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Crystal structure of a Low Molecular Weight Phosphotyrosine phosphatase from Vibrio choleraeO395


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.152 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Atomic resolution crystal structure of VcLMWPTP-1 from Vibrio cholerae O395: insights into a novel mode of dimerization in the low molecular weight protein tyrosine phosphatase family.

Nath, S.Banerjee, R.Sen, U.

(2014) Biochem.Biophys.Res.Commun. 450: 390-395

  • DOI: 10.1016/j.bbrc.2014.05.129

  • PubMed Abstract: 
  • Low molecular weight protein tyrosine phosphatase (LMWPTP) is a group of phosphotyrosine phosphatase ubiquitously found in a wide range of organisms ranging from bacteria to mammals. Dimerization in the LMWPTP family has been reported earlier which f ...

    Low molecular weight protein tyrosine phosphatase (LMWPTP) is a group of phosphotyrosine phosphatase ubiquitously found in a wide range of organisms ranging from bacteria to mammals. Dimerization in the LMWPTP family has been reported earlier which follows a common mechanism involving active site residues leading to an enzymatically inactive species. Here we report a novel form of dimerization in a LMWPTP from Vibrio cholera 0395 (VcLMWPTP-1). Studies in solution reveal the existence of the dimer in solution while kinetic study depicts the active form of the enzyme. This indicates that the mode of dimerization in VcLMWPTP-1 is different from others where active site residues are not involved in the process. A high resolution (1.45Å) crystal structure of VcLMWPTP-1 confirms a different mode of dimerization where the active site is catalytically accessible as evident by a tightly bound substrate mimicking ligand, MOPS at the active site pocket. Although being a member of a prokaryotic protein family, VcLMWPTP-1 structure resembles very closely to LMWPTP from a eukaryote, Entamoeba histolytica. It also delineates the diverse surface properties around the active site of the enzyme.


    Organizational Affiliation

    Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, 1/AF, Bidhannagar, Kolkata 700064, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphotyrosine protein phosphatase
A, B, C, D
155Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)Mutation(s): 0 
EC: 3.1.3.48
Find proteins for A0A0H3ALA8 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395))
Go to UniProtKB:  A0A0H3ALA8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
MPO
Query on MPO

Download SDF File 
Download CCD File 
A, B, C, D
3[N-MORPHOLINO]PROPANE SULFONIC ACID
C7 H15 N O4 S
DVLFYONBTKHTER-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.152 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 87.470α = 90.00
b = 87.470β = 90.00
c = 73.850γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
PHASERphasing
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-02
    Type: Initial release
  • Version 1.1: 2015-06-17
    Type: Database references