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Literature summary extracted from

  • Chen, K.E.; Li, M.Y.; Chou, C.C.; Ho, M.R.; Chen, G.C.; Meng, T.C.; Wang, A.H.
    Substrate specificity and plasticity of FERM-containing protein tyrosine phosphatases (2015), Structure, 23, 653-664 .
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.1.3.48 purified recombinant enzyme mutants D811A/C842S, D811E/C842S, D811A/H812F/C842S/M883G, Y676I, and D811E in complex with substrate Eps15846-854, and with mutant Eps15846-854 P450V, X-ray diffraction structure determination and analysis at 1.26-1.72 A resolution Homo sapiens

Protein Variants

EC Number Protein Variants Comment Organism
3.1.3.48 D811A/C842S site-directed mutagenesis, analysis of binding structure of substrate Eps15846-854 compared to wild-type enzyme and enzyme PTP1B Homo sapiens
3.1.3.48 D811A/H812F/C842S/M883G site-directed mutagenesis, analysis of binding structure of substrate Eps15846-854 compared to wild-type enzyme and enzyme PTP1B. THe mutant acts as a surrogate of the PTP1B active site, in complex with substrate Eps15846-854. Introduction of M883G substitution increased the flexibility of the side chain of Q886, thus facilitating interaction between F812 and the pTyr-Pro motif. In this complex structure, the phenyl side chain of F812 is shifted 3.7 A away from the active site pocket Homo sapiens
3.1.3.48 D811E site-directed mutagenesis, analysis of binding structure of substrate Eps15846-854 compared to wild-type enzyme and enzyme PTP1B Homo sapiens
3.1.3.48 D811E/C842S site-directed mutagenesis, analysis of binding structure of substrate Eps15846-854 compared to wild-type enzyme and enzyme PTP1B Homo sapiens
3.1.3.48 H812F site-directed mutagenesis, analysis of binding structure of substrate Eps15846-854 compared to wild-type enzyme and enzyme PTP1B. The H812F mutant form of PTPN3 behaves similarly to the wild-type PTP1B, showing a 9fold increase in Km and a 3.6fold decrease in kcat relative to the wild-type PTPN3 Homo sapiens
3.1.3.48 additional information ectopic expression of the D811E or H812F mutant form of PTPN3 fails to reduce the level of endogenous EGFR and the phosphorylation of mitogen-activated protein kinase (MAPK) in response to EGF stimulation. Transfection of human embryonic kidney HEK293T cells with the wild-type PTPN3 significantly decreases EGF-induced Y849 phosphorylation of Eps15, whereas ectopic expression of the D811E or H812F mutant form of PTPN3 does not affect the Y849 phosphorylation levels of Eps15. In the H1975 line-derived from human non-small-cell lung cancer, in which the wild-type form of PTPN3 can downregulate EGFR signaling via dephosphorylating Eps15, ectopic expression of the D811E or H812F mutant form of PTPN3 fails to reduce the level of endogenous EGFR and the phosphorylation of mitogen-activated protein kinase (MAPK) in response to EGF stimulation Homo sapiens
3.1.3.48 Y46A site-directed mutagenesis, substitution of Y46 with alalnine in PTP1B results in a 380fold increase in Km using pNPP as a substrate Homo sapiens
3.1.3.48 Y676I site-directed mutagenesis, analysis of binding structure of substrate Eps15846-854 compared to wild-type enzyme and enzyme PTP1B, mutant Y676I mutant loses the catalytic activity completely Homo sapiens

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.1.3.48 orthovanadate
-
 Homo sapiens

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.1.3.48 0.0215
-
 [Eps15 peptide846-854 P850V]-tyrosine phosphate recombinant wild-type enzyme, pH and temperature not specified in the publication Homo sapiens
3.1.3.48 0.0438
-
 [Eps15 peptide846-854]-tyrosine phosphate recombinant wild-type enzyme, pH and temperature not specified in the publication Homo sapiens

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
3.1.3.48 [a protein]-tyrosine phosphate + H2O Homo sapiens
-
 [a protein]-tyrosine + phosphate
-
 ?
3.1.3.48 [Eps15 peptide]-tyrosine phosphate + H2O Homo sapiens substrate is a phosphopeptide fragment of substrate epidermal growth factor receptor. Eps15 is a scaffolding adaptor that regulates endocytosis and trafficking of the EGFR and is a substrate for enzyme PTPN3 [Eps15 peptide]-tyrosine + phosphate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
3.1.3.48 Homo sapiens P18031
-
-
3.1.3.48 Homo sapiens P26045
-
-
3.1.3.48 Homo sapiens Q12923
-
-
3.1.3.48 Homo sapiens Q15678
-
-
3.1.3.48 Homo sapiens Q16825
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.1.3.48 4-nitrophenyl phosphate + H2O
-
 Homo sapiens 4-nitrophenol + phosphate
-
 ?
3.1.3.48 additional information the [Eps15 peptide]-tyrosine phosphate is a phosphopeptide fragment of substrate epidermal growth factor receptor. Eps15 is a scaffolding adaptor that regulates endocytosis and trafficking of the EGFR and is a substrate for PTP enzyme PTPN3. A conserved aspartic acid, which functions as a general acid for nucleophilic attack on the substrate in the first step of catalysis, must appear in the WPD loop among active PTPs, except for enzyme PTPN21, this critical residue in PTPN21 is substituted with a glutamic acid, thus resulting in a WPE loop instead. Enzyme PTPN21 shows no activity with 4-nitrophenyl phosphate or Eps15846-854 peptide as substrate in the phosphatase activity assay. Once the glutamic acid in the WPE loop is replaced by an aspartic acid, the E1067D mutant form of PTPN21PTP exhibits a significantly higher level of phosphatase activity compared with its wild-type counterpart Homo sapiens ?
-
 ?
3.1.3.48 additional information the [Eps15 peptide]-tyrosine phosphate is a phosphopeptide fragment of substrate epidermal growth factor receptor. Eps15 is a scaffolding adaptor that regulates endocytosis and trafficking of the EGFR and is a substrate for PTP enzyme PTPN3. Analysis of enzymes PTPN13 and PTPN14 within the FERM domain-containing PTP subfamily, overview. The catalytic domain of enzyme PTP1B cannot dephosphorylate Eps15846-854 or Eps15836-858 efficiently compared with wild-type PTPN3, supporting a critical role of H812 in recognition of Eps15. The position of H812 in PTPN3 is a phenylalanine (F182) in PTP1B, His812 of PTPN3 plays a central role in substrate specificity. Enzyme PTPN13 binds to Eps15846-854 more strongly largely because of the unique H2379 responsible for substrate recognition. The other difference is an aspartic acid (D2380) in PTPN13 instead of a glycine residue in PTPN3 inside the WPD loop. The presence of an additional aspartic acid suggests that the side chain of H2379 in PTPN13 might interact with the side chains of D2378 and D2380. Such interaction likely causes a perturbation of H2379, rendering this particular residue unable to form a stable stacked-like contact to Eps15846-854, wild-type PTPN13 shows a 3fold increase in Km compared with PTPN3 Homo sapiens ?
-
 ?
3.1.3.48 additional information the [Eps15 peptide]-tyrosine phosphate is a phosphopeptide fragment of substrate epidermal growth factor receptor. Eps15 is a scaffolding adaptor that regulates endocytosis and trafficking of the EGFR and is a substrate for PTP enzyme PTPN3. Analysis of enzymes PTPN13 and PTPN14 within the FERM domain-containing PTP subfamily, overview. The catalytic domain of enzyme PTP1B cannot dephosphorylate Eps15846-854 or Eps15836-858 efficiently compared with wild-type PTPN3, supporting a critical role of H812 in recognition of Eps15. The position of H812 in PTPN3 is a phenylalanine (F182) in PTP1B, His812 of PTPN3 plays a central role in substrate specificity. Enzyme PTPN14 shows a substitution of tyrosine in the pY loop with an isoleucin. The wild-type PTPN14PTP is catalytically inactive when four structurally characterized phosphopeptides are used as the substrate in the assay Homo sapiens ?
-
 ?
3.1.3.48 additional information the [Eps15 peptide]-tyrosine phosphate is a phosphopeptide fragment of substrate epidermal growth factor receptor. Eps15 is a scaffolding adaptor that regulates endocytosis and trafficking of the EGFR and is a substrate for PTP enzyme PTPN3. The catalytic domain of PTP1B cannot dephosphorylate Eps15846-854 or Eps15836-858 efficiently compared with wild-type N3PTP, supporting a critical role of H812 in recognition of Eps15. The position of H812 in PTPN3 is a phenylalanine (F182) in PTP1B, His812 of PTPN3 plays a central role in substrate specificity Homo sapiens ?
-
 ?
3.1.3.48 [a protein]-tyrosine phosphate + H2O
-
 Homo sapiens [a protein]-tyrosine + phosphate
-
 ?
3.1.3.48 [Eps15 peptide846-854 P850V]-tyrosine phosphate + H2O
-
 Homo sapiens [Eps15 peptide846-854 P850V]-tyrosine + phosphate
-
 ?
3.1.3.48 [Eps15 peptide846-854]-tyrosine phosphate + H2O
-
 Homo sapiens [Eps15 peptide846-854]-tyrosine + phosphate
-
 ?
3.1.3.48 [Eps15 peptide846-854]-tyrosine phosphate + H2O active with enzyme mutant F182H, wild-type shows poor activity Homo sapiens [Eps15 peptide846-854]-tyrosine + phosphate
-
 ?
3.1.3.48 [Eps15 peptide]-tyrosine phosphate + H2O substrate is a phosphopeptide fragment of substrate epidermal growth factor receptor. Eps15 is a scaffolding adaptor that regulates endocytosis and trafficking of the EGFR and is a substrate for enzyme PTPN3 Homo sapiens [Eps15 peptide]-tyrosine + phosphate
-
 ?
3.1.3.48 [Eps15 peptide]-tyrosine phosphate + H2O substrate is a phosphopeptide fragment of substrate epidermal growth factor receptor. Eps15 is a scaffolding adaptor that regulates endocytosis and trafficking of the EGFR and is a substrate for enzyme PTPN3. Pro850 of Eps15 and His812 of PTPN3 plays a central role in substrate specificity. E811 in WPE loop is unfavorable to act as a general acid during dephosphorylation. Critical role of the additional residue Tyr676 of PTPN3. The atypical binding conformation of Eps15 is mediated by its pTyr-Pro motif Homo sapiens [Eps15 peptide]-tyrosine + phosphate
-
 ?

Synonyms

EC Number Synonyms Comment Organism
3.1.3.48 N3PTP
-
 Homo sapiens
3.1.3.48 protein tyrosine phosphatase
-
 Homo sapiens
3.1.3.48 protein tyrosine phosphatase N3
-
 Homo sapiens
3.1.3.48 PTP
-
 Homo sapiens
3.1.3.48 PTP1B
-
 Homo sapiens
3.1.3.48 PTP1N13
-
 Homo sapiens
3.1.3.48 PTP1N21
-
 Homo sapiens
3.1.3.48 PTPH1
-
 Homo sapiens
3.1.3.48 PTPN14
-
 Homo sapiens
3.1.3.48 PTPN3
-
 Homo sapiens

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.1.3.48 13.4
-
 [Eps15 peptide846-854 P850V]-tyrosine phosphate recombinant wild-type enzyme, pH and temperature not specified in the publication Homo sapiens
3.1.3.48 17.3
-
 [Eps15 peptide846-854]-tyrosine phosphate recombinant wild-type enzyme, pH and temperature not specified in the publication Homo sapiens

General Information

EC Number General Information Comment Organism
3.1.3.48 evolution protein tyrosine phosphatase N3 (PTPN3/PTPH1) belongs to a subfamily of five PTPs that contain an N-terminal 4.1 protein, ezrin, radixin, and moesin (FERM) plasma membrane-localization domain and a C-terminal catalytic domain. PTPs in this subfamily can be further divided into two types based on the presence of a PDZ domain Homo sapiens
3.1.3.48 additional information a conserved aspartic acid, which functions as a general acid for nucleophilic attack on the substrate in the first step of catalysis, must appear in the WPD loop among active PTPs Homo sapiens
3.1.3.48 additional information a conserved aspartic acid, which functions as a general acid for nucleophilic attack on the substrate in the first step of catalysis, must appear in the WPD loop among active PTPs, except for enzyme PTPN21, this critical residue in PTPN21 is substituted with a glutamic acid, thus resulting in a WPE loop instead. The WPE loop is a key region responsible for the catalytic inertness of PTPN21 Homo sapiens
3.1.3.48 additional information specific recognition of Eps15 by enzyme PTPN3 and members in the FERM domain-containing PTP subfamily comprising PTPN4, N13, N14, and N21, overview. Pro850 of Eps15 and His812 of PTPN3 plays a central role in substrate specificity. E811 in WPE loop is unfavorable to act as a general acid during dephosphorylation. Identification of residues responsible for substrate specificity in the subfamily, overview. Critical role of the additional residue Tyr676 of PTPN3, which is replaced by Ile939 in PTPN14, in recognition of tyrosine phosphorylated Eps15. The WPD loop necessary for catalysis is present in all members but not PTPN21. A conserved aspartic acid, which functions as a general acid for nucleophilic attack on the substrate in the first step of catalysis, must appear in the WPD loop among active PTPs. Superposition of the N3PTP D811A/C842SEps15846-854 complex structure with other known PTP phosphopeptide structures. Residues H812 and D811 in PTPN3 are essential for regulating Eps15-dependent EGFR/MAPK signaling In vivo Homo sapiens

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
3.1.3.48 395
-
 [Eps15 peptide846-854]-tyrosine phosphate recombinant wild-type enzyme, pH and temperature not specified in the publication Homo sapiens
3.1.3.48 623.3
-
 [Eps15 peptide846-854 P850V]-tyrosine phosphate recombinant wild-type enzyme, pH and temperature not specified in the publication Homo sapiens