PDBsum entry 2ixf

Hydrolase

PDB id: 2ixf

Contents

Protein chains

255 a.a.

Ligands

ATP ×4

GOL ×5

Metals

_MG ×4

Waters ×968

References listed in PDB file

Key reference

Title

Distinct structural and functional properties of the atpase sites in an asymmetric abc transporter.

Authors

E.Procko, I.Ferrin-O'Connell, S.L.Ng, R.Gaudet.

Ref.

Mol Cell, 2006, 24, 51-62. [DOI no: 10.1016/j.molcel.2006.07.034]

PubMed id

17018292

Abstract

The ABC transporter associated with antigen processing (TAP) shuttles cytosolic peptides into the endoplasmic reticulum for loading onto class I MHC molecules. Transport is fueled by ATP binding and hydrolysis at two distinct cytosolic ATPase sites. One site comprises consensus motifs shared among most ABC transporters, while the second has substituted, degenerate motifs. Biochemical and crystallography experiments with a TAP cytosolic domain demonstrate that the consensus ATPase site has high catalytic activity and facilitates ATP-dependent dimerization of the cytosolic domains, which is an important conformational change during transport. In contrast, the degenerate site is defective in dimerization and ATP hydrolysis. Full-length TAP mutagenesis demonstrates the necessity for at least one consensus site, supporting our conclusion that the consensus site is the principal facilitator of substrate transport. Since asymmetry of the ATPase site motifs is a feature of many mammalian homologs, our proposed model has broad implications for ABC transporters.

Figure 3.
Figure 3. Crystal Structures of Three TAP1-NBD Constructs with ATP
(A) TAP1-NBD D→N·ATP is a dimer with two ATP-Mg^2+ at the interface. The two NBDs, colored light and dark blue, are viewed from the TMDs looking down onto the NBDs. Important functional motifs are highlighted in one active site.
(B) NBDs from the three structures were superimposed via their ATPase subdomains (lighter shades). This demonstrates rigid-body motions of the helical subdomain (darker shades).
(C and D) σA-weighted 2F[o]–F[c] map, contoured at 1.3 σ, for the consensus (TAP1-NBD D→Q/Q→H) (C) and hybrid (TAP1-NBD D→N) (D) active sites. The putative hydrolytic water is labeled.
(E) The degenerate TAP1-NBD SG→AV/D→N signature motif structure (magenta) superimposed onto the consensus active site (green). Polar contacts from S621 of the consensus signature motif are shown.
(F) Stereoview of the superposition in (E), zooming in on the two residues that differ between the consensus (green) and degenerate (magenta) signature motifs. The van der Waals radii of V622 and a Mg^2+-coordinated water are shown with a dotted surface, demonstrating a steric clash.

Figure 6.
Figure 6. Model of ATP-Dependent Peptide Transport
Two opposing models are discussed. In model 1, the preferred model, peptide binding stimulates a conformational change in TAP2-NBD, facilitating ATP binding and NBD dimerization. This is coupled to peptide transport. In model 2, the NBDs have instrinsic ability to form an ATP-dependent dimer, and peptide binding stimulates ATP hydrolysis and NBD dissociation, which drives peptide translocation. TAP1 is green, TAP2 is blue, and peptide is red.

The above figures are reprinted by permission from Cell Press: Mol Cell (2006, 24, 51-62) copyright 2006.