Nucleic Acids Research Advance Access originally published online on December 11, 2008
Nucleic Acids Research 2009 37(3):762-770; doi:10.1093/nar/gkn988
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Nucleic Acids Research, 2009, Vol. 37, No. 3 762-770
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Structural Biology |
The structure of M.EcoKI Type I DNA methyltransferase with a DNA mimic antirestriction protein
1Astbury Centre, Institute of Molecular and Cellular Biology, University of Leeds, UK, 2Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology in Warsaw, Trojdena 4, PL-02-109 Warsaw, 3Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland, 4School of Chemistry, University of Edinburgh, The Kings’ Buildings, Edinburgh, EH9 3JJ, UK and 5Bioinformatics Laboratory, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614 Poznan, Poland
*To whom correspondence should be addressed. Tel: +44 131 650 4735; Fax: +44 131 650 6453; Email: david.dryden{at}ed.ac.uk
Received October 16, 2008. Revised November 20, 2008. Accepted November 21, 2008.
Type-I DNA restriction–modification (R/M) systems are important agents in limiting the transmission of mobile genetic elements responsible for spreading bacterial resistance to antibiotics. EcoKI, a Type I R/M enzyme from Escherichia coli, acts by methylation- and sequence-specific recognition, leading to either methylation of DNA or translocation and cutting at a random site, often hundreds of base pairs away. Consisting of one specificity subunit, two modification subunits, and two DNA translocase/endonuclease subunits, EcoKI is inhibited by the T7 phage antirestriction protein ocr, a DNA mimic. We present a 3D density map generated by negative-stain electron microscopy and single particle analysis of the central core of the restriction complex, the M.EcoKI M2S1 methyltransferase, bound to ocr. We also present complete atomic models of M.EcoKI in complex with ocr and its cognate DNA giving a clear picture of the overall clamp-like operation of the enzyme. The model is consistent with a large body of experimental data on EcoKI published over 40 years.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
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