8Y0L | pdb_00008y0l

beta-glucosidase from Thermoascus aurantiacus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.201 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

A thermostable and highly active fungal GH3 beta-glucosidase generated by random and saturation mutagenesis.

Matsuzaki, C.Hidaka, M.Nakashima, Y.Honda, Y.Koyanagi, T.Ishikawa, K.Katoh, T.Katayama, T.Kumagai, H.

(2025) Proc Jpn Acad Ser B Phys Biol Sci 101: 177-195

  • DOI: https://doi.org/10.2183/pjab.101.011
  • Primary Citation of Related Structures:  
    8Y0L, 8Y0M

  • PubMed Abstract: 

    Enhancing the thermostability of cellulose-degrading enzymes is pivotal for establishing an efficient bioconversion system from cellulosic materials to value-added compounds. Here, by introducing random and saturation mutagenesis into the Thermoascus aurantiacus β-glucosidase gene, we generated a hyperthermostable mutant with five amino acid substitutions. Analysis of temperature-induced unfolding revealed the involvement of each replacement in the increased T m value. Structural analysis showed that all replacements are located at the periphery of the catalytic pocket. D433N replacement, which had a pronounced thermostabilizing effect (ΔT m = 4.5°C), introduced an additional hydrogen bond with a backbone carbonyl oxygen in a long loop structure. The mutant enzyme expressed in Kluyveromyces marxianus exhibited a T m of 82°C and hydrolyzed cellobiose with k cat and K m values of 200 s -1 and 1.8 mM, respectively. When combined with a thermostable endoglucanase, the mutant enzyme released 20% more glucose than wild-type enzyme from cellulosic material. The mutant enzyme is therefore a noteworthy addition to the existing repertoire of thermostable β-glucosidases.


  • Organizational Affiliation
    • Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
beta-glucosidase
A, B, C, D
861Thermoascus aurantiacusMutation(s): 0 
Gene Names: bgl1
EC: 3.2.1.21
UniProt
Find proteins for Q0ZUL0 (Thermoascus aurantiacus)
Explore Q0ZUL0 
Go to UniProtKB:  Q0ZUL0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0ZUL0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NOJ (Subject of Investigation/LOI)
Query on NOJ

Download Ideal Coordinates CCD File 
H [auth A],
L [auth B],
P [auth C],
T [auth D]
1-DEOXYNOJIRIMYCIN
C6 H13 N O4
LXBIFEVIBLOUGU-JGWLITMVSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
I [auth B]
J [auth B]
E [auth A],
F [auth A],
G [auth A],
I [auth B],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
O [auth C],
Q [auth D],
R [auth D],
S [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.201 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.175 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.945α = 90
b = 149.752β = 90
c = 175.529γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-30
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Database references