3HO7

Crystal structure of OxyR from Porphyromonas gingivalis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Structures of the Porphyromonas gingivalis OxyR regulatory domain explain differences in expression of the OxyR regulon in Escherichia coli and P. gingivalis.

Svintradze, D.V.Peterson, D.L.Collazo-Santiago, E.A.Lewis, J.P.Wright, H.T.

(2013) Acta Crystallogr.,Sect.D 69: 2091-2103

  • DOI: 10.1107/S0907444913019471
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • OxyR transcriptionally regulates Escherichia coli oxidative stress response genes through a reversibly reducible cysteine disulfide biosensor of cellular redox status. Structural changes induced by redox changes in these cysteines are conformationall ...

    OxyR transcriptionally regulates Escherichia coli oxidative stress response genes through a reversibly reducible cysteine disulfide biosensor of cellular redox status. Structural changes induced by redox changes in these cysteines are conformationally transmitted to the dimer subunit interfaces, which alters dimer and tetramer interactions with DNA. In contrast to E. coli OxyR regulatory-domain structures, crystal structures of Porphyromonas gingivalis OxyR regulatory domains show minimal differences in dimer configuration on changes in cysteine disulfide redox status. This locked configuration of the P. gingivalis OxyR regulatory-domain dimer closely resembles the oxidized (activating) form of the E. coli OxyR regulatory-domain dimer. It correlates with the observed constitutive activation of some oxidative stress genes in P. gingivalis and is attributable to a single amino-acid insertion in P. gingivalis OxyR relative to E. coli OxyR. Modelling of full-length P. gingivalis, E. coli and Neisseria meningitidis OxyR-DNA complexes predicts different modes of DNA binding for the reduced and oxidized forms of each.


    Organizational Affiliation

    OCMB Philips Institute, School of Dentistry, Virginia Commonwealth University, Richmond, VA 23298-0566, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OxyR
A, B
232Porphyromonas gingivalis (strain ATCC BAA-308 / W83)Mutation(s): 0 
Gene Names: oxyR
Find proteins for Q7MXD3 (Porphyromonas gingivalis (strain ATCC BAA-308 / W83))
Go to UniProtKB:  Q7MXD3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.219 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 55.819α = 110.63
b = 55.795β = 102.82
c = 56.711γ = 114.63
Software Package:
Software NamePurpose
d*TREKdata reduction
PHENIXmodel building
PHENIXphasing
CrystalCleardata collection
CrystalCleardata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-06-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance
  • Version 1.2: 2013-01-16
    Type: Atomic model
  • Version 1.3: 2013-10-02
    Type: Database references
  • Version 1.4: 2014-01-08
    Type: Database references