9W4B | pdb_00009w4b

Crystal structure of beta-glucosidase CaBGL

PDB DOI: https://doi.org/10.2210/pdb9W4B/pdb

Classification: HYDROLASE
Organism(s): Caldicellulosiruptor sp.
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2025-07-31 Released: 2025-10-15
Deposition Author(s): You, C., Feng, Y.G.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

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
View more details

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

PubMed: 41043783 Search on PubMed
DOI: https://doi.org/10.1016/j.biortech.2025.133424
Primary Citation 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.

Macromolecule Content

Total Structure Weight: 646.17 kDa
Atom Count: 46,367
Modeled Residue Count: 5,432
Deposited Residue Count: 5,448
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
beta-glucosidase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	454	Caldicellulosiruptor sp.	Mutation(s): 0 EC: 3.2.1.21

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain VA [auth L] SDF format, chain UA [auth L] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain SA [auth K] SDF format, chain RA [auth K] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain PA [auth J] SDF format, chain OA [auth J] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain MA [auth I] SDF format, chain LA [auth I] SDF format, chain JA [auth H] SDF format, chain IA [auth H] SDF format, chain GA [auth G] SDF format, chain FA [auth G] SDF format, chain DA [auth F] SDF format, chain CA [auth F] SDF format, chain AA [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain VA [auth L] MOL2 format, chain UA [auth L] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain SA [auth K] MOL2 format, chain RA [auth K] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth J] MOL2 format, chain OA [auth J] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth I] MOL2 format, chain LA [auth I] MOL2 format, chain JA [auth H] MOL2 format, chain IA [auth H] MOL2 format, chain GA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain AA [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain VA [auth L] mmCIF format, chain UA [auth L] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain SA [auth K] mmCIF format, chain RA [auth K] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth J] mmCIF format, chain OA [auth J] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth I] mmCIF format, chain LA [auth I] mmCIF format, chain JA [auth H] mmCIF format, chain IA [auth H] mmCIF format, chain GA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain AA [auth E]	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		Interactions Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain MA [auth I] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth J] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain R [auth B] Focus chain RA [auth K] Focus chain SA [auth K] Focus chain T [auth C] Focus chain U [auth C] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain LA [auth I] Focus chain MA [auth I] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth J] Focus chain PA [auth J] Focus chain Q [auth B] Focus chain R [auth B] Focus chain RA [auth K] Focus chain SA [auth K] Focus chain T [auth C] Focus chain U [auth C] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Y [auth E] SDF format, chain V [auth D] SDF format, chain TA [auth L] SDF format, chain S [auth C] SDF format, chain QA [auth K] SDF format, chain P [auth B] SDF format, chain NA [auth J] SDF format, chain M [auth A] SDF format, chain KA [auth I] SDF format, chain HA [auth H] SDF format, chain EA [auth G] SDF format, chain BA [auth F] MOL2 format, chain Y [auth E] MOL2 format, chain V [auth D] MOL2 format, chain TA [auth L] MOL2 format, chain S [auth C] MOL2 format, chain QA [auth K] MOL2 format, chain P [auth B] MOL2 format, chain NA [auth J] MOL2 format, chain M [auth A] MOL2 format, chain KA [auth I] MOL2 format, chain HA [auth H] MOL2 format, chain EA [auth G] MOL2 format, chain BA [auth F] mmCIF format, chain Y [auth E] mmCIF format, chain V [auth D] mmCIF format, chain TA [auth L] mmCIF format, chain S [auth C] mmCIF format, chain QA [auth K] mmCIF format, chain P [auth B] mmCIF format, chain NA [auth J] mmCIF format, chain M [auth A] mmCIF format, chain KA [auth I] mmCIF format, chain HA [auth H] mmCIF format, chain EA [auth G] mmCIF format, chain BA [auth F]	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		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain QA [auth K] Focus chain S [auth C] Focus chain TA [auth L] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain KA [auth I] Focus chain M [auth A] Focus chain NA [auth J] Focus chain P [auth B] Focus chain QA [auth K] Focus chain S [auth C] Focus chain TA [auth L] Focus chain V [auth D] Focus chain Y [auth E]