{"database":"JPOST Repository","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Wiff":["https://storage.jpostdb.org/JPST000235/files/131019hi_03_02.wiff.scan","https://storage.jpostdb.org/JPST000235/files/131019hi_02_01.wiff.scan","https://storage.jpostdb.org/JPST000235/files/131116hi_02_a1.wiff","https://storage.jpostdb.org/JPST000235/files/131116hi_02_a1.wiff.scan","https://storage.jpostdb.org/JPST000235/files/131116hi_03_a2.wiff","https://storage.jpostdb.org/JPST000235/files/131116hi_03_a2.wiff.scan","https://storage.jpostdb.org/JPST000235/files/131019hi_03_02.wiff","https://storage.jpostdb.org/JPST000235/files/131019hi_02_01.wiff"],"Mzid":["https://storage.jpostdb.org/JPST000235/files/F073776.mzid","https://storage.jpostdb.org/JPST000235/files/F073169.mzid","https://storage.jpostdb.org/JPST000235/files/F073170.mzid","https://storage.jpostdb.org/JPST000235/files/F073777.mzid"],"Mgf":["https://storage.jpostdb.org/JPST000235/files/131116hi_03_a2.mgf","https://storage.jpostdb.org/JPST000235/files/131019hi_02_01.mgf","https://storage.jpostdb.org/JPST000235/files/131116hi_02_a1.mgf","https://storage.jpostdb.org/JPST000235/files/131019hi_03_02.mgf"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"omics_type":["Proteomics"],"submitter":["Yasushi Ishihama"],"species":["Homo Sapiens (human)"],"full_dataset_link":["https://repository.jpostdb.org/entry/JPST000235"],"submitter_affiliation":["Kyoto university"],"sample_protocol":[""],"repository":["jPOST"],"data_protocol":[""],"pubmed_abstract":["Protein kinase A (PKA or cAMP-dependent protein kinase) is a serine/threonine kinase that plays essential roles in the regulation of proliferation, differentiation, and apoptosis. To better understand the functions of PKA, it is necessary to elucidate the direct interplay between PKA and their substrates in living human cells. To identify kinase target substrates in a high-throughput manner, we first quantified the change of phosphoproteome in the cells of which PKA activity was perturbed by drug stimulations. LC-MS/MS analyses identified 2755 and 3191 phosphopeptides from experiments with activator or inhibitor of PKA. To exclude potential indirect targets of PKA, we built a computational model to characterize the kinase sequence specificity toward the substrate target site based on known kinase-substrate relationships. Finally, by combining the sequence recognition model with the quantitative changes in phosphorylation measured in the two drug perturbation experiments, we identified 29 reliable candidates of PKA targeting residues in living cells including 8 previously known substrates. Moreover, 18 of these sites were confirmed to be site-specifically phosphorylated in vitro. Altogether this study proposed a confident list of PKA substrate candidates, expanding our knowledge of PKA signaling network."],"pubmed_title":["Identifications of Putative PKA Substrates with Quantitative Phosphoproteomics and Primary-Sequence-Based Scoring."],"pubmed_authors":["Imamura Haruna H, Wagih Omar O, Niinae Tomoya T, Sugiyama Naoyuki N, Beltrao Pedro P, Ishihama Yasushi Y"],"name_synonyms":["6beta, NKH-477., Colforsin, colforsinum, cAMP Dependent Protein Kinase, Cyclic AMP-Dependent Protein Kinase, 5-(acetyloxy)-3-ethenyldodecahydro-6, 10b-trihydroxy-3, cAMP, N, Coleonol, number, 13-epoxy-1alpha, Adenosine Cyclic Monophosphate-Dependent Protein Kinases, NKH477, N-Dimethyl-beta-alanine-5-(acetyloxy)-3-ethenyldodecahydro-10, 1-b)pyran-1-one, 10a-pentamethyl-, cAMP Dependent Protein Kinases, 9alpha-trihydroxylabd-14-en-11-one, presence, cAMP Protein Kinase, primary structure of sequence macromolecule, cAMP-Dependent, 10, Coleonolk, Cyclic AMP Dependent Protein Kinase, colforsina, 1-b)pyran-6-yl Ester HCl, count in organism, Adenosine Cyclic Monophosphate Dependent Protein Kinases, colforsine, 1H-Naphtho(2, 4a, 7beta-acetoxy-8, sequence, Protein Kinases, cAMP-Dependent Protein Kinases, colforsin, cAMP-Dependent Protein Kinase, 7, Forskolin, NKH 477, Protein Kinase, 10a-pentamethyl-1-oxo-1H-naphtho(2, Cyclic AMP Dependent Protein Kinases, 10b-dihydroxy-3, Protein Kinase A"],"pubmed_abstract_synonyms":["glycogen synthase kinase activity, liquid chromatography tandem mass spectroscopy, 6353, Dmel_CG3263, protein kinase A activity, Activity, Product, FALL39, 5'-cyclic monophosphate, L-Threonine, type I programmed cell death, CG18677, phosphorylation, Social Controls, CG12452, Prp4 protein kinase activity, 2-Amino-3-hydroxypropionic acid, Extrinsic Pathway Apoptoses, ATP-protein transphosphorylase activity, cAMP-dependent protein kinase, Pharmaceutical Product, ATP:protein phosphotransferase (non-specific) activity, CAP-18, Protein Kinases, Dpck, mitogen-activated protein kinase activity, Kinase, RI, C13orf8, Formal Social Controls, Cyclic AMP Dependent Protein Kinases, Protein Kinase A, Threonin, C, cAMP Dependent Protein Kinase, LCMSMS, Man (Taxonomy), pre-mortem, cAMP, CG4379, Pk72A, ZNF828, 3', 5' cAMP-dependent protein kinase complex, CG15862, cAMP-Dependent, Raf kinase activity, Social, Cyclic AMP Dependent Protein Kinase, serine kinase activity, Intrinsic Pathway Apoptosis, DmelCG6117, 5' cAMP-dependent protein kinase activity, 2-amino-3-hydroxypropanoic acid, atypical protein kinase C activity, medicine, Classic, Pharmaceutical, Classical Apoptosis, mitogen-activated S6 kinase activity, protein-aspartyl kinase activity, cAMP-Dependent Protein Kinases, ATP Phosphotransferases, ATP, p82 kinase activity, HSD26, LC-MS2, Caspase-Dependent Apoptosis, Modern, betaIIPKC, cyclic AMP-dependent protein kinase complex, LC-MS/MS, CG42341, CAP18, pka-C1, 5'-phosphate, CAMP, M phase-specific cdc2 kinase activity, Wee-kinase activity, signaling (initiator) caspase activity, Cyclic AMP, induction of apoptosis, pka-R1, 3-Hydroxyalanine, Intrinsic Pathway, MAPK, Extrinsic Pathway Apoptosis, 5'-cAMP-dependent protein kinase complex, Cos-1, RII[[DR]], Pharmaceutic, Caspase-Dependent, pka-c1, serine protein kinase activity, region, 5-23, PKA C, phosphorylase B kinase kinase activity, Transphosphorylases, Epistemology, protein glutamyl kinase activity, CHAMP, Control, CG6117, non-specific serine/threonine protein kinase activity, Adenosine Cyclic Monophosphate-Dependent Protein Kinases, Dmel_CG12452, pka-RII, cAMP Dependent Protein Kinases, Controls, human, Intrinsic Pathway Apoptoses, living, hydroxyalkyl-protein kinase activity, SNF1-RELATED PROTEIN KINASE 2-2, WEE1Hu, DmelCG4379, ATP:protein phosphotransferase (cAMP-dependent) activity, induction of apoptosis by p53, PKA RII, antagonists and inhibitors, SNF1-related protein kinase 2.2, serine-specific protein kinase activity, liquid chromatography-tandem mass spectroscopy, dPKA, epsilon PKC, PkaC1, PKAcA, Adenosine 3', HIPK2, cytidine 3', Extrinsic Pathway, RII, L Serine, Epa, Wee 1-like kinase activity, L-Serine, Protein Kinase, Dcpk, Regulation, Classical, adenosine 3', Apoptoses, PKAC1, Regulations, ribosomal S6 protein kinase activity, CRAMP, calcium/phospholipid-dependent protein kinase activity, human being, Cyclic AMP-Dependent Protein Kinase, glycogen synthase A kinase activity, glycogen synthase kinase 3 activity, caspase-dependent programmed cell death, number, Pk?5, Caspase Dependent Apoptosis, PKA-C3, PKA-C-3, PKA-C1, presence, BcDNA:GM01761, phosphorylase b kinase kinase activity, activation of apoptosis, LC-MS-MS, Human, 5'-Cyclic AMP, Homo sapiens, Pka-RI, Cyclic adenylic acid, LC-MSMS, l(2)cos[[1]], serine(threonine) protein kinase activity, BG02142, Type I, AMPK, ribosomal protein S6 kinase II activity, Phosphotransferase, Man, 18304, T-antigen kinase activity, Drugs, galactosyltransferase-associated kinase activity, study, protein-serine kinase activity, Pka-C, PKAR, PkaR, STK32, inhibiteur, PKa-R2, PKa-R1, L Threonine, PKAc, Transphosphorylase, apoptosis activator activity, ATP-protein phosphotransferase, cAMP Protein Kinase, protein kinase (phosphorylating) activity, PKA-R1, DmelCG15862, 5'-cyclophosphate-dependent protein kinase activity, Adenosine Cyclic Monophosphate Dependent Protein Kinases, PKA-R2, drugs, Cos, SNRK2-2, inhibidor, CdkA, protein-cysteine kinase activity, Raf-1, Classic Apoptosis, Hpr kinase activity, Dc0, STK22, site, Preparation, casein kinase (phosphorylating) activity, DRI, PKA-RI, single organism signaling., Apoptosis, Pharmaceuticals, PKA Cl, inhibitors, Products, Cos1, 5'-cyclophosphate-dependent protein kinase complex, l(2)s4402, Formal Social Control, drug, DC0, DC2, Phosphorylations, dPKA-RI, inhibitor, CG3263, CdkR, protein serine kinase activity, Phosphotransferases, Cell, protein phosphokinase activity, cos1, Serin, count in organism, twitchin kinase activity, LC/MS/MS, PKAi, cyclic AMP-dependent protein kinase activity, SRK2D, pkA, PKA, Pka, Phosphopeptide, PKAr, PKC, 5'-cyclic phosphate, Social Control, Programmed Cell Death, AP50 kinase activity, Protein, dcO, DCO, Dco, sequence, intrinsic catalyst activity, protein kinase p58 activity, Pka-RII, serine/threonine protein kinase activity, antagonists, threonine-specific protein kinase activity, apoptosis signaling, pka, pka C1, pKA, dr[[1]], LL37, SPK-2-2, PKA C3, FALL-39, apoptosis, Pharmaceutic Preparations, Kinases, dco, 5'-(hydrogen phosphate), 5'-cAMP-dependent protein kinase activity, dsk1, PKA-RII, 5'-CYCLIC-MONOPHOSPHATE, 5'-cyclic monophosphate-responsive protein kinase activity, atypical PKC activity, primary structure of sequence macromolecule, DmelCG42341, Classic Apoptoses, Drug, PKA CI, Preparations, signalling process, apoptotic program, Modern Man, l(2)01272, ADENOSINE-3', commitment to apoptosis, liquid chromatography tandem mass spectrometry, regulation, cAMP-Dependent Protein Kinase, Pharmaceutical Products, PROTEIN KINASE, protein serine-threonine kinase activity, General activity, A-kinase activity, Pharmaceutical Preparation"],"pubmed_title_synonyms":["glycogen synthase kinase activity, 6353, ribosomal S6 protein kinase activity, calcium/phospholipid-dependent protein kinase activity, Dmel_CG3263, protein kinase A activity, glycogen synthase A kinase activity, glycogen synthase kinase 3 activity, number, Pk?5, PKA-C3, PKA-C-3, PKA-C1, presence, CG18677, BcDNA:GM01761, phosphorylase b kinase kinase activity, CG12452, Prp4 protein kinase activity, Pka-RI, ATP-protein transphosphorylase activity, cAMP-dependent protein kinase, ATP:protein phosphotransferase (non-specific) activity, l(2)cos[[1]], serine(threonine) protein kinase activity, Dpck, mitogen-activated protein kinase activity, BG02142, RI, AMPK, ribosomal protein S6 kinase II activity, 18304, T-antigen kinase activity, galactosyltransferase-associated kinase activity, C, protein-serine kinase activity, Pka-C, PKAR, PkaR, CG4379, STK32, Pk72A, 3', 5' cAMP-dependent protein kinase complex, PKa-R2, PKa-R1, PKAc, CG15862, Raf kinase activity, protein kinase (phosphorylating) activity, PKA-R1, DmelCG15862, serine kinase activity, 5'-cyclophosphate-dependent protein kinase activity, PKA-R2, Cos, DmelCG6117, 5' cAMP-dependent protein kinase activity, CdkA, protein-cysteine kinase activity, atypical protein kinase C activity, Raf-1, Hpr kinase activity, Dc0, mitogen-activated S6 kinase activity, STK22, protein-aspartyl kinase activity, casein kinase (phosphorylating) activity, DRI, PKA-RI, p82 kinase activity, PKA Cl, Cos1, 5'-cyclophosphate-dependent protein kinase complex, l(2)s4402, DC0, betaIIPKC, cyclic AMP-dependent protein kinase complex, DC2, dPKA-RI, CG42341, CG3263, CdkR, protein serine kinase activity, pka-C1, protein phosphokinase activity, M phase-specific cdc2 kinase activity, Wee-kinase activity, cos1, count in organism, twitchin kinase activity, PKAi, cyclic AMP-dependent protein kinase activity, pkA, PKA, Pka, PKAr, pka-R1, PKC, MAPK, AP50 kinase activity, 5'-cAMP-dependent protein kinase complex, Cos-1, dcO, DCO, Dco, sequence, RII[[DR]], intrinsic catalyst activity, pka-c1, serine protein kinase activity, protein kinase p58 activity, Pka-RII, serine/threonine protein kinase activity, 5-23, threonine-specific protein kinase activity, PKA C, phosphorylase B kinase kinase activity, pka, pka C1, pKA, dr[[1]], PKA C3, protein glutamyl kinase activity, dco, CG6117, non-specific serine/threonine protein kinase activity, Dmel_CG12452, pka-RII, 5'-cAMP-dependent protein kinase activity, dsk1, PKA-RII, 5'-cyclic monophosphate-responsive protein kinase activity, atypical PKC activity, DmelCG42341, PKA CI, hydroxyalkyl-protein kinase activity, WEE1Hu, DmelCG4379, ATP:protein phosphotransferase (cAMP-dependent) activity, PKA RII, serine-specific protein kinase activity, dPKA, epsilon PKC, PkaC1, l(2)01272, PKAcA, HIPK2, cytidine 3', primary structure of sequence macromolecule., RII, Epa, Wee 1-like kinase activity, Dcpk, adenosine 3', protein serine-threonine kinase activity, PKAC1, A-kinase activity"],"description_synonyms":["glycogen synthase kinase activity, liquid chromatography tandem mass spectroscopy, 6353, Dmel_CG3263, protein kinase A activity, Activity, Product, determination, L-Threonine, CG18677, phosphorylation, brl, CG12452, Prp4 protein kinase activity, 2-Amino-3-hydroxypropionic acid, ATP-protein transphosphorylase activity, cAMP-dependent protein kinase, Pharmaceutical Product, ATP:protein phosphotransferase (non-specific) activity, Protein Kinases, Dpck, mitogen-activated protein kinase activity, Kinase, RI, Cyclic AMP Dependent Protein Kinases, Protein Kinase A, Threonin, C, cAMP Dependent Protein Kinase, LCMSMS, pre-mortem, cAMP, CG4379, Pk72A, 3', 5' cAMP-dependent protein kinase complex, CG15862, cAMP-Dependent, Raf kinase activity, Cyclic AMP Dependent Protein Kinase, serine kinase activity, DmelCG6117, 5' cAMP-dependent protein kinase activity, 2-amino-3-hydroxypropanoic acid, atypical protein kinase C activity, medicine, Pharmaceutical, signaling process, mitogen-activated S6 kinase activity, protein-aspartyl kinase activity, cAMP-Dependent Protein Kinases, ATP Phosphotransferases, SIMPLE, ATP, single organism signaling, p82 kinase activity, LC-MS2, betaIIPKC, cyclic AMP-dependent protein kinase complex, LC-MS/MS, CG42341, pka-C1, Expanded, M phase-specific cdc2 kinase activity, Wee-kinase activity, pka-R1, 3-Hydroxyalanine, MAPK, PIG7, 1270, 5'-cAMP-dependent protein kinase complex, Cos-1, RII[[DR]], Pharmaceutic, pka-c1, serine protein kinase activity, region, 5-23, PKA C, phosphorylase B kinase kinase activity, Transphosphorylases, Epistemology, protein glutamyl kinase activity, expanded, CG6117, non-specific serine/threonine protein kinase activity, Ex, Adenosine Cyclic Monophosphate-Dependent Protein Kinases, Dmel_CG12452, pka-RII, cAMP Dependent Protein Kinases, living, hydroxyalkyl-protein kinase activity, WEE1Hu, DmelCG4379, ATP:protein phosphotransferase (cAMP-dependent) activity, PKA RII, antagonists and inhibitors, enlarged, serine-specific protein kinase activity, liquid chromatography-tandem mass spectroscopy, dPKA, epsilon PKC, PkaC1, PKAcA, HIPK2, cytidine 3', l(2)ey, RII, L Serine, Epa, Wee 1-like kinase activity, L-Serine, Protein Kinase, Dcpk, adenosine 3', PKAC1, big, ribosomal S6 protein kinase activity, calcium/phospholipid-dependent protein kinase activity, biological signaling, Cyclic AMP-Dependent Protein Kinase, glycogen synthase A kinase activity, glycogen synthase kinase 3 activity, Pk?5, PKA-C3, PKA-C-3, PKA-C1, BcDNA:GM01761, phosphorylase b kinase kinase activity, LC-MS-MS, large, DmelCG4114, Pka-RI, LC-MSMS, l(2)cos[[1]], serine(threonine) protein kinase activity, BG02142, AMPK, ribosomal protein S6 kinase II activity, Phosphotransferase, 18304, T-antigen kinase activity, Drugs, galactosyltransferase-associated kinase activity, study, protein-serine kinase activity, Pka-C, anatomical systems, PKAR, PkaR, STK32, inhibiteur, PKa-R2, PKa-R1, L Threonine, PKAc, Transphosphorylase, cAMP Protein Kinase, protein kinase (phosphorylating) activity, PKA-R1, DmelCG15862, 5'-cyclophosphate-dependent protein kinase activity, Adenosine Cyclic Monophosphate Dependent Protein Kinases, PKA-R2, drugs, Cos, inhibidor, CdkA, protein-cysteine kinase activity, Raf-1, great, Hpr kinase activity, Dc0, STK22, site, Preparation, casein kinase (phosphorylating) activity, DRI, PKA-RI, TP53I7, Pharmaceuticals, signalling., PKA Cl, inhibitors, Products, Cos1, 5'-cyclophosphate-dependent protein kinase complex, l(2)s4402, drug, DC0, CG4114, DC2, Phosphorylations, dPKA-RI, inhibitor, CG3263, CdkR, protein serine kinase activity, Phosphotransferases, Cell, protein phosphokinase activity, cos1, Serin, twitchin kinase activity, LC/MS/MS, PKAi, cyclic AMP-dependent protein kinase activity, pkA, PKA, Pka, Phosphopeptide, PKAr, PKC, AP50 kinase activity, chemical analysis, dcO, DCO, Dco, intrinsic catalyst activity, protein kinase p58 activity, Pka-RII, serine/threonine protein kinase activity, antagonists, threonine-specific protein kinase activity, pka, pka C1, pKA, dr[[1]], PKA C3, Pharmaceutic Preparations, Kinases, dco, 5'-cAMP-dependent protein kinase activity, dsk1, PKA-RII, 5'-cyclic monophosphate-responsive protein kinase activity, atypical PKC activity, signalling, DmelCG42341, Drug, l(2)01270, PKA CI, Preparations, signalling process, l(2)01272, liquid chromatography tandem mass spectrometry, assay, cAMP-Dependent Protein Kinase, Pharmaceutical Products, protein serine-threonine kinase activity, General activity, A-kinase activity, Pharmaceutical Preparation"],"additional_accession":[]},"is_claimable":false,"name":"Identifications of protein kinase A substrates with quantitative phosphoproteomics and primary-sequence based scoring.(forskolin)","description":"Protein kinase A (PKA) is a serine/threonine kinase who plays essential roles in the complex signalling pathways. To better understand the functionalities, it is necessary to elucidate direct interplays between PKA and their substrates in living system. In order to screen them in a high-throughput manner, we firstly quantified the change of phosphoproteome in the cells of which PKA activity was perturbed by drag stimulations. LC-MS/MS analysis identified 2,755 and 3,191 phosphopeptides from either experiments with activator or inhibitor of PKA. To exclude indirect targets of PKA, we built the simple model to characterize the kinase sequential specificity to its substrate recognitions based on the known kinase-substrate relationships. Finally, by applying the metric to the sites of which phosphorylation were changed due to the drug stimulations, we identified 29 reliable candidates of PKA targeting residues in living cells including 8 known substrates. Moreover, 18 sites out of them were confirmed to be site-specifically phosphorylated in vitro. Altogether this study proposed confident list of PKA substrate and expanded the knowledge of PKA signalling network.","dates":{"publication":"Wed Feb 14 00:00:00 GMT 2018"},"accession":"PXD005922","cross_references":{"TAXONOMY":["9606"],"pubmed":["28287266"]}}