3HIF

The crystal structure of apo wild type CAP at 3.6 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.295 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding.

Sharma, H.Yu, S.Kong, J.Wang, J.Steitz, T.A.

(2009) Proc.Natl.Acad.Sci.USA 106: 16604-16609

  • DOI: 10.1073/pnas.0908380106
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The binding of cAMP to the Escherichia coli catabolite gene activator protein (CAP) produces a conformational change that enables it to bind specific DNA sequences and regulate transcription, which it cannot do in the absence of the nucleotide. The c ...

    The binding of cAMP to the Escherichia coli catabolite gene activator protein (CAP) produces a conformational change that enables it to bind specific DNA sequences and regulate transcription, which it cannot do in the absence of the nucleotide. The crystal structures of the unliganded CAP containing a D138L mutation and the unliganded WT CAP were determined at 2.3 and 3.6 A resolution, respectively, and reveal that the two DNA binding domains have dimerized into one rigid body and their two DNA recognition helices become buried. The WT structure shows multiple orientations of this rigid body relative to the nucleotide binding domain supporting earlier biochemical data suggesting that the inactive form exists in an equilibrium among different conformations. Comparison of the structures of the liganded and unliganded CAP suggests that cAMP stabilizes the active DNA binding conformation of CAP through the interactions that the N(6) of the adenosine makes with the C-helices. These interactions are associated with the reorientation and elongation of the C-helices that precludes the formation of the inactive structure.


    Organizational Affiliation

    Departments of Chemistry and Molecular Biophysics and Biochemistry, Yale University, Howard Hughes Medical Institute, New Haven, CT 06511, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Catabolite gene activator
A, B, C, D, E, F
210Escherichia coli (strain K12)Gene Names: crp (cap, csm)
Find proteins for P0ACJ8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ACJ8
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.59 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.295 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 125.291α = 90.00
b = 125.291β = 90.00
c = 224.677γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
DMphasing
HKL-2000data reduction
HKL-2000data collection
DMmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance