2WIB

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


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:  

  • 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 an ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FERROUS IRON TRANSPORT PROTEIN B
A, B
267Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)Mutation(s): 0 
Gene Names: feoB
Find proteins for A6TF32 (Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578))
Go to UniProtKB:  A6TF32
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GDPKd: 11800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.56 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.222 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 86.552α = 90.00
b = 184.688β = 90.00
c = 38.168γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
CrystalCleardata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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