1O9R

The X-ray crystal structure of Agrobacterium tumefaciens Dps, a member of the family that protect DNA without binding


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Dps Protein of Agrobacterium Tumefaciens Does not Bind to DNA But Protects It Toward Oxidative Cleavage: X-Ray Crystal Structure, Iron Binding, and Hydroxyl-Radical Scavenging Properties

Ceci, P.Ilari, A.Falvo, E.Chiancone, E.

(2003) J.Biol.Chem. 278: 20319

  • DOI: 10.1074/jbc.M302114200

  • PubMed Abstract: 
  • Agrobacterium tumefaciens Dps (DNA-binding proteins from starved cells), encoded by the dps gene located on the circular chromosome of this plant pathogen, was cloned, and its structural and functional properties were determined in vitro. In Escheric ...

    Agrobacterium tumefaciens Dps (DNA-binding proteins from starved cells), encoded by the dps gene located on the circular chromosome of this plant pathogen, was cloned, and its structural and functional properties were determined in vitro. In Escherichia coli Dps, the family prototype, the DNA binding properties are thought to be associated with the presence of the lysine-containing N-terminal tail that extends from the protein surface into the solvent. The x-ray crystal structure of A. tumefaciens Dps shows that the positively charged N-terminal tail, which is 11 amino acids shorter than in the E. coli protein, is blocked onto the protein surface. This feature accounts for the lack of interaction with DNA. The intersubunit ferroxidase center characteristic of Dps proteins is conserved and confers to the A. tumefaciens protein a ferritin-like activity that manifests itself in the capacity to oxidize and incorporate iron in the internal cavity and to release it after reduction. In turn, sequestration of Fe(II) correlates with the capacity of A. tumefaciens Dps to reduce the production of hydroxyl radicals from H2O2 through Fenton chemistry. These data demonstrate conclusively that DNA protection from oxidative damage in vitro does not require formation of a Dps-DNA complex. In vivo, the hydroxyl radical scavenging activity of A. tumefaciens Dps may be envisaged to act in concert with catalase A to counteract the toxic effect of H2O2, the major component of the plant defense system when challenged by the bacterium.


    Related Citations: 
    • Structure of the Neutrophil-Activating Protein from Helicobacter Pylori
      Zanotti, G.,Papinutto, E.,Dundon, W.G.,Battistutta, R.,Seveso, M.,Giudice, G.D.,Rappuoli, R.,Montecucco, C.
      (2002) J.Mol.Biol. 323: 125
    • Structure of Two Iron-Binding Proteins from Bacillus Anthracis
      Papinutto, E.,Dundon, W.G.,Pitulis, N.,Battistutta, R.,Montecucco, C.,Zanotti, G.
      (2002) J.Biol.Chem. 277: 15093
    • The Dodecameric Ferritin from Listeria Innocua Contains a Novel Intersubunit Iron-Binding Site
      Ilari, A.,Stefanini, S.,Chiancone, E.,Tsernoglou, D.
      (2000) Nat.Struct.Mol.Biol. 7: 38
    • The Crystal Structure of Dps, a Ferritin Homolog that Binds and Protects DNA
      Grant, R.A.,Filman, D.J.,Finkel, S.E.,Kolter, R.,Hogle, J.M.
      (1998) Nat.Struct.Mol.Biol. 5: 294


    Organizational Affiliation

    Consiglio Nazionale delle Ricerche 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
AGROBACTERIUM TUMEFACIENS DPS
A, B, C, D, E, F
162Agrobacterium fabrum (strain C58 / ATCC 33970)Gene Names: dps
EC: 1.16.-.-
Find proteins for Q8UCK6 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Go to UniProtKB:  Q8UCK6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
FE
Query on FE

Download SDF File 
Download CCD File 
A, B, C, D, E, F
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
B, E
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.170 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 106.046α = 90.00
b = 90.349β = 90.00
c = 105.656γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-05-29
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance