Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota

Titouan Jaunet-Lahary, Tatsuro Shimamura (), Masahiro Hayashi, Norimichi Nomura, Kouta Hirasawa, Tetsuya Shimizu, Masao Yamashita, Naotaka Tsutsumi, Yuta Suehiro, Keiichi Kojima, Yuki Sudo, Takashi Tamura, Hiroko Iwanari, Takao Hamakubo, So Iwata, Kei-ichi Okazaki (), Teruhisa Hirai () and Atsuko Yamashita ()
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Titouan Jaunet-Lahary: National Institutes of Natural Sciences
Tatsuro Shimamura: Kyoto University
Masahiro Hayashi: Okayama University
Norimichi Nomura: Kyoto University
Kouta Hirasawa: Kyoto University
Tetsuya Shimizu: RIKEN SPring-8 Center
Masao Yamashita: RIKEN SPring-8 Center
Naotaka Tsutsumi: Okayama University
Yuta Suehiro: Okayama University
Keiichi Kojima: Okayama University
Yuki Sudo: Okayama University
Takashi Tamura: Okayama University
Hiroko Iwanari: The University of Tokyo
Takao Hamakubo: The University of Tokyo
So Iwata: Kyoto University
Kei-ichi Okazaki: National Institutes of Natural Sciences
Teruhisa Hirai: RIKEN SPring-8 Center
Atsuko Yamashita: Okayama University

Nature Communications, 2023, vol. 14, issue 1, 1-15

Abstract: Abstract An oxalate-degrading bacterium in the gut microbiota absorbs food-derived oxalate to use this as a carbon and energy source, thereby reducing the risk of kidney stone formation in host animals. The bacterial oxalate transporter OxlT selectively uptakes oxalate from the gut to bacterial cells with a strict discrimination from other nutrient carboxylates. Here, we present crystal structures of oxalate-bound and ligand-free OxlT in two distinct conformations, occluded and outward-facing states. The ligand-binding pocket contains basic residues that form salt bridges with oxalate while preventing the conformational switch to the occluded state without an acidic substrate. The occluded pocket can accommodate oxalate but not larger dicarboxylates, such as metabolic intermediates. The permeation pathways from the pocket are completely blocked by extensive interdomain interactions, which can be opened solely by a flip of a single side chain neighbouring the substrate. This study shows the structural basis underlying metabolic interactions enabling favourable symbiosis.

Date: 2023
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Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36883-5

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DOI: 10.1038/s41467-023-36883-5

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