Mechanism of Nucleotidyltransfer Reaction and Role of Mg2D Ion in Sugar Nucleotidyltransferases.

Sugar nucleotidyl transferases (SNTs) catalyze nucleotidyltransfer reactions to form sugar-nucleotides and pyrophosphate in the presence of two Mg2þ ions (Mg2þ
A and Mg2þ
B). We unveil the mechanism and free energetics of nucleotidyl
transfer reaction in an 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 Mg2þ ions in catalyzing the
reaction. Of great significance, we are able to compare the free energy barrier for the reaction with that for the Mg2þ-assisted
release of the product (i.e., pyrophosphate) into the solution, shedding light on the general mechanistic and kinetic aspects of
catalysis by SNTs.