Crystal Structure of the PTPL1/FAP-1 Human Tyrosine Phosphatase Mutated in Colorectal Cancer

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 Å 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 solventexposed 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.Protein-tyrosine phosphatase-L1 (PTPL1) 1 is a non-receptor protein-tyrosine phosphatase and is the largest of the known 107 protein-tyrosine phosphatases (PTPs), comprising 2485 residues (1). The N terminus contains a kinase non-catalytic C-lobe (KIND) domain (residues 3-190), a new protein module identified recently (2), and a four-point-one/ezrin/radixin/moesin (FERM) domain (residues 568 -781). PTPL1 also contains five PSD-95/Drosophila disc large/zonula occludens (PDZ) domains located between residues 1102 and 1990 and a proteintyrosine phosphatase domain at its C terminus (residues 2087-2485). PTPL1 is the only tyrosine phosphatase possessing this domain organization (1). The non-catalytic region of PTPL1 is likely to regulate its cellular localization and/or interaction of PTPL1 with other regulators and/or substrates (reviewed in Ref.3). The non-catalytic domain of PTPL1 does not appear to control PTPL1 activity directly as the isolated catalytic domain of PTPL1 possesses the same activity as full-length PTPL1 (4).Recent studies have provided initial evidence that PTPL1 may play a role in regulating PI 3-kinase-dependent signaling pathways that regulate cell growth and survival responses. This was first based on the finding that overexpression of PTPL1 in a breast cancer cell line induced the dephosphorylation of the...

PTPL1: a large phosphatase with a split personality

“…In HeLa cells, PTPL1 localizes to the centrosomes during metaphase and to the midbody during cytokinesis [14]. Even though the PTP domains of protein tyrosine phosphatases share a high degree of sequence similarity [15], the crystal structure of the PTP domain of PTPL1 reveals a secondary phosphotyrosine binding pocket next to the active site, which is similar to that found in the structure of PTP1B [16]. Consistent with a functional role for this pocket in substrate recognition, monophosphorylated substrates are dephosphorylated by PTPL1 more slowly when compared to bi-or tri-phosphorylated substrates [16].…”

“…Even though the PTP domains of protein tyrosine phosphatases share a high degree of sequence similarity [15], the crystal structure of the PTP domain of PTPL1 reveals a secondary phosphotyrosine binding pocket next to the active site, which is similar to that found in the structure of PTP1B [16]. Consistent with a functional role for this pocket in substrate recognition, monophosphorylated substrates are dephosphorylated by PTPL1 more slowly when compared to bi-or tri-phosphorylated substrates [16]. The five PDZ domains within PTPL1 are responsible for direct binding to interacting proteins, which could either directly recruit phosphatase substrates or provide a multi-protein scaffold for the indirect binding of substrate proteins.…”

“…When the five missense mutations in the catalytic domain of PTPL1 were studied in vitro, four mutations led to amino-acid substitutions but without altered phosphatase activity. The fifth led to the M2307T [16], where M2307 is a highly conserved residue among PTPs [15]. This M2307T produced a protein with a seven-fold higher K m and two-fold lower k cat potentially leading to a decrease in the catalytic activity of PTPL1 [16].…”

The Putative Tumor Suppressor Gene PTPN13/PTPL1 Induces Apoptosis through Insulin Receptor Substrate-1 Dephosphorylation

“…Although several studies have identified potential substrates for PTPL1, among which ephrin B is the most documented (25), our study is the first that associates in vivo dephosphorylation and functional assays with in vitro and in vivo substrate trapping experiments. A crystal structure study of the PTPL1 catalytic domain shows that this enzyme, like PTP1B, interacts with and preferentially dephosphorylates bisphosphorylated insulin receptor peptides (26). However, specificity of PTPL1 for peptides from other multiphosphorylated proteins implicated in this transduction pathway, like IRS-1, has not yet been tested.…”

Regulation of TRP channel TRPM2 by the tyrosine phosphatase PTPL1

“…PTPL1, also called PTP-BAS (31), hPTP1E (4), or Fasassociated phosphatase-1 (FAP-1) (43), is one of the largest protein tyrosine phosphatases with 2,485 amino acids (3). It contains a kinase noncatalytic C-lobe domain and a four-pointone/ezrin/radixin/moesin domain in the NH 2 terminus, five PDZ domains between residues 1102 and 1990, and a protein tyrosine phosphatase domain in the COOH terminus (10,13,48). The four-point-one/ezrin/radixin/moesin domain may be necessary for targeting of PTPL1 to the apical surface of the plasma membrane (13), and the PDZ domains play a role in regulating the intracellular localization of PTPL1 and its interaction with other substrates and proteins (22,25,26).…”