The budding yeast Saccharomyces cerevisiae contains two homologues of bacterial IscA proteins, designated Isa1p and Isa2p. Bacterial IscA is a product of the isc (iron-sulfur cluster) operon and has been suggested to participate in Fe-S cluster formation or repair. To test the function of yeast Isa1p and Isa2p, single or combinatorial disruptions were introduced in ISA1 and ISA2. The resultant isa⌬ mutants were viable but exhibited a dependency on lysine and glutamate for growth and a respiratory deficiency due to an accumulation of mutations in mitochondrial DNA. As with other yeast genes proposed to function in Fe-S cluster assembly, mitochondrial iron concentration was significantly elevated in the isa mutants, and the activities of the Fe-S cluster-containing enzymes aconitase and succinate dehydrogenase were dramatically reduced. An inspection of Isa-like proteins from bacteria to mammals revealed three invariant cysteine residues, which in the case of Isa1p and Isa2p are essential for function and may be involved in iron binding. As predicted, Isa1p is targeted to the mitochondrial matrix. However, Isa2p is present within the intermembrane space of the mitochondria. Our deletion analyses revealed that Isa2p harbors a bipartite N-terminal leader sequence containing a mitochondrial import signal linked to a second sequence that targets Isa2p to the intermembrane space. Both signals are needed for Isa2p function. A model for the nonredundant roles of Isa1p and Isa2p in delivering iron to sites of the Fe-S cluster assembly is discussed.Iron-sulfur (Fe-S) cluster prosthetic groups play a key role in a wide range of enzymatic reactions, as well as serving as regulatory switches. Key enzymes containing Fe-S clusters include aconitase and succinate dehydrogenase (SDH) in the tricarboxylic acid cycle, the Rieske iron-sulfur protein in the respiratory chain, homoaconitase, which is required for fungal lysine biosynthesis, the nitrogenase iron protein involved in nitrogen fixation, and iron-responsive element binding protein 1, which regulates ferritin and transferrin receptor production in mammals (4,22,32,36,37).The formation of Fe-S clusters has been most thoroughly studied in the case of nitrogenase from the nitrogen-fixing bacterium Azotobacter vinelandii (56). The proteins responsible for the synthesis, maturation, and regulation of nitrogenase are encoded by genes present on the nif operon (19). Two proteins implicated in biosynthesis of the nitrogenase Fe-S cluster include NifS and NifU (19). NifS is a cysteine desulfurase that produces the inorganic sulfide for the cluster (57), whereas NifU is speculated to participate in Fe mobilization for the Fe-S cofactor (11,54,55). An additional protein encoded by nif, Orf6, may also be involved in assembly of the nitrogenase cluster, although its precise role is unknown.The recently identified iscSUA-hscBA-fdx operon from A. vinelandii contains genes exhibiting strong homology to nifS, nifU, and orf6 (55). Additionally, this operon encodes the molecular chaperones Hs...