1CGP

CATABOLITE GENE ACTIVATOR PROTEIN (CAP)/DNA COMPLEX + ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Work: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees.

Schultz, S.C.Shields, G.C.Steitz, T.A.

(1991) Science 253: 1001-1007

  • DOI: 10.1126/science.1653449
  • Primary Citation of Related Structures:  
    1CGP

  • PubMed Abstract: 
  • The 3 angstrom resolution crystal structure of the Escherichia coli catabolite gene activator protein (CAP) complexed with a 30-base pair DNA sequence shows that the DNA is bent by 90 degrees. This bend results almost entirely from two 40 degrees kinks that occur between TG/CA base pairs at positions 5 and 6 on each side of the dyad axis of the complex ...

    The 3 angstrom resolution crystal structure of the Escherichia coli catabolite gene activator protein (CAP) complexed with a 30-base pair DNA sequence shows that the DNA is bent by 90 degrees. This bend results almost entirely from two 40 degrees kinks that occur between TG/CA base pairs at positions 5 and 6 on each side of the dyad axis of the complex. DNA sequence discrimination by CAP derives both from sequence-dependent distortion of the DNA helix and from direct hydrogen-bonding interactions between three protein side chains and the exposed edges of three base pairs in the major groove of the DNA. The structure of this transcription factor--DNA complex provides insights into possible mechanisms of transcription activation.


    Related Citations: 
    • Crystal Structure of a cAMP-Independent Form of Catabolite Gene Activator Protein with Adenosine Substituted in One of Two cAMP-Binding Sites
      Vaney, M.-C., Gilliland, G.L., Harman, J.G., Peterkofsky, A., Weber, I.T.
      (1989) Biochemistry 28: 4568

    Organizational Affiliation

    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (CATABOLITE GENE ACTIVATOR PROTEIN (CAP))E [auth A],
F [auth B]
205Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0ACJ8 (Escherichia coli (strain K12))
Explore P0ACJ8 
Go to UniProtKB:  P0ACJ8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ACJ8
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*CP*GP*AP*AP*AP*AP*GP*TP*GP*TP*GP*AP*CP*AP*TP*AP*T)-3')A [auth C],
C [auth E]
18synthetic construct
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
DNA (5'-D(*GP*TP*CP*AP*CP*AP*CP*TP*TP*TP*TP*CP*G)-3')B [auth D],
D [auth F]
13synthetic construct
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CMP
Query on CMP

Download Ideal Coordinates CCD File 
G [auth A],
H [auth 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: 3.00 Å
  • R-Value Work: 0.235 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138α = 90
b = 152.6β = 90
c = 76γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-01-31
    Type: Initial release
  • Version 1.1: 2008-05-22
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-02-15
    Changes: Source and taxonomy, Structure summary