4LP1

Crystal structure of CyaY protein from Psychromonas ingrahamii in complex with Eu(III)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.803 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural characterization of metal binding to a cold-adapted frataxin

Noguera, M.E.Roman, E.A.Rigal, J.B.Cousido-Siah, A.Mitschler, A.Podjarny, A.Santos, J.

(2015) J.Biol.Inorg.Chem. 20: 653-664

  • DOI: 10.1007/s00775-015-1251-9
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Frataxin is an evolutionary conserved protein that participates in iron metabolism. Deficiency of this small protein in humans causes a severe neurodegenerative disease known as Friedreich's ataxia. A number of studies indicate that frataxin binds ir ...

    Frataxin is an evolutionary conserved protein that participates in iron metabolism. Deficiency of this small protein in humans causes a severe neurodegenerative disease known as Friedreich's ataxia. A number of studies indicate that frataxin binds iron and regulates Fe-S cluster biosynthesis. Previous structural studies showed that metal binding occurs mainly in a region of high density of negative charge. However, a comprehensive characterization of the binding sites is required to gain further insights into the mechanistic details of frataxin function. In this work, we have solved the X-ray crystal structures of a cold-adapted frataxin from a psychrophilic bacterium in the presence of cobalt or europium ions. We have identified a number of metal-binding sites, mainly solvent exposed, several of which had not been observed in previous studies on mesophilic homologues. No major structural changes were detected upon metal binding, although the structures exhibit significant changes in crystallographic B-factors. The analysis of these B-factors, in combination with crystal packing and RMSD among structures, suggests the existence of localized changes in the internal motions. Based on these results, we propose that bacterial frataxins possess binding sites of moderate affinity for a quick capture and transfer of iron to other proteins and for the regulation of Fe-S cluster biosynthesis, modulating interactions with partner proteins.


    Organizational Affiliation

    Instituto de Química y Físico-Química Biológicas, Universidad de Buenos Aires, Junín 956, 1113AAD, Buenos Aires, Argentina.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein CyaY
A, B
105Psychromonas ingrahamii (strain 37)Mutation(s): 0 
Gene Names: cyaY
Find proteins for A1SR01 (Psychromonas ingrahamii (strain 37))
Go to UniProtKB:  A1SR01
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EU3
Query on EU3

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.803 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.213 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.821α = 90.00
b = 49.992β = 90.43
c = 46.580γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PHASERphasing
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-16
    Type: Initial release
  • Version 1.1: 2016-09-21
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description