Discussion

Proteins’ functions are more closely related to their three-dimensional structure than to their amino acid sequence; therefore a structural comparison of the respiratory enzymes is crucial in understanding the molecular evolution of NORs and COXs.

Common NOR structure

• Calcium ion bridging heme b and b3 is common to the NORs
• Calcium ion found in P.aeruginosa cNOR was found in the same position and with the same ligands as in the qNOR.
• The Glu429 ligand in qNOR is one of the five conserved and functionally important glutamate residues in the NOR family. 

The diagram above shows the common structure of cNOR with NorC being coloured in blue and NorB in green. Calcium is coloured in red, and from images under "structure" you can see that this is in the same position as in qNOR. 

cbb₃ oxidase

·         Has the same position of the calcium ion which is present in the NORs, and the environment of the calcium ion is also similar.

Aerobic COXs (A- and B-type oxidases)

• These don’t have the calcium ion; it is replaced by positively charged groups from two conserved arginine residues.
• It is therefore probable to say that the COXs are evolutionary distinct from the cbb₃ oxidases and NORs. 
• This is consistent with their functional aspects: NOR has some O₂ reduction activity, and cbb₃oxidase has some NO reduction activity, whereas the A- and B-type oxidases show little or no NO reduction activity.

Structural comparison of the hydrophilic domains

·         In the A- and B-type oxidase, the hydrophilic domain of subunit II is the cupredoxin fold, whereas in NORs and cbb₃ oxidase, their hydrophilic domains shows a cyt-c fold.

      From the table below, I have boxed some of the structural similarities. And concluding from this table, it is likely that cNOR has more evolutionary links with both qNOR and the cbb₃ oxidase but that qNOR and cbb₃ are not directly related.

( http://www.ncbi.nlm.nih.gov/pubmed/22266822

A qNOR-like enzyme has been found

• Can catalyse the formation of N₂ to O₂ from 2NO, was discovered in an the bacteria Candidatus Methylomirabilis oxyfera showing nitrite driven anaerobic methane oxidation, and it is an important target for finding out the evolution of the bioenergetics system.
• Because nitrogen oxides were already present on early Earth, the findings of Katharina F. Ettwig et al. opens up the possibility that oxygen was available to microbial metabolism before the evolution of oxygenic photosynthesis. (http://www.nature.com/nature/journal/v464/n7288/full/nature08883.html)