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PDBsum entry 3mbp

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Periplasmic binding protein PDB id
3mbp
Jmol
Contents
Protein chain
370 a.a. *
Ligands
GLC-GLC-GLC
Waters ×244
* Residue conservation analysis
PDB id:
3mbp
Name: Periplasmic binding protein
Title: Maltodextrin-binding protein with bound maltotriose
Structure: Maltodextrin-binding protein. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k12. Cellular_location: periplasm. Gene: male
Resolution:
1.70Å     R-factor:   0.164    
Authors: J.C.Spurlino,F.A.Quiocho
Key ref:
F.A.Quiocho et al. (1997). Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport/chemosensory receptor. Structure, 5, 997. PubMed id: 9309217 DOI: 10.1016/S0969-2126(97)00253-0
Date:
25-Jun-97     Release date:   24-Dec-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0AEX9  (MALE_ECOLI) -  Maltose-binding periplasmic protein
Seq:
Struc:
396 a.a.
370 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   5 terms 
  Biological process     transport   7 terms 
  Biochemical function     transporter activity     4 terms  

 

 
DOI no: 10.1016/S0969-2126(97)00253-0 Structure 5:997 (1997)
PubMed id: 9309217  
 
 
Extensive features of tight oligosaccharide binding revealed in high-resolution structures of the maltodextrin transport/chemosensory receptor.
F.A.Quiocho, J.C.Spurlino, L.E.Rodseth.
 
  ABSTRACT  
 
BACKGROUND: Active-transport processes perform a vital function in the life of a cell, maintaining cell homeostasis and allowing access of nutrients. Maltodextrin/maltose-binding protein (MBP; M(r) = 40k) is a receptor protein which serves as an initial high-affinity binding component of the active-transport system of maltooligosaccharides in bacteria. MBP also participates in chemotaxis towards maltooligosaccharides. The interaction between MBP and specific cytoplasmic membrane proteins initiates either active transport or chemotaxis. In order to gain new understanding of the function of MBP, especially its versatility in binding different linear and cyclic oligosaccharides with similar affinities, we have undertaken high-resolution X-ray analysis of three oligosaccharide-bound structures. RESULTS: The structures of MBP complexed with maltose, maltotriose and maltotetraose have been refined to high resolutions (1.67 to 1.8 A). These structures provide details at the atomic level of many features of oligosaccharide binding. The structures reveal differences between buried and surface binding sites and show the importance of hydrogen bonds and van der Waals interactions, especially those resulting from aromatic residue stacking. Insights are provided into the structural plasticity of the protein, the binding affinity and the binding specificity with respect to alpha/beta anomeric preference and oligosaccharide length. In addition, the structures demonstrate the different conformations that can be adopted by the oligosaccharide within the complex. CONCLUSIONS: MBP has a two-domain structure joined by a hinge-bending region which contains the substrate-binding groove. The bound maltooligosaccharides have a ribbon-like structure: the edges of the ribbon are occupied by polar hydroxyl groups and the flat surfaces are composed of nonpolar patches of the sugar ring faces. The polar groups and nonpolar patches are heavily involved in forming hydrogen bonds and van der Waals contacts, respectively, with complimentary residues in the groove. Hinge-bending between the two domains enables the participation of both domains in the binding and sequestering of the oligosaccharides. Changes in the subtle contours of the binding site allow binding of maltodextrins of varying length with similarly high affinities. The fact that the three bound structures are essentially identical ensures productive interaction with the oligomeric membrane proteins, which are distinct for transport and chemotaxis.
 
  Selected figure(s)  
 
Figure 4.
Figure 4. Schematic diagram of the hydrogen bonds between the maltodextrin-binding protein and maltose (a), maltotriose (b) and maltotetraose (c). Hydrogen bonds are shown as dashed lines.
 
  The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 997-0) copyright 1997.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21376731 C.Haupt, M.Bereza, S.T.Kumar, B.Kieninger, I.Morgado, P.Hortschansky, G.Fritz, C.Röcken, U.Horn, and M.Fändrich (2011).
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21132840 J.R.Perilla, O.Beckstein, E.J.Denning, and T.B.Woolf (2011).
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Allosteric control of ligand-binding affinity using engineered conformation-specific effector proteins.
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PDB code: 3pgf
20497229 T.Eitinger, D.A.Rodionov, M.Grote, and E.Schneider (2011).
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Structural analysis of the intracellular domain of (pro)renin receptor fused to maltose-binding protein.
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PDB codes: 3lbs 3lc8
20497336 D.W.Abbott, M.A.Higgins, S.Hyrnuik, B.Pluvinage, A.Lammerts van Bueren, and A.B.Boraston (2010).
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PDB codes: 2xd2 2xd3
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PDB code: 3hst
20535468 I.H.Walker, P.C.Hsieh, and P.D.Riggs (2010).
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Position-specific incorporation of fluorescent non-natural amino acids into maltose-binding protein for detection of ligand binding by FRET and fluorescence quenching.
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PDB codes: 2o7i 3i5o
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Crystal structure of a catalytic intermediate of the maltose transporter.
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Structural basis for cyclodextrin recognition by Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein.
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Selective, reversible, reagentless maltose biosensing with core-shell semiconducting nanoparticles.
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Molecular dynamics simulations of the periplasmic ferric-hydroxamate binding protein FhuD.
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Joint X-ray and NMR refinement of the yeast L30e-mRNA complex.
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PDB code: 1t0k
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PDB codes: 1mh3 1mh4
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The link module from ovulation- and inflammation-associated protein TSG-6 changes conformation on hyaluronan binding.
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PDB codes: 1o7b 1o7c
12824478 D.R.Smyth, M.K.Mrozkiewicz, W.J.McGrath, P.Listwan, and B.Kobe (2003).
Crystal structures of fusion proteins with large-affinity tags.
  Protein Sci, 12, 1313-1322.  
12592028 F.A.Saul, M.Mourez, B.Vulliez-Le Normand, N.Sassoon, G.A.Bentley, and J.M.Betton (2003).
Crystal structure of a defective folding protein.
  Protein Sci, 12, 577-585.
PDB code: 1lax
12919326 S.R.Leliveld, M.H.Noteborn, and J.P.Abrahams (2003).
Prevalent conformations and subunit exchange in the biologically active apoptin protein multimer.
  Eur J Biochem, 270, 3619-3627.  
12486124 Y.Mishima, K.Momma, W.Hashimoto, B.Mikami, and K.Murata (2003).
Crystal structure of AlgQ2, a macromolecule (alginate)-binding protein of Sphingomonas sp. A1, complexed with an alginate tetrasaccharide at 1.6-A resolution.
  J Biol Chem, 278, 6552-6559.
PDB code: 1j1n
11863465 D.E.Benson, A.E.Haddy, and H.W.Hellinga (2002).
Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design.
  Biochemistry, 41, 3262-3269.  
12163068 L.S.Mizoue, and W.J.Chazin (2002).
Engineering and design of ligand-induced conformational change in proteins.
  Curr Opin Struct Biol, 12, 459-463.  
12381848 R.M.de Lorimier, J.J.Smith, M.A.Dwyer, L.L.Looger, K.M.Sali, C.D.Paavola, S.S.Rizk, S.Sadigov, D.W.Conrad, L.Loew, and H.W.Hellinga (2002).
Construction of a fluorescent biosensor family.
  Protein Sci, 11, 2655-2675.  
11709169 C.Steegborn, O.Danot, R.Huber, and T.Clausen (2001).
Crystal structure of transcription factor MalT domain III: a novel helix repeat fold implicated in regulated oligomerization.
  Structure, 9, 1051-1060.
PDB code: 1hz4
11533486 D.E.Benson, D.W.Conrad, R.M.de Lorimier, S.A.Trammell, and H.W.Hellinga (2001).
Design of bioelectronic interfaces by exploiting hinge-bending motions in proteins.
  Science, 293, 1641-1644.  
11344330 J.D.Fox, R.B.Kapust, and D.S.Waugh (2001).
Single amino acid substitutions on the surface of Escherichia coli maltose-binding protein can have a profound impact on the solubility of fusion proteins.
  Protein Sci, 10, 622-630.  
11524684 J.S.Marvin, and H.W.Hellinga (2001).
Manipulation of ligand binding affinity by exploitation of conformational coupling.
  Nat Struct Biol, 8, 795-798.  
11320244 J.S.Marvin, and H.W.Hellinga (2001).
Conversion of a maltose receptor into a zinc biosensor by computational design.
  Proc Natl Acad Sci U S A, 98, 4955-4960.  
11381122 Y.Liu, A.Manna, R.Li, W.E.Martin, R.C.Murphy, A.L.Cheung, and G.Zhang (2001).
Crystal structure of the SarR protein from Staphylococcus aureus.
  Proc Natl Acad Sci U S A, 98, 6877-6882.
PDB code: 1hsj
10866829 D.I.Kreimer, H.Malak, J.R.Lakowicz, S.Trakhanov, E.Villar, and V.L.Shnyrov (2000).
Thermodynamics and dynamics of histidine-binding protein, the water-soluble receptor of histidine permease. Implications for the transport of high and low affinity ligands.
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10913296 J.Kormos, P.E.Johnson, E.Brun, P.Tomme, L.P.McIntosh, C.A.Haynes, and D.G.Kilburn (2000).
Binding site analysis of cellulose binding domain CBD(N1) from endoglucanse C of Cellulomonas fimi by site-directed mutagenesis.
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10630988 M.Muraki, K.Harata, N.Sugita, and K.I.Sato (2000).
Protein-carbohydrate interactions in human lysozyme probed by combining site-directed mutagenesis and affinity labeling.
  Biochemistry, 39, 292-299.
PDB codes: 1d6p 1d6q
10601853 P.Van Gelder, F.Dumas, J.P.Rosenbusch, and M.Winterhalter (2000).
Oriented channels reveal asymmetric energy barriers for sugar translocation through maltoporin of Escherichia coli.
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PDB code: 1mg1
10559198 L.M.Veenhoff, and B.Poolman (1999).
Substrate recognition at the cytoplasmic and extracellular binding site of the lactose transport protein of Streptococcus thermophilus.
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Dual affinity labeling of the active site of human lysozyme with an N-acetyllactosamine derivative: first ligand assisted recognition of the second ligand.
  Biochemistry, 38, 540-548.
PDB code: 1re2
9927672 Y.Zhang, P.J.Gardina, A.S.Kuebler, H.S.Kang, J.A.Christopher, and M.D.Manson (1999).
Model of maltose-binding protein/chemoreceptor complex supports intrasubunit signaling mechanism.
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9558324 A.K.Schmidt, S.Cottaz, H.Driguez, and G.E.Schulz (1998).
Structure of cyclodextrin glycosyltransferase complexed with a derivative of its main product beta-cyclodextrin.
  Biochemistry, 37, 5909-5915.
PDB code: 3cgt
9651355 D.G.Vassylyev, H.Tomitori, K.Kashiwagi, K.Morikawa, and K.Igarashi (1998).
Crystal structure and mutational analysis of the Escherichia coli putrescine receptor. Structural basis for substrate specificity.
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PDB code: 1a99
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Maltose/maltodextrin system of Escherichia coli: transport, metabolism, and regulation.
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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 code is shown on the right.