6ENG | pdb_00006eng

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.257 (Depositor), 0.274 (DCC)
R-Value Work:
0.200 (Depositor), 0.213 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.8b01928
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0AES6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BHW Query on BHW Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	Coumermycin A1 C₅₅ H₅₉ N₅ O₂₀ WTIJXIZOODAMJT-DHFGXMAYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], L [auth B], M [auth B], N [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], J [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain O [auth B] SDF format, chain F [auth A] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A] mmCIF format, chain O [auth B] mmCIF format, chain F [auth A]	F [auth A], O [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain O [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.257 (Depositor), 0.274 (DCC)
R-Value Work: 0.200 (Depositor), 0.213 (DCC)
R-Value Observed: 0.203 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-04-10

Deposition Author(s):

Vanden Broeck, A.

McEwen, A.G.

Lamour, V.

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 (Full details and data files)

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