Structural characterization of the microbial enzyme urocanate reductase mediating imidazole propionate production

Raminta Venskutonytė,Olof Stenström,Fredrik Bäckhed,Muhammad Tanweer Khan,Mikael Akke,Ara Koh,Karin Lindkvist-Petersson,Annika Lundqvist

doi:10.1038/s41467-021-21548-y

Abstract

The human microbiome can produce metabolites that modulate insulin signaling. Type 2 diabetes patients have increased circulating concentrations of the microbially produced histidine metabolite, imidazole propionate (ImP) and administration of ImP in mice resulted in impaired glucose tolerance. Interestingly, the fecal microbiota of the patients had increased capacity to produce ImP, which is mediated by the bacterial enzyme urocanate reductase (UrdA). Here, we describe the X-ray structures of the ligand-binding domains of UrdA in four different states, representing the structural transitions along the catalytic reaction pathway of this unexplored enzyme linked to disease in humans. The structures in combination with functional data provide key insights into the mechanism of action of UrdA that open new possibilities for drug development strategies targeting type 2 diabetes.

Highlights

The human microbiome can produce metabolites that modulate insulin signaling
An improved understanding of the unexplored enzyme urocanate reductase (UrdA) is of clear medical interest
The overall structural properties of UrdA′ are similar to the well-studied soluble flavocytochrome c3 fumarate reductase from Shewanella oneidensis, but specific residues contribute to selectivity for urocanate in UrdA

Summary

Introduction

The human microbiome can produce metabolites that modulate insulin signaling. Type 2 diabetes patients have increased circulating concentrations of the microbially produced histidine metabolite, imidazole propionate (ImP) and administration of ImP in mice resulted in impaired glucose tolerance. The fecal microbiota of type 2 diabetes patients has an increased capacity to produce imidazole propionate (ImP), which is catalyzed by the bacterial enzyme urocanate reductase (UrdA)[3]. The structure of UrdA′ was determined at four specific states: an ADP-bound structure without substrate at 1.1 Å resolution, and three FAD-bound structures in complex with either the substrate urocanate (1.56 Å) or the product ImP (1.40 Å), or without any ligand bound (2.56 Å). Both full-length UrdA and UrdA′ showed specific activity toward urocanate but not to fumarate, suggesting that the functional integrity and substrate specificity are conserved in the two-domain construct. Our detailed comparison of the four structures gives valuable insights into the mechanism of action of this enzyme, revealing that specific residues, in combination with larger conformational changes, regulate substrate access, and product release

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Conclusion