PDBsum entry 1qz0

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hydrolase/hydrolase inhibitor PDB id
Protein chains
282 a.a. *
Waters ×603
* Residue conservation analysis
PDB id:
Name: Hydrolase/hydrolase inhibitor
Title: Crystal structure of the yersinia pestis phosphatase yoph in 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)
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
15-Sep-03     Release date:   25-Nov-03    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
O68720  (O68720_YERPE) -  Targeted effector protein
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.  - Protein-tyrosine-phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protein tyrosine phosphate + H2O = protein tyrosine + phosphate
Protein tyrosine phosphate
+ H(2)O
protein tyrosine
Bound ligand (Het Group name = FTY)
matches with 45.00% similarity
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     dephosphorylation   2 terms 
  Biochemical function     phosphatase activity     2 terms  


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.
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.