2ZHG

Crystal structure of SoxR in complex with DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 

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This is version 1.1 of the entry. See complete history


Literature

Crystal structure of the [2Fe-2S] oxidative-stress sensor SoxR bound to DNA

Watanabe, S.Kita, A.Kobayashi, K.Miki, K.

(2008) Proc Natl Acad Sci U S A 105: 4121-4126

  • DOI: 10.1073/pnas.0709188105
  • Primary Citation of Related Structures:  
    2ZHG, 2ZHH

  • PubMed Abstract: 
  • The [2Fe-2S] transcription factor SoxR, a member of the MerR family, functions as a bacterial sensor of oxidative stress such as superoxide and nitric oxide. SoxR is activated by reversible one-electron oxidation of the [2Fe-2S] cluster and then enhances the production of various antioxidant proteins through the soxRS regulon ...

    The [2Fe-2S] transcription factor SoxR, a member of the MerR family, functions as a bacterial sensor of oxidative stress such as superoxide and nitric oxide. SoxR is activated by reversible one-electron oxidation of the [2Fe-2S] cluster and then enhances the production of various antioxidant proteins through the soxRS regulon. In the active state, SoxR and other MerR family proteins activate transcription from unique promoters, which have a long 19- or 20-bp spacer between the -35 and -10 operator elements, by untwisting the promoter DNA. Here, we show the crystal structures of SoxR and its complex with the target promoter in the oxidized (active) state. The structures reveal that the [2Fe-2S] cluster of SoxR is completely solvent-exposed and surrounded by an asymmetric environment stabilized by interaction with the other subunit. The asymmetrically charged environment of the [2Fe-2S] cluster probably causes redox-dependent conformational changes of SoxR and the target promoter. Compared with the promoter structures with the 19-bp spacer previously studied, the DNA structure is more sharply bent, by approximately 1 bp, with the two central base pairs holding Watson-Crick base pairs. Comparison of the target promoter sequences of the MerR family indicates that the present DNA structure represents the activated conformation of the target promoter with a 20-bp spacer in the MerR family.


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Redox-sensitive transcriptional activator soxRB [auth A]154Escherichia coli K-12Mutation(s): 0 
Gene Names: soxRmarCb4063JW4024
UniProt
Find proteins for P0ACS2 (Escherichia coli (strain K12))
Explore P0ACS2 
Go to UniProtKB:  P0ACS2
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*DGP*DCP*DCP*DTP*DCP*DAP*DAP*DGP*DTP*DTP*DAP*DAP*DCP*DTP*DTP*DGP*DAP*DGP*DGP*DC)-3')A [auth B]20N/A
    Protein Feature View
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    • Reference Sequence
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    FES
    Query on FES

    Download Ideal Coordinates CCD File 
    C [auth A]FE2/S2 (INORGANIC) CLUSTER
    Fe2 S2
    NIXDOXVAJZFRNF-UHFFFAOYSA-N
     Ligand Interaction
    DTT
    Query on DTT

    Download Ideal Coordinates CCD File 
    D [auth A]2,3-DIHYDROXY-1,4-DITHIOBUTANE
    C4 H10 O2 S2
    VHJLVAABSRFDPM-IMJSIDKUSA-N
     Ligand Interaction
    GOL
    Query on GOL

    Download Ideal Coordinates CCD File 
    E [auth A]GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.80 Å
    • R-Value Free: 0.281 
    • R-Value Work: 0.243 
    • R-Value Observed: 0.243 
    • Space Group: P 61 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 53.374α = 90
    b = 53.374β = 90
    c = 355.159γ = 120
    Software Package:
    Software NamePurpose
    CNSrefinement
    HKL-2000data collection
    HKL-2000data reduction
    HKL-2000data scaling
    SOLVEphasing

    Structure Validation

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    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2008-03-25
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Source and taxonomy, Version format compliance