Crystal structure of the inactive mutant Monocot (Maize ZMGlu1) beta-glucosidase ZMGluE191D in complex with the competitive inhibitor dhurrin

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 

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The mechanism of substrate (aglycone) specificity in beta-glucosidases is revealed by crystal structures of mutant maize beta-glucosidase-DIMBOA, -DIMBOAGlc, and -dhurrin complexes.

Czjzek, M.Cicek, M.Zamboni, V.Bevan, D.R.Henrissat, B.Esen, A.

(2000) Proc Natl Acad Sci U S A 97: 13555-13560

  • DOI: https://doi.org/10.1073/pnas.97.25.13555
  • Primary Citation of Related Structures:  
    1E4L, 1E4N, 1E55, 1E56

  • PubMed Abstract: 

    The mechanism and the site of substrate (i.e., aglycone) recognition and specificity were investigated in maize beta-glucosidase (Glu1) by x-ray crystallography by using crystals of a catalytically inactive mutant (Glu1E191D) in complex with the natural substrate 2-O-beta-d-glucopyranosyl-4-hydroxy-7-methoxy-1,4-benzoxazin-3-one (DIMBOAGlc), the free aglycone DIMBOA, and competitive inhibitor para-hydroxy-S-mandelonitrile beta-glucoside (dhurrin). The structures of these complexes and of the free enzyme were solved at 2.1-, 2.1-, 2.0-, and 2.2-A resolution, respectively. The structural data from the complexes allowed us to visualize an intact substrate, free aglycone, or a competitive inhibitor in the slot-like active site of a beta-glucosidase. These data show that the aglycone moiety of the substrate is sandwiched between W378 on one side and F198, F205, and F466 on the other. Thus, specific conformations of these four hydrophobic amino acids and the shape of the aglycone-binding site they form determine aglycone recognition and substrate specificity in Glu1. In addition to these four residues, A467 interacts with the 7-methoxy group of DIMBOA. All residues but W378 are variable among beta-glucosidases that differ in substrate specificity, supporting the conclusion that these sites are the basis of aglycone recognition and binding (i.e., substrate specificity) in beta-glucosidases. The data also provide a plausible explanation for the competitive binding of dhurrin to maize beta-glucosidases with high affinity without being hydrolyzed.

  • Organizational Affiliation

    Architecture et Fonction des Macromolecules Biologiques, Centre National de la Recherche Scientifique, 31 Chemin Joseph Aiguier, F13402 Marseille cedex 20, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
512Zea maysMutation(s): 1 
Find proteins for P49235 (Zea mays)
Explore P49235 
Go to UniProtKB:  P49235
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49235
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
DHR Binding MOAD:  1E55 Ki: 7.60e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.8α = 90
b = 95β = 90
c = 117.5γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALAdata 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: 2000-12-11
    Type: Initial release
  • Version 1.1: 2015-10-14
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary