One is enough: insights into the two-metal ion nuclease mechanism from global analysis and computational studies

The mechanistic details of metallonuclease reactions, typically supported by Mg(II), have a long and contentious history. Two-metal ion mechanisms have enjoyed much favor, based largely in the multitude of X-ray crystal structures of these enzymes with more than one metal ion per active site. Most recently, this mechanism has come under challenge. Reviewed herein are the applications of different experimental strategies that collectively support a mechanism in which only one metal ion is necessary for nucleic acid hydrolysis. Based on global kinetic analysis, analysis of reactions in which the nonsupportive Ca(II) is added, and a number of computational approaches, secondary sites are proposed to either be occupied by activity-modulating metal ions or occupied in turn by a single metal that changes position during the course of the reaction.