5FRU

crystal structure of the phenol-responsive sensory domain of the transcription activator PoxR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Analysis of the Phenol-Responsive Sensory Domain of the Transcription Activator Poxr

Patil, V.V.Park, K.-H.Lee, S.-G.Woo, E.J.

(2016) Structure 624: 24

  • DOI: https://doi.org/10.1016/j.str.2016.03.006
  • Primary Citation of Related Structures:  
    5FRU, 5FRV, 5FRW, 5FRX, 5FRY, 5FRZ, 5FS0

  • PubMed Abstract: 

    Positive phenol-degradative gene regulator (PoxR) is a σ(54)-dependent AAA+ ATPase transcription activator that regulates the catabolism of phenols. The PoxR sensory domain detects phenols and relays signals for the activation of transcription. Here we report the first structure of the phenol sensory domain bound to phenol and five derivatives. It exists as a tightly intertwined homodimer with a phenol-binding pocket buried inside, placing two C termini on the same side of the dimer. His102 and Trp130 interact with the hydroxyl group of the phenol in a cavity surrounded by rigid hydrophobic residues on one side and a flexible region on the other. Each monomer has a V4R fold with a unique zinc-binding site. A shift at the C-terminal helix suggests that there is a possible conformational change upon ligand binding. The results provide a structural basis of chemical effector binding for transcriptional regulation with broad implications for protein engineering.


  • Organizational Affiliation

    Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea; Department of Bio-Analytical science, University of Science and Technology, Daejeon 305-333, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Positive phenol-degradative gene regulator
A, B
211Ralstonia sp. E2Mutation(s): 0 
Gene Names: poxR
UniProt
Find proteins for O84957 (Ralstonia sp. E2)
Explore O84957 
Go to UniProtKB:  O84957
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO84957
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.634α = 90
b = 66.516β = 90
c = 106.039γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-04-13
    Changes: Database references
  • Version 1.2: 2016-04-20
    Changes: Database references
  • Version 1.3: 2019-10-16
    Changes: Data collection, Other
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary