Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex.

Acenaphthenes; Anti-Bacterial Agents; Heterocyclic Compounds, 3-Ring; Multiprotein Complexes; Nucleoproteins; DVF0PR037D (gepotidacin); EC 5.99.1.3 (DNA Gyrase); Acenaphthenes/metabolism; Anti-Bacterial Agents/metabolism; Cryoelectron Microscopy; DNA Gyrase/metabolism/ultrastructure; Escherichia coli; Heterocyclic Compounds, 3-Ring/metabolism; Models, Molecular; Multiprotein Complexes/ultrastructure; Nucleoproteins/metabolism/ultrastructure; Single Molecule Imaging

Abstract :

[en] 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.

Disciplines :

Biochemistry, biophysics & molecular biology

Author, co-author :

Vanden Broeck, Arnaud ; Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France. ; Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France. ; Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France. ; Université de Strasbourg, Illkirch, France.

Lotz, Christophe ; Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France. ; Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France. ; Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France. ; Université de Strasbourg, Illkirch, France.

Ortiz, Julio ; Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France. ; Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France. ; Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France. ; Université de Strasbourg, Illkirch, France.

Lamour, Valérie ; Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch Cedex, France. lamourv@igbmc.fr. ; Centre National de Recherche Scientifique (CNRS) UMR 7104, Illkirch, France. lamourv@igbmc.fr. ; Institut National de Santé et de Recherche Médicale (INSERM) U1258, Illkirch, France. lamourv@igbmc.fr. ; Université de Strasbourg, Illkirch, France. lamourv@igbmc.fr. ; Hôpitaux Universitaires de Strasbourg, 1 Place de l'Hôpital, 67091, Strasbourg Cedex, France. lamourv@igbmc.fr.

Language :

English

Title :

Cryo-EM structure of the complete E. coli DNA gyrase nucleoprotein complex.

Publication date :

30 October 2019

Journal title :

Nature Communications

eISSN :

2041-1723

Publisher :

Nature Publishing Group, London, Gb

Volume :

Issue :

Pages :

4935

Peer reviewed :

Peer Reviewed verified by ORBi

Available on ORBi :

since 01 October 2024

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