PDBsum entry 1wch

Hydrolase

PDB id: 1wch

Contents

Protein chain

308 a.a. *

Ligands

PO4 ×3

Waters ×280

* Residue conservation analysis

PDB id:

1wch

Name:

Hydrolase

Title:

Crystal structure of ptpl1 human tyrosine phosphatase mutated in colorectal cancer - evidence for a second phosphotyrosine substrate recognition pocket

Structure:

Protein tyrosine phosphatase, non-receptor type 13. Chain: a. Fragment: residues 2163-2477. Synonym: protein tyrosine phosphatase like 1, protein tyrosine phosphatase 1e, ptp-e1, hptpe1, ptp-bas, protein tyrosine phosphatase ptpl1, fas-associated protein tyrosine phosphatase 1, fap-1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.85Å R-factor: 0.177 R-free: 0.204

Authors:

F.Villa,M.Deak,G.B.Bloomberg,D.R.Alessi,D.M.F.Van Aalten

Key ref:

F.Villa et al. (2005). Crystal structure of the PTPL1/FAP-1 human tyrosine phosphatase mutated in colorectal cancer: evidence for a second phosphotyrosine substrate recognition pocket. J Biol Chem, 280, 8180-8187. PubMed id: 15611135 DOI: 10.1074/jbc.M412211200

Date:

16-Nov-04 Release date: 14-Dec-04

Protein chain

Q12923  (PTN13_HUMAN) -  Tyrosine-protein phosphatase non-receptor type 13 from Homo sapiens

Seq: 2485 a.a.

Struc: 308 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.3.48 - protein-tyrosine-phosphatase.
• Reaction: O-phospho-L-tyrosyl-[protein] + H2O = L-tyrosyl-[protein] + phosphate

O-phospho-L-tyrosyl-[protein] + H2O = L-tyrosyl-[protein] + phosphate (Bound ligand (Het Group name = PO4) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1074/jbc.M412211200

J Biol Chem 280:8180-8187 (2005)

PubMed id: 15611135

Crystal structure of the PTPL1/FAP-1 human tyrosine phosphatase mutated in colorectal cancer: evidence for a second phosphotyrosine substrate recognition pocket.

F.Villa, M.Deak, G.B.Bloomberg, D.R.Alessi, D.M.van Aalten.

ABSTRACT

Protein-tyrosine phosphatase-L1 (PTPL1, also known as FAP-1, PTP1E, PTP-BAS, and PTPN13) is mutated in a significant number of colorectal tumors and may play a role in down-regulating signaling responses mediated by phosphatidylinositol 3-kinase, although the precise substrates are as yet unknown. In this study, we describe a 1.8 A resolution crystal structure of a fully active fragment of PTPL1 encompassing the catalytic domain. PTPL1 adopts the standard PTP fold, albeit with an unusually positioned additional N-terminal helix, and shows an ordered phosphate in the active site. Interestingly, a positively charged pocket is located near the PTPL1 catalytic site, reminiscent of the second phosphotyrosine binding site in PTP1B, which is required to dephosphorylate peptides containing two adjacent phosphotyrosine residues (as occurs for example in the activated insulin receptor). We demonstrate that PTPL1, like PTP1B, interacts with and dephosphorylates a bis-phosphorylated insulin receptor peptide more efficiently than monophosphorylated peptides, indicating that PTPL1 may down-regulate the phosphatidylinositol 3-kinase pathway, by dephosphorylating insulin or growth factor receptors that contain tandem phosphotyrosines. The structure also reveals that four out of five PTPL1 mutations found in colorectal cancers are located on solvent-exposed regions remote from the active site, consistent with these mutants being normally active. In contrast, the fifth mutation, which changes Met-2307 to Thr, is close to the active site cysteine and decreases activity significantly. Our studies provide the first molecular description of the PTPL1 catalytic domain and give new insight into the function of PTPL1.

Selected figure(s)

Figure 1.
FIG. 1. Comparison of the structure of the catalytic domain of PTPL1 and PTP1B. A, overall ribbon structure of the PTPL1 catalytic domain (residues 2152-2485) phosphate complex (left panel). A 2 F[o] - F[c], [calc] electron density map for the phosphate molecule is drawn in red and displays well ordered density. The key features of the structure that are described under the Introduction are indicated in magenta. The N-terminal 0 helix that replaces the 7 helix on PTP1B is displayed in yellow. Shown in stick representation are Cys-2408, Asp-2378, Arg-2205, Ile-2458, and Met-2307. The electrostatic potential of the surface of PTPL1 and the location of the positively charged primary and secondary phosphotyrosine binding pockets are indicated (right panel). The blue areas (+6kT) represent highly positively charged residues, and the red areas (-6kT) represent highly negatively charged residues. B, overall ribbon structure of the PTP1B catalytic domain (residues 1-298, left panel). The electrostatic potential of the surface of PTP1B, calculated without the peptide bound to the enzyme, complexed to the phosphorylated insulin receptor peptide phosphorylated at residues equivalent to Tyr-1162 and Tyr-1163 on the insulin receptor that are located in the primary and secondary phosphotyrosine binding pockets, respectively is shown in the right panel.

Figure 3.
FIG. 3. Comparison of the catalytic and secondary phosphotyrosine binding site of PTPL1 and PTP1B. A, a ribbon drawing of the catalytic center of PTPL1 displaying the electron density of the phosphate molecule shown in red. Shown in stick representation are Cys-2408; Asp-2378 in the WPD loop; Gln-2452 from the Q-loop. Also shown are the His-2448, Gln-2221, Gly-2449, and Arg-2444 that make up the secondary phosphotyrosine binding pocket. Superimposed on the structure is a model of how the phosphorylated insulin receptor peptide (ETDY(P)Y(P)R) might interact with PTPL1 based on the structure of this peptide with PTP1B. B, a ribbon drawing of the catalytic center of PTP1B complexed to the phosphorylated insulin receptor peptide (ETDY(P)Y(P)R). Shown in stick representation are Ser-215 (replacing the catalytic cysteine in trapping mutant PTP1B-C215S); Asp-181 in the WPD loop; Gln-262 from the Q-loop. Also shown are the Arg-24, Met-258, Gly-259, and Arg-254 in the secondary phosphotyrosine binding pocket. Note that His-2448 located on the loop between 5 and 6 in PTPL1 is structurally replacing Arg-24 in PTP1B located on the 2'-helix.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 8180-8187) copyright 2005.

Figures were selected by an automated process.