ExplorEnz: EC 4.1.1.*

Displaying entries 101-127 of 127.

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4.1.1.101

Accepted name:

malolactic enzyme

Reaction:

(S)-malate = (S)-lactate + CO₂

Other name(s):

mleA (gene name); mleS (gene name)

Systematic name:

(S)-malate carboxy-lyase

Comments:

The enzyme is involved in the malolactic fermentation of wine, which results in a natural decrease in acidity and favorable changes in wine flavors. It has been purified from several lactic acid bacteria, including Leuconostoc mesenteroides [1], Lactobacillus plantarum [2], and Oenococcus oeni [3,4]. The enzyme contains a tightly bound NAD⁺ cofactor and requires Mn²⁺.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc

References:

1.	Lonvaud-Funel, A. and de Saad, A.M. Purification and properties of a malolactic Enzyme from a strain of Leuconostoc mesenteroides isolated from grapes. Appl. Environ. Microbiol. 43 (1982) 357–361. [PMID: 16345941]
2.	Caspritz, G. and Radler, F. Malolactic enzyme of Lactobacillus plantarum. Purification, properties, and distribution among bacteria. J. Biol. Chem. 258 (1983) 4907–4910. [PMID: 6833282]
3.	Naouri, P., Chagnaud, P., Arnaud, A. and Galzy, P. Purification and properties of a malolactic enzyme from Leuconostoc oenos ATCC 23278. J. Basic Microbiol. 30 (1990) 577–585. [DOI] [PMID: 2097345]
4.	Schumann, C., Michlmayr, H., Del Hierro, A.M., Kulbe, K.D., Jiranek, V., Eder, R. and Nguyen, T.H. Malolactic enzyme from Oenococcus oeni: heterologous expression in Escherichia coli and biochemical characterization. Bioengineered 4 (2013) 147–152. [DOI] [PMID: 23196745]

[EC 4.1.1.101 created 2015]

4.1.1.102

Accepted name:

phenacrylate decarboxylase

Reaction:

(1) 4-coumarate = 4-vinylphenol + CO₂
(2) trans-cinnamate = styrene + CO₂
(3) ferulate = 4-vinylguaiacol + CO₂

Glossary:

4-coumarate = 3-(4-hydroxyphenyl)prop-2-enoate
trans-cinnamate = (2E)-3-phenylprop-2-enoate
ferulate = 4-hydroxy-3-methoxycinnamate

Other name(s):

FDC1 (gene name); ferulic acid decarboxylase

Systematic name:

3-phenylprop-2-enoate carboxy-lyase

Comments:

The enzyme, found in fungi, catalyses the decarboxylation of phenacrylic acids present in plant cell walls. It requires a prenylated flavin cofactor that is produced by EC 2.5.1.129, flavin prenyltransferase.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc, PDB

References:

1.	Mukai, N., Masaki, K., Fujii, T., Kawamukai, M. and Iefuji, H. PAD1 and FDC1 are essential for the decarboxylation of phenylacrylic acids in Saccharomyces cerevisiae. J. Biosci. Bioeng. 109 (2010) 564–569. [DOI] [PMID: 20471595]
2.	Bhuiya, M.W., Lee, S.G., Jez, J.M. and Yu, O. Structure and mechanism of ferulic acid decarboxylase (FDC1) from Saccharomyces cerevisiae. Appl. Environ. Microbiol. 81 (2015) 4216–4223. [DOI] [PMID: 25862228]
3.	Payne, K.A., White, M.D., Fisher, K., Khara, B., Bailey, S.S., Parker, D., Rattray, N.J., Trivedi, D.K., Goodacre, R., Beveridge, R., Barran, P., Rigby, S.E., Scrutton, N.S., Hay, S. and Leys, D. New cofactor supports α,β-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition. Nature 522 (2015) 497–501. [DOI] [PMID: 26083754]

[EC 4.1.1.102 created 2015]

4.1.1.103

Accepted name:

γ-resorcylate decarboxylase

Reaction:

2,6-dihydroxybenzoate = 1,3-dihydroxybenzene + CO₂

Glossary:

2,6-dihydroxybenzoate = γ-resorcylate
1,3-dihydroxybenzene = resorcinol

Other name(s):

graF (gene name); tsdA (gene name)

Systematic name:

2,6-dihydroxybenzoate carboxy-lyase

Comments:

The enzyme, characterized from several bacterial strains, is involved in the degradation of γ-resorcylate. It contains a zinc ion and a water molecule at the active site. The reaction is reversible, but equilibrium greatly favors the decarboxylation reaction.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc, PDB

References:

1.	Yoshida, M., Fukuhara, N. and Oikawa, T. Thermophilic, reversible γ-resorcylate decarboxylase from Rhizobium sp. strain MTP-10005: purification, molecular characterization, and expression. J. Bacteriol. 186 (2004) 6855–6863. [DOI] [PMID: 15466039]
2.	Ishii, Y., Narimatsu, Y., Iwasaki, Y., Arai, N., Kino, K. and Kirimura, K. Reversible and nonoxidative γ-resorcylic acid decarboxylase: characterization and gene cloning of a novel enzyme catalyzing carboxylation of resorcinol, 1,3-dihydroxybenzene, from Rhizobium radiobacter. Biochem. Biophys. Res. Commun. 324 (2004) 611–620. [DOI] [PMID: 15474471]
3.	Matsui, T., Yoshida, T., Yoshimura, T. and Nagasawa, T. Regioselective carboxylation of 1,3-dihydroxybenzene by 2,6-dihydroxybenzoate decarboxylase of Pandoraea sp. 12B-2. Appl. Microbiol. Biotechnol. 73 (2006) 95–102. [DOI] [PMID: 16683134]
4.	Goto, M., Hayashi, H., Miyahara, I., Hirotsu, K., Yoshida, M. and Oikawa, T. Crystal structures of nonoxidative zinc-dependent 2,6-dihydroxybenzoate (γ-resorcylate) decarboxylase from Rhizobium sp. strain MTP-10005. J. Biol. Chem. 281 (2006) 34365–34373. [DOI] [PMID: 16963440]
5.	Kasai, D., Araki, N., Motoi, K., Yoshikawa, S., Iino, T., Imai, S., Masai, E. and Fukuda, M. γ-Resorcylate catabolic-pathway genes in the soil actinomycete Rhodococcus jostii RHA1. Appl. Environ. Microbiol. 81 (2015) 7656–7665. [DOI] [PMID: 26319878]

[EC 4.1.1.103 created 2016]

4.1.1.104

Accepted name:

3-dehydro-4-phosphotetronate decarboxylase

Reaction:

(1) 3-dehydro-4-phospho-L-erythronate = glycerone phosphate + CO₂
(2) 3-dehydro-4-phospho-D-erythronate = glycerone phosphate + CO₂

For diagram of erythronate and threonate catabolism, click here

Glossary:

L-erythronate = (2S,3S)-2,3,4-trihydroxybutanoate
D-erythronate = (2R,3R)-2,3,4-trihydroxybutanoate

Other name(s):

otnC (gene name)

Systematic name:

3-dehydro-4-phosphotetronate carboxy-lyase

Comments:

The enzyme, characterized from bacteria, is involved in D-erythronate and L-threonate catabolism.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc, PDB

References:

Zhang, X., Carter, M.S., Vetting, M.W., San Francisco, B., Zhao, S., Al-Obaidi, N.F., Solbiati, J.O., Thiaville, J.J., de Crecy-Lagard, V., Jacobson, M.P., Almo, S.C. and Gerlt, J.A. Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars. Proc. Natl. Acad. Sci. USA 113 (2016) E4161–E4169. [DOI] [PMID: 27402745]

[EC 4.1.1.104 created 2017]

4.1.1.105

Accepted name:

L-tryptophan decarboxylase

Reaction:

L-tryptophan = tryptamine + CO₂

For diagram of psilocybin biosynthesis, click here

Other name(s):

psiD (gene name); TDC (gene name)

Systematic name:

L-tryptophan carboxy-lyase

Comments:

The enzyme has been characterized from bacteria, plants, and fungi. Unlike EC 4.1.1.28, aromatic-L-amino-acid decarboxylase, this enzyme is specific for L-tryptophan.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc, PDB

References:

1.	Noe, W., Mollenschott, C. and Berlin, J. Tryptophan decarboxylase from Catharanthus roseus cell suspension cultures: purification, molecular and kinetic data of the homogenous protein. Plant Mol. Biol. 3 (1984) 281–288. [DOI] [PMID: 24310513]
2.	Buki, K.G., Vinh, D.Q. and Horvath, I. Partial purification and some properties of tryptophan decarboxylase from a Bacillus strain. Acta Microbiol Hung 32 (1985) 65–73. [PMID: 4036551]
3.	Nakazawa, H., Kumagai, H. and Yamada, H. Constitutive aromatic L-amino acid decarboxylase from Micrococcus percitreus. Biochem. Biophys. Res. Commun. 61 (1974) 75–82. [DOI] [PMID: 4441405]
4.	Lopez-Meyer, M. and Nessler, C.L. Tryptophan decarboxylase is encoded by two autonomously regulated genes in Camptotheca acuminata which are differentially expressed during development and stress. Plant J. 11 (1997) 1167–1175. [DOI] [PMID: 9225462]
5.	Fricke, J., Blei, F. and Hoffmeister, D. Enzymatic synthesis of psilocybin. Angew. Chem. Int. Ed. Engl. 56 (2017) 12352–12355. [DOI] [PMID: 28763571]

[EC 4.1.1.105 created 2017]

4.1.1.106

Accepted name:

fatty acid photodecarboxylase

Reaction:

a long-chain fatty acid + hν = a long-chain alkane + CO₂

Other name(s):

FAP (gene name)

Systematic name:

fatty acid carboxy-lyase (light-dependent, alkane-forming)

Comments:

This algal enzyme, characterized from the green algae Chlorella variabilis and Chlamydomonas reinhardtii, is dependent on blue light, which photooxidizes its FAD cofactor. The enzyme acts on fatty acids in the range of C₁₂ to C₂₂, with a higher efficiency for C₁₆ to C₁₇ chains, and forms an alkane product that is one carbon shorter than the substrate. The enzyme can also act on unsaturated fatty acids, forming the respective alkenes, but does not generate a new double bond.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc, PDB

References:

Sorigue, D., Legeret, B., Cuine, S., Blangy, S., Moulin, S., Billon, E., Richaud, P., Brugiere, S., Coute, Y., Nurizzo, D., Muller, P., Brettel, K., Pignol, D., Arnoux, P., Li-Beisson, Y., Peltier, G. and Beisson, F. An algal photoenzyme converts fatty acids to hydrocarbons. Science 357 (2017) 903–907. [DOI] [PMID: 28860382]

[EC 4.1.1.106 created 2017]

4.1.1.107

Accepted name:

3,4-dihydroxyphenylacetaldehyde synthase

Reaction:

L-dopa + O₂ + H₂O = 3,4-dihydroxyphenylacetaldehyde + CO₂ + NH₃ + H₂O₂

For diagram of phenylacetaldehyde, 4-hydroxyphenylacetaldehyde and 3,4-dihydroxyacetaldehyde biosynthesis, click here

Glossary:

L-dopa = 3,4-dihydroxyphenylalanine

Other name(s):

DHPAA synthase

Systematic name:

L-dopa carboxy-lyase (oxidative-deaminating)

Comments:

A pyridoxal 5′-phosphate protein. The enzyme, isolated from the mosquito Aedes aegypti, catalyses the production of 3,4-dihydroxylphenylacetaldehyde directly from L-dopa. Dopamine is not formed as an intermediate (cf. EC 4.1.1.28, aromatic-L-amino-acid decarboxylase). The enzyme is specific for L-dopa and does not react with other aromatic amino acids with the exception of a low activity with α-methyl-L-dopa.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc, PDB

References:

1.	Vavricka, C., Han, Q., Huang, Y., Erickson, S.M., Harich, K., Christensen, B.M. and Li, J. From L-dopa to dihydroxyphenylacetaldehyde: a toxic biochemical pathway plays a vital physiological function in insects. PLoS One 6:e16124 (2011). [DOI] [PMID: 21283636]

[EC 4.1.1.107 created 2017]

4.1.1.108

Accepted name:

4-hydroxyphenylacetaldehyde synthase

Reaction:

L-tyrosine + O₂ + H₂O = (4-hydroxyphenyl)acetaldehyde + CO₂ + NH₃ + H₂O₂

For diagram of phenylacetaldehyde, 4-hydroxyphenylacetaldehyde and 3,4-dihydroxyacetaldehyde biosynthesis, click here

Other name(s):

TYRDC-2 (gene name)

Systematic name:

L-tyrosine carboxy-lyase (oxidative-deaminating)

Comments:

A pyridoxal 5′-phosphate protein. The enzyme, isolated from the the plant Petroselinum crispum (parsley), catalyses the production of 4-hydroxyphenylacetaldehyde directly from L-tyrosine. Tyramine is not formed as an intermediate. The enzyme has a low activity with L-dopa (cf. EC 4.1.1.107, 3,4-dihydroxyphenylacetaldehyde synthase).

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc, PDB

References:

1.	Torrens-Spence, M.P., Gillaspy, G., Zhao, B., Harich, K., White, R.H. and Li, J. Biochemical evaluation of a parsley tyrosine decarboxylase results in a novel 4-hydroxyphenylacetaldehyde synthase enzyme. Biochem. Biophys. Res. Commun. 418 (2012) 211–216. [DOI] [PMID: 22266321]
2.	Torrens-Spence, M.P., Liu, P., Ding, H., Harich, K., Gillaspy, G. and Li, J. Biochemical evaluation of the decarboxylation and decarboxylation-deamination activities of plant aromatic amino acid decarboxylases. J. Biol. Chem. 288 (2013) 2376–2387. [DOI] [PMID: 23204519]

[EC 4.1.1.108 created 2017]

4.1.1.109

Accepted name:

phenylacetaldehyde synthase

Reaction:

L-phenylalanine + O₂ + H₂O = phenylacetaldehyde + CO₂ + NH₃ + H₂O₂

For diagram of phenylacetaldehyde, 4-hydroxyphenylacetaldehyde and 3,4-dihydroxyacetaldehyde biosynthesis, click here

Other name(s):

PAAS (gene name)

Systematic name:

L-phenylalanine carboxy-lyase (oxidative-deaminating)

Comments:

A pyridoxal 5′-phosphate protein. The enzyme, isolated from the the plants Petunia hybrida and a Rosa hybrid, catalyses the production of phenylacetaldehyde directly from L-phenylalanine. The enzyme is specific for L-phenylalanine and does not accept other aromatic amino acids as substrates.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc, PDB

References:

Kaminaga, Y., Schnepp, J., Peel, G., Kish, C.M., Ben-Nissan, G., Weiss, D., Orlova, I., Lavie, O., Rhodes, D., Wood, K., Porterfield, D.M., Cooper, A.J., Schloss, J.V., Pichersky, E., Vainstein, A. and Dudareva, N. Plant phenylacetaldehyde synthase is a bifunctional homotetrameric enzyme that catalyzes phenylalanine decarboxylation and oxidation. J. Biol. Chem. 281 (2006) 23357–23366. [DOI] [PMID: 16766535]

[EC 4.1.1.109 created 2017]

4.1.1.110

Accepted name:

bisphosphomevalonate decarboxylase

Reaction:

(R)-3,5-bisphosphomevalonate = isopentenyl phosphate + CO₂ + phosphate

Other name(s):

mevalonate 3,5-bisphosphate decarboxylase

Systematic name:

(R)-3,5-bisphosphomevalonate carboxy-lyase (isopentenyl-phosphate-forming)

Comments:

The enzyme participates in an alternative mevalonate pathway that takes place in extreme acidophiles of the Thermoplasmatales order. cf. EC 4.1.1.99, phosphomevalonate decarboxylase.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc, PDB

References:

1.	Vinokur, J.M., Cummins, M.C., Korman, T.P. and Bowie, J.U. An adaptation to life in acid through a novel mevalonate pathway. Sci. Rep. 6 (2016) 39737. [DOI] [PMID: 28004831]

[EC 4.1.1.110 created 2018]

4.1.1.111

Accepted name:

siroheme decarboxylase

Reaction:

siroheme = 12,18-didecarboxysiroheme + 2 CO₂

For diagram of siroheme decarboxylase, click here

Other name(s):

sirohaem decarboxylase; nirDLHG (gene name); ahbAB (gene name)

Systematic name:

siroheme carboxy-lyase

Comments:

The enzyme from archaea is involved in an alternative heme biosynthesis pathway. The enzyme from denitrifying bacteria is involved in the heme d1 biosynthesis pathway.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc, PDB

References:

1.	Bali, S., Lawrence, A.D., Lobo, S.A., Saraiva, L.M., Golding, B.T., Palmer, D.J., Howard, M.J., Ferguson, S.J. and Warren, M.J. Molecular hijacking of siroheme for the synthesis of heme and d1 heme. Proc. Natl. Acad. Sci. USA 108 (2011) 18260–18265. [DOI] [PMID: 21969545]
2.	Kuhner, M., Haufschildt, K., Neumann, A., Storbeck, S., Streif, J. and Layer, G. The alternative route to heme in the methanogenic archaeon Methanosarcina barkeri. Archaea 2014:327637 (2014). [DOI] [PMID: 24669201]
3.	Palmer, D.J., Schroeder, S., Lawrence, A.D., Deery, E., Lobo, S.A., Saraiva, L.M., McLean, K.J., Munro, A.W., Ferguson, S.J., Pickersgill, R.W., Brown, D.G. and Warren, M.J. The structure, function and properties of sirohaem decarboxylase^--an enzyme with structural homology to a transcription factor family that is part of the alternative haem biosynthesis pathway. Mol. Microbiol. 93 (2014) 247–261. [DOI] [PMID: 24865947]
4.	Haufschildt, K., Schmelz, S., Kriegler, T.M., Neumann, A., Streif, J., Arai, H., Heinz, D.W. and Layer, G. The crystal structure of siroheme decarboxylase in complex with iron-uroporphyrin III reveals two essential histidine residues. J. Mol. Biol. 426 (2014) 3272–3286. [DOI] [PMID: 25083922]

[EC 4.1.1.111 created 2018]

4.1.1.112

Accepted name:

oxaloacetate decarboxylase

Reaction:

oxaloacetate = pyruvate + CO₂

Other name(s):

oxaloacetate β-decarboxylase; oxalacetic acid decarboxylase; oxalate β-decarboxylase; oxaloacetate carboxy-lyase

Systematic name:

oxaloacetate carboxy-lyase (pyruvate-forming)

Comments:

Requires a divalent metal cation. The enzymes from the fish Gadus morhua (Atlantic cod) and the bacterium Micrococcus luteus prefer Mn²⁺, while those from the bacteria Pseudomonas putida and Pseudomonas aeruginosa prefer Mg²⁺. Unlike EC 7.2.4.2 [oxaloacetate decarboxylase (Na⁺ extruding)], there is no evidence of the enzyme’s involvement in Na⁺ transport.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9024-98-0

References:

1.	Schmitt, A., Bottke, I. and Siebert, G. Eigenschaften einer Oxaloacetat-Decarboxylase aus Dorschmuskulatur. Hoppe-Seyler's Z. Physiol. Chem. 347 (1966) 18–34. [PMID: 5972993]
2.	Herbert, D. Oxalacetic carboxylase of Micrococcus lysodeikticus. Methods Enzymol. 1 (1955) 753–757.
3.	Horton, A.A. and Kornberg, H.L. Oxaloacetate 4-carboxy-lyase from Pseudomonas ovalis chester. Biochim. Biophys. Acta 89 (1964) 381–383. [PMID: 14205502]
4.	Sender, P.D., Martin, M.G., Peiru, S. and Magni, C. Characterization of an oxaloacetate decarboxylase that belongs to the malic enzyme family. FEBS Lett. 570 (2004) 217–222. [PMID: 15251467]
5.	Narayanan, B.C., Niu, W., Han, Y., Zou, J., Mariano, P.S., Dunaway-Mariano, D. and Herzberg, O. Structure and function of PA4872 from Pseudomonas aeruginosa, a novel class of oxaloacetate decarboxylase from the PEP mutase/isocitrate lyase superfamily. Biochemistry 47 (2008) 167–182. [PMID: 18081320]

[EC 4.1.1.112 created 1961 as EC 4.1.1.3, modified 1986, modified 2000, part transferred 2018 to EC 4.1.1.112]

4.1.1.113

Accepted name:

trans-aconitate decarboxylase

Reaction:

trans-aconitate = itaconate + CO₂

Glossary:

trans-aconitate = (E)-prop-1-ene-1,2,3-tricarboxylate
itaconate = 2-methylenesuccinate

Other name(s):

TAD1 (gene name)

Systematic name:

trans-aconitate carboxy-lyase (itaconate-forming)

Comments:

The enzyme, characterized from the smut fungus Ustilago maydis, is involved in an alternative pathway for the biosynthesis of itaconate. cf. EC 4.1.1.6, cis-aconitate decarboxylase.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc

References:

1.	Geiser, E., Przybilla, S.K., Friedrich, A., Buckel, W., Wierckx, N., Blank, L.M. and Bolker, M. Ustilago maydis produces itaconic acid via the unusual intermediate trans-aconitate. Microb. Biotechnol. 9 (2016) 116–126. [PMID: 26639528]

[EC 4.1.1.113 created 2018]

4.1.1.114

Accepted name:

cis-3-alkyl-4-alkyloxetan-2-one decarboxylase

Reaction:

a cis-3-alkyl-4-alkyloxetan-2-one = a cis-alkene + CO₂

Other name(s):

oleB (gene name)

Systematic name:

cis-3-alkyl-4-alkyloxetan-2-one carboxy-lyase (cis-alkene-forming)

Comments:

The enzyme, found in certain bacterial species, catalyses the last step in a pathway for the production of olefins.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc

References:

1.	Christenson, J.K., Richman, J.E., Jensen, M.R., Neufeld, J.Y., Wilmot, C.M. and Wackett, L.P. β-Lactone synthetase found in the olefin biosynthesis pathway. Biochemistry 56 (2017) 348–351. [DOI] [PMID: 28029240]
2.	Christenson, J.K., Jensen, M.R., Goblirsch, B.R., Mohamed, F., Zhang, W., Wilmot, C.M. and Wackett, L.P. Active multienzyme assemblies for long-chain olefinic hydrocarbon biosynthesis. J. Bacteriol. 199 (2017) . [PMID: 28223313]

[EC 4.1.1.114 created 2018]

4.1.1.115

Accepted name:

indoleacetate decarboxylase

Reaction:

(1H-indol-3-yl)acetate = skatole + CO₂

For diagram of indoleacetic acid biosynthesis, click here

Glossary:

(1H-indol-3-yl)acetate = indoleacetate
skatole = 3-methyl-1H-indole

Other name(s):

IAD

Systematic name:

(1H-indol-3-yl)acetate carboxy-lyase (skatole-forming)

Comments:

This glycyl radical enzyme has been isolate from a number of bacterial species. Skatole contributes to the characteristic smell of animal faeces.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc

References:

1.	Liu, D., Wei, Y., Liu, X., Zhou, Y., Jiang, L., Yin, J., Wang, F., Hu, Y., Nanjaraj Urs, A.N., Liu, Y., Ang, E.L., Zhao, S., Zhao, H. and Zhang, Y. Indoleacetate decarboxylase is a glycyl radical enzyme catalysing the formation of malodorant skatole. Nat. Commun. 9:4224 (2018). [PMID: 30310076]

[EC 4.1.1.115 created 2019]

4.1.1.116

Accepted name:

D-ornithine/D-lysine decarboxylase

Reaction:

(1) D-ornithine = putrescine + CO₂
(2) D-lysine = cadaverine + CO₂

For diagram of spermine biosynthesis, click here

Glossary:

cadaverine = pentane-1,5-diamine
putrescine = butane-1,4-diamine

Other name(s):

dokD (gene name); DOKDC

Systematic name:

D-ornithine/D-lysine carboxy-lyase

Comments:

The enzyme, characterized from the bacterium Salmonella typhimurium LT2, is specific for D-ornithine and D-lysine. Requires pyridoxal 5′-phosphate.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc, PDB

References:

1.	Phillips, R.S., Poteh, P., Miller, K.A. and Hoover, T.R. STM2360 encodes a D-ornithine/D-lysine decarboxylase in Salmonella enterica serovar typhimurium. Arch. Biochem. Biophys. 634 (2017) 83–87. [PMID: 29024617]

[EC 4.1.1.116 created 2019]

4.1.1.117

Accepted name:

2-[(L-alanin-3-ylcarbamoyl)methyl]-2-hydroxybutanedioate decarboxylase

Reaction:

2-[(L-alanin-3-ylcarbamoyl)methyl]-2-hydroxybutanedioate = 2-[(2-aminoethylcarbamoyl)methyl]-2-hydroxybutanedioate + CO₂

Glossary:

staphyloferrin B = 5-[(2-{[(3S)-5-{[(2S)-2-amino-2-carboxyethyl]amino}-3-carboxy-3-hydroxy-5-oxopentanoyl]amino}ethyl)amino]-2,5-dioxopentanoate

Other name(s):

sbnH (gene name)

Systematic name:

2-[(L-alanin-3-ylcarbamoyl)methyl]-2-hydroxybutanedioate carboxy-lyase (2-[(2-aminoethylcarbamoyl)methyl]-2-hydroxybutanedioate-forming)

Comments:

The enzyme, characterized from the bacterium Staphylococcus aureus, participates in the biosynthesis of the siderophore staphyloferrin B.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc

References:

1.	Cheung, J., Beasley, F.C., Liu, S., Lajoie, G.A. and Heinrichs, D.E. Molecular characterization of staphyloferrin B biosynthesis in Staphylococcus aureus. Mol. Microbiol. 74 (2009) 594–608. [PMID: 19775248]

[EC 4.1.1.117 created 2019]

4.1.1.118

Accepted name:

isophthalyl-CoA decarboxylase

Reaction:

isophthalyl-CoA = benzoyl-CoA + CO₂

Other name(s):

IPCD

Systematic name:

isophthalyl-CoA carboxy-lyase

Comments:

The enzyme, characterized from the bacterium Syntrophorhabdus aromaticivorans, participates in an anaerobic isophthalate degradation pathway. The enzyme requires a prenylated flavin mononucleotide cofactor.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc

References:

1.	Junghare, M., Spiteller, D. and Schink, B. Anaerobic degradation of xenobiotic isophthalate by the fermenting bacterium Syntrophorhabdus aromaticivorans. ISME J. 13 (2019) 1252–1268. [PMID: 30647456]

[EC 4.1.1.118 created 2019]

4.1.1.119

Accepted name:

phenylacetate decarboxylase

Reaction:

phenylacetate = toluene + CO₂

Other name(s):

phdB (gene name)

Systematic name:

phenylacetate carboxy-lyase

Comments:

This bacterial enzyme, isolated from anoxic, toluene-producing microbial communities, is a glycyl radical enzyme. It needs to be activated by a dedicated activating enzyme (PhdA). The activase catalyses the reductive cleavage of AdoMet, producing a 5′-deoxyadenosyl radical that leads to the production of the glycyl radical in PhdB.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc

References:

1.	Zargar, K., Saville, R., Phelan, R.M., Tringe, S.G., Petzold, C.J., Keasling, J.D. and Beller, H.R. In vitro characterization of phenylacetate decarboxylase, a novel enzyme catalyzing toluene biosynthesis in an anaerobic microbial community. Sci. Rep. 6:31362 (2016). [PMID: 27506494]
2.	Beller, H.R., Rodrigues, A.V., Zargar, K., Wu, Y.W., Saini, A.K., Saville, R.M., Pereira, J.H., Adams, P.D., Tringe, S.G., Petzold, C.J. and Keasling, J.D. Discovery of enzymes for toluene synthesis from anoxic microbial communities. Nat. Chem. Biol. 14 (2018) 451–457. [PMID: 29556105]
3.	Rodrigues, A.V., Tantillo, D.J., Mukhopadhyay, A., Keasling, J.D. and Beller, H. Insights into the mechanism of phenylacetate decarboxylase (PhdB), a toluene-producing glycyl radical enzyme. ChemBioChem (2019) . [PMID: 31512343]

[EC 4.1.1.119 created 2019]

4.1.1.120

Accepted name:

3-oxoisoapionate decarboxylase

Reaction:

3-oxoisoapionate = L-erythrulose + CO₂

Glossary:

3-oxoisoapionate = 2,4-dihydroxy-2-(hydroxymethyl)-3-oxobutanoate

Other name(s):

oiaC (gene name)

Systematic name:

3-oxoisoapionate carboxy-lyase

Comments:

The enzyme, characterized from several bacterial species, is involved in the degradation of D-apionate. Stereospecificity of 3-oxoisoapionate has not been determined.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc

References:

Carter, M.S., Zhang, X., Huang, H., Bouvier, J.T., Francisco, B.S., Vetting, M.W., Al-Obaidi, N., Bonanno, J.B., Ghosh, A., Zallot, R.G., Andersen, H.M., Almo, S.C. and Gerlt, J.A. Functional assignment of multiple catabolic pathways for D-apiose. Nat. Chem. Biol. 14 (2018) 696–705. [DOI] [PMID: 29867142]

[EC 4.1.1.120 created 2020]

4.1.1.121

Accepted name:

3-oxoisoapionate-4-phosphate decarboxylase

Reaction:

3-oxoisoapionate 4-phosphate = L-erythrulose 1-phosphate + CO₂

Glossary:

3-oxoisoapionate = 2,4-dihydroxy-2-(hydroxymethyl)-3-oxobutanoate

Other name(s):

oiaX (gene name)

Systematic name:

3-oxoisoapionate 4-phosphate carboxy-lyase

Comments:

The enzyme, characterized from several bacterial species, participates in the degradation of D-apionate. It belongs to the RuBisCO-like-protein (RLP) superfamily. Stereospecificity of 3-oxoisoapionate 4-phosphate has not been determined.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc

References:

[EC 4.1.1.121 created 2020]

4.1.1.122

Accepted name:

L-cysteate decarboxylase

Reaction:

L-cysteate = taurine + CO₂

Other name(s):

CAD

Systematic name:

L-cysteate carboxy-lyase (taurine-forming)

Comments:

Requires pyridoxal 5′-phosphate. The enzyme, characterized from chicken, is specific for L-cysteate and has poor activity with 3-sulfino-L-alanine. cf. EC 4.1.1.29, sulfinoalanine decarboxylase.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc

References:

1.	Malatesta, M., Mori, G., Acquotti, D., Campanini, B., Peracchi, A., Antin, P.B. and Percudani, R. Birth of a pathway for sulfur metabolism in early amniote evolution. Nat Ecol Evol 4 (2020) 1239–1246. [DOI] [PMID: 32601391]

[EC 4.1.1.122 created 2022]

4.1.1.123

Accepted name:

phenyl-phosphate phosphatase/carboxylase

Reaction:

4-hydroxybenzoate + phosphate = phenyl phosphate + CO₂ + H₂O

Other name(s):

phenyl phosphate carboxylase

Systematic name:

4-hydroxybenzoate carboxy-lyase (phenyl phosphate-forming)

Comments:

The enzyme, characterized from the bacterium Thauera aromatica, participates in an anaerobic phenol degradation pathway. It catalyses the para dephosphorylation and carboxylation of phenylphosphate to 4-hydroxybenzoate. The enzyme from Thauera aromatica consists of four different subunits and requires K⁺ and a divalent metal cation (Mg²⁺ or Mn²⁺) for activity. It is strongly inhibited by oxygen.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc

References:

1.	Schuhle, K. and Fuchs, G. Phenylphosphate carboxylase: a new C-C lyase involved in anaerobic phenol metabolism in Thauera aromatica. J. Bacteriol. 186 (2004) 4556–4567. [DOI] [PMID: 15231788]

[EC 4.1.1.123 created 2022]

4.1.1.124

Accepted name:

malonyl-[acp] decarboxylase

Reaction:

malonyl-[acp] = acetyl-[acp] + CO₂

Other name(s):

decarboxylative ketosynthase; bryQ (gene name); mupG (gene name); pksF (gene name); curC (gene name); jamG (gene name); pedM (gene name)

Systematic name:

malonyl-[acyl-carrier protein] carboxy-lyase

Comments:

This family of enzymes participates in a process that introduces a methyl branch into nascent polyketide products. The process begins with EC 4.1.1.124, malonyl-[acp] decarboxylase, which converts the common extender unit malonyl-[acp] to acetyl-[acp]. The enzyme is a mutated form of a ketosynthase enzyme, in which a Cys residue in the active site is modified to a Ser residue, leaving the decarboxylase function intact, but nulifying the ability of the enzyme to form a carbon-carbon bond. Next, EC 2.3.3.22, 3-carboxymethyl-3-hydroxy-acyl-[acp] synthase, utilizes the acetyl group to introduce the branch at the β position of 3-oxoacyl intermediates attached to a polyketide synthase, forming a 3-hydroxy-3-carboxymethyl intermediate. This is followed by dehydration catalysed by EC 4.2.1.181, 3-carboxymethyl-3-hydroxy-acyl-[acp] dehydratase (often referred to as an ECH₁ domain), leaving a 3-carboxymethyl group and forming a double bond between the α and β carbons. The process concludes with decarboxylation catalysed by EC 4.1.1.125, 4-carboxy-3-alkylbut-2-enoyl-[acp] decarboxylase (often referred to as an ECH₂ domain), leaving a methyl branch at the β carbon. The enzymes are usually encoded by a cluster of genes referred to as an "HMGS cassette", based on the similarity of the key enzyme to EC 2.3.3.10, hydroxymethylglutaryl-CoA synthase. cf. EC 4.1.1.87, malonyl-[malonate decarboxylase] decarboxylase.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc

References:

1.	Simunovic, V. and Muller, R. 3-hydroxy-3-methylglutaryl-CoA-like synthases direct the formation of methyl and ethyl side groups in the biosynthesis of the antibiotic myxovirescin A. Chembiochem 8 (2007) 497–500. [DOI] [PMID: 17330904]
2.	Wu, J., Hothersall, J., Mazzetti, C., O'Connell, Y., Shields, J.A., Rahman, A.S., Cox, R.J., Crosby, J., Simpson, T.J., Thomas, C.M. and Willis, C.L. In vivo mutational analysis of the mupirocin gene cluster reveals labile points in the biosynthetic pathway: the "leaky hosepipe" mechanism. Chembiochem 9 (2008) 1500–1508. [DOI] [PMID: 18465759]
3.	Buchholz, T.J., Rath, C.M., Lopanik, N.B., Gardner, N.P., Hakansson, K. and Sherman, D.H. Polyketide β-branching in bryostatin biosynthesis: identification of surrogate acetyl-ACP donors for BryR, an HMG-ACP synthase. Chem. Biol. 17 (2010) 1092–1100. [DOI] [PMID: 21035732]

[EC 4.1.1.124 created 2023]

4.1.1.125

Accepted name:

4-carboxy-3-alkylbut-2-enoyl-[acp] decarboxylase

Reaction:

a 4-carboxy-3-alkylbut-2-enoyl-[acp] = a 3-alkylbut-2-enoyl-[acp] + CO₂

Other name(s):

aprG (gene name); corG (gene name); pedI (gene name); mupK (gene name); 3-carboxymethyl-alk-2-enyl-[acyl-carrier protein] decarboxylase

Systematic name:

4-carboxy-3-alkylbut-2-enoyl-[acyl-carrier protein] carboxy-lyase

Comments:

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc

References:

1.	Geders, T.W., Gu, L., Mowers, J.C., Liu, H., Gerwick, W.H., Hakansson, K., Sherman, D.H. and Smith, J.L. Crystal structure of the ECH₂ catalytic domain of CurF from Lyngbya majuscula. Insights into a decarboxylase involved in polyketide chain β-branching. J. Biol. Chem. 282 (2007) 35954–35963. [DOI] [PMID: 17928301]
2.	Erol, O., Schaberle, T.F., Schmitz, A., Rachid, S., Gurgui, C., El Omari, M., Lohr, F., Kehraus, S., Piel, J., Muller, R. and Konig, G.M. Biosynthesis of the myxobacterial antibiotic corallopyronin A. Chembiochem 11 (2010) 1253–1265. [DOI] [PMID: 20503218]
3.	Grindberg, R.V., Ishoey, T., Brinza, D., Esquenazi, E., Coates, R.C., Liu, W.T., Gerwick, L., Dorrestein, P.C., Pevzner, P., Lasken, R. and Gerwick, W.H. Single cell genome amplification accelerates identification of the apratoxin biosynthetic pathway from a complex microbial assemblage. PLoS One 6:e18565 (2011). [DOI] [PMID: 21533272]

[EC 4.1.1.125 created 2023]

4.1.1.126

Accepted name:

anhydromevalonate phosphate decarboxylase

Reaction:

trans-anhydromevalonate 5-phosphate = 3-methylbut-3-en-1-yl phosphate + CO₂

Glossary:

trans-anhydromevalonate 5-phosphate = (2E)-3-methyl-5-phosphooxypent-2-enoate
3-methylbut-3-en-1-yl phosphate = isopentenyl phosphate

Systematic name:

trans-anhydromevalonate 5-phosphate carboxy-lyase

Comments:

The enzyme catalyses a step in the archaeal prenyl diphosphate biosynthesis pathway. It requires a prenylated flavin cofactor that is produced by EC 2.5.1.129, flavin prenyltransferase.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc

References:

1.	Yoshida, R., Yoshimura, T. and Hemmi, H. Reconstruction of the "archaeal" mevalonate pathway from the methanogenic archaeon Methanosarcina mazei in Escherichia coli cells. Appl. Environ. Microbiol. 86:e02889-19 (2020). [DOI] [PMID: 31924615]

[EC 4.1.1.126 created 2023]

4.1.1.127

Accepted name:

carboxyaminopropylagmatine decarboxylase

Reaction:

N¹-[(S)-3-amino-3-carboxypropyl]agmatine = N¹-(3-aminopropyl)agmatine + CO₂

Glossary:

N¹-[(S)-3-amino-3-carboxypropyl]agmatine = carboxyaminopropylagmatine
N¹-(3-aminopropyl)agmatine = aminopropylagmatine

Other name(s):

sll0873 (locus name)

Systematic name:

N¹-[(S)-3-amino-3-carboxypropyl]agmatine carboxy-lyase

Comments:

A pyridoxal 5′-phosphate protein. The enzyme, characterized from the cyanobacterium Synechocystis sp. PCC 6803, participates in a biosynthetic pathway for spermidine.

Links to other databases:

BRENDA, EXPASY, KEGG, MetaCyc

References:

1.	Xi, H., Nie, X., Gao, F., Liang, X., Li, H., Zhou, H., Cai, Y. and Yang, C. A bacterial spermidine biosynthetic pathway via carboxyaminopropylagmatine. Sci Adv 9:eadj9075 (2023). [DOI] [PMID: 37878710]

[EC 4.1.1.127 created 2024]