Structural basis for the reaction cycle of DASS dicarboxylate transporters

  1. David B Sauer
  2. Noah Trebesch
  3. Jennifer J Marden
  4. Nicolette Cocco
  5. Jinmei Song
  6. Akiko Koide
  7. Shohei Koide
  8. Emad Tajkhorshid  Is a corresponding author
  9. Da-Neng Wang  Is a corresponding author
  1. New York University School of Medicine, United States
  2. University of Illinois at Urbana-Champaign, United States
  3. University of Illinoi Urbana-Champaign, United States

Abstract

Citrate, α-ketoglutarate and succinate are TCA cycle intermediates that also play essential roles in metabolic signaling and cellular regulation. These di- and tricarboxylates are imported into the cell by the divalent anion sodium symporter (DASS) family of plasma membrane transporters, which contains both cotransporters and exchangers. While DASS proteins transport substrates via an elevator mechanism, to date structures are only available for a single DASS cotransporter protein in a substrate-bound, inward-facing state. We report multiple cryo-EM and X-ray structures in four different states, including three hitherto unseen states, along with molecular dynamics simulations, of both a cotransporter and an exchanger. Comparison of these outward- and inward-facing structures reveal how the transport domain translates and rotates within the framework of the scaffold domain through the transport cycle. Additionally, we propose that DASS transporters ensure substrate coupling by a charge-compensation mechanism, and by structural changes upon substrate release.

Data availability

Cryo-EM maps and models have been deposited in the Protein Data Bank and EMDB database, respectively, for VcINDY-Na+ in amphipol (6WU3, EMD-21904), VcINDY-Na+-Fab84 in nanodisc (6WW5, EMD-21928), LaINDY-apo (6WU1, EMD-21902), LaINDY-aKG (6WU4, EMD-21905), and LaINDY-malate (6WU2, EMD-21903). X-ray derived models and diffraction data have been deposited in the Protein Data Bank for LaINDY-malate-aKG (6WTW) and VcINDY-TTP (6WTX). Coordinates of representative LaINDY structures from MD simulations of the Co-S and Ci-S states will be made publicly available on Zenodo (DOI: 10.5281/zenodo.3965996). Bond length analysis code is available at https://github.com/DavidBSauer/bond_length_analysis.

Article and author information

Author details

  1. David B Sauer

    Skirball Institute, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9291-4640
  2. Noah Trebesch

    Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5536-4862
  3. Jennifer J Marden

    Skirball Institute, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Nicolette Cocco

    Skirball Institute, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Jinmei Song

    Skirball Institute, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Akiko Koide

    Perlmutter Cancer Center, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  7. Shohei Koide

    Perlmutter Cancer Center, New York University School of Medicine, New York, United States
    Competing interests
    The authors declare that no competing interests exist.
  8. Emad Tajkhorshid

    Biochemistry, University of Illinoi Urbana-Champaign, Urbana, United States
    For correspondence
    emad@illinois.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8434-1010
  9. Da-Neng Wang

    Skirball Institute, New York University School of Medicine, New York, United States
    For correspondence
    Da-Neng.Wang@med.nyu.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6496-4699

Funding

National Institutes of Health (R01NS108151)

  • Da-Neng Wang

Department of Defense (W81XWH-16-1-0153)

  • David B Sauer

National Science Foundation (1746047)

  • Noah Trebesch

National Institutes of Health (T32GM088118)

  • Nicolette Cocco

Blue Waters and XSEDE (TG-MCA06N060)

  • Emad Tajkhorshid

National Institutes of Health (R01GM121994)

  • Da-Neng Wang

National Institutes of Health (R01DK099023)

  • Da-Neng Wang

National Institutes of Health (U54GM095315)

  • Da-Neng Wang

National Institutes of Health (P41GM104601)

  • Emad Tajkhorshid

National Institutes of Health (R01GM067887)

  • Emad Tajkhorshid

TESS Research Foundation

  • Da-Neng Wang

American Epilepsy Society (AES2017SD3)

  • Da-Neng Wang

American Cancer Society (129844-PF-17-135-01-TBE)

  • David B Sauer

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

Reviewing Editor

  1. Merritt Maduke, Stanford University School of Medicine, United States

Version history

  1. Received: July 23, 2020
  2. Accepted: August 31, 2020
  3. Accepted Manuscript published: September 1, 2020 (version 1)
  4. Version of Record published: October 13, 2020 (version 2)

Copyright

© 2020, Sauer 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. David B Sauer
  2. Noah Trebesch
  3. Jennifer J Marden
  4. Nicolette Cocco
  5. Jinmei Song
  6. Akiko Koide
  7. Shohei Koide
  8. Emad Tajkhorshid
  9. Da-Neng Wang
(2020)
Structural basis for the reaction cycle of DASS dicarboxylate transporters
eLife 9:e61350.
https://doi.org/10.7554/eLife.61350

Share this article

https://doi.org/10.7554/eLife.61350

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