Metal-mediated hydrolysis of biological phosphate esters - A critical analysis of the essential metal ion stoichiometry for magnesium-dependent nuclease activation

Metal-mediated hydrolysis of phosphate esters is a common catalytic pathway in nucleic acid biochemistry. Two distinct models are principally invoked in mechanistic discussions of these reactions for magnesium-dependent nuclease activation, namely, the one-versus two-metal-ion pathways. By careful consideration of the available experimental data on a variety of enzymes (including the Klenow fragment of DNA pol I, exonuclease III, ribonuclease H domains of HIV reverse transcriptase and the homologous Escherichia coli enzyme, avian sarcoma virus integrase, Eco RI and Eco RV restriction endonucleases, and ribozymes), it is demonstrated that the two-metal-ion paradigm cannot be substantiated as a bona fide mechanism on the basis of the published structural data. The origins of the problems with this model are traced to fundamental issues in solution chemistry. These factors help to explain and resolve the often dichotomous results obtained from X-ray crystallography versus solution studies.