4K2F

Structure of Pseudomonas aeruginosa PvdQ bound to BRD-A08522488


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Identification of Inhibitors of PvdQ, an Enzyme Involved in the Synthesis of the Siderophore Pyoverdine.

Wurst, J.M.Drake, E.J.Theriault, J.R.Jewett, I.T.VerPlank, L.Perez, J.R.Dandapani, S.Palmer, M.Moskowitz, S.M.Schreiber, S.L.Munoz, B.Gulick, A.M.

(2014) Acs Chem.Biol. 9: 1536-1544

  • DOI: 10.1021/cb5001586
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pseudomonas aeruginosa produces the peptide siderophore pyoverdine, which is used to acquire essential Fe(3+) ions from the environment. PvdQ, an Ntn hydrolase, is required for the biosynthesis of pyoverdine. PvdQ knockout strains are not infectious ...

    Pseudomonas aeruginosa produces the peptide siderophore pyoverdine, which is used to acquire essential Fe(3+) ions from the environment. PvdQ, an Ntn hydrolase, is required for the biosynthesis of pyoverdine. PvdQ knockout strains are not infectious in model systems, suggesting that disruption of siderophore production via PvdQ inhibition could be exploited as a target for novel antibacterial agents, by preventing cells from acquiring iron in the low iron environments of most biological settings. We have previously described a high-throughput screen to identify inhibitors of PvdQ that identified inhibitors with IC50 values of ∼100 μM. Here, we describe the discovery of ML318, a biaryl nitrile inhibitor of PvdQ acylase. ML318 inhibits PvdQ in vitro (IC50 = 20 nM) by binding in the acyl-binding site, as confirmed by the X-ray crystal structure of PvdQ bound to ML318. Additionally, the PvdQ inhibitor is active in a whole cell assay, preventing pyoverdine production and limiting the growth of P. aeruginosa under iron-limiting conditions.


    Organizational Affiliation

    The Broad Institute , Cambridge, Massachusetts 02142, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acyl-homoserine lactone acylase PvdQ
A
170Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: pvdQ (qsc112)
EC: 3.5.1.97
Find proteins for Q9I194 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9I194
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Acyl-homoserine lactone acylase PvdQ
B
546Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: pvdQ (qsc112)
EC: 3.5.1.97
Find proteins for Q9I194 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9I194
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
A08
Query on A08

Download SDF File 
Download CCD File 
B
(2S)-(4-chlorophenyl)(6-chloropyridin-2-yl)ethanenitrile
C13 H8 Cl2 N2
KFUYTJBERFHHIL-NSHDSACASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A08IC50: 40 nM (99) BINDINGDB
A08IC50: 40 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.168 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 120.280α = 90.00
b = 166.020β = 90.00
c = 94.190γ = 90.00
Software Package:
Software NamePurpose
Blu-Icedata collection
REFMACrefinement
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-06-18
    Type: Initial release
  • Version 1.1: 2014-07-30
    Type: Database references