Enzyme Nomenclature

Continued from EC 4.2.3.151-203

EC 4.2.99

Other Carbon-Oxygen Lyases

Contents

EC 4.2.99.1 now EC 4.2.2.2
EC 4.2.99.2 now EC 4.2.3.1
EC 4.2.99.3 now EC 4.2.2.2
EC 4.2.99.4 now EC 4.2.2.20 and EC 4.2.2.21
EC 4.2.99.5 deleted
EC 4.2.99.6 deleted, included in EC 4.2.2.5, EC 4.2.2.20 and EC 4.2.2.21
EC 4.2.99.7 now EC 4.2.3.2
EC 4.2.99.8 now EC 2.5.1.47
EC 4.2.99.9 now EC 2.5.1.48
EC 4.2.99.10 now EC 2.5.1.49
EC 4.2.99.11 now EC 4.2.3.3
EC 4.2.99.12 carboxymethyloxysuccinate lyase
EC 4.2.99.13 now EC 2.5.1.50
EC 4.2.99.14 now EC 2.5.1.51
EC 4.2.99.15 now EC 2.5.1.52
EC 4.2.99.16 now EC 2.5.1.53
EC 4.2.99.17 now EC 4.2.99.14
EC 4.2.99.18 DNA-(apurinic or apyrimidinic site) lyase
EC 4.2.99.19 now EC 4.4.1.23
EC 4.2.99.20 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
EC 4.2.99.21 isochorismate lyase
EC 4.2.99.22 tuliposide A-converting enzyme
EC 4.2.99.23 tuliposide B-converting enzyme
EC 4.2.99.24 thebaine synthase

Entries

[EC 4.2.99.1 Transferred entry: now EC 4.2.2.1 hyaluronate lyase (EC 4.2.99.1 created 1961, deleted 1972)]

[EC 4.2.99.2 Transferred entry: now EC 4.2.3.1, threonine synthase (EC 4.2.99.2 created 1961, deleted 2000)]

[EC 4.2.99.3 Transferred entry: now EC 4.2.2.2 pectate lyase (EC 4.2.99.3 created 1965, deleted 1972)]

[EC 4.2.99.4 Transferred entry: now EC 4.2.2.3 alginate lyase (EC 4.2.99.4 created 1965, deleted 1972)]

[EC 4.2.99.5 Deleted entry: polyglucuronide lyase (EC 4.2.99.5 created 1965, deleted 1972)]

[EC 4.2.99.6 Deleted entry: chondroitin sulfate lyase. Now included with EC 4.2.2.4 (chondroitin ABC lyase) and EC 4.2.2.5 (chondroitin AC lyase) (EC 4.2.99.6 created 1965, deleted 1972)]

[EC 4.2.99.7 Transferred entry: now EC 4.2.3.2, ethanolamine-phosphate phospho-lyase (EC 4.2.99.7 created 1972, deleted 2000)]

[EC 4.2.99.8 Transferred entry: now EC 2.5.1.47, cysteine synthase (EC 4.2.99.8 created 1972, modified 1976, modified 1990, deleted 2002)]

[EC 4.2.99.9 Transferred entry: now EC 2.5.1.48, cystathionine γ-synthase (EC 4.2.99.9 created 1972, deleted 2002)]

[EC 4.2.99.10 Transferred entry: now EC 2.5.1.49, O-acetylhomoserine aminocarboxypropyltransferase (EC 4.2.99.10 created 1972, deleted 2002)]

[EC 4.2.99.11 Transferred entry: now EC 4.2.3.3, methylglyoxal synthase (EC 4.2.99.11 created 1972, deleted 2000)]

EC 4.2.99.12

Accepted name: carboxymethyloxysuccinate lyase

Reaction: carboxymethyloxysuccinate = fumarate + glycolate

Other name(s): carbon-oxygen lyase; carboxymethyloxysuccinate glycolate-lyase

Systematic name: carboxymethyloxysuccinate glycolate-lyase (fumarate-forming)

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 53167-89-8

References:

1. Peterson, D. and Llaneza, J. Identification of a carbon-oxygen lyase activity cleaving the ether linkage in carboxymethyloxysuccinic acid. Arch. Biochem. Biophys. 162 (1974) 135-146. [PMID: 4831330]

[EC 4.2.99.12 created 1976]

[EC 4.2.99.13 Transferred entry: now EC 2.5.1.50, zeatin 9-aminocarboxyethyltransferase (EC 4.2.99.13 created 1984, deleted 2002)]

[EC 4.2.99.14 Transferred entry: now EC 2.5.1.51, β-pyrazolylalanine synthase (EC 4.2.99.14 created 1989 (EC 4.2.99.17 incorporated 1992), deleted 2002)]

[EC 4.2.99.15 Transferred entry: now EC 2.5.1.52, L-mimosine synthase (EC 4.2.99.15 created 1989, deleted 2002)]

[EC 4.2.99.16 Transferred entry: now EC 2.5.1.53, uracilylalanine synthase (EC 4.2.99.16 created 1990, deleted 2002)]

[EC 4.2.99.17 Deleted entry: listed as EC 4.2.99.14 β-pyrazolylalanine synthase (acetylserine) (EC 4.2.99.17 created 1992, deleted 1992)]

EC 4.2.99.18

Accepted name: DNA-(apurinic or apyrimidinic site) lyase

Reaction: The C-O-P bond 3' to the apurinic or apyrimidinic site in DNA is broken by a β-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-phosphate

Other name(s): AP lyase; AP endonuclease class I; endodeoxyribonuclease (apurinic or apyrimidinic); deoxyribonuclease (apurinic or apyrimidinic); E. coli endonuclease III; phage-T4 UV endonuclease; Micrococcus luteus UV endonuclease; AP site-DNA 5'-phosphomonoester-lyase; X-ray endonuclease III

Systematic name: DNA-(apurinic or apyrimidinic site) 5'-phosphomonoester-lyase

Comments: 'Nicking' of the phosphodiester bond is due to a lyase-type reaction, not hydrolysis. This group of enzymes was previously listed as endonucleases, under EC 3.1.25.2.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 61811-29-8

References:

1. Bailly, V., Sente, B. and Verly, W.G. Bacteriophage-T4 and Micrococcus luteus UV endonucleases are not endonucleases but β-elimination and sometimes βδ-elimination catalysts. Biochem. J. 259 (1989) 751-759. [PMID: 2471512]

2. Bailly, V. and Verly, W.G. Escherichia coli endonuclease III is not an endonuclease but a β-elimination catalyst. Biochem. J. 242 (1987) 565-572. [PMID: 2439070]

3. Bailly, V. and Verly, W.G. AP endonucleases and AP lyases. Nucleic Acids Res. 17 (1989) 3617-3618. [PMID: 2471157]

4. Manoharan, M., Mazumder, A., Ransom, S.C., Gerlt, J.A. and Bolton, P.H. Mechanism of UV endonuclease-V cleavage of abasic sites in DNA determined by C-13 labeling. J. Am. Chem. Soc. 110 (1988) 2690-2691.

[EC 4.2.99.18 created 1978 as EC 3.1.25.2, transferred 1992 to EC 4.2.99.18]

[EC 4.2.99.19 Transferred entry: Now EC 4.4.1.23, 2-hydroxypropyl-CoM lyase. The enzyme was incorrectly classified as acting on a C-O bond rather than a C-S bond (EC 4.2.99.19 created 2001, deleted 2005)]

EC 4.2.99.20

Accepted name: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase

Reaction: 5-enolpyruvoyl-6-hydroxy-2-succinylcyclohex-3-ene-1-carboxylate = (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate + pyruvate

For diagram of reaction, click here.

Other name(s): 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid synthase; 6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate synthase; SHCHC synthase; MenH; YfbB

Systematic name: 5-enolpyruvoyl-6-hydroxy-2-succinylcyclohex-3-ene-1-carboxylate pyruvate-lyase [(1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate-forming)

Comments: This enzyme is involved in the biosynthesis of vitamin K2 (menaquinone). In most anaerobes and all Gram-positive aerobes, menaquinone is the sole electron transporter in the respiratory chain and is essential for their survival. It had previously been thought that the reactions carried out by this enzyme and EC 2.2.1.9, 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase, were carried out by a single enzyme but this has since been disproved [2].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 122007-88-9

References:

1. Jiang, M., Chen, X., Guo, Z.F., Cao, Y., Chen, M. and Guo, Z. Identification and characterization of (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase in the menaquinone biosynthesis of Escherichia coli. Biochemistry 47 (2008) 3426-3434. [PMID: 18284213]

2. Jiang, M., Cao, Y., Guo, Z.F., Chen, M., Chen, X. and Guo, Z. Menaquinone biosynthesis in Escherichia coli: identification of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate as a novel intermediate and re-evaluation of MenD activity. Biochemistry 46 (2007) 10979-10989. [PMID: 17760421]

[EC 4.2.99.20 created 2008 (EC 2.5.1.64 created 2003, part-incorporated 2008)]

EC 4.2.99.21

Accepted name: isochorismate lyase

Reaction: isochorismate = salicylate + pyruvate

Other name(s): salicylate biosynthesis protein pchB; pyochelin biosynthetic protein PchB; isochorismate pyruvate lyase

Systematic name: isochorismate pyruvate-lyase (salicylate-forming)

Comments: This enzyme is part of the pathway of salicylate formation from chorismate, and forms an integral part of pathways that produce salicylate-derived siderophores, such as pyochelin and yersiniabactin.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Serino, L., Reimmann, C., Baur, H., Beyeler, M., Visca, P. and Haas, D. Structural genes for salicylate biosynthesis from chorismate in Pseudomonas aeruginosa. Mol. Gen. Genet. 249 (1995) 217-228. [PMID: 7500944]

2. Kerbarh, O., Ciulli, A., Howard, N.I. and Abell, C. Salicylate biosynthesis: overexpression, purification, and characterization of Irp9, a bifunctional salicylate synthase from Yersinia enterocolitica. J. Bacteriol. 187 (2005) 5061-5066. [PMID: 16030197]

[EC 4.2.99.21 created 2010]

EC 4.2.99.22

Accepted name: tuliposide A-converting enzyme

Reaction: 6-tuliposide A = tulipalin A + D-glucose

For diagram of reaction click here.

Glossary: 6-tuliposide A = 6-O-(4-hydroxy-2-methylenebutanoyl)-D-glucose
tulipalin A = 2-methylenebutanolactone

Other name(s): tuliposide-converting enzyme; 6-O-(4'-hydroxy-2'-methylenebutyryl)-D-glucose acyltransferase (lactone-forming); TCA; TCEA

Systematic name: 6-tuliposide A D-glucose-lyase (tulipalin A forming)

Comments: Isolated from the plant Tulipa gesneriana (tulip). The reaction is an intramolecular transesterification producing the lactone. The enzyme also has a weak activity with 6-tuliposide B and 6-O-benzoyl-D-glucose.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:

References:

1. Kato, Y., Shoji, K., Ubukata, M., Shigetomi, K., Sato, Y., Nakajima, N. and Ogita, S. Purification and characterization of a tuliposide-converting enzyme from bulbs of Tulipa gesneriana. Biosci. Biotechnol. Biochem. 73 (2009) 1895-1897. [PMID: 19661715]

2. Nomura, T., Ogita, S. and Kato, Y. A novel lactone-forming carboxylesterase: molecular identification of a tuliposide A-converting enzyme in tulip. Plant Physiol. 159 (2012) 565-578. [PMID: 22474185]

[EC 4.2.99.22 created 2013]

EC 4.2.99.23

Accepted name: tuliposide B-converting enzyme

Reaction: 6-tuliposide B = tulipalin B + D-glucose

Glossary: 6-tuliposide B = 6-O-[(3S)-3,4-dihydroxy-2-methylenebutanoyl]-D-glucose
tulipalin B = (4S)-4-hydroxy-3-methylideneoxolan-2-one

Systematic name: 6-tuliposide B D-glucose-lyase (tulipalin B-forming)

Comments: The enzyme, characterized from pollen of the plant Tulipa gesneriana (tulip), catalyses the intramolecular transesterification of 6-tuliposide B to form the antibiotic aglycon tulipalin B as a sole product. It does not catalyse the hydrolysis of 6-tuliposide B to form a hydroxy acid. The enzyme has marginal activity with 6-tuliposide A. cf. EC 4.2.99.22, tuliposide A-converting enzyme.

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:

References:

1. Nomura, T., Murase, T., Ogita, S. and Kato, Y. Molecular identification of tuliposide B-converting enzyme: a lactone-forming carboxylesterase from the pollen of tulip. Plant J. 83 (2015) 252-262. [PMID: 25997073]

[EC 4.2.99.23 created 2016]

EC 4.2.99.24

Accepted name: thebaine synthase

Reaction: salutaridinol 7-O-acetate = thebaine + acetate

For diagram of reaction click here

Other name(s): THS

Systematic name: salutaridinol 7-O-acetate acetate-lyase (thebaine forming)

Comments: Isolated from the plant Papaver somniferum (opium poppy). The reaction occurs spontaneously when the pH is between 8-9, but the enzyme is required at the physiological pH, which is close to 7.

Links to other databases: BRENDA, EXPASY, ExplorEnz, KEGG, MetaCyc, CAS registry number:

References:

1. Chen, X., Hagel, J.M., Chang, L., Tucker, J.E., Shiigi, S.A., Yelpaala, Y., Chen, H.Y., Estrada, R., Colbeck, J., Enquist-Newman, M., Ibanez, A.B., Cottarel, G., Vidanes, G.M. and Facchini, P.J. A pathogenesis-related 10 protein catalyzes the final step in thebaine biosynthesis. Nat. Chem. Biol. 14 (2018) 738-743. [PMID: 29807982]

[EC 4.2.99.24 created 2019]


Continued with EC 4.3
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