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Classification of common functional loops of kinase super‐families
Author(s) -
FernandezFuentes Narcis,
Hermoso Antoni,
Espadaler Jordi,
Querol Enrique,
Aviles Francesc X.,
Oliva Baldomero
Publication year - 2004
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20136
Subject(s) - subclass , kinase , loop (graph theory) , computational biology , set (abstract data type) , biology , function (biology) , computer science , bioinformatics , pattern recognition (psychology) , genetics , artificial intelligence , mathematics , combinatorics , programming language , antibody
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.