Dissection of the DNA Mimicry of the Bacteriophage T7 Ocr Protein using Chemical Modification

• Published in: Journal of molecular biology 2009-08, Vol.391 (3), p.565-576
• Main Authors: Stephanou, Augoustinos S., Roberts, Gareth A., Cooper, Laurie P., Clarke, David J., Thomson, Andrew R., MacKay, C. Logan, Nutley, Margaret, Cooper, Alan, Dryden, David T.F.
• Format: Article
• Language: English
• Subjects: Bacteria; Bacteriophage T7; Binding, Competitive; Chemical modification; Dimerization; DNA - chemistry; DNA mimic; Methyltransferases - chemistry; Molecular Mimicry; Nucleic Acid Conformation; Protein Folding; restriction/modification system; Viral Proteins - chemistry
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2009.06.020

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.