Evolutionary variation and adaptation in a conserved protein kinase allosteric network: Implications for inhibitor design

Biochimica et Biophysica Acta - Proteins and Proteomics

Volumn 1834, Issue 7, 2013, Pages 1322-1329

  Oruganty, Krishnadev ^a   Kannan, Natarajan ^a,b  

^a University of Georgia   (United States)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

DFG out; EPK ELK network; Imatinib; Protein kinase; Strain switch

Indexed keywords

ADENOSINE TRIPHOSPHATE; ALANINE; ASPARTIC ACID; GLUTAMIC ACID; PHOSPHATE; PROTEIN KINASE;

ALLOSTERISM; ARTICLE; CATALYSIS; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME ACTIVATION; EVOLUTIONARY ADAPTATION; GEOMETRY; HYDROGEN BOND; NEOPLASM; PRIORITY JOURNAL;

ALLOSTERIC REGULATION; ALLOSTERIC SITE; ARCHAEA; BACTERIA; BENZAMIDES; BIOCATALYSIS; DRUG DESIGN; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; GENETIC VARIATION; HUMANS; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MODELS, MOLECULAR; NEOPLASMS; PHOSPHORYLATION; PIPERAZINES; PROTEIN KINASE INHIBITORS; PROTEIN KINASES; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTO-ONCOGENE PROTEINS C-PIM-1; PYRIMIDINES;

EID: 84878885457     PISSN: 15709639     EISSN: 18781454     Source Type: Journal    
DOI: 10.1016/j.bbapap.2013.02.040     Document Type: Article

References (33)

1. G. Manning, D.B. Whyte, R. Martinez, T. Hunter, and S. Sudarsanam The protein kinase complement of the human genome Science 298 2002 1912 1934 (Pubitemid 35425239)
2. N. Jura, X. Zhang, N.F. Endres, M.A. Seeliger, T. Schindler, and J. Kuriyan Catalytic control in the EGF receptor and its connection to general kinase regulatory mechanisms Mol. Cell 42 2011 9 22
3. S.S. Taylor, and A.P. Kornev Protein kinases: evolution of dynamic regulatory proteins Trends Biochem. Sci. 36 2011 65 77
4. Z. Shi, K.A. Resing, and N.G. Ahn Networks for the allosteric control of protein kinases Curr. Opin. Struct. Biol. 16 2006 686 692 (Pubitemid 44827734)
5. B. Nolen, S. Taylor, and G. Ghosh Regulation of protein kinases; controlling activity through activation segment conformation Mol Cell 15 2004 661 675 (Pubitemid 39194898)
6. M. Huse, and J. Kuriyan The conformational plasticity of protein kinases Cell 109 2002 275 282 (Pubitemid 34606870)
7. L.N. Johnson, M.E. Noble, and D.J. Owen Active and inactive protein kinases: structural basis for regulation Cell 85 1996 149 158 (Pubitemid 26118158)
8. S.K. Hanks, and T. Hunter Protein kinases 6. The eukaryotic protein kinase superfamily: kinase (catalytic) domain structure and classification FASEB J. 9 1995 576 596
9. N. Kannan, S.S. Taylor, Y. Zhai, J.C. Venter, and G. Manning Structural and functional diversity of the microbial kinome PLoS Biol. 5 2007 e17
10. J.A. Endicott, M.E. Noble, and L.N. Johnson The structural basis for control of eukaryotic protein kinases Annu. Rev. Biochem. 81 2012 587 613
11. A. Krupa, and N. Srinivasan Anamika Genome-wide comparative analyses of domain organisation of repertoires of protein kinases of Arabidopsis thaliana and Oryza sativa Gene 380 2006 1 13 (Pubitemid 44293158)
12. S.C. Robertson, J. Tynan, and D.J. Donoghue RTK mutations and human syndromes: when good receptors turn bad Trends Genet. 16 2000 368
13. L.N. Johnson Protein kinase inhibitors: contributions from structure to clinical compounds Q. Rev. Biophys. 42 2009 1 40
14. N. Kannan, and A.F. Neuwald Did protein kinase regulatory mechanisms evolve through elaboration of a simple structural component? J. Mol. Biol. 351 2005 956 972 (Pubitemid 41133444)
15. C.J. Leonard, L. Aravind, and E.V. Koonin Novel families of putative protein kinases in bacteria and archaea: evolution of the "eukaryotic" protein kinase superfamily Genome Res. 8 1998 1038 1047 (Pubitemid 28532492)
16. G.A. McKay, P.R. Thompson, and G.D. Wright Broad spectrum aminoglycoside phosphotransferase type III from Enterococcus: overexpression, purification, and substrate specificity Biochemistry 33 1994 6936 6944 (Pubitemid 24190818)
17. G.L. Clary, C.F. Tsai, and R.W. Guynn Substrate specificity of choline kinase Arch. Biochem. Biophys. 254 1987 214 221 (Pubitemid 17068814)
18. H. Yamaguchi, M. Matsushita, A.C. Nairn, and J. Kuriyan Crystal structure of the atypical protein kinase domain of a TRP channel with phosphotransferase activity Mol Cell 7 2001 1047 1057 (Pubitemid 32525751)
19. J. Zheng, and Z. Jia Structure of the bifunctional isocitrate dehydrogenase kinase/phosphatase Nature 465 2010 961 965
20. M. Funaki, H. Katagiri, K. Inukai, M. Kikuchi, and T. Asano Structure and function of phosphatidylinositol-3,4 kinase Cell. Signal. 12 2000 135 142 (Pubitemid 30126030)
21. A.P. Kornev, N.M. Haste, S.S. Taylor, and L.F. Eyck Surface comparison of active and inactive protein kinases identifies a conserved activation mechanism Proc. Natl. Acad. Sci. U. S. A. 103 2006 17783 17788 (Pubitemid 44852237)
22. A.P. Kornev, S.S. Taylor, and L.F. Ten Eyck A helix scaffold for the assembly of active protein kinases Proc. Natl. Acad. Sci. U. S. A. 105 2008 14377 14382
23. K. Oruganty, N.S. Talathi, Z.A. Wood, and N. Kannan Identification of a hidden strain switch provides clues to an ancient structural mechanism in protein kinases Proc. Natl. Acad. Sci. 110 2012 924 929
24. A.F. Neuwald Rapid detection, classification and accurate alignment of up to a million or more related protein sequences Bioinformatics 25 2009 1869 1875
25. R.D. Finn, J. Mistry, J. Tate, P. Coggill, A. Heger, and J.E. Pollington The Pfam protein families database Nucleic Acids Res. 38 2010 D211 D222
26. W. Kabsch, and C. Sander Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features Biopolymers 22 1983 2577 2637
27. V.B. Chen, W.B. Arendall 3rd, J.J. Headd, D.A. Keedy, R.M. Immormino, and G.J. Kapral MolProbity: all-atom structure validation for macromolecular crystallography Acta Crystallogr. D: Biol. Crystallogr. 66 2010 12 21
28. K.C. Qian, L. Wang, E.R. Hickey, J. Studts, K. Barringer, and C. Peng Structural basis of constitutive activity and a unique nucleotide binding mode of human Pim-1 kinase J. Biol. Chem. 280 2005 6130 6137 (Pubitemid 40280098)
29. S.A. Forbes, N. Bindal, S. Bamford, C. Cole, C.Y. Kok, and D. Beare COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer Nucleic Acids Res. 39 2011 D945 D950
30. L.R. Masterson, C. Cheng, T. Yu, M. Tonelli, A. Kornev, and S.S. Taylor Dynamics connect substrate recognition to catalysis in protein kinase A Nat. Chem. Biol. 6 2010 821 828
31. S. Ferreira-Cerca, V. Sagar, T. Schafer, M. Diop, A.M. Wesseling, and H. Lu ATPase-dependent role of the atypical kinase Rio2 on the evolving pre-40S ribosomal subunit Nat. Struct. Mol. Biol. 19 2012 1316 1323
32. G.H. Su, R. Bansal, K.M. Murphy, E. Montgomery, C.J. Yeo, and R.H. Hruban ACVR1B (ALK4, activin receptor type 1B) gene mutations in pancreatic carcinoma Proc. Natl. Acad. Sci. U. S. A. 98 2001 3254 3257 (Pubitemid 32220832)
33. Schrodinger, LLC, The PyMOL molecular graphics system, Version 1.3r1, in, 2010.