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Huang LK, Huang YC, Chen PC, Lee CH, Lin SM, Hsu YHH, Pan RL. Exploration of the Catalytic Cycle Dynamics of Vigna Radiata H +-Translocating Pyrophosphatases Through Hydrogen-Deuterium Exchange Mass Spectrometry. J Membr Biol 2023; 256:443-458. [PMID: 37955797 DOI: 10.1007/s00232-023-00295-9] [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: 04/25/2023] [Accepted: 10/11/2023] [Indexed: 11/14/2023]
Abstract
Vigna radiata H+-translocating pyrophosphatases (VrH+-PPases, EC 3.6.1.1) are present in various endomembranes of plants, bacteria, archaea, and certain protozoa. They transport H+ into the lumen by hydrolyzing pyrophosphate, which is a by-product of many essential anabolic reactions. Although the crystal structure of H+-PPases has been elucidated, the H+ translocation mechanism of H+-PPases in the solution state remains unclear. In this study, we used hydrogen-deuterium exchange (HDX) coupled with mass spectrometry (MS) to investigate the dynamics of H+-PPases between the previously proposed R state (resting state, Apo form), I state (intermediate state, bound to a substrate analog), and T state (transient state, bound to inorganic phosphate). When hydrogen was replaced by proteins in deuterium oxide solution, the backbone hydrogen atoms, which were exchanged with deuterium, were identified through MS. Accordingly, we used deuterium uptake to examine the structural dynamics and conformational changes of H+-PPases in solution. In the highly conserved substrate binding and proton exit regions, HDX-MS revealed the existence of a compact conformation with deuterium exchange when H+-PPases were bound with a substrate analog and product. Thus, a novel working model was developed to elucidate the in situ catalytic mechanism of pyrophosphate hydrolysis and proton transport. In this model, a proton is released in the I state, and the TM5 inner wall serves as a proton piston.
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Affiliation(s)
- Li-Kun Huang
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No.101, Sec. 2, Kuangfu Rd., Hsinchu City, 30013, Taiwan, Republic of China
| | - Yi-Cyuan Huang
- Department of Chemistry, Tunghai University, No.1727, Sec. 4, Taiwan Boulevard, Taichung, 40704, Taiwan, Republic of China
| | - Pin-Chuan Chen
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No.101, Sec. 2, Kuangfu Rd., Hsinchu City, 30013, Taiwan, Republic of China
| | - Ching-Hung Lee
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No.101, Sec. 2, Kuangfu Rd., Hsinchu City, 30013, Taiwan, Republic of China
| | - Shih-Ming Lin
- Department of Biotechnology and Bioindustry Sciences, National Cheng Kung University, Tainan, 70101, Taiwan, Republic of China
| | - Yuan-Hao Howard Hsu
- Department of Chemistry, Tunghai University, No.1727, Sec. 4, Taiwan Boulevard, Taichung, 40704, Taiwan, Republic of China.
| | - Rong-Long Pan
- Department of Life Science and Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, No.101, Sec. 2, Kuangfu Rd., Hsinchu City, 30013, Taiwan, Republic of China.
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Malinen AM, Anashkin VA, Orlov VN, Bogachev AV, Lahti R, Baykov AA. Pre‐steady‐state kinetics and solvent isotope effects support the “billiard‐type” transport mechanism in
Na
+
‐translocating pyrophosphatase. Protein Sci 2022; 31:e4394. [PMID: 36040263 PMCID: PMC9405524 DOI: 10.1002/pro.4394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/23/2022] [Accepted: 07/12/2022] [Indexed: 11/10/2022]
Abstract
Membrane‐bound pyrophosphatase (mPPase) found in microbes and plants is a membrane H+ pump that transports the H+ ion generated in coupled pyrophosphate hydrolysis out of the cytoplasm. Certain bacterial and archaeal mPPases can in parallel transport Na+ via a hypothetical “billiard‐type” mechanism, also involving the hydrolysis‐generated proton. Here, we present the functional evidence supporting this coupling mechanism. Rapid‐quench and pulse‐chase measurements with [32P]pyrophosphate indicated that the chemical step (pyrophosphate hydrolysis) is rate‐limiting in mPPase catalysis and is preceded by a fast isomerization of the enzyme‐substrate complex. Na+, whose binding is a prerequisite for the hydrolysis step, is not required for substrate binding. Replacement of H2O with D2O decreased the rates of pyrophosphate hydrolysis by both Na+‐ and H+‐transporting bacterial mPPases, the effect being more significant than with a non‐transporting soluble pyrophosphatase. We also show that the Na+‐pumping mPPase of Thermotoga maritima resembles other dimeric mPPases in demonstrating negative kinetic cooperativity and the requirement for general acid catalysis. The findings point to a crucial role for the hydrolysis‐generated proton both in H+‐pumping and Na+‐pumping by mPPases.
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Affiliation(s)
- Anssi M. Malinen
- Department of Life Technologies University of Turku Turku Finland
| | - Viktor A. Anashkin
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
| | - Victor N. Orlov
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
| | - Alexander V. Bogachev
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
| | - Reijo Lahti
- Department of Life Technologies University of Turku Turku Finland
| | - Alexander A. Baykov
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
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The Mechanism of Energy Coupling in H +/Na +-Pumping Membrane Pyrophosphatase-Possibilities and Probabilities. Int J Mol Sci 2022; 23:ijms23169504. [PMID: 36012762 PMCID: PMC9408878 DOI: 10.3390/ijms23169504] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/12/2022] [Accepted: 08/21/2022] [Indexed: 11/17/2022] Open
Abstract
Membrane pyrophosphatases (mPPases) found in plant vacuoles and some prokaryotes and protists are ancient cation pumps that couple pyrophosphate hydrolysis with the H+ and/or Na+ transport out of the cytoplasm. Because this function is reversible, mPPases play a role in maintaining the level of cytoplasmic pyrophosphate, a known regulator of numerous metabolic reactions. mPPases arouse interest because they are among the simplest membrane transporters and have no homologs among known ion pumps. Detailed phylogenetic studies have revealed various subtypes of mPPases and suggested their roles in the evolution of the "sodium" and "proton" bioenergetics. This treatise focuses on the mechanistic aspects of the transport reaction, namely, the coupling step, the role of the chemically produced proton, subunit cooperation, and the relationship between the proton and sodium ion transport. The available data identify H+-PPases as the first non-oxidoreductase pump with a "direct-coupling" mechanism, i.e., the transported proton is produced in the coupled chemical reaction. They also support a "billiard" hypothesis, which unifies the H+ and Na+ transport mechanisms in mPPase and, probably, other transporters.
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