1Z9C

Crystal structure of OhrR bound to the ohrA promoter: Structure of MarR family protein with operator DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of an OhrR-ohrA Operator Complex Reveals the DNA Binding Mechanism of the MarR Family.

Hong, M.Fuangthong, M.Helmann, J.D.Brennan, R.G.

(2005) Mol.Cell 20: 131-141

  • DOI: 10.1016/j.molcel.2005.09.013
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The mechanisms by which Bacillus subtilis OhrR, a member of the MarR family of transcription regulators, binds the ohrA operator and is induced by oxidation of its lone cysteine residue by organic hydroperoxides to sulphenic acid are unknown. Here, w ...

    The mechanisms by which Bacillus subtilis OhrR, a member of the MarR family of transcription regulators, binds the ohrA operator and is induced by oxidation of its lone cysteine residue by organic hydroperoxides to sulphenic acid are unknown. Here, we describe the crystal structures of reduced OhrR and an OhrR-ohrA operator complex. To bind DNA, OhrR employs a chimeric winged helix-turn-helix DNA binding motif, which is composed of extended eukaryotic-like wings, prokaryotic helix-turn-helix motifs, and helix-helix elements. The reactivity of the peroxide-sensing cysteine is not modulated by proximal basic residues but largely by the positive dipole of helix alpha1. Induction originates from the alleviation of intersubunit steric clash between the sulphenic acid moieties of the oxidized sensor cysteines and nearby tyrosines and methionines. The structure of the OhrR-ohrA operator complex reveals the DNA binding mechanism of the entire MarR family and suggests a common inducer binding pocket.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Oregon Health and Science University, Portland, OR 97239, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Organic hydroperoxide resistance transcriptional regulator
A, B, C, D, E, F
147Bacillus subtilis (strain 168)Mutation(s): 1 
Gene Names: ohrR (ykmA)
Find proteins for O34777 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34777
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (29-MER)G,I,K29N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (29-MER)H,J,L29N/A
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 81.899α = 90.00
b = 80.960β = 100.20
c = 109.340γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
CCP4data scaling
SCALAdata scaling
PDB_EXTRACTdata extraction
MOSFLMdata reduction
EPMRphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-25
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance