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: 2.90 Å
  • R-Value Work: 0.233 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    1CMK

  • 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 catalytic subunit ternary complex (Zheng, J ...

    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: 
    • 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 D Biol Crystallogr 49: 381
    • 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 D Biol Crystallogr 49: 362
    • 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
    • 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
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNITA [auth E]350Sus scrofaMutation(s): 0 
Gene Names: PRKACA
EC: 2.7.11.11
UniProt
Find proteins for P36887 (Sus scrofa)
Explore P36887 
Go to UniProtKB:  P36887
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
cAMP-dependent protein kinase inhibitor, alpha formB [auth I]22Homo sapiensMutation(s): 0 
Gene Names: PKIAPRKACN1
UniProt & NIH Common Fund Data Resources
Find proteins for P61925 (Homo sapiens)
Explore P61925 
Go to UniProtKB:  P61925
PHAROS:  P61925
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR (Subject of Investigation/LOI)
Query on MYR

Download Ideal Coordinates CCD File 
C [auth E]MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
IOD
Query on IOD

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.52α = 90
b = 171.52β = 90
c = 171.52γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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