1O3S

PROTEIN-DNA RECOGNITION AND DNA DEFORMATION REVEALED IN CRYSTAL STRUCTURES OF CAP-DNA COMPLEXES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.260 
  • R-Value Observed: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: Alteration of DNA Binding Specificity Through Alteration of DNA Kinking

Chen, S.Gunasekera, A.Zhang, X.Kunkel, T.A.Ebright, R.H.Berman, H.M.

(2001) J Mol Biol 314: 75-82

  • DOI: 10.1006/jmbi.2001.5090
  • Primary Citation of Related Structures:  
    1O3S

  • PubMed Abstract: 
  • The catabolite activator protein (CAP) sharply bends DNA in the CAP-DNA complex, introducing a DNA kink, with a roll angle of approximately 40 degrees and a twist angle of approximately 20 degrees, between positions 6 and 7 of the DNA half-site, 5'-A ...

    The catabolite activator protein (CAP) sharply bends DNA in the CAP-DNA complex, introducing a DNA kink, with a roll angle of approximately 40 degrees and a twist angle of approximately 20 degrees, between positions 6 and 7 of the DNA half-site, 5'-A(1)A(2)A(3)T(4)G(5)T(6)G(7)A(8)T(9)C(10)T(11)-3' ("primary kink"). CAP recognizes the base-pair immediately 5' to the primary-kink site, T:A(6), through an "indirect-readout" mechanism involving sequence effects on the energetics of primary-kink formation. CAP recognizes the base-pair immediately 3' to the primary-kink site, G:C(7), through a "direct-readout" mechanism involving formation of a hydrogen bond between Glu181 of CAP and G:C(7). Here, we report that substitution of the carboxylate side-chain of Glu181 of CAP by the one-methylene-group-shorter carboxylate side-chain of Asp changes DNA binding specificity at position 6 of the DNA half site, changing specificity for T:A(6) to specificity for C:G(6), and we report a crystallographic analysis defining the structural basis of the change in specificity. The Glu181-->Asp substitution eliminates the primary kink and thus eliminates indirect-readout-based specificity for T:A(6). The Glu181-->Asp substitution does not eliminate hydrogen-bond formation with G:C(7), and thus does not eliminate direct-readout-based specificity for G:C(7).


    Related Citations: 
    • Indirect Readout of DNA Sequence at the Primary-kink Site in the CAP-DNA Complex: DNA Binding Specificity Based on Energetics of DNA Kinking
      Chen, S., Vojtechovsky, J., Parkinson, G.N., Ebright, R.H., Berman, H.M.
      (2001) J Mol Biol 314: 63

    Organizational Affiliation

    Department of Chemistry and The Waksman Institute, Rutgers, the State University of New Jersey, 610 Taylor Road, Piscataway, NJ, 08854-8087, USA



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CATABOLITE GENE ACTIVATOR PROTEINA200Escherichia coliMutation(s): 1 
Find proteins for P0ACJ8 (Escherichia coli (strain K12))
Explore P0ACJ8 
Go to UniProtKB:  P0ACJ8
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)-3'B11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*TP*AP*GP*AP*TP*CP*GP*CP*AP*TP*TP*TP*TP*T)-3'C15N/A
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      CMP
      Query on CMP

      Download CCD File 
      A
      ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
      C10 H12 N5 O6 P
      IVOMOUWHDPKRLL-KQYNXXCUSA-N
       Ligand Interaction
      External Ligand Annotations 
      IDBinding Affinity (Sequence Identity %)
      DNAKd :  0.014000000432133675   nM  PDBBind
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.00 Å
      • R-Value Free: 0.308 
      • R-Value Work: 0.260 
      • R-Value Observed: 0.260 
      • Space Group: P 31 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 78.05α = 90
      b = 78.05β = 90
      c = 142.79γ = 120
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALAdata scaling
      AMoREphasing
      CNSrefinement
      CCP4data scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History 

      • Version 1.0: 2003-04-08
        Type: Initial release
      • Version 1.1: 2008-04-26
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance