2VXX

X-ray structure of DpsA from Thermosynechococcus elongatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Thermosynechococcus Elongatus Dpsa Binds Zn(II) at a Unique Three Histidine-Containing Ferroxidase Center and Utilizes O2 as Iron Oxidant with Very High Efficiency, Unlike the Typical Dps Proteins.

Alaleona, F.Franceschini, S.Ceci, P.Ilari, A.Chiancone, E.

(2010) FEBS J. 277: 903

  • DOI: 10.1111/j.1742-4658.2009.07532.x

  • PubMed Abstract: 
  • The cyanobacterium Thermosynechococcus elongatus is one the few bacteria to possess two Dps proteins, DpsA-Te and Dps-Te. The present characterization of DpsA-Te reveals unusual structural and functional features that differentiate it from Dps-Te and ...

    The cyanobacterium Thermosynechococcus elongatus is one the few bacteria to possess two Dps proteins, DpsA-Te and Dps-Te. The present characterization of DpsA-Te reveals unusual structural and functional features that differentiate it from Dps-Te and the other known Dps proteins. Notably, two Zn(II) are bound at the ferroxidase center, owing to the unique substitution of a metal ligand at the A-site (His78 in place of the canonical aspartate) and to the presence of a histidine (His164) in place of a hydrophobic residue at a metal-coordinating distance in the B-site. Only the latter Zn(II) is displaced by incoming iron, such that Zn(II)-Fe(III) complexes are formed upon oxidation, as indicated by absorbance and atomic emission spectroscopy data. In contrast to the typical behavior of Dps proteins, where Fe(II) oxidation by H(2)O(2) is about 100-fold faster than by O(2), in DpsA-Te the ferroxidation efficiency of O(2) is very high and resembles that of H(2)O(2). Oxygraphic experiments show that two Fe(II) are required to reduce O(2), and that H(2)O(2) is not released into solution at the end of the reaction. On this basis, a reaction mechanism is proposed that also takes into account the formation of Zn(II)-Fe(III) complexes. The physiological significance of the DpsA-Te behavior is discussed in the framework of a possible localization of the protein at the thylakoid membranes, where photosynthesis takes place, with the consequent increased formation of reactive oxygen species.


    Organizational Affiliation

    C.N.R. Institute of Molecular Biology and Pathology, Department of Biochemical Sciences A. Rossi-Fanelli, University of Rome La Sapienza, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
STARVATION INDUCED DNA BINDING PROTEIN
A, B, C, D
192Thermosynechococcus elongatus (strain BP-1)Mutation(s): 0 
Gene Names: dpsA
Find proteins for Q8DL82 (Thermosynechococcus elongatus (strain BP-1))
Go to UniProtKB:  Q8DL82
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B, C, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

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B, C
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
B, C, D
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.165 
  • Space Group: I 2 3
Unit Cell:
Length (Å)Angle (°)
a = 174.504α = 90.00
b = 174.504β = 90.00
c = 174.504γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
DENZOdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-05-07
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance