Continued from EC 3.6.4
EC 3.7 Acting on Carbon-Carbon Bonds
EC 3.8 Acting on Halide Bonds
EC 3.9 Acting on Phosphorus-Nitrogen Bonds
EC 3.10 Acting on Sulfur-Nitrogen Bonds
EC 3.11 Acting on Carbon-Phosphorus Bonds
EC 3.12 Acting on Sulfur-Sulfur Bonds
EC 3.13 Acting on Carbon-Sulfur Bonds
EC 3.7.1 In Ketonic Substances
Accepted name: oxaloacetase
Reaction: oxaloacetate + H2O = oxalate + acetate
Other name(s):oxalacetic hydrolase
Systematic name: oxaloacetate acetylhydrolase
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9024-89-9
References:
1. Hayaishi, O., Shimazono, H., Katagiri, M. and Saito, Y. Enzymatic formation of oxalate and acetate from oxaloacetate. J. Am. Chem. Soc. 78 (1956) 5126-5127.
Accepted name: fumarylacetoacetase
Reaction: 4-fumarylacetoacetate + H2O = acetoacetate + fumarate
For diagram of reaction click here.
Other name(s): β-diketonase; fumarylacetoacetate hydrolase
Systematic name: 4-fumarylacetoacetate fumarylhydrolase
Comments: Also acts on other 3,5- and 2,4-dioxo acids.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9032-59-1
References:
1. Connors, W.M. and Stotz, E. The purification and properties of a triacetic acid-hydrolyzing enzyme. J. Biol. Chem. 178 (1949) 881-890.
2. Edwards, S.W. and Knox, W.E. Homogentisate metabolism: the isomerization of maleylacetoacetate by an enzyme which requires glutathione. J. Biol. Chem. 220 (1956) 79-91.
3. Meister, A. and Greenstein, J.P. Enzymatic hydrolysis of 2,4-diketo acids. J. Biol. Chem. 175 (1948) 573-588.
Accepted name: kynureninase
Reaction: L-kynurenine + H2O = anthranilate + L-alanine
For diagram of reaction click here.
Systematic name: L-kynurenine hydrolase
Comments: A pyridoxal-phosphate protein. Also acts on 3'-hydroxykynurenine and some other (3-arylcarbonyl)-alanines.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9024-78-6
References:
1. Jakoby, W.B. and Bonner, D.M. Kynureninase from Neurospora: purification and properties. J. Biol. Chem. 205 (1953) 699-707. [PMID: 13129248]
2. Jakoby, W.B. and Bonner, D.M. Kynureninase from Neurospora: interactions of enzyme with substrates, coenzyme and amines. J. Biol. Chem. 205 (1953) 709-715. [PMID: 13129249]
3. Knox, W.E. The relation of liver kynureninase to tryptophan metabolism in pyridoxine deficiency. Biochem. J. 53 (1953) 379-385. [PMID: 13032082]
4. Wiss, O. and Weber, F. Die Reindarstellung der Kynureninase. Hoppe-Seyler's Z. Physiol. Chem. 304 (1956) 232-240.
Accepted name: phloretin hydrolase
Reaction: phloretin + H2O = phloretate + phloroglucinol
For diagram of reaction click here.
Glossary: phloretin = 3-(4-hydroxyphenyl)-1-(2,4,6-trihydroxyphenyl)propan-1-one
phloretate = 3-(4-hydroxyphenyl)propanoate
phloroglucinol = benzene-1,3,5-triol
Other name(s): ErPhy; lactase-phlorerin hydrolase; C-acylphenol hydrolase; 2',4,4',6'-tetrahydroxydehydrochalcone 1,3,5-trihydroxybenzenehydrolase (incorrect)
Systematic name: phloretin acylhydrolase (phloroglucinol forming)
Comments: Also hydrolyses other C-acylated phenols related to phloretin. Isolated from the fungus Aspergillus niger and the bacteria Pantoea agglomerans and Eubacterium ramulus.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37289-38-6
References:
1. Chatterjee, A.K. and Gibbins, L.N. Metabolism of phloridzin by Erwinia herbicola: nature of the degradation products, and the purification and properties of phloretin hydrolase. J. Bacteriol. 100 (1969) 594-600. [PMID: 5354935]
2. Minamikawa, T., Jayasankar, N.P., Bohm, B.A., Taylor, I.E. and Towers, G.H. An inducible hydrolase from Aspergillus niger, acting on carbon-carbon bonds, for phlorrhizin and other C-acylated phenols. Biochem. J. 116 (1970) 889-897. [PMID: 5441377]
3. Schoefer, L., Braune, A. and Blaut, M. Cloning and expression of a phloretin hydrolase gene from Eubacterium ramulus and characterization of the recombinant enzyme. Appl. Environ. Microbiol. 70 (2004) 6131-6137. [PMID: 15466559]
Accepted name: acylpyruvate hydrolase
Reaction: A 3-acylpyruvate + H2O = a carboxylate + pyruvate
Systematic name: 3-acylpyruvate acylhydrolase
Comments: Acts on formylpyruvate, 2,4-dioxopentanoate, 2,4-dioxohexanoate and 2,4-dioxoheptanoate.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 54004-67-0
References:
1. Watson, G.H., Houghton, C. and Cain, R.B. Microbial metabolism of the pyridine ring. The metabolism of pyridine-3,4-diol (3,4-dihydroxypyridine) by Agrobacterium sp. Biochem. J. 140 (1974) 277-292. [PMID: 4375963]
Accepted name: acetylpyruvate hydrolase
Reaction: acetylpyruvate + H2O = acetate + pyruvate
Systematic name: 2,4-dioxopentanoate acetylhydrolase
Comments: Highly specific; does not act on pyruvate, oxaloacetate, maleylpyruvate, fumarylpyruvate or acetylacetone.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, Metacyc, KEGG, CAS registry number: 56214-30-3
References:
1. Davey, J.F. and Ribbons, D.W. Metabolism of resorcinylic compounds by bacteria. Purification and properties of acetylpyruvate hydrolase from Pseudomonas putida 01. J. Biol. Chem. 250 (1975) 3826-3830. [PMID: 236305]
Accepted name: β-diketone hydrolase
Reaction: nonane-4,6-dione + H2O = pentan-2-one + butanoate
Other name(s): oxidized PVA hydrolase
Systematic name: nonane-4,6-dione acylhydrolase
Comments: Also acts on the product of the action of EC 1.1.3.18 secondary-alcohol oxidase, on polyvinyl alcohols; involved in the bacterial degradation of polyvinyl alcohol.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 97955-12-9
References:
1. Sakai, K., Hamada, N. and Watanabe, Y. Separation of secondary alcohol oxidase and oxidized poly(vinyl alcohol) hydrolase by hydrophobic and dye-ligand chromatographies. Agric. Biol. Chem. 47 (1983) 153-155.
2. Sakai, K., Hamada, N. and Watanabe, Y. A new enzyme, β-diketone hydrolase: a component of a poly(vinyl alcohol)-degrading enzyme preparation. Agric. Biol. Chem. 49 (1985) 1901-1902.
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.
Accepted name: 2-hydroxymuconate-6-semialdehyde hydrolase
Reaction: 2-hydroxymuconate-6-semialdehyde + H2O = formate + 2-oxopent-4-enoate
For diagram of reaction click here.
Glossary: 2-hydroxymuconate-6-semialdehyde = (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate
Other name(s): 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase; 2-hydroxymuconic semialdehyde hydrolase; HMSH; HOD hydrolase; xylF (gene name); 2-hydroxymuconate-semialdehyde formylhydrolase; 2-hydroxymuconate-semialdehyde hydrolase
Systematic name: 2-hydroxymuconate-6-semialdehyde formylhydrolase
Comments: The enzyme is involved in the degradation of catechols.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 54004-61-4
References:
1. Sala-Trepat, J.M. and Evans, W.C. The meta cleavage of catechol by Azotobacter species. 4-Oxalocrotonate pathway. Eur. J. Biochem. 20 (1971) 400-413. [PMID: 4325686]
2. Harayama, S., Rekik, M., Wasserfallen, A. and Bairoch, A. Evolutionary relationships between catabolic pathways for aromatics: conservtion of gene order and nucleotide sequences of catechol oxidation genes of pWW0 and NAH7 plasmids. MGG Mol. Gen. Genet. 210 (1987) 241-247. [PMID: 3481421]
3. Diaz, E. and Timmis, K.N. Identification of functional residues in a 2-hydroxymuconic semialdehyde hydrolase. A new member of the α/β hydrolase-fold family of enzymes which cleaves carbon-carbon bonds. J. Biol. Chem. 270 (1995) 6403-6411. [PMID: 7890778]
Accepted name: cyclohexane-1,3-dione hydrolase
Reaction: cyclohexane-1,3-dione + H2O = 5-oxohexanoate
Other name(s): 1,3-cyclohexanedione hydrolase; cyclohexane-1,3-dione acylhydrolase (decyclizing)
Systematic name: cyclohexane-1,3-dione acylhydrolase (ring-opening)
Comments: Highly specific; does not act on other dione derivatives of cyclohexane, cyclopentane or cycloheptane.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 123516-46-1
References:
1. Dangel, W., Tschech, A. and Fuchs, G. Enzyme reactions involved in anaerobic cyclohexanol metabolism by a denitrifying Pseudomonas species. Arch. Microbiol. 152 (1989) 273-279.
Accepted name: cyclohexane-1,2-dione hydrolase
Reaction: cyclohexane-1,2-dione + H2O = 6-oxohexanoate
Other name(s): cyclohexane-1,2-dione acylhydrolase (decyclizing)
Systematic name: cyclohexane-1,2-dione acylhydrolase (ring-opening)
Comments: Highly specific; does not act on cyclohexanone or cyclohexane-1,3-dione as substrate.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Harder, J. Anaerobic degradation of cyclohexane-1,2-diol by a new Azoarcus species. Arch. Microbiol. 168 (1997) 199-204.
2. Fraas, S., Steinbach, A.K., Tabbert, A., Harder, J., Ermler, U., Tittmann, K., Meyer, A. and Kroneck P.M.H. Cyclohexane-1,2-dione hydrolase: A new tool to degrade alicyclic compounds. J. Mol. Catalysis B: Enzymatic 61 (2009) 47-49.
Accepted name: cobalt-precorrin 5A hydrolase
Reaction: cobalt-precorrin-5A + H2O = cobalt-precorrin-5B + acetaldehyde + 2 H+
For diagram click here.
Other name(s): CbiG (gene name)
Systematic name: obalt-precorrin 5A acylhydrolase
Comments: This enzyme hydrolyses the ring A acetate δ-lactone of cobalt-precorrin-5A resulting in the loss of the C-20 carbon and its attached methyl group in the form of acetaldehyde. This is a key reaction in the contraction of the porphyrin-type tetrapyrrole ring and its conversion to a corrin ring in the anaerobic (early cobalt insertion) adenosylcobalamin biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Kajiwara, Y., Santander, P.J., Roessner, C.A., Perez, L.M. and Scott, A.I. Genetically engineered synthesis and structural characterization of cobalt-precorrin 5A and -5B, two new intermediates on the anaerobic pathway to vitamin B12: definition of the roles of the CbiF and CbiG enzymes. J. Am. Chem. Soc. 128 (2006) 9971-9978. [PMID: 16866557]
Accepted name: 2-hydroxy-6-oxo-6-(2-aminophenyl)hexa-2,4-dienoate hydrolase
Reaction: (2E,4E)-6-(2-aminophenyl)-2-hydroxy-6-oxohexa-2,4-dienoate + H2O = anthranilate + (2E)-2-hydroxypenta-2,4-dienoate
Other name(s): CarC
Systematic name: (2E,4E)-6-(2-aminophenyl)-2-hydroxy-6-oxohexa-2,4-dienoate acylhydrolase
Comments: This enzyme catalyses the third step in the aerobic degradation pathway of carbazole. The effect of the presence of an amino group or hydroxyl group at the 2'-position of the substrate is small. The enzyme has no cofactor requirement [2].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Nojiri, H., Taira, H., Iwata, K., Morii, K., Nam, J.W., Yoshida, T., Habe, H., Nakamura, S., Shimizu, K., Yamane, H. and Omori, T. Purification and characterization of meta-cleavage compound hydrolase from a carbazole degrader Pseudomonas resinovorans strain CA10. Biosci. Biotechnol. Biochem. 67 (2003) 36-45. [PMID: 12619671]
2. Riddle, R.R., Gibbs, P.R., Willson, R.C. and Benedik, M.J. Purification and properties of 2-hydroxy-6-oxo-6-(2'-aminophenyl)hexa-2,4-dienoic acid hydrolase involved in microbial degradation of carbazole. Protein Expr. Purif. 28 (2003) 182-189. [PMID: 12651123]
Accepted name: 2-hydroxy-6-oxonona-2,4-dienedioate hydrolase
Reaction: (1) (2Z,4E)-2-hydroxy-6-oxonona-2,4-diene-1,9-dioate + H2O = (2Z)-2-hydroxypenta-2,4-dienoate + succinate
(2) (2Z,4E,7E)-2-hydroxy-6-oxonona-2,4,7-triene-1,9-dioate + H2O = (2Z)-2-hydroxypenta-2,4-dienoate + fumarate
For diagram of reaction click here or click here.
Other name(s): mhpC (gene name)
Systematic name: (2Z,4E)-2-hydroxy-6-oxona-2,4-dienedioate succinylhydrolase
Comments: This enzyme catalyses a step in a pathway of phenylpropanoid compounds degradation. The first step of the enzyme mechanism involves a reversible keto-enol tautomerization [4].
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Burlingame, R. and Chapman, P.J. Catabolism of phenylpropionic acid and its 3-hydroxy derivative by Escherichia coli. J. Bacteriol. 155 (1983) 113-121. [PMID: 6345502]
2. Burlingame, R.P., Wyman, L. and Chapman, P.J. Isolation and characterization of Escherichia coli mutants defective for phenylpropionate degradation. J. Bacteriol. 168 (1986) 55-64. [PMID: 3531186]
3. Lam, W. W. Y and Bugg, T. D. H. Chemistry of extradiol aromatic ring cleavage: isolation of a stable dienol ring fission intermediate and stereochemistry of its enzymatic hydrolytic clevage. J. Chem. Soc., Chem. Commun. 10 (1994) 1163-1164.
4. Lam, W.W. and Bugg, T.D. Purification, characterization, and stereochemical analysis of a C-C hydrolase: 2-hydroxy-6-keto-nona-2,4-diene-1,9-dioic acid 5,6-hydrolase. Biochemistry 36 (1997) 12242-12251. [PMID: 9315862]
5. Ferrández, A., García, J.L. and Díaz, E. Genetic characterization and expression in heterologous hosts of the 3-(3-hydroxyphenyl)propionate catabolic pathway of Escherichia coli K-12. J. Bacteriol. 179 (1997) 2573-2581. [PMID: 9098055]
6. Díaz, E., Ferrández, A. and García, J.L. Characterization of the hca cluster encoding the dioxygenolytic pathway for initial catabolism of 3-phenylpropionic acid in Escherichia coli K-12. J. Bacteriol. 180 (1998) 2915-2923. [PMID: 9603882]
[EC 3.7.1.15 Transferred entry: (+)-caryolan-1-ol synthase. Now listed as EC 4.2.1.138 (+)-caryolan-1-ol synthase (EC 3.7.1.15 created 2011, deleted 2013)]
[EC 3.7.1.16 Transferred entry: oxepin-CoA hydrolase. Now listed as EC 3.3.2.12 oxepin-CoA hydrolase (EC 3.7.1.16 created 2011, deleted 2013)]
Accepted name: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
Reaction: (1E,2Z)-3-hydroxy-5,9,17-trioxo-4,5:9,10-disecoandrosta-1(10),2-dien-4-oate + H2O = 3-[(3aS,4S,7aS)-7a-methyl-1,5-dioxo-octahydro-1H-inden-4-yl]propanoate + (2Z,4Z)-2-hydroxyhexa-2,4-dienoate
Other name(s): tesD (gene name); hsaD (gene name)
Systematic name: 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase ( (2Z,4Z)-2-hydroxyhexa-2,4-dienoate-forming)
Comments: The enzyme is involved in the bacterial degradation of the steroid ring structure, and is involved in degradation of multiple steroids, such as testosterone [1], cholesterol [2], and sitosterol.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Horinouchi, M., Hayashi, T., Koshino, H., Kurita, T. and Kudo, T. Identification of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid, 4-hydroxy-2-oxohexanoic acid, and 2-hydroxyhexa-2,4-dienoic acid and related enzymes involved in testosterone degradation in Comamonas testosteroni TA441. Appl. Environ. Microbiol. 71 (2005) 5275-5281. [PMID: 16151114]
2. Van der Geize, R., Yam, K., Heuser, T., Wilbrink, M.H., Hara, H., Anderton, M.C., Sim, E., Dijkhuizen, L., Davies, J.E., Mohn, W.W. and Eltis, L.D. A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into Mycobacterium tuberculosis survival in macrophages. Proc. Natl. Acad. Sci. USA 104 (2007) 1947-1952. [PMID: 17264217]
3. Lack, N., Lowe, E.D., Liu, J., Eltis, L.D., Noble, M.E., Sim, E. and Westwood, I.M. Structure of HsaD, a steroid-degrading hydrolase, from Mycobacterium tuberculosis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 2-7. [PMID: 18097091]
4. Lack, N.A., Yam, K.C., Lowe, E.D., Horsman, G.P., Owen, R.L., Sim, E. and Eltis, L.D. Characterization of a carbon-carbon hydrolase from Mycobacterium tuberculosis involved in cholesterol metabolism. J. Biol. Chem. 285 (2010) 434-443. [PMID: 19875455]
Accepted name: 6-oxocamphor hydrolase
Reaction: bornane-2,6-dione + H2O = [(1S)-4-hydroxy-2,2,3-trimethylcyclopent-3-enyl]acetate
For diagram of reaction click here and mechanism click here.
Glossary: α-campholonate = (4-hydroxy-2,2,3-trimethylcyclopent-3-enyl)acetate (enol form) = (2,2,3-trimethyl-4-oxocyclopentyl)acetate (keto form)
Other name(s): OCH; camK (gene name)
Systematic name: bornane-2,6-dione hydrolase
Comments: Isolated from Rhodococcus sp. The bornane ring system is cleaved by a retro-Claisen reaction to give the enol of α-campholonate. When separate from the enzyme the enol is tautomerised to the keto form as a 6:1 mixture of [(1S,3R)-2,2,3-trimethyl-4-oxocyclopentyl]acetate and [(1S,3S)-2,2,3-trimethyl-4-oxocyclopentyl]acetate.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Grogan, G., Roberts, G.A., Bougioukou, D., Turner, N.J. and Flitsch, S.L. The desymmetrization of bicyclic β-diketones by an enzymatic retro-Claisen reaction. A new reaction of the crotonase superfamily. J. Biol. Chem. 276 (2001) 12565-12572. [PMID: 11278926]
2. Whittingham, J.L., Turkenburg, J.P., Verma, C.S., Walsh, M.A. and Grogan, G. The 2-Å crystal structure of 6-oxo camphor hydrolase. New structural diversity in the crotonase superfamily. J. Biol. Chem. 278 (2003) 1744-1750. [PMID: 12421807]
3. Leonard, P.M. and Grogan, G. Structure of 6-oxo camphor hydrolase H122A mutant bound to its natural product, (2S,4S)-α-campholinic acid: mutant structure suggests an atypical mode of transition state binding for a crotonase homolog. J. Biol. Chem. 279 (2004) 31312-31317. [PMID: 15138275]
Accepted name: 2,6-dihydroxypseudooxynicotine hydrolase
Reaction: 1-(2,6-dihydroxypyridin-3-yl)-4-(methylamino)butan-1-one + H2O = 2,6-dihydroxypyridine + 4-methylaminobutanoate
For diagram of reaction click here.
Glossary: 1-(2,6-dihydroxypyridin-3-yl)-4-(methylamino)butan-1-one = 2,6-dihydroxypseudooxynicotine
Systematic name: 1-(2,6-dihydroxypyridin-3-yl)-4-(methylamino)butan-1-one hydrolase
Comments: The enzyme, characterized from the soil bacterium Arthrobacter nicotinovorans, participates in nicotine degradation.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Gherna, R.L., Richardson, S.H. and Rittenberg, S.C. The bacterial oxidation of nicotine. VI. The metabolism of 2,6-dihydroxypseudooxynicotine. J. Biol. Chem. 240 (1965) 3669-3674. [PMID: 5835946]
2. Sachelaru, P., Schiltz, E., Igloi, G.L. and Brandsch, R. An α/β-fold C—C bond hydrolase is involved in a central step of nicotine catabolism by Arthrobacter nicotinovorans. J. Bacteriol. 187 (2005) 8516-8519. [PMID: 16321959]
Accepted name: 3-fumarylpyruvate hydrolase
Reaction: 3-fumarylpyruvate + H2O = fumarate + pyruvate
Other name(s): nagK (gene name); naaD (gene name)
Systematic name: 3-fumarylpyruvate hydrolase
Comments: The enzyme is involved in bacterial degradation of 5-substituted salicylates, including gentisate (5-hydroxysalicylate), 5-nitrosalicylate and 5-halosalicylates.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Zhou, N.Y., Fuenmayor, S.L. and Williams, P.A. nag genes of Ralstonia (formerly Pseudomonas) sp. strain U2 encoding enzymes for gentisate catabolism. J. Bacteriol. 183 (2001) 700-708. [PMID: 11133965]
2. Qu, Y. and Spain, J.C. Molecular and biochemical characterization of the 5-nitroanthranilic acid degradation pathway in Bradyrhizobium sp. strain JS329. J. Bacteriol. 193 (2011) 3057-3063. [PMID: 21498645]
Accepted name: 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
Reaction: 6-oxocyclohex-1-ene-1-carbonyl-CoA + 2 H2O = 3-hydroxypimeloyl-CoA (overall reaction)
(1a) 6-oxocyclohex-1-ene-1-carbonyl-CoA + H2O = 2-hydroxy-6-oxocyclohexane-1-carbonyl-CoA
(1b) 2-hydroxy-6-oxocyclohexane-1-carbonyl-CoA + H2O = 3-hydroxypimeloyl-CoA
For diagram of reaction click here.
Glossary: 3-hydroxypimeloyl-CoA = 3-hydroxy-6-carboxyhexanoyl-CoA
Other name(s): 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase; 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase (decyclizing)
Systematic name: 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase (ring-opening)
Comments: The enzyme, which participates in the anaerobic benzoyl-CoA degradation pathway in certain organisms, catalyses the addition of one molecule of water to the double bound of 6-oxocyclohex-1-ene-1-carbonyl-CoA followed by the hydrolytic C-C cleavage of the alicyclic ring.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Laempe, D., Jahn, M. and Fuchs, G. 6-Hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase and 6-oxocyclohex-1-ene-1-carbonyl-CoA hydrolase, enzymes of the benzoyl-CoA pathway of anaerobic aromatic metabolism in the denitrifying bacterium Thauera aromatica. Eur. J. Biochem. 263 (1999) 420-429. [PMID: 10406950]
2. Kuntze, K., Shinoda, Y., Moutakki, H., McInerney, M.J., Vogt, C., Richnow, H.H. and Boll, M. 6-Oxocyclohex-1-ene-1-carbonyl-coenzyme A hydrolases from obligately anaerobic bacteria: characterization and identification of its gene as a functional marker for aromatic compounds degrading anaerobes. Environ Microbiol 10 (2008) 1547-1556. [PMID: 18312395]
Accepted name: 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (decyclizing)
Reaction: 3D-3,5/4-trihydroxycyclohexa-1,2-dione + H2O = 5-deoxy-D-glucuronate
For diagram of reaction click here.
Glossary: 3D-3,5/4-trihydroxycyclohexa-1,2-dione = (3R,4S,5R)-3,4,5-trihydroxycyclohexane-1,2-dione
Other name(s): IolD; THcHDO hydrolase; 3D-3,5/4-trihydroxycyclohexa-1,2-dione hydrolase (decyclizing); 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (decyclizing)
Systematic name: 3D-3,5/4-trihydroxycyclohexa-1,2-dione hydrolase (ring-opening)
Comments: The enzyme, found in the bacterium Bacillus subtilis, is part of the myo-inositol degradation pathway leading to acetyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Yoshida, K., Yamaguchi, M., Morinaga, T., Kinehara, M., Ikeuchi, M., Ashida, H. and Fujita, Y. myo-Inositol catabolism in Bacillus subtilis. J. Biol. Chem. 283 (2008) 10415-10424. [PMID: 18310071]
Accepted name: maleylpyruvate hydrolase
Reaction: 3-maleylpyruvate + H2O = maleate + pyruvate
Glossary: 3-maleylpyruvate = (2Z)-4,6-dioxohept-2-enedioate
Other name(s): hbzF (gene name)
Systematic name: (2Z)-4,6-dioxohept-2-enedioate acylhydrolase
Comments: The enzyme, characterized from the bacterium Pseudomonas alcaligenes NCIMB 9867, catalyses the hydrolysis of 3-maleylpyruvate, the ring-cleavage product of gentisate. The enzyme can also act on a number of maleylpyruvate derivatives, such as (2E)-2-methyl-4,6-dioxohept-2-enedioate and (2E)-3-methyl-4,6-dioxohept-2-enedioate. Activated by Mn2+. May be identical to EC 3.7.1.5, acylpyruvate hydrolase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Hopper, D.J., Chapman, P.J. and Dagley, S. The enzymic degradation of alkyl-substituted gentisates, maleates and malates. Biochem. J. 122 (1971) 29-40. [PMID: 5124802]
2. Bayly, R.C., Chapman, P.J., Dagley, S. and Di Berardino, D. Purification and some properties of maleylpyruvate hydrolase and fumarylpyruvate hydrolase from Pseudomonas alcaligenes, J. Bacteriol. 143 (1980) 70-77. [PMID: 7400101]
3. Liu, K., Liu, T.T. and Zhou, N.Y. HbzF catalyzes direct hydrolysis of maleylpyruvate in the gentisate pathway of Pseudomonas alcaligenes NCIMB 9867. Appl. Environ. Microbiol. 79 (2013) 1044-1047. [PMID: 23204427]
Accepted name: 2,4-diacetylphloroglucinol hydrolase
Reaction: 2,4-diacetylphloroglucinol + H2O = 2-acetylphloroglucinol + acetate
Glossary: phloroglucinol = benzene-1,3,5-triol
2,4-diacetylphloroglucinol = 1,1'-(2,4,6-trihydroxybenzene-1,3-diyl)diethan-1-one
Other name(s): PhlG
Systematic name: 2,4-diacetylphloroglucinol acetylhydrolase
Comments: Requires Zn2+. Isolated from the bacteria Pseudomonas fluorescens, Pseudomonas sp. YGJ3 and Mycobacterium abscessus 103. It reduces the antibiotic activity of 2,4-diacetylphloroglucinol.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Bottiglieri, M. and Keel, C. Characterization of PhlG, a hydrolase that specifically degrades the antifungal compound 2,4-diacetylphloroglucinol in the biocontrol agent Pseudomonas fluorescens CHA0. Appl. Environ. Microbiol. 72 (2006) 418-427. [PMID: 16391073]
2. He, Y.X., Huang, L., Xue, Y., Fei, X., Teng, Y.B., Rubin-Pitel, S.B., Zhao, H. and Zhou, C.Z. Crystal structure and computational analyses provide insights into the catalytic mechanism of 2,4-diacetylphloroglucinol hydrolase PhlG from Pseudomonas fluorescens. J. Biol. Chem. 285 (2010) 4603-4611. [PMID: 20018877]
3. Saitou, H., Watanabe, M. and Maruyama, K. Molecular and catalytic properties of 2,4-diacetylphloroglucinol hydrolase (PhlG) from Pseudomonas sp. YGJ3. Biosci. Biotechnol. Biochem. 76 (2012) 1239-1241. [PMID: 22790955]
4. Zhang, Z., Jiang, Y.L., Wu, Y. and He, Y.X. Crystallization and preliminary X-ray diffraction analysis of a putative carbon-carbon bond hydrolase from Mycobacterium abscessus 103. Acta Crystallogr. F Struct. Biol. Commun. 71 (2015) 239-242. [PMID: 25664803]
Accepted name: 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase
Reaction: (2Z,4E)-2-hydroxy-6-oxohepta-2,4-dienoate + H2O = (2Z)-2-hydroxypenta-2,4-dienoate + acetate
Other name(s): 2-hydroxy-5-methylmuconate semialdehyde hydrolase; todF (gene name)
Systematic name: 2-hydroxy-6-oxohepta-2,4-dienoate acetylhydrolase
Comments: A bacterial enzyme that participates in the degradation of toluene and 2-nitrotoluene.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Kukor, J.J. and Olsen, R.H. Genetic organization and regulation of a meta cleavage pathway for catechols produced from catabolism of toluene, benzene, phenol, and cresols by Pseudomonas pickettii PKO1. J. Bacteriol. 173 (1991) 4587-4594. [PMID: 1856161]
2. Menn, F.M., Zylstra, G.J. and Gibson, D.T. Location and sequence of the todF gene encoding 2-hydroxy-6-oxohepta-2,4-dienoate hydrolase in Pseudomonas putida F1. Gene 104 (1991) 91-94. [PMID: 1916282]
3. Haigler, B.E., Wallace, W.H. and Spain, J.C. Biodegradation of 2-nitrotoluene by Pseudomonas sp. strain JS42. Appl. Environ. Microbiol. 60 (1994) 3466-3469. [PMID: 7944378]
Accepted name: 2,4-didehydro-3-deoxy-L-rhamnonate hydrolase
Reaction: 2,4-didehydro-3-deoxy-L-rhamnonate + H2O = pyruvate + (S)-lactate
For diagram of reaction click here
Other name(s): L-2,4-diketo-3-deoxyrhamnonate hydrolase; lra6 (gene name)
Systematic name: 2,4-didehydro-3-deoxy-L-rhamnonate hydrolase
Comments: The enzyme, characterized from the bacterium Sphingomonas sp. SKA58, participates in an L-rhamnose degradation pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Watanabe, S. and Makino, K. Novel modified version of nonphosphorylated sugar metabolism - an alternative L-rhamnose pathway of Sphingomonas sp. FEBS J. 276 (2009) 1554-1567. [PMID: 19187228]
[EC 3.7.1.27 Transferred entry: neryl diphosphate diphosphatase. Now EC 3.1.7.13, neryl diphosphate diphosphatase. (EC 3.7.1.27 created 2020, deleted 2021)]
Accepted name: 3-oxoisoapionate-4-phosphate transcarboxylase/hydrolase
Reaction: 3-oxoisoapionate 4-phosphate + H2O = glycolate + 3-phospho-D-glycerate
Glossary: 3-oxoisoapionate = 2,4-dihydroxy-2-(hydroxymethyl)-3-oxobutanoate
Other name(s): oiaT (gene name)
Systematic name: 3-oxoisoapionate-4-phosphate transcarboxylase/glycolylhydrolase (3-phospho-D-glycerate-forming)
Comments: The enzyme, which belongs to the RuBisCO-like-protein (RLP) superfamily, has been characterized from several bacterial species. It participates in the degradation of D-apionate. The reaction is initiated by decarboxylation to generate a stabilized enediolate intermediate, with the sequestered CO2 carboxylating the adjacent enediolate carbon atom. The resulting 3-ketose-1-phosphate intermediate is hydrolysed, as in the authentic RuBisCO-catalysed reaction, to generate glycolate and 3-phospho-D-glycerate. Stereospecificity of 3-oxoisoapionate 4-phosphate has not been determined.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Carter, M.S., Zhang, X., Huang, H., Bouvier, J.T., Francisco, B.S., Vetting, M.W., Al-Obaidi, N., Bonanno, J.B., Ghosh, A., Zallot, R.G., Andersen, H.M., Almo, S.C. and Gerlt, J.A. Functional assignment of multiple catabolic pathways for D-apiose. Nat. Chem. Biol. 14 (2018) 696-705. [PMID: 29867142]
EC 3.8.1 In C-Halide Compounds
Accepted name: (S)-2-haloacid dehalogenase
Reaction: (S)-2-haloacid + H2O = (R)-2-hydroxyacid + halide
For diagram click here.
Other name(s): 2-haloacid dehalogenase[ambiguous]; 2-haloacid halidohydrolase [ambiguous][ambiguous]; 2-haloalkanoic acid dehalogenase; 2-haloalkanoid acid halidohydrolase; 2-halocarboxylic acid dehalogenase II; DL-2-haloacid dehalogenase[ambiguous]; L-2-haloacid dehalogenase; L-DEX
Systematic name: (S)-2-haloacid halidohydrolase
Comments: Acts on acids of short chain lengths, C2 to C4, with inversion of configuration at C-2. [See also EC 3.8.1.9 (R)-2-haloacid dehalogenase, EC 3.8.1.10 2-haloacid dehalogenase (configuration-inverting) and EC 3.8.1.11 2-haloacid dehalogenase (configuration-retaining)]
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37289-39-7
References:
1. Goldman, P., Milne, G.W.A. and Keister, D.B. Carbon-halogen bond cleavage. 3. Studies on bacterial halidohyrolases. J. Biol. Chem. 243 (1968) 428-434. [PMID: 5635785]
2. Motosugi, M., Esaki, N. and Soda, K. Preparation and properties of 2-halo acid dehalogenase from Pseudomonas putida. Agric. Biol. Chem. 46 (1982) 837-838.
3. Klages, M., Krauss, S. and Lingens, F. 2-Haloacid dehalogenase from a 4-chlorobenzoate-degrading Pseudomonas spec. CBS 3. Hoppe-Seyler's Z. Physiol. Chem. 364 (1983) 529-535. [PMID: 6873881]
4. Diez, A., Prieto, M.I., Alvarez, M.J., Bautista, J.M., Garrido, J. and Puyet, A. Improved catalytic performance of a 2-haloacid dehalogenase from Azotobacter sp. by ion-exchange immobilisation. Biochem. Biophys. Res. Commun. 220 (1996) 828-833. [PMID: 8607850]
5. Mörsberger, F.-M., Müller, R., Otto, M.K., Lingens, F. and Kulbe, K.D. Purification and characterization of 2-halocarboxylic acid dehalogenase II from Pseudomonas spec. CBS 3. Biol. Chem. Hoppe-Seyler 372 (1991) 915-922. [PMID: 1772590]
6. Köhler, R., Brokamp, A., Schwarze, R., Reiting, R.H. and Schmidt, F.R.J. Characteristics and DNA-sequence of a cryptic haloalkanoic acid dehalogenase from Agrobacterium tumefaciens RS5. Curr. Microbiol. 36 (1998) 96-101. [PMID: 9425247]
7. Motosugi, K., Esahi, N. and Soda, K. Bacterial assimilation of D- and L-2-chloropropionates and occurrence of a new dehalogenase. Arch. Microbiol. 131, (1982) 179-183. [PMID: 7103659]
8. Kurihara, T., Esaki, N. and Soda, K. Bacterial 2-haloacid dehalogenases: structures and reaction mechanisms. J. Mol. Catal., B Enzym. 10, (2000) 57-65.
9. Soda, K., Kurihara, T., Liu, J.-Q., Nardi-Dei, V., Park, C., Miyagi, M., Tsunasawa, S. and Esaki, N. Bacterial 2-haloacid dehalogenases: Structures and catalytic properties. Pure Appl. Chem. 68, (1996) 2097-2103.
Accepted name: haloacetate dehalogenase
Reaction: haloacetate + H2O = glycolate + halide
Other name(s): monohaloacetate dehalogenase
Systematic name: haloacetate halidohydrolase
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37289-40-0
References:
1. Goldman, P. The enzymatic cleavage of the carbon-fluorine bond in fluoroacetate.J. Biol. Chem. 240 (1965) 3434-3438.
2. Goldman, P. and Milne, G.W.A. Carbon-fluorine bond cleavage. II. Studies on the mechanism of the defluorination of fluoroacetate. J. Biol. Chem. 241 (1966) 5557-5559. [PMID: 5928195]
[EC 3.8.1.4 Transferred entry: now EC 1.97.1.10 thyroxine 5'-deiodinase (EC 3.8.1.4 created 1984, deleted 2003)]
Accepted name: haloalkane dehalogenase
Reaction: 1-haloalkane + H2O = a primary alcohol + halide
Other name(s): 1-chlorohexane halidohydrolase; 1-haloalkane dehalogenase
Systematic name: 1-haloalkane halidohydrolase
Comments: Acts on a wide range of 1-haloalkanes, haloalcohols, haloalkenes and some haloaromatic compounds.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 95990-29-7
References:
1. Keuning, S., Janssen, D.B. and Witholt, B. Purification and characterization of hydrolytic haloalkane dehalogenase from Xanthobacter autotrophicus GJ10. J. Bacteriol. 163 (1985) 635-639. [PMID: 4019411]
2. Scholtz, R., Leisinger, T., Suter, F. and Cook, A.M. Characterization of 1-chlorohexane halidohydrolase, a dehalogenase of wide substrate range from an Arthrobacter sp. J. Bacteriol. 169 (1987) 5016-5021. [PMID: 3667524]
3. Yokota, T., Omori, T. and Kodama, T. Purification and properties of haloalkane dehalogenase from Corynebacterium sp. strain m15-3. J. Bacteriol. 169 (1987) 4049-4054. [PMID: 3624201]
Accepted name: 4-chlorobenzoate dehalogenase
Reaction: 4-chlorobenzoate + H2O = 4-hydroxybenzoate + chloride
Other name(s): halobenzoate dehalogenase
Systematic name: 4-chlorobenzoate chlorohydrolase
Comments: Catalyses the first step in the degradation of chlorobenzoate in Pseudomonas. In many microorganisms, this activity comprises three separate enzymes, EC 6.2.1.33 (4-chlorobenzoate—CoA ligase), EC 3.8.1.7 (4-chlorobenzoyl-CoA dehalogenase) and EC 3.1.2.23 (4-hydroxybenzoyl-CoA thioesterase).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 94047-11-7
References:
1. Müller, R., Thiele, J., Klages, U. and Lingens, F. Incorporation of [18O]water into 4-hydroxybenzoic acid in the reaction of 4-chlorobenzoate dehalogenase from Pseudomonas spec. CBS 3. Biochem. Biophys. Res. Commun. 124 (1984) 178-182. [PMID: 6497878]
2. Heppel, L.A., Porterfield, V.T. Enzymatic dehalogenation of certain brominated and chlorinated compounds. J. Biol. Chem. 176 (1948) 763-769.
Accepted name: 4-chlorobenzoyl-CoA dehalogenase
Reaction: 4-chlorobenzoyl-CoA + H2O = 4-hydroxybenzoyl CoA + chloride
Systematic name: 4-chlorobenzoyl CoA chlorohydrolase
Comments: specific for dehalogenation at the 4-position. Can dehalogenate substrates bearing fluorine, chlorine, bromine and iodine in the 4-position. This enzyme is part of the bacterial 2,4-dichlorobenzoate degradation pathway.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 141583-18-8
References:
1. Chang, K.H., Liang, P.H., Beck, W., Scholten, J.D., Dunaway-Mariano, D. Isolation and characterization of the three polypeptide components of 4-chlorobenzoate dehalogenase from Pseudomonas sp. strain CBS-3. Biochemistry 31 (1992) 5605-5610. [PMID: 1610806]
2. Crooks, G.P., Copley, S.D. Purification and characterization of 4-chlorobenzoyl CoA dehalogenase from Arthrobacter sp. strain 4-CB1. Biochemistry, 33 (1994) 11645-11649. [PMID: 7918379]
Accepted name: atrazine chlorohydrolase
Reaction: atrazine + H2O = 4-(ethylamino)-2-hydroxy-6-(isopropylamino)-1,3,5-triazine + chloride
For diagram of reaction click here.
Glossary: atrazine = 6-chloro-N-ethyl-N′-isopropyl-1,3,5-triazine-2,4-diamine
hydroxyatrazine = 4-(ethylamino)-6-(isopropylamino)-1,3,5-triazin-2-ol
Other name(s): AtzA
Systematic name: atrazine chlorohydrolase
Comments: Involved in the degradation of the herbicide atrazine, 2-chloro-4-(ethylamino)-6-(isopropylamino)-1,3,5-triazine, in bacteria.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 168680-16-8
References:
1. de Souza, M.L., Wackett, L.P., Boundy-Mills, K.L., Mandelbaum, R.T. and Sadowsky, M.J. Cloning, characterization, and expression of a gene region from Pseudomonas sp. strain ADP involved in the dechlorination of atrazine. Appl. Environ. Microbiol. 61 (1995) 3373-3378. [PMID: 7574646]
2. de Souza, M.L., Sadowsky, M.J. and Wackett, L.P. Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: gene sequence, enzyme purification, and protein characterization. J. Bacteriol. 178 (1996) 4894-4900. [PMID: 8759853]
Accepted name: (R)-2-haloacid dehalogenase
Reaction: (R)-2-haloacid + H2O = (S)-2-hydroxyacid + halide
Other name(s): 2-haloalkanoic acid dehalogenase[ambiguous]; 2-haloalkanoid acid halidohydrolase[ambiguous]; D-2-haloacid dehalogenase; D-DEX
Systematic name: (R)-2-haloacid halidohydrolase
Comments: Acts on acids of short chain lengths, C2 to C4, with inversion of configuration at C-2. [See also EC 3.8.1.2 (S)-2-haloacid dehalogenase, EC 3.8.1.10 2-haloacid dehalogenase (configuration-inverting) and EC 3.8.1.11 2-haloacid dehalogenase (configuration-retaining)]
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 119345-29-8
References:
1. Smith, J.M., Harrison, K. and Colby, J. Purification and characterization of D-2-haloacid dehalogenase from Pseudomonas putida strain AJ1/23. J. Gen. Microbiol. 136 (1990) 881-886. [PMID: 2380688]
2. Leigh, J.A., Skinner, A.J. and Cooper, R.A. Partial purification, stereospecificity and stoichiometry of three dehalogenases from a Rhizobium species. FEMS Microbiol. Lett. 49 (1988) 353-356.
3. Soda, K., Kurihara, T., Liu, J.-Q., Nardi-Dei, V., Park, C., Miyagi, M., Tsunasawa, S. and Esaki, N. Bacterial 2-haloacid dehalogenases: Structures and catalytic properties. Pure Appl. Chem. 68 (1996) 2097-2103.
Accepted name: 2-haloacid dehalogenase (configuration-inverting)
Reaction: (1) (S)-2-haloacid + H2O = (R)-2-hydroxyacid + halide
(2) (R)-2-haloacid + H2O = (S)-2-hydroxyacid + halide
For diagram click here.
Other name(s): 2-haloalkanoic acid dehalogenase; 2-haloalkanoid acid halidohydrolase; DL-2-haloacid dehalogenase; DL-2-haloacid dehalogenase (inversion of configuration); DL-2-haloacid halidohydrolase (inversion of configuration); DL-DEXi
Systematic name: (S)-2-haloacid dehalogenase (configuration-inverting)
Comments: Dehalogenates both (S)- and (R)-2-haloalkanoic acids to the corresponding (R)- and (S)-hydroxyalkanoic acids, respectively, with inversion of configuration at C-2. The enzyme from Pseudomonas sp. 113 acts on 2-haloalkanoic acids whose carbon chain lengths are five or less. [See also EC 3.8.1.2 (S)-2-haloacid dehalogenase, EC 3.8.1.9 (R)-2-haloacid dehalogenase and EC 3.8.1.11 2-haloacid dehalogenase (configuration-retaining)]
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Motosugi, K., Esahi, N. and Soda, K. Bacterial assimilation of D- and L-2-chloropropionates and occurrence of a new dehalogenase. Arch. Microbiol. 131 (1982) 179-183. [PMID: 7103659]
2. Motosugi, K., Esahi, N. and Soda, K. Purification and properties of a new enzyme, DL-2-haloacid dehalogenase, from Pseudomonas sp. J. Bacteriol. 150 (1982) 522-527. [PMID: 7068529]
3. Motosugi, K., Esahi, N. and Soda, K. Enzymatic preparation of D- and L-lactic acid from racemic 2-chloropropionic acid. Biotechnol. Bioeng. 26 (1984) 805-806.
4. Kurihara, T., Esaki, N. and Soda, K. Bacterial 2-haloacid dehalogenases: structures and reaction mechanisms. J. Mol. Catal., B Enzym. 10 (2000) 57-65.
5. Liu, J.-Q., Kurihara, T., Hasan, A.K.M.Q., Nardi-Dei, V., Koshikawa, H., Esaki, N. and Soda, K. Purification and characterization of thermostable and nonthermostable 2-haloacid dehalogenases with different stereospecificities from Pseudomonas sp. strain YL. Appl. Environ. Microbiol. 60 (1994) 2389-2393. [PMID: 8074519]
6. Cairns, S.S., Cornish, A. and Cooper, R.A. Cloning, sequencing and expression in Escherichia coli of two Rhizobium sp. genes encoding haloalkanoate dehalogenases of opposite stereospecificity. Eur. J. Biochem. 235 (1996) 744-749. [PMID: 8654424]
7. Leigh, J.A., Skinner, A.J. and Cooper, R.A. Partial purification, stereospecificity and stoichiometry of three dehalogenases from a Rhizobium species. FEMS Microbiol. Lett. 49 (1988) 353-356.
8. Weightman, A.J., Weightman, A.L. and Slater, J.H. Stereospecificity of 2-monochloropropionate dehalogenation by the two dehalogenases of Pseudomonas P3: evidence for two different dehalogenation mechanisms. J. Gen. Microbiol. 128 (1982) 1755-1762. [PMID: 7142958]
9. Soda, K., Kurihara, T., Liu, J.-Q., Nardi-Dei, V., Park, C., Miyagi, M., Tsunasawa, S. and Esaki, N. Bacterial 2-haloacid dehalogenases: Structures and catalytic properties. Pure Appl. Chem. 68 (1996) 2097-2103.
Accepted name: 2-haloacid dehalogenase (configuration-retaining)
Reaction: (1) (S)-2-haloacid + H2O = (S)-2-hydroxyacid + halide
(2) (R)-2-haloacid + H2O = (R)-2-hydroxyacid + halide
Other name(s): 2-haloalkanoic acid dehalogenase; 2-haloalkanoid acid halidohydrolase; DL-2-haloacid dehalogenase; DL-DEXr
Systematic name: (S)-2-haloacid dehalogenase (configuration-retaining)
Comments: Dehalogenates both (S)- and (R)-2-haloalkanoic acids to the corresponding (S)- and (R)-hydroxyalkanoic acids, respectively, with retention of configuration at C-2. [See also EC 3.8.1.2 (S)-2-haloacid dehalogenase, EC 3.8.1.9 (R)-2-haloacid dehalogenase and EC 3.8.1.10 2-haloacid dehalogenase (configuration-inverting)]
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Weightman, A.J., Weightman, A.L. and Slater, J.H. Stereospecificity of 2-monochloropropionate dehalogenation by the two dehalogenases of Pseudomonas P3: evidence for two different dehalogenation mechanisms. J. Gen. Microbiol. 128 (1982) 1755-1762. [PMID: 7142958]
2. Soda, K., Kurihara, T., Liu, J.-Q., Nardi-Dei, V., Park, C., Miyagi, M., Tsunasawa, S. and Esaki, N. Bacterial 2-haloacid dehalogenases: Structures and catalytic properties. Pure Appl. Chem. 68 (1996) 2097-2103.
[EC 3.8.2.1 Transferred entry: diisopropyl-fluorophosphatase. Now listed as EC 3.1.8.2 diisopropyl-fluorophosphatase (EC 3.8.2.1 created 1961, modified 1976, deleted 1992)]
Accepted name: diisopropyl-fluorophosphatase
Reaction: diisopropyl fluorophosphate + H2O = diisopropyl phosphate + fluoride
Other name(s): DFPase; tabunase; somanase; organophosphorus acid anhydrolase; organophosphate acid anhydrase; OPA anhydrase (ambiguous); diisopropylphosphofluoridase; dialkylfluorophosphatase; diisopropyl phosphorofluoridate hydrolase; isopropylphosphorofluoridase; diisopropylfluorophosphonate dehalogenase
Systematic name: diisopropyl-fluorophosphate fluorohydrolase
Comments: Acts on phosphorus anhydride bonds (such as phosphorus-halide and phosphorus-cyanide) in organophosphorus compounds (including ‘nerve gases’). Inhibited by chelating agents; requires divalent cations. Related to EC 3.1.8.1 aryldialkylphosphatase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Augustinsson, K.-B. and Heimburger, G. Enzymatic hydrolysis of organophosphorus compounds. I. Occurrence of enzymes hydrolysing dimethyl-amido-ethoxy-phosphoryl cyanide (Tabun). Acta Chem. Scand. 8 (1954) 753-761.
2. Augustinsson, K.-B. and Heimburger, G. Enzymatic hydrolysis of organophosphorus compounds. II. Analysis of reaction products in experiments with Tabun and some properties of blood plasma tabunase. Acta Chem. Scand. 8 (1954) 762-767.
3. Augustinsson, K.-B. and Heimburger, G. Enzymatic hydrolysis of organophosphorus compounds. IV. Specificity studies. Acta Chem. Scand. 8 (1954) 1533-1541.
4. Cohen, J.A. and Warringa, M.G.P.J. Purification and properties of dialkylfluorophosphatase. Biochim. Biophys. Acta 26 (1957) 29-39. [PMID: 13479457]
5. Mounter, L.A. Enzymic hydrolysis of organophosphorus compounds. In: Boyer, P.D., Lardy, H. and Myrbäck, K. (Ed.), The Enzymes, 2nd edn, vol. 4, Academic Press, New York, 1960, pp. 541-550.
6. Reiner, E., Aldridge, W.N. and Hoskin, C.G. (Ed.), Enzymes Hydrolysing Organophosphorus Compounds, Ellis Horwood, Chichester, UK, 1989.
Accepted name: phosphoamidase
Reaction: N-phosphocreatine + H2O = creatine + phosphate
Other name(s): creatine phosphatase
Systematic name: phosphamide hydrolase
Comments: Also acts on N-phospho-arginine and other phosphoamides. Possibly identical with EC 3.1.3.9 (glucose-6-phosphatase) or EC 3.1.3.16 (protein-serine/threonine phosphatase).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9001-79-0
References:
1. Parvin, R. and Smith, R.A. Phosphoramidates. V. Probable identity of rat liver microsomal glucose 6-phosphatase, phosphoramidase, and phosphoramidate-hexose phosphotransferase. Biochemistry 8 (1969) 1748. [PMID: 4308726]
2. Singer, M.F. and Fruton, J.S. Some properties of beef spleen phosphoamidase. J. Biol. Chem. 229 (1957) 111-119.
3. Sundarajan, T.A. and Sarma, P.S. Substrate specificity of phosphoprotein phosphatase from spleen. Biochem. J. 71 (1959) 537-544.
Accepted name: protein arginine phosphatase
Reaction: a [protein]-Nω-phospho-L-arginine + H2O = a [protein]-L-arginine + phosphate
Other name(s): YwlE
Systematic name: [protein]-Nω-phospho-L-arginine phosphohydrolase
Comments: The enzyme, characterized from Gram-positive bacteria, hydrolyses the phosphoramidate (P-N) bond of Nω-phospho-L-arginine residues in proteins and peptides that were phosphorylated by EC 2.7.14.1, protein-arginine-kinase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Fuhrmann, J., Mierzwa, B., Trentini, D.B., Spiess, S., Lehner, A., Charpentier, E. and Clausen, T. Structural basis for recognizing phosphoarginine and evolving residue-specific protein phosphatases in gram-positive bacteria. Cell Rep 3 (2013) 1832-1839. [PMID: 23770242]
2. Trentini, D.B., Fuhrmann, J., Mechtler, K. and Clausen, T. Chasing phosphoarginine proteins: development of a selective enrichment method using a phosphatase trap. LID - mcp.O113.035790 [pii. Mol. Cell. Proteomics (2014) . [PMID: 24825175]
3. Elsholz, A.K., Turgay, K., Michalik, S., Hessling, B., Gronau, K., Oertel, D., Mader, U., Bernhardt, J., Becher, D., Hecker, M. and Gerth, U. Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis. Proc. Natl. Acad. Sci. USA 109 (2012) 7451-7456. [PMID: 22517742]
Accepted name: phosphohistidine phosphatase
Reaction: a [protein]-N-phospho-L-histidine + H2O = a [protein]-L-histidine + phosphate
Other name(s): PHPT1 (gene name); protein histidine phosphatase; PHP
Systematic name: [protein]-N-phospho-L-histidine phosphohydrolase
Comments: This eukaryotic enzyme dephosphorylates phosphorylated histidine residues within proteins and peptides. The enzyme acts on phosphate groups attached to both the pros- and tele-nitrogen atoms, but the pros- position is somewhat preferred (by a factor of two at the most) [4]. The substrate specificity depends on the amino acid sequence or structural context of the phosphohistidine in a phosphoprotein. The enzyme is also active on free phosphoramidate [1,4] and peptide-bound phospholysine [5].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Ek, P., Pettersson, G., Ek, B., Gong, F., Li, J.P. and Zetterqvist, O. Identification and characterization of a mammalian 14-kDa phosphohistidine phosphatase. Eur. J. Biochem. 269 (2002) 5016-5023. [PMID: 12383260]
2. Klumpp, S., Hermesmeier, J., Selke, D., Baumeister, R., Kellner, R. and Krieglstein, J. Protein histidine phosphatase: a novel enzyme with potency for neuronal signaling. J Cereb Blood Flow Metab 22 (2002) 1420-1424. [PMID: 12468887]
3. Baumer, N., Maurer, A., Krieglstein, J. and Klumpp, S. Expression of protein histidine phosphatase in Escherichia coli, purification, and determination of enzyme activity. Methods Mol Biol 365 (2007) 247-260. [PMID: 17200567]
4. Attwood, P.V., Ludwig, K., Bergander, K., Besant, P.G., Adina-Zada, A., Krieglstein, J. and Klumpp, S. Chemical phosphorylation of histidine-containing peptides based on the sequence of histone H4 and their dephosphorylation by protein histidine phosphatase. Biochim. Biophys. Acta 1804 (2010) 199-205. [PMID: 19836471]
5. Ek, P., Ek, B. and Zetterqvist, O. Phosphohistidine phosphatase 1 (PHPT1) also dephosphorylates phospholysine of chemically phosphorylated histone H1 and polylysine. Ups J Med Sci 120 (2015) 20-27. [PMID: 25574816]
Accepted name: N-sulfoglucosamine sulfohydrolase
Reaction: N-sulfo-D-glucosamine + H2O = D-glucosamine + sulfate
Other name(s): sulfoglucosamine sulfamidase; heparin sulfamidase; 2-desoxy-D-glucoside-2-sulphamate sulphohydrolase (sulphamate sulphohydrolase)
Systematic name: N-sulfo-D-glucosamine sulfohydrolase
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37289-41-1
References:
1. Dietrich, C.P. Enzymic degradation of heparin. A sulphamidase and a sulphoesterase from Flavobacterium heparinum. Biochem. J. 111 (1969) 91-95. [PMID: 5775690]
2. Mahuran, D., Clements, P. and Hopwood, J. A rapid four column purification of 2-deoxy-D-glucoside-2-sulphamate sulphohydrolase from human liver. Biochim. Biophys. Acta 757 (1983) 359-365. [PMID: 6849981]
Accepted name: cyclamate sulfohydrolase
Reaction: cyclohexylsulfamate + H2O = cyclohexylamine + sulfate
Other name(s): cyclamate sulfamatase; cyclamate sulfamidase; cyclohexylsulfamate sulfamidase
Systematic name: cyclohexylsulfamate sulfohydrolase
Comments: Also readily hydrolyses aliphatic sulfamates with 3 to 8 carbons.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, EAWAG-BBD , CAS registry number: 52228-00-9
References:
1. Niimura, T., Tokieda, T. and Yamaha, T. Partial purification and some properties of cyclamate sulfamatase. J. Biochem. (Tokyo) 75 (1974) 407-417. [PMID: 4209783]
Accepted name: phosphonoacetaldehyde hydrolase
Reaction: phosphonoacetaldehyde + H2O = acetaldehyde + phosphate
For diagram of reaction click here.
Other name(s): phosphonatase; 2-phosphonoacetylaldehyde phosphonohydrolase
Systematic name: 2-oxoethylphosphonate phosphonohydrolase
Comments: This enzyme destabilizes the C-P bond, by forming an imine between one of its lysine residues and the carbonyl group of the substrate, thus allowing this, normally stable, bond to be broken. The mechanism is similar to that used by EC 4.1.2.13, fructose-bisphosphate aldolase, to break a C-C bond. Belongs to the haloacetate dehalogenase family.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37289-42-2
References:
1. La Nauze, J.M. and Rosenberg, H. The identification of 2-phosphonoacetaldehyde as an intermediate in the degradation of 2-aminoethylphosphonate by Bacillus cereus. Biochim. Biophys. Acta 165 (1968) 438-447. [PMID: 4982500]
2. La Nauze, J.M., Rosenberg, H. and Shaw, D.C. The enzymic cleavage of the carbon-phosphorus bond: purification and properties of phosphonatase. Biochim. Biophys. Acta 212 (1970) 332-350. [PMID: 4989158]
3. La Nauze, J.M., Coggins, J.R. and Dixon, H.B.F. Aldolase-like imine formation in the mechanism of action of phosphonoacetaldehyde hydrolase. Biochem. J. 165 (1977) 409-411. [PMID: 200222]
4. Olsen, D.B., Hepburn, T.W., Moos, M., Mariano, P.S. and Dunaway-Mariano, D. Substrate binding and catalytic groups of the P-C bond cleaving enzyme, phosphonoacetaldehyde hydrolase. Biochemistry 27 (1988) 2229-2234. [PMID: 3132206]
5. Baker, A.S., Ciocci, M.J., Metcalf, W.W., Kim, J., Babbitt, P.C., Wanner, B.L., Martin, B.M. and Dunaway-Mariano, D. Insights into the mechanism of catalysis by the P-C bond-cleaving enzyme phosphonoacetaldehyde hydrolase derived from gene sequence analysis and mutagenesis. Biochemistry 37 (1998) 9305-9315. [PMID: 9649311]
Accepted name: phosphonoacetate hydrolase
Reaction: phosphonoacetate + H2O = acetate + phosphate
Systematic name: phosphonoacetate phosphonohydrolase
Comments: a zinc-dependent enzyme. Belongs to the alkaline phosphatase superfamily of zinc-dependent hydrolases.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 153570-68-4
References:
1. McGrath, J.W., Wisdom, G.B., McMullan, G., Larkin, M.J., Quinn, J.P. The purification and properties of phosphonoacetate hydrolase, a novel carbon-phosphorus bond-cleavage enzyme from Pseudomonas fluorescens 23F. Eur. J. Biochem. 234 (1995) 225-230. [PMID: 8529644]
Accepted name: phosphonopyruvate hydrolase
Reaction: 3-phosphonopyruvate + H2O = pyruvate + phosphate
For diagram of reaction click here.
Other name(s): PPH
Comments: Highly specific for phosphonopyruvate as substrate [2]. The reaction is not inhibited by phosphate but is inhibited by the phosphonates phosphonoformic acid, hydroxymethylphosphonic acid and 3-phosphonopropanoic acid [2]. The enzyme is activated by the divalent cations Co2+, Mg2+ and Mn2+. This enzyme is a member of the phosphoenolpyruvate mutase/isocitrate lyase superfamily [3].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Ternan, N.G., Hamilton, J.T. and Quinn, J.P. Initial in vitro characterisation of phosphonopyruvate hydrolase, a novel phosphate starvation-independent, carbon-phosphorus bond cleavage enzyme in Burkholderia cepacia Pal6. Arch. Microbiol. 173 (2000) 35-41. [PMID: 10648102]
2. Kulakova, A.N., Wisdom, G.B., Kulakov, L.A. and Quinn, J.P. The purification and characterization of phosphonopyruvate hydrolase, a novel carbon-phosphorus bond cleavage enzyme from Variovorax sp. Pal2. J. Biol. Chem. 278 (2003) 23426-23431. [PMID: 12697754]
3. Chen, C.C., Han, Y., Niu, W., Kulakova, A.N., Howard, A., Quinn, J.P., Dunaway-Mariano, D. and Herzberg, O. Structure and kinetics of phosphonopyruvate hydrolase from Variovorax sp. Pal2: new insight into the divergence of catalysis within the PEP mutase/isocitrate lyase superfamily. Biochemistry 45 (2006) 11491-11504. [PMID: 16981709]
Accepted name: trithionate hydrolase
Reaction: trithionate + H2O = thiosulfate + sulfate + 2 H+
Systematic name: trithionate thiosulfohydrolase
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 115004-90-5
References:
1. Lu, W.-P. and Kelly, D.P. Cellular location and partial purification of the 'thiosulfate oxidizing enzyme' and 'trithionate hydrolase' from Thiobacillus tepidarius. J. Gen. Microbiol. 134 (1988) 877-885.
2. Trudinger, P.A. The metabolism of trithionate by Thiobacillus X. Aust. J. Biol. Sci. 17 (1964) 459-468.
EC 3.13.1 Acting on Carbon-Sulfur Bonds
Accepted name: UDP-sulfoquinovose synthase
Reaction: UDP-α-D-sulfoquinovopyranose + H2O = UDP-α-D-glucose + sulfite
For diagram of the reaction, click here
Other name(s): sulfite:UDP-glucose sulfotransferase; UDPsulfoquinovose synthase
Systematic name: UDP-6-sulfo-6-deoxyglucose sulfohydrolase
Comments: Requires NAD+, which appears to oxidize UDP-α-D-glucose to UDP-4-dehydroglucose, which dehydrates to UDP-4-dehydro-6-deoxygluc-5-enose, to which sulfite is added. The reaction is completed when the substrate is rehydrogenated at C-4. The enzyme from Arabidopsis thaliana is specific for UDP-Glc and sulfite.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB CAS registry number:
References:
1. Essigmann, B., Gler, S., Narang, R.A., Linke, D. and Benning, C. Phosphate availability affects the thylakoid lipid composition and the expression of SQD1, a gene required for sulfolipid biosynthesis in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 95 (1998) 1950-1955. [PMID: 9465123]
2. Essigmann, B., Hespenheide, B.M., Kuhn, L.A. and Benning, C. Prediction of the active-site structure and NAD+ binding in SQD1, a protein essential for sulfolipid biosynthesis in Arabidopsis. Arch. Biochem. Biophys. 369 (1999) 30-41. [PMID: 10462438]
3. Mulichak, A.M., Theisen, M.J., Essigmann, B., Benning, C. and Garavito, R.M. Crystal structure of SQD1, an enzyme involved in the biosynthesis of the plant sulfolipid headgroup donor UDP-sulfoquinovose. Proc. Natl. Acad. Sci. USA 96 (1999) 13097-13102. [PMID: 10557279]
4. Sanda, S., Leustek, T., Theisen, M., Garavito, R.M. and Benning, C. Recombinant Arabidopsis SQD1 converts UDP-glucose and sulfite to the sulfolipid head group precursor UDP-sulfoquinovose in vitro. J. Biol. Chem. 276 (2001) 3941-3946. [PMID: 11073956]
[EC 3.13.1.2 Deleted entry: 5-deoxyribos-5-ylhomocysteinase. The activity is most probably attributable to EC 4.4.1.21, S-ribosylhomocysteine lyase. (EC 3.13.1.2 created 1972 as EC 3.3.1.3, transferred 2001 to EC 3.2.1.148, transferred 2004 to EC 3.13.1.2, deleted 2005)]
Accepted name: 2'-hydroxybiphenyl-2-sulfinate desulfinase
Reaction: 2'-hydroxybiphenyl-2-sulfinate + H2O = 2-hydroxybiphenyl + sulfite
For diagram click here.
Other name(s): gene dszB-encoded hydrolase; 2-(2-hydroxyphenyl) benzenesulfinate:H2O hydrolase; DszB; HBPSi desulfinase; 2-(2-hydroxyphenyl) benzenesulfinate sulfohydrolase; HPBS desulfinase; 2-(2-hydroxyphenyl)benzenesulfinate hydrolase; 2-(2'-hydroxyphenyl)benzenesulfinate desulfinase; 2-(2-hydroxyphenyl)benzenesulfinate desulfinase
Systematic name: 2'-hydroxybiphenyl-2-sulfinate sulfohydrolase
Comments: The enzyme from Rhodococcus sp. strain IGTS8 is encoded by the plasmid-encoded dibenzothiophene-desulfurization (dsz) operon. The enzyme has a narrow substrate specificity with biphenyl-2-sulfinate being the only other substrate known to date [2].
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB CAS registry number: 198154-06-2
References:
1. Oldfield, C., Pogrebinsky, O., Simmonds, J., Ölson, E.S. and Kulpa, C.F. Elucidation of the metabolic pathway for dibenzothiophene desulfurization by Rhodococcus sp. strain IGTS8 (ATCC 53968). Microbiology 143 (1997) 2961-2973. [PMID: 9308179]
2. Nakayama, N., Matsubara, T., Ohshiro, T., Moroto, Y., Kawata, Y., Koizumi, K., Hirakawa, Y., Suzuki, M., Maruhashi, K., Izumi, Y. and Kurane, R. A novel enzyme, 2'-hydroxybiphenyl-2-sulfinate desulfinase (DszB), from a dibenzothiophene-desulfurizing bacterium Rhodococcus erythropolis KA2-5-1: gene overexpression and enzyme characterization. Biochim. Biophys. Acta 1598 (2002) 122-130. [PMID: 12147352]
3. Watkins, L.M., Rodriguez, R., Schneider, D., Broderick, R., Cruz, M., Chambers, R., Ruckman, E., Cody, M. and Mrachko, G.T. Purification and characterization of the aromatic desulfinase, 2-(2'-hydroxyphenyl)benzenesulfinate desulfinase. Arch. Biochem. Biophys. 415 (2003) 14-23. [PMID: 12801508]
Accepted name: 3-sulfinopropanoyl-CoA desulfinase
Reaction: 3-sulfinopropanoyl-CoA + H2O = propanoyl-CoA + sulfite
Other name(s): 3SP-CoA desulfinase; AcdDPN7; 3-sulfinopropionyl-CoA desulfinase
Systematic name: 3-sulfinopropanoyl-CoA sulfinohydrolase
Comments: The enzyme from the β-proteobacterium Advenella mimigardefordensis contains one non-covalently bound FAD per subunit.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Schurmann, M., Deters, A., Wubbeler, J.H. and Steinbuchel, A. A novel 3-sulfinopropionyl coenzyme A (3SP-CoA) desulfinase from Advenella mimigardefordensis strain DPN7T acting as a key enzyme during catabolism of 3,3'-dithiodipropionic acid is a member of the acyl-CoA dehydrogenase superfamily. J. Bacteriol. 195 (2013) 1538-1551. [PMID: 23354747]
2. Schurmann, M., Demming, R.M., Krewing, M., Rose, J., Wubbeler, J.H. and Steinbuchel, A. Identification of 3-sulfinopropionyl coenzyme A (CoA) desulfinases within the Acyl-CoA dehydrogenase superfamily. J. Bacteriol. 196 (2014) 882-893. [PMID: 24317404]
Accepted name: carbon disulfide hydrolase
Reaction: carbon disulfide + 2 H2O = CO2 + 2 hydrogen sulfide (overall reaction)
(1a) carbon disulfide + H2O = carbonyl sulfide + hydrogen sulfide
(1b) carbonyl sulfide + H2O = CO2 + hydrogen sulfide
Other name(s): CS2 hydrolase (misleading); carbon disulfide lyase; CS2-converting enzyme; carbon disulphide-lyase (decarboxylating)
Systematic name: carbon-disulfide hydrogen-sulfide-lyase (decarboxylating)
Comments: The enzyme contains Zn2+. The hyperthermophilic archaeon Acidianus sp. A1-3 obtains energy by the conversion of carbon disulfide to hydrogen sulfide, with carbonyl sulfide as an intermediate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Smeulders, M.J., Barends, T.R., Pol, A., Scherer, A., Zandvoort, M.H., Udvarhelyi, A., Khadem, A.F., Menzel, A., Hermans, J., Shoeman, R.L., Wessels, H.J., van den Heuvel, L.P., Russ, L., Schlichting, I., Jetten, M.S. and Op den Camp, H.J. Evolution of a new enzyme for carbon disulphide conversion by an acidothermophilic archaeon. Nature 478 (2011) 412-416. [PMID: 22012399]
Accepted name: [CysO sulfur-carrier protein]-S-L-cysteine hydrolase
Reaction: [CysO sulfur-carrier protein]-Gly-NH-CH2-C(O)-S-L-cysteine + H2O = [CysO sulfur-carrier protein]-Gly-NH-CH2-COOH + L-cysteine
Other name(s): mec (gene name)
Systematic name: [CysO sulfur-carrier protein]-S-L-cysteine sulfohydrolase
Comments: Requires Zn2+. The enzyme, characterized from the bacterium Mycobacterium tuberculosis, participates in an L-cysteine biosynthesis pathway. It acts on the product of EC 2.5.1.113, [CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Burns, K.E., Baumgart, S., Dorrestein, P.C., Zhai, H., McLafferty, F.W. and Begley, T.P. Reconstitution of a new cysteine biosynthetic pathway in Mycobacterium tuberculosis. J. Am. Chem. Soc. 127 (2005) 11602-11603. [PMID: 16104727]
Accepted name: carbonyl sulfide hydrolase
Reaction: carbonyl sulfide + H2O = hydrogen sulfide + CO2
Other name(s): COSase; COS hydrolase; cos (gene name)
Systematic name: carbonyl sulfide hydrogen-sulfide-lyase (decarboxylating)
Comments: The enzyme, characterized from the bacterium Thiobacillus thioparus, catalyses a step in the degradation pathway of thiocyanate. This activity is also catalysed by the archaeal EC 3.13.1.5, carbon disulfide lyase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Ogawa, T., Noguchi, K., Saito, M., Nagahata, Y., Kato, H., Ohtaki, A., Nakayama, H., Dohmae, N., Matsushita, Y., Odaka, M., Yohda, M., Nyunoya, H. and Katayama, Y. Carbonyl sulfide hydrolase from Thiobacillus thioparus strain THI115 is one of the β-carbonic anhydrase family enzymes. J. Am. Chem. Soc. 135 (2013) 3818-3825. [PMID: 23406161]
[EC 3.13.1.8 Transferred entry: S-adenosyl-L-methionine hydrolase (adenosine-forming), now classified as EC 3.13.2.3, S-adenosyl-L-methionine hydrolase (adenosine-forming) (EC 3.13.1.8 created 2018, deleted 2022)]
Accepted name: S-inosyl-L-homocysteine hydrolase
Reaction: S-inosyl-L-homocysteine + H2O = inosine + L-homocysteine
Other name(s): SIHH
Systematic name: S-inosyl-L-homocysteine hydrolase (inosine-forming)
Comments: The enzyme, characterized from the methanogenic archaeon Methanocaldococcus jannaschii, binds an NAD+ cofactor. It participates in an alternative pathway for the regeneration of S-adenosyl-L-methionine from S-adenosyl-L-homocysteine that involves the deamination of the latter to S-inosyl-L-homocysteine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Miller, D., Xu, H. and White, R.H. S-Inosyl-L-homocysteine hydrolase, a novel enzyme involved in S-adenosyl-L-methionine recycling. J. Bacteriol. 197 (2015) 2284-2291. [PMID: 25917907]
Accepted name: adenosylhomocysteinase
Reaction: S-adenosyl-L-homocysteine + H2O = L-homocysteine + adenosine
For diagram of reaction mechanism, click here
Other name(s): S-adenosylhomocysteine synthase; S-adenosylhomocysteine hydrolase (ambiguous); adenosylhomocysteine hydrolase; S-adenosylhomocysteinase; SAHase; AdoHcyase
Systematic name: S-adenosyl-L-homocysteine hydrolase
Comments: The enzyme contains one tightly bound NAD+ per subunit. This appears to bring about a transient oxidation at C-3' of the 5'-deoxyadenosine residue, thus labilizing the thioether bond [2] (for mechanism, click here), cf. EC 5.5.1.4, inositol-3-phosphate synthase.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, CAS registry number:
References:
1. de la Haba, G. and Cantoni, G.L. The enzymatic synthesis of S-adenosyl-L-homocysteine from adenosine and homocysteine. J. Biol. Chem. 234 (1959) 603-608. [PMID: 13641268]
2. Palmer, J.L. and Abeles, R.H. The mechanism of action of S-adenosylhomocysteinase. J. Biol. Chem. 254 (1979) 1217-1226. [PMID: 762125]
[EC 3.13.2.2 Transferred entry: S-adenosyl-L-methionine hydrolase (L-homoserine-forming). Now classified as EC 4.4.1.42, S-adenosyl-L-methionine lyase (EC 3.13.2.2 created 1972 as EC 3.3.1.2, modified 1976, modified 2018, transferred 2022 to EC 3.13.2.2, deleted 2022)]
Accepted name: (R)-S-adenosyl-L-methionine hydrolase (adenosine-forming)
Reaction: (R)-S-adenosyl-L-methionine + H2O = adenosine + L-methionine
Other name(s): SAM hydroxide adenosyltransferase
Systematic name: (R)-S-adenosyl-L-methionine hydrolase (adenosine-forming)
Comments: The enzyme, found in bacteria and archaea, is involved in removing the (R) isomer of S-adenosyl-L-methionine from the cell. It catalyses a nucleophilic attack of water at the C5' carbon of S-adenosyl-L-methionine to generate adenosine and L-methionine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Eustaquio, A.S., Harle, J., Noel, J.P. and Moore, B.S. S-Adenosyl-L-methionine hydrolase (adenosine-forming), a conserved bacterial and archaeal protein related to SAM-dependent halogenases. ChemBioChem 9 (2008) 2215-2219. [PMID: 18720493]
2. Deng, H., McMahon, S.A., Eustaquio, A.S., Moore, B.S., Naismith, J.H. and O'Hagan, D. Mechanistic insights into water activation in SAM hydroxide adenosyltransferase (duf-62). ChemBioChem 10 (2009) 2455-2459. [PMID: 19739191]
3. Kornfuehrer, T., Romanowski, S., de Crecy-Lagard, V., Hanson, A.D. and Eustaquio, A.S. An enzyme containing the conserved domain of unknown function DUF62 acts as a stereoselective (Rs ,Sc)-S-adenosylmethionine hydrolase. Chembiochem 21 (2020) 3495-3499. [PMID: 32776704]
Accepted name: lanthipeptide synthase
Reaction: (1) a [protein]-L-serine + a [protein]-L-cysteine = a [protein] with lanthionine crosslink + H2O (overall reaction)
(1a) a [protein]-L-serine = a [protein]-2-aminoprop-2-enoate + H2O
(1b) a [protein]-2-aminoprop-2-enoate + a [protein]-L-cysteine = a [protein] with lanthionine crosslink
(2) a [protein]-L-threonine + a [protein]-L-cysteine = a [protein] with 3-methyllanthionine crosslink + H2O (overall reaction)
(2a) a [protein]-L-threonine = a [protein]-(Z)-2-aminobutenoate + H2O
(2b) a [protein]-(Z)-2-aminobutenoate + a [protein]-L-cysteine = a [protein] with 3-methyllanthionine crosslink
Other name(s): lanthipeptide synthetase
Systematic name: [protein]-(methyl)lanthionine hydrolase
Comments: The lanthipeptides are a family of ribosomally synthesized and post-translationally modified peptides (RiPPs) that is characterized by the presence of multiple lanthionine (Lan) and 3-methyllanthionine (MeLan) crosslinks, which are formed by lanthipeptide synthases. These enzymes catalyse dehydration of Ser/Thr residues, followed by intramolecular addition of the thiol group of a Cys residue to the dehydro amino acids, which results in the formation of the thioether crosslinks of (methyl)lanthionine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Li, B., Yu, J.P., Brunzelle, J.S., Moll, G.N., van der Donk, W.A. and Nair, S.K. Structure and mechanism of the lantibiotic cyclase involved in nisin biosynthesis. Science 311 (2006) 1464-1467. [PMID: 16527981]
2. Willey, J.M. and van der Donk, W.A. Lantibiotics: peptides of diverse structure and function. Annu. Rev. Microbiol. 61 (2007) 477-501. [PMID: 17506681]
3. Li, B. and van der Donk, W.A. Identification of essential catalytic residues of the cyclase NisC involved in the biosynthesis of nisin. J. Biol. Chem. 282 (2007) 21169-21175. [PMID: 17513866]
4. Goto, Y., Li, B., Claesen, J., Shi, Y., Bibb, M.J. and van der Donk, W.A. Discovery of unique lanthionine synthetases reveals new mechanistic and evolutionary insights. PLoS Biol. 8 (2010) e1000339. [PMID: 20351769]
5. Zhang, Q., Yu, Y., Velasquez, J.E. and van der Donk, W.A. Evolution of lanthipeptide synthetases. Proc. Natl. Acad. Sci. USA 109 (2012) 18361-18366. [PMID: 23071302]