5N7O | pdb_00005n7o

EthR2 in complex with SMARt-420 compound

• PDB DOI: https://doi.org/10.2210/pdb5N7O/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2017-02-21 Released: 2017-04-26 
• Deposition Author(s): Wohlkonig, A., Wintjens, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.248 (Depositor), 0.257 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of the interaction between spiroisoxazoline SMARt-420 and the Mycobacterium tuberculosis repressor EthR2.

Wohlkonig, A., Remaut, H., Moune, M., Tanina, A., Meyer, F., Desroses, M., Steyaert, J., Willand, N., Baulard, A.R., Wintjens, R.

(2017) Biochem Biophys Res Commun 487: 403-408

• PubMed: 28416386 
• DOI: https://doi.org/10.1016/j.bbrc.2017.04.074
• Primary Citation Related Structures: 
  5N7O


• PubMed Abstract: 
  

  Inhibition of transcriptional regulators of bacterial pathogens with the aim of reprogramming their metabolism to modify their antibiotic susceptibility constitutes a promising therapeutic strategy. One example is the bio-activation of the anti-tubercular pro-drug ethionamide, which activity could be enhanced by inhibiting the transcriptional repressor EthR. Recently, we discovered that inhibition of a second transcriptional repressor, EthR2, leads to the awakening of a new ethionamide bio-activation pathway. The x-ray structure of EthR2 was solved at 2.3 Å resolution in complex with a compound called SMARt-420 (Small Molecule Aborting Resistance). Detailed comparison and structural analysis revealed interesting insights for the upcoming structure-based design of EthR2 inhibitors as an alternative to revert ethionamide resistance in Mycobacterium tuberculosis.

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Organizational Affiliation: 
• Center for Structural Biology, Vlaams Instituut voor Biotechnology (VIB), Pleinlaan 2, B-1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium.
Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France.
Laboratory of Biopolymers and Supramolecular Nanomaterials, Faculty of Pharmacy, Université Libre de Bruxelles, B-1050 Brussels, Belgium.
Univ. Lille, Inserm, Institut Pasteur de Lille, U1177 - Drugs and Molecules for Living Systems, F-59000 Lille, France.
Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204 - CIIL - Center for Infection and Immunity of Lille, F-59000 Lille, France. Electronic address: [e-mail].
Laboratory of Biopolymers and Supramolecular Nanomaterials, Faculty of Pharmacy, Université Libre de Bruxelles, B-1050 Brussels, Belgium. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 48.93 kDa 
• Atom Count: 2,968 
• Modeled Residue Count: 382 
• Deposited Residue Count: 442 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable transcriptional regulatory protein	A, B	221	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: Rv0078, LH57_00450
UniProt
Find proteins for O53623 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O53623  Go to UniProtKB:  O53623

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
69Y	C [auth A], D [auth B]	4,4,4-trifluoro-1-(3-phenyl-1-oxa-2,8-diazaspiro[4.5]dec-2-en-8-yl)butan-1-one C17 H19 F3 N2 O2 IBVDSAFESRHIBV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.248 (Depositor), 0.257 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.4	α = 90
b = 74.29	β = 90
c = 91.5	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-26 
Deposition Author(s): Wohlkonig, A., Wintjens, R.

Revision History  

• Version 1.0: 2017-04-26
  Type: Initial release
  
• Version 1.1: 2017-05-10
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description