Aspartic Acid 397 in Subunit B of the Na+-pumping NADH:Quinone Oxidoreductase from Vibrio cholerae Forms Part of a Sodium-binding Site, Is Involved in Cation Selectivity, and Affects Cation-binding Site Cooperativity

Shea, Michael; Juárez, Óscar; Cho, Jonathan; Barquera, Blanca

doi:10.1074/jbc.m113.510776

Cited by 16 publications

(32 citation statements)

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“…7D), as have been demonstrated before (6,15). The second binding site is located in NqrB, in which residue NqrB Asp-397 plays an important role in the cooperative behavior and in determining the size of the cation that can be bound (15). Although the operation of the two sites is important for the optimal work of Na ϩ -NQR, the enzyme can be functional with only one sodium-binding site, possibly the one located in NqrD/NqrE (15).…”

Section: Discussionsupporting

confidence: 62%

“…Once the first sodium is bound, the accessibility of the second binding site increases, producing positive cooperativity between the sites (Fig. 7D), as have been demonstrated before (6,15). The second binding site is located in NqrB, in which residue NqrB Asp-397 plays an important role in the cooperative behavior and in determining the size of the cation that can be bound (15).…”

Section: Discussionmentioning

confidence: 57%

“…These enzymes are multimeric complexes that are organized in modules that can act independently, allowing the operation of the ping-pong mechanism. This type of module organization is also found in Na ϩ -NQR, with the NADH dehydrogenase module located in the NqrF subunit (26,43), CoQ-1 reduction in the NqrB subunit (19,20), and sodium transport in the NqrB and NqrD/ NqrE subunits (14,15,17,30). The hexa-uni ping-pong mechanism is conformational in character, because the individual binding sites of the substrates are not preformed (or are inaccessible in certain states), which confirms our previous hypothesis that the enzyme undergoes multiple conformational changes (5,16,19,30).…”

Section: Discussionmentioning

confidence: 98%

“…7C). This sodium-binding site could be found in NqrE/NqrD subunits (15). Once the first sodium is bound, the accessibility of the second binding site increases, producing positive cooperativity between the sites (Fig.…”

Section: Discussionmentioning

confidence: 99%

“…The NqrB subunit contains the attachment site for one covalently bound FMN molecule (13), as well some of the structures involved in the transport of sodium, including one of the at least two sodium-binding sites (14 -17). Indeed, the mutation of aspartate residue 397 affects the positive cooperativity of the sites (15), changes the cation selectivity, and produces an uncoupling effect in the presence of potassium (17). Recent crystallographic data have shown that NqrB contains 10 transmembrane helices (12), with an organization that allows the transport of sodium.…”

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confidence: 99%

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The Kinetic Reaction Mechanism of the Vibrio cholerae Sodium-dependent NADH Dehydrogenase

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Mezic

et al. 2015

Journal of Biological Chemistry

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Section: Discussionsupporting

confidence: 62%

Section: Discussionmentioning

confidence: 57%

Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

mentioning

confidence: 99%

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The Kinetic Reaction Mechanism of the Vibrio cholerae Sodium-dependent NADH Dehydrogenase

Tuz

Mezic

et al. 2015

Journal of Biological Chemistry

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Sodium as Coupling Cation in Respiratory Energy Conversion

Fritz

Steuber

2016

The Alkali Metal Ions: Their Role for Life

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Among the alkali cations, Na(+) has an extraordinary role in living cells since it is used to charge the battery of life. To this end, sophisticated protein complexes in biological membranes convert chemical energy obtained from oxidation of NADH, or hydrolysis of ATP, into an electrochemical gradient of sodium ions. Cells use this so-called sodium-motive force stored in energy-converting membranes for important processes like uptake of nutrients, motility, or expulsion of toxic compounds. The Na(+) pumps act in concert with other enzymes embedded in the lipid membrane, and together they form the respiratory chain which achieves the oxidation of NADH derived from nutrients under formation of an electrochemical sodium (or proton) gradient. We explain why Na(+) pumps are important model systems for the homologous, proton-translocating complexes, and hope to convince the reader that studying the Na(+)-translocating ATP synthase from the unimpressive bacterium Ilyobacter tartaricus had a big impact on our understanding of energy conversion by human ATP synthase. The Na(+)-translocating systems described here are either driven by the oxidation of NADH, the carrier of redox equivalents of cells, or by the hydrolysis of adenosine 5'-triphosphate, the universal high-energy compound of cells. The electrochemical energy provided by these respiratory Na(+) pumps, the NADH dehydrogenase or the ATPase, drives other Na(+) transport systems like the bacterial flagellum discussed in the last part of this chapter. The flagellar motor does not represent a Na(+) pump, but like ATPase, it operates by a rotational mechanism. By comparing these two Na(+) -translocating, rotary machines, we obtain new insight into the possible mechanisms of Na(+) transport through the stator proteins of the flagellar motor. Na(+) pumps are widespread in pathogenic bacteria where they play an important role in metabolism, making them novel targets for antibiotics.

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Molecular dynamics modeling of the Vibrio cholera Na+-translocating NADH:quinone oxidoreductase NqrB–NqrD subunit interface

et al. 2021

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The Na+-translocating NADH:quinone oxidoreductase (Na+-NQR) is the major Na+ pump in aerobic pathogens such as Vibrio cholerae. The interface between two of the NQR subunits, NqrB and NqrD, has been proposed to harbor a binding site for inhibitors of Na+-NQR. While the mechanisms underlying Na+-NQR function and inhibition remain underinvestigated, their clarification would facilitate the design of compounds suitable for clinical use against pathogens containing Na+-NQR. An in silico model of the NqrB–D interface suitable for use in molecular dynamics simulations was successfully constructed. A combination of algorithmic and manual methods was used to reconstruct portions of the two subunits unresolved in the published crystal structure and validate the resulting structure. Hardware and software optimizations that improved the efficiency of the simulation were considered and tested. The geometry of the reconstructed complex compared favorably to the published V. cholerae Na+-NQR crystal structure. Results from one 1 µs, three 150 ns and two 50 ns molecular dynamics simulations illustrated the stability of the system and defined the limitations of this model. When placed in a lipid bilayer under periodic boundary conditions, the reconstructed complex was completely stable for at least 1 µs. However, the NqrB–D interface underwent a non-physiological transition after 350 ns.

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Aspartic Acid 397 in Subunit B of the Na+-pumping NADH:Quinone Oxidoreductase from Vibrio cholerae Forms Part of a Sodium-binding Site, Is Involved in Cation Selectivity, and Affects Cation-binding Site Cooperativity

Abstract: Background: Na ϩ -NQR is the main sodium pump in Vibrio cholerae.

Cited by 16 publications

References 19 publications

The Kinetic Reaction Mechanism of the Vibrio cholerae Sodium-dependent NADH Dehydrogenase

The Kinetic Reaction Mechanism of the Vibrio cholerae Sodium-dependent NADH Dehydrogenase

Sodium as Coupling Cation in Respiratory Energy Conversion

Molecular dynamics modeling of the Vibrio cholera Na+-translocating NADH:quinone oxidoreductase NqrB–NqrD subunit interface

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