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Chen P, Chen X, Song X, He A, Zheng Y, Li X, Tian R. Dissecting phospho-motif-dependent Shc1 interactome using long synthetic protein fragments. Chem Sci 2024; 15:d4sc02350a. [PMID: 39184293 PMCID: PMC11342145 DOI: 10.1039/d4sc02350a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 08/10/2024] [Indexed: 08/27/2024] Open
Abstract
Activated receptor tyrosine kinases (RTKs) rely on the assembly of signaling proteins into high-dimensional protein complexes for signal transduction. Shc1, a prototypical scaffold protein, plays a pivotal role in directing phosphotyrosine (pY)-dependent protein complex formation for numerous RTKs typically through its two pY-binding domains. The three conserved pY sites within its CH1 region (Shc1CH1) hold particular significance due to their substantial contribution to its functions. However, how Shc1 differentially utilizes these sites to precisely coordinate protein complex assembly remains unclear. Here, we employed multiple peptide ligation techniques to synthesize an array of long protein fragments (107 amino acids) covering a significant portion of the Shc1CH1 region with varying phosphorylation states at residues Y239, 240, 313, and S335. By combining these phospho-Shc1CH1 fragments with integrated proteomics sample preparation and quantitative proteomic analysis, we were able to comprehensively resolve the site-specific interactomes of Shc1 with single amino acid resolution. By applying this approach to different cancer cell lines, we demonstrated that these phospho-Shc1CH1 fragments can be effectively used as a diagnostic tool to assess cell type-specific RTK signaling networks. Collectively, these biochemical conclusions help to better understand the sophisticated organization of pY-dependent Shc1 adaptor protein complexes and their functional roles in cancer.
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Affiliation(s)
- Peizhong Chen
- Department of Chemistry, College of Science, Southern University of Science and Technology Shenzhen 518055 China
- Department of Chemistry, State Key Lab of Synthetic Chemistry, University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Xiong Chen
- Department of Chemistry, College of Science, Southern University of Science and Technology Shenzhen 518055 China
- Shenzhen Key Laboratory of Functional Proteomics, Guangming Advanced Research Institute, Southern University of Science and Technology Shenzhen 518055 China
| | - Xiaolei Song
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics Beijing 102206 China
| | - An He
- Department of Chemistry, College of Science, Southern University of Science and Technology Shenzhen 518055 China
| | - Yong Zheng
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics Beijing 102206 China
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, School of Basic Medicine, School of Rehabilitation Medicine, Gannan Medical University Ganzhou 341000 China
| | - Xuechen Li
- Department of Chemistry, State Key Lab of Synthetic Chemistry, University of Hong Kong Pokfulam Road Hong Kong SAR P. R. China
| | - Ruijun Tian
- Department of Chemistry, College of Science, Southern University of Science and Technology Shenzhen 518055 China
- Shenzhen Key Laboratory of Functional Proteomics, Guangming Advanced Research Institute, Southern University of Science and Technology Shenzhen 518055 China
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics Beijing 102206 China
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2
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Tsygankov AY. TULA Proteins in Men, Mice, Hens, and Lice: Welcome to the Family. Int J Mol Sci 2023; 24:ijms24119126. [PMID: 37298079 DOI: 10.3390/ijms24119126] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
The two members of the UBASH3/STS/TULA protein family have been shown to critically regulate key biological functions, including immunity and hemostasis, in mammalian biological systems. Negative regulation of signaling through immune receptor tyrosine-based activation motif (ITAM)- and hemITAM-bearing receptors mediated by Syk-family protein tyrosine kinases appears to be a major molecular mechanism of the down-regulatory effect of TULA-family proteins, which possess protein tyrosine phosphatase (PTP) activity. However, these proteins are likely to carry out some PTP-independent functions as well. Whereas the effects of TULA-family proteins overlap, their characteristics and their individual contributions to cellular regulation also demonstrate clearly distinct features. Protein structure, enzymatic activity, molecular mechanisms of regulation, and biological functions of TULA-family proteins are discussed in this review. In particular, the usefulness of the comparative analysis of TULA proteins in various metazoan taxa, for identifying potential roles of TULA-family proteins outside of their functions already established in mammalian systems, is examined.
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Affiliation(s)
- Alexander Y Tsygankov
- Sol Sherry Thrombosis Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA
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3
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Zaman A, French JB, Carpino N. The Sts Proteins: Modulators of Host Immunity. Int J Mol Sci 2023; 24:8834. [PMID: 37240179 PMCID: PMC10218301 DOI: 10.3390/ijms24108834] [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: 04/20/2023] [Revised: 05/08/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
The suppressor of TCR signaling (Sts) proteins, Sts-1 and Sts-2, are a pair of closely related signaling molecules that belong to the histidine phosphatase (HP) family of enzymes by virtue of an evolutionarily conserved C-terminal phosphatase domain. HPs derive their name from a conserved histidine that is important for catalytic activity and the current evidence indicates that the Sts HP domain plays a critical functional role. Sts-1HP has been shown to possess a readily measurable protein tyrosine phosphatase activity that regulates a number of important tyrosine-kinase-mediated signaling pathways. The in vitro catalytic activity of Sts-2HP is significantly lower than that of Sts-1HP, and its signaling role is less characterized. The highly conserved unique structure of the Sts proteins, in which additional domains, including one that exhibits a novel phosphodiesterase activity, are juxtaposed together with the phosphatase domain, suggesting that Sts-1 and -2 occupy a specialized intracellular signaling niche. To date, the analysis of Sts function has centered predominately around the role of Sts-1 and -2 in regulating host immunity and other responses associated with cells of hematopoietic origin. This includes their negative regulatory role in T cells, platelets, mast cells and other cell types, as well as their less defined roles in regulating host responses to microbial infection. Regarding the latter, the use of a mouse model lacking Sts expression has been used to demonstrate that Sts contributes non-redundantly to the regulation of host immunity toward a fungal pathogen (C. albicans) and a Gram-negative bacterial pathogen (F. tularensis). In particular, Sts-/- animals demonstrate significant resistance to lethal infections of both pathogens, a phenotype that is correlated with some heightened anti-microbial responses of phagocytes derived from mutant mice. Altogether, the past several years have seen steady progress in our understanding of Sts biology.
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Affiliation(s)
- Anika Zaman
- Graduate Program in Molecular and Cellular Pharmacology, Stony Brook University, Stony Brook, NY 11794, USA;
| | - Jarrod B. French
- Hormel Institute, University of Minnesota, 801 16th Ave NE, Austin, MN 55912, USA;
| | - Nick Carpino
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY 11794, USA
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4
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Yin Y, Frank D, Zhou W, Kaur N, French JB, Carpino N. An unexpected 2-histidine phosphoesterase activity of suppressor of T-cell receptor signaling protein 1 contributes to the suppression of cell signaling. J Biol Chem 2020; 295:8514-8523. [PMID: 32371395 DOI: 10.1074/jbc.ra120.013482] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 04/30/2020] [Indexed: 11/06/2022] Open
Abstract
The suppressor of T-cell receptor (TCR) signaling (Sts) proteins Sts-1 and Sts-2 suppress receptor-mediated signaling pathways in various immune cells, including the TCR pathway in T cells and the Dectin-1 signaling pathway in phagocytes. As multidomain enzymes, they contain an N-terminal ubiquitin-association domain, a central Src homology 3 domain, and a C-terminal histidine phosphatase domain. Recently, a 2-histidine (2H) phosphoesterase motif was identified within the N-terminal portion of Sts. The 2H phosphoesterase motif defines an evolutionarily ancient protein domain present in several enzymes that hydrolyze cyclic phosphate bonds on different substrates, including cyclic nucleotides. It is characterized by two invariant histidine residues that play a critical role in catalytic activity. Consistent with its assignment as a phosphoesterase, we demonstrate here that the Sts-1 2H phosphoesterase domain displays catalytic, saturable phosphodiesterase activity toward the dinucleotide 2',3'-cyclic NADP. The enzyme exhibited a high degree of substrate specificity and selectively generated the 3'-nucleotide as the sole product. Sts-1 also had phosphodiesterase catalytic activity toward a 5-mer RNA oligonucleotide containing a 2',3'-cyclic phosphate group at its 3' terminus. To investigate the functional significance of Sts-1 2H phosphoesterase activity, we generated His-to-Ala variants and examined their ability to negatively regulate cellular signaling pathways. Substitution of either conserved histidine compromised the ability of Sts-1 to suppress signaling pathways downstream of both the TCR and the Dectin-1 receptor. Our results identify a heretofore unknown cellular enzyme activity associated with Sts-1 and indicate that this catalytic activity is linked to specific cell-signaling outcomes.
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Affiliation(s)
- Yue Yin
- Department of Chemistry, Stony Brook University, Stony Brook, New York, USA
| | - David Frank
- Department of Microbiology and Immunology, Stony Brook University Medical Center, Stony Brook, New York, USA
| | - Weijie Zhou
- Department of Chemistry, Stony Brook University, Stony Brook, New York, USA
| | - Neena Kaur
- Department of Microbiology and Immunology, Stony Brook University Medical Center, Stony Brook, New York, USA
| | - Jarrod B French
- Department of Chemistry, Stony Brook University, Stony Brook, New York, USA .,Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Nick Carpino
- Department of Microbiology and Immunology, Stony Brook University Medical Center, Stony Brook, New York, USA
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5
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Tsygankov AY. TULA proteins as signaling regulators. Cell Signal 2019; 65:109424. [PMID: 31639493 DOI: 10.1016/j.cellsig.2019.109424] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/16/2019] [Accepted: 09/18/2019] [Indexed: 10/25/2022]
Abstract
Two members of the UBASH3/STS/TULA family exhibit a unique protein domain structure, which includes a histidine phosphatase domain, and play a key role in regulating cellular signaling. UBASH3A/STS-2/TULA is mostly a lymphoid protein, while UBASH3B/STS-1/TULA-2 is expressed ubiquitously. Dephosphorylation of tyrosine-phosphorylated proteins by TULA-2 and, probably to a lesser extent, by TULA critically contribute to the molecular basis of their regulatory effect. The notable differences between the effects of the two family members on cellular signaling and activation are likely to be linked to the difference between their specific enzymatic activities. However, these differences might also be related to the functions of their domains other than the phosphatase domain and independent of their phosphatase activity. The down-regulation of the Syk/Zap-70-mediated signaling, which to-date appears to be the best-studied regulatory effect of TULA family, is discussed in detail in this publication.
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Affiliation(s)
- Alexander Y Tsygankov
- Sol Sherry Thrombosis Research Center, Fels Institute for Cancer Research and Department of Microbiology and Immunology, Lewis Katz School of Medicine at Temple University, 3400 N. Broad Street, Philadelphia, PA, 19140, United States.
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Zhou W, Yin Y, Smith E, Chou J, Shumate J, Scampavia L, Spicer TP, Carpino N, French JB. Discovery and Characterization of Two Classes of Selective Inhibitors of the Suppressor of the TCR Signaling Family of Proteins. ACS Infect Dis 2019; 5:250-259. [PMID: 30485744 DOI: 10.1021/acsinfecdis.8b00238] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The suppressor of T-cell receptor signaling (Sts) proteins, Sts-1, has recently emerged as a potential immunostimulatory target for drug development. Genetic inactivation of the Sts proteins dramatically increases host survival of systemic infection and leads to improved pathogen clearance. The protein tyrosine phosphatase (PTP) activity of these proteins arises from a C-terminal 2-histidine phosphatase (HP) domain. To identify new inhibitors of the HP activity of Sts-1, we miniaturized a phosphatase assay to a 1536-well format and conducted a 20 580 compound screen. Among the hits were two classes of structurally related compounds, tetracycline variants and sulfonated azo dyes. These hits had low micromolar to nanomolar IC50 values. Orthogonal screening confirmed the validity of these inhibitors and demonstrated that both act competitively on Sts-1 phosphatase activity. When tested on other PTPs, PTP1B and SHP1, it was found that the tetracycline PTP1B, SHP1, the tetracycline variant (doxycycline), and the sulfonated azo dye (Congo red) are selective inhibitors of Sts-1HP, with selectivity indices ranging from 19 to as high as 200. The planar polyaromatic moieties present in both classes of compounds suggested a common binding mode. The mutation of either tryptophan 494 or tyrosine 596, located near the active site of the protein, reduced the Ki of the inhibitors from 3- to 18-fold, indicating that these residues may help to promote the binding of substrates with aromatic groups. This work provides new insights into substrate selectivity mechanisms and describes two classes of compounds that can serve as probes of function or as a basis for future drug discovery.
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Affiliation(s)
| | | | - Emery Smith
- Department of Molecular Medicine, Scripps Research Molecular Screening Center, Scripps Research, 130 Scripps Way, Jupiter, Florida 33458, United States
| | | | - Justin Shumate
- Department of Molecular Medicine, Scripps Research Molecular Screening Center, Scripps Research, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Louis Scampavia
- Department of Molecular Medicine, Scripps Research Molecular Screening Center, Scripps Research, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Timothy P. Spicer
- Department of Molecular Medicine, Scripps Research Molecular Screening Center, Scripps Research, 130 Scripps Way, Jupiter, Florida 33458, United States
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7
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Zhou W, Yin Y, Weinheimer AS, Kaur N, Carpino N, French JB. Structural and Functional Characterization of the Histidine Phosphatase Domains of Human Sts-1 and Sts-2. Biochemistry 2017; 56:4637-4645. [PMID: 28759203 DOI: 10.1021/acs.biochem.7b00638] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The suppressor of T cell signaling (Sts) proteins, Sts-1 and Sts-2, are homologous phosphatases that negatively regulate signaling pathways downstream of the T cell receptor. Functional inactivation of Sts-1 and Sts-2 in a murine model leads to resistance to systemic infection by the opportunistic pathogen, Candida albicans. This suggests that modulation of the host immune response by inhibiting Sts function may be a viable strategy for treating these deadly fungal pathogen infections. To better understand the molecular determinants of function and structure, we characterized the structure and steady-state kinetics of the histidine phosphatase domains of human Sts-1 (Sts-1HP) and Sts-2 (Sts-2HP). We determined the X-ray crystal structures of unliganded Sts-1HP and Sts-1HP in complex with sulfate to 2.5 and 1.9 Å, respectively, and the structure of Sts-2HP with sulfate to 2.4 Å. The steady-state kinetic analysis shows, as expected, that Sts-1HP has a phosphatase activity significantly higher than that of Sts-2HP and that the human and mouse proteins behave similarly. In addition, comparison of the phosphatase activity of full-length Sts-1 protein to Sts-1HP reveals similar kinetics, indicating that Sts-1HP is a functional surrogate for the native protein. We also tested known phosphatase inhibitors and determined that the SHP-1 inhibitor, PHPS1, is a potent inhibitor of Sts-1 (Ki = 1.05 ± 0.15 μM). Finally, we demonstrated that human Sts-1 has robust phosphatase activity against the substrate, Zap-70, in a cell-based assay. Collectively, these data suggest that the human Sts proteins are druggable targets and provide a structural basis for future drug development efforts.
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Affiliation(s)
- Weijie Zhou
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Yue Yin
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Alexandra S Weinheimer
- Department of Biochemistry and Cell Biology, Stony Brook University , Stony Brook, New York 11794, United States
| | - Neena Kaur
- Department of Molecular Genetics and Microbiology, Stony Brook University , Stony Brook, New York 11794, United States
| | - Nick Carpino
- Department of Molecular Genetics and Microbiology, Stony Brook University , Stony Brook, New York 11794, United States
| | - Jarrod B French
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.,Department of Biochemistry and Cell Biology, Stony Brook University , Stony Brook, New York 11794, United States
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8
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Abstract
PGAM5 is a mitochondrial membrane protein that functions as an atypical Ser/Thr phosphatase and is a regulator of oxidative stress response, necroptosis, and autophagy. Here we present several crystal structures of PGAM5 including the activating N-terminal regulatory sequences, providing a model for structural plasticity, dimerization of the catalytic domain, and the assembly into an enzymatically active dodecameric form. Oligomeric states observed in structures were supported by hydrogen exchange mass spectrometry, size-exclusion chromatography, and analytical ultracentrifugation experiments in solution. We report that the catalytically important N-terminal WDPNWD motif acts as a structural integrator assembling PGAM5 into a dodecamer, allosterically activating the phosphatase by promoting an ordering of the catalytic loop. Additionally the observed active site plasticity enabled visualization of essential conformational rearrangements of catalytic elements. The comprehensive biophysical characterization offers detailed structural models of this key mitochondrial phosphatase that has been associated with the development of diverse diseases. PGAM5 catalytic domain shares phosphoglycerate mutase fold and forms stable dimer WDPNWD motif allosterically activates the fully active dodecameric form Crystal structures reveal conformational plasticity of the PGAM5 active site
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