5EZ0

CRYSTAL STRUCTURE OF THE PTPN4 PDZ DOMAIN COMPLEXED WITH THE PDZ BINDING MOTIF OF THE MITOGEN ACTIVATED PROTEIN KINASE P38GAMMA.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Molecular Basis of the Interaction of the Human Protein Tyrosine Phosphatase Non-receptor Type 4 (PTPN4) with the Mitogen-activated Protein Kinase p38 gamma.

Maisonneuve, P.Caillet-Saguy, C.Vaney, M.C.Bibi-Zainab, E.Sawyer, K.Raynal, B.Haouz, A.Delepierre, M.Lafon, M.Cordier, F.Wolff, N.

(2016) J Biol Chem 291: 16699-16708

  • DOI: 10.1074/jbc.M115.707208
  • Primary Citation of Related Structures:  
    5EYZ, 5EZ0

  • PubMed Abstract: 
  • The human protein tyrosine phosphatase non-receptor type 4 (PTPN4) prevents cell death induction in neuroblastoma and glioblastoma cell lines in a PDZ·PDZ binding motifs-dependent manner, but the cellular partners of PTPN4 involved in cell protection are unknown ...

    The human protein tyrosine phosphatase non-receptor type 4 (PTPN4) prevents cell death induction in neuroblastoma and glioblastoma cell lines in a PDZ·PDZ binding motifs-dependent manner, but the cellular partners of PTPN4 involved in cell protection are unknown. Here, we described the mitogen-activated protein kinase p38γ as a cellular partner of PTPN4. The main contribution to the p38γ·PTPN4 complex formation is the tight interaction between the C terminus of p38γ and the PDZ domain of PTPN4. We solved the crystal structure of the PDZ domain of PTPN4 bound to the p38γ C terminus. We identified the molecular basis of recognition of the C-terminal sequence of p38γ that displays the highest affinity among all endogenous partners of PTPN4. We showed that the p38γ C terminus is also an efficient inducer of cell death after its intracellular delivery. In addition to recruiting the kinase, the binding of the C-terminal sequence of p38γ to PTPN4 abolishes the catalytic autoinhibition of PTPN4 and thus activates the phosphatase, which can efficiently dephosphorylate the activation loop of p38γ. We presume that the p38γ·PTPN4 interaction promotes cellular signaling, preventing cell death induction.


    Related Citations: 
    • Peptides targeting the PDZ domain of PTPN4 are efficient inducers of glioblastoma cell death.
      Babault, N., Cordier, F., Lafage, M., Cockburn, J., Haouz, A., Prehaud, C., Rey, F.A., Delepierre, M., Buc, H., Lafon, M., Wolff, N.
      (2011) Structure 19: 1518

    Organizational Affiliation

    From the Département de Biologie Structurale et Chimie, Unité de Résonance Magnétique Nucléaire des Biomolécules, UMR 3528 and nicolas.wolff@pasteur.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 4A, B, C, D107Homo sapiensMutation(s): 0 
Gene Names: PTPN4
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P29074 (Homo sapiens)
Explore P29074 
Go to UniProtKB:  P29074
PHAROS:  P29074
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 12E, F, G, H11Homo sapiensMutation(s): 0 
Gene Names: MAPK12hCG_2039437
EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for B5MDL5 (Homo sapiens)
Explore B5MDL5 
Go to UniProtKB:  B5MDL5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
I [auth D], J [auth G]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.564α = 90
b = 76.121β = 90
c = 198.676γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2016-06-15
    Changes: Database references
  • Version 1.2: 2016-08-17
    Changes: Database references
  • Version 1.3: 2017-12-20
    Changes: Database references, Structure summary