Structural basis of chiral wrap and T-segment capture by <i>Escherichia coli</i> DNA gyrase

Journal article

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

Authors: Michalczyk, E; Pakosz-Stępień, Z; Liston, JD; Gittins, O; Pabis, M

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: National Academy of Sciences
• Journal: Proceedings of the National Academy of Sciences
• Volume: 121
• Issue: 49
• Pages: e2407398121-e2407398121
• Publication date: 2024-11-26
• DOI: 10.1073/pnas.2407398121
• EISSN: 1091-6490
• ISSN: 0027-8424
• Language: English
• Keywords: Crystallography; Gene; Biochemistry; Biology; Topoisomerase; Biophysics; DNA gyrase; Chemistry; Stereochemistry; DNA replication; ATP hydrolysis; Escherichia coli; Enzyme; ATPase; DNA; DNA supercoil