9UPT | pdb_00009upt

Structure of AtBgl1A, a GH1 beta-Glucosidase from Acetivibrio thermocellus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free: 
    0.215 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.173 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-Based Engineering to Improve Thermostability of At Bgl1A beta ‐Glucosidase.

Pitchayatanakorn, P.Putthasang, P.Chomngam, S.Jongkon, N.Choowongkomon, K.Kongsaeree, P.Fushinobu, S.Kongsaeree, P.T.

(2025) ACS Omega 10: 27153-27164

  • DOI: https://doi.org/10.1021/acsomega.5c02381
  • Primary Citation of Related Structures:  
    9UPT

  • PubMed Abstract: 

    β-Glucosidases are essential enzymes in cellulose degradation and hold significant promise for industrial applications, particularly in biorefinery processes. This study focused on the structural and functional characterization of At Bgl1A, a glycoside hydrolase family 1 β-glucosidase from , and its rational engineering to enhance thermostability. At Bgl1A exhibited over 400-fold higher specificity for laminaribiose than cellobiose, supporting its physiological role in laminaribiose metabolism. The crystal structure of the wild-type At Bgl1A was determined at 2.37-Å resolution, and served as a guide for the design of thermostabilizing mutations. Among variants, the A17S/S39T/T105V triple mutant showed the most significant improvement in thermostability, with a 145 min increase in half-life at 70 and a 5.6 °C elevation in inactivation temperature, while retaining comparable kinetic efficiency. This mutant also outperformed both the wild-type At Bgl1A and commercial enzyme in hydrolyzing cellulose and laminaran at both 60 and 70 °C. Molecular dynamics simulations and residue interaction analyses suggested that the enhanced thermostability was associated with additional hydrogen bonds, van der Waals contacts, and hydrophobic interactions introduced by the mutations. These findings provide valuable insights into the structural determinants of thermostability in GH1 β-glucosidases and demonstrate the potential of rational protein engineering for developing robust biocatalysts for industrial biomass conversion.


  • Organizational Affiliation
    • Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-glucosidase A469Acetivibrio thermocellus ATCC 27405Mutation(s): 0 
Gene Names: bglACthe_0212
EC: 3.2.1.21
UniProt
Find proteins for P26208 (Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372))
Explore P26208 
Go to UniProtKB:  P26208
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26208
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.37 Å
  • R-Value Free:  0.215 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.173 (DCC) 
Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.27α = 90
b = 158.27β = 90
c = 53.962γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentNRCT5-RSA63002-09

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-07-23
    Changes: Database references