2DGA

Crystal structure of hexameric beta-glucosidase in wheat


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Molecular and Structural Characterization of Hexameric beta-D-Glucosidases in Wheat and Rye.

Sue, M.Yamazaki, K.Yajima, S.Nomura, T.Matsukawa, T.Iwamura, H.Miyamoto, T.

(2006) Plant Physiol 141: 1237-1247

  • DOI: https://doi.org/10.1104/pp.106.077693
  • Primary Citation of Related Structures:  
    2DGA

  • PubMed Abstract: 

    The wheat (Triticum aestivum) and rye (Secale cereale) beta-D-glucosidases hydrolyze hydroxamic acid-glucose conjugates, exist as different types of isozyme, and function as oligomers. In this study, three cDNAs encoding beta-D-glucosidases (TaGlu1a, TaGlu1b, and TaGlu1c) were isolated from young wheat shoots. Although the TaGlu1s share very high sequence homology, the mRNA level of Taglu1c was much lower than the other two genes in 48- and 96-h-old wheat shoots. The expression ratio of each gene was different between two wheat cultivars. Recombinant TaGlu1b expressed in Escherichia coli was electrophoretically distinct fromTaGlu1a and TaGlu1c. Furthermore, coexpression of TaGlu1a and TaGlu1b gave seven bands on a native-PAGE gel, indicating the formation of both homo- and heterohexamers. One distinctive property of the wheat and rye glucosidases is that they function as hexamers but lose activity when dissociated into smaller oligomers or monomers. The crystal structure of hexameric TaGlu1b was determined at a resolution of 1.8 A. The N-terminal region was located at the dimer-dimer interface and plays a crucial role in hexamer formation. Mutational analyses revealed that the aromatic side chain at position 378, which is located at the entrance to the catalytic center, plays an important role in substrate binding. Additionally, serine-464 and leucine-465 of TaGlu1a were shown to be critical in the relative specificity for DIMBOA-glucose (2-O-beta-D-glucopyranosyl-4-hydroxy-7-methoxy-1,4-benzoxazin-3-one) over DIBOA-glucose (7-demethoxy-DIMBOA-glucose).


  • Organizational Affiliation

    Department of Applied Biology and Chemistry , Tokyo University of Agriculture, Setagaya, Tokyo 156-8502, Japan. sue@nodai.ac.jp


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-glucosidase565Triticum aestivumMutation(s): 0 
Gene Names: Taglu1b
EC: 3.2.1.21 (PDB Primary Data), 3.2.1.182 (UniProt)
UniProt
Find proteins for Q1XH05 (Triticum aestivum)
Explore Q1XH05 
Go to UniProtKB:  Q1XH05
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ1XH05
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.65α = 90
b = 194.65β = 90
c = 194.65γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-07-04
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary