Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB)

Proposed Changes to the Enzyme List

The entries below are proposed additions and amendments to the Enzyme Nomenclature list. The entries below are proposed additions and amendments to the Enzyme Nomenclature list. They were prepared for the NC-IUBMB by Kristian Axelsen, Ron Caspi, Ture Damhus, Shinya Fushinobu, Julia Hauenstein, Antje Jäde, Masaaki Kotera, Andrew McDonald, Gerry Moss, Ida Schomburg and Keith Tipton. Comments and suggestions on these draft entries should be sent to Dr Andrew McDonald (Department of Biochemistry, Trinity College Dublin, Dublin 2, Ireland). The date on which an enzyme will be made official is appended after the EC number. To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.

An asterisk before "EC' indicates that this is an amendment to an existing enzyme rather than a new enzyme entry.


Contents

EC 1.1.1.434 2-dehydro-3-deoxy-L-fuconate 4-dehydrogenase (12 January 2023)
EC 1.1.1.435 L-fucose dehydrogenase (12 January 2023)
EC 1.1.1.436 lactate dehydrogenase (NAD+,ferredoxin) (12 January 2023)
EC 1.1.1.437 5-dehydrofumagillol 5-reductase (12 January 2023)
EC 1.3.1.110 transferred now EC 1.1.1.436 (12 January 2023)
EC 1.3.1.125 acrylate reductase (12 January 2023)
EC 1.3.2.4 fumarate reductase (cytochrome) (12 January 2023)
EC 1.4.2.2 nicotine dehydrogenase (12 January 2023)
EC 1.4.2.3 pseudooxynicotine dehydrogenase (12 January 2023)
EC 1.4.3.24 transferred now EC 1.4.2.3 (12 January 2023)
EC 1.4.3.27 homospermidine oxidase (12 January 2023)
EC 1.14.11.80 methylcytosine dioxygenase (12 January 2023)
EC 1.14.11.81 (–)-cyclopenine synthase (12 January 2023)
EC 1.14.11.82 5-dehydro-6-demethoxyfumagillol dioxygenase (12 January 2023)
*EC 1.14.13.211 rifampicin monooxygenase (12 January 2023)
*EC 1.14.14.173 2,4,6-trichlorophenol monooxygenase (12 January 2023)
EC 1.14.14.184 5-dehydro-6-demethoxyfumagillol synthase (12 January 2023)
EC 1.21.98.5 tetraether lipid synthase (12 January 2023)
EC 2.1.1.386 small RNA 2'-O-methyltransferase (12 January 2023)
EC 2.1.1.387 5-dehydro-6-demethoxy-6-hydroxyfumagillol O-methyltransferase (12 January 2023)
EC 2.3.1.311 tRNA carboxymetyluridine synthase (12 January 2023)
EC 2.4.1.390 4,3-α-glucanotransferase (12 January 2023)
EC 2.4.1.391 β-1,2-glucosyltransferase (12 January 2023)
EC 2.4.1.392 3-O-β-D-glucopyranosyl-β-D-glucuronide phosphorylase (12 January 2023)
EC 2.5.1.4 transferred now EC 4.4.1.42 (12 January 2023)
EC 2.6.1.8 deleted (12 January 2023)
EC 2.7.1.239 α-D-ribose-1-phosphate 5-kinase (ATP) (12 January 2023)
EC 2.7.8.48 ceramide phosphoethanolamine synthase (12 January 2023)
EC 3.1.1.120 L-fucono-1,5-lactonase (12 January 2023)
EC 3.1.3.109 ribulose-1,5-bisphosphate 5-phosphatase (12 January 2023)
EC 3.2.1.218 α-3'-ketoglucosidase (12 January 2023)
EC 3.2.1.219 palatinase (12 January 2023)
EC 3.5.1.61 transferred now EC 4.3.3.8 (12 January 2023)
EC 3.6.1.76 prenyl-diphosphate phosphatase (12 January 2023)
EC 3.13.2.2 transferred now EC 4.4.1.42 (12 January 2023)
*EC 4.1.3.27 anthranilate synthase (12 January 2023)
EC 4.1.99.27 cyclopenase (12 January 2023)
EC 4.2.2.28 α-L-rhamnosyl-(1→4)-β-D-glucuronate lyase (12 January 2023)
EC 4.2.3.206 (–)-cyatha-3,12-diene synthase (12 January 2023)
EC 4.2.3.207 neoverrucosan-5β-ol synthase (12 January 2023)
EC 4.2.3.208 verrucosan-2β-ol synthase (12 January 2023)
EC 4.2.3.209 (R)-axinyssene synthase (12 January 2023)
EC 4.2.3.210 lydicene synthase (12 January 2023)
EC 4.2.3.211 (+)-exo-β-bergamotene synthase (12 January 2023)
EC 4.3.3.8 mimosinase (12 January 2023)
EC 4.4.1.42 S-adenosyl-L-methionine lyase (12 January 2023)
EC 4.4.1.43 canavanine-γ-lyase (12 January 2023)
EC 4.8.1.5 thiohydroximate-O-sulfate sulfate/sulfur-lyase (nitrile-forming) (12 January 2023)
EC 4.8.1.6 N-(sulfonatooxy)alkenimidothioic acid sulfate-lyase (epithionitrile-forming) (12 January 2023)
EC 4.8.1.7 phenyl-N-(sulfonatooxy)methanimidothioate sulfolyase (12 January 2023)
EC 4.8.1.8 N-(sulfonatooxy)prop-2-enimidothioate sulfolyase (12 January 2023)
EC 5.3.3.24 neopinone isomerase (12 January 2023)
EC 7.1.3.2 transferred now EC 7.2.3.1 (12 January 2023)
EC 7.2 Catalysing the translocation of inorganic cations (12 January 2023)
EC 7.2.3 Linked to the hydrolysis of diphosphate (12 January 2023)
EC 7.2.3.1 Na+-exporting diphosphatase (12 January 2023)

EC 1.1.1.434

Accepted name: 2-dehydro-3-deoxy-L-fuconate 4-dehydrogenase

Reaction: 2-dehydro-3-deoxy-L-fuconate + NAD+ = 2,4-didehydro-3-deoxy-L-fuconate + NADH + H+

For diagram of reaction click here

Glossary: 2-dehydro-3-deoxy-L-fuconate = (4S,5S)-4,5-dihydroxy-2-oxohexanoate
2,4-didehydro-3-deoxy-L-fuconate = (5S)-5-hydroxy-2,4-dioxohexanoate

Systematic name: 2-dehydro-3-deoxy-L-fuconate:NAD+ 4-oxidoreductase

Comments: The enzyme, originally described from the bacterium Xanthomonas campestris pv. campestris, participates in an L-fucose degradation pathway. It can also act on 2-dehydro-3-deoxy-L-galactonate and 2-dehydro-3-deoxy-D-pentonate.

References:

1. Yew, W.S., Fedorov, A.A., Fedorov, E.V., Rakus, J.F., Pierce, R.W., Almo, S.C. and Gerlt, J.A. Evolution of enzymatic activities in the enolase superfamily: L-fuconate dehydratase from Xanthomonas campestris. Biochemistry 45 (2006) 14582-14597. [PMID: 17144652]

2. Watanabe, S., Fukumori, F., Nishiwaki, H., Sakurai, Y., Tajima, K. and Watanabe, Y. Novel non-phosphorylative pathway of pentose metabolism from bacteria. Sci. Rep. 9 (2019) 155. [PMID: 30655589]

[EC 1.1.1.434 created 2022]

EC 1.1.1.435

Accepted name: L-fucose dehydrogenase

For diagram of reaction click here

Reaction: β-L-fucopyranose + NADP+ = L-fucono-1,5-lactone + NADPH + H+

Systematic name: β-L-fucopyranose:NADP+ 1-oxidoreductase

Comments: The enzyme, characterized from the bacterium Burkholderia multivorans, participates in an L-fucose degradation pathway. The enzyme catalyses the oxidation of β-L-fucopyranose to L-fucono-1,5-lactone, which is unstable and is rapidly converted to L-fucono-1,4-lactone. The α anomer is not recognized. The enzyme can also act on β-L-galactopyranose and D-arabinose with lower activity. NADP is a better cosubstrate than NAD.

References:

1. Hobbs, M.E., Vetting, M., Williams, H.J., Narindoshvili, T., Kebodeaux, D.M., Hillerich, B., Seidel, R.D., Almo, S.C. and Raushel, F.M. Discovery of an L-fucono-1,5-lactonase from cog3618 of the amidohydrolase superfamily. Biochemistry 52 (2013) 239-253. [PMID: 23214453]

[EC 1.1.1.435 created 2022]

EC 1.1.1.436

Accepted name: lactate dehydrogenase (NAD+,ferredoxin)

Reaction: lactate + 2 NAD+ + 2 reduced ferredoxin [iron-sulfur] cluster = pyruvate + 2 NADH + 2 oxidized ferredoxin [iron-sulfur] cluster

Other name(s): electron bifurcating LDH/Etf complex

Systematic name: lactate:NAD+,ferredoxin oxidoreductase

Comments: The enzyme, isolated from the bacterium Acetobacterium woodii, uses flavin-based electron confurcation to drive endergonic lactate oxidation with NAD+ as oxidant at the expense of simultaneous exergonic electron flow from reduced ferredoxin to NAD+.

References:

1. Weghoff, M.C., Bertsch, J. and Muller, V. A novel mode of lactate metabolism in strictly anaerobic bacteria. Environ. Microbiol. 17 (2015) 670-677. [PMID: 24762045]

[EC 1.1.1.436 created 2015 as EC 1.3.1.110, transferred 2022 to EC 1.1.1.436]

EC 1.1.1.437

Accepted name: 5-dehydrofumagillol 5-reductase

Reaction: fumagillol + NADP+ = 5-dehydrofumagillol + NADPH + H+

For diagram of reaction click here

Glossary: fumagillol = (3R,4S,5S,6R)-5-methoxy-4-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]-1-oxaspiro[2.5]octan-6-ol

Other name(s): af490 (gene name); Fma-KR

Systematic name: fumagillol:NADP+ 5-oxidoreductase

Comments: The enzyme, characterized from the mold Aspergillus fumigatus, participates in the biosynthesis of the meroterpenoid fumagillin. It is a partial polyketide synthase (PKS) consisting of only a dehydratase (DH) and a ketoreductase (KR) domain.

References:

1. Lin, H.C., Tsunematsu, Y., Dhingra, S., Xu, W., Fukutomi, M., Chooi, Y.H., Cane, D.E., Calvo, A.M., Watanabe, K. and Tang, Y. Generation of complexity in fungal terpene biosynthesis: discovery of a multifunctional cytochrome P450 in the fumagillin pathway. J. Am. Chem. Soc. 136 (2014) 4426-4436. [PMID: 24568283]

[EC 1.1.1.437 created 2022]

[EC 1.3.1.110 Transferred entry: lactate dehydrogenase (NAD+, ferredoxin). Now EC 1.1.1.436, lactate dehydrogenase (NAD+,ferredoxin) (EC 1.3.1.110 created 2015, deleted 2022)]

EC 1.3.1.125

Accepted name: acrylate reductase

Reaction: propanoate + NAD+ = acrylate + NADH + H+

Other name(s): ard (gene name); NADH:acrylate oxidoreductase

Systematic name: propanoate:NAD+ oxidoreductase

Comments: The enzyme, characterized from the marine bacterium Vibrio harveyi, enables the organism to utilize acrylate as the terminal electron acceptor for NADH regeneration under anaerobic conditions.

References:

1. Bertsova, Y.V., Serebryakova, M.V., Baykov, A.A. and Bogachev, A.V. A novel, NADH-dependent acrylate reductase in Vibrio harveyi. Appl. Environ. Microbiol. 88 (2022) e0051922. [PMID: 35612301]

[EC 1.3.1.125 created 2022]

EC 1.3.2.4

Accepted name: fumarate reductase (cytochrome)

Reaction: succinate + 2 ferricytochrome c = fumarate + 2 ferrocytochrome c

Other name(s): fccA (gene name); fcc3 (gene name); flavocytochrome c3

Systematic name: succinate:ferricytochrome-c oxidoreductase

Comments: Contains a non-covalently bound FAD cofactor and four heme c groups. The enzyme, characterized from the bacterium Shewanella frigidimarina, is a soluble periplasmic protein that functions as a terminal electron acceptor during anaerobic growth. The direct electron donor is the membrane-bound tetraheme c-type cytochrome CymA (EC 7.1.1.8, quinol—cytochrome-c reductase), which receives the electrons from the membrane quinol pool.

References:

1. Pealing, S.L., Black, A.C., Manson, F.D., Ward, F.B., Chapman, S.K. and Reid, G.A. Sequence of the gene encoding flavocytochrome c from Shewanella putrefaciens: a tetraheme flavoenzyme that is a soluble fumarate reductase related to the membrane-bound enzymes from other bacteria. Biochemistry 31 (1992) 12132-12140. [PMID: 1333793]

2. Pealing, S.L., Cheesman, M.R., Reid, G.A., Thomson, A.J., Ward, F.B. and Chapman, S.K. Spectroscopic and kinetic studies of the tetraheme flavocytochrome c from Shewanella putrefaciens NCIMB400. Biochemistry 34 (1995) 6153-6158. [PMID: 7742319]

3. Gordon, E.HJ., Pealing, S.L., Chapman, S.K., Ward, F.B. and Reid, G.A. Physiological function and regulation of flavocytochrome c3, the soluble fumarate reductase from Shewanella putrefaciens NCIMB 400. Microbiology (Reading) 144 (1998) 937-945. [PMID: 9579067]

4. Doherty, M.K., Pealing, S.L., Miles, C.S., Moysey, R., Taylor, P., Walkinshaw, M.D., Reid, G.A. and Chapman, S.K. Identification of the active site acid/base catalyst in a bacterial fumarate reductase: a kinetic and crystallographic study. Biochemistry 39 (2000) 10695-10701. [PMID: 10978153]

5. Reid, G.A., Miles, C.S., Moysey, R.K., Pankhurst, K.L. and Chapman, S.K. Catalysis in fumarate reductase. Biochim. Biophys Acta 1459 (2000) 310-315. [PMID: 11004445]

6. Schwalb, C., Chapman, S.K. and Reid, G.A. The membrane-bound tetrahaem c-type cytochrome CymA interacts directly with the soluble fumarate reductase in Shewanella. Biochem Soc Trans. 30 (2002) 658-662. [PMID: 12196158]

[EC 1.3.2.4 created 2022]

EC 1.4.2.2

Accepted name: nicotine dehydrogenase

Reaction: (S)-nicotine + 2 ferricytochrome c = N-methylmyosmine + 2 ferrocytochrome c + 2 H+

Glossary: (S)-nicotine = 3-[(S)-1-methylpyrrolidin-2-yl]pyridine
N-methylmyosamine = 3-(1-methyl-4,5-dihydro-1H-pyrrol-2-yl)pyridine

Other name(s): nicA2 (gene name)

Systematic name: (S)-nicotine:cytochrome c oxidoreductase (N-methylmimosine-forming)

Comments: The enzyme, characterized from the bacterium Pseudomonas putida S16, contains an FAD cofactor and belongs to the flavin-containing amine oxidase family. The enzyme from this bacterium is specific for the c-type cytochrome CycN. The product undergoes spontaneous hydrolysis to form pseudooxynicotine.

References:

1. Tang, H., Wang, L., Wang, W., Yu, H., Zhang, K., Yao, Y. and Xu, P. Systematic unraveling of the unsolved pathway of nicotine degradation in Pseudomonas. PLoS Genet. 9 (2013) e1003923. [PMID: 24204321]

2. Dulchavsky, M., Clark, C.T., Bardwell, J.CA. and Stull, F. A cytochrome c is the natural electron acceptor for nicotine oxidoreductase. Nat. Chem. Biol. 17 (2021) 344-350. [PMID: 33432238]

[EC 1.4.2.2 created 2022]

EC 1.4.2.3

Accepted name: pseudooxynicotine dehydrogenase

Reaction: pseudooxynicotine + H2O + 2 ferricytochrome c = 4-oxo-4-(pyridin-3-yl)butanal + methylamine + 2 ferrocytochrome c + 2 H+

Glossary: pseudooxynicotine = 4-(methylamino)-1-(pyridin-3-yl)butan-1-one

Other name(s): pnaO (gene name)

Systematic name: 4-(methylamino)-1-(pyridin-3-yl)butan-1-one:c-type cytochrome oxidoreductase (methylamine releasing)

Comments: Contains one non-covalently bound FAD molecule per dimer. This enzyme, characterized from the soil bacteria Pseudomonas sp. HZN6 and Pseudomonas putida S16, is involved the nicotine degradation.

References:

1. Qiu, J., Ma, Y., Wen, Y., Chen, L., Wu, L. and Liu, W. Functional identification of two novel genes from Pseudomonas sp. strain HZN6 involved in the catabolism of nicotine. Appl. Environ. Microbiol. 78 (2012) 2154-2160. [PMID: 22267672]

2. Choudhary, V., Wu, K., Zhang, Z., Dulchavsky, M., Barkman, T., Bardwell, J.CA. and Stull, F. The enzyme pseudooxynicotine amine oxidase from Pseudomonas putida S16 is not an oxidase, but a dehydrogenase. J. Biol. Chem. (2022) 102251. [PMID: 35835223]

[EC 1.4.2.3 created 2012 as EC 1.4.3.24, transferred 2022 to EC 1.4.2.3]

[EC 1.4.3.24 Transferred entry: pseudooxynicotine oxidase, now classified as EC 1.4.2.3, pseudooxynicotine dehydrogenase (EC 1.4.3.24 created 2012, deleted 2022)]

EC 1.4.3.27

Accepted name: homospermidine oxidase

Reaction: sym-homospermidine + 2 O2 + H2O = 1-formylpyrrolizidine + 2 H2O2 + 2 NH3 (overall reaction)
(1a) sym-homospermidine + O2 = N-(4-aminobutylpyrrolinium) ion + H2O2 + NH3
(1b) N-(4-aminobutylpyrrolinium) ion + O2 + H2O = N-(4-oxobutylpyrrolinium) ion + NH3 + H2O2
(1c) N-(4-oxobutylpyrrolinium) ion = 1-formylpyrrolizidine (spontaneous)

Glossary: (-)-trachelanthamidine = (1R,7aS)-hexahydro-1H-pyrrolizin-1-ylmethanol

Other name(s): HSO

Systematic name: homospermidine:oxygen oxidase (deaminating, cyclizing)

Comments: The copper-containing enzyme has been isolated from the plant Heliotropium indicum. It is involved in the biosynthesis of the pyrrolizidine alkaloid (-)-trachelanthamidine which acts as a secondary metabolite for the defense against herbivores. The oxidation of sym-homospermidine proceeds in three steps and results in a cyclization.

References:

1. Zakaria, M.M., Stegemann, T., Sievert, C., Kruse, L.H., Kaltenegger, E., Girreser, U., Cicek, S.S., Nimtz, M. and Ober, D. Insights into polyamine metabolism: homospermidine is double-oxidized in two discrete steps by a single copper-containing amine oxidase in pyrrolizidine alkaloid biosynthesis. Plant Cell 34 (2022) 2364-2382. [PMID: 35212762]

[EC 1.4.3.27 created 2022]

EC 1.14.11.80

Accepted name: methylcytosine dioxygenase

Reaction: (1) 5-methylcytosine in DNA + 2-oxoglutarate + O2 = 5-hydroxymethylcytosine in DNA + succinate + CO2
(2) 5-hydroxymethylcytosine in DNA + 2-oxoglutarate + O2 = 5-formylcytosine in DNA + succinate + CO2 + H2O
(3) 5-formylcytosine in DNA + 2-oxoglutarate + O2 = 5-carboxycytosine in DNA + succinate + CO2

Other name(s): TET1 (gene name); TET2 (gene name); TET3 (gene name)

Systematic name: 5-methylcytosine in DNA,2-oxoglutarate:oxygen oxidoreductase

Comments: The TET proteins mediate iterative oxidation of 5-methylcytosine in DNA (5mc) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC are recognized by EC 3.2.2.29, thymine-DNA glycosylase (TDG), which excises them, leaving an apyrimidinic site. Coupled with the base excision repair (BER) pathway, these activities result in a cytosine demethylation pathway.

References:

1. Ito, S., D'Alessio, A.C., Taranova, O.V., Hong, K., Sowers, L.C. and Zhang, Y. Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification. Nature 466 (2010) 1129-1133. [PMID: 20639862]

2. Ito, S., Shen, L., Dai, Q., Wu, S.C., Collins, L.B., Swenberg, J.A., He, C. and Zhang, Y. Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333 (2011) 1300-1303. [PMID: 21778364]

3. He, Y.F., Li, B.Z., Li, Z., Liu, P., Wang, Y., Tang, Q., Ding, J., Jia, Y., Chen, Z., Li, L., Sun, Y., Li, X., Dai, Q., Song, C.X., Zhang, K., He, C. and Xu, G.L. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333 (2011) 1303-1307. [PMID: 21817016]

4. Maiti, A. and Drohat, A.C. Thymine DNA glycosylase can rapidly excise 5-formylcytosine and 5-carboxylcytosine: potential implications for active demethylation of CpG sites. J. Biol. Chem. 286 (2011) 35334-35338. [PMID: 21862836]

5. Zhang, L., Lu, X., Lu, J., Liang, H., Dai, Q., Xu, G.L., Luo, C., Jiang, H. and He, C. Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA. Nat. Chem. Biol. 8 (2012) 328-330. [PMID: 22327402]

[EC 1.14.11.80 created 2022]

EC 1.14.11.81

Accepted name: (–)-cyclopenine synthase

Reaction: (1) cyclopeptine + 2-oxoglutarate + O2 = dehydrocyclopeptine + succinate + CO2 + H2O
(2) dehydrocyclopeptine + 2-oxoglutarate + O2 = (–)-cyclopenine + succinate + CO2

Glossary: cyclopeptine = (3S)-3-benzyl-4-methyl-3,4-dihydro-1H-1,4-benzodiazepine-2,5-dione
(–)-cyclopenine = (3S,3'R)-4-methyl-3'-phenyl-1H-spiro[1,4-benzodiazepine-3,2'-oxirane]-2,5-dione

Other name(s): asqJ (gene name)

Systematic name: cyclopeptine,2-oxoglutarate:oxygen oxidoreductase ((–)-cyclopenine-forming)

Comments: This fungal enzyme is involved in the biosynthesis of quinolone compounds. it catalyses two oxidation reactions: the first reaction results in a desaturation; the second reaction is a monooxygenation of the double bond, forming an epoxide. The enzyme is also active with 4'-methoxycyclopeptine.

References:

1. Nover, L. and Luckner, M. Mixed functional oxygenations during the biosynthesis of cyclopenin and cyclopenol, benzodiazepine alkaloids of Penicillium cyclopium westling. Incorporation of molecular oxygen and NIH-shift. FEBS Lett. 3 (1969) 292-296. [PMID: 11947032]

2. Ishikawa, N., Tanaka, H., Koyama, F., Noguchi, H., Wang, C.C., Hotta, K. and Watanabe, K. Non-heme dioxygenase catalyzes atypical oxidations of 6,7-bicyclic systems to form the 6,6-quinolone core of viridicatin-type fungal alkaloids. Angew. Chem. Int. Ed. Engl. 53 (2014) 12880-12884. [PMID: 25251934]

3. Brauer, A., Beck, P., Hintermann, L. and Groll, M. Structure of the dioxygenase AsqJ: Mechanistic insights into a one-pot multistep quinolone antibiotic biosynthesis. Angew. Chem. Int. Ed. Engl. 55 (2016) 422-426. [PMID: 26553478]

4. Chang, W.C., Li, J., Lee, J.L., Cronican, A.A. and Guo, Y. Mechanistic investigation of a non-heme iron enzyme catalyzed epoxidation in (–)-4'-methoxycyclopenin biosynthesis. J. Am. Chem. Soc. 138 (2016) 10390-10393. [PMID: 27442345]

5. Song, X., Lu, J. and Lai, W. Mechanistic insights into dioxygen activation, oxygen atom exchange and substrate epoxidation by AsqJ dioxygenase from quantum mechanical/molecular mechanical calculations. Phys Chem Chem Phys 19 (2017) 20188-20197. [PMID: 28726913]

6. Liao, H.J., Li, J., Huang, J.L., Davidson, M., Kurnikov, I., Lin, T.S., Lee, J.L., Kurnikova, M., Guo, Y., Chan, N.L. and Chang, W.C. Insights into the desaturation of cyclopeptin and its C3 epimer catalyzed by a non-heme Iron enzyme: structural characterization and mechanism elucidation. Angew. Chem. Int. Ed. Engl. 57 (2018) 1831-1835. [PMID: 29314482]

7. Mader, S.L., Brauer, A., Groll, M. and Kaila, V.RI. Catalytic mechanism and molecular engineering of quinolone biosynthesis in dioxygenase AsqJ. Nat. Commun. 9 (2018) 1168. [PMID: 29563492]

8. Wojdyla, Z. and Borowski, T. On how the binding cavity of AsqJ dioxygenase controls the desaturation reaction regioselectivity: a QM/MM study. J. Biol. Inorg. Chem. 23 (2018) 795-808. [PMID: 29876666]

9. Li, J., Liao, H.J., Tang, Y., Huang, J.L., Cha, L., Lin, T.S., Lee, J.L., Kurnikov, I.V., Kurnikova, M.G., Chang, W.C., Chan, N.L. and Guo, Y. Epoxidation catalyzed by the nonheme iron(II)- and 2-oxoglutarate-dependent oxygenase, AsqJ: mechanistic elucidation of oxygen atom transfer by a ferryl intermediate. J. Am. Chem. Soc. 142 (2020) 6268-6284. [PMID: 32131594]

10. Tang, H., Tang, Y., Kurnikov, I.V., Liao, H.J., Chan, N.L., Kurnikova, M.G., Guo, Y. and Chang, W.C. Harnessing the substrate promiscuity of dioxygenase AsqJ and developing efficient chemoenzymatic synthesis for quinolones. ACS Catal. 11 (2021) 7186-7192. [PMID: 35721870]

[EC 1.14.11.81 created 2022]

EC 1.14.11.82

Accepted name: 5-dehydro-6-demethoxyfumagillol dioxygenase

Reaction: 5-dehydro-6-demethoxyfumagillol + 2-oxoglutarate + O2 = 5-dehydro-6-demethoxy-6-hydroxyfumagillol + succinate + CO2

For diagram of reaction click here

Glossary: fumagillol = (3R,4S,5S,6R)-5-methoxy-4-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]-1-oxaspiro[2.5]octan-6-ol

Other name(s): fmaF (gene name); Fma-C6H

Systematic name: 5-dehydro-6-demethoxyfumagillol,2-oxoglutarate:oxygen oxidoreductase (6-hydroxylating)

Comments: Requires iron(II). The enzyme, characterized from the mold Aspergillus fumigatus, participates in the biosynthesis of the meroterpenoid fumagillin.

References:

1. Lin, H.C., Tsunematsu, Y., Dhingra, S., Xu, W., Fukutomi, M., Chooi, Y.H., Cane, D.E., Calvo, A.M., Watanabe, K. and Tang, Y. Generation of complexity in fungal terpene biosynthesis: discovery of a multifunctional cytochrome P450 in the fumagillin pathway. J. Am. Chem. Soc. 136 (2014) 4426-4436. [PMID: 24568283]

[EC 1.14.11.82 created 2022]

*EC 1.14.13.211

Accepted name: rifampicin monooxygenase

Reaction: rifampicin + NAD(P)H + O2 = 2-hydroxyrifampicin + NAD(P)+ + H2O

For diagram of reaction click here

Glossary: rifampicin = (2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-5,6,9,17,19-pentahydroxy-23-methoxy-2,4,12,16,18,20,22-heptamethyl-8-{[(E)-(4-methylpiperazin-1-yl)imino]methyl}-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca-1,11,13-trienoimino)nathpho[2,1-b]furan-21-yl acetate

Other name(s): RIF-O; ROX; RIFMO; rifampicin:NAD(P)H:oxygen oxidoreductase (2'-N-hydroxyrifampicin-forming) (incorrect)

Systematic name: rifampicin:NAD(P)H:oxygen oxidoreductase (C2-hydroxyrifampicin-forming; ring-cleaving)

Comments: The enzyme has been found in a variety of environmental bacteria, notably Rhodococcus, Nocardia, and Streptomyces. It hydroxylates C-2 of rifampicin leading to its macro-ring cleaving.

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

References:

1. Andersen, S.J., Quan, S., Gowan, B. and Dabbs, E.R. Monooxygenase-like sequence of a Rhodococcus equi gene conferring increased resistance to rifampin by inactivating this antibiotic. Antimicrob. Agents Chemother. 41 (1997) 218-221. [PMID: 8980786]

2. Hoshino, Y., Fujii, S., Shinonaga, H., Arai, K., Saito, F., Fukai, T., Satoh, H., Miyazaki, Y. and Ishikawa, J. Monooxygenation of rifampicin catalyzed by the rox gene product of Nocardia farcinica: structure elucidation, gene identification and role in drug resistance. J. Antibiot. (Tokyo) 63 (2010) 23-28. [PMID: 19942945]

3. Koteva, K., Cox, G., Kelso, J.K., Surette, M.D., Zubyk, H.L., Ejim, L., Stogios, P., Savchenko, A., Sørensen, D. and Wright, G.D. Rox, a rifamycin resistance enzyme with an unprecedented mechanism of action. Cell Chem Biol 25 (2018) 403-412.e5. [PMID: 29398560]

4. Liu, L.K., Dai, Y., Abdelwahab, H., Sobrado, P. and Tanner, J.J. Structural evidence for rifampicin monooxygenase inactivating rifampicin by cleaving Its ansa-bridge. Biochemistry 57 (2018) 2065-2068. [PMID: 29578336]

[EC 1.14.13.211 created 2016, modified 2022]

*EC 1.14.14.173

Accepted name: 2,4,6-trichlorophenol monooxygenase

Reaction: 2,4,6-trichlorophenol + FADH2 + O2 = 6-chloro-2-hydroxy-1,4-benzoquinone + 2 Cl- + FAD (overall reaction)
(1a) 2,4,6-trichlorophenol + FADH2 + O2 = 2,6-dichloro-1,4-benzoquinone + Cl- + FAD + H2O
(1b) 2,6-dichloro-1,4-benzoquinone + H2O = 6-chloro-2-hydroxy-1,4-benzoquinone + Cl-

Other name(s): tcpA (gene name)

Systematic name: 2,4,6-trichlorophenol,FADH2:oxygen oxidoreductase (dechlorinating)

Comments: The enzyme, characterized from Cupriavidus pinatubonensis, participates in the degradation of 2,4,6-trichlorophenol, a compound that has been used for decades as a wood preservative. The enzyme is a multifunctional flavin-dependent monooxygenase that catalyses two different reactions to displace two chlorine atoms, a monooxygenase reaction followed by a hydrolysis reaction that takes advantage of the reactivity of the product of the first reaction, 2,6-dichloro-1,4-benzoquinone [2]. The large amount of FADH2 that is required is generated by a dedicated flavin reductase (TcpB). cf. EC 1.14.14.172, 3,5,6-trichloropyridin-2-ol monooxygenase.

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

References:

1. Louie, T.M., Webster, C.M. and Xun, L. Genetic and biochemical characterization of a 2,4,6-trichlorophenol degradation pathway in Ralstonia eutropha JMP134. J. Bacteriol. 184 (2002) 3492-3500. [PMID: 12057943]

2. Xun, L. and Webster, C.M. A monooxygenase catalyzes sequential dechlorinations of 2,4,6-trichlorophenol by oxidative and hydrolytic reactions. J. Biol. Chem. 279 (2004) 6696-6700. [PMID: 14662756]

3. Hayes, R.P., Webb, B.N., Subramanian, A.K., Nissen, M., Popchock, A., Xun, L. and Kang, C. Structural and catalytic differences between two FADH2-dependent monooxygenases: 2,4,5-TCP 4-monooxygenase (TftD) from Burkholderia cepacia AC1100 and 2,4,6-TCP 4-monooxygenase (TcpA) from Cupriavidus necator JMP134. Int. J. Mol. Sci. 13 (2012) 9769-9784. [PMID: 22949829]

[EC 1.14.14.173 created 2020, modified 2022]

EC 1.14.14.184

Accepted name: 5-dehydro-6-demethoxyfumagillol synthase

Reaction: (+)-exo-β-bergamotene + 2 [reduced NADPH—hemoprotein reductase] + 3 O2 = 5-dehydro-6-demethoxyfumagillol + 2 [oxidized NADPH—hemoprotein reductase] + 3 H2O (overall reaction)
(1a) (+)-exo-β-bergamotene + [reduced NADPH—hemoprotein reductase] + O2 = (5R)-hydroxy-(+)-exo-β-bergamotene + [oxidized NADPH—hemoprotein reductase] + H2O
(1b) (5R)-hydroxy-(+)-exo-β-bergamotene + O2 = (3S)-3-[2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]-4-methylidenecyclohexan-1-one + H2O
(1c) (3S)-3-[2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]-4-methylidenecyclohexan-1-one + [reduced NADPH—hemoprotein reductase] + O2 = 5-dehydro-6-demethoxyfumagillol + [oxidized NADPH—hemoprotein reductase] + H2O

For diagram of reaction click here

Glossary: (+)-exo-β-bergamotene = β-trans-bergamotene = (1S,5S,6R)-6-methyl-2-methylidene-6-(4-methylpent-3-enyl)bicyclo[3.1.1]heptane
fumagillol = (3R,4S,5S,6R)-5-methoxy-4-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]-1-oxaspiro[2.5]octan-6-ol
fumagillin = (2E,4E,6E,8E)-10-({(3R,4S,5S,6R)-5-methoxy-4-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]-1-oxaspiro[2.5]oct-6-yl}oxy)-10-oxodeca-2,4,6,8-tetraenoate

Other name(s): fumagillin multifunctional cytochrome P450 monooxygenase; Fma-P450; fmaG (gene name)

Systematic name: (+)-exo-β-bergamotene,[reduced NADPH—hemoprotein reductase] oxidoreductase (5-dehydro-6-demethoxyfumagillol-producing)

Comments: The enzyme, characterized from the mold Aspergillus fumigatus, catalyses a complex transformation comprising hydroxylation, bicyclic ring-opening, and two epoxidations, generating the sesquiterpenoid core skeleton of fumagillin.

References:

1. Lin, H.C., Tsunematsu, Y., Dhingra, S., Xu, W., Fukutomi, M., Chooi, Y.H., Cane, D.E., Calvo, A.M., Watanabe, K. and Tang, Y. Generation of complexity in fungal terpene biosynthesis: discovery of a multifunctional cytochrome P450 in the fumagillin pathway. J. Am. Chem. Soc. 136 (2014) 4426-4436. [PMID: 24568283]

[EC 1.14.14.184 created 2022]

EC 1.21.98.5

Accepted name: tetraether lipid synthase

Reaction: (1) 2 a 2,3-bis-O-phytanyl-sn-glycero-phospholipid + 4 S-adenosyl-L-methionine + 2 reduced acceptor = a glycerol dibiphytanyl glycerol tetraether phospholipid + 4 L-methionine + 4 5'-deoxyadenosine + 2 acceptor
(2) a 3-bis-O-phytanyl-sn-glycero-phospholipid + 2 S-adenosyl-L-methionine + reduced acceptor = a macrocyclic archaeol phospholipid + 2 L-methionine + 2 5'-deoxyadenosine + acceptor

Glossary: 2,3-bis-O-phytanyl-sn-glycerol = archaeol

Other name(s): GDGT/MA synthase; GDGT/MAS; tetraether synthase; Tes; Mj0619 (locus name)

Systematic name: a 2,3-bis-O-phytanyl-sn-glycero-phospholipid:S-adenosyl-L-methionine,acceptor oxidoreductase (cyclyzing)

Comments: This archaeal enzyme catalyses a C—C bond formation during the biosynthesis of tetraether lipids. The bond is formed between the termini of two lipid tails from two glycerophospholipids to generate the macrocycle glycerol dibiphytanyl glycerol tetraether (GDGT). The enzyme does not distinguish whether the two lipids are connected in antiparallel or parallel geometry, resulting in formation of two forms of the product, which are known as caldarchaeol and isocaldarchaeol, respectively. The enzyme can also form macrocyclic archaeol phospholipids by joining the two lipid tails of a single substrate molecule. Even though the reaction shown here describes phospholipid substrates, the enzyme can also act on glycolipids or lipids that contains mixed types of polar head groups. The enzyme is a radical SAM enzyme that contains 3 [4Fe-4S] clusters and one mononuclear rubredoxin-like iron ion, each found in a separate domain. The enzyme uses the 5'-deoxyadenosyl radical to initiate the reaction, which involves the formation of an intermediate bond between the substrate carbon and a sulfur of one of the [4Fe-4S] clusters. Two radicals are needed per C-C bond formed. The source of the required additional electrons is not known.

References:

1. Zeng, Z., Chen, H., Yang, H., Chen, Y., Yang, W., Feng, X., Pei, H. and Welander, P.V. Identification of a protein responsible for the synthesis of archaeal membrane-spanning GDGT lipids. Nat. Commun. 13 (2022) 1545. [PMID: 35318330]

2. Lloyd, C.T., Iwig, D.F., Wang, B., Cossu, M., Metcalf, W.W., Boal, A.K. and Booker, S.J. Discovery, structure, and mechanism of a tetraether lipid synthase. Nature (2022) . [PMID: 35882349]

[EC 1.21.98.5 created 2022]

EC 2.1.1.386

Accepted name: small RNA 2'-O-methyltransferase

Reaction: S-adenosyl-L-methionine + an [sRNA]-3'-end ribonucleotide = S-adenosyl-L-homocysteine + an [sRNA]-3'-end 2'-O-methylated ribonucleotide

Glossary: sRNA = small RNA

Other name(s): HENMT1 (gene name); HEN1 (gene name)

Systematic name: S-adenosyl-L-methionine:[sRNA]-3'-end ribonucleotide 2'-O-methyltransferase

Comments: The enzyme adds a 2'-O-methyl group to the ribose of the last nucleotide in several types of small RNAs (sRNAs), protecting the 3'-end of sRNAs from uridylation activity and subsequent degradation.

References:

1. Park, W., Li, J., Song, R., Messing, J. and Chen, X. CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr. Biol. 12 (2002) 1484-1495. [PMID: 12225663]

2. Yu, B., Yang, Z., Li, J., Minakhina, S., Yang, M., Padgett, R.W., Steward, R. and Chen, X. Methylation as a crucial step in plant microRNA biogenesis. Science 307 (2005) 932-935. [PMID: 15705854]

3. Kirino, Y. and Mourelatos, Z. 2'-O-methyl modification in mouse piRNAs and its methylase. Nucleic Acids Symp Ser (Oxf) (2007) 417-418. [PMID: 18029764]

4. Huang, Y., Ji, L., Huang, Q., Vassylyev, D.G., Chen, X. and Ma, J.B. Structural insights into mechanisms of the small RNA methyltransferase HEN1. Nature 461 (2009) 823-827. [PMID: 19812675]

5. Peng, L., Zhang, F., Shang, R., Wang, X., Chen, J., Chou, J.J., Ma, J., Wu, L. and Huang, Y. Identification of substrates of the small RNA methyltransferase Hen1 in mouse spermatogonial stem cells and analysis of its methyl-transfer domain. J. Biol. Chem. 293 (2018) 9981-9994. [PMID: 29703750]

[EC 2.1.1.386 created 2022]

EC 2.1.1.387

Accepted name: 5-dehydro-6-demethoxy-6-hydroxyfumagillol O-methyltransferase

Reaction: S-adenosyl-L-methionine + 5-dehydro-6-demethoxy-6-hydroxyfumagillol = S-adenosyl-L-homocysteine + 5-dehydrofumagillol

For diagram of reaction click here

Glossary: fumagillol = (3R,4S,5S,6R)-5-methoxy-4-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]-1-oxaspiro[2.5]octan-6-ol

Other name(s): Fma-MT; fmaD (gene name); af390-400 (gene name)

Systematic name: S-adenosyl-L-methionine:5-dehydro-6-demethoxy-6-hydroxyfumagillol 6-O-methyltransferase

Comments: The enzyme, characterized from the mold Aspergillus fumigatus, participates in the biosynthesis of the meroterpenoid fumagillin.

References:

1. Lin, H.C., Tsunematsu, Y., Dhingra, S., Xu, W., Fukutomi, M., Chooi, Y.H., Cane, D.E., Calvo, A.M., Watanabe, K. and Tang, Y. Generation of complexity in fungal terpene biosynthesis: discovery of a multifunctional cytochrome P450 in the fumagillin pathway. J. Am. Chem. Soc. 136 (2014) 4426-4436. [PMID: 24568283]

[EC 2.1.1.387 created 2022]

EC 2.3.1.311

Accepted name: tRNA carboxymetyluridine synthase

Reaction: acetyl-CoA + uridine34 in tRNA + S-adenosyl-L-methionine + H2O = CoA + 5-(carboxymethyl)uridine34 in tRNA + L-methionine + 5'-deoxyadenosine

Other name(s): elongator complex; ELP3

Systematic name: acetyl-CoA:tRNA uridine carboxymethyltransferase

Comments: The enzyme, found in eukaryotes, most archaea, and some bacteria, catalyses the first step in modification of the wobble uridine base of certain tRNAs. In eukaryotes the enzyme is a complex of six conserved subunits, with ELP3 being the catalytic subunit. In archaea and bacteria the enzyme consists of a single subunit, homologous to ELP3. The enzyme contains an [4Fe-4S] cluster and uses radical chemistry. A 5'-deoxyadenosyl radical generated in the radical AdoMet (SAM) domain attacks the acetyl-CoA donor, activating its methyl group, which forms a C-C bond with C5 of the uridine moiety.

References:

1. Paraskevopoulou, C., Fairhurst, S.A., Lowe, D.J., Brick, P. and Onesti, S. The Elongator subunit Elp3 contains a Fe4S4 cluster and binds S-adenosylmethionine. Mol. Microbiol. 59 (2006) 795-806. [PMID: 16420352]

2. Selvadurai, K., Wang, P., Seimetz, J. and Huang, R.H. Archaeal Elp3 catalyzes tRNA wobble uridine modification at C5 via a radical mechanism. Nat. Chem. Biol. 10 (2014) 810-812. [PMID: 25151136]

3. Lin, T.Y., Abbassi, N.EH., Zakrzewski, K., Chramiec-Glabik, A., Jemiola-Rzeminska, M., Rozycki, J. and Glatt, S. The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase. Nat. Commun. 10 (2019) 625. [PMID: 30733442]

[EC 2.3.1.311 created 2022]

EC 2.4.1.390

Accepted name: 4,3-α-glucanotransferase

Reaction: formation of a mixed (1→4)/(1→3)-α-D-glucan from (1→4)-α-D-glucans

Other name(s): gtfB (gene name) (ambiguous)

Systematic name: (1→4)-α-D-glucan:(1→4)/(1→3)-α-D-glucan 3-α-D-glucosyltransferase

Comments: The enzyme, characterized from the bacterium Lactobacillus fermentum NCC 2970, possesses hydrolysis and transglycosylase activities on malto-oligosaccharides with a degree of polymerization of at least 6, as well as polymers such as amylose, potato starch, and amylopectin. The enzyme, which belongs to glycoside hydrolase 70 (GH70) family, attaches the glucosyl residues by α(1→3) linkages in both linear and branched orientations. While capable of forming large polymers, the enzyme produces mainly oligosaccharides in vitro.

References:

1. Gangoiti, J., van Leeuwen, S.S., Gerwig, G.J., Duboux, S., Vafiadi, C., Pijning, T. and Dijkhuizen, L. 4,3-α-Glucanotransferase, a novel reaction specificity in glycoside hydrolase family 70 and clan GH-H. Sci. Rep. 7 (2017) 39761. [PMID: 28059108]

2. Pijning, T., Gangoiti, J., Te Poele, E.M., Borner, T. and Dijkhuizen, L. Insights into broad-specificity starch modification from the crystal structure of Limosilactobacillus reuteri NCC 2613 4,6-α-glucanotransferase GtfB. J. Agric. Food Chem. 69 (2021) 13235-13245. [PMID: 34708648]

[EC 2.4.1.390 created 2022]

EC 2.4.1.391

Accepted name: β-1,2-glucosyltransferase

Reaction: [(1→2)-β-D-glucosyl]n + a D-glucoside = [(1→2)-β-D-glucosyl]n-1 + a β-D-glucosyl-(1→2)-D-glucoside

Systematic name: 1,2-β-D-glucan:D-glucoside 2-β-D-glucosyltransferase (configuration-retaining)

Comments: The enzyme, characterized from the bacterium Ignavibacterium album, transfers a glucosyl residue from the non-reducing end of a 1,2-β-D-glucan to a glucose residue of an acceptor molecule, forming a β(1,2) linkage. The donor molecule can be as small as sophorose (which contains two glucosyl residues). The enzyme has a very broad specificity for the acceptor, and can act on various aryl- and alkyl-glucosides. In addition, the accepting glucose unit can be in either α or β configuration.

References:

1. Kobayashi, K., Shimizu, H., Tanaka, N., Kuramochi, K., Nakai, H., Nakajima, M. and Taguchi, H. Characterization and structural analyses of a novel glycosyltransferase acting on the β-1,2-glucosidic linkages. J. Biol. Chem. 298 (2022) 101606. [PMID: 35065074]

[EC 2.4.1.391 created 2022]

EC 2.4.1.392

Accepted name: 3-O-β-D-glucopyranosyl-β-D-glucuronide phosphorylase

Reaction: a 3-O-β-D-glucosyl-β-D-glucuronoside + phosphate = a β-D-glucuronoside + α-D-glucopyranose 1-phosphate

Other name(s): PBOR_13355 (locus name)

Systematic name: 3-O-β-D-glucopyranosyl-β-D-glucuronide:phosphate α-D-glucosyltransferase

Comments: The enzyme, characterized from the bacterium Paenibacillus borealis, catalyses a reversible reaction, transferring a glucosyl residue attached by a β(1,3) linkage to a D-glucuronate residue (either free or as a part of a β-D-glucuronide) to a free phosphate, generating α-D-glucopyranose 1-phosphate

References:

1. Isono, N., Mizutani, E., Hayashida, H., Katsuzaki, H. and Saburi, W. Functional characterization of a novel GH94 glycoside phosphorylase, 3-O-β-D-glucopyranosyl β-D-glucuronide phosphorylase, and implication of the metabolic pathway of acidic carbohydrates in Paenibacillus borealis. Biochem. Biophys. Res. Commun. 625 (2022) 60-65. [PMID: 35947916]

[EC 2.4.1.392 created 2022]

[EC 2.5.1.4 Transferred entry: adenosylmethionine cyclotransferase. Now classified as EC 4.4.1.42, S-adenosyl-L-methionine lyase (EC 2.5.1.4 created 1965, deleted 2022)]

[EC 2.6.1.8 Deleted entry: 2,5-diaminovalerate transaminase (EC 2.6.1.8 created 1961, modified 1982, deleted 2022)]

EC 2.7.1.239

Accepted name: α-D-ribose-1-phosphate 5-kinase (ATP)

Reaction: ATP + α-D-ribose-1-phosphate = ADP + α-D-ribose 1,5-bisphosphate

Systematic name: ATP:α-D-ribose-1-phosphate 5-phosphotransferase

Comments: The enzyme, characterized from the halophilic archaeon Halopiger xanaduensis, participates in a non-carboxylating pentose bisphosphate pathway for nucleoside degradation, which is found in some halophilic archaea. cf. EC 2.7.1.212, α-D-ribose-1-phosphate 5-kinase (ADP).

References:

1. Sato, T., Utashima, S.H., Yoshii, Y., Hirata, K., Kanda, S., Onoda, Y., Jin, J.Q., Xiao, S., Minami, R., Fukushima, H., Noguchi, A., Manabe, Y., Fukase, K. and Atomi, H. A non-carboxylating pentose bisphosphate pathway in halophilic archaea. Commun Biol 5 (2022) 1290. [PMID: 36434094]

[EC 2.7.1.239 created 2022]

EC 2.7.8.48

Accepted name: ceramide phosphoethanolamine synthase

Reaction: CDP-ethanolamine + a ceramide = a ceramide phosphorylethanolamine + CMP

Other name(s): Cpes (gene name)

Systematic name: CDP-ethanolamine:ceramide phosphoethanolaminyltransferase

Comments: The enzyme, studied from the fly Drosophila melanogaster, has homologues among the invertebrates, but not in other animal phyla. Its product, ceramide phosphoethanolamine, is synthesized as the main sphingolipid in cell membranes of arthropods, such as Drosophila and Musca, and is common in worms, bees, spiders, and scorpions. It has also been reported in deep-sea mussels and some sea snails, as well as protozoans and oomycetes. The enzyme requires a Mn(II) cofactor.

References:

1. Vacaru, A.M., Tafesse, F.G., Ternes, P., Kondylis, V., Hermansson, M., Brouwers, J.F., Somerharju, P., Rabouille, C. and Holthuis, J.C. Sphingomyelin synthase-related protein SMSr controls ceramide homeostasis in the ER. J. Cell Biol. 185 (2009) 1013-1027. [PMID: 19506037]

2. Vacaru, A.M., van den Dikkenberg, J., Ternes, P. and Holthuis, J.C. Ceramide phosphoethanolamine biosynthesis in Drosophila is mediated by a unique ethanolamine phosphotransferase in the Golgi lumen. J. Biol. Chem. 288 (2013) 11520-11530. [PMID: 23449981]

[EC 2.7.8.48 created 2022]

EC 3.1.1.120

Accepted name: L-fucono-1,5-lactonase

For diagram of reaction click here

Reaction: L-fucono-1,5-lactone + H2O = L-fuconate

Systematic name: L-fucono-1,5-lactone lactonohydrolase

Comments: The enzyme, characterized from the bacterium Burkholderia multivorans, participates in an L-fucose degradation pathway. The enzyme exhibits catalytic activity for the hydrolysis of several lactones, including L-fucono-1,4-lactone, D-arabinono-1,4-lactone, L-xylono-1,4-lactone, and L-galactono-1,4-lactone, but L-fucono-1,5-lactone is the best substrate.

References:

1. Hobbs, M.E., Vetting, M., Williams, H.J., Narindoshvili, T., Kebodeaux, D.M., Hillerich, B., Seidel, R.D., Almo, S.C. and Raushel, F.M. Discovery of an L-fucono-1,5-lactonase from cog3618 of the amidohydrolase superfamily. Biochemistry 52 (2013) 239-253. [PMID: 23214453]

[EC 3.1.1.120 created 2022]

EC 3.1.3.109

Accepted name: ribulose-1,5-bisphosphate 5-phosphatase

Reaction: D-ribulose-1,5-bisphosphate + H2O = D-ribulose 1-phosphate + phosphate

Other name(s): RuBP 5-phosphatase

Systematic name: D-ribulose-1,5-bisphosphate 5-phosphohydrolase

Comments: The enzyme, characterized from the halophilic archaeon Halopiger xanaduensis, participates in a non-carboxylating pentose bisphosphate pathway for nucleoside degradation, which is found in some halophilic archaea. The enzyme requires both monovalent and divalent ions for optimal activity.

References:

1. Sato, T., Utashima, S.H., Yoshii, Y., Hirata, K., Kanda, S., Onoda, Y., Jin, J.Q., Xiao, S., Minami, R., Fukushima, H., Noguchi, A., Manabe, Y., Fukase, K. and Atomi, H. A non-carboxylating pentose bisphosphate pathway in halophilic archaea. Commun Biol 5 (2022) 1290. [PMID: 36434094]

[EC 3.1.3.109 created 2022]

EC 3.2.1.218

Accepted name: α-3'-ketoglucosidase

Reaction: 3'-dehydrosucrose + H2O = 3-dehydro-D-glucopyranose + β-D-fructofuranose

Other name(s): 3'-keto-α-D-gluco-disaccharide hydrolase; α-3-ketoglucosidase (incorrect); 3-keto-glucoside hydrolase

Systematic name: 3'-dehydrosucrose 3'-dehydroglucohydrolase

Comments: The enzyme, originally characterized from the bacterium Agrobacterium tumefaciens, is specific for disaccharides that contain a 3-dehydro-α-D-glucose at the non-reducing end such as 3'-dehydrosucrose and 3'-dehydro-α,α-trehalose. It has no activity with disaccharides in which the glucose is in β conformation, and greatly reduced activity with disaccharides with an unmodified 3' position.

References:

1. Hayano, K. and Fukui, S. Alpha-3-ketoglucosidase of Agrobacterium tumefaciens. J. Bacteriol. 101 (1970) 692-697. [PMID: 5438043]

2. Liu, H., Shiver, A.L., Price, M.N., Carlson, H.K., Trotter, V.V., Chen, Y., Escalante, V., Ray, J., Hern, K.E., Petzold, C.J., Turnbaugh, P.J., Huang, K.C., Arkin, A.P. and Deutschbauer, A.M. Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments. Cell Rep. 34 (2021) 108789. [PMID: 33657378]

[EC 3.2.1.218 created 2022]

EC 3.2.1.219

Accepted name: palatinase

Reaction: palatinose + H2O = α-D-glucopyranose + D-fructofuranose

Glossary: palatinose = 6-O-α-D-glucopyranosyl-D-fructofuranose

Other name(s): palQ (gene name)

Systematic name: palatinose α-1,6-glucohydrolase

Comments: The enzyme, characterized from the bacterium Erwinia rhapontici, is specific for palatinose.

References:

1. Bornke, F., Hajirezaei, M. and Sonnewald, U. Cloning and characterization of the gene cluster for palatinose metabolism from the phytopathogenic bacterium Erwinia rhapontici. J. Bacteriol. 183 (2001) 2425-2430. [PMID: 11274100]

[EC 3.2.1.219 created 2022]

[EC 3.5.1.61 Transferred entry: mimosinase. Now EC 4.3.3.8, mimosinase (EC 3.5.1.61 created 1989, deleted 2022)]

EC 3.6.1.76

Accepted name: prenyl-diphosphate phosphatase

Reaction: (1) prenyl diphosphate + H2O = prenyl phosphate + phosphate
(2) 3-methylbut-3-en-1-yl diphosphate + H2O = 3-methylbut-3-en-1-yl phosphate + phosphate

Glossary: isopentenyl = 3-methylbut-3-en-1-yl
prenyl = 3-methylbut-2-en-1-yl = dimethylallyl
dimethylallyl diphosphate = DMAPP
isopentenyl diphosphate = IPP

Systematic name: prenyl diphosphate/3-methylbut-3-en-1-yl diphosphate phosphohydrolase

Comments: The enzyme, characterized from the methanogenic archaeon Methanosarcina mazei, belongs to the Nudix hydrolase family (a superfamily of hydrolytic enzymes capable of cleaving nucleoside diphosphates linked to a moiety). Its main purpose is to provide the substrate for EC 2.5.1.129, flavin prenyltransferase.

References:

1. Ishibashi, Y., Matsushima, N., Ito, T. and Hemmi, H. Isopentenyl diphosphate/dimethylallyl diphosphate-specific Nudix hydrolase from the methanogenic archaeon Methanosarcina mazei. Biosci. Biotechnol. Biochem. 86 (2022) 246-253. [PMID: 34864834]

[EC 3.6.1.76 created 2022]

[EC 3.13.2.2 Transferred entry: S-adenosyl-L-methionine hydrolase (L-homoserine-forming). Now classified as EC 4.4.1.42, S-adenosyl-L-methionine lyase (EC 3.13.2.2 created 1972 as EC 3.3.1.2, modified 1976, modified 2018, transferred 2022 to EC 3.13.2.2, transferred 2022 to EC 4.4.1.42, deleted 2022)]

*EC 4.1.3.27

Accepted name: anthranilate synthase

Reaction: chorismate + L-glutamine = anthranilate + pyruvate + L-glutamate (overall reaction)
(1a) L-glutamine + H2O = L-glutamate + NH3
(1b) chorismate + NH3 = (2S)-2-amino-4-deoxychorismate + H2O
(1c) (2S)-2-amino-4-deoxychorismate = anthranilate + pyruvate

For diagram of reaction, click here

Other name(s): anthranilate synthetase; chorismate lyase; chorismate pyruvate-lyase (amino-accepting); TrpDE

Systematic name: chorismate pyruvate-lyase (amino-accepting; anthranilate-forming)

Comments: The enzyme, found in plants, fungi and bacteria is composed of two parts, a glutaminase subunit and a lyase subunit. The glutaminase produces ammonia that is channeled to the lyase subunit. In the absence of the glutaminase, the lyase can convert ammonia and chorismate into anthranilate. In some organisms, this enzyme is part of a multifunctional protein, together with one or more other components of the system for the biosynthesis of tryptophan [EC 2.4.2.18 (anthranilate phosphoribosyltransferase), EC 4.1.1.48 (indole-3-glycerol-phosphate synthase), EC 4.2.1.20 (tryptophan synthase) and EC 5.3.1.24 (phosphoribosylanthranilate isomerase)].

Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9031-59-8

References:

1. Baker, T. and Crawford, I.P. Anthranilate synthetase. Partial purification and some kinetic studies on the enzyme from Escherichia coli. J. Biol. Chem. 241 (1966) 5577-5584. [PMID: 5333199]

2. Creighton, T.E. and Yanofsky, C. Chorismate to tryptophan (Escherichia coli) - anthranilate synthetase, PR transferase, PRA isomerase, InGP synthetase, tryptophan synthetase. Methods Enzymol. 17A (1970) 365-380.

3. Hütter, R., Niederberger, P. and DeMoss, J.A. Tryptophan synthetic genes in eukaryotic microorganisms. Annu. Rev. Microbiol. 40 (1986) 55-77. [PMID: 3535653]

4. Ito, J. and Yanofsky, C. Anthranilate synthetase, an enzyme specified by the tryptophan operon of Escherichia coli: Comparative studies on the complex and the subunits. J. Bacteriol. 97 (1969) 734-742. [PMID: 4886290]

5. Zalkin, H. and Kling, D. Anthranilate synthetase. Purification and properties of component I from Salmonella typhimurium. Biochemistry 7 (1968) 3566-3573. [PMID: 4878701]

6. Morollo, A.A. and Bauerle, R. Characterization of composite aminodeoxyisochorismate synthase and aminodeoxyisochorismate lyase activities of anthranilate synthase. Proc. Natl. Acad. Sci. USA 90 (1993) 9983-9987. [PMID: 8234345]

7. Kanno, T., Kasai, K., Ikejiri-Kanno, Y., Wakasa, K. and Tozawa, Y. In vitro reconstitution of rice anthranilate synthase: distinct functional properties of the α subunits OASA1 and OASA2. Plant Mol. Biol. 54 (2004) 11-22. [PMID: 15159631]

[EC 4.1.3.27 created 1972, modified 2022]

EC 4.1.99.27

Accepted name: cyclopenase

Reaction: (–)-cyclopenine = viridicatin + methyl isocyanate

Glossary: (–)-cyclopenine = (3S,3'R)-4-methyl-3'-phenyl-1H-spiro[1,4-benzodiazepine-3,2'-oxirane]-2,5-dione
viridicatin = 3-hydroxy-4-phenyl-1H-quinolin-2-one

Other name(s): asqI (gene name)

Systematic name: (–)-cyclopenine methyl-isocyanate lyase (viridicatin-forming)

Comments: This fungal enzyme catalyses a key reaction in the biosynthesis of quinolone compounds, converting the benzodiazepine structure into a quinolone structure. The enzyme is also active with (–)-4'-methoxycyclopenine.

References:

1. Kishimoto, S., Hara, K., Hashimoto, H., Hirayama, Y., Champagne, P.A., Houk, K.N., Tang, Y. and Watanabe, K. Enzymatic one-step ring contraction for quinolone biosynthesis. Nat. Commun. 9 (2018) 2826. [PMID: 30026518]

[EC 4.1.99.27 created 2022]

EC 4.2.2.28

Accepted name: α-L-rhamnosyl-(1→4)-β-D-glucuronate lyase

Reaction: an α-L-rhamnose-(1→4)-β-D-glucuronide = α-L-rhamnopyranose + a 4-deoxy-α-L-threo-hex-4-enopyranuronoside

Other name(s): L-rhamnose-α-1,4-D-glucuronate lyase; FoRham (gene name)

Systematic name: α-L-rhamnosyl-(1→4)-β-D-glucuronate lyase

Comments: The enzyme, characterized from the phytopathogenic fungus Fusarium oxysporum, removes the rhamnosyl residue from α-L-rhamnosyl-(1→4)-β-D-glucuronate or from oligosaccharides that contain this motif at the non-reducing end, leaving an unsaturated glucuronate residue. Among its natural substrates is the type II arabinogalactan component of gum arabic.

References:

1. Kondo, T., Kichijo, M., Maruta, A., Nakaya, M., Takenaka, S., Arakawa, T., Fushinobu, S. and Sakamoto, T. Structural and functional analysis of gum arabic L-rhamnose-α-1,4-D-glucuronate lyase establishes a novel polysaccharide lyase family. J. Biol. Chem. 297 (2021) 101001. [PMID: 34303708]

[EC 4.2.2.28 created 2022]

EC 4.2.3.206

Accepted name: (–)-cyatha-3,12-diene synthase

Reaction: geranylgeranyl diphosphate = (–)-cyatha-3,12-diene + diphosphate

Diagram of reaction click here

Glossary: (–)-cyatha-3,12-diene = (3aS,5aS,10aS)-3a,5a,8-trimethyl-1-(propan-2-yl)-2,3,4,5,6,9,10,10a-octahydrocyclohepta[e]indene

Other name(s): eriG (gene name); CyaTC

Systematic name: geranylgeranyl diphosphate-lyase [(–)-cyatha-3,12-diene-forming]

Comments: The enzyme, characterized from the fungi Hericium erinaceus and Cyathus africanus, requires Mg2+ for activity.

References:

1. Yang, Y.L., Zhang, S., Ma, K., Xu, Y., Tao, Q., Chen, Y., Chen, J., Guo, S., Ren, J., Wang, W., Tao, Y., Yin, W.B. and Liu, H. Discovery and characterization of a new family of diterpene cyclases in bacteria and fungi. Angew. Chem. Int. Ed. Engl. 56 (2017) 4749-4752. [PMID: 28371074]

[EC 4.2.3.206 created 2022]

EC 4.2.3.207

Accepted name: neoverrucosan-5β-ol synthase

Reaction: geranylgeranyl diphosphate + H2O = neoverrucosan-5β-ol + diphosphate

Diagram of reaction click here

Glossary: neoverrucosan-5β-ol = (1aS,3R,3aS,5aR,8bR,8cS,12S,14S)-1a,3a,5a-trimethyl-8-(propan-2-yl)tetradecahydrocyclopenta[a]cyclopropa[h]naphthalen-3-ol

Other name(s): SapTC1

Systematic name: geranylgeranyl- diphosphate diphosphate-lyase (neoverrucosan-5β-ol-forming)

Comments: Requires Mg2+. Characterized from the marine bacterium Saprospira grandis.

References:

1. Yang, Y.L., Zhang, S., Ma, K., Xu, Y., Tao, Q., Chen, Y., Chen, J., Guo, S., Ren, J., Wang, W., Tao, Y., Yin, W.B. and Liu, H. Discovery and characterization of a new family of diterpene cyclases in bacteria and fungi. Angew. Chem. Int. Ed. Engl. 56 (2017) 4749-4752. [PMID: 28371074]

[EC 4.2.3.207 created 2022]

EC 4.2.3.208

Accepted name: verrucosan-2β-ol synthase

Reaction: geranylgeranyl diphosphate + H2O = verrucosan-2β-ol + diphosphate

Diagram of reaction click here

Glossary: verrucosan-2β-ol = (1S,3aR,5aS,6aR,7aR,8S,8aR,9bR)-1-(propan-2-yl)tetradecahydrocyclopenta[a]cyclopropa[g]naphthalene-8-ol

Other name(s): ChlTC2

Systematic name: geranylgeranyl-diphosphate diphosphate-lyase (verrucosan-2β-ol-forming)

Comments: Requires Mg2+. Characterized from the bacterium Chloroflexus aurantiacus.

References:

1. Yang, Y.L., Zhang, S., Ma, K., Xu, Y., Tao, Q., Chen, Y., Chen, J., Guo, S., Ren, J., Wang, W., Tao, Y., Yin, W.B. and Liu, H. Discovery and characterization of a new family of diterpene cyclases in bacteria and fungi. Angew. Chem. Int. Ed. Engl. 56 (2017) 4749-4752. [PMID: 28371074]

[EC 4.2.3.208 created 2022]

EC 4.2.3.209

Accepted name: (R)-axinyssene synthase

Reaction: geranylgeranyl diphosphate = (R)-axinyssene + diphosphate

Diagram of reaction click here

Glossary: (R)-axinyssene = (4R)-4-[(5E)-6,10-dimethylundeca-1,5,9-trien-2-yl]-1-methylcyclohexene

Other name(s): CysTC2

Systematic name: geranylgeranyl-diphosphate diphosphate-lyase [(R)-axinyssene-forming]

Comments: Requires Mg2+. Characterized from the bacterium Archangium violaceum.

References:

1. Yang, Y.L., Zhang, S., Ma, K., Xu, Y., Tao, Q., Chen, Y., Chen, J., Guo, S., Ren, J., Wang, W., Tao, Y., Yin, W.B. and Liu, H. Discovery and characterization of a new family of diterpene cyclases in bacteria and fungi. Angew. Chem. Int. Ed. Engl. 56 (2017) 4749-4752. [PMID: 28371074]

[EC 4.2.3.209 created 2022]

EC 4.2.3.210

Accepted name: lydicene synthase

Reaction: geranylgeranyl diphosphate = lydicene + diphosphate

Diagram of reaction click here

Glossary: lydicene = (4aR,6aS)-2,2,4α,6α,9-pentamethyl-2,3,4,5,6,7,10,11-octahydro-1Hcyclohepta[a]naphthalene

Other name(s): StlTC

Systematic name: geranylgerany-diphosphate diphosphate-lyase (lydicene-forming)

Comments: Requires Mg2+. Characterized from the bacterium Streptomyces lydicus.

References:

1. Yang, Y.L., Zhang, S., Ma, K., Xu, Y., Tao, Q., Chen, Y., Chen, J., Guo, S., Ren, J., Wang, W., Tao, Y., Yin, W.B. and Liu, H. Discovery and characterization of a new family of diterpene cyclases in bacteria and fungi. Angew. Chem. Int. Ed. Engl. 56 (2017) 4749-4752. [PMID: 28371074]

[EC 4.2.3.210 created 2022]

EC 4.2.3.211

Accepted name: (+)-exo-β-bergamotene synthase

Reaction: (2E,6E)-farnesyl diphosphate = (+)-exo-β-bergamotene + diphosphate

Diagram of reaction click here and mechanism click here

Glossary: (+)-exo-β-bergamotene = β-trans-bergamotene = (1S,5S,6R)-6-methyl-2-methylidene-6-(4-methylpent-3-enyl)bicyclo[3.1.1]heptane
fumagillin = w(2E,4E,6E,8E)-10-({(3R,4S,5S,6R)-5-methoxy-4-[(2R,3R)-2-methyl-3-(3-methylbut-2-en-1-yl)oxiran-2-yl]-1-oxaspiro[2.5]oct-6-yl}oxy)-10-oxodeca-2,4,6,8-tetraenoate

Systematic name: (2E,6E)-farnesyl-diphosphate diphosphate-lyase [(+)-exo-β-bergamotene-forming]

Comments: The enzyme, characterized from the mold Aspergillus fumigatus, participates in the biosynthesis of the meroterpenoid fumagillin.

References:

1. Lin, H.C., Chooi, Y.H., Dhingra, S., Xu, W., Calvo, A.M. and Tang, Y. The fumagillin biosynthetic gene cluster in Aspergillus fumigatus encodes a cryptic terpene cyclase involved in the formation of β-trans-bergamotene. J. Am. Chem. Soc. 135 (2013) 4616-4619. [PMID: 23488861]

[EC 4.2.3.211 created 2022]

EC 4.3.3.8

Accepted name: mimosinase

Reaction: L-mimosine + H2O = 3-hydroxy-4H-pyrid-4-one + pyruvate + ammonia (overall reaction)
(1a) L-mimosine = 3-hydroxy-4H-pyrid-4-one + 2-aminoprop-2-enoate
(1b) 2-aminoprop-2-enoate = 2-iminopropanoate
(1c) 2-iminopropanoate + H2O = pyruvate + ammonia

Glossary: L-mimosine = (2S)-2-amino-3-[3-hydroxy-4-oxopyridin-1(4H)-yl]propanoate

Other name(s): mimosine amidohydrolase (incorrect)

Systematic name: (2S)-2-amino-3-[3-hydroxy-4-oxopyridin-1(4H)-yl]propanoate 3-hydroxy-4H-pyrid-4-one-lyase (2-aminoprop-2-enoate-forming)

Comments: A pyridoxal-phosphate protein. The enzyme degrades the toxic amino acid L-mimosine. It cleaves a carbon-nitrogen bond, releasing 3-hydroxy-4H-pyrid-4-one and an unstable enamine product that tautomerizes to an imine form, which undergoes a hydrolytic deamination to form pyruvate and ammonia. It is thought to have evolved from EC 4.4.1.13, cysteine-S-conjugate β-lyase. It has been described in both mimosine-producing plants and some bacteria.

References:

1. Tangendjaja, B., Lowry, J.B. and Wills, R.H. Isolation of a mimosine degrading enzyme from Leucaena leaf. J. Sci. Food Agric. 37 (1986) 523-526.

2. Negi, V.S., Bingham, J.P., Li, Q.X. and Borthakur, D. A carbon-nitrogen lyase from Leucaena leucocephala catalyzes the first step of mimosine degradation. Plant Physiol. 164 (2014) 922-934. [PMID: 24351687]

3. Oogai, S., Fukuta, M., Watanabe, K., Inafuku, M. and Oku, H. Molecular characterization of mimosinase and cystathionine β-lyase in the Mimosoideae subfamily member Mimosa pudica. J. Plant Res. 132 (2019) 667-680. [PMID: 31368041]

4. Oogai, S., Fukuta, M., Inafuku, M. and Oku, H. Isolation and characterization of mimosine degrading enzyme from Arthrobacter sp. Ryudai-S1. World J. Microbiol. Biotechnol. 38 (2022) 172. [PMID: 35908235]

[EC 4.3.3.8 created 1989 as EC 3.5.1.61, transferred 2022]

EC 4.4.1.42

Accepted name: S-adenosyl-L-methionine lyase

Reaction: S-adenosyl-L-methionine = L-homoserine lactone + S-methyl-5'-thioadenosine

Other name(s): T3p01 (gene name); SAM lyase; SAMase; adenosylmethionine cyclotransferase; S-adenosyl-L-methionine alkyltransferase (cyclizing)

Systematic name: S-adenosyl-L-methionine S-methyl-5'-thioadenosine-lyase (cyclizing; L-homoserine lactone-forming)

Comments: The enzyme was originally described from the yeast Saccharomyces cerevisiae (as EC 2.5.1.4), though it had not been well characterized. It was also incorrectly described from several bacteriophages as a hydrolase (EC 3.13.2.2). Later work has shown the bacteriophage enzyme to be a lyase. The enzyme binds its substrate at the border between two subunits of a trimeric complex in a position that prevents it from interacting with water. Instead, the substrate reacts with itself and splits in two. The product, L-homoserine lactone, spontaneously hydrolyses to L-homoserine.

References:

1. Mudd, S.H. The mechanism of the enzymatic cleavage of S-adenosylmethionine to α-amino-γ-butyrolactone. J. Biol. Chem. 234 (1959) 1784-1786. [PMID: 13672964]

2. Mudd, S.H. Enzymatic cleavage of S-adenosylmethionine. J. Biol. Chem. 234 (1959) 87-92. [PMID: 13610898]

3. Hausmann, R. Synthesis of an S-adenosylmethionine-cleaving enzyme in T3-infected Escherichia coli and its disturbance by co-infection with enzymatically incompetent bacteriophage. J. Virol. 1 (1967) 57-63. [PMID: 4918233]

4. Studier, F.W. and Movva, N.R. SAMase gene of bacteriophage T3 is responsible for overcoming host restriction. J. Virol. 19 (1976) 136-145. [PMID: 781304]

5. Guo, X., Soderholm, A., Kanchugal, P., S., Isaksen, G.V., Warsi, O., Eckhard, U., Triguis, S., Gogoll, A., Jerlstrom-Hultqvist, J., Aqvist, J., Andersson, D.I. and Selmer, M. Structure and mechanism of a phage-encoded SAM lyase revises catalytic function of enzyme family. Elife 10 (2021) . [PMID: 33567250]

[EC 4.4.1.42 created 2022 (EC 2.5.1.4 created 1965, incorporated 2022, EC 3.13.2.2 created 1972 as EC 3.3.1.2, modified 1976, modified 2018, transferred 2022 to EC 3.13.2.2, incorporated 2022)]

EC 4.4.1.43

Accepted name: canavanine-γ-lyase

Reaction: L-canavanine + H2O = L-homoserine + N-hydroxyguanidine (overall reaction)
(1a) L-canavanine = vinylglycine + N-hydroxyguanidine
(1b) vinylglycine = (2E)-2-aminobut-2-enoate (spontaneous)
(1c) (2E)-2-aminobut-2-enoate + H2O = L-homoserine (spontaneous)

Other name(s): CangL

Systematic name: L-canavanine N-hydroxyguanidine-lyase (L-homoserine-forming)

Comments: A pyridoxal-phosphate protein. The enzyme, characterized from the bacterium Pseudomonas canavaninivorans, cleaves a carbon-oxygen bond, releasing N-hydroxyguanidine and an unstable enamine product that tautomerizes to an imine form, which is attacked by a water molecule to form L-homoserine.

References:

1. Hauth, F., Buck, H., Stanoppi, M., and Hartig, J. S. Canavanine utilization via homoserine and hydroxyguanidine by a PLP-dependent γ-lyase in Pseudomonadaceae and Rhizobiales. RSC Chemical Biology (0) .

[EC 4.4.1.43 created 2022]

EC 4.8.1.5

Accepted name: thiohydroximate-O-sulfate sulfate/sulfur-lyase (nitrile-forming)

Reaction: an N-(sulfonatooxy)alkanimidothioate = a nitrile + sulfate + sulfur

Glossary: an N-(sulfonatooxy)alkanimidothioate = a thiohydroximate-O-sulfate

Other name(s): NSP (gene name); nitrile-specifier protein

Systematic name: thiohydroximate-O-sulfate sulfate/sulfur-lyase (nitrile-forming)

Comments: The enzyme is involved in the breakdown of glucosinolates. It can act on both aliphatic and aromatic glucosinolates, and forms nitrile-containing products. cf. EC 4.8.1.6, N-(sulfonatooxy)alkenimidothioic acid sulfate-lyase (epithionitrile-forming), and EC 4.8.1.7, phenyl-N-(sulfonatooxy)methanimidothioate sulfolyase.

References:

1. Kissen, R. and Bones, A.M. Nitrile-specifier proteins involved in glucosinolate hydrolysis in Arabidopsis thaliana. J. Biol. Chem. 284 (2009) 12057-12070. [PMID: 19224919]

2. Burow, M., Losansky, A., Muller, R., Plock, A., Kliebenstein, D.J. and Wittstock, U. The genetic basis of constitutive and herbivore-induced ESP-independent nitrile formation in Arabidopsis. Plant Physiol. 149 (2009) 561-574. [PMID: 18987211]

[EC 4.8.1.5 created 2022]

EC 4.8.1.6

Accepted name: N-(sulfonatooxy)alkenimidothioic acid sulfate-lyase (epithionitrile-forming)

Reaction: N-(sulfonatooxy)alkenimidothioic acid with a terminal double bond = an epithionitrile + sulfate

Other name(s): ESP (gene name); epithionitrile-specifier protein; epithiospecifier protein

Systematic name: N-(sulfonatooxy)alkenimidothioic acid sulfate-lyase (epithionitrile-forming)

Comments: The enzyme is involved in the breakdown of glucosinolates. It acts only on aliphatic N-(sulfonatooxy)alkenimidothioic acids produced from ω-alkenyl-glucosinolates, and forms epithionitrile-containing products. cf. EC 4.8.1.5, thiohydroximate-O-sulfate sulfate/sulfur-lyase (nitrile-forming), and EC 4.8.1.7, phenyl-N-(sulfonatooxy)methanimidothioate sulfolyase.

References:

1. Lambrix, V., Reichelt, M., Mitchell-Olds, T., Kliebenstein, D.J. and Gershenzon, J. The Arabidopsis epithiospecifier protein promotes the hydrolysis of glucosinolates to nitriles and influences Trichoplusia ni herbivory. Plant Cell 13 (2001) 2793-2807. [PMID: 11752388]

2. Zabala M. de, T., Grant, M., Bones, A.M., Bennett, R., Lim, Y.S., Kissen, R. and Rossiter, J.T. Characterisation of recombinant epithiospecifier protein and its over-expression in Arabidopsis thaliana. Phytochemistry 66 (2005) 859-867. [PMID: 15845404]

[EC 4.8.1.6 created 2022]

EC 4.8.1.7 Accepted name: phenyl-N-(sulfonatooxy)methanimidothioate sulfolyase

Accepted name: phenyl-N-(sulfonatooxy)methanimidothioate sulfolyase

Reaction: phenyl-N-(sulfonatooxy)methanimidothioate = benzylthiocyanate + sulfate

For diagram of reaction click here

Glossary: glucotropaeolin = 1-S-[(1Z)-2-phenyl-N-(sulfonatooxy)ethanimidoyl]-1-thio-β-D-glucopyranose

Other name(s): TFP (gene name) (ambiguous); thiocyanate-forming protein (ambiguous)

Systematic name: phenyl-N-(sulfonatooxy)methanimidothioate sulfate-lyase (benzylthiocyanate-forming)

Comments: The enzyme, characterized from the plant Lepidium sativum, is involved in the breakdown of the glucosinolate glucotropaeolin. Depending on the substrate, it can also form simple nitrile- and epithionitrile-containing products. cf. EC 4.8.1.5, thiohydroximate-O-sulfate sulfate/sulfur-lyase (nitrile-forming), and EC 4.8.1.6, N-(sulfonatooxy)alkenimidothioic acid sulfate-lyase (epithionitrile-forming).

References:

1. Burow, M., Bergner, A., Gershenzon, J. and Wittstock, U. Glucosinolate hydrolysis in Lepidium sativum - identification of the thiocyanate-forming protein. Plant Mol. Biol. 63 (2007) 49-61. [PMID: 17139450]

[EC 4.8.1.7 created 2022]

EC 4.8.1.8

Accepted name: N-(sulfonatooxy)prop-2-enimidothioate sulfolyase

Reaction: (1) N-(sulfonatooxy)prop-2-enimidothioate = prop-2-enylthiocyanate + sulfate
(2) N-(sulfonatooxy)prop-2-enimidothioate = 2-(thiiran-2-yl)acetonitrile + sulfate

Other name(s): TFP (gene name) (ambiguous); thiocyanate-forming protein (ambiguous)

Systematic name: N-(sulfonatooxy)prop-2-enimidothioate sulfate-lyase (prop2-enylthiocyanate-forming)

Comments: The enzyme, characterized from the plant Thlaspi arvense, is involved in the breakdown of the glucosinolate sinigrin. Depending on the substrate, it can also form simple nitrile-containing products. cf. EC 4.8.1.5, thiohydroximate-O-sulfate sulfate/sulfur-lyase (nitrile-forming) and EC 4.8.1.6, N-(sulfonatooxy)alkenimidothioic acid sulfate-lyase (epithionitrile-forming).

References:

1. Kuchernig, J.C., Backenkohler, A., Lubbecke, M., Burow, M. and Wittstock, U. A thiocyanate-forming protein generates multiple products upon allylglucosinolate breakdown in Thlaspi arvense. Phytochemistry 72 (2011) 1699-1709. [PMID: 21783213]

2. Gumz, F., Krausze, J., Eisenschmidt, D., Backenkohler, A., Barleben, L., Brandt, W. and Wittstock, U. The crystal structure of the thiocyanate-forming protein from Thlaspi arvense, a kelch protein involved in glucosinolate breakdown. Plant Mol. Biol. 89 (2015) 67-81. [PMID: 26260516]

3. Eisenschmidt-Bonn, D., Schneegans, N., Backenkohler, A., Wittstock, U. and Brandt, W. Structural diversification during glucosinolate breakdown: mechanisms of thiocyanate, epithionitrile and simple nitrile formation. Plant J. 99 (2019) 329-343. [PMID: 30900313]

[EC 4.8.1.8 created 2022]

EC 5.3.3.24

Accepted name: neopinone isomerase

Reaction: neopinone = codeinone

For diagram of reaction click here

Glossary: neopinone = 3-methoxy-17-methyl-8,14-didehydro-4,5α-epoxymorphinan-6-one
codeinone = 3-methoxy-17-methyl-7,8-didehydro-4,5α-epoxymorphinan-6-one

Other name(s): NISO (gene name)

Systematic name: neopinone Δ87-isomerase

Comments: The enzyme, characterized from the opium poppy (Papaver somniferum), participates in the biosynthesis of morphine. It also catalyses the isomerization of neomorphinone and morphinone.

References:

1. Dastmalchi, M., Chen, X., Hagel, J.M., Chang, L., Chen, R., Ramasamy, S., Yeaman, S. and Facchini, P.J. Neopinone isomerase is involved in codeine and morphine biosynthesis in opium poppy. Nat. Chem. Biol. 15 (2019) 384-390. [PMID: 30886433]

[EC 5.3.3.24 created 2022]

[EC 7.1.3.2 Transferred entry: Na+-exporting diphosphatase. Now EC 7.2.3.1, Na+-exporting diphosphatase (EC 7.1.3.2 created 2021, deleted 2022)]

EC 7.2 Catalysing the translocation of inorganic cations

EC 7.2.3 Linked to the hydrolysis of diphosphate

EC 7.2.3.1

Accepted name: Na+-exporting diphosphatase

Reaction: diphosphate + H2O + Na+[side 1] = 2 phosphate + Na+[side 2]

Other name(s): Na+-translocating membrane pyrophosphatase; sodium-translocating pyrophosphatase

Systematic name: diphosphate phosphohydrolase (Na+-transporting)

Comments: Requires Na+ and K+. This enzyme, found in some bacteria and archaea, couples the energy from diphosphate hydrolysis to active sodium translocation across the membrane. The enzyme is electrogenic, as the Na+ transport results in generation of a positive potential in the inner side of the membrane.

References:

1. Belogurov, G.A., Malinen, A.M., Turkina, M.V., Jalonen, U., Rytkonen, K., Baykov, A.A. and Lahti, R. Membrane-bound pyrophosphatase of Thermotoga maritima requires sodium for activity. Biochemistry 44 (2005) 2088-2096. [PMID: 15697234]

2. Malinen, A.M., Belogurov, G.A., Baykov, A.A. and Lahti, R. Na+-pyrophosphatase: a novel primary sodium pump. Biochemistry 46 (2007) 8872-8878. [PMID: 17605473]

3. Luoto, H.H., Belogurov, G.A., Baykov, A.A., Lahti, R. and Malinen, A.M. Na+-translocating membrane pyrophosphatases are widespread in the microbial world and evolutionarily precede H+-translocating pyrophosphatases. J. Biol. Chem. 286 (2011) 21633-21642. [PMID: 21527638]

[EC 7.2.3.1 created 2021 as EC 7.1.3.2, transferred 2022 to EC 7.2.3.1]


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