Mechanism of nucleotidyltransfer reaction and role of Mg2+ ion in sugar nucleotidyltransferases

Abstract Sugar nucleotidyl transferases (SNTs) catalyze nucleotidyltransfer reactions to form sugar-nucleotides and pyrophosphate, in the presence of two Mg2+ ions (Mg2+A and Mg2+B). We unveil the mechanism and free energetics of nucleotidyl transfer reaction in a SNT called GlmU through hybrid quantum mechanics/molecular mechanics molecular dynamics simulations and free energy calculations. The study identifies the roles of the active site residues and the Mg2+ ions in catalyzing the reaction. Of great significance, we are able to compare the free energy barrier for the reaction with that for the Mg2+ assisted release of the product (i.e. pyrophosphate) into the solution, shedding light on the general mechanistic and kinetic aspects of catalysis by SNTs.