1CMK

CRYSTAL STRUCTURES OF THE MYRISTYLATED CATALYTIC SUBUNIT OF CAMP-DEPENDENT PROTEIN KINASE REVEAL OPEN AND CLOSED CONFORMATIONS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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: 1559-1573

  • DOI: 10.1002/pro.5560021003

  • PubMed Abstract: 
  • Three crystal structures, representing two distinct conformational states, of the mammalian catalytic subunit of cAMP-dependent protein kinase were solved using molecular replacement methods starting from the refined structure of the recombinant cata ...

    Three crystal structures, representing two distinct conformational states, of the mammalian catalytic subunit of cAMP-dependent protein kinase were solved using molecular replacement methods starting from the refined structure of the recombinant catalytic subunit ternary complex (Zheng, J., et al., 1993a, Biochemistry 32, 2154-2161). These structures correspond to the free apoenzyme, a binary complex with an iodinated inhibitor peptide, and a ternary complex with both ATP and the unmodified inhibitor peptide. The apoenzyme and the binary complex crystallized in an open conformation, whereas the ternary complex crystallized in a closed conformation similar to the ternary complex of the recombinant enzyme. The model of the binary complex, refined at 2.9 A resolution, shows the conformational changes associated with the open conformation. These can be described by a rotation of the small lobe and a displacement of the C-terminal 30 residues. This rotation of the small lobe alters the cleft interface in the active-site region surrounding the glycine-rich loop and Thr 197, a critical phosphorylation site. In addition to the conformational changes, the myristylation site, absent in the recombinant enzyme, was clearly defined in the binary complex. The myristic acid binds in a deep hydrophobic pocket formed by four segments of the protein that are widely dispersed in the linear sequence. The N-terminal 40 residues that lie outside the conserved catalytic core are anchored by the N-terminal myristylate plus an amphipathic helix that spans both lobes and is capped by Trp 30. Both posttranslational modifications, phosphorylation and myristylation, contribute directly to the stable structure of this enzyme.


    Related Citations: 
    • Crystal Structure of the Catalytic Subunit of Camp-Dependent Protein Kinase
      Knighton, D.R.,Zheng, J.,Ten Eyck, L.F.,Ashford, V.A.,Xuong, N.-H.,Taylor, S.S.,Sowadski, J.M.
      (1991) Science 253: 407
    • The Crystal Structure of the Mammalian Catalytic Subunit of Camp-Dependent Protein Kinase and a Di-Iodinated Pki(5-24) Inhibitor Peptide Displays an Open Conformation
      Karlsson, R.,Zheng, J.,Xuong, N.-H.,Taylor, S.S.,Sowadski, J.M.
      (1993) Acta Crystallogr.,Sect.D 49: 381
    • 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.-H.,Taylor, S.S.,Sowadski, J.M.
      (1993) Biochemistry 32: 2154
    • Structure of a Peptide Inhibitor Bound to the Catalytic Subunit of Cyclic Adenosine Monophosphate-Dependent Protein Kinase
      Knighton, D.R.,Zheng, J.,Ten Eyck, L.F.,Xuong, N.-H.,Taylor, S.S.,Sowadski, J.M.
      (1991) Science 253: 414
    • Differential Labeling and Identification of the Cysteine-Containing Tryptic Peptides of Catalytic Subunit from Porcine Heart Camp-Dependent Protein Kinase
      Nelson, N.C.,Taylor, S.S.
      (1981) J.Biol.Chem. 256: 3743
    • 2.2 Angstroms 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
    • Expression of the Catalytic Subunit of Camp-Dependent Protein Kinase in Escherichia Coli
      Slice, L.W.,Taylor, S.S.
      (1989) J.Biol.Chem. 264: 20940


    Organizational Affiliation

    Department of Chemistry, University of California at San Diego, La Jolla 92093.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT
E
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
cAMP-dependent protein kinase inhibitor, alpha form
I
22Homo sapiensGene Names: PKIA (PRKACN1)
Find proteins for P61925 (Homo sapiens)
Go to Gene View: PKIA
Go to UniProtKB:  P61925
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download SDF File 
Download CCD File 
E
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

Download SDF File 
Download CCD File 
I
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
E
L-PEPTIDE LINKINGC3 H8 N O6 PSER
TPO
Query on TPO
E
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.233 
  • Space Group: P 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 171.520α = 90.00
b = 171.520β = 90.00
c = 171.520γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-05-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-07-18
    Type: Source and taxonomy