7K5E | pdb_00007k5e

1.75 A resolution structure of WT BfrB from Pseudomonas aeruginosa in complex with a protein-protein interaction inhibitor JAG-5-7

PDB DOI: https://doi.org/10.2210/pdb7K5E/pdb

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

Deposited: 2020-09-16 Released: 2020-12-16
Deposition Author(s): Lovell, S., Battaile, K.P., Soldano, A., Punchi-Hewage, A., Meraz, K., Annor-Gyamfi, J.K., Yao, H., Bunce, R.A., Rivera, M.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.213 (Depositor), 0.219 (DCC)
R-Value Work:
0.182 (Depositor), 0.192 (DCC)
R-Value Observed:
0.183 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Small Molecule Inhibitors of the Bacterioferritin (BfrB)-Ferredoxin (Bfd) Complex Kill Biofilm-Embedded Pseudomonas aeruginosa Cells.

Soldano, A., Yao, H., Punchi Hewage, A.N.D., Meraz, K., Annor-Gyamfi, J.K., Bunce, R.A., Battaile, K.P., Lovell, S., Rivera, M.

(2021) ACS Infect Dis 7: 123-140

PubMed: 33269912 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acsinfecdis.0c00669
Primary Citation Related Structures:
7K5E, 7K5F, 7K5G, 7K5H

PubMed Abstract:
Bacteria depend on a well-regulated iron homeostasis to survive adverse environments. A key component of the iron homeostasis machinery is the compartmentalization of Fe ³⁺ in bacterioferritin and its subsequent mobilization as Fe ²⁺ to satisfy metabolic requirements. In Pseudomonas aeruginosa Fe ³⁺ is compartmentalized in bacterioferritin (BfrB), and its mobilization to the cytosol requires binding of a ferredoxin (Bfd) to reduce the stored Fe ³⁺ and release the soluble Fe ²⁺. Blocking the BfrB-Bfd complex in P. aeruginosa by deletion of the bfd gene triggers an irreversible accumulation of Fe ³⁺ in BfrB, concomitant cytosolic iron deficiency and significant impairment of biofilm development. Herein we report that small molecules developed to bind BfrB at the Bfd binding site block the BfrB-Bfd complex, inhibit the mobilization of iron from BfrB in P. aeruginosa cells, elicit a bacteriostatic effect on planktonic cells, and are bactericidal to cells embedded in mature biofilms.

Organizational Affiliation

Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, Louisiana 70803, United States.

Macromolecule Content

Total Structure Weight: 229.68 kDa
Atom Count: 17,271
Modeled Residue Count: 1,872
Deposited Residue Count: 1,896
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ferroxidase	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9HY79
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain DA [auth L] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain Z [auth H] SDF format, chain X [auth F] SDF format, chain P [auth B] SDF format, chain N [auth A] MOL2 format, chain DA [auth L] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Z [auth H] MOL2 format, chain X [auth F] MOL2 format, chain P [auth B] MOL2 format, chain N [auth A] mmCIF format, chain DA [auth L] mmCIF format, chain R [auth C] mmCIF format, chain U [auth D] mmCIF format, chain Z [auth H] mmCIF format, chain X [auth F] mmCIF format, chain P [auth B] mmCIF format, chain N [auth A]	DA [auth L] N [auth A] P [auth B] R [auth C] U [auth D] DA [auth L], N [auth A], P [auth B], R [auth C], U [auth D], X [auth F], Z [auth H]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain DA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth F] Focus chain Z [auth H] Interactions & Density Focus chain DA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth F] Focus chain Z [auth H]
VXM (Subject of Investigation/LOI) Query on VXM Download:Ideal Coordinates CCD File SDF format, chain AA [auth H] SDF format, chain CA [auth J] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth G] SDF format, chain W [auth E] SDF format, chain BA [auth I] MOL2 format, chain AA [auth H] MOL2 format, chain CA [auth J] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth G] MOL2 format, chain W [auth E] MOL2 format, chain BA [auth I] mmCIF format, chain AA [auth H] mmCIF format, chain CA [auth J] mmCIF format, chain Q [auth B] mmCIF format, chain S [auth C] mmCIF format, chain V [auth D] mmCIF format, chain Y [auth G] mmCIF format, chain W [auth E] mmCIF format, chain BA [auth I]	AA [auth H] BA [auth I] CA [auth J] Q [auth B] S [auth C] AA [auth H], BA [auth I], CA [auth J], Q [auth B], S [auth C], V [auth D], W [auth E], Y [auth G]	4-{[(5-fluoro-2-hydroxyphenyl)methyl]amino}-1H-isoindole-1,3(2H)-dione C₁₅ H₁₁ F N₂ O₃ KOZDXWZBBVAXGG-UHFFFAOYSA-N		Interactions Focus chain AA [auth H] Focus chain BA [auth I] Focus chain CA [auth J] Focus chain Q [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth E] Focus chain Y [auth G] Interactions & Density Focus chain AA [auth H] Focus chain BA [auth I] Focus chain CA [auth J] Focus chain Q [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain W [auth E] Focus chain Y [auth G]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain T [auth D] SDF format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain T [auth D] MOL2 format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain T [auth D] mmCIF format, chain O [auth B]	M [auth A], O [auth B], T [auth D]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain O [auth B] Focus chain T [auth D] Interactions & Density Focus chain M [auth A] Focus chain O [auth B] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.213 (Depositor), 0.219 (DCC)
R-Value Work: 0.182 (Depositor), 0.192 (DCC)
R-Value Observed: 0.183 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.852	α = 90
b = 194.284	β = 90
c = 203.14	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-12-16

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI125529

Revision History (Full details and data files)

Version 1.0: 2020-12-16
Type: Initial release
Version 1.1: 2021-01-20
Changes: Database references
Version 1.2: 2023-10-18
Changes: Data collection, Database references, Refinement description