Nucleic Acids Research Advance Access originally published online on July 21, 2008
Nucleic Acids Research 2008 36(14):4778-4787; doi:10.1093/nar/gkn448
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Nucleic Acids Research, 2008, Vol. 36, No. 14 4778-4787
© 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 |
Structural analysis of the genetic switch that regulates the expression of restriction-modification genes
1Biophysics Laboratories, School of Biological Sciences, Institute of Biomedical and Biomolecular Sciences, University of Portsmouth, Portsmouth PO1 2DT, UK and 2Section Electron Microscopy, Department of Molecular Cell Biology, Leiden University Medical Center (LUMC), PO Box 9600, 2300RC Leiden, The Netherlands
*To whom correspondence should be addressed. Tel: +1 02392 842 678; Fax: +1 02392 842 053; Email: geoff.kneale{at}port.ac.uk
Received May 27, 2008. Revised June 20, 2008. Accepted June 28, 2008.
Controller (C) proteins regulate the timing of the expression of restriction and modification (R–M) genes through a combination of positive and negative feedback circuits. A single dimer bound to the operator switches on transcription of the C-gene and the endonuclease gene; at higher concentrations, a second dimer bound adjacently switches off these genes. Here we report the first structure of a C protein–DNA operator complex, consisting of two C protein dimers bound to the native 35 bp operator sequence of the R–M system Esp1396I. The structure reveals a role for both direct and indirect DNA sequence recognition. The structure of the DNA in the complex is highly distorted, with severe compression of the minor groove resulting in a 50° bend within each operator site, together with a large expansion of the major groove in the centre of the DNA sequence. Cooperative binding between dimers governs the concentration-dependent activation–repression switch and arises, in part, from the interaction of Glu25 and Arg35 side chains at the dimer–dimer interface. Competition between Arg35 and an equivalent residue of the 
70 subunit of RNA polymerase for the Glu25 site underpins the switch from activation to repression of the endonuclease gene.
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