Cytochrome c oxidase, the terminal enzyme of the respiratory chains of mitochondria and aerobic bacteria, catalyzes electron transfer from cytochrome c to molecular oxygen. The enzyme belongs to the haem-copper-containing oxidases superfamily.

Burkholderia pseudomallei is the causative agent of melioidosis, a serious disease of humans and animals that occurs primarily in South East Asia, Northern Australia and other tropical areas. In this study, recombinant plasmid carrying a 2.0 kb insert DNA from a Burkholderia pseudomallei genomic DNA library was subjected to automated DNA sequencing. The resulting sequence was analysed and was found to have a 1536 bp open reading frame. This sequence was predicted to encode a putative cytochrome c oxidase.

Further analysis using sequence alignments and tertiary structure analysis tools demonstrated that the hypothetical B. pseudomallei cytochrome c oxidase is similar to cytochrome c oxidases from other organisms such as Thermus thermophilus (36% protein sequence identity), Paracoccus denitrificans and bovine heart mitochondrial, the latter two which crystal structures available. The deduced 512 residue protein sequence includes the six canonical histidine residues involved in binding the low spin heme B and the binuclear center Cu_B/hemeA.

A protein structure model was predicted for the putative gene using comparative modelling methods. This technique of modelling called comparative or homology modelling is based upon the knowledge that sequence similarity can translate to possible conservation of functional structures (structurally conserved regions). The cytochrome c oxidase protein sequence was designated as the target sequence and compared against a database of known structures. A protein structure with significant sequence identity was chosen as a template structure. The tertiary structure coordinates are then transferred from the template to the target. The regions of the target sequence which do not have sequence identity with the template, or structurally variable regions, are then refined. The predicted tertiary structure of the hypothetical protein is consistent with previous models of electron transfer for cytochrome c oxidase. Therefore, a target sequence with relatively low sequence identity to a template sequence (36%), was able to be identified and its function and possible mechanisms explained using purely in-silico or computational methods.