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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 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 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.

SUBMITTER: Vithani N

PROVIDER: S-EPMC7399479 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Mechanism of Nucleotidyltransfer Reaction and Role of Mg2+ Ion in Sugar Nucleotidyltransferases.

Vithani Neha N Prakash Balaji B Nair Nisanth N NN

Biophysical journal 20200624 3

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 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 ...[more]

PMID: 32645293

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