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

Experimental Data Snapshot

  • Resolution: 1.45 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.180 

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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: https://doi.org/10.1074/jbc.M302114200
  • Primary Citation of Related Structures:  

  • 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 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.

  • 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
162Agrobacterium tumefaciensMutation(s): 0 
Find proteins for Q8UCK6 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore Q8UCK6 
Go to UniProtKB:  Q8UCK6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8UCK6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on TRS

Download Ideal Coordinates CCD File 
I [auth B],
N [auth E]
C4 H12 N O3
Query on EDO

Download Ideal Coordinates CCD File 
L [auth D]1,2-ETHANEDIOL
C2 H6 O2
Query on FE

Download Ideal Coordinates CCD File 
G [auth A]
H [auth B]
J [auth C]
K [auth D]
M [auth E]
G [auth A],
H [auth B],
J [auth C],
K [auth D],
M [auth E],
O [auth F]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.45 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.180 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.046α = 90
b = 90.349β = 90
c = 105.656γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-29
    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: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description