Theoretical Study of the Catalytic Mechanism of DNA-(N4-Cytosine)-Methyltransferase from the Bacterium Proteus vulgaris

Abstract

In this paper the reaction mechanism for methylation of cytosine at the exocyclic N4 position catalyzed by M.PvuII has been explored by means of hybrid quantum mechanics/molecular mechanics (QM/MM) methods. A reaction model was prepared by placing a single cytosine base in the active site of the enzyme. In this model the exocyclic amino group of the base establishes hydrogen bond interactions with the hydroxyl oxygen atom of Ser53 and the carbonyl oxygen atom of Pro54. The reaction mechanism involves a direct methyl transfer from AdoMet to the N4 atom and a proton transfer from this atom to Ser53, which in turn transfers a proton to Asp96. Different timings for the proton transfers and methylation steps have been explored at the AM1/MM and B3LYP/MM levels including localization and characterization of stationary structures. At our best estimate the reaction proceeds by means of a simultaneous but asynchronous proton transfer from Ser53 to Asp96 and from N4 of cytosine to Ser53 followed by a direct methyl transfer from AdoMet to the exocyclic N4 of cytosine.