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Structural basis of chiral wrap and T-segment capture by Escherichia coli DNA gyrase

Michalczyk, Elizabeth; Pakosz-Stępień, Zuzanna; Liston, Jonathon D.; Gittins, Olivia; Pabis, Marta; Heddle, Jonathan G.; Ghilarov, Dmitry

Structural basis of chiral wrap and T-segment capture by            Escherichia coli            DNA gyrase Thumbnail


Authors

Elizabeth Michalczyk

Olivia Gittins olivia.v.gittins@durham.ac.uk
Postdoctoral Research Associate

Marta Pabis

Dmitry Ghilarov



Abstract

Type II topoisomerase DNA gyrase transduces the energy of ATP hydrolysis into the negative supercoiling of DNA. The postulated catalytic mechanism involves stabilization of a chiral DNA loop followed by the passage of the T-segment through the temporarily cleaved G-segment resulting in sign inversion. The molecular basis for this is poorly understood as the chiral loop has never been directly observed. We have obtained high-resolution cryoEM structures of Escherichia coli gyrase with chirally wrapped 217 bp DNA with and without the fluoroquinolone moxifloxacin (MFX). Each structure constrains a positively supercoiled figure-of-eight DNA loop stabilized by a GyrA β-pinwheel domain which has the structure of a flat disc. By comparing the catalytic site of the native drug-free and MFX-bound gyrase structures both of which contain a single metal ion, we demonstrate that the enzyme is observed in a native precatalytic state. Our data imply that T-segment trapping is not dependent on the dimerization of the ATPase domains which appears to only be possible after strand passage has taken place.

Citation

Michalczyk, E., Pakosz-Stępień, Z., Liston, J. D., Gittins, O., Pabis, M., Heddle, J. G., & Ghilarov, D. (2024). Structural basis of chiral wrap and T-segment capture by Escherichia coli DNA gyrase. Proceedings of the National Academy of Sciences, 121(49), Article e2407398121. https://doi.org/10.1073/pnas.2407398121

Journal Article Type Article
Acceptance Date Oct 17, 2024
Online Publication Date Nov 26, 2024
Publication Date Dec 3, 2024
Deposit Date Nov 27, 2024
Publicly Available Date Nov 27, 2024
Journal Proceedings of the National Academy of Sciences
Print ISSN 0027-8424
Electronic ISSN 1091-6490
Publisher National Academy of Sciences
Peer Reviewed Peer Reviewed
Volume 121
Issue 49
Article Number e2407398121
DOI https://doi.org/10.1073/pnas.2407398121
Keywords Models, Molecular, Escherichia coli - metabolism - enzymology - genetics, DNA Gyrase - metabolism - chemistry, Moxifloxacin - chemistry, Cryoelectron Microscopy, Catalytic Domain, Topoisomerase II Inhibitors - chemistry - pharmacology, antibiotics, DNA crossover, topoisomerase, DNA, Superhelical - metabolism - chemistry, molecular machine, Nucleic Acid Conformation, DNA-binding protein, DNA, Bacterial - metabolism, Fluoroquinolones - chemistry - pharmacology
Public URL https://durham-repository.worktribe.com/output/3107520

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