PDBsum entry 2ixe

Hydrolase

PDB id: 2ixe

Contents

Protein chains

251 a.a. *

Ligands

ATP ×2

PO4

Metals

_MG ×2

Waters ×332

* Residue conservation analysis

PDB id:

2ixe

Name:

Hydrolase

Title:

Crystal structure of the atpase domain of tap1 with atp (d645n mutant)

Structure:

Antigen peptide transporter 1. Chain: a, d. Fragment: atpase domain, residues 465-725. Synonym: tap1, apt1, peptide transporter tap1, atp-binding cassette sub-family b member 2. Engineered: yes. Mutation: yes. Other_details: transporter associated with antigen processing 1 (tap1)

Source:

Rattus norvegicus. Rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PDB file)

Resolution:

2.00Å R-factor: 0.202 R-free: 0.241

Authors:

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

Key ref:

E.Procko et al. (2006). Distinct structural and functional properties of the ATPase sites in an asymmetric ABC transporter. Mol Cell, 24, 51-62. PubMed id: 17018292 DOI: 10.1016/j.molcel.2006.07.034

Date:

07-Jul-06 Release date: 11-Oct-06

Protein chains

P36370  (TAP1_RAT) -  Antigen peptide transporter 1 from Rattus norvegicus

Seq: 725 a.a.

Struc: 251 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.7.4.2.14 - ABC-type antigen peptide transporter.
• Reaction: a peptide antigen(in) + ATP + H2O = a peptide antigen(out) + ADP + phosphate + H⁺

peptide antigen(in) + ATP (Bound ligand (Het Group name = ATP) corresponds exactly) + H2O = peptide antigen(out) + ADP + phosphate + H(+) (Bound ligand (Het Group name = PO4) corresponds exactly)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.molcel.2006.07.034

Mol Cell 24:51-62 (2006)

PubMed id: 17018292

Distinct structural and functional properties of the ATPase sites in an asymmetric ABC transporter.

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

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.

Selected figure(s)

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.

Figures were selected by the author.