Tailoring the specificity of the type C feruloyl esterase FoFaeC from Fusarium oxysporum towards methyl sinapate by rational redesign based on small molecule docking simulations

PLoS One. 2018 May 24;13(5):e0198127. doi: 10.1371/journal.pone.0198127. eCollection 2018.

Abstract

The type C feruloyl esterase FoFaeC from Fusarium oxysporum is a newly discovered enzyme with high potential for use in the hydrolysis of lignocellulosic biomass but it shows low activity towards sinapates. In this work, small molecule docking simulations were employed in order to identify important residues for the binding of the four model methyl esters of hydroxycinnamic acids, methyl ferulate/caffeate/sinapate/p-coumarate, to the predicted structure of FoFaeC. Subsequently rational redesign was applied to the enzyme' active site in order to improve its specificity towards methyl sinapate. A double mutation (F230H/T202V) was considered to provide hydrophobic environment for stabilization of the methoxy substitution on sinapate and a larger binding pocket. Five mutant clones and the wild type were produced in Pichia pastoris and biochemically characterized. All clones showed improved activity, substrate affinity, catalytic efficiency and turnover rate compared to the wild type against methyl sinapate, with clone P13 showing a 5-fold improvement in catalytic efficiency. Although the affinity of all mutant clones was improved against the four model substrates, the catalytic efficiency and turnover rate decreased for the substrates containing a hydroxyl substitution.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Carboxylic Ester Hydrolases / chemistry
  • Carboxylic Ester Hydrolases / genetics
  • Carboxylic Ester Hydrolases / metabolism*
  • Catalysis
  • Cinnamates / chemistry
  • Cinnamates / metabolism*
  • Drug Design*
  • Fusarium / enzymology*
  • Fusarium / genetics
  • Gene Expression Regulation, Enzymologic / drug effects*
  • Models, Molecular
  • Molecular Docking Simulation
  • Mutation*
  • Sequence Homology
  • Small Molecule Libraries / pharmacology*
  • Substrate Specificity

Substances

  • Cinnamates
  • Small Molecule Libraries
  • methyl-p-coumarate
  • antithiamine factor
  • Carboxylic Ester Hydrolases
  • feruloyl esterase

Grants and funding

This work was supported by grant from European Union- Large scale integrating project targeted to SMEs “Optimized esterase biocatalysts for cost-effective industrial production (OPTIBIOCAT)” grant agreement no. 613868, co-funded within the FP7 Knowledge Based Bio-Economy (KBBE). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.