The mitochondrial ADP/ATP carrier (AAC), which has six transmembrane regions (TM) with cytosolic N- and C-termini, exchanges matrix ATP for cytosolic ADP in the mitochondrial inner membrane. Structural aspects of the bovine type 1 AAC (bAAC1) and the yeast type 2 AAC (yAAC2) are quite similar, whereas the molecular activity of yAAC2 is four times higher than that of bAAC1. To examine the relationship between the structure and the functional difference, substrate transport activities of serial chimeric proteins having N-terminal bAAC1 and C-terminal yAAC2 were estimated from growth activities of their yeast transformants on a medium containing non-fermentable glycerol. The chimera having the boundary of bAAC1 and yAAC2 between a TM and its C-terminal adjoining loop had activity, but chimera having the boundary between a TM and its N-sided loop did not. These results indicate that a set of a TM and its C-sided loop is important to the AAC function. In addition, the mutant, in which the first TM and its C-sided loop (the first matrix loop) in yAAC2 are replaced with those of bAAC1, exhibited a change in reactivity for a SH cross-linking reagent copper-o-phenanthroline, suggesting that the interaction of these regions is also involved in the structural feature of AAC. Because the mutant had similar transport activities to bAAC1, the structural property provided by the interaction between the first TM and the first matrix loop is probably involved in activity of AAC.