Classification of common functional loops of kinase super-families

Narcis Fernandez-Fuentes, Antoni Hermoso, Jordi Espadaler, Enrique Querol, Francesc X Aviles, Baldomero Oliva

Research output: Contribution to journalArticlepeer-review

21 Citations (SciVal)

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.
Original languageEnglish
Pages (from-to)539-555
Number of pages17
JournalProteins: Structure, Function and Genetics
Volume56
Issue number3
Early online date16 Apr 2004
DOIs
Publication statusPublished - 15 Aug 2004

Keywords

  • protein-loops classification
  • P-loop
  • protein-motifs
  • kinases
  • comparative modeling

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