Conformation of peptides bound to the transporter associated with antigen processing (TAP)

Herget, Meike; Baldauf, Christoph; Schölz, Christian; Parcej, David; Wiesmüller, Karl‐Heinz; Tampé, Robert; Abele, Rupert; Bordignon, Enrica

doi:10.1073/pnas.1012355108

Cited by 51 publications

(78 citation statements)

References 28 publications

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“…The presented work offers a structural rationale for future studies on mammalian ABC exporters with asymmetric ATP-binding sites including the medically important transporters MRP1, SUR1, TAP1/2, and CFTR (33)(34)(35)(36).…”

Section: Discussionmentioning

confidence: 99%

Structural basis for allosteric cross-talk between the asymmetric nucleotide binding sites of a heterodimeric ABC exporter

Höhl

Hürlimann

Böhm

et al. 2014

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

Self Cite

110

153

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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...

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Section: Discussionmentioning

confidence: 99%

Structural basis for allosteric cross-talk between the asymmetric nucleotide binding sites of a heterodimeric ABC exporter

Höhl

Hürlimann

Böhm

et al. 2014

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

Self Cite

110

153

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“…Peptide binding to the ATP-binding cassette (ABC) transporter associated with antigen processing (TAP) was studied with peptides with a length of 7, 9, and 15 residues that were labeled with iodo-acetamido proxyl at the second and second-to-last residue (127). TAP binds peptides with a length of 8-16 residues with comparable affinity.…”

Section: Conformational Changesmentioning

confidence: 99%

DEER Distance Measurements on Proteins

Jeschke

2012

Annu. Rev. Phys. Chem.

921

1,073

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Distance distributions between paramagnetic centers in the range from 1.8 to 6 nm in membrane proteins and up to 10 nm in deuterated soluble proteins can be measured by the DEER technique. The number of paramagnetic centers and their relative orientation can be characterized. DEER does not require crystallization and is not limited with respect to the size of the protein or protein complex. Diamagnetic proteins are accessible by site-directed spin labeling. To characterize structure or structural changes, the experimental protocols were optimized and techniques for artifact suppression were introduced. Data analysis programs were developed and it was realized that interpretation of the distance distributions must take into account the conformational distribution of spin labels. First methods have appeared for deriving structural models from a small number of distance constraints. The current scope and limitations of the technique are illustrated.

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“…peptides of 8 to 40 residues, into the lumen of the endoplasmic reticulum for loading onto MHC class I molecules. EPR spectroscopy and simulations based on a rotamer library were used to reveal conformational details about the bound peptides (Herget et al, 2011). …”

Section: Conformation Of Peptides Bound To Tapmentioning

confidence: 99%

“…Site-Directed Spin Labeling and Electron Paramagnetic Resonance (EPR) Spectroscopy: A Versatile Tool to Study Protein-Protein Interactions 441 the authors to the conclusion that peptides bind to TAP in an extended kinked structure, analogous to those bound to MHC class I proteins (Herget et al, 2011).…”

mentioning

confidence: 99%

Site-Directed Spin Labeling and Electron Paramagnetic Resonance (EPR) Spectroscopy: A Versatile Tool to Study Protein-Protein Interactions

Klare¹

2012

Protein Interactions

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Conformation of peptides bound to the transporter associated with antigen processing (TAP)

Cited by 51 publications

References 28 publications

Structural basis for allosteric cross-talk between the asymmetric nucleotide binding sites of a heterodimeric ABC exporter

Structural basis for allosteric cross-talk between the asymmetric nucleotide binding sites of a heterodimeric ABC exporter

DEER Distance Measurements on Proteins

Site-Directed Spin Labeling and Electron Paramagnetic Resonance (EPR) Spectroscopy: A Versatile Tool to Study Protein-Protein Interactions

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