The Enzyme Database

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. They were prepared for the NC-IUBMB by Kristian Axelsen, Ron Caspi, Ture Damhus, Shinya Fushinobu, Julia Hauenstein, Antje Jäde, Ingrid Keseler, 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 To prevent confusion please do not quote new EC numbers until they are incorporated into the main list.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 1.1.1.32 deleted
EC 1.1.1.33 deleted
EC 1.3.8.17 dehydro coenzyme F420 reductase
EC 1.3.8.17 dehydro coenzyme F420 reductase
*EC 1.5.1.20 methylenetetrahydrofolate reductase [NAD(P)H]
*EC 1.5.99.4 nicotine 6-hydroxylase
*EC 1.8.4.16 thioredoxin:protein disulfide reductase
*EC 1.8.7.2 ferredoxin:thioredoxin reductase
*EC 1.14.14.97 methyltetrahydroprotoberberine 14-monooxygenase
*EC 1.14.20.7 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming)
*EC 2.1.1.122 (S)-tetrahydroprotoberberine N-methyltransferase
EC 2.1.1.388 proline betaine—corrinoid protein Co-methyltransferase
EC 2.1.1.389 [methyl-Co(III) quaternary-amine-specific corrinoid protein]—tetrahydrofolate methyltransferase
EC 2.1.1.390 gentamicin X2 methyltransferase
EC 2.3.1.312 D-glutamate N-acetyltransferase
EC 2.3.1.313 NAD-dependent lipoamidase
EC 2.3.2.37 ergosteryl-3β-O-L-aspartate synthase
EC 2.4.1.393 MMP α-(1→4)-mannosyltransferase
EC 2.4.99.26 O-antigen ligase
EC 2.4.99.27 O-antigen polymerase Wzy
EC 2.5.1.157 rRNA small subunit aminocarboxypropyltransferase
*EC 2.7.7.61 citrate lyase holo-[acyl-carrier protein] synthase
EC 2.7.11.27 transferred
EC 2.7.11.35 CRIK-subfamily protein kinase
*EC 3.1.1.29 peptidyl-tRNA hydrolase
EC 3.1.1.121 ergosteryl-3β-O-L-aspartate hydrolase
*EC 3.2.1.115 branched-dextran exo-1,2-α-glucosidase
EC 3.2.1.220 ipecoside β-D-glucosidase
EC 3.4.11.27 archaeal arginyl aminopeptidase
*EC 3.4.19.1 acylaminoacyl-peptidase
EC 3.5.1.138 lipoamidase
EC 4.1.2.64 2-dehydro-3-deoxy-L-fuconate aldolase
EC 4.1.99.28 3′-dehydrocarminate deglycosidase
EC 4.2.99.25 unsaturated pyranuronate lyase
EC 4.3.1.33 (R)-1-hydroxy-2-aminoethylphosphonate ammonia-lyase
EC 5.1.1.25 N-acetyl-D-glutamate racemase
EC 6.3.2.31 coenzyme F420-0:L-glutamate ligase
EC 6.3.2.31 coenzyme F420-0:L-glutamate ligase
*EC 6.3.2.34 coenzyme F420-1:γ-L-glutamate ligase
*EC 7.1.1.2 NADH:ubiquinone reductase (H+-translocating)
EC 7.5.2.14 ABC-type homopolymeric O-antigen exporter

EC 1.1.1.32
Deleted entry: mevaldate reductase, now included with EC 1.1.1.1, alcohol dehydrogenase.
[EC 1.1.1.32 created 1961, deleted 2022]
 
 
EC 1.1.1.33
Deleted entry: mevaldate reductase (NADPH), now included with EC 1.1.1.2, alcohol dehydrogenase (NADP+).
[EC 1.1.1.33 created 1961, deleted 2022]
 
 
EC 1.3.8.17
Accepted name: dehydro coenzyme F420 reductase
Reaction: oxidized coenzyme F420-0 + FMN = dehydro coenzyme F420-0 + FMNH2
Glossary: dehydro coenzyme F420-0 = 2-{[5-deoxy-5-(8-hydroxy-2,4-dioxopyrimidino[4,5-b]quinolin-10(2H)-yl)-L-ribityloxy]hydroxyphosphoryloxy}prop-2-enoate
Other name(s): fbiB (gene name)
Systematic name: oxidized coenzyme F420-0:FMN oxidoreductase
Comments: This enzyme is involved in the biosynthesis of factor 420 (coenzyme F420), a redox-active compound found in all methanogenic archaea, as well as some eubacteria. In some eubacteria the enzyme is multifunctional, also catalysing the activities of EC 6.3.2.31, coenzyme F420-0:L-glutamate ligase, and EC 6.3.2.34, coenzyme F420-1:γ-L-glutamate ligase.
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Bashiri, G., Antoney, J., Jirgis, E.NM., Shah, M.V., Ney, B., Copp, J., Stuteley, S.M., Sreebhavan, S., Palmer, B., Middleditch, M., Tokuriki, N., Greening, C., Scott, C., Baker, E.N. and Jackson, C.J. A revised biosynthetic pathway for the cofactor F420 in prokaryotes. Nat. Commun. 10:1558 (2019). [DOI] [PMID: 30952857]
[EC 1.3.8.17 created 2021]
 
 
*EC 1.5.1.20
Accepted name: methylenetetrahydrofolate reductase [NAD(P)H]
Reaction: 5-methyltetrahydrofolate + NAD(P)+ = 5,10-methylenetetrahydrofolate + NAD(P)H + H+
For diagram of folate cofactor, click here and for diagram of C1 metabolism, click here
Other name(s): MTHFR (gene name)
Systematic name: 5-methyltetrahydrofolate:NAD(P)+ oxidoreductase
Comments: A flavoprotein (FAD). The enzyme catalyses the reversible conversion of 5,10-methylenetetrahydrofolate to 5-methyltetrahydrofolate, playing an important role in folate metabolism by regulating the distribution of one-carbon moieties between cellular methylation reactions and nucleic acid synthesis. This enzyme, characterized from Protozoan parasites of the genus Leishmania, is unique among similar characterized eukaryotic enzymes in that it lacks the C-terminal allosteric regulatory domain (allowing it to catalyse a reversible reaction) and uses NADH and NADPH with equal efficiency under physiological conditions. cf. EC 1.5.1.53, methylenetetrahydrofolate reductase (NADPH); EC 1.5.1.54, methylenetetrahydrofolate reductase (NADH); and EC 1.5.7.1, methylenetetrahydrofolate reductase (ferredoxin).
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 71822-25-8
References:
1.  Vickers, T.J., Orsomando, G., de la Garza, R.D., Scott, D.A., Kang, S.O., Hanson, A.D. and Beverley, S.M. Biochemical and genetic analysis of methylenetetrahydrofolate reductase in Leishmania metabolism and virulence. J. Biol. Chem. 281 (2006) 38150–38158. [DOI] [PMID: 17032644]
[EC 1.5.1.20 created 1978 as EC 1.1.1.171, transferred 1984 to EC 1.5.1.20 (EC 1.7.99.5 incorporated 2005), modified 2005., modified 2021, modified 2023]
 
 
*EC 1.5.99.4
Accepted name: nicotine 6-hydroxylase
Reaction: (S)-nicotine + acceptor + H2O = (S)-6-hydroxynicotine + reduced acceptor
For diagram of nicotine catabolism by arthrobacter, click here
Other name(s): nicotine oxidase; D-nicotine oxidase; nicotine:(acceptor) 6-oxidoreductase (hydroxylating); L-nicotine oxidase; nicotine dehydrogenase (incorrect)
Systematic name: nicotine:acceptor 6-oxidoreductase (hydroxylating)
Comments: A metalloprotein (FMN). The enzyme can act on both the naturally found (S)-enantiomer and the synthetic (R)-enantiomer of nicotine, with retention of configuration in both cases [4].
Links to other databases: BRENDA, EAWAG-BBD, EXPASY, KEGG, CAS registry number: 37256-31-8
References:
1.  Behrman, E.J. and Stanier, R.Y. The bacterial oxidation of nicotinic acid. J. Biol. Chem. 228 (1957) 923–945. [PMID: 13475371]
2.  Decker, K. and Bleeg, H. Induction and purification of stereospecific nicotine oxidizing enzymes from Arthrobacter oxidans. Biochim. Biophys. Acta 105 (1965) 313–324. [PMID: 5849820]
3.  Hochstein, L.I. and Dalton, B.P. The purification and properties of nicotine oxidase. Biochim. Biophys. Acta 139 (1967) 56–68. [DOI] [PMID: 4962139]
4.  Hochstein, L.I. and Rittenberg, S.C. The bacterial oxidation of nicotine. II. The isolation of the first oxidative product and its identification as (1)-6-hydroxynicotine. J. Biol. Chem. 234 (1959) 156–160. [PMID: 13610912]
[EC 1.5.99.4 created 1972, modified 2023]
 
 
*EC 1.8.4.16
Accepted name: thioredoxin:protein disulfide reductase
Reaction: a [protein] with reduced L-cysteine residues + thioredoxin disulfide = a [protein] carrying a disulfide bond + thioredoxin (overall reaction)
(1a) a [thioredoxin:protein disulfide reductase] with reduced L-cysteine residues + thioredoxin disulfide = a [thioredoxin:protein disulfide reductase] carrying a disulfide bond + thioredoxin
(1b) a [thioredoxin:protein disulfide reductase] carrying a disulfide bond + a [protein] with reduced L-cysteine residues = a [thioredoxin:protein disulfide reductase] with reduced L-cysteine residues + a [protein] carrying a disulfide bond
Other name(s): dsbD (gene name); dipZ (gene name)
Systematic name: thioredoxin:protein disulfide oxidoreductase (dithiol-forming)
Comments: The DsbD protein is found in Gram-negative bacteria and transfers electrons from cytoplasmic thioredoxin to the periplasmic substrate proteins DsbC, DsbG and CcmG, reducing disulfide bonds in the target proteins to dithiols. NrdH redoxins, which are found in Gram-positive bacteria, catalyse a similar reaction.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Missiakas, D., Schwager, F. and Raina, S. Identification and characterization of a new disulfide isomerase-like protein (DsbD) in Escherichia coli. EMBO J. 14 (1995) 3415–3424. [DOI] [PMID: 7628442]
2.  Gordon, E.H., Page, M.D., Willis, A.C. and Ferguson, S.J. Escherichia coli DipZ: anatomy of a transmembrane protein disulphide reductase in which three pairs of cysteine residues, one in each of three domains, contribute differentially to function. Mol. Microbiol. 35 (2000) 1360–1374. [DOI] [PMID: 10760137]
3.  Katzen, F. and Beckwith, J. Transmembrane electron transfer by the membrane protein DsbD occurs via a disulfide bond cascade. Cell 103 (2000) 769–779. [DOI] [PMID: 11114333]
4.  Goulding, C.W., Sawaya, M.R., Parseghian, A., Lim, V., Eisenberg, D. and Missiakas, D. Thiol-disulfide exchange in an immunoglobulin-like fold: structure of the N-terminal domain of DsbD. Biochemistry 41 (2002) 6920–6927. [DOI] [PMID: 12033924]
5.  Katzen, F. and Beckwith, J. Role and location of the unusual redox-active cysteines in the hydrophobic domain of the transmembrane electron transporter DsbD. Proc. Natl. Acad. Sci. USA 100 (2003) 10471–10476. [DOI] [PMID: 12925743]
6.  Rozhkova, A. and Glockshuber, R. Thermodynamic aspects of DsbD-mediated electron transport. J. Mol. Biol. 380 (2008) 783–788. [DOI] [PMID: 18571669]
7.  Si, M.R., Zhang, L., Yang, Z.F., Xu, Y.X., Liu, Y.B., Jiang, C.Y., Wang, Y., Shen, X.H. and Liu, S.J. NrdH Redoxin enhances resistance to multiple oxidative stresses by acting as a peroxidase cofactor in Corynebacterium glutamicum. Appl. Environ. Microbiol. 80 (2014) 1750–1762. [DOI] [PMID: 24375145]
[EC 1.8.4.16 created 2019, modified 2023]
 
 
*EC 1.8.7.2
Accepted name: ferredoxin:thioredoxin reductase
Reaction: 2 reduced ferredoxin + thioredoxin disulfide + 2 H+ = 2 oxidized ferredoxin + thioredoxin
Systematic name: ferredoxin:thioredoxin disulfide oxidoreductase
Comments: The enzyme contains a [4Fe-4S] cluster and internal disulfide. It forms a mixed disulfide with thioredoxin on one side, and docks ferredoxin on the other side, enabling two one-electron transfers. The reduced thioredoxins generated by the enzyme activate the Calvin cycle enzymes EC 3.1.3.11 (fructose-bisphosphatase), EC 3.1.3.37 (sedoheptulose-bisphosphatase) and EC 2.7.1.19 (phosphoribulokinase) as well as other chloroplast enzymes by disulfide reduction.
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Buchanan, B.B. Regulation of CO2 assimilation in oxygenic photosynthesis: the ferredoxin/thioredoxin system. Perspective on its discovery, present status, and future development. Arch. Biochem. Biophys. 288 (1991) 1–9. [DOI] [PMID: 1910303]
2.  Chow, L.P., Iwadate, H., Yano, K., Kamo, M., Tsugita, A., Gardet-Salvi, L., Stritt-Etter, A.L. and Schurmann, P. Amino acid sequence of spinach ferredoxin:thioredoxin reductase catalytic subunit and identification of thiol groups constituting a redox-active disulfide and a [4Fe-4S] cluster. Eur. J. Biochem. 231 (1995) 149–156. [DOI] [PMID: 7628465]
3.  Staples, C.R., Ameyibor, E., Fu, W., Gardet-Salvi, L., Stritt-Etter, A.L., Schurmann, P., Knaff, D.B. and Johnson, M.K. The function and properties of the iron-sulfur center in spinach ferredoxin: thioredoxin reductase: a new biological role for iron-sulfur clusters. Biochemistry 35 (1996) 11425–11434. [DOI] [PMID: 8784198]
[EC 1.8.7.2 created 2010, modified 2023]
 
 
*EC 1.14.14.97
Accepted name: methyltetrahydroprotoberberine 14-monooxygenase
Reaction: (1) (S)-cis-N-methylcanadine + [reduced NADPH—hemoprotein reductase] + O2 = allocryptopine + [oxidized NADPH—hemoprotein reductase] + H2O
(2) (S)-cis-N-methylstylopine + [reduced NADPH—hemoprotein reductase] + O2 = protopine + [oxidized NADPH—hemoprotein reductase] + H2O
For diagram of canadine biosynthesis, click here and for diagram of stylopine biosynthesis, click here
Other name(s): methyltetrahydroprotoberberine 14-hydroxylase; (S)-cis-N-methyltetrahydroberberine 14-monooxygenase; (S)-cis-N-methyltetrahydroprotoberberine-14-hydroxylase; CYP82N4 (gene name); (S)-N-methylcanadine,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (14-hydroxylating); (S)-cis-N-methylstylopine 14-hydroxylase
Systematic name: (S)-cis-N-methylcanadine,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (14-hydroxylating)
Comments: A cytochrome P-450 (heme-thiolate) protein involved in the biosynthesis of isoquinoline alkaloids in plants. It also hydroxylates (S)-cis-N-methyltetrahydrothalifendine, and (S)-cis-N-methyltetrahydropalmatine.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 113478-42-5
References:
1.  Rueffer, M. and Zenk, M.H. Enzymatic formation of protopines by a microsomal cytochrome-P-450 system of Corydalis vaginans. Tetrahedron Lett. 28 (1987) 5307–5310. [DOI]
2.  Beaudoin, G.A. and Facchini, P.J. Isolation and characterization of a cDNA encoding (S)-cis-N-methylstylopine 14-hydroxylase from opium poppy, a key enzyme in sanguinarine biosynthesis. Biochem. Biophys. Res. Commun. 431 (2013) 597–603. [DOI] [PMID: 23313486]
[EC 1.14.14.97 created 1990 as EC 1.14.13.37, transferred 2018 to EC 1.14.14.97, modified 2023]
 
 
*EC 1.14.20.7
Accepted name: 2-oxoglutarate/L-arginine monooxygenase/decarboxylase (succinate-forming)
Reaction: L-arginine + 2-oxoglutarate + O2 = L-glutamate 5-semialdehyde + guanidine + succinate + CO2 (overall reaction)
(1a) L-arginine + 2-oxoglutarate + O2 = 5-hydroxy-L-arginine + succinate + CO2
(1b) 5-hydroxy-L-arginine = L-glutamate 5-semialdehyde + guanidine
Other name(s): ethene-forming enzyme; ethylene-forming enzyme; EFE
Systematic name: L-arginine,2-oxoglutarate:oxygen oxidoreductase (succinate-forming)
Comments: This is one of two simultaneous reactions catalysed by the enzyme, which is responsible for ethene (ethylene) production in bacteria of the Pseudomonas syringae group. In the other reaction [EC 1.13.12.19, 2-oxoglutarate dioxygenase (ethene-forming)] the enzyme catalyses the dioxygenation of 2-oxoglutarate forming ethene and three molecules of carbon dioxide.The enzyme catalyses two cycles of the ethene-forming reaction for each cycle of the succinate-forming reaction, so that the stoichiometry of the products ethene and succinate is 2:1. The product of the enzyme, L-glutamate 5-semialdehyde, exists in equilibrium with the cyclic form (S)-1-pyrroline-5-carboxylate.
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Nagahama, K., Ogawa, T., Fujii, T., Tazaki, M., Tanase, S., Morino, Y. and Fukuda, H. Purification and properties of an ethylene-forming enzyme from Pseudomonas syringae pv. phaseolicola PK2. J. Gen. Microbiol. 137 (1991) 2281–2286. [DOI] [PMID: 1770346]
2.  Fukuda, H., Ogawa, T., Tazaki, M., Nagahama, K., Fujii, T., Tanase, S. and Morino, Y. Two reactions are simultaneously catalyzed by a single enzyme: the arginine-dependent simultaneous formation of two products, ethylene and succinate, from 2-oxoglutarate by an enzyme from Pseudomonas syringae. Biochem. Biophys. Res. Commun. 188 (1992) 483–489. [DOI] [PMID: 1445291]
3.  Fukuda, H., Ogawa, T., Ishihara, K., Fujii, T., Nagahama, K., Omata, T., Inoue, Y., Tanase, S. and Morino, Y. Molecular cloning in Escherichia coli, expression, and nucleotide sequence of the gene for the ethylene-forming enzyme of Pseudomonas syringae pv. phaseolicola PK2. Biochem. Biophys. Res. Commun. 188 (1992) 826–832. [DOI] [PMID: 1445325]
4.  Martinez, S., Fellner, M., Herr, C.Q., Ritchie, A., Hu, J. and Hausinger, R.P. Structures and mechanisms of the non-heme Fe(II)- and 2-oxoglutarate-dependent ethylene-forming enzyme: substrate binding creates a twist. J. Am. Chem. Soc. 139 (2017) 11980–11988. [DOI] [PMID: 28780854]
[EC 1.14.20.7 created 2011 as EC 1.14.11.34, transferred 2018 to EC 1.14.20.7, modified 2023]
 
 
*EC 2.1.1.122
Accepted name: (S)-tetrahydroprotoberberine N-methyltransferase
Reaction: S-adenosyl-L-methionine + an (S)-7,8,13,14-tetrahydroprotoberberine = S-adenosyl-L-homocysteine + an (S)-cis-N-methyl-7,8,13,14-tetrahydroprotoberberine
For diagram of canadine biosynthesis, click here, for diagram of noscapine biosynthesis, click here and for diagram of stylopine biosynthesis, click here
Other name(s): tetrahydroprotoberberine cis-N-methyltransferase
Systematic name: S-adenosyl-L-methionine:(S)-7,8,13,14-tetrahydroprotoberberine cis-N-methyltransferase
Comments: Involved in the biosynthesis of isoquinoline alkaloids in plants. Substrates include (S)-canadine, (S)-stylopine, and (S)-tetrahydropalmatine.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 106878-42-6
References:
1.  Rueffer, M., Zumstein, G., Zenk, M.H. Partial purification and characterization of S-adenosyl-L-methionine:(S)-tetrahydroprotoberberine cis-N-methyltransferase from suspension-cultured cells of Eschscholtzia and Corydalis. Phytochemistry 29 (1990) 3727–3733. [DOI]
2.  Liscombe, D.K. and Facchini, P.J. Molecular cloning and characterization of tetrahydroprotoberberine cis-N-methyltransferase, an enzyme involved in alkaloid biosynthesis in opium poppy. J. Biol. Chem. 282 (2007) 14741–14751. [DOI] [PMID: 17389594]
3.  Liscombe, D.K., Ziegler, J., Schmidt, J., Ammer, C. and Facchini, P.J. Targeted metabolite and transcript profiling for elucidating enzyme function: isolation of novel N-methyltransferases from three benzylisoquinoline alkaloid-producing species. Plant J. 60 (2009) 729–743. [DOI] [PMID: 19624470]
[EC 2.1.1.122 created 1999, modified 2023]
 
 
EC 2.1.1.388
Accepted name: proline betaine—corrinoid protein Co-methyltransferase
Reaction: L-proline betaine + a [Co(I) quaternary-amine-specific corrinoid protein] = a [methyl-Co(III) quaternary-amine-specific corrinoid protein] + N-methyl-L-proline
Glossary: L-proline betaine = (2S)-1,1-dimethylpyrrolidinium-2-carboxylate
Other name(s): mtpB (gene name)
Systematic name: L-proline betaine:[Co(I) quaternary-amine-specific corrinoid protein] Co-methyltransferase
Comments: The enzyme, characterized from the bacterium Eubacterium limosum, is a component of a system that transfers a methyl group from L-proline betaine to tetrahydrofolate, as part of an L-proline betaine degradation pathway. The resulting 5-methyltetrahydrofolate is processed to acetyl-CoA via the Wood—Ljungdahl pathway.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Picking, J.W., Behrman, E.J., Zhang, L. and Krzycki, J.A. MtpB, a member of the MttB superfamily from the human intestinal acetogen Eubacterium limosum, catalyzes proline betaine demethylation. J. Biol. Chem. 294 (2019) 13697–13707. [DOI] [PMID: 31341018]
[EC 2.1.1.388 created 2023]
 
 
EC 2.1.1.389
Accepted name: [methyl-Co(III) quaternary-amine-specific corrinoid protein]—tetrahydrofolate methyltransferase
Reaction: a [methyl-Co(III) quaternary-amine-specific corrinoid protein] + tetrahydrofolate = N5-methyltetrahydrofolate + a [Co(I) quaternary-amine-specific corrinoid protein]
Other name(s): mtqA (gene name) (ambiguous); [methyl-Co(III) MtqC corrinoid protein]—tetrahydrofolate methyltransferase
Systematic name: [methyl-Co(III) quaternary-amine-specific corrinoid protein]:tetrahydrofolate methyltransferase
Comments: The enzyme, characterized from the acetogenic gut bacterium Eubacterium limosum, participates in a pathway for the degradation of some quaternary amine compounds (L-proline betaine and L-carnitine). The enzyme catalyses the transfer of a methyl group bound to the cobalt cofactor of a dedicated corrinoid protein (bacterial MtqC) to tetrahydrofolate. The resulting 5-methyltetrahydrofolate is processed to acetyl-CoA via the Wood—Ljungdahl pathway.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Picking, J.W., Behrman, E.J., Zhang, L. and Krzycki, J.A. MtpB, a member of the MttB superfamily from the human intestinal acetogen Eubacterium limosum, catalyzes proline betaine demethylation. J. Biol. Chem. 294 (2019) 13697–13707. [DOI] [PMID: 31341018]
2.  Kountz, D.J., Behrman, E.J., Zhang, L. and Krzycki, J.A. MtcB, a member of the MttB superfamily from the human gut acetogen Eubacterium limosum, is a cobalamin-dependent carnitine demethylase. J. Biol. Chem. 295 (2020) 11971–11981. [DOI] [PMID: 32571881]
[EC 2.1.1.389 created 2023]
 
 
EC 2.1.1.390
Accepted name: gentamicin X2 methyltransferase
Reaction: gentamicin X2 + 2 S-adenosyl-L-methionine + reduced acceptor = geneticin + 5′-deoxyadenosine + L-methionine + S-adenosyl-L-homocysteine + oxidized acceptor (overall reaction)
(1a) S-adenosyl-L-methionine + cob(I)alamin = S-adenosyl-L-homocysteine + methylcob(III)alamin
(1b) methylcob(III)alamin + gentamicin X2 + S-adenosyl-L-methionine = cob(III)alamin + geneticin + 5′-deoxyadenosine + L-methionine
(1c) cob(III)alamin + reduced acceptor = cob(I)alamin + oxidized acceptor
Glossary: geneticin = G418 = (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-β-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2,7-dideoxy-D-glycero-α-D-gluco-heptopyranoside
Other name(s): genK (gene name); gntK (gene name); gentamicin C-methyltransferase (ambiguous)
Systematic name: S-adenosyl-L-methionine:gentamicin X2 C6′-methyltransferase
Comments: The enzyme, isolated from the bacterium Micromonospora echinospora, has a single [4Fe-4S] cluster per monomer. It is a radical S-adenosyl-L-methionine (SAM) enzyme with a methylcob(III)alamin cofactor. The enzyme uses two molecues of SAM for the reaction. One molecule forms a 5′-deoxyadenosyl radical, while the other is used to methylate the cobalamin cofactor. It catalyses methylation of the 6′-carbon of gentamicin X2 (GenX2) to produce genetricin (G418) during the biosynthesis of gentamicins. The 6′-pro-R-hydrogen atom of GenX2 is stereoselectively abstracted by the 5′-deoxyadenosyl radical and methylation occurs with retention of configuration at C6′. The regeneration of cob(I)alamin from cob(III)alamin is carried out with an as yet unidentified electron donor.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Kim, J.Y., Suh, J.W., Kang, S.H., Phan, T.H., Park, S.H. and Kwon, H.J. Gene inactivation study of gntE reveals its role in the first step of pseudotrisaccharide modifications in gentamicin biosynthesis. Biochem. Biophys. Res. Commun. 372 (2008) 730–734. [DOI] [PMID: 18533111]
2.  Hong, W. and Yan, L. Identification of gntK, a gene required for the methylation of purpurosamine C-6′ in gentamicin biosynthesis. J. Gen. Appl. Microbiol. 58 (2012) 349–356. [DOI] [PMID: 23149679]
3.  Kim, H.J., McCarty, R.M., Ogasawara, Y., Liu, Y.N., Mansoorabadi, S.O., LeVieux, J. and Liu, H.W. GenK-catalyzed C-6′ methylation in the biosynthesis of gentamicin: isolation and characterization of a cobalamin-dependent radical SAM enzyme. J. Am. Chem. Soc. 135 (2013) 8093–8096. [DOI] [PMID: 23679096]
4.  Kim, H.J., Liu, Y.N., McCarty, R.M. and Liu, H.W. Reaction Catalyzed by GenK, a Cobalamin-Dependent Radical S-Adenosyl-l-methionine Methyltransferase in the Biosynthetic Pathway of Gentamicin, Proceeds with Retention of Configuration. J. Am. Chem. Soc. 139 (2017) 16084–16087. [DOI] [PMID: 29091410]
[EC 2.1.1.390 created 2023]
 
 
EC 2.3.1.312
Accepted name: D-glutamate N-acetyltransferase
Reaction: acetyl-CoA + D-glutamate = N-acetyl-D-glutamate + CoA
Other name(s): dgcN (gene name)
Systematic name: acetyl-CoA:D-glutamate N-acetyltransferase
Comments: The enzyme, present in bacteria and archaea, participates in a pathway for the degradation of D-glutamate. The enzyme from the marine bacterium Pseudoalteromonas sp. CF6-2 can also acetylate D-glutamine, D-aspartate, and D-asparagine with lower activity.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Yu, Y., Wang, P., Cao, H.Y., Teng, Z.J., Zhu, Y., Wang, M., McMinn, A., Chen, Y., Xiang, H., Zhang, Y.Z., Chen, X.L. and Zhang, Y.Q. Novel D-glutamate catabolic pathway in marine Proteobacteria and halophilic archaea. ISME J. (2023) . [DOI] [PMID: 36690779]
[EC 2.3.1.312 created 2023]
 
 
EC 2.3.1.313
Accepted name: NAD-dependent lipoamidase
Reaction: [lipoyl-carrier protein]-N6-[(R)-lipoyl]-L-lysine + NAD+ + H2O = [lipoyl-carrier protein]-L-lysine + 2′′-O-lipoyl-ADP-D-ribose + nicotinamide
Other name(s): SIRT4; srtN (gene name); cobB (gene name)
Systematic name: [lipoyl-carrier protein]-N6-[(R)-lipoyl]-L-lysine:NAD+ lipoyltranferase (NAD+-hydrolysing; 2′′-O-lipoyl-ADP-D-ribose-forming)
Comments: The enzyme, a member of the sirtuin family, removes the lipoyl group from the dihydrolipoamide acyltransferase (E2) component of 2-oxo acid dehydrogenase complexes such as EC 1.2.1.104, pyruvate dehydrogenase system. The enzyme often has additional activities and can remove other modifications of lysine residues such as acetyl and biotinyl groups. cf. EC 3.5.1.138, lipoamidase.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Mathias, R.A., Greco, T.M., Oberstein, A., Budayeva, H.G., Chakrabarti, R., Rowland, E.A., Kang, Y., Shenk, T. and Cristea, I.M. Sirtuin 4 is a lipoamidase regulating pyruvate dehydrogenase complex activity. Cell 159 (2014) 1615–1625. [DOI] [PMID: 25525879]
2.  Rowland, E.A., Greco, T.M., Snowden, C.K., McCabe, A.L., Silhavy, T.J. and Cristea, I.M. Sirtuin lipoamidase activity is conserved in bacteria as a regulator of metabolic enzyme complexes. mBio 8:e01096-17 (2017). [DOI] [PMID: 28900027]
3.  Betsinger, C.N. and Cristea, I.M. Mitochondrial function, metabolic regulation, and human disease viewed through the prism of sirtuin 4 (SIRT4) functions. J. Proteome Res. 18 (2019) 1929–1938. [DOI] [PMID: 30913880]
[EC 2.3.1.313 created 2023]
 
 
EC 2.3.2.37
Accepted name: ergosteryl-3β-O-L-aspartate synthase
Reaction: L-aspartyl-tRNAAsp + ergosterol = tRNAAsp + 1-(ergostan-3β-yl)-L-aspartate
Other name(s): ErdS
Systematic name: L-aspartyl-tRNAAsp:ergosterol-3β-O-L-aspartyltransferase
Comments: The enzyme, detected in fungal species that belong to the Ascomycota and Basidiomycota phyla and characterized from Aspergillus fumigatus, is bifunctional. The AspRS domain catalyses the transfer of L-aspartate to tRNAAsp (EC 6.1.1.12), while the second domain carries out the transfer of L-aspartate to the 3β-hydroxyl of ergosterol.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Yakobov, N., Fischer, F., Mahmoudi, N., Saga, Y., Grube, C.D., Roy, H., Senger, B., Grob, G., Tatematsu, S., Yokokawa, D., Mouyna, I., Latge, J.P., Nakajima, H., Kushiro, T. and Becker, H.D. RNA-dependent sterol aspartylation in fungi. Proc. Natl. Acad. Sci. USA 117 (2020) 14948–14957. [DOI] [PMID: 32541034]
[EC 2.3.2.37 created 2023]
 
 
EC 2.4.1.393
Accepted name: MMP α-(1→4)-mannosyltransferase
Reaction: GDP-α-D-mannose + [3-O-methyl-α-D-mannosyl-(1→4)]n-3-O-methyl-α-D-mannose = α-D-mannosyl-(1→4)-[3-O-methyl-α-D-mannosyl-(1→4)]n-3-O-methyl-α-D-mannose + GDP
Glossary: MMP = α-D-mannosyl-(1→4)-[3-O-methyl-α-D-mannosyl-(1→4)]n-1-O,3-O-dimethyl-α-D-mannose
Other name(s): manT (gene name)
Systematic name: GDP-α-D-mannose:[3-O-methyl-α-D-mannosyl-(1→4)]n-3-O-methyl-α-D-mannose [(1→4)-α-D-mannosyl]transferase
Comments: The enzyme, present in mycobacterial species that produce a 3-O-methylmannose polysaccharide (MMP), is involved in recycling and biosynthesis of the polymer. The enzyme has the highest activity with 3-O-methylated mannosides with 4-6 residues. The residue at the reducing end of the substrate is often dimethylated, with the second methyl group attached at the O-1 position.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Maranha, A., Costa, M., Ripoll-Rozada, J., Manso, J.A., Miranda, V., Mendes, V.M., Manadas, B., Macedo-Ribeiro, S., Ventura, M.R., Pereira, P.JB. and Empadinhas, N. Self-recycling and partially conservative replication of mycobacterial methylmannose polysaccharides. Commun Biol 6:108 (2023). [DOI] [PMID: 36707645]
[EC 2.4.1.393 created 2023]
 
 
EC 2.4.99.26
Accepted name: O-antigen ligase
Reaction: a lipid-linked O antigen + a lipid A-core oligosaccharide = a lipopolysaccharide + a polyisoprenyl diphosphate
Other name(s): waaL (gene name); surface polymer:lipid A-core ligase; rfaL (gene name)
Systematic name: lipid-linked O-antigen:lipid A-core oligosaccharide O-antigen transferase (configuration-inverting)
Comments: This Gram-negative bacterial enzyme attaches the polymerized O antigen molecule to the outer core region of the lipid A-core oligosaccharide, finalizing the biosynthesis of the lipopolysaccharide. Prior to the reaction the two substrates are attached to the periplasmic-facing side of the inner membrane, and the enzyme transfers the O-antigen from its polyprenyl diphosphate membrane anchor (usually ditrans,octacis-undecaprenyl diphosphate) to a terminal sugar of the lipid A-core oligosaccharide. Despite the popular name "ligase", the enzyme is not a real ligase, as the reaction does not involve the hydrolysis of a phosphate bond in a triphosphate. The enzyme is embedded in the inner membrane and often has 12 trans-membrane segments. It is a metal-independent inverting glycosyltransferase, and in some cases it can attach surface polymers other than O-antigens to the lipid A-core oligosaccharide.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  MacLachlan, P.R., Kadam, S.K. and Sanderson, K.E. Cloning, characterization, and DNA sequence of the rfaLK region for lipopolysaccharide synthesis in Salmonella typhimurium LT2. J. Bacteriol. 173 (1991) 7151–7163. [DOI] [PMID: 1657881]
2.  Whitfield, C., Amor, P.A. and Koplin, R. Modulation of the surface architecture of gram-negative bacteria by the action of surface polymer:lipid A-core ligase and by determinants of polymer chain length. Mol. Microbiol. 23 (1997) 629–638. [DOI] [PMID: 9157235]
3.  Ruan, X., Loyola, D.E., Marolda, C.L., Perez-Donoso, J.M. and Valvano, M.A. The WaaL O-antigen lipopolysaccharide ligase has features in common with metal ion-independent inverting glycosyltransferases. Glycobiology 22 (2012) 288–299. [DOI] [PMID: 21983211]
4.  Ruan, X., Monjaras Feria, J., Hamad, M. and Valvano, M.A. Escherichia coli and Pseudomonas aeruginosa lipopolysaccharide O-antigen ligases share similar membrane topology and biochemical properties. Mol. Microbiol. 110 (2018) 95–113. [DOI] [PMID: 30047569]
[EC 2.4.99.26 created 2023]
 
 
EC 2.4.99.27
Accepted name: O-antigen polymerase Wzy
Reaction: n lipid-linked O-antigen repeat units = a lipid-linked O antigen + (n−1) polyisoprenyl diphosphate
Other name(s): wzy (gene name); rfc (gene name); Wzy O-antigen polymerase; Wzy polymerase
Systematic name: lipid-linked O-antigen repeat unit:O-antigen O-antigen repeat-unit transferase
Comments: The Wzy-type polymerase polymerizes O antigen repeat unit oligosaccharides that are anchored to the periplasmic face of the inner membrane, forming an O antigen polysaccharide that is still anchored to the membrane. A Wzz chain length regulator (sometimes referred to as an O-antigen co-polymerase) normally interacts with Wzy to confer a distinctive modal chain length distribution. The resultant polysaccharide is transferred from the membrane anchor to the lipid A-core oligosaccharide by EC 2.4.99.26, O-antigen ligase, forming a complete lipopolysaccharide structure. There is an enormous diversity of O antigen polymerases with different specificities, reflecting the variability in the structure and composition of O-antigens.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Collins, L.V. and Hackett, J. Molecular cloning, characterization, and nucleotide sequence of the rfc gene, which encodes an O-antigen polymerase of Salmonella typhimurium. J. Bacteriol. 173 (1991) 2521–2529. [DOI] [PMID: 1707412]
2.  Woodward, R., Yi, W., Li, L., Zhao, G., Eguchi, H., Sridhar, P.R., Guo, H., Song, J.K., Motari, E., Cai, L., Kelleher, P., Liu, X., Han, W., Zhang, W., Ding, Y., Li, M. and Wang, P.G. In vitro bacterial polysaccharide biosynthesis: defining the functions of Wzy and Wzz. Nat. Chem. Biol. 6 (2010) 418–423. [DOI] [PMID: 20418877]
3.  Kenyon, J.J. and Reeves, P.R. The Wzy O-antigen polymerase of Yersinia pseudotuberculosis O:2a has a dependence on the Wzz chain-length determinant for efficient polymerization. FEMS Microbiol. Lett. 349 (2013) 163–170. [DOI] [PMID: 24164168]
4.  Islam, S.T., Huszczynski, S.M., Nugent, T., Gold, A.C. and Lam, J.S. Conserved-residue mutations in Wzy affect O-antigen polymerization and Wzz-mediated chain-length regulation in Pseudomonas aeruginosa PAO1. Sci. Rep. 3:3441 (2013). [DOI] [PMID: 24309320]
5.  Islam, S.T. and Lam, J.S. Synthesis of bacterial polysaccharides via the Wzx/Wzy-dependent pathway. Can. J. Microbiol. 60 (2014) 697–716. [DOI] [PMID: 25358682]
6.  Nath, P. and Morona, R. Mutational analysis of the major periplasmic loops of Shigella flexneri Wzy: identification of the residues affecting O antigen modal chain length control, and Wzz-dependent polymerization activity. Microbiology (Reading) 161 (2015) 774–785. [DOI] [PMID: 25627441]
7.  Merino, S., Gonzalez, V. and Tomas, J.M. The first sugar of the repeat units is essential for the Wzy polymerase activity and elongation of the O-antigen lipopolysaccharide. Future Microbiol 11 (2016) 903–918. [DOI] [PMID: 27357519]
[EC 2.4.99.27 created 2023]
 
 
EC 2.5.1.157
Accepted name: rRNA small subunit aminocarboxypropyltransferase
Reaction: S-adenosyl-L-methionine + an N1-methylpseudouridine in rRNA = S-methyl-5′-thioadenosine + an N1-methyl-N3-[(3S)-3-aminocarboxypropyl]-pseudouridine in rRNA
Other name(s): TSR3 (gene name)
Systematic name: S-adenosyl-L-methionine:rRNA N1-methylpseudouridine 3-[(3S)-3-amino-3-carboxypropyl]transferase
Comments: The enzyme, found in all eukaryotes and some archaea, catalyses the final step in production of the modified rRNA nucleotide N1-methyl-N3-[(3S)-aminocarboxypropyl]-pseudouridine (m1acp3ψ). This modified nucleotide is present in the small subunit of ribosomal RNA (18S in eukaryotes and 16S in archaea). cf. EC 2.5.1.114, tRNAPhe (4-demethylwyosine37-C7) aminocarboxypropyltransferase, and EC 2.5.1.108, 2-(3-amino-3-carboxypropyl)histidine synthase.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Meyer, B., Wurm, J.P., Sharma, S., Immer, C., Pogoryelov, D., Kotter, P., Lafontaine, D.L., Wohnert, J. and Entian, K.D. Ribosome biogenesis factor Tsr3 is the aminocarboxypropyl transferase responsible for 18S rRNA hypermodification in yeast and humans. Nucleic Acids Res. 44 (2016) 4304–4316. [DOI] [PMID: 27084949]
[EC 2.5.1.157 created 2023]
 
 
*EC 2.7.7.61
Accepted name: citrate lyase holo-[acyl-carrier protein] synthase
Reaction: 2′-(5-triphosphoribosyl)-3′-dephospho-CoA + apo-[citrate (pro-3S)-lyase] = diphosphate + holo-[citrate (pro-3S)-lyase]
For diagram of reaction, click here
Other name(s): 2′-(5′′-phosphoribosyl)-3′-dephospho-CoA transferase; 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate lyase; CitX; holo-ACP synthase (ambiguous); 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate lyase adenylyltransferase; 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate lyase 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA transferase; 2′-(5′′-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate-lyase adenylyltransferase; holo-citrate lyase synthase (incorrect); 2′-(5-triphosphoribosyl)-3′-dephospho-CoA:apo-citrate-lyase 2′-(5-phosphoribosyl)-3′-dephospho-CoA-transferase
Systematic name: 2′-(5-triphosphoribosyl)-3′-dephospho-CoA:apo-[citrate (pro-3S)-lyase] 2′-(5-phosphoribosyl)-3′-dephospho-CoA-transferase
Comments: The γ-subunit of EC 4.1.3.6, citrate (pro-3S) lyase, serves as an acyl-carrier protein (ACP) and contains the cofactor 2′-(5-triphosphoribosyl)-3′-dephospho-CoA [1,3]. Synthesis and attachment of the cofactor requires the concerted action of this enzyme and EC 2.4.2.52, triphosphoribosyl-dephospho-CoA synthase [1]. In the enzyme from Escherichia coli, the cofactor is attached to serine-14 of the ACP via a phosphodiester bond.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 312492-44-7
References:
1.  Schneider, K., Dimroth, P. and Bott, M. Biosynthesis of the prosthetic group of citrate lyase. Biochemistry 39 (2000) 9438–9450. [DOI] [PMID: 10924139]
2.  Schneider, K., Dimroth, P. and Bott, M. Identification of triphosphoribosyl-dephospho-CoA as precursor of the citrate lyase prosthetic group. FEBS Lett. 483 (2000) 165–168. [DOI] [PMID: 11042274]
3.  Schneider, K., Kästner, C.N., Meyer, M., Wessel, M., Dimroth, P. and Bott, M. Identification of a gene cluster in Klebsiella pneumoniae which includes citX, a gene required for biosynthesis of the citrate lyase prosthetic group. J. Bacteriol. 184 (2002) 2439–2446. [DOI] [PMID: 11948157]
[EC 2.7.7.61 created 2002, modified 2008, modified 2023]
 
 
EC 2.7.11.27
Transferred entry: [acetyl-CoA carboxylase] kinase. Now classified under EC 2.7.11.31, 5-AMP-activated protein kinase.
[EC 2.7.11.27 created 1990 as EC 2.7.1.128 (EC 2.7.1.111 created 1984, incorporated 1992), transferred 2005 to EC 2.7.11.27, deleted 2022]
 
 
EC 2.7.11.35
Accepted name: CRIK-subfamily protein kinase
Reaction: (1) ATP + [protein]-L-serine = ADP + [protein]-O-phospho-L-serine
(2) ATP + [protein]-L-threonine = ADP + [protein]-O-phospho-L-threonine
Other name(s): CRIK; CIT; SGK21; Citron; Citron-K; Sticky/Citron Kinase; Citron Rho-Interacting Kinase
Comments: Requires Mg2+. Peptide array data show a preference for phosphorylation of Thr over Ser and a preference for basic residues in the -5 to -1 positions [1]. CRIK is an animal-specific protein kinase that phosphorylates myosin light chain (cf. EC 2.7.11.18, myosin-light-chain kinase) and is involved in cytokinesis in both mammals and Drosophila. Human CRIK phosphorylates myosin light chain, MYL9/MRLC1 on T19/S20 [2] and GLI2 on S149 [3]. Drosophila CRIK (sticky) interacts with the kinesins Nebbish and Pavarotti, and human CRIK interacts with their orthologs, KIF14 and KIF23/MKLP1 to promote midbody formation during cytokinesis [4]. In Drosophila, CRIK/Sticky catalytic activity was required for this function. Human CRIK is mostly highly expressed in brain, and mutations that alter splicing or kinase activity lead to microcephaly [5, 6], as do knockouts in mouse and rat, and mutations in its interacting partner, the kinesin KIF14 [6].
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Johnson, J.L., Yaron, T.M., Huntsman, E.M., Kerelsky, A., Song, J., Regev, A., Lin, T.Y., Liberatore, K., Cizin, D.M., Cohen, B.M., Vasan, N., Ma, Y., Krismer, K., Robles, J.T., van de Kooij, B., van Vlimmeren, A.E., Andree-Busch, N., Kaufer, N.F., Dorovkov, M.V., Ryazanov, A.G., Takagi, Y., Kastenhuber, E.R., Goncalves, M.D., Hopkins, B.D., Elemento, O., Taatjes, D.J., Maucuer, A., Yamashita, A., Degterev, A., Uduman, M., Lu, J., Landry, S.D., Zhang, B., Cossentino, I., Linding, R., Blenis, J., Hornbeck, P.V., Turk, B.E., Yaffe, M.B. and Cantley, L.C. An atlas of substrate specificities for the human serine/threonine kinome. Nature 613 (2023) 759–766. [DOI] [PMID: 36631611]
2.  Yamashiro, S., Totsukawa, G., Yamakita, Y., Sasaki, Y., Madaule, P., Ishizaki, T., Narumiya, S. and Matsumura, F. Citron kinase, a Rho-dependent kinase, induces di-phosphorylation of regulatory light chain of myosin II. Mol. Biol. Cell 14 (2003) 1745–1756. [DOI] [PMID: 12802051]
3.  Xing, Z., Lin, A., Li, C., Liang, K., Wang, S., Liu, Y., Park, P.K., Qin, L., Wei, Y., Hawke, D.H., Hung, M.C., Lin, C. and Yang, L. lncRNA directs cooperative epigenetic regulation downstream of chemokine signals. Cell 159 (2014) 1110–1125. [DOI] [PMID: 25416949]
4.  Bassi, Z.I., Audusseau, M., Riparbelli, M.G., Callaini, G. and D'Avino, P.P. Citron kinase controls a molecular network required for midbody formation in cytokinesis. Proc. Natl. Acad. Sci. USA 110 (2013) 9782–9787. [DOI] [PMID: 23716662]
5.  Shaheen, R., Hashem, A., Abdel-Salam, G.M., Al-Fadhli, F., Ewida, N. and Alkuraya, F.S. Mutations in CIT, encoding citron rho-interacting serine/threonine kinase, cause severe primary microcephaly in humans. Hum Genet 135 (2016) 1191–1197. [DOI] [PMID: 27503289]
6.  Li, H., Bielas, S.L., Zaki, M.S., Ismail, S., Farfara, D., Um, K., Rosti, R.O., Scott, E.C., Tu, S., Chi, N.C., Gabriel, S., Erson-Omay, E.Z., Ercan-Sencicek, A.G., Yasuno, K., Caglayan, A.O., Kaymakcalan, H., Ekici, B., Bilguvar, K., Gunel, M. and Gleeson, J.G. Biallelic mutations in citron kinase link mitotic cytokinesis to human primary microcephaly. Am. J. Hum. Genet. 99 (2016) 501–510. [DOI] [PMID: 27453578]
[EC 2.7.11.35 created 2023]
 
 
*EC 3.1.1.29
Accepted name: peptidyl-tRNA hydrolase
Reaction: N-substituted aminoacyl-tRNA + H2O = N-substituted amino acid + tRNA
Other name(s): aminoacyl-transfer ribonucleate hydrolase; N-substituted aminoacyl transfer RNA hydrolase; aminoacyl-tRNA hydrolase; PTH1 (gene name); PTH2 (gene name); pth (gene name); spoVC (gene name); PTRH1 (gene name); PTRH2 (gene name)
Systematic name: peptidyl-tRNA peptidylhydrolase
Comments: The enzyme acts on premature protein synthesis products that dissociate from stalled ribosomes, cleaving the peptidyl chains and restoring functionality to the tRNA. In most organisms mutants with limited Pth activity accumulate peptidyl-tRNAs, reducing the availability of uncharged tRNAs below the limit that is necessary for protein synthesis and impairing cell growth. Two distinct classes of the enzyme, Pth and Pth2, have been identified. While most enzymes can recognize and cleave N-acylated aminoacyl-tRNAs, they are not able to act on N-formyl-methionyl-tRNA.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9054-98-2
References:
1.  Cuzin, F., Kretchmer, N., Greenberg, R.E., Hurwitz, R. and Chapeville, F. Enzymatic hydrolysis of N-substituted aminoacyl-tRNA. Proc. Natl. Acad. Sci. USA 58 (1967) 2079–2086. [DOI] [PMID: 4866985]
2.  Kossel, H. and RajBhandary, U.L. Studies on polynucleotides. LXXXVI. Enzymic hydrolysis of N-acylaminoacyl-transfer RNA. J. Mol. Biol. 35 (1968) 539–560. [DOI] [PMID: 4877004]
3.  Jost, J.-P. and Bock, R.M. Enzymatic hydrolysis of N-substituted aminoacyl transfer ribonucleic acid in yeast. J. Biol. Chem. 244 (1969) 5866–5873. [DOI] [PMID: 4981785]
4.  Menninger, J.R. Accumulation of peptidyl tRNA is lethal to Escherichia coli. J. Bacteriol. 137 (1979) 694–696. [DOI] [PMID: 368041]
5.  Dutka, S., Meinnel, T., Lazennec, C., Mechulam, Y. and Blanquet, S. Role of the 1-72 base pair in tRNAs for the activity of Escherichia coli peptidyl-tRNA hydrolase. Nucleic Acids Res. 21 (1993) 4025–4030. [DOI] [PMID: 7690473]
6.  Menez, J., Buckingham, R.H., de Zamaroczy, M. and Campelli, C.K. Peptidyl-tRNA hydrolase in Bacillus subtilis, encoded by spoVC, is essential to vegetative growth, whereas the homologous enzyme in Saccharomyces cerevisiae is dispensable. Mol. Microbiol. 45 (2002) 123–129. [DOI] [PMID: 12100553]
7.  Rosas-Sandoval, G., Ambrogelly, A., Rinehart, J., Wei, D., Cruz-Vera, L.R., Graham, D.E., Stetter, K.O., Guarneros, G. and Soll, D. Orthologs of a novel archaeal and of the bacterial peptidyl-tRNA hydrolase are nonessential in yeast. Proc. Natl. Acad. Sci. USA 99 (2002) 16707–16712. [DOI] [PMID: 12475929]
8.  De Pereda, J.M., Waas, W.F., Jan, Y., Ruoslahti, E., Schimmel, P. and Pascual, J. Crystal structure of a human peptidyl-tRNA hydrolase reveals a new fold and suggests basis for a bifunctional activity. J. Biol. Chem. 279 (2004) 8111–8115. [DOI] [PMID: 14660562]
[EC 3.1.1.29 created 1972, modified 2023]
 
 
EC 3.1.1.121
Accepted name: ergosteryl-3β-O-L-aspartate hydrolase
Reaction: 1-(ergostan-3β-yl) L-aspartate + H2O = ergosterol + L-aspartate
Other name(s): ErdH
Systematic name: ergosteryl-3β-O-L-aspartate aminoacylesterase
Comments: The enzyme has been detected in fungal species that belong to the Ascomycota and Basidiomycota phyla, and has been characterized from the fungus Aspergillus fumigatus.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Yakobov, N., Fischer, F., Mahmoudi, N., Saga, Y., Grube, C.D., Roy, H., Senger, B., Grob, G., Tatematsu, S., Yokokawa, D., Mouyna, I., Latge, J.P., Nakajima, H., Kushiro, T. and Becker, H.D. RNA-dependent sterol aspartylation in fungi. Proc. Natl. Acad. Sci. USA 117 (2020) 14948–14957. [DOI] [PMID: 32541034]
[EC 3.1.1.121 created 2023]
 
 
*EC 3.2.1.115
Accepted name: branched-dextran exo-1,2-α-glucosidase
Reaction: Hydrolysis of (1→2)-α-D-glucosidic linkages at the branch points of dextrans and related polysaccharides, producing free D-glucose
Other name(s): dextran 1,2-α-glucosidase; dextran α-1,2-debranching enzyme; 1,2-α-D-glucosyl-branched-dextran 2-glucohydrolase
Systematic name: (1→2)-α-D-glucosyl-branched-dextran 2-glucohydrolase
Comments: Has a much lower activity with kojibiose and kojitriose.
Links to other databases: BRENDA, EXPASY, KEGG, CAS registry number: 72840-94-9
References:
1.  Kobayashi, M., Mitsuishi, Y., and Matsuda, K. Pronounced hydrolysis of highly branched dextrans with a new type of dextranase. Biochem. Biophys. Res. Commun. 80(2) (1978) 306–312. [DOI] [PMID: 623663]
2.  Mitsuishi, Y., Kobayashi, M. and Matsuda, K. Dextran α-1,2-debranching enzyme from Flavobacterium sp. M-73: its production and purification. Agric. Biol. Chem. 43 (1979) 2283–2290. [DOI]
3.  Mitsuishi, Y., Kobayashi, M. and Matsuda, K. Dextran α-(1→2)-debranching enzyme from Flavobacterium sp. M-73. Properties and mode of action. Carbohydr. Res. 83 (1980) 303–313. [DOI] [PMID: 7407800]
4.  Miyazaki, T., Tanaka, H., Nakamura, S., Dohra, H. and Funane, K. Identification and characterization of dextran α-1,2-debranching enzyme from Microbacterium dextranolyticum. J. Appl. Glycosci. (1999) 70 (2023) 15–24. [DOI] [PMID: 37033117]
[EC 3.2.1.115 created 1989, modified 2023]
 
 
EC 3.2.1.220
Accepted name: ipecoside β-D-glucosidase
Reaction: (1) ipecoside + H2O = ipecoside aglycone + D-glucopyranose
(2) N-deacetylipecoside + H2O = N-deacetylipecoside aglycone + D-glucopyranose
(3) 6-O-methyl-N-deacetylipecoside + H2O = 6-O-methyl-N-deacetylipecoside aglycone + D-glucopyranose
Glossary: ipecoside = methyl (2S,3R,4S)-4-{[(1R)-2-acetyl-6,7-dihydroxy-1,2,3,4-tetrahydro-1-isoquinolinyl]methyl}-2-(β-D-glucopyranosyloxy)-3-vinyl-3,4-dihydro-2H-pyran-5-carboxylate
Other name(s): 6-O-methyl-deacetylisoipecoside β-glucosidase; IpeGlu1
Systematic name: ipecoside glucohydrolase
Comments: The enzyme, isolated from the roots of the plant Carapichea ipecacuanha, preferentially hydrolyses glucosidic ipecoside alkaloids except for their lactams, but shows poor or no activity toward other substrates. IpeGlu1 activity is extremely poor toward 7-O-methyl and 6,7-O,O-dimethyl derivatives. However, 6-O-methyl derivatives are hydrolysed as efficiently as non-methylated substrates. IpeGlu1 accepts both 1α(S)-N-deacetylisoipecoside and 1β(R)-N-deacetylipecoside epimers as substrate, with preference for the 1β(R)-epimer. 6-O-methyl-N-deacetylisoipecoside is an intermediate in the biosynthesis of the medicinal alkaloid emetine.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Nomura, T., Quesada, A.L. and Kutchan, T.M. The new β-D-glucosidase in terpenoid-isoquinoline alkaloid biosynthesis in Psychotria ipecacuanha. J. Biol. Chem. 283 (2008) 34650–34659. [DOI] [PMID: 18927081]
[EC 3.2.1.220 created 2023]
 
 
EC 3.4.11.27
Accepted name: archaeal arginyl aminopeptidase
Reaction: Release of an N-terminal L-arginine from a protein with only minimal activity against other amino acids. L-Arg-7-amido-4-methylcoumarin is the best artificial substrate.
Other name(s): arginyl aminopeptidase PH1704; PH1704; PfpI peptidase; C56.001 (Merops Identifier)
Comments: The enzyme from the archaeon Pyrococcus horikoshii OT3 is thermostable. In that enzyme Cys100 is the nucleophile responsible for the proteolytic activity, while Tyr120 regulates the catalytic conformation of Cys100 through a hydrogen bond, thereby affecting enzyme activity. The activity with L-Arginine is 90-300 times higher than with other N-terminal amino acids. The enzyme shows low endopeptidase activity.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Du, X., Choi, I.G., Kim, R., Wang, W., Jancarik, J., Yokota, H. and Kim, S.H. Crystal structure of an intracellular protease from Pyrococcus horikoshii at 2-Å resolution. Proc. Natl. Acad. Sci. USA 97 (2000) 14079–14084. [DOI] [PMID: 11114201]
2.  Zhan, D., Han, W. and Feng, Y. Experimental and computational studies indicate the mutation of Glu12 to increase the thermostability of oligomeric protease from Pyrococcus horikoshii. J Mol Model 17 (2011) 1241–1249. [DOI] [PMID: 20711794]
3.  Zhan, D., Bai, A., Yu, L., Han, W. and Feng, Y. Characterization of the PH1704 protease from Pyrococcus horikoshii OT3 and the critical functions of Tyr120. PLoS One 9:e103902 (2014). [DOI] [PMID: 25192005]
[EC 3.4.11.27 created 2023]
 
 
*EC 3.4.19.1
Accepted name: acylaminoacyl-peptidase
Reaction: (1) cleavage of an N-acetyl or N-formyl amino acid from the N-terminus of a polypeptide
(2) internal cleavage of oxidized and glycated proteins
Other name(s): acylamino-acid-releasing enzyme; N-acylpeptide hydrolase; N-formylmethionine (fMet) aminopeptidase; α-N-acylpeptide hydrolase; oxidized protein hydrolase; acylpeptide hydrolase; AARE; AAP; OPH; AAH; APEH; ACPH
Comments: This is a bifunctional serine protease that has exopeptidase activity against Nα-acylated peptides and endopeptidase activity against oxidized and glycated proteins. In its exopeptidase mode the enzyme cleaves an N-acetyl or N-formyl amino acid from the N-terminus of a polypeptide. This class of enzymes is evolutionary deeply conserved and is found in bacteria, archaea, animals and plants with different quartenary structures. In humans, malfunction is linked to different types of cancer and sarcoma cell viability. In peptidase family S9 (prolyl oligopeptidase family).
Links to other databases: BRENDA, EXPASY, KEGG, MEROPS, PDB, CAS registry number: 73562-30-8
References:
1.  Tsunazawa, S., Narita, K. and Ogata, K. Acylamino acid-releasing enzyme from rat liver. J. Biochem. (Tokyo) 77 (1975) 89–102. [DOI] [PMID: 1137989]
2.  Fujino, T., Watanabe, K., Beppu, M., Kikugawa, K. and Yasuda, H. Identification of oxidized protein hydrolase of human erythrocytes as acylpeptide hydrolase. Biochim. Biophys Acta 1478 (2000) 102–112. [DOI] [PMID: 10719179]
3.  Yamauchi, Y., Ejiri, Y., Toyoda, Y. and Tanaka, K. Identification and biochemical characterization of plant acylamino acid-releasing enzyme. J. Biochem. 134 (2003) 251–257. [DOI] [PMID: 12966075]
4.  Bartlam, M., Wang, G., Yang, H., Gao, R., Zhao, X., Xie, G., Cao, S., Feng, Y. and Rao, Z. Crystal structure of an acylpeptide hydrolase/esterase from Aeropyrum pernix K1. Structure 12 (2004) 1481–1488. [DOI] [PMID: 15296741]
5.  Shimizu, K., Kiuchi, Y., Ando, K., Hayakawa, M. and Kikugawa, K. Coordination of oxidized protein hydrolase and the proteasome in the clearance of cytotoxic denatured proteins. Biochem. Biophys. Res. Commun. 324 (2004) 140–146. [DOI] [PMID: 15464994]
6.  Nakai, A., Yamauchi, Y., Sumi, S. and Tanaka, K. Role of acylamino acid-releasing enzyme/oxidized protein hydrolase in sustaining homeostasis of the cytoplasmic antioxidative system. Planta 236 (2012) 427–436. [DOI] [PMID: 22398639]
7.  Gogliettino, M., Cocca, E., Sandomenico, A., Gratino, L., Iaccarino, E., Calvanese, L., Rossi, M. and Palmieri, G. Selective inhibition of acylpeptide hydrolase in SAOS-2 osteosarcoma cells: is this enzyme a viable anticancer target. Mol. Biol. Rep. 48 (2021) 1505–1519. [DOI] [PMID: 33471263]
8.  Kiss-Szeman, A.J., Straner, P., Jakli, I., Hosogi, N., Harmat, V., Menyhard, D.K. and Perczel, A. Cryo-EM structure of acylpeptide hydrolase reveals substrate selection by multimerization and a multi-state serine-protease triad. Chem. Sci. 13 (2022) 7132–7142. [DOI] [PMID: 35799812]
[EC 3.4.19.1 created 1978 as EC 3.4.14.3, transferred 1981 to EC 3.4.19.1, modified 2023]
 
 
EC 3.5.1.138
Accepted name: lipoamidase
Reaction: a [lipoyl-carrier protein]-N6-[(R)-lipoyl]-L-lysine + H2O = a [lipoyl-carrier protein]-L-lysine + (R)-lipoate
Other name(s): pyruvate dehydrogenase inactivase
Systematic name: [lipoyl-carrier protein]-N6-[(R)-lipoyl]-L-lysine amidohydrolase
Comments: The enzyme, characterized from the bacterium Enterococcus faecalis, is a member of the Ser-Ser-Lys triad amidohydrolase family. cf. EC 2.3.1.313, NAD-dependent lipoamidase.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Reed, L.J., Koike, M., Levitch, M.E., Leach, F.R. Studies on the nature and reactions of protein-bound lipoic acid. J. Biol. Chem. 232 (1958) 143–158. [DOI] [PMID: 13549405]
2.  Suzuki, K, Reed L.J. Lipoamidase. J. Biol. Chem. 238 (1963) 4021–4025. [DOI] [PMID: 14086741]
3.  Jiang, Y. and Cronan, J.E. Expression cloning and demonstration of Enterococcus faecalis lipoamidase (pyruvate dehydrogenase inactivase) as a Ser-Ser-Lys triad amidohydrolase. J. Biol. Chem. 280 (2005) 2244–2256. [DOI] [PMID: 15528186]
[EC 3.5.1.138 created 2023]
 
 
EC 4.1.2.64
Accepted name: 2-dehydro-3-deoxy-L-fuconate aldolase
Reaction: 2-dehydro-3-deoxy-L-fuconate = pyruvate + (S)-lactaldehyde
Other name(s): 2-keto-3-deoxy-L-fuconate aldolase; L-2-keto-3-deoxyfuconate aldolase; fucH (gene name)
Systematic name: 2-dehydro-3-deoxy-L-fuconate (S)-lactaldehyde-lyase (pyruvate-forming)
Comments: The enzyme, characterized from the bacteria Veillonella ratti and Campylobacter jejuni, participates in an L-fucose degradation pathway. It also has significant activity with 2-dehydro-3-deoxy-D-pentonate (cf. EC 4.1.2.28, 2-dehydro-3-deoxy-D-pentonate aldolase).
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Watanabe, S. Characterization of L-2-keto-3-deoxyfuconate aldolases in a nonphosphorylating L-fucose metabolism pathway in anaerobic bacteria. J. Biol. Chem. 295 (2020) 1338–1349. [DOI] [PMID: 31914410]
[EC 4.1.2.64 created 2023]
 
 
EC 4.1.99.28
Accepted name: 3′-dehydrocarminate deglycosidase
Reaction: 3′-dehydrocarminate = 1,5-anhydro-D-erythro-hex-1-en-3-ulose + kermesate
For diagram of carminate catabolism, click here
Glossary: carminate = 7-(β-D-glucopyranosyl)-3,5,6,8-tetrahydroxy-1-methyl-9,10-dioxo-9,10-dihydroanthracene-2-carboxylate
kermesate = 3,5,6,8-tetrahydroxy-1-methyl-9,10-dioxo-9,10-dihydroanthracene-2-carboxylate
1,5-anhydro-D-erythro-hex-1-en-3-ulose = (2R,3R)-3,5-dihydroxy-2-(hydroxymethyl)-2,3-dihydropyran-4-one
Other name(s): carBC (gene names)
Systematic name: 3′-dehydrocarminate lyase (kermesate-forming)
Comments: Requires Mg2+. This enzyme, isolated from the bacterium Microbacterium 5-2b, participates in a carminate degradation pathway. Following the activity of EC 1.1.3.50, C-glycoside oxidase, it cleaves the C—C bond in 3′-dehydrocarminate. The sugar moiety is released lacking a hydroxyl at position 1, and containing a double bond between C-1 and C-2. The enzyme shows weak activity with other 3′-dehydro-C-glucosides.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Mori, T., Kumano, T., He, H., Watanabe, S., Senda, M., Moriya, T., Adachi, N., Hori, S., Terashita, Y., Kawasaki, M., Hashimoto, Y., Awakawa, T., Senda, T., Abe, I. and Kobayashi, M. C-Glycoside metabolism in the gut and in nature: Identification, characterization, structural analyses and distribution of C-C bond-cleaving enzymes. Nat. Commun. 12:6294 (2021). [DOI] [PMID: 34728636]
[EC 4.1.99.28 created 2023]
 
 
EC 4.2.99.25
Accepted name: unsaturated pyranuronate lyase
Reaction: (1) 4-deoxy-L-erythro-hex-4-enopyranuronate = (4S,5S)-4,5-dihydroxy-2,6-dioxohexanoate
(2) 4-deoxy-L-threo-hex-4-enopyranuronate = (4S,5R)-4,5-dihydroxy-2,6-dioxohexanoate
Glossary: 4-deoxy-L-erythro-hex-4-enopyranuronate = 4,5-unsaturated D-galacturonate
4-deoxy-L-threo-hex-4-enopyranuronate = 4,5-unsaturated D-mannuronate/L-guluronate
(4S,5S)-4,5-dihydroxy-2,6-dioxohexanoate = 5-keto-4-deoxyuronate
(4S,5R)-4,5-dihydroxy-2,6-dioxohexanoate = 5-dehydro-4-deoxy-D-glucuronate
Other name(s): kdgF (gene name)
Systematic name: 4,5-unsaturated pyranuronate lyase (ring-opening)
Comments: The enzyme, found in bacteria and archaea, is involved in the degradation of polysaccharides such as alginate and pectin. The enzyme catalyses a pyranose ring-opening reaction followed by enol-keto tautomerization.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Hobbs, J.K., Lee, S.M., Robb, M., Hof, F., Barr, C., Abe, K.T., Hehemann, J.H., McLean, R., Abbott, D.W. and Boraston, A.B. KdgF, the missing link in the microbial metabolism of uronate sugars from pectin and alginate. Proc. Natl. Acad. Sci. USA 113 (2016) 6188–6193. [DOI] [PMID: 27185956]
[EC 4.2.99.25 created 2023]
 
 
EC 4.3.1.33
Accepted name: (R)-1-hydroxy-2-aminoethylphosphonate ammonia-lyase
Reaction: (1R)-(2-amino-1-hydroxyethyl)phosphonate = phosphonoacetaldehyde + NH3 (overall reaction)
(1a) (1R)-(2-amino-1-hydroxyethyl)phosphonate = (E)-2-aminoethenylphosphonate + H2O
(1b) (E)-2-aminoethenylphosphonate + H2O = phosphonoacetaldehyde + NH3
Glossary: phosphonoacetaldehyde = (2-oxoethyl)phosphonate
Other name(s): pbfA (gene name)
Systematic name: (1R)-(2-amino-1-hydroxyethyl)phosphonate ammonia-lyase
Comments: A pyridoxal 5′-phosphate enzyme. This bacterial enzyme, characterized from the marine bacterium Vibrio splendidus, expands the substrate scope of a widespread pathway for the degradation of 2-aminoethylphosphonate. The enzyme is highly specific and does not act on the S enantiomer of 1-hydroxy-2-aminoethylphosphonate or other structurally related compounds.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Zangelmi, E., Stankovic, T., Malatesta, M., Acquotti, D., Pallitsch, K. and Peracchi, A. Discovery of a new, recurrent enzyme in bacterial phosphonate degradation: (R)-1-hydroxy-2-aminoethylphosphonate ammonia-lyase. Biochemistry 60 (2021) 1214–1225. [DOI] [PMID: 33830741]
[EC 4.3.1.33 created 2023]
 
 
EC 5.1.1.25
Accepted name: N-acetyl-D-glutamate racemase
Reaction: N-acetyl-D-glutamate = N-acetyl-L-glutamate
Other name(s): dgcA (gene name)
Systematic name: N-acetyl-glutamate racemase
Comments: The enzyme, present in bacteria and archaea, participates in a pathway for the degradation of D-glutamate.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Yu, Y., Wang, P., Cao, H.Y., Teng, Z.J., Zhu, Y., Wang, M., McMinn, A., Chen, Y., Xiang, H., Zhang, Y.Z., Chen, X.L. and Zhang, Y.Q. Novel D-glutamate catabolic pathway in marine Proteobacteria and halophilic archaea. ISME J. (2023) . [DOI] [PMID: 36690779]
[EC 5.1.1.25 created 2023]
 
 
EC 6.3.2.31
Accepted name: coenzyme F420-0:L-glutamate ligase
Reaction: GTP + coenzyme F420-0 + L-glutamate = GDP + phosphate + coenzyme F420-1
For diagram of coenzyme F420 biosynthesis, click here
Glossary: coenzyme F420 = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate
Other name(s): CofE-AF; MJ0768; CofE
Systematic name: L-glutamate:coenzyme F420-0 ligase (GDP-forming)
Comments: This protein catalyses the successive addition of two glutamate residues to factor F420 (coenzyme F420) by two distinct and independent reactions. In the reaction described here the enzyme attaches a glutamate via its α-amine group to F420-0. In the second reaction (EC 6.3.2.34, coenzyme F420-1:γ-L-glutamate ligase) it catalyses the addition of a second L-glutamate residue to the γ-carboxyl of the first glutamate.
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Li, H., Graupner, M., Xu, H. and White, R.H. CofE catalyzes the addition of two glutamates to F420-0 in F420 coenzyme biosynthesis in Methanococcus jannaschii. Biochemistry 42 (2003) 9771–9778. [DOI] [PMID: 12911320]
2.  Nocek, B., Evdokimova, E., Proudfoot, M., Kudritska, M., Grochowski, L.L., White, R.H., Savchenko, A., Yakunin, A.F., Edwards, A. and Joachimiak, A. Structure of an amide bond forming F420:γ-glutamyl ligase from Archaeoglobus fulgidus — a member of a new family of non-ribosomal peptide synthases. J. Mol. Biol. 372 (2007) 456–469. [DOI] [PMID: 17669425]
[EC 6.3.2.31 created 2010]
 
 
*EC 6.3.2.34
Accepted name: coenzyme F420-1:γ-L-glutamate ligase
Reaction: GTP + coenzyme F420-1 + L-glutamate = GDP + phosphate + coenzyme γ-F420-2
For diagram of coenzyme F420 biosynthesis, click here
Glossary: coenzyme F420 = N-(N-{O-[5-(8-hydroxy-2,4-dioxo-2,3,4,10-tetrahydropyrimido[4,5-b]quinolin-10-yl)-5-deoxy-L-ribityl-1-phospho]-(S)-lactyl}-γ-L-glutamyl)-L-glutamate
Other name(s): F420:γ-glutamyl ligase; CofE-AF; MJ0768; CofE
Systematic name: L-glutamate:coenzyme F420-1 ligase (GDP-forming)
Comments: This protein catalyses the successive addition of two glutamate residues to factor 420 (coenzyme F420) by two distinct and independent reactions. In the first reaction (EC 6.3.2.31, coenzyme F420-0:L-glutamate ligase) the enzyme attaches a glutamate via its α-amine group to F420-0. In the second reaction, which is described here, the enzyme catalyses the addition of a second L-glutamate residue to the γ-carboxyl of the first glutamate.
Links to other databases: BRENDA, EXPASY, KEGG, PDB
References:
1.  Li, H., Graupner, M., Xu, H. and White, R.H. CofE catalyzes the addition of two glutamates to F420-0 in F420 coenzyme biosynthesis in Methanococcus jannaschii. Biochemistry 42 (2003) 9771–9778. [DOI] [PMID: 12911320]
2.  Nocek, B., Evdokimova, E., Proudfoot, M., Kudritska, M., Grochowski, L.L., White, R.H., Savchenko, A., Yakunin, A.F., Edwards, A. and Joachimiak, A. Structure of an amide bond forming F420:γ-glutamyl ligase from Archaeoglobus fulgidus — a member of a new family of non-ribosomal peptide synthases. J. Mol. Biol. 372 (2007) 456–469. [DOI] [PMID: 17669425]
[EC 6.3.2.34 created 2010, modified 2023]
 
 
*EC 7.1.1.2
Accepted name: NADH:ubiquinone reductase (H+-translocating)
Reaction: NADH + H+ + an ubiquinone + 4 H+[side 1] = NAD+ + an ubiquinol + 4 H+[side 2]
Other name(s): ubiquinone reductase (ambiguous); type 1 dehydrogenase; complex 1 dehydrogenase; coenzyme Q reductase (ambiguous); complex I (electron transport chain); complex I (mitochondrial electron transport); complex I (NADH:Q1 oxidoreductase); dihydronicotinamide adenine dinucleotide-coenzyme Q reductase (ambiguous); DPNH-coenzyme Q reductase (ambiguous); DPNH-ubiquinone reductase (ambiguous); mitochondrial electron transport complex 1; mitochondrial electron transport complex I; NADH coenzyme Q1 reductase; NADH-coenzyme Q oxidoreductase (ambiguous); NADH-coenzyme Q reductase (ambiguous); NADH-CoQ oxidoreductase (ambiguous); NADH-dehydrogenase (ubiquinone) (ambiguous); NADH-CoQ reductase (ambiguous); NADH-ubiquinone reductase (ambiguous); NADH-ubiquinone oxidoreductase (ambiguous); NADH-ubiquinone-1 reductase; reduced nicotinamide adenine dinucleotide-coenzyme Q reductase (ambiguous); NADH:ubiquinone oxidoreductase complex; NADH-Q6 oxidoreductase (ambiguous); electron transfer complex I; NADH2 dehydrogenase (ubiquinone)
Systematic name: NADH:ubiquinone oxidoreductase
Comments: The enzyme is a very large complex that participates in electron transfer chains of mitochondria and aerobic bacteria, transferring two electrons from NADH to a ubiquinone in the membrane's ubiquinone pool while pumping additional protons across the membrane, generating proton motive force. Different reports disagree whether the enzyme pumps 3 or 4 protons. Reversed electron transport through this enzyme can reduce NAD+ to NADH.
Links to other databases: BRENDA, EXPASY, KEGG, PDB, CAS registry number: 9028-04-0
References:
1.  Hatefi, Y., Ragan, C.I. and Galante, Y.M. The enzymes and the enzyme complexes of the mitochondrial oxidative phosphorylation system. In: Martonosi, A. (Ed.), The Enzymes of Biological Membranes, 2nd edn, vol. 4, Plenum Press, New York, 1985, pp. 1–70.
2.  Herter, S.M., Kortluke, C.M. and Drews, G. Complex I of Rhodobacter capsulatus and its role in reverted electron transport. Arch. Microbiol. 169 (1998) 98–105. [DOI] [PMID: 9446680]
3.  Hunte, C., Zickermann, V. and Brandt, U. Functional modules and structural basis of conformational coupling in mitochondrial complex I. Science 329 (2010) 448–451. [DOI] [PMID: 20595580]
4.  Efremov, R.G., Baradaran, R. and Sazanov, L.A. The architecture of respiratory complex I. Nature 465 (2010) 441–445. [DOI] [PMID: 20505720]
5.  Wikstrom, M. and Hummer, G. Stoichiometry of proton translocation by respiratory complex I and its mechanistic implications. Proc. Natl. Acad. Sci. USA 109 (2012) 4431–4436. [DOI] [PMID: 22392981]
[EC 7.1.1.2 created 1961 as EC 1.6.5.3, deleted 1965, reinstated 1983, modified 2011, modified 2013, transferred 2018 to EC 7.1.1.2, modified 2023]
 
 
EC 7.5.2.14
Accepted name: ABC-type homopolymeric O-antigen exporter
Reaction: ATP + a lipid-linked O antigen[cytosol] + H2O = ADP + phosphate + a lipid-linked O antigen[periplasm]
Other name(s): wzm (gene name); wzt (gene name)
Systematic name: ATP phosphohydrolase (ABC-type, homopolymeric O-antigen exporting)
Comments: Unlike heteropolymeric O antigens, which are polymerized in the periplasm by EC 2.4.99.27, O antigen polymerase Wzy, homopolymeric O antigens are polymerized inside the cytoplasm by a progressive transfer of sugar monomers to a growing chain attached to a polyprenyl diphosphate membrane anchor. When the chain reaches its full length it is transported across the cytoplasmic membrane by this ABC-type transporter, which consists of an ATP-binding subunit (Wzt) and an integral membrane protein (Wzm). Wzm proteins are poorly conserved in their primary sequence. Once in the periplasm, the O antigen is ligated to the lipid A-core complex by EC 2.4.99.26, O-antigen ligase.
Links to other databases: BRENDA, EXPASY, KEGG
References:
1.  Kido, N., Torgov, V.I., Sugiyama, T., Uchiya, K., Sugihara, H., Komatsu, T., Kato, N. and Jann, K. Expression of the O9 polysaccharide of Escherichia coli: sequencing of the E. coli O9 rfb gene cluster, characterization of mannosyl transferases, and evidence for an ATP-binding cassette transport system. J. Bacteriol. 177 (1995) 2178–2187. [DOI] [PMID: 7536735]
2.  Rocchetta, H.L. and Lam, J.S. Identification and functional characterization of an ABC transport system involved in polysaccharide export of A-band lipopolysaccharide in Pseudomonas aeruginosa. J. Bacteriol. 179 (1997) 4713–4724. [DOI] [PMID: 9244257]
3.  Cuthbertson, L., Powers, J. and Whitfield, C. The C-terminal domain of the nucleotide-binding domain protein Wzt determines substrate specificity in the ATP-binding cassette transporter for the lipopolysaccharide O-antigens in Escherichia coli serotypes O8 and O9a. J. Biol. Chem. 280 (2005) 30310–30319. [DOI] [PMID: 15980069]
4.  Cuthbertson, L., Kimber, M.S. and Whitfield, C. Substrate binding by a bacterial ABC transporter involved in polysaccharide export. Proc. Natl. Acad. Sci. USA 104 (2007) 19529–19534. [DOI] [PMID: 18032609]
5.  Mann, E., Mallette, E., Clarke, B.R., Kimber, M.S. and Whitfield, C. The Klebsiella pneumoniae O12 ATP-binding cassette (ABC) transporter recognizes the terminal residue of its O-antigen polysaccharide substrate. J. Biol. Chem. 291 (2016) 9748–9761. [DOI] [PMID: 26934919]
6.  Mann, E., Kelly, S.D., Al-Abdul-Wahid, M.S., Clarke, B.R., Ovchinnikova, O.G., Liu, B. and Whitfield, C. Substrate recognition by a carbohydrate-binding module in the prototypical ABC transporter for lipopolysaccharide O-antigen from Escherichia coli O9a. J. Biol. Chem. 294 (2019) 14978–14990. [DOI] [PMID: 31416837]
[EC 7.5.2.14 created 2023]
 
 


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