PMID: 11929612Apr 4, 2002Paper

RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited--bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure

BMC Bioinformatics
Janusz M Bujnicki, Leszek Rychlewski

Abstract

Escherichia coli guanine-N2 (m2G) methyltransferases (MTases) RsmC and RsmD modify nucleosides G1207 and G966 of 16S rRNA. They possess a common MTase domain in the C-terminus and a variable region in the N-terminus. Their C-terminal domain is related to the YbiN family of hypothetical MTases, but nothing is known about the structure or function of the N-terminal domain. Using a combination of sequence database searches and fold recognition methods it has been demonstrated that the N-termini of RsmC and RsmD are related to each other and that they represent a "degenerated" version of the C-terminal MTase domain. Novel members of the YbiN family from Archaea and Eukaryota were also indentified. It is inferred that YbiN and both domains of RsmC and RsmD are closely related to a family of putative MTases from Gram-positive bacteria and Archaea, typified by the Mj0882 protein from M. jannaschii (1dus in PDB). Based on the results of sequence analysis and structure prediction, the residues involved in cofactor binding, target recognition and catalysis were identified, and the mechanism of the guanine-N2 methyltransfer reaction was proposed. Using the known Mj0882 structure, a comprehensive analysis of sequence-structure-function rel...Continue Reading

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Citations

Feb 24, 2005·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Elodie NédélecMichel Termier
Oct 30, 2008·Nucleic Acids Research·Augusto Simoes-BarbosaPatricia J Johnson
Dec 26, 2006·The Journal of Biological Chemistry·Dmitry V LesnyakOlga A Dontsova
Mar 29, 2007·Nucleic Acids Research·Petr V SergievOlga A Dontsova
Dec 1, 2004·EcoSal Plus·James Ofengand, Mark Del Campo
May 9, 2006·Journal of Molecular Biology·Niels Møller Andersen, Stephen Douthwaite
Oct 18, 2005·BMC Structural Biology·Piotr Z Kozbial, Arcady R Mushegian

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