3SR9 | pdb_00003sr9

Crystal structure of mouse PTPsigma


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.272 (Depositor), 0.231 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3SR9

This is version 1.1 of the entry. See complete history

Literature

Structural insights into the homology and differences between mouse protein tyrosine phosphatase-sigma and human protein tyrosine phosphatase-sigma

Hou, L.Wang, J.Zhou, Y.Li, J.Zang, Y.Li, J.

(2011) Acta Biochim Biophys Sin (Shanghai) 43: 977-988

  • DOI: https://doi.org/10.1093/abbs/gmr095
  • Primary Citation Related Structures: 
    3SR9

  • PubMed Abstract: 

    Protein tyrosine phosphatases PTP-sigma (PTPσ) plays an important role in the development of the nervous system and nerve regeneration. Although cumulative studies about the function of PTPσ have been reported, yet limited data have been reported about the crystal structure and in vitro activity of mouse PTPσ. Here we report the crystal structure of mouse PTPσ tandem phosphatase domains at 2.4 Å resolution. Then we compared the crystal structure of mouse PTPσ with human PTPσ and found that they are very similar, superimposing with a root mean square deviation of 0.45 Å for 517 equivalent Cα atoms. But some residues in mouse PTPσ form loops while corresponding residues in human PTPσ form β-sheets or α-helices. Furthermore, we also compared in vitro activities of mouse PTPσ with human PTPσ and found that mouse PTPσ has 25-fold higher specific activity than human PTPσ does toward O-methyl fluorescein phosphate (OMFP) as the substrate. However, there is no significant activity difference between the mouse and the human enzyme detected with p-nitrophenylphosphate (pNPP) as the substrate. Mouse PTPσ and human PTPσ have different substrate specificities toward OMFP and pNPP as substrates. This work gives clues for further study of PTPσ.


  • Organizational Affiliation
    • School of Life Science, East China Normal University, Shanghai, China.

Macromolecule Content 

  • Total Structure Weight: 67.21 kDa 
  • Atom Count: 4,686 
  • Modeled Residue Count: 568 
  • Deposited Residue Count: 583 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor-type tyrosine-protein phosphatase S583Mus musculusMutation(s): 0 
Gene Names: Ptprs
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for B0V2N1 (Mus musculus)
Explore B0V2N1 
Go to UniProtKB:  B0V2N1
IMPC:  MGI:97815
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0V2N1
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.272 (Depositor), 0.231 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.653α = 90
b = 94.653β = 90
c = 124.201γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references, Refinement description