Similarity of cytochrome c oxidases in different organisms

Abstract

Most of biological oxygen reduction is catalyzed by the heme-copper oxygen reductases. These enzymes are redox-driven proton pumps that take part in generating the proton gradient in both prokaryotes and mitochondria that drives synthesis of ATP. The enzymes have been divided into three evolutionarily-related groups: the A-, B-, and C-families. Recent comparative studies suggest that all oxygen reductases perform the same chemistry for oxygen reduction and comprise the same essential elements of the proton pumping mechanism, such as the proton loading and kinetic gating sites, which, however, appear to be different in different families. All species of the A-family, however, demonstrate remarkable similarity of the central processing unit of the enzyme, as revealed by their recent crystal structures. Here we demonstrate that cytochrome c oxidases (CcO) of such diverse organisms as a mammal (bovine heart mitochondrial CcO), photosynthetic bacteria (Rhodobacter sphaeroides CcO), and soil bacteria (Paracoccus denitrificans CcO) are not only structurally similar, but almost identical in microscopic electrostatics and thermodynamics properties of their key amino-acids. By using pK(a) calculations of some of the key residues of the catalytic site, D- and K- proton input, and putative proton output channels of these three different enzymes, we demonstrate that the microscopic properties of key residues are almost identical, which strongly suggests the same mechanism in these species. The quantitative precision with which the microscopic physical properties of these enzymes have remained constant despite different evolutionary routes undertaken is striking.

Fig.1

(A) The key structural elements of the proposed pumping mechanism of CcO and the sequence of transitions during one pumping cycle. Two protonation sites, PLS and one in BNC, are shown as H-circles. PT and ET steps are shown by blue and red arrows, respectively. (B) The schematics of the model. The key assumption of the model is that the proton transfer rate upon ET between the hemes (step 2) is much higher along the pumping channel 3 than along the chemical channel 5, in other words step 3 occurs before step 5.

Fig.2

Location of key residues in bovine cytochrome c oxidase. The residues are mainly distributed in subunit A, but those located in subunit B are marked with the letter “B” at the end of its label. D- and K-channel residues are shown in blue and brown color, respectively. Possible key residues of exit pathways are in purple color. Ligands of Cu_B co-factor are in red color and the hemes along with the salt-bridged Arginines are shown in cyan color.

Fig.3

Superimposed CcO Catalytic Centers: Bovine (red), R. sphaeroides (blue), P. denitrificans (cyan). The key residue labels correspond to the bovine structure. The structure matching has been done by VMD program and corresponds to the best fitting of heme porphyrin rings.