EC 2.1.1.1 to EC 2.1.1.50See 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 2.1.1.399.
EC 2.1.1.51 to EC 2.1.1.100
EC 2.1.1.101 to EC 2.1.1.150
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 2.1.1.399
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]
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]
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]
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]
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]
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, PDB, 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]
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]
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]
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]
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]
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]
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]
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]
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, Metacyc, PDB, 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]
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.
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]
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, PDB, 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]
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]
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]
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]
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]
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]
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]
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]
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.
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]
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]
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]
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]
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]
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 2.3.1.182 Transferred entry: (R)-citramalate synthase. Now classified as EC 2.3.3.21, (R)-citramalate synthase. (EC 2.3.1.182 created 2007, deleted 2021)]
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]
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]
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]
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]
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]
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]
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]
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]
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]
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, PDB, 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]
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, PDB, 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 2.1.1.194 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)]
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, PDB, 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]
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, PDB, 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]
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]
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, 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]
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]
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, PDB, 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]