1J3H

Crystal structure of apoenzyme cAMP-dependent protein kinase catalytic subunit


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Dynamic Features of cAMP-dependent Protein Kinase Revealed by Apoenzyme Crystal Structure

Akamine, P.MadhusudanWu, J.Xuong, N.-H.Ten Eyck, L.F.Taylor, S.S.

(2003) J.Mol.Biol. 327: 159-171


  • PubMed Abstract: 
  • To better understand the mechanism of ligand binding and ligand-induced conformational change, the crystal structure of apoenzyme catalytic (C) subunit of adenosine-3',5'-cyclic monophosphate (cAMP)-dependent protein kinase (PKA) was solved. The apoe ...

    To better understand the mechanism of ligand binding and ligand-induced conformational change, the crystal structure of apoenzyme catalytic (C) subunit of adenosine-3',5'-cyclic monophosphate (cAMP)-dependent protein kinase (PKA) was solved. The apoenzyme structure (Apo) provides a snapshot of the enzyme in the first step of the catalytic cycle, and in this unliganded form the PKA C subunit adopts an open conformation. A hydrophobic junction is formed by residues from the small and large lobes that come into close contact. This "greasy" patch may lubricate the shearing motion associated with domain rotation, and the opening and closing of the active-site cleft. Although Apo appears to be quite dynamic, many important residues for MgATP binding and phosphoryl transfer in the active site are preformed. Residues around the adenine ring of ATP and residues involved in phosphoryl transfer from the large lobe are mostly preformed, whereas residues involved in ribose binding and in the Gly-rich loop are not. Prior to ligand binding, Lys72 and the C-terminal tail, two important ATP-binding elements are also disordered. The surface created in the active site is contoured to bind ATP, but not GTP, and appears to be held in place by a stable hydrophobic core, which includes helices C, E, and F, and beta strand 6. This core seems to provide a network for communicating from the active site, where nucleotide binds, to the peripheral peptide-binding F-to-G helix loop, exemplified by Phe239. Two potential lines of communication are the D helix and the F helix. The conserved Trp222-Phe238 network, which lies adjacent to the F-to-G helix loop, suggests that this network would exist in other protein kinases and may be a conserved means of communicating ATP binding from the active site to the distal peptide-binding ledge.


    Related Citations: 
    • Structure of the mammalian catalytic subunit of cAMP-dependent protein kinase and an inhibitor peptide displays an open conformation
      Karlsson, R.,Zheng, J.,Xuong, N.,Taylor, S.S.,Sowadski, J.M.
      (1993) Acta Crystallogr.,Sect.D 49: 381
    • Crystal structure of a transition state mimic of the catalytic subunit of cAMP-dependent protein kinase
      Madhusudan,Akamine, P.,Xuong, N.H.,Taylor, S.S.
      (2002) Nat.Struct.Mol.Biol. 9: 273
    • A binary complex of the catalytic subunit of cAMP-dependent protein kinase and adenosine further defines conformational flexibility
      Narayana, N.,Cox, S.,Nguyen-huu, X.,Ten Eyck, L.F.,Taylor, S.S.
      (1997) Structure 5: 921
    • Crystal structures of the myristylated catalytic subunit of cAMP-dependent protein kinase reveal open and closed conformations
      Zheng, J.,Knighton, D.R.,Xuong, N.H.,Taylor, S.S.,Sowadski, J.M.,Ten Eyck, L.F.
      (1993) Protein Sci. 2: 1559
    • Crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MgATP and peptide inhibitor
      Zheng, J.,Knighton, D.R.,Ten Eyck, L.F.,Karlsson, R.,Xuong, N.,Taylor, S.S.,Sowadski, J.M.
      (1993) Biochemistry 32: 2154


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California-San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0654, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-dependent protein kinase, alpha-catalytic subunit
A, B
350Mus musculusMutation(s): 0 
Gene Names: Prkaca (Pkaca)
EC: 2.7.11.11
Find proteins for P05132 (Mus musculus)
Go to UniProtKB:  P05132
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
A, B
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
CME
Query on CME
A, B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.257 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.776α = 90.00
b = 143.601β = 105.71
c = 62.809γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-04
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance