3S3E

Crystal structure of the catalytic domain of PTP10D from Drosophila melanogaster


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Conformational basis for substrate recruitment in protein tyrosine phosphatase 10D

Madan, L.L.Gopal, B.

(2011) Biochemistry 50: 10114-10125

  • DOI: 10.1021/bi201092q
  • Primary Citation of Related Structures:  3S3F, 3S3H, 3S3K

  • PubMed Abstract: 
  • The coordinated activity of protein tyrosine phosphatases (PTPs) is crucial for the initiation, modulation, and termination of diverse cellular processes. The catalytic activity of this protein depends on a nucleophilic cysteine at the active site th ...

    The coordinated activity of protein tyrosine phosphatases (PTPs) is crucial for the initiation, modulation, and termination of diverse cellular processes. The catalytic activity of this protein depends on a nucleophilic cysteine at the active site that mediates the hydrolysis of the incoming phosphotyrosine substrate. While the role of conserved residues in the catalytic mechanism of PTPs has been extensively examined, the diversity in the mechanisms of substrate recognition and modulation of catalytic activity suggests that other, less conserved sequence and structural features could contribute to this process. Here we describe the crystal structures of Drosophila melanogaster PTP10D in the apo form as well as in a complex with a substrate peptide and an inhibitor. These studies reveal the role of aromatic ring stacking interactions at the boundary of the active site of PTPs in mediating substrate recruitment. We note that phenylalanine 76, of the so-called KNRY loop, is crucial for orienting the phosphotyrosine residue toward the nucleophilic cysteine. Mutation of phenylalanine 76 to leucine results in a 60-fold decrease in the catalytic efficiency of the enzyme. Fluorescence measurements with a competitive inhibitor, p-nitrocatechol sulfate, suggest that Phe76 also influences the formation of the enzyme-substrate intermediate. The structural and biochemical data for PTP10D thus highlight the role of relatively less conserved residues in PTP domains in both substrate recruitment and modulation of reaction kinetics.


    Organizational Affiliation

    Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tyrosine-protein phosphatase 10D
A, B
307Drosophila melanogasterGene Names: Ptp10D
EC: 3.1.3.48
Find proteins for P35992 (Drosophila melanogaster)
Go to UniProtKB:  P35992
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BU1
Query on BU1

Download SDF File 
Download CCD File 
B
1,4-BUTANEDIOL
C4 H10 O2
WERYXYBDKMZEQL-UHFFFAOYSA-N
 Ligand Interaction
1BO
Query on 1BO

Download SDF File 
Download CCD File 
A, B
1-BUTANOL
BUTAN-1-OL
C4 H10 O
LRHPLDYGYMQRHN-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download SDF File 
Download CCD File 
A, B
ISOPROPYL ALCOHOL
2-PROPANOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.205 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 102.460α = 90.00
b = 102.460β = 90.00
c = 171.842γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
HKL-2000data collection
PHASERphasing
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2011-05-18 
  • Released Date: 2011-11-02 
  • Deposition Author(s): Madan, L.L., Gopal, B.

Revision History 

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2013-07-03
    Type: Database references