The Enzyme Database

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EC 3.2.1.124     
Accepted name: 3-deoxy-2-octulosonidase
Reaction: Endohydrolysis of the β-ketopyranosidic linkages of 3-deoxy-D-manno-2-octulosonate in capsular polysaccharides
Other name(s): 2-keto-3-deoxyoctonate hydrolase; octulosylono hydrolase; octulofuranosylono hydrolase; octulopyranosylonohydrolase
Systematic name: capsular-polysaccharide 3-deoxy-D-manno-2-octulosonohydrolase
Comments: The enzyme from a bacteriophage catalyses the depolymerization of capsular polysaccharides containing 3-deoxy-2-octulosonide in the cell wall of Escherichia coli.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 103171-48-8
References:
1.  Altmann, F., Kwiatkowski, B., Stirm, S., März, L. and Unger, F.M. A bacteriophage-associated glycanase cleaving β-pyranosidic linkages of 3-deoxy-D-manno-2-octulosonic acid (KDO). Biochem. Biophys. Res. Commun. 136 (1986) 329–335. [DOI] [PMID: 3707579]
[EC 3.2.1.124 created 1989]
 
 
EC 3.2.1.144     
Accepted name: 3-deoxyoctulosonase
Reaction: 3-deoxyoctulosonyl-lipopolysaccharide + H2O = 3-deoxyoctulosonic acid + lipopolysaccharide
Other name(s): α-Kdo-ase
Systematic name: 3-deoxyoctulosonyl-lipopolysaccharide hydrolase
Comments: Releases Kdo (α- and β-linked 3-deoxy-D-manno-octulosonic acid) from different lipopolysaccharides, including Re-LPS from Escherichia coli and Salmonella, Rd-LPS from S. minnesota, and de-O-acyl-re-LPS. 4-Methylumbelliferyl-α-Kdo (α-Kdo-OMec) is also a substrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 199128-67-1
References:
1.  Li, Y.T., Wang, L.X., Pavlova, N.V., Li, S.C. and Lee, Y.C. α-KDOase activity in oyster and synthesis of α- and β-4-methylumbelliferyl ketosides of 3-deoxy-D-manno-octulosonic acid (KDO). J. Biol. Chem. 272 (1997) 26419–26424. [DOI] [PMID: 9334217]
[EC 3.2.1.144 created 2000]
 
 
EC 3.4.19.9     
Accepted name: folate γ-glutamyl hydrolase
Reaction: tetrahydropteroyl-(γ-glutamyl)n + (n-1) H2O = 5,6,7,8-tetrahydrofolate + (n-1) L-glutamate
For diagram of folate biosynthesis (late stages), click here
Other name(s): GGH (gene name); conjugase; folate conjugase; lysosomal γ-glutamyl carboxypeptidase; γ-Glu-X carboxypeptidase; pteroyl-poly-γ-glutamate hydrolase; carboxypeptidase G; folic acid conjugase; poly(γ-glutamic acid) endohydrolase; polyglutamate hydrolase; poly(glutamic acid) hydrolase II; pteroylpoly-γ-glutamyl hydrolase; γ-glutamyl hydrolase
Systematic name: tetrahydropteroyl-poly-γ-glutamyl γ-glutamyl hydrolase
Comments: The enzyme, which occurs only in animals and plants, can be either endo- and/or exopeptidase. It acts on tetrahydropteroyl polyglutamates and their modified forms, as well as the polyglutamates of the folate breakdown product N-(4-aminobenzoyl)-L-glutamate (pABA-Glu). The initial cleavage may release either monoglutamate or poly-γ-glutamate of two or more residues, depending on the specific enzyme. For example, GGH1 from the plant Arabidopsis thaliana cleaves pentaglutamates, mainly to di- and triglutamates, whereas GGH2 from the same organism yields mainly monoglutamates. The enzyme is lysosomal (and secreted) in animals and vacuolar in plants. In peptidase family C26.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, MEROPS, PDB, CAS registry number: 9074-87-7
References:
1.  McGuire, J.J. and Coward, J.K. Pteroylpolyglutamates: biosynthesis, degradation and function.. In: Blakley, R.L. and Benkovic, S.J. (Ed.), Folates and Pterins, John Wiley and Sons, New York, 1984, pp. 135–191.
2.  Wang, Y., Nimec, Z., Ryan, T.J., Dias, J.A. and Galivan, J. The properties of the secreted γ-glutamyl hydrolases from H35 hepatoma cells. Biochim. Biophys. Acta 1164 (1993) 227–235. [DOI] [PMID: 8343522]
3.  Yao, R., Rhee, M.S. and Galivan, J. Effects of γ-glutamyl hydrolase on folyl and antifolylpolyglutamates in cultured H35 hepatoma cells. Mol. Pharmacol. 48 (1995) 505–511. [PMID: 7565632]
4.  Yao, R., Schneider, E., Ryan, T.J. and Galivan, J. Human γ-glutamyl hydrolase: cloning and characterization of the enzyme expressed in vitro. Proc. Natl. Acad. Sci. USA 93 (1996) 10134–10138. [DOI] [PMID: 8816764]
5.  Yao, R., Nimec, Z., Ryan, T.J. and Galivan, J. Identification, cloning, and sequencing of a cDNA coding for rat γ-glutamyl hydrolase. J. Biol. Chem. 271 (1996) 8525–8528. [DOI] [PMID: 8621474]
6.  Orsomando, G., de la Garza, R.D., Green, B.J., Peng, M., Rea, P.A., Ryan, T.J., Gregory, J.F., 3rd and Hanson, A.D. Plant γ-glutamyl hydrolases and folate polyglutamates: characterization, compartmentation, and co-occurrence in vacuoles. J. Biol. Chem. 280 (2005) 28877–28884. [PMID: 15961386]
7.  Akhtar, T.A., McQuinn, R.P., Naponelli, V., Gregory, J.F., 3rd, Giovannoni, J.J. and Hanson, A.D. Tomato γ-glutamylhydrolases: expression, characterization, and evidence for heterodimer formation. Plant Physiol. 148 (2008) 775–785. [PMID: 18757550]
[EC 3.4.19.9 created 1972 as EC 3.4.12.10, transferred 1978 to EC 3.4.22.12, transferred 1992 to EC 3.4.19.9, modified 1997, modified 2018]
 
 
EC 3.4.21.97     
Accepted name: assemblin
Reaction: Cleaves -Ala┼Ser- and -Ala┼Ala- bonds in the scaffold protein
Comments: Involved in the breakdown of the scaffold protein during the late stages of assembly of the herpes-virus virion. Inhibited by diisopropyl fluorophosphate. Type example of peptidase family S21. Catalytic residues are His, Ser, His, a combination not known for any other peptidase, and the protein fold also is unique. Known from herpes viruses of several types, cytomegalovirus, Epstein-Barr virus and human herpesvirus 3
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, MEROPS, PDB, CAS registry number: 139691-88-6
References:
1.  Chen, P., Tsuge, H., Almassy, R.J., Gribskov, C.L., Katoh, S., Vanderpool, D.L., Margosiak, S.A., Pinko, C., Matthews, D.A. and Kan, C.C. Structure of the human cytomegalovirus protease catalytic domain reveals a novel serine protease fold and catalytic triad. Cell 86 (1996) 477–483. [DOI] [PMID: 8797829]
2.  Darke, P.L. Herpesvirus assemblin. In: Barrett, A.J., Rawlings, N.D. and Woessner, J.F. (Ed.), Handbook of Proteolytic Enzymes, Academic Press, London, 1998, pp. 470–472.
[EC 3.4.21.97 created 2000]
 
 
EC 3.5.1.7     
Accepted name: ureidosuccinase
Reaction: N-carbamoyl-L-aspartate + H2O = L-aspartate + CO2 + NH3
Systematic name: N-carbamoyl-L-aspartate amidohydrolase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9024-81-1
References:
1.  Lieberman, I. and Kornberg, A. Enzymatic synthesis and breakdown of a pyrimidine, orotic acid. III. Ureidosuccinase. J. Biol. Chem. 212 (1955) 909–920. [PMID: 14353892]
[EC 3.5.1.7 created 1961]
 
 
EC 3.5.1.29     
Accepted name: 2-(acetamidomethylene)succinate hydrolase
Reaction: 2-(acetamidomethylene)succinate + 2 H2O = acetate + succinate semialdehyde + NH3 + CO2
Other name(s): α-(N-acetylaminomethylene)succinic acid hydrolase
Systematic name: 2-(acetamidomethylene)succinate amidohydrolase (deaminating, decarboxylating)
Comments: Involved in the degradation of pyridoxin in Pseudomonas.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37289-09-1
References:
1.  Huynh, M.S. and Snell, E.E. Enzymes of vitamin B6 degradation. Purification and properties of two N-acetylamidohydrolases. J. Biol. Chem. 260 (1985) 2379–2383. [PMID: 3972793]
2.  Nyns, E.J., Zach, D. and Snell, E.E. The bacterial oxidation of vitamin B6. 8. Enzymatic breakdown of α-(N-acetylaminomethylene) succinic acid. J. Biol. Chem. 244 (1969) 2601–2605. [PMID: 5769993]
[EC 3.5.1.29 created 1972]
 
 
EC 3.5.2.3     
Accepted name: dihydroorotase
Reaction: (S)-dihydroorotate + H2O = N-carbamoyl-L-aspartate
For diagram of pyrimidine biosynthesis, click here
Other name(s): carbamoylaspartic dehydrase; dihydroorotate hydrolase
Systematic name: (S)-dihydroorotate amidohydrolase
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9024-93-5
References:
1.  Cooper, C. and Wilson, D.W. Biosynthesis of pyrimidines. Fed. Proc. 13 (1954) 194.
2.  Lieberman, I. and Kornberg, A. Enzymatic synthesis and breakdown of a pyrimidine, orotic acid. II. Dihydroorotic acid, ureidosuccinic acid, and 5-carboxymethylhydantoin. J. Biol. Chem. 207 (1954) 911–924. [PMID: 13163076]
[EC 3.5.2.3 created 1961]
 
 
EC 3.5.2.4     
Accepted name: carboxymethylhydantoinase
Reaction: L-5-carboxymethylhydantoin + H2O = N-carbamoyl-L-aspartate
Other name(s): hydantoin hydrolase
Systematic name: L-5-carboxymethylhydantoin amidohydrolase
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number: 9025-14-3
References:
1.  Lieberman, I. and Kornberg, A. Enzymatic synthesis and breakdown of a pyrimidine, orotic acid. II. Dihydroorotic acid, ureidosuccinic acid, and 5-carboxymethylhydantoin. J. Biol. Chem. 207 (1954) 911–924. [PMID: 13163076]
[EC 3.5.2.4 created 1961]
 
 
EC 3.7.1.8     
Accepted name: 2,6-dioxo-6-phenylhexa-3-enoate hydrolase
Reaction: 2,6-dioxo-6-phenylhexa-3-enoate + H2O = benzoate + 2-oxopent-4-enoate
Other name(s): HOHPDA hydrolase
Systematic name: 2,6-dioxo-6-phenylhexa-3-enoate benzoylhydrolase
Comments: Cleaves the products from biphenol, 3-isopropylcatechol and 3-methylcatechol produced by EC 1.13.11.39 biphenyl-2,3-diol 1,2-dioxygenase, by ring-fission at a -CO-C bond. Involved in the breakdown of biphenyl-related compounds by Pseudomonas sp.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 102925-38-2
References:
1.  Omori, T., Sugimura, K., Ishigooka, H. and Minoda, Y. Purification and some properties of a 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid hydrolyzing enzyme from Pseudomonas cruciviae S93 B1 involved in the degradation of biphenyl. Agric. Biol. Chem. 50 (1986) 931–937.
[EC 3.7.1.8 created 1989]
 
 
EC 4.1.2.4     
Accepted name: deoxyribose-phosphate aldolase
Reaction: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde
For diagram of reaction, click here
Other name(s): phosphodeoxyriboaldolase; deoxyriboaldolase; deoxyribose-5-phosphate aldolase; 2-deoxyribose-5-phosphate aldolase; 2-deoxy-D-ribose-5-phosphate acetaldehyde-lyase
Systematic name: 2-deoxy-D-ribose-5-phosphate acetaldehyde-lyase (D-glyceraldehyde-3-phosphate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9026-97-5
References:
1.  Hoffee, P.A. 2-Deoxyribose-5-phosphate aldolase of Salmonella typhimurium: purification and properties. Arch. Biochem. Biophys. 126 (1968) 795–802. [DOI] [PMID: 4879701]
2.  Jedziniak, J.A. and Lionetti, F.J. Purification and properties of deoxyriboaldolase from human erythrocytes. Biochim. Biophys. Acta 212 (1970) 478–487. [DOI] [PMID: 4989681]
3.  Racker, E. Enzymatic synthesis and breakdown of desoxyribose phosphate. J. Biol. Chem. 196 (1952) 347–365. [PMID: 12980976]
4.  Hoffee, P. Rosen, O.M. and Horecker, B.L. The mechanism of action of aldolases. VI. Crystallization of deoxyribose 5-phosphate aldolase and the number of active sites. J. Biol. Chem. 240 (1965) 1512–1516. [PMID: 14285485]
[EC 4.1.2.4 created 1961]
 
 
EC 4.1.2.23     
Accepted name: 3-deoxy-D-manno-octulosonate aldolase
Reaction: 3-deoxy-D-manno-octulosonate = pyruvate + D-arabinose
Other name(s): 2-keto-3-deoxyoctonate aldolase; KDOaldolase; 3-deoxyoctulosonic aldolase; 2-keto-3-deoxyoctonic aldolase; 3-deoxy-D-manno-octulosonic aldolase; 3-deoxy-D-manno-octulosonate D-arabinose-lyase
Systematic name: 3-deoxy-D-manno-octulosonate D-arabinose-lyase (pyruvate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 9026-95-3
References:
1.  Ghalambor, M.A. and Heath, E.C. The biosynthesis of cell wall lipopolysaccharide in Escherichia coli. V. Purification and properties of 3-deoxy-D-manno-octulosonate aldolase. J. Biol. Chem. 241 (1966) 3222–3227. [PMID: 5912115]
[EC 4.1.2.23 created 1972]
 
 
EC 4.1.2.63     
Accepted name: 2-hydroxyacyl-CoA lyase
Reaction: (1) a 2-hydroxy-3-methyl-Cn-fatty-acyl-CoA = a 2-methyl-branched Cn-1-fatty aldehyde + formyl-CoA
(2) a (2R)-2-hydroxy-Cn-long-chain fatty acyl-CoA = a Cn-1-long-chain fatty aldehyde + formyl-CoA
Other name(s): HACL1 (gene name); 2-hydroxyphytanoyl-CoA lyase; 2-HPCL
Systematic name: 2-hydroxy-3-methyl fatty-CoA formyl-CoA lyase (2-methyl branched fatty aldehyde-forming)
Comments: Requires Mg2+ and thiamine diphosphate. This peroxisomal enzyme, found in animals, is involved in the α-oxidation of 3-methyl-branched fatty acids like phytanic acid and the shortening of 2-hydroxy long-chain fatty acids.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Foulon, V., Antonenkov, V.D., Croes, K., Waelkens, E., Mannaerts, G.P., Van Veldhoven, P.P. and Casteels, M. Purification, molecular cloning, and expression of 2-hydroxyphytanoyl-CoA lyase, a peroxisomal thiamine pyrophosphate-dependent enzyme that catalyzes the carbon-carbon bond cleavage during α-oxidation of 3-methyl-branched fatty acids. Proc. Natl. Acad. Sci. USA 96 (1999) 10039–10044. [DOI] [PMID: 10468558]
2.  Foulon, V., Sniekers, M., Huysmans, E., Asselberghs, S., Mahieu, V., Mannaerts, G.P., Van Veldhoven, P.P. and Casteels, M. Breakdown of 2-hydroxylated straight chain fatty acids via peroxisomal 2-hydroxyphytanoyl-CoA lyase: a revised pathway for the α-oxidation of straight chain fatty acids. J. Biol. Chem. 280 (2005) 9802–9812. [DOI] [PMID: 15644336]
3.  Casteels, M., Sniekers, M., Fraccascia, P., Mannaerts, G.P. and Van Veldhoven, P.P. The role of 2-hydroxyacyl-CoA lyase, a thiamin pyrophosphate-dependent enzyme, in the peroxisomal metabolism of 3-methyl-branched fatty acids and 2-hydroxy straight-chain fatty acids. Biochem Soc Trans. 35 (2007) 876–880. [DOI] [PMID: 17956236]
[EC 4.1.2.63 created 2021]
 
 
EC 4.4.1.28     
Accepted name: L-cysteine desulfidase
Reaction: L-cysteine + H2O = sulfide + NH3 + pyruvate (overall reaction)
(1a) L-cysteine = 2-aminoprop-2-enoate + sulfide
(1b) 2-aminoprop-2-enoate = 2-iminopropanoate (spontaneous)
(1c) 2-iminopropanoate + H2O = pyruvate + NH3 (spontaneous)
Other name(s): L-cysteine desulfhydrase
Systematic name: L-cysteine sulfide-lyase (deaminating; pyruvate-forming)
Comments: The enzyme from the archaeon Methanocaldococcus jannaschii contains a [4Fe-4S] cluster and is specific for L-cysteine (cf. EC 4.4.1.1, cystathionine γ-lyase). It cleaves a carbon-sulfur bond releasing sulfide and the unstable enamine product 2-aminoprop-2-enoate that tautomerizes to an imine form, which undergoes a hydrolytic deamination to form pyruvate and ammonia. The same reaction can also be catalysed by some pyridoxal-phosphate proteins (cf. EC 4.4.1.1, cystathionine γ-lyase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Tchong, S.I., Xu, H. and White, R.H. L-Cysteine desulfidase: an [4Fe-4S] enzyme isolated from Methanocaldococcus jannaschii that catalyzes the breakdown of L-cysteine into pyruvate, ammonia, and sulfide. Biochemistry 44 (2005) 1659–1670. [DOI] [PMID: 15683250]
[EC 4.4.1.28 created 2014]
 
 
EC 4.6.1.13     
Accepted name: phosphatidylinositol diacylglycerol-lyase
Reaction: 1-phosphatidyl-1D-myo-inositol = 1D-myo-inositol 1,2-cyclic phosphate + 1,2-diacyl-sn-glycerol
For diagram of 1-phosphatidyl-myo-inositol metabolism, click here
Other name(s): monophosphatidylinositol phosphodiesterase; phosphatidylinositol phospholipase C; 1-phosphatidylinositol phosphodiesterase; 1-phosphatidyl-D-myo-inositol inositolphosphohydrolase (cyclic-phosphate-forming); 1-phosphatidyl-1D-myo-inositol diacylglycerol-lyase (1,2-cyclic-phosphate-forming)
Systematic name: 1-phosphatidyl-1D-myo-inositol 1,2-diacyl-sn-glycerol-lyase (1D-myo-inositol-1,2-cyclic-phosphate-forming)
Comments: This enzyme is bacterial. Activity is also found in animals, but this activity is due to the presence of EC 3.1.4.11, phosphoinositide phospholipase C.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37288-19-0
References:
1.  Allan, D. and Michell, R.H. Phosphatidylinositol cleavage catalysed by the soluble fraction from lymphocytes. Activity at pH5.5 and pH7.0. Biochem. J. 142 (1974) 591–597. [PMID: 4377210]
2.  Friedel, R.O., Brown, J.D. and Durell, J. Monophosphatidyl inositol inositolphosphohydrolase in guinea-pig brain. Biochim. Biophys. Acta 144 (1967) 684–686. [DOI] [PMID: 4294905]
3.  Irvine, R.F. The enzymology of stimulated inositol lipid turnover. Cell Calcium 3 (1982) 295–309. [DOI] [PMID: 6297738]
4.  Michell, R.H. and Allan, D. Inositol cyclic phosphate as a product of phosphatidylinositol breakdown by phospholipase C (Bacillus cereus). FEBS Lett. 53 (1975) 302–304. [DOI] [PMID: 236918]
5.  Low, M.G. and Finean, J.B. Release of alkaline phosphatase from membranes by a phosphatidylinositol-specific phospholipase C. Biochem. J. 167 (1977) 281–284. [PMID: 588258]
6.  Henner, D.J., Yang, M., Chen, E., Helmikss, R. and Low, M.G. Sequence of the Bacillus thuringiensis phosphatidylinositol-specific phospholipase C. Nucleic Acids Res. 16 (1988) 10383. [DOI] [PMID: 3194218]
[EC 4.6.1.13 created 1972 as EC 3.1.4.10, modified 1976, transferred 2002 to EC 4.6.1.13]
 
 
EC 4.8.1.5     
Accepted name: thiohydroximate-O-sulfate sulfate/sulfur-lyase (nitrile-forming)
Reaction: an N-(sulfonatooxy)alkanimidothioate = a nitrile + sulfate + sulfur
Glossary: an N-(sulfonatooxy)alkanimidothioate = a thiohydroximate-O-sulfate
Other name(s): NSP (gene name); nitrile-specifier protein
Systematic name: thiohydroximate-O-sulfate sulfate/sulfur-lyase (nitrile-forming)
Comments: The enzyme is involved in the breakdown of glucosinolates. It can act on both aliphatic and aromatic glucosinolates, and forms nitrile-containing products. cf. EC 4.8.1.6, N-(sulfonatooxy)alkenimidothioic acid sulfate-lyase (epithionitrile-forming), and EC 4.8.1.7, phenyl-N-(sulfonatooxy)methanimidothioate sulfolyase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kissen, R. and Bones, A.M. Nitrile-specifier proteins involved in glucosinolate hydrolysis in Arabidopsis thaliana. J. Biol. Chem. 284 (2009) 12057–12070. [DOI] [PMID: 19224919]
2.  Burow, M., Losansky, A., Muller, R., Plock, A., Kliebenstein, D.J. and Wittstock, U. The genetic basis of constitutive and herbivore-induced ESP-independent nitrile formation in Arabidopsis. Plant Physiol. 149 (2009) 561–574. [DOI] [PMID: 18987211]
[EC 4.8.1.5 created 2022]
 
 
EC 4.8.1.6     
Accepted name: N-(sulfonatooxy)alkenimidothioic acid sulfate-lyase (epithionitrile-forming)
Reaction: N-(sulfonatooxy)alkenimidothioic acid with a terminal double bond = an epithionitrile + sulfate
Other name(s): ESP (gene name); epithionitrile-specifier protein; epithiospecifier protein
Systematic name: N-(sulfonatooxy)alkenimidothioic acid sulfate-lyase (epithionitrile-forming)
Comments: The enzyme is involved in the breakdown of glucosinolates. It acts only on aliphatic N-(sulfonatooxy)alkenimidothioic acids produced from ω-alkenyl-glucosinolates, and forms epithionitrile-containing products. cf. EC 4.8.1.5, thiohydroximate-O-sulfate sulfate/sulfur-lyase (nitrile-forming), and EC 4.8.1.7, phenyl-N-(sulfonatooxy)methanimidothioate sulfolyase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lambrix, V., Reichelt, M., Mitchell-Olds, T., Kliebenstein, D.J. and Gershenzon, J. The Arabidopsis epithiospecifier protein promotes the hydrolysis of glucosinolates to nitriles and influences Trichoplusia ni herbivory. Plant Cell 13 (2001) 2793–2807. [DOI] [PMID: 11752388]
2.  Zabala M. de, T., Grant, M., Bones, A.M., Bennett, R., Lim, Y.S., Kissen, R. and Rossiter, J.T. Characterisation of recombinant epithiospecifier protein and its over-expression in Arabidopsis thaliana. Phytochemistry 66 (2005) 859–867. [DOI] [PMID: 15845404]
[EC 4.8.1.6 created 2022]
 
 
EC 4.8.1.7     
Accepted name: phenyl-N-(sulfonatooxy)methanimidothioate sulfolyase
Reaction: phenyl-N-(sulfonatooxy)methanimidothioate = benzylthiocyanate + sulfate
For diagram of glucotropeolin biosynthesis and catabolism, click here
Glossary: glucotropaeolin = 1-S-[(1Z)-2-phenyl-N-(sulfonatooxy)ethanimidoyl]-1-thio-β-D-glucopyranose
Other name(s): TFP (gene name) (ambiguous); thiocyanate-forming protein (ambiguous)
Systematic name: phenyl-N-(sulfonatooxy)methanimidothioate sulfate-lyase (benzylthiocyanate-forming)
Comments: The enzyme, characterized from the plant Lepidium sativum, is involved in the breakdown of the glucosinolate glucotropaeolin. Depending on the substrate, it can also form simple nitrile- and epithionitrile-containing products. cf. EC 4.8.1.5, thiohydroximate-O-sulfate sulfate/sulfur-lyase (nitrile-forming), and EC 4.8.1.6, N-(sulfonatooxy)alkenimidothioic acid sulfate-lyase (epithionitrile-forming).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Burow, M., Bergner, A., Gershenzon, J. and Wittstock, U. Glucosinolate hydrolysis in Lepidium sativum - identification of the thiocyanate-forming protein. Plant Mol. Biol. 63 (2007) 49–61. [DOI] [PMID: 17139450]
[EC 4.8.1.7 created 2022]
 
 
EC 4.8.1.8     
Accepted name: N-(sulfonatooxy)prop-2-enimidothioate sulfolyase
Reaction: (1) N-(sulfonatooxy)prop-2-enimidothioate = prop-2-enylthiocyanate + sulfate
(2) N-(sulfonatooxy)prop-2-enimidothioate = 2-(thiiran-2-yl)acetonitrile + sulfate
Other name(s): TFP (gene name) (ambiguous); thiocyanate-forming protein (ambiguous)
Systematic name: N-(sulfonatooxy)prop-2-enimidothioate sulfate-lyase (prop2-enylthiocyanate-forming)
Comments: The enzyme, characterized from the plant Thlaspi arvense, is involved in the breakdown of the glucosinolate sinigrin. Depending on the substrate, it can also form simple nitrile-containing products. cf. EC 4.8.1.5, thiohydroximate-O-sulfate sulfate/sulfur-lyase (nitrile-forming) and EC 4.8.1.6, N-(sulfonatooxy)alkenimidothioic acid sulfate-lyase (epithionitrile-forming).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Kuchernig, J.C., Backenkohler, A., Lubbecke, M., Burow, M. and Wittstock, U. A thiocyanate-forming protein generates multiple products upon allylglucosinolate breakdown in Thlaspi arvense. Phytochemistry 72 (2011) 1699–1709. [DOI] [PMID: 21783213]
2.  Gumz, F., Krausze, J., Eisenschmidt, D., Backenkohler, A., Barleben, L., Brandt, W. and Wittstock, U. The crystal structure of the thiocyanate-forming protein from Thlaspi arvense, a kelch protein involved in glucosinolate breakdown. Plant Mol. Biol. 89 (2015) 67–81. [DOI] [PMID: 26260516]
3.  Eisenschmidt-Bonn, D., Schneegans, N., Backenkohler, A., Wittstock, U. and Brandt, W. Structural diversification during glucosinolate breakdown: mechanisms of thiocyanate, epithionitrile and simple nitrile formation. Plant J. 99 (2019) 329–343. [DOI] [PMID: 30900313]
[EC 4.8.1.8 created 2022]
 
 
EC 5.3.1.13     
Accepted name: arabinose-5-phosphate isomerase
Reaction: D-arabinose 5-phosphate = D-ribulose 5-phosphate
For diagram of D-arabinose catabolism, click here
Other name(s): kdsD (gene name); gutQ (gene name); arabinose phosphate isomerase; phosphoarabinoisomerase; D-arabinose-5-phosphate ketol-isomerase
Systematic name: D-arabinose-5-phosphate aldose-ketose-isomerase
Comments: The enzyme is involved in the pathway for synthesis of 3-deoxy-D-manno-octulosonate (Kdo), a component of bacterial lipopolysaccharides and plant call walls.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9023-86-3
References:
1.  Volk, W.A. Purification and properties of phosphoarabinoisomerase from Propionibacterium pentosaceum. J. Biol. Chem. 235 (1960) 1550–1553.
2.  Lim, R. and Cohen, S.S. D-Phosphoarabinoisomerase and D-ribulokinase in Escherichia coli. J. Biol. Chem. 241 (1966) 4304–4315. [PMID: 5332197]
3.  Meredith, T.C. and Woodard, R.W. Identification of GutQ from Escherichia coli as a D-arabinose 5-phosphate isomerase. J. Bacteriol. 187 (2005) 6936–6942. [DOI] [PMID: 16199563]
4.  Gourlay, L.J., Sommaruga, S., Nardini, M., Sperandeo, P., Deho, G., Polissi, A. and Bolognesi, M. Probing the active site of the sugar isomerase domain from E. coli arabinose-5-phosphate isomerase via X-ray crystallography. Protein Sci. 19 (2010) 2430–2439. [DOI] [PMID: 20954237]
5.  Chiu, H.J., Grant, J.C., Farr, C.L., Jaroszewski, L., Knuth, M.W., Miller, M.D., Elsliger, M.A., Deacon, A.M., Godzik, A., Lesley, S.A. and Wilson, I.A. Structural analysis of arabinose-5-phosphate isomerase from Bacteroides fragilis and functional implications. Acta Crystallogr. D Biol. Crystallogr. 70 (2014) 2640–2651. [DOI] [PMID: 25286848]
[EC 5.3.1.13 created 1965]
 
 
EC 6.2.1.4     
Accepted name: succinate—CoA ligase (GDP-forming)
Reaction: GTP + succinate + CoA = GDP + phosphate + succinyl-CoA
For diagram of the citric-acid cycle, click here
Other name(s): succinyl-CoA synthetase (GDP-forming); succinyl coenzyme A synthetase (guanosine diphosphate-forming); succinate thiokinase (ambiguous); succinic thiokinase (ambiguous); succinyl coenzyme A synthetase (ambiguous); succinate-phosphorylating enzyme (ambiguous); P-enzyme; SCS (ambiguous); G-STK; succinyl coenzyme A synthetase (GDP-forming); succinyl CoA synthetase (ambiguous)
Systematic name: succinate:CoA ligase (GDP-forming)
Comments: Itaconate can act instead of succinate, and ITP instead of GTP.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9014-36-2
References:
1.  Hager, L.P. Succinyl CoA synthetase. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 6, Academic Press, New York, 1962, pp. 387–399.
2.  Kaufman, S., Gilvarg, C., Cori, O. and Ochoa, S. Enzymatic oxidation of α-ketoglutarate and coupled phosphorylation. J. Biol. Chem. 203 (1953) 869–888. [PMID: 13084656]
3.  Mazumder, R., Sanadi, D.R. and Rodwell, W.V. Purification and properties of hog kidney succinic thiokinase. J. Biol. Chem. 235 (1960) 2546–2550. [PMID: 13768680]
4.  Sanadi, D.R., Gibson, D.M. and Ayengar, P. Guanosine triphosphate, the primary product of phosphorylation coupled to the breakdown of succinyl coenzyme A. Biochim. Biophys. Acta 14 (1954) 434–436. [DOI] [PMID: 13181903]
[EC 6.2.1.4 created 1961]
 
 
EC 6.2.1.7     
Accepted name: cholate—CoA ligase
Reaction: (1) ATP + cholate + CoA = AMP + diphosphate + choloyl-CoA
(2) ATP + (25R)-3α,7α,12α-trihydroxy-5β-cholestan-26-oate + CoA = AMP + diphosphate + (25R)-3α,7α,12α-trihydroxy-5β-cholestanoyl-CoA
For diagram of cholic acid conjugates biosynthesis, click here and for diagram of cholic acid biosynthesis (sidechain), click here
Glossary: cholate = 3α,7α,12α-trihydroxy-5β-cholan-24-oate
trihydroxycoprostanoate = 3α,7α,12α-trihydroxy-5β-cholestan-26-oate
Other name(s): BAL; bile acid CoA ligase; bile acid coenzyme A ligase; choloyl-CoA synthetase; choloyl coenzyme A synthetase; cholic thiokinase; cholate thiokinase; cholic acid:CoA ligase; 3α,7α,12α-trihydroxy-5β-cholestanoyl coenzyme A synthetase; 3α,7α,12α-trihydroxy-5β-cholestanoate-CoA ligase; 3α,7α,12α-trihydroxy-5β-cholestanoate-CoA synthetase; THCA-CoA ligase; 3α,7α,12α-trihydroxy-5β-cholestanate—CoA ligase; 3α,7α,12α-trihydroxy-5β-cholestanate:CoA ligase (AMP-forming); cholyl-CoA synthetase; trihydroxycoprostanoyl-CoA synthetase
Systematic name: cholate:CoA ligase (AMP-forming)
Comments: Requires Mg2+ for activity. The mammalian enzyme is membrane-bound and catalyses the first step in the conjugation of bile acids with amino acids, converting bile acids into their acyl-CoA thioesters. Chenodeoxycholate, deoxycholate, lithocholate and trihydroxycoprostanoate can also act as substrates [7]. The bacterial enzyme is soluble and participates in an anaerobic bile acid 7 α-dehydroxylation pathway [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9027-90-1
References:
1.  Elliott, W.H. The enzymic activation of cholic acid by guinea-pig-liver microsomes. Biochem. J. 62 (1956) 427–433. [PMID: 13303991]
2.  Elliott, W.H. The breakdown of adenosine triphosphate accompanying cholic acid activation by guinea-pig liver microsomes. Biochem. J. 65 (1957) 315–321. [PMID: 13403911]
3.  Prydz, K., Kase, B.F., Björkhem, I. and Pedersen, J.I. Subcellular localization of 3α,7α-dihydroxy- and 3α,7α,12α-trihydroxy-5β-cholestanoyl-coenzyme A ligase(s) in rat liver. J. Lipid Res. 29 (1988) 997–1004. [PMID: 3183523]
4.  Schepers, L., Casteels, M., Verheyden, K., Parmentier, G., Asselberghs, S., Eyssen, H.J. and Mannaerts, G.P. Subcellular distribution and characteristics of trihydroxycoprostanoyl-CoA synthetase in rat liver. Biochem. J. 257 (1989) 221–229. [PMID: 2521999]
5.  Mallonee, D.H., Adams, J.L. and Hylemon, P.B. The bile acid-inducible baiB gene from Eubacterium sp. strain VPI 12708 encodes a bile acid-coenzyme A ligase. J. Bacteriol. 174 (1992) 2065–2071. [DOI] [PMID: 1551828]
6.  Wheeler, J.B., Shaw, D.R. and Barnes, S. Purification and characterization of a rat liver bile acid coenzyme A ligase from rat liver microsomes. Arch. Biochem. Biophys. 348 (1997) 15–24. [DOI] [PMID: 9390170]
7.  Falany, C.N., Xie, X., Wheeler, J.B., Wang, J., Smith, M., He, D. and Barnes, S. Molecular cloning and expression of rat liver bile acid CoA ligase. J. Lipid Res. 43 (2002) 2062–2071. [PMID: 12454267]
[EC 6.2.1.7 created 1961 (EC 6.2.1.29 created 1992, incorporated 2005), modified 2005]
 
 
EC 6.2.1.34     
Accepted name: trans-feruloyl-CoA synthase
Reaction: ferulic acid + CoA + ATP = feruloyl-CoA + products of ATP breakdown
For diagram of reaction, click here
Other name(s): trans-feruloyl-CoA synthetase; trans-ferulate:CoASH ligase (ATP-hydrolysing); ferulate:CoASH ligase (ATP-hydrolysing)
Systematic name: ferulate:CoA ligase (ATP-hydrolysing)
Comments: Requires Mg2+. It has not yet been established whether AMP + diphosphate or ADP + phosphate are formed in this reaction.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Narbad, A. and Gasson, M.J. Metabolism of ferulic acid via vanillin using a novel CoA-dependent pathway in a newly-isolated strain of Pseudomonas fluorescens. Microbiology 144 (1998) 1397–1405. [DOI] [PMID: 9611814]
2.  Pometto, A.L. and Crawford, D.L. Whole-cell bioconversion of vanillin to vanillic acid by Streptomyces viridosporus. Appl. Environ. Microbiol. 45 (1983) 1582–1585. [PMID: 6870241]
[EC 6.2.1.34 created 2000]
 
 
EC 6.3.2.18     
Accepted name: γ-glutamylhistamine synthase
Reaction: ATP + L-glutamate + histamine = products of ATP breakdown + Nα-γ-L-glutamylhistamine
Other name(s): γ-glutaminylhistamine synthetase; γ-GHA synthetase
Systematic name: L-glutamate:histamine ligase
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 82904-08-3
References:
1.  Stein, C. and Weinreich, D. An in vitro characterization of γ-glutamylhistamine synthetase: a novel enzyme catalyzing histamine metabolism in the central nervous system of the marine mollusk, Aplysia californica. J. Neurochem. 38 (1982) 204–214. [DOI] [PMID: 6125565]
[EC 6.3.2.18 created 1986]
 
 


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