1YTS

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.174 
  • R-Value Observed: 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
  • Primary Citation of Related Structures:  
    1YTS

  • 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 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 ...

    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: 
    • Dissecting the Catalytic Mechanism of Protein-Tyrosine Phosphatases
      Zhang, Z.-Y., Wang, Y., Dixon, J.E.
      (1994) Proc Natl Acad Sci U S A 91: 1624
    • 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
    • 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

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
YERSINIA PROTEIN TYROSINE PHOSPHATASEA278Yersinia enterocoliticaMutation(s): 0 
Gene Names: yop51yopH
EC: 3.1.3.48
UniProt
Find proteins for P15273 (Yersinia enterocolitica)
Explore P15273 
Go to UniProtKB:  P15273
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A], C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.4α = 90
b = 49.8β = 90
c = 100.4γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
SDMSdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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