Abstract
BackgroundProtein kinase A (cAMP-dependent kinase, PKA) is a serine/threonine kinase, for which ca. 150 substrate proteins are known. Based on a refinement of the recognition motif using the available experimental data, we wished to apply the simplified substrate protein binding model for accurate prediction of PKA phosphorylation sites, an approach that was previously successful for the prediction of lipid posttranslational modifications and of the PTS1 peroxisomal translocation signal.ResultsApproximately 20 sequence positions flanking the phosphorylated residue on both sides have been found to be restricted in their sequence variability (region -18...+23 with the site at position 0). The conserved physical pattern can be rationalized in terms of a qualitative binding model with the catalytic cleft of the protein kinase A. Positions -6...+4 surrounding the phosphorylation site are influenced by direct interaction with the kinase in a varying degree. This sequence stretch is embedded in an intrinsically disordered region composed preferentially of hydrophilic residues with flexible backbone and small side chain. This knowledge has been incorporated into a simplified analytical model of productive binding of substrate proteins with PKA.ConclusionThe scoring function of the pkaPS predictor can confidently discriminate PKA phosphorylation sites from serines/threonines with non-permissive sequence environments (sensitivity of ~96% at a specificity of ~94%). The tool "pkaPS" has been applied on the whole human proteome. Among new predicted PKA targets, there are entirely uncharacterized protein groups as well as apparently well-known families such as those of the ribosomal proteins L21e, L22 and L6.AvailabilityThe supplementary data as well as the prediction tool as WWW server are available at .ReviewersErik van Nimwegen (Biozentrum, University of Basel, Switzerland), Sandor Pongor (International Centre for Genetic Engineering and Biotechnology, Trieste, Italy), Igor Zhulin (University of Tennessee, Oak Ridge National Laboratory, USA).
Highlights
Protein kinase A is a serine/threonine kinase, for which ca. 150 substrate proteins are known
Overview The whole work consist of two major parts – first, the derivation of the property pattern that characterizes sequence segments with Protein kinase A (PKA) phosphorylation sites and, second, the development and the validation of a prediction tool for the recognition of PKA phosphorylation sites in query sequences
The following four sections of the Results ("The motif length", "Positive charge in the N-terminal flank", "Polarity and flexibility in the C-terminal flank", "Phylogenetic variation of the substrate binding site of PKA") are dedicated to the derivation of the sequence motif coding for PKA phosphorylation sites
Summary
Protein kinase A (cAMP-dependent kinase, PKA) is a serine/threonine kinase, for which ca. 150 substrate proteins are known. Phosphorylation plays a key role in a large set of signal transduction pathways and is known to regulate the functions of a vast number of different proteins. Are substrate motifs for phosphorylation found in proteins from various cellular contexts, there are >500 kinases [1] with at least partly non-overlapping substrate specificities encoded in each of the higher eukaryote genomes. This broad distribution, coupled with the potential medical applications, makes them interesting research targets with regard to their role in signaling cascades. A low false-positive prediction rate is especially important in this context
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