1FOT

STRUCTURE OF THE UNLIGANDED CAMP-DEPENDENT PROTEIN KINASE CATALYTIC SUBUNIT FROM SACCHAROMYCES CEREVISIAE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the unliganded cAMP-dependent protein kinase catalytic subunit from Saccharomyces cerevisiae.

Mashhoon, N.Carmel, G.Pflugrath, J.W.Kuret, J.

(2001) Arch.Biochem.Biophys. 387: 11-19

  • DOI: 10.1006/abbi.2000.2241

  • PubMed Abstract: 
  • The structure of TPK1delta, a truncated variant of the cAMP-dependent protein kinase catalytic subunit from Saccharomyces cerevisiae, was determined in an unliganded state at 2.8 A resolution and refined to a crystallographic R-factor of 19.4%. Compa ...

    The structure of TPK1delta, a truncated variant of the cAMP-dependent protein kinase catalytic subunit from Saccharomyces cerevisiae, was determined in an unliganded state at 2.8 A resolution and refined to a crystallographic R-factor of 19.4%. Comparison of this structure to that of its fully liganded mammalian homolog revealed a highly conserved protein fold comprised of two globular lobes. Within each lobe, root mean square deviations in Calpha positions averaged approximately equals 0.9 A. In addition, a phosphothreonine residue was found in the C-terminal domain of each enzyme. Further comparison of the two structures suggests that a trio of conformational changes accompanies ligand-binding. The first consists of a 14.7 degrees rigid-body rotation of one lobe relative to the other and results in closure of the active site cleft. The second affects only the glycine-rich nucleotide binding loop, which moves approximately equals 3 A to further close the active site and traps the nucleotide substrate. The third is localized to a C-terminal segment that makes direct contact with ligands and the ligand-binding cleft. In addition to resolving the conformation of unliganded enzyme, the model shows that the salient features of the cAMP-dependent protein kinase are conserved over long evolutionary distances.


    Related Citations: 
    • Crystallization and Preliminary X-ray Analysis of the cAMP-Depende Protein Kinase Catalytic Subunit from Saccharomyces cerevisiae
      Kuret, J.,Pflugrath, J.W.
      (1991) Biochemistry 30: 10595


    Organizational Affiliation

    Biophysics Program, Ohio State University Medical School, Columbus 43210, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CAMP-DEPENDENT PROTEIN KINASE TYPE 1
A
318Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: TPK1 (PKA1, SRA3)
EC: 2.7.11.11
Find proteins for P06244 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: TPK1
Go to UniProtKB:  P06244
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.194 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 61.000α = 90.00
b = 61.000β = 90.00
c = 322.000γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
PHASESphasing
FSdata scaling
CNSrefinement
MADNESSdata reduction
PROTEINdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-06-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description