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 6EWX | pdb_00006ewx

Structure of Pragmin pseudo-kinase reveals a dimerization mechanism to regulate protein tyrosine phosphorylation and nuclear transcription


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free: 
    0.246 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6EWX

This is version 1.2 of the entry. See complete history. 

Literature

Dimerization of the Pragmin Pseudo-Kinase Regulates Protein Tyrosine Phosphorylation.

Lecointre, C., Simon, V., Kerneur, C., Allemand, F., Fournet, A., Montarras, I., Pons, J.L., Gelin, M., Brignatz, C., Urbach, S., Labesse, G., Roche, S.

(2018) Structure 26: 545-554.e4

  • DOI: https://doi.org/10.1016/j.str.2018.01.017
  • Primary Citation Related Structures: 
    6EWX

  • PubMed Abstract: 

    The pseudo-kinase and signaling protein Pragmin has been linked to cancer by regulating protein tyrosine phosphorylation via unknown mechanisms. Here we present the crystal structure of the Pragmin 906-1,368 amino acid C terminus, which encompasses its kinase domain. We show that Pragmin contains a classical protein-kinase fold devoid of catalytic activity, despite a conserved catalytic lysine (K997). By proteomics, we discovered that this pseudo-kinase uses the tyrosine kinase CSK to induce protein tyrosine phosphorylation in human cells. Interestingly, the protein-kinase domain is flanked by N- and C-terminal extensions forming an original dimerization domain that regulates Pragmin self-association and stimulates CSK activity. A1329E mutation in the C-terminal extension destabilizes Pragmin dimerization and reduces CSK activation. These results reveal a dimerization mechanism by which a pseudo-kinase can induce protein tyrosine phosphorylation. Further sequence-structure analysis identified an additional member (C19orf35) of the superfamily of dimeric Pragmin/SgK269/PEAK1 pseudo-kinases.


  • Organizational Affiliation: 
    • CRBM, "Equipe Labellisée Ligue Contre le Cancer", Univ Montpellier, CNRS, 34000 Montpellier, France.

Macromolecule Content 

  • Total Structure Weight: 107.92 kDa 
  • Atom Count: 5,705 
  • Modeled Residue Count: 717 
  • Deposited Residue Count: 968 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PEAK1-related kinase-activating pseudokinase 1
A, B
484Rattus norvegicusMutation(s): 0 
Gene Names: Prag1, Pragmin, RGD1311793_predicted, rCG_43329
UniProt
Find proteins for D3ZMK9 (Rattus norvegicus)
Explore D3ZMK9 
Go to UniProtKB:  D3ZMK9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD3ZMK9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.77 Å
  • R-Value Free:  0.246 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.43α = 90
b = 58.92β = 118.48
c = 110.64γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
INCaFrancePLBIO-2011-150
French National Research AgencyFranceANR-10-INBS-05

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-31
    Type: Initial release
  • Version 1.1: 2018-04-18
    Changes: Data collection, Database references
  • Version 1.2: 2024-05-08
    Changes: Data collection, Database references