Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs

Janine Mok, Philip M. Kim, Hugo Y.K. Lam, Stacy Piccirillo, Xiuqiong Zhou, Grace R. Jeschke, Douglas L. Sheridan, Sirlester A. Parker, Ved Desai, Miri Jwa, Elisabetta Cameroni, Hengyao Niu, Matthew Good, Attila Remenyi, Jia Lin Nianhan Ma, Yi Jun Sheu, Holly E. Sassi, Richelle Sopko, Clarence S.M. Chan, Claudio De VirgilioNancy M. Hollingsworth, Wendell A. Lim, David F. Stern, Bruce Stillman, Brenda J. Andrews, Mark B. Gerstein, Michael Snyder, Benjamin E. Turk

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223 Citations (Scopus)

Abstract

Phosphorylation is a universal mechanism for regulating cell behavior in eukaryotes. Although protein kinases target short linear sequence motifs on their substrates, the rules for kinase substrate recognition are not completely understood. We used a rapid peptide screening approach to determine consensus phosphorylation site motifs targeted by 61 of the 122 kinases in Saccharomyces cerevisiae. By correlating these motifs with kinase primary sequence, we uncovered previously unappreciated rules for determining specificity within the kinase family, including a residue determining P-3 arginine specificity among members of the CMGC [CDK (cyclin-dependent kinase), MAPK (mitogen-activated protein kinase), GSK (glycogen synthase kinase), and CDK-like] group of kinases. Furthermore, computational scanning of the yeast proteome enabled the prediction of thousands of new kinasesubstrate relationships. We experimentally verified several candidate substrates of the Prk1 family of kinases in vitro and in vivo and identified a protein substrate of the kinase Vhs1. Together, these results elucidate how kinase catalytic domains recognize their phosphorylation targets and suggest general avenues for the identification of previously unknown kinase substrates across eukaryotes.

Original languageEnglish
Pages (from-to)ra12
JournalScience Signaling
Volume3
Issue number109
DOIs
Publication statusPublished - Feb 16 2010

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ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Mok, J., Kim, P. M., Lam, H. Y. K., Piccirillo, S., Zhou, X., Jeschke, G. R., Sheridan, D. L., Parker, S. A., Desai, V., Jwa, M., Cameroni, E., Niu, H., Good, M., Remenyi, A., Ma, J. L. N., Sheu, Y. J., Sassi, H. E., Sopko, R., Chan, C. S. M., ... Turk, B. E. (2010). Deciphering protein kinase specificity through large-scale analysis of yeast phosphorylation site motifs. Science Signaling, 3(109), ra12. https://doi.org/10.1126/scisignal.2000482