3E1J

Crystal structure of E. coli Bacterioferritin (BFR) with an unoccupied ferroxidase centre (APO-BFR).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 

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This is version 1.1 of the entry. See complete history


Literature

Structural basis for iron mineralization by bacterioferritin

Crow, A.Lawson, T.L.Lewin, A.Moore, G.R.Le Brun, N.E.

(2009) J Am Chem Soc 131: 6808-6813

  • DOI: 10.1021/ja8093444
  • Primary Citation of Related Structures:  
    3E1O, 3E1P, 3E1J, 3E1L, 3E1M, 3E1N

  • PubMed Abstract: 
  • Ferritin proteins function to detoxify, solubilize and store cellular iron by directing the synthesis of a ferric oxyhydroxide mineral solubilized within the protein's central cavity. Here, through the application of X-ray crystallographic and kinetic methods, we report significant new insight into the mechanism of mineralization in a bacterioferritin (BFR) ...

    Ferritin proteins function to detoxify, solubilize and store cellular iron by directing the synthesis of a ferric oxyhydroxide mineral solubilized within the protein's central cavity. Here, through the application of X-ray crystallographic and kinetic methods, we report significant new insight into the mechanism of mineralization in a bacterioferritin (BFR). The structures of nonheme iron-free and di-Fe(2+) forms of BFR showed that the intrasubunit catalytic center, known as the ferroxidase center, is preformed, ready to accept Fe(2+) ions with little or no reorganization. Oxidation of the di-Fe(2+) center resulted in a di-Fe(3+) center, with bridging electron density consistent with a mu-oxo or hydro bridged species. The mu-oxo bridged di-Fe(3+) center appears to be stable, and there is no evidence that Fe(3+)species are transferred into the core from the ferroxidase center. Most significantly, the data also revealed a novel Fe(2+) binding site on the inner surface of the protein, lying approximately 10 A directly below the ferroxidase center, coordinated by only two residues, His46 and Asp50. Kinetic studies of variants containing substitutions of these residues showed that the site is functionally important. In combination, the data support a model in which the ferroxidase center functions as a true catalytic cofactor, rather than as a pore for the transfer of iron into the central cavity, as found for eukaryotic ferritins. The inner surface iron site appears to be important for the transfer of electrons, derived from Fe(2+) oxidation in the cavity, to the ferroxidase center. Bacterioferritin may represent an evolutionary link between ferritins and class II di-iron proteins not involved in iron metabolism.


    Organizational Affiliation

    Centre for Molecular and Structural Biochemistry, School of Chemical Sciences and Pharmacy, University of East Anglia, Norwich NR4 7TJ, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BacterioferritinABCDEFGHABCDEFGHIJKL
158Escherichia coli K-12Mutation(s): 0 
Gene Names: bfrb3336JW3298
EC: 1.16.3.1
Find proteins for P0ABD3 (Escherichia coli (strain K12))
Explore P0ABD3 
Go to UniProtKB:  P0ABD3
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.242 
  • R-Value Observed: 0.243 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 208.216α = 90
b = 208.216β = 90
c = 142.457γ = 90
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance