3L91

Structure of Pseudomonas aerugionsa PvdQ bound to octanoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1021/cb2002973
  • Primary Citation of Related Structures:  
    3L91, 3L94, 3SRA, 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl-homoserine lactone acylase pvdQ subunit alpha170Pseudomonas aeruginosaMutation(s): 0 
Gene Names: PA2385pvdQqsc112
EC: 3.5.1.97
UniProt
Find proteins for Q9I194 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I194 
Go to UniProtKB:  Q9I194
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I194
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Acyl-homoserine lactone acylase pvdQ subunit beta546Pseudomonas aeruginosaMutation(s): 0 
Gene Names: PA2385pvdQqsc112
EC: 3.5.1.97
UniProt
Find proteins for Q9I194 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I194 
Go to UniProtKB:  Q9I194
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I194
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OCA
Query on OCA

Download Ideal Coordinates CCD File 
H [auth B]OCTANOIC ACID (CAPRYLIC ACID)
C8 H16 O2
WWZKQHOCKIZLMA-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.289α = 90
b = 165.281β = 90
c = 93.998γ = 90
Software Package:
Software NamePurpose
CHESSdata collection
SOLVEphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-01-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-04-17
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary