4HJQ

SHP-1 catalytic domain WPD loop closed


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8013 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.165 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

SHP Family Protein Tyrosine Phosphatases Adopt Canonical Active-Site Conformations in the Apo and Phosphate-Bound States.

Alicea-Velazquez, N.L.Boggon, T.J.

(2013) Protein Pept.Lett. 20: 1039-1048

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein tyrosine phosphatase (PTP) catalytic domains undergo a series of conformational changes in order to mediate dephosphorylation of their tyrosine phosphorylated substrates. An important conformational change occurs in the Tryptophan-Proline-Asp ...

    Protein tyrosine phosphatase (PTP) catalytic domains undergo a series of conformational changes in order to mediate dephosphorylation of their tyrosine phosphorylated substrates. An important conformational change occurs in the Tryptophan-Proline-Aspartic acid (WPD) loop, which contains the conserved catalytic aspartate. Upon substrate binding, the WPD loop transitions from the 'open' to the 'closed' state, thus allowing optimal positioning of the catalytic aspartate for substrate dephosphorylation. The dynamics of WPD loop conformational changes have previously been studied for PTP1B, HePTP, and the bacterial phosphatase YopH, but have not yet been comprehensively studied for the nonreceptor tyrosine phosphatase SHP-1 (PTPN6). To structurally describe the changes in WPD loop conformation in SHP-1, we have determined the 1.4 Å crystal structure of the catalytic domain of SHP-1 in the Apo state and the 1.8 Å crystal structure of the SHP-1 catalytic domain in complex with a phosphate ion. We provide structural analysis for the WPD loop closed state of SHP phosphatases and the conformational changes that occur upon WPD loop closure.


    Organizational Affiliation

    Department of Pharmacology, Yale University School of Medicine, 333 Cedar St., SHM B-316A, New Haven, CT 06520, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein phosphatase non-receptor type 6
A, B
308Homo 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
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8013 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.165 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 45.642α = 102.39
b = 57.783β = 94.71
c = 77.319γ = 110.01
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-04-03
    Type: Initial release
  • Version 1.1: 2013-08-21
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Advisory, Refinement description