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Proteins. 2004 Aug 15;56(3):539-55.

Classification of common functional loops of kinase super-families.

Author information

1
Institut de Biotecnologia i Biomedicina and Department de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.

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.

PMID:
15229886
DOI:
10.1002/prot.20136
[Indexed for MEDLINE]

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