A signal capture and proofreading mechanism for the KDEL-receptor explains selectivity and dynamic range in ER retrieval

Abstract

ER proteins of widely differing abundance are retrieved from the Golgi by the KDEL-receptor. Abundant ER proteins tend to have KDEL rather than HDEL signals, whereas ADEL and DDEL are not used in most organisms. Here, we explore the mechanism of selective retrieval signal capture by the KDEL-receptor and how HDEL binds with ten-fold higher affinity than KDEL. Our results show the carboxyl-terminus of the retrieval signal moves along a ladder of arginine residues as it enters the binding pocket of the receptor. Gatekeeper residues D50 and E117 at the entrance of this pocket exclude ADEL and DDEL sequences. D50N/E117Q mutation of human KDEL-receptors changes the selectivity to ADEL and DDEL. However, further analysis of HDEL, KDEL and RDEL-bound receptor structures shows that affinity differences are explained by interactions between the variable -4 H/K/R position of the signal and W120, rather than D50 or E117. Together, these findings explain KDEL-receptor selectivity, and how signal variants increase dynamic range to support efficient ER retrieval of low and high abundance proteins.

Data availability

Atomic coordinates for the models have been deposited in the Protein Data Bank (PDB) under accession codes 6Y7V and 6ZXR.Data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 1, 1Sup1, 1Sup2, 2, 3, 3Sup1, 4, 4Sup1, 6, 6Sup1, 6Sup2, 7, and 7Sup1.

The following previously published data sets were used

Article and author information

Author details

  1. Andreas Gerondopoulos

    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  2. Philipp Bräuer

    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-4127-2638
  3. Tomoaki Sobajima

    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0753-5361
  4. Zhiyi Wu

    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7615-7851
  5. Joanne L Parker

    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  6. Philip Biggin

    Biochemistry, University of Oxford, Oxford, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5100-8836
  7. Francis A Barr Ph.D.

    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    For correspondence
    francis.barr@bioch.ox.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7518-253X
  8. Simon Newstead

    Department of Biochemistry, University of Oxford, Oxford, United Kingdom
    For correspondence
    simon.newstead@bioch.ox.ac.uk
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-7432-2270

Funding

Wellcome Trust (219531/Z/19/Z,203741/Z/16/A and 109133/Z/15/A)

  • Zhiyi Wu

Engineering and Physical Sciences Research Council (EP/R029407/1)

  • Andreas Gerondopoulos
  • Philipp Bräuer
  • Tomoaki Sobajima

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

Reviewing Editor

  1. Adam Linstedt, Carnegie Mellon University, United States

Version history

  1. Received: March 14, 2021
  2. Accepted: June 16, 2021
  3. Accepted Manuscript published: June 17, 2021 (version 1)
  4. Version of Record published: July 1, 2021 (version 2)
  5. Version of Record updated: July 15, 2021 (version 3)
  6. Version of Record updated: July 22, 2021 (version 4)

Copyright

© 2021, Gerondopoulos 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. Andreas Gerondopoulos
  2. Philipp Bräuer
  3. Tomoaki Sobajima
  4. Zhiyi Wu
  5. Joanne L Parker
  6. Philip Biggin
  7. Francis A Barr Ph.D.
  8. Simon Newstead
(2021)
A signal capture and proofreading mechanism for the KDEL-receptor explains selectivity and dynamic range in ER retrieval
eLife 10:e68380.
https://doi.org/10.7554/eLife.68380

Share this article

https://doi.org/10.7554/eLife.68380

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