2CF7

Asp74Ala mutant crystal structure for Dps-like peroxide resistance protein Dpr from Streptococcus suis.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Iron incorporation in Streptococcus suis Dps-like peroxide resistance protein Dpr requires mobility in the ferroxidase center and leads to the formation of a ferrihydrite-like core.

Kauko, A.Pulliainen, A.T.Haataja, S.Meyer-Klaucke, W.Finne, J.Papageorgiou, A.C.

(2006) J. Mol. Biol. 364: 97-109

  • DOI: 10.1016/j.jmb.2006.08.061
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Dps-like peroxide resistance protein (Dpr) is a dodecameric protein that protects the human and swine pathogen Streptococcus suis from hydrogen peroxide by removing free Fe2+ from the cytosol. Subsequent oxidation of iron by Dpr results in the de ...

    The Dps-like peroxide resistance protein (Dpr) is a dodecameric protein that protects the human and swine pathogen Streptococcus suis from hydrogen peroxide by removing free Fe2+ from the cytosol. Subsequent oxidation of iron by Dpr results in the deposition of Fe3+ inside the protein's central cavity. Structural changes that occur in the ferroxidase center were studied by X-ray crystallography after soaking Dpr crystals with Fe2+ in the presence of sodium dithionite. Twelve iron-binding sites were identified with each site formed by residues Asp74 and Glu78 from one subunit, and Asp63, His47 and His59 from a 2-fold symmetry-related subunit. Compared to the iron-free Dpr, Asp74 and Glu78 were found to be the most flexible amino acid residues and able to adopt a variety of conformations in different subunits. The crystal structure of an Asp74Ala Dpr mutant soaked with a Fe2+ -solution revealed variations in the Asp63 position and no iron bound to the ferroxidase center. These results indicate an intrinsic flexibility in the active site that may be important for the catalytic reaction and subsequent nucleation events. Two iron cores with remarkably different features were identified in Dpr using X-ray absorption spectroscopy. Purified Dpr was found to have a small-size iron core with only approximately 16 iron atoms/dodecamer forming a ferritin-like ferrihydrite structure. Because of its size, this core represents the smallest iron core identified so far in ferritins and other Dps-like proteins. A large-size core (approximately 180 iron atoms/dodecamer) formed after incubating the protein with a ferrous solution shows differences in iron coordination compared to the small size core. Characterization of the two iron cores in Dpr could provide insights into nucleation events and the mechanism of iron core growth in the Dps family of proteins.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DPR
A, B, C, D, E, F, G, H, I, J, K, L
165Streptococcus suisMutation(s): 1 
Gene Names: dps (dpr)
EC: 1.16.-.-
Find proteins for P0CB53 (Streptococcus suis)
Go to UniProtKB:  P0CB53
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EPE
Query on EPE

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Download CCD File 
B, E, G, K
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
HEPES
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
J, K
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
D, J, K
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.153 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 106.930α = 90.00
b = 133.670β = 90.00
c = 135.630γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
AMoREphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-09-28
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2019-03-13
    Type: Data collection, Database references, Experimental preparation, Other
  • Version 1.4: 2019-07-24
    Type: Data collection