Motion in Yersinia Protein Tyrosine Phosphatase [tyrphos]

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Classification Known Fragment Motion, Hinge Mechanism [F-h-2]

Structures
1YPT Conformation 2 [ PartsList ]
1YTS Conformation 1 [ PartsList ]
1YTN [ PartsList ]

Description
The binding of tungstate to the Yop51 PTPase from Yersinia induces a loop conformational change that moving an aspartic acid into the active site. Small perturbations occuring in the active site residues, especially around Arg 409, trigger the loop to close. Loop closure significantly decreases the solvent accessibility of the bound oxyanion and could effectively shield catalytic intermediates from phosphate acceptors other than water.
The loop moves up to 6 A and positions Asp 356 carboxylate within 3.8 A of the tungstate oxygen analogous to the Oeta phosphoester oxygen of a phosphotyrosine substrate.
The conformational change between the unliganded and oxyanion-bound structures probably originates from small perturbations immediately adjacent to the ligand binding site.
The two core structures superimpose with an overall RMSD of 0.83 A for all paired Calphas, but the Calpha RMSD for residues 351-359 is 3.6 A. The loop moves up to 6 A to close over the active site.

Particular values describing motion
Creation Date = 19970822
Modification Date = 19970822
Domain 1 (residue selection) = 1-350, 360-409 (from lit.)
Domain 2 (residue selection) = 351-359 (from lit.)
Maximum CA displacement (A) = 6 (from lit.)
Experimental Methods = x (Traditional x-ray)

References
Z Jia, D Barford, A J Flint, and N K Tonks (1995). Structural Basis for Phosphotyrosine Peptide Recognition by Protein Tyrosine Phosphatase 1B. Sci. 268:1754-1758. [Medline info for 97352620]
Stuckey JA, Schubert HL, Fauman EB, Zhang ZY, Dixon JE, Saper MA. (1994). Crystal structure of Yersinia protein tyrosine phosphatase at 2.5 A and the complex with tungstate. Nature 1994 370:571-5. [Medline info for 94329181]
Schubert HL, Fauman EB, Stuckey JA, Dixon JE, Saper MA. (1995) A ligand-induced conformational change in the Yersinia protein tyrosine phosphatase. Protein Sci., 4:1904-13 [Medline info for 96100656]

Data and Graphics
Graphic-2 Link to a web page
Full-Text-1 Full Text of Protein Science article
Graphic-1 Overall Motion adapted from Prot. Sci. Article

GO terms associated with structures
Molecular functionphosphoprotein phosphatase activity, protein tyrosine phosphatase activity
Biological processprotein amino acid dephosphorylation

Morphs

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Best representative
Morph Morph name Structure #1 Structure #2 Residues
Yersinia Protein Tyrosine Phosphatase upload [ A ] upload [ A ] 278

User-submitted morphs
Morph Morph name Structure #1 Structure #2 Residues
048580-28226 PTPase upload [ A ] upload [ A ] 278


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Copyright 1995-2005 M. Gerstein, W. Krebs, S. Flores, N. Echols, and others
Email: Mark.Gerstein _at_ yale.edu