Structure and Function of a Microbial Oxidase

Oxygen is essential for the survival of various life forms. When cells convert nutrients into energy, oxygen is converted into water as the last step of the respiratory chain. The enzyme responsible for this process is oxidase.

While humans have only one type of oxidase, the bacterial model organism E. coli has three. In order to better understand why E. coli and other bacteria need multiple oxidases, researchers have determined the molecular structure of the cytochrome bd oxidase from E. coli, an oxidase that is found only in bacteria and microbial archaea. The results were published yesterday in Nature Communications.

The eponymous cytochromes, two of type b and one of type d, are the key iron-containing groups that enable the function of oxidase. At the cytochrome d, the oxygen is bound and converted to water. The structure determination revealed that the architecture of cytochrome bd oxidase from E. coli is very similar to the structure of another bacterium, Geobacillus thermodenitrificans. “However, to our great surprise, we discovered that a cytochrome b and cytochrome d have changed positions and thus the site of oxygen conversion within the enzyme,” says senior author Thorsten Friedrich of the University of Freiburg.

The cause of this change could be that the cytochrome bd oxidase might fulfill a second function: In addition to the energy production, it can serve to protect against oxidative stress and stress by nitroxides. Particularly pathogenic bacterial strains show a high activity of cytochrome bd oxidase. Since humans do not have this type of oxidase, these results might furthermore provide important indications on the development of new antimicrobials that target the cytochrome bd oxidase of pathogens such as Mycobacteria.

Important for this success was the new high-performance electron microscope, which has been operated since 2018. “Cytochrome bd oxidase was a challenging sample for cryo-electron microscopy because it is one of the smallest membrane proteins whose structure has been determined with this technique,” says coauthor Bettina Böttcher of the Rudolf Virchow Center.

Special features of this technique are extremely low temperatures down to –180 °C and a resolution that moves in the order of atoms. It makes it possible to study biological molecules and complexes in solution that have been previously snap-frozen and to reconstruct their three-dimensional structure. With a voltage of 300,000 volts, the microscope accelerates the electrons with which it “scans” the samples.

Image: Structure of the cytochrome bd oxidase. The experimental data are shown in gray and the derived molecular model is colored. The excision enlargement shows the area in which the three cytochromes are bound. Image courtesy of Rudolf-Virchow-Zentrum / University of Würzburg.