4JVA

Crystal Structure of RIIbeta(108-402) bound to HE33, a N6 di-propyl substituted cAMP analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Implementing Fluorescence Anisotropy Screening and Crystallographic Analysis to Define PKA Isoform-Selective Activation by cAMP Analogs.

Brown, S.H.Cheng, C.Y.Saldanha, S.A.Wu, J.Cottam, H.B.Sankaran, B.Taylor, S.S.

(2013) Acs Chem.Biol. 8: 2164-2172

  • DOI: 10.1021/cb400247t
  • Primary Citation of Related Structures:  4JV4

  • PubMed Abstract: 
  • Cyclic AMP (cAMP) is a ubiquitous second messenger that regulates many proteins, most notably cAMP-dependent protein kinase (PKA). PKA holoenzymes (comprised of two catalytic (C) and two regulatory (R) subunits) regulate a wide variety of cellular pr ...

    Cyclic AMP (cAMP) is a ubiquitous second messenger that regulates many proteins, most notably cAMP-dependent protein kinase (PKA). PKA holoenzymes (comprised of two catalytic (C) and two regulatory (R) subunits) regulate a wide variety of cellular processes, and its functional diversity is amplified by the presence of four R-subunit isoforms, RIα, RIβ, RIIα, and RIIβ. Although these isoforms all respond to cAMP, they are functionally nonredundant and exhibit different biochemical properties. In order to understand the functional differences between these isoforms, we screened cAMP derivatives for their ability to selectively activate RI and RII PKA holoenzymes using a fluorescence anisotropy assay. Our results indicate that RIα holoenzymes are selectively activated by C8-substituted analogs and RIIβ holoenzymes by N6-substituted analogs, where HE33 is the most prominent RII activator. We also solved the crystal structures of both RIα and RIIβ bound to HE33. The RIIβ structure shows the bulky aliphatic substituent of HE33 is fully encompassed by a pocket comprising of hydrophobic residues. RIα lacks this hydrophobic lining in Domain A, and the side chains are displaced to accommodate the HE33 dipropyl groups. Comparison between cAMP-bound structures reveals that RIIβ, but not RIα, contains a cavity near the N6 site. This study suggests that the selective activation of RII over RI isoforms by N6 analogs is driven by the spatial and chemical constraints of Domain A and paves the way for the development of potent noncyclic nucleotide activators to specifically target PKA iso-holoenyzmes.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, ‡Department of Pharmacology and Howard Hughes Medical Institute, §Moores Cancer Center, University of California , San Diego, La Jolla, California 92037-0654, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase type II-beta regulatory subunit
A
305Rattus norvegicusGene Names: Prkar2b
Find proteins for P12369 (Rattus norvegicus)
Go to UniProtKB:  P12369
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1OR
Query on 1OR

Download SDF File 
Download CCD File 
A
(2R,4aR,6R,7R,7aS)-6-[6-(dipropylamino)-9H-purin-9-yl]tetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinine-2,7-diol 2-oxide
C16 H24 N5 O6 P
QNRWJSITNIAJDB-XNIJJKJLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.238 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 54.514α = 90.00
b = 54.514β = 90.00
c = 199.960γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
ADSCdata collection
HKL-2000data reduction
PHASESphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-10-30
    Type: Database references