1M0V | pdb_00001m0v

NMR STRUCTURE OF THE TYPE III SECRETORY DOMAIN OF YERSINIA YOPH COMPLEXED WITH THE SKAP-HOM PHOSPHO-PEPTIDE N-acetyl-DEpYDDPF-NH2


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 360 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report

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This is version 1.4 of the entry. See complete history

Literature

Solution structure and phosphopeptide binding to the N-terminal domain of Yersinia YopH: comparison with a crystal structure

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

(2002) Biochemistry 41: 11425-11437

  • DOI: https://doi.org/10.1021/bi026333l
  • Primary Citation Related Structures: 
    1M0V

  • PubMed Abstract: 

    Virulence of pathogenic bacteria of the genus Yersinia requires the injection of six effector proteins into the cytoplasm of host cells. The amino-terminal domain of one of these effectors, the tyrosine phosphatase YopH, is essential for translocation of YopH, as well as for targeting it to phosphotyrosine-containing substrates of the type pYxxP. We report the high-resolution solution structure of the N-terminal domain (residues 1-129) from the Yersinia pseudotuberculosis YopH (YopH-NT) in complex with N-acetyl-DEpYDDPF-NH(2), a peptide derived from an in vivo protein substrate. In contrast to the domain-swapped dimer observed in a crystal structure of the same protein (Smith, C. L., Khandelwal, P., Keliikuli, K., Zuiderweg, E. R. P., and Saper, M. A. (2001) Mol. Microbiol. 42, 967-979), YopH-NT is monomeric in solution. The peptide binding site is located on a beta-hairpin that becomes the crossover point in the dimer structure. The binding site has several characteristics that are reminiscent of SH2 domains, which also bind to pYxxP sequences.


  • Organizational Affiliation
    • Biophysics Research Division, University of Michigan, 930 North University Avenue, Ann Arbor, Michigan 48109-1055, USA.

Macromolecule Content 

  • Total Structure Weight: 15.89 kDa 
  • Atom Count: 1,053 
  • Modeled Residue Count: 139 
  • Deposited Residue Count: 145 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PROTEIN-TYROSINE PHOSPHATASE YOPH136Yersinia pseudotuberculosisMutation(s): 0 
EC: 3.1.3.48
UniProt
Find proteins for P08538 (Yersinia pseudotuberculosis serotype I (strain IP32953))
Explore P08538 
Go to UniProtKB:  P08538
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08538
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
SKAP55 homologue9N/AMutation(s): 1 
UniProt
Find proteins for Q3UND0 (Mus musculus)
Explore Q3UND0 
Go to UniProtKB:  Q3UND0
Entity Groups
UniProt GroupQ3UND0
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
B
L-PEPTIDE LINKINGC9 H12 N O6 PTYR

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 360 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-07-24
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-23
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-11-20
    Changes: Data collection, Structure summary