Dissemin is shutting down on January 1st, 2025

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Oxford University Press, Nucleic Acids Research, 9(51), p. 4508-4518, 2023

DOI: 10.1093/nar/gkad260

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Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology

This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Postprint: archiving allowed
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Data provided by SHERPA/RoMEO

Abstract

Abstract A methyltransferase ribozyme (MTR1) was selected in vitro to catalyze alkyl transfer from exogenous O6-methylguanine (O6mG) to a target adenine N1, and recently, high-resolution crystal structures have become available. We use a combination of classical molecular dynamics, ab initio quantum mechanical/molecular mechanical (QM/MM) and alchemical free energy (AFE) simulations to elucidate the atomic-level solution mechanism of MTR1. Simulations identify an active reactant state involving protonation of C10 that hydrogen bonds with O6mG:N1. The deduced mechanism involves a stepwise mechanism with two transition states corresponding to proton transfer from C10:N3 to O6mG:N1 and rate-controlling methyl transfer (19.4 kcal·mol−1 barrier). AFE simulations predict the pKa for C10 to be 6.3, close to the experimental apparent pKa of 6.2, further implicating it as a critical general acid. The intrinsic rate derived from QM/MM simulations, together with pKa calculations, enables us to predict an activity–pH profile that agrees well with experiment. The insights gained provide further support for a putative RNA world and establish new design principles for RNA-based biochemical tools.