Classification of common functional loops of kinase super-families.
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.
Fernandez-Fuentes
Narcis
N
Institut de Biotecnologia i Biomedicina and Department de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
Hermoso
Antoni
A
Espadaler
Jordi
J
Querol
Enrique
E
Aviles
Francesc X
FX
Oliva
Baldomero
B
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
D010770:Phosphotransferases; D011494:Protein Kinases