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Juyoux P, Galdadas I, Gobbo D, von Velsen J, Pelosse M, Tully M, Vadas O, Gervasio FL, Pellegrini E, Bowler MW. Architecture of the MKK6-p38α complex defines the basis of MAPK specificity and activation. Science 2023; 381:1217-1225. [PMID: 37708276 PMCID: PMC7615176 DOI: 10.1126/science.add7859] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 08/09/2023] [Indexed: 09/16/2023]
Abstract
The mitogen-activated protein kinase (MAPK) p38α is a central component of signaling in inflammation and the immune response and is, therefore, an important drug target. Little is known about the molecular mechanism of its activation by double phosphorylation from MAPK kinases (MAP2Ks), because of the challenge of trapping a transient and dynamic heterokinase complex. We applied a multidisciplinary approach to generate a structural model of p38α in complex with its MAP2K, MKK6, and to understand the activation mechanism. Integrating cryo-electron microscopy with molecular dynamics simulations, hydrogen-deuterium exchange mass spectrometry, and experiments in cells, we demonstrate a dynamic, multistep phosphorylation mechanism, identify catalytically relevant interactions, and show that MAP2K-disordered amino termini determine pathway specificity. Our work captures a fundamental step of cell signaling: a kinase phosphorylating its downstream target kinase.
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Affiliation(s)
- Pauline Juyoux
- European Molecular Biology Laboratory (EMBL), Grenoble, France
| | - Ioannis Galdadas
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Dorothea Gobbo
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
| | - Jill von Velsen
- European Molecular Biology Laboratory (EMBL), Grenoble, France
| | - Martin Pelosse
- European Molecular Biology Laboratory (EMBL), Grenoble, France
| | - Mark Tully
- European Synchrotron Radiation Facility, Grenoble, France
| | - Oscar Vadas
- Protein and peptide purification platform, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Francesco Luigi Gervasio
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- School of Pharmaceutical Sciences, University of Geneva, Geneva, Switzerland
- Department of Chemistry, University College London, London, UK
- Institute of Structural and Molecular Biology, University College London, London, UK
- Swiss Institute of Bioinformatics, Geneva, Switzerland
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2
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Huang C, Ji C, Wang J. Current thoughts on cellular functions of numb-associated kinases. Mol Biol Rep 2023; 50:4645-4652. [PMID: 37014568 PMCID: PMC10072014 DOI: 10.1007/s11033-023-08372-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 03/02/2023] [Indexed: 04/05/2023]
Abstract
Members of the Numb-associated kinase family of serine/threonine kinases play an essential role in many cellular processes, such as endocytosis, autophagy, dendrite morphogenesis, osteoblast differentiation, and the regulation of the Notch pathway. Numb-associated kinases have been relevant to diverse diseases, including neuropathic pain, Parkinson's disease, and prostate cancer. Therefore, they are considered potential therapeutic targets. In addition, it is reported that Numb-associated kinases have been involved in the life cycle of multiple viruses such as hepatitis C virus (HCV), Ebola virus (EBOV), and dengue virus (DENV). Recently, Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to threaten global health. Studies show that Numb-associated kinases are implicated in the infection of SARS-CoV-2 which can be suppressed by Numb-associated kinases inhibitors. Thus, Numb-associated kinases are proposed as potential host targets for broad-spectrum antiviral strategies. We will focus on the recent advances in Numb-associated kinases-related cellular functions and their potential as host targets for viral infections in this review. Questions that remained unknown on the cellular functions of Numb-associated kinases will also be discussed.
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Affiliation(s)
- Chenxi Huang
- Department of Biology, Faculty of Environment and Life, Beijing University of Technology, 100124, Beijing, China
| | - Cuicui Ji
- Department of Biology, Faculty of Environment and Life, Beijing University of Technology, 100124, Beijing, China.
| | - Juan Wang
- Department of Biology, Faculty of Environment and Life, Beijing University of Technology, 100124, Beijing, China.
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3
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Rangwala AM, Mingione VR, Georghiou G, Seeliger MA. Kinases on Double Duty: A Review of UniProtKB Annotated Bifunctionality within the Kinome. Biomolecules 2022; 12:biom12050685. [PMID: 35625613 PMCID: PMC9138534 DOI: 10.3390/biom12050685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 01/27/2023] Open
Abstract
Phosphorylation facilitates the regulation of all fundamental biological processes, which has triggered extensive research of protein kinases and their roles in human health and disease. In addition to their phosphotransferase activity, certain kinases have evolved to adopt additional catalytic functions, while others have completely lost all catalytic activity. We searched the Universal Protein Resource Knowledgebase (UniProtKB) database for bifunctional protein kinases and focused on kinases that are critical for bacterial and human cellular homeostasis. These kinases engage in diverse functional roles, ranging from environmental sensing and metabolic regulation to immune-host defense and cell cycle control. Herein, we describe their dual catalytic activities and how they contribute to disease pathogenesis.
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4
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Conservation of the unusual dimeric JmjC fold of JMJD7 from Drosophila melanogaster to humans. Sci Rep 2022; 12:6065. [PMID: 35410347 PMCID: PMC9001643 DOI: 10.1038/s41598-022-10028-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/30/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractThe JmjC family of 2-oxoglutarate dependent oxygenases catalyse a range of hydroxylation and demethylation reactions in humans and other animals. Jumonji domain-containing 7 (JMJD7) is a JmjC (3S)-lysyl-hydroxylase that catalyses the modification of Developmentally Regulated GTP Binding Proteins 1 and 2 (DRG1 and 2); JMJD7 has also been reported to have histone endopeptidase activity. Here we report biophysical and biochemical studies on JMJD7 from Drosophila melanogaster (dmJMJD7). Notably, crystallographic analyses reveal that the unusual dimerization mode of JMJD7, which involves interactions between both the N- and C-terminal regions of both dmJMJD7 monomers and disulfide formation, is conserved in human JMJD7 (hsJMJD7). The results further support the assignment of JMJD7 as a lysyl hydroxylase and will help enable the development of selective inhibitors for it and other JmjC oxygenases.
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5
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Westrip CAE, Zhuang Q, Hall C, Eaton CD, Coleman ML. Developmentally regulated GTPases: structure, function and roles in disease. Cell Mol Life Sci 2021; 78:7219-7235. [PMID: 34664086 PMCID: PMC8629797 DOI: 10.1007/s00018-021-03961-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/13/2021] [Accepted: 09/28/2021] [Indexed: 01/01/2023]
Abstract
GTPases are a large superfamily of evolutionarily conserved proteins involved in a variety of fundamental cellular processes. The developmentally regulated GTP-binding protein (DRG) subfamily of GTPases consists of two highly conserved paralogs, DRG1 and DRG2, both of which have been implicated in the regulation of cell proliferation, translation and microtubules. Furthermore, DRG1 and 2 proteins both have a conserved binding partner, DRG family regulatory protein 1 and 2 (DFRP1 and DFRP2), respectively, that prevents them from being degraded. Similar to DRGs, the DFRP proteins have also been studied in the context of cell growth control and translation. Despite these proteins having been implicated in several fundamental cellular processes they remain relatively poorly characterized, however. In this review, we provide an overview of the structural biology and biochemistry of DRG GTPases and discuss current understanding of DRGs and DFRPs in normal physiology, as well as their emerging roles in diseases such as cancer.
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Affiliation(s)
- Christian A E Westrip
- Tumour Oxygenase Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Qinqin Zhuang
- Tumour Oxygenase Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Institute of Inflammation and Ageing, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Charlotte Hall
- Tumour Oxygenase Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Charlotte D Eaton
- Tumour Oxygenase Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
- Neurological Surgery, School of Medicine, University of California, 1450 Third St, San Francisco, CA, 94158, USA
| | - Mathew L Coleman
- Tumour Oxygenase Group, Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
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6
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Manandhar SP, Siddiqah IM, Cocca SM, Gharakhanian E. A kinase cascade on the yeast lysosomal vacuole regulates its membrane dynamics: conserved kinase Env7 is phosphorylated by casein kinase Yck3. J Biol Chem 2020; 295:12262-12278. [PMID: 32647006 PMCID: PMC7443493 DOI: 10.1074/jbc.ra119.012346] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 06/02/2020] [Indexed: 01/15/2023] Open
Abstract
Membrane fusion/fission is a highly dynamic and conserved process that responds to intra- and extracellular signals. Whereas the molecular machineries involved in membrane fusion/fission have been dissected, regulation of membrane dynamics remains poorly understood. The lysosomal vacuole of budding yeast (Saccharomyces cerevisiae) has served as a seminal model in studies of membrane dynamics. We have previously established that yeast ENV7 encodes an ortholog of STK16-related kinases that localizes to the vacuolar membrane and downregulates vacuolar membrane fusion. Additionally, we have previously reported that Env7 phosphorylation in vivo depends on YCK3, a gene that encodes a vacuolar membrane casein kinase I (CKI) homolog that nonredundantly functions in fusion regulation. Here, we report that Env7 physically interacts with and is directly phosphorylated by Yck3. We also establish that Env7 vacuole fusion/fission regulation and vacuolar localization are mediated through its Yck3-dependent phosphorylation. Through extensive site-directed mutagenesis, we map phosphorylation to the Env7 C terminus and confirm that Ser-331 is a primary and preferred phosphorylation site. Phospho-deficient Env7 mutants were defective in negative regulation of membrane fusion, increasing the number of prominent vacuoles, whereas a phosphomimetic substitution at Ser-331 increased the number of fragmented vacuoles. Bioinformatics approaches confirmed that Env7 Ser-331 is within a motif that is highly conserved in STK16-related kinases and that it also anchors an SXXS CKI phosphorylation motif (328SRFS331). This study represents the first report on the regulatory mechanism of an STK16-related kinase. It also points to regulation of vacuolar membrane dynamics via a novel Yck3-Env7 kinase cascade.
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Affiliation(s)
- Surya P Manandhar
- Department of Biological Sciences, California State University at Long Beach, Long Beach, California, USA
| | - Ikha M Siddiqah
- Department of Biological Sciences, California State University at Long Beach, Long Beach, California, USA
| | - Stephanie M Cocca
- Department of Biological Sciences, California State University at Long Beach, Long Beach, California, USA
| | - Editte Gharakhanian
- Department of Biological Sciences, California State University at Long Beach, Long Beach, California, USA.
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7
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Wells C, Couñago RM, Limas JC, Almeida TL, Cook JG, Drewry DH, Elkins JM, Gileadi O, Kapadia NR, Lorente-Macias A, Pickett JE, Riemen A, Ruela-de-Sousa RR, Willson TM, Zhang C, Zuercher WJ, Zutshi R, Axtman AD. SGC-AAK1-1: A Chemical Probe Targeting AAK1 and BMP2K. ACS Med Chem Lett 2020; 11:340-345. [PMID: 32184967 DOI: 10.1021/acsmedchemlett.9b00399] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/23/2019] [Indexed: 12/12/2022] Open
Abstract
Inhibitors based on a 3-acylaminoindazole scaffold were synthesized to yield potent dual AAK1/BMP2K inhibitors. Optimization furnished a small molecule chemical probe (SGC-AAK1-1, 25) that is potent and selective for AAK1/BMP2K over other NAK family members, demonstrates narrow activity in a kinome-wide screen, and is functionally active in cells. This inhibitor represents one of the best available small molecule tools to study the functions of AAK1 and BMP2K.
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Affiliation(s)
- Carrow Wells
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC−CH), Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC−CH, Chapel Hill, North Carolina 27599, United States
| | - Rafael M. Couñago
- SGC, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-886, Brazil
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, UNICAMP, Campinas, SP 13083-875, Brazil
| | - Juanita C. Limas
- Department of Pharmacology, UNC−CH, Chapel Hill, North Carolina 27599, United States
| | - Tuanny L. Almeida
- SGC, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-886, Brazil
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, UNICAMP, Campinas, SP 13083-875, Brazil
| | - Jeanette Gowen Cook
- Department of Biochemistry and Biophysics, UNC−CH, Chapel Hill, North Carolina 27599, United States
| | - David H. Drewry
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC−CH), Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC−CH, Chapel Hill, North Carolina 27599, United States
| | - Jonathan M. Elkins
- SGC, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-886, Brazil
- SGC, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, U.K
| | - Opher Gileadi
- SGC, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-886, Brazil
- SGC, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, U.K
| | - Nirav R. Kapadia
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC−CH), Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC−CH, Chapel Hill, North Carolina 27599, United States
| | - Alvaro Lorente-Macias
- Departamento de Química Farmacéutica y Orgánica, University of Granada, Granada, 18071, Spain
| | - Julie E. Pickett
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC−CH), Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC−CH, Chapel Hill, North Carolina 27599, United States
| | - Alexander Riemen
- Luceome Biotechnologies, LLC, Tucson, Arizona 85719, United States
| | - Roberta R. Ruela-de-Sousa
- SGC, Departamento de Genética e Evolução, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-886, Brazil
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, UNICAMP, Campinas, SP 13083-875, Brazil
| | - Timothy M. Willson
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC−CH), Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC−CH, Chapel Hill, North Carolina 27599, United States
| | - Cunyu Zhang
- Platform Technology Sciences, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - William J. Zuercher
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC−CH), Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC−CH, Chapel Hill, North Carolina 27599, United States
- Lineberger Comprehensive Cancer Center (LCCC), UNC−CH, Chapel Hill, North Carolina 27599, United States
| | - Reena Zutshi
- Luceome Biotechnologies, LLC, Tucson, Arizona 85719, United States
| | - Alison D. Axtman
- Structural Genomics Consortium (SGC), UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill (UNC−CH), Chapel Hill, North Carolina 27599, United States
- Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, UNC−CH, Chapel Hill, North Carolina 27599, United States
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8
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Haltenhof T, Kotte A, De Bortoli F, Schiefer S, Meinke S, Emmerichs AK, Petermann KK, Timmermann B, Imhof P, Franz A, Loll B, Wahl MC, Preußner M, Heyd F. A Conserved Kinase-Based Body-Temperature Sensor Globally Controls Alternative Splicing and Gene Expression. Mol Cell 2020; 78:57-69.e4. [PMID: 32059760 DOI: 10.1016/j.molcel.2020.01.028] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/12/2019] [Accepted: 01/27/2020] [Indexed: 12/24/2022]
Abstract
Homeothermic organisms maintain their core body temperature in a narrow, tightly controlled range. Whether and how subtle circadian oscillations or disease-associated changes in core body temperature are sensed and integrated in gene expression programs remain elusive. Furthermore, a thermo-sensor capable of sensing the small temperature differentials leading to temperature-dependent sex determination (TSD) in poikilothermic reptiles has not been identified. Here, we show that the activity of CDC-like kinases (CLKs) is highly responsive to physiological temperature changes, which is conferred by structural rearrangements within the kinase activation segment. Lower body temperature activates CLKs resulting in strongly increased phosphorylation of SR proteins in vitro and in vivo. This globally controls temperature-dependent alternative splicing and gene expression, with wide implications in circadian, tissue-specific, and disease-associated settings. This temperature sensor is conserved across evolution and adapted to growth temperatures of diverse poikilotherms. The dynamic temperature range of reptilian CLK homologs suggests a role in TSD.
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Affiliation(s)
- Tom Haltenhof
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Ana Kotte
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Francesca De Bortoli
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Samira Schiefer
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Stefan Meinke
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Ann-Kathrin Emmerichs
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Kristina Katrin Petermann
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Bernd Timmermann
- Sequencing Core Facility, Max-Planck-Institute for Molecular Genetics, Ihnestraße 63-73, Berlin 14195, Germany
| | - Petra Imhof
- Freie Universität Berlin, Institute of Theoretical Physics, Arnimallee 14, 14195 Berlin, Germany
| | - Andreas Franz
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany; Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Bernhard Loll
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Markus C Wahl
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of Structural Biochemistry, Takustrasse 6, 14195 Berlin, Germany; Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, 12489 Berlin, Germany
| | - Marco Preußner
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany
| | - Florian Heyd
- Freie Universität Berlin, Institute of Chemistry and Biochemistry, Laboratory of RNA Biochemistry, Takustrasse 6, 14195 Berlin, Germany.
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9
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Li B, Wang X, Rutz B, Wang R, Tamalunas A, Strittmatter F, Waidelich R, Stief CG, Hennenberg M. The STK16 inhibitor STK16-IN-1 inhibits non-adrenergic and non-neurogenic smooth muscle contractions in the human prostate and the human male detrusor. Naunyn Schmiedebergs Arch Pharmacol 2019; 393:829-842. [PMID: 31867686 DOI: 10.1007/s00210-019-01797-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 12/12/2019] [Indexed: 01/25/2023]
Abstract
Mixed lower urinary tract symptoms (LUTS) (voiding symptoms suggestive of benign prostatic hyperplasia plus storage symptoms, which can be caused by overactive bladder) are common in men. Unwanted contraction of prostate and/or bladder smooth muscle has been implied in the pathophysiology of male LUTS. Here, we examined effects of the serine/threonine kinase 16 (STK16) inhibitor STK16-IN-1 on contraction of human tissues from the prostate and male detrusor. Tissues were obtained from radical prostatectomy and radical cystectomy. Contractions were studied in an organ bath and STK16 expressions by Western blot analyses and fluorescence staining. In prostate tissues, STK16-IN-1 (1 μM) inhibited contractions induced by endothelin-1 and the thromboxane A2 analog U46619. Contractions of prostate tissues induced by noradrenaline, the α1-agonists phenylephrine and methoxamine, or electric field stimulation (EFS) were not changed by STK16-IN-1. In male detrusor tissues, STK16-IN-1 inhibited contractions induced by the cholinergic agonists carbachol and metacholine, and contractions induced by U46619. EFS-induced contractions of detrusor tissues were not changed by STK16-IN-1. Western blot analyses of prostate and detrusor tissues revealed bands matching the molecular weight of STK16. Fluorescence staining of prostate tissues using STK16 antibodies resulted in immunoreactivity in smooth muscle cells. STK16-IN-1 selectively inhibits non-adrenergic/non-neurogenic smooth muscle contractions in the male prostate and to limited extent in the bladder. Because non-adrenergic contractions in the male LUTS may account for limited efficacy of α1-blockers and for α1-blocker-resistant symptoms, studies assessing add-on of STK16-IN-1 to α1-blockers in mixed LUTS appear feasible.
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Affiliation(s)
- Bingsheng Li
- Department of Urology, University Hospital, LMU Munich, Munich, Germany
| | - Xiaolong Wang
- Department of Urology, University Hospital, LMU Munich, Munich, Germany
| | - Beata Rutz
- Department of Urology, University Hospital, LMU Munich, Munich, Germany
| | - Ruixiao Wang
- Department of Urology, University Hospital, LMU Munich, Munich, Germany
| | | | | | | | - Christian G Stief
- Department of Urology, University Hospital, LMU Munich, Munich, Germany
| | - Martin Hennenberg
- Department of Urology, University Hospital, LMU Munich, Munich, Germany. .,Urologische Klinik und Poliklinik, LMU Munich, Marchioninistr. 15, 81377, Munich, Germany.
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10
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Tyr198 is the Essential Autophosphorylation Site for STK16 Localization and Kinase Activity. Int J Mol Sci 2019; 20:ijms20194852. [PMID: 31574902 PMCID: PMC6801969 DOI: 10.3390/ijms20194852] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/17/2019] [Accepted: 09/25/2019] [Indexed: 12/22/2022] Open
Abstract
STK16, reported as a Golgi localized serine/threonine kinase, has been shown to participate in multiple cellular processes, including the TGF-β signaling pathway, TGN protein secretion and sorting, as well as cell cycle and Golgi assembly regulation. However, the mechanisms of the regulation of its kinase activity remain underexplored. It was known that STK16 is autophosphorylated at Thr185, Ser197, and Tyr198 of the activation segment in its kinase domain. We found that STK16 localizes to the cell membrane and the Golgi throughout the cell cycle, but mutations in the auto-phosphorylation sites not only alter its subcellular localization but also affect its kinase activity. In particular, the Tyr198 mutation alone significantly reduced the kinase activity of STK16, abolished its Golgi and membrane localization, and affected the cell cycle progression. This study demonstrates that a single site autophosphorylation of STK16 could affect its localization and function, which provides insights into the molecular regulatory mechanism of STK16's kinase activity.
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11
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Wang J, Ji X, Liu J, Zhang X. Serine/Threonine Protein Kinase STK16. Int J Mol Sci 2019; 20:ijms20071760. [PMID: 30974739 PMCID: PMC6480182 DOI: 10.3390/ijms20071760] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 04/05/2019] [Accepted: 04/08/2019] [Indexed: 12/18/2022] Open
Abstract
STK16 (Ser/Thr kinase 16, also known as Krct/PKL12/MPSK1/TSF-1) is a myristoylated and palmitoylated Ser/Thr protein kinase that is ubiquitously expressed and conserved among all eukaryotes. STK16 is distantly related to the other kinases and belongs to the NAK kinase family that has an atypical activation loop architecture. As a membrane-associated protein that is primarily localized to the Golgi, STK16 has been shown to participate in the TGF-β signaling pathway, TGN protein secretion and sorting, as well as cell cycle and Golgi assembly regulation. This review aims to provide a comprehensive summary of the progress made in recent research about STK16, ranging from its distribution, molecular characterization, post-translational modification (fatty acylation and phosphorylation), interactors (GlcNAcK/DRG1/MAL2/Actin/WDR1), and related functions. As a relatively underexplored kinase, more studies are encouraged to unravel its regulation mechanisms and cellular functions.
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Affiliation(s)
- Junjun Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China.
| | - Xinmiao Ji
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.
| | - Juanjuan Liu
- School of Life Sciences, Anhui University, Hefei 230601, China.
| | - Xin Zhang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China.
- Science Island Branch of Graduate School, University of Science and Technology of China, Hefei 230026, China.
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, China.
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12
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Ohbayashi N, Murayama K, Kato‐Murayama M, Kukimoto‐Niino M, Uejima T, Matsuda T, Ohsawa N, Yokoyoma S, Nojima H, Shirouzu M. Structural Basis for the Inhibition of Cyclin G-Associated Kinase by Gefitinib. ChemistryOpen 2018; 7:721-727. [PMID: 30214852 PMCID: PMC6129943 DOI: 10.1002/open.201800177] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Indexed: 02/03/2023] Open
Abstract
Gefitinib is the molecular target drug for advanced non-small-cell lung cancer. The primary target of gefitinib is the positive mutation of epidermal growth factor receptor, but it also inhibits cyclin G-associated kinase (GAK). To reveal the molecular bases of GAK and gefitinib binding, structure analyses were conducted and determined two forms of the gefitinib-bound nanobody⋅GAK kinase domain complex structures. The first form, GAK_1, has one gefitinib at the ATP binding pocket, whereas the second form, GAK_2, binds one each in the ATP binding site and a novel binding site adjacent to the activation segment C-terminal helix, a unique element of the Numb-associated kinase family. In the novel binding site, gefitinib binds in the hydrophobic groove around the activation segment, disrupting the conserved hydrogen bonds for the catalytic activity. These structures suggest possibilities for the development of selective GAK inhibitors for viral infections, such as the hepatitis C virus.
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Affiliation(s)
- Naomi Ohbayashi
- Division of Structural and Synthetic BiologyRIKEN Center for Life Science Technologies1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
| | - Kazutaka Murayama
- RIKEN Center for Biosystems Dynamics Research1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
- Graduate School of Biomedical EngineeringTohoku University2-1 Seiryomachi, AobaSendai980-8575Japan
| | - Miyuki Kato‐Murayama
- RIKEN Center for Biosystems Dynamics Research1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
| | - Mutsuko Kukimoto‐Niino
- RIKEN Center for Biosystems Dynamics Research1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
| | - Tamami Uejima
- RIKEN Center for Biosystems Dynamics Research1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
| | - Takayoshi Matsuda
- Division of Structural and Synthetic BiologyRIKEN Center for Life Science Technologies1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
| | - Noboru Ohsawa
- Division of Structural and Synthetic BiologyRIKEN Center for Life Science Technologies1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
| | - Shigeyuki Yokoyoma
- RIKEN Structural Biology Laboratory1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
| | - Hiroshi Nojima
- Department of Molecular GeneticsOsaka University3-1 Yamadaoka, SuitaOsaka565-0871Japan
| | - Mikako Shirouzu
- RIKEN Center for Biosystems Dynamics Research1-7-22 Suehiro-cho, TsurumiYokohama230-0045Japan
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13
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A Serine/Threonine Kinase 16-Based Phospho-Proteomics Screen Identifies WD Repeat Protein-1 As A Regulator Of Constitutive Secretion. Sci Rep 2018; 8:13049. [PMID: 30158666 PMCID: PMC6115458 DOI: 10.1038/s41598-018-31426-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/14/2018] [Indexed: 01/03/2023] Open
Abstract
The plasma membrane of polarized hepatocytes is functionally divided into two domains: the apical and basolateral. Our focus is to define the molecular basis of polarized protein sorting of newly-synthesized membrane and secretory proteins in WIF-B cells, an excellent model system for polarized hepatocytes. We determined that MAL2 (myelin and lymphocyte protein 2) and its binding partner, serine/threonine kinase 16 (STK16) regulate basolateral constitutive secretion. Because STK16 is a constitutively active kinase, we reasoned that constitutively phosphorylated substrates must participate in constitutive secretion. To identify either STK16 substrates or other proteins that regulate constitutive secretion, we took a proteomics approach. Post-nuclear supernatants from cells expressing wild type or a kinase-dead (E202A) STK16 were separated on 2D gels and immunoblotted with antibodies against phospho-serine/threonine residues. Sixteen spots were identified from E202A-expressing cells that reproducibly displayed decreased immunoreactivity. From these spots, 28 proteins were identified as possible STK16 substrates. Out of these 28 possible substrates, 25% of them encode predicted STK16 phosphorylation consensus sites, with WD repeat containing protein-1 (WDR1) encoding two such sites. Based on this finding and on the finding that actin remodeling is required for hepatic secretion, we further confirmed that WDR1 is a phosphoprotein that regulates secretion.
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14
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STK16 regulates actin dynamics to control Golgi organization and cell cycle. Sci Rep 2017; 7:44607. [PMID: 28294156 PMCID: PMC5353726 DOI: 10.1038/srep44607] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/09/2017] [Indexed: 11/30/2022] Open
Abstract
STK16 is a ubiquitously expressed, myristoylated, and palmitoylated serine/threonine protein kinase with underexplored functions. Recently, it was shown to be involved in cell division but the mechanism remains unclear. Here we found that human STK16 localizes to the Golgi complex throughout the cell cycle and plays important roles in Golgi structure regulation. STK16 knockdown or kinase inhibition disrupts actin polymers and causes fragmented Golgi in cells. In vitro assays show that STK16 directly binds to actin and regulates actin dynamics in a concentration- and kinase activity-dependent way. In addition, STK16 knockdown or kinase inhibition not only delays mitotic entry and prolongs mitosis, but also causes prometaphase and cytokinesis arrest. Therefore, we revealed STK16 as a novel actin binding protein that resides in the Golgi, which regulates actin dynamics to control Golgi structure and participate in cell cycle progression.
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15
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Env7p Associates with the Golgin Protein Imh1 at the trans-Golgi Network in Candida albicans. mSphere 2016; 1:mSphere00080-16. [PMID: 27504497 PMCID: PMC4973633 DOI: 10.1128/msphere.00080-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 06/29/2016] [Indexed: 12/16/2022] Open
Abstract
A multitier regulation exists at the trans-Golgi network in all higher organisms. We report a palmitoylated protein kinase, Env7, that functions at the TGN interface by interacting with two more TGN-resident proteins, namely, Imh1 and Arl1. Palmitoylation seems to be important for the specific localization. This study focuses on the involvement of a ubiquitous protein kinase, whose substrates had not yet been reported from any organism, as an upstream signaling component that modulates the activity of the Imh1-Arl1 complex crucial for maintaining membrane asymmetry. Virulence is significantly diminished in an Env7 mutant. The functioning of this protein in C. albicans seems to be quite different from its nearest homologue in S. cerervisiae, which reflects the evolutionary divergence between these two organisms. Vesicular dynamics is one of the very important aspects of cellular physiology, an imbalance of which leads to the disorders or diseases in higher eukaryotes. We report the functional characterization of a palmitoylated protein kinase from Candida albicans whose homologue in Saccharomyces cerevisiae has been reported to be involved in negative regulation of membrane fusion and was named Env7. However, the downstream target of this protein remains to be identified. Env7 in C. albicans (CaEnv7) could be isolated from the membrane fraction and localized to vesicular structures associated with the Golgi apparatus. Our work reports Env7 in C. albicans as a new player involved in maintaining the functional dynamics at the trans-Golgi network (TGN) by interacting with two other TGN-resident proteins, namely, Imh1p and Arl1p. Direct interaction could be detected between Env7p and the golgin protein Imh1p. Env7 is itself phosphorylated (Env7p) and phosphorylates Imh1 in vivo. An interaction between Env7 and Imh1 is required for the targeted localization of Imh1. CaEnv7 has a putative palmitoylation site toward both N and C termini. An N-terminal palmitoylation-defective strain retains its ability to phosphorylate Imh1 in vitro. An ENV7 homozygous mutant showed compromised filamentation in solid media and attenuated virulence, whereas an overexpressed strain affected cell wall integrity. Thus, Env7 plays a subtle but important role at the level of multitier regulation that exists at the TGN. IMPORTANCE A multitier regulation exists at the trans-Golgi network in all higher organisms. We report a palmitoylated protein kinase, Env7, that functions at the TGN interface by interacting with two more TGN-resident proteins, namely, Imh1 and Arl1. Palmitoylation seems to be important for the specific localization. This study focuses on the involvement of a ubiquitous protein kinase, whose substrates had not yet been reported from any organism, as an upstream signaling component that modulates the activity of the Imh1-Arl1 complex crucial for maintaining membrane asymmetry. Virulence is significantly diminished in an Env7 mutant. The functioning of this protein in C. albicans seems to be quite different from its nearest homologue in S. cerervisiae, which reflects the evolutionary divergence between these two organisms.
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16
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Liu F, Wang J, Yang X, Li B, Wu H, Qi S, Chen C, Liu X, Yu K, Wang W, Zhao Z, Wang A, Chen Y, Wang L, Gray NS, Liu J, Zhang X, Liu Q. Discovery of a Highly Selective STK16 Kinase Inhibitor. ACS Chem Biol 2016; 11:1537-43. [PMID: 27082499 DOI: 10.1021/acschembio.6b00250] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
STK16, a serine/threonine protein kinase, is ubiquitously expressed and is conserved among all eukaryotes. STK16 has been implicated to function in a variety of cellular processes such as VEGF and cargo secretion, but the pathways through which these effects are mediated remain to be elucidated. Through screening of our focused library of kinase inhibitors, we discovered a highly selective ATP competitive inhibitor, STK16-IN-1, which exhibits potent inhibitory activity against STK16 kinase (IC50: 0.295 μM) with excellent selectivity across the kinome as assessed using the KinomeScan profiling assay (S score (1) = 0.0). In MCF-7 cells, treatment with STK16-IN-1 results in a reduction in cell number and accumulation of binucleated cells, which can be recapitulated by RNAi knockdown of STK16. Co-treatment of STK16-IN-1 with chemotherapeutics such as cisplatin, doxorubicin, colchicine, and paclitaxel results in a slight potentiation of the antiproliferative effects of the chemotherapeutics. STK16-IN-1 provides a useful tool compound for further elucidating the biological functions of STK16.
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Affiliation(s)
- Feiyang Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1110, Hefei, Anhui 230031, People’s Republic of China
- University of Science and Technology of China, Hefei, Anhui 230036, People’s Republic of China
| | - Jinhua Wang
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 250 Longwood Ave, SGM 628, Boston, Massachusetts 02115, United States
| | - Xingxing Yang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1110, Hefei, Anhui 230031, People’s Republic of China
| | - Binhua Li
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1110, Hefei, Anhui 230031, People’s Republic of China
- CHMFL-HCMTC Target Therapy Joint Laboratory, Shushanhu Road, Hefei, Anhui 230031, People’s Republic of China
| | - Hong Wu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1110, Hefei, Anhui 230031, People’s Republic of China
- University of Science and Technology of China, Hefei, Anhui 230036, People’s Republic of China
| | - Shuang Qi
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1110, Hefei, Anhui 230031, People’s Republic of China
- CHMFL-HCMTC Target Therapy Joint Laboratory, Shushanhu Road, Hefei, Anhui 230031, People’s Republic of China
| | - Cheng Chen
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1110, Hefei, Anhui 230031, People’s Republic of China
- CHMFL-HCMTC Target Therapy Joint Laboratory, Shushanhu Road, Hefei, Anhui 230031, People’s Republic of China
| | - Xiaochuan Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1110, Hefei, Anhui 230031, People’s Republic of China
- University of Science and Technology of China, Hefei, Anhui 230036, People’s Republic of China
| | - Kailin Yu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1110, Hefei, Anhui 230031, People’s Republic of China
- University of Science and Technology of China, Hefei, Anhui 230036, People’s Republic of China
| | - Wenchao Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1110, Hefei, Anhui 230031, People’s Republic of China
- CHMFL-HCMTC Target Therapy Joint Laboratory, Shushanhu Road, Hefei, Anhui 230031, People’s Republic of China
| | - Zheng Zhao
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1110, Hefei, Anhui 230031, People’s Republic of China
- CHMFL-HCMTC Target Therapy Joint Laboratory, Shushanhu Road, Hefei, Anhui 230031, People’s Republic of China
| | - Aoli Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1110, Hefei, Anhui 230031, People’s Republic of China
- University of Science and Technology of China, Hefei, Anhui 230036, People’s Republic of China
| | - Yongfei Chen
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1110, Hefei, Anhui 230031, People’s Republic of China
- CHMFL-HCMTC Target Therapy Joint Laboratory, Shushanhu Road, Hefei, Anhui 230031, People’s Republic of China
| | - Li Wang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1110, Hefei, Anhui 230031, People’s Republic of China
- CHMFL-HCMTC Target Therapy Joint Laboratory, Shushanhu Road, Hefei, Anhui 230031, People’s Republic of China
| | - Nathanael S. Gray
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, 250 Longwood Ave, SGM 628, Boston, Massachusetts 02115, United States
| | - Jing Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1110, Hefei, Anhui 230031, People’s Republic of China
- CHMFL-HCMTC Target Therapy Joint Laboratory, Shushanhu Road, Hefei, Anhui 230031, People’s Republic of China
| | - Xin Zhang
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1110, Hefei, Anhui 230031, People’s Republic of China
| | - Qingsong Liu
- High Magnetic Field Laboratory, Chinese Academy of Sciences, 350 Shushanhu Road, P.O. Box 1110, Hefei, Anhui 230031, People’s Republic of China
- University of Science and Technology of China, Hefei, Anhui 230036, People’s Republic of China
- CHMFL-HCMTC Target Therapy Joint Laboratory, Shushanhu Road, Hefei, Anhui 230031, People’s Republic of China
- Hefei Science
Center, Chinese Academy of Sciences, Shushanhu Road, Hefei, Anhui 230031, People’s Republic of China
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17
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Sorrell FJ, Szklarz M, Abdul Azeez KR, Elkins JM, Knapp S. Family-wide Structural Analysis of Human Numb-Associated Protein Kinases. Structure 2016; 24:401-11. [PMID: 26853940 PMCID: PMC4780864 DOI: 10.1016/j.str.2015.12.015] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 12/18/2015] [Accepted: 12/22/2015] [Indexed: 01/22/2023]
Abstract
The highly diverse Numb-associated kinase (NAK) family has been linked to broad cellular functions including receptor-mediated endocytosis, Notch pathway modulation, osteoblast differentiation, and dendrite morphogenesis. Consequently, NAK kinases play a key role in a diverse range of diseases from Parkinson's and prostate cancer to HIV. Due to the plasticity of this kinase family, NAK kinases are often inhibited by approved or investigational drugs and have been associated with side effects, but they are also potential drug targets. The presence of cysteine residues in some NAK family members provides the possibility for selective targeting via covalent inhibition. Here we report the first high-resolution structures of kinases AAK1 and BIKE in complex with two drug candidates. The presented data allow a comprehensive structural characterization of the NAK kinase family and provide the basis for rational design of selective NAK inhibitors. First crystal structures of AAK1 and BIKE solved, completing the NAK family Structural analysis of NAKs performed, revealing unusual family architecture 144 clinical kinase inhibitors screened against AAK1, BIKE, GAK, and MPSK1 Nanomolar and covalent inhibitors discovered from clinical kinase library
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Affiliation(s)
- Fiona J Sorrell
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute (TDI), University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Marta Szklarz
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute (TDI), University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Kamal R Abdul Azeez
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute (TDI), University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Jon M Elkins
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute (TDI), University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium and Target Discovery Institute (TDI), University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK; Institute for Pharmaceutical Chemistry, Buchmann Institute for Life Sciences Campus Riedberg, Goethe-University Frankfurt, 60438 Frankfurt am Main, Germany.
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18
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Alexander LT, Möbitz H, Drueckes P, Savitsky P, Fedorov O, Elkins JM, Deane CM, Cowan-Jacob SW, Knapp S. Type II Inhibitors Targeting CDK2. ACS Chem Biol 2015; 10:2116-25. [PMID: 26158339 DOI: 10.1021/acschembio.5b00398] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Kinases can switch between active and inactive conformations of the ATP/Mg(2+) binding motif DFG, which has been explored for the development of type I or type II inhibitors. However, factors modulating DFG conformations remain poorly understood. We chose CDK2 as a model system to study the DFG in-out transition on a target that was thought to have an inaccessible DFG-out conformation. We used site-directed mutagenesis of key residues identified in structural comparisons in conjunction with biochemical and biophysical characterization of the generated mutants. As a result, we identified key residues that facilitate the DFG-out movement, facilitating binding of type II inhibitors. However, surprisingly, we also found that wild type CDK2 is able to bind type II inhibitors. Using protein crystallography structural analysis of the CDK2 complex with an aminopyrimidine-phenyl urea inhibitor (K03861) revealed a canonical type II binding mode and the first available type II inhibitor CDK2 cocrystal structure. We found that the identified type II inhibitors compete with binding of activating cyclins. In addition, analysis of the binding kinetics of the identified inhibitors revealed slow off-rates. The study highlights the importance of residues that may be distant to the ATP binding pocket in modulating the energetics of the DFG-out transition and hence inhibitor binding. The presented data also provide the foundation for a new class of slow off-rate cyclin-competitive CDK2 inhibitors targeting the inactive DFG-out state of this important kinase target.
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Affiliation(s)
- Leila T. Alexander
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
- Department
of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, United Kingdom
| | - Henrik Möbitz
- Novartis Institutes of Biomedical Research, Basel, Switzerland, Novartis Pharma AG, Postfach, CH-4002 Basel, Switzerland
| | - Peter Drueckes
- Novartis Institutes of Biomedical Research, Basel, Switzerland, Novartis Pharma AG, Postfach, CH-4002 Basel, Switzerland
| | - Pavel Savitsky
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
| | - Oleg Fedorov
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford, OX3 7FZ, United Kingdom
| | - Jonathan M. Elkins
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford, OX3 7FZ, United Kingdom
| | - Charlotte M. Deane
- Department
of Statistics, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, United Kingdom
| | - Sandra W. Cowan-Jacob
- Novartis Institutes of Biomedical Research, Basel, Switzerland, Novartis Pharma AG, Postfach, CH-4002 Basel, Switzerland
| | - Stefan Knapp
- Structural
Genomics Consortium, University of Oxford, Old Road Campus Research Building,
Roosevelt Drive, Oxford, OX3 7DQ, United Kingdom
- Target
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford, OX3 7FZ, United Kingdom
- Institute
for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Max-von-Laue-Str.
9, D-60438 Frankfurt
am Main, Germany
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19
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Serine/threonine kinase 16 and MAL2 regulate constitutive secretion of soluble cargo in hepatic cells. Biochem J 2014; 463:201-13. [PMID: 25084525 DOI: 10.1042/bj20140468] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
MAL2 (myelin and lymphocyte protein 2) is thought to regulate at least two steps in the hepatic apical transcytotic pathway. As vesicle budding and delivery at each step are driven by complex machineries, we predicted that MAL2 participates in several large protein complexes with multiple binding partners. To identify novel MAL2 interactors, we performed split-ubiquitin yeast two-hybrid assays and identified STK16 (serine/threonine kinase 16) as a putative interactor which we verified morphologically and biochemically. As STK16 is a Golgi-associated constitutively active kinase implicated in regulating secretion and because of the massive constitutive secretory capacity of hepatic cells, we tested whether MAL2 and STK16 function in secretion. Expression of a dominant-negative kinase-dead STK16 mutant (E202A) or knockdown of MAL2 impaired secretion that correlated with decreased expression of albumin and haptoglobin. By using 19°C temperature blocks and lysosome deacidification, we determined that E202A expression or MAL2 knockdown did not interfere with albumin synthesis or processing, but led to albumin lysosomal degradation. We conclude that MAL2 and the constitutively active STK16 function to sort secretory soluble cargo into the constitutive secretory pathway at the TGN (trans-Golgi network) in polarized hepatocytes.
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20
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Abstract
GAK (cyclin G-associated kinase) is a key regulator of clathrin-coated vesicle trafficking and plays a central role during development. Additionally, due to the unusually high plasticity of its catalytic domain, it is a frequent ‘off-target’ of clinical kinase inhibitors associated with respiratory side effects of these drugs. In the present paper, we determined the crystal structure of the GAK catalytic domain alone and in complex with specific single-chain antibodies (nanobodies). GAK is constitutively active and weakly associates in solution. The GAK apo structure revealed a dimeric inactive state of the catalytic domain mediated by an unusual activation segment interaction. Co-crystallization with the nanobody NbGAK_4 trapped GAK in a dimeric arrangement similar to the one observed in the apo structure, whereas NbGAK_1 captured the activation segment of monomeric GAK in a well-ordered conformation, representing features of the active kinase. The presented structural and biochemical data provide insight into the domain plasticity of GAK and demonstrate the utility of nanobodies to gain insight into conformational changes of dynamic molecules. In addition, we present structural data on the binding mode of ATP mimetic inhibitors and enzyme kinetic data, which will support rational inhibitor design of inhibitors to reduce the off-target effect on GAK. Cyclin G-associated kinase (GAK) is a regulator of clathrin-coated vesicle trafficking. The determined crystal structures of GAK in complex with specific single chain antibodies (nanobodies) revealed the domain plasticity of this kinase and unusual activation segment architecture.
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21
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Manandhar SP, Calle EN, Gharakhanian E. Distinct palmitoylation events at the amino-terminal conserved cysteines of Env7 direct its stability, localization, and vacuolar fusion regulation in S. cerevisiae. J Biol Chem 2014; 289:11431-11442. [PMID: 24610781 DOI: 10.1074/jbc.m113.524082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Palmitoylation at cysteine residues is the only known reversible form of lipidation and has been implicated in protein membrane association as well as function. Many palmitoylated proteins have regulatory roles in dynamic cellular processes, including membrane fusion. Recently, we identified Env7 as a conserved and palmitoylated protein kinase involved in negative regulation of membrane fusion at the lysosomal vacuole. Env7 contains a palmitoylation consensus sequence, and substitution of its three consecutive cysteines (Cys(13)-Cys(15)) results in a non-palmitoylated and cytoplasmic Env7. In this study, we further dissect and define the role(s) of individual cysteines of the consensus sequence in various properties of Env7 in vivo. Our results indicate that more than one of the cysteines serve as palmitoylation substrates, and any pairwise combination is essential and sufficient for near wild type levels of Env7 palmitoylation, membrane localization, and phosphorylation. Furthermore, individually, each cysteine can serve as a minimum requirement for distinct aspects of Env7 behavior and function in cells. Cys(13) is sufficient for membrane association, Cys(15) is essential for the fusion regulatory function of membrane-bound Env7, and Cys(14) and Cys(15) are redundantly essential for protection of membrane-bound Env7 from proteasomal degradation. A role for Cys(14) and Cys(15) in correct sorting at the membrane is also discussed. Thus, palmitoylation at the N-terminal cysteines of Env7 directs not only its membrane association but also its stability, phosphorylation, and cellular function.
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Affiliation(s)
- Surya P Manandhar
- Department of Biological Sciences, California State University, Long Beach, California 90840
| | - Erika N Calle
- Department of Biological Sciences, California State University, Long Beach, California 90840
| | - Editte Gharakhanian
- Department of Biological Sciences, California State University, Long Beach, California 90840.
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22
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Pérez-Arellano I, Spínola-Amilibia M, Bravo J. Human Drg1 is a potassium-dependent GTPase enhanced by Lerepo4. FEBS J 2013; 280:3647-57. [PMID: 23711155 DOI: 10.1111/febs.12356] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 05/15/2013] [Accepted: 05/23/2013] [Indexed: 11/26/2022]
Abstract
Human Drg1, a guanine nucleotide binding protein conserved in archaea and eukaryotes, is regulated by Lerepo4. Together they form a complex which interacts with translating ribosomes. Here we have purified and characterized the GTPase activity of Drg1 and three variants, a shortened mutant depleted of the TGS domain, a phosphomimicking mutant and a construct with the two combined mutations. Our data reveal that potassium strongly stimulates the GTPase activity, without changing the monomeric status of Drg1 and that this activity is notably reduced in the mutants. The nature of Lerepo4 association has also been investigated. Dissecting the role of the different domains revealed that Dfrp domain is the sole responsible for the Drg1 increase in thermal stability and the four fold stimulation over its catalytic activity. Lerepo4 action leaves Drg1 affinity for nucleotides unaffected, feasibly favoring a switch I reorientation, mainly via the TGS domain. Drg1 displayed a high temperature optimum of activity at 42°C, suggesting the ability of being active under possible heat stress conditions.
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Affiliation(s)
- Isabel Pérez-Arellano
- Instituto de Biomedicina de Valencia, Consejo Superior de Investigaciones Científicas, Valencia, Spain
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Saccharomyces cerevisiae Env7 is a novel serine/threonine kinase 16-related protein kinase and negatively regulates organelle fusion at the lysosomal vacuole. Mol Cell Biol 2012; 33:526-42. [PMID: 23166297 DOI: 10.1128/mcb.01303-12] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Membrane fusion depends on conserved components and is responsible for organelle biogenesis and vesicular trafficking. Yeast vacuoles are dynamic structures analogous to mammalian lysosomes. We report here that yeast Env7 is a novel palmitoylated protein kinase ortholog that negatively regulates vacuolar membrane fusion. Microscopic and biochemical studies confirmed the localization of tagged Env7 at the vacuolar membrane and implicated membrane association via the palmitoylation of its N-terminal Cys13 to -15. In vitro kinase assays established Env7 as a protein kinase. Site-directed mutagenesis of the Env7 alanine-proline-glutamic acid (APE) motif Glu269 to alanine results in an unstable kinase-dead allele that is stabilized and redistributed to the detergent-resistant fraction by interruption of the proteasome system in vivo. Palmitoylation-deficient Env7C13-15S is also kinase dead and mislocalizes to the cytoplasm. Microscopy studies established that env7Δ is defective in maintaining fragmented vacuoles during hyperosmotic response and in buds. ENV7 function is not redundant with a similar role of vacuolar membrane kinase Yck3, as the two do not share a substrate, and ENV7 is not a suppressor of yck3Δ. Bayesian phylogenetic analyses strongly support ENV7 as an ortholog of the gene encoding human STK16, a Golgi apparatus protein kinase with undefined function. We propose that Env7 function in fusion/fission dynamics may be conserved within the endomembrane system.
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Francis SM, Gas ME, Daugeron MC, Bravo J, Séraphin B. Rbg1-Tma46 dimer structure reveals new functional domains and their role in polysome recruitment. Nucleic Acids Res 2012; 40:11100-14. [PMID: 23002146 PMCID: PMC3510508 DOI: 10.1093/nar/gks867] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Developmentally Regulated GTP-binding (DRG) proteins are highly conserved GTPases that associate with DRG Family Regulatory Proteins (DFRP). The resulting complexes have recently been shown to participate in eukaryotic translation. The structure of the Rbg1 GTPase, a yeast DRG protein, in complex with the C-terminal region of its DFRP partner, Tma46, was solved by X-ray diffraction. These data reveal that DRG proteins are multimodular factors with three additional domains, helix–turn–helix (HTH), S5D2L and TGS, packing against the GTPase platform. Surprisingly, the S5D2L domain is inserted in the middle of the GTPase sequence. In contrast, the region of Tma46 interacting with Rbg1 adopts an extended conformation typical of intrinsically unstructured proteins and contacts the GTPase and TGS domains. Functional analyses demonstrate that the various domains of Rbg1, as well as Tma46, modulate the GTPase activity of Rbg1 and contribute to the function of these proteins in vivo. Dissecting the role of the different domains revealed that the Rbg1 TGS domain is essential for the recruitment of this factor in polysomes, supporting further the implication of these conserved factors in translation.
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Affiliation(s)
- Sandrea M Francis
- Instituto de Biomedicina de Valencia (IBV-CSIC), Calle Jaime Roig, 11, Valencia E-46010, Spain
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25
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Endicott JA, Noble MEM, Johnson LN. The structural basis for control of eukaryotic protein kinases. Annu Rev Biochem 2012; 81:587-613. [PMID: 22482904 DOI: 10.1146/annurev-biochem-052410-090317] [Citation(s) in RCA: 312] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Eukaryotic protein kinases are key regulators of cell processes. Comparison of the structures of protein kinase domains, both alone and in complexes, allows generalizations to be made about the mechanisms that regulate protein kinase activation. Protein kinases in the active state adopt a catalytically competent conformation upon binding of both the ATP and peptide substrates that has led to an understanding of the catalytic mechanism. Docking sites remote from the catalytic site are a key feature of several substrate recognition complexes. Mechanisms for kinase activation through phosphorylation, additional domains or subunits, by scaffolding proteins and by kinase dimerization are discussed.
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Affiliation(s)
- Jane A Endicott
- Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
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26
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Rabiller M, Getlik M, Klüter S, Richters A, Tückmantel S, Simard JR, Rauh D. Proteus in the world of proteins: conformational changes in protein kinases. Arch Pharm (Weinheim) 2010; 343:193-206. [PMID: 20336692 DOI: 10.1002/ardp.201000028] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The 512 protein kinases encoded by the human genome are a prime example of nature's ability to create diversity by introducing variations to a highly conserved theme. The activity of each kinase domain is controlled by layers of regulatory mechanisms involving different combinations of post-translational modifications, intramolecular contacts, and intermolecular interactions. Ultimately, they all achieve their effect by favoring particular conformations that promote or prevent the kinase domain from catalyzing protein phosphorylation. The central role of kinases in various diseases has encouraged extensive investigations of their biological function and three-dimensional structures, yielding a more detailed understanding of the mechanisms that regulate protein kinase activity by conformational changes. In the present review, we discuss these regulatory mechanisms and show how conformational changes can be exploited for the design of specific inhibitors that lock protein kinases in inactive conformations. In addition, we highlight recent developments to monitor ligand-induced structural changes in protein kinases and for screening and identifying inhibitors that stabilize enzymatically incompetent kinase conformations.
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Affiliation(s)
- Matthias Rabiller
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
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27
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Eswaran J, Knapp S. Insights into protein kinase regulation and inhibition by large scale structural comparison. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1804:429-32. [PMID: 19854302 PMCID: PMC2845818 DOI: 10.1016/j.bbapap.2009.10.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2009] [Revised: 10/06/2009] [Accepted: 10/08/2009] [Indexed: 12/11/2022]
Abstract
Protein structure determination of soluble globular protein domains has developed into an efficient routine technology which can now be applied to generate and analyze structures of entire human protein families. In the kinase area, several kinase families still lack comprehensive structural analysis. Nevertheless, Structural Genomics (SG) efforts contributed more than 40 kinase catalytic domain structures during the past 4 years providing a rich resource of information for large scale comparisons of kinase active sites. Moreover, many of the released structures are inhibitor complexes that offer chemical starting points for development of selective and potent inhibitors. Here we discuss the currently available structural data and strategies that can be utilized for the development of highly selective inhibitors.
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Affiliation(s)
- Jeyanthy Eswaran
- Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford Old Road Campus Building, Oxford OX3 7DQ, UK.
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28
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Bamborough P, Drewry D, Harper G, Smith GK, Schneider K. Assessment of chemical coverage of kinome space and its implications for kinase drug discovery. J Med Chem 2009; 51:7898-914. [PMID: 19035792 DOI: 10.1021/jm8011036] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
More than 500 compounds chosen to represent kinase inhibitor space have been screened against a panel of over 200 protein kinases. Significant results include the identification of hits against new kinases including PIM1 and MPSK1, and the expansion of the inhibition profiles of several literature compounds. A detailed analysis of the data through the use of affinity fingerprints has produced findings with implications for biological target selection, the choice of tool compounds for target validation, and lead discovery and optimization. In a detailed examination of the tyrosine kinases, interesting relationships have been found between targets and compounds. Taken together, these results show how broad cross-profiling can provide important insights to assist kinase drug discovery.
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Affiliation(s)
- Paul Bamborough
- Molecular Discovery Research, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, UK.
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29
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Filippakopoulos P, Kofler M, Hantschel O, Gish GD, Grebien F, Salah E, Neudecker P, Kay LE, Turk BE, Superti-Furga G, Pawson T, Knapp S. Structural coupling of SH2-kinase domains links Fes and Abl substrate recognition and kinase activation. Cell 2008; 134:793-803. [PMID: 18775312 PMCID: PMC2572732 DOI: 10.1016/j.cell.2008.07.047] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2008] [Revised: 06/23/2008] [Accepted: 07/29/2008] [Indexed: 11/05/2022]
Abstract
The SH2 domain of cytoplasmic tyrosine kinases can enhance catalytic activity and substrate recognition, but the molecular mechanisms by which this is achieved are poorly understood. We have solved the structure of the prototypic SH2-kinase unit of the human Fes tyrosine kinase, which appears specialized for positive signaling. In its active conformation, the SH2 domain tightly interacts with the kinase N-terminal lobe and positions the kinase αC helix in an active configuration through essential packing and electrostatic interactions. This interaction is stabilized by ligand binding to the SH2 domain. Our data indicate that Fes kinase activation is closely coupled to substrate recognition through cooperative SH2-kinase-substrate interactions. Similarly, we find that the SH2 domain of the active Abl kinase stimulates catalytic activity and substrate phosphorylation through a distinct SH2-kinase interface. Thus, the SH2 and catalytic domains of active Fes and Abl pro-oncogenic kinases form integrated structures essential for effective tyrosine kinase signaling.
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Affiliation(s)
- Panagis Filippakopoulos
- Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Oxford OX3 7DQ, UK
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