4QUM

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

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:  
    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 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. 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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 3A306Homo sapiensMutation(s): 2 
Gene Names: PTPH1PTPN3
EC: 3.1.3.48
Find proteins for P26045 (Homo sapiens)
Explore P26045 
Go to UniProtKB:  P26045
NIH Common Fund Data Resources
PHAROS  P26045
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Mitogen-activated protein kinase 12B9Homo sapiensMutation(s): 1 
Gene Names: MAPK12ERK6SAPK3
EC: 2.7.11.24
Find proteins for P53778 (Homo sapiens)
Explore P53778 
Go to UniProtKB:  P53778
NIH Common Fund Data Resources
PHAROS  P53778
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PTR
Query on PTR
BL-PEPTIDE LINKINGC9 H12 N O6 PTYR
TPO
Query on TPO
BL-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.52 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.491α = 90
b = 75.491β = 90
c = 109.605γ = 120
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 

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