LRET-derived HADDOCK structural models describe the conformational heterogeneity required for DNA cleavage by the Mre11-Rad50 DNA damage repair complex

  1. Marella D Canny
  2. Michael Latham  Is a corresponding author
  1. Texas Tech University, United States

Abstract

The Mre11-Rad50-Nbs1 protein complex is one of the first responders to DNA double strand breaks. Studies have shown that the catalytic activities of the evolutionarily conserved Mre11-Rad50 (MR) core complex depend on an ATP-dependent global conformational change that takes the macromolecule from an open, extended structure in the absence of ATP to a closed, globular structure when ATP is bound. We have previously identified an additional ‘partially open’ conformation using Luminescence Resonance Energy Transfer (LRET) experiments. Here, a combination of LRET and the molecular docking program HADDOCK was used to further investigate this partially open state and identify three conformations of MR in solution: closed, partially open, and open, which are in addition to the extended, apo conformation. Mutants disrupting specific Mre11-Rad50 interactions within each conformation were used in nuclease activity assays on a variety of DNA substrates to help put the three states into a functional perspective. LRET data collected on MR bound to DNA demonstrate that the three conformations also exist when nuclease substrates are bound. These models were further supported with SAXS data which corroborate the presence of multiple states in solution. Together, the data suggest a mechanism for the nuclease activity of the MR complex along the DNA.

Data availability

All data generated or analysed during this study are available from the DRYAD database under the doi: https://doi.org/10.5061/dryad.qfttdz0h6

The following data sets were generated

Article and author information

Author details

  1. Marella D Canny

    Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9884-5575
  2. Michael Latham

    Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, United States
    For correspondence
    michael.latham@ttu.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2209-5798

Funding

National Institute of General Medical Sciences (1R35GM128906)

  • Michael Latham

Cancer Prevention and Research Institute of Texas (RP180553)

  • Michael Latham

Welch Foundation (D-1876)

  • Michael Latham

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

Reviewing Editor

  1. Maria Spies, University of Iowa, United States

Version history

  1. Received: April 20, 2021
  2. Preprint posted: August 4, 2021 (view preprint)
  3. Accepted: January 26, 2022
  4. Accepted Manuscript published: January 27, 2022 (version 1)
  5. Version of Record published: February 8, 2022 (version 2)
  6. Version of Record updated: February 22, 2022 (version 3)

Copyright

© 2022, Canny & Latham

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. Marella D Canny
  2. Michael Latham
(2022)
LRET-derived HADDOCK structural models describe the conformational heterogeneity required for DNA cleavage by the Mre11-Rad50 DNA damage repair complex
eLife 11:e69579.
https://doi.org/10.7554/eLife.69579

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https://doi.org/10.7554/eLife.69579

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