PDBsum entry 3mbp

Go to PDB code: 
protein ligands links
Periplasmic binding protein PDB id
Protein chain
370 a.a. *
Waters ×244
* Residue conservation analysis
PDB id:
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
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
25-Jun-97     Release date:   24-Dec-97    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P0AEX9  (MALE_ECOLI) -  Maltose-binding periplasmic protein
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.
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).
Pattern recognition with a fibril-specific antibody fragment reveals the surface variability of natural amyloid fibrils.
  J Mol Biol, 408, 529-540.  
21280116 G.M.Clore (2011).
Exploring sparsely populated states of macromolecules by diamagnetic and paramagnetic NMR relaxation.
  Protein Sci, 20, 229-246.  
21132840 J.R.Perilla, O.Beckstein, E.J.Denning, and T.B.Woolf (2011).
Computing ensembles of transitions from stable states: Dynamic importance sampling.
  J Comput Chem, 32, 196-209.  
21053338 S.Brown, and S.Mathiasen (2011).
Particle-dissociating peptides.
  Adv Mater, 23, 132-135.  
21378967 S.S.Rizk, M.Paduch, J.H.Heithaus, E.M.Duguid, A.Sandstrom, and A.A.Kossiakoff (2011).
Allosteric control of ligand-binding affinity using engineered conformation-specific effector proteins.
  Nat Struct Mol Biol, 18, 437-442.
PDB code: 3pgf
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.  
21420935 Y.Zhang, X.Gao, and R.Michael Garavito (2011).
Structural analysis of the intracellular domain of (pro)renin receptor fused to maltose-binding protein.
  Biochem Biophys Res Commun, 407, 674-679.
PDB codes: 3lbs 3lc8
20497336 D.W.Abbott, M.A.Higgins, S.Hyrnuik, B.Pluvinage, A.Lammerts van Bueren, and A.B.Boraston (2010).
The molecular basis of glycogen breakdown and transport in Streptococcus pneumoniae.
  Mol Microbiol, 77, 183-199.
PDB codes: 2xd2 2xd3
20363939 H.A.Watkins, and E.N.Baker (2010).
Structural and functional characterization of an RNase HI domain from the bifunctional protein Rv2228c from Mycobacterium tuberculosis.
  J Bacteriol, 192, 2878-2886.
PDB code: 3hst
20535468 I.H.Walker, P.C.Hsieh, and P.D.Riggs (2010).
Mutations in maltose-binding protein that alter affinity and solubility properties.
  Appl Microbiol Biotechnol, 88, 187-197.  
21150123 S.Fushinobu (2010).
Unique sugar metabolic pathways of bifidobacteria.
  Biosci Biotechnol Biochem, 74, 2374-2384.  
20101644 V.Zoete, A.Grosdidier, M.Cuendet, and O.Michielin (2010).
Use of the FACTS solvation model for protein-ligand docking calculations. Application to EADock.
  J Mol Recognit, 23, 457-461.  
20175182 Y.Hori, Y.Egashira, R.Kamiura, and K.Kikuchi (2010).
Noncovalent-interaction-promoted ligation for protein labeling.
  Chembiochem, 11, 646-648.  
19846313 A.K.Mittermaier, and L.E.Kay (2009).
Observing biological dynamics at atomic resolution using NMR.
  Trends Biochem Sci, 34, 601-611.  
  19193996 C.S.Souza, L.C.Ferreira, L.Thomas, J.A.Barbosa, and A.Balan (2009).
Crystallization, data collection and data processing of maltose-binding protein (MalE) from the phytopathogen Xanthomonas axonopodis pv. citri.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 105-107.  
19522502 G.M.Clore, and J.Iwahara (2009).
Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes.
  Chem Rev, 109, 4108-4139.  
19626709 H.Fu, G.R.Grimsley, A.Razvi, J.M.Scholtz, and C.N.Pace (2009).
Increasing protein stability by improving beta-turns.
  Proteins, 77, 491-498.  
19301314 I.Iijima, and T.Hohsaka (2009).
Position-specific incorporation of fluorescent non-natural amino acids into maltose-binding protein for detection of ligand binding by FRET and fluorescence quenching.
  Chembiochem, 10, 999.  
19285508 M.A.Higgins, D.W.Abbott, M.J.Boulanger, and A.B.Boraston (2009).
Blood group antigen recognition by a solute-binding protein from a serotype 3 strain of Streptococcus pneumoniae.
  J Mol Biol, 388, 299-309.
PDB code: 2w7y
19801540 M.J.Cuneo, L.S.Beese, and H.W.Hellinga (2009).
Structural analysis of semi-specific oligosaccharide recognition by a cellulose-binding protein of thermotoga maritima reveals adaptations for functional diversification of the oligopeptide periplasmic binding protein fold.
  J Biol Chem, 284, 33217-33223.
PDB codes: 2o7i 3i5o
19490104 N.Matsumoto, M.Yamada, Y.Kurakata, H.Yoshida, S.Kamitori, A.Nishikawa, and T.Tonozuka (2009).
Crystal structures of open and closed forms of cyclo/maltodextrin-binding protein.
  FEBS J, 276, 3008-3019.
PDB codes: 2zym 2zyn 2zyo
19300437 R.P.Berntsson, M.K.Doeven, F.Fusetti, R.H.Duurkens, D.Sengupta, S.J.Marrink, A.M.Thunnissen, B.Poolman, and D.J.Slotboom (2009).
The structural basis for peptide selection by the transport receptor OppA.
  EMBO J, 28, 1332-1340.
PDB codes: 3drf 3drg 3drh 3dri 3drj 3drk
18375760 A.A.Pioszak, and H.E.Xu (2008).
Molecular recognition of parathyroid hormone by its G protein-coupled receptor.
  Proc Natl Acad Sci U S A, 105, 5034-5039.
PDB code: 3c4m
18074341 A.D.Hill, and P.J.Reilly (2008).
A Gibbs free energy correlation for automated docking of carbohydrates.
  J Comput Chem, 29, 1131-1141.  
18477634 A.Nigham, L.Tucker-Kellogg, I.Mihalek, C.Verma, and D.Hsu (2008).
pFlexAna: detecting conformational changes in remotely related proteins.
  Nucleic Acids Res, 36, W246-W251.  
18931781 G.M.Clore (2008).
Visualizing lowly-populated regions of the free energy landscape of macromolecular complexes by paramagnetic relaxation enhancement.
  Mol Biosyst, 4, 1058-1069.  
18307765 J.A.Potter, R.E.Randall, and G.L.Taylor (2008).
Crystal structure of human IPS-1/MAVS/VISA/Cardif caspase activation recruitment domain.
  BMC Struct Biol, 8, 11.
PDB code: 2vgq
19019243 M.J.Cuneo, L.S.Beese, and H.W.Hellinga (2008).
Ligand-induced conformational changes in a thermophilic ribose-binding protein.
  BMC Struct Biol, 8, 50.
PDB codes: 2fn8 2fn9
18332142 R.Suzuki, J.Wada, T.Katayama, S.Fushinobu, T.Wakagi, H.Shoun, H.Sugimoto, A.Tanaka, H.Kumagai, H.Ashida, M.Kitaoka, and K.Yamamoto (2008).
Structural and thermodynamic analyses of solute-binding Protein from Bifidobacterium longum specific for core 1 disaccharide and lacto-N-biose I.
  J Biol Chem, 283, 13165-13173.
PDB codes: 2z8d 2z8e 2z8f
18004759 S.O.Yesylevskyy, V.N.Kharkyanen, and A.P.Demchenko (2008).
The blind search for the closed states of hinge-bending proteins.
  Proteins, 71, 831-843.  
17400245 C.Park, S.Zhou, J.Gilmore, and S.Marqusee (2007).
Energetics-based protein profiling on a proteomic scale: identification of proteins resistant to proteolysis.
  J Mol Biol, 368, 1426-1437.  
17960247 C.Tang, C.D.Schwieters, and G.M.Clore (2007).
Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR.
  Nature, 449, 1078-1082.
PDB code: 2v93
17581234 H.H.Kuo, C.Chan, L.L.Burrows, and C.M.Deber (2007).
Hydrophobic interactions in complexes of antimicrobial peptides with bacterial polysaccharides.
  Chem Biol Drug Des, 69, 405-412.  
  17768345 J.Wada, R.Suzuki, S.Fushinobu, M.Kitaoka, T.Wakagi, H.Shoun, H.Ashida, H.Kumagai, T.Katayama, and K.Yamamoto (2007).
Purification, crystallization and preliminary X-ray analysis of the galacto-N-biose-/lacto-N-biose I-binding protein (GL-BP) of the ABC transporter from Bifidobacterium longum JCM1217.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 751-753.  
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
17371546 T.Tonozuka, A.Sogawa, M.Yamada, N.Matsumoto, H.Yoshida, S.Kamitori, K.Ichikawa, M.Mizuno, A.Nishikawa, and Y.Sakano (2007).
Structural basis for cyclodextrin recognition by Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein.
  FEBS J, 274, 2109-2120.
PDB codes: 2dfz 2zyk
16565082 D.Shaya, A.Tocilj, Y.Li, J.Myette, G.Venkataraman, R.Sasisekharan, and M.Cygler (2006).
Crystal structure of heparinase II from Pedobacter heparinus and its complex with a disaccharide product.
  J Biol Chem, 281, 15525-15535.
PDB codes: 2fuq 2fut
16440087 M.G.Sandros, V.Shete, and D.E.Benson (2006).
Selective, reversible, reagentless maltose biosensing with core-shell semiconducting nanoparticles.
  Analyst, 131, 229-235.  
16326912 Z.A.Sands, A.Grottesi, and M.S.Sansom (2006).
The intrinsic flexibility of the Kv voltage sensor and its implications for channel gating.
  Biophys J, 90, 1598-1606.  
15659363 J.D.Dattelbaum, L.L.Looger, D.E.Benson, K.M.Sali, R.B.Thompson, and H.W.Hellinga (2005).
Analysis of allosteric signal transduction mechanisms in an engineered fluorescent maltose biosensor.
  Protein Sci, 14, 284-291.  
16158230 K.D.Krewulak, C.M.Shepherd, and H.J.Vogel (2005).
Molecular dynamics simulations of the periplasmic ferric-hydroxamate binding protein FhuD.
  Biometals, 18, 375-386.  
16143635 T.Stockner, H.J.Vogel, and D.P.Tieleman (2005).
A salt-bridge motif involved in ligand binding and large-scale domain motions of the maltose-binding protein.
  Biophys J, 89, 3362-3371.  
15614971 A.Saito, Z.Fujimoto, E.Minami, H.Mizuno, K.Miyashita, H.Schrempf, and M.Momma (2004).
Crystallization and preliminary X-ray analysis of the Streptomyces olivaceoviridis NgcE binding protein of the ABC transporter for N-acetylglucosamine.
  Acta Crystallogr D Biol Crystallogr, 60, 2358-2360.  
15281134 D.B.Sherman, S.Zhang, J.B.Pitner, and A.Tropsha (2004).
Evaluation of the relative stability of liganded versus ligand-free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method.
  Proteins, 56, 828-838.  
15555998 G.Guntas, S.F.Mitchell, and M.Ostermeier (2004).
A molecular switch created by in vitro recombination of nonhomologous genes.
  Chem Biol, 11, 1483-1487.  
15242593 J.A.Chao, and J.R.Williamson (2004).
Joint X-ray and NMR refinement of the yeast L30e-mRNA complex.
  Structure, 12, 1165-1176.
PDB code: 1t0k
14660599 K.S.Bak-Jensen, G.André, T.E.Gottschalk, G.Paës, V.Tran, and B.Svensson (2004).
Tyrosine 105 and threonine 212 at outermost substrate binding subsites -6 and +4 control substrate specificity, oligosaccharide cleavage patterns, and multiple binding modes of barley alpha-amylase 1.
  J Biol Chem, 279, 10093-10102.  
12538894 A.Ke, and C.Wolberger (2003).
Insights into binding cooperativity of MATa1/MATalpha2 from the crystal structure of a MATa1 homeodomain-maltose binding protein chimera.
  Protein Sci, 12, 306-312.
PDB codes: 1mh3 1mh4
12972412 C.D.Blundell, D.J.Mahoney, A.Almond, P.L.DeAngelis, J.D.Kahmann, P.Teriete, A.R.Pickford, I.D.Campbell, and A.J.Day (2003).
The link module from ovulation- and inflammation-associated protein TSG-6 changes conformation on hyaluronan binding.
  J Biol Chem, 278, 49261-49270.
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 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, 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.
  Eur J Biochem, 267, 4242-4252.  
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.
  Biochemistry, 39, 8844-8852.  
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.
  Eur J Biochem, 267, 79-84.  
10200260 B.Kobe, R.J.Center, B.E.Kemp, and P.Poumbourios (1999).
Crystal structure of human T cell leukemia virus type 1 gp21 ectodomain crystallized as a maltose-binding protein chimera reveals structural evolution of retroviral transmembrane proteins.
  Proc Natl Acad Sci U S A, 96, 4319-4324.
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.
  J Biol Chem, 274, 33244-33250.  
9888793 M.Muraki, K.Harata, N.Sugita, and K.Sato (1999).
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.
  Proc Natl Acad Sci U S A, 96, 939-944.  
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.
  J Biol Chem, 273, 17604-17609.
PDB code: 1a99
  9529892 W.Boos, and H.Shuman (1998).
Maltose/maltodextrin system of Escherichia coli: transport, metabolism, and regulation.
  Microbiol Mol Biol Rev, 62, 204-229.  
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.