1TQ5

Crystal Structure of YhhW from Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural and biochemical analysis reveal pirins to possess quercetinase activity.

Adams, M.Jia, Z.

(2005) J Biol Chem 280: 28675-28682

  • DOI: https://doi.org/10.1074/jbc.M501034200
  • Primary Citation of Related Structures:  
    1TQ5

  • PubMed Abstract: 

    Pirin is a recently identified eukaryotic protein implicated in transcriptional activation and apoptosis. Homologues of Pirin are highly conserved in both prokaryotes and eukaryotes, but their function remains poorly understood. We present here the crystal structure of the yhhW gene product, a putative Pirin homologue, from Escherichia coli and confirm its structural similarity to Pirin. The YhhW protein displays a bicupin fold with a single N-terminal metal coordination site. Molecular surface comparisons of YhhW and Pirin with structurally similar proteins suggested quercetin as a potential ligand. We demonstrate that both bacterial and human Pirins have quercetinase activity, which is inhibited by the addition of typical inhibitors of the quercetin 2,3-dioxygenase reaction. We also demonstrate the release of carbon monoxide as a reaction product. This is the first report of enzymatic activity for any member of the Pirin family and may be an important connection to their roles in transcriptional regulation.


  • Organizational Affiliation

    Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein yhhW242Escherichia coliMutation(s): 7 
Gene Names: YHHWB3439
EC: 1.13.11.24
UniProt
Find proteins for P46852 (Escherichia coli (strain K12))
Explore P46852 
Go to UniProtKB:  P46852
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46852
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.204 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.769α = 90
b = 62.769β = 90
c = 98.053γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary