1
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Partipilo M, Jan Slotboom D. The S-component fold: a link between bacterial transporters and receptors. Commun Biol 2024; 7:610. [PMID: 38773269 PMCID: PMC11109136 DOI: 10.1038/s42003-024-06295-2] [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: 01/18/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024] Open
Abstract
The processes of nutrient uptake and signal sensing are crucial for microbial survival and adaptation. Membrane-embedded proteins involved in these functions (transporters and receptors) are commonly regarded as unrelated in terms of sequence, structure, mechanism of action and evolutionary history. Here, we analyze the protein structural universe using recently developed artificial intelligence-based structure prediction tools, and find an unexpected link between prominent groups of microbial transporters and receptors. The so-called S-components of Energy-Coupling Factor (ECF) transporters, and the membrane domains of sensor histidine kinases of the 5TMR cluster share a structural fold. The discovery of their relatedness manifests a widespread case of prokaryotic "transceptors" (related proteins with transport or receptor function), showcases how artificial intelligence-based structure predictions reveal unchartered evolutionary connections between proteins, and provides new avenues for engineering transport and signaling functions in bacteria.
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Affiliation(s)
- Michele Partipilo
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Dirk Jan Slotboom
- Department of Biochemistry, Groningen Institute of Biomolecular Sciences & Biotechnology, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.
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2
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Exapicheidou IA, Shams A, Ibrahim H, Tsarenko A, Backenköhler M, Hamed MM, Diamanti E, Volkamer A, Slotboom DJ, Hirsch AKH. Hit optimization by dynamic combinatorial chemistry on Streptococcus pneumoniae energy-coupling factor transporter ECF-PanT. Chem Commun (Camb) 2024; 60:870-873. [PMID: 38164786 DOI: 10.1039/d3cc04738e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Herein, we present the first application of target-directed dynamic combinatorial chemistry (tdDCC) to the whole complex of the highly dynamic transmembrane, energy-coupling factor (ECF) transporter ECF-PanT in Streptococcus pneumoniae. In addition, we successfully employed the tdDCC technique as a hit-identification and -optimization strategy that led to the identification of optimized ECF inhibitors with improved activity. We characterized the best compounds regarding cytotoxicity and performed computational modeling studies on the crystal structure of ECF-PanT to rationalize their binding mode. Notably, docking studies showed that the acylhydrazone linker is able to maintain the crucial interactions.
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Affiliation(s)
- Ioulia Antonia Exapicheidou
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
- Saarland University, Department of Pharmacy, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Atanaz Shams
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
- Saarland University, Department of Pharmacy, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Hamza Ibrahim
- Data Driven Drug Design Group, Center for Bioinformatics, Saarland Informatics Campus E2.1, Saarland University, Saarbrücken 66123, Germany
| | - Aleksei Tsarenko
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Michael Backenköhler
- Data Driven Drug Design Group, Center for Bioinformatics, Saarland Informatics Campus E2.1, Saarland University, Saarbrücken 66123, Germany
| | - Mostafa M Hamed
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
| | - Eleonora Diamanti
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
| | - Andrea Volkamer
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
- Data Driven Drug Design Group, Center for Bioinformatics, Saarland Informatics Campus E2.1, Saarland University, Saarbrücken 66123, Germany
| | - Dirk J Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, The Netherlands
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany.
- Saarland University, Department of Pharmacy, Campus Building E8.1, 66123, Saarbrücken, Germany
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3
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Diamanti E, Souza PCT, Setyawati I, Bousis S, Monjas L, Swier LJYM, Shams A, Tsarenko A, Stanek WK, Jäger M, Marrink SJ, Slotboom DJ, Hirsch AKH. Identification of inhibitors targeting the energy-coupling factor (ECF) transporters. Commun Biol 2023; 6:1182. [PMID: 37985798 PMCID: PMC10662466 DOI: 10.1038/s42003-023-05555-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 11/08/2023] [Indexed: 11/22/2023] Open
Abstract
The energy-coupling factor (ECF) transporters are a family of transmembrane proteins involved in the uptake of vitamins in a wide range of bacteria. Inhibition of the activity of these proteins could reduce the viability of pathogens that depend on vitamin uptake. The central role of vitamin transport in the metabolism of bacteria and absence from humans make the ECF transporters an attractive target for inhibition with selective chemical probes. Here, we report on the identification of a promising class of inhibitors of the ECF transporters. We used coarse-grained molecular dynamics simulations on Lactobacillus delbrueckii ECF-FolT2 and ECF-PanT to profile the binding mode and mechanism of inhibition of this novel chemotype. The results corroborate the postulated mechanism of transport and pave the way for further drug-discovery efforts.
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Affiliation(s)
- Eleonora Diamanti
- Helmholtz Institute for Pharmaceutical Research (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, D-66123, Saarbrücken, Germany
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, UMR 5086 CNRS and University of Lyon, Lyon, France
- Laboratoire de Biologie et Modélisation de la Cellule (UMR 5239, Inserm, U1293) and Centre Blaise Pascal, École Normale Supérieure de Lyon, Université Claude Bernard Lyon 1 and CNRS, 46 Allée d'Italie, 69007, Lyon, France
| | - Inda Setyawati
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
- Department of Biochemistry, Bogor Agricultural University, Dramaga, 16680, Bogor, Indonesia
| | - Spyridon Bousis
- Helmholtz Institute for Pharmaceutical Research (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, D-66123, Saarbrücken, Germany
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747, AG Groningen, the Netherlands
| | - Leticia Monjas
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Lotteke J Y M Swier
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Atanaz Shams
- Helmholtz Institute for Pharmaceutical Research (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, D-66123, Saarbrücken, Germany
| | - Aleksei Tsarenko
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Weronika K Stanek
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Manuel Jäger
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747, AG Groningen, the Netherlands
| | - Siewert J Marrink
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Dirk J Slotboom
- Biomolecular Sciences and Biotechnology Institute University of Groningen Nijenborgh 4, 9747AG, Groningen, The Netherlands
| | - Anna K H Hirsch
- Helmholtz Institute for Pharmaceutical Research (HIPS) - Helmholtz Centre for Infection Research (HZI), Campus Building E 8.1, D-66123, Saarbrücken, Germany.
- Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany.
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, NL-9747, AG Groningen, the Netherlands.
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4
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Thangaratnarajah C, Nijland M, Borges-Araújo L, Jeucken A, Rheinberger J, Marrink SJ, Souza PCT, Paulino C, Slotboom DJ. Expulsion mechanism of the substrate-translocating subunit in ECF transporters. Nat Commun 2023; 14:4484. [PMID: 37491368 PMCID: PMC10368641 DOI: 10.1038/s41467-023-40266-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/20/2023] [Indexed: 07/27/2023] Open
Abstract
Energy-coupling factor (ECF)-type transporters mediate the uptake of micronutrients in many bacteria. They consist of a substrate-translocating subunit (S-component) and an ATP-hydrolysing motor (ECF module) Previous data indicate that the S-component topples within the membrane to alternately expose the binding site to either side of the membrane. In many ECF transporters, the substrate-free S-component can be expelled from the ECF module. Here we study this enigmatic expulsion step by cryogenic electron microscopy and reveal that ATP induces a concave-to-convex shape change of two long helices in the motor, thereby destroying the S-component's docking site and allowing for its dissociation. We show that adaptation of the membrane morphology to the conformational state of the motor may favour expulsion of the substrate-free S-component when ATP is bound and docking of the substrate-loaded S-component after hydrolysis. Our work provides a picture of bilayer-assisted chemo-mechanical coupling in the transport cycle of ECF transporters.
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Affiliation(s)
- Chancievan Thangaratnarajah
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Mark Nijland
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Luís Borges-Araújo
- Molecular Microbiology and Structural Biochemistry, CNRS and University of Lyon, 69367, Lyon, France
| | - Aike Jeucken
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Jan Rheinberger
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany
| | - Siewert J Marrink
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Molecular Dynamics Group, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Paulo C T Souza
- Molecular Microbiology and Structural Biochemistry, CNRS and University of Lyon, 69367, Lyon, France
| | - Cristina Paulino
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Electron Microscopy Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
- Biochemistry Center, University of Heidelberg, Im Neuenheimer Feld 328, 69120, Heidelberg, Germany.
| | - Dirk J Slotboom
- Faculty of Science and Engineering, Groningen Biomolecular Sciences and Biotechnology, Membrane Enzymology Group, University of Groningen, 9747 AG, Groningen, The Netherlands.
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5
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Rivera-Lugo R, Huang S, Lee F, Méheust R, Iavarone AT, Sidebottom AM, Oldfield E, Portnoy DA, Light SH. Distinct Energy-Coupling Factor Transporter Subunits Enable Flavin Acquisition and Extracytosolic Trafficking for Extracellular Electron Transfer in Listeria monocytogenes. mBio 2023; 14:e0308522. [PMID: 36744898 PMCID: PMC9973259 DOI: 10.1128/mbio.03085-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/05/2023] [Indexed: 02/07/2023] Open
Abstract
A variety of electron transfer mechanisms link bacterial cytosolic electron pools with functionally diverse redox activities in the cell envelope and extracellular space. In Listeria monocytogenes, the ApbE-like enzyme FmnB catalyzes extracytosolic protein flavinylation, covalently linking a flavin cofactor to proteins that transfer electrons to extracellular acceptors. L. monocytogenes uses an energy-coupling factor (ECF) transporter complex that contains distinct substrate-binding, transmembrane, ATPase A, and ATPase A' subunits (RibU, EcfT, EcfA, and EcfA') to import environmental flavins, but the basis of extracytosolic flavin trafficking for FmnB flavinylation remains poorly defined. In this study, we show that the EetB and FmnA proteins are related to ECF transporter substrate-binding and transmembrane subunits, respectively, and are essential for exporting flavins from the cytosol for flavinylation. Comparisons of the flavin import versus export capabilities of L. monocytogenes strains lacking different ECF transporter subunits demonstrate a strict directionality of substrate-binding subunit transport but partial functional redundancy of transmembrane and ATPase subunits. Based on these results, we propose that ECF transporter complexes with different subunit compositions execute directional flavin import/export through a broadly conserved mechanism. Finally, we present genomic context analyses that show that related ECF exporter genes are distributed across members of the phylum Firmicutes and frequently colocalize with genes encoding flavinylated extracytosolic proteins. These findings clarify the basis of ECF transporter export and extracytosolic flavin cofactor trafficking in Firmicutes. IMPORTANCE Bacteria import vitamins and other essential compounds from their surroundings but also traffic related compounds from the cytosol to the cell envelope where they serve various functions. Studying the foodborne pathogen Listeria monocytogenes, we find that the modular use of subunits from a prominent class of bacterial transporters enables the import of environmental vitamin B2 cofactors and the extracytosolic trafficking of a vitamin B2-derived cofactor that facilitates redox reactions in the cell envelope. These studies clarify the basis of bidirectional small-molecule transport across the cytoplasmic membrane and the assembly of redox-active proteins within the cell envelope and extracellular space.
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Affiliation(s)
- Rafael Rivera-Lugo
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Shuo Huang
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
| | - Frank Lee
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Raphaël Méheust
- Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d’Évry, Université Paris-Saclay, CNRS, Evry, France
| | - Anthony T. Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, Berkeley, California, USA
| | | | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Daniel A. Portnoy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, California, USA
| | - Samuel H. Light
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
- Department of Microbiology, University of Chicago, Chicago, Illinois, USA
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6
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Tordai H, Suhajda E, Sillitoe I, Nair S, Varadi M, Hegedus T. Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology. Int J Mol Sci 2022; 23:8877. [PMID: 36012140 PMCID: PMC9408558 DOI: 10.3390/ijms23168877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/05/2022] [Accepted: 08/07/2022] [Indexed: 02/06/2023] Open
Abstract
The number of unique transmembrane (TM) protein structures doubled in the last four years, which can be attributed to the revolution of cryo-electron microscopy. In addition, AlphaFold2 (AF2) also provided a large number of predicted structures with high quality. However, if a specific protein family is the subject of a study, collecting the structures of the family members is highly challenging in spite of existing general and protein domain-specific databases. Here, we demonstrate this and assess the applicability and usability of automatic collection and presentation of protein structures via the ABC protein superfamily. Our pipeline identifies and classifies transmembrane ABC protein structures using the PFAM search and also aims to determine their conformational states based on special geometric measures, conftors. Since the AlphaFold database contains structure predictions only for single polypeptide chains, we performed AF2-Multimer predictions for human ABC half transporters functioning as dimers. Our AF2 predictions warn of possibly ambiguous interpretation of some biochemical data regarding interaction partners and call for further experiments and experimental structure determination. We made our predicted ABC protein structures available through a web application, and we joined the 3D-Beacons Network to reach the broader scientific community through platforms such as PDBe-KB.
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Affiliation(s)
- Hedvig Tordai
- Department of Biophysics and Radiation Biology, Semmelweis University, 1085 Budapest, Hungary
| | - Erzsebet Suhajda
- Department of Biophysics and Radiation Biology, Semmelweis University, 1085 Budapest, Hungary
- Faculty of Electrical Engineering and Informatics, Budapest University of Technology and Economics, 1111 Budapest, Hungary
- Wigner Research Centre for Physics, 1121 Budapest, Hungary
| | - Ian Sillitoe
- Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - Sreenath Nair
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton CB10 1SD, UK
| | - Mihaly Varadi
- European Bioinformatics Institute, European Molecular Biology Laboratory, Hinxton CB10 1SD, UK
| | - Tamas Hegedus
- Department of Biophysics and Radiation Biology, Semmelweis University, 1085 Budapest, Hungary
- ELKH-SE Biophysical Virology Research Group, Eötvös Loránd Research Network, 1052 Budapest, Hungary
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7
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Kiefer AF, Bousis S, Hamed MM, Diamanti E, Haupenthal J, Hirsch AKH. Structure-Guided Optimization of Small-Molecule Folate Uptake Inhibitors Targeting the Energy-Coupling Factor Transporters. J Med Chem 2022; 65:8869-8880. [PMID: 35709475 PMCID: PMC9289886 DOI: 10.1021/acs.jmedchem.1c02114] [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] [Indexed: 11/29/2022]
Abstract
![]()
Here, we report on
a potent class of substituted ureidothiophenes
targeting energy-coupling factor (ECF) transporters, an unexplored
target that is not addressed by any antibiotic in the market. Since
the ECF module is crucial for the vitamin transport mechanism, the
prevention of substrate uptake should ultimately lead to cell death.
By utilizing a combination of virtual and functional whole-cell screening
of our in-house library, the membrane-bound protein mediated uptake
of folate could be effectively inhibited. Structure-based optimization
of our hit yielded low-micromolar inhibitors, whereby the most active
compounds showed in addition potent antimicrobial activities against
a panel of clinically relevant Gram-positive pathogens without significant
cytotoxic effects.
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Affiliation(s)
- Alexander F Kiefer
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Spyridon Bousis
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany
| | - Mostafa M Hamed
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Eleonora Diamanti
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany.,Helmholtz International Lab for Anti-Infectives, Campus E8.1, 66123 Saarbrücken, Germany
| | - Jörg Haupenthal
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany
| | - Anna K H Hirsch
- Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS)-Helmholtz Centre for Infection Research (HZI), Campus E8.1, 66123 Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus E8.1, 66123 Saarbrücken, Germany.,Helmholtz International Lab for Anti-Infectives, Campus E8.1, 66123 Saarbrücken, Germany
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8
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Younus I, Kochkina S, Choi CC, Sun W, Ford RC. ATP-Binding Cassette Transporters: Snap-on Complexes? Subcell Biochem 2022; 99:35-82. [PMID: 36151373 DOI: 10.1007/978-3-031-00793-4_2] [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] [Indexed: 06/16/2023]
Abstract
ATP-binding cassette (ABC) transporters are one of the largest families of membrane proteins in prokaryotic organisms. Much is now understood about the structure of these transporters and many reviews have been written on that subject. In contrast, less has been written on the assembly of ABC transporter complexes and this will be a major focus of this book chapter. The complexes are formed from two cytoplasmic subunits that are highly conserved (in terms of their primary and three-dimensional structures) across the whole family. These ATP-binding subunits give rise to the name of the family. They must assemble with two transmembrane subunits that will typically form the permease component of the transporter. The transmembrane subunits have been found to be surprisingly diverse in structure when the whole family is examined, with seven distinct folds identified so far. Hence nucleotide-binding subunits appear to have been bolted on to a variety of transmembrane platforms during evolution, leading to a greater variety in function. Furthermore, many importers within the family utilise a further external substrate-binding component to trap scarce substrates and deliver them to the correct permease components. In this chapter, we will discuss whether assembly of the various ABC transporter subunits occurs with high fidelity within the crowded cellular environment and whether promiscuity in assembly of transmembrane and cytoplasmic components can occur. We also discuss the new AlphaFold protein structure prediction tool which predicts a new type of transmembrane domain fold within the ABC transporters that is associated with cation exporters of bacteria and plants.
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Affiliation(s)
- Iqra Younus
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Sofia Kochkina
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Cheri C Choi
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Wenjuan Sun
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Robert C Ford
- Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, UK.
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9
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Insights into the bilayer-mediated toppling mechanism of a folate-specific ECF transporter by cryo-EM. Proc Natl Acad Sci U S A 2021; 118:2105014118. [PMID: 34408021 DOI: 10.1073/pnas.2105014118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Energy-coupling factor (ECF)-type transporters are small, asymmetric membrane protein complexes (∼115 kDa) that consist of a membrane-embedded, substrate-binding protein (S component) and a tripartite ATP-hydrolyzing module (ECF module). They import micronutrients into bacterial cells and have been proposed to use a highly unusual transport mechanism, in which the substrate is dragged across the membrane by a toppling motion of the S component. However, it remains unclear how the lipid bilayer could accommodate such a movement. Here, we used cryogenic electron microscopy at 200 kV to determine structures of a folate-specific ECF transporter in lipid nanodiscs and detergent micelles at 2.7- and 3.4-Å resolution, respectively. The structures reveal an irregularly shaped bilayer environment around the membrane-embedded complex and suggest that toppling of the S component is facilitated by protein-induced membrane deformations. In this way, structural remodeling of the lipid bilayer environment is exploited to guide the transport process.
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10
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Elevator-type mechanisms of membrane transport. Biochem Soc Trans 2021; 48:1227-1241. [PMID: 32369548 PMCID: PMC7329351 DOI: 10.1042/bst20200290] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 03/29/2020] [Accepted: 03/31/2020] [Indexed: 12/13/2022]
Abstract
Membrane transporters are integral membrane proteins that mediate the passage of solutes across lipid bilayers. These proteins undergo conformational transitions between outward- and inward-facing states, which lead to alternating access of the substrate-binding site to the aqueous environment on either side of the membrane. Dozens of different transporter families have evolved, providing a wide variety of structural solutions to achieve alternating access. A sub-set of structurally diverse transporters operate by mechanisms that are collectively named 'elevator-type'. These transporters have one common characteristic: they contain a distinct protein domain that slides across the membrane as a rigid body, and in doing so it 'drags" the transported substrate along. Analysis of the global conformational changes that take place in membrane transporters using elevator-type mechanisms reveals that elevator-type movements can be achieved in more than one way. Molecular dynamics simulations and experimental data help to understand how lipid bilayer properties may affect elevator movements and vice versa.
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11
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Setyawati I, Stanek WK, Majsnerowska M, Swier LJYM, Pardon E, Steyaert J, Guskov A, Slotboom DJ. In vitro reconstitution of dynamically interacting integral membrane subunits of energy-coupling factor transporters. eLife 2020; 9:64389. [PMID: 33350937 PMCID: PMC7755397 DOI: 10.7554/elife.64389] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/02/2020] [Indexed: 01/03/2023] Open
Abstract
Energy-coupling factor (ECF) transporters mediate import of micronutrients in prokaryotes. They consist of an integral membrane S-component (that binds substrate) and ECF module (that powers transport by ATP hydrolysis). It has been proposed that different S-components compete for docking onto the same ECF module, but a minimal liposome-reconstituted system, required to substantiate this idea, is lacking. Here, we co-reconstituted ECF transporters for folate (ECF-FolT2) and pantothenate (ECF-PanT) into proteoliposomes, and assayed for crosstalk during active transport. The kinetics of transport showed that exchange of S-components is part of the transport mechanism. Competition experiments suggest much slower substrate association with FolT2 than with PanT. Comparison of a crystal structure of ECF-PanT with previously determined structures of ECF-FolT2 revealed larger conformational changes upon binding of folate than pantothenate, which could explain the kinetic differences. Our work shows that a minimal in vitro system with two reconstituted transporters recapitulates intricate kinetics behaviour observed in vivo.
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Affiliation(s)
- Inda Setyawati
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Biochemistry Department, Bogor Agricultural University, Bogor, Indonesia
| | - Weronika K Stanek
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Maria Majsnerowska
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Lotteke J Y M Swier
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Els Pardon
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Jan Steyaert
- Structural Biology Brussels, Vrije Universiteit Brussel, VUB, Brussels, Belgium.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium
| | - Albert Guskov
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.,Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Dirk J Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
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12
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Turner ME, Huynh K, Carroll RK, Ahn SJ, Rice KC. Characterization of the Streptococcus mutans SMU.1703c-SMU.1702c Operon Reveals Its Role in Riboflavin Import and Response to Acid Stress. J Bacteriol 2020; 203:e00293-20. [PMID: 33077636 PMCID: PMC7950412 DOI: 10.1128/jb.00293-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/15/2020] [Indexed: 11/20/2022] Open
Abstract
Streptococcus mutans utilizes numerous metabolite transporters to obtain essential nutrients in the "feast or famine" environment of the human mouth. S. mutans and most other streptococci are considered auxotrophic for several essential vitamins including riboflavin (vitamin B2), which is used to generate key cofactors and to perform numerous cellular redox reactions. Despite the well-known contributions of this vitamin to central metabolism, little is known about how S. mutans obtains and metabolizes B2 The uncharacterized protein SMU.1703c displays high sequence homology to the riboflavin transporter RibU. Deletion of SMU.1703c hindered S. mutans growth in complex and defined medium in the absence of saturating levels of exogenous riboflavin, whereas deletion of cotranscribed SMU.1702c alone had no apparent effect on growth. Expression of SMU.1703c in a Bacillus subtilis riboflavin auxotroph functionally complemented growth in nonsaturating riboflavin conditions. S. mutans was also able to grow on flavin adenine dinucleotide (FAD) or flavin mononucleotide (FMN) in an SMU.1703c-dependent manner. Deletion of SMU.1703c and/or SMU.1702c impacted S. mutans acid stress tolerance, as all mutants showed improved growth at pH 5.5 compared to that of the wild type when medium was supplemented with saturating riboflavin. Cooccurrence of SMU.1703c and SMU.1702c, a hypothetical PAP2 family acid phosphatase gene, appears unique to the streptococci and may suggest a connection of SMU.1702c to the acquisition or metabolism of flavins within this genus. Identification of SMU.1703c as a RibU-like riboflavin transporter furthers our understanding of how S. mutans acquires essential micronutrients within the oral cavity and how this pathogen successfully competes within nutrient-starved oral biofilms.IMPORTANCE Dental caries form when acid produced by oral bacteria erodes tooth enamel. This process is driven by the fermentative metabolism of cariogenic bacteria, most notably Streptococcus mutans Nutrient acquisition is key in the competitive oral cavity, and many organisms have evolved various strategies to procure carbon sources or necessary biomolecules. B vitamins, such as riboflavin, which many oral streptococci must scavenge from the oral environment, are necessary for survival within the competitive oral cavity. However, the primary mechanism and proteins involved in this process remain uncharacterized. This study is important because it identifies a key step in S. mutans riboflavin acquisition and cofactor generation, which may enable the development of novel anticaries treatment strategies via selective targeting of metabolite transporters.
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Affiliation(s)
- Matthew E Turner
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Khanh Huynh
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
| | - Ronan K Carroll
- Department of Biological Sciences, Ohio University, Athens, Ohio, USA
| | - Sang-Joon Ahn
- Department of Oral Biology, College of Dentistry, University of Florida, Gainesville, Florida, USA
| | - Kelly C Rice
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA
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13
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Ford RC, Hellmich UA. What monomeric nucleotide binding domains can teach us about dimeric ABC proteins. FEBS Lett 2020; 594:3857-3875. [PMID: 32880928 DOI: 10.1002/1873-3468.13921] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/06/2020] [Accepted: 08/24/2020] [Indexed: 12/12/2022]
Abstract
The classic conceptualization of ATP binding cassette (ABC) transporter function is an ATP-dependent conformational change coupled to transport of a substrate across a biological membrane via the transmembrane domains (TMDs). The binding of two ATP molecules within the transporter's two nucleotide binding domains (NBDs) induces their dimerization. Despite retaining the ability to bind nucleotides, isolated NBDs frequently fail to dimerize. ABC proteins without a TMD, for example ABCE and ABCF, have NBDs tethered via elaborate linkers, further supporting that NBD dimerization does not readily occur for isolated NBDs. Intriguingly, even in full-length transporters, the NBD-dimerized, outward-facing state is not as frequently observed as might be expected. This leads to questions regarding what drives NBD interaction and the role of the TMDs or linkers. Understanding the NBD-nucleotide interaction and the subsequent NBD dimerization is thus pivotal for understanding ABC transporter activity in general. Here, we hope to provide new insights into ABC protein function by discussing the perplexing issue of (missing) NBD dimerization in isolation and in the context of full-length ABC proteins.
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Affiliation(s)
- Robert C Ford
- Faculty of Biology Medicine and Health, The University of Manchester, UK
| | - Ute A Hellmich
- Department of Chemistry, Johannes Gutenberg-University, Mainz, Germany.,Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University, Frankfurt, Germany
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14
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Verplaetse E, André-Leroux G, Duhutrel P, Coeuret G, Chaillou S, Nielsen-Leroux C, Champomier-Vergès MC. Heme Uptake in Lactobacillus sakei Evidenced by a New Energy Coupling Factor (ECF)-Like Transport System. Appl Environ Microbiol 2020; 86:e02847-19. [PMID: 32680867 PMCID: PMC7480364 DOI: 10.1128/aem.02847-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 07/05/2020] [Indexed: 12/27/2022] Open
Abstract
Lactobacillus sakei is a nonpathogenic lactic acid bacterium and a natural inhabitant of meat ecosystems. Although red meat is a heme-rich environment, L. sakei does not need iron or heme for growth, although it possesses a heme-dependent catalase. Iron incorporation into L. sakei from myoglobin and hemoglobin was previously shown by microscopy and the L. sakei genome reveals the complete equipment for iron and heme transport. Here, we report the characterization of a five-gene cluster (from lsa1836 to lsa1840 [lsa1836-1840]) encoding a putative metal iron ABC transporter. Interestingly, this cluster, together with a heme-dependent catalase gene, is also conserved in other species from the meat ecosystem. Our bioinformatic analyses revealed that the locus might correspond to a complete machinery of an energy coupling factor (ECF) transport system. We quantified in vitro the intracellular heme in the wild type (WT) and in our Δlsa1836-1840 deletion mutant using an intracellular heme sensor and inductively coupled plasma mass spectrometry for quantifying incorporated 57Fe heme. We showed that in the WT L. sakei, heme accumulation occurs rapidly and massively in the presence of hemin, while the deletion mutant was impaired in heme uptake; this ability was restored by in trans complementation. Our results establish the main role of the L. sakei Lsa1836-1840 ECF-like system in heme uptake. Therefore, this research outcome sheds new light on other possible functions of ECF-like systems.IMPORTANCELactobacillus sakei is a nonpathogenic bacterial species exhibiting high fitness in heme-rich environments such as meat products, although it does not need iron or heme for growth. Heme capture and utilization capacities are often associated with pathogenic species and are considered virulence-associated factors in the infected hosts. For these reasons, iron acquisition systems have been deeply studied in such species, while for nonpathogenic bacteria the information is scarce. Genomic data revealed that several putative iron transporters are present in the genome of the lactic acid bacterium L. sakei In this study, we demonstrate that one of them is an ECF-like ABC transporter with a functional role in heme transport. Such evidence has not yet been brought for an ECF; therefore, our study reveals a new class of heme transport system.
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Affiliation(s)
- Emilie Verplaetse
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | | | - Philippe Duhutrel
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Gwendoline Coeuret
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Stéphane Chaillou
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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15
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Jochim A, Adolf L, Belikova D, Schilling NA, Setyawati I, Chin D, Meyers S, Verhamme P, Heinrichs DE, Slotboom DJ, Heilbronner S. An ECF-type transporter scavenges heme to overcome iron-limitation in Staphylococcus lugdunensis. eLife 2020; 9:e57322. [PMID: 32515736 PMCID: PMC7299338 DOI: 10.7554/elife.57322] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/09/2020] [Indexed: 01/03/2023] Open
Abstract
Energy-coupling factor type transporters (ECF) represent trace nutrient acquisition systems. Substrate binding components of ECF-transporters are membrane proteins with extraordinary affinity, allowing them to scavenge trace amounts of ligand. A number of molecules have been described as substrates of ECF-transporters, but an involvement in iron-acquisition is unknown. Host-induced iron limitation during infection represents an effective mechanism to limit bacterial proliferation. We identified the iron-regulated ECF-transporter Lha in the opportunistic bacterial pathogen Staphylococcus lugdunensis and show that the transporter is specific for heme. The recombinant substrate-specific subunit LhaS accepted heme from diverse host-derived hemoproteins. Using isogenic mutants and recombinant expression of Lha, we demonstrate that its function is independent of the canonical heme acquisition system Isd and allows proliferation on human cells as sources of nutrient iron. Our findings reveal a unique strategy of nutritional heme acquisition and provide the first example of an ECF-transporter involved in overcoming host-induced nutritional limitation.
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Affiliation(s)
- Angelika Jochim
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of TübingenTübingenGermany
| | - Lea Adolf
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of TübingenTübingenGermany
| | - Darya Belikova
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of TübingenTübingenGermany
| | | | - Inda Setyawati
- Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningenNetherlands
| | - Denny Chin
- Department of Microbiology and Immunology, University of Western OntarioLondonCanada
| | | | | | - David E Heinrichs
- Department of Microbiology and Immunology, University of Western OntarioLondonCanada
| | - Dirk J Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute, University of GroningenGroningenNetherlands
| | - Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of TübingenTübingenGermany
- German Centre for Infection Research (DZIF), Partner Site TübingenTübingenGermany
- (DFG) Cluster of Excellence EXC 2124 Controlling Microbes to Fight InfectionsTübingenGermany
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16
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Membrane mediated toppling mechanism of the folate energy coupling factor transporter. Nat Commun 2020; 11:1763. [PMID: 32273501 PMCID: PMC7145868 DOI: 10.1038/s41467-020-15554-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 03/13/2020] [Indexed: 01/12/2023] Open
Abstract
Energy coupling factor (ECF) transporters are responsible for the uptake of micronutrients in bacteria and archaea. They consist of an integral membrane unit, the S-component, and a tripartite ECF module. It has been proposed that the S-component mediates the substrate transport by toppling over in the membrane when docking onto an ECF module. Here, we present multi-scale molecular dynamics simulations and in vitro experiments to study the molecular toppling mechanism of the S-component of a folate-specific ECF transporter. Simulations reveal a strong bending of the membrane around the ECF module that provides a driving force for toppling of the S-component. The stability of the toppled state depends on the presence of non-bilayer forming lipids, as confirmed by folate transport activity measurements. Together, our data provide evidence for a lipid-dependent toppling-based mechanism for the folate-specific ECF transporter, a mechanism that might apply to other ECF transporters.
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17
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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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18
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Finkenwirth F, Sippach M, Pecina SN, Gäde M, Ruta J, Ricke A, Bondarenko E, Klare JP, Zinke M, Lange S, Lange A, Steinhoff HJ, Eitinger T. Dynamic interactions of CbiN and CbiM trigger activity of a cobalt energy-coupling-factor transporter. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1862:183114. [PMID: 31666178 DOI: 10.1016/j.bbamem.2019.183114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 10/01/2019] [Accepted: 10/08/2019] [Indexed: 11/26/2022]
Abstract
Energy-coupling factor (ECF) transporters for uptake of vitamins and transition-metal ions into prokaryotic cells share a common architecture consisting of a substrate-specific integral membrane protein (S), a transmembrane coupling protein (T) and two cytoplasmic ATP-binding-cassette-family ATPases. S components rotate within the membrane to expose their binding pockets alternately to the exterior and the cytoplasm. In contrast to vitamin transporters, metal-specific systems rely on additional proteins with essential but poorly understood functions. CbiN, a membrane protein composed of two transmembrane helices tethered by an extracytoplasmic loop of 37 amino-acid residues represents the auxiliary component that temporarily interacts with the CbiMQO2 Co2+ transporter. CbiN was previously shown to induce significant Co2+ transport activity in the absence of CbiQO2 in cells producing the S component CbiM plus CbiN or a Cbi(MN) fusion. Here we analyzed the mode of interaction between the two protein domains. Any deletion in the CbiN loop abolished transport activity. In silico predicted protein-protein contacts between segments of the CbiN loop and loops in CbiM were confirmed by cysteine-scanning mutagenesis and crosslinking. Likewise, an ordered structure of the CbiN loop was observed by electron paramagnetic resonance analysis after site-directed spin labeling. The N-terminal loop of CbiM containing three of four metal ligands was partially immobilized in wild-type Cbi(MN) but completely immobile in inactive variants with CbiN loop deletions. Decreased dynamics of the inactive form was also detected by solid-state nuclear magnetic resonance of isotope-labeled protein in proteoliposomes. In conclusion, CbiM-CbiN loop-loop interactions facilitate metal insertion into the binding pocket.
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Affiliation(s)
- Friedrich Finkenwirth
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Michael Sippach
- Fachbereich Physik, Universität Osnabrück, 49076 Osnabrück, Germany
| | - Sinah N Pecina
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Mario Gäde
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Julia Ruta
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Adrian Ricke
- Fachbereich Physik, Universität Osnabrück, 49076 Osnabrück, Germany
| | - Elena Bondarenko
- Fachbereich Physik, Universität Osnabrück, 49076 Osnabrück, Germany
| | - Johann P Klare
- Fachbereich Physik, Universität Osnabrück, 49076 Osnabrück, Germany
| | - Maximilian Zinke
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Sascha Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany
| | - Adam Lange
- Department of Molecular Biophysics, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany; Institut für Biologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | | | - Thomas Eitinger
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, 10099 Berlin, Germany.
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19
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Finkenwirth F, Eitinger T. ECF-type ABC transporters for uptake of vitamins and transition metal ions into prokaryotic cells. Res Microbiol 2019; 170:358-365. [PMID: 31283960 DOI: 10.1016/j.resmic.2019.06.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 12/15/2022]
Abstract
Energy-coupling factor (ECF) transporters mediate the uptake of micronutrients in prokaryotes. They consist of two ATP-binding-cassette family ATPases, a transmembrane coupling protein (T component) and a substrate-binding membrane protein (S component). ECF transporters for Co2+ and Ni2+ ions have one or two additional proteins with extracytoplasmic regions but poorly understood function. Homologs of T components with a predicted localization in plastids are widespread in plants but their physiological role is unclear. S components in eukaryotes are very rare and restricted to biotin-specific variants. Apart from a potential contribution to the export of flavins to serve the assembly of extracytoplasmic electron transfer chains, ECF transporters function as importers.
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Affiliation(s)
- Friedrich Finkenwirth
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Thomas Eitinger
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany.
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20
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Santos JA, Rempel S, Mous ST, Pereira CT, Ter Beek J, de Gier JW, Guskov A, Slotboom DJ. Functional and structural characterization of an ECF-type ABC transporter for vitamin B12. eLife 2018; 7:35828. [PMID: 29809140 PMCID: PMC5997447 DOI: 10.7554/elife.35828] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/26/2018] [Indexed: 01/01/2023] Open
Abstract
Vitamin B12 (cobalamin) is the most complex B-type vitamin and is synthetized exclusively in a limited number of prokaryotes. Its biologically active variants contain rare organometallic bonds, which are used by enzymes in a variety of central metabolic pathways such as L-methionine synthesis and ribonucleotide reduction. Although its biosynthesis and role as co-factor are well understood, knowledge about uptake of cobalamin by prokaryotic auxotrophs is scarce. Here, we characterize a cobalamin-specific ECF-type ABC transporter from Lactobacillus delbrueckii, ECF-CbrT, and demonstrate that it mediates the specific, ATP-dependent uptake of cobalamin. We solved the crystal structure of ECF-CbrT in an apo conformation to 3.4 Å resolution. Comparison with the ECF transporter for folate (ECF-FolT2) from the same organism, reveals how the identical ECF module adjusts to interact with the different substrate binding proteins FolT2 and CbrT. ECF-CbrT is unrelated to the well-characterized B12 transporter BtuCDF, but their biochemical features indicate functional convergence.
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Affiliation(s)
- Joana A Santos
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Stephan Rempel
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Sandra Tm Mous
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | | | - Josy Ter Beek
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Jan-Willem de Gier
- Department of Biochemistry and Biophysics, Center for Biomembrane Research, Stockholm University, Stockholm, Sweden
| | - Albert Guskov
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands
| | - Dirk J Slotboom
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Groningen, The Netherlands.,Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands
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21
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Crystal Structure of a Group I Energy Coupling Factor Vitamin Transporter S Component in Complex with Its Cognate Substrate. Cell Chem Biol 2017; 23:827-836. [PMID: 27447050 PMCID: PMC5037267 DOI: 10.1016/j.chembiol.2016.06.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 05/18/2016] [Accepted: 06/02/2016] [Indexed: 12/27/2022]
Abstract
Energy coupling factor (ECF) transporters are responsible for the uptake of essential scarce nutrients in prokaryotes. This ATP-binding cassette transporter family comprises two subgroups that share a common architecture forming a tripartite membrane protein complex consisting of a translocation component and ATP hydrolyzing module and a substrate-capture (S) component. Here, we present the crystal structure of YkoE from Bacillus subtilis, the S component of the previously uncharacterized group I ECF transporter YkoEDC. Structural and biochemical analyses revealed the constituent residues of the thiamine-binding pocket as well as an unexpected mode of vitamin recognition. In addition, our experimental and bioinformatics data demonstrate major differences between YkoE and group II ECF transporters and indicate how group I vitamin transporter S components have diverged from other group I and group II ECF transporters. The crystal structure of a group I ECF transporter S component was determined The thiamine-bound structure was determined in lipidic environment The structure reveals major differences to group II S components CGMD simulations indicate the orientation of the protein in the membrane
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22
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Finkenwirth F, Kirsch F, Eitinger T. Complex Stability During the Transport Cycle of a Subclass I ECF Transporter. Biochemistry 2017; 56:4578-4583. [DOI: 10.1021/acs.biochem.7b00390] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Friedrich Finkenwirth
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Franziska Kirsch
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Thomas Eitinger
- Institut für Biologie/Mikrobiologie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
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23
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Structure and mechanism of a group-I cobalt energy coupling factor transporter. Cell Res 2017; 27:675-687. [PMID: 28322252 DOI: 10.1038/cr.2017.38] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 02/08/2017] [Accepted: 02/15/2017] [Indexed: 12/20/2022] Open
Abstract
Energy-coupling factor (ECF) transporters are a large family of ATP-binding cassette transporters recently identified in microorganisms. Responsible for micronutrient uptake from the environment, ECF transporters are modular transporters composed of a membrane substrate-binding component EcfS and an ECF module consisting of an integral membrane scaffold component EcfT and two cytoplasmic ATP binding/hydrolysis components EcfA/A'. ECF transporters are classified into groups I and II. Currently, the molecular understanding of group-I ECF transporters is very limited, partly due to a lack of transporter complex structural information. Here, we present structures and structure-based analyses of the group-I cobalt ECF transporter CbiMNQO, whose constituting subunits CbiM/CbiN, CbiQ, and CbiO correspond to the EcfS, EcfT, and EcfA components of group-II ECF transporters, respectively. Through reconstitution of different CbiMNQO subunits and determination of related ATPase and transporter activities, the substrate-binding subunit CbiM was found to stimulate CbiQO's basal ATPase activity. The structure of CbiMQO complex was determined in its inward-open conformation and that of CbiO in β, γ-methyleneadenosine 5'-triphosphate-bound closed conformation. Structure-based analyses revealed interactions between different components, substrate-gating function of the L1 loop of CbiM, and conformational changes of CbiO induced by ATP binding and product release within the CbiMNQO transporter complex. These findings enabled us to propose a working model of the CbiMNQO transporter, in which the transport process requires the rotation or toppling of both CbiQ and CbiM, and CbiN might function in coupling conformational changes between CbiQ and CbiM.
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Karpowich NK, Song J, Wang DN. An Aromatic Cap Seals the Substrate Binding Site in an ECF-Type S Subunit for Riboflavin. J Mol Biol 2016; 428:3118-30. [PMID: 27312125 DOI: 10.1016/j.jmb.2016.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/07/2016] [Accepted: 06/07/2016] [Indexed: 10/21/2022]
Abstract
ECF transporters are a family of active membrane transporters for essential micronutrients, such as vitamins and trace metals. Found exclusively in archaea and bacteria, these transporters are composed of four subunits: an integral membrane substrate-binding subunit (EcfS), a transmembrane coupling subunit (EcfT), and two ATP-binding cassette ATPases (EcfA and EcfA'). We have characterized the structural basis of substrate binding by the EcfS subunit for riboflavin from Thermotoga maritima, TmRibU. TmRibU binds riboflavin with high affinity, and the protein-substrate complex is exceptionally stable in solution. The crystal structure of riboflavin-bound TmRibU reveals an electronegative binding pocket at the extracellular surface in which the substrate is completely buried. Analysis of the intermolecular contacts indicates that nearly every available substrate hydrogen bond is satisfied. A conserved aromatic residue at the extracellular end of TM5, Tyr130, caps the binding site to generate a substrate-bound, occluded state, and non-conservative mutation of Tyr130 reduces the stability of this conformation. Using a novel fluorescence binding assay, we find that an aromatic residue at this position is essential for high-affinity substrate binding. Comparison with other S subunit structures suggests that TM5 and Loop5-6 contain a dynamic, conserved motif that plays a key role in gating substrate entry and release by S subunits of ECF transporters.
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Affiliation(s)
- Nathan K Karpowich
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.
| | - Jinmei Song
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA
| | - Da-Neng Wang
- The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, and Department of Cell Biology, New York University School of Medicine, 540 First Avenue, New York, NY 10016, USA.
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25
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Structural insight in the toppling mechanism of an energy-coupling factor transporter. Nat Commun 2016; 7:11072. [PMID: 27026363 PMCID: PMC4820897 DOI: 10.1038/ncomms11072] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 02/17/2016] [Indexed: 11/08/2022] Open
Abstract
Energy-coupling factor (ECF) transporters mediate uptake of micronutrients in prokaryotes. The transporters consist of an S-component that binds the transported substrate and an ECF module (EcfAA′T) that binds and hydrolyses ATP. The mechanism of transport is poorly understood but presumably involves an unusual step in which the membrane-embedded S-component topples over to carry the substrate across the membrane. In many ECF transporters, the S-component dissociates from the ECF module after transport. Subsequently, substrate-bound S-components out-compete the empty proteins for re-binding to the ECF module in a new round of transport. Here we present crystal structures of the folate-specific transporter ECF–FolT from Lactobacillus delbrueckii. Interaction of the ECF module with FolT stabilizes the toppled state, and simultaneously destroys the high-affinity folate-binding site, allowing substrate release into the cytosol. We hypothesize that differences in the kinetics of toppling can explain how substrate-loaded FolT out-competes apo-FolT for association with the ECF module. Prokaryotes use energy-coupling factor transporters to uptake required micronutrients and an unusual toppling mechanism has been proposed for their function. Here, the authors provide structural support for this mechanism, allowing direct visualization of the toppled state.
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26
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Monjas L, Swier LJYM, de Voogd AR, Oudshoorn RC, Hirsch AKH, Slotboom DJ. Design and synthesis of thiamine analogues to study their binding to the ECF transporter for thiamine in bacteria. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00022c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This work presents new small molecules that bind to the protein ThiT, which confers substrate specificity to the Energy-Coupling Factor (ECF) transporter for thiamine. Further development of the molecules may lead to compounds with antimicrobial activity.
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Affiliation(s)
- L. Monjas
- Stratingh Institute for Chemistry
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - L. J. Y. M. Swier
- Groningen Biomolecular Sciences and Biotechnology Institute
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - A. R. de Voogd
- Stratingh Institute for Chemistry
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - R. C. Oudshoorn
- Groningen Biomolecular Sciences and Biotechnology Institute
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - A. K. H. Hirsch
- Stratingh Institute for Chemistry
- University of Groningen
- 9747 AG Groningen
- The Netherlands
| | - D. J. Slotboom
- Groningen Biomolecular Sciences and Biotechnology Institute
- University of Groningen
- 9747 AG Groningen
- The Netherlands
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27
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Majsnerowska M, Ter Beek J, Stanek WK, Duurkens RH, Slotboom DJ. Competition between Different S-Components for the Shared Energy Coupling Factor Module in Energy Coupling Factor Transporters. Biochemistry 2015. [PMID: 26217920 DOI: 10.1021/acs.biochem.5b00609] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Energy coupling factor (ECF) transporters take up micronutrients in Bacteria and Archaea. They consist of a membrane-embedded S-component that provides substrate specificity and a three-subunit ECF module that couples ATP hydrolysis to transport. The S-components ThiT (for thiamin) and NiaX (for niacin) from Lactococcus lactis form complexes with the same ECF module. Here, we assayed the uptake of thiamin and niacin in Escherichia coli cells expressing the transporter genes. We demonstrate that the two different S-components compete for the ECF module, and that competition is more efficient in the presence of the transported substrate. The data suggest that binding and release of the S-components is a step in the transport cycle.
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Affiliation(s)
- Maria Majsnerowska
- †Department of Biochemistry, University of Groningen, Groningen Biomolecular Science and Biotechnology Institute, Nijenborg 4, 9747 AG Groningen, The Netherlands.,‡University of Groningen, Zernike Institute for Advanced Materials, Nijenborg 4, 9747 AG Groningen, The Netherlands
| | - Josy Ter Beek
- †Department of Biochemistry, University of Groningen, Groningen Biomolecular Science and Biotechnology Institute, Nijenborg 4, 9747 AG Groningen, The Netherlands.,‡University of Groningen, Zernike Institute for Advanced Materials, Nijenborg 4, 9747 AG Groningen, The Netherlands
| | - Weronika K Stanek
- †Department of Biochemistry, University of Groningen, Groningen Biomolecular Science and Biotechnology Institute, Nijenborg 4, 9747 AG Groningen, The Netherlands
| | - Ria H Duurkens
- †Department of Biochemistry, University of Groningen, Groningen Biomolecular Science and Biotechnology Institute, Nijenborg 4, 9747 AG Groningen, The Netherlands
| | - Dirk J Slotboom
- †Department of Biochemistry, University of Groningen, Groningen Biomolecular Science and Biotechnology Institute, Nijenborg 4, 9747 AG Groningen, The Netherlands.,‡University of Groningen, Zernike Institute for Advanced Materials, Nijenborg 4, 9747 AG Groningen, The Netherlands
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28
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Zhao Q, Wang C, Wang C, Guo H, Bao Z, Zhang M, Zhang P. Structures of FolT in substrate-bound and substrate-released conformations reveal a gating mechanism for ECF transporters. Nat Commun 2015. [PMID: 26198469 PMCID: PMC4525288 DOI: 10.1038/ncomms8661] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Energy-coupling factor (ECF) transporters are a new family of ABC transporters that consist of four subunits, two cytoplasmic ATPases EcfA and EcfA' and two transmembrane proteins namely EcfS for substrate-specific binding and EcfT for energy coupling. Here, we report the 3.2-Å resolution crystal structure of the EcfS protein of a folate ECF transporter from Enterococcus faecalis-EfFolT, a close homologue of FolT from Lactobacillus brevis-LbFolT. Structural and biochemical analyses reveal the residues constituting the folate-binding pocket and determining the substrate-binding specificity. Structural comparison of the folate-bound EfFolT with the folate-free LbFolT contained in the holotransporter complex discloses significant conformational change at the L1 loop, and reveals a gating mechanism of ECF transporters in which the L1 loop of EcfS acts as a gate in the substrate binding and release. Substrate specificity of ECF transporters is determined by the transmembrane EcfS protein subunit. Here Zhao et al. present substrate-bound and substrate-released structures of a bacterial folate transporter EcfS and suggest a gating mechanism for ECF transporters.
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Affiliation(s)
- Qin Zhao
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chengcheng Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Chengyuan Wang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Hui Guo
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhihao Bao
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Minhua Zhang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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29
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Pyridoxamine is a substrate of the energy-coupling factor transporter HmpT. Cell Discov 2015; 1:15014. [PMID: 27462413 PMCID: PMC4860826 DOI: 10.1038/celldisc.2015.14] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/28/2015] [Indexed: 12/12/2022] Open
Abstract
Energy-coupling factor (ECF) transporters belong to a novel family of proteins that forms a subset within the ATP-binding cassette (ABC) transporter family. These proteins are responsible for the uptake of micronutrients in bacteria. ECF transporters are composed of four proteins: the A- and A′-components, the T-component and the S-component. One of the ECF transporters, named HmpT, was crystallized in the apo form with all four components. It is currently unknown whether HmpT serves as a transporter for hydroxymethyl pyrimidine or the different forms of vitamin B6 (pyridoxine, pyridoxal or pyridoxamine). Using a combination of molecular dynamics (MD) simulations and mass spectrometry, we have identified pyridoxamine to be the preferred substrate of HmpT. Mass spectra show that the mass of the substrate from the HmpT–substrate complex matches that of pyridoxamine. MD simulations likewise indicate that pyridoxamine interacts most strongly with most of the conserved residues of the S-component (Glu 41, His 84 and Gln 43) compared with the other vitamin B6 forms. Furthermore, the simulations have implied that loops 1 and 5 of the S-component can participate in the gating action for HmpT.
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30
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ATP binding drives substrate capture in an ECF transporter by a release-and-catch mechanism. Nat Struct Mol Biol 2015; 22:565-71. [PMID: 26052893 PMCID: PMC4634891 DOI: 10.1038/nsmb.3040] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 05/05/2015] [Indexed: 01/07/2023]
Abstract
ECF transporters are a family of active transporters for vitamins. They are composed of four subunits: a membrane-embedded substrate-binding subunit (EcfS), a transmembrane coupling subunit (EcfT) and two ATP-binding-cassette ATPases (EcfA and EcfA'). We have investigated the mechanism of the ECF transporter for riboflavin from the pathogen Listeria monocytogenes, LmECF-RibU. Using structural and biochemical approaches, we found that ATP binding to the EcfAA' ATPases drives a conformational change that dissociates the S subunit from the EcfAA'T ECF module. Upon release from the ECF module, the RibU S subunit then binds the riboflavin transport substrate. We also find that S subunits for distinct substrates compete for the ATP-bound state of the ECF module. Our results explain how ECF transporters capture the transport substrate and reproduce the in vivo observations on S-subunit competition for which the family was named.
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31
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Finkenwirth F, Sippach M, Landmesser H, Kirsch F, Ogienko A, Grunzel M, Kiesler C, Steinhoff HJ, Schneider E, Eitinger T. ATP-dependent Conformational Changes Trigger Substrate Capture and Release by an ECF-type Biotin Transporter. J Biol Chem 2015; 290:16929-42. [PMID: 25991724 DOI: 10.1074/jbc.m115.654343] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Indexed: 11/06/2022] Open
Abstract
Energy-coupling factor (ECF) transporters for vitamins and metal ions in prokaryotes consist of two ATP-binding cassette-type ATPases, a substrate-specific transmembrane protein (S component) and a transmembrane protein (T component) that physically interacts with the ATPases and the S component. The mechanism of ECF transporters was analyzed upon reconstitution of a bacterial biotin transporter into phospholipid bilayer nanodiscs. ATPase activity was not stimulated by biotin and was only moderately reduced by vanadate. A non-hydrolyzable ATP analog was a competitive inhibitor. As evidenced by cross-linking of monocysteine variants and by site-specific spin labeling of the Q-helix followed by EPR-based interspin distance analyses, closure and reopening of the ATPase dimer (BioM2) was a consequence of ATP binding and hydrolysis, respectively. A previously suggested role of a stretch of small hydrophobic amino acid residues within the first transmembrane segment of the S units for S unit/T unit interactions was structurally and functionally confirmed for the biotin transporter. Cross-linking of this segment in BioY (S) using homobifunctional thiol-reactive reagents to a coupling helix of BioN (T) indicated a reorientation rather than a disruption of the BioY/BioN interface during catalysis. Fluorescence emission of BioY labeled with an environmentally sensitive fluorophore was compatible with an ATP-induced reorientation and consistent with a hypothesized toppling mechanism. As demonstrated by [(3)H]biotin capture assays, ATP binding stimulated substrate capture by the transporter, and subsequent ATP hydrolysis led to substrate release. Our study represents the first experimental insight into the individual steps during the catalytic cycle of an ECF transporter in a lipid environment.
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Affiliation(s)
| | - Michael Sippach
- the Fachbereich Physik, Universität Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany
| | - Heidi Landmesser
- Institut für Biologie/Physiologie der Mikroorganismen, Humboldt-Universität zu Berlin, Chausseestrasse 117, 10115 Berlin, Germany and
| | | | | | | | | | - Heinz-Jürgen Steinhoff
- the Fachbereich Physik, Universität Osnabrück, Barbarastrasse 7, 49076 Osnabrück, Germany
| | - Erwin Schneider
- Institut für Biologie/Physiologie der Mikroorganismen, Humboldt-Universität zu Berlin, Chausseestrasse 117, 10115 Berlin, Germany and
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32
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Swier LJYM, Monjas L, Guskov A, de Voogd AR, Erkens GB, Slotboom DJ, Hirsch AKH. Structure-based design of potent small-molecule binders to the S-component of the ECF transporter for thiamine. Chembiochem 2015; 16:819-26. [PMID: 25676607 DOI: 10.1002/cbic.201402673] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Indexed: 12/20/2022]
Abstract
Energy-coupling factor (ECF) transporters are membrane-protein complexes that mediate vitamin uptake in prokaryotes. They bind the substrate through the action of a specific integral membrane subunit (S-component) and power transport by hydrolysis of ATP in the three-subunit ECF module. Here, we have studied the binding of thiamine derivatives to ThiT, a thiamine-specific S-component. We designed and synthesized derivatives of thiamine that bind to ThiT with high affinity; this allowed us to evaluate the contribution of the functional groups to the binding affinity. We determined six crystal structures of ThiT in complex with our derivatives. The structure of the substrate-binding site in ThiT remains almost unchanged despite substantial differences in affinity. This work indicates that the structural organization of the binding site is robust and suggests that substrate release, which is required for transport, requires additional changes in conformation in ThiT that might be imposed by the ECF module.
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Affiliation(s)
- Lotteke J Y M Swier
- Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands) http://www.rug.nl/research/membrane-enzymology/
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