Mechanistic Dichotomy in the Activation of SAM by Radical SAM Enzymes: QM/MM Modeling Deciphers the Determinant

Abstract Activation of S-adenosyl methionine (SAM) is an initiating step in hundreds of thousands of radical SAM enzymes that catalyze over 80 diverse types of reactions. The fundamental mechanisms, however, remain unclear. In this work, via multistate QM/MM theory, we report our discovery that the SAM activation mechanism in the radical SAM enzymes Dph2 and PFL-AE is controlled by the binding structure of SAM to a [4Fe–4S] cluster cofactor. Two distinguishing types of SAM binding structures, different in the orientation of the C–S bond to be cleaved in SAM relative to the SAM-binding iron, led separately to a concerted and a stepwise pathway to form the Ω-type species, a key type of bio-organometallic intermediates captured experimentally for these two enzymes. This theoretically deciphered determinant from Dph2 and PFL-AE for the mechanistic dichotomy enables a prediction of the SAM activation pathway adopted in many other radical SAM enzymes, which opens up an avenue for understanding the SAM activation in the radical SAM enzymes.