2WIC

Crystal Structures of the N-terminal Intracellular Domain of FeoB from Klebsiella Pneumoniae in GMPPNP binding state


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural Fold, Conservation and Fe(II) Binding of the Intracellular Domain of Prokaryote Feob.

Hung, K.-W.Chang, Y.-W.Eng, E.T.Chen, J.-H.Chen, Y.-C.Sun, Y.-J.Hsiao, C.-D.Dong, G.Spasov, K.A.Unger, V.M.Huang, T.-H.

(2010) J Struct Biol 170: 501

  • DOI: 10.1016/j.jsb.2010.01.017
  • Primary Citation of Related Structures:  
    2WIA, 2WIB, 2WIC, 3K53

  • PubMed Abstract: 
  • FeoB is a G-protein coupled membrane protein essential for Fe(II) uptake in prokaryotes. Here, we report the crystal structures of the intracellular domain of FeoB (NFeoB) from Klebsiella pneumoniae (KpNFeoB) and Pyrococcus furiosus (PfNFeoB) with and without bound ligands ...

    FeoB is a G-protein coupled membrane protein essential for Fe(II) uptake in prokaryotes. Here, we report the crystal structures of the intracellular domain of FeoB (NFeoB) from Klebsiella pneumoniae (KpNFeoB) and Pyrococcus furiosus (PfNFeoB) with and without bound ligands. In the structures, a canonical G-protein domain (G domain) is followed by a helical bundle domain (S-domain), which despite its lack of sequence similarity between species is structurally conserved. In the nucleotide-free state, the G-domain's two switch regions point away from the binding site. This gives rise to an open binding pocket whose shallowness is likely to be responsible for the low nucleotide-binding affinity. Nucleotide binding induced significant conformational changes in the G5 motif which in the case of GMPPNP binding was accompanied by destabilization of the switch I region. In addition to the structural data, we demonstrate that Fe(II)-induced foot printing cleaves the protein close to a putative Fe(II)-binding site at the tip of switch I, and we identify functionally important regions within the S-domain. Moreover, we show that NFeoB exists as a monomer in solution, and that its two constituent domains can undergo large conformational changes. The data show that the S-domain plays important roles in FeoB function.


    Related Citations: 
    • Sequencing and Analysis of the Large Virulence Plasmid Plvpk of Klebsiella Pneumoniae Cg43.
      Chen, Y., Chang, H., Lai, Y., Pan, C., Tsai, S., Peng, H.
      (2004) Gene 337: 189

    Organizational Affiliation

    Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan, ROC.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FERROUS IRON TRANSPORT PROTEIN BA267Klebsiella pneumoniaeMutation(s): 0 
UniProt
Find proteins for A6TF32 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Explore A6TF32 
Go to UniProtKB:  A6TF32
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GNP (Subject of Investigation/LOI)
Query on GNP

Download Ideal Coordinates CCD File 
B [auth A]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GNP PDBBind:  2WIC Kd: 4100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.215 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.897α = 90
b = 106.897β = 90
c = 106.897γ = 90
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance