6GKA

20 minute Fe2+ soak structure of SynFtn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Reaction of O2with a diiron protein generates a mixed-valent Fe2+/Fe3+center and peroxide.

Bradley, J.M.Svistunenko, D.A.Pullin, J.Hill, N.Stuart, R.K.Palenik, B.Wilson, M.T.Hemmings, A.M.Moore, G.R.Le Brun, N.E.

(2019) Proc Natl Acad Sci U S A 116: 2058-2067

  • DOI: 10.1073/pnas.1809913116
  • Primary Citation of Related Structures:  
    5OUW, 5OUZ, 6GKA, 6GKB, 6GKC

  • PubMed Abstract: 
  • The gene encoding the cyanobacterial ferritin Syn Ftn is up-regulated in response to copper stress. Here, we show that, while Syn Ftn does not interact directly with copper, it is highly unusual in several ways. First, its catalytic diiron ferroxidase center is unlike those of all other characterized prokaryotic ferritins and instead resembles an animal H-chain ferritin center ...

    The gene encoding the cyanobacterial ferritin Syn Ftn is up-regulated in response to copper stress. Here, we show that, while Syn Ftn does not interact directly with copper, it is highly unusual in several ways. First, its catalytic diiron ferroxidase center is unlike those of all other characterized prokaryotic ferritins and instead resembles an animal H-chain ferritin center. Second, as demonstrated by kinetic, spectroscopic, and high-resolution X-ray crystallographic data, reaction of O 2 with the di-Fe 2+ center results in a direct, one-electron oxidation to a mixed-valent Fe 2+ /Fe 3+ form. Iron-O 2 chemistry of this type is currently unknown among the growing family of proteins that bind a diiron site within a four α-helical bundle in general and ferritins in particular. The mixed-valent form, which slowly oxidized to the more usual di-Fe 3+ form, is an intermediate that is continually generated during mineralization. Peroxide, rather than superoxide, is shown to be the product of O 2 reduction, implying that ferroxidase centers function in pairs via long-range electron transfer through the protein resulting in reduction of O 2 bound at only one of the centers. We show that electron transfer is mediated by the transient formation of a radical on Tyr40, which lies ∼4 Å from the diiron center. As well as demonstrating an expansion of the iron-O 2 chemistry known to occur in nature, these data are also highly relevant to the question of whether all ferritins mineralize iron via a common mechanism, providing unequivocal proof that they do not.


    Organizational Affiliation

    Centre for Molecular and Structural Biochemistry, School of Chemistry, University of East Anglia, Norwich NR4 7TJ, United Kingdom; n.le-brun@uea.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FerritinA178Synechococcus sp. CC9311Mutation(s): 0 
Gene Names: sync_1539
EC: 1.16.3.2
UniProt
Find proteins for Q0I9X8 (Synechococcus sp. (strain CC9311))
Explore Q0I9X8 
Go to UniProtKB:  Q0I9X8
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 
  • Space Group: F 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 177.26α = 90
b = 177.26β = 90
c = 177.26γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/IO21884/1

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-01-30
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-13
    Changes: Data collection, Database references