The Candida albicans CDR1 and CDR2 genes code for highly homologous ATP-binding cassette (ABC) transporters which are overexpressed in azole-resistant clinical isolates and which confer resistance to multiple drugs by actively transporting their substrates out of the cells. These transporters are formed by two homologous halves, each with an intracellular domain containing an ATP-binding site followed by a membrane-associated domain. We have expressed Cdr1p and Cdr2p in Saccharomyces cerevisiae to investigate their functions. The two proteins were properly expressed and functional, as determined by Western blotting, drug susceptibility assays, and rhodamine efflux. Using total membrane proteins from these transformants, we showed that Cdr1p and Cdr2p bind to the photoreactive analogue of rhodamine 123, [125 I]iodoaryl azidorhodamine 123 (IAARh123). IAARh123 photoaffinity labeling of membranes prepared from cells expressing either the N half or the C half of Cdr2p, or both, demonstrated that both halves contribute to rhodamine binding and can bind to rhodamine independently. Interestingly, Cdr1p was found to confer hypersusceptibility to FK520, an immunosuppressant and antifungal agent, whereas Cdr2p conferred resistance to this compound, uncovering a major functional difference between the two transporters. Furthermore, when administered in combination with azoles, FK520 sensitized cells expressing CDR1 but not those expressing CDR2. Finally, we showed that Cdr2p confers hypersusceptibility to hydrogen peroxide and resistance to diamide, while Cdr1p has no effect against these oxidative agents. Taken together, our results demonstrate that, despite a high level of structural conservation, Cdr1p and Cdr2p exhibit major functional differences, suggesting distinct biological functions.Multidrug resistance (MDR) or pleiotropic drug resistance (PDR) is characterized by cellular cross-resistance to a broad spectrum of structurally and functionally unrelated cytotoxic compounds. It operates in a wide variety of cell types and involves the overexpression of membrane-associated transporters functioning as drug efflux pumps. Many of these transporters belong to the ATP-binding cassette (ABC) superfamily and contain highly conserved consensus sequences for ATP binding and hydrolysis (34). Well-characterized ABC transporters involved in MDR in mammalian cells include P glycoprotein type 1 (P-gp1) and the MDR-associated protein type 1 (MRP1), whose overexpression causes resistance to several anticancer drugs (2, 35). In the yeast Saccharomyces cerevisiae, overexpression of the ABC transporters Pdr5p and Snq2p has been shown to confer resistance to several different compounds with antifungal activities (6). Pdr5p and Snq2p are homologous proteins formed by two similar halves, each with an N-terminal hydrophilic domain that contains the ABC motif followed by a C-terminal hydrophobic domain with six predicted transmembrane (TM) segments, a structure characteristic of the PDR subfamily of ABC transporters ([ABC-TM] 2 ) (14, 67). ...