Structural Biochemistry/Enzyme/Radical-SAM Enzyme
The diversity of proteins and nucleic acids is much due to the many mechanisms that allow site-specific additions of chemical groups into macromolecules. These modifications done to macromolecules were considered to be only nucleophilic, such has in DNA methylation. However, after the discovery of the Radical-SAM (S-Adenosylmethionine) enzyme family, a lot of protein and RNA modification reactions were found to be done through radical mechanisms rather than nucleophilic mechanisms. Because free radicals are very reactive, it allows any site of the target substrate to be activated for modification. So, this free radical mechanism discovery expanded the number of modified monomers, creating diversity. However, these reactions are more difficult to control. The study of these radical-based mechanisms through Radical-SAM enzymes are still at the beginning stages. These mechanisms require detail structural characterization of enzymes in complex polymers, which is a problem since the 3-D structures for many of these polymers are unknown still.
Many modifications can occur through radical mechanisms. Protein modifications, the simplest being the glycyl radical, can occur via radical mechanisms. In addition, these radical-based mechanisms are also at work in post-transciptional modifications of nucleosides. These Radical-SAM enzymes creates a radical in a specific polymer, and this radical can bind to methyls, thiols, and other groups, creating more complex molecules. Glycine radicalization done by converting a glycine into the radical form, generated by a "Radical-SAM" activase. This process causes a conformational change in the structure. Radical-SAM enzymes also are involved in the addition of methylthio (CH3 and SH) groups into proteins and transfer RNAs. First, there is a hydrogen atom abstraction by the 5'-deoxyadenosyl radical. Then, there is a sulfuration of the substrate radical to make an intermediate thiol. Lastly, there is a nucleophilic methylation by SAM. Then, two different activities happen, both SAM dependent. First, the catalyze radical C-H to C-S. Second, they function as SAM-dependent methyltransferases.
Structural organization of Radical-SAM enzymes
These SAM enzymes have a conserved core with a mixture of alpha and beta structure forms. A six-stranded parallel B-sheet binds SAM and a [4Fe-4S] cluster at equivalent positions for all the radical enzymes. SAM binds at the groove formed between adjacent B-strands connected to alpha helices that pack on opposite surfaces of the B-sheet. This specific packing geometry produces a concave surface that has different degrees of curvature based on the specific Radical-SAM enzyme family. These different degrees of curvature are very important because it contributes to their specificity for diverse substrates ranging from small molecules to macromolecules.
Atta, Mohamed, Mulliez, Etienne, etc. "S-Adenosylmethionine-dependent radical-based modification of biological macromolecules." Current Opinion in Structural Biology. 2010.