title: Classification of common functional loops of kinase super-families.
abstract: A structural classification of loops has been obtained from a set of 141 protein structures classified as kinases. A total of 1813 loops was classified into 133 subclasses (9 betabeta(links), 15 betabeta(hairpins), 31 alpha-alpha, 46 alpha-beta and 32 beta-alpha). Functional information and specific features relating subclasses and function were included in the classification. Functional loops such as the P-loop (shared by different folds) or the Gly-rich-loop, among others, were classified into structural motifs. As a result, a common mechanism of catalysis and substrate binding was proved for most kinases. Additionally, the multiple-alignment of loop sequences made within each subclass was shown to be useful for comparative modeling of kinase loops. The classification is summarized in a kinase loop database located at http://sbi.imim.es/archki.
authors.affiliation: Institut de Biotecnologia i Biomedicina and Department de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
authors.forename: Narcis
authors.initials: N
authors.lastname: Fernandez-Fuentes
authors.forename: Antoni
authors.initials: A
authors.lastname: Hermoso
authors.forename: Jordi
authors.initials: J
authors.lastname: Espadaler
authors.forename: Enrique
authors.initials: E
authors.lastname: Querol
authors.forename: Francesc X
authors.initials: FX
authors.lastname: Aviles
authors.forename: Baldomero
authors.initials: B
authors.lastname: Oliva
mesh_terms: D020816:Amino Acid Motifs; D020134:Catalytic Domain; D030562:Databases, Protein; D008956:Models, Chemical; D010770:Phosphotransferases / Q000737:chemistry* / Q000145:classification*; D011494:Protein Kinases / Q000737:chemistry; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D040681:Structural Homology, Protein; D013329:Structure-Activity Relationship
chemical_list: D010770:Phosphotransferases; D011494:Protein Kinases