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PDBsum entry 1wch
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the ptpl1/fap-1 human tyrosine phosphatase mutated in colorectal cancer: evidence for a second phosphotyrosine substrate recognition pocket.
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Authors
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F.Villa,
M.Deak,
G.B.Bloomberg,
D.R.Alessi,
D.M.Van aalten.
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Ref.
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J Biol Chem, 2005,
280,
8180-8187.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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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.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2005,
280,
8180-8187)
copyright 2005.
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