The Enzyme Database

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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 2.1.1.200     
Accepted name: tRNA (cytidine32/uridine32-2′-O)-methyltransferase
Reaction: (1) S-adenosyl-L-methionine + cytidine32 in tRNA = S-adenosyl-L-homocysteine + 2′-O-methylcytidine32 in tRNA
(2) S-adenosyl-L-methionine + uridine32 in tRNA = S-adenosyl-L-homocysteine + 2′-O-methyluridine32 in tRNA
Other name(s): YfhQ; tRNA:Cm32/Um32 methyltransferase; TrMet(Xm32); TrmJ
Systematic name: S-adenosyl-L-methionine:tRNA (cytidine32/uridine32-2′-O)-methyltransferase
Comments: In Escherichia coli YfhQ is the only methyltransferase responsible for the formation of 2′-O-methylcytidine32 in tRNA. No methylation of cytosine34 in tRNALeu(CAA). In vitro the enzyme 2-O-methylates cytidine32 of tRNASer1 and uridine32 of tRNAGln2.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Purta, E., van Vliet, F., Tkaczuk, K.L., Dunin-Horkawicz, S., Mori, H., Droogmans, L. and Bujnicki, J.M. The yfhQ gene of Escherichia coli encodes a tRNA:Cm32/Um32 methyltransferase. BMC Mol. Biol. 7:23 (2006). [DOI] [PMID: 16848900]
[EC 2.1.1.200 created 2011]
 
 
EC 2.1.1.201     
Accepted name: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase
Reaction: S-adenosyl-L-methionine + 2-methoxy-6-all-trans-polyprenyl-1,4-benzoquinol = S-adenosyl-L-homocysteine + 6-methoxy-3-methyl-2-all-trans-polyprenyl-1,4-benzoquinol
For diagram of ubiquinol biosynthesis, click here
Other name(s): ubiE (gene name, ambiguous)
Systematic name: S-adenosyl-L-methionine:2-methoxy-6-all-trans-polyprenyl-1,4-benzoquinol 5-C-methyltransferase
Comments: This enzyme is involved in ubiquinone biosynthesis. Ubiquinones from different organisms have a different number of prenyl units (for example, ubiquinone-6 in Saccharomyces, ubiquinone-9 in rat and ubiquinone-10 in human), and thus the natural substrate for the enzymes from different organisms has a different number of prenyl units. However, the enzyme usually shows a low degree of specificity regarding the number of prenyl units. For example, when the COQ5 gene from Saccharomyces cerevisiae is introduced into Escherichia coli, it complements the respiratory deficiency of an ubiE mutant [3]. The bifunctional enzyme from Escherichia coli also catalyses the methylation of demethylmenaquinol-8 (this activity is classified as EC 2.1.1.163) [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Lee, P.T., Hsu, A.Y., Ha, H.T. and Clarke, C.F. A C-methyltransferase involved in both ubiquinone and menaquinone biosynthesis: isolation and identification of the Escherichia coli ubiE gene. J. Bacteriol. 179 (1997) 1748–1754. [DOI] [PMID: 9045837]
2.  Young, I.G., McCann, L.M., Stroobant, P. and Gibson, F. Characterization and genetic analysis of mutant strains of Escherichia coli K-12 accumulating the biquinone precursors 2-octaprenyl-6-methoxy-1,4-benzoquinone and 2-octaprenyl-3-methyl-6-methoxy-1,4-benzoquinone. J. Bacteriol. 105 (1971) 769–778. [PMID: 4323297]
3.  Dibrov, E., Robinson, K.M. and Lemire, B.D. The COQ5 gene encodes a yeast mitochondrial protein necessary for ubiquinone biosynthesis and the assembly of the respiratory chain. J. Biol. Chem. 272 (1997) 9175–9181. [DOI] [PMID: 9083048]
4.  Barkovich, R.J., Shtanko, A., Shepherd, J.A., Lee, P.T., Myles, D.C., Tzagoloff, A. and Clarke, C.F. Characterization of the COQ5 gene from Saccharomyces cerevisiae. Evidence for a C-methyltransferase in ubiquinone biosynthesis. J. Biol. Chem. 272 (1997) 9182–9188. [DOI] [PMID: 9083049]
[EC 2.1.1.201 created 2011]
 
 
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 2.1.1.203     
Accepted name: tRNA (cytosine34-C5)-methyltransferase
Reaction: S-adenosyl-L-methionine + cytosine34 in tRNA precursor = S-adenosyl-L-homocysteine + 5-methylcytosine34 in tRNA precursor
Other name(s): hTrm4 Mtase; hTrm4 methyltransferase; hTrm4 (gene name); tRNA:m5C-methyltransferase (ambiguous)
Systematic name: S-adenosyl-L-methionine:tRNA (cytosine34-C5)-methyltransferase
Comments: The human enzyme is specific for C5-methylation of cytosine34 in tRNA precursors. The intron in the human pre-tRNALeu(CAA) is indispensable for the C5-methylation of cytosine in the first position of the anticodon. It is not able to form 5-methylcytosine at positions 48 and 49 of human and yeast tRNA precursors [1].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Brzezicha, B., Schmidt, M., Makalowska, I., Jarmolowski, A., Pienkowska, J. and Szweykowska-Kulinska, Z. Identification of human tRNA:m5C methyltransferase catalysing intron-dependent m5C formation in the first position of the anticodon of the pre-tRNA Leu (CAA). Nucleic Acids Res. 34 (2006) 6034–6043. [DOI] [PMID: 17071714]
[EC 2.1.1.203 created 1976 as EC 2.1.1.29, part transferred 2011 to EC 2.1.1.203]
 
 
EC 2.1.1.204     
Accepted name: tRNA (cytosine38-C5)-methyltransferase
Reaction: S-adenosyl-L-methionine + cytosine38 in tRNA = S-adenosyl-L-homocysteine + 5-methylcytosine38 in tRNA
Other name(s): hDNMT2 (gene name); DNMT2 (gene name); TRDMT1 (gene name)
Systematic name: S-adenosyl-L-methionine:tRNA (cytosine38-C5)-methyltransferase
Comments: The eukaryotic enzyme catalyses methylation of cytosine38 in the anti-codon loop of tRNAAsp(GTC), tRNAVal(AAC) and tRNAGly(GCC). Methylation by Dnmt2 protects tRNAs against stress-induced cleavage by ribonuclease [3].
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Goll, M.G., Kirpekar, F., Maggert, K.A., Yoder, J.A., Hsieh, C.L., Zhang, X., Golic, K.G., Jacobsen, S.E. and Bestor, T.H. Methylation of tRNAAsp by the DNA methyltransferase homolog Dnmt2. Science 311 (2006) 395–398. [DOI] [PMID: 16424344]
2.  Jurkowski, T.P., Meusburger, M., Phalke, S., Helm, M., Nellen, W., Reuter, G. and Jeltsch, A. Human DNMT2 methylates tRNA(Asp) molecules using a DNA methyltransferase-like catalytic mechanism. RNA 14 (2008) 1663–1670. [DOI] [PMID: 18567810]
3.  Schaefer, M., Pollex, T., Hanna, K., Tuorto, F., Meusburger, M., Helm, M. and Lyko, F. RNA methylation by Dnmt2 protects transfer RNAs against stress-induced cleavage. Genes Dev. 24 (2010) 1590–1595. [DOI] [PMID: 20679393]
[EC 2.1.1.204 created 1976 as EC 2.1.1.29, part transferred 2011 to EC 2.1.1.204]
 
 
EC 2.1.1.205     
Accepted name: tRNA (cytidine32/guanosine34-2′-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + cytidine32/guanosine34 in tRNA = S-adenosyl-L-homocysteine + 2′-O-methylcytidine32/2′-O-methylguanosine34 in tRNA
Other name(s): Trm7p
Systematic name: S-adenosyl-L-methionine:tRNA (cytidine32/guanosine34-2′-O)-methyltransferase
Comments: The enzyme from Saccharomyces cerevisiae catalyses the formation of 2′-O-methylnucleotides at positions 32 and 34 of the yeast tRNAPhe, tRNATrp and, possibly, tRNALeu.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Pintard, L., Lecointe, F., Bujnicki, J.M., Bonnerot, C., Grosjean, H. and Lapeyre, B. Trm7p catalyses the formation of two 2′-O-methylriboses in yeast tRNA anticodon loop. EMBO J. 21 (2002) 1811–1820. [DOI] [PMID: 11927565]
[EC 2.1.1.205 created 2011]
 
 
EC 2.1.1.206     
Accepted name: tRNA (cytidine56-2′-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + cytidine56 in tRNA = S-adenosyl-L-homocysteine + 2′-O-methylcytidine56 in tRNA
Other name(s): aTrm56; tRNA ribose 2′-O-methyltransferase aTrm56; PAB1040 (gene name)
Systematic name: S-adenosyl-L-methionine:tRNA (cytidine56-2′-O)-methyltransferase
Comments: The archaeal enzyme specifically catalyses the S-adenosyl-L-methionine dependent 2′-O-ribose methylation of cytidine at position 56 in tRNA transcripts.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Renalier, M.H., Joseph, N., Gaspin, C., Thebault, P. and Mougin, A. The Cm56 tRNA modification in archaea is catalyzed either by a specific 2′-O-methylase, or a C/D sRNP. RNA 11 (2005) 1051–1063. [DOI] [PMID: 15987815]
2.  Kuratani, M., Bessho, Y., Nishimoto, M., Grosjean, H. and Yokoyama, S. Crystal structure and mutational study of a unique SpoU family archaeal methylase that forms 2′-O-methylcytidine at position 56 of tRNA. J. Mol. Biol. 375 (2008) 1064–1075. [DOI] [PMID: 18068186]
[EC 2.1.1.206 created 2011]
 
 
EC 2.1.1.207     
Accepted name: tRNA (cytidine34-2′-O)-methyltransferase
Reaction: (1) S-adenosyl-L-methionine + cytidine34 in tRNA = S-adenosyl-L-homocysteine + 2′-O-methylcytidine34 in tRNA
(2) S-adenosyl-L-methionine + 5-carboxymethylaminomethyluridine34 in tRNALeu = S-adenosyl-L-homocysteine + 5-carboxymethylaminomethyl-2′-O-methyluridine34 in tRNALeu
Other name(s): yibK (gene name); methyltransferase yibK; TrmL; tRNA methyltransferase L; tRNA (cytidine34/5-carboxymethylaminomethyluridine34-2′-O)-methyltransferase
Systematic name: S-adenosyl-L-methionine:tRNA (cytidine34/5-carboxymethylaminomethyluridine34-2′-O)-methyltransferase
Comments: The enzyme from Escherichia coli catalyses the 2′-O-methylation of cytidine or 5-carboxymethylaminomethyluridine at the wobble position at nucleotide 34 in tRNALeuCmAA and tRNALeucmnm5UmAA. The enzyme is selective for the two tRNALeu isoacceptors and only methylates these when they present the correct anticodon loop sequence and modification pattern. Specifically, YibK requires a pyrimidine nucleoside at position 34, it has a clear preference for an adenosine at position 35, and it fails to methylate without prior addition of the N6-(isopentenyl)-2-methylthioadenosine modification at position 37.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Benitez-Paez, A., Villarroya, M., Douthwaite, S., Gabaldon, T. and Armengod, M.E. YibK is the 2′-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors. RNA 16 (2010) 2131–2143. [DOI] [PMID: 20855540]
[EC 2.1.1.207 created 2011]
 
 
EC 2.1.1.208     
Accepted name: 23S rRNA (uridine2479-2′-O)-methyltransferase
Reaction: S-adenosyl-L-methionine + uridine2479 in 23S rRNA = S-adenosyl-L-homocysteine + 2′-O-methyluridine2479 in 23S rRNA
Other name(s): AviRb
Systematic name: S-adenosyl-L-methionine:23S rRNA (uridine2479-2′-O)-methyltransferase
Comments: Streptomyces viridochromogenes produces the antibiotic avilamycin A which binds to the 50S ribosomal subunit to inhibit protein synthesis. To protect itself from the antibiotic, Streptomyces viridochromogenes utilizes two methyltransferases, 23S rRNA (uridine2479-2′-O)-methyltransferase and EC 2.1.1.209 [23S rRNA (guanine2535-N1)-methyltransferase], whose actions confer avilamycin resistance to the RNA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Mosbacher, T.G., Bechthold, A. and Schulz, G.E. Structure and function of the antibiotic resistance-mediating methyltransferase AviRb from Streptomyces viridochromogenes. J. Mol. Biol. 345 (2005) 535–545. [DOI] [PMID: 15581897]
2.  Treede, I., Jakobsen, L., Kirpekar, F., Vester, B., Weitnauer, G., Bechthold, A. and Douthwaite, S. The avilamycin resistance determinants AviRa and AviRb methylate 23S rRNA at the guanosine 2535 base and the uridine 2479 ribose. Mol. Microbiol. 49 (2003) 309–318. [DOI] [PMID: 12828631]
3.  Weitnauer, G., Gaisser, S., Trefzer, A., Stockert, S., Westrich, L., Quiros, L.M., Mendez, C., Salas, J.A. and Bechthold, A. An ATP-binding cassette transporter and two rRNA methyltransferases are involved in resistance to avilamycin in the producer organism Streptomyces viridochromogenes Tu57. Antimicrob. Agents Chemother. 45 (2001) 690–695. [DOI] [PMID: 11181344]
[EC 2.1.1.208 created 2011]
 
 
EC 2.1.1.209     
Accepted name: 23S rRNA (guanine2535-N1)-methyltransferase
Reaction: S-adenosyl-L-methionine + guanine2535 in 23S rRNA = S-adenosyl-L-homocysteine + N1-methylguanine2535 in 23S rRNA
Other name(s): AviRa
Systematic name: S-adenosyl-L-methionine:23S rRNA (guanine2535-N1)-methyltransferase
Comments: Streptomyces viridochromogenes produces the antibiotic avilamycin A which binds to the 50S ribosomal subunit to inhibit protein synthesis. To protect itself from the antibiotic, Streptomyces viridochromogenes utilizes two methyltransferases, 23S rRNA (guanine2535-N1)-methyltransferase and EC 2.1.1.208 [23S rRNA (uridine2479-2-O)-methyltransferase], whose actions confer avilamycin resistance to the RNA.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc
References:
1.  Treede, I., Jakobsen, L., Kirpekar, F., Vester, B., Weitnauer, G., Bechthold, A. and Douthwaite, S. The avilamycin resistance determinants AviRa and AviRb methylate 23S rRNA at the guanosine 2535 base and the uridine 2479 ribose. Mol. Microbiol. 49 (2003) 309–318. [DOI] [PMID: 12828631]
2.  Weitnauer, G., Gaisser, S., Trefzer, A., Stockert, S., Westrich, L., Quiros, L.M., Mendez, C., Salas, J.A. and Bechthold, A. An ATP-binding cassette transporter and two rRNA methyltransferases are involved in resistance to avilamycin in the producer organism Streptomyces viridochromogenes Tu57. Antimicrob. Agents Chemother. 45 (2001) 690–695. [DOI] [PMID: 11181344]
3.  Mosbacher, T.G., Bechthold, A. and Schulz, G.E. Crystal structure of the avilamycin resistance-conferring methyltransferase AviRa from Streptomyces viridochromogenes. J. Mol. Biol. 329 (2003) 147–157. [DOI] [PMID: 12742024]
[EC 2.1.1.209 created 2011]
 
 


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