1
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Wiuf A, Steffen JH, Becares ER, Grønberg C, Mahato DR, Rasmussen SGF, Andersson M, Croll T, Gotfryd K, Gourdon P. The two-domain elevator-type mechanism of zinc-transporting ZIP proteins. SCIENCE ADVANCES 2022; 8:eabn4331. [PMID: 35857505 PMCID: PMC9278863 DOI: 10.1126/sciadv.abn4331] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 05/27/2022] [Indexed: 05/13/2023]
Abstract
Zinc is essential for all organisms and yet detrimental at elevated levels. Hence, homeostasis of this metal is tightly regulated. The Zrt/Irt-like proteins (ZIPs) represent the only zinc importers in metazoans. Mutations in human ZIPs cause serious disorders, but the mechanism by which ZIPs transfer zinc remains elusive. Hitherto, structural information is only available for a model member, BbZIP, and as a single, ion-bound conformation, precluding mechanistic insights. Here, we elucidate an inward-open metal-free BbZIP structure, differing substantially in the relative positions of the two separate domains of ZIPs. With accompanying coevolutional analyses, mutagenesis, and uptake assays, the data point to an elevator-type transport mechanism, likely shared within the ZIP family, unifying earlier functional data. Moreover, the structure reveals a previously unknown ninth transmembrane segment that is important for activity in vivo. Our findings outline the mechanistic principles governing ZIP-protein transport and enhance the molecular understanding of ZIP-related disorders.
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Affiliation(s)
- Anders Wiuf
- Department of Biomedical Sciences, University of Copenhagen, Mærsk Tower 7-9, Nørre Allé 14, DK-2200 Copenhagen, Denmark
| | - Jonas Hyld Steffen
- Department of Biomedical Sciences, University of Copenhagen, Mærsk Tower 7-9, Nørre Allé 14, DK-2200 Copenhagen, Denmark
| | - Eva Ramos Becares
- Department of Biomedical Sciences, University of Copenhagen, Mærsk Tower 7-9, Nørre Allé 14, DK-2200 Copenhagen, Denmark
| | - Christina Grønberg
- Department of Biomedical Sciences, University of Copenhagen, Mærsk Tower 7-9, Nørre Allé 14, DK-2200 Copenhagen, Denmark
| | - Dhani Ram Mahato
- Department of Chemistry, Umeå University, Linnaeus Väg 10, SE-901 87 Umeå, Sweden
| | - Søren G. F. Rasmussen
- Department of Neuroscience, University of Copenhagen, Maersk Tower 7-5, Nørre Allé 14, DK-2200 Copenhagen, Denmark
| | - Magnus Andersson
- Department of Chemistry, Umeå University, Linnaeus Väg 10, SE-901 87 Umeå, Sweden
| | - Tristan Croll
- Cambridge Institute for Medical Research, Department of Haematology, University of Cambridge, Keith Peters Building, Hills Rd., Cambridge CB2 0XY, UK
| | - Kamil Gotfryd
- Department of Biomedical Sciences, University of Copenhagen, Mærsk Tower 7-9, Nørre Allé 14, DK-2200 Copenhagen, Denmark
| | - Pontus Gourdon
- Department of Biomedical Sciences, University of Copenhagen, Mærsk Tower 7-9, Nørre Allé 14, DK-2200 Copenhagen, Denmark
- Department of Experimental Medical Science, Lund University, Sölvegatan 19, SE-221 84 Lund, Sweden
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2
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Miyamoto A, Yamanaka T, Suzuki S, Kunii K, Kurono K, Yoshimi A, Hidaka M, Ogasawara S, Nanatani K, Abe K. Oligomeric state of the aspartate:alanine transporter (AspT) from Tetragenococcus halophilus. J Biochem 2022; 172:217-224. [PMID: 35818339 PMCID: PMC9527358 DOI: 10.1093/jb/mvac057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/30/2022] [Indexed: 11/12/2022] Open
Abstract
The aspartate:alanine exchanger family of membrane transporters includes industrially important transporters such as succinate exporter and glutamate exporter. No high-resolution structure is available from this family so far, and the transport mechanism of these transporters also remains unclear. In the present study, we focus on the oligomeric status of the aspartate:alanine antiporter (AspT) of Tetragenococcus halophilus, which is the prototype of this family. To investigate the oligomeric structure of AspT, we established a system that produces high yields of highly purified AspT and determined the oligomeric structure of AspT by analysis with size exclusion chromatography coupled with multi-angle light scattering and blue native PAGE and by comparison of the wild-type AspT with a single-cysteine mutant that forms spontaneous inter-molecular thiol crosslinking. All the results consistently support the notion that AspT is a homodimer in solutions and in membranes.
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Affiliation(s)
- Akari Miyamoto
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-0845 Japan
| | - Takashi Yamanaka
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-0845 Japan
| | - Satomi Suzuki
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-0845 Japan
| | - Kota Kunii
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-0845 Japan
| | - Kenichiro Kurono
- LS-Project, Shoko Science Co., Ltd., Aoba-ku, Yokohama, 225-0012 Japan
| | - Akira Yoshimi
- Microbial Genomics Laboratory, New Industry Creation Hatchery Center, Tohoku University, Sendai, Miyagi, 980-8579, Japan
| | - Masafumi Hidaka
- Laboratory of Molecular Enzymology, Department of Molecular Cell Science, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-0845 Japan
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, 263-8522 Japan.,Molecular Chirality Research Center, Chiba University, Chiba, 263-8522 Japan.,Membrane Protein Research and Molecular Chirality Research Centers, Chiba University, Chiba 263-8522, Japan
| | - Kei Nanatani
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-0845 Japan.,Structural Biology Group, Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, Miyagi, 980-8573, Japan
| | - Keietsu Abe
- Laboratory of Applied Microbiology, Department of Microbial Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, Miyagi, 980-0845 Japan.,Microbial Genomics Laboratory, New Industry Creation Hatchery Center, Tohoku University, Sendai, Miyagi, 980-8579, Japan
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3
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Sauer DB, Wang B, Sudar JC, Song J, Marden J, Rice WJ, Wang DN. The ups and downs of elevator-type di-/tricarboxylate membrane transporters. FEBS J 2022; 289:1515-1523. [PMID: 34403567 PMCID: PMC9832446 DOI: 10.1111/febs.16158] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/27/2021] [Accepted: 08/16/2021] [Indexed: 01/13/2023]
Abstract
The divalent anion sodium symporter (DASS) family contains both sodium-driven anion cotransporters and anion/anion exchangers. The family belongs to a broader ion transporter superfamily (ITS), which comprises 24 families of transporters, including those of AbgT antibiotic efflux transporters. The human proteins in the DASS family play major physiological roles and are drug targets. We recently determined multiple structures of the human sodium-dependent citrate transporter (NaCT) and the succinate/dicarboxylate transporter from Lactobacillus acidophilus (LaINDY). Structures of both proteins show high degrees of structural similarity to the previously determined VcINDY fold. Conservation between these DASS protein structures and those from the AbgT family indicates that the VcINDY fold represents the overall protein structure for the entire ITS. The new structures of NaCT and LaINDY are captured in the inward- or outward-facing conformations, respectively. The domain arrangements in these structures agree with a rigid body elevator-type transport mechanism for substrate translocation across the membrane. Two separate NaCT structures in complex with a substrate or an inhibitor allowed us to explain the inhibition mechanism and propose a detailed classification scheme for grouping disease-causing mutations in the human protein. Structural understanding of multiple kinetic states of DASS proteins is a first step toward the detailed characterization of their entire transport cycle.
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Affiliation(s)
- David B. Sauer
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Bing Wang
- Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY 10016, USA
| | - Joseph C. Sudar
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Jinmei Song
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - Jennifer Marden
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
| | - William J. Rice
- Cryo-Electron Microscopy Core, New York University School of Medicine, New York, NY 10016, USA
| | - Da-Neng Wang
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY 10016, USA
- Department of Cell Biology, New York University School of Medicine, New York, NY 10016, USA
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4
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High-speed atomic force microscopy reveals a three-state elevator mechanism in the citrate transporter CitS. Proc Natl Acad Sci U S A 2022; 119:2113927119. [PMID: 35101979 PMCID: PMC8833178 DOI: 10.1073/pnas.2113927119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2021] [Indexed: 12/16/2022] Open
Abstract
As cellular membranes are impermeable to most molecules, transporter proteins are typically present in the membrane to transport small molecules in or out of the cell. Due to the small, nanometer size of these transporters, it is challenging to study their transport mechanism. Here, we use advanced microscopy approaches to study in real time and at the single-molecule level the mode of action of the dimeric CitS tranpsorter. Using high-speed atomic force microscopy, we visualize the dynamic, elevator-like movement of the transporter, and we reveal that the two protomers move independently. We also discovered an intermediate state, reminiscent of another, unrelated transporter, indicating that independent evolutionary pathways have led to similar three-state elevator mechanisms. The secondary active transporter CitS shuttles citrate across the cytoplasmic membrane of gram-negative bacteria by coupling substrate translocation to the transport of two Na+ ions. Static crystal structures suggest an elevator type of transport mechanism with two states: up and down. However, no dynamic measurements have been performed to substantiate this assumption. Here, we use high-speed atomic force microscopy for real-time visualization of the transport cycle at the level of single transporters. Unexpectedly, instead of a bimodal height distribution for the up and down states, the experiments reveal movements between three distinguishable states, with protrusions of ∼0.5 nm, ∼1.0 nm, and ∼1.6 nm above the membrane, respectively. Furthermore, the real-time measurements show that the individual protomers of the CitS dimer move up and down independently. A three-state elevator model of independently operating protomers resembles the mechanism proposed for the aspartate transporter GltPh. Since CitS and GltPh are structurally unrelated, we conclude that the three-state elevators have evolved independently.
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5
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Sauer DB, Trebesch N, Marden JJ, Cocco N, Song J, Koide A, Koide S, Tajkhorshid E, Wang DN. Structural basis for the reaction cycle of DASS dicarboxylate transporters. eLife 2020; 9:e61350. [PMID: 32869741 PMCID: PMC7553777 DOI: 10.7554/elife.61350] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 08/31/2020] [Indexed: 01/09/2023] Open
Abstract
Citrate, α-ketoglutarate and succinate are TCA cycle intermediates that also play essential roles in metabolic signaling and cellular regulation. These di- and tricarboxylates are imported into the cell by the divalent anion sodium symporter (DASS) family of plasma membrane transporters, which contains both cotransporters and exchangers. While DASS proteins transport substrates via an elevator mechanism, to date structures are only available for a single DASS cotransporter protein in a substrate-bound, inward-facing state. We report multiple cryo-EM and X-ray structures in four different states, including three hitherto unseen states, along with molecular dynamics simulations, of both a cotransporter and an exchanger. Comparison of these outward- and inward-facing structures reveal how the transport domain translates and rotates within the framework of the scaffold domain through the transport cycle. Additionally, we propose that DASS transporters ensure substrate coupling by a charge-compensation mechanism, and by structural changes upon substrate release.
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Affiliation(s)
- David B Sauer
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Noah Trebesch
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Jennifer J Marden
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Nicolette Cocco
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Jinmei Song
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
| | - Akiko Koide
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Department of Medicine, New York University School of MedicineNew YorkUnited States
| | - Shohei Koide
- Perlmutter Cancer Center, New York University School of MedicineNew YorkUnited States
- Department of Medicine, New York University School of MedicineNew YorkUnited States
- Department of Biochemistry and Molecular Pharmacology, New York University School of MedicineNew YorkUnited States
| | - Emad Tajkhorshid
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-ChampaignUrbanaUnited States
| | - Da-Neng Wang
- Skirball Institute of Biomolecular Medicine, New York University School of MedicineNew YorkUnited States
- Department of Cell Biology, New York University School of MedicineNew YorkUnited States
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6
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Abstract
Energy-coupling factor (ECF)-type ATP-binding cassette (ABC) transporters catalyze membrane transport of micronutrients in prokaryotes. Crystal structures and biochemical characterization have revealed that ECF transporters are mechanistically distinct from other ABC transport systems. Notably, ECF transporters make use of small integral membrane subunits (S-components) that are predicted to topple over in the membrane when carrying the bound substrate from the extracellular side of the bilayer to the cytosol. Here, we review the phylogenetic diversity of ECF transporters as well as recent structural and biochemical advancements that have led to the postulation of conceptually different mechanistic models. These models can be described as power stroke and thermal ratchet. Structural data indicate that the lipid composition and bilayer structure are likely to have great impact on the transport function. We argue that study of ECF transporters could lead to generic insight into membrane protein structure, dynamics, and interaction.
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Affiliation(s)
- S Rempel
- Gr oningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands; , ,
| | - W K Stanek
- Gr oningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands; , ,
| | - D J Slotboom
- Gr oningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, The Netherlands; , , .,Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
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7
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Computational studies of membrane proteins: from sequence to structure to simulation. Curr Opin Struct Biol 2017; 45:133-141. [DOI: 10.1016/j.sbi.2017.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 11/19/2022]
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8
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Structural insights into the elevator-like mechanism of the sodium/citrate symporter CitS. Sci Rep 2017; 7:2548. [PMID: 28566738 PMCID: PMC5451387 DOI: 10.1038/s41598-017-02794-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 04/19/2017] [Indexed: 11/09/2022] Open
Abstract
The sodium-dependent citrate transporter of Klebsiella pneumoniae (KpCitS) belongs to the 2-hydroxycarboxylate transporter (2-HCT) family and allows the cell to use citrate as sole carbon and energy source in anaerobic conditions. Here we present crystal structures of KpCitS in citrate-bound outward-facing, citrate-bound asymmetric, and citrate-free inward-facing state. The structures reveal that the KpCitS dimerization domain remains stationary throughout the transport cycle due to a hydrogen bond network as well as extensive hydrophobic interactions. In contrast, its transport domain undergoes a ~35° rigid-body rotation and a ~17 Å translocation perpendicular to the membrane to expose the substrate-binding site alternately to either side of the membrane. Furthermore, homology models of two other 2-HCT proteins based on the KpCitS structure offer structural insights into their differences in substrate specificity at a molecular level. On the basis of our results and previous biochemical data, we propose that the activity of the 2-HCT CitS involves an elevator-like movement in which the transport domain itself traverses the lipid bilayer, carrying the substrate into the cell in a sodium-dependent manner.
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