1.65 A resolution structure of Apo BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor (analog 12)

Experimental Data Snapshot

  • Resolution: 1.65 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Small Molecule Inhibitors of the BfrB-Bfd Interaction Decrease Pseudomonas aeruginosa Fitness and Potentiate Fluoroquinolone Activity.

Punchi Hewage, A.N.D.Yao, H.Nammalwar, B.Gnanasekaran, K.K.Lovell, S.Bunce, R.A.Eshelman, K.Phaniraj, S.M.Lee, M.M.Peterson, B.R.Battaile, K.P.Reitz, A.B.Rivera, M.

(2019) J Am Chem Soc 141: 8171-8184

  • DOI: https://doi.org/10.1021/jacs.9b00394
  • Primary Citation of Related Structures:  
    6NLF, 6NLG, 6NLI, 6NLJ, 6NLK, 6NLL, 6NLM, 6NLN

  • PubMed Abstract: 

    The iron storage protein bacterioferritin (BfrB) is central to bacterial iron homeostasis. The mobilization of iron from BfrB, which requires binding by a cognate ferredoxin (Bfd), is essential to the regulation of cytosolic iron levels in P. aeruginosa. This paper describes the structure-guided development of small molecule inhibitors of the BfrB-Bfd protein-protein interaction. The process was initiated by screening a fragment library and followed by obtaining the structure of a fragment hit bound to BfrB. The structural insights were used to develop a series of 4-(benzylamino)- and 4-((3-phenylpropyl)amino)-isoindoline-1,3-dione analogs that selectively bind BfrB at the Bfd binding site. Challenging P. aeruginosa cells with the 4-substituted isoindoline analogs revealed a dose-dependent growth phenotype. Further investigation determined that the analogs elicit a pyoverdin hyperproduction phenotype that is consistent with blockade of the BfrB-Bfd interaction and ensuing irreversible accumulation of iron in BfrB, with concomitant depletion of iron in the cytosol. The irreversible accumulation of iron in BfrB prompted by the 4-substituted isoindoline analogs was confirmed by visualization of BfrB-iron in P. aeruginosa cell lysates separated on native PAGE gels and stained for iron with Ferene S. Challenging P. aeruginosa cultures with a combination of commercial fluoroquinolone and our isoindoline analogs results in significantly lower cell survival relative to treatment with either antibiotic or analog alone. Collectively, these findings furnish proof of concept for the usefulness of small molecule probes designed to dysregulate bacterial iron homeostasis by targeting a protein-protein interaction pivotal for iron storage in the bacterial cell.

  • Organizational Affiliation

    Department of Chemistry , University of Kansas , 2030 Becker Drive , Lawrence , Kansas 66047 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
158Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: bfrBPA3531
Find proteins for Q9HY79 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HY79 
Go to UniProtKB:  Q9HY79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HY79
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.65 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.291α = 90
b = 195.014β = 90
c = 203.22γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI125529
National Science Foundation (NSF, United States)United StatesMCB1615767
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30 GM110761

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-06-19
    Changes: Data collection, Database references
  • Version 1.2: 2019-06-26
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description