EC 4 Lyases

EC 4.1.1.74

Recommended name: indolepyruvate decarboxylase

Reaction: 3-(indol-3-yl)pyruvate = 2-(indol-3-yl)acetaldehyde + CO₂

Systematic name: indol-3-yl-pyruvate carboxy-lyase

Comments: thiamin diphosphate and Mg²⁺-dependent. More specific than EC 4.1.1.1.

References:

1. Koga, J. Structure and function of indolepyruvate decarboxylase, a key enzyme in indole-3-pyruvic acid biosynthesis. Biochim. Biophys. Acta 1249 (1995) 1-13. [PMID: 7766676]

EC 4.1.1.75

Recommended name: 5-guanidino-2-oxopentanoate decarboxylase

Reaction: 5-guanidino-2-oxo-pentanoate = 4-guanidinobutanoate + CO₂

Other name(s): -ketoarginine decarboxylase

Systematic name: 2-oxo-5-guanidinopentanoate carboxy-lyase

Comments: enzyme activity is dependent on the presence of thiamin diphosphate and a divalent cation.

References:

1.Vanderbilt, A.S., Gaby, N.S., Rodwell, V.W. Intermediates and enzymes between -ketoarginine and -guanidinobutyrate in the L-arginine catabolic pathway of Pseudomonas putida. J. Biol. Chem. 250 (1975) 5322-5329. [PMID: 237915]

EC 4.1.1.76

Recommended name: arylmalonate decarboxylase

Reaction: 2-aryl-2-methylmalonate = 2-arylpropionate + CO₂

Other name(s): AMDASE

Systematic name: 2-aryl-2-methylmalonate carboxy-lyase

References:

1. Miyamoto, K., Ohta, H. Cloning and heterologous expression of a novel arylmalonate decarboxylase gene from Alcaligenes bronchisepticus KU 1201. Appl. Microbiol. Biotechnol. 38 (1992) 234-238. [PMID: 1369144]

EC 4.1.1.77

Recommended name: 4-oxalocrotonate decarboxylase

Reaction: 4-oxalocrotonate = 2-oxopent-4-enoate + CO₂

Systematic name: 4-oxalocrotonate carboxy-lyase

Comments: involved in the meta-cleavage pathway for the degradation of phenols, cresols and catechols

References:

1.Shingler, V., Marklund, U., Powlowski, J. Nucleotide sequence and functional analysis of the complete phenol/3,4-dimethylphenol catabolic pathway of Pseudomonas sp. strain CF600. J. Bacteriol. 174 (1992) 711-724. [PMID: 1732207]

EC 4.1.2.39

Recommended name: hydroxynitrilase

Reaction: 2-hydroxyisobutyronitrile = cyanide + acetone

Other name(s): hydroxynitrile lyase; oxynitrilase

Systematic name: 2-hydroxyisobutyronitrile acetone-lyase

Comments: the enzyme from Hevea (rubber tree) and Manihot spp. (cassava) accepts aliphatic and aromatic hydroxynitriles, unlike EC 4.1.2.11, which does not act on aliphatic hydroxynitriles. 2-Hydroxyisobutyronitrile (acetone cyanohydrin) is liberated by glycosidase action on linamarin.

References:

1. Selmar, D., Lieberei, R., Biehl, B., Conn, E.E. -Hydroxynitrile lyase in Hevea brasiliensis and its significance for rapid cyanogenesis. Physiol. Plant 75 (1989) 97-101.

EC 4.1.2.40

Recommended name: tagatose-bisphosphate aldolase

Reaction: D-tagatose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate

Systematic name: D-tagatose-1,6-bisphosphate triosephosphate lyase

Comments: enzyme activity is stimulated by certain divalent cations. It is involved in the tagatose 6-phosphate pathway of lactose catabolism in bacteria.

References:

1. Anderson, R.L., Markwell, J.P. D-Tagatose-1,6-bisphosphate aldolase (Class II) from Klebsiella pneumoniae. Methods Enzymol. 90 (1982) 323-324.

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 4.1.99.7

Recommended name: aristolochene synthase

Reaction: trans,trans-farnesyl diphosphate = aristolochene + diphosphate

Other name(s): sesquiterpene cyclase

Systematic name: trans,trans-farnesyl diphosphate aristolochene-lyase

Comments: The initial internal cyclization produces the monocyclic intermediate germacrene A; further cyclization and methyl transfer converts the intermediate into aristolochene. The enzyme from Penicillium roqueforti requires magnesium and manganese ions. Aristolochene is the likely parent compound for a number of sesquiterpenes produced by filamentous fungi.

References:

1. Cane, D.E., Prabhakaran, P.C., Oliver, J.S., McIlwaine, D.B. Aristolochene biosynthesis. Stereochemistry of the deprotonation steps in the enzymatic cyclization of farnesyl pyrophosphate. J. Am. Chem. Soc. 112 (1990) 3209-3210.

2. Cane, D.E., Prabhakaran, P.C., Salaski, E.J., Harrison, P.M.H., Noguchi, H., Rawlings, B.J. Aristolochene biosynthesis and enzymatic cyclization of farnesyl pyrophosphate. J. Am. Chem. Soc. 111 (1989) 8914-8916.

3. Hohn, T.M., Plattner, R.D. Purification and characterization of the sesquiterpene cyclase aristolochene synthase from Penicillium roqueforti. Arch. Biochem. Biophys. 272 (1989) 137-143. [PMID: 2544140]

4. Proctor, R.H., Hohn, T.M. Aristolochene synthase. Isolation, characterization, and bacterial expression of a sesquiterpenoid biosynthetic gene (Ari1) from Penicillium roqueforti. J. Biol. Chem. 268 (1993) 4543-4548. [PMID: 8440737]

EC 4.2.1.96

Recommended name: 4a-hydroxytetrahydrobiopterin dehydratase

Reaction: (6R)-6-(L-erythro-1,2-dihydroxypropyl)-5,6,7,8-tetrahydro-4a-hydroypterin = (6R)-6-(L-erythro-1,2-dihydroxypropyl)-7,8-dihydro-6H-pterin + H₂O

Other name(s): 4-hydroxy-tetrahydropterin dehydratase; pterin-4-carbinolamine dehydratase

Systematic name: 4a-hydroxytetrahydrobiopterin hydro-lyase

Comments: catalyses the dehydration of 4a-hydroxytetrahydrobiopterins

References:

1. Hauer, C.R., Rebrin, I., Thöny, B., Neuheiser, F., Curtius, H.C., Hunziker, P., Blau, N., Ghisla, S., Heizmann, C.W. Phenylalanine hydroxylase-stimulating protein: pterin-4-carbinolamine dehydratase from rat and human liver. J. Biol. Chem. 268 (1993) 4828-4831. [PMID: 8444860]

EC 4.2.1.97

Recommended name: phaseollidin hydratase

Reaction: phaseollidin hydrate = phaseollidin + H₂O

Systematic name: phaseollidin-hydrate hydro-lyase

Comments: the enzyme from Fusarium solani, which is distinct from kievitone hydratase (EC 4.2.1.95), hydrates the methylbutenyl side-chain of the isoflavonoid phytoalexin, phaseollidin.

References:

1. Turbek, C.S., Smith, D.A., Schardl, C.L. An extracellular enzyme from Fusarium solani f.sp. phaseoli, which catalyses hydration of the isoflavonoid phytoalexin, phaseollidin. FEMS Microbiol. Lett. 94 (1992) 187-190. [PMID: 1521768]

EC 4.2.1.98

Recommended name: 16-hydroxyprogesterone dehydratase

Reaction: 16-hydroxyprogesterone = 16,17-didehydroprogesterone + H₂O

Other name(s): hydroxyprogesterone dehydroxylase

Systematic name: 16-hydroxyprogesterone hydro-lyase

Comments: 16-hydroxypregnenolone is also a substrate.

References:

1. Glass, T.L., Lamppa, R.S. Purification and properties of 16-hydroxyprogesterone dehydroxylase Eubacterium sp. strain 144. Biochim. Biophys. Acta 837 (1985) 103-110. [PMID: 4052439]

EC 4.2.1.99

Recommended name: 2-methylisocitrate dehydratase

Reaction: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate = (Z)-but-2-ene-1,2,3-tricarboxylate + H₂O

Other name(s): (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate hydro-lyase

Systematic name: (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate hydro-lyase

Comments: the enzyme from the fungus Yarrowia lipolytica (Saccharomycopsis) does not act on isocitrate.

References:

1. Aoki, H., Uchiyama, H., Umetsu, H., Tabuchi, T. Isolation of 2-methylisocitrate dehydratase, a new enzyme serving in the methylcitric acid cycle for propionate metabolism, from Yarrowia lipolytica. Biosci. Biotechnol. Biochem. 59 (1995) 1825-1828

2. Tabuchi, T., Umetsu, H., Aoki, H., Uchiyama, H. Characteristics of 2-methylisocitrate dehydratase, isolated from Yarrowia lipolytica, in comparison to aconitase. Biosci. Biotechnol. Biochem. 59 (1995) 2013-2017.

EC 4.2.2.13

Recommended name: exo-(1fi4)--D-glucan lyase

Reaction: linear -glucan = glucose + 1,5-anhydro-D-fructose

Other name(s): -(1fi4)-glucan 1,5-anhydro-D-fructose eliminase; -1,4-glucan exo-lyase; -1,4-glucan lyase

Systematic name: (1fi4)--D-glucan exo-4-lyase (1,5-anhydro-D-fructose-forming)

Comments: the enzyme catalyses the sequential degradation of (14)--D-glucans from the non-reducing end with the release of 1,5-anhydro-D-fructose. Thus, for an -glucan containing n (14)-linked glucose units, the final products are 1 glucose plus (n-1) 1,5-anhydro-D-fructose. Maltose, maltosaccharides and amylose are all completely degraded. It does not degrade (16)--gucosidic bonds and thus the degradation of a branched glucan, such as amylopectin or glycogen, will result in the formation of 1,5-anhydro-D-fructose plus a limit dextrin.

References:

1. Yu, S., Kenne, L., Pedersén, M. -1,4-Glucan lyase, a new class of starch/glycogen degrading enzyme. I. Efficient purification and characterization from red seaweeds. Biochim. Biophys. Acta 1156 (1993) 313-320. [PMID: 8461323]

2. Yu, S., Pedersén, M. -1,4-Glucan lyase, a new class of starch/glycogen degrading enzyme. II. Subcellular localization and partial amino-acid sequence. Planta 191 (1993) 137-142.

EC 4.3.1.14

Recommended name: 3-aminobutyryl-CoA ammonia-lyase

Reaction: L-3-aminobutyryl-CoA = crotonoyl-CoA + NH₃₊

Other name(s): L-3-aminobutyryl-CoA deaminase

Systematic name: L-3-aminobutyryl-CoA ammonia-lyase

Comments: hydroxylamine can replace ammonia as a substrate. Crotonoyl-pantetheine can replace crotonoyl-CoA but it is a poorer substrate.

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]

EC 4.3.1.15

Recommended name: diaminopropionate ammonia-lyase

Reaction: 2,3-diaminopropionate = pyruvate + 2 ammonia

Other name(s): diaminopropionatase; ,-diaminopropionate ammonia-lyase

Systematic name: 2,3-diaminopropionate ammonia-lyase

Comments: a pyridoxal phosphate enzyme. Active towards both D- and L-diaminopropionate. D- and L-Serine are poor substrates.

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]

EC 4.6.1.10

Recommended name: 6-pyruvoyltetrahydropterin synthase

Reaction: 6-(L-erythro-1,2-dihydroxypropyl 3-triphosphate)-7,8-dihydropteridin = 6-(1,2-dioxopropyl)-5,6,7,8-tetrahydropterin + triphosphate

Systematic name: 2-amino-4-oxo-6-(erythro-1',2',3'-trihydroxypropyl)-7,8-dihydroxypterdine triphosphate triphosphate lyase

Comments: catalyses triphosphate elimination and an intramolecular redox reaction in the presence of Mg²⁺. It has been identified in human liver. The product is 6-pyruvoyltetrahydrobiopterin.

References:

1. Milstien, S., Kaufman, S. The biosynthesis of tetrahydrobiopterin in rat brain. Purification and characterization of 6-pyruvoyl-tetrahydrobiopterin(2'-oxo) reductase. J. Biol. Chem. 264 (1989) 8066-8073. [PMID: 2656673]

2. Thöny, B., Leimbacher, W., Bürgisser, D., Heinzmann, C.W. Human 6-pyruvoyl-tetrahydrobiopterin synthase: cDNA cloning and heterologous expression of the recombinant enzyme. Biochem. Biophys. Res. Commun. 189 (1992) 1437-1443. [PMID: 1282802]

EC 4.6.1.11

Recommended name: (+)--cadinene synthase

Reaction: 2-trans,6-trans-farnesyl diphosphate = (+)--cadinene + diphosphate

Systematic name: 2-trans,6-trans-farnesyl-diphosphate diphosphate-lyase (cyclizing, (+)--cadinene-forming)

Comments: the sesquiterpenoid (+)--cadinene is an intermediate in phytoalexin biosynthesis. Mg²⁺ is required for activity.

References:

1. Davis, G.D., Essenberg, M. (+)--Cadinene is a product of sesquiterpene cyclase activity in cotton. Phytochemistry 39 (1995) 553-567.

2. Chen, X.-Y., Chen, Y., Heinstein, P., Davisson, V.J. Cloning, expression and characterization of (+)--cadinene synthase: a catalyst for cotton phytoalexin biosynthesis. Arch. Biochem. Biophys. 324 (1995) 255-266. [PMID: 8554317]

3. Davis, E.M., Tsuji, J., Davis, G.D., Pierce, M.L., Essenberg, M. Purification of (+)--cadinene synthase, a sesquiterpene cyclase from bacteria-inoculated cotton foliar tissue. Phytochemistry 41 (1996) 1047-1055.

AMENDMENTS TO EXISTING ENTRIES

EC 4.1.1.29

Recommended name: sulfinoalanine decarboxylase

Reaction: 3-sulfino-L-alanine = hypotaurine + CO₂

Other names: cysteine-sulfinate decarboxylase

Systematic name: 3-sulfino-L-alanine carboxy-lyase

Comments: a pyridoxal-phosphate protein. Also acts on L-cysteate. The 1992 edition of the Enzyme List erroneously gave the name sulfoalanine decarboxylase to this enzyme.

References:

1. Guion-Rain, M.C., Portemer, C., Chatagner, F. Rat liver cysteine sulfinate decarboxylase: purification, new appraisal of molecular weight and determination of catalytic properties. Biochim. Biophys. Acta 384 (1975) 265-276. [PMID: 236774]

2. Jacobsen, J.G., Thomas, L.L., Smith, L.H., Jr. Properties and distribution of L-cysteine sulfinate carboxy-lyase. Biochim. Biophys. Acta 85 (1964) 103-116.

EC 4.1.2.10

Recommended name: mandelonitrile lyase

Reaction: mandelonitrile = cyanide + benzaldehyde

Other name(s): hydroxynitrile lyase; (R)-oxynitrilase

Systematic name: mandelonitrile benzaldehyde-lyase

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).

References:

1. Becker, W., Benthin, U., Eschenhof, E., Pfeil, E. [Cyanohydrin synthesis. II. Purification and properties of oxynitrilase of bitter almonds (Prunus communis).] [German] Biochem. Z. 337 (1963) 156-166.

2. Becker, W., Pfeil, E. Die Darstellung kristallisierter Oxynitrilase aus bitteren Mandeln (Prunus comm. Stks). Naturwissenschaften 51 (1964) 193.

3. Gross, M., Jacobs, G.H., Poulton, J.E. A rapid and sensitive spectrophotometric assay for prunasin hydrolase activity employing purified mandelonitrile lyase. Anal. Biochem. 119 (1982) 25-30. [PMID: 6803611]

4. Xu, L.-L., Singh, B.K., Conn, E.E. Purification and characterization of mandelonitrile lyase from Prunus lyonii. Arch. Biochem. Biophys. 250 (1986) 322-328. [PMID: 3777939]

5. Yemm, R.S., Poulton, J.E. Isolation and characterization of multiple forms of mandelonitrile lyase from mature black cherry (Prunus serotina Ehrh.) seeds. Arch. Biochem. Biophys. 247 (1986) 440-445. [PMID: 3717954]

EC 4.1.2.11

Recommended name: hydroxymandelonitrile lyase

Reaction: (S)-4-hydroxymandelonitrile = cyanide + 4-hydroxybenzaldehyde

Other name(s): hydroxynitrile lyase

Systematic name: (S)-4-hydroxymandelonitrile hydroxybenzaldehyde-lyase

Comments: does not accept aliphatic hydroxynitriles, unlike EC 4.1.2.10 and 4.1.2.39.

References:

1. Bové, C., Conn, E.E. Metabolism of aromatic compounds in higher plants II. Purification and properites of the oxynitrilase of Sorghum vulgare. J. Biol. Chem. 236 (1961) 207-210.

2. Seely, M.K., Criddle, R.S., 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]

EC 4.1.2.13

Recommended name: fructose-bisphosphate aldolase

Reaction: D-fructose 1,6-bisphosphate = glycerone phosphate + D-glyceraldehyde 3-phosphate

Other name(s): aldolase; fructose-1,6-bisphosphate triosephosphate-lyase

Systematic name: D-fructose-1,6-bisphosphate D-glyceraldehyde-3-phosphate-lyase

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

References:

1. Horecker, B.L., Tsolas, O.and Lai, C.Y. Aldolases. In Boyer, P.D., (Ed.) The Enzymes, 3rd ed., vol.7, p.213, Academic Press, New York, 1972, p. 213-25.

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]

EC 4.2.1.78

Recommended name: (S)-norcoclaurine synthase

Reaction: 4-(2-aminoethyl)benzene-1,2-diol + 4-hydroxyphenylacetaldehyde = (S)-norcoclaurine + H₂O

Other name(s): (S)-norlaudanosoline synthase

Systematic name: 4-hydroxyphenylacetaldehyde hydro-lyase (adding dopamine)

Comments: the reaction makes a 6-membered ring by forming a bond between C-6 of the 3,4-dihydroxyphenyl group of the dopamine and C-1 of the aldehyde in the imine formed between the substrates. The product is the precursor of the benzylisoquinoline alkaloids in plants. The enzyme, formerly known as (S)-norlaudanosoline synthase, will also catalyse the reaction of 4-(2-aminoethyl)benzene-1,2-diol + (3,4-dihydroxyphenyl)acetaldehyde to form (S)-norlaudanosoline, but this alkaloid has not been found to occur in plants.

References:

1. Stadler, R., Zenk, M.H. A revision of the generally accepted pathway for the biosynthesis of the benzotetrahydroisoquinoline reticuline. Liebigs Ann. Chem. (1990) 555-562.

2. Stadler, R., Kutchan, T.M., Zenk, M.H. (S)-Norcoclaurine is the central intermediate in benzylisoquinoline alkaloid biosynthesis. Phytochemistry 28 (1989) 1083-1086.