Crystal Structure of the DNA binding domain of E.coli FUR (Ferric Uptake Regulator)

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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Structural changes of Escherichia coli ferric uptake regulator during metal-dependent dimerization and activation explored by NMR and X-ray crystallography

Pecqueur, L.D'Autreaux, B.Dupuy, J.Nicolet, Y.Jacquamet, L.Brutscher, B.Michaud-Soret, I.Bersch, B.

(2006) J Biol Chem 281: 21286-21295

  • DOI: https://doi.org/10.1074/jbc.M601278200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Ferric uptake regulator (Fur) is a global bacterial regulator that uses iron as a cofactor to bind to specific DNA sequences. Escherichia coli Fur is usually isolated as a homodimer with two metal sites per subunit. Metal binding to the iron site induces protein activation; however the exact role of the structural zinc site is still unknown. Structural studies of three different forms of the Escherichia coli Fur protein (nonactivated dimer, monomer, and truncated Fur-(1-82)) were performed. Dimerization of the oxidized monomer was followed by NMR in the presence of a reductant (dithiothreitol) and Zn(II). Reduction of the disulfide bridges causes only local structure variations, whereas zinc addition to reduced Fur induces protein dimerization. This demonstrates for the first time the essential role of zinc in the stabilization of the quaternary structure. The secondary structures of the mono- and dimeric forms are almost conserved in the N-terminal DNA-binding domain, except for the first helix, which is not present in the nonactivated dimer. In contrast, the C-terminal dimerization domain is well structured in the dimer but appears flexible in the monomer. This is also confirmed by heteronuclear Overhauser effect data. The crystal structure at 1.8A resolution of a truncated protein (Fur-(1-82)) is described and found to be identical to the N-terminal domain in the monomeric and in the metal-activated state. Altogether, these data allow us to propose an activation mechanism for E. coli Fur involving the folding/unfolding of the N-terminal helix.

  • Organizational Affiliation

    Laboratoire de Résonance Magnétique Nucléaire des Protéines, Institut de Biologie Structurale Jean-Pierre Ebel (Unité Mixte de Recherche 5075 CNRS/Commissariat à l'Energie Atomique/Université Joseph Fourier), F-38027 Grenoble Cedex 1.

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferric uptake regulation protein
A, B
83Escherichia coli BL21Mutation(s): 0 
Gene Names: FUR(P0A9A9)
Find proteins for P0A9A9 (Escherichia coli (strain K12))
Explore P0A9A9 
Go to UniProtKB:  P0A9A9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A9A9
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CD

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
R [auth B]
Query on GOL

Download Ideal Coordinates CCD File 
C3 H8 O3
Query on CL

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
L [auth A]
M [auth A]
N [auth A]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
S [auth B],
T [auth B],
U [auth B],
V [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.5α = 90
b = 159.27β = 90
c = 28.65γ = 90
Software Package:
Software NamePurpose
XNEMOdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance