2ZYK

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 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 pr ...

    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.


    Related Citations: 
    • Crystal structures of open and closed forms of cyclo/maltodextrin-binding protein
      Matsumoto, M.,Yamada, M.,Kurakata, Y.,Yoshida, H.,Kamitori, S.,Nishikawa, A.,Tonozuka, T.
      (2009) Febs J. 276: 3008


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Solute-binding protein
A, B, C, D
397Thermoactinomyces vulgarisMutation(s): 0 
Gene Names: orf-3
Find proteins for Q9AJF5 (Thermoactinomyces vulgaris)
Go to UniProtKB:  Q9AJF5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLC
Query on GLC

Download SDF File 
Download CCD File 
A, B, C, D
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.222 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 167.399α = 90.00
b = 95.270β = 131.56
c = 117.130γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSrefinement
ADSCdata collection
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance