8Y9Q | pdb_00008y9q

b-glucosidase from Thermotoga profunda Tp-BGL

• PDB DOI: https://doi.org/10.2210/pdb8Y9Q/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga profunda
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-07 Released: 2025-02-12 
• Deposition Author(s): Guo, Y., Chen, A.
• Funding Organization(s): Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.172 (Depositor), 0.174 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.154 (Depositor) 

Starting Model: experimental

Literature

Structural insights and functional characterization of a novel beta-glucosidase derived from Thermotoga profunda.

Guo, Y., Chen, A., Liu, K., Ji, C.

(2024) Biochem Biophys Res Commun 732: 150405-150405

• PubMed: 39033552 
• DOI: https://doi.org/10.1016/j.bbrc.2024.150405
• Primary Citation Related Structures: 
  8Y9Q


• PubMed Abstract: 
  

  β-Glucosidase is a crucial cellulase, as its activity determines the efficiency of cellulose hydrolysis into glucose. This study addresses the functional and structural characteristics of Thermotoga profunda β-glucosidase (Tp-BGL). Tp-BGL exhibited a K _m of 0.3798 mM for p-nitrophenyl-β-d-glucopyranoside (pNPGlc) and 4.44 mM for cellobiose, with k _cat /K _m of 1211.16 and 4.18 s ^-1  mM ^-1 , respectively. In addition, Tp-BGL showed significant pH adaptability and thermal stability, with a T _m of 85.7 °C and retaining >90 % of its activity after incubation at 80 °C for 90 min. The crystal structure of Tp-BGL was resolved at 1.95 Å resolution, and reveals a typical TIM barrel structure. Comparative structural analysis highlighted that the major distinction between Tp-BGL and the other glucosidases lies in their loop regions.

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Organizational Affiliation: 
• School of Life Sciences, Fudan University, Shanghai, 200433, China.
School of Life Sciences, Fudan University, Shanghai, 200433, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 104.42 kDa 
• Atom Count: 8,401 
• Modeled Residue Count: 896 
• Deposited Residue Count: 896 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
b-glucosidase	A, B	448	Thermotoga profunda	Mutation(s): 0  EC: 3.2.1.21 (PDB Primary Data), 3.2.1.23 (UniProt)
UniProt
Find proteins for P22498 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore P22498  Go to UniProtKB:  P22498

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL (Subject of Investigation/LOI)	C [auth A], D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.172 (Depositor), 0.174 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.154 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.709	α = 90
b = 179.709	β = 90
c = 89.033	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	phasing
autoPROC	data reduction
autoPROC	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-02-12 
Deposition Author(s): Guo, Y., Chen, A.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2021YFC2301500

Revision History  

• Version 1.0: 2025-02-12
  Type: Initial release