9W4B | pdb_00009w4b

Crystal structure of beta-glucosidase CaBGL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 
    0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.190 (Depositor) 

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

Engineering of beta-glucosidase CaBGL with improved performance in cellulose hydrolysis.

You, C.Zheng, X.Qi, K.Dong, S.Liu, Y.J.Chen, C.Cui, Q.Feng, Y.

(2025) Bioresour Technol 440: 133424-133424

  • DOI: https://doi.org/10.1016/j.biortech.2025.133424
  • Primary Citation of Related Structures:  
    9W4B, 9W4F

  • PubMed Abstract: 

    β-Glucosidase (BGL) plays a crucial role in lignocellulose utilization by alleviating cellobiose inhibition of cellulases. Incorporation of the BGL from Caldicellulosiruptor sp. F32 (CaBGL) enhanced the overall efficiency of the consolidated bio-saccharification process. To optimize BGL performance under industrial conditions, we established a thermostable green fluorescent protein-based high-throughput screening platform coupled with structure-informed semi-rational design, enabling the generation of functionally enhanced CaBGL mutants. This approach identified mutant M418T, which exhibited more than two-fold catalytic activity compared to that of wild type in both the absence and presence of glucose at various concentrations. In vitro cellulose saccharification showed that M418T increased the saccharification rate coefficient by 43.27 % compared to the wild-type. The mechanisms underlying its improved property were further elucidated through structural analysis and molecular docking. Consequently, this work presents an effective approach for enhancing the performance of CaBGL and demonstrates the potential of a promising catalyst in lignocellulose conversion.


  • Organizational Affiliation
    • CAS Key Laboratory of Biofuels, Shandong Provincial Key Laboratory of Synthetic Biology, Shandong Engineering Research Center of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao 266101, China; Qingdao Engineering Laboratory of Single Cell Oil, Qingdao New Energy Shandong Laboratory, 189 Songling Road, Qingdao 266101, China; Shandong Energy Institute, 189 Songling Road, Qingdao 266101, China; University of Chinese Academy of Sciences, Beijing 100049, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
beta-glucosidase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
454Caldicellulosiruptor sp.Mutation(s): 0 
EC: 3.2.1.21
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth E]
CA [auth F]
DA [auth F]
FA [auth G]
GA [auth G]
AA [auth E],
CA [auth F],
DA [auth F],
FA [auth G],
GA [auth G],
IA [auth H],
JA [auth H],
LA [auth I],
MA [auth I],
N [auth A],
O [auth A],
OA [auth J],
PA [auth J],
Q [auth B],
R [auth B],
RA [auth K],
SA [auth K],
T [auth C],
U [auth C],
UA [auth L],
VA [auth L],
W [auth D],
X [auth D],
Z [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth F]
EA [auth G]
HA [auth H]
KA [auth I]
M [auth A]
BA [auth F],
EA [auth G],
HA [auth H],
KA [auth I],
M [auth A],
NA [auth J],
P [auth B],
QA [auth K],
S [auth C],
TA [auth L],
V [auth D],
Y [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free:  0.233 (Depositor), 0.234 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.190 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.84α = 90
b = 221.66β = 90
c = 236.22γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
Aimlessdata scaling
xia2data reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32200030
National Natural Science Foundation of China (NSFC)China32170051

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release
  • Version 1.1: 2025-10-22
    Changes: Database references