The co-factor-induced pre-active conformation in PhoB

Experimental Data Snapshot

  • Resolution: 2.08 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

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The Cofactor-Induced Pre-Active Conformation in Phob.

Sola, M.Drew, D.L.Blanco, A.G.Gomis-Ruth, F.X.Coll, M.

(2006) Acta Crystallogr D Biol Crystallogr 62: 1046

  • DOI: https://doi.org/10.1107/S0907444906024541
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    PhoB is an Escherichia coli transcription factor from a two-component signal transduction system that is sensitive to limiting environmental phosphate conditions. It consists of an N-terminal receiver domain (RD) and a C-terminal DNA-binding domain. The protein is activated upon phosphorylation at the RD, an event that depends on Mg(2+) binding. The structure of PhoB RD in complex with Mg(2+) is presented, which shows three protomers in the asymmetric unit that interact across two different surfaces. One association is symmetric and has been described as a non-active dimerization contact; the other involves the alpha4-beta5-alpha5 interface and recalls the contact found in activated PhoB. However, here this last interaction is not perfectly symmetric and helix alpha4, which in the activated molecule undergoes a helical shift, becomes strongly destabilized in one of the interacting monomers. All protomers bind the cation in a similar manner but, interestingly, at the prospective binding site for the phosphate moiety the side chains of either Glu88 (in helix alpha4) or Trp54 alternate and interact with active-site atoms. When Glu88 is inside the cavity, helix alpha4 is arranged similarly to the unliganded wild-type structure. However, if Trp54 is present, the helix loses its contacts with the active-site cavity and vanishes. Accordingly, the presence of Trp54 in the active site induces a flexible state in helix alpha4, potentially allowing a helical shift that phosphorylation would eventually stabilize.

  • Organizational Affiliation

    Institut de Biologia Molecular de Barcelona, CSIC, Parc Científic de Barcelona, c/ Josep Samitier 1-5, 08028 Barcelona, Spain. msvcri@ibmb.csic.es

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C
127Escherichia coliMutation(s): 0 
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
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.08 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.742α = 90
b = 105.829β = 90
c = 135.51γ = 90
Software Package:
Software NamePurpose

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other