PDBsum entry 1pty

Hydrolase

PDB id: 1pty

Contents

Protein chain

298 a.a.

Ligands

PTR ×2

Metals

_MG

Waters ×263

References listed in PDB file

Key reference

Title

Identification of a second aryl phosphate-Binding site in protein-Tyrosine phosphatase 1b: a paradigm for inhibitor design.

Authors

Y.A.Puius, Y.Zhao, M.Sullivan, D.S.Lawrence, S.C.Almo, Z.Y.Zhang.

Ref.

Proc Natl Acad Sci U S A, 1997, 94, 13420-13425. [DOI no: 10.1073/pnas.94.25.13420]

PubMed id

9391040

Abstract

The structure of the catalytically inactive mutant (C215S) of the human protein-tyrosine phosphatase 1B (PTP1B) has been solved to high resolution in two complexes. In the first, crystals were grown in the presence of bis-(para-phosphophenyl) methane (BPPM), a synthetic high-affinity low-molecular weight nonpeptidic substrate (Km = 16 microM), and the structure was refined to an R-factor of 18. 2% at 1.9 A resolution. In the second, crystals were grown in a saturating concentration of phosphotyrosine (pTyr), and the structure was refined to an R-factor of 18.1% at 1.85 A. Difference Fourier maps showed that BPPM binds PTP1B in two mutually exclusive modes, one in which it occupies the canonical pTyr-binding site (the active site), and another in which a phosphophenyl moiety interacts with a set of residues not previously observed to bind aryl phosphates. The identification of a second pTyr molecule at the same site in the PTP1B/C215S-pTyr complex confirms that these residues constitute a low-affinity noncatalytic aryl phosphate-binding site. Identification of a second aryl phosphate binding site adjacent to the active site provides a paradigm for the design of tight-binding, highly specific PTP1B inhibitors that can span both the active site and the adjacent noncatalytic site. This design can be achieved by tethering together two small ligands that are individually targeted to the active site and the proximal noncatalytic site.

Figure 3.
Fig. 3. Stereo representations of the binding modes of BPPM A (a), BPPM B (b), and pTyr B (c). Contacts represented by dashed lines are distances less than 3.6 Å, except for certain interactions with aromatic rings. Interactions between the amide nitrogens of residues 216-221 and the phosphate groups of ligand A are too numerous to represent. [Diagrams were generated with the program O (16)].

Figure 4.
Fig. 4. Schematic representations of the interactions between PTP1B/C215S and BPPM A (a), BPPM B (b), and pTyr B (c). A distance cutoff^ of 3.6 Å was used, except for certain interactions with aromatic^ rings.

Secondary reference #1

Title

Potent low molecular weight substrates for protein-Tyrosine phosphatase.

Authors

J.Montserat, L.Chen, D.S.Lawrence, Z.Y.Zhang.

Ref.

J Biol Chem, 1996, 271, 7868-7872.

PubMed id

8631832

Secondary reference #2

Title

Structural basis for phosphotyrosine peptide recognition by protein tyrosine phosphatase 1b.

Authors

Z.Jia, D.Barford, A.J.Flint, N.K.Tonks.

Ref.

Science, 1995, 268, 1754-1758. [DOI no: 10.1126/science.7540771]

PubMed id

7540771

Secondary reference #3

Title

Crystal structure of human protein tyrosine phosphatase 1b.

Authors

D.Barford, A.J.Flint, N.K.Tonks.

Ref.

Science, 1994, 263, 1397-1404. [DOI no: 10.1126/science.8128219]

PubMed id

8128219