1B00

PHOB RECEIVER DOMAIN FROM ESCHERICHIA COLI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.210 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Three-dimensional crystal structure of the transcription factor PhoB receiver domain.

Sola, M.Gomis-Ruth, F.X.Serrano, L.Gonzalez, A.Coll, M.

(1999) J Mol Biol 285: 675-687

  • DOI: 10.1006/jmbi.1998.2326
  • Primary Citation of Related Structures:  
    1B00

  • PubMed Abstract: 
  • PhoB is the response regulator of the two-component signal transduction system activated under phosphate starvation conditions. This protein is a transcription factor that activates more than 30 genes of the pho regulon and consists of two domains: a DNA binding domain and a dimerization domain, the latter being homologous to the receiver domain described for two-component response regulators ...

    PhoB is the response regulator of the two-component signal transduction system activated under phosphate starvation conditions. This protein is a transcription factor that activates more than 30 genes of the pho regulon and consists of two domains: a DNA binding domain and a dimerization domain, the latter being homologous to the receiver domain described for two-component response regulators. Activation by phosphorylation induces dimerization of the protein and the consequent binding to the DNA direct repeat pho box, where it promotes the binding of RNA polymerase. In the absence of phosphorylation, the activating dimerization process can be mimicked by deletion of the DNA binding domain. The three-dimensional crystal structure of the receiver domain of PhoB from Escherichia coli has been solved by multiple anomalous diffraction using a gold derivative obtained by co-crystallization, and refined using data to 1.9 A resolution. The crystal structure reveals an alpha/beta doubly wound fold, similar to other known receivers, the most conspicuous difference being the displacement of helix alpha4 towards its N terminus. The active site includes the acidic triad Asp53 (the site of phosphorylation), Asp10 and Glu9. Lys105, from loop beta5alpha5, and Glu88, from helix alpha4, interact with Asp53 via an H-bond and a water bridge, respectively. In the asymmetric unit of the crystal there are two molecules linked by a complementary hydrophobic surface, which involves helix alpha1, loop beta5alpha5 and the N terminus of helix alpha5, and is connected to the active site through the fully conserved residue Lys105 from loop beta5alpha5. The possibility that this surface is the functional surface used for the activating dimerization is discussed.


    Related Citations: 
    • Overexpression, Purification, Crystallization and Preliminary X-Ray Diffraction Analysis of the Receiver Domain of Phob
      Sola, M., Rueth, F.-X.G., Serrano, L., Gonzalez, A., Coll, M.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 1460

    Organizational Affiliation

    CID-CSIC, Jordi Girona 18-26, Barcelona, 08034, Spain.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOBA, B127Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AFJ5 (Escherichia coli (strain K12))
Explore P0AFJ5 
Go to UniProtKB:  P0AFJ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AFJ5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.11α = 90
b = 60.42β = 90
c = 119.97γ = 90
Software Package:
Software NamePurpose
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-11-19
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance