ATP binding cassette (ABC) transporters mediate vital transport processes in every living cell. ATP hydrolysis, which fuels transport, displays positive cooperativity in numerous ABC transporters. In particular, heterodimeric ABC exporters exhibit pronounced allosteric coupling between a catalytically impaired degenerate site, where nucleotides bind tightly, and a consensus site, at which ATP is hydrolyzed in every transport cycle. Whereas the functional phenomenon of cooperativity is well described, its structural basis remains poorly understood. Here, we present the apo structure of the heterodimeric ABC exporter TM287/288 and compare it to the previously solved structure with adenosine 5′-(β,γ-imido)triphosphate (AMP-PNP) bound at the degenerate site. In contrast to other ABC exporter structures, the nucleotide binding domains (NBDs) of TM287/288 remain in molecular contact even in the absence of nucleotides, and the arrangement of the transmembrane domains (TMDs) is not influenced by AMP-PNP binding, a notion confirmed by double electron-electron resonance (DEER) measurements. Nucleotide binding at the degenerate site results in structural rearrangements, which are transmitted to the consensus site via two D-loops located at the NBD interface. These loops owe their name from a highly conserved aspartate and are directly connected to the catalytically important Walker B motif. The D-loop at the degenerate site ties the NBDs together even in the absence of nucleotides and substitution of its aspartate by alanine is well-tolerated. By contrast, the D-loop of the consensus site is flexible and the aspartate to alanine mutation and conformational restriction by cross-linking strongly reduces ATP hydrolysis and substrate transport.membrane transport | X-ray crystallography | allosteric communication A BC exporters are found in every organism (1, 2). They minimally consist of four domains and exist as homodimers or heterodimers. Two transmembrane domains (TMDs) span the membrane with a total of 12 transmembrane helices and form the substrate permeation pathway by alternating between inward-and outward-oriented states (Fig. S1A). A pair of nucleotide binding domains (NBDs) is connected to the TMDs via coupling helices and drive conformational cycling of the transporter by binding and hydrolysis of ATP, a process which is linked to NBD dimerization and dissociation (3).In their closed state, the NBDs sandwich two ATP molecules at the dimer interface by composite ATP binding sites involving conserved sequence motifs contributed by both subunits (4, 5). The A-loop and Walker A motif of one NBD and the ABC signature motif of the opposite NBD are involved in nucleotide binding. The Walker B glutamate and the switch-loop histidine constitute a catalytic dyad required for ATP hydrolysis (6, 7). In heterodimeric ABC exporters with asymmetric ATP binding sites, these catalytic residues are noncanonical at the degenerate site and ATP is therefore primarily, if not exclusively, hydrolyzed at the consensus site (8). The Q-and D...

ABC exporters pump substrates across the membrane by coupling ATP-driven movements of nucleotide binding domains (NBDs) to the transmembrane domains (TMDs), which switch between inward- and outward-facing (IF, OF) orientations. DEER measurements on the heterodimeric ABC exporter TM287/288 from Thermotoga maritima, which contains a non-canonical ATP binding site, revealed that in the presence of nucleotides the transporter exists in an IF/OF equilibrium. While ATP binding was sufficient to partially populate the OF state, nucleotide trapping in the pre- or post-hydrolytic state was required for a pronounced conformational shift. At physiologically high temperatures and in the absence of nucleotides, the NBDs disengage asymmetrically while the conformation of the TMDs remains unchanged. Nucleotide binding at the degenerate ATP site prevents complete NBD separation, a molecular feature differentiating heterodimeric from homodimeric ABC exporters. Our data suggest hydrolysis-independent closure of the NBD dimer, which is further stabilized as the consensus site nucleotide is committed to hydrolysis.DOI: http://dx.doi.org/10.7554/eLife.20236.001

Background: ABC exporters are suggested to hydrolyze ATP sequentially implying the existence of asymmetries. Results: An in vitro selected binder (DARPin) was identified that binds to homodimeric MsbA at a stoichiometric ratio of 1:1. Conclusion:The DARPin recognizes asymmetries in MsbA. Significance: Selected binding proteins are useful tools to recognize membrane transporters in novel conformational states.

ATP-binding cassette (ABC) transporters couple the translocation of solutes across membranes to ATP hydrolysis. Crystal structures of the Escherichia coli maltose importer (MalFGK 2 ) in complex with its substrate binding protein (MalE) provided unprecedented insights in the mechanism of substrate translocation, leaving the MalE-transporter interactions still poorly understood. Using pulsed EPR and cross-linking methods we investigated the effects of maltose and MalE on complex formation and correlated motions of the MalK 2 nucleotide-binding domains (NBDs A TP-binding cassette (ABC) systems are found in all kingdoms of life, forming one of the largest protein superfamilies (1-4). ABC transporters comprise two transmembrane domains (TMDs) that form the translocation pathway and two nucleotide-binding domains (NBDs) that bind and hydrolyze ATP. Based on biochemical and structural evidence, all ABC transporters are thought to function by an "alternate-access" mode, with the translocation path shuttling between an inward-facing and outward-facing conformation in response to substrate and ATP binding, the latter causing the NBD dimer to close (5).Canonical ABC importers are subdivided into type I and type II based on structural and biochemical evidence (6) and are dependent on extracellular (or periplasmic) substrate binding proteins (SBPs) (4), which play a crucial role in initial steps of the transport cycle (7-10). SBPs generally consist of two symmetrical lobes that rotate toward each other upon substrate binding (11).The type I maltose transporter of Escherichia coli/Salmonella is probably the best understood ABC transporter to date (12). It is composed of the periplasmic maltose binding protein, MalE, the membrane-integral subunits, MalF and MalG, and the nucleotidebinding subunits (NBDs), MalK 2 . The available crystal structures in the pretranslocation, ATP-, and vanadate-trapped states (13-16) have largely contributed to the understanding of the details of the inward-to outward-facing mechanism. The posthydrolytic state has not yet been crystallized, but data exist proposing this state to have a distinct structure from the other three known crystal snapshots (8, 9). MalE interacts with the transporter throughout the nucleotide cycle (15-18), and the X-ray structures revealed the switch of the binding protein from the liganded (closed) to the substrate-free (open) conformation concomitantly with ATP binding to the NBDs. Despite all these structural insights, the response of the transporter to substrate availability is poorly understood. Furthermore, the mechanism behind the stimulation of the ATPase activity of the transporter by unliganded MalE (10, 19) is still elusive (20,21).Our results show that the apo-and ADP-states of the transporter bind both open and closed MalE, but the complex adopts different periplasmic configurations. The ATP-state of the transporter can bind either closed MalE, inducing its opening and release of substrate to MalF or directly unliganded MalE, which generates a futile cycle. I...