Extremely 'open' clamp structure of DNA gyrase: role of the Corynebacteriales GyrB specific insert

Experimental Data Snapshot

  • Resolution: 3.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


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

Petrella, S.Capton, E.Raynal, B.Giffard, C.Thureau, A.Bonnete, F.Alzari, P.M.Aubry, A.Mayer, C.

(2019) Structure 27: 579-589.e5

  • DOI: https://doi.org/10.1016/j.str.2019.01.004
  • Primary Citation of Related Structures:  
    6GAU, 6GAV

  • PubMed 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.

  • Organizational Affiliation

    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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA gyrase subunit B,DNA gyrase subunit A
A, B
1,179Mycobacterium tuberculosisMutation(s): 0 
Gene Names: gyrBgyrARv0006MTCY10H4.04
Find proteins for P9WG47 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WG47 
Go to UniProtKB:  P9WG47
Find proteins for P9WG45 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WG45 
Go to UniProtKB:  P9WG45
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP9WG45P9WG47
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.30 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.177 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.523α = 75.64
b = 96.782β = 64.44
c = 105.791γ = 65.8
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-02-20
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-05-08
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2019-10-16
    Changes: Data collection
  • Version 1.4: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description