Using a Library of Structural Templates to Recognise Catalytic Sites and Explore their Evolution in Homologous Families

• Published in: Journal of molecular biology 2005-04, Vol.347 (3), p.565-581
• Main Authors: Torrance, James W., Bartlett, Gail J., Porter, Craig T., Thornton, Janet M.
• Format: Article
• Language: English
• Subjects: active site; Algorithms; Animals; Bacterial Proteins - chemistry; Catalytic Domain; catalytic residue; catalytic site atlas; Databases, Protein; Evolution, Molecular; function prediction; Humans; Models, Molecular; Molecular Structure; Protein Structure, Tertiary; structural template
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2005.01.044

Catalytic site structure is normally highly conserved between distantly related enzymes. As a consequence, templates representing catalytic sites have the potential to succeed at function prediction in cases where methods based on sequence or overall structure fail. There are many methods for searching protein structures for matches to structural templates, but few validated template libraries to use with these methods. We present a library of structural templates representing catalytic sites, based on information from the scientific literature. Furthermore, we analyse homologous template families to discover the diversity within families and the utility of templates for active site recognition. Templates representing the catalytic sites of homologous proteins mostly differ by less than 1 Å root mean square deviation, even when the sequence similarity between the two proteins is low. Within these sets of homologues there is usually no discernible relationship between catalytic site structure similarity and sequence similarity. Because of this structural conservation of catalytic sites, the templates can discriminate between matches to related proteins and random matches with over 85% sensitivity and predictive accuracy. Templates based on protein backbone positions are more discriminating than those based on side-chain atoms. These analyses show encouraging prospects for prediction of functional sites in structural genomics structures of unknown function, and will be of use in analyses of convergent evolution and exploring relationships between active site geometry and chemistry. The template library can be queried via a web server at www.ebi.ac.uk/thornton-srv/databases/CSS and is available for download.