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PDBsum entry 1ytw

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Hydrolase PDB id
1ytw
Jmol
Contents
Protein chain
283 a.a. *
Ligands
WO4
SO4
Waters ×139
* Residue conservation analysis
PDB id:
1ytw
Name: Hydrolase
Title: Yersinia ptpase complexed with tungstate
Structure: Yersinia protein tyrosine phosphatase. Chain: a. Fragment: catalytic domain, residues 163 - 468. Synonym: yop51, yop2b, pasteurella x, ptpase, yop51delta162. Engineered: yes. Other_details: tungstate and sulfate ligands
Source: Yersinia enterocolitica. Organism_taxid: 630. Strain: w22703. Cell_line: bl21. Gene: yop51. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.40Å     R-factor:   0.179    
Authors: E.B.Fauman,H.L.Schubert,M.A.Saper
Key ref:
E.B.Fauman et al. (1996). The X-ray crystal structures of Yersinia tyrosine phosphatase with bound tungstate and nitrate. Mechanistic implications. J Biol Chem, 271, 18780-18788. PubMed id: 8702535 DOI: 10.1074/jbc.271.31.18780
Date:
01-May-96     Release date:   08-Nov-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P15273  (YOPH_YEREN) -  Tyrosine-protein phosphatase YopH
Seq:
Struc:
468 a.a.
283 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.3.1.3.48  - Protein-tyrosine-phosphatase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Protein tyrosine phosphate + H2O = protein tyrosine + phosphate
Protein tyrosine phosphate
+ H(2)O
= protein tyrosine
+ 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  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.271.31.18780 J Biol Chem 271:18780-18788 (1996)
PubMed id: 8702535  
 
 
The X-ray crystal structures of Yersinia tyrosine phosphatase with bound tungstate and nitrate. Mechanistic implications.
E.B.Fauman, C.Yuvaniyama, H.L.Schubert, J.A.Stuckey, M.A.Saper.
 
  ABSTRACT  
 
X-ray crystal structures of the Yersinia tyrosine phosphatase (PTPase) in complex with tungstate and nitrate have been solved to 2. 4-A resolution. Tetrahedral tungstate, WO42-, is a competitive inhibitor of the enzyme and is isosteric with the substrate and product of the catalyzed reaction. Planar nitrate, NO3-, is isosteric with the PO3 moiety of a phosphotransfer transition state. The crystal structures of the Yersinia PTPase with and without ligands, together with biochemical data, permit modeling of key steps along the reaction pathway. These energy-minimized models are consistent with a general acid-catalyzed, in-line displacement of the phosphate moiety to Cys403 on the enzyme, followed by attack by a nucleophilic water molecule to release orthophosphate. This nucleophilic water molecule is identified in the crystal structure of the nitrate complex. The active site structure of the PTPase is compared to alkaline phosphatase, which employs a similar phosphomonoester hydrolysis mechanism. Both enzymes must stabilize charges at the nucleophile, the PO3 moiety of the transition state, and the leaving group. Both an associative (bond formation preceding bond cleavage) and a dissociative (bond cleavage preceding bond formation) mechanism were modeled, but a dissociative-like mechanism is favored for steric and chemical reasons. Since nearly all of the 47 invariant or highly conserved residues of the PTPase domain are clustered at the active site, we suggest that the mechanism postulated for the Yersinia enzyme is applicable to all the PTPases.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Energy-minimized atomic model of a substrate hexapeptide, Asp-Ala-Asp-Glu-Tyr(P)-Leu, bound to the Yersinia PTPase. The molecular surface of the protein atoms from the PTPase-WO[4] crystal structure is shown in cyan. This surface has been sliced (dark blue surface) to reveal a deep active site pocket into which a model of a substrate hexapeptide was manually docked and subsequently energy minimized. The hexapeptide carbon, nitrogen, oxygen, and phosphorus atoms are shown in yellow, blue, red, and yellow, respectively. The peptide substrate runs from N terminus on the left of the figure to C terminus on the right.
Figure 4.
Fig. 4. Comparison of the active sites of Yersinia PTPase and E. coli alkaline phosphatase (Protein Data Bank entry 1ALK). Alkaline phosphatase is indicated by the pale gray bonds and boxed residue labels. The PTPase-WO[4] crystal structure is indicated by colored bonds and bold residue labels. Coordinates were superimposed based on the positions of the anion, the nucleophile, and the guanidinium groups of the arginines. Both enzymes catalyze hydrolysis of phosphomonoesters and must stabilize charges at the nucleophile, the PO[3] moiety, and the leaving group.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1996, 271, 18780-18788) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20300652 D.E.Almonacid, E.R.Yera, J.B.Mitchell, and P.C.Babbitt (2010).
Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function.
  PLoS Comput Biol, 6, e1000700.  
19267450 L.J.Juszczak, and R.Z.Desamero (2009).
Extension of the tryptophan chi2,1 dihedral angle-W3 band frequency relationship to a full rotation: correlations and caveats.
  Biochemistry, 48, 2777-2787.  
19140798 T.A.Brandão, H.Robinson, S.J.Johnson, and A.C.Hengge (2009).
Impaired acid catalysis by mutation of a protein loop hinge residue in a YopH mutant revealed by crystal structures.
  J Am Chem Soc, 131, 778-786.
PDB codes: 3f99 3f9a 3f9b
17382260 T.Strahl, and J.Thorner (2007).
Synthesis and function of membrane phosphoinositides in budding yeast, Saccharomyces cerevisiae.
  Biochim Biophys Acta, 1771, 353-404.  
17766352 Z.Huang, and C.F.Wong (2007).
A mining minima approach to exploring the docking pathways of p-nitrocatechol sulfate to YopH.
  Biophys J, 93, 4141-4150.  
16892390 A.Lavecchia, S.Cosconati, V.Limongelli, and E.Novellino (2006).
Modeling of Cdc25B dual specifity protein phosphatase inhibitors: docking of ligands and enzymatic inhibition mechanism.
  ChemMedChem, 1, 540-550.  
  16569237 D.L.Scott, G.Diez, and W.H.Goldmann (2006).
Protein-lipid interactions: correlation of a predictive algorithm for lipid-binding sites with three-dimensional structural data.
  Theor Biol Med Model, 3, 17.  
16698773 X.Hu, and C.E.Stebbins (2006).
Dynamics of the WPD loop of the Yersinia protein tyrosine phosphatase.
  Biophys J, 91, 948-956.  
15860562 L.W.Yang, X.Liu, C.J.Jursa, M.Holliman, A.J.Rader, H.A.Karimi, and I.Bahar (2005).
iGNM: a database of protein functional motions based on Gaussian Network Model.
  Bioinformatics, 21, 2978-2987.  
15008850 J.M.Otaki, and H.Yamamoto (2004).
Species-specific color-pattern modifications of butterfly wings.
  Dev Growth Differ, 46, 1.  
15459456 J.M.Otaki, and H.Yamamoto (2004).
Color-pattern modifications and speciation in butterflies of the genus Vanessa and its related genera Cynthia and Bassaris.
  Zoolog Sci, 21, 967-976.  
12660160 A.Yamashita, K.Maeda, and Y.Maéda (2003).
Crystal structure of CapZ: structural basis for actin filament barbed end capping.
  EMBO J, 22, 1529-1538.
PDB code: 1izn
14506477 C.E.Stebbins, and J.E.Galán (2003).
Priming virulence factors for delivery into the host.
  Nat Rev Mol Cell Biol, 4, 738-743.  
11980490 H.Deng, R.Callender, Z.Huang, and Z.Y.Zhang (2002).
Is the PTPase-vanadate complex a true transition state analogue?
  Biochemistry, 41, 5865-5872.  
11468356 G.Scapin, S.Patel, V.Patel, B.Kennedy, and E.Asante-Appiah (2001).
The structure of apo protein-tyrosine phosphatase 1B C215S mutant: more than just an S --> O change.
  Protein Sci, 10, 1596-1605.
PDB code: 1i57
10777720 G.H.Peters, T.M.Frimurer, J.N.Andersen, and O.H.Olsen (2000).
Molecular dynamics simulations of protein-tyrosine phosphatase 1B. II. substrate-enzyme interactions and dynamics.
  Biophys J, 78, 2191-2200.  
10978163 W.Chen, M.Wilborn, and J.Rudolph (2000).
Dual-specific Cdc25B phosphatase: in search of the catalytic acid.
  Biochemistry, 39, 10781-10789.  
10447891 C.Persson, R.Nordfelth, K.Andersson, A.Forsberg, H.Wolf-Watz, and M.Fällman (1999).
Localization of the Yersinia PTPase to focal complexes is an important virulence mechanism.
  Mol Microbiol, 33, 828-838.  
  10368138 E.Härtig, U.Schiek, K.U.Vollack, and W.G.Zumft (1999).
Nitrate and nitrite control of respiratory nitrate reduction in denitrifying Pseudomonas stutzeri by a two-component regulatory system homologous to NarXL of Escherichia coli.
  J Bacteriol, 181, 3658-3665.  
9799489 F.Wang, W.Li, M.R.Emmett, C.L.Hendrickson, A.G.Marshall, Y.L.Zhang, L.Wu, and Z.Y.Zhang (1998).
Conformational and dynamic changes of Yersinia protein tyrosine phosphatase induced by ligand binding and active site mutation and revealed by H/D exchange and electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry.
  Biochemistry, 37, 15289-15299.  
9548920 G.H.Peters, T.M.Frimurer, and O.H.Olsen (1998).
Electrostatic evaluation of the signature motif (H/V)CX5R(S/T) in protein-tyrosine phosphatases.
  Biochemistry, 37, 5383-5393.  
  9409151 W.G.Zumft (1997).
Cell biology and molecular basis of denitrification.
  Microbiol Mol Biol Rev, 61, 533-616.  
9063884 Z.Y.Zhang, and L.Wu (1997).
The single sulfur to oxygen substitution in the active site nucleophile of the Yersinia protein-tyrosine phosphatase leads to substantial structural and functional perturbations.
  Biochemistry, 36, 1362-1369.  
8987394 E.B.Fauman, and M.A.Saper (1996).
Structure and function of the protein tyrosine phosphatases.
  Trends Biochem Sci, 21, 413-417.  
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 codes are shown on the right.