1H49

CRYSTAL STRUCTURE OF THE INACTIVE DOUBLE MUTANT OF THE MAIZE BETA-GLUCOSIDASE ZMGLU1-E191D-F198V IN COMPLEX WITH DIMBOA-GLUCOSIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mutational and Structural Analysis of Aglycone Specificity in Maize and Sorghum Beta-Glucosidases

Verdoucq, L.Czjzek, M.Moriniere, J.Bevan, D.R.Esen, A.

(2003) J Biol Chem 278: 25055

  • DOI: 10.1074/jbc.M301978200
  • Primary Citation of Related Structures:  
    1H49

  • PubMed Abstract: 
  • Plant beta-glucosidases display varying substrate specificities. The maize beta-glucosidase isozyme Glu1 (ZmGlu1) hydrolyzes a broad spectrum of substrates in addition to its natural substrate DIMBOA-Glc (2-O-beta-d-glucopyranosyl-4-hydroxy-7-methoxy ...

    Plant beta-glucosidases display varying substrate specificities. The maize beta-glucosidase isozyme Glu1 (ZmGlu1) hydrolyzes a broad spectrum of substrates in addition to its natural substrate DIMBOA-Glc (2-O-beta-d-glucopyranosyl-4-hydroxy-7-methoxy-1,4-benzoxaxin-3-one), whereas the sorghum beta-glucosidase isozyme Dhr1 (SbDhr1) hydrolyzes exclusively its natural substrate dhurrin (p-hydroxy-(S)-mandelonitrile-beta-d-glucoside). Structural data from cocrystals of enzyme-substrate and enzyme-aglycone complexes have shown that five amino acid residues (Phe198, Phe205, Trp378, Phe466, and Ala467) are located in the aglycone-binding site of ZmGlu1 and form the basis of aglycone recognition and binding, hence substrate specificity. To study the mechanism of substrate specificity further, mutant beta-glucosidases were generated by replacing Phe198, Phe205, Asp261, Met263, Phe377, Phe466, Ala467, and Phe473 of Glu1 by Dhr1 counterparts. The effects of mutations on enzyme activity and substrate specificity were studied using both natural and artificial substrates. The simple mutant replacing Phe198 by a valine had the most drastic effect on activity, because the capacity of this enzyme to hydrolyze beta-glucosides was almost completely abolished. The analysis of this mutation was completed by a structural study of the double mutant ZmGlu1-E191D,F198V in complex with the natural substrate. The structure reveals that the single mutation F198V causes a cascade of conformational changes, which are unpredictable by standard molecular modeling techniques. Some other mutations led to drastic effects: replacing Asp261 by an asparagine decreases the catalytic efficiency of this simple mutant by 75% although replacing Tyr473 by a phenylalanine increase its efficiency by 300% and also provides a new substrate specificity by hydrolyzing dhurrin.


    Related Citations: 
    • 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

    Organizational Affiliation

    Department of Biology, Virginia Polytechnic Institute and State University, Blacksburg 24061, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
BETA-GLUCOSIDASEA, B512Zea maysMutation(s): 2 
Gene Names: GLU1
EC: 3.2.1.21 (PDB Primary Data), 3.2.1.182 (UniProt)
Find proteins for P49235 (Zea mays)
Explore P49235 
Go to UniProtKB:  P49235
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HBO
Query on HBO

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
BGC
Query on BGC

Download CCD File 
A, B
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.145α = 90
b = 114.088β = 93.88
c = 80.126γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary