Substrate promiscuity in DNA methyltransferase M.PvuII. A mechanistic insight

M.PvuII is a DNA methyltransferase from the bacterium Proteus vulgaris that catalyzes methylation of cytosine at the N4 position. This enzyme also displays promiscuous activity catalyzing methylation of adenine at the N6 position. In this work we use QM/MM methods to investigate the reaction mechanism of this promiscuous activity. We found that N6 methylation in M.PvuII takes place by means of a stepwise mechanism in which deprotonation of the exocyclic amino group is followed by the methyl transfer. Deprotonation involves two residues of the active site, Ser53 and Asp96, while methylation takes place directly from the AdoMet cofactor to the target nitrogen atom. The same reaction mechanism was described for cytosine methylation in the same enzyme, while the reversal timing, that is methylation followed by deprotonation, has been described in M.TaqI, an enzyme that catalyzes the N6-adenine DNA methylation from Thermus aquaticus. These mechanistic findings can be useful to understand the evolutionary paths followed by N-methyltransferases.This work was supported by the Ministerio de Ciencia e Innovación project CTQ2009-14541-C02-02, Generalitat Valenciana projects ACOMP/2011/028, ACOM/2012/243, GV/2012/053 and Universitat de Valencia project UV-INV-AE11-40931. J.A. and M.R. thank Ministerio Ciencia e Innovación for a doctoral grant and a ‘Juan de la Cierva’ contract, respectively. The authors acknowledge computational facilities of the Servei d’Informàtica de la Universitat de València in the ‘Tirant’ supercomputer, which is part of the Spanish Supercomputing Network