CryoEM structures of open dimers of Gyrase A in complex with DNA illuminate mechanism of strand passage

  1. Katarzyna M Soczek
  2. Tim Grant
  3. Peter B Rosenthal
  4. Alfonso Mondragon  Is a corresponding author
  1. Northwestern University, United States
  2. MRC National Institute for Medical Research, United Kingdom
  3. The Francis Crick Institute, United Kingdom

Abstract

Gyrase is a unique type IIA topoisomerase that uses ATP hydrolysis to maintain the negatively supercoiled state of bacterial DNA. In order to perform its function, gyrase undergoes a sequence of conformational changes that consist of concerted gate openings, DNA cleavage, and DNA strand passage events. Structures where the transported DNA molecule (T-segment) is trapped by the A subunit have not been observed. Here we present the cryoEM structures of two oligomeric complexes of open gyrase A dimers and DNA. The protein subunits in these complexes were solved to 4 Å and 5.16 Å resolution. One of the complexes traps a linear DNA molecule, a putative T-segment, which interacts with the open gyrase A dimers in two states, representing steps either prior to or after passage through the DNA-gate. The structures locate the T-segment in important intermediate conformations of the catalytic cycle and provide insights into gyrase-DNA interactions and mechanism.

Data availability

Coordinates and EM maps were deposited in the PDB and EMDB with accession codes: PDB entry ID 6N1R and EMDB entry ID EMD-9318, PDB entry ID 6N1Q and EMDB entry ID EMD-9317, and PDB entry ID 6N1P and EMDB entry ID EMD-9316.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Katarzyna M Soczek

    Department of Molecular Biosciences, Northwestern University, Evanston, United States
    Competing interests
    The authors declare that no competing interests exist.
  2. Tim Grant

    Division of Physical Biochemistry, MRC National Institute for Medical Research, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  3. Peter B Rosenthal

    The Francis Crick Institute, London, United Kingdom
    Competing interests
    The authors declare that no competing interests exist.
  4. Alfonso Mondragon

    Department of Molecular Biosciences, Northwestern University, Evanston, United States
    For correspondence
    a-mondragon@northwestern.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0423-6323

Funding

National Institutes of Health (R01-GM051350)

  • Alfonso Mondragon

Wellcome (FC001143)

  • Peter B Rosenthal

Cancer Research UK (FC001143)

  • Peter B Rosenthal

Medical Research Council (FC001143)

  • Tim Grant
  • Peter B Rosenthal

National Institutes of Health (R35-GM118108)

  • Alfonso Mondragon

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

Reviewing Editor

  1. Andrea Musacchio, Max Planck Institute of Molecular Physiology, Germany

Version history

  1. Received: August 17, 2018
  2. Accepted: November 9, 2018
  3. Accepted Manuscript published: November 20, 2018 (version 1)
  4. Version of Record published: December 7, 2018 (version 2)

Copyright

© 2018, Soczek 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. Katarzyna M Soczek
  2. Tim Grant
  3. Peter B Rosenthal
  4. Alfonso Mondragon
(2018)
CryoEM structures of open dimers of Gyrase A in complex with DNA illuminate mechanism of strand passage
eLife 7:e41215.
https://doi.org/10.7554/eLife.41215

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https://doi.org/10.7554/eLife.41215

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