6EFU | pdb_00006efu

Crystal structure of the double mutant L167W / P172L of the beta-glucosidase from Trichoderma harzianum

• PDB DOI: https://doi.org/10.2210/pdb6EFU/pdb

• Classification: HYDROLASE
• Organism(s): Trichoderma harzianum
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-08-17 Released: 2019-06-26 
• Deposition Author(s): Morais, M.A.B., Santos, C.A., Tonoli, C.C.C., Souza, A.P., Murakami, M.T.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.221 (Depositor), 0.223 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

An engineered GH1 beta-glucosidase displays enhanced glucose tolerance and increased sugar release from lignocellulosic materials.

Santos, C.A., Morais, M.A.B., Terrett, O.M., Lyczakowski, J.J., Zanphorlin, L.M., Ferreira-Filho, J.A., Tonoli, C.C.C., Murakami, M.T., Dupree, P., Souza, A.P.

(2019) Sci Rep 9: 4903-4903

• PubMed: 30894609 
• DOI: https://doi.org/10.1038/s41598-019-41300-3
• Primary Citation Related Structures: 
  6EFU


• PubMed Abstract: 
  

  β-glucosidases play a critical role among the enzymes in enzymatic cocktails designed for plant biomass deconstruction. By catalysing the breakdown of β-1, 4-glycosidic linkages, β-glucosidases produce free fermentable glucose and alleviate the inhibition of other cellulases by cellobiose during saccharification. Despite this benefit, most characterised fungal β-glucosidases show weak activity at high glucose concentrations, limiting enzymatic hydrolysis of plant biomass in industrial settings. In this study, structural analyses combined with site-directed mutagenesis efficiently improved the functional properties of a GH1 β-glucosidase highly expressed by Trichoderma harzianum (ThBgl) under biomass degradation conditions. The tailored enzyme displayed high glucose tolerance levels, confirming that glucose tolerance can be achieved by the substitution of two amino acids that act as gatekeepers, changing active-site accessibility and preventing product inhibition. Furthermore, the enhanced efficiency of the engineered enzyme in terms of the amount of glucose released and ethanol yield was confirmed by saccharification and simultaneous saccharification and fermentation experiments using a wide range of plant biomass feedstocks. Our results not only experimentally confirm the structural basis of glucose tolerance in GH1 β-glucosidases but also demonstrate a strategy to improve technologies for bioethanol production based on enzymatic hydrolysis.

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Organizational Affiliation: 
• Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil.
University of Cambridge, Department of Biochemistry, Cambridge, UK.
Laboratório Nacional de Ciência e Tecnologia do Bioetanol, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil.
Natural Material Innovation Centre, University of Cambridge, Cambridge, UK.
OpenPlant Synthetic Biology Research Centre, Department of Plant Sciences, University of Cambridge, Cambridge, UK.
Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, SP, Brazil.
Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil. [e-mail].
Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 106.81 kDa 
• Atom Count: 7,818 
• Modeled Residue Count: 929 
• Deposited Residue Count: 932 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-glucosidase	A, B	466	Trichoderma harzianum	Mutation(s): 2  Gene Names: bgl, CI102_8745 EC: 3.2.1.21
UniProt
Find proteins for A0A2T4AR08 (Trichoderma harzianum CBS 226.95) Explore A0A2T4AR08  Go to UniProtKB:  A0A2T4AR08

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NO3	C [auth A], D [auth A], E [auth B], F [auth B], G [auth B]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.221 (Depositor), 0.223 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.612	α = 90
b = 96.213	β = 90
c = 96.445	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-06-26 
Deposition Author(s): Morais, M.A.B., Santos, C.A., Tonoli, C.C.C., Souza, A.P., Murakami, M.T.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2015092020
Sao Paulo Research Foundation (FAPESP)	Brazil	15269820

Revision History  

• Version 1.0: 2019-06-26
  Type: Initial release
  
• Version 1.1: 2020-01-01
  Changes: Author supporting evidence
• Version 1.2: 2023-10-11
  Changes: Data collection, Database references, Refinement description