8ZNW | pdb_00008znw

Crystal structure of beta-glucosidase Cba3 from Cellulomonas biazotea in complex with glucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.188 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.154 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 
    0.156 (Depositor) 

Starting Model: experimental
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Literature

Glucose binding to the gatekeeper region induces the glucose stimulation of beta-glucosidase Cba3 from Cellulomonas biazotea.

Kim, D.Nam, K.H.Kim, I.J.

(2025) Int J Biol Macromol 319: 145590-145590

  • DOI: https://doi.org/10.1016/j.ijbiomac.2025.145590
  • Primary Citation of Related Structures:  
    8ZNV, 8ZNW

  • PubMed Abstract: 

    The transition from an economy reliant on fossil fuels to a sustainable bioeconomy that utilizes renewable biomass feedstock to produce chemicals, bioplastics, and biofuels is imperative. β-Glucosidase (BGL) is essential for hydrolyzing cellooligosaccharides in lignocellulosic biomass to generate glucose. During biomass degradation, glucose can inhibit or stimulate BGL activity. Accordingly, identifying and characterizing glucose-stimulated and glucose-tolerant BGL has become a major research focus in industrial BGL applications. In the current study, BGL Cba3 from Cellulomonas biazotea-a cellulose-degrading bacterium-(CbiCba3) demonstrated glucose-stimulated and glucose-tolerant properties. The hydrolase activity of CbiCba3 increased by 1.3-fold in the presence of 31.25 mM glucose and was maintained at glucose concentrations up to 500 mM. The crystal structure of glucose-bound CbiCba3 shows that the glucose molecule binds the glycone and gatekeeper regions. The occupancy of the glucose molecule in the gatekeeper region reduces the substrate-accessible entrance and induces conformational changes in the Gln295 and Val310 side chains, narrowing the substrate entrance. Mutagenesis studies revealed that glucose binding the gatekeeper region is responsible for glucose stimulation; this binding site of CbiCba3 is distinct from those previously reported for glucose-stimulated BGLs. Meanwhile, Trp323 and Asn176 in CbiCba3 form a narrow substrate-binding channel at the aglycone site associated with glucose tolerance. Although Asn176 is not conserved in other glucose-tolerant BGLs, their channel widths are similar. These results highlight the significant glucose-stimulated and glucose-tolerant properties of CbiCba3, providing valuable insights for BGL protein engineering to enhance enzyme activity for more efficient biotechnological applications.


  • Organizational Affiliation
    • Division of Applied Life Sciences, Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-glucosidase447Cellulomonas biazoteaMutation(s): 0 
Gene Names: cba3bglBCBZ_21620
EC: 3.2.1.21
UniProt
Find proteins for G1C1T5 (Cellulomonas biazotea)
Explore G1C1T5 
Go to UniProtKB:  G1C1T5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG1C1T5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.188 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.154 (Depositor), 0.169 (DCC) 
  • R-Value Observed: 0.156 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.08α = 90
b = 72.354β = 108.14
c = 78.381γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2021R1I1A1A01050838
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2022R1I1A1A01072158

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-28
    Type: Initial release
  • Version 1.1: 2025-12-10
    Changes: Database references