7E5J

Crystal structure of beta-glucosidase from Thermoanaerobacterium saccharolyticum

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 

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Literature

Biochemical and Structural Analysis of a Glucose-Tolerant beta-Glucosidase from the Hemicellulose-Degrading Thermoanaerobacterium saccharolyticum.

Kim, I.J., Bornscheuer, U.T., Nam, K.H.

(2022) Molecules 27

  • DOI: https://doi.org/10.3390/molecules27010290
  • Primary Citation of Related Structures:  
    7E5J

  • PubMed Abstract: 

    • β-Glucosidases (Bgls) convert cellobiose and other soluble cello-oligomers into glucose and play important roles in fundamental biological processes, providing energy sources in living organisms. Bgls are essential terminal enzymes of cellulose degradation systems and attractive targets for lignocellulose-based biotechnological applications ...

    β-Glucosidases (Bgls) convert cellobiose and other soluble cello-oligomers into glucose and play important roles in fundamental biological processes, providing energy sources in living organisms. Bgls are essential terminal enzymes of cellulose degradation systems and attractive targets for lignocellulose-based biotechnological applications. Characterization of novel Bgls is important for broadening our knowledge of this enzyme class and can provide insights into its further applications. In this study, we report the biochemical and structural analysis of a Bgl from the hemicellulose-degrading thermophilic anaerobe Thermoanaerobacterium saccharolyticum (TsaBgl). TsaBgl exhibited its maximum hydrolase activity on p -nitrophenyl-β-d-glucopyranoside at pH 6.0 and 55 °C. The crystal structure of TsaBgl showed a single (β/α) 8 TIM-barrel fold, and a β8-α14 loop, which is located around the substrate-binding pocket entrance, showing a unique conformation compared with other structurally known Bgls. A Tris molecule inhibited enzyme activity and was bound to the active site of TsaBgl coordinated by the catalytic residues Glu163 (proton donor) and Glu351 (nucleophile). Titration experiments showed that TsaBgl belongs to the glucose-tolerant Bgl family. The gatekeeper site of TsaBgl is similar to those of other glucose-tolerant Bgls, whereas Trp323 and Leu170, which are involved in glucose tolerance, show a unique configuration. Our results therefore improve our knowledge about the Tris-mediated inhibition and glucose tolerance of Bgl family members, which is essential for their industrial application.

    Organizational Affiliation: 

    POSTECH Biotech Center, Pohang University of Science and Technology, Pohang 37673, Korea.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-glucosidaseA446Thermoanaerobacterium saccharolyticum JW/SL-YS485Mutation(s): 0 
Gene Names: Tsac_2208
EC: 3.2.1.21
UniProt
Find proteins for I3VXG7 (Thermoanaerobacterium saccharolyticum (strain DSM 8691 / JW/SL-YS485))
Explore I3VXG7 
Go to UniProtKB:  I3VXG7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI3VXG7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TRS (Subject of Investigation/LOI)
Query on TRS
Download Ideal Coordinates CCD File 
B [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]		SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.71 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.141 
  • R-Value Observed: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.139α = 90
b = 71.293β = 90
c = 99.24γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2022-02-23 
    • Deposition Author(s): Nam, K.H.
Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2017R1D1A1B03033087
National Research Foundation (NRF, Korea)Korea, Republic OfNRF-2017M3A9F6029736

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-23
    Type: Initial release
  • Version 1.1: 2022-08-31
    Changes: Database references