The Enzyme Database

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EC 1.14.19.72     
Accepted name: (–)-pluviatolide synthase
Reaction: (–)-matairesinol + [reduced NADPH—hemoprotein reductase] + O2 = (–)-pluviatolide + [oxidized NADPH—hemoprotein reductase] + 2 H2O
For diagram of podophyllotoxin biosynthesis, click here
Glossary: (–)-matairesinol = 3R,4R)-3,4-bis[(4-hydroxy-3-methoxyphenyl)methyl]oxolan-2-one
(–)-pluviatolide = ((3R,4R)-4-(2H-1,3-benzodioxol-5-ylmethyl)-3-[(4-hydroxy-3-methoxyphenyl)methyl]oxolan-2-one
Other name(s): CYP719A23 (gene name)
Systematic name: (–)-matairesinol,[reduced NADPH—hemoprotein reductase]:oxygen oxidoreductase (methylenedioxy-bridge-forming)
Comments: A cytochrome P-450 (heme-thiolate) protein. The enzyme from the plants Sinopodophyllum hexandrum and Podophyllum peltatum catalyses the formation of a methylenedioxy-bridge. It is involved in the biosynthesis of podophyllotoxin, a non-alkaloid toxin lignan whose derivatives are important anticancer drugs.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Marques, J.V., Kim, K.W., Lee, C., Costa, M.A., May, G.D., Crow, J.A., Davin, L.B. and Lewis, N.G. Next generation sequencing in predicting gene function in podophyllotoxin biosynthesis. J. Biol. Chem. 288 (2013) 466–479. [DOI] [PMID: 23161544]
[EC 1.14.19.72 created 2016 as EC 1.14.21.11, transferred 2018 to EC 1.14.19.72]
 
 
EC 1.14.20.8     
Accepted name: (–)-deoxypodophyllotoxin synthase
Reaction: (–)-yatein + 2-oxoglutarate + O2 = (–)-deoxypodophyllotoxin + succinate + CO2 + H2O
For diagram of podophyllotoxin biosynthesis, click here
Glossary: (–)-yatein = (3R,4R)-4-(1,3-benzodioxol-5-ylmethyl)-3-(3,4,5-trimethoxybenzyl)dihydrofuran-2(3H)-one
(–)-deoxypodophyllotoxin = (5R,5aR,8aR)-5-(3,4,5-trimethoxyphenyl)-5,8,8a,9-tetrahydrofuro[3′,4′:6,7]naphtho[2,3-d][1,3]dioxol-6(5a)-one
Other name(s): 2-ODD (gene name)
Systematic name: (–)-yatein,2-oxoglutarate:oxygen oxidoreductase (ring-forming)
Comments: The enzyme, characterized from the plant Sinopodophyllum hexandrum (mayapple), is involved in the biosynthetic pathway of podophyllotoxin, a non-alkaloid toxin lignan whose derivatives are important anticancer drugs. It catalyses the closure of the central six-membered ring in the aryltetralin scaffold.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Lau, W. and Sattely, E.S. Six enzymes from mayapple that complete the biosynthetic pathway to the etoposide aglycone. Science 349 (2015) 1224–1228. [DOI] [PMID: 26359402]
[EC 1.14.20.8 created 2016 as EC 1.14.11.50, transferred 2018 to EC 1.14.20.8]
 
 
EC 1.14.20.14     
Accepted name: hapalindole-type alkaloid chlorinase
Reaction: (1) hapalindole U + 2-oxoglutarate + O2 + chloride = hapalindole G + succinate + CO2 + H2O
(2)12-epi-fischerindole U + 2-oxoglutarate + O2 + chloride = 12-epi-fischerindole G + succinate + CO2 + H2O
For diagram of hapalindole/fischerindole biosynthesis, click here
Glossary: 12-epi-fischerindole U = (6aS,9S,10R,10aS)-9-ethenyl-10-isocyano-6,6,9-trimethyl-5,6,6a,7,8,9,10,10a-octahydroindeno[2,1-b]indole
12-epi-fischerindole G = (6aR,8R,9S,10R,10aS)-8-chloro-9-ethenyl-10-isocyano-6,6,9-trimethyl-5,6,6a,7,8,9,10,10a-octahydroindeno[2,1-b]indole
Other name(s): ambO5 (gene name); welO5 (gene name)
Systematic name: 12-epi-fischerindole U,2-oxoglutarate:oxygen oxidoreductase (13-halogenating)
Comments: The enzyme, characterized from hapalindole-type alkaloids-producing cyanobacteria, is a specialized iron(II)/2-oxoglutarate-dependent oxygenase that catalyses the chlorination of its substrates in a reaction that requires oxygen, chloride ions, iron(II) and 2-oxoglutarate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Hillwig, M.L. and Liu, X. A new family of iron-dependent halogenases acts on freestanding substrates. Nat. Chem. Biol. 10 (2014) 921–923. [PMID: 25218740]
2.  Zhu, Q., Hillwig, M.L., Doi, Y. and Liu, X. Aliphatic halogenase enables late-stage C-H functionalization: selective synthesis of a brominated fischerindole alkaloid with enhanced antibacterial activity. ChemBioChem 17 (2016) 466–470. [PMID: 26749394]
3.  Hillwig, M.L., Zhu, Q., Ittiamornkul, K. and Liu, X. Discovery of a promiscuous non-heme iron halogenase in ambiguine alkaloid biogenesis: implication for an evolvable enzyme family for late-stage halogenation of aliphatic carbons in small molecules. Angew. Chem. Int. Ed. Engl. 55 (2016) 5780–5784. [PMID: 27027281]
[EC 1.14.20.14 created 2018]
 
 
EC 1.14.21.11      
Transferred entry: (–)-pluviatolide synthase. Now EC 1.14.19.72, (–)-pluviatolide synthase
[EC 1.14.21.11 created 2016, deleted 2018]
 
 
EC 1.14.99.9      
Transferred entry: steroid 17α-monooxygenase, now classified as EC 1.14.14.19, steroid 17α-monooxygenase
[EC 1.14.99.9 created 1961 as EC 1.99.1.9, transferred 1965 to EC 1.14.1.7, transferred 1972 to EC 1.14.99.9, modified 2013, deleted 2015]
 
 
EC 1.14.99.21     
Accepted name: Latia-luciferin monooxygenase (demethylating)
Reaction: Latia luciferin + reduced acceptor + 2 O2 = oxidized Latia luciferin + CO2 + formate + acceptor + H2O + hν
Glossary: Latia-luciferin = (E)-2-methyl-4-(2,6,6-trimethylcyclohex-1-en-1-yl)but-1-en-1-yl formate
Other name(s): luciferase (Latia luciferin); Latia luciferin monooxygenase (demethylating)
Systematic name: Latia-luciferin,hydrogen-donor:oxygen oxidoreductase (demethylating)
Comments: A flavoprotein. Latia is a bioluminescent mollusc. The reaction possibly involves two enzymes, an oxygenase followed by a monooxygenase for the actual light-emitting step.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 62213-54-1
References:
1.  Shimomura, O. and Johnson, F.H. The structure of Latia luciferin. Biochemistry 7 (1968) 1734–1738. [PMID: 5650377]
2.  Shimomura, O., Johnson, F.H. and Kohama, Y. Reactions involved in bioluminescence systems of limpet (Latia neritoides) and luminous bacteria. Proc. Natl. Acad. Sci. USA 69 (1972) 2086–2089. [DOI] [PMID: 4506078]
[EC 1.14.99.21 created 1976, modified 1982]
 
 
EC 1.14.99.42      
Transferred entry: zeaxanthin 7,8-dioxygenase. Now EC 1.13.11.84, crocetin dialdehyde synthase
[EC 1.14.99.42 created 2011, modified 2014, deleted 2017]
 
 
EC 1.14.99.60     
Accepted name: 3-demethoxyubiquinol 3-hydroxylase
Reaction: 6-methoxy-3-methyl-2-(all-trans-polyprenyl)-1,4-benzoquinol + a reduced acceptor + O2 = 3-demethylubiquinol + acceptor + H2O
Glossary: 3-demethylubiquinol = 3-methoxy-6-methyl-5-(all trans-polyprenyl)benzene-1,2,4-triol
Other name(s): 6-methoxy-3-methyl-2-(all-trans-polyprenyl)-1,4-benzoquinol 5-hydroxylase; COQ7 (gene name); clk-1 (gene name); ubiF (gene name)
Systematic name: 6-methoxy-3-methyl-2-(all-trans-polyprenyl)-1,4-benzoquinol,acceptor:oxygen oxidoreductase (5-hydroxylating)
Comments: The enzyme catalyses the last hydroxylation reaction during the biosynthesis of ubiquinone.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Marbois, B.N. and Clarke, C.F. The COQ7 gene encodes a protein in Saccharomyces cerevisiae necessary for ubiquinone biosynthesis. J. Biol. Chem. 271 (1996) 2995–3004. [PMID: 8621692]
2.  Vajo, Z., King, L.M., Jonassen, T., Wilkin, D.J., Ho, N., Munnich, A., Clarke, C.F. and Francomano, C.A. Conservation of the Caenorhabditis elegans timing gene clk-1 from yeast to human: a gene required for ubiquinone biosynthesis with potential implications for aging. Mamm Genome 10 (1999) 1000–1004. [PMID: 10501970]
3.  Kwon, O., Kotsakis, A. and Meganathan, R. Ubiquinone (coenzyme Q) biosynthesis in Escherichia coli: identification of the ubiF gene. FEMS Microbiol. Lett. 186 (2000) 157–161. [PMID: 10802164]
4.  Stenmark, P., Grunler, J., Mattsson, J., Sindelar, P.J., Nordlund, P. and Berthold, D.A. A new member of the family of di-iron carboxylate proteins. Coq7 (clk-1), a membrane-bound hydroxylase involved in ubiquinone biosynthesis. J. Biol. Chem. 276 (2001) 33297–33300. [PMID: 11435415]
5.  Tran, U.C., Marbois, B., Gin, P., Gulmezian, M., Jonassen, T. and Clarke, C.F. Complementation of Saccharomyces cerevisiae coq7 mutants by mitochondrial targeting of the Escherichia coli UbiF polypeptide: two functions of yeast Coq7 polypeptide in coenzyme Q biosynthesis. J. Biol. Chem. 281 (2006) 16401–16409. [PMID: 16624818]
[EC 1.14.99.60 created 2018]
 
 
EC 1.16.5.1      
Transferred entry: ascorbate ferrireductase (transmembrane). Now EC 7.2.1.3, ascorbate ferrireductase (transmembrane)
[EC 1.16.5.1 created 2011, deleted 2018]
 
 
EC 1.17.1.2      
Transferred entry: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase, now classified as EC 1.17.7.4, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase.
[EC 1.17.1.2 created 2003, modified 2009, deleted 2016]
 
 
EC 1.17.98.1      
Deleted entry: bile-acid 7α-dehydroxylase. Now known to be catalyzed by multiple enzymes.
[EC 1.17.98.1 created 2005 as EC 1.17.1.6, transferred 2006 to EC 1.17.99.5, transferred 2014 to EC 1.17.98.1, deleted 2016]
 
 
EC 1.17.99.5      
Transferred entry: bile-acid 7α-dehydroxylase. Now classified as EC 1.17.98.1, bile-acid 7α-dehydroxylase.
[EC 1.17.99.5 created 2005 as EC 1.17.1.6, transferred 2006 to EC 1.17.99.5, deleted 2014]
 
 
EC 1.18.1.6     
Accepted name: adrenodoxin-NADP+ reductase
Reaction: 2 reduced adrenodoxin + NADP+ + H+ = 2 oxidized adrenodoxin + NADPH
Other name(s): adrenodoxin reductase; nicotinamide adenine dinucleotide phosphate-adrenodoxin reductase; AdR; NADPH:adrenal ferredoxin oxidoreductase; NADPH-adrenodoxin reductase
Systematic name: reduced adrenodoxin:NADP+ oxidoreductase
Comments: A flavoprotein (FAD). The enzyme, which transfers electrons from NADPH to adrenodoxin molecules, is the first component of the mitochondrial cytochrome P-450 electron transfer systems, and is involved in the biosynthesis of all steroid hormones.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Omura, T., Sanders, E., Estabrook, R.W., Cooper, D.Y. and Rosenthal, O. Isolation from adrenal cortex of a nonheme iron protein and a flavoprotein functional as a reduced triphosphopyridine nucleotide-cytochrome P-450 reductase. Arch. Biochem. Biophys. 117 (1966) 660–673.
2.  Chu, J.W. and Kimura, T. Studies on adrenal steroid hydroxylases. Molecular and catalytic properties of adrenodoxin reductase (a flavoprotein). J. Biol. Chem. 248 (1973) 2089–2094. [PMID: 4144106]
3.  Sugiyama, T. and Yamano, T. Purification and crystallization of NADPH-adrenodoxin reductase from bovine adrenocortical mitochondria. FEBS Lett. 52 (1975) 145–148. [DOI] [PMID: 235468]
4.  Hanukoglu, I. and Jefcoate, C.R. Mitochondrial cytochrome P-450scc. Mechanism of electron transport by adrenodoxin. J. Biol. Chem. 255 (1980) 3057–3061. [PMID: 6766943]
5.  Hanukoglu, I. and Hanukoglu, Z. Stoichiometry of mitochondrial cytochromes P-450, adrenodoxin and adrenodoxin reductase in adrenal cortex and corpus luteum. Implications for membrane organization and gene regulation. Eur. J. Biochem. 157 (1986) 27–31. [DOI] [PMID: 3011431]
6.  Hanukoglu, I. and Gutfinger, T. cDNA sequence of adrenodoxin reductase. Identification of NADP-binding sites in oxidoreductases. Eur. J. Biochem. 180 (1989) 479–484. [DOI] [PMID: 2924777]
7.  Ziegler, G.A., Vonrhein, C., Hanukoglu, I. and Schulz, G.E. The structure of adrenodoxin reductase of mitochondrial P450 systems: electron transfer for steroid biosynthesis. J. Mol. Biol. 289 (1999) 981–990. [DOI] [PMID: 10369776]
[EC 1.18.1.6 created 1965 as EC 1.6.99.4, transferred 1972 as EC 1.6.7.1, transferred 1978 to EC 1.18.1.2, part transferred 2012 to EC 1.18.1.6, modified 2016]
 
 
EC 1.97.1.12     
Accepted name: photosystem I
Reaction: reduced plastocyanin + oxidized ferredoxin + hν = oxidized plastocyanin + reduced ferredoxin
Systematic name: plastocyanin:ferredoxin oxidoreductase (light-dependent)
Comments: Contains chlorophyll, phylloquinones, carotenoids and [4Fe-4S] clusters. Cytochrome c6 can act as an alternative electron donor, and flavodoxin as an alternative acceptor in some species.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Takabe, T., Iwasaki, Y., Hibino, T. and Ando, T. Subunit composition of photosystem I complex that catalyzes light-dependent transfer of electrons from plastocyanin to ferredoxin. J. Biochem. 110 (1991) 622–627. [PMID: 1778985]
2.  van Thor, J.J., Geerlings, T.H., Matthijs, H.C. and Hellingwerf, K.J. Kinetic evidence for the PsaE-dependent transient ternary complex photosystem I/Ferredoxin/Ferredoxin:NADP+ reductase in a cyanobacterium. Biochemistry 38 (1999) 12735–12746. [DOI] [PMID: 10504244]
3.  Chitnis, P.R. Photosystem I: function and physiology. Annu. Rev. Plant Physiol. Plant Mol. Biol. 52 (2001) 593–626. [DOI] [PMID: 11337410]
4.  Amunts, A., Toporik, H., Borovikova, A. and Nelson, N. Structure determination and improved model of plant photosystem I. J. Biol. Chem. 285 (2010) 3478–3486. [DOI] [PMID: 19923216]
[EC 1.97.1.12 created 2011]
 
 
EC 2.1.1.20     
Accepted name: glycine N-methyltransferase
Reaction: S-adenosyl-L-methionine + glycine = S-adenosyl-L-homocysteine + sarcosine
Glossary: sarcosine = N-methylglycine
Other name(s): glycine methyltransferase; S-adenosyl-L-methionine:glycine methyltransferase; GNMT
Systematic name: S-adenosyl-L-methionine:glycine N-methyltransferase
Comments: This enzyme is thought to play an important role in the regulation of methyl group metabolism in the liver and pancreas by regulating the ratio between S-adenosyl-L-methionine and S-adenosyl-L-homocysteine. It is inhibited by 5-methyltetrahydrofolate pentaglutamate [4]. Sarcosine, which has no physiological role, is converted back into glycine by the action of EC 1.5.8.3, sarcosine dehydrogenase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37228-72-1
References:
1.  Blumenstein, J. and Williams, G.R. Glycine methyltransferase. Can. J. Biochem. Physiol. 41 (1963) 201–210. [PMID: 13971907]
2.  Ogawa, H., Gomi, T., Takusagawa, F. and Fujioka, M. Structure, function and physiological role of glycine N-methyltransferase. Int. J. Biochem. Cell Biol. 30 (1998) 13–26. [DOI] [PMID: 9597750]
3.  Yeo, E.J., Briggs, W.T. and Wagner, C. Inhibition of glycine N-methyltransferase by 5-methyltetrahydrofolate pentaglutamate. J. Biol. Chem. 274 (1999) 37559–37564. [DOI] [PMID: 10608809]
4.  Martinov, M.V., Vitvitsky, V.M., Mosharov, E.V., Banerjee, R. and Ataullakhanov, F.I. A substrate switch: a new mode of regulation in the methionine metabolic pathway. J. Theor. Biol. 204 (2000) 521–532. [DOI] [PMID: 10833353]
5.  Takata, Y., Huang, Y., Komoto, J., Yamada, T., Konishi, K., Ogawa, H., Gomi, T., Fujioka, M. and Takusagawa, F. Catalytic mechanism of glycine N-methyltransferase. Biochemistry 42 (2003) 8394–8402. [DOI] [PMID: 12859184]
6.  Pakhomova, S., Luka, Z., Grohmann, S., Wagner, C. and Newcomer, M.E. Glycine N-methyltransferases: a comparison of the crystal structures and kinetic properties of recombinant human, mouse and rat enzymes. Proteins 57 (2004) 331–337. [DOI] [PMID: 15340920]
[EC 2.1.1.20 created 1972, modified 2005]
 
 
EC 2.1.1.25     
Accepted name: phenol O-methyltransferase
Reaction: S-adenosyl-L-methionine + phenol = S-adenosyl-L-homocysteine + anisole
Other name(s): PMT
Systematic name: S-adenosyl-L-methionine:phenol O-methyltransferase
Comments: Acts on a wide variety of simple alkyl-, methoxy- and halo-phenols.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number: 37256-94-3
References:
1.  Axelrod, J. and Daly, J. Phenol-O-methyltransferase. Biochim. Biophys. Acta 159 (1968) 472–478. [DOI] [PMID: 5657870]
[EC 2.1.1.25 created 1972]
 
 
EC 2.1.1.35     
Accepted name: tRNA (uracil54-C5)-methyltransferase
Reaction: S-adenosyl-L-methionine + uracil54 in tRNA = S-adenosyl-L-homocysteine + 5-methyluracil54 in tRNA
Other name(s): transfer RNA uracil54 5-methyltransferase; transfer RNA uracil54 methylase; tRNA uracil54 5-methyltransferase; m5U54-methyltransferase; tRNA:m5U54-methyltransferase; RUMT; TrmA; 5-methyluridine54 tRNA methyltransferase; tRNA(uracil-54,C5)-methyltransferase; Trm2; tRNA(m5U54)methyltransferase
Systematic name: S-adenosyl-L-methionine:tRNA (uracil54-C5)-methyltransferase
Comments: Unlike this enzyme, EC 2.1.1.74 (methylenetetrahydrofolate—tRNA-(uracil54-C5)-methyltransferase (FADH2-oxidizing)), uses 5,10-methylenetetrahydrofolate and FADH2 to supply the atoms for methylation of U54 [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 37257-02-6
References:
1.  Björk, G.R. and Svensson, I. Studies on microbial RNA. Fractionation of tRNA methylases from Saccharomyces cerevisiae. Eur. J. Biochem. 9 (1969) 207–215. [DOI] [PMID: 4896260]
2.  Greenberg, R. and Dudock, B. Isolation and characterization of m5U-methyltransferase from Escherichia coli. J. Biol. Chem. 255 (1980) 8296–8302. [PMID: 6997293]
3.  Hurwitz, J., Gold, M. and Anders, M. The enzymatic methylation of ribonucleic acid and deoxyribonucleic acid. 3. Purification of soluble ribonucleic acid-methylating enzymes. J. Biol. Chem. 239 (1964) 3462–3473. [PMID: 14245404]
4.  Delk, A.S., Nagle, D.P., Jr. and Rabinowitz, J.C. Methylenetetrahydrofolate-dependent biosynthesis of ribothymidine in transfer RNA of Streptococcus faecalis. Evidence for reduction of the 1-carbon unit by FADH2. J. Biol. Chem. 255 (1980) 4387–4390. [PMID: 6768721]
5.  Kealey, J.T., Gu, X. and Santi, D.V. Enzymatic mechanism of tRNA (m5U54)methyltransferase. Biochimie 76 (1994) 1133–1142. [DOI] [PMID: 7748948]
6.  Gu, X., Ivanetich, K.M. and Santi, D.V. Recognition of the T-arm of tRNA by tRNA (m5U54)-methyltransferase is not sequence specific. Biochemistry 35 (1996) 11652–11659. [DOI] [PMID: 8794745]
7.  Becker, H.F., Motorin, Y., Sissler, M., Florentz, C. and Grosjean, H. Major identity determinants for enzymatic formation of ribothymidine and pseudouridine in the TΨ-loop of yeast tRNAs. J. Mol. Biol. 274 (1997) 505–518. [DOI] [PMID: 9417931]
8.  Walbott, H., Leulliot, N., Grosjean, H. and Golinelli-Pimpaneau, B. The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-methyltransferase provides insights into its tRNA specificity. Nucleic Acids Res. 36 (2008) 4929–4940. [DOI] [PMID: 18653523]
[EC 2.1.1.35 created 1972, modified 2011]
 
 
EC 2.1.1.93      
Deleted entry: xanthotoxol O-methyltransferase. Enzyme is identical to EC 2.1.1.70, 8-hydroxyfuranocoumarin 8-O-methyltransferase
[EC 2.1.1.93 created 1989, deleted 2008]
 
 
EC 2.1.1.179     
Accepted name: 16S rRNA (guanine1405-N7)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine1405 in 16S rRNA = S-adenosyl-L-homocysteine + N7-methylguanine1405 in 16S rRNA
Other name(s): methyltransferase Sgm; m7G1405 Mtase; Sgm Mtase; Sgm; sisomicin-gentamicin methyltransferase; sisomicin-gentamicin methylase; GrmA; RmtB; RmtC; ArmA
Systematic name: S-adenosyl-L-methionine:16S rRNA (guanine1405-N7)-methyltransferase
Comments: The enzyme from the antibiotic-producing bacterium Micromonospora zionensis specifically methylates guanine1405 at N7 in 16S rRNA, thereby rendering the ribosome resistant to 4,6-disubstituted deoxystreptamine aminoglycosides, which include gentamicins and kanamycins [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Husain, N., Tkaczuk, K.L., Tulsidas, S.R., Kaminska, K.H., Cubrilo, S., Maravic-Vlahovicek, G., Bujnicki, J.M. and Sivaraman, J. Structural basis for the methylation of G1405 in 16S rRNA by aminoglycoside resistance methyltransferase Sgm from an antibiotic producer: a diversity of active sites in m7G methyltransferases. Nucleic Acids Res. 38 (2010) 4120–4132. [DOI] [PMID: 20194115]
2.  Savic, M., Lovric, J., Tomic, T.I., Vasiljevic, B. and Conn, G.L. Determination of the target nucleosides for members of two families of 16S rRNA methyltransferases that confer resistance to partially overlapping groups of aminoglycoside antibiotics. Nucleic Acids Res. 37 (2009) 5420–5431. [DOI] [PMID: 19589804]
3.  Tomic, T.I., Moric, I., Conn, G.L. and Vasiljevic, B. Aminoglycoside resistance genes sgm and kgmB protect bacterial but not yeast small ribosomal subunits in vitro despite high conservation of the rRNA A-site. Res. Microbiol. 159 (2008) 658–662. [DOI] [PMID: 18930134]
4.  Savic, M., Ilic-Tomic, T., Macmaster, R., Vasiljevic, B. and Conn, G.L. Critical residues for cofactor binding and catalytic activity in the aminoglycoside resistance methyltransferase Sgm. J. Bacteriol. 190 (2008) 5855–5861. [DOI] [PMID: 18586937]
5.  Maravic Vlahovicek, G., Cubrilo, S., Tkaczuk, K.L. and Bujnicki, J.M. Modeling and experimental analyses reveal a two-domain structure and amino acids important for the activity of aminoglycoside resistance methyltransferase Sgm. Biochim. Biophys. Acta 1784 (2008) 582–590. [DOI] [PMID: 18343347]
6.  Kojic, M., Topisirovic, L. and Vasiljevic, B. Cloning and characterization of an aminoglycoside resistance determinant from Micromonospora zionensis. J. Bacteriol. 174 (1992) 7868–7872. [DOI] [PMID: 1447159]
7.  Schmitt, E., Galimand, M., Panvert, M., Courvalin, P. and Mechulam, Y. Structural bases for 16 S rRNA methylation catalyzed by ArmA and RmtB methyltransferases. J. Mol. Biol. 388 (2009) 570–582. [DOI] [PMID: 19303884]
8.  Wachino, J., Shibayama, K., Kimura, K., Yamane, K., Suzuki, S. and Arakawa, Y. RmtC introduces G1405 methylation in 16S rRNA and confers high-level aminoglycoside resistance on Gram-positive microorganisms. FEMS Microbiol. Lett. 311 (2010) 56–60. [DOI] [PMID: 20722735]
9.  Liou, G.F., Yoshizawa, S., Courvalin, P. and Galimand, M. Aminoglycoside resistance by ArmA-mediated ribosomal 16S methylation in human bacterial pathogens. J. Mol. Biol. 359 (2006) 358–364. [DOI] [PMID: 16626740]
[EC 2.1.1.179 created 2010]
 
 
EC 2.1.1.180     
Accepted name: 16S rRNA (adenine1408-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + adenine1408 in 16S rRNA = S-adenosyl-L-homocysteine + N1-methyladenine1408 in 16S rRNA
Other name(s): kanamycin-apramycin resistance methylase; 16S rRNA:m1A1408 methyltransferase; KamB; NpmA; 16S rRNA m1A1408 methyltransferase
Systematic name: S-adenosyl-L-methionine:16S rRNA (adenine1408-N1)-methyltransferase
Comments: The enzyme provides a panaminoglycoside-resistant nature through interference with the binding of aminoglycosides toward the A site of 16S rRNA through N1-methylation at position adenine1408 [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Beauclerk, A.A. and Cundliffe, E. Sites of action of two ribosomal RNA methylases responsible for resistance to aminoglycosides. J. Mol. Biol. 193 (1987) 661–671. [DOI] [PMID: 2441068]
2.  Koscinski, L., Feder, M. and Bujnicki, J.M. Identification of a missing sequence and functionally important residues of 16S rRNA:m1A1408 methyltransferase KamB that causes bacterial resistance to aminoglycoside antibiotics. Cell Cycle 6 (2007) 1268–1271. [DOI] [PMID: 17495534]
3.  Holmes, D.J., Drocourt, D., Tiraby, G. and Cundliffe, E. Cloning of an aminoglycoside-resistance-encoding gene, kamC, from Saccharopolyspora hirsuta: comparison with kamB from Streptomyces tenebrarius. Gene 102 (1991) 19–26. [DOI] [PMID: 1840536]
4.  Wachino, J., Shibayama, K., Kurokawa, H., Kimura, K., Yamane, K., Suzuki, S., Shibata, N., Ike, Y. and Arakawa, Y. Novel plasmid-mediated 16S rRNA m1A1408 methyltransferase, NpmA, found in a clinically isolated Escherichia coli strain resistant to structurally diverse aminoglycosides. Antimicrob. Agents Chemother. 51 (2007) 4401–4409. [DOI] [PMID: 17875999]
[EC 2.1.1.180 created 2010]
 
 
EC 2.1.1.184     
Accepted name: 23S rRNA (adenine2085-N6)-dimethyltransferase
Reaction: 2 S-adenosyl-L-methionine + adenine2085 in 23S rRNA = 2 S-adenosyl-L-homocysteine + N6-dimethyladenine2085 in 23S rRNA
Other name(s): ErmC′ methyltransferase; ermC methylase; ermC 23S rRNA methyltransferase; rRNA:m6A methyltransferase ErmC′; ErmC′; rRNA methyltransferase ErmC′
Systematic name: S-adenosyl-L-methionine:23S rRNA (adenine2085-N6)-dimethyltransferase
Comments: ErmC is a methyltransferase that confers resistance to the macrolide-lincosamide-streptogramin B group of antibiotics by catalysing the methylation of 23S rRNA at adenine2085.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Zhong, P., Pratt, S.D., Edalji, R.P., Walter, K.A., Holzman, T.F., Shivakumar, A.G. and Katz, L. Substrate requirements for ErmC′ methyltransferase activity. J. Bacteriol. 177 (1995) 4327–4332. [DOI] [PMID: 7543473]
2.  Denoya, C. and Dubnau, D. Mono- and dimethylating activities and kinetic studies of the ermC 23 S rRNA methyltransferase. J. Biol. Chem. 264 (1989) 2615–2624. [PMID: 2492520]
3.  Denoya, C.D. and Dubnau, D. Site and substrate specificity of the ermC 23S rRNA methyltransferase. J. Bacteriol. 169 (1987) 3857–3860. [DOI] [PMID: 2440853]
4.  Bussiere, D.E., Muchmore, S.W., Dealwis, C.G., Schluckebier, G., Nienaber, V.L., Edalji, R.P., Walter, K.A., Ladror, U.S., Holzman, T.F. and Abad-Zapatero, C. Crystal structure of ErmC′, an rRNA methyltransferase which mediates antibiotic resistance in bacteria. Biochemistry 37 (1998) 7103–7112. [DOI] [PMID: 9585521]
5.  Schluckebier, G., Zhong, P., Stewart, K.D., Kavanaugh, T.J. and Abad-Zapatero, C. The 2.2 Å structure of the rRNA methyltransferase ErmC′ and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism. J. Mol. Biol. 289 (1999) 277–291. [DOI] [PMID: 10366505]
6.  Maravic, G., Bujnicki, J.M., Feder, M., Pongor, S. and Flogel, M. Alanine-scanning mutagenesis of the predicted rRNA-binding domain of ErmC′ redefines the substrate-binding site and suggests a model for protein-RNA interactions. Nucleic Acids Res. 31 (2003) 4941–4949. [PMID: 12907737]
[EC 2.1.1.184 created 1976 as EC 2.1.1.48, part transferred 2010 to EC 2.1.1.184]
 
 
EC 2.1.1.187     
Accepted name: 23S rRNA (guanine745-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine745 in 23S rRNA = S-adenosyl-L-homocysteine + N1-methylguanine745 in 23S rRNA
Other name(s): Rlma(I); Rlma1; 23S rRNA m1G745 methyltransferase; YebH; RlmAI methyltransferase; ribosomal RNA(m1G)-methylase (ambiguous); rRNA(m1G)methylase (ambiguous); RrmA (ambiguous); 23S rRNA:m1G745 methyltransferase
Systematic name: S-adenosyl-L-methionine:23S rRNA (guanine745-N1)-methyltransferase
Comments: The enzyme specifically methylates guanine745 at N1 in 23S rRNA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Liu, M., Novotny, G.W. and Douthwaite, S. Methylation of 23S rRNA nucleotide G745 is a secondary function of the RlmAI methyltransferase. RNA 10 (2004) 1713–1720. [DOI] [PMID: 15388872]
2.  Gustafsson, C. and Persson, B.C. Identification of the rrmA gene encoding the 23S rRNA m1G745 methyltransferase in Escherichia coli and characterization of an m1G745-deficient mutant. J. Bacteriol. 180 (1998) 359–365. [PMID: 9440525]
3.  Das, K., Acton, T., Chiang, Y., Shih, L., Arnold, E. and Montelione, G.T. Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site. Proc. Natl. Acad. Sci. USA 101 (2004) 4041–4046. [DOI] [PMID: 14999102]
4.  Hansen, L.H., Kirpekar, F. and Douthwaite, S. Recognition of nucleotide G745 in 23 S ribosomal RNA by the rrmA methyltransferase. J. Mol. Biol. 310 (2001) 1001–1010. [DOI] [PMID: 11501991]
5.  Liu, M. and Douthwaite, S. Methylation at nucleotide G745 or G748 in 23S rRNA distinguishes Gram-negative from Gram-positive bacteria. Mol. Microbiol. 44 (2002) 195–204. [DOI] [PMID: 11967079]
[EC 2.1.1.187 created 1976 as EC 2.1.1.51, part transferred 2010 to EC 2.1.1.187]
 
 
EC 2.1.1.195     
Accepted name: cobalt-precorrin-5B (C1)-methyltransferase
Reaction: S-adenosyl-L-methionine + cobalt-precorrin-5B = S-adenosyl-L-homocysteine + cobalt-precorrin-6A
For diagram of anaerobic corrin biosynthesis (part 1), click here
Glossary: cobalt-precorrin-6A = cobalt-precorrin-6x
Other name(s): cobalt-precorrin-6A synthase; CbiD
Systematic name: S-adenosyl-L-methionine:cobalt-precorrin-5B C1-methyltransferase
Comments: This enzyme catalyses the C-1 methylation of cobalt-precorrin-5B in the anaerobic (early cobalt insertion) pathway of adenosylcobalamin biosynthesis. See EC 2.1.1.152, precorrin-6A synthase (deacetylating), for the C1-methyltransferase that participates in the aerobic cobalamin biosynthesis pathway.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Roper, J.M., Raux, E., Brindley, A.A., Schubert, H.L., Gharbia, S.E., Shah, H.N. and Warren, M.J. The enigma of cobalamin (Vitamin B12) biosynthesis in Porphyromonas gingivalis. Identification and characterization of a functional corrin pathway. J. Biol. Chem. 275 (2000) 40316–40323. [DOI] [PMID: 11007789]
2.  Roessner, C.A., Williams, H.J. and Scott, A.I. Genetically engineered production of 1-desmethylcobyrinic acid, 1-desmethylcobyrinic acid a,c-diamide, and cobyrinic acid a,c-diamide in Escherichia coli implies a role for CbiD in C-1 methylation in the anaerobic pathway to cobalamin. J. Biol. Chem. 280 (2005) 16748–16753. [DOI] [PMID: 15741157]
3.  Moore, S.J., Lawrence, A.D., Biedendieck, R., Deery, E., Frank, S., Howard, M.J., Rigby, S.E. and Warren, M.J. Elucidation of the anaerobic pathway for the corrin component of cobalamin (vitamin B12). Proc. Natl. Acad. Sci. USA 110 (2013) 14906–14911. [DOI] [PMID: 23922391]
[EC 2.1.1.195 created 2010]
 
 
EC 2.1.1.202     
Accepted name: multisite-specific tRNA:(cytosine-C5)-methyltransferase
Reaction: (1) S-adenosyl-L-methionine + cytosine34 in tRNA precursor = S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
(2) S-adenosyl-L-methionine + cytosine40 in tRNA precursor = S-adenosyl-L-homocysteine + 5-methylcytosine40 in tRNA precursor
(3) S-adenosyl-L-methionine + cytosine48 in tRNA = S-adenosyl-L-homocysteine + 5-methylcytosine48 in tRNA
(4) S-adenosyl-L-methionine + cytosine49 in tRNA = S-adenosyl-L-homocysteine + 5-methylcytosine49 in tRNA
Other name(s): multisite-specific tRNA:m5C-methyltransferase; TRM4 (gene name, gene corresponding to ORF YBL024w)
Systematic name: S-adenosyl-L-methionine:tRNA (cytosine-C5)-methyltransferase
Comments: The enzyme from Saccharomyces cerevisiae is responsible for complete 5-methylcytosine methylations of yeast tRNA. The incidence of modification depends on the cytosine position in tRNA. At positions 34 and 40, 5-methylcytosine is found only in two yeast tRNAs (tRNALeu(CUA) and tRNAPhe(GAA), respectively), whereas most other elongator yeast tRNAs bear either 5-methylcytosine48 or 5-methylcytosine49, but never both in the same tRNA molecule [1]. The formation of 5-methylcytosine34 and 5-methylcytosine40 is a strictly intron-dependent process, whereas the formation of 5-methylcytosine48 and 5-methylcytosine49 is an intron-independent process [2,3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Motorin, Y. and Grosjean, H. Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: identification of the gene and substrate specificity of the enzyme. RNA 5 (1999) 1105–1118. [PMID: 10445884]
2.  Jiang, H.Q., Motorin, Y., Jin, Y.X. and Grosjean, H. Pleiotropic effects of intron removal on base modification pattern of yeast tRNAPhe: an in vitro study. Nucleic Acids Res. 25 (1997) 2694–2701. [DOI] [PMID: 9207014]
3.  Strobel, M.C. and Abelson, J. Effect of intron mutations on processing and function of Saccharomyces cerevisiae SUP53 tRNA in vitro and in vivo. Mol. Cell Biol. 6 (1986) 2663–2673. [DOI] [PMID: 3537724]
4.  Walbott, H., Husson, C., Auxilien, S. and Golinelli-Pimpaneau, B. Cysteine of sequence motif VI is essential for nucleophilic catalysis by yeast tRNA m5C methyltransferase. RNA 13 (2007) 967–973. [DOI] [PMID: 17475914]
[EC 2.1.1.202 created 1976 as EC 2.1.1.29, part transferred 2011 to EC 2.1.1.202]
 
 
EC 2.1.1.216     
Accepted name: tRNA (guanine26-N2)-dimethyltransferase
Reaction: 2 S-adenosyl-L-methionine + guanine26 in tRNA = 2 S-adenosyl-L-homocysteine + N2-dimethylguanine26 in tRNA
Other name(s): Trm1p; TRM1; tRNA (m22G26)dimethyltransferase
Systematic name: S-adenosyl-L-methionine:tRNA (guanine26-N2)-dimethyltransferase
Comments: The enzyme dissociates from its tRNA substrate between the two consecutive methylation reactions. In contrast to EC 2.1.1.215, tRNA (guanine26-N2/guanine27-N2)-dimethyltransferase, this enzyme does not catalyse the methylation of guanine27 in tRNA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Constantinesco, F., Motorin, Y. and Grosjean, H. Characterisation and enzymatic properties of tRNA(guanine26, N2,N2-dimethyltransferase (Trm1p) from Pyrococcus furiosus. J. Mol. Biol. 291 (1999) 375–392. [DOI] [PMID: 10438627]
2.  Constantinesco, F., Benachenhou, N., Motorin, Y. and Grosjean, H. The tRNA(guanine-26,N2-N2) methyltransferase (Trm1) from the hyperthermophilic archaeon Pyrococcus furiosus: cloning, sequencing of the gene and its expression in Escherichia coli. Nucleic Acids Res. 26 (1998) 3753–3761. [DOI] [PMID: 9685492]
3.  Liu, J., Liu, J. and Straby, K.B. Point and deletion mutations eliminate one or both methyl group transfers catalysed by the yeast TRM1 encoded tRNA (m22G26)dimethyltransferase. Nucleic Acids Res. 26 (1998) 5102–5108. [DOI] [PMID: 9801306]
4.  Liu, J., Zhou, G.Q. and Straby, K.B. Caenorhabditis elegans ZC376.5 encodes a tRNA (m22G26)dimethyltransferance in which 246arginine is important for the enzyme activity. Gene 226 (1999) 73–81. [DOI] [PMID: 10048958]
[EC 2.1.1.216 created 2011 (EC 2.1.1.32 created 1972, part transferred 2011 to EC 2.1.1.216)]
 
 
EC 2.1.1.219     
Accepted name: tRNA (adenine57-N1/adenine58-N1)-methyltransferase
Reaction: 2 S-adenosyl-L-methionine + adenine57/adenine58 in tRNA = 2 S-adenosyl-L-homocysteine + N1-methyladenine57/N1-methyladenine58 in tRNA
Other name(s): TrmI; PabTrmI; AqTrmI; MtTrmI
Systematic name: S-adenosyl-L-methionine:tRNA (adenine57/adenine58-N1)-methyltransferase
Comments: The enzyme catalyses the formation of N1-methyladenine at two adjacent positions (57 and 58) in the T-loop of certain tRNAs (e.g. tRNAAsp). Methyladenosine at position 57 is an obligatory intermediate for the synthesis of methylinosine, which is commonly found at position 57 of archaeal tRNAs.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Roovers, M., Wouters, J., Bujnicki, J.M., Tricot, C., Stalon, V., Grosjean, H. and Droogmans, L. A primordial RNA modification enzyme: the case of tRNA (m1A) methyltransferase. Nucleic Acids Res. 32 (2004) 465–476. [DOI] [PMID: 14739239]
2.  Guelorget, A., Roovers, M., Guerineau, V., Barbey, C., Li, X. and Golinelli-Pimpaneau, B. Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase. Nucleic Acids Res. 38 (2010) 6206–6218. [DOI] [PMID: 20483913]
[EC 2.1.1.219 created 2011 (EC 2.1.1.36 created 1972, part transferred 2011 to EC 2.1.1.219)]
 
 
EC 2.1.1.228     
Accepted name: tRNA (guanine37-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine37 in tRNA = S-adenosyl-L-homocysteine + N1-methylguanine37 in tRNA
For diagram of wyosine biosynthesis, click here
Other name(s): TrmD; tRNA (m1G37) methyltransferase; transfer RNA (m1G37) methyltransferase; Trm5p; TRMT5; tRNA-(N1G37) methyltransferase; MJ0883 (gene name)
Systematic name: S-adenosyl-L-methionine:tRNA (guanine37-N1)-methyltransferase
Comments: This enzyme is important for the maintenance of the correct reading frame during translation. Unlike TrmD from Escherichia coli, which recognizes the G36pG37 motif preferentially, the human enzyme (encoded by TRMT5) also methylates inosine at position 37 [4].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Takeda, H., Toyooka, T., Ikeuchi, Y., Yokobori, S., Okadome, K., Takano, F., Oshima, T., Suzuki, T., Endo, Y. and Hori, H. The substrate specificity of tRNA (m1G37) methyltransferase (TrmD) from Aquifex aeolicus. Genes Cells 11 (2006) 1353–1365. [DOI] [PMID: 17121543]
2.  Lee, C., Kramer, G., Graham, D.E. and Appling, D.R. Yeast mitochondrial initiator tRNA is methylated at guanosine 37 by the Trm5-encoded tRNA (guanine-N1-)-methyltransferase. J. Biol. Chem. 282 (2007) 27744–27753. [DOI] [PMID: 17652090]
3.  O'Dwyer, K., Watts, J.M., Biswas, S., Ambrad, J., Barber, M., Brule, H., Petit, C., Holmes, D.J., Zalacain, M. and Holmes, W.M. Characterization of Streptococcus pneumoniae TrmD, a tRNA methyltransferase essential for growth. J. Bacteriol. 186 (2004) 2346–2354. [DOI] [PMID: 15060037]
4.  Brule, H., Elliott, M., Redlak, M., Zehner, Z.E. and Holmes, W.M. Isolation and characterization of the human tRNA-(N1G37) methyltransferase (TRM5) and comparison to the Escherichia coli TrmD protein. Biochemistry 43 (2004) 9243–9255. [DOI] [PMID: 15248782]
5.  Goto-Ito, S., Ito, T., Ishii, R., Muto, Y., Bessho, Y. and Yokoyama, S. Crystal structure of archaeal RNA(m1G37)methyltransferase aTrm5. Proteins 72 (2008) 1274–1289. [DOI] [PMID: 18384044]
6.  Ahn, H.J., Kim, H.W., Yoon, H.J., Lee, B.I., Suh, S.W. and Yang, J.K. Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition. EMBO J. 22 (2003) 2593–2603. [DOI] [PMID: 12773376]
[EC 2.1.1.228 created 2011 (EC 2.1.1.31 created 1971, part transferred 2011 to EC 2.1.1.228)]
 
 
EC 2.1.1.229     
Accepted name: tRNA (carboxymethyluridine34-5-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + carboxymethyluridine34 in tRNA = S-adenosyl-L-homocysteine + 5-(2-methoxy-2-oxoethyl)uridine34 in tRNA
Glossary: 5-methoxycarboxymethyluridine = 5-(2-methoxy-2-oxoethyl)uridine
Other name(s): ALKBH8; ABH8; Trm9; tRNA methyltransferase 9
Systematic name: S-adenosyl-L-methionine:tRNA (carboxymethyluridine34-5-O)-methyltransferase
Comments: The enzyme catalyses the posttranslational modification of uridine residues at the wobble position 34 of the anticodon loop of tRNA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Fu, D., Brophy, J.A., Chan, C.T., Atmore, K.A., Begley, U., Paules, R.S., Dedon, P.C., Begley, T.J. and Samson, L.D. Human AlkB homolog ABH8 Is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival. Mol. Cell Biol. 30 (2010) 2449–2459. [DOI] [PMID: 20308323]
2.  Songe-Møller, L., van den Born, E., Leihne, V., Vågbø, C.B., Kristoffersen, T., Krokan, H.E., Kirpekar, F., Falnes, P.Ø. and Klungland, A. Mammalian ALKBH8 possesses tRNA methyltransferase activity required for the biogenesis of multiple wobble uridine modifications implicated in translational decoding. Mol. Cell Biol. 30 (2010) 1814–1827. [DOI] [PMID: 20123966]
3.  Kalhor, H.R. and Clarke, S. Novel methyltransferase for modified uridine residues at the wobble position of tRNA. Mol. Cell Biol. 23 (2003) 9283–9292. [DOI] [PMID: 14645538]
[EC 2.1.1.229 created 2011]
 
 
EC 2.1.1.273     
Accepted name: benzoate O-methyltransferase
Reaction: S-adenosyl-L-methionine + benzoate = S-adenosyl-L-homocysteine + methyl benzoate
Other name(s): BAMT; S-adenosyl-L-methionine:benzoic acid carboxyl methyltransferase
Systematic name: S-adenosyl-L-methionine:benzoate O-methyltransferase
Comments: While the enzyme from the plant Zea mays is specific for benzoate [6], the enzymes from Arabidopsis species and Clarkia breweri also catalyse the reaction of EC 2.1.1.274, salicylate 1-O-methyltransferase [1,5]. In snapdragon (Antirrhinum majus) two isoforms are found, one specific for benzoate [2,3] and one that is also active towards salicylate [4]. The volatile product is an important scent compound in some flowering species [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ross, J.R., Nam, K.H., D'Auria, J.C. and Pichersky, E. S-Adenosyl-L-methionine:salicylic acid carboxyl methyltransferase, an enzyme involved in floral scent production and plant defense, represents a new class of plant methyltransferases. Arch. Biochem. Biophys. 367 (1999) 9–16. [DOI] [PMID: 10375393]
2.  Dudareva, N., Murfitt, L.M., Mann, C.J., Gorenstein, N., Kolosova, N., Kish, C.M., Bonham, C. and Wood, K. Developmental regulation of methyl benzoate biosynthesis and emission in snapdragon flowers. Plant Cell 12 (2000) 949–961. [PMID: 10852939]
3.  Murfitt, L.M., Kolosova, N., Mann, C.J. and Dudareva, N. Purification and characterization of S-adenosyl-L-methionine:benzoic acid carboxyl methyltransferase, the enzyme responsible for biosynthesis of the volatile ester methyl benzoate in flowers of Antirrhinum majus. Arch. Biochem. Biophys. 382 (2000) 145–151. [DOI] [PMID: 11051108]
4.  Negre, F., Kolosova, N., Knoll, J., Kish, C.M. and Dudareva, N. Novel S-adenosyl-L-methionine:salicylic acid carboxyl methyltransferase, an enzyme responsible for biosynthesis of methyl salicylate and methyl benzoate, is not involved in floral scent production in snapdragon flowers. Arch. Biochem. Biophys. 406 (2002) 261–270. [DOI] [PMID: 12361714]
5.  Chen, F., D'Auria, J.C., Tholl, D., Ross, J.R., Gershenzon, J., Noel, J.P. and Pichersky, E. An Arabidopsis thaliana gene for methylsalicylate biosynthesis, identified by a biochemical genomics approach, has a role in defense. Plant J. 36 (2003) 577–588. [DOI] [PMID: 14617060]
6.  Köllner, T.G., Lenk, C., Zhao, N., Seidl-Adams, I., Gershenzon, J., Chen, F. and Degenhardt, J. Herbivore-induced SABATH methyltransferases of maize that methylate anthranilic acid using s-adenosyl-L-methionine. Plant Physiol. 153 (2010) 1795–1807. [DOI] [PMID: 20519632]
[EC 2.1.1.273 created 2013]
 
 
EC 2.1.1.278     
Accepted name: indole-3-acetate O-methyltransferase
Reaction: S-adenosyl-L-methionine + (indol-3-yl)acetate = S-adenosyl-L-homocysteine + methyl (indol-3-yl)acetate
Other name(s): IAA carboxylmethyltransferase; IAMT
Systematic name: S-adenosyl-L-methionine:(indol-3-yl)acetate O-methyltransferase
Comments: Binds Mg2+. The enzyme is found in plants and is important for regulation of the plant hormone (indol-3-yl)acetate. The product, methyl (indol-3-yl)acetate is inactive as hormone [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Zubieta, C., Ross, J.R., Koscheski, P., Yang, Y., Pichersky, E. and Noel, J.P. Structural basis for substrate recognition in the salicylic acid carboxyl methyltransferase family. Plant Cell 15 (2003) 1704–1716. [DOI] [PMID: 12897246]
2.  Li, L., Hou, X., Tsuge, T., Ding, M., Aoyama, T., Oka, A., Gu, H., Zhao, Y. and Qu, L.J. The possible action mechanisms of indole-3-acetic acid methyl ester in Arabidopsis. Plant Cell Rep. 27 (2008) 575–584. [DOI] [PMID: 17926040]
3.  Zhao, N., Ferrer, J.L., Ross, J., Guan, J., Yang, Y., Pichersky, E., Noel, J.P. and Chen, F. Structural, biochemical, and phylogenetic analyses suggest that indole-3-acetic acid methyltransferase is an evolutionarily ancient member of the SABATH family. Plant Physiol. 146 (2008) 455–467. [DOI] [PMID: 18162595]
[EC 2.1.1.278 created 2013]
 
 
EC 2.1.1.279     
Accepted name: trans-anol O-methyltransferase
Reaction: (1) S-adenosyl-L-methionine + trans-anol = S-adenosyl-L-homocysteine + trans-anethole
(2) S-adenosyl-L-methionine + isoeugenol = S-adenosyl-L-homocysteine + isomethyleugenol
Glossary: trans-anol = 4-[(1E)-prop-1-en-1-yl]phenol
trans-anethole = 1-methoxy-4-[(1E)-prop-1-en-1-yl]benzene
Other name(s): AIMT1; S-adenosyl-L-methionine:t-anol/isoeugenol O-methyltransferase; t-anol O-methyltransferase
Systematic name: S-adenosyl-L-methionine:trans-anol O-methyltransferase
Comments: The enzyme from anise (Pimpinella anisum) is highly specific for substrates in which the double bond in the propenyl side chain is located between C7 and C8, and, in contrast to EC 2.1.1.146, (iso)eugenol O-methyltransferase, does not have activity with eugenol or chavicol.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Koeduka, T., Baiga, T.J., Noel, J.P. and Pichersky, E. Biosynthesis of t-anethole in anise: characterization of t-anol/isoeugenol synthase and an O-methyltransferase specific for a C7-C8 propenyl side chain. Plant Physiol. 149 (2009) 384–394. [DOI] [PMID: 18987218]
[EC 2.1.1.279 created 2013]
 
 
EC 2.1.1.282     
Accepted name: tRNAPhe 7-[(3-amino-3-carboxypropyl)-4-demethylwyosine37-N4]-methyltransferase
Reaction: S-adenosyl-L-methionine + 7-[(3S)-(3-amino-3-carboxypropyl)]-4-demethylwyosine37 in tRNAPhe = S-adenosyl-L-homocysteine + 7-[(3S)-(3-amino-3-carboxypropyl)]wyosine37 in tRNAPhe
For diagram of wyosine biosynthesis, click here
Glossary: wyosine = 4,6-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
wybutosine = yW = 7-{(3S)-4-methoxy-3-[(methoxycarbonyl)amino]-4-oxobutyl}-4,5-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
Other name(s): TYW3 (gene name); tRNA-yW synthesizing enzyme-3
Systematic name: S-adenosyl-L-methionine:tRNAPhe 7-[(3S)-(3-amino-3-carboxypropyl)-4-demethylwyosine-N4]-methyltransferase
Comments: The enzyme is involved in the biosynthesis of hypermodified tricyclic bases found at position 37 of certain tRNAs. These modifications are important for translational reading-frame maintenance. The enzyme is found in all eukaryotes and in some archaea, but not in bacteria. The eukaryotic enzyme is involved in the biosynthesis of wybutosine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Noma, A., Kirino, Y., Ikeuchi, Y. and Suzuki, T. Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 25 (2006) 2142–2154. [DOI] [PMID: 16642040]
[EC 2.1.1.282 created 2013, modified 2014]
 
 
EC 2.1.1.286     
Accepted name: 25S rRNA (adenine2142-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + adenine2142 in 25S rRNA = S-adenosyl-L-homocysteine + N1-methyladenine2142 in 25S rRNA
Other name(s): BMT2 (gene name); 25S rRNA m1A2142 methyltransferase
Systematic name: S-adenosyl-L-methionine:25S rRNA (adenine2142-N1)-methyltransferase
Comments: In the yeast Saccharomyces cerevisiae this methylation is important for resistance towards hydrogen peroxide and the antibiotic anisomycin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Sharma, S., Watzinger, P., Kotter, P. and Entian, K.D. Identification of a novel methyltransferase, Bmt2, responsible for the N-1-methyl-adenosine base modification of 25S rRNA in Saccharomyces cerevisiae. Nucleic Acids Res. 41 (2013) 5428–5443. [DOI] [PMID: 23558746]
[EC 2.1.1.286 created 2013]
 
 
EC 2.1.1.287     
Accepted name: 25S rRNA (adenine645-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + adenine645 in 25S rRNA = S-adenosyl-L-homocysteine + N1-methyladenine645 in 25S rRNA
Other name(s): 25S rRNA m1A645 methyltransferase; Rrp8
Systematic name: S-adenosyl-L-methionine:25S rRNA (adenine645-N1)-methyltransferase
Comments: The enzyme is found in eukaryotes. The adenine position refers to rRNA in the yeast Saccharomyces cerevisiae, in which the enzyme is important for ribosome biogenesis.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Peifer, C., Sharma, S., Watzinger, P., Lamberth, S., Kotter, P. and Entian, K.D. Yeast Rrp8p, a novel methyltransferase responsible for m1A 645 base modification of 25S rRNA. Nucleic Acids Res. 41 (2013) 1151–1163. [DOI] [PMID: 23180764]
[EC 2.1.1.287 created 2013]
 
 
EC 2.1.1.290     
Accepted name: tRNAPhe [7-(3-amino-3-carboxypropyl)wyosine37-O]-methyltransferase
Reaction: S-adenosyl-L-methionine + 7-[(3S)-3-amino-3-carboxypropyl]wyosine37 in tRNAPhe = S-adenosyl-L-homocysteine + 7-[(3S)-3-amino-3-(methoxycarbonyl)propyl]wyosine37 in tRNAPhe
For diagram of wyosine biosynthesis, click here
Glossary: wyosine = 4,6-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
wybutosine = yW = 7-[(3S)-3-(methoxycarbonyl)-3-(methoxycarbonylamino)propyl]-4,5-dimethyl-3-(β-D-ribofuranosyl)-3,4-dihydro-9H-imidazo[1,2-a]purin-9-one
Other name(s): TYW4 (ambiguous); tRNA-yW synthesizing enzyme-4 (ambiguous)
Systematic name: S-adenosyl-L-methionine:tRNAPhe {7-[(3S)-3-amino-3-carboxypropyl]wyosine37-O}-methyltransferase
Comments: The enzyme is found only in eukaryotes, where it is involved in the biosynthesis of wybutosine, a hypermodified tricyclic base found at position 37 of certain tRNAs. The modification is important for translational reading-frame maintenance. In some species that produce hydroxywybutosine the enzyme uses 7-(2-hydroxy-3-amino-3-carboxypropyl)wyosine37 in tRNAPhe as substrate. The enzyme also has the activity of EC 2.3.1.231, tRNAPhe 7-[(3S)-4-methoxy-(3-amino-3-carboxypropyl)wyosine37-O]-carbonyltransferase [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Noma, A., Kirino, Y., Ikeuchi, Y. and Suzuki, T. Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 25 (2006) 2142–2154. [DOI] [PMID: 16642040]
2.  Suzuki, Y., Noma, A., Suzuki, T., Ishitani, R. and Nureki, O. Structural basis of tRNA modification with CO2 fixation and methylation by wybutosine synthesizing enzyme TYW4. Nucleic Acids Res. 37 (2009) 2910–2925. [DOI] [PMID: 19287006]
3.  Kato, M., Araiso, Y., Noma, A., Nagao, A., Suzuki, T., Ishitani, R. and Nureki, O. Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification. Nucleic Acids Res. 39 (2011) 1576–1585. [DOI] [PMID: 20972222]
[EC 2.1.1.290 created 2013]
 
 
EC 2.1.1.317     
Accepted name: sphingolipid C9-methyltransferase
Reaction: S-adenosyl-L-methionine + a (4E,8E)-sphinga-4,8-dienine ceramide = S-adenosyl-L-homocysteine + a 9-methyl-(4E,8E)-sphinga-4,8-dienine ceramide
Systematic name: S-adenosyl-L-methionine:(4E,8E)-sphinga-4,8-dienine ceramide C-methyltransferase
Comments: The enzyme, characterized from the fungi Komagataella pastoris and Fusarium graminearum, acts only on ceramides and has no activity with free sphingoid bases or glucosylceramides.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Ternes, P., Sperling, P., Albrecht, S., Franke, S., Cregg, J.M., Warnecke, D. and Heinz, E. Identification of fungal sphingolipid C9-methyltransferases by phylogenetic profiling. J. Biol. Chem. 281 (2006) 5582–5592. [DOI] [PMID: 16339149]
2.  Ramamoorthy, V., Cahoon, E.B., Thokala, M., Kaur, J., Li, J. and Shah, D.M. Sphingolipid C-9 methyltransferases are important for growth and virulence but not for sensitivity to antifungal plant defensins in Fusarium graminearum. Eukaryot Cell 8 (2009) 217–229. [DOI] [PMID: 19028992]
[EC 2.1.1.317 created 2015]
 
 
EC 2.1.1.321     
Accepted name: type III protein arginine methyltransferase
Reaction: S-adenosyl-L-methionine + [protein]-L-arginine = S-adenosyl-L-homocysteine + [protein]-Nω-methyl-L-arginine
Other name(s): PRMT7 (gene name)
Systematic name: S-adenosyl-L-methionine:[protein]-L-arginine N-methyltransferase ([protein]-Nω-methyl-L-arginine-forming)
Comments: Type III protein arginine methyltransferases catalyse the single methylation of one of the terminal nitrogen atoms of the guanidino group in an L-arginine residue within a protein. Unlike type I and type II protein arginine methyltransferases, which also catalyse this reaction, type III enzymes do not methylate the substrate any further. cf. EC 2.1.1.319, type I protein arginine methyltransferase, EC 2.1.1.320, type II protein arginine methyltransferase, and EC 2.1.1.322, type IV protein arginine methyltransferase.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Miranda, T.B., Miranda, M., Frankel, A. and Clarke, S. PRMT7 is a member of the protein arginine methyltransferase family with a distinct substrate specificity. J. Biol. Chem. 279 (2004) 22902–22907. [DOI] [PMID: 15044439]
2.  Gonsalvez, G.B., Tian, L., Ospina, J.K., Boisvert, F.M., Lamond, A.I. and Matera, A.G. Two distinct arginine methyltransferases are required for biogenesis of Sm-class ribonucleoproteins. J. Cell Biol. 178 (2007) 733–740. [DOI] [PMID: 17709427]
3.  Feng, Y., Hadjikyriacou, A. and Clarke, S.G. Substrate specificity of human protein arginine methyltransferase 7 (PRMT7): the importance of acidic residues in the double E loop. J. Biol. Chem. 289 (2014) 32604–32616. [DOI] [PMID: 25294873]
[EC 2.1.1.321 created 2015]
 
 
EC 2.1.1.323     
Accepted name: (–)-pluviatolide 4-O-methyltransferase
Reaction: S-adenosyl-L-methionine + (–)-pluviatolide = S-adenosyl-L-homocysteine + (–)-bursehernin
For diagram of podophyllotoxin biosynthesis, click here
Glossary: (–)-pluviatolide = (3R,4R)-4-(2H-1,3-benzodioxol-5-ylmethyl)-3-[(4-hydroxy-3-methoxyphenyl)methyl]oxolan-2-one
(–)-bursehernin = (3R,4R)-4-(2H-1,3-benzodioxol-5-ylmethyl)-3-[(3,4-dimethoxyphenyl)methyl]oxolan-2-one
Other name(s): OMT3 (gene name)
Systematic name: S-adenosyl-L-methionine:(–)-pluviatolide 4-O-methyltransferase
Comments: The enzyme, characterized from the plant Sinopodophyllum hexandrum, is involved in the biosynthetic pathway of podophyllotoxin, a non-alkaloid toxin lignan whose derivatives are important anticancer drugs.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lau, W. and Sattely, E.S. Six enzymes from mayapple that complete the biosynthetic pathway to the etoposide aglycone. Science 349 (2015) 1224–1228. [DOI] [PMID: 26359402]
[EC 2.1.1.323 created 2016]
 
 
EC 2.1.1.330     
Accepted name: 5′-demethylyatein 5′-O-methyltransferase
Reaction: S-adenosyl-L-methionine + (–)-5′-demethylyatein = S-adenosyl-L-homocysteine + (–)-yatein
For diagram of podophyllotoxin biosynthesis, click here
Glossary: (–)-5′-demethylyatein = (3R,4R)-4-(2,3-benzodioxol-5-ylmethyl)-3-(3-hydroxy-4,5-dimethoxybenzyl)dihydrofuran-2(3H)-one
(–)-yatein = (3R,4R)-4-(1,3-benzodioxol-5-ylmethyl)-3-(3,4,5-trimethoxybenzyl)dihydrofuran-2(3H)-one
Other name(s): OMT1 (gene name)
Systematic name: S-adenosyl-L-methionine:(–)-5′-demethylyatein 5′-O-methyltransferase
Comments: The enzyme, characterized from the plant Sinopodophyllum hexandrum, is involved in the biosynthetic pathway of podophyllotoxin, a non-alkaloid toxin lignan whose derivatives are important anticancer drugs.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lau, W. and Sattely, E.S. Six enzymes from mayapple that complete the biosynthetic pathway to the etoposide aglycone. Science 349 (2015) 1224–1228. [DOI] [PMID: 26359402]
[EC 2.1.1.330 created 2016]
 
 
EC 2.1.1.346     
Accepted name: U6 snRNA m6A methyltransferase
Reaction: S-adenosyl-L-methionine + adenine in U6 snRNA = S-adenosyl-L-homocysteine + N6-methyladenine in U6 snRNA
Other name(s): METTL16 (gene name)
Systematic name: S-adenosyl-L-methionine:adenine in U6 snRNA methyltransferase
Comments: This enzyme, found in vertebrates, methylates a specific adenine in a hairpin structure of snRNA. The effects of the binding of the methyltransferase to its substrate is important for the regulation of the activity of an isoform of EC 2.5.1.6, methionine adenosyltransferase, that produces S-adenosyl-L-methionine [1,2]. The enzyme also binds (and maybe methylates) the lncRNAs XIST and MALAT1 as well as a number of pre-mRNAs at specific positions often found in the intronic regions [2].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Pendleton, K.E., Chen, B., Liu, K., Hunter, O.V., Xie, Y., Tu, B.P. and Conrad, N.K. The U6 snRNA m6A methyltransferase METTL16 regulates SAM synthetase intron retention. Cell 169 (2017) 824–835.e14. [DOI] [PMID: 28525753]
2.  Warda, A.S., Kretschmer, J., Hackert, P., Lenz, C., Urlaub, H., Hobartner, C., Sloan, K.E. and Bohnsack, M.T. Human METTL16 is a N6-methyladenosine (m6A) methyltransferase that targets pre-mRNAs and various non-coding RNAs. EMBO Rep. 18 (2017) 2004–2014. [DOI] [PMID: 29051200]
[EC 2.1.1.346 created 2018]
 
 
EC 2.1.1.360     
Accepted name: [histone H3]-lysine79 N-trimethyltransferase
Reaction: 3 S-adenosyl-L-methionine + a [histone H3]-L-lysine79 = 3 S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine79 (overall reaction)
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine79 = S-adenosyl-L-homocysteine + a [histone H3]-N6-methyl-L-lysine79
(1b) S-adenosyl-L-methionine + a [histone H3]-N6-methyl-L-lysine79 = S-adenosyl-L-homocysteine + a [histone H3]-N6,N6-dimethyl-L-lysine79
(1c) S-adenosyl-L-methionine + a [histone H3]-N6,N6-dimethyl-L-lysine79 = S-adenosyl-L-homocysteine + a [histone H3]-N6,N6,N6-trimethyl-L-lysine79
Other name(s): DOT1L (gene name); KMT4 (gene name)
Systematic name: S-adenosyl-L-methionine:[histone H3]-L-lysine79 N6-trimethyltransferase
Comments: The enzyme successively methylates the L-lysine79 residue of histone H3 (H3K79), ultimately generating a trimethylated form. These modifications influence the binding of chromatin-associated proteins. This is the only known methylation event of a lysine residue within the core region of a histone, as all other such modifications occur at the tail.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Feng, Q., Wang, H., Ng, H.H., Erdjument-Bromage, H., Tempst, P., Struhl, K. and Zhang, Y. Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain. Curr. Biol. 12 (2002) 1052–1058. [PMID: 12123582]
2.  Ng, H.H., Feng, Q., Wang, H., Erdjument-Bromage, H., Tempst, P., Zhang, Y. and Struhl, K. Lysine methylation within the globular domain of histone H3 by Dot1 is important for telomeric silencing and Sir protein association. Genes Dev. 16 (2002) 1518–1527. [PMID: 12080090]
3.  Min, J., Feng, Q., Li, Z., Zhang, Y. and Xu, R.M. Structure of the catalytic domain of human DOT1L, a non-SET domain nucleosomal histone methyltransferase. Cell 112 (2003) 711–723. [PMID: 12628190]
4.  Steger, D.J., Lefterova, M.I., Ying, L., Stonestrom, A.J., Schupp, M., Zhuo, D., Vakoc, A.L., Kim, J.E., Chen, J., Lazar, M.A., Blobel, G.A. and Vakoc, C.R. DOT1L/KMT4 recruitment and H3K79 methylation are ubiquitously coupled with gene transcription in mammalian cells. Mol. Cell Biol. 28 (2008) 2825–2839. [PMID: 18285465]
[EC 2.1.1.360 created 1976 as EC 2.1.1.43, modified 1982, modified 1983, part transferred 2019 to EC 2.1.1.360]
 
 
EC 2.1.1.362     
Accepted name: [histone H4]-N-methyl-L-lysine20 N-methyltransferase
Reaction: S-adenosyl-L-methionine + a [histone H4]-N6-methyl-L-lysine20 = S-adenosyl-L-homocysteine + a [histone H4]-N6,N6-dimethyl-L-lysine20
Other name(s): KMT5B (gene name); KMT5C (gene name); SUV420H1 (gene name); SUV420H2 (gene name)
Systematic name: S-adenosyl-L-methionine:[histone H4]-N6-methyl-L-lysine20 N6-methyltransferase
Comments: This entry describes a group of enzymes that catalyse a single methylation of monomethylated lysine20 of histone H4 (H4K20m1, generated by EC 2.1.1.361, [histone H4]-lysine20 N-methyltransferase), forming the dimethylated form. This modification is broadly distributed across the genome and is likely important for general chromatin-mediated processes. The double-methylated form of lysine20 in histone H4 is the most abundant methylation state of this residue and is found on ~80% of all histone H4 molecules. Full activity of the enzyme requires that the lysine at position 9 of histone H3 is trimethylated.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Schotta, G., Lachner, M., Sarma, K., Ebert, A., Sengupta, R., Reuter, G., Reinberg, D. and Jenuwein, T. A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin. Genes Dev. 18 (2004) 1251–1262. [PMID: 15145825]
2.  Jorgensen, S., Schotta, G. and Sorensen, C.S. Histone H4 lysine 20 methylation: key player in epigenetic regulation of genomic integrity. Nucleic Acids Res. 41 (2013) 2797–2806. [PMID: 23345616]
3.  Wu, H., Siarheyeva, A., Zeng, H., Lam, R., Dong, A., Wu, X.H., Li, Y., Schapira, M., Vedadi, M. and Min, J. Crystal structures of the human histone H4K20 methyltransferases SUV420H1 and SUV420H2. FEBS Lett. 587 (2013) 3859–3868. [PMID: 24396869]
4.  Southall, S.M., Cronin, N.B. and Wilson, J.R. A novel route to product specificity in the Suv4-20 family of histone H4K20 methyltransferases. Nucleic Acids Res. 42 (2014) 661–671. [PMID: 24049080]
5.  Weirich, S., Kudithipudi, S. and Jeltsch, A. Specificity of the SUV4-20H1 and SUV4-20H2 protein lysine methyltransferases and methylation of novel substrates. J. Mol. Biol. 428 (2016) 2344–2358. [PMID: 27105552]
[EC 2.1.1.362 created 1976 as EC 2.1.1.43, modified 1982, modified 1983, part transferred 2019 to EC 2.1.1.362]
 
 
EC 2.1.1.365     
Accepted name: MMP 1-O-methyltransferase
Reaction: S-adenosyl-L-methionine + 3,3′-di-O-methyl-4α-mannobiose = S-adenosyl-L-homocysteine + 1,3,3′-tri-O-methyl-4α-mannobiose
Glossary: 3,3′-di-O-methyl-4α-mannobiose = 3-O-methyl-α-D-mannopyranosyl-(1→4)-3-O-methyl-α-D-mannopyranose
Other name(s): MeT1; 3-O-methylmannose polysaccharide 1-O-methyltransferase
Systematic name: S-adenosyl-L-methionine:3,3′-di-O-methyl-4α-mannobiose 1-O-methyltransferase
Comments: Requires Mg2+. The enzyme, characterized from the bacterium Mycolicibacterium hassiacum, participates in the biosynthesis of 3-O-methylmannose polysaccharides (MMP), which are intracellular polymethylated polysaccharides implicated in the modulation of fatty acid metabolism in nontuberculous mycobacteria. The methylation catalysed by this enzyme was shown to block the reducing end of 3,3′-di-O-methyl-α-mannobiose, a probable early precursor of the 3-O-methylmannose polysaccharides.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Ripoll-Rozada, J., Costa, M., Manso, J.A., Maranha, A., Miranda, V., Sequeira, A., Ventura, M.R., Macedo-Ribeiro, S., Pereira, P.JB. and Empadinhas, N. Biosynthesis of mycobacterial methylmannose polysaccharides requires a unique 1-O-methyltransferase specific for 3-O-methylated mannosides. Proc. Natl. Acad. Sci. USA 116 (2019) 835–844. [DOI] [PMID: 30606802]
[EC 2.1.1.365 created 2020]
 
 
EC 2.1.1.379     
Accepted name: [methyl coenzyme M reductase]-L-arginine C-5-methyltransferase
Reaction: 2 S-adenosyl-L-methionine + a [methyl coenzyme-M reductase]-L-arginine + reduced acceptor = S-adenosyl-L-homocysteine + L-methionine + 5′-deoxyadenosine + a [methyl coenzyme-M reductase]-(5S)-C-methyl-L-arginine + acceptor
Other name(s): methanogenesis marker protein 10; Mmp10
Systematic name: S-adenosyl-L-methionine:[methyl coenzyme M reductase]-L-arginine C-5-(S)-methyltransferase
Comments: The enzyme, present in methanogenic archaea, catalyses a modification of an L-arginine residue at the active site of EC 2.8.4.1, coenzyme-B sulfoethylthiotransferase (better known as methyl-coenzyme M reductase), which catalyses the last and methane-releasing step of methanogenesis. The enzyme is a radical AdoMet (radical SAM) enzyme and contains a [4Fe-4S] cluster and a Coα-[α-(5-hydroxybenzimidazolyl)]-cobamide cofactor. The methyl group, which is derived from S-adenosyl-L-methionine, is transferred to the cob(I)amide cofactor, forming methylcob(III)amide as an intermediate carrier, before being transferred to the arginine residue.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Deobald, D., Adrian, L., Schone, C., Rother, M. and Layer, G. Identification of a unique radical SAM methyltransferase required for the sp3-C-methylation of an arginine residue of methyl-coenzyme M reductase. Sci. Rep. 8:7404 (2018). [DOI] [PMID: 29743535]
2.  Radle, M.I., Miller, D.V., Laremore, T.N. and Booker, S.J. Methanogenesis marker protein 10 (Mmp10) from Methanosarcina acetivorans is a radical S-adenosylmethionine methylase that unexpectedly requires cobalamin. J. Biol. Chem. 294 (2019) 11712–11725. [DOI] [PMID: 31113866]
3.  Lyu, Z., Shao, N., Chou, C.W., Shi, H., Patel, R., Duin, E.C. and Whitman, W.B. Posttranslational methylation of arginine in methyl coenzyme M reductase has a profound impact on both methanogenesis and growth of Methanococcus maripaludis. J. Bacteriol. 202 (2020) . [DOI] [PMID: 31740491]
[EC 2.1.1.379 created 2021]
 
 
EC 2.1.2.5     
Accepted name: glutamate formimidoyltransferase
Reaction: 5-formimidoyltetrahydrofolate + L-glutamate = tetrahydrofolate + N-formimidoyl-L-glutamate
Other name(s): FTCD (gene name); glutamate formyltransferase; formiminoglutamic acid transferase; formiminoglutamic formiminotransferase; glutamate formiminotransferase
Systematic name: 5-formimidoyltetrahydrofolate:L-glutamate N-formimidoyltransferase
Comments: The enzyme also catalyses formyl transfer from 5-formyltetrahydrofolate to L-glutamate. In eukaryotes, it occurs as a bifunctional enzyme that also has formimidoyltetrahydrofolate cyclodeaminase (EC 4.3.1.4) activity.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9032-83-1
References:
1.  Miller, A. and Waelsch, H. Formimino transfer from formamidinoglutaric acid to tetrahydrofolic acid. J. Biol. Chem. 228 (1957) 397–417. [PMID: 13475327]
2.  Silverman, M., Keresztesy, J.C., Koval, G.J. and Gardiner, R.C. Citrovorium factor and the synthesis of formylglutamic acid. J. Biol. Chem. 226 (1957) 83–94. [PMID: 13428739]
3.  Tabor, H. and Wyngarden, L. The enzymatic formation of formiminotetrahydrofolic acid, 5,10-methenyltetrahydrofolic acid, and 10-formyltetrahydrofolic acid in the metabolism of formiminoglutamic acid. J. Biol. Chem. 234 (1959) 1830–1849. [PMID: 13672973]
4.  Kohls, D., Sulea, T., Purisima, E.O., MacKenzie, R.E. and Vrielink, A. The crystal structure of the formiminotransferase domain of formiminotransferase-cyclodeaminase: implications for substrate channeling in a bifunctional enzyme. Structure 8 (2000) 35–46. [PMID: 10673422]
5.  Mao, Y., Vyas, N.K., Vyas, M.N., Chen, D.H., Ludtke, S.J., Chiu, W. and Quiocho, F.A. Structure of the bifunctional and Golgi-associated formiminotransferase cyclodeaminase octamer. EMBO J. 23 (2004) 2963–2971. [PMID: 15272307]
6.  Jeanguenin, L., Lara-Nunez, A., Pribat, A., Mageroy, M.H., Gregory, J.F., 3rd, Rice, K.C., de Crecy-Lagard, V. and Hanson, A.D. Moonlighting glutamate formiminotransferases can functionally replace 5-formyltetrahydrofolate cycloligase. J. Biol. Chem. 285 (2010) 41557–41566. [PMID: 20952389]
[EC 2.1.2.5 created 1961, modified 2000 (EC 2.1.2.6 created 1965, incorporated 1984)]
 
 
EC 2.1.2.13     
Accepted name: UDP-4-amino-4-deoxy-L-arabinose formyltransferase
Reaction: 10-formyltetrahydrofolate + UDP-4-amino-4-deoxy-β-L-arabinopyranose = 5,6,7,8-tetrahydrofolate + UDP-4-deoxy-4-formamido-β-L-arabinopyranose
For diagram of UDP-4-amino-4-deoxy-β-L-arabinose biosynthesis, click here
Other name(s): UDP-L-Ara4N formyltransferase; ArnAFT
Systematic name: 10-formyltetrahydrofolate:UDP-4-amino-4-deoxy-β-L-arabinose N-formyltransferase
Comments: The activity is part of a bifunctional enzyme also performing the reaction of EC 1.1.1.305 [UDP-glucuronic acid dehydrogenase (UDP-4-keto-hexauronic acid decarboxylating)].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB
References:
1.  Breazeale, S.D., Ribeiro, A.A., McClerren, A.L. and Raetz, C.R.H. A formyltransferase required for polymyxin resistance in Escherichia coli and the modification of lipid A with 4-amino-4-deoxy-L-arabinose. Identification and function of UDP-4-deoxy-4-formamido-L-arabinose. J. Biol. Chem. 280 (2005) 14154–14167. [DOI] [PMID: 15695810]
2.  Gatzeva-Topalova, P.Z., May, A.P. and Sousa, M.C. Crystal structure and mechanism of the Escherichia coli ArnA (PmrI) transformylase domain. An enzyme for lipid A modification with 4-amino-4-deoxy-L-arabinose and polymyxin resistance. Biochemistry 44 (2005) 5328–5338. [DOI] [PMID: 15807526]
3.  Williams, G.J., Breazeale, S.D., Raetz, C.R.H. and Naismith, J.H. Structure and function of both domains of ArnA, a dual function decarboxylase and a formyltransferase, involved in 4-amino-4-deoxy-L-arabinose biosynthesis. J. Biol. Chem. 280 (2005) 23000–23008. [DOI] [PMID: 15809294]
4.  Gatzeva-Topalova, P.Z., May, A.P. and Sousa, M.C. Structure and mechanism of ArnA: conformational change implies ordered dehydrogenase mechanism in key enzyme for polymyxin resistance. Structure 13 (2005) 929–942. [DOI] [PMID: 15939024]
5.  Yan, A., Guan, Z. and Raetz, C.R.H. An undecaprenyl phosphate-aminoarabinose flippase required for polymyxin resistance in Escherichia coli. J. Biol. Chem. 282 (2007) 36077–36089. [DOI] [PMID: 17928292]
[EC 2.1.2.13 created 2010]
 
 
EC 2.2.1.6     
Accepted name: acetolactate synthase
Reaction: 2 pyruvate = 2-acetolactate + CO2
For diagram of reaction mechanism, click here
Glossary: thiamine diphosphate = 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-diphosphoethyl)-4-methyl-1,3-thiazolium
Other name(s): α-acetohydroxy acid synthetase; α-acetohydroxyacid synthase; α-acetolactate synthase; α-acetolactate synthetase; acetohydroxy acid synthetase; acetohydroxyacid synthase; acetolactate pyruvate-lyase (carboxylating); acetolactic synthetase
Systematic name: pyruvate:pyruvate acetaldehydetransferase (decarboxylating)
Comments: This enzyme requires thiamine diphosphate. The reaction shown is in the pathway of biosynthesis of valine; the enzyme can also transfer the acetaldehyde from pyruvate to 2-oxobutanoate, forming 2-ethyl-2-hydroxy-3-oxobutanoate, also known as 2-aceto-2-hydroxybutanoate, a reaction in the biosynthesis of isoleucine.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 9027-45-6
References:
1.  Bauerle, R.H., Freundlich, M., Størmer, F.C. and Umbarger, H.E. Control of isoleucine, valine and leucine biosynthesis. II. Endproduct inhibition by valine of acetohydroxy acid synthetase in Salmonella typhimurium. Biochim. Biophys. Acta 92 (1964) 142–149. [PMID: 14243762]
2.  Huseby, N.E., Christensen, T.B., Olsen, B.R. and Størmer, F.C. The pH 6 acetolactate-forming enzyme from Aerobacter aerogenes. Subunit structure. Eur. J. Biochem. 20 (1971) 209–214. [DOI] [PMID: 5560406]
3.  Størmer, F.C., Solberg, Y. and Hovig, T. The pH 6 acetolactate-forming enzyme from Aerobacter aerogenes. Molecular properties. Eur. J. Biochem. 10 (1969) 251–260. [DOI] [PMID: 5823101]
4.  Barak, Z., Chipman, D.M. and Gollop, N. Physiological implications of the specificity of acetohydroxy acid synthase isozymes of enteric bacteria. J. Bacteriol. 169 (1987) 3750–3756. [DOI] [PMID: 3301814]
[EC 2.2.1.6 created 1972 as EC 4.1.3.18, transferred 2002 to EC 2.2.1.6]
 
 
EC 2.2.1.12     
Accepted name: 3-acetyloctanal synthase
Reaction: pyruvate + (E)-oct-2-enal = (S)-3-acetyloctanal + CO2
Other name(s): pigD (gene name)
Systematic name: pyruvate:(E)-oct-2-enal acetaldehydetransferase (decarboxylating)
Comments: Requires thiamine diphosphate. The enzyme, characterized from the bacterium Serratia marcescens, participates in the biosynthesis of the antibiotic prodigiosin. The enzyme decarboxylates pyruvate, followed by attack of the resulting two-carbon fragment on (E)-oct-2-enal, resulting in a Stetter reaction. In vitro the enzyme can act on a number of α,β-unsaturated carbonyl compounds, including aldehydes and ketones, and can catalyse both 1-2 and 1-4 carboligations depending on the substrate.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Williamson, N.R., Simonsen, H.T., Ahmed, R.A., Goldet, G., Slater, H., Woodley, L., Leeper, F.J. and Salmond, G.P. Biosynthesis of the red antibiotic, prodigiosin, in Serratia: identification of a novel 2-methyl-3-n-amyl-pyrrole (MAP) assembly pathway, definition of the terminal condensing enzyme, and implications for undecylprodigiosin biosynthesis in Streptomyces. Mol. Microbiol. 56 (2005) 971–989. [DOI] [PMID: 15853884]
2.  Dresen, C., Richter, M., Pohl, M., Ludeke, S. and Müller, M. The enzymatic asymmetric conjugate umpolung reaction. Angew. Chem. Int. Ed. Engl. 49 (2010) 6600–6603. [DOI] [PMID: 20669204]
3.  Kasparyan, E., Richter, M., Dresen, C., Walter, L.S., Fuchs, G., Leeper, F.J., Wacker, T., Andrade, S.L., Kolter, G., Pohl, M. and Müller, M. Asymmetric Stetter reactions catalyzed by thiamine diphosphate-dependent enzymes. Appl. Microbiol. Biotechnol. 98 (2014) 9681–9690. [DOI] [PMID: 24957249]
[EC 2.2.1.12 created 2014]
 
 
EC 2.3.1.39     
Accepted name: [acyl-carrier-protein] S-malonyltransferase
Reaction: malonyl-CoA + an [acyl-carrier protein] = CoA + a malonyl-[acyl-carrier protein]
For diagram of malonate decarboxylase, click here
Other name(s): [acyl carrier protein]malonyltransferase; FabD; malonyl coenzyme A-acyl carrier protein transacylase; malonyl transacylase; malonyl transferase; malonyl-CoA-acyl carrier protein transacylase; malonyl-CoA:[acyl-carrier-protein] S-malonyltransferase; malonyl-CoA:ACP transacylase; malonyl-CoA:ACP-SH transacylase; malonyl-CoA:AcpM transacylase; malonyl-CoA:acyl carrier protein transacylase; malonyl-CoA:acyl-carrier-protein transacylase; malonyl-CoA/dephospho-CoA acyltransferase; MAT; MCAT; MdcH
Systematic name: malonyl-CoA:[acyl-carrier protein] S-malonyltransferase
Comments: This enzyme, along with EC 2.3.1.38, [acyl-carrier-protein] S-acetyltransferase, is essential for the initiation of fatty-acid biosynthesis in bacteria. This enzyme also provides the malonyl groups for polyketide biosynthesis [7]. The product of the reaction, malonyl-ACP, is an elongation substrate in fatty-acid biosynthesis. In Mycobacterium tuberculosis, holo-ACP (the product of EC 2.7.8.7, holo-[acyl-carrier-protein] synthase) is the preferred substrate [5]. This enzyme also forms part of the multienzyme complexes EC 4.1.1.88, biotin-independent malonate decarboxylase and EC 7.2.4.4, biotin-dependent malonate decarboxylase. Malonylation of ACP is immediately followed by decarboxylation within the malonate-decarboxylase complex to yield acetyl-ACP, the catalytically active species of the decarboxylase [12]. In the enzyme from Klebsiella pneumoniae, methylmalonyl-CoA can also act as a substrate but acetyl-CoA cannot [10] whereas the enzyme from Pseudomonas putida can use both as substrates [11]. The ACP subunit found in fatty-acid biosynthesis contains a pantetheine-4′-phosphate cofactor; that from malonate decarboxylase also contains pantetheine-4′-phosphate but in the form of a 2′-(5-triphosphoribosyl)-3′-dephospho-CoA cofactor.
Links to other databases: BRENDA, EXPASY, GTD, KEGG, MetaCyc, PDB, CAS registry number: 37257-17-3
References:
1.  Alberts, A.W., Majerus, P.W. and Vagelos, P.R. Acetyl-CoA acyl carrier protein transacylase. Methods Enzymol. 14 (1969) 50–53. [DOI]
2.  Prescott, D.J. and Vagelos, P.R. Acyl carrier protein. Adv. Enzymol. Relat. Areas Mol. Biol. 36 (1972) 269–311. [DOI] [PMID: 4561013]
3.  Williamson, I.P. and Wakil, S.J. Studies on the mechanism of fatty acid synthesis. XVII. Preparation and general properties of acetyl coenzyme A and malonyl coenzyme A-acyl carrier protein transacylases. J. Biol. Chem. 241 (1966) 2326–2332. [DOI] [PMID: 5330116]
4.  Joshi, V.C. and Wakil, S.J. Studies on the mechanism of fatty acid synthesis. XXVI. Purification and properties of malonyl-coenzyme A--acyl carrier protein transacylase of Escherichia coli. Arch. Biochem. Biophys. 143 (1971) 493–505. [DOI] [PMID: 4934182]
5.  Kremer, L., Nampoothiri, K.M., Lesjean, S., Dover, L.G., Graham, S., Betts, J., Brennan, P.J., Minnikin, D.E., Locht, C. and Besra, G.S. Biochemical characterization of acyl carrier protein (AcpM) and malonyl-CoA:AcpM transacylase (mtFabD), two major components of Mycobacterium tuberculosis fatty acid synthase II. J. Biol. Chem. 276 (2001) 27967–27974. [DOI] [PMID: 11373295]
6.  Keatinge-Clay, A.T., Shelat, A.A., Savage, D.F., Tsai, S.C., Miercke, L.J., O'Connell, J.D., 3rd, Khosla, C. and Stroud, R.M. Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA:ACP transacylase. Structure 11 (2003) 147–154. [DOI] [PMID: 12575934]
7.  Szafranska, A.E., Hitchman, T.S., Cox, R.J., Crosby, J. and Simpson, T.J. Kinetic and mechanistic analysis of the malonyl CoA:ACP transacylase from Streptomyces coelicolor indicates a single catalytically competent serine nucleophile at the active site. Biochemistry 41 (2002) 1421–1427. [DOI] [PMID: 11814333]
8.  Hoenke, S., Schmid, M. and Dimroth, P. Sequence of a gene cluster from Klebsiella pneumoniae encoding malonate decarboxylase and expression of the enzyme in Escherichia coli. Eur. J. Biochem. 246 (1997) 530–538. [DOI] [PMID: 9208947]
9.  Koo, J.H. and Kim, Y.S. Functional evaluation of the genes involved in malonate decarboxylation by Acinetobacter calcoaceticus. Eur. J. Biochem. 266 (1999) 683–690. [DOI] [PMID: 10561613]
10.  Hoenke, S. and Dimroth, P. Formation of catalytically active acetyl-S-malonate decarboxylase requires malonyl-coenzyme A:acyl carrier protein transacylase as auxiliary enzyme. Eur. J. Biochem. 259 (1999) 181–187. [DOI] [PMID: 9914491]
11.  Chohnan, S., Fujio, T., Takaki, T., Yonekura, M., Nishihara, H. and Takamura, Y. Malonate decarboxylase of Pseudomonas putida is composed of five subunits. FEMS Microbiol. Lett. 169 (1998) 37–43. [DOI] [PMID: 9851033]
12.  Dimroth, P. and Hilbi, H. Enzymic and genetic basis for bacterial growth on malonate. Mol. Microbiol. 25 (1997) 3–10. [DOI] [PMID: 11902724]
[EC 2.3.1.39 created 1972, modified 2006, modified 2008]
 
 
EC 2.3.1.108     
Accepted name: α-tubulin N-acetyltransferase
Reaction: acetyl-CoA + [α-tubulin]-L-lysine = CoA + [α-tubulin]-N6-acetyl-L-lysine
Other name(s): ATAT1 (gene name); MEC17 (gene name); α-tubulin acetylase; TAT; α-tubulin acetyltransferase; tubulin N-acetyltransferase (ambiguous); acetyl-CoA:α-tubulin-L-lysine N-acetyltransferase; acetyl-CoA:[α-tubulin]-L-lysine 6-N-acetyltransferase
Systematic name: acetyl-CoA:[α-tubulin]-L-lysine N6-acetyltransferase
Comments: The enzyme is conserved from protists to mammals and is present in flowering plants. In most organisms it acetylates L-lysine at position 40 of α-tubulin.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 99889-90-4
References:
1.  Greer, K., Maruta, H., L'Hernault, S.W. and Rosenbaum, J.L. α-Tubulin acetylase activity in isolated Chlamydomonas flagella. J. Cell Biol. 101 (1985) 2081–2084. [PMID: 4066751]
2.  Akella, J.S., Wloga, D., Kim, J., Starostina, N.G., Lyons-Abbott, S., Morrissette, N.S., Dougan, S.T., Kipreos, E.T. and Gaertig, J. MEC-17 is an α-tubulin acetyltransferase. Nature 467 (2010) 218–222. [DOI] [PMID: 20829795]
3.  Shida, T., Cueva, J.G., Xu, Z., Goodman, M.B. and Nachury, M.V. The major α-tubulin K40 acetyltransferase αTAT1 promotes rapid ciliogenesis and efficient mechanosensation. Proc. Natl. Acad. Sci. USA 107 (2010) 21517–21522. [DOI] [PMID: 21068373]
4.  Taschner, M., Vetter, M. and Lorentzen, E. Atomic resolution structure of human α-tubulin acetyltransferase bound to acetyl-CoA. Proc. Natl. Acad. Sci. USA 109 (2012) 19649–19654. [DOI] [PMID: 23071318]
5.  Friedmann, D.R., Aguilar, A., Fan, J., Nachury, M.V. and Marmorstein, R. Structure of the α-tubulin acetyltransferase, αTAT1, and implications for tubulin-specific acetylation. Proc. Natl. Acad. Sci. USA 109 (2012) 19655–19660. [DOI] [PMID: 23071314]
6.  Kalebic, N., Sorrentino, S., Perlas, E., Bolasco, G., Martinez, C. and Heppenstall, P.A. αTAT1 is the major α-tubulin acetyltransferase in mice. Nat. Commun. 4:1962 (2013). [DOI] [PMID: 23748901]
[EC 2.3.1.108 created 1989, modified 2021]
 
 


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