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>C=CH- + NH2-RContinued from EC 4.2.99
>C=CH- + NH2-ROthers, however, catalyse elimination of another component, e.g. water, which is followed by spontaneous reactions that lead to breakage of the C-N bond, e.g.
as in EC 4.3.1.17 (L-serine ammonia-lyase), so that the overall reaction is
>CH2-CO- + NH3Sections
EC 4.3.1 Ammonia-Lyases
EC 4.3.2 Lyases Acting on Amides, Amidines, etc.
EC 4.3.3 Amine-Lyases
EC 4.3.99 Other Carbon-Nitrogen Lyases
Accepted name: aspartate ammonia-lyase
Reaction: L-aspartate = fumarate + NH3
Other name(s): aspartase; fumaric aminase; L-aspartase; L-aspartate ammonia-lyase
Systematic name: L-aspartate ammonia-lyase (fumarate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9027-30-9
References:
1. Ellfolk, N. Studies on aspartase. 1. Quantitative separation of aspartase from bacterial cells, and its partial purification. Acta Chem. Scand. 7 (1953) 824-830.
Accepted name: methylaspartate ammonia-lyase
Reaction: L-threo-3-methylaspartate = mesaconate + NH3
Other name(s): β-methylaspartase; 3-methylaspartase; L-threo-3-methylaspartate ammonia-lyase
Systematic name: L-threo-3-methylaspartate ammonia-lyase (mesaconate-forming)
Comments: A cobalamin protein.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9033-26-5
References:
1. Barker, H.A., Smyth, R.O., Wawszkiewicz, E.J., Lee, M.N. and Wilson, R.M. Enzymic preparation and characterization of an α-L-β-methylaspartic acid. Arch. Biochem. Biophys. 78 (1958) 468-476.
2. Bright, H.J. and Ingraham, L.L. The preparation of crystalline β-methylaspartase. Biochim. Biophys. Acta 44 (1960) 586-588. [PMID: 13618029]
Accepted name: histidine ammonia-lyase
Reaction: L-histidine = urocanate + NH3
For diagram of reaction click here
Glossary: urocanate = (E)-3-(imidazol-4-yl)propenoate
Other name(s): histidase; histidinase; histidine α-deaminase; L-histidine ammonia-lyase
Systematic name: L-histidine ammonia-lyase (urocanate-forming)
Comments: This enzyme is a member of the aromatic amino acid lyase family, other members of which are EC 4.3.1.23 (tyrosine ammonia-lyase), EC 4.3.1.24 (phenylalanine ammonia-lyase) and EC 4.3.1.25 (phenylalanine/tyrosine ammonia-lyase). The enzyme contains the cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO), which is common to this family [4]. This unique cofactor is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine [5]. This enzyme catalyses the first step in the degradation of histidine and the product, urocanic acid, is further metabolized to glutamate [2,3].
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9013-75-6
References:
1. Mehler, A.H. and Tabor, H. Deamination of histidine to form urocanic acid in liver. J. Biol. Chem. 201 (1953) 775-784. [PMID: 13061415]
2. Watts, K.T., Mijts, B.N., Lee, P.C., Manning, A.J. and Schmidt-Dannert, C. Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family. Chem. Biol. 13 (2006) 1317-1326. [PMID: 17185227]
3. Poppe, L. and Rétey, J. Friedel-Crafts-type mechanism for the enzymatic elimination of ammonia from histidine and phenylalanine. Angew. Chem. Int. Ed. Engl. 44 (2005) 3668-3688. [PMID: 15906398]
4. Louie, G.V., Bowman, M.E., Moffitt, M.C., Baiga, T.J., Moore, B.S. and Noel, J.P. Structural determinants and modulation of substrate specificity in phenylalanine-tyrosine ammonia-lyases. Chem. Biol. 13 (2006) 1327-1338. [PMID: 17185228]
5. Schwede, T.F., Rétey, J. and Schulz, G.E. Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile. Biochemistry 38 (1999) 5355-5361. [PMID: 10220322]
Accepted name: formimidoyltetrahydrofolate cyclodeaminase
Reaction: 5-formimidoyltetrahydrofolate = 5,10-methenyltetrahydrofolate + NH3
For diagram of reaction click here (another example).
Other name(s): formiminotetrahydrofolate cyclodeaminase; 5-formimidoyltetrahydrofolate ammonia-lyase (cyclizing)
Systematic name: 5-formimidoyltetrahydrofolate ammonia-lyase (cyclizing; 5,10-methenyltetrahydrofolate-forming)
Comments: In eukaroytes, occurs as a bifunctional enzyme that also has glutamate formimidoyltransferase (EC 2.1.2.5) activity.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9032-05-7
References:
1. Rabinowitz, J.C. and Pricer, W.E. Formimino-tetrahydrofolic acid and methenyltetrahydrofolic acid as intermediates in the formation of N10-formyltetrahydrofolic acid. J. Am. Chem. Soc. 78 (1956) 5702-5704.
[EC 4.3.1.5 Transferred entry: phenylalanine ammonia-lyase. Now divided into EC 4.3.1.23 (tyrosine ammonia-lyase), EC 4.3.1.24 (phenylalanine ammonia-lyase) and EC 4.3.1.25 (phenylalanine/tyrosine ammonia-lyase). (EC 4.3.1.5 created 1965, deleted 2008)]
Accepted name: β-alanyl-CoA ammonia-lyase
Reaction: β-alanyl-CoA = acryloyl-CoA + NH3
Other name(s): β-alanyl coenzyme A ammonia-lyase; β-alanyl-CoA ammonia-lyase
Systematic name: β-alanyl-CoA ammonia-lyase (acryloyl-CoA-forming)
Comments: The reaction has only been demonstrated in the direction of addition of ammonia.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, CAS registry number: 9024-29-7
References:
1. Stadtman, E.R. The enzymic synthesis of β-alanyl coenzyme A. J. Am. Chem. Soc. 77 (1955) 5765-5766.
Accepted name: ethanolamine ammonia-lyase
Reaction: ethanolamine = acetaldehyde + NH3
Other name(s): ethanolamine deaminase; ethanolamine ammonia-lyase
Systematic name: ethanolamine ammonia-lyase (acetaldehyde-forming)
Comments: A cobalamin protein.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9054-69-7
References:
1. Bradbeer, C. The clostridial fermentations of choline and ethanolamine. 1. Preparation and properties of cell-free extracts. J. Biol. Chem. 240 (1965) 4669-4474. [PMID: 5846987]
2. Bradbeer, C. The clostridial fermentations of choline and ethanolamine. II. Requirement for a cobamide coenzyme by an ethanolamine deaminase. J. Biol. Chem. 240 (1965) 4675-4681. [PMID: 5846988]
3. Kaplan, B.H. and Stadtman, E.R. Ethanolamine deaminase, a cobamide coenzyme-dependent enzyme. I. Purification, assay, and properties of the enzyme. J. Biol. Chem. 243 (1968) 1787-1793. [PMID: 4297225]
[EC 4.3.1.8 Transferred entry: now EC 2.5.1.61 hydroxymethylbilane synthase. (EC 4.3.1.8 created 1972, deleted 2003)]
Accepted name: glucosaminate ammonia-lyase
Reaction: D-glucosaminate = 2-dehydro-3-deoxy-D-gluconate + NH3
Glossary: glucosaminate = 2-amino-2-deoxy-D-gluconate
Other name(s): glucosaminic dehydrase; D-glucosaminate dehydratase; D-glucosaminic acid dehydrase; aminodeoxygluconate dehydratase; 2-amino-2-deoxy-D-gluconate hydro-lyase (deaminating); aminodeoxygluconate ammonia-lyase; 2-amino-2-deoxy-D-gluconate ammonia-lyase; D-glucosaminate ammonia-lyase
Systematic name: D-glucosaminate ammonia-lyase (isomerizing; 2-dehydro-3-deoxy-D-gluconate-forming)
Comments: Contains pyridoxal phosphate.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37290-91-8
References:
1. Imanaga, Y. Metabolism of D-glucosamine. III. Enzymic degradation of D-glucosaminic acid. J. Biochem. (Tokyo) 45 (1958) 647-650.
2. Merrick, J.M. and Roseman, S. D-Glucosaminic acid dehydrase. Methods Enzymol. 9 (1966) 657-660.
3. Iwamoto, R., Imanaga, Y. and Soda, K. D-Glucosaminate dehydratase from Agrobacterium radiobacter. Physicochemical and enzymological properties. J. Biochem. (Tokyo) 91 (1982) 283-289. [PMID: 7068563]
4. Iwamoto, R., Taniki, H., Koishi, J. and Nakura, S. D-Glucosaminate aldolase activity of D-glucosaminate dehydratase from Pseudomonas fluorescens and its requirement for Mn2+ ion. Biosci. Biotechnol. Biochem. 59 (1995) 408-411. [PMID: 7766176]
Accepted name: serine-sulfate ammonia-lyase
Reaction: L-serine O-sulfate + H2O = pyruvate + NH3 + sulfate
Other name(s): (L-SOS)lyase
Systematic name: L-serine-O-sulfate ammonia-lyase (pyruvate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9054-70-0
References:
1. Thomas, J.H. and Tudball, N. Studies on the enzymic degradation of L-serine O-sulphate by a rat liver preparation. Biochem. J. 105 (1967) 467-472. [PMID: 5583990]
[EC 4.3.1.11 Deleted entry: dihydroxyphenylalanine ammonia-lyase. The entry had been drafted on the basis of a single abstract that did not provide experimental evidence of the enzyme-catalysed reaction. (EC 4.3.1.11 created 1972, deleted 2007)]
Accepted name: ornithine cyclodeaminase
Reaction: L-ornithine = L-proline + NH3
For diagram click here.
Other name(s): ornithine cyclase; ornithine cyclase (deaminating); L-ornithine ammonia-lyase (cyclizing)
Systematic name: L-ornithine ammonia-lyase (cyclizing; L-proline-forming)
Comments: Requires NAD+. The enzyme is a member of the μ-crystallin protein family [4]. The reaction is stimulated by the presence of ADP or ATP and is inhibited by O2 [2].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9054-76-6
References:
1. Costilow, R.N. and Laycock, L. Ornithine cyclase (deaminating). Purification of a protein that converts ornithine to proline and definition of the optimal assay conditions. J. Biol. Chem. 246 (1971) 6655-6660. [PMID: 4399881]
2. Muth, W.L. and Costilow, R.N. Ornithine cyclase (deaminating). II. Properties of the homogeneous enzyme. J. Biol. Chem. 249 (1974) 7457-7462. [PMID: 4373469]
3. Espineda, C.E., Linford, A.S., Devine, D. and Brusslan, J.A. The AtCAO gene, encoding chlorophyll a oxygenase, is required for chlorophyll b synthesis in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 96 (1999) 10507-10511. [PMID: 10468639]
4. Goodman, J.L., Wang, S., Alam, S., Ruzicka, F.J., Frey, P.A. and Wedekind, J.E. Ornithine cyclodeaminase: structure, mechanism of action, and implications for the μ-crystallin family. Biochemistry 43 (2004) 13883-13891. [PMID: 15518536]
5. Alam, S., Wang, S.C., Ruzicka, F.J., Frey, P.A. and Wedekind, J.E. Crystallization and X-ray diffraction analysis of ornithine cyclodeaminase from Pseudomonas putida. Acta Crystallogr. D Biol. Crystallogr. 60 (2004) 941-944. [PMID: 15103146]
Accepted name: carbamoyl-serine ammonia-lyase
Reaction: O-carbamoyl-L-serine + H2O = pyruvate + 2 NH3 + CO2
Other name(s): O-carbamoyl-L-serine deaminase; carbamoylserine deaminase; O-carbamoyl-L-serine ammonia-lyase (pyruvate-forming)
Systematic name: O-carbamoyl-L-serine ammonia-lyase (decarboxylating; pyruvate-forming)
Comments: A pyridoxal-phosphate protein.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 52227-64-2
References:
1. Cooper, A.J.L. and Meister, A. Enzymatic conversion of O-carbamyl-L-serine to pyruvate and ammonia. Biochem. Biophys. Res. Commun. 55 (1973) 780-787. [PMID: 4399881]
Accepted name: 3-aminobutyryl-CoA ammonia-lyase
Reaction: L-3-aminobutyryl-CoA = crotonoyl-CoA + NH3
Other name(s): L-3-aminobutyryl-CoA deaminase; L-3-aminobutyryl-CoA ammonia-lyase
Systematic name: L-3-aminobutyryl-CoA ammonia-lyase (crotonoyl-CoA-forming)
Comments: Hydroxylamine can replace ammonia as a substrate. Crotonoyl-pantetheine can replace crotonoyl-CoA but it is a poorer substrate.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 55467-41-9
References:
1. Jeng, I.-M., Barker, H.A. Purification and properties of L-3-aminobutyryl coenzyme A deaminase from a lysine-fermenting Clostridium. J. Biol. Chem. 249 (1974) 6578-6584. [PMID: 4420467]
2. Barker, H.A., Kahn, J.M., Chew, S. Enzymes involved in 3,5-diaminohexanoate degradation by Brevibacterium sp. J. Bacteriol. 143 (1980) 1165-1170. [PMID: 7410315]
Accepted name: diaminopropionate ammonia-lyase
Reaction: 2,3-diaminopropanoate + H2O = pyruvate + 2 NH3
Other name(s): diaminopropionatase; α,β-diaminopropionate ammonia-lyase; 2,3-diaminopropionate ammonia-lyase; 2,3-diaminopropanoate ammonia-lyase
Systematic name: 2,3-diaminopropanoate ammonia-lyase (adding water; pyruvate-forming)
Comments: A pyridoxal phosphate enzyme. Active towards both D- and L-diaminopropanoate. D- and L-serine are poor substrates.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 51901-19-0
References:
1. Nagasawa, T., Tanizawa, K., Satoda, T., Yamada, H. Diaminopropionate ammonia-lyase from Salmonella typhimurium. Purification and characterization of the crystalline enzyme, and sequence determination of the pyridoxal 5'-phosphate binding peptide. J. Biol. Chem. 263 (1988) 958-964. [PMID: 3275662]
Accepted name: threo-3-hydroxy-L-aspartate ammonia-lyase
Reaction: threo-3-hydroxy-L-aspartate = oxaloacetate + NH3
Other name(s): L-threo-3-hydroxyaspartate dehydratase; threo-3-hydroxyaspartate ammonia-lyase
Systematic name: threo-3-hydroxy-L-aspartate ammonia-lyase (oxaloacetate-forming)
Comments: A pyridoxal-phosphate protein. The enzyme, purified from the bacterium Pseudomonas sp. T62, is highly specific, and does not accept any other stereoisomer of 3-hydroxyaspartate. Different from EC 4.3.1.20, erythro-3-hydroxy-L-aspartate ammonia-lyase and EC 4.3.1.27, threo-3-hydroxy-D-aspartate ammonia-lyase. Requires a divalent cation such as Mn2+, Mg2+, or Ca2+.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 248270-70-4
References:
1. Wada, M., Matsumoto, T., Nakamori, S., Sakamoto, M., Kataoka, M., Liu, J.-Q., Itoh, N., Yamada, H. and Shimizu, S. Purification and characterization of a novel enzyme, L-threo-3-hydroxyaspartate dehydratase, from Pseudomonas sp. T62. FEMS Microbiol. Lett. 179 (1999) 147-151. [PMID: 10481099]
Accepted name: L-serine ammonia-lyase
Reaction: L-serine = pyruvate + NH3
Other name(s): serine deaminase; L-hydroxyaminoacid dehydratase; L-serine deaminase; L-serine dehydratase; L-serine hydro-lyase (deaminating)
Systematic name: L-serine ammonia-lyase (pyruvate-forming)
Comments: A pyridoxal-phosphate protein. This reaction is also carried out by EC 4.3.1.19 threonine ammonia-lyase, from a number of sources. The reaction catalysed probably involves initial elimination of water (hence the enzyme's original classification as EC 4.2.1.13, L-serine dehydratase), followed by isomerization and hydrolysis of the product with C-N bond breakage.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9014-27-1
References:
1. Ramos, F. and Wiame, J.-M. Occurrence of a catabolic L-serine (L-threonine) deaminase in Saccharomyces cerevisiae. Eur. J. Biochem. 123 (1982) 571-576. [PMID: 7042346]
2. Simon, D., Hoshino, J. and Kröger, H. L-Serine dehydratase from rat liver. Purification and some properties. Biochim. Biophys. Acta 321 (1973) 361-368. [PMID: 4750769]
3. Suda, M. and Nakagawa, H. L-Serine dehydratase (rat liver). Methods Enzymol. 17B (1971) 346-351.
4. Sagers, R.D. and Carter, J. E. L-Serine dehydratase (Clostridium acidiurica). Methods Enzymol. 17B (1971) 351-356.
5. Robinson, W.G. and Labow, R. L-Serine dehydratase (Escherichia coli). Methods Enzymol. 17B (1971) 356-360.
Accepted name: D-serine ammonia-lyase
Reaction: D-serine = pyruvate + NH3
Other name(s): D-hydroxyaminoacid dehydratase; D-serine dehydrase; D-hydroxy amino acid dehydratase; D-serine hydrolase; D-serine dehydratase (deaminating); D-serine deaminase; D-serine hydro-lyase (deaminating); D-serine ammonia-lyase
Systematic name: D-serine ammonia-lyase (pyruvate-forming)
Comments: A pyridoxal-phosphate protein. Also acts, slowly, on D-threonine. The reaction catalysed probably involves initial elimination of water (hence the enzyme's original classification as EC 4.2.1.14, D-serine dehydratase), followed by isomerization and hydrolysis of the product with C-N bond breakage.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9015-88-7
References:
1. Dupourque, D., Newton, W.A. and Snell, E.E. Purification and properties of D-serine dehydrase from Escherichia coli. J. Biol. Chem. 241 (1966) 1233-1238. [PMID: 5327100]
2. Metzler, D.E. and Snell, E.E. Deamination of serine. II. D-Serine dehydrase, a vitamin B6 enzyme from Escherichia coli. J. Biol. Chem. 198 (1952) 363-373. [PMID: 12999751]
Accepted name: threonine ammonia-lyase
Reaction: L-threonine = 2-oxobutanoate + NH3
For diagram of reaction click here.
Other name(s): threonine deaminase; L-serine dehydratase; serine deaminase; L-threonine dehydratase; threonine dehydrase; L-threonine deaminase; threonine dehydratase; L-threonine hydro-lyase (deaminating); L-threonine ammonia-lyase
Systematic name: L-threonine ammonia-lyase (2-oxobutanoate-forming)
Comments: The enzyme from many sources is a pyridoxal-phosphate protein; that from Pseudomonas putida is not. The enzyme from a number of sources also acts on L-serine, cf. EC 4.3.1.17, L-serine ammonia-lyase. The reaction catalysed probably involves initial elimination of water (hence the enzyme's original classification as EC 4.2.1.16, threonine dehydratase), followed by isomerization and hydrolysis of the product with C-N bond breakage.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, UM-BBD, CAS registry number: 774231-81-1
References:
1. Cohn, M.S. and Phillips, A.T. Purification and characterization of a B6-independent threonine dehydratase from Pseudomonas putida. Biochemistry 13 (1974) 1208-1214. [PMID: 4814721]
2. Nishimura, J.S. and Greenberg, D.M. Purification and properties of L-threonine dehydrase of sheep liver. J. Biol. Chem. 236 (1961) 2684-2691. [PMID: 14479973]
3. Phillips, A.T. and Wood, W.A. The mechanism of action of 5'-adenylic acid-activated threonine dehydrase. J. Biol. Chem. 240 (1965) 4703-4309. [PMID: 5321308]
4. Shizuta, Y., Nakazawa, A., Tokushige, M. and Hayaishi, O. Studies on the interaction between regulatory enzymes and effectors. 3. Crystallization and characterization of adenosine 5'-monophosphate-dependent threonine deaminase from Escherichia coli. J. Biol. Chem. 244 (1969) 1883-1889. [PMID: 4889010]
Accepted name: erythro-3-hydroxy-L-aspartate ammonia-lyase
Reaction: erythro-3-hydroxy-L-aspartate = oxaloacetate + ammonia
Other name(s): erythro-β-hydroxyaspartate dehydratase; erythro-3-hydroxyaspartate dehydratase; erythro-3-hydroxy-Ls-aspartate hydro-lyase (deaminating); erythro-3-hydroxy-Ls-aspartate ammonia-lyase
Systematic name: erythro-3-hydroxy-L-aspartate ammonia-lyase (oxaloacetate-forming)
Comments: A pyridoxal-phosphate protein. The enzyme, which was characterized from the bacterium Paracoccus denitrificans NCIMB 8944, is highly specific for the L-isomer of erythro-3-hydroxyaspartate. Different from EC 4.3.1.16, threo-3-hydroxy-L-aspartate ammonia-lyase and EC 4.3.1.27, threo-3-hydroxy-D-aspartate ammonia-lyase. Requires a divalent cation such as Mn2+, Mg2+, and Ca2+.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37290-74-7
References:
1. Gibbs, R.G. and Morris, J.G. Purification and properties of erythro-β-hydroxyaspartate dehydratase from Micrococcus denitrificans. Biochem. J. 97 (1965) 547-554. [PMID: 16749162]
[EC 4.3.1.21 Deleted entry: aminodeoxygluconate ammonia-lyase. Enzyme is identical to EC 4.3.1.9, glucosaminate ammonia-lyase (EC 4.3.1.21 created 1965 as EC 4.2.1.26, transferred 2002 to EC 4.3.1.21, deleted 2004)]
Accepted name: 3,4-dihydroxyphenylalanine reductive deaminase
Reaction: L-dopa + 2 NADH = 3,4-dihydroxyphenylpropanoate + 2 NAD+ + NH3
Glossary: L-dopa = 3,4-dihydroxy-L-phenylalanine
Other name(s): reductive deaminase; DOPA-reductive deaminase; DOPARDA
Systematic name: 3,4-dihydroxy-L-phenylalanine ammonia-lyase (3,4-dihydroxyphenylpropanoate-forming)
Comments: Forms part of the L-phenylalanine-catabolism pathway in the anoxygenic phototrophic bacterium Rhodobacter sphaeroides OU5. NADPH is oxidized more slowly than NADH.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Ranjith, N.K., Sasikala, Ch. and Ramana, Ch.V. Catabolism of L-phenylalanine and L-tyrosine by Rhodobacter sphaeroides OU5 occurs through 3,4-dihydroxyphenylalanine. Res. Microbiol. 158 (2007) 506-511. [PMID: 17616348]
Accepted name: tyrosine ammonia-lyase
Reaction: L-tyrosine = trans-p-hydroxycinnamate + NH3
Other name(s): TAL; tyrase; L-tyrosine ammonia-lyase
Systematic name: L-tyrosine ammonia-lyase (trans-p-hydroxycinnamate-forming)
Comments: This enzyme is a member of the aromatic amino acid lyase family, other members of which are EC 4.3.1.3 (histidine ammonia-lyase), EC 4.3.1.24 (phenylalanine ammonia-lyase) and EC 4.3.1.25 (phenylalanine/tyrosine ammonia-lyase). The enzyme contains the cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO), which is common to this family [1]. This unique cofactor is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine [3]. The enzyme is far more active with tyrosine than with phenylalanine as substrate, but the substrate specificity can be switched by mutation of a single amino acid (H89F) in the enzyme from the bacterium Rhodobacter sphaeroides [1,2].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 1030840-68-6
References:
1. Louie, G.V., Bowman, M.E., Moffitt, M.C., Baiga, T.J., Moore, B.S. and Noel, J.P. Structural determinants and modulation of substrate specificity in phenylalanine-tyrosine ammonia-lyases. Chem. Biol. 13 (2006) 1327-1338. [PMID: 17185228]
2. Watts, K.T., Mijts, B.N., Lee, P.C., Manning, A.J. and Schmidt-Dannert, C. Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family. Chem. Biol. 13 (2006) 1317-1326. [PMID: 17185227]
3. Schwede, T.F., Rétey, J. and Schulz, G.E. Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile. Biochemistry 38 (1999) 5355-5361. [PMID: 10220322]
Accepted name: phenylalanine ammonia-lyase
Reaction: L-phenylalanine = trans-cinnamate + NH3
For diagram of reaction click here
Other name(s): phenylalanine deaminase; phenylalanine ammonium-lyase; PAL; L-phenylalanine ammonia-lyase; Phe ammonia-lyase
Systematic name: L-phenylalanine ammonia-lyase (trans-cinnamate-forming)
Comments: This enzyme is a member of the aromatic amino acid lyase family, other members of which are EC 4.3.1.3 (histidine ammonia-lyase) and EC 4.3.1.23 (tyrosine ammonia-lyase) and EC 4.3.1.25 (phenylalanine/tyrosine ammonia-lyase). The enzyme contains the cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO), which is common to this family [3]. This unique cofactor is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine [9]. The enzyme from some species is highly specific for phenylalanine [7,8].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9024-28-6
References:
1. Koukol, J. and Conn, E.E. The metabolism of aromatic compounds in higher plants. IV. Purification and properties of the phenylalanine deaminase of Hordeum vulgare. J. Biol. Chem. 236 (1961) 2692-2698. [PMID: 14458851]
2. Young, M.R. and Neish, A.C. Properties of the ammonia-lyases deaminating phenylalanine and related compounds in Triticum sestivum and Pteridium aquilinum. Phytochemistry 5 (1966) 1121-1132.
3. Louie, G.V., Bowman, M.E., Moffitt, M.C., Baiga, T.J., Moore, B.S. and Noel, J.P. Structural determinants and modulation of substrate specificity in phenylalanine-tyrosine ammonia-lyases. Chem. Biol. 13 (2006) 1327-1338. [PMID: 17185228]
4. Calabrese, J.C., Jordan, D.B., Boodhoo, A., Sariaslani, S. and Vannelli, T. Crystal structure of phenylalanine ammonia lyase: multiple helix dipoles implicated in catalysis. Biochemistry 43 (2004) 11403-11416. [PMID: 15350127]
5. Ritter, H. and Schulz, G.E. Structural basis for the entrance into the phenylpropanoid metabolism catalyzed by phenylalanine ammonia-lyase. Plant Cell 16 (2004) 3426-3436. [PMID: 15548745]
6. Watts, K.T., Mijts, B.N., Lee, P.C., Manning, A.J. and Schmidt-Dannert, C. Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family. Chem. Biol. 13 (2006) 1317-1326. [PMID: 17185227]
7. Appert, C., Logemann, E., Hahlbrock, K., Schmid, J. and Amrhein, N. Structural and catalytic properties of the four phenylalanine ammonia-lyase isoenzymes from parsley (Petroselinum crispum Nym.). Eur. J. Biochem. 225 (1994) 491-499. [PMID: 7925471]
8. Cochrane, F.C., Davin, L.B. and Lewis, N.G. The Arabidopsis phenylalanine ammonia lyase gene family: kinetic characterization of the four PAL isoforms. Phytochemistry 65 (2004) 1557-1564. [PMID: 15276452]
9. Schwede, T.F., Rétey, J. and Schulz, G.E. Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile. Biochemistry 38 (1999) 5355-5361. [PMID: 10220322]
Accepted name: phenylalanine/tyrosine ammonia-lyase
Reaction: (1) L-phenylalanine = trans-cinnamate + NH3
(2) L-tyrosine = trans-p-hydroxycinnamate + NH3
Other name(s): PTAL; bifunctional PAL
Systematic name: L-phenylalanine(or L-tyrosine):trans-cinnamate(or trans-p-hydroxycinnamate) ammonia-lyase
Comments: This enzyme is a member of the aromatic amino acid lyase family, other members of which are EC 4.3.1.3 (histidine ammonia-lyase), EC 4.3.1.23 (tyrosine ammonia-lyase) and EC 4.3.1.24 (phenylalanine ammonia-lyase). The enzyme from some monocots, including maize, and from the yeast Rhodosporidium toruloides, deaminate L-phenylalanine and L-tyrosine with similar catalytic efficiency [3]. The enzyme contains the cofactor 3,5-dihydro-5-methylidene-4H-imidazol-4-one (MIO), which is common to this family [3]. This unique cofactor is formed autocatalytically by cyclization and dehydration of the three amino-acid residues alanine, serine and glycine [4].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Rösler, J., Krekel, F., Amrhein, N. and Schmid, J. Maize phenylalanine ammonia-lyase has tyrosine ammonia-lyase activity. Plant Physiol. 113 (1997) 175-179. [PMID: 9008393]
2. Watts, K.T., Mijts, B.N., Lee, P.C., Manning, A.J. and Schmidt-Dannert, C. Discovery of a substrate selectivity switch in tyrosine ammonia-lyase, a member of the aromatic amino acid lyase family. Chem. Biol. 13 (2006) 1317-1326. [PMID: 17185227]
3. Louie, G.V., Bowman, M.E., Moffitt, M.C., Baiga, T.J., Moore, B.S. and Noel, J.P. Structural determinants and modulation of substrate specificity in phenylalanine-tyrosine ammonia-lyases. Chem. Biol. 13 (2006) 1327-1338. [PMID: 17185228]
4. Schwede, T.F., Rétey, J. and Schulz, G.E. Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile. Biochemistry 38 (1999) 5355-5361. [PMID: 10220322]
Accepted name: chromopyrrolate synthase
Reaction: 2 2-imino-3-(7-chloroindol-3-yl)propanoate = dichlorochromopyrrolate + NH3
For diagram of reaction click here
Other name(s): RebD; chromopyrrolic acid synthase
Systematic name: 2-imino-3-(7-chloroindol-3-yl)propanoate ammonia-lyase (dichlorochromopyrrolate-forming)
Comments: This enzyme catalyses a step in the biosynthesis of rebeccamycin, an indolocarbazole alkaloid produced by the Actinobacterium Lechevalieria aerocolonigenes. The enzyme is a dimeric heme-protein oxidase that catalyses the oxidative dimerization of two L-tryptophan-derived molecules to form dichlorochromopyrrolic acid, the precursor for the fused six-ring indolocarbazole scaffold of rebeccamycin [1]. Contains one molecule of heme b per monomer, as well as non-heme iron that is not part of an iron-sulfur center [2]. The enzyme also possesses catalase activity.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Nishizawa, T., Gruschow, S., Jayamaha, D.H., Nishizawa-Harada, C. and Sherman, D.H. Enzymatic assembly of the bis-indole core of rebeccamycin. J. Am. Chem. Soc. 128 (2006) 724-725. [PMID: 16417354]
2. Howard-Jones, A.R. and Walsh, C.T. Enzymatic generation of the chromopyrrolic acid scaffold of rebeccamycin by the tandem action of RebO and RebD. Biochemistry 44 (2005) 15652-15663. [PMID: 16313168]
Accepted name: threo-3-hydroxy-D-aspartate ammonia-lyase
Reaction: threo-3-hydroxy-D-aspartate = oxaloacetate + NH3
Other name(s): D-threo-3-hydroxyaspartate dehydratase
Systematic name: threo-3-hydroxy-D-aspartate ammonia-lyase (oxaloacetate-forming)
Comments: A pyridoxal-phosphate protein. The enzyme, purified from the bacterium Delftia sp. HT23, also has activity against L-threo-3-hydroxyaspartate, L-erythro-3-hydroxyaspartate, and D-serine. Different from EC 4.3.1.20, erythro-3-hydroxy-L-aspartate ammonia-lyase and EC 4.3.1.16, threo-3-hydroxy-L-aspartate ammonia-lyase. Requires a divalent cation such as Mn2+, Co2+ or Ni2+.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Maeda, T., Takeda, Y., Murakami, T., Yokota, A. and Wada, M. Purification, characterization and amino acid sequence of a novel enzyme, D-threo-3-hydroxyaspartate dehydratase, from Delftia sp. HT23. J. Biochem. 148 (2010) 705-712. [PMID: 20843822]
Accepted name: L-lysine cyclodeaminase
Reaction: L-lysine = L-pipecolate + NH3
Other name(s): rapL (gene name); fkbL (gene name); tubZ (gene name); visC (gene name)
Systematic name: L-lysine ammonia-lyase (cyclizing; ammonia-forming)
Comments: Requires bound NAD+. The enzyme produces the non-proteinogenic amino acid L-pipecolate, which is incorporated into multiple secondary metabolite products, including rapamycin, tobulysin, virginiamycin and pristinamycin.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Khaw, L.E., Bohm, G.A., Metcalfe, S., Staunton, J. and Leadlay, P.F. Mutational biosynthesis of novel rapamycins by a strain of Streptomyces hygroscopicus NRRL 5491 disrupted in rapL, encoding a putative lysine cyclodeaminase. J. Bacteriol. 180 (1998) 809-814. [PMID: 9473033]
2. Gatto, G.J., Jr., Boyne, M.T., 2nd, Kelleher, N.L. and Walsh, C.T. Biosynthesis of pipecolic acid by RapL, a lysine cyclodeaminase encoded in the rapamycin gene cluster. J. Am. Chem. Soc. 128 (2006) 3838-3847. [PMID: 16536560]
3. Tsotsou, G.E. and Barbirato, F. Biochemical characterisation of recombinant Streptomyces pristinaespiralis L-lysine cyclodeaminase. Biochimie 89 (2007) 591-604. [PMID: 17291665]
Accepted name: argininosuccinate lyase
Reaction: 2-(Nω-L-arginino)succinate = fumarate + L-arginine
For diagram click here.
Other name(s): arginosuccinase; argininosuccinic acid lyase; arginine-succinate lyase; N-(L-argininosuccinate) arginine-lyase; ω-N-(L-arginino)succinate arginine-lyase
Systematic name: 2-(Nω-L-arginino)succinate arginine-lyase (fumarate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9027-34-3
References:
1. Davison, D.C. and Elliott, W.H. Enzymic reaction between arginine and fumarate in plant and animal tissue. Nature 169 (1952) 313-314. [PMID: 14910762]
Accepted name: adenylosuccinate lyase
Reaction: (1) N6-(1,2-dicarboxyethyl)AMP = fumarate + AMP
(2) (S)-2-[5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamido]succinate = fumarate + 5-amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxamide
For diagram click here and another example click here.
Other name(s): adenylosuccinase; succino AMP-lyase; N6-(1,2-dicarboxyethyl)AMP AMP-lyase; 6-N-(1,2-dicarboxyethyl)AMP AMP-lyase
Systematic name: N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming)
Comments: Also acts on 1-(5-phosphoribosyl)-4-(N-succinocarboxamide)-5-aminoimidazole.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9027-81-0
References:
1. Carter, C.E. and Cohen, L.H. The preparation and properties of adenylosuccinase and adenylosuccinic acid. J. Biol. Chem. 222 (1956) 17-30. [PMID: 13366975]
Accepted name: ureidoglycolate lyase
Reaction: (S)-ureidoglycolate = glyoxylate + urea
For diagram click here.
Other name(s): ureidoglycolatase; ureidoglycolase; ureidoglycolate hydrolase; (S)-ureidoglycolate urea-lyase
Systematic name: (S)-ureidoglycolate urea-lyase (glyoxylate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, CAS registry number: 9014-57-7
References:
1. Trijbels, F. and Vogels, G.D. Allantoate and ureidoglycolate degradation by Pseudomonas aeruginosa. Biochim. Biophys. Acta 132 (1967) 115-126. [PMID: 67202055]
Accepted name: purine imidazole-ring cyclase
Reaction: DNA 4,6-diamino-5-formamidopyrimidine = DNA adenine + H2O
Other name(s): DNA-4,6-diamino-5-formamidopyrimidine C8-N9-lyase (cyclizing); DNA-4,6-diamino-5-formamidopyrimidine 8-C,9-N-lyase (cyclizing)
Systematic name: DNA-4,6-diamino-5-formamidopyrimidine C8-N9-lyase (cyclizing; DNA-adenine-forming)
Comments: Also acts on 2,6-diamino-5-formamido-3,4-dihydro-4-oxopyrimidine residues. Brings about the reclosure of the imidazole rings of purine residues damaged by γ-rays.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 95990-28-6
References:
1. Chetsanga, C.J. and Grigorian, C. In situ enzymatic reclosure of opened imidazole rings of purines in DNA damaged by γ-irradiation. Proc. Natl. Acad. Sci. USA 82 (1985) 633-637. [PMID: 3856219]
Accepted name: peptidylamidoglycolate lyase
Reaction: peptidylamidoglycolate = peptidyl amide + glyoxylate
Other name(s): α-hydroxyglycine amidating dealkylase; peptidyl-α-hydroxyglycine α-amidating lyase; HGAD; PGL; PAL; peptidylamidoglycolate peptidylamide-lyase
Systematic name: peptidylamidoglycolate peptidyl-amide-lyase (glyoxylate-forming)
Comments: The enzyme acts on the product of the reaction catalysed by EC 1.14.17.3 peptidylglycine monooxygenase, thus removing a terminal glycine residue and leaving a des-glycine peptide amide.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 131689-50-4
References:
1. Katapodis, A.G., Ping, D. and May, S.W. A novel enzyme from bovine neurointermediate pituitary catalyzes dealkylation of α-hydroxyglycine derivatives, thereby functioning sequentially with peptidylglycine α-amidating monooxygenase in peptide amidation. Biochemistry 29 (1990) 6115-6120. [PMID: 2207061]
Accepted name: γ-L-glutamyl-butirosin B γ-glutamyl cyclotransferase
Reaction: γ-L-glutamyl-butirosin B = butirosin B + 5-oxoproline
Glossary: γ-L-glutamyl-butirosin B = (1R,2R,3S,4R,6S)-6-amino-4-{[(2R)-4-(L-γ-glutamylamino)-2-hydroxybutanoyl]amino}-3-hydroxy-2-(α-D-ribofuranosyloxy)cyclohexyl
Other name(s): btrG (gene name)
Systematic name: γ-L-glutamyl-butirosin B γ-glutamyl cyclotransferase (5-oxoproline producing)
Comments: The enzyme catalyses the last step in the biosynthesis of the aminoglycoside antibiotic butirosin B. The enzyme acts as a cyclotransferase, cleaving the amide bond via transamidation using the α-amine of the terminal γ-L-glutamate of the side chain, releasing it as the cyclic 5-oxoproline.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Llewellyn, N.M., Li, Y. and Spencer, J.B. Biosynthesis of butirosin: transfer and deprotection of the unique amino acid side chain. Chem. Biol. 14 (2007) 379-386. [PMID: 17462573]
EC 4.3.3.5 4'-demethylrebeccamycin synthase
EC 4.3.3.6 pyridoxal 5'-phosphate synthase (glutamine hydrolysing)
EC 4.3.3.7 4-hydroxy-tetrahydrodipicolinate synthase
Accepted name: 3-ketovalidoxylamine C-N-lyase
Reaction: 4-nitrophenyl-3-ketovalidamine = 4-nitroaniline + 5-D-(5/6)-5-C-(hydroxymethyl)-2,6-dihydroxycyclohex-2-en-1-one
Other name(s): 3-ketovalidoxylamine A C-N-lyase; p-nitrophenyl-3-ketovalidamine p-nitroaniline lyase; 4-nitrophenyl-3-ketovalidamine 4-nitroaniline-lyase
Systematic name: 4-nitrophenyl-3-ketovalidamine 4-nitroaniline-lyase [5-D-(5/6)-5-C-(hydroxymethyl)-2,6-dihydroxycyclohex-2-en-1-one-forming]
Comments: Requires Ca2+. Eliminates 4-nitroaniline from 4-nitrophenyl-3-ketovalidamine, or 4-nitrophenol from 4-nitrophenyl-α-D-3-dehydroglucoside. Involved in the degradation of the fungicide validamycin A by Flavobacterium saccharophilum.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 99889-98-2
References:
1. Asano, N., Takeuchi, M., Ninomiya, K., Kameda, Y. and Matsui, K. Microbial degradation of validamycin A by Flavobacterium saccharophilum. Enzymatic cleavage of C-N linkage in validoxylamine A. J. Antibiot. 37 (1984) 859-867. [PMID: 6548220]
2. Takeuchi, M., Asano, N., Kameda, Y. and Matsui, K. Purification and properties of 3-ketovalidoxylamine A C-N lyase from Flavobacterium saccharophilum. J. Biochem. (Tokyo) 98 (1985) 1631-1638. [PMID: 4093450]
Accepted name: strictosidine synthase
Reaction: 3-α(S)-strictosidine + H2O = tryptamine + secologanin
For diagram click here.
Other name(s): strictosidine synthetase; STR; 3-α(S)-strictosidine tryptamine-lyase
Systematic name: 3-α(S)-strictosidine tryptamine-lyase (secologanin-forming)
Comments: Catalyses a Pictet-Spengler reaction between the aldehyde group of secologanin and the amino group of tryptamine [4,5]. Involved in the biosynthesis of the monoterpenoid indole alkaloids.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 69669-72-3
References:
1. Treimer, J.K. and Zenk, M.H. Purification and properties of strictosidine synthase, the key enzyme in indole alkaloid formation. Eur. J. Biochem. 101 (1979) 225-233. [PMID: 510306]
2. Kutchan, T.M. Strictosidine: from alkaloid to enzyme to gene. Phytochemistry 32 (1993) 493-506. [PMID: 7763429]
3. de Waal, A., Meijer, A.H. and Verpoorte, R. Strictosidine synthase from Catharanthus roseus: purification and characterization of multiple forms. Biochem. J. 306 (1995) 571-580. [PMID: 7887913]
4. Ruppert, M., Woll, J., Giritch, A., Genady, E., Ma, X. and Stöckigt, J. Functional expression of an ajmaline pathway-specific esterase from Rauvolfia in a novel plant-virus expression system. Planta 222 (2005) 888-898. [PMID: 16133216]
5. McCoy, E., Galan, M.C. and O'Connor, S.E. Substrate specificity of strictosidine synthase. Bioorg. Med. Chem. Lett. 16 (2006) 2475-2478. [PMID: 16481164]
6. Ma, X., Panjikar, S., Koepke, J., Loris, E. and Stöckigt, J. The structure of Rauvolfia serpentina strictosidine synthase is a novel six-bladed β-propeller fold in plant proteins. Plant Cell 18 (2006) 907-920. [PMID: 16531499]
Accepted name: deacetylisoipecoside synthase
Reaction: deacetylisoipecoside + H2O = dopamine + secologanin
For diagram click here.
Glossary: dopamine = 4-(2-aminoethyl)benzene-1,2-diol
Other name(s): deacetylisoipecoside dopamine-lyase
Systematic name: deacetylisoipecoside dopamine-lyase (secologanin-forming)
Comments: The enzyme from the leaves of Alangium lamarckii differs in enantiomeric specificity from EC 4.3.3.4 deacetylipecoside synthase. The product is rapidly converted to demethylisoalangiside.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 192827-94-4
References:
1. DeEknamkul, W., Ounaroon, A., Tanahashi, T., Kutchan, T. and Zenk, M.H. Enzymatic condensation of dopamine and secologanin by cell-free extracts of Alangium lamarckii. Phytochemistry 45 (1997) 477-484.
Accepted name: deacetylipecoside synthase
Reaction: deacetylipecoside + H2O = dopamine + secologanin
For diagram click here.
Glossary: dopamine = 4-(2-aminoethyl)benzene-1,2-diol
Other name(s): deacetylipecoside dopamine-lyase
Systematic name: deacetylipecoside dopamine-lyase (secologanin-forming)
Comments: The enzyme from the leaves of Alangium lamarckii differs in enantiomeric specificity from EC 4.3.3.3 deacetylisoipecoside synthase. The product is rapidly converted to demethylalangiside.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 192827-93-3
References:
1. DeEknamkul, W., Ounaroon, A., Tanahashi, T., Kutchan, T. and Zenk, M.H. Enzymatic condensation of dopamine and secologanin by cell-free extracts of Alangium lamarckii. Phytochemistry 45 (1997) 477-484.
Accepted name: 4'-demethylrebeccamycin synthase
Reaction: 4'-O-demethylrebeccamycin + H2O = dichloro-arcyriaflavin A + β-D-glucose
For diagram of reaction click here
Glossary: dichloro-arcyriaflavin A = rebeccamycin aglycone
Other name(s): arcyriaflavin A N-glycosyltransferase; RebG
Systematic name: 4'-demethylrebeccamycin D-glucose-lyase
Comments: This enzyme catalyses a step in the biosynthesis of rebeccamycin, an indolocarbazole alkaloid produced by the Actinobacterium Lechevalieria aerocolonigenes. The enzyme is a glycosylase, and acts in the reverse direction to that shown. It has a wide substrate range, and was shown to glycosylate several substrates, including the staurosporine aglycone, EJG-III-108A, J-104303, 6-N-methyl-arcyriaflavin C and indolo-[2,3-a]-carbazole [1,2].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Ohuchi, T., Ikeda-Araki, A., Watanabe-Sakamoto, A., Kojiri, K., Nagashima, M., Okanishi, M. and Suda, H. Cloning and expression of a gene encoding N-glycosyltransferase (ngt) from Saccharothrix aerocolonigenes ATCC39243. J. Antibiot. (Tokyo) 53 (2000) 393-403. [PMID: 10866221]
2. Zhang, C., Albermann, C., Fu, X., Peters, N.R., Chisholm, J.D., Zhang, G., Gilbert, E.J., Wang, P.G., Van Vranken, D.L. and Thorson, J.S. RebG- and RebM-catalyzed indolocarbazole diversification. Chembiochem 7 (2006) 795-804. [PMID: 16575939]
Accepted name: pyridoxal 5'-phosphate synthase (glutamine hydrolysing)
Reaction: D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate (overall reaction)
(1a) L-glutamine + H2O = L-glutamate + NH3
(1b) D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + NH3 = pyridoxal 5'-phosphate + 4 H2O + phosphate
Other name(s): PdxST; pyridoxal 5'-phosphate synthase (glutamine hydrolyzing)
Systematic name: D-ribose 5-phosphate,D-glyceraldehyde 3-phosphate pyridoxal 5'-phosphate-lyase
Comments: The ammonia is provided by the glutaminase subunit and channeled to the active site of the lyase subunit by a 100 Å tunnel. The enzyme can also use ribulose 5-phosphate and dihydroxyacetone phosphate. The enzyme complex is found in aerobic bacteria, archaea, fungi and plants.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Burns, K.E., Xiang, Y., Kinsland, C.L., McLafferty, F.W. and Begley, T.P. Reconstitution and biochemical characterization of a new pyridoxal-5'-phosphate biosynthetic pathway. J. Am. Chem. Soc. 127 (2005) 3682-3683. [PMID: 15771487]
2. Raschle, T., Amrhein, N. and Fitzpatrick, T.B. On the two components of pyridoxal 5'-phosphate synthase from Bacillus subtilis. J. Biol. Chem. 280 (2005) 32291-32300. [PMID: 16030023]
3. Strohmeier, M., Raschle, T., Mazurkiewicz, J., Rippe, K., Sinning, I., Fitzpatrick, T.B. and Tews, I. Structure of a bacterial pyridoxal 5'-phosphate synthase complex. Proc. Natl. Acad. Sci. USA 103 (2006) 19284-19289. [PMID: 17159152]
4. Raschle, T., Arigoni, D., Brunisholz, R., Rechsteiner, H., Amrhein, N. and Fitzpatrick, T.B. Reaction mechanism of pyridoxal 5'-phosphate synthase. Detection of an enzyme-bound chromophoric intermediate. J. Biol. Chem. 282 (2007) 6098-6105. [PMID: 17189272]
5. Hanes, J.W., Keresztes, I. and Begley, T.P. Trapping of a chromophoric intermediate in the Pdx1-catalyzed biosynthesis of pyridoxal 5'-phosphate. Angew. Chem. Int. Ed. Engl. 47 (2008) 2102-2105. [PMID: 18260082]
6. Hanes, J.W., Burns, K.E., Hilmey, D.G., Chatterjee, A., Dorrestein, P.C. and Begley, T.P. Mechanistic studies on pyridoxal phosphate synthase: the reaction pathway leading to a chromophoric intermediate. J. Am. Chem. Soc. 130 (2008) 3043-3052. [PMID: 18271580]
7. Hanes, J.W., Keresztes, I. and Begley, T.P. 13C NMR snapshots of the complex reaction coordinate of pyridoxal phosphate synthase. Nat. Chem. Biol. 4 (2008) 425-430. [PMID: 18516049]
8. Wallner, S., Neuwirth, M., Flicker, K., Tews, I. and Macheroux, P. Dissection of contributions from invariant amino acids to complex formation and catalysis in the heteromeric pyridoxal 5-phosphate synthase complex from Bacillus subtilis. Biochemistry 48 (2009) 1928-1935. [PMID: 19152323]
Accepted name: 4-hydroxy-tetrahydrodipicolinate synthase
Reaction: pyruvate + L-aspartate-4-semialdehyde = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O
For diagram of reaction click here.
Glossary: (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
Other name(s): dihydrodipicolinate synthase (incorrect); dihydropicolinate synthetase (incorrect); dihydrodipicolinic acid synthase (incorrect); L-aspartate-4-semialdehyde hydro-lyase (adding pyruvate and cyclizing); dapA (gene name).
Systematic name: L-aspartate-4-semialdehyde hydro-lyase [adding pyruvate and cyclizing; (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate-forming]
Comments: Studies of the enzyme from the bacterium Escherichia coli have shown that the reaction can be divided into three consecutive steps: Schiff base formation between pyruvate and an active-site lysine, the addition of L-aspartate-semialdehyde, and finally transimination leading to cyclization with simultaneous dissociation of the product.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Yugari, Y. and Gilvarg, C. The condensation step in diaminopimelate synthesis. J. Biol. Chem. 240 (1965) 4710-4716. [PMID: 5321309]
2. Blickling, S., Renner, C., Laber, B., Pohlenz, H.D., Holak, T.A. and Huber, R. Reaction mechanism of Escherichia coli dihydrodipicolinate synthase investigated by X-ray crystallography and NMR spectroscopy. Biochemistry 36 (1997) 24-33. [PMID: 8993314]
3. Devenish, S.R., Blunt, J.W. and Gerrard, J.A. NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase. J Med Chem 53 (2010) 4808-4812. [PMID: 20503968]
4. Soares da Costa, T.P., Muscroft-Taylor, A.C., Dobson, R.C., Devenish, S.R., Jameson, G.B. and Gerrard, J.A. How essential is the 'essential' active-site lysine in dihydrodipicolinate synthase. Biochimie 92 (2010) 837-845. [PMID: 20353808]
Accepted name: carboxybiotin decarboxylase
Reaction: a carboxybiotinyl-[protein] + n Na+in + H+out = CO2 + a biotinyl-[protein] + n Na+out (n = 1—2)
For diagram of the reaction click here
Other name(s): MadB; carboxybiotin protein decarboxylase
Systematic name: carboxybiotinyl-[protein] carboxy-lyase
Comments: The integral membrane protein MadB from the anaerobic bacterium Malonomonas rubra is a component of the multienzyme complex EC 4.1.1.89, biotin-dependent malonate decarboxylase. The free energy of the decarboxylation reaction is used to pump Na+ out of the cell. The enzyme is a member of the Na+-translocating decarboxylase family, other members of which include EC 4.1.1.3 (oxaloacetate decarboxylase) and EC 4.1.1.41 (methylmalonyl-CoA decarboxylase) [2].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Berg, M., Hilbi, H. and Dimroth, P. Sequence of a gene cluster from Malonomonas rubra encoding components of the malonate decarboxylase Na+ pump and evidence for their function. Eur. J. Biochem. 245 (1997) 103-115. [PMID: 9128730]
2. Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3-10. [PMID: 11902724]
Accepted name: 7-carboxy-7-deazaguanine synthase
Reaction: 6-carboxy-5,6,7,8-tetrahydropterin = 7-carboxy-7-carbaguanine + NH3
For diagram of reaction click here.
Glossary: 7-carboxy-7-carbaguanine = 7-carboxy-7-deazaguanine
Other name(s): 7-carboxy-7-carbaguanine synthase; queE (gene name)
Systematic name: 6-carboxy-5,6,7,8-tetrahydropterin ammonia-lyase
Comments: The enzyme is a member of the superfamily of S-adenosyl-L-methionine-dependent radical (radical AdoMet) enzymes. Binds a [4Fe-4S] cluster that is coordinated by 3 cysteines and an exchangeable S-adenosyl-L-methionine molecule. The reaction is part of the biosynthesis pathway of queuosine.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. McCarty, R.M., Somogyi, A., Lin, G., Jacobsen, N.E. and Bandarian, V. The deazapurine biosynthetic pathway revealed: in vitro enzymatic synthesis of preQ0 from guanosine 5'-triphosphate in four steps. Biochemistry 48 (2009) 3847-3852. [PMID: 19354300]
Accepted name: choline trimethylamine-lyase
Reaction: choline = trimethylamine + acetaldehyde
Other name(s): cutC (gene name)
Systematic name: choline trimethylamine-lyase (acetaldehyde-forming)
Comments: The enzyme utilizes a glycine radical to break the C-N bond in choline. Found in choline-degrading anaerobic bacteria.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Craciun, S. and Balskus, E.P. Microbial conversion of choline to trimethylamine requires a glycyl radical enzyme. Proc. Natl. Acad. Sci. USA 109 (2012) 21307-21312. [PMID: 23151509]