2010
Deciphering Protein Kinase Specificity Through Large-Scale Analysis of Yeast Phosphorylation Site Motifs
Mok J, Kim PM, Lam HY, Piccirillo S, Zhou X, Jeschke GR, Sheridan DL, Parker SA, Desai V, Jwa M, Cameroni E, Niu H, Good M, Remenyi A, Nianhan J, Sheu YJ, Sassi HE, Sopko R, Chan CS, De Virgilio C, Hollingsworth NM, Lim WA, Stern DF, Stillman B, Andrews BJ, Gerstein MB, Snyder M, Turk BE. Deciphering Protein Kinase Specificity Through Large-Scale Analysis of Yeast Phosphorylation Site Motifs. Science Signaling 2010, 3: ra12. PMID: 20159853, PMCID: PMC2846625, DOI: 10.1126/scisignal.2000482.Peer-Reviewed Original ResearchConceptsPhosphorylation site motifsSite motifShort linear sequence motifsKinase substrate recognitionKinase-substrate relationshipsProtein kinase specificityKinase catalytic domainLinear sequence motifsPrediction of thousandsCMGC groupKinase specificityPhosphorylation targetsKinase substrateYeast proteomeSequence motifsSubstrate recognitionKinase familyProtein substratesCatalytic domainProtein kinaseLarge-scale analysisPrimary sequenceCandidate substratesComputational scanningKinase
2008
Regulation of the Rad53 protein kinase in signal amplification by oligomer assembly and disassembly
Jia-Lin Ma N, Stern DF. Regulation of the Rad53 protein kinase in signal amplification by oligomer assembly and disassembly. Cell Cycle 2008, 7: 808-817. PMID: 18239457, DOI: 10.4161/cc.7.6.5595.Peer-Reviewed Original ResearchConceptsRad53 activationDNA damageOligomer assemblyRad53 kinase activityRad53 protein kinaseAbsence of Mec1DNA damage responseSignal transduction processesMammalian Chk2Autophosphorylation activityGenetic requirementsCheckpoint responseChk2 activationDamage responseEffector kinaseProtein kinaseKinase activityRad53Forms oligomersTransduction processesSCD domainsInduced oligomerizationOligomer formationOligomerizationChk2
2006
Global Analysis of Protein Phosphorylation in Yeast
Ptacek J, Devgan G, Michaud G, Zhu H, Zhu X, Fasolo J, Guo H, Jona G, Breitkreutz A, Sopko R, McCartney R, Schmidt M, Rachidi N, Lee S, Mah A, Meng L, Stark M, Stern D, De Virgilio C, Tyers M, Andrews B, Gerstein M, Schweitzer B, Predki P, Snyder M. Global Analysis of Protein Phosphorylation in Yeast. The FASEB Journal 2006, 20: a1308-a1308. DOI: 10.1096/fasebj.20.5.a1308.Peer-Reviewed Original ResearchProtein phosphorylationProtein kinaseNovel regulatory moduleDifferent biochemical functionsNumber of kinasesMajor regulatory mechanismSame cellular compartmentSame functional categoryYeast kinasesCellular rolesCyclin subunitPhosphorylation eventsRegulatory modulesYeast proteinsVivo substratePhosphorylation resultsBiochemical functionsRelated kinasesTranscription factorsCellular compartmentsFunctional categoriesBiochemical understandingRegulatory mechanismsDifferent proteinsKinase
2005
Activation of the Checkpoint Kinase Rad53 by the Phosphatidyl Inositol Kinase-like Kinase Mec1*
Ma JL, Lee SJ, Duong JK, Stern DF. Activation of the Checkpoint Kinase Rad53 by the Phosphatidyl Inositol Kinase-like Kinase Mec1*. Journal Of Biological Chemistry 2005, 281: 3954-3963. PMID: 16365046, DOI: 10.1074/jbc.m507508200.Peer-Reviewed Original ResearchConceptsPhosphorylation-dependent mechanismDNA damageKinase activityDNA replication checkpoint pathwayRad53 kinase activityCheckpoint kinase Rad53Essential protein kinaseReplication checkpoint pathwayActivation of Rad53Protein kinase activityMammalian Chk2Rad53 phosphorylationRad53 activationRad53Protein kinaseDownstream responsesCheckpoint pathwayOrthologsAutophosphorylationKinasePhosphorylationIntermolecular mechanismActivationPIKKsComplexesPhosphoproteomics for oncology discovery and treatment
Stern DF. Phosphoproteomics for oncology discovery and treatment. Expert Opinion On Therapeutic Targets 2005, 9: 851-860. PMID: 16083347, DOI: 10.1517/14728222.9.4.851.Peer-Reviewed Original ResearchConceptsPhosphoproteomic analysisProtein phosphorylationReversible protein phosphorylationSignal transduction pathwaysCellular regulationProtein kinaseTransduction pathwaysHuman cancersDevelopment of drugsPathwayPhosphorylationGood targetImportant insightsCancer therapyCancer drugsPhosphoproteomicsCellsIndividual tumorsPowerful toolKinaseRegulationIntermediary levelDiscoveryTargetIdentificationThe Plk1 Polo Box Domain Mediates a Cell Cycle and DNA Damage Regulated Interaction with Chk2
Tsvetkov LM, Tsekova RT, Xu X, Stern DF. The Plk1 Polo Box Domain Mediates a Cell Cycle and DNA Damage Regulated Interaction with Chk2. Cell Cycle 2005, 4: 602-610. PMID: 15876876, DOI: 10.4161/cc.4.4.1599.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsCatalytic DomainCell CycleCell Cycle ProteinsCell DivisionCell SeparationCheckpoint Kinase 2DNA DamageDNA RepairG2 PhaseGenetic VectorsGlutathione TransferaseHeLa CellsHumansImmunoblottingImmunoprecipitationIn Vitro TechniquesMitosisPhosphorylationProtein BindingProtein KinasesProtein Serine-Threonine KinasesProtein Structure, TertiaryProto-Oncogene ProteinsSignal TransductionConceptsPlk1 polo-box domainDNA damage checkpointPolo-box domainPolo-like kinase 1Eukaryotic proteinsDamage checkpointMitotic regulationBox domainRegulated interactionPlk1 activityProtein kinaseSignaling cascadesChk2Kinase 1Tumor suppressorCell cycleDNA damageS phasePlk1M phaseMitosisMultiple processesPotential mechanismsPhosphorylatesKinaseRegulation of CHK2 by DNA-dependent Protein Kinase*
Li J, Stern DF. Regulation of CHK2 by DNA-dependent Protein Kinase*. Journal Of Biological Chemistry 2005, 280: 12041-12050. PMID: 15668230, DOI: 10.1074/jbc.m412445200.Peer-Reviewed Original ResearchMeSH KeywordsAndrostadienesAntigens, NuclearAtaxia Telangiectasia Mutated ProteinsCell Cycle ProteinsCells, CulturedCheckpoint Kinase 2DNADNA DamageDNA-Activated Protein KinaseDNA-Binding ProteinsEnzyme ActivationHumansKu AutoantigenNuclear ProteinsPhosphorylationProtein Serine-Threonine KinasesTumor Suppressor ProteinsWortmanninConceptsActivation of Chk2DNA-PKChk2 phosphorylationDNA damageDNA-Dependent Protein Kinase Catalytic SubunitProtein Kinase Catalytic SubunitDNA-dependent protein kinaseFunctional DNA-PKRegulation of Chk2Kinase catalytic subunitRegulation of DNAChk2 kinase activityATM-deficient cellsDiverse cellular responsesKinase inhibitor wortmanninATM-defective cellsChk2 activationExposure of cellsCatalytic subunitProtein kinaseKinase activityChk2Inhibitor wortmanninRabbit reticulocytesCellular responsesInteraction of Chromatin-associated Plk1 and Mcm7*
Tsvetkov L, Stern DF. Interaction of Chromatin-associated Plk1 and Mcm7*. Journal Of Biological Chemistry 2005, 280: 11943-11947. PMID: 15654075, DOI: 10.1074/jbc.m413514200.Peer-Reviewed Original ResearchMeSH KeywordsCell Cycle ProteinsCells, CulturedChromatinDNA DamageDNA ReplicationDNA-Binding ProteinsHumansImmunoprecipitationMinichromosome Maintenance Complex Component 3Minichromosome Maintenance Complex Component 7MitosisNuclear ProteinsPhosphorylationProtein KinasesProtein Serine-Threonine KinasesProto-Oncogene ProteinsTranscription FactorsConceptsPolo-box domainEndogenous Plk1Mcm2-7 protein complexPBD of Plk1DNA damage checkpointMultifunctional protein kinaseInteraction of chromatinFull-length Plk1Soluble chromatin fractionMinichromosome maintenance proteinsChromosome segregationMitotic exitDamage checkpointPlk1 interactsMitotic structuresProtein complexesMitotic entryDNA replicationChromatin fractionProtein kinaseMitotic eventsMaintenance proteinsCell cyclePlk1MCM7
2004
Phosphorylation of Plk1 at S137 and T210 is Inhibited in Response to DNA Damage
Tsvetkov L, Stern DF. Phosphorylation of Plk1 at S137 and T210 is Inhibited in Response to DNA Damage. Cell Cycle 2004, 4: 166-171. PMID: 15611664, DOI: 10.4161/cc.4.1.1348.Peer-Reviewed Original ResearchMeSH KeywordsAtaxia Telangiectasia Mutated ProteinsCaffeineCDC2 Protein KinaseCdc25 PhosphatasesCell Cycle ProteinsCell DivisionCell Line, TumorCheckpoint Kinase 1Checkpoint Kinase 2Cyclin BDNA DamageDNA-Binding ProteinsDoxorubicinEnzyme ActivationG2 PhaseHumansMitosisNocodazolePhosphorylationProtein KinasesProtein Serine-Threonine KinasesProto-Oncogene ProteinsSerineSignal TransductionStaurosporineThreonineTumor Suppressor ProteinsConceptsDNA damage checkpointThreonine 210Damage checkpointPlk1 phosphorylationDNA damageCdc2/cyclin B kinaseATR-dependent checkpoint pathwayChk2 protein kinaseDNA damage-induced inhibitionATM/ATRCyclin B kinasePolo-like kinase 1Phosphorylation of PLK1Activation of Cdc25CNuclear importPhosphopeptide mappingMitotic entryActivation loopPhosphorylation sitesVivo phosphorylationPlk1 activityKinase domainProtein kinasePrevents phosphorylationActive mutant
2003
Rad53 Phosphorylation Site Clusters Are Important for Rad53 Regulation and Signaling
Lee SJ, Schwartz MF, Duong JK, Stern DF. Rad53 Phosphorylation Site Clusters Are Important for Rad53 Regulation and Signaling. Molecular And Cellular Biology 2003, 23: 6300-6314. PMID: 12917350, PMCID: PMC180918, DOI: 10.1128/mcb.23.17.6300-6314.2003.Peer-Reviewed Original ResearchMeSH KeywordsAlanineAmino Acid SubstitutionBinding SitesCell Cycle ProteinsCheckpoint Kinase 2DNA DamageFungal ProteinsIntracellular Signaling Peptides and ProteinsMAP Kinase Kinase 1Mitogen-Activated Protein Kinase KinasesMutationPhosphorylationProtein KinasesProtein Serine-Threonine KinasesProtein Structure, TertiarySaccharomyces cerevisiae ProteinsSaccharomycetalesSchizosaccharomyces pombe ProteinsSignal TransductionConceptsDNA damage-induced interactionsPhosphorylation of Rad53Rad53 kinase activityTel1-dependent mannerEssential protein kinaseDNA damageConsensus phosphorylation sitesRad53 activationRad53 phosphorylationFHA domainPhosphorylation sitesCheckpoint functionUpstream kinaseYeast Rad53Protein kinaseRad53Kinase activityAlanine substitutionsReplication blockadeBasal interactionSubstitution mutationsImpaired interactionDun1Mec1Site clustersFHA Domain-Mediated DNA Checkpoint Regulation of Rad53
Schwartz MF, Lee SJ, Duong JK, Eminaga S, Stern DF. FHA Domain-Mediated DNA Checkpoint Regulation of Rad53. Cell Cycle 2003, 2: 381-394. PMID: 12851493, DOI: 10.4161/cc.2.4.457.Peer-Reviewed Original ResearchConceptsDNA damage checkpoint pathwayDamage checkpoint pathwayFHA domainReplication blocksCheckpoint pathwayChromatin assembly factor Asf1Phosphorylation-dependent associationDNA damageDNA replication checkpointActivation of Rad53Phosphopeptide binding domainsReplication checkpointReplicational stressDNA checkpointCheckpoint defectRad53Checkpoint regulationCatalytic domainProtein kinaseFHA1Binding domainsAsf1FHA2Persistent activationPathway
1998
Rad53 FHA Domain Associated with Phosphorylated Rad9 in the DNA Damage Checkpoint
Sun Z, Hsiao J, Fay D, Stern D. Rad53 FHA Domain Associated with Phosphorylated Rad9 in the DNA Damage Checkpoint. Science 1998, 281: 272-274. PMID: 9657725, DOI: 10.1126/science.281.5374.272.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceCell Cycle ProteinsCheckpoint Kinase 2DNA DamageDNA ReplicationFungal ProteinsG2 PhaseHydroxyureaMethyl MethanesulfonateMitosisMutationOligopeptidesPeptidesPhosphorylationProtein KinasesProtein Serine-Threonine KinasesSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsTranscription, GeneticConceptsRad53 phosphorylationRad53 protein kinaseDNA damage signalsDNA damage checkpointProtein-binding domainsCell cycle phase arrestRNR3 transcriptionRad9 proteinFHA domainDamage checkpointG2/M cell cycle phase arrestCell divisionProtein kinaseSaccharomyces cerevisiaeDamage signalsRad9DNA damageRad53Phase arrestPhosphorylationCheckpointDomainCerevisiaeTranscriptionKinase
1997
Mutations in SPK1/RAD53 that specifically abolish checkpoint but not growth-related functions
Fay DS, Sun Z, Stern D. Mutations in SPK1/RAD53 that specifically abolish checkpoint but not growth-related functions. Current Genetics 1997, 31: 97-105. PMID: 9021124, DOI: 10.1007/s002940050181.Peer-Reviewed Original ResearchMeSH KeywordsAllelesCell Cycle ProteinsCheckpoint Kinase 2Cloning, MolecularElectrophoresis, Polyacrylamide GelGene Expression Regulation, EnzymologicGene Expression Regulation, FungalMutagenesisPlasmidsProtein KinasesProtein Serine-Threonine KinasesSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence DeletionTransformation, GeneticConceptsCheckpoint functionKinase domainKinase activityEssential protein kinaseWild-type levelsGrowth-related functionsCheckpoint arrestProtein kinaseDeletional analysisN-terminusSPK1Cell cycleMutant allelesGrowth activityMutationsRad53Normal rateSaccharomycesMultiple stagesKinaseDomainCheckpointActivityAllelesRegulation
1996
Spk1/Rad53 is regulated by Mec1-dependent protein phosphorylation in DNA replication and damage checkpoint pathways.
Sun Z, Fay DS, Marini F, Foiani M, Stern DF. Spk1/Rad53 is regulated by Mec1-dependent protein phosphorylation in DNA replication and damage checkpoint pathways. Genes & Development 1996, 10: 395-406. PMID: 8600024, DOI: 10.1101/gad.10.4.395.Peer-Reviewed Original ResearchMeSH KeywordsAlkaline PhosphataseCell CycleCell Cycle ProteinsCell DivisionCheckpoint Kinase 2DNA DamageDNA ReplicationDNA, FungalFungal ProteinsGene Expression Regulation, FungalGenes, FungalHydroxyureaImmunoblottingIntracellular Signaling Peptides and ProteinsMethyl MethanesulfonateMutagenesisPhosphorylationPrecipitin TestsProtein KinasesProtein Serine-Threonine KinasesSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSignal TransductionTemperatureConceptsProtein kinaseCheckpoint pathwayEssential protein kinaseDamage checkpoint pathwayDamage-induced phosphorylationKinase-defective formG1/S boundarySignal transduction pathwaysRegulation of phosphorylationTreatment of cellsCheckpoint functionCdc mutantsDNA replicationProtein phosphorylationUpstream kinaseCheckpoint arrestRegulated phosphorylationTransduction pathwaysKinase activityCell cyclePhosphorylationS boundaryDamage DNACycle arrestKinase
1995
ScSpk1 Spk1 (S. cerevisiae)
Zheng P, Fay D, Stern D. ScSpk1 Spk1 (S. cerevisiae). 1995, 126-127. DOI: 10.1016/b978-012324719-3/50028-5.Peer-Reviewed Original ResearchKinase domainProtein kinaseMluI cell cycle boxS-phase-specific genesS phase-specific expressionPhase-specific genesPhase-specific expressionTyr kinase activitySer/ThrSpecific protein kinasesProtein tyrosine kinasesTranscriptional regulationMutant cellsNuclear proteinsNuclear localizationKinase activitySPK1DNA damageKinaseDNA synthesisProteinRepair synthesisGenesLatter activityImportant role
1993
SPK1 is an essential S-phase-specific gene of Saccharomyces cerevisiae that encodes a nuclear serine/threonine/tyrosine kinase.
Zheng P, Fay DS, Burton J, Xiao H, Pinkham JL, Stern DF. SPK1 is an essential S-phase-specific gene of Saccharomyces cerevisiae that encodes a nuclear serine/threonine/tyrosine kinase. Molecular And Cellular Biology 1993, 13: 5829-5842. PMID: 8355715, PMCID: PMC360328, DOI: 10.1128/mcb.13.9.5829.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceCell Cycle ProteinsCheckpoint Kinase 2Chromosome MappingDNA RepairFungal ProteinsGene ExpressionGene Expression Regulation, FungalGenes, FungalMolecular Sequence DataMutagenesis, InsertionalNuclear ProteinsOligodeoxyribonucleotidesPromoter Regions, GeneticProtein KinasesProtein Serine-Threonine KinasesRestriction MappingRNA, MessengerS PhaseSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence AlignmentSubstrate SpecificityConceptsSerine/threonine/tyrosine kinasesS-phase-specific transcriptionCell cycle-dependent transcriptionS-phase-specific genesDual-specificity protein kinaseImmune complex kinase assayTyr kinase activityTyrosine protein kinaseDNA synthesisExcision repair genesBudded cellsCEN plasmidGenomic libraryPositive regulatorProtein-SerKinase assaysProtein kinaseNuclear localizationNucleotide sequenceBox elementKinase activityGenetic techniquesSPK1Tyrosine kinaseUpstream region
1991
Spk1, a new kinase from Saccharomyces cerevisiae, phosphorylates proteins on serine, threonine, and tyrosine.
Stern DF, Zheng P, Beidler DR, Zerillo C. Spk1, a new kinase from Saccharomyces cerevisiae, phosphorylates proteins on serine, threonine, and tyrosine. Molecular And Cellular Biology 1991, 11: 987-1001. PMID: 1899289, PMCID: PMC359764, DOI: 10.1128/mcb.11.2.987.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsBase SequenceBinding SitesCell Cycle ProteinsCheckpoint Kinase 2Cloning, MolecularEscherichia coliFungal ProteinsGene LibraryGenes, FungalImmunoblottingMolecular Sequence DataProtein KinasesProtein Serine-Threonine KinasesProtein-Tyrosine KinasesRecombinant ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence Homology, Nucleic AcidSerineSubstrate SpecificityThreonineTyrosineConceptsSerine/threonine kinaseProtein kinaseFusion proteinThreonine kinaseTyrosine phosphorylationGlutathione S-transferase fusion proteinCyclic AMP-dependent protein kinaseAMP-dependent protein kinaseSerine protein kinaseSerine/threonineCalmodulin-dependent protein kinase IICalcium/calmodulin-dependent protein kinase IITyrosine protein kinaseOpen reading frameProtein kinase IILambda gt11 libraryPutative kinaseNew kinasesThreonine phosphorylationCatalytic subunitSaccharomyces cerevisiaeBacterial proteinsReading frameAntiphosphotyrosine antibodyKinase II
1989
The Ick tyrosine protein kinase interacts with the cytoplasmic tail of the CD4 glycoprotein through its unique amino-terminal domain
Shaw A, Amrein K, Hammond C, Stern D, Sefton B, Rose J. The Ick tyrosine protein kinase interacts with the cytoplasmic tail of the CD4 glycoprotein through its unique amino-terminal domain. Cell 1989, 59: 627-636. PMID: 2582490, DOI: 10.1016/0092-8674(89)90008-1.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBase SequenceCD4 AntigensCytoplasmHeLa CellsHumansLymphocyte Specific Protein Tyrosine Kinase p56(lck)Macromolecular SubstancesMembrane GlycoproteinsMolecular Sequence DataMutationOligonucleotide ProbesPhosphoproteinsPlasmidsProtein BindingProtein MultimerizationProtein-Tyrosine KinasesT-LymphocytesTransfectionConceptsAmino-terminal domainCytoplasmic domainTyrosine protein kinase p56lckUnique amino-terminal domainT cell-specific proteinsTyrosine protein kinaseSpecific transmembrane proteinsCell-specific proteinsIntracellular tyrosine kinaseAmino-terminal residuesCarboxy-terminal residuesTransmembrane proteinCytoplasmic tailSrc familyProtein kinaseKinase p56lckTyrosine kinaseHeLa cellsCell surfaceProteinDeleted formsSurface glycoproteinP56lckKinaseResidues