3AIW

Crystal structure of beta-glucosidase in rye complexed with 2-deoxy-2-fluoroglucoside and dinitrophenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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: https://doi.org/10.1016/j.plantsci.2010.09.001
  • Primary Citation of Related Structures:  
    3AIQ, 3AIR, 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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-glucosidase564Secale cerealeMutation(s): 0 
Gene Names: ScGlu
EC: 3.2.1.21
UniProt
Find proteins for Q9FYS3 (Secale cereale)
Explore Q9FYS3 
Go to UniProtKB:  Q9FYS3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9FYS3
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DNF
Query on DNF

Download Ideal Coordinates CCD File 
B [auth A]2,4-DINITROPHENOL
C6 H4 N2 O5
UFBJCMHMOXMLKC-UHFFFAOYSA-N
G2F
Query on G2F

Download Ideal Coordinates CCD File 
C [auth A]2-deoxy-2-fluoro-alpha-D-glucopyranose
C6 H11 F O5
ZCXUVYAZINUVJD-UKFBFLRUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.686α = 90
b = 194.686β = 90
c = 194.686γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



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
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary