Nature's Anaerobic Toolkit: Glycyl Radical Enzymes and Their Expanding Functional and Mechanistic Diversity

Nature has devised an array of enzymatic cofactors that enable challenging chemical transformations to occur on a time scale compatible with biological life. The glycyl radical enzyme (GRE) superfamily, for example, highlights the catalytic power of protein-based amino acid radicals. GREs utilize a persistent radical housed on the α-carbon of a C-terminally conserved glycine residue to accomplish diverse chemical reactions in anaerobic environments. This radical cofactor is post-translationally installed on the mature, folded protein by a radical S-adenosyl-L-methionine (RS) activating enzyme (GRE-AE; activase) specific to each GRE. The catalytic repertoire of GREs is diverse, spanning ribonucleotide reduction for DNA synthesis, acetyl-CoA formation in anaerobic primary metabolism, dehydration reactions in secondary metabolism, decarboxylation reactions in aromatic amino acid fermentation, and hydrocarbon activation in anaerobic bacteria, enabling their survival on crude oil as a carbon source. Pyruvate formate lyase (PFL), the founding member of the GRE superfamily, was first identified several decades ago. In recent years, sequencing technology has enabled the annotation of thousands of unique GRE-encoding sequences. Several dozen of the identified GREs have been characterized further, providing insight into the structure, mechanism, and regulation of this multitudinous and diverse enzyme family. Here, we introduce the superfamily, summarize what is known about their activation and catalysis, note conserved structural features, expand on the previously identified GRE classes, highlight GRE-associated bacterial microcompartments, and discuss the future and outlook of the GRE superfamily.