6ENG

Crystal structure of the 43K ATPase domain of Escherichia coli gyrase B in complex with an aminocoumarin

• PDB DOI: https://doi.org/10.2210/pdb6ENG/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-10-04 Released: 2019-04-10 
• Deposition Author(s): Vanden Broeck, A., McEwen, A.G., Lamour, V.
• Funding Organization(s): French National Research Agency

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.257 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

Starting Model: experimental

Literature

Structural Basis for DNA Gyrase Interaction with Coumermycin A1.

Vanden Broeck, A., McEwen, A.G., Chebaro, Y., Potier, N., Lamour, V.

(2019) J Med Chem 62: 4225-4231

• PubMed: 30920824 
• DOI: https://doi.org/10.1021/acs.jmedchem.8b01928
• Primary Citation of Related Structures:  
  6ENG, 6ENH


• PubMed Abstract: 
  

  Coumermycin A1 is a natural aminocoumarin that inhibits bacterial DNA gyrase, a member of the GHKL proteins superfamily. We report here the first cocrystal structures of gyrase B bound to coumermycin A1, revealing that one coumermycin A1 molecule traps simultaneously two ATP-binding sites. The inhibited dimers from different species adopt distinct sequence-dependent conformations, alternative to the ATP-bound form. These structures provide a basis for the rational development of coumermycin A1 derivatives for antibiotherapy and biotechnology applications.

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Organizational Affiliation: 

Integrated Structural Biology Department, IGBMC, UMR7104 CNRS, U1258 Inserm, University of Strasbourg, Illkirch 67404 , France.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: SAXS, gel filtration, mass spectrometry

Macromolecule Content

• Total Structure Weight: 89.47 kDa 
• Atom Count: 6,407 
• Modelled Residue Count: 750 
• Deposited Residue Count: 792 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	A, B	396	Escherichia coli K-12	Mutation(s): 0  Gene Names: gyrB, acrB, cou, himB, hisU, nalC, parA, pcbA, b3699, JW5625 EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0AES6 (Escherichia coli (strain K12)) Explore P0AES6  Go to UniProtKB:  P0AES6

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BHW	K [auth B]	Coumermycin A1 C55 H59 N5 O20 WTIJXIZOODAMJT-DHFGXMAYSA-N
PG4	E [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PO4	C [auth A], D [auth A], L [auth B], M [auth B], N [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
K	H [auth A], I [auth A], J [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
CL	F [auth A], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.257 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.83	α = 90
b = 128.07	β = 90
c = 159.76	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
BUSTER	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-04-10 
Deposition Author(s): Vanden Broeck, A., McEwen, A.G., Lamour, V.

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Funding Organization	Location	Grant Number
French National Research Agency	France	ANR-10-INSB-05-01
French National Research Agency	France	ANR-10-LABX-0030-INRT

Revision History  

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