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

Neha Vithani; Balaji Prakash; Nisanth N Nair

doi:10.1016/j.bpj.2020.06.017

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

Biophys J. 2020 Aug 4;119(3):619-627. doi: 10.1016/j.bpj.2020.06.017. Epub 2020 Jun 24.

Authors

Neha Vithani¹, Balaji Prakash², Nisanth N Nair³

Affiliations

¹ Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, India.
² Department of Molecular Nutrition, CSIR-Central Food Technological Research Institute, Mysore, India. Electronic address: [email protected].
³ Department of Chemistry, Indian Institute of Technology, Kanpur, India. Electronic address: [email protected].

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Catalysis
Catalytic Domain
Molecular Dynamics Simulation
Nucleotidyltransferases* / metabolism
Sugars*

Substances

Sugars
Nucleotidyltransferases