1K46

Crystal Structure of the Type III Secretory Domain of Yersinia YopH Reveals a Domain-Swapped Dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the type III secretion and substrate-binding domain of Yersinia YopH phosphatase.

Smith, C.L.Khandelwal, P.Keliikuli, K.Zuiderweg, E.R.Saper, M.A.

(2001) Mol Microbiol 42: 967-979

  • DOI: 10.1046/j.0950-382x.2001.02711.x
  • Primary Citation of Related Structures:  
    1K46

  • PubMed Abstract: 
  • Pathogenic strains of Yersinia deploy a type III secretion system to inject the potent tyrosine phosphatase YopH into host cells, where it dephosphorylates focal adhesion-associated substrates. The amino-terminal, non-catalytic domain of YopH is bifu ...

    Pathogenic strains of Yersinia deploy a type III secretion system to inject the potent tyrosine phosphatase YopH into host cells, where it dephosphorylates focal adhesion-associated substrates. The amino-terminal, non-catalytic domain of YopH is bifunctional; it is essential for the secretion and binding of the specific chaperone SycH, but also targets the catalytic domain to substrates in the infected cell. We describe the 2.2 A resolution crystal structure of residues 1-129 of YopH from Yersinia pseudotuberculosis. The amino-terminal alpha-helix (2-17), comprising the secretion signal, and beta-strand (24-28) of one molecule exchange with another molecule to form a domain-swapped dimer. Nuclear magnetic resonance (NMR) and gel filtration experiments demonstrated that YopH(1-129) could exist as a monomer and/or a dimer in solution. The topology of the dimer and the dynamics of a monomeric form in solution observed by NMR imply that YopH has the propensity to unfold partially. The dimer is probably not important physiologically, but may mimic how SycH binds to the exposed non-polar surfaces of a partially unfolded YopH. Phosphopeptide-induced perturbations in NMR chemical shifts define a substrate-binding surface on YopH(1-129) that includes residues previously shown by mutagenesis to be essential for YopH function.


    Related Citations: 
    • Identification of Residues in the N-terminal Domain of the Yersinia Tyrosine Phosphatase that are Critical for Substrate Recognition
      Montagna, L.G., Ivanov, M.I., Bliska, J.B.
      (2001) J Biol Chem 276: 5005
    • Identification of an Amino-terminal Substrate-binding Domain in the Yersinia Tyrosine Phosphatase that is Required for Efficient Recognition of Focal Adhesion Targets
      Black, D.S., Montagna, L.G., Zitsmann, S., Bliska, J.B.
      (1998) Mol Microbiol 29: 1263

    Organizational Affiliation

    Department of Biological Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109-1055, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN-TYROSINE PHOSPHATASE YOPHA136Yersinia pseudotuberculosisMutation(s): 0 
Gene Names: yopH
EC: 3.1.3.48
Find proteins for P08538 (Yersinia pseudotuberculosis serotype I (strain IP32953))
Explore P08538 
Go to UniProtKB:  P08538
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.224 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.9α = 90
b = 120.7β = 90
c = 48.8γ = 90
Software Package:
Software NamePurpose
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance