4QUM

Crystal structure of PTPN3 (PTPH1) in complex with a dually phosphorylated MAPK12 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.516 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1126/scisignal.2005722
  • Primary Citation of Related Structures:  

  • 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 combin ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein phosphatase non-receptor type 3
A
306Homo sapiensMutation(s): 2 
Gene Names: PTPN3 (PTPH1)
EC: 3.1.3.48
Find proteins for P26045 (Homo sapiens)
Go to Gene View: PTPN3
Go to UniProtKB:  P26045
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Mitogen-activated protein kinase 12
B
9Homo sapiensMutation(s): 1 
Gene Names: MAPK12 (ERK6, SAPK3)
EC: 2.7.11.24
Find proteins for P53778 (Homo sapiens)
Go to Gene View: MAPK12
Go to UniProtKB:  P53778
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
TPO
Query on TPO
B
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.516 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.197 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 75.491α = 90.00
b = 75.491β = 90.00
c = 109.605γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data reduction
Blu-Icedata collection
PHASESphasing
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2018-07-18
    Type: Advisory, Data collection