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bioRxiv · 10.64898/2026.05.24.727522

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

Imrich, C. N.·Backman, L. R. F.·Allworth, A. P.·Andorfer, M. C.·Paris, J. C.·Greeley, N. M.·Fu, B.·Balskus, E. P.·Drennan, C. L.
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Abstract

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 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 skatole's 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.

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Imrich, C. N., Backman, L. R. F., Allworth, A. P., Andorfer, M. C., Paris, J. C., Greeley, N. M., Fu, B., Balskus, E. P., Drennan, C. L.. 2026-05-25. The Structural Basis of Malodorant Skatole Formation by the Glycyl Radical Enzyme Indoleacetate Decarboxylase. https://doi.org/10.64898/2026.05.24.727522

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