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Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK

Author

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  • Masahiro Fukuda

    (Graduate School of Science, The University of Tokyo
    Global Research Cluster)

  • Hironori Takeda

    (Graduate School of Science, The University of Tokyo
    Global Research Cluster)

  • Hideaki E. Kato

    (Graduate School of Science, The University of Tokyo
    Global Research Cluster
    Present address: Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA.)

  • Shintaro Doki

    (Graduate School of Science, The University of Tokyo
    Global Research Cluster)

  • Koichi Ito

    (Graduate School of Frontier Sciences, The University of Tokyo)

  • Andrés D. Maturana

    (Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho)

  • Ryuichiro Ishitani

    (Graduate School of Science, The University of Tokyo
    Global Research Cluster)

  • Osamu Nureki

    (Graduate School of Science, The University of Tokyo
    Global Research Cluster)

Abstract

NarK belongs to the nitrate/nitrite porter (NNP) family in the major facilitator superfamily (MFS) and plays a central role in nitrate uptake across the membrane in diverse organisms, including archaea, bacteria, fungi and plants. Although previous studies provided insight into the overall structure and the substrate recognition of NarK, its molecular mechanism, including the driving force for nitrate transport, remained elusive. Here we demonstrate that NarK is a nitrate/nitrite antiporter, using an in vitro reconstituted system. Furthermore, we present the high-resolution crystal structures of NarK from Escherichia coli in the nitrate-bound occluded, nitrate-bound inward-open and apo inward-open states. The integrated structural, functional and computational analyses reveal the nitrate/nitrite antiport mechanism of NarK, in which substrate recognition is coupled to the transport cycle by the concomitant movement of the transmembrane helices and the key tyrosine and arginine residues in the substrate-binding site.

Suggested Citation

  • Masahiro Fukuda & Hironori Takeda & Hideaki E. Kato & Shintaro Doki & Koichi Ito & Andrés D. Maturana & Ryuichiro Ishitani & Osamu Nureki, 2015. "Structural basis for dynamic mechanism of nitrate/nitrite antiport by NarK," Nature Communications, Nature, vol. 6(1), pages 1-12, November.
    • Handle: RePEc:nat:natcom:v:6:y:2015:i:1:d:10.1038_ncomms8097
    DOI: 10.1038/ncomms8097
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    1. Shanyun Wang & Bangrui Lan & Longbin Yu & Manyi Xiao & Liping Jiang & Yu Qin & Yucheng Jin & Yuting Zhou & Gawhar Armanbek & Jingchen Ma & Manting Wang & Mike S. M. Jetten & Hanqin Tian & Guibing Zhu , 2024. "Ammonium-derived nitrous oxide is a global source in streams," Nature Communications, Nature, vol. 15(1), pages 1-9, December.
    2. 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.
    3. Philip Schmiege & Linda Donnelly & Nadia Elghobashi-Meinhardt & Chia-Hsueh Lee & Xiaochun Li, 2024. "Structure and inhibition of the human lysosomal transporter Sialin," Nature Communications, Nature, vol. 15(1), pages 1-11, December.

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