InterPro domain: IPR023268

RNA (C5-cytosine) methyltransferases (RCMTs) catalyse the transfer of a methyl group to the 5th carbon of a cytosine base in RNA sequences to produce C5-methylcytosine. RCMTs use the cofactor S-adenosyl-L-methionine (SAM) as a methyl donor [ 1 ]. The catalytic mechanism of RCMTs involves an attack by the thiolate of a Cys residue on position 6 of the target cytosine base to form a covalent link, thereby activating C5 for methyl-group transfer. Following the addition of the methyl group, a second Cys residue acts as a general base in the beta-elimination of the proton from the methylated cytosine ring. The free enzyme is restored and the methylated product is released [ 2 ].

Numerous putative RCMTs have been identified in archaea, bacteria and eukaryota [ 3 , 4 ]; most are predicted to be nuclear or nucleolar proteins [ 5 ]. The Escherichia coli Ribosomal RNA Small-subunit Methyltransferase Beta (RSMB) FMU (FirMicUtes) represents the first protein identified and characterised as a cytosine-specific RNA methyltransferase. RSMB was reported to catalyse the formation of C5-methylcytosine at position 967 of 16S rRNA [ 6 , 7 ].

A classification of RCMTs has been proposed on the basis of sequence similarity [ 8 ]. According to this classification, RCMTs are divided into 8 distinct subfamilies [ 8 ]. Recently, a new RCMT subfamily, termed RCMT9, was identified [ 8 ]. Members of the RCMT contain a core domain, responsible for the cytosine-specific RNA methyltransferase activity. This 'catalytic' domain adopts the Rossman fold for the accommodation of the cofactor SAM [ 8 ]. The RCMT subfamilies are also distinguished by N-terminal and C-terminal extensions, variable both in size and sequence [ 9 ].

Proteins related to the RsmB subfamily of RCMTs have been detected in the genomes of Viridiplantae [ 9 ]. They were provisionally assigned to the RsmB subfamily [ 9 ], which hitherto was considered to be restricted to Eubacteria, based solely on similarity to the prototypic member of this subfamily, the E.coli protein [ 9 , 9 ].

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2. RNA methyltransferases utilize two cysteine residues in the formation of 5-methylcytosine. Biochemistry 41, 11218-25
3. Exposition of a family of RNA m(5)C methyltransferases from searching genomic and proteomic sequences. Nucleic Acids Res. 27, 3138-45
4. Phylogenetic analysis of the eukaryotic RNA (cytosine-5)-methyltransferases. Genomics 93, 350-7
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