1. Structural Biology and Molecular Biophysics

Structural insights into sodium transport by the oxaloacetate decarboxylase sodium pump

  1. Xin Xu
  2. Huigang Shi
  3. Xiaowen Gong
  4. Ying Gao
  5. Xinzheng Zhang  Is a corresponding author
  6. Song Xiang  Is a corresponding author
  1. Tianjin Medical University, China
  2. Institute of Biophysics, Chinese Academy of Sciences, China
  3. Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, China
https://doi.org/10.7554/eLife.53853
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  1. Xin Xu
  2. Huigang Shi
  3. Xiaowen Gong
  4. Ying Gao
  5. Xinzheng Zhang
  6. Song Xiang
(2020)
Structural insights into sodium transport by the oxaloacetate decarboxylase sodium pump
eLife 9:e53853.
https://doi.org/10.7554/eLife.53853
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Abstract

The oxaloacetate decarboxylase sodium pump (OAD) is a unique primary-active transporter that utilizes the free energy derived from oxaloacetate decarboxylation for sodium transport across the cell membrane. It is composed of 3 subunits: the a subunit catalyzes carboxyl-transfer from oxaloacetate to biotin, the membrane integrated β subunit catalyzes the subsequent carboxyl-biotin decarboxylation and the coupled sodium transport, the γ subunit interacts with the a and β subunits and stabilizes the OAD complex. We present here structure of the Salmonella typhimurium OAD βγ sub-complex. The structure revealed that the β and γ subunits form a β3γ3 hetero-hexamer with extensive interactions between the subunits and shed light on the OAD holo-enzyme assembly. Structure-guided functional studies provided insights into the sodium binding sites in the β subunit and the coupling between carboxyl-biotin decarboxylation and sodium transport by the OAD β subunit.

Data availability

The cryo-EM structure of the StOAD βγ sub-complex and related data have been deposited into the protein data bank (https://www.pdb.org) and the electron microscopy data bank (https://www.ebi.ac.uk/pdbe/emdb/), with the accession numbers 6IWW and EMD-9743, respectively. The crystal structure of the StOAD βγ sub-complex and the diffraction data have been deposited into the protein data bank with the accession number 6IVA. Source data for Figure 4c-d, Figure 4-figure supplement 1, Figure 5b-c, Figure 5-figure supplement 1, Figure 6a, Figure 6-figure supplement 1, and Figure 6-figure supplement 2a-b are provided.

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Author details

  1. Xin Xu

    Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, China
    Competing interests
    The authors declare that no competing interests exist.

  2. Huigang Shi

    National Laboratory of Biomacromolecules, CAS center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
    Competing interests
    The authors declare that no competing interests exist.

  3. Xiaowen Gong

    CAS Key Laboratory of Nutrition, Metabolism and Food safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
    Competing interests
    The authors declare that no competing interests exist.

  4. Ying Gao

    CAS Key Laboratory of Nutrition, Metabolism and Food safety, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
    Competing interests
    The authors declare that no competing interests exist.

  5. Xinzheng Zhang

    National Laboratory of Biomacromolecules, CAS center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
    For correspondence
    xzzhang@ibp.ac.cn
    Competing interests
    The authors declare that no competing interests exist.

  6. Song Xiang

    Department of Biochemistry and Molecular Biology, Tianjin Medical University, Tianjin, China
    For correspondence
    xiangsong@tmu.edu.cn
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9314-4684

Funding

National Natural Science Foundation of China (31870769)

  • Song Xiang

National Natural Science Foundation of China (31570743)

  • Song Xiang

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. José D Faraldo-Gómez, National Heart, Lung and Blood Institute, National Institutes of Health, United States

Version history

  1. Received: November 22, 2019
  2. Accepted: May 22, 2020
  3. Accepted Manuscript published: May 27, 2020 (version 1)
  4. Version of Record published: June 5, 2020 (version 2)

Copyright

© 2020, Xu et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Xin Xu
  2. Huigang Shi
  3. Xiaowen Gong
  4. Ying Gao
  5. Xinzheng Zhang
  6. Song Xiang
(2020)
Structural insights into sodium transport by the oxaloacetate decarboxylase sodium pump
eLife 9:e53853.
https://doi.org/10.7554/eLife.53853

Share this article

https://doi.org/10.7554/eLife.53853

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