1MC0

Regulatory Segment of Mouse 3',5'-Cyclic Nucleotide Phosphodiesterase 2A, Containing the GAF A and GAF B Domains


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 

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This is version 1.2 of the entry. See complete history


Literature

The two GAF domains in phosphodiesterase 2A have distinct roles in dimerization and in cGMP binding.

Martinez, S.E.Wu, A.Y.Glavas, N.A.Tang, X.B.Turley, S.Hol, W.G.Beavo, J.A.

(2002) Proc Natl Acad Sci U S A 99: 13260-13265

  • DOI: 10.1073/pnas.192374899
  • Primary Citation of Related Structures:  
    1MC0

  • PubMed Abstract: 
  • Cyclic nucleotide phosphodiesterases (PDEs) regulate all pathways that use cGMP or cAMP as a second messenger. Five of the 11 PDE families have regulatory segments containing GAF domains, 3 of which are known to bind cGMP. In PDE2 binding of cGMP to the GAF domain causes an activation of the catalytic activity by a mechanism that apparently is shared even in the adenylyl cyclase of Anabaena, an organism separated from mouse by 2 billion years of evolution ...

    Cyclic nucleotide phosphodiesterases (PDEs) regulate all pathways that use cGMP or cAMP as a second messenger. Five of the 11 PDE families have regulatory segments containing GAF domains, 3 of which are known to bind cGMP. In PDE2 binding of cGMP to the GAF domain causes an activation of the catalytic activity by a mechanism that apparently is shared even in the adenylyl cyclase of Anabaena, an organism separated from mouse by 2 billion years of evolution. The 2.9-A crystal structure of the mouse PDE2A regulatory segment reported in this paper reveals that the GAF A domain functions as a dimerization locus. The GAF B domain shows a deeply buried cGMP displaying a new cGMP-binding motif and is the first atomic structure of a physiological cGMP receptor with bound cGMP. Moreover, this cGMP site is located well away from the region predicted by previous mutagenesis and structural genomic approaches.


    Organizational Affiliation

    Departments of Pharmacology, and Biochemistry and Biological Structure, Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3',5'-cyclic nucleotide phosphodiesterase 2AA368Mus musculusMutation(s): 0 
Gene Names: Pde2a
EC: 3.1.4.35 (PDB Primary Data), 3.1.4.17 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q922S4 (Mus musculus)
Explore Q922S4 
Go to UniProtKB:  Q922S4
IMPC:  MGI:2446107
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ922S4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PCG
Query on PCG

Download Ideal Coordinates CCD File 
B [auth A]CYCLIC GUANOSINE MONOPHOSPHATE
C10 H12 N5 O7 P
ZOOGRGPOEVQQDX-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.86 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.221 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.2α = 90
b = 136.2β = 90
c = 149.1γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-10-02
    Type: Initial release
  • Version 1.1: 2008-03-19
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance