How do Gepotidacin and Zoliflodacin stabilize DNA cleavage complexes with bacterial Type IIA topoisomerases? 1. Experimental definition of metal binding sites

Morgan, Harry, Nicholls, Robert A., Warren, Anna J., Ward, Simon E. ORCID: https://orcid.org/0000-0002-8745-8377, Evans, Gwyndaf, Long, Fei, Murshudov, Garib N., Duman, Ramona and Bax, Benjamin D. 2024. How do Gepotidacin and Zoliflodacin stabilize DNA cleavage complexes with bacterial Type IIA topoisomerases? 1. Experimental definition of metal binding sites. International Journal of Molecular Sciences 25 (21) , 11688. 10.3390/ijms252111688

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Abstract

One of the challenges for experimental structural biology in the 21st century is to see chemical reactions happen. Staphylococcus aureus (S. aureus) DNA gyrase is a type IIA topoisomerase that can create temporary double-stranded DNA breaks to regulate DNA topology. Drugs, such as gepotidacin, zoliflodacin and the quinolone moxifloxacin, can stabilize these normally transient DNA strand breaks and kill bacteria. Crystal structures of uncleaved DNA with a gepotidacin precursor (2.1 Å GSK2999423) or with doubly cleaved DNA and zoliflodacin (or with its progenitor QPT-1) have been solved in the same P61 space-group (a = b ≈ 93 Å, c ≈ 412 Å). This suggests that it may be possible to observe the two DNA cleavage steps (and two DNA-religation steps) in this P61 space-group. Here, a 2.58 Å anomalous manganese dataset in this crystal form is solved, and four previous crystal structures (1.98 Å, 2.1 Å, 2.5 Å and 2.65 Å) in this crystal form are re-refined to clarify crystal contacts. The structures clearly suggest a single moving metal mechanism—presented in an accompanying (second) paper. A previously published 2.98 Å structure of a yeast topoisomerase II, which has static disorder around a crystallographic twofold axis, was published as containing two metals at one active site. Re-refined coordinates of this 2.98 Å yeast structure are consistent with other type IIA topoisomerase structures in only having one metal ion at each of the two different active sites.

Item Type:	Article
Date Type:	Published Online
Status:	Published
Schools:	Medicine Biosciences
Additional Information:	License information from Publisher: LICENSE 1: URL: https://creativecommons.org/licenses/by/4.0/, Type: open-access
Publisher:	MDPI
ISSN:	1661-6596
Date of First Compliant Deposit:	8 November 2024
Date of Acceptance:	25 October 2024
Last Modified:	04 Dec 2024 10:27
URI:	https://orca.cardiff.ac.uk/id/eprint/173768

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