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Abstract
Deubiquitinases (DUBs) play important roles and therefore are potential drug targets in various diseases including cancer and neurodegeneration. In this review, we recapitulate structure-function studies of the most studied DUBs including USP7, USP22, CYLD, UCHL1, BAP1, A20, as well as ataxin 3 and connect them to regulatory mechanisms and their growing protein interaction networks. We then describe DUBs that have been associated with endocrine carcinogenesis with a focus on prostate, ovarian, and thyroid cancer, pheochromocytoma, and adrenocortical carcinoma. The goal is enhancing our understanding of the connection between dysregulated DUBs and cancer to permit the design of therapeutics and to establish biomarkers that could be used in diagnosis and prognosis.
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Affiliation(s)
- Roland Pfoh
- Department of BiologyYork University, 4700 Keele Street, Toronto, Ontario, Canada, M3J1P3
| | - Ira Kay Lacdao
- Department of BiologyYork University, 4700 Keele Street, Toronto, Ontario, Canada, M3J1P3
| | - Vivian Saridakis
- Department of BiologyYork University, 4700 Keele Street, Toronto, Ontario, Canada, M3J1P3
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102
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Erzberger JP, Stengel F, Pellarin R, Zhang S, Schaefer T, Aylett CHS, Cimermančič P, Boehringer D, Sali A, Aebersold R, Ban N. Molecular architecture of the 40S⋅eIF1⋅eIF3 translation initiation complex. Cell 2015; 158:1123-1135. [PMID: 25171412 PMCID: PMC4151992 DOI: 10.1016/j.cell.2014.07.044] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 05/29/2014] [Accepted: 07/29/2014] [Indexed: 11/25/2022]
Abstract
Eukaryotic translation initiation requires the recruitment of the large, multiprotein eIF3 complex to the 40S ribosomal subunit. We present X-ray structures of all major components of the minimal, six-subunit Saccharomyces cerevisiae eIF3 core. These structures, together with electron microscopy reconstructions, cross-linking coupled to mass spectrometry, and integrative structure modeling, allowed us to position and orient all eIF3 components on the 40S⋅eIF1 complex, revealing an extended, modular arrangement of eIF3 subunits. Yeast eIF3 engages 40S in a clamp-like manner, fully encircling 40S to position key initiation factors on opposite ends of the mRNA channel, providing a platform for the recruitment, assembly, and regulation of the translation initiation machinery. The structures of eIF3 components reported here also have implications for understanding the architecture of the mammalian 43S preinitiation complex and the complex of eIF3, 40S, and the hepatitis C internal ribosomal entry site RNA. X-ray structures of major yeast eIF3 components and subcomplexes Crosslinking coupled to mass-spectrometry analysis of 40S⋅eIF1⋅eIF3 complex Integrative modeling reveals architecture of 40S⋅eIF1⋅eIF3 complex
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Affiliation(s)
- Jan P Erzberger
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
| | - Florian Stengel
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland
| | - Riccardo Pellarin
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, UCSF MC 2552, Byers Hall Room 503B, 1700 4th Street, San Francisco, CA 94158-2330, USA
| | - Suyang Zhang
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Tanja Schaefer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Christopher H S Aylett
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Peter Cimermančič
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, UCSF MC 2552, Byers Hall Room 503B, 1700 4th Street, San Francisco, CA 94158-2330, USA
| | - Daniel Boehringer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, UCSF MC 2552, Byers Hall Room 503B, 1700 4th Street, San Francisco, CA 94158-2330, USA
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Auguste-Piccard-Hof 1, 8093 Zurich, Switzerland; Faculty of Science, University of Zurich, 8006 Zurich, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Otto-Stern-Weg 5, 8093 Zurich, Switzerland.
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103
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Hu Y, Wu Y, Li Q, Zhang W, Jin C. Solution structure of yeast Rpn9: insights into proteasome lid assembly. J Biol Chem 2015; 290:6878-89. [PMID: 25631053 DOI: 10.1074/jbc.m114.626762] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The regulatory particle (RP) of the 26 S proteasome functions in preparing polyubiquitinated substrates for degradation. The lid complex of the RP contains an Rpn8-Rpn11 heterodimer surrounded by a horseshoe-shaped scaffold formed by six proteasome-COP9/CSN-initiation factor (PCI)-containing subunits. The PCI domains are essential for lid assembly, whereas the detailed molecular mechanisms remain elusive. Recent cryo-EM studies at near-atomic resolution provided invaluable information on the RP architecture in different functional states. Nevertheless, atomic resolution structural information on the RP is still limited, and deeper understanding of RP assembly mechanism requires further studies on the structures and interactions of individual subunits or subcomplexes. Herein we report the high-resolution NMR structures of the PCI-containing subunit Rpn9 from Saccharomyces cerevisiae. The 45-kDa protein contains an all-helical N-terminal domain and a C-terminal PCI domain linked via a semiflexible hinge. The N-terminal domain mediates interaction with the ubiquitin receptor Rpn10, whereas the PCI domain mediates interaction with the neighboring PCI subunit Rpn5. The Rpn9-Rpn5 interface highlights two structural motifs on the winged helix module forming a hydrophobic center surrounded by ionic pairs, which is a common pattern for all PCI-PCI interactions in the lid. The results suggest that divergence in surface composition among different PCI pairs may contribute to the modulation of lid assembly.
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Affiliation(s)
- Yunfei Hu
- From the Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering
| | - Yujie Wu
- From the Beijing Nuclear Magnetic Resonance Center, College of Life Sciences, and
| | - Qianwen Li
- From the Beijing Nuclear Magnetic Resonance Center, College of Life Sciences, and
| | - Wenbo Zhang
- From the Beijing Nuclear Magnetic Resonance Center, College of Life Sciences, and
| | - Changwen Jin
- From the Beijing Nuclear Magnetic Resonance Center, College of Chemistry and Molecular Engineering, College of Life Sciences, and Beijing National Laboratory for Molecular Sciences, Peking University, Beijing 100871, China
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104
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Base-CP proteasome can serve as a platform for stepwise lid formation. Biosci Rep 2015; 35:BSR20140173. [PMID: 26182356 PMCID: PMC4438304 DOI: 10.1042/bsr20140173] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 01/26/2015] [Indexed: 12/14/2022] Open
Abstract
26S proteasome, a major regulatory protease in eukaryotes, consists of a 20S proteolytic core particle (CP) capped by a 19S regulatory particle (RP). The 19S RP is divisible into base and lid sub-complexes. Even within the lid, subunits have been demarcated into two modules: module 1 (Rpn5, Rpn6, Rpn8, Rpn9 and Rpn11), which interacts with both CP and base sub-complexes and module 2 (Rpn3, Rpn7, Rpn12 and Rpn15) that is attached mainly to module 1. We now show that suppression of RPN11 expression halted lid assembly yet enabled the base and 20S CP to pre-assemble and form a base-CP. A key role for Regulatory particle non-ATPase 11 (Rpn11) in bridging lid module 1 and module 2 subunits together is inferred from observing defective proteasomes in rpn11–m1, a mutant expressing a truncated form of Rpn11 and displaying mitochondrial phenotypes. An incomplete lid made up of five module 1 subunits attached to base-CP was identified in proteasomes isolated from this mutant. Re-introducing the C-terminal portion of Rpn11 enabled recruitment of missing module 2 subunits. In vitro, module 1 was reconstituted stepwise, initiated by Rpn11–Rpn8 heterodimerization. Upon recruitment of Rpn6, the module 1 intermediate was competent to lock into base-CP and reconstitute an incomplete 26S proteasome. Thus, base-CP can serve as a platform for gradual incorporation of lid, along a proteasome assembly pathway. Identification of proteasome intermediates and reconstitution of minimal functional units should clarify aspects of the inner workings of this machine and how multiple catalytic processes are synchronized within the 26S proteasome holoenzymes. Defective proteasome 19S regulatory particles (RPs) were identified in rpn11f–m1, a proteasomal mutant with mitochondrial phenotypes. The Rpn11 subunit initiates assembly of a five-subunit lid module competent to integrate into pre-assembled base-20S core particle (CP), with subsequent recruitment of remaining lid subunits.
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105
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Desmyter A, Spinelli S, Roussel A, Cambillau C. Camelid nanobodies: killing two birds with one stone. Curr Opin Struct Biol 2015; 32:1-8. [PMID: 25614146 DOI: 10.1016/j.sbi.2015.01.001] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2014] [Revised: 12/23/2014] [Accepted: 01/05/2015] [Indexed: 01/09/2023]
Abstract
In recent years, the use of single-domain camelid immunoglobulins, termed vHHs or nanobodies, has seen increasing growth in biotechnology, pharmaceutical applications and structure/function research. The usefulness of nanobodies in structural biology is now firmly established, as they provide access to new epitopes in concave and hinge regions - and stabilize them. These sites are often associated with enzyme inhibition or receptor neutralization, and, at the same time, provide favorable surfaces for crystal packing. Remarkable results have been achieved by using nanobodies with flexible multi-domain proteins, large complexes and, last but not least, membrane proteins. While generating nanobodies is still a rather long and expensive procedure, the advent of naive libraries might be expected to facilitate the whole process.
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Affiliation(s)
- Aline Desmyter
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, France; Centre National de la Recherche Scientifique, AFMB, UMR 7257, case 932, 13288 Marseille Cedex 09, France
| | - Silvia Spinelli
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, France; Centre National de la Recherche Scientifique, AFMB, UMR 7257, case 932, 13288 Marseille Cedex 09, France
| | - Alain Roussel
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, France; Centre National de la Recherche Scientifique, AFMB, UMR 7257, case 932, 13288 Marseille Cedex 09, France
| | - Christian Cambillau
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, France; Centre National de la Recherche Scientifique, AFMB, UMR 7257, case 932, 13288 Marseille Cedex 09, France.
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106
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Antibody Fragments Defining Biologically Relevant Conformations of Target Proteins. Antibodies (Basel) 2014. [DOI: 10.3390/antib3040289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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107
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Gu ZC, Enenkel C. Proteasome assembly. Cell Mol Life Sci 2014; 71:4729-45. [PMID: 25107634 PMCID: PMC11113775 DOI: 10.1007/s00018-014-1699-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 07/30/2014] [Accepted: 07/31/2014] [Indexed: 10/24/2022]
Abstract
In eukaryotic cells, proteasomes are highly conserved protease complexes and eliminate unwanted proteins which are marked by poly-ubiquitin chains for degradation. The 26S proteasome consists of the proteolytic core particle, the 20S proteasome, and the 19S regulatory particle, which are composed of 14 and 19 different subunits, respectively. Proteasomes are the second-most abundant protein complexes and are continuously assembled from inactive precursor complexes in proliferating cells. The modular concept of proteasome assembly was recognized in prokaryotic ancestors and applies to eukaryotic successors. The efficiency and fidelity of eukaryotic proteasome assembly is achieved by several proteasome-dedicated chaperones that initiate subunit incorporation and control the quality of proteasome assemblies by transiently interacting with proteasome precursors. It is important to understand the mechanism of proteasome assembly as the proteasome has key functions in the turnover of short-lived proteins regulating diverse biological processes.
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Affiliation(s)
- Zhu Chao Gu
- Department of Biochemistry, University of Toronto, Medical Sciences Building, 1 King’s College Circle, Toronto, ON M5S 1A8 Canada
| | - Cordula Enenkel
- Department of Biochemistry, University of Toronto, Medical Sciences Building, 1 King’s College Circle, Toronto, ON M5S 1A8 Canada
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108
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Mansour W, Nakasone MA, von Delbrück M, Yu Z, Krutauz D, Reis N, Kleifeld O, Sommer T, Fushman D, Glickman MH. Disassembly of Lys11 and mixed linkage polyubiquitin conjugates provides insights into function of proteasomal deubiquitinases Rpn11 and Ubp6. J Biol Chem 2014; 290:4688-4704. [PMID: 25389291 DOI: 10.1074/jbc.m114.568295] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Protein homeostasis is largely dependent on proteolysis by the ubiquitin-proteasome system. Diverse polyubiquitin modifications are reported to target cellular proteins to the proteasome. At the proteasome, deubiquitination is an essential preprocessing event that contributes to degradation efficiency. We characterized the specificities of two proteasome-associated deubiquitinases (DUBs), Rpn11 and Ubp6, and explored their impact on overall proteasome DUB activity. This was accomplished by constructing a panel of well defined ubiquitin (Ub) conjugates, including homogeneous linkages of varying lengths as well as a heterogeneously modified target. Rpn11 and Ubp6 processed Lys(11) and Lys(63) linkages with comparable efficiencies that increased with chain length. In contrast, processing of Lys(48) linkages by proteasome was inversely correlated to chain length. Fluorescently labeled tetra-Ub chains revealed endo-chain preference for Ubp6 acting on Lys(48) and random action for Rpn11. Proteasomes were more efficient at deconjugating identical substrates than their constituent DUBs by roughly 2 orders of magnitude. Incorporation into proteasomes significantly enhanced enzymatic efficiency of Rpn11, due in part to alleviation of the autoinhibitory role of its C terminus. The broad specificity of Rpn11 could explain how proteasomes were more effective at disassembling a heterogeneously modified conjugate compared with homogeneous Lys(48)-linked chains. The reduced ability to disassemble homogeneous Lys(48)-linked chains longer than 4 Ub units may prolong residency time on the proteasome.
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Affiliation(s)
- Wissam Mansour
- From the Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Mark A Nakasone
- From the Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel,; the Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742
| | - Maximilian von Delbrück
- the Max-Delbrück-Zentrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany, and
| | - Zanlin Yu
- From the Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Daria Krutauz
- From the Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Noa Reis
- From the Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Oded Kleifeld
- the Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne 3800, Australia
| | - Thomas Sommer
- the Max-Delbrück-Zentrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13125 Berlin, Germany, and
| | - David Fushman
- the Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, Maryland 20742
| | - Michael H Glickman
- From the Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel,.
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109
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Birol M, Enchev RI, Padilla A, Stengel F, Aebersold R, Betzi S, Yang Y, Hoh F, Peter M, Dumas C, Echalier A. Structural and biochemical characterization of the Cop9 signalosome CSN5/CSN6 heterodimer. PLoS One 2014; 9:e105688. [PMID: 25144743 PMCID: PMC4140821 DOI: 10.1371/journal.pone.0105688] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Accepted: 07/23/2014] [Indexed: 11/18/2022] Open
Abstract
The Cop9 signalosome complex (CSN) regulates the functional cycle of the major E3 ubiquitin ligase family, the cullin RING E3 ubiquitin ligases (CRLs). Activated CRLs are covalently modified by the ubiquitin-like protein Nedd8 (neural precursor cell expressed developmentally down-regulated protein 8). CSN serves an essential role in myriad cellular processes by reversing this modification through the isopeptidase activity of its CSN5 subunit. CSN5 alone is inactive due to an auto-inhibited conformation of its catalytic domain. Here we report the molecular basis of CSN5 catalytic domain activation and unravel a molecular hierarchy in CSN deneddylation activity. The association of CSN5 and CSN6 MPN (for Mpr1/Pad1 N-terminal) domains activates its isopeptidase activity. The CSN5/CSN6 module, however, is inefficient in CRL deneddylation, indicating a requirement of further elements in this reaction such as other CSN subunits. A hybrid molecular model of CSN5/CSN6 provides a structural framework to explain these functional observations. Docking this model into a published CSN electron density map and using distance constraints obtained from cross-linking coupled to mass-spectrometry, we find that the C-termini of the CSN subunits could form a helical bundle in the centre of the structure. They likely play a key scaffolding role in the spatial organization of CSN and precise positioning of the dimeric MPN catalytic core.
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Affiliation(s)
- Melissa Birol
- Centre de Biochimie Structurale, Unité Mixte de Recherche (UMR) 5048, Centre National de Recherche Scientifique (CNRS), Université Montpellier 1 (UM1), Université Montpellier 2 (UM2), Montpellier, France
- Institut national de la santé et de la recherche médicale (INSERM) U1054, Paris, France
| | | | - André Padilla
- Centre de Biochimie Structurale, Unité Mixte de Recherche (UMR) 5048, Centre National de Recherche Scientifique (CNRS), Université Montpellier 1 (UM1), Université Montpellier 2 (UM2), Montpellier, France
- Institut national de la santé et de la recherche médicale (INSERM) U1054, Paris, France
| | - Florian Stengel
- ETH Zurich, Department of Biology, Institute of Molecular Systems Biology, Zurich, Switzerland
| | - Ruedi Aebersold
- ETH Zurich, Department of Biology, Institute of Molecular Systems Biology, Zurich, Switzerland
- Faculty of Science, University of Zurich, Zurich, Switzerland
| | - Stéphane Betzi
- Centre de Recherche en Cancérologie de Marseille, Centre de Biochimie Structurale, Unité Mixte de Recherche (UMR) 7258, Institut national de la santé et de la recherche médicale (INSERM) U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Yinshan Yang
- Centre de Biochimie Structurale, Unité Mixte de Recherche (UMR) 5048, Centre National de Recherche Scientifique (CNRS), Université Montpellier 1 (UM1), Université Montpellier 2 (UM2), Montpellier, France
- Institut national de la santé et de la recherche médicale (INSERM) U1054, Paris, France
| | - François Hoh
- Centre de Biochimie Structurale, Unité Mixte de Recherche (UMR) 5048, Centre National de Recherche Scientifique (CNRS), Université Montpellier 1 (UM1), Université Montpellier 2 (UM2), Montpellier, France
- Institut national de la santé et de la recherche médicale (INSERM) U1054, Paris, France
| | - Matthias Peter
- ETH Zurich, Department of Biology, Institute of Biochemistry, Zurich, Switzerland
| | - Christian Dumas
- Centre de Biochimie Structurale, Unité Mixte de Recherche (UMR) 5048, Centre National de Recherche Scientifique (CNRS), Université Montpellier 1 (UM1), Université Montpellier 2 (UM2), Montpellier, France
- Institut national de la santé et de la recherche médicale (INSERM) U1054, Paris, France
| | - Aude Echalier
- Centre de Biochimie Structurale, Unité Mixte de Recherche (UMR) 5048, Centre National de Recherche Scientifique (CNRS), Université Montpellier 1 (UM1), Université Montpellier 2 (UM2), Montpellier, France
- Institut national de la santé et de la recherche médicale (INSERM) U1054, Paris, France
- * E-mail:
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110
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Förster F, Schuller JM, Unverdorben P, Aufderheide A. Emerging mechanistic insights into AAA complexes regulating proteasomal degradation. Biomolecules 2014; 4:774-94. [PMID: 25102382 PMCID: PMC4192671 DOI: 10.3390/biom4030774] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 06/11/2014] [Accepted: 07/21/2014] [Indexed: 12/25/2022] Open
Abstract
The 26S proteasome is an integral element of the ubiquitin-proteasome system (UPS) and, as such, responsible for regulated degradation of proteins in eukaryotic cells. It consists of the core particle, which catalyzes the proteolysis of substrates into small peptides, and the regulatory particle, which ensures specificity for a broad range of substrates. The heart of the regulatory particle is an AAA-ATPase unfoldase, which is surrounded by non-ATPase subunits enabling substrate recognition and processing. Cryo-EM-based studies revealed the molecular architecture of the 26S proteasome and its conformational rearrangements, providing insights into substrate recognition, commitment, deubiquitylation and unfolding. The cytosol proteasomal degradation of polyubiquitylated substrates is tuned by various associating cofactors, including deubiquitylating enzymes, ubiquitin ligases, shuttling ubiquitin receptors and the AAA-ATPase Cdc48/p97. Cdc48/p97 and its cofactors function upstream of the 26S proteasome, and their modular organization exhibits some striking analogies to the regulatory particle. In archaea PAN, the closest regulatory particle homolog and Cdc48 even have overlapping functions, underscoring their intricate relationship. Here, we review recent insights into the structure and dynamics of the 26S proteasome and its associated machinery, as well as our current structural knowledge on the Cdc48/p97 and its cofactors that function in the ubiquitin-proteasome system (UPS).
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Affiliation(s)
- Friedrich Förster
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Martinsried D-82152, Germany.
| | - Jan M Schuller
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Martinsried D-82152, Germany.
| | - Pia Unverdorben
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Martinsried D-82152, Germany.
| | - Antje Aufderheide
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Martinsried D-82152, Germany.
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111
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Crystal structure of the human COP9 signalosome. Nature 2014; 512:161-5. [PMID: 25043011 DOI: 10.1038/nature13566] [Citation(s) in RCA: 178] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Accepted: 06/06/2014] [Indexed: 12/26/2022]
Abstract
Ubiquitination is a crucial cellular signalling process, and is controlled on multiple levels. Cullin-RING E3 ubiquitin ligases (CRLs) are regulated by the eight-subunit COP9 signalosome (CSN). CSN inactivates CRLs by removing their covalently attached activator, NEDD8. NEDD8 cleavage by CSN is catalysed by CSN5, a Zn(2+)-dependent isopeptidase that is inactive in isolation. Here we present the crystal structure of the entire ∼350-kDa human CSN holoenzyme at 3.8 Å resolution, detailing the molecular architecture of the complex. CSN has two organizational centres: a horseshoe-shaped ring created by its six proteasome lid-CSN-initiation factor 3 (PCI) domain proteins, and a large bundle formed by the carboxy-terminal α-helices of every subunit. CSN5 and its dimerization partner, CSN6, are intricately embedded at the core of the helical bundle. In the substrate-free holoenzyme, CSN5 is autoinhibited, which precludes access to the active site. We find that neddylated CRL binding to CSN is sensed by CSN4, and communicated to CSN5 with the assistance of CSN6, resulting in activation of the deneddylase.
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112
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113
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114
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Deep classification of a large cryo-EM dataset defines the conformational landscape of the 26S proteasome. Proc Natl Acad Sci U S A 2014; 111:5544-9. [PMID: 24706844 DOI: 10.1073/pnas.1403409111] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The 26S proteasome is a 2.5 MDa molecular machine that executes the degradation of substrates of the ubiquitin-proteasome pathway. The molecular architecture of the 26S proteasome was recently established by cryo-EM approaches. For a detailed understanding of the sequence of events from the initial binding of polyubiquitylated substrates to the translocation into the proteolytic core complex, it is necessary to move beyond static structures and characterize the conformational landscape of the 26S proteasome. To this end we have subjected a large cryo-EM dataset acquired in the presence of ATP and ATP-γS to a deep classification procedure, which deconvolutes coexisting conformational states. Highly variable regions, such as the density assigned to the largest subunit, Rpn1, are now well resolved and rendered interpretable. Our analysis reveals the existence of three major conformations: in addition to the previously described ATP-hydrolyzing (ATPh) and ATP-γS conformations, an intermediate state has been found. Its AAA-ATPase module adopts essentially the same topology that is observed in the ATPh conformation, whereas the lid is more similar to the ATP-γS bound state. Based on the conformational ensemble of the 26S proteasome in solution, we propose a mechanistic model for substrate recognition, commitment, deubiquitylation, and translocation into the core particle.
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