tRNA (C5-cytosine) methyltransferase, NCL1 (IPR023270)

Short name: RCMT_NCL1

Overlapping homologous superfamilies


Family relationships


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 [PMID: 12826405]. 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 [PMID: 12220187].

Numerous putative RCMTs have been identified in archaea, bacteria and eukaryota [PMID: 10454610, PMID: 19135144]; most are predicted to be nuclear or nucleolar proteins [PMID: 20007150]. 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 [PMID: 10194318, PMID: 10026269].

A classification of RCMTs has been proposed on the basis of sequence similarity [PMID: 10454610]. According to this classification, RCMTs are divided into 8 distinct subfamilies [PMID: 10454610]. Recently, a new RCMT subfamily, termed RCMT9, was identified [PMID: 19135144]. Members of the RCMT contain a core domain, responsible for the cytosine-specific RNA methyltransferase activity. This 'catalytic' domain adopts the Rossmann fold for the accommodation of the cofactor SAM [PMID: 15121902]. The RCMT subfamilies are also distinguished by N-terminal and C-terminal extensions, variable both in size and sequence [PMID: 10454610].

The prototypical member of the Nuclear protein 1 RCMT subfamily, the S. cerevisiae NCL1 (also known as Trm4), has been demonstrated to methylate cytosine to C5-methylcytosine at positions 34, 40, 48 and 49 in different intron- containing tRNAs and tRNA precursors [PMID: 10445884]. Its human homologue, MISU/NSUN2, was found to catalyse the formation of C5-methylcytosine at position 34 of intron-containing pre-tRNAs [PMID: 17215513]; it was not able to modify tRNAs at positions 48 or 49. It was also shown to be involved in Myc-mediated proliferation of cancer cells [PMID: 16713953].

GO terms

Biological Process

No terms assigned in this category.

Molecular Function

GO:0016428 tRNA (cytosine-5-)-methyltransferase activity

Cellular Component

No terms assigned in this category.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.