1O3T

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 63-74

  • DOI: 10.1006/jmbi.2001.5089
  • Primary Citation of Related Structures:  
    1O3T, 1O3R, 1O3Q

  • PubMed Abstract: 
  • The catabolite activator protein (CAP) makes no direct contact with the consensus base-pair T:A at position 6 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' but, nevertheless, exhibits strong specificity for T:A at position ...

    The catabolite activator protein (CAP) makes no direct contact with the consensus base-pair T:A at position 6 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' but, nevertheless, exhibits strong specificity for T:A at position 6. Binding of CAP results in formation of a sharp 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. The consensus base-pair T:A at position 6 and the consensus base-pair G:C at position 7 form a T:A/G:C step, which is known to be associated with DNA flexibility. It has been proposed that specificity for T:A at position 6 is a consequence of formation of the DNA kink between positions 6 and 7, and of effects of the T:A(6)/G:C(7) step on the geometry of DNA kinking, or the energetics of DNA kinking. In this work, we determine crystallographic structures of CAP-DNA complexes having the consensus base-pair T:A at position 6 or the non-consensus base-pair C:G at position 6. We show that complexes containing T:A or C:G at position 6 exhibit similar overall DNA bend angles and local geometries of DNA kinking. We infer that indirect readout in this system does not involve differences in the geometry of DNA kinking but, rather, solely differences in the energetics of DNA kinking. We further infer that the main determinant of DNA conformation in this system is protein-DNA interaction, and not DNA sequence.


    Related Citations: 
    • 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

    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 PROTEINAB200Escherichia coliMutation(s): 0 
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(*GP*CP*GP*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)-3'C, F14N/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*TP*CP*G)-3'D, E17N/A
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      CMP
      Query on CMP

      Download CCD File 
      A, B
      ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
      C10 H12 N5 O6 P
      IVOMOUWHDPKRLL-KQYNXXCUSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.80 Å
      • R-Value Free: 0.303 
      • R-Value Work: 0.230 
      • R-Value Observed: 0.230 
      • Space Group: C 2 2 21
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 136.99α = 90
      b = 152.8β = 90
      c = 76.06γ = 90
      Software Package:
      Software NamePurpose
      VRIEDdata reduction
      AMoREphasing
      CNSrefinement
      VRIEDdata 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
      • Version 1.3: 2017-10-04
        Changes: Refinement description