Enzyme Nomenclature

EC 2.1.1 (continued)

Methyltransferases

Continued from:
EC 2.1.1.1 to EC 2.1.1.50
EC 2.1.1.51 to EC 2.1.1.100
EC 2.1.1.101 to EC 2.1.1.150
See separate file for EC 2.1.1.201 to EC 2.1.1.250, EC 2.1.1.251 to EC 2.1.1.300 and EC 2.1.1.301 to EC 2.1.1.365.

Contents

EC 2.1.1.151 cobalt-factor II C20-methyltransferase
EC 2.1.1.152 precorrin-6A synthase (deacetylating)
EC 2.1.1.153 vitexin 2"-O-rhamnoside 7-O-methyltransferase
EC 2.1.1.154 isoliquiritigenin 2'-O-methyltransferase
EC 2.1.1.155 kaempferol 4'-O-methyltransferase
EC 2.1.1.156 glycine/sarcosine N-methyltransferase
EC 2.1.1.157 sarcosine/dimethylglycine N-methyltransferase
EC 2.1.1.158 7-methylxanthosine synthase
EC 2.1.1.159 theobromine synthase
EC 2.1.1.160 caffeine synthase
EC 2.1.1.161 dimethylglycine N-methyltransferase
EC 2.1.1.162 glycine/sarcosine/dimethylglycine N-methyltransferase
EC 2.1.1.163 demethylmenaquinone methyltransferase
EC 2.1.1.164 demethylrebeccamycin-D-glucose O-methyltransferase
EC 2.1.1.165 methyl halide transferase
EC 2.1.1.166 23S rRNA (uridine2552-2'-O-)-methyltransferase
EC 2.1.1.167 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase
EC 2.1.1.168 21S rRNA (uridine2791-2'-O)-methyltransferase
EC 2.1.1.169 tricetin 3',4',5'-O-trimethyltransferase
EC 2.1.1.170 16S rRNA (guanine527-N7)-methyltransferase
EC 2.1.1.171 16S rRNA (guanine966-N2)-methyltransferase
EC 2.1.1.172 16S rRNA (guanine1207-N2)-methyltransferase
EC 2.1.1.173 23S rRNA (guanine2445-N2)-methyltransferase
EC 2.1.1.174 23S rRNA (guanine1835-N2)-methyltransferase
EC 2.1.1.175 tricin synthase
EC 2.1.1.176 16S rRNA (cytosine967-C5)-methyltransferase
EC 2.1.1.177 23S rRNA (pseudouridine1915-N3)-methyltransferase
EC 2.1.1.178 16S rRNA (cytosine1407-C5)-methyltransferase
EC 2.1.1.179 16S rRNA (guanine1405-C7)-methyltransferase
EC 2.1.1.180 16S rRNA (adenine1408-N1)-methyltransferase
EC 2.1.1.181 23S rRNA (adenine1618-N6)-methyltransferase
EC 2.1.1.182 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase
EC 2.1.1.183 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase
EC 2.1.1.184 23S rRNA (adenine2085-N6)-dimethyltransferase
EC 2.1.1.185 23S rRNA (guanosine2251-2'-O)-methyltransferase
EC 2.1.1.186 23S rRNA (cytidine2498-2'-O)-methyltransferase
EC 2.1.1.187 23S rRNA (guanine745-N1)-methyltransferase
EC 2.1.1.188 23S rRNA (guanine748-N1)-methyltransferase
EC 2.1.1.189 23S rRNA (uracil747-C5)-methyltransferase
EC 2.1.1.190 23S rRNA (uracil1939-C5)-methyltransferase
EC 2.1.1.191 23S rRNA (cytosine1962-C5)-methyltransferase
EC 2.1.1.192 23S rRNA (adenine2503-C2)-methyltransferase
EC 2.1.1.193 16S rRNA (uracil1498-N3)-methyltransferase
EC 2.1.1.194 deleted, a mixture of EC 2.1.1.192 and EC 2.1.1.224
EC 2.1.1.195 cobalt-precorrin-5B (C1)-methyltransferase
EC 2.1.1.196 cobalt-precorrin-6B (C15)-methyltransferase [decarboxylating]
EC 2.1.1.197 malonyl-[acyl-carrier protein] O-methyltransferase
EC 2.1.1.198 16S rRNA (cytidine1402-2'-O)-methyltransferase
EC 2.1.1.199 16S rRNA (cytidine1402-N4)-methyltransferase
EC 2.1.1.200 tRNA (cytidine32/uridine32-2'-O)-methyltransferase

See the following files for:
EC 2.1.1.201 to EC 2.1.1.250
EC 2.1.1.251 to EC 2.1.1.300
EC 2.1.1.301 to EC 2.1.1.365

Entries

EC 2.1.1.151

Accepted name: cobalt-factor II C20-methyltransferase

Reaction: S-adenosyl-L-methionine + cobalt-factor II = S-adenosyl-L-homocysteine + cobalt-factor III

For diagram click here.

Other name(s): CbiL

Systematic name: S-adenosyl-L-methionine:cobalt-factor-II C20-methyltransferase

Comments: This enzyme participates in the anaerobic (early cobalt insertion) cobalamin biosynthesis pathway. See EC 2.1.1.130, precorrin-2 C20-methyltransferase, for the equivalent enzyme that participates in the aerobic cobalamin biosynthesis pathway.

Comments: Involved in the anaerobic biosynthesis of vitamin B12.

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

References:

1. Spencer, P., Stolowich, N.J., Sumner, L.W. and Scott, A.I. Definition of the redox states of cobalt-precorrinoids: investigation of the substrate and redox specificity of CbiL from Salmonella typhimurium. Biochemistry 37 (1998) 14917-14927. [PMID: 9778368]

[EC 2.1.1.151 created 2004]

EC 2.1.1.152

Accepted name: precorrin-6A synthase (deacetylating)

Reaction: S-adenosyl-L-methionine + precorrin-5 + H2O = S-adenosyl-L-homocysteine + precorrin-6A + acetate

For diagram click here and mechanism here.

Other name(s): precorrin-6X synthase (deacetylating); CobF

Systematic name: S-adenosyl-L-methionine:precorrin-5 C1-methyltransferase (deacetylating)

Comments: The enzyme, which participates in the aerobic (late cobalt insertion) cobalamin biosythesis pathway, catalyses two reactions -the methylation of carbon C1 of precorrin-5, and its deacetylation, forming precorrin-6A. See EC 2.1.1.195, cobalt-precorrin-5B (C1)-methyltransferase, for the C1-methyltransferase that participates in the anaerobic cobalamin biosynthesis pathway.

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

References:

1. Debussche, L., Thibaut, D., Cameron, B., Crouzet, J. and Blanche, F. Biosynthesis of the corrin macrocycle of coenzyme B12 in Pseudomonas denitrificans. J. Bacteriol. 175 (1993) 7430-7440. [PMID: 8226690]

2. Warren, M.J., Raux, E., Schubert, H.L. and Escalante-Semerena, J.C. The biosynthesis of adenosylcobalamin (vitamin B12). Nat. Prod. Rep. 19 (2002) 390-412. [PMID: 12195810]

[EC 2.1.1.152 created 2004]

EC 2.1.1.153

Accepted name: vitexin 2"-O-rhamnoside 7-O-methyltransferase

Reaction: S-adenosyl-L-methionine + vitexin 2"-O-β-L-rhamnoside = S-adenosyl-L-homocysteine + 7-O-methylvitexin 2"-O-β-L-rhamnoside

For diagram click here.

Systematic name: S-adenosyl-L-methionine:vitexin-2"-O-β-L-rhamnoside 7-O-methyltransferase

Comments: The flavonoids vitexin and isovitexin 2"-O-arabinoside do not act as substrates for the enzyme from oats (Avena sativa).

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 90698-29-6

References:

1. Knogge, W. and Weissenbock, G. Purification, characterization, and kinetic mechanism of S-adenosyl-L-methionine: vitexin 2"-O-rhamnoside 7-O-methyltransferase of Avena sativa L. Eur. J. Biochem. 140 (1984) 113-118. [PMID: 6705789]

[EC 2.1.1.153 created 2004]

EC 2.1.1.154

Accepted name: isoliquiritigenin 2'-O-methyltransferase

Reaction: S-adenosyl-L-methionine + isoliquiritigenin = S-adenosyl-L-homocysteine + 2'-O-methylisoliquiritigenin

For diagram click here.

Glossary: isoliquiritigenin = 4,2',4'-trihydroxychalcone

Other name(s): chalcone OMT; CHMT

Systematic name: S-adenosyl-L-methionine:isoliquiritigenin 2'-O-methyltransferase

Comments: Not identical to EC 2.1.1.65, licodione 2'-O-methyltransferase [2]. While EC 2.1.1.154, isoliquiritigenin 2'-O-methyltransferase can use licodione as a substrate, EC 2.1.1.65 cannot use isoliquiritigenin as a substrate.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 139317-14-9

References:

1. Maxwell, C.A., Edwards, R. and Dixon R.A. Identification, purification, and characterization of S-adenosyl-L-methionine: isoliquiritigenin 2'-O-methyltransferase from alfalfa (Medicago sativa L.). Arch. Biochem. Biophys. 293 (1992) 158-166. [PMID: 1731632]

2. Ichimura, M., Furuno, T., Takahashi, T., Dixon, R.A. and Ayabe, S. Enzymic O-methylation of isoliquiritigenin and licodione in alfalfa and licorice cultures. Phytochemistry 44 (1997) 991-995. [PMID: 9055445]

[EC 2.1.1.154 created 2004]

EC 2.1.1.155

Accepted name: kaempferol 4'-O-methyltransferase

Reaction: S-adenosyl-L-methionine + kaempferol = S-adenosyl-L-homocysteine + kaempferide

For diagram click here.

Glossary: kaempferide = 3,5,7-trihydroxy-4'-methoxyflavone

Other name(s): S-adenosyl-L-methionine:flavonoid 4'-O-methyltransferase; F 4'-OMT

Systematic name: S-adenosyl-L-methionine:kaempferol 4'-O-methyltransferase

Comments: The enzyme acts on the hydroxy group in the 4'-position of some flavones, flavanones and isoflavones. Kaempferol, apigenin and kaempferol triglucoside are substrates, as is genistein, which reacts more slowly. Compounds with an hydroxy group in the 3' and 4' positions, such as quercetin and eriodictyol, do not act as substrates. Similar to EC 2.1.1.75, apigenin 4'-O-methyltransferase and EC 2.1.1.83, 3,7-dimethylquercetin 4'-O-methyltransferase.

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 80747-20-2

References:

1. Curir, P., Lanzotti, V., Dolci, M., Dolci, P., Pasini, C. and Tollin, G. Purification and properties of a new S-adenosyl-L-methionine:flavonoid 4'-O-methyltransferase from carnation (Dianthus caryophyllus L.). Eur. J. Biochem. 270 (2003) 3422-3431. [PMID: 12899699]

[EC 2.1.1.155 created 2004]

EC 2.1.1.156

Accepted name: glycine/sarcosine N-methyltransferase

Reaction: 2 S-adenosyl-L-methionine + glycine = 2 S-adenosyl-L-homocysteine + N,N-dimethylglycine (overall reaction)
(1a) S-adenosyl-L-methionine + glycine = S-adenosyl-L-homocysteine + sarcosine

(1b) S-adenosyl-L-methionine + sarcosine = S-adenosyl-L-homocysteine + N,N-dimethylglycine

Glossary: sarcosine = N-methylglycine

Other name(s): ApGSMT; glycine-sarcosine methyltransferase; GSMT; GMT; glycine sarcosine N-methyltransferase; S-adenosyl-L-methionine:sarcosine N-methyltransferase

Systematic name: S-adenosyl-L-methionine:glycine(or sarcosine) N-methyltransferase [sarcosine(or N,N-dimethylglycine)-forming]

Comments: Cells of the oxygen-evolving halotolerant cyanobacterium Aphanocthece halophytica synthesize betaine from glycine by a three-step methylation process. This is the first enzyme and it leads to the formation of either sarcosine or N,N-dimethylglycine, which is further methylated to yield betaine (N,N,N-trimethylglycine) by the action of EC 2.1.1.157, sarcosine/dimethylglycine N-methyltransferase. Differs from EC 2.1.1.20, glycine N-methyltransferase, as it can further methylate the product of the first reaction. Acetate, dimethylglycine and S-adenosyl-L-homocysteine can inhibit the reaction [3].

Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 294210-82-5

References:

1. Nyyssölä, A., Kerovuo, J., Kaukinen, P., von Weymarn, N. and Reinikainen, T. Extreme halophiles synthesize betaine from glycine by methylation. J. Biol. Chem. 275 (2000) 22196-22201. [PMID: 10896953]

2. Nyyssölä, A., Reinikainen, T. and Leisola, M. Characterization of glycine sarcosine N-methyltransferase and sarcosine dimethylglycine N-methyltransferase. Appl. Environ. Microbiol. 67 (2001) 2044-2050. [PMID: 11319079]

3. Waditee, R., Tanaka, Y., Aoki, K., Hibino, T., Jikuya, H., Takano, J., Takabe, T. and Takabe, T. Isolation and functional characterization of N-methyltransferases that catalyze betaine synthesis from glycine in a halotolerant photosynthetic organism Aphanothece halophytica. J. Biol. Chem. 278 (2003) 4932-4942. [PMID: 12466265]

[EC 2.1.1.156 created 2005]

EC 2.1.1.157

Accepted name: sarcosine/dimethylglycine N-methyltransferase

Reaction: 2 S-adenosyl-L-methionine + sarcosine = 2 S-adenosyl-L-homocysteine + betaine (overall reaction)
(1) S-adenosyl-L-methionine + sarcosine = S-adenosyl-L-homocysteine + N,N-dimethylglycine

(2) S-adenosyl-L-methionine + N,N-dimethylglycine = S-adenosyl-L-homocysteine + betaine

Glossary: sarcosine = N-methylglycine
betaine = glycine betaine = N,N,N-trimethylglycine

Other name(s): ApDMT; sarcosine-dimethylglycine methyltransferase; SDMT; sarcosine dimethylglycine N-methyltransferase; S-adenosyl-L-methionine:N,N-dimethylglycine N-methyltransferase

Systematic name: S-adenosyl-L-methionine:sarcosine(or N,N-dimethylglycine) N-methyltransferase [N,N-dimethylglycine(or betaine)-forming]

Comments: Cells of the oxygen-evolving halotolerant cyanobacterium Aphanocthece halophytica synthesize betaine from glycine by a three-step methylation process. The first enzyme, EC 2.1.1.156, glycine/sarcosine N-methyltransferase, leads to the formation of either sarcosine or N,N-dimethylglycine, which is further methylated to yield betaine (N,N,N-trimethylglycine) by the action of this enzyme. Both of these enzymes can catalyse the formation of N,N-dimethylglycine from sarcosine [3]. The reactions are strongly inhibited by S-adenosyl-L-homocysteine.

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

References:

1. Nyyssölä, A., Kerovuo, J., Kaukinen, P., von Weymarn, N. and Reinikainen, T. Extreme halophiles synthesize betaine from glycine by methylation. J. Biol. Chem. 275 (2000) 22196-22201. [PMID: 10896953]

2. Nyyssölä, A., Reinikainen, T. and Leisola, M. Characterization of glycine sarcosine N-methyltransferase and sarcosine dimethylglycine N-methyltransferase. Appl. Environ. Microbiol. 67 (2001) 2044-2050. [PMID: 11319079]

3. Waditee, R., Tanaka, Y., Aoki, K., Hibino, T., Jikuya, H., Takano, J., Takabe, T. and Takabe, T. Isolation and functional characterization of N-methyltransferases that catalyze betaine synthesis from glycine in a halotolerant photosynthetic organism Aphanothece halophytica. J. Biol. Chem. 278 (2003) 4932-4942. [PMID: 12466265]

[EC 2.1.1.157 created 2005]

EC 2.1.1.158

Accepted name: 7-methylxanthosine synthase

Reaction: S-adenosyl-L-methionine + xanthosine = S-adenosyl-L-homocysteine + 7-methylxanthosine

For diagram of reaction click here

Other name(s): xanthosine methyltransferase; XMT; xanthosine:S-adenosyl-L-methionine methyltransferase; CtCS1; CmXRS1; CaXMT1; CmXRS1; S-adenosyl-L-methionine:xanthosine 7-N-methyltransferase

Systematic name: S-adenosyl-L-methionine:xanthosine N7-methyltransferase

Comments: The enzyme is specific for xanthosine, as XMP and xanthine cannot act as substrates [2,4]. The enzyme does not have N1- or N3- methylation activity [2]. This is the first methylation step in the production of caffeine.

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

References:

1. Negishi, O., Ozawa, T. and Imagawa, H. The role of xanthosine in the biosynthesis of caffeine in coffee plants. Agric. Biol. Chem. 49 (1985) 2221-2222.

2. Mizuno, K., Kato, M., Irino, F., Yoneyama, N., Fujimura, T. and Ashihara, H. The first committed step reaction of caffeine biosynthesis: 7-methylxanthosine synthase is closely homologous to caffeine synthases in coffee (Coffea arabica L.). FEBS Lett. 547 (2003) 56-60. [PMID: 12860386]

3. Uefuji, H., Ogita, S., Yamaguchi, Y., Koizumi, N. and Sano, H. Molecular cloning and functional characterization of three distinct N-methyltransferases involved in the caffeine biosynthetic pathway in coffee plants. Plant Physiol. 132 (2003) 372-380. [PMID: 12746542]

4. Yoneyama, N., Morimoto, H., Ye, C.X., Ashihara, H., Mizuno, K. and Kato, M. Substrate specificity of N-methyltransferase involved in purine alkaloids synthesis is dependent upon one amino acid residue of the enzyme. Mol. Genet. Genomics 275 (2006) 125-135. [PMID: 16333668]

[EC 2.1.1.158 created 2007]

EC 2.1.1.159

Accepted name: theobromine synthase

Reaction: S-adenosyl-L-methionine + 7-methylxanthine = S-adenosyl-L-homocysteine + 3,7-dimethylxanthine

For diagram of reaction click here

Glossary: theobromine = 3,7-dimethylxanthine
paraxanthine = 1,7-dimethylxanthine

Other name(s): monomethylxanthine methyltransferase; MXMT; CTS1; CTS2; S-adenosyl-L-methionine:7-methylxanthine 3-N-methyltransferase

Systematic name: S-adenosyl-L-methionine:7-methylxanthine N3-methyltransferase

Comments: This is the third enzyme in the caffeine-biosynthesis pathway. This enzyme can also catalyse the conversion of paraxanthine into caffeine, although the paraxanthine pathway is considered to be a minor pathway for caffeine biosynthesis [2,3].

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

References:

1. Ogawa, M., Herai, Y., Koizumi, N., Kusano, T. and Sano, H. 7-Methylxanthine methyltransferase of coffee plants. Gene isolation and enzymatic properties. J. Biol. Chem. 276 (2001) 8213-8218. [PMID: 11108716]

2. Uefuji, H., Ogita, S., Yamaguchi, Y., Koizumi, N. and Sano, H. Molecular cloning and functional characterization of three distinct N-methyltransferases involved in the caffeine biosynthetic pathway in coffee plants. Plant Physiol. 132 (2003) 372-380. [PMID: 12746542]

3. Yoneyama, N., Morimoto, H., Ye, C.X., Ashihara, H., Mizuno, K. and Kato, M. Substrate specificity of N-methyltransferase involved in purine alkaloids synthesis is dependent upon one amino acid residue of the enzyme. Mol. Genet. Genomics 275 (2006) 125-135. [PMID: 16333668]

[EC 2.1.1.159 created 2007]

EC 2.1.1.160

Accepted name: caffeine synthase

Reaction: (1) S-adenosyl-L-methionine + 3,7-dimethylxanthine = S-adenosyl-L-homocysteine + 1,3,7-trimethylxanthine
(2) S-adenosyl-L-methionine + 1,7-dimethylxanthine = S-adenosyl-L-homocysteine + 1,3,7-trimethylxanthine
(3) S-adenosyl-L-methionine + 7-methylxanthine = S-adenosyl-L-homocysteine + 3,7-dimethylxanthine

For diagram of reaction click here

Glossary: theobromine = 3,7-dimethylxanthine
paraxanthine = 1,7-dimethylxanthine
caffeine = 1,3,7-trimethylxanthine

Other name(s): dimethylxanthine methyltransferase, 3N-methyltransferase; DXMT; CCS1; S-adenosyl-L-methionine:3,7-dimethylxanthine 1-N-methyltransferase

Systematic name: S-adenosyl-L-methionine:3,7-dimethylxanthine N1-methyltransferase

Comments: Paraxanthine is the best substrate for this enzyme but the paraxanthine pathway is considered to be a minor pathway for caffeine biosynthesis [2,3].

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

References:

1. Kato, M., Mizuno, K., Fujimura, T., Iwama, M., Irie, M., Crozier, A. and Ashihara, H. Purification and characterization of caffeine synthase from tea leaves. Plant Physiol. 120 (1999) 579-586. [PMID: 10364410]

2. Mizuno, K., Okuda, A., Kato, M., Yoneyama, N., Tanaka, H., Ashihara, H. and Fujimura, T. Isolation of a new dual-functional caffeine synthase gene encoding an enzyme for the conversion of 7-methylxanthine to caffeine from coffee (Coffea arabica L.). FEBS Lett. 534 (2003) 75-81. [PMID: 12527364]

3. Uefuji, H., Ogita, S., Yamaguchi, Y., Koizumi, N. and Sano, H. Molecular cloning and functional characterization of three distinct N-methyltransferases involved in the caffeine biosynthetic pathway in coffee plants. Plant Physiol. 132 (2003) 372-380. [PMID: 12746542]

4. Kato, M., Mizuno, K., Crozier, A., Fujimura, T. and Ashihara, H. Caffeine synthase gene from tea leaves. Nature 406 (2000) 956-957. [PMID: 10984041]

[EC 2.1.1.160 created 2007]

EC 2.1.1.161

Accepted name: dimethylglycine N-methyltransferase

Reaction: S-adenosyl-L-methionine + N,N-dimethylglycine = S-adenosyl-L-homocysteine + betaine

Glossary: betaine = glycine betaine = N,N,N-trimethylglycine

Other name(s): BsmB; DMT

Systematic name: S-adenosyl-L-methionine:N,N-dimethylglycine N-methyltransferase (betaine-forming)

Comments: This enzyme, from the marine cyanobacterium Synechococcus sp. WH8102, differs from 2.1.1.157, sarcosine/dimethylglycine N-methyltransferase in that it cannot use sarcosine as an alternative substrate [1]. Betaine is a 'compatible solute' that enables cyanobacteria to cope with osmotic stress by maintaining a positive cellular turgor.

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

References:

1. Lu, W.D., Chi, Z.M. and Su, C.D. Identification of glycine betaine as compatible solute in Synechococcus sp. WH8102 and characterization of its N-methyltransferase genes involved in betaine synthesis. Arch. Microbiol. 186 (2006) 495-506. [PMID: 17019606]

[EC 2.1.1.161 created 2007]

EC 2.1.1.162

Accepted name: glycine/sarcosine/dimethylglycine N-methyltransferase

Reaction: 3 S-adenosyl-L-methionine + glycine = 3 S-adenosyl-L-homocysteine + betaine (overall reaction)
(1a) S-adenosyl-L-methionine + glycine = S-adenosyl-L-homocysteine + sarcosine
(1b) S-adenosyl-L-methionine + sarcosine = S-adenosyl-L-homocysteine + N,N-dimethylglycine
(1c) S-adenosyl-L-methionine + N,N-dimethylglycine = S-adenosyl-L-homocysteine + betaine

Glossary: sarcosine = N-methylglycine
betaine = glycine betaine = N,N,N-trimethylglycine

Other name(s): GSDMT; glycine sarcosine dimethylglycine N-methyltransferase

Systematic name: S-adenosyl-L-methionine:glycine(or sarcosine or N,N-dimethylglycine) N-methyltransferase [sarcosine(or N,N-dimethylglycine or betaine)-forming]

Comments: Unlike EC 2.1.1.156 (glycine/sarcosine N-methyltransferase), EC 2.1.1.157 (sarcosine/dimethylglycine N-methyltransferase) and EC 2.1.1.161 (dimethylglycine N-methyltransferase), this enzyme, from the halophilic methanoarchaeon Methanohalophilus portucalensis, can methylate glycine and all of its intermediates to form the compatible solute betaine [1].

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

References:

1. Lai, M.C., Wang, C.C., Chuang, M.J., Wu, Y.C. and Lee, Y.C. Effects of substrate and potassium on the betaine-synthesizing enzyme glycine sarcosine dimethylglycine N-methyltransferase from a halophilic methanoarchaeon Methanohalophilus portucalensis. Res. Microbiol. 157 (2006) 948-955. [PMID: 17098399]

[EC 2.1.1.162 created 2007]

EC 2.1.1.163

Accepted name: demethylmenaquinone methyltransferase

Reaction: a demethylmenaquinone + S-adenosyl-L-methionine = a menaquinol + S-adenosyl-L-homocysteine

For diagram of reaction click here.

Other name(s): S-adenosyl-L-methione—DMK methyltransferase; demethylmenaquinone C-methylase; 2-heptaprenyl-1,4-naphthoquinone methyltransferase; 2-demethylmenaquinone methyltransferase; S-adenosyl-L-methione:2-demethylmenaquinone methyltransferase

Systematic name: S-adenosyl-L-methione:demethylmenaquinone methyltransferase

Comments: The enzyme catalyses the last step in menaquinone biosynthesis. It is able to accept substrates with varying polyprenyl side chain length (the chain length is determined by polyprenyl diphosphate synthase)[1]. The enzyme from Escherichia coli also catalyses the conversion of 2-methoxy-6-octaprenyl-1,4-benzoquinone to 5-methoxy-2-methyl-3-octaprenyl-1,4-benzoquinone during the biosynthesis of ubiquinone [4]. The enzyme probably acts on menaquinol rather than menaquinone.

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

References:

1. Koike-Takeshita, A., Koyama, T. and Ogura, K. Identification of a novel gene cluster participating in menaquinone (vitamin K2) biosynthesis. Cloning and sequence determination of the 2-heptaprenyl-1,4-naphthoquinone methyltransferase gene of Bacillus stearothermophilus. J. Biol. Chem. 272 (1997) 12380-12383. [PMID: 9139683]

2. Wissenbach, U., Ternes, D. and Unden, G. An Escherichia coli mutant containing only demethylmenaquinone, but no menaquinone: effects on fumarate, dimethylsulfoxide, trimethylamine N-oxide and nitrate respiration. Arch. Microbiol. 158 (1992) 68-73. [PMID: 1444716]

3. Catala, F., Azerad, R. and Lederer, E. Sur les propriétés de la desméthylménaquinone C-méthylase de Mycobacterium phlei. Int. Z. Vitaminforsch. 40 (1970) 363-373. [PMID: 5450997]

4. 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. [PMID: 9045837]

[EC 2.1.1.163 created 2009]

EC 2.1.1.164

Accepted name: demethylrebeccamycin-D-glucose O-methyltransferase

Reaction: 4'-demethylrebeccamycin + S-adenosyl-L-methionine = rebeccamycin + S-adenosyl-L-homocysteine

For diagram of reaction click here

Other name(s): RebM

Systematic name: S-adenosyl-L-methionine:demethylrebeccamycin-D-glucose O-methyltransferase

Comments: Catalyses the last step in the biosynthesis of rebeccamycin, an indolocarbazole alkaloid produced by the bacterium Lechevalieria aerocolonigenes. The enzyme is able to use a wide variety substrates, tolerating variation on the imide heterocycle, deoxygenation of the sugar moiety, and even indolocarbazole glycoside anomers [1]. The enzyme is a member of the general acid/base-dependent O-methyltransferase family [2].

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

References:

1. Zhang, C., Albermann, C., Fu, X., Peters, N.R., Chisholm, J.D., Zhang, G., Gilbert, E.J., Wang, P.G., Van Vranken, D.L. and Thorson, J.S. RebG- and RebM-catalyzed indolocarbazole diversification. Chembiochem 7 (2006) 795-804. [PMID: 16575939]

2. Singh, S., McCoy, J.G., Zhang, C., Bingman, C.A., Phillips, G.N., Jr. and Thorson, J.S. Structure and mechanism of the rebeccamycin sugar 4'-O-methyltransferase RebM. J. Biol. Chem. 283 (2008) 22628-22636. [PMID: 18502766]

[EC 2.1.1.164 created 2010]

EC 2.1.1.165

Accepted name: methyl halide transferase

Reaction: S-adenosyl-L-methionine + iodide = S-adenosyl-L-homocysteine + methyl iodide

Other name(s): MCT; methyl chloride transferase; S-adenosyl-L-methionine:halide/bisulfide methyltransferase; AtHOL1; AtHOL2; AtHOL3; HARMLESS TO OZONE LAYER protein; HMT; S-adenosyl-L-methionine: halide ion methyltransferase; SAM:halide ion methyltransferase

Systematic name: S-adenosylmethionine:iodide methyltransferase

Comments: This enzyme contributes to the methyl halide emissions from Arabidopsis [6].

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

References:

1. Ni, X. and Hager, L.P. Expression of Batis maritima methyl chloride transferase in Escherichia coli. Proc. Natl. Acad. Sci. USA 96 (1999) 3611-3615. [PMID: 10097085]

2. Saxena, D., Aouad, S., Attieh, J. and Saini, H.S. Biochemical characterization of chloromethane emission from the wood-rotting fungus Phellinus pomaceus. Appl. Environ. Microbiol. 64 (1998) 2831-2835. [PMID: 9687437]

3. Attieh, J.M., Hanson, A.D. and Saini, H.S. Purification and characterization of a novel methyltransferase responsible for biosynthesis of halomethanes and methanethiol in Brassica oleracea. J. Biol. Chem. 270 (1995) 9250-9257. [PMID: 7721844]

4. Itoh, N., Toda, H., Matsuda, M., Negishi, T., Taniguchi, T. and Ohsawa, N. Involvement of S-adenosylmethionine-dependent halide/thiol methyltransferase (HTMT) in methyl halide emissions from agricultural plants: isolation and characterization of an HTMT-coding gene from Raphanus sativus (daikon radish). BMC Plant Biol. 9 (2009) 116. [PMID: 19723322]

5. Ohsawa, N., Tsujita, M., Morikawa, S. and Itoh, N. Purification and characterization of a monohalomethane-producing enzyme S-adenosyl-L-methionine: halide ion methyltransferase from a marine microalga, Pavlova pinguis. Biosci. Biotechnol. Biochem. 65 (2001) 2397-2404. [PMID: 11791711]

6. Nagatoshi, Y.and Nakamura, T. Characterization of three halide methyltransferases in Arabidopsis thaliana. Plant Biotechnol 24 (2007) 503-506.

[EC 2.1.1.165 created 2010]

EC 2.1.1.166

Accepted name: 23S rRNA (uridine2552-2'-O-)-methyltransferase

Reaction: S-adenosyl-L-methionine + uridine2552 in 23S rRNA = S-adenosyl-L-homocysteine + 2'-O-methyluridine2552 in 23S rRNA

Other name(s): Um(2552) 23S ribosomal RNA methyltransferase; heat shock protein RrmJ; RrmJ; FTSJ; Um2552 methyltransferase

Systematic name: S-adenosyl-L-methionine:23S rRNA (uridine2552-2'-O-)-methyltransferase

Comments: The enzyme catalyses the 2'-O methylation of the universally conserved U2552 in the A loop of 23S rRNA [3].

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

References:

1. Caldas, T., Binet, E., Bouloc, P., Costa, A., Desgres, J. and Richarme, G. The FtsJ/RrmJ heat shock protein of Escherichia coli is a 23 S ribosomal RNA methyltransferase. J. Biol. Chem. 275 (2000) 16414-16419. [PMID: 10748051]

2. Hager, J., Staker, B.L., Bugl, H. and Jakob, U. Active site in RrmJ, a heat shock-induced methyltransferase. J. Biol. Chem. 277 (2002) 41978-41986. [PMID: 12181314]

3. Hager, J., Staker, B.L. and Jakob, U. Substrate binding analysis of the 23S rRNA methyltransferase RrmJ. J. Bacteriol. 186 (2004) 6634-6642. [PMID: 15375145]

4. Bugl, H., Fauman, E.B., Staker, B.L., Zheng, F., Kushner, S.R., Saper, M.A., Bardwell, J.C. and Jakob, U. RNA methylation under heat shock control. Mol. Cell 6 (2000) 349-360. [PMID: 10983982]

[EC 2.1.1.166 created 2010]

EC 2.1.1.167

Accepted name: 27S pre-rRNA (guanosine2922-2'-O)-methyltransferase

Reaction: S-adenosyl-L-methionine + guanosine2922 in 27S pre-rRNA = S-adenosyl-L-homocysteine + 2'-O-methylguanosine2922 in 27S pre-rRNA

Other name(s): Spb1p (gene name); YCL054W (gene name)

Systematic name: S-adenosyl-L-methionine:27S pre-rRNA (guanosine2922-2'-O-)-methyltransferase

Comments: Spb1p is a site-specific 2'-O-ribose RNA methyltransferase that catalyses the formation of 2'-O-methylguanosine2922, a universally conserved position of the catalytic center of the ribosome that is essential for translation. 2'-O-Methylguanosine2922 is formed at a later stage of the processing, during the maturation of of the 27S pre-rRNA. In absence of snR52, Spb1p can also catalyse the formation of uridine2921 [1].

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

References:

1. Lapeyre, B. and Purushothaman, S.K. Spb1p-directed formation of Gm2922 in the ribosome catalytic center occurs at a late processing stage. Mol. Cell 16 (2004) 663-669. [PMID: 15546625]

2. Bonnerot, C., Pintard, L. and Lutfalla, G. Functional redundancy of Spb1p and a snR52-dependent mechanism for the 2'-O-ribose methylation of a conserved rRNA position in yeast. Mol. Cell 12 (2003) 1309-1315. [PMID: 14636587]

[EC 2.1.1.167 created 2010]

EC 2.1.1.168

Accepted name: 21S rRNA (uridine2791-2'-O)-methyltransferase

Reaction: S-adenosyl-L-methionine + uridine2791 in 21S rRNA = S-adenosyl-L-homocysteine + 2'-O-methyluridine2791 in 21S rRNA

Other name(s): MRM2 (gene name); mitochondrial 21S rRNA methyltransferase; mitochondrial rRNA MTase 2

Systematic name: S-adenosyl-L-methionine:21S rRNA (uridine2791-2'-O-)-methyltransferase

Comments: The enzyme catalyses the methylation of uridine2791 of mitochondrial 21S rRNA.

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

References:

1. Pintard, L., Bujnicki, J.M., Lapeyre, B. and Bonnerot, C. MRM2 encodes a novel yeast mitochondrial 21S rRNA methyltransferase. EMBO J. 21 (2002) 1139-1147. [PMID: 11867542]

[EC 2.1.1.168 created 2010]

EC 2.1.1.169

Accepted name: tricetin 3',4',5'-O-trimethyltransferase

Reaction: (1) 3 S-adenosyl-L-methionine + tricetin = 3 S-adenosyl-L-homocysteine + 3',4',5'-O-trimethyltricetin (overall reaction)
(1a) S-adenosyl-L-methionine + tricetin = S-adenosyl-L-homocysteine + 3'-O-methyltricetin
(1b) S-adenosyl-L-methionine + 3'-O-methyltricetin = S-adenosyl-L-homocysteine + 3',5'-O-dimethyltricetin
(1c) S-adenosyl-L-methionine + 3',5'-O-dimethyltricetin = S-adenosyl-L-homocysteine + 3',4',5'-O-trimethyltricetin

Other name(s): FOMT; TaOMT1; TaCOMT1; TaOMT2

Systematic name: S-adenosyl-L-methionine:tricetin 3',4',5'-O-trimethyltransferase

Comments: The enzyme from Triticum aestivum catalyses the sequential O-methylation of tricetin via 3'-O-methyltricetin, 3',5'-O-methyltricetin to 3',4',5'-O-trimethyltricetin [2].

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

References:

1. Kornblatt, J.A., Zhou, J.M. and Ibrahim, R.K. Structure-activity relationships of wheat flavone O-methyltransferase: a homodimer of convenience. FEBS J. 275 (2008) 2255-2266. [PMID: 18397325]

2. Zhou, J.M., Gold, N.D., Martin, V.J., Wollenweber, E. and Ibrahim, R.K. Sequential O-methylation of tricetin by a single gene product in wheat. Biochim. Biophys. Acta 1760 (2006) 1115-1124. [PMID: 16730127]

3. Zhou, J.M., Seo, Y.W. and Ibrahim, R.K. Biochemical characterization of a putative wheat caffeic acid O-methyltransferase. Plant Physiol. Biochem. 47 (2009) 322-326. [PMID: 19211254]

[EC 2.1.1.169 created 2010]

EC 2.1.1.170

Accepted name: 16S rRNA (guanine527-N7)-methyltransferase

Reaction: S-adenosyl-L-methionine + guanine527 in 16S rRNA = S-adenosyl-L-homocysteine + N7-methylguanine527 in 16S rRNA

Other name(s): ribosomal RNA small subunit methyltransferase G; 16S rRNA methyltransferase RsmG; GidB; rsmG (gene name)

Systematic name: S-adenosyl-L-methionine:16S rRNA (guanine527-N7)-methyltransferase

Comments: The enzyme specifically methylates guanine527 at N7 in 16S rRNA.

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

References:

1. Okamoto, S., Tamaru, A., Nakajima, C., Nishimura, K., Tanaka, Y., Tokuyama, S., Suzuki, Y. and Ochi, K. Loss of a conserved 7-methylguanosine modification in 16S rRNA confers low-level streptomycin resistance in bacteria. Mol. Microbiol. 63 (2007) 1096-1106. [PMID: 17238915]

2. Romanowski, M.J., Bonanno, J.B. and Burley, S.K. Crystal structure of the Escherichia coli glucose-inhibited division protein B (GidB) reveals a methyltransferase fold. Proteins 47 (2002) 563-567. [PMID: 12001236]

[EC 2.1.1.170 created 2010]

EC 2.1.1.171

Accepted name: 16S rRNA (guanine966-N2)-methyltransferase

Reaction: S-adenosyl-L-methionine + guanine966 in 16S rRNA = S-adenosyl-L-homocysteine + N2-methylguanine966 in 16S rRNA

Other name(s): yhhF (gene name); rsmD (gene name); m2G966 methyltransferase

Systematic name: S-adenosyl-L-methionine:16S rRNA (guanine966-N2)-methyltransferase

Comments: The enzyme efficiently methylates guanine966 of the assembled 30S subunits in vitro. Protein-free 16S rRNA is not a substrate for RsmD [1]. The enzyme specifically methylates guanine966 at N2 in 16S rRNA.

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

References:

1. Lesnyak, D.V., Osipiuk, J., Skarina, T., Sergiev, P.V., Bogdanov, A.A., Edwards, A., Savchenko, A., Joachimiak, A. and Dontsova, O.A. Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure. J. Biol. Chem. 282 (2007) 5880-5887. [PMID: 17189261]

[EC 2.1.1.171 created 1976 as EC 2.1.1.52, part transferred 2010 to EC 2.1.1.171]

EC 2.1.1.172

Accepted name: 16S rRNA (guanine1207-N2)-methyltransferase

Reaction: S-adenosyl-L-methionine + guanine1207 in 16S rRNA = S-adenosyl-L-homocysteine + N2-methylguanine1207 in 16S rRNA

Other name(s): m2G1207 methyltransferase

Systematic name: S-adenosyl-L-methionine:16S rRNA (guanine1207-N2)-methyltransferase

Comments: The enzyme reacts well with 30S subunits reconstituted from 16S RNA transcripts and 30S proteins but is almost inactive with the corresponding free RNA [1]. The enzyme specifically methylates guanine1207 at N2 in 16S rRNA.

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

References:

1. Tscherne, J.S., Nurse, K., Popienick, P. and Ofengand, J. Purification, cloning, and characterization of the 16 S RNA m2G1207 methyltransferase from Escherichia coli. J. Biol. Chem. 274 (1999) 924-929. [PMID: 9873033]

2. Sunita, S., Purta, E., Durawa, M., Tkaczuk, K.L., Swaathi, J., Bujnicki, J.M. and Sivaraman, J. Functional specialization of domains tandemly duplicated within 16S rRNA methyltransferase RsmC. Nucleic Acids Res. 35 (2007) 4264-4274. [PMID: 17576679]

[EC 2.1.1.172 created 1976 as EC 2.1.1.52, part transferred 2010 to EC 2.1.1.172]

EC 2.1.1.173

Accepted name: 23S rRNA (guanine2445-N2)-methyltransferase

Reaction: S-adenosyl-L-methionine + guanine2445 in 23S rRNA = S-adenosyl-L-homocysteine + N2-methylguanine2445 in 23S rRNA

Other name(s): ycbY (gene name); rlmL (gene name)

Systematic name: S-adenosyl-L-methionine:23S rRNA (guanine2445-N2)-methyltransferase

Comments: The enzyme methylates 23S rRNA in vitro, assembled 50S subunits are not a substrate [1]. The enzyme specifically methylates guanine2445 at N2 in 23S rRNA.

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

References:

1. Lesnyak, D.V., Sergiev, P.V., Bogdanov, A.A. and Dontsova, O.A. Identification of Escherichia coli m2G methyltransferases: I. the ycbY gene encodes a methyltransferase specific for G2445 of the 23 S rRNA. J. Mol. Biol. 364 (2006) 20-25. [PMID: 17010378]

[EC 2.1.1.173 created 1976 as EC 2.1.1.52, part transferred 2010 to EC 2.1.1.173]

EC 2.1.1.174

Accepted name: 23S rRNA (guanine1835-N2)-methyltransferase

Reaction: S-adenosyl-L-methionine + guanine1835 in 23S rRNA = S-adenosyl-L-homocysteine + N2-methylguanine1835 in 23S rRNA

Other name(s): ygjO (gene name); rlmG (gene name); ribosomal RNA large subunit methyltransferase G

Systematic name: S-adenosyl-L-methionine:23S rRNA (guanine1835-N2)-methyltransferase

Comments: The enzyme methylates 23S rRNA in vitro, assembled 50S subunits are not a substrate [1]. The enzyme specifically methylates guanine1835 at N2 in 23S rRNA.

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

References:

1. Sergiev, P.V., Lesnyak, D.V., Bogdanov, A.A. and Dontsova, O.A. Identification of Escherichia coli m2G methyltransferases: II. The ygjO gene encodes a methyltransferase specific for G1835 of the 23 S rRNA. J. Mol. Biol. 364 (2006) 26-31. [PMID: 17010380]

[EC 2.1.1.174 created 1976 as EC 2.1.1.52, part transferred 2010 to EC 2.1.1.174]

EC 2.1.1.175

Accepted name: tricin synthase

Reaction: (1) 2 S-adenosyl-L-methionine + tricetin = 2 S-adenosyl-L-homocysteine + 3',5'-O-dimethyltricetin
(1a) S-adenosyl-L-methionine + tricetin = S-adenosyl-L-homocysteine + 3'-O-methyltricetin
(1b) S-adenosyl-L-methionine + 3'-O-methyltricetin = S-adenosyl-L-homocysteine + 3',5'-O-dimethyltricetin

Glossary: tricin = 3',5'-O-dimethyltricetin

Other name(s): ROMT-17; ROMT-15; HvOMT1; ZmOMT1

Systematic name: S-adenosyl-L-methionine:tricetin 3',5'-O-dimethyltransferase

Comments: The enzymes from Oryza sativa (ROMT-15 and ROMT-17) catalyses the stepwise methylation of tricetin to its 3'-mono- and 3',5'-dimethyl ethers. In contrast with the wheat enzyme (EC 2.1.1.169, tricetin 3',4',5'-O-trimethyltransferase), tricetin dimethyl ether is not converted to its 3',4',5'-trimethylated ether derivative [1]. The enzymes from Hordeum vulgare (HvOMT1) and from Zea mays (ZmOMT1) form the 3',5'-dimethyl derivative as the major product [2].

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

References:

1. Lee, Y.J., Kim, B.G., Chong, Y., Lim, Y. and Ahn, J.H. Cation dependent O-methyltransferases from rice. Planta 227 (2008) 641-647. [PMID: 17943312]

2. Zhou, J.-M., Fukushi, Y., Wollenweber, E., Ibrahim, R.K. Characterization of two O-methyltransferase-like genes in barley and maize. Pharm. Biol. 46 (2008) 26-34.

[EC 2.1.1.175 created 2010]

EC 2.1.1.176

Accepted name: 16S rRNA (cytosine967-C5)-methyltransferase

Reaction: S-adenosyl-L-methionine + cytosine967 in 16S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine967 in 16S rRNA

Other name(s): rsmB (gene name); fmu (gene name); 16S rRNA m5C967 methyltransferase

Systematic name: S-adenosyl-L-methionine:16S rRNA (cytosine967-C5)-methyltransferase

Comments: The enzyme specifically methylates cytosine967 at C5 in 16S rRNA.

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

References:

1. Tscherne, J.S., Nurse, K., Popienick, P., Michel, H., Sochacki, M. and Ofengand, J. Purification, cloning, and characterization of the 16S RNA m5C967 methyltransferase from Escherichia coli. Biochemistry 38 (1999) 1884-1892. [PMID: 10026269]

2. Gu, X.R., Gustafsson, C., Ku, J., Yu, M. and Santi, D.V. Identification of the 16S rRNA m5C967 methyltransferase from Escherichia coli. Biochemistry 38 (1999) 4053-4057. [PMID: 10194318]

3. Foster, P.G., Nunes, C.R., Greene, P., Moustakas, D. and Stroud, R.M. The first structure of an RNA m5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate. Structure 11 (2003) 1609-1620. [PMID: 14656444]

[EC 2.1.1.176 created 2010]

EC 2.1.1.177

Accepted name: 23S rRNA (pseudouridine1915-N3)-methyltransferase

Reaction: S-adenosyl-L-methionine + pseudouridine1915 in 23S rRNA = S-adenosyl-L-homocysteine + N3-methylpseudouridine1915 in 23S rRNA

Other name(s): YbeA; RlmH; pseudouridine methyltransferase; m3Ψ methyltransferase; Ψ1915-specific methyltransferase; rRNA large subunit methyltransferase H

Systematic name: S-adenosyl-L-methionine:23S rRNA (pseudouridine1915-N3)-methyltransferase

Comments: YbeA does not methylate uridine at position 1915 [1].

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

References:

1. Ero, R., Peil, L., Liiv, A. and Remme, J. Identification of pseudouridine methyltransferase in Escherichia coli. RNA 14 (2008) 2223-2233. [PMID: 18755836]

2. Purta, E., Kaminska, K.H., Kasprzak, J.M., Bujnicki, J.M. and Douthwaite, S. YbeA is the m3Ψ methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA. RNA 14 (2008) 2234-2244. [PMID: 18755835]

[EC 2.1.1.177 created 2010]

EC 2.1.1.178

Accepted name: 16S rRNA (cytosine1407-C5)-methyltransferase

Reaction: S-adenosyl-L-methionine + cytosine1407 in 16S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine1407 in 16S rRNA

Other name(s): RNA m5C methyltransferase YebU; RsmF; YebU

Systematic name: S-adenosyl-L-methionine:16S rRNA (cytosine1407-C5)-methyltransferase

Comments: The enzyme specifically methylates cytosine1407 at C5 in 16S rRNA.

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

References:

1. Andersen, N.M. and Douthwaite, S. YebU is a m5C methyltransferase specific for 16 S rRNA nucleotide 1407. J. Mol. Biol. 359 (2006) 777-786. [PMID: 16678201]

2. Hallberg, B.M., Ericsson, U.B., Johnson, K.A., Andersen, N.M., Douthwaite, S., Nordlund, P., Beuscher, A.E., 4th and Erlandsen, H. The structure of the RNA m5C methyltransferase YebU from Escherichia coli reveals a C-terminal RNA-recruiting PUA domain. J. Mol. Biol. 360 (2006) 774-787. [PMID: 16793063]

[EC 2.1.1.178 created 2010]

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 specifically methylates guanine1405 at N7 in 16S rRNA. The enzyme from the antibiotic-producing bacterium Micromonospora zionensis methylates guanine1405 in 16S rRNA to 7-methylguanine, 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, CAS registry number:

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. [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. [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. [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. [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. [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. [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. [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. [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. [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, CAS registry number:

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. [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. [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. [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. [PMID: 17875999]

[EC 2.1.1.180 created 2010]

EC 2.1.1.181

Accepted name: 23S rRNA (adenine1618-N6)-methyltransferase

Reaction: S-adenosyl-L-methionine + adenine1618 in 23S rRNA = S-adenosyl-L-homocysteine + N6-methyladenine1618 in 23S rRNA

Other name(s): rRNA large subunit methyltransferase F; YbiN protein; rlmF (gene name); m6A1618 methyltransferase

Systematic name: S-adenosyl-L-methionine:23S rRNA (adenine1618-N6)-methyltransferase

Comments: The recombinant YbiN protein is able to methylate partially deproteinized 50 S ribosomal subunit, but neither the completely assembled 50 S subunits nor completely deproteinized 23 S rRNA [1].

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

References:

1. Sergiev, P.V., Serebryakova, M.V., Bogdanov, A.A. and Dontsova, O.A. The ybiN gene of Escherichia coli encodes adenine-N6 methyltransferase specific for modification of A1618 of 23 S ribosomal RNA, a methylated residue located close to the ribosomal exit tunnel. J. Mol. Biol. 375 (2008) 291-300. [PMID: 18021804]

[EC 2.1.1.181 created 1976 as EC 2.1.1.48, part transferred 2010 to EC 2.1.1.181]

EC 2.1.1.182

Accepted name: 16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase

Reaction: 4 S-adenosyl-L-methionine + adenine1518/adenine1519 in 16S rRNA = 4 S-adenosyl-L-homocysteine + N6-dimethyladenine1518/N6-dimethyladenine1519 in 16S rRNA

Other name(s): S-adenosylmethionine-6-N',N'-adenosyl (rRNA) dimethyltransferase; KsgA; ksgA methyltransferase

Systematic name: S-adenosyl-L-methionine:16S rRNA (adenine1518-N6/adenine1519-N6)-dimethyltransferase

Comments: KsgA introduces the most highly conserved ribosomal RNA modification, the dimethylation of adenine1518 and adenine1519 in 16S rRNA. Strains lacking the methylase are resistant to kasugamycin [1].

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

References:

1. Helser, T.L., Davies, J.E. and Dahlberg, J.E. Change in methylation of 16S ribosomal RNA associated with mutation to kasugamycin resistance in Escherichia coli. Nat. New Biol. 233 (1971) 12-14. [PMID: 4329247]

2. Helser, T.L., Davies, J.E. and Dahlberg, J.E. Mechanism of kasugamycin resistance in Escherichia coli. Nat. New Biol. 235 (1972) 6-9. [PMID: 4336392]

3. van Buul, C.P. and van Knippenberg, P.H. Nucleotide sequence of the ksgA gene of Escherichia coli: comparison of methyltransferases effecting dimethylation of adenosine in ribosomal RNA. Gene 38 (1985) 65-72. [PMID: 3905517]

4. Formenoy, L.J., Cunningham, P.R., Nurse, K., Pleij, C.W. and Ofengand, J. Methylation of the conserved A1518-A1519 in Escherichia coli 16S ribosomal RNA by the ksgA methyltransferase is influenced by methylations around the similarly conserved U1512.G1523 base pair in the 3' terminal hairpin. Biochimie 76 (1994) 1123-1128. [PMID: 7538324]

5. O'Farrell, H.C., Scarsdale, J.N. and Rife, J.P. Crystal structure of KsgA, a universally conserved rRNA adenine dimethyltransferase in Escherichia coli. J. Mol. Biol. 339 (2004) 337-353. [PMID: 15136037]

6. Poldermans, B., Roza, L. and Van Knippenberg, P.H. Studies on the function of two adjacent N6,N6-dimethyladenosines near the 3' end of 16 S ribosomal RNA of Escherichia coli. III. Purification and properties of the methylating enzyme and methylase-30 S interactions. J. Biol. Chem. 254 (1979) 9094-9100. [PMID: 383712]

7. Demirci, H., Belardinelli, R., Seri, E., Gregory, S.T., Gualerzi, C., Dahlberg, A.E. and Jogl, G. Structural rearrangements in the active site of the Thermus thermophilus 16S rRNA methyltransferase KsgA in a binary complex with 5'-methylthioadenosine. J. Mol. Biol. 388 (2009) 271-282. [PMID: 19285505]

8. Tu, C., Tropea, J.E., Austin, B.P., Court, D.L., Waugh, D.S. and Ji, X. Structural basis for binding of RNA and cofactor by a KsgA methyltransferase. Structure 17 (2009) 374-385. [PMID: 19278652]

[EC 2.1.1.182 created 1976 as EC 2.1.1.48, part transferred 2010 to EC 2.1.1.182]

EC 2.1.1.183

Accepted name: 18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase

Reaction: 4 S-adenosyl-L-methionine + adenine1779/adenine1780 in 18S rRNA = 4 S-adenosyl-L-homocysteine + N6-dimethyladenine1779/N6-dimethyladenine1780 in 18S rRNA

Other name(s): 18S rRNA dimethylase Dim1p; Dim1p; ScDim1; m2(6)A dimethylase; KIDIM1

Systematic name: S-adenosyl-L-methionine:18S rRNA (adenine1779-N6/adenine1780-N6)-dimethyltransferase

Comments: DIM1 is involved in pre-rRNA processing [1].

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

References:

1. Lafontaine, D., Vandenhaute, J. and Tollervey, D. The 18S rRNA dimethylase Dim1p is required for pre-ribosomal RNA processing in yeast. Genes Dev. 9 (1995) 2470-2481. [PMID: 7590228]

2. Lafontaine, D.L., Preiss, T. and Tollervey, D. Yeast 18S rRNA dimethylase Dim1p: a quality control mechanism in ribosome synthesis. Mol. Cell Biol. 18 (1998) 2360-2370. [PMID: 9528805]

3. Pulicherla, N., Pogorzala, L.A., Xu, Z., O. Farrell, H.C., Musayev, F.N., Scarsdale, J.N., Sia, E.A., Culver, G.M. and Rife, J.P. Structural and functional divergence within the Dim1/KsgA family of rRNA methyltransferases. J. Mol. Biol. 391 (2009) 884-893. [PMID: 19520088]

4. Lafontaine, D., Delcour, J., Glasser, A.L., Desgres, J. and Vandenhaute, J. The DIM1 gene responsible for the conserved m6(2)Am6(2)A dimethylation in the 3'-terminal loop of 18 S rRNA is essential in yeast. J. Mol. Biol. 241 (1994) 492-497. [PMID: 8064863]

5. O'Farrell, H.C., Pulicherla, N., Desai, P.M. and Rife, J.P. Recognition of a complex substrate by the KsgA/Dim1 family of enzymes has been conserved throughout evolution. RNA 12 (2006) 725-733. [PMID: 16540698]

[EC 2.1.1.183 created 1976 as EC 2.1.1.48, part transferred 2010 to EC 2.1.1.183]

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, CAS registry number:

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. [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. [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. [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. [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 2.1.1.185

Accepted name: 23S rRNA (guanosine2251-2'-O)-methyltransferase

Reaction: S-adenosyl-L-methionine + guanosine2251 in 23S rRNA = S-adenosyl-L-homocysteine + 2'-O-methylguanosine2251 in 23S rRNA

Other name(s): rlmB (gene name); yifH (gene name)

Systematic name: S-adenosyl-L-methionine:23S rRNA (guanosine2251-2'-O)-methyltransferase

Comments: The enzyme catalyses the methylation of guanosine2251, a modification conserved in the peptidyltransferase domain of 23S rRNA.

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

References:

1. Lovgren, J.M. and Wikstrom, P.M. The rlmB gene is essential for formation of Gm2251 in 23S rRNA but not for ribosome maturation in Escherichia coli. J. Bacteriol. 183 (2001) 6957-6960. [PMID: 11698387]

2. Michel, G., Sauve, V., Larocque, R., Li, Y., Matte, A. and Cygler, M. The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot. Structure 10 (2002) 1303-1315. [PMID: 12377117]

[EC 2.1.1.185 created 2010]

EC 2.1.1.186

Accepted name: 23S rRNA (cytidine2498-2'-O)-methyltransferase

Reaction: S-adenosyl-L-methionine + cytidine2498 in 23S rRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA

Other name(s): YgdE; rRNA large subunit methyltransferase M; RlmM

Systematic name: S-adenosyl-L-methionine:23S rRNA (cytidine2498-2'-O)-methyltransferase

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

References:

1. Purta, E., O'Connor, M., Bujnicki, J.M. and Douthwaite, S. YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA. Mol. Microbiol. 72 (2009) 1147-1158. [PMID: 19400805]

[EC 2.1.1.186 created 2010]

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, CAS registry number:

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. [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. [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. [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. [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 2.1.1.188

Accepted name: 23S rRNA (guanine748-N1)-methyltransferase

Reaction: S-adenosyl-L-methionine + guanine748 in 23S rRNA = S-adenosyl-L-homocysteine + N1-methylguanine748 in 23S rRNA

Other name(s): Rlma(II); Rlma2; 23S rRNA m1G748 methyltransferase; RlmaII; Rlma II; tylosin-resistance methyltransferase RlmA(II); TlrB; rRNA large subunit methyltransferase II

Systematic name: S-adenosyl-L-methionine:23S rRNA (guanine748-N1)-methyltransferase

Comments: The enzyme specifically methylates guanine748 at N1 in 23S rRNA. The methyltransferase RlmAII confers resistance to the macrolide antibiotic tylosin in the drug-producing strain Streptomyces fradiae [1].

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

References:

1. Douthwaite, S., Crain, P.F., Liu, M. and Poehlsgaard, J. The tylosin-resistance methyltransferase RlmAII (TlrB) modifies the N-1 position of 23S rRNA nucleotide G748. J. Mol. Biol. 337 (2004) 1073-1077. [PMID: 15046978]

2. Liu, M., Kirpekar, F., Van Wezel, G.P. and Douthwaite, S. The tylosin resistance gene tlrB of Streptomyces fradiae encodes a methyltransferase that targets G748 in 23S rRNA. Mol. Microbiol. 37 (2000) 811-820. [PMID: 10972803]

3. Lebars, I., Yoshizawa, S., Stenholm, A.R., Guittet, E., Douthwaite, S. and Fourmy, D. Structure of 23S rRNA hairpin 35 and its interaction with the tylosin-resistance methyltransferase RlmAII. EMBO J. 22 (2003) 183-192. [PMID: 12514124]

4. Lebars, I., Husson, C., Yoshizawa, S., Douthwaite, S. and Fourmy, D. Recognition elements in rRNA for the tylosin resistance methyltransferase RlmAII. J. Mol. Biol. 372 (2007) 525-534. [PMID: 17673230]

5. Douthwaite, S., Jakobsen, L., Yoshizawa, S. and Fourmy, D. Interaction of the tylosin-resistance methyltransferase RlmAII at its rRNA target differs from the orthologue RlmAI. J. Mol. Biol. 378 (2008) 969-975. [PMID: 18406425]

6. 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. [PMID: 11967079]

[EC 2.1.1.188 created 1976 as EC 2.1.1.51, part transferred 2010 to EC 2.1.1.188]

EC 2.1.1.189

Accepted name: 23S rRNA (uracil747-C5)-methyltransferase

Reaction: S-adenosyl-L-methionine + uracil747 in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil747 in 23S rRNA

Other name(s): YbjF; RumB; RNA uridine methyltransferase B

Systematic name: S-adenosyl-L-methionine:23S rRNA (uracil747-C5)-methyltransferase

Comments: The enzyme specifically methylates uracil747 at C5 in 23S rRNA.

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

References:

1. Madsen, C.T., Mengel-Jorgensen, J., Kirpekar, F. and Douthwaite, S. Identifying the methyltransferases for m5U747 and m5U1939 in 23S rRNA using MALDI mass spectrometry. Nucleic Acids Res. 31 (2003) 4738-4746. [PMID: 12907714]

[EC 2.1.1.189 created 2010]

EC 2.1.1.190

Accepted name: 23S rRNA (uracil1939-C5)-methyltransferase

Reaction: S-adenosyl-L-methionine + uracil1939 in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil1939 in 23S rRNA

Other name(s): RumA; RNA uridine methyltransferase A; YgcA

Systematic name: S-adenosyl-L-methionine:23S rRNA (uracil1939-C5)-methyltransferase

Comments: The enzyme specifically methylates uracil1939 at C5 in 23S rRNA [1]. The enzyme contains an [4Fe-4S] cluster coordinated by four conserved cysteine residues [2].

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

References:

1. Agarwalla, S., Kealey, J.T., Santi, D.V. and Stroud, R.M. Characterization of the 23 S ribosomal RNA m5U1939 methyltransferase from Escherichia coli. J. Biol. Chem. 277 (2002) 8835-8840. [PMID: 11779873]

2. Lee, T.T., Agarwalla, S. and Stroud, R.M. Crystal structure of RumA, an iron-sulfur cluster containing E. coli ribosomal RNA 5-methyluridine methyltransferase. Structure 12 (2004) 397-407. [PMID: 15016356]

3. Madsen, C.T., Mengel-Jorgensen, J., Kirpekar, F. and Douthwaite, S. Identifying the methyltransferases for m5U747 and m5U1939 in 23S rRNA using MALDI mass spectrometry. Nucleic Acids Res. 31 (2003) 4738-4746. [PMID: 12907714]

4. Persaud, C., Lu, Y., Vila-Sanjurjo, A., Campbell, J.L., Finley, J. and O'Connor, M. Mutagenesis of the modified bases, m5U1939 and Ψ2504, in Escherichia coli 23S rRNA. Biochem. Biophys. Res. Commun. 392 (2010) 223-227. [PMID: 20067766]

5. Agarwalla, S., Stroud, R.M. and Gaffney, B.J. Redox reactions of the iron-sulfur cluster in a ribosomal RNA methyltransferase, RumA: optical and EPR studies. J. Biol. Chem. 279 (2004) 34123-34129. [PMID: 15181002]

6. Lee, T.T., Agarwalla, S. and Stroud, R.M. A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function. Cell 120 (2005) 599-611. [PMID: 15766524]

[EC 2.1.1.190 created 2010]

EC 2.1.1.191

Accepted name: 23S rRNA (cytosine1962-C5)-methyltransferase

Reaction: S-adenosyl-L-methionine + cytosine1962 in 23S rRNA = S-adenosyl-L-homocysteine + 5-methylcytosine1962 in 23S rRNA

Other name(s): RlmI; rRNA large subunit methyltransferase I; YccW

Systematic name: S-adenosyl-L-methionine:23S rRNA (cytosine1962-C5)-methyltransferase

Comments: The enzyme specifically methylates cytosine1962 at C5 in 23S rRNA.

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

References:

1. Purta, E., O'Connor, M., Bujnicki, J.M. and Douthwaite, S. YccW is the m5C methyltransferase specific for 23S rRNA nucleotide 1962. J. Mol. Biol. 383 (2008) 641-651. [PMID: 18786544]

2. Sunita, S., Tkaczuk, K.L., Purta, E., Kasprzak, J.M., Douthwaite, S., Bujnicki, J.M. and Sivaraman, J. Crystal structure of the Escherichia coli 23S rRNA:m5C methyltransferase RlmI (YccW) reveals evolutionary links between RNA modification enzymes. J. Mol. Biol. 383 (2008) 652-666. [PMID: 18789337]

[EC 2.1.1.191 created 2010]

EC 2.1.1.192

Accepted name: 23S rRNA (adenine2503-C2)-methyltransferase

Reaction: (1) 2 S-adenosyl-L-methionine + adenine2503 in 23S rRNA + 2 reduced [2Fe-2S] ferredoxin = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine2503 in 23S rRNA + 2 oxidized [2Fe-2S] ferredoxin
(2) 2 S-adenosyl-L-methionine + adenine37 in tRNA + 2 reduced [2Fe-2S] ferredoxin = S-adenosyl-L-homocysteine + L-methionine + 5'-deoxyadenosine + 2-methyladenine37 in tRNA + 2 oxidized [2Fe-2S] ferredoxin

Other name(s): RlmN; YfgB; Cfr

Systematic name: S-adenosyl-L-methionine:23S rRNA (adenine2503-C2)-methyltransferase

Comments: Contains an [4Fe-4S] cluster [2]. This enzyme is a member of the ‘AdoMet radical’ (radical SAM) family. S-Adenosyl-L-methionine acts as both a radical generator and as the source of the appended methyl group. RlmN first transfers an CH2 group to a conserved cysteine (Cys355 in Escherichia coli) [6], the generated radical from a second S-adenosyl-L-methionine then attacks the methyl group, exctracting a hydrogen. The formed radical forms a covalent intermediate with the adenine group of the tRNA [9]. RlmN is an endogenous enzyme used by the cell to refine functions of the ribosome in protein synthesis [2]. The enzyme methylates adenosine by a radical mechanism with CH2 from the S-adenosyl-L-methionine and retention of the hydrogen at C-2 of adenosine2503 of 23S rRNA. It will also methylate 8-methyladenosine2503 of 23S rRNA. cf. EC 2.1.1.224 [23S rRNA (adenine2503-C8)-methyltransferase].

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

References:

1. Toh, S.M., Xiong, L., Bae, T. and Mankin, A.S. The methyltransferase YfgB/RlmN is responsible for modification of adenosine 2503 in 23S rRNA. RNA 14 (2008) 98-106. [PMID: 18025251]

2. Yan, F., LaMarre, J.M., Röhrich, R., Wiesner, J., Jomaa, H., Mankin, A.S. and Fujimori, D.G. RlmN and Cfr are radical SAM enzymes involved in methylation of ribosomal RNA. J. Am. Chem. Soc. 132 (2010) 3953-3964. [PMID: 20184321]

3. Yan, F. and Fujimori, D.G. RNA methylation by radical SAM enzymes RlmN and Cfr proceeds via methylene transfer and hydride shift. Proc. Natl. Acad. Sci. USA 108 (2011) 3930-3934. [PMID: 21368151]

4. Grove, T.L., Benner, J.S., Radle, M.I., Ahlum, J.H., Landgraf, B.J., Krebs, C. and Booker, S.J. A radically different mechanism for S-adenosylmethionine-dependent methyltransferases. Science 332 (2011) 604-607. [PMID: 21415317]

5. Boal, A.K., Grove, T.L., McLaughlin, M.I., Yennawar, N.H., Booker, S.J. and Rosenzweig, A.C. Structural basis for methyl transfer by a radical SAM enzyme. Science 332 (2011) 1089-1092. [PMID: 21527678]

6. Grove, T.L., Radle, M.I., Krebs, C. and Booker, S.J. Cfr and RlmN contain a single [4Fe-4S] cluster, which directs two distinct reactivities for S-adenosylmethionine: methyl transfer by SN2 displacement and radical generation. J. Am. Chem. Soc. 133 (2011) 19586-19589. [PMID: 21916495]

7. McCusker, K.P., Medzihradszky, K.F., Shiver, A.L., Nichols, R.J., Yan, F., Maltby, D.A., Gross, C.A. and Fujimori, D.G. Covalent intermediate in the catalytic mechanism of the radical S-adenosyl-L-methionine methyl synthase RlmN trapped by mutagenesis. J. Am. Chem. Soc. 134 (2012) 18074-18081. [PMID: 23088750]

8. Benitez-Paez, A., Villarroya, M. and Armengod, M.E. The Escherichia coli RlmN methyltransferase is a dual-specificity enzyme that modifies both rRNA and tRNA and controls translational accuracy. RNA 18 (2012) 1783-1795. [PMID: 22891362]

9. Silakov, A., Grove, T.L., Radle, M.I., Bauerle, M.R., Green, M.T., Rosenzweig, A.C., Boal, A.K. and Booker, S.J. Characterization of a cross-linked protein-nucleic acid substrate radical in the reaction catalyzed by RlmN. J. Am. Chem. Soc. 136 (2014) 8221-8228. [PMID: 24806349]

[EC 2.1.1.192 created 2010, modified 2011, modified 2014]

EC 2.1.1.193

Accepted name: 16S rRNA (uracil1498-N3)-methyltransferase

Reaction: S-adenosyl-L-methionine + uracil1498 in 16S rRNA = S-adenosyl-L-homocysteine + N3-methyluracil1498 in 16S rRNA

Other name(s): DUF558 protein; YggJ; RsmE; m3U1498 specific methyltransferase

Systematic name: S-adenosyl-L-methionine:16S rRNA (uracil1498-N3)-methyltransferase

Comments: The enzyme specifically methylates uracil1498 at N3 in 16S rRNA.

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

References:

1. Basturea, G.N., Rudd, K.E. and Deutscher, M.P. Identification and characterization of RsmE, the founding member of a new RNA base methyltransferase family. RNA 12 (2006) 426-434. [PMID: 16431987]

2. Basturea, G.N. and Deutscher, M.P. Substrate specificity and properties of the Escherichia coli 16S rRNA methyltransferase, RsmE. RNA 13 (2007) 1969-1976. [PMID: 17872509]

[EC 2.1.1.193 created 2010]

[EC 2.1.1.194 Deleted entry: 23S rRNA (adenine2503-C2,C8)-dimethyltransferase. A mixture of EC 2.1.1.192 (23S rRNA (adenine2503-C2)-methyltransferase) and EC 2.1.1.224 (23S rRNA (adenine2503-C8)-methyltransferase) (EC 2.1.1.194 created 2010, deleted 2011)]

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 click here.

Glossary: cobalt-precorrin-6A = cobalt-precorrin-6x

Other name(s): cobalt-precorrin-6A synthase; CbiD (gene name)

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.

Comments: This enzyme catalyses the C-1 methylation of cobalt-precorrin-5B in the anaerobic (early cobalt insertion) pathway of adenosylcobalamin biosynthesis.

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

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. [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. [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. [PMID: 23922391]

[EC 2.1.1.195 created 2010]

EC 2.1.1.196

Accepted name: cobalt-precorrin-6B (C15)-methyltransferase [decarboxylating]

Reaction: cobalt-precorrin-6B + S-adenosyl-L-methionine = cobalt-precorrin-7 + S-adenosyl-L-homocysteine + CO2

For diagram of reaction, click here

Other name(s): cbiT (gene name); S-adenosyl-L-methionine:precorrin-7 C15-methyltransferase (C12-decarboxylating); cobalt-precorrin-7 (C15)-methyltransferase [decarboxylating]

Systematic name: S-adenosyl-L-methionine:precorrin-6B C15-methyltransferase (C12-decarboxylating)

Comments: This enzyme, which participates in the anaerobic (early cobalt insertion) adenosylcobalamin biosynthesis pathway, catalyses both methylation at C-15 and decarboxylation of the C-12 acetate side chain of cobalt-precorrin-6B. The equivalent activity in the aerobic adenosylcobalamin biosynthesis pathway is catalysed by the bifunctional enzyme EC 2.1.1.132, precorrin-6B C5,15-methyltransferase (decarboxylating).

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

References:

1. Keller, J.P., Smith, P.M., Benach, J., Christendat, D., deTitta, G.T. and Hunt, J.F. The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferase. Structure 10 (2002) 1475-1487. [PMID: 12429089]

2. Santander, P.J., Kajiwara, Y., Williams, H.J. and Scott, A.I. Structural characterization of novel cobalt corrinoids synthesized by enzymes of the vitamin B12 anaerobic pathway. Bioorg. Med. Chem. 14 (2006) 724-731. [PMID: 16198574]

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. [PMID: 23922391]

[EC 2.1.1.196 created 2010, modified 2013]

EC 2.1.1.197

Accepted name: malonyl-[acyl-carrier protein] O-methyltransferase

Reaction: S-adenosyl-L-methionine + malonyl-[acyl-carrier protein] = S-adenosyl-L-homocysteine + malonyl-[acyl-carrier protein] methyl ester

Other name(s): BioC

Systematic name: S-adenosyl-L-methionine:malonyl-[acyl-carrier protein] O-methyltransferase

Comments: Involved in an early step of biotin biosynthesis in Gram-negative bacteria. This enzyme catalyses the transfer of a methyl group to the ω-carboxyl group of malonyl-[acyl-carrier protein] forming a methyl ester. The methyl ester is recognized by the fatty acid synthetic enzymes, which process it via the fatty acid elongation cycle to give pimelyl-[acyl-carrier-protein] methyl ester [5]. While the enzyme can also accept malonyl-CoA, it has a much higher activity with malonyl-[acyl-carrier protein] [6]

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

References:

1. Del Campillo-Campbell, A., Kayajanian, G., Campbell, A. and Adhya, S. Biotin-requiring mutants of Escherichia coli K-12. J. Bacteriol. 94 (1967) 2065-2066. [PMID: 4864413]

2. Rolfe, B. and Eisenberg, M.A. Genetic and biochemical analysis of the biotin loci of Escherichia coli K-12. J. Bacteriol. 96 (1968) 515-524. [PMID: 4877129]

3. Otsuka, A.J., Buoncristiani, M.R., Howard, P.K., Flamm, J., Johnson, C., Yamamoto, R., Uchida, K., Cook, C., Ruppert, J. and Matsuzaki, J. The Escherichia coli biotin biosynthetic enzyme sequences predicted from the nucleotide sequence of the bio operon. J. Biol. Chem. 263 (1988) 19577-19585. [PMID: 3058702]

4. Cleary, P.P. and Campbell, A. Deletion and complementation analysis of biotin gene cluster of Escherichia coli. J. Bacteriol. 112 (1972) 830-839. [PMID: 4563978]

5. Lin, S., Hanson, R.E. and Cronan, J.E. Biotin synthesis begins by hijacking the fatty acid synthetic pathway. Nat. Chem. Biol. 6 (2010) 682-688. [PMID: 20693992]

6. Lin, S. and Cronan, J.E. The BioC O-Methyltransferase Catalyzes Methyl Esterification of Malonyl-Acyl Carrier Protein, an Essential Step in Biotin Synthesis. J. Biol. Chem. (2012) . [PMID: 22965231]

[EC 2.1.1.197 created 2010, modified 2013]

EC 2.1.1.198

Accepted name: 16S rRNA (cytidine1402-2'-O)-methyltransferase

Reaction: S-adenosyl-L-methionine + cytidine1402 in 16S rRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine1402 in 16S rRNA

Other name(s): RsmI; YraL

Systematic name: S-adenosyl-L-methionine:16S rRNA (cytidine1402-2'-O)-methyltransferase

Comments: RsmI catalyses the 2'-O-methylation of cytidine1402 and RsmH (EC 2.1.1.199) catalyses the N4-methylation of cytidine1402 in 16S rRNA. Both methylations are necessary for efficient translation initiation at the UUG and GUG codons.

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

References:

1. Kimura, S. and Suzuki, T. Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA. Nucleic Acids Res. 38 (2010) 1341-1352. [PMID: 19965768]

[EC 2.1.1.198 created 2010]

EC 2.1.1.199

Accepted name: 16S rRNA (cytidine1402-N4)-methyltransferase

Reaction: S-adenosyl-L-methionine + cytidine1402 in 16S rRNA = S-adenosyl-L-homocysteine + N4-methylcytidine1402 in 16S rRNA

Other name(s): RsmH; MraW

Systematic name: S-adenosyl-L-methionine:16S rRNA (cytidine1402-N4)-methyltransferase

Comments: RsmH catalyses the N4-methylation of cytidine1402 and RsmI (EC 2.1.1.198) catalyses the 2'-O-methylation of cytidine1402 in 16S rRNA. Both methylations are necessary for efficient translation initiation at the UUG and GUG codons.

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

References:

1. Kimura, S. and Suzuki, T. Fine-tuning of the ribosomal decoding center by conserved methyl-modifications in the Escherichia coli 16S rRNA. Nucleic Acids Res. 38 (2010) 1341-1352. [PMID: 19965768]

[EC 2.1.1.199 created 2010]

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, CAS registry number:

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 (2006) 23. [PMID: 16848900]

[EC 2.1.1.200 created 2011]


Continued with EC 2.1.1.251 to EC 2.1.1.257
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