6RKS

E. coli DNA Gyrase - DNA binding and cleavage domain in State 1 without TOPRIM insertion

Summary for 6RKS

• Entry DOI: 10.2210/pdb6rks/pdb
• EMDB information: 4909
• Descriptor: DNA gyrase subunit A, DNA gyrase subunit B, DNA Strand 1, ... (5 entities in total)
• Functional Keywords: isomerase, complex, dna gyrase, inhibitor, dna binding protein
• Biological source: Escherichia coli K-12; More
• Total number of polymer chains: 8
• Total formula weight: 394364.33

Authors

Vanden Broeck, A.,Lamour, V. (deposition date: 2019-04-30, release date: 2019-11-06, Last modification date: 2024-05-22)

Primary citation

Vanden Broeck, A.,Lotz, C.,Ortiz, J.,Lamour, V.
Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex.
Nat Commun, 10:4935-4935, 2019

PubMed Abstract: DNA gyrase is an essential enzyme involved in the homeostatic control of DNA supercoiling and the target of successful antibacterial compounds. Despite extensive studies, a detailed architecture of the full-length DNA gyrase from the model organism E. coli is still missing. Herein, we report the complete structure of the E. coli DNA gyrase nucleoprotein complex trapped by the antibiotic gepotidacin, using phase-plate single-particle cryo-electron microscopy. Our data unveil the structural and spatial organization of the functional domains, their connections and the position of the conserved GyrA-box motif. The deconvolution of two states of the DNA-binding/cleavage domain provides a better understanding of the allosteric movements of the enzyme complex. The local atomic resolution in the DNA-bound area reaching up to 3.0 Å enables the identification of the antibiotic density. Altogether, this study paves the way for the cryo-EM determination of gyrase complexes with antibiotics and opens perspectives for targeting conformational intermediates.

PubMed: 31666516
DOI: 10.1038/s41467-019-12914-y

Experimental method

ELECTRON MICROSCOPY (4 Å)