3SRA

Structure of Pseudomonas aerugionsa PvdQ covalently acylated with myristic acid from PVDIq


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Characterization and High-Throughput Screening of Inhibitors of PvdQ, an NTN Hydrolase Involved in Pyoverdine Synthesis.

Drake, E.J.Gulick, A.M.

(2011) Acs Chem.Biol. 6: 1277-1286

  • DOI: 10.1021/cb2002973
  • Primary Citation of Related Structures:  3L91, 3L94, 3SRB, 3SRC

  • PubMed Abstract: 
  • The human pathogen Pseudomonas aeruginosa produces a variety of virulence factors including pyoverdine, a nonribosomally produced peptide siderophore. The maturation pathway of the pyoverdine peptide is complex and provides a unique target for inhibi ...

    The human pathogen Pseudomonas aeruginosa produces a variety of virulence factors including pyoverdine, a nonribosomally produced peptide siderophore. The maturation pathway of the pyoverdine peptide is complex and provides a unique target for inhibition. Within the pyoverdine biosynthetic cluster is a periplasmic hydrolase, PvdQ, that is required for pyoverdine production. However, the precise role of PvdQ in the maturation pathway has not been biochemically characterized. We demonstrate herein that the initial module of the nonribosomal peptide synthetase PvdL adds a myristate moiety to the pyoverdine precursor. We extracted this acylated precursor, called PVDIq, from a pvdQ mutant strain and show that the PvdQ enzyme removes the fatty acid catalyzing one of the final steps in pyoverdine maturation. Incubation of PVDIq with crystals of PvdQ allowed us to capture the acylated enzyme and confirm through structural studies the chemical composition of the incorporated acyl chain. Finally, because inhibition of siderophore synthesis has been identified as a potential antibiotic strategy, we developed a high-throughput screening assay and tested a small chemical library for compounds that inhibit PvdQ activity. Two compounds that block PvdQ have been identified, and their binding within the fatty acid binding pocket was structurally characterized.


    Organizational Affiliation

    Hauptman-Woodward Medical Research Institute and Department of Structural Biology, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, New York 14203-1102, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Acyl-homoserine lactone acylase pvdQ
A
163Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)Gene Names: pvdQ (qsc112)
EC: 3.5.1.97
Find proteins for Q9I194 (Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228))
Go to UniProtKB:  Q9I194
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Acyl-homoserine lactone acylase pvdQ
B
546Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)Gene Names: pvdQ (qsc112)
EC: 3.5.1.97
Find proteins for Q9I194 (Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228))
Go to UniProtKB:  Q9I194
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download SDF File 
Download CCD File 
B
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.182 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 120.168α = 90.00
b = 166.622β = 90.00
c = 93.746γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction
Blu-Icedata collection
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-09-21
    Type: Initial release
  • Version 1.1: 2011-11-30
    Type: Database references