A novel, large-scale method for the purification of cytochrome-c oxidase from the yeast Saccharomyces cerevisiae is described. The isolation procedure gave highly pure and active enzyme at high yields. The purified enzyme exhibited a heme dprotein ratio of 9.1 nmoVmg and revealed twelve protein bands after Tricine/SDSPAGE. N-terminal sequencing showed that eleven of the corresponding proteins were identical to those recently described by Taanman and Capaldi [Taanman, J.-W. & Capaldi, R. A. (1992) J. Biol. Chem. 267, 22481-2248.51. 15 of the N-terminal residues of the 12th band were identical to subunit VIII indicating that this band represents a dimer of subunit VIII (Mr 5364). We conclude that subunit XI1 postulated by Taanman and Capaldi is the subunit VIII dimer and that cytochrome-c oxidase contains eleven rather than twelve subunits.We obtained the complete sequence of subunit VIa by Edman degradation. The protein contains more than 25 % of charged amino acids and hydropathy analysis predicts one membrane-spanning helix.The purified enzyme had a turnover number of 1500 s-' and the ionic-strength dependence of the K, value for cytochrome-c was similar to that described for other preparations of cytochrome-c oxidase. This was al:io true for the cyanide-binding characteristics of the preparation. When the enzyme was isolated in the presence of chloride, more than 90% of the preparation showed fast cyanide-binding kinetics and was resistant to formate incubation, indicating that chloride was bound to the binuclear center. When the enzyme was isolated in the absence of chloride, approximately 70% of the preparation was in the fast form. This high content of fast enzyme was also reflected in the characteristics of optical and EPR spectra for cytochrome-c oxidase purified with our method.Keywo,rds. Cytochrome-c oxidase ; Saccharomyces cerevisiae ; mitochondria ; subunit composition.Cytochronie-c oxidase is the terminal enzyme of the mitochondrial electron-transfer chain catalyzing reduction of oxygen to water [l], The three largest subunits of the eukaryotic enzyme are encoded by mitochondria1 DNA and form the functional core, as they contain all redox centers and are homologous to the subunits of bacterial oxidases [2]. Two hemes (a and a,) and Cu, are ligated by subunit I and the Cu, center is ligated by subunit I1 [3 -51. In addition mitochondria1 cytochrome-c oxidases consists of up to ten nuclear-coded subunits [6]. Most preparations of Saccharomyces cerevisiae cytochroine-c oxidase contain only six nuclear-coded subunits [7], but recently three more bands were identified by SDSPAGE in a small-scale preparation using dodecyl maltoside as a detergent by Taanman and Capaldi [8]. Two o€ the additional bands could be sequenced and turned out to be the homologs to subunits VIa [9] and VIb [lo] of the bovine enzyme. The third band migrated too close to subunit VI to he sequenced in the 21% polyacrylamide Laemmli gel used by these authors [8]. In this study we describe a large-scale preparation for yeast cytochrome...