Dissection of the DNA mimicry of the bacteriophage T7 Ocr protein using chemical modification

Stephanou, A. S., Roberts, G. A., Cooper, L. P., Clarke, D. J., Thomson, A. R., MacKay, C. L., Nutley, M., Cooper, A. and Dryden, D. T.F. (2009) Dissection of the DNA mimicry of the bacteriophage T7 Ocr protein using chemical modification. Journal of Molecular Biology, 391(3), pp. 565-576. (doi:10.1016/j.jmb.2009.06.020) (PMID:19523474) (PMCID:PMC2806950)

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Abstract

The homodimeric Ocr (overcome classical restriction) protein of bacteriophage T7 is a molecular mimic of double-stranded DNA and a highly effective competitive inhibitor of the bacterial type I restriction/modification system. The surface of Ocr is replete with acidic residues that mimic the phosphate backbone of DNA. In addition, Ocr also mimics the overall dimensions of a bent 24-bp DNA molecule. In this study, we attempted to delineate these two mechanisms of DNA mimicry by chemically modifying the negative charges on the Ocr surface. Our analysis reveals that removal of about 46% of the carboxylate groups per Ocr monomer results in an ∼ 50-fold reduction in binding affinity for a methyltransferase from a model type I restriction/modification system. The reduced affinity between Ocr with this degree of modification and the methyltransferase is comparable with the affinity of DNA for the methyltransferase. Additional modification to remove ∼ 86% of the carboxylate groups further reduces its binding affinity, although the modified Ocr still binds to the methyltransferase via a mechanism attributable to the shape mimicry of a bent DNA molecule. Our results show that the electrostatic mimicry of Ocr increases the binding affinity for its target enzyme by up to ∼ 800-fold.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Nutley, Mrs Margaret and Cooper, Professor Alan and Thomson, Dr Andrew
Authors: Stephanou, A. S., Roberts, G. A., Cooper, L. P., Clarke, D. J., Thomson, A. R., MacKay, C. L., Nutley, M., Cooper, A., and Dryden, D. T.F.
Subjects:Q Science > QD Chemistry
College/School:College of Science and Engineering > School of Chemistry
Journal Name:Journal of Molecular Biology
ISSN:0022-2836
ISSN (Online):1089-8638
Published Online:10 June 2009
Copyright Holders:Copyright © 2009 Elsevier Ltd.
First Published:First published in Journal of Molecular Biology 391(5): 565-576
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
352051The BBSRC/EPSRC Biological Microcalorimetry FacilityAlan CooperBiotechnology and Biological Sciences Research Council (BBSRC)B20089Chemistry