2W7N

Crystal Structure of KorA Bound to Operator DNA: Insight into Repressor Cooperation in RP4 Gene Regulation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.172 

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This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of Kora Bound to Operator DNA: Insight Into Repressor Cooperation in Rp4 Gene Regulation

Koenig, B.Mueller, J.J.Lanka, E.Heinemann, U.

(2009) Nucleic Acids Res 37: 1915

  • DOI: 10.1093/nar/gkp044
  • Primary Citation of Related Structures:  
    2W7N

  • PubMed Abstract: 
  • KorA is a global repressor in RP4 which regulates cooperatively the expression of plasmid genes whose products are involved in replication, conjugative transfer and stable inheritance. The structure of KorA bound to an 18-bp DNA duplex that contains the symmetric operator sequence and incorporates 5-bromo-deoxyuridine nucleosides has been determined by multiple-wavelength anomalous diffraction phasing at 1 ...

    KorA is a global repressor in RP4 which regulates cooperatively the expression of plasmid genes whose products are involved in replication, conjugative transfer and stable inheritance. The structure of KorA bound to an 18-bp DNA duplex that contains the symmetric operator sequence and incorporates 5-bromo-deoxyuridine nucleosides has been determined by multiple-wavelength anomalous diffraction phasing at 1.96-A resolution. KorA is present as a symmetric dimer and contacts DNA via a helix-turn-helix motif. Each half-site of the symmetric operator DNA binds one copy of the protein in the major groove. As confirmed by mutagenesis, recognition specificity is based on two KorA side chains forming hydrogen bonds to four bases within each operator half-site. KorA has a unique dimerization module shared by the RP4 proteins TrbA and KlcB. We propose that these proteins cooperate with the global RP4 repressor KorB in a similar manner via this dimerization module and thus regulate RP4 inheritance.


    Organizational Affiliation

    Max-Delbrück-Center for Molecular Medicine, Berlin, Germany.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRFB TRANSCRIPTIONAL REPRESSOR PROTEINA, B101Escherichia coliMutation(s): 0 
Gene Names: trfBkorA
Find proteins for P03052 (Escherichia coli)
Explore P03052 
Go to UniProtKB:  P03052
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*AP*TP*GP*TP*TP*TP*AP*GP*CP *TP*AP*AP*AP*CP*AP*AP*G)-3'C [auth E], E [auth G]18Escherichia coli
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*BRUP*BRUP*GP*TP*TP*TP*AP*GP*CP*TP*AP *AP*AP*CP*AP*BRUP*T)-3'D [auth F], F [auth H]18Escherichia coli
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.85 Å
      • R-Value Free: 0.201 
      • R-Value Work: 0.170 
      • R-Value Observed: 0.172 
      • Space Group: P 1 21 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 44.83α = 90
      b = 115.45β = 114
      c = 49.88γ = 90
      Software Package:
      Software NamePurpose
      REFMACrefinement
      XDSdata reduction
      XDSdata scaling
      XDSphasing

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2009-02-17
        Type: Initial release
      • Version 1.1: 2011-05-08
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance
      • Version 1.3: 2019-01-30
        Changes: Data collection, Experimental preparation, Other
      • Version 1.4: 2019-05-22
        Changes: Data collection, Derived calculations, Experimental preparation