Classification of common functional loops of kinase super-families

Proteins
Narcis Fernandez-FuentesBaldomero Oliva

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.

References

Nov 1, 1990·Trends in Biochemical Sciences·M SarasteA Wittinghofer
Jan 1, 1985·Advances in Protein Chemistry·G D RoseJ A Smith
Nov 15, 1994·Structure·A V Efimov
Nov 4, 1994·Journal of Molecular Biology·S Henikoff, J G Henikoff
Feb 11, 1994·Journal of Molecular Biology·H J Müller-Dieckmann, G E Schulz
Jan 12, 1996·Journal of Molecular Biology·R T WintjensS J Wodak
May 21, 1996·Biochemistry·M A SinevE Haas
May 23, 1996·Nature·K Fritz-WolfW Kabsch
Jun 25, 1996·Proceedings of the National Academy of Sciences of the United States of America·R M XuX Cheng
Jan 1, 1997·Trends in Biochemical Sciences·T Hunter, G D Plowman
Dec 1, 1996·Computer Applications in the Biosciences : CABIOS·R W HooftG Vriend
Feb 13, 1997·Nature·F SicheriJ Kuriyan
Mar 7, 1997·Journal of Molecular Biology·B OlivaM J Sternberg
May 20, 1998·Structure·A MatteL T Delbaere
Jun 20, 1998·Journal of Molecular Biology·T KrellA J Lapthorn
Jul 17, 1998·Nature Structural Biology·A M MulichakR M Garavito
Jul 22, 1998·Proceedings of the National Academy of Sciences of the United States of America·G ZhouM S Chapman
Dec 8, 1998·Biochemistry·I I MathewsS E Ealick
Dec 16, 1998·FEBS Letters·J K RaoA Wlodawer
Mar 17, 1999·Biochimica Et Biophysica Acta·P W Schenk, B E Snaar-Jagalska

❮ Previous
Next ❯

Citations

Feb 6, 2010·BMC Bioinformatics·Leslie RegadAnne-Claude Camproux
Jun 30, 2007·BMC Bioinformatics·Sungroh YoonRuss B Altman
Nov 1, 2012·Cell Communication and Signaling : CCS·Stephan M Feller, Marc Lewitzky
Nov 23, 2013·Nucleic Acids Research·Jaume BonetBaldo Oliva
Jul 17, 2009·Protein Science : a Publication of the Protein Society·Manoj TyagiAlexandre G de Brevern
Nov 18, 2005·Proteins·Marco De VivoMaurizio Recanatini

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.