2JBA

PhoB response regulator receiver domain constitutively-active double mutant D53A and Y102C.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

The X-Ray Crystal Structures of Two Constitutively Active Mutants of the Escherichia Coli Phob Receiver Domain Give Insights Into Activation.

Arribas-Bosacoma, R.Kim, S.-K.Ferrer-Orta, C.Blanco, A.G.Pereira, P.J.B.Gomis-Ruth, F.X.Wanner, B.L.Coll, M.Sola, M.

(2007) J.Mol.Biol. 366: 626

  • DOI: 10.1016/j.jmb.2006.11.038
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The PhoR/PhoB two-component system is a key regulatory protein network enabling Escherichia coli to respond to inorganic phosphate (Pi) starvation conditions by turning on Pho regulon genes for more efficient Pi uptake and use of alternative phosphor ...

    The PhoR/PhoB two-component system is a key regulatory protein network enabling Escherichia coli to respond to inorganic phosphate (Pi) starvation conditions by turning on Pho regulon genes for more efficient Pi uptake and use of alternative phosphorus sources. Under environmental Pi depletion, the response regulator (RR) component, PhoB, is phosphorylated at the receiver domain (RD), a process that requires Mg(2+) bound at the active site. Phosphorylation of the RD relieves the inhibition of the PhoB effector domain (ED), a DNA-binding region that binds to Pho regulon promoters to activate transcription. The molecular details of the activation are proposed to involve dimerization of the RD and a conformational change in the RD detected by the ED. The structure of the PhoB RD shows a symmetrical interaction involving alpha1, loop beta5alpha5 and N terminus of alpha5 elements, also seen in the complex of PhoB RD with Mg(2+), in which helix alpha4 highly increases its flexibility. PhoB RD in complex with Mg(2+) and BeF(3) (an emulator of the phosphate moiety) undergoes a dramatic conformational change on helix alpha4 and shows another interaction involving alpha4, beta5 and alpha5 segments. We have selected a series of constitutively active PhoB mutants (PhoB(CA)) that are able to turn on the Pho regulon promoters in the absence phosphorylation and, as they cannot be inactivated, should therefore mimic the active RD state of PhoB and its functional oligomerisation. We have analysed the PhoB(CA) RD crystal structures of two such mutants, Asp53Ala/Tyr102Cys and Asp10Ala/Asp53Glu. Interestingly, both mutants reproduce the homodimeric arrangement through the symmetric interface encountered in the unbound and magnesium-bound wild-type PhoB RD structures. Besides, the mutant RD structures show a modified active site organization as well as changes at helix alpha4 that correlate with repositioning of surrounding residues, like the active-site events indicator Trp54, putatively redifining the interaction with the ED in the full-length protein.


    Related Citations: 
    • 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


    Organizational Affiliation

    Institut de Biologia Molecular de Barcelona (CSIC), c/Jordi Girona 18-26, 08034 Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
A
127Escherichia coli (strain K12)Mutation(s): 2 
Gene Names: phoB
Find proteins for P0AFJ5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFJ5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
B
127Escherichia coli (strain K12)Mutation(s): 2 
Gene Names: phoB
Find proteins for P0AFJ5 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AFJ5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 44.907α = 90.00
b = 47.631β = 99.34
c = 59.703γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-01-04
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance