1E56

Crystal structure of the inactive mutant Monocot (Maize ZMGlu1) beta-glucosidase ZMGluE191D in complex with the natural substrate DIMBOA-beta-D-glucoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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.USA 97: 13555

  • DOI: 10.1073/pnas.97.25.13555
  • Primary Citation of Related Structures:  1E4L, 1E4N, 1E55
  • Also Cited By: 1H49

  • 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 natu ...

    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.


    Related Citations: 
    • Expression of Soluble and Catalytically Active Plant (Monocot) Beta-Glucosidases in E. Coli
      Cicek, M.,Esen, A.
      (1999) Biotechnol.Bioeng. 63: 392


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BETA-GLUCOSIDASE
A, B
512Zea maysGene Names: GLU1
EC: 3.2.1.182, 3.2.1.21
Find proteins for P49235 (Zea mays)
Go to UniProtKB:  P49235
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
A, B
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
HBO
Query on HBO

Download SDF File 
Download CCD File 
A, B
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: 2.1 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 93.100α = 90.00
b = 95.300β = 90.00
c = 119.700γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-12-11
    Type: Initial release
  • Version 1.1: 2015-09-16
    Type: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Source and taxonomy, Structure summary, Version format compliance