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Mechanism of DNA entrapment by the MukBEF SMC complex and its inhibition by a viral DNA mimic

View ORCID ProfileFrank Bürmann, View ORCID ProfileBryony Clifton, Sophie Koekemoer, View ORCID ProfileOliver J. Wilkinson, View ORCID ProfileDari Kimanius, View ORCID ProfileMark S. Dillingham, View ORCID ProfileJan Löwe
doi: https://doi.org/10.1101/2024.10.02.616235
Frank Bürmann
1MRC Laboratory of Molecular Biology, Structural Studies, Francis Crick Avenue, CB2 0QH, Cambridge, UK
2University of Oxford, Department of Biochemistry, South Parks Rd, OX1 3QU, Oxford, UK
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  • For correspondence: [email protected] [email protected] [email protected]
Bryony Clifton
3University of Bristol, School of Biochemistry, DNA:Protein Interactions Unit, Bristol, BS8 1TD, UK
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Sophie Koekemoer
3University of Bristol, School of Biochemistry, DNA:Protein Interactions Unit, Bristol, BS8 1TD, UK
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Oliver J. Wilkinson
3University of Bristol, School of Biochemistry, DNA:Protein Interactions Unit, Bristol, BS8 1TD, UK
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Dari Kimanius
1MRC Laboratory of Molecular Biology, Structural Studies, Francis Crick Avenue, CB2 0QH, Cambridge, UK
4CZ Imaging Institute, 3400 Bridge Parkway, Redwood City, CA 94065, USA
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Mark S. Dillingham
3University of Bristol, School of Biochemistry, DNA:Protein Interactions Unit, Bristol, BS8 1TD, UK
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Jan Löwe
1MRC Laboratory of Molecular Biology, Structural Studies, Francis Crick Avenue, CB2 0QH, Cambridge, UK
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  • For correspondence: [email protected] [email protected] [email protected]
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Summary

Ring-like structural maintenance of chromosomes (SMC) complexes are crucial for genome organization and operate through mechanisms of DNA entrapment and loop extrusion. Here, we explore the DNA loading process of the bacterial SMC complex MukBEF. Using electron cryomicroscopy (cryo-EM), we demonstrate that ATP binding opens one of MukBEF’s three potential DNA entry gates, exposing a DNA capture site that positions DNA at the open neck gate. We discover that the gp5.9 protein of bacteriophage T7 blocks this capture site by DNA mimicry, thereby preventing DNA loading and inactivating MukBEF. We propose a comprehensive and unidirectional loading mechanism in which DNA is first captured at the complex’s periphery and then ingested through the DNA entry gate, powered by a single cycle of ATP hydrolysis. These findings illuminate a fundamental aspect of how ubiquitous DNA organizers are primed for genome maintenance and demonstrate how this process can be disrupted by viruses.

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Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 02, 2024.
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Mechanism of DNA entrapment by the MukBEF SMC complex and its inhibition by a viral DNA mimic
Frank Bürmann, Bryony Clifton, Sophie Koekemoer, Oliver J. Wilkinson, Dari Kimanius, Mark S. Dillingham, Jan Löwe
bioRxiv 2024.10.02.616235; doi: https://doi.org/10.1101/2024.10.02.616235
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Mechanism of DNA entrapment by the MukBEF SMC complex and its inhibition by a viral DNA mimic
Frank Bürmann, Bryony Clifton, Sophie Koekemoer, Oliver J. Wilkinson, Dari Kimanius, Mark S. Dillingham, Jan Löwe
bioRxiv 2024.10.02.616235; doi: https://doi.org/10.1101/2024.10.02.616235

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