5J8R

Crystal Structure of the Catalytic Domain of Human Protein Tyrosine Phosphatase non-receptor Type 12 - K61R mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.043 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.239 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure and substrate specificity of PTPN12.

Li, H.Yang, F.Liu, C.Xiao, P.Xu, Y.F.Liang, Z.L.Liu, C.Wang, H.M.Wang, W.J.Zheng, W.S.Zhang, W.Ma, X.Y.He, D.F.Song, X.Y.Cui, F.A.Xu, Z.G.Yi, F.Sun, J.P.Yu, X.

(2016) Cell Rep 15: 1-14

  • DOI: 10.1016/j.celrep.2016.04.016

  • PubMed Abstract: 
  • PTPN12 is an important tumor suppressor that plays critical roles in various physiological processes. However, the molecular basis underlying the substrate specificity of PTPN12 remains uncertain. Here, enzymological and crystallographic studies have ...

    PTPN12 is an important tumor suppressor that plays critical roles in various physiological processes. However, the molecular basis underlying the substrate specificity of PTPN12 remains uncertain. Here, enzymological and crystallographic studies have enabled us to identify two distinct structural features that are crucial determinants of PTPN12 substrate specificity: the pY+1 site binding pocket and specific basic charged residues along its surface loops. Key structurally plastic regions and specific residues in PTPN12 enabled recognition of different HER2 phosphorylation sites and regulated specific PTPN12 functions. In addition, the structure of PTPN12 revealed a CDK2 phosphorylation site in a specific PTPN12 loop. Taken together, our results not only provide the working mechanisms of PTPN12 for desphosphorylation of its substrates but will also help in designing specific inhibitors of PTPN12.


    Organizational Affiliation

    Key Laboratory Experimental Teratology of the Ministry of Education and Department of Physiology, Shandong University School of Medicine, 44 Wenhua Xi Road, Jinan, Shandong 250012, China; Department of Molecular Biology and Biochemistry, Shandong University School of Medicine, 44 Wenhua Xi Road, Jinan, Shandong 250012, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein phosphatase non-receptor type 12
A, B, C, D
311Homo sapiensMutation(s): 1 
Gene Names: PTPN12
EC: 3.1.3.48
Find proteins for Q05209 (Homo sapiens)
Go to Gene View: PTPN12
Go to UniProtKB:  Q05209
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.043 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.239 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 129.938α = 90.00
b = 129.938β = 90.00
c = 278.757γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the National Key Basic Research Program of ChinaChina2013CB967700
the National Key Basic Research Program of ChinaChina2012CB910402

Revision History 

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-05-18
    Type: Database references