A New Type of Na+-Driven ATP Synthase Membrane Rotor with a Two-Carboxylate Ion-Coupling Motif

Schulz, Sarah; Iglesias-Cans, Marina C.; Krah, Alexander; Yıldız, Özkan; Leone, Vanessa; Matthies, Doreen; Cook, Gregory M.; Faraldo‐Gómez, José D.; Meier, Thomas

doi:10.1371/journal.pbio.1001596

Cited by 59 publications

(59 citation statements)

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“…2) is very similar to that observed in other high-resolution c-ring structures resolved using detergent-based crystallization buffers 12,17,13,28,26 . We have previously shown, for a H + -coupled c-ring, that this is the configuration of the sites that face the membrane during the enzyme’s rotary cycle 34 .…”

Section: Resultssupporting

confidence: 85%

High-resolution structure and mechanism of an F/V-hybrid rotor ring in a Na+-coupled ATP synthase

et al. 2014

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All rotary ATPases catalyze the interconversion of ATP and ADP-Pi through a mechanism that is coupled to the transmembrane flow of H+ or Na+. Physiologically, however, F/A-type enzymes specialize in ATP synthesis driven by downhill ion diffusion, while eukaryotic V-type ATPases function as ion pumps. To begin to rationalize the molecular basis for this functional differentiation, we solved the crystal structure of the Na+-driven membrane rotor of the Acetobacterium woodii ATP synthase, at 2.1 Å resolution. Unlike known structures, this rotor ring is a 9:1 heteromer of F- and V-type c-subunits, and therefore features a hybrid configuration of ion-binding sites along its circumference. Molecular and kinetic simulations are used to dissect the mechanisms of Na+ recognition and rotation of this c-ring, and to explain the functional implications of the V-type c-subunit. These structural and mechanistic insights indicate an evolutionary path between synthases and pumps involving adaptations in the rotor ring.

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Section: Resultssupporting

confidence: 85%

High-resolution structure and mechanism of an F/V-hybrid rotor ring in a Na+-coupled ATP synthase

et al. 2014

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“…The determination of the selectivity of the I. tartaricus c-ring has enabled us to challenge a previously proposed theoretical framework, based on MD simulations, with which we have compared and rationalized the functional specificity of different rotary ATPases (17,29,30,33). The quantitative agreement between computational and experimental results obtained here validates that approach and therefore substantiates the principle of ion selectivity derived from it.…”

Section: Discussionsupporting

confidence: 73%

“…The functional ion-binding sites in the c-subunit rings of all rotary ATPases are located along the outer circumference of the structure, approximately halfway across the transmembrane region (21,23,(31)(32)(33)(34)(35). The amino acid composition of these binding sites varies across species, but invariably they feature at least one carboxylic side chain (most commonly glutamate).…”

Section: Resultsmentioning

confidence: 99%

“…The amino acid composition of these binding sites varies across species, but invariably they feature at least one carboxylic side chain (most commonly glutamate). In rotary ATPases that are physiologically coupled to the H + gradient, this conserved side chain enables H + binding to the c-ring through protonation (36,37); in enzymes coupled to Na + , as in I. tartaricus, the carboxylate group coordinates the bound Na + directly (21,33,35). Carboxylic amino acids are, however, often found elsewhere in the c-subunits, usually at either side of the transmembrane region.…”

Section: Resultsmentioning

confidence: 99%

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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

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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“…In addition, our pKa calculations show that amongst the two scenarios, deprotonation of D371 incurs a substantially higher free energy penalty than deprotonation of E255, and therefore we conclude that, out of this dyad of ionisable side chains, D371 is more likely to carry the proton. This result is in good agreement with a previous study on a molecular rotor, where two carboxylate groups bind to a sodium ion during the Na + translocation mechanism, but one carboxylate group is protonated at any time (Na + bound or unbound) under physiological conditions [68]. Our finding is also in agreement with the observation that the E255Q mutant has been shown to markedly decrease transport activity in intact cells (NorM-VC) [19].…”

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confidence: 93%

Insights into the ion-coupling mechanism in the MATE transporter NorM-VC

Krah

Zachariae

2017

Phys. Biol.

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Bacteria have developed a variety of different mechanisms to defend themselves from compounds that are toxic to them, such as antibiotics. One of these defence mechanisms is the expulsion of drugs or other noxious compounds by multidrug efflux pumps. Multidrug and toxic compound extrusion (MATE) transporters are efflux pumps that extrude metabolic waste and a variety of antibiotics out of the cell, using an ion gradient as energy source. They function via an alternative-access mechanism. When ions bind in the outward facing conformation, a large conformational change to the inward facing conformation is induced, from which the ion is released and the extruded chemical compound is bound. NorM proteins, which are usually coupled to a Na + gradient, are members of the MATE family. However, for NorM-VC from Vibrio cholerae, it has been shown that this MATE transporter is additionally coupled to protons. How H + and Na + binding are coupled mechanistically to enable drug antiport is not well understood. In this study, we use molecular dynamics simulations to illuminate the sequence of ion binding event that enable efflux. Understanding this antiport mechanism is important to support the development of novel compounds that specifically inhibit the functional cycle of NorM transporters.3

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A New Type of Na+-Driven ATP Synthase Membrane Rotor with a Two-Carboxylate Ion-Coupling Motif

Abstract: Multi-disciplinary methods reveal a novel type of ion binding in the rotor ring of the F1Fo-ATP synthase from the opportunistic pathogen Fusobacterium nucleatum.

Cited by 59 publications

References 50 publications

High-resolution structure and mechanism of an F/V-hybrid rotor ring in a Na+-coupled ATP synthase

High-resolution structure and mechanism of an F/V-hybrid rotor ring in a Na+-coupled ATP synthase

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

Insights into the ion-coupling mechanism in the MATE transporter NorM-VC

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A New Type of Na+-Driven ATP Synthase Membrane Rotor with a Two-Carboxylate Ion-Coupling Motif

Abstract: Multi-disciplinary methods reveal a novel type of ion binding in the rotor ring of the F1Fo-ATP synthase from the opportunistic pathogen Fusobacterium nucleatum.

Cited by 59 publications

References 50 publications

High-resolution structure and mechanism of an F/V-hybrid rotor ring in a Na+-coupled ATP synthase

High-resolution structure and mechanism of an F/V-hybrid rotor ring in a Na+-coupled ATP synthase

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

Insights into the ion-coupling mechanism in the MATE transporter NorM-VC

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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