Mechanism of the Escherichia coli DNA T:G-mismatch Endonuclease (Vsr protein) Probed with Thiophosphate-containing Oligodeoxynucleotides

• Published in: Journal of molecular biology 2005-10, Vol.353 (3), p.692-703
• Main Authors: Elliott, Sarah L., Brazier, John, Cosstick, Richard, Connolly, Bernard A.
• Format: Article
• Language: English
• Subjects: Base Pairing; Base Sequence; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; Endodeoxyribonucleases - chemistry; Escherichia coli; Escherichia coli - genetics; Hydrolysis; Kinetics; Molecular Probes; nuclease; Oligodeoxyribonucleotides - chemistry; Phosphates - chemistry; phosphodiester bond hydrolysis; phosphorothioates; phosphorothiolates; Stereoisomerism; Vsr endonuclease
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2005.08.048

The mechanism of the Escherichia coli DNA T:G mismatch endonuclease (Vsr) has been investigated using oligodeoxynucleotides substituted, at the scissile phosphate, with isomeric phosphorothioates and a 3′-phosphorothiolate. Binding and kinetic data with the phosphorothioates/phosphorothiolate indicate that the two magnesium ions, which constitute essential co-factors, are required to stabilise the extra negative charge developed on the phosphate as the transition state is formed. Additionally one of the magnesium ions serves to activate the leaving group (the non-bridging 3′-oxygen atom of the scissile phosphate) during the hydrolysis reaction. Stereochemical analysis, using the R p phosphorothioate isomer, indicates that Vsr carries out a hydrolytic reaction with inversion of stereochemistry at phosphorus, compatible with an in-line attack of water and a pentacovalent transition state with trigonal bipyramidal geometry. In conjunction with structures of Vsr bound to its products, these data allow the reconstruction of the enzyme–substrate complex and a comprehensive description of the hydrolysis mechanism.