6ZWT

Crystal structure of DNA-binding domain of OmpR of two-component system of Acinetobacter baumannii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Targeting virulence regulation to disarm Acinetobacter baumannii pathogenesis.

Trebosc, V.Lucchini, V.Narwal, M.Wicki, B.Gartenmann, S.Schellhorn, B.Schill, J.Bourotte, M.Frey, D.Grunberg, J.Trauner, A.Ferrari, L.Felici, A.Champion, O.L.Gitzinger, M.Lociuro, S.Kammerer, R.A.Kemmer, C.Pieren, M.

(2022) Virulence 13: 1868-1883

  • DOI: https://doi.org/10.1080/21505594.2022.2135273
  • Primary Citation of Related Structures:  
    6ZWT

  • PubMed Abstract: 

    The development of anti-virulence drug therapy against Acinetobacter baumannii infections would provide an alternative to traditional antibacterial therapy that are increasingly failing. Here, we demonstrate that the OmpR transcriptional regulator plays a pivotal role in the pathogenesis of diverse A. baumannii clinical strains in multiple murine and G. mellonella invertebrate infection models. We identified OmpR-regulated genes using RNA sequencing and further validated two genes whose expression can be used as robust biomarker to quantify OmpR inhibition in A. baumannii . Moreover, the determination of the structure of the OmpR DNA binding domain of A. baumannii and the development of in vitro protein-DNA binding assays enabled the identification of an OmpR small molecule inhibitor. We conclude that OmpR is a valid and unexplored target to fight A. baumannii infections and we believe that the described platform combining in silico methods, in vitro OmpR inhibitory assays and in vivo G. mellonella surrogate infection model will facilitate future drug discovery programs.


  • Organizational Affiliation

    BioVersys AG, Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Two-component response regulator
A, B, C, D
114Acinetobacter baumannii SDFMutation(s): 0 
Gene Names: ompRABSDF0250
UniProt
Find proteins for B0VPC9 (Acinetobacter baumannii (strain SDF))
Explore B0VPC9 
Go to UniProtKB:  B0VPC9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0VPC9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.47α = 90.07
b = 49.703β = 99.01
c = 52.727γ = 103.98
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
InnosuisseSwitzerland18838.1 PFLS-LS

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-11
    Type: Initial release
  • Version 1.1: 2023-03-01
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description