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

Experimental Data Snapshot

  • Resolution: 2.19 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 

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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: https://doi.org/10.1021/bi050005e
  • Primary Citation of Related Structures:  
    2BJY, 2BK6, 2BKC

  • 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 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.

  • Organizational Affiliation

    Istituto di Biologia e Patologia Molecolari CNR, Dipartimento di Scienze Biochimiche, Università La Sapienza, P.le A. Moro, 5, 00185 Roma, 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
156Listeria innocuaMutation(s): 1 
Find proteins for P80725 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262))
Explore P80725 
Go to UniProtKB:  P80725
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80725
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.19 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.212 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 136.33α = 90
b = 136.33β = 90
c = 242.489γ = 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: 2005-02-14
    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: 2018-02-28
    Changes: Database references, Source and taxonomy
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description