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PDBsum entry 2fgj

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protein ligands Protein-protein interface(s) links
Transport protein PDB id
2fgj
Jmol
Contents
Protein chains
241 a.a. *
Ligands
ATP ×4
Waters ×196
* Residue conservation analysis
PDB id:
2fgj
Name: Transport protein
Title: Crystal structure of the abc-cassette h662a mutant of hlyb w atp
Structure: Alpha-hemolysin translocation atp-binding protein chain: a, b, c, d. Fragment: amino acids 467-707. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: hlyb. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.60Å     R-factor:   0.211     R-free:   0.279
Authors: J.Zaitseva,C.Oswald,T.Jumpertz,S.Jenewein,I.B.Holland,L.Schm
Key ref:
J.Zaitseva et al. (2006). A structural analysis of asymmetry required for catalytic activity of an ABC-ATPase domain dimer. EMBO J, 25, 3432-3443. PubMed id: 16858415 DOI: 10.1038/sj.emboj.7601208
Date:
22-Dec-05     Release date:   08-Aug-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P08716  (HLYBP_ECOLX) -  Alpha-hemolysin translocation ATP-binding protein HlyB
Seq:
Struc:
 
Seq:
Struc:
707 a.a.
241 a.a.*
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 1 residue position (black cross)

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

 

 
DOI no: 10.1038/sj.emboj.7601208 EMBO J 25:3432-3443 (2006)
PubMed id: 16858415  
 
 
A structural analysis of asymmetry required for catalytic activity of an ABC-ATPase domain dimer.
J.Zaitseva, C.Oswald, T.Jumpertz, S.Jenewein, A.Wiedenmann, I.B.Holland, L.Schmitt.
 
  ABSTRACT  
 
The ATP-binding cassette (ABC)-transporter haemolysin (Hly)B, a central element of a Type I secretion machinery, acts in concert with two additional proteins in Escherichia coli to translocate the toxin HlyA directly from the cytoplasm to the exterior. The basic set of crystal structures necessary to describe the catalytic cycle of the isolated HlyB-NBD (nucleotide-binding domain) has now been completed. This allowed a detailed analysis with respect to hinge regions, functionally important key residues and potential energy storage devices that revealed many novel features. These include a structural asymmetry within the ATP dimer that was significantly enhanced in the presence of Mg2+, indicating a possible functional asymmetry in the form of one open and one closed phosphate exit tunnel. Guided by the structural analysis, we identified two amino acids, closing one tunnel by an apparent salt bridge. Mutation of these residues abolished ATP-dependent cooperativity of the NBDs. The implications of these new findings for the coupling of ATP binding and hydrolysis to functional activity are discussed.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 The catalytic cycle of the HlyB-NBD. Crystal structures of the monomeric nucleotide-free (Schmitt et al, 2003), dimeric ATP-bound (H662A and E631Q) and monomeric ADP-bound (wild type, E631Q and H662A) forms (this study) are shown. For simplicity, the structure of the ATP/Mg^2+-bound form (Zaitseva et al, 2005a) is not shown. The catalytic domain is colored in light yellow and the helical domain in light tan. Conserved motifs are highlighted and color-coded as follows: Walker A (residues 502–510, blue), Q-loop (residues 549–556, brown), ABC-signature motif (residues 606–610, red), Pro-loop (residues 623–625, orange), Walker B (residues 626–630, magenta), D-loop (residues 634–637, black) and H-loop (residues 661–663, green). Bound ligands are shown in ball-and-stick representation. K[D] values were taken from Zaitseva et al (2005b).
Figure 2.
Figure 2 Nucleotide-binding sites. Stereoview of the ATP-binding (A) and ATP/Mg^2+-binding(B) sites. Color-coding is identical to Figure 1. Direct and water-mediated protein–ATP interactions are highlighted in yellow. Water molecules are shown as blue spheres and Mg^2+ as a green sphere. The interaction between D637 of the D-loop of the trans monomer and S504 of the Walker A motif of the cis monomer is indicated. ATP and amino acids involved in ligand interactions are shown in ball-and-stick representation. ^* indicates conserved motifs of the trans monomer participating in ATP coordination. (C) Stereoview of the ADP-binding site. ADP and residues involved in ligand interactions are shown in ball-and-stick representation, water molecules are blue spheres, protein–ADP interactions are highlighted in green and ADP–water interactions in blue. Color-coding is identical to Figure 1. The interaction between the side chain of Q550 and the amide backbone of T633 is highlighted by a dashed, brown line.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 3432-3443) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20855293 B.Meineke, B.Schwer, R.Schaffrath, and S.Shuman (2011).
Determinants of eukaryal cell killing by the bacterial ribotoxin PrrC.
  Nucleic Acids Res, 39, 687-700.  
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.  
20061384 A.Siarheyeva, R.Liu, and F.J.Sharom (2010).
Characterization of an asymmetric occluded state of P-glycoprotein with two bound nucleotides: implications for catalysis.
  J Biol Chem, 285, 7575-7586.  
21059948 C.Orelle, F.J.Alvarez, M.L.Oldham, A.Orelle, T.E.Wiley, J.Chen, and A.L.Davidson (2010).
Dynamics of alpha-helical subdomain rotation in the intact maltose ATP-binding cassette transporter.
  Proc Natl Acad Sci U S A, 107, 20293-20298.  
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.  
19996093 J.W.Weng, K.N.Fan, and W.N.Wang (2010).
The conformational transition pathway of ATP binding cassette transporter MsbA revealed by atomistic simulations.
  J Biol Chem, 285, 3053-3063.  
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
20162627 O.Doppelt-Azeroual, F.Delfaud, F.Moriaud, and A.G.de Brevern (2010).
Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins.
  Protein Sci, 19, 847-867.  
19132955 A.Siarheyeva, and F.J.Sharom (2009).
The ABC transporter MsbA interacts with lipid A and amphipathic drugs at different sites.
  Biochem J, 419, 317-328.  
19426129 C.Schölz, and R.Tampé (2009).
The peptide-loading complex--antigen translocation and MHC class I loading.
  Biol Chem, 390, 783-794.  
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.  
19948960 G.Bozkurt, G.Stjepanovic, F.Vilardi, S.Amlacher, K.Wild, G.Bange, V.Favaloro, K.Rippe, E.Hurt, B.Dobberstein, and I.Sinning (2009).
Structural insights into tail-anchored protein binding and membrane insertion by Get3.
  Proc Natl Acad Sci U S A, 106, 21131-21136.
PDB codes: 3iqw 3iqx
18955484 H.T.Lin, V.N.Bavro, N.P.Barrera, H.M.Frankish, S.Velamakanni, H.W.van Veen, C.V.Robinson, M.I.Borges-Walmsley, and A.R.Walmsley (2009).
MacB ABC Transporter Is a Dimer Whose ATPase Activity and Macrolide-binding Capacity Are Regulated by the Membrane Fusion Protein MacA.
  J Biol Chem, 284, 1145-1154.  
19368888 J.Timmins, E.Gordon, S.Caria, G.Leonard, S.Acajjaoui, M.S.Kuo, V.Monchois, and S.McSweeney (2009).
Structural and mutational analyses of Deinococcus radiodurans UvrA2 provide insight into DNA binding and damage recognition by UvrAs.
  Structure, 17, 547-558.
PDB codes: 2vf7 2vf8
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.  
19748342 S.Newstead, P.W.Fowler, P.Bilton, E.P.Carpenter, P.J.Sadler, D.J.Campopiano, M.S.Sansom, and S.Iwata (2009).
Insights into how nucleotide-binding domains power ABC transport.
  Structure, 17, 1213-1222.
PDB code: 3fvq
19544044 V.Kos, and R.C.Ford (2009).
The ATP-binding cassette family: a structural perspective.
  Cell Mol Life Sci, 66, 3111-3126.  
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.  
18421494 G.Cui, Z.R.Zhang, A.R.O'Brien, B.Song, and N.A.McCarty (2008).
Mutations at arginine 352 alter the pore architecture of CFTR.
  J Membr Biol, 222, 91.  
18497752 H.de Wet, P.Proks, M.Lafond, J.Aittoniemi, M.S.Sansom, S.E.Flanagan, E.R.Pearson, A.T.Hattersley, and F.M.Ashcroft (2008).
A mutation (R826W) in nucleotide-binding domain 1 of ABCC8 reduces ATPase activity and causes transient neonatal diabetes.
  EMBO Rep, 9, 648-654.  
18304008 J.R.Riordan (2008).
CFTR function and prospects for therapy.
  Annu Rev Biochem, 77, 701-726.  
19053284 K.M.Westfahl, J.A.Merten, A.H.Buchaklian, and C.S.Klug (2008).
Functionally important ATP binding and hydrolysis sites in Escherichia coli MsbA.
  Biochemistry, 47, 13878-13886.  
18790847 P.C.Wen, and E.Tajkhorshid (2008).
Dimer opening of the nucleotide binding domains of ABC transporters after ATP hydrolysis.
  Biophys J, 95, 5100-5110.  
18715873 R.Masia, and C.G.Nichols (2008).
Functional clustering of mutations in the dimer interface of the nucleotide binding folds of the sulfonylurea receptor.
  J Biol Chem, 283, 30322-30329.  
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.  
17972020 D.Nikles, and R.Tampé (2007).
Targeted degradation of ABC transporters in health and disease.
  J Bioenerg Biomembr, 39, 489-497.  
17158291 H.W.Pinkett, A.T.Lee, P.Lum, K.P.Locher, and D.C.Rees (2007).
An inward-facing conformation of a putative metal-chelate-type ABC transporter.
  Science, 315, 373-377.
PDB code: 2nq2
16937116 K.J.Linton, and C.F.Higgins (2007).
Structure and function of ABC transporters: the ATP switch provides flexible control.
  Pflugers Arch, 453, 555-567.  
17545154 M.L.Daus, M.Grote, P.Müller, M.Doebber, A.Herrmann, H.J.Steinhoff, E.Dassa, and E.Schneider (2007).
ATP-driven MalK dimer closure and reopening and conformational changes of the "EAA" motifs are crucial for function of the maltose ATP-binding cassette transporter (MalFGK2).
  J Biol Chem, 282, 22387-22396.  
17485460 P.M.Jones, and A.M.George (2007).
Nucleotide-dependent allostery within the ABC transporter ATP-binding cassette: a computational study of the MJ0796 dimer.
  J Biol Chem, 282, 22793-22803.  
18058211 Z.E.Sauna, I.W.Kim, and S.V.Ambudkar (2007).
Genomics and the mechanism of P-glycoprotein (ABCB1).
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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 codes are shown on the right.