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Huang X, Sun S, Wang X, Fan F, Zhou Q, Lu S, Cao Y, Wang QW, Dong MQ, Yao J, Sui SF. Mechanistic insights into the SNARE complex disassembly. SCIENCE ADVANCES 2019; 5:eaau8164. [PMID: 30989110 PMCID: PMC6457932 DOI: 10.1126/sciadv.aau8164] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 02/19/2019] [Indexed: 05/16/2023]
Abstract
NSF (N-ethylmaleimide-sensitive factor) and α-SNAP (α-soluble NSF attachment protein) bind to the SNARE (soluble NSF attachment protein receptor) complex, the minimum machinery to mediate membrane fusion, to form a 20S complex, which disassembles the SNARE complex for reuse. We report the cryo-EM structures of the α-SNAP-SNARE subcomplex and the NSF-D1D2 domain in the 20S complex at 3.9- and 3.7-Å resolutions, respectively. Combined with the biochemical and electrophysiological analyses, we find that α-SNAPs use R116 through electrostatic interactions and L197 through hydrophobic interactions to apply force mainly on two positions of the VAMP protein to execute disassembly process. Furthermore, we define the interaction between the amino terminus of the SNARE helical bundle and the pore loop of the NSF-D1 domain and demonstrate its essential role as a potential anchor for SNARE complex disassembly. Our studies provide a rotation model of α-SNAP-mediated disassembly of the SNARE complex.
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Affiliation(s)
- Xuan Huang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shan Sun
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaojing Wang
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Fenghui Fan
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qiang Zhou
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shan Lu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yong Cao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Qiu-Wen Wang
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jun Yao
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, IDG/McGovern Institute for Brain Research, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Sen-Fang Sui
- State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
- Corresponding author.
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Kienle N, Kloepper TH, Fasshauer D. Shedding light on the expansion and diversification of the Cdc48 protein family during the rise of the eukaryotic cell. BMC Evol Biol 2016; 16:215. [PMID: 27756227 PMCID: PMC5070193 DOI: 10.1186/s12862-016-0790-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Accepted: 10/04/2016] [Indexed: 11/22/2022] Open
Abstract
Background A defining feature of eukaryotic cells is the presence of various distinct membrane-bound compartments with different metabolic roles. Material exchange between most compartments occurs via a sophisticated vesicle trafficking system. This intricate cellular architecture of eukaryotes appears to have emerged suddenly, about 2 billion years ago, from much less complex ancestors. How the eukaryotic cell acquired its internal complexity is poorly understood, partly because no prokaryotic precursors have been found for many key factors involved in compartmentalization. One exception is the Cdc48 protein family, which consists of several distinct classical ATPases associated with various cellular activities (AAA+) proteins with two consecutive AAA domains. Results Here, we have classified the Cdc48 family through iterative use of hidden Markov models and tree building. We found only one type, Cdc48, in prokaryotes, although a set of eight diverged members that function at distinct subcellular compartments were retrieved from eukaryotes and were probably present in the last eukaryotic common ancestor (LECA). Pronounced changes in sequence and domain structure during the radiation into the LECA set are delineated. Moreover, our analysis brings to light lineage-specific losses and duplications that often reflect important biological changes. Remarkably, we also found evidence for internal duplications within the LECA set that probably occurred during the rise of the eukaryotic cell. Conclusions Our analysis corroborates the idea that the diversification of the Cdc48 family is closely intertwined with the development of the compartments of the eukaryotic cell. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0790-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nickias Kienle
- Département des neurosciences fondamentales, Université de Lausanne, Rue du Bugnon 9, CH-1005, Lausanne, Switzerland
| | - Tobias H Kloepper
- Sir William Dunn School of Pathology, Research Group Cell Biology of Intercellular Signaling, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Dirk Fasshauer
- Département des neurosciences fondamentales, Université de Lausanne, Rue du Bugnon 9, CH-1005, Lausanne, Switzerland.
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Starr ML, Hurst LR, Fratti RA. Phosphatidic Acid Sequesters Sec18p from cis-SNARE Complexes to Inhibit Priming. Traffic 2016; 17:1091-109. [PMID: 27364524 DOI: 10.1111/tra.12423] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 06/28/2016] [Accepted: 06/28/2016] [Indexed: 01/08/2023]
Abstract
Yeast vacuole fusion requires the activation of cis-SNARE complexes through priming carried out by Sec18p/N-ethylmaleimide sensitive factor and Sec17p/α-SNAP. The association of Sec18p with vacuolar cis-SNAREs is regulated in part by phosphatidic acid (PA) phosphatase production of diacylglycerol (DAG). Inhibition of PA phosphatase activity blocks the transfer of membrane-associated Sec18p to SNAREs. Thus, we hypothesized that Sec18p associates with PA-rich membrane microdomains before transferring to cis-SNARE complexes upon PA phosphatase activity. Here, we examined the direct binding of Sec18p to liposomes containing PA or DAG. We found that Sec18p preferentially bound to liposomes containing PA compared with those containing DAG by approximately fivefold. Additionally, using a specific PA-binding domain blocked Sec18p binding to PA-liposomes and displaced endogenous Sec18p from isolated vacuoles. Moreover, the direct addition of excess PA blocked the priming activity of isolated vacuoles in a manner similar to chemically inhibiting PA phosphatase activity. These data suggest that the conversion of PA to DAG facilitates the recruitment of Sec18p to cis-SNAREs. Purified vacuoles from yeast lacking the PA phosphatase Pah1p showed reduced Sec18p association with cis-SNAREs and complementation with plasmid-encoded PAH1 or recombinant Pah1p restored the interaction. Taken together, this demonstrates that regulating PA concentrations by Pah1p activity controls SNARE priming by Sec18p.
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Affiliation(s)
- Matthew L Starr
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Logan R Hurst
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Rutilio A Fratti
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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Chang LF, Chen S, Liu CC, Pan X, Jiang J, Bai XC, Xie X, Wang HW, Sui SF. Structural characterization of full-length NSF and 20S particles. Nat Struct Mol Biol 2012; 19:268-75. [PMID: 22307055 DOI: 10.1038/nsmb.2237] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2011] [Accepted: 12/20/2011] [Indexed: 11/09/2022]
Abstract
The 20S particle, which is composed of the N-ethylmaleimide-sensitive factor (NSF), soluble NSF attachment proteins (SNAPs) and the SNAP receptor (SNARE) complex, has an essential role in intracellular vesicle fusion events. Using single-particle cryo-EM and negative stain EM, we reconstructed four related three-dimensional structures: Chinese hamster NSF hexamer in the ATPγS, ADP-AlFx and ADP states, and the 20S particle. These structures reveal a parallel arrangement between the D1 and D2 domains of the hexameric NSF and characterize the nucleotide-dependent conformational changes in NSF. The structure of the 20S particle shows that it holds the SNARE complex at two interaction interfaces around the C terminus and N-terminal half of the SNARE complex, respectively. These findings provide insight into the molecular mechanism underlying disassembly of the SNARE complex by NSF.
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Affiliation(s)
- Lei-Fu Chang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing, China
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Requirements for the catalytic cycle of the N-ethylmaleimide-Sensitive Factor (NSF). BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2011; 1823:159-71. [PMID: 21689688 DOI: 10.1016/j.bbamcr.2011.06.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 05/23/2011] [Accepted: 06/06/2011] [Indexed: 12/23/2022]
Abstract
The N-ethylmaleimide-Sensitive Factor (NSF) was one of the initial members of the ATPases Associated with various cellular Activities Plus (AAA(+)) family. In this review, we discuss what is known about the mechanism of NSF action and how that relates to the mechanisms of other AAA(+) proteins. Like other family members, NSF binds to a protein complex (i.e., SNAP-SNARE complex) and utilizes ATP hydrolysis to affect the conformations of that complex. SNAP-SNARE complex disassembly is essential for SNARE recycling and sustained membrane trafficking. NSF is a homo-hexamer; each protomer is composed of an N-terminal domain, NSF-N, and two adjacent AAA-domains, NSF-D1 and NSF-D2. Mutagenesis analysis has established specific roles for many of the structural elements of NSF-D1, the catalytic ATPase domain, and NSF-N, the SNAP-SNARE binding domain. Hydrodynamic analysis of NSF, labeled with (Ni(2+)-NTA)(2)-Cy3, detected conformational differences in NSF, in which the ATP-bound conformation appears more compact than the ADP-bound form. This indicates that NSF undergoes significant conformational changes as it progresses through its ATP-hydrolysis cycle. Incorporating these data, we propose a sequential mechanism by which NSF uses NSF-N and NSF-D1 to disassemble SNAP-SNARE complexes. We also illustrate how analytical centrifugation might be used to study other AAA(+) proteins.
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Dokudovskaya S, Waharte F, Schlessinger A, Pieper U, Devos DP, Cristea IM, Williams R, Salamero J, Chait BT, Sali A, Field MC, Rout MP, Dargemont C. A conserved coatomer-related complex containing Sec13 and Seh1 dynamically associates with the vacuole in Saccharomyces cerevisiae. Mol Cell Proteomics 2011; 10:M110.006478. [PMID: 21454883 DOI: 10.1074/mcp.m110.006478] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The presence of multiple membrane-bound intracellular compartments is a major feature of eukaryotic cells. Many of the proteins required for formation and maintenance of these compartments share an evolutionary history. Here, we identify the SEA (Seh1-associated) protein complex in yeast that contains the nucleoporin Seh1 and Sec13, the latter subunit of both the nuclear pore complex and the COPII coating complex. The SEA complex also contains Npr2 and Npr3 proteins (upstream regulators of TORC1 kinase) and four previously uncharacterized proteins (Sea1-Sea4). Combined computational and biochemical approaches indicate that the SEA complex proteins possess structural characteristics similar to the membrane coating complexes COPI, COPII, the nuclear pore complex, and, in particular, the related Vps class C vesicle tethering complexes HOPS and CORVET. The SEA complex dynamically associates with the vacuole in vivo. Genetic assays indicate a role for the SEA complex in intracellular trafficking, amino acid biogenesis, and response to nitrogen starvation. These data demonstrate that the SEA complex is an additional member of a family of membrane coating and vesicle tethering assemblies, extending the repertoire of protocoatomer-related complexes.
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Zhao C, Matveeva EA, Ren Q, Whiteheart SW. Dissecting the N-ethylmaleimide-sensitive factor: required elements of the N and D1 domains. J Biol Chem 2009; 285:761-72. [PMID: 19887446 DOI: 10.1074/jbc.m109.056739] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
N-Ethylmaleimide-sensitive factor (NSF) is a homo-hexameric member of the AAA(+) (ATPases associated with various cellular activities plus) family. It plays an essential role in most intracellular membrane trafficking through its binding to and disassembly of soluble NSF attachment protein (SNAP) receptor (SNARE) complexes. Each NSF protomer contains an N-terminal domain (NSF-N) and two AAA domains, a catalytic NSF-D1 and a structural NSF-D2. This study presents detailed mutagenesis analyses of NSF-N and NSF-D1, dissecting their roles in ATP hydrolysis, SNAP.SNARE binding, and complex disassembly. Our results show that a positively charged surface on NSF-N, bounded by Arg(67) and Lys(105), and the conserved residues in the central pore of NSF-D1 (Tyr(296) and Gly(298)) are involved in SNAP.SNARE binding but not basal ATP hydrolysis. Mutagenesis of Sensor 1 (Thr(373)-Arg(375)), Sensor 2 (Glu(440)-Glu(442)), and Arginine Fingers (Arg(385) and Arg(388)) in NSF-D1 shows that each region plays a discrete role. Sensor 1 is important for basal ATPase activity and nucleotide binding. Sensor 2 plays a role in ATP- and SNAP-dependent SNARE complex binding and disassembly but does so in cis and not through inter-protomer interactions. Arginine Fingers are important for SNAP.SNARE complex-stimulated ATPase activity and complex disassembly. Mutants at these residues have a dominant-negative phenotype in cells, suggesting that Arginine Fingers function in trans via inter-protomer interactions. Taken together, these data establish functional roles for many of the structural elements of the N domain and of the D1 ATP-binding site of NSF.
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Affiliation(s)
- Chunxia Zhao
- Department of Molecular and Cellular Biochemistry, University of Kentucky Medical Center, Lexington, Kentucky 40536-0509, USA
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Zhao C, Slevin JT, Whiteheart SW. Cellular functions of NSF: not just SNAPs and SNAREs. FEBS Lett 2007; 581:2140-9. [PMID: 17397838 PMCID: PMC1948069 DOI: 10.1016/j.febslet.2007.03.032] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Accepted: 03/07/2007] [Indexed: 12/26/2022]
Abstract
N-ethylmaleimide sensitive factor (NSF) is an ATPases associated with various cellular activities protein (AAA), broadly required for intracellular membrane fusion. NSF functions as a SNAP receptor (SNARE) chaperone which binds, through soluble NSF attachment proteins (SNAPs), to SNARE complexes and utilizes the energy of ATP hydrolysis to disassemble them thus facilitating SNARE recycling. While this is a major function of NSF, it does seem to interact with other proteins, such as the AMPA receptor subunit, GluR2, and beta2-AR and is thought to affect their trafficking patterns. New data suggest that NSF may be regulated by transient post-translational modifications such as phosphorylation and nitrosylation. These new aspects of NSF function as well as its role in SNARE complex dynamics will be discussed.
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Affiliation(s)
- Chunxia Zhao
- Departmental of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, USA
| | - John T. Slevin
- Neurology Service, Department of Veterans Affairs Medical Center, Departments of Neurology and Molecular and Biomedical Pharmacology, University of Kentucky Medical Center, Lexington, KY, USA
| | - Sidney W. Whiteheart
- Departmental of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, Lexington, KY, USA
- *Corresponding author. 741 South Limestone, BBSRB B261, Lexington, KY 40536, USA. Phone: 1-859-257-4882. Fax: 1-859-257-2283. E-mail address:
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Abstract
Vascular injury triggers endothelial exocytosis of granules, releasing pro-inflammatory and pro-thrombotic mediators into the blood. Nitric oxide (NO) and reactive oxygen species (ROS) limit vascular inflammation and thrombosis by inhibiting endothelial exocytosis. NO decreases exocytosis by regulating the activity of the N-ethylmaleimide-sensitive factor (NSF), a central component of the exocytic machinery. NO nitrosylates specific cysteine residues of NSF, thereby inhibiting NSF disassembly of the soluble NSF attachment protein receptor (SNARE). NO also modulates exocytosis of other cells; for example, NO regulates platelet activation by inhibiting alpha-granule secretion from platelets. Other radicals besides NO can regulate exocytosis as well. For example, H(2)O(2) inhibits exocytosis by oxidizing NSF. Using site-directed mutagenesis, we have defined the critical cysteine residues of NSF, and found that one particular cysteine residue, C264, renders NSF sensitive to oxidative stress. Since radicals such as NO and H(2)O(2) inhibit NSF and decrease exocytosis, NSF may act as a redox sensor, modulating exocytosis in response to changes in oxidative stress.
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Affiliation(s)
- Charles J Lowenstein
- Department of Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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10
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Shiozawa K, Goda N, Shimizu T, Mizuguchi K, Kondo N, Shimozawa N, Shirakawa M, Hiroaki H. The common phospholipid-binding activity of the N-terminal domains of PEX1 and VCP/p97. FEBS J 2006; 273:4959-71. [PMID: 17018057 DOI: 10.1111/j.1742-4658.2006.05494.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PEX1 is a type II AAA-ATPase that is indispensable for biogenesis and maintenance of the peroxisome, an organelle responsible for the primary metabolism of lipids, such as beta-oxidation and lipid biosynthesis. Recently, we demonstrated a striking structural similarity between its N-terminal domain and those of other membrane-related AAA-ATPases, such as valosine-containing protein (p97). The N-terminal domain of valosine-containing protein serves as an interface to its adaptor proteins p47 and Ufd1, whereas the physiologic interaction partner of the N-terminal domain of PEX1 remains unknown. Here we found that N-terminal domains isolated from valosine-containing protein, as well as from PEX1, bind phosphoinositides. The N-terminal domain of PEX1 appears to preferentially bind phosphatidylinositol 3-monophosphate and phosphatidylinositol 4-monophosphate, whereas the N-terminal domain of valosine-containing protein displays broad and nonspecific lipid binding. Although N-ethylmaleimide-sensitive fusion protein, CDC48 and Ufd1 have structures similar to that of valosine-containing protein, they displayed lipid specificity similar to that of the N-terminal domain of PEX1 in the assays. By mutational analysis, we demonstrate that a conserved arginine surrounded by hydrophobic residues is essential for lipid binding, despite very low sequence similarity between PEX1 and valosine-containing protein.
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Affiliation(s)
- Kumiko Shiozawa
- International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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11
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Deshmukh MV, John M, Coles M, Peters J, Baumeister W, Kessler H. Inter-domain orientation and motions in VAT-N explored by residual dipolar couplings and 15N backbone relaxation. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2006; 44 Spec No:S89-S100. [PMID: 16826545 DOI: 10.1002/mrc.1837] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The N-terminal domain of VAT (Valosine-containing protein-like ATPase of Thermoplasma acidophilum), VAT-N (20.5 kDa), is considered to be the primary substrate-recognition site of the complex. The solution structure of VAT-N derived in our laboratory using conventionally obtained NMR restraints shows the existence of two equally sized sub-domains, VAT-Nn and VAT-Nc, together forming a kidney-shaped overall structure. The putative substrate-binding site of VAT-N involves free loops and a highly charged groove located on the surface of the protein. Alternatively, the opening of the cleft between the domains to accommodate substrate has been proposed to be part of the functional mechanism. We have used the residual dipolar couplings (RDCs) obtained in a bicelle medium to refine the structure of VAT-N. The long-range information available from RDCs both defines the sub-domain orientation and probes possible inter-domain motions. In addition, 15N backbone relaxation data were obtained and analysed within the model-free framework. Together, the data provides a refined structure with improved local geometry, but with the overall kidney shape intact. Further, the protein is rigid overall, with no evidence of inter-domain motions.
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Affiliation(s)
- Mandar V Deshmukh
- Department Chemie, Technische Universität München, Lichtenbergstrasse 4, 85747, Garching, Germany
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12
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DeLaBarre B, Brunger AT. Nucleotide dependent motion and mechanism of action of p97/VCP. J Mol Biol 2005; 347:437-52. [PMID: 15740751 DOI: 10.1016/j.jmb.2005.01.060] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2004] [Revised: 01/18/2005] [Accepted: 01/21/2005] [Indexed: 11/29/2022]
Abstract
The AAA (ATPases associated with a variety of cellular activities) family of proteins bind, hydrolyze, and release ATP to effect conformational changes, assembly, or disassembly upon their binding partners and substrate molecules. One of the members of this family, the hexameric p97/valosin-containing protein p97/VCP, is essential for the dislocation of misfolded membrane proteins from the endoplasmic reticulum. Here, we observe large motions and dynamic changes of p97/VCP as it proceeds through the ATP hydrolysis cycle. The analysis is based on crystal structures of four representative ATP hydrolysis states: APO, AMP-PNP, hydrolysis transition state ADP x AlF3, and ADP bound. Two of the structures presented herein, ADP and AMP-PNP bound, are new structures, and the ADP x AlF3 structure was re-refined to higher resolution. The largest motions occur at two stages during the hydrolysis cycle: after, but not upon, nucleotide binding and then following nucleotide release. The motions occur primarily in the D2 domain, the D1 alpha-helical domain, and the N-terminal domain, relative to the relatively stationary and invariant D1alpha/beta domain. In addition to the motions, we observed a transition from a rigid state to a flexible state upon loss of the gamma-phosphate group, and a further increase in flexibility within the D2 domains upon nucleotide release. The domains within each protomer of the hexameric p97/VCP deviate from strict 6-fold symmetry, with the more flexible ADP state exhibiting greater asymmetry compared to the relatively rigid ADP x AlF3 state, suggesting a mechanism of action in which hydrolysis and conformational changes move about the hexamer in a processive fashion.
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Affiliation(s)
- Byron DeLaBarre
- Howard Hughes Medical Institute, and Department of Molecular and Cellular Physiology, and Stanford Synchrotron Radiation Laboratory, Stanford University, J.H. Clark Center E300-C, 318 Campus Drive, Stanford, CA 94305-5432, USA
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13
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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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Whiteheart SW, Matveeva EA. Multiple binding proteins suggest diverse functions for the N-ethylmaleimide sensitive factor. J Struct Biol 2004; 146:32-43. [PMID: 15037235 DOI: 10.1016/j.jsb.2003.09.015] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2003] [Revised: 09/12/2003] [Indexed: 01/12/2023]
Abstract
The hexameric ATPase, N-ethylmaleimide sensitive factor (NSF), is essential to vesicular transport and membrane fusion because it affects the conformations and associations of the soluble NSF attachment protein receptor (SNARE) proteins. NSF binds SNAREs through adaptors called soluble NSF attachment proteins (alpha- or beta-SNAP) and disassembles SNARE complexes to recycle the monomers. NSF contains three domains, two nucleotide-binding domains (NSF-D1 and -D2) and an amino terminal domain (NSF-N) that is required for SNAP-SNARE complex binding. Mutagenesis studies indicate that a cleft between the two sub-domains of NSF-N is critical for binding. The structural conservation of N domains in NSF, p97/VCP, and VAT suggests that a similar type of binding site could mediate substrate recognition by other AAA proteins. In addition to SNAP-SNARE complexes, NSF also binds other proteins and protein complexes such as AMPA receptor subunits (GluR2), beta2-adrenergic receptor, beta-Arrestin1, GATE-16, LMA1, rabs, and rab-containing complexes. The potential for these interactions indicates a broader role for NSF in the assembly/disassembly cycles of several cellular complexes and suggests that NSF may have specific regulatory effects on the functions of the proteins involved in these complexes. The structural requirements for these interactions and their physiological significance will be discussed.
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Affiliation(s)
- Sidney W Whiteheart
- Department of Molecular and Cellular Biochemistry, University of Kentucky College of Medicine, 800 Rose Street, Lexington, KY 40536, USA.
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Abstract
N-Ethylmaleimide sensitive factor (NSF) and p97/valosin-containing protein (VCP) are distantly related members of the ATPases associated with a variety of cellular activities (AAA) family of proteins. While both proteins have been implied in cellular morphology changes involving membrane compartments or vesicles, more recent evidence seems to imply that NSF is primarily involved in the soluble NSF attachment receptor (SNARE)-mediated vesicle fusion by disassembling the SNARE complex whereas p97/VCP is primarily involved in the extraction of membrane proteins. These functional differences are now corroborated by major structural differences based on recent crystallographic and cryo-electron microscopy studies. This review discusses these recent findings.
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Affiliation(s)
- Axel T Brunger
- Howard Hughes Medical Institute, and Department of Molecular and Cellular Physiology, and Stanford Synchrotron Radiation Laboratory, Stanford University, James H. Clark Center E300-C, 318 Campus Drive, Stanford, CA 94305-5432, USA.
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16
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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: 315] [Impact Index Per Article: 15.0] [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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17
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Affiliation(s)
- Josep Rizo
- Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, Texas 75390, USA.
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18
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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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19
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Pullikuth AK, Gill SS. In vivo membrane trafficking role for an insect N-ethylmaleimide-sensitive factor which is developmentally regulated in endocrine cells. J Exp Biol 2002; 205:911-26. [PMID: 11916988 DOI: 10.1242/jeb.205.7.911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SUMMARY
The hexameric ATPase, N-ethylmaleimide-sensitive factor (NSF) is implicated in the release of neurotransmitters and in mediating fusion between intracellular membranes. Due to the conservation of proteins in constitutive and regulated membrane fusion reactions, NSF and its downstream targets have been predicted also to participate in fusion reactions underlying endocrine function, but there is little experimental evidence to support such a role for NSF in insect neuroendocrine secretion. Here we have characterized the NSF orthologue (MsNSF) from the endocrine model for development Manduca sexta. MsNSF is developmentally regulated in endocrine organs of the protocerebral complex. Enrichment of MsNSF in corpora cardiaca (CC) and not in corpora allata (CA) indicates that it might play a preferential role in releasing hormones produced in CC. Endocrine/paracrine cells of the enteric system in M. sexta exhibit selective MsNSF enrichment. Together the data point to a more selective participation of MsNSF in development of M. sexta by its involvement in a subset of factors, whereas other as-yet-unidentified homolog(s) might regulate secretion from CA and a large set of endocrine/paracrine cells. We further characterized the in vivo role of MsNSF by heterologous expression. In contrast to vertebrate NSF, MsNSF is functional in yeast membrane fusion in vivo. MsNSF rectifies defects in SEC18 (yeast NSF homologue) at nearly all discernible steps where Sec18p has been implicated in the biosynthetic route. This underscores the utility of our approach to delineate functional roles for proteins from systems that are not currently amenable to in vitroreconstitution.
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Affiliation(s)
- Ashok K Pullikuth
- Department of Cell Biology and Neuroscience, University of California, Riverside, CA 92521, USA
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20
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Littleton JT, Barnard RJ, Titus SA, Slind J, Chapman ER, Ganetzky B. SNARE-complex disassembly by NSF follows synaptic-vesicle fusion. Proc Natl Acad Sci U S A 2001; 98:12233-8. [PMID: 11593041 PMCID: PMC59797 DOI: 10.1073/pnas.221450198] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Soluble N-ethylmaleimide-sensitive fusion attachment protein receptor (SNARE)-mediated fusion of synaptic vesicles with the presynaptic-plasma membrane is essential for communication between neurons. Disassembly of the SNARE complex requires the ATPase N-ethylmaleimide-sensitive fusion protein (NSF). To determine where in the synaptic-vesicle cycle NSF functions, we have undertaken a genetic analysis of comatose (dNSF-1) in Drosophila. Characterization of 16 comatose mutations demonstrates that NSF mediates disassembly of SNARE complexes after synaptic-vesicle fusion. Hypomorphic mutations in NSF cause temperature-sensitive paralysis, whereas null mutations result in lethality. Genetic-interaction studies with para demonstrate that blocking evoked fusion delays the accumulation of assembled SNARE complexes and behavioral paralysis that normally occurs in comatose mutants, indicating NSF activity is not required in the absence of vesicle fusion. In addition, the entire vesicle pool can be depleted in shibire comatose double mutants, demonstrating that NSF activity is not required for the fusion step itself. Multiple rounds of vesicle fusion in the absence of NSF activity poisons neurotransmission by trapping SNAREs into cis-complexes. These data indicate that NSF normally dissociates and recycles SNARE proteins during the interval between exocytosis and endocytosis. In the absence of NSF activity, there are sufficient fusion-competent SNAREs to exocytose both the readily released and the reserve pool of synaptic vesicles.
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Affiliation(s)
- J T Littleton
- Center for Learning and Memory and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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21
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Brunger AT. Structure of proteins involved in synaptic vesicle fusion in neurons. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2001; 30:157-71. [PMID: 11340056 DOI: 10.1146/annurev.biophys.30.1.157] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The fusion of vesicles with target membranes is controlled by a complex network of protein-protein and protein-lipid interactions. Structures of the SNARE complex, synaptotagmin III, nSec1, domains of the NSF chaperone and its adaptor SNAP, and Rab3 and some of its effectors provide the framework for developing molecular models of vesicle fusion and for designing experiments to test these models.
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Affiliation(s)
- A T Brunger
- The Howard Hughes Medical Institute and Department of Molecular and Cellular Physiology, Neurology and Neurological Sciences, and Stanford Synchrotron Radiation Laboratory, Stanford University, Stanford, California 94305, USA.
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22
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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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23
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Abstract
The AAA+ superfamily of ATPases, which contain a homologous ATPase module, are found in all kingdoms of living organisms where they participate in diverse cellular processes including membrane fusion, proteolysis and DNA replication. Recent structural studies have revealed that they usually form ring-shaped oligomers, which are crucial for their ATPase activities and mechanisms of action. These ring-shaped oligomeric complexes are versatile in their mode of action, which collectively seem to involve some form of disruption of molecular or macromolecular structure; unfolding of proteins, disassembly of protein complexes, unwinding of DNA, or alteration of the state of DNA-protein complexes. Thus, the AAA+ proteins represent a novel type of molecular chaperone. Comparative analyses have also revealed significant similarities and differences in structure and molecular mechanism between AAA+ ATPases and other ring-shaped ATPases.
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Affiliation(s)
- T Ogura
- Division of Molecular Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto 862-0976, Japan.
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24
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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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25
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Schepers A, Diffley JF. Mutational analysis of conserved sequence motifs in the budding yeast cdc6 protein 1 1Edited by M. Yaniv. J Mol Biol 2001; 308:597-608. [PMID: 11350163 DOI: 10.1006/jmbi.2001.4637] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Cdc6 protein is required to load a complex of Mcm2-7 family members (the MCM complex) into prereplicative complexes at budding yeast origins of DNA replication. Cdc6p is a member of the AAA(+) superfamily of proteins, which includes the prokaryotic and eukaryotic clamp loading proteins. These proteins share a number of conserved regions of homology and a common three-dimensional architecture. Two of the conserved sequence motifs are the Walker A and B motifs that are involved in nucleotide metabolism and are essential for Cdc6p function in vivo. Here, we analyse mutants in the other conserved sequence motifs. Several of these mutants are temperature-sensitive for growth and are unable to recruit the MCM complex to chromatin at the restrictive temperature. In one such temperature-sensitive mutant, a highly conserved asparagine residue in the sensor I motif was changed to alanine. Overexpression of this mutant protein is lethal. This phenotype is very similar to the phenotype previously described for a mutation in the Walker B motif, suggesting a common role for sensor I and the Walker B motif in Cdc6 function.
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Affiliation(s)
- A Schepers
- Clare Hall Laboratories, Imperial Cancer Research Fund, South Mimms, EN6 3LD, UK
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26
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Brunger AT. Structural insights into the molecular mechanism of calcium-dependent vesicle-membrane fusion. Curr Opin Struct Biol 2001; 11:163-73. [PMID: 11297924 DOI: 10.1016/s0959-440x(00)00186-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The fusion of vesicles with target membranes is controlled by a complex network of protein-protein and protein-lipid interactions. Recently determined structures of the SNARE complex, synaptotagmin III, nSec1, domains of the NSF chaperone and its adaptor (SNAP), and Rab3 and some of its effectors provide the framework for developing molecular models of vesicle fusion and for designing experiments to test these models. Ultimately, knowledge of the structures of higher-order complexes and their dynamic behavior will be required to obtain a full understanding of the vesicle fusion protein machinery.
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Affiliation(s)
- A T Brunger
- The Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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27
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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: 357] [Impact Index Per Article: 14.9] [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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28
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Abstract
The fusion of intracellular vesicles with their target membranes is an essential feature of the compartmental structure of eukaryotic cells. This process requires proteins that dictate the targeting of a vesicle to the correct cellular location, mediate bilayer fusion and, in some systems, regulate the precise time at which fusion occurs. Recent biophysical and structural studies of these proteins have begun to provide a foundation for understanding their functions at a molecular level.
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Affiliation(s)
- K M Misura
- Departments of Structural Biology and Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305-5126, USA
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29
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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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30
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Paz Y, Elazar Z, Fass D. Structure of GATE-16, membrane transport modulator and mammalian ortholog of autophagocytosis factor Aut7p. J Biol Chem 2000; 275:25445-50. [PMID: 10856287 DOI: 10.1074/jbc.c000307200] [Citation(s) in RCA: 119] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The GATE-16 protein participates in intra-Golgi transport and can associate with the N-ethylmaleimide-sensitive fusion protein and with Golgi SNAREs. The yeast ortholog of GATE-16 is the autophagocytosis factor Aut7p. GATE-16 is also closely related to the GABA receptor-associated protein (GABARAP), which has been proposed to cluster neurotransmitter receptors by mediating interaction with the cytoskeleton, and to the light chain-3 subunit of the neuronal microtubule-associated protein complex. Here, we present the crystal structure of GATE-16 refined to 1.8 A resolution. GATE-16 contains a ubiquitin fold decorated by two additional N-terminal helices. Proteins with strong structural similarity but no detectable sequence homology to GATE-16 include Ras effectors that mediate diverse downstream functions, but each interacts with Ras by forming pseudo-continuous beta-sheets. The GATE-16 surface suggests that it binds its targets in a similar manner. Moreover, a second potential protein-protein interaction site on GATE-16 may explain the adapter activity observed for members of the GATE-16 family.
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Affiliation(s)
- Y Paz
- Department of Structural Biology and Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
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31
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Affiliation(s)
- R D Vale
- Howard Hughes Medical Institute and the Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California 94143, USA.
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32
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Abstract
We present a summary of the structures of 13 proteins involved in the docking and fusion of intracellular transport vesicles to their target membranes.
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Affiliation(s)
- J A Ybe
- G.W. Hooper Foundation, Box 0552, Department of Microbiology and Immunology, Department of Biopharmaceutical Sciences, University of California, 513 Parnassus Avenue, San Francisco, CA 94143, USA
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33
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Abstract
The fusion of vesicles with target membranes is controlled by a complex network of protein-protein and protein-lipid interactions. Recent structures of the SNARE complex, synaptotagmin III, nSec1, domains of NSF and its adaptor SNAP, along with Rab3 and some of its effectors, provide the framework for developing molecular models of vesicle fusion and for designing experiments to test these models. Ultimately, this knowledge of the structures of higher-order complexes and their dynamic behavior will allow us to obtain a full understanding of the vesicle fusion protein machinery.
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Affiliation(s)
- A T Brunger
- Department of Molecular Biophysics and Biochemistry, The Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.
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