4JVI

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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.1371/journal.ppat.1003508
  • Primary Citation of Related Structures:  
    4JVC, 4JVD, 4JVI

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator MvfR216Pseudomonas aeruginosaMutation(s): 0 
Gene Names: mvfRPA14_51340PqsR
UniProt
Find proteins for A0A0H2Z7A6 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore A0A0H2Z7A6 
Go to UniProtKB:  A0A0H2Z7A6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2Z7A6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QZN
Query on QZN

Download Ideal Coordinates CCD File 
B [auth A]3-amino-7-chloro-2-nonylquinazolin-4(3H)-one
C17 H24 Cl N3 O
PLTFJOYTWYIUIG-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
QZN PDBBind:  4JVI IC50: 5000 (nM) from 1 assay(s)
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 = 118.441α = 90
b = 118.441β = 90
c = 115.409γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
SOLVEphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2024-03-20
    Changes: Data collection, Database references, Derived calculations