Cytochrome caa3, a cytochrome c oxidase from Thermus thermophilus, has been purified and extensively characterized as a two-subunit enzyme containing the metal centers characteristic of cytochrome c oxidases (cytochromes a and a3; copper centers CuA and CuB) and an additional cytochrome c (Fee, J. A., Kuila, D., Mather, M. W., and Yoshida, T. (1986) Biochim. Biophys. Acta 853, 153-185). We have now cloned and sequenced the genes encoding the subunits of this enzyme. The smaller subunit consists of a typical oxidase subunit II sequence fused to a cytochrome c domain (Mather, M. W., Springer, P., and Fee, J. A. (1991) J. Biol. Chem. 266, 5025-5035). The larger subunit, the A-protein, is encoded by a fusion gene lying immediately downstream of the subunit IIc gene. The 5' portion of this gene encodes an oxidase subunit I homolog, whereas the 3' portion is homologous to oxidase subunits III. The A-protein from the purified enzyme appears too small from SDS-polyacrylamide gel electrophoresis and quantitative amino acid analyses to be a complete subunit I/III fusion, but it is currently not known if proteolytic processing occurs. Analyses of the sequences of oxidase subunits are presented which clearly identify T. thermophilus cytochrome caa3 as a bona fide member of the greater family of heme- and copper-requiring oxidases. As one consequence, it is confirmed that the set of invariant histidine residues (potential ligands of the metal centers) in cytochrome c oxidase subunits I and II is reduced to 8. Possible topological and helix packing models are developed based on considerations of homology, hydropathy, and variability.