2XGW

ZINC-BOUND CRYSTAL STRUCTURE OF STREPTOCOCCUS PYOGENES DPR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Characterization and Biological Implications of Di-Zinc Binding in the Ferroxidase Center of Streptococcus Pyogenes Dpr.

Haikarainen, T.Tsou, C.-C.Wu, J.-J.Papageorgiou, A.C.

(2010) Biochem Biophys Res Commun 398: 361

  • DOI: 10.1016/j.bbrc.2010.06.071
  • Primary Citation of Related Structures:  
    2XGW

  • PubMed Abstract: 
  • Dps proteins contain a ferroxidase site that binds and oxidizes iron, thereby preventing hydroxyl radical formation by Fenton reaction. Although the involvement of a di-iron ferroxidase site has been suggested, X-ray crystal structures of various Dps mem ...

    Dps proteins contain a ferroxidase site that binds and oxidizes iron, thereby preventing hydroxyl radical formation by Fenton reaction. Although the involvement of a di-iron ferroxidase site has been suggested, X-ray crystal structures of various Dps members have shown either one or two iron cations with various occupancies despite the high structural conservation of the site. Similarly, structural studies with zinc, a redox-stable replacement for iron, have shown the binding of either one or two zinc ions. Here, the crystal structure of Streptococcus pyogenes Dpr in complex with zinc reveals the binding of two zinc cations in the ferroxidase center and an additional zinc-binding site at the surface of the protein. The results suggest a structural basis for the protection of Streptococcus pyogenes in zinc stress conditions and provide a clear evidence for a di-zinc and di-iron ferroxidase site in Streptococcus pyogenes Dpr protein.


    Organizational Affiliation

    Turku Centre for Biotechnology, University of Turku and Abo Akademi University, Finland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEROXIDE RESISTANCE PROTEIN A199Streptococcus pyogenesMutation(s): 0 
Find proteins for Q99YU7 (Streptococcus pyogenes serotype M1)
Explore Q99YU7 
Go to UniProtKB:  Q99YU7
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: F 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 187.12α = 90
b = 187.12β = 90
c = 187.12γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    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