3PS5

Crystal structure of the full-length Human Protein Tyrosine Phosphatase SHP-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.225 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of human protein tyrosine phosphatase SHP-1 in the open conformation.

Wang, W.Liu, L.Song, X.Mo, Y.Komma, C.Bellamy, H.D.Zhao, Z.J.Zhou, G.W.

(2011) J.Cell.Biochem. 112: 2062-2071

  • DOI: 10.1002/jcb.23125

  • PubMed Abstract: 
  • SHP-1 belongs to the family of non-receptor protein tyrosine phosphatases (PTPs) and generally acts as a negative regulator in a variety of cellular signaling pathways. Previously, the crystal structures of the tail-truncated SHP-1 and SHP-2 revealed ...

    SHP-1 belongs to the family of non-receptor protein tyrosine phosphatases (PTPs) and generally acts as a negative regulator in a variety of cellular signaling pathways. Previously, the crystal structures of the tail-truncated SHP-1 and SHP-2 revealed an autoinhibitory conformation. To understand the regulatory mechanism of SHP-1, we have determined the crystal structure of the full-length SHP-1 at 3.1 Å. Although the tail was disordered in current structure, the huge conformational rearrangement of the N-SH2 domain and the incorporation of sulfate ions into the ligand-binding site of each domain indicate that the SHP-1 is in the open conformation. The N-SH2 domain in current structure is shifted away from the active site of the PTP domain to the other side of the C-SH2 domain, resulting in exposure of the active site. Meanwhile, the C-SH2 domain is twisted anticlockwise by about 110°. In addition, a set of new interactions between two SH2 domains and between the N-SH2 and the catalytic domains is identified, which could be responsible for the stabilization of SHP-1 in the open conformation. Based on the structural comparison, a model for the activation of SHP-1 is proposed.


    Organizational Affiliation

    Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein phosphatase non-receptor type 6
A
595Homo sapiensMutation(s): 1 
Gene Names: PTPN6 (HCP, PTP1C)
EC: 3.1.3.48
Find proteins for P29350 (Homo sapiens)
Go to Gene View: PTPN6
Go to UniProtKB:  P29350
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.1 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.225 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 231.919α = 90.00
b = 231.919β = 90.00
c = 78.852γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data scaling
MAR345dtbdata collection
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-08-24
    Type: Database references