6Y2V

Crystal structure of the double mutant L13R I16K of Low Molecular Weight Protein Tyrosine Phosphatase (LMW-PTP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Computational and structure-guided design of phosphoinositide substrate specificity into the tyrosine specific LMW-PTP enzyme.

Egbe, E.Levy, C.W.Tabernero, L.

(2020) PLoS One 15: e0235133-e0235133

  • DOI: 10.1371/journal.pone.0235133
  • Primary Citation of Related Structures:  
    6Y2W, 6Y2V

  • PubMed Abstract: 
  • We have used a combination of computational and structure-based redesign of the low molecular weight protein tyrosine phosphatase, LMW-PTP, to create new activity towards phosphoinositide substrates for which the wild-type enzyme had little or no activity ...

    We have used a combination of computational and structure-based redesign of the low molecular weight protein tyrosine phosphatase, LMW-PTP, to create new activity towards phosphoinositide substrates for which the wild-type enzyme had little or no activity. The redesigned enzymes retain catalytic activity despite residue alterations in the active site, and kinetic experiments confirmed specificity for up to four phosphoinositide substrates. Changes in the shape and overall volume of the active site where critical to facilitate access of the new substrates for catalysis. The kinetics data suggest that both the position and the combination of amino acid mutations are important for specificity towards the phosphoinositide substrates. The introduction of basic residues proved essential to establish new interactions with the multiple phosphate groups in the inositol head, thus promoting catalytically productive complexes. The crystallographic structures of the top-ranking designs confirmed the computational predictions and showed that residue substitutions do not alter the overall folding of the phosphatase or the conformation of the active site P-loop. The engineered LMW-PTP mutants with new activities can be useful reagents in investigating cell signalling pathways and offer the potential for therapeutic applications.


    Organizational Affiliation

    School of Biological Sciences, Faculty of Biology Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, England, United Kingdom.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Low molecular weight phosphotyrosine protein phosphataseA158Homo sapiensMutation(s): 2 
Gene Names: ACP1
EC: 3.1.3.48 (PDB Primary Data), 3.1.3.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P24666 (Homo sapiens)
Explore P24666 
Go to UniProtKB:  P24666
PHAROS:  P24666
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGE
Query on PGE

Download Ideal Coordinates CCD File 
B [auth A]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.625α = 90
b = 41.287β = 91.809
c = 56.898γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-02-17 
  • Released Date: 2020-07-22 
  • Deposition Author(s): Levy, C.

Funding OrganizationLocationGrant Number
Commonwealth Scholarship Commission (United Kingdom)United Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-22
    Type: Initial release