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Nucleic Acids Research 2006 34(7):1992-2005; doi:10.1093/nar/gkl132
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Published online 13 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

Structural model for the multisubunit Type IC restriction–modification DNA methyltransferase M.EcoR124I in complex with DNA

Agnieszka Obarska, Alex Blundell1, Marcin Feder, Stepánka Vejsadová1,2, Eva Sisáková2, Marie Weiserová2, Janusz M. Bujnicki and Keith Firman1,*

Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology Trojdena 4, 02-109 Warsaw, Poland 1 IBBS Biophysics Laboratories, School of Biological Sciences, University of Portsmouth King Henry Building, King Henry I Street, Portsmouth PO1 2DY, UK 2 Institute of Microbiology, Czech Academy of Sciences Videnska 1083, 142 20 Prague 4, Czech Republic

*To whom all correspondence should be addressed. Tel: +44 2392 842059; Fax: +44 2392 842070; Email: keith.firman{at}port.ac.uk

Received November 25, 2005. Revised December 16, 2005. Accepted March 14, 2006.

Recent publication of crystal structures for the putative DNA-binding subunits (HsdS) of the functionally uncharacterized Type I restriction–modification (R-M) enzymes MjaXIP and MgeORF438 have provided a convenient structural template for analysis of the more extensively characterized members of this interesting family of multisubunit molecular motors. Here, we present a structural model of the Type IC M.EcoR124I DNA methyltransferase (MTase), comprising the HsdS subunit, two HsdM subunits, the cofactor AdoMet and the substrate DNA molecule. The structure was obtained by docking models of individual subunits generated by fold-recognition and comparative modelling, followed by optimization of inter-subunit contacts by energy minimization. The model of M.EcoR124I has allowed identification of a number of functionally important residues that appear to be involved in DNA-binding. In addition, we have mapped onto the model the location of several new mutations of the hsdS gene of M.EcoR124I that were produced by misincorporation mutagenesis within the central conserved region of hsdS, we have mapped all previously identified DNA-binding mutants of TRD2 and produced a detailed analysis of the location of surface-modifiable lysines. The model structure, together with location of the mutant residues, provides a better background on which to study protein–protein and protein–DNA interactions in Type I R-M systems.


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Home page
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J. Youell and K. Firman
EcoR124I: from Plasmid-Encoded Restriction-Modification System to Nanodevice
Microbiol. Mol. Biol. Rev., June 1, 2008; 72(2): 365 - 377.
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