-ray structure of the dimeric cytochrome bc1 complex from the soil bacterium Paracoccus denitrificans at 2.7-Å resolution

The respiratory cytochrome bc₁ complex is a fundamental enzyme in biological energy conversion. It couples electron transfer from ubiquinol to cytochrome c to generation of proton motive force which fuels ATP synthesis. The complex from the α-proteobacterium P. denitrificans, a model for the medically relevant mitochondrial complexes, lacked structural characterization. Here we show by LILBID mass spectrometry that truncation of the organism-specific, acidic N-terminus of cytochrome c₁ changes the oligomerization state of the enzyme to a dimer. The fully functional complex was crystallized and the X-ray structure determined at 2.7-Å resolution. It has high structural homology to mitochondrial complexes and to the Rhodobacter sphaeroides complex especially for subunits cytochrome b and ISP. Species-specific binding of the inhibitor stigmatellin is noteworthy. Interestingly, cytochrome c₁ shows structural differences even between the two Rhodobacteraceae complexes. A diverse cytochrome c₁ surface faces the ISP domain indicating that no specific docking interface is required for this electron transfer step. Anchoring points of the acidic N-termini of cytochrome c₁ and yeast subunit QCR6p on the same side of the core domain of cytochrome c₁ support their similar function. A model of the electron transfer complex with membrane-anchored cytochrome c₅₅₂, the natural substrate, shows that it can adopt the same orientation as the soluble substrate in the yeast complex. The full structural integrity of the P. denitrificans variant underpins previous mechanistic studies on intermonomer electron transfer and paves the way for using this model system to address open questions of structure/function relationships and inhibitor binding.