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

Edited by Ruma BanerjeeThe Na ؉ -pumping NADH-quinone oxidoreductase (Na ؉ -NQR) is the first enzyme of the respiratory chain and the main ion transporter in many marine and pathogenic bacteria, including Vibrio cholerae. I]PAD-2, rather than being competitively suppressed in the presence of other inhibitors, is enhanced under some experimental conditions. To explain these apparently paradoxical results, we propose models for the catalytic reaction of Na ؉ -NQR and its interactions with inhibitors on the basis of the biochemical and biophysical results reported here and in previous work.The Na ϩ -pumping NADH-quinone oxidoreductase (Na ϩ -NQR) 2 is the first enzyme of the respiratory chain and the main ion transporter in many marine and pathogenic bacteria, such as Vibrio cholerae and Haemophilus influenzae (1, 2). Na ϩ -NQR obtains energy by oxidizing NADH and reducing ubiquinone, which allows it to generate an electrochemical Na ϩ gradient across the inner bacterial membrane. The enzyme is an integral membrane complex consisting of six subunits (NqrA-F) encoded by the nqr operon (2). There is a consensus that the electron transfer takes place through a series of five redox cofactors as follows: a FAD; a 2Fe-2S center; two covalently bound FMN, and a riboflavin (3-5). Different studies have intensively investigated the locations and redox properties of the cofactors of the enzyme (6 -12); however, the exact locations of the ubiquinone-binding site(s) and the Na ϩ transport pathway, as well as the mechanism that couples Na ϩ transport to the electron transfer, still remain elusive.A recently published X-ray crystallographic study provided important information about the structure of V. cholerae Na ϩ -NQR (13), but the model includes several features that are difficult to reconcile with previous biochemical and/or biophysical functional characterizations (11). For instance, the spatial distances between several pairs of redox cofactors in the proposed electron transfer pathway are too large to support physiological rates of electron transfer; for example, the edge-toedge distance between the [2Fe-2S] cluster in NqrF and the Fe(Cys) 4 in NqrD (33.4 Å) and between the FMN and the riboflavin cofactor in NqrB (29.3 Å). The fact that electron transfer between these cofactors takes place indicates that the subunits harboring the cofactors undergo large conformational changes during turnover that decrease these spatial gaps (13).Additionally, the crystallographic model lacks an anticipated tightly bound quinone, which has been reported in the enzyme preparations from different laboratories (4,6,8) and suggested to be located in NqrA on the basis of photoaffinity labeling and NMR studies (7,9). In the crystallographic model, the NqrA subunit includes a deep cavity that is large enough to accommodate a ubiquinone molecule, but the cavity is ϳ20 Å above the predicted membrane surface and the distance between the cavity and the riboflavin in NqrB subunit is too large (Ͼ40 Å) to be consistent with electron transfer during tu...

RNF is a redox-driven ion (Na+ and in one case possibly H+) transporter present in many prokaryotes. It has been proposed that RNF performs a variety of reactions in different organisms, delivering low-potential reducing equivalents for specific cellular processes. RNF shares strong homology with the Na+-pumping respiratory enzyme Na+-NQR, although there are significant differences in subunit and redox cofactor composition. Here we report a topological analysis of the six subunits of RNF from Vibrio cholerae. Although individual subunits from other organisms have previously been studied, this is the first complete, experimentally derived, analysis of RNF from any one source. This has allowed us to identify and confirm key properties of RNF. The putative NADH binding site in RnfC is located on the cytoplasmic side of the membrane. FeS centers in RnfB and RnfC are also located on the cytoplasmic side. However, covalently attached FMNs in RnfD and RnfG are both located in the periplasm. RNF also contains a number of acidic residues that correspond to functionally important groups in Na+-NQR. The acidic residues involved in Na+ uptake and many of those implicated in Na+ translocation are topologically conserved. The topology of RNF closely matches the topology represented in the newly published structure of Na+-NQR, consistent with the close relation between the two enzymes. The topology of RNF is discussed in the context of the current structural model of Na+-NQR, and the proposed functionality of the RNF complex itself.

The sodium-pumping NADH:ubiquinone oxidoreductase (Na+-NQR) is a bacterial respiratory enzyme that obtains energy from the redox reaction between NADH and ubiquinone and uses this energy to create an electrochemical Na+ gradient across the cell membrane. A number of acidic residues in transmembrane helices have been shown to be important for Na+ translocation. One of these, Asp-397 in the NqrB subunit, is a key residue for Na+ uptake and binding. In this study, we show that when this residue is replaced with asparagine, the enzyme acquires a new sensitivity to K+; in the mutant, K+ both activates the redox reaction and uncouples it from the ion translocation reaction. In the wild-type enzyme, Na+ (or Li+) accelerates turnover while K+ alone does not activate. In the NqrB-D397N mutant, K+ accelerates the same internal electron transfer step (2Fe-2S → FMNC) that is accelerated by Na+. This is the same step that is inhibited in mutants in which Na+ uptake is blocked. NqrB-D397N is able to translocate Na+ and Li+, but when K+ is introduced, no ion translocation is observed, regardless of whether Na+ or Li+ is present. Thus, this mutant, when it turns over in the presence of K+, is the first, and currently the only, example of an uncoupled Na+-NQR. The fact the redox reaction and ion pumping become decoupled from each other only in the presence of K+ provides a switch that promises to be a useful experimental tool.

The sodium-pumping NADH:quinone oxidoreductase (Na + -NQR) is a bacterial enzyme that oxidizes NADH, reduces ubiquinone, and translocates Na + across the membrane. We previously identified three acidic residues in the membranespanning helices, near the cytosol, NqrB-D397, NqrD-D133, and NqrE-E95, as candidates likely to be involved in Na + uptake, and replacement of any one of them by a non-acidic residue affects the Na + -dependent kinetics of the enzyme. Here, we have inquired further into the role of the NqrE-E95 residue by constructing a series of mutants in which this residue is replaced by amino acids with charges and/or sizes different from those of the glutamate of the wild-type enzyme. All of the mutants showed altered steadystate kinetics with the acceleration of turnover by Na + greatly diminished. Selected mutants were studied by other physical methods. Membrane potential measurements showed that NqrE-E95D and A are significantly less efficient in ion transport. NqrE-E95A, Q, and D were studied by transient kinetic measurements of the reduction of the enzyme by NADH. In all three cases, the results indicated inhibition of the electron-transfer step in which the FMN C becomes reduced. This is the first Na +dependent step and is associated with Na + uptake by the enzyme. Electrochemical measurements on NqrE-E95Q showed that the Na + dependence of the redox potential of the FMN cofactors has been lost. The fact that the mutations at the NqrE-E95 site have specific effects related to translocation of Na + and Li + strongly indicates a definite role for NqrE-E95 in the cation transport process of Na + -NQR.