2HWN

Crystal Structure of RII alpha Dimerization/Docking domain of PKA bound to the D-AKAP2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Dynamic Mechanism for AKAP Binding to RII Isoforms of cAMP-Dependent Protein Kinase.

Kinderman, F.S.Kim, C.von Daake, S.Ma, Y.Pham, B.Q.Spraggon, G.Xuong, N.H.Jennings, P.A.Taylor, S.S.

(2006) Mol.Cell 24: 397-408

  • DOI: 10.1016/j.molcel.2006.09.015

  • PubMed Abstract: 
  • A kinase-anchoring proteins (AKAPs) target PKA to specific microdomains by using an amphipathic helix that docks to N-terminal dimerization and docking (D/D) domains of PKA regulatory (R) subunits. To understand specificity, we solved the crystal str ...

    A kinase-anchoring proteins (AKAPs) target PKA to specific microdomains by using an amphipathic helix that docks to N-terminal dimerization and docking (D/D) domains of PKA regulatory (R) subunits. To understand specificity, we solved the crystal structure of the helical motif from D-AKAP2, a dual-specific AKAP, bound to the RIIalpha D/D domain. The 1.6 Angstrom structure reveals how this dynamic, hydrophobic docking site is assembled. A stable, hydrophobic docking groove is formed by the helical interface of two RIIalpha protomers. The flexible N terminus of one protomer is then recruited to the site, anchored to the peptide through two essential isoleucines. The other N terminus is disordered. This asymmetry provides greater possibilities for AKAP docking. Although there is strong discrimination against RIalpha in the N terminus of the AKAP helix, the hydrophobic groove discriminates against RIIalpha. RIalpha, with a cavity in the groove, can accept a bulky tryptophan, whereas RIIalpha requires valine.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, San Diego, California 92093, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase type II-alpha regulatory subunit
A, B, C, D
45Rattus norvegicusMutation(s): 0 
Gene Names: Prkar2a
Find proteins for P12368 (Rattus norvegicus)
Go to UniProtKB:  P12368
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
A Kinase binding peptide
E, F
22Macaca fascicularisMutation(s): 0 
Find proteins for Q4R5S0 (Macaca fascicularis)
Go to UniProtKB:  Q4R5S0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.208 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 99.551α = 90.00
b = 44.561β = 124.07
c = 72.802γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
AMoREphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-08-01 
  • Released Date: 2006-11-21 
  • Deposition Author(s): Kinderman, F., Kim, C.

Revision History 

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Refinement description, Version format compliance