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Faltova L, Jiang K, Frey D, Wu Y, Capitani G, Prota AE, Akhmanova A, Steinmetz MO, Kammerer RA. Crystal Structure of a Heterotetrameric Katanin p60:p80 Complex. Structure 2019; 27:1375-1383.e3. [PMID: 31353241 DOI: 10.1016/j.str.2019.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 05/27/2019] [Accepted: 07/05/2019] [Indexed: 10/26/2022]
Abstract
Katanin is a microtubule-severing enzyme that is crucial for many cellular processes. Katanin consists of two subunits, p60 and p80, that form a stable complex. The interaction between subunits is mediated by the p60 N-terminal microtubule-interacting and -trafficking domain (p60-MIT) and the p80 C-terminal domain (p80-CTD). Here, we performed a biophysical characterization of the mouse p60-MIT:p80-CTD heterodimer and show that this complex can assemble into heterotetramers. We identified two mutations that enhance heterotetramer formation and determined the X-ray crystal structure of this mutant complex. The structure revealed a domain-swapped heterotetramer consisting of two p60-MIT:p80-CTD heterodimers. Structure-based sequence alignments suggest that heterotetramerization of katanin might be a common feature of various species. Furthermore, we show that enhanced heterotetramerization of katanin impairs its microtubule end-binding properties and increases the enzyme's microtubule lattice binding and severing activities. Therefore, our findings suggest the existence of different katanin oligomers that possess distinct functional properties.
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Affiliation(s)
- Lenka Faltova
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Kai Jiang
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands; The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan 430071, China; Medical Research Institute, Wuhan University, Wuhan 430071, China
| | - Daniel Frey
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Yufan Wu
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Guido Capitani
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Andrea E Prota
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland
| | - Anna Akhmanova
- Cell Biology, Department of Biology, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands.
| | - Michel O Steinmetz
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland; Biozentrum, University of Basel, 4056 Basel, Switzerland.
| | - Richard A Kammerer
- Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institut, 5232 Villigen PSI, Switzerland.
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Iwaya N, Akiyama K, Goda N, Tenno T, Fujiwara Y, Hamada D, Ikura T, Shirakawa M, Hiroaki H. Effect of Ca2+ on the microtubule-severing enzyme p60-katanin. Insight into the substrate-dependent activation mechanism. FEBS J 2012; 279:1339-52. [PMID: 22325007 DOI: 10.1111/j.1742-4658.2012.08528.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Katanin p60 (p60-katanin) is a microtubule (MT)-severing enzyme and its activity is regulated by the p80 subunit (adaptor-p80). p60-katanin consists of an N-terminal domain, followed by a single ATPase associated with various cellular activities (AAA) domain. We have previously shown that the N-terminal domain serves as the binding site for MT, the substrate of p60-katanin. In this study, we show that the same domain shares another interface with the C-terminal domain of adaptor-p80. We further show that Ca(2+) ions inhibit the MT-severing activity of p60-katanin, whereas the MT-binding activity is preserved in the presence of Ca(2+). In detail, the basal ATPase activity of p60-katanin is stimulated twofold by both MTs and the C-terminal domain of adaptor-p80, whereas Ca(2+) reduces elevated ATPase activity to the basal level. We identify the Ca(2+) -binding site at the end of helix 2 of the N-terminal domain, which is different from the MT-binding interface. On the basis of these observations, we propose a speculative model in which spatial rearrangement of the N-terminal domain relative to the C-terminal AAA domain may be important for productive ATP hydrolysis towards MT-severing. Our model can explain how Ca(2+) regulates both severing and ATP hydrolysis activity, because the Ca(2+) -binding site on the N-terminal domain moves close to the AAA domain during MT severing.
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Affiliation(s)
- Naoko Iwaya
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
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Fujiwara Y, Fujiwara KI, Goda N, Iwaya N, Tenno T, Shirakawa M, Hiroaki H. Structure and function of the N-terminal nucleolin binding domain of nuclear valosin-containing protein-like 2 (NVL2) harboring a nucleolar localization signal. J Biol Chem 2011; 286:21732-41. [PMID: 21474449 PMCID: PMC3122229 DOI: 10.1074/jbc.m110.174680] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 02/28/2011] [Indexed: 11/06/2022] Open
Abstract
The N-terminal regions of AAA-ATPases (ATPase associated with various cellular activities) often contain a domain that defines the distinct functions of the enzymes, such as substrate specificity and subcellular localization. As described herein, we have determined the solution structure of an N-terminal unique domain isolated from nuclear valosin-containing protein (VCP)-like protein 2 (NVL2(UD)). NVL2(UD) contains three α helices with an organization resembling that of a winged helix motif, whereas a pair of β-strands is missing. The structure is unique and distinct from those of other known type II AAA-ATPases, such as VCP. Consequently, we identified nucleolin from a HeLa cell extract as a binding partner of this domain. Nucleolin contains a long (∼300 amino acids) intrinsically unstructured region, followed by the four tandem RNA recognition motifs and the C-terminal glycine/arginine-rich domain. Binding analyses revealed that NVL2(UD) potentially binds to any of the combinations of two successive RNA binding domains in the presence of RNA. Furthermore, NVL2(UD) has a characteristic loop, in which the key basic residues RRKR are exposed to the solvent at the edge of the molecule. The mutation study showed that these residues are necessary and sufficient for nucleolin-RNA complex binding as well as nucleolar localization. Based on the observations presented above, we propose that NVL2 serves as an unfoldase for the nucleolin-RNA complex. As inferred from its RNA dependence and its ATPase activity, NVL2 might facilitate the dissociation and recycling of nucleolin, thereby promoting efficient ribosome biogenesis.
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Affiliation(s)
- Yoshie Fujiwara
- From the Division of Structural Biology, Graduate School of Medicine, and
- the Global Center of Excellence Program for Integrative Membrane Biology, Kobe University, 7-5-1 Kusunokicho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
- the Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Kawaguchi Center Building, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ken-ichiro Fujiwara
- the Field of Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Shionogi Research Laboratories, Shionogi & Co., Ltd., 5-12-4 Sagisu, Fukushima-ku, Osaka 553-0002, Japan, and
| | - Natsuko Goda
- From the Division of Structural Biology, Graduate School of Medicine, and
- the Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Kawaguchi Center Building, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Naoko Iwaya
- From the Division of Structural Biology, Graduate School of Medicine, and
- the Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Kawaguchi Center Building, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
- the Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takeshi Tenno
- From the Division of Structural Biology, Graduate School of Medicine, and
- the Global Center of Excellence Program for Integrative Membrane Biology, Kobe University, 7-5-1 Kusunokicho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - Masahiro Shirakawa
- the Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hidekazu Hiroaki
- From the Division of Structural Biology, Graduate School of Medicine, and
- the Global Center of Excellence Program for Integrative Membrane Biology, Kobe University, 7-5-1 Kusunokicho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
- the Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Kawaguchi Center Building, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
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Iwaya N, Kuwahara Y, Fujiwara Y, Goda N, Tenno T, Akiyama K, Mase S, Tochio H, Ikegami T, Shirakawa M, Hiroaki H. A common substrate recognition mode conserved between katanin p60 and VPS4 governs microtubule severing and membrane skeleton reorganization. J Biol Chem 2010; 285:16822-9. [PMID: 20339000 DOI: 10.1074/jbc.m110.108365] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Katanin p60 (kp60), a microtubule-severing enzyme, plays a key role in cytoskeletal reorganization during various cellular events in an ATP-dependent manner. We show that a single domain isolated from the N terminus of mouse katanin p60 (kp60-NTD) binds to tubulin. The solution structure of kp60-NTD was determined by NMR. Although their sequence similarities were as low as 20%, the structure of kp60-NTD revealed a striking similarity to those of the microtubule interacting and trafficking (MIT) domains, which adopt anti-parallel three-stranded helix bundle. In particular, the arrangement of helices 2 and 3 is well conserved between kp60-NTD and the MIT domain from Vps4, which is a homologous protein that promotes disassembly of the endosomal sorting complexes required for transport III membrane skeleton complex. Mutation studies revealed that the positively charged surface formed by helices 2 and 3 binds tubulin. This binding mode resembles the interaction between the MIT domain of Vps4 and Vps2/CHMP1a, a component of endosomal sorting complexes required for transport III. Our results show that both the molecular architecture and the binding modes are conserved between two AAA-ATPases, kp60 and Vps4. A common mechanism is evolutionarily conserved between two distinct cellular events, one that drives microtubule severing and the other involving membrane skeletal reorganization.
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Affiliation(s)
- Naoko Iwaya
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-ku, Kyoto 615-8530, Japan
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Manjasetty BA, Turnbull AP, Panjikar S, Büssow K, Chance MR. Automated technologies and novel techniques to accelerate protein crystallography for structural genomics. Proteomics 2008; 8:612-25. [PMID: 18210369 DOI: 10.1002/pmic.200700687] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The sequence infrastructure that has arisen through large-scale genomic projects dedicated to protein analysis, has provided a wealth of information and brought together scientists and institutions from all over the world. As a consequence, the development of novel technologies and methodologies in proteomics research is helping to unravel the biochemical and physiological mechanisms of complex multivariate diseases at both a functional and molecular level. In the late sixties, when X-ray crystallography had just been established, the idea of determining protein structure on an almost universal basis was akin to an impossible dream or a miracle. Yet only forty years after, automated protein structure determination platforms have been established. The widespread use of robotics in protein crystallography has had a huge impact at every stage of the pipeline from protein cloning, over-expression, purification, crystallization, data collection, structure solution, refinement, validation and data management- all of which have become more or less automated with minimal human intervention necessary. Here, recent advances in protein crystal structure analysis in the context of structural genomics will be discussed. In addition, this review aims to give an overview of recent developments in high throughput instrumentation, and technologies and strategies to accelerate protein structure/function analysis.
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Affiliation(s)
- Babu A Manjasetty
- Case Center for Synchrotron Biosciences, National Synchrotron Light Source, Brookhaven National Laboratory, Upton, NY11973, USA.
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