Glycyl radical enzymes and their impact on microbial physiology

Glycyl radical enzymes (GRE) use radical-based biochemistry to catalyze the cleavage or formation of the carbon-carbon and carbon-heteroatom bonds found in organic molecules. These evolutionarily ancient enzymes are highly oxygen-sensitive but widespread in obligate as well as facultative anaerobes. When synthesized, GRE lack activity. The radical must be installed through the action of an activating enzyme (AE) that belongs to the radical S-adenosylmethionine superfamily. Typically, each GRE has a dedicated GRE-AE. Hydrogen atom abstraction from a highly conserved glycine residue located within the GRE's C-terminal domain introduces the radical into its storage location. Upon substrate binding, the radical is transferred to a conserved cysteine residue within the active site, transiently generating a thiyl radical species and initiating catalysis. There are currently five biochemical classes of GRE. Nevertheless, these GRE classes share a common mechanism of glycyl-radical storage and thiyl radical-mediated generation of a substrate radical. GRE exhibit similar tertiary structures and conserved active sites, but otherwise show limited primary structural conservation. These features are consistent with them diverging from an ancient common ancestor. Recent genome mining analyses, combined with structural and biochemical studies, are revealing the ubiquity of GRE, especially in uncultured gut microbiota and in association with disease states. Moreover, GRE are predominant in environmental microbiota associated with anaerobic degradation of hydrocarbons. GRE now have mainly catabolic roles in fermentative heterotrophs, but their universal involvement in anaerobic DNA synthesis and in other chemically challenging reactions suggests earlier in evolution biosynthesis of organic molecules might have been their main function.