Curation of characterized glycoside hydrolases of fungal origin

Database (Oxford). 2011 May 26;2011:bar020. doi: 10.1093/database/bar020. Print 2011.

Abstract

Fungi produce a wide range of extracellular enzymes to break down plant cell walls, which are composed mainly of cellulose, lignin and hemicellulose. Among them are the glycoside hydrolases (GH), the largest and most diverse family of enzymes active on these substrates. To facilitate research and development of enzymes for the conversion of cell-wall polysaccharides into fermentable sugars, we have manually curated a comprehensive set of characterized fungal glycoside hydrolases. Characterized glycoside hydrolases were retrieved from protein and enzyme databases, as well as literature repositories. A total of 453 characterized glycoside hydrolases have been cataloged. They come from 131 different fungal species, most of which belong to the phylum Ascomycota. These enzymes represent 46 different GH activities and cover 44 of the 115 CAZy GH families. In addition to enzyme source and enzyme family, available biochemical properties such as temperature and pH optima, specific activity, kinetic parameters and substrate specificities were recorded. To simplify comparative studies, enzyme and species abbreviations have been standardized, Gene Ontology terms assigned and reference to supporting evidence provided. The annotated genes have been organized in a searchable, online database called mycoCLAP (Characterized Lignocellulose-Active Proteins of fungal origin). It is anticipated that this manually curated collection of biochemically characterized fungal proteins will be used to enhance functional annotation of novel GH genes. Database URL: http://mycoCLAP.fungalgenomics.ca/.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cellulase / genetics
  • Databases, Protein
  • Fungi / enzymology*
  • Fungi / genetics
  • Genes, Fungal / genetics
  • Glycoside Hydrolases / genetics*
  • Molecular Sequence Annotation / methods*
  • Species Specificity

Substances

  • Glycoside Hydrolases
  • Cellulase