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
Further reading
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Under physiological conditions, proteins continuously undergo structural fluctuations on different timescales. Some conformations are only sparsely populated, but still play a key role in protein function. Thus, meaningful structure–function frameworks must include structural ensembles rather than only the most populated protein conformations. To detail protein plasticity, modern structural biology combines complementary experimental and computational approaches. In this review, we survey available computational approaches that integrate sparse experimental data from electron paramagnetic resonance spectroscopy with molecular modeling techniques to derive all-atom structural models of rare protein conformations. We also propose strategies to increase the reliability and improve efficiency using deep learning approaches, thus advancing the field of integrative structural biology.
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