9GGQ

E.coli gyrase holocomplex with cleaved chirally wrapped 217 bp DNA fragment and moxifloxacin

Summary for 9GGQ

• Entry DOI: 10.2210/pdb9ggq/pdb
• Related: 9GBV
• EMDB information: 51339
• Descriptor: DNA gyrase subunit A, DNA gyrase subunit B, Mu217R, ... (7 entities in total)
• Functional Keywords: dna gyrase, type ii topoisomerase, moxifloxacin, dna crossover, isomerase
• Biological source: Escherichia coli; More
• Total number of polymer chains: 8
• Total formula weight: 642648.89

Authors

Ghilarov, D.,Heddle, J.G.,Pabis, M. (deposition date: 2024-08-13, release date: 2024-09-11, Last modification date: 2024-12-04)

Primary citation

Michalczyk, E.,Pakosz-Stepien, Z.,Liston, J.D.,Gittins, O.,Pabis, M.,Heddle, J.G.,Ghilarov, D.
Structural basis of chiral wrap and T-segment capture by Escherichia coli DNA gyrase.
Proc.Natl.Acad.Sci.USA, 121:e2407398121-e2407398121, 2024

PubMed 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 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.

PubMed: 39589884
DOI: 10.1073/pnas.2407398121

Experimental method

ELECTRON MICROSCOPY (2.6 Å)