ABSTRACT The alternative oxidase (AOX) is a member of the family of di-iron proteins, in which the catalytic centre consists of a pair of iron atoms ligated by carboxylate (aspartate and glutamate) and histidine ligands within a four helix bundle. Recently sequenced bacterial AOXs are homologues of the rubrerythrin domains of rubrerythrin and nigerythrin and so the crystal structure of Desulfovibrio vulgaris rubrerythrin (PDB accession code 1S2Z) was used as the basis for a simple model of AOX. The putative iron ligands were identified by analysis of their distribution in other di-iron proteins and protein sequence analysis and the putative quinone binding site was identified by sequence analysis. The pattern of hydropathy of the four helices implies that AOX is partially embedded in the membrane and that the quinone binding site is located on the most hydrophobic helix opposite residues associated with mutations conferring inhibitor resistance. These results may be used for further analysis using structure prediction software and subsequent site-directed mutagenesis of the putative quinone binding site, the aspartate residue involved in stabilising the di-iron histidine ligands and other physically significant residues. http://www.ijbst.org/Home/papers-published/ijbst-2009-volume-2-issue-9