spacer
spacer

PDBsum entry 1oxu

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Transport protein PDB id
1oxu
Jmol
Contents
Protein chains
353 a.a. *
Ligands
ADP ×3
Metals
_MG ×3
IOD ×60
Waters ×810
* Residue conservation analysis
PDB id:
1oxu
Name: Transport protein
Title: Crystal structure of glcv, the abc-atpase of the glucose abc transporter from sulfolobus solfataricus
Structure: Abc transporter, atp binding protein. Chain: a, b, c. Synonym: glcv, glucose. Engineered: yes
Source: Sulfolobus solfataricus. Organism_taxid: 2287. Gene: glcv. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.10Å     R-factor:   0.195     R-free:   0.256
Authors: G.Verdon,S.V.Albers,B.W.Dijkstra,A.J.Driessen,A.M.Thunnissen
Key ref:
G.Verdon et al. (2003). Crystal structures of the ATPase subunit of the glucose ABC transporter from Sulfolobus solfataricus: nucleotide-free and nucleotide-bound conformations. J Mol Biol, 330, 343-358. PubMed id: 12823973 DOI: 10.1016/S0022-2836(03)00575-8
Date:
03-Apr-03     Release date:   17-Jun-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q97UY8  (Q97UY8_SULSO) -  ABC transporter, ATP binding protein (Glucose)
Seq:
Struc:
353 a.a.
353 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     ATP-binding cassette (ABC) transporter complex   1 term 
  Biological process     metabolic process   4 terms 
  Biochemical function     transporter activity     6 terms  

 

 
DOI no: 10.1016/S0022-2836(03)00575-8 J Mol Biol 330:343-358 (2003)
PubMed id: 12823973  
 
 
Crystal structures of the ATPase subunit of the glucose ABC transporter from Sulfolobus solfataricus: nucleotide-free and nucleotide-bound conformations.
G.Verdon, S.V.Albers, B.W.Dijkstra, A.J.Driessen, A.M.Thunnissen.
 
  ABSTRACT  
 
The ABC-ATPase GlcV energizes a binding protein-dependent ABC transporter that mediates glucose uptake in Sulfolobus solfataricus. Here, we report high-resolution crystal structures of GlcV in different states along its catalytic cycle: distinct monomeric nucleotide-free states and monomeric complexes with ADP-Mg(2+) as a product-bound state, and with AMPPNP-Mg(2+) as an ATP-like bound state. The structure of GlcV consists of a typical ABC-ATPase domain, comprising two subdomains, connected by a linker region to a C-terminal domain of unknown function. Comparisons of the nucleotide-free and nucleotide-bound structures of GlcV reveal re-orientations of the ABCalpha subdomain and the C-terminal domain relative to the ABCalpha/beta subdomain, and switch-like rearrangements in the P-loop and Q-loop regions. Additionally, large conformational differences are observed between the GlcV structures and those of other ABC-ATPases, further emphasizing the inherent flexibility of these proteins. Notably, a comparison of the monomeric AMPPNP-Mg(2+)-bound GlcV structure with that of the dimeric ATP-Na(+)-bound LolD-E171Q mutant reveals a +/-20 degrees rigid body re-orientation of the ABCalpha subdomain relative to the ABCalpha/beta subdomain, accompanied by a local conformational difference in the Q-loop. We propose that these differences represent conformational changes that may have a role in the mechanism of energy-transduction and/or allosteric control of the ABC-ATPase activity in bacterial importers.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Stereo views of the nucleotide-binding site of GlcV in (a) nucleotide-free form A, (b) nucleotide-free form B, (c) the GlcV-ADP-Mg2+ complex and (d) the GlcV-AMPPNP-Mg2+ complex. For the complexes, a portion of a 2F[o] -F[c] simulated annealing electron density omit map[63.] is shown, contoured at 1s and covering the nucleotide, the magnesium ion and its coordinating water molecules. Residues and ligands in the nucleotide-binding site are shown in ball-and-stick representation. The P-loop is coloured in purple.
Figure 4.
Figure 4. A representation of the interactions stabilizing the nucleotide, the magnesium ion and its coordinating water molecules (red dots) in (a) the GlcV-ADP-Mg2+ complex and (b) the GlcV-AMPPNP-Mg2+ complex. Distances are in Å and residue colouring is identical with that used in Figure 1 and Figure 2.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 330, 343-358) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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.  
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
  19074458 A.V.Cideciyan, M.Swider, T.S.Aleman, Y.Tsybovsky, S.B.Schwartz, E.A.Windsor, A.J.Roman, A.Sumaroka, J.D.Steinberg, S.G.Jacobson, E.M.Stone, and K.Palczewski (2009).
ABCA4 disease progression and a proposed strategy for gene therapy.
  Hum Mol Genet, 18, 931-941.  
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.  
19707853 J.P.Mornon, P.Lehn, and I.Callebaut (2009).
Molecular models of the open and closed states of the whole human CFTR protein.
  Cell Mol Life Sci, 66, 3469-3486.  
18831048 P.M.Jones, and A.M.George (2009).
Opening of the ADP-bound active site in the ABC transporter ATPase dimer: evidence for a constant contact, alternating sites model for the catalytic cycle.
  Proteins, 75, 387-396.  
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.  
  18540059 A.S.Ethayathulla, Y.Bessho, A.Shinkai, B.Padmanabhan, T.P.Singh, P.Kaur, and S.Yokoyama (2008).
Purification, crystallization and preliminary X-ray diffraction analysis of the putative ABC transporter ATP-binding protein from Thermotoga maritima.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 64, 498-500.  
19325794 C.Oswald, S.H.Smits, E.Bremer, and L.Schmitt (2008).
Microseeding - a powerful tool for crystallizing proteins complexed with hydrolyzable substrates.
  Int J Mol Sci, 9, 1131-1141.  
18489584 I.Carrier, and P.Gros (2008).
Investigating the role of the invariant carboxylate residues E552 and E1197 in the catalytic activity of Abcb1a (mouse Mdr3).
  FEBS J, 275, 3312-3324.  
17951296 J.Weng, J.Ma, K.Fan, and W.Wang (2008).
The conformational coupling and translocation mechanism of vitamin B12 ATP-binding cassette transporter BtuCD.
  Biophys J, 94, 612-621.  
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.  
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.  
18198173 Y.Shi, X.Chen, Z.Wu, W.Shi, Y.Yang, N.Cui, C.Jiang, and R.W.Harrison (2008).
cAMP-dependent protein kinase phosphorylation produces interdomain movement in SUR2B leading to activation of the vascular KATP channel.
  J Biol Chem, 283, 7523-7530.  
17208306 C.A.McDevitt, and R.Callaghan (2007).
How can we best use structural information on P-glycoprotein to design inhibitors?
  Pharmacol Ther, 113, 429-441.  
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.  
16710701 M.Herget, and R.Tampé (2007).
Intracellular peptide transporters in human--compartmentalization of the "peptidome".
  Pflugers Arch, 453, 591-600.  
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.  
17764951 S.J.Lee, A.Böhm, M.Krug, and W.Boos (2007).
The ABC of binding-protein-dependent transport in Archaea.
  Trends Microbiol, 15, 389-397.  
17623846 T.Prakash, K.S.Sandhu, N.K.Singh, Y.Bhasin, C.Ramakrishnan, and S.K.Brahmachari (2007).
Structural assessment of glycyl mutations in invariantly conserved motifs.
  Proteins, 69, 617-632.  
17295059 X.B.Chang (2007).
A molecular understanding of ATP-dependent solute transport by multidrug resistance-associated protein MRP1.
  Cancer Metastasis Rev, 26, 15-37.  
16541253 C.Oswald, I.B.Holland, and L.Schmitt (2006).
The motor domains of ABC-transporters. What can structures tell us?
  Naunyn Schmiedebergs Arch Pharmacol, 372, 385-399.  
16352607 D.W.Zhang, G.A.Graf, R.D.Gerard, J.C.Cohen, and H.H.Hobbs (2006).
Functional asymmetry of nucleotide-binding domains in ABCG5 and ABCG8.
  J Biol Chem, 281, 4507-4516.  
16877382 E.O.Oloo, E.Y.Fung, and D.P.Tieleman (2006).
The dynamics of the MgATP-driven closure of MalK, the energy-transducing subunit of the maltose ABC transporter.
  J Biol Chem, 281, 28397-28407.  
16604273 J.M.Lubelska, M.Jonuscheit, C.Schleper, S.V.Albers, and A.J.Driessen (2006).
Regulation of expression of the arabinose and glucose transporter genes in the thermophilic archaeon Sulfolobus solfataricus.
  Extremophiles, 10, 383-391.  
16858415 J.Zaitseva, C.Oswald, T.Jumpertz, S.Jenewein, A.Wiedenmann, I.B.Holland, and L.Schmitt (2006).
A structural analysis of asymmetry required for catalytic activity of an ABC-ATPase domain dimer.
  EMBO J, 25, 3432-3443.
PDB codes: 2ff7 2ffa 2ffb 2fgj 2fgk
17036051 M.Mense, P.Vergani, D.M.White, G.Altberg, A.C.Nairn, and D.C.Gadsby (2006).
In vivo phosphorylation of CFTR promotes formation of a nucleotide-binding domain heterodimer.
  EMBO J, 25, 4728-4739.  
16547024 X.Guo, R.W.Harrison, and P.C.Tai (2006).
Nucleotide-dependent dimerization of the C-terminal domain of the ABC transporter CvaB in colicin V secretion.
  J Bacteriol, 188, 2383-2391.  
17128986 X.Guo, X.Chen, I.T.Weber, R.W.Harrison, and P.C.Tai (2006).
Molecular basis for differential nucleotide binding of the nucleotide-binding domain of ABC-transporter CvaB.
  Biochemistry, 45, 14473-14480.  
16585747 Y.Ito, H.Matsuzawa, S.Matsuyama, S.Narita, and H.Tokuda (2006).
Genetic analysis of the mode of interplay between an ATPase subunit and membrane subunits of the lipoprotein-releasing ATP-binding cassette transporter LolCDE.
  J Bacteriol, 188, 2856-2864.  
17038124 Y.Ito, K.Kanamaru, N.Taniguchi, S.Miyamoto, and H.Tokuda (2006).
A novel ligand bound ABC transporter, LolCDE, provides insights into the molecular mechanisms underlying membrane detachment of bacterial lipoproteins.
  Mol Microbiol, 62, 1064-1075.  
15837203 A.Karcher, K.Büttner, B.Märtens, R.P.Jansen, and K.P.Hopfner (2005).
X-ray structure of RLI, an essential twin cassette ABC ATPase involved in ribosome biogenesis and HIV capsid assembly.
  Structure, 13, 649-659.
PDB code: 1yqt
15711166 A.Pohorille, K.Schweighofer, and M.A.Wilson (2005).
The origin and early evolution of membrane channels.
  Astrobiology, 5, 1.  
15616192 D.J.Schmidt, D.J.Rose, W.M.Saxton, and S.Strome (2005).
Functional analysis of cytoplasmic dynein heavy chain in Caenorhabditis elegans with fast-acting temperature-sensitive mutations.
  Mol Biol Cell, 16, 1200-1212.  
16326809 G.Lu, J.M.Westbrooks, A.L.Davidson, and J.Chen (2005).
ATP hydrolysis is required to reset the ATP-binding cassette dimer into the resting-state conformation.
  Proc Natl Acad Sci U S A, 102, 17969-17974.
PDB codes: 2awn 2awo
15889153 J.Zaitseva, S.Jenewein, T.Jumpertz, I.B.Holland, and L.Schmitt (2005).
H662 is the linchpin of ATP hydrolysis in the nucleotide-binding domain of the ABC transporter HlyB.
  EMBO J, 24, 1901-1910.
PDB code: 1xef
  15596536 L.Csanády, K.W.Chan, A.C.Nairn, and D.C.Gadsby (2005).
Functional roles of nonconserved structural segments in CFTR's NH2-terminal nucleotide binding domain.
  J Gen Physiol, 125, 43-55.  
15980069 L.Cuthbertson, J.Powers, and C.Whitfield (2005).
The C-terminal domain of the nucleotide-binding domain protein Wzt determines substrate specificity in the ATP-binding cassette transporter for the lipopolysaccharide O-antigens in Escherichia coli serotypes O8 and O9a.
  J Biol Chem, 280, 30310-30319.  
16107340 O.Dalmas, C.Orelle, A.E.Foucher, C.Geourjon, S.Crouzy, A.Di Pietro, and J.M.Jault (2005).
The Q-loop disengages from the first intracellular loop during the catalytic cycle of the multidrug ABC transporter BmrA.
  J Biol Chem, 280, 36857-36864.  
16246032 P.Vergani, C.Basso, M.Mense, A.C.Nairn, and D.C.Gadsby (2005).
Control of the CFTR channel's gates.
  Biochem Soc Trans, 33, 1003-1007.  
15729345 P.Vergani, S.W.Lockless, A.C.Nairn, and D.C.Gadsby (2005).
CFTR channel opening by ATP-driven tight dimerization of its nucleotide-binding domains.
  Nature, 433, 876-880.  
  15767296 S.G.Bompadre, J.H.Cho, X.Wang, X.Zou, Y.Sohma, M.Li, and T.C.Hwang (2005).
CFTR gating II: Effects of nucleotide binding on the stability of open states.
  J Gen Physiol, 125, 377-394.  
15063852 A.Böhm, and W.Boos (2004).
Gene regulation in prokaryotes by subcellular relocalization of transcription factors.
  Curr Opin Microbiol, 7, 151-156.  
15189142 A.L.Davidson, and J.Chen (2004).
ATP-binding cassette transporters in bacteria.
  Annu Rev Biochem, 73, 241-268.  
15452563 C.F.Higgins, and K.J.Linton (2004).
The ATP switch model for ABC transporters.
  Nat Struct Mol Biol, 11, 918-926.  
15551867 C.van der Does, and R.Tampé (2004).
How do ABC transporters drive transport?
  Biol Chem, 385, 927-933.  
15308647 E.O.Oloo, and D.P.Tieleman (2004).
Conformational transitions induced by the binding of MgATP to the vitamin B12 ATP-binding cassette (ABC) transporter BtuCD.
  J Biol Chem, 279, 45013-45019.  
14685259 H.A.Lewis, S.G.Buchanan, S.K.Burley, K.Conners, M.Dickey, M.Dorwart, R.Fowler, X.Gao, W.B.Guggino, W.A.Hendrickson, J.F.Hunt, M.C.Kearins, D.Lorimer, P.C.Maloney, K.W.Post, K.R.Rajashankar, M.E.Rutter, J.M.Sauder, S.Shriver, P.H.Thibodeau, P.J.Thomas, M.Zhang, X.Zhao, and S.Emtage (2004).
Structure of nucleotide-binding domain 1 of the cystic fibrosis transmembrane conductance regulator.
  EMBO J, 23, 282-293.
PDB codes: 1q3h 1r0w 1r0x 1r0y 1r0z 1r10
15159567 J.Zaitseva, I.B.Holland, and L.Schmitt (2004).
The role of CAPS buffer in expanding the crystallization space of the nucleotide-binding domain of the ABC transporter haemolysin B from Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 60, 1076-1084.  
15313236 K.P.Locher (2004).
Structure and mechanism of ABC transporters.
  Curr Opin Struct Biol, 14, 426-431.  
15355964 Q.Zhao, and X.B.Chang (2004).
Mutation of the aromatic amino acid interacting with adenine moiety of ATP to a polar residue alters the properties of multidrug resistance protein 1.
  J Biol Chem, 279, 48505-48512.  
15382245 T.Ose, T.Fujie, M.Yao, N.Watanabe, and I.Tanaka (2004).
Crystal structure of the ATP-binding cassette of multisugar transporter from Pyrococcus horikoshii OT3.
  Proteins, 57, 635-638.
PDB codes: 1v43 1vci
14527411 J.Chen, G.Lu, J.Lin, A.L.Davidson, and F.A.Quiocho (2003).
A tweezers-like motion of the ATP-binding cassette dimer in an ABC transport cycle.
  Mol Cell, 12, 651-661.
PDB codes: 1q12 1q1b 1q1e
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.