Literature DB >> 18436524

The annotation of both human and mouse kinomes in UniProtKB/Swiss-Prot: one small step in manual annotation, one giant leap for full comprehension of genomes.

Silvia Braconi Quintaje1, Sandra Orchard.   

Abstract

Biomolecule phosphorylation by protein kinases is a fundamental cell signaling process in all living cells. Following the comprehensive cataloguing of the protein kinase complement of the human genome (Manning, G., Whyte, D. B., Martinez, R., Hunter, T., and Sudarsanam, S. (2002) The protein kinase complement of the human genome. Science 298, 1912-1934), this review will detail the state-of-the-art human and mouse kinase proteomes as provided in the UniProtKB/Swiss-Prot protein knowledgebase. The sequences of the 480 classical and up to 24 atypical protein kinases now believed to exist in the human genome and 484 classical and up to 24 atypical kinases within the mouse genome have been reviewed and, where necessary, revised. Extensive annotation has been added to each entry. In an era when a wealth of new databases is emerging on the Internet, UniProtKB/Swiss-Prot makes available to the scientific community the most up-to-date and in-depth annotation of these proteins with access to additional external resources linked from within each entry. Incorrect sequence annotations resulting from errors and artifacts have been eliminated. Each entry will be constantly reviewed and updated as new information becomes available with the orthologous enzymes in related species being annotated in a parallel effort and complete kinomes being completed as sequences become available. This ensures that the mammalian kinomes available from UniProtKB/Swiss-Prot are of a consistently high standard with each separate entry acting both as a valuable information resource and a central portal to a wealth of further detail via extensive cross-referencing.

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Year:  2008        PMID: 18436524      PMCID: PMC2500232          DOI: 10.1074/mcp.R700001-MCP200

Source DB:  PubMed          Journal:  Mol Cell Proteomics        ISSN: 1535-9476            Impact factor:   5.911


  40 in total

Review 1.  Cellular signaling through multifunctional Ca2+/calmodulin-dependent protein kinase II.

Authors:  T R Soderling; B Chang; D Brickey
Journal:  J Biol Chem       Date:  2000-11-28       Impact factor: 5.157

2.  The Gene Ontology (GO) database and informatics resource.

Authors:  M A Harris; J Clark; A Ireland; J Lomax; M Ashburner; R Foulger; K Eilbeck; S Lewis; B Marshall; C Mungall; J Richter; G M Rubin; J A Blake; C Bult; M Dolan; H Drabkin; J T Eppig; D P Hill; L Ni; M Ringwald; R Balakrishnan; J M Cherry; K R Christie; M C Costanzo; S S Dwight; S Engel; D G Fisk; J E Hirschman; E L Hong; R S Nash; A Sethuraman; C L Theesfeld; D Botstein; K Dolinski; B Feierbach; T Berardini; S Mundodi; S Y Rhee; R Apweiler; D Barrell; E Camon; E Dimmer; V Lee; R Chisholm; P Gaudet; W Kibbe; R Kishore; E M Schwarz; P Sternberg; M Gwinn; L Hannick; J Wortman; M Berriman; V Wood; N de la Cruz; P Tonellato; P Jaiswal; T Seigfried; R White
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

3.  IntEnz, the integrated relational enzyme database.

Authors:  Astrid Fleischmann; Michael Darsow; Kirill Degtyarenko; Wolfgang Fleischmann; Sinéad Boyce; Kristian B Axelsen; Amos Bairoch; Dietmar Schomburg; Keith F Tipton; Rolf Apweiler
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

4.  Two novel protein-tyrosine kinases, each with a second phosphotransferase-related catalytic domain, define a new class of protein kinase.

Authors:  A F Wilks; A G Harpur; R R Kurban; S J Ralph; G Zürcher; A Ziemiecki
Journal:  Mol Cell Biol       Date:  1991-04       Impact factor: 4.272

Review 5.  A human protein atlas based on antibody proteomics.

Authors:  Anja Persson; Sophia Hober; Mathias Uhlén
Journal:  Curr Opin Mol Ther       Date:  2006-06

6.  The activating dual phosphorylation of MAPK by MEK is nonprocessive.

Authors:  W R Burack; T W Sturgill
Journal:  Biochemistry       Date:  1997-05-20       Impact factor: 3.162

7.  A phosphoserine/threonine-binding pocket in AGC kinases and PDK1 mediates activation by hydrophobic motif phosphorylation.

Authors:  Morten Frödin; Torben L Antal; Bettina A Dümmler; Claus J Jensen; Maria Deak; Steen Gammeltoft; Ricardo M Biondi
Journal:  EMBO J       Date:  2002-10-15       Impact factor: 11.598

8.  The PIF-binding pocket in PDK1 is essential for activation of S6K and SGK, but not PKB.

Authors:  R M Biondi; A Kieloch; R A Currie; M Deak; D R Alessi
Journal:  EMBO J       Date:  2001-08-15       Impact factor: 11.598

9.  DrugBank: a comprehensive resource for in silico drug discovery and exploration.

Authors:  David S Wishart; Craig Knox; An Chi Guo; Savita Shrivastava; Murtaza Hassanali; Paul Stothard; Zhan Chang; Jennifer Woolsey
Journal:  Nucleic Acids Res       Date:  2006-01-01       Impact factor: 16.971

10.  Mitotic regulation by NIMA-related kinases.

Authors:  Laura O'regan; Joelle Blot; Andrew M Fry
Journal:  Cell Div       Date:  2007-08-29       Impact factor: 5.130

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  24 in total

1.  Differential effects of PKA-controlled CaMKK2 variants on neuronal differentiation.

Authors:  Wenguang Cao; Muhammad Sohail; Guodong Liu; Geremy A Koumbadinga; Vincent G Lobo; Jiuyong Xie
Journal:  RNA Biol       Date:  2011-11-01       Impact factor: 4.652

Review 2.  Phosphoproteomic analysis: an emerging role in deciphering cellular signaling in human embryonic stem cells and their differentiated derivatives.

Authors:  Brian T D Tobe; Junjie Hou; Andrew M Crain; Ilyas Singec; Evan Y Snyder; Laurence M Brill
Journal:  Stem Cell Rev Rep       Date:  2012-03       Impact factor: 5.739

3.  In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution.

Authors:  Nozomu Yachie; Rintaro Saito; Junichi Sugahara; Masaru Tomita; Yasushi Ishihama
Journal:  Mol Cell Proteomics       Date:  2009-01-09       Impact factor: 5.911

4.  Computational analysis of kinase inhibitor selectivity using structural knowledge.

Authors:  Yu-Chen Lo; Tianyun Liu; Kari M Morrissey; Satoko Kakiuchi-Kiyota; Adam R Johnson; Fabio Broccatelli; Yu Zhong; Amita Joshi; Russ B Altman
Journal:  Bioinformatics       Date:  2019-01-15       Impact factor: 6.937

Review 5.  Human Protein Reference Database and Human Proteinpedia as resources for phosphoproteome analysis.

Authors:  Renu Goel; H C Harsha; Akhilesh Pandey; T S Keshava Prasad
Journal:  Mol Biosyst       Date:  2011-12-08

6.  MimoSA: a system for minimotif annotation.

Authors:  Jay Vyas; Ronald J Nowling; Thomas Meusburger; David Sargeant; Krishna Kadaveru; Michael R Gryk; Vamsi Kundeti; Sanguthevar Rajasekaran; Martin R Schiller
Journal:  BMC Bioinformatics       Date:  2010-06-16       Impact factor: 3.169

Review 7.  Evolution of SH2 domains and phosphotyrosine signalling networks.

Authors:  Bernard A Liu; Piers D Nash
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2012-09-19       Impact factor: 6.237

Review 8.  Current understanding of LRRK2 in Parkinson's disease: biochemical and structural features and inhibitor design.

Authors:  Soumya Ray; Min Liu
Journal:  Future Med Chem       Date:  2012-09       Impact factor: 3.808

9.  KEA: kinase enrichment analysis.

Authors:  Alexander Lachmann; Avi Ma'ayan
Journal:  Bioinformatics       Date:  2009-01-28       Impact factor: 6.937

Review 10.  From protein sequences to 3D-structures and beyond: the example of the UniProt knowledgebase.

Authors:  Ursula Hinz
Journal:  Cell Mol Life Sci       Date:  2009-12-31       Impact factor: 9.261

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