Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 28314.77 
• Atom Count: 1533 
• Residue Count: 255 
• Unique protein chains: 1

3G1O

EthR from Mycobacterium tuberculosis in complex with compound BDM14500

• DOI: 10.2210/pdb3G1O/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
• Expression System: Escherichia coli


• Deposited: 2009-01-30 Released: 2009-07-21 
• Deposition Author(s): Willand, N., Dirie, B., Carette, X., Bifani, P., Singhal, A., Desroses, M., Leroux, F., Willery, E., Mathys, V., Deprez-Poulain, R., Delcroix, G., Frenois, F., Aumercier, M., Locht, C., Villeret, V., Deprez, B., Baulard, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.277 
• R-Value Work: 0.208 

Literature

Synthetic EthR inhibitors boost antituberculous activity of ethionamide.

Willand, N., Dirie, B., Carette, X., Bifani, P., Singhal, A., Desroses, M., Leroux, F., Willery, E., Mathys, V., Deprez-Poulain, R., Delcroix, G., Frenois, F., Aumercier, M., Locht, C., Villeret, V., Deprez, B., Baulard, A.R.

(2009) NAT.MED. (N.Y.) 15: 537-544

• PubMed: 19412174 
• DOI: 10.1038/nm.1950
• Primary Citation of Related Structures:  
  3G1M, 3G1L
• Also Cited By: 3QPL


• PubMed Abstract: 
  

The side effects associated with tuberculosis therapy bring with them the risk of noncompliance and subsequent drug resistance. Increasing the therapeutic index of antituberculosis drugs should thus improve treatment effectiveness. Several antituberculosis compounds require in situ metabolic activation to become inhibitory. Various thiocarbamide-containing drugs, including ethionamide, are activated by the mycobacterial monooxygenase EthA, the production of which is controlled by the transcriptional repressor EthR. Here we identify drug-like inhibitors of EthR that boost the bioactivation of ethionamide. Compounds designed and screened for their capacity to inhibit EthR-DNA interaction were co-crystallized with EthR. We exploited the three-dimensional structures of the complexes for the synthesis of improved analogs that boosted the ethionamide potency in culture more than tenfold. In Mycobacterium tuberculosis-infected mice, one of these analogs, BDM31343, enabled a substantially reduced dose of ethionamide to lessen the mycobacterial load as efficiently as the conventional higher-dose treatment. This provides proof of concept that inhibiting EthR improves the therapeutic index of thiocarbamide derivatives, which should prompt reconsideration of their use as first-line drugs.

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Related Citations: 

• EthR, a repressor of the TetR/CamR family implicated in ethionamide resistance in mycobacteria, octamerizes cooperatively on its operator.
  Engohang-Ndong, J.,Baillat, D.,Aumercier, M.,Bellefontaine, F.,Besra, G.S.,Locht, C.,Baulard, A.R.
  (2004) Mol.Microbiol. 51: 175
• Structure of EthR in a ligand bound conformation reveals therapeutic perspectives against tuberculosis.
  Frenois, F.,Engohang-Ndong, J.,Locht, C.,Baulard, A.R.,Villeret, V.
  (2004) Mol.Cell 16: 301
• Insights into mechanisms of induction and ligands recognition in the transcriptional repressor EthR from Mycobacterium tuberculosis.
  Frenois, F.,Baulard, A.R.,Villeret, V.
  (2006) Tuberculosis 86: 110




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Organizational Affiliation: 

Institut National de la Santé et de la Recherche Médicale, Lille, France.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
TRANSCRIPTIONAL REGULATORY REPRESSOR PROTEIN (TETR-FAMILY) ETHR	A	255	Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)	Mutation(s): 0  Gene Names: ethR (etaR)
Find proteins for P9WMC1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Go to UniProtKB:  P9WMC1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
RF1	A	tert-butyl 4-(3-thiophen-2-yl-1,2,4-oxadiazol-5-yl)piperidine-1-carboxylate C16 H21 N3 O3 S METBQPRXNZHZMB-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
RF1	IC50: 38000 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.277 
• R-Value Work: 0.208 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 121.230	α = 90.00
b = 121.230	β = 90.00
c = 33.680	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data scaling
REFMAC	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-01-30 
• Released Date: 2009-07-21 
• Deposition Author(s): Willand, N., Dirie, B., Carette, X., Bifani, P., Singhal, A., Desroses, M., Leroux, F., Willery, E., Mathys, V., Deprez-Poulain, R., Delcroix, G., Frenois, F., Aumercier, M., Locht, C., Villeret, V., Deprez, B., Baulard, A.R.

Revision History 

• Version 1.0: 2009-07-21
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance
• Version 1.2: 2014-02-19
  Type: Database references