6NLI

1.90 A resolution structure of WT BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor (analog 11)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

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: 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 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 , Louisiana State University , 229A Choppin Hall , Baton Rouge , Louisiana 70803 , United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ferroxidase
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J, K, L
158Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: bfrBPA3531
EC: 1.16.3.1
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
BA [auth E], EA [auth F], MA [auth J], N [auth A], QA [auth L], T [auth C], X [auth D]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
KTM (Subject of Investigation/LOI)
Query on KTM

Download Ideal Coordinates CCD File 
CA [auth E] , HA [auth G] , JA [auth H] , LA [auth I] , NA [auth J] , O [auth A] , R [auth B] , U [auth C] , 
CA [auth E], HA [auth G], JA [auth H], LA [auth I], NA [auth J], O [auth A], R [auth B], U [auth C], Y [auth D]
4-{[(2-hydroxyphenyl)methyl]amino}-1H-isoindole-1,3(2H)-dione
C15 H12 N2 O3
LGIZVMOUWUZRKO-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

Download Ideal Coordinates CCD File 
AA [auth D] , DA [auth E] , FA [auth F] , GA [auth F] , IA [auth G] , KA [auth H] , OA [auth J] , P [auth A] , 
AA [auth D], DA [auth E], FA [auth F], GA [auth F], IA [auth G], KA [auth H], OA [auth J], P [auth A], PA [auth K], RA [auth L], S [auth B], V [auth C], Z [auth D]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download Ideal Coordinates CCD File 
M [auth A], Q [auth B], W [auth D]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
KTM Binding MOAD:  6NLI Kd: 1.10e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.168 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.546α = 90
b = 194.227β = 90
c = 202.759γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



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