Structural and functional diversity calls for a new classification of ABC transporters
Members of the ATP‐binding cassette (ABC) transporter superfamily translocate a broad spectrum of chemically diverse substrates. While their eponymous ATP‐binding cassette in the nucleotide‐binding domains (NBDs) is highly conserved, their transmembrane domains (TMDs) forming the translocation pathw...
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| Published in | FEBS letters Vol. 594; no. 23; pp. 3767 - 3775 |
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| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Wiley
01.12.2020
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| Subjects | |
| Online Access | Get full text |
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| Abstract | Members of the ATP‐binding cassette (ABC) transporter superfamily translocate a broad spectrum of chemically diverse substrates. While their eponymous ATP‐binding cassette in the nucleotide‐binding domains (NBDs) is highly conserved, their transmembrane domains (TMDs) forming the translocation pathway exhibit distinct folds and topologies, suggesting that during evolution the ancient motor domains were combined with different transmembrane mechanical systems to orchestrate a variety of cellular processes. In recent years, it has become increasingly evident that the distinct TMD folds are best suited to categorize the multitude of ABC transporters. We therefore propose a new ABC transporter classification that is based on structural homology in the TMDs. |
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| AbstractList | Members of the ATP-binding cassette (ABC) transporter superfamily translocate a broad spectrum of chemically diverse substrates. While their eponymous ATP-binding cassette in the nucleotide-binding domains (NBDs) is highly conserved, their transmembrane domains (TMDs) forming the translocation pathway exhibit distinct folds and topologies, suggesting that during evolution the ancient motor domains were combined with different transmembrane mechanical systems to orchestrate a variety of cellular processes. In recent years, it has become increasingly evident that the distinct TMD folds are best suited to categorize the multitude of ABC transporters. We therefore propose a new ABC transporter classification that is based on structural homology in the TMDs. Members of the ATP-binding cassette (ABC) transporter superfamily translocate a broad spectrum of chemically diverse substrates. While their eponymous ATP-binding cassette in the nucleotide-binding domains (NBDs) is highly conserved, their transmembrane domains (TMDs) forming the translocation pathway exhibit distinct folds and topologies, suggesting that during evolution the ancient motor domains were combined with different transmembrane mechanical systems to orchestrate a variety of cellular processes. In recent years, it has become increasingly evident that the distinct TMD folds are best suited to categorize the multitude of ABC transporters. We therefore propose a new ABC transporter classification that is based on structural homology in the TMDs.Members of the ATP-binding cassette (ABC) transporter superfamily translocate a broad spectrum of chemically diverse substrates. While their eponymous ATP-binding cassette in the nucleotide-binding domains (NBDs) is highly conserved, their transmembrane domains (TMDs) forming the translocation pathway exhibit distinct folds and topologies, suggesting that during evolution the ancient motor domains were combined with different transmembrane mechanical systems to orchestrate a variety of cellular processes. In recent years, it has become increasingly evident that the distinct TMD folds are best suited to categorize the multitude of ABC transporters. We therefore propose a new ABC transporter classification that is based on structural homology in the TMDs. Members of the ATP-binding cassette (ABC) transporter superfamily translocate a broad spectrum of chemically diverse substrates. While their eponymous ATP-binding cassette in the nucleotide-binding domains (NBDs) is highly conserved, their transmembrane domains (TMDs) forming the translocation pathway exhibit distinct folds and topologies, suggesting that during evolution, the ancient motor domains were combined with different transmembrane mechanical systems to orchestrate a variety of cellular processes. In recent years, it has become increasingly evident that the distinct TMD folds are best suited to categorize the multitude of ABC transporters. We therefore propose a new ABC transporter classification that currently comprises seven different types based on structural homology in the TMDs. |
| Author | Koronakis, Vassilis Zhang, Peng Tampé, Robert Lill, Roland Holland, I. Barry Zheng, Hongjin Yan, Nieng Lee, Youngsook Chang, Geoffrey Poolman, Bert Wen, Po‐Chao Murakami, Satoshi Beis, Konstantinos Váradi, András Lewinson, Oded Aller, Stephen G. Dean, Michael Slotboom, Dirk J. Ekiert, Damian Rosenbaum, Daniel Duong Van Hoa, Franck Kato, Hiroaki Gong, Xin Chen, Lei Carpenter, Elisabeth P. Pinkett, Heather W. Ueda, Kazumitsu Ford, Robert Tieleman, D. Peter Thomas, Christoph Schneider, Erwin Shyng, Show‐Ling Schmitt, Lutz Sarkadi, Balazs Kahne, Daniel K. Martinoia, Enrico Dassa, Elie Huang, Yihua Shi, Yigong Tajkhorshid, Emad Zimmer, Jochen Koth, Christopher M. Gaudet, Rachelle |
| AuthorAffiliation | 30 Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA 9 Institut Pasteur, Paris Cedex 15, France 27 Department of Life Science, Tokyo Institute of Technology, Yokohama, Japan 31 Institute of Enzymology, Research Center for Natural Sciences (RCNS), Budapest, Hungary 39 Department of Molecular Biology, Princeton University, NJ, USA 10 Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, USA 34 Institute of Biology, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, China 23 Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel 13 Faculty of Biology, Medicine and Health, The University of Manchester, UK 22 Division of Integrative Bioscience and Biotechnology, POSTECH, Pohang, Korea 36 Department of Biochemistry, Center for Biophysics and Quantitative Biology, NIH Center for Macromolecular Mod |
| AuthorAffiliation_xml | – name: 3 Department of Life Sciences, Imperial College London, London South Kensington, UK – name: 8 Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China – name: 31 Institute of Enzymology, Research Center for Natural Sciences (RCNS), Budapest, Hungary – name: 15 Department of Biology, Southern University of Science and Technology, Shenzhen, China – name: 35 Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA – name: 19 Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Japan – name: 24 Institut für Zytobiologie, Philipps-Universität Marburg, Germany – name: 30 Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA – name: 27 Department of Life Science, Tokyo Institute of Technology, Yokohama, Japan – name: 2 Department of Pharmacology and Toxicology, University of Alabama at Birmingham, AL, USA – name: 11 Department of Biochemistry and Molecular Biology, Faculty of Medicine, Life Sciences Institute, University of British Columbia, Vancouver, BC, Canada – name: 17 National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China – name: 26 International Research Centre for Environmental Membrane Biology, Foshan University, Foshan, China – name: 21 Structural Biology, Genentech Inc., South San Francisco, CA, USA – name: 22 Division of Integrative Bioscience and Biotechnology, POSTECH, Pohang, Korea – name: 10 Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Gaithersburg, MD, USA – name: 36 Department of Biochemistry, Center for Biophysics and Quantitative Biology, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, IL, USA – name: 18 Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA – name: 23 Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, Haifa, Israel – name: 16 Institute for Integrative Biology of the Cell (I2BC), Université Paris-Sud, Orsay, France – name: 5 Structural Genomics Consortium, University of Oxford, UK – name: 20 Department of Pathology, University of Cambridge, UK – name: 14 Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA – name: 28 Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA – name: 39 Department of Molecular Biology, Princeton University, NJ, USA – name: 37 Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, AB, Canada – name: 7 State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Peking University, Beijing, China – name: 29 Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, The Netherlands – name: 32 Institute of Biochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany – name: 38 Institute for Integrated Cell-Material Sciences (WPI-iCeMS), KUIAS, Kyoto University, Japan – name: 1 Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Germany – name: 6 Skaggs School of Pharmacy and Pharmaceutical Sciences and Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, CA, USA – name: 12 Department of Cell Biology and Department of Microbiology, New York University School of Medicine, NY, USA – name: 33 Department of Biology/Microbial Physiology, Humboldt-University of Berlin, Germany – name: 13 Faculty of Biology, Medicine and Health, The University of Manchester, UK – name: 9 Institut Pasteur, Paris Cedex 15, France – name: 25 Department of Plant and Microbial Biology, University Zurich, Switzerland – name: 34 Institute of Biology, Westlake Institute for Advanced Study, School of Life Sciences, Westlake University, Hangzhou, China – name: 42 Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA, USA – name: 40 National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China – name: 41 Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, USA – name: 4 Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, UK |
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Peter orcidid: 0000-0001-5507-0688 surname: Tieleman fullname: Tieleman, D. Peter organization: University of Calgary – sequence: 36 givenname: Kazumitsu orcidid: 0000-0003-2980-6078 surname: Ueda fullname: Ueda, Kazumitsu organization: Kyoto University – sequence: 37 givenname: András orcidid: 0000-0002-2722-7120 surname: Váradi fullname: Váradi, András organization: Research Center for Natural Sciences (RCNS) – sequence: 38 givenname: Po‐Chao orcidid: 0000-0002-6049-6904 surname: Wen fullname: Wen, Po‐Chao organization: University of Illinois at Urbana‐Champaign – sequence: 39 givenname: Nieng surname: Yan fullname: Yan, Nieng organization: Princeton University – sequence: 40 givenname: Peng surname: Zhang fullname: Zhang, Peng organization: Chinese Academy of Sciences – sequence: 41 givenname: Hongjin surname: Zheng fullname: Zheng, Hongjin organization: University of Colorado Anschutz Medical Campus – sequence: 42 givenname: Jochen surname: Zimmer fullname: Zimmer, Jochen organization: University of Virginia School of Medicine – sequence: 43 givenname: Robert orcidid: 0000-0002-0403-2160 surname: Tampé fullname: Tampé, Robert email: tampe@em.uni-frankfurt.de organization: Goethe University Frankfurt |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/32978974$$D View this record in MEDLINE/PubMed https://hal.science/hal-02968374$$DView record in HAL |
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| Keywords | X-ray crystallography primary active transporters membrane proteins sequence alignment molecular machines phylogeny ABC transporters structural biology ATPases cryo-EM ABC Transporters |
| Language | English |
| License | Attribution 2020 The Authors. FEBS Letters published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies. Distributed under a Creative Commons Attribution 4.0 International License: http://creativecommons.org/licenses/by/4.0 This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. http://creativecommons.org/licenses/by/4.0 |
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| Notes | Edited by Gergely Szakács ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 ObjectType-Review-3 content type line 23 PMCID: PMC8386196 CT and RT wrote the manuscript with contributions from all coauthors. This review is the quintessence of a resumed discussion that started at the FEBS Advanced Lecture Course on the Biochemistry of Membrane Proteins in Budapest (2019) and continued at the FEBS Conference on ATP-Binding Cassette (ABC) Proteins in Innsbruck (2020). The discussion included a vivid exchange of thoughts via hundreds of emails and remote video sessions during the global COVID-19 pandemic. In addition to the authors listed, we received positive feedbacks on our proposed classification from several further leading scientists in the ABC transporter field. Yet, as they felt that their contribution was too small, they decided not to accept authorship. Author contributions |
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| Snippet | Members of the ATP‐binding cassette (ABC) transporter superfamily translocate a broad spectrum of chemically diverse substrates. While their eponymous... Members of the ATP-binding cassette (ABC) transporter superfamily translocate a broad spectrum of chemically diverse substrates. While their eponymous... |
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| SubjectTerms | ABC transporters ATPases cryo‐EM evolution functional diversity Life Sciences membrane proteins molecular machines phylogeny primary active transporters sequence alignment structural biology X‐ray crystallography |
| Title | Structural and functional diversity calls for a new classification of ABC transporters |
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