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Architecture and assembly of the archaeal Cdc48*20S proteasome. Proc Natl Acad Sci U S A 2014; 111:E1687-94. [PMID: 24711419 DOI: 10.1073/pnas.1404823111] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
ATP-dependent proteases maintain protein quality control and regulate diverse intracellular functions. Proteasomes are primarily responsible for these tasks in the archaeal and eukaryotic domains of life. Even the simplest of these proteases function as large complexes, consisting of the 20S peptidase, a barrel-like structure composed of four heptameric rings, and one or two AAA+ (ATPase associated with a variety of cellular activities) ring hexamers, which use cycles of ATP binding and hydrolysis to unfold and translocate substrates into the 20S proteolytic chamber. Understanding how the AAA+ and 20S components of these enzymes interact and collaborate to execute protein degradation is important, but the highly dynamic nature of prokaryotic proteasomes has hampered structural characterization. Here, we use electron microscopy to determine the architecture of an archaeal Cdc48 ⋅ 20S proteasome, which we stabilized by site-specific cross-linking. This complex displays coaxial alignment of Cdc48 and 20S and is enzymatically active, demonstrating that AAA+ unfoldase wobbling with respect to 20S is not required for function. In the complex, the N-terminal domain of Cdc48, which regulates ATP hydrolysis and degradation, packs against the D1 ring of Cdc48 in a coplanar fashion, constraining mechanisms by which the N-terminal domain alters 20S affinity and degradation activity.
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2
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Hubert Á, Mitani Y, Tamura T, Boicu M, Nagy I. Protein complex purification from Thermoplasma acidophilum using a phage display library. J Microbiol Methods 2014; 98:15-22. [DOI: 10.1016/j.mimet.2013.12.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 12/12/2013] [Accepted: 12/12/2013] [Indexed: 11/27/2022]
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3
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Cryo-electron tomography in biology and medicine. Ann Anat 2009; 191:427-45. [PMID: 19559584 DOI: 10.1016/j.aanat.2009.04.003] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Accepted: 04/23/2009] [Indexed: 12/16/2022]
Abstract
During the last six decades electron microscopy (EM) has been essential to ultra-structural studies of the cell to understand the fundamentals of cellular morphology and processes underlying diseases. More recently, electron tomography (ET) has emerged as a novel approach able to provide three-dimensional (3D) information on cells and tissues at molecular level. Electron tomography is comparable to medical tomographic techniques like CAT, PET and MRI in the sense that it provides a 3D view of an object, yet it does so at a cellular scale and with nanometer resolution. Electron tomography has the unique ability to visualize molecular assemblies, cytoskeletal elements and organelles within cells. The three-dimensional perspective it provides has revised our understanding of cellular organization and its relation with morphological changes in normal development and disease. Cryo-electron tomography of vitrified samples at cryogenic temperatures combines excellent structural preservation with direct high-resolution imaging. The use of cryo-preparation and imaging techniques eliminates artifacts induced by plastic embedding and staining of the samples is circumvented. This review describes the technique of cryo-electron tomography, its basic principles, cryo-specimen preparation, tomographic data acquisition and image processing. A number of illustrative examples ranging from whole cells, cytoskeletal filaments, viruses and organelles are presented along with a comprehensive list of research articles employing cryo-electron tomography as the key ultrastuctural technique.
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4
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Davies JM, Brunger AT, Weis WI. Improved structures of full-length p97, an AAA ATPase: implications for mechanisms of nucleotide-dependent conformational change. Structure 2008; 16:715-26. [PMID: 18462676 DOI: 10.1016/j.str.2008.02.010] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Revised: 02/11/2008] [Accepted: 02/11/2008] [Indexed: 10/22/2022]
Abstract
The ATPases associated with various cellular activities (AAA) protein p97 has been implicated in a variety of cellular processes, including endoplasmic reticulum-associated degradation and homotypic membrane fusion. p97 belongs to a subgroup of AAA proteins that contains two nucleotide binding domains, D1 and D2. We determined the crystal structure of D2 at 3.0 A resolution. This model enabled rerefinement of full-length p97 in different nucleotide states against previously reported low-resolution diffraction data to significantly improved R values and Ramachandran statistics. Although the overall fold remained similar, there are significant improvements, especially around the D2 nucleotide binding site. The rerefinement illustrates the importance of knowledge of high-resolution structures of fragments covering most of the whole molecule. The structures suggest that nucleotide hydrolysis is transformed into larger conformational changes by pushing of one D2 domain by its neighbor in the hexamer, and transmission of nucleotide-state information through the D1-D2 linker to displace the N-terminal, effector binding domain.
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Affiliation(s)
- Jason M Davies
- Department of Structural Biology, Stanford University, Stanford, CA 94305-5432, USA
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5
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Pye VE, Dreveny I, Briggs LC, Sands C, Beuron F, Zhang X, Freemont PS. Going through the motions: the ATPase cycle of p97. J Struct Biol 2006; 156:12-28. [PMID: 16621604 DOI: 10.1016/j.jsb.2006.03.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2006] [Revised: 03/01/2006] [Accepted: 03/03/2006] [Indexed: 12/12/2022]
Abstract
p97 (VCP, Cdc48), a type II AAA+ ATPase family member, is ubiquitous, essential, highly abundant, and involved in a diverse range of biological functions with roles in membrane fusion, endoplasmic-reticulum associated degradation, transcriptional activation, and cell cycle control. As such, dysfunction of this protein has serious pathological consequences and has been implicated in a variety of cancers and neurodegenerative diseases. p97 has a large number of adaptor proteins through which it transmits energy from ATPase activity to conformational changes which are then exerted onto target proteins. p97 has been studied by a variety of biochemical and structural techniques at various resolutions and stages throughout its ATPase cycle. From these studies, many models have been proposed and consequently a single model for p97's action cannot be suggested. Many questions about the mechanism of p97 still remain, including whether the protomers act in a concerted manner and crucially how the induced changes in p97 are transmitted to its adaptor proteins and target substrates. The elucidation of p97's mechanism is not only important in furthering our knowledge of this intriguing protein and its many functions, but subsequently in the development of potential therapies for diseases associated with p97 dysfunction.
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Affiliation(s)
- Valerie E Pye
- Division of Molecular Biosciences, Centre for Structural Biology, Faculty of Natural Sciences, Imperial College London, London SW7 2AZ, UK
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6
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Maupin-Furlow JA, Humbard MA, Kirkland PA, Li W, Reuter CJ, Wright AJ, Zhou G. Proteasomes from Structure to Function: Perspectives from Archaea. Curr Top Dev Biol 2006; 75:125-69. [PMID: 16984812 DOI: 10.1016/s0070-2153(06)75005-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Insight into the world of proteolysis has expanded considerably over the past decade. Energy-dependent proteases, such as the proteasome, are no longer viewed as nonspecific degradative enzymes associated solely with protein catabolism but are intimately involved in controlling biological processes that span life to death. The proteasome maintains this exquisite control by catalyzing the precisely timed and rapid turnover of key regulatory proteins. Proteasomes also interplay with chaperones to ensure protein quality and to readjust the composition of the proteome following stress. Archaea encode proteasomes that are highly related to those of eukaryotes in basic structure and function. Investigations of archaeal proteasomes coupled with those of eukaryotes has greatly facilitated our understanding of the molecular mechanisms that govern regulated protein degradation by this elaborate nanocompartmentalized machine.
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Affiliation(s)
- Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida Gainesville, Florida 32611, USA
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7
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Gerega A, Rockel B, Peters J, Tamura T, Baumeister W, Zwickl P. VAT, the thermoplasma homolog of mammalian p97/VCP, is an N domain-regulated protein unfoldase. J Biol Chem 2005; 280:42856-62. [PMID: 16236712 DOI: 10.1074/jbc.m510592200] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Thermoplasma VCP-like ATPase from Thermoplasma acidophilum (VAT) ATPase is a member of the two-domain AAA ATPases and homologous to the mammalian p97/VCP and NSF proteins. We show here that the VAT ATPase complex unfolds green fluorescent protein (GFP) labeled with the ssrA-degradation tag. Increasing the Mg2+ concentration derepresses the ATPase activity and concomitantly stimulates the unfolding activity of VAT. Similarly, the VATDeltaN complex, a mutant of VAT deleted for the N domain, displays up to 24-fold enhanced ATP hydrolysis and 250-fold enhanced GFP unfolding activity when compared with wild-type VAT. To determine the individual contribution of the two AAA domains to ATP hydrolysis and GFP unfolding we performed extensive site-directed mutagenesis of the Walker A, Walker B, sensor-1, and pore residues in both AAA domains. Analysis of the VAT mutant proteins, where ATP hydrolysis was confined to a single AAA domain, revealed that the first domain (D1) is sufficient to exert GFP unfolding indistinguishable from wild-type VAT, while the second AAA domain (D2), although active, is significantly less efficient than wild-type VAT. A single conserved aromatic residue in the D1 section of the pore was found to be essential for GFP unfolding. In contrast, two neighboring residues in the D2 section of the pore had to be exchanged simultaneously, to achieve a drastic inhibition of GFP unfolding.
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Affiliation(s)
- Alexandra Gerega
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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8
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Davies JM, Tsuruta H, May AP, Weis WI. Conformational changes of p97 during nucleotide hydrolysis determined by small-angle X-Ray scattering. Structure 2005; 13:183-95. [PMID: 15698563 DOI: 10.1016/j.str.2004.11.014] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2004] [Revised: 11/15/2004] [Accepted: 11/22/2004] [Indexed: 11/26/2022]
Abstract
Valosin-containing protein (VCP)/p97 is an AAA family ATPase that has been implicated in the removal of misfolded proteins from the endoplasmic reticulum and in membrane fusion. p97 forms a homohexamer whose protomers consist of an N-terminal (N) domain responsible for binding to effector proteins, followed by two AAA ATPase domains, D1 and D2. Small-angle X-ray scattering (SAXS) measurements of p97 in the presence of AMP-PNP (ATP state), ADP-AlF(x) (hydrolysis transition state), ADP, or no nucleotide reveal major changes in the positions of the N domains with respect to the hexameric ring during the ATP hydrolysis cycle. Nucleotide binding and hydrolysis experiments indicate that D2 inhibits nucleotide exchange by D1. The data suggest that the conversion of the chemical energy of ATP hydrolysis into mechanical work on substrates involves transmission of conformational changes generated by D2 through D1 to move N.
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Affiliation(s)
- Jason M Davies
- Department of Structural Biology, Stanford University School of Medicine, 299 Campus Drive West, Stanford, California 94305, USA
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9
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Zhang X, Stoffels K, Wurzbacher S, Schoofs G, Pfeifer G, Banerjee T, Parret AHA, Baumeister W, De Mot R, Zwickl P. The N-terminal coiled coil of the Rhodococcus erythropolis ARC AAA ATPase is neither necessary for oligomerization nor nucleotide hydrolysis. J Struct Biol 2004; 146:155-65. [PMID: 15037247 DOI: 10.1016/j.jsb.2003.10.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2003] [Revised: 10/17/2003] [Indexed: 11/18/2022]
Abstract
Deletion mutants of the Rhodococcus erythropolis ARC AAA ATPase were generated and characterized by biochemical analysis and electron microscopy. Based on sequence comparisons the ARC protein was divided into three consecutive regions, the N-terminal coiled coil, the central ARC-specific inter domain and the C-terminal AAA domain. When the ARC AAA domain was expressed separately it formed aggregates of undefined structure. However, when the AAA domain was expressed in conjunction with the preceeding inter domain, but without the N-terminal coiled coil, high-molecular weight-complexes were formed (ARC-DeltaCC) which showed an N-ethylmaleimide-sensitive ATPase activity. In 2D crystallization experiments the ARC-DeltaCC particles yielded crystals nearly identical to those formed by the wild-type ARC complexes. Thus, the N-terminal coiled coil, which was proposed to have a role in the assembly of and/or interaction between the eukaryotic AAA ATPases in the 26S proteasome, is neither essential for assembly nor for ATP hydrolysis of the ARC ATPase. The N-terminal domain of related AAA ATPases mediates the interaction with substrates or co-factors, suggesting a regulatory function for the N-terminal coiled coil of the ARC ATPase. Surprisingly, the mutant ARC protein ARC-DeltaAAA consisting of the N-terminal coiled coil and the central inter domain, but deleted for the C-terminal AAA domain, was shown to form a dodecameric complex with sixfold symmetry. This suggests an important role of the inter domain for the ordered assembly of the ARC ATPase.
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Affiliation(s)
- Xujia Zhang
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, D-82152 Martinsried, Germany
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10
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Huyton T, Pye VE, Briggs LC, Flynn TC, Beuron F, Kondo H, Ma J, Zhang X, Freemont PS. The crystal structure of murine p97/VCP at 3.6A. J Struct Biol 2004; 144:337-48. [PMID: 14643202 DOI: 10.1016/j.jsb.2003.10.007] [Citation(s) in RCA: 155] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
p97/VCP is a member of the AAA ATPase family and has roles in both membrane fusion and ubiquitin dependent protein degradation. Here, we present a 3.6A crystal structure of murine p97 in which D2 domain has been modelled as poly-alanine and the remaining approximately 100 residues are absent. The resulting structure illustrates a head-to-tail packing arrangement of the two p97 AAA domains in a natural hexameric state with D1 ADP bound and D2 nucleotide free. The head-to-tail packing arrangement observed in this structure is in contrast to our previously predicted tail-to-tail packing model. The linker between the D1 and D2 domains is partially disordered, suggesting a flexible nature. Normal mode analysis of the crystal structure suggests anti-correlated motions and distinct conformational states of the two AAA domains.
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Affiliation(s)
- Trevor Huyton
- Department of Biological Sciences, Imperial College London, South Kensington SW7 2AZ, UK
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11
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Yuan X, Simpson P, Mckeown C, Kondo H, Uchiyama K, Wallis R, Dreveny I, Keetch C, Zhang X, Robinson C, Freemont P, Matthews S. Structure, dynamics and interactions of p47, a major adaptor of the AAA ATPase, p97. EMBO J 2004; 23:1463-73. [PMID: 15029246 PMCID: PMC391063 DOI: 10.1038/sj.emboj.7600152] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2003] [Accepted: 02/11/2004] [Indexed: 11/09/2022] Open
Abstract
p47 is a major adaptor molecule of the cytosolic AAA ATPase p97. The principal role of the p97-p47 complex is in regulation of membrane fusion events. Mono-ubiquitin recognition by p47 has also been shown to be crucial in the p97-p47-mediated Golgi membrane fusion events. Here, we describe the high-resolution solution structures of the N-terminal UBA domain and the central domain (SEP) from p47. The p47 UBA domain has the characteristic three-helix bundle fold and forms a highly stable complex with ubiquitin. We report the interaction surfaces of the two proteins and present a structure for the p47 UBA-ubiquitin complex. The p47 SEP domain adopts a novel fold with a betabetabetaalphaalphabeta secondary structure arrangement, where beta4 pairs in a parallel fashion to beta1. Based on biophysical studies, we demonstrate a clear propensity for the self-association of p47. Furthermore, p97 N binding abolishes p47 self-association, revealing the potential interaction surfaces for recognition of other domains within p97 or the substrate.
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Affiliation(s)
- Xuemei Yuan
- Department of Biological Sciences, Wolfson Laboratories, Imperial College London, South Kensington, London, UK
- Centre for Structural Biology, Imperial College London, South Kensington, London, UK
| | - Peter Simpson
- Department of Biological Sciences, Wolfson Laboratories, Imperial College London, South Kensington, London, UK
- Centre for Structural Biology, Imperial College London, South Kensington, London, UK
| | - Ciaran Mckeown
- Department of Biological Sciences, Wolfson Laboratories, Imperial College London, South Kensington, London, UK
- Centre for Structural Biology, Imperial College London, South Kensington, London, UK
| | - Hisao Kondo
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Keiji Uchiyama
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Russell Wallis
- Department of Glycobiology, University of Oxford, Oxford, UK
| | - Ingrid Dreveny
- Department of Biological Sciences, Wolfson Laboratories, Imperial College London, South Kensington, London, UK
- Centre for Structural Biology, Imperial College London, South Kensington, London, UK
| | | | - Xiaodong Zhang
- Department of Biological Sciences, Wolfson Laboratories, Imperial College London, South Kensington, London, UK
- Centre for Structural Biology, Imperial College London, South Kensington, London, UK
| | - Carol Robinson
- Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Paul Freemont
- Department of Biological Sciences, Wolfson Laboratories, Imperial College London, South Kensington, London, UK
- Centre for Structural Biology, Imperial College London, South Kensington, London, UK
| | - Stephen Matthews
- Department of Biological Sciences, Wolfson Laboratories, Imperial College London, South Kensington, London, UK
- Centre for Structural Biology, Imperial College London, South Kensington, London, UK
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12
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DeLaBarre B, Brunger AT. Complete structure of p97/valosin-containing protein reveals communication between nucleotide domains. Nat Struct Mol Biol 2003; 10:856-63. [PMID: 12949490 DOI: 10.1038/nsb972] [Citation(s) in RCA: 319] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2003] [Accepted: 07/28/2003] [Indexed: 11/09/2022]
Abstract
The ATPase p97/VCP affects multiple events within the cell. These events include the alteration of both nuclear and mitotic Golgi membranes, the dislocation of ubiquitylated proteins from the endoplasmic reticulum and regulation of the NF-kappa b pathway. Here we present the crystal structure of full-length Mus musculus p97/VCP in complex with a mixture of ADP and ADP-AlF(x) at a resolution of 4.7 A. This is the first complete hexameric structure of a protein containing tandem AAA (ATPases associated with a variety of cellular activities) domains. Comparison of the crystal structure and cryo-electron microscopy (EM) reconstructions reveals large conformational changes in the helical subdomains during the hydrolysis cycle. Structural and functional data imply a communication mechanism between the AAA domains. A Zn(2+) occludes the central pore of the hexamer, suggesting that substrate does not thread through the pore of the molecule.
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Affiliation(s)
- Byron DeLaBarre
- Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Stanford University, James H. Clark Center E300-C, 318 Campus Drive, Stanford, California 94305-5432, USA
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13
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Maupin-Furlow JA, Kaczowka SJ, Reuter CJ, Zuobi-Hasona K, Gil MA. Archaeal proteasomes: potential in metabolic engineering. Metab Eng 2003; 5:151-63. [PMID: 12948749 DOI: 10.1016/s1096-7176(03)00030-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Archaea are a valuable source of enzymes for industrial and scientific applications because of their ability to survive extreme conditions including high salt and temperature. Thanks to advances in molecular biology and genetics, archaea are also attractive hosts for metabolic engineering. Understanding how energy-dependent proteases and chaperones function to maintain protein quality control is key to high-level synthesis of recombinant products. In archaea, proteasomes are central players in energy-dependent proteolysis and form elaborate nanocompartments that degrade proteins into oligopeptides by processive hydrolysis. The catalytic core responsible for this proteolytic activity is the 20S proteasome, a barrel-shaped particle with a central channel and axial gates on each end that limit substrate access to a central proteolytic chamber. AAA proteins (ATPases associated with various cellular activities) are likely to play several roles in mediating energy-dependent proteolysis by the proteasome. These include ATP binding/hydrolysis, substrate binding/unfolding, opening of the axial gates, and translocation of substrate into the proteolytic chamber.
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Affiliation(s)
- Julie A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Room 1052, Building 981, Gainesville, FL 32611-0700, USA.
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14
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Abstract
Proteasomes are large, multisubunit proteases that are found, in one form or another, in all domains of life and play a critical role in intracellular protein degradation. Although they have substantial structural similarity, the proteasomes of bacteria, archaea, and eukaryotes show many differences in architecture and subunit composition. This article discusses possible paths by which proteasomes may have evolved from simple precursors to the highly complicated and diverse complexes observed today.
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Affiliation(s)
- C Volker
- SmithKline Beecham Pharmaceuticals, UP 1345, 1250 South Collegeville Road, Collegeville, PA 19426-0989, USA
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15
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Maupin-Furlow JA, Kaczowka SJ, Ou MS, Wilson HL. Archaeal proteasomes: proteolytic nanocompartments of the cell. ADVANCES IN APPLIED MICROBIOLOGY 2002; 50:279-338. [PMID: 11677686 DOI: 10.1016/s0065-2164(01)50008-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- J A Maupin-Furlow
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611-0700, USA
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16
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Rockel B, Jakana J, Chiu W, Baumeister W. Electron cryo-microscopy of VAT, the archaeal p97/CDC48 homologue from Thermoplasma acidophilum. J Mol Biol 2002; 317:673-81. [PMID: 11955016 DOI: 10.1006/jmbi.2002.5448] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
VAT (valosine containing protein-like ATPase from Thermoplasma acidophilum), an archaeal member of the AAA-family (ATPases associated with a variety of cellular activities) that possesses foldase as well as unfoldase-activity, forms homo-hexameric rings like its eukaryotic homologues p97 and CDC48. The VAT-monomer exhibits the tripartite domain architecture typical for type II AAA-ATPases: N-D1-D2, whereby N is the substrate binding N-terminal domain preceding domains D1 and D2, both containing AAA-modules. Recent 3-D reconstructions of VAT and p97 as obtained by electron microscopy suffer from weakly represented N-domains, probably a consequence of their flexible linkage to the hexameric core. Here we used electron cryo-microscopy and 3-D reconstruction of single particles in order to generate a 3-D model of VAT at 2.3 nm resolution. The hexameric core of the VAT-complex (diameter 13.2 nm, height 8.4 nm) encloses a central cavity and the substrate-binding N-domains are clearly arranged in the upper periphery. Comparison with the p97 3-D reconstruction and the recently determined crystal structure of p97-N-D1 suggests a tail-to-tail arrangement of D1 and D2 in VAT.
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Affiliation(s)
- Beate Rockel
- Max-Planck-Institut für Biochemie, Abteilung Molekulare Strukturbiologie, Am Klopferspitz 18 a, 82152 Martinsried, Germany.
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17
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Frangakis AS, Hegerl R. Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion. J Struct Biol 2001; 135:239-50. [PMID: 11722164 DOI: 10.1006/jsbi.2001.4406] [Citation(s) in RCA: 291] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Electron tomography is a powerful technique capable of giving unique insights into the three-dimensional structural organization of pleomorphic biological objects. However, visualization and interpretation of the resulting volumetric data are hampered by an extremely low signal-to-noise ratio, especially when ice-embedded biological specimens are investigated. Usually, isosurface representation or volume rendering of such data is hindered without any further signal enhancement. We propose a novel technique for noise reduction based on nonlinear anisotropic diffusion. The approach combines efficient noise reduction with excellent signal preservation and is clearly superior to conventional methods (e.g., low-pass and median filtering) and invariant wavelet transform filtering. The gain in the signal-to-noise ratio is verified and demonstrated by means of Fourier shell correlation. Improved visualization performance after processing the 3D images is demonstrated with two examples, tomographic reconstructions of chromatin and of a mitochondrion. Parameter settings and discretization stencils are presented in detail.
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Affiliation(s)
- A S Frangakis
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, Martinsried, D-82152, Germany
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18
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Yuan X, Shaw A, Zhang X, Kondo H, Lally J, Freemont PS, Matthews S. Solution structure and interaction surface of the C-terminal domain from p47: a major p97-cofactor involved in SNARE disassembly. J Mol Biol 2001; 311:255-63. [PMID: 11478859 DOI: 10.1006/jmbi.2001.4864] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
p47 is the major protein identified in complex with the cytosolic AAA ATPase p97. It functions as an essential cofactor of p97-regulated membrane fusion, which has been suggested to disassemble t-t-SNARE complexes and prepare them for further rounds of membrane fusion. Here, we report the high-resolution NMR structure of the C-terminal domain from p47. It comprises a UBX domain and a 13 residue long structured N-terminal extension. The UBX domain adopts a characteristic ubiquitin fold with a betabetaalphabetabetaalphabeta secondary structure arrangement. Three hydrophobic residues from the N-terminal extension pack closely against a cleft in the UBX domain. We also identify, for the first time, the p97 interaction surface using NMR chemical shift perturbation studies.
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Affiliation(s)
- X Yuan
- Department of Biological Sciences, Wolfson Laboratories, Imperial College of Science Technology and Medicine, London, South Kensington, SW7 2AY, UK
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19
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Ruepp A, Rockel B, Gutsche I, Baumeister W, Lupas AN. The Chaperones of the archaeon Thermoplasma acidophilum. J Struct Biol 2001; 135:126-38. [PMID: 11580262 DOI: 10.1006/jsbi.2001.4402] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Chaperonesare an essential component of a cell's ability to respond to environmental challenges. Chaperones have been studied primarily in bacteria, but in recent years it has become apparent that some classes of chaperones either are very divergent in bacteria relative to archaea and eukaryotes or are missing entirely. In contrast, a high degree of similarity was found between the chaperonins of archaea and those of the eukaryotic cytosol, which has led to the establishment of archaeal model systems. The archaeon most extensively used for such studies is Thermoplasma acidophilum, which thrives at 59 degrees C and pH 2. Here we review information on its chaperone complement in light of the recently determined genome sequence.
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Affiliation(s)
- A Ruepp
- Department of Molecular Structural Biology, Max-Planck-Institute for Biochemistry, Am Klopferspitz 18a, Martinsried, D-82152, Germany
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20
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May AP, Whiteheart SW, Weis WI. Unraveling the mechanism of the vesicle transport ATPase NSF, the N-ethylmaleimide-sensitive factor. J Biol Chem 2001; 276:21991-4. [PMID: 11301340 DOI: 10.1074/jbc.r100013200] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- A P May
- Department of Structural Biology and Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, California 94305, USA
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21
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Affiliation(s)
- S Dalal
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
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22
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Whiteheart SW, Schraw T, Matveeva EA. N-ethylmaleimide sensitive factor (NSF) structure and function. INTERNATIONAL REVIEW OF CYTOLOGY 2001; 207:71-112. [PMID: 11352269 DOI: 10.1016/s0074-7696(01)07003-6] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Our understanding of the molecular mechanisms of membrane trafficking advanced at a rapid rate during the 1990s. As one of the initial protein components of the trafficking machinery to be identified, N-ethylmaleimide sensitive factor (NSF) has served as a reference point in many of these recent studies. This hexameric ATPase is essential for most of the membrane-trafficking events in a cell. Initially, due to its ATPase activity, NSF was thought to be the motor that drove membrane fusion. Subsequent studies have shown that NSF actually plays the role of a chaperone by activating SNAP receptor proteins (SNAREs) so that they can participate in membrane fusion. In this review we will examine the initial characterization of NSF, its role in membrane fusion events, and what new structural information can tell us about NSF's mechanism of action.
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Affiliation(s)
- S W Whiteheart
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington 40536, USA
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23
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Rouiller I, Butel VM, Latterich M, Milligan RA, Wilson-Kubalek EM. A major conformational change in p97 AAA ATPase upon ATP binding. Mol Cell 2000; 6:1485-90. [PMID: 11163220 DOI: 10.1016/s1097-2765(00)00144-1] [Citation(s) in RCA: 135] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
AAA ATPases play central roles in cellular activities. The ATPase p97, a prototype of this superfamily, participates in organelle membrane fusion. Cryoelectron microscopy and single-particle analysis revealed that a major conformational change of p97 during the ATPase cycle occurred upon nucleotide binding and not during hydrolysis as previously hypothesized. Furthermore, our study indicates that six p47 adaptor molecules bind to the periphery of the ring-shaped p97 hexamer. Taken together, these results provide a revised model of how this and possibly other AAA ATPases can translate nucleotide binding into conformational changes of associated binding partners.
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Affiliation(s)
- I Rouiller
- Department of Cell Biology, Scripps Research Institute, La Jolla, CA 92037, USA
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24
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Zhang X, Shaw A, Bates PA, Newman RH, Gowen B, Orlova E, Gorman MA, Kondo H, Dokurno P, Lally J, Leonard G, Meyer H, van Heel M, Freemont PS. Structure of the AAA ATPase p97. Mol Cell 2000; 6:1473-84. [PMID: 11163219 DOI: 10.1016/s1097-2765(00)00143-x] [Citation(s) in RCA: 356] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
p97, an abundant hexameric ATPase of the AAA family, is involved in homotypic membrane fusion. It is thought to disassemble SNARE complexes formed during the process of membrane fusion. Here, we report two structures: a crystal structure of the N-terminal and D1 ATPase domains of murine p97 at 2.9 A resolution, and a cryoelectron microscopy structure of full-length rat p97 at 18 A resolution. Together, these structures show that the D1 and D2 hexamers pack in a tail-to-tail arrangement, and that the N domain is flexible. A comparison with NSF D2 (ATP complex) reveals possible conformational changes induced by ATP hydrolysis. Given the D1 and D2 packing arrangement, we propose a ratchet mechanism for p97 during its ATP hydrolysis cycle.
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Affiliation(s)
- X Zhang
- Molecular Structure and Function Laboratory, Imperial Cancer Research Fund, London SW7 2AY, United Kingdom
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25
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Rockel B, Guckenberger R, Gross H, Tittmann P, Baumeister W. Rotary and unidirectional metal shadowing of VAT: localization of the substrate-binding domain. J Struct Biol 2000; 132:162-8. [PMID: 11162738 DOI: 10.1006/jsbi.2000.4313] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
AAA-ATPases have important roles in manifold cellular processes. VAT (valosine-containing protein-like ATPase of Thermoplasma acidophilum), a hexameric archaeal member of this family, has the tripartite domain structure N-D1-D2 that is characteristic of many members of this family. N, the N-terminal domain of 20.5 kDa, has been implicated in substrate binding. We have applied rotary and unidirectional shadowing to VAT and an N-terminally deleted mutant, VAT(Delta N), in order to map the location of this domain. For the analysis of data derived from unidirectionally shadowed samples we used a new approach combining eigenvector analysis with surface relief reconstruction. Averages of rotary shadowed particles as well as relief reconstructions map the N-terminal domains to the periphery of the hexameric complex and reveal their bipartite structure. Thus, this method appears to be well suited to study the conformational changes that occur during the functional cycle of the protein.
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Affiliation(s)
- B Rockel
- Abteilung Molekulare Strukturbiologie, Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, 82152 Martinsried, Germany
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26
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Coles M, Diercks T, Liermann J, Gröger A, Rockel B, Baumeister W, Koretke KK, Lupas A, Peters J, Kessler H. The solution structure of VAT-N reveals a 'missing link' in the evolution of complex enzymes from a simple betaalphabetabeta element. Curr Biol 1999; 9:1158-68. [PMID: 10531028 DOI: 10.1016/s0960-9822(00)80017-2] [Citation(s) in RCA: 80] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND The VAT protein of the archaebacterium Thermoplasma acidophilum, like all other members of the Cdc48/p97 family of AAA ATPases, has two ATPase domains and a 185-residue amino-terminal substrate-recognition domain, VAT-N. VAT shows activity in protein folding and unfolding and thus shares the common function of these ATPases in disassembly and/or degradation of protein complexes. RESULTS Using nuclear magnetic resonance (NMR) spectroscopy, we found that VAT-N is composed of two equally sized subdomains. The amino-terminal subdomain VAT-Nn (comprising residues Met1-Thr92) forms a double-psi beta-barrel whose pseudo-twofold symmetry is mirrored by an internal sequence repeat of 42 residues. The carboxy-terminal subdomain VAT-Nc (comprising residues Glu93-Gly185) forms a novel six-stranded beta-clam fold. Together, VAT-Nn and VAT-Nc form a kidney-shaped structure, in close agreement with results from electron microscopy. Sequence and structure analyses showed that VAT-Nn is related to numerous proteins including prokaryotic transcription factors, metabolic enzymes, the protease cofactors UFD1 and PrlF, and aspartic proteinases. These proteins map out an evolutionary path from simple homodimeric transcription factors containing a single copy of the VAT-Nn repeat to complex enzymes containing four copies. CONCLUSIONS Our results suggest that VAT-N is a precursor of the aspartic proteinases that has acquired peptide-binding activity while remaining proteolytically incompetent. We propose that the binding site of the protein is similar to that of aspartic proteinases, in that it lies between the psi-loops of the amino-terminal beta-barrel and that it coincides with a crescent-shaped band of positive charge extending across the upper face of the molecule.
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Affiliation(s)
- M Coles
- Institut für Organische Chemie und Biochemie, Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
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Golbik R, Lupas AN, Koretke KK, Baumeister W, Peters J. The Janus face of the archaeal Cdc48/p97 homologue VAT: protein folding versus unfolding. Biol Chem 1999; 380:1049-62. [PMID: 10543442 DOI: 10.1515/bc.1999.131] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Members of the AAA family of ATPases have been implicated in chaperone-like activities. We used the archaeal Cdc48/p97 homologue VAT as a model system to investigate the effect of an AAA protein on the folding and unfolding of two well-studied, heterologous substrates, cyclophilin and penicillinase. We found that, depending on the Mg2+ concentration, VAT assumes two states with maximum rates of ATP hydrolysis that differ by an order of magnitude. In the low-activity state, VAT accelerated the refolding of penicillinase, whereas in the high-activity state, it accelerated its unfolding. Both reactions were ATP-dependent. In its interaction with cyclophilin, VAT was ATP-independent and only promoted refolding. The N-terminal domain of VAT, which lacks ATPase activity, also accelerated the refolding of cyclophilin but showed no effect on penicillinase. VAT appears to be structurally equivalent over its entire length to Sec18/NSF, suggesting that these results apply more broadly to group II AAA proteins.
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Affiliation(s)
- R Golbik
- Department of Biochemistry, Martin-Luther-University, Halle-Wittenberg, Halle, Germany
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