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 To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.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 1.1.3.50 C-glycoside oxidase (1 August 2022)
EC 2.3.1.309 [β-tubulin]-L-lysine N-acetyltransferase (1 August 2022)
EC 2.3.1.310 benzoylsuccinyl-CoA thiolase (1 August 2022)
EC 2.7.7.108 protein adenylyltransferase (1 August 2022)
EC 3.1.3.81 transferred now EC 3.6.1.75 (1 August 2022)
EC 3.6.1.75 diacylglycerol diphosphate phosphatase (1 August 2022)
EC 4.3.2.11 (3R)-3-[(carboxylmethyl)amino]fatty acid synthase (1 August 2022)
EC 6.2.1.76 malonate–CoA ligase (1 August 2022)

EC 1.1.3.50

Accepted name: C-glycoside oxidase

Reaction: carminate + O2 = 3'-dehydrocarminate + H2O2

Glossary: carminate = 7-carboxy-4,6-dihydroxy-8-methyl-9,10-dioxo-2-[(2S,3R,4R,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]anthracene-1,3-diolate

Other name(s): carA (gene name)

Systematic name: carminate:oxygen 3'-oxidoreductase (H2O2-forming)

Comments: A flavoprotein (FAD). This bacterial enzyme participates in degradation of certain C-glucosides by catalysing the oxidation of the hydroxyl group at position 3 of the glycose moiety. The enzyme was found active with assorted C-glycosides, such as carminate, mangiferin, and C6-glycosylated flavonoids, but not with D-glucose or C8-glycosylated flavonoids.

References:

1. Kumano, T., Hori, S., Watanabe, S., Terashita, Y., Yu, H.Y., Hashimoto, Y., Senda, T., Senda, M. and Kobayashi, M. FAD-dependent C-glycoside-metabolizing enzymes in microorganisms: Screening, characterization, and crystal structure analysis. Proc. Natl. Acad. Sci. USA 118 (2021) . [PMID: 34583991]

[EC 1.1.3.50 created 2022]

EC 2.3.1.309

Accepted name: [β-tubulin]-L-lysine N-acetyltransferase

Reaction: acetyl-CoA + a [β-tubulin]-L-lysine = CoA + a [β-tubulin]-N6-acetyl-L-lysine

Other name(s): San; NatE; NAA50 (gene name)

Systematic name: acetyl-CoA:[β-tubulin]-L-lysine N6-acetyltransferase

Comments: The enzyme acetylates L-lysine at position 252 of β-tubulin, which is located at the interface of α/β-tubulin heterodimers and interacts with the phosphate group of the α-tubulin-bound GTP. The acetylation is thought to attenuate tubulin incorporation into microtubules. The enzyme catalysing this activity (NAA50) also catalyses the acetylation of certain N-terminal methionyl residues. That activity is classified as EC 2.3.1.258, N-terminal methionine Nα-acetyltransferase NatE. cf. EC 2.3.1.108, α-tubulin N-acetyltransferase.

References:

1. Chu, C.W., Hou, F., Zhang, J., Phu, L., Loktev, A.V., Kirkpatrick, D.S., Jackson, P.K., Zhao, Y. and Zou, H. A novel acetylation of β-tubulin by San modulates microtubule polymerization via down-regulating tubulin incorporation. Mol. Biol. Cell 22 (2011) 448-456. [PMID: 21177827]

[EC 2.3.1.309 created 2022]

EC 2.3.1.310

Accepted name: benzoylsuccinyl-CoA thiolase

Reaction: (S)-2-benzoylsuccinyl-CoA + CoA = benzoyl-CoA + succinyl-CoA

Other name(s): bbsAB (gene names)

Systematic name: (S)-2-benzoylsuccinyl-CoA:CoA benzoyltransferase (benzoyl-CoA-forming)

Comments: The enzyme, characterized from the bacteria Thauera aromatica and Geobacter metallireducens, participates in an anaerobic toluene degradation pathway.

References:

1. Leuthner, B. and Heider, J. Anaerobic toluene catabolism of Thauera aromatica: the bbs operon codes for enzymes of β oxidation of the intermediate benzylsuccinate. J. Bacteriol. 182 (2000) 272-277. [PMID: 10629170]

2. Weidenweber, S., Schuhle, K., Lippert, M.L., Mock, J., Seubert, A., Demmer, U., Ermler, U. and Heider, J. Finis tolueni: a new type of thiolase with an integrated Zn-finger subunit catalyzes the final step of anaerobic toluene metabolism. FEBS J. (2022) . [PMID: 35313080]

[EC 2.3.1.310 created 2022]

EC 2.7.7.108

Accepted name: protein adenylyltransferase

Reaction: (1) ATP + a [protein]-L-serine = diphosphate + a [protein]-O-(5′-adenylyl)-L-serine
(1) ATP + a [protein]-L-threonine = diphosphate + a [protein]-O-(5′-adenylyl)-L-threonine
(1) ATP + a [protein]-L-tyrosine = diphosphate + a [protein]-O-(5′-adenylyl)-L-tyrosine

Other name(s): AMPylase; selO (gene name); FMP40 (gene name); SELENOO (gene name); IbpA; VopS; DrrA; FICD (gene name)

Systematic name: [protein] L-serine/L-threonine/L-tyrosine adenylyltransferase

Comments: The enzyme, commonly referred to as AMPylase, transfers an adenylyl (adenosine 5'-phosphate) group from ATP to L-serine, L-threonine, and L-tyrosine residues in its target protein substrates. AMPylation is found in both prokaryotes and eukaryotes. In bacteria AMPylases are abundant enzymes that either regulate the function of endogenous bacterial proteins or are translocated into host cells to hijack host cell signalling processes. Metazoans AMPylases are either enzymes containing a conserved Fic domain that primarily modify the ER-resident chaperone BiP, or mitochondrial selenocysteine-containing proteins (SelO) involved in redox signalling.

References:

1. Xiao, J., Worby, C.A., Mattoo, S., Sankaran, B. and Dixon, J.E. Structural basis of Fic-mediated adenylylation. Nat. Struct. Mol. Biol. 17 (2010) 1004-1010. [PMID: 20622875]

2. Palanivelu, D.V., Goepfert, A., Meury, M., Guye, P., Dehio, C. and Schirmer, T. Fic domain-catalyzed adenylylation: insight provided by the structural analysis of the type IV secretion system effector BepA. Protein Sci. 20 (2011) 492-499. [PMID: 21213248]

3. Truttmann, M.C., Cruz, V.E., Guo, X., Engert, C., Schwartz, T.U. and Ploegh, H.L. The Caenorhabditis elegans protein FIC-1 is an AMPylase that covalently modifies heat-shock 70 family proteins, translation elongation factors and histones. PLoS Genet. 12 (2016) e1006023. [PMID: 27138431]

4. Sreelatha, A., Yee, S.S., Lopez, V.A., Park, B.C., Kinch, L.N., Pilch, S., Servage, K.A., Zhang, J., Jiou, J., Karasiewicz-Urbanska, M., Lobocka, M., Grishin, N.V., Orth, K., Kucharczyk, R., Pawlowski, K., Tomchick, D.R. and Tagliabracci, V.S. Protein AMPylation by an evolutionarily conserved pseudokinase. Cell 175 (2018) 809-821. [PMID: 30270044]

5. Bardwell, L. Pseudokinases: Flipping the ATP for AMPylation. Curr. Biol. 29 (2019) R23-R25. [PMID: 30620911]

6. Chatterjee, B.K. and Truttmann, M.C. Fic and non-Fic AMPylases: protein AMPylation in metazoans. Open Biol 11 (2021) 210009. [PMID: 33947243]

[EC 2.7.7.108 created 2022]

[EC 3.1.3.81 Transferred entry: diacylglycerol diphosphate phosphatase. Now EC 3.6.1.75, diacylglycerol diphosphate phosphatase (EC 3.1.3.81 created 2010, deleted 2022)]

EC 3.6.1.75

Accepted name: diacylglycerol diphosphate phosphatase

Reaction: 1,2-diacyl-sn-glycerol 3-diphosphate + H2O = 1,2-diacyl-sn-glycerol 3-phosphate + phosphate

Other name(s): DGPP phosphatase; DGPP phosphohydrolase; DPP1; DPPL1; DPPL2; PAP2; pyrophosphate phosphatase

Systematic name: 1,2-diacyl-sn-glycerol 3-phosphate phosphohydrolase

Comments: The bifunctional enzyme catalyses the dephosphorylation of diacylglycerol diphosphate to phosphatidate and the subsequent dephosphorylation of phosphatidate to diacylglycerol (cf. phosphatidate phosphatase (EC 3.1.3.4)). It regulates intracellular levels of diacylglycerol diphosphate and phosphatidate, phospholipid molecules believed to play a signalling role in stress response [6]. The phosphatase activity of the bifunctional enzyme is Mg2+-independent and N-ethylmaleimide-insensitive and is distinct from the Mg2+-dependent and N-ethylmaleimide-sensitive enzyme EC 3.1.3.4 (phosphatidate phosphatase) [5].The diacylglycerol pyrophosphate phosphatase activity in Saccharomyces cerevisiae is induced by zinc depletion, by inositol supplementation, and when cells enter the stationary phase [4].

References:

1. Dillon, D.A., Wu, W.I., Riedel, B., Wissing, J.B., Dowhan, W. and Carman, G.M. The Escherichia coli pgpB gene encodes for a diacylglycerol pyrophosphate phosphatase activity. J. Biol. Chem. 271 (1996) 30548-30553. [PMID: 8940025]

2. Dillon, D.A., Chen, X., Zeimetz, G.M., Wu, W.I., Waggoner, D.W., Dewald, J., Brindley, D.N. and Carman, G.M. Mammalian Mg2+-independent phosphatidate phosphatase (PAP2) displays diacylglycerol pyrophosphate phosphatase activity. J. Biol. Chem. 272 (1997) 10361-10366. [PMID: 9099673]

3. Wu, W.I., Liu, Y., Riedel, B., Wissing, J.B., Fischl, A.S. and Carman, G.M. Purification and characterization of diacylglycerol pyrophosphate phosphatase from Saccharomyces cerevisiae. J. Biol. Chem. 271 (1996) 1868-1876. [PMID: 8567632]

4. Oshiro, J., Han, G.S. and Carman, G.M. Diacylglycerol pyrophosphate phosphatase in Saccharomyces cerevisiae. Biochim. Biophys. Acta 1635 (2003) 1-9. [PMID: 14642771]

5. Carman, G.M. Phosphatidate phosphatases and diacylglycerol pyrophosphate phosphatases in Saccharomyces cerevisiae and Escherichia coli. Biochim. Biophys. Acta 1348 (1997) 45-55. [PMID: 9370315]

6. Han, G.S., Johnston, C.N., Chen, X., Athenstaedt, K., Daum, G. and Carman, G.M. Regulation of the Saccharomyces cerevisiae DPP1-encoded diacylglycerol pyrophosphate phosphatase by zinc. J. Biol. Chem. 276 (2001) 10126-10133. [PMID: 11139591]

[EC 3.6.1.75 created 2010 as EC 3.1.3.81, 2022 transferred to EC 3.6.1.75]

EC 4.3.2.11

Accepted name: (3R)-3-[(carboxylmethyl)amino]fatty acid synthase

Reaction: (3R)-3-[(carboxylmethyl)amino]fatty acid + an [acyl-carrier protein] = a (2E)-unsaturated fatty acyl-[acyl-carrier protein] + glycine + H2O

Other name(s): scoD (gene name); mmaD (gene name)

Systematic name: (3R)-3-[(carboxylmethyl)amino]fatty acid glycine-lyase ((2E)-unsaturated fatty acyl-[acyl-carrier protein]-forming)

Comments: The enzyme, found in some actinobacterial species, participates in the biosynthesis of isonitrile-containing lipopeptides. It catalyses the formation of (3R)-3-[(carboxylmethyl)amino]fatty acid by the addition of glycine and the release of the product from the acyl-carrier protein.

References:

1. Harris, N.C., Sato, M., Herman, N.A., Twigg, F., Cai, W., Liu, J., Zhu, X., Downey, J., Khalaf, R., Martin, J., Koshino, H. and Zhang, W. Biosynthesis of isonitrile lipopeptides by conserved nonribosomal peptide synthetase gene clusters in Actinobacteria. Proc. Natl. Acad. Sci. USA 114 (2017) 7025-7030. [PMID: 28634299]

2. Harris, N.C., Born, D.A., Cai, W., Huang, Y., Martin, J., Khalaf, R., Drennan, C.L. and Zhang, W. Isonitrile formation by a non-heme iron(II)-dependent oxidase/decarboxylase. Angew. Chem. Int. Ed. Engl. 57 (2018) 9707-9710. [PMID: 29906336]

[EC 4.3.2.11 created 2022]

EC 6.2.1.76

Accepted name: malonate—CoA ligase

Reaction: ATP + malonate + CoA = AMP + phosphate + malonyl-CoA

Other name(s): ACSF3 (gene name); AAE13 (gene name); malonyl-CoA synthetase

Systematic name: malonate:CoA ligase (AMP-forming)

Comments: The enzyme, found in mitochondria, detoxifies malonate, which is a potent inhibitor of mitochondrial respiration, and provides malonyl-CoA to the mitochondrial fatty acid biosynthesis pathway.

References:

1. Gueguen, V., Macherel, D., Jaquinod, M., Douce, R. and Bourguignon, J. Fatty acid and lipoic acid biosynthesis in higher plant mitochondria. J. Biol. Chem. 275 (2000) 5016-5025. [PMID: 10671542]

2. Witkowski, A., Thweatt, J. and Smith, S. Mammalian ACSF3 protein is a malonyl-CoA synthetase that supplies the chain extender units for mitochondrial fatty acid synthesis. J. Biol. Chem. 286 (2011) 33729-33736. [PMID: 21846720]

3. Chen, H., Kim, H.U., Weng, H. and Browse, J. Malonyl-CoA synthetase, encoded by ACYL ACTIVATING ENZYME13, is essential for growth and development of Arabidopsis. Plant Cell 23 (2011) 2247-2262. [PMID: 21642549]

4. Guan, X. and Nikolau, B.J. AAE13 encodes a dual-localized malonyl-CoA synthetase that is crucial for mitochondrial fatty acid biosynthesis. Plant J. 85 (2016) 581-593. [PMID: 26836315]

5. Bowman, C.E., Rodriguez, S., Selen Alpergin, E.S., Acoba, M.G., Zhao, L., Hartung, T., Claypool, S.M., Watkins, P.A. and Wolfgang, M.J. The mammalian malonyl-CoA synthetase ACSF3 is required for mitochondrial protein malonylation and metabolic efficiency. Cell Chem. Biol. 24 (2017) 673-684.e4. [PMID: 28479296]

6. Bowman, C.E. and Wolfgang, M.J. Role of the malonyl-CoA synthetase ACSF3 in mitochondrial metabolism. Adv Biol Regul 71 (2019) 34-40. [PMID: 30201289]

[EC 6.2.1.76 created 2022]


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