2P1X

Crystal structure analysis of the complex between CyaY and Eu(III)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Understanding the binding properties of an unusual metal-binding protein-a study of bacterial frataxin

Pastore, C.Franzese, M.Sica, F.Temussi, P.Pastore, A.

(2007) Febs J. 274: 4199-4210

  • DOI: 10.1111/j.1742-4658.2007.05946.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Deficiency of the small mitochondrial protein frataxin causes Friedreich's ataxia, a severe neurodegenerative pathology. Frataxin, which has been highly conserved throughout evolution, is thought to be involved in, among other processes, Fe-S cluster ...

    Deficiency of the small mitochondrial protein frataxin causes Friedreich's ataxia, a severe neurodegenerative pathology. Frataxin, which has been highly conserved throughout evolution, is thought to be involved in, among other processes, Fe-S cluster formation. Independent evidence shows that it binds iron directly, although with very distinct features and low affinity. Here, we have carried out an extensive study of the binding properties of CyaY, the bacterial ortholog of frataxin, to different divalent and trivalent cations, using NMR and X-ray crystallography. We demonstrate that the protein has low cation specificity and contains multiple binding sites able to chelate divalent and trivalent metals with low affinity. Binding does not involve cavities or pockets, but exposed glutamates and aspartates, which are residues that are unusual for iron chelation when not assisted by histidines and/or cysteines. We have related how such an ability to bind cations on a relatively large area through an electrostatic mechanism could be a valuable asset for protein function.


    Related Citations: 
    • Solution structure of the bacterial frataxin ortholog, CyaY: mapping the iron binding sites
      Nair, M.,Adinolfi, S.,Pastore, C.,Kelly, G.,Temussi, P.,Pastore, A.
      (2004) Structure 12: 2037
    • Crystal structure of Escherichia coli CyaY protein reveals a previously unidentified fold for the evolutionarily conserved frataxin family
      Cho, S.J.,Lee, M.G.,Yang, J.K.,Lee, J.Y.,Song, H.K.,Suh, S.W.
      (2000) Proc.Natl.Acad.Sci.Usa 97: 8932


    Organizational Affiliation

    National Institute for Medical Research, London, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein cyaY
A
106Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: cyaY
Find proteins for P27838 (Escherichia coli (strain K12))
Go to UniProtKB:  P27838
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EU3
Query on EU3

Download SDF File 
Download CCD File 
A
EUROPIUM (III) ION
Eu
LNBHUCHAFZUEGJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.199 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 43.859α = 90.00
b = 43.859β = 90.00
c = 98.717γ = 120.00
Software Package:
Software NamePurpose
MAR345dtbdata collection
SHELXL-97refinement
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-03-06 
  • Released Date: 2007-10-02 
  • Deposition Author(s): Sica, F., Franzese, M.

Revision History 

  • Version 1.0: 2007-10-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance