6NLM

1.90 A resolution structure of WT BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor (analog 15)

• PDB DOI:  https://doi.org/10.2210/pdb6NLM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-01-08 Released: 2019-05-08 
• Deposition Author(s): Lovell, S., Punchi-Hewage, A., Battaile, K.P., Yao, H., Nammalwar, B., Gnanasekaran, K.K., Bunce, R.A., Reitz, A.B., Rivera, M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.184 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 

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

• PubMed: 31038945 
• 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.

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Organizational Affiliation: 

Department of Chemistry , Louisiana State University , 229A Choppin Hall , Baton Rouge , Louisiana 70803 , United States.

Biological Assembly 1  

Global Symmetry: Octahedral - O  (3D View)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 234.66 kDa 
• Atom Count: 17,216 
• Modelled Residue Count: 1,863 
• Deposited Residue Count: 1,896 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferroxidase	A, B, C, D, E, F, G, H, I, J, K, L	158	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: bfrB, PA3531 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	BA [auth D], IA [auth F], NA [auth H], O [auth A], S [auth B], X [auth C], YA [auth L]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
KT1	AA [auth D], EA [auth E], HA [auth F], KA [auth G], MA [auth H], N [auth A], QA [auth I], R [auth B], SA [auth J], VA [auth K], W [auth C], XA [auth L]	4-{[3-(4-hydroxy-2-methoxyphenyl)propyl]amino}-1H-isoindole-1,3(2H)-dione C18 H18 N2 O4 MCHANSUEWHRRRQ-UHFFFAOYSA-N
PG4	CA [auth D], DA [auth D], FA [auth E], GA [auth E], JA [auth F], LA [auth G], OA [auth H], P [auth A], PA [auth H], RA [auth I], T [auth B], TA [auth J], U [auth B], UA [auth J], V [auth B], WA [auth K], Y [auth C]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
FE2	M [auth A], Q [auth B], Z [auth D]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
KT1	Binding MOAD:  6NLM	Kd: 5000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.184 
• R-Value Work: 0.152 
• R-Value Observed: 0.153 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 130.247	α = 90
b = 194.97	β = 90
c = 203.03	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-05-08 
Deposition Author(s): Lovell, S., Punchi-Hewage, A., Battaile, K.P., Yao, H., Nammalwar, B., Gnanasekaran, K.K., Bunce, R.A., Reitz, A.B., Rivera, M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI125529
National Science Foundation (NSF, United States)	United States	MCB1615767
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30 GM110761

Revision History  

• 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