4RI5

Crystal structure of PTPN3 (PTPH1) D811E mutant in complex with metavanadate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Substrate specificity and plasticity of FERM-containing protein tyrosine phosphatases.

Chen, K.E.Li, M.Y.Chou, C.C.Ho, M.R.Chen, G.C.Meng, T.C.Wang, A.H.

(2015) Structure 23: 653-664

  • DOI: 10.1016/j.str.2015.01.017
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Epidermal growth factor receptor (EGFR) pathway substrate 15 (Eps15) is a newly identified substrate for protein tyrosine phosphatase N3 (PTPN3), which belongs to the FERM-containing PTP subfamily comprising five members including PTPN3, N4, N13, N14 ...

    Epidermal growth factor receptor (EGFR) pathway substrate 15 (Eps15) is a newly identified substrate for protein tyrosine phosphatase N3 (PTPN3), which belongs to the FERM-containing PTP subfamily comprising five members including PTPN3, N4, N13, N14, and N21. We solved the crystal structures of the PTPN3-Eps15 phosphopeptide complex and found that His812 of PTPN3 and Pro850 of Eps15 are responsible for the specific interaction between them. We defined the critical role of the additional residue Tyr676 of PTPN3, which is replaced by Ile939 in PTPN14, in recognition of tyrosine phosphorylated Eps15. The WPD loop necessary for catalysis is present in all members but not PTPN21. We identified that Glu instead of Asp in the WPE loop contributes to the catalytic incapability of PTPN21 due to an extended distance beyond protonation targeting a phosphotyrosine substrate. Together with in vivo validations, our results provide novel insights into the substrate specificity and plasticity of FERM-containing PTPs.


    Organizational Affiliation

    Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 115, Taiwan; National Core Facility for Protein Structural Analysis, Academia Sinica, Taipei 115, Taiwan; Graduate Institute of Translational Medicine, College of Medical Science and Technology, Taipei Medical University, Taipei 110, Taiwan. Electronic address: ahjwang@gate.sinica.edu.tw.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein phosphatase non-receptor type 3A, B306Homo sapiensMutation(s): 1 
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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
VN4
Query on VN4

Download CCD File 
A, B
oxido(dioxo)vanadium
O3 V
ALTWGIIQPLQAAM-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
A, B
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.162α = 90
b = 96.071β = 90
c = 141.722γ = 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 

  • Version 1.0: 2015-03-11
    Type: Initial release
  • Version 1.1: 2018-07-18
    Changes: Advisory, Data collection, Database references