Accepted name: trans-feruloyl-CoA hydratase
Reaction: 4-hydroxy-3-methoxyphenyl-β-hydroxypropanoyl-CoA = feruloyl-CoA + H2O
Other name(s): trans-feruloyl-CoA hydro-lyase (incorrect); 4-hydroxy-3-methoxyphenyl-β-hydroxypropanoyl-CoA hydro-lyase (trans-feruloyl-CoA-forming)
Systematic name: 4-hydroxy-3-methoxyphenyl-β-hydroxypropanoyl-CoA hydro-lyase (feruloyl-CoA-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 197462-62-7
References:
1. Narbad, A. and Gasson, M.J. Metabolism of ferulic acid via vanillin using a novel CoA-dependent pathway in a newly-isolated strain of Pseudomonas fluorescens. Microbiology 144 (1998) 1397-1405. [PMID: 9611814]
2. Pometto, A.L. and Crawford, D.L. Whole-cell bioconversion of vanillin to vanillic acid by Streptomyces viridosporus. Appl. Environ. Microbiol. 45 (1983) 1582-1585. [PMID: 6870241]
[EC 4.2.1.102 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, EXPASY, KEGG, Metacyc, UM-BBD, CAS registry number: 358974-06-8
References:
1. Goda, M., Hashimoto, Y., Shimizu, S. and Kobayashi, M. Discovery of a novel enzyme, isonitrile hydratase, involved in nitrogen-carbon triple bond cleavage. J. Biol. Chem. 276 (2001) 23480-23485. [PMID: 11306561]
Accepted name: cyanase
Reaction: cyanate + HCO3– + 2 H+ = NH3 + 2 CO2 (overall reaction)
(1a) cyanate + HCO3– + H+ = carbamate + CO2
(1b) carbamate + H+ = NH3 + CO2 (spontaneous)
For diagram click here.
Glossary: cyanate = NCO-
carbamate = H2N-CO-O-
Other name(s): cyanate lyase; cyanate hydrolase; cyanase; cyanate aminohydrolase; cyanate C-N-lyase; cyanate hydratase
Systematic name: carbamate hydro-lyase
Comments: This enzyme, which is found in bacteria and plants, is used to decompose cyanate, which can be used as the sole source of nitrogen [6,7]. Reaction (1) can be considered as the reverse of 'carbamate = cyanate + H2O', where this is assisted by reaction with bicarbonate and carbon dioxide (see mechanism above) [2], and hence is classified in sub-subclass 4.2.1. Bicarbonate functions as a recycling substrate [2].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, UM-BBD, CAS registry number: 37289-24-0
References:
1. Anderson, P.M. Purification and properties of the inducible enzyme cyanase. Biochemistry 19 (1980) 2882-2888. [PMID: 6994799]
2. Johnson, W.V. and Anderson, P.M. Bicarbonate is a recycling substrate for cyanase. J. Biol. Chem. 262 (1987) 9021-9025. [PMID: 3110153]
3. Taussig, A. The synthesis of the induced enzyme, "cyanase", in E. coli. Biochim. Biophys. Acta 44 (1960) 510-519. [PMID: 13775509]
4. Taussig, A. Some properties of the induced enzyme cyanase. Can. J. Biochem. 43 (1965) 1063-1069. [PMID: 5322950]
5. Anderson, P.M., Korte, J.J. and Holcomb, T.A. Reaction of the N-terminal methionine residues in cyanase with diethylpyrocarbonate. Biochemistry 33 (1994) 14121-14125. [PMID: 7947823]
6. Kozliak, E.I., Fuchs, J.A., Guilloton, M.B. and Anderson, P.M. Role of bicarbonate/CO2 in the inhibition of Escherichia coli growth by cyanate. J. Bacteriol. 177 (1995) 3213-3219. [PMID: 7768821]
7. Walsh, M.A., Otwinowski, Z., Perrakis, A., Anderson, P.M. and Joachimiak, A. Structure of cyanase reveals that a novel dimeric and decameric arrangement of subunits is required for formation of the enzyme active site. Structure 8 (2000) 505-514. [PMID: 10801492]
Accepted name: 2-hydroxyisoflavanone dehydratase
Reaction: 2,7,4'-trihydroxyisoflavanone = daidzein + H2O
See diagram for reaction in genistein or daidzein biosynthesis.
Glossary: daidzein = 7,4'-dihydroxyisoflavone
Other name(s): 2,7,4′-trihydroxyisoflavanone hydro-lyase
Systematic name: 2,7,4′-trihydroxyisoflavanone hydro-lyase (daidzein-forming)
Comments: Catalyses the final step in the formation of the isoflavonoid skeleton. The reaction also occurs spontaneously.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 166800-10-8
References:
1. Hakamatsuka, T., Mori, K., Ishida, S., Ebizuka, Y and Sankawa, U. Purification of 2-hydroxyisoflavanone dehydratase from the cell cultures of Pueraria lobata. Phytochemistry 49 (1998) 497-505.
Accepted name: bile-acid 7α-dehydratase
Reaction: 7α,12α-dihydroxy-3-oxochol-4-enoate = 12α-hydroxy-3-oxochola-4,6-dienoate + H2O
For diagram click here.
Other name(s): 7α,12α-dihydroxy-3-oxochol-4-enoate hydro-lyase
Systematic name: 7α,12α-dihydroxy-3-oxochol-4-enoate hydro-lyase (12α-hydroxy-3-oxochola-4,6-dienoate-forming)
Comments: The enzyme from Eubacterium sp. strain VPI 12708 can also use 7α-hydroxy-3-oxochol-4-enoate as a substrate but not 7α,12α-dihydroxy-3-oxochol-5β-anoate, 3α,7α,12α-trihydroxychol-5β-anoate or 7β-hydroxy-3-oxochol-4-enoate.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. 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]
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: N4-acetyl-L-2,4-diaminobutanoate = L-ectoine + H2O
For diagram, click here
Glossary: ectoine = (4S)-2-methyl-1,4,5,6-tetrahydropyrimidine-4-carboxylate
Other name(s): N-acetyldiaminobutyrate dehydratase; N-acetyldiaminobutanoate dehydratase; L-ectoine synthase; EctC; N4-acetyl-L-2,4-diaminobutanoate hydro-lyase; 4-N-acetyl-L-2,4-diaminobutanoate hydro-lyase; 4-N-acetyl-L-2,4-diaminobutanoate hydro-lyase (L-ectoine-forming)
Systematic name: N4-acetyl-L-2,4-diaminobutanoate hydro-lyase (L-ectoine-forming)
Comments: Ectoine is an osmoprotectant that is found in halophilic eubacteria. This is the third enzyme in the ectoine-biosynthesis pathway, the other enzymes involved being EC 2.6.1.76, diaminobutyrate—2-oxoglutarate transaminase and EC 2.3.1.178, diaminobutyrate acetyltransferase [1,2].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Peters, P., Galinski, E.A. and Truper, H.G. The biosynthesis of ectoine. FEMS Microbiol. Lett. 71 (1990) 157-162.
2. Ono, H., Sawada, K., Khunajakr, N., Tao, T., Yamamoto, M., Hiramoto, M., Shinmyo, A., Takano, M. and Murooka, Y. Characterization of biosynthetic enzymes for ectoine as a compatible solute in a moderately halophilic eubacterium, Halomonas elongata. J. Bacteriol. 181 (1999) 91-99. [PMID: 9864317]
3. Kuhlmann, A.U. and Bremer, E. Osmotically regulated synthesis of the compatible solute ectoine in Bacillus pasteurii and related Bacillus spp. Appl. Environ. Microbiol. 68 (2002) 772-783. [PMID: 11823218]
4. Louis, P. and Galinski, E.A. Characterization of genes for the biosynthesis of the compatible solute ectoine from Marinococcus halophilus and osmoregulated expression in Escherichia coli. Microbiology 143 (1997) 1141-1149. [PMID: 9141677]
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, EXPASY, KEGG, Metacyc, PDB, UM-BBD, CAS registry number: 101920-80-3
References:
1. Yu, S. and Fiskesund, R. The anhydrofructose pathway and its possible role in stress response and signaling. Biochim. Biophys. Acta 1760 (2006) 1314-1322. [PMID: 16822618]
2. Yu, S. Enzymatic description of the anhydrofructose pathway of glycogen degradation. II. Gene identification and characterization of the reactions catalyzed by aldos-2-ulose dehydratase that converts 1,5-anhydro-D-fructose to microthecin with ascopyrone M as the intermediate. Biochim. Biophys. Acta 1723 (2005) 63-73. [PMID: 15716041]
3. Broberg, A., Kenne, L. and Pedersén, M. Presence of microthecin in the red alga Gracilariopsis lemaneiformis and its formation from 1,5-anhydro-D-fructose. Phytochemistry 41 (1996) 151-154.
4. Gabriel, J., Volc, J., Sedmera, P., Daniel, G. and Kubátová, E. Pyranosone dehydratase from the basidiomycete Phanerochaete chrysosporium: improved purification, and identification of 6-deoxy-D-glucosone and D-xylosone reaction products. Arch. Microbiol. 160 (1993) 27-34. [PMID: 8352649]
5. Yu, S., Refdahl, C. and Lundt, I. Enzymatic description of the anhydrofructose pathway of glycogen degradation; I. Identification and purification of anhydrofructose dehydratase, ascopyrone tautomerase and α-1,4-glucan lyase in the fungus Anthracobia melaloma. Biochim. Biophys. Acta 1672 (2004) 120-129. [PMID: 15110094]
Accepted name: 1,5-anhydro-D-fructose dehydratase
Reaction: 1,5-anhydro-D-fructose = 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose + H2O
For diagram click here.
Glossary: 1,5-anhydro-D-fructose = 1,5-anhydro-D-arabino-hex-2-ulose = (4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)dihydro-2H-pyran-3(4H)-one
ascopyrone M = 1,5-anhydro-4-deoxy-D-glycero-hex-3-en-2-ulose = (6S)-4-hydroxy-6-(hydroxymethyl)-2H-pyran-3(6H)-one
Other name(s): 1,5-anhydro-D-fructose 4-dehydratase; 1,5-anhydro-D-fructose hydrolyase; 1,5-anhydro-D-arabino-hex-2-ulose dehydratase; AFDH; AF dehydratase; 1,5-anhydro-D-fructose hydro-lyase
Systematic name: 1,5-anhydro-D-fructose hydro-lyase (ascopyrone-M-forming)
Comments: This enzyme catalyses one of the steps in the anhydrofructose pathway, which leads to the degradation of glycogen and starch via 1,5-anhydro-D-fructose [1,2]. The other enzymes involved in this pathway are EC 4.2.1.110 (aldos-2-ulose dehydratase), EC 4.2.2.13 [exo-(1→4)-α-D-glucan lyase] and EC 5.3.2.7 (ascopyrone tautomerase). Requires divalent (Ca2+ or Mg2+) or monovalent cations (Na+) for optimal activity. Unlike EC 4.2.1.110, aldos-2-ulose dehydratase, the enzyme is specific for 1,5-anhydro-D-fructose as substrate and shows no activity towards aldose-2-uloses such as 2-dehydroglucose [1,2,3]. In addition, it is inhibited by its end-product ascopyrone M [2] and it cannot convert ascopyrone M into microthecin, as can EC 4.2.1.110.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, UM-BBD, CAS registry number:
References:
1. Yu, S., Refdahl, C. and Lundt, I. Enzymatic description of the anhydrofructose pathway of glycogen degradation; I. Identification and purification of anhydrofructose dehydratase, ascopyrone tautomerase and α-1,4-glucan lyase in the fungus Anthracobia melaloma. Biochim. Biophys. Acta 1672 (2004) 120-129. [PMID: 15110094]
2. Yu, S. and Fiskesund, R. The anhydrofructose pathway and its possible role in stress response and signaling. Biochim. Biophys. Acta 1760 (2006) 1314-1322. [PMID: 16822618]
3. Yu, S. Enzymatic description of the anhydrofructose pathway of glycogen degradation. II. Gene identification and characterization of the reactions catalyzed by aldos-2-ulose dehydratase that converts 1,5-anhydro-D-fructose to microthecin with ascopyrone M as the intermediate. Biochim. Biophys. Acta 1723 (2005) 63-73. [PMID: 15716041]
Accepted name: acetylene hydratase
Reaction: acetaldehyde = acetylene + H2O
Other name(s): AH; acetaldehyde hydro-lyase
Systematic name: acetaldehyde hydro-lyase (acetylene-forming)
Comments: This is a non-redox-active enzyme that contains two molybdopterin guanine dinucleotide (MGD) cofactors, a tungsten centre and a cubane type [4Fe-4S] cluster [2]. The tungsten centre binds a water molecule that is activated by an adjacent aspartate residue, enabling it to attack acetylene bound in a distinct hydrophobic pocket [2]. Ethylene cannot act as a substrate [1].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, UM-BBD, CAS registry number: 75788-81-7
References:
1. Rosner, B.M. and Schink, B. Purification and characterization of acetylene hydratase of Pelobacter acetylenicus, a tungsten iron-sulfur protein. J. Bacteriol. 177 (1995) 5767-5772. [PMID: 7592321]
2. Seiffert, G.B., Ullmann, G.M., Messerschmidt, A., Schink, B., Kroneck, P.M. and Einsle, O. Structure of the non-redox-active tungsten/[4Fe:4S] enzyme acetylene hydratase. Proc. Natl. Acad. Sci. USA 104 (2007) 3073-3077. [PMID: 17360611]
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 hydrolyase (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 dihomocitrate and trihomocitrate as well as the non-physiological substrate tetrahomocitrate. cis-Aconitate and threo-DL-isocitrate cannot act as substrates, and (S)-homocitrate and trans-homoaconitate act as inhibitors of the enzyme.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Drevland, R.M., Jia, Y., Palmer, D.R. and Graham, D.E. Methanogen homoaconitase catalyzes both hydrolyase reactions in coenzyme B biosynthesis. J. Biol. Chem. 283 (2008) 28888-28896. [PMID: 18765671]
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
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
Glossary: acrylyl-CoA = acryloyl-CoA
3-hydroxypropionyl-CoA = 3-hydroxypropanoyl-CoA
Systematic name: 3-hydroxypropionyl-CoA hydro-lyase
Comments: Catalyses a step in the 3-hydroxypropionate/4-hydroxybutyrate cycle, an autotrophic CO2 fixation pathway found in some thermoacidophilic archaea [1]. The enzyme from Metallosphaera sedula acts nearly equally as well on (S)-3-hydroxybutanoyl-CoA but not (R)-3-hydroxybutanoyl-CoA [2].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Berg, I.A., Kockelkorn, D., Buckel, W. and Fuchs, G. A 3-hydroxypropionate/4-hydroxybutyrate autotrophic carbon dioxide assimilation pathway in Archaea. Science 318 (2007) 1782-1786. [PMID: 18079405]
2. Teufel, R., Kung, J.W., Kockelkorn, D., Alber, B.E. and Fuchs, G. 3-hydroxypropionyl-coenzyme A dehydratase and acryloyl-coenzyme A reductase, enzymes of the autotrophic 3-hydroxypropionate/4-hydroxybutyrate cycle in the Sulfolobales. J. Bacteriol. 191 (2009) 4572-4581. [PMID: 19429610]
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 = protocatechuate + H2O
Systematic name: 3-dehydroshikimate hydro-lyase
Comments: Catalyses an early step in the biosynthesis of petrobactin, a siderophore produced by many bacteria, including the human pathogen Bacillus anthracis. Requires divalent ions, with a preference for Mn2+.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Fox, D.T., Hotta, K., Kim, C.Y. and Koppisch, A.T. The missing link in petrobactin biosynthesis: asbF encodes a (–)-3-dehydroshikimate dehydratase. Biochemistry 47 (2008) 12251-12253. [PMID: 18975921]
2. Pfleger, B.F., Kim, Y., Nusca, T.D., Maltseva, N., Lee, J.Y., Rath, C.M., Scaglione, J.B., Janes, B.K., Anderson, E.C., Bergman, N.H., Hanna, P.C., Joachimiak, A. and Sherman, D.H. Structural and functional analysis of AsbF: origin of the stealth 3,4-dihydroxybenzoic acid subunit for petrobactin biosynthesis. Proc. Natl. Acad. Sci. USA 105 (2008) 17133-17138. [PMID: 18955706]
Accepted name: enoyl-CoA hydratase 2
Reaction: (3R)-3-hydroxyacyl-CoA = (2E)-2-enoyl-CoA + H2O
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 = but-3-enoyl-CoA + H2O
Glossary: 4-hydroxybutanoyl-CoA = 4-hydroxybutyryl-CoA
but-3-enoyl-CoA = vinylacetyl-CoA
Systematic name: 4-hydroxybutanoyl-CoA hydro-lyase
Comments: Contains FAD and a [3Fe-4S] iron-sulfur cluster. The enzyme is often present as a bifunctional enzyme, catalysing the dehydration of 4-hydroxybutanoyl-CoA to but-3-enoyl-CoA followed by isomerization of the later to crotonyl-CoA (EC 5.3.3.3). The enzyme has been characterized from several microorganisms, including Clostridium kluyveri, where it participates in succinate fermentation [1,2], Clostridium aminobutyricum, where it participates in 4-aminobutyrate degradation [3,4], and Metallosphaera sedula, where it participates in the 3-hydroxypropionate/4-hydroxybutyrate cycle, an autotrophic CO2 fixation pathway found in some thermoacidophilic archaea [5].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Bartsch, R.G. and Barker, H.A. A vinylacetyl isomerase from Clostridium kluyveri. Arch. Biochem. Biophys. 92 (1961) 122-132. [PMID: 13687513]
2. Scherf, U., Sohling, B., Gottschalk, G., Linder, D. and Buckel, W. Succinate-ethanol fermentation in Clostridium kluyveri: purification and characterisation of 4-hydroxybutyryl-CoA dehydratase/vinylacetyl-CoA 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
Systematic name: (8E)-9-[(1E,3E)-nona-1,3-dien-1-yloxy]non-8-enoate synthase
Comments: A heme-thiolate protein (P450) [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, 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, PDB, Metacyc, CAS registry number:
References:
1. Hoshino, T., Nakano, S., Kondo, T., Sato, T. and Miyoshi, A. Squalene-hopene cyclase: final deprotonation reaction, conformational analysis for the cyclization of (3R,S)-2,3-oxidosqualene and further evidence for the requirement of an isopropylidene moiety both for initiation of the polycyclization cascade and for the formation of the 5-membered E-ring. Org Biomol Chem 2 (2004) 1456-1470. [PMID: 15136801]
2. Sato, T., Kouda, M. and Hoshino, T. Site-directed mutagenesis experiments on the putative deprotonation site of squalene-hopene cyclase from Alicyclobacillus acidocaldarius. Biosci. Biotechnol. Biochem. 68 (2004) 728-738. [PMID: 15056909]
Accepted name: D-lactate dehydratase
Reaction: (R)-lactate = methylglyoxal + H2O
Glossary: methylglyoxal = 2-oxopropanal
Other name(s): glyoxylase III
Systematic name: (R)-lactate hydro-lyase
Comments: The enzyme converts methylglyoxal to D-lactate in a single glutathione (GSH)-independent step. The other known route for this conversion is the two-step GSH-dependent pathway catalysed by EC 4.4.1.5 (lactoylglutathione lyase) and EC 3.1.2.6 (hydroxyacylglutathione hydrolase).
Links to other databases: BRENDA, EXPASY, KEGG, PDB, Metacyc, CAS registry number:
References:
1. Misra, K., Banerjee, A.B., Ray, S. and Ray, M. Glyoxalase III from Escherichia coli: a single novel enzyme for the conversion of methylglyoxal into D-lactate without reduced glutathione. Biochem. J. 305 ( Pt 3) (1995) 999-1003. [PMID: 7848303]
2. Subedi, K.P., Choi, D., Kim, I., Min, B. and Park, C. Hsp31 of Escherichia coli K-12 is glyoxalase III. Mol. Microbiol. 81 (2011) 926-936. [PMID: 21696459]
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, EXPASY, KEGG, Metacyc, UM-BBD, CAS registry number:
References:
1. Horinouchi, M., Hayashi, T., Koshino, H., Kurita, T. and Kudo, T. Identification of 9,17-dioxo-1,2,3,4,10,19-hexanorandrostan-5-oic acid, 4-hydroxy-2-oxohexanoic acid, and 2-hydroxyhexa-2,4-dienoic acid and related enzymes involved in testosterone degradation in Comamonas testosteroni TA441. Appl. Environ. Microbiol. 71 (2005) 5275-5281. [PMID: 16151114]
Accepted name: copal-8-ol diphosphate hydratase
Reaction: (13E)-8α-hydroxylabda-13-en-15-yl diphosphate = geranylgeranyl diphosphate + H2O
For diagram of reaction click here.
Glossary: (13E)-8α-hydroxylabda-13-en-15-yl diphosphate = copal-8-ol diphosphate
Other name(s): CcCLS
Systematic name: geranylgeranyl-diphosphate hydro-lyase [(13E)-8α-hydroxylabda-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-[acyl-carrier protein] dehydratase
Reaction: a very-long-chain (3R)-3-hydroxyacyl-[acyl-carrier protein] = a very-long-chain trans-2,3-dehydroacyl-[acyl-carrier protein] + 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-[acyl-carrier protein] 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, 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]