3AIQ

Crystal structure of beta-glucosidase in wheat complexed with an aglycone DIMBOA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.195 

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Literature

Active-site architecture of benzoxazinone-glucoside beta-D-glucosidases in Triticeae

Sue, M.Nakamura, C.Miyamoto, T.Yajima, S.

(2011) Plant Sci 180: 268-275

  • DOI: 10.1016/j.plantsci.2010.09.001
  • Primary Citation of Related Structures:  
    3AIQ, 3AIR, 3AIS, 3AIU, 3AIV, 3AIW

  • PubMed Abstract: 
  • The β-D-glucosidases from wheat (Triticum aestivum) and rye (Secale cereale) hydrolyze benzoxazinone-glucose conjugates. Although wheat and rye glucosidases have high sequence identity, they have different substrate preferences; the wheat enzyme favors DIMBOA-Glc (2-O-β-D-glucopyranosyl-4-hydroxy-7-methoxy-1,4-benzoxazin-3-one) over DIBOA-Glc (7-demethoxy-DIMBOA-Glc), whereas the rye enzyme preference is the opposite ...

    The β-D-glucosidases from wheat (Triticum aestivum) and rye (Secale cereale) hydrolyze benzoxazinone-glucose conjugates. Although wheat and rye glucosidases have high sequence identity, they have different substrate preferences; the wheat enzyme favors DIMBOA-Glc (2-O-β-D-glucopyranosyl-4-hydroxy-7-methoxy-1,4-benzoxazin-3-one) over DIBOA-Glc (7-demethoxy-DIMBOA-Glc), whereas the rye enzyme preference is the opposite. To investigate the mechanism of substrate binding, we analyzed crystal structures of an inactive mutant of the wheat glucosidase complexed with the natural substrate DIMBOA-Glc, wheat and rye glucosidases complexed with an aglycone DIMBOA, and wheat and rye glucosidases complexed with an inhibitor 2-fluoro-2-deoxy-β-D-glucose. The binding position of substrate in the active site was determined but interaction between the substrate and Ser-464 or Leu-465 was not observed, although amino acid residues at these two positions are the only structural distinctions between wheat and rye glucosidase catalytic pockets. Variation at these two positions alters the width of the pocket entrance, which may relate to observed differences in substrate specificity. The side chain of Glu-462 that forms hydrogen bonds with the glucose moiety of DIMBOA-Glc moved deeper into the pocket upon substrate binding, and mutation of this residue dramatically decreased enzyme activity.


    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
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-glucosidaseA565Triticum aestivumMutation(s): 0 
Gene Names: Taglu1bGLU1B
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HBO
Query on HBO

Download Ideal Coordinates CCD File 
B [auth A]2,4-DIHYDROXY-7-(METHYLOXY)-2H-1,4-BENZOXAZIN-3(4H)-ONE
C9 H9 N O5
GDNZNIJPBQATCZ-SECBINFHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.195 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 193.962α = 90
b = 193.962β = 90
c = 193.962γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-04
    Changes: Database references