2VXX

X-ray structure of DpsA from Thermosynechococcus elongatus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1111/j.1742-4658.2009.07532.x
  • Primary Citation of Related Structures:  
    2VXX

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
STARVATION INDUCED DNA BINDING PROTEIN
A, B, C, D
192Synechococcus elongatusMutation(s): 0 
UniProt
Find proteins for Q8DL82 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DL82 
Go to UniProtKB:  Q8DL82
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DL82
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
J [auth B]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
K [auth B],
O [auth C],
R [auth D]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth B]
H [auth B]
L [auth C]
E [auth A],
F [auth A],
G [auth B],
H [auth B],
L [auth C],
M [auth C],
P [auth D],
Q [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE
Query on FE

Download Ideal Coordinates CCD File 
I [auth B],
N [auth C]
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: I 2 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.504α = 90
b = 174.504β = 90
c = 174.504γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description