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Structure. 2019 Apr 2;27(4):579-589.e5. doi: 10.1016/j.str.2019.01.004. Epub 2019 Feb 7.

Overall Structures of Mycobacterium tuberculosis DNA Gyrase Reveal the Role of a Corynebacteriales GyrB-Specific Insert in ATPase Activity.

Author information

1
Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France; Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France. Electronic address: stephanie.petrella@pasteur.fr.
2
Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses-Paris, Cimi-Paris, INSERM U1135, National Reference Center for Mycobacteria, Laboratoire de Bactériologie-Hygiène, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, 75013 Paris, France.
3
Plateforme de Biophysique Moléculaire, Institut Pasteur, CNRS UMR 3528, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France.
4
Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France; Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France.
5
Synchrotron SOLEIL, l'Orme des Merisiers, 91410 Saint Aubin, France.
6
Laboratoire de Biologie Physico-Chimique des Protéines Membranaires, Institut de Biologie Physico-Chimique, CNRS UMR7099 and Université Paris Didérot, 13 rue Pierre et Marie Curie, 75005 Paris, France.
7
Sorbonne Université, Centre d'Immunologie et des Maladies Infectieuses-Paris, Cimi-Paris, INSERM U1135, National Reference Center for Mycobacteria, Laboratoire de Bactériologie-Hygiène, AP-HP, Hôpitaux Universitaires Pitié-Salpêtrière - Charles Foix, 75013 Paris, France. Electronic address: alexandra.aubry@sorbonne-universite.fr.

Abstract

Despite sharing common features, previous studies have shown that gyrases from different species have been modified throughout evolution to modulate their properties. Here, we report two crystal structures of Mycobacterium tuberculosis DNA gyrase, an apo and AMPPNP-bound form at 2.6-Å and 3.3-Å resolution, respectively. These structures provide high-resolution structural data on the quaternary organization and interdomain connections of a gyrase (full-length GyrB-GyrA57)2 thus providing crucial inputs on this essential drug target. Together with small-angle X-ray scattering studies, they revealed an "extremely open" N-gate state, which persists even in the DNA-free gyrase-AMPPNP complex and an unexpected connection between the ATPase and cleavage core domains mediated by two Corynebacteriales-specific motifs, respectively the C-loop and DEEE-loop. We show that the C-loop participates in the stabilization of this open conformation, explaining why this gyrase has a lower ATPase activity. Our results image a conformational state which might be targeted for drug discovery.

KEYWORDS:

ATPase activity; Corynebacteriales; DNA gyrase; DNA-binding protein; Mycobacterium tuberculosis; SAXS experiments; X-ray structure; fluoroquinolone; molecular machine; type IIA topoisomerases

PMID:
30744994
DOI:
10.1016/j.str.2019.01.004

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