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Pérez Carrillo VH, Rose-Sperling D, Tran MA, Wiedemann C, Hellmich UA. Backbone NMR assignment of the nucleotide binding domain of the Bacillus subtilis ABC multidrug transporter BmrA in the post-hydrolysis state. BIOMOLECULAR NMR ASSIGNMENTS 2022; 16:81-86. [PMID: 34988902 PMCID: PMC9068644 DOI: 10.1007/s12104-021-10063-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/22/2021] [Indexed: 05/11/2023]
Abstract
ATP binding cassette (ABC) proteins are present in all phyla of life and form one of the largest protein families. The Bacillus subtilis ABC transporter BmrA is a functional homodimer that can extrude many different harmful compounds out of the cell. Each BmrA monomer is composed of a transmembrane domain (TMD) and a nucleotide binding domain (NBD). While the TMDs of ABC transporters are sequentially diverse, the highly conserved NBDs harbor distinctive conserved motifs that enable nucleotide binding and hydrolysis, interdomain communication and that mark a protein as a member of the ABC superfamily. In the catalytic cycle of an ABC transporter, the NBDs function as the molecular motor that fuels substrate translocation across the membrane via the TMDs and are thus pivotal for the entire transport process. For a better understanding of the structural and dynamic consequences of nucleotide interactions within the NBD at atomic resolution, we determined the 1H, 13C and 15N backbone chemical shift assignments of the 259 amino acid wildtype BmrA-NBD in its post-hydrolytic, ADP-bound state.
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Affiliation(s)
- Victor Hugo Pérez Carrillo
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Dania Rose-Sperling
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Mai Anh Tran
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Christoph Wiedemann
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany
| | - Ute A Hellmich
- Faculty of Chemistry and Earth Sciences, Institute of Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstraße 10, 07743, Jena, Germany.
- Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max von Laue Str. 9, 60438, Frankfurt, Germany.
- Cluster of Excellence "Balance of the Microverse", Friedrich Schiller University Jena, 07743, Jena, Germany.
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2
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Structural insights into the catalytic cycle of a bacterial multidrug ABC efflux pump. J Mol Biol 2022; 434:167541. [DOI: 10.1016/j.jmb.2022.167541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/02/2022] [Accepted: 03/09/2022] [Indexed: 12/19/2022]
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3
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Oepen K, Özbek H, Schüffler A, Liermann JC, Thines E, Schneider D. Myristic Acid Inhibits the Activity of the Bacterial ABC Transporter BmrA. Int J Mol Sci 2021; 22:ijms222413565. [PMID: 34948362 PMCID: PMC8707315 DOI: 10.3390/ijms222413565] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022] Open
Abstract
ATP-binding cassette (ABC) transporters are conserved in all kingdoms of life, where they transport substrates against a concentration gradient across membranes. Some ABC transporters are known to cause multidrug resistances in humans and are able to transport chemotherapeutics across cellular membranes. Similarly, BmrA, the ABC transporter of Bacillus subtilis, is involved in excretion of certain antibiotics out of bacterial cells. Screening of extract libraries isolated from fungi revealed that the C14 fatty acid myristic acid has an inhibitory effect on the BmrA ATPase as well as the transport activity. Thus, a natural membrane constituent inhibits the BmrA activity, a finding with physiological consequences as to the activity and regulation of ABC transporter activities in biological membranes.
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Affiliation(s)
- Kristin Oepen
- Department of Chemistry, Johannes Gutenberg-University, 55128 Mainz, Germany; (K.O.); (J.C.L.)
| | - Hüseyin Özbek
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), 55128 Mainz, Germany; (H.Ö.); (A.S.); (E.T.)
| | - Anja Schüffler
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), 55128 Mainz, Germany; (H.Ö.); (A.S.); (E.T.)
| | - Johannes C. Liermann
- Department of Chemistry, Johannes Gutenberg-University, 55128 Mainz, Germany; (K.O.); (J.C.L.)
| | - Eckhard Thines
- Institut für Biotechnologie und Wirkstoff-Forschung gGmbH (IBWF), 55128 Mainz, Germany; (H.Ö.); (A.S.); (E.T.)
- Institute of Molecular Physiology, Johannes Gutenberg-University, 55128 Mainz, Germany
| | - Dirk Schneider
- Department of Chemistry, Johannes Gutenberg-University, 55128 Mainz, Germany; (K.O.); (J.C.L.)
- Institute of Molecular Physiology, Johannes Gutenberg-University, 55128 Mainz, Germany
- Correspondence: ; Tel.: +49-6131-39-25833
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4
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Rismondo J, Schulz LM. Not Just Transporters: Alternative Functions of ABC Transporters in Bacillus subtilis and Listeria monocytogenes. Microorganisms 2021; 9:microorganisms9010163. [PMID: 33450852 PMCID: PMC7828314 DOI: 10.3390/microorganisms9010163] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/07/2021] [Accepted: 01/10/2021] [Indexed: 12/24/2022] Open
Abstract
ATP-binding cassette (ABC) transporters are usually involved in the translocation of their cognate substrates, which is driven by ATP hydrolysis. Typically, these transporters are required for the import or export of a wide range of substrates such as sugars, ions and complex organic molecules. ABC exporters can also be involved in the export of toxic compounds such as antibiotics. However, recent studies revealed alternative detoxification mechanisms of ABC transporters. For instance, the ABC transporter BceAB of Bacillus subtilis seems to confer resistance to bacitracin via target protection. In addition, several transporters with functions other than substrate export or import have been identified in the past. Here, we provide an overview of recent findings on ABC transporters of the Gram-positive organisms B. subtilis and Listeria monocytogenes with transport or regulatory functions affecting antibiotic resistance, cell wall biosynthesis, cell division and sporulation.
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Feng Z, Liu D, Liu Z, Liang Y, Wang Y, Liu Q, Liu Z, Zang Z, Cui Y. Cloning and Functional Characterization of Putative Escherichia coli ABC Multidrug Efflux Transporter YddA. J Microbiol Biotechnol 2020; 30:982-995. [PMID: 32347079 PMCID: PMC9728188 DOI: 10.4014/jmb.2003.03003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 04/23/2020] [Indexed: 12/15/2022]
Abstract
A putative multidrug efflux gene, yddA, was cloned from the Escherichia coli K-12 strain. A drugsensitive strain of E. coli missing the main multidrug efflux pump AcrB was constructed as a host and the yddA gene was knocked out in wild-type (WT) and drug-sensitive E. coliΔacrB to study the yddA function. Sensitivity to different substrates of WT E.coli, E. coliΔyddA, E. coliΔacrB and E. coliΔacrBΔyddA strains was compared with minimal inhibitory concentration (MIC) assays and fluorescence tests. MIC assay and fluorescence test results showed that YddA protein was a multidrug efflux pump that exported multiple substrates. Three inhibitors, ortho-vanadate, carbonyl cyanide m-chlorophenylhydrazone (CCCP), and reserpine, were used in fluorescence tests. Ortho-vanadate and reserpine significantly inhibited the efflux and increased accumulation of ethidium bromide and norfloxacin, while CCCP had no significant effect on YddA-regulated efflux. The results indicated that YddA relies on energy released from ATP hydrolysis to transfer the substrates and YddA is an ABC-type multidrug exporter. Functional study of unknown ATP-binding cassette (ABC) superfamily transporters in the model organism E. coli is conducive to discovering new multidrug resistance-reversal targets and providing references for studying other ABC proteins of unknown function.
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Affiliation(s)
- Zhenyue Feng
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China,College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Defu Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Ziwen Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Yimin Liang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Yanhong Wang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Qingpeng Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Zhenhua Liu
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Zhongjing Zang
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China
| | - Yudong Cui
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China,College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, P.R. China,Corresponding author Phone/Fax: +459-6031177 E-mail:
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6
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Multidrug ABC transporters in bacteria. Res Microbiol 2019; 170:381-391. [DOI: 10.1016/j.resmic.2019.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Revised: 06/12/2019] [Accepted: 06/17/2019] [Indexed: 12/23/2022]
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Raghuraman H, Chatterjee S, Das A. Site-Directed Fluorescence Approaches for Dynamic Structural Biology of Membrane Peptides and Proteins. Front Mol Biosci 2019; 6:96. [PMID: 31608290 PMCID: PMC6774292 DOI: 10.3389/fmolb.2019.00096] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 09/11/2019] [Indexed: 12/31/2022] Open
Abstract
Membrane proteins mediate a number of cellular functions and are associated with several diseases and also play a crucial role in pathogenicity. Due to their importance in cellular structure and function, they are important drug targets for ~60% of drugs available in the market. Despite the technological advancement and recent successful outcomes in determining the high-resolution structural snapshot of membrane proteins, the mechanistic details underlining the complex functionalities of membrane proteins is least understood. This is largely due to lack of structural dynamics information pertaining to different functional states of membrane proteins in a membrane environment. Fluorescence spectroscopy is a widely used technique in the analysis of functionally-relevant structure and dynamics of membrane protein. This review is focused on various site-directed fluorescence (SDFL) approaches and their applications to explore structural information, conformational changes, hydration dynamics, and lipid-protein interactions of important classes of membrane proteins that include the pore-forming peptides/proteins, ion channels/transporters and G-protein coupled receptors.
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Affiliation(s)
- H. Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, Kolkata, India
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8
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Mathieu K, Javed W, Vallet S, Lesterlin C, Candusso MP, Ding F, Xu XN, Ebel C, Jault JM, Orelle C. Functionality of membrane proteins overexpressed and purified from E. coli is highly dependent upon the strain. Sci Rep 2019; 9:2654. [PMID: 30804404 PMCID: PMC6390180 DOI: 10.1038/s41598-019-39382-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/22/2019] [Indexed: 11/24/2022] Open
Abstract
Overexpression of correctly folded membrane proteins is a fundamental prerequisite for functional and structural studies. One of the most commonly used expression systems for the production of membrane proteins is Escherichia coli. While misfolded proteins typically aggregate and form inclusions bodies, membrane proteins that are addressed to the membrane and extractable by detergents are generally assumed to be properly folded. Accordingly, GFP fusion strategy is often used as a fluorescent proxy to monitor their expression and folding quality. Here we investigated the functionality of two different multidrug ABC transporters, the homodimer BmrA from Bacillus subtilis and the heterodimer PatA/PatB from Streptococcus pneumoniae, when produced in several E. coli strains with T7 expression system. Strikingly, while strong expression in the membrane of several strains could be achieved, we observed drastic differences in the functionality of these proteins. Moreover, we observed a general trend in which mild detergents mainly extract the population of active transporters, whereas a harsher detergent like Fos-choline 12 could solubilize transporters irrespective of their functionality. Our results suggest that the amount of T7 RNA polymerase transcripts may indirectly but notably impact the structure and activity of overexpressed membrane proteins, and advise caution when using GFP fusion strategy.
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Affiliation(s)
- Khadija Mathieu
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France
| | - Waqas Javed
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France.,Université Grenoble Alpes, CNRS, CEA, IBS, 38000, Grenoble, France
| | - Sylvain Vallet
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France
| | - Christian Lesterlin
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France
| | - Marie-Pierre Candusso
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France
| | - Feng Ding
- Department of Chemistry & Biochemistry, Old Dominion University, Norfolk, VA, 23529, USA
| | - Xiaohong Nancy Xu
- Department of Chemistry & Biochemistry, Old Dominion University, Norfolk, VA, 23529, USA
| | - Christine Ebel
- Université Grenoble Alpes, CNRS, CEA, IBS, 38000, Grenoble, France
| | - Jean-Michel Jault
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France.
| | - Cédric Orelle
- Université de Lyon, CNRS, UMR 5086 "Molecular Microbiology and Structural Biochemistry", IBCP, 69367, Lyon, France.
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9
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Breyton C, Javed W, Vermot A, Arnaud CA, Hajjar C, Dupuy J, Petit-Hartlein I, Le Roy A, Martel A, Thépaut M, Orelle C, Jault JM, Fieschi F, Porcar L, Ebel C. Assemblies of lauryl maltose neopentyl glycol (LMNG) and LMNG-solubilized membrane proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2019; 1861:939-957. [PMID: 30776334 DOI: 10.1016/j.bbamem.2019.02.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 02/08/2019] [Accepted: 02/08/2019] [Indexed: 12/11/2022]
Abstract
Laurylmaltose neopentylglycol (LMNG) bears two linked hydrophobic chains of equal length and two hydrophilic maltoside groups. It arouses a strong interest in the field of membrane protein biochemistry, since it was shown to efficiently solubilize and stabilize membrane proteins often better than the commonly used dodecylmaltopyranoside (DDM), and to allow structure determination of some challenging membrane proteins. However, LMNG was described to form large micelles, which could be unfavorable for structural purposes. We thus investigated its auto-assemblies and the association state of different membrane proteins solubilized in LMNG by analytical ultracentrifugation, size exclusion chromatography coupled to light scattering, centrifugation on sucrose gradient and/or small angle scattering. At high concentrations (in the mM range), LMNG forms long rods, and it stabilized the membrane proteins investigated herein, i.e. a bacterial multidrug transporter, BmrA; a prokaryotic analogous of the eukaryotic NADPH oxidases, SpNOX; an E. coli outer membrane transporter, FhuA; and the halobacterial bacteriorhodopsin, bR. BmrA, in the Apo and the vanadate-inhibited forms showed reduced kinetics of limited proteolysis in LMNG compared to DDM. Both SpNOX and BmrA display an increased specific activity in LMNG compared to DDM. The four proteins form LMNG complexes with their usual quaternary structure and with usual amount of bound detergent. No heterogeneous complexes related to the large micelle size of LMNG alone were observed. In conditions where LMNG forms assemblies of large size, FhuA crystals diffracting to 4.0 Å were obtained by vapor diffusion. LMNG large micelle size thus does not preclude membrane protein homogeneity and crystallization.
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Affiliation(s)
- Cécile Breyton
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Waqas Javed
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France; University of Lyon, CNRS, UMR5086, Molecular Microbiology and Structural Biochemistry, IBCP, Lyon 69367, France
| | - Annelise Vermot
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Charles-Adrien Arnaud
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Christine Hajjar
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Jérôme Dupuy
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Isabelle Petit-Hartlein
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Aline Le Roy
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Anne Martel
- Institut Max Von Laue Paul Langevin, 38042 Grenoble, France
| | - Michel Thépaut
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Cédric Orelle
- University of Lyon, CNRS, UMR5086, Molecular Microbiology and Structural Biochemistry, IBCP, Lyon 69367, France
| | - Jean-Michel Jault
- University of Lyon, CNRS, UMR5086, Molecular Microbiology and Structural Biochemistry, IBCP, Lyon 69367, France
| | - Franck Fieschi
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France
| | - Lionel Porcar
- Institut Max Von Laue Paul Langevin, 38042 Grenoble, France
| | - Christine Ebel
- Univ. Grenoble Alpes, CNRS, CEA, Institute for Structural Biology (IBS), 38000 Grenoble, France.
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10
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Lu WJ, Lin HJ, Janganan TK, Li CY, Chin WC, Bavro VN, Lin HTV. ATP-Binding Cassette Transporter VcaM from Vibrio cholerae is Dependent on the Outer Membrane Factor Family for Its Function. Int J Mol Sci 2018; 19:ijms19041000. [PMID: 29584668 PMCID: PMC5979437 DOI: 10.3390/ijms19041000] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 03/23/2018] [Accepted: 03/25/2018] [Indexed: 11/16/2022] Open
Abstract
Vibrio cholerae ATP-binding cassette transporter VcaM (V. cholerae ABC multidrug resistance pump) has previously been shown to confer resistance to a variety of medically important drugs. In this study, we set to analyse its properties both in vitro in detergent-solubilised state and in vivo to differentiate its dependency on auxiliary proteins for its function. We report the first detailed kinetic parameters of purified VcaM and the rate of phosphate (Pi) production. To determine the possible functional dependencies of VcaM on the tripartite efflux pumps we then utilized different E. coli strains lacking the principal secondary transporter AcrB (Acriflavine resistance protein), as well as cells lacking the outer membrane factor (OMF) TolC (Tolerance to colicins). Consistent with the ATPase function of VcaM we found it to be susceptible to sodium orthovanadate (NaOV), however, we also found a clear dependency of VcaM function on TolC. Inhibitors targeting secondary active transporters had no effects on either VcaM-conferred resistance or Hoechst 33342 accumulation, suggesting that VcaM might be capable of engaging with the TolC-channel without periplasmic mediation by additional transporters. Our findings are indicative of VcaM being capable of a one-step substrate translocation from cytosol to extracellular space utilising the TolC-channel, making it the only multidrug ABC-transporter outside of the MacB-family with demonstrable TolC-dependency.
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Affiliation(s)
- Wen-Jung Lu
- Department of Food Science, National Taiwan Ocean University, No. 2, Pei-Ning Road, Keelung 202, Taiwan.
| | - Hsuan-Ju Lin
- Department of Food Science, National Taiwan Ocean University, No. 2, Pei-Ning Road, Keelung 202, Taiwan.
| | - Thamarai K Janganan
- School of Life Sciences, University of Bedfordshire, University Square, Luton LU1 3JU, UK.
| | - Cheng-Yi Li
- Department of Food Science, National Taiwan Ocean University, No. 2, Pei-Ning Road, Keelung 202, Taiwan.
| | - Wei-Chiang Chin
- Department of Food Science, National Taiwan Ocean University, No. 2, Pei-Ning Road, Keelung 202, Taiwan.
| | - Vassiliy N Bavro
- School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK.
| | - Hong-Ting Victor Lin
- Department of Food Science, National Taiwan Ocean University, No. 2, Pei-Ning Road, Keelung 202, Taiwan.
- Center of Excellence for the Oceans, National Taiwan Ocean University, No. 2, Pei-Ning Road, Keelung 202, Taiwan.
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11
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3D cryo-electron reconstruction of BmrA, a bacterial multidrug ABC transporter in an inward-facing conformation and in a lipidic environment. J Mol Biol 2014; 426:2059-69. [PMID: 24630999 DOI: 10.1016/j.jmb.2014.03.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 03/01/2014] [Accepted: 03/04/2014] [Indexed: 11/21/2022]
Abstract
ABC (ATP-binding cassette) membrane exporters are efflux transporters of a wide diversity of molecule across the membrane at the expense of ATP. A key issue regarding their catalytic cycle is whether or not their nucleotide-binding domains (NBDs) are physically disengaged in the resting state. To settle this controversy, we obtained structural data on BmrA, a bacterial multidrug homodimeric ABC transporter, in a membrane-embedded state. BmrA in the apostate was reconstituted in lipid bilayers forming a mixture of ring-shaped structures of 24 or 39 homodimers. Three-dimensional models of the ring-shaped structures of 24 or 39 homodimers were calculated at 2.3 nm and 2.5 nm resolution from cryo-electron microscopy, respectively. In these structures, BmrA adopts an inward-facing open conformation similar to that found in mouse P-glycoprotein structure with the NBDs separated by 3 nm. Both lipidic leaflets delimiting the transmembrane domains of BmrA were clearly resolved. In planar membrane sheets, the NBDs were even more separated. BmrA in an ATP-bound conformation was determined from two-dimensional crystals grown in the presence of ATP and vanadate. A projection map calculated at 1.6 nm resolution shows an open outward-facing conformation. Overall, the data are consistent with a mechanism of drug transport involving large conformational changes of BmrA and show that a bacterial ABC exporter can adopt at least two open inward conformations in lipid membrane.
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12
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Optimized purification of a heterodimeric ABC transporter in a highly stable form amenable to 2-D crystallization. PLoS One 2011; 6:e19677. [PMID: 21602923 PMCID: PMC3094339 DOI: 10.1371/journal.pone.0019677] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Accepted: 04/06/2011] [Indexed: 12/24/2022] Open
Abstract
Optimized protocols for achieving high-yield expression, purification and reconstitution of membrane proteins are required to study their structure and function. We previously reported high-level expression in Escherichia coli of active BmrC and BmrD proteins from Bacillus subtilis, previously named YheI and YheH. These proteins are half-transporters which belong to the ABC (ATP-Binding Cassette) superfamily and associate in vivo to form a functional transporter able to efflux drugs. In this report, high-yield purification and functional reconstitution were achieved for the heterodimer BmrC/BmrD. In contrast to other detergents more efficient for solubilizing the transporter, dodecyl-ß-D-maltoside (DDM) maintained it in a drug-sensitive and vanadate-sensitive ATPase-competent state after purification by affinity chromatography. High amounts of pure proteins were obtained which were shown either by analytical ultracentrifugation or gel filtration to form a monodisperse heterodimer in solution, which was notably stable for more than one month at 4°C. Functional reconstitution using different lipid compositions induced an 8-fold increase of the ATPase activity (kcat∼5 s−1). We further validated that the quality of the purified BmrC/BmrD heterodimer is suitable for structural analyses, as its reconstitution at high protein densities led to the formation of 2-D crystals. Electron microscopy of negatively stained crystals allowed the calculation of a projection map at 20 Å resolution revealing that BmrC/BmrD might assemble into oligomers in a lipidic environment.
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13
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Seantier B, Dezi M, Gubellini F, Berquand A, Godefroy C, Dosset P, Lévy D, Milhiet PE. Transfer on hydrophobic substrates and AFM imaging of membrane proteins reconstituted in planar lipid bilayers. J Mol Recognit 2011; 24:461-6. [DOI: 10.1002/jmr.1070] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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14
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Pérez-Victoria I, Pérez-Victoria FJ, Roldán-Vargas S, García-Hernández R, Carvalho L, Castanys S, Gamarro F, Morales JC, Pérez-Victoria JM. Non-reducing trisaccharide fatty acid monoesters: Novel detergents in membrane biochemistry. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:717-26. [DOI: 10.1016/j.bbamem.2010.11.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 11/18/2010] [Accepted: 11/22/2010] [Indexed: 11/30/2022]
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15
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Do Cao MA, Crouzy S, Kim M, Becchi M, Cafiso DS, Di Pietro A, Jault JM. Probing the conformation of the resting state of a bacterial multidrug ABC transporter, BmrA, by a site-directed spin labeling approach. Protein Sci 2009; 18:1507-20. [PMID: 19479721 DOI: 10.1002/pro.141] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Previously published 3-D structures of a prototypic ATP-binding cassette (ABC) transporter, MsbA, have been recently corrected revealing large rigid-body motions possibly linked to its catalytic cycle. Here, a closely related multidrug bacterial ABC transporter, BmrA, was studied using site-directed spin labeling by focusing on a region connecting the transmembrane domain and the nucleotide-binding domain (NBD). Electron paramagnetic resonance (EPR) spectra of single spin-labeled cysteine mutants suggests that, in the resting state, this sub-domain essentially adopts a partially extended conformation, which is consistent with the crystal structures of MsbA and Sav1866. Interestingly, one of the single point mutants (Q333C) yielded an immobilized EPR spectrum that could arise from a direct interaction with a vicinal tyrosine residue. Inspection of different BmrA models pointed to Y408, within the NBD, as the putative interacting partner, and its mutation to a Phe residue indeed dramatically modified the EPR spectra of the spin labeled Q333C. Moreover, unlike the Y408F mutation, the Y408A mutation abolished both ATPase activity and drug transport of BmrA, suggesting that a nonpolar bulky residue is required at this position. The spatial proximity of Q333 and Y408 was also confirmed by formation of a disulfide bond when both Q333 and T407 (or S409) were replaced jointly by a cysteine residue. Overall, these results indicate that the two regions surrounding Q333 and Y408 are close together in the 3-D structure of BmrA and that residues within these two sub-domains are essential for proper functioning of this transporter.
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Affiliation(s)
- Marie-Ange Do Cao
- Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS-Université Lyon I and IFR 128, 7 passage du Vercors, 69367 Lyon Cedex 07, France
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16
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Torres C, Galián C, Freiberg C, Fantino JR, Jault JM. The YheI/YheH heterodimer from Bacillus subtilis is a multidrug ABC transporter. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2009; 1788:615-22. [DOI: 10.1016/j.bbamem.2008.12.012] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Revised: 12/12/2008] [Accepted: 12/22/2008] [Indexed: 12/12/2022]
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17
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Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol Mol Biol Rev 2008; 72:317-64, table of contents. [PMID: 18535149 DOI: 10.1128/mmbr.00031-07] [Citation(s) in RCA: 933] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
SUMMARY ATP-binding cassette (ABC) systems are universally distributed among living organisms and function in many different aspects of bacterial physiology. ABC transporters are best known for their role in the import of essential nutrients and the export of toxic molecules, but they can also mediate the transport of many other physiological substrates. In a classical transport reaction, two highly conserved ATP-binding domains or subunits couple the binding/hydrolysis of ATP to the translocation of particular substrates across the membrane, through interactions with membrane-spanning domains of the transporter. Variations on this basic theme involve soluble ABC ATP-binding proteins that couple ATP hydrolysis to nontransport processes, such as DNA repair and gene expression regulation. Insights into the structure, function, and mechanism of action of bacterial ABC proteins are reported, based on phylogenetic comparisons as well as classic biochemical and genetic approaches. The availability of an increasing number of high-resolution structures has provided a valuable framework for interpretation of recent studies, and realistic models have been proposed to explain how these fascinating molecular machines use complex dynamic processes to fulfill their numerous biological functions. These advances are also important for elucidating the mechanism of action of eukaryotic ABC proteins, because functional defects in many of them are responsible for severe human inherited diseases.
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18
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Rao DK, Kaur P. The Q-loop of DrrA is involved in producing the closed conformation of the nucleotide binding domains and in transduction of conformational changes between DrrA and DrrB. Biochemistry 2008; 47:3038-50. [PMID: 18237140 DOI: 10.1021/bi701699a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
DrrA and DrrB proteins form an ATP-dependent efflux pump for doxorubicin and daunorubicin in Streptomyces peucetius. DrrA, the catalytic subunit, forms a complex with the integral membrane protein DrrB. Previous studies have provided evidence for strong interaction between these two proteins, which was found to be critical for binding of ATP to DrrA and for stability of DrrB. Chemical cross-linking experiments carried out previously showed that in the resting state of the complex DrrA and DrrB are in contact with each other. Use of a cysteine-to-amine cross-linker then allowed identification of the N-terminal cytoplasmic tail of DrrB (residues 1-53) as the primary region of contact with DrrA. In this study, single-cysteine substitutions were introduced into different domains of DrrA in a strain already containing the S23C substitution in the N-terminal tail of DrrB. By using different arm-length disulfide cross-linkers, we found that a cysteine placed in the Q-loop region of DrrA traps DrrA in the dimeric state, thus indicating that in the closed conformation the Q-loops from opposing subunits are in the proximity of each other. Furthermore, the same region of DrrA was also found to interact with the N-terminus of DrrB, although the A-A interaction was much more prominent than the A-B interaction under these conditions. On the basis of additional data shown here, we propose that the interaction of the Q-loop with the N-terminal cytoplasmic tail of DrrB identifies an important step in the communication of conformational changes between DrrA and DrrB. The significance of these findings in the mechanism of the DrrAB complex is discussed, and a model based on analyses of different conformations of DrrA and DrrB is presented.
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Affiliation(s)
- Divya K Rao
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, USA
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19
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Lubelski J, Konings WN, Driessen AJM. Distribution and physiology of ABC-type transporters contributing to multidrug resistance in bacteria. Microbiol Mol Biol Rev 2007; 71:463-76. [PMID: 17804667 PMCID: PMC2168643 DOI: 10.1128/mmbr.00001-07] [Citation(s) in RCA: 208] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Membrane proteins responsible for the active efflux of structurally and functionally unrelated drugs were first characterized in higher eukaryotes. To date, a vast number of transporters contributing to multidrug resistance (MDR transporters) have been reported for a large variety of organisms. Predictions about the functions of genes in the growing number of sequenced genomes indicate that MDR transporters are ubiquitous in nature. The majority of described MDR transporters in bacteria use ion motive force, while only a few systems have been shown to rely on ATP hydrolysis. However, recent reports on MDR proteins from gram-positive organisms, as well as genome analysis, indicate that the role of ABC-type MDR transporters in bacterial drug resistance might be underestimated. Detailed structural and mechanistic analyses of these proteins can help to understand their molecular mode of action and may eventually lead to the development of new strategies to counteract their actions, thereby increasing the effectiveness of drug-based therapies. This review focuses on recent advances in the analysis of ABC-type MDR transporters in bacteria.
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Affiliation(s)
- Jacek Lubelski
- Department of Molecular Microbiology, University of Groningen, Kerklaan 30, NL-9751 NN Haren, The Netherlands
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20
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Ravaud S, Do Cao MA, Jidenko M, Ebel C, Le Maire M, Jault JM, Di Pietro A, Haser R, Aghajari N. The ABC transporter BmrA from Bacillus subtilis is a functional dimer when in a detergent-solubilized state. Biochem J 2006; 395:345-53. [PMID: 16405427 PMCID: PMC1422757 DOI: 10.1042/bj20051719] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
BmrA from Bacillus subtilis is a half-size ABC (ATP-binding cassette) transporter involved in multidrug resistance. Although its supramolecular organization has been investigated after reconstitution in a lipid bilayer environment, and shows a dimeric and possibly a tetrameric form, the precise quaternary structure in a detergent-solubilized state has never been addressed. In the present study, BmrA was purified from Escherichia coli membranes using an optimized purification protocol and different detergents. Furthermore, the ATPase activity of BmrA and the quantity of bound lipids and detergent were determined, and the oligomeric state was analysed using SEC (size-exclusion chromatography) and analytical ultracentrifugation. The activity and the quaternary structure of BmrA appeared to be strongly influenced by the type and concentration of the detergent used. SEC data showed that BmrA could be purified in a functional form in 0.05 and 0.01% DDM (n-dodecyl-beta-D-maltoside) and was homogeneous and monodisperse with an R(s) (Stokes radius) of 5.6 nm that is compatible with a dimer structure. Sedimentation-velocity and equilibrium experiments unequivocally supported that BmrA purified in DDM is a dimer and excluded the presence of other oligomeric states. These observations, which are discussed in relation to results obtained in proteoliposomes, also constitute an important first step towards crystallographic studies of BmrA structure.
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Affiliation(s)
- Stéphanie Ravaud
- *Laboratoire de BioCristallographie, Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/UCBL, IFR 128 BioSciences Lyon-Gerland, 7 Passage du Vercors, F-69367 Lyon Cedex 07, France
| | - Marie-Ange Do Cao
- †Laboratoire de Protéines de Résistance aux Agents Chimiothérapeutiques, Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/UCBL, IFR 128 BioSciences Lyon-Gerland, 7 Passage du Vercors, F-69367 Lyon Cedex 07, France
| | - Marie Jidenko
- ‡DBJC/SBFM, URA 2096 CNRS/CEA and LRA17V (Commissariat à l'Energie Atomique/Université Paris XI), Bâtiment 528, 91191 Gif-sur-Yvette Cedex, France
| | - Christine Ebel
- §Laboratoire de Biophysique Moléculaire, Institut de Biologie Structurale, UMR 5075 CEA/CNRS/UJF, 41 rue Jules Horowitz, 38027 Grenoble Cedex 01, France
| | - Marc Le Maire
- ‡DBJC/SBFM, URA 2096 CNRS/CEA and LRA17V (Commissariat à l'Energie Atomique/Université Paris XI), Bâtiment 528, 91191 Gif-sur-Yvette Cedex, France
| | - Jean-Michel Jault
- ∥Laboratoire de Biophysique Moléculaire et Cellulaire, DRDC, UMR 5090 CNRS/CEA/UJF, CEA, 17 rue des Martyrs, Bâtiment K, 38054 Grenoble Cedex 09, France
| | - Attilio Di Pietro
- †Laboratoire de Protéines de Résistance aux Agents Chimiothérapeutiques, Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/UCBL, IFR 128 BioSciences Lyon-Gerland, 7 Passage du Vercors, F-69367 Lyon Cedex 07, France
| | - Richard Haser
- *Laboratoire de BioCristallographie, Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/UCBL, IFR 128 BioSciences Lyon-Gerland, 7 Passage du Vercors, F-69367 Lyon Cedex 07, France
| | - Nushin Aghajari
- *Laboratoire de BioCristallographie, Institut de Biologie et Chimie des Protéines, UMR 5086 CNRS/UCBL, IFR 128 BioSciences Lyon-Gerland, 7 Passage du Vercors, F-69367 Lyon Cedex 07, France
- To whom correspondence should be addressed (email )
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Hanekop N, Zaitseva J, Jenewein S, Holland IB, Schmitt L. Molecular insights into the mechanism of ATP-hydrolysis by the NBD of the ABC-transporter HlyB. FEBS Lett 2005; 580:1036-41. [PMID: 16330029 DOI: 10.1016/j.febslet.2005.11.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2005] [Revised: 11/03/2005] [Accepted: 11/04/2005] [Indexed: 02/08/2023]
Abstract
The ABC-transporter HlyB is a central element of the Type I protein secretion machinery, dedicated to export the E. coli toxin HlyA in a single step across the two membranes of the cell envelope. Here, we discuss recent insights into the structure and the mechanism of ATP-hydrolysis by the NBD of HlyB. Combining structural and biochemical data, we have suggested that substrate-assisted catalysis (SAC), but not general base catalysis, is responsible for ATP-hydrolysis in this NBD and might also operate in other NBDs. Finally, the implications and advantages of SAC are discussed in the context of ATP-induced dimerization of the NBDs.
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Affiliation(s)
- N Hanekop
- Institute of Biochemistry, Heinrich Heine University Duesseldorf, Universitaetsstr. 1, 40225 Duesseldorf, Germany
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22
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Dalmas O, Orelle C, Foucher AE, Geourjon C, Crouzy S, Di Pietro A, Jault JM. The Q-loop Disengages from the First Intracellular Loop during the Catalytic Cycle of the Multidrug ABC Transporter BmrA. J Biol Chem 2005; 280:36857-64. [PMID: 16107340 DOI: 10.1074/jbc.m503266200] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The ATP-binding cassette is the most abundant family of transporters including many medically relevant members and gathers both importers and exporters involved in the transport of a wide variety of substrates. Although three high resolution three-dimensional structures have been obtained for a prototypic exporter, MsbA, two have been subjected to much criticism. Here, conformational changes of BmrA, a multidrug bacterial transporter structurally related to MsbA, have been studied. A three-dimensional model of BmrA, based on the "open" conformation of Escherichia coli MsbA, was probed by simultaneously introducing two cysteine residues, one in the first intracellular loop of the transmembrane domain and the other in the Q-loop of the nucleotide-binding domain (NBD). Intramolecular disulfide bonds could be created in the absence of any effectors, which prevented both drug transport and ATPase activity. Interestingly, addition of ATP/Mg plus vanadate strongly prevented this bond formation in a cysteine double mutant, whereas ATP/Mg alone was sufficient when the ATPase-inactive E504Q mutation was also introduced, in agreement with additional BmrA models where the ATP-binding sites are positioned at the NBD/NBD interface. Furthermore, cross-linking between the two cysteine residues could still be achieved in the presence of ATP/Mg plus vanadate when homobifunctional cross-linkers separated by more than 13 Angstrom were added. Altogether, these results give support to the existence, in the resting state, of a monomeric conformation of BmrA similar to that found within the open MsbA dimer and show that a large motion is required between intracellular loop 1 and the nucleotide-binding domain for the proper functioning of a multidrug ATP-binding cassette transporter.
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Affiliation(s)
- Olivier Dalmas
- Institut de Biologie et Chimie des Protéines, Unité Mixte de Recherche 5086 CNRS-UCBL1 and IFR 128, 7 Passage du Vercors, 69367 Lyon Cedex 07, France
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