3EAT

Crystal structure of the PvcB (PA2255) protein from Pseudomonas aeruginosa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Three-dimensional structures of Pseudomonas aeruginosa PvcA and PvcB, two proteins involved in the synthesis of 2-isocyano-6,7-dihydroxycoumarin.

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

(2008) J.Mol.Biol. 384: 193-205

  • DOI: 10.1016/j.jmb.2008.09.027
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The pvcABCD operon of Pseudomonas aeruginosa encodes four proteins (PA2254, PA2255, PA2256, and PA2257) that form a cluster that is responsible for the synthesis of a cyclized isocyano derivative of tyrosine. These proteins, which were identified ori ...

    The pvcABCD operon of Pseudomonas aeruginosa encodes four proteins (PA2254, PA2255, PA2256, and PA2257) that form a cluster that is responsible for the synthesis of a cyclized isocyano derivative of tyrosine. These proteins, which were identified originally as being responsible for a step in the maturation of the chromophore of the peptide siderophore pyoverdine, have been identified recently as belonging to a family of proteins that produce small organic isonitriles. We report that strains harboring a disruption in the pvcA or pvcB genes are able to grow in iron-depleted conditions and to produce pyoverdine. Additionally, we have determined the three-dimensional crystal structures of PvcA and PvcB. The structure of PvcA demonstrates a novel enzyme architecture that is built upon a Rossmann fold. We have analyzed the sequence conservation of enzymes within this family and identified six conserved motifs. These regions of the protein cluster around a putative active site cavity. The structure of the PvcB protein confirms it is a member of the Fe2+/alpha-ketoglutarate-dependent oxygenase family of enzymes. The active site of PvcB is compared to the structures of other family members and suggests that a conformational change to order several loops will accompany the binding of ligands.


    Organizational Affiliation

    Hauptman-Woodward Medical Research Institute, Department of Structural Biology, State University of New York at Buffalo, 700 Ellicott St, Buffalo, NY 14203-1102, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyoverdine biosynthesis protein PvcB
X
293Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: pvcB
Find proteins for Q9I1L4 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q9I1L4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
X
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.187 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 125.350α = 90.00
b = 125.350β = 90.00
c = 107.110γ = 120.00
Software Package:
Software NamePurpose
SnBphasing
HKL-2000data reduction
Blu-Icedata collection
REFMACrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-10-14
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance