8S7O | pdb_00008s7o

M. tuberculosis gyrase holocomplex with 150 bp DNA and BDM71403

• PDB DOI: https://doi.org/10.2210/pdb8S7O/pdb
• EM Map EMD-19782: EMDB EMDataResource
• NAKB: 8S7O

• Classification: DNA BINDING PROTEIN
• Organism(s): Mycobacterium tuberculosis, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-03-04 Released: 2025-03-19 
• Deposition Author(s): Gedeon, A., Yab, E., Dinut, A., Sadowski, E., Capton, E., Dreneau, A., Gioia, B., Piveteau, C., Djaout, K., Lecat, E., Wehenkel, A.M., Gubellini, F., Mechaly, A., Alzari, P.M., Deprez, B., Baulard, A., Aubry, A., Willand, N., Petrella, S.
• Funding Organization(s): IdEx Universite Paris Cite, Agence Nationale de la Recherche (ANR), Fondation pour la Recherche Medicale (FRM)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular mechanism of a triazole-containing inhibitor of Mycobacterium tuberculosis DNA gyrase.

Gedeon, A., Yab, E., Dinut, A., Sadowski, E., Capton, E., Dreneau, A., Petit, J., Gioia, B., Piveteau, C., Djaout, K., Lecat, E., Wehenkel, A.M., Gubellini, F., Mechaly, A., Alzari, P.M., Deprez, B., Baulard, A., Aubry, A., Willand, N., Petrella, S.

(2024) iScience 27: 110967-110967

• PubMed: 39429773 
• DOI: https://doi.org/10.1016/j.isci.2024.110967
• Primary Citation Related Structures: 
  8S7K, 8S7O


• PubMed Abstract: 
  

  Antimicrobial resistance remains a persistent and pressing public health concern. Here, we describe the synthesis of original triazole-containing inhibitors targeting the DNA gyrase, a well-validated drug target for developing new antibiotics. Our compounds demonstrate potent antibacterial activity against various pathogenic bacteria, with notable potency against Mycobacterium tuberculosis ( Mtb ). Moreover, one hit, compound 10a , named BDM71403, was shown to be more potent in Mtb than the NBTI of reference, gepotidacin. Mechanistic enzymology assays reveal a competitive interaction of BDM71403 with fluoroquinolones within the Mtb gyrase cleavage core. High-resolution cryo-electron microscopy structural analysis provides detailed insights into the ternary complex formed by the Mtb gyrase, double-stranded DNA, and either BDM71403 or gepotidacin, providing a rational framework to understand the superior in vitro efficacy on Mtb . This study highlights the potential of triazole-based scaffolds as promising gyrase inhibitors, offering new avenues for drug development in the fight against antimicrobial resistance.

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Organizational Affiliation: 
• Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Unité de Microbiologie Structurale, 75015 Paris, France.
Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for living Systems, 59000 Lille, France.
Cimi-Paris, INSERM U1135, Sorbonne Université, AP-HP. Sorbonne Université, Laboratoire de Bactériologie-Hygiène, CNR des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, 75005 Paris, France.
Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Center for Infection and Immunity of Lille, 59000 Lille, France.
Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Bacterial Cell Cycle Mechanisms Unit, 75015 Paris, France.
Institut Pasteur, Plate-Forme de Cristallographie, CNRS UMR 3528, 75015 Paris, France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 426.52 kDa 
• Atom Count: 11,253 
• Modeled Residue Count: 1,381 
• Deposited Residue Count: 3,330 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit A	A, C	837	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: gyrA, Rv0006, MTCY10H4.04 EC: 5.6.2.2
UniProt
Find proteins for P9WG47 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WG47  Go to UniProtKB:  P9WG47

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	B, D	678	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: gyrB, Rv0005, MTCY10H4.03 EC: 5.6.2.2
UniProt
Find proteins for P9WG45 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WG45  Go to UniProtKB:  P9WG45

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*GP*AP*AP*GP*GP*GP*GP*TP*AP*AP*TP*AP*CP*T)-3')	E	150	synthetic construct

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*GP*AP*AP*GP*GP*GP*GP*TP*AP*AP*TP*AP*CP*T)-3')	F	150	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1H5Q (Subject of Investigation/LOI)	G [auth E]	6-[[2-[1-(6-methoxy-1,5-naphthyridin-4-yl)-1,2,3-triazol-4-yl]ethylamino]methyl]-4H-1,4-benzothiazin-3-one C22 H21 N7 O2 S IFTKOVLUZDBNBQ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487:

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-03-19 
Deposition Author(s): Gedeon, A., Yab, E., Dinut, A., Sadowski, E., Capton, E., Dreneau, A., Gioia, B., Piveteau, C., Djaout, K., Lecat, E., Wehenkel, A.M., Gubellini, F., Mechaly, A., Alzari, P.M., Deprez, B., Baulard, A., Aubry, A., Willand, N., Petrella, S.

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Funding Organization	Location	Grant Number
IdEx Universite Paris Cite	France	--
Agence Nationale de la Recherche (ANR)	France	ANR-18-IDEX-0001
Fondation pour la Recherche Medicale (FRM)	France	EQU202303016284

Revision History  

• Version 1.0: 2025-03-19
  Type: Initial release
  
• Version 1.1: 2026-05-13
  Changes: Data collection, Database references