2CJZ

crystal structure of the c472s mutant of human protein tyrosine phosphatase ptpn5 (step, striatum enriched phosphatase) in complex with phosphotyrosine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Large-Scale Structural Analysis of the Classical Human Protein Tyrosine Phosphatome.

Barr, A.J., Ugochukwu, E., Lee, W.H., King, O.N.F., Filippakopoulos, P., Alfano, I., Savitsky, P., Burgess-Brown, N.A., Muller, S., Knapp, S.

(2009) Cell 136: 352

  • DOI: 10.1016/j.cell.2008.11.038
  • Primary Citation of Related Structures:  
  • Also Cited By: 4NND, 4ICZ

  • PubMed Abstract: 

    • Protein tyrosine phosphatases (PTPs) play a critical role in regulating cellular functions by selectively dephosphorylating their substrates. Here we present 22 human PTP crystal structures that, together with prior structural knowledge, enable a com ...

    Protein tyrosine phosphatases (PTPs) play a critical role in regulating cellular functions by selectively dephosphorylating their substrates. Here we present 22 human PTP crystal structures that, together with prior structural knowledge, enable a comprehensive analysis of the classical PTP family. Despite their largely conserved fold, surface properties of PTPs are strikingly diverse. A potential secondary substrate-binding pocket is frequently found in phosphatases, and this has implications for both substrate recognition and development of selective inhibitors. Structural comparison identified four diverse catalytic loop (WPD) conformations and suggested a mechanism for loop closure. Enzymatic assays revealed vast differences in PTP catalytic activity and identified PTPD1, PTPD2, and HDPTP as catalytically inert protein phosphatases. We propose a "head-to-toe" dimerization model for RPTPgamma/zeta that is distinct from the "inhibitory wedge" model and that provides a molecular basis for inhibitory regulation. This phosphatome resource gives an expanded insight into intrafamily PTP diversity, catalytic activity, substrate recognition, and autoregulatory self-association.

    Organizational Affiliation: 

    University of Oxford, Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, Headington, Oxford, OX3 7DQ, UK. alastair.barr@sgc.ox.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HUMAN PROTEIN TYROSINE PHOSPHATASE PTPN5
A
305Homo sapiensMutation(s): 1 
Gene Names: PTPN5
EC: 3.1.3.48
Find proteins for P54829 (Homo sapiens)
Go to Gene View: PTPN5
Go to UniProtKB:  P54829
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO
Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
PTR
Query on PTR
Download SDF File 
Download CCD File 
A
O-PHOSPHOTYROSINE
PHOSPHONOTYROSINE
C9 H12 N O6 P
DCWXELXMIBXGTH-QMMMGPOBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.342α = 90.00
b = 64.348β = 90.00
c = 100.781γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.2: 2012-06-20
    Type: Other
  • Version 1.3: 2018-01-24
    Type: Structure summary