Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 24.61 kDa 
• Atom Count: 1619 
• Residue Count: 203 
• Unique protein chains: 1

4JVI

Crystal structure of PqsR co-inducer binding domain of Pseudomonas aeruginosa with inhibitor 3NH2-7Cl-C9QZN

• DOI: 10.2210/pdb4JVI/pdb

• Classification: TRANSCRIPTION REGULATOR/INHIBITOR
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-03-25 Released: 2013-08-07 
• Deposition Author(s): Ilangovan, A., Williams, P., Emsley, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.263 
• R-Value Work: 0.204 
• R-Value Observed: 0.207 

Literature

Structural basis for native agonist and synthetic inhibitor recognition by the Pseudomonas aeruginosa quorum sensing regulator PqsR (MvfR).

Ilangovan, A., Fletcher, M., Rampioni, G., Pustelny, C., Rumbaugh, K., Heeb, S., Camara, M., Truman, A., Chhabra, S.R., Emsley, J., Williams, P.

(2013) PLoS Pathog 9: e1003508-e1003508

• PubMed: 23935486 
• DOI: 10.1371/journal.ppat.1003508
• Primary Citation of Related Structures:  
  4JVI, 4JVC, 4JVD


• PubMed Abstract: 
  

Bacterial populations co-ordinate gene expression collectively through quorum sensing (QS), a cell-to-cell communication mechanism employing diffusible signal molecules. The LysR-type transcriptional regulator (LTTR) protein PqsR (MvfR) is a key component of alkyl-quinolone (AQ)-dependent QS in Pseudomonas aeruginosa. PqsR is activated by 2-alkyl-4-quinolones including the Pseudomonas quinolone signal (PQS; 2-heptyl-3-hydroxy-4(1H)-quinolone), its precursor 2-heptyl-4-hydroxyquinoline (HHQ) and their C9 congeners, 2-nonyl-3-hydroxy-4(1H)-quinolone (C9-PQS) and 2-nonyl-4-hydroxyquinoline (NHQ). These drive the autoinduction of AQ biosynthesis and the up-regulation of key virulence determinants as a function of bacterial population density. Consequently, PqsR constitutes a potential target for novel antibacterial agents which attenuate infection through the blockade of virulence. Here we present the crystal structures of the PqsR co-inducer binding domain (CBD) and a complex with the native agonist NHQ. We show that the structure of the PqsR CBD has an unusually large ligand-binding pocket in which a native AQ agonist is stabilized entirely by hydrophobic interactions. Through a ligand-based design strategy we synthesized and evaluated a series of 50 AQ and novel quinazolinone (QZN) analogues and measured the impact on AQ biosynthesis, virulence gene expression and biofilm development. The simple exchange of two isosteres (OH for NH₂) switches a QZN agonist to an antagonist with a concomitant impact on the induction of bacterial virulence factor production. We also determined the complex crystal structure of a QZN antagonist bound to PqsR revealing a similar orientation in the ligand binding pocket to the native agonist NHQ. This structure represents the first description of an LTTR-antagonist complex. Overall these studies present novel insights into LTTR ligand binding and ligand-based drug design and provide a chemical scaffold for further anti-P. aeruginosa virulence drug development by targeting the AQ receptor PqsR.

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Organizational Affiliation: 

Centre for Biomolecular Sciences, University of Nottingham, University Park, Nottingham, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcriptional regulator MvfR	A	216	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: mvfR, PA14_51340, PqsR
Find proteins for A0A0H2Z7A6 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Explore A0A0H2Z7A6  Go to UniProtKB:  A0A0H2Z7A6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
QZN	A	3-amino-7-chloro-2-nonylquinazolin-4(3H)-one C17 H24 Cl N3 O PLTFJOYTWYIUIG-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
QZN	IC50 :  5000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.263 
• R-Value Work: 0.204 
• R-Value Observed: 0.207 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 118.441	α = 90
b = 118.441	β = 90
c = 115.409	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
SOLVE	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-03-25 
• Released Date: 2013-08-07 
Deposition Author(s): Ilangovan, A., Williams, P., Emsley, J.

Revision History 

• Version 1.0: 2013-08-07
  Type: Initial release
  
• Version 1.1: 2014-02-12
  Changes: Database references
• Version 1.2: 2019-12-04
  Changes: Data collection