2BK6

The X-ray crystal structure of the Listeria innocua H31G Dps mutant.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The unusual intersubunit ferroxidase center of Listeria innocua Dps is required for hydrogen peroxide detoxification but not for iron uptake. A study with site-specific mutants.

Ilari, A.Latella, M.C.Ceci, P.Ribacchi, F.Su, M.Giangiacomo, L.Stefanini, S.Chasteen, N.D.Chiancone, E.

(2005) Biochemistry 44: 5579-5587

  • DOI: 10.1021/bi050005e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The role of the ferroxidase center in iron uptake and hydrogen peroxide detoxification was investigated in Listeria innocua Dps by substituting the iron ligands His31, His43, and Asp58 with glycine or alanine residues either individually or in combin ...

    The role of the ferroxidase center in iron uptake and hydrogen peroxide detoxification was investigated in Listeria innocua Dps by substituting the iron ligands His31, His43, and Asp58 with glycine or alanine residues either individually or in combination. The X-ray crystal structures of the variants reveal only small alterations in the ferroxidase center region compared to the native protein. Quenching of the protein fluorescence was exploited to assess stoichiometry and affinity of metal binding. Substitution of either His31 or His43 decreases Fe(II) affinity significantly with respect to wt L. innocua Dps (K approximately 10(5) vs approximately 10(7) M(-)(1)) but does not alter the binding stoichiometry [12 Fe(II)/dodecamer]. In the H31G-H43G and H31G-H43G-D58A variants, binding of Fe(II) does not take place with measurable affinity. Oxidation of protein-bound Fe(II) increases the binding stoichiometry to 24 Fe(III)/dodecamer. However, the extent of fluorescence quenching upon Fe(III) binding decreases, and the end point near 24 Fe(III)/dodecamer becomes less distinct with increase in the number of mutated residues. In the presence of dioxygen, the mutations have little or no effect on the kinetics of iron uptake and in the formation of micelles inside the protein shell. In contrast, in the presence of hydrogen peroxide, with increase in the number of substitutions the rate of iron oxidation and the capacity to inhibit Fenton chemistry, thereby protecting DNA from oxidative damage, appear increasingly compromised, a further indication of the role of ferroxidation in conferring peroxide tolerance to the bacterium.


    Related Citations: 
    • 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


    Organizational Affiliation

    Istituto di Biologia e Patologia Molecolari CNR, Dipartimento di Scienze Biochimiche, Università La Sapienza, P.le A. Moro, 5, 00185 Roma, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NON-HEME IRON-CONTAINING FERRITIN
A, B, C, D, E, F
156Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)Mutation(s): 1 
Gene Names: dps (flp, fri)
EC: 1.16.-.-
Find proteins for P80725 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262))
Go to UniProtKB:  P80725
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.211 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 136.330α = 90.00
b = 136.330β = 90.00
c = 242.489γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
REFMACrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-14
    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: 2018-02-28
    Type: Database references, Source and taxonomy