Continued from EC 4.1.1.51 to EC 4.1.1.127
Accepted name: ketotetrose-phosphate aldolase
Reaction: erythrulose 1-phosphate = glycerone phosphate + formaldehyde
Other name(s): phosphoketotetrose aldolase; erythrulose-1-phosphate synthetase; erythrose-1-phosphate synthase; erythrulose-1-phosphate formaldehyde-lyase
Systematic name: erythrulose-1-phosphate formaldehyde-lyase (glycerone-phosphate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, CAS registry number: 9024-45-7
References:
1. Charalampous, F.C. and Mueller, G.C. Synthesis of erythrulose phosphate by a soluble enzyme from rat tissue. J. Biol. Chem. 201 (1953) 161-173.
[EC 4.1.2.3 Deleted entry: pentosealdolase (EC 4.1.2.3 created 1961, deleted 1972)]
Accepted name: deoxyribose-phosphate aldolase
Reaction: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde
For diagram of mechanism click here.
Other name(s): phosphodeoxyriboaldolase; deoxyriboaldolase; deoxyribose-5-phosphate aldolase; 2-deoxyribose-5-phosphate aldolase; 2-deoxy-D-ribose-5-phosphate acetaldehyde-lyase
Systematic name: 2-deoxy-D-ribose-5-phosphate acetaldehyde-lyase (D-glyceraldehyde-3-phosphate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9026-97-5
References:
1. Hoffee, P.A. 2-Deoxyribose-5-phosphate aldolase of Salmonella typhimurium: purification and properties. Arch. Biochem. Biophys. 126 (1968) 795-802 [PMID: 4879701]
2. Jedziniak, J.A. and Lionetti, F.J. Purification and properties of deoxyriboaldolase from human erythrocytes. Biochim. Biophys. Acta 212 (1970) 478-487. [PMID: 4989681]
3. Racker, E. Enzymatic synthesis and breakdown of desoxyribose phosphate. J. Biol. Chem. 196 (1952) 347-365.
4. Hoffee, P. Rosen, O.M. and Horecker, B.L. The mechanism of action of aldolases. VI. Crystallization of deoxyribose 5-phosphate aldolase and the number of active sites. J. Biol. Chem. 240 (1965) 1512-1516.
Accepted name: L-threonine aldolase
Reaction: L-threonine = glycine + acetaldehyde
Other name(s): L-threonine acetaldehyde-lyase
Systematic name: L-threonine acetaldehyde-lyase (glycine-forming)
Comments: A pyridoxal-phosphate protein. This enzyme is specific for L-threonine and can not utilize L-allo-threonine. Different from EC 4.1.2.49, L-allo-threonine aldolase, and EC 4.1.2.48, low-specificity L-threonine aldolase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 62213-23-4
References:
1. Dainty, R.H. Purification and properties of threonine aldolase from Clostridium pasteurianum. Biochem. J. 117 (1970) 585-592. [PMID: 5419751]
2. Karasek, M.A. and Greenberg, D.M. Studies on the properties of threonine aldolases. J. Biol. Chem. 227 (1957) 191-205. [PMID: 13449064]
[EC 4.1.2.6 Deleted entry: allothreonine aldolase. Reaction is due to EC 2.1.2.1 glycine hydroxymethyltransferase) (EC 4.1.2.6 created 1961, deleted 1972)]
[EC 4.1.2.7 Deleted entry: ketose-1-phosphate aldolase. Now included with EC 4.1.2.13 fructose-bisphosphate aldolase (EC 4.1.2.7 created 1961, deleted 1972)]
Accepted name: indole-3-glycerol-phosphate lyase
Reaction: (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate = indole + D-glyceraldehyde 3-phosphate
For diagram click here.
Other name(s): tryptophan synthase α; TSA; indoleglycerolphosphate aldolase; indole glycerol phosphate hydrolase; indole synthase; indole-3-glycerolphosphate D-glyceraldehyde-3-phosphate-lyase; indole-3-glycerol phosphate lyase; IGL; BX1; (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate D-glyceraldehyde-3-phosphate-lyase
Systematic name: (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate D-glyceraldehyde-3-phosphate-lyase (indole-forming)
Comments: Forms part of the defence mechanism against insects and microbial pathogens in the grass family, Gramineae, where it catalyses one of the steps in the formation of the cyclic hydroxamic acids 2,4-dihydroxy-2H-1,4-benzoxazin-3(4H)-one (DIBOA) and 2,4-dihydroxy-7-methoxy-2H-1,4-benzoxazin-3(4H)-one (DIMBOA) [1]. This enzyme resembles the α-subunit of EC 4.2.1.20, tryptophan synthase [3] but, unlike tryptophan synthase, its activity is independent of the β-subunit and free indole is released [2].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9014-52-2
References:
1. Yanofsky, C. The enzymatic conversion of anthranilic acid to indole. J. Biol. Chem. 223 (1956) 171-184. [PMID: 13376586]
2. Frey, M., Chomet, P., Glawischnig, E., Stettner, C., Grün, S., Winklmair, A., Eisenreich, W., Bacher, A., Meeley, R.B., Briggs, S.P., Simcox, K. and Gierl, A. Analysis of a chemical plant defense mechanism in grasses. Science 277 (1997) 696-699.
3. Frey, M., Stettner, C., Paré, P.W., Schmelz, E.A., Tumlinson, J.H. and Gierl, A. An herbivore elicitor activates the gene for indole emission in maize. Proc. Natl. Acad. Sci. USA 97 (2000) 14801-14806. [PMID: 11106389]
4. Melanson, D., Chilton, M.D., Masters-Moore, D. and Chilton, W.S. A deletion in an indole synthase gene is responsible for the DIMBOA-deficient phenotype of bxbx maize. Proc. Natl. Acad. Sci. USA 94 (1997) 13345-13350. [PMID: 9371848]
Accepted name: phosphoketolase
Reaction: D-xylulose 5-phosphate + phosphate = acetyl phosphate + D-glyceraldehyde 3-phosphate + H2O
Glossary: thiamine diphosphate
Other name(s): D-xylulose-5-phosphate D-glyceraldehyde-3-phosphate-lyase (phosphate-acetylating)
Systematic name: D-xylulose-5-phosphate D-glyceraldehyde-3-phosphate-lyase (adding phosphate; acetyl-phosphate-forming)
Comments: A thiamine-diphosphate protein.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9031-75-8
References:
1. Heath, E.C., Hurwitz, J., Horecker, B.L. and Ginsburg, A. Pentose fermentation by Lactobacillus plantarum. I. The cleavage of xylulose 5-phosphate by phosphoketolase. J. Biol. Chem. 231 (1958) 1009-1029.
2. Schramm, M., Klybas, V. and Racker, E. Phospholytic cleavage of fructose-6-phosphate by fructose-6-phosphate phosphoketolase from Acetobacter xylinum. J. Biol. Chem. 233 (1958) 1283-1288.
Accepted name: (R)-mandelonitrile lyase
Reaction: (R)-mandelonitrile = cyanide + benzaldehyde
Other name(s): (R)-oxynitrilase; oxynitrilase; D-oxynitrilase; D-α-hydroxynitrile lyase; mandelonitrile benzaldehyde-lyase; PaHNL; AtHNL; PhaMDL; (R)-HNL; (R)-PeHNL; (R)-hydroxynitrile lyase; R-selective hydroxynitrile lyase; R-selective HNL; (R)-(+)-mandelonitrile lyase
Systematic name: (R)-mandelonitrile benzaldehyde-lyase (cyanide-forming)
Comments: A variety of enzymes from different sources and with different properties. Some are flavoproteins, others are not. Active towards a number of aromatic and aliphatic hydroxynitriles (cyanohydrins).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9024-43-5
References:
1. Ueatrongchit, T., Kayo, A., Komeda, H., Asano, Y. and H-Kittikun, A. Purification and characterization of a novel (R)-hydroxynitrile lyase from Eriobotrya japonica (Loquat). Biosci. Biotechnol. Biochem. 72 (2008) 1513-1522. [PMID: 18540101]
2. Lin, G., Han, S. and Li, Z. Enzymic synthesis of (R)-cyanohydrins by three (R)-oxynitrilase sources in micro-aqueous organic medium. Tetrahedron 55 (1999) 3531-3540.
3. de Gonzalo, G., Brieva, R. and Gotor, V. (R)-Oxynitrilase-catalyzed transformation of ω-hydroxyalkanals. J. Mol. Catal. B 19-20 (2002) 223-230.
4. Ueatrongchit, T., Tamura, K., Ohmiya, T., H-Kittikun, A. and Asano, Y. Hydroxynitrile lyase from Passiflora edulis. Purification, characteristics and application in asymmetric synthesis of (R)-mandelonitrile. Enzyme Microb. Technol. 46 (2010) 456-465.
5. Andexer, J., von Langermann, J., Mell, A., Bocola, M., Kragl, U., Eggert, T. and Pohl, M. An R-selective hydroxynitrile lyase from Arabidopsis thaliana with an α/β-hydrolase fold. Angew. Chem. Int. Ed. Engl. 46 (2007) 8679-8681. [PMID: 17907254]
6. Guterl, J.K., Andexer, J.N., Sehl, T., von Langermann, J., Frindi-Wosch, I., Rosenkranz, T., Fitter, J., Gruber, K., Kragl, U., Eggert, T. and Pohl, M. Uneven twins: comparison of two enantiocomplementary hydroxynitrile lyases with α/β-hydrolase fold. J. Biotechnol. 141 (2009) 166-173. [PMID: 19433222]
Accepted name: hydroxymandelonitrile lyase
Reaction: (S)-4-hydroxymandelonitrile = cyanide + 4-hydroxybenzaldehyde
Other name(s): hydroxynitrile lyase; oxynitrilase; Sorghum hydroxynitrile lyase; (S)-4-hydroxymandelonitrile hydroxybenzaldehyde-lyase
Systematic name: (S)-4-hydroxymandelonitrile hydroxybenzaldehyde-lyase
Comments: Does not accept aliphatic hydroxynitriles, unlike EC 4.1.2.10 (mandelonitrile lyase), EC 4.1.2.46 [aliphatic (R)-hydroxynitrile lyase] and EC 4.1.2.47 [(S)-hydroxynitrile ketone-lyase (cyanide forming)].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9075-38-1
References:
1. Bové, C. and Conn, E.E. Metabolism of aromatic compounds in higher plants. II. Purification and properties of the oxynitrilase of Sorghum vulgare. J. Biol. Chem. 236 (1961) 207-210. [PMID: 16495254]
2. Seely, M.K., Criddle, R.S. and Conn, E.E. The metabolism of aromatic compounds in higher plants. 8. On the requirement of hydroxynitrile lyase for flavin. J. Biol. Chem. 241 (1966) 4457-4462. [PMID: 5922969]
Accepted name: 2-dehydropantoate aldolase
Reaction: 2-dehydropantoate = 3-methyl-2-oxobutanoate + formaldehyde
Glossary: pantoate = 2,4-dihydroxy-3,3-dimethylbutanoate
Other name(s): ketopantoaldolase; 2-dehydropantoate formaldehyde-lyase
Systematic name: 2-dehydropantoate formaldehyde-lyase (3-methyl-2-oxobutanoate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9024-51-5
References:
1. McIntosh, E.N., Purko, M. and Wood, W.A. Ketopantoate formation by a hydroxymethylation enzyme from Escherichia coli. J. Biol. Chem. 228 (1957) 499-510.
Accepted name: fructose-bisphosphate aldolase
Reaction: D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
For diagram of reaction click here (mechanism), alternatives click here or click here.
Other name(s): aldolase; fructose-1,6-bisphosphate triosephosphate-lyase; fructose diphosphate aldolase; diphosphofructose aldolase; fructose 1,6-diphosphate aldolase; ketose 1-phosphate aldolase; phosphofructoaldolase; zymohexase; fructoaldolase; fructose 1-phosphate aldolase; fructose 1-monophosphate aldolase; 1,6-Diphosphofructose aldolase; SMALDO; D-fructose-1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase
Systematic name: D-fructose-1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase (glycerone-phosphate-forming)
Comments: Also acts on (3S,4R)-ketose 1-phosphates. The yeast and bacterial enzymes are zinc proteins. The enzymes increase electron-attraction by the carbonyl group, some (Class I) forming a protonated imine with it, others (Class II), mainly of microbial origin, polarizing it with a metal ion, e.g. zinc.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9024-52-6
References:
1. Horecker, B.L., Tsolas, O. and Lai, C.Y. Aldolases, in Boyer, P.D. (Ed.), The Enzymes, 3rd edn., vol. 7, Academic Press, New York, 1972, pp. 213-258.
2. Alefounder, P.R., Baldwin, S.A., Perham, R.N., Short, N.J. Cloning, sequence analysis and over-expression of the gene for the class II fructose 1,6-bisphosphate aldolase of Escherichia coli. Biochem. J. 257 (1989) 529-534. [PMID: 2649077]
Accepted name: 2-dehydro-3-deoxy-phosphogluconate aldolase
Reaction: 2-dehydro-3-deoxy-6-phospho-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
For diagram of reaction click here.
Other name(s): phospho-2-keto-3-deoxygluconate aldolase; KDPG aldolase; phospho-2-keto-3-deoxygluconic aldolase; 2-keto-3-deoxy-6-phosphogluconic aldolase; 2-keto-3-deoxy-6-phosphogluconate aldolase; 6-phospho-2-keto-3-deoxygluconate aldolase; ODPG aldolase; 2-oxo-3-deoxy-6-phosphogluconate aldolase; 2-keto-3-deoxygluconate-6-P-aldolase; 2-keto-3-deoxygluconate-6-phosphate aldolase; 2-dehydro-3-deoxy-D-gluconate-6-phosphate D-glyceraldehyde-3-phosphate-lyase; 2-dehydro-3-deoxy-D-gluconate-6-phosphate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)
Systematic name: 2-dehydro-3-deoxy-6-phosphate-D-gluconate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)
Comments: The enzyme shows no activity with 2-dehydro-3-deoxy-6-phosphate-D-galactonate. cf. EC 4.1.2.55, 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase [2]. Also acts on 2-oxobutanoate [1].
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9024-53-7
References:
1. Meloche, H.P. and Wood, W.A. Crystallization and characteristics of 2-keto-3-deoxy-6-phosphogluconic aldolase. J. Biol. Chem. 239 (1964) 3515-3518. [PMID: 14245411]
2. Barran, L.R. and Wood, W.A. The mechanism of 2-keto-3-deoxy-6-phosphogluconate aldolase. 3. Nature of the inactivation by fluorodinitrobenzene. J. Biol. Chem. 246 (1971) 4028-4035. [PMID: 5561473]
[EC 4.1.2.15 Transferred entry: now EC 2.5.1.54, 3-deoxy-7-phosphoheptulonate synthase (EC 4.1.2.15 created 1965, modified 1976, deleted 2002)]
[EC 4.1.2.16 Transferred entry: now EC 2.5.1.55, 3-deoxy-8-phosphooctulonate synthase (EC 4.1.2.16 created 1965, deleted 2002)]
Accepted name: L-fuculose-phosphate aldolase
Reaction: L-fuculose 1-phosphate = glycerone phosphate + (S)-lactaldehyde
Other name(s): L-fuculose 1-phosphate aldolase; fuculose aldolase; L-fuculose-1-phosphate lactaldehyde-lyase
Systematic name: L-fuculose-1-phosphate (S)-lactaldehyde-lyase (glycerone-phosphate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9024-54-8
References:
1. Ghalambor, M.A. and Heath, E.C. The biosynthesis of cell wall lipopolysaccharide in Escherichia coli. IV. Purification and properties of cytidine monophosphate 3-deoxy-D-manno-octulosonate synthetase. J. Biol. Chem. 241 (1966) 3216-3221. [PMID: 5330266]
2. Dreyer, M.K. and Schulz, G.E. The spatial structure of the class II L-fuculose-1-phosphate aldolase from Escherichia coli. J. Mol. Biol. 231 (1993) 549-553. [PMID: 8515438]
3. Dreyer, M.K. and Schulz, G.E. Catalytic mechanism of the metal-dependent fuculose aldolase from Escherichia coli as derived from the structure. J. Mol. Biol. 259 (1996) 458-466. [PMID: 8676381]
Accepted name: 2-dehydro-3-deoxy-L-pentonate aldolase
Reaction: 2-dehydro-3-deoxy-L-pentonate = pyruvate + glycolaldehyde
For diagram of reaction click here.
Other name(s): 2-keto-3-deoxy-L-pentonate aldolase; 2-keto-3-deoxy-L-arabonate aldolase; 2-keto-3-deoxy-D-xylonate aldolase; 3-deoxy-D-pentulosonic acid aldolase; 2-dehydro-3-deoxy-L-pentonate glycolaldehyde-lyase
Systematic name: 2-dehydro-3-deoxy-L-pentonate glycolaldehyde-lyase (pyruvate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, CAS registry number: 9076-49-7
References:
1. Dahms, A.S. and Anderson, R.L. 2-Keto-3-deoxy-L-arabonate aldolase and its role in a new pathway of L-arabinose degradation. Biochem. Biophys. Res. Commun. 36 (1969) 809-814. [PMID: 5808295]
Accepted name: rhamnulose-1-phosphate aldolase
Reaction: L-rhamnulose 1-phosphate = glycerone phosphate + (S)-lactaldehyde
For diagram of reaction click here.
Other name(s): rhamnulose phosphate aldolase; L-rhamnulose 1-phosphate aldolase; L-rhamnulose-phosphate aldolase; L-rhamnulose-1-phosphate lactaldehyde-lyase
Systematic name: L-rhamnulose-1-phosphate (S)-lactaldehyde-lyase (glycerone-phosphate-forming)
Links to other databases: BRENDA, EXPASY, GTD, KEGG, Metacyc, PDB, CAS registry number: 9054-58-4
References:
1. Chiu, T.-H. and Feingold, D.S. L-Rhamnulose 1-phosphate aldolase from Escherichia coli. Crystallization and properties. Biochemistry 8 (1969) 98-108. [PMID: 4975916]
2. Sawada, H. and Takagi, Y. The metabolism of L-rhamnose in Escherichia coli. 3. L-Rhamulose-phosphate aldolase. Biochim. Biophys. Acta 92 (1964) 26-32.
Accepted name: 2-dehydro-3-deoxyglucarate aldolase
Reaction: 2-dehydro-3-deoxy-D-glucarate = pyruvate + 2-hydroxy-3-oxopropanoate
Glossary: 2-hydroxy-3-oxopropanoate = tartronate semialdehyde
Other name(s): 2-keto-3-deoxyglucarate aldolase; α-keto-β-deoxy-D-glucarate aldolase; 2-dehydro-3-deoxy-D-glucarate tartronate-semialdehyde-lyase; 2-dehydro-3-deoxy-D-glucarate tartronate-semialdehyde-lyase (pyruvate-forming)
Systematic name: 2-dehydro-3-deoxy-D-glucarate 2-hydroxy-3-oxopropanoate-lyase (pyruvate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37290-56-5
References:
1. Fish, D.C. and Blumenthal, H.J. 2-Keto-3-deoxy-D-glucarate aldolase. Methods Enzymol. 9 (1966) 529-534.
Accepted name: 2-dehydro-3-deoxy-6-phosphogalactonate aldolase
Reaction: 2-dehydro-3-deoxy-6-phospho-D-galactonate = pyruvate + D-glyceraldehyde 3-phosphate
Other name(s): 6-phospho-2-keto-3-deoxygalactonate aldolase; phospho-2-keto-3-deoxygalactonate aldolase; 2-keto-3-deoxy-6-phosphogalactonic aldolase; phospho-2-keto-3-deoxygalactonic aldolase; 2-keto-3-deoxy-6-phosphogalactonic acid aldolase; (KDPGal)aldolase; 2-dehydro-3-deoxy-D-galactonate-6-phosphate D-glyceraldehyde-3-phosphate-lyase; 2-dehydro-3-deoxy-D-galactonate-6-phosphate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)
Systematic name: 2-dehydro-3-deoxy-6-phospho-D-galactonate D-glyceraldehyde-3-phospho-lyase (pyruvate-forming)
Comments: The enzyme catalyses the last reaction in a D-galactose degradation pathway. cf. EC 4.1.2.55, 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 9030-99-3
References:
1. Shuster, C.W. 2-Keto-3-deoxy-6-phosphogalactonic acid aldolase. Methods Enzymol. 9 (1966) 524-528.
Accepted name: fructose-6-phosphate phosphoketolase
Reaction: D-fructose 6-phosphate + phosphate = acetyl phosphate + D-erythrose 4-phosphate + H2O
Systematic name: D-fructose-6-phosphate D-erythrose-4-phosphate-lyase (adding phosphate; phosphate-acetylating)
Comments: Also acts on D-xylulose 5-phosphate.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37290-57-6
References:
1. Schramm, M., Klybas, V. and Racker, E. Phospholytic cleavage of fructose-6-phosphate by fructose-6-phosphate phosphoketolase from Acetobacter xylinum. J. Biol. Chem. 233 (1958) 1283-1288.
Accepted name: 3-deoxy-D-manno-octulosonate aldolase
Reaction: 3-deoxy-D-manno-octulosonate = pyruvate + D-arabinose
Other name(s): 2-keto-3-deoxyoctonate aldolase; KDOaldolase; 3-deoxyoctulosonic aldolase; 2-keto-3-deoxyoctonic aldolase; 3-deoxy-D-manno-octulosonic aldolase; 3-deoxy-D-manno-octulosonate D-arabinose-lyase
Systematic name: 3-deoxy-D-manno-octulosonate D-arabinose-lyase (pyruvate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9026-95-3
References:
1. Ghalambor, M.A. and Heath, E.C. The biosynthesis of cell wall lipopolysaccharide in Escherichia coli. V. Purification and properties of 3-deoxy-D-manno-octulosonate aldolase. J. Biol. Chem. 241 (1966) 3222-3227. [PMID: 5912115]
Accepted name: dimethylaniline-N-oxide aldolase
Reaction: N,N-dimethylaniline N-oxide = N-methylaniline + formaldehyde
Other name(s): microsomal oxidase II; microsomal N-oxide dealkylase; N,N-dimethylaniline-N-oxide formaldehyde-lyase
Systematic name: N,N-dimethylaniline-N-oxide formaldehyde-lyase (N-methylaniline-forming)
Comments: Acts on various N,N-dialkylarylamides.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37290-58-7
References:
1. Machinist, J.M., Orme-Johnson, W.H. and Ziegler, D.M. Microsomal oxidases. II. Properties of a pork liver microsomal N-oxide dealkylase. Biochemistry 5 (1966) 2939-2943. [PMID: 5961882]
Accepted name: dihydroneopterin aldolase
Reaction: 7,8-dihydroneopterin = 6-(hydroxymethyl)-7,8-dihydropterin + glycolaldehyde
For diagram of reaction click here or click here.
Other name(s): 7,8-dihydroneopterin aldolase; 2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8-dihydropteridine glycolaldehyde-lyase; 2-amino-4-hydroxy-6-(D-erythro-1,2,3-trihydroxypropyl)-7,8-dihydropteridine glycolaldehyde-lyase (2-amino-4-hydroxy-6-hydroxymethyl-7,8-dihydropteridine-forming); DHNA; mptD (gene name); folB (gene name)
Systematic name: 7,8-dihydroneopterin glycolaldehyde-lyase [6-(hydroxymethyl)-7,8-dihydropterin-forming]
Comments: The enzyme participates in folate (in bacteria, plants and fungi) and methanopterin (in archaea) biosynthesis. The enzymes from the bacterium Escherichia coli and the plant Arabidopsis thaliana also catalyse the epimerisation of the 2' hydroxy-group (EC 5.1.99.8, 7,8-dihydroneopterin epimerase) [2,3]. The enzyme from the bacterium Mycobacterium tuberculosis is trifunctional and also catalyses EC 5.1.99.8 and EC 1.13.11.81, 7,8-dihydroneopterin oxygenase [6]. The enzyme from the yeast Saccharomyces cerevisiae also catalyses the two subsequent steps in the folate biosynthesis pathway - EC 2.7.6.3, 2-amino-4-hydroxy-6-hydroxymethyldihydropteridine diphosphokinase, and EC 2.5.1.15, dihydropteroate synthase [4].
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37290-59-8
References:
1. Mathis, J.B. and Brown, G.M. The biosynthesis of folic acid. XI. Purification and properties of dihydroneopterin aldolase. J. Biol. Chem. 245 (1970) 3015-3025. [PMID: 4912541]
2. Haussmann, C., Rohdich, F., Schmidt, E., Bacher, A. and Richter, G. Biosynthesis of pteridines in Escherichia coli. Structural and mechanistic similarity of dihydroneopterin-triphosphate epimerase and dihydroneopterin aldolase. J. Biol. Chem. 273 (1998) 17418-17424. [PMID: 9651328]
3. Goyer, A., Illarionova, V., Roje, S., Fischer, M., Bacher, A. and Hanson, A.D. Folate biosynthesis in higher plants. cDNA cloning, heterologous expression, and characterization of dihydroneopterin aldolases. Plant Physiol. 135 (2004) 103-111. [PMID: 15107504]
4. Güldener, U., Koehler, G.J., Haussmann, C., Bacher, A., Kricke, J., Becher, D. and Hegemann, J.H. Characterization of the Saccharomyces cerevisiae Fol1 protein: starvation for C1 carrier induces pseudohyphal growth. Mol. Biol. Cell 15 (2004) 3811-3828. [PMID: 15169867]
5. Czekster, C.M. and Blanchard, J.S. One substrate, five products: reactions catalyzed by the dihydroneopterin aldolase from Mycobacterium tuberculosis. J. Am. Chem. Soc. 134 (2012) 19758-19771. [PMID: 23150985]
6. Wang, Y., Xu, H., Grochowski, L.L. and White, R.H. Biochemical characterization of a dihydroneopterin aldolase used for methanopterin biosynthesis in methanogens. J. Bacteriol. 196 (2014) 3191-3198. [PMID: 24982305]
7. Blaszczyk, J., Lu, Z., Li, Y., Yan, H. and Ji, X. Crystallographic and molecular dynamics simulation analysis of Escherichia coli dihydroneopterin aldolase. Cell Biosci 4 (2014) 52. [PMID: 25264482]
Accepted name: phenylserine aldolase
Reaction: L-threo-3-phenylserine = glycine + benzaldehyde
Other name(s): L-threo-3-phenylserine benzaldehyde-lyase
Systematic name: L-threo-3-phenylserine benzaldehyde-lyase (glycine-forming)
Comments: A pyridoxal-phosphate protein.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37290-60-1
References:
1. Bruns, F.H. and Fiedler, L. Enzymatic cleavage and synthesis of L-threo-β-phenylserine and L-erythro-β-phenylserine. Nature 181 (1958) 1533-1534. [PMID: 13566053]
Accepted name: sphinganine-1-phosphate aldolase
Reaction: sphinganine 1-phosphate = phosphoethanolamine + palmitaldehyde
Other name(s): dihydrosphingosine 1-phosphate aldolase; sphinganine-1-phosphate alkanal-lyase; sphinganine-1-phosphate lyase; sphinganine-1-phosphate palmitaldehyde-lyase
Systematic name: sphinganine-1-phosphate palmitaldehyde-lyase (phosphoethanolamine-forming)
Comments: A pyridoxal-phosphate protein.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 39391-27-0
References:
1. Stoffel, W., Le Kim, D. and Sticht, G. Distribution and properties of dihydrosphingosine-1-phosphate aldolase (sphinganine-1-phosphate alkanal-lyase). Hoppe-Seyler's Z. Physiol. Chem. 350 (1969) 1233-1241. [PMID: 5389296]
Accepted name: 2-dehydro-3-deoxy-D-pentonate aldolase
Reaction: 2-dehydro-3-deoxy-D-pentonate = pyruvate + glycolaldehyde
Other name(s): 2-keto-3-deoxy-D-pentonate aldolase; 3-deoxy-D-pentulosonic acid aldolase; 2-dehydro-3-deoxy-D-pentonate glycolaldehyde-lyase
Systematic name: 2-dehydro-3-deoxy-D-pentonate glycolaldehyde-lyase (pyruvate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 55326-36-8
References:
1. Dahms, A.S. 3-Deoxy-D-pentulosonic acid aldolase and its role in a new pathway of D-xylose degradation. Biochem. Biophys. Res. Commun. 60 (1974) 1433-1439. [PMID: 4423285]
2. Dahms, A.S. and Donald, A. 2-Keto-3-deoxy-D-xylonate aldolase (3-deoxy-D-pentulosonic acid aldolase). Methods Enzymol. 90 (1982) 269-272. [PMID: 7154955]
Accepted name: 5-dehydro-2-deoxyphosphogluconate aldolase
Reaction: 5-dehydro-2-deoxy-D-gluconate 6-phosphate = glycerone phosphate + malonate semialdehyde
For diagram of reaction click here.
Other name(s): phospho-5-keto-2-deoxygluconate aldolase; 5-dehydro-2-deoxy-D-gluconate-6-phosphate malonate-semialdehyde-lyase
Systematic name: 5-dehydro-2-deoxy-D-gluconate-6-phosphate malonate-semialdehyde-lyase (glycerone-phosphate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 62213-25-6
References:
1. Anderson, W.A. and Magasanik, B. The pathway of myo-inositol degradation in Aerobacter aerogenes. Conversion of 2-deoxy-5-keto-D-gluconic acid to glycolytic intermediates. J. Biol. Chem. 246 (1971) 5662-5675. [PMID: 4328832]
[EC 4.1.2.30 Transferred entry: 17α-hydroxyprogesterone aldolase. Now EC 1.14.14.32, 17α-hydroxyprogesterone deacetylase (EC 4.1.2.30 created 1976, deleted 2016)]
[EC 4.1.2.31 Deleted entry: 2-oxo-4-hydroxyglutarate aldolase. Now included with EC 4.1.3.16 4-hydroxy-2-oxoglutarate aldolase (EC 4.1.2.31 created 1978, deleted 1982)]
Accepted name: trimethylamine-oxide aldolase
Reaction: trimethylamine N-oxide = dimethylamine + formaldehyde
Other name(s): trimethylamine N-oxide formaldehyde-lyase; trimethylamine N-oxide aldolase; trimethylamine N-oxide demethylase; trimethylamine-N-oxide formaldehyde-lyase
Systematic name: trimethylamine-N-oxide formaldehyde-lyase (dimethylamine-forming)
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, CAS registry number: 72561-08-1
References:
1. Large, P.J. Non-oxidative demethylation of trimethyl N-oxide by Pseudomonas aminovorans. FEBS Lett. 18 (1971) 297-300.
2. Myers, P.A. and Zatman, L.J. The metabolism of trimethylamine N-oxide by Bacillus PM6. Biochem. J. 121 (1971) 10P only. [PMID: 5116524]
Accepted name: fucosterol-epoxide lyase
Reaction: (24R,241R)-fucosterol epoxide = desmosterol + acetaldehyde
Glossary: (24R,241R)-fucosterol epoxide = (3β,24R,28R)-24,28-epoxystigmast-5-en-3-ol
Other name(s): (24R,24'R)-fucosterol-epoxide acetaldehyde-lyase; (24R,24'R)-fucosterol-epoxide acetaldehyde-lyase (desmosterol-forming)
Systematic name: (24R,241R)-fucosterol-epoxide acetaldehyde-lyase (desmosterol-forming)
Comments: The insect enzyme is involved in the conversion of sitosterol into cholesterol.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 99676-42-3
References:
1. Prestwich, G.D., Angelastro, M., De Palma, A. and Perino, M.A. Fucosterol epoxide lyase of insects: synthesis of labeled substrates and development of a partition assay. Anal. Biochem. 151 (1985) 315-326. [PMID: 3913328]
Accepted name: 4-(2-carboxyphenyl)-2-oxobut-3-enoate aldolase
Reaction: (3Z)-4-(2-carboxyphenyl)-2-oxobut-3-enoate + H2O = 2-formylbenzoate + pyruvate
For diagram of reaction click here.
Other name(s): 2'-carboxybenzalpyruvate aldolase; (3E)-4-(2-carboxyphenyl)-2-oxobut-3-enoate 2-carboxybenzaldehyde-lyase; (3Z)-4-(2-carboxyphenyl)-2-oxobut-3-enoate 2-carboxybenzaldehyde-lyase
Systematic name: (3Z)-4-(2-carboxyphenyl)-2-oxobut-3-enoate 2-formylbenzoate-lyase (pyruvate-forming)
Comments: Involved, with EC 1.13.11.38 (1-hydroxy-2-naphthoate 1,2-dioxygenase), in the metabolism of phenanthrene in bacteria.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, Metacyc, CAS registry number: 86611-90-7
References:
1. Barnsley, E.A. Phthalate pathway of phenanthrene metabolism: formation of 2'-carboxybenzalpyruvate. J. Bacteriol. 154 (1983) 113-117. [PMID: 6833175]
Accepted name: propioin synthase
Reaction: 2 propanal = 4-hydroxy-3-hexanone
Other name(s): 4-hydroxy-3-hexanone aldolase; 4-hydroxy-3-hexanone propanal-lyase
Systematic name: 4-hydroxy-3-hexanone propanal-lyase (propanal-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 114189-86-5
References:
1. Morimoto, S., Azuma, K., Oshima, T. and Sakamoto, M. Purification and properties of a new enzyme, propioin synthase in bakers' yeast which forms propioin from propionaldehyde. J. Ferment. Technol. 66 (1988) 7-12.
Accepted name: lactate aldolase
Reaction: (S)-lactate = formate + acetaldehyde
Other name(s): lactate synthase; (S)-lactate acetaldehyde-lyase
Systematic name: (S)-lactate acetaldehyde-lyase (formate-forming)
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 110777-33-8
References:
1. Gulyi, M.F. and Silonova, N.V. [Various metabolic reactions of formate in animal tissues.] Ukr. Biokhim. Zh. 59 (1987) 29-35. [PMID: 3629727] (in Russian)
[EC 4.1.2.37 Deleted entry: hydroxynitrilase. Now covered by EC 4.1.2.46 [aliphatic (R)-hydroxynitrile lyase] and EC 4.1.2.47 [(S)-hydroxynitrile ketone-lyase (cyanide forming)] (EC 4.1.2.37 created 1992 (EC 4.1.2.39 created 1999, incorporated 2007), deleted 2011)]
Accepted name: benzoin aldolase
Reaction: 2-hydroxy-1,2-diphenylethanone = 2 benzaldehyde
benzoin = 2-hydroxy-1,2-diphenylethanone
Glossary: thiamine diphosphate
Other name(s): benzaldehyde lyase; 2-hydroxy-1,2-diphenylethanone benzaldehyde-lyase
Systematic name: 2-hydroxy-1,2-diphenylethanone benzaldehyde-lyase (benzaldehyde-forming)
Comments: A thiamine-diphosphate protein.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 122097-01-2
References:
1. González, B. and Vicuña, R. Benzaldehyde lyase, a novel thiamine PPi-requiring enzyme, from Pseudomonas fluorescens biovar I. J. Bacteriol. 171 (1989) 2401-2405. [PMID: 2496105]
[EC 4.1.2.39 Deleted entry: hydroxynitrilase. The enzyme is identical to EC 4.1.2.37, hydroxynitrilase. (EC 4.1.2.39 created 1999, deleted 2007)]
Accepted name: tagatose-bisphosphate aldolase
Reaction: D-tagatose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate
Other name(s): D-tagatose-1,6-bisphosphate triosephosphate lyase
Systematic name: D-tagatose 1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase
Comments: enzyme activity is stimulated by certain divalent cations. It is involved in the tagatose 6-phosphate pathway of lactose catabolism in bacteria.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 39433-95-9
References:
1. Anderson, R.L., Markwell, J.P. D-Tagatose-1,6-bisphosphate aldolase (Class II) from Klebsiella pneumoniae. Methods Enzymol. 90 (1982) 232-234. [PMID: 6759854].
2. Van Rooijen, R.J., Van Schalkwijk, S., De Vos, W.M. Molecular cloning, characterization, and nucleotide sequence of the tagatose 6-phosphate pathway gene cluster of the lactose operon of Lactococcus lactis. J. Biol. Chem. 266 (1991) 7176-7181. [PMID: 1901863]
[EC 4.1.2.41 Transferred entry: vanillin synthase. Now included with EC 4.1.2.61, feruloyl-CoA hydratase/lyase (EC 4.1.2.41 created 2000, deleted 2020)]
Accepted name: D-threonine aldolase
Reaction: (1) D-threonine = glycine + acetaldehyde
(2) D-allo-threonine = glycine + acetaldehyde
Glossary: D-threonine = (2R,3S)-2-amino-3-hydroxybutanoic acid
D-allo-hreonine = (2R,3R)-2-amino-3-hydroxybutanoic acid
Other name(s): D-TA; DTA; low specificity D-TA; low specificity D-threonine aldolase
Systematic name: D-threonine acetaldehyde-lyase (glycine-forming)
Comments: A pyridoxal-phosphate protein that is activated by divalent metal cations (e.g. Co2+, Ni2+, Mn2+ or Mg2+) [1,2]. The reaction is reversible, which can lead to the interconversion of D-threonine and D-allo-threonine [1]. Several other D-β-hydroxy-α-amino acids, such as D-β-phenylserine, D-β-hydroxy-α-aminovaleric acid and D-β-3,4-dihydroxyphenylserine, can also act as substrate [1].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Kataoka, M., Ikemi, M., Morikawa, T., Miyoshi, T., Nishi, K., Wada, M., Yamada, H. and Shimizu, S. Isolation and characterization of D-threonine aldolase, a pyridoxal-5'-phosphate-dependent enzyme from Arthrobacter sp. DK-38. Eur. J. Biochem. 248 (1997) 385-393. [PMID: 9346293]
2. Liu, J.Q., Dairi, T., Itoh, N., Kataoka, M., Shimizu, S. and Yamada, H. A novel metal-activated pyridoxal enzyme with a unique primary structure, low specificity D-threonine aldolase from Arthrobacter sp. Strain DK-38. Molecular cloning and cofactor characterization. J. Biol. Chem. 273 (1998) 16678-16685. [PMID: 9642221]
3. Liu, J.Q., Odani, M., Dairi, T., Itoh, N., Shimizu, S. and Yamada, H. A new route to L-threo-3-[4-(methylthio)phenylserine], a key intermediate for the synthesis of antibiotics: recombinant low-specificity D-threonine aldolase-catalyzed stereospecific resolution. Appl. Microbiol. Biotechnol. 51 (1999) 586-591. [PMID: 10390816]
4. Liu, J.Q., Odani, M., Yasuoka, T., Dairi, T., Itoh, N., Kataoka, M., Shimizu, S. and Yamada, H. Gene cloning and overproduction of low-specificity D-threonine aldolase from Alcaligenes xylosoxidans and its application for production of a key intermediate for parkinsonism drug. Appl. Microbiol. Biotechnol. 54 (2000) 44-51. [PMID: 10952004]
5. Liu, J.Q., Dairi, T., Itoh, N., Kataoka, M., Shimizu, S. and Yamada, H. Diversity of microbial threonine aldolases and their application. J. Mol. Catal. B 10 (2000) 107-115.
6. Paiardini, A., Contestabile, R., D'Aguanno, S., Pascarella, S. and Bossa, F. Threonine aldolase and alanine racemase: novel examples of convergent evolution in the superfamily of vitamin B6-dependent enzymes. Biochim. Biophys. Acta 1647 (2003) 214-219. [PMID: 12686135]
Accepted name: 3-hexulose-6-phosphate synthase
Reaction: D-arabino-hex-3-ulose 6-phosphate = D-ribulose 5-phosphate + formaldehyde
For diagram of reaction, click here
Other name(s): D-arabino-3-hexulose 6-phosphate formaldehyde-lyase; 3-hexulosephosphate synthase; 3-hexulose phosphate synthase; HPS
Systematic name: D-arabino-3-hexulose-6-phosphate formaldehyde-lyase (D-ribulose-5-phosphate-forming)
Comments: Requires Mg2+ or Mn2+ for maximal activity [1]. The enzyme is specific for formaldehyde and D-ribulose 5-phosphate as substrates. Ribose 5-phosphate, xylulose 5-phosphate, allulose 6-phosphate and fructose 6-phosphate cannot act as substrate. This enzyme, along with EC 5.3.1.27, 6-phospho-3-hexuloisomerase, plays a key role in the ribulose-monophosphate cycle of formaldehyde fixation, which is present in many microorganisms that are capable of utilizing C1-compounds [1]. The hyperthermophilic and anaerobic archaeon Pyrococcus horikoshii OT3 constitutively produces a bifunctional enzyme that sequentially catalyses the reactions of this enzyme and EC 5.3.1.27, 6-phospho-3-hexuloisomerase [6]. This enzyme is a member of the orotidine 5'-monophosphate decarboxylase (OMPDC) suprafamily [5].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Ferenci, T., Strøm, T. and Quayle, J.R. Purification and properties of 3-hexulose phosphate synthase and phospho-3-hexuloisomerase from Methylococcus capsulatus. Biochem. J. 144 (1974) 477-486. [PMID: 4219834]
2. Kato, N., Ohashi, H., Tani, Y. and Ogata, K. 3-Hexulosephosphate synthase from Methylomonas aminofaciens 77a. Purification, properties and kinetics. Biochim. Biophys. Acta 523 (1978) 236-244. [PMID: 564713]
3. Yanase, H., Ikeyama, K., Mitsui, R., Ra, S., Kita, K., Sakai, Y. and Kato, N. Cloning and sequence analysis of the gene encoding 3-hexulose-6-phosphate synthase from the methylotrophic bacterium, Methylomonas aminofaciens 77a, and its expression in Escherichia coli. FEMS Microbiol. Lett. 135 (1996) 201-205. [PMID: 8595859]
4. Yurimoto, H., Kato, N. and Sakai, Y. Assimilation, dissimilation, and detoxification of formaldehyde, a central metabolic intermediate of methylotrophic metabolism. Chem. Rec. 5 (2005) 367-375. [PMID: 16278835]
5. Kato, N., Yurimoto, H. and Thauer, R.K. The physiological role of the ribulose monophosphate pathway in bacteria and archaea. Biosci. Biotechnol. Biochem. 70 (2006) 10-21. [PMID: 16428816]
6. Orita, I., Yurimoto, H., Hirai, R., Kawarabayasi, Y., Sakai, Y. and Kato, N. The archaeon Pyrococcus horikoshii possesses a bifunctional enzyme for formaldehyde fixation via the ribulose monophosphate pathway. J. Bacteriol. 187 (2005) 3636-3642. [PMID: 15901685]
7. Kato, N., Miyamoto, N., Shimao, M. and Sakazawa, C. 3-Hexulose phosphate pynthase from a new facultative methylotroph, Mycobacterium gastri MB19. Agric. Biol. Chem. 52 (1988) 265-2661.
Accepted name: 2,3-epoxybenzoyl-CoA dihydrolase
Reaction: 2,3-epoxy-2,3-dihydrobenzoyl-CoA + 2 H2O = 3,4-didehydroadipyl-CoA semialdehyde + formate
For diagram of reaction click here and mechanism click here.
Other name(s): 2,3-dihydro-2,3-dihydroxybenzoyl-CoA lyase/hydrolase (deformylating); BoxC; dihydrodiol transforming enzyme; benzoyl-CoA oxidation component C; 2,3-dihydro-2,3-dihydroxybenzoyl-CoA 3,4-didehydroadipyl-CoA semialdehyde-lyase (formate-forming); benzoyl-CoA-dihydrodiol lyase (incorrect); 2,3-dihydro-2,3-dihydroxybenzoyl-CoA 3,4-didehydroadipyl-CoA-semialdehyde-lyase (formate-forming)
Systematic name: 2,3-epoxy-2,3-dihydrobenzoyl-CoA 3,4-didehydroadipyl-CoA-semialdehyde-lyase (formate-forming)
Comments: The enzyme is involved in the aerobic benzoyl-CoA catabolic pathway of the bacterium Azoarcus evansii. The enzyme converts 2,3-epoxy-2,3-dihydroxybenzoyl-CoA to its oxepin form prior to the ring-opening and the formation of a dialdehyde intermediate.
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Gescher, J., Eisenreich, W., Worth, J., Bacher, A. and Fuchs, G. Aerobic benzoyl-CoA catabolic pathway in Azoarcus evansii: studies on the non-oxygenolytic ring cleavage enzyme. Mol. Microbiol. 56 (2005) 1586-1600. [PMID: 15916608]
2. Rather, L.J., Knapp, B., Haehnel, W. and Fuchs, G. Coenzyme A-dependent aerobic metabolism of benzoate via epoxide formation. J. Biol. Chem. 285 (2010) 20615-20624. [PMID: 20452977]
Accepted name: trans-o-hydroxybenzylidenepyruvate hydratase-aldolase
Reaction: (3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate + H2O = salicylaldehyde + pyruvate
For diagram of reaction, click here
Glossary: (3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate = (E)-2'-hydroxybenzylidenepyruvate
salicylaldehyde = 2-hydroxybenzaldehyde
Other name(s): 2'-hydroxybenzalpyruvate aldolase; NsaE; tHBPA hydratase-aldolase
Systematic name: (3E)-4-(2-hydroxyphenyl)-2-oxobut-3-enoate hydro-lyase
Comments: This enzyme is involved in naphthalene degradation. The enzyme catalyses a retro-aldol reaction in vitro, and it accepts a broad range of aldehydes and 4-substituted 2-oxobut-3-enoates as substrates [4].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Kuhm, A.E., Knackmuss, H.J. and Stolz, A. Purification and properties of 2'-hydroxybenzalpyruvate aldolase from a bacterium that degrades naphthalenesulfonates. J. Biol. Chem. 268 (1993) 9484-9489. [PMID: 8486638]
2. Keck, A., Conradt, D., Mahler, A., Stolz, A., Mattes, R. and Klein, J. Identification and functional analysis of the genes for naphthalenesulfonate catabolism by Sphingomonas xenophaga BN6. Microbiology 152 (2006) 1929-1940. [PMID: 16804169]
3. Eaton, R.W. Organization and evolution of naphthalene catabolic pathways: sequence of the DNA encoding 2-hydroxychromene-2-carboxylate isomerase and trans-o-hydroxybenzylidenepyruvate hydratase-aldolase from the NAH7 plasmid. J. Bacteriol. 176 (1994) 7757-7762. [PMID: 8002605]
4. Eaton, R.W. trans-o-Hydroxybenzylidenepyruvate hydratase-aldolase as a biocatalyst. Appl. Environ. Microbiol. 66 (2000) 2668-2672. [PMID: 10831455]
Accepted name: aliphatic (R)-hydroxynitrile lyase
Reaction: (2R)-2-hydroxy-2-methylbutanenitrile = cyanide + butan-2-one
Other name(s): (R)-HNL; (R)-oxynitrilase; (R)-hydroxynitrile lyase; LuHNL
Systematic name: (2R)-2-hydroxy-2-methylbutanenitrile butan-2-one-lyase (cyanide forming)
Comments: The enzyme contains Zn2+ [1]. The enzyme catalyses the stereoselective synthesis of aliphatic (R)-cyanohydrins [1]. No activity towards mandelonitrile and 4-hydroxymandelonitrile [5]. Natural substrates for the (R)-oxynitrilase from Linum usitatissimum are acetone and butan-2-one, which are the building blocks of the cyanogen glycosides in Linum, linamarin and lotaustralin, or linustatin and neolinustatin, respectively [4].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Trummler, K., Roos, J., Schwaneberg, U., Effenberger, F., Frster, S., Pfizenmaier, K., Wajant, H. Expression of the Zn2+-containing hydroxynitrile lyase from flax (Linum usitatissimum) in Pichia pastoris - utilization of the recombinant enzyme for enzymatic analysis and site-directed mutagenesis. Plant Sci. 139 (1998) 19-27.
2. Trummler, K. and Wajant, H. Molecular cloning of acetone cyanohydrin lyase from flax (Linum usitatissimum). Definition of a novel class of hydroxynitrile lyases. J. Biol. Chem. 272 (1997) 4770-4774. [PMID: 9030531]
3. Albrecht, J., Jansen, I.and Kula, M.R. Improved purification of an (R)-oxynitrilase from Linum usitatissimum (flax) and investigation of the substrate range. Biotechnol. Appl. Biochem. 17 (1993) 191-203.
4. Xu, L.-L., Singh, B.K. and Conn, E.E. Purification and characterization of acetone cyanohydrin lyase from Linum usitatissimum. Arch. Biochem. Biophys. 263 (1988) 256-263. [PMID: 3377504]
5. Cabirol, F.L., Tan, P.L., Tay, B., Cheng, S., Hanefeld, U. and Sheldon, R.A. Linum usitatissimum hydroxynitrile lyase cross-linked enzyme aggregates: a recyclable enantioselective catalyst. Adv. Synth. Catal. 350 (2008) 2329-2338.
6. Breithaupt, H., Pohl, M., Bnigk, W., Heim, P., Schimz, K.-L. and Kula, M.-R. Cloning and expression of (R)-hydroxynitrile lyase from Linum usitatissimum (flax). J. Mol. Catal. B 6 (1999) 315-332.
Accepted name: (S)-hydroxynitrile lyase
Reaction: (1) an aliphatic (S)-hydroxynitrile = cyanide + an aliphatic aldehyde or ketone
(2) an aromatic (S)-hydroxynitrile = cyanide + an aromatic aldehyde
Other name(s): (S)-cyanohydrin producing hydroxynitrile lyase; (S)-oxynitrilase; (S)-HbHNL; (S)-MeHNL; hydroxynitrile lyase; oxynitrilase; HbHNL; MeHNL; (S)-selective hydroxynitrile lyase; (S)-cyanohydrin carbonyl-lyase (cyanide forming)
Systematic name: (S)-cyanohydrin lyase (cyanide forming)
Comments: Hydroxynitrile lyases catalyses the the cleavage of hydroxynitriles into cyanide and the corresponding aldehyde or ketone. In nature the liberation of cyanide serves as a defense mechanism against herbivores and microbial attack in plants. In vitro the enzymes from Manihot esculenta and Hevea brasiliensis accept a broad range of aliphatic and aromatic carbonyl compounds as substrates and catalyse the formation of (S)-hydroxynitriles [1,10].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Förster, S., Roos, J., Effenberger, F., Wajant, H. and Sprauer, A. The first recombinant hydroxynitrile lyase and its application in the synthesis of (S)-cyanohydrins. Angew. Chem. Int. Ed. 35 (1996) 437-439.
2. Bühler, H., Effenberger, F., Förster, S., Roos, J. and Wajant, H. Substrate specificity of mutants of the hydroxynitrile lyase from Manihot esculenta. Chembiochem. 4 (2003) 211-216. [PMID: 12616635]
3. Semba, H., Dobashi, Y. and Matsui, T. Expression of hydroxynitrile lyase from Manihot esculenta in yeast and its application in (S)-mandelonitrile production using an immobilized enzyme reactor. Biosci. Biotechnol. Biochem. 72 (2008) 1457-1463. [PMID: 18540112]
4. Avi, M., Wiedner, R.M., Griengl, H. and Schwab, H. Improvement of a stereoselective biocatalytic synthesis by substrate and enzyme engineering: 2-hydroxy-(4'-oxocyclohexyl)acetonitrile as the model. Chemistry 14 (2008) 11415-11422. [PMID: 19006143]
5. von Langermann, J., Guterl, J.K., Pohl, M., Wajant, H. and Kragl, U. Hydroxynitrile lyase catalyzed cyanohydrin synthesis at high pH-values. Bioprocess Biosyst Eng 31 (2008) 155-161. [PMID: 18204865]
6. Schmidt, A., Gruber, K., Kratky, C. and Lamzin, V.S. Atomic resolution crystal structures and quantum chemistry meet to reveal subtleties of hydroxynitrile lyase catalysis. J. Biol. Chem. 283 (2008) 21827-21836. [PMID: 18524775]
7. Gartler, G., Kratky, C. and Gruber, K. Structural determinants of the enantioselectivity of the hydroxynitrile lyase from Hevea brasiliensis. J. Biotechnol. 129 (2007) 87-97. [PMID: 17250917]
8. Wagner, U.G., Schall, M., Hasslacher, M., Hayn, M., Griengl, H., Schwab, H. and Kratky, C. Crystallization and preliminary X-ray diffraction studies of a hydroxynitrile lyase from Hevea brasiliensis. Acta Crystallogr. D Biol. Crystallogr. 52 (1996) 591-593. [PMID: 15299689]
9. Schmidt, M., Herve, S., Klempier, N. and Griengl, H. Preparation of optically active cyanohydrins using the (S)-hydroxynitrile lyase from Hevea brasiliensis. Tetrahedron 52 (1996) 7833-7840.
10. Klempier, N. and Griengl, H. Aliphatic (S)-cyanohydrins by enzyme catalyzed synthesis. Tetrahedron Lett. 34 (1993) 4769-4772.
Accepted name: low-specificity L-threonine aldolase
Reaction: (1) L-threonine = glycine + acetaldehyde
(2) L-allo-threonine = glycine + acetaldehyde
Other name(s): LtaE
Systematic name: L-threonine/L-allo-threonine acetaldehyde-lyase (glycine-forming)
Comments: Requires pyridoxal phosphate. The low-specificity L-threonine aldolase can act on both L-threonine and L-allo-threonine [1,2]. The enzyme from Escherichia coli can also act on L-threo-phenylserine and L-erythro-phenylserine [4]. The enzyme can also catalyse the aldol condensation of glycolaldehyde and glycine to form 4-hydroxy-L-threonine, an intermediate of pyridoxal phosphate biosynthesis [3]. Different from EC 4.1.2.5, L-threonine aldolase, and EC 4.1.2.49, L-allo-threonine aldolase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Yamada, H., Kumagai, H., Nagate, T. and Yoshida, H. Crystalline threonine aldolase from Candida humicola. Biochem. Biophys. Res. Commun. 39 (1970) 53-58. [PMID: 5438301]
2. Kumagai, H., Nagate, T., Yoshida, H. and Yamada, H. Threonine aldolase from Candida humicola. II. Purification, crystallization and properties. Biochim. Biophys. Acta 258 (1972) 779-790. [PMID: 5017702]
3. Liu, J.Q., Nagata, S., Dairi, T., Misono, H., Shimizu, S. and Yamada, H. The GLY1 gene of Saccharomyces cerevisiae encodes a low-specific L-threonine aldolase that catalyzes cleavage of L-allo-threonine and L-threonine to glycine—expression of the gene in Escherichia coli and purification and characterization of the enzyme. Eur. J. Biochem. 245 (1997) 289-293. [PMID: 9151955]
4. Liu, J.Q., Dairi, T., Itoh, N., Kataoka, M., Shimizu, S. and Yamada, H. Gene cloning, biochemical characterization and physiological role of a thermostable low-specificity L-threonine aldolase from Escherichia coli. Eur. J. Biochem. 255 (1998) 220-226. [PMID: 9692922]
5. Kim, J., Kershner, J.P., Novikov, Y., Shoemaker, R.K. and Copley, S.D. Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5'-phosphate synthesis. Mol. Syst. Biol. 6 (2010) 436. [PMID: 21119630]
Accepted name: L-allo-threonine aldolase
Reaction: L-allo-threonine = glycine + acetaldehyde
Systematic name: L-allo-threonine acetaldehyde-lyase (glycine-forming)
Comments: Requires pyridoxal phosphate. This enzyme, characterized from the bacterium Aeromonas jandaei, is specific for L-allo-threonine and can not act on either L-threonine or L-serine. Different from EC 4.1.2.5, L-threonine aldolase, and EC 4.1.2.48, low-specificity L-threonine aldolase. A previously listed enzyme with this name, EC 4.1.2.6, was deleted in 1971 after it was found to be identical to EC 2.1.2.1, glycine hydroxymethyltransferase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Kataoka, M., Wada, M., Nishi, K., Yamada, H. and Shimizu, S. Purification and characterization of L-allo-threonine aldolase from Aeromonas jandaei DK-39. FEMS Microbiol. Lett. 151 (1997) 245-248. [PMID: 9228760]
Accepted name: 6-carboxytetrahydropterin synthase
Reaction: 7,8-dihydroneopterin 3'-triphosphate + H2O = 6-carboxy-5,6,7,8-tetrahydropterin + acetaldehyde + triphosphate
For diagram of reaction click here.
Glossary: 7,8-dihydroneopterin 3'-triphosphate = 2-amino-6-[(1S,2R)-1,2-dihydroxy-3-triphosphooxypropyl]-4-oxo-2,3,7,8-tetrahydropteridine
6-carboxy-5,6,7,8-tetrahydropterin = 2-amino-4-oxo-2,3,5,6,7,8-hexahydropteridine-6-carboxylate
Other name(s): CPH4 synthase; queD (gene name)
Systematic name: 7,8-dihydroneopterin 3'-triphosphate acetaldehyde-lyase (6-carboxy-5,6,7,8-tetrahydropterin and triphosphate-forming)
Comments: Binds Zn2+. Isolated from the bacteria Bacillus subtilis and Escherichia coli. The reaction is part of the biosynthesis pathway of queuosine.The enzyme from Escherichia coli can also convert 6-pyruvoyl-5,6,7,8-tetrahydropterin and sepiapterin to 6-carboxy-5,6,7,8-tetrahydropterin [2].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Cicmil, N. and Shi, L. Crystallization and preliminary X-ray characterization of queD from Bacillus subtilis, an enzyme involved in queuosine biosynthesis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 64 (2008) 119-122. [PMID: 18259064]
2. McCarty, R.M., Somogyi, A. and Bandarian, V. Escherichia coli QueD is a 6-carboxy-5,6,7,8-tetrahydropterin synthase. Biochemistry 48 (2009) 2301-2303. [PMID: 19231875]
Accepted name: 2-dehydro-3-deoxy-D-gluconate aldolase
Reaction: 2-dehydro-3-deoxy-D-gluconate = pyruvate + D-glyceraldehyde
For diagram of reaction click here.
Other name(s): Pto1279 (gene name); KDGA; KDG-specific aldolase
Systematic name: 2-dehydro-3-deoxy-D-gluconate D-glyceraldehyde-lyase (pyruvate-forming)
Comments: The enzyme from the archaeon Picrophilus torridus is involved in D-glucose and D-galactose catabolism via the nonphosphorylative variant of the Entner-Doudoroff pathway. In the direction of aldol synthesis the enzyme catalyses the formation of 2-dehydro-3-deoxy-D-gluconate and 2-dehydro-3-deoxy-D-galactonate at a similar ratio. It shows no activity with 2-dehydro-3-deoxy-D-gluconate 6-phosphate. cf. EC 4.1.2.14, 2-dehydro-3-deoxy-phosphogluconate aldolase.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Reher, M., Fuhrer, T., Bott, M. and Schonheit, P. The nonphosphorylative Entner-Doudoroff pathway in the thermoacidophilic euryarchaeon Picrophilus torridus involves a novel 2-keto-3-deoxygluconate- specific aldolase. J. Bacteriol. 192 (2010) 964-974. [PMID: 20023024]
Accepted name: 4-hydroxy-2-oxoheptanedioate aldolase
Reaction: 4-hydroxy-2-oxoheptanedioate = pyruvate + succinate semialdehyde
Other name(s): 2,4-dihydroxyhept-2-enedioate aldolase; HHED aldolase; 4-hydroxy-2-ketoheptanedioate aldolase; HKHD aldolase; HpcH; HpaI; 4-hydroxy-2-oxoheptanedioate succinate semialdehyde lyase (pyruvate-forming)
Systematic name: 4-hydroxy-2-oxoheptanedioate succinate-semialdehyde-lyase (pyruvate-forming)
Comments: Requires Co2+ or Mn2+ for activity. The enzyme is also able to catalyse the aldol cleavage of 4-hydroxy-2-oxopentanoate and 4-hydroxy-2-oxohexanoate, and can use 2-oxobutanoate as carbonyl donor, with lower efficiency. In the reverse direction, is able to condense a range of aldehyde acceptors with pyruvate. The enzyme from the bacterium Escherichia coli produces a racemic mixture of (4R)- and (4S)-hydroxy-2-oxoheptanedioate [4].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Wang, W. and Seah, S.Y. Purification and biochemical characterization of a pyruvate-specific class II aldolase, HpaI. Biochemistry 44 (2005) 9447-9455. [PMID: 15996099]
2. Rea, D., Fulop, V., Bugg, T.D. and Roper, D.I. Structure and mechanism of HpcH: a metal ion dependent class II aldolase from the homoprotocatechuate degradation pathway of Escherichia coli. J. Mol. Biol. 373 (2007) 866-876. [PMID: 17881002]
3. Wang, W. and Seah, S.Y. The role of a conserved histidine residue in a pyruvate-specific class II aldolase. FEBS Lett 582 (2008) 3385-3388. [PMID: 18775708]
4. Wang, W., Baker, P. and Seah, S.Y.K. Comparison of two metal-dependent pyruvate aldolases related by convergent evolution: substrate specificity, kinetic mechanism, and substrate channeling. Biochemistry 49 (2010) 3774-3782. [PMID: 20364820]
Accepted name: 2-keto-3-deoxy-L-rhamnonate aldolase
Reaction: 2-dehydro-3-deoxy-L-rhamnonate = pyruvate + (S)-lactaldehyde
For diagram of reaction click here or click here
Glossary: 2-dehydro-3-deoxy-L-rhamnonate = 3,6-dideoxy-L-erythro-hex-2-ulosonate
Other name(s): KDR aldolase; 2-dehydro-3-deoxyrhamnonate aldolase; 2-keto-3-deoxy acid sugar aldolase; YfaU; 2-dehydro-3-deoxy-L-rhamnonate (S)-lactaldehyde lyase (pyruvate-forming); 2-dehydro-3-deoxy-L-rhamnonate (R)-lactaldehyde lyase (pyruvate-forming)
Systematic name: 2-dehydro-3-deoxy-L-rhamnonate (S)-lactaldehyde-lyase (pyruvate-forming)
Comments: Requires Mg2+ for activity. The enzyme can also use 2-oxo-3-deoxy-L-mannonate, 2-oxo-3-deoxy-L-lyxonate and 4-hydroxy-2-ketoheptane-1,7-dioate (HKHD) as substrates [2].
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Rakus, J.F., Fedorov, A.A., Fedorov, E.V., Glasner, M.E., Hubbard, B.K., Delli, J.D., Babbitt, P.C., Almo, S.C. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase. Biochemistry 47 (2008) 9944-9954. [PMID: 18754693]
2. Rea, D., Hovington, R., Rakus, J.F., Gerlt, J.A., Fulop, V., Bugg, T.D. and Roper, D.I. Crystal structure and functional assignment of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12. Biochemistry 47 (2008) 9955-9965. [PMID: 18754683]
Accepted name: L-threo-3-deoxy-hexylosonate aldolase
Reaction: 2-dehydro-3-deoxy-L-galactonate = pyruvate + L-glyceraldehyde
Other name(s): GAAC; LGA1
Systematic name: 2-dehydro-3-deoxy-L-galactonate L-glyceraldehyde-lyase (pyruvate-forming)
Comments: The enzyme takes part in a D-galacturonate degradation pathway in the fungi Aspergillus niger and Trichoderma reesei (Hypocrea jecorina).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Hilditch, S., Berghall, S., Kalkkinen, N., Penttila, M. and Richard, P. The missing link in the fungal D-galacturonate pathway: identification of the L-threo-3-deoxy-hexulosonate aldolase. J. Biol. Chem. 282 (2007) 26195-26201. [PMID: 17609199]
2. Martens-Uzunova, E.S. and Schaap, P.J. An evolutionary conserved D-galacturonic acid metabolic pathway operates across filamentous fungi capable of pectin degradation. Fungal Genet. Biol. 45 (2008) 1449-1457. [PMID: 18768163]
Accepted name: 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase
Reaction: (1) 2-dehydro-3-deoxy-6-phospho-D-gluconate = pyruvate + D-glyceraldehyde 3-phosphate
(2) 2-dehydro-3-deoxy-6-phospho-D-galactonate = pyruvate + D-glyceraldehyde 3-phosphate
For diagram of reaction click here.
Other name(s): 2-keto-3-deoxygluconate aldolase (ambiguous); KDGA (ambiguous)
Systematic name: 2-dehydro-3-deoxy-6-phosphate-D-gluconate/2-dehydro-3-deoxy-6-phosphate-D-galactonate D-glyceraldehyde-3-phosphate-lyase (pyruvate-forming)
Comments: In the archaeon Sulfolobus solfataricus the enzyme is involved in glucose and galactose catabolism via the branched variant of the Entner-Doudoroff pathway. It utilizes 2-dehydro-3-deoxy-6-phosphate-D-gluconate and 2-dehydro-3-deoxy-6-phosphate-D-galactonate with similar catalytic efficiency. In vitro the enzyme can also catalyse the cleavage of the non-phosphorylated forms 2-dehydro-3-deoxy-D-gluconate and 2-dehydro-3-deoxy-D-galactonate with much lower catalytic efficiency. cf. EC 4.1.2.21, 2-dehydro-3-deoxy-6-phosphogalactonate aldolase, and EC 4.1.2.14, 2-dehydro-3-deoxy-phosphogluconate aldolase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Buchanan, C.L., Connaris, H., Danson, M.J., Reeve, C.D. and Hough, D.W. An extremely thermostable aldolase from Sulfolobus solfataricus with specificity for non-phosphorylated substrates. Biochem. J. 343 (1999) 563-570. [PMID: 10527934]
2. Lamble, H.J., Theodossis, A., Milburn, C.C., Taylor, G.L., Bull, S.D., Hough, D.W. and Danson, M.J. Promiscuity in the part-phosphorylative Entner-Doudoroff pathway of the archaeon Sulfolobus solfataricus. FEBS Lett 579 (2005) 6865-6869. [PMID: 16330030]
3. Wolterink-van Loo, S., van Eerde, A., Siemerink, M.A., Akerboom, J., Dijkstra, B.W. and van der Oost, J. Biochemical and structural exploration of the catalytic capacity of Sulfolobus KDG aldolases. Biochem. J. 403 (2007) 421-430. [PMID: 17176250]
Accepted name: 2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate synthase
Reaction: 2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate = glycerone phosphate + L-aspartate 4-semialdehyde
For diagram of reaction click here and mechanism click here.
Other name(s): griI (gene name)
Systematic name: 2-amino-4,5-dihydroxy-6-oxo-7-(phosphooxy)heptanoate L-aspartate 4-semialdehyde-lyase (glycerone phosphate-forming)
Comments: Part of the pathway for the biosynthesis of grixazone, a mixture of yellow pigments produced by the bacterium Streptomyces griseus.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Suzuki, H., Ohnishi, Y., Furusho, Y., Sakuda, S. and Horinouchi, S. Novel benzene ring biosynthesis from C3 and C4 primary metabolites by two enzymes. J. Biol. Chem. 281 (2006) 36944-36951. [PMID: 17003031]
Accepted name: sulfofructosephosphate aldolase
Reaction: 6-deoxy-6-sulfo-D-fructose 1-phosphate = glycerone phosphate + (2S)-3-sulfolactaldehyde
For diagram of reaction click here.
Glossary: glycerone phosphate = dihydroxyacetone phosphate = 3-hydroxy-2-oxopropyl phosphate
(2S)-3-sulfolactaldehyde = (2S)-2-hydroxy-3-oxopropane-1-sulfonate
Other name(s): yihT (gene name)
Systematic name: 6-deoxy-6-sulfofructose-1-phosphate 2-hydroxy-3-oxopropane-1-sulfonate-lyase (glycerone-phosphate-forming)
Comments: The enzyme, characterized from the bacterium Escherichia coli, is involved in the degradation pathway of sulfoquinovose, the polar headgroup of sulfolipids found in the photosynthetic membranes of all higher plants, mosses, ferns, algae, and most photosynthetic bacteria, as well as the surface layer of some archaea.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Denger, K., Weiss, M., Felux, A.K., Schneider, A., Mayer, C., Spiteller, D., Huhn, T., Cook, A.M. and Schleheck, D. Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle. Nature 507 (2014) 114-117. [PMID: 24463506]
Accepted name: 2-dehydro-3,6-dideoxy-6-sulfogluconate aldolase
Reaction: 2-dehydro-3,6-dideoxy-6-sulfo-D-gluconate = (2S)-3-sulfolactaldehyde + pyruvate
For diagram of reaction click here.
Glossary: (2S)-3-sulfolactaldehyde = (2S)-2-hydroxy-3-oxopropane-1-sulfonate
Other name(s): KDSG aldolase
Systematic name: 2-dehydro-3,6-dideoxy-6-sulfo-D-gluconate-lyase (pyruvate-forming)
Comments: The enzyme, characterized from the bacterium Pseudomonas putida SQ1, participates in a sulfoquinovose degradation pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Felux, A.K., Spiteller, D., Klebensberger, J. and Schleheck, D. Entner-Doudoroff pathway for sulfoquinovose degradation in Pseudomonas putida SQ1. Proc. Natl. Acad. Sci. USA 112 (2015) E4298-E4305. [PMID: 26195800]
Accepted name: dihydroneopterin phosphate aldolase
Reaction: 7,8-dihydroneopterin 3'-phosphate = 6-(hydroxymethyl)-7,8-dihydropterin + glycolaldehyde phosphate
Other name(s): H2NMP aldolase
Systematic name: 7,8-dihydroneopterin 3'-phosphate glycolaldehyde phosphate-lyase [6-(hydroxymethyl)-7,8-dihydropterin-forming]
Comments: The enzyme participates in methanopterin biosynthesis the archaeon Pyrococcus furiosus. The enzyme is specific for 7,8-dihydroneopterin 3'-phosphate. cf. EC 4.1.2.25, dihydroneopterin aldolase and EC 4.1.2.60, dihydroneopterin triphosphate aldolase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. de Crecy-Lagard, V., Phillips, G., Grochowski, L.L., El Yacoubi, B., Jenney, F., Adams, M.W., Murzin, A.G. and White, R.H. Comparative genomics guided discovery of two missing archaeal enzyme families involved in the biosynthesis of the pterin moiety of tetrahydromethanopterin and tetrahydrofolate. ACS Chem. Biol. 7 (2012) 1807-1816. [PMID: 22931285]
Accepted name: dihydroneopterin triphosphate aldolase
Reaction: 7,8-dihydroneopterin 3'-triphosphate = 6-(hydroxymethyl)-7,8-dihydropterin + glycolaldehyde triphosphate
Other name(s): PTPS-III
Systematic name: 7,8-dihydroneopterin 3'-triphosphate glycolaldehyde phosphate-lyase [6-(hydroxymethyl)-7,8-dihydropterin-forming]
Comments: The enzyme, which participates in a pathway for folate biosynthesis, is found in the Stramenopiles, a large group that includes oomycetes, various microalgae and brown algae, as well as in several bacterial phyla. It provides a bypass mechanism compensating for the lack of EC 4.1.2.25, dihydroneopterin aldolase. In the malaria parasite Plasmodium falciparum the enzyme is bifunctional and also catalyses the activity of EC 4.2.3.12, 6-pyruvoyltetrahydropterin synthase. cf. EC 4.1.2.59, dihydroneopterin phosphate aldolase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
References:
1. Dittrich, S., Mitchell, S.L., Blagborough, A.M., Wang, Q., Wang, P., Sims, P.F. and Hyde, J.E. An atypical orthologue of 6-pyruvoyltetrahydropterin synthase can provide the missing link in the folate biosynthesis pathway of malaria parasites. Mol. Microbiol. 67 (2008) 609-618. [PMID: 18093090]
2. Hyde, J.E., Dittrich, S., Wang, P., Sims, P.F., de Crecy-Lagard, V. and Hanson, A.D. Plasmodium falciparum: a paradigm for alternative folate biosynthesis in diverse microorganisms. Trends Parasitol. 24 (2008) 502-508. [PMID: 18805734]
3. Pribat, A., Jeanguenin, L., Lara-Nunez, A., Ziemak, M.J., Hyde, J.E., de Crecy-Lagard, V. and Hanson, A.D. 6-Pyruvoyltetrahydropterin synthase paralogs replace the folate synthesis enzyme dihydroneopterin aldolase in diverse bacteria. J. Bacteriol. 191 (2009) 4158-4165. [PMID: 19395485]
Accepted name: feruloyl-CoA hydratase/lyase
Reaction: feruloyl-CoA + H2O = vanillin + acetyl-CoA (overall reaction)
(1a) feruloyl-CoA + H2O = 3-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propanoyl-CoA
(1b) 3-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propanoyl-CoA = vanillin + acetyl-CoA
For diagram of reaction click here
Other name(s): hydroxycinnamoyl-CoA hydratase lyase; enoyl-CoA hydratase/aldolase; HCHL; ferB (gene name); couA (gene name)
Systematic name: feruloyl-CoA hydro-lyase/vanillin-lyase (acetyl-CoA-forming)
Comments: The enzyme is a member of the enoyl-CoA hydratase/isomerase superfamily. It catalyses a two-step process involving first the hydration of the double bond of feruloyl-CoA and then the cleavage of the resultant β-hydroxy thioester by retro-aldol reaction. (E)-caffeoyl-CoA and (E)-4-coumaroyl-CoA are also substrates.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Pometto, A.L. and Crawford, D.L. Whole-cell bioconversion of vanillin to vanillic acid by Streptomyces viridosporus. Appl. Environ. Microbiol. 45 (1983) 1582-1585. [PMID: 6870241]
2. Narbad, A. and Gasson, M.J. Metabolism of ferulic acid via vanillin using a novel CoA-dependent pathway in a newly-isolated strain of Pseudomonas fluorescens. Microbiology 144 (1998) 1397-1405. [PMID: 9611814]
3. Gasson, M.J., Kitamura, Y., McLauchlan, W.R., Narbad, A., Parr, A.J., Parsons, E.L., Payne, J., Rhodes, M.J. and Walton, N.J. Metabolism of ferulic acid to vanillin. A bacterial gene of the enoyl-SCoA hydratase/isomerase superfamily encodes an enzyme for the hydration and cleavage of a hydroxycinnamic acid SCoA thioester. J. Biol. Chem. 273 (1998) 4163-4170. [PMID: 9461612]
4. Overhage, J., Priefert, H. and Steinbuchel, A. Biochemical and genetic analyses of ferulic acid catabolism in Pseudomonas sp. Strain HR199. Appl. Environ. Microbiol. 65 (1999) 4837-4847. [PMID: 10543794]
5. Bennett, J.P., Bertin, L., Moulton, B., Fairlamb, I.J., Brzozowski, A.M., Walton, N.J. and Grogan, G. A ternary complex of hydroxycinnamoyl-CoA hydratase-lyase (HCHL) with acetyl-CoA and vanillin gives insights into substrate specificity and mechanism. Biochem. J. 414 (2008) 281-289. [PMID: 18479250]
6. Hirakawa, H., Schaefer, A.L., Greenberg, E.P. and Harwood, C.S. Anaerobic p-coumarate degradation by Rhodopseudomonas palustris and identification of CouR, a MarR repressor protein that binds p-coumaroyl coenzyme A. J. Bacteriol. 194 (2012) 1960-1967. [PMID: 22328668]
7. Yang, W., Tang, H., Ni, J., Wu, Q., Hua, D., Tao, F. and Xu, P. Characterization of two Streptomyces enzymes that convert ferulic acid to vanillin. PLoS One 8 (2013) e67339. [PMID: 23840666]
Accepted name: 5-deoxyribulose 1-phosphate aldolase
Reaction: (1) 5-deoxy-D-ribulose 1-phosphate = glycerone phosphate + acetaldehyde
(2) S-methyl-5-thio-D-ribulose 1-phosphate = glycerone phosphate + (2-methylsulfanyl)acetaldehyde
Other name(s): 5-(methylthio)ribulose-1-phosphate aldolase; ald2 (gene name)
Systematic name: 5-deoxy-D-ribulose 1-phosphate acetaldehyde-lyase (glycerone-phosphate-forming)
Comments: The enzyme, originally characterized from the bacterium Rhodospirillum rubrum, is involved in degradation pathways for 5'-deoxyadenosine and S-methyl-5'-thioadenosine, which are formed from S-adenosyl-L-methionine (SAM, AdoMet) by radical SAM enzymes and other types of SAM-dependent enzymes, respectively. The enzyme requires a divalent metal cation, with Co2+ producing the highest activity.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. North, J.A., Miller, A.R., Wildenthal, J.A., Young, S.J. and Tabita, F.R. Microbial pathway for anaerobic 5'-methylthioadenosine metabolism coupled to ethylene formation. Proc. Natl. Acad. Sci. USA 114 (2017) E10455-E10464. [PMID: 29133429]
2. North, J.A., Wildenthal, J.A., Erb, T.J., Evans, B.S., Byerly, K.M., Gerlt, J.A. and Tabita, F.R. A bifunctional salvage pathway for two distinct S-adenosylmethionine by-products that is widespread in bacteria, including pathogenic Escherichia coli. Mol. Microbiol. (2020) . [PMID: 31950558]
Accepted name: 2-hydroxyacyl-CoA lyase
Reaction: (1) a 2-hydroxy-3-methyl-Cn-fatty-acyl-CoA = a 2-methyl-branched Cn-1-fatty aldehyde + formyl-CoA
(2) a (2R)-2-hydroxy-Cn-long-chain fatty acyl-CoA = a Cn-1-long-chain fatty aldehyde + formyl-CoA
Other name(s): HACL1 (gene name); 2-hydroxyphytanoyl-CoA lyase; 2-HPCL
Systematic name: 2-hydroxy-3-methyl fatty-CoA formyl-CoA lyase (2-methyl branched fatty aldehyde-forming)
Comments: Requires Mg2+ and thiamine diphosphate. This peroxisomal enzyme, found in animals, is involved in the α-oxidation of 3-methyl-branched fatty acids like phytanic acid and the shortening of 2-hydroxy long-chain fatty acids.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Foulon, V., Antonenkov, V.D., Croes, K., Waelkens, E., Mannaerts, G.P., Van Veldhoven, P.P. and Casteels, M. Purification, molecular cloning, and expression of 2-hydroxyphytanoyl-CoA lyase, a peroxisomal thiamine pyrophosphate-dependent enzyme that catalyzes the carbon-carbon bond cleavage during α-oxidation of 3-methyl-branched fatty acids. Proc. Natl. Acad. Sci. USA 96 (1999) 10039-10044. [PMID: 10468558]
2. Foulon, V., Sniekers, M., Huysmans, E., Asselberghs, S., Mahieu, V., Mannaerts, G.P., Van Veldhoven, P.P. and Casteels, M. Breakdown of 2-hydroxylated straight chain fatty acids via peroxisomal 2-hydroxyphytanoyl-CoA lyase: a revised pathway for the α-oxidation of straight chain fatty acids. J. Biol. Chem. 280 (2005) 9802-9812. [PMID: 15644336]
3. Casteels, M., Sniekers, M., Fraccascia, P., Mannaerts, G.P. and Van Veldhoven, P.P. The role of 2-hydroxyacyl-CoA lyase, a thiamin pyrophosphate-dependent enzyme, in the peroxisomal metabolism of 3-methyl-branched fatty acids and 2-hydroxy straight-chain fatty acids. Biochem Soc Trans. 35 (2007) 876-880. [PMID: 17956236]
Accepted name: 2-dehydro-3-deoxy-L-fuconate aldolase
Reaction: 2-dehydro-3-deoxy-L-fuconate = pyruvate + (S)-lactaldehyde
Other name(s): 2-keto-3-deoxy-L-fuconate aldolase; L-2-keto-3-deoxyfuconate aldolase; fucH (gene name)
Systematic name: 2-dehydro-3-deoxy-L-fuconate (S)-lactaldehyde-lyase (pyruvate-forming)
Comments: The enzyme, characterized from the bacteria Veillonella ratti and Campylobacter jejuni, participates in an L-fucose degradation pathway. It also has significant activity with 2-dehydro-3-deoxy-D-pentonate (cf. EC 4.1.2.28, 2-dehydro-3-deoxy-D-pentonate aldolase).
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Watanabe, S. Characterization of L-2-keto-3-deoxyfuconate aldolases in a nonphosphorylating L-fucose metabolism pathway in anaerobic bacteria. J. Biol. Chem. 295 (2020) 1338-1349. [PMID: 31914410]
Accepted name: ferulate hydratase/lyase
Reaction: ferulate + H2O = vanillin + acetate (overall reaction)
(1a) ferulate + H2O = 3-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propanoate
(1b) 3-hydroxy-3-(4-hydroxy-3-methoxyphenyl)propanoate = vanillin + acetate
For diagram of reaction click here
Glossary: ferulate = 4-hydroxy-3-methoxycinnamate
vanillin = 4-hydroxy-3-methoxybenzaldehyde
Other name(s): vanillin synthase; VpVan; VAN; ferulate aldolase
Systematic name: ferulate acetate-lyase (vanillin-forming)
Comments: The enzyme is located in the chloroplasts of vanilla pods of the orchid Vanilla planifolia. It also converts ferulic acid 4-O-β-D-glucopyranoside to vanillin 4-O-β-D-glucopyranoside.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Gallage, N.J., Hansen, E.H., Kannangara, R., Olsen, C.E., Motawia, M.S., Jørgensen, K., Holme, I., Hebelstrup, K., Grisoni, M. and Møller, B.L. Vanillin formation from ferulic acid in Vanilla planifolia is catalysed by a single enzyme. Nat. Commun. 5 (2014) 4037. [PMID: 24941968]
2. Kundu, A. Vanillin biosynthetic pathways in plants. Planta 245 (2017) 1069-1078. [PMID: 28357540]
3. Gallage, N.J., Jørgensen, K., Janfelt, C., Nielsen, A.JZ., Naake, T., Dunski, E., Dalsten, L., Grisoni, M. and Møller, B.L. The intracellular localization of the vanillin biosynthetic machinery in pods of Vanilla planifolia. Plant Cell Physiol. 59 (2018) 304-318. [PMID: 29186560]
Accepted name: 4-coumarate hydratase/lyase
Reaction: 4-coumarate + H2O = 4-hydroxybenzaldehyde + acetate (overall reaction)
(1a) 4-coumarate + H2O = 3-hydroxy-3-(4-hydroxyphenyl)propanoate
(1b) 3-hydroxy-3-(4-hydroxyphenyl)propanoate = 4-hydroxybenzaldehyde + acetate
Glossary: 4-coumarate = (2E)-3-(4-hydroxyphenyl)acrylate = (2E)-3-(4-hydroxyphenyl)prop-2-enoate
Other name(s): 4-hydroxybenzaldehyde synthase; 4HBS
Systematic name: 4-coumarate acetate-lyase (4-hydroxybenzaldehyde-forming)
Comments: The enzyme has been purified from vanilla pods of the orchid Vanilla planifolia. It is highly specific for 4-coumarate. Similar compounds such as cinnamate, caffeate, sinapate and o-coumarate are not substrates.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
References:
1. Podstolski, A., Havkin-Frenkel, D., Malinowski, J., Blount, J.W., Kourteva, G. and Dixon, R.A. Unusual 4-hydroxybenzaldehyde synthase activity from tissue cultures of the vanilla orchid Vanilla planifolia. Phytochemistry 61 (2002) 611-620. [PMID: 12423881]