[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)]
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, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, 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]
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 (1a) can be considered an equivalent of 'cyanate + H2O = carbamate', where the water molecule is provided by the dehydration of bicarbonate to carbon dioxide [2], and hence the enzyme is classified as a hydrolase.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, 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]
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, PDB, 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.
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, PDB, 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]
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]
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, PDB, 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]
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]
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, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, 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]
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, EAWAG-BBD, EXPASY, KEGG, Metacyc, 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]
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, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, 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]
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]
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 dihomoaconitate and trihomoaconitate as well as the non-physiological substrate tetrahomoaconitate. 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]
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]
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, PDB, 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]
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]
Accepted name: 3-dehydroshikimate dehydratase
Reaction: 3-dehydro-shikimate = 3,4-dihydroxybenzoate + 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]
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]
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, PDB, 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 Δ3-Δ2-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 Δ3-Δ2-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]
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]
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]
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]
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]
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]
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]
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, PDB, 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]
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]
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, Metacyc, PDB, 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]
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, Metacyc, PDB, 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]
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]
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, EAWAG-BBD, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Horinouchi, M., Hayashi, T., Koshino, H., Kurita, T. and Kudo, T. Identification of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid, 4-hydroxy-2-oxohexanoic acid, and 2-hydroxyhexa-2,4-dienoic acid and related enzymes involved in testosterone degradation in Comamonas testosteroni TA441. Appl. Environ. Microbiol. 71 (2005) 5275-5281. [PMID: 16151114]
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]
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]
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]
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, PDB, 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]
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]
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]
Accepted name: pterocarpan synthase
Reaction: a (4R)-4,2'-dihydroxyisoflavan = a pterocarpan + H2O
For diagram of reaction click here
Glossary: an isoflavan = an isoflavonoid with a 3,4-dihydro-3-aryl-2H-1-benzopyran skeleton.
(-)-medicarpin = (6aR,11aR)-9-methoxy-6a,11a-dihydro-6H-[1]benzofuro[3,2-c]chromen-3-ol
(+)-medicarpin = (6aS,11aS)-9-methoxy-6a,11a-dihydro-6H-[1]benzofuro[3,2-c]chromen-3-ol
(-)-maackiain = (6aR,12aR)-6a,12a-dihydro-6H-[1,3]dioxolo[5,6][1]benzofuro[3,2-c]chromen-3-ol
(+)-maackiain = (6aS,12aS)-6a,12a-dihydro-6H-[1,3]dioxolo[5,6][1]benzofuro[3,2-c]chromen-3-ol
(+)-pterocarpan = (6aR,11aR)-6a,11a-dihydro-6H-[1]benzofuran[3,2-c][1]benzopyran
Other name(s): medicarpin synthase; medicarpan synthase; 7,2'-dihydroxy-4'-methoxyisoflavanol dehydratase; 2',7-dihydroxy-4'-methoxyisoflavanol dehydratase; DMI dehydratase; DMID; 2'-hydroxyisoflavanol 4,2'-dehydratase; PTS (gene name); 4'-methoxyisoflavan-2',4,7-triol hydro-lyase [(-)-medicarpin-forming]
Systematic name: (4R)-4,2'-dihydroxyisoflavan hydro-lyase (pterocarpan-forming)
Comments: The enzyme catalyses the formation of the additional ring in pterocarpan, the basic structure of phytoalexins produced by leguminous plants, including (-)-medicarpin, (+)-medicarpin, (-)-maackiain and (+)-maackiain. The enzyme requires that the hydroxyl group at C-4 of the substrate is in the (4R) configuration. The configuration of the hydrogen atom at C-3 determines whether the pterocarpan is the (+)- or (-)-enantiomer. The enzyme contains amino acid motifs characteristic of dirigent proteins.
Links to other databases: BRENDA, EXPASY, ExplorEnz, IUBMB, KEGG, MetaCyc, PDB, 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]
3. Uchida, K., Akashi, T. and Aoki, T. The missing link in leguminous pterocarpan biosynthesis is a dirigent domain-containing protein with isoflavanol dehydratase activity. Plant Cell Physiol 58 (2017) 398-408. [PMID: 28394400]
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]
Accepted name: 2-dehydro-3-deoxy-D-arabinonate dehydratase
Reaction: 2-dehydro-3-deoxy-D-arabinonate = 2,5-dioxopentanoate + H2O
For diagram of reaction click here.
Glossary: 2-dehydro-3-deoxy-D-arabinonate = 2-dehydro-3-deoxy-D-xylonate = 3-deoxy-L-glycero-pent-2-ulonate
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, PDB, 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]
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]
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]
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, PDB, 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]
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]
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]
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, PDB, 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]
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, PDB, 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]
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]
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, PDB, 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]
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, PDB, 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]
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, PDB, 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]
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]
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, PDB, 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]
Accepted name: (methylthio)acryloyl-CoA hydratase
Reaction: 3-(methylsulfanyl)acryloyl-CoA + 2 H2O = acetaldehyde + methanethiol + CoA + CO2 (overall reaction)
(1a) 3-(methylsulfanyl)acryloyl-CoA + H2O = 3-hydroxy-3-(methylsulfanyl)propanoyl-CoA
(1b) 3-hydroxy-3-(methylsulfanyl)propanoyl-CoA = 3-oxopropanoyl-CoA + methanethiol
(1c) 3-oxopropanoyl-CoA + H2O = 3-oxopropanoate + CoA
(1d) 3-oxopropanoate = acetaldehyde + CO2
Glossary: 3-(methylsulfanyl)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, PDB, 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]
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, PDB, 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]
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, PDB, 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]
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, PDB, 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]
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, PDB, 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]
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]
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]
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]
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, PDB, 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]
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]
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]
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]
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 [4Fe-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]
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 + NH3 (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 + NH3 (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]
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]
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]
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, PDB, 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]
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.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
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]
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]
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]
Accepted name: (R)-3-(aryl)lactoyl-CoA dehydratase
Reaction: (1) (R)-3-(phenyl)lactoyl-CoA = (E)-cinnamoyl-CoA + H2O
(2) (R)-3-(4-hydroxyphenyl)lactoyl-CoA = (E)-4-coumaroyl-CoA + H2O
(3) (R)-3-(indol-3-yl)lactoyl-CoA = 3-(indol-3-yl)acryloyl-CoA + H2O
Other name(s): fldBC (gene names); (R)-phenyllactoyl-CoA dehydratase; aryllactyl-CoA dehydratase
Systematic name: (R)-3-(aryl)lactoyl-CoA hydro-lyase
Comments: The enzyme, found in some amino acid-fermenting anaerobic bacteria, participates in the fermentation pathways of L-phenylalanine, L-tyrosine, and L-tryptophan. It is a heterodimeric protein consisting of the FldB and FldC polypeptides, both of which contain an [4Fe-4S]cluster, and forms a complex with EC 2.8.3.17, 3-(aryl)acryloyl-CoA:(R)-3-(aryl)lactate CoA-transferase (FldA). In order to catalyse the reaction, the enzyme requires one high-energy electron that transiently reduces the electrophilic thiol ester carbonyl of the substrate to a nucleophilic ketyl radical anion, facilitating the elimination of the hydroxyl group. This electron, which is provided by by EC 5.6.1.10, (R)-2-hydroxyacyl-CoA dehydratase activating ATPase, needs to be supplied only once, before the first reaction takes place, as it is regenerated at the end of each reaction cycle. The enzyme acts on (R)-3-(aryl)lactoyl-CoAs produced by FldA, and regenerates the CoA donors used by that enzyme.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Dickert, S., Pierik, A.J., Linder, D. and Buckel, W. The involvement of coenzyme A esters in the dehydration of (R)-phenyllactate to (E)-cinnamate by Clostridium sporogenes. Eur. J. Biochem. 267 (2000) 3874-3884. [PMID: 10849007]
2. Dickert, S., Pierik, A.J. and Buckel, W. Molecular characterization of phenyllactate dehydratase and its initiator from Clostridium sporogenes. Mol. Microbiol. 44 (2002) 49-60. [PMID: 11967068]
3. Kim, J., Hetzel, M., Boiangiu, C.D. and Buckel, W. Dehydration of (R)-2-hydroxyacyl-CoA to enoyl-CoA in the fermentation of α-amino acids by anaerobic bacteria. FEMS Microbiol. Rev. 28 (2004) 455-468. [PMID: 15374661]
4. Kim, J., Darley, D.J., Buckel, W. and Pierik, A.J. An allylic ketyl radical intermediate in clostridial amino-acid fermentation. Nature 452 (2008) 239-242. [PMID: 18337824]
5. Dodd, D., Spitzer, M.H., Van Treuren, W., Merrill, B.D., Hryckowian, A.J., Higginbottom, S.K., Le, A., Cowan, T.M., Nolan, G.P., Fischbach, M.A. and Sonnenburg, J.L. A gut bacterial pathway metabolizes aromatic amino acids into nine circulating metabolites. Nature 551 (2017) 648-652. [PMID: 29168502]
Accepted name: L-lyxonate dehydratase
Reaction: L-lyxonate = 2-dehydro-3-deoxy-L-arabinonate + H2O
Glossary: L-lyxonate = (2R,3R,4S)-2,3,4,5-tetrahydroxypentanoate
Other name(s): lyxD (gene name)
Systematic name: L-lyxonate hydro-lyase
Comments: The enzyme, characterized from several bacterial species, is involved in an L-lyxonate degradation pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Ghasempur, S., Eswaramoorthy, S., Hillerich, B.S., Seidel, R.D., Swaminathan, S., Almo, S.C. and Gerlt, J.A. Discovery of a novel L-lyxonate degradation pathway in Pseudomonas aeruginosa PAO1. Biochemistry 53 (2014) 3357-3366. [PMID: 24831290]
Accepted name: (2S)-3-sulfopropanediol dehydratase
Reaction: (2S)-2,3-dihydroxypropane-1-sulfonate = 3-oxopropane-1-sulfonate + H2O
Glossary: (2S)-2,3-dihydroxypropane-1-sulfonic acid = (2S)-3-sulfopropanediol = (S)-DHPS
Other name(s): hpfG (gene name); (S)-DHPS dehydratase
Systematic name: (2S)-2,3-dihydroxypropane-1-sulfonate hydro-lyase
Comments: The enzyme, characterized from the bacterium Klebsiella oxytoca, participates in (2S)-2,3-dihydroxypropane-1-sulfonate degradation. The active form of the enzyme contains a glycyl radical that is generated by a dedicated activating enzyme via chemistry involving S-adenosyl-L-methionine (AdoMet) and a [4Fe-4S] cluster.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Liu, J., Wei, Y., Lin, L., Teng, L., Yin, J., Lu, Q., Chen, J., Zheng, Y., Li, Y., Xu, R., Zhai, W., Liu, Y., Liu, Y., Cao, P., Ang, E.L., Zhao, H., Yuchi, Z. and Zhang, Y. Two radical-dependent mechanisms for anaerobic degradation of the globally abundant organosulfur compound dihydroxypropanesulfonate. Proc. Natl. Acad. Sci. USA 117 (2020) 15599-15608. [PMID: 32571930]
Accepted name: difructose-dianhydride-III synthase
Reaction: inulobiose = α-D-fructofuranose-β-D-fructofuranose 2',1:2,3'-dianhydride + H2O
Glossary: difructose anhydride III = α-D-fructofuranose-β-D-fructofuranose 2',1:2,3'-dianhydride
inulobiose = β-D-fructofuranosyl-(2→1)-D-fructose
Other name(s): DFA-IIIase; difructose anhydride III hydrolase
Systematic name: inulobiose hydro-lyase (α-D-fructofuranose-β-D-fructofuranose 2',1:2,3'-dianhydride-forming)
Comments: The enzyme participates in an inulin degradation pathway, in which it forms inulobiose from difructose anhydride III. A conformational change in the enzyme from the bacterium Pseudarthrobacter chlorophenolicus results in it also catalysing the activity of EC 4.2.2.18, inulin fructotransferase (DFA-III-forming).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Tanaka, T., Uchiyama, T., Kobori, H. and Tanaka, K. Enzymic hydrolysis of di-D-fructofuranose 1, 2'; 2, 3' dianhydride with Arthrobacter ureafaciens, J. Biochem. 78 (1975) 1201-1206. [PMID: 1225919]
2. Neubauer, A., Walter, M., and Buchholz, K. Formation of inulobiose from difructoseanhydride III catalysed by a lysate from Arthrobacter ureafaciens ATCC 21124. Biocatalysis and Biotransformation 18 (2000) 443-455.
3. Saito, K., Sumita, Y., Nagasaka, Y., Tomita, F. and Yokota, A. Molecular cloning of the gene encoding the di-D-fructofuranose 1,2':2,3' dianhydride hydrolysis enzyme (DFA IIIase) from Arthrobacter sp. H65-7. J. Biosci. Bioeng. 95 (2003) 538-540. [PMID: 16233453]
4. Yu, S., Wang, X., Zhang, T., Stressler, T., Fischer, L., Jiang, B. and Mu, W. Identification of a novel di-D-fructofuranose 1,2':2,3' dianhydride (DFA III) hydrolysis enzyme from Arthrobacter aurescens SK8.001. PLoS One 10 (2015) e0142640. [PMID: 26555784]
5. Yu, S., Shen, H., Cheng, Y., Zhu, Y., Li, X., and Mu, W. Structural and functional basis of difructose anhydride III hydrolase, which sequentially converts inulin using the same catalytic residue. ACS Catalysis 8 (2018) 10683-10697.
Accepted name: difructose-anhydride-I synthase
Reaction: inulobiose = bis-D-fructose 2',1:2,1'-dianhydride + H2O
Glossary: α-D-fructofuranose-β-D-fructofuranose 2',1:2,1'-dianhydride = bis-D-fructose 2',1:2,1'-dianhydride = difructose anhydride I = DFA-I
Other name(s): DFAIase; inulobiose hydrolase; bis-D-fructose 2',1:2,1'-dianhydride fructohydrolase
Systematic name: inulobiose hydro-lyase (α-D-fructofuranose-β-D-fructofuranose 2',1:2,1'-dianhydride-forming)
Comments: The enzyme, studied in the fungus Aspergillus fumigatus, may participate in an inulin degradation pathway in which it converts the product of EC 4.2.2.17, inulin fructotransferase (DFA-I-forming), to inulobiose, though in vitro activity was higher in the direction of DFA-I formation.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Matsuyama, T. and Tanaka, K. On the enzyme of Aspergillus fumigatus producing difructose anhydride I from inulobiose. Agric. Biol. Chem. 53 (1989) 831-832.
2. Matsuyama, T., Tanaka, K., Mashiko, M. and Kanamoto, M. Enzymic formation of di-D-fructose 1,2'; 2,1' dianhydride from inulobiose by Aspergillus fumigatus, J. Biochem. (Tokyo) 92 (1982) 1325-1328. [PMID: 6757245]
Accepted name: (E)-benzylidenesuccinyl-CoA hydratase
Reaction: (R,S)-2-(α-hydroxybenzyl)succinyl-CoA = (E)-benzylidenesuccinyl-CoA + H2O
Other name(s): bbsH (gene name)
Systematic name: (R,S)-2-(α-hydroxybenzyl)succinyl-CoA hydro-lyase
Comments: The enzyme, purified from the bacterium Thauera aromatica, is involved in an anaerobic toluene degradation pathway in which it catalyses the hydration of (E)-benzylidenesuccinyl-CoA.
References:
1. von Horsten, S., Lippert, M.L., Geisselbrecht, Y., Schuhle, K., Schall, I., Essen, L.O. and Heider, J. Inactive pseudoenzyme subunits in heterotetrameric BbsCD, a novel short-chain alcohol dehydrogenase involved in anaerobic toluene degradation. FEBS J. (2021) . [PMID: 34601806]
Accepted name: 3-carboxymethyl-3-hydroxy-acyl-[acp] dehydratase
Reaction: a 3-carboxymethyl-3-hydroxy-acyl-[acyl-carrier protein] = a 4-carboxy-3-alkylbut-2-enoyl-[acyl-carrier protein] + H2O
Other name(s): aprF (gene name); corF (gene name); curE (gene name); pedL (gene name); 3-carboxymethyl-3-hydroxy-acyl-[acyl-carrier protein] dehydratase
Systematic name: 3-carboxymethyl-3-hydroxy-acyl-[acyl-carrier protein] hydro-lyase
Comments: This family of enzymes participates in a process that introduces a methyl branch into nascent polyketide products. The process begins with EC 4.1.1.124, malonyl-[acp] decarboxylase, which converts the common extender unit malonyl-[acp] to acetyl-[acp]. The enzyme is a mutated form of a ketosynthase enzyme, in which a Cys residue in the active site is modified to a Ser residue, leaving the decarboxylase function intact, but nulifying the ability of the enzyme to form a carbon-carbon bond. Next, EC 2.3.3.22, 3-carboxymethyl-3-hydroxy-acyl-[acp] synthase, utilizes the acetyl group to introduce the branch at the β position of 3-oxoacyl intermediates attached to a polyketide synthase, forming a 3-hydroxy-3-carboxymethyl intermediate. This is followed by dehydration catalysed by EC 4.2.1.181, 3-carboxymethyl-3-hydroxy-acyl-[acp] dehydratase (often referred to as an ECH1 domain), leaving a 3-carboxymethyl group and forming a double bond between the α and β carbons. The process concludes with decarboxylation catalysed by EC 4.1.1.125, 4-carboxy-3-alkylbut-2-enoyl-[acp] decarboxylase (often referred to as an ECH2 domain), leaving a methyl branch at the β carbon. The enzymes are usually encoded by a cluster of genes referred to as an "HMGS cassette", based on the similarity of the key enzyme to EC 2.3.3.10, hydroxymethylglutaryl-CoA synthase. cf. EC 4.2.1.18, methylglutaconyl-CoA hydratase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Gu, L., Jia, J., Liu, H., Hakansson, K., Gerwick, W.H. and Sherman, D.H. Metabolic coupling of dehydration and decarboxylation in the curacin A pathway: functional identification of a mechanistically diverse enzyme pair. J. Am. Chem. Soc. 128 (2006) 9014-9015. [PMID: 16834357]
2. Gu, L., Wang, B., Kulkarni, A., Geders, T.W., Grindberg, R.V., Gerwick, L., Hakansson, K., Wipf, P., Smith, J.L., Gerwick, W.H. and Sherman, D.H. Metamorphic enzyme assembly in polyketide diversification. Nature 459 (2009) 731-735. [PMID: 19494914]
3. Erol, O., Schaberle, T.F., Schmitz, A., Rachid, S., Gurgui, C., El Omari, M., Lohr, F., Kehraus, S., Piel, J., Muller, R. and Konig, G.M. Biosynthesis of the myxobacterial antibiotic corallopyronin A. Chembiochem 11 (2010) 1253-1265. [PMID: 20503218]
4. Grindberg, R.V., Ishoey, T., Brinza, D., Esquenazi, E., Coates, R.C., Liu, W.T., Gerwick, L., Dorrestein, P.C., Pevzner, P., Lasken, R. and Gerwick, W.H. Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage. PLoS One 6 (2011) e18565. [PMID: 21533272]
Accepted name: phosphomevalonate dehydratase
Reaction: (R)-5-phosphomevalonate = (2E)--3-methyl-5-phosphooxypent-2-enoate + H2O
Glossary:(2E)-3-methyl-5-phosphooxypent-2-enoate = trans-anhydromevalonate 5-phosphate
Systematic name: (R)-5-phosphomevalonate hydro-lyase
Comments: The enzyme catalyses a step in an archaeal prenyl diphosphate biosynthesis pathway. It belongs to the aconitase X family, and contains a [4Fe-4S] cluster.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Hayakawa, H., Motoyama, K., Sobue, F., Ito, T., Kawaide, H., Yoshimura, T. and Hemmi, H. Modified mevalonate pathway of the archaeon Aeropyrum pernix proceeds via trans-anhydromevalonate 5-phosphate. Proc. Natl. Acad. Sci. USA 115 (2018) 10034Ð10039. [PMID: 30224495]
2. Yoshida, R., Yoshimura, T. and Hemmi, H. Reconstruction of the "archaeal" mevalonate pathway from the methanogenic archaeon Methanosarcina mazei in Escherichia coli cells. Appl. Environ. Microbiol. 86 (2020) e02889-19. [PMID: 31924615]
3. Komeyama, M., Kanno, K., Mino, H., Yasuno, Y., Shinada, T., Ito, T. and Hemmi, H. A [4Fe-4S] cluster resides at the active center of phosphomevalonate dehydratase, a key enzyme in the archaeal modified mevalonate pathway. Front Microbiol. 14 (2023) 1150353. [PMID: 36992929]
Accepted name: etheroleic acid synthase
Reaction: (9Z,11E,13S)-13-hydroperoxy-9,11-octadecadienoate = (9Z,11E)-12-[(1E)-hex-1-en-1-yloxy]dodeca-9,11-dienoate + H2O
Glossary: (9Z,11E)-12-[(1E)-hex-1-en-1-yloxy]dodeca-9,11-dienoic acid = etheroleic acid
(9Z,11E,13S)-13-hydroperoxy-9,11-octadecadienoic acid = 13(S)-HPOD
Other name(s): colneleic acid/etheroleic acid synthase; 13/9-DES; 9/13-DES; 13/9-divinyl ether synthase; (9Z,11E)-12-[(1E)-hex-1-en-1-yloxy]dodeca-9,11-dienoate synthase
Systematic name: (9Z,11E,13S)-13-hydroperoxy-9,11-octadecadienoate lyase
Comments: A heme-thiolate protein (P-450) occurring in several plants, including Allium sativum (garlic) and Selaginella moellendorffii (spikemoss). The enzyme also catalyses the reaction of EC 4.2.1.121, colneleate synthase, to a lesser extent.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Grechkin, A.N., Fazliev, F.N. and Mukhtarova, L.S. The lipoxygenase pathway in garlic (Allium sativum L.) bulbs: detection of the novel divinyl ether oxylipins. FEBS Lett. 371 (1995) 159-162. [PMID: 7672118]
2. Stumpe, M., Carsjens, J.G., Gobel, C. and Feussner, I. Divinyl ether synthesis in garlic bulbs. J. Exp. Bot. 59 (2008) 907-915. [PMID: 18326559]
3. Gorina, S.S., Toporkova, Y.Y., Mukhtarova, L.S., Smirnova, E.O., Chechetkin, I.R., Khairutdinov, B.I., Gogolev, Y.V. and Grechkin, A.N. Oxylipin biosynthesis in spikemoss Selaginella moellendorffii: Molecular cloning and identification of divinyl ether synthases CYP74M1 and CYP74M3. Biochim. Biophys Acta 1861 (2016) 301-309. [PMID: 26776054]