CryoEM structures of open dimers of Gyrase A in complex with DNA illuminate mechanism of strand passage
- Northwestern University, United States
- MRC National Institute for Medical Research, United Kingdom
- 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.
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Tetrahedral oligomeric complex of GyrA N-terminal fragment, solved by cryoEM in tetrahedral symmetryElectron Microscopy Data Bank, EMD-9318.
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Dihedral oligomeric complex of GyrA N-terminal fragment, solved by cryoEM in D2 symmetryElectron Microscopy Data Bank, EMD-9317.
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Dihedral oligomeric complex of GyrA N-terminal fragment with DNA, solved by cryoEM in C2 symmetryElectron Microscopy Data Bank, EMD-9316.
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Structural plasticity of the Bacillus subtilis GyrA homodimerProtein Data Bank, 4DDQ.
Article and author information
Author details
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.
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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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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