EC 4.2.1 Hydro-Lyases
EC 4.2.2 Acting on Polysaccharides
EC 4.2.99 Other Carbon-Oxygen Lyases
EC 4.2.1 Hydro-Lyases
EC 4.2.1.1 carbonic anhydrase
EC 4.2.1.2 fumarate hydratase
EC 4.2.1.3 aconitate hydratase
EC 4.2.1.4 deleted now known to be a partial reaction catalysed by EC 4.2.1.3
EC 4.2.1.5 arabinonate dehydratase
EC 4.2.1.6 galactonate dehydratase
EC 4.2.1.7 altronate dehydratase
EC 4.2.1.8 mannonate dehydratase
EC 4.2.1.9 dihydroxy-acid dehydratase
EC 4.2.1.10 3-dehydroquinate dehydratase
EC 4.2.1.11 phosphopyruvate hydratase
EC 4.2.1.12 phosphogluconate dehydratase
EC 4.2.1.13 now EC 4.3.1.17
EC 4.2.1.14 now EC 4.3.1.18
EC 4.2.1.15 now EC 4.4.1.1
EC 4.2.1.16 now EC 4.3.1.19
EC 4.2.1.17 enoyl-CoA hydratase
EC 4.2.1.18 methylglutaconyl-CoA hydratase
EC 4.2.1.19 imidazoleglycerol-phosphate dehydratase
EC 4.2.1.20 tryptophan synthase
EC 4.2.1.21 now EC 4.2.1.22
EC 4.2.1.22 cystathionine β-synthase
EC 4.2.1.23 deleted
EC 4.2.1.24 porphobilinogen synthase
EC 4.2.1.25 L-arabinonate dehydratase
EC 4.2.1.26 now EC 4.3.1.9
EC 4.2.1.27 acetylenecarboxylate hydratase
EC 4.2.1.28 propanediol dehydratase
EC 4.2.1.29 now EC 4.99.1.6
EC 4.2.1.30 glycerol dehydratase
EC 4.2.1.31 maleate hydratase
EC 4.2.1.32 L(+)-tartrate dehydratase
EC 4.2.1.33 3-isopropylmalate dehydratase
EC 4.2.1.34 (S)-2-methylmalate dehydratase
EC 4.2.1.35 (R)-2-methylmalate dehydratase
EC 4.2.1.36 homoaconitate hydratase
EC 4.2.1.37 now EC 3.3.2.4
EC 4.2.1.38 now EC 4.3.1.20
EC 4.2.1.39 gluconate dehydratase
EC 4.2.1.40 glucarate dehydratase
EC 4.2.1.41 5-dehydro-4-deoxyglucarate dehydratase
EC 4.2.1.42 galactarate dehydratase
EC 4.2.1.43 2-dehydro-3-deoxy-L-arabinonate dehydratase
EC 4.2.1.44 myo-inosose-2 dehydratase
EC 4.2.1.45 CDP-glucose 4,6-dehydratase
EC 4.2.1.46 dTDP-glucose 4,6-dehydratase
EC 4.2.1.47 GDP-mannose 4,6-dehydratase
EC 4.2.1.48 D-glutamate cyclase
EC 4.2.1.49 urocanate hydratase
EC 4.2.1.50 pyrazolylalanine synthase
See the following file for:
EC 4.2.1.51 to EC 4.2.1.100
EC 4.2.1.101 to EC 4.2.1.183
Accepted name: carbonate dehydratase
Reaction: H2CO3 = CO2 + H2O
Other name(s): carbonic anhydrase; anhydrase; carbonate anhydrase; carbonic acid anhydrase; carboxyanhydrase; carbonic anhydrase A; carbonate hydro-lyase
Systematic name: carbonate hydro-lyase (carbon-dioxide-forming)
Comments: A zinc protein.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9001-03-0
References:
1. Keilin, D. and Mann, T. Carbonic anhydrase. Nature 144 (1939) 442-443.
2. Murakami, H. and Sly, W.S. Purification and characterization of human salivary carbonic anhydrase. J. Biol. Chem. 262 (1987) 1382-1388. [PMID: 2433278]
Accepted name: fumarate hydratase
Reaction: (S)-malate = fumarate + H2O
For diagram of reaction click here or (another example or another example).
Other name(s): fumarase; L-malate hydro-lyase; (S)-malate hydro-lyase
Systematic name: (S)-malate hydro-lyase (fumarate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9032-88-6
References:
1. Alberty, R.A. Fumarase, in Boyer, P.D., Lardy, H. and Myrbäck, K. (Eds.), The Enzymes, 2nd edn., vol. 5, Academic Press, New York, 1961, pp. 531-544.
2. Kanarek, L. and Hill, R.L. The preparation and characterization of fumarase from swine heart muscle. J. Biol. Chem. 239 (1964) 4202-4206. [PMID: 14247669]
Accepted name: aconitate hydratase
Reaction: citrate = isocitrate (overall reaction)
(1a) citrate = cis-aconitate + H2O
(1b) cis-aconitate + H2O = isocitrate
For diagram click here and mechanism click here (see also glyoxylate cycle and citric acid cycle).
Glossary: isocitrate = (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate (previously known as threo-Ds-isocitrate)
cis-aconitate = (Z)-prop-1-ene-1,2,3-tricarboxylate
Other name(s): cis-aconitase; aconitase; AcnB; 2-methylaconitate hydratase; citrate(isocitrate) hydro-lyase
Systematic name: citrate(isocitrate) hydro-lyase (cis-aconitate-forming)
Comments: Besides interconverting citrate and cis-aconitate, it also interconverts cis-aconitate with isocitrate and, hence, interconverts citrate and isocitrate. The equilibrium mixture is 91% citrate, 6% isocitrate and 3% aconitate. cis-Aconitate is used to designate the isomer (Z)-prop-1-ene-1,2,3-tricarboxylate. An iron-sulfur protein, containing a [4Fe-4S] cluster to which the substrate binds.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9024-25-3
References:
1. Dickman, S.R. Aconitase. In: Boyer, P.D., Lardy, H. and Myrbäck, K (Eds.), The Enzymes, 2nd ed., vol. 5, Academic Press, New York, 1961, pp. 495-510.
2. Morrison, J.F. The purification of aconitase. Biochem. J. 56 (1954) 99-105. [PMID: 13126098]
3. Lauble, H., Kennedy, M.C., Beinert, H. and Stout, C.D. Crystal structures of aconitase with trans-aconitate and nitrocitrate bound. J. Mol. Biol. 237 (1994) 437-451. [PMID: 8151704]
[EC 4.2.1.4 Deleted entry: citrate dehydratase. Now known to be a partial reaction catalysed by EC 4.2.1.3, aconitate hydratase. (EC 4.2.1.4 created 1961, deleted 2013)]
Accepted name: arabinonate dehydratase
Reaction: D-arabinonate = 2-dehydro-3-deoxy-D-arabinonate + H2O
For diagram of reaction click here.
Other name(s): D-arabinonate hydro-lyase
Systematic name: D-arabinonate hydro-lyase (2-dehydro-3-deoxy-D-arabinonate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9024-36-6
References:
1. Palleroni, N.J. and Doudoroff, M. Characterization and properties of 2-keto-3-deoxy-D-arabonic acid. J. Biol. Chem. 223 (1956) 499-508 [PMID: 13376619]
For diagram of reaction click here.
Accepted name: galactonate dehydratase
Reaction: D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O
For diagram of reaction click here.
Other name(s): D-galactonate dehydrase; D-galactonate dehydratase; D-galactonate hydro-lyase
Systematic name: D-galactonate hydro-lyase (2-dehydro-3-deoxy-D-galactonate-forming)
Comments: The enzyme shows no activity with D-gluconate [2]. cf. EC 4.2.1.140, gluconate/galactonate dehydratase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9024-38-8
References:
1. De Ley, J. and Doudoroff, M. The metabolism of D-galactose in Pseudomonas saccarophila. J. Biol. Chem. 227 (1957) 745-757. [PMID: 13462997]
2. Donald, A., Sibley, D., Lyons, D.E. and Dahms, A.S. D-Galactonate dehydrase. Purification and properties. J. Biol. Chem. 254 (1979) 2132-2137. [PMID: 422572]
Accepted name: altronate dehydratase
Reaction: D-altronate = 2-dehydro-3-deoxy-D-gluconate + H2O
For diagram of reaction click here.
Other name(s): D-altronate hydro-lyase
Systematic name: D-altronate hydro-lyase (2-dehydro-3-deoxy-D-gluconate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 62213-26-7
References:
1. Smiley, J.D. and Ashwell, G. Uronic acid metabolism in bacteria. III. Purification and properties of D-altronic acid and D-mannonic acid dehydrases in Escherichia coli. J. Biol. Chem. 235 (1960) 1571-1575. [PMID: 13831814]
Accepted name: mannonate dehydratase
Reaction: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O
For diagram of reaction click here.
Other name(s): mannonic hydrolase; mannonate hydrolyase; altronic hydro-lyase; altronate hydrolase; D-mannonate hydrolyase; D-mannonate hydro-lyase
Systematic name: D-mannonate hydro-lyase (2-dehydro-3-deoxy-D-gluconate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9024-31-1
References:
1. Ashwell, G., Wahba, A.J. and Hickman, J. A new pathway of uronic acid metabolism. Biochim. Biophys. Acta 30 (1958) 186-187.
2. Robert-Baudouy, J.M. and Stoeber, F.R. [Purification and properties of D-mannonate hydrolyase from Escherichia coli K12]. Biochim. Biophys. Acta 309 (1973) 473-485. [PMID: 4581499]
Accepted name: dihydroxy-acid dehydratase
Reaction: 2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O
For diagram of reaction click here.
Other name(s): acetohydroxyacid dehydratase; α,β-dihydroxyacid dehydratase; 2,3-dihydroxyisovalerate dehydratase; α,β-dihydroxyisovalerate dehydratase; dihydroxy acid dehydrase; DHAD; 2,3-dihydroxy-acid hydro-lyase; 2,3-dihydroxy-acid hydro-lyase (3-methyl-2-oxobutanoate-forming)
Systematic name: 2,3-dihydroxy-3-methylbutanoate hydro-lyase (3-methyl-2-oxobutanoate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9024-32-2
References:
1. Kanamori, M. and Wixom, R.L. Studies in valine biosynthesis. V. Characteristics of the purified dihydroxyacid dehydratase from spinach leaves. J. Biol. Chem. 238 (1963) 998-1005.
2. Myers, J.W. Dihydroxy acid dehydrase: an enzyme involved in the biosynthesis of isoleucine and valine. J. Biol. Chem. 236 (1961) 1414-1418. [PMID: 13727223]
Accepted name: 3-dehydroquinate dehydratase
Reaction: 3-dehydroquinate = 3-dehydroshikimate + H2O
For diagram click here and mechanism here.
Glossary: quinate = (1R,3R,4R,5R)-1,3,4,5-tetrahydroxycyclohexanecarboxylic acid and is a cyclitol carboxylate
The numbering system used for the 3-dehydroquinate is that of the recommendations on cyclitols, sections I-8 and I-9: and is shown in the reaction diagram). The use of the term '5-dehydroquinate' for this compound is based on an earlier system of numbering.
Other name(s): 3-dehydroquinate hydrolase; DHQase; dehydroquinate dehydratase; 3-dehydroquinase; 5-dehydroquinase; dehydroquinase; 5-dehydroquinate dehydratase; 5-dehydroquinate hydro-lyase; 3-dehydroquinate hydro-lyase
Systematic name: 3-dehydroquinate hydro-lyase (3-dehydroshikimate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9012-66-2
References:
1. Mitsuhashi, S. and Davis, B.D. Aromatic biosynthesis. XII. Conversion of 5-dehydroquinic acid to 5-dehydroshikimic acid by 5-dehydroquinase. Biochim. Biophys. Acta 15 (1954) 54-61. [PMID: 13198937]
2. Mitsuhashi, S. and Davis, B.D. Aromatic biosynthesis. XII. Conversion of quinic acid to 5-dehydroquinic acid by quinic dehydrogenase. Biochim. Biophys. Acta 15 (1954) 268-280. [PMID: 13208693]
Accepted name: phosphopyruvate hydratase
Reaction: 2-phospho-D-glycerate = phosphoenolpyruvate + H2O
For diagram of reaction click here.
Other name(s): enolase; 2-phosphoglycerate dehydratase; 14-3-2-protein; nervous-system specific enolase; phosphoenolpyruvate hydratase; 2-phosphoglycerate dehydratase; 2-phosphoglyceric dehydratase; 2-phosphoglycerate enolase; γ-enolase; 2-phospho-D-glycerate hydro-lyase
Systematic name: 2-phospho-D-glycerate hydro-lyase (phosphoenolpyruvate-forming)
Comments: Also acts on 3-phospho-D-erythronate.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9014-08-8
References:
1. Holt, A. and Wold, F. The isolation and characterization of rabbit muscle enolase. J. Biol. Chem. 236 (1961) 3227-3231. [PMID: 13908561]
2. Malmström, B.G. Enolase, in Boyer, P.D., Lardy, H. and Myrbäck, K. (Eds.), The Enzymes, 2nd edn., vol. 5, Academic Press, New York, 1961, pp. 471-494.
3. Westhead, E.W. and McLain, G. Purification of brewers' and bakers' yeast enolase yielding a single active component. J. Biol. Chem. 239 (1964) 2464-2468.
Accepted name: phosphogluconate dehydratase
Reaction: 6-phospho-D-gluconate = 2-dehydro-3-deoxy-6-phospho-D-gluconate + H2O
Other name(s): 6-phosphogluconate dehydratase; 6-phosphogluconic dehydrase; gluconate-6-phosphate dehydratase; gluconate 6-phosphate dehydratase; 6-phosphogluconate dehydrase; 6-phospho-D-gluconate hydro-lyase
Systematic name: 6-phospho-D-gluconate hydro-lyase (2-dehydro-3-deoxy-6-phospho-D-gluconate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9024-33-3
References:
1. Meloche, H.P. and Wood, W.A. The mechanism of 6-phosphogluconic dehydrase. J. Biol. Chem. 239 (1964) 3505-3510.
[EC 4.2.1.13 Transferred entry: now EC 4.3.1.17, L-serine ammonia-lyase (EC 4.2.1.13 created 1961, deleted 2001)]
[EC 4.2.1.14 Transferred entry: now EC 4.3.1.18, D-serine ammonia-lyase (EC 4.2.1.14 created 1961, deleted 2001)]
[EC 4.2.1.15 Deleted entry: homoserine dehydratase. Identical with EC 4.4.1.1 cystathionine γ-lyase (EC 4.2.1.15 created 1961, deleted 1972)]
[EC 4.2.1.16 Transferred entry: now EC 4.3.1.19, threonine ammonia-lyase (EC 4.2.1.16 created 1961, deleted 2001)]
Accepted name: enoyl-CoA hydratase
Reaction: (3S)-3-hydroxyacyl-CoA = trans-2(or 3)-enoyl-CoA + H2O
For diagram of reaction click here.
Other name(s): enoyl hydrase; unsaturated acyl-CoA hydratase; β-hydroxyacyl-CoA dehydrase; β-hydroxyacid dehydrase; acyl coenzyme A hydrase; crotonase; crotonyl hydrase; 2-octenoyl coenzyme A hydrase; enoyl coenzyme A hydratase; 2-enoyl-CoA hydratase; short-chain enoyl-CoA hydratase; ECH; trans-2-enoyl-CoA hydratase; short-chain enoyl-CoA hydratase; enoyl coenzyme A hydrase (D); enoyl coenzyme A hydrase (L); short chain enoyl coenzyme A hydratase; D-3-hydroxyacyl-CoA dehydratase
Systematic name: (3S)-3-hydroxyacyl-CoA hydro-lyase
Comments: Acts in the reverse direction. With cis-compounds, yields (3R)-3-hydroxyacyl-CoA. cf. EC 4.2.1.74 long-chain-enoyl-CoA hydratase.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9027-13-8
References:
1. Moskowitz, G.J. and Merrick, J.M. Metabolism of poly-β-hydroxybutyrate. II. Enzymatic synthesis of D-(–)-β-hydroxybutyryl coenzyme A by an enoyl hydrase from Rhodospirillum rubrum. Biochemistry 8 (1969) 2748-2755. [PMID: 5808333]
2. Stern, J.R. Thioltranscrotylase and β-hydroxybutyryl CoA racemase activities of crystalline crotonase. Biochim. Biophys. Acta 26 (1957) 641-643.
Accepted name: methylglutaconyl-CoA hydratase
Reaction: (S)-3-hydroxy-3-methylglutaryl-CoA = trans-3-methylglutaconyl-CoA + H2O
For diagram click here.
Other name(s): methylglutaconyl coenzyme A hydratase; 3-methylglutaconyl CoA hydratase; methylglutaconase; (S)-3-hydroxy-3-methylglutaryl-CoA hydro-lyase
Systematic name: (S)-3-hydroxy-3-methylglutaryl-CoA hydro-lyase (trans-3-methylglutaconyl-CoA-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9024-24-2
References:
1. Hilz, H., Knappe, J., Ringelmann, E. and Lynen, F. Methylglutaconase, eine neue Hydratase, die am Stoffwechsel verzweigter Carbonsäuren beteiligt ist. Biochem. Z. 329 (1958) 476-489. [PMID: 13535602]
Accepted name: imidazoleglycerol-phosphate dehydratase
Reaction: D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate = 3-(imidazol-4-yl)-2-oxopropyl phosphate + H2O
For diagram click here.
Other name(s): IGP dehydratase; D-erythro-1-(imidazol-4-yl)glycerol 3-phosphate hydro-lyase
Systematic name: D-erythro-1-(imidazol-4-yl)glycerol-3-phosphate hydro-lyase [3-(imidazol-4-yl)-2-oxopropyl-phosphate-forming]
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9024-35-5
References:
1. Ames, B.N. The biosynthesis of histidine: D-erythro-Imidazoleglycerol phosphate dehydrase. J. Biol. Chem. 228 (1957) 131-143. [PMID: 13475302]
Accepted name: tryptophan synthase
Reaction: L-serine + 1-C-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + D-glyceraldehyde 3-phosphate + H2O (overall reaction)
(1a) 1-C-(indol-3-yl)glycerol 3-phosphate = indole + D-glyceraldehyde 3-phosphate
(1b) L-serine + indole = L-tryptophan + H2O
For diagram of reaction click here and mechanism click here
Other name(s): L-tryptophan synthetase; indoleglycerol phosphate aldolase; tryptophan desmolase; tryptophan synthetase; L-serine hydro-lyase (adding indoleglycerol-phosphate)
Systematic name: L-serine hydro-lyase [adding 1-C-(indol-3-yl)glycerol 3-phosphate, L-tryptophan and glyceraldehyde-3-phosphate-forming]
Comments: A pyridoxal-phosphate protein. The α-subunit catalyses the conversion of 1-C-(indol-3-yl)glycerol 3-phosphate to indole and glyceraldehyde 3-phosphate (this reaction was listed formerly as EC 4.1.2.8). The indole migrates to the β-subunit where, in the presence of pyridoxal 5'-phosphate, it is combined with L-serine to form L-tryptophan. In some organisms this enzyme is part of a multifunctional protein that also includes one or more of the enzymes EC 2.4.2.18 (anthranilate phosphoribosyltransferase), EC 4.1.1.48 (indole-3-glycerol-phosphate synthase), EC 4.1.3.27 (anthranilate synthase) and EC 5.3.1.24 (phosphoribosylanthranilate isomerase). In thermophilic organisms, where the high temperature enhances diffusion and causes the loss of indole, a protein similar to the β subunit can be found (EC 4.2.1.122). That enzyme cannot combine with the α unit of EC 4.2.1.20 to form a complex.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9014-52-2
References:
1. Crawford, I.P. and Yanofsky, C. On the separation of the tryptophan synthetase of Escherichia coli into two protein components. Proc. Natl. Acad. Sci. USA 44 (1958) 1161-1170. [PMID: 16590328]
2. Creighton, T.E. and Yanofsky, C. Chorismate to tryptophan (Escherichia coli) - anthranilate synthetase, PR transferase, PRA isomerase, InGP synthetase, tryptophan synthetase. Methods Enzymol. 17A (1970) 365-380.
3. Hütter, R., Niederberger, P. and DeMoss, J.A. Tryptophan synthetic genes in eukaryotic microorganisms. Annu. Rev. Microbiol. 40 (1986) 55-77. [PMID: 3535653]
4. Hyde, C.C., Ahmed, S.A., Padlan, E.A., Miles, E.W. and Davies, D.R. Three-dimensional structure of the tryptophan synthase α2β2 multienzyme complex from Salmonella typhimurium. J. Biol. Chem. 263 (1988) 17857-17871. [PMID: 3053720]
5. Woehl, E. and Dunn, M.F. Mechanisms of monovalent cation action in enzyme catalysis: the tryptophan synthase α-, β-, and αβ-reactions. Biochemistry 38 (1999) 7131-7141. [PMID: 10353823]
[EC 4.2.1.21 Deleted entry: cystathionine β-synthase. Now EC 4.2.1.22 cystathionine β-synthase (EC 4.2.1.21 created 1961, deleted 1964)]
Accepted name: cystathionine β-synthase
Reaction: L-serine + L-homocysteine = L-cystathionine + H2O
For diagram of reaction click here.
Other name(s): serine sulfhydrase; β-thionase; methylcysteine synthase; cysteine synthase (incorrect); serine sulfhydrylase; L-serine hydro-lyase (adding homocysteine)
Systematic name: L-serine hydro-lyase (adding homocysteine; L-cystathionine-forming)
Comments: A pyridoxal-phosphate protein. A multifunctional enzyme: catalyses β-replacement reactions between L-serine, L-cysteine, cysteine thioethers, or some other β-substituted α-L-amino acids, and a variety of mercaptans.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9023-99-8
References:
1. Braunstein, A.E., Goryachinkova, E.V., Tolosa, E.A., Willhardt, I.H. and Yefremova, L.L. Specificity and some other properties of liver serine sulphhydrase: evidence for its identity with cystathionine-synthase. Biochim. Biophys. Acta, 242 (1971) 247-260. [PMID: 5121611]
2. Nakagawa, H. and Kimura, H. Purification and properties of cystathionine synthetase synthetase from rat liver: separation of cystathionine synthetase from serine dehydratase. Biochem. Biophys. Res. Commun. 32 (1968) 209-214. [PMID: 5672136]
3. Schlossmann, K., Brüggemann, J. and Lynen, F. Biosynthese des Cysteins. I. Nachweis und Isolierung der Serinsulfhydrase aus Bäckerhefe. Biochem. Z. 336 (1962) 258-273.
[EC 4.2.1.23 Deleted entry: methylcysteine synthase. The reaction was due to a side-reaction of EC 4.2.1.22 cystathionine β-synthase (EC 4.2.1.23 created 1961, deleted 1972)]
Accepted name: porphobilinogen synthase
Reaction: 2 5-aminolevulinate = porphobilinogen + 2 H2O
For diagram of reaction click here.
Other name(s): aminolevulinate dehydratase; δ-aminolevulinate dehydratase; δ-aminolevulinic acid dehydrase; δ-aminolevulinic acid dehydratase; aminolevulinic dehydratase; δ-aminolevulinic dehydratase; 5-levulinic acid dehydratase; 5-aminolevulinate hydro-lyase (adding 5-aminolevulinate and cyclizing)
Systematic name: 5-aminolevulinate hydro-lyase (adding 5-aminolevulinate and cyclizing; porphobilinogen-forming)
Comments: The enzyme catalyses the asymmetric condensation and cyclization of two 5-aminolevulinate molecules, which is the first common step in the biosynthesis of tetrapyrrole pigments such as porphyrin, chlorophyll, vitamin B12, siroheme, phycobilin, and cofactor F430. The enzyme is widespread, being essential in organisms that carry out respiration, photosynthesis, or methanogenesis. The enzymes from most organisms utilize metal ions (Zn2+, Mg2+, K+, and Na+) as cofactors that reside at multiple sites, including the active site and allosteric sites. Enzymes from archaea, yeast, and metazoa (including human) contain Zn2+ at the active site. In humans, the enzyme is a primary target for the environmental toxin Pb. The enzymes from some organisms utilize a dynamic equilibrium between architecturally distinct multimeric assemblies as a means for allosteric regulation.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9036-37-7
References:
1. Gibson, K.D., Neuberger, A. and Scott, J.J. The purification and properties of δ-aminolaevulic acid dehydrase. Biochem. J. 61 (1955) 618-629. [PMID: 13276347]
2. Komai, H. and Neilands, J.B. The metalloprotein nature of Ustilago δ-aminolevulinate dehydratase. Biochim. Biophys. Acta 171 (1969) 311-320. [PMID: 5773436]
3. Yamasaki, H. and Moriyama, T. δ-Aminolevulinic acid dehydratase of Mycobacterium phlei. Biochim. Biophys. Acta 227 (1971) 698-705. [PMID: 4998716]
4. Mitchell, L.W. and Jaffe, E.K. Porphobilinogen synthase from Escherichia coli is a Zn(II) metalloenzyme stimulated by Mg(II). Arch. Biochem. Biophys. 300 (1993) 169-177. [PMID: 8424649]
5. Jaffe, E.K., Ali, S., Mitchell, L.W., Taylor, K.M., Volin, M. and Markham, G.D. Characterization of the role of the stimulatory magnesium of Escherichia coli porphobilinogen synthase. Biochemistry 34 (1995) 244-251. [PMID: 7819203]
6. Warren, M.J., Cooper, J.B., Wood, S.P. and Shoolingin-Jordan, P.M. Lead poisoning, haem synthesis and 5-aminolaevulinic acid dehydratase. Trends Biochem. Sci. 23 (1998) 217-221. [PMID: 9644976]
7. Jaffe, E.K. and Lawrence, S.H. Allostery and the dynamic oligomerization of porphobilinogen synthase. Arch. Biochem. Biophys. 519 (2012) 144-153. [PMID: 22037356]
8. Tian, B.X., Erdtman, E. and Eriksson, L.A. Catalytic mechanism of porphobilinogen synthase: the chemical step revisited by QM/MM calculations. J. Phys. Chem. B 116 (2012) 12105-12112. [PMID: 22974111]
Accepted name: L-arabinonate dehydratase
Reaction: L-arabinonate = 2-dehydro-3-deoxy-L-arabinonate + H2O
For diagram of reaction click here.
Other name(s): L-arabonate dehydrase; L-arabonate dehydratase; L-arabinonate hydro-lyase
Systematic name: L-arabinonate hydro-lyase (2-dehydro-3-deoxy-L-arabinonate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9024-30-0
References:
1. Weimberg, R. L-2-Keto-4,5-dihydroxyvaleric acid: an intermediate in the oxidation of L-arabinose by Pseudomonase saccharophila. J. Biol. Chem. 234 (1959) 727-732. [PMID: 13654251]
[EC 4.2.1.26 Transferred entry: now EC 4.3.1.9, aminodeoxygluconate ammonia-lyase (EC 4.2.1.26 created 1965, deleted 2002)]
Accepted name: acetylenecarboxylate hydratase
Reaction: 3-oxopropanoate = propynoate + H2O
Other name(s): acetylenemonocarboxylate hydratase; alkynoate hydratase; acetylenemonocarboxylate hydrase; acetylenemonocarboxylic acid hydrase; malonate-semialdehyde dehydratase; 3-oxopropanoate hydro-lyase
Systematic name: 3-oxopropanoate hydro-lyase (propynoate-forming)
Comments: The reaction is effectively irreversible, favouring oxopropanoate (malonic semialdehyde) and its tautomers. Also acts on but-3-ynoate forming acetoacetate. The mechanism appears to involve hydration of the acetylene to 3-hydroxypropenoate, which will spontaneously tautomerize to 3-oxopropanoate. It is thus analogous to EC 4.1.1.78, acetylenedicarboxylate decarboxylase, in its mechanism.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9024-26-4
References:
1. Van den Tweel, W.J.J. and De Bont, J.A.M. Metabolism of 3-butyn-1-ol by Pseudomonas BB1. J. Gen. Microbiol. 131 (1985) 3155-3162. [PMID: 16525953]
2. Yamada, E.W. and Jakoby, W.B. Enzymatic utilization of acetylenic compounds. II. Acetylenemonocarboxylic acid hydrase. J. Biol. Chem. 234 (1959) 941-945. [PMID: 13654296]
Accepted name: propanediol dehydratase
Reaction: propane-1,2-diol = propanal + H2O
Other name(s): meso-2,3-butanediol dehydrase; diol dehydratase; DL-1,2-propanediol hydro-lyase; diol dehydrase; adenosylcobalamin-dependent diol dehydratase; propanediol dehydrase; coenzyme B12-dependent diol dehydrase; 1,2-propanediol dehydratase; dioldehydratase; propane-1,2-diol hydro-lyase
Systematic name: propane-1,2-diol hydro-lyase (propanal-forming)
Comments: Two different forms of the enzyme have been described. One form requires a cobamide cofactor, while the other is a glycyl radical enzyme. The cobamide-dependent enzyme has been shown to also dehydrate ethylene glycol to acetaldehyde.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9026-90-8
References:
1. Abeles, R.H. and Lee, H.A., Jr. An intramolecular oxidation-reduction requiring a cobamide coenzyme. J. Biol. Chem. 236 (1961) 2347-2350. [PMID: 13680987]
2. Lee, H.A. and Abeles, R.H. Purification and properties of dioldehydrase, and enzyme requiring a cobamide coenzyme. J. Biol. Chem. 238 (1963) 2367-2373. [PMID: 13929077]
3. Forage, R.G. and Foster, M.A. Glycerol fermentation in Klebsiella pneumoniae: functions of the coenzyme B12-dependent glycerol and diol dehydratases. J. Bacteriol. 149 (1982) 413-419. [PMID: 7035429]
4. LaMattina, J.W., Keul, N.D., Reitzer, P., Kapoor, S., Galzerani, F., Koch, D.J., Gouvea, I.E. and Lanzilotta, W.N. 1,2-Propanediol Dehydration in Roseburia inulinivorans: Structural basis for substrate and enantiomer selectivity. J. Biol. Chem 291 (2016) 15515-15526. [PMID: 27252380]
[EC 4.2.1.29 Transferred entry: now EC 4.99.1.6, indoleacetaldoxime dehydratase. The enzyme was classified incorrectly as a C-O lyase when the bond broken is a N-O bond. (EC 4.2.1.29 created 1965, deleted 2004)
Accepted name: glycerol dehydratase
Reaction: glycerol = 3-hydroxypropanal + H2O
Other name(s): glycerol dehydrase; glycerol hydro-lyase
Systematic name: glycerol hydro-lyase (3-hydroxypropanal-forming)
Comments: wo different forms of the enzyme have been described. One form requires a cobamide cofactor, while the other is a glycyl radical enzyme.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9077-68-3
References:
1. Smiley, K.L. and Sobolov, M. A cobamide-requiring glycerol dehydrase from an acrolein-forming Lactobacillus. Arch. Biochem. Biophys. 97 (1962) 538-543.
2. Schneider, Z. and Pawelkiewicz, J. The properties of glycerol dehydratase isolated from Aerobacter aerogenes, and the properties of the apoenzyme subunits. Acta Biochim. Pol. 13 (1966) 311-328. [PMID: 5962440]
3. Schneider, Z., Larsen, E.G., Jacobsen, G., Johnson, B.C. and Pawelkiewicz, J. Purification and properties of glycerol dehydrase. J. Biol. Chem. 245 (1970) 3388-3396. [PMID: 4989992]
4. Forage, R.G. and Foster, M.A. Glycerol fermentation in Klebsiella pneumoniae: functions of the coenzyme B12-dependent glycerol and diol dehydratases. J. Bacteriol. 149 (1982) 413-419. [PMID: 7035429]
5. O'Brien, J.R., Raynaud, C., Croux, C., Girbal, L., Soucaille, P. and Lanzilotta, W.N. Insight into the mechanism of the B12-independent glycerol dehydratase from Clostridium butyricum: preliminary biochemical and structural characterization. Biochemistry 43 (2004) 4635-4645. [PMID: 15096031]
Accepted name: maleate hydratase
Reaction: (R)-malate = maleate + H2O
Other name(s): D-malate hydro-lyase; malease; (R)-malate hydro-lyase
Systematic name: (R)-malate hydro-lyase (maleate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 37290-71-4
References:
1. Britten, J.S., Morell, H. and Taggart, J.V. Anion activation of maleate hydratase. Biochim. Biophys. Acta 185 (1969) 220-227. [PMID: 5796106]
2. Sacks, W. and Jensen, C.O. Malease, a hydrase from corn kernals. J. Biol. Chem. 192 (1951) 231-236.
Accepted name: L(+)-tartrate dehydratase
Reaction: (R,R)-tartrate = oxaloacetate + H2O
Other name(s): tartrate dehydratase; tartaric acid dehydrase; L-tartrate dehydratase; L-(+)-tartaric acid dehydratase; (R,R)-tartrate hydro-lyase
Systematic name: (R,R)-tartrate hydro-lyase (oxaloacetate-forming)
Comments: The enzyme exists in an inactive low-molecular-mass form, which is converted into active enzyme in the presence of Fe2+ and thiol. cf. EC 4.2.1.81 D(–)-tartrate dehydratase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9014-40-8
References:
1. Hurlbert, R.E. and Jakoby, W.B. Tartaric acid metabolism. I. Subunits of L(+)-tartaric acid dehydrase. J. Biol. Chem. 240 (1965) 2772-2777. [PMID: 14342293]
Accepted name: 3-isopropylmalate dehydratase
Reaction: (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate (overall reaction)
(1a) (2R,3S)-3-isopropylmalate = 2-isopropylmaleate + H2O
(1b) 2-isopropylmaleate + H2O = (2S)-2-isopropylmalate
For diagram of reaction click here.
Glossary: α-isopropylmalate = (2S)-2-isopropylmalate
β-isopropylmalate = (2R,3S)-3-isopropylmalate
Other name(s): (2R,3S)-3-isopropylmalate hydro-lyase; β-isopropylmalate dehydratase; isopropylmalate isomerase; α-isopropylmalate isomerase; 3-isopropylmalate hydro-lyase
Systematic name: (2R,3S)-3-isopropylmalate hydro-lyase (2-isopropylmaleate-forming)
Comments: Forms part of the leucine biosynthesis pathway. The enzyme brings about the interconversion of the two isomers of isopropylmalate. It contains an iron-sulfur cluster.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37290-72-5
References:
1. Gross, S.R., Burns, R.O. and Umbarger, H.E. The biosynthesis of leucine. II. The enzymic isomerization of β-carboxy-β-hydroxyisocaproate and α-hydroxy-β-carboxyisocaproate. Biochemistry 2 (1963) 1046-1052. [PMID: 14087357]
2. Calvo, J. M., Stevens, C. M., Kalyanpur, M. G., and Umbarger, H. E. The absolute configuration of α-hydroxy-β-carboxyisocaproic acid (3-isopropylmalic acid), an intermediate in leucine biosynthesis. Biochemistry 3 (1964) 2024-2027. [PMID: 14269331]
3. Cole, F.E., Kalyanpur, M. G. and Stevens, C. M. Absolute configuration of α-isopropylmalate and the mechanism of its conversion to β-isopropylmalate in the biosynthesis of leucine. Biochemistry 12 (1973) 3346-3350. [PMID: 4270046]
4. Jang, S. and Imlay, J.A. Micromolar intracellular hydrogen peroxide disrupts metabolism by damaging iron-sulfur enzymes. J. Biol. Chem. 282 (2007) 929-937. [PMID: 17102132]
Accepted name: (S)-2-methylmalate dehydratase
Reaction: (S)-2-methylmalate = 2-methylfumarate + H2O
Other name(s): mesaconate hydratase; (+)-citramalate hydro-lyase; L-citramalate hydrolase; citramalate dehydratase; (+)-citramalic hydro-lyase; mesaconate mesaconase; mesaconase; (S)-2-methylmalate hydro-lyase
Systematic name: (S)-2-methylmalate hydro-lyase (2-methylfumarate-forming)
Comments: Also hydrates fumarate to (S)-malate.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, CAS registry number: 9027-94-5
References:
1. Blair, A.H. and Barker, H.A. Assay and purification of (+)-citramalate hydro-lyase components from Clostridium tetanomorphum. J. Biol. Chem. 241 (1966) 400-408. [PMID: 5903732]
2. Wang, C.C. and Barker, H.A. Purification and properties of L-citramalate hydrolyase. J. Biol. Chem. 244 (1969) 2516-2526. [PMID: 5769987]
Accepted name: (R)-2-methylmalate dehydratase
Reaction: (R)-2-methylmalate = 2-methylmaleate + H2O
Other name(s): citraconate hydratase; citraconase; citramalate hydro-lyase; (–)-citramalate hydro-lyase; (R)-2-methylmalate hydro-lyase
Systematic name: (R)-2-methylmalate hydro-lyase (2-methylmaleate-forming)
Comments: Requires Fe2+.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9027-92-3
References:
1. Subramanian, S.S. and Raghavendra Rao, M.R. Purification and properties of citraconase. J. Biol. Chem. 243 (1968) 2367-2372. [PMID: 4296839]
2. Raghavendra Rao, M.R., Subramanian, S.S., Rahatekar, H.I. and Paranjape, S.V. Enzymatic hydration of citraconate to (–)citramalate. Biochem. Biophys. Res. Commun. 12 (1963) 78-82. [PMID: 13973053]
Accepted name: homoaconitate hydratase
Reaction: (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate = (Z)-but-1-ene-1,2,4-tricarboxylate + H2O
For diagram click here.
Glossary: cis-homoaconitate = (Z)-but-1-ene-1,2,4-tricarboxylate
(R)-homocitrate = (2R)-2-hydroxybutane-1,2,4-tricarboxylate
homoisocitrate = (–)-threo-homoisocitrate = (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate
homocitrate = (2R)-2-hydroxybutane-1,2,4-tricarboxylate
homoisocitrate = (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate
Other name(s): homoaconitase; cis-homoaconitase; HACN; Lys4; LysF; 2-hydroxybutane-1,2,4-tricarboxylate hydro-lyase (incorrect)
Systematic name: (1R,2S)-1-hydroxybutane-1,2,4-tricarboxylate hydro-lyase [(Z)-but-1-ene-1,2,4-tricarboxylate-forming]
Comments: Requires a [4Fe-4S] cluster for activity. The enzyme from the hyperthermophilic eubacterium Thermus thermophilus can catalyse the reaction shown above but cannot catalyse the previously described reaction, i.e. formation of homocitrate by hydration of cis-homoaconitate. The enzyme responsible for the conversion of cis-homoaconitate into homocitrate in T. thermophilus is unknown at present but the reaction can be catalysed in vitro using aconitate hydratase from pig (EC 4.2.1.3) [2].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9030-68-6
References:
1. Strassman, M. and Ceci, L.N. Enzymatic formation of cis-homoaconitic acid, an intermediate in lysine biosynthesis in yeast. J. Biol. Chem. 241 (1966) 5401-5407. [PMID: 5954805]
2. Jia, Y., Tomita, T., Yamauchi, K., Nishiyama, M. and Palmer, D.R. Kinetics and product analysis of the reaction catalysed by recombinant homoaconitase from Thermus thermophilus. Biochem. J. 396 (2006) 479-485. [PMID: 16524361]
3. Zabriskie, T.M. and Jackson, M.D. Lysine biosynthesis and metabolism in fungi. Nat. Prod. Rep. 17 (2000) 85-97. [PMID: 10714900]
[EC 4.2.1.37 Transferred entry: now EC 3.3.2.4 trans-epoxysuccinate hydrolase (EC 4.2.1.37 created 1972, deleted 1992)]
[EC 4.2.1.38 Transferred entry: now EC 4.3.1.20, erythro-3-hydroxyaspartate ammonia-lyase (EC 4.2.1.38 created 1972, deleted 2001)]
Accepted name: gluconate dehydratase
Reaction: D-gluconate = 2-dehydro-3-deoxy-D-gluconate + H2O
For diagram of reaction click here.
Other name(s): D-gluconate dehydratase; D-gluconate hydro-lyase
Systematic name: D-gluconate hydro-lyase (2-dehydro-3-deoxy-D-gluconate-forming)
Comments: The enzyme shows no activity with D-galactonate [2]. cf. EC 4.2.1.140, gluconate/galactonate dehydratase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37290-75-8
References:
1. Andreesen, J.R. and Gottschalk, G. The occurrence of a modified Entner-Doudoroff pathway in Clostridium aceticum. Arch. Mikrobiol. 69 (1969) 160-170. [PMID: 5383859]
2. Bender, R. and Gottschalk, G. Purification and properties of D-gluconate dehydratase from Clostridium pasteurianum. Eur. J. Biochem. 40 (1973) 309-321. [PMID: 4772682]
Accepted name: glucarate dehydratase
Reaction: D-glucarate = 5-dehydro-4-deoxy-D-glucarate + H2O
Other name(s): D-glucarate dehydratase; D-glucarate hydro-lyase
Systematic name: D-glucarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9059-02-3
References:
1. Blumenthal, H.J. D-Glucarate dehydrase. Methods Enzymol. 9 (1966) 660-665.
Accepted name: 5-dehydro-4-deoxyglucarate dehydratase
Reaction: 5-dehydro-4-deoxy-D-glucarate = 2,5-dioxopentanoate + H2O + CO2
Other name(s): 5-keto-4-deoxy-glucarate dehydratase; 5-keto-4-deoxy-glucarate dehydratase; deoxyketoglucarate dehydratase; D-4-deoxy-5-ketoglucarate hydro-lyase; 5-dehydro-4-deoxy-D-glucarate hydro-lyase (decarboxylating)
Systematic name: 5-dehydro-4-deoxy-D-glucarate hydro-lyase (decarboxylating; 2,5-dioxopentanoate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37290-77-0
References:
1. Jeffcoat, R., Hassall, H. and Dagley, S. Purification and properties of D-4-deoxy-5-oxoglucarate hydro-lyase (decarboxylating). Biochem. J. 115 (1969) 977-983. [PMID: 4982840]
Accepted name: galactarate dehydratase
Reaction: galactarate = (2R,3S)-2,3-dihydroxy-5-oxohexanedioate + H2O
Glossary: galactarate = (2R,3S,4R,5S)-2,3,4,5-tetrahydroxyhexanedioate
(2R,3S)-2,3-dihydroxy-5-oxohexanedioate = 3-deoxy-L-threo-hex-2-ulosarate
Other name(s): D-galactarate hydro-lyase; D-galactarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming); talrD (gene name)/galrD (gene name)
Systematic name: galactarate hydro-lyase (5-dehydro-4-deoxy-D-glucarate-forming)
Comments: The enzyme from the bacterium Escherichia coli is specific for galactarate [2], while the enzyme from Salmonella typhimurium also has activity with L-talarate (cf. EC 4.2.1.156, L-talarate dehydratase) [3]. cf. EC 4.2.1.158, galactarate dehydratase (D-threo-forming).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37290-78-1
References:
1. Blumenthal, H.J. and Jepson, T. Galactarate dehydrase. Methods Enzymol. 9 (1966) 665-669.
2. Hubbard, B.K., Koch, M., Palmer, D.R., Babbitt, P.C. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: characterization of the (D)-glucarate/galactarate catabolic pathway in Escherichia coli. Biochemistry 37 (1998) 14369-14375. [PMID: 9772162]
3. 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]
4. 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: 2-dehydro-3-deoxy-L-arabinonate dehydratase
Reaction: 2-dehydro-3-deoxy-L-arabinonate = 2,5-dioxopentanoate + H2O
For diagram of reaction click here.
Other name(s): 2-keto-3-deoxy-L-arabinonate dehydratase; 2-dehydro-3-deoxy-L-arabinonate hydro-lyase
Systematic name: 2-dehydro-3-deoxy-L-arabinonate hydro-lyase (2,5-dioxopentanoate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37263-10-8
References:
1. Stoolmiller, A.C. and Abeles, R.H. Formation of α-ketoglutaric semialdehyde from L-2-keto-3-deoxyarabonic acid and isolation of L-2-keto-3-deoxyarabonate dehydratase from Pseudomonas saccharophila. J. Biol. Chem. 241 (1966) 5764-5771. [PMID: 5954356]
Accepted name: myo-inosose-2 dehydratase
Reaction: 2,4,6/3,5-pentahydroxycyclohexanone = 3,5/4-trihydroxycyclohexa-1,2-dione + H2O
For diagram of reaction click here.
Other name(s): inosose 2,3-dehydratase; ketoinositol dehydratase; 2,4,6/3,5-pentahydroxycyclohexanone hydro-lyase
Systematic name: 2,4,6/3,5-pentahydroxycyclohexanone hydro-lyase (3,5/4-trihydroxycyclohexa-1,2-dione-forming)
Comments: Requires Co2+ or Mn2+.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37290-79-2
References:
1. Berman, T. and Magasanik, B. The pathway of myo-inositol degradation in Aerobacter aerogenes. Dehydrogenation and dehydration. J. Biol. Chem. 241 (1966) 800-806. [PMID: 5905122]
Accepted name: CDP-glucose 4,6-dehydratase
Reaction: CDP-glucose = CDP-4-dehydro-6-deoxy-D-glucose + H2O
Other name(s): cytidine diphosphoglucose oxidoreductase; CDP-glucose 4,6-hydro-lyase
Systematic name: CDP-glucose 4,6-hydro-lyase (CDP-4-dehydro-6-deoxy-D-glucose-forming)
Comments: Requires bound NAD+.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37259-55-5
References:
1. Hey, A.E. and Elbein, A.D. Biosynthesis of tyvelose. The purification and properties of cytidine diphosphate D-glucose oxidoreductase. J. Biol. Chem. 241 (1966) 5473-5478. [PMID: 4380946]
2. Matsuhashi, S., Matsuhashi, M., Brown, J.G. and Strominger, J.L. Enzymatic synthesis of cytidine diphosphate 3,6-dideoxyhexoses. 3. Cytidine diphosphate D-glucose oxidoreductase. J. Biol. Chem. 241 (1966) 4283-4287. [PMID: 4288651]
3. Melo, A., Elliott, H. and Glaser, L. The mechanism of 6-deoxyhexose synthesis. I. Intramolecular hydrogen transfer catalyzed by deoxythymidine diphosphate D-glucose oxidoreductase. J. Biol. Chem. 243 (1968) 1467-1474. [PMID: 4869560]
Accepted name: dTDP-glucose 4,6-dehydratase
Reaction: dTDP-α-D-glucose = dTDP-4-dehydro-6-deoxy-α-D-glucose + H2O
For diagram click here.
Other name(s): thymidine diphosphoglucose oxidoreductase; TDP-glucose oxidoreductase; dTDP-glucose 4,6-hydro-lyase; dTDP-glucose 4,6-hydro-lyase (dTDP-4-dehydro-6-deoxy-D-glucose-forming)
Systematic name: dTDP-α-D-glucose 4,6-hydro-lyase (dTDP-4-dehydro-6-deoxy-α-D-D-glucose-forming)
Comments: Requires bound NAD+.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37259-54-4
References:
1. Gilbert, J.M., Matsuhashi, M. and Strominger, J.L. Thymidine diphosphate 4-acetamido-4,6-dideoxyhexoses. II. Purification and properties of thymidine diphosphate D-glucose oxidoreductase. J. Biol. Chem. 240 (1965) 1305-1308. [PMID: 14284740]
2. Melo, A., Elliott, H. and Glaser, L. The mechanism of 6-deoxyhexose synthesis. I. Intramolecular hydrogen transfer catalyzed by deoxythymidine diphosphate D-glucose oxidoreductase. J. Biol. Chem. 243 (1968) 1467-1774. [PMID: 4869560]
3. Wang, S.-F. and Gabriel, O. Biological mechanisms involved in the formation of deoxy sugars. V. Isolation and crystallization of thymidine diphosphate-D-glucose oxidoreductase from Escherichia coli B. J. Biol. Chem. 244 (1969) 3430-3437. [PMID: 4307450]
4. Hegeman, A.D., Gross, J.W. and Frey, P.A. Probing catalysis by Escherichia coli dTDP-glucose-4,6-dehydratase: identification and preliminary characterization of functional amino acid residues at the active site. Biochemistry 40 (2001) 6598-6610. [PMID: 11380254]
5. Gross, J.W., Hegeman, A.D., Gerratana, B. and Frey, P.A. Dehydration is catalyzed by glutamate-136 and aspartic acid-135 active site residues in Escherichia coli dTDP-glucose 4,6-dehydratase. Biochemistry 40 (2001) 12497-12504. [PMID: 11601973]
Accepted name: GDP-mannose 4,6-dehydratase
Reaction: GDP-α-D-mannose = GDP-4-dehydro-α-D-rhamnose + H2O
For diagram click here.
Other name(s): guanosine 5′-diphosphate-D-mannose oxidoreductase; guanosine diphosphomannose oxidoreductase; guanosine diphosphomannose 4,6-dehydratase; GDP-D-mannose dehydratase; GDP-D-mannose 4,6-dehydratase; Gmd; GDP-mannose 4,6-hydro-lyase; GDP-mannose 4,6-hydro-lyase (GDP-4-dehydro-6-deoxy-D-mannose-forming)
Systematic name: GDP-α-D-mannose 4,6-hydro-lyase (GDP-4-dehydro-α-D-rhamnose-forming)
Comments: The bacterial enzyme requires bound NAD+. This enzyme forms the first step in the biosynthesis of GDP-D-rhamnose and GDP-L-fucose. In Aneurinibacillus thermoaerophilus L420-91T, this enzyme acts as a bifunctional enzyme, catalysing the above reaction as well as the reaction catalysed by EC 1.1.1.281, GDP-4-dehydro-6-deoxy-D-mannose reductase [5]. Belongs to the short-chain dehydrogenase/reductase enzyme family, having homologous structures and a conserved catalytic triad of Lys, Tyr and Ser/Thr residues [6].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37211-59-9
References:
1. Elbein, A.D. and Heath, E.C. The biosynthesis of cell wall lipopolysaccharide in Escherichia coli. II. Guanosine diphosphate 4-keto-6-deoxy-D-mannose, an intermediate in the biosynthesis of guanosine diphosphate colitose. J. Biol. Chem. 240 (1965) 1926-1931. [PMID: 14299611]
2. Liao, T.-H. and Barber, G.A. Purification of guanosine 5'-diphosphate D-mannose oxidoreductase from Phaseolus vulgaris. Biochim. Biophys. Acta 276 (1972) 85-93. [PMID: 5047712]
3. Melo, A., Elliott, H. and Glaser, L. The mechanism of 6-deoxyhexose synthesis. I. Intramolecular hydrogen transfer catalyzed by deoxythymidine diphosphate D-glucose oxidoreductase. J. Biol. Chem. 243 (1968) 1467-1474. [PMID: 4869560]
4. Sullivan, F.X., Kumar, R., Kriz, R., Stahl, M., Xu, G.Y., Rouse, J., Chang, X.J., Boodhoo, A., Potvin, B. and Cumming, D.A. Molecular cloning of human GDP-mannose 4,6-dehydratase and reconstitution of GDP-fucose biosynthesis in vitro. J. Biol. Chem. 273 (1988) 8193-8202. [PMID: 9525924]
5. Kneidinger, B., Graninger, M., Adam, G., Puchberger, M., Kosma, P., Zayni, S. and Messner, P. Identification of two GDP-6-deoxy-D-lyxo-4-hexulose reductases synthesizing GDP-D-rhamnose in Aneurinibacillus thermoaerophilus L420-91T. J. Biol. Chem. 276 (2001) 5577-5583. [PMID: 11096116]
6. Mulichak, A.M., Bonin, C.P., Reiter, W.D. and Garavito, R.M. Structure of the MUR1 GDP-mannose 4,6-dehydratase from Arabidopsis thaliana: implications for ligand binding and specificity. Biochemistry 41 (2000) 15578-15589. [PMID: 12501186]
Accepted name: D-glutamate cyclase
Reaction: D-glutamate = 5-oxo-D-proline + H2O
Other name(s): D-glutamate hydro-lyase (cyclizing)
Systematic name: D-glutamate hydro-lyase (cyclizing; 5-oxo-D-proline-forming)
Comments: Also acts on various derivatives of D-glutamate.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37290-80-5
References:
1. Meister, A., Bukenberger, M.W. and Strassburger, M. The optically-specific enzymatic cyclization of D-glutamate. Biochem. Z. 338 (1963) 217-229. [PMID: 14087295]
Accepted name: urocanate hydratase
Reaction: 3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate = urocanate + H2O
For diagram click here and probable mechanism here.
Glossary: urocanate = (E)-3-(imidazol-4-yl)propenoate
Other name(s): urocanase; 3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate hydro-lyase
Systematic name: 3-(5-oxo-4,5-dihydro-3H-imidazol-4-yl)propanoate hydro-lyase (urocanate-forming)
Comments: Contains tightly bound NAD+.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9014-58-8
References:
1. Rétey, J. The urocanase story: a novel role of NAD+ as electrophile. Arch. Biochem. Biophys. 314 (1994) 1-16. [PMID: 7944380]
2. Hassall, H. and Greenberg, D.M. Urocanase (beef liver). Methods Enzymol. 17B (1971) 84-88.
3. Kaminskas, E., Kimhi, Y. and Magasanik, B. Urocanase and N-formimino-L-glutamate formiminohydrolase of Bacillus subtilis, two enzymes of the histidine degradation pathway. J. Biol. Chem. 245 (1970) 3536-3544. [PMID: 4990470]
4. Swaine, D. The effect of substrate analogues on the activity of cat liver urocanase. Biochim. Biophys. Acta 178 (1969) 609-618. [PMID: 5784906]
Accepted name: pyrazolylalanine synthase
Reaction: L-serine + pyrazole = 3-(pyrazol-1-yl)-L-alanine + H2O
Other name(s): β-pyrazolylalaninase; β-(1-pyrazolyl)alanine synthase; L-serine hydro-lyase (adding pyrazole)
Systematic name: L-serine hydro-lyase [adding pyrazole; 3-(pyrazol-1-yl)-L-alanine-forming]
Comments: A pyridoxal-phosphate protein.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37290-81-6
References:
1. Dunnill, P.M. and Fowden, L. The biosynthesis of β-pyrazol-1-ylalanine. J. Exp. Bot. 14 (1963) 237-248.