Structure-based sequence alignment of three AdoMet-dependent DNA methyltransferases

Streptogramin B biosynthesis in Streptomyces pristinaespiralis and Streptomyces virginiae: molecular characterization of the last structural peptide synthetase gene

“…Others are found in the sequence of enniatin synthetase (2,13), and seven are found in cyclosporin A synthetase (18,30). Detailed structural data available for a great number of S-adenosine-dependent methyltransferases have suggested a common structure for these enzymes (21,23). The PPS methylase domains clearly contain signature motif I, which is involved in making direct contacts with the methionine moiety of S-adenosyl-L-methionine (23).…”

Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: Identification of the gene and substrate specificity of the enzyme

“…The results of a search for putative RNA:m 5 Cmethyltransferases from different Archaea are noteworthy+ The complete genomic sequences of four representatives of this life domain are now accessible+ A BLAST search detected five homologous, but distinct proteins in Pyrococcus horikoshii, three in Archaeoglobus fulgidus, and only one in Methanococcus jannaschii+ No corresponding sequences have been detected in the complete genome of Methanobacterium thermoautotrophicum+ Unfortunately, information on the presence of m 5 C in tRNA from these organisms remains extremely limited+ Indeed, only two tRNA species from M. thermoautotrophicum have been sequenced and none contains m 5 C at either position 48 or 49, although unmodified cytosine is present (Gu et al+, 1984)+ Inspection of tRNA sequences from other Archaea reveals that m 5 C is in fact present at several positions in tRNA (positions 39, 40, 48, 49, 50, and 51) (Gupta, 1984;Auffinger & Westhof, 1998)+ Taken together these data may indicate that the corresponding tRNA:m 5 C-methyltransferase(s) may be present in certain Archaeal organisms while totally absent in others+ Moreover, m 5 C residues were detected in 16S and 23S rRNAs from Sulfolobus solfataricus (Noon et al+, 1998), supporting the idea that rRNA-specific m 5 C-methyltransferases exist at least in this archaeon+ Lastly, the genomes of the most extensively studied higher eukaryotes (mouse and human) contain proteins of the family that are homologous to yeast The enzymatic formation of modified nucleoside m 5 C in RNA should have some points in common with m 5 C methylation in DNA+ The enzymes (MTases) acting on DNA have been detected in most living organisms, and the mechanism of DNA methylation was rather well studied by different approaches (reviewed in Adams, 1995;Cheng, 1995;Roberts, 1995;Cheng & Blumenthal, 1996)+ In addition, the crystal structures of M+HpaI DNA:m 5 C-methyltransferase in binary complex with AdoMet and in ternary complex with AdoMet and a substrate analog have been resolved (Cheng et al+, 1993;Klimasauskas et al+, 1994)+ Despite very similar substrates (polynucleotide chain RNA/DNA and AdoMet) and a common reaction product (5-methylcytidine), the two enzymatic families (DNA and RNA m 5 C-methyltransferases) display very little homology at the level of amino acid sequences+ At least five highly conserved sequence motifs have been detected in DNA:m 5 Cmethylases (Posfai et al+, 1989;Malone et al+, 1995;O'Gara et al+, 1995), two of them corresponding, in fact, to common Adomet-binding motifs+ Despite great divergence in amino acid sequences, both DNA and RNA:m 5 C-methyltransferases share the highly conserved dipeptide sequence (PC) in the second Adometbinding motif (Block III on Fig+ 1), whereas this dipeptide (PC) is not obligatorily conserved in other Adometbinding methylases+ In the case of DNA:m 5 C-methylases, the PC sequence is part of the enzyme active site, with the cysteine residue binding covalently to the target cytosine …”

Critical residues of Semliki Forest virus RNA capping enzyme involved in methyltransferase and guanylyltransferase-like activities

“…7) (10,12). Structure-guided analyses have revealed additional single amino acid residues often conserved in MTs (16,21). The G-loop (after ␤-strand 1) and the loops after ␤-strands 2 and 3 interact with AdoMet.…”