Structural Superimposition

Abstact

The ability of SAM-dependent enzymes to accept S-adenosyl-d-methionine [d-SAM, (S(S),R(Calpha))-SAM] instead of the native cofactor S-adenosyl-l-methionine [l-SAM, (S(S),S(Calpha))-SAM] remains largely unexplored. Challenging the stereochemical preference of SAM-dependent enzymes, we investigated the ability of different enzyme classes to accept d-SAM. Contrary to common assumptions, the tested N- and O-methyltransferases (MTs), as well as one of the examined C-MTs accepted d-SAM. Docking studies suggest that acceptance of d-SAM by C-MTs may be influenced by the angle between the transferable methyl group of SAM and the nucleophilic carbon of the substrate, along with enzyme and substrate flexibility. In addition to conventional MTs, the radical SAM glutamine C-MT QCMT showed low but detectable methylation activity with d-SAM. Furthermore, the azetidine-2-carboxylic acid synthase AzeJ not only uses d-SAM but also incorporates the stereocentre of d-methionine into the cyclic amino acid product. The pyridoxal 5'-phosphate (PLP)-dependent enzyme 1-aminocyclopropyl-1-carboxylic acid synthase (ACCS) also showed detectable turnover with d-SAM. These findings broaden the understanding of enzyme stereoselectivity, provide an overview of d-SAM-utilising enzymes, and identify the first enzyme systems that may serve as starting points for engineering efforts aimed at shifting cofactor preference towards d-SAM.