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Krishnan H, Ahmed S, Hubbard SR, Miller WT. Biochemical characterization of the Drosophila insulin receptor kinase and longevity-associated mutants. FASEB J 2024; 38:e23355. [PMID: 38071609 DOI: 10.1096/fj.202301948r] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023]
Abstract
Drosophila melanogaster (fruit fly) insulin receptor (D-IR) is highly homologous to the human counterpart. Like the human pathway, D-IR responds to numerous insulin-like peptides to activate cellular signals that regulate growth, development, and lipid metabolism in fruit flies. Allelic mutations in the D-IR kinase domain elevate life expectancy in fruit flies. We developed a robust heterologous expression system to express and purify wild-type and longevity-associated mutant D-IR kinase domains to investigate enzyme kinetics and substrate specificities. D-IR exhibits remarkable similarities to the human insulin receptor kinase domain but diverges in substrate preferences. We show that longevity-associated mutations reduce D-IR catalytic activity. Deletion of the unique kinase insert domain portion or mutations proximal to activating tyrosines do not influence kinase activity, suggesting their potential role in substrate recruitment and downstream signaling. Through biochemical investigations, this study enhances our comprehension of D-IR's role in Drosophila physiology, complementing genetic studies and expanding our knowledge on the catalytic functions of this conserved signaling pathway.
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Affiliation(s)
- Harini Krishnan
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Sultan Ahmed
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, USA
| | - Stevan R Hubbard
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York, USA
- Department of Veterans Affairs Medical Center, Northport, New York, USA
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2
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Arwood ML, Liu Y, Harkins SK, Weinstock DM, Yang L, Stevenson KE, Plana OD, Dong J, Cirka H, Jones KL, Virtanen AT, Gupta DG, Ceas A, Lawney B, Yoda A, Leahy C, Hao M, He Z, Choi HG, Wang Y, Silvennoinen O, Hubbard SR, Zhang T, Gray NS, Li LS. New scaffolds for type II JAK2 inhibitors overcome the acquired G993A resistance mutation. Cell Chem Biol 2023; 30:618-631.e12. [PMID: 37290440 PMCID: PMC10495080 DOI: 10.1016/j.chembiol.2023.05.007] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 02/07/2023] [Accepted: 05/18/2023] [Indexed: 06/10/2023]
Abstract
Recurrent JAK2 alterations are observed in myeloproliferative neoplasms, B-cell acute lymphoblastic leukemia, and other hematologic malignancies. Currently available type I JAK2 inhibitors have limited activity in these diseases. Preclinical data support the improved efficacy of type II JAK2 inhibitors, which lock the kinase in the inactive conformation. By screening small molecule libraries, we identified a lead compound with JAK2 selectivity. We highlight analogs with on-target biochemical and cellular activity and demonstrate in vivo activity using a mouse model of polycythemia vera. We present a co-crystal structure that confirms the type II binding mode of our compounds with the "DFG-out" conformation of the JAK2 activation loop. Finally, we identify a JAK2 G993A mutation that confers resistance to the type II JAK2 inhibitor CHZ868 but not to our analogs. These data provide a template for identifying novel type II kinase inhibitors and inform further development of agents targeting JAK2 that overcome resistance.
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Affiliation(s)
- Matthew L Arwood
- Molecular and Translational Cancer Biology Program, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Yao Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Shannon K Harkins
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - David M Weinstock
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Cancer Biology Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Biological and Biomedical Sciences Program, Harvard Medical School, Boston, MA 02115, USA
| | - Lei Yang
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kristen E Stevenson
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Olivia D Plana
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jingyun Dong
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Skirball Institute of Biomolecular Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Haley Cirka
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kristen L Jones
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Anniina T Virtanen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Dikshat G Gupta
- Molecular and Translational Cancer Biology Program, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Amanda Ceas
- Molecular and Translational Cancer Biology Program, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Brian Lawney
- Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Akinori Yoda
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Catharine Leahy
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Mingfeng Hao
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Zhixiang He
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hwan Geun Choi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yaning Wang
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Olli Silvennoinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Institute of Biotechnology, HiLIFE Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Stevan R Hubbard
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Skirball Institute of Biomolecular Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Tinghu Zhang
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - Loretta S Li
- Molecular and Translational Cancer Biology Program, Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA; Department of Pediatrics, Division of Hematology, Oncology, and Stem Cell Transplantation, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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3
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Caveney NA, Saxton RA, Waghray D, Glassman CR, Tsutsumi N, Hubbard SR, Garcia KC. Structural basis of Janus kinase trans-activation. Cell Rep 2023; 42:112201. [PMID: 36867534 PMCID: PMC10180219 DOI: 10.1016/j.celrep.2023.112201] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [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: 11/04/2022] [Revised: 01/09/2023] [Accepted: 02/16/2023] [Indexed: 03/04/2023] Open
Abstract
Janus kinases (JAKs) mediate signal transduction downstream of cytokine receptors. Cytokine-dependent dimerization is conveyed across the cell membrane to drive JAK dimerization, trans-phosphorylation, and activation. Activated JAKs in turn phosphorylate receptor intracellular domains (ICDs), resulting in the recruitment, phosphorylation, and activation of signal transducer and activator of transcription (STAT)-family transcription factors. The structural arrangement of a JAK1 dimer complex with IFNλR1 ICD was recently elucidated while bound by stabilizing nanobodies. While this revealed insights into the dimerization-dependent activation of JAKs and the role of oncogenic mutations in this process, the tyrosine kinase (TK) domains were separated by a distance not compatible with the trans-phosphorylation events between the TK domains. Here, we report the cryoelectron microscopy structure of a mouse JAK1 complex in a putative trans-activation state and expand these insights to other physiologically relevant JAK complexes, providing mechanistic insight into the crucial trans-activation step of JAK signaling and allosteric mechanisms of JAK inhibition.
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Affiliation(s)
- Nathanael A Caveney
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert A Saxton
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Deepa Waghray
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Caleb R Glassman
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Naotaka Tsutsumi
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Stevan R Hubbard
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - K Christopher Garcia
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
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4
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Levine RL, Hubbard SR. Unlocking the secrets to Janus kinase activation. Science 2022; 376:139-140. [PMID: 35389811 DOI: 10.1126/science.abo7788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The full-length structure of a Janus kinase provides insights for drug development.
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Affiliation(s)
- Ross L Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Stevan R Hubbard
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY, USA
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5
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Tada T, Zhou H, Dcosta BM, Samanovic MI, Chivukula V, Herati RS, Hubbard SR, Mulligan MJ, Landau NR. Increased resistance of SARS-CoV-2 Omicron variant to neutralization by vaccine-elicited and therapeutic antibodies. EBioMedicine 2022; 78:103944. [PMID: 35465948 PMCID: PMC9021600 DOI: 10.1016/j.ebiom.2022.103944] [Citation(s) in RCA: 78] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/22/2022] [Accepted: 03/03/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND SARS-CoV-2 vaccines currently authorized for emergency use have been highly successful in preventing infection and lessening disease severity. The vaccines maintain effectiveness against earlier SARS-CoV-2 Variants of Concern but the heavily mutated, highly transmissible Omicron variant presents an obstacle both to vaccine protection and monoclonal antibody therapies. METHODS Pseudotyped lentiviruses were incubated with serum from vaccinated and boosted donors or therapeutic monoclonal antibody and then applied to target cells. After 2 days, luciferase activity was measured in a microplate luminometer. Resistance mutations of the Omicron spike were identified using point-mutated spike protein pseudotypes and mapped onto the three-dimensional spike protein structure. FINDINGS Virus with the Omicron spike protein was 26-fold resistant to neutralization by recovered donor sera and 26-34-fold resistance to Pfizer BNT162b2 and Moderna vaccine-elicited antibodies following two immunizations. A booster immunization increased neutralizing titres against Omicron. Neutralizing titres against Omicron were increased in the sera with a history of prior SARS-CoV-2 infection. Analysis of the therapeutic monoclonal antibodies showed that the Regeneron and Eli Lilly monoclonal antibodies were ineffective against the Omicron pseudotype while Sotrovimab and Evusheld were partially effective. INTERPRETATION The results highlight the benefit of a booster immunization to protect against the Omicron variant and demonstrate the challenge to monoclonal antibody therapy. The decrease in neutralizing titres against Omicron suggest that much of the vaccine efficacy may rely on T cells. FUNDING The work was funded by grants from the NIH to N.R.L. (DA046100, AI122390 and AI120898) and 55 to M.J.M. (UM1AI148574).
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Affiliation(s)
- Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA
| | - Hao Zhou
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA
| | - Belinda M Dcosta
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA
| | - Marie I Samanovic
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Vidya Chivukula
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA
| | - Ramin S Herati
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Stevan R Hubbard
- Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY, USA
| | - Mark J Mulligan
- NYU Langone Vaccine Center and Department of Medicine, NYU Grossman School of Medicine, New York, NY, USA
| | - Nathaniel R Landau
- Department of Microbiology, NYU Grossman School of Medicine, 430 East 29th Street, Alexandria West Building, Rm 509, New York, NY 10016, USA.
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Wilmes S, Hafer M, Vuorio J, Tucker JA, Winkelmann H, Löchte S, Stanly TA, Pulgar Prieto KD, Poojari C, Sharma V, Richter CP, Kurre R, Hubbard SR, Garcia KC, Moraga I, Vattulainen I, Hitchcock IS, Piehler J. Mechanism of homodimeric cytokine receptor activation and dysregulation by oncogenic mutations. Science 2020; 367:643-652. [PMID: 32029621 PMCID: PMC8117407 DOI: 10.1126/science.aaw3242] [Citation(s) in RCA: 87] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 10/08/2019] [Accepted: 12/20/2019] [Indexed: 12/11/2022]
Abstract
Homodimeric class I cytokine receptors are assumed to exist as preformed dimers that are activated by ligand-induced conformational changes. We quantified the dimerization of three prototypic class I cytokine receptors in the plasma membrane of living cells by single-molecule fluorescence microscopy. Spatial and spatiotemporal correlation of individual receptor subunits showed ligand-induced dimerization and revealed that the associated Janus kinase 2 (JAK2) dimerizes through its pseudokinase domain. Oncogenic receptor and hyperactive JAK2 mutants promoted ligand-independent dimerization, highlighting the formation of receptor dimers as the switch responsible for signal activation. Atomistic modeling and molecular dynamics simulations based on a detailed energetic analysis of the interactions involved in dimerization yielded a mechanistic blueprint for homodimeric class I cytokine receptor activation and its dysregulation by individual mutations.
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Affiliation(s)
- Stephan Wilmes
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Maximillian Hafer
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Joni Vuorio
- Department of Physics, University of Helsinki, Helsinki, Finland
- Computational Physics Laboratory, Tampere University, Tampere, Finland
| | - Julie A Tucker
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Hauke Winkelmann
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Sara Löchte
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Tess A Stanly
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Katiuska D Pulgar Prieto
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Chetan Poojari
- Department of Physics, University of Helsinki, Helsinki, Finland
| | - Vivek Sharma
- Department of Physics, University of Helsinki, Helsinki, Finland
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Christian P Richter
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Rainer Kurre
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany
| | - Stevan R Hubbard
- Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - K Christopher Garcia
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
- Department of Molecular and Cellular Physiology and Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ignacio Moraga
- Division of Cell Signalling and Immunology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ilpo Vattulainen
- Department of Physics, University of Helsinki, Helsinki, Finland.
- Computational Physics Laboratory, Tampere University, Tampere, Finland
| | - Ian S Hitchcock
- York Biomedical Research Institute and Department of Biology, University of York, Heslington, York YO10 5DD, UK.
| | - Jacob Piehler
- Department of Biology and Center of Cellular Nanoanalytics, University of Osnabrück, 49076 Osnabrück, Germany.
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Ji T, Corbalán-García S, Hubbard SR. Correction: Crystal structure of the C-terminal four-helix bundle of the potassium channel KCa3.1. PLoS One 2018; 13:e0205540. [PMID: 30286164 PMCID: PMC6171962 DOI: 10.1371/journal.pone.0205540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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8
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Hammarén HM, Virtanen AT, Abraham BG, Peussa H, Hubbard SR, Silvennoinen O. Janus kinase 2 activation mechanisms revealed by analysis of suppressing mutations. J Allergy Clin Immunol 2018; 143:1549-1559.e6. [PMID: 30092288 DOI: 10.1016/j.jaci.2018.07.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 09/01/2017] [Revised: 06/30/2018] [Accepted: 07/24/2018] [Indexed: 12/18/2022]
Abstract
BACKGROUND Janus kinases (JAKs; JAK1 to JAK3 and tyrosine kinase 2) mediate cytokine signals in the regulation of hematopoiesis and immunity. JAK2 clinical mutations cause myeloproliferative neoplasms and leukemia, and the mutations strongly concentrate in the regulatory pseudokinase domain Janus kinase homology (JH) 2. Current clinical JAK inhibitors target the tyrosine kinase domain and lack mutation and pathway selectivity. OBJECTIVE We sought to characterize mechanisms and differences for pathogenic and cytokine-induced JAK2 activation to enable design of novel selective JAK inhibitors. METHODS We performed a systematic analysis of JAK2 activation requirements using structure-guided mutagenesis, cell-signaling assays, microscopy, and biochemical analysis. RESULTS Distinct structural requirements were identified for activation of different pathogenic mutations. Specifically, the predominant JAK2 mutation, V617F, is the most sensitive to structural perturbations in multiple JH2 elements (C helix [αC], Src homology 2-JH2 linker, and ATP binding site). In contrast, activation of K539L is resistant to most perturbations. Normal cytokine signaling shows distinct differences in activation requirements: JH2 ATP binding site mutations have only a minor effect on signaling, whereas JH2 αC mutations reduce homomeric (JAK2-JAK2) erythropoietin signaling and almost completely abrogate heteromeric (JAK2-JAK1) IFN-γ signaling, potentially by disrupting a dimerization interface on JH2. CONCLUSIONS These results suggest that therapeutic approaches targeting the JH2 ATP binding site and αC could be effective in inhibiting most pathogenic mutations. JH2 ATP site targeting has the potential for reduced side effects by retaining erythropoietin and IFN-γ functions. Simultaneously, however, we identified the JH2 αC interface as a potential target for pathway-selective JAK inhibitors in patients with diseases with unmutated JAK2, thus providing new insights into the development of novel pharmacologic interventions.
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Affiliation(s)
- Henrik M Hammarén
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Anniina T Virtanen
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | | | - Heidi Peussa
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Stevan R Hubbard
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York, NY; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY
| | - Olli Silvennoinen
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland; Fimlab Laboratories, Tampere, Finland; Institute of Biotechnology, University of Helsinki, Helsinki, Finland.
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Ji T, Corbalán-García S, Hubbard SR. Crystal structure of the C-terminal four-helix bundle of the potassium channel KCa3.1. PLoS One 2018; 13:e0199942. [PMID: 29953543 PMCID: PMC6023178 DOI: 10.1371/journal.pone.0199942] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [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: 04/18/2018] [Accepted: 06/15/2018] [Indexed: 11/18/2022] Open
Abstract
KCa3.1 (also known as SK4 or IK1) is a mammalian intermediate-conductance potassium channel that plays a critical role in the activation of T cells, B cells, and mast cells, effluxing potassium ions to maintain a negative membrane potential for influxing calcium ions. KCa3.1 shares primary sequence similarity with three other (low-conductance) potassium channels: KCa2.1, KCa2.2, and KCa2.3 (also known as SK1–3). These four homotetrameric channels bind calmodulin (CaM) in the cytoplasmic region, and calcium binding to CaM triggers channel activation. Unique to KCa3.1, activation also requires phosphorylation of a single histidine residue, His358, in the cytoplasmic region, which relieves copper-mediated inhibition of the channel. Near the cytoplasmic C-terminus of KCa3.1 (and KCa2.1–2.3), secondary-structure analysis predicts the presence of a coiled-coil/heptad repeat. Here, we report the crystal structure of the C-terminal coiled-coil region of KCa3.1, which forms a parallel four-helix bundle, consistent with the tetrameric nature of the channel. Interestingly, the four copies of a histidine residue, His389, in an ‘a’ position within the heptad repeat, are observed to bind a copper ion along the four-fold axis of the bundle. These results suggest that His358, the inhibitory histidine in KCa3.1, might coordinate a copper ion through a similar binding mode.
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Affiliation(s)
- Tianyang Ji
- Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States of America
| | - Senena Corbalán-García
- Department of Biochemistry and Molecular Biology-A, School of Veterinary, Regional Campus of International Excellence "Campus Mare Nostrum", Biomedical Research Institute of Murcia (IMIB-Arrixaca), University of Murcia, Murcia, Spain
| | - Stevan R. Hubbard
- Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, United States of America
- * E-mail:
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Abstract
JAK2 is a member of the Janus kinase (JAKs) family of non-receptor protein tyrosine kinases, which includes JAK1-3 and TYK2. JAKs serve as the cytoplasmic signaling components of cytokine receptors and are activated through cytokine-mediated trans-phosphorylation, which leads to receptor phosphorylation and recruitment and phosphorylation of signal transducer and activator of transcription (STAT) proteins. JAKs are unique among tyrosine kinases in that they possess a pseudokinase domain, which is just upstream of the C-terminal tyrosine kinase domain. A wealth of biochemical and clinical data have established that the pseudokinase domain of JAKs is crucial for maintaining a low basal (absence of cytokine) level of tyrosine kinase activity. In particular, gain-of-function mutations in the JAK genes, most frequently, V617F in the pseudokinase domain of JAK2, have been mapped in patients with blood disorders, including myeloproliferative neoplasms and leukemias. Recent structural and biochemical studies have begun to decipher the molecular mechanisms that maintain the basal, low-activity state of JAKs and that, via mutation, lead to constitutive activity and disease. This review will examine these mechanisms and describe how this knowledge could potentially inform drug development efforts aimed at obtaining a mutant (V617F)-selective inhibitor of JAK2.
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Affiliation(s)
- Stevan R. Hubbard
- Department of Biochemistry and Molecular Pharmacology, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, United States
- *Correspondence: Stevan R. Hubbard,
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Petersen MC, Madiraju AK, Gassaway BM, Marcel M, Nasiri AR, Butrico G, Marcucci MJ, Zhang D, Abulizi A, Zhang XM, Philbrick W, Hubbard SR, Jurczak MJ, Samuel VT, Rinehart J, Shulman GI. Insulin receptor Thr1160 phosphorylation mediates lipid-induced hepatic insulin resistance. J Clin Invest 2016; 126:4361-4371. [PMID: 27760050 DOI: 10.1172/jci86013] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Accepted: 09/08/2016] [Indexed: 02/06/2023] Open
Abstract
Nonalcoholic fatty liver disease (NAFLD) is a risk factor for type 2 diabetes (T2D), but whether NAFLD plays a causal role in the pathogenesis of T2D is uncertain. One proposed mechanism linking NAFLD to hepatic insulin resistance involves diacylglycerol-mediated (DAG-mediated) activation of protein kinase C-ε (PKCε) and the consequent inhibition of insulin receptor (INSR) kinase activity. However, the molecular mechanism underlying PKCε inhibition of INSR kinase activity is unknown. Here, we used mass spectrometry to identify the phosphorylation site Thr1160 as a PKCε substrate in the functionally critical INSR kinase activation loop. We hypothesized that Thr1160 phosphorylation impairs INSR kinase activity by destabilizing the active configuration of the INSR kinase, and our results confirmed this prediction by demonstrating severely impaired INSR kinase activity in phosphomimetic T1160E mutants. Conversely, the INSR T1160A mutant was not inhibited by PKCε in vitro. Furthermore, mice with a threonine-to-alanine mutation at the homologous residue Thr1150 (InsrT1150A mice) were protected from high fat diet-induced hepatic insulin resistance. InsrT1150A mice also displayed increased insulin signaling, suppression of hepatic glucose production, and increased hepatic glycogen synthesis compared with WT controls during hyperinsulinemic clamp studies. These data reveal a critical pathophysiological role for INSR Thr1160 phosphorylation and provide further mechanistic links between PKCε and INSR in mediating NAFLD-induced hepatic insulin resistance.
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12
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Srivastava S, Panda S, Li Z, Fuhs SR, Hunter T, Thiele DJ, Hubbard SR, Skolnik EY. Histidine phosphorylation relieves copper inhibition in the mammalian potassium channel KCa3.1. eLife 2016; 5. [PMID: 27542194 PMCID: PMC5005030 DOI: 10.7554/elife.16093] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 08/14/2016] [Indexed: 12/02/2022] Open
Abstract
KCa2.1, KCa2.2, KCa2.3 and KCa3.1 constitute a family of mammalian small- to intermediate-conductance potassium channels that are activated by calcium-calmodulin. KCa3.1 is unique among these four channels in that activation requires, in addition to calcium, phosphorylation of a single histidine residue (His358) in the cytoplasmic region, by nucleoside diphosphate kinase-B (NDPK-B). The mechanism by which KCa3.1 is activated by histidine phosphorylation is unknown. Histidine phosphorylation is well characterized in prokaryotes but poorly understood in eukaryotes. Here, we demonstrate that phosphorylation of His358 activates KCa3.1 by antagonizing copper-mediated inhibition of the channel. Furthermore, we show that activated CD4+ T cells deficient in intracellular copper exhibit increased KCa3.1 histidine phosphorylation and channel activity, leading to increased calcium flux and cytokine production. These findings reveal a novel regulatory mechanism for a mammalian potassium channel and for T-cell activation, and highlight a unique feature of histidine versus serine/threonine and tyrosine as a regulatory phosphorylation site. DOI:http://dx.doi.org/10.7554/eLife.16093.001
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Affiliation(s)
- Shekhar Srivastava
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States.,Division of Nephrology, New York University School of Medicine, New York, United States.,Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University, New York, United States
| | - Saswati Panda
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States.,Division of Nephrology, New York University School of Medicine, New York, United States.,Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University, New York, United States
| | - Zhai Li
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States.,Division of Nephrology, New York University School of Medicine, New York, United States.,Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University, New York, United States
| | - Stephen R Fuhs
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, United States
| | - Dennis J Thiele
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, United States.,Department of Biochemistry, Duke University School of Medicine, Durham, United States
| | - Stevan R Hubbard
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States.,Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University, New York, United States
| | - Edward Y Skolnik
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States.,Division of Nephrology, New York University School of Medicine, New York, United States.,Kimmel Center for Biology and Medicine, Skirball Institute of Biomolecular Medicine, New York University, New York, United States
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13
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Abstract
Activating JAK2 mutants cause hematological malignancies. Current clinical type I JAK2 inhibitors effectively relieve symptoms but fail to resolve the disease. In this issue of Cancer Cell, two articles by Wu and colleagues and Meyer and colleagues characterize a type II JAK2 inhibitor that is effective in preclinical models of JAK2-dependent myeloproliferative neoplasms and B cell acute lymphoblastic leukemia.
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Affiliation(s)
- Olli Silvennoinen
- School of Medicine, University of Tampere, Biokatu 8, 33014 Tampere, Finland; Clinical Hematology, Department of Internal Medicine, Tampere University Hospital, Medisiinarinkatu 3, 33520 Tampere, Finland.
| | - Stevan R Hubbard
- Kimmel Center for Biology and Medicine at the Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
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14
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Cabail MZ, Li S, Lemmon E, Bowen ME, Hubbard SR, Miller WT. The insulin and IGF1 receptor kinase domains are functional dimers in the activated state. Nat Commun 2015; 6:6406. [PMID: 25758790 DOI: 10.1038/ncomms7406] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 01/26/2015] [Indexed: 12/31/2022] Open
Abstract
The insulin receptor (IR) and insulin-like growth factor-1 receptor (IGF1R) are highly related receptor tyrosine kinases with a disulfide-linked homodimeric architecture. Ligand binding to the receptor ectodomain triggers tyrosine autophosphorylation of the cytoplasmic domains, which stimulates catalytic activity and creates recruitment sites for downstream signalling proteins. Whether the two phosphorylated tyrosine kinase domains within the receptor dimer function independently or cooperatively to phosphorylate protein substrates is not known. Here we provide crystallographic, biophysical and biochemical evidence demonstrating that the phosphorylated kinase domains of IR and IGF1R form a specific dimeric arrangement involving an exchange of the juxtamembrane region proximal to the kinase domain. In this dimer, the active position of α-helix C in the kinase N lobe is stabilized, which promotes downstream substrate phosphorylation. These studies afford a novel strategy for the design of small-molecule IR agonists as potential therapeutic agents for type 2 diabetes.
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Affiliation(s)
- M Zulema Cabail
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Shiqing Li
- Department of Biochemistry and Molecular Pharmacology, Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - Eric Lemmon
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Mark E Bowen
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, USA
| | - Stevan R Hubbard
- Department of Biochemistry and Molecular Pharmacology, Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, New York 10016, USA
| | - W Todd Miller
- Department of Physiology and Biophysics, Stony Brook University, Stony Brook, New York 11794, USA
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15
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Samanovic MI, Tu S, Novák O, Iyer LM, McAllister FE, Aravind L, Gygi SP, Hubbard SR, Strnad M, Darwin KH. Proteasomal control of cytokinin synthesis protects Mycobacterium tuberculosis against nitric oxide. Mol Cell 2015; 57:984-994. [PMID: 25728768 DOI: 10.1016/j.molcel.2015.01.024] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Revised: 12/17/2014] [Accepted: 01/16/2015] [Indexed: 12/19/2022]
Abstract
One of several roles of the Mycobacterium tuberculosis proteasome is to defend against host-produced nitric oxide (NO), a free radical that can damage numerous biological macromolecules. Mutations that inactivate proteasomal degradation in Mycobacterium tuberculosis result in bacteria that are hypersensitive to NO and attenuated for growth in vivo, but it was not known why. To elucidate the link between proteasome function, NO resistance, and pathogenesis, we screened for suppressors of NO hypersensitivity in a mycobacterial proteasome ATPase mutant and identified mutations in Rv1205. We determined that Rv1205 encodes a pupylated proteasome substrate. Rv1205 is a homolog of the plant enzyme LONELY GUY, which catalyzes the production of hormones called cytokinins. Remarkably, we report that an obligate human pathogen secretes several cytokinins. Finally, we determined that the Rv1205-dependent accumulation of cytokinin breakdown products is likely responsible for the sensitization of Mycobacterium tuberculosis proteasome-associated mutants to NO.
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Affiliation(s)
- Marie I Samanovic
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Shengjiang Tu
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - Ondřej Novák
- Department of Metabolomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, 78371 Olomouc, Czech Republic; Laboratory of Growth Regulators, Institute of Experimental Botany AS CR, 78371 Olomouc, Czech Republic
| | - Lakshminarayan M Iyer
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
| | - Fiona E McAllister
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - L Aravind
- National Center for Biotechnology Information, National Library of Medicine, NIH, Bethesda, MD 20894, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Stevan R Hubbard
- Department of Biochemistry and Molecular Pharmacology, The Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Miroslav Strnad
- Department of Metabolomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, 78371 Olomouc, Czech Republic; Laboratory of Growth Regulators, Institute of Experimental Botany AS CR, 78371 Olomouc, Czech Republic
| | - K Heran Darwin
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA.
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16
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Abstract
Structural and biochemical studies by Ferrao et al. (2014) in this issue demonstrate that dimerization of the kinase domain of IRAK4 is crucial for its activation, but with conditions: after-not before-receptor recruitment and before-not after-autophosphorylation.
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Affiliation(s)
- Stevan R Hubbard
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
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17
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Abstract
When insulin-like growth factor-1 (IGF1) binds to its receptor, a physical constraint is released that allows the two transmembrane helices to come together to facilitate activation of the receptor.
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Affiliation(s)
- Stevan R Hubbard
- Stevan R Hubbard is in the Kimmel Center for Biology and Medicine at the Skirball Institute and the Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, United States
| | - W Todd Miller
- W Todd Miller is in the Department of Physiology and Biophysics, Stony Brook University, Stony Brook, United States
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18
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Shan Y, Gnanasambandan K, Ungureanu D, Kim ET, Hammarén H, Yamashita K, Silvennoinen O, Shaw DE, Hubbard SR. Molecular basis for pseudokinase-dependent autoinhibition of JAK2 tyrosine kinase. Nat Struct Mol Biol 2014; 21:579-84. [PMID: 24918548 DOI: 10.1038/nsmb.2849] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 06/04/2014] [Indexed: 12/31/2022]
Abstract
Janus kinase-2 (JAK2) mediates signaling by various cytokines, including erythropoietin and growth hormone. JAK2 possesses tandem pseudokinase and tyrosine-kinase domains. Mutations in the pseudokinase domain are causally linked to myeloproliferative neoplasms (MPNs) in humans. The structure of the JAK2 tandem kinase domains is unknown, and therefore the molecular bases for pseudokinase-mediated autoinhibition and pathogenic activation remain obscure. Using molecular dynamics simulations of protein-protein docking, we produced a structural model for the autoinhibitory interaction between the JAK2 pseudokinase and kinase domains. A striking feature of our model, which is supported by mutagenesis experiments, is that nearly all of the disease mutations map to the domain interface. The simulations indicate that the kinase domain is stabilized in an inactive state by the pseudokinase domain, and they offer a molecular rationale for the hyperactivity of V617F, the predominant JAK2 MPN mutation.
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Affiliation(s)
- Yibing Shan
- 1] D. E. Shaw Research, New York, New York, USA. [2]
| | - Kavitha Gnanasambandan
- 1] Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA. [2]
| | - Daniela Ungureanu
- School of Medicine, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Eric T Kim
- D. E. Shaw Research, New York, New York, USA
| | - Henrik Hammarén
- School of Medicine, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Kazuo Yamashita
- Systems Immunology Laboratory, Immunology Frontier Research Center, Osaka University, Suita, Japan
| | - Olli Silvennoinen
- School of Medicine, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - David E Shaw
- 1] D. E. Shaw Research, New York, New York, USA. [2] Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, USA
| | - Stevan R Hubbard
- Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
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19
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Abstract
Grb14, a member of the Grb7-10-14 family of cytoplasmic adaptor proteins, is a tissue-specific negative regulator of insulin signaling. Grb7-10-14 contain several signaling modules, including a Ras-associating (RA) domain, a pleckstrin-homology (PH) domain, a family-specific BPS (between PH and SH2) region, and a C-terminal Src-homology-2 (SH2) domain. We showed previously that the RA and PH domains, along with the BPS region and SH2 domain, are necessary for downregulation of insulin signaling. Here, we report the crystal structure at 2.4-Å resolution of the Grb14 RA and PH domains in complex with GTP-loaded H-Ras (G12V). The structure reveals that the Grb14 RA and PH domains form an integrated structural unit capable of binding simultaneously to small GTPases and phosphoinositide lipids. The overall mode of binding of the Grb14 RA domain to activated H-Ras is similar to that of the RA domains of RalGDS and Raf1 but with important distinctions. The integrated RA-PH structural unit in Grb7-10-14 is also found in a second adaptor family that includes Rap1-interacting adaptor molecule (RIAM) and lamellipodin, proteins involved in actin-cytoskeleton rearrangement. The structure of Grb14 RA-PH in complex with H-Ras represents the first detailed molecular characterization of tandem RA-PH domains bound to a small GTPase and provides insights into the molecular basis for specificity.
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Affiliation(s)
- Rohini Qamra
- Kimmel Center for Biology and Medicine of the Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
| | - Stevan R. Hubbard
- Kimmel Center for Biology and Medicine of the Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, United States of America
- * E-mail:
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20
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Abstract
Unlike prototypical receptor tyrosine kinases (RTKs), which are single-chain polypeptides, the insulin receptor (InsR) is a preformed, covalently linked tetramer with two extracellular α subunits and two membrane-spanning, tyrosine kinase-containing β subunits. A single molecule of insulin binds asymmetrically to the ectodomain, triggering a conformational change that is transmitted to the cytoplasmic kinase domains, which facilitates their trans-phosphorylation. As in prototypical RTKs, tyrosine phosphorylation in the juxtamembrane region of InsR creates recruitment sites for downstream signaling proteins (IRS [InsR substrate] proteins, Shc) containing a phosphotyrosine-binding (PTB) domain, and tyrosine phosphorylation in the kinase activation loop stimulates InsR's catalytic activity. For InsR, phosphorylation of the activation loop, which contains three tyrosine residues, also creates docking sites for adaptor proteins (Grb10/14, SH2B2) that possess specialized Src homology-2 (SH2) domains, which are dimeric and engage two phosphotyrosines in the activation loop.
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Affiliation(s)
- Stevan R Hubbard
- Kimmel Center for Biology and Medicine of the Skirball Institute and Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York 10016, USA.
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21
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Wynne JP, Wu J, Su W, Mor A, Patsoukis N, Boussiotis VA, Hubbard SR, Philips MR. Rap1-interacting adapter molecule (RIAM) associates with the plasma membrane via a proximity detector. ACTA ACUST UNITED AC 2012; 199:317-30. [PMID: 23045549 PMCID: PMC3471229 DOI: 10.1083/jcb.201201157] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Ras association and PH domains of RIAM function as a proximity detector for activated Rap1 and PI(4,5)P2. Adaptive immunity depends on lymphocyte adhesion that is mediated by the integrin lymphocyte functional antigen 1 (LFA-1). The small guanosine triphosphatase Rap1 regulates LFA-1 adhesiveness through one of its effectors, Rap1-interacting adapter molecule (RIAM). We show that RIAM was recruited to the lymphocyte plasma membrane (PM) through its Ras association (RA) and pleckstrin homology (PH) domains, both of which were required for lymphocyte adhesion. The N terminus of RIAM inhibited membrane translocation. In vitro, the RA domain bound both Rap1 and H-Ras with equal but relatively low affinity, whereas in vivo only Rap1 was required for PM association. The PH domain bound phosphoinositol 4,5-bisphosphate (PI(4,5)P2) and was responsible for the spatial distribution of RIAM only at the PM of activated T cells. We determined the crystal structure of the RA and PH domains and found that, despite an intervening linker of 50 aa, the two domains were integrated into a single structural unit, which was critical for proper localization to the PM. Thus, the RA-PH domains of RIAM function as a proximity detector for activated Rap1 and PI(4,5)P2.
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Affiliation(s)
- Joseph P Wynne
- Cancer Institute, NYU School of Medicine, New York, NY 10016, USA
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22
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Burns KE, McAllister FE, Schwerdtfeger C, Mintseris J, Cerda-Maira F, Noens EE, Wilmanns M, Hubbard SR, Melandri F, Ovaa H, Gygi SP, Darwin KH. Mycobacterium tuberculosis prokaryotic ubiquitin-like protein-deconjugating enzyme is an unusual aspartate amidase. J Biol Chem 2012; 287:37522-9. [PMID: 22942282 DOI: 10.1074/jbc.m112.384784] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Deamidase of Pup (Dop), the prokaryotic ubiquitin-like protein (Pup)-deconjugating enzyme, is critical for the full virulence of Mycobacterium tuberculosis and is unique to bacteria, providing an ideal target for the development of selective chemotherapies. We used a combination of genetics and chemical biology to characterize the mechanism of depupylation. We identified an aspartate as a potential nucleophile in the active site of Dop, suggesting a novel protease activity to target for inhibitor development.
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Affiliation(s)
- Kristin E Burns
- Department of Microbiology, New York University, New York, New York 10016, USA
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23
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Bandaranayake RM, Ungureanu D, Shan Y, Shaw DE, Silvennoinen O, Hubbard SR. Crystal structures of the JAK2 pseudokinase domain and the pathogenic mutant V617F. Nat Struct Mol Biol 2012; 19:754-9. [PMID: 22820988 PMCID: PMC3414675 DOI: 10.1038/nsmb.2348] [Citation(s) in RCA: 172] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 06/26/2012] [Indexed: 11/09/2022]
Abstract
The protein tyrosine kinase JAK2 mediates signaling through numerous cytokine receptors. JAK2 possesses a pseudokinase domain (JH2) and a tyrosine kinase domain (JH1). Through unknown mechanisms, JH2 regulates the catalytic activity of JH1, and hyperactivating mutations in the JH2 region of human JAK2 cause myeloproliferative neoplasms (MPNs). We showed previously that JAK2 JH2 is, in fact, catalytically active. Here we present crystal structures of human JAK2 JH2, including both wild type and the most prevalent MPN mutant, V617F. The structures reveal that JH2 adopts the fold of a prototypical protein kinase but binds Mg-ATP noncanonically. The structural and biochemical data indicate that the V617F mutation rigidifies α-helix C in the N lobe of JH2, facilitating trans-phosphorylation of JH1. The crystal structures of JH2 afford new opportunities for the design of novel JAK2 therapeutics targeting MPNs.
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Affiliation(s)
- Rajintha M Bandaranayake
- Structural Biology Program, Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York, USA
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24
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Zhang W, Coldefy AS, Hubbard SR, Burden SJ. Agrin binds to the N-terminal region of Lrp4 protein and stimulates association between Lrp4 and the first immunoglobulin-like domain in muscle-specific kinase (MuSK). J Biol Chem 2011; 286:40624-30. [PMID: 21969364 DOI: 10.1074/jbc.m111.279307] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Neuromuscular synapse formation depends upon coordinated interactions between motor neurons and muscle fibers, leading to the formation of a highly specialized postsynaptic membrane and a highly differentiated nerve terminal. Synapse formation begins as motor axons approach muscles that are prepatterned in the prospective synaptic region in a manner that depends upon Lrp4, a member of the LDL receptor family, and muscle-specific kinase (MuSK), a receptor tyrosine kinase. Motor axons supply Agrin, which binds Lrp4 and stimulates further MuSK phosphorylation, stabilizing nascent synapses. How Agrin binds Lrp4 and stimulates MuSK kinase activity is poorly understood. Here, we demonstrate that Agrin binds to the N-terminal region of Lrp4, including a subset of the LDLa repeats and the first of four β-propeller domains, which promotes association between Lrp4 and MuSK and stimulates MuSK kinase activity. In addition, we show that Agrin stimulates the formation of a functional complex between Lrp4 and MuSK on the surface of myotubes in the absence of the transmembrane and intracellular domains of Lrp4. Further, we demonstrate that the first Ig-like domain in MuSK, which shares homology with the NGF-binding region in Tropomyosin Receptor Kinase (TrKA), is required for MuSK to bind Lrp4. These findings suggest that Lrp4 is a cis-acting ligand for MuSK, whereas Agrin functions as an allosteric and paracrine regulator to promote association between Lrp4 and MuSK.
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Affiliation(s)
- Wei Zhang
- Molecular Neurobiology Program, Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University Medical School, New York, New York 10016, USA
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25
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Abstract
In this issue, Lupardus et al. (2011) provide images, obtained by electron microscopy, of a complete cytokine signaling complex, offering clues into the mechanism by which binding of cytokines to their cognate receptors triggers trans-phosphorylation and activation of Janus kinases.
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Affiliation(s)
- Stevan R Hubbard
- Structural Biology Program, Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA.
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26
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Cerda-Maira FA, Pearce MJ, Fuortes M, Bishai WR, Hubbard SR, Darwin KH. Molecular analysis of the prokaryotic ubiquitin-like protein (Pup) conjugation pathway in Mycobacterium tuberculosis. Mol Microbiol 2011; 77:1123-35. [PMID: 20636328 DOI: 10.1111/j.1365-2958.2010.07276.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Proteins targeted for degradation by the Mycobacterium proteasome are post-translationally tagged with prokaryotic ubiquitin-like protein (Pup), an intrinsically disordered protein of 64 residues. In a process termed 'pupylation', Pup is synthesized with a terminal glutamine, which is deamidated to glutamate by Dop (deamidase of Pup) prior to attachment to substrate lysines by proteasome accessory factor A (PafA). Importantly, PafA was previously shown to be essential to cause lethal infections by Mycobacterium tuberculosis (Mtb) in mice. In this study we show that Dop, like PafA, is required for the full virulence of Mtb. Additionally, we show that Dop is not only involved in the deamidation of Pup, but also needed to maintain wild-type steady state levels of pupylated proteins in Mtb. Finally, using structural models and site-directed mutagenesis our data suggest that Dop and PafA are members of the glutamine synthetase fold family of proteins.
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Affiliation(s)
- Francisca A Cerda-Maira
- New York University School of Medicine, Department of Microbiology, 550 First Avenue, New York, NY 10016, USA
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27
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Bergamin E, Hallock PT, Burden SJ, Hubbard SR. The cytoplasmic adaptor protein Dok7 activates the receptor tyrosine kinase MuSK via dimerization. Mol Cell 2010; 39:100-9. [PMID: 20603078 DOI: 10.1016/j.molcel.2010.06.007] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Revised: 03/08/2010] [Accepted: 04/16/2010] [Indexed: 12/29/2022]
Abstract
Formation of the vertebrate neuromuscular junction requires, among others proteins, Agrin, a neuronally derived ligand, and the following muscle proteins: LRP4, the receptor for Agrin; MuSK, a receptor tyrosine kinase (RTK); and Dok7 (or Dok-7), a cytoplasmic adaptor protein. Dok7 comprises a pleckstrin-homology (PH) domain, a phosphotyrosine-binding (PTB) domain, and C-terminal sites of tyrosine phosphorylation. Unique among adaptor proteins recruited to RTKs, Dok7 is not only a substrate of MuSK, but also an activator of MuSK's kinase activity. Here, we present the crystal structure of the Dok7 PH-PTB domains in complex with a phosphopeptide representing the Dok7-binding site on MuSK. The structure and biochemical data reveal a dimeric arrangement of Dok7 PH-PTB that facilitates trans-autophosphorylation of the kinase activation loop. The structure provides the molecular basis for MuSK activation by Dok7 and for rationalizing several Dok7 loss-of-function mutations found in patients with congenital myasthenic syndromes.
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Affiliation(s)
- Elisa Bergamin
- Structural Biology Program, Kimmel Center for Biology and Medicine of the Skirball Institute and Department of Pharmacology, New York University School of Medicine, New York, NY 10016, USA
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28
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Depetris RS, Wu J, Hubbard SR. Erratum: Structural and functional studies of the Ras-associating and pleckstrin-homology domains of Grb10 and Grb14. Nat Struct Mol Biol 2009. [DOI: 10.1038/nsmb1209-1331a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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29
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Stiegler AL, Burden SJ, Hubbard SR. Crystal structure of the frizzled-like cysteine-rich domain of the receptor tyrosine kinase MuSK. J Mol Biol 2009; 393:1-9. [PMID: 19664639 DOI: 10.1016/j.jmb.2009.07.091] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2009] [Revised: 07/26/2009] [Accepted: 07/30/2009] [Indexed: 12/18/2022]
Abstract
Muscle-specific kinase (MuSK) is an essential receptor tyrosine kinase for the establishment and maintenance of the neuromuscular junction (NMJ). Activation of MuSK by agrin, a neuronally derived heparan-sulfate proteoglycan, and LRP4 (low-density lipoprotein receptor-related protein-4), the agrin receptor, leads to clustering of acetylcholine receptors on the postsynaptic side of the NMJ. The ectodomain of MuSK comprises three immunoglobulin-like domains and a cysteine-rich domain (Fz-CRD) related to those in Frizzled proteins, the receptors for Wnts. Here, we report the crystal structure of the MuSK Fz-CRD at 2.1 A resolution. The structure reveals a five-disulfide-bridged domain similar to CRDs of Frizzled proteins but with a divergent C-terminal region. An asymmetric dimer present in the crystal structure implicates surface hydrophobic residues that may function in homotypic or heterotypic interactions to mediate co-clustering of MuSK, rapsyn, and acetylcholine receptors at the NMJ.
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Affiliation(s)
- Amy L Stiegler
- Structural Biology Program, Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA
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30
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Abstract
The activation process for the epidermal growth factor receptor (EGFR) involves formation of an asymmetric dimer of the tyrosine kinase domains. Jura et al. (2009) in this issue and Brewer et al. (2009) in Molecular Cell now demonstrate that the juxtamembrane region of EGFR plays a crucial role in stabilizing this dimer.
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Affiliation(s)
- Stevan R Hubbard
- Structural Biology Program, Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA.
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31
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Kim N, Stiegler AL, Cameron TO, Hallock PT, Gomez AM, Huang JH, Hubbard SR, Dustin ML, Burden SJ. Lrp4 is a receptor for Agrin and forms a complex with MuSK. Cell 2008; 135:334-42. [PMID: 18848351 DOI: 10.1016/j.cell.2008.10.002] [Citation(s) in RCA: 492] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 09/12/2008] [Accepted: 10/01/2008] [Indexed: 12/14/2022]
Abstract
Neuromuscular synapse formation requires a complex exchange of signals between motor neurons and skeletal muscle fibers, leading to the accumulation of postsynaptic proteins, including acetylcholine receptors in the muscle membrane and specialized release sites, or active zones in the presynaptic nerve terminal. MuSK, a receptor tyrosine kinase that is expressed in skeletal muscle, and Agrin, a motor neuron-derived ligand that stimulates MuSK phosphorylation, play critical roles in synaptic differentiation, as synapses do not form in their absence, and mutations in MuSK or downstream effectors are a major cause of a group of neuromuscular disorders, termed congenital myasthenic syndromes (CMS). How Agrin activates MuSK and stimulates synaptic differentiation is not known and remains a fundamental gap in our understanding of signaling at neuromuscular synapses. Here, we report that Lrp4, a member of the LDLR family, is a receptor for Agrin, forms a complex with MuSK, and mediates MuSK activation by Agrin.
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Affiliation(s)
- Natalie Kim
- Molecular Neurobiology Program, Skirball Institute of Biomolecular Medicine, Helen and Martin Kimmel Center for Biology and Medicine, NYU Medical School, New York, NY 10016, USA
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32
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Li S, Depetris RS, Barford D, Chernoff J, Hubbard SR. Crystal structure of a complex between protein tyrosine phosphatase 1B and the insulin receptor tyrosine kinase. Structure 2008; 13:1643-51. [PMID: 16271887 DOI: 10.1016/j.str.2005.07.019] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2005] [Revised: 07/28/2005] [Accepted: 07/28/2005] [Indexed: 02/03/2023]
Abstract
Protein tyrosine phosphatase 1B (PTP1B) is a highly specific negative regulator of insulin receptor signaling in vivo. The determinants of PTP1B specificity for the insulin receptor versus other receptor tyrosine kinases are largely unknown. Here, we report a crystal structure at 2.3 A resolution of the catalytic domain of PTP1B (trapping mutant) in complex with the phosphorylated tyrosine kinase domain of the insulin receptor (IRK). The crystallographic asymmetric unit contains two PTP1B-IRK complexes that interact through an IRK dimer interface. Rather than binding to a phosphotyrosine in the IRK activation loop, PTP1B binds instead to the opposite side of the kinase domain, with the phosphorylated activation loops sequestered within the IRK dimer. The crystal structure provides evidence for a noncatalytic mode of interaction between PTP1B and IRK, which could be important for the selective recruitment of PTP1B to the insulin receptor.
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Affiliation(s)
- Shiqing Li
- Structural Biology Program, Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, New York 10016, USA
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33
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Wu J, Li W, Craddock BP, Foreman KW, Mulvihill MJ, Ji QS, Miller WT, Hubbard SR. Small-molecule inhibition and activation-loop trans-phosphorylation of the IGF1 receptor. EMBO J 2008; 27:1985-94. [PMID: 18566589 DOI: 10.1038/emboj.2008.116] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Accepted: 05/20/2008] [Indexed: 11/09/2022] Open
Abstract
The insulin-like growth factor-1 receptor (IGF1R) is a receptor tyrosine kinase (RTK) that has a critical role in mitogenic signalling during embryogenesis and an antiapoptotic role in the survival and progression of many human tumours. Here, we present the crystal structure of the tyrosine kinase domain of IGF1R (IGF1RK), in its unphosphorylated state, in complex with a novel compound, cis-3-[3-(4-methyl-piperazin-l-yl)-cyclobutyl]-1-(2-phenyl-quinolin-7-yl)-imidazo[1,5-a]pyrazin-8-ylamine (PQIP), which we show is a potent inhibitor of both the unphosphorylated (basal) and phosphorylated (activated) states of the kinase. PQIP interacts with residues in the ATP-binding pocket and in the activation loop, which confers specificity for IGF1RK and the highly related insulin receptor (IR) kinase. In this crystal structure, the IGF1RK active site is occupied by Tyr1135 from the activation loop of an symmetry (two-fold)-related molecule. This dimeric arrangement affords, for the first time, a visualization of the initial trans-phosphorylation event in the activation loop of an RTK, and provides a molecular rationale for a naturally occurring mutation in the activation loop of the IR that causes type II diabetes mellitus.
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Affiliation(s)
- Jinhua Wu
- Structural Biology Program, Kimmel Center for Biology and Medicine of the Skirball Institute of Biomolecular Medicine, Department of Pharmacology, New York University School of Medicine, New York, NY 10016, USA
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34
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Abstract
The long-awaited structure of the effector portion of IRE1, the endoplasmic reticulum stress transducer, is published in this issue of Cell (Lee et al., 2008). This structure provides new insight into the mysterious coupling of kinase and endoribonuclease activities in the oldest, most-conserved branch of the unfolded protein response in eukaryotes.
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Affiliation(s)
- David Ron
- Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY 10016, USA.
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35
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Wu J, Tseng YD, Xu CF, Neubert TA, White MF, Hubbard SR. Structural and biochemical characterization of the KRLB region in insulin receptor substrate-2. Nat Struct Mol Biol 2008; 15:251-8. [DOI: 10.1038/nsmb.1388] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2007] [Accepted: 01/10/2008] [Indexed: 11/09/2022]
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36
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Abstract
The human laminin receptor (LamR) interacts with many ligands, including laminin, prions, Sindbis virus, and the polyphenol (-)-epigallocatechin-3-gallate (EGCG), and has been implicated in a number of diseases. LamR is overexpressed on tumor cells, and targeting LamR elicits anti-cancer effects. Here, we report the crystal structure of human LamR, which provides insights into its function and should facilitate the design of novel therapeutics targeting LamR.
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Affiliation(s)
- Kelly V Jamieson
- Gene Therapy Center, Cancer Institute and Department of Pathology, New York University School of Medicine, New York, New York 10016
| | - Jinhua Wu
- Structural Biology Program, Kimmel Center for Biology and Medicine of the Skirball Institute, and Department of Pharmacology, New York University School of Medicine, New York, New York 10016
| | - Stevan R Hubbard
- Structural Biology Program, Kimmel Center for Biology and Medicine of the Skirball Institute, and Department of Pharmacology, New York University School of Medicine, New York, New York 10016.
| | - Daniel Meruelo
- Gene Therapy Center, Cancer Institute and Department of Pathology, New York University School of Medicine, New York, New York 10016.
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37
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Abstract
Receptor tyrosine kinases (RTKs) are essential components of signal transduction pathways that mediate cell-to-cell communication. These single-pass transmembrane receptors, which bind polypeptide ligands - mainly growth factors - play key roles in processes such as cellular growth, differentiation, metabolism and motility. Recent progress has been achieved towards an understanding of the precise (and varied) mechanisms by which RTKs are activated by ligand binding and by which signals are propagated from the activated receptors to downstream targets in the cell.
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Affiliation(s)
- Stevan R Hubbard
- Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
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38
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Stiegler AL, Burden SJ, Hubbard SR. Crystal structure of the agrin-responsive immunoglobulin-like domains 1 and 2 of the receptor tyrosine kinase MuSK. J Mol Biol 2006; 364:424-33. [PMID: 17011580 PMCID: PMC1752213 DOI: 10.1016/j.jmb.2006.09.019] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2006] [Revised: 08/30/2006] [Accepted: 09/05/2006] [Indexed: 10/24/2022]
Abstract
Muscle-specific kinase (MuSK) is a receptor tyrosine kinase expressed exclusively in skeletal muscle, where it is required for formation of the neuromuscular junction. MuSK is activated by agrin, a neuron-derived heparan sulfate proteoglycan. Here, we report the crystal structure of the agrin-responsive first and second immunoglobulin-like domains (Ig1 and Ig2) of the MuSK ectodomain at 2.2 A resolution. The structure reveals that MuSK Ig1 and Ig2 are Ig-like domains of the I-set subfamily, which are configured in a linear, semi-rigid arrangement. In addition to the canonical internal disulfide bridge, Ig1 contains a second, solvent-exposed disulfide bridge, which our biochemical data indicate is critical for proper folding of Ig1 and processing of MuSK. Two Ig1-2 molecules form a non-crystallographic dimer that is mediated by a unique hydrophobic patch on the surface of Ig1. Biochemical analyses of MuSK mutants introduced into MuSK(-/-) myotubes demonstrate that residues in this hydrophobic patch are critical for agrin-induced MuSK activation.
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Affiliation(s)
- Amy L Stiegler
- Structural Biology Program, Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, NY 10016, USA
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39
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Abstract
A study by Zhang et al. (2006) in this issue of Cell provides compelling evidence that the tyrosine kinase domain of the epidermal growth factor receptor (EGFR) is activated by the formation of an asymmetric dimer, with one kinase domain in the EGF-mediated dimer activating the other through an allosteric mechanism.
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Affiliation(s)
- Stevan R Hubbard
- Structural Biology Program, Skirball Institute of Biomolecular Medicine, and Department of Pharmacology, New York University School of Medicine, New York, NY 10016, USA
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40
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Bergamin E, Wu J, Hubbard SR. Structural Basis for Phosphotyrosine Recognition by Suppressor of Cytokine Signaling-3. Structure 2006; 14:1285-92. [PMID: 16905102 DOI: 10.1016/j.str.2006.06.011] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2006] [Revised: 06/12/2006] [Accepted: 06/16/2006] [Indexed: 10/24/2022]
Abstract
Suppressor of cytokine signaling (SOCS) proteins are indispensable negative regulators of cytokine-stimulated Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling pathways. SOCS proteins (SOCS1-7 and CIS) consist of a variable N-terminal region, a central Src homology-2 (SH2) domain, and a C-terminal SOCS box. The N-terminal region in SOCS1 and SOCS3 includes the so-called kinase inhibitory region that has been shown to inhibit the catalytic activity of JAK2. Here, we present a crystal structure at 2.0 A resolution of the N-terminally extended SH2 domain of SOCS3 in complex with its phosphopeptide target on the cytokine receptor gp130. The structure reveals that major insertions in the EF and BG loops of the SOCS3 SH2 domain are responsible for binding to gp130 with high affinity and specificity. In addition, the structure provides insights into the possible mechanisms by which SOCS3 and SOCS1 inhibit JAK2 kinase activity.
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Affiliation(s)
- Elisa Bergamin
- Structural Biology Program, Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, New York 10016, USA
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41
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Hu J, Hubbard SR. Structural basis for phosphotyrosine recognition by the Src homology-2 domains of the adapter proteins SH2-B and APS. J Mol Biol 2006; 361:69-79. [PMID: 16824542 DOI: 10.1016/j.jmb.2006.05.070] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2006] [Revised: 05/30/2006] [Accepted: 05/31/2006] [Indexed: 11/25/2022]
Abstract
SH2-B, APS, and Lnk constitute a family of adapter proteins that modulate signaling by protein tyrosine kinases. These adapters contain an N-terminal dimerization region, a pleckstrin homology domain, and a C-terminal Src homology-2 (SH2) domain. SH2-B is recruited via its SH2 domain to various protein tyrosine kinases, including Janus kinase-2 (Jak2) and the insulin receptor. Here, we present the crystal structure at 2.35 A resolution of the SH2 domain of SH2-B in complex with a phosphopeptide representing the SH2-B recruitment site in Jak2 (pTyr813). The structure reveals a canonical SH2 domain-phosphopeptide binding mode, but with specific recognition of a glutamate at the +1 position relative to phosphotyrosine, in addition to recognition of a hydrophobic residue at the +3 position. Biochemical studies of SH2-B and APS demonstrate that, although the SH2 domains of these two adapter proteins share 79% sequence identity, the SH2-B SH2 domain binds preferentially to Jak2, whereas the APS SH2 domain has higher affinity for the insulin receptor. This differential specificity is attributable to the difference in the oligomeric states of the two SH2 domains: monomeric for SH2-B and dimeric for APS.
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Affiliation(s)
- Junjie Hu
- Structural Biology Program, Skirball Institute of Biomolecular Medicine, and Department of Pharmacology, New York University School of Medicine, NY 10016, USA.
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42
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Depetris RS, Hu J, Gimpelevich I, Holt LJ, Daly RJ, Hubbard SR. Structural basis for inhibition of the insulin receptor by the adaptor protein Grb14. Mol Cell 2006; 20:325-33. [PMID: 16246733 PMCID: PMC4526137 DOI: 10.1016/j.molcel.2005.09.001] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2005] [Revised: 08/25/2005] [Accepted: 09/02/2005] [Indexed: 11/20/2022]
Abstract
Grb14, a member of the Grb7 adaptor protein family, possesses a pleckstrin homology (PH) domain, a C-terminal Src homology-2 (SH2) domain, and an intervening stretch of approximately 45 residues known as the BPS region, which is unique to this adaptor family. Previous studies have demonstrated that Grb14 is a tissue-specific negative regulator of insulin receptor signaling and that inhibition is mediated by the BPS region. We have determined the crystal structure of the Grb14 BPS region in complex with the tyrosine kinase domain of the insulin receptor. The structure reveals that the N-terminal portion of the BPS region binds as a pseudosubstrate inhibitor in the substrate peptide binding groove of the kinase. Together with the crystal structure of the SH2 domain, we present a model for the interaction of Grb14 with the insulin receptor, which indicates how Grb14 functions as a selective protein inhibitor of insulin signaling.
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Affiliation(s)
- Rafael S. Depetris
- Structural Biology Program, Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, New York 10016
| | - Junjie Hu
- Structural Biology Program, Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, New York 10016
| | - Ilana Gimpelevich
- Structural Biology Program, Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, New York 10016
| | - Lowenna J. Holt
- Cancer Research Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Roger J. Daly
- Cancer Research Program, Garvan Institute of Medical Research, Sydney, NSW 2010, Australia
| | - Stevan R. Hubbard
- Structural Biology Program, Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, New York 10016
- Correspondence:
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43
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Hines AC, Parang K, Kohanski RA, Hubbard SR, Cole PA. Bisubstrate analog probes for the insulin receptor protein tyrosine kinase: molecular yardsticks for analyzing catalytic mechanism and inhibitor design. Bioorg Chem 2005; 33:285-97. [PMID: 16023488 DOI: 10.1016/j.bioorg.2005.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2005] [Revised: 02/23/2005] [Accepted: 02/28/2005] [Indexed: 12/30/2022]
Abstract
Bisubstrate analogs have the potential to provide enhanced specificity for protein kinase inhibition and tools to understand catalytic mechanism. Previous efforts led to the design of a peptide-ATP conjugate bisubstrate analog utilizing aminophenylalanine in place of tyrosine and a thioacetyl linker to the gamma-phosphate of ATP which was a potent inhibitor of the insulin receptor kinase (IRK). In this study, we have examined the contributions of various electrostatic and structural elements in the bisubstrate analog to IRK binding affinity. Three types of changes (seven specific analogs in all) were introduced: a Tyr isostere of the previous aminophenylalanine moiety, modifications of the spacer between the adenine and the peptide, and deletions and substitutions within the peptide moiety. These studies allowed a direct evaluation of the hydrogen bond strength between the anilino nitrogen of the bisubstrate analog and the enzyme catalytic base Asp and showed that it contributes 2.5 kcal/mol of binding energy, in good agreement with previous predictions. Modifications of the linker length resulted in weakened inhibitory affinity, consistent with the geometric requirements of an enzyme-catalyzed dissociative transition state. Alterations in the peptide motif generally led to diminished inhibitory potency, and only some of these effects could be rationalized based on prior kinetic and structural studies. Taken together, these results suggest that a combination of mechanism-based design and empirical synthetic manipulation will be necessary in producing optimized protein kinase bisubstrate analog inhibitors.
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Affiliation(s)
- Aliya C Hines
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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44
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Hu J, Hubbard SR. Structural characterization of a novel Cbl phosphotyrosine recognition motif in the APS family of adapter proteins. J Biol Chem 2005; 280:18943-9. [PMID: 15737992 DOI: 10.1074/jbc.m414157200] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Cbl adapter proteins typically function to down-regulate activated protein tyrosine kinases and other signaling proteins by coupling them to the ubiquitination machinery for degradation by the proteasome. Cbl proteins bind to specific tyrosine-phosphorylated sequences in target proteins via the tyrosine kinase-binding (TKB) domain, which comprises a four-helix bundle, an EF-hand calcium-binding domain, and a non-conventional Src homology-2 domain. The previously derived consensus sequence for phosphotyrosine recognition by the Cbl TKB domain is NXpY(S/T)XXP (X denotes lesser residue preference), wherein specificity is conferred primarily by residues C-terminal to the phosphotyrosine. Cbl is recruited to and phosphorylated by the insulin receptor in adipose cells through the adapter protein APS. APS is phosphorylated by the insulin receptor on a C-terminal tyrosine residue, which then serves as a binding site for the Cbl TKB domain. Using x-ray crystallography, site-directed mutagenesis, and calorimetric studies, we have characterized the interaction between the Cbl TKB domain and the Cbl recruitment site in APS, which contains a sequence motif, RA(V/I)XNQpY(S/T), that is conserved in the related adapter proteins SH2-B and Lnk. These studies reveal a novel mode of phosphopeptide interaction with the Cbl TKB domain, in which N-terminal residues distal to the phosphotyrosine directly contact residues of the four-helix bundle of the TKB domain.
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Affiliation(s)
- Junjie Hu
- Structural Biology Program, Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, New York 10016, USA
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45
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Hubbard SR, Greenall RJ, Woolfson MM. On the application of direct methods to oligonucleotide crystallography. Acta Crystallogr D Biol Crystallogr 2005; 50:833-41. [PMID: 15299350 DOI: 10.1107/s0907444994005615] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The direct methods program SAYTAN was applied to simulated data at various resolutions from three oligonucleotides. Success in solving the structures was found to depend more upon the resolution of the data than upon errors in the data or the complexity of the structure. Collecting the data at a reduced temperature has little effect, unless it alters the mosaicity of the crystal or changes the resolution of the data. The presence of a heavy atom dramatically improved the phase refinement, particularly at low resolution.
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Affiliation(s)
- S R Hubbard
- Department of Physics, University of York, Heslington, England
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46
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Affiliation(s)
- Stevan R Hubbard
- Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York 10016, USA.
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47
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Abstract
A study by Wan et al. in this issue of Cell demonstrates that the majority of oncogenic mutations in the B-Raf protein kinase result in increased catalytic activity, through disruption of the autoinhibited state of the kinase domain. Surprisingly, several mutations lead to impaired B-Raf kinase activity, yet these mutants are nevertheless capable of stimulating downstream signaling through transactivation of C-Raf.
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Affiliation(s)
- Stevan R Hubbard
- Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, NY 10016, USA
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48
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Abstract
The adaptor protein APS is a substrate of the insulin receptor and couples receptor activation with phosphorylation of Cbl to facilitate glucose uptake. The interaction with the activated insulin receptor is mediated by the Src homology 2 (SH2) domain of APS. Here, we present the crystal structure of the APS SH2 domain in complex with the phosphorylated tyrosine kinase domain of the insulin receptor. The structure reveals a novel dimeric configuration of the APS SH2 domain, wherein the C-terminal half of each protomer is structurally divergent from conventional, monomeric SH2 domains. The APS SH2 dimer engages two kinase molecules, with pTyr-1158 of the kinase activation loop bound in the canonical phosphotyrosine binding pocket of the SH2 domain and a second phosphotyrosine, pTyr-1162, coordinated by two lysine residues in beta strand D. This structure provides a molecular visualization of one of the initial downstream recruitment events following insulin activation of its dimeric receptor.
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Affiliation(s)
- Junjie Hu
- Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, NY 10016, USA
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49
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Li S, Covino ND, Stein EG, Till JH, Hubbard SR. Structural and biochemical evidence for an autoinhibitory role for tyrosine 984 in the juxtamembrane region of the insulin receptor. J Biol Chem 2003; 278:26007-14. [PMID: 12707268 DOI: 10.1074/jbc.m302425200] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tyrosine 984 in the juxtamembrane region of the insulin receptor, between the transmembrane helix and the cytoplasmic tyrosine kinase domain, is conserved among all insulin receptor-like proteins from hydra to humans. Crystallographic studies of the tyrosine kinase domain and proximal juxtamembrane region reveal that Tyr-984 interacts with several other conserved residues in the N-terminal lobe of the kinase domain, stabilizing a catalytically nonproductive position of alpha-helix C. Steady-state kinetics measurements on the soluble kinase domain demonstrate that replacement of Tyr-984 with phenylalanine results in a 4-fold increase in kcat in the unphosphorylated (basal state) enzyme. Moreover, mutation of Tyr-984 in the full-length insulin receptor results in significantly elevated receptor phosphorylation levels in cells, both in the absence of insulin and following insulin stimulation. These data demonstrate that Tyr-984 plays an important structural role in maintaining the quiescent, basal state of the insulin receptor. In addition, the structural studies suggest a possible target site for small molecule activators of the insulin receptor, with potential use in the treatment of noninsulin-dependent diabetes mellitus.
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Affiliation(s)
- Shiqing Li
- Skirball Institute of Biomolecular Medicine and Department of Pharmacology, New York University School of Medicine, New York, New York 10016, USA
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50
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