1. Structural Biology and Molecular Biophysics
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Structural basis of ClpXP recognition and unfolding of ssrA-tagged substrates

  1. Xue Fei
  2. Tristan A Bell
  3. Sarah R Barkow
  4. Tania A Baker
  5. Robert T Sauer  Is a corresponding author
  1. Massachusetts Institute of Technology, United States
Research Article
  • Cited 3
  • Views 1,073
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Cite this article as: eLife 2020;9:e61496 doi: 10.7554/eLife.61496

Abstract

When ribosomes fail to complete normal translation, all cells have mechanisms to ensure degradation of the resulting partial proteins to safeguard proteome integrity. In E. coli and other eubacteria, the tmRNA system rescues stalled ribosomes and adds an ssrA tag or degron to the C-terminus of the incomplete protein, which directs degradation by the AAA+ ClpXP protease. Here, we present cryo-EM structures of ClpXP bound to the ssrA degron. C-terminal residues of the ssrA degron initially bind in the top of an otherwise closed ClpX axial channel and subsequently move deeper into an open channel. For short-degron protein substrates, we show that unfolding can occur directly from the initial closed-channel complex. For longer-degron substrates, our studies illuminate how ClpXP transitions from specific recognition into a nonspecific unfolding and translocation machine. Many AAA+ proteases and protein-remodeling motors are likely to employ similar multistep recognition and engagement strategies.

Article and author information

Author details

  1. Xue Fei

    Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Tristan A Bell

    Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Sarah R Barkow

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Tania A Baker

    Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0737-3411
  5. Robert T Sauer

    Department of Biology, Massachusetts Institute of Technology, Cambridge, United States
    For correspondence
    bobsauer@mit.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1719-5399

Funding

National Institute of General Medical Sciences (GM-101988)

  • Robert T 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. Andrew P Carter, MRC Laboratory of Molecular Biology, United Kingdom

Publication history

  1. Received: July 27, 2020
  2. Accepted: October 21, 2020
  3. Accepted Manuscript published: October 22, 2020 (version 1)
  4. Version of Record published: November 9, 2020 (version 2)

Copyright

© 2020, Fei 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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