The structures of mitochondrial transporters and uncoupling proteins are 3-fold pseudosymmetrical, but their substrates and coupling ions are not. Thus, deviations from symmetry are to be expected in the substrate and ion-binding sites in the central aqueous cavity. By analyzing the 3-fold pseudosymmetrical repeats from which their sequences are made, conserved asymmetric residues were found to cluster in a region of the central cavity identified previously as the common substrate-binding site. Conserved symmetrical residues required for the transport mechanism were found at the water-membrane interfaces, and they include the three PX T he members of the mitochondrial transporter or carrier family translocate nucleotides, amino acids, inorganic ions, keto acids, and vitamins across the mitochondrial inner membrane (1, 2). Uncoupling proteins, which generate heat by dissipating the proton electrochemical gradient, also belong to the family (3-5). The amino acid sequences have 3 homologous repeats (6) and a structure with pseudosymmetry (7). Each repeat is folded into 2 transmembrane ␣-helices linked by a short ␣-helix on the matrix side (8) and contains the signature motif PX[DE]XX[RK] (9). The proline residues kink the oddnumbered transmembrane ␣-helices H1, H3, and H5, and the charged residues form a salt-bridge network connecting the C-terminal end of the transmembrane ␣-helices, closing the transporter on the matrix side (8). During the transport cycle, the carriers form the cytoplasmic and matrix states in which the substrate-binding site of the carrier is open to the mitochondrial intermembrane space and matrix, respectively (10). According to the single binding center-gating pore mechanism, interconversion of the 2 conformational states via a transition intermediate leads to substrate translocation (11). In agreement, in the cytoplasmic state, a central substrate-binding site has been identified by applying chemical and distance constraints to comparative models (12, 13). The substrates bind to 3 major sites on the even-numbered ␣-helices, which are related by symmetry and located approximately in the middle of the membrane. In molecular dynamics simulations, ADP binds to the ADP/ATP carrier at the common substrate-binding site (14). The structural changes required for the translocation of the substrate are unknown, but docking of the substrate could disrupt the matrix salt bridge network, allowing the transporter to convert to the matrix state (12, 13). The yeast ADP/ATP carriers function as monomers (15), and other mitochondrial transporters are likely to operate in the same way.Residues that are important for the transport mechanism are likely to be symmetrical, whereas residues involved in substrate binding will be asymmetrical reflecting the asymmetry of the substrates. By scoring the symmetry of residues in the sequence repeats, we have identified the substrate-binding sites and salt bridge networks that are important for the transport mechanism in family members. No preexisting molecular structure i...