1
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Martínez Felices JM, Barreto YB, Thangaratnarajah C, Whittaker JJ, Alencar AM, Guskov A, Slotboom DJ. Cobalamin decyanation by the membrane transporter BtuM. Structure 2024:S0969-2126(24)00140-0. [PMID: 38733996 DOI: 10.1016/j.str.2024.04.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 03/04/2024] [Accepted: 04/15/2024] [Indexed: 05/13/2024]
Abstract
BtuM is a bacterial cobalamin transporter that binds the transported substrate in the base-off state, with a cysteine residue providing the α-axial coordination of the central cobalt ion via a sulfur-cobalt bond. Binding leads to decyanation of cobalamin variants with a cyano group as the β-axial ligand. Here, we report the crystal structures of untagged BtuM bound to two variants of cobalamin, hydroxycobalamin and cyanocobalamin, and unveil the native residue responsible for the β-axial coordination, His28. This coordination had previously been obscured by non-native histidines of His-tagged BtuM. A model in which BtuM initially binds cobinamide reversibly with low affinity (KD = 4.0 μM), followed by the formation of a covalent bond (rate constant of 0.163 s-1), fits the kinetics data of substrate binding and decyanation of the cobalamin precursor cobinamide by BtuM. The covalent binding mode suggests a mechanism not used by any other transport protein.
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Affiliation(s)
- Jose M Martínez Felices
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands
| | - Yan Borges Barreto
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands; Instituto de Física, Universidade de São Paulo, São Paulo 05508-090, São Paulo, Brazil
| | - Chancievan Thangaratnarajah
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands
| | - Jacob J Whittaker
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands
| | - Adriano M Alencar
- Instituto de Física, Universidade de São Paulo, São Paulo 05508-090, São Paulo, Brazil
| | - Albert Guskov
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands
| | - Dirk J Slotboom
- Groningen Biomolecular and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 4, Groningen 9474 AG, the Netherlands.
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2
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Irfan, Soleja N, Mohsin M. FRET-based probe for ratiometric detection and imaging of folic acid in real-time. Anal Biochem 2023; 679:115285. [PMID: 37586674 DOI: 10.1016/j.ab.2023.115285] [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: 07/10/2023] [Revised: 08/12/2023] [Accepted: 08/13/2023] [Indexed: 08/18/2023]
Abstract
Inadequate folic acid intake is linked to diseases such as megaloblastic anemia, neural tube defects, and hyperhomocysteinemia, increasing the risk of vascular disease and thrombosis. Folic acid, a cofactor in various enzymes, can be produced by plants and bacteria, but not by humans and other animals. L-5-methyl-tetrahydrofolate (L-5-methyl-THF) is the primary dietary folate form, transported in circulation for cellular metabolism. Traditional methods of determining folic acid levels are unreliable and time-consuming. SenFol (Sensor for folic acid) is a fluorescence resonance energy transfer (FRET)-based nanosensor that we have developed by inserting folic acid-binding protein (FolT) as the folate detecting domain between the pair of enhanced cyan fluorescent protein (ECFP) and Venus. The developed sensor is highly specific, produces a quick signal, which is pH stable, and delivers precise, ratiometric readings in cell-based experiments. The projected affinity score of folic acid with FolT was -7.4 kcal/mol. The apparent affinity (Kd) of SenFol for folic acid is 28.49 × 10-9 M, with a detection range of 5 × 10-9 M to 5 × 10-7 M, and a maximum FRET ratio change of 0.45. WT SenFol, a highly efficient folic acid nanosensor, can dynamically detect intracellular folic acid content in E. coli, yeast, and HEK-293 T cells, confirming its potential.
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Affiliation(s)
- Irfan
- Department of Biosciences, Jamia Millia Islamia, New Delhi-110025, India
| | - Neha Soleja
- Department of Biosciences, Jamia Millia Islamia, New Delhi-110025, India
| | - Mohd Mohsin
- Department of Biosciences, Jamia Millia Islamia, New Delhi-110025, India.
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3
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Newstead S. Structural basis for recognition and transport of folic acid in mammalian cells. Curr Opin Struct Biol 2022; 74:102353. [PMID: 35303537 PMCID: PMC7612623 DOI: 10.1016/j.sbi.2022.102353] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/29/2022] [Accepted: 02/08/2022] [Indexed: 12/19/2022]
Abstract
Structural studies on mammalian vitamin transport lag behind other metabolites. Folates, also known as B9 vitamins, are essential cofactors in one-carbon transfer reactions in biology. Three different systems control folate uptake in the human body; folate receptors function to capture and internalise extracellular folates via endocytosis, whereas two major facilitator superfamily transporters, the reduced folate carrier (RFC; SLC19A1) and proton-coupled folate transporter (PCFT; SLC46A1) control the transport of folates across cellular membranes. Targeting specific folate transporters is being pursued as a route to developing new antifolates with improved pharmacology. Recent structures of the proton-coupled folate transporter, PCFT, revealed key insights into antifolate recognition and the mechanism of proton-coupled transport. Combined with previously determined structures of folate receptors and new predictions for the structure of the RFC, we are now able to develop a structure-based understanding of folate and antifolate recognition to accelerate efforts in antifolate drug development.
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Affiliation(s)
- Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK.
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4
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Vermaas JV, Mayne CG, Shinn E, Tajkhorshid E. Assembly and Analysis of Cell-Scale Membrane Envelopes. J Chem Inf Model 2022; 62:602-617. [PMID: 34910495 PMCID: PMC8903035 DOI: 10.1021/acs.jcim.1c01050] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The march toward exascale computing will enable routine molecular simulation of larger and more complex systems, for example, simulation of entire viral particles, on the scale of approximately billions of atoms─a simulation size commensurate with a small bacterial cell. Anticipating the future hardware capabilities that will enable this type of research and paralleling advances in experimental structural biology, efforts are currently underway to develop software tools, procedures, and workflows for constructing cell-scale structures. Herein, we describe our efforts in developing and implementing an efficient and robust workflow for construction of cell-scale membrane envelopes and embedding membrane proteins into them. A new approach for construction of massive membrane structures that are stable during the simulations is built on implementing a subtractive assembly technique coupled with the development of a structure concatenation tool (fastmerge), which eliminates overlapping elements based on volumetric criteria rather than adding successive molecules to the simulation system. Using this approach, we have constructed two "protocells" consisting of MARTINI coarse-grained beads to represent cellular membranes, one the size of a cellular organelle and another the size of a small bacterial cell. The membrane envelopes constructed here remain whole during the molecular dynamics simulations performed and exhibit water flux only through specific proteins, demonstrating the success of our methodology in creating tight cell-like membrane compartments. Extended simulations of these cell-scale structures highlight the propensity for nonspecific interactions between adjacent membrane proteins leading to the formation of protein microclusters on the cell surface, an insight uniquely enabled by the scale of the simulations. We anticipate that the experiences and best practices presented here will form the basis for the next generation of cell-scale models, which will begin to address the addition of soluble proteins, nucleic acids, and small molecules essential to the function of a cell.
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Affiliation(s)
- Josh V. Vermaas
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401,;
| | - Christopher G. Mayne
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Eric Shinn
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801,;
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5
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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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6
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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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7
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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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8
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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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9
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Rodionova IA, Goodacre N, Do J, Hosseinnia A, Babu M, Uetz P, Saier MH. The uridylyltransferase GlnD and tRNA modification GTPase MnmE allosterically control Escherichia coli folylpoly-γ-glutamate synthase FolC. J Biol Chem 2018; 293:15725-15732. [PMID: 30089654 DOI: 10.1074/jbc.ra118.004425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 07/31/2018] [Indexed: 01/20/2023] Open
Abstract
Folate derivatives are important cofactors for enzymes in several metabolic processes. Folate-related inhibition and resistance mechanisms in bacteria are potential targets for antimicrobial therapies and therefore a significant focus of current research. Here, we report that the activity of Escherichia coli poly-γ-glutamyl tetrahydrofolate/dihydrofolate synthase (FolC) is regulated by glutamate/glutamine-sensing uridylyltransferase (GlnD), THF-dependent tRNA modification enzyme (MnmE), and UDP-glucose dehydrogenase (Ugd) as shown by direct in vitro protein-protein interactions. Using kinetics analyses, we observed that GlnD, Ugd, and MnmE activate FolC many-fold by decreasing the K half of FolC for its substrate l-glutamate. Moreover, FolC inhibited the GTPase activity of MnmE at low GTP concentrations. The growth phenotypes associated with these proteins are discussed. These results, obtained using direct in vitro enzyme assays, reveal unanticipated networks of allosteric regulatory interactions in the folate pathway in E. coli and indicate regulation of polyglutamylated tetrahydrofolate biosynthesis by the availability of nitrogen sources, signaled by the glutamine-sensing GlnD protein.
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Affiliation(s)
- Irina A Rodionova
- From the Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116,
| | - Norman Goodacre
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284, and
| | - Jimmy Do
- From the Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116
| | - Ali Hosseinnia
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Mohan Babu
- Department of Biochemistry, University of Regina, Regina, Saskatchewan S4S 0A2, Canada
| | - Peter Uetz
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284, and
| | - Milton H Saier
- From the Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, California 92093-0116,
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10
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Luo JS, Huang J, Zeng DL, Peng JS, Zhang GB, Ma HL, Guan Y, Yi HY, Fu YL, Han B, Lin HX, Qian Q, Gong JM. A defensin-like protein drives cadmium efflux and allocation in rice. Nat Commun 2018; 9:645. [PMID: 29440679 PMCID: PMC5811569 DOI: 10.1038/s41467-018-03088-0] [Citation(s) in RCA: 192] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 01/18/2018] [Indexed: 01/07/2023] Open
Abstract
Pollution by heavy metals limits the area of land available for cultivation of food crops. A potential solution to this problem might lie in the molecular breeding of food crops for phytoremediation that accumulate toxic metals in straw while producing safe and nutritious grains. Here, we identify a rice quantitative trait locus we name cadmium (Cd) accumulation in leaf 1 (CAL1), which encodes a defensin-like protein. CAL1 is expressed preferentially in root exodermis and xylem parenchyma cells. We provide evidence that CAL1 acts by chelating Cd in the cytosol and facilitating Cd secretion to extracellular spaces, hence lowering cytosolic Cd concentration while driving long-distance Cd transport via xylem vessels. CAL1 does not appear to affect Cd accumulation in rice grains or the accumulation of other essential metals, thus providing an efficient molecular tool to breed dual-function rice varieties that produce safe grains while remediating paddy soils.
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Affiliation(s)
- Jin-Song Luo
- National Key Laboratory of Plant Molecular Genetics and CAS center for excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, 410128, China
| | - Jing Huang
- National Key Laboratory of Plant Molecular Genetics and CAS center for excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, Nanning, 530004, China
| | - Da-Li Zeng
- China National Rice Research Institute, Hangzhou, 310006, China
| | - Jia-Shi Peng
- National Key Laboratory of Plant Molecular Genetics and CAS center for excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Guo-Bin Zhang
- National Key Laboratory of Plant Molecular Genetics and CAS center for excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hai-Ling Ma
- National Key Laboratory of Plant Molecular Genetics and CAS center for excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Guan
- National Key Laboratory of Plant Molecular Genetics and CAS center for excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hong-Ying Yi
- National Key Laboratory of Plant Molecular Genetics and CAS center for excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yan-Lei Fu
- National Key Laboratory of Plant Molecular Genetics and CAS center for excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Bin Han
- National Key Laboratory of Plant Molecular Genetics and CAS center for excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hong-Xuan Lin
- National Key Laboratory of Plant Molecular Genetics and CAS center for excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Qian Qian
- China National Rice Research Institute, Hangzhou, 310006, China.
| | - Ji-Ming Gong
- National Key Laboratory of Plant Molecular Genetics and CAS center for excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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11
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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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12
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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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13
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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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14
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Lewinson O, Livnat-Levanon N. Mechanism of Action of ABC Importers: Conservation, Divergence, and Physiological Adaptations. J Mol Biol 2017; 429:606-619. [PMID: 28104364 DOI: 10.1016/j.jmb.2017.01.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 01/08/2023]
Abstract
The past decade has seen a remarkable surge in structural characterization of ATP binding cassette (ABC) transporters, which have spurred a more focused functional analysis of these elaborate molecular machines. As a result, it has become increasingly apparent that there is a substantial degree of mechanistic variation between ABC transporters that function as importers, which correlates with their physiological roles. Here, we summarize recent advances in ABC importers' structure-function studies and provide an explanation as to the origin of the different mechanisms of action.
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Affiliation(s)
- Oded Lewinson
- Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, 31096 Haifa, Israel.
| | - Nurit Livnat-Levanon
- Department of Biochemistry, The Bruce and Ruth Rappaport Faculty of Medicine, The Technion-Israel Institute of Technology, 31096 Haifa, Israel
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15
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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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16
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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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17
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Liu H, Li D, Li Y, Hou T. Atomistic molecular dynamics simulations of ATP-binding cassette transporters. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Hui Liu
- College of Pharmaceutical Sciences; Zhejiang University; Hangzhou China
| | - Dan Li
- College of Pharmaceutical Sciences; Zhejiang University; Hangzhou China
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM); Soochow University; Suzhou China
| | - Tingjun Hou
- College of Pharmaceutical Sciences; Zhejiang University; Hangzhou China
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18
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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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