Author ORCID Identifier

https://orcid.org/0000-0002-7502-7780 : John Hayward

https://orcid.org/0000-0002-2956-9781 : James W. Gauld

Document Type

Article

Publication Date

2017

Publication Title

Physical Chemistry Chemical Physics

Issue

37

First Page

25598

Last Page

25609

DOI

10.1039/c7cp02969a

Abstract

Glutaminyl-tRNA synthetase (GlnRS) catalyzes the aminoacylation of glutamine to the corresponding tRNAGln. However, most bacteria and all archaea lack GlnRS and thus an indirect noncanonical aminoacylation is required. With the assistance of a non-discriminating version of Glutamyl-tRNA synthetases (ND-GluRS) the tRNAGln is misaminoacylated by glutamate. In this study, we have computationally investigated the aminoacylation mechanism in GlnRS and ND-GluRS employing Molecular Dynamics (MD) simulations, Quantum Mechanics (QM) cluster and Quantum Mechanics/Molecular Mechanics (QM/MM) calculations. Our investigations demonstrated the feasibility of a water-mediated, substrate-assisted catalysis pathway with rate limiting steps occurring at energy barriers of 25.0 and 25.4 kcal mol−1 for GlnRS and ND-GluRS, respectively. A conserved lysine residue participates in a second proton transfer to facilitate the departure of the adenosine monophosphate (AMP) group. Thermodynamically stable (−29.9 and −9.3 kcal mol−1 for GlnRS and ND-GluRS) product complexes are obtained only when the AMP group is neutral.

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