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Wilkens S, Khan MM, Knight K, Oot R. Tender love and disassembly: How a TLDc domain protein breaks the V-ATPase. Bioessays 2023; 45:e2200251. [PMID: 37183929 PMCID: PMC10392918 DOI: 10.1002/bies.202200251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 04/13/2023] [Accepted: 05/03/2023] [Indexed: 05/16/2023]
Abstract
Vacuolar ATPases (V-ATPases, V1 Vo -ATPases) are rotary motor proton pumps that acidify intracellular compartments, and, when localized to the plasma membrane, the extracellular space. V-ATPase is regulated by a unique process referred to as reversible disassembly, wherein V1 -ATPase disengages from Vo proton channel in response to diverse environmental signals. Whereas the disassembly step of this process is ATP dependent, the (re)assembly step is not, but requires the action of a heterotrimeric chaperone referred to as the RAVE complex. Recently, an alternative pathway of holoenzyme disassembly was discovered that involves binding of Oxidation Resistance 1 (Oxr1p), a poorly characterized protein implicated in oxidative stress response. Unlike conventional reversible disassembly, which depends on enzyme activity, Oxr1p induced dissociation can occur in absence of ATP. Yeast Oxr1p belongs to the family of TLDc domain containing proteins that are conserved from yeast to mammals, and have been implicated in V-ATPase function in a variety of tissues. This brief perspective summarizes what we know about the molecular mechanisms governing both reversible (ATP dependent) and Oxr1p driven (ATP independent) V-ATPase dissociation into autoinhibited V1 and Vo subcomplexes.
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Affiliation(s)
- Stephan Wilkens
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
| | - Md. Murad Khan
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
| | - Kassidy Knight
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
| | - Rebecca Oot
- Department of Biochemistry & Molecular Biology, SUNY Upstate Medical University, Syracuse, NY
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Structure and dynamics of rotary V 1 motor. Cell Mol Life Sci 2018; 75:1789-1802. [PMID: 29387903 PMCID: PMC5910484 DOI: 10.1007/s00018-018-2758-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 12/25/2017] [Accepted: 01/18/2018] [Indexed: 12/14/2022]
Abstract
Rotary ATPases are unique rotary molecular motors that function as energy conversion machines. Among all known rotary ATPases, F1-ATPase is the best characterized rotary molecular motor. There are many high-resolution crystal structures and the rotation dynamics have been investigated in detail by extensive single-molecule studies. In contrast, knowledge on the structure and rotation dynamics of V1-ATPase, another rotary ATPase, has been limited. However, recent high-resolution structural studies and single-molecule studies on V1-ATPase have provided new insights on how the catalytic sites in this molecular motor change its conformation during rotation driven by ATP hydrolysis. In this review, we summarize recent information on the structural features and rotary dynamics of V1-ATPase revealed from structural and single-molecule approaches and discuss the possible chemomechanical coupling scheme of V1-ATPase with a focus on differences between rotary molecular motors.
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Isaka Y, Ekimoto T, Kokabu Y, Yamato I, Murata T, Ikeguchi M. Rotation Mechanism of Molecular Motor V 1-ATPase Studied by Multiscale Molecular Dynamics Simulation. Biophys J 2017; 112:911-920. [PMID: 28297650 PMCID: PMC5355535 DOI: 10.1016/j.bpj.2017.01.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 01/06/2017] [Accepted: 01/30/2017] [Indexed: 11/28/2022] Open
Abstract
Enterococcus hirae V1-ATPase is a molecular motor composed of the A3B3 hexamer ring and the central stalk. In association with ATP hydrolysis, three catalytic AB pairs in the A3B3 ring undergo conformational changes, which lead to a 120° rotation of the central stalk. To understand how the conformational changes of three catalytic pairs induce the 120° rotation of the central stalk, we performed multiscale molecular dynamics (MD) simulations in which coarse-grained and all-atom MD simulations were combined using a fluctuation matching methodology. During the rotation, a catalytic AB pair spontaneously adopted an intermediate conformation, which was not included in the initial inputs of the simulations and was essentially close to the “bindable-like” structure observed in a recently solved crystal structure. Furthermore, the creation of a space between the bindable-like and tight pairs was required for the central stalk to rotate without steric hindrance. These cooperative rearrangements of the three catalytic pairs are crucial for the rotation of the central stalk.
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Affiliation(s)
- Yuta Isaka
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, Japan
| | - Toru Ekimoto
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, Japan
| | - Yuichi Kokabu
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, Japan
| | - Ichiro Yamato
- Department of Biological Science and Technology, Tokyo University of Science, Katsushika-ku, Tokyo, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Inage, Chiba, Japan; JST, PRESTO, Inage, Chiba, Japan
| | - Mitsunori Ikeguchi
- Graduate School of Medical Life Science, Yokohama City University, Tsurumi, Yokohama, Japan.
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Suzuki K, Mizutani K, Maruyama S, Shimono K, Imai FL, Muneyuki E, Kakinuma Y, Ishizuka-Katsura Y, Shirouzu M, Yokoyama S, Yamato I, Murata T. Crystal structures of the ATP-binding and ADP-release dwells of the V 1 rotary motor. Nat Commun 2016; 7:13235. [PMID: 27807367 PMCID: PMC5095293 DOI: 10.1038/ncomms13235] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 09/14/2016] [Indexed: 12/21/2022] Open
Abstract
V1-ATPases are highly conserved ATP-driven rotary molecular motors found in various membrane systems. We recently reported the crystal structures for the Enterococcus hirae A3B3DF (V1) complex, corresponding to the catalytic dwell state waiting for ATP hydrolysis. Here we present the crystal structures for two other dwell states obtained by soaking nucleotide-free V1 crystals in ADP. In the presence of 20 μM ADP, two ADP molecules bind to two of three binding sites and cooperatively induce conformational changes of the third site to an ATP-binding mode, corresponding to the ATP-binding dwell. In the presence of 2 mM ADP, all nucleotide-binding sites are occupied by ADP to induce conformational changes corresponding to the ADP-release dwell. Based on these and previous findings, we propose a V1-ATPase rotational mechanism model.
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Affiliation(s)
- Kano Suzuki
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Kenji Mizutani
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan
| | - Shintaro Maruyama
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Kazumi Shimono
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi 274-8510, Japan
| | - Fabiana L. Imai
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Eiro Muneyuki
- Department of Physics, Faculty of Science and Engineering, Chuo University, 1-13-27 Kasuga, Tokyo 112-8551, Japan
| | - Yoshimi Kakinuma
- Laboratory of Molecular Physiology and Genetics, Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
| | - Yoshiko Ishizuka-Katsura
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Mikako Shirouzu
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Shigeyuki Yokoyama
- RIKEN Structural Biology Laboratory, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Ichiro Yamato
- Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda-shi, Chiba 278-8510, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
- Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
- JST, PRESTO, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
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Iino R, Ueno H, Minagawa Y, Suzuki K, Murata T. Rotational mechanism of Enterococcus hirae V1-ATPase by crystal-structure and single-molecule analyses. Curr Opin Struct Biol 2015; 31:49-56. [PMID: 25796033 DOI: 10.1016/j.sbi.2015.02.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Revised: 02/03/2015] [Accepted: 02/23/2015] [Indexed: 11/25/2022]
Abstract
In ion-transporting rotary ATPases, the mechanical rotation of inner rotor subunits against other stator subunits in the complex mediates conversion of chemical free energy from ATP hydrolysis into electrochemical potential by pumping ions across the cell membrane. To fully understand the rotational mechanism of energy conversion, it is essential to analyze a target sample by multiple advanced methods that differ in spatiotemporal resolutions and sample environments. Here, we describe such a strategy applied to the water-soluble V1 moiety of Enterococcus hirae V-ATPase; this strategy involves integration of crystal structure studies and single-molecule analysis of rotary dynamics and torque generation. In addition, we describe our current model of the chemo-mechanical coupling scheme obtained by this approach, as well as future prospects.
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Affiliation(s)
- Ryota Iino
- Okazaki Institute for Integrative Bioscience, Institute for Molecular Science, National Institutes of Natural Sciences, Aichi 444-8787, Japan; Department of Functional Molecular Science, School of Physical Sciences, The Graduate University for Advanced Studies (SOKENDAI), Kanagawa 240-0193, Japan.
| | - Hiroshi Ueno
- Department of Physics, Faculty of Science and Engineering, Chuo University, Tokyo 112-8551, Japan
| | - Yoshihiro Minagawa
- Department of Applied Chemistry, The University of Tokyo, Tokyo 113-8656, Japan
| | - Kano Suzuki
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba 263-8522, Japan; JST, PRESTO, Chiba 263-8522, Japan.
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Ma W, Schulten K. Mechanism of substrate translocation by a ring-shaped ATPase motor at millisecond resolution. J Am Chem Soc 2015; 137:3031-40. [PMID: 25646698 PMCID: PMC4393844 DOI: 10.1021/ja512605w] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Ring-shaped, hexameric ATPase motors fulfill key functions in cellular processes, such as genome replication, transcription, or protein degradation, by translocating a long substrate through their central pore powered by ATP hydrolysis. Despite intense research efforts, the atomic-level mechanism transmitting chemical energy from hydrolysis into mechanical force that translocates the substrate is still unclear. Here we employ all-atom molecular dynamics simulations combined with advanced path sampling techniques and milestoning analysis to characterize how mRNA substrate is translocated by an exemplary homohexameric motor, the transcription termination factor Rho. We find that the release of hydrolysis product (ADP + Pi) triggers the force-generating process of Rho through a 0.1 millisecond-long conformational transition, the time scale seen also in experiment. The calculated free energy profiles and kinetics show that Rho unidirectionally translocates the single-stranded RNA substrate via a population shift of the conformational states of Rho; upon hydrolysis product release, the most favorable conformation shifts from the pretranslocation state to the post-translocation state. Via two previously unidentified intermediate states, the RNA chain is seen to be pulled by six K326 side chains, whose motions are induced by highly coordinated relative translation and rotation of Rho's six subunits. The present study not only reveals in new detail the mechanism employed by ring-shaped ATPase motors, for example the use of loosely bound and tightly bound hydrolysis reactant and product states to coordinate motor action, but also provides an effective approach to identify allosteric sites of multimeric enzymes in general.
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