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El Badaoui L, Barr AJ. Analysis of Receptor-Type Protein Tyrosine Phosphatase Extracellular Regions with Insights from AlphaFold. Int J Mol Sci 2024; 25:820. [PMID: 38255894 PMCID: PMC10815196 DOI: 10.3390/ijms25020820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
The receptor-type protein tyrosine phosphatases (RPTPs) are involved in a wide variety of physiological functions which are mediated via their diverse extracellular regions. They play key roles in cell-cell contacts, bind various ligands and are regulated by dimerization and other processes. Depending on the subgroup, they have been described as everything from 'rigid rods' to 'floppy tentacles'. Here, we review current experimental structural knowledge on the extracellular region of RPTPs and draw on AlphaFold structural predictions to provide further insights into structure and function of these cellular signalling molecules, which are often mutated in disease and are recognised as drug targets. In agreement with experimental data, AlphaFold predicted structures for extracellular regions of R1, and R2B subgroup RPTPs have an extended conformation, whereas R2B RPTPs are twisted, reflecting their high flexibility. For the R3 PTPs, AlphaFold predicts that members of this subgroup adopt an extended conformation while others are twisted, and that certain members, such as CD148, have one or more large, disordered loop regions in place of fibronectin type 3 domains suggested by sequence analysis.
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Affiliation(s)
| | - Alastair J. Barr
- School of Life Sciences, University of Westminster, 115 New Cavendish Street, London W1W 6UW, UK;
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Kubota C, Torii R, Hosaka M, Takeuchi T, Gomi H, Torii S. Phogrin Regulates High-Fat Diet-Induced Compensatory Pancreatic β-Cell Growth by Switching Binding Partners. Nutrients 2024; 16:169. [PMID: 38201998 PMCID: PMC10780347 DOI: 10.3390/nu16010169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/26/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
The receptor protein tyrosine phosphatase phogrin primarily localizes to hormone secretory granules in neuroendocrine cells. Concurrent with glucose-stimulated insulin secretion, phogrin translocates to pancreatic β-cell plasma membranes, where it interacts with insulin receptors (IRs) to stabilize insulin receptor substrate 2 (IRS2) that, in turn, contributes to glucose-responsive β-cell growth. Pancreatic β-cell development was not altered in β-cell-specific, phogrin-deficient mice, but the thymidine incorporation rate decreased in phogrin-deficient islets with a moderate reduction in IRS2 protein expression. In this study, we analyzed the β-cell response to high-fat diet stress and found that the compensatory expansion in β-cell mass was significantly suppressed in phogrin-deficient mice. Phogrin-IR interactions occurred only in high-fat diet murine islets and proliferating β-cell lines, whereas they were inhibited by the intercellular binding of surface phogrin under confluent cell culture conditions. Thus, phogrin could regulate glucose-stimulated compensatory β-cell growth by changing its binding partner from another β-cell phogrin to IR in the same β-cells.
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Affiliation(s)
- Chisato Kubota
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-8512, Gunma, Japan (T.T.)
- Department of Nutrition, Takasaki University of Health and Welfare, Takasaki 370-0033, Gunma, Japan
| | - Ryoko Torii
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-8512, Gunma, Japan (T.T.)
| | - Masahiro Hosaka
- Department of Biotechnology, Akita Prefectural University, Akita 010-0195, Akita, Japan;
| | - Toshiyuki Takeuchi
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-8512, Gunma, Japan (T.T.)
| | - Hiroshi Gomi
- Department of Veterinary Anatomy, College of Bioresource Sciences, Nihon University, Fujisawa 252-0880, Kanagawa, Japan;
| | - Seiji Torii
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi 371-8512, Gunma, Japan (T.T.)
- Center for Food Science and Wellness, Gunma University, Maebashi 371-8511, Gunma, Japan
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Noguera ME, Jakoncic J, Ermácora MR. High-resolution structure of intramolecularly proteolyzed human mucin-1 SEA domain. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1868:140361. [PMID: 31923589 DOI: 10.1016/j.bbapap.2020.140361] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 01/04/2020] [Accepted: 01/06/2020] [Indexed: 01/26/2023]
Abstract
SEA domains are ubiquitous in large proteins associated with highly glycosylated environments. Certain SEA domains undergo intramolecular proteolysis involving a nucleophilic attack of a serine hydroxyl group on the preceding glycine carbonyl. The mucin-1 (MUC1) SEA domain has been extensively investigated as a model of intramolecular proteolysis. Since neither a general base, a general acid, nor an oxyanion hole could be identified in MUC1 SEA, it has been suggested that proteolysis is accelerated by a non-planarity of the scissile peptide bond imposed by protein folding. A reactant distorted peptide bond has been also invoked to explain the autoproteolysis of several unrelated proteins. However, the only evidence of peptide distortion in MUC1 SEA stems from molecular dynamic simulations of the reactant modeled upon a single NMR structure of the cleaved product. We report the first high-resolution X-ray structure of cleaved MUC1 SEA. Structural comparison with uncleaved SEA domains suggests that the number of residues evolutionarily inserted in the cleaved loop of MUC1 SEA precludes the formation of a properly hydrogen-bonded beta turn. By sequence analysis, we show that this conformational frustration is shared by all known cleaved SEA domains. In addition, alternative conformations of the uncleaved precursor could be modeled in which the scissile peptide bond is planar. The implications of these structures for autoproteolysis are discussed in the light of the previous research on autoproteolysis.
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Affiliation(s)
- Martín E Noguera
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Argentina; Instituto de Química y Físico-Química Biológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Jean Jakoncic
- Photon Science Directorate, Brookhaven National Laboratory, Upton, New York, United States
| | - Mario R Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Argentina; Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes,Argentina.
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Toledo PL, Torkko JM, Müller A, Wegbrod C, Sönmez A, Solimena M, Ermácora MR. ICA512 RESP18 homology domain is a protein-condensing factor and insulin fibrillation inhibitor. J Biol Chem 2019; 294:8564-8576. [PMID: 30979722 DOI: 10.1074/jbc.ra119.007607] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/09/2019] [Indexed: 12/19/2022] Open
Abstract
Type 1 diabetes islet cell autoantigen 512 (ICA512/IA-2) is a tyrosine phosphatase-like intrinsic membrane protein involved in the biogenesis and turnover of insulin secretory granules (SGs) in pancreatic islet β-cells. Whereas its membrane-proximal and cytoplasmic domains have been functionally and structurally characterized, the role of the ICA512 N-terminal segment named "regulated endocrine-specific protein 18 homology domain" (RESP18HD), which encompasses residues 35-131, remains largely unknown. Here, we show that ICA512 RESP18HD residues 91-131 encode for an intrinsically disordered region (IDR), which in vitro acts as a condensing factor for the reversible aggregation of insulin and other β-cell proteins in a pH and Zn2+-regulated fashion. At variance with what has been shown for other granule cargoes with aggregating properties, the condensing activity of ICA512 RESP18HD is displayed at a pH close to neutral, i.e. in the pH range found in the early secretory pathway, whereas it is resolved at acidic pH and Zn2+ concentrations resembling those present in mature SGs. Moreover, we show that ICA512 RESP18HD residues 35-90, preceding the IDR, inhibit insulin fibrillation in vitro Finally, we found that glucose-stimulated secretion of RESP18HD upon exocytosis of SGs from insulinoma INS-1 cells is associated with cleavage of its IDR, conceivably to prevent its aggregation upon exposure to neutral pH in the extracellular milieu. Taken together, these findings point to ICA512 RESP18HD being a condensing factor for protein sorting and granulogenesis early in the secretory pathway and for prevention of amyloidogenesis.
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Affiliation(s)
- Pamela L Toledo
- Grupo de Biología Estructural y Biotecnología, Universidad Nacional de Quilmes, 1876 Bernal, Buenos Aires, Argentina; IMBICE, CONICET-CIC-Universidad Nacional de La Plata, B1906APO La Plata, Buenos Aires, Argentina
| | - Juha M Torkko
- Grupo de Biología Estructural y Biotecnología, Universidad Nacional de Quilmes, 1876 Bernal, Buenos Aires, Argentina; IMBICE, CONICET-CIC-Universidad Nacional de La Plata, B1906APO La Plata, Buenos Aires, Argentina; Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Andreas Müller
- Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Carolin Wegbrod
- Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Anke Sönmez
- Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
| | - Michele Solimena
- Department of Molecular Diabetology, University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; Paul Langerhans Institute Dresden of the Helmholtz Center Munich at the University Hospital and Faculty of Medicine, TU Dresden, 01307 Dresden, Germany; German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany; Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany.
| | - Mario R Ermácora
- Grupo de Biología Estructural y Biotecnología, Universidad Nacional de Quilmes, 1876 Bernal, Buenos Aires, Argentina; IMBICE, CONICET-CIC-Universidad Nacional de La Plata, B1906APO La Plata, Buenos Aires, Argentina.
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Pei J, Grishin NV. Expansion of divergent SEA domains in cell surface proteins and nucleoporin 54. Protein Sci 2017; 26:617-630. [PMID: 27977898 DOI: 10.1002/pro.3096] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 12/13/2022]
Abstract
SEA (sea urchin sperm protein, enterokinase, agrin) domains, many of which possess autoproteolysis activity, have been found in a number of cell surface and secreted proteins. Despite high sequence divergence, SEA domains were also proposed to be present in dystroglycan based on a conserved autoproteolysis motif and receptor-type protein phosphatase IA-2 based on structural similarity. The presence of a SEA domain adjacent to the transmembrane segment appears to be a recurring theme in quite a number of type I transmembrane proteins on the cell surface, such as MUC1, dystroglycan, IA-2, and Notch receptors. By comparative sequence and structural analyses, we identified dystroglycan-like proteins with SEA domains in Capsaspora owczarzaki of the Filasterea group, one of the closest single-cell relatives of metazoans. We also detected novel and divergent SEA domains in a variety of cell surface proteins such as EpCAM, α/ε-sarcoglycan, PTPRR, collectrin/Tmem27, amnionless, CD34, KIAA0319, fibrocystin-like protein, and a number of cadherins. While these proteins are mostly from metazoans or their single cell relatives such as choanoflagellates and Filasterea, fibrocystin-like proteins with SEA domains were found in several other eukaryotic lineages including green algae, Alveolata, Euglenozoa, and Haptophyta, suggesting an ancient evolutionary origin. In addition, the intracellular protein Nucleoporin 54 (Nup54) acquired a divergent SEA domain in choanoflagellates and metazoans.
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Affiliation(s)
| | - Nick V Grishin
- Howard Hughes Medical Institute.,Department of Biophysics and Department of Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX, 75390, USA
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Stability of proICA512/IA-2 and its targeting to insulin secretory granules require β4-sheet-mediated dimerization of its ectodomain in the endoplasmic reticulum. Mol Cell Biol 2015; 35:914-27. [PMID: 25561468 DOI: 10.1128/mcb.00994-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The type 1 diabetes autoantigen ICA512/IA-2/RPTPN is a receptor protein tyrosine phosphatase of the insulin secretory granules (SGs) which regulates the size of granule stores, possibly via cleavage/signaling of its cytosolic tail. The role of its extracellular region remains unknown. Structural studies indicated that β2- or β4-strands in the mature ectodomain (ME ICA512) form dimers in vitro. Here we show that ME ICA512 prompts proICA512 dimerization in the endoplasmic reticulum. Perturbation of ME ICA512 β2-strand N-glycosylation upon S508A replacement allows for proICA512 dimerization, O-glycosylation, targeting to granules, and conversion, which are instead precluded upon G553D replacement in the ME ICA512 β4-strand. S508A/G553D and N506A/G553D double mutants dimerize but remain in the endoplasmic reticulum. Removal of the N-terminal fragment (ICA512-NTF) preceding ME ICA512 allows an ICA512-ΔNTF G553D mutant to exit the endoplasmic reticulum, and ICA512-ΔNTF is constitutively delivered to the cell surface. The signal for SG sorting is located within the NTF RESP18 homology domain (RESP18-HD), whereas soluble NTF is retained in the endoplasmic reticulum. Hence, we propose that the ME ICA512 β2-strand fosters proICA512 dimerization until NTF prevents N506 glycosylation. Removal of this constraint allows for proICA512 β4-strand-induced dimerization, exit from the endoplasmic reticulum, O-glycosylation, and RESP18-HD-mediated targeting to granules.
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