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PDBsum entry 1qz0
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Hydrolase/hydrolase inhibitor PDB id
1qz0

 

 

 

 

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Contents
Protein chains
282 a.a. *
Ligands
ASP-GLU-FTY-LEU-
NH2 ×2
ASP-ALA-ASP-GLU-
FTY-LEU-NH2 ×2
Waters ×603
* Residue conservation analysis
PDB id:
1qz0
Name: Hydrolase/hydrolase inhibitor
Title: Crystal structure of the yersinia pestis phosphatase yoph in complex with a phosphotyrosyl mimetic-containing hexapeptide
Structure: Protein-tyrosine phosphatase yoph. Chain: a, b. Fragment: catalytic domain, residues 164-468. Synonym: virulence protein. Engineered: yes. Mutation: yes. Asp-ala-asp-glu-fty-leu-nh2. Chain: c, d, e, f. Engineered: yes
Source: Yersinia pestis. Organism_taxid: 632. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes
Biol. unit: Trimer (from PQS)
Resolution:
1.50Å     R-factor:   0.188     R-free:   0.209
Authors: J.Phan,K.Lee,S.Cherry,J.E.Tropea,T.R.Burke Jr,D.S.Waugh
Key ref:
J.Phan et al. (2003). High-resolution structure of the Yersinia pestis protein tyrosine phosphatase YopH in complex with a phosphotyrosyl mimetic-containing hexapeptide. Biochemistry, 42, 13113-13121. PubMed id: 14609321 DOI: 10.1021/bi030156m
Date:
15-Sep-03     Release date:   25-Nov-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
O68720  (O68720_YERPE) -  protein-tyrosine-phosphatase from Yersinia pestis
Seq:
Struc: 		468 a.a.
282 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.3.1.3.48  - protein-tyrosine-phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: O-phospho-L-tyrosyl-[protein] + H2O = L-tyrosyl-[protein] + phosphate
O-phospho-L-tyrosyl-[protein]
 + H2O
 = L-tyrosyl-[protein]
 + phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    Key reference    
 
 
DOI no: 10.1021/bi030156m Biochemistry 42:13113-13121 (2003)
PubMed id: 14609321  
 
 
High-resolution structure of the Yersinia pestis protein tyrosine phosphatase YopH in complex with a phosphotyrosyl mimetic-containing hexapeptide.
J.Phan, K.Lee, S.Cherry, J.E.Tropea, T.R.Burke, D.S.Waugh.
 
  ABSTRACT  
 
Yersinia pestis, the causative agent of bubonic plague, secretes a eukaryotic-like protein tyrosine phosphatase (PTPase) termed Yersinia outer protein H (YopH) that is essential for virulence. We have determined, for the first time, the crystal structure of the YopH PTPase domain in complex with a nonhydrolyzable substrate analogue, the hexapeptide mimetic Ac-DADE-F(2)Pmp-L-NH(2). As anticipated, the mode of ligand binding in the active site is similar to the way in which the corresponding phosphohexapeptide binds to the structurally homologous human PTP1B. Unexpectedly, however, the crystal structure also revealed a second substrate-binding site in YopH that is not present in PTP1B. The mode of binding and structural conformation of the hexapeptide analogue is quite different in the two sites. Although the biological function of the second substrate-binding site remains to be investigated, the structure of a substrate analogue in the active site of Y. pestis YopH opens the door for the structure-based design and optimization of therapeutic countermeasures to combat this potential agent of bioterrorism.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21118379 M.Leone, E.Barile, R.Dahl, and M.Pellecchia (2011).
Design and NMR studies of cyclic peptides targeting the N-terminal domain of the protein tyrosine phosphatase YopH.
  Chem Biol Drug Des, 77, 12-19.  
20350805 F.Liu, R.M.Hakami, B.Dyas, M.Bahta, G.T.Lountos, D.S.Waugh, R.G.Ulrich, and T.R.Burke (2010).
A rapid oxime linker-based library approach to identification of bivalent inhibitors of the Yersinia pestis protein-tyrosine phosphatase, YopH.
  Bioorg Med Chem Lett, 20, 2813-2816.  
19845408 Z.Huang, and C.F.Wong (2009).
Docking flexible peptide to flexible protein by molecular dynamics using two implicit-solvent models: an evaluation in protein kinase and phosphatase systems.
  J Phys Chem B, 113, 14343-14354.  
18240386 C.E.Hubbard, and A.M.Barrios (2008).
A highly efficient route to enantiomerically pure l-N-Bz-Pmp(t-Bu)2-OH and incorporation into a peptide-based protein tyrosine phosphatase inhibitor.
  Bioorg Med Chem Lett, 18, 679-681.  
18081726 J.E.Trosky, A.D.Liverman, and K.Orth (2008).
Yersinia outer proteins: Yops.
  Cell Microbiol, 10, 557-565.  
16098211 C.E.Stebbins (2005).
Structural microbiology at the pathogen-host interface.
  Cell Microbiol, 7, 1227-1236.  
16271885 C.Grundner, H.L.Ng, and T.Alber (2005).
Mycobacterium tuberculosis protein tyrosine phosphatase PtpB structure reveals a diverged fold and a buried active site.
  Structure, 13, 1625-1634.
PDB code: 1ywf
15684325 H.J.Nam, F.Poy, H.Saito, and C.A.Frederick (2005).
Structural basis for the function and regulation of the receptor protein tyrosine phosphatase CD45.
  J Exp Med, 201, 441-452.
PDB codes: 1ygr 1ygu
15720545 M.I.Ivanov, J.A.Stuckey, H.L.Schubert, M.A.Saper, and J.B.Bliska (2005).
Two substrate-targeting sites in the Yersinia protein tyrosine phosphatase co-operate to promote bacterial virulence.
  Mol Microbiol, 55, 1346-1356.
PDB codes: 1xxp 1xxv
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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