Structural aspects of the functional modules in human protein kinase- Cα deduced from comparative analyses

Proteins: Structure, Function and Genetics

Volumn 26, Issue 2, 1996, Pages 217-235

  Srinivasan, N ^a   Bax, Ben ^a   Blundell, Tom L ^a   Parker, Peter J ^b  

^a UNIVERSITY OF LONDON   (United Kingdom)

^b IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

Author keywords

catalytic region; comparative modeling; cysteine rich domain; phosphorylation; pseudo substrate specificity; synaptotagmin

Indexed keywords

ARGININE; CALCIUM BINDING PROTEIN; CYCLIC AMP DEPENDENT PROTEIN KINASE; LYSINE; PHORBOL ESTER; PROTEIN KINASE C; SYNAPTOTAGMIN; ZINC FINGER PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME PHOSPHORYLATION; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; HUMAN; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN LIPID INTERACTION;

AMINO ACID SEQUENCE; CALCIUM; CATALYSIS; CRYSTALLOGRAPHY, X-RAY; HUMANS; ISOENZYMES; LIPID METABOLISM; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PHOSPHORYLATION; PROTEIN FOLDING; PROTEIN KINASE C; PROTEIN KINASE C-ALPHA; SEQUENCE HOMOLOGY, AMINO ACID; STRUCTURE-ACTIVITY RELATIONSHIP; ZINC;

EID: 0029969880     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199610)26:2<217::AID-PROT11>3.0.CO;2-S     Document Type: Article

References (89)

1. Takai, Y., Kishimoto, A., Inoue, M., Nishizuka, Y. Studies on a cyclic nucleotide-independent protein kinase and its proenzyme in mammalian tissues. I. Purification and characterization of an active enzyme from bovine cerebellum. J. Biol. Chem. 252:7603-7609, 1977.
2. Inoue, M., Kishimoto, A., Takai, Y., Nishizuka, Y. Studies on a cyclic nucleotide-independent protein kinase and its proenzyme in mammalian tissues. J. Biol. Chem. 252: 7610-7616, 1977.
3. Hunter, T., Cooper, J.A. Viral oncogenes and tyrosine phosphorylation. In "The Enzymes." Vol. 17. Boyer, P.D., Krebs, E.G. (eds.). Orlando, FL: Academic Press, 1986: 191-246.
4. Edelman, A.M., Blumenthal, D.K., Krebs, E.G. Protein serine threonine kinases. Annu. Rev. Biochem. 56:567-613, 1987.
5. Hanks, S.K., Quinn, A.M., Hunter, T. The protein kinase family - conserved features and deduced phytogeny of catalytic domains. Science 241:42-52, 1988.
6. Dekker, L.V., Parker, P.J. Protein kinase C - a question of specificity. Trends Biochem. Sci. 19:73-77, 1994.
7. Dekker, L.V., Palmer, R.H., Parker, P.J. The protein kinase C and protein kinase C related gene families. Curr. Opin. Struct. Biol. 5:396-402, 1995.
8. Ashendel, C.L. A phorbol ester receptor - a phospholipid regulated protein kinase. Biochim. Biophys. Acta 822: 219-242, 1985.
9. Alkon, D.L. Memory storage and neural systems. Sci. Am. 261:42-50, 1989.
10. Otte, A.P., Kramer, I.M., Durston, A.J. Protein kinase C and the regulation of Xenopus ectoderm. Science 251:570-573, 1991.
11. Stabel, S., Parker, P.J. Protein kinase C. Pharm. Ther. 51:71-95, 1991.
12. Hug, H., Sarre, T.F. Protein kinase C isoenzymes - divergence in signal transduction. Biochem. J. 291:329-343, 1993.
13. Nishizuka, Y. The role of protein kinase C in cell surface signal transduction and tumour promotion. Nature 308: 693-695, 1984.
14. Nishizuka, Y. Intracellular signalling by hydrolysis of phospholipids and activation of protein kinase C. Science 258:607-614, 1992.
15. Asaoka, Y., Nakamura, S., Yoshida, K., Nishizuka, Y. Protein kinase C, calcium and phospholipid degradation. Trends Biochem. Sci. 17:414-417, 1992.
16. Cazaubon, S.M., Parker, P.J. Identification of the phosphorylated region responsible for the permissive activation of protein kinase C. J. Biol. Chem. 268:17559-17563, 1993.
17. Cazaubon, S.M., Bornancin, F., Parker, P.J. Threonine-497 is a critical site for permissive activation of protein kinase Ca. Biochem. J. 301:443-448, 1994.
18. Pears, C., Stabel, S., Cazaubon, S., Parker, P.J. Studies on the phosphorylation of protein kinase Ca. Biochem. J. 283: 515-518, 1992.
19. Ono, Y., Fujii, T., Ogita, K., Kikkawa, U., Igarashi, K., Nishizuka, Y. Protein kinase ζ subspecies from rat brain: Its structure, expression and properties. Proc. Natl. Acad. Sci. USA 86:3099-3103, 1989.
20. Hommel, U., Zurini, M., Luyten, M. Solution structure of a cysteine-rich domain of rat protein kinase C. Nature Struct. Biol. 1:383-387, 1994.
21. Zhang, G., Kazanietz, M.G., Blumberg, P.M., Hurley, J.H. Crystal structure of the Cys2 activator-binding domain of protein kinase Cδ in complex with phorbol ester. Cell 81: 917-924, 1995.
22. Luo, J.H., Weinstein, I.B. Calcium-dependent activation of protein kinase C - the role of the C2 domain in divalent cation selectivity. J. Biol. Chem. 268:23580-23584, 1993.
23. Quest, A.F.G., Bell, R.M. The regulatory region of protein kinase C-γ - studies of phorbol ester binding to individual and combined functional segments expressed as glutathione S-transferase fusion proteins indicate a complex mechanism of regulation by phospholipids, phorbol esters and divalent cations. J. Biol. Chem. 269:20000-20012, 1994.
24. Perin, M.S., Fried, V.A., Mignery, G.A., Jahn, R., Sudhof, T.C. Phospholipid binding by a synaptic vesicle protein homologous to the regulatory region of protein kinase C. Nature 345:260-263, 1990.
25. 2+/phospholipid binding fold. Cell 80:929-938, 1995.
26. Pears, C., Kour, G., House, C., Kemp, B., Parker, P. Mutagenesis of the pseudo-substrate site of protein kinase C leads to activation. Eur. J. Biochem. 194:89-94, 1990.
27. House, C., Kemp, B.E. Protein kinase C contains a pseudosubstrate prototype in its regulatory domain. Science 238:1726-1728, 1987.
28. Parker, P.J., Kour, G., Marais, R.M., Mitchell, F., Pears, C., Schaap, D., Stabel, S., Webster, C. Protein kinase C - a family affair. Mol. Cell Endocrinol. 65:1-11, 1989.
29. Pap, E.H.W., Bastiaens, P.I.H., Borst, J.W., Vandenberg, P.A.W., Vanhoek, A., Snoek, G.T., Wirtz, K.W.A., Visser, A.J.W.G. Quantitation of the interaction of protein kinase-C with diacylglycerol and phosphoinositides by time-resolved deduction of resonance energy-transfer. Biochemistry 32:13310-13317, 1993.
30. Nakanishi, H., Brewer, K., Exton, J. Activation of the ζ isozyme of protein kinase C by phosphatidylinositol 3,4,5-triphosphate. J. Biol. Chem. 268:13-16, 1993.
31. Singh, S.S., Chauhan, A., Brockerhoff, H., Chauhan, V.P.S. Activation of protein kinase C by phosphatidylinositol 3,4,5-triphosphate. Biochem. Biophys. Res. Commun. 195:104-112, 1993.
32. Taylor, S.S., Knighton, D.R., Zheng, J.H., Sowadski, J.M., Gibbs, C.S., Zoller, M.J. A template for the protein kinase family. Trends Biochem. Sci. 18:84-89, 1993.
33. Taylor, S.S., Radzio-Andzelm, E. Three protein kinase structures define a common motif. Structure 2:345-355, 1994.
34. Wei, L., Hubbard, S.R., Smith, R.F., Ellis, L. Protein kinase superfamily - comparison of sequence data with three-dimensional structures. Curr. Opin. Struct. Biol. 4:450-455, 1994.
35. Knighton, D.R., Pearson, R.B., Sowadski, J.M., Means, A.R., Teneyck, L.F., Taylor, S.S., Kemp, B.E. Structural basis for the intrasteric regulation of myosin light chain kinases. Science 258:130-135, 1992.
36. Knighton, D.R., Cadena, D.L., Zheng, J.H., Teneyck, L.F., Taylor, S.S., Sowadski, J.M., Gill, G.N. Structural features that specify tyrosine kinase activity deduced from homology modelling of the epidermal growth factor receptor. Proc. Natl. Acad. Sci. USA 90:5001-5005, 1993.
37. Endicott, J.A., Nurse, P., Johnson, L.N. Mutational analysis supports a structural model for the cell cycle protein kinase p34. Protein Eng. 7:243-253, 1994.
38. Finkenzeller, G., Marine, D., Hug, H. Sequence of human protein kinase C α. Nucleic Acids Res. 18:2183-2183, 1990.
39. Knighton, D.R., Zheng, J.H., Teneyck, L.F., Ashford, V.A., Xuong, N.H., Taylor, S.S., Sowadski, J.M. Crystal structure of the catalytic sub-unit of cyclic adenosine monophosphate dependent protein kinase. Science 253:407-414, 1991.
40. Knighton, D.R., Bell, S.M., Zheng, J.H., Teneyck, L.F., Xuong, N.H., Taylor, S.S., Sowadski, J.M. 2.0Å refined crystal structure of the catalytic sub-unit of cAMP dependent protein kinase complexed with a peptide inhibitor and detergent. Acta Crystallogr. D49:357-361, 1993.
41. Zheng, J.H., Knighton, D.R., Teneyck, L.F., Karlsson, R., Xuong, N.H., Taylor, S.S., Sowadski, J.M. Crystal structure of the catalytic sub-unit of cAMP dependent protein kinase complexed with MgATP and peptide inhibitor. Biochemistry 32:2154-2161, 1993.
42. deBondt, H.L., Rosenblatt, J., Jancarik, J., Jones, H.D., Morgan, D.O., Kim, S.H. Crystal structure of cyclin dependent kinase 2. Nature 363:595-602, 1993.
43. Knighton, D.R., Zheng, J.H., Teneyck, L.F., Xuong, N.H., Taylor, S.S., Sowadski, J.M. Structure of a peptide inhibitor bound to the catalytic sub-unit of cyclic adenosinemonophosphate dependent protein kinase. Science 253: 414-420, 1991.
44. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Beyer, E.F. Jr., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., Tasumi M. The protein data bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
45. 2+ adenylyl imidodiphosphate and inhibitor peptide PKI(5-24). EMBO J. 12:849-859, 1993.
46. Šali, A., Blundell, T.L. Definition of topological equivalence in protein structures - a procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J. Mol. Biol. 212: 403-428, 1990.
47. Zhu, Z.-Y., Sali, A., Blundell, T.L. A variable gap penalty function and feature weights for protein 3-D structure comparisons. Protein Eng. 5:43-51, 1992.
48. Srinivasan, N., Blundell, T.L. An evaluation of the performance of an automatic procedure for comparative modelling of protein tertiary structure. Protein Eng. 6:501-512, 1993.
49. Zhang, F., Strand, A., Robbins, D., Cobb, M.H., Goldsmith, E.J. Atomic structure of the MAP kinase ERK2 at 2.3Å resolution. Nature 367:704-711, 1994.
50. Hu, S.-H., Parker, M.W., Lei, J.Y., Wilce, M.C.J., Benian, G.M., Kemp, B.E. Insights into autoregulation from the crystal structure of twitchin kinase. Nature 369:581-584, 1994.
51. Xu, R.M., Carmel, G., Sweet, R.M., Kuret, J., Cheng, X.D. Crystal-structure of casein kiuase-1, a phosphate-directed protein kinase. EMBO J. 14:1015-1023, 1995.
52. Owen, D.J., Noble, M.E.M., Garman, E.F., Papageorgiou, A.C., Johnson, L.N. Two structures of the catalytic domain of phosphorylase kinase: An active protein kinase complexed with substrate analogue and product. Structure 3:467-482, 1995.
53. Jeffrey, P.D., Russo, A.A., Polyak, K., Gibbs, E., Hurwitz, J., Massague, J., Pavletich, N.P. Mechanism of CDK activation revealed by the structure of a cyclinA-CDK2 complex. Nature 376:313-320, 1995.
54. Schulzegahmen, U., Brandsen, J., Jones, H.D., Morgan, D.O., Meijer, L., Vesely, J., Kim, S.H. Multiple-modes of ligand recognition crystal structures of cyclin-dependent protein-kinase-2 in complex with ATP and two inhibitors, olomoucine and isopentenyladenine. Proteins 22:378-391, 1995.
55. Hubbard, S.R., Wei, L., Ellis, L., Hendrickson, W.A. Crystal structure of the tyrosine kinase domain of the human insulin receptor. Nature 372:746-754, 1994.
56. Blundell, T., Carney, D., Gardner, S., Hayes, F., Howlin, B., Hubbard, T., Overington, J., Singh, D.A., Sibanda, B.L., Sutcliffe, M. Knowledge-based protein modelling and design. Eur. J. Biochem. 172:513-520, 1988.
57. Topham, C.M., McLeod, A., Eisenmenger, F., Overington, J.P., Johnson, M.S., Blundell, T.L. Fragment ranking in modelling of protein structure - conformationally constrained environmental amino acid substitution tables. J. Mol. Biol. 229:104-220, 1993.
58. Sutcliffe, M.J., Hayes, F.R.F., Blundell, T.L. Knowledge-based modelling of homologous proteins. 2. Rules for the conformations of substituted sidechains. Protein Eng. 1:385-392, 1987.
59. Weiner, S.J., Kollman, P.A., Case, D.A., Singh, D.C., Ghio, C., Alagona, G., Profeta, S., Weiner, P. A new force-field for molecular mechanical simulation of nucleic acids and proteins. J. Am. Chem. Soc. 106:765-784, 1984.
60. Jones, T.A. Graphics model building and refinement system for macromolecules. J. Appl. Crystallogr. 11:272-282, 1978.
61. Doolittle, R.F. Similar amino acid sequences. Chance or common ancestry. Science 214:149-159, 1981.
62. Veron, M., Radzioandzelm, E., Tsigelny, I., Teneyck, L.F., Taylor, S.S. A conserved helix motif complements the protein kinase core. Proc. Natl. Acad. Sci. USA 90:10618-10622, 1993.
63. Hanks, S.K. Eukaryotic protein kinases. Curr. Opin. Struct. Biol. 1:369-383, 1991.
64. Su, L., Parissenti, A.M., Riedel, H. Functional carboxyl terminal deletion map of protein kinase C α. Receptors Channels 1:1-9, 1993.
65. Overington, J.P., Johnson, M.S., Šali, A., Blundell, T.L. Tertiary structural constraints on protein evolutionary diversity - templates, key residues and structure prediction. Proc. R. Soc. (Lond.) 241:132-145, 1990.
66. Johnson, M.S., Overington, J.P., Blundell, T.L. Alignment and searching for common protein folds using a data bank of structural templates. J. Mol. Biol. 231:735-752, 1993.
67. Nicholls, A., Sharp, K.A., Honig, B. Protein folding and association - insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11:281-296, 1991.
68. Soderling, T.R. Protein kinases. Regulation by autoinhibitory domains. J. Biol. Chem. 265:1823-1826, 1990.
69. Smith, M.K., Colbran, R.J., Soderling, T.R. Specificities of autoinhibitory domain peptides for four protein kinases. J. Biol. Chem. 265:1837-1840, 1990.
70. Orr, J.W., Newton, A.C. Requirement for negative charge on activation loop of protein kinase C. J. Biol. Chem. 269: 27715-27718, 1994.
71. Orr, J.W., Newton, A.C. Intrapeptide regulation of protein kinase C. J. Biol. Chem. 269:8383-8387, 1994.
72. Orr, J.W., Keranen, L.M., Newton, A.C. Reversible exposure of the pseudosubstrate domain of protein kinase C by phosphatidylserine and diacylglycerol. J. Biol. Chem. 267: 15263-15266, 1992.
73. Stahl, M.L., Ferenz, C.R., Kelleher, K.L., Kriz, R.W., Knopf, J.F. Sequence similarity of phospholipase C with the non-catalytic region of src. Nature 332:269-272, 1988.
74. Vongel, U.S., Dixon, R.A.F., Schaber, M.D., Diehl, R.E., Marshall, M.S., Scolnick, E.M., Sigal, I.S., Gibbs, J.B. Cloning of bovine GAP and its interaction with oncogenic ras p21. Nature 335:90-93, 1988.
75. 2+-dependent translocation domain with homology to PKC and GAP. Cell 65:1043-1051, 1991.
76. 2+-independent catalytic domain. J. Biol. Chem. 269: 18239-18249, 1994.
77. Gerloff, D.L., Chelvanayagam, G., Benner, S.A. A predicted consensus structure for the protein-kinase C2 homology (C2H) domain. The repeating unit of synaptotagmin. Proteins 22:299-310, 1995.
78. Ponting, C.P., Parker, P.J. Extending the C2 domain family: C2s in PKCs, δ, ε, η, θ, phospholipases, GAPs and perform. Protein Sci. 5:162-166, 1996.
79. Bazzi, M.D., Neisestuen, G.L. Protein kinase C interaction with calcium: A phospholipid dependent process. Biochemistry 29:7624-7630, 1990.
80. Orr, J.W., Newton, A.C. Interaction of protein kinase C with phosphatidylserine II. Specificity and regulation. Biochemistry 31:4567-4573, 1992.
81. Quest, A.F.G., Bardes, E.S.G., Bell, R.M. A phorbol ester binding domain of protein kinase C γ - deletion analysis of the CYS2 domain defines a minimal 43 amino acid peptide. J. Biol. Chem. 269:2961-2970, 1994.
82. Rando, R.R., Kishi, Y. Structural basis of protein kinase-C activation by diacylglycerols and tumor promoters. Biochemistry 31:2211-2218, 1992.
83. Newman, R.H., Carpenter, E., Freemont, P.S., Blundell, T.L., Parker, P.J. Microcrystals of the β(1) isoenzyme of protein kinase C - an electron-microscopic study. Biochem. J. 298:391-393, 1994.
84. Xiao, B., Smerdom, S.J., Jones, D.H., Dodson, C.G., Soneji, Y., Aitken, A., Gamblin, S.J. Structure of a 14-3-3 protein and implications for coordination of multiple signalling pathways. Nature 376:188-191, 1995.
85. Liu, D., Bienkowska, J., Petosa, C., Collier, R.J., Fu, H., Liddington, R. Crystal structure of a zeta isoform of the 14-3-3 protein. Nature 376:191-194, 1995.
86. Jones, D.H., Ley, S., Aitken, A. Isoforms of 14-3-3 protein can form homo and hetero dimers in vitro. Implications for function as adaptor proteins. FEBS Lett. 368:55-58, 1995.
87. Kolch, W., Heldecker, G., Kochs, G., Hummel, R., Vahldi, H., Mischak, H., Filkenzeller, G., Marme, D., Rapp, U.R. Protein kinase Ca activates RAF-1 by direct phosphorylation. Nature 364:249-252, 1993.
88. Coussens, L., Parker, P.J., Rhee, L., Yangfeng, T.L., Chen, E., Waterfield, M.D., Francke, U., Ullrich, A. Multiple and distinct forms of bovine and human protein kinase C suggest diversity in cellular signalling pathways. Science 233: 859-866, 1986.
89. Evans, S.V. SETOR-hardware lighted three-dimensional solid model representations of macromolecules. J. Mol. Graph. 11:134-138, 1993.