title: Toward mechanistic classification of enzyme functions.
abstract: Classification of enzyme function should be quantitative, computationally accessible, and informed by sequences and structures to enable use of genomic information for functional inference and other applications. Large-scale studies have established that divergently evolved enzymes share conserved elements of structure and common mechanistic steps and that convergently evolved enzymes often converge to similar mechanisms too, suggesting that reaction mechanisms could be used to develop finer-grained functional descriptions than provided by the Enzyme Commission (EC) system currently in use. Here we describe how evolution informs these structure-function mappings and review the databases that store mechanisms of enzyme reactions along with recent developments to measure ligand and mechanistic similarities. Together, these provide a foundation for new classifications of enzyme function.
authors.affiliation: Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, 1700 4th Street, MC 2550, San Francisco, CA 94158, USA.
authors.forename: Daniel E
authors.initials: DE
authors.lastname: Almonacid
authors.forename: Patricia C
authors.initials: PC
authors.lastname: Babbitt
mesh_terms: D000465:Algorithms; D002384:Catalysis; D030562:Databases, Protein; D004798:Enzymes / Q000737:chemistry* / Q000145:classification* / Q000235:genetics / Q000378:metabolism; D019143:Evolution, Molecular; D013329:Structure-Activity Relationship
chemical_list: D004798:Enzymes