CARD12, NLRC4) and AIM2 inflammasomes all have clear physiological roles in vivo. NLRP2, NLRP6, NLRP7, NLRP10 and NLRP12 have been demonstrated to modulate caspase-1 activity in vitro but the significance of this is unclear (Mariathasan and Monack, 2007). NLRP3 and AIM2 bind the protein 'apoptosis-associated speck-like protein containing a CARD' (ASC, also called PYCARD), via a PYD-PYD domain interaction. This in turn recruits procaspase-1 through a CARD-CARD interaction. NLRP1 and IPAF contain CARD domains and can bind procaspase-1 directly, though both are stimulated by ASC. Oligomerization of NLRPs is believed to bring procaspases into close proximity, leading to 'induced proximity' auto-activation (Boatright et al. 2003). This leads to formation of the active caspase tetramer. NLRPs are generally considered to be cytoplasmic proteins, but there is evidence for cytoplasmic-nuclear shuttling of the family member CIITA (LeibundGut-Landmann et al. 2004) and tissue/cell dependent NALP1 expression in the nucleus of neurons and lymphocytes (Kummer et al. 2007); the significance of this remains unclear.
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Direct role of ChREBP.Mlx in regulating hepatic glucose-responsive genes.
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Quantitative analysis of EGFRvIII cellular signaling networks reveals a combinatorial therapeutic strategy for glioblastoma
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The presence of reactive oxygen species (ROS) leads to the oxidation of thioredoxin and consequent release of TXNIP (Zhou et al. 2010). The source of the ROS is unclear but they are known to be essential for caspase-1 activation (Cruz et al. 2007) and are produced in response to all known NLRP3 activators (Dostert et al. 2008, Zhou et al. 2010). The freed TXNIP binds NLRP3 and is proposed to activate the NLRP3 inflammasome, explaining how ROS can bring about NLRP3 activation.
The NLRP3 (Cryopyrin) inflammasome is currently the best characterized. It consists of NLRP3, ASC (PYCARD) and procaspase-1; CARD8 (Cardinal) is also suggested to be a component. It is activated by a number of pathogens and bacterial toxins as well as diverse PAMPs, danger-associated molecular patterns (DAMPS) such as hyaluronan and uric acid, and exogenous irritants such as silica and asbestos (see Table S1 Schroder & Tschopp, 2010). Mutations in NLRP3 which lead to constitutive activation are linked to the human diseases Muckle-Wells syndrome, familial cold autoinflammatory syndrome and NOMID (Ting et al. 2006), characterized by skin rashes and other symptoms associated with generalized inflammation. The cause of these symptoms is uncontrolled IL-1 beta production. Multiple studies have shown that activation of the NLRP3 inflammasome by particulate activators (e.g. Hornung et al. 2008) requires phagocytosis, but this is not required for the response to ATP, which is mediated by the P2X7 receptor (Kahlenberg & Dubyak, 2004) and appears to involve the pannexin membrane channel (Pellegrin & Suprenenant 2006). Direct binding of activators to NLRP3 has not been demonstrated and the exact process of activation is unclear, though it is speculated to involve changes in conformation that free the NACHT domain for oligomerization (Inohara & Nunez 2001, 2003).
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.
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.
Transporter associated with antigen processing (TAP) prefers peptides 8-16 residues long, slightly longer than the canonical 8-10 residue peptides that fit into class I MHC binding sites. These longer peptides are further trimmed at their N-termini by the ER-associated aminopeptidase (ERAP). ERAP trims peptides to a length of 8-10 residues, suitable for loading into the MHC class I binding groove.
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.
Beta glucuronidase deficiency: report of clinical, radiologic, and biochemical features of a new mucopolysaccharidosis
Intracellular foreign or aberrant host proteins are cleaved into peptide fragments of a precise size, such that they can be loaded on to class I MHC molecules and presented externally to cytotoxic T cells. The ubiquitin-26S proteasome system plays a central role in the generation of these class I MHC antigens. Ubiquitination is the mechanism of adding ubiquitin to lysine residues on substrate protein leading to the formation of a polyubiquitinated substrate. This process involves three classes of enzyme, an E1 ubiquitin-activating enzyme, an E2 ubiquitin-conjugating enzyme, and an E3 ubiquitin ligase. Polyubiquitination through lysine-48 (K48) generally targets the substrate protein for proteasomal destruction. The protease responsible for the degradation of K48-polyubiquitinated proteins is the 26S proteasome. This proteasome is a two subunit protein complex composed of the 20S (catalytic core) and 19S (regulatory) proteasome complexes. The proteasome eliminates most of the foreign and non-functional proteins from the cell by degrading them into short peptides; only a small fraction of the peptides generated are of the correct length to be presented by the MHC class I system. It has been calculated that between 994 and 3122 protein molecules have to be degraded for the formation of a single, stable MHC class I complex at the cell surface, with an average effciency of 1 in 2000 (Kloetzel et al. 2004, Princiotta et al. 2003).
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).
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).
Some peptides generated by the 26S proteasome are too long to bind to MHC class I molecules. These N-terminal extended precursor peptides may be trimmed by cytosolic aminopeptidases, such as Tripeptidyl peptidase II (TPP2), puromycin-sensitive aminopeptidase (PSA), bleomycin hydrolase (BH), and leucine aminopeptidase (LAP).
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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).
The human gene ATP7B encodes the copper-transporting ATPase 2 (ATP7B, ATPase2, Wilson's protein) which is expressed mainly in the liver, brain and kidneys (Bull et al, 1993). ATP7B resides on the trans-Golgi membrane where it it thought to sequester copper from the cytosol into the golgi (Yang et al, 1997). Defects in ATP7B are the cause of Wilson disease (WD), an autosomal recessive disorder of copper metabolism characterized by the toxic accumulation of copper in a number of organs, particularly the liver and brain (Thomas et al, 1995).
The 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 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).
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.
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.
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C1-Tetrahydrofolate synthase from rabbit liver. Structural and kinetic properties of the enzyme and its two domains.
Identification of the cDNA encoding human 6-phosphogluconolactonase, the enzyme catalyzing the second step of the pentose phosphate pathway(1)
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Primary structure and tissue distribution of human 4-aminobutyrate aminotransferase
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triphopsphoric acid 1-xanthosin-5'-yl ester
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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=936901
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=77343
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_98914.9
Molecular variation in relation to purine metabolism
J Clin Pathol Suppl (R Coll Pathol) 8:48-63
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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_125665.1
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=1475048
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1470070
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_92006.9
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_4368.1
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=77253
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_33389.10
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236223
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234181
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234179
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_98369.9
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5323.1
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_122149.1
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=4234178
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=1222342
Structures of human cytosolic NADP-dependent isocitrate dehydrogenase reveal a novel self-regulatory mechanism of activity
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_161011.1
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Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236020
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_163300.2
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=77252
Frizzled/PCP signalling: a conserved mechanism regulating cell polarity and directed motility
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2872447
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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_31777.10
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=2872443
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234187
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5571.1
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=77255
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_82884.9
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=4236372
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236122
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_163434.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_81776.9
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=4236255
P-glycoprotein-mediated active efflux of the anti-HIV1 nucleoside abacavir limits cellular accumulation and brain distribution
Cloning, tissue distribution, and functional analysis of the human Na+/N+ exchanger isoform, NHE3
Matrix metalloproteinases: old dogs with new tricks
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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=77269
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5544.1
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=4234201
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_76260.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_80423.9
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=983022
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_76416.2
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=77261
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=983018
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2800.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_76371.2
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=4234196
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=983012
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_76265.2
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=983015
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_138546.5
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_158125.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4231085
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_108610.9
The Wilson disease gene: spectrum of mutations and their consequences
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_87185.9
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=4236182
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235128
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235130
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=74016
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5631.2
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=4236318
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234184
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234185
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3421.1
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=4231084
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4231095
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=77276
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235413
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234197
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_106191.9
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=4235415
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235414
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_154111.3
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5705.1
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=4235417
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234199
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236180
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_103922.9
alpha,alpha'-Trehalose 6-phosphate [ChEBI:10201]
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_120718.3
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234889
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_105903.9
adenosine 5'-monophosphate [ChEBI:16027]
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234894
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_33644.10
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236234
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_86935.9
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=4236235
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_82093.9
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=74112
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_3654.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_88891.9
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=4236184
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=77272
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_90179.9
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_76054.2
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=77273
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=983025
Proline and glycine control protein self-organization into elastomeric or amyloid fibrils
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_76873.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2294.2
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=983013
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4234210
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_76197.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_110677.9
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=983017
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236123
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=983010
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_76136.2
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=983020
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_76277.2
5'-Phosphoribosyl-N-formylglycinamide [ChEBI:18272]
Regulation of Endoplasmic Reticulum Stress-induced Cell Death by ATF4 in Neuroectodermal Tumor Cells
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235039
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235036
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235033
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5668.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_130760.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236284
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=983011
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_76713.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_76690.2
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=983019
Xenobiotic, bile acid, and cholesterol transporters: function and regulation
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_76736.2
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=983023
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_75946.2
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=983029
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_76349.2
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=983024
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236287
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_146168.5
3-Phospho-D-glyceroyl phosphate [ChEBI:16001]
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236183
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_102443.9
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=4236285
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_130032.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4236286
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_139735.5
Mycothiol is essential for growth of Mycobacterium tuberculosis Erdman
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=76633
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235291
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=76632
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235294
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5211.1
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235292
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_2762.2
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_144050.5
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235259
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=76629
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4235257
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The molecular basis of human 3-methylcrotonyl-CoA carboxylase deficiency.
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Cloning and expression of functional shikimate dehydrogenase (EC 1.1.1.25) from Mycobacterium tuberculosis H37Rv
The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis reveals a common catalytic scaffold and ancestry for type I and type II enzymes
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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
ERBB2, also known as HER2 or NEU, is a receptor tyrosine kinase (RTK) belonging to the EGFR family. ERBB2 possesses an extracellular domain that does not bind any known ligand, contrary to other EGFR family members, a single transmembrane domain, and an intracellular domain consisting of an active kinase and a C-tail with multiple tyrosine phosphorylation sites. Inactive ERBB2 is associated with a chaperone heat shock protein 90 (HSP90) and its co-chaperone CDC37 (Xu et al. 2001, Citri et al. 2004, Xu et al. 2005). In addition, ERBB2 is associated with ERBB2IP (also known as ERBIN or LAP2), a protein responsible for proper localization of ERBB2. In epithelial cells, ERBB2IP restricts expression of ERBB2 to basolateral plasma membrane regions (Borg et al. 2000). ERBB2 becomes activated by forming a heterodimer with another ligand-activated EGFR family member, either EGFR, ERBB3 or ERBB4, which is accompanied by dissociation of chaperoning proteins HSP90 and CDC37 (Citri et al. 2004), as well as ERBB2IP (Borg et al. 2000) from ERBB2. ERBB2 heterodimers function to promote cell proliferation, cell survival and differentiation, depending on the cellular context. ERBB2 can also be activated by homodimerization when it is overexpressed, in cancer for example. In cells expressing both ERBB2 and EGFR, EGF stimulation of EGFR leads to formation of both ERBB2:EGFR heterodimers (Wada et al. 1990, Karunagaran et al. 1996) and EGFR homodimers. Heterodimers of ERBB2 and EGFR trans-autophosphorylate on twelve tyrosine residues, six in the C-tail of EGFR and six in the C-tail of ERBB2 - Y1023, Y1139, Y1196, Y1221, Y1222 and Y1248 (Margolis et al. 1989, Hazan et al. 1990,Walton et al. 1990, Helin et al. 1991, Ricci et al. 1995, Pinkas-Kramarski 1996). Phosphorylated tyrosine residues in the C-tail of EGFR and ERBB2 serve as docking sites for downstream signaling molecules. Three key signaling pathways activated by ERBB2:EGFR heterodimers are RAF/MAP kinase cascade, PI3K-induced AKT signaling, and signaling by phospholipase C gamma (PLCG1). Downregulation of EGFR signaling is mediated by ubiquitin ligase CBL, and is shown under Signaling by EGFR. In cells expressing ERBB2 and ERBB3, ERBB3 activated by neuregulin NRG1 or NRG2 binding (Tzahar et al. 1994) forms a heterodimer with ERBB2 (Pinkas-Kramarski et al. 1996, Citri et al. 2004). ERBB3 is the only EGFR family member with no kinase activity, and can only function in heterodimers, with ERBB2 being its preferred heterodimerization partner. After heterodimerization, ERBB2 phosphorylates ten tyrosine residues in the C-tail of ERBB3, Y1054, Y1197, Y1199, Y1222, Y1224, Y1260, Y1262, Y1276, Y1289 and Y1328 (Prigent et al. 1994, Pinkas-Kramarski et al. 1996, Vijapurkar et al. 2003, Li et al. 2007) that subsequently serve as docking sites for downstream signaling molecules, resulting in activation of PI3K-induced AKT signaling and RAF/MAP kinase cascade. Signaling by ERBB3 is downregulated by the action of RNF41 ubiquitin ligase, also known as NRDP1. In cells expressing ERBB2 and ERBB4, ligand stimulated ERBB4 can either homodimerize or form heterodimers with ERBB2 (Li et al. 2007), resulting in trans-autophosphorylation of ERBB2 and ERBB4 on C-tail tyrosine residues that will subsequently serve as docking sites for downstream signaling molecules, leading to activation of RAF/MAP kinase cascade and, in the case of ERBB4 CYT1 isoforms, PI3K-induced AKT signaling (Hazan et al. 1990, Cohen et al. 1996, Li et al. 2007, Kaushansky et al. 2008). Signaling by ERBB4 is downregulated by the action of WWP1 and ITCH ubiquitin ligases, and is shown under Signaling by ERBB4.
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Neurotrophins (NGF, BDNF, NT-3, NT-4/5) play pivotal roles in survival, differentiation, and plasticity of neurons in the peripheral and central nervous system. They are produced, and secreted in minute amounts, by a variety of tissues. They signal through two types of receptors: TRK tyrosine kinase receptors (TRKA, TRKB, TRKC), which specifically interact with the different neurotrophins, and p75NTR, which interacts with all neurotrophins. TRK receptors are reported in a variety of tissues in addition to neurons. p75NTRs are also widespread. Neurotrophins and their receptors are synthesized as several different splice variants, which differ in terms of their biological activities. The nerve growth factor (NGF) was the first growth factor to be identified and has served as a model for studying the mechanisms of action of neurotrophins and growth factors. The mechanisms by which NGF generates diverse cellular responses have been studied extensively in the rat pheochromocytoma cell line PC12. When exposed to NGF, PC12 cells exit the cell cycle and differentiate into sympathetic neuron-like cells. Current data show that signalling by the other neurotrophins is similar to NGF signalling.
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The role of autophosphorylation sites on PDGF receptors are to provide docking sites for downstream signal transduction molecules which contain SH2 domains. The SH2 domain is a conserved motif of around 100 amino acids that can bind a phosphorylated tyrosine residue. These downstream molecules are activated upon binding to, or phosphorylated by, the receptor kinases intrinsic to PDGF receptors. Some of the dowstream molecules are themselves enzymes, such as phosphatidylinositol 3'-kinase (PI3K), phospholipase C (PLC-gamma), the Src family of tyrosine kinases, the tyrosine phosphatase SHP2, and a GTPase activating protein (GAP) for Ras. Others such as Grb2 are adaptor molecules which link the receptor with downstream catalytic molecules.
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Platelet-derived Growth Factor (PDGF) is a potent stimulator of growth and motility of connective tissue cells such as fibroblasts and smooth muscle cells as well as other cells such as capillary endothelial cells and neurons.The PDGF family of growth factors is composed of four different polypeptide chains encoded by four different genes. The classical PDGF chains, PDGF-A and PDGF-B, and more recently discovered PDGF-C and PDGF-D. The four PDGF chains assemble into disulphide-bonded dimers via homo- or heterodimerization, and five different dimeric isoforms have been described so far; PDGF-AA, PDGF-AB, PDGF-BB, PDGF-CC and PDGF-DD. It is notable that no heterodimers involving PDGF-C and PDGF-D chains have been described. PDGF exerts its effects by binding to, and activating, two protein tyrosine kinase (PTK) receptors, alpha and beta. These receptors dimerize and undergo autophosphorylation. The phosphorylation sites then attract downstream effectors to transduct the signal into the cell.
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Activation of PLCG1 signaling is observed only in the presence of ERBB2:EGFR heterodimers, with PLCG1 binding to phosphorylated tyrosine Y992 and Y1173 in the C-tail of EGFR (Chattopadhyay et al. 1999), and potentially Y1023 in the C-tail of ERBB2 (Fazioli et al. 1991, Cohen et al. 1996).
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Innate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
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Humans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first critical hours and days of exposure to a new pathogen, our innate immune system.
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The activation of phosphlipase C-gamma (PLC-gamma) and subsequent mobilization of calcium from intracellular stores are essential for neurotrophin secretion. PLC-gamma is activated through the phosphorylation by TrkA receptor kinase and this form hydrolyses PIP2 to generate inositol tris-phosphate (IP3) and diacylglycerol (DAG). IP3 promotes the release of Ca2+ from internal stores and this results in activation of enzymes such as protein kinase C and Ca2+ calmodulin-regulated protein kinases.
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Trk receptors signal from the plasma membrane and from intracellular membranes, particularly from early endosomes. Signalling from the plasma membrane is fast but transient; signalling from endosomes is slower but long lasting. Signalling from the plasma membrane is annotated here. TRK signalling leads to proliferation in some cell types and neuronal differentiation in others. Proliferation is the likely outcome of short term signalling, as observed following stimulation of EGFR (EGF receptor). Long term signalling via TRK receptors, instead, was clearly shown to be required for neuronal differentiation in response to neurotrophins.
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DNAX activation protein of 12kDa (DAP12) is an immunoreceptor tyrosine-based activation motif (ITAM)-bearing adapter molecule that transduces activating signals in natural killer (NK) and myeloid cells. It mediates signalling for multiple cell-surface receptors expressed by these cells, associating with receptor chains through complementary charged transmembrane amino acids that form a salt-bridge in the context of the hydrophobic lipid bilayer (Lanier et al. 1998). DAP12 homodimers associate with a variety of receptors expressed by macrophages, monocytes and myeloid cells including TREM2, Siglec H and SIRP-beta, as well as activating KIR, LY49 and the NKG2C proteins expressed by NK cells. DAP12 is expressed at the cell surface, with most of the protein lying on the cytoplasmic side of the membrane (Turnbull & Colonna 2007, Tessarz & Cerwenka 2008).
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Replication factors required for SV40 DNA replication in vitro. II. Switching of DNA polymerase alpha and delta during initiation of leading and lagging strand synthesis.
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When dissociated Galpha-GTP and Gbeta-gamma can activate or inhibit different signalling cascades and effector proteins. The precise pathways depends on the identity of the alpha and beta/gamma subtypes.
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Opioids are chemical substances similar to opiates, the active substances found in opium (morphine, codeine etc.). Opioid action is mediated by the receptors for endogenous opioids; peptides such as the enkephalins, the endorphins or the dynorphins. Opioids possess powerful analgesic and sedative effects, and are widely used as pain-killers. Their main side-effect is the rapid establishment of a strong addiction. Opioids receptors are G-protein coupled receptors (GPCR). There are four classes of receptors: mu (MOR), kappa (KOR) and delta (DOR), and the nociceptin receptor (NOP).
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Calcium, as the ion Ca2+, is essential in many biological processes. The majority of Ca2+ in many organisms is bound to phosphates which form skeletal structures and also buffer Ca2+ levels in extracellular fluids (typically 1 millimolar). Intracellular free Ca2+, by contrast, is 10,000 times lower than the outside of the cell (typically 10 micromolar). This concentration gradient is used to import Ca2+ into cells where it acts as a second messenger.
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Kinetics and morphology of self-assembly of an elastin-like polypeptide based on the alternating domain arrangement of human tropoelastin
The phospholipase C (PLC) family of enzymes is both diverse and complex. The isoforms beta, gamma and delta (each have subtypes) make up the members of this family. PLC hydrolyzes phosphatidylinositol bisphosphate (PIP2) into two second messengers, inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG). IP3 mobilizes intracellular calcium stores while DAG activates protein kinase C isoforms which are involved in regulatory functions.
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The classic signalling route for G alpha (q) is activation of phospholipase C beta thereby triggering phosphoinositide hydrolysis, calcium mobilization and protein kinase C activation. This provides a path to calcium-regulated kinases and phosphatases, GEFs, MAP kinase cassettes and other proteins that mediate cellular responses ranging from granule secretion, integrin activation, and aggregation in platelets. Gq participates in many other signalling events including direct interaction with RhoGEFs that stimulate RhoA activity and inhibition of PI3K. Both in vitro and in vivo, the G-protein Gq seems to be the predominant mediator of the activation of platelets.
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G protein-coupled receptors (GPCRs) are classically defined as the receptor, G-protein and downstream effectors, the alpha subunit of the G-protein being the primary signaling molecule. However, it has become clear that this greatly oversimplifies the complexities of GPCR signaling (see Gurevich & Gurevich, 2008). The beta:gamma G-protein dimer is also involved in downstream signaling (Smrcka, 2008), and some receptors form part of metastable complexes of receptor and accessory proteins such as the arrestins. GPCRs are involved in many diverse signaling events (Kristiansen 2004), using a variety of pathways that include modulation of adenylyl cyclase, phospholipase C, the mitogen activated protein kinases (MAPKs), extracellular signal regulated kinase (ERK) c-Jun-NH2-terminal kinase (JNK) and p38 MAPK.
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The classical signalling mechanism for G alpha (i) is inhibition of the cAMP dependent pathway through inhibition of adenylate cyclase. Decreased production of cAMP from ATP results in decreased activity of cAMP-dependent protein kinases.
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The heterotrimeric G protein Gz, is a member of the Gi family. Unlike other Gi family members it lacks an ADP ribosylation site cysteine four residues from the carboxyl terminus and is thus pertussis toxin-insensitive. It inhibits adenylyl cyclase types I, V and VI. G alpha (z) interacts with the Rap1 GTPase activating protein (Rap1GAP) to attenuate Rap1 signaling. Like all G-proteins Gz has an intrinsic GTPase activity, but this activity tends to be lower for the pertussis toxin insensitive G-proteins, most strikingly so for Gz, whose kcat value for GTP hydrolysis is 200-fold lower than those of Gs or Gi (Grazziano et al. 1989). Gz knockout mice have disrupted platelet aggregation at physiological concentrations of epinephrine and responses to several neuroactive drugs are altered (Yang et al. 2000).
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The activation of adenylyl (adenylate) cyclase (AC) results in the production of adenosine-3',5'-monophosphate i.e. cyclic AMP. Humans have 9 genes encoding membrane-associated AC and one encoding a soluble AC. Two of the classes of heterotrimeric G-proteins are named according to their effect on AC; Gs stimulates all membrane-bound ACs (the s in Gs denotes AC stimulatory); the Gi class inhibits some AC isoforms, particularly 5 and 6. Beta-gamma subunits of heterotrimeric G-proteins can also regulate AC. Ca2+/Calmodulin activates some AC isoforms (1, 8 and 3) but is inhibitory to others (5 and 6).
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The general function of the G alpha (s) subunit (Gs) is to activate adenylate cyclase, which in turn produces cAMP, leading to the activation of cAMP-dependent protein kinases (often referred to collectively as Protein Kinase A). The signal from the ligand-stimulated GPCR is amplified because the receptor can activate several Gs heterotrimers before it is inactivated.
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NaPO(4) cotransport type III (PiT1) expression in human embryonic kidney cells and regulation by PTH
Emerging roles for E2F: beyond the G1/S transition and DNA replication.
5-methyltetrahydrofolyl polyglutamate macromolecule
5-methyltetrahydrofolyl polyglutamate macromolecule [ChEBI:63907]
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_5250.2
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Exosomes mediate stromal mobilization of autocrine Wnt-PCP signaling in breast cancer cell migration
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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_20939.2
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Aminoacyl tRNA synthetases and their connections to disease
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Expression and characterization of a human mitochondrial phenylalanyl-tRNA synthetase
CREB phosphorylation through the activation of Adenylate Cyclase
Human phosphoglycerate kinase. I. Crystallization and characterization of normal enzyme
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Cytosolic aldehyde dehydrogenase (ALDH1) variants found in alcohol flushers
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(R,R)-3,3'-thiobis-(2-aminopropanoic acid)
(R,R)-2,6-diamino-4-thiaheptanedioic acid
Glycoprotein folding, quality control and ER-associated degradation
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Neurotrophin-regulated signalling pathways
Philos Trans R Soc Lond B Biol Sci 361:1545-64
Rv2131c from Mycobacterium tuberculosis is a CysQ 3'-phosphoadenosine-5'-phosphatase
Pathways of DNA double-strand break repair during the mammalian cell cycle.
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Identification of the INO1 gene of Mycobacterium tuberculosis H37Rv reveals a novel class of inositol-1-phosphate synthase enzyme
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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_27301.1
ChEBI:11805 3-hydroxy-2-methylpropanoate
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Mutations and polymorphisms in GUSB gene in mucopolysaccharidosis VII (Sly Syndrome)
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Studies on the metabolic fate of n-3 polyunsaturated fatty acids
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Three pathways for trehalose biosynthesis in mycobacteria
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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_17073.1
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Endogenous synthesis of coenzyme Q in eukaryotes
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L-Glutamate 5-semialdehyde [ChEBI:17232]
Identification of inflammatory gene modules based on variations of human endothelial cell responses to oxidized lipids
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Characterization of Mycobacterium tuberculosis mycothiol S-conjugate amidase
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The vitelliform macular dystrophy protein defines a new family of chloride channels
Proc. Natl. Acad. Sci. U.S.A. 99:4008-13
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Wnt/Fz signaling and the cytoskeleton: potential roles in tumorigenesis
Hormone-sensitive lipase: control of intracellular tri-(di-)acylglycerol and cholesteryl ester hydrolysis
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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_93191.9
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_32765.10
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Production of formyl-CoA during peroxisomal alpha-oxidation of 3-methyl-branched fatty acids
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Endoplasmic reticulum (ER) chaperone regulation and survival of cells compensating for deficiency in the ER stress response kinase, PERK
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Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate
Proline hydroxylation of collagens synthesized at different temperatures in vivo by two poikilothermic species
Proximal events in Wnt signal transduction
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Principles of bioactive lipid signalling: lessons from sphingolipids
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Recent developments in the investigation of inherited metabolic disorders using cultured human cells.
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ABC transporters and cholesterol metabolism
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The TREM receptor family and signal integration
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(S)-alpha-amino-beta-phenylpropionic acid
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Atomic structure of GTP cyclohydrolase I
Diseases associated with visual transduction
The challenge of new drug discovery for tuberculosis
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CATALYTIC ACTIVITY Phosphoenolpyruvate + 3-phosphoshikimate = phosphate + 5-O-(1-carboxyvinyl)-3-phosphoshikimate.PATHWAY Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 6/7.SUBUNIT Monomer.SIMILARITY Belongs to the EPSP synthase family.
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EMILIN-1 deficiency induces elastogenesis and vascular cell defects
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Secretion of Wnt ligands requires Evi, a conserved transmembrane protein
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Wntless, a conserved membrane protein dedicated to the secretion of Wnt proteins from signaling cells
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Renal physiology of SLC26 anion exchangers
Human Na(+)/H(+) exchanger isoform 6 is found in recycling endosomes of cells, not in mitochondria
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Frequent deletions at Xq28 indicate genetic heterogeneity in Hunter syndrome
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Pyruvate metabolism and Citric Acid (TCA) cycle
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5-Phosphoribose 1-diphosphate biosynthesis
Synthesis of cytosolic 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) from D-ribose 5-phosphate
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Sequence of the human iduronate 2-sulfatase (IDS) gene
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AGPAT6 is a novel microsomal glycerol-3-phosphate acyltransferase
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Human frataxin is an allosteric switch that activates the Fe-S cluster biosynthetic complex
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Which DNA polymerases are used for DNA-repair in eukaryotes?
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Functions and regulatory mechanisms of Gq-signaling pathways
Mycobacterium tuberculosis expresses methionine sulphoxide reductases A and B that protect from killing by nitrite and hypochlorite
Silica crystals and aluminum salts activate the NALP3 inflammasome through phagosomal destabilization
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Characterization of phospholipase D activity in bovine photoreceptor membranes
Cleavage site specificity and conformational selection in type I collagen degradation
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Regulation of mammalian liver methionine adenosyltransferase
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A novel cardiolipin-remodeling pathway revealed by a gene encoding an endoplasmic reticulum-associated acyl-CoA:lysocardiolipin acyltransferase (ALCAT1) in mouse
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Identification, cloning, expression, and purification of three novel human calcium-independent phospholipase A2 family members possessing triacylglycerol lipase and acylglycerol transacylase activities
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Monounsaturated fatty acid modification of Wnt protein: its role in Wnt secretion
Vitamins B6 activation to pyridoxal phosphate
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Uptake of sulfur in Mycobacterium tuberculosis happens exclusively through sulfate assimiliation, an abundant molecule in the bacterium's environment. All enzymes participating in this process are non-redundant ie they are essential enzymes. Sulfate is first taken up via an ABC transporter and appended to AMP giving APS and PAPS, which can be considered the activated forms of sulfate and are used in cysteine and sulfolipid biosynthesis (Bhave et al, 2007).
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Crystal structure of an Hsp90-geldanamycin complex: targeting of a protein chaperone by an antitumor agent
Novel D761Y and common secondary T790M mutations in epidermal growth factor receptor-mutant lung adenocarcinomas with acquired resistance to kinase inhibitors
Disorders of proline and hydroxyproline metabolism
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1821-1838
Mycothiol and its adducts that result from detoxification can be readily cleaved into smaller molecules. The mycothiol pool therefore serves as storage for unstable cysteine and sugars. (Rawat and Av-Gay, 2007; Newton et al, 2008)
Inositol polyphosphates: a new frontier for regulating gene expression
Disorders of tetrahydrobiopterin and related biogenic amines
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1725-1776
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1777-1805
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1965-1970
Organic acidemias due to defects in lysine oxidation: 2-ketoadipic acidemia and glutaric acidemia
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 2195-2204
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1909-1963
Characterization of the Mycobacterium tuberculosis H37Rv alkyl hydroperoxidase AhpC points to the importance of ionic interactions in oligomerization and activity
In stress situations, Mycobacteria express enzymes for a second pathway that enables cysteine synthesis from serine pathway products, here from phosphoserine. The details of the sulfur donor are not established (Agren et al, 2008).
Maple syrup urine disease (branched-chain ketoaciduria)
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1971-2005
Characterization of human UDP-glucose dehydrogenase. CYS-276 is required for the second of two successive oxidations
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Human glutamine phosphoribosylpyrophosphate amidotransferase. Kinetic and regulatory properties
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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)
ATP-binding cassette sub-family G member 4
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ATP-binding cassette sub-family D member 2
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ATP-binding cassette sub-family D member 3
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 1857-1895
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Multidrug resistance-associated protein 3
ATP-binding cassette sub-family C member 3
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Mycobacterium tuberculosis and the intimate discourse of a chronic infection
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ATP-binding cassette sub-family C member 9
Multidrug resistance-associated protein 7
ATP-binding cassette sub-family B member 5
Multidrug resistance-associated protein 6
ATP-binding cassette transporter sub-family C member 8
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 2125-2163
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Synthesis and interconversion of nucleotide di- and triphosphates
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Identification of the mycothiol synthase gene (mshD) encoding the acetyltransferase producing mycothiol in actinomycetes
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Half-site reactivity in 6-phosphogluconate dehydrogenase from human erythrocytes
Adrenoleukodystrophy gene: unexpected homology to a protein involved in peroxisome biogenesis
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CATALYTIC ACTIVITY Hydrogen sulfide + 6 oxidized ferredoxin + 3 H(2)O = sulfite + 6 reduced ferredoxin + 6 H(+).COFACTOR Binds 1 siroheme per subunit.COFACTOR Binds 1 4Fe-4S cluster per subunit.SUBUNIT Monomer.MISCELLANEOUS Was identified as a high-confidence drug target.SIMILARITY Belongs to the nitrite and sulfite reductase 4Fe-4S domain family.
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FUNCTION: Part of a binding-protein-dependent transport system. Probably responsible for the translocation of the substrate across the membrane (By similarity).
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Beta-oxidation of very long chain fatty acids
Long-chain fatty acid transport protein 6
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all-trans-decaprenyl diphosphate [ChEBI:61011]
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Long-chain fatty acid transport protein 4
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Molecular characterization of methylmalonate semialdehyde dehydrogenase deficiency
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Solute carrier family 2, facilitated glucose transporter member 12
Solute carrier family 2, facilitated glucose transporter member 10
Sodium-dependent phosphate transporter 2
The structure and function of G-protein-coupled receptors
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Sodium-dependent phosphate transporter 1
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The characterization of gene mutations for human glucose phosphate isomerase deficiency associated with chronic hemolytic anemia
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Essentials of Glycobiology, 2nd edition (Book)
CATALYTIC ACTIVITY D-glucose 6-phosphate = 1D-myo-inositol 3-phosphate.PTM Pupylated at Lys-73 by the prokaryotic ubiquitin-like protein Pup, which leads to its degradation by the proteasome.MISCELLANEOUS Was identified as a natural substrate of the M.tuberculosis proteasome.SIMILARITY Belongs to the myo-inositol 1-phosphate synthase family.
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Mechanisms of glycerophospholipid homeostasis in mammalian cells
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Sanfilippo syndrome type C: deficiency of acetyl-CoA:alpha-glucosaminide N-acetyltransferase in skin fibroblasts
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De novo purine nucleotide biosynthesis: cloning of human and avian cDNAs encoding the trifunctional glycinamide ribonucleotide synthetase-aminoimidazole ribonucleotide synthetase-glycinamide ribonucleotide transformylase by functional complementation in E. coli
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Disease-causing missense mutations affect enzymatic activity, stability and oligomerization of glutaryl-CoA dehydrogenase (GCDH)
Heparin and heparan sulfate: biosynthesis, structure and function
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Loss of signaling through the G protein, Gz, results in abnormal platelet activation and altered responses to psychoactive drugs
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Isolated 2-methylbutyrylglycinuria caused by short/branched-chain acyl-CoA dehydrogenase deficiency: identification of a new enzyme defect, resolution of its molecular basis, and evidence for distinct acyl-CoA dehydrogenases in isoleucine and valine metabolism.
CATALYTIC ACTIVITY L-histidinol phosphate + H(2)O = L-histidinol + phosphate.PATHWAY Amino-acid biosynthesis; L-histidine biosynthesis; L-histidine from 5-phospho-alpha-D-ribose 1-diphosphate: step 8/9.INDUCTION When comparing gene expression levels of the four IMPase family genes in exponential cultures of M.tuberculosis, the level of cysQ is the highest, almost equal to sigA; impA and impC are expressed at approximately 40% of this level, while suhB is lowest, at 12% of the cysQ level.DISRUPTION PHENOTYPE Strains lacking this gene appear to be not viable, even in the presence of high levels of exogenous inositol.SIMILARITY Belongs to the inositol monophosphatase family.
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Tryptophan metabolism in the central nervous system: medical implications
Regulation of cell growth-dependent expression of mammalian CDC6 gene by the cell cycle transcription factor E2F.
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Glycosaminoglycan-mediated coacervation of tropoelastin abolishes the critical concentration, accelerates coacervate formation, and facilitates spherule fusion: implications for tropoelastin microassembly
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ChEBI:61088 S-nitroso-L-cysteinylglycine
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TRP channels: sensors and transducers of gasotransmitter signals
4-cis-decenoyl-CoA transits through the first step of the saturated beta-oxidation spiral to yield 2-trans-4-cis-decadienoyl-CoA.
trans,cis-Lauro-2,6-dienoyl-CoA transits through the saturated beta-oxidation spiral a single time to yield 4-cis-decenoyl-CoA.
The second of the two accessory enzymes, 2,4-dienoyl-CoA reductase catalyses an oxidation-reduction (redox) reaction to yield 3-trans-decenoyl-CoA.
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The sixth pass through the beta-oxidation spiral picks up where the last left off with the saturated fatty acid hexanoyl-CoA and produces butanoyl-CoA. Four enzymatic steps are required starting with SCAD CoA dehydrogenase (Short Chain) activity, followed by the enoyl-CoA hydratase activity of crotonase, the 3-hydroxyacyl-CoA dehydrogenase activity of the short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD), and completed by the ketoacyl-CoA thiolase activity, present in the mitochondrial membrane associated trifunctional protein.
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At the beginning of this reaction, 1 molecule of 'FAD', and 1 molecule of 'Butanoyl-CoA' are present. At the end of this reaction, 1 molecule of 'Crotonoyl-CoA', and 1 molecule of 'FADH2' are present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'acyl-CoA dehydrogenase activity' of 'SCAD acyl-CoA dehydrogenase homotetramer'.
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At the beginning of this reaction, 1 molecule of 'Crotonoyl-CoA', and 1 molecule of 'H2O' are present. At the end of this reaction, 1 molecule of '(S)-3-Hydroxybutanoyl-CoA' is present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'enoyl-CoA hydratase activity' of 'enoyl-CoA hydratase hexamer'.
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The seventh and final pass through the beta-oxidation spiral picks up where the last left off with the saturated fatty acid butanoyl-CoA and at the third step produces acetoacetyl-CoA, which can be used to generate 2 acetyl-CoA molecules or can be turned toward the synthesis of ketone bodies pathway. Four enzymatic steps are required starting with SCAD CoA dehydrogenase (Short Chain) activity, followed by the enoyl-CoA hydratase activity of crotonase, the 3-hydroxyacyl-CoA dehydrogenase activity of the short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD). The final enzymatic step, creating two acetyl-CoA molecules requires a specific ketoacyl-CoA thiolase, Acetoacetyl-CoA thiolase.
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Once fatty acids have been imported into the mitochondrial matrix by the carnitine acyltransferases, the beta-oxidation spiral begins. Each turn of this spiral concludes with the repetitive removal of two carbon units from the fatty acyl chain. beta-oxidation of saturated fatty acids (fatty acids with even numbered carbon chains and no double bonds) involves four different enzymatic steps: oxidation, hydration, a second oxidation, and a concluding thiolysis step, resulting in the two-carbon acetyl-CoA and a newly CoA primed acyl-CoA for the next turn of the spiral.
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Linoleoyl-CoA transits through the saturated beta-oxidation spiral three times. With each turn of the spiral two carbon atoms are removed until the double bond is reached.
At the beginning of this reaction, 1 molecule of 'cis,cis-3,6-Dodecadienoyl-CoA' is present. At the end of this reaction, 1 molecule of 'trans,cis-Lauro-2,6-dienoyl-CoA ' is present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'dodecenoyl-CoA delta-isomerase activity' of '3,2-trans-enoyl-CoA isomerase Homodimer'.
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Acetyl-CoA acetyltransferase tetramer (ACAT1) in the mitochondrial matrix catalyzes the reversible reaction of acetoacetyl-CoA and CoA to form two molecules of acetyl-CoA (Middleton et al. 1986).
3-Oxoacid CoA-transferase dimer (OXCT1) in the mitochondrial matrix catalyzes the reversible reaction of acetoacetate and succinyl-CoA to form acetoacetyl-CoA and succinate (Kassovska-Bratinova et al. 1996).
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At the beginning of this reaction, 1 molecule of 'D-methylmalonyl-CoA' is present. At the end of this reaction, 1 molecule of 'L-methylmalonyl-CoA' is present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'methylmalonyl-CoA epimerase activity' of 'methylmalonyl-CoA epimerase'.
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Methylmalonyl-CoA mutase (MUT aka MCM) (Jansen et al. 1989) utilises adenosylcobalamin (AdoCbl) as a cofactor and transfers an adenosyl group from AdoCbl to methylmalonyl-CoA to form succinyl-CoA, a precursor for the citric acid cycle. MUT has a homodimeric structure and is located in the mitochondrial matrix. Defects in MUT cause methylmalonic aciduria, mut type (MMAM; MIM:251000), an often fatal disorder of organic acid metabolism (Worgan et al. 2006). Methylmalonic aciduria type A protein (MMAA) is thought to act as a chaperone to MUT, the enzyme which utilises adenosylcobalamin (AdoCbl) as a cofactor. MMAA is suggested to play a dual role with regards to MUT protection and reactivation. Some AdoCbl-dependent enzymes undergo suicide inactivation after catalysis due to the oxidative inactivation of Cbl. MMAA is thought to play a protective role to prevent MUT being inactivated in this way. After the catalytic cycle when MUT is inactive, MMAA increases the enzymatic activity of MUT through exchange of the damaged cofactor. Whether this happens via GTP-mediated hydrolysis is unknown at present (Takahashi-Iniguez et al. 2011, Froese et al. 2010). Bacterial AdoCbl-containing enzymes possess reactivating factors which release the inactivated cofactor to allow the resulting apoenzyme to reconstitute into an active form. A bacterial orthologue of MMAA, MeaB, forms a stable complex with MUT and plays a role in its protection and reactivation (Padovani & Banerjee 2006). Defects in MMAA cause methylmalonic aciduria type cblA (cblA aka methylmalonic aciduria type A or vitamin B12-responsive methylmalonicaciduria of cblA complementation type; MIM:251100). Affected individuals accumulate methylmalonic acid in the blood and urine and are prone to potentially life threatening acidotic crises in infancy or early childhood (Dobson et al. 2002, Lerner-Ellis et al. 2004).
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Once the second of the two double bonds has been reached 3,2-trans-enoyl-CoA isomerase, changes the spatial conformation of the second double bond from cis to trans. This step yields trans-dec-2-enoyl-CoA, which then enters the saturated beta-oxidation pathway.
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The complete beta-oxidation spiral produces and consumes intermediates with a trans configuration. Mitochondrial beta-oxidation of unsaturated fatty acids leads to intermediates not compatible with the four enzymatic steps responsible for the beta-oxidation of saturated fatty acids. Unsaturated fatty acids that have bonds in the cis configuration require three separate enzymatic steps to prepare these molecules for the beta-oxidation pathway. The further processing of these intermediates requires additional enzymes, depending on the position of the double bonds in the original fatty acids. Described here is the beta-oxidation of linoleoyl-CoA.
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Acetyl-CoA acetyltransferase tetramer (ACAT1) in the mitochondrial matrix catalyzes the reversible reaction of two molecules of acetyl-CoA to form acetoacetyl-CoA and CoA (Middleton et al. 1986).
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In a healthy, well-nourished individual, the production of ketone bodies occurs at a relatively low rate. During periods of normal physiological responses to carbohydrate shortages, the liver increases the production of ketone bodies from acetyl-CoA generated from fatty acid oxidation. This allows heart and skeletal muscle to use ketone bodies as the primary source of energy, thereby preserving the limited glucose supply for use in brain tissue. In untreated diabetes mellitus, a huge buildup of ketone bodies occurs due to an increase in fatty acid oxidation. The production of ketone bodies exceeds the ability of peripheral tissues to oxidize them, and results in lowering the pH of blood. Blood acidification is dangerous, chiefly as it impairs the ability of hemoglobin to bind oxygen. Ketone body synthesis proceeds via the synthesis of ccetoacetic acid in three steps from acetyl CoA, followed by the reduction of acetoacetic acid to beta-hydroxybutyrate. In the body, these reactions occur in the mitochondria of liver cells (Sass 2011).
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Propionyl-CoA is a product of the catabolism of the amino acids, leucine, methionine, and threonine, and of the beta-oxidation of fatty acids with odd numbers of carbon atoms. The three reactions of this pathway convert propionyl-CoA to succinyl-CoA, an intermediate of the citric acid cycle. Through these reactions, carbon atoms from these sources can be fully oxidized to produce energy, or can be directed to gluconeogenesis. The three reactions of propionyl-CoA catabolism take place in the mitochondrial matrix.
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Beta-oxidation begins once fatty acids have been imported into the mitochondrial matrix by carnitine acyltransferases. The beta-oxidation spiral of fatty acids metabolism involves the repetitive removal of two carbon units from the fatty acyl chain. There are four steps to this process: oxidation, hydration, a second oxidation, and finally thiolysis. The last step releases the two-carbon acetyl-CoA and a ready primed acyl-CoA that takes another turn down the spiral. In total each turn of the beta-oxidation spiral produces one NADH, one FADH2, and one acetyl-CoA. Further oxidation of acetyl-CoA via the tricarboxylic acid cycle generates additional FADH2 and NADH. All reduced cofactors are used by the mitochondrial electron transport chain to form ATP. The complete oxidation of a fatty acid molecule produces numerous ATP molecules. Palmitate, used as the model here, produces 129 ATPs. Beta-oxidation pathways differ for saturated and unsaturated fatty acids. The beta-oxidation of saturated fatty acids requires four different enzymatic steps. Beta-oxidation produces and consumes intermediates with a trans configuration; unsaturated fatty acids that have bonds in the cis configuration require three separate enzymatic steps to prepare these molecules for the beta-oxidation pathway.
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At the beginning of this reaction, 1 molecule of 'Decanoyl-CoA', and 1 molecule of 'FAD' are present. At the end of this reaction, 1 molecule of 'trans-Dec-2-enoyl-CoA', and 1 molecule of 'FADH2' are present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'acyl-CoA dehydrogenase activity' of 'MCAD acyl-CoA dehydrogenase homotetramer'.
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At the beginning of this reaction, 1 molecule of '2-trans-Dodecenoyl-CoA', and 1 molecule of 'H2O' are present. At the end of this reaction, 1 molecule of '(S)-3-Hydroxydodecanoyl-CoA' is present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'enoyl-CoA hydratase activity' of 'enoyl-CoA hydratase hexamer'.
At the beginning of this reaction, 1 molecule of 'Lauroyl-CoA', and 1 molecule of 'FAD' are present. At the end of this reaction, 1 molecule of 'FADH2', and 1 molecule of '2-trans-Dodecenoyl-CoA' are present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'acyl-CoA dehydrogenase activity' of 'LCAD acyl-CoA dehydrogenase homotetramer'.
The third pass through the beta-oxidation spiral picks up where the last left off with the saturated fatty acid lauroyl-CoA and produces decanoyl-CoA. Four enzymatic steps are required starting with LCAD CoA dehydrogenase (Long Chain) activity, followed by the enoyl-CoA hydratase activity of crotonase, the 3-hydroxyacyl-CoA dehydrogenase activity of the short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD), and completed by the ketoacyl-CoA thiolase activity, present in the mitochondrial membrane associated trifunctional protein. Note that the 3-hydroxyacyl-CoA dehydrogenase activity of SCHAD is not actually limited to short chain fatty acids, in fact SCHAD has a broad substrate specificity.
At the beginning of this reaction, 1 molecule of '3-Oxododecanoyl-CoA', and 1 molecule of 'CoA' are present. At the end of this reaction, 1 molecule of 'Decanoyl-CoA', and 1 molecule of 'Acetyl-CoA' are present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'transferase activity' of 'Trifunctional Protein'.
trans,trans-Farnesyl diphosphate [ChEBI:10700]
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The collagen fibril: the almost crystalline structure
At the beginning of this reaction, 1 molecule of 'trans-Tetradec-2-enoyl-CoA', and 1 molecule of 'H2O' are present. At the end of this reaction, 1 molecule of '(S)-3-Hydroxytetradecanoyl-CoA' is present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'enoyl-CoA hydratase activity' of 'Trifunctional Protein'.
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At the beginning of this reaction, 1 molecule of 'NAD+', and 1 molecule of '(S)-3-Hydroxytetradecanoyl-CoA' are present. At the end of this reaction, 1 molecule of 'H+', 1 molecule of '3-Oxotetradecanoyl-CoA', and 1 molecule of 'NADH' are present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the '3-hydroxyacyl-CoA dehydrogenase activity' of 'Trifunctional Protein'.
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At the beginning of this reaction, 1 molecule of '3-Oxotetradecanoyl-CoA', and 1 molecule of 'CoA' are present. At the end of this reaction, 1 molecule of 'Lauroyl-CoA', and 1 molecule of 'Acetyl-CoA' are present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'transferase activity' of 'Trifunctional Protein'.
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The second pass through the beta-oxidation spiral starts with the saturated fatty acid myristoyl-CoA (from the first swing through the beta oxidation spiral) and produces lauroyl-CoA. Four enzymatic steps are required starting with LCAD CoA dehydrogenase (Long Chain) activity, followed by three enzymatic steps, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase, and ketoacyl-CoA thiolase activities, all present in the mitochondrial membrane associated trifunctional protein.
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At the beginning of this reaction, 1 molecule of 'myristoyl-CoA', and 1 molecule of 'FAD' are present. At the end of this reaction, 1 molecule of 'FADH2', and 1 molecule of 'trans-Tetradec-2-enoyl-CoA' are present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'acyl-CoA dehydrogenase activity' of 'LCAD acyl-CoA dehydrogenase homotetramer'.
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At the beginning of this reaction, 1 molecule of '3-Oxohexanoyl-CoA', and 1 molecule of 'CoA' are present. At the end of this reaction, 1 molecule of 'Acetyl-CoA', and 1 molecule of 'Butanoyl-CoA' are present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'transferase activity' of 'Trifunctional Protein'.
At the beginning of this reaction, 1 molecule of 'trans-Hex-2-enoyl-CoA', and 1 molecule of 'H2O' are present. At the end of this reaction, 1 molecule of '(S)-Hydroxyhexanoyl-CoA' is present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'enoyl-CoA hydratase activity' of 'enoyl-CoA hydratase hexamer'.
At the beginning of this reaction, 1 molecule of 'Hexanoyl-CoA', and 1 molecule of 'FAD' are present. At the end of this reaction, 1 molecule of 'trans-Hex-2-enoyl-CoA', and 1 molecule of 'FADH2' are present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'acyl-CoA dehydrogenase activity' of 'SCAD acyl-CoA dehydrogenase homotetramer'.
The fifth pass through the beta-oxidation spiral picks up where the last left off with the saturated fatty acid octanoyl-CoA and produces hexanoyl-CoA. Four enzymatic steps are required starting with MCAD CoA dehydrogenase (Medium Chain) activity, followed by the enoyl-CoA hydratase activity of crotonase, the 3-hydroxyacyl-CoA dehydrogenase activity of the short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD), and completed by the ketoacyl-CoA thiolase activity, present in the mitochondrial membrane associated trifunctional protein.
Enzymatic and nonenzymatic cross-linking of collagen and elastin
At the beginning of this reaction, 1 molecule of 'H2O', and 1 molecule of 'trans-Oct-2-enoyl-CoA' are present. At the end of this reaction, 1 molecule of '(S)-Hydroxyoctanoyl-CoA' is present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'enoyl-CoA hydratase activity' of 'enoyl-CoA hydratase hexamer'.
At the beginning of this reaction, 1 molecule of '3-Oxooctanoyl-CoA', and 1 molecule of 'CoA' are present. At the end of this reaction, 1 molecule of 'Hexanoyl-CoA', and 1 molecule of 'Acetyl-CoA' are present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'transferase activity' of 'Trifunctional Protein'.
The fourth pass through the beta-oxidation spiral picks up where the last left off with the saturated fatty acid decanoyl-CoA and produces octanoyl-CoA. Four enzymatic steps are required starting with MCAD CoA dehydrogenase (Medium Chain) activity, followed by the enoyl-CoA hydratase activity of crotonase, the 3-hydroxyacyl-CoA dehydrogenase activity of the short chain 3-hydroxyacyl-CoA dehydrogenase (SCHAD), and completed by the ketoacyl-CoA thiolase activity, present in the mitochondrial membrane associated trifunctional protein. Note that the 3-hydroxyacyl-CoA dehydrogenase activity of SCHAD is not actually limited to short chain fatty acids, in fact SCHAD has a broad substrate specificity.
At the beginning of this reaction, 1 molecule of 'Octanoyl-CoA', and 1 molecule of 'FAD' are present. At the end of this reaction, 1 molecule of 'FADH2', and 1 molecule of 'trans-Oct-2-enoyl-CoA' are present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'acyl-CoA dehydrogenase activity' of 'MCAD acyl-CoA dehydrogenase homotetramer'.
At the beginning of this reaction, 1 molecule of 'trans-Dec-2-enoyl-CoA', and 1 molecule of 'H2O' are present. At the end of this reaction, 1 molecule of '(S)-Hydroxydecanoyl-CoA' is present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'enoyl-CoA hydratase activity' of 'enoyl-CoA hydratase hexamer'.
Gly-X-Y tripeptide frequencies in collagen: a context for host-guest triple-helical peptides
At the beginning of this reaction, 1 molecule of '3-Oxodecanoyl-CoA', and 1 molecule of 'CoA' are present. At the end of this reaction, 1 molecule of 'Acetyl-CoA', and 1 molecule of 'Octanoyl-CoA' are present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'transferase activity' of 'Trifunctional Protein'.
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The thiol-based redox networks of pathogens: unexploited targets in the search for new drugs
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Triacylglycerol is a major energy store in the body and its hydrolysis to yield fatty acids and glycerol is a tightly regulated part of energy metabolism. A central part in this regulation is played by hormone-sensitive lipase (HSL), a neutral lipase abundant in adipocytes and skeletal and cardiac muscle, but also abundant in ovarian and adrenal tissue, where it mediates cholesterol ester hydrolysis, yielding cholesterol for steroid biosynthesis. The hormones to which it is sensitive include catecholamines (e.g., epinephrine), ACTH, and glucagon, all of which trigger signaling cascades that lead to its phosphorylation and activation, and insulin, which sets off events leading to its dephosphorylation and inactivation (Holm et al. 2000; Kraemer and Shen 2002). The processes of triacylglycerol and cholesterol ester hydrolysis are also regulated by subcellular compartmentalization: these lipids are packaged in cytosolic particles and the enzymes responsible for their hydrolysis, and perhaps for additional steps in their metabolism, are organized at the surfaces of these particles (e.g., Brasaemle et al. 2004). This organization is dynamic: the inactive form of HSL is not associated with the particles, but is translocated there after being phosphorylated. Conversely, perilipin, a major constituent of the particle surface, appears to block access of enzymes to the lipids within the particle; its phosphorylation allows greater access. Here, HSL-mediated triacylglycerol hydrolysis is described as a pathway containing twelve reactions. The first six of these involve activation: phosphorylation of HSL, dimerization of HSL, disruption of CGI-58:perilipin complexes at the surfaces of cytosolic lipid particles, phosphorylation of perilipin, association of phosphorylated HSL with FABP, and translocation of HSL from the cytosol to the surfaces of lipid particles. The next four reactions are the hydrolysis reactions themselves: the hydrolysis of cholesterol esters, and the successive removal of three fatty acids from triacylglycerol. The last two reactions, dephosphorylation of perilipin and HSL, negatively regulate the pathway. These events are outlined in the figure below. Inputs (substrates) and outputs (products) of individual reactions are connected by black arrows; blue lines connect output activated enzymes to the other reactions that they catalyze. Despite the undoubted importance of these reactions in normal human energy metabolism and in the pathology of diseases such as type II diabetes, they have been studied only to a limited extent in human cells and tissues. Most experimental data are derived instead from two rodent model systems: primary adipocytes from rats, and mouse 3T3-L1 cells induced to differentiate into adipocytes.
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Processes annotated here include the digestion of dietary lipids, sterol uptake, the formation and turnover of lipoproteins (chylomicrons, VLDL, LDL, and HDL), and the mobilization of fatty acids through the action of hormone-sensitive lipase.
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While fatty acid synthesis from acetyl CoA proceeds in the cytosol, most acetyl CoA in the cell is generated within the mitochondria, by oxidative decarboxylation of the pyruvate derived from glycolysis, as well as from a number of reactions of amino acid catabolism. Mitochondrial Acetyl-CoA is transported to cytoplasm as citrate to participate in fatty acid biosynthesis. Mitochondrial citrate synthase, a tricarboxylic acid transporter in the inner mitochondrial membrane, and cytosolic citrate lyase are involved in this transport.
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Association of cytosolic FAS into multimers is linked to increased catalytic activity (Locke et al. 2008).
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Cytosolic fatty acid synthase (FAS) complex catalyzes the reaction of acetyl-CoA with 7 malonyl-CoA and 14 NADHP + 14 H+ to form a molecule of palmitate and 7 CO2, 14 NADP+, 8 CoASH, and 6 H2O. The process proceeds via the successive condensations of malonyl groups onto the growing acyl chain,each followed by loss of CO2 and three steps of reduction (Smith et al. 2003).
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Hydroxysteroid (17-beta) dehydrogenase 12 (HSD17B12) catalyzes the reaction of 3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA) and NADPH + H+ to form 3-hydroxyoctadecanoyl-CoA and NADP+. This activity of HSD17B12 protein and its localization to the endoplasmic reticulum membrane was established in studies of transfected cells expressing the protein (Moon and Horton 2003).
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Very long-chain fatty acyl-CoA molecules are synthesized from palmitic acid (C16) or other fatty acids that are synthesized de novo or obtained from the diet. Before they can be elongated, these fatty acids are activated by conversion to fatty acyl-CoAs in reactions catalyzed by the five members of the ACSL (acyl-CoA synthetase long-chain) enzyme family. Elongation proceeds by a four-step reaction sequence parallel to that responsible for the synthesis of palmitate (C16) from acetyl-CoA and malonyl-CoA: a molecule of malonyl-CoA condenses with the long chain fatty acyl-CoA forming a 3-oxoacyl-CoA containing two more carbon atoms than the starting long chain fatty acyl-CoA and CO2. This reaction is catalyzed by one of the seven members of the ELOVL (Elongation of very long chain fatty acids protein) enzyme family. The 3-oxoacyl-CoA is reduced to a 3-hydroxyacyl-CoA by HSD17B12 (hydroxysteroid (17-beta) dehydrogenase 12), 3-hydroxyacyl-CoA is dehydrated to a trans-2,3-enoyl-CoA, and the trans-2,3-enoyl-CoA is reduced to a fatty acid two carbon atoms longer than the input one by TECR (trans-2,3-enoyl-CoA reductase) enzyme. All of these enzyme activities are associated with separate polypeptides associated with the endoplasmic reticulum membrane, unlike the multifunctional and cytosolic FAS complex responsible for synthesis of palmitic acid (Jakobsson ea 2006; Nugteren 1965). The specific reactions annotated here mediate the synthesis of stearoyl-CoA (3-hydroxyoctadecanoyl-CoA) from palmitate, as well as the activation and condensation with malonyl-CoA of arachidonic acid, a 20-carbon unsaturated fatty acid that plays a central role in the synthesis of prostaglandins and related hormones. Human cells contain a wide range of very long chain fatty acids, and the enzymes involved in these reactions are believed to have broader substrate specificities than are shown in these annotations, but few direct experimental data are available to support more extensive annotations.
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HDL particles play a central role in the reverse transport of cholesterol, the process by which cholesterol in tissues other than the liver is returned to the liver for conversion to bile salts and excretion from the body and provided to tissues such as the adrenals and gonads for steroid hormone synthesis (Tall et al. 2008). HDL particles are heterogeneous and can be fractionated into sub-populations based on their electrophoretic mobility, their density, or their content of various apolipoproteins. Sub-populations yielded by any one fractionation strategy, however, remain heterogeneous with respect to the other two parameters (Kontush and Chapman 2006). All HDL particles share two key features: they are assembled on a protein scaffold provided by apolipoprotein A-I (apoA-I), and they are recycled to allow a net flow of lipids from peripheral tissues to the liver and steroidogenic tissues while allowing apoA-I molecules to be re-used. The HDL life cycle annotated here does not capture the full complexity of HDL structure and function but rather is an attempt to outline the key steps by which HDL particles assemble and transfer their lipid content. These steps include the assembly of nascent (discoidal) HDL particles on newly synthesized apoA-I, a process that in the body occurs primarily in the liver, the loading of discoidal HDL with additional lipid through interaction with cells carrying excess cholesterol (transformation to spherical HDL), the conversion of HDL-associated cholesterol to cholesterol esters (remodeling of spherical HDL), the transfer of HDL lipids to target cells with the regeneration of pre-beta HDL (lipid-poor apoA-I), and the conversion of pre-beta HDL to discoidal HDL to complete the cycle. Additional reactions provide houekeeping functions needed for the efficient operation of the cycle: binding and release of CETP, dispersal of byproducts of the CETP reaction, and export and degradation of excess apoA-I protein. Finally, the function of torcetrapib as an inhibitor of CETP function is annotated.
Rat monoacylglycerol lipase (MGLL) catalyzes the hydrolysis of 2-acylglycerol to yield glycerol + fatty acid (Tornqvist and Belfrage 1976; Fredrikson et al. 1986). Localization of the enzyme to lipid particles is plausible, given its low solubility and its involvement in acylglycerol metabolism, but this localization has not been directly experimentally verified. The human reaction is inferred from the well-studied rat one.
Because of their hydrophobicity, lipids are found in the extracellular spaces of the human body primarily in the form of lipoprotein complexes. Chylomicrons form in the small intestine and transport dietary lipids to other tissues in the body. Very low density lipoproteins (VLDL) form in the liver and transport triacylglycerol synthesized there to other tissues of the body. As they circulate, VLDL are acted on by lipoprotein lipases on the endothelial surfaces of blood vessels, liberating fatty acids and glycerol to be taken up by tissues and converting the VLDL first to intermediate density lipoproteins (IDL) and then to low density lipoproteins (LDL). IDL and LDL are cleared from the circulation via a specific cell surface receptor, found in the body primarily on the surfaces of liver cells. High density lipoprotein (HDL) particles, initially formed primarily by the liver, shuttle several kinds of lipids between tissues and other lipoproteins. Notably, they are responsible for the so-called reverse transport of cholesterol from peripheral tissues to LDL for return to the liver. Three aspects of lipoprotein function are currently annotated in Reactome: chylomicron-mediated lipid transport, LDL endocytosis and degradation, and HDL-mediated lipid transport.
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At the beginning of this reaction, 1 molecule of 'H2O', and 1 molecule of 'trans-Hexadec-2-enoyl-CoA' are present. At the end of this reaction, 1 molecule of '(S)-3-Hydroxyhexadecanoyl-CoA' is present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'enoyl-CoA hydratase activity' of 'Trifunctional Protein'.
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At the beginning of this reaction, 1 molecule of 'NAD+', and 1 molecule of '(S)-3-Hydroxyhexadecanoyl-CoA' are present. At the end of this reaction, 1 molecule of '3-Oxopalmitoyl-CoA', 1 molecule of 'H+', and 1 molecule of 'NADH' are present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the '3-hydroxyacyl-CoA dehydrogenase activity' of 'Trifunctional Protein'.
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The overall process of triglyceride (triacylglycerol) biosynthesis consists of four biochemical pathways: fatty acyl-CoA biosynthesis, conversion of fatty acyl-CoA to phosphatidic acid, conversion of phosphatidic acid to diacylglycerol, and conversion fo diacylglycerol to triacylglycerol.
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At the beginning of this reaction, 1 molecule of 'palmitoyl-CoA', and 1 molecule of 'FAD' are present. At the end of this reaction, 1 molecule of 'FADH2', and 1 molecule of 'trans-Hexadec-2-enoyl-CoA' are present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'acyl-CoA dehydrogenase activity' of 'VLCAD acyl-CoA dehydrogenase homodimer'.
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At the beginning of this reaction, 1 molecule of '3-Oxopalmitoyl-CoA', and 1 molecule of 'CoA' are present. At the end of this reaction, 1 molecule of 'Acetyl-CoA', and 1 molecule of 'myristoyl-CoA' are present. This reaction takes place in the 'mitochondrial matrix' and is mediated by the 'transferase activity' of 'Trifunctional Protein'.
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This first pass through the beta-oxidation spiral starts with the saturated fatty acid palmitoyl-CoA and produces myristoyl-CoA. Four enzymatic steps are required, starting with VLCAD CoA dehydrogenase (Very Long Chain) activity, followed by three enzymatic steps, enoyl-CoA hydratase, 3-hydroxyacyl-CoA dehydrogenase, and ketoacyl-CoA thiolase activities, all present in the mitochondrial membrane associated trifunctional protein.
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Glycosylation-induced conformational modification positively regulates receptor-receptor association: a study with an aberrant epidermal growth factor receptor (EGFRvIII/DeltaEGFR) expressed in cancer cells
At the endoplasmic reticulum (ER) membrane, 1-acyl-lysophosphatidic acid (LPA) is acylated to phosphatidic acid (PA) by the enzymes 1-acyl-sn-glycerol-3-phosphate acyltransferases (AGPAT1 through 11), and lysophosphatidylcholine acyltransferase (LPCAT1) (Aguado and Campbell 1998). See recent review by Agarwal (2012, in press). AGPAT1, 2, 3 and LPCAT1 have been characterized biochemically (AGPAT1, 2: Yamashita et al. 2007, West et al. 1997, Aguado and Campbell 1998, Gale et al. 2006; AGPAT3: Agarwal et al. 2006; LPCAT1: Nakanishi et al. 2006, Chen et al. 2006). Two additional proteins, AGPAT4 and AGPAT5, are inferred to have such activity based on studies of homologous mouse enzymes (Lu et al. 2005). These enzymes differ in their tissue specific patterns of expression in the body and in their preferences for specific acyl CoA molecules (Shindou and Shimizu 2009; Takeuchi and Reue 2009).
Either of GPAM or GPAT2 (glycerol-3-phosphate acyltransferase, mitochondrial; glycerol-3-phosphate acyltransferase 2, mitochondrial) associated with the outer mitochondrial membrane catalyzes the reaction of cytosolic glycerol 3-phosphate and acyl-CoA to form 1-acylglycerol 3-phosphate and CoASH. The biochemical properties and location of human GPAM have been established through studies of the recombinant protein (Chen et al. 2008); those features of GPAT2 have been inferred from the properties of its rat homologue and those of GPAM. GPAM and GPAT2 differ in their their preferences for acyl-CoA substrates (Shindou & Shimizu 2009) and in their expression patterns in the body (Takeuchi & Reue 2009).
Glycerol can be a source for glycerol-3-phosphate, in which case, a phosphate form ATP is transferred to glycerol by glycerol kinase forming glycerol-3-phosphate and ADP.
Fatty acyl-CoA biosynthesis involves following steps: -Palmitate synthesis catalyzed by Acetyl-CoA carboxylase and Fatty acid synthase -Conversion of palmitic acid to long chain fatty acids and -Conversion of long chain fatty acids to fatty acyl-CoA by acyl-CoA synthases.
Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv
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Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA
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Calcium signalling: past, present and future
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Rich tapestry of G protein-coupled receptor signaling and regulatory mechanisms
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Metabolism of steroid hormones and vitamin D
Human X-linked phosphoribosylpyrophosphate synthetase superactivity is associated with distinct point mutations in the PRPS1 gene
Expression, localization, structural, and functional characterization of pFGE, the paralog of the Calpha-formylglycine-generating enzyme
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3,4-Hyp Glu-Gal-Hyl-collagen alpha-1(XV)
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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_27338.2
3,4-Hyp Glu-Gal-Hyl-collagen alpha-1(XVIII) chain
3,4-hydroxyprolyl-collagen alpha-1(XVIII) chain
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4-hydroxyprolyl-collagen alpha-1(XVIII) chain
4-Hyp 5-Gal-Hyl-collagen alpha-1(XVIII) chain
Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27536.1
4-Hyp 5-Hyl-collagen alpha-1(XVIII) chain
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3,4-Hyp 5-Gal-Hyl-collagen alpha-1(XVIII) chain
3,4-Hyp 5-Hyl-collagen alpha-1(XVIII) chain
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_157781.3
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The mitochondrial electron transport and oxidative phosphorylation system
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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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4-Hyp Glu-Gal-Hyl-collagen alpha-1(VIII) chain
4-hydroxyprolyl-collagen alpha-1(VIII) chain
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4-hydroxyprolyl collagen alpha-1(VIII) chain
4-Hyp 5-Gal-Hyl-collagen alpha-1(VIII) chain
4-Hyp 5-Hyl-collagen alpha-1(VIII) chain
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Glu-Gal-Hyl-collagen alpha-1(VIII) chain
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5-hydroxylysyl-collagen alpha-1(VIII) chain
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3,4-hydroxyprolyl-collagen alpha-1(VIII) chain
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_27294.1
3,4-Hyp Glu-Gal-Hyl-collagen alpha-1(VIII) chain
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3,4-Hyp 5-Hyl-collagen alpha-1(VIII) chain
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Expression of human thymidylate synthase in Escherichia coli
3,4-hydroxyprolyl-collagen alpha-1(IX) chain
3,4-Hyp 5-Hyl-collagen alpha-1(IX) chain
3,4-Hyp Glu-Gal-Hyl-collagen alpha-1(IX) chain
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4-Hyp 5-Gal-Hyl-collagen alpha-1(IX) chain
4-hydroxyprolyl-collagen alpha-1(IX) chain
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4-Hyp Glu-Gal-Hyl-collagen alpha-1(IX) chain
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4-hydroxyprolyl collagen alpha-1(IX) chain
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5-hydroxylysyl-collagen alpha-1(IX) chain
Phospholipid meets all-trans-retinal: the making of RPE bisretinoids
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3,4-Hyp 5-Gal-Hyl-collagen alpha-1(IX) chain
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Functional characterization of human 1-acylglycerol-3-phosphate acyltransferase isoform 8: cloning, tissue distribution, gene structure, and enzymatic activity
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The nucleoside diphosphate kinase D (NM23-H4) binds the inner mitochondrial membrane with high affinity to cardiolipin and couples nucleotide transfer with respiration
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The sulfur-containing amino acids: an overview
Advances in the understanding of cobalamin assimilation and metabolism
Signalling via integrins: implications for cell survival and anticancer strategies
Proteoglycan-collagen XV in human tissues is seen linking banded collagen fibers subjacent to the basement membrane
FUNCTION Removes the phosphate from trehalose 6-phosphate to produce free trehalose.CATALYTIC ACTIVITY Trehalose 6-phosphate + H(2)O = trehalose + phosphate.COFACTOR Divalent cation. Manganese or magnesium.ENZYME REGULATION Inhibited by EDTA and calcium. Diumycin and moenomycin stimulate activity at concentrations of up to 100 ug/ml, and then inhibit at higher concentrations.PATHWAY Glycan biosynthesis; trehalose biosynthesis.MISCELLANEOUS Was identified as a high-confidence drug target.SIMILARITY Belongs to the trehalose phosphatase family.
Intracellular calcium release from human platelets: different messengers for multiple stores
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
4-hydroxyprolyl collagen alpha-1(XXV) chain
4-Hyp Glu-Gal-Hyl-collagen alpha-1(XXV) chain
4-hydroxyprolyl-collagen alpha-1(XXV) chain
4-Hyp 5-Gal-Hyl-collagen alpha-1(XXV) chain
Overexpression of the normal phosphoribosylpyrophosphate synthetase 1 isoform undelies catalytic superactivity of human phosphoribosylpyrophosphate synthetase
5-hydroxylysyl-collagen alpha-1(XXV) chain
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_11294.1
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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_11734.2
3,4-Hyp 5-Hyl collagen alpha-1(VII) chain
3,4-Hyp Glu-Gal-Hyl collagen alpha-1(VII) chain
3,4-Hyp 5-Gal-Hyl collagen alpha-1(VII) chain
3,4-Hyp 5-Gal-Hyl-collagen alpha-1(XXV) chain
3,4-hydroxyprolyl-collagen alpha-1(XXV) chain
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Reactome stable identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_93162.9
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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_11409.2
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=197256
3,4-Hyp 5-Hyl-collagen alpha-1(XXV) chain
3,4-Hyp Glu-Gal-Hyl-collagen alpha-1(XXV) chain
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Glu-Gal-Hyl-collagen alpha-1(XVIII) chain
5-hydroxylysyl-collagen alpha-1(XVIII) chain
4-hydroxyprolyl collagen alpha-1(XVIII) chain
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Type XII and XIV collagens mediate interactions between banded collagen fibers in vitro and may modulate extracellular matrix deformability
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Inflammasome components NALP 1 and 3 show distinct but separate expression profiles in human tissues suggesting a site-specific role in the inflammatory response
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The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book)
4-Hyp Glu-Gal-Hyl-collagen alpha-1(XVIII) chain
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Biochemistry of signal transduction and regulation
Glu-Gal-Hyl-collagen alpha-1(XV) endostatin-XV
5-Gal-Hyl-collagen alpha-1(XV) endostatin-XV
5-hydroxylysyl-collagen alpha-1(XV) endostatin-XV
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DNA-3-methyladenine glycosylase (EC 3.2.2.21) (3-methyladenine DNA glycosidase) (ADPG) (3-alkyladenine DNA glycosylase) (N-methylpurine- DNA glycosirase)
4-hydroxyprolyl collagen alpha-1(XV) endostatin-XV
DNA repair protein REV1 ecNumber2.7.7.-/ecNumber
Heteroduplex DNA with D-loop structure with extended pairing between invading strand and complementary heteroduplex strand and containing newly synthesized ends
Endonuclease III-like protein 1 (EC 4.2.99.18)
repaired DNA template:nascent mRNA hybrid
damaged DNA substrate:nascent mRNA hybrid with dual incisions
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Molecular cloning of SLC26A7, a novel member of the SLC26 sulfate/anion transporter family, from high endothelial venules and kidney
Hemostasis and Thrombosis: Basic Principles and Clinical Practice
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Expression cloning of an oxysterol 7alpha-hydroxylase selective for 24-hydroxycholesterol
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Structures of lung cancer-derived EGFR mutants and inhibitor complexes: mechanism of activation and insights into differential inhibitor sensitivity
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3,4-Hyp 5-Gal-Hyl-collagen alpha-1(XV) endostatin-XV
3,4-Hyp Glu-Gal-Hyl-collagen alpha-1(XV) endostatin-XV
3,4-Hyp 5-Hyl-collagen alpha-1(XV) endostatin-XV
4-Hyp 5-Gal-Hyl-collagen alpha-1(XV) endostatin-XV
3,4-hydroxyprolyl-collagen alpha-1(XV) endostatin-XV
Elongated DNA template with bypassed lesion
4-Hyp Glu-Gal-Hyl-collagen alpha-1(XV) endostatin-XV
Epidermal growth factor receptor: elements of intracellular communication
damaged DNA substrate with misinserted bases
4-Hyp 5-Hyl-collagen alpha-1(XV) endostatin-XV
damaged DNA substrate inserted with correct base complement
Repaired DNA after oxidative dealkylation
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Glycosaminoglycans mediate the coacervation of human tropoelastin through dominant charge interactions involving lysine side chains
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3,4-hydroxyprolyl collagen alpha-1(VII) chain
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4-Hyp 5-Gal-Hyl collagen alpha-1(VII) chain
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Double-strand DNA containing a hypoxanthine
Double-strand DNA containing an ethenoadenine
Double-strand DNA containing a 3-methyladenine
5-hydroxylysyl collagen alpha-1(VII) chain
4-hydroxyprolyl collagen alpha-1(VII) chain
Mucin-type O-glycosylation and its potential use in drug and vaccine development
4-Hyp Glu-Gal-Hyl collagen alpha-1(VII) chain
Epidermal growth factor receptors with tyrosine kinase domain mutations exhibit reduced Cbl association, poor ubiquitylation, and down-regulation but are efficiently internalized
Double-strand DNA containing a thymine glycol
Double-strand DNA containing a formamidopyrimidine
Double-strand DNA containing a dihydrouracil
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Double-strand DNA containing a cytosine glycol
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DNA containing an apurinic/apyrimidinic (AP) site
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Double-strand DNA containing an adenine opposite to an 8-oxo guanine
Platelets in thrombotic and non-thrombotic disorders.
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Fatty acid, triacylglycerol, and ketone body metabolism
Sinauer Associates, Inc., P.O. Box 407 23 Plumtree Road, Sunderland, MA 01375 U.S.A.
Collagen type VII fibril (name copied from entity in Homo sapiens)
Cleaved collagen type XV multimer (name copied from entity in Homo sapiens)
Collagen type XV multimer (name copied from entity in Homo sapiens)
Ca/calmodulin activated Adenylate Cyclase
Mucopolysaccharidosis IV A: molecular cloning of the human N-acetylgalactosamine-6-sulfatase gene (GALNS) and analysis of the 5'-flanking region
Human adrenoleukodystrophy protein and related peroxisomal ABC transporters interact with the peroxisomal assembly protein PEX19p
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Human ornithine transcarbamylase: crystallographic insights into substrate recognition and conformational changes
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Glycine and taurine conjugation of bile acids by a single enzyme. Molecular cloning and expression of human liver bile acid CoA:amino acid N-acyltransferase.
Fat and beyond: the diverse biology of PPARgamma
Human mitochondrial phosphoenolpyruvate carboxykinase 2 gene. Structure, chromosomal localization and tissue-specific expression
Non-vesicular lipid transport by lipid-transfer proteins and beyond
3alpha,7alpha,12alpha-trihydroxy-5beta-cholan-24-one-CoA and CoASH react to form choloyl-CoA (3alpha,7alpha,12alpha-trihydroxy-5beta-cholan-24-one-CoA) and propionyl CoA. This reaction, in the peroxisomal matrix, is catalyzed by peroxisomal thiolase 2 (sterol carrier protein 2).
The isomerization of 25(R) DHCA-CoA to 25(S) DHCA-CoA, catalyzed by 2-methylacyl-CoA racemase, occurs in the peroxisomal matrix.
THCA (25(R) 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoate) , coenzyme A, and ATP react to form the CoA conjugate of 25(R) THCA, AMP, and pyrophosphate. This cytosolic reaction is catalyzed by SLC27A5 (BACS). SLC27A2 (VLCS) also catalyzes this reaction; the relative contributions of the two enzymes to de novo bile acid synthesis in vivo are not certain (Mihalik et al. 2002).
DHCA (25(R) 3alpha,7alpha-dihydroxy-5beta-cholestanoate), coenzyme A, and ATP react to form the CoA conjugate of 25(R) DHCA, AMP, and pyrophosphate. This cytosolic reaction is catalyzed by SLC27A2 (VLCS). SLC27A5 (BACS) also catalyzes this reaction; the relative contributions of the two enzymes to de novo bile acid synthesis in vivo are not certain (Mihalik et al. 2002).
The isomerization of 25(R) THCA-CoA to 25(S) THCA-CoA, catalyzed by 2-methylacyl-CoA racemase, occurs in the peroxisomal matrix.
DHCA (25(R) 3alpha,7alpha-dihydroxy-5beta-cholestanoate) , coenzyme A, and ATP react to form the CoA conjugate of 25(R) DHCA, AMP, and pyrophosphate. This cytosolic reaction is catalyzed by SLC27A5 (BACS). SLC27A2 (VLCS) also catalyzes this reaction; the relative contributions of the two enzymes to de novo bile acid synthesis in vivo are not certain (Mihalik et al. 2002).
Cholesterol, NADPH + H+, and O2 form 7alpha-cholesterol (5-cholesten-3beta, 7alpha-diol), NADP+,and H2O, in a reaction catalyzed by CYP7A1 (cholesterol 7alpha-hydroylase) in the endoplasmic reticulum membrane. In the body, this enzyme is expressed only in liver, and its expression is tightly regulated at the level of transcription to determine the overall rate of bile acid and bile salt production (Russell 2003; Pullinger et al. 2002).
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).
THCA (25(R) 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoate), coenzyme A, and ATP react to form the CoA conjugate of 25(R) THCA, AMP, and pyrophosphate. This cytosolic reaction is catalyzed by SLC27A2 (VLCS). SLC27A5 (BACS) also catalyzes this reaction; the relative contributions of the two enzymes to de novo bile acid synthesis in vivo are not certain (Mihalik et al. 2002).
Molecular cloning of a functional thrombin receptor reveals a novel proteolytic mechanism of receptor activation
7-Alpha-hydroxycholest-4-en-3-one, NADPH + H+, and O2 form 7-alpha,12-alpha-dihydroxycholest-4-en-3-one + NADP+ + H2O. This reaction is catalyzed by sterol 12alpha hydroxylase (CYP8B1), an enzyme associated with the endoplasmic reticulum membrane. While the human gene has been cloned (Gafvels et al. 1999), its protein product has not been characterized, and the enzymatic properties of human CYP8B1 protein are inferred from those of its well-characterized rabbit homolog (Ishida et al. 1992).
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Desmosterol is reduced by NADPH + H+ to form cholesterol and NADP+, catalyzed by DHCR24 associated with the endoplasmic reticulum membrane.
Lanosterol, NADPH + H+, and O2 react to form 4,4-dimethylcholesta-8(9),14,24-trien-3beta-ol, NADP+, H2O and formate. This oxidative demethylation reaction, in the endoplasmic reticulum, is catalyzed by lanosterol 14alpha-demethylase (CYP51A1). Although the reaction is annotated here as a single concerted event, studies with purified rat enzyme indicate that the methyl group is converted successively to an alcohol and an aldehyde before being released as formate (Trzaskos et al. 1986; Fischer et al. 1991; Gaylor 2002).
Cytosolic isopentenyl diphosphate isomerase (IPP isomerase) catalyzes an essential activation step in the isoprenoid biosynthetic pathway. It rearranges isopentenyl pyrophosphate into its highly electrophilic isomer, dimethylallyl pyrophosphate (DMAPP). IPP isomerase may also be located in human peroxisomes but it's function there is not clear.
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 conversion of isocitrate to 2-oxoglutarate (alpha-ketoglutarate) with the concomitant synthesis of NADPH from NADP+ is thought to play a significant role in supplying NADPH for other reactions in both the cytosol and the peroxisome (Geisbrecht and Gould 1999).
Cytosolic IDH1 (isocitrate dehydrogenase 1) homodimer catalyzes the reaction of isocitrate and NADP+ to form 2-oxoglutarate, CO2, and NADPH + H+. The same enzyme can also localize to peroxisomes (Geisbrecht and Gould 1999; Xu et al. 2004).
Why calcium-stimulated adenylyl cyclases?
Peroxisomal IDH1 (isocitrate dehydrogenase 1) homodimer catalyzes the reaction of isocitrate and NADP+ to form 2-oxoglutarate, CO2, and NADPH + H+. The same enzyme can also localize to the cytosol in at least some cell types (Geisbrecht and Gould 1999; Xu et al. 2004).
1-Acylglycerol-3-phosphate is synthesized from dihydroxyacetone phosphate, an acyl CoA molecule and NADPH + H+ in four reactions catalyzed by peroxisomal enzymes, either in the matrix of the organelle or associated with its membrane. These reactions are annotated here for palmityl (C16:0) CoA. In a series of less well-characterized reactions in the cytosol and endoplasmic reticulum, these molecules are converted to ether lipids (plasmalogens). The functions of plasmalogens are not well understood. They are an abundant subclass of phospholipids, however, and defects in their metabolism are associated with serious human disease (de Vet et al. 1999; Nagan and Zoeller 2001).
Peroxisomal alkylglycerone phosphate synthase (AGPS) catalyzes the reaction of 1-palmitoylglycerone phosphate and hexadecanol to form O-hexadecylglycerone phosphate and palmitate. The active form of the enzyme is post-translationally cleaved to remove its 58 aminoterminal residues, has a molecule of FAD as a cofactor, and occurs in the peroxisome as a complex with glyceronephosphate O-acyltransferase (GNPAT) (Biermann et al. 1999; Bierman and van den Bosch 1999; de Vet et al. 2000).
Peroxisomal glyceronephosphate O-acyltransferase (GNPAT) catalyzes the reaction of palmitoyl-CoA and DHAP to form 1-palmitoyl glycerone phosphate (1-palmitoyl dihydroxyacetone phosphate) and CoASH. The active form of the enzyme is one subunit of a heterotrimer with two molecules of the alkylglycerone phosphate synthase (AGPS) enzyme (Biermann et al. 1999). It was first purified and characterized biochemically by Ofman and Wanders (1994). Mutations in the GNPAT gene are associated with rhizomelic chondrodysplasia type 2 (Ofman et al. 1998, 2001).
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Oncogenic transformation by inhibitor-sensitive and -resistant EGFR mutants
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Phytanic acid arises through ruminant metabolism of chlorophyll and enters the human diet as a constituent of dairy products (Baxter 1968). It can act as an agonist for PPAR and other nuclear hormone receptors, but its normal role in human physiology, if any, is unclear. It is catabolized via a five-step alpha-oxidation reaction sequence that yields pristanoyl-CoA, which is turn is a substrate for beta-oxidation. These reactions take place in the peroxisomal matrix and their failure is associated with Refsum disease (Wanders et al. 2003).
VLCS (very long chain acyl-CoA synthetase), associated with the inner surface of the peroxisomal membrane, catalyzes the reaction of pristanate, CoA-SH and ATP to form pristanoyl-CoA, AMP and pyrophosphate (Steinberg et al. 1999).
Peroxisomal SCPx (Non-specific lipid transfer protein; SCP2) catalyzes the reaction of 3-ketopristanoyl-CoA and CoASH to form 4,8,12-trimethyltridecanoyl-CoA and propionyl-CoA. Both intact SCPx and an SCPx fragment corresponding to approximately the 430 aminoterminal residues of the protein are catalytically active in vitro; the latter form may predominate in vivo. Consistent with the role of SCPx in the beta-oxidation of branched-chain fatty acids in vitro, mutations in the protein are associated with elevated levels of pristanic acid in the blood in vivo and the development of neurological defects (Ferdinandusse et al. 2000, 2006).
Peroxisomal 2-methylacyl-CoA racemase (AMACR) catalyzes the isomerization of (2R)-pristanoyl-CoA to form (2S)-pristanoyl-CoA. The active form of the enzyme is a monomer (Schmitz et al. 1995; Amery et al. 2000; Ferdinandusse et al. 2000).
Pristanoyl-CoA, generated in the peroxisome by alpha-oxidation of dietary phytanic acid, is further catabolized by three cycles of peroxisomal beta-oxidation to yield 4,8-dimethylnonanoyl-CoA, acetyl-CoA and two molecules of propionyl-CoA. These molecules in turn are converted to carnitine conjugates, which can be transported to mitochondria (Wanders and Waterham 2006, Verhoeven et al. 1998, Ferdinandusse et al. 1999).
Peroxisomal ACOT8 catalyzes the hydrolysis of acetyl-CoA to form acetate and CoASH (Jones et al. 1999; Wanders and Waterham 2006).
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).
Homodimeric ABCD1 associated with the peroxisomal membrane mediates the uptake of cytosolic very long chain fatty acyl CoAs such as hexacosanoyl-CoA into the peroxisomal matrix. While the requirement for this uptake step in the catabolism of very long chain fatty acids is well-established, direct evidence for the function of ABCD1 as a transporter comes only from studies of its ability to restore peroxisomal long chain fatty acid catabolism in yeast strains whose endogenous transporters have been disrupted by mutation. ABCD1 is inferred to function as a dimer like other members of the ABCD transporter family. The energy requirements of peroxisomal fatty acid uptake (other ABCD transporter-mediated reactions are coupled to ATP hydrolysis) have not been established (van Roermund et al. 2008).
Peroxisomal HACL1 catalyzes the reaction of 2-hydroxyphytanoyl-CoA to form pristanal and formyl-CoA. The active form of the enzyme is a homotetramer, with one Mg++ and one molecule of thiamin pyrophosphate bound to each monomer (Croes et al. 1997; Foulon et al. 1999).
VLCS (very long chain acyl-CoA synthetase), associated with the inner surface of the peroxisomal membrane, cayalyzes the reaction of phytanate, CoA-SH, and ATP to form phytanoyl-CoA, AMP, and pyrophosphate (Steinberg et al. 1999).
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Ether lipid biosynthesis: alkyl-dihydroxyacetonephosphate synthase protein deficiency leads to reduced dihydroxyacetonephosphate acyltransferase activities
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The ACADM gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The ABCB4 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
FAD-linked mitochondrial glycerol 3-phosphate dehydrogenase (GPD2, alias: mGPDH) and its NAD-linked cytosolic isoform (GPD1, alias:cGPDH) constitute glycerol phosphate shuttle. GPD2 catalyzes the unidirectional conversion of glycerol-3-phosphate (G-3-P) to dihydroxyacetone phosphate (DHAP) with concomitant reduction of the enzyme-bound FAD. Impaired activity of GPD2 has been suggested to be one of the primary causes of insulin secretory defects in beta-cells and thus it is a candidate gene for type 2 diabetes.
Acetoacetate, beta-hydroxybutyrate, and acetone collectively are called ketone bodies. The first two are synthesized from acetyl-CoA, in the mitochondria of liver cells; acetone is formed by spontaneous decarboxylation of acetoacetate. Ketone body synthesis in liver is effectively irreversible because the enzyme that catalyzes the conversion of acetoacetate to acetoacetyl-CoA is not present in liver cells. Ketone bodies, unlike fatty acids and triglycerides, are water-soluble. They are exported from the liver, and are taken up by other tissues, notably brain and skeletal and cardiac muscle. There, they are broken down to acetyl-CoA which is oxidized via the TCA cycle to yield energy. In a normal person, this pathway of ketone body synthesis and utilization is most active during extended periods of fasting. Under these conditions, mobilization and breakdown of stored fatty acids generates abundant acetyl-CoA acetyl-CoA in liver cells for synthesis of ketone bodies, and their utilization in other tissues minimizes the demand of these tissues for glucose (Sass 2011).
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 FATP1 (SLC27A1) gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The CYP7A1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The levels of acetone in ketone bodies are much lower than those of acetoacetic acid and beta-hydroxybutyric acid. Acetone cannot be converted back to acetyl-CoA, and is excreted in urine, or breathed out through the lungs. Extrahepatic tissues utilize ketone bodies by converting the beta-hydroxybutyrate successively to acetoacetate, acetoacetatyl-CoA, finally to acetyl-CoA (Sass 2011).
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Maturation of collagen Ketoimine cross-links by an alternative mechanism to pyridinoline formation in cartilage
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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.
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Absorption of chlorophyll phytol in normal man and in patients with Refsum's disease
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Sterol transfer by ABCG5 and ABCG8: in vitro assay and reconstitution
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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
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The epoxidation of arachidonic acid by cytochrome P450s (CYPs) results in the formation of unique bioactive lipid mediators termed epoxyeicosatrienoic acids (EETs). Each double bond has been shown to be susceptible to oxidation, resulting in 5,6-EET, 8,9-EET, 11,12-EET, and 14,15-EET. The majority of the EET biological activities are diminished by the hydrolysis to the corresponding dihydroxyeicosatrienoic acids (DHET) (Capdevila et al. 2000, Buczynski et al. 2009, Vance & Vance 2008).
Epoxide hydrolase 2 (EPHX2) hydrolyses 5,6-, 8,9-, 11,12-, and 14,15-epoxyeicosatrienoic acids ("EET(1)") to their corresponding dihydroxyeicosatrienoic acids ("DHET(1)") (Werner et al. 2002; Gomez et al. 2004). The majority of the EET biological activities are diminished by this hydrolysis.
SGPL1 (sphingosine-1-phosphate lyase 1), associated with the endoplasmic reticulum membrane, catalyzes the cleavage of cytosolic sphinganine (dihydrosphingosine) 1-phosphate to form phosphoethanolamine and hexadecanal (Van Veldhoven et al. 2000; Fyrst and Saba 2008).
Eicosanoids, oxygenated, 20-carbon fatty acids, are autocrine and paracrine signaling molecules that modulate physiological processes including pain, fever, inflammation, blood clot formation, smooth muscle contraction and relaxation, and the release of gastric acid. Eicosanoids are synthesized in humans primarily from arachidonic acid (all-cis 5,8,11,14-eicosatetraenoic acid) that is released from membrane phospholipids. Once released, arachidonic acid is acted on by prostaglandin G/H synthases (PTGS, also known as cyclooxygenases (COX)) to form prostaglandins and thromboxanes, by arachidonate lipoxygenases (ALOX) to form leukotrienes, epoxygenases (cytochrome P450s and epoxide hydrolase) to form epoxides such as 15-eicosatetraenoic acids, and omega-hydrolases (cytochrome P450s) to form hydroxyeicosatetraenoic acids (Buczynski et al. 2009, Vance & Vance 2008). Levels of free arachidonic acid in the cell are normally very low so the rate of synthesis of eicosanoids is determined primarily by the activity of phospholipase A2, which mediates phospholipid cleavage to generate free arachidonic acid. The enzymes involved in arachidonic acid metabolism are typically constitutively expressed so the subset of these enzymes expressed by a cell determines the range of eicosanoids it can synthesize. Eicosanoids are unstable, undergoing conversion to inactive forms with half-times under physiological conditions of seconds or minutes. Many of these reactions appear to be spontaneous.
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Prostacyclin synthase (PTGIS) aka CYP8A1 mediates the isomerisation of prostaglandin H2 (PGH2) to prostaglandin I2 (PGI2) aka prostacyclin (Wada et al. 2004). This reaction is not coupled with any P450 reductase proteins nor consumes NADPH.
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The bioactive prostaglandin (PG) signalling molecules, including PGA2, PGE2, PGF2a, and PGI2 (prostacyclin) are synthesised from arachidonic acid and its products by various prostaglandin synthase type enzymes. Prostaglandin H2 (PGH2) is the starting point for the synthesis of Thromboxanes (TXs) (Buczynski et al. 2009, Vance & Vance 2008). PGs and TXs are collectively known as the prostanoids. Two enzymes, PTGS1 and 2 (COX1 and 2) both catalyze the two-step conversion of arachidonic acid to PGH2. PTGS1 is constitutively expressed in many cell types while PTGS2 is induced in response to stress and mediates the syntheses of prostaglandins associated with pain, fever, and inflammation. Aspirin irreversibly inactivates both enzymes (though it acts more efficiently on PTGS1), explaining both its antiinflammatory effects and side effects like perturbed gastic acid secretion. Drugs like celecoxib, by specifically inhibiting PTGS2, have a strong anti-inflammatory effect with fewer side effects. These PTGS2-specific drugs, however, probably because of their effects on the balance of prostaglandin synthesis in platelets and endothelial cells, can also promote blood clot formation (Buczynski et al. 2009; Stables & Gilroy 2011).
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On formation, leukotriene C4 (LTC4) is exported to the extracellular region by the ABCC1 transporter (Sjolinder et al. 1999, Lam et al. 1989) and processed further by cleavage reactions.
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Leukotrienes (LTs) are biologically active molecules formed in response to inflammatory stimuli. They cause contraction of bronchial smooth muscles, stimulation of vascular permeability, and attraction and activation of leukocytes. LTs were discovered in 1938 and were termed the "slow release substance" (SRS) until their structures were determined in 1979 and they were then renamed to leukotrienes. LTs are derived from arachidonic acid through action by arachidonate 5-lipoxygenase (ALOX5). Cysteinyl leukotrienes (LTC4, LTD4, and LTE4) are generated as products derived from leukotriene A4 (LTA4). Eoxins are generated from leukotrienes (LTs) and resemble cysteinyl leukotrienes but have a different three-dimensional structure (Murphy & Gijon 2007, Hammarstrom 1983, MA.Claesson 2009, Vance & Vance 2008, Buczynski et al. 2009).
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Linoleic acid (LA, 18:2(n-6)) is an omega-6 fatty acid obtained through diet, mainly from vegetable oils. Omega-6 fatty acids helps stimulate skin and hair growth, maintain bone health, regulate metabolism, and maintain the reproductive system. All the desaturation and elongation steps occur in the endoplasmic reticulum (ER) except for the final step which requires translocation to peroxisomes for partial beta-oxidation. The linoleic acid pathway involves the following steps: 18:2(n-6)-->18:3(n-6)--> 20:3(n-6)-->20:4(n-6)-->22:4(n-6)-->24:4(n-6)-->24:5(n-6)-->22:5(n-6). Two desaturation enzymes are involved in this process: delta-6 desaturase which converts 18:2(n-6) to 18:3 (n-6) and 24:4(n-6) to 24:5(n-6) respectively, and delta-5 desaturase which converts 20:3(n-6) to 20:4(n-6). (Sprecher 2002).
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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).
SIMILARITY Belongs to the SecD/SecF family. SecF subfamily.
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SIMILARITY Belongs to the SecD/SecF family. SecD subfamily.
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At the end of this reaction, 1 molecule of 'citrate lyase monomer' is present. This reaction takes place in the 'nucleus'.
Lipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphingolipids, eicosanoids, cholesterol, bile salts, steroid hormones, and fat-soluble vitamins. They function as a major source of energy (fatty acids, triacylglycerols, and ketone bodies), are major constituents of cell membranes (cholesterol and phospholipids), play a major role in their own digestion and uptake (bile salts), and participate in numerous signaling and regulatory processes (steroid hormones, eicosanoids, phosphatidylinositols, and sphingolipids). Because of their poor solubility in water, most lipids in extracellular spaces in the human body are found as complexes with specific carrier proteins. Regulation of the formation and movement of these lipoprotein complexes is a critical aspect of human lipid metabolism, and lipoprotein abnormalities are associated with major human disease processes including atherosclerosis and diabetes. The central steroid in human biology is cholesterol, obtained from animal fats consumed in the diet or synthesized de novo from acetyl-coenzyme A. (Vegetable fats contain various sterols but no cholesterol.) Cholesterol is an essential constituent of lipid bilayer membranes and is the starting point for the biosyntheses of bile acids and salts, steroid hormones, and vitamin D. Bile acids and salts are mostly synthesized in the liver. They are released into the intestine and function as detergents to solubilize dietary fats. Steroid hormones are mostly synthesized in the adrenal gland and gonads. They regulate energy metabolism and stress responses (glucocorticoids), salt balance (mineralocorticoids), and sexual development and function (androgens and estrogens). At the same time, chronically elevated cholesterol levels in the body are associated with the formation of atherosclerotic lesions and hence increased risk of heart attacks and strokes. The human body lacks a mechanism for degrading excess cholesterol, although an appreciable amount is lost daily in the form of bile salts and acids that escape recycling. Aspects of lipid metabolism currently annotated in Reactome include lipid digestion, mobilization, and transport; fatty acid, triacylglycerol, and ketone body metabolism; peroxisomal lipid metabolism; phospholipid and sphingolipid metabolism; cholesterol biosynthesis; bile acid and bile salt metabolism; and steroid hormone biosynthesis.
The length of the polyisoprenoid chain of ubiquinone aka coenzyme Q (Q), varies depending on the species involved: it is 6 in budding yeast, Saccharomyces cerevisiae, (Q6) and 10 in humans (Q10). Most ubiquinone is naturally reduced to ubiquinol (Q10H2 in humans) and it is this form which dominates in most human tissues. It functions as an ubiquitous coenzyme in redox reactions and its ability both to associate with complexes I and III of the electron transport chain and to move freely in the inner mitochondrial membrane are central to its role in electron transport. In eukaryotes ubiquinones/ubiquinols are also found in other membranes such as the endoplasmic reticulum, Golgi vesicles, lysosomes and peroxisomes. Ubiquinol/ubiquinone is synthesized in the following way. Initially, the polyisoprenoid tail is assembled by a polyprenyl diphosphate synthase. Next, 4 hydroxybenzoate polyprenyltransferase (COQ2) catalyses the formation of the covalent linkage between the benzoquinone head group and the tail to produce 4 hydroxy 3 polyprenyl benzoic acid intermediate (DHB, 3 decaprenyl 4 hydroxybenzoic acid in humans). There follows modifications of the aromatic ring starting with hydroxylation, followed by O methylation, and decarboxylation to form the 2 methoxy 6 polyprenyl phenol intermediate (DMPhOH ; 2 methoxy 6 decaprenylphenol in humans). Following this, two additional methylations, one C methylation, and one O methylation step, finally generate the fully substituted hydroquinone, ubiquinol (Szkopinska 2000, Kagan & Quinn 2000, Tran & Clarke 2007, Kawamukai 2009).
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The polyprenyl diphosphate synthase consists of a tetramer comprising two units of decaprenyl-diphosphate synthase subunit 1 (PDSS1) and two units of decaprenyl-diphosphate synthase subunit 2 (PDSS2). It catalyses the combination of 2-trans,6-trans-farnesyl diphosphate (FPP) with isopentenyl diphosphate (IPPP) to form the polyisoprenoid tail all-trans-decaprenyl diphosphate (all-E-10PrP2) (Saiki et al. 2005, Tekle et al. 2008).
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2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial (COQ5) catalyses the C-methyltransferase conversion of 2-methoxy-6-decaprenyl-1,4-benzoquinol (MDMQ10H2) to 6-methoxy-3-methyl-2-decaprenyl-1,4-benzoquinol (DMQ10H2). This reaction is inferred from the equivalent reaction in yeast (Barkovich et al. 1997).
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The steps involved in the synthesis of glycosphingolipids (sphingolipids with one or more sugars attached) are annotated here (Gault et al. 2010).
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Sphingolipids are derivatives of long chain sphingoid bases such as sphingosine (trans-1,3-dihydroxy 2-amino-4-octadecene), an 18-carbon unsaturated amino alcohol which is the most abundant sphingoid base in mammals. Amide linkage of a fatty acid to sphingosine yields ceramides. Esterification of phosphocholine to ceramides yields sphingomyelin, and ceramide glycosylation yields glycosylceramides. Introduction of sialic acid residues yields gangliosides. These molecules appear to be essential components of cell membranes, and intermediates in the pathways of sphingolipid synthesis and breakdown modulate processes including apoptosis and T cell trafficking. While sphingolipids are abundant in a wide variety of foodstuffs, these dietary molecules are mostly degraded by the intestinal flora and intestinal enzymes. The body primarily depends on de novo synthesis for its sphingolipid supply (Hannun and Obeid 2008; Merrill 2002). De novo synthesis proceeds in four steps: the condensation of palmitoyl-CoA and serine to form 3-ketosphinganine, the reduction of 3-ketosphinganine to sphinganine, the acylation of sphinganine with a long-chain fatty acyl CoA to form dihydroceramide, and the desaturation of dihydroceramide to form ceramide. Other sphingolipids involved in signaling are derived from ceramide and its biosynthetic intermediates. These include sphinganine (dihydrosphingosine) 1-phosphate, phytoceramide, sphingosine, and sphingosine 1-phosphate. Sphingomyelin is synthesized in a single step in the membrane of the Golgi apparatus from ceramides generated in the endoplasmic reticulum (ER) membrane and transferred to the Golgi by CERT (ceramide transfer protein), an isoform of COL4A3BP that is associated with the ER membrane as a complex with PPM1L (protein phosphatase 1-like) and VAPA or VAPB (VAMP-associated proteins A or B). Sphingomyelin synthesis appears to be regulated primarily at the level of this transport process through the reversible phosphorylation of CERT (Saito et al. 2008).
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The main steps involved in de novo sphingolipid synthesis are annotated here (Merrill 2002, Gault et al. 2010).
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Neutral ceramidase (ASAH2) is an enzyme localised to the plasma membrane that catalyses the hydrolysis of ceramide to sphingosine and free fatty acid (Hwang et al. 2005, Galadari et al. 2006).
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Molecular mechanism of phase I and phase II drug-metabolizing enzymes: implications for detoxification
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SGPL1 (sphingosine-1-phosphate lyase 1), associated with the endoplasmic reticulum membrane, catalyzes the cleavage of cytosolic sphingosine 1-phosphate to form phosphoethanolamine and hexadec-2-enal (Van Veldhoven et al. 2000; Fyrst and Saba 2008).
gamma-L-Glutamyl-L-cysteine [ChEBI:17515]
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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).
Mitochondrial isocitrate dehydrogenase IDH2 catalyzes the irreversible reaction of isocitrate and NADP+ to form alpha ketoglutarate, CO2, and NADPH + H+ (Hartong et al. 2008). The structure of the active human enzyme has not been determined experimentally, but is inferred to be a homodimer with one Mn++ bound to each subunit based on detailed studies of the homologous pig enzyme (Ceccarelli et al. 2002). NADP-specific IDH2 was the first isocitrate dehydrogenase isoenzyme to be characterized in biochemical studies of the mammalian TCA cycle (Ochoa 1948). Later work with yeast revealed the existence of both NADP-specific (IDH2-homologous) and NAD-specific (IDH3-homologous) enzymes and demonstrated the ADP-dependence of the latter (Kornberg and Pricer 1951), consistent with the now widely accepted view that IDH3 mediates the conversion of isocitrate to alpha-ketoglutarate in the TCA cycle. The physiological function of IDH2 is thus unclear. The recent observation that individuals homozygous for IDH3 mutations that sharply reduce its activity do not show symptoms of deficient energy metabolism in most tissues raises the possibility that the IDH2 reaction may play an accessory role in the TCA cycle (Hartong et al. 2008).
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At the end of this reaction, 1 molecule of 'Fatty acid synthase ' is present. This reaction takes place in the 'nucleus'.
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At the end of this reaction, 1 molecule of '1-acyl-sn-glycerol-3-phosphate acyltransferase alpha ' is present. This reaction takes place in the 'nucleus'.
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ChREBP (Carbohydrate Response Element Binding Protein) is a large multidomain protein containing a nuclear localization signal near its amino terminus, polyproline domains, a basic helix-loop-helix-leucine zipper domain, and a leucine-zipper-like domain (Uyeda et al., 2002). Its dephosphorylation in response to molecular signals associated with the well-fed state allows it to enter the nucleus, interact with MLX protein, and bind to ChRE DNA sequence motifs near Acetyl-CoA carboxylase, Fatty acid synthase, and Pyruvate kinase (L isoform) genes (Ishi et al.2004). This sequence of events is outlined schematically in the picture below (adapted from Kawaguchi et al. (2001) - copyright (2001) National Academy of Sciences, U.S.A.).
Many hormones that affect individual physiological processes including the regulation of appetite, absorption, transport, and oxidation of foodstuffs influence energy metabolism pathways. While insulin mediates the storage of excess nutrients, glucagon is involved in the mobilization of energy resources in response to low blood glucose levels, principally by stimulating hepatic glucose output. Small doses of glucagon are sufficient to induce significant glucose elevations. These hormone-driven regulatory pathways enable the body to sense and respond to changed amounts of nutrients in the blood and demands for energy. Glucagon and Insulin act through various metabolites and enzymes that target specific steps in metabolic pathways for sugar and fatty acids. The processes responsible for the long-term control of fat synthesis and short term control of glycolysis by key metabolic products and enzymes are annotated in this module as six specific pathways: Pathway 1. Glucagon signalling in metabolic pathways: In response to low blood glucose, pancreatic alpha-cells release glucagon. The binding of glucagon to its receptor results in increased cAMP synthesis, and Protein Kinase A (PKA) activation. Pathway 2. PKA mediated phosphorylation:PKA phosphorylates key enzymes, e.g., 6-Phosphofructo-2-kinase /Fructose-2,6-bisphosphatase (PF2K-Pase) at serine 36, and regulatory proteins, e.g., Carbohydrate Response Element Binding Protein (ChREBP) at serine 196 and threonine 666. Insulin mediated responses to high blood glucose will be annotated in future versions of Reactome. In brief, the binding of insulin to its receptor leads to increased protein phosphatase activity and to hydrolysis of cAMP by cAMP phosphodiesterase. These events counteract the regulatory effects of glucagon. Pathway 3: Insulin stimulates increased synthesis of Xylulose-5-phosphate (Xy-5-P). Activation of the insulin receptor results indirectly in increased Xy-5-P synthesis from Glyceraldehyde-3-phosphate and Fructose-6-phosphate. Xy-5-P, a metabolite of the pentose phosphate pathway, stimulates protein phosphatase PP2A. Pathway 4: AMP Kinase (AMPK) mediated response to high AMP:ATP ratio: In response to diet with high fat content or low energy levels, the cytosolic AMP:ATP ratio is increased. AMP triggers a complicated cascade of events. In this module we have annotated only the phosphorylation of ChREBP by AMPK at serine 568, which inactivates this transcription factor. Pathway 5: Dephosphorylation of key metabolic factors by PP2A: Xy-5-P activated PP2A efficiently dephosphorylates phosphorylated PF2K-Pase resulting in the higher output of F-2,6-P2 that enhances PFK activity in the glycolytic pathway. PP2A also dephosphorylates (and thus activates) cytosolic and nuclear ChREBP. Pathway 6: Transcriptional activation of metabolic genes by ChREBP: Dephosphorylated ChREBP activates the transcription of genes involved in glucose metabolism such as pyruvate kinase, and lipogenic genes such as acetyl-CoA carboxylase, fatty acid synthetase, acyl CoA synthase and glycerol phosphate acyl transferase. The illustration below summarizes this network of events. Black lines are metabolic reactions, red lines are negative regulatory events, and green lines are positive regulatory events (figure reused with permission from Veech (2003) - Copyright (2003) National Academy of Sciences, U.S.A.).
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The first and rate-limiting enzyme in tetrahydrobiopterin de novo biosynthesis is GTP cyclohydrolase I (GCH1, GTPCHI). Three different isoforms are produced but only isoform 1 is functionally active (Gütlich et al. 1994). GCH1 is functional as a homodecamer. First, a monomer of GCH1 forms a dimer. Then five dimers arrange into a ring-like structure to form the homodecamer (Nar et al. 1995).
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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.
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.
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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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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D2HDGH associated with the mitochondrial inner membrane catalyzes the FAD-dependent reaction of (R)-2-hydroxyglutarate to form 2-oxoglutarate (Achouri et al. 2004). D2HDGH mutations are associated with high levels of (R)-2-hydroxyglutarate in vivo and variable neurological symptoms (Struys et al. 2005; Wanders and Mooyer 1995)).
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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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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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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.
Mitochondria are often described as the "powerhouse" of a cell as it is here that energy is largely released from the oxidation of food. Reducing equivalents generated from beta-oxidation of fatty acids and from the Krebs cycle enter the electron transport chain (also called the respiratory chain). During a series of redox reactions, electrons travel down the chain releasing their energy in controlled steps. These reactions drive the active transport of H+ ions from the mitochondrial matrix , through the inner membrane to the intermembrane space. The respiratory chain consists of five main types of carrier; flavins, iron-sulfur centres, quinones, cytochromes (heme proteins) and copper. The two main reducing equivalents entering the respiratory chain are NADH and FADH2. NADH is linked through the NADH-specific dehydrogenase whereas FADH2 is reoxidised within succinate dehydrogenase and a ubiquinone reductase of the fatty acid oxidation pathway. Oxygen is the final acceptor of electrons and with H+ ions, is converted to form water, the end product of aerobic cellular respiration. A proton electrochemical gradient (often called protonmotive force) is established across the inner membrane, with positive charge in the intermembrane space relative to the matrix. Protons driven by the proton-motive force, can enter ATP synthase thus returning to the mitochondrial matrix. ATP synthases use this exergonic flow to form ATP in the matrix, a process called chemiosmotic coupling. A by-product of this process is heat generation. An antiport, ATP-ADP translocase, preferentially exports ATP from the matrix thereby maintaining a high ADP:ATP ratio in the matrix. The tight coupling of electron flow to ATP synthesis means oxygen consumption is dependent on ADP availability (termed respiratory control). High ADP (low ATP) increases electron flow thereby increasing oxygen consumption and low ADP (high ATP) decreases electron flow and thereby decreases oxygen consumption. There are many inhibitors of mitochondrial ATP synthesis. Most act by either blocking the flow of electrons (eg cyanide, carbon monoxide, rotenone) or uncoupling electron flow from ATP synthesis (eg dinitrophenol). Thermogenin is a natural protein found in brown fat. Newborn babies have a large amount of brown fat and the heat generated by thermogenin is an alternative to ATP synthesis (and thus electron flow only produces heat) and allows the maintenance of body temperature in newborns. The electron transport chain is located in the inner mitochondrial membrane and comprises some 80 proteins organized in four enzymatic complexes (I-IV). Complex V generates ATP but has no electron transfer activity. In addition to these 5 complexes, there are also two electron shuttle molecules; Coenzyme Q (also known as ubiquinone, CoQ) and Cytochrome c (Cytc). These two molecules shuttle electrons between the large complexes in the chain. How many ATPs are generated by this process? Theoretically, for each glucose molecule, 32 ATPs can be produced. As electrons drop from NADH to oxygen in the chain, the number of protons pumped out and returning through ATP synthase can produce 2.5 ATPs per electron pair. For each pair donated by FADH2, only 1.5 ATPs can be formed. Twelve pairs of electrons are removed from each glucose molecule; 10 by NAD+ = 25 ATPs 2 by FADH2 = 3 ATPs. Making a total of 28 ATPs. However, 2 ATPs are formed during the Krebs' cycle and 2 ATPs formed during glycolysis for each glucose molecule therefore making a total ATP yield of 32 ATPs. In reality, the energy from the respiratory chain is used for other processes (such as active transport of important ions and molecules) so under conditions of normal respiration, the actual ATP yield probably does not reach 32 ATPs. The reducing equivalents that fuel the electron transport chain, namely NADH and FADH2, are produced by the Krebs cycle (TCA cycle) and the beta-oxidation of fatty acids. At three steps in the Krebs cycle (isocitrate conversion to oxoglutarate; oxoglutarate conversion to succinyl-CoA; Malate conversion to oxaloacetate), a pair of electrons (2e-) are removed and transferred to NAD+, forming NADH and H+. At a single step, a pair of electrons are removed from succinate, reducing FAD to FADH2. From the beta-oxidation of fatty acids, one step in the process forms NADH and H+ and another step forms FADH2. Cytoplasmic NADH, generated from glycolysis, has to be oxidized to reform NAD+, essential for glycolysis, otherwise glycolysis would cease to function. There is no carrier that transports NADH directly into the mitochondrial matrix and the inner mitochondrial membrane is impermeable to NADH so the cell uses two shuttle systems to move reducing equivalents into the mitochondrion and regenerate cytosolic NAD+. The first is the glycerol phosphate shuttle, which uses electrons from cytosolic NADH to produce FADH2 within the inner membrane. These electrons then flow to Coenzyme Q. Complex I is bypassed so only 1.5 ATPs can be formed per NADH via this route. The overall balanced equation, summing all the reactions in this system, is NADHcytosol + H+cytosol + NAD+mito -> NAD+cytosol + NADHmito + H+mito The malate-aspartate shuttle uses the oxidation of malate to generate NADH in the mitochondrial matrix. This NADH can then be fed directly to complex I and thus can form 3 ATPs via the respiratory chain. The overall balanced equation is NADHcytosol + H+cytosol + FADinner memb -> NAD+cytosol + FADH2 inner memb Both of these shuttle systems regenerate cytosolic NAD+. The entry point for NADH is complex I (NADH dehydrogenase) and the entry point for FADH2 is Coenzyme Q. The input of electrons from fatty acid oxidation via ubiquinone is complicated and not shown in the diagram.
Oxidation of fatty acids and pyruvate in the mitochondrial matrix yield large amounts of NADH. The respiratory electron transport chain couples the re-oxidation of this NADH to NAD+ to the export of protons from the mitochonrial matrix, generating a chemiosmotic gradient across the inner mitochondrial membrane. This gradient is used to drive the synthesis of ATP; it can also be bypassed by uncoupling proteins to generate heat, a reaction in brown fat that may be important in regulation of body temperature in newborn children.
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Pyruvate metabolism and the citric acid (TCA) cycle together link the processes of energy metabolism in a human cell with one another and with key biosynthetic reactions. Pyruvate, derived from the reversible oxidation of lactate or transamination of alanine, can be converted to acetyl CoA. Other sources of acetyl CoA include breakdown of free fatty acids and ketone bodies in the fasting state. Acetyl CoA can enter the citric acid cycle, a major source of reducing equivalents used to synthesize ATP, or enter biosynthetic pathways. In addition to its role in energy generation, the citric acid cycle is a source of carbon skeletons for amino acid metabolism and other biosynthetic processes. One such process included here is the interconversion of 2-hydroxyglutarate, probably derived from porphyrin and amino acid metabolism, and 2-oxoglutarate (alpha-ketoglutarate), a citric acid cycle intermediate.
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Electron transfer flavoprotein, ETF, a 63kDa heterodimer composed of alpha and beta subunit, binds one FAD and one AMP per dimer. ETF resides on the matrix face of the mitochondrial inner membrane. Reducing equivalents from the beta-oxidation of fatty acyl CoAs are transferred to ETF, reducing the ETF-bound FAD to FADH2.
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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).
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TetraHCA (25(R) 3alpha,7alpha,12alpha,24(S)-tetrahydroxy-5beta-cholestanoate), coenzyme A, and ATP react to form the CoA conjugate of 25(R) TetraHCA, AMP, pyrophosphate and water. This cytosolic reaction is catalyzed by SLC27A5 (BACS). SLC27A2 (VLCS) also catalyzes this reaction; the relative contributions of the two enzymes to de novo bile acid synthesis in vivo are not certain (Mihalik et al. 2002).
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3,7,24THCA (25(R) 3alpha,7alpha,24(S)-trihydroxy-5beta-cholestanoate), coenzyme A, and ATP react to form the CoA conjugate of 3,7,24THCA, AMP, pyrophosphate and water. This cytosolic reaction is catalyzed by SLC27A5 (BACS). SLC27A2 (VLCS) also catalyzes this reaction; the relative contributions of the two enzymes to de novo bile acid synthesis in vivo are not certain (Mihalik et al. 2002).
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TetraHCA (25(R) 3alpha,7alpha,12alpha,24(S)-tetrahydroxy-5beta-cholestanoate), coenzyme A, and ATP react to form the CoA conjugate of 25(R) TetraHCA, AMP, pyrophosphate and water. This cytosolic reaction is catalyzed by SLC27A2 (VLCS). SLC27A5 (BACS) also catalyzes this reaction; the relative contributions of the two enzymes to de novo bile acid synthesis in vivo are not certain (Mihalik et al. 2002).
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3,7,24THCA (25(R) 3alpha,7alpha,24(S)-trihydroxy-5beta-cholestanoate), coenzyme A, and ATP react to form the CoA conjugate of 3,7,24THCA, AMP, pyrophosphate and water. This cytosolic reaction is catalyzed by SLC27A2 (VLCS). SLC27A5 (BACS) also catalyzes this reaction; the relative contributions of the two enzymes to de novo bile acid synthesis in vivo are not certain (Mihalik et al. 2002).
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A molecule of glycocholate, glycochenodeoxycholate, taurocholate, or taurochenodeoxycholate is transported from the cytosol to the extracellular space, coupled to the hydrolysis of a molecule of cytosolic ATP to ADP and orthophosphate. This reaction is mediated by ABCB11 (bile salt export pump). In the body, this reaction mediates the release of bile salts from the liver cells into the bile (Kullak-Ublick et al. 2004); the role of ABCB11 in the reaction is confirmed by the observed failure of bile salt export in patients in whom the transporter is defective (Noe et al. 2005).
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In the liver, synthesis of bile acids and bile salts is initiated with the conversion of cholesterol to 7alpha-hydroxycholesterol and of 7alpha-hydroxycholesterol to 4-cholesten-7alpha-ol-3-one. The pathway then branches: hydroxylation of 4-cholesten-7alpha-ol-3-one to 4-cholesten-7alpha, 12alpha-diol-3-one leads ultimately to the formation of cholate, while its reduction to 5beta-cholestan-7alpha-ol-3-one leads to chenodeoxycholate formation. The amounts of substrate following each branch appear to be determined by abundance of the hydroxylase enzyme: in human liver, cholate synthesis predominates. In both branches, reactions in the cytosol, the mitochondrial matrix, and the peroxisomal matrix result in modifications to the ring structure, shortening and oxidation of the side chain, conversion to a Coenzyme A derivative, and conjugation with the amino acids glycine or taurine. In the body, glycocholate, taurocholate, glycochenodeoxycholate, and taurochenodeoxycholate are released from hepatocytes into the bile and ultimately into the lumen of the small intestine, where they function as detergents to solubilize dietary fats. The liver synthetic pathway also yields small amounts of bile acids, cholate and deoxycholate, which may play a feedback role in regulating the bile acid synthetic pathway (Russell 2003). These reactions are outlined in the figure below.
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24-hydroxycholesterol, NADPH + H+, and O2 react to form cholest-5-ene-3beta,7alpha,24-triol, NADP+, and H2O. This hydroxylation reaction is catalyzed by CYP39A1 in the membrane of the endoplasmic reticulum. In the body, expression of CYP39A1 is restricted to the liver.
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4-Cholesten-7alpha,24(S)-diol-3-one, NADPH + H+, and O2 form 4-cholesten-7-alpha,12-alpha,24(S)-triol-3-one + NADP+ + H2O. This reaction is catalyzed by sterol 12alpha hydroxylase (CYP8B1), an enzyme associated with the endoplasmic reticulum membrane. While the human gene has been cloned (Gafvels et al. 1999), its protein product has not been characterized, and the enzymatic properties of human CYP8B1 protein are inferred from those of its well-characterized rabbit homolog (Ishida et al. 1992).
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Choloyl-CoA and water react to form cholate and CoASH. This reaction, catalyzed by acyl-coenzyme A thioesterase 8, occurs in the peroxisomal matrix (Jones et al. 1999; Hunt et al. 2002). While bile salts are the major product of the de novo biosynthetic pathway in the normal human liver, bile acids are major feedback regulators of this pathway and this hydrolysis reaction is thought to play a role in generating them (Russell 2003).
3alpha,7alpha-dihydroxy-5beta-cholan-24-one-CoA and CoASH react to form chenodeoxycholoyl-CoA (3alpha,7alpha-dihydroxy-5beta-cholan-24-one-CoA) and propionyl CoA. This reaction, in the peroxisomal matrix, is catalyzed by peroxisomal thiolase 2 (sterol carrier protein 2).
The role of small leucine-rich proteoglycans in collagen fibrillogenesis
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FUNCTION Lipoamide dehydrogenase is an essential component of the alpha-ketoacid dehydrogenase complexes, namely the pyruvate dehydrogenase (PDH) complex, the branched-chain alpha-ketoacid dehydrogenase (BCKADH) complex, and likely also the 2-oxoglutarate dehydrogenase (ODH) complex. Catalyzes the reoxidation of dihydrolipoyl groups which are covalently attached to the lipoate acyltransferase components (E2) of the complexes. Is also able to catalyze the transhydrogenation of NADH and thio-NAD(+) in the absence of D,L-lipoamide, and the NADH-dependent reduction of quinones in vitro.FUNCTION Together with AhpC, AhpD and DlaT, Lpd constitutes an NADH-dependent peroxidase active against hydrogen and alkyl peroxides as well as serving as a peroxynitrite reductase, thus protecting the bacterium against reactive nitrogen intermediates and oxidative stress generated by the host immune system.FUNCTION Appears to be essential for Mtb pathogenesis.CATALYTIC ACTIVITY Protein N(6)-(dihydrolipoyl)lysine + NAD(+) = protein N(6)-(lipoyl)lysine + NADH.COFACTOR Binds 1 FAD per subunit.ENZYME REGULATION Triazaspirodimethoxybenzoyls are high-nanomolar inhibitors of M.tuberculosis Lpd and are non-competitive versus NADH, NAD(+), and lipoamide and >100-fold selective compared to human Lpd.SUBUNIT Homodimer. Identified in a complex with AhpC, AhpD and DlaT. Also makes part of the PDH complex, consisting of multiple copies of AceE (E1), DlaT (E2) and Lpd (E3), and of the BCKADH complex, consisting of multiple copies of BkdA/BkdB (E1), BkdC (E2) and Lpd (E3).DISRUPTION PHENOTYPE Cells lacking this gene grow, albeit poorly, in standard medium with dextrose, glycerol, and fatty acids as carbon sources, but fail to grow on carbohydrates. They are less resistant than wild-type to exposition to mildly acidified nitrite, but are more resistant to oxidative stress in the form of H(2)O(2) in vitro. Lpd-deficient strains are severely attenuated in wild-type and immunodeficient mice. In contrast to wild-type or DlaT lacking strains, strains lacking Lpd are unable to grow on leucine or isoleucine. Disruption of this gene also leads to extraordinary accumulations of pyruvate and branched chain amino and keto acids.MISCELLANEOUS The active site is a redox-active disulfide bond.SIMILARITY Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family.
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Of the 20-40 grams of bile salts released daily by the liver, all but approximately 0.5 grams are reabsorbed from the intestine, returned to the liver, and re-used. This recycling involves a series of transport processes: uptake by enterocytes mediated by ASBT (SLC10A2), traversal of the enterocyte cytosol mediated by ileal bile acid binding protein (I-BABP - FABP6), efflux from enterocytes mediated by MRP3 (ABCC3), travel through the portal blood as a complex with albumin, and uptake by hepatocytes mediated by Na+-taurocholate transporting protein (NTPC - SLC10A1) and, to a lesser extent by organic anion transporting proteins A, C, and 8 (OATPA - SLCO1A2, OATPC - SLCO1B1, and OATP-8 - SLCO1B3). Once returned to the hepatocyte cytosol, bile acids (generated in the intestine by the action of bacteria on secreted bile salts) are activated by conjugation with coenzyme A, then coupled to glycine or taurine, regenerating bile salts for re-export into the bile, mediated by the bile salt export pump, ABCB11 (Kullak-Ublick et al. 2004; Mihalik et al. 2002; Trauner and Boyer 2003). Unmodified bile salts returned to the hepatocyte cytosol can be re-exported by ABCB11 without further modification.
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In a healthy adult human, about 500 mg of cholesterol is converted to bile salts daily (Russell 2003). The major pathway for bile salt synthesis in the liver begins with the conversion of cholesterol to 7alpha-hydroxycholesterol. Bile salt synthesis can also begin with the synthesis of an oxysterol - 24-hydroxycholesterol or 27-hydroxycholesterol. In the body, the initial steps of these two pathways occur in extrahepatic tissues, generating intermediates that are transported to the liver and converted to bile salts via the 7alpha-hydroxycholesterol pathway. These extrahepatic pathways contribute little to the total synthesis of bile salts, but are thought to play important roles in cholesterol homeostasis (Javitt 2002).
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Cholate or chenodeoxycholate, coenzyme A, and ATP react to form their CoA conjugates, AMP, pyrophosphate and water. This reaction is catalyzed by SLC27A5 (BACS) associated with the endoplasmic reticulum membrane, but the substrates and products are cytosolic (Mihalik et al. 2002).
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In the body, 27-hydroxycholesterol is synthesized in multiple tissues, exported to the liver, and converted there to bile acids and bile salts. This pathway is only a minor source of bile acids and bile salts, but may play a significant role particularly in the mobilization of cholesterol from lung phagocytes (Bjorkhem et al. 1994; Babiker et al. 1999; Javitt 2002). In the liver, conversion of 27-hydroxycholesterol to bile acids and bile salts is initiated with hydroxylation and oxidoreductase reactions to form 4-cholesten-7alpha,27-diol-3-one. The pathway then branches: hydroxylation of 4-cholesten-7alpha,27-diol-3-one to 4-cholesten-7alpha,12alpha,27-triol-3-one leads ultimately to the formation of cholate, while its reduction to 5beta-cholestan-7alpha,27-diol-3-one leads to chenodeoxycholate formation. In both branches, reactions in the cytosol, the mitochondrial matrix, and the peroxisomal matrix result in modifications to the ring structure, shortening and oxidation of the side chain, conversion to a Coenzyme A derivative, and conjugation with the amino acids glycine or taurine (Russell 2003). These reactions are outlined in the figure below. The final nine reactions are identical to ones of bile salt synthesis initiated by 7alpha-hydroxylation and are shown as arrows with no substrates.
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25-hydroxycholesterol is 7alpha-hydroxylated to cholest-5-ene-3beta,7alpha,25-triol by CYP7B1.
27-hydroxycholesterol, NADPH + H+, and O2 react to form cholest-5-ene-3beta,7alpha,27-triol, H2O, and NADP+. This reaction is catalyzed by CYP7B1 in the endoplasmic reticulum membrane. Defects in CYB7B1 are associated with failure of 7alpha-hydroxylation in vivo, and with liver damage, confirming both the function of the enzyme and the central role of the liver in this metabolic process (Setchell et al. 1998).
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4-Cholesten-7alpha,27-diol-3-one, NADPH + H+, and O2 form 4-Cholesten-7alpha,12alpha,27-triol-3-one + NADP+ + H2O. This reaction is catalyzed by sterol 12alpha hydroxylase (CYP8B1), an enzyme associated with the endoplasmic reticulum membrane. While the human gene has been cloned (Gafvels et al. 1999), its protein product has not been characterized, and the enzymatic properties of human CYP8B1 protein are inferred from those of its well-characterized rabbit homolog (Ishida et al. 1992).
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In the body, 24-hydroxycholesterol is synthesized in the brain, exported to the liver, and converted there to bile acids and bile salts. This pathway is only a minor source of bile acids and bile salts, but appears to be critical for the disposal of excess cholesterol from the brain (Bjorkhem et al. 1998; Javitt 2002). In the liver, conversion of 24-hydroxycholesterol to bile acids and bile salts is initiated with hydroxylation and oxidoreductase reactions to form 4-cholesten-7alpha,24(S)-diol-3-one. The pathway then branches: hydroxylation of 4-cholesten-7alpha,24(S)-diol-3-one to 4-cholesten-7alpha,12alpha,24(S)-triol-3-one leads ultimately to the formation of cholate, while its reduction to 5beta-cholestan-7alpha,24(S)-diol-3-one leads to chenodeoxycholate formation. In both branches, reactions in the cytosol, the mitochondrial matrix, and the peroxisomal matrix result in modifications to the ring structure, shortening and oxidation of the side chain, conversion to a Coenzyme A derivative, and conjugation with the amino acids glycine or taurine (Russell 2003). These reactions are outlined in the figure below. The final three reactions are identical to ones of bile salt synthesis initiated by 7alpha-hydroxylation and are shown as arrows with no substrates.
The isomerization of 3,7,24THCA-CoA to (24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA, catalyzed by 2-methylacyl-CoA racemase, occurs in the peroxisomal matrix.
The isomerization of 25(R) TetraHCA-CoA to (24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA, catalyzed by 2-methylacyl-CoA racemase, occurs in the peroxisomal matrix.
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Dihydroxyacetone phosphate (DHAP) is converted to 1-acyl glycerone 3-phosphate (GO3P) by the enzyme dihydroxyacetone phosphate acyltransferase (GNPAT) (de Vet et al. 1999, Ofman et al. 1994). This reaction step links Glycerolipid metabolism to Ether lipid metabolism.
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Glycerol-3-phosphate (G3P) is acylated to 1-acyl lysophosphatidic acid (LPA) by the enzymes glycerol-3-phosphate acyltransferase 1 (GPAT, also known as GPAM) and glycerol-3-phosphate acyltransferase 2 (GPAT2), at the outer mitochondrial (OM) membrane (Shindou & Shimizu 2009, Chen et al. 2008, Takeuchi & Reue 2009).
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SLC4 base (HCO3 -, CO3 2-) transporters: classification, function, structure, genetic diseases, and knockout models
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In the de novo synthesis of phosphatidic acid (PA), lysophosphatidic acid (LPA) is initially formed by the esterification of sn-1 by glycerol 3-phosphate acyltransferase (GPAT) from glycerol 3-phosphate (G3P). Next, LPA is converted to PA by a LPA acyltransferase (AGPAT, also known as LPAAT). In addition to this, PA is also formed when phosphatidylcholine (PC) is hydrolyzed by phospholipase D1/2 (PLD1/2). PA is involved in acyl chain remodeling via cleavage by phospholipases followed by reacylation by acyltransferases (Ghomashchi et al. 2010, Singer et al. 2002, Prasad et al. 2011, Shindou & Shimizu 2009, Cao et al. 2006).
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At the endoplasmic reticulum (ER) membrane, monoglyceride lipase (MGLL) hydrolyzes 2-monoacylglycerol (2-MAG) to form a fatty acid and glycerol (Dinh et al. 2004, Zvonok et al. 2008, Bertrand et al. 2010, Labar et al. 2010).
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Acyl chain remodeling of triacylglycerol (TAG) and diacylglycerol (DAG) progresses through their hydrolysis by patatin-like phospholipase domain-containing proteins 2/3 (PNPLA2/3). DAG is reacylated back to TAG by acylglycerol O-acyltransferase 1/2 (DGAT1/2), while DAG and its hydrolysis product 2-monoacylglycerol (2-MAG) are transacylated back to TAG by PNPLA2/3. In addition, the DAG hydrolysis product 2-MAG is subsequently hydrolyzed to fatty acid and glycerol by monoglyceride lipase (MGLL) (Jenkins et al. 2004).
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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).
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Functional genomics reveals extended roles of the Mycobacterium tuberculosis stress response factor sigmaH
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The 17HSD family of enzymes catalyze the final step in the synthesis of estradiol and testosterone. They convert inactive 17-ketosteroids to their active 17beta-hydroxy forms. Androstenedione, a ketosteroid, is reduced to testosterone, a highly potent androgen, by the enzyme 17beta-hydroxysteroid dehydrogenase isoform III (17HSD3). The other human isoforms of 17HSDs to take part in the final steps of active steroid biosynthesis are types 1 and VII, which reduce estrone to estradiol. Corticotropin (Adrenocorticotropic hormone, ACTH) acts through the ACTH receptor called melanocortin receptor type 2 (MC2R) to stimulate steroidogenesis, increasing the production of androgens (McKenna et al, 1997). In males, Lutropin (LH) stimulates testosterone production.
In a healthy adult human, about 500 mg of cholesterol is converted to bile salts daily. Newly synthesized bile salts are secreted into the bile and released into the small intestine where they emulsify dietary fats (Russell 2003). About 95% of the bile salts in the intestine are recovered and returned to the liver (Kullak-Ublick et al. 2004; Trauner and Boyer 2002). The major pathway for bile salt synthesis in the liver begins with the conversion of cholesterol to 7alpha-hydroxycholesterol. Bile salt synthesis can also begin with the synthesis of an oxysterol - 24-hydroxycholesterol or 27-hydroxycholesterol. In the body, the initial steps of these two pathways occur in extrahepatic tissues, generating intermediates that are transported to the liver and converted to bile salts via the 7alpha-hydroxycholesterol pathway. These extrahepatic pathways contribute little to the total synthesis of bile salts, but are thought to play important roles in extrahepatic cholesterol homeostasis (Javitt 2002).
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.
Androgens are the determining factors for male development and behaviour in vertebrates (Miller 2002).
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DHA-CoA preferentially moves back to the ER, perhaps as a free fatty acid. This conversion is usually catalysed by acyl-CoA thioesterases (ACOTs). No specific acyl-CoA thioesterase enzyme has been identified for the peroxisomal metabolism of DHA-CoA, but the peroxisomal ACOT8 has a wide substrate specificity and is likely to be responsible (Ferdinandusse et al. 2003, Hunt & Alexson. 2008).
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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).
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The 24-carbon tetracosahexaenoyl-CoA (6,9,12,15,18,21-24:6(n-3) is transported to peroxisomes to undergo a putative single cycle of peroxisomal beta-oxidation, producing Docosahexaenoic Acid (DHA) (Sprecher 2002, Luthria et al. 1996).
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) (this reaction) and the classic 3-ketoacyl-CoA thiolase (Ferdinandusse et al. 2001).
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Prior to this reaction all the enzymes involved in the desaturation and elongation of linoleic acid are located in the ER, but for this last step tetracosapentaenoyl-CoA must be transferred to the peroxisomes for partial beta-oxidation to docosapentaenoyl-CoA (DPA-CoA, 4,7,10,13,16-22:5(n-6)) (Su et al. 2001).
Expression and characterization of human mitochondrial ferredoxin reductase in Escherichia coli
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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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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).
Sulphatase activities are regulated by the interaction of sulphatase-modifying factor 1 with SUMF2
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Phospholipids contain a polar head group and two long-chain fatty acyl moieties, one of which is generally unsaturated. The head group is a glycerol or serine phosphate attached to a polar group such as choline. These molecules are a major constituent of cellular membranes, where their diverse structures and asymmetric distributions play major roles in determining membrane properties (Dowhan 1997). The four major classes of phospholipids in human plasma membranes are phosphatidylethanolamine, phosphatidylserine, phosphatidylcholine, and sphingomyelin. The first three are derivatives of glycerol while sphingomyelin is a derivative of serine. Here, pathways for the metabolism of glycerophospholipids, phosphphatidylinositol (PI), and sphingolipids are annotated.
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).
Acyl chain remodeling of cardiolipin (CL) occurs in the inner mitochondria membranes (IM) via hydrolysis by phopholipases and subsequent reacylation by acyltransferases. At the endoplasmic reticulum (ER) membrane the situation is more complicated with monolysocardiolipin (MLCL) involved in hydrolysis and subsequent reacylation back to CL (Zachman et al. 2010, Malhotra et al. 2009, Xu et al. 2003, Taylor & Hatch 2009, Cao et al. 2004, Zhao et al. 2009, Buckland et al. 1998).
At the inner mitochondrial membrane (IM), the trifunctional enzyme HADH (3-hydroxyacyl-CoA dehydrogenase), an octamer of four alpha (HADHA) and four beta (HADHB) subunits, acylates monolysocardiolipin (MLCL) to cardiolipin (CL) (Taylor & Hatch 2009).
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Acetyl-coenzyme A synthetase 2-like, mitochondrial
acyl-CoA synthetase short-chain family member 1
Acetyl-coenzyme A synthetase, cytoplasmic
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The control of mammalian DNA replication: a brief history of space and timing.
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NADPH:adrenodoxin oxidoreductase, mitochondrial
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Structures of isobutyryl-CoA dehydrogenase and enzyme-product complex: comparison with isovaleryl- and short-chain acyl-CoA dehydrogenases
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Human cationic amino acid transporters hCAT-1, hCAT-2A, and hCAT-2B: three related carriers with distinct transport properties
Allelism, non-allelism, and genetic compounds among the mucopolysaccharidoses
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Ca(2+)/calmodulin activated adenylyl cyclase
Novel mutations in 3-phosphoglycerate dehydrogenase (PHGDH) are distributed throughout the protein and result in altered enzyme kinetics
Beta-galactosidase deficiency (beta-galactosidosis): GM1 gangliosidosis and Morquio B disease
The Metabolic and Molecular Bases of Inherited Disease, 8th ed (Book): 3775-3809
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Recombinant human elastin polypeptides self-assemble into biomaterials with elastin-like properties
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N-acyl-phosphatidylethanolamine-hydrolyzing phospholipase D
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High affinity cationic amino acid transporter 1
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Isocitrate dehydrogenase (NADP) cytoplasmic R132H
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Low affinity cationic amino acid transporter 2, isoform B
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4-aminobutyrate aminotransferase, mitochondrial
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Succinate-semialdehyde dehydrogenase, mitochondrial
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Plasma membrane calcium-transporting ATPase 1
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Structural analysis of the human hydroxyindole-O-methyltransferase gene. Presence of two distinct promoters.
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ChEBI:57701 5-enolpyruvyl shikimate-3-phosphate
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Rad52 and Ku bind to different DNA structures produced early in double-strand break repair.
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Analysis and update of the human solute carrier (SLC) gene superfamily
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Oxidized LDL-induced endolysosomal phospholipidosis and enzymatically modified LDL-induced foam cell formation determine specific lipid species modulation in human macrophages
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Molecular cloning, sequencing and expression of the cDNA of the mitochondrial form of phosphoenolpyruvate carboxykinase from human liver
Characterization of purine nucleoside phosphorylase from human granulocytes and its metabolism of deoxyribonucleosides
Deficiency of carbohydrate response element-binding protein (ChREBP) reduces lipogenesis as well as glycolysis
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The Mycobacterium tuberculosis high-affinity iron importer, IrtA, contains an FAD-binding domain
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Plasma membrane calcium-transporting ATPase 3
Plasma membrane calcium-transporting ATPase 2
Plasma membrane calcium-transporting ATPase 4
Mammalian ABC transporters in health and disease
The role of calmodulin recruitment in Ca2+ stimulation of adenylyl cyclase type 8
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Prostaglandins, thromboxanes, leukotrienes, and cytochrome P-450 metabolites of arachidonic acid
4-Hyp 5-Gal-Hyl collagen alpha-3(V) propeptide
3,4-hydroxyprolyl collagen alpha-3(V) propeptide
3,4-Hyp Glu-Gal-Hyl collagen alpha-3(V) propeptide
3,4-Hyp 5-Hyl collagen alpha-3(V) propeptide
3,4-Hyp 5-Gal-Hyl collagen alpha-3(V) propeptide
Membrane-bound enzymes of cholesterol synthesis from lanosterol
Cholesterol, hydroxycholesterols, and bile acids
Proteomic analysis of proteins associated with lipid droplets of basal and lipolytically stimulated 3T3-L1 adipocytes
The glutamate/GABA-glutamine cycle: aspects of transport, neurotransmitter homeostasis and ammonia transfer
Complete amino acid sequence of human phosphoglycerate kinase. Isolation and amino acid sequence of tryptic peptides.
3,4-Hyp 5-Gal-Hyl-collagen alpha-1(VIII) chain
4-Hyp 5-Hyl collagen alpha-3(V) propeptide
4-Hyp Glu-Gal-Hyl collagen alpha-3(V) propeptide
4-hydroxyprolyl collagen alpha-3(V) propeptide
5-Gal-Hyl collagen alpha-3(V) propeptide
5-hydroxylysyl collagen alpha-3(V) propeptide
Glu-Gal-Hyl collagen alpha-3(V) propeptide
Atherosclerosis and sterol 27-hydroxylase: evidence for a role of this enzyme in elimination of cholesterol from human macrophages
Nitric oxide scavenging and detoxification by the Mycobacterium tuberculosis haemoglobin, HbN in Escherichia coli
The SLC20 family of proteins: dual functions as sodium-phosphate cotransporters and viral receptors
The SLC26 gene family of multifunctional anion exchangers
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Identification and characterization of HAOX1, HAOX2, and HAOX3, three human peroxisomal 2-hydroxy acid oxidases
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The tissue inhibitors of metalloproteinases (TIMPs): an ancient family with structural and functional diversity
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Update on interconversions of vitamin B-6 with its coenzyme
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Antigen processing and presentation by the class I major histocompatibility complex
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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).
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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.
Cytosolic GMP synthase (GMPS) catalyzes the reaction of xanthosine 5'-monophosphate (XMP), ATP, glutamine and water to form guanosine 5'-monophosphate (GMP), AMP, glutamate and pyrophosphate. GMPS is a monomer (Hirst et al. 1994; Nakamura and Lou 1995).
The 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).
Cloning and characterization of the aroA gene from Mycobacterium tuberculosis
Cytosolic ADAL (Adenosine DeAminase-Like) catalyzes the reaction of N6-methyl-AMP and water to form IMP and methylamine. The active form of the enzyme is a protein monomer complexed with a zinc ion (Murakami et al. 2011).
Cytosolic adenosine deaminase (ADA) catalyzes the hydrolysis of 2'deoxyadenosine and adenosine to yield deoxyinosine and inosine, respectively, plus ammonia (Akeson et al. 1988). Unpublished crystallographic data (PDB 3IAR) indicate that the human enzyme is a monomer.
Cytosolic nucleoside phosphorylase (NP) trimer catalyzes the reversible reaction of hypoxanthine with ribose 1-phosphate or deoxyribose 1-phosphate to form inosine or deoxyinosine and orthophosphate (Ealick et al. 1990; Wiginton et al. 1980). While NP is active with either ribose 1-phosphate or deoxyribose 1-phosphate in vitro, levels of deoxyribose 1-phosphate are normally low in vivo, limiting the extent of this reaction. NP deficiency in vivo is associated with defects in purine nucleotide salvage and leads to immunodeficiency (Williams et al. 1987).
Cytosolic nucleoside phosphorylase (NP) trimer catalyzes the reversible reaction of guanine with ribose 1-phosphate or deoxyribose 1-phosphate to form guanosine or deoxyguanosine and orthophosphate (Ealick et al. 1990; Wiginton et al. 1980). While NP is active with either ribose 1-phosphate or deoxyribose 1-phosphate in vitro, levels of deoxyribose 1-phosphate are normally low in vivo, limiting the extent of this reaction. NP deficiency in vivo is associated with defects in purine nucleotide salvage and leads to immunodeficiency (Williams et al. 1987).
Endoplasmic reticulum stress induction of insulin-like growth factor-binding protein-1 involves ATF4
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).
Pannexin-1 mediates large pore formation and interleukin-1beta release by the ATP-gated P2X7 receptor
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PRPP stimulates the dissociation of phosphoribosyl pyrophosphate amidotransferase tetramers to form dimers (Holmes et al. 1973a,b).
Cytosolic AMP, GMP, and IMP stimulate the association of phosphoribosyl pyrophosphate amidotransferase (PPAT) dimers to form tetramers (Holmes et al. 1973a,b).
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The irreversible transfer of an amino group from L-glutamine to 5'-phosphoribosylformylglycinamide (FGAR), forming 5'-phosphoribosylformylglycinamidine (FGAM) and glutamate, accompanied by the conversion of ATP to ADP and orthophosphate, is catalyzed by phosphoribosylformylglycinamidine synthetase. The human enzyme has been purified and characterized biochemically (Barnes et al. 1994). Fluoresence microscopy studies of cultured human cells have shown that the enzyme is cytosolic and suggest that it may co-localize with other enzymes of de novo IMP biosynthesis under some metabolic conditions (An et al. 2008).
The irreversible transfer of a formyl group to cytosolic 5-phosphoribosylglycinamide (GAR) to form 5'-phosphoribosylformylglycinamide (FGAR) is catalyzed by the phosphoribosylglycinamide formyltransferase domain of the trifunctional protein, "phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase" (GART) (Aimi et al. 1990; Zhang et al. 2002). Fluoresence microscopy studies of cultured human cells have shown that GART is cytosolic and suggest that it may co-localize with other enzymes of de novo IMP biosynthesis under some metabolic conditions (Gooljarsingh et al. 2001; An et al. 2008).
The synthesis of cytosolic 5-phosphoribosylglycinamide from 5-phosphoribosylamine and glycine, accompanied by the conversion of ATP to ADP and orthophosphate, is catalyzed by the phosphoribosylglycinamide synthetase domain of the trifunctional protein, "phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase" (GART) (Aimi et al. 1990). The active form of the protein is cytosolic (Gooljarsingh et al. 2001; An et al. 2008).
Cytosolic PPAT (phosphoribosyl pyrophosphate amidotransferase) catalyzes the reaction of 5-phospho-alpha-D-ribose 1-diphosphate (PRPP), water, and L-glutamine to form 5-phosphoribosylamine, L-glutamate, and pyrophosphate. This event is the committed step in de novo purine synthesis. The reaction itself is reversible, but it is pulled strongly in the direction of 5'-phosphoribosylamine synthesis by the irreversible hydrolysis of the pyrophosphate that is also formed in the reaction. Fluoresence microscopy studies of cultured human cells have shown that PPAT is cytosolic and suggest that it may co-localize with other enzymes of de novo IMP biosynthesis under some metabolic conditions (An et al. 2008). The PPAT enzyme is inferred to be an iron-sulfur protein, like its well-characterized B. subtilis homologue, because incubation of purified enzyme with molecular oxygen or chelating agents inactivates it, and activity can be restored by incubation with ferrous iron and inorganic sulfide. The stoichiometry of the iron-sulfur moiety and its role in enzyme activity remain unknown (Itakura and Holmes 1979). The fully active form of the enzyme is a dimer, which can associate further to form a tetramer with sharply reduced activity (Holmes et al. 1973b; Iwahana et al. 1993). Interaction of the enzyme with inosine 5'-monophosphate (IMP), guanosine 5'-monophosphate (GMP), and adenosine 5'-monophosphate (AMP), end products of de novo purine biosynthesis, favors tetramer formation, while interaction with 5-phospho-alpha-D-ribose 1-diphosphate (PRPP), a required substrate, favors formation of the active dimer. Kinetic studies suggest that the enzyme's binding site for GMP and IMP is separate from its AMP binding site (Holmes et al. 1973a).
The reversible synthesis of inosine 5'-monophosphate from 5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide (FAICAR) is catalyzed by the IMP cyclohydrolase activity of the bifunctional 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase enzyme. This cytosolic protein occurs primarily as a dimer (Rayl et al. 1996; Vergis et al. 2001) and may further associate with other enzymes of de novo IMP biosynthesis under some metabolic conditions (An et al. 2008).
The irreversible transfer of a formyl group to 5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR), to yield 5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide (FAICAR), is catalyzed by the phosphoribosylaminoimidazolecarboxamide formyltransferase activity of the bifunctional 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase enzyme. This cytosolic protein occurs primarily as a dimer (Rayl et al. 1996; Vergis et al. 2001) and may further associate with other enzymes of de novo IMP biosynthesis under some metabolic conditions (An et al. 2008).
The human nm23-H4 gene product is a mitochondrial nucleoside diphosphate kinase
Comparative analysis of gene regulation by the transcription factor PPARalpha between mouse and human
The reversible conversion of 5'-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide (SAICAR) to 5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR) and fumarate is catalyzed by adenylosuccinate lyase. The active form of this enzyme is a cytosolic tetramer (Stone et al. 1993), and fluoresence microscopy of cultured human cells suggests that it may associate with other enzymes of de novo IMP biosynthesis under some metabolic conditions (An et al. 2008). The enzyme also catalyzes the conversion of adenylosuccinate to adenosine 5'-monophosphate and fumarate. Humans lacking the enzyme accumulate dephosphorylated forms of both substrates, indicating that the enzyme mediates both reactions in vivo as well (Race et al. 2000).
The irreversible synthesis of cytosolic 5'-phosphoribosyl-5-aminoimidazole (AIR) from 5'-phosphoribosylformylglycinamidine (FGAM), accompanied by the conversion of ATP to ADP and orthophosphate, is catalyzed by the phosphoribosylaminoimidazole synthetase domain of the trifunctional protein, "phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase" (GART) (Aimi et al. 1990). The active form of the protein is cytosolic and may co-localize with other enzymes of de novo IMP biosynthesis under some metabolic conditions (Gooljarsingh et al. 2001; An et al. 2008).
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Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib
Structure and chromosomal assignment of the sterol 12alpha-hydroxylase gene (CYP8B1) in human and mouse: eukaryotic cytochrome P-450 gene devoid of introns
The murine and human cholesterol 7alpha-hydroxylase gene promoters are differentially responsive to regulation by fatty acids mediated via peroxisome proliferator-activated receptor alpha
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Conversion of NO2 to NO by reduced coenzyme F420 protects mycobacteria from nitrosative damage
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Crystallization and properties of human liver ornithine aminotransferase
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Receptor specificity of the fibroblast growth factor family. The complete mammalian FGF family.
Trans-synaptic transmission of vesicular Wnt signals through Evi/Wntless
(5Z,13E)-(15S)-6,9alpha-Epoxy-11alpha,15-dihydroxyprosta-5,13-dienoate [ChEBI:15552]
Structural and functional organization of the animal fatty acid synthase.
Cetuximab monotherapy and cetuximab plus irinotecan in irinotecan-refractory metastatic colorectal cancer
Characterization of a glutathione metabolic mutant of Mycobacterium tuberculosis and its resistance to glutathione and nitrosoglutathione
The microsomal cardiolipin remodeling enzyme acyl-CoA lysocardiolipin acyltransferase is an acyltransferase of multiple anionic lysophospholipids
'L-Phe [cytosol]' positively regulates 'GCH1 reduces GTP to dihydroneopterin triphosphate'
Nerve growth factor signaling, neuroprotection, and neural repair
'Zn2+ [mitochondrial matrix]' positively regulates '(R)-2-hydroxyglutarate + FAD => 2-oxoglutarate + FADH2'
'Co2+ [mitochondrial matrix]' positively regulates '(R)-2-hydroxyglutarate + FAD => 2-oxoglutarate + FADH2'
'IMP [cytosol]' positively regulates 'Formation of phosphoribosyl pyrophosphate amidotransferase tetramer'
'Mn2+ [mitochondrial matrix]' positively regulates '(R)-2-hydroxyglutarate + FAD => 2-oxoglutarate + FADH2'
'GMP [cytosol]' positively regulates 'Formation of phosphoribosyl pyrophosphate amidotransferase tetramer'
'AMP [cytosol]' positively regulates 'Formation of phosphoribosyl pyrophosphate amidotransferase tetramer'
'Dissociation of phosphoribosyl pyrophosphate amidotransferase tetramer' positively regulates '5-phospho-alpha-D-ribose 1-diphosphate (PRPP) + H2O + L-glutamine <=> 5-phosphoribosylamine + L-glutamate +pyrophosphate'
'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'
Basement membrane structure in situ: evidence for lateral associations in the type IV collagen network
'XMP [cytosol]' negatively regulates 'IMP + H2O + NAD+ => XMP + NADH + H+ [IMPDH1,2]'
'GDP [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
4,4-Dimethyl-5alpha-cholesta-8,14,24-trien-3beta-ol [ChEBI:1743]
'ATP [cytosol]' positively regulates 'NDP + reduced thioredoxin => dNDP + oxidized thioredoxin + H2O'
'GMP [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
'D-Fructose 1,6-bisphosphate [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
'ADS [cytosol]' negatively regulates 'IMP + L-Aspartate + GTP => Adenylosuccinate + GDP + Pi [ADSS]'
'Mg2+ [cytosol]' is required for 'ITPA hydrolyses XTP to XMP'
'Mg2+ [cytosol]' is required for 'ITPA hydrolyses dITP to dIMP'
'Mg2+ [cytosol]' is required for 'ITPA hydrolyses ITP to IMP'
'dATP [cytosol]' negatively regulates 'NDP + reduced thioredoxin => dNDP + oxidized thioredoxin + H2O'
The extracellular matrix: not just pretty fibrils
Novel molecular defects of the delta-aminolevulinate dehydratase gene in a patient with inherited acute hepatic porphyria
'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]'
'HCYS [cytosol]' positively regulates 'Excess homocysteine yields homolanthionine and H2S'
'Pb2+ [mitochondrial matrix]' negatively regulates 'FECH binds Fe2+ to PRIN9 to form heme'
'Cys [cytosol]' positively regulates 'Excess cysteine yields lanthionine and H2S'
Large complex globular domains of type VII procollagen contribute to the structure of anchoring fibrils
Molecular determinants of metalloproteinase substrate specificity: matrix metalloproteinase substrate binding domains, modules, and exosites
Peroxisomal fatty acid oxidation disorders and 58 kDa sterol carrier protein X (SCPx). Activity measurements in liver and fibroblasts using a newly developed method.
ERAAP synergizes with MHC class I molecules to make the final cut in the antigenic peptide precursors in the endoplasmic reticulum
Recent studies with the electron microscope on ordered aggregates of the tropocollagen macromolecule
Aspects of Protein Structure (Book): 289-300
Hydroxylation of proline and lysine residues in collagens and other animal and plant proteins.
Post-translational modification of proteins (Book): 1-51
The in situ conformation and axial location of the intermolecular cross-linked non-helical telopeptides of type I collagen
Dysregulation of TGF-beta activation contributes to pathogenesis in Marfan syndrome
The high-resolution structure of the NADP(H)-binding component (dIII) of proton-translocating transhydrogenase from human heart mitochondria
Collagens, Suprastructures, and Collagen Fibril Assembly
The Extracellular Matrix: An Overview (Book): 77-115
Synthesis of substrates in N-glycan biosythesis
Negative regulation of dE2F1 by cyclin-dependent kinases controls cell cycle timing
The Drosophila tweety family: molecular candidates for large-conductance Ca2+-activated Cl- channels
Prog Nucleic Acid Res Mol Biol 42:259-287
Characterization and tRNA recognition of mammalian mitochondrial seryl-tRNA synthetase
Cross-talk between the allosteric effector-binding sites in mouse ribonucleotide reductase
Human HRD1 promoter carries a functional unfolded protein response element to which XBP1 but not ATF6 directly binds
New regulatory mechanisms of TGF-beta receptor function
The ferritins: molecular properties, iron storage function and cellular regulation
Neurotransmitter Receptor Binding And Downstream Transmission In The Postsynaptic Cell
G protein betagamma subunits: central mediators of G protein-coupled receptor signaling
FUNCTION Catalyzes the NAD(P)H-dependent reduction of mycothione (the oxidized disulfide form of mycothiol) to mycothiol.CATALYTIC ACTIVITY 2 mycothiol + NAD(P)(+) = mycothione + NAD(P)H.COFACTOR Binds 1 FAD per subunit.SUBUNIT Homodimer.SIMILARITY Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family.
Identification of a dehydrogenase acting on D-2-hydroxyglutarate
4-Hydroxyphenylacetaldehyde [ChEBI:15621]
The NOD: a signaling module that regulates apoptosis and host defense against pathogens
PPARs: therapeutic targets for metabolic disease
Desaturation and chain elongation of n - 3 and n - 6 polyunsaturated fatty acids in the human CaCo-2 cell line
Genomic organization of the human phosphomannose isomerase (MPI) gene and mutation analysis in patients with congenital disorders of glycosylation type Ib (CDG-Ib)
Structure and sequence of the human alpha-L-iduronidase gene
Supramolecular interactions in the dermo-epidermal junction zone: anchoring fibril-collagen VII tightly binds to banded collagen fibrils
Integrating signals from RTKs to ERK/MAPK
xanthosine 5'-monophosphate [ChEBI:15652]
Proteoglycans and Sulfated Glycosaminoglycans
Characteristics of human types 1, 2 and 3 17 beta-hydroxysteroid dehydrogenase activities: oxidation/reduction and inhibition
Role of the CCAAT enhancer binding proteins (C/EBPs) in adipocyte differentiation
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.
Cytosolic phophoribosyl pyrophosphate synthetase catalyzes the reaction of D-ribose 5-phosphate and ATP to form 5-phospho-alpha-D-ribose and AMP. Three isoforms of the enzyme have been described. The first has been purified and characterized biochemically (Fox and Kelley 1971). The others are known only as inferred protein products of cloned genes; their catalytic properties have not been determined.
Cytosolic phosphoribosyl pyrophosphate synthetase 1 catalyzes the reaction of D-ribose 5-phosphate and dATP to form 5-phospho-alpha-D-ribose 1-diphosphate and 2'-deoxyadenosine 5'-monophosphate. While phosphoribosyl pyrophosphate synthetase 1 works well with either ATP or dATP as a substrate in vitro, the extent of the dATP reaction in vivo is unclear, as cellular dATP concentrations are normally very low (Fox and Kelley 1971).
The pentose phosphate pathway is responsible for the generation of a substantial fraction of the cytoplasmic NADPH required for biosynthetic reactions, and for the generation of ribose 5-phosphate for nucleotide synthesis. Although the pentose phosphate pathway and glycolysis are distinct, they involve three common intermediates, glucose 6-phosphate, glyceraldehyde 3-phosphate, and fructose 6-phosphate, so the two pathways are interconnected. The pentose phosphate pathway consists of eight reactions:1. Conversion glucose 6-phosphate to D-glucono-1,5-lactone 6-phosphate, with the formation of NADPH; 2. Conversion of D-glucono-1,5-lactone 6-phosphate to 6-phospho-D-gluconate; 3. Conversion of 6-phospho-D-gluconate to ribulose 5-phosphate, with the formation of NADPH; 4. Conversion of ribulose 5-phosphate to xylulose 5-phosphate; 5. Conversion of ribulose 5-phosphate to ribose 5-phosphate; 6. Rearrangement of ribose 5-phosphate and xylulose 5-phosphate to form sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate; 7. Rearrangement of sedoheptulose 7-phosphate and glyceraldehyde 3-phosphate to form erythrose 4-phosphate and fructose 6-phosphate; and 8. Rearrangement of xylulose 5-phosphate and erythrose 4-phosphate to form glyceraldehyde 3-phosphate and fructose-6-phosphate. The oxidative branch of the pentose phosphate pathway, reactions 1-3, generates NADPH and pentose 5-phosphate. The non-oxidative branch of the pathway, reactions 4-8, converts pentose 5-phosphate to other sugars. The overall pathway can operate to generate only NADPH (glucose 6-phosphate is converted to pentose 5-phosphates, which are directed to the synthesis of fructose 6-phosphate and glyceraldehyde 3-phosphate, which in turn are converted back to glucose 6-phosphate). The reactions of the non-oxidative branch can operate to generate net amounts of ribose 5-phosphate with no production of NADPH. Net flux through this network of reactions appears to depend on the metabolic state of the cell and the nature of the biosynthetic reactions underway (Casazza and Veech 1987). G6PD, the enzyme that catalyzes the first reaction of the pathway, is more extensively mutated in human populations than any other enzyme, pehaps because these mutant alleles confer malaria resistance (Luzzatto and Afolayan 1968). Mutations affecting other parts of the pathway are rare, though several have been described and studies of their effects have contributed to our understanding of the normal flux of metabolites through this network of reactions (Wamelink et al. 2008).
Cytosolic ribulose-5-phosphate-3-epimerase (RPE) catalyzes the reversible interconversion of D-xylulose 5-phosphate and D-ribulose 5-phosphate (Bose and 1985). The electrophoretic properties of RPE activity detected in extracts of mouse-human somatic cell hybrids suggest that the active form of the enzyme is a homodimer (Spencer and Hopkinson 1980).
Cytosolic ribulose-5-phosphate-3-epimerase (RPE) catalyzes the reversible interconversion of D-ribulose 5-phosphate and D-xylulose 5-phosphate (Bose and 1985). The electrophoretic properties of RPE activity detected in extracts of mouse-human somatic cell hybrids suggest that the active form of the enzyme is a homodimer (Spencer and Hopkinson 1980).
Cytosolic phosphogluconate dehydrogenase (PGD) catalyzes the reaction of 6-phospho-D-gluconate and NADP+ to form D-ribulose 5-phosphate, CO2, and NADPH + H+ (Beutler and Kuhl 1985; Rippa et al. 1998). The PGD enzyme is dimeric (Dallocchio et al. 1985).
(S)-2-Methyl-3-oxopropanoyl-CoA [ChEBI:15466]
(R)-2-Methyl-3-oxopropanoyl-CoA [ChEBI:15465]
N-sulphoglucosamine sulphohydrolase (SGSH) hydrolyses the sulfate group from the terminal N-sulphoglucosamine residue of heparan sulfate (Scott et al. 1995). Defects in SGSH cause mucopolysaccharidosis type IIIA (MPSIIIA, MIM:252900), also called Sanfilippo syndrome A (Weber et al. 1997).
Alpha-N-acetylglucosaminidase (NAGLU) also hydrolyses another nonreducing, terminal N-acetyl-D-glucosamine residue from heparan sulfate. The active form of the enzyme (77kDa) is derived from an 82kDa precursor (Weber et al. 1996). Defects in NAGLU cause Mucopolysaccharidosis type IIIB (MPSIIIB, MIM:252920), also known as Sanfilippo syndrome type B (Beesley et al. 2005).
The SLC26A1 and 2 genes encode proteins that facilitate sulfate uptake into cells. The mechanism by which these transporters work is unclear but may be enhanced by extracellular halides or acidic pH environments, cotransporting protons electroneutrally. SLC26A1 encodes the sulfate anion transporter 1 (SAT1) (Regeer et al. 2003) which can transport sulfate and oxalate across the basolateral membrane of epithelial cells. It is most abundantly expressed in the liver and kidney, with lower levels expressed in many other parts of the body. SLC26A2 is ubiquitously expressed and encodes a sulfate transporter (Diastrophic dysplasia protein, DTD, DTDST) (Hastbacka et al. 1994). This transporter provides sulfate for proteoglycan sulfation which is needed for cartilage development. Defects in SLC26A2 are implicated in the pathogenesis of several human chondrodysplasias.
PAPS (3'-phosphoadenosine-5'-phosphosulfate), which functions as a sulfate donor in the cell, is synthesized from sulfate and two molecules of ATP in a two-step process (Robbins & Lipmann 1958) catalyzed in vertebrates by a bifunctional enzyme (Venkatachalam et al. 1998). PAPS synthesis takes place in the cytosol, and it is either consumed there in the sulfonation of a variety of hormones and xenobiotics, or it is transported to the Golgi apparatus and consumed in the synthesis of proteoglycans like chondroitin sulfate. Two isoforms of the human bifunctional enzyme are known, mutations in one of which are associated with defects in proteoglycan biosynthesis (Girard et al. 1998, ul Haque et al. 1998).
Inositol monophosphatase 1 (IMPA1) and 2 (IMPA2) homodimers dephosphorylate inositol 1-phosphate (I1P) to inositol (Ins). In vitro, IMPA1 and 2 differ in their pH optima and IMPA1 has a significantly greater activity on IP4 than does IMPA2 (McAllister et al. 1992, Ohnishi et al. 2007).
Inositol monophosphatase 1 (IMPA1) and 2 (IMPA2) homodimers dephosphorylate inositol 4-phosphate (I4P) to inositol (Ins). In vitro, IMPA1 and 2 differ in their pH optima and IMPA1 has a significantly greater activity on IP4 than does IMPA2 (Ohnishi et al. 2007).
The acronym HS-GAG is used to describe both heparin and heparan sulfate. HS-GAG is a member of the glycosaminoglycan family and consists of a variably sulfated repeating disaccharide unit, the most common one (50% of the total) being glucuronic acid (GlcA) linked to N-acetylglucosamine (GlcNAc). GlcA can be epimerized to iduronic acid. Higher degrees of sulfation and iduronic acid content in the polysaccharide chain confers the name heparin rather than heparan sulfate to the chain. HS-GAG, like the majority of GAGs in the body, are linked to core proteins, forming proteoglycans (mucopolysaccharides). Two or three HS-GAG chains attach to a core protein on the cell surface or in the extracellular matrix (Sasisekharan & Venkataraman 2000). HS-GAG bound to a core protein can regulate many biological processes such as angiogenesis, blood coagulation and tumour metastasis (Stringer & Gallagher 1997, Tumova et al. 2000). Degradation of HS-GAG is required to maintain a natural turnover of GAGs. Defects in the degradative enzymes result in lysosomal storage diseases, where GAGs build up rather than being broken down and having pathological effects (Ballabio & Gieselmann 2009).
Lysosomal degradation of glycoproteins is part of the cellular homeostasis of glycosylation (Winchester 2005). The steps outlined below describe the degradation of heparan sulfate/heparin. Complete degradation of glycoproteins is required to avoid build up of glycosaminoglycan fragments which can cause lysosomal storage diseases. The proteolysis of the core protein of the glycoprotein is not shown here.
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.
Glycosaminoglycans (GAGs) are long, unbranched polysaccharides containing a repeating disaccharide unit composed of a hexosamine (either N-acetylgalactosamine (GalNAc) or N-acetylglucosamine (GlcNAc)) and a uronic acid (glucuronate or iduronate). They can be heavily sulfated. GAGs are located primarily in the extracellular matrix (ECM) and on cell membranes, acting as a lubricating fluid for joints and as part of signalling processes. They have structural roles in connective tissue, cartilage, bone and blood vessels (Esko et al. 2009). GAGs are degraded in the lysosome as part of their natural turnover. Defects in the lysosomal enzymes responsible for the metabolism of membrane-associated GAGs lead to lysosomal storage diseases called mucopolysaccharidoses (MPS). MPSs are characterised by the accumulation of GAGs in lysosomes resulting in chronic, progressively debilitating disorders that in many instances lead to severe psychomotor retardation and premature death (Cantz & Gehler 1976, Clarke 2008). The biosynthesis and breakdown of the main GAGs (hyaluronate, keratan sulfate, chondroitin sulfate, dermatan sulfate and heparan sulfate) is described here.
mitochondrial fatty acid beta-oxidation of saturated fatty acids
Inositol phosphates IP2, IP and the six-carbon cyclic alcohol inositol (Ins) are produced by various phosphatases and the inositol-3-phosphate synthase 1 (ISYNA1) (Ju et al. 2004, Ohnishi et al. 2007, Irvine & Schell 2001, Bunney & Katan 2010).
Inositol phosphates (IPs) are molecules involves in signalling processes in eukaryotes. myo-Inositol consists of a six-carbon cyclic alcohol with an axial 2-hydroxy and five equatorial hydroxyls. Mono-, di-, and triphosphorylation of the inositol ring generates a wide variety of stereochemically distinct signalling entities. Inositol 1,4,5-trisphosphate (I(1,4,5)P3), is formed when the phosphoinositide phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) is hydrolysed by a phospholipase C isozyme. An array of inositol trisphosphate (IP3) and tetrakisphosphate (IP4) molecules are synthesised by the action of various kinases and phosphatases in the cytosol. These species then transport between the cytosol and the nucleus where they are acted on by inositol polyphosphate multikinase (IPMK), inositol-pentakisphosphate 2-kinase (IPPK), inositol hexakisphosphate kinase 1 (IP6K1) and 2 (IP6K2), to produce IP5, IP6, IP7, and IP8 molecules. Some of these nuclear produced IPs transport back to the cytosol where they are converted to an even wider variety of IPs, by kinases and phosphatases, including the di- and triphospho inositol phosphates aka pyrophosphates (Irvine & Schell 2001, Bunney & Katan 2010, Alcazar-Romain & Wente 2008, York 2006, Monserrate and York 2010).
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).
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).
Inositol monophosphatase 1 (IMPA1) and 2 (IMPA2) homodimers dephosphorylate inositol 3-phosphate (I3P) to inositol (Ins). In vitro, IMPA1 and 2 differ in their pH optima and IMPA1 has a significantly greater activity on IP4 than does IMPA2 (Ohnishi et al. 2007).
NPC1L1 protein mediates the uptake of dietary sterols from the gut lumen. These include cholesterol and plant sterols (phytosterols). Half to two-thirds of the 250-500 milligrams of cholesterol consumed daily from a typical western diet is taken up by this route and exported from enterocytes into the lymph in chylomicrons. Of the 200-400 milligrams of dietary phytosterol, only about 5% is absorbed.The drug ezetimibe interferes with NPC1L1-mediated sterol uptake (Oram and Vaughan 2006). Both cholesterol and phytosterols are secreted from the liver into the bile (Salen et al. 1970). Mutations affecting the ABCG5/8 transporter complex inhibit this process (e.g., Berge et al. 2000), while the molecular details of sterol export in human cells have not been worked out, they can be inferred from the properties of the homologous mouse proteins (Graf et al. 2003; Wang et al. 2006).
ABCG5/8 in the plasma membrane mediates the ATP-dependent export of cytosolic sterols (cholesterol and phytosterols). Mutations affecting the ABCG5/8 proteins are associated with the accumulation of high levels of cholesterol and phytosterols in the body, demonstrating the specificity and physiological importance of this process (Berge et al. 2000). Human ABCG5/8 has not been studied in detail, but the homologous mouse protein complex mediate ATP-dependent sterol export (Wang et al. 2006). The mouse proteins localize to the apical plasma membranes of enterocytes and hepatocytes, consistent with the hypothesis that in vivo ABCG5/8 mediates sterol export into the gut lumen and from hepatocytes into the bile (Graf et al. 2003).
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.
Biochemical genetics of the pentose phosphate cycle: human ribose 5-phosphate isomerase (RPI) and ribulose 5-phosphate 3-epimerase (RPE)
In an ATP-dependent reaction, ABCG1 mediates the movement of intracellular cholesterol to the extracellular face of the plasma membrane. In a tissue culture model system, the active form of ABCG1 is predominantly a tetramer (Vuaghan and Oram 2005). The number of lipid molecules transported per ATP consumed is not known.
The way Wnt works: Components and mechanism
(2S,3S)-3-Hydroxy-2-methylbutanoyl-CoA [ChEBI:15449]
Phospholipase C-gamma as a signal-transducing element
Human sphingosine-1-phosphate lyase: cDNA cloning, functional expression studies and mapping to chromosome 10q22(1)
Extracellular matrix metalloproteinase 2 levels are regulated by the low density lipoprotein-related scavenger receptor and thrombospondin 2
Sphingosine-1-phosphate lyase in development and disease: sphingolipid metabolism takes flight
Synthesis and recycling of tetrahydrobiopterin in endothelial function and vascular disease
Ca2+ entry, efflux and release in smooth muscle
Genetic heterogeneity and clinical variability in the Sanfilippo syndrome (types A, B, and C)
3alpha,7alpha-Dihydroxy-5beta-cholestanoyl-CoA [ChEBI:1709]
4,8,12-Trimethyltridecanoyl-CoA [ChEBI:1757]
2'-deoxyadenosine 5'-monophosphate [ChEBI:17713]
Mechanisms of human DNA repair: an update.
Structural and functional characterization of human NAD kinase
The 7 TM G-protein-coupled receptor target family
The role of cis-trans isomerization of peptide bonds in the coil leads to and comes from triple helix conversion of collagen
Three conformationally distinct domains in the amino-terminal segment of type III procollagen and its rapid triple helix leads to and comes from coil transition
The structure and function of cartilage proteoglycans
Molecular basis of GM1 gangliosidosis and Morquio disease, type B. Structure-function studies of lysosomal beta-galactosidase and the non-lysosomal beta-galactosidase-like protein
Refined crystal structure of cytoplasmic malate dehydrogenase at 2.5-A resolution
Structural basis of the interaction between integrin alpha6beta4 and plectin at the hemidesmosomes
Glycosylation and palmitoylation of Wnt-3a are coupled to produce an active form of Wnt-3a
The known unknowns of antigen processing and presentation
CATALYTIC ACTIVITY 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate = 3-dehydroquinate + phosphate.PATHWAY Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 2/7.MISCELLANEOUS Was identified as a high-confidence drug target.SIMILARITY Belongs to the dehydroquinate synthase family.
CATALYTIC ACTIVITY 3-dehydroquinate = 3-dehydroshikimate + H(2)O.PATHWAY Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 3/7.SUBUNIT Homododecamer.MISCELLANEOUS Was identified as a high-confidence drug target.SIMILARITY Belongs to the type-II 3-dehydroquinase family.
FUNCTION Catalyzes the specific phosphorylation of the 3-hydroxyl group of shikimic acid using ATP as a cosubstrate.CATALYTIC ACTIVITY ATP + shikimate = ADP + shikimate 3-phosphate.COFACTOR Binds 1 magnesium ion per subunit.PATHWAY Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 5/7.SUBUNIT Monomer.DOMAIN Consists of three domains: the CORE domain which forms the binding site for nucleotides, the LID domain which closes over the active site upon ATP or shikimate binding, and the substrate-binding domain which functions to recognize and bind shikimate.MISCELLANEOUS The phosphoryl transfer proceeds by an in-line associative mechanism. The random sequential binding of shikimate and nucleotide is associated with domain movements that suggest a synergic mechanism by which binding of the first substrate may enhance the affinity for the second substrate.MISCELLANEOUS Was identified as a high-confidence drug target.SIMILARITY Belongs to the shikimate kinase family.
Glycogen metabolism and glycolytic enzymes
Structure and mechanism of the alkyl hydroperoxidase AhpC, a key element of the Mycobacterium tuberculosis defense system against oxidative stress
Single eubacterial origin of eukaryotic sulfide:quinone oxidoreductase, a mitochondrial enzyme conserved from the early evolution of eukaryotes during anoxic and sulfidic times
FUNCTION Binds oxygen cooperatively with very high affinity (P(50) = 0.013 mmHg at 20 degrees Celsius) because of a fast combination (25 microM(-1).s(-1)) and a slow dissociation (0.2 s(-1)) rate.COFACTOR Binds 1 heme group per subunit.SUBUNIT Homodimer.MISCELLANEOUS Was identified as a high-confidence drug target.SIMILARITY Belongs to the truncated hemoglobin family. Group I subfamily.
Constitutive and inducible expression and regulation of vascular endothelial growth factor
FUNCTION Part of the ABC transporter complex CysAWTP involved in sulfate/thiosulfate import. Responsible for energy coupling to the transport system.CATALYTIC ACTIVITY ATP + H(2)O + sulfate(Out) = ADP + phosphate + sulfate(In).SIMILARITY Belongs to the ABC transporter superfamily. Sulfate/tungstate importer (TC 3.A.1.6) family.SIMILARITY Contains 1 ABC transporter domain.
FATP1 channels exogenous FA into 1,2,3-triacyl-sn-glycerol and down-regulates sphingomyelin and cholesterol metabolism in growing 293 cells
Expression, purification, and kinetic characterization of recombinant human adenylosuccinate lyase
Biology, structure and mechanism of P-type ATPases
FUNCTION Catalyzes the conversion of O-acetylserine (OAS) to cysteine through the elimination of acetate and addition of hydrogen sulfide.CATALYTIC ACTIVITY O(3)-acetyl-L-serine + H(2)S = L-cysteine + acetate.COFACTOR Pyridoxal phosphate.ENZYME REGULATION Competitively inhibited by a four-residue peptide derived from the C-terminus of serine acetyltransferase (CysE). This suggests that CysK1 may associate with CysE in vivo to form a bi-enzyme complex, in which the OASS activity is down-regulated.PATHWAY Amino-acid biosynthesis; L-cysteine biosynthesis; L-cysteine from L-serine: step 2/2.SUBUNIT Homodimer.SIMILARITY Belongs to the cysteine synthase/cystathionine beta-synthase family.
A conserved mechanism for sulfonucleotide reduction
Collagen XV is necessary for modeling of the extracellular matrix and its deficiency predisposes to cardiomyopathy
Functional characterization by genetic complementation of aroB-encoded dehydroquinate synthase from Mycobacterium tuberculosis H37Rv and its heterologous expression and purification
Purification, molecular cloning, and expression of 2-hydroxyphytanoyl-CoA lyase, a peroxisomal thiamine pyrophosphate-dependent enzyme that catalyzes the carbon-carbon bond cleavage during alpha-oxidation of 3-methyl-branched fatty acids
Molecular cloning, cDNA sequence, and bacterial expression of human glutamine:fructose-6-phosphate amidotransferase
Enzyme hyperspecificity. Rejection of threonine by the valyl-tRNA synthetase by misacylation and hydrolytic editing
Nucleotide binding to nucleoside diphosphate kinases: X-ray structure of human NDPK-A in complex with ADP and comparison to protein kinases
The canonical Notch signaling pathway: unfolding the activation mechanism
A human purine nucleoside phosphorylase deficiency caused by a single base change
Folding mechanism of the triple helix in type-III collagen and type-III pN-collagen. Role of disulfide bridges and peptide bond isomerization
Sanfilippo disease type D: deficiency of N-acetylglucosamine-6-sulfate sulfatase required for heparan sulfate degradation
Tripeptidyl peptidase II is the major peptidase needed to trim long antigenic precursors, but is not required for most MHC class I antigen presentation
Biochemistry of the initial steps of mycothiol biosynthesis
Lead-induced abnormalities of porphyrin metabolism. The relationship with iron deficiency.
Methylation pharmacogenetics: catechol O-methyltransferase, thiopurine methyltransferase, and histamine N-methyltransferase
Immunoelectron microscopy of type X collagen: supramolecular forms within embryonic chick cartilage
alpha-D-Glucose 6-phosphate [ChEBI:17665]
Inositol monophosphate phosphatase genes of Mycobacterium tuberculosis
Identification and expression of a cDNA for human glycolate oxidase
Molecular genetics of mucopolysaccharidosis type IIIA and IIIB: Diagnostic, clinical, and biological implications
Molecular mechanisms of MHC class I-antigen processing: redox considerations
Expression of human asparagine synthetase in Escherichia coli
Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation
An overview of sphingolipid metabolism: from synthesis to breakdown
Functional analysis of ABCA8, a new drug transporter
Differential activation of recombinant human acetyl-CoA carboxylases 1 and 2 by citrate
Platelet activation, signaling and aggregation
Distinct flippases translocate glycerophospholipids and oligosaccharide diphosphate dolichols across the endoplasmic reticulum
Alkyl-dihydroxyacetone phosphate synthase and dihydroxyacetone phosphate acyltransferase form a protein complex in peroxisomes
(2E,4E,6Z,8E)-3,7-dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acid
Bone morphogenetic protein receptors and signal transduction
Peroxisome proliferator-activated receptor alpha target genes
Mutations in HYAL1, a member of a tandemly distributed multigene family encoding disparate hyaluronidase activities, cause a newly described lysosomal disorder, mucopolysaccharidosis IX
Proc. Natl. Acad. Sci. U.S.A. 96:6296-300
Tolerance of reactive oxygen produced by macrophages
The expression of AhpC in Mycobacteria does not correlate with virulence; instead, the most important parts of the antioxidant system in Mtb appear to be the lipid cell wall, the enzymes SodB/SodC (superoxide dismutases), and the catalase/peroxidase KatG. Together with the enzyme system that acts on nitrosative stress and the sequestration of iron, these appear to be critical in defending against the macrophage's production of ROS/RNS, and enable the bacterium to exist in the phagosome for extended periods (Zahrt & Deretic 2002).
Dermal collagen fibrils are hybrids of type I and type III collagen molecules
The human sugar-phosphate/phosphate exchanger family SLC37
Annu Rev Plant Physiol Plant Mol Biol 50:473-503
Expression, purification, and characterization of Mycobacterium tuberculosis mycothione reductase
New drugs and regimens for treatment of TB
Transcriptional Regulation of White Adipocyte Differentiation
Distinct phosphotyrosines on a growth factor receptor bind to specific molecules that mediate different signaling pathways
Isolation and characterization of argininosuccinate synthetase from human liver.
D-Glucono-1,5-lactone 6-phosphate [ChEBI:16938]
Leber congenital amaurosis: genes, proteins and disease mechanisms
Molecular interactions of biglycan and decorin with elastic fiber components: biglycan forms a ternary complex with tropoelastin and microfibril-associated glycoprotein 1
The role of calcium-independent phospholipase A2 in cardiolipin remodeling in the spontaneously hypertensive heart failure rat heart
The biochemistry and physiology of nucleotides
WNT secretion and signalling in human disease
ChEBI:16975 1-acyl-sn-glycerol 3-phosphate
Human cationic amino acid transporter hCAT-3 is preferentially expressed in peripheral tissues
Hereditary disorders of connective tissue
Abcg2/Bcrp1 mediates the polarized transport of antiretroviral nucleosides abacavir and zidovudine
Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.
Degradation of cysteine and homocysteine
The regulation of size and form in the assembly of collagen fibrils in vivo
Two forms of Wilson disease protein produced by alternative splicing are localized in distinct cellular compartments
Characterization of a leukotriene C4 export mechanism in human platelets: possible involvement of multidrug resistance-associated protein 1
Control of muscle ryanodine receptor calcium release channels by proteins in the sarcoplasmic reticulum lumen
Molecular cloning and sequence analysis of cDNA encoding human cholesterol 7 alpha-hydroxylase
alpha-D-Galactose 1-phosphate [ChEBI:17973]
3'-Phosphoadenylyl sulfate [ChEBI:17980]
D-Fructose 1,6-bisphosphate [ChEBI:16905]
The trifunctional sulfate-activating complex (SAC) of Mycobacterium tuberculosis
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.
Clinical and biochemical manifestations of hyaluronidase deficiency
Mechanisms of accurate translesion synthesis by human DNA polymerase eta.
ChREBP activates metabolic gene expression
The molecular basis of Sanfilippo syndrome type B
Effects of fibrillin-1 degradation on microfibril ultrastructure
Rational design of a drug for Alzheimer's disease with cholinesterase inhibitory and neuroprotective activity
Identification of the human cytochrome P450, P450RAI-2, which is predominantly expressed in the adult cerebellum and is responsible for all-trans-retinoic acid metabolism
L-2-Aminoadipate 6-semialdehyde [ChEBI:17917]
(5Z,8Z,11Z)-14,15-Epoxyicosa-5.8.11-trienoic acid
all-cis-14,15-epoxyeicosa-5,8,11-trienoic acid
14,15-epoxy-5Z,8Z,11Z-icosatrienoic acid
(5Z,8Z,11Z)-14,15-Epoxyeicosa-5.8.11-trienoic acid
14,15-epoxy-5Z,8Z,11Z-eicosatrienoic acid
Preferential DNA repair of an active gene in human cells.
Comparison of the enzymatic activities of human galactokinase GALK1 and a related human galactokinase protein GK2
The content of pentose-cycle intermediates in liver in starved, fed ad libitum and meal-fed rats.
Critical role for Ebf1 and Ebf2 in the adipogenic transcriptional cascade
Formation and metabolism of prebeta-migrating, lipid-poor apolipoprotein A-I
A yeast chromosomal origin of DNA replication defined by multiple functional elements.
Molecular identification of human glutamine- and ammonia-dependent NAD synthetases. Carbon-nitrogen hydrolase domain confers glutamine dependency.
Matrix metalloproteinases and the regulation of tissue remodelling
Communication between the synapse and the nucleus in neuronal development, plasticity, and disease
Protein phosphatase 2Cepsilon is an endoplasmic reticulum integral membrane protein that dephosphorylates the ceramide transport protein CERT to enhance its association with organelle membranes
Novel mutations in Sanfilippo A syndrome: implications for enzyme function
Mechanisms of transcription-coupled DNA repair.
(S)-alpha-amino-beta-(3-indolyl)-propionic acid
Congenital Disorders of Glycosylation Overview
beta-catenin destruction complex: insights and questions from a structural perspective
eNOS, COX-2, and prostacyclin production are impaired in endothelial cells from diabetics
mitochondrial fatty acid beta-oxidation of unsaturated fatty acids
Xeroderma pigmentosum variant (XP-V) correcting protein from HeLa cells has a thymine dimer bypass DNA polymerase activity.
Synthesis of bile acids and bile salts via 24-hydroxycholesterol
The crystal structure of human cytosolic serine hydroxymethyltransferase: a target for cancer chemotherapy
Fibulin-5 interacts with fibrillin-1 molecules and microfibrils
Reactive nitrogen and oxygen intermediates and bacterial defenses: unusual adaptations in Mycobacterium tuberculosis
Docosahexaenoic acid synthesis in human skin fibroblasts involves peroxisomal retroconversion of tetracosahexaenoic acid
Activating and inhibitory functions of DAP12
Tuberculosis: what we don't know can, and does, hurt us
Enzymatic degradation of dopamine by COMT
Proteoglycan-collagen interactions and sub-fibrillar structure in collagen fibrils: implications in the development and remodelling of connective tissues
3-Hydroxy-N6,N6,N6-trimethyl-L-lysine [ChEBI:15786]
Nicotinate phosphoribosyltransferase of human erythrocytes. Purification and properties.
Interchain disulfide bonds at the COOH-terminal end of procollagen synthesized by matrix-free cells from chick embryonic tendon and cartilage
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
ChEBI:17899 7alpha-hydroxycholest-4-en-3-one
(S)-2-Amino-3-(p-hydroxyphenyl)propionic acid
Superoxide production and electron transport in mitochondrial oxidation of dihydroorotic acid.
Lysosomal disorders: from storage to cellular damage
Nicotinate D-ribonucleotide [ChEBI:7561]
Bile salt transporters: molecular characterization, function, and regulation
(R)-4'-Phosphopantothenoyl-L-cysteine [ChEBI:328]
D-2-Hydroxyglutaric aciduria: unravelling the biochemical pathway and the genetic defect
Vesicle pools, docking, priming, and release
Fractionation and characterization of a cyclic adenine ribonucleotide formed by tissue particles
NAGLU mutations underlying Sanfilippo syndrome type B
The function of the human homolog of Saccharomyces cerevisiae REV1 is required for mutagenesis induced by UV light.
FGF signaling pathways in endochondral and intramembranous bone development and human genetic disease
Palmitoylglycerone phosphate [ChEBI:7900]
Facilitative Na+-independent glucose transporters
Human arylamine N-acetyltransferase genes: isolation, chromosomal localization, and functional expression
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Mitochondrial Iron-Sulfur Cluster Biogenesis
Structure-function relationship in the evolution of elastin
Mice deficient in small leucine-rich proteoglycans: novel in vivo models for osteoporosis, osteoarthritis, Ehlers-Danlos syndrome, muscular dystrophy, and corneal diseases
Developmental control of a G1-S transcriptional program in Drosophila
Molecular analysis of patients with beta-glucuronidase deficiency presenting as hydrops fetalis or as early mucopolysaccharidosis VII
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The enzymes, regulation, and genetics of bile acid synthesis
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Succinyl CoA: 3-oxoacid CoA transferase (SCOT): human cDNA cloning, human chromosomal mapping to 5p13, and mutation detection in a SCOT-deficient patient
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2-Methyl-3-hydroxybutyryl-CoA dehydrogenase deficiency is caused by mutations in the HADH2 gene.
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HEDJ, an Hsp40 co-chaperone localized to the endoplasmic reticulum of human cells
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Peroxisome proliferator-activated receptor alpha (PPARalpha ) turnover by the ubiquitin-proteasome system controls the ligand-induced expression level of its target genes
UDP-N-acetyl-D-galactosamine [ChEBI:9820]
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Beta oxidation of myristoyl-CoA to lauroyl-CoA
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Mutations in the gene encoding peroxisomal sterol carrier protein X (SCPx) cause leukencephalopathy with dystonia and motor neuropathy
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Activation of ATF6 and an ATF6 DNA binding site by the endoplasmic reticulum stress response
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Human glutamine phosphoribosylpyrophosphate amidotransferase. Two molecular forms interconvertible by purine ribonucleotides and phosphoribosylpyrophosphate
Molecular analysis of a series of alleles in humans with reduced activity at the triosephosphate isomerase locus
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HDL, ABC Transporters, and Cholesterol Efflux: Implications for the Treatment of Atherosclerosis
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Structure of human cytidine deaminase bound to a potent inhibitor
Antimicrobial reactive oxygen and nitrogen species: concepts and controversies
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Biosynthesis of mycothiol starts from glucose-6-phosphate and proceeds directly to myo-inositol-1-phosphate, contrary to phosphatidylinositol synthesis. One of the following steps, the removal of the phosphate group, is catalyzed by a still unknown phosphatase. The pathway is essential in M. tuberculosis (Newton et al, 2006; Sareen et al., 2003)
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Cloning and overexpression in soluble form of functional shikimate kinase and 5-enolpyruvylshikimate 3-phosphate synthase enzymes from Mycobacterium tuberculosis
Solution structure and dynamics of the lipoic acid-bearing domain of human mitochondrial branched-chain alpha-keto acid dehydrogenase complex
Recombinational DNA repair and human disease.
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Human SGBS cells - a unique tool for studies of human fat cell biology
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Developmental regulation and cellular distribution of human cytosolic malate dehydrogenase (MDH1)
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Supramolecular Structure of Cartilage Matrix
Dynamics of Bone and Cartilage Metabolism (Book): 407-418
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Isolation of a candidate gene for Menkes disease and evidence that it encodes a copper-transporting ATPase
Mechanisms underlying differential responses to FGF signaling
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Molecular cloning of human mitochondrial glycerophosphate dehydrogenase gene: genomic structure, chromosomal localization, and existence of a pseudogene
Origin, Recognition, Signaling and Repair of DNA Double-Strand Breaks in Mammalian Cells
Damage Surveillance and Repair (Keith Caldecott, editor)1-40
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Isolation of a candidate gene for Menkes disease that encodes a potential heavy metal binding protein
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Common and distinct elements in cellular signaling via EGF and FGF receptors
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Determination of the organisation of coding sequences within the iduronate sulphate sulphatase (IDS) gene
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Beta-oxidation of long-chain fatty acids by human fibroblasts: evidence for a novel long-chain acyl-coenzyme A dehydrogenase.
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Functionality of alternative splice forms of the first enzymes involved in human molybdenum cofactor biosynthesis
Glycyl tRNA synthetase mutations in Charcot-Marie-Tooth disease type 2D and distal spinal muscular atrophy type V
Ror-family receptor tyrosine kinases in noncanonical Wnt signaling: their implications in developmental morphogenesis and human diseases
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Cellular signaling by fibroblast growth factor receptors
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cAMP-dependent protein kinase: framework for a diverse family of regulatory enzymes
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ABCB5-mediated doxorubicin transport and chemoresistance in human malignant melanoma
Type VI collagen microfibrils: evidence for a structural association with hyaluronan
Comparison of cytochrome P450 (CYP) genes from the mouse and human genomes, including nomenclature recommendations for genes, pseudogenes and alternative-splice variants
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NGF signalling via TRKA from the plasma membrane
Uroporphyrinogen decarboxylase: complete human gene sequence and molecular study of three families with hepatoerythropoietic porphyria
Mutations in TMEM76* cause mucopolysaccharidosis IIIC (Sanfilippo C syndrome)
3alpha,7alpha-Dihydroxy-5beta-cholanic acid
Topology of acyltransferase motifs and substrate specificity and accessibility in 1-acyl-sn-glycero-3-phosphate acyltransferase 1
Synthesis of lysophosphatidic acid from dihydroxyacetone phosphate
G proteins: transducers of receptor-generated signals
Biogenesis of iron-sulfur clusters in mammalian cells: new insights and relevance to human disease
Mini-review: Specificity and expression of CIITA, the master regulator of MHC class II genes
Molecular cloning, genomic organization, and functional expression of Na+/H+ exchanger isoform 5 (NHE5) from human brain
Structural features of a superfamily of zinc-endopeptidases: the metzincins
Indirect inhibition of mitochondrial dihydroorotate dehydrogenase activity by nitric oxide.
Peroxisome proliferator-activated receptors, coactivators, and downstream targets
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
The role of non-P450 enzymes in drug oxidation
O-phospho-L-serine and the thiocarboxylated sulfur carrier protein CysO-COSH are substrates for CysM, a cysteine synthase from Mycobacterium tuberculosis
A new biochemical subtype of the Sanfilippo syndrome: characterization of the storage material in cultured fibroblasts of Sanfilippo C patients
Polyamines: metabolism and implications in human diseases
Differential expression of fibrillin-3 adds to microfibril variety in human and avian, but not rodent, connective tissues
3alpha,7alpha-Dihydroxy-5beta-cholestanate [ChEBI:1707]
Cold Spring Harb Perspect Biol 3:a004978
Frataxin and mitochondrial FeS cluster biogenesis
Identification of the human mitochondrial linoleoyl-coenzyme A monolysocardiolipin acyltransferase (MLCL AT-1)
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Disorders of cholesterol biosynthesis: prototypic metabolic malformation syndromes
Making heads or tails of phospholipids in mitochondria
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The crystal structure of human phosphoglucose isomerase at 1.6 A resolution: implications for catalytic mechanism, cytokine activity and haemolytic anaemia
5'-adenosinephosphosulfate lies at a metabolic branch point in mycobacteria
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5,10-methylenetetrahydrofolate polyglutamate
5,10-methylenetetrahydrofolate polyglutamate macromolecule
5,10-methylenetetrahydrofolate polyglutamate macromolecule [ChEBI:60473]
A novel human cytochrome P450, CYP26C1, involved in metabolism of 9-cis and all-trans isomers of retinoic acid
The cysteine switch: a principle of regulation of metalloproteinase activity with potential applicability to the entire matrix metalloproteinase gene family
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A complete inventory of all enzymes in the eukaryotic methionine salvage pathway
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Fibrillin-integrin interactions in health and disease
Purification, cloning, complementary DNA structure, and predicted amino acid sequence of human estradiol 17 beta-dehydrogenase
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A regulatory role for 1-acylglycerol-3-phosphate-O-acyltransferase 2 in adipocyte differentiation
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Opposing roles for ATF6alpha and ATF6beta in endoplasmic reticulum stress response gene induction
Mycothiol-dependent proteins in actinomycetes
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Dealing with methionine/homocysteine sulfur: cysteine metabolism to taurine and inorganic sulfur
Xylulose 5-phosphate mediates glucose-induced lipogenesis by xylulose 5-phosphate-activated protein phosphatase in rat liver
Crystal structure of human D-amino acid oxidase: context-dependent variability of the backbone conformation of the VAAGL hydrophobic stretch located at the si-face of the flavin ring
Cloning and characterization of the human beta-glucuronidase gene
Building collagen molecules, fibrils, and suprafibrillar structures
Identification and characterization of human mitochondrial tryptophanyl-tRNA synthetase
Chapter 3 Activation of TRP Channels in Mammalian Systems
Identification of 14 novel GLB1 mutations, including five deletions, in 19 patients with GM1 gangliosidosis from South America
Crystal structure of human ABAD/HSD10 with a bound inhibitor: implications for design of Alzheimer's disease therapeutics
The Wnt/Ca2+ pathway: a new vertebrate Wnt signaling pathway takes shape
Induction of CHOP expression by amino acid limitation requires both ATF4 expression and ATF2 phosphorylation
Electron Transport from NADPH to Ferredoxin
Peroxisome proliferator-activated receptor alpha (PPARalpha) and athero-sclerosis
Curr Drug Targets Cardiovasc Haematol Disord 5:513-23
Mutations in the MMAA gene in patients with the cblA disorder of vitamin B12 metabolism
The triglyceride lipases of the pancreas
Molecular cloning, primary structure, and expression of the human growth factor-activatable Na+/H+ antiporter
Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure
Calmodulin: a prototypical calcium sensor
Analysis of GPIIb/IIIa receptor number by quantification of 7E3 binding to human platelets
Enzymatic synthesis and properties of 5-phosphoribosylpyrophosphate
Ornithine delta-aminotransferase mutations in gyrate atrophy. Allelic heterogeneity and functional consequences.
A humble hexose monophosphate pathway metabolite regulates short- and long-term control of lipogenesis
A tyrosine-phosphorylated carboxy-terminal peptide of the fibroblast growth factor receptor (Flg) is a binding site for the SH2 domain of phospholipase C-gamma 1
Antigen Presentation: Folding, assembly and peptide loading of class I MHC
The bisretinoids of retinal pigment epithelium
AKT/PKB signaling: navigating downstream
Effect of trehalose on protein structure
The citric acid (TCA) cycle and respiratory electron transport
Reversal of DNA alkylation damage by two human dioxygenases.
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Expression and characterization of the human mitochondrial leucyl-tRNA synthetase
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ATP-binding cassette sub-family G member 1
Recognition and association of DNA glycosylase with site containing an affected pyrimidine
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6-phosphogluconate dehydrogenase, decarboxylating
SUBUNIT Part of the essential Sec protein translocation apparatus which comprises SecA, SecYEG and auxiliary proteins SecDF. Other proteins may also be involved (By similarity). Monomer and homodimer.SIMILARITY Belongs to the SecA family.
Cardiolipin hydrolysis by human phospholipases A2. The multiple enzymatic activities of human cytosolic phospholipase A2
phosphoribosyl pyrophosphate synthetase 1
Phosphoribosyl pyrophosphate synthetase I
Ribose-phosphate pyrophosphokinase I (EC 2.7.6.1) (Phosphoribosyl pyrophosphate synthetase I) (PPRibP) (PRS-I)
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Isozymes of human phosphofructokinase in blood cells and cultured cell lines: molecular and genetic evidence for a trigenic system
Glucuronidation and the UDP-glucuronosyltransferases in health and disease
FUNCTION Essential for protein export.SIMILARITY Belongs to the SecE/SEC61-gamma family.
MISCELLANEOUS Was identified as a high-confidence drug target.SIMILARITY Belongs to the SecY/SEC61-alpha family.
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Deletion of mouse Porcn blocks Wnt ligand secretion and reveals an ectodermal etiology of human focal dermal hypoplasia/Goltz syndrome
Proc. Natl. Acad. Sci. U.S.A. 108:12752-7
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Substrate specificity of human nucleoside-diphosphate kinase revealed by transient kinetic analysis
Homologues of O-phosphopantetheine-L-serine-FASN
Adipocyte-specific transcription factor ARF6 is a heterodimeric complex of two nuclear hormone receptors, PPAR gamma and RXR alpha
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ChEBI:16436 3-Methoxy-4-hydroxyphenylglycol
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Neurotransmitter Clearance In The Synaptic Cleft
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3,2-trans-enoyl-CoA isomerase, mitochondrial precursor
Acyl-CoA dehydrogenase, short-chain specific, mitochondrial precursor
Acyl-CoA dehydrogenase, long-chain specific, mitochondrial precursor
Trifunctional enzyme beta subunit, mitochondrial precursor
Acyl-CoA dehydrogenase, medium-chain specific, mitochondrial precursor
Enoyl-CoA hydratase, mitochondrial precursor
Lysophosphatidic acid acyltransferase-alpha
1-acylglycerol-3-phosphate O- acyltransferase 1
1-acyl-sn-glycerol-3-phosphate acyltransferase alpha
Lysophosphatidic acid acyltransferase-beta
1-acylglycerol-3-phosphate O- acyltransferase 2
1-acyl-sn-glycerol-3-phosphate acyltransferase beta
Long chain 3-hydroxyacyl-CoA dehydrogenase
Trifunctional enzyme alpha subunit, mitochondrial precursor
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Glycerol-3-phosphate acyltransferase, mitochondrial
Molecular and structural mapping of collagen fibril interactions
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Selective inhibition of heterotrimeric Gs signaling. Targeting the receptor-G protein interface using a peptide minigene encoding the Galpha(s) carboxyl terminus
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SecA2 functions in the secretion of superoxide dismutase A and in the virulence of Mycobacterium tuberculosis
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Developmental adaptation of the mouse cardiovascular system to elastin haploinsufficiency
A human testis-specific mRNA for phosphoribosylpyrophosphate synthetase that initiates from a non-AUG codon
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Interaction of osteopontin with fibronectin and other extracellular matrix molecules
Diacylglycerol, when simplicity becomes complex
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Functional genomics reveals the sole sulphate transporter of the Mycobacterium tuberculosis complex and its relevance to the acquisition of sulphur in vivo
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2,4,6,8-Nonatetraenoic acid, 3,7-dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-, (all-E)-
3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexene-1-yl)-2,4,6,8-nonatetraenoic acid (ECL)
(all-E)-3,7-Dimethyl-9-(2,6,6-trimethyl-1-cyclohexen-1-yl)-2,4,6,8-nonatetraenoic acid
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The enzymic chain elongation of fatty acids by rat-liver microsomes
Pentose phosphate pathway (hexose monophosphate shunt)
Homologous recombinational repair of DNA ensures mammalian chromosome stability
Inborn errors of cobalamin absorption and metabolism
Am J Med Genet C Semin Med Genet 157:33-44
Metabolism of gammalinolenic acid in human neutrophils
Mutations in the gene encoding peroxisomal alpha-methylacyl-CoA racemase cause adult-onset sensory motor neuropathy
Tropoelastin massively associates during coacervation to form quantized protein spheres
Reactive oxygen and nitrogen intermediates in the relationship between mammalian hosts and microbial pathogens
Human phosphoribosylpyrophosphate synthetase
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Acyl-CoA dehydrogenase, very-long-chain specific, mitochondrial precursor
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Purification and properties of short chain acyl-CoA, medium chain acyl-CoA, and isovaleryl-CoA dehydrogenases from human liver.
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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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Glucosamine--fructose-6-phosphate aminotransferase (isomerizing) 2
The molecular and fibrillar structure of collagen and its relationship to the mechanical properties of connective tissue
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Construction of a model for the aggregation and cross-linking region (7S domain) of type IV collagen based upon an evaluation of the primary structure of the alpha 1 and alpha 2 chains in this region
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Galactose-1-phosphate uridylyltransferase
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Phosphoenolpyruvate carboxykinase (GTP), mitochondrial
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HDL as a target in the treatment of atherosclerotic cardiovascular disease
Phosphoenolpyruvate carboxykinase, cytosolic (GTP)
phosphoenolpyruvate carboxykinase 1 (soluble)
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Glutamine- dependent asparagine synthetase
Asparagine synthetase (glutamine-hydrolyzing)
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Cloning of a complete protein-coding sequence of human platelet-type phosphofructokinase isozyme from pancreatic islet.
GM1-gangliosidosis (genetic beta-galactosidase deficiency): identification of four mutations in different clinical phenotypes among Japanese patients
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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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Enzymatic degradation of Dopamine by monoamine oxidase
(2R)-2-Hydroxy-3-(phosphonooxy)-propanal [ChEBI:29052]
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The Mycobacterium tuberculosis cysD and cysNC genes form a stress-induced operon that encodes a tri-functional sulfate-activating complex
Elimination of cholesterol as cholestenoic acid in human lung by sterol 27-hydroxylase: evidence that most of this steroid in the circulation is of pulmonary origin
CATALYTIC ACTIVITY Peptide-L-methionine + thioredoxin disulfide + H(2)O = peptide-L-methionine (S)-S-oxide + thioredoxin.CATALYTIC ACTIVITY L-methionine + thioredoxin disulfide + H(2)O = L-methionine (S)-S-oxide + thioredoxin.SIMILARITY Belongs to the MsrA Met sulfoxide reductase family.
Tropoelastin interacts with cell-surface glycosaminoglycans via its COOH-terminal domain
Suprastructures of extracellular matrices: paradigms of functions controlled by aggregates rather than molecules
Siroheme- and [Fe4-S4]-dependent NirA from Mycobacterium tuberculosis is a sulfite reductase with a covalent Cys-Tyr bond in the active site
CATALYTIC ACTIVITY 2 superoxide + 2 H(+) = O(2) + H(2)O(2).COFACTOR Binds 1 copper ion per subunit.ENZYME REGULATION Inhibited by the copper chelator diethyl dithiocarbamate.SUBUNIT Homodimer.MISCELLANEOUS Does not bind zinc ions. Has normal enzyme activity in the absence of zinc ions.SIMILARITY Belongs to the Cu-Zn superoxide dismutase family.CAUTION Lacks two conserved histidine residues that bind copper and zinc.
Gastrin-CREB signalling pathway via PKC and MAPK
Structure and function of the radical enzyme ribonucleotide reductase
FUNCTION Antioxidant protein with alkyl hydroperoxidase activity. Required for the reduction of the AhpC active site cysteine residues and for the regeneration of the AhpC enzyme activity.FUNCTION Together with AhpC, DlaT and Lpd, constitutes an NADH-dependent peroxidase active against hydrogen and alkyl peroxides as well as serving as a peroxynitrite reductase, thus protecting the bacterium against reactive nitrogen intermediates and oxidative stress generated by the host immune system.CATALYTIC ACTIVITY 2 R'-SH + ROOH = R'-S-S-R' + H(2)O + ROH.SUBUNIT Homotrimer. Identified in a complex with AhpC, DlaT and Lpd.SIMILARITY Belongs to the AhpD family.
Coacervation characteristics of recombinant human tropoelastin
Role of platelet-derived growth factors in physiology and medicine
Assignment of human beta-galactosidase-A gene to 3p21.33 by fluorescence in situ hybridization
Bile salt-dependent lipase: its pathophysiological implications
FUNCTION In its thiocarboxylated form (CysO-COSH), is the sulfur donor in the CysM-dependent cysteine biosynthetic pathway. May be of particular importance for cysteine biosynthesis in the persistent phase of M.tuberculosis.PATHWAY Amino-acid biosynthesis; L-cysteine biosynthesis.INDUCTION Up-regulated under oxidative stress conditions.PTM Thiocarboxylated by MoeZ.PTM A covalent CysO-cysteine adduct is formed by the action of CysM. The structure of the adduct seems to be first a S-(glycyl)-cysteinate which leads to a N-(glycyl)-cysteinate after a S->N acyl shift.SIMILARITY Belongs to the sulfur carrier protein CysO family.
The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction
Self-assembly of basement membrane collagen
Transmembrane transport of small molecules
Crystal structure of human guanosine monophosphate reductase 2 (GMPR2) in complex with GMP
Peroxisome proliferator-activated receptors: a nuclear receptor signaling pathway in lipid physiology
Full mass spectrometric characterization of human monoacylglycerol lipase generated by large-scale expression and single-step purification
Biosynthetic studies of A2E, a major fluorophore of retinal pigment epithelial lipofuscin
N-acylphosphatidylethanolamine-hydrolyzing phospholipase D: a novel enzyme of the beta-lactamase fold family releasing anandamide and other N-acylethanolamines
Error-prone DNA polymerases: novel structures and the benefits of infidelity.
Tetrahydrobiopterin biosynthesis, regeneration and functions
Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits
Identification and subcellular localization of a novel Cu,Zn superoxide dismutase of Mycobacterium tuberculosis
Resolution of D-loop structures through Holliday junction intermediates
Mutant human adenosine deaminase alleles and their expression by transfection into fibroblasts
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Activation of Chaperone Genes by XBP1(S)
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Characterization of an acyl-coA thioesterase that functions as a major regulator of peroxisomal lipid metabolism
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Spatial expression patterns and biochemical properties distinguish a second myo-inositol monophosphatase IMPA2 from IMPA1
FUNCTION Catalyzes the ATP-dependent condensation of GlcN-Ins and L-cysteine to form L-Cys-GlcN-Ins.CATALYTIC ACTIVITY 1-O-(2-amino-2-deoxy-alpha-D-glucopyranosyl)-1D-myo-inositol + L-cysteine + ATP = 1-O-(2-(L-cysteinamido)-2-deoxy-alpha-D-glucopyranosyl)-1D-myo-inositol + AMP + diphosphate.SIMILARITY Belongs to the class-I aminoacyl-tRNA synthetase family. MshC subfamily.
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Emilin, a component of elastic fibers preferentially located at the elastin-microfibrils interface
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Regulation of collagen fibril nucleation and initial fibril assembly involves coordinate interactions with collagens V and XI in developing tendon
Analysis of the putative role of 24-carbon polyunsaturated fatty acids in the biosynthesis of docosapentaenoic (22:5n-6) and docosahexaenoic (22:6n-3) acids
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3alpha,7alpha,12alpha-Trihydroxy-5beta-cholanic acid
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Biotransformation of xenobiotics by amine oxidases
The DNA replication fork in eukaryotic cells.
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Lipidomic discovery of deoxysiderophores reveals a revised mycobactin biosynthesis pathway in Mycobacterium tuberculosis
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Three enzymatic activities catalyze the oxidation of sulfide to thiosulfate in mammalian and invertebrate mitochondria
Purification and characterization of an alpha-methylacyl-CoA racemase from human liver
Baillieres Clin Endocrinol Metab 7:551-86
Mutations in the facilitative glucose transporter GLUT10 alter angiogenesis and cause arterial tortuosity syndrome
NOD-like receptors: role in innate immunity and inflammatory disease
Folic acid: nutritional biochemistry, molecular biology, and role in disease processes
N-hydroxy-4-aminobiphenyl O-acetylated conjugate
N-hydroxy-4-aminobiphenyl O-acetylated conjugate [ChEBI:16395]
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Mechanism of action and in vivo role of platelet-derived growth factor
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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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Cloning of the human MCCA and MCCB genes and mutations therein reveal the molecular cause of 3-methylcrotonyl-CoA: carboxylase deficiency.
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(2-trans,4-cis)-deca-2,4-dienoyl-CoA [ChEBI:29119]
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The generation and the manipulation of human multipotent adipose-derived stem cells
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Carnitine biosynthesis. beta-Hydroxylation of trimethyllysine by an alpha-ketoglutarate-dependent mitochondrial dioxygenase.
Matrix proteoglycans: from molecular design to cellular function
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Advanced In Protein Chemistry 17:227-302
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Molecular physiology of bestrophins: multifunctional membrane proteins linked to best disease and other retinopathies
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Trimerization and triple helix stabilization of the collagen XIX NC2 domain
Human mucopolysaccharidosis IIID: clinical, biochemical, morphological and immunohistochemical characteristics
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Molecular characterization of a phospholipase D generating anandamide and its congeners
ABH2 mediated Reversal of Alkylation Damage
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Human homologue of murine tumor rejection antigen gp96: 5'-regulatory and coding regions and relationship to stress-induced proteins
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FUNCTION Catalyzes the transfer of glucose from a nucleoside diphosphate-glucose to glucose-6-phosphate to form trehalose-6-phosphate and nucleoside diphosphate. TPS is specific for the glucosyl acceptor but not for the glucosyl donor. Most active with the purine sugar nucleotides than the pyrimidine sugar nucleotides.CATALYTIC ACTIVITY Nucleoside diphosphate-glucose + D-glucose 6-phosphate = trehalose 6-phosphate + nucleoside diphosphate.ENZYME REGULATION Activity is increased about twofold by 10 mM manganese. ADP, at 10 mM concentration, inhibits the formation of trehalose-P by 70% with either UDP-glucose or GDP-glucose as substrate, but GDP, also at 10 mM, only inhibits the reaction with UDP-glucose (50%) but not with GDP-glucose.PATHWAY Glycan biosynthesis; trehalose biosynthesis.SUBUNIT Homotetramer.SIMILARITY Belongs to the glycosyltransferase 20 family.
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Membrane type 1 matrix metalloproteinase digests interstitial collagens and other extracellular matrix macromolecules
Complete amino acid sequence of human phosphoglycerate kinase. Cyanogen bromide peptides and complete amino acid sequence.
Two new proteases in the MHC class I processing pathway
Crystal structure of Homo sapiens protein LOC79017
Differential hydrolysis of phospholipid molecular species during activation of human platelets with thrombin and collagen
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Identification of eukaryotic DNA replication proteins using simian virus 40 in vitro replication system.
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Extracellular matrix degradation and remodeling in development and disease
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
PTM: gamma carboxylation, hypusine formation and arylsulfatase activation
Matrix Metalloproteinases and TIMPs (Book)
Cdc6 is regulated by E2F and is essential for DNA replication in mammalian cells.
Expression of Gs alpha in Escherichia coli. Purification and properties of two forms of the protein
(S)-alpha-Amino-1H-imidazole-4-propionic acid
Cytochrome P450s and other enzymes in drug metabolism and toxicity
Human 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/inosine 5'-monophosphate cyclohydrolase. A bifunctional protein requiring dimerization for transformylase activity but not for cyclohydrolase activity
Phosphorylation of nucleosides and nucleoside analogs by mammalian nucleoside monophosphate kinases
Interfacial kinetic and binding properties of the complete set of human and mouse groups I, II, V, X, and XII secreted phospholipases A2
Removal of the flap by FEN-1 leads to the generation of a nick between the 3'-end of the upstream Okazaki fragment and the 5'-end of the downstream Okazaki fragment. DNA ligase I then seals the nicks between adjacent processed Okazaki fragments to generate intact double-stranded DNA.
The key event that allows the processive synthesis on the lagging strand, is polymerase switching from pol alpha to pol delta, as on the leading strand. However, the processive synthesis on the lagging strand proceeds very differently. DNA synthesis is discontinuous, and involves the formation of short fragments called the Okazaki fragments. During the synthesis of Okazaki fragments, the RNA primer is folded into a single-stranded flap, which is removed by endonucleases. This is followed by the ligation of adjacent Okazaki fragments.
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.
Adenosine triphosphate-adenosine-5'-monophosphate phosphotransferase from normal human liver mitochondria. Isolation, chemical properties, and immunochemical comparison with Duchenne muscular dystrophic serum aberrant adenylate kinase
Due to the antiparallel nature of DNA, DNA polymerization is unidirectional, and one strand is synthesized discontinuously. This strand is called the lagging strand. Although the polymerase switching on the lagging strand is very similar to that on the leading strand, the processive synthesis on the two strands proceeds quite differently. Short DNA fragments, about 100 bases long, called Okazaki fragments are synthesized on the RNA-DNA primers first. Strand-displacement synthesis occurs, whereby the primer-containing 5'-terminus of the adjacent Okazaki fragment is folded into a single-stranded flap structure. This flap structure is removed by endonucleases, and the adjacent Okazaki fragments are joined by DNA ligase.
Accurate and efficient genome duplication requires coordinated processes to replicate two template strands at eucaryotic replication forks. Knowledge of the fundamental reactions involved in replication fork progression is derived largely from biochemical studies of the replication of simian virus and from yeast genetic studies. Since duplex DNA forms an anti-parallel structure, and DNA polymerases are unidirectional, one of the new strands is synthesized continuously in the direction of fork movement. This strand is designated as the leading strand. The other strand grows in the direction away from fork movement, and is called the lagging strand. Several specific interactions among the various proteins involved in DNA replication underlie the mechanism of DNA synthesis, on both the leading and lagging strands, at a DNA replication fork. These interactions allow the replication enzymes to cooperate in the replication process (Hurwitz et al 1990; Brush et al 1996; Ayyagari et al 1995; Budd & Campbell 1997; Bambara et al 1997).
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.
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.
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.
Heparan sulfate/heparin (HS-GAG) metabolism
Cloning, expression, and characterization of a human inosine triphosphate pyrophosphatase encoded by the itpa gene
Lysine uptake by cloned hCAT-2B: comparison with hCAT-1 and with trophoblast surface membranes
Genetic analysis of superoxide dismutase, the 23 kilodalton antigen of Mycobacterium tuberculosis
XBP1 controls diverse cell type- and condition-specific transcriptional regulatory networks
Accumulation of dietary cholesterol in sitosterolemia caused by mutations in adjacent ABC transporters
Human amidophosphoribosyltransferase. An oxygen-sensitive iron-sulfur protein
alpha-linolenic (omega3) and linoleic (omega6) acid metabolism
FUNCTION Is involved in the biosynthesis of trehalose but not in that of capsular glucan and glycogen.CATALYTIC ACTIVITY Hydrolysis of (1->4)-alpha-D-glucosidic linkage in 4-alpha-D-((1->4)-alpha-D-glucanosyl)(n) trehalose to yield trehalose and (1->4)-alpha-D-glucan.PATHWAY Glycan biosynthesis; trehalose biosynthesis.DISRUPTION PHENOTYPE Inactivation of treZ does not affect the production of both capsular alpha-D-glucan and glycogen. Cells lacking this gene are not affected in their multiplication or persistence in the BALB/c mouse infection model.SIMILARITY Belongs to the glycosyl hydrolase 13 family.
CATALYTIC ACTIVITY 4-((1->4)-alpha-D-glucosyl)(n-1)-D-glucose = 1-alpha-D-((1->4)-alpha-D-glucosyl)(n-1)-alpha-D-glucopyranoside.SIMILARITY Belongs to the glycosyl hydrolase 13 family.
The molecular mechanism of lead inhibition of human porphobilinogen synthase
Translesion synthesis by DNA polymerases bypassing lesion on DNA template
Release of arachidonate from diglyceride in human platelets requires the sequential action of a diglyceride lipase and a monoglyceride lipase
Mitochondrial targeting signals and mature peptides of 3-methylcrotonyl-CoA carboxylase
ChEBI:58394 (4R,5S,6R)-4,5,6-trihydroxy-2-oxo-7-(phosphonatooxy)heptanoate(3-)
Mechanistic implications of mutations to the active site lysine of porphobilinogen synthase
Sanfilippo syndrome type C: mutation spectrum in the heparan sulfate acetyl-CoA: alpha-glucosaminide N-acetyltransferase (HGSNAT) gene
Endostatins derived from collagens XV and XVIII differ in structural and binding properties, tissue distribution and anti-angiogenic activity
A second canon. Functions and mechanisms of beta-catenin-independent Wnt signaling
Structure-function analysis of the bestrophin family of anion channels
Involvement of prolyl 4-hydroxylase in the assembly of trimeric minicollagen XII. Study in a baculovirus expression system
Versican interacts with fibrillin-1 and links extracellular microfibrils to other connective tissue networks
Cell signaling by receptor tyrosine kinases
Human liver long-chain 3-hydroxyacyl-coenzyme A dehydrogenase is a multifunctional membrane-bound beta-oxidation enzyme of mitochondria.
cDNA cloning and mapping of a novel subtype of glutamine:fructose-6-phosphate amidotransferase (GFAT2) in human and mouse
Functional shikimate dehydrogenase from Mycobacterium tuberculosis H37Rv: purification and characterization
Structures of the human orotidine-5'-monophosphate decarboxylase support a covalent mechanism and provide a framework for drug design
Tissue distribution and cDNA cloning of a human fatty acid transport protein (hsFATP4)
A quantitative model of human DNA base excision repair. I. Mechanistic insights
Sulfotransferases in the bioactivation of xenobiotics
Functional characterization of three novel tissue-specific anion exchangers SLC26A7, -A8, and -A9
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Identification of the peroxisomal beta-oxidation enzymes involved in the biosynthesis of docosahexaenoic acid
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Antigen presentation and the ubiquitin-proteasome system in host-pathogen interactions
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Regulation of nuclear processes by inositol polyphosphates
Metabolic enzymes of mycobacteria linked to antioxidant defense by a thioredoxin-like protein
Primate Genome Gain and Loss: A Bone Dysplasia, Muscular Dystrophy, and Bone Cancer Syndrome Resulting from Mutated Retroviral-Derived MTAP Transcripts
Overview of steroidogenic enzymes in the pathway from cholesterol to active steroid hormones
KARAP/DAP12/TYROBP: three names and a multiplicity of biological functions
FUNCTION Catalyzes the reversible interconversion of maltose and trehalose by transglucosylation. Also displays amylase activity, catalyzing the endohydrolysis of (1->4)-alpha-D-glucosidic linkages in glycogen and maltooligosaccharides such as maltoheptaose, to produce maltose which then can be converted to trehalose. TreS probably plays a key role in the utilization of trehalose for the production of glycogen, and might also function as a sensor and/or regulator of trehalose levels within the cell. Thus, when trehalose levels in the cell become dangerously low, TreS could expedite the conversion of glycogen to maltose via its amylase activity and then convert the maltose to trehalose; but this enzyme also could expedite or promote the conversion of trehalose to glycogen when cytoplasmic trehalose levels become too high.CATALYTIC ACTIVITY Maltose = alpha,alpha-trehalose.CATALYTIC ACTIVITY Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units.PATHWAY Glycan biosynthesis; glycogen biosynthesis.DISRUPTION PHENOTYPE Cells lacking this gene are as virulent as wild-type in mice. It is not possible to inactivate Rv3032 in a mutant lacking treS, suggesting the joint essentiality of the different alpha-(1->4)-glucans biosynthesis pathways involving these two genes.MISCELLANEOUS Was identified as a high-confidence drug target.SIMILARITY Belongs to the glycosyl hydrolase 13 family. TreS subfamily.
Regulation of repair of alkylation damage in mammalian genomes.
Prog Nucleic Acid Res Mol Biol 44:109-42
N-retinylidene-N-retinylphosphatidylethanolamine [ChEBI:52592]
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Another look at collagen V and XI molecules
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Cloning and characterization of murine 1-acyl-sn-glycerol 3-phosphate acyltransferases and their regulation by PPARalpha in murine heart
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Gamma linolenic acid: an antiinflammatory omega-6 fatty acid
Tissue-differential expression of two distinct genes for phosphoribosyl pyrophosphate synthetase and existence of the testic-specific transcript
Spectrum of mutations in mut methylmalonic acidemia and identification of a common Hispanic mutation and haplotype
The complex route to MHC class I-peptide complexes
a-ketoisocaproate, a-keto b-methylvalerate, a-ketoisovalerate
isovaleryl-CoA, a-methylbutyryl-CoA, isobutyryl-CoA
PGYM b dimer:AMP (name copied from entity in Homo sapiens)
GALE dimer (name copied from entity in Homo sapiens)
G6PD dimer (name copied from entity in Homo sapiens)
G6PD tetramer (name copied from entity in Homo sapiens)
PGD dimer (name copied from entity in Homo sapiens)
RPE dimer (name copied from entity in Homo sapiens)
Structure and functions of human oxysterol 7alpha-hydroxylase cDNAs and gene CYP7B1
phosphoribosyl pyrophosphate synthetase 1 holoenzyme (name copied from entity in Homo sapiens)
phosphoribosyl pyrophosphate synthetase holoenzyme
ACADVL dimer (name copied from entity in Homo sapiens)
IMPA2 dimer (name copied from entity in Homo sapiens)
IMPA2:Mg2+ (name copied from entity in Homo sapiens)
IMPA1 dimer (name copied from entity in Homo sapiens)
IMPA1:Mg2+ (name copied from entity in Homo sapiens)
ABCG5:ABCG8 heterodimer (name copied from entity in Homo sapiens)
ABCG1 dimer (name copied from entity in Homo sapiens)
dimerized CEL:bile salt complex (name copied from entity in Homo sapiens)
CEL:bile salt complex (name copied from entity in Homo sapiens)
Citrate lyase homotetramer (name copied from entity in Homo sapiens)
FAS dimer (name copied from entity in Homo sapiens)
Cholesterol homeostasis in human brain: turnover of 24S-hydroxycholesterol and evidence for a cerebral origin of most of this oxysterol in the circulation
Phosphate transporters: a tale of two solute carrier families
Nanomechanical heterogeneity in the gap and overlap regions of type I collagen fibrils with implications for bone heterogeneity
Ligand-induced, receptor-mediated dimerization and activation of EGF receptor
Mitochondrial aspartyl-tRNA synthetase deficiency causes leukoencephalopathy with brain stem and spinal cord involvement and lactate elevation
Regulation of the biosynthesis of 4,7,10,13,16,19-docosahexaenoic acid
PGM1:Mg++ (name copied from entity in Homo sapiens)
pyruvate carboxylase holoenzyme (name copied from entity in Homo sapiens)
malate dehydrogenase 1 dimer (name copied from entity in Homo sapiens)
phosphoglycerate kinase 1 complex (name copied from entity in Homo sapiens)
enolase 1 dimer, (alpha) (name copied from entity in Homo sapiens)
PGYB b dimer:AMP (name copied from entity in Homo sapiens)
PGYM dimer, b form (name copied from entity in Homo sapiens)
PGM2:Mg++ (name copied from entity in Homo sapiens)
PGYB dimer b form (name copied from entity in Homo sapiens)
The sodium phosphate cotransporter family SLC34
EPHX2 dimer (name copied from entity in Homo sapiens)
HADH octamer (name copied from entity in Homo sapiens)
ACHE tetramer (name copied from entity in Homo sapiens)
ACHE dimer (name copied from entity in Homo sapiens)
GCH1 decamer (name copied from entity in Homo sapiens)
PDSS1:Mg2+ (name copied from entity in Homo sapiens)
Isozymes of human phosphofructokinase: identification and subunit structural characterization of a new system
PDSS1/2 tetramer (name copied from entity in Homo sapiens)
NNT dimer (name copied from entity in Homo sapiens)
fumarate hydratase tetramer (name copied from entity in Homo sapiens)
GCH1 dimer (name copied from entity in Homo sapiens)
IDH2 dimer (name copied from entity in Homo sapiens)
The SLC2 family of facilitated hexose and polyol transporters
ETF (reduced) (name copied from entity in Homo sapiens)
ETF (name copied from entity in Homo sapiens)
PPAT tetramer (name copied from entity in Homo sapiens)
PPAT dimer (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)
adenylosuccinate synthetase like 1 holoenzyme (name copied from entity in Homo sapiens)
adenylosuccinate synthetase holoenzyme dimer (name copied from entity in Homo sapiens)
Isoforms of mammalian adenylyl cyclase: multiplicities of signaling
2xMUT:AdoCbl (name copied from entity in Homo sapiens)
2xMMAA:2xMUT:AdoCbl (name copied from entity in Homo sapiens)
DECR1 tetramer (name copied from entity in Homo sapiens)
DCI dimer (name copied from entity in Homo sapiens)
ACADS tetramer (name copied from entity in Homo sapiens)
ACADM tetramer (name copied from entity in Homo sapiens)
ECHS1 hexamer (name copied from entity in Homo sapiens)
ACADL tetramer (name copied from entity in Homo sapiens)
Trifunctional Protein (name copied from entity in Homo sapiens)
2xMMAA (name copied from entity in Homo sapiens)
2xMMAA:2xMUT (name copied from entity in Homo sapiens)
ABCD1 homodimer (name copied from entity in Homo sapiens)
HACL1 holoenzyme monomer (name copied from entity in Homo sapiens)
AGPS:FAD (name copied from entity in Homo sapiens)
GNPAT:AGPS complex (name copied from entity in Homo sapiens)
ACAT1 tetramer (name copied from entity in Homo sapiens)
2xMUT (name copied from entity in Homo sapiens)
HACL1 tetramer (name copied from entity in Homo sapiens)
OXCT1 dimer (name copied from entity in Homo sapiens)
IDH1 dimer (name copied from entity in Homo sapiens)
IDI1 or 2 (name copied from entity in Homo sapiens)
MGLL dimer (name copied from entity in Homo sapiens)
5,10-methenyltetrahydrofolate polyglutamate
HGPRT homotetramer (name copied from entity in Homo sapiens)
NP trimer (name copied from entity in Homo sapiens)
APRT homodimer (name copied from entity in Homo sapiens)
adenylosuccinate synthetase holoenzyme (name copied from entity in Homo sapiens)
ADAL:Zn (name copied from entity in Homo sapiens)
UMPS dimer (name copied from entity in Homo sapiens)
dihydroorotate dehydrogenase holoenzyme (name copied from entity in Homo sapiens)
CAD hexamer (name copied from entity in Homo sapiens)
GMPR2 tetramer (name copied from entity in Homo sapiens)
GMPR tetramer (name copied from entity in Homo sapiens)
DUT trimer (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)
CDA tetramer (name copied from entity in Homo sapiens)
An IFN-gamma-induced aminopeptidase in the ER, ERAP1, trims precursors to MHC class I-presented peptides
The ER aminopeptidase ERAP1 enhances or limits antigen presentation by trimming epitopes to 8-9 residues
Another important antioxidant activity is the KatG catalase/peroxidase which also activates the anti-tuberculosis drug isoniazid (Nagy et al. 1997).
H2O2 gets scavenged by unsaturated lipid
Due to their abundance in Mycobacteria, lipids fulfill a buffering role in the tolerance of antioxidants. Lipid production is triggered by oxidative stress. The peroxidated lipid can be reduced by AhpC (Chauhan & Mande 2001).
Inducible overproduction of the Aspergillus nidulans pentafunctional AROM protein and the type-I and -II 3-dehydroquinases from Salmonella typhi and Mycobacterium tuberculosis
glucosaminyl-inositol and cysteine are ligated to desacetylmycothiol
Ligation of glucosamine-inositol with the amino acid cysteine is zinc-dependent. The catalyzing enzyme MshC is a homologue of Cys-tRNA synthetase (Sareen et al, 2002)
acetylglucosamine-inositol-phosphate is dephosphorylated
The enzyme to catalyze dephosphorylation of Glc-NAc-Ins-P is still unknown. Several candidate phosphatases have been characterized. The most likely is Rv3137 which was shown to be essential in M. tuberculosis (Newton et al, 2006; Movahedzadeh, 2010)
Purification and properties of uroporphyrinogen decarboxylase from human erythrocytes. A single enzyme catalyzing the four sequential decarboxylations of uroporphyrinogens I and III.
acetylglucosamine is transferred from UDP-GlcNAc onto inositol-1-phosphate
MshA catalyzes the transfer of acetylglucosamine from UDP-GlcNAc onto inositol-1-phosphate. From biochemical and crystal studies, there is an absolute requirement for the phosphate as substrate (Newton et al, 2006; Vetting, 2008).
glucose-6-phosphate is converted to inositol-1-phosphate
M. tuberculosis utilizes myo-inositol-1-phosphate for mycothiol biosynthesis. This substrate comes nearly exclusively from the conversion of glucose-6-phosphate by Ino1. However, mutants devoid of Ino1 still have minimal amounts of mycothiol, so another reaction appears to provide Ins-P in small amounts, most likely the phosphorylation of uptaken inositol (Bachhawat and Mande, 1999; Mohavedzadeh et al, 2004; Newton et al, 2006; Newton et al, 2008).
Iron is reduced and separates from mycobactin
The IrtA transporter has a flavin reductase domain very much like Fre from E.coli that can probably act as ferrisiderophore reductase to relieve incoming loaded mycobactin from its Fe3+ by reducing it to Fe2+. Furthermore Rv2895c, which co-precipitates with IrtB and therefore is probably part of the transporter complex, has such a domain as well (Farhana et al. 2008).
Mtb bacterioferritin BfrA oxidises Fe2+ to Fe3+, migrates them to its centre, and collects thousands of them as FeO(OH) in the central mineral core from which they can be later remobilised (Reddy et al. 2012).
Carboxymycobactin and mycobactin exchange their iron load
Carboxymycobactin and mycobactin exchange their iron loads. This interplay between polar and nonpolar siderophore is unique to Mtb. However, mycobactin can gather iron from nonpolar regions of the host cell by itself too (Madigan et al. 2012).
The ABC-type transporter IrtA, probably complexed with IrtB and ViuB (Rv2895c), specifically transports iron-loaded mycobactin into the cytosol (Ryndak et al. 2009).
Mtb bacterioferritin BfrB oxidises Fe2+ to Fe3+, migrates them to its centre, and collects thousands of them as FeO(OH) in the central mineral core from which they can be later remobilised (Harrison & Arrosio 1996, Khare et al. 2011).
Adenylate cyclase converts ATP to 3',5'-cyclic AMP (cAMP) and pyrophosphate
Carboxymycobactin is the more polar siderophore of Mtb and it is localized, after its secretion, in the phagosomal lumen. The transporters for export and secretion of this molecule are still unknown (Madigan et al. 2012).
Carboxymycobactin binds iron from lactoferrin
Since bacterial siderophores bind iron with much greater affinity, they can scavenge iron ions from loaded lactoferrin (Madigan et al. 2012).
Mycobactin is the lipophilic siderophore of Mtb. After export into the periplasmic space, it localizes to the bacterium's cell wall. The responsible transporter activity is still unknown (Madigan et al. 2012).
Transcriptional activation of Citrate lyase monomer gene by ChREBP:MLX
Transcriptional induction of the human asparagine synthetase gene during the unfolded protein response does not require the ATF6 and IRE1/XBP1 arms of the pathway
Transcriptional activation of FAS monomer gene by ChREBP:MLX
Transcriptional activation of GP-acyl transferase gene by ChREBP:MLX
Expression of Phosphoenolpyruvate carboxykinase 1 (PEPCK-C)
Cleavage and shedding of E-cadherin after induction of apoptosis
Reduction of peroxidated lipids depends on reduced AhpC, the only alkyl hydoperoxidase in Mtb (Chauhan & Mande 2001).
Peroxiredoxin AhpC gets its reducing equivalents through a cascade of proteins via AhpD, a disulfide reductase, DlaT, a lipoylated disulfide reductase, and, finally, from Lpd, the NADH-dependent dihydrolipoyl reductase. The latter two are also part of the pyruvate dehydrogenase complex (Venugopal et al. 2011).
The peroxiredoxin AhpC can be alternatively reactivated by TrxA (Jaeger et al. 2004).
TrxB is an NADPH-dependent thioredoxin reductase that reactivates TrxA (Jaeger et al. 2006).
The Tpx peroxiredoxin is reactivated by either TrxA or TrxB1 (Jaeger et al. 2006).
The enzyme in Mtb known to reduce F420 is the glucose-6-phosphate dehydrogenase Fgd1 (Bashiri et al. 2008).
Although there is no direct evidence for CysE catalyzing the acetylation of serine, it has 58% identity with the serine acetyltransferase of Corynebacterium glutamicum and is upregulated in stress conditions (Haitani et al, 2006; Schnell et al, 2007; Mehra and Kaushal, 2009).
Three molecules of reduced ferredoxin are needed to reduce sulfite to sulfide. Electrons are transferred to sulfite with the help of Sir, an enzyme with siroheme and an iron-sulfur cluster as cofactors (Schnell et al, 2005; Pinto et al, 2007).
Reduction and cleavage of the sulfate moiety of APS happens in two distinct steps. First, the C-terminal cysteine of CysH binds sulfite to form an enzyme-thiosulfonate intermediate, which is then reduced by a thioredoxin (donating two electrons, thereby freeing two protons) (Williams et al, 2002; Carroll et al, 2005).
Beta oxidation of lauroyl-CoA to decanoyl-CoA-CoA
PAPS dephosphorylation, as the reverse reaction to APS phosphorylation, may have a regulatory role in the sulfate metabolism of M. tuberculosis (Hatzios et al, 2008).
Energy for the phosphorylation of APS comes from the hydrolysis of a GTP molecule. The resulting PAPS is used in M. tuberculosis by several sulfotransferases for the production of sulfolipids (Pinto et al, 2004; Sun et al, 2005).
Sufate is first activated by adding it to ATP, giving APS. Although both sulfate adenylyltransferase and APS kinase activities reside in the same enzyme complex, the intermediate APS is not channeled within the complex. Its accessibility ensures the functionality of the cysteine biosynthetic pathway (Pinto et al, 2004; Sun et al, 2005).
Mucopolysaccharidosis type IVA (Morquio A disease): clinical review and current treatment
The sulfate transporter of M. tuberculosis, a typical ABC transporter family ATPase, is the sole membrane transport protein in sulfate assimilation. It consists of the CysT/CysW/CysA proteins in 1:1:2 stoichiometry. cysA null mutants in M. bovis were unable to take up sulfate but could be rescued by M. tuberculosis cysA (Wooff et al, 2002).
Glucanotrehalose is hydrolyzed to 1,4-alpha-glucan and trehalose
From the glucanotrehalose, the enzyme TreZ cleaves one molecule of trehalose, leaving a linear glucan that is two sugars shorter than before. This is the rate-limiting step in the TreYZ pathway of trehalose biosynthesis (De Smet et al, 2000).
sulfate binds to SubI outside the membrane
The sulfate binding protein is localized in the plasma membrane using a lipid anchor. It is associated with the ATP sulfate influx pump and binds sulfate and probably also thiosulfate anions from the extracellular space (Wooff et al, 2002).
Maltose is converted to trehalose. The enzymatic activity of TreS for this reaction is 2-5 fold stronger than for the reverse reaction (De Smet et al, 2000).
1,4-alpha-glucan is converted to glucanotrehalose
Linear alpha-1,4-glucans are modified at one end to a glucanotrehalose by the enzyme TreY (De Smet et al, 2000).
Mycothiol is recycled using a reduction equivalent (NADPH/H+) and the help of the mycothione reductase enzyme. Although a mtr null mutant was obtained by McAdam and coworkers in M. tuberculosis, another study by Sassetti suggests the enzyme is essential in the H37Rv strain. It appears possible that thioredoxin reductases can provide some enzymatic rest activity. (Patel and Blanchard, 1999; Rawat and Av-Gay, 2007)
The oxidation of mycothiol provides electrons for the maintenance of cell redox homeostasis. In which reactions exactly those electrons are used is unknown. A possibility is the existence of MSH-dependent peroxidases. (Rawat and Av-Gay, 2007)
Trehalose-6-phosphate is hydrolyzed to trehalose
Hydrolysis of trehalose phosphate, catalyzed by OtsB2, gives trehalose. The enzyme needs magnesium for its activity. A second homologue, OtsB1 is non-functional (De Smet et al, 2000; Edavana et al, 2004).
Glucose is transferred from UDP-glucose onto glucose-6-phosphate
Trehalose phosphate synthase, which is a tetramer in solution, catalyzes the transfer of glucose from UDP onto glucose-6-phosphate. The enzyme is stimulated by manganese ions and can also accept ADP-, CDP-, GDP- and TDP-glucose as well as UDP-glucose (De Smet et al, 2000; Pan et al, 2008).
formylmycothiol hydrolyzes into mycothiol and formate
Formylmycothiol, like any S-formyl ester, is unstable and quickly hydrolyzes into mycothiol and formate (Vogt et al, 2003).
mycothiol S-conjugate is cleaved into mercapturic acid and GlcN-Ins
The hydrolysis of the mycothiol S-conjugate, catalyzed by the Mca amidase, results in a so called mercapturic acid (acetylcysteine adduct) of the toxin, and glucosaminyl-inositol which is recycled to mycothiol (Steffek et al, 2003).
mycothiol binds formaldehyde and is dehydrogenated
In the detoxification of formaldehyde, mycothiol first binds to the molecule forming a hydroxymethyl adduct intermediate (M-S-CH2OH, not shown), which is dehydrogenated by the bifunctional MscR enzyme to formylmycothiol (Vogt et al, 2003).
FGFR activation in skeletal disorders: too much of a good thing
desacetylmycothiol is acetylated to mycothiol using acetyl-CoA
The final step to yield mycothiol is an acetylation using acetyl-CoA. Compounds with other acyl groups can be produced spontaneously without the MshD enzyme and can have mycothiol activity. This explains low levels of mycothiol-like activity and traces of formyl- and succinyl-Cys-GlcN-Ins in MshD null mutants (Koledin et al, 2002)
acetylglucosamine-inositol is deacetylated by Mca
A small part of deacetylase activity required in the step producing glucosaminylinositol comes from the mycothiol S-conjugate amidase Mca. The hydrolaswe also needs zinc for its activity (Steffek et al, 2003).
mycothiol is cleaved to acetylcysteine and glucosaminylinositol
The degradation of mycothiol proceeds through its cleavage into acetylcysteine and glucosaminylinositol which both are completely degradable further. (Steffek et al, 2003)
mycothiol conjugates with electrophilic xenobiotic
Although mycothiol is able to conjugate by itself with electrophilic substances, analogously to glutathione in eukaryotes, it is possible there are specific MSH transferases for the catalysis of this reaction in cases where the substrate is more inert (Rawat and Av-Gay, 2007).
The identification of a distinct export step following the biosynthesis of leukotriene C4 by human eosinophils
Expression cloning of a human cDNA encoding folylpoly(gamma-glutamate) synthetase and determination of its primary structure
Dephosphorylation of EPSP yields chorismate
AroF in complex with reduced FMN catalyzes the dehydration and phosphate cleavage of EPSP, yielding chorismate. The cofactor FMN is reduced by NADPH which makes the enzyme stable in aerobic conditions and is known from similar fungal enzymes (Ely et al, 2008).
Condensation with cleavage of one phosphate group of shikimate 3-phosphate and phosphoenolpyruvate to EPSP is catalyzed by AroA (Garbe et al, 1990).
Enolase isoenzymes in rat tissues. Electrophoretic, chromatographic, immunological and kinetic properties
cleavage of L-cysteine from carrier protein
After serine was transferred onto its sulfhydryl group, a metallopeptidase cleaves the cysteine molecule from the sulfur carrier protein (Burns et al, 2005).
Cysteine from cystathionine and vice versa
The pyridoxalphosphate-dependent enzyme MetB not only catalyzes destruction of cystathonine to cysteine but also the transfer of homoserine onto cysteine to yield cystathione from O-succinyl-L-homoserine. This ensures that cysteine and methionine can be interconverted when the need arises. (Wheeler et al, 2005)
The first committed step in the biosynthesis of chorismate is the fusion of D-erythrose-4-phosphate with phosphoenolpyruvate, catalyzed by AroG (Rizzi et al, 2005; Webby et al, 2005).
Cyclization and dephosphorylation of DAHP, catalyzed by AroB, establishes the C6 ring in the pathway which is then only modified in the remaining five reactions (Mendonca et al, 2007).
AroQ, which catalyzes the dehydratation of 3-dehydroquinate (DHQ) to 3-dehydroshikimate (DHS), is a type II DHQ dehydratase. Unlike fungi DHQ dehydratases, AroQ doesn't take part in catabolism reactions (Moore et al, 1992).
The dimeric form of AroE catalyzes the hydration of dehydroshikimate. The reaction is reversible with high efficiency (Magalhaes et al, 2002; Fonseca et al, 2006).
Shikimate kinase (AroK) phosphorylates shikimate to shikimate 3-phosphate, using ATP (Oliveira et al, 2001).
deacetylation of O-acetylserine and sulfhydrylation using CysK2
Expression of the other enzyme catalyzing the sulfhydrylation of O-acetylserine, CysK2, is increased by oxidative stress (Mehra and Kaushal, 2009; Schnell et al, 2007).
deacetylation of O-acetylserine and sulfhydrylation using CysK1
Sulfhydrylation of O-acetylserine (OAS) is a four step process, as was shown with CysK1, consisting of 1) addition of OAS to pyridoxal phosphate, 2) deacetylation, 3) sulfhydrylation and 4) cleavage of cysteine. It remains to be shown that the enzyme binds to CysE, resulting in a bifunctional complex. Activity of CysK1 is not essential for M. tuberculosis (Schnell et al, 2007).
Similar to thiamine or pterine biosynthesis, the sulfide carrier protein CysO serves as substrate to the pyridoxal phosphate-dependent, dimeric CysM which transfers O-phosphoserine onto the sulfur (OLeary et al, 2008; Agren et al, 2008).
MoeZ appears to catalyze the transfer of sulfur (here sulfide) onto the sulfur carrier protein CysO where the C-terminus carboxyl group becomes a thiocarboxyl group. The small molecule substrate, as well as the exact enzymatic activity of MoeZ, is unknown (Burns et al, 2005).
Regulation of purine synthesis de novo in human fibroblasts by purine nucleotides and phosphoribosylpyrophosphate
Proximal tubular handling of phosphate: A molecular perspective
A network model for the organization of type IV collagen molecules in basement membranes
Biosynthesis of tricarboxylic acids by carbon dioxide fixation; enzymatic mechanisms
Stability of elastin in the developing mouse aorta: a quantitative radioautographic study
ChEBI:59629 N-ethylsuccinimide-mycothiol conjugate
ChEBI:59634 3-(1-ethyl-2,5-dioxopyrrolidin-3-yl)sulfanylpropanoic acid
3-(1-ethyl-2,5-dioxopyrrolidin-3-yl)sulfanylpropanoic acid
ChEBI:59632 (2R)-2-acetamido-3-phenacylsulfanylpropanoic acid
(2R)-2-acetamido-3-phenacylsulfanylpropanoic acid
Interfacial kinetic and binding properties of mammalian group IVB phospholipase A2 (cPLA2beta) and comparison with the other cPLA2 isoforms
ChEBI:59630 acetophenone-mycothiol conjugate
Human UDP-glucuronosyltransferases: metabolism, expression, and disease
A unified model for apical caspase activation
Characterization of human D-amino acid oxidase
S-methyl-5-thio-?-D-ribose 1-phosphate(2?)
ChEBI:58533 S-methyl-5-thio-?-D-ribose 1-phosphate(2?)
Mucopolysaccharidosis IV A: assignment of the human N-acetylgalactosamine-6-sulfate sulfatase (GALNS) gene to chromosome 16q24
ChEBI:52442 1-O-(2-acetamido-2-deoxy-alpha-D-glucopyranosyl)-1D-myo-inositol
ChEBI:52443 GlcNAc-(alpha1,1)-1D-Ins-3-P
No cysteine auxotrophs of Mycobacterium tuberculosis are known. This suggests redundant pathways for sulfur uptake and cysteine biosynthesis. Indeed, there is full interconversion between taken up sulfate/sulfide, cysteine, and methionine via cystathionine. (Schnell and Schneider, 2010)
Proteinases of the bone morphogenetic protein-1 family convert procollagen VII to mature anchoring fibril collagen
E2F mediates developmental and cell cycle regulation of ORC1 in Drosophila
Cloning of full-length methylmalonyl-CoA mutase from a cDNA library using the polymerase chain reaction
Collagens: molecular biology, diseases, and potentials for therapy
Aldehyde dehydrogenase, a diphosphopyridine nucleotide-linked enzyme
MISCELLANEOUS Was identified as a high-confidence drug target.SIMILARITY Belongs to the cysteine synthase/cystathionine beta-synthase family.
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
The molecular structure of human tissue type XV presents a unique conformation among the collagens
ATP-binding cassette (ABC) transporters in human metabolism and diseases
Human Sulfotransferases and Their Role in Chemical Metabolism
Structural characterization of VGVAPG, an elastin-derived peptide
The non-reducing disaccharide trehalose is found in insects, plants, and microorganisms. In bacteria, it is a storage energy source and is essential for the survival of many stress conditions. In mycobacteria, trehalose is also part of the cell wall and of the 'cord factor' which is important for entry into the host (Elbein et al, 2003; Tropis et al, 2005; Jain & Roy, 2009) M. tuberculosis has three ways to synthesize trehalose: from UDP-glucose and glucose phosphate (the OtsAB pathway), from maltose (the TreS pathway), and from glycogen (TreYZ pathway). The OtsAB pathway was shown to be essential for the organism. It is not known, however, whether or not the essentiality of trehalose for the mycobacterial growth is directly connected to the biosynthesis of cell wall mycolates (De Smet et al, 2000; Murphy et al, 2005)
The juxtamembrane region of the EGF receptor functions as an activation domain
Recombinant human collagen XV regulates cell adhesion and migration
Biosynthesis of diphosphopyridine nucleotide. II. Enzymatic aspects.
Characterization of distinct nuclear and mitochondrial forms of human deoxyuridine triphosphate nucleotidohydrolase
Mtb encounters a vastly changed environment, soon after it gets internalized by macrophages. The compartment it resides in, the phagosome, is acidified and devoid of important metal ions. It is flooded with reactive oxygen and nitrogen species. And steps will be soon taken by the macrophage to "mature" the phagosome with all kinds of lysosomal digestive enzymes. However, unlike most other bacteria species Mtb. has evolved solutions to each of these threats and, after making sure these are installed, it soon will enter a dormant state (de Chastellier, 2009; Flannagan et al, 2009). A combination of the host defense and the response of the infecting bacillus (active and passive) ensure suppression of bacterial metabolic activity and replication, resulting in a non-replicating state (Russell 2011, Russell et al. 2010).
Adhesion-modulating/matricellular ECM protein families: a structural, functional and evolutionary appraisal
The NMR solution structure of human glutaredoxin in the fully reduced form
The Ca2+-pumping ATPase of plasma membranes. Purification, reconstitution and properties
ribose 1-phosphate, deoxyribose 1-phosphate
Post-translational palmitoylation and glycosylation of Wnt-5a are necessary for its signalling
Chromosomal replication initiates and terminates at random sequences but at regular intervals in the ribosomal DNA of Xenopus early embryos.
Helical model of nucleation and propagation to account for the growth of type I collagen fibrils from symmetrical pointed tips: a special example of self-assembly of rod-like monomers
Intrinsic activity and stability of bifunctional human UMP synthase and its two separate catalytic domains, orotate phosphoribosyltransferase and orotidine-5'-phosphate decarboxylase
Collagenous transmembrane proteins: recent insights into biology and pathology
PC and PE synthesis: mixed micellar analysis of the cholinephosphotransferase and ethanolaminephosphotransferase activities of human choline/ethanolamine phosphotransferase 1 (CEPT1)
FUNCTION Part of the ABC transporter complex IrtAB involved in iron import. Transmembrane domains (TMD) form a pore in the membrane and the ATP-binding domain (NBD) is responsible for energy generation. Required for replication in human macrophages and in mouse lungs.COFACTOR FAD.INDUCTION Repressed by iron and IdeR.DOMAIN In IrtA the ATP-binding domain (NBD) and the transmembrane domain (TMD) are fused.DOMAIN The FAD-binding domain could function as a flavin/ferric reductase necessary to release iron from the siderophore complex, making it available for utilization.SIMILARITY Belongs to the ABC transporter superfamily. Siderophore-Fe(3+) uptake transporter (SIUT) (TC 3.A.1.21) family.SIMILARITY Contains 1 ABC transmembrane type-1 domain.SIMILARITY Contains 1 ABC transporter domain.SIMILARITY Contains 1 FAD-binding FR-type domain.CAUTION PubMed:18461140 reports that IrtA is a siderophore exporter, however this activity could be due to functional differences of IrtA in the molecular context of M.smegmatis and M.tuberculosis.
FUNCTION Part of the ABC transporter complex IrtAB involved in iron import. Transmembrane domains (TMD) form a pore in the membrane and the ATP-binding domain (NBD) is responsible for energy generation. Required for replication in human macrophages and in mouse lungs.INDUCTION Repressed by iron and IdeR.DOMAIN In IrtB the ATP-binding domain (NBD) and the transmembrane domain (TMD) are fused.DISRUPTION PHENOTYPE Mutants show normal growth in iron-sufficient conditions, but show a growth defect under iron-deficient conditions.SIMILARITY Belongs to the ABC transporter superfamily. Siderophore-Fe(3+) uptake transporter (SIUT) (TC 3.A.1.21) family.SIMILARITY Contains 1 ABC transmembrane type-1 domain.SIMILARITY Contains 1 ABC transporter domain.CAUTION PubMed:18461140 reports that IrtB forms a siderophore importer with Rv2895c, however this activity could be due to functional differences of IrtB in the molecular context of M.smegmatis and M.tuberculosis.
Molecular cloning of the human UMP synthase gene and characterization of point mutations in two hereditary orotic aciduria families
Identification and characterization of a lysophosphatidylcholine acyltransferase in alveolar type II cells
Functional expression of the canalicular bile salt export pump of human liver
The neurotransmitter cycle and quantal size
Oxidative demethylation of 1-EtA damaged DNA By ABH2
Oxidative demethylation of 3-MeC damaged DNA By ABH2
The ABCC family mediates organic anion transport
Ligation of newly synthesized repair patch to incised DNA in TC-NER
ABCD1/D2/D3 mediate long chain fatty acid transport in to peroxisomes
Ligation of DNA and formation of Holliday structures following repair synthesis
Ligation of newly synthesized repair patch to incised DNA in GG-NER
Oxidative demethylation of 3-MeC damaged DNA By ABH3
Oxidative demethylation of 1-EtA damaged DNA By ABH3
Oxidative demethylation of 1-MeA damaged DNA By ABH3
The human bile salt export pump: characterization of substrate specificity and identification of inhibitors
CoA-dependent methylmalonate-semialdehyde dehydrogenase, a unique member of the aldehyde dehydrogenase superfamily. cDNA cloning, evolutionary relationships, and tissue distribution
Cleavage of dihydrouracil by hNTH1 glycosylase
Cleavage of cytosine glycol by hNTH1 glycosylase
Cleavage of formamidopyrimidine by hNTH1 glycosylase
Insertion of correct bases opposite to the lesion by Pol eta
Oxidative demethylation of 1-MeA damaged DNA By ABH2
Binding of REV1 to lesioned DNA template
Misinsertion of bases opposite to the lesion by HREV1
FUNCTION Protease that hydrolyzes the covalent CysO-cysteine adduct synthesized by CysM to release L-cysteine and regenerate CysO.CATALYTIC ACTIVITY [CysO]-L-cysteine + H(2)O = [CysO] + L-cysteine.COFACTOR Zinc.ENZYME REGULATION Inhibited by EDTA in vitro.PATHWAY Amino-acid biosynthesis; L-cysteine biosynthesis.INDUCTION Up-regulated under oxidative stress conditions.DISRUPTION PHENOTYPE Strains lacking this gene are shown to be attenuated in macrophages.SIMILARITY Belongs to the peptidase M67A family.SIMILARITY Contains 1 MPN (JAB/Mov34) domain.
Binding of Pol eta to lesioned DNA template
SUMF2 inhibits SUMF1-mediated activation of arylsulfatases
Formation of glucosamine 6-phosphate from fructose 6-phosphate and glutamine
Fructose 6-phosphate isomerizes to Mannose 6-phosphate
Addition of GlcNAc to the Tn antigen via an alpha-1,3 linkage forms a Core 5 glycoprotein
Cleavage of 3-methyladenine by MPG glycosylase
Cleavage 8-oxo guanine by MYH glycosylase
MYH glycosylase mediated recognition and binding of an adenine opposite to an 8-oxo guanine
MPG glycosylase mediated recognition and binding of hypoxanthine
Cleavage of hypoxanthine by MPG glycosylase
hNTH1 glycosylase mediated recognition and binding of cytosine glycol
Cleavage of ethenoadenine by MPG glycosylase
hNTH1 glycosylase mediated recognition and binding of thymine glycol
Cleavage of thymine glycol by hNTH1 glycosylase
hNTH1 glycosylase mediated recognition and binding of dihydrouracil
hNTH1 glycosylase mediated recognition and binding of formamidopyrimidine
How nucleotide excision repair protects against cancer.
Generation of major histocompatibility complex class I antigens: functional interplay between proteasomes and TPPII
Post-proteasomal antigen processing for major histocompatibility complex class I presentation
tyrosine + tRNA(Tyr) + ATP => Tyr-tRNA(Tyr) + AMP + pyrophosphate
tryptophan + tRNA(Trp) + ATP => Trp-tRNA(Trp) + AMP + pyrophosphate
valine + tRNA(Val) + ATP => Val-tRNA(Val) + AMP + pyrophosphate
MPG glycosylase mediated recognition and binding of 3-methyladenine
MPG glycosylase mediated recognition and binding of ethenoadenine
Mutations in the Delta1-pyrroline 5-carboxylate dehydrogenase gene cause type II hyperprolinemia.
Selectivity in post-translational biotin addition to five human carboxylases
glycine + tRNA(Gly) + ATP => Gly-tRNA(Gly) + AMP + pyrophosphate
leucine + tRNA(Leu) + ATP => Leu-tRNA(Leu) + AMP + pyrophosphate
aspartate + tRNA(Asp) + ATP => Asp-tRNA(Asp) + AMP + pyrophosphate
glutamate + tRNA(Glu) + ATP => Glu-tRNA(Glu) + AMP + pyrophosphate
serine + tRNA(Ser) + ATP => Ser-tRNA(Ser) + AMP + pyrophosphate
proline + tRNA(Pro) + ATP => Pro-tRNA(Pro) + AMP + pyrophosphate
phenylalanine + tRNA(Phe) + ATP => Phe-tRNA(Phe) + AMP + pyrophosphate
methionine + tRNA(Met) + ATP => Met-tRNA(Met) + AMP + pyrophosphate
lysine + tRNA(Lys) + ATP => Lys-tRNA(Lys) + AMP + pyrophosphate
Oxidation of 3-Methoxytyramine to homovanillic acid
oxidation of dopamine to 3,4dihydroxyphenylacetic acid (DOPAC)
Methylation of 3,4-dihydroxyphenylacetic acid to homovanillic acid
Conversion of GABA to Succinate Semialdehyde
Conversion of succinate semialdehyde to succinate
methylation of Dopamine to form 3-Methoxytyramine
ATP2B1-4 transport cytosolic Ca2+ to extracellular region
Peroxynitrite oxidizes methionine residues
Peroxynitrite oxidizes methionine residues (Pryor et al. 1994).
Addition of galactose to the Tn antigen via an alpha-1,3 linkage forms a Core 8 glycoprotein
Glucose 6-phosphate is isomerized to form fructose-6-phosphate
alpha-D-glucose 6-phosphate <=> D-fructose 6-phosphate
Addition of GlcNAc to the Tn antigen via a beta-1,6 linkage forms a Core 6 glycoprotein
Addition of GalNAc to the Tn antigen via an alpha-1,6 linkage forms a Core 7 glycoprotein
SLC7A3 (CAT-3)-mediated uptake of cationic amino acids
SLC7A2, isoform B (CAT-2B)-mediated uptake of cationic amino acids
SLC7A2, isoform A (CAT-2A)-mediated uptake of cationic amino acids
Characterization of solanesyl and decaprenyl diphosphate synthases in mice and humans
Human 1-D-myo-inositol-3-phosphate synthase is functional in yeast
The ontogeny of human drug-metabolizing enzymes: phase II conjugation enzymes and regulatory mechanisms
Matrix metalloproteinase degradation of extracellular matrix: biological consequences
Insights from retinitis pigmentosa into the roles of isocitrate dehydrogenases in the Krebs cycle
FUNCTION Catalyzes the conversion of the sulfur carrier protein CysO to CysO-thiocarboxylate. The reaction is thought to proceed in two steps: first, ATP-dependent activation of CysO as acyl-adenylate (CysO-COOAMP), followed by sulfur transfer to give CysO-thiocarboxylate (CysO-COSH) (Probable). The sulfur source is unknown.INDUCTION Up-regulated under oxidative stress conditions.SIMILARITY In the N-terminal section; belongs to the HesA/MoeB/ThiF family.SIMILARITY Contains 1 rhodanese domain.
Horror autoinflammaticus: the molecular pathophysiology of autoinflammatory disease (*)
Completion of mammalian lagging strand DNA replication using purified proteins.
Lanosterol 14 alpha-methyl demethylase. Isolation and characterization of the third metabolically generated oxidative demethylation intermediate.
MscR reduces nitrosomycothiol to ammonia
MscR is an alcohol dehydrogenase that can probably reduce nitrosomycothiol with the help of NADH/H+ reducing equivalents to the sulfinamide which then presumably decomposes to the thione and ammonia (Vogt et al. 2003).
Nitrosyl is scavenged by mycothiol (MSH), which is functionally analogous to glutathione, which mycobacteria do not possess (Miller et al. 2007).
Peroxynitrite is reduced to nitrite by Tpx
Tpx, like AhpC, is a peroxiredoxin with alkylhydroperoxidase, peroxidase, and peroxynitritase activities. Peroxynitrite is detoxified to nitrite (Jaeger et al. 2006, Rho et al. 2006).
The peroxiredoxin AhpE participates in reducing peroxynitrite to nitrite, but how it is recycled back to the reduced form is still unknown (Hugo et al. 2009).
The versatile AhpC reduces hydrogen peroxide to water (Bryk et al. 2002).
Copper-containing superoxide dismutase is localized in the plasma membrane of the bacterium where it catalyzes the reduction of superoxide (Wu et al. 1998).
Iron-containing superoxide dismutase is localized both within and without the bacterium where it catalyzes the reduction of superoxide (Zhang et al. 1991).
Superoxide dismutase SodB is secreted via the Sec transport complex (Braunstein et al. 2003).
Nitrosoglutathione gets cleaved to Cys(NO)-Gly
Most gamma-glutamyl transpeptidases (GGT) cleave both glutathione and glutathione conjugates. Mtb GGT cleaves nitrosoglutathione )GSNO) to Cys(NO)-Gly, thus making it soluble for transport into the cytosol (Dayaram et al. 2006).
MsrA/B reduces peptide-methionine S/R-sulfoxides
MsrA and MsrB are enzymes that can both reduce the S- and R-stereoisomers of (peptidyl-) methionine sulfoxide. The exact nature of the accompanying thioredoxin is not settled, but it is predicted to be TrxA. The whole methionine-MsrA/B-thioredoxin-and-reductase system is an important part of NO detoxification in Mtb (St John et al. 2001, Lee et al. 2009).
Changes in methionine adenosyltransferase and S-adenosylmethionine homeostasis in alcoholic rat liver
Am J Physiol Gastrointest Liver Physiol 279:G178-85
Copper export from cells by copper-transporting ATPase1
ATP7A transports cytosolic Cu2+ to extracellular region
Copper sequestration by copper-transporting ATPase 2
ATP7B transports cytosolic Cu2+ to Golgi lumen
Trimming of N-ter extended precursor fragments by cytosolic aminopeptidases
Superoxide can enter the bacterium when acidic conditions apply. Together with a proton it forms the hydroperoxyl radical (Nathan & Shiloh 2000, Zahrt & Deretic 2002, Warner & Mizrahi 2006, Spagnolo et al, 2004).
Heme proteins, especially the truncated globin GlbN in Mtb possess oxygen-dependent nitric oxide dioxygenase activity, where the heme that is oxidized to ferriheme in the process will need to be reduced in a second step to activate the protein again. The responsible heme protein reductase is unknown (Ouellet et al. 2002, Pathania et al. 2002).
Nitrogen dioxide is reduced to NO by F420
The archaeal cofactor F420 reduces toxic nitrogen dioxide that can be produced when NO and oxygen combine. F420 itself is reduced by the enzyme Fgd (Purwantini & Mukhopadyay 2008).
Peroxynitrite is reduced to nitrite by AhpC
AhpC is an unusual peroxiredoxin - it has three cysteine residues that participate in the reduction of toxic peroxynitrite to nitrite. In a second step, another thioredoxin or the reductase chain AhpD/DlaT/Lpd is needed for reactivation (Guimaraes et al. 2005).
The crystal structure of 1-D-myo-inosityl 2-acetamido-2-deoxy-alpha-D-glucopyranoside deacetylase (MshB) from Mycobacterium tuberculosis reveals a zinc hydrolase with a lactate dehydrogenase fold
Na+/H+ exchanger transport (at early endosome membrane)
Na+/H+ exchanger transport (at cell membrane)
Na+/H+ exchanger transport (at late endosome membrane)
Na+/H+ exchanger transport (at trans-golgi membrane)
FATP1, 4 and 6 can mediate the influx of long chain fatty acids into cells
HMIT co-transports myo-inositol with a proton
ABCA8, B1 and B5 mediate xenobiotic efflux
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
6Z,9Z,12Z,15Z,18Z-tetracosapentaenoyl-CoA (TPA-CoA)
(4Z,7Z,10Z,13Z,16Z,19Z)-Docosahexaenoic acid
6Z,9Z,12Z,15Z,18Z,21Z-tetracosahexaenoyl-CoA (THA-CoA)
Purine ribonucleoside monophosphate biosynthesis
Feedback regulation of EGFR signalling: decision making by early and delayed loops
CATALYTIC ACTIVITY ATP + sulfate = diphosphate + adenylyl sulfate.CATALYTIC ACTIVITY ATP + adenylyl sulfate = ADP + 3'-phosphoadenylyl sulfate.PATHWAY Sulfur metabolism; hydrogen sulfide biosynthesis; sulfite from sulfate: step 1/3.PATHWAY Sulfur metabolism; hydrogen sulfide biosynthesis; sulfite from sulfate: step 2/3.SUBUNIT Heterodimer composed of CysD, the smaller subunit, and CysNC.INDUCTION Induced by sulfur limitation and oxidative stress. Repressed by the presence of cysteine.SIMILARITY In the N-terminal section; belongs to the GTP-binding elongation factor family. CysN/NodQ subfamily.SIMILARITY In the C-terminal section; belongs to the APS kinase family.
(24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA
25(R) 3alpha,7alpha,12alpha,24(S)-tetrahydroxy-5beta-cholestanoyl-CoA
(24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA
25(R) 3alpha,7alpha,24(S)-trihydroxy-5beta-cholestanoyl-CoA
Identification of a novel amidase motif in neutral ceramidase
25(S) 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA
25(R) 3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA
25(S) 3alpha,7alpha-dihydroxy-5beta-cholestanoyl-CoA
2xNAPRT1 (name copied from entity in Homo sapiens)
4xNADK:Zn2+ (name copied from entity in Homo sapiens)
2xMTHFD1 (name copied from entity in Homo sapiens)
6x(Btn-MCCC1:MCCC2) (name copied from entity in Homo sapiens)
NADSYN1 homohexamer (name copied from entity in Homo sapiens)
4x(Btn-PC:Mn2+) (name copied from entity in Homo sapiens)
3alpha, 7alpha, 12alpha-trihydroxy-5beta-cholestanoate
3xMMAB (name copied from entity in Homo sapiens)
2xPNPO:2xFMN (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)
nucleoside diphosphate kinase 1A:5B heterohexamer (name copied from entity in Homo sapiens)
ribonucleotide reductase M2B (TP53 inducible) dimer (name copied from entity in Homo sapiens)
ribonucleotide reductase M2B (TP53 inducible) variant (name copied from entity in Homo sapiens)
ribonucleotide reductase M2 polypeptide dimer (name copied from entity in Homo sapiens)
ribonucleotide reductase (name copied from entity in Homo sapiens)
ribonucleotide reductase M1 polypeptide dimer (name copied from entity in Homo sapiens)
Mechanism of aminoacylation of tRNA. Proof of the aminoacyl adenylate pathway for the isoleucyl- and tyrosyl-tRNA synthetases from Escherichia coli K12
Arylamine N-acetyltransferases and drug response
Carbohydrate response element binding protein directly promotes lipogenic enzyme gene transcription
FUNCTION Catalyzes an aldol-like condensation reaction between phosphoenolpyruvate (PEP) and D-erythrose 4-phosphate (E4P) to generate 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAH7P) and inorganic phosphate.CATALYTIC ACTIVITY Phosphoenolpyruvate + D-erythrose 4-phosphate + H(2)O = 3-deoxy-D-arabino-hept-2-ulosonate 7-phosphate + phosphate.COFACTOR Binds 2 divalent cations per subunit. The enzyme is active with manganese, cobalt or cadmium ions.ENZYME REGULATION Feedback inhibited by tryptophan, tyrosine, phenylalanine and chorismate.PATHWAY Metabolic intermediate biosynthesis; chorismate biosynthesis; chorismate from D-erythrose 4-phosphate and phosphoenolpyruvate: step 1/7.SUBUNIT Homodimer. Interacts with Rv0948c.SIMILARITY Belongs to the class-II DAHP synthase family.
Molybdenum cofactor biosynthesis and deficiency
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
Conversion of mitochondrial THF to THF-polyglutamate
Tetrahydrofolate polyglutamate (THF polyglutamate) + serine <=> 5,10-methyleneTHF polyglutamate + glycine
Characterization of a human gene conferring sensitivity to infection by gibbon ape leukemia virus
Localization by fluorescence in situ hybridization of the human functional beta-glucuronidase gene (GUSB) to 7q11.21 --> q11.22 and two pseudogenes to 5p13 and 5q13
5,10-methyleneTHF polyglutamate + glycine <=> tetrahydrofolate polyglutamate (THF polyglutamate) + serine
5,10-methyleneTHF polyglutamate + NADP+ <=> 5,10-methenylTHF polyglutamate + NADPH + H+
Sulfhydrylation and ring cleavage of precursor Z
ornithine + alpha-ketoglutarate <=> glutamate + L-glutamate gamma-semialdehyde [OAT]
5,10-methenylTHF polyglutamate + H2O <=> 10-formylTHF polyglutamate
MMAB transfers adenosyl group from ATP to B12s
ABCC1 transports cytosolic Cbl to extracellular region
A phospho-ribosyl group is added to quinolinate
Cytoslic carboxylases translocate to mitochondrial matrix
Human very-long-chain acyl-CoA synthetase: cloning, topography, and relevance to branched-chain fatty acid metabolism
Cascade regulation of terminal adipocyte differentiation by three members of the C/EBP family of leucine zipper proteins
Mitochondrial tRNA import: are there distinct mechanisms?
A phosphoribosyl group is added to nicotinate to form nicotinate mononucleotide (NaMN)
Conversion of cytosolic THF to THF-polyglutamate
Conversion of cytosolic 5-methyltetrahydrofolate (5-methylTHF) to 5-methylTHF-polyglutamate
isobutyryl-CoA + FAD => methacrylyl-CoA + FADH2
alpha-methyl-acetoacetyl-CoA + CoA => propionyl-CoA + acetyl-CoA
alpha-methylacetoacetyl-CoA + NADH + H+ <=> alpha-methyl-beta-hydroxybutyryl-CoA + NAD+
FUNCTION Catalyzes the transfer of a N-acetyl-glucosamine moiety to 1D-myo-inositol 3-phosphate to produce 1D-myo-inositol 2-acetamido-2-deoxy-glucopyranoside 3-phosphate in the mycothiol biosynthesis pathway.CATALYTIC ACTIVITY UDP-N-acetyl-D-glucosamine + 1D-myo-inositol 3-phosphate = UDP + 1-O-(2-acetamido-2-deoxy-alpha-D-glucopyranosyl)-1D-myo-inositol 3-phosphate.SIMILARITY Belongs to the glycosyltransferase group 1 family. MshA subfamily.
tyrosine + alpha-ketoglutarate <=> p-hydroxyphenylpyruvate + glutamate
p-hydroxyphenylpyruvate + glutamate <=> tyrosine + alpha-ketoglutarate
alpha-aminoadipic semialdehyde + NAD+ => alpha-aminoadipate + NADH + H+
glutaryl-CoA + FAD => crotonyl-CoA + FADH2 + CO2
methylmalonyl semialdehyde + NADH + H+ <=> beta-hydroxyisobutyrate + NAD+
methylmalonate semialdehyde + NAD+ + CoA => propionyl-CoA + CO2 + NADH + H+
Crystal structure of human dihydrolipoamide dehydrogenase: NAD+/NADH binding and the structural basis of disease-causing mutations
beta-hydroxyisobutyryl-CoA + H2O => beta-hydroxyisobutyrate + CoA
beta-hydroxyisobutyrate + NAD+ <=> methylmalonyl semialdehyde + NADH + H+
Herp is dually regulated by both the endoplasmic reticulum stress-specific branch of the unfolded protein response and a branch that is shared with other cellular stress pathways
glutamate + ATP + NADPH + H+ => L-glutamate gamma-semialdehyde + NADP+ + ADP + orthophosphate [P5CS]
glutamate + L-glutamate gamma-semialdehyde <=> ornithine + alpha-ketoglutarate [OAT]
aspartate + glutamine + ATP <=> asparagine + glutamate + AMP + pyrophosphate [ASNS]
Tuberculosis chemotherapy: the influence of bacillary stress and damage response pathways on drug efficacy
beta-methylcrotonyl-CoA + ATP + CO2 <=> beta-methylglutaconyl-CoA + ADP + orthophosphate + H2O [MCCA]
beta-methylglutaconyl-CoA + ADP + orthophosphate + H2O <=> beta-methylcrotonyl-CoA + ATP + CO2 [MCCA]
alpha-methylbutyryl-CoA + FAD => tiglyl-CoA + FADH2
alpha-methyl-beta-hydroxybutyryl-CoA + NAD+ <=> alpha-methylacetoacetyl-CoA + NADH + H+
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
isovaleryl-CoA + FAD => beta-methylcrotonyl-CoA + FADH2
Enzymes and reactions at the eukaryotic DNA replication fork.
The Mycobacterium tuberculosis Rv2540c DNA sequence encodes a bifunctional chorismate synthase
An estimate of the mean length of collagen fibrils in rat tail-tendon as a function of age
PLP from oxidation of pyridoxine phosphate
PLP from oxidation of pyridoxamine phosphate
Phosphopantothenoylcysteine is decarboxylated
cDNA cloning of human and rat brain myo-inositol monophosphatase. Expression and characterization of the human recombinant enzyme
7alpha,26-dihydroxycholest-4-en-3-one [ChEBI:48825]
2-Hydroxy-1,2,3-propanetricarboxylic acid
Molecular physiology of cation-coupled Cl- cotransport: the SLC12 family
5-oxoproline can be formed from gamma-glutamyl-AA products
abacavir monophosphate + H2O => carbovir monophosphate + cyclopropylamine
Deamination of abacavir monophosphate to form carbovir monophosphate
carbovir diphosphate + ATP => carbovir triphosphate + ADP
Transfer of Electrons from NADPH to FDXR
abacavir [cytosol] + ATP + H2O => abacavir[extracellular] + ADP + phosphate
2-oxoglutarate + NADPH + H+ => (R)-2-hydroxyglutarate + NADP+ [mutant IDH1]
HSP90 is inactivated by binding to benzaquinoid ansamycins
Collagen cross-linking. Purification and substrate specificity of lysyl oxidase
SLC7A1 (CAT-1)-mediated uptake of cationic amino acids
Synthesis of Prostaglandins (PG) and Thromboxanes (TX)
The extended protein kinase C superfamily
Beta-enolase deficiency, a new metabolic myopathy of distal glycolysis
Structure of human argininosuccinate synthetase
Acta Crystallogr D Biol Crystallogr 64:279-86
Homocysteine is degraded to oxobutanoate and H2S
Excess homocysteine yields homolanthionine and H2S
SQR oxidizes sulfide to bound persulfide
Excess cysteine yields lanthionine and H2S
Two molecules of ALA condense to form porphobilinogen (PBG)
ALAD octamer associates with Pb++, forming a catalytically inactive complex
Cystathionine is formed from homocysteine and serine
Old and new generation lipid mediators in acute inflammation and resolution
SAM is sythesized from methionine's reaction with ATP
beta-hydroxy-trimethyllysine => gamma-butyrobetaine aldehyde + glycine
argininosuccinate <=> fumarate + arginine
ATP + aspartate + citrulline <=> argininosuccinate + AMP + pyrophosphate
glycine + O2 => glyoxylate + H2O2 + NH4+
Methylation of N-acetyl-5-HT to form melatonin
carbamoyl phosphate + ornithine => citrulline + orthophosphate
ABH3 mediated Reversal of Alkylation Damage
L-glutamate gamma-semialdehyde + NAD+ => glutamate + NADH + H+
2 ATP + NH4+ + HCO3- => 2 ADP + orthophosphate + carbamoyl phosphate [mitochondrial]
2 ATP + NH4+ + HCO3- => 2 ADP + orthophosphate + carbamoyl phosphate
Formation of 5-oxoproline from gamma-glutamylcysteine
3,4-dihydroxybenzoate can be O-methylated
The acetyl group from acetyl-CoA is transferred to the NAT2
UDP-glucose is oxidised to UDP-glucuronate
Oxidative deamination of Phenyethylamine by MAOB
Oxidative deamination of 5-Hydroxytryptamine by MAOA
acetate + CoA + ATP => acetyl-CoA + AMP + pyrophosphate [cytosolic]
acetate + CoA + ATP => acetyl-CoA + AMP + pyrophosphate [mitochondrial]
Novel mutant-selective EGFR kinase inhibitors against EGFR T790M
The complete digestion of human milk triacylglycerol in vitro requires gastric lipase, pancreatic colipase-dependent lipase, and bile salt-stimulated lipase
Dietary tyramine is oxidatively deaminated to an aldehyde by MAOB
CYP26C1 deactivates 9-cis-retinoic acid by 4-hydroxylation
CYP26B1 also deactivates all-trans-retinoic acid by 4-hydroxylation
CYP26A1 breaks down all-trans-retinoic acid by 4-hydroxylation
GLUT8, a novel member of the sugar transport facilitator family with glucose transport activity
Ferrous iron is inserted into protoporphyrin IX to form heme
Oxidation of protoporphyrinogen IX to protoporphyrin IX
Uroporphyrinogen I is decarboxylated to form coproporphyrinogen I
Uroporphyrinogen III is decarboxylated to form coproporphyrinogen III
Four PBGs combine through deamination to form hydroxymethylbilane (HMB)
Am. J. Physiol., Cell Physiol. 302:C943-65
Truncated hemoglobin HbN protects Mycobacterium bovis from nitric oxide
Biosynthesis and metabolism of leukotrienes
ChEBI:37623 7alpha,25-dihydroxycholesterol
Human protoporphyrinogen oxidase: expression, purification, and characterization of the cloned enzyme
Multiple thioredoxin-mediated routes to detoxify hydroperoxides in Mycobacterium tuberculosis
Humans possess two mitochondrial ferredoxins, Fdx1 and Fdx2, with distinct roles in steroidogenesis, heme, and Fe/S cluster biosynthesis
ChEBI:37643 (25S)-3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA
ChEBI:37642 (25R)-3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA
ChEBI:37640 (24S)-7alpha,24-dihydroxycholesterol
Mitochondrial energy-linked nicotinamide nucleotide transhydrogenase. Membrane topography of the bovine enzyme
Characterization of MOCS1A, an oxygen-sensitive iron-sulfur protein involved in human molybdenum cofactor biosynthesis
MPG glycosylase:hypoxanthine complex (name copied from entity in Homo sapiens)
REV1:damaged DNA template complex (name copied from entity in Homo sapiens)
DNA containing an MPG-bound apurinic/apyrimidinic site (name copied from entity in Homo sapiens)
hNTH1 glycosylase:cytosine glycol complex (name copied from entity in Homo sapiens)
MYH glycosylase:adenine complex (name copied from entity in Homo sapiens)
DNA containing an MYH-bound apurinic/apyrimidinic site (name copied from entity in Homo sapiens)
hNTH1 glycosylase:thymine glycol complex (name copied from entity in Homo sapiens)
DNA containing a hNTH1-bound apurinic/apyrimidinic site (name copied from entity in Homo sapiens)
hNTH1 glycosylase:dihydrouracil complex (name copied from entity in Homo sapiens)
hNTH1 glycosylase: foramidopyrimidine complex (name copied from entity in Homo sapiens)
Pol eta:damaged DNA template complex (name copied from entity in Homo sapiens)
REV1:lesioned DNA template with misinserted bases (name copied from entity in Homo sapiens)
Pol eta:lesioned DNA template inserted with correct base complement (name copied from entity in Homo sapiens)
ABCD1:ABCD2 (name copied from entity in Homo sapiens)
ABCD1:ABCD3 (name copied from entity in Homo sapiens)
ABCD2:ABCD3 (name copied from entity in Homo sapiens)
ABCG4 dimer (name copied from entity in Homo sapiens)
Localized unfolding of collagen explains collagenase cleavage near imino-poor sites
Human retinoic acid (RA) 4-hydroxylase (CYP26) is highly specific for all-trans-RA and can be induced through RA receptors in human breast and colon carcinoma cells
The sodium/glucose cotransport family SLC5
Phosphoinositide signalling in cancer: beyond PI3K and PTEN
Beta oxidation of hexanoyl-CoA to butanoyl-CoA
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
Molecular basis of multidrug transport by ABC transporters
Microsomal enzymes of cholesterol biosynthesis. Purification of lanosterol 14 alpha-methyl demethylase cytochrome P-450 from hepatic microsomes.
A novel adenylyl cyclase sequence cloned from the human erythroleukemia cell line
Beta oxidation of butanoyl-CoA to acetyl-CoA
The Nod-like receptor (NLR) family: a tale of similarities and differences
In vitro processing of the human alkyl-dihydroxyacetonephosphate synthase precursor
NADPH + NAD+ + H+ [cytosol] => NADP+ + NADH + H+ [mitochondrial matrix]
Amino acid synthesis and interconversion (transamination)
Human liver alcohol dehydrogenase: purification, composition, and catalytic features.
5-phosphoribosylglycinamide (GAR) + 10-formyl-tetrahydrofolate => 5'-phosphoribosylformylglycinamide (FGAR) + tetrahydrofolate
5'-phosphoribosylformylglycinamide (FGAR) + L-glutamine + ATP + H2O => 5'-phosphoribosylformylglycinamidine (FGAM) + L-glutamate + adenosine 5'-diphosphate + orthophosphate
FGAR + L-Glutamine + ATP + H2O => FGAM + L-Glutamate + ADP + Pi
5-phospho-alpha-D-ribose 1-diphosphate (PRPP) + H2O + L-glutamine <=> 5-phosphoribosylamine + L-glutamate +pyrophosphate
PRPP + H2O + L-Glutamine => 5-Phosphoribosylamine + L-Glutamate + PPi
5-phosphoribosylamine + glycine + ATP => 5-phosphoribosylglycinamide (GAR) + ADP + orthophosphate
5-Phosphoribosylamine + Glycine + ATP => GAR + ADP + Pi
Formation of phosphoribosyl pyrophosphate amidotransferase tetramer
Dissociation of phosphoribosyl pyrophosphate amidotransferase tetramer
(R)-2-hydroxyglutarate + FAD => 2-oxoglutarate + FADH2
Reducing equivalents from beta-oxidation of fatty acids transfer to ETF
5'-phosphoribosylformylglycinamidine (FGAM) + ATP => 5'-phosphoribosyl-5-aminoimidazole (AIR) + ADP + orthophosphate
5'-phosphoribosyl-5-aminoimidazole-4-N-succinocarboxamide (SAICAR) <=> 5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR) + fumarate
5'-phosphoribosyl-5-aminoimidazole-4-carboxamide (AICAR) + 10-formyltetrahydrofolate => 5'-phosphoribosyl-5-formaminoimidazole-4-carboxamide (FAICAR) + tetrahydrofolate
adenylosuccinate => adenosine 5'-monophosphate + fumarate
(2'-deoxy)adenosine + H2O => (2'-deoxy)inosine + NH3 [ADA]
Deamination of N6-methyl-AMP to form IMP
N6-methyl-AMP + H2O => IMP + methylamine
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]
Reduction of androstenedione to testosterone
Cytosolic cholate and chenodeoxycholate are conjugated with Coenzyme A (SLC27A5 BACS)
25-hydroxycholesterol is 7alpha-hydroxylated by CYP7B1
Antigenic analysis of the major human phosphoglucomutase isozymes: PGM1, PGM2, PGM3 and PGM4
2-MAG is hydrolyzed to fatty acid and glycerol by MGLL
AcCho is hydrolyzed to Cho and acetate by ACHE
Acetylcholine clearance from synaptic cleft
DHAP is converted to 1-acyl GO3P by GNPAT
Impaired expression and function of the bile salt export pump due to three novel ABCB11 mutations in intrahepatic cholestasis
G3P is acylated to 1-acyl LPA by GPAM/GPAT2 (OM)
Formation of DHA-CoA catalysed by sterol carrier protein X (SCPx)
Conversion of DHA-CoA to docosahexaenoic acid (DHA)
Translocation of tetracosahexaenoyl-CoA to peroxisomes
Prostacyclin synthase (CYP8A1) mediates the isomerization of prostaglandin H2 to prostaglandin I2
Translocation of tetracosapentaenoyl-CoA to peroxisomes
Phosphorylation of carbovir enantiomers by cellular enzymes determines the stereoselectivity of antiviral activity
LTC4 is exported from the cytosol by ABCC1
ABCC1 mediates LTC4 export from the cell
EET(1) is hydrolysed to DHET(1) by EPHX2
sphinganine 1-phosphate => phosphoethanolamine + hexadecanal
sphingosine 1-phosphate => phosphoethanolamine + hexadec-2-enal
Neutral ceramidase hydrolyses ceramide into sphingosine and free fatty acid (plasma membrane)
DAHP synthase from Mycobacterium tuberculosis H37Rv: cloning, expression, and purification of functional enzyme
FPP and IPPP are combined into all-E-10PrP2 by PDSS1/2 tetramer
MDMQ10H2 is methylated to DMQ10H2 by COQ5
GCH1 reduces GTP to dihydroneopterin triphosphate
isocitrate + NADP+ => alpha-ketoglutarate + CO2 + NADPH + H+ [IDH2]
Wnt/beta-catenin signaling: components, mechanisms, and diseases
(d)NTP + ADP <=> (d)NDP + ATP [NME1,2,3]
(d)NDP + ATP <=> (d)NTP + ADP [NME1,2,3]
thioredoxin, reduced (cytosol) <=> thioredoxin, reduced (nucleus)
thioredoxin, oxidized (nucleus) <=> thioredoxin, oxidized (cytosol)
Reduction of nuclear ribonucleoside 5'-diphosphates to deoxyribonucleoside 5'-diphosphates (thioredoxin)
NDP + reduced thioredoxin => dNDP + oxidized thioredoxin + H2O
Reduction of cytosolic ribonucleoside 5'-diphosphates to deoxyribonucleoside 5'-diphosphates (thioredoxin)
Dopamine clearance from the synaptic cleft
Sulfation and sulfotransferases 1: Sulfotransferase molecular biology: cDNAs and genes
Resistance to thromboembolism in PI3Kgamma-deficient mice
L-glutamine + 2 ATP + HCO3- + H2O => carbamoyl phosphate + L-glutamate + 2 ADP + orthophosphate
bicarbonate and glutamine combine to form carbamoyl phosphate
(deoxy)inosine + orthophosphate <=> hypoxanthine + (deoxy)ribose 1-phosphate [NP]
(deoxy)guanosine + orthophosphate <=> guanine + (deoxy)ribose 1-phosphate [NP]
GMP + NADPH + H+ => IMP + NADP+ + NH4+ [GMPR,GMPR2]
condensation of N-Carbamoyl-L-aspartate to form (S)-Dihydroorotate (ring closure)
N-carbamoyl L-aspartate + H+ <=> (S)-dihydroorotate + H2O
carbamoyl phosphate + L-aspartate <=> N-carbamoyl L-aspartate + orthophosphate
carbamoyl phosphate and L-aspartate combine to form N-Carbamoyl-L-aspartate
guanine or hypoxanthine + PRPP => GMP or IMP + PPi [HPRT1]
Expression and characterization of a human pyruvate carboxylase variant by retroviral gene transfer
hypoxanthine + (deoxy)ribose 1-phosphate <=> (deoxy)inosine + orthophosphate [NP]
guanine + (deoxy)ribose 1-phosphate <=> (deoxy)guanosine + orthophosphate [NP]
Sulfation in high endothelial venules: cloning and expression of the human PAPS synthetase
(deoxy)cytidine + H2O => (deoxy)uridine + NH4+ [CDA]
deamination of 2'-Deoxycytidine to 2'-Deoxyuridine
thymine or uracil + 2-deoxy-D-ribose 1-phosphate <=> thymidine or deoxyuridine + orthophosphate [TYMP]
thymidine or deoxyuridine + orthophosphate <=> thymine or uracil + 2-deoxy-D-ribose 1-phosphate [TYMP]
Cloning and expression of two human lysophosphatidic acid acyltransferase cDNAs that enhance cytokine-induced signaling responses in cells
(S)-dihydroorotate + ubiquinone => orotate + ubiquinol
oxidation of (S)-Dihydroorotate to form Orotate
decarboxylation of Orotidine 5'-phosphate to form Uridine 5'-phosphate
orotidine 5'-monophosphate => uridine 5'-monophosphate + CO2
orotate + 5-phospho-alpha-D-ribose 1-diphosphate (PRPP) <=> orotidine 5'-monophosphate (OMP) + pyrophosphate
phosphoribosylation of orotate to form oritidine 5'-phosphate (OMP)
dUMP + N5,N10-methylene tetrahydrofolate => TMP + dihydrofolate
hydrolysis of 2'-deoxyuridine 5'-triphosphate to form 2'-deoxyuridine 5'-phosphate
CNDP2 (name copied from entity in Homo sapiens)
CTH tetramer:PXLP (name copied from entity in Homo sapiens)
CBS tetramer (name copied from entity in Homo sapiens)
Rat liver adenosine triphosphate:adenosine monophosphate phosphotransferase activity. II. Subcellular localization of adenylate kinase isozymes
(S)-3-Hydroxyisobutyryl-CoA [ChEBI:28259]
Hydroxyacid oxidase 1:Flavin mononucleotide complex (name copied from entity in Homo sapiens)
HAO1 tetramer (name copied from entity in Homo sapiens)
MAT II heterotetramer (name copied from entity in Homo sapiens)
MAT II homodimer (name copied from entity in Homo sapiens)
MAT I homotetramer (name copied from entity in Homo sapiens)
MAT I/III (Mg, K cofactors) (name copied from entity in Homo sapiens)
MTAP trimer (name copied from entity in Homo sapiens)
ASL tetramer (name copied from entity in Homo sapiens)
D-amino-acid oxidase:FAD complex (name copied from entity in Homo sapiens)
DAO dimer (name copied from entity in Homo sapiens)
Protection and reactivation of human methylmalonyl-CoA mutase by MMAA protein
Biochem. Biophys. Res. Commun. 404:443-7
The major sites of cellular phospholipid synthesis and molecular determinants of Fatty Acid and lipid head group specificity
ALDH7A1 tetramer (name copied from entity in Homo sapiens)
GCDH tetramer (name copied from entity in Homo sapiens)
TAT dimer (name copied from entity in Homo sapiens)
ALDH4A1 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)
HIBADH tetramer (name copied from entity in Homo sapiens)
ACAD8 tetramer (name copied from entity in Homo sapiens)
HSD17B10 tetramer (name copied from entity in Homo sapiens)
ACADSB tetramer (name copied from entity in Homo sapiens)
IVD tetramer (name copied from entity in Homo sapiens)
FUNCTION Together with AhpD, DlaT and Lpd, constitutes an NADH-dependent peroxidase active against hydrogen and alkyl peroxides as well as serving as a peroxynitrite reductase, thus protecting the bacterium against reactive nitrogen intermediates and oxidative stress generated by the host immune system. Does not however seem to play a role in detoxification of isoniazid.CATALYTIC ACTIVITY 2 R'-SH + ROOH = R'-S-S-R' + H(2)O + ROH.SUBUNIT Homodimer; disulfide-linked, upon oxidation. It has been shown to form 10-mers. The crystal structure of Ser-176 implies that the reduced protein may form a 10- or 12-mer during the catalytic cycle. Identified in a complex with AhpD, DlaT and Lpd.INDUCTION Induced in isoniazid (INH)-resistant, KatG-deficient strains as well as in INH-sensitive strains when challenged with the drug. Increased expression in these strains probably compensates for loss of katG activity in detoxification of organic peroxides. A possible member of the dormancy regulon. Induced in response to reduced oxygen tension (hypoxia). It is hoped that this regulon will give insight into the latent, or dormant phase of infection.MISCELLANEOUS In the absence of both Cys-174 and Cys-176 the enzyme may adopt a 1-Cys Prx-type mechanism, which would account for the apparent suppression of the Ala-174 mutation by Ala-176.SIMILARITY Belongs to the AhpC/TSA family.SIMILARITY Contains 1 thioredoxin domain.
Male pseudohermaphroditism caused by mutations of testicular 17 beta-hydroxysteroid dehydrogenase 3
alpha-keto acid dehydrogenase E3 homodimer (name copied from entity in Homo sapiens)
alpha-keto acid dehydrogenase E3 holoenzyme (name copied from entity in Homo sapiens)
branched-chain alpha-ketoacid dehydrogenase complex (name copied from entity in Homo sapiens)
branched-chain alpha-ketoacid dehydrogenase E1 complex (name copied from entity in Homo sapiens)
PSPH:Mg++ dimer (name copied from entity in Homo sapiens)
PHGHD tetramer (name copied from entity in Homo sapiens)
ASNS dimer (name copied from entity in Homo sapiens)
delta-1-pyrroline-5-carboxylate synthetase dimers
OAT hexamer (name copied from entity in Homo sapiens)
P5CS short isoform, dimer (name copied from entity in Homo sapiens)
P5CS long isoform, dimer (name copied from entity in Homo sapiens)
Proteinases involved in matrix turnover during cartilage and bone breakdown
4xSHMT1 (name copied from entity in Homo sapiens)
holo-MOCS1 (name copied from entity in Homo sapiens)
2xMOCS2-CO-S(1-):2xMOCS2B (name copied from entity in Homo sapiens)
2xMOCS2A:2xMOCS2B (name copied from entity in Homo sapiens)
Thiolysis of 3alpha,7alpha,12alpha-trihydroxy-5beta-cholan-24-one-CoA yields choloyl-CoA (3alpha,7alpha,12alpha-trihydroxy-5beta-cholan-24-one-CoA) and propionyl CoA
3alpha,7alpha,12alpha-trihydroxy-5beta-cholan-24-one-CoA + CoASH => choloyl-CoA (3alpha,7alpha,12alpha-trihydroxy-5beta-cholan-24-one-CoA) + propionyl CoA
Isomerization of 25(R) DHCA-CoA to 25(S) DHCA-CoA
Hydrolysis of choloyl-CoA to cholate and CoASH
Review of epidermal growth factor receptor biology
Thiolysis of 3alpha,7alpha-dihydroxy-5beta-cholan-24-one-CoA yields chenodeoxycholoyl-CoA (3alpha,7alpha-dihydroxy-5beta-cholan-24-one-CoA) and propionyl CoA
3alpha,7alpha-dihydroxy-5beta-cholan-24-one-CoA + CoASH => chenodeoxycholoyl-CoA (3alpha,7alpha-dihydroxy-5beta-cholan-24-one-CoA) + propionyl CoA
Isomerization of 25(R) THCA-CoA to 25(S) THCA-CoA
DHCA + ATP + CoASH => 25(R) DHCA-CoA + AMP + pyrophosphate (SCLS25A5 "BACS")
DHCA is conjugated with Coenzyme A (SLC27A5 BACS)
Collagen type VII -NC2 trimer (name copied from entity in Homo sapiens)
Collagen type VII -NC2 hexamer (name copied from entity in Homo sapiens)
Collagen type VII hexamer (name copied from entity in Homo sapiens)
Collagen alpha-1(VII) trimer (name copied from entity in Homo sapiens)
MPG glycosylase:ethenoadenine complex (name copied from entity in Homo sapiens)
MPG glycosylase:3-methyladenine complex (name copied from entity in Homo sapiens)
Tropoelastin aggregate (name copied from entity in Homo sapiens)
THCA + ATP + CoASH => 25(R) THCA-CoA + AMP + pyrophosphate (SCLS25A5 "BACS")
THCA is conjugated with Coenzyme A (SLC27A5 BACS)
Cholesterol + NADPH + H+ + O2 => 7-alpha-hydroxycholesterol + NADP+ + H2O
Cholesterol is hydroxylated to 7alpha-hydroxycholesterol by CYP7A1
Collagen type XXV (name copied from entity in Homo sapiens)
7-alpha-hydroxycholest-4-en-3-one + NADPH + H+ + O2 => 7-alpha,12-alpha-dihydroxycholest-4-en-3-one + NADP+ + H2O
4-Cholesten-7alpha-ol-3-one is 12alpha-hydroxylated to 7-alpha,12-alpha-dihydroxycholest-4-en-3-one
C-linked procollagen type XXV trimer (name copied from entity in Homo sapiens)
THCA + ATP + CoASH => 25(R) THCA-CoA + AMP + pyrophosphate (SLC27A2 "VLCS")
THCA is conjugated with Coenzyme A (SLC27A2 VLCS)
C-linked procollagen type XVIII trimer (name copied from entity in Homo sapiens)
DHCA + ATP + CoASH => 25(R) DHCA-CoA + AMP + pyrophosphate (SLC27A2 "VLCS")
DHCA is conjugated with Coenzyme A (SLC27A2 VLCS)
4-Cholesten-7alpha,27-diol-3-one + NADPH + H+ + O2 => 4-Cholesten-7alpha,12alpha,27-triol-3-one + NADP+ + H2O
4-Cholesten-7alpha,27-diol-3-one is 12alpha-hydroxylated to 4-Cholesten-7alpha,12alpha,27-triol-3-one
27-hydroxycholesterol + NADPH + H+ + O2 => cholest-5-ene-3beta,7alpha,27-triol + H2O + NADP+
27-hydroxycholesterol is 7alpha-hydroxylated
Isomerization of 3,7,24THCA-CoA to (24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA
3,7,24THCA-CoA => (24R, 25R) 3alpha,7alpha,24-trihydroxy-5beta-cholestanoyl-CoA
Isomerization of 25(R) TetraHCA-CoA to (24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA
25(R) TetraHCA-CoA => (24R, 25R) 3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA
3,7,24THCA + ATP + CoASH => 3,7,24THCA-CoA + AMP + pyrophosphate + H2O (SLC27A2 "VLCS")
3,7,24THCA is conjugated with Coenzyme A (SLC27A2 VLCS)
TetraHCA + ATP + CoASH => 25(R) THCA-CoA + AMP + pyrophosphate + H2O (SLC27A2 "VLCS")
TetraHCA is conjugated with Coenzyme A (SLC27A2 VLCS)
3,7,24THCA + ATP + CoASH => 3,7,24THCA-CoA + AMP + pyrophosphate + H2O (SCLS25A5 "BACS")
3,7,24THCA is conjugated with Coenzyme A (SLC27A5 BACS)
KARS dimer (name copied from entity in Homo sapiens)
GARS dimer (name copied from entity in Homo sapiens)
YARS2 dimer (name copied from entity in Homo sapiens)
SARS2 dimer (name copied from entity in Homo sapiens)
C-linked procollagen alpha-3(V) trimer (name copied from entity in Homo sapiens)
C-linked procollagen type XV trimer (name copied from entity in Homo sapiens)
C-linked procollagen type VII trimer (name copied from entity in Homo sapiens)
4-Cholesten-7alpha,24(S)-diol-3-one + NADPH + H+ + O2 => 4-cholesten-7-alpha,12-alpha,24(S)-triol-3-one + NADP+ + H2O
4-Cholesten-7alpha,24(S)-diol-3-one is 12alpha-hydroxylated to 4-cholesten-7-alpha,12-alpha,24(S)-triol-3-one
TetraHCA + ATP + CoASH => 25(R) TetraHCA-CoA + AMP + pyrophosphate + H2O (SCLS25A5 "BACS")
TetraHCA is conjugated with Coenzyme A (SLC27A5 BACS)
Transport (efflux) of bile salts by ABCB11 (bile salt export pump)
DARS2 dimer (name copied from entity in Homo sapiens)
24-hydroxycholesterol + NADPH + H+ + O2 => cholest-5-ene-3beta,7alpha,24-triol + NADP+ + H2O
24-hydroxycholesterol is 7alpha-hydroxylated to yield cholest-5-ene-3beta,7alpha,24-triol
Homodimer of 4 aminobutyrate aminotransferase (name copied from entity in Homo sapiens)
IDH1 R132H dimer (name copied from entity in Homo sapiens)
De novo sphingolipid biosynthesis: a necessary, but dangerous, pathway
HSP90:Benzoquinoid ansamycins (name copied from entity in Homo sapiens)
HSP90 (name copied from entity in Homo sapiens)
Adenylate cyclase (Mg2+ cofactor) (name copied from entity in Homo sapiens)
FDXR:FADH2 (name copied from entity in Homo sapiens)
FDXR:FAD (name copied from entity in Homo sapiens)
GGCT (name copied from entity in Homo sapiens)
isocitrate + NADP+ => 2-oxoglutarate + CO2 + NADPH + H+
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
desmosterol + NADPH + H+ => cholesterol + NADP+
lanosterol + 3 NADPH + 3 H+ + 3 O2 => 4,4-dimethylcholesta-8(9),14,24-trien-3beta-ol + 3 NADP+ + 4 H2O + formate
Lanosterol is oxidatively demethylated to 4,4-dimethylcholesta-8(9),14,24-trien-3beta-ol
Isopentenyl pyrophosphate rearranges to dimethylallyl pyrophosphate
MAOA-FAD complex (name copied from entity in Homo sapiens)
6xUGDH (name copied from entity in Homo sapiens)
2xPPO:FAD (name copied from entity in Homo sapiens)
2xUROD (name copied from entity in Homo sapiens)
MAOB-FAD complex (name copied from entity in Homo sapiens)
2x(FECH:2Fe-2S cluster) (name copied from entity in Homo sapiens)
8x(ALAD:Zn2+) (name copied from entity in Homo sapiens)
SQR:FAD (name copied from entity in Homo sapiens)
HMBS:DIPY (name copied from entity in Homo sapiens)
8xALAD:Pb2+:Zn2+ (name copied from entity in Homo sapiens)
The mucopolysaccharidoses: inborn errors of glycosaminoglycan catabolism
Beta oxidation of octanoyl-CoA to hexanoyl-CoA
Human adenine phosphoribosyltransferase. Affinity purification, subunit structure, amino acid composition, and peptide mapping.
Regulation of Lipid Metabolism by Peroxisome proliferator-activated receptor alpha (PPARalpha)
Phytanic acid alpha-oxidation, new insights into an old problem: a review
3-(4-Hydroxyphenyl)pyruvate [ChEBI:1431]
Functional expression of human mutant phosphofructokinase in yeast: genetic defects in French Canadian and Swiss patients with phosphofructokinase deficiency
Studies on the properties and tissue distribution of the isozymes of guanylate kinase in man
Immunocytochemical localization of the Menkes copper transport protein (ATP7A) to the trans-Golgi network
6-Phosphogluconate dehydrogenase: the mechanism of action investigated by a comparison of the enzyme from different species
A new sperm-specific Na+/H+ exchanger required for sperm motility and fertility
Molecular basis for membrane phospholipid diversity: why are there so many lipids?
On the mechanism of sensing unfolded protein in the endoplasmic reticulum
Subcellular targeting and trafficking of nitric oxide synthases
Inhibition of collagen fibrillogenesis by cells expressing soluble extracellular domains of DDR1 and DDR2
Interconversion of 2-oxoglutarate and 2-hydroxyglutarate
A dityrosyl-diiron radical cofactor center is essential for human ribonucleotide reductases
Formation of interchain disulfide bonds and helical structure during biosynthesis of procollagen by embryonic tendon cells
Transport of vitamins, nucleosides, and related molecules
SLC26A9 is a Cl(-) channel regulated by the WNK kinases
FUNCTION: Ferredoxins are iron-sulfur proteins that transfer electrons in a wide variety of metabolic reactions (By similarity).
(24R,25R)-3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestan-26-oyl-CoA [ChEBI:52050]
Complete reconstitution of the human coenzyme A biosynthetic pathway via comparative genomics
N-Acetyl-1-D-myo-inosityl-2-amino-2-deoxy-alpha-D-glucopyranoside deacetylase (MshB) is a key enzyme in mycothiol biosynthesis
The multidrug transporter, a double-edged sword
Human cholesterol 7alpha-hydroxylase (CYP7A1) deficiency has a hypercholesterolemic phenotype
G(1) to S transition: more than a cell cycle engine switch.
Human methionine synthase: cDNA cloning and identification of mutations in patients of the cblG complementation group of folate/cobalamin disorders
NLR proteins: integral members of innate immunity and mediators of inflammatory diseases
Structure of human isovaleryl-CoA dehydrogenase at 2.6 A resolution: structural basis for substrate specificity,.
Protein interactions with nitric oxide synthases: controlling the right time, the right place, and the right amount of nitric oxide
Cloning and characterization of SLC26A6, a novel member of the solute carrier 26 gene family
The biochemistry, metabolism and inherited defects of the pentose phosphate pathway: a review
Relevance of aggregation properties of tropoelastin to the assembly and structure of elastic fibers
J. Ultrastruct. Mol. Struct. Res. 94:209-16
The cysteine biosynthetic pathway using the intermediate O-acetylserine is well preserved among bacteria, and it is also the main pathway in M. tuberculosis in normal medium. It depends on a six electron reduction of sulfite to sulfide (Bhave et al, 2007; Pinto et al, 2007).
The quality control of MHC class I peptide loading
Molecular cloning of a novel member of the GLUT family of transporters, SLC2a10 (GLUT10), localized on chromosome 20q13.1: a candidate gene for NIDDM susceptibility
Extracellular transsulfuration generates hydrogen sulfide from homocysteine and protects endothelium from redox stress
Am J Physiol Heart Circ Physiol 299:H1568-76
New roles for cysteine and transsulfuration enzymes: production of H2S, a neuromodulator and smooth muscle relaxant
Molecular characterization of two galactosemia mutations: correlation of mutations with highly conserved domains in galactose-1-phosphate uridyl transferase
Mutational analysis of 105 mucopolysaccharidosis type VI patients
Di- and triphosphopyridine nucleotide isocitric dehydrogenases in yeast
Signal transduction via platelet-derived growth factor receptors
Inflammasomes: guardians of cytosolic sanctity
Adrenodoxin: structure, stability, and electron transfer properties
Morquio A syndrome: cloning, sequence, and structure of the human N-acetylgalactosamine 6-sulfatase (GALNS) gene
DAP10- and DAP12-associated receptors in innate immunity
Function of Nod-like receptors in microbial recognition and host defense
Identification of the gene encoding the enzyme deficient in mucopolysaccharidosis IIIC (Sanfilippo disease type C)
Purification and characterization of recombinant human liver glycolate oxidase
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
ATF6-alpha is a transmembrane protein that normally resides in the Endoplasmic Reticulum (ER) membrane. Here its luminal C-terminal domain is associated with BiP, shielding 2 Golgi-targeting regions and thus keeping ATF6-alpha in the ER. Upon interaction of BiP with unfolded proteins in the ER, ATF6-alpha dissociates and transits to the Golgi where it is cleaved by the S1P and S2P proteases that reside in the Golgi, releasing the N-terminal domain of ATF6-alpha into the cytosol. After transiting to the nucleus, the N-terminal domain acts as a transcription factor to activate genes encoding chaperones.
The N-terminal fragment of ATF6-alpha contains a bZIP domain and binds the sequence CCACG in ER Stress Response Elements (ERSEs). ATF6-alpha binds ERSEs together with the heterotrimeric transcription factor NF-Y, which binds the sequence CCAAT in the ERSEs, and together the two factors activate transcription of ER stress-responsive genes. Evidence from overexpression and knockdowns indicates that ATF6-alpha is a potent activator but its homolog ATF6-beta is not and ATF6-beta may actually reduce expression of ER stress proteins.
The Endoplasmin (HSP90B1) gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
Purification and characterization of 7 alpha-hydroxy-4-cholesten-3-one 12 alpha-hydroxylase
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.
The GFPT1 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The DNAJB11 gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
The ACADVL gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
A current review of fatty acid transport proteins (SLC27)
ATF4 is a transcription factor and activates expression of IL-8, MCP1, IGFBP-1, CHOP, HERP1 and ATF3.
The Aspariagine Synthetase (ASNS) gene is transcribed to yield mRNA and the mRNA is translated to yield protein.
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.
Three-dimensional structure of human erythrocytic purine nucleoside phosphorylase at 3.2 A resolution
The Unfolded Protein Response (UPR) is a regulatory system that protects the Endoplasmic Reticulum (ER) from overload. The UPR is provoked by the accumulation of improperly folded protein in the ER during times of unusually high secretion activity. Analysis of mutants with altered UPR, however, shows that the UPR is also required for normal development and function of secretory cells. One level at which the URP operates is transcriptional and translational regulation: mobilization of ATF6 and IRE1 leads to increased transcription of genes encoding chaperones, and mobilization of PERK (pancreatic eIF2alpha kinase) leads to phosphorylation of the translation initiation factor eIF2alpha and global down-regulation of protein synthesis. These three regulatory pathways are annotated here.
PERK is a single-pass transmembrane protein located in the endoplasmic reticulum (ER) membrane such that the N-terminus of PERK is luminal and the C-terminus is cytosolic. PERK is maintained in an inactive form by interaction of its luminal domain with BiP, an ER chaperone. BiP also binds unfolded proteins and so BiP dissociates from PERK when unfolded proteins accumulate in the ER. Dissociated PERK monomers spontaneously form homodimers and the homodimeric form of PERK possesses kinase activity in its cytosolic C-terminal domain. The kinase specifically phosphorylates the translation factor eIF2alpha at Ser52, resulting in an arrest of translation. Thus translation of proteins targeted to the ER is downregulated. The translation arrest also causes depletion of Cyclin D1, a rapidly turned over protein. The depletion of Cyclin D1 in turn causes arrest of the cell cycle in G1 phase.
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).
Protein metabolism comprises the pathways of translation, post-translational modification and protein folding.
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).
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.
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.
Functional structure and composition of the extracellular matrix
Cytosolic malate dehydrogenase catalyzes the reaction of malate and NAD+ to form oxaloacetate and NADH + H+ (Lo et al. 2005). The dimeric structure of the human dehydrogenase is inferred from that established for its well-studied pig homolog (Birktoft et al. 1989).
Cytosolic phosphoglucomutase (PGM) catalyzes the reversible conversion of glucose 6-phosphate to glucose 1-phosphate (Drago et al. 1991). Two PGM isoenzymes, both monomers, have been identified. PGM1 is the major form found in most tissues except erythrocytes, where PGM2 is abundant (March et al. 1993; Parrington et al. 1968; Putt et al. 1993). PGM2 also has substantial phosphopentomutase activity and its primary physiological in normal tissues in vivo is not clear.
The reactions of gluconeogenesis convert mitochondrial pyruvate to cytosolic glucose 6-phosphate which in turn can be hydrolyzed to glucose and exported from the cell. Gluconeogenesis is confined to cells of the liver and kidney and enables glucose synthesis from molecules such as lactate and alanine and other amino acids when exogenous glucose is not available (reviewed, e.g., by Gerich 1993). The process of gluconeogenesis as diagrammed below occurs in two parts: a network of reactions converts mitochondrial pyruvate to cytosolic phosphoenolpyruvate; then phosphoenolpyruvate is converted to glucose 6-phosphate in a single sequence of cytosolic reactions. Three variants of the first part of the process are physiologically important. 1) A series of transport and transamination reactions convert mitochondrial oxaloacetate to cytosolic oxaloacetate which is converted to phosphoenolpyruvate by a hormonally regulated, cytosolic isoform of phosphoenolpyruvate carboxykinase. This variant allows regulated glucose synthesis from lactate. 2) Mitochondrial oxaloacetate is reduced to malate, which is exported to the cytosol and re-oxidized to oxaloacetate. This variant provides reducing equivalents to the cytosol, needed for glucose synthesis from amino acids such as alanine and glutamine. 3) Constitutively expressed mitochondrial phosphoenolpyruvate carboxykinase catalyzes the conversion of mitochondrial oxaloacetate to phosphoenolpyruvate which is then transported to the cytosol. The exact path followed by any one molecule of pyruvate through this reaction network is determined by the tissue in which the reactions are occurring, the source of the pyruvate, and the physiological stress that triggered gluconeogenesis. In all cases, the synthesis of glucose from two molecules of pyruvate requires the generation and consumption of two reducing equivalents as cytosolic NADH + H+. For pyruvate derived from lactate (variants 1 and 3), NADH + H+ is generated with the oxidation of lactate to pyruvate in the cytosol (a reaction of pyruvate metabolism not shown in the diagram). For pyruvate derived from amino acids (variant 2), mitochondrial NADH + H+ generated by glutamate dehydrogenase (a reaction of amino acid metabolism, not shown) is used to reduce oxaloacetate to malate, which is transported to the cytosol and re-oxidized, generating cytosolic NADH + H+. The synthesis of glucose from pyruvate also requires the consumption of six high-energy phosphates, four from ATP and two from GTP. In the second part of gluconeogenesis, cytosolic phosphoenolpyruvate, however derived, is converted to fructose 1,6-bisphosphate by reactions that are the reverse of steps of glycolysis. Hydrolysis of fructose 1,6-bisphosphate to fructose 6-phosphate is catalyzed by fructose 1,6-bisphosphatase, and fructose 6-phosphate is reversibly isomerized to glucose 6-phosphate.
The reversible isomerization of fructose-6-phosphate to form glucose-6-phosphate is catalyzed by cytosolic phosphoglucose isomerase (Noltman 1972; Xu and Beutler 1994; Tsuboi et al. 1958).
The reversible conversion of glyceraldehyde-3-phosphate to dihydroxyacetone phosphate is catalyzed by cytosolic triose phosphate isomerase (Watanabe et al. 1996; Lu et al. 1984).
Cytosolic phosphoglycerate kinase complexed with magnesium catalyzes the reversible phosphorylation of 3-phosphoglycerate to form 1,3-bisphosphoglycerate (Huang et al. 1980a, 1980b).
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.
PCK2 (phosphoenolcarboxykinase), located in the mitochondrial matrix, catalyzes the physiologically irreversible reaction of oxaloacetate and GTP to form phosphoenolpyruvate, GDP, and CO2 (Modaressi et al. 1996, 1998).
The transfer of a high-energy phosphate bond from GTP to oxaloacetate, to form phosphoenolpyruvate, GDP, and CO2, is catalyzed by cytosolic phosphoenolpyruvate carboxykinase (Dunten et al. 2002). This reaction is irreversible under physiological conditions.
Glycogen, a highly branched glucose polymer, is formed and broken down in most human tissues, but is most abundant in liver and muscle, where it serves as a major stored fuel. Glycogen metabolism has been studied in most detail in muscle, although considerable experimental data are available concerning these reactions in liver as well. Glycogen metabolism in other tissues has not been studied as extensively, and is thought to resemble the muscle process (Hers 1976; Lomako et al. 2004; Villar-Palasi and Larner 1970). Glycogen synthesis involves five reactions. The first two, conversion of glucose 6-phosphate to glucose 1-phosphate and synthesis of UDP-glucose from glucose 1-phosphate and UTP, are shared with several other pathways. The next three reactions, the auto-catalyzed synthesis of a glucose oligomer on glycogenin, the linear extension of the glucose oligomer catalyzed by glycogen synthase, and the formation of branches catalyzed by glycogen branching enzyme, are unique to glycogen synthesis. These reactions are shown in the figure. Repetition of the last two reactions generates large, extensively branched glycogen polymers. The catalysis of several of these reactions by distinct isozymes in liver and muscle allows them to be regulated independently in the two tissues.
Cytosolic, non-phosphorylated PGYB dimers (b form) can reversibly bind AMP. This reaction is inferred from the AMP-binding properties of human PGYL and closely homologous PGYM proteins from other species (Newgard et al. 1989; Rath et al. 2000).
Cytosolic, non-phosphorylated PGYB dimers (b form) complexed with AMP can reversibly dissociate. This reaction is inferred from the AMP-binding properties of the closely homologous PGYM complex (Rath et al. 2000).
Cytosolic galactokinase (GALK1) catalyzes the reaction of ATP and D-galactose to form ADP and D-galactose 1-phosphate (Ai at al. 1995).
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).
Cytosolic galactose-1-phosphate uridylyltransferase (GALT) catalyzes the reaction of alpha-D-galactose 1-phosphate and UDP glucose to form D-glucose 1-phosphate and UDP galactose (Reichardt et al. 1991).
Cytosolic, non-phosphorylated PGYM dimers (b form) complexed with AMP can reversibly dissociate (Rath et al. 2000).
Cytosolic, non-phosphorylated PGYM dimers (b form) can reversibly bind AMP. This reaction is negatively regulated by ATP and glucose 6-phosphate and is the means by which high levels of these molecules repress PGYM activity (Rath et al. 2000).
Glycogen breakdown occurs via the same chemical steps in all tissues but is separately regulated via tissue specific isozymes and signaling pathways that enable distinct physiological fates for liver glycogen and that in other tissues. Glycogen phosphorylase, which can be activated by phosphorylase kinase, catalyzes the removal of glucose residues as glucose 1-phosphate from the ends of glycogen branches. The final four residues of each branch are removed in two steps catalyzed by debranching enzyme, and further glycogen phosphorylase activity completes the process of glycogen breakdown. The figure shows the actions of phosphorylase and debranching enzyme. The first glucose residue in each branch is released as free glucose; all other residues are released as glucose 1-phosphate. The latter molecule can be converted to glucose 6-phosphate in a step shared with other pathways (Villar-Palasi and Larner 1970; Hers 1976).
Cytosolic phosphoglucomutase (PGM) catalyzes the reversible conversion of glucose 1-phosphate to glucose 6-phosphate. Two PGM isoenzymes, both monomers, have been identified. PGM1 is the major form found in most tissues except erythrocytes, where PGM2 is abundant (March et al. 1993; Parrington et al. 1968; Putt et al. 1993). PGM2 also has substantial phosphopentomutase activity and its primary physiological in normal tissues in vivo is not clear.
Toward the full set of human mitochondrial aminoacyl-tRNA synthetases: characterization of AspRS and TyrRS
The main sources of galactose in the human diet are milk and milk products. The disaccharide lactose from these sources is hydrolyzed in the intestine to its constituent monosaccharides, glucose and galactose. Galactose is metabolized primarily in the liver in a sequence of three reactions that yield one molecule of glucose 1-phosphate per molecule of galactose. First, it is phosphorylated to yield galactose 1-phosphate. Then, galactose 1-phosphate and UDP-glucose react to form UDP-galactose and glucose 1-phosphate, and UDP-galactose undergoes epimerization to form UDP-glucose. In a reaction shared with other pathways, glucose 1-phosphate can be converted into glucose 6-phosphate (Holton et al. 2001; Elsas and Lai 2001).
Cytosolic glucose-6-phosphate dehydrogenase (G6PD) catalyzes the reaction of glucose 6-phosphate and NADP+ to form D-glucono-1,5-lactone 6-phosphate and , and NADPH + H+. Biochemical studies indicate that both G6PD dimers and tetramers are catalytically active and capable or forming under physiological conditions in vivo (Au et al. 2000). Mutations that reduce the catalytic efficientcy of G6PD are remarkably common in human populations; these appear to have a protective effect against malaria (e.g., Luzzatto and Afolayan 1968).
Cytosolic 6-phosphogluconolactonase (PGLS) catalyzes the hydrolysis of D-glucono-1,5-lactone 6-phosphate to form 6-phospho-D-gluconate (Beutler and Kuhl 1985; Collard et al. 1999).
Functional analysis of the purified anandamide-generating phospholipase D as a member of the metallo-beta-lactamase family
Comparison of the intracellular signaling responses by three chimeric fibroblast growth factor receptors in PC12 cells
Mannose-6-phosphate isomerase (MPI) converts Fructose 6-phosphate to Mannose 6-phosphate (Proudfoot AE et al, 1994). Defects in this gene are associated with congenital disorder of glycosylation type 1B (CDG1B). Oral administration of mannose is an efficient therapy against this defect (Schollen E et al, 2000).
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).
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.
Sulfatase activity requires a unique posttranslational modification (PTM) of a catalytic cysteine residue into a formylglycine. This modification is impaired in patients with multiple sulfatase deficiency (MSD) due to defects in the SUMF1 (sulfatase-modifying factor 1) gene responsible for this PTM. SUMF2 can inhibit the activity of SUMF1 thereby providing a mechanism for the regulation of sulfatase activation (Ghosh 2007, Diez-Roux & Ballabio 2005).
After translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the body. These modifications include the vitamin K-dependent attachment of carboxyl groups to glutamate residues and the conversion of lysine residues to hypusine.
Sulfatase-modifying factor 2 (SUMF2, also called C-alpha-formylglycine-generating enzyme 2, pFGE) is the paralogue of SUMF1. While SUMF1 can modify a critical residue on arylsulfatases to confer activity to them, SUMF2 lacks this ability (Mariappan et al. 2005) and instead, SUMF2 can inhibit the action of SUMF1 by dimerising with it (Zito et al. 2005). SUMF2 can interact with sulfatases with and without SUMF1 (Zito et al. 2005).
DNA synthesis occurs in the S phase, or the synthesis phase, of the cell cycle. The cell duplicates its hereditary material, and two copies of the chromosome are formed. As DNA replication continues, the E type cyclins shared by the G1 and S phases, are destroyed and the levels of the mitotic cyclins rise.
The 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.
The actual synthesis of DNA occurs in the S phase of the cell cycle. This includes the initiation of DNA replication, when the first nucleotide of the new strand is laid down during the synthesis of the primer. The DNA replication preinitiation events begin in late M or early G1 phase.
An unknown N-acetylgalactosaminyltransferase mediates the transfer of GalNAc is transferred to Tn antigens via an alpha-1,6 linkage to create Core 7 mucins (Brockhausen et al. 2009).
An unknown galactosyltransferase mediates the transfer of galactose is transferred to Tn antigens via an alpha-1,3 linkage to create Core 8 mucins (Brockhausen et al. 2009).
Mucins are a family of high molecular weight, heavily glycosylated proteins (glycoconjugates) produced by epithelial tissues in most metazoa. Mucins' key characteristic is their ability to form gels; therefore they are a key component in most gel-like secretions, serving functions from lubrication to cell signalling to forming chemical barriers. To date, there are approximately 20 genes that express mucins. Mature mucins are composed of two distinct regions: (1) The amino- and carboxy-terminal regions are very lightly glycosylated, but rich in cysteines. The cysteine residues participate in establishing disulfide linkages within and among mucin monomers. (2) A large central region rich in serine, threonine and proline residues called the variable number of tandem repeat (VNTR) region which can become heavily O-glycosylated with hundreds of O-GalNAc glycans. N-acetyl-galactosamine (GalNAc) is the first glycan to be attached, forming the simplest mucin O-glycan. After this, several different pathways are possible generating "core" structures. Four core structures are commonly formed, several others are possible but infrequent. O-linked glycans are often capped by the addition of a sialic acid residue, terminating the addition of any more O-glycans (Brockhausen et al, 2009; Tarp and Clausen, 2008).
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.
Signalling functions and biochemical properties of pertussis toxin-resistant G-proteins
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.
An unknown N-acetylglucosaminyltransferase mediates the transfer of GlcNAc to Tn antigens via an alpha-1,3 linkage to create Core 5 mucins (Brockhausen et al. 2009).
An unknown N-acetylglucosaminyltransferase mediates the transfer of GlcNAc to Tn antigens via an beta-1,6 linkage to create Core 6 mucins (Brockhausen et al. 2009).
GDP-mannose is the mannose donor for the first 5 mannose addition reactions in the N-glycan precursor synthesis, and also for the synthesis of Dolichyl-phosphate-mannose involved in other mannose transfer reactions. It is synthesized from fructose 6-phosphate and GTP in three steps.
Reactions for the synthesis of the small nucleotide-linked sugar substrates that are used in the synthesis of the N-glycan precursor and in the later steps of glycosylation are annotated here. All these nucleotide-linked sugar donors are synthesized in the cytosol; however, to participate in the later reactions of N-glycan precursor biosynthesis (when the glycan is oriented toward the lumen of the endoplasmic reticulum (ER)), these substrates must be attached to a dolichyl-phosphate molecule and then flipped toward the luminal side of the ER, through a mechanism which is still not known but which involves a different protein than the one that mediates the flipping of the LLO itself (Sanyal S et al, 2008). Two of the genes encoding enzymes involved in these reactions, MPI and PMM2, are known to be associated with Congenital Disorders of Glycosylation (CDG) diseases of type I. Of these, CDG-Ia, associated with defects in PMM2, is the most frequent CDG disease reported.
Electrophilic substance-mercapturic acid
Electrophilic substrate-mycothiol conjugate
Proteasome and peptidase function in MHC-class-I-mediated antigen presentation
FUNCTION Bifunctional enzyme with both catalase and broad-spectrum peroxidase activity. Displays also NADH oxidase, isoniazid (INH) lyase and isonicotinoyl-NAD synthase activity. May play a role in the intracellular survival of mycobacteria. May be involved in DNA repair. Partly complements recA-deficient E.coli cells exposed to UV radiation, mitomycin C or hydrogen peroxide. Increases resistance to mitomycin C in E.coli cells deficient for either uvrA, uvrB or uvrC.CATALYTIC ACTIVITY Donor + H(2)O(2) = oxidized donor + 2 H(2)O.CATALYTIC ACTIVITY 2 H(2)O(2) = O(2) + 2 H(2)O.COFACTOR Binds 1 heme B (iron-protoporphyrin IX) group per subunit.SUBUNIT Homodimer.INDUCTION By treatment with H(2)O(2). Repressed by FurA.DISRUPTION PHENOTYPE Cells show isoniazid (INH) resistance and are more sensitive to oxidative stress.MISCELLANEOUS In contrast to the Synechocystis sp. enzyme, no Trp radical is formed on the distal Trp residue (Trp-91).MISCELLANEOUS The action of antitubercular drug isoniazid (INH) is dependent on its activation by KatG to form an isonicotinoyl-NAD adduct (IN-NAD). Resistance to INH can be due to mutations that reduces KatG activity.MISCELLANEOUS Was identified as a high-confidence drug target.SIMILARITY Belongs to the peroxidase family. Peroxidase/catalase subfamily.
FUNCTION Catalyzes the transfer of acetyl from acetyl-CoA to desacetylmycothiol (Cys-GlcN-Ins) to form mycothiol.CATALYTIC ACTIVITY Desacetylmycothiol + acetyl-CoA = CoA + mycothiol.SUBUNIT Monomer.MISCELLANEOUS The N-terminal acetyl-CoA does not function as substrate in the catalyzed reaction, but is believed to have a structural role.MISCELLANEOUS Was identified as a high-confidence drug target.SIMILARITY Belongs to the acetyltransferase family. MshD subfamily.SIMILARITY Contains 2 N-acetyltransferase domains.
Elastic fiber formation: a dynamic view of extracellular matrix assembly using timer reporters
In analogy to glutathione, mycothiol is part of the detoxification machinery of the M. tuberculosis cell. The biotransformation of electrophilic toxins consists of creating an adduct with mycothiol, its cleavage into a "mercapturic acid" and glucosaminyl-inositol (with which mycothiol is recycled), and transport of the mercapturic acid through the membrane. The protein(s) catalyzing the transport are still unidentified. Further molecules that are changed to less dangerous entities with the help of mycothiol are formaldehyde and the nitrosyl radical (Rawat and Av-Gay, 2007; Newton et al, 2008).
Collagen fibrillogenesis: fibronectin, integrins, and minor collagens as organizers and nucleators
Phagocytosis of retinal rod and cone photoreceptors
5-Hydroxyindoleacetaldehyde [ChEBI:2070]
Nucleotide receptor signaling in platelets
Structural and catalytic properties and homology modelling of the human nucleoside diphosphate kinase C, product of the DRnm23 gene
Collagen biosynthesis and modifying enzymes
Steroidogenic electron transport in adrenal cortex mitochondria
Acyl-CoA:lysophospholipid acyltransferases
Molecular cloning and nucleotide sequence of a full-length cDNA for human alpha enolase
Human multidrug-resistant cell lines: increased mdr1 expression can precede gene amplification
Structural and enzymatic analysis of MshA from Corynebacterium glutamicum: substrate-assisted catalysis
Crystal structures of MMP-1 and -13 reveal the structural basis for selectivity of collagenase inhibitors
Oxidative demethylation by Escherichia coli AlkB directly reverts DNA base damage.
Employment of the epidermal growth factor receptor in growth factor-independent signaling pathways
Insig-mediated degradation of HMG CoA reductase stimulated by lanosterol, an intermediate in the synthesis of cholesterol
Glycogenin: the primer for mammalian and yeast glycogen synthesis
Control of matrix metalloproteinase catalytic activity
Phosphoribosylpyrophosphate synthesis from glucose decreases during amino acid starvation of human lymphoblasts
Association with HSP90 inhibits Cbl-mediated down-regulation of mutant epidermal growth factor receptors
The sodium/calcium exchanger family-SLC8
Genomic organization, tissue distribution and deletion mutation of human pyridoxine 5'-phosphate oxidase
Antimicrobial mechanisms of phagocytes and bacterial evasion strategies
CATALYTIC ACTIVITY Thioredoxin + NADP(+) = thioredoxin disulfide + NADPH.MISCELLANEOUS The active site is a redox-active disulfide bond.MISCELLANEOUS Was identified as a high-confidence drug target.SIMILARITY Belongs to the class-II pyridine nucleotide-disulfide oxidoreductase family.
Measurement and subcellular distribution of choloyl-CoA synthetase and bile acid-CoA:amino acid N-acyltransferase activities in rat liver
Wnt and calcium signaling: beta-catenin-independent pathways
10-formyltetrahydrofolyl polyglutamate macromolecule [ChEBI:28010]
10-formyltetrahydrofolyl polyglutamate macromolecule
Regulation of matrix metalloproteinase activity in health and disease
Molecular analysis of human argininosuccinate lyase: mutant characterization and alternative splicing of the coding region
Identification of isobutyryl-CoA dehydrogenase and its deficiency in humans.
cis,cis-3,6-Dodecadienoyl-CoA [ChEBI:28002]
Molecular cloning, expression, and characterization of human bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthase and its functional domains
Purification and some properties of a monoacylglycerol-hydrolyzing enzyme of rat adipose tissue
Database identifier. Use this URL to connect to the web page of this instance in Reactome: http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=4233558
One- and two-electron oxidations of methionine by peroxynitrite
Acidosis, acid-sensing ion channels, and neuronal cell death
Beta oxidation of palmitoyl-CoA to myristoyl-CoA
Purification of, generation of monoclonal antibodies to, and mapping of phosphoribosyl N-formylglycinamide amidotransferase
Mycobacterium tuberculosis biological processes
Mycobacterium tuberculosis H37Rv is the laboratory strain most widely used of the pathogen M. tuberculosis, an actinobacterium that carries many properties of its family to the extreme. It is not only interesting as one of the top three bacterial killers, with one third of the world having a dormant infection, but also as a model for other mycobacteria regarding the processes of slow growing, dormancy, host interaction, very long chain fatty acid biosynthesis, outer cell wall assembly, as well as sulfolipid, siderophore, and mycothiol biosynthesis. M. tuberculosis produces mycolic and phthioceranic acids, the fatty acids with the longest carbon atom chains known. With up to 20 hours, it has the longest reproduction time in mycobacteria. In human macrophages in dormant state, it spends decades without reproduction. Consequently, to fully investigate these properties new methods will have to be invented. While the treatment of an M. tuberculosis infection appears standard in Western countries, it still involves six months of a regime of three antibiotics that have been known for a long time. Not unexpectedly, acceptance and adherence to such a prolonged therapy are less than desired, and this contributes to spontaneous resistance from an already higher than average mutation rate of M. tuberculosis due to replication errors. Fueled by the HIV advance, strains of this bacterium are on the rise with resistance to all used antibiotics. For this reason, M. tuberculosis is the testbed of new antibiotics development, and it offers the opportunity of many unique and essential biochemical pathways. (Camus et al. 2002; Leibert and Rom, 2010)
Characterization of human type I and type II IMP dehydrogenases
Characterization of collagen types XII and XIV from fetal bovine cartilage
Class I MHC mediated antigen processing & presentation
Biglycan organizes collagen VI into hexagonal-like networks resembling tissue structures
Cellular targets for activation by the E2F1 transcription factor include DNA synthesis- and G1/S-regulatory genes
Phospholipase C-gamma: diverse roles in receptor-mediated calcium signaling
Gly-3-P+FAD->DHAP+FADH2 (catalyzed by mitochondrial Gly-Phos dehydrogenase)
2-hydroxyphytanoyl-CoA => pristanal + formyl-CoA
phytanate + CoA-SH + ATP => phytanoyl-CoA + AMP + pyrophosphate
Peroxisomal uptake of very long-chain fatty acyl CoA
palmitoyl-CoA + DHAP => 1-palmitoylglycerone phosphate + CoASH
1-palmitoylglycerone phosphate + hexadecanol => O-hexadecylglycerone phosphate + palmitate
pristanate + CoA-SH + ATP => pristanoyl-CoA + AMP + pyrophosphate
Isomerization of (2R)-pristanoyl-CoA to (2S)-pristanoyl-CoA
3-ketopristanoyl-CoA + CoASH => 4,8,12-trimethyltridecanoyl-CoA + propionyl-CoA
DNA replication initiates at multiple sites on plasmid DNA in Xenopus egg extracts.
A mutational analysis of the yeast proliferating cell nuclear antigen indicates distinct roles in DNA replication and DNA repair.
A model for interstitial collagen catabolism by mammalian collagenases
ATF6 as a transcription activator of the endoplasmic reticulum stress element: thapsigargin stress-induced changes and synergistic interactions with NF-Y and YY1
Fibroblast growth factors and their receptors in cancer
lysophosphatidic acid + fatty acyl CoA => phosphatidic acid + CoA (1)
1-acyl-glycerol 3-phosphate + acyl-CoA => 1,2-diacyl-glycerol 3-phosphate + CoASH
1-acyl LPA is acylated to PA by AGPAT (LPAAT)
glycerol 3-phosphate + acyl-CoA => 1-acylglycerol 3-phosphate + CoASH [mitochondrial membrane-associated]
Conversion of glycerol-3-phosphate to lysophosphatidic acid
Conversion of Glycerol to Glycerol-3-phosphate
3-oxooctadecanoyl-CoA (3-oxostearoyl-CoA) + NADPH + H+ => 3-hydroxyoctadecanoyl-CoA + NADP+
acetyl-CoA + 7 malonyl-CoA + 14 NADHP + 14 H+ => palmitate + 7 CO2 + 14 NADP+ + 8 CoASH + 6 H2O
Conversion of malonyl-CoA and acetyl-CoA to palmitate
Formation of fatty acid synthase (FAS) dimer
Generation of Cytoplasmic Acetyl CoA from Citrate
Crystal structure of human recombinant ornithine aminotransferase.
Reduction of 2-trans-4-cis-decadienoyl-CoA to form 3-trans-decenoyl-CoA
dehydrogenation of 4-cis-decenoyl-CoA to form 2-trans-4-cis-decadienoyl-CoA
D-methylmalonyl-CoA <=> L-methylmalonyl-CoA
Isomerization of 3-trans-decenoyl-CoA to form trans-dec-2-enoyl-CoA
MUT transfers adenosyl group from AdoCbl to L-MM-CoA
acetoacetate + succinyl-CoA <=> acetoacetyl-CoA + succinate
Krüppel-like transcription factor KLF5 is a key regulator of adipocyte differentiation
The ubiquitously expressed human CYP51 encodes lanosterol 14 alpha-demethylase, a cytochrome P450 whose expression is regulated by oxysterols
Isomerization of cis,cis-3,6-Dodecadienoyl-CoA to form trans,cis-Lauro-2,6-dienoyl-CoA
Removal of 2 Carbon atoms from trans,cis-Lauro-2,6-dienoyl-CoA to form 4-cis-decenoyl-CoA
Removal of six carbons from Linoleoyl-CoA to form cis,cis-3,6- Dodecadienoyl-CoA
Molecular mechanisms of ligand binding, signaling, and regulation within the superfamily of G-protein-coupled receptors: molecular modeling and mutagenesis approaches to receptor structure and function
Sprinter: a novel transmembrane protein required for Wg secretion and signaling
Mucopolysaccharidosis type II (Hunter syndrome): a clinical review and recommendations for treatment in the era of enzyme replacement therapy
D-glyceraldehyde 3-phosphate <=> dihydroxyacetone phosphate
D-fructose 6-phosphate <=> alpha-D-Glucose 6-phosphate
alpha-D-Glucose 6-phosphate <=> D-Glucose 1-phosphate
PGYB dimer, b form + 2 AMP <=> PGYB b dimer:AMP complex
Inositol phosphate synthesis and the nuclear processes they affect
ATP + D-galactose => ADP + D-galactose 1-phosphate
D-galactose 1-phosphate + UDP-glucose <=> D-glucose 1-phosphate + UDP-galactose
PGYB b dimer:AMP complex <=> PGYB dimer, b form + 2 AMP
PGYM dimer, b form + 2 AMP <=> PGYM b dimer:AMP complex
PGYM b dimer:AMP complex <=> PGYM dimer, b form + 2 AMP
D-Glucose 1-phosphate <=> alpha-D-Glucose 6-phosphate
dihydroxyacetone phosphate <=> D-glyceraldehyde 3-phosphate
1,3-Bisphosphoglycerate and ADP react to form 3-phosphoglycerate and ATP
1,3-bisphospho-D-glycerate + ADP <=> 3-phospho-D-glycerate + ADP
D-fructose 6-phosphate + ATP => D-fructose 1,6-bisphosphate + ADP
ATP + 3-Phospho-D-glycerate <=> ADP + 1,3-bisphospho-D-glycerate
oxaloacetate + GTP => phosphoenolpyruvate + GDP + CO2 [mitochondrial matrix]
Phosphoenolpyruvate + H2O <=> 2-Phospho-D-glycerate
(S)-malate + NAD+ <=> oxaloacetate + NADH + H+
malate + NAD+ <=> oxaloacetate + NADH + H+
Oxaloacetate and GTP react to form phosphoenolpyruvate, CO2, and GDP [cytosol]
oxaloacetate + GTP => phosphoenolpyruvate + GDP + CO2 [cytosol]
2-Phospho-D-glycerate <=> Phosphoenolpyruvate + H2O
Pyruvate, CO2, and ATP react to form oxaloacetate, ADP, and orthophosphate
Pyruvate + CO2 + ATP => ADP + Orthophosphate + Oxaloacetate
N-sulphoglucosamine sulphohydrolase (SGSH) hydrolyses another sulfate from the N-sulphoglucosamine residue of heparan sulfate
I4P is dephosphorylated to Ins by IMPA1/2 in the cytosol
I1P is dephosphorylated to Ins by IMPA1/2 in the cytosol
I3P is dephosphorylated to Ins by IMPA1/2 in the cytosol
Digestion of cholesterol esters by extracellular CEL (bile salt-dependent lipase)
Digestion of monoacylglycerols by extracellular CEL (bile salt-dependent lipase)
Digestion of triacylglycerols by extracellular CEL (bile salt-dependent lipase)
sterols[cytosol] + ATP => sterols[extracellular] + ADP + Pi
ABCG5:ABCG8-mediated export of cholesterol and phytosterols
ABCG1-mediated transport of intracellular cholesterol to the cell surface
2-acylglycerol + H2O -> glycerol + fatty acid
Diversity of the mammalian sodium/proton exchanger SLC9 gene family
6-phospho-D-gluconate + NADP+ => D-ribulose 5-phosphate + CO2 + NADPH + H+
D-ribulose 5-phosphate <=> xylulose 5-phosphate
alpha-D-glucose 6-phosphate + NADP+ => D-glucono-1,5-lactone 6-phosphate + NADPH + H+
D-glucono-1,5-lactone 6-phosphate + H2O => 6-phospho-D-gluconate
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
SLC26A1,2 transport extracellular SO4(2-) to cytosol
xylulose 5-phosphate <=> D-ribulose 5-phosphate
D-ribose 5-phosphate + 2'-deoxyadenosine 5'-triphosphate (dATP) => 5-Phospho-alpha-D-ribose 1-diphosphate (PRPP) + 2'-deoxyadenosine 5'-monophosphate
N-sulphoglucosamine sulphohydrolase (SGSH) hydrolyses sulfate from the N-sulphoglucosamine residue of heparan sulfate
Glucose transporters (GLUT and SGLT): expanded families of sugar transport proteins
Identification of a novel glucose transporter-like protein-GLUT-12
Am J Physiol Endocrinol Metab 282:E733-8
Despite substantial degradation, 2-arachidonoylglycerol is a potent full efficacy agonist mediating CB(1) receptor-dependent G-protein activation in rat cerebellar membranes
Regulated expression of three C/EBP isoforms during adipose conversion of 3T3-L1 cells
Gefitinib-sensitizing EGFR mutations in lung cancer activate anti-apoptotic pathways
A review of the pharmacokinetics of abacavir
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
The unfolded protein response is an important regulator of inflammatory genes in endothelial cells
5,10-methenyltetrahydrofolate polyglutamate [ChEBI:65049]
The role of mitochondria in cellular iron-sulfur protein biogenesis and iron metabolism
Mutational analysis of a patient with mucopolysaccharidosis type VII, and identification of pseudogenes
Interactions of fibrillin-1 with heparin/heparan sulfate, implications for microfibrillar assembly
Phytanic acid and pristanic acid are oxidized by sequential peroxisomal and mitochondrial reactions in cultured fibroblasts
Human argininosuccinate lyase: a structural basis for intragenic complementation
Interferon-gamma can stimulate post-proteasomal trimming of the N terminus of an antigenic peptide by inducing leucine aminopeptidase
Planar cell polarity signaling: from fly development to human disease
Interactions between the endoplasmic reticulum, mitochondria, plasma membrane and other subcellular organelles
Characterizing the specificity and cooperation of aminopeptidases in the cytosol and endoplasmic reticulum during MHC class I antigen presentation
ABC transporters in cellular lipid trafficking
Mechanistic and mutational studies of Escherichia coli molybdopterin synthase clarify the final step of molybdopterin biosynthesis
gene ontology term for cellular function
Collagen fibrillogenesis in vitro: interaction of types I and V collagen regulates fibril diameter
Diseases caused by defects in the visual cycle: retinoids as potential therapeutic agents
Annu. Rev. Pharmacol. Toxicol. 47:469-512
Primary structure and tissue-specific expression of human beta-hydroxyisobutyryl-coenzyme A hydrolase.