The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.


Furnham, N; Holliday, GL; de Beer, TA; Jacobsen, JO; Pearson, WR; Thornton, JM; (2013) The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic acids research, 42 (Database issue). D485-9. ISSN 0305-1048 DOI: https://doi.org/10.1093/nar/gkt1243

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Abstract

: Understanding which are the catalytic residues in an enzyme and what function they perform is crucial to many biology studies, particularly those leading to new therapeutics and enzyme design. The original version of the Catalytic Site Atlas (CSA) (http://www.ebi.ac.uk/thornton-srv/databases/CSA) published in 2004, which catalogs the residues involved in enzyme catalysis in experimentally determined protein structures, had only 177 curated entries and employed a simplistic approach to expanding these annotations to homologous enzyme structures. Here we present a new version of the CSA (CSA 2.0), which greatly expands the number of both curated (968) and automatically annotated catalytic sites in enzyme structures, utilizing a new method for annotation transfer. The curated entries are used, along with the variation in residue type from the sequence comparison, to generate 3D templates of the catalytic sites, which in turn can be used to find catalytic sites in new structures. To ease the transfer of CSA annotations to other resources a new ontology has been developed: the Enzyme Mechanism Ontology, which has permitted the transfer of annotations to Mechanism, Annotation and Classification in Enzymes (MACiE) and UniProt Knowledge Base (UniProtKB) resources. The CSA database schema has been re-designed and both the CSA data and search capabilities are presented in a new modern web interface.<br/>

Item Type: Article
Faculty and Department: Faculty of Infectious and Tropical Diseases > Dept of Pathogen Molecular Biology
PubMed ID: 24319146
Web of Science ID: 331139800072
URI: http://researchonline.lshtm.ac.uk/id/eprint/2374031

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