Abstract By catalysing the microbial formation of methane, methyl-coenzyme M reductase has a central role in the global levels of this greenhouse gas 1,2 . The activity of methyl-coenzyme M reductase is profoundly affected by several unique post-translational modifications 3–6 , such as a unique C -methylation reaction catalysed by methanogenesis marker protein 10 (Mmp10), a radical S- adenosyl- l -methionine (SAM) enzyme 7,8 . Here we report the spectroscopic investigation and atomic resolution structure of Mmp10 from Methanosarcina acetivorans , a unique B 12 (cobalamin)-dependent radical SAM enzyme 9 . The structure of Mmp10 reveals a unique enzyme architecture with four metallic centres and critical structural features involved in the control of catalysis. In addition, the structure of the enzyme–substrate complex offers a glimpse into a B 12 -dependent radical SAM enzyme in a precatalytic state. By combining electron paramagnetic resonance spectroscopy, structural biology and biochemistry, our study illuminates the mechanism by which the emerging superfamily of B 12 -dependent radical SAM enzymes catalyse chemically challenging alkylation reactions and identifies distinctive active site rearrangements to provide a structural rationale for the dual use of the SAM cofactor for radical and nucleophilic chemistry.