1. Biochemistry and Chemical Biology
  2. Structural Biology and Molecular Biophysics
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Structure of Vps4 with circular peptides and implications for translocation of two polypeptide chains by AAA+ ATPases

  1. Han Han
  2. James M Fulcher
  3. Venkata P Dandey
  4. Janet H Iwasa
  5. Wesley I Sundquist
  6. Michael S Kay
  7. Peter S Shen  Is a corresponding author
  8. Christopher P Hill  Is a corresponding author
  1. University of Utah School of Medicine, United States
  2. New York Structural Biology Center, United States
Research Article
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Cite this article as: eLife 2019;8:e44071 doi: 10.7554/eLife.44071

Abstract

Many AAA+ ATPases form hexamers that unfold protein substrates by translocating them through their central pore. Multiple structures have shown how a helical assembly of subunits binds a single strand of substrate, and indicate that translocation results from the ATP-driven movement of subunits from one end of the helical assembly to the other end. To understand how more complex substrates are bound and translocated, we demonstrated that linear and cyclic versions of peptides bind to the S. cerevisiae AAA+ ATPase Vps4 with similar affinities, and determined cryo-EM structures of cyclic peptide complexes. The peptides bind in a hairpin conformation, with one primary strand equivalent to the single chain peptide ligands, while the second strand returns through the translocation pore without making intimate contacts with Vps4. These observations indicate a general mechanism by which AAA+ ATPases may translocate a variety of substrates that include extended chains, hairpins, and crosslinked polypeptide chains.

Data availability

The refined model comprising the Vps4 ATPase domains of subunits A-E and the cyclic peptide is accessible via the PDB (RRID: SCR_012820; PDB ID: 6NDY) together with the 3.6 Å map from the combined dataset (RRID: SCR_003207, EMDB Accession Number EMD-0443). The complete model, including regions not subjected to atomic refinement such as the 12 Vta1VSL domains and subunit F, is also available via the PDB (PDB ID: 6OO2), together with the map containing Vta1VSL densities at all six Vps4 interfaces (RRID: SCR_003207, EMDB Accession Number EMD-20142). The two maps derived from the cF30 and cFF30 complex datasets individually, and the three maps for subunit F, have been deposited to the EMDB (RRID: SCR_ 003207, EMDB Accession Numbers EMD-20144, EMD-20147, EMD-20139, EMD-20140, EMD-20141).

The following data sets were generated

Article and author information

Author details

  1. Han Han

    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0361-4254
  2. James M Fulcher

    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9033-3623
  3. Venkata P Dandey

    National Resource for Automated Molecular Microscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States
    Competing interests
    No competing interests declared.
  4. Janet H Iwasa

    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
    Competing interests
    No competing interests declared.
  5. Wesley I Sundquist

    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
    Competing interests
    Wesley I Sundquist, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-9988-6021
  6. Michael S Kay

    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
    Competing interests
    No competing interests declared.
  7. Peter S Shen

    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
    For correspondence
    peter.shen@biochem.utah.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-6256-6910
  8. Christopher P Hill

    Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States
    For correspondence
    chris@biochem.utah.edu
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6796-7740

Funding

National Institutes of Health (P50 GM082545)

  • Han Han
  • James M Fulcher
  • Janet H Iwasa
  • Michael S Kay
  • Peter S Shen
  • Christopher P Hill

National Institutes of Health (R01 GM112080)

  • Wesley I Sundquist

National Institutes of Health (P41 GM103310)

  • Venkata P Dandey

New York State Foundation for Science, Technology and Innovation

  • Venkata P Dandey

Simons Foundation (SF349247)

  • Venkata P Dandey

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

Reviewing Editor

  1. James M Berger, Johns Hopkins University School of Medicine, United States

Publication history

  1. Received: December 1, 2018
  2. Accepted: June 11, 2019
  3. Accepted Manuscript published: June 11, 2019 (version 1)
  4. Version of Record published: July 1, 2019 (version 2)

Copyright

© 2019, Han 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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