Active site rearrangement and structural divergence in prokaryotic respiratory oxidases

Abstract

Cytochrome bd–type quinol oxidases catalyze the reduction of molecular oxygen to water in the respiratory chain of many human-pathogenic bacteria. They are structurally unrelated to mitochondrial cytochrome c oxidases and are therefore a prime target for the development of antimicrobial drugs. We determined the structure of the Escherichia coli cytochrome bd-I oxidase by single-particle cryo–electron microscopy to a resolution of 2.7 angstroms. Our structure contains a previously unknown accessory subunit CydH, the L-subfamily–specific Q-loop domain, a structural ubiquinone-8 cofactor, an active-site density interpreted as dioxygen, distinct water-filled proton channels, and an oxygen-conducting pathway. Comparison with another cytochrome bd oxidase reveals structural divergence in the family, including rearrangement of high-spin hemes and conformational adaption of a transmembrane helix to generate a distinct oxygen-binding site.

Mycobacteria tolerate carbon monoxide by remodelling their respiratory chain

“…The cytochrome bcc - aa 3 complex is a supercomplex composed of components analogous to mitochondrial complex III and IV; it is primarily synthesized under optimal growth conditions (19) and is the more efficient of the two oxidases given it acts as a proton pump (18). Alternatively, cytochrome bd oxidase is non-proton pumping and is therefore less efficient, but is thought to have a higher O 2 affinity and is induced during hypoxia (20, 21). Cytochrome aa 3 oxidases are members of the heme-copper oxidase superfamily with binuclear heme-copper active sites that are highly susceptible to inhibition by ligands like CO, nitric oxide (NO), cyanide (CN - ) and hydrogen sulphide (H 2 S) (22).…”

“…Cytochrome aa 3 oxidases are members of the heme-copper oxidase superfamily with binuclear heme-copper active sites that are highly susceptible to inhibition by ligands like CO, nitric oxide (NO), cyanide (CN - ) and hydrogen sulphide (H 2 S) (22). Cytochrome bd oxidases are unrelated to heme-copper oxidases and utilise dual b and d hemes in their active site for O 2 reduction (21). In a number of bacteria, cytochrome bd oxidase is important for resistance to oxidative and nitrosative stress, as well as to NO, CN and H 2 S, suggesting its active site is less susceptible to inhibition by non-O 2 ligands (23-25).…”

The long Q‐loop of Escherichia coli cytochrome bd oxidase is required for assembly and structural integrity

“…). In accordance with the different positions of the dioxygen binding sites, the positions of heme b 595 and d are interchanged in the E. coli enzyme with respect to the G. thermodenitrificans oxidase .…”

“…). Surprisingly, E. coli bd oxidase contains a fourth subunit called either CydY or CydH that is not encoded in the cyd operon but derives from the orphan gene ynhF . CydY is located in a hydrophobic cleft shaped by TM helices 1 and 9 of CydA and is absent in the G. thermodenitrificans enzyme.…”

“…The Q‐loop of CydA is in close proximity to heme b 558 , the primary electron acceptor, implying a function in quinol oxidation . Due to the presence of a short (S) or a long (L) Q‐loop, the family of bd oxidases is classified into the S‐ and L‐subfamilies .…”