1ZRF

4 crystal structures of CAP-DNA with all base-pair substitutions at position 6, CAP-[6C;17G]ICAP38 DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.225 

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: recognition of pyrimidine-purine and purine-purine steps.

Napoli, A.A.Lawson, C.L.Ebright, R.H.Berman, H.M.

(2006) J.Mol.Biol. 357: 173-183

  • DOI: 10.1016/j.jmb.2005.12.051
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The catabolite activator protein (CAP) bends DNA in the CAP-DNA complex, typically introducing 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-si ...

    The catabolite activator protein (CAP) bends DNA in the CAP-DNA complex, typically introducing 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, 5'-A1A2A3T4G5T6G7A8T9C10T11 -3' ("primary kink"). In previous work, we showed that CAP recognizes the nucleotide immediately 5' to the primary-kink site, T6, through an "indirect-readout" mechanism involving sequence effects on energetics of primary-kink formation. Here, to understand further this example of indirect readout, we have determined crystal structures of CAP-DNA complexes containing each possible nucleotide at position 6. The structures show that CAP can introduce a DNA kink at the primary-kink site with any nucleotide at position 6. The DNA kink is sharp with the consensus pyrimidine-purine step T6G7 and the non-consensus pyrimidine-purine step C6G7 (roll angles of approximately 42 degrees, twist angles of approximately 16 degrees ), but is much less sharp with the non-consensus purine-purine steps A6G7 and G6G7 (roll angles of approximately 20 degrees, twist angles of approximately 17 degrees). We infer that CAP discriminates between consensus and non-consensus pyrimidine-purine steps at positions 6-7 solely based on differences in the energetics of DNA deformation, but that CAP discriminates between the consensus pyrimidine-purine step and non-consensus purine-purine steps at positions 6-7 both based on differences in the energetics of DNA deformation and based on qualitative differences in DNA deformation. The structures further show that CAP can achieve a similar, approximately 46 degrees per DNA half-site, overall DNA bend through a sharp DNA kink, a less sharp DNA kink, or a smooth DNA bend. Analysis of these and other crystal structures of CAP-DNA complexes indicates that there is a large, approximately 28 degrees per DNA half-site, out-of-plane component of CAP-induced DNA bending in structures not constrained by end-to-end DNA lattice interactions and that lattice contacts involving CAP tend to involve residues in or near biologically functional surfaces.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology and Waksman Institute Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Catabolite gene activator
A, B
209Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: crp (cap, csm)
Find proteins for P0ACJ8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ACJ8
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*AP*TP*TP*TP*CP*GP*AP*AP*AP*AP*AP*TP*GP*CP*GP*AP*T)-3'W,Y17N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*TP*AP*GP*AP*TP*CP*GP*CP*AP*TP*TP*TP*TP*TP*CP*GP*AP*AP*AP*T)-3'X,Z21N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DIO
Query on DIO

Download SDF File 
Download CCD File 
A, B
1,4-DIETHYLENE DIOXIDE
C4 H8 O2
RYHBNJHYFVUHQT-UHFFFAOYSA-N
 Ligand Interaction
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: 2.1 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.225 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 61.778α = 90.00
b = 77.745β = 90.00
c = 154.813γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data scaling
DENZOdata reduction
CNSrefinement
CBASSdata collection
PHASERphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-21
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description