8Z2Y | pdb_00008z2y

High-resolution crystal structure of exo-beta-(1,3)-glucanase from Aspergillus oryzae (AoBgl) as a complex with glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 
    0.185 (Depositor), 0.189 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.162 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of Aspergillus oryzae exo-beta-(1,3)-glucanase reveal insights into oligosaccharide binding, recognition, and hydrolysis.

Banerjee, B.Kamale, C.K.Suryawanshi, A.B.Dasgupta, S.Noronha, S.Bhaumik, P.

(2025) FEBS Lett 599: 53-73

  • DOI: https://doi.org/10.1002/1873-3468.15045
  • Primary Citation Related Structures: 
    8Z2W, 8Z2X, 8Z2Y

  • PubMed Abstract: 

    Exo-β-(1,3)-glucanases are promising enzymes for use in the biofuel industry as they hydrolyse sugars such as laminarin, a major constituent of the algal cell wall. This study reports structural and biochemical characterizations of Aspergillus oryzae exo-β-(1,3)-glucanase (AoBgl) belonging to the GH5 family. Purified AoBgl hydrolyses β-(1,3)-glycosidic linkages of the oligosaccharide laminaritriose and the polysaccharide laminarin effectively. We have determined three high-resolution structures of AoBgl: (a) the apo form at 1.75 Å, (b) the complexed form with bound cellobiose at 1.73 Å and (c) the glucose-bound form at 1.20 Å. The crystal structures, molecular dynamics simulation studies and site-directed mutagenesis reveal the mode of substrate binding and interactions at the active site. The results also indicate that AoBgl effectively hydrolyses trisaccharides and higher oligosaccharides. The findings from our structural and biochemical studies would aid in rational engineering efforts to generate superior AoBgl variants and similar GH5 enzymes for their industrial use.


  • Organizational Affiliation
    • Department of Biosciences and Bioengineering, IIT Bombay, Mumbai, India.

Macromolecule Content 

  • Total Structure Weight: 45.91 kDa 
  • Atom Count: 3,529 
  • Modeled Residue Count: 382 
  • Deposited Residue Count: 411 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glucan 1,3-beta-glucosidase A411Aspergillus oryzaeMutation(s): 0 
Gene Names: exgAexg1AO090003000990
EC: 3.2.1.58
UniProt
Find proteins for Q7Z9L3 (Aspergillus oryzae (strain ATCC 42149 / RIB 40))
Explore Q7Z9L3 
Go to UniProtKB:  Q7Z9L3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z9L3
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BGC
(Subject of Investigation/LOI)

Query on BGC



Download:Ideal Coordinates CCD File
D [auth A],
F [auth A]
beta-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
GOL
(Subject of Investigation/LOI)

Query on GOL



Download:Ideal Coordinates CCD File
C [auth A],
E [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
(Subject of Investigation/LOI)

Query on EDO



Download:Ideal Coordinates CCD File
B [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
(Subject of Investigation/LOI)

Query on CL



Download:Ideal Coordinates CCD File
G [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
(Subject of Investigation/LOI)

Query on NA



Download:Ideal Coordinates CCD File
H [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free:  0.185 (Depositor), 0.189 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.162 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.29α = 90
b = 81.29β = 90
c = 114.74γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Biotechnology (DBT, India)IndiaBT/PR41982/PBD/26/822/2021

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2025-01-29
    Changes: Database references