Mechanism of Nucleotidyltransfer Reaction and Role of Mg Ion in Sugar Nucleotidyltransferases

Overview

Journal Biophys J

Publisher Cell Press

Specialty Biophysics

Date 2020 Jul 10

PMID 32645293

Citations 1

Authors

Neha Vithani

Balaji Prakash

Nisanth N Nair

Affiliations

Soon will be listed here.

Abstract

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

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