Classification of protein kinases on the basis of both kinase and non-kinase regions

PLoS ONE

Volumn 5, Issue 9, 2010, Pages 1-12

  Martin, Juliette ^a,b,c,d   Anamika, Krishanpal ^a,e   Srinivasan, Narayanaswamy ^a,e  

^a INDIAN INSTITUTE OF SCIENCE   (India)

^b INRA Institut National de la Recherche Agronomique   (France)

^c UNIVERSITÉ DE LYON   (France)

^d University Lyon i   (France)

^e UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; PROTEIN KINASE;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CATALYSIS; CONTROLLED STUDY; ENTAMOEBA HISTOLYTICA; ENZYME ANALYSIS; ENZYME STRUCTURE; PROTEIN DOMAIN; PROTEIN FAMILY; QUANTITATIVE ANALYSIS; SEQUENCE ALIGNMENT; SEQUENCE DATABASE; SEQUENCE HOMOLOGY; VALIDATION PROCESS; CHEMISTRY; CLASSIFICATION; GENETICS; HUMAN; METABOLISM; MOLECULAR GENETICS; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE;

ENTAMOEBA HISTOLYTICA; PROTOZOA;

ALGORITHMS; AMINO ACID SEQUENCE; DATABASES, PROTEIN; HUMANS; MOLECULAR SEQUENCE DATA; PROTEIN KINASES; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT;

EID: 77958536829     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012460     Document Type: Article

References (52)

1. Krupa A, Abhinandan K, Srinivasan N (2004) KinG: a database of protein kinases in genomes. Nucleic Acids Res 32: D153-155.
2. Cohen P (2002) Protein kinases-the major drug targets of the twenty-first century? Nat Rev Drug Discov 1: 309-315.
3. Han E, McGonigal T (2007) Role of focal adhesion kinase in human cancer: a potential target for drug discovery. Anticancer Agents Med Chem 7: 681-684.
4. Hardie D (2007) AMP-activated protein kinase as a drug target. Annu Rev Pharmacol Toxicol 47: 185-210.
5. Hunter T, Plowman G (1997) The protein kinases of budding yeast: six score and more. Trends Biochem Sci 22: 18-22.
6. Plowman G, Sudarsanam S, Bingham J, Whyte D, Hunter T (1999) The protein kinases of Caenorhabditis elegans: a model for signal transduction in multicellular organisms. Proc Natl Acad Sci USA 96: 13603-13610.
7. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S (2002) The protein kinase complement of the human genome. Science 298: 1912-1934.
8. Krupa A, Srinivasan N (2002) The repertoire of protein kinases encoded in the draft version of the human genome: atypical variations and uncommon domain combinations. Genome Biol 3: RESEARCH0066.
9. Kostich M, English J, Madison V, Gheyas F, Wang L, et al. (2002) Human members of the eukaryotic protein kinase family. Genome Biol 3: RESEARCH0043.
10. Caenepeel S, Charydczak G, Sudarsanam S, Hunter T, Manning G (2004) The mouse kinome: discovery and comparative genomics of all mouse protein kinases. Proc Natl Acad Sci USA 101: 11707-11712.
11. Ward P, Equinet L, Packer J, Doerig C (2004) Protein kinases of the human malaria parasite Plasmodium falciparum: the kinome of a divergent eukaryote. BMC Genomics 5: 79.
12. Champion A, Kreis M, Mockaitis K, Picaud A, Henry Y (2004) Arabidopsis kinome: after the casting. Funct Integr Genomics 4: 163-187.
13. Shiu S, Karlowski W, Pan R, Tzeng Y, Mayer K, et al. (2004) Comparative analysis of the receptor-like kinase family in Arabidopsis and rice. Plant Cell 16: 1220-1234.
14. Srinivasan N, Krupa A (2005) A genomic perspective of protein kinases in Plasmodium falciparum. Proteins 58: 180-189.
15. Krupa A, Srinivasan N (2005) Diversity in domain architectures of Ser/Thr kinases and their homologues in prokaryotes. BMC Genomics 6: 129.
16. Krupa A, Anamika, Srinivasan N. (2006) Genome-wide comparative analyses of domain organisation of repertoires of protein kinases of Arabidopsis thaliana and Oryza sativa. Gene 380: 1-13.
17. Goldberg J, Manning G, Liu A, Fey P, Pilcher K, et al. (2006) The dictyostelium kinome-analysis of the protein kinases from a simple model organism. PLoS Genet 2: e38.
18. Bradham C, Foltz K, Beane W, Arnone M, Rizzo F, et al. (2006) The sea urchin kinome: a first look. Dev Biol 300: 180-193.
19. Dardick C, Chen J, Richter T, Ouyang S, Ronald P (2007) The rice kinase database. A phylogenomic database for the rice kinome. Plant Physiol 143: 579-586.
20. Anamika K, Srinivasan N (2007) Comparative kinomics of Plasmodium organisms: unity in diversity. Protein Pept Lett 14: 509-517.
21. Kannan N, Taylor S, Zhai Y, Venter J, Manning G (2007) Structural and functional diversity of the microbial kinome. PLoS Biol 5: e17.
22. Anamika K, Bhattacharya A, Srinivasan N (2008) Analysis of the protein kinome of Entamoeba histolytica. Proteins 71: 995-1006.
23. Martin DM, Miranda-Saavedra D, Barton GJ (2009) Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases. Nucleic Acids Res 37: D244-250.
24. Hanks S, Quinn A, Hunter T (1988) The protein kinase family: conserved features and deduced phylogeny of the catalytic domains. Science 241: 42-52.
25. Hanks S, Hunter T (1995) Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification. FASEB J 9: 576-596.
26. Smith C, Shindyalov I, Veretnik S, Gribskov M, Taylor S, et al. (1997) The protein kinase resource. Trends Biochem Sci 22: 444-446.
27. Niedner R, Buzko O, Haste N, Taylor A, Gribskov M, et al. (2006) Protein kinase resource: an integrated environment for phosphorylation research. Proteins 63: 78-86.
28. Manning G, Plowman G, Hunter T, Sudarsanam S (2002) Evolution of protein kinase signaling from yeast to man. Trends Biochem Sci 27: 514-520.
29. Miranda-Saavedra D, Barton GJ (2007) Classification and functional annotation of eukaryotic protein kinases. Proteins 68: 893-914.
30. Buzko O, Shokat K (2002) A kinase sequence database: sequence alignments and family assignment. Bioinformatics 18: 1274-1275.
31. Gribskov M, Fana F, Harper J, Hope D, Harmon A, et al. (2001) PlantsP: a functional genomics database for plant phosphorylation. Nucleic Acids Res 29: 111-113.
32. Tchieu J, Fana F, Fink J, Harper J, Nair T, et al. (2003) The PlantsP and PlantsT Functional Genomics Databases. Nucleic Acids Res 31: 342-344.
33. Cheek S, Zhang H, Grishin NV (2002) Sequence and structure classification of kinases. J Mol Biol 320: 855-881.
34. Cheek S, Ginalski K, Zhang H, Grishin N (2005) A comprehensive update of the sequence and structure classification of kinases. BMC Struct Biol 5: 6.
35. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, et al. (2004) The pfam protein families database. Nucleic Acids Res 32: D138-D141.
36. Tatusov R, Koonin E, Lipman D (1997) A genomic perspective on protein families. Science 278: 631-637.
37. Tatusov R, Fedorova N, Jackson J, Jacobs A, Kiryutin B, et al. (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4: 41.
38. Scheeff ED, Bourne PE (2005) Structural evolution of the protein kinase-like superfamily. PLoS Comput Biol 1: e49.
39. Jacobs M, Caron P, Hare B (2008) Classifying protein kinase structures guides use of ligand-selectivity profiles to predict inactive conformations: structure of lck/imatinib complex. Proteins 70: 1451-1460.
40. Kelil A, Wang S, Brzezinski R, Fleury A (2007) CLUSS: clustering of protein sequences based on a new similarity measure. BMC Bioinformatics 8: 286.
41. Zheng J, Knighton DR, ten Eyck LF, Karlsson R, Xuong N, et al. (1993) Crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MgATP and peptide inhibitor. Biochemistry 32: 2154-2161.
42. Deshmukh K, Anamika K, Srinivasan N. (2009) Evolution of domain combinations in protein kinases and its implications for functional diversity. Prog Biophys Mol Biol.
43. Katamine S, Notario V, Rao CD, Miki T, Cheah MS, et al. (1988) Primary structure of the human fgr proto-oncogene product p55c-fgr. Mol Cell Biol 8: 259-266.
44. Toshima J, Toshima JY, Takeuchi K, Mori R, Mizuno K (2001) Cofilin phosphorylation and actin reorganization activities of testicular protein kinase 2 and its predominant expression in testicular Sertoli cells. J Biol Chem 276: 31449-31458.
45. Gowri VS, Tina KG, Krishnadev O, Srinivasan N (2007) Strategies for the effective identification of remotely related sequences in multiple PSSM search approach. Proteins 67: 789-794.
46. Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, et al. (2002) CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res 30: 281-283.
47. Eddy SR (1998) Profile hidden markov models. Bioinformatics 14: 755-763.
48. Anamika K, Garnier N, Srinivasan N (2009) Functional diversity of human protein kinase splice variants marks significant expansion of human kinome. BMC Genomics 10: 622.
49. Rice I P Longden, Bleasby A, Bleasby A (2000) Emboss: The European molecular biology open software suite. Trends in Genetics 16: 276-277.
50. R Development Core Team (2007) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org. ISBN 3-900051-07-0.
51. Datta S, Datta S (2006) Methods for evaluating clustering algorithms for gene expression data using a reference set of functional classes. BMC Bioinformatics 7: 397.
52. Gouet P, Robert X, Courcelle E (2003) ESPript/ENDscript: Extracting and rendering sequence and 3D information from atomic structures of proteins. Nucleic Acids Res 31: 3320-3323.