Bioinformatic analysis of α/β-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities

Protein Eng Des Sel. 2012 Nov;25(11):689-97. doi: 10.1093/protein/gzs068. Epub 2012 Oct 4.


Superfamily of alpha-beta hydrolases is one of the largest groups of structurally related enzymes with diverse catalytic functions. Bioinformatic analysis was used to study how lipase and amidase catalytic activities are implemented into the same structural framework. Subfamily-specific positions--conserved within lipases and peptidases but different between them--that were supposed to be responsible for functional discrimination have been identified. Mutations at subfamily-specific positions were used to introduce amidase activity into Candida antarctica lipase B (CALB). Molecular modeling was implemented to evaluate influence of selected residues on binding and catalytic conversion of amide substrate by corresponding library of mutants. In silico screening was applied to select reactive enzyme-substrate complexes that satisfy knowledge-based criteria of amidase catalytic activity. Selected CALB variants with substitutions at subfamily-specific positions Gly39, Thr103, Trp104, and Leu278 were produced and showed significant improvement of experimentally measured amidase activity. Based on these results, we suggest that value of subfamily-specific positions should be further explored in order to develop a systematic tool to study structure-function relationship in enzymes and to use this information for rational enzyme engineering.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amidohydrolases / chemistry
  • Amidohydrolases / metabolism*
  • Amino Acid Substitution
  • Candida / chemistry
  • Candida / enzymology*
  • Candida / genetics
  • Catalytic Domain
  • Computational Biology / methods*
  • Fungal Proteins / chemistry
  • Fungal Proteins / genetics
  • Fungal Proteins / metabolism*
  • Humans
  • Hydrolases / chemistry
  • Hydrolases / metabolism*
  • Lipase / chemistry
  • Lipase / genetics
  • Lipase / metabolism*
  • Molecular Dynamics Simulation
  • Protein Conformation
  • Protein Engineering


  • Fungal Proteins
  • Hydrolases
  • Lipase
  • lipase B, Candida antarctica
  • Amidohydrolases
  • amidase