4QUN

Crystal structure of the PTPN3 (PTPH1) catalytic domain C842S mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Reciprocal allosteric regulation of p38 gamma and PTPN3 involves a PDZ domain-modulated complex formation.

Chen, K.E.Lin, S.Y.Wu, M.J.Ho, M.R.Santhanam, A.Chou, C.C.Meng, T.C.Wang, A.H.J.

(2014) Sci Signal 7: ra98-ra98

  • DOI: https://doi.org/10.1126/scisignal.2005722
  • Primary Citation of Related Structures:  
    4QUM, 4QUN

  • PubMed Abstract: 
  • The mitogen-activated protein kinase p38γ (also known as MAPK12) and its specific phosphatase PTPN3 (also known as PTPH1) cooperate to promote Ras-induced oncogenesis. We determined the architecture of the PTPN3-p38γ complex by a hybrid method combining x-ray crystallography, small-angle x-ray scattering, and chemical cross-linking coupled to mass spectrometry ...

    The mitogen-activated protein kinase p38γ (also known as MAPK12) and its specific phosphatase PTPN3 (also known as PTPH1) cooperate to promote Ras-induced oncogenesis. We determined the architecture of the PTPN3-p38γ complex by a hybrid method combining x-ray crystallography, small-angle x-ray scattering, and chemical cross-linking coupled to mass spectrometry. A unique feature of the glutamic acid-containing loop (E-loop) of the phosphatase domain defined the substrate specificity of PTPN3 toward fully activated p38γ. The solution structure revealed the formation of an active-state complex between p38γ and the phosphatase domain of PTPN3. The PDZ domain of PTPN3 stabilized the active-state complex through an interaction with the PDZ-binding motif of p38γ. This interaction alleviated autoinhibition of PTPN3, enabling efficient tyrosine dephosphorylation of p38γ. Our findings may enable structure-based drug design targeting the PTPN3-p38γ interaction as an anticancer therapeutic.


    Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei 11581, Taiwan. National Core Facility for Protein Structural Analysis, Academia Sinica, Taipei 11581, Taiwan. Institute of Biochemical Sciences, National Taiwan University, Taipei 10717, Taiwan. Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 11047, Taiwan. tcmeng@gate.sinica.edu.tw ahjwang@gate.sinica.edu.tw.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 3
A, B
306Homo sapiensMutation(s): 1 
Gene Names: PTPH1PTPN3
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P26045 (Homo sapiens)
Explore P26045 
Go to UniProtKB:  P26045
PHAROS:  P26045
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26045
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.74α = 90
b = 97β = 90
c = 138.207γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASESphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-12-10
    Type: Initial release