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Wybenga-Groot LE, Tench AJ, Simpson CD, Germain JS, Raught B, Moran MF, McGlade CJ. SLAP2 Adaptor Binding Disrupts c-CBL Autoinhibition to Activate Ubiquitin Ligase Function. J Mol Biol 2021; 433:166880. [PMID: 33617900 DOI: 10.1016/j.jmb.2021.166880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 02/05/2021] [Accepted: 02/12/2021] [Indexed: 10/22/2022]
Abstract
CBL is a RING type E3 ubiquitin ligase that functions as a negative regulator of tyrosine kinase signaling and loss of CBL E3 function is implicated in several forms of leukemia. The Src-like adaptor proteins (SLAP/SLAP2) bind to CBL and are required for CBL-dependent downregulation of antigen receptor, cytokine receptor, and receptor tyrosine kinase signaling. Despite the established role of SLAP/SLAP2 in regulating CBL activity, the nature of the interaction and the mechanisms involved are not known. To understand the molecular basis of the interaction between SLAP/SLAP2 and CBL, we solved the crystal structure of CBL tyrosine kinase binding domain (TKBD) in complex with SLAP2. The carboxy-terminal region of SLAP2 adopts an α-helical structure which binds in a cleft between the 4H, EF-hand, and SH2 domains of the TKBD. This SLAP2 binding site is remote from the canonical TKBD phospho-tyrosine peptide binding site but overlaps with a region important for stabilizing CBL in its autoinhibited conformation. In addition, binding of SLAP2 to CBL in vitro activates the ubiquitin ligase function of autoinhibited CBL. Disruption of the CBL/SLAP2 interface through mutagenesis demonstrated a role for this protein-protein interaction in regulation of CBL E3 ligase activity in cells. Our results reveal that SLAP2 binding to a regulatory cleft of the TKBD provides an alternative mechanism for activation of CBL ubiquitin ligase function.
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Affiliation(s)
- Leanne E Wybenga-Groot
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Program in Cell Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; SPARC BioCentre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada.
| | - Andrea J Tench
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Program in Cell Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, ON M5G 2M9, Canada
| | - Craig D Simpson
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Program in Cell Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada
| | - Jonathan St Germain
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Brian Raught
- Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, ON M5G 2M9, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 1L7, Canada
| | - Michael F Moran
- Program in Cell Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; SPARC BioCentre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Molecular Genetics, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - C Jane McGlade
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Program in Cell Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada; Department of Medical Biophysics, University of Toronto, 610 University Avenue, Toronto, ON M5G 2M9, Canada.
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2
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Wybenga-Groot LE, McGlade CJ. Sleuthing biochemical evidence to elucidate unassigned electron density in a CBL-SLAP2 crystal complex. Acta Crystallogr F Struct Biol Commun 2021; 77:37-46. [PMID: 33620036 DOI: 10.1107/s2053230x21000911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 01/26/2021] [Indexed: 11/10/2022]
Abstract
The Src-like adaptor proteins (SLAP/SLAP2) bind to CBL E3 ubiquitin ligase to downregulate antigen, cytokine and tyrosine kinase receptor signalling. In contrast to the phosphotyrosine-dependent binding of CBL substrates through its tyrosine kinase-binding domain (TKBD), CBL TKBD associates with the C-terminal tail of SLAP2 in a phospho-independent manner. To understand the distinct nature of this interaction, a purification protocol for SLAP2 in complex with CBL TKBD was established and the complex was crystallized. However, determination of the complex crystal structure was hindered by the apparent degradation of SLAP2 during the crystallization process, such that only the CBL TKBD residues could initially be modelled. Close examination of the CBL TKBD structure revealed a unique dimer interface that included two short segments of electron density of unknown origin. To elucidate which residues of SLAP2 to model into this unassigned density, a co-expression system was generated to test SLAP2 deletion mutants and define the minimal SLAP2 binding region. SLAP2 degradation products were also analysed by mass spectrometry. The model-building and map-generation features of the Phenix software package were employed, leading to successful modelling of the C-terminal tail of SLAP2 into the unassigned electron-density segments.
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Affiliation(s)
- Leanne E Wybenga-Groot
- SPARC BioCentre, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
| | - C Jane McGlade
- Program in Cell Biology, The Hospital for Sick Children, 686 Bay Street, Toronto, Ontario M5G 0A4, Canada
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3
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Saraon P, Snider J, Kalaidzidis Y, Wybenga-Groot LE, Weiss K, Rai A, Radulovich N, Drecun L, Vučković N, Vučetić A, Wong V, Thériault B, Pham NA, Park JH, Datti A, Wang J, Pathmanathan S, Aboualizadeh F, Lyakisheva A, Yao Z, Wang Y, Joseph B, Aman A, Moran MF, Prakesch M, Poda G, Marcellus R, Uehling D, Samaržija M, Jakopović M, Tsao MS, Shepherd FA, Sacher A, Leighl N, Akhmanova A, Al-Awar R, Zerial M, Stagljar I. A drug discovery platform to identify compounds that inhibit EGFR triple mutants. Nat Chem Biol 2020; 16:577-586. [PMID: 32094923 DOI: 10.1038/s41589-020-0484-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 01/27/2020] [Indexed: 12/21/2022]
Abstract
Receptor tyrosine kinases (RTKs) are transmembrane receptors of great clinical interest due to their role in disease. Historically, therapeutics targeting RTKs have been identified using in vitro kinase assays. Due to frequent development of drug resistance, however, there is a need to identify more diverse compounds that inhibit mutated but not wild-type RTKs. Here, we describe MaMTH-DS (mammalian membrane two-hybrid drug screening), a live-cell platform for high-throughput identification of small molecules targeting functional protein-protein interactions of RTKs. We applied MaMTH-DS to an oncogenic epidermal growth factor receptor (EGFR) mutant resistant to the latest generation of clinically approved tyrosine kinase inhibitors (TKIs). We identified four mutant-specific compounds, including two that would not have been detected by conventional in vitro kinase assays. One of these targets mutant EGFR via a new mechanism of action, distinct from classical TKI inhibition. Our results demonstrate how MaMTH-DS is a powerful complement to traditional drug screening approaches.
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Affiliation(s)
- Punit Saraon
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Jamie Snider
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Yannis Kalaidzidis
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Konstantin Weiss
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Ankit Rai
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Nikolina Radulovich
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Luka Drecun
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Nika Vučković
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Adriana Vučetić
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Victoria Wong
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Brigitte Thériault
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Jin H Park
- Department of Pharmacology and Cancer Biology Institute, Yale University, New Haven, CT, USA.,Department of Pharmacology, Weill Cornell Medicine, New York, NY, USA
| | - Alessandro Datti
- Network Biology Collaborative Centre, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Agriculture, Food, and Environmental Sciences, University of Perugia, Perugia, Italy
| | - Jenny Wang
- Network Biology Collaborative Centre, Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Shivanthy Pathmanathan
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | | | - Anna Lyakisheva
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Zhong Yao
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Yuhui Wang
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Babu Joseph
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Ahmed Aman
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Michael F Moran
- Peter Gilgan Centre for Research and Learning, Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Michael Prakesch
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gennady Poda
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Richard Marcellus
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - David Uehling
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Miroslav Samaržija
- Department for Lung Diseases Jordanovac, Clinical Hospital Centre Zagreb, University of Zagreb, Zagreb, Croatia
| | - Marko Jakopović
- Department for Lung Diseases Jordanovac, Clinical Hospital Centre Zagreb, University of Zagreb, Zagreb, Croatia
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Frances A Shepherd
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Adrian Sacher
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Natasha Leighl
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Anna Akhmanova
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht, the Netherlands
| | - Rima Al-Awar
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
| | - Marino Zerial
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Igor Stagljar
- Donnelly Centre, University of Toronto, Toronto, Ontario, Canada. .,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada. .,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada. .,Mediterranean Institute for Life Sciences, Split, Croatia.
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4
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Scott BM, Wybenga-Groot LE, McGlade CJ, Heon E, Peisajovich SG, Chang BSW. Screening of Chemical Libraries Using a Yeast Model of Retinal Disease. SLAS Discov 2019; 24:969-977. [PMID: 31556794 DOI: 10.1177/2472555219875934] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Retinitis pigmentosa (RP) is a degenerative retinal disease, often caused by mutations in the G-protein-coupled receptor rhodopsin. The majority of pathogenic rhodopsin mutations cause rhodopsin to misfold, including P23H, disrupting its crucial ability to respond to light. Previous screens to discover pharmacological chaperones of rhodopsin have primarily been based on rescuing rhodopsin trafficking and localization to the plasma membrane. Here, we present methods utilizing a yeast-based assay to screen for compounds that rescue the ability of rhodopsin to activate an associated downstream G-protein signaling cascade. We engineered a yeast strain in which human rhodopsin variants were genomically integrated, and were able to demonstrate functional coupling to the yeast mating pathway, leading to fluorescent protein expression. We confirmed that a known pharmacological chaperone, 9-cis retinal, could partially rescue light-dependent activation of a disease-associated rhodopsin mutation (P23H) expressed in yeast. These novel yeast strains were used to perform a phenotypic screen of 4280 compounds from the LOPAC1280 library and a peptidomimetic library, to discover novel pharmacological chaperones of rhodopsin. The fluorescence-based assay was robust in a 96-well format, with a Z' factor of 0.65 and a signal-to-background ratio of above 14. One compound was selected for additional analysis, but it did not appear to rescue rhodopsin function in yeast. The methods presented here are amenable to future screens of small-molecule libraries, as they are robust and cost-effective. We also discuss how these methods could be further modified or adapted to perform screens of more compounds in the future.
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Affiliation(s)
- Benjamin M Scott
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.,Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA.,Biosystems and Biomaterials Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | | | - C Jane McGlade
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Program in Cell Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Elise Heon
- Department of Ophthalmology and Vision Science, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sergio G Peisajovich
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Belinda S W Chang
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.,Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Centre for the Analysis of Genome Evolution and Function, University of Toronto, ON, Canada
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5
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Krieger JR, Wybenga-Groot LE, Tong J, Bache N, Tsao MS, Moran MF. Evosep One Enables Robust Deep Proteome Coverage Using Tandem Mass Tags while Significantly Reducing Instrument Time. J Proteome Res 2019; 18:2346-2353. [DOI: 10.1021/acs.jproteome.9b00082] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | | | | | | | - Ming S. Tsao
- Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, ON, Canada M5G 2C1
- Department of Laboratory Medicine and Pathobiology, University of Toronto, 1 King’s College Circle, Toronto, ON, Canada M5S 1A8
- Department of Medical Biophysics, University of Toronto, 101 College Street, Toronto, ON, Canada M5G 1L7
| | - Michael F. Moran
- Department of Molecular Genetics, University of Toronto, 1 King’s College Circle, Toronto, ON, Canada M5S 1A8
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6
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Jin LL, Wybenga-Groot LE, Tong J, Taylor P, Minden MD, Trudel S, McGlade CJ, Moran MF. Tyrosine phosphorylation of the Lyn Src homology 2 (SH2) domain modulates its binding affinity and specificity. Mol Cell Proteomics 2015; 14:695-706. [PMID: 25587033 DOI: 10.1074/mcp.m114.044404] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Src homology 2 (SH2) domains are modular protein structures that bind phosphotyrosine (pY)-containing polypeptides and regulate cellular functions through protein-protein interactions. Proteomics analysis showed that the SH2 domains of Src family kinases are themselves tyrosine phosphorylated in blood system cancers, including acute myeloid leukemia, chronic lymphocytic leukemia, and multiple myeloma. Using the Src family kinase Lyn SH2 domain as a model, we found that phosphorylation at the conserved SH2 domain residue Y(194) impacts the affinity and specificity of SH2 domain binding to pY-containing peptides and proteins. Analysis of the Lyn SH2 domain crystal structure supports a model wherein phosphorylation of Y(194) on the EF loop modulates the binding pocket that engages amino acid side chains at the pY+2/+3 position. These data indicate another level of regulation wherein SH2-mediated protein-protein interactions are modulated by SH2 kinases and phosphatases.
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Affiliation(s)
- Lily L Jin
- From the ‡Molecular Structure and Function, The Hospital For Sick Children, 686 Bay Street, Toronto, M5G 0A4, Canada; ‡‡Departments of Molecular Genetics, Medical Science Building, Room 4386, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Leanne E Wybenga-Groot
- §Cell Biology, The Hospital For Sick Children, 686 Bay Street, Toronto, M5G 0A4, Canada; ¶The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital For Sick Children, 686 Bay Street, Toronto, M5G 0A4, Canada
| | - Jiefei Tong
- From the ‡Molecular Structure and Function, The Hospital For Sick Children, 686 Bay Street, Toronto, M5G 0A4, Canada
| | - Paul Taylor
- From the ‡Molecular Structure and Function, The Hospital For Sick Children, 686 Bay Street, Toronto, M5G 0A4, Canada
| | - Mark D Minden
- ‖Medical Biophysics, University of Toronto, Medical Science Building, Room 4386, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; **The Princess Margaret Cancer Center, 610 University Avenue, M5G 2M9, Toronto, Canada
| | - Suzanne Trudel
- ‖Medical Biophysics, University of Toronto, Medical Science Building, Room 4386, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; **The Princess Margaret Cancer Center, 610 University Avenue, M5G 2M9, Toronto, Canada
| | - C Jane McGlade
- §Cell Biology, The Hospital For Sick Children, 686 Bay Street, Toronto, M5G 0A4, Canada; ¶The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital For Sick Children, 686 Bay Street, Toronto, M5G 0A4, Canada; ‖Medical Biophysics, University of Toronto, Medical Science Building, Room 4386, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Michael F Moran
- From the ‡Molecular Structure and Function, The Hospital For Sick Children, 686 Bay Street, Toronto, M5G 0A4, Canada; ‡‡Departments of Molecular Genetics, Medical Science Building, Room 4386, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; **The Princess Margaret Cancer Center, 610 University Avenue, M5G 2M9, Toronto, Canada
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7
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Wybenga-Groot LE, Ho CS, Sweeney FD, Ceccarelli DF, McGlade CJ, Durocher D, Sicheri F. Structural basis of Rad53 kinase activation by dimerization and activation segment exchange. Cell Signal 2014; 26:1825-36. [PMID: 24815189 DOI: 10.1016/j.cellsig.2014.05.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 05/02/2014] [Indexed: 01/08/2023]
Abstract
The protein kinase Rad53 is a key regulator of the DNA damage checkpoint in budding yeast. Its human ortholog, CHEK2, is mutated in familial breast cancer and mediates apoptosis in response to genotoxic stress. Autophosphorylation of Rad53 at residue Thr354 located in the kinase activation segment is essential for Rad53 activation. In this study, we assessed the requirement of kinase domain dimerization and the exchange of its activation segment during the Rad53 activation process. We solved the crystal structure of Rad53 in its dimeric form and found that disruption of the observed head-to-tail, face-to-face dimer structure decreased Rad53 autophosphorylation on Thr354 in vitro and impaired Rad53 function in vivo. Moreover, we provide critical functional evidence that Rad53 trans-autophosphorylation may involve the interkinase domain exchange of helix αEF via an invariant salt bridge. These findings suggest a mechanism of autophosphorylation that may be broadly applicable to other protein kinases.
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Affiliation(s)
- Leanne E Wybenga-Groot
- The Arthur and Sonia Labatt Brain Tumour Research Centre and Program in Cell Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada.
| | - Cynthia S Ho
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.
| | - Frédéric D Sweeney
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada; Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
| | - Derek F Ceccarelli
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada.
| | - C Jane McGlade
- The Arthur and Sonia Labatt Brain Tumour Research Centre and Program in Cell Biology, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8, Canada.
| | - Daniel Durocher
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada; Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
| | - Frank Sicheri
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada; Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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8
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Wolting CD, Griffiths EK, Sarao R, Prevost BC, Wybenga-Groot LE, McGlade CJ. Biochemical and computational analysis of LNX1 interacting proteins. PLoS One 2011; 6:e26248. [PMID: 22087225 PMCID: PMC3210812 DOI: 10.1371/journal.pone.0026248] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Accepted: 09/23/2011] [Indexed: 12/18/2022] Open
Abstract
PDZ (Post-synaptic density, 95 kDa, Discs large, Zona Occludens-1) domains are protein interaction domains that bind to the carboxy-terminal amino acids of binding partners, heterodimerize with other PDZ domains, and also bind phosphoinositides. PDZ domain containing proteins are frequently involved in the assembly of multi-protein complexes and clustering of transmembrane proteins. LNX1 (Ligand of Numb, protein X 1) is a RING (Really Interesting New Gene) domain-containing E3 ubiquitin ligase that also includes four PDZ domains suggesting it functions as a scaffold for a multi-protein complex. Here we use a human protein array to identify direct LNX1 PDZ domain binding partners. Screening of 8,000 human proteins with isolated PDZ domains identified 53 potential LNX1 binding partners. We combined this set with LNX1 interacting proteins identified by other methods to assemble a list of 220 LNX1 interacting proteins. Bioinformatic analysis of this protein list was used to select interactions of interest for future studies. Using this approach we identify and confirm six novel LNX1 binding partners: KCNA4, PAK6, PLEKHG5, PKC-alpha1, TYK2 and PBK, and suggest that LNX1 functions as a signalling scaffold.
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Affiliation(s)
- Cheryl D. Wolting
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Canada
| | - Emily K. Griffiths
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Canada
| | - Renu Sarao
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Canada
| | - Brittany C. Prevost
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Canada
| | - Leanne E. Wybenga-Groot
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Canada
| | - C. Jane McGlade
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Canada
- * E-mail:
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9
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Littler DR, Walker JR, Davis T, Wybenga-Groot LE, Finerty PJ, Newman E, Mackenzie F, Dhe-Paganon S. A conserved mechanism of autoinhibition for the AMPK kinase domain: ATP-binding site and catalytic loop refolding as a means of regulation. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:143-51. [PMID: 20124709 DOI: 10.1107/s1744309109052543] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Accepted: 12/07/2009] [Indexed: 12/16/2022]
Abstract
The AMP-activated protein kinase (AMPK) is a highly conserved trimeric protein complex that is responsible for energy homeostasis in eukaryotic cells. Here, a 1.9 A resolution crystal structure of the isolated kinase domain from the alpha2 subunit of human AMPK, the first from a multicellular organism, is presented. This human form adopts a catalytically inactive state with distorted ATP-binding and substrate-binding sites. The ATP site is affected by changes in the base of the activation loop, which has moved into an inhibited DFG-out conformation. The substrate-binding site is disturbed by changes within the AMPKalpha2 catalytic loop that further distort the enzyme from a catalytically active form. Similar structural rearrangements have been observed in a yeast AMPK homologue in response to the binding of its auto-inhibitory domain; restructuring of the kinase catalytic loop is therefore a conserved feature of the AMPK protein family and is likely to represent an inhibitory mechanism that is utilized during function.
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Affiliation(s)
- Dene R Littler
- The Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.
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10
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Abstract
Eph receptor tyrosine kinases regulate many important biological processes. In the present study, we explored the substrate specificity of the EphA4 receptor tyrosine kinase using peptide arrays. We define a consensus substrate motif for EphA4 and go on to identify and test a number of potential EphA4 substrates and map their putative site(s) of phosphorylation. Cotransfection studies validate two of the predicted substrates: Nck2 and Dok1. Our findings identify several potential EphA4 substrates and demonstrate the general utility of using peptide arrays to rapidly identify and map protein kinase phosphorylation sites.
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Affiliation(s)
- Neil Warner
- Program in Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
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11
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Wiesner S, Wybenga-Groot LE, Warner N, Lin H, Pawson T, Forman-Kay JD, Sicheri F. A change in conformational dynamics underlies the activation of Eph receptor tyrosine kinases. EMBO J 2006; 25:4686-96. [PMID: 16977320 PMCID: PMC1589994 DOI: 10.1038/sj.emboj.7601315] [Citation(s) in RCA: 81] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2006] [Accepted: 08/08/2006] [Indexed: 02/03/2023] Open
Abstract
Eph receptor tyrosine kinases (RTKs) mediate numerous developmental processes. Their activity is regulated by auto-phosphorylation on two tyrosines within the juxtamembrane segment (JMS) immediately N-terminal to the kinase domain (KD). Here, we probe the molecular details of Eph kinase activation through mutational analysis, X-ray crystallography and NMR spectroscopy on auto-inhibited and active EphB2 and EphA4 fragments. We show that a Tyr750Ala gain-of-function mutation in the KD and JMS phosphorylation independently induce disorder of the JMS and its dissociation from the KD. Our X-ray analyses demonstrate that this occurs without major conformational changes to the KD and with only partial ordering of the KD activation segment. However, conformational exchange for helix alphaC in the N-terminal KD lobe and for the activation segment, coupled with increased inter-lobe dynamics, is observed upon kinase activation in our NMR analyses. Overall, our results suggest that a change in inter-lobe dynamics and the sampling of catalytically competent conformations for helix alphaC and the activation segment rather than a transition to a static active conformation underlies Eph RTK activation.
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Affiliation(s)
- Silke Wiesner
- Structural Biology and Biochemistry, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Leanne E Wybenga-Groot
- Program in Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Neil Warner
- Program in Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hong Lin
- Structural Biology and Biochemistry, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Tony Pawson
- Program in Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave., Toronto, Ontario, Canada M5G 1X5. Tel.: +1 416 586 8262; Fax: +1 416 586 8869; E-mail:
| | - Julie D Forman-Kay
- Structural Biology and Biochemistry, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Hospital for Sick Children, 555 University Ave., Toronto, Ontario, Canada M5G 1X8. Tel.: +1 416 813 5358; Fax: +1 416 813 5022; E-mail:
| | - Frank Sicheri
- Program in Systems Biology, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, Ontario, Canada
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Ave., Toronto, Ontario, Canada M5G 1X5. Tel.: +1 416 586 8471; Fax: +1 416 586 8869; E-mail:
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Burk DL, Ghuman N, Wybenga-Groot LE, Berghuis AM. X-ray structure of the AAC(6')-Ii antibiotic resistance enzyme at 1.8 A resolution; examination of oligomeric arrangements in GNAT superfamily members. Protein Sci 2003; 12:426-37. [PMID: 12592013 PMCID: PMC2312454 DOI: 10.1110/ps.0233503] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The rise of antibiotic resistance as a public health concern has led to increased interest in studying the ways in which bacteria avoid the effects of antibiotics. Enzymatic inactivation by several families of enzymes has been observed to be the predominant mechanism of resistance to aminoglycoside antibiotics such as kanamycin and gentamicin. Despite the importance of acetyltransferases in bacterial resistance to aminoglycoside antibiotics, relatively little is known about their structure and mechanism. Here we report the three-dimensional atomic structure of the aminoglycoside acetyltransferase AAC(6')-Ii in complex with coenzyme A (CoA). This structure unambiguously identifies the physiologically relevant AAC(6')-Ii dimer species, and reveals that the enzyme structure is similar in the AcCoA and CoA bound forms. AAC(6')-Ii is a member of the GCN5-related N-acetyltransferase (GNAT) superfamily of acetyltransferases, a diverse group of enzymes that possess a conserved structural motif, despite low sequence homology. AAC(6')-Ii is also a member of a subset of enzymes in the GNAT superfamily that form multimeric complexes. The dimer arrangements within the multimeric GNAT superfamily members are compared, revealing that AAC(6')-Ii forms a dimer assembly that is different from that observed in the other multimeric GNAT superfamily members. This different assembly may provide insight into the evolutionary processes governing dimer formation.
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Affiliation(s)
- David L Burk
- Departments of Biochemistry and Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada
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Wybenga-Groot LE, Baskin B, Ong SH, Tong J, Pawson T, Sicheri F. Structural basis for autoinhibition of the Ephb2 receptor tyrosine kinase by the unphosphorylated juxtamembrane region. Cell 2001; 106:745-57. [PMID: 11572780 DOI: 10.1016/s0092-8674(01)00496-2] [Citation(s) in RCA: 236] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Eph receptor tyrosine kinase family is regulated by autophosphorylation within the juxtamembrane region and the kinase activation segment. We have solved the X-ray crystal structure to 1.9 A resolution of an autoinhibited, unphosphorylated form of EphB2 comprised of the juxtamembrane region and the kinase domain. The structure, supported by mutagenesis data, reveals that the juxtamembrane segment adopts a helical conformation that distorts the small lobe of the kinase domain, and blocks the activation segment from attaining an activated conformation. Phosphorylation of conserved juxtamembrane tyrosines would relieve this autoinhibition by disturbing the association of the juxtamembrane segment with the kinase domain, while liberating phosphotyrosine sites for binding SH2 domains of target proteins. We propose that the autoinhibitory mechanism employed by EphB2 is a more general device through which receptor tyrosine kinases are controlled.
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Affiliation(s)
- L E Wybenga-Groot
- Program in Molecular Biology and Cancer, Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Ontario M5G 1X5, Toronto, Canada
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Wybenga-Groot LE, Draker K, Wright GD, Berghuis AM. Crystal structure of an aminoglycoside 6'-N-acetyltransferase: defining the GCN5-related N-acetyltransferase superfamily fold. Structure 1999; 7:497-507. [PMID: 10378269 DOI: 10.1016/s0969-2126(99)80066-5] [Citation(s) in RCA: 118] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND The predominant mechanism of antibiotic resistance employed by pathogenic bacteria against the clinically used aminoglycosides is chemical modification of the drug. The detoxification reactions are catalyzed by enzymes that promote either the phosphorylation, adenylation or acetylation of aminoglycosides. Structural studies of these aminoglycoside-modifying enzymes may assist in the development of therapeutic agents that could circumvent antibiotic resistance. In addition, such studies may shed light on the development of antibiotic resistance and the evolution of different enzyme classes. RESULTS The crystal structure of the aminoglycoside-modifying enzyme aminoglycoside 6'-N-acetyltransferase type li (AAC(6')-li) in complex with the cofactor acetyl coenzyme A has been determined at 2.7 A resolution. The structure establishes that this acetyltransferase belongs to the GCN5-related N-acetyltransferase superfamily, which includes such enzymes as the histone acetyltransferases GCN5 and Hat1. CONCLUSIONS Comparison of the AAC(6')-li structure with the crystal structures of two other members of this superfamily, Serratia marcescens aminoglycoside 3-N-acetyltransferase and yeast histone acetyltransferase Hat1, reveals that of the 84 residues that are structurally similar, only three are conserved and none can be implicated as catalytic residues. Despite the negligible sequence identity, functional studies show that AAC(6')-li possesses protein acetylation activity. Thus, AAC(6')-li is both a structural and functional homolog of the GCN5-related histone acetyltransferases.
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Affiliation(s)
- L E Wybenga-Groot
- Department of Biochemistry, McMaster University, Hamilton, ON, Canada
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