1O3T

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.303 
  • R-Value Work: 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:  1O3Q, 1O3R

  • 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: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
CATABOLITE GENE ACTIVATOR PROTEIN
A, B
200Escherichia coli (strain K12)Gene Names: crp (cap, csm)
Find proteins for P0ACJ8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ACJ8
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*GP*CP*GP*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)-3'C,F14N/A
Entity ID: 2
MoleculeChainsLengthOrganism
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 SDF File 
Download CCD File 
A, B
ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE
CYCLIC AMP; CAMP
C10 H12 N5 O6 P
IVOMOUWHDPKRLL-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.303 
  • R-Value Work: 0.230 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 136.990α = 90.00
b = 152.800β = 90.00
c = 76.060γ = 90.00
Software Package:
Software NamePurpose
VRIEDdata scaling
VRIEDdata reduction
AMoREphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description