The Structural Basis of Malodorant Skatole Formation by the Glycyl Radical Enzyme Indoleacetate Decarboxylase

Glycyl radical enzymes (GREs) catalyze challenging chemical reactions using a post-translationally installed glycyl radical cofactor. One such enzyme, indoleacetate decarboxylase (IAD), performs the radical-based decarboxylation of indole-3-acetate (I3A) to form the malodorant molecule skatole. In addition to being an odor nuisance, skatole is a human and livestock lung toxin, a suspected carcinogen, and a mosquito attractant, all of which impact human health, agriculture, food production, and wastewater treatment. Here, we use cryogenic electron microscopy to solve a 2.45-[A] resolution structure of indoleacetate decarboxylase from the gut bacterium Olsenella uli. We observe IAD in a homotetrameric form with the substrate I3A bound in all four protomers. The positioning of the I3A in the active site is unexpected and is more consistent with a Kolbe-type decarboxylation mechanism, i.e. a decarboxylation initiated by a 1-electron oxidation of the carboxylate moiety rather than being initiated by hydrogen atom transfer (HAT). Previously, a high deuterium content in skatole from IAD assays in D2O was used to support a HAT mechanism over a Kolbe-type mechanism. However, we show here that deuterium content does not necessarily inform on mechanism as IAD can catalyze the exchange of skatoles 3'-methyl hydrogens post-turnover. Structural comparisons show that both IAD and HPAD display structural features that are not found in other characterized GREs, suggesting that they represent a distinct GRE-subclass. Collectively, these insights will inform IAD inhibitor design aimed at decreasing skatole production. Significance StatementGlycyl radical enzymes (GREs) are a superfamily of enzymes that catalyze challenging chemical reactions in anaerobic environments. One such enzyme, indoleacetate decarboxylase (IAD) performs a C-C bond cleavage and decarboxylation reaction on the tryptophan metabolite indole-3-acetate (I3A). Decarboxylation of I3A by IAD forms the malodorant molecule skatole which negatively impacts human health, livestock health, odor emissions, the environment, and food production. Here, we present the first structure of IAD with I3A bound, revealing the substrate binding mode and active site architecture. This work provides new insight into the catalytic mechanism of the enzyme and illuminates new avenues for control of the odor nuisance skatole.