1PA9

Yersinia Protein-Tyrosine Phosphatase complexed with pNCS (Yop51,Pasteurella X,Ptpase,Yop51delta162) (Catalytic Domain, Residues 163-468) Mutant With Cys 235 Replaced By Arg (C235r)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Crystal structure of the Yersinia protein-tyrosine phosphatase YopH complexed with a specific small molecule inhibitor

Sun, J.P.Wu, L.Fedorov, A.A.Almo, S.C.Zhang, Z.Y.

(2003) J Biol Chem 278: 33392-33399

  • DOI: https://doi.org/10.1074/jbc.M304693200
  • Primary Citation of Related Structures:  
    1PA9

  • PubMed Abstract: 

    The pathogenic bacteria Yersinia are causative agents in human diseases ranging from gastrointestinal syndromes to bubonic plague. There is increasing risk of misuse of infectious agents, such as Yersinia pestis, as weapons of terror as well as instruments of warfare for mass destruction. Because the phosphatase activity of the Yersinia protein tyrosine phosphatase, YopH, is essential for virulence in the Yersinia pathogen, potent and selective YopH inhibitors are expected to serve as novel anti-plague agents. We have identified a specific YopH small molecule inhibitor, p-nitrocatechol sulfate (pNCS), which exhibits a Ki value of 25 microM for YopH and displays a 13-60-fold selectivity in favor of YopH against a panel of mammalian PTPs. To facilitate the understanding of the underlying molecular basis for tight binding and specificity, we have determined the crystal structure of YopH in complex with pNCS at a 2.0-A resolution. The structural data are corroborated by results from kinetic analyses of the interactions of YopH and its site-directed mutants with pNCS. The results show that while the interactions of the sulfuryl moiety and the phenyl ring with the YopH active site contribute to pNCS binding affinity, additional interactions of the hydroxyl and nitro groups in pNCS with Asp-356, Gln-357, Arg-404, and Gln-446 are responsible for the increased potency and selectivity. In particular, we note that residues Arg-404, Glu-290, Asp-356, and a bound water (WAT185) participate in a unique H-bonding network with the hydroxyl group ortho to the sulfuryl moiety, which may be exploited to design more potent and specific YopH inhibitors.


  • Organizational Affiliation

    Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, New York 10461, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein-tyrosine phosphatase yopH284Yersinia enterocoliticaMutation(s): 1 
Gene Names: YOPH OR YOP51
EC: 3.1.3.48
UniProt
Find proteins for P15273 (Yersinia enterocolitica)
Explore P15273 
Go to UniProtKB:  P15273
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15273
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CSN
Query on CSN

Download Ideal Coordinates CCD File 
B [auth A]N,4-DIHYDROXY-N-OXO-3-(SULFOOXY)BENZENAMINIUM
C6 H5 N O7 S
XMCCOOONGGUOLA-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CSN PDBBind:  1PA9 Ki: 2.50e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.36α = 90
b = 55.9β = 90
c = 97.84γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-04
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-07-29
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.4: 2021-10-27
    Changes: Database references
  • Version 1.5: 2023-08-16
    Changes: Data collection, Refinement description