1E1F

Crystal structure of a Monocot (Maize ZMGlu1) beta-glucosidase in complex with p-Nitrophenyl-beta-D-thioglucoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

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This is version 1.4 of the entry. See complete history


Literature

Crystal Structure of a Monocotyledon (Maize Zmglu1) Beta-Glucosidase and a Model of its Complex with P-Nitrophenyl Beta-D-Thioglucoside

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

(2001) Biochem J 354: 37

  • DOI: 10.1042/0264-6021:3540037
  • Primary Citation of Related Structures:  
    1E1E, 1E1F

  • PubMed Abstract: 
  • The maize beta-glucosidase isoenzymes ZMGlu1 and ZMGlu2 hydrolyse the abundant natural substrate DIMBOAGlc (2-O-beta-D-glucopyranosyl-4-hydroxy-7-methoxy-1,4-benzoxazin-3-one), whose aglycone DIMBOA (2,4-hydroxy-7-methoxy-1,4-benzoxazin-3-one) is the major defence chemical protecting seedlings and young plant parts against herbivores and other pests ...

    The maize beta-glucosidase isoenzymes ZMGlu1 and ZMGlu2 hydrolyse the abundant natural substrate DIMBOAGlc (2-O-beta-D-glucopyranosyl-4-hydroxy-7-methoxy-1,4-benzoxazin-3-one), whose aglycone DIMBOA (2,4-hydroxy-7-methoxy-1,4-benzoxazin-3-one) is the major defence chemical protecting seedlings and young plant parts against herbivores and other pests. The two isoenzymes hydrolyse DIMBOAGlc with similar kinetics but differ from each other and their sorghum homologues with respect to specificity towards other substrates. To gain insights into the mechanism of substrate (i.e. aglycone) specificity between the two maize isoenzymes and their sorghum homologues, ZMGlu1 was produced in Escherichia coli, purified, crystallized and its structure solved at 2.5 Angstrom resolution by X-ray crystallography. In addition, the complex of ZMGlu1 with the non-hydrolysable inhibitor p-nitrophenyl beta-D-thioglucoside was crystallized and, based on the partial electron density, a model for the inhibitor molecule within the active site is proposed. The inhibitor is located in a slot-like active site where its aromatic aglycone is held by stacking interactions with Trp-378. Whereas some of the atoms on the non-reducing end of the glucose moiety can be modelled on the basis of the electron density, most of the inhibitor atoms are highly disordered. This is attributed to the requirement of the enzyme to accommodate two different species, namely the substrate in its ground state and in its distorted conformation, for catalysis.


    Organizational Affiliation

    Architecture et Fonction des Macromolecules Biologiques-AFMB-UMR 6098, CNRS and Universités d'Aix-Marseille I et II, 31 Chemin Joseph Aiguier, F13402 Marseille Cedex 20, France. czjzek@afmb.cnrs-mrs.fr



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-GLUCOSIDASEA, B512Zea maysMutation(s): 0 
Gene Names: GLU1
EC: 3.2.1.21 (PDB Primary Data), 3.2.1.182 (UniProt)
UniProt
Find proteins for P49235 (Zea mays)
Explore P49235 
Go to UniProtKB:  P49235
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PSG (Subject of Investigation/LOI)
Query on PSG

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]4-nitrophenyl 1-thio-beta-D-glucopyranoside
C12 H15 N O7 S
IXFOBQXJWRLXMD-ZIQFBCGOSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.64α = 90
b = 118.15β = 94.33
c = 80.88γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-19
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-07-05
    Changes: Data collection
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Other, Structure summary