4EC2

Crystal structure of trimeric frataxin from the yeast Saccharomyces cerevisiae, complexed with ferrous


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.260 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The molecular basis of iron-induced oligomerization of frataxin and the role of the ferroxidation reaction in oligomerization.

Soderberg, C.A.Rajan, S.Shkumatov, A.V.Gakh, O.Schaefer, S.Ahlgren, E.C.Svergun, D.I.Isaya, G.Al-Karadaghi, S.

(2013) J Biol Chem 288: 8156-8167

  • DOI: 10.1074/jbc.M112.442285
  • Primary Citation of Related Structures:  
    4EC2

  • PubMed Abstract: 
  • The role of the mitochondrial protein frataxin in iron storage and detoxification, iron delivery to iron-sulfur cluster biosynthesis, heme biosynthesis, and aconitase repair has been extensively studied during the last decade. However, still no general consensus exists on the details of the mechanism of frataxin function and oligomerization ...

    The role of the mitochondrial protein frataxin in iron storage and detoxification, iron delivery to iron-sulfur cluster biosynthesis, heme biosynthesis, and aconitase repair has been extensively studied during the last decade. However, still no general consensus exists on the details of the mechanism of frataxin function and oligomerization. Here, using small-angle x-ray scattering and x-ray crystallography, we describe the solution structure of the oligomers formed during the iron-dependent assembly of yeast (Yfh1) and Escherichia coli (CyaY) frataxin. At an iron-to-protein ratio of 2, the initially monomeric Yfh1 is converted to a trimeric form in solution. The trimer in turn serves as the assembly unit for higher order oligomers induced at higher iron-to-protein ratios. The x-ray crystallographic structure obtained from iron-soaked crystals demonstrates that iron binds at the trimer-trimer interaction sites, presumably contributing to oligomer stabilization. For the ferroxidation-deficient D79A/D82A variant of Yfh1, iron-dependent oligomerization may still take place, although >50% of the protein is found in the monomeric state at the highest iron-to-protein ratio used. This demonstrates that the ferroxidation reaction controls frataxin assembly and presumably the iron chaperone function of frataxin and its interactions with target proteins. For E. coli CyaY, the assembly unit of higher order oligomers is a tetramer, which could be an effect of the much shorter N-terminal region of this protein. The results show that understanding of the mechanistic features of frataxin function requires detailed knowledge of the interplay between the ferroxidation reaction, iron-induced oligomerization, and the structure of oligomers formed during assembly.


    Related Citations: 
    • Oligomerization propensity and flexibility of yeast frataxin studied by x-ray crystallography and small-angle x-ray scattering
      Soderberg, C.A.G., Shkumatov, A.V., Rajan, S., Gakh, O., Svergun, D.I., Isaya, G., Al-karadaghi, S.
      (2011) J Mol Biol 414: 783
    • The structures of frataxin oligomers reveal the mechanism for the delivery and detoxification of iron
      Karlberg, T., Schagerlof, U., Gakh, O., Park, S., Ryde, U., Lindahl, M., Leath, K., Garman, E., Isaya, G., Al-karadaghi, S.
      (2006) Structure 14: 1535

    Organizational Affiliation

    Center for Molecular Protein Science, Institute for Chemistry and Chemical Engineering, Lund University, P. O. Box 124, SE-221 00 Lund, Sweden. Electronic address: salam.al-karadaghi@biochemistry.lu.se.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Frataxin homolog, mitochondrialA123Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: YFH1YDL120W
EC: 1.16.3.1
UniProt
Find proteins for Q07540 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q07540 
Go to UniProtKB:  Q07540
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07540
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE2
Query on FE2

Download Ideal Coordinates CCD File 
B [auth A]FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.260 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.57α = 90
b = 121.57β = 90
c = 121.57γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-30
    Type: Initial release
  • Version 1.1: 2013-05-22
    Changes: Database references
  • Version 1.2: 2018-03-07
    Changes: Advisory, Data collection