Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 32.93 kDa 
• Atom Count: 2694 
• Modelled Residue Count: 281 
• Deposited Residue Count: 288 
• Unique protein chains: 1

4HJP

SHP-1 catalytic domain WPD loop open

• PDB DOI: 10.2210/pdb4HJP/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-10-13 Released: 2013-04-03 
• Deposition Author(s): Alicea-Velazquez, N.L., Boggon, T.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.186 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 

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

• PubMed: 23514039 
• DOI: 10.2174/09298665113209990041
• Primary Citation of Related Structures:  
  4HJP, 4HJQ


• 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-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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 6	A	288	Homo sapiens	Mutation(s): 0  Gene Names: HCP, PTP1C, PTPN6, SHP-1 (PTPN6) EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P29350 (Homo sapiens) Explore P29350  Go to UniProtKB:  P29350
PHAROS:  P29350

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.186 
• R-Value Work: 0.164 
• R-Value Observed: 0.165 
• Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.482	α = 90
b = 57.388	β = 90
c = 110.808	γ = 90

Software Package:

Software Name	Purpose
CBASS	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-13 
• Released Date: 2013-04-03 
Deposition Author(s): Alicea-Velazquez, N.L., Boggon, T.J.

Revision History  

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2013-08-21
  Changes: Database references
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence