1YTW

YERSINIA PTPASE COMPLEXED WITH TUNGSTATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The X-ray crystal structures of Yersinia tyrosine phosphatase with bound tungstate and nitrate. Mechanistic implications.

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

(1996) J.Biol.Chem. 271: 18780-18788

  • DOI: 10.1074/jbc.271.31.18780
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • X-ray crystal structures of the Yersinia tyrosine phosphatase (PTPase) in complex with tungstate and nitrate have been solved to 2. 4-A resolution. Tetrahedral tungstate, WO42-, is a competitive inhibitor of the enzyme and is isosteric with the subst ...

    X-ray crystal structures of the Yersinia tyrosine phosphatase (PTPase) in complex with tungstate and nitrate have been solved to 2. 4-A resolution. Tetrahedral tungstate, WO42-, is a competitive inhibitor of the enzyme and is isosteric with the substrate and product of the catalyzed reaction. Planar nitrate, NO3-, is isosteric with the PO3 moiety of a phosphotransfer transition state. The crystal structures of the Yersinia PTPase with and without ligands, together with biochemical data, permit modeling of key steps along the reaction pathway. These energy-minimized models are consistent with a general acid-catalyzed, in-line displacement of the phosphate moiety to Cys403 on the enzyme, followed by attack by a nucleophilic water molecule to release orthophosphate. This nucleophilic water molecule is identified in the crystal structure of the nitrate complex. The active site structure of the PTPase is compared to alkaline phosphatase, which employs a similar phosphomonoester hydrolysis mechanism. Both enzymes must stabilize charges at the nucleophile, the PO3 moiety of the transition state, and the leaving group. Both an associative (bond formation preceding bond cleavage) and a dissociative (bond cleavage preceding bond formation) mechanism were modeled, but a dissociative-like mechanism is favored for steric and chemical reasons. Since nearly all of the 47 invariant or highly conserved residues of the PTPase domain are clustered at the active site, we suggest that the mechanism postulated for the Yersinia enzyme is applicable to all the PTPases.


    Related Citations: 
    • 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
    • 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.,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 A 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


    Organizational Affiliation

    Biophysics Research Division and the Department of Biological Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
YERSINIA PROTEIN TYROSINE PHOSPHATASE
A
306Yersinia enterocoliticaMutation(s): 0 
Gene Names: yopH (yop51)
EC: 3.1.3.48
Find proteins for P15273 (Yersinia enterocolitica)
Go to UniProtKB:  P15273
Small Molecules
Ligands 2 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
WO4
Query on WO4

Download SDF File 
Download CCD File 
A
TUNGSTATE(VI)ION
O4 W
PBYZMCDFOULPGH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.300α = 90.00
b = 49.800β = 90.00
c = 100.600γ = 90.00
Software Package:
Software NamePurpose
PHASESphasing
X-PLORphasing
PROCORdata reduction
XSCALEdata scaling
X-PLORmodel building
X-PLORrefinement
MADNESdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-11-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-03-21
    Type: Data collection