Cryo-EM structures of Na(+)-pumping NADH-ubiquinone oxidoreductase from Vibrio cholerae

The Na(+)-pumping NADH-ubiquinone oxidoreductase (Na(+)-NQR) couples electron transfer from NADH to ubiquinone with Na(+)-pumping, generating an electrochemical Na(+) gradient that is essential for energy-consuming reactions in bacteria. Since Na(+)-NQR is exclusively found in prokaryotes, it is a promising target for highly selective antibiotics. However, the molecular mechanism of inhibition is not well-understood for lack of the atomic structural information about an inhibitor-bound state. Here we present cryo-electron microscopy structures of Na(+)-NQR from Vibrio cholerae with or without a bound inhibitor at 2.5- to 3.1-Å resolution. The structures reveal the arrangement of all six redox cofactors including a herein identified 2Fe-2S cluster located between the NqrD and NqrE subunits. A large part of the hydrophilic NqrF is barely visible in the density map, suggesting a high degree of flexibility. This flexibility may be responsible to reducing the long distance between the 2Fe-2S centers in NqrF and NqrD/E. Two different types of specific inhibitors bind to the N-terminal region of NqrB, which is disordered in the absence of inhibitors. The present study provides a foundation for understanding the function of Na(+)-NQR and the binding manner of specific inhibitors.