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of Life Sciences, University of Dundee, Scotland, United Kingdom"],"cell_type":["Not available"],"repository":["GPMDB"],"pubmed_abstract":["The focus of the present study was to characterize the phosphoproteome of cytotoxic T cells and to explore the role of the serine threonine kinase PKD2 (Protein Kinase D2) in the phosphorylation networks of this key lymphocyte population. We used Stable Isotope Labeling of Amino acids in Culture (SILAC) combined with phosphopeptide enrichment and quantitative mass-spectrometry to determine the impact of PKD2 loss on the cytotoxic T cells phosphoproteome. We identified 15,871 phosphorylations on 3505 proteins in cytotoxic T cells. 450 phosphosites on 281 proteins were down-regulated and 300 phosphosites on 196 proteins were up-regulated in PKD2 null cytotoxic T cells. These data give valuable new insights about the protein phosphorylation networks operational in effector T cells and reveal that PKD2 regulates directly and indirectly about 5% of the cytotoxic T-cell phosphoproteome. PKD2 candidate substrates identified in this study include proteins involved in two distinct biological functions: regulation of protein sorting and intracellular vesicle trafficking, and control of chromatin structure, transcription, and translation. In other cell types, PKD substrates include class II histone deacetylases such as HDAC7 and actin regulatory proteins such as Slingshot. The current data show these are not PKD substrates in primary T cells revealing that the functional role of PKD isoforms is different in different cell lineages."],"pubmed_title":["Quantitative phosphoproteomics of cytotoxic T cells to reveal protein kinase d 2 regulated networks."],"pubmed_authors":["Navarro María N MN,Goebel Juergen J,Hukelmann Jens L JL,Cantrell Doreen A DA,","Navarro María N MN, Goebel Juergen J, Hukelmann Jens L JL, Cantrell Doreen A DA"],"name_synonyms":["protein kinase Cmu, Protein kinase D, protein kinase C mu, PKD1 kinase, number, mouse, nPKC-D1, PKCmu, presence, Cell, human, protein kinase C, count in organism, rat, count, mu, nPKC-mu, Protein kinase C mu type, 2.7.11.13, quantitative, Pkcm protein, PRKD1 protein, PRKCM protein, mouse., protein kinase D1, Prkcm protein, presence or absence in organism"],"description_synonyms":["data, Beliefs, PLXN5, mol, PKD2, Aminokarbonsaeure, PKD4, Aminosaeure, nPKC-D2, Proteins, Aminocarbonsaeure, number, Nl1, Phosphorylations, FBN, Gene, PLEXIN-B1, Mell1, Cultural Backgrounds, AI325941, presence, Cell, PC2, SeP, Belief, ACMICD, Spectroscopy, polypeptide, Background, count in organism, Cultural Background, Experiment, CEH, count, Cultures, MMEL2, ECTOL1, Cultural, Protein, Gene Products, NEPII, NL1, TRPP2, MFS1, Cell., NL2, Analysis, SEH, WMS, WMS2, Backgrounds, SEP, amino acids, cell, Spectrum, Spectrometry, APKD2, proteins, MASS, Amino, Pc-2, sEP, OCTD, Protein Gene Products, Gene Proteins, RGD1559992, Custom, SSKS, SELP, C030034P18Rik, Customs, Eph2, Acids, quantitative, GPHYSD2, E430016J11Rik, RWDD5, NEP2, SGS, presence or absence in organism"],"pubmed_title_synonyms":["protein kinase Cmu, Protein kinase D, protein kinase C mu, PKD1 kinase, number, mouse, nPKC-D1, PKCmu, presence, Cell, human, protein kinase C, count in organism, rat, count, mu, nPKC-mu, Protein kinase C mu type, 2.7.11.13, quantitative, Pkcm protein, PRKD1 protein, PRKCM protein, mouse., protein kinase D1, Prkcm protein, presence or absence in organism"],"pubmed_abstract_synonyms":["protein translation, Class I Histone Deacetylases, transcription, Beliefs, conformation, Aminosaeure, nPKC-D2, cytotoxic T cell, Deacetylase, Aminocarbonsaeure, number, FBN, Gene, L-Threonine, killer T lymphocyte, Isotope-Coded Affinity, PKD2 enzyme, HDRP, presence, phosphorylation, protein amino acid phosphorylation, lymphocytes, School-Age, Background, HD7b, HD7a, Roles, ECTOL1, Cultural, PKC-MU, Prkcm, Gene Products, HDAC7B, Concepts, HDAC7A, TRPP2, alpha-beta cytotoxic T-cell, transcription regulator activity, Histone Deacetylase Complexes, Kinase, Analysis, Isotopically-Coded Affinity, WMS, Chromatins, Isotopically-Coded Affinity Tagging, Backgrounds, PRKCM, MITR, HDAC, study, School-Age Populations, Hdac7a, FOCUS, amino acids, killer T-lymphocyte, reference sample, cell, Spectrum, 5830434K02Rik, killer T-cell, present in organism, proteins, L Threonine, Population, cytotoxic T-cell, Class II Histone Deacetylases, OCTD, RGD1559992, DNA-dependent, Stable, Custom, Deacetylase Complexes, Role Concepts, chromosome scaffold, Isotope-Coded Affinity Tagging, C030034P18Rik, Customs, School Age Population, ATP Phosphotransferases, Tagging, GPHYSD2, relational structural quality, alpha-beta cytotoxic T lymphocyte, Cell Lineages., Stable Isotope Labeling, ATP, SGS, cytolytic T-lymphocyte, Controlled, HDAC9B, PKCM, data, Controlling, cellular transcription, protein anabolism, mFLJ00062, protein biosynthetic process, alpha-beta cytotoxic T-lymphocyte, DNA-dependent transcription, PKD2, PKD1, PKD4, Aminokarbonsaeure, killer T cell, Proteins, Phosphorylations, Cultural Backgrounds, AI325941, Labeling, Histone, HDAC9FL, Cell, Phosphotransferases, Deacetylases, PC2, Concept, Belief, ACMICD, Spectroscopy, polypeptide, Isotope, count in organism, Cultural Background, Role Concept, count, PKD, Lineage, Cultures, Stable Isotope, School Age, Protein, Role, protein formation, protein biosynthesis, MFS1, cytotoxic T lymphocyte, HD7, Isotope Coded Affinity Tagging, HD9, WMS2, Transphosphorylases, Populations, HD7A, distinct, Kinases, Histone Deacetylase, HDAC7, Lineages, Spectrometry, APKD2, MASS, Isotope Labeling, Amino, Affinity Tagging, School Age Populations, Isotopically-Coded, cytotoxic T-lymphocyte, Pc-2, Protein Gene Products, cytolytic T-cell, Pkcm, Gene Proteins, CD8-positive, protein synthesis, Complexes, SSKS, HDAC Proteins, Isotope-Coded, L Serine, Acids, regulation, School-Age Population, threonine, quantitative, L-Serine, E430016J11Rik, CTL, RWDD5, presence or absence in organism"],"view_count":["33"],"citation_count":["0"],"search_count":["5"],"full_dataset_link":["http://gpmdb.thegpm.org/~/dblist_gpmnum/gpmnum=GPM32320004050"],"search_domains":["dbgap_ncbi~0","patentfamilies~0","rfam~0","merops~0","complex-portal~0","uniprot~0","wormbaseparasite~0","embl-covid19~0","reactome~0","emdb~0","wgs_masters~0","ebiweb_resources~0","opentargets_genetics~0","biomodels_all~0","ipd-mhc~0","ebiweb_teams~0","taxonomy~0","genome_assembly~0","sc-experiments~0","ebiweb_people~0","enzymeportal_enzymes~0","ipd-nhkir~0","cellosaurus~0","pdbe~0","chebi~0","patentproteins~0","interpro7~0","uniref~0","chembl~0","pdbekb~0","gpcrdb~0","hgnc~0","sc-genes~0","intact~0","rhea~0","ebiweb_training~0","alphafold~0","imgt-hla~0","patentnucleotides~0","ensemblroot~0","eva_studies~0","non-coding~0","europepmc~0","pubmed~1","identifiers_registry~0","pdbechem~0","hpa-covid19~0","eva-variants-covid19~0","biosamples~0","gwas_catalog~0","biotools~0","tls_masters~0","mesh~0","coding~0","sra~0","opentargets~0","efo~0","embl-pathogen~0","project~0","pride~1","human_diseases~0","geo_datasets~0","embl~0","treefam~0","uniparc~0","ols~0","dgva~0","intenz~0","go~0","tsa_masters~0","biosamples-covid19~0","ebiweb_corporate~0","omim~0","lrg~0","earlycause-molecular-sequences~0","ipd-kir~0","empiar~0","rnacentral~0","orcid_data_claims~0","gpmdb~2","lineage-covid19~0","metagenomics~0","pfam~0","pride archive~1","varsite~0"],"reanalysis_count":["0"],"submitter_keywords":["Resource Reanalysis"],"citation_count_scaled":["0.0"],"reanalysis_count_scaled":["0.0"],"view_count_scaled":["0.010178901912399754"],"download_count_scaled":["0.0"],"normalized_connections":["1.0"],"additional_accession":[]},"is_claimable":false,"name":"Quantitative phosphoproteomics of cytotoxic T cells to reveal Protein Kinase D 2 regulated networks.","description":"Data from ProteomeXchange, PXD ID: PXD001076. Experiment: JG-N2, file: JG-N2-12.mzml. Published as part of Mol Cell Proteomics. 2014 Sep 29  . From the Abstract: {{i}} ... We used Stable Isotope of Amino acids in Culture (SILAC) combined with phosphopeptide enrichment and quantitative mass-spectrometry to determine the impact of PKD2 loss on the cytotoxic T cells phosphoproteome. We identified 15,871 phosphorylations on 3,505 proteins in cytotoxic T cells ...{{/i}}","dates":{"submission":"2014-10-07"},"accession":"GPM32320004050","cross_references":{"pubmed":["25266776"],"Pride":["PXD001076"],"pride":[],"Pride Archive":["PXD001076"]}}