1A25

C2 DOMAIN FROM PROTEIN KINASE C (BETA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

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


Literature

Structure of the protein kinase Cbeta phospholipid-binding C2 domain complexed with Ca2+.

Sutton, R.B.Sprang, S.R.

(1998) Structure 6: 1395-1405

  • DOI: https://doi.org/10.1016/s0969-2126(98)00139-7
  • Primary Citation of Related Structures:  
    1A25

  • PubMed Abstract: 

    Conventional isoforms (alpha, beta and gamma) of protein kinase C (PKC) are synergistically activated by phosphatidylserine and Ca2+; both bind to C2 domains located within the PKC amino-terminal regulatory regions. C2 domains contain a bipartite or tripartite Ca2+-binding site formed by opposing loops at one end of the protein. Neither the structural basis for cooperativity between phosphatidylserine and Ca2+, nor the binding site for phosphatidylserine are known. The structure of the C2 domain from PKCbeta complexed with Ca2+ and o-phospho-L-serine has been determined to 2.7 A resolution using X-ray crystallography. The eight-stranded, Greek key beta-sandwich fold of PKCbeta-C2 is similar to that of the synaptotagmin I type I C2 domain. Three Ca2+ ions, one at a novel site, were located, each sharing common aspartate ligands. One of these ligands is donated by a dyad-related C2 molecule. A phosphoserine molecule binds to a lysine-rich cluster in C2. Shared ligation among the three Ca2+ ions suggests that they bind cooperatively to PKCbeta-C2. Cooperativity may be compromised by the accumulation of positive charge in the binding site as successive ions are bound. Model building shows that the C1 domain could provide carboxylate and carbonyl ligands for two of the three Ca2+ sites. Ca2+-mediated interactions between the two domains could contribute to enzyme activation as well as to the creation of a positively charged phosphatidylserine-binding site.


  • Organizational Affiliation

    Howard Hughes Medical Institute Department of Biochemistry The University of Texas Southwestern Medical Center 5323 Harry Hines Blvd. Dallas, TX 75235-9050, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN KINASE C (BETA)
A, B
149Rattus norvegicusMutation(s): 0 
EC: 2.7.1 (PDB Primary Data), 2.7.11.13 (UniProt)
Membrane Entity: Yes 
UniProt
Find proteins for P68403 (Rattus norvegicus)
Explore P68403 
Go to UniProtKB:  P68403
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP68403
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.798α = 90
b = 77.798β = 90
c = 140.826γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-06
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-02
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-05-22
    Changes: Data collection