Insights into the stereochemical mechanism of the B12-dependent radical SAM glutamine C- methyltransferase (QCMT)

Methyl-coenzyme M reductase (MCR) is a crucial enzyme for methanogenesis and harbors several unusual post-translational modifications. Recent studies have identified glutamine C-methyltransferase (QCMT), as a B12-dependent radical SAM enzyme responsible for methylating a glutamine residue within the MCR active site. B12-dependent radical SAM enzymes have the remarkable ability to alkylate unactivated Csp2- and Csp3-atoms in a stereoselective manner. However, the factors influencing the stereo-selectivity and catalytic properties of this emerging superfamily of enzymes remain poorly understood. Here, we report the mechanistic, structural, and biochemical investigation of several QCMTs. Our findings reveal significant differences among them, notably in their ability to bind cobalamin. In addition, our data support that Cα H-atom abstraction and methyl transfer are not concerted but rather independent processes that require motion within the enzyme’s active site. We also demonstrate that QCMT catalyzes novel reactions, including the formation of unnatural C-methylated residues, peptide epimerization, reversible H-atom abstraction, and the direct conversion of glycine into D-alanine. Overall, our data are consistent with QCMT being a unique and versatile biocatalyst allowing for the installation of unnatural post-translational modifications and provide a structural and biochemical rationale for the control of the stereochemistry by B12-dependent radical SAM enzymes. The authors show that glutamine C-methyltransferase (QCMT), although catalzying a highly stereo- and regio-selective transformation, possesses unanticipated catalytic promiscuity that results in peptide epimerization, hydrogen-atom exchange, and alkylation.