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acetate]Continued from EC 4.1.2
EC 4.1.3 Oxo-Acid-Lyases
EC 4.1.99 Other Carbon-Carbon Lyases
Accepted name: isocitrate lyase
Reaction: isocitrate = succinate + glyoxylate
For diagram of reaction click here.
Glossary: isocitrate = (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate (previously known as threo-Ds-isocitrate)
Other name(s): isocitrase; isocitritase; isocitratase; threo-Ds-isocitrate glyoxylate-lyase; isocitrate glyoxylate-lyase
Systematic name: isocitrate glyoxylate-lyase (succinate-forming)
Comments: The isomer of isocitrate involved is (1R,2S)-1-hydroxypropane-1,2,3-tricarboxylate [3].
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9045-78-7
References:
1. McFadden, B.A. and Howes, W.V. Crystallisation and some properties of isocitrate lyase from Pseudomonas indigofera. J. Biol. Chem. 238 (1963) 1737-1742.
2. Shiio, I, Shiio, T. and McFadden, B.A. Isocitrate lyase from Pseudomonas indigofera. I. Preparation, amino acid composition and molecular weight. Biochim. Biophys. Acta 96 (1965) 114-122.
3. Vickery, H.B. A suggested new nomenclature for the isomers of isocitric acid. J. Biol. Chem. 237 (1962) 1739-1741.
[EC 4.1.3.2 Transferred entry: now EC 2.3.3.9, malate synthase (EC 4.1.3.2 created 1961, deleted 2002)]
Accepted name: N-acetylneuraminate lyase
Reaction: N-acetylneuraminate = N-acetyl-D-mannosamine + pyruvate
Other name(s): N-acetylneuraminic acid aldolase; acetylneuraminate lyase; sialic aldolase; sialic acid aldolase; sialate lyase; N-acetylneuraminic aldolase; neuraminic aldolase; N-acetylneuraminate aldolase; neuraminic acid aldolase; N-acetylneuraminic acid aldolase; neuraminate aldolase; N-acetylneuraminic lyase; N-acetylneuraminic acid lyase; NPL; NALase; NANA lyase; acetylneuraminate pyruvate-lyase; N-acetylneuraminate pyruvate-lyase
Systematic name: N-acetylneuraminate pyruvate-lyase (N-acetyl-D-mannosamine-forming)
Comments: Also acts on N-glycoloylneuraminate, and on O-acetylated sialic acids, other than 4-O-acetylated derivatives.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9027-60-5
References:
1. Comb, D.G. and Roseman, S. The sialic acids. I. The structure and enzymatic synthesis of N-acetylneuraminic acid. J. Biol. Chem. 235 (1960) 2529-2537.
2. Schauer, R. Chemistry, metabolism, and biological functions of sialic acids. Adv. Carbohydr. Chem. Biochem. 40 (1982) 131-234. [PMID: 6762816]
Accepted name: hydroxymethylglutaryl-CoA lyase
Reaction: (S)-3-hydroxy-3-methylglutaryl-CoA = acetyl-CoA + acetoacetate
For diagram click here.
Other name(s): hydroxymethylglutaryl coenzyme A-cleaving enzyme; hydroxymethylglutaryl coenzyme A lyase; 3-hydroxy-3-methylglutaryl coenzyme A lyase; 3-hydroxy-3-methylglutaryl CoA cleaving enzyme; 3-hydroxy-3-methylglutaryl-CoA lyase; (S)-3-hydroxy-3-methylglutaryl-CoA acetoacetate-lyase
Systematic name: (S)-3-hydroxy-3-methylglutaryl-CoA acetoacetate-lyase (acetyl-CoA-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9030-83-5
References:
1. Bachhawat, B.K., Robinson, W.G. and Coon, M.J. The enzymatic cleavage of β-hydroxy-β-methylglutaryl coenzyme A to acetoacetate and acetyl coenzyme A. J. Biol. Chem. 216 (1955) 727-736.
[EC 4.1.3.5 Transferred entry: now EC 2.3.3.10, hydroxymethylglutaryl-CoA synthase (EC 4.1.3.5 created 1961, deleted 2002)]
Accepted name: citrate (pro-3S)-lyase
Reaction: citrate = acetate + oxaloacetate
Other name(s): citrase; citratase; citritase; citridesmolase; citrate aldolase; citric aldolase; citrate lyase; citrate oxaloacetate-lyase, citrate oxaloacetate-lyase [(pro-3S)-CH2COO-acetate]
Systematic name: citrate oxaloacetate-lyase (forming acetate from the pro-S carboxymethyl group of citrate)
Comments: The enzyme can be dissociated into components, two of which are identical with EC 2.8.3.10 (citrate CoA-transferase) and EC 4.1.3.34 (citryl-CoA lyase). EC 3.1.2.16 (citrate lyase deacetylase), deacetylates and inactivates the enzyme.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9012-83-3
References:
1. Dagley, S. and Dawes, E.A. Citridesmolase: its properties and mode of action. Biochim. Biophys. Acta 17 (1955) 177-184. [PMID: 13239657]
2. Dimroth, P., Loyal, R. and Eggerer, H. Characterization of the isolated transferase subunit of citrate lyase as a CoA-transferase. Evidence ag ainst a covalent enzyme-substrate intermediate. Eur. J. Biochem. 80 (1977) 479-488. [PMID: 336371]
[EC 4.1.3.7 Transferred entry: now EC 2.3.3.1, citrate (Si)-synthase (EC 4.1.3.7 created 1961, deleted 2002)]
[EC 4.1.3.8 Transferred entry: now EC 2.3.3.8, ATP citrate synthase (EC 4.1.3.8 created 1965, modified 1986, deleted 2002)]
[EC 4.1.3.9 Transferred entry: now EC 2.3.3.11, 2-hydroxyglutarate synthase (EC 4.1.3.9 created 1965, deleted 2002)]
[EC 4.1.3.10 Transferred entry: now EC 2.3.3.7, 3-ethylmalate synthase (EC 4.1.3.10 created 1965, modified 1983, deleted 2002)]
[EC 4.1.3.11 Transferred entry: now EC 2.3.3.12, 3-propylmalate synthase (EC 4.1.3.11 created 1972, deleted 2002)]
[EC 4.1.3.12 Transferred entry: now EC 2.3.3.13, 2-isopropylmalate synthase (EC 4.1.3.12 created 1972, deleted 2002)]
Accepted name: oxalomalate lyase
Reaction: 3-oxalomalate = oxaloacetate + glyoxylate
Other name(s): 3-oxalomalate glyoxylate-lyase
Systematic name: 3-oxalomalate glyoxylate-lyase (oxaloacetate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37290-63-4
References:
1. Sekizawa, Y., Maragoudakis, M.E., King, T.E. and Cheldelin, V.H. Glutamate biosynthesis in an organism lacking a Krebs tricarboxylic acid cycle. V. Isolation of α-hydroxy-γ-ketoglutarate (HKG) in Acetobacter suboxydans. Biochemistry 5 (1966) 2392-2398. [PMID: 6005666]
Accepted name: L-erythro-3-hydroxyaspartate aldolase
Reaction: L-erythro-3-hydroxy-aspartate = glycine + glyoxylate
Other name(s): L-erythro-β-hydroxyaspartate aldolase; L-erythro-β-hydroxyaspartate glycine-lyase; erythro-3-hydroxy-Ls-aspartate glyoxylate-lyase
Systematic name: L-erythro-3-hydroxy-aspartate glyoxylate-lyase (glycine-forming)
Comments: A pyridoxal-phosphate protein. The enzyme, purified from the bacterium Paracoccus denitrificans NCIMB 8944, is strictly specific for the L-erythro stereoisomer of 3-hydroxyaspartate. Different from EC 4.1.3.41, erythro-3-hydroxy-D-aspartate aldolase. Requires a divalent cation.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37290-64-5
References:
1. Gibbs, R.G. and Morris, J.G. Assay and properties of β-hydroxyaspartate aldolase from Micrococcus denitrificans. Biochim. Biophys. Acta 85 (1964) 501-503. [PMID: 14194868]
[EC 4.1.3.15 Transferred entry: now EC 2.2.1.5, 2-hydroxy-3-oxoadipate synthase (EC 4.1.3.15 created 1972, deleted 2002)]
Accepted name: 4-hydroxy-2-oxoglutarate aldolase
Reaction: 4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate
Other name(s): 2-oxo-4-hydroxyglutarate aldolase; hydroxyketoglutaric aldolase; 4-hydroxy-2-ketoglutaric aldolase; 2-keto-4-hydroxyglutaric aldolase; 4-hydroxy-2-ketoglutarate aldolase; 2-keto-4-hydroxyglutarate aldolase; 2-oxo-4-hydroxyglutaric aldolase; DL-4-hydroxy-2-ketoglutarate aldolase; hydroxyketoglutarate aldolase; 2-keto-4-hydroxybutyrate aldolase; 4-hydroxy-2-oxoglutarate glyoxylate-lyase; KHGA
Systematic name: 4-hydroxy-2-oxoglutarate glyoxylate-lyase (pyruvate-forming)
Comments: The enzymes from rat liver and bovine liver act on both enantiomers of 4-hydroxy-2-oxoglutarate. cf. EC 4.1.3.42, L-4-hydroxy-2-oxoglutarate aldolase.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9030-81-3
References:
1. Kuratomi, K. and Fukunaga, K. The metabolism of γ-hydroxyglutamate in rat liver. I. Enzymic synthesis of γ-hydroxy-α-ketoglutarate from pyruvate and glyoxalate. Biochim. Biophys. Acta 78 (1963) 617-628.
2. Kobes, R.D. and Dekker, E.E. 2-Keto-4-hydroxyglutarate aldolase of bovine liver. Purification, criteria of purity, and general properties. J. Biol. Chem. 244 (1969) 1919-1925. [PMID: 5780845]
3. Lane, R.S., Shapley, A. and Dekker, E.E. 2-keto-4-hydroxybutyrate aldolase. Identification as 2-keto-4-hydroxyglutarate aldolase, catalytic properties, and role in the mammalian metabolism of L-homoserine. Biochemistry 10 (1971) 1353-1364. [PMID: 5580656]
4. Scholtz, J.M. and Schuster, S.M. Regulation of rat liver 4-hydroxy-2-ketoglutarate aldolase. Biochim. Biophys. Acta 869 (1986) 192-196. [PMID: 3942759]
Accepted name: 4-hydroxy-4-methyl-2-oxoglutarate aldolase
Reaction: (1) 4-hydroxy-4-methyl-2-oxoglutarate = 2 pyruvate
(2) 2-hydroxy-4-oxobutane-1,2,4-tricarboxylate = oxaloacetate + pyruvate
For diagram of reaction click here.
Other name(s): pyruvate aldolase; γ-methyl-γ-hydroxy-α-ketoglutaric aldolase; 4-hydroxy-4-methyl-2-ketoglutarate aldolase; 4-hydroxy-4-methyl-2-oxoglutarate pyruvate-lyase; HMG aldolase; CHA aldolase; 4-carboxy-4-hydroxy-2-oxoadipate aldolase
Systematic name: 4-hydroxy-4-methyl-2-oxoglutarate pyruvate-lyase (pyruvate-forming)
Comments: Requires a divalent metal ion [3]. This enzyme participates in the degradation of protocatechuate (via the meta-cleavage pathway), phthalate, syringate and gallate [1-3]. The enzyme from Pseudomonas ochraceae can also cleave 4-hydroxy-2-oxoglutarate to glyoxylate and pyruvate, and also catalyses the reaction of EC 4.1.1.3 (oxaloacetate decarboxylase) [3].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37290-65-6
References:
1. Tack, B.F., Chapman, P.J. and Dagley, S. Purification and properties of 4-hydroxy-4-methyl-2-oxoglutarate aldolase. J. Biol. Chem. 247 (1972) 6444-6449. [PMID: 5076765]
2. Wood, W.A. 2-Keto-3-deoxy-6-phosphogluconic and related aldolases. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 7, Academic Press, New York, 1972, pp. 281-302.
3. Maruyama, K. Purification and properties of 2-pyrone-4,6-dicarboxylate hydrolase. J. Biochem. (Tokyo) 93 (1983) 557-565. [PMID: 6841353]
4. Nogales, J., Canales, A., Jimenez-Barbero, J., Serra, B., Pingarron, J.M., Garcia, J.L. and Diaz, E. Unravelling the gallic acid degradation pathway in bacteria: the gal cluster from Pseudomonas putida. Mol. Microbiol. 79 (2011) 359-374. [PMID: 21219457]
[EC 4.1.3.18 Transferred entry: now EC 2.2.1.6, acetolactate synthase (EC 4.1.3.18 created 1972, deleted 2002)]
[EC 4.1.3.19 Transferred entry: now EC 2.5.1.56, N-acetylneuraminate synthase (EC 4.1.2.19 created 1972, deleted 2002)]
[EC 4.1.3.20 Transferred entry: now EC 2.5.1.57, N-acylneuraminate-9-phosphate synthase (EC 4.1.3.20 created 1972, deleted 2002)]
[EC 4.1.3.21 Transferred entry: now EC 2.3.3.14, homocitrate synthase (EC 4.1.3.21 created 1972, deleted 2002)]
Accepted name: citramalate lyase
Reaction: (2S)-2-hydroxy-2-methylbutanedioate = acetate + pyruvate
For diagram click here.
Glossary: (+)-citramalate = (2S)-2-hydroxy-2-methylbutanedioate
Other name(s): citramalate pyruvate-lyase; citramalate synthase; citramalic-condensing enzyme; citramalate synthetase; citramalic synthase; (S)-citramalate lyase; (+)-citramalate pyruvate-lyase; citramalate pyruvate lyase; (3S)-citramalate pyruvate-lyase; (2S)-2-hydroxy-2-methylbutanedioate pyruvate-lyase
Systematic name: (2S)-2-hydroxy-2-methylbutanedioate pyruvate-lyase (acetate-forming)
Comments: The enzyme can be dissociated into components, two of which are identical with EC 2.8.3.11 (citramalate CoA-transferase) and EC 4.1.3.25 (citramalyl-CoA lyase).
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9027-93-4
References:
1. Barker, H.A. Citramalate lyase of Clostridium tetanomorphum. Arch. Mikrobiol. 59 (1967) 4-12. [PMID: 4301387]
2. Dimroth, P., Buckel, W., Loyal, R. and Eggerer, H. Isolation and function of the subunits of citramalate lyase and formation of hybrids with the subunits of citrate lyase. Eur. J. Biochem. 80 (1977) 469-477. [PMID: 923590]
[EC 4.1.3.23 Transferred entry: now EC 2.3.3.2, decylcitrate synthase (EC 4.1.3.23 created 1972, deleted 2002)]
Accepted name: malyl-CoA lyase
Reaction: (3S)-3-carboxy-3-hydroxypropanoyl-CoA = acetyl-CoA + glyoxylate
Other name(s): malyl-coenzyme A lyase; (3S)-3-carboxy-3-hydroxypropanoyl-CoA glyoxylate-lyase
Systematic name: (3S)-3-carboxy-3-hydroxypropanoyl-CoA glyoxylate-lyase (acetyl-CoA-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 37290-67-8
References:
1. Tuboi, S. and Kikuchi, G. Enzymic cleavage of malyl-Coenzyme A into acetyl-Coenzyme A and glyoxylic acid. Biochim. Biophys. Acta 96 (1965) 148-153.
Accepted name: citramalyl-CoA lyase
Reaction: (3S)-citramalyl-CoA = acetyl-CoA + pyruvate
Other name(s): citramalyl coenzyme A lyase; (+)-CMA-CoA lyase; (3S)-citramalyl-CoA pyruvate-lyase
Systematic name: (3S)-citramalyl-CoA pyruvate-lyase (acetyl-CoA-forming)
Comments: The enzyme is a component of EC 4.1.3.22 citramalate lyase. Also acts on (3S)-citramalyl thioacyl-carrier protein.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37290-68-9
References:
1. Cooper, R.A. and Kornberg, H.L. The utilization of itaconate by Pseudomonas sp. Biochem. J. 91 (1964) 82-91. [PMID: 4284209]
2. Dimroth, P., Buckel, W., Loyal, R. and Eggerer, H. Isolation and function of the subunits of citramalate lyase and formation of hybrids with the subunits of citrate lyase. Eur. J. Biochem. 80 (1977) 469-477. [PMID: 923590]
Accepted name: 3-hydroxy-3-isohexenylglutaryl-CoA lyase
Reaction: 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA = 7-methyl-3-oxooct-6-enoyl-CoA + acetate
Other name(s): β-hydroxy-β-isohexenylglutaryl CoA-lyase; hydroxyisohexenylglutaryl-CoA:acetatelyase; 3-hydroxy-3-isohexenylglutaryl coenzyme A lyase; 3-hydroxy-3-isohexenylglutaryl-CoA isopentenylacetoacetyl-CoA-lyase
Systematic name: 3-hydroxy-3-(4-methylpent-3-en-1-yl)glutaryl-CoA acetate-lyase (7-methyl-3-oxooct-6-enoyl-CoA-forming)
Comments: Also acts on the hydroxy derivative of farnesoyl-CoA.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37290-69-0
References:
1. Seubert, W. and Fass, E. Untersuchungen über den bakterielle Abbau von Isoprenoiden. IV. Reinigung und Eigenschaftender β-Isohexenylglutaconyl-CoA-hydratase und β-Hydroxy-β-isohexenylglutaryl-CoA-lyase. Biochem. Z. 341 (1964) 23-34.
Accepted name: anthranilate synthase
Reaction: chorismate + L-glutamine = anthranilate + pyruvate + L-glutamate
For diagram of reaction click here.
Other name(s): anthranilate synthetase; chorismate lyase; chorismate pyruvate-lyase (amino-accepting); TrpE
Systematic name: chorismate pyruvate-lyase (amino-accepting; anthranilate-forming)
Comments: In some organisms, this enzyme is part of a multifunctional protein, together with one or more other components of the system for the biosynthesis of tryptophan [EC 2.4.2.18 (anthranilate phosphoribosyltransferase ), EC 4.1.1.48 (indole-3-glycerol-phosphate synthase), EC 4.2.1.20 (tryptophan synthase) and EC 5.3.1.24 (phosphoribosylanthranilate isomerase)]. The native enzyme in the complex uses either glutamine or, less efficiently, NH3. The enzyme separated from the complex uses NH3 only.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9031-59-8
References:
1. Baker, T. and Crawford, I.P. Anthranilate synthetase. Partial purification and some kinetic studies on the enzyme from Escherichia coli. J. Biol. Chem. 241 (1966) 5577-5584. [PMID: 5333199]
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 biosynthetic genes in eukaryotic microorganisms. Annu. Rev. Microbiol. 40 (1986) 55-77. [PMID: 16526091]
4. Ito, J. and Yanofsky, C. Anthranilate synthetase, an enzyme specified by the tryptophan operon of Escherichia coli: Comparative studies on the complex and the subunits. J. Bacteriol. 97 (1969) 734-742. [PMID: 4886290]
5. Zalkin, H. and Kling, D. Anthranilate synthetase. Purification and properties of component I from Salmonella typhimurium. Biochemistry 7 (1968) 3566-3573. [PMID: 4878701]
[EC 4.1.3.28 Transferred entry: now EC 2.3.3.3, citrate (Re)-synthase (EC 4.1.3.28 created 1972, deleted 2002)]
[EC 4.1.3.29 Transferred entry: now EC 2.3.3.4, decylhomocitrate synthase (EC 4.1.3.29 created 1976, deleted 2002)]
Accepted name: methylisocitrate lyase
Reaction: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = pyruvate + succinate
Glossary: (2S,3R)-2-methylisocitrate = (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = threo-Ds-2-methylisocitrate
Other name(s): 2-methylisocitrate lyase; MICL; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate pyruvate-lyase
Systematic name: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate pyruvate-lyase (succinate-forming)
Comments: The enzyme acts on threo-Ds-2-methylisocitrate, but not on threo-Ds-isocitrate, threo-DL-isocitrate or erythro-Ls-isocitrate.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 57827-77-7
References:
1. Tabuchi, T. and Satoh, T. Distinction between isocitrate lyase and methylisocitrate lyase in Candida lipolytica. Agric. Biol. Chem. 40 (1976) 1863-1869.
2. Tabuchi, T. and Satoh, T. Purification and properties of methylisocitrate lyase, a key enzyme in propionate metabolism, from Candida lipolytica. Agric. Biol. Chem. 41 (1977) 169-174.
[EC 4.1.3.31 Transferred entry: now EC 2.3.3.5, 2-methylcitrate synthase (EC 4.1.3.31 created 1978, deleted 2002)]
Accepted name: 2,3-dimethylmalate lyase
Reaction: (2R,3S)-2,3-dimethylmalate = propanoate + pyruvate
For diagram click here.
Other name(s): 2,3-dimethylmalate pyruvate-lyase
Systematic name: (2R,3S)-2,3-dimethylmalate pyruvate-lyase (propanoate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, CAS registry number: 73562-28-4
References:
1. Pirzer, P., Lill, U. and Eggerer, H. Nicotinic acid metabolism. 2,3-Dimethylmalate lyase. Hoppe-Seyler's Z. Physiol. Chem. 360 (1979) 1693-1702. [PMID: 527937]
[EC 4.1.3.33 Transferred entry: now EC 2.3.3.6, 2-ethylmalate synthase (EC 4.1.3.33 created 1983, deleted 2002)]
Accepted name: citryl-CoA lyase
Reaction: (3S)-citryl-CoA = acetyl-CoA + oxaloacetate
Other name(s): (3S)-citryl-CoA oxaloacetate-lyase
Systematic name: (3S)-citryl-CoA oxaloacetate-lyase (acetyl-CoA-forming)
Comments: The enzyme is a component of EC 4.1.3.6 {[citrate (pro-3S)-lyase]}and EC 2.3.3.8 [ATP citrate synthase]. Also acts on (3S)-citryl thioacyl-carrier protein.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 131095-35-7
References:
1. Dimroth, P., Loyal, R. and Eggerer, H. Characterization of the isolated transferase subunit of citrate lyase as a CoA-transferase. Evidence against a covalent enzyme-substrate intermediate. Eur. J. Biochem. 80 (1977) 479-488. [PMID: 336371]
2. Lill, U., Schreil, A. and Eggerer, H. Isolation of enzymically active fragments formed by limited proteolysis of ATP citrate lyase. Eur. J. Biochem. 125 (1982) 645-650. [PMID: 6749502]
Accepted name: (1-hydroxycyclohexan-1-yl)acetyl-CoA lyase
Reaction: (1-hydroxycyclohexan-1-yl)acetyl-CoA = acetyl-CoA + cyclohexanone
For reaction pathway click here.
Other name(s): (1-hydroxycyclohexan-1-yl)acetyl-CoA cyclohexanone-lyase
Systematic name: (1-hydroxycyclohexan-1-yl)acetyl-CoA cyclohexanone-lyase (acetyl-CoA-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 71343-09-4
References:
1. Ougham, H.J. and Trudgill, P.W. Metabolism of cyclohexaneacetic acid and cyclohexanebutyric acid by Arthrobacter sp. strain CA1. J. Bacteriol. 150 (1982) 1172-1182. [PMID: 7076617]
Accepted name: 1,4-dihydroxy-2-naphthoyl-CoA synthase
Reaction: 4-(2-carboxyphenyl)-4-oxobutanoyl-CoA = 1,4-dihydroxy-2-naphthoyl-CoA + H2O
For diagram of reaction, click here.
Other name(s): naphthoate synthase; 1,4-dihydroxy-2-naphthoate synthase; dihydroxynaphthoate synthase; o-succinylbenzoyl-CoA 1,4-dihydroxy-2-naphthoate-lyase (cyclizing); MenB; o-succinylbenzoyl-CoA dehydratase (cyclizing)
Systematic name: 4-(2-carboxyphenyl)-4-oxobutanoyl-CoA dehydratase (cyclizing)
Comments: This enzyme is involved in the synthesis of 1,4-dihydroxy-2-naphthoate, a branch point metabolite leading to the biosynthesis of menaquinone (vitamin K2, in bacteria), phylloquinone (vitamin K1 in plants), and many plant pigments. The coenzyme A group is subsequently removed from the product by EC 3.1.2.28, 1,4-dihydroxy-2-naphthoyl-CoA hydrolase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 61328-42-5
References:
1. Meganathan, R. and Bentley, R. Menaquinone (vitamin K2) biosynthesis: conversion of o-succinylbenzoic acid to 1,4-dihydroxy-2-naphthoic acid by Mycobacterium phlei enzymes. J. Bacteriol. 140 (1979) 92-98. [PMID: 500558]
2. Kolkmann, R. and Leistner, E. 4-(2'-Carboxyphenyl)-4-oxobutyryl coenzyme A ester, an intermediate in vitamin K2 (menaquinone) biosynthesis. Z. Naturforsch. C: Sci. 42 (1987) 1207-1214. [PMID: 2966501]
3. Johnson, T.W., Shen, G., Zybailov, B., Kolling, D., Reategui, R., Beauparlant, S., Vassiliev, I.R., Bryant, D.A., Jones, A.D., Golbeck, J.H. and Chitnis, P.R. Recruitment of a foreign quinone into the A(1) site of photosystem I. I. Genetic and physiological characterization of phylloquinone biosynthetic pathway mutants in Synechocystis sp. pcc 6803. J. Biol. Chem. 275 (2000) 8523-8530. [PMID: 10722690]
4. Truglio, J.J., Theis, K., Feng, Y., Gajda, R., Machutta, C., Tonge, P.J. and Kisker, C. Crystal structure of Mycobacterium tuberculosis MenB, a key enzyme in vitamin K2 biosynthesis. J. Biol. Chem. 278 (2003) 42352-42360. [PMID: 12909628]
[EC 4.1.3.37 Transferred entry: now EC 2.2.1.7, 1-deoxy-D-xylulose 5-phosphate synthase (EC 4.1.3.37 created 2001, deleted 2002)]
Accepted name: aminodeoxychorismate lyase
Reaction: 4-amino-4-deoxychorismate = 4-aminobenzoate + pyruvate
For diagram of reaction click here (folate biosynthesis).
Other name(s): enzyme X; 4-amino-4-deoxychorismate lyase; 4-amino-4-deoxychorismate pyruvate-lyase
Systematic name: 4-amino-4-deoxychorismate pyruvate-lyase (4-aminobenzoate-forming)
Comments: A pyridoxal-phosphate protein. Forms part of the folate biosynthesis pathway. Acts on 4-amino-4-deoxychorismate, the product of EC 6.3.5.8, aminodeoxychorismate synthase, to form p-aminobenzoate.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 132264-33-6
References:
1. Ye, Q.Z., Liu, J. and Walsh, C.T. p-Aminobenzoate synthesis in Escherichia coli: purification and characterization of PabB as aminodeoxychorismate synthase and enzyme X as aminodeoxychorismate lyase. Proc. Natl. Acad. Sci. USA 87 (1990) 9391-9395. [PMID: 2251281]
2. Green, J.M., Merkel, W.K. and Nichols, B.P. Characterization and sequence of Escherichia coli pabC, the gene encoding aminodeoxychorismate lyase, a pyridoxal phosphate-containing enzyme. J. Bacteriol. 174 (1992) 5317-5323. [PMID: 1644759]
3. Nakai, T., Mizutani, H., Miyahara, I., Hirotsu, K., Takeda, S., Jhee, K.H., Yoshimura, T. and Esaki, N. Three-dimensional structure of 4-amino-4-deoxychorismate lyase from Escherichia coli. J. Biochem. 128 (2000) 29-38. [PMID: 10876155]
Accepted name: 4-hydroxy-2-oxovalerate aldolase
Reaction: 4-hydroxy-2-oxopentanoate = acetaldehyde + pyruvate
For diagram of reaction click here and another click here and another.
Glossary: valerate = pentanoate
Other name(s): 4-hydroxy-2-ketovalerate aldolase; HOA; DmpG; 4-hydroxy-2-oxovalerate pyruvate-lyase; 4-hydroxy-2-oxopentanoate pyruvate-lyase
Systematic name: 4-hydroxy-2-oxopentanoate pyruvate-lyase (acetaldehyde-forming)
Comments: Requires Mn2+ for maximal activity [1]. The enzyme from Pseudomonas putida is also stimulated by the presence of NADH [1]. In Pseudomonas species, this enzyme forms part of a bifunctional enzyme with EC 1.2.1.10, acetaldehyde dehydrogenase (acetylating). It catalyses the penultimate step in the meta-cleavage pathway for the degradation of phenols, methylphenols and catechol [1].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, UM-BBD, CAS registry number: 37325-52-3
References:
1. Manjasetty, B.A., Powlowski, J. and Vrielink, A. Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate. Proc. Natl. Acad. Sci. USA 100 (2003) 6992-6997. [PMID: 12764229]
2. Powlowski, J., Sahlman, L. and Shingler, V. Purification and properties of the physically associated meta-cleavage pathway enzymes 4-hydroxy-2-ketovalerate aldolase and aldehyde dehydrogenase (acylating) from Pseudomonas sp. strain CF600. J. Bacteriol. 175 (1993) 377-385. [PMID: 8419288]
3. Manjasetty, B.A., Croteau, N., Powlowski, J. and Vrielink, A. Crystallization and preliminary X-ray analysis of dmpFG-encoded 4-hydroxy-2-ketovalerate aldolase—aldehyde dehydrogenase (acylating) from Pseudomonas sp. strain CF600. Acta Crystallogr. D Biol. Crystallogr. 57 (2001) 582-585. [PMID: 11264589]
Accepted name: chorismate lyase
Reaction: chorismate = 4-hydroxybenzoate + pyruvate
For diagram of reaction click here.
Other name(s): CL; CPL; UbiC
Systematic name: chorismate pyruvate-lyase (4-hydroxybenzoate-forming)
Comments: This enzyme catalyses the first step in the biosynthesis of ubiquinone in Escherichia coli and other Gram-negative bacteria [1]. The yeast Saccharomyces cerevisiae can synthesize ubiquinone from either chorismate or tyrosine [3].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Nichols, B.P. and Green, J.M. Cloning and sequencing of Escherichia coli ubiC and purification of chorismate lyase. J. Bacteriol. 174 (1992) 5309-5316. [PMID: 1644758]
2. Siebert, M., Severin, K. and Heide, L. Formation of 4-hydroxybenzoate in Escherichia coli: characterization of the ubiC gene and its encoded enzyme chorismate pyruvate-lyase. Microbiology 140 (1994) 897-904. [PMID: 8012607]
3. Meganathan, R. Ubiquinone biosynthesis in microorganisms. FEMS Microbiol. Lett. 203 (2001) 131-139. [PMID: 11583838]
Accepted name: 3-hydroxy-D-aspartate aldolase
Reaction: (1) threo-3-hydroxy-D-aspartate = glycine + glyoxylate
(2) D-erythro-3-hydroxyaspartate = glycine + glyoxylate
Other name(s): D-3-hydroxyaspartate aldolase
Systematic name: 3-hydroxy-D-aspartate glyoxylate-lyase (glycine-forming)
Comments: A pyridoxal-phosphate protein. The enzyme, purified from the bacterium Paracoccus denitrificans IFO 13301, is strictly D-specific as to the α-position of the substrate, but accepts both the threo and erythro forms at the β-position. The erythro form is a far better substrate (about 100 fold). The enzyme can also accept D-allothreonine, D-threonine, erythro-3-phenyl-D-serine and threo-3-phenyl-D-serine. Different from EC 4.1.3.14, erythro-3-hydroxy-L-aspartate aldolase. Requires a divalent cation, such as Mg2+, Mn2+ or Co2+.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Liu, J.Q., Dairi, T., Itoh, N., Kataoka, M. and Shimizu, S. A novel enzyme, D-3-hydroxyaspartate aldolase from Paracoccus denitrificans IFO 13301: purification, characterization, and gene cloning. Appl. Microbiol. Biotechnol. 62 (2003) 53-60. [PMID: 12835921]
Accepted name: (4S)-4-hydroxy-2-oxoglutarate aldolase
Reaction: (4S)-4-hydroxy-2-oxoglutarate = pyruvate + glyoxylate
Glossary: (4S)-4-hydroxy-2-oxoglutatrate = (S)-2-hydroxy-4-oxopentanedioate = L-4-hydroxy-2-oxoglutarate
Other name(s): 2-oxo-4-hydroxyglutarate aldolase (ambiguous); hydroxyketoglutaric aldolase (ambiguous); 4-hydroxy-2-ketoglutaric aldolase (ambiguous); 2-keto-4-hydroxyglutaric aldolase (ambiguous); 4-hydroxy-2-ketoglutarate aldolase (ambiguous); 2-keto-4-hydroxyglutarate aldolase (ambiguous); 2-oxo-4-hydroxyglutaric aldolase (ambiguous); hydroxyketoglutarate aldolase (ambiguous); 2-keto-4-hydroxybutyrate aldolase (ambiguous); 4-hydroxy-2-oxoglutarate glyoxylate-lyase (ambiguous); eda (gene name)
Systematic name: (4S)-4-hydroxy-2-oxoglutarate glyoxylate-lyase (pyruvate-forming)
Comments: The enzyme from the bacterium Escherichia coli is specific for the (S) enantiomer. That enzyme is trifunctional, and also catalyses the reactions of EC 4.1.1.3, oxaloacetate decarboxylase and EC 4.1.2.14, 2-dehydro-3-deoxy-phosphogluconate aldolase. cf. EC 4.1.3.16, 4-hydroxy-2-oxoglutarate aldolase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Nishihara, H. and Dekker, E.E. Purification, substrate specificity and binding, β-decarboxylase activity, and other properties of Escherichia coli 2-keto-4-hydroxyglutarate aldolase. J. Biol. Chem. 247 (1972) 5079-5087. [PMID: 4560498]
2. Patil, R.V. and Dekker, E.E. Cloning, nucleotide sequence, overexpression, and inactivation of the Escherichia coli 2-keto-4-hydroxyglutarate aldolase gene. J. Bacteriol. 174 (1992) 102-107. [PMID: 1339418]
Accepted name: tryptophanase
Reaction: L-tryptophan + H2O = indole + pyruvate + NH3
Other name(s): L-tryptophanase; L-tryptophan indole-lyase (deaminating)
Systematic name: L-tryptophan indole-lyase (deaminating; pyruvate-forming)
Comments: A pyridoxal-phosphate protein, requiring K+. Also catalyses 2,3-elimination and β-replacement reactions of some indole-substituted tryptophan analogues of L-cysteine, L-serine and other 3-substituted amino acids.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9024-00-4
References:
1. Burns, R.O. and DeMoss, R.D. Properties of tryptophanase from Escherichia coli. Biochim. Biophys. Acta 65 (1962) 233-244. [PMID: 14017164]
2. Cowell, J.L., Maser, K. and DeMoss, R.D. Tryptophanase from Aeromonas liquifaciens. Purification, molecular weight and some chemical, catalytic and immunological properties. Biochim. Biophys. Acta 315 (1973) 449-463.
3. Newton, W.A., Morino, Y. and Snell, E.E. Properties of crystalline tryptophanase. J. Biol. Chem. 240 (1965) 1211-1218. [PMID: 14284727]
Accepted name: tyrosine phenol-lyase
Reaction: L-tyrosine + H2O = phenol + pyruvate + NH3
Other name(s): β-tyrosinase; L-tyrosine phenol-lyase (deaminating)
Systematic name: L-tyrosine phenol-lyase (deaminating; pyruvate-forming)
Comments: A pyridoxal-phosphate protein. The enzyme also slowly catalyses pyruvate formation from D-tyrosine, S-methyl-L-cysteine, L-cysteine, L-serine and D-serine.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9059-31-8
References:
1. Kumagai, H., Yamada, H., Matsui, H., Ohkishi, H. and Ogata, K. Tyrosine phenol lyase. I. Purification, crystallization, and properties. J. Biol. Chem. 245 (1970) 1767-1772. [PMID: 4908868]
2. Kumagai, H., Yamada, H., Matsui, H., Ohkishi, H. and Ogata, K. Tyrosine phenol lyase. II. Cofactor requirements. J. Biol. Chem. 245 (1970) 1773-1777. [PMID: 4908869]
Accepted name: deoxyribodipyrimidine photo-lyase
Reaction: cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA)
For diagram click here.
Other name(s): photoreactivating enzyme; DNA photolyase; DNA-photoreactivating enzyme; DNA cyclobutane dipyrimidine photolyase; DNA photolyase; deoxyribonucleic photolyase; deoxyribodipyrimidine photolyase; photolyase; PRE; PhrB photolyase; deoxyribonucleic cyclobutane dipyrimidine photolyase; phr A photolyase; dipyrimidine photolyase (photosensitive); deoxyribonucleate pyrimidine dimer lyase (photosensitive)
Systematic name: deoxyribocyclobutadipyrimidine pyrimidine-lyase
Comments: A flavoprotein (FAD), containing a second chromophore group. The enzyme catalyses the reactivation by light of irradiated DNA. A similar reactivation of irradiated RNA is probably due to a separate enzyme.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37290-70-3
References:
1. Eker, A.P.M. and Fichtinger-Schepman, A.M.J. Studies on a DNA photoreactivating enzyme from Streptomyces griseus. II. Purification of the enzyme. Biochim. Biophys. Acta 378 (1975) 54-63. [PMID: 804322]
2. Sancar, G.B., Smith, F.W., Reid, R., Payne, G., Levy, M. and Sancar, A. Action mechanism of Escherichia coli DNA photolyase. I. Formation of the enzyme-substrate complex. J. Biol. Chem. 262 (1987) 478-485. [PMID: 3539939]
3. Setlow, J.K. and Bollum, F.J. The minimum size of the substrate for yeast photoreactivating enzyme. Biochim. Biophys. Acta 157 (1968) 233-237. [PMID: 5649902]
[EC 4.1.99.4 Transferred entry: now EC 3.5.99.7, 1-aminocyclopropane-1-carboxylate deaminase (EC 4.1.99.4 created 1981, deleted 2002)]
Accepted name: octadecanal decarbonylase
Reaction: octadecanal + O2 + 2 NADPH + 2 H+ = heptadecane + formate + H2O + 2 NADP+
Other name(s): decarbonylase; aldehyde decarbonylase
Systematic name: octadecanal alkane-lyase
Comments: Contains a diiron center. Involved in the biosynthesis of alkanes. The enzyme from the cyanobacterium Nostoc punctiforme PCC 73102 is only active in vitro in the presence of ferredoxin, ferredoxin reductase and NADPH, and produces mostly C15 to C17 alkanes [2,3]. The enzyme from pea (Pisum sativum) produces alkanes of chain length C18 to C32 and is inhibited by metal-chelating agents [1]. The substrate for this enzyme is formed by EC 1.2.1.80, acyl-[acyl-carrier protein] reductase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 94185-90-7
References:
1. Cheesbrough, T.M. and, K olattukudy, P.E. Alkane biosynthesis by decarbonylation of aldehydes catalyzed by a particulate preparation from Pisum sativum. Proc. Natl. Acad. Sci. USA 81 (1984) 6613-6617. [PMID: 6593720]
2. Schirmer, A., Rude, M.A., Li, X., Popova, E. and del Cardayre, S.B. Microbial biosynthesis of alkanes. Science 329 (2010) 559-562. [PMID: 20671186]
3. Warui, D.M., Li, N., Norgaard, H., Krebs, C., Bollinger, J.M. and Booker, S.J. Detection of formate, rather than carbon monoxide, as the stoichiometric coproduct in conversion of fatty aldehydes to alkanes by a cyanobacterial aldehyde decarbonylase. J. Am. Chem. Soc. 133 (2011) 3316-3319. [PMID: 21341652]
[EC 4.1.99.6 Transferred entry: now EC 4.2.3.6, trichodiene synthase (EC 4.1.99.6 created 1989, deleted 2000)]
[EC 4.1.99.7 Transferred entry: now EC 4.2.3.9, aristolochene synthase (EC 4.1.99.7 created 1992 as EC 2.5.1.40, transferred 1999 to EC 4.1.99.7, deleted 2000)]
[EC 4.1.99.8 Transferred entry: now EC 4.2.3.14, pinene synthase (EC 4.1.99.8 created 2000, deleted 2000)]
[EC 4.1.99.9 Transferred entry: now EC 4.2.3.15, myrcene synthase (EC 4.1.99.9 created 2000, deleted 2000)]
[EC 4.1.99.10 Transferred entry: now EC 4.2.3.16, trichodiene synthase (EC 4.1.99.10 created 2000, deleted 2000)]
Accepted name: benzylsuccinate synthase
Reaction: benzylsuccinate = toluene + fumarate
For diagram of reaction click here.
Other name(s): benzylsuccinate fumarate-lyase
Systematic name: benzylsuccinate fumarate-lyase (toluene-forming)
Comments: A glycyl radical enzyme that is inhibited by benzyl alcohol, benzaldehyde, phenylhydrazine and is inactivated by oxygen.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, UM-BBD, CAS registry number: 209264-18-6
References:
1. Beller, H.R. and Spormann, A.M. Analysis of the novel benzylsuccinate synthase reaction for anaerobic toluene activation based on structural studies of the product. J. Bacteriol. 180 (1998) 5454-5457. [PMID: 9765580]
2. Leuthner, B., Leutwein, C., Schultz, H., Hörth, P., Haehnel, W., Schiltz, E., Schägger, H. and Heider, J. Biochemical and genetic characterisation of benzylsuccinate synthase from Thauera aromatica: a new glycyl radical enzyme catalysing the first step in anaerobic toluene metabolism. Mol. Microbiol. 28 (1998) 615-628. [PMID: 9632263]
Accepted name: 3,4-dihydroxy-2-butanone-4-phosphate synthase
Reaction: D-ribulose 5-phosphate = formate + L-3,4-dihydroxybutan-2-one 4-phosphate
For diagram of reaction click here
Other name(s): DHBP synthase; L-3,4-dihydroxybutan-2-one-4-phosphate synthase
Systematic name: D-ribulose 5-phosphate formate-lyase (L-3,4-dihydroxybutan-2-one 4-phosphate-forming)
Comments: Requires a divalent cation, preferably Mg2+, for activity [1]. The reaction involves an intramolecular skeletal rearrangement, with the bonds in D-ribulose 5-phosphate that connect C-3 and C-5 to C-4 being broken, C-4 being removed as formate and reconnection of C-3 and C-5 [1]. The phosphorylated four-carbon product (L-3,4-dihydroxybutan-2-one 4-phosphate) is an intermediate in the biosynthesis of riboflavin [1].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Volk, R. and Bacher, A. Studies on the 4-carbon precursor in the biosynthesis of riboflavin. Purification and properties of L-3,4-dihydroxy-2-butanone-4-phosphate synthase. J. Biol. Chem. 265 (1990) 19479-19485. [PMID: 2246238]
2. Liao, D.I., Calabrese, J.C., Wawrzak, Z., Viitanen, P.V. and Jordan, D.B. Crystal structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase of riboflavin biosynthesis. Structure 9 (2001) 11-18. [PMID: 11342130]
3. Kelly, M.J., Ball, L.J., Krieger, C., Yu, Y., Fischer, M., Schiffmann, S., Schmieder, P., Kühne, R., Bermel, W., Bacher, A., Richter, G. and Oschkinat, H. The NMR structure of the 47-kDa dimeric enzyme 3,4-dihydroxy-2-butanone-4-phosphate synthase and ligand binding studies reveal the location of the active site. Proc. Natl. Acad. Sci. USA 98 (2001) 13025-13030. [PMID: 11687623]
4. Liao, D.I., Zheng, Y.J., Viitanen, P.V. and Jordan, D.B. Structural definition of the active site and catalytic mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase. Biochemistry 41 (2002) 1795-1806. [PMID: 11827524]
5. Fischer, M., Römisch, W., Schiffmann, S., Kelly, M., Oschkinat, H., Steinbacher, S., Huber, R., Eisenreich, W., Richter, G. and Bacher, A. Biosynthesis of riboflavin in archaea studies on the mechanism of 3,4-dihydroxy-2-butanone-4-phosphate synthase of Methanococcus jannaschii. J. Biol. Chem. 277 (2002) 41410-41416. [PMID: 12200440]
6. Steinbacher, S., Schiffmann, S., Richter, G., Huber, R., Bacher, A. and Fischer, M. Structure of 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with divalent metal ions and the substrate ribulose 5-phosphate: implications for the catalytic mechanism. J. Biol. Chem. 278 (2003) 42256-42265. [PMID: 12904291]
7. Steinbacher, S., Schiffmann, S., Bacher, A. and Fischer, M. Metal sites in 3,4-dihydroxy-2-butanone 4-phosphate synthase from Methanococcus jannaschii in complex with the substrate ribulose 5-phosphate. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 1338-1340. [PMID: 15213409]
8. Echt, S., Bauer, S., Steinbacher, S., Huber, R., Bacher, A. and Fischer, M. Potential anti-infective targets in pathogenic yeasts: structure and properties of 3,4-dihydroxy-2-butanone 4-phosphate synthase of Candida albicans. J. Mol. Biol. 341 (2004) 1085-1096. [PMID: 15328619]
Accepted name: (6-4)DNA photolyase
Reaction: (6-4) photoproduct (in DNA) = 2 pyrimidine residues (in DNA)
For diagram of reaction, click here.
Other name(s): DNA photolyase; H64PRH; NF-10; phr (6-4); PL-(6-4); OtCPF1; (6-4) PHR; At64PHR
Systematic name: (6-4) photoproduct pyrimidine-lyase
Comments: A flavoprotein (FAD). The overall repair reaction consists of two distinct steps, one of which is light-independent and the other one light-dependent. In the initial light-independent step, a 6-iminium ion is thought to be generated via proton transfer induced by two histidines highly conserved among the (6-4) photolyases. This intermediate spontaneously rearranges to form an oxetane intermediate by intramolecular nucleophilic attack. In the subsequent light-driven reaction, one electron is believed to be transferred from the fully reduced FAD cofactor (FADH-) to the oxetane intermediate thus forming a neutral FADH radical and an anionic oxetane radical, which spontaneously fractures. The excess electron is then back-transferred to the flavin radical restoring the fully reduced flavin cofactor and a pair of pyrimidine bases [2].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Hitomi, K., DiTacchio, L., Arvai, A.S., Yamamoto, J., Kim, S.T., Todo, T., Tainer, J.A., Iwai, S., Panda, S. and Getzoff, E.D. Functional motifs in the (6-4) photolyase crystal structure make a comparative framework for DNA repair photolyases and clock cryptochromes. Proc. Natl. Acad. Sci. USA 106 (2009) 6962-6967. [PMID: 19359474]
2. Schleicher, E., Hitomi, K., Kay, C.W., Getzoff, E.D., Todo, T. and Weber, S. Electron nuclear double resonance differentiates complementary roles for active site histidines in (6-4) photolyase. J. Biol. Chem. 282 (2007) 4738-4747. [PMID: 17164245]
Accepted name: spore photoproduct lyase
Reaction: (5R)-5,6-dihydro-5-(thymidin-7-yl)thymidine (in double-helical DNA) = thymidylyl-(3'→5')-thymidylate (in double-helical DNA)
For diagram of reaction click here
Other name(s): SAM; SP lyase; SPL; SplB; SplG
Systematic name: spore photoproduct pyrimidine-lyase
Comments: This enzyme is a member of the 'AdoMet radical' (radical SAM) family. The enzyme binds a [4Fe-4S] cluster. The cluster is coordinated by 3 cysteines and an exchangeable SAM molecule [3]. The 5'-deoxy-adenosine radical formed after electron transfer from the [4Fe-4S] cluster to the S-adenosyl-L-methionine, initiates the repair by abstracting the C-6 hydrogen of the spore photoproduct lesion. During the second part of the repair process the SAM molecule is regenerated [3].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37290-70-3
References:
1. Chandor, A., Berteau, O., Douki, T., Gasparutto, D., Sanakis, Y., Ollagnier-de-Choudens, S., Atta, M. and Fontecave, M. Dinucleotide spore photoproduct, a minimal substrate of the DNA repair spore photoproduct lyase enzyme from Bacillus subtilis. J. Biol. Chem. 281 (2006) 26922-26931. [PMID: 16829676]
2. Pieck, J.C., Hennecke, U., Pierik, A.J., Friedel, M.G. and Carell, T. Characterization of a new thermophilic spore photoproduct lyase from Geobacillus stearothermophilus (SplG) with defined lesion containing DNA substrates. J. Biol. Chem. 281 (2006) 36317-36326. [PMID: 16968710]
3. Buis, J.M., Cheek, J., Kalliri, E. and Broderick, J.B. Characterization of an active spore photoproduct lyase, a DNA repair enzyme in the radical S-adenosylmethionine superfamily. J. Biol. Chem. 281 (2006) 25994-26003. [PMID: 16829680]
4. Mantel, C., Chandor, A., Gasparutto, D., Douki, T., Atta, M., Fontecave, M., Bayle, P.-A., Mouesca, J.-M. and Bardet, M. Combined NMR and DFT studies for the absolute configuration elucidation of the spore photoproduct, a UV-induced DNA lesion. J. Am. Chem. Soc. 130 (2008) 16978-16984. [PMID: 19012397]
5. Silver, S.C., Chandra, T., Zilinskas, E., Ghose, S., Broderick, W.E. and Broderick, J.B. Complete stereospecific repair of a synthetic dinucleotide spore photoproduct by spore photoproduct lyase. J. Biol. Inorg. Chem. 15 (2010) 943-955. [PMID: 20405152]
[EC 4.1.99.15 Deleted entry: S-specific spore photoproduct lyase. This enzyme was classified on the basis of an incorrect reaction. The activity is covered by EC 4.1.99.14, spore photoproduct lyase (EC 4.1.99.15 created 2009, deleted 2010)]
Accepted name: geosmin synthase
Reaction: (1E,4S,5E,7R)-germacra-1(10),5-dien-11-ol + H2O = (–)-geosmin + acetone
For diagram of reaction click here and mechanism click here.
Systematic name: germacradienol geosmin-lyase (acetone forming)
Comments: Requires Mg2+. Geosmin is the cause of the characteristic smell of moist soil. It is a bifunctional enzyme. The N-terminal part of the enzyme is EC 4.2.3.22, germacradienol synthase, and forms germacradienol from farnesyl diphosphate. The C-terminal part of the enzyme catalyses the conversion of germacradienol to geosmin via (1S,4aS,8aS)-1,4a-dimethyl-1,2,3,4,4a,5,6,8a-octahydronaphthalene.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Jiang, J., He, X. and Cane, D.E. Geosmin biosynthesis. Streptomyces coelicolor germacradienol/germacrene D synthase converts farnesyl diphosphate to geosmin. J. Am. Chem. Soc. 128 (2006) 8128-8129. [PMID: 16787064]
2. Cane, D.E., He, X., Kobayashi, S., Omura, S. and Ikeda, H. Geosmin biosynthesis in Streptomyces avermitilis. Molecular cloning, expression, and mechanistic study of the germacradienol/geosmin synthase. J. Antibiot. (Tokyo) 59 (2006) 471-479. [PMID: 17080683]
3. Jiang, J., He, X. and Cane, D.E. Biosynthesis of the earthy odorant geosmin by a bifunctional Streptomyces coelicolor enzyme. Nat. Chem. Biol. 3 (2007) 711-715. [PMID: 17873868]
Accepted name: phosphomethylpyrimidine synthase
Reaction: 5-amino-1-(5-phospho-D-ribosyl)imidazole + S-adenosyl-L-methionine = 4-amino-2-methyl-5-phosphomethylpyrimidine + 5'-deoxyadenosine + L-methionine + formate + CO
For diagram of reaction click here.
Other name(s): thiC (gene name)
Systematic name: 5-amino-1-(5-phospho-D-ribosyl)imidazole formate-lyase (decarboxylating, 4-amino-2-methyl-5-phosphomethylpyrimidine-forming)
Comments: Binds a 4Fe-4S cluster that is coordinated by 3 cysteines and an exchangeable S-adenosyl-L-methionine molecule. The first stage of catalysis is reduction of the S-adenosyl-L-methionine to produce L-methionine and a 5'-deoxyadenosin-5'-yl radical that is crucial for the conversion of the substrate. Part of the pathway for thiamine biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Chatterjee, A., Li, Y., Zhang, Y., Grove, T.L., Lee, M., Krebs, C., Booker, S.J., Begley, T.P. and Ealick, S.E. Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily. Nat. Chem. Biol. 4 (2008) 758-765. [PMID: 18953358]
2. Martinez-Gomez, N.C., Poyner, R.R., Mansoorabadi, S.O., Reed, G.H. and Downs, D.M. Reaction of AdoMet with ThiC generates a backbone free radical. Biochemistry 48 (2009) 217-219. [PMID: 19113839]
3. Chatterjee, A., Hazra, A.B., Abdelwahed, S., Hilmey, D.G. and Begley, T.P. A "radical dance" in thiamin biosynthesis: mechanistic analysis of the bacterial hydroxymethylpyrimidine phosphate synthase. Angew. Chem. Int. Ed. Engl. 49 (2010) 8653-8656. [PMID: 20886485]
Accepted name: cyclic pyranopterin phosphate synthase
Reaction: GTP = cyclic pyranopterin phosphate + diphosphate
For diagram of reaction click here and mechanism click here.
Glossary: cPMP = cyclic pyranopterin monophosphate = precursor Z = 8-amino-2,12,12-trihydroxy-4a,5a,6,9,11,11a,12,12a-octahydro[1,3,2]dioxaphosphinino[4',5':5,6]pyrano[3,2-g]pteridin-10(4H)-one 2-oxide = 8-amino-2,12,12-trihydroxy-4,4a,5a,6,9,10,11,11a,12,12a-decahydro-[1,3,2]dioxaphosphinino[4',5':5,6]pyrano[3,2-g]pteridine 2-oxide
Other name(s): MOCS1A; MoaA; MoaC; molybdenum cofactor biosynthesis protein 1; cyclic pyranopterin monophosphate synthase; GTP 8,9-lyase (cyclic pyranopterin monophosphate-forming)
Systematic name: GTP 8,9-lyase (cyclic pyranopterin phosphate-forming)
Comments: The enzyme catalyses an early step in the biosynthesis of the molybdenum cofactor (MoCo). The enzyme MoaA from bacteria and the human enzyme MOCS1A each contain two oxygen-sensitive FeS clusters. The enzyme is a member of the superfamily of S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes. In bacteria, the reaction is catalysed by MoaA and requires the action of MoaC. The latter protein is equivalent to the C-terminal domain of the eukaryotic enzyme MOCS1A which does not need further protein components to perform the reaction.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Rieder, C., Eisenreich, W., O'Brien, J., Richter, G., Götze, E., Boyle, P., Blanchard, S., Bacher, A. and Simon, H. Rearrangement reactions in the biosynthesis of molybdopterin - an NMR study with multiply 13C/15N labelled precursors. Eur. J. Biochem. 255 (1998) 24-36. [PMID: 9692897]
2. Wuebbens, M.M. and Rajagopalan, K.V. Investigation of the early steps of molybdopterin biosynthesis in Escherichia coli through the use of in vivo labeling studies. J. Biol. Chem. 270 (1995) 1082-1087. [PMID: 7836363]
3. Hänzelmann, P., Hernandez, H.L., Menzel, C., Garcia-Serres, R., Huynh, B.H., Johnson, M.K., Mendel, R.R. and Schindelin, H. Characterization of MOCS1A, an oxygen-sensitive iron-sulfur protein involved in human molybdenum cofactor biosynthesis. J. Biol. Chem. 279 (2004) 34721-34732. [PMID: 15180982]
4. Hänzelmann, P. and Schindelin, H. Crystal structure of the S-adenosylmethionine-dependent enzyme MoaA and its implications for molybdenum cofactor deficiency in humans. Proc. Natl. Acad. Sci. USA 101 (2004) 12870-12875. [PMID: 15317939]
5. Sanishvili, R., Beasley, S., Skarina, T., Glesne, D., Joachimiak, A., Edwards, A. and Savchenko, A. The crystal structure of Escherichia coli MoaB suggests a probable role in molybdenum cofactor synthesis. J. Biol. Chem. 279 (2004) 42139-42146. [PMID: 15269205]
6. Hänzelmann, P. and Schindelin, H. Binding of 5'-GTP to the C-terminal FeS cluster of the radical S-adenosylmethionine enzyme MoaA provides insights into its mechanism. Proc. Natl. Acad. Sci. USA 103 (2006) 6829-6834. [PMID: 16632608]
7. Lees, N.S., Hänzelmann, P., Hernandez, H.L., Subramanian, S., Schindelin, H., Johnson, M.K. and Hoffman, B.M. ENDOR spectroscopy shows that guanine N1 binds to [4Fe-4S] cluster II of the S-adenosylmethionine-dependent enzyme MoaA: mechanistic implications. J. Am. Chem. Soc. 131 (2009) 9184-9185. [PMID: 19566093]
Accepted name: 2-iminoacetate synthase
Reaction: L-tyrosine + S-adenosyl-L-methionine + reduced acceptor = 2-iminoacetate + 4-methylphenol + 5'-deoxyadenosine + L-methionine + acceptor + 2 H+
For diagram of reaction click here.
Glossary: 4-methylphenol = 4-cresol = p-cresol
Other name(s): thiH (gene name)
Systematic name: L-tyrosine 4-methylphenol-lyase (2-iminoacetate-forming)
Comments: Binds a 4Fe-4S cluster that is coordinated by 3 cysteines and an exchangeable S-adenosyl-L-methionine molecule. The first stage of catalysis is reduction of the S-adenosyl-L-methionine to produce methionine and a 5-deoxyadenosin-5-yl radical that is crucial for the conversion of the substrate. Part of the pathway for thiamine biosynthesis.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Leonardi, R., Fairhurst, S.A., Kriek, M., Lowe, D.J. and Roach, P.L. Thiamine biosynthesis in Escherichia coli: isolation and initial characterisation of the ThiGH complex. FEBS Lett. 539 (2003) 95-99. [PMID: 12650933]
2. Kriek, M., Martins, F., Challand, M.R., Croft, A. and Roach, P.L. Thiamine biosynthesis in Escherichia coli: identification of the intermediate and by-product derived from tyrosine. Angew. Chem. Int. Ed. Engl. 46 (2007) 9223-9226. [PMID: 17969213]
3. Kriek, M., Martins, F., Leonardi, R., Fairhurst, S.A., Lowe, D.J. and Roach, P.L. Thiazole synthase from Escherichia coli: an investigation of the substrates and purified proteins required for activity in vitro. J. Biol. Chem. 282 (2007) 17413-17423. [PMID: 17403671]