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PDBsum entry 2ixg

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Hydrolase PDB id
2ixg
Jmol
Contents
Protein chain
254 a.a. *
Ligands
ATP
GOL
Waters ×45
* Residue conservation analysis
PDB id:
2ixg
Name: Hydrolase
Title: Crystal structure of the atpase domain of tap1 with atp (s621a, g622v, d645n mutant)
Structure: Antigen peptide transporter 1. Chain: a. Fragment: atpase domain, residues 465-725. Synonym: tap1, apt1, peptide transporter tap1, atp-binding sub-family b member 2. Engineered: yes. Mutation: yes. Other_details: transporter associated with antigen processi (tap1)
Source: Rattus norvegicus. Rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
2.70Å     R-factor:   0.217     R-free:   0.267
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:
08-Jul-06     Release date:   11-Oct-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P36370  (TAP1_RAT) -  Antigen peptide transporter 1
Seq:
Struc:
 
Seq:
Struc:
725 a.a.
254 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleotide binding     4 terms  

 

 
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22447242 M.Hohl, C.Briand, M.G.Grütter, and M.A.Seeger (2012).
Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation.
  Nat Struct Mol Biol, 19, 395-402.
PDB code: 3qf4
23000901 V.M.Korkhov, S.A.Mireku, and K.P.Locher (2012).
Structure of AMP-PNP-bound vitamin B12 transporter BtuCD-F.
  Nature, 490, 367-372.
PDB code: 4fi3
21194365 R.P.Gupta, P.Kueppers, L.Schmitt, and R.Ernst (2011).
The multidrug transporter Pdr5: a molecular diode?
  Biol Chem, 392, 53-60.  
21315686 R.Yang, Y.X.Hou, C.A.Campbell, K.Palaniyandi, Q.Zhao, A.J.Bordner, and X.B.Chang (2011).
Glutamine residues in Q-loops of multidrug resistance protein MRP1 contribute to ATP binding via interaction with metal cofactor.
  Biochim Biophys Acta, 1808, 1790-1796.  
  20876359 A.Szollosi, P.Vergani, and L.Csanády (2010).
Involvement of F1296 and N1303 of CFTR in induced-fit conformational change in response to ATP binding at NBD2.
  J Gen Physiol, 136, 407-423.  
19721454 A.Theodoratos, B.Whittle, A.Enders, D.C.Tscharke, C.M.Roots, C.C.Goodnow, and A.M.Fahrer (2010).
Mouse strains with point mutations in TAP1 and TAP2.
  Immunol Cell Biol, 88, 72-78.  
20644544 D.Parcej, and R.Tampé (2010).
ABC proteins in antigen translocation and viral inhibition.
  Nat Chem Biol, 6, 572-580.  
20454684 J.Aittoniemi, H.de Wet, F.M.Ashcroft, and M.S.Sansom (2010).
Asymmetric switching in a homodimeric ABC transporter: a simulation study.
  PLoS Comput Biol, 6, e1000762.  
20799350 L.Kelly, H.Fukushima, R.Karchin, J.M.Gow, L.W.Chinn, U.Pieper, M.R.Segal, D.L.Kroetz, and A.Sali (2010).
Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains.
  Protein Sci, 19, 2110-2121.  
  20421370 M.F.Tsai, M.Li, and T.C.Hwang (2010).
Stable ATP binding mediated by a partial NBD dimer of the CFTR chloride channel.
  J Gen Physiol, 135, 399-414.  
20823549 M.Haffke, A.Menzel, Y.Carius, D.Jahn, and D.W.Heinz (2010).
Structures of the nucleotide-binding domain of the human ABCB6 transporter and its complexes with nucleotides.
  Acta Crystallogr D Biol Crystallogr, 66, 979-987.
PDB codes: 3nh6 3nh9 3nha 3nhb
19961541 R.Ernst, P.Kueppers, J.Stindt, K.Kuchler, and L.Schmitt (2010).
Multidrug efflux pumps: substrate selection in ATP-binding cassette multidrug efflux pumps--first come, first served?
  FEBS J, 277, 540-549.  
20150177 S.Atwell, C.G.Brouillette, K.Conners, S.Emtage, T.Gheyi, W.B.Guggino, J.Hendle, J.F.Hunt, H.A.Lewis, F.Lu, I.I.Protasevich, L.A.Rodgers, R.Romero, S.R.Wasserman, P.C.Weber, D.Wetmore, F.F.Zhang, and X.Zhao (2010).
Structures of a minimal human CFTR first nucleotide-binding domain as a monomer, head-to-tail homodimer, and pathogenic mutant.
  Protein Eng Des Sel, 23, 375-384.
PDB codes: 2pze 2pzf 2pzg
  19704900 C.De Marcos Lousa, D.Dietrich, B.Johnson, S.A.Baldwin, M.J.Holdsworth, F.L.Theodoulou, and A.Baker (2009).
The NBDs that wouldn't die: A cautionary tale of the use of isolated nucleotide binding domains of ABC transporters.
  Commun Integr Biol, 2, 97-99.  
19426129 C.Schölz, and R.Tampé (2009).
The peptide-loading complex--antigen translocation and MHC class I loading.
  Biol Chem, 390, 783-794.  
19019987 D.Dietrich, H.Schmuths, C.d.e. .M.Lousa, J.M.Baldwin, S.A.Baldwin, A.Baker, F.L.Theodoulou, and M.J.Holdsworth (2009).
Mutations in the Arabidopsis peroxisomal ABC transporter COMATOSE allow differentiation between multiple functions in planta: insights from an allelic series.
  Mol Biol Cell, 20, 530-543.  
18957373 D.Muallem, and P.Vergani (2009).
Review. ATP hydrolysis-driven gating in cystic fibrosis transmembrane conductance regulator.
  Philos Trans R Soc Lond B Biol Sci, 364, 247-255.  
19261456 E.Procko, and R.Gaudet (2009).
Antigen processing and presentation: TAPping into ABC transporters.
  Curr Opin Immunol, 21, 84-91.  
19254551 J.Weng, J.Ma, K.Fan, and W.Wang (2009).
Asymmetric conformational flexibility in the ATP-binding cassette transporter HI1470/1.
  Biophys J, 96, 1918-1930.  
19691360 Y.X.Hou, C.Z.Li, K.Palaniyandi, P.M.Magtibay, L.Homolya, B.Sarkadi, and X.B.Chang (2009).
Effects of putative catalytic base mutation E211Q on ABCG2-mediated methotrexate transport.
  Biochemistry, 48, 9122-9131.  
18535149 A.L.Davidson, E.Dassa, C.Orelle, and J.Chen (2008).
Structure, function, and evolution of bacterial ATP-binding cassette systems.
  Microbiol Mol Biol Rev, 72, 317.  
18675588 M.Raghavan, N.Del Cid, S.M.Rizvi, and L.R.Peters (2008).
MHC class I assembly: out and about.
  Trends Immunol, 29, 436-443.  
18356296 R.Ernst, P.Kueppers, C.M.Klein, T.Schwarzmueller, K.Kuchler, and L.Schmitt (2008).
A mutation of the H-loop selectively affects rhodamine transport by the yeast multidrug ABC transporter Pdr5.
  Proc Natl Acad Sci U S A, 105, 5069-5074.  
18088596 R.Yang, R.Scavetta, and X.B.Chang (2008).
The hydroxyl group of S685 in Walker A motif and the carboxyl group of D792 in Walker B motif of NBD1 play a crucial role for multidrug resistance protein folding and function.
  Biochim Biophys Acta, 1778, 454-465.  
18311911 S.Park, B.B.Lim, C.Perez-Terzic, G.Mer, and A.Terzic (2008).
Interaction of asymmetric ABCC9-encoded nucleotide binding domains determines KATP channel SUR2A catalytic activity.
  J Proteome Res, 7, 1721-1728.  
17068338 C.L.Perria, V.Rajamanickam, P.E.Lapinski, and M.Raghavan (2006).
Catalytic site modifications of TAP1 and TAP2 and their functional consequences.
  J Biol Chem, 281, 39839-39851.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.