Conformational dynamics of the nucleotide binding domains and the power stroke of a heterodimeric ABC transporter

Mishra, Shailendra; Verhalen, Brandy; Stein, Richard A.; Wen, Po‐Chao; Tajkhorshid, Emad; Mchaourab, Hassane S.

doi:10.7554/elife.02740

Cited by 121 publications

(176 citation statements)

References 57 publications

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“…It is commonly thought that homodimeric multi‐drug ABC transporters adopt an outward‐open conformation upon nucleotide binding (Dawson & Locher, 2006; Ward et al , 2007). In contrast, heterodimeric ABC exporters assume this outward‐open conformation upon ATP hydrolysis (in the form of ADP‐VO 4 ; Mishra et al , 2014). McjD is the first report of a homodimeric ABC exporter that does not form a stable wide‐open state on the periplasmic side in the presence of nucleotides.…”

Section: Discussionmentioning

confidence: 99%

Structural basis for antibacterial peptide self‐immunity by the bacterial ABC transporter McjD

et al. 2017

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Certain pathogenic bacteria produce and release toxic peptides to ensure either nutrient availability or evasion from the immune system. These peptides are also toxic to the producing bacteria that utilize dedicated ABC transporters to provide self‐immunity. The ABC transporter McjD exports the antibacterial peptide MccJ25 in Escherichia coli. Our previously determined McjD structure provided some mechanistic insights into antibacterial peptide efflux. In this study, we have determined its structure in a novel conformation, apo inward‐occluded and a new nucleotide‐bound state, high‐energy outward‐occluded intermediate state, with a defined ligand binding cavity. Predictive cysteine cross‐linking in E. coli membranes and PELDOR measurements along the transport cycle indicate that McjD does not undergo major conformational changes as previously proposed for multi‐drug ABC exporters. Combined with transport assays and molecular dynamics simulations, we propose a novel mechanism for toxic peptide ABC exporters that only requires the transient opening of the cavity for release of the peptide. We propose that shielding of the cavity ensures that the transporter is available to export the newly synthesized peptides, preventing toxic‐level build‐up.

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Section: Discussionmentioning

confidence: 99%

Structural basis for antibacterial peptide self‐immunity by the bacterial ABC transporter McjD

et al. 2017

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“…This methodology has been successfully applied to define coupled conformational cycles for a number of transporter classes (13,(26)(27)(28)(29)(30)(31)(32). We find that patterns of distance distributions between pairs of spin labels monitoring the intra-and extracellular sides of Mhp1 are consistent with isomerization between the crystallographic inward-and outward-facing conformations.…”

mentioning

confidence: 86%

Conformational cycle and ion-coupling mechanism of the Na ⁺ /hydantoin transporter Mhp1

Kazmier

Sharma

Islam

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

147

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Ion-dependent transporters of the LeuT-fold couple the uptake of physiologically essential molecules to transmembrane ion gradients. Defined by a conserved 5-helix inverted repeat that encodes common principles of ion and substrate binding, the LeuTfold has been captured in outward-facing, occluded, and inwardfacing conformations. However, fundamental questions relating to the structural basis of alternating access and coupling to ion gradients remain unanswered. Here, we used distance measurements between pairs of spin labels to define the conformational cycle of the Na + -coupled hydantoin symporter Mhp1 from Microbacterium liquefaciens. Our results reveal that the inward-facing and outward-facing Mhp1 crystal structures represent sampled intermediate states in solution. Here, we provide a mechanistic context for these structures, mapping them into a model of transport based on ion-and substrate-dependent conformational equilibria. In contrast to the Na + /leucine transporter LeuT, our results suggest that Na + binding at the conserved second Na + binding site does not change the energetics of the inward-and outward-facing conformations of Mhp1. Comparative analysis of ligand-dependent alternating access in LeuT and Mhp1 lead us to propose that different coupling schemes to ion gradients may define distinct conformational mechanisms within the LeuT-fold class.EPR | DEER | Na + -coupled symport | conformational dynamics | transport mechanism

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“…MsbA is located in the inner membrane of Gram-negative bacteria, where it transports lipid A from the inner to the outer leaflet (9,10). MsbA has been crystallized in inward-and outward-facing conformations (11) and has also been extensively studied by different spectroscopic techniques (12)(13)(14)(15)(16)(17)(18). Several studies point to large motions between the nucleotide-free "open" inward-facing conformation (NBDs separated by tens of Angstroms) and the ATP-bound "closed" outward-facing conformation (tightly associated NBDs).…”

Section: Atp-binding Cassette (Abc)mentioning

confidence: 99%

The Lipid Bilayer Modulates the Structure and Function of an ATP-binding Cassette Exporter

Zoghbi

Cooper

Altenberg

2016

Journal of Biological Chemistry

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ATP-binding cassette exporters use the energy of ATP hydrolysis to transport substrates across membranes by switching between inward-and outward-facing conformations. Essentially all structural studies of these proteins have been performed with the proteins in detergent micelles, locked in specific conformations and/or at low temperature. Here, we used luminescence resonance energy transfer spectroscopy to study the prototypical ATP-binding cassette exporter MsbA reconstituted in nanodiscs at 37°C while it performs ATP hydrolysis. We found major differences when comparing MsbA in these native-like conditions with double electron-electron resonance data and the crystal structure of MsbA in the open inward-facing conformation. The most striking differences include a significantly smaller separation between the nucleotide-binding domains and a larger fraction of molecules with associated nucleotide-binding domains in the nucleotide-free apo state. These studies stress the importance of studying membrane proteins in an environment that approaches physiological conditions. ATP-binding cassette (ABC)2 transporters constitute one of the largest families of membrane proteins and are found in all domains of life (1-3). They can be either importers (most prokaryote ABC transporters) or exporters (most mammal ABC transporters) (1-3). The core structure of ABC proteins consists of two transmembrane domains that form the translocation pathway and two conserved nucleotide-binding domains (NBDs) that bind and hydrolyze ATP (1-3), a process essential for their function. Binding of ATP promotes the formation of an NBD dimer in a head to tail orientation (4, 5). In the resulting structure two ATP molecules are "sandwiched" at the dimer interface, and residues from both NBDs form each of the two nucleotide-binding sites (1, 4, 5). NBD dimerization is essential for ATP hydrolysis and requires ATP binding to both nucleotide-binding sites (6), whereas dissociation of the dimers occurs following hydrolysis at only one of the two sites (7). This ATP-dependent NBDs dimerization/dissociation process is coupled to rearrangements of the transmembrane helices, switching the transporters from an inward-facing conformation (dissociated NBDs) to an outward-facing conformation (dimeric NBDs), with the concomitant translocation of substrate (1, 3).Two of the most studied ABC exporters are the multidrug resistance protein P-glycoprotein (MDR1 and ABCB1) that plays a role in the resistance to chemotherapy of some forms of cancer (3),and its bacterial homolog, the lipid flippase MsbA (8). MsbA is located in the inner membrane of Gram-negative bacteria, where it transports lipid A from the inner to the outer leaflet (9, 10). MsbA has been crystallized in inward-and outward-facing conformations (11) and has also been extensively studied by different spectroscopic techniques (12-18). Several studies point to large motions between the nucleotide-free "open" inward-facing conformation (NBDs separated by tens of Angstroms) and the ATP-bound "closed" outw...

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Conformational dynamics of the nucleotide binding domains and the power stroke of a heterodimeric ABC transporter

Cited by 121 publications

References 57 publications

Structural basis for antibacterial peptide self‐immunity by the bacterial ABC transporter McjD

Structural basis for antibacterial peptide self‐immunity by the bacterial ABC transporter McjD

Conformational cycle and ion-coupling mechanism of the Na ⁺ /hydantoin transporter Mhp1

The Lipid Bilayer Modulates the Structure and Function of an ATP-binding Cassette Exporter

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Conformational dynamics of the nucleotide binding domains and the power stroke of a heterodimeric ABC transporter

Cited by 121 publications

References 57 publications

Structural basis for antibacterial peptide self‐immunity by the bacterial ABC transporter McjD

Structural basis for antibacterial peptide self‐immunity by the bacterial ABC transporter McjD

Conformational cycle and ion-coupling mechanism of the Na + /hydantoin transporter Mhp1

The Lipid Bilayer Modulates the Structure and Function of an ATP-binding Cassette Exporter

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Conformational cycle and ion-coupling mechanism of the Na ⁺ /hydantoin transporter Mhp1