The mitochondrial ADP/ATP carrier imports ADP from the cytosol and exports ATP from the mitochondrial matrix. The carrier cycles by an unresolved mechanism between the cytoplasmic state, in which the carrier accepts ADP from the cytoplasm, and the matrix state, in which it accepts ATP from the mitochondrial matrix. Here we present the structures of the yeast ADP/ATP carriers Aac2p and Aac3p in the cytoplasmic state. The carriers have three domains and are closed at the matrix side by three interdomain salt-bridge interactions, one of which is braced by a glutamine residue. Glutamine braces are conserved in mitochondrial carriers and contribute to an energy barrier, preventing the conversion to the matrix state unless substrate binding occurs. At the cytoplasmic side a second salt-bridge network forms during the transport cycle, as demonstrated by functional analysis of mutants with charge-reversed networks. Analyses of the domain structures and properties of the interdomain interfaces indicate that interconversion between states involves movement of the even-numbered α-helices across the surfaces of the odd-numbered α-helices by rotation of the domains. The odd-numbered α-helices have an L-shape, with proline or serine residues at the kinks, which functions as a lever-arm, coupling the substrate-induced disruption of the matrix network to the formation of the cytoplasmic network. The simultaneous movement of three domains around a central translocation pathway constitutes a unique mechanism among transport proteins. These findings provide a structural description of transport by mitochondrial carrier proteins, consistent with an alternating-access mechanism.membrane protein | cardiolipin binding | X-ray crystallography | serine kinks | adenine nucleotide translocase M itochondrial carriers are a family of proteins that transport a diverse range of nucleotides, amino acids, inorganic ions, fatty acids, keto acids, and cofactors across the inner mitochondrial membrane (1). The carriers link the biochemical pathways in the cytoplasm with those in the mitochondrial matrix, thereby playing key roles in many aspects of cell physiology. There are many rare, but severe, human diseases associated with defective mitochondrial carriers (2).The ADP/ATP carriers are archetypal members of the mitochondrial carrier family (3). ADP/ATP carriers play the essential role of importing ADP into the mitochondrial matrix, where it can be phosphorylated by ATP synthase, and of exporting newly synthesized ATP into the cytosol, replenishing the cell with metabolic energy. ADP/ATP carriers have been intensively studied, because of their high natural abundance and the availability of specific inhibitors, which lock the carrier in two distinct states. The atractylosides, such as carboxyatractyloside (CATR) (4, 5), lock the carrier in the cytosolic state (c-state) with the substrate-binding site accessible to the intermembrane space, which is confluent with the cytosol. Bongkrekic acid (6) locks the carrier in the matrix state (m-state), wit...

SummaryMitochondrial ADP/ATP carriers transport ADP into the mitochondrial matrix for ATP synthesis, and ATP out to fuel the cell, by cycling between cytoplasmic-open and matrix-open states. The structure of the cytoplasmic-open state is known, but it has proved difficult to understand the transport mechanism in the absence of a structure in the matrix-open state. Here, we describe the structure of the matrix-open state locked by bongkrekic acid bound in the ADP/ATP-binding site at the bottom of the central cavity. The cytoplasmic side of the carrier is closed by conserved hydrophobic residues, and a salt bridge network, braced by tyrosines. Glycine and small amino acid residues allow close-packing of helices on the matrix side. Uniquely, the carrier switches between states by rotation of its three domains about a fulcrum provided by the substrate-binding site. Because these features are highly conserved, this mechanism is likely to apply to the whole mitochondrial carrier family.Video Abstract

The mitochondrial ADP/ATP carrier imports ADP from the cytosol and exports ATP from the mitochondrial matrix, providing key steps in oxidative phosphorylation in eukaryotic organisms. The transport protein belongs to the mitochondrial carrier family, a large transporter family in the inner membrane of mitochondria. It is one of the best studied members of the family and serves as a paradigm for the molecular mechanism of mitochondrial carriers. Structurally, the carrier consists of three homologous domains, each composed of two transmembrane α--helices linked with a loop and short α--helix on the matrix side. The transporter cycles between a cytoplasmic and matrix conformation in which a central substrate binding site is alternately accessible to these compartments for binding of ADP or ATP. On both the cytoplasmic and matrix side of the carrier are networks consisting of three salt bridges each. In the cytoplasmic conformation, the matrix salt bridge network is formed and the cytoplasmic network is disrupted, opening the central substrate binding site to the intermembrane space and cytosol, whereas the converse occurs in the matrix conformation. In the transport cycle, tighter substrate binding in the intermediate states allows the interconversion of conformations by lowering the energy barrier for disruption and formation of these networks, opening and closing the carrier to either side of the membrane in an alternating way. The simultaneous 2 rotation of three domains around a central translocation pathway constitutes a unique mechanism among transport proteins.