5E3J

The response regulator RstA is a potential drug target for Acinetobacter baumannii


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The Response Regulator BfmR Is a Potential Drug Target for Acinetobacter baumannii.

Russo, T.A.Manohar, A.Beanan, J.M.Olson, R.MacDonald, U.Graham, J.Umland, T.C.

(2016) mSphere 1

  • DOI: https://doi.org/10.1128/mSphere.00082-16
  • Primary Citation of Related Structures:  
    5E3J

  • PubMed Abstract: 

    Identification and validation is the first phase of target-based antimicrobial development. BfmR (RstA), a response regulator in a two-component signal transduction system (TCS) in Acinetobacter baumannii, is an intriguing potential antimicrobial target. A unique characteristic of BfmR is that its inhibition would have the dual benefit of significantly decreasing in vivo survival and increasing sensitivity to selected antimicrobials. Studies on the clinically relevant strain AB307-0294 have shown BfmR to be essential in vivo. Here, we demonstrate that this phenotype in strains AB307-0294 and AB908 is mediated, in part, by enabling growth in human ascites fluid and serum. Further, BfmR conferred resistance to complement-mediated bactericidal activity that was independent of capsular polysaccharide. Importantly, BfmR also increased resistance to the clinically important antimicrobials meropenem and colistin. BfmR was highly conserved among A. baumannii strains. The crystal structure of the receiver domain of BfmR was determined, lending insight into putative ligand binding sites. This enabled an in silico ligand binding analysis and a blind docking strategy to assess use as a potential druggable target. Predicted binding hot spots exist at the homodimer interface and the phosphorylation site. These data support pursuing the next step in the development process, which includes determining the degree of inhibition needed to impact growth/survival and the development a BfmR activity assay amenable to high-throughput screening for the identification of inhibitors. Such agents would represent a new class of antimicrobials active against A. baumannii which could be active against other Gram-negative bacilli that possess a TCS with shared homology. IMPORTANCE Increasing antibiotic resistance in bacteria, particularly Gram-negative bacilli, has significantly affected the ability of physicians to treat infections, with resultant increased morbidity, mortality, and health care costs. In fact, some strains of bacteria are resistant to all available antibiotics, such as Acinetobacter baumannii, which is the focus of this report. Therefore, the development of new antibiotics active against these resistant strains is urgently needed. In this study, BfmR is further validated as an intriguing target for a novel class of antibiotics. Successful inactivation of BfmR would confer the multiple benefits of a decreased ability of A. baumannii to survive in human body fluids, increased sensitivity to complement-mediated bactericidal activity and, importantly, increased sensitivity to other antibiotics. Structural studies support the potential for this "druggable" target, as they identify the potential for small-molecule binding at functionally relevant sites. Next-phase high-throughput screening studies utilizing BfmR are warranted.


  • Organizational Affiliation

    Veterans Administration Western New York Healthcare System, Buffalo, New York, USA; Department of Medicine, University at Buffalo, State University of New York, Buffalo, New York, USA; Department of Microbiology and Immunology, University at Buffalo, State University of New York, Buffalo, New York, USA; The Witebsky Center for Microbial Pathogenesis, University at Buffalo, State University of New York, Buffalo, New York, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Response regulator RstA
A, B
132Acinetobacter baumannii AB307-0294Mutation(s): 0 
Gene Names: ABBFA_002866
UniProt
Find proteins for D0C9D6 (Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / JCM 6841 / CCUG 19606 / CIP 70.34 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81))
Explore D0C9D6 
Go to UniProtKB:  D0C9D6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD0C9D6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.015α = 90
b = 52.015β = 90
c = 197.861γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Blu-Icedata collection
SCALEPACKdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Telemedicine and Advance Technical Research CenterUnited StatesW23RYX1055N607
Interdisciplinary Grant from the University at BuffaloUnited States--
Veterans AdministrationUnited States--
Department of Energy (DOE, United States)United StatesDE-AC02-76SF00515
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41GM103393

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-06-29
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description