Crystal structure of cyclo/maltodextrin-binding protein complexed with gamma-cyclodextrin

Experimental Data Snapshot

  • Resolution: 2.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 

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Structural basis for cyclodextrin recognition by Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein

Tonozuka, T.Sogawa, A.Yamada, M.Matsumoto, N.Yoshida, H.Kamitori, S.Ichikawa, K.Mizuno, M.Nishikawa, A.Sakano, Y.

(2007) FEBS J 274: 2109-2120

  • DOI: https://doi.org/10.1111/j.1742-4658.2007.05753.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of a Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein (TvuCMBP) complexed with gamma-cyclodextrin has been determined. Like Escherichia coli maltodextrin-binding protein (EcoMBP) and other bacterial sugar-binding proteins, TvuCMBP consists of two domains, an N- and a C-domain, both of which are composed of a central beta-sheet surrounded by alpha-helices; the domains are joined by a hinge region containing three segments. gamma-Cyclodextrin is located at a cleft formed by the two domains. A common functional conformational change has been reported in this protein family, which involves switching from an open form to a sugar-transporter bindable form, designated a closed form. The TvuCMBP-gamma-cyclodextrin complex structurally resembles the closed form of EcoMBP, indicating that TvuCMBP complexed with gamma-cyclodextrin adopts the closed form. The fluorescence measurements also showed that the affinities of TvuCMBP for cyclodextrins were almost equal to those for maltooligosaccharides. Despite having similar folds, the sugar-binding site of the N-domain part of TvuCMBP and other bacterial sugar-binding proteins are strikingly different. In TvuCMBP, the side-chain of Leu59 protrudes from the N-domain part into the sugar-binding cleft and orients toward the central cavity of gamma-cyclodextrin, thus Leu59 appears to play the key role in binding. The cleft of the sugar-binding site of TvuCMBP is also wider than that of EcoMBP. These findings suggest that the sugar-binding site of the N-domain part and the wide cleft are critical in determining the specificity of TvuCMBP for gamma-cyclodextrin.

  • Organizational Affiliation

    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Japan. tonozuka@cc.tuat.ac.jp

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Solute-binding protein
A, B, C, D
397Thermoactinomyces vulgarisMutation(s): 0 
Gene Names: orf-3
Find proteins for Q9AJF5 (Thermoactinomyces vulgaris)
Explore Q9AJF5 
Go to UniProtKB:  Q9AJF5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9AJF5
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
E, F, G, H
Glycosylation Resources
GlyTouCan:  G28503YQ
GlyCosmos:  G28503YQ
Experimental Data & Validation

Experimental Data

  • Resolution: 2.50 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 167.399α = 90
b = 95.27β = 131.56
c = 117.13γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary