Structural basis for the drug extrusion mechanism by a MATE multidrug transporter

Tanaka, Yoshiki; Hipolito, Christopher J.; Maturana, Andrés D.; Ito, Koichi; Kuroda, Teruo; Higuchi, Takashi; Katoh, Takayuki; Kato, Hideaki; Hattori, Motoyuki; Kumazaki, Kaoru; Tsukazaki, Tomoya; Ishitani, Ryuichiro; Suga, Hiroaki; Nureki, Osamu

doi:10.1038/nature12014

Cited by 224 publications

(304 citation statements)

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“…At the molecular level, the architecture of pmf-and smf-driven membrane proteins within the same family has consistently been found to be largely conserved (20)(21)(22)(23)(24)(25)(26)(27)(28). Thus, it appears as if the Na + or H + specificity of these systems is dictated by localized variations in their amino acid sequence, rather than by major structural or mechanistic adaptations.…”

mentioning

confidence: 95%

On the principle of ion selectivity in Na ⁺ /H ⁺ -coupled membrane proteins: Experimental and theoretical studies of an ATP synthase rotor

Leone

Pogoryelov

Meier

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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Numerous membrane transporters and enzymes couple their mechanisms to the permeation of Na + or H + , thereby harnessing the energy stored in the form of transmembrane electrochemical potential gradients to sustain their activities. The molecular and environmental factors that control and modulate the ion specificity of most of these systems are, however, poorly understood. Here, we use isothermal titration calorimetry to determine the Na + /H + selectivity of the ion-driven membrane rotor of an F-type ATP synthase. Consistent with earlier theoretical predictions, we find that this rotor is significantly H + selective, although not sufficiently to be functionally coupled to H + , owing to the large excess of Na + in physiological settings. The functional Na + specificity of this ATP synthase thus results from two opposing factors, namely its inherent chemical selectivity and the relative availability of the coupling ion. Further theoretical studies of this membrane rotor, and of two others with a much stronger and a slightly weaker H + selectivity, indicate that, although the inherent selectivity of their ion-binding sites is largely set by the balance of polar and hydrophobic groups flanking a conserved carboxylic side chain, subtle variations in their structure and conformational dynamics, for a similar chemical makeup, can also have a significant contribution. We propose that the principle of ion selectivity outlined here may provide a rationale for the differentiation of Na + -and H + -coupled systems in other families of membrane transporters and enzymes. molecular motor | ion-coupled transport | binding thermodynamics | energy transduction | membrane bioenergetics G radients in the electrochemical potential of H + or Na + across biological membranes sustain a wide range of essential cellular process. The resulting proton or sodium motive forces (pmf, smf) are the predominant energy source for secondary-active membrane transporters, which mediate the uptake of many substances required by the cell (1-3), and also enable pathogenic bacteria to protect themselves from human-made antibiotics and other toxic compounds (4-6). Downhill membrane permeation of Na + and H + across the membrane also powers the ATP synthase (7), which produces most of cellular ATP, and energizes the rotation of bacterial flagella (8). Thus, the importance of this mode of energy transduction in cells cannot be overstated. Nevertheless, little is known about the factors that control and modulate the specificity for Na + or H + in most of these processes.It seems clear, although, that there is no correlation between function type and ion specificity; that is, the same process in different species can be coupled to either Na + or H + (2, 5-7, 9-11). Organism-specific environmental factors, such as temperature or pH, also do not provide a consistent rationale; for example, ATP synthases from thermoalkaliphilic bacteria use a H + gradient despite the scarcity of H + and the potentially greater degree of H + leakage across the membrane at hig...

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mentioning

confidence: 95%

On the principle of ion selectivity in Na ⁺ /H ⁺ -coupled membrane proteins: Experimental and theoretical studies of an ATP synthase rotor

Leone

Pogoryelov

Meier

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

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“…In addition, the crystal structures have also revealed different locations of cationand substrate-binding sites, suggesting a mechanistic diversity among MATE transporters. In the structure of drug-bound NorM_NG, the binding site is located close to the membraneperiplasm interface, whereas in the structure of PfMATE, the drug binding pocket was published to be in the N-lobe cavity, which is halfway in the transmembrane region (9,11). Despite the report of the crystal structures of MATE transporters, no detailed biochemical characterization and substrate binding studies have been performed so far.…”

mentioning

confidence: 96%

“…ϩ Translocation-Asp-41 PfMATE (corresponding to NorM_PS ) was reported to be involved in H ϩ translocation by changing its protonation state: the change may trigger the reorganization of the interaction network, thereby inducing the structural transition between the straight and bent conformations of TMH1 (11). Moreover, another orthologue of NorM_PS , Asp-40 DinFϪBH was proposed to be a competition site for substrate and H ϩ (10).…”

Section: Asp-38 Is Involved In Hmentioning

confidence: 99%

Identification of the High-affinity Substrate-binding Site of the Multidrug and Toxic Compound Extrusion (MATE) Family Transporter from Pseudomonas stutzeri

Nie

Grell

Malviya

et al. 2016

Journal of Biological Chemistry

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Multidrug and toxic compound extrusion (MATE) transportThe ability of all living organisms to protect themselves against toxic substances is essential for their survival. Organisms acquire this ability through evolutionary force (1). Due to the development of scientific knowledge, more and more medical drugs are being developed and applied. As a consequence, general defense mechanisms to resist antibiotics, drugs, and other toxic compounds have been evolved in bacteria (2). Being one of those defense mechanisms, the active extrusion of the toxic compounds from the cells plays an important role (3). In bacteria, the extrusion is often carried out by multidrug transporters, which are integral membrane proteins. They are classified into five distinct families: ATP-binding cassette, multidrug and toxic compound extrusion (MATE), 4 major facilitator superfamily, resistance nodulation division, and small multidrug resistance transporters (4).In 1999, the MATE family proteins were first recognized as a new group of the multidrug transporters, existing in all three domains of life (5). Most members of this family consist of a single chain of 450 -550 amino acid residues and exhibit 12 putative transmembrane helices (TMHs). Up to now, about 900 proteins have been annotated as MATE transporters on the basis of amino acid sequence similarities. Moreover, a subclassification of the MATE family has been suggested, NorM-, DinF-(DNA damage-inducible protein F), and eukaryotic subfamily (4, 6, 7). Various compounds can be recognized by NorM proteins, including dyes, fluoroquinolones, and aminoglycosides (7). As secondary active transporters, MATE proteins utilize transmembrane Na ϩ or H ϩ electrochemical gradients to extrude toxic compounds.So far atomic structures of four MATE transporters have been reported in their putative outward-facing states, in both drug-bound and/or drug-free states. NorM_VC from Vibrio cholerae and NorM_NG from Neisseria gonorrhoeae, are both Na ϩ driven, whereas PfMATE from Pyrococcus furiosus and DinF-BH from Bacillus halodurans are published to be H ϩ -dependent antiporters (8 -11). All these four proteins contain 12 TMHs with intracellular N and C termini, and possess a hydrophobic internal cavity, formed by two symmetric bundles with 6 TMHs each. The two bundles are linked by a cytoplasmic loop between the 6th and 7th TMH. All MATE proteins share about 40% sequence similarity, and they employ the same rockerswitch mechanism for substrate extrusion (12). In addition, the crystal structures have also revealed different locations of cationand substrate-binding sites, suggesting a mechanistic diversity among MATE transporters. In the structure of drug-bound NorM_NG, the binding site is located close to the membraneperiplasm interface, whereas in the structure of PfMATE, the

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“…1 The researchers are now collaborating with PeptiDream Inc. to develop compounds with improved drug-like properties that hit medically relevant targets.…”

Section: By Chris Cain Senior Writermentioning

confidence: 99%

RaPID results

Cain¹

2013

Science-Business eXchange

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SciBX that the export mechanism is the most important new piece of information provided by these structures.Hendrick van Veen, senior lecturer in the Department of Pharmacology at the University of Cambridge, agreed. "One key finding of the current structure is that it provides new insights into the question of how substrate transport is coupled to the movement of protons," he said. "Based on [the MATEs'] structures, the researchers propose that when a proton binds to the MATE transporter, it switches the conformation to allow the dissociation of the toxin molecule into the extracellular environment. "Geoffrey Chang, whose team crystalized the first MATE transporter in 2010, said the resolution of the new transporter structures was critical to enabling the new insights. Chang's structure of the Vibrio cholera Na + MATE transporter NorM was resolved at 3.65 Å. The series of structures presented in the new work range from 2.1-3 Å.Chang is a professor of pharmacology at the University of California, San Diego.Nureki now plans to conduct studies on more therapeutically relevant MATE proteins, including those from pathogenic bacteria and humans, and to solve the structures of the transporters complexed with specific inhibitory peptides. "Our inhibitory cyclic peptide paves the way toward the development of efficient inhibitors against previously undruggable MATE transporters," he said. "Unfortunately, because traditional antibiotics are small and readily transported out by MATEs, it was difficult to discover potent inhibitors. The thioether-macrocyclic peptides are the right molecular size to fit into the active pocket of MATE and effectively clog it and inhibit its function. " RaPID resultsSuga said the team plans to use RaPID to optimize inhibitory peptides with unnatural and d-amino acids, which are more resistant to proteases found in the blood and can increase cell permeability compared with unmodified l-amino acids.van Veen said he was impressed that the cyclic peptides were able to block transport without entering the cell. "The researchers have identified a new type of inhibitor for MATE that acts by binding to outward-facing MATE from the exterior of the cell. This represents a very promising approach to inhibit multidrug transporters in a clinical setting because the inhibitor does not need to enter the cell to exert its action, " he said.van Veen and Chang both said the next key advance for understanding MATE transport will come from solving the structure of an inward-facing MATE transporter.Robert Stavenger, group leader at GlaxoSmithKline plc and project coordinator for TRANSLOCATION, an Innovative Medicines

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Structural basis for the drug extrusion mechanism by a MATE multidrug transporter

Cited by 224 publications

References 39 publications

On the principle of ion selectivity in Na ⁺ /H ⁺ -coupled membrane proteins: Experimental and theoretical studies of an ATP synthase rotor

On the principle of ion selectivity in Na ⁺ /H ⁺ -coupled membrane proteins: Experimental and theoretical studies of an ATP synthase rotor

Identification of the High-affinity Substrate-binding Site of the Multidrug and Toxic Compound Extrusion (MATE) Family Transporter from Pseudomonas stutzeri

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Structural basis for the drug extrusion mechanism by a MATE multidrug transporter

Cited by 224 publications

References 39 publications

On the principle of ion selectivity in Na + /H + -coupled membrane proteins: Experimental and theoretical studies of an ATP synthase rotor

On the principle of ion selectivity in Na + /H + -coupled membrane proteins: Experimental and theoretical studies of an ATP synthase rotor

Identification of the High-affinity Substrate-binding Site of the Multidrug and Toxic Compound Extrusion (MATE) Family Transporter from Pseudomonas stutzeri

RaPID results

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On the principle of ion selectivity in Na ⁺ /H ⁺ -coupled membrane proteins: Experimental and theoretical studies of an ATP synthase rotor

On the principle of ion selectivity in Na ⁺ /H ⁺ -coupled membrane proteins: Experimental and theoretical studies of an ATP synthase rotor