Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 117.58 kDa 
• Atom Count: 8594 
• Residue Count: 982 
• Unique protein chains: 1

1E55

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

• DOI: 10.2210/pdb1E55/pdb

• Classification: HYDROLASE
• Organism(s): Zea mays
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-07-18 Released: 2000-12-11 
• Deposition Author(s): Czjzek, M., Cicek, M., Bevan, D.R., Zamboni, V., Henrissat, B., Esen, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.235 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

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 U S A 97: 13555-13560

• PubMed: 11106394 
• DOI: 10.1073/pnas.97.25.13555
• Primary Citation of Related Structures:  
  1E56, 1E55, 1E4N, 1E4L


• 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.

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Related Citations: 

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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-GLUCOSIDASE	A, B	512	Zea mays	Mutation(s): 1  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	A, B	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
DHR	A, B	(2S)-HYDROXY(4-HYDROXYPHENYL)ETHANENITRILE C8 H7 N O2 HOOOPXDSCKBLFG-MRVPVSSYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DHR	Ki:  76000   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• 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 = 91.8	α = 90
b = 95	β = 90
c = 117.5	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-07-18 
• Released Date: 2000-12-11 
Deposition Author(s): Czjzek, M., Cicek, M., Bevan, D.R., Zamboni, V., Henrissat, B., Esen, A.

Revision History 

• 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