1FOT

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.6 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
  • Structures With Same Primary Citation

  • 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 1A318Saccharomyces cerevisiaeMutation(s): 1 
EC: 2.7.1.37 (PDB Primary Data), 2.7.11.11 (UniProt)
Find proteins for P06244 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06244 
Go to UniProtKB:  P06244
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
AL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.194 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61α = 90
b = 61β = 90
c = 322γ = 120
Software Package:
Software NamePurpose
CNSrefinement
X-PLORrefinement
PHASESphasing
MADNESSdata reduction
FSdata scaling
PROTEINdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-06-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-04-18
    Changes: Data collection
  • Version 1.5: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.6: 2019-08-14
    Changes: Data collection