Why Nature Uses Radical SAM Enzymes so Widely: Electron Nuclear Double Resonance Studies of Lysine 2,3-Aminomutase Show the 5′-dAdo• "Free Radical" Is Never Free

Lysine 2,3-aminomutase (LAM) is a radical S-adenosyl-L-methionine (SAM) enzyme and, like other members of this superfamily, LAM utilizes radical-generating machinery comprising SAM anchored to the unique Fe of a [4Fe-4S] cluster via a classical five-membered N,O chelate ring. Catalysis is initiated by reductive cleavage of the SAM S-CS' bond, which creates the highly reactive S'-deoxyadenosyl radical (5'-dAdo center dot), the same radical generated by homolytic Co-C bond cleavage in B-12 radical enzymes. The SAM surrogate S-3',4'-anhydroadenosyl-L-methionine (anSAM) can replace SAM as a cofactor in the isomerization of L-alpha-lysine to L-beta-lysine by LAM, via the stable allylic anhydroadenosyl radical (anAdo center dot). Here electron nuclear double resonance (ENDOW spectroscopy of the anAdo center dot radical in the presence of C-13, H-2, and N-15-labeled lysine completes the picture of how the active site of LAM from Clostridium subterminale SB4 "tames" the 5'-dAdoo center dot radical, preventing it from carrying out harmful side reactions: this "free radical" in LAM is never free. The low steric demands of the radical-generating [4Fe-4S]/SAM construct allow the substrate target to bind adjacent to the S-CS' bond, thereby enabling the 5'-dAdoo center dot radical created by cleavage of this bond to react with its partners by undergoing small motions, similar to 0.6 angstrom toward the target and similar to 1.5 angstrom overall, that are controlled by tight van der Waals contact with its partners. We suggest that the accessibility to substrate and ready control of the reactive CS' radical, with "van der Waals control" of small motions throughout the catalytic cycle, is common within the radical SAM enzyme superfamily and is a major reason why these enzymes are the preferred means of initiating radical reactions in nature.