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Strauss J, Wilkinson C, Vidilaseris K, de Castro Ribeiro OM, Liu J, Hillier J, Wichert M, Malinen AM, Gehl B, Jeuken LJ, Pearson AR, Goldman A. Functional and structural asymmetry suggest a unifying principle for catalysis in membrane-bound pyrophosphatases. EMBO Rep 2024; 25:853-875. [PMID: 38182815 PMCID: PMC10897367 DOI: 10.1038/s44319-023-00037-x] [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: 08/24/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 01/07/2024] Open
Abstract
Membrane-bound pyrophosphatases (M-PPases) are homodimeric primary ion pumps that couple the transport of Na+- and/or H+ across membranes to the hydrolysis of pyrophosphate. Their role in the virulence of protist pathogens like Plasmodium falciparum makes them an intriguing target for structural and functional studies. Here, we show the first structure of a K+-independent M-PPase, asymmetric and time-dependent substrate binding in time-resolved structures of a K+-dependent M-PPase and demonstrate pumping-before-hydrolysis by electrometric studies. We suggest how key residues in helix 12, 13, and the exit channel loops affect ion selectivity and K+-activation due to a complex interplay of residues that are involved in subunit-subunit communication. Our findings not only explain ion selectivity in M-PPases but also why they display half-of-the-sites reactivity. Based on this, we propose, for the first time, a unified model for ion-pumping, hydrolysis, and energy coupling in all M-PPases, including those that pump both Na+ and H+.
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Affiliation(s)
- Jannik Strauss
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
- Numaferm GmbH, Düsseldorf, Germany
| | - Craig Wilkinson
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
| | - Keni Vidilaseris
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland
| | - Orquidea M de Castro Ribeiro
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland
| | - Jianing Liu
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland
| | - James Hillier
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK
- Bio-Rad Laboratories Ltd., Watford, UK
| | - Maximilian Wichert
- Leiden Institute of Chemistry, University Leiden, PO Box 9502, 2300 RA, Leiden, The Netherlands
| | - Anssi M Malinen
- Department of Life Technologies, University of Turku, FIN-20014, Turku, Finland
| | - Bernadette Gehl
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland
- Department of Applied Physics, Aalto University, FI-00076, AALTO, Espoo, Finland
| | - Lars Jc Jeuken
- Leiden Institute of Chemistry, University Leiden, PO Box 9502, 2300 RA, Leiden, The Netherlands
| | - Arwen R Pearson
- Institute for Nanostructure and Solid State Physics, Hamburg Centre for Ultrafast Imaging, Universität Hamburg, 22761, Hamburg, Germany
| | - Adrian Goldman
- Astbury Centre for Structural and Molecular Biology, University of Leeds, LS2 9JT, Leeds, UK.
- Molecular and Integrative Biosciences, Biological and Environmental Sciences, University of Helsinki, 00100, Helsinki, Finland.
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H +-Translocating Membrane-Bound Pyrophosphatase from Rhodospirillum rubrum Fuels Escherichia coli Cells via an Alternative Pathway for Energy Generation. Microorganisms 2023; 11:microorganisms11020294. [PMID: 36838259 PMCID: PMC9959109 DOI: 10.3390/microorganisms11020294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 01/11/2023] [Accepted: 01/14/2023] [Indexed: 01/24/2023] Open
Abstract
Inorganic pyrophosphatases (PPases) catalyze an essential reaction, namely, the hydrolysis of PPi, which is formed in large quantities as a side product of numerous cellular reactions. In the majority of living species, PPi hydrolysis is carried out by soluble cytoplasmic PPase (S-PPases) with the released energy dissipated in the form of heat. In Rhodospirillum rubrum, part of this energy can be conserved by proton-pumping pyrophosphatase (H+-PPaseRru) in the form of a proton electrochemical gradient for further ATP synthesis. Here, the codon-harmonized gene hppaRru encoding H+-PPaseRru was expressed in the Escherichia coli chromosome. We demonstrate, for the first time, that H+-PPaseRru complements the essential native S-PPase in E. coli cells. 13C-MFA confirmed that replacing native PPase to H+-PPaseRru leads to the re-distribution of carbon fluxes; a statistically significant 36% decrease in tricarboxylic acid (TCA) cycle fluxes was found compared with wild-type E. coli MG1655. Such a flux re-distribution can indicate the presence of an additional method for energy generation (e.g., ATP), which can be useful for the microbiological production of a number of compounds, the biosynthesis of which requires the consumption of ATP.
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Baykov AA, Anashkin VA, Malinen AM, Bogachev AV. The Mechanism of Energy Coupling in H +/Na +-Pumping Membrane Pyrophosphatase-Possibilities and Probabilities. Int J Mol Sci 2022; 23:9504. [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] [MESH Headings] [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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Affiliation(s)
- Alexander A. Baykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119899, Russia
| | - Viktor A. Anashkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119899, Russia
| | - Anssi M. Malinen
- Department of Life Technologies, University of Turku, FIN-20014 Turku, Finland
| | - Alexander V. Bogachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119899, Russia
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