4DFY | pdb_00004dfy

Crystal structure of R194A mutant of cAMP-dependent protein kinase with unphosphorylated activation loop


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.286 (Depositor), 0.284 (DCC) 
  • R-Value Work: 
    0.252 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 
    0.253 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

Structural basis for the regulation of protein kinase a by activation loop phosphorylation.

Steichen, J.M.Kuchinskas, M.Keshwani, M.M.Yang, J.Adams, J.A.Taylor, S.S.

(2012) J Biological Chem 287: 14672-14680

  • DOI: https://doi.org/10.1074/jbc.M111.335091
  • Primary Citation Related Structures: 
    4DFY

  • PubMed Abstract: 

    The catalytic subunit of cAMP-dependent protein kinase (PKA) is a member of the AGC group of protein kinases. Whereas PKA has served as a structural model for the protein kinase superfamily, all previous structures of the catalytic subunit contain a phosphorylated activation loop. To understand the structural effects of activation loop phosphorylation at Thr-197 we used a PKA mutant that does not autophosphorylate at Thr-197. The enzyme crystallized in the apo-state, and the structure was solved to 3.0 Å. The N-lobe is rotated by 18° relative to the wild-type apoenzyme, which illustrates that the enzyme likely exists in a wide range of conformations in solution due to the uncoupling of the N- and C-lobes. Several regions of the protein including the activation loop are disordered in the structure, and there are alternate main chain conformations for the magnesium positioning loop and catalytic loop causing a complete loss of hydrogen bonding between these two active site structural elements. These alterations are reflected in a 20-fold decrease in the apparent phosphoryl transfer rate as measured by pre-steady-state kinetic methods.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093, USA.

Macromolecule Content 

  • Total Structure Weight: 85.59 kDa 
  • Atom Count: 4,991 
  • Modeled Residue Count: 624 
  • Deposited Residue Count: 742 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
cAMP-dependent protein kinase catalytic subunit alphaA,
B [auth E]
371Mus musculusMutation(s): 1 
Gene Names: PrkacaPkaca
EC: 2.7.11.11
UniProt
Find proteins for P05132 (Mus musculus)
Explore P05132 
Go to UniProtKB:  P05132
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05132
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SEP
Query on SEP
A,
B [auth E]
L-PEPTIDE LINKINGC3 H8 N O6 PSER

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.286 (Depositor), 0.284 (DCC) 
  • R-Value Work:  0.252 (Depositor), 0.245 (DCC) 
  • R-Value Observed: 0.253 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.745α = 90
b = 95.745β = 90
c = 173.959γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-02-15
    Type: Initial release
  • Version 1.1: 2012-02-29
    Changes: Database references
  • Version 1.2: 2012-05-16
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-10-30
    Changes: Structure summary