7WWH | pdb_00007wwh

Crystal structure of the Geobacillus thermoglucosidasius feruloyl esterase GthFAE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 
    0.203 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history

Literature

Structure-guided rational design of the Geobacillus thermoglucosidasius feruloyl esterase GthFAE to improve its thermostability.

Yang, W.Sun, L.Dong, P.Chen, Y.Zhang, H.Huang, X.Wu, L.Chen, L.Jing, D.Wu, Y.

(2022) Biochem Biophys Res Commun 600: 117-122

  • DOI: https://doi.org/10.1016/j.bbrc.2022.02.074
  • Primary Citation Related Structures: 
    7WWH

  • PubMed Abstract: 

    Feruloyl esterases are indispensable biocatalysts catalyzing the cleavage of ester bonds between polysaccharides and their hydroxycinnamoyl cross-links. GthFAE from Geobacillus thermoglucosidasius was identified as a thermophilic alkaline feruloyl esterase with potential applications in paper manufacturing. To improve the enzymatic properties rationally and efficiently, the structure of GthFAE was solved at 1.9 Å, revealing a core domain of classical α/β hydrolase fold and an inserted α/β cap domain. In silico analysis based on it helped us to investigate whether the residues at the active center have positive effects on the stability, and how. Several site-directed mutations were conducted, of which substitutions at residues T41 and T150 apparently improved the thermostability. The combination mutant T41N/T150R exhibited an optimal temperature of 65 °C, a 6.4 °C higher T m compared to wild type by 80 °C, and a 35-fold longer in half-life (201 min) at 70 °C. Molecular dynamics simulations further illustrated that the structure of T41N/T150R was more stable than the wild type and T150R stabilized the cap domain by introducing salt bridges to the region with E154 and D164. This study not only highlighted residues within the active center on their thermostability improving effects, but also contributed to the prospective industrial application of GthFAE.


  • Organizational Affiliation
    • Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, College of Life Science, Fujian Normal University, Fuzhou, 350117, China.

Macromolecule Content 

  • Total Structure Weight: 56.35 kDa 
  • Atom Count: 4,365 
  • Modeled Residue Count: 502 
  • Deposited Residue Count: 504 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Alpha/beta hydrolase
A, B
252Parageobacillus thermoglucosidasiusMutation(s): 0 
Gene Names: DV712_01095

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free:  0.203 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.183 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.038α = 90
b = 87.41β = 95.97
c = 69.456γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other government--

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-09
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Refinement description