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

Author

Listed:
  • 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
    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
    RIKEN SPring-8 Center
    Okayama University)

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.

Suggested Citation

  • Titouan Jaunet-Lahary & Tatsuro Shimamura & Masahiro Hayashi & Norimichi Nomura & Kouta Hirasawa & Tetsuya Shimizu & Masao Yamashita & Naotaka Tsutsumi & Yuta Suehiro & Keiichi Kojima & Yuki Sudo & Ta, 2023. "Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-36883-5
    DOI: 10.1038/s41467-023-36883-5
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    References listed on IDEAS

    as
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