Enzyme Nomenclature

EC 4.2.1 (continued)

Hydro-Lyases

Continued from EC 4.2.1.1 to EC 4.2.1.50

Contents

EC 4.2.1.101 trans-feruloyl-CoA hydratase
EC 4.2.1.102 now EC 4.2.1.100
EC 4.2.1.103 cyclohexyl-isocyanide hydratase
EC 4.2.1.104 cyanase
EC 4.2.1.105 2-hydroxyisoflavanone dehydratase
EC 4.2.1.106 bile-acid 7α-dehydratase
EC 4.2.1.107 3α,7α,12αtrihydroxy-5β-cholest-24-enoyl-CoA dehydratase
EC 4.2.1.108 ectoine synthase
EC 4.2.1.109 methylthioribulose 1-phosphate dehydratase
EC 4.2.1.110 aldos-2-ulose dehydratase
EC 4.2.1.111 1,5-anhydro-D-fructose dehydratase
EC 4.2.1.112 acetylene hydratase
EC 4.2.1.113 o-succinylbenzoate synthase
EC 4.2.1.114 methanogen homoaconitase
EC 4.2.1.115 UDP-N-acetylglucosamine 4,6-dehydratase (inverting)
EC 4.2.1.116 3-hydroxypropionyl-CoA dehydratase
EC 4.2.1.117 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)
EC 4.2.1.118 3-dehydroshikimate dehydratase
EC 4.2.1.119 enoyl-CoA hydratase 2
EC 4.2.1.120 4-hydroxybutanoyl-CoA dehydratase
EC 4.2.1.121 colneleate synthase
EC 4.2.1.122 tryptophan synthase (indole-salvaging)
EC 4.2.1.123 tetrahymanol synthase
EC 4.2.1.124 arabidiol synthase
EC 4.2.1.125 dammarenediol II synthase
EC 4.2.1.126 N-acetylmuramic acid 6-phosphate etherase
EC 4.2.1.127 linalool dehydratase
EC 4.2.1.128 lupan-3β,20-diol synthase
EC 4.2.1.129 squalene—hopanol cyclase
EC 4.2.1.130 D-lactate dehydratase
EC 4.2.1.131 carotenoid 1,2-hydratase
EC 4.2.1.132 2-hydroxyhexa-2,4-dienoate hydratase
EC 4.2.1.133 copal-8-ol diphosphate hydratase
EC 4.2.1.134 very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase
EC 4.2.1.135 UDP-N-acetylglucosamine 4,6-dehydratase (configuration-retaining)
EC 4.2.1.136 ADP-dependent NAD(P)H-hydrate dehydratase
EC 4.2.1.137 sporulenol synthase
EC 4.2.1.138 (+)-caryolan-1-ol synthase
EC 4.2.1.139 medicarpin synthase
EC 4.2.1.140 gluconate/galactonate dehydratase
EC 4.2.1.141 2-dehydro-3-deoxy-D-arabinonate dehydratase
EC 4.2.1.142 5'-oxoaverantin cyclase
EC 4.2.1.143 versicolorin B synthase
EC 4.2.1.144 3-amino-5-hydroxybenzoate synthase
EC 4.2.1.145 capreomycidine synthase
EC 4.2.1.146 L-galactonate dehydratase
EC 4.2.1.147 5,6,7,8-tetrahydromethanopterin hydro-lyase
EC 4.2.1.148 2-methylfumaryl-CoA hydratase
EC 4.2.1.149 crotonobetainyl-CoA hydratase
EC 4.2.1.150 short-chain-enoyl-CoA hydratase
EC 4.2.1.151 chorismate dehydratase
EC 4.2.1.152 hydroperoxy icosatetraenoate dehydratase
EC 4.2.1.153 3-methylfumaryl-CoA hydratase
EC 4.2.1.154 tetracenomycin F2 cyclase
EC 4.2.1.155 methylthioacryloyl-CoA hydratase
EC 4.2.1.156 L-talarate dehydratase
EC 4.2.1.157 (R)-2-hydroxyisocaproyl-CoA dehydratase
EC 4.2.1.158 galactarate dehydratase (D-threo-forming)
EC 4.2.1.159 dTDP-4-dehydro-6-deoxy-α-D-glucopyranose 2,3-dehydratase
EC 4.2.1.160 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one isomerase/dehydratase
EC 4.2.1.161 bisanhydrobacterioruberin hydratase
EC 4.2.1.162 6-deoxy-6-sulfo-D-gluconate dehydratase
EC 4.2.1.163 2-oxo-hept-4-ene-1,7-dioate hydratase
EC 4.2.1.164 dTDP-4-dehydro-2,6-dideoxy-D-glucose 3-dehydratase
EC 4.2.1.165 chlorophyllide a 31-hydratase
EC 4.2.1.166 phosphinomethylmalate isomerase
EC 4.2.1.167 (R)-2-hydroxyglutaryl-CoA dehydratase
EC 4.2.1.168 GDP-4-dehydro-6-deoxy-α-D-mannose 3-dehydratase
EC 4.2.1.169 3-vinyl bacteriochlorophyllide d 31-hydratase
EC 4.2.1.170 2-(ω-methylthio)alkylmalate dehydratase
EC 4.2.1.171 cis-L-3-hydroxyproline dehydratase
EC 4.2.1.172 trans-4-hydroxy-L-proline dehydratase
EC 4.2.1.173 ent-8α-hydroxylabd-13-en-15-yl diphosphate synthase
EC 4.2.1.174 peregrinol diphosphate synthase

Entries

EC 4.2.1.101

Accepted name: trans-feruloyl-CoA hydratase

Reaction: 4-hydroxy-3-methoxyphenyl-β-hydroxypropanoyl-CoA = feruloyl-CoA + H2O

Other name(s): trans-feruloyl-CoA hydro-lyase (incorrect); 4-hydroxy-3-methoxyphenyl-β-hydroxypropanoyl-CoA hydro-lyase (trans-feruloyl-CoA-forming)

Systematic name: 4-hydroxy-3-methoxyphenyl-β-hydroxypropanoyl-CoA hydro-lyase (feruloyl-CoA-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 197462-62-7

References:

1. Narbad, A. and Gasson, M.J. Metabolism of ferulic acid via vanillin using a novel CoA-dependent pathway in a newly-isolated strain of Pseudomonas fluorescens. Microbiology 144 (1998) 1397-1405. [PMID: 9611814]

2. Pometto, A.L. and Crawford, D.L. Whole-cell bioconversion of vanillin to vanillic acid by Streptomyces viridosporus. Appl. Environ. Microbiol. 45 (1983) 1582-1585. [PMID: 6870241]

[EC 4.2.1.101 created 2000]

[EC 4.2.1.102 Transferred entry: now EC 4.2.1.100 cyclohexa-1,5-diene-1-carbonyl-CoA hydratase (EC 4.2.1.102 created 2001, deleted 2001)]

EC 4.2.1.103

Accepted name: cyclohexyl-isocyanide hydratase

Reaction: N-cyclohexylformamide = cyclohexyl isocyanide + H2O

Other name(s): isonitrile hydratase; N-cyclohexylformamide hydro-lyase

Systematic name: N-cyclohexylformamide hydro-lyase (cyclohexyl-isocyanide-forming)

Comments: The enzyme from Pseudomonas putida strain N19-2 can also catalyse the hydration of other isonitriles to the corresponding N-substituted formamides. The enzyme has no metal requirements.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, UM-BBD, CAS registry number: 358974-06-8

References:

1. Goda, M., Hashimoto, Y., Shimizu, S. and Kobayashi, M. Discovery of a novel enzyme, isonitrile hydratase, involved in nitrogen-carbon triple bond cleavage. J. Biol. Chem. 276 (2001) 23480-23485. [PMID: 11306561]

[EC 4.2.1.103 created 2001]

EC 4.2.1.104

Accepted name: cyanase

Reaction: cyanate + HCO3 + 2 H+ = NH3 + 2 CO2 (overall reaction)
(1a) cyanate + HCO3 + H+ = carbamate + CO2
(1b) carbamate + H+ = NH3 + CO2 (spontaneous)

For diagram click here.

Glossary: cyanate = NCO-
carbamate = H2N-CO-O-

Other name(s): cyanate lyase; cyanate hydrolase; cyanase; cyanate aminohydrolase; cyanate C-N-lyase; cyanate hydratase

Systematic name: carbamate hydro-lyase

Comments: This enzyme, which is found in bacteria and plants, is used to decompose cyanate, which can be used as the sole source of nitrogen [6,7]. Reaction (1) can be considered as the reverse of 'carbamate = cyanate + H2O', where this is assisted by reaction with bicarbonate and carbon dioxide (see mechanism above) [2], and hence is classified in sub-subclass 4.2.1. Bicarbonate functions as a recycling substrate [2].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, UM-BBD, CAS registry number: 37289-24-0

References:

1. Anderson, P.M. Purification and properties of the inducible enzyme cyanase. Biochemistry 19 (1980) 2882-2888. [PMID: 6994799]

2. Johnson, W.V. and Anderson, P.M. Bicarbonate is a recycling substrate for cyanase. J. Biol. Chem. 262 (1987) 9021-9025. [PMID: 3110153]

3. Taussig, A. The synthesis of the induced enzyme, "cyanase", in E. coli. Biochim. Biophys. Acta 44 (1960) 510-519. [PMID: 13775509]

4. Taussig, A. Some properties of the induced enzyme cyanase. Can. J. Biochem. 43 (1965) 1063-1069. [PMID: 5322950]

5. Anderson, P.M., Korte, J.J. and Holcomb, T.A. Reaction of the N-terminal methionine residues in cyanase with diethylpyrocarbonate. Biochemistry 33 (1994) 14121-14125. [PMID: 7947823]

6. Kozliak, E.I., Fuchs, J.A., Guilloton, M.B. and Anderson, P.M. Role of bicarbonate/CO2 in the inhibition of Escherichia coli growth by cyanate. J. Bacteriol. 177 (1995) 3213-3219. [PMID: 7768821]

7. Walsh, M.A., Otwinowski, Z., Perrakis, A., Anderson, P.M. and Joachimiak, A. Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site. Structure 8 (2000) 505-514. [PMID: 10801492]

[EC 4.2.1.104 created 1972 as EC 3.5.5.3, transferred 1990 to EC 4.3.99.1, transferred 2001 to EC 4.2.1.104, modified 2007]

EC 4.2.1.105

Accepted name: 2-hydroxyisoflavanone dehydratase

Reaction: (1) 2,4',7-trihydroxyisoflavanone = daidzein + H2O
(2) 2,4',5,7-tetrahydroxyisoflavanone = genistein + H2O

For diagram of reaction click here or click here.

Glossary: daidzein = 4',7-dihydroxyisoflavone
genistein = 4',5,7-dihydroxyisoflavone

Other name(s): 2,7,4'-trihydroxyisoflavanone hydro-lyase; 2,7,4'-trihydroxyisoflavanone hydro-lyase (daidzein-forming)

Systematic name: 2,4',7-trihydroxyisoflavanone hydro-lyase (daidzein-forming)

Comments: Catalyses the final step in the formation of the isoflavonoid skeleton. The reaction also occurs spontaneously.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 166800-10-8

References:

1. Hakamatsuka, T., Mori, K., Ishida, S., Ebizuka, Y and Sankawa, U. Purification of 2-hydroxyisoflavanone dehydratase from the cell cultures of Pueraria lobata. Phytochemistry 49 (1998) 497-505.

[EC 4.2.1.105 created 2004, modified 2013]

EC 4.2.1.106

Accepted name: bile-acid 7α-dehydratase

Reaction: 7α,12α-dihydroxy-3-oxochol-4-en-24-oyl-CoA = 12α-hydroxy-3-oxochola-4,6-dien-24-oyl-CoA + H2O

For diagram of reaction click here.

Other name(s): baiE (gene name); 7α,12α-dihydroxy-3-oxochol-4-enoate hydro-lyase; 7α,12α-dihydroxy-3-oxochol-4-enoate hydro-lyase (12α-hydroxy-3-oxochola-4,6-dienoate-forming)

Systematic name: 7α,12α-dihydroxy-3-oxochol-4-enoyl-CoA hydro-lyase (12α-hydroxy-3-oxochola-4,6-dienoyl-CoA-forming)

Comments: This enzyme, characterized from the gut bacterium Clostridium scindens (previously known as Eubacterium sp. strain VPI 12708), participates in the 7-dehydroxylation process associated with bile acid degradation.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Mallonee, D.H., White, W.B. and Hylemon, P.B. Cloning and sequencing of a bile acid-inducible operon from Eubacterium sp. strain VPI 12708. J. Bacteriol. 172 (1990) 7011-7019. [PMID: 2254270]

2. Dawson, J.A., Mallonee, D.H., Björkhem, I. and Hylemon, P.B. Expression and characterization of a C24 bile acid 7α-dehydratase from Eubacterium sp. strain VPI 12708 in Escherichia coli. J. Lipid Res. 37 (1996) 1258-1267. [PMID: 8808760]

3. Bhowmik, S., Chiu, H.P., Jones, D.H., Chiu, H.J., Miller, M.D., Xu, Q., Farr, C.L., Ridlon, J.M., Wells, J.E., Elsliger, M.A., Wilson, I.A., Hylemon, P.B. and Lesley, S.A. Structure and functional characterization of a bile acid 7α dehydratase BaiE in secondary bile acid synthesis. Proteins 84 (2016) 316-331. [PMID: 26650892]

[EC 4.2.1.106 created 2005, modified 2016]

EC 4.2.1.107

Accepted name: 3α,7α,12α-trihydroxy-5β-cholest-24-enoyl-CoA hydratase

Reaction: (24R,25R)-3α,7α,12α,24-tetrahydroxy-5β-cholestanoyl-CoA = (24E)-3α,7α,12α-trihydroxy-5β-cholest-24-enoyl-CoA + H2O

For diagram click here.

Other name(s): 46 kDa hydratase 2; (24R,25R)-3α,7α,12α,24-tetrahydroxy-5β-cholestanoyl-CoA hydro-lyase

Systematic name: (24R,25R)-3α,7α,12α,24-tetrahydroxy-5β-cholestanoyl-CoA hydro-lyase [(24E)-3α,7α,12α-trihydroxy-5β-cholest-24-enoyl-CoA-forming]

Comments: This enzyme forms part of the rat peroxisomal multifunctional enzyme perMFE-2, which also exhibits a dehydrogenase activity. The enzyme is involved in the β-oxidation of the cholesterol side chain in the cholic-acid-biosynthesis pathway.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 152787-68-3

References:

1. Qin, Y.M., Haapalainen, A.M., Conry, D., Cuebas, D.A., Hiltunen, J.K. and Novikov, D.K. Recombinant 2-enoyl-CoA hydratase derived from rat peroxisomal multifunctional enzyme 2: role of the hydratase reaction in bile acid synthesis. Biochem. J. 328 (1997) 377-382. [PMID: 9371691]

2. Xu, R. and Cuebas, D.A. The reactions catalyzed by the inducible bifunctional enzyme of rat liver peroxisomes cannot lead to the formation of bile acids. Biochem. Biophys. Res. Commun. 221 (1996) 271-278. [PMID: 8619845]

3. Kinoshita, T., Miyata, M., Ismail, S.M., Fujimoto, Y., Kakinuma, K., Kokawa, N.I. and Morisaki, M. Synthesis and determination of stereochemistry of four diastereoisomers at the C-24 and C-25 positions of 3α,7α,12α,24-tetrahydroxy-5β-cholestan-26-oic acid and cholic acid. Chem. Pharm. Bull. 36 (1988) 134-141.

4. Fujimoto, Y., Kinoshita, T., Oya, I., Kakinuma, K., Ismail, S.M., Sonoda, Y., Sato, Y. and Morisaki, M. Non-stereoselective conversion of the four diastereoisomers at the C-24 and C-25 positions of 3α,7α,12α,24-tetrahydroxy-5β-cholestan-26-oic acid and cholic acid. Chem. Pharm. Bull. 36 (1988) 142-145.

5. Kurosawa, T., Sato, M., Nakano, H., Fujiwara, M., Murai, T., Yoshimura, T. and Hashimoto, T. Conjugation reactions catalyzed by bifunctional proteins related to β-oxidation in bile acid biosynthesis. Steroids 66 (2001) 107-114. [PMID: 11146090]

6. Russell, D.W. The enzymes, regulation, and genetics of bile acid synthesis. Annu. Rev. Biochem. 72 (2003) 137-174. [PMID: 12543708]

[EC 4.2.1.107 created 2005]

EC 4.2.1.108

Accepted name: ectoine synthase

Reaction: (2S)-4-acetamido-2-aminobutanoate = L-ectoine + H2O

For diagram of reaction click here.

Glossary: ectoine = (4S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylate

Other name(s): ectC (gene name); N-acetyldiaminobutyrate dehydratase; N-acetyldiaminobutanoate dehydratase; L-ectoine synthase; 4-N-acetyl-L-2,4-diaminobutanoate hydro-lyase (L-ectoine-forming); N4-acetyl-L-2,4-diaminobutanoate hydro-lyase (L-ectoine-forming)

Systematic name: (2S)-4-acetamido-2-aminobutanoate (L-ectoine-forming)

Comments: Ectoine is an osmoprotectant that is found in halophilic eubacteria. This enzyme is part of the ectoine biosynthesis pathway and only acts in the direction of ectoine formation. cf. EC 3.5.4.44, ectoine hydrolase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Peters, P., Galinski, E.A. and Truper, H.G. The biosynthesis of ectoine. FEMS Microbiol. Lett. 71 (1990) 157-162.

2. Ono, H., Sawada, K., Khunajakr, N., Tao, T., Yamamoto, M., Hiramoto, M., Shinmyo, A., Takano, M. and Murooka, Y. Characterization of biosynthetic enzymes for ectoine as a compatible solute in a moderately halophilic eubacterium, Halomonas elongata. J. Bacteriol. 181 (1999) 91-99. [PMID: 9864317]

3. Kuhlmann, A.U. and Bremer, E. Osmotically regulated synthesis of the compatible solute ectoine in Bacillus pasteurii and related Bacillus spp. Appl. Environ. Microbiol. 68 (2002) 772-783. [PMID: 11823218]

4. Louis, P. and Galinski, E.A. Characterization of genes for the biosynthesis of the compatible solute ectoine from Marinococcus halophilus and osmoregulated expression in Escherichia coli. Microbiology 143 (1997) 1141-1149. [PMID: 9141677]

5. Schwibbert, K., Marin-Sanguino, A., Bagyan, I., Heidrich, G., Lentzen, G., Seitz, H., Rampp, M., Schuster, S.C., Klenk, H.P., Pfeiffer, F., Oesterhelt, D. and Kunte, H.J. A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581 T. Environ. Microbiol. 13 (2011) 1973-1994. [PMID: 20849449]

[EC 4.2.1.108 created 2006, modified 2017]

EC 4.2.1.109

Accepted name: methylthioribulose 1-phosphate dehydratase

Reaction: S-methyl-5-thio-D-ribulose 1-phosphate = 5-(methylthio)-2,3-dioxopentyl phosphate + H2O

For diagram click here.

Other name(s): 1-PMT-ribulose dehydratase; S-methyl-5-thio-D-ribulose-1-phosphate hydro-lyase

Systematic name: S-methyl-5-thio-D-ribulose-1-phosphate 4-hydro-lyase [5-(methylthio)-2,3-dioxopentyl-phosphate-forming]

Comments: This enzyme forms part of the methionine-salvage pathway.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 1114239-22-3

References:

1. Furfine, E.S. and Abeles, R.H. Intermediates in the conversion of 5'-S-methylthioadenosine to methionine in Klebsiella pneumoniae. J. Biol. Chem. 263 (1988) 9598-9606. [PMID: 2838472]

2. Wray, J.W. and Abeles, R.H. The methionine salvage pathway in Klebsiella pneumoniae and rat liver. Identification and characterization of two novel dioxygenases. J. Biol. Chem. 270 (1995) 3147-3153. [PMID: 7852397]

[EC 4.2.1.109 created 2006]

EC 4.2.1.110

Accepted name: aldos-2-ulose dehydratase

Reaction: 1,5-anhydro-D-fructose = 2-hydroxy-2-(hydroxymethyl)-2H-pyran-3(6H)-one + H2O (overall reaction)
(1a) 1,5-anhydro-D-fructose = 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose + H2O
(1b) 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose = 2-hydroxy-2-(hydroxymethyl)-2H-pyran-3(6H)-one

For diagram click here.

Glossary: 1,5-anhydro-D-fructose = 1,5-anhydro-D-arabino-hex-2-ulose = (4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)dihydro-2H-pyran-3(4H)-one
ascopyrone M = 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose = (6S)-4-hydroxy-6-(hydroxymethyl)-2H-pyran-3(6H)-one
microthecin = 2-hydroxy-2-(hydroxymethyl)-2H-pyran-3(6H)-one

Other name(s): pyranosone dehydratase; AUDH; 1,5-anhydro-D-fructose dehydratase (microthecin-forming)

Systematic name: 1,5-anhydro-D-fructose hydro-lyase (microthecin-forming)

Comments: This enzyme catalyses two of the steps in the anhydrofructose pathway, which leads to the degradation of glycogen and starch via 1,5-anhydro-D-fructose [1,2]. The other enzymes involved in this pathway are EC 4.2.1.111 (1,5-anhydro-D-fructose dehydratase), EC 4.2.2.13 (exo-(1→4)-α-D-glucan lyase) and EC 5.3.2.7 (ascopyrone tautomerase). Aldose-2-uloses such as 2-dehydroglucose can also act as substrates, but more slowly [1,2,4]. This is a bifunctional enzyme that acts as both a lyase and as an isomerase [2]. Differs from EC 4.2.1.111, which can carry out only reaction (1a) and requires a cofactor for activity [5].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, UM-BBD, CAS registry number: 101920-80-3

References:

1. Yu, S. and Fiskesund, R. The anhydrofructose pathway and its possible role in stress response and signaling. Biochim. Biophys. Acta 1760 (2006) 1314-1322. [PMID: 16822618]

2. Yu, S. Enzymatic description of the anhydrofructose pathway of glycogen degradation. II. Gene identification and characterization of the reactions catalyzed by aldos-2-ulose dehydratase that converts 1,5-anhydro-D-fructose to microthecin with ascopyrone M as the intermediate. Biochim. Biophys. Acta 1723 (2005) 63-73. [PMID: 15716041]

3. Broberg, A., Kenne, L. and Pedersén, M. Presence of microthecin in the red alga Gracilariopsis lemaneiformis and its formation from 1,5-anhydro-D-fructose. Phytochemistry 41 (1996) 151-154.

4. Gabriel, J., Volc, J., Sedmera, P., Daniel, G. and Kubátová, E. Pyranosone dehydratase from the basidiomycete Phanerochaete chrysosporium: improved purification, and identification of 6-deoxy-D-glucosone and D-xylosone reaction products. Arch. Microbiol. 160 (1993) 27-34. [PMID: 8352649]

5. Yu, S., Refdahl, C. and Lundt, I. Enzymatic description of the anhydrofructose pathway of glycogen degradation; I. Identification and purification of anhydrofructose dehydratase, ascopyrone tautomerase and α-1,4-glucan lyase in the fungus Anthracobia melaloma. Biochim. Biophys. Acta 1672 (2004) 120-129. [PMID: 15110094]

[EC 4.2.1.110 created 2006]

EC 4.2.1.111

Accepted name: 1,5-anhydro-D-fructose dehydratase

Reaction: 1,5-anhydro-D-fructose = 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose + H2O

For diagram click here.

Glossary: 1,5-anhydro-D-fructose = 1,5-anhydro-D-arabino-hex-2-ulose = (4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)dihydro-2H-pyran-3(4H)-one
ascopyrone M = 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose = (6S)-4-hydroxy-6-(hydroxymethyl)-2H-pyran-3(6H)-one

Other name(s): 1,5-anhydro-D-fructose 4-dehydratase; 1,5-anhydro-D-fructose hydrolyase; 1,5-anhydro-D-arabino-hex-2-ulose dehydratase; AFDH; AF dehydratase; 1,5-anhydro-D-fructose hydro-lyase

Systematic name: 1,5-anhydro-D-fructose hydro-lyase (ascopyrone-M-forming)

Comments: This enzyme catalyses one of the steps in the anhydrofructose pathway, which leads to the degradation of glycogen and starch via 1,5-anhydro-D-fructose [1,2]. The other enzymes involved in this pathway are EC 4.2.1.110 (aldos-2-ulose dehydratase), EC 4.2.2.13 [exo-(1→4)-α-D-glucan lyase] and EC 5.3.2.7 (ascopyrone tautomerase). Requires divalent (Ca2+ or Mg2+) or monovalent cations (Na+) for optimal activity. Unlike EC 4.2.1.110, aldos-2-ulose dehydratase, the enzyme is specific for 1,5-anhydro-D-fructose as substrate and shows no activity towards aldose-2-uloses such as 2-dehydroglucose [1,2,3]. In addition, it is inhibited by its end-product ascopyrone M [2] and it cannot convert ascopyrone M into microthecin, as can EC 4.2.1.110.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, UM-BBD, CAS registry number:

References:

1. Yu, S., Refdahl, C. and Lundt, I. Enzymatic description of the anhydrofructose pathway of glycogen degradation; I. Identification and purification of anhydrofructose dehydratase, ascopyrone tautomerase and α-1,4-glucan lyase in the fungus Anthracobia melaloma. Biochim. Biophys. Acta 1672 (2004) 120-129. [PMID: 15110094]

2. Yu, S. and Fiskesund, R. The anhydrofructose pathway and its possible role in stress response and signaling. Biochim. Biophys. Acta 1760 (2006) 1314-1322. [PMID: 16822618]

3. Yu, S. Enzymatic description of the anhydrofructose pathway of glycogen degradation. II. Gene identification and characterization of the reactions catalyzed by aldos-2-ulose dehydratase that converts 1,5-anhydro-D-fructose to microthecin with ascopyrone M as the intermediate. Biochim. Biophys. Acta 1723 (2005) 63-73. [PMID: 15716041]

[EC 4.2.1.111 created 2006]

EC 4.2.1.112

Accepted name: acetylene hydratase

Reaction: acetaldehyde = acetylene + H2O

Other name(s): AH; acetaldehyde hydro-lyase

Systematic name: acetaldehyde hydro-lyase (acetylene-forming)

Comments: This is a non-redox-active enzyme that contains two molybdopterin guanine dinucleotide (MGD) cofactors, a tungsten centre and a cubane type [4Fe-4S] cluster [2]. The tungsten centre binds a water molecule that is activated by an adjacent aspartate residue, enabling it to attack acetylene bound in a distinct hydrophobic pocket [2]. Ethylene cannot act as a substrate [1].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, UM-BBD, CAS registry number: 75788-81-7

References:

1. Rosner, B.M. and Schink, B. Purification and characterization of acetylene hydratase of Pelobacter acetylenicus, a tungsten iron-sulfur protein. J. Bacteriol. 177 (1995) 5767-5772. [PMID: 7592321]

2. Seiffert, G.B., Ullmann, G.M., Messerschmidt, A., Schink, B., Kroneck, P.M. and Einsle, O. Structure of the non-redox-active tungsten/[4Fe:4S] enzyme acetylene hydratase. Proc. Natl. Acad. Sci. USA 104 (2007) 3073-3077. [PMID: 17360611]

[EC 4.2.1.112 created 2007]

EC 4.2.1.113

Accepted name: o-succinylbenzoate synthase

Reaction: (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate = 2-succinylbenzoate + H2O

For diagram click here.

Glossary: 2-succinylbenzoate = o-succinylbenzoate = 4-(2-carboxyphenyl)-4-oxobutanoate

Other name(s): o-succinylbenzoic acid synthase; OSB synthase; OSBS; 2-succinylbenzoate synthase; MenC

Systematic name: (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate hydro-lyase (2-succinylbenzoate-forming)

Comments: Belongs to the enolase superfamily and requires divalent cations, preferably Mg2+ or Mn2+, for activity. Forms part of the vitamin-K-biosynthesis pathway.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Sharma, V., Meganathan, R. and Hudspeth, M.E. Menaquinone (vitamin K2) biosynthesis: cloning, nucleotide sequence, and expression of the menC gene from Escherichia coli. J. Bacteriol. 175 (1993) 4917-4921. [PMID: 8335646]

2. Klenchin, V.A., Taylor Ringia, E.A., Gerlt, J.A. and Rayment, I. Evolution of enzymatic activity in the enolase superfamily: structural and mutagenic studies of the mechanism of the reaction catalyzed by o-succinylbenzoate synthase from Escherichia coli. Biochemistry 42 (2003) 14427-14433. [PMID: 14661953]

3. Palmer, D.R., Garrett, J.B., Sharma, V., Meganathan, R., Babbitt, P.C. and Gerlt, J.A. Unexpected divergence of enzyme function and sequence: "N-acylamino acid racemase" is o-succinylbenzoate synthase. Biochemistry 38 (1999) 4252-4258. [PMID: 10194342]

4. Thompson, T.B., Garrett, J.B., Taylor, E.A., Meganathan, R., Gerlt, J.A. and Rayment, I. Evolution of enzymatic activity in the enolase superfamily: structure of o-succinylbenzoate synthase from Escherichia coli in complex with Mg2+ and o-succinylbenzoate. Biochemistry 39 (2000) 10662-10676. [PMID: 10978150]

5. Taylor Ringia, E.A., Garrett, J.B., Thoden, J.B., Holden, H.M., Rayment, I. and Gerlt, J.A. Evolution of enzymatic activity in the enolase superfamily: functional studies of the promiscuous o-succinylbenzoate synthase from Amycolatopsis. Biochemistry 43 (2004) 224-229. [PMID: 14705949]

[EC 4.2.1.113 created 2007]

EC 4.2.1.114

Accepted name: methanogen homoaconitase

Reaction: (R)-2-hydroxybutane-1,2,4-tricarboxylate + H2O = (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate (overall reaction)
(1a) (R)-2-hydroxybutane-1,2,4-tricarboxylate = (Z)-but-1-ene-1,2,4-tricarboxylate + H2O
(1b) (Z)-but-1-ene-1,2,4-tricarboxylate + H2O = (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate

Glossary: cis-homoaconitate = (Z)-but-1-ene-1,2,4-tricarboxylate
(R)-homocitrate = (R)-2-hydroxybutane-1,2,4-tricarboxylate
homoisocitrate = (–)-threo-homoisocitrate = (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate

Other name(s): methanogen HACN

Systematic name: (R)-2-hydroxybutane-1,2,4-tricarboxylate hydro-lyase [(1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate-forming]

Comments: This enzyme catalyses several reactions in the pathway of coenzyme-B biosynthesis in methanogenic archaea. Requires a [4Fe-4S] cluster for activity. In contrast to EC 4.2.1.36, homoaconitate hydratase, this enzyme can catalyse both the dehydration of (R)-homocitrate to form cis-homoaconitate and the subsequent hydration reaction that forms homoisocitrate. In addition to cis-homoaconitate, the enzyme can also catalyse the hydration of the physiological substrates dihomocitrate and trihomocitrate as well as the non-physiological substrate tetrahomocitrate. cis-Aconitate and threo-DL-isocitrate cannot act as substrates, and (S)-homocitrate and trans-homoaconitate act as inhibitors of the enzyme.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Drevland, R.M., Jia, Y., Palmer, D.R. and Graham, D.E. Methanogen homoaconitase catalyzes both hydrolyase reactions in coenzyme B biosynthesis. J. Biol. Chem. 283 (2008) 28888-28896. [PMID: 18765671]

[EC 4.2.1.114 created 2009]

EC 4.2.1.115

Accepted name: UDP-N-acetylglucosamine 4,6-dehydratase (inverting)

Reaction: UDP-N-acetyl-α-D-glucosamine = UDP-2-acetamido-2,6-dideoxy-β-L-arabino-hex-4-ulose + H2O

For diagram of reaction click here and mechanism click here.

Glossary: pseudaminic acid = 5,7-bis(acetylamino)-3,5,7,9-tetradeoxy-L-glycero-α-L-manno-2-nonulopyranosonic acid

Other name(s): FlaA1; UDP-N-acetylglucosamine 5-inverting 4,6-dehydratase; PseB; UDP-N-acetylglucosamine hydro-lyase (inverting; UDP-2-acetamido-2,6-dideoxy-β-L-arabino-hex-4-ulose-forming)

Systematic name: UDP-N-acetyl-α-D-glucosamine hydro-lyase (inverting; UDP-2-acetamido-2,6-dideoxy-β-L-arabino-hex-4-ulose-forming)

Comments: Contains NADP+ as a cofactor. This is the first enzyme in the biosynthetic pathway of pseudaminic acid [3], a sialic-acid-like sugar that is unique to bacteria and is used by Helicobacter pylori to modify its flagellin. This enzyme plays a critical role in H. pylori's pathogenesis, being involved in the synthesis of both functional flagella and lipopolysaccharides [1,2]. It is completely inhibited by UDP-galactose. The reaction results in the chirality of the C-5 atom being inverted. It is thought that Lys-133 acts sequentially as a catalytic acid, protonating the C-6 hydroxy group and as a catalytic base, abstracting the C-5 proton, resulting in the elimination of water. This enzyme belongs to the short-chain dehydrogenase/reductase family of enzymes.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Ishiyama, N., Creuzenet, C., Miller, W.L., Demendi, M., Anderson, E.M., Harauz, G., Lam, J.S. and Berghuis, A.M. Structural studies of FlaA1 from Helicobacter pylori reveal the mechanism for inverting 4,6-dehydratase activity. J. Biol. Chem. 281 (2006) 24489-24495. [PMID: 16651261]

2. Schirm, M., Soo, E.C., Aubry, A.J., Austin, J., Thibault, P. and Logan, S.M. Structural, genetic and functional characterization of the flagellin glycosylation process in Helicobacter pylori. Mol. Microbiol. 48 (2003) 1579-1592. [PMID: 12791140]

3. Schoenhofen, I.C., McNally, D.J., Brisson, J.R. and Logan, S.M. Elucidation of the CMP-pseudaminic acid pathway in Helicobacter pylori: synthesis from UDP-N-acetylglucosamine by a single enzymatic reaction. Glycobiology 16 (2006) 8C-14C. [PMID: 16751642]

[EC 4.2.1.115 created 2009]

EC 4.2.1.116

Accepted name: 3-hydroxypropionyl-CoA dehydratase

Reaction: 3-hydroxypropanoyl-CoA = acryloyl-CoA + H2O

For diagram of reaction click here (another example and anther example.

Glossary: acryloyl-CoA = acrylyl-CoA
3-hydroxypropanoyl-CoA = 3-hydroxypropionyl-CoA

Other name(s): 3-hydroxypropionyl-CoA hydro-lyase; 3-hydroxypropanoyl-CoA dehydratase

Systematic name: 3-hydroxypropanoyl-CoA hydro-lyase

Comments: Catalyses a step in the 3-hydroxypropanoate/4-hydroxybutanoate cycle, an autotrophic CO2 fixation pathway found in some thermoacidophilic archaea [1]. The enzyme from Metallosphaera sedula acts nearly equally as well on (S)-3-hydroxybutanoyl-CoA but not (R)-3-hydroxybutanoyl-CoA [2].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Berg, I.A., Kockelkorn, D., Buckel, W. and Fuchs, G. A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318 (2007) 1782-1786. [PMID: 18079405]

2. Teufel, R., Kung, J.W., Kockelkorn, D., Alber, B.E. and Fuchs, G. 3-hydroxypropionyl-coenzyme A dehydratase and acryloyl-coenzyme A reductase, enzymes of the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle in the Sulfolobales. J. Bacteriol. 191 (2009) 4572-4581. [PMID: 19429610]

[EC 4.2.1.116 created 2009]

EC 4.2.1.117

Accepted name: 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming)

Reaction: (2S,3S)-2-methylcitrate = 2-methyl-trans-aconitate + H2O

Glossary: (2S,3S)-2-methylcitrate = (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate
2-methyl-trans-aconitate = (2E)-but-2-ene-1,2,3-tricarboxylate

Systematic name: (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate hydro-lyase (2-methyl-trans-aconitate forming)

Comments: Catalyses the dehydration of (2S,3S)-2-methylcitrate, forming the trans isomer of 2-methyl-aconitate (unlike EC 4.2.1.79, which forms only the cis isomer). Part of a propionate degradation pathway. The enzyme from Shewanella oneidensis can also accept citrate and cis-aconitate, but activity with (2S,3S)-2-methylcitrate was approximately 2.5-fold higher. 2-methylisocitrate and isocitrate were not substrates [1]. An iron-sulfur protein.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Grimek, T.L. and Escalante-Semerena, J.C. The acnD genes of Shewenella oneidensis and Vibrio cholerae encode a new Fe/S-dependent 2-methylcitrate dehydratase enzyme that requires prpF function in vivo. J. Bacteriol. 186 (2004) 454-462. [PMID: 14702315]

[EC 4.2.1.117 created 2009]

EC 4.2.1.118

Accepted name: 3-dehydroshikimate dehydratase

Reaction: 3-dehydro-shikimate = protocatechuate + H2O

Systematic name: 3-dehydroshikimate hydro-lyase

Comments: Catalyses an early step in the biosynthesis of petrobactin, a siderophore produced by many bacteria, including the human pathogen Bacillus anthracis. Requires divalent ions, with a preference for Mn2+.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Fox, D.T., Hotta, K., Kim, C.Y. and Koppisch, A.T. The missing link in petrobactin biosynthesis: asbF encodes a (–)-3-dehydroshikimate dehydratase. Biochemistry 47 (2008) 12251-12253. [PMID: 18975921]

2. Pfleger, B.F., Kim, Y., Nusca, T.D., Maltseva, N., Lee, J.Y., Rath, C.M., Scaglione, J.B., Janes, B.K., Anderson, E.C., Bergman, N.H., Hanna, P.C., Joachimiak, A. and Sherman, D.H. Structural and functional analysis of AsbF: origin of the stealth 3,4-dihydroxybenzoic acid subunit for petrobactin biosynthesis. Proc. Natl. Acad. Sci. USA 105 (2008) 17133-17138. [PMID: 18955706]

[EC 4.2.1.118 created 2009]

EC 4.2.1.119

Accepted name: enoyl-CoA hydratase 2

Reaction: (3R)-3-hydroxyacyl-CoA = (2E)-2-enoyl-CoA + H2O

For diagram of reaction click here.

Other name(s): 2-enoyl-CoA hydratase 2; AtECH2; ECH2; MaoC; MFE-2; PhaJAc; D-3-hydroxyacyl-CoA hydro-lyase; D-specific 2-trans-enoyl-CoA hydratase

Systematic name: (3R)-3-hydroxyacyl-CoA hydro-lyase

Comments: This enzyme catalyses a hydration step in peroxisomal β-oxidation. The human multifunctional enzyme type 2 (MFE-2) is a 79000 Da enzyme composed of three functional units: (3R)-hydroxyacyl-CoA dehydrogenase, 2-enoyl-CoA hydratase 2 and sterol carrier protein 2-like units [1]. The enzymes from Aeromonas caviae [4] and Arabidopsis thaliana [5] are monofunctional enzymes. 2-Enoyl-CoA hydratase 3 from Candida tropicalis is a part from multifunctional enzyme type 2 [3].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Koski, K.M., Haapalainen, A.M., Hiltunen, J.K. and Glumoff, T. Crystal structure of 2-enoyl-CoA hydratase 2 from human peroxisomal multifunctional enzyme type 2. J. Mol. Biol. 345 (2005) 1157-1169. [PMID: 15644212]

2. Fukui, T., Shiomi, N. and Doi, Y. Expression and characterization of (R)-specific enoyl coenzyme A hydratase involved in polyhydroxyalkanoate biosynthesis by Aeromonas caviae. J. Bacteriol. 180 (1998) 667-673. [PMID: 9457873]

3. Koski, M.K., Haapalainen, A.M., Hiltunen, J.K. and Glumoff, T. Crystallization and preliminary crystallographic data of 2-enoyl-CoA hydratase 2 domain of Candida tropicalis peroxisomal multifunctional enzyme type 2. Acta Crystallogr. D Biol. Crystallogr. 59 (2003) 1302-1305. [PMID: 12832794]

4. Hisano, T., Fukui, T., Iwata, T. and Doi, Y. Crystallization and preliminary X-ray analysis of (R)-specific enoyl-CoA hydratase from Aeromonas caviae involved in polyhydroxyalkanoate biosynthesis. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 145-147. [PMID: 11134939]

5. Goepfert, S., Hiltunen, J.K. and Poirier, Y. Identification and functional characterization of a monofunctional peroxisomal enoyl-CoA hydratase 2 that participates in the degradation of even cis-unsaturated fatty acids in Arabidopsis thaliana. J. Biol. Chem. 281 (2006) 35894-35903. [PMID: 16982622]

6. Engeland, K. and Kindl, H. Evidence for a peroxisomal fatty acid β-oxidation involving D-3-hydroxyacyl-CoAs. Characterization of two forms of hydro-lyase that convert D-(–)-3-hydroxyacyl-CoA into 2-trans-enoyl-CoA. Eur. J. Biochem. 200 (1991) 171-178. [PMID: 1879422]

[EC 4.2.1.119 created 2009]

EC 4.2.1.120

Accepted name: 4-hydroxybutanoyl-CoA dehydratase

Reaction: 4-hydroxybutanoyl-CoA = (E)-but-2-enoyl-CoA + H2O

For diagram of reaction click here.

Glossary: 4-hydroxybutanoyl-CoA = 4-hydroxybutyryl-CoA
(E)-but-2-enoyl-CoA = crotonyl-CoA

Systematic name: 4-hydroxybutanoyl-CoA hydro-lyase

Comments: Contains FAD and a [4Fe-4S] iron-sulfur cluster. The enzyme has been characterized from several microorganisms, including Clostridium kluyveri, where it participates in succinate fermentation [1,2], Clostridium aminobutyricum, where it participates in 4-aminobutyrate degradation [3,4], and Metallosphaera sedula, where it participates in the 3-hydroxypropionate/4-hydroxybutyrate cycle, an autotrophic CO2 fixation pathway found in some thermoacidophilic archaea [5].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Bartsch, R.G. and Barker, H.A. A vinylacetyl isomerase from Clostridium kluyveri. Arch. Biochem. Biophys. 92 (1961) 122-132. [PMID: 13687513]

2. Scherf, U., Sohling, B., Gottschalk, G., Linder, D. and Buckel, W. Succinate-ethanol fermentation in Clostridium kluyveri: purification and characterisation of 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA Δ32-isomerase. Arch. Microbiol. 161 (1994) 239-245. [PMID: 8161284]

3. Scherf, U. and Buckel, W. Purification and properties of an iron-sulfur and FAD-containing 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA Δ32-isomerase from Clostridium aminobutyricum. Eur. J. Biochem. 215 (1993) 421-429. [PMID: 8344309]

4. Muh, U., Cinkaya, I., Albracht, S.P. and Buckel, W. 4-Hydroxybutyryl-CoA dehydratase from Clostridium aminobutyricum: characterization of FAD and iron-sulfur clusters involved in an overall non-redox reaction. Biochemistry 35 (1996) 11710-11718. [PMID: 8794752]

5. Berg, I.A., Kockelkorn, D., Buckel, W. and Fuchs, G. A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318 (2007) 1782-1786. [PMID: 18079405]

[EC 4.2.1.120 created 2009]

EC 4.2.1.121

Accepted name: colneleate synthase

Reaction: (9S,10E,12Z)-9-hydroperoxyoctadeca-10,12-dienoate = (8E)-9-[(1E,3Z)-nona-1,3-dien-1-yloxy]non-8-enoate + H2O

Glossary: colneleate = (8E)-9-[(1E,3Z)-nona-1,3-dien-1-yloxy]non-8-enoate

Other name(s): 9-divinyl ether synthase; 9-DES; CYP74D; CYP74D1; CYP74 cytochrome P-450; DES1; (8E)-9-[(1E,3E)-nona-1,3-dien-1-yloxy]non-8-enoate synthase

Systematic name: (9S,10E,12Z)-9-hydroperoxyoctadeca-10,12-dienoate hydro-lyase

Comments: A heme-thiolate protein (P-450) [2]. It catalyses the selective removal of pro-R hydrogen at C-8 in the biosynthesis of colneleic acid [4]. It forms also (8E)-9-[(1E,3Z,6Z)-nona-1,3,6-trien-1-yloxy]non-8-enoic acid (i.e. colnelenate) from (9S,10E,12Z,15Z)-9-hydroperoxy-10,12,15-octadecatrienoate. The corresponding 13-hydroperoxides are poor substrates [1,3]. The divinyl ethers colneleate and colnelenate have antimicrobial activity.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Stumpe, M., Kandzia, R., Gobel, C., Rosahl, S. and Feussner, I. A pathogen-inducible divinyl ether synthase (CYP74D) from elicitor-treated potato suspension cells. FEBS Lett. 507 (2001) 371-376. [PMID: 11696374]

2. Itoh, A. and Howe, G.A. Molecular cloning of a divinyl ether synthase. Identification as a CYP74 cytochrome P-450. J. Biol. Chem. 276 (2001) 3620-3627. [PMID: 11060314]

3. Fammartino, A., Cardinale, F., Gobel, C., Mene-Saffrane, L., Fournier, J., Feussner, I. and Esquerre-Tugaye, M.T. Characterization of a divinyl ether biosynthetic pathway specifically associated with pathogenesis in tobacco. Plant Physiol. 143 (2007) 378-388. [PMID: 17085514]

4. Hamberg, M. Hidden stereospecificity in the biosynthesis of divinyl ether fatty acids. FEBS J. 272 (2005) 736-743. [PMID: 15670154]

[EC 4.2.1.121 created 2011, modified 2014]

EC 4.2.1.122

Accepted name: tryptophan synthase (indole-salvaging)

Reaction: L-serine + indole = L-tryptophan + H2O

Other name(s): tryptophan synthase β2

Systematic name: L-serine hydro-lyase [adding indole, L-tryptophan-forming]

Comments: Most mesophilic bacteria have a multimeric tryptophan synthase complex (EC 4.2.1.20) that forms L-tryptophan from L-serine and 1-C-(indol-3-yl)glycerol 3-phosphate via an indole intermediate. This intermediate, which is formed by the α subunits, is transferred in an internal tunnel to the β units, which convert it to tryptophan. In thermophilic organisms the high temperature enhances diffusion and causes the loss of indole. This enzyme, which does not combine with the α unit to form a complex, salvages the lost indole back to L-tryptophan. It has a much lower Km for indole than the β subunit of EC 4.2.1.20.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Hettwer, S. and Sterner, R. A novel tryptophan synthase β-subunit from the hyperthermophile Thermotoga maritima. Quaternary structure, steady-state kinetics, and putative physiological role. J. Biol. Chem. 277 (2002) 8194-8201. [PMID: 11756459]

[EC 4.2.1.122 created 2011]

EC 4.2.1.123

Accepted name: tetrahymanol synthase

Reaction: tetrahymanol = squalene + H2O

For diagram of reaction click here.

Glossary: tetrahymanol = gammaceran-3β-ol

Other name(s): squalene–tetrahymanol cyclase

Systematic name: squalene hydro-lyase (tetrahymanol forming)

Comments: The reaction occurs in the reverse direction.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Saar, J., Kader, J.C., Poralla, K. and Ourisson, G. Purification and some properties of the squalene-tetrahymanol cyclase from Tetrahymena thermophila. Biochim. Biophys. Acta 1075 (1991) 93-101. [PMID: 1892870]

2. Giner, J.L., Rocchetti, S., Neunlist, S., Rohmer, M. and Arigoni, D. Detection of 1,2-hydride shifts in the formation of euph-7-ene by the squalene-tetrahymanol cyclase of Tetrahymena pyriformis. Chem. Commun. (Camb.) (2005) 3089-3091. [PMID: 15959594]

[EC 4.2.1.123 created 2011]

EC 4.2.1.124

Accepted name: arabidiol synthase

Reaction: arabidiol = (3S)-2,3-epoxy-2,3-dihydrosqualene + H2O

For diagram of reaction click here.

Glossary: arabidiol = (13R)-malabarica-17,21-diene-3β,14-diol

Other name(s): PEN1 (gene name); (S)-squalene-2,3-epoxide hydro-lyase (arabidiol forming)

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene hydro-lyase (arabidiol forming)

Comments: The reaction occurs in the reverse direction.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Xiang, T., Shibuya, M., Katsube, Y., Tsutsumi, T., Otsuka, M., Zhang, H., Masuda, K. and Ebizuka, Y. A new triterpene synthase from Arabidopsis thaliana produces a tricyclic triterpene with two hydroxyl groups. Org Lett 8 (2006) 2835-2838. [PMID: 16774269]

[EC 4.2.1.124 created 2011]

EC 4.2.1.125

Accepted name: dammarenediol II synthase

Reaction: dammarenediol II = (3S)-2,3-epoxy-2,3-dihydrosqualene + H2O

For diagram of reaction click here.

Other name(s): dammarenediol synthase; 2,3-oxidosqualene (20S)-dammarenediol cyclase; DDS; (S)-squalene-2,3-epoxide hydro-lyase (dammarenediol-II forming)

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene hydro-lyase (dammarenediol-II forming)

Comments: The reaction occurs in the reverse direction.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Tansakul, P., Shibuya, M., Kushiro, T. and Ebizuka, Y. Dammarenediol-II synthase, the first dedicated enzyme for ginsenoside biosynthesis, in Panax ginseng. FEBS Lett. 580 (2006) 5143-5149. [PMID: 16962103]

2. Han, J.Y., Kwon, Y.S., Yang, D.C., Jung, Y.R. and Choi, Y.E. Expression and RNA interference-induced silencing of the dammarenediol synthase gene in Panax ginseng. Plant Cell Physiol. 47 (2006) 1653-1662. [PMID: 17088293]

[EC 4.2.1.125 created 2011]

EC 4.2.1.126

Accepted name: N-acetylmuramic acid 6-phosphate etherase

Reaction: (R)-lactate + N-acetyl-D-glucosamine 6-phosphate = N-acetylmuramate 6-phosphate + H2O

Other name(s): MurNAc-6-P etherase; MurQ

Systematic name: (R)-lactate hydro-lyase (adding N-acetyl-D-glucosamine 6-phosphate; N-acetylmuramate 6-phosphate-forming)

Comments: This enzyme, along with EC 2.7.1.170, anhydro-N-acetylmuramic acid kinase, is required for the utilization of anhydro-N-acetylmuramic acid in proteobacteria. The substrate is either imported from the medium or derived from the bacterium's own cell wall murein during cell wall recycling.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:

References:

1. Jaeger, T., Arsic, M. and Mayer, C. Scission of the lactyl ether bond of N-acetylmuramic acid by Escherichia coli "etherase". J. Biol. Chem. 280 (2005) 30100-30106. [PMID: 15983044]

2. Uehara, T., Suefuji, K., Valbuena, N., Meehan, B., Donegan, M. and Park, J.T. Recycling of the anhydro-N-acetylmuramic acid derived from cell wall murein involves a two-step conversion to N-acetylglucosamine-phosphate. J. Bacteriol. 187 (2005) 3643-3649. [PMID: 15901686]

3. Uehara, T., Suefuji, K., Jaeger, T., Mayer, C. and Park, J.T. MurQ etherase is required by Escherichia coli in order to metabolize anhydro-N-acetylmuramic acid obtained either from the environment or from its own cell wall. J. Bacteriol. 188 (2006) 1660-1662. [PMID: 16452451]

4. Hadi, T., Dahl, U., Mayer, C. and Tanner, M.E. Mechanistic studies on N-acetylmuramic acid 6-phosphate hydrolase (MurQ): an etherase involved in peptidoglycan recycling. Biochemistry 47 (2008) 11547-11558. [PMID: 18837509]

5. Jaeger, T. and Mayer, C. N-acetylmuramic acid 6-phosphate lyases (MurNAc etherases): role in cell wall metabolism, distribution, structure, and mechanism. Cell. Mol. Life Sci. 65 (2008) 928-939. [PMID: 18049859]

[EC 4.2.1.126 created 2011]

EC 4.2.1.127

Accepted name: linalool dehydratase

Reaction: linalool = myrcene + H2O

For diagram click here.

Glossary: linalool = 3,7-dimethylocta-1,6-dien-3-ol

Other name(s): linalool hydro-lyase (myrcene-forming)

Systematic name: (3S)-linalool hydro-lyase (myrcene-forming)

Comments: In absence of oxygen the bifunctional linalool dehydratase-isomerase can catalyse in vitro two reactions, the hydration of myrcene to (3S)-linalool and the isomerization of (3S)-linalool to geraniol, the latter activity being classified as EC 5.4.4.4, geraniol isomerase.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Brodkorb, D., Gottschall, M., Marmulla, R., Lüddeke, F. and Harder, J. Linalool dehydratase-isomerase, a bifunctional enzyme in the anaerobic degradation of monoterpenes. J. Biol. Chem. 285 (2010) 30436-30442. [PMID: 20663876]

2. Lüddeke, F. and Harder, J. Enantiospecific (S)-(+)-linalool formation from β-myrcene by linalool dehydratase-isomerase. Z. Naturforsch. C 66 (2011) 409–412. [PMID: 21950166]

[EC 4.2.1.127 created 2011]

EC 4.2.1.128

Accepted name: lupan-3β,20-diol synthase

Reaction: lupan-3β,20-diol = (3S)-2,3-epoxy-2,3-dihydrosqualene + H2O

For diagram of reaction click here.

Other name(s): LUP1 (gene name); (S)-squalene-2,3-epoxide hydro-lyase (lupan-3β,20-diol forming)

Systematic name: (3S)-2,3-epoxy-2,3-dihydrosqualene hydro-lyase (lupan-3β,20-diol forming)

Comments: The reaction occurs in the reverse direction. The recombinant enzyme from Arabidopsis thaliana gives a 1:1 mixture of lupeol and lupan-3β,20-diol with small amounts of β-amyrin, germanicol, taraxasterol and ψ-taraxasterol. See EC 5.4.99.41 (lupeol synthase).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Segura, M.J., Meyer, M.M. and Matsuda, S.P. Arabidopsis thaliana LUP1 converts oxidosqualene to multiple triterpene alcohols and a triterpene diol. Org. Lett. 2 (2000) 2257-2259. [PMID: 10930257]

2. Kushiro, T., Hoshino, M., Tsutsumi, T., Kawai, K., Shiro, M., Shibuya, M. and Ebizuka, Y. Stereochemical course in water addition during LUP1-catalyzed triterpene cyclization. Org. Lett. 8 (2006) 5589-5592. [PMID: 17107079]

[EC 4.2.1.128 created 2011]

EC 4.2.1.129

Accepted name: squalene—hopanol cyclase

Reaction: hopan-22-ol = squalene + H2O

For diagram of reaction click here.

Other name(s): squalene—hopene cyclase (ambiguos)

Systematic name: hopan-22-ol hydro-lyase

Comments: The enzyme produces the cyclization products hopene (cf. EC 5.4.99.17) and hopanol from squalene at a constant ratio of 5:1.

Links to other databases: BRENDA, EXPASY, KEGG, PDB, Metacyc, CAS registry number:

References:

1. Hoshino, T., Nakano, S., Kondo, T., Sato, T. and Miyoshi, A. Squalene-hopene cyclase: final deprotonation reaction, conformational analysis for the cyclization of (3R,S)-2,3-oxidosqualene and further evidence for the requirement of an isopropylidene moiety both for initiation of the polycyclization cascade and for the formation of the 5-membered E-ring. Org Biomol Chem 2 (2004) 1456-1470. [PMID: 15136801]

2. Sato, T., Kouda, M. and Hoshino, T. Site-directed mutagenesis experiments on the putative deprotonation site of squalene-hopene cyclase from Alicyclobacillus acidocaldarius. Biosci. Biotechnol. Biochem. 68 (2004) 728-738. [PMID: 15056909]

[EC 4.2.1.129 created 2011]

EC 4.2.1.130

Accepted name: D-lactate dehydratase

Reaction: (R)-lactate = 2-oxopropanal + H2O

Glossary: methylglyoxal = 2-oxopropanal
(R)-lactate = D-lactate

Other name(s): glyoxylase III; GLO3

Systematic name: (R)-lactate hydro-lyase

Comments: The enzyme, described from the fungi Candida albicans and Schizosaccharomyces pombe, converts 2-oxopropanal to (R)-lactate in a single glutathione (GSH)-independent step. The other known route for this conversion is the two-step GSH-dependent pathway catalysed by EC 4.4.1.5 (lactoylglutathione lyase) and EC 3.1.2.6 (hydroxyacylglutathione hydrolase).

Links to other databases: BRENDA, EXPASY, KEGG, PDB, Metacyc, CAS registry number:

References:

1. Hasim, S., Hussin, N.A., Alomar, F., Bidasee, K.R., Nickerson, K.W. and Wilson, M.A. A glutathione-independent glyoxalase of the DJ-1 superfamily plays an important role in managing metabolically generated methylglyoxal in Candida albicans. J. Biol. Chem. 289 (2014) 1662-1674. [PMID: 24302734]

2. Zhao, Q., Su, Y., Wang, Z., Chen, C., Wu, T. and Huang, Y. Identification of glutathione (GSH)-independent glyoxalase III from Schizosaccharomyces pombe. BMC Evol Biol 14 (2014) 86. [PMID: 24758716]

[EC 4.2.1.130 created 2011]

EC 4.2.1.131

Accepted name: carotenoid 1,2-hydratase

Reaction: (1) 1-hydroxy-1,2-dihydrolycopene = lycopene + H2O
(2) 1,1'-dihydroxy-1,1',2,2'-tetrahydrolycopene = 1-hydroxy-1,2-dihydrolycopene + H2O

For diagram of reaction click here or click here

Other name(s): CrtC

Systematic name: lycopene hydro-lyase (1-hydroxy-1,2-dihydrolycopene-forming)

Comments: In Rubrivivax gelatinosus [1] and Thiocapsa roseopersicina [2] both products are formed, whereas Rhodobacter capsulatus [1] only gives 1-hydroxy-1,2-dihydrolycopene. Also acts on neurosporene giving 1-hydroxy-1,2-dihydroneurosporene with both organism but 1,1'-dihydroxy-1,1',2,2'-tetrahydroneurosporene only with Rubrivivax gelatinosus.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Steiger, S., Mazet, A. and Sandmann, G. Heterologous expression, purification, and enzymatic characterization of the acyclic carotenoid 1,2-hydratase from Rubrivivax gelatinosus. Arch. Biochem. Biophys. 414 (2003) 51-58. [PMID: 12745254]

2. Hiseni, A., Arends, I.W. and Otten, L.G. Biochemical characterization of the carotenoid 1,2-hydratases (CrtC) from Rubrivivax gelatinosus and Thiocapsa roseopersicina. Appl. Microbiol. Biotechnol. (2011) . [PMID: 21590288]

[EC 4.2.1.131 created 2011]

EC 4.2.1.132

Accepted name: 2-hydroxyhexa-2,4-dienoate hydratase

Reaction: 4-hydroxy-2-oxohexanoate = (2Z,4Z)-2-hydroxyhexa-2,4-dienoate + H2O

Other name(s): tesE (gene name); hsaE (gene name)

Systematic name: 4-hydroxy-2-oxohexanoate hydro-lyase [(2Z,4Z)-2-hydroxyhexa-2,4-dienoate-forming]

Comments: This enzyme catalyses a late step in the bacterial steroid degradation pathway. The product, 4-hydroxy-2-oxohexanoate, forms a 2-hydroxy-4-hex-2-enolactone under acidic conditions.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, 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]

[EC 4.2.1.132 created 2012]

EC 4.2.1.133

Accepted name: copal-8-ol diphosphate hydratase

Reaction: (13E)-8α-hydroxylabd-13-en-15-yl diphosphate = geranylgeranyl diphosphate + H2O

For diagram of reaction click here.

Glossary: (13E)-8α-hydroxylabd-13-en-15-yl diphosphate = copal-8-ol diphosphate

Other name(s): CcCLS

Systematic name: geranylgeranyl-diphosphate hydro-lyase [(13E)-8α-hydroxylabd-13-en-15-yl diphosphate forming]

Comments: Requires Mg2+. The enzyme was characterized from the plant Cistus creticus subsp. creticus.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Falara, V., Pichersky, E. and Kanellis, A.K. A copal-8-ol diphosphate synthase from the angiosperm Cistus creticus subsp. creticus is a putative key enzyme for the formation of pharmacologically active, oxygen-containing labdane-type diterpenes. Plant Physiol. 154 (2010) 301-310. [PMID: 20595348]

[EC 4.2.1.133 created 2012]

EC 4.2.1.134

Accepted name: very-long-chain (3R)-3-hydroxyacyl-CoA dehydratase

Reaction: a very-long-chain (3R)-3-hydroxyacyl-CoA = a very-long-chain trans-2,3-dehydroacyl-CoA + H2O

Glossary: a very-long-chain acyl-CoA = an acyl-CoA thioester where the acyl chain contains 23 or more carbon atoms.

Other name(s): PHS1 (gene name); PAS2 (gene name)

Systematic name: very-long-chain (3R)-3-hydroxyacyl-CoA hydro-lyase

Comments: This is the third component of the elongase, a microsomal protein complex responsible for extending palmitoyl-CoA and stearoyl-CoA (and modified forms thereof) to very-long chain acyl CoAs. cf. EC 2.3.1.199, very-long-chain 3-oxoacyl-CoA synthase, EC 1.1.1.330, very-long-chain 3-oxoacyl-CoA reductase, and EC 1.3.1.93, very-long-chain enoyl-CoA reductase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Bach, L., Michaelson, L.V., Haslam, R., Bellec, Y., Gissot, L., Marion, J., Da Costa, M., Boutin, J.P., Miquel, M., Tellier, F., Domergue, F., Markham, J.E., Beaudoin, F., Napier, J.A. and Faure, J.D. The very-long-chain hydroxy fatty acyl-CoA dehydratase PASTICCINO2 is essential and limiting for plant development. Proc. Natl. Acad. Sci. USA 105 (2008) 14727-14731. [PMID: 18799749]

2. Kihara, A., Sakuraba, H., Ikeda, M., Denpoh, A. and Igarashi, Y. Membrane topology and essential amino acid residues of Phs1, a 3-hydroxyacyl-CoA dehydratase involved in very long-chain fatty acid elongation. J. Biol. Chem. 283 (2008) 11199-11209. [PMID: 18272525]

[EC 4.2.1.134 created 2012, modified 2014]

EC 4.2.1.135

Accepted name: UDP-N-acetylglucosamine 4,6-dehydratase (configuration-retaining)

Reaction: UDP-N-acetyl-α-D-glucosamine = UDP-2-acetamido-2,6-dideoxy-α-D-xylo-hex-4-ulose + H2O

For diagram of reaction click here and mechanism click here.

Glossary: N,N'-diacetylbacillosamine = 2,4-diacetamido-2,4,6-trideoxy-α-D-glucopyranose

Other name(s): PglF

Systematic name: UDP-N-acetyl-α-D-glucosamine hydro-lyase (configuration-retaining; UDP-2-acetamido-2,6-dideoxy-α-D-xylo-hex-4-ulose-forming)

Comments: Contains NAD+ as a cofactor [2]. This is the first enzyme in the biosynthetic pathway of N,N'-diacetylbacillosamine [1], the first carbohydrate in the glycoprotein N-linked heptasaccharide in Campylobacter jejuni. This enzyme belongs to the short-chain dehydrogenase/reductase family of enzymes.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Schoenhofen, I.C., McNally, D.J., Vinogradov, E., Whitfield, D., Young, N.M., Dick, S., Wakarchuk, W.W., Brisson, J.R. and Logan, S.M. Functional characterization of dehydratase/aminotransferase pairs from Helicobacter and Campylobacter: enzymes distinguishing the pseudaminic acid and bacillosamine biosynthetic pathways. J. Biol. Chem. 281 (2006) 723-732. [PMID: 16286454]

2. Olivier, N.B., Chen, M.M., Behr, J.R. and Imperiali, B. In vitro biosynthesis of UDP-N,N'-diacetylbacillosamine by enzymes of the Campylobacter jejuni general protein glycosylation system. Biochemistry 45 (2006) 13659-13669. [PMID: 17087520]

[EC 4.2.1.135 created 2012]

EC 4.2.1.136

Accepted name: ADP-dependent NAD(P)H-hydrate dehydratase

Reaction: (1) ADP + (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide = AMP + phosphate + NADH
(2) ADP + (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide phosphate = AMP + phosphate + NADPH

Glossary: (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide = (S)-NADH-hydrate = (S)-NADHX
(6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine dinucleotide phosphate = (S)-NADPH-hydrate = (S)-NADPHX

Other name(s): (6S)-β-6-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase(ADP-hydrolysing); (6S)-6-β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase (ADP-hydrolysing; NADH-forming)

Systematic name: (6S)-6β-hydroxy-1,4,5,6-tetrahydronicotinamide-adenine-dinucleotide hydro-lyase (ADP-hydrolysing; NADH-forming)

Comments: Acts equally well on hydrated NADH and hydrated NADPH. NAD(P)H spontaneously hydrates to both the (6S)- and (6R)- isomers. The enzyme from bacteria consists of two domains, one of which acts as an NAD(P)H-hydrate epimerase that interconverts the two isomers to a 60:40 ratio (cf. EC 5.1.99.6), while the other catalyses the dehydration. Hence the enzyme can restore the complete mixture of isomers into NAD(P)H. The enzyme has no activity with ATP, contrary to the enzyme from eukaryotes (cf. EC 4.2.1.93, ATP-dependent NAD(P)H-hydrate dehydratase).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Marbaix, A.Y., Noel, G., Detroux, A.M., Vertommen, D., Van Schaftingen, E. and Linster, C.L. Extremely conserved ATP- or ADP-dependent enzymatic system for nicotinamide nucleotide repair. J. Biol. Chem. 286 (2011) 41246-41252. [PMID: 21994945]

[EC 4.2.1.136 created 2012]

EC 4.2.1.137

Accepted name: sporulenol synthase

Reaction: sporulenol = tetraprenyl-β-curcumene + H2O

For diagram of reaction click here.

Glossary: sporulenol = (1R,2R,4aS,4bR,6aS,10aS,10bR,12aS)-2,4b,7,7,10a,12a-hexamethyl-1-[(3R)-3-(4-methylcyclohexa-1,4-dien-1-yl)butyl]octadecahydrochrysen-2-ol

Other name(s): sqhC (gene name)

Systematic name: tetraprenyl-β-curcumene—sporulenol cyclase

Comments: The reaction occurs in the reverse direction. Isolated from Bacillus subtilis. Similar sesquarterpenoids are present in a number of Bacillus species.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Sato, T., Yoshida, S., Hoshino, H., Tanno, M., Nakajima, M. and Hoshino, T. Sesquarterpenes (C35 terpenes) biosynthesized via the cyclization of a linear C35 isoprenoid by a tetraprenyl-β-curcumene synthase and a tetraprenyl-β-curcumene cyclase: identification of a new terpene cyclase. J. Am. Chem. Soc. 133 (2011) 9734-9737. [PMID: 21627333]

[EC 4.2.1.137 created 2012]

EC 4.2.1.138

Accepted name: (+)-caryolan-1-ol synthase

Reaction: (+)-β-caryophyllene + H2O = (+)-caryolan-1-ol

For diagram of reaction click here.

Glossary: (+)-caryolan-1-ol = (1S,2R,5S,8R)-4,4,8-trimethyltricyclo[6.3.1.02,5]dodecan-1-ol

Other name(s): GcoA

Systematic name: (+)-β-caryophyllene hydrolase [cyclizing, (+)-caryolan-1-ol-forming]

Comments: A multifunctional enzyme which also forms (+)-β-caryophyllene from farnesyl diphosphate [EC 4.2.3.89, (+)-β-caryophyllene synthase].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Nakano, C., Horinouchi, S. and Ohnishi, Y. Characterization of a novel sesquiterpene cyclase involved in (+)-caryolan-1-ol biosynthesis in Streptomyces griseus. J. Biol. Chem. 286 (2011) 27980-27987. [PMID: 21693706]

[EC 4.2.1.138 created 2011 as EC 3.7.1.15, transferred 2013 to EC 4.2.1.138]

EC 4.2.1.139

Accepted name: medicarpin synthase

Reaction: 7,2'-dihydroxy-4'-methoxyisoflavanol = (–)-medicarpin + H2O

For diagram of reaction click here.

Glossary: (–)-medicarpin = (6aR,11aR)-9-methoxy-6a,11a-dihydro-6H-[1]benzofuro[3,2-c]chromen-3-ol

Other name(s): medicarpan synthase; 7,2'-dihydroxy-4'-methoxyisoflavanol; DMI dehydratase; DMID

Systematic name: 7,2'-dihydroxy-4'-methoxyisoflavanol hydro-lyase [(–)-medicarpin-forming]

Comments: Isolated from the plant Medicago sativa (alfalfa). Catalyses the final step in the biosynthesis of medicarpin, the main pterocarpan phytoalexin in alfalfa.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Guo, L., Dixon, R.A. and Paiva, N.L. The 'pterocarpan synthase' of alfalfa: association and co-induction of vestitone reductase and 7,2'-dihydroxy-4'-methoxy-isoflavanol (DMI) dehydratase, the two final enzymes in medicarpin biosynthesis. FEBS Lett 356 (1994) 221-225. [PMID: 7805842]

2. Guo, L., Dixon, R.A. and Paiva, N.L. Conversion of vestitone to medicarpin in alfalfa (Medicago sativa L.) is catalyzed by two independent enzymes. Identification, purification, and characterization of vestitone reductase and 7,2'-dihydroxy-4'-methoxyisoflavanol dehydratase. J. Biol. Chem. 269 (1994) 22372-22378. [PMID: 8071365]

[EC 4.2.1.139 created 2013]

EC 4.2.1.140

Accepted name: gluconate/galactonate dehydratase

Reaction: (1) D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O
(2) D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O

For diagram of reaction click here.

Other name(s): gluconate dehydratase (ambiguous); Sso3198 (gene name); Pto0485 (gene name)

Systematic name: D-gluconate/D-galactonate hydro-lyase

Comments: The enzyme is involved in glucose and galactose catabolism via the nonphosphorylative variant of the Entner-Doudoroff pathway in Picrophilus torridus [3] and via the branched variant of the Entner-Doudoroff pathway in Sulfolobus solfataricus [1,2]. In vitro it utilizes D-gluconate with 6-10 fold higher catalytic efficiency than D-galactonate [1,3]. It requires Mg2+ for activity [1,2]. cf. EC 4.2.1.6, galactonate dehydratase, and EC 4.2.1.39, gluconate dehydratase.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Lamble, H.J., Milburn, C.C., Taylor, G.L., Hough, D.W. and Danson, M.J. Gluconate dehydratase from the promiscuous Entner-Doudoroff pathway in Sulfolobus solfataricus. FEBS Lett 576 (2004) 133-136. [PMID: 15474024]

2. Ahmed, H., Ettema, T.J., Tjaden, B., Geerling, A.C., van der Oost, J. and Siebers, B. The semi-phosphorylative Entner-Doudoroff pathway in hyperthermophilic archaea: a re-evaluation. Biochem. J. 390 (2005) 529-540. [PMID: 15869466]

3. Reher, M., Fuhrer, T., Bott, M. and Schonheit, P. The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase. J. Bacteriol. 192 (2010) 964-974. [PMID: 20023024]

[EC 4.2.1.140 created 2013]

EC 4.2.1.141

Accepted name: 2-dehydro-3-deoxy-D-arabinonate dehydratase

Reaction: 2-dehydro-3-deoxy-D-arabinonate = 2,5-dioxopentanoate + H2O

Systematic name: 2-dehydro-3-deoxy-D-arabinonate hydro-lyase (2,5-dioxopentanoate-forming)

Comments: The enzyme participates in pentose oxidation pathways that convert pentose sugars to the tricarboxylic acid cycle intermediate 2-oxoglutarate.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Brouns, S.J., Walther, J., Snijders, A.P., van de Werken, H.J., Willemen, H.L., Worm, P., de Vos, M.G., Andersson, A., Lundgren, M., Mazon, H.F., van den Heuvel, R.H., Nilsson, P., Salmon, L., de Vos, W.M., Wright, P.C., Bernander, R. and van der Oost, J. Identification of the missing links in prokaryotic pentose oxidation pathways: evidence for enzyme recruitment. J. Biol. Chem. 281 (2006) 27378-27388. [PMID: 16849334]

2. Brouns, S.J., Barends, T.R., Worm, P., Akerboom, J., Turnbull, A.P., Salmon, L. and van der Oost, J. Structural insight into substrate binding and catalysis of a novel 2-keto-3-deoxy-D-arabinonate dehydratase illustrates common mechanistic features of the FAH superfamily. J. Mol. Biol. 379 (2008) 357-371. [PMID: 18448118]

3. Johnsen, U., Dambeck, M., Zaiss, H., Fuhrer, T., Soppa, J., Sauer, U. and Schonheit, P. D-Xylose degradation pathway in the halophilic archaeon Haloferax volcanii. J. Biol. Chem. 284 (2009) 27290-27303. [PMID: 19584053]

[EC 4.2.1.141 created 2013]

EC 4.2.1.142

Accepted name: 5'-oxoaverantin cyclase

Reaction: 5'-oxoaverantin = (1'S,5'S)-averufin + H2O

For diagram of reaction click here.

Glossary: 5'-oxoaverantin = 1,3,6,8-tetrahydroxy-2-[(1S)-1-hydroxy-5-oxohexyl]anthracene-9,10-dione
averufin = 7,9,11-trihydroxy-2-methyl-3,4,5,6-tetrahydro-2,6-epoxy-2H-anthra[2,3-b]oxocin-8,13-dione

Other name(s): OAVN cyclase

Systematic name: 5'-oxoaverantin hydro-lyase [(1'S,5'S)-averufin forming]

Comments: Isolated from the aflatoxin-producing mold Aspergillus parasiticus. The enzyme also catalyses the conversion of versiconal to versicolorin B (EC 4.2.1.143, versicolorin B synthase). Involved in aflatoxin biosynthesis.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Sakuno, E., Yabe, K. and Nakajima, H. Involvement of two cytosolic enzymes and a novel intermediate, 5'-oxoaverantin, in the pathway from 5'-hydroxyaverantin to averufin in aflatoxin biosynthesis. Appl. Environ. Microbiol. 69 (2003) 6418-6426. [PMID: 14602595]

2. Sakuno, E., Wen, Y., Hatabayashi, H., Arai, H., Aoki, C., Yabe, K. and Nakajima, H. Aspergillus parasiticus cyclase catalyzes two dehydration steps in aflatoxin biosynthesis. Appl. Environ. Microbiol. 71 (2005) 2999-3006. [PMID: 15932995]

[EC 4.2.1.142 created 2013]

EC 4.2.1.143

Accepted name: versicolorin B synthase

Reaction: versiconal = versicolorin B + H2O

For diagram of reaction click here.

Glossary: versiconal = (2S,3S)-2,4,6,8-tetrahydroxy-3-(2-hydroxyethyl)anthra[2,3-b]furan-5,10-dione
versicolorin B = (3aR,12bS)-8,10,12-trihydroxy-1,2,3a,12b-tetrahydroanthra[2,3-b]furo[3,2-d]furan-6,11-dione

Other name(s): versiconal cyclase; VBS

Systematic name: versiconal hydro-lyase (versicolorin-B forming)

Comments: Isolated from the aflatoxin-producing mold Aspergillus parasiticus. Involved in aflatoxin biosynthesis.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Lin, B.K. and Anderson, J.A. Purification and properties of versiconal cyclase from Aspergillus parasiticus. Arch. Biochem. Biophys. 293 (1992) 67-70. [PMID: 1731640]

2. McGuire, S.M., Silva, J.C., Casillas, E.G. and Townsend, C.A. Purification and characterization of versicolorin B synthase from Aspergillus parasiticus. Catalysis of the stereodifferentiating cyclization in aflatoxin biosynthesis essential to DNA interaction. Biochemistry 35 (1996) 11470-11486. [PMID: 8784203]

3. Silva, J.C., Minto, R.E., Barry, C.E., 3rd, Holland, K.A. and Townsend, C.A. Isolation and characterization of the versicolorin B synthase gene from Aspergillus parasiticus. Expansion of the aflatoxin b1 biosynthetic gene cluster. J. Biol. Chem. 271 (1996) 13600-13608. [PMID: 8662689]

4. Silva, J.C. and Townsend, C.A. Heterologous expression, isolation, and characterization of versicolorin B synthase from Aspergillus parasiticus. A key enzyme in the aflatoxin B1 biosynthetic pathway. J. Biol. Chem. 272 (1997) 804-813. [PMID: 8995367]

[EC 4.2.1.143 created 2013]

EC 4.2.1.144

Accepted name: 3-amino-5-hydroxybenzoate synthase

Reaction: 5-amino-5-deoxy-3-dehydroshikimate = 3-amino-5-hydroxybenzoate + H2O

For diagram of reaction click here.

Other name(s): AHBA synthase; rifK (gene name)

Systematic name: 5-amino-5-deoxy-3-dehydroshikimate hydro-lyase (3-amino-5-hydroxybenzoate-forming)

Comments: A pyridoxal 5'-phosphate enzyme. The enzyme from the bacterium Amycolatopsis mediterranei participates in the pathway for rifamycin B biosynthesis. The enzyme also functions as a transaminase earlier in the pathway, producing UDP-α-D-kanosamine [3].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Kim, C.G., Yu, T.W., Fryhle, C.B., Handa, S. and Floss, H.G. 3-Amino-5-hydroxybenzoic acid synthase, the terminal enzyme in the formation of the precursor of mC7N units in rifamycin and related antibiotics. J. Biol. Chem. 273 (1998) 6030-6040. [PMID: 9497318]

2. Eads, J.C., Beeby, M., Scapin, G., Yu, T.W. and Floss, H.G. Crystal structure of 3-amino-5-hydroxybenzoic acid (AHBA) synthase. Biochemistry 38 (1999) 9840-9849. [PMID: 10433690]

3. Floss, H.G., Yu, T.W. and Arakawa, K. The biosynthesis of 3-amino-5-hydroxybenzoic acid (AHBA), the precursor of mC7N units in ansamycin and mitomycin antibiotics: a review. J. Antibiot. (Tokyo) 64 (2011) 35-44. [PMID: 21081954]

[EC 4.2.1.144 created 2013]

EC 4.2.1.145

Accepted name: capreomycidine synthase

Reaction: (2S,3S)-3-hydroxyarginine = (2S,3R)-capreomycidine + H2O

Glossary: (2S,3R)-capreomycidine = (S)-2-amino-2-[(R)-2-iminohexahydropyrimidin-4-yl]acetic acid

Other name(s): VioD (ambiguous)

Systematic name: (2S,3S)-3-hydroxyarginine hydro-lyase (cyclizing, (2S,3R)-capreomycidine-forming)

Comments: A pyridoxal 5'-phosphate protein. The enzyme is involved in the biosynthesis of the cyclic pentapeptide antibiotic viomycin.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Yin, X., McPhail, K.L., Kim, K.J. and Zabriskie, T.M. Formation of the nonproteinogenic amino acid (2S,3R)-capreomycidine by VioD from the viomycin biosynthesis pathway. ChemBioChem. 5 (2004) 1278-1281. [PMID: 15368581]

2. Ju, J., Ozanick, S.G., Shen, B. and Thomas, M.G. Conversion of (2S)-arginine to (2S,3R)-capreomycidine by VioC and VioD from the viomycin biosynthetic pathway of Streptomyces sp. strain ATCC11861. ChemBioChem. 5 (2004) 1281-1285. [PMID: 15368582]

[EC 4.2.1.145 created 2013]

EC 4.2.1.146

Accepted name: L-galactonate dehydratase

Reaction: L-galactonate = 2-dehydro-3-deoxy-L-galactonate + H2O

Other name(s): LGD1

Systematic name: L-galactonate hydro-lyase (2-dehydro-3-deoxy-L-galactonate-forming)

Comments: The enzyme takes part in a D-galacturonate degradation pathway in the fungi Trichoderma reesei (Hypocrea jecorina) and Aspergillus niger.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Kuorelahti, S., Jouhten, P., Maaheimo, H., Penttila, M. and Richard, P. L-Galactonate dehydratase is part of the fungal path for D-galacturonic acid catabolism. Mol. Microbiol. 61 (2006) 1060-1068. [PMID: 16879654]

2. Martens-Uzunova, E.S. and Schaap, P.J. An evolutionary conserved D-galacturonic acid metabolic pathway operates across filamentous fungi capable of pectin degradation. Fungal Genet. Biol. 45 (2008) 1449-1457. [PMID: 18768163]

[EC 4.2.1.146 created 2013]

EC 4.2.1.147

Accepted name: 5,6,7,8-tetrahydromethanopterin hydro-lyase

Reaction: 5,6,7,8-tetrahydromethanopterin + formaldehyde = 5,10-methylenetetrahydromethanopterin + H2O

Other name(s): formaldehyde-activating enzyme

Systematic name: 5,6,7,8-tetrahydromethanopterin hydro-lyase (formaldehyde-adding, tetrahydromethanopterin-forming)

Comments: Found in methylotrophic bacteria and methanogenic archaea.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Vorholt, J.A., Marx, C.J., Lidstrom, M.E. and Thauer, R.K. Novel formaldehyde-activating enzyme in Methylobacterium extorquens AM1 required for growth on methanol. J. Bacteriol. 182 (2000) 6645-6650. [PMID: 11073907]

2. Acharya, P., Goenrich, M., Hagemeier, C.H., Demmer, U., Vorholt, J.A., Thauer, R.K. and Ermler, U. How an enzyme binds the C1 carrier tetrahydromethanopterin. Structure of the tetrahydromethanopterin-dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1. J. Biol. Chem. 280 (2005) 13712-13719. [PMID: 15632161]

[EC 4.2.1.147 created 2014]

EC 4.2.1.148

Accepted name: 2-methylfumaryl-CoA hydratase

Reaction: (2R,3S)-2-methylmalyl-CoA = 2-methylfumaryl-CoA + H2O

For diagram of reaction click here.

Glossary: (2R,3S)-2-methylmalyl-CoA = L-erythro-β-methylmalyl-CoA = (2R,3S)-2-methyl-3-carboxy-3-hydroxypropanoyl-CoA
2-methylfumaryl-CoA = (E)-3-carboxy-2-methylprop-2-enoyl-CoA

Other name(s): Mcd; erythro-β-methylmalonyl-CoA hydrolyase; mesaconyl-coenzyme A hydratase (ambiguous); mesaconyl-C1-CoA hydratase

Systematic name: (2R,3S)-2-methylmalyl-CoA hydro-lyase (2-methylfumaryl-CoA-forming)

Comments: The enzyme from the bacterium Chloroflexus aurantiacus is part of the 3-hydroxypropanoate cycle for carbon assimilation.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Zarzycki, J., Schlichting, A., Strychalsky, N., Muller, M., Alber, B.E. and Fuchs, G. Mesaconyl-coenzyme A hydratase, a new enzyme of two central carbon metabolic pathways in bacteria. J. Bacteriol. 190 (2008) 1366-1374. [PMID: 18065535]

[EC 4.2.1.148 created 2014]

EC 4.2.1.149

Accepted name: crotonobetainyl-CoA hydratase

Reaction: L-carnitinyl-CoA = (E)-4-(trimethylammonio)but-2-enoyl-CoA + H2O

Glossary: L-carnitinyl-CoA = (3R)-3-hydroxy-4-(trimethylammonio)butanoyl-CoA
(E)-4-(trimethylammonio)but-2-enoyl-CoA = crotonobetainyl-CoA

Other name(s): CaiD; L-carnityl-CoA dehydratase

Systematic name: L-carnitinyl-CoA hydro-lyase [(E)-4-(trimethylammonio)but-2-enoyl-CoA-forming]

Comments: The enzyme is also able to use crotonyl-CoA as substrate, with low efficiency [2].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Engemann, C., Elssner, T. and Kleber, H.P. Biotransformation of crotonobetaine to L-(–)-carnitine in Proteus sp. Arch. Microbiol. 175 (2001) 353-359. [PMID: 11409545]

2. Elssner, T., Engemann, C., Baumgart, K. and Kleber, H.P. Involvement of coenzyme A esters and two new enzymes, an enoyl-CoA hydratase and a CoA-transferase, in the hydration of crotonobetaine to L-carnitine by Escherichia coli. Biochemistry 40 (2001) 11140-11148. [PMID: 11551212]

3. Engemann, C., Elssner, T., Pfeifer, S., Krumbholz, C., Maier, T. and Kleber, H.P. Identification and functional characterisation of genes and corresponding enzymes involved in carnitine metabolism of Proteus sp. Arch. Microbiol. 183 (2005) 176-189. [PMID: 15731894]

[EC 4.2.1.149 created 2014]

EC 4.2.1.150

Accepted name: short-chain-enoyl-CoA hydratase

Reaction: a short-chain (3S)-3-hydroxyacyl-CoA = a short-chain trans-2-enoyl-CoA + H2O

Other name(s): 3-hydroxybutyryl-CoA dehydratase; crotonase; crt (gene name)

Systematic name: short-chain-(3S)-3-hydroxyacyl-CoA hydro-lyase

Comments: The enzyme from the bacterium Clostridium acetobutylicum is part of the central fermentation pathway and plays a key role in the production of both acids and solvents. It is specific for short, C4-C6, chain length substrates and exhibits an extremely high turnover number for crotonyl-CoA. cf. EC 4.2.1.17, enoyl-CoA hydratase and EC 4.2.1.74, long-chain-enoyl-CoA hydratase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Waterson, R.M., Castellino, F.J., Hass, G.M. and Hill, R.L. Purification and characterization of crotonase from Clostridium acetobutylicum. J. Biol. Chem. 247 (1972) 5266-5271. [PMID: 5057466]

2. Waterson, R.M. and Conway, R.S. Enoyl-CoA hydratases from Clostridium acetobutylicum and Escherichia coli. Methods Enzymol. 71 Pt C (1981) 421-430. [PMID: 7024731]

3. Boynton, Z.L., Bennet, G.N. and Rudolph, F.B. Cloning, sequencing, and expression of clustered genes encoding β-hydroxybutyryl-coenzyme A (CoA) dehydrogenase, crotonase, and butyryl-CoA dehydrogenase from Clostridium acetobutylicum ATCC 824. J. Bacteriol. 178 (1996) 3015-3024. [PMID: 8655474]

[EC 4.2.1.150 created 2014]

EC 4.2.1.151

Accepted name: chorismate dehydratase

Reaction: chorismate = 3-[(1-carboxyvinyl)oxy]benzoate + H2O

For diagram of reaction click here.

Other name(s): MqnA

Systematic name: chorismate hydro-lyase (3-[(1-carboxyvinyl)oxy]benzoate-forming)

Comments: The enzyme, found in several bacterial species, is part of the futalosine pathway for menaquinone biosynthesis.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Mahanta, N., Fedoseyenko, D., Dairi, T. and Begley, T.P. Menaquinone biosynthesis: formation of aminofutalosine requires a unique radical SAM enzyme. J. Am. Chem. Soc. 135 (2013) 15318-15321. [PMID: 24083939]

[EC 4.2.1.151 created 2014]

EC 4.2.1.152

Accepted name: hydroperoxy icosatetraenoate dehydratase

Reaction: a hydroperoxyicosatetraenoate = an oxoicosatetraenoate + H2O

Glossary: (12R)-HPETE = (5Z,8Z,10E,12R,14Z)-12-hydroperoxyicosa-5,8,10,14-tetraenoate
(12S)-HPETE = (5Z,8Z,10E,12S,14Z)-12-hydroperoxyicosa-5,8,10,14-tetraenoate
12-KETE = 12-oxo-ETE = (5Z,8Z,10E,14Z)-12-oxoicosa-5,8,10,14-tetraenoate
(8R)-HPETE = (5Z,8R,9E,11Z,14Z)-8-hydroperoxyicosa-5,9,11,14-tetraenoate
(15R)-HPETE = (5Z,8Z,11Z,13E,15R)-15-hydroperoxyicosa-5,8,11,13-tetraenoate

Other name(s): epidermal lipoxygenase-3 (ambiguous); eLOX3 (ambiguous)

Systematic name: hydroperoxyicosatetraenoate hydro-lyase (oxoicosatetraenoate-forming)

Comments: Binds Fe2+. The mammalian enzymes accept a range of hydroperoxyicosatetraenoates (HPETE). The human enzyme has highest activity with (12R)-HPETE, followed by (12S)-HPETE and (15R)-HPETE with much lower efficiency. The murine enzyme has highest activity with (8R)-HPETE followed by (8S)-HPETE. All HPETE isoforms are converted to the corresponding oxoicosatetraenoate forms (KETE) [2]. The enzymes also catalyse the reaction of EC 5.4.4.7, hydroperoxy icosatetraenoate isomerase.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Yu, Z., Schneider, C., Boeglin, W.E., Marnett, L.J. and Brash, A.R. The lipoxygenase gene ALOXE3 implicated in skin differentiation encodes a hydroperoxide isomerase. Proc. Natl. Acad. Sci. USA 100 (2003) 9162-9167. [PMID: 12881489]

2. Yu, Z., Schneider, C., Boeglin, W.E. and Brash, A.R. Human and mouse eLOX3 have distinct substrate specificities: implications for their linkage with lipoxygenases in skin. Arch. Biochem. Biophys. 455 (2006) 188-196. [PMID: 17045234]

3. Zheng, Y. and Brash, A.R. Dioxygenase activity of epidermal lipoxygenase-3 unveiled: typical and atypical features of its catalytic activity with natural and synthetic polyunsaturated fatty acids. J. Biol. Chem. 285 (2010) 39866-39875. [PMID: 20921226]

[EC 4.2.1.152 created 2014]

EC 4.2.1.153

Accepted name: 3-methylfumaryl-CoA hydratase

Reaction: (S)-citramalyl-CoA = 3-methylfumaryl-CoA + H2O

For diagram of reaction click here.

Glossary: (S)-citramalyl-CoA = (3S)-3-carboxy-3-hydroxybutanoyl-CoA
3-methylfumaryl-CoA = (E)-3-carboxybut-2-enoyl-CoA

Other name(s): Meh; mesaconyl-C4-CoA hydratase; mesaconyl-coenzyme A hydratase (ambiguous)

Systematic name: (S)-citramalyl-CoA hydro-lyase (3-methylfumaryl-CoA-forming)

Comments: The enzyme from the bacterium Chloroflexus aurantiacus is part of the 3-hydroxypropanoate cycle for carbon assimilation.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Zarzycki, J., Brecht, V., Muller, M. and Fuchs, G. Identifying the missing steps of the autotrophic 3-hydroxypropionate CO2 fixation cycle in Chloroflexus aurantiacus. Proc. Natl. Acad. Sci. USA 106 (2009) 21317-21322. [PMID: 19955419]

[EC 4.2.1.153 created 2014]

EC 4.2.1.154

Accepted name: tetracenomycin F2 cyclase

Reaction: tetracenomycin F2 = tetracenomycin F1 + H2O

For diagram of reaction click here.

Glossary: tetracenomycin F1 = 3,8,10,12-tetrahydroxy-1-methyl-11-oxo-6,11-dihydro-2-tetracenecarboxylate = 6,11-dihydro-3,8,10,12-tetrahydroxy-1-methyl-11-oxonaphthacene-2-carboxylate
tetracenomycin F2 = (3E)-4-(3-acetyl-4,5,7-trihydroxy-10-oxo-9,10-dihydroanthracen-2-yl)-3-hydroxybut-3-enoate

Other name(s): tcmI (gene name)

Systematic name: tetracenomycin F2 hydro-lyase (tetracenomycin-F1-forming)

Comments: The enzyme is involved in biosynthesis of the anthracycline antibiotic tetracenomycin C by the bacterium Streptomyces glaucescens.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Shen, B. and Hutchinson, C.R. Tetracenomycin F2 cyclase: intramolecular aldol condensation in the biosynthesis of tetracenomycin C in Streptomyces glaucescens. Biochemistry 32 (1993) 11149-11154. [PMID: 8218177]

2. Thompson, T.B., Katayama, K., Watanabe, K., Hutchinson, C.R. and Rayment, I. Structural and functional analysis of tetracenomycin F2 cyclase from Streptomyces glaucescens. A type II polyketide cyclase. J. Biol. Chem. 279 (2004) 37956-37963. [PMID: 15231835]

[EC 4.2.1.154 created 2014]

EC 4.2.1.155

Accepted name: (methylthio)acryloyl-CoA hydratase

Reaction: 3-(methylthio)acryloyl-CoA + 2 H2O = acetaldehyde + methanethiol + CoA + CO2 (overall reaction)
(1a) 3-(methylthio)acryloyl-CoA + H2O = 3-hydroxy-3-(methylthio)propanoyl-CoA
(1b) 3-hydroxy-3-(methylthio)propanoyl-CoA = 3-oxopropanoyl-CoA + methanethiol
(1c) 3-oxopropanoyl-CoA + H2O = 3-oxopropanoate + CoA
(1d) 3-oxopropanoate = acetaldehyde + CO2

Glossary: 3-(methylthio)acryloyl-CoA = 3-(methylsulfanyl)prop-2-enoyl-CoA

Other name(s): DmdD

Systematic name: 3-(methylsulfanyl)prop-2-enoyl-CoA hydro-lyase (acetaldehyde-forming)

Comments: The enzyme is involved in the degradation of 3-(dimethylsulfonio)propanoate, an osmolyte produced by marine phytoplankton. Isolated from the bacterium Ruegeria pomeroyi.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Tan, D., Crabb, W.M., Whitman, W.B. and Tong, L. Crystal structure of DmdD, a crotonase superfamily enzyme that catalyzes the hydration and hydrolysis of methylthioacryloyl-CoA. PLoS One 8 (2013) e63870. [PMID: 23704947]

[EC 4.2.1.155 created 2015]

EC 4.2.1.156

Accepted name: L-talarate dehydratase

Reaction: L-altarate = 5-dehydro-4-deoxy-D-glucarate + H2O

Glossary: L-altrarate = L-talarate = (2R,3R,4S,5R)-2,3,4,5-tetrahydroxyhexanedioate

Other name(s): L-talarate hydro-lyase

Systematic name: L-altarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming)

Comments: Requires Mg2+. The enzyme, isolated from the bacteria Salmonella typhimurium and Polaromonas sp. JS666, also has activity with galactarate (cf. EC 4.2.1.42, galactarate dehydratase).

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Yew, W.S., Fedorov, A.A., Fedorov, E.V., Almo, S.C. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: L-talarate/galactarate dehydratase from Salmonella typhimurium LT2. Biochemistry 46 (2007) 9564-9577. [PMID: 17649980]

[EC 4.2.1.156 created 2015]

EC 4.2.1.157

Accepted name: (R)-2-hydroxyisocaproyl-CoA dehydratase

Reaction: (R)-2-hydroxy-4-methylpentanoyl-CoA = 4-methylpent-2-enoyl-CoA + H2O

Other name(s): 2-hydroxyisocaproyl-CoA dehydratase; HadBC

Systematic name: (R)-2-hydroxy-4-methylpentanoyl-CoA hydro-lyase

Comments: The enzyme, isolated from the bacterium Peptoclostridium difficile, is involved in the reductive branch of L-leucine fermentation. It catalyses an α/β-dehydration, which depends on the reductive formation of ketyl radicals on the substrate generated by injection of a single electron from the ATP-dependent activator protein HadI.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Kim, J., Darley, D. and Buckel, W. 2-Hydroxyisocaproyl-CoA dehydratase and its activator from Clostridium difficile. FEBS J. 272 (2005) 550-561. [PMID: 15654892]

2. Knauer, S.H., Buckel, W. and Dobbek, H. Structural basis for reductive radical formation and electron recycling in (R)-2-hydroxyisocaproyl-CoA dehydratase. J. Am. Chem. Soc. 133 (2011) 4342-4347. [PMID: 21366233]

[EC 4.2.1.157 created 2015]

EC 4.2.1.158

Accepted name: galactarate dehydratase (D-threo-forming)

Reaction: galactarate = (2S,3R)-2,3-dihydroxy-5-oxohexanedioate + H2O

Glossary: galactarate = (2R,3S,4R,5S)-2,3,4,5-tetrahydroxyhexanedioate
(2S,3R)-2,3-dihydroxy-5-oxohexanedioate = 3-deoxy-D-threo-hex-2-ulosarate

Systematic name: galactarate hydro-lyase (3-deoxy-D-threo-hex-2-ulosarate-forming)

Comments: The enzyme has been characterized from the bacterium Oceanobacillus iheyensis. cf. EC 4.2.1.42, galactarate dehydratase.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Rakus, J.F., Kalyanaraman, C., Fedorov, A.A., Fedorov, E.V., Mills-Groninger, F.P., Toro, R., Bonanno, J., Bain, K., Sauder, J.M., Burley, S.K., Almo, S.C., Jacobson, M.P. and Gerlt, J.A. Computation-facilitated assignment of the function in the enolase superfamily: a regiochemically distinct galactarate dehydratase from Oceanobacillus iheyensis. Biochemistry 48 (2009) 11546-11558. [PMID: 19883118]

[EC 4.2.1.158 created 2015]

EC 4.2.1.159

Accepted name: dTDP-4-dehydro-6-deoxy-α-D-glucopyranose 2,3-dehydratase

Reaction: dTDP-4-dehydro-6-deoxy-α-D-glucopyranose = dTDP-3,4-didehydro-2,6-dideoxy-α-D-glucose + H2O (overall reaction)
(1a) dTDP-4-dehydro-6-deoxy-α-D-glucopyranose = dTDP-2,6-dideoxy-D-glycero-hex-2-enos-4-ulose + H2O
(1b) dTDP-2,6-dideoxy-D-glycero-hex-2-enos-4-ulose = dTDP-3,4-didehydro-2,6-dideoxy-α-D-glucose (spontaneous)

For diagram of reaction click here.

Other name(s): jadO (gene name); evaA (gene name); megBVI (gene name); eryBV (gene name); mtmV (gene name); oleV (gene name); spnO (gene name); TDP-4-keto-6-deoxy-D-glucose 2,3-dehydratase; dTDP-4-dehydro-6-deoxy-α-D-glucopyranose hydro-lyase (dTDP-(2R,6S)-2,4-dihydroxy-6-methyl-2,6-dihydropyran-3-one-forming)

Systematic name: dTDP-4-dehydro-6-deoxy-α-D-glucopyranose hydro-lyase (dTDP-2,6-dideoxy-D-glycero-hex-2-enos-4-ulose-forming)

Comments: The enzyme participates in the biosynthesis of several deoxysugars, including β-L-4-epi-vancosamine, α-L-megosamine, L- and D-olivose, D-oliose, D-mycarose, forosamine and β-L-digitoxose. In vitro the intermediate can undergo a spontaneous decomposition to maltol [2,3].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Aguirrezabalaga, I., Olano, C., Allende, N., Rodriguez, L., Brana, A.F., Mendez, C. and Salas, J.A. Identification and expression of genes involved in biosynthesis of L-oleandrose and its intermediate L-olivose in the oleandomycin producer Streptomyces antibioticus. Antimicrob. Agents Chemother. 44 (2000) 1266-1275. [PMID: 10770761]

2. Chen, H., Thomas, M.G., Hubbard, B.K., Losey, H.C., Walsh, C.T. and Burkart, M.D. Deoxysugars in glycopeptide antibiotics: enzymatic synthesis of TDP-L-epivancosamine in chloroeremomycin biosynthesis. Proc. Natl. Acad. Sci. USA 97 (2000) 11942-11947. [PMID: 11035791]

3. Gonzalez, A., Remsing, L.L., Lombo, F., Fernandez, M.J., Prado, L., Brana, A.F., Kunzel, E., Rohr, J., Mendez, C. and Salas, J.A. The mtmVUC genes of the mithramycin gene cluster in Streptomyces argillaceus are involved in the biosynthesis of the sugar moieties. Mol. Gen. Genet. 264 (2001) 827-835. [PMID: 11254130]

4. Wang, L., White, R.L. and Vining, L.C. Biosynthesis of the dideoxysugar component of jadomycin B: genes in the jad cluster of Streptomyces venezuelae ISP5230 for L-digitoxose assembly and transfer to the angucycline aglycone. Microbiology 148 (2002) 1091-1103. [PMID: 11932454]

5. Hong, L., Zhao, Z., Melancon, C.E., 3rd, Zhang, H. and Liu, H.W. In vitro characterization of the enzymes involved in TDP-D-forosamine biosynthesis in the spinosyn pathway of Saccharopolyspora spinosa. J. Am. Chem. Soc. 130 (2008) 4954-4967. [PMID: 18345667]

6. Useglio, M., Peiru, S., Rodriguez, E., Labadie, G.R., Carney, J.R. and Gramajo, H. TDP-L-megosamine biosynthesis pathway elucidation and megalomicin a production in Escherichia coli. Appl. Environ. Microbiol. 76 (2010) 3869-3877. [PMID: 20418422]

[EC 4.2.1.159 created 2015]

EC 4.2.1.160

Accepted name: 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one isomerase/dehydratase

Reaction: 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one = 7,8-dihydroneopterin 3'-phosphate + H2O

Systematic name: 2,5-diamino-6-(5-phospho-D-ribosylamino)pyrimidin-4(3H)-one cyclohydrolase

Comments: The enzyme participates in a folate biosynthesis pathway in Chlamydia.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Adams, N.E., Thiaville, J.J., Proestos, J., Juarez-Vazquez, A.L., McCoy, A.J., Barona-Gomez, F., Iwata-Reuyl, D., de Crecy-Lagard, V. and Maurelli, A.T. Promiscuous and adaptable enzymes fill "holes" in the tetrahydrofolate pathway in Chlamydia species. MBio 5 (2014) e01378. [PMID: 25006229]

[EC 4.2.1.160 created 2015]

EC 4.2.1.161

Accepted name: bisanhydrobacterioruberin hydratase

Reaction: bacterioruberin = bisanhydrobacterioruberin + 2 H2O (overall reaction)
(1a) bacterioruberin = monoanhydrobacterioruberin + H2O
(1b) monoanhydrobacterioruberin = bisanhydrobacterioruberin + H2O

For diagram of reaction click here.

Glossary: bisanhydrobacterioruberin = 2,2'-bis(3-methylbut-2-enyl)-3,4,3',4'-tetradehydro-1,2,1',2'-tetrahydro-ψ,ψ-carotene-1,1'-diol
monoanhydrobacterioruberin = 2-(3-hydroxy-3-methylbutyl)-2'-(3-methylbut-2-enyl)-3,4,3',4'-tetradehydro-1,2,1',2'-tetrahydro-ψ,ψ-carotene-1,1'-diol

Other name(s): CruF; C50 carotenoid 2'',3''-hydratase

Systematic name: bacterioruberin hydro-lyase (bisanhydrobacterioruberin-forming)

Comments: The enzyme, isolated from the archaeon Haloarcula japonica, is involved in the biosynthesis of the C50 carotenoid bacterioruberin. In this pathway it catalyses the introduction of hydroxyl groups to C3'' and C3''' of bisanhydrobacterioruberin to generate bacterioruberin.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Yang, Y., Yatsunami, R., Ando, A., Miyoko, N., Fukui, T., Takaichi, S. and Nakamura, S. Complete biosynthetic pathway of the C50 carotenoid bacterioruberin from lycopene in the extremely halophilic archaeon Haloarcula japonica. J. Bacteriol. 197 (2015) 1614-1623. [PMID: 25712483]

[EC 4.2.1.161 created 2015]

EC 4.2.1.162

Accepted name: 6-deoxy-6-sulfo-D-gluconate dehydratase

Reaction: 6-deoxy-6-sulfo-D-gluconate = 2-dehydro-3,6-dideoxy-6-sulfo-D-gluconate + H2O

For diagram of reaction click here.

Other name(s): SG dehydratase

Systematic name: 6-deoxy-6-sulfo-D-gluconate hydro-lyase (2-dehydro-3,6-dideoxy-6-sulfo-D-gluconate-forming)

Comments: The enzyme, characterized from the bacterium Pseudomonas putida SQ1, participates in a sulfoquinovose degradation pathway.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Felux, A.K., Spiteller, D., Klebensberger, J. and Schleheck, D. Entner-Doudoroff pathway for sulfoquinovose degradation in Pseudomonas putida SQ1. Proc. Natl. Acad. Sci. USA 112 (2015) E4298-E4305. [PMID: 26195800]

[EC 4.2.1.162 created 2016]

EC 4.2.1.163

Accepted name: 2-oxo-hept-4-ene-1,7-dioate hydratase

Reaction: (4Z)-2-oxohept-4-enedioate + H2O = (4S)-4-hydroxy-2-oxoheptanedioate

Other name(s): HpcG

Systematic name: (4S)-4-hydroxy-2-oxoheptanedioate hydro-lyase [(4Z)-2-oxohept-4-enedioate-forming]

Comments: Requires Mg2+ [2]. Part of a 4-hydroxyphenylacetate degradation pathway in Escherichia coli C.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Burks, E.A., Johnson, W.H., Jr. and Whitman, C.P. Stereochemical and isotopic labeling studies of 2-oxo-hept-4-ene-1,7-dioate hydratase: evidence for an enzyme-catalyzed ketonization step in the hydration reaction. J. Am. Chem. Soc. 120 (1998) 7665-7675.

2. Izumi, A., Rea, D., Adachi, T., Unzai, S., Park, S.Y., Roper, D.I. and Tame, J.R. Structure and mechanism of HpcG, a hydratase in the homoprotocatechuate degradation pathway of Escherichia coli, J. Mol. Biol. 370 (2007) 899-911. [PMID: 17559873]

[EC 4.2.1.163 created 2016]

EC 4.2.1.164

Accepted name: dTDP-4-dehydro-2,6-dideoxy-D-glucose 3-dehydratase

Reaction: dTDP-4-dehydro-2,6-dideoxy-α-D-threo-hexopyranose + 2 reduced ferredoxin [iron-sulfur] cluster + 2 H+ = dTDP-4-dehydro-2,3,6-trideoxy-α-D-hexopyranose + H2O + 2 oxidized ferredoxin [iron-sulfur] cluster

For diagram of reaction click here.

Other name(s): SpnQ; TDP-4-keto-2,6-dideoxy-D-glucose 3-dehydrase

Systematic name: dTDP-2,6-dideoxy-α-D-threo-hexopyranose hydro-lyase (dTDP-2,3,6-trideoxy-α-D-hexopyranose-forming)

Comments: A pyridoxal-phosphate protein. The enzyme, isolated from the bacterium Saccharopolyspora spinosa, participates in the biosynthesis of forosamine. Requires ferredoxin/ferredoxin reductase or flavodoxin/flavodoxin reductase [1].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Hong, L., Zhao, Z. and Liu, H.W. Characterization of SpnQ from the spinosyn biosynthetic pathway of Saccharopolyspora spinosa: mechanistic and evolutionary implications for C-3 deoxygenation in deoxysugar biosynthesis. J. Am. Chem. Soc. 128 (2006) 14262-14263. [PMID: 17076492]

2. Hong, L., Zhao, Z., Melancon, C.E., 3rd, Zhang, H. and Liu, H.W. In vitro characterization of the enzymes involved in TDP-D-forosamine biosynthesis in the spinosyn pathway of Saccharopolyspora spinosa. J. Am. Chem. Soc. 130 (2008) 4954-4967. [PMID: 18345667]

[EC 4.2.1.164 created 2016]

EC 4.2.1.165

Accepted name: chlorophyllide a 31-hydratase

Reaction: (1) 3-devinyl-3-(1-hydroxyethyl)-chlorophyllide a = chlorophyllide a + H2O
(2) 3-deacetyl-3-(1-hydroxyethyl)-bacteriochlorophyllide a = 3-deacetyl-3-vinyl-bacteriochlorophyllide a + H2O

For diagram of reaction click here.

Other name(s): bchF (gene name)

Systematic name: chlorophyllide-a 31-hydro-lyase

Comments: The enzyme, together with EC 1.3.7.15, chlorophyllide-a reductase, and EC 1.1.1.396, bacteriochlorophyllide-a dehydrogenase, is involved in the conversion of chlorophyllide a to bacteriochlorophyllide a. The enzymes can act in multiple orders, resulting in the formation of different intermediates, but the final product of the cumulative action of the three enzymes is always bacteriochlorophyllide a. The enzyme catalyses the hydration of a vinyl group on ring A, converting it to a hydroxyethyl group.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Pudek, M.R. and Richards, W.R. A possible alternate pathway of bacteriochlorophyll biosynthesis in a mutant of Rhodopseudomonas sphaeroides. Biochemistry 14 (1975) 3132-3137. [PMID: 1080053]

2. Burke, D.H., Alberti, M. and Hearst, J.E. bchFNBH bacteriochlorophyll synthesis genes of Rhodobacter capsulatus and identification of the third subunit of light-independent protochlorophyllide reductase in bacteria and plants. J. Bacteriol. 175 (1993) 2414-2422. [PMID: 8385667]

3. Lange, C., Kiesel, S., Peters, S., Virus, S., Scheer, H., Jahn, D. and Moser, J. Broadened substrate specificity of 3-hydroxyethyl bacteriochlorophyllide a dehydrogenase (BchC) indicates a new route for the biosynthesis of bacteriochlorophyll a. J. Biol. Chem. 290 (2015) 19697-19709. [PMID: 26088139]

4. Harada, J., Teramura, M., Mizoguchi, T., Tsukatani, Y., Yamamoto, K. and Tamiaki, H. Stereochemical conversion of C3-vinyl group to 1-hydroxyethyl group in bacteriochlorophyll c by the hydratases BchF and BchV: adaptation of green sulfur bacteria to limited-light environments. Mol. Microbiol. 98 (2015) 1184-1198. [PMID: 26331578]

[EC 4.2.1.165 created 2016]

EC 4.2.1.166

Accepted name: phosphinomethylmalate isomerase

Reaction: phosphinomethylmalate = phosphinomethylisomalate (overall reaction)
(1a) phosphinomethylmalate = 2-(phosphinatomethylidene)butanedioate + H2O
(1b) 2-(phosphinatomethylidene)butanedioate + H2O = phosphinomethylisomalate

Other name(s): pmi (gene name)

Systematic name: phosphinomethylmalate(phosphinomethylisomalate) hydro-lyase (cis-aconitate-forming)

Comments: The enzyme, characterized from the bacterium Streptomyces viridochromogenes, is involved in bialaphos biosynthesis. The enzyme from the bacterium Kitasatospora phosalacinea participates in the biosynthesis of the related compound phosalacine. Both compounds contain the nonproteinogenic amino acid L-phosphinothricin that acts as a potent inhibitor of EC 6.3.1.2, glutamine synthetase. The similar enzyme EC 4.2.1.3, aconitate hydratase, cannot catalyse this reaction.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Heinzelmann, E., Kienzlen, G., Kaspar, S., Recktenwald, J., Wohlleben, W. and Schwartz, D. The phosphinomethylmalate isomerase gene pmi, encoding an aconitase-like enzyme, is involved in the synthesis of phosphinothricin tripeptide in Streptomyces viridochromogenes. Appl. Environ. Microbiol. 67 (2001) 3603-3609. [PMID: 11472937]

[EC 4.2.1.166 created 2016]

EC 4.2.1.167

Accepted name: (R)-2-hydroxyglutaryl-CoA dehydratase

Reaction: (R)-2-hydroxyglutaryl-CoA = (E)-glutaconyl-CoA + H2O

Other name(s): hgdAB (gene names)

Systematic name: (R)-2-hydroxyglutaryl-CoA hydro-lyase ((E)-glutaconyl-CoA-forming)

Comments: The enzymes from the bacteria Acidaminococcus fermentans and Clostridium symbiosum are involved in the fermentation of L-glutamate. The enzyme contains [4F-4S] clusters, FMNH2 and riboflavin. It must be activated by an activator protein. Once activated, it can catalyse many turnovers.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Buckel, W. The reversible dehydration of (R)-2-hydroxyglutarate to (E)-glutaconate. Eur. J. Biochem. 106 (1980) 439-447. [PMID: 7398622]

2. Schweiger, G., Dutscho, R. and Buckel, W. Purification of 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. An iron-sulfur protein. Eur. J. Biochem. 169 (1987) 441-448. [PMID: 3691501]

3. Muller, U. and Buckel, W. Activation of (R)-2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans. Eur. J. Biochem. 230 (1995) 698-704. [PMID: 7607244]

4. Hans, M., Sievers, J., Muller, U., Bill, E., Vorholt, J.A., Linder, D. and Buckel, W. 2-hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum. Eur. J. Biochem. 265 (1999) 404-414. [PMID: 10491198]

5. Locher, K.P., Hans, M., Yeh, A.P., Schmid, B., Buckel, W. and Rees, D.C. Crystal structure of the Acidaminococcus fermentans 2-hydroxyglutaryl-CoA dehydratase component A. J. Mol. Biol. 307 (2001) 297-308. [PMID: 11243821]

6. Parthasarathy, A., Pierik, A.J., Kahnt, J., Zelder, O. and Buckel, W. Substrate specificity of 2-hydroxyglutaryl-CoA dehydratase from Clostridium symbiosum: toward a bio-based production of adipic acid. Biochemistry 50 (2011) 3540-3550. [PMID: 21434666]

[EC 4.2.1.167 created 2016]

EC 4.2.1.168

Accepted name: GDP-4-dehydro-6-deoxy-α-D-mannose 3-dehydratase

Reaction: GDP-4-dehydro-α-D-rhamnose + L-glutamate = GDP-4-dehydro-3,6-dideoxy-α-D-mannose + 2-oxoglutarate + ammonia (overall reaction)
(1a) GDP-4-dehydro-α-D-rhamnose + L-glutamate = GDP-(2S,3S,6R)-3-hydroxy-5-amino-6-methyl-3,6-dihydro-2H-pyran + 2-oxoglutarate + H2O
(1b) GDP-(2S,3S,6R)-3-hydroxy-5-amino-6-methyl-3,6-dihydro-2H-pyran = GDP-(2S,3S,6R)-3-hydroxy-5-imino-6-methyloxane (spontaneous)
(1c) GDP-(2S,3S,6R)-3-hydroxy-5-imino-6-methyloxane + H2O = GDP-4-dehydro-3,6-dideoxy-α-D-mannose + ammonia (spontaneous)

For diagram of reaction click here.

Glossary: GDP-4-dehydro-α-D-rhamnose = GDP-4-dehydro-6-deoxy-α-D-mannose

Other name(s): colD (gene name)

Systematic name: GDP-4-dehydro-α-D-rhamnose 3-hydrolyase

Comments: This enzyme, involved in β-L-colitose biosynthesis, is a unique vitamin-B6-dependent enzyme. In the first step of catalysis, the bound pyridoxal phosphate (PLP) cafactor is transaminated to the pyridoxamine 5'-phosphate (PMP) form of vitamin B6, using L-glutamate as the amino group donor. The PMP cofactor then forms a Schiff base with the sugar substrate and the resulting adduct undergoes a 1,4-dehydration to eliminate the 3-OH group. Hydrolysis of the product from the enzyme restores the PLP cofactor and results in the release of an unstable enamine intermediate. This intermediate tautomerizes to form an imine form, which hydrolyses spontaneously, releasing ammonia and forming the final product.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Alam, J., Beyer, N. and Liu, H.W. Biosynthesis of colitose: expression, purification, and mechanistic characterization of GDP-4-keto-6-deoxy-D-mannose-3-dehydrase (ColD) and GDP-L-colitose synthase (ColC). Biochemistry 43 (2004) 16450-16460. [PMID: 15610039]

2. Cook, P.D. and Holden, H.M. A structural study of GDP-4-keto-6-deoxy-D-mannose-3-dehydratase: caught in the act of geminal diamine formation. Biochemistry 46 (2007) 14215-14224. [PMID: 17997582]

[EC 4.2.1.168 created 2016]

EC 4.2.1.169

Accepted name: 3-vinyl bacteriochlorophyllide d 31-hydratase

Reaction: a 3-(1-hydroxyethyl) bacteriochlorophyllide d = a 3-vinyl bacteriochlorophyllide d + H2O

For diagram of reaction click here.

Other name(s): bchV (gene name)

Systematic name: 3-vinylbacteriochlorophyllide-d 31-hydro-lyase

Comments: This enzyme, found in green sulfur bacteria (Chlorobiaceae) and green flimentous bacteria (Chloroflexaceae), is involved in the biosynthesis of bacteriochlorophylls c, d and e. It acts in the direction of hydration, and the hydroxyl group that is formed is essential for the ability of the resulting bacteriochlorophylls to self-aggregate in the chlorosomes, unique light-harvesting antenna structures found in these organisms. The product is formed preferentially in the (R)-configuration.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Frigaard, N.U., Chew, A.G., Li, H., Maresca, J.A. and Bryant, D.A. Chlorobium tepidum: insights into the structure, physiology, and metabolism of a green sulfur bacterium derived from the complete genome sequence. Photosynth. Res. 78 (2003) 93-117. [PMID: 16245042]

2. Harada, J., Teramura, M., Mizoguchi, T., Tsukatani, Y., Yamamoto, K. and Tamiaki, H. Stereochemical conversion of C3-vinyl group to 1-hydroxyethyl group in bacteriochlorophyll c by the hydratases BchF and BchV: adaptation of green sulfur bacteria to limited-light environments. Mol. Microbiol. 98 (2015) 1184-1198. [PMID: 26331578]

[EC 4.2.1.169 created 2016]

EC 4.2.1.170

Accepted name: 2-(ω-methylthio)alkylmalate dehydratase

Reaction: (1) a 2-[(ω-methylthio)alkyl]malate = a 2-[(ω-methylthio)alkyl]maleate + H2O
(2) a 3-[(ω-methylthio)alkyl]malate = a 2-[(ω-methylthio)alkyl]maleate + H2O

For diagram of reaction click here.

Other name(s): IPMI (gene name)

Systematic name: 2-[(ω-methylthio)alkyl]malate hydro-lyase (2-[(ω-methylthio)alkyl]maleate-forming)

Comments: The enzyme, characterized from the plant Arabidopsis thaliana, is involved in the L-methionine side-chain elongation pathway, forming substrates for the biosynthesis of aliphatic glucosinolates. By catalysing a dehydration of a 2-[(ω-methylthio)alkyl]maleate, followed by a hydration at a different position, the enzyme achieves the isomerization of its substrates. The enzyme is a heterodimer comprising a large and a small subunits. The large subunit can also bind to an alternative small subunit, forming EC 4.2.1.33, 3-isopropylmalate dehydratase, which participates in L-leucine biosynthesis.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Knill, T., Reichelt, M., Paetz, C., Gershenzon, J. and Binder, S. Arabidopsis thaliana encodes a bacterial-type heterodimeric isopropylmalate isomerase involved in both Leu biosynthesis and the Met chain elongation pathway of glucosinolate formation. Plant Mol. Biol. 71 (2009) 227-239. [PMID: 19597944]

[EC 4.2.1.170 created 2016]

EC 4.2.1.171

Accepted name: cis-L-3-hydroxyproline dehydratase

Reaction: cis-3-hydroxy-L-proline = 1-pyrroline-2-carboxylate + H2O

Glossary: 1-pyrroline-2-carboxylate = 4,5-dihydro-3H-pyrrole-2-carboxylate

Other name(s): cis-L-3-hydroxyproline hydro-lyase; c3LHypD

Systematic name: cis-3-hydroxy-L-proline hydro-lyase (1-pyrroline-2-carboxylate-forming)

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Zhang, X., Kumar, R., Vetting, M.W., Zhao, S., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. A unique cis-3-hydroxy-L-proline dehydratase in the enolase superfamily. J. Am. Chem. Soc. 137 (2015) 1388-1391. [PMID: 25608448]

[EC 4.2.1.171 created 2017]

EC 4.2.1.172

Accepted name: trans-4-hydroxy-L-proline dehydratase

Reaction: trans-4-hydroxy-L-proline = (S)-1-pyrroline-5-carboxylate + H2O

Glossary: 1-pyrroline = 3,4-dihydro-2H-pyrrole

Systematic name: trans-4-hydroxy-L-proline hydro-lyase

Comments: The enzyme has been characterized from the bacterium Peptoclostridium difficile. The active form contains a glycyl radical that is generated by a dedicated activating enzyme via chemistry involving S-adenosyl-L-methionine (SAM) and a [4Fe-4S] cluster.

References:

1. Levin, B.J., Huang, Y.Y., Peck, S.C., Wei, Y., Martinez-Del Campo, A., Marks, J.A., Franzosa, E.A., Huttenhower, C. and Balskus, E.P. A prominent glycyl radical enzyme in human gut microbiomes metabolizes trans-4-hydroxy-L-proline. Science 355 (2017) . [PMID: 28183913]

[EC 4.2.1.172 created 2017]

EC 4.2.1.173

Accepted name: ent-8α-hydroxylabd-13-en-15-yl diphosphate synthase

Reaction: ent-8α-hydroxylabd-13-en-15-yl diphosphate = geranylgeranyl diphosphate + H2O

For diagram of reaction click here

Other name(s): SmCPS4

Systematic name: geranylgeranyl-diphosphate hydro-lyase (ent-8α-hydroxylabd-13-en-15-yl diphosphate forming)

Comments: Isolated from the plant Salvia miltiorrhiza (red sage).

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Cui, G., Duan, L., Jin, B., Qian, J., Xue, Z., Shen, G., Snyder, J.H., Song, J., Chen, S., Huang, L., Peters, R.J. and Qi, X. Functional divergence of diterpene syntheses in the medicinal plant Salvia miltiorrhiza. Plant Physiol. 169 (2015) 1607-1618. [PMID: 26077765]

[EC 4.2.1.173 created 2017]

EC 4.2.1.174

Accepted name: peregrinol diphosphate synthase

Reaction: peregrinol diphosphate = geranylgeranyl diphosphate + H2O

For diagram of reaction click here

Glossary: peregrinol diphosphate = (13E)-9-hydroxy-8α-labda-13-en-15-yl diphosphate

Other name(s): MvCPS1

Systematic name: geranylgeranyl-diphosphate hydro-lyase (peregrinol diphosphate forming)

Comments: Isolated from the plant Marrubium vulgare (white horehound). Involved in marrubiin biosynthesis.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Zerbe, P., Chiang, A., Dullat, H., O'Neil-Johnson, M., Starks, C., Hamberger, B. and Bohlmann, J. Diterpene synthases of the biosynthetic system of medicinally active diterpenoids in Marrubium vulgare. Plant J. 79 (2014) 914-927. [PMID: 24990389]

[EC 4.2.1.174 created 2017]


Continued with EC 4.2.2 to EC 4.2.99
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