1
|
Steuber J, Fritz G. The Na +-translocating NADH:quinone oxidoreductase (Na +-NQR): Physiological role, structure and function of a redox-driven, molecular machine. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149485. [PMID: 38955304 DOI: 10.1016/j.bbabio.2024.149485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
Abstract
Many bacterial processes are powered by the sodium motive force (smf) and in case of pathogens, the smf contributes to virulence. Vibrio cholerae, the causative agent of Cholera disease, possesses a Na+-translocating NADH:quinone oxidoreductase (NQR), a six-subunit membrane protein assembly. The 3D structure of NQR revealed the arrangement of the six subunits NqrABCDEF, the position of all redox cofactors (four flavins, two [2Fe-2S] centers) and the binding sites for the substrates NADH (in NqrF) and ubiquinone (in NqrB). Upon oxidation of NADH, electrons are shuttled twice across the membrane, starting with cytoplasmic FADNqrF and electron transfer to the [2Fe2S] clusterNqrF and from there to an intra-membranous [2Fe-2S] clusterNqrDE, periplasmic FMNNqrC, FMNNqrB and from there to riboflavinNqrB. This riboflavin is located at the cytoplasmic entry site of the sodium channel in NqrB, and it donates electrons to ubiquinone-8 positioned at the cytoplasmic side of NqrB. Targeting the substrate binding sites of NQR is a promising strategy to identify new inhibitors against many bacterial pathogens. Detailed structural information on the binding mode of natural inhibitors and small molecules in the active sites of NQR is now available, paving the way for the development of new antibiotics. The NQR shows different conformations as revealed in recent cryo-EM and crystallographic studies combined with spectroscopic analyses. These conformations represent distinct steps in the catalytic cycle. Considering the structural and functional data available, we propose a mechanism of Na+-NQR based on conformational coupling of electron transfer and Na+ translocation reaction steps.
Collapse
Affiliation(s)
- Julia Steuber
- Institute of Biology, Department of Cellular Microbiology, University of Hohenheim, Garbenstr. 30, 70599 Stuttgart, Germany.
| | - Günter Fritz
- Institute of Biology, Department of Cellular Microbiology, University of Hohenheim, Garbenstr. 30, 70599 Stuttgart, Germany.
| |
Collapse
|
2
|
Zhang L, Einsle O. Architecture of the RNF1 complex that drives biological nitrogen fixation. Nat Chem Biol 2024; 20:1078-1085. [PMID: 38890433 DOI: 10.1038/s41589-024-01641-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 05/10/2024] [Indexed: 06/20/2024]
Abstract
Biological nitrogen fixation requires substantial metabolic energy in form of ATP as well as low-potential electrons that must derive from central metabolism. During aerobic growth, the free-living soil diazotroph Azotobacter vinelandii transfers electrons from the key metabolite NADH to the low-potential ferredoxin FdxA that serves as a direct electron donor to the dinitrogenase reductases. This process is mediated by the RNF complex that exploits the proton motive force over the cytoplasmic membrane to lower the midpoint potential of the transferred electron. Here we report the cryogenic electron microscopy structure of the nitrogenase-associated RNF complex of A. vinelandii, a seven-subunit membrane protein assembly that contains four flavin cofactors and six iron-sulfur centers. Its function requires the strict coupling of electron and proton transfer but also involves major conformational changes within the assembly that can be traced with a combination of electron microscopy and modeling.
Collapse
Affiliation(s)
- Lin Zhang
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany.
| |
Collapse
|
3
|
Fritz G, Kroneck PMH, Steuber J. The power supply for biological nitrogen fixation. Nat Chem Biol 2024:10.1038/s41589-024-01663-9. [PMID: 38987384 DOI: 10.1038/s41589-024-01663-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Affiliation(s)
- Günter Fritz
- Department of Cellular Microbiology, Institute of Biology, University of Hohenheim, Stuttgart, Germany
| | - Peter M H Kroneck
- Department of Biology, Faculty of Sciences, University of Konstanz, Konstanz, Germany
| | - Julia Steuber
- Department of Cellular Microbiology, Institute of Biology, University of Hohenheim, Stuttgart, Germany.
| |
Collapse
|
4
|
Aziz I, Kayastha K, Kaltwasser S, Vonck J, Welsch S, Murphy BJ, Kahnt J, Wu D, Wagner T, Shima S, Ermler U. Structural and mechanistic basis of the central energy-converting methyltransferase complex of methanogenesis. Proc Natl Acad Sci U S A 2024; 121:e2315568121. [PMID: 38530900 PMCID: PMC10998594 DOI: 10.1073/pnas.2315568121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/24/2024] [Indexed: 03/28/2024] Open
Abstract
Methanogenic archaea inhabiting anaerobic environments play a crucial role in the global biogeochemical material cycle. The most universal electrogenic reaction of their methane-producing energy metabolism is catalyzed by N 5-methyl-tetrahydromethanopterin: coenzyme M methyltransferase (MtrABCDEFGH), which couples the vectorial Na+ transport with a methyl transfer between the one-carbon carriers tetrahydromethanopterin and coenzyme M via a vitamin B12 derivative (cobamide) as prosthetic group. We present the 2.08 Å cryo-EM structure of Mtr(ABCDEFG)3 composed of the central Mtr(ABFG)3 stalk symmetrically flanked by three membrane-spanning MtrCDE globes. Tetraether glycolipids visible in the map fill gaps inside the multisubunit complex. Putative coenzyme M and Na+ were identified inside or in a side-pocket of a cytoplasmic cavity formed within MtrCDE. Its bottom marks the gate of the transmembrane pore occluded in the cryo-EM map. By integrating Alphafold2 information, functionally competent MtrA-MtrH and MtrA-MtrCDE subcomplexes could be modeled and thus the methyl-tetrahydromethanopterin demethylation and coenzyme M methylation half-reactions structurally described. Methyl-transfer-driven Na+ transport is proposed to be based on a strong and weak complex between MtrCDE and MtrA carrying vitamin B12, the latter being placed at the entrance of the cytoplasmic MtrCDE cavity. Hypothetically, strongly attached methyl-cob(III)amide (His-on) carrying MtrA induces an inward-facing conformation, Na+ flux into the membrane protein center and finally coenzyme M methylation while the generated loosely attached (or detached) MtrA carrying cob(I)amide (His-off) induces an outward-facing conformation and an extracellular Na+ outflux. Methyl-cob(III)amide (His-on) is regenerated in the distant active site of the methyl-tetrahydromethanopterin binding MtrH implicating a large-scale shuttling movement of the vitamin B12-carrying domain.
Collapse
Affiliation(s)
- Iram Aziz
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Kanwal Kayastha
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Susann Kaltwasser
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Janet Vonck
- Structural Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Sonja Welsch
- Central Electron Microscopy Facility, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Bonnie J. Murphy
- Redox and Metalloprotein Research Group, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Jörg Kahnt
- Max Planck Institute for Terrestrial Microbiology, MarburgD-35043, Germany
| | - Di Wu
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| | - Tristan Wagner
- Max Planck Institute for Marine Microbiology, BremenD-28359, Germany
| | - Seigo Shima
- Max Planck Institute for Terrestrial Microbiology, MarburgD-35043, Germany
| | - Ulrich Ermler
- Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am MainD-60438, Germany
| |
Collapse
|
5
|
Hau JL, Schleicher L, Herdan S, Simon J, Seifert J, Fritz G, Steuber J. Functionality of the Na +-translocating NADH:quinone oxidoreductase and quinol:fumarate reductase from Prevotella bryantii inferred from homology modeling. Arch Microbiol 2023; 206:32. [PMID: 38127130 PMCID: PMC10739449 DOI: 10.1007/s00203-023-03769-5] [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: 10/05/2023] [Revised: 11/20/2023] [Accepted: 11/23/2023] [Indexed: 12/23/2023]
Abstract
Members of the family Prevotellaceae are Gram-negative, obligate anaerobic bacteria found in animal and human microbiota. In Prevotella bryantii, the Na+-translocating NADH:quinone oxidoreductase (NQR) and quinol:fumarate reductase (QFR) interact using menaquinone as electron carrier, catalyzing NADH:fumarate oxidoreduction. P. bryantii NQR establishes a sodium-motive force, whereas P. bryantii QFR does not contribute to membrane energization. To elucidate the possible mode of function, we present 3D structural models of NQR and QFR from P. bryantii to predict cofactor-binding sites, electron transfer routes and interaction with substrates. Molecular docking reveals the proposed mode of menaquinone binding to the quinone site of subunit NqrB of P. bryantii NQR. A comparison of the 3D model of P. bryantii QFR with experimentally determined structures suggests alternative pathways for transmembrane proton transport in this type of QFR. Our findings are relevant for NADH-dependent succinate formation in anaerobic bacteria which operate both NQR and QFR.
Collapse
Affiliation(s)
- Jann-Louis Hau
- Institute of Biology, University of Hohenheim, Garbenstraße 30, 70599, Stuttgart, Germany
| | - Lena Schleicher
- Institute of Biology, University of Hohenheim, Garbenstraße 30, 70599, Stuttgart, Germany
- HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen-Weg 3, 70599, Stuttgart, Germany
| | - Sebastian Herdan
- Institute of Biology, University of Hohenheim, Garbenstraße 30, 70599, Stuttgart, Germany
- HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen-Weg 3, 70599, Stuttgart, Germany
| | - Jörg Simon
- Microbial Energy Conservation and Biotechnology, Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, 64287, Darmstadt, Germany
| | - Jana Seifert
- HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen-Weg 3, 70599, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Emil-Wolff-Straße 8, 70599, Stuttgart, Germany
| | - Günter Fritz
- Institute of Biology, University of Hohenheim, Garbenstraße 30, 70599, Stuttgart, Germany
| | - Julia Steuber
- Institute of Biology, University of Hohenheim, Garbenstraße 30, 70599, Stuttgart, Germany.
- HoLMiR-Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Leonore-Blosser-Reisen-Weg 3, 70599, Stuttgart, Germany.
| |
Collapse
|