2IYN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.,Sect.D 62: 1046

  • DOI: 10.1107/S0907444906024541

  • 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. ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
A, B, C
127Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: phoB
Find proteins for P0AFJ5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFJ5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.231 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 50.742α = 90.00
b = 105.829β = 90.00
c = 135.510γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance