2CGP | pdb_00002cgp

CATABOLITE GENE ACTIVATOR PROTEIN/DNA COMPLEX, ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE

• PDB DOI: https://doi.org/10.2210/pdb2CGP/pdb
• NAKB: 2CGP

• Classification: TRANSCRIPTION/DNA
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1997-01-31 Released: 1998-02-04 
• Deposition Author(s): Passner, J.M., Steitz, T.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.296 (Depositor), 0.291 (DCC) 
• R-Value Work: 
  0.232 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

The structure of a CAP-DNA complex having two cAMP molecules bound to each monomer.

Passner, J.M., Steitz, T.A.

(1997) Proc Natl Acad Sci U S A 94: 2843-2847

• PubMed: 9096308 
• DOI: https://doi.org/10.1073/pnas.94.7.2843
• Primary Citation Related Structures: 
  2CGP


• PubMed Abstract: 
  

  The 2.2 A resolution crystal structure of the Escherichia coli catabolite gene activator protein (CAP) complexed with cAMP and a 46-bp DNA fragment reveals a second cAMP molecule bound to each protein monomer. The second cAMP is in the syn conformation and is located on the DNA binding domain interacting with the helix-turn-helix, a beta-hairpin from the regulatory domain and the DNA (via water molecules). The presence of this second cAMP site resolves the apparent discrepancy between the NMR and x-ray data on the conformation of cAMP, and explains the cAMP concentration-dependent behaviors of the protein. In addition, this site's close proximity to mutations affecting transcriptional activation and its water-mediated interactions with a DNA recognition residue (E181) and DNA raise the possibility that this site has biological relevance.

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Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.27 kDa 
• Atom Count: 2,303 
• Modeled Residue Count: 226 
• Deposited Residue Count: 236 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (CATABOLITE GENE ACTIVATOR PROTEIN)	C [auth A]	210	Escherichia coli	Mutation(s): 0
UniProt
Find proteins for P0ACJ8 (Escherichia coli (strain K12)) Explore P0ACJ8  Go to UniProtKB:  P0ACJ8

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*TP*CP*AP*CP*AP*TP*TP*AP*AP*T)-3')	A [auth B]	11	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*TP*AP*AP*TP*GP*TP*GP*AP*CP*AP*TP*AP*T)-3')	B [auth C]	15	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CMP	D [auth A], E [auth A]	ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE C10 H12 N5 O6 P IVOMOUWHDPKRLL-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.296 (Depositor), 0.291 (DCC) 
• R-Value Work:  0.232 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.19	α = 90
b = 79.19	β = 90
c = 140.4	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-02-04 
Deposition Author(s): Passner, J.M., Steitz, T.A.

Revision History  

• Version 1.0: 1998-02-04
  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: 2023-08-02
  Changes: Database references, Derived calculations, Refinement description