Mechanism and Catalytic Site Atlas

Introduction

The C5′ of the dA moiety of AdoMet is close (3.9 Å) to the substrate C6, which is poised to abstract the C6 hydrogen after reductive cleavage of AdoMet. Mg(II) may facilitate this H-atom abstraction through its interaction with both the carbonyl and carboxylate moieties of the substrate. After substrate radical formation, a number of routes are possible to generate the five-membered pyrrole ring, all of which are reminiscent of group migration reactions that are catalysed by adenosylcobalamin-dependent and AdoMet radical mutases.

By analogy to lysine aminomutases, one may envision a migration through an azocyclopropyl radical intermediate that is stabilised by resonance. Alternatively, the rearrangement may proceed by ring opening followed by a 5-exo-trig ring closure, resulting in the pyrroline ring. Next, the amino-centred radical would re-abstract a hydrogen atom from dA-H to reform AdoMet for use in a subsequent catalytic cycle, forming a gem-amino carboxylate pyrrole-like ring. The next step, elimination of the amino group must be enzyme catalysed based on the stereoselective loss of deuterium from the substrate C7 position. Here, enzyme-bound Mg(II) could act as a Lewis acid; alternatively, the protein C-terminal carboxylic acid group could promote the reaction through its interaction with the six-membered ring of substrate. Subsequent deprotonation of the pro-R C8 proton of either intermediate would lead to the final aromatised product.