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PDBsum entry 2qi9
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protein ligands Protein-protein interface(s) links
Membrane protein PDB id
2qi9

 

 

 

 

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Contents
Protein chains
324 a.a. *
248 a.a. *
245 a.a. *
Ligands
PO4 ×2
SO4 ×6
1PE ×2
PEG ×4
Waters ×16
* Residue conservation analysis
PDB id:
2qi9
Name: Membrane protein
Title: Abc-transporter btucd in complex with its periplasmic binding protein btuf
Structure: Vitamin b12 import system permease protein btuc. Chain: a, b. Engineered: yes. Mutation: yes. Vitamin b12 import atp-binding protein btud. Chain: c, d. Synonym: vitamin b12-transporting atpase. Engineered: yes. Mutation: yes.
Source: Escherichia coli. Organism_taxid: 562. Gene: btuc. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: btud. Gene: btuf.
Resolution:
2.60Å     R-factor:   0.262     R-free:   0.280
Authors: R.N.Hvorup,B.A.Goetz,M.Niederer,K.Hollenstein,E.Perozo,K.P.Locher
Key ref: R.N.Hvorup et al. (2007). Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF. Science, 317, 1387-1390. PubMed id: 17673622
Date:
03-Jul-07     Release date:   14-Aug-07    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P06609  (BTUC_ECOLI) -  Vitamin B12 import system permease protein BtuC from Escherichia coli (strain K12)
Seq:
Struc: 		326 a.a.
324 a.a.*
Protein chains
Pfam   ArchSchema ?
P06611  (BTUD_ECOLI) -  Vitamin B12 import ATP-binding protein BtuD from Escherichia coli (strain K12)
Seq:
Struc: 		249 a.a.
248 a.a.*
Protein chain
Pfam   ArchSchema ?
P37028  (BTUF_ECOLI) -  Vitamin B12-binding protein from Escherichia coli (strain K12)
Seq:
Struc: 		266 a.a.
245 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 8 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains C, D: E.C.7.6.2.8  - ABC-type vitamin B12 transporter.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: an R-cob(III)alamin(out) + ATP + H2O = an R-cob(III)alamin(in) + ADP + phosphate + H+
R-cob(III)alamin(out)
 + ATP
 + H2O
 = R-cob(III)alamin(in)
 +
ADP
Bound ligand (Het Group name = PO4)
corresponds exactly 		+ phosphate
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
Science 317:1387-1390 (2007)
PubMed id: 17673622  
 
 
Asymmetry in the structure of the ABC transporter-binding protein complex BtuCD-BtuF.
R.N.Hvorup, B.A.Goetz, M.Niederer, K.Hollenstein, E.Perozo, K.P.Locher.
 
  ABSTRACT  
 
BtuCD is an adenosine triphosphate-binding cassette (ABC) transporter that translocates vitamin B12 from the periplasmic binding protein BtuF into the cytoplasm of Escherichia coli. The 2.6 angstrom crystal structure of a complex BtuCD-F reveals substantial conformational changes as compared with the previously reported structures of BtuCD and BtuF. The lobes of BtuF are spread apart, and B12 is displaced from the binding pocket. The transmembrane BtuC subunits reveal two distinct conformations, and the translocation pathway is closed to both sides of the membrane. Electron paramagnetic resonance spectra of spin-labeled cysteine mutants reconstituted in proteoliposomes are consistent with the conformation of BtuCD-F that was observed in the crystal structure. A comparison with BtuCD and the homologous HI1470/71 protein suggests that the structure of BtuCD-F may reflect a posttranslocation intermediate.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
23142986 J.S.Woo, A.Zeltina, B.A.Goetz, and K.P.Locher (2012).
X-ray structure of the Yersinia pestis heme transporter HmuUV.
  Nat Struct Mol Biol, 19, 1310-1315.
PDB code: 4g1u
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
  21488101 A.S.Oliveira, A.M.Baptista, and C.M.Soares (2011).
Conformational changes induced by ATP-hydrolysis in an ABC transporter: A molecular dynamics study of the Sav1866 exporter.
  Proteins, 79, 1977-1990.  
21194366 B.C.Chu, and H.J.Vogel (2011).
A structural and functional analysis of type III periplasmic and substrate binding proteins: their role in bacterial siderophore and heme transport.
  Biol Chem, 392, 39-52.  
20497229 T.Eitinger, D.A.Rodionov, M.Grote, and E.Schneider (2011).
Canonical and ECF-type ATP-binding cassette importers in prokaryotes: diversity in modular organization and cellular functions.
  FEMS Microbiol Rev, 35, 3.  
21269440 Y.Peng, Y.Luo, T.Yu, X.Xu, K.Fan, Y.Zhao, and K.Yang (2011).
A Blue Native-PAGE analysis of membrane protein complexes in Clostridium thermocellum.
  BMC Microbiol, 11, 22.  
20659291 E.Bordignon, M.Grote, and E.Schneider (2010).
The maltose ATP-binding cassette transporter in the 21st century--towards a structural dynamic perspective on its mode of action.
  Mol Microbiol, 77, 1354-1366.  
19961540 I.D.Kerr, P.M.Jones, and A.M.George (2010).
Multidrug efflux pumps: the structures of prokaryotic ATP-binding cassette transporter efflux pumps and implications for our understanding of eukaryotic P-glycoproteins and homologues.
  FEBS J, 277, 550-563.  
19940001 J.A.Lundbaek, S.A.Collingwood, H.I.Ingólfsson, R.Kapoor, and O.S.Andersen (2010).
Lipid bilayer regulation of membrane protein function: gramicidin channels as molecular force probes.
  J R Soc Interface, 7, 373-395.  
20810662 J.C.Grigg, J.Cheung, D.E.Heinrichs, and M.E.Murphy (2010).
Specificity of Staphyloferrin B recognition by the SirA receptor from Staphylococcus aureus.
  J Biol Chem, 285, 34579-34588.  
19826804 K.McLuskey, A.W.Roszak, Y.Zhu, and N.W.Isaacs (2010).
Crystal structures of all-alpha type membrane proteins.
  Eur Biophys J, 39, 723-755.  
20667175 K.R.Vinothkumar, and R.Henderson (2010).
Structures of membrane proteins.
  Q Rev Biophys, 43, 65.  
20656493 M.Fischer, Q.Y.Zhang, R.E.Hubbard, and G.H.Thomas (2010).
Caught in a TRAP: substrate-binding proteins in secondary transport.
  Trends Microbiol, 18, 471-478.  
20173761 O.Lewinson, A.T.Lee, K.P.Locher, and D.C.Rees (2010).
A distinct mechanism for the ABC transporter BtuCD-BtuF revealed by the dynamics of complex formation.
  Nat Struct Mol Biol, 17, 332-338.  
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
20154136 V.Eckey, D.Weidlich, H.Landmesser, U.Bergmann, and E.Schneider (2010).
The second extracellular loop of pore-forming subunits of ATP-binding cassette transporters for basic amino acids plays a crucial role in interaction with the cognate solute binding protein(s).
  J Bacteriol, 192, 2150-2159.  
  21078867 Z.Kopeikin, Y.Sohma, M.Li, and T.C.Hwang (2010).
On the mechanism of CFTR inhibition by a thiazolidinone derivative.
  J Gen Physiol, 136, 659-671.  
19642870 C.Oswald, S.H.Smits, M.Höing, E.Bremer, and L.Schmitt (2009).
Structural analysis of the choline-binding protein ChoX in a semi-closed and ligand-free conformation.
  Biol Chem, 390, 1163-1170.
PDB code: 3hcq
19234479 D.C.Rees, E.Johnson, and O.Lewinson (2009).
ABC transporters: the power to change.
  Nat Rev Mol Cell Biol, 10, 218-227.  
19053133 D.Parcej, and R.Tampé (2009).
Solute-binding sites in ABC transporters for recognition, occlusion and trans-inhibition.
  ChemMedChem, 4, 25-28.  
19418088 G.K.Wang, J.Calderon, S.J.Jaw, and S.Y.Wang (2009).
State-dependent block of Na+ channels by articaine via the local anesthetic receptor.
  J Membr Biol, 229, 1-9.  
19883597 H.H.Loeffler, and A.Kitao (2009).
Collective dynamics of periplasmic glutamine binding protein upon domain closure.
  Biophys J, 97, 2541-2549.  
19159494 J.P.Becker, G.Depret, F.Van Bambeke, P.M.Tulkens, and M.Prévost (2009).
Molecular models of human P-glycoprotein in two different catalytic states.
  BMC Struct Biol, 9, 3.  
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.  
18957379 K.P.Locher (2009).
Review. Structure and mechanism of ATP-binding cassette transporters.
  Philos Trans R Soc Lond B Biol Sci, 364, 239-245.  
19479721 M.A.Do Cao, S.Crouzy, M.Kim, M.Becchi, D.S.Cafiso, A.Di Pietro, and J.M.Jault (2009).
Probing the conformation of the resting state of a bacterial multidrug ABC transporter, BmrA, by a site-directed spin labeling approach.
  Protein Sci, 18, 1507-1520.  
19224345 M.Dean (2009).
ABC transporters, drug resistance, and cancer stem cells.
  J Mammary Gland Biol Neoplasia, 14, 3-9.  
19395376 M.Grote, Y.Polyhach, G.Jeschke, H.J.Steinhoff, E.Schneider, and E.Bordignon (2009).
Transmembrane signaling in the maltose ABC transporter MalFGK2-E: periplasmic MalF-P2 loop communicates substrate availability to the ATP-bound MalK dimer.
  J Biol Chem, 284, 17521-17526.  
19376876 M.J.Gray, and J.C.Escalante-Semerena (2009).
In vivo analysis of cobinamide salvaging in Rhodobacter sphaeroides strain 2.4.1.
  J Bacteriol, 191, 3842-3851.  
19004000 R.Shi, A.Proteau, J.Wagner, Q.Cui, E.O.Purisima, A.Matte, and M.Cygler (2009).
Trapping open and closed forms of FitE: a group III periplasmic binding protein.
  Proteins, 75, 598-609.
PDB codes: 3be5 3be6
19453273 U.A.Hellmich, and C.Glaubitz (2009).
NMR and EPR studies of membrane transporters.
  Biol Chem, 390, 815-834.  
19544044 V.Kos, and R.C.Ford (2009).
The ATP-binding cassette family: a structural perspective.
  Cell Mol Life Sci, 66, 3111-3126.  
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.  
18539464 K.Schauer, D.A.Rodionov, and H.de Reuse (2008).
New substrates for TonB-dependent transport: do we only see the 'tip of the iceberg'?
  Trends Biochem Sci, 33, 330-338.  
18776017 M.F.Del Papa, and M.Perego (2008).
Ethanolamine activates a sensor histidine kinase regulating its utilization in Enterococcus faecalis.
  J Bacteriol, 190, 7147-7156.  
18567630 M.Grote, E.Bordignon, Y.Polyhach, G.Jeschke, H.J.Steinhoff, and E.Schneider (2008).
A comparative electron paramagnetic resonance study of the nucleotide-binding domains' catalytic cycle in the assembled maltose ATP-binding cassette importer.
  Biophys J, 95, 2924-2938.  
  18808385 M.J.Gray, N.K.Tavares, and J.C.Escalante-Semerena (2008).
The genome of Rhodobacter sphaeroides strain 2.4.1 encodes functional cobinamide salvaging systems of archaeal and bacterial origins.
  Mol Microbiol, 70, 824-836.  
18212011 M.K.Doeven, G.van den Bogaart, V.Krasnikov, and B.Poolman (2008).
Probing receptor-translocator interactions in the oligopeptide ABC transporter by fluorescence correlation spectroscopy.
  Biophys J, 94, 3956-3965.  
18948194 M.L.Oldham, A.L.Davidson, and J.Chen (2008).
Structural insights into ABC transporter mechanism.
  Curr Opin Struct Biol, 18, 726-733.  
18621668 N.S.Kadaba, J.T.Kaiser, E.Johnson, A.Lee, and D.C.Rees (2008).
The high-affinity E. coli methionine ABC transporter: structure and allosteric regulation.
  Science, 321, 250-253.
PDB codes: 3dhw 3dhx
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.  
18676641 P.Sompornpisut, B.Roux, and E.Perozo (2008).
Structural refinement of membrane proteins by restrained molecular dynamics and solvent accessibility data.
  Biophys J, 95, 5349-5361.  
18511655 S.Gerber, M.Comellas-Bigler, B.A.Goetz, and K.P.Locher (2008).
Structural basis of trans-inhibition in a molybdate/tungstate ABC transporter.
  Science, 321, 246-250.
PDB code: 3d31
18075584 C.Olesen, M.Picard, A.M.Winther, C.Gyrup, J.P.Morth, C.Oxvig, J.V.Møller, and P.Nissen (2007).
The structural basis of calcium transport by the calcium pump.
  Nature, 450, 1036-1042.
PDB codes: 3b9b 3b9r 3ba6
17972020 D.Nikles, and R.Tampé (2007).
Targeted degradation of ABC transporters in health and disease.
  J Bioenerg Biomembr, 39, 489-497.  
17961142 M.L.Daus, S.Berendt, S.Wuttge, and E.Schneider (2007).
Maltose binding protein (MalE) interacts with periplasmic loops P2 and P1 respectively of the MalFG subunits of the maltose ATP binding cassette transporter (MalFGK(2)) from Escherichia coli/Salmonella during the transport cycle.
  Mol Microbiol, 66, 1107-1122.  
18033289 M.L.Oldham, D.Khare, F.A.Quiocho, A.L.Davidson, and J.Chen (2007).
Crystal structure of a catalytic intermediate of the maltose transporter.
  Nature, 450, 515-521.
PDB code: 2r6g
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.

 

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