1
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Reiners JJ, Mathieu PA, Gargano M, George I, Shen Y, Callaghan JF, Borch RF, Mattingly RR. Synergistic Suppression of NF1 Malignant Peripheral Nerve Sheath Tumor Cell Growth in Culture and Orthotopic Xenografts by Combinational Treatment with Statin and Prodrug Farnesyltransferase Inhibitor PAMAM G4 Dendrimers. Cancers (Basel) 2023; 16:89. [PMID: 38201517 PMCID: PMC10778372 DOI: 10.3390/cancers16010089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/16/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024] Open
Abstract
Neurofibromatosis type 1 (NF1) is a disorder in which RAS is constitutively activated due to the loss of the Ras-GTPase-activating activity of neurofibromin. RAS must be prenylated (i.e., farnesylated or geranylgeranylated) to traffic and function properly. Previous studies showed that the anti-growth properties of farnesyl monophosphate prodrug farnesyltransferase inhibitors (FTIs) on human NF1 malignant peripheral nerve sheath tumor (MPNST) cells are potentiated by co-treatment with lovastatin. Unfortunately, such prodrug FTIs have poor aqueous solubility. In this study, we synthesized a series of prodrug FTI polyamidoamine generation 4 (PAMAM G4) dendrimers that compete with farnesyl pyrophosphate for farnesyltransferase (Ftase) and assessed their effects on human NF1 MPNST S462TY cells. The prodrug 3-tert-butylfarnesyl monophosphate FTI-dendrimer (i.e., IG 2) exhibited improved aqueous solubility. Concentrations of IG 2 and lovastatin (as low as 0.1 μM) having little to no effect when used singularly synergistically suppressed cell proliferation, colony formation, and induced N-RAS, RAP1A, and RAB5A deprenylation when used in combination. Combinational treatment had no additive or synergistic effects on the proliferation/viability of immortalized normal rat Schwann cells, primary rat hepatocytes, or normal human mammary epithelial MCF10A cells. Combinational, but not singular, in vivo treatment markedly suppressed the growth of S462TY xenografts established in the sciatic nerves of immune-deficient mice. Hence, prodrug farnesyl monophosphate FTIs can be rendered water-soluble by conjugation to PAMAM G4 dendrimers and exhibit potent anti-tumor activity when combined with clinically achievable statin concentrations.
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Affiliation(s)
- John J. Reiners
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA; (J.J.R.J.); (P.A.M.); (M.G.)
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Patricia A. Mathieu
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA; (J.J.R.J.); (P.A.M.); (M.G.)
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Mary Gargano
- Institute of Environmental Health Sciences, Wayne State University, Detroit, MI 48201, USA; (J.J.R.J.); (P.A.M.); (M.G.)
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Irene George
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; (I.G.); (R.F.B.)
- Currently College of Arts and Sciences, Ohio State University, Columbus, OH 43210, USA
| | - Yimin Shen
- Department of Radiology, Wayne State University, Detroit, MI 48201, USA;
| | - John F. Callaghan
- Department of Pharmacology and Toxicology, East Carolina University, Greenville, NC 27834, USA;
| | - Richard F. Borch
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907, USA; (I.G.); (R.F.B.)
| | - Raymond R. Mattingly
- Department of Pharmacology, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Pharmacology and Toxicology, East Carolina University, Greenville, NC 27834, USA;
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2
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Marchwicka A, Kamińska D, Monirialamdari M, Błażewska KM, Gendaszewska-Darmach E. Protein Prenyltransferases and Their Inhibitors: Structural and Functional Characterization. Int J Mol Sci 2022; 23:ijms23105424. [PMID: 35628237 PMCID: PMC9141697 DOI: 10.3390/ijms23105424] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/07/2022] [Accepted: 05/09/2022] [Indexed: 02/06/2023] Open
Abstract
Protein prenylation is a post-translational modification controlling the localization, activity, and protein–protein interactions of small GTPases, including the Ras superfamily. This covalent attachment of either a farnesyl (15 carbon) or a geranylgeranyl (20 carbon) isoprenoid group is catalyzed by four prenyltransferases, namely farnesyltransferase (FTase), geranylgeranyltransferase type I (GGTase-I), Rab geranylgeranyltransferase (GGTase-II), and recently discovered geranylgeranyltransferase type III (GGTase-III). Blocking small GTPase activity, namely inhibiting prenyltransferases, has been proposed as a potential disease treatment method. Inhibitors of prenyltransferase have resulted in substantial therapeutic benefits in various diseases, such as cancer, neurological disorders, and viral and parasitic infections. In this review, we overview the structure of FTase, GGTase-I, GGTase-II, and GGTase-III and summarize the current status of research on their inhibitors.
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Affiliation(s)
- Aleksandra Marchwicka
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-537 Lodz, Poland; (A.M.); (D.K.)
| | - Daria Kamińska
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-537 Lodz, Poland; (A.M.); (D.K.)
| | - Mohsen Monirialamdari
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland; (M.M.); (K.M.B.)
| | - Katarzyna M. Błażewska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, 90-924 Lodz, Poland; (M.M.); (K.M.B.)
| | - Edyta Gendaszewska-Darmach
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, 90-537 Lodz, Poland; (A.M.); (D.K.)
- Correspondence:
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3
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Gutkowska M, Kaus‐Drobek M, Hoffman‐Sommer M, Małgorzata Pamuła M, Daria Leja A, Perycz M, Lichocka M, Witek A, Wojtas M, Dadlez M, Swiezewska E, Surmacz L. Impact of C-terminal truncations in the Arabidopsis Rab escort protein (REP) on REP-Rab interaction and plant fertility. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1400-1421. [PMID: 34592024 PMCID: PMC9293207 DOI: 10.1111/tpj.15519] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
Lipid anchors are common post-translational modifications for proteins engaged in signaling and vesicular transport in eukaryotic cells. Rab proteins are geranylgeranylated at their C-termini, a modification which is important for their stable binding to lipid bilayers. The Rab escort protein (REP) is an accessory protein of the Rab geranylgeranyl transferase (RGT) complex and it is obligatory for Rab prenylation. While REP-Rab interactions have been studied by biochemical, structural, and genetic methods in animals and yeast, data on the plant RGT complex are still limited. Here we use hydrogen-deuterium exchange mass spectrometry (HDX-MS) to describe the structural basis of plant REP-Rab binding. The obtained results show that the interaction of REP with Rabs is highly dynamic and involves specific structural changes in both partners. In some cases the Rab and REP regions involved in the interaction are molecule-specific, and in other cases they are common for a subset of Rabs. In particular, the C-terminus of REP is not involved in binding of unprenylated Rab proteins in plants, in contrast to mammalian REP. In line with this, a C-terminal REP truncation does not have pronounced phenotypic effects in planta. On the contrary, a complete lack of functional REP leads to male sterility in Arabidopsis: pollen grains develop in the anthers, but they do not germinate efficiently and hence are unable to transmit the mutated allele. The presented data show that the mechanism of action of REP in the process of Rab geranylgeranylation is different in plants than in animals or yeast.
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Affiliation(s)
- Małgorzata Gutkowska
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Magdalena Kaus‐Drobek
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
- Mossakowski Medical Research CentrePolish Academy of Sciencesul. Pawinskiego 5, 02‐106WarsawPoland
| | - Marta Hoffman‐Sommer
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | | | - Anna Daria Leja
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Małgorzata Perycz
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
- Institute of Computer SciencePolish Academy of Sciencesul. Jana Kazimierza 501‐248WarsawPoland
| | - Małgorzata Lichocka
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Agnieszka Witek
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Magdalena Wojtas
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Michał Dadlez
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Ewa Swiezewska
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
| | - Liliana Surmacz
- Institute of Biochemistry and BiophysicsPolish Academy of Sciencesul. Pawinskiego 5a, 02‐106WarsawPoland
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4
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Chang HY, Cheng TH, Wang AHJ. Structure, catalysis, and inhibition mechanism of prenyltransferase. IUBMB Life 2020; 73:40-63. [PMID: 33246356 PMCID: PMC7839719 DOI: 10.1002/iub.2418] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 11/02/2020] [Accepted: 11/14/2020] [Indexed: 12/31/2022]
Abstract
Isoprenoids, also known as terpenes or terpenoids, represent a large family of natural products composed of five‐carbon isopentenyl diphosphate or its isomer dimethylallyl diphosphate as the building blocks. Isoprenoids are structurally and functionally diverse and include dolichols, steroid hormones, carotenoids, retinoids, aromatic metabolites, the isoprenoid side‐chain of ubiquinone, and isoprenoid attached signaling proteins. Productions of isoprenoids are catalyzed by a group of enzymes known as prenyltransferases, such as farnesyltransferases, geranylgeranyltransferases, terpenoid cyclase, squalene synthase, aromatic prenyltransferase, and cis‐ and trans‐prenyltransferases. Because these enzymes are key in cellular processes and metabolic pathways, they are expected to be potential targets in new drug discovery. In this review, six distinct subsets of characterized prenyltransferases are structurally and mechanistically classified, including (1) head‐to‐tail prenyl synthase, (2) head‐to‐head prenyl synthase, (3) head‐to‐middle prenyl synthase, (4) terpenoid cyclase, (5) aromatic prenyltransferase, and (6) protein prenylation. Inhibitors of those enzymes for potential therapies against several diseases are discussed. Lastly, recent results on the structures of integral membrane enzyme, undecaprenyl pyrophosphate phosphatase, are also discussed.
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Affiliation(s)
- Hsin-Yang Chang
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Tien-Hsing Cheng
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
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5
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Bazzicalupo AL, Ruytinx J, Ke Y, Coninx L, Colpaert JV, Nguyen NH, Vilgalys R, Branco S. Fungal heavy metal adaptation through single nucleotide polymorphisms and copy‐number variation. Mol Ecol 2020; 29:4157-4169. [DOI: 10.1111/mec.15618] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 08/19/2020] [Indexed: 12/15/2022]
Affiliation(s)
- Anna L. Bazzicalupo
- Department of Microbiology and Immunology Montana State University Bozeman MT USA
| | - Joske Ruytinx
- Research Group of Microbiology Department of Bioengineering Sciences Vrije Universiteit Brussel Brussels Belgium
| | - Yi‐Hong Ke
- Biology Department Duke University Durham NC USA
| | - Laura Coninx
- Biology Department Centre for Environmental Sciences Hasselt University Diepenbeek Belgium
| | - Jan V. Colpaert
- Biology Department Centre for Environmental Sciences Hasselt University Diepenbeek Belgium
| | - Nhu H. Nguyen
- Department of Tropical Plant and Soil Sciences University of Hawai'i at Mānoa Honolulu HI USA
| | | | - Sara Branco
- Department of Integrative Biology University of Colorado Denver Denver CO USA
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6
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Batkhishig D, Enkhbayar P, Kretsinger RH, Matsushima N. A strong correlation between consensus sequences and unique super secondary structures in leucine rich repeats. Proteins 2020; 88:840-852. [DOI: 10.1002/prot.25876] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 01/03/2020] [Accepted: 01/25/2020] [Indexed: 12/24/2022]
Affiliation(s)
- Dashdavaa Batkhishig
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied SciencesNational University of Mongolia Ulaanbaatar Mongolia
- Department of Physics, School of Mathematics and Natural SciencesMongolian National University of Education Ulaanbaatar Mongolia
| | - Purevjav Enkhbayar
- Laboratory of Bioinformatics and Systems Biology, Department of Information and Computer Science, School of Engineering and Applied SciencesNational University of Mongolia Ulaanbaatar Mongolia
| | | | - Norio Matsushima
- Division of Bioinformatics, Institute of Tandem Repeats Noboribetsu Japan
- Center for Medical Education, Sapporo Medical University Sapporo Japan
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7
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Shirakawa R, Goto-Ito S, Goto K, Wakayama S, Kubo H, Sakata N, Trinh DA, Yamagata A, Sato Y, Masumoto H, Cheng J, Fujimoto T, Fukai S, Horiuchi H. A SNARE geranylgeranyltransferase essential for the organization of the Golgi apparatus. EMBO J 2020; 39:e104120. [PMID: 32128853 DOI: 10.15252/embj.2019104120] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 01/22/2020] [Accepted: 01/31/2020] [Indexed: 01/08/2023] Open
Abstract
Protein prenylation is essential for many cellular processes including signal transduction, cytoskeletal reorganization, and membrane trafficking. Here, we identify a novel type of protein prenyltransferase, which we named geranylgeranyltransferase type-III (GGTase-III). GGTase-III consists of prenyltransferase alpha subunit repeat containing 1 (PTAR1) and the β subunit of RabGGTase. Using a biotinylated geranylgeranyl analogue, we identified the Golgi SNARE protein Ykt6 as a substrate of GGTase-III. GGTase-III transfers a geranylgeranyl group to mono-farnesylated Ykt6, generating doubly prenylated Ykt6. The crystal structure of GGTase-III in complex with Ykt6 provides structural basis for Ykt6 double prenylation. In GGTase-III-deficient cells, Ykt6 remained in a singly prenylated form, and the Golgi SNARE complex assembly was severely impaired. Consequently, the Golgi apparatus was structurally disorganized, and intra-Golgi protein trafficking was delayed. Our findings reveal a fourth type of protein prenyltransferase that generates geranylgeranyl-farnesyl Ykt6. Double prenylation of Ykt6 is essential for the structural and functional organization of the Golgi apparatus.
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Affiliation(s)
- Ryutaro Shirakawa
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Sakurako Goto-Ito
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan
| | - Kota Goto
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Shonosuke Wakayama
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Haremaru Kubo
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Natsumi Sakata
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Duc Anh Trinh
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
| | - Atsushi Yamagata
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan
| | - Yusuke Sato
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan
| | - Hiroshi Masumoto
- Biomedical Research Support Center, Nagasaki University School of Medicine, Nagasaki, Japan
| | - Jinglei Cheng
- Department of Anatomy and Molecular Cell Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toyoshi Fujimoto
- Research Institute for Diseases of Old Age, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shuya Fukai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, Japan
| | - Hisanori Horiuchi
- Department of Molecular and Cellular Biology, Institute of Development, Aging and Cancer, Tohoku University, Sendai, Japan
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8
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Pająk B, Kania E, Gołaszewska A, Orzechowski A. Preliminary Study on Clusterin Protein (sCLU) Expression in PC-12 Cells Overexpressing Wild-Type and Mutated (Swedish) AβPP genes Affected by Non-Steroid Isoprenoids and Water-Soluble Cholesterol. Int J Mol Sci 2019; 20:E1481. [PMID: 30909654 PMCID: PMC6470582 DOI: 10.3390/ijms20061481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 03/04/2019] [Accepted: 03/18/2019] [Indexed: 02/07/2023] Open
Abstract
In this study we attempted to verify the hypothesis that the mevalonate pathway affects amyloid beta precursor protein (AβPP) processing and regulates clusterin protein levels. AβPP expression was monitored by green fluorescence (FL) and Western blot (WB). WB showed soluble amyloid protein precursor alpha (sAβPPα) presence in AβPP-wt cells and Aβ expression in AβPP-sw cells. Nerve growth factor (NGF)-differentiated rat neuronal pheochromocytoma PC-12 cells were untreated/treated with statins alone or together with non-sterol isoprenoids. Co-treatment with mevalonate, dolichol, ubiquinol, farnesol, geranylgeraniol, or water-soluble cholesterol demonstrated statin-dependent neurotoxicity resulted from the attenuated activity of mevalonate pathway rather than lower cholesterol level. Atorvastatin (50 μM) or simvastatin (50 μM) as well as cholesterol chelator methyl-β-cyclodextrin (0.2 mM) diminished cell viability (p < 0.05) and clusterin levels. Interestingly, co-treatment with mevalonate, dolichol, ubiquinol, farnesol, geranylgeraniol, or water-soluble cholesterol stimulated (p < 0.05) clusterin expression. Effects of non-sterol isoprenoids, but not water soluble cholesterol (Chol-PEG), were the most significant in mock-transfected cells. Geranylgeraniol (GGOH) overcame atorvastatin (ATR)-dependent cytotoxicity. This effect does not seem to be dependent on clusterin, as its level became lower after GGOH. The novelty of these findings is that they show that the mevalonate (MEV) pathway rather than cholesterol itself plays an important role in clusterin expression levels. In mock-transfected, rather than in AβPP-overexpressing cells, GGOH/farnesol (FOH) exerted a protective effect. Thus, protein prenylation with GGOH/FOH might play substantial role in neuronal cell survival.
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Affiliation(s)
- Beata Pająk
- Independent Laboratory of Genetics and Molecular Biology, Kaczkowski Military Institute of Hygiene and Epidemiology, Kozielska 4, 01-163 Warsaw, Poland.
| | - Elżbieta Kania
- Tumor Cell Death Laboratory, Cancer Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK.
| | - Anita Gołaszewska
- Department of Neuroendocrinology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland.
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences ⁻ SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland.
| | - Arkadiusz Orzechowski
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences ⁻ SGGW, Nowoursynowska 159, 02-776 Warsaw, Poland.
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9
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Jiang H, Zhang X, Chen X, Aramsangtienchai P, Tong Z, Lin H. Protein Lipidation: Occurrence, Mechanisms, Biological Functions, and Enabling Technologies. Chem Rev 2018; 118:919-988. [PMID: 29292991 DOI: 10.1021/acs.chemrev.6b00750] [Citation(s) in RCA: 275] [Impact Index Per Article: 45.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Protein lipidation, including cysteine prenylation, N-terminal glycine myristoylation, cysteine palmitoylation, and serine and lysine fatty acylation, occurs in many proteins in eukaryotic cells and regulates numerous biological pathways, such as membrane trafficking, protein secretion, signal transduction, and apoptosis. We provide a comprehensive review of protein lipidation, including descriptions of proteins known to be modified and the functions of the modifications, the enzymes that control them, and the tools and technologies developed to study them. We also highlight key questions about protein lipidation that remain to be answered, the challenges associated with answering such questions, and possible solutions to overcome these challenges.
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Affiliation(s)
- Hong Jiang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Xiaoyu Zhang
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Xiao Chen
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Pornpun Aramsangtienchai
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Zhen Tong
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
| | - Hening Lin
- Howard Hughes Medical Institute, Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States
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10
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Shi W, Zeng Q, Kunkel BN, Running MP. Arabidopsis Rab Geranylgeranyltransferases Demonstrate Redundancy and Broad Substrate Specificity in Vitro. J Biol Chem 2015; 291:1398-410. [PMID: 26589801 DOI: 10.1074/jbc.m115.673491] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Indexed: 11/06/2022] Open
Abstract
Posttranslational lipid modifications mediate the membrane attachment of Rab GTPases, facilitating their function in regulating intracellular vesicular trafficking. In Arabidopsis, most Rab GTPases have two C-terminal cysteines and potentially can be double-geranylgeranylated by heterodimeric Rab geranylgeranyltransferases (Rab-GGTs). Genes encoding two putative α subunits and two putative β subunits of Rab-GGTs have been annotated in the Arabidopsis thaliana genome, but little is known about Rab-GGT activity in Arabidopsis. In this study, we demonstrate that four different heterodimers can be formed between putative Arabidopsis Rab-GGT α subunits RGTA1/RGTA2 and β subunits RGTB1/RGTB2, but only RGTA1·RGTB1 and RGTA1·RGTB2 exhibit bona fide Rab-GGT activity, and they are biochemically redundant in vitro. We hypothesize that RGTA2 function might be disrupted by a 12-amino acid insertion in a conserved motif. We present evidence that Arabidopsis Rab-GGTs may have preference for prenylation of C-terminal cysteines in particular positions. We also demonstrate that Arabidopsis Rab-GGTs can not only prenylate a great variety of Rab GTPases in the presence of Rab escort protein but, unlike Rab-GGT in yeast and mammals, can also prenylate certain non-Rab GTPases independently of Rab escort protein. Our findings may help to explain some of the phenotypes of Arabidopsis protein prenyltransferase mutants.
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Affiliation(s)
- Wan Shi
- From the Department of Biology, Washington University, Saint Louis, Missouri 63130
| | - Qin Zeng
- the Donald Danforth Plant Science Center, Saint Louis, Missouri 63132, and
| | - Barbara N Kunkel
- From the Department of Biology, Washington University, Saint Louis, Missouri 63130
| | - Mark P Running
- the Department of Biology, University of Louisville, Louisville, Kentucky 40292
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11
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Abstract
In pathogen resistant plants, solvent-exposed residues in the leucine-rich repeat (LRR) proteins are thought to mediate resistance by recognizing plant pathogen elicitors. In potato, the gene Gro1-4 confers resistance to Globodera rostochiensis. The investigation of variability in different copies of this gene represents a good model for the verification of positive selection mechanisms. Two datasets of Gro1 LRR sequences were constructed, one derived from the Gro1-4 gene, belonging to different cultivated and wild Solanum species, and the other belonging to paralogues of a resistant genotype. Analysis of nonsynonymous to synonymous substitution rates (K(a)/K(s)) highlighted 14 and six amino acids with K(a)/K(s) >1 in orthologue and paralogue datasets, respectively. Selection analysis revealed that the leucine-rich regions accumulate variability in a very specific way, and we found that some combinations of amino acids in these sites might be involved in pathogen recognition. The results confirm previous studies on positive selection in the LRR domain of R protein in Arabidopsis and other model plants and extend these to wild Solanum species. Moreover, positively selected sites in the Gro1 LRR domain show that coevolution mainly occurred in two regions on the internal surface of the three-dimensional horseshoe structure of the domain, albeit with different evolutionary forces between paralogues and orthologues.
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12
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Wieninger SA, Ullmann GM. CoMoDo: Identifying Dynamic Protein Domains Based on Covariances of Motion. J Chem Theory Comput 2015; 11:2841-54. [DOI: 10.1021/acs.jctc.5b00150] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Silke A. Wieninger
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, 95447 Bayreuth, Germany
| | - G. Matthias Ullmann
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, 95447 Bayreuth, Germany
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13
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Palsuledesai CC, Distefano MD. Protein prenylation: enzymes, therapeutics, and biotechnology applications. ACS Chem Biol 2015; 10:51-62. [PMID: 25402849 PMCID: PMC4301080 DOI: 10.1021/cb500791f] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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Protein
prenylation is a ubiquitous covalent post-translational modification
found in all eukaryotic cells, comprising attachment of either a farnesyl
or a geranylgeranyl isoprenoid. It is essential for the proper cellular
activity of numerous proteins, including Ras family GTPases and heterotrimeric
G-proteins. Inhibition of prenylation has been extensively investigated
to suppress the activity of oncogenic Ras proteins to achieve antitumor
activity. Here, we review the biochemistry of the prenyltransferase
enzymes and numerous isoprenoid analogs synthesized to investigate
various aspects of prenylation and prenyltransferases. We also give
an account of the current status of prenyltransferase inhibitors as
potential therapeutics against several diseases including cancers,
progeria, aging, parasitic diseases, and bacterial and viral infections.
Finally, we discuss recent progress in utilizing protein prenylation
for site-specific protein labeling for various biotechnology applications.
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Affiliation(s)
- Charuta C. Palsuledesai
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Mark D. Distefano
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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14
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Wotske M, Wu Y, Wolters DA. Liquid Chromatographic Analysis and Mass Spectrometric Identification of Farnesylated Peptides. Anal Chem 2012; 84:6848-55. [DOI: 10.1021/ac301437m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Marina Wotske
- Department of Analytical Chemistry, Ruhr-University of Bochum, Bochum, Germany
| | - Yaowen Wu
- Department of Physical Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund,
Germany
| | - Dirk A. Wolters
- Department of Analytical Chemistry, Ruhr-University of Bochum, Bochum, Germany
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15
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Gutkowska M, Swiezewska E. Structure, regulation and cellular functions of Rab geranylgeranyl transferase and its cellular partner Rab Escort Protein. Mol Membr Biol 2012; 29:243-56. [DOI: 10.3109/09687688.2012.693211] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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16
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Deraeve C, Guo Z, Bon RS, Blankenfeldt W, DiLucrezia R, Wolf A, Menninger S, Stigter EA, Wetzel S, Choidas A, Alexandrov K, Waldmann H, Goody RS, Wu YW. Psoromic acid is a selective and covalent Rab-prenylation inhibitor targeting autoinhibited RabGGTase. J Am Chem Soc 2012; 134:7384-91. [PMID: 22480322 DOI: 10.1021/ja211305j] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Post-translational attachment of geranylgeranyl isoprenoids to Rab GTPases, the key organizers of intracellular vesicular transport, is essential for their function. Rab geranylgeranyl transferase (RabGGTase) is responsible for prenylation of Rab proteins. Recently, RabGGTase inhibitors have been proposed to be potential therapeutics for treatment of cancer and osteoporosis. However, the development of RabGGTase selective inhibitors is complicated by its structural and functional similarity to other protein prenyltransferases. Herein we report identification of the natural product psoromic acid (PA) that potently and selectively inhibits RabGGTase with an IC(50) of 1.3 μM. Structure-activity relationship analysis suggested a minimal structure involving the depsidone core with a 3-hydroxyl and 4-aldehyde motif for binding to RabGGTase. Analysis of the crystal structure of the RabGGTase:PA complex revealed that PA forms largely hydrophobic interactions with the isoprenoid binding site of RabGGTase and that it attaches covalently to the N-terminus of the α subunit. We found that in contrast to other protein prenyltransferases, RabGGTase is autoinhibited through N-terminal (α)His2 coordination with the catalytic zinc ion. Mutation of (α)His dramatically enhances the reaction rate, indicating that the activity of RabGGTase is likely regulated in vivo. The covalent binding of PA to the N-terminus of the RabGGTase α subunit seems to potentiate its interaction with the active site and explains the selectivity of PA for RabGGTase. Therefore, psoromic acid provides a new starting point for the development of selective RabGGTase inhibitors.
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Affiliation(s)
- Céline Deraeve
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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17
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Fu TM, Almqvist J, Liang YH, Li L, Huang Y, Su XD. Crystal structures of cobalamin-independent methionine synthase (MetE) from Streptococcus mutans: a dynamic zinc-inversion model. J Mol Biol 2011; 412:688-97. [PMID: 21840320 DOI: 10.1016/j.jmb.2011.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 08/01/2011] [Accepted: 08/02/2011] [Indexed: 11/17/2022]
Abstract
Cobalamin-independent methionine synthase (MetE) catalyzes the direct transfer of a methyl group from methyltetrahydrofolate to l-homocysteine to form methionine. Previous studies have shown that the MetE active site coordinates a zinc atom, which is thought to act as a Lewis acid and plays a role in the activation of thiol. Extended X-ray absorption fine structure studies and mutagenesis experiments identified the zinc-binding site in MetE from Escherichia coli. Further structural investigations of MetE from Thermotoga maritima lead to the proposition of two models: "induced fit" and "dynamic equilibrium", to account for the catalytic mechanisms of MetE. Here, we present crystal structures of oxidized and zinc-replete MetE from Streptococcus mutans at the physiological pH. The structures reveal that zinc is mobile in the active center and has the possibility to invert even in the absence of homocysteine. These structures provide evidence for the dynamic equilibrium model.
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Affiliation(s)
- Tian-Min Fu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, PR China
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18
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Placzek AT, Krzysiak AJ, Gibbs RA. Chemical Probes of Protein Prenylation. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/b978-0-12-415922-8.00005-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
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19
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Sasaki D, Fujihashi M, Okuyama N, Kobayashi Y, Noike M, Koyama T, Miki K. Crystal structure of heterodimeric hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 reveals that the small subunit is directly involved in the product chain length regulation. J Biol Chem 2010; 286:3729-40. [PMID: 21068379 DOI: 10.1074/jbc.m110.147991] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Hexaprenyl diphosphate synthase from Micrococcus luteus B-P 26 (Ml-HexPPs) is a heterooligomeric type trans-prenyltransferase catalyzing consecutive head-to-tail condensations of three molecules of isopentenyl diphosphates (C(5)) on a farnesyl diphosphate (FPP; C(15)) to form an (all-E) hexaprenyl diphosphate (HexPP; C(30)). Ml-HexPPs is known to function as a heterodimer of two different subunits, small and large subunits called HexA and HexB, respectively. Compared with homooligomeric trans-prenyltransferases, the molecular mechanism of heterooligomeric trans-prenyltransferases is not yet clearly understood, particularly with respect to the role of the small subunits lacking the catalytic motifs conserved in most known trans-prenyltransferases. We have determined the crystal structure of Ml-HexPPs both in the substrate-free form and in complex with 7,11-dimethyl-2,6,10-dodecatrien-1-yl diphosphate ammonium salt (3-DesMe-FPP), an analog of FPP. The structure of HexB is composed of mostly antiparallel α-helices joined by connecting loops. Two aspartate-rich motifs (designated the first and second aspartate-rich motifs) and the other characteristic motifs in HexB are located around the diphosphate part of 3-DesMe-FPP. Despite the very low amino acid sequence identity and the distinct polypeptide chain lengths between HexA and HexB, the structure of HexA is quite similar to that of HexB. The aliphatic tail of 3-DesMe-FPP is accommodated in a large hydrophobic cleft starting from HexB and penetrating to the inside of HexA. These structural features suggest that HexB catalyzes the condensation reactions and that HexA is directly involved in the product chain length control in cooperation with HexB.
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Affiliation(s)
- Daisuke Sasaki
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, Kyoto 606-8502, Japan
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20
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Nguyen UTT, Goody RS, Alexandrov K. Understanding and exploiting protein prenyltransferases. Chembiochem 2010; 11:1194-201. [PMID: 20432425 DOI: 10.1002/cbic.200900727] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Uyen T T Nguyen
- Laboratory of Synthetic Protein Chemistry, The Rockefeller University, New York, NY 10065, USA
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21
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Detecting internally symmetric protein structures. BMC Bioinformatics 2010; 11:303. [PMID: 20525292 PMCID: PMC2894822 DOI: 10.1186/1471-2105-11-303] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Accepted: 06/03/2010] [Indexed: 11/30/2022] Open
Abstract
Background Many functional proteins have a symmetric structure. Most of these are multimeric complexes, which are made of non-symmetric monomers arranged in a symmetric manner. However, there are also a large number of proteins that have a symmetric structure in the monomeric state. These internally symmetric proteins are interesting objects from the point of view of their folding, function, and evolution. Most algorithms that detect the internally symmetric proteins depend on finding repeating units of similar structure and do not use the symmetry information. Results We describe a new method, called SymD, for detecting symmetric protein structures. The SymD procedure works by comparing the structure to its own copy after the copy is circularly permuted by all possible number of residues. The procedure is relatively insensitive to symmetry-breaking insertions and deletions and amplifies positive signals from symmetry. It finds 70% to 80% of the TIM barrel fold domains in the ASTRAL 40 domain database and 100% of the beta-propellers as symmetric. More globally, 10% to 15% of the proteins in the ASTRAL 40 domain database may be considered symmetric according to this procedure depending on the precise cutoff value used to measure the degree of perfection of the symmetry. Symmetrical proteins occur in all structural classes and can have a closed, circular structure, a cylindrical barrel-like structure, or an open, helical structure. Conclusions SymD is a sensitive procedure for detecting internally symmetric protein structures. Using this procedure, we estimate that 10% to 15% of the known protein domains may be considered symmetric. We also report an initial, overall view of the types of symmetries and symmetric folds that occur in the protein domain structure universe.
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22
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Hála M, Soukupová H, Synek L, Zárský V. Arabidopsis RAB geranylgeranyl transferase beta-subunit mutant is constitutively photomorphogenic, and has shoot growth and gravitropic defects. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 62:615-27. [PMID: 20180921 DOI: 10.1111/j.1365-313x.2010.04172.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
RAB GTPases are important directional regulators of intracellular vesicle transport. Membrane localization of RAB GTPases is mediated by C-terminal double geranylgeranylation. This post-translational modification is catalyzed by the alpha-beta-heterodimer catalytic core of RAB geranylgeranyl transferase (RAB-GGT), which cooperates with the RAB escort protein (REP) that presents a nascent RAB. Here, we show that RAB-geranylgeranylation activity is significantly reduced in two homozygous mutants of the major Arabidopsis beta-subunit of RAB-GGT (AtRGTB1), resulting in unprenylated RAB GTPases accumulation in the cytoplasm. Both endocytosis and exocytosis are downregulated in rgtb1 homozygotes defective in shoot growth and morphogenesis. Root gravitropism is normal in rgtb1 roots, but is significantly compromised in shoots. Mutants are defective in etiolation and show constitutive photomorphogenic phenotypes that cannot be rescued by brassinosteroid treatment, similarly to the det3 mutant that is also defective in the secretory pathway. Transcriptomic analysis revealed an upregulation of specific RAB GTPases in etiolated wild-type plants. Taken together, these data suggest that the downregulation of the secretory pathway is interpreted as a photomorphogenic signal in Arabidopsis.
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Affiliation(s)
- Michal Hála
- Institute of Experimental Botany, Academy of Sciences of the Czech Republic, Rozvojova 263, 165 02 Prague 6, Czech Republic
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23
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Hovlid ML, Edelstein RL, Henry O, Ochocki J, DeGraw A, Lenevich S, Talbot T, Young VG, Hruza AW, Lopez-Gallego F, Labello NP, Strickland CL, Schmidt-Dannert C, Distefano MD. Synthesis, properties, and applications of diazotrifluropropanoyl-containing photoactive analogs of farnesyl diphosphate containing modified linkages for enhanced stability. Chem Biol Drug Des 2010; 75:51-67. [PMID: 19954434 DOI: 10.1111/j.1747-0285.2009.00914.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Photoactive analogs of farnesyl diphosphate (FPP) are useful probes in studies of enzymes that employ this molecule as a substrate. Here, we describe the preparation and properties of two new FPP analogs that contain diazotrifluoropropanoyl photophores linked to geranyl diphosphate via amide or ester linkages. The amide-linked analog (3) was synthesized in 32P-labeled form from geraniol in seven steps. Experiments with Saccharomyces cerevisiae protein farnesyltransferase (ScPFTase) showed that 3 is an alternative substrate for the enzyme. Photolysis experiments with [(32)P]3 demonstrate that this compound labels the beta-subunits of both farnesyltransferase and geranylgeranyltransferase (types 1 and 2). However, the amide-linked probe 3 undergoes a rearrangement to a photochemically unreactive isomeric triazolone upon long term storage making it inconvenient to use. To address this stability issue, the ester-linked analog 4 was prepared in six steps from geraniol. Computational analysis and X-ray crystallographic studies suggest that 4 binds to protein farnesyl transferase (PFTase) in a similar fashion as FPP. Compound 4 is also an alternative substrate for PFTase, and a 32P-labeled form selectively photocrosslinks the beta-subunit of ScPFTase as well as E. coli farnesyldiphosphate synthase and a germacrene-producing sesquiterpene synthase from Nostoc sp. strain PCC7120 (a cyanobacterial source). Finally, nearly exclusive labeling of ScPFTase in crude E. coli extract was observed, suggesting that [32P]4 manifests significant selectivity and should hence be useful for identifying novel FPP-utilizing enzymes in crude protein preparations.
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Affiliation(s)
- Marisa L Hovlid
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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24
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Chan LN, Hart C, Guo L, Nyberg T, Davies BSJ, Fong LG, Young SG, Agnew BJ, Tamanoi F. A novel approach to tag and identify geranylgeranylated proteins. Electrophoresis 2010; 30:3598-606. [PMID: 19784953 DOI: 10.1002/elps.200900259] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A recently developed proteomic strategy, the "GG-azide"-labeling approach, is described for the detection and proteomic analysis of geranylgeranylated proteins. This approach involves metabolic incorporation of a synthetic azido-geranylgeranyl analog and chemoselective derivatization of azido-geranylgeranyl-modified proteins by the "click" chemistry, using a tetramethylrhodamine-alkyne. The resulting conjugated proteins can be separated by 1-D or 2-D and pH fractionation, and detected by fluorescence imaging. This method is compatible with downstream LC-MS/MS analysis. Proteomic analysis of conjugated proteins by this approach identified several known geranylgeranylated proteins as well as Rap2c, a novel member of the Ras family. Furthermore, prenylation of progerin in mouse embryonic fibroblast cells was examined using this approach, demonstrating that this strategy can be used to study prenylation of specific proteins. The "GG-azide"-labeling approach provides a new tool for the detection and proteomic analysis of geranylgeranylated proteins, and it can readily be extended to other post-translational modifications.
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Affiliation(s)
- Lai N Chan
- Departments of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095-1489, USA
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25
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Hindle KL, Bella J, Lovell SC. Quantitative analysis and prediction of curvature in leucine-rich repeat proteins. Proteins 2009; 77:342-58. [PMID: 19452560 DOI: 10.1002/prot.22440] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Leucine-rich repeat (LRR) proteins form a large and diverse family. They have a wide range of functions most of which involve the formation of protein-protein interactions. All known LRR structures form curved solenoids, although there is large variation in their curvature. It is this curvature that determines the shape and dimensions of the inner space available for ligand binding. Unfortunately, large-scale parameters such as the overall curvature of a protein domain are extremely difficult to predict. Here, we present a quantitative analysis of determinants of curvature of this family. Individual repeats typically range in length between 20 and 30 residues and have a variety of secondary structures on their convex side. The observed curvature of the LRR domains correlates poorly with the lengths of their individual repeats. We have, therefore, developed a scoring function based on the secondary structure of the convex side of the protein that allows prediction of the overall curvature with a high degree of accuracy. We also demonstrate the effectiveness of this method in selecting a suitable template for comparative modeling. We have developed an automated, quantitative protocol that can be used to predict accurately the curvature of leucine-rich repeat proteins of unknown structure from sequence alone. This protocol is available as an online resource at http://www.bioinf.manchester.ac.uk/curlrr/.
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Affiliation(s)
- K Lauren Hindle
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK
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26
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Baron RA, Tavaré R, Figueiredo AC, Błazewska KM, Kashemirov BA, McKenna CE, Ebetino FH, Taylor A, Rogers MJ, Coxon FP, Seabra MC. Phosphonocarboxylates inhibit the second geranylgeranyl addition by Rab geranylgeranyl transferase. J Biol Chem 2008; 284:6861-8. [PMID: 19074143 PMCID: PMC2652301 DOI: 10.1074/jbc.m806952200] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rab geranylgeranyl transferase (RGGT) catalyzes the post-translational
geranylgeranyl (GG) modification of (usually) two C-terminal cysteines in Rab
GTPases. Here we studied the mechanism of the Rab geranylgeranylation reaction
by bisphosphonate analogs in which one phosphonate group is replaced by a
carboxylate (phosphonocarboxylate, PC). The phosphonocarboxylates used were
3-PEHPC, which was previously reported, and
2-hydroxy-3-imidazo[1,2-a]pyridin-3-yl-2-phosphonopropionic
acid ((+)-3-IPEHPC), a >25-fold more potent related compound as measured by
both IC50 and Ki.(+)-3-IPEHPC behaves as a
mixed-type inhibitor with respect to GG pyrophosphate (GGPP) and an
uncompetitive inhibitor with respect to Rab substrates. We propose that
phosphonocarboxylates prevent only the second GG transfer onto Rabs based on
the following evidence. First, geranylgeranylation of Rab proteins ending with
a single cysteine motif such as CAAX, is not affected by the
inhibitors, either in vitro or in vivo. Second, the addition
of an -AAX sequence onto Rab-CC proteins protects the substrate from
inhibition by the inhibitors. Third, we demonstrate directly that in the
presence of (+)-3-IPEHPC, Rab-CC and Rab-CXC proteins are modified by
only a single GG addition. The presence of (+)-3-IPEHPC resulted in a
preference for the Rab N-terminal cysteine to be modified first, suggesting an
order of cysteine geranylgeranylation in RGGT catalysis. Our results further
suggest that the inhibitor binds to a site distinct from the GGPP-binding site
on RGGT. We suggest that phosphonocarboxylate inhibitors bind to a GG-cysteine
binding site adjacent to the active site, which is necessary to align the
mono-GG-Rab for the second GG addition. These inhibitors may represent a novel
therapeutic approach in Rab-mediated diseases.
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Affiliation(s)
- Rudi A Baron
- Molecular Medicine, National Heart and Lung Institute, Imperial College London, London SW7 2AZ, United Kingdom
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27
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Levisson M, Sun L, Hendriks S, Swinkels P, Akveld T, Bultema JB, Barendregt A, van den Heuvel RHH, Dijkstra BW, van der Oost J, Kengen SWM. Crystal structure and biochemical properties of a novel thermostable esterase containing an immunoglobulin-like domain. J Mol Biol 2008; 385:949-62. [PMID: 19013466 DOI: 10.1016/j.jmb.2008.10.075] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2008] [Revised: 10/24/2008] [Accepted: 10/27/2008] [Indexed: 11/26/2022]
Abstract
Comparative analysis of the genome of the hyperthermophilic bacterium Thermotoga maritima revealed a hypothetical protein (EstA) with typical esterase features. The EstA protein was functionally produced in Escherichia coli and purified to homogeneity. It indeed displayed esterase activity with optima at or above 95 degrees C and at pH 8.5, with a preference for esters with short acyl chains (C2-C10). Its 2.6-A-resolution crystal structure revealed a classical alpha/beta hydrolase domain with a catalytic triad consisting of a serine, an aspartate, and a histidine. EstA is irreversibly inhibited by the organophosphate paraoxon. A 3.0-A-resolution structure confirmed that this inhibitor binds covalently to the catalytic serine residue of EstA. Remarkably, the structure also revealed the presence of an N-terminal immunoglobulin (Ig)-like domain, which is unprecedented among esterases. EstA forms a hexamer both in the crystal and in solution. Electron microscopy showed that the hexamer in solution is identical with the hexamer in the crystal, which is formed by two trimers, with the N-terminal domains facing each other. Mutational studies confirmed that residues Phe89, Phe112, Phe116, Phe246, and Trp377 affect enzyme activity. A truncated mutant of EstA, in which the Ig-like domain was removed, showed only 5% of wild-type activity, had lower thermostability, and failed to form hexamers. These data suggest that the Ig-like domain plays an important role in the enzyme multimerization and activity of EstA.
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Affiliation(s)
- Mark Levisson
- Laboratory of Microbiology, Department of Agrotechnology and Food Sciences, Wageningen University, Dreijenplein 10, 6703 HB Wageningen, The Netherlands.
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28
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Pavkov T, Egelseer EM, Tesarz M, Svergun DI, Sleytr UB, Keller W. The structure and binding behavior of the bacterial cell surface layer protein SbsC. Structure 2008; 16:1226-37. [PMID: 18682224 DOI: 10.1016/j.str.2008.05.012] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2008] [Revised: 04/30/2008] [Accepted: 05/01/2008] [Indexed: 10/21/2022]
Abstract
Surface layers (S-layers) comprise the outermost cell envelope component of most archaea and many bacteria. Here we present the structure of the bacterial S-layer protein SbsC from Geobacillus stearothermophilus, showing a very elongated and flexible molecule, with strong and specific binding to the secondary cell wall polymer (SCWP). The crystal structure of rSbsC((31-844)) revealed a novel fold, consisting of six separate domains, which are connected by short flexible linkers. The N-terminal domain exhibits positively charged residues regularly spaced along the putative ligand binding site matching the distance of the negative charges on the extended SCWP. Upon SCWP binding, a considerable stabilization of the N-terminal domain occurs. These findings provide insight into the processes of S-layer attachment to the underlying cell wall and self-assembly, and also accommodate the observed mechanical strength, the polarity of the S-layer, and the pronounced requirement for surface flexibility inherent to cell growth and division.
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Affiliation(s)
- Tea Pavkov
- Institute of Molecular Biosciences, Structural Biology, University of Graz, Humboldtsrasse 50/3, 8010 Graz, Austria
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29
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Chavas LM, Ihara K, Kawasaki M, Torii S, Uejima T, Kato R, Izumi T, Wakatsuki S. Elucidation of Rab27 Recruitment by Its Effectors: Structure of Rab27a Bound to Exophilin4/Slp2-a. Structure 2008; 16:1468-77. [DOI: 10.1016/j.str.2008.07.015] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2008] [Revised: 07/18/2008] [Accepted: 07/21/2008] [Indexed: 01/03/2023]
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30
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Structures of RabGGTase-substrate/product complexes provide insights into the evolution of protein prenylation. EMBO J 2008; 27:2444-56. [PMID: 18756270 DOI: 10.1038/emboj.2008.164] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2008] [Accepted: 07/28/2008] [Indexed: 11/08/2022] Open
Abstract
Post-translational isoprenylation of proteins is carried out by three related enzymes: farnesyltransferase, geranylgeranyl transferase-I, and Rab geranylgeranyl transferase (RabGGTase). Despite the fact that the last one is responsible for the largest number of individual protein prenylation events in the cell, no structural information is available on its interaction with substrates and products. Here, we present structural and biophysical analyses of RabGGTase in complex with phosphoisoprenoids as well as with the prenylated peptides that mimic the C terminus of Rab7 GTPase. The data demonstrate that, unlike other protein prenyl transferases, both RabGGTase and its substrate RabGTPases completely 'outsource' their specificity for each other to an accessory subunit, the Rab escort protein (REP). REP mediates the placement of the C terminus of RabGTPase into the active site of RabGGTase through a series protein-protein interactions of decreasing strength and selectivity. This arrangement enables RabGGTase to prenylate any cysteine-containing sequence. On the basis of our structural and thermodynamic data, we propose that RabGGTase has evolved from a GGTase-I-like molecule that 'learned' to interact with a recycling factor (GDI) that, in turn, eventually gave rise to REP.
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Abstract
Zinc bioinorganic chemistry has emphasized the role of the metal ion on the structure and function of the protein. There is, more recently, an increasing appreciation of the role of zinc proteins in a variety of human diseases. This critical review, aimed at both bioinorganic and medicinal chemists, shows how apparently widely-diverging diseases share the common mechanistic approaches of targeting the essential function of the metal ion to inhibit activity. Protein structure and function is briefly summarized in the context of its clinical relevance. The status of current and potential inhibitors is discussed along with the prospects for future developments (162 references).
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Affiliation(s)
- A I Anzellotti
- Department of Chemistry, Virginia Commonwealth University, PO Box 842006, Richmond, VA23284, USA
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Metal active site elasticity linked to activation of homocysteine in methionine synthases. Proc Natl Acad Sci U S A 2008; 105:3286-91. [PMID: 18296644 DOI: 10.1073/pnas.0709960105] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Enzymes possessing catalytic zinc centers perform a variety of fundamental processes in nature, including methyl transfer to thiols. Cobalamin-independent (MetE) and cobalamin-dependent (MetH) methionine synthases are two such enzyme families. Although they perform the same net reaction, transfer of a methyl group from methyltetrahydrofolate to homocysteine (Hcy) to form methionine, they display markedly different catalytic strategies, modular organization, and active site zinc centers. Here we report crystal structures of zinc-replete MetE and MetH, both in the presence and absence of Hcy. Structural investigation of the catalytic zinc sites of these two methyltransferases reveals an unexpected inversion of zinc geometry upon binding of Hcy and displacement of an endogenous ligand in both enzymes. In both cases a significant movement of the zinc relative to the protein scaffold accompanies inversion. These structures provide new information on the activation of thiols by zinc-containing enzymes and have led us to propose a paradigm for the mechanism of action of the catalytic zinc sites in these and related methyltransferases. Specifically, zinc is mobile in the active sites of MetE and MetH, and its dynamic nature helps facilitate the active site conformational changes necessary for thiol activation and methyl transfer.
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Watanabe M, Fiji HDG, Guo L, Chan L, Kinderman SS, Slamon DJ, Kwon O, Tamanoi F. Inhibitors of protein geranylgeranyltransferase I and Rab geranylgeranyltransferase identified from a library of allenoate-derived compounds. J Biol Chem 2008; 283:9571-9. [PMID: 18230616 DOI: 10.1074/jbc.m706229200] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Protein geranylgeranylation is critical for the function of a number of proteins such as RhoA, Rac, and Rab. Protein geranylgeranyltransferase I (GGTase-I) and Rab geranylgeranyltransferase (RabGGTase) catalyze these modifications. In this work, we first describe the identification and characterization of small molecule inhibitors of GGTase-I (GGTI) with two novel scaffolds from a library consisting of allenoate-derived compounds. These compounds exhibit specific inhibition of GGTase-I and act by competing with a substrate protein. Derivatization of a carboxylic acid emanating from the core ring of one of the GGTI compounds dramatically improves their cellular activity. The improved GGTI compounds inhibit proliferation of a variety of human cancer cell lines and cause G(1) cell cycle arrest and induction of p21(CIP1/WAF1). We also report the identification of novel small molecule inhibitors of RabGGTase. These compounds were identified first by screening our GGTI compounds for those that also exhibited RabGGTase inhibition. This led to the discovery of a common structural feature for RabGGTase inhibitors: the presence of a characteristic six-atom aliphatic tail attached to the penta-substituted pyrrolidine core. Further screening led to the identification of compounds with preferential inhibition of RabGGTase. These compounds inhibit RabGGTase activity by competing with the substrate protein. These novel compounds may provide valuable reagents to study protein geranylgeranylation.
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Affiliation(s)
- Masaru Watanabe
- Microbiology, Immunology, and Molecular Genetics, Jonsson Comprehensive Cancer Center, University of California-Los Angeles, 609 Charles E. Young Drive, Los Angeles, CA 90095, USA
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Raposo G, Marks MS. Melanosomes--dark organelles enlighten endosomal membrane transport. Nat Rev Mol Cell Biol 2007; 8:786-97. [PMID: 17878918 PMCID: PMC2786984 DOI: 10.1038/nrm2258] [Citation(s) in RCA: 379] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Melanosomes are tissue-specific lysosome-related organelles of pigment cells in which melanins are synthesized and stored. Analyses of the trafficking and fate of melanosomal components are beginning to reveal how melanosomes are formed through novel pathways from early endosomal intermediates. These studies unveil generalized structural and functional modifications of the endosomal system in specialized cells, and provide unexpected insights into the biogenesis of multivesicular bodies and how compartmentalization regulates protein refolding. Moreover, genetic disorders that affect the biogenesis of melanosomes and other lysosome-related organelles have shed light onto the molecular machinery that controls specialized endosomal sorting events.
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Affiliation(s)
- Graça Raposo
- Institut Curie, Centre de Recherche, Paris, F-75248 France.
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Rasteiro R, Pereira-Leal JB. Multiple domain insertions and losses in the evolution of the Rab prenylation complex. BMC Evol Biol 2007; 7:140. [PMID: 17705859 PMCID: PMC1994686 DOI: 10.1186/1471-2148-7-140] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2007] [Accepted: 08/17/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Rab proteins are regulators of vesicular trafficking, requiring a lipid modification for proper function, prenylation of C-terminal cysteines. This is catalysed by a complex of a catalytic heterodimer (Rab Geranylgeranyl Transferase - RabGGTase) and an accessory protein (Rab Escort Protein. REP). Components of this complex display domain insertions relative to paralogous proteins. The function of these inserted domains is unclear. RESULTS We profiled the domain architecture of the components of the Rab prenylation complex in evolution. We identified the orthologues of the components of the Rab prenylation machinery in 43 organisms, representing the crown eukaryotic groups. We characterize in detail the domain structure of all these components and the phylogenetic relationships between the individual domains. CONCLUSION We found different domain insertions in different taxa, in alpha-subunits of RGGTase and REP. Our results suggest that there were multiple insertions, expansions and contractions in the evolution of this prenylation complex.
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Affiliation(s)
- Rita Rasteiro
- Instituto Gulbenkian de Ciência, Apartado 14, P-2781-901 Oeiras Portugal
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36
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Matsushima N, Tanaka T, Enkhbayar P, Mikami T, Taga M, Yamada K, Kuroki Y. Comparative sequence analysis of leucine-rich repeats (LRRs) within vertebrate toll-like receptors. BMC Genomics 2007; 8:124. [PMID: 17517123 PMCID: PMC1899181 DOI: 10.1186/1471-2164-8-124] [Citation(s) in RCA: 266] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Accepted: 05/21/2007] [Indexed: 12/15/2022] Open
Abstract
Background Toll-like receptors (TLRs) play a central role in innate immunity. TLRs are membrane glycoproteins and contain leucine rich repeat (LRR) motif in the ectodomain. TLRs recognize and respond to molecules such as lipopolysaccharide, peptidoglycan, flagellin, and RNA from bacteria or viruses. The LRR domains in TLRs have been inferred to be responsible for molecular recognition. All LRRs include the highly conserved segment, LxxLxLxxNxL, in which "L" is Leu, Ile, Val, or Phe and "N" is Asn, Thr, Ser, or Cys and "x" is any amino acid. There are seven classes of LRRs including "typical" ("T") and "bacterial" ("S"). All known domain structures adopt an arc or horseshoe shape. Vertebrate TLRs form six major families. The repeat numbers of LRRs and their "phasing" in TLRs differ with isoforms and species; they are aligned differently in various databases. We identified and aligned LRRs in TLRs by a new method described here. Results The new method utilizes known LRR structures to recognize and align new LRR motifs in TLRs and incorporates multiple sequence alignments and secondary structure predictions. TLRs from thirty-four vertebrate were analyzed. The repeat numbers of the LRRs ranges from 16 to 28. The LRRs found in TLRs frequently consists of LxxLxLxxNxLxxLxxxxF/LxxLxx ("T") and sometimes short motifs including LxxLxLxxNxLxxLPx(x)LPxx ("S"). The TLR7 family (TLR7, TLR8, and TLR9) contain 27 LRRs. The LRRs at the N-terminal part have a super-motif of STT with about 80 residues. The super-repeat is represented by STTSTTSTT or _TTSTTSTT. The LRRs in TLRs form one or two horseshoe domains and are mostly flanked by two cysteine clusters including two or four cysteine residue. Conclusion Each of the six major TLR families is characterized by their constituent LRR motifs, their repeat numbers, and their patterns of cysteine clusters. The central parts of the TLR1 and TLR7 families and of TLR4 have more irregular or longer LRR motifs. These central parts are inferred to play a key role in the structure and/or function of their TLRs. Furthermore, the super-repeat in the TLR7 family suggests strongly that "bacterial" and "typical" LRRs evolved from a common precursor.
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Affiliation(s)
- Norio Matsushima
- School of Health Sciences, Sapporo Medical University, Hokkaido 060-8556, Japan
| | - Takanori Tanaka
- RIKEN Genomic Sciences Center, Yokohama, Kanagawa 230-0045, Japan
| | - Purevjav Enkhbayar
- Faculty of Biology, National University of Mongolia, Ulaanbaatar-210646/377, Mongolia
| | - Tomoko Mikami
- School of Health Sciences, Sapporo Medical University, Hokkaido 060-8556, Japan
- Department of Nursing, Sapporo City University, Sapporo, Hokkaido 060-0011, Japan
| | - Masae Taga
- School of Health Sciences, Sapporo Medical University, Hokkaido 060-8556, Japan
- Department of Nursing, Sapporo City University, Sapporo, Hokkaido 060-0011, Japan
| | - Keiko Yamada
- School of Health Sciences, Sapporo Medical University, Hokkaido 060-8556, Japan
| | - Yoshio Kuroki
- Department of Biochemistry, School of Medicine, Sapporo Medical University, Hokkaido 060-8556, Japan
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Gelb MH, Brunsveld L, Hrycyna CA, Michaelis S, Tamanoi F, Van Voorhis WC, Waldmann H. Therapeutic intervention based on protein prenylation and associated modifications. Nat Chem Biol 2006; 2:518-28. [PMID: 16983387 PMCID: PMC2892741 DOI: 10.1038/nchembio818] [Citation(s) in RCA: 156] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In eukaryotic cells, a specific set of proteins are modified by C-terminal attachment of 15-carbon farnesyl groups or 20-carbon geranylgeranyl groups that function both as anchors for fixing proteins to membranes and as molecular handles for facilitating binding of these lipidated proteins to other proteins. Additional modification of these prenylated proteins includes C-terminal proteolysis and methylation, and attachment of a 16-carbon palmitoyl group; these modifications augment membrane anchoring and alter the dynamics of movement of proteins between different cellular membrane compartments. The enzymes in the protein prenylation pathway have been isolated and characterized. Blocking protein prenylation is proving to be therapeutically useful for the treatment of certain cancers, infection by protozoan parasites and the rare genetic disease Hutchinson-Gilford progeria syndrome.
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Affiliation(s)
- Michael H Gelb
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA.
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Sommerhalter M, Zhang Y, Rosenzweig AC. Solution structure of the COMMD1 N-terminal domain. J Mol Biol 2006; 365:715-21. [PMID: 17097678 PMCID: PMC2706016 DOI: 10.1016/j.jmb.2006.10.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2006] [Revised: 10/03/2006] [Accepted: 10/09/2006] [Indexed: 11/17/2022]
Abstract
COMMD1 is the prototype of a new protein family that plays a role in several important cellular processes, including NF-kappaB signaling, sodium transport, and copper metabolism. The COMMD proteins interact with one another via a conserved C-terminal domain, whereas distinct functions are predicted to result from a variable N-terminal domain. The COMMD proteins have not been characterized biochemically or structurally. Here, we present the solution structure of the N-terminal domain of COMMD1 (N-COMMD1, residues 1-108). This domain adopts an alpha-helical structure that bears little resemblance to any other helical protein. The compact nature of N-COMMD1 suggests that full-length COMMD proteins are modular, consistent with specific functional properties for each domain. Interactions between N-COMMD1 and partner proteins may occur via complementary electrostatic surfaces. These data provide a new foundation for biochemical characterization of COMMD proteins and for probing COMMD1 protein-protein interactions at the molecular level.
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Affiliation(s)
- Monika Sommerhalter
- Departments of Biochemistry, Molecular Biology, and Cell Biology and of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
| | - Yongbo Zhang
- Weinberg College of Arts and Sciences Structural Biology NMR Facility, Northwestern University, Evanston, Illinois 60208, USA
| | - Amy C. Rosenzweig
- Departments of Biochemistry, Molecular Biology, and Cell Biology and of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
- Corresponding author, Email address of corresponding author:
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39
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Protein Prenylation: An (Almost) Comprehensive Overview on Discovery History, Enzymology, and Significance in Physiology and Disease. MONATSHEFTE FUR CHEMIE 2006. [DOI: 10.1007/s00706-006-0534-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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40
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Leung KF, Baron R, Seabra MC. Thematic review series: Lipid Posttranslational Modifications. Geranylgeranylation of Rab GTPases. J Lipid Res 2006; 47:467-75. [PMID: 16401880 DOI: 10.1194/jlr.r500017-jlr200] [Citation(s) in RCA: 188] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Rab GTPases require special machinery for protein prenylation, which include Rab escort protein (REP) and Rab geranylgeranyl transferase (RGGT). The current model of Rab geranylgeranylation proposes that REP binds Rab and presents it to RGGT. After geranylgeranylation of Rab C-terminal cysteines, REP delivers the prenylated protein to membranes. The REP-like protein Rab GDP dissociation inhibitor (RabGDI) then recycles the prenylated Rab between the membrane and the cytosol. The recent solution of crystal structures of the Rab prenylation machinery has helped to refine this model and provided further insights. The hydrophobic prenyl binding pocket of RGGT and geranylgeranyl transferase type-I (GGT-I) differs from that of farnesyl transferase (FT). A bulky tryptophan residue in FT restricts the size of the pocket, whereas in RGGT and GGT-I, this position is occupied by smaller residues. A highly conserved phenylalanine in REP, which is absent in RabGDI, is critical for the formation of the REP:RGGT complex. Finally, a geranylgeranyl binding site conserved in REP and RabGDI has been identified within helical domain II. The postprenylation events, including the specific targeting of Rabs to target membranes and the requirement for single versus double geranylgeranylation by different Rabs, remain obscure and should be the subject of future studies.
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Affiliation(s)
- Ka Fai Leung
- Molecular and Cellular Medicine, Division of Biomedical Sciences, Imperial College London, London SW7 2AZ, UK
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41
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Lane KT, Beese LS. Thematic review series: lipid posttranslational modifications. Structural biology of protein farnesyltransferase and geranylgeranyltransferase type I. J Lipid Res 2006; 47:681-99. [PMID: 16477080 DOI: 10.1194/jlr.r600002-jlr200] [Citation(s) in RCA: 183] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
More than 100 proteins necessary for eukaryotic cell growth, differentiation, and morphology require posttranslational modification by the covalent attachment of an isoprenoid lipid (prenylation). Prenylated proteins include members of the Ras, Rab, and Rho families, lamins, CENPE and CENPF, and the gamma subunit of many small heterotrimeric G proteins. This modification is catalyzed by the protein prenyltransferases: protein farnesyltransferase (FTase), protein geranylgeranyltransferase type I (GGTase-I), and GGTase-II (or RabGGTase). In this review, we examine the structural biology of FTase and GGTase-I (the CaaX prenyltransferases) to establish a framework for understanding the molecular basis of substrate specificity and mechanism. These enzymes have been identified in a number of species, including mammals, fungi, plants, and protists. Prenyltransferase structures include complexes that represent the major steps along the reaction path, as well as a number of complexes with clinically relevant inhibitors. Such complexes may assist in the design of inhibitors that could lead to treatments for cancer, viral infection, and a number of deadly parasitic diseases.
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Affiliation(s)
- Kimberly T Lane
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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42
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Pan J, Yeung SCJ. Recent advances in understanding the antineoplastic mechanisms of farnesyltransferase inhibitors. Cancer Res 2005; 65:9109-12. [PMID: 16230362 DOI: 10.1158/0008-5472.can-05-2635] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Farnesyltransferase (FTase) inhibitors (FTI) have broad antineoplastic actions targeting both cancer cells and mesenchymal cells involved in tumor angiogenesis. The small GTPases H-Ras, Rheb, and RhoB and the centromere proteins CENP-E and CENP-F are relevant targets of farnesylation inhibition; however, their relative importance in the antineoplastic effect of FTIs may vary in different cell types at different stages of the cell cycle and at different stages in oncogenesis. Three recent studies argue that Ras-independent and perhaps even FTase-independent properties are important to the antineoplastic action of this class of drugs. In mice, genetic ablation of FTase does not abolish the oncogenic activity of Ras, limiting the original conception of FTIs as an effective means to target Ras in cancer cells. FTase may not be the sole molecular target of these agents, and one study has suggested that FTIs act by targeting geranylgeranyl transferase II. Lastly, we have obtained evidence that induction of reactive oxygen species and reactive oxygen species-mediated DNA damage by FTIs may be critical for their antineoplastic action as a class. Together, these findings may alter thinking about how to apply FTIs in the clinic.
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Affiliation(s)
- Jingxuan Pan
- Department of Leukemia, General Internal Medicine, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA
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Lackner MR, Kindt RM, Carroll PM, Brown K, Cancilla MR, Chen C, de Silva H, Franke Y, Guan B, Heuer T, Hung T, Keegan K, Lee JM, Manne V, O'Brien C, Parry D, Perez-Villar JJ, Reddy RK, Xiao H, Zhan H, Cockett M, Plowman G, Fitzgerald K, Costa M, Ross-Macdonald P. Chemical genetics identifies Rab geranylgeranyl transferase as an apoptotic target of farnesyl transferase inhibitors. Cancer Cell 2005; 7:325-36. [PMID: 15837622 DOI: 10.1016/j.ccr.2005.03.024] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 11/05/2004] [Accepted: 03/23/2005] [Indexed: 10/25/2022]
Abstract
A chemical genetics approach identified a cellular target of several proapoptotic farnesyl transferase inhibitors (FTIs). Treatment with these FTIs caused p53-independent apoptosis in Caenorhabditis elegans, which was mimicked by knockdown of endosomal trafficking proteins, including Rab5, Rab7, the HOPS complex, and notably the enzyme Rab geranylgeranyl transferase (RabGGT). These FTIs were found to inhibit mammalian RabGGT with potencies that correlated with their proapoptotic activity. Knockdown of RabGGT induced apoptosis in mammalian cancer cell lines, and both RabGGT subunits were overexpressed in several tumor tissues. These findings validate RabGGT, and by extension endosomal function, as a therapeutically relevant target for modulation of apoptosis, and enhance our understanding of the mechanism of action of FTIs.
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Affiliation(s)
- Mark R Lackner
- Exelixis Inc., 170 Harbor Way, South San Francisco, California 94083, USA
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Abstract
Protein farnesylation is a lipid posttranslational modification required for the cancer-causing activity of proteins such as the GTPase Ras. Although farnesyltransferase inhibitors (FTIs) are in clinical trials, their mechanism of action and the role of protein farnesylation in normal physiology are ill understood. In this issue of Cancer Cell, two articles shed light on these important issues. Protein farnesylation was found to be essential for early embryogenesis, dispensable for adult homeostasis, and critical for progression but not initiation of tumorigenesis. Furthermore, Rab geranylgeranyltransferase was identified as a target for some FTIs. This minireview discusses the implications of these findings on normal physiology, malignant transformation, and cancer therapy.
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Affiliation(s)
- Saïd M Sebti
- Drug Discovery Program, H. Lee Moffitt Cancer Center & Research Institute, Department of Interdisciplinary Oncology, University of South Florida College of Medicine, Tampa, Florida 33612, USA.
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Watzke A, Brunsveld L, Durek T, Alexandrov K, Rak A, Goody RS, Waldmann H. Chemical biology of protein lipidation: semi-synthesis and structure elucidation of prenylated RabGTPases. Org Biomol Chem 2005; 3:1157-64. [PMID: 15785799 DOI: 10.1039/b417573e] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Rab/Ypt guanosine triphosphatases (GTPases) represent a family of key membrane traffic regulators in eukaryotic cells. For their function Rab/Ypt proteins require double modification with two covalently bound geranylgeranyl lipid moieties at the C-terminus. Generally, prenylated proteins are very difficult to obtain by recombinant or enzymatic methods. We generated prenylated RabGTPases using a combination of chemical synthesis and protein engineering. This semi-synthesis depends largely on the availability of functionalized prenylated peptides corresponding to the proteins' native structure or modifications. We developed solution phase and solid phase strategies for the generation of peptides corresponding to the prenylated C-terminus of Rab7 GTPase in preparative amounts enabling us to crystallize the mono-prenylated Ypt1:RabGDI complex. The structure of the complex provides a structural basis for the ability of RabGDI to inhibit the release of nucleotide by Rab proteins and a molecular basis for understanding a RabGDI mutant that causes mental retardation in humans.
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Affiliation(s)
- Anja Watzke
- Max-Planck-Institut für Molekulare Physiologie, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany
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Pejchal R, Ludwig ML. Cobalamin-independent methionine synthase (MetE): a face-to-face double barrel that evolved by gene duplication. PLoS Biol 2004; 3:e31. [PMID: 15630480 PMCID: PMC539065 DOI: 10.1371/journal.pbio.0030031] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2004] [Accepted: 11/17/2004] [Indexed: 12/05/2022] Open
Abstract
Cobalamin-independent methionine synthase (MetE) catalyzes the transfer of a methyl group from methyltetrahydrofolate to L-homocysteine (Hcy) without using an intermediate methyl carrier. Although MetE displays no detectable sequence homology with cobalamin-dependent methionine synthase (MetH), both enzymes require zinc for activation and binding of Hcy. Crystallographic analyses of MetE from T. maritima reveal an unusual dual-barrel structure in which the active site lies between the tops of the two (βα)8 barrels. The fold of the N-terminal barrel confirms that it has evolved from the C-terminal polypeptide by gene duplication; comparisons of the barrels provide an intriguing example of homologous domain evolution in which binding sites are obliterated. The C-terminal barrel incorporates the zinc ion that binds and activates Hcy. The zinc-binding site in MetE is distinguished from the (Cys)3Zn site in the related enzymes, MetH and betaine–homocysteine methyltransferase, by its position in the barrel and by the metal ligands, which are histidine, cysteine, glutamate, and cysteine in the resting form of MetE. Hcy associates at the face of the metal opposite glutamate, which moves away from the zinc in the binary E·Hcy complex. The folate substrate is not intimately associated with the N-terminal barrel; instead, elements from both barrels contribute binding determinants in a binary complex in which the folate substrate is incorrectly oriented for methyl transfer. Atypical locations of the Hcy and folate sites in the C-terminal barrel presumably permit direct interaction of the substrates in a ternary complex. Structures of the binary substrate complexes imply that rearrangement of folate, perhaps accompanied by domain rearrangement, must occur before formation of a ternary complex that is competent for methyl transfer. By solving the structure of MetE, the authors have shed light on how the chemically difficult transfer of a methyl group from methyltetrahydrofolate to homocysteine can occur
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Affiliation(s)
- Robert Pejchal
- 1Department of Biological Chemistry, University of MichiganAnn Arbor, MichiganUnited States of America
| | - Martha L Ludwig
- 1Department of Biological Chemistry, University of MichiganAnn Arbor, MichiganUnited States of America
- 2Biophysics Research Division, University of MichiganAnn Arbor, MichiganUnited States of America
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Zhang Z, Hu W, Cano L, Lee TD, Chen DJ, Chen Y. Solution structure of the C-terminal domain of Ku80 suggests important sites for protein-protein interactions. Structure 2004; 12:495-502. [PMID: 15016365 DOI: 10.1016/j.str.2004.02.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2003] [Accepted: 11/14/2003] [Indexed: 10/26/2022]
Abstract
The solution structure of Ku80 CTD from residue 566 to 732 has been solved in order to gain insights into the mechanisms of its interactions with other proteins. The structure reveals a topology similar to several common scaffolds for protein-protein interactions, in the absence of significant sequence similarity to these proteins. Conserved surface amino acid residues are clustered on two main surface areas, which are likely involved in mediating interactions between Ku80 and other proteins. The Ku70/Ku80 heterodimer has been shown to be involved in at least three processes, nonhomologous end joining, transcription, and telomere maintenance, and thus it needs to interact with different proteins involved in these different processes. The three-dimensional structure of the Ku80 C-terminal domain and the availability of NMR chemical shift assignments provide a basis for further investigation of the interactions between Ku80 and other proteins in these Ku-dependent cellular functions.
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Affiliation(s)
- Ziming Zhang
- Division of Immunology, Beckman Research Institute of the City of Hope, Duarte, CA 91010, USA
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Taylor JS, Reid TS, Terry KL, Casey PJ, Beese LS. Structure of mammalian protein geranylgeranyltransferase type-I. EMBO J 2004; 22:5963-74. [PMID: 14609943 PMCID: PMC275430 DOI: 10.1093/emboj/cdg571] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Protein geranylgeranyltransferase type-I (GGTase-I), one of two CaaX prenyltransferases, is an essential enzyme in eukaryotes. GGTase-I catalyzes C-terminal lipidation of >100 proteins, including many GTP- binding regulatory proteins. We present the first structural information for mammalian GGTase-I, including a series of substrate and product complexes that delineate the path of the chemical reaction. These structures reveal that all protein prenyltransferases share a common reaction mechanism and identify specific residues that play a dominant role in determining prenyl group specificity. This hypothesis was confirmed by converting farnesyltransferase (15-C prenyl substrate) into GGTase-I (20-C prenyl substrate) with a single point mutation. GGTase-I discriminates against farnesyl diphosphate (FPP) at the product turnover step through the inability of a 15-C FPP to displace the 20-C prenyl-peptide product. Understanding these key features of specificity is expected to contribute to optimization of anti-cancer and anti-parasite drugs.
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Affiliation(s)
- Jeffrey S Taylor
- Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA
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Seebacher J, Ji M, Vahrenkamp H. (Neocuproin)zinc Thiolates: Attempts at Modeling Cobalamin-Independent Methionine Synthase. Eur J Inorg Chem 2004. [DOI: 10.1002/ejic.200300501] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Abstract
Covalent attachment of lipophilic moieties to proteins influences interaction with membranes and membrane microdomains, as well as signal transduction. The most common forms of fatty acylation include modification of the N-terminal glycine of proteins by N-myristoylation and/or attachment of palmitate to internal cysteine residues. Protein prenylation involves attachment of farnesyl or geranylgeranyl moieties via thio-ether linkage to cysteine residues at or near the C-terminus. Attachment of each of these lipophilic groups is catalyzed by a distinct enzyme or set of enzymes: N-myristoyl transferase for N-myristoylation, palmitoyl acyl transferases for palmitoylation, and farnesyl or geranylgeranyl transferases for prenylation. The distinct nature of the lipid modification determines the strength of membrane interaction of the modified protein as well as the specificity of membrane targeting. Clusters of basic residues can also synergize with the lipophilic group to promote membrane binding and targeting. The final destination of the modified protein is influenced by multiple factors, including the localization of the modifying enzymes, protein/protein interactions, and the lipid composition of the acceptor membrane. In particular, much interest has been focused on the ability of fatty acylated proteins to preferentially partition into membrane rafts, subdomains of the plasma membrane that are enriched in cholesterol and glycosphingolipids. Lipid raft localization is necessary for efficient signal transduction in a wide variety of systems, including signaling by T and B cell receptors, Ras, and growth factor receptors. However, certain membrane subdomains, such as caveolae, can serve as reservoirs for inactive signaling proteins. Heterogeneity in the types of membrane subdomains, as well as in the types of lipophilic groups that are attached to proteins, provide an additional level of complexity in the regulation of signaling by membrane bound proteins.
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Affiliation(s)
- Marilyn D Resh
- Member and Professor, Cell Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
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