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Nucleic Acids Research 2006 34(6):1925-1934; doi:10.1093/nar/gkl116
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Published online 5 April 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Article

Crystal structure of Bacillus subtilis TrmB, the tRNA (m7G46) methyltransferase

Ingrid Zegers, Daniel Gigot1, Françoise van Vliet2, Catherine Tricot2, Stéphane Aymerich3, Janusz M. Bujnicki4,*, Jan Kosinski4 and Louis Droogmans1,*

Laboratorium Ultrastructuur, Vrije Universiteit Brussel Pleinlaan 2, B-1050 Brussel, Belgium 1 Laboratoire de Microbiologie, Université Libre de Bruxelles Institut de Recherches Microbiologiques J.-M. Wiame, Avenue E. Gryson 1, B-1070 Bruxelles, Belgium 2 Institut de Recherches Microbiologiques J.-M. Wiame, Avenue E. Gryson 1 B-1070 Bruxelles, Belgium 3 Microbiologie et Génétique Moléculaire, INRA (UMR1238) and CNRS (UMR2585), Institut National Agronomique Paris-Grignon F-78850 Thiverval-Grignon, France 4 Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology ul. Ks. Trojdena 4, 02-109 Warsaw, Poland

*To whom correspondence should be addressed. Tel: +32 2 526 7283; Fax: +32 2 526 7273; Email: ldroogma{at}ulb.ac.be

*Correspondence may also be addressed to Janusz M. Bujnicki. Tel: +48 22 597 0750; Fax: +48 22 597 0715; Email: iamb{at}genesilico.pl

Received December 20, 2005. Revised January 10, 2006. Accepted March 11, 2006.

The structure of Bacillus subtilis TrmB (BsTrmB), the tRNA (m7G46) methyltransferase, was determined at a resolution of 2.1 Å. This is the first structure of a member of the TrmB family to be determined by X-ray crystallography. It reveals a unique variant of the Rossmann-fold methyltransferase (RFM) structure, with the N-terminal helix folded on the opposite site of the catalytic domain. The architecture of the active site and a computational docking model of BsTrmB in complex with the methyl group donor S-adenosyl-L-methionine and the tRNA substrate provide an explanation for results from mutagenesis studies of an orthologous enzyme from Escherichia coli (EcTrmB). However, unlike EcTrmB, BsTrmB is shown here to be dimeric both in the crystal and in solution. The dimer interface has a hydrophobic core and buries a potassium ion and five water molecules. The evolutionary analysis of the putative interface residues in the TrmB family suggests that homodimerization may be a specific feature of TrmBs from Bacilli, which may represent an early stage of evolution to an obligatory dimer.


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