1CDK

CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT (E.C.2.7.1.37) (PROTEIN KINASE A) COMPLEXED WITH PROTEIN KINASE INHIBITOR PEPTIDE FRAGMENT 5-24 (PKI(5-24) ISOELECTRIC VARIANT CA) AND MN2+ ADENYLYL IMIDODIPHOSPHATE (MNAMP-PNP) AT PH 5.6 AND 7C AND 4C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Phosphotransferase and substrate binding mechanism of the cAMP-dependent protein kinase catalytic subunit from porcine heart as deduced from the 2.0 A structure of the complex with Mn2+ adenylyl imidodiphosphate and inhibitor peptide PKI(5-24).

Bossemeyer, D.Engh, R.A.Kinzel, V.Ponstingl, H.Huber, R.

(1993) EMBO J. 12: 849-859


  • PubMed Abstract: 
  • The crystal structure of the porcine heart catalytic subunit of cAMP-dependent protein kinase in a ternary complex with the MgATP analogue MnAMP-PNP and a pseudosubstrate inhibitor peptide, PKI(5-24), has been solved at 2.0 A resolution from monoclin ...

    The crystal structure of the porcine heart catalytic subunit of cAMP-dependent protein kinase in a ternary complex with the MgATP analogue MnAMP-PNP and a pseudosubstrate inhibitor peptide, PKI(5-24), has been solved at 2.0 A resolution from monoclinic crystals of the catalytic subunit isoform CA. The refinement is presently at an R factor of 0.194 and the active site of the molecule is well defined. The glycine-rich phosphate anchor of the nucleotide binding fold motif of the protein kinase is a beta ribbon acting as a flap with conformational flexibility over the triphosphate group. The glycines seem to be conserved to avoid steric clash with ATP. The known synergistic effects of substrate binding can be explained by hydrogen bonds present only in the ternary complex. Implications for the kinetic scheme of binding order are discussed. The structure is assumed to represent a phosphotransfer competent conformation. The invariant conserved residue Asp166 is proposed to be the catalytic base and Lys168 to stabilize the transition state. In some tyrosine kinases Lys168 is functionally replaced by an Arg displaced by two residues in the primary sequence, suggesting invariance in three-dimensional space. The structure supports an in-line transfer with a pentacoordinate transition state at the phosphorus with very few nuclear movements.


    Related Citations: 
    • 2.2 Angstrom Refined Crystal Structure of the Catalytic Subunit of cAMP-Dependent Protein Kinase Complexed with Mnatp and a Peptide Inhibitor
      Zheng, J.,Trafny, E.A.,Knighton, D.R.,Xuong, N.-H.,Taylor, S.S.,Ten Eyck, L.F.,Sowadski, J.M.
      (1993) Acta Crystallogr.,Sect.D 49: 362
    • A Sequence Variant in the N-Terminal Region of the Catalytic Subunit of the cAMP-Dependent Protein Kinase
      Hotz, A.,Konig, N.,Kretschmer, J.,Maier, G.,Ponstingl, H.,Kinzel, V.
      (1989) FEBS Lett. 256: 115
    • Crystal Structures of the Myristylated Catalytic Subunit Ofcamp-Dependent Kinase Reveal Open and Closed Conformation
      Zheng, J.,Knighton, D.R.,Xuong, N.-H.,Taylor, S.S.,Sowadski, J.M.,Ten Eyck, L.F.
      (1993) Protein Sci. 2: 1559
    • Regulation by Phosphorylation of Reversible Association of a Myristoylated Protein Kinase C Substrate with the Plasma Membrane
      Thelen, M.,Rosen, A.,Nairn, A.C.,Aderem, A.
      (1991) Nature 351: 320
    • Crystal Structure of the Catalytic Subunit of Cyclic Adenosine Monophosphate Dependent-Protein Kinase
      Knighton, D.R.,Zheng, J.H.,Ten Eyck, L.F.,Ashford, V.A.,Xuong, N.-H.,Taylor, S.S.,Sowadski, J.M.
      (1991) Science 253: 407
    • Characterization of Genomic Clones Coding for the C-Alpha and C-Beta Subunits of Mouse Camp Dependent Protein Kinase
      Chrivia, J.C.,Uhler, M.D.,Mcknight, G.S.
      (1988) J.Biol.Chem. 263: 5739
    • Structure of a Peptide Inhibitor Bound to the Catalytic Subunit of a Cyclic Adenosine Monophosphate-Dependent Protein Kinase
      Knighton, D.R.,Zheng, J.,Ten Eyck, L.F.,Xoung, N.-H.,Taylor, S.S.,Sowadski, J.M.
      (1991) Science 253: 414


    Organizational Affiliation

    Deutsches Krebsforschungzentrum, Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CAMP-DEPENDENT PROTEIN KINASE
A, B
350Sus scrofaGene Names: PRKACA
EC: 2.7.11.11
Find proteins for P36887 (Sus scrofa)
Go to Gene View: PRKACA
Go to UniProtKB:  P36887
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN KINASE INHIBITOR
I, J
20Oryctolagus cuniculusGene Names: PKIA (PRKACN1)
Find proteins for P61926 (Oryctolagus cuniculus)
Go to Gene View: PKIA
Go to UniProtKB:  P61926
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
MYR
Query on MYR

Download SDF File 
Download CCD File 
A, B
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, B
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Work: 0.197 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 107.610α = 90.00
b = 80.600β = 88.59
c = 110.100γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-07-18
    Type: Source and taxonomy