Enzyme Nomenclature

Continued from EC 3.6.4

EC 3.7 and EC 3.13

Sections

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 Acting on Carbon-Carbon Bonds

EC 3.7.1 In Ketonic Substances

Contents

EC 3.7.1.1 oxaloacetase
EC 3.7.1.2 fumarylacetoacetase
EC 3.7.1.3 kynureninase
EC 3.7.1.4 phloretin hydrolase
EC 3.7.1.5 acylpyruvate hydrolase
EC 3.7.1.6 acetylpyruvate hydrolase
EC 3.7.1.7 β-diketone hydrolase
EC 3.7.1.8 2,6-dioxo-6-phenylhexa-3-enoate hydrolase
EC 3.7.1.9 2-hydroxymuconate-semialdehyde hydrolase
EC 3.7.1.10 cyclohexane-1,3-dione hydrolase
EC 3.7.1.11 cyclohexane-1,2-dione hydrolase
EC 3.7.1.12 cobalt-precorrin 5A hydrolase
EC 3.7.1.13 2-hydroxy-6-oxo-6-(2-aminobiphenyl)hexa-2,4-dienoate hydrolase
EC 3.7.1.14 2-hydroxy-6-oxonona-2,4-dienedioate hydrolase
EC 3.7.1.15 transferred now EC 4.2.1.138
EC 3.7.1.16 transferred now EC 3.3.2.12
EC 3.7.1.17 4,5:9,10-diseco-3-hydroxy-5,9,17-trioxoandrosta-1(10),2-diene-4-oate hydrolase
EC 3.7.1.18 6-oxocamphor hydrolase
EC 3.7.1.19 2,6-dihydroxypseudooxynicotine hydrolase
EC 3.7.1.20 3-fumarylpyruvate hydrolase
EC 3.7.1.21 6-oxocyclohex-1-ene-1-carbonyl-CoA hydratase
EC 3.7.1.22 3D-(3,5/4)-trihydroxycyclohexane-1,2-dione acylhydrolase (decyclizing)
EC 3.7.1.23 maleylpyruvate hydrolase

Entries

EC 3.7.1.1

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.

[EC 3.7.1.1 created 1961]

EC 3.7.1.2

Accepted name: fumarylacetoacetase

Reaction: 4-fumarylacetoacetate + H2O = acetoacetate + fumarate

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, EXPASY, KEGG, Metacyc, PDB, UM-BBD, 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.

[EC 3.7.1.2 created 1961]

EC 3.7.1.3

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.

[EC 3.7.1.3 created 1965]

EC 3.7.1.4

Accepted name: phloretin hydrolase

Reaction: phloretin + H2O = phloretate + phloroglucinol

Other name(s): lactase-phlorizin hydrolase

Systematic name: 2',4,4',6'-tetrahydroxydehydrochalcone 1,3,5-trihydroxybenzenehydrolase

Comments: Also hydrolyses other C-acylated phenols related to phloretin.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37289-38-6

References:

1. Minamikawa, T., Jayasankar, N.P., Bohm, B.A., Taylor, I.E.P and Towers, G.H.N. 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]

[EC 3.7.1.4 created 1972]

EC 3.7.1.5

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, EXPASY, KEGG, Metacyc, PDB, UM-BBD, 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]

[EC 3.7.1.5 created 1976]

EC 3.7.1.6

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, EXPASY, Metacyc, KEGG, UM-BBD, 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]

[EC 3.7.1.6 created 1984]

EC 3.7.1.7

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, 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.

[EC 3.7.1.7 created 1989]

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, EXPASY, KEGG, Metacyc, PDB, UM-BBD, 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 3.7.1.9

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, EXPASY, KEGG, Metacyc, UM-BBD, 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]

[EC 3.7.1.9 created 1990, modified 2013]

EC 3.7.1.10

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.

[EC 3.7.1.10 created 1992]

EC 3.7.1.11

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, 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.

[EC 3.7.1.11 created 2009]

EC 3.7.1.12

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]

[EC 3.7.1.12 created 2010]

EC 3.7.1.13

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]

[EC 3.7.1.13 created 2010]

EC 3.7.1.14

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, EXPASY, KEGG, Metacyc, PDB, UM-BBD, 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 3.7.1.14 created 2011, modified 2012]

[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)]

EC 3.7.1.17

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, EXPASY, KEGG, Metacyc, PDB, UM-BBD, 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]

[EC 3.7.1.17 created 2012]

EC 3.7.1.18

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, 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]

[EC 3.7.1.18 created 2012]

EC 3.7.1.19

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, 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]

[EC 3.7.1.19 created 2012]

EC 3.7.1.20

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]

[EC 3.7.1.20 created 2012]

EC 3.7.1.21

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]

[EC 3.7.1.21 created 2014]

EC 3.7.1.22

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]

[EC 3.7.1.22 created 2014]

EC 3.7.1.23

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]

[EC 3.7.1.23 created 2016]


EC 3.8 Acting on Halide Bonds

EC 3.8.1 In C-Halide Compounds

Contents

EC 3.8.1.1 alkylhalidase
EC 3.8.1.2 (S)-2-haloacid dehalogenase
EC 3.8.1.3 haloacetate dehalogenase
EC 3.8.1.4 now EC 1.97.1.10
EC 3.8.1.5 haloalkane dehalogenase
EC 3.8.1.6 4-chlorobenzoate dehalogenase
EC 3.8.1.7 4-chlorobenzoyl-CoA dehalogenase
EC 3.8.1.8 atrazine chlorohydrolase
EC 3.8.1.9 (R)-2-haloacid dehalogenase
EC 3.8.1.10 2-haloacid dehalogenase (configuration-inverting)
EC 3.8.1.11 2-haloacid dehalogenase (configuration-retaining)


Entries

EC 3.8.1.1

Accepted name: alkylhalidase

Reaction: bromochloromethane + H2O = formaldehyde + bromide + chloride

Other name(s): halogenase; haloalkane halidohydrolase; haloalkane dehalogenase

Systematic name: alkyl-halide halidohydrolase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9025-22-3

References:

1. Heppel, L.A. and Porterfield, V.T. Enzymatic dehalogenation of certain brominated and chlorinated compounds. J. Biol. Chem. 176 (1948) 763-769.

[EC 3.8.1.1 created 1961]

EC 3.8.1.2

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; (R,S)-2-haloacid dehalogenase (configuration-inverting)

Systematic name: (S)-2-haloacid dehalogenase (configuration-inverting)

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, EXPASY, KEGG, Metacyc, PDB, UM-BBD, 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.

[EC 3.8.1.2 created 1972, modified 2003]

EC 3.8.1.3

Accepted name: haloacetate dehalogenase

Reaction: haloacetate + H2O = glycolate + halide

Other name(s): monohaloacetate dehalogenase

Systematic name: haloacetate halidohydrolase

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, UM-BBD, 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 3.8.1.3 created 1972]

[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)]

EC 3.8.1.5

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, EXPASY, KEGG, Metacyc, PDB, UM-BBD, 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]

[EC 3.8.1.5 created 1989]

EC 3.8.1.6

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.

[EC 3.8.1.6 created 1989, modified 1999]

EC 3.8.1.7

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, EXPASY, KEGG, Metacyc, PDB, UM-BBD, 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]

[EC 3.8.1.7 created 1999]

EC 3.8.1.8

Accepted name: atrazine chlorohydrolase

Reaction: atrazine + H2O = 4-(ethylamino)-2-hydroxy-6-(isopropylamino)-1,3,5-triazine + chloride

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, EXPASY, KEGG, Metacyc, UM-BBD, 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]

[EC 3.8.1.8 created 2000]

EC 3.8.1.9

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, 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.

[EC 3.8.1.9 created 2003]

EC 3.8.1.10

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, 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.

[EC 3.8.1.10 created 2003]

EC 3.8.1.11

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 3.8.1.11 created 2003]


[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)]


EC 3.9 Acting on Phosphorus-Nitrogen Bonds

Contents

EC 3.9.1.1 phosphoamidase
EC 3.9.1.2 protein arginine phosphatase
EC 3.9.1.3 phosphohistidine phosphatase

Entries

EC 3.9.1.1

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, 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.

[EC 3.9.1.1 created 1961]

EC 3.9.1.2

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, 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]

[EC 3.9.1.2 created 2014]

EC 3.9.1.3

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, 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]

[EC 3.9.1.3 created 2016]


EC 3.10 Acting on Sulfur-Nitrogen Bonds

Contents

EC 3.10.1.1 N-sulfoglucosamine sulfohydrolase
EC 3.10.1.2 cyclamate sulfohydrolase


Entries

EC 3.10.1.1

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, 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]

[EC 3.10.1.1 created 1972, modified 1981, modified 1982]

EC 3.10.1.2

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, UM-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]

[EC 3.10.1.2 created 1976, modified 1981]


EC 3.11 Acting on Carbon-Phosphorus Bonds

Contents

EC 3.11.1.1 phosphonoacetaldehyde hydrolase
EC 3.11.1.2 phosphonoacetate hydrolase
EC 3.11.1.3 phosphonopyruvate hydrolase

Entries

EC 3.11.1.1

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]

[EC 3.11.1.1 created 1972, modified 1976, modified 2001]

EC 3.11.1.2

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]

[EC 3.11.1.2 created 1999]

EC 3.11.1.3

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]

[EC 3.11.1.3 created 2007]


EC 3.12 Acting on Sulfur-Sulfur Bonds

EC 3.12.1.1

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 3.12.1.1 created 1990]


EC 3.13 Acting on Carbon-Sulfur Bonds

Contents

EC 3.13.1.1 UDP-sulfoquinovose synthase
EC 3.13.1.2 deleted probably EC 4.4.1.21
EC 3.13.1.3 2'-hydroxybiphenyl-2-sulfinate desulfinase
EC 3.13.1.4 3-sulfinopropanoyl-CoA desulfinase


EC 3.13.1.1

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 3.13.1.1 created 2001, modified 2010]

[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)]

EC 3.13.1.3

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, EXPASY, KEGG, Metacyc, PDB UM-BBD, 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]

[EC 3.13.1.3 created 2000 as EC 3.1.2.24, transferred 2005 to EC 3.13.1.3]

EC 3.13.1.4

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, 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]

[EC 3.13.1.4 created 2014]


Continued with EC 4 Lyases
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