1YTS

A LIGAND-INDUCED CONFORMATIONAL CHANGE IN THE YERSINIA PROTEIN TYROSINE PHOSPHATASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A ligand-induced conformational change in the Yersinia protein tyrosine phosphatase.

Schubert, H.L.Fauman, E.B.Stuckey, J.A.Dixon, J.E.Saper, M.A.

(1995) Protein Sci. 4: 1904-1913

  • DOI: 10.1002/pro.5560040924
  • Also Cited By: 2I42

  • PubMed Abstract: 
  • Protein tyrosine phosphatases (PTPases) play critical roles in the intracellular signal transduction pathways that regulate cell transformation, growth, and proliferation. The structures of several different PTPases have revealed a conserved active s ...

    Protein tyrosine phosphatases (PTPases) play critical roles in the intracellular signal transduction pathways that regulate cell transformation, growth, and proliferation. The structures of several different PTPases have revealed a conserved active site architecture in which a phosphate-binding loop, together with an invariant arginine, cradle the phosphate of a phosphotyrosine substrate and poise it for nucleophilic attack by an invariant cysteine nucleophile. We previously reported that binding of tungstate to the Yop51 PTPase from Yersinia induced a loop conformational change that moved aspartic acid 356 into the active site, where it can function as a general acid. This is consistent with the aspartic acid donating a proton to the tyrosyl leaving group during the initial hydrolysis step. In this report, using a similar structure of the inactive Cys 403-->Ser mutant of the Yersinia PTPase complexed with sulfate, we detail the structural and functional details of this conformational change. In response to oxyanion binding, small perturbations occur in active site residues, especially Arg 409, and trigger the loop to close. Interestingly, the peptide bond following Asp 356 has flipped to ligate a buried, active site water molecule that also hydrogen bonds to the bound sulfate anion and two invariant glutamines. Loop closure also significantly decreases the solvent accessibility of the bound oxyanion and could effectively shield catalytic intermediates from phosphate acceptors other than water. We speculate that the intrinsic loop flexibility of different PTPases may be related to their catalytic rate and may play a role in the wide range of activities observed within this enzyme family.


    Related Citations: 
    • Expression, Purification, and Physicochemical Characterization of a Recombinant Yersinia Protein Tyrosine Phosphatase
      Zhang, Z.-Y.,Clemens, J.C.,Schubert, H.L.,Stuckey, J.A.,Fischer, M.W.F.,Hume, D.M.,Saper, M.A.,Dixon, J.E.
      (1992) J.Biol.Chem. 267: 23759
    • Crystal Structure of Yersinia Protein Tyrosine Phosphatase at 2.5 Angstroms and the Complex with Tungstate
      Stuckey, J.A.,Schubert, H.L.,Fauman, E.B.,Zhang, Z.-Y.,Dixon, J.E.,Saper, M.A.
      (1994) Nature 370: 571
    • Dissecting the Catalytic Mechanism of Protein-Tyrosine Phosphatases
      Zhang, Z.-Y.,Wang, Y.,Dixon, J.E.
      (1994) Proc.Natl.Acad.Sci.USA 91: 1624


    Organizational Affiliation

    Biophysics Research Division, University of Michigan, Ann Arbor 48109-1055, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YERSINIA PROTEIN TYROSINE PHOSPHATASE
A
278Yersinia enterocoliticaGene Names: yopH (yop51)
EC: 3.1.3.48
Find proteins for P15273 (Yersinia enterocolitica)
Go to UniProtKB:  P15273
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.400α = 90.00
b = 49.800β = 90.00
c = 100.400γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-07-10
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance