PDBsum entry 1ytw

Hydrolase

PDB id: 1ytw

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

Protein chain

P15273  (YOPH_YEREN) -  Tyrosine-protein phosphatase YopH from Yersinia enterocolitica

Seq: 468 a.a.

Struc: 283 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.1.3.48 - protein-tyrosine-phosphatase.
• Reaction: 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: 10.1074/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.