2008
Mammalian mitochondria have the innate ability to import tRNAs by a mechanism distinct from protein import
Rubio MA, Rinehart JJ, Krett B, Duvezin-Caubet S, Reichert AS, Söll D, Alfonzo JD. Mammalian mitochondria have the innate ability to import tRNAs by a mechanism distinct from protein import. Proceedings Of The National Academy Of Sciences Of The United States Of America 2008, 105: 9186-9191. PMID: 18587046, PMCID: PMC2453747, DOI: 10.1073/pnas.0804283105.Peer-Reviewed Original ResearchConceptsProtein importMammalian mitochondriaImport systemSubcellular RNA fractionsMitochondrial tRNA genesMitochondrial electrochemical gradientMitochondrial genomeTRNA genesTranscribed tRNAsHuman mitochondriaDefective mitochondriaProtein factorsFiber cellsHeterologous RNATRNACytosolic factorsSufficient ATPRNA fractionHuman cellsHuman diseasesProtein synthesisMitochondriaElectrochemical gradientOligonucleotide primersVitro systemCharacterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation
Sherrer RL, O’Donoghue P, Söll D. Characterization and evolutionary history of an archaeal kinase involved in selenocysteinyl-tRNA formation. Nucleic Acids Research 2008, 36: 1247-1259. PMID: 18174226, PMCID: PMC2275090, DOI: 10.1093/nar/gkm1134.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphatasesAdenosine TriphosphateAmino Acid SequenceArchaeal ProteinsBinding SitesEvolution, MolecularKineticsMethanococcalesModels, MolecularMutationPhosphotransferasesPhylogenyProtein Structure, TertiaryRNA, Transfer, Amino AcylSequence AlignmentSingle-Strand Specific DNA and RNA EndonucleasesSubstrate SpecificityConceptsATPase active sitePhosphate-binding loopInduced fit mechanismRxxxR motifEvolutionary historyWalker BKinase familyPhylogenetic analysisSep-tRNARelated kinasesPSTKBiochemical characterizationSynthase convertsFit mechanismKinaseATPase activityPlasmodium speciesMotifActive siteSerHigh affinityDecreased activityArchaeaSepSecSSer18
2006
Structure of the unusual seryl‐tRNA synthetase reveals a distinct zinc‐dependent mode of substrate recognition
Bilokapic S, Maier T, Ahel D, Gruic‐Sovulj I, Söll D, Weygand‐Durasevic I, Ban N. Structure of the unusual seryl‐tRNA synthetase reveals a distinct zinc‐dependent mode of substrate recognition. The EMBO Journal 2006, 25: 2498-2509. PMID: 16675947, PMCID: PMC1478180, DOI: 10.1038/sj.emboj.7601129.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAmino Acid SequenceAnimalsArchaeal ProteinsBinding SitesCrystallography, X-RayDimerizationEnzyme ActivationHumansMethanosarcina barkeriModels, MolecularMolecular Sequence DataMolecular StructureProtein Structure, QuaternarySequence AlignmentSequence Homology, Amino AcidSerineSerine-tRNA LigaseSubstrate SpecificityThreonineConceptsSeryl-tRNA synthetaseTRNA-binding domainMinimal sequence similarityResolution crystal structureAmino acid substratesActive site zinc ionSequence similaritySubstrate recognitionSerRSsSerine substrateMotif 1Methanogenic archaeaMutational analysisProtein ligandsEnzymatic activityArchaeaAminoacyl-tRNA synthetase systemsDistinct mechanismsAbsolute requirementRecognition mechanismSynthetase systemSynthetaseIon ligandsZinc ionsEucaryotes
2005
RNA-Dependent Cysteine Biosynthesis in Archaea
Sauerwald A, Zhu W, Major TA, Roy H, Palioura S, Jahn D, Whitman WB, Yates JR, Ibba M, Söll D. RNA-Dependent Cysteine Biosynthesis in Archaea. Science 2005, 307: 1969-1972. PMID: 15790858, DOI: 10.1126/science.1108329.Peer-Reviewed Original ResearchConceptsCysteine biosynthesisSep-tRNAComparative genomic analysisCys-tRNA synthasePhosphoseryl-tRNA synthetaseCys-tRNACysteine auxotrophyMost organismsMethanocaldococcus jannaschiiMethanococcus maripaludisGenetic codeGenomic analysisEssential enzymeO-phosphoserineBiosynthesisRNA synthetaseOrganismsSepRSSynthetasePartial purificationCysteineSole routeArchaeaSepCysSJannaschii
2002
tRNA‐dependent amino acid discrimination by yeast seryl‐tRNA synthetase
Gruic‐Sovulj I, Landeka I, Söll D, Weygand‐Durasevic I. tRNA‐dependent amino acid discrimination by yeast seryl‐tRNA synthetase. The FEBS Journal 2002, 269: 5271-5279. PMID: 12392560, DOI: 10.1046/j.1432-1033.2002.03241.x.Peer-Reviewed Original ResearchConceptsSeryl-tRNA synthetaseYeast seryl-tRNA synthetaseCognate tRNA moleculesAmino acid discriminationAminoacyl-tRNA synthetasesAmino acid substratesSimilar amino acidsAmino acid serineGenetic codeEnzyme active siteTRNA moleculesActive siteYeast SerRSConformational changesAcid substratesAmino acidsSerineSynthetaseStoichiometric analysisDifferent affinitiesEnzymeAccurate translationTRNASerSynthetasesSaccharomyces
1997
Glutamyl-tRNA sythetase.
Freist W, Gauss D, Söll D, Lapointe J. Glutamyl-tRNA sythetase. Biological Chemistry 1997, 378: 1313-29. PMID: 9426192.Peer-Reviewed Original ResearchConceptsGlutamyl-tRNA synthetaseGlutaminyl-tRNA synthetaseAminoacyl-tRNA synthetasesNegative eubacteriaBacterial glutamyl-tRNA synthetasesATP/PPiHigh molecular mass complexesClass I aminoacyl-tRNA synthetasesCytoplasm of eukaryotesE. coli GlnRSGlutamyl-tRNA synthetasesMolecular mass complexesN-terminal halfC-terminal halfAmino acid residuesDihydrouridine (DHU) armPhylogenetic studiesSpecific amidotransferaseGlutamyl-prolylMass complexesTRNA synthetasesCognate tRNAAcid residuesAcceptor stemSynthetasesGlutaminyl-tRNA synthetase.
Freist W, Gauss D, Ibba M, Söll D. Glutaminyl-tRNA synthetase. Biological Chemistry 1997, 378: 1103-17. PMID: 9372179.Peer-Reviewed Original ResearchConceptsE. coli GlnRSGlutaminyl-tRNA synthetaseGlutamyl-tRNA synthetaseMammalian enzymeCommon ancestorPositive eubacteriaCognate tRNAMultienzyme complexTRNA moleculesGlnRArtificial mutantsAcceptor stemAnticodon loopMolecular massAmino acidsCatalytic siteEnzymeSynthetaseEubacteriaArchaebacteriaTRNAMutantsOrganellesAncestorComplexes
1996
Genetic analysis of functional connectivity between substrate recognition domains ofEscherichia coli glutaminyl-tRNA synthetase
Kitabatake M, Inokuchi H, Ibba M, Hong K, Söll D. Genetic analysis of functional connectivity between substrate recognition domains ofEscherichia coli glutaminyl-tRNA synthetase. Molecular Genetics And Genomics 1996, 252: 717-722. PMID: 8917315, DOI: 10.1007/bf02173978.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAmino Acyl-tRNA SynthetasesCatalysisEscherichia coliMutagenesis, Site-DirectedProtein Structure, TertiarySubstrate SpecificityConceptsGlutaminyl-tRNA synthetaseWild-type enzymeSubstrate discriminationDouble mutantSubstrate recognition domainThree-dimensional structureAnticodon recognitionSubstrate specificityTRNA bindingGenetic analysisAcceptor stemRecognition domainC171Ternary complexExtensive interactionsMutantsPotential involvementG mutationEnzymeHigh KmSynthetaseMutationsActive siteE222GlnRTransfer RNA‐dependent cognate amino acid recognition by an aminoacyl‐tRNA synthetase.
Hong K, Ibba M, Weygand‐Durasevic I, Rogers M, Thomann H, Söll D. Transfer RNA‐dependent cognate amino acid recognition by an aminoacyl‐tRNA synthetase. The EMBO Journal 1996, 15: 1983-1991. PMID: 8617245, PMCID: PMC450117, DOI: 10.1002/j.1460-2075.1996.tb00549.x.Peer-Reviewed Original ResearchConceptsAmino acid recognitionEscherichia coli glutaminyl-tRNA synthetaseAccuracy of aminoacylationProtein-RNA interactionsRole of tRNAGlutaminyl-tRNA synthetaseAmino acid affinityCharacterization of mutantsAminoacyl-tRNA synthetaseAmino acid activationSpecific interactionsSubstrate recognitionEnzyme active siteGlnRActive siteAcceptor stemTRNAAminoacylationAcid affinityPosition 235TerminusSynthetaseObserved roleGlnTRNAGln
1995
A broadly applicable continuous spectrophotometric assay for measuring aminoacyl-tRNA synthetase activity
Lloyd A, Thomann H, Ibba M, Soöll D. A broadly applicable continuous spectrophotometric assay for measuring aminoacyl-tRNA synthetase activity. Nucleic Acids Research 1995, 23: 2886-2892. PMID: 7659511, PMCID: PMC307126, DOI: 10.1093/nar/23.15.2886.Peer-Reviewed Original Research
1991
Histidine tRNA guanylyltransferase from Saccharomyces cerevisiae. I. Purification and physical properties.
Pande S, Jahn D, Söll D. Histidine tRNA guanylyltransferase from Saccharomyces cerevisiae. I. Purification and physical properties. Journal Of Biological Chemistry 1991, 266: 22826-22831. PMID: 1660461, DOI: 10.1016/s0021-9258(18)54428-8.Peer-Reviewed Original ResearchConceptsAdditional nucleotidesHistidine tRNA genesPolymin P precipitationTRNA genesSodium dodecyl sulfate-polyacrylamide gel electrophoresisDodecyl sulfate-polyacrylamide gel electrophoresisTRNA speciesSulfate-polyacrylamide gel electrophoresisRate zonal sedimentationHomodimeric structureGuanylyltransferaseRelative molecular weightTRNAATP-agaroseGel filtrationAbolishes activityHistidine tRNANative enzymeGuanosine residuesAcceptor RNAEnzymatic activityUnfractionated tRNAGuanosine substrateZonal sedimentationGel electrophoresis
1990
Purification and functional characterization of the Glu-tRNA(Gln) amidotransferase from Chlamydomonas reinhardtii.
Jahn D, Kim Y, Ishino Y, Chen M, Söll D. Purification and functional characterization of the Glu-tRNA(Gln) amidotransferase from Chlamydomonas reinhardtii. Journal Of Biological Chemistry 1990, 265: 8059-8064. PMID: 1970821, DOI: 10.1016/s0021-9258(19)39038-6.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAmmoniaAsparagineAzo CompoundsBinding SitesChlamydomonasElectrophoresis, Polyacrylamide GelEnzyme ActivationGlutamatesGlutamic AcidGlutamineMagnesiumMolecular WeightNitrogenous Group TransferasesNorleucinePhosphorylationProtein DenaturationRNA, Transfer, Amino AcylSpectrophotometrySubstrate SpecificityTransferasesConceptsChlamydomonas reinhardtiiGlutamyl-tRNA synthetaseGlycerol gradient sedimentationSodium dodecyl sulfate-polyacrylamide gelsDodecyl sulfate-polyacrylamide gelsAmide donorSulfate-polyacrylamide gelsGlutamine-dependent reactionGlutamine amidotransferasesPresence of ATPGreen algaeSpecific amidotransferaseFunctional characterizationGlutaminyl-tRNAAmidotransferaseLow glutaminase activityApparent MrGradient sedimentationAlpha 2 structureReinhardtiiEnzymeATPGlutaminase activityStable complexesAmmonia-dependent reaction
1989
Structure of E. coli Glutaminyl-tRNA Synthetase Complexed with tRNAGln and ATP at 2.8 Å Resolution
Rould M, Perona J, Söll D, Steitz T. Structure of E. coli Glutaminyl-tRNA Synthetase Complexed with tRNAGln and ATP at 2.8 Å Resolution. Science 1989, 246: 1135-1142. PMID: 2479982, DOI: 10.1126/science.2479982.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAmino Acyl-tRNA SynthetasesAnticodonBase CompositionBase SequenceBinding SitesBiological EvolutionChemical PhenomenaChemistry, PhysicalCrystallizationEscherichia coliMolecular Sequence DataMolecular StructureNucleic Acid ConformationRNA, BacterialRNA, FungalRNA, Transfer, Amino Acid-SpecificRNA, Transfer, GlnX-Ray Diffraction
1988
Escherichia coli glutaminyl-tRNA synthetase: a single amino acid replacement relaxes rRNA specificity.
Uemura H, Conley J, Yamao F, Rogers J, Söll D. Escherichia coli glutaminyl-tRNA synthetase: a single amino acid replacement relaxes rRNA specificity. Protein Sequences And Data Analysis 1988, 1: 479-85. PMID: 2464170.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseTRNA bindingEscherichia coli glutaminyl-tRNA synthetaseExtensive homology searchesSingle amino acid replacementSingle amino acid changeRegion of homologyAminoacyl-tRNA synthetasesAmino acid replacementsAminoacyl adenylate formationAmino acids 235Amino acid changesLittle apparent similarityGlnS geneTRNA discriminationHomology searchGene productsAcid replacementsShare regionsDifferent tRNAsShort stretchesGenetic selectionAcid changesAsn changeHomology
1974
Involvement of the anticodon region of Escherichia coli tRNAGln and tRNAGlu in the specific interaction with cognate aminoacyl-tRNA synthetase Alteration of the 2-thiouridine derivatives located in the anticodon of the tRNAs by BrCN or sulfur deprivation
Seno T, Agris P, Söll D. Involvement of the anticodon region of Escherichia coli tRNAGln and tRNAGlu in the specific interaction with cognate aminoacyl-tRNA synthetase Alteration of the 2-thiouridine derivatives located in the anticodon of the tRNAs by BrCN or sulfur deprivation. Biochimica Et Biophysica Acta 1974, 349: 328-338. PMID: 4366808, DOI: 10.1016/0005-2787(74)90120-8.Peer-Reviewed Original ResearchAdenosine TriphosphateAmino Acyl-tRNA SynthetasesCarbon RadioisotopesChromatography, Ion ExchangeCyanogen BromideDiphosphatesEscherichia coliGlutamatesGlutamineKineticsPhosphorus RadioisotopesProtein BiosynthesisRNA, BacterialRNA, TransferSpectrophotometry, UltravioletThiouridineTransfer RNA Aminoacylation
1972
Glutamyl Transfer Ribonucleic Acid Synthetase of Escherichia coli I. PURIFICATION AND PROPERTIES
Lapointe J, Söll D. Glutamyl Transfer Ribonucleic Acid Synthetase of Escherichia coli I. PURIFICATION AND PROPERTIES. Journal Of Biological Chemistry 1972, 247: 4966-4974. PMID: 4341531, DOI: 10.1016/s0021-9258(19)44925-9.Peer-Reviewed Original ResearchAdenosine TriphosphateAlkylationAmino AcidsAmino Acyl-tRNA SynthetasesAnimalsCatalysisCentrifugation, ZonalChromatographyDiphosphatesDrug StabilityElectrophoresisElectrophoresis, DiscEscherichia coliGlutamatesHot TemperatureHydroxyapatitesIsoelectric FocusingMacromolecular SubstancesMolecular WeightOxidation-ReductionPhosphorus IsotopesRabbitsUltracentrifugationGlutamyl Transfer Ribonucleic Acid Synthetase of Escherichia coli II. INTERACTION WITH INTACT GLUTAMYL TRANSFER RIBONUCLEIC ACID
Lapointe J, Söll D. Glutamyl Transfer Ribonucleic Acid Synthetase of Escherichia coli II. INTERACTION WITH INTACT GLUTAMYL TRANSFER RIBONUCLEIC ACID. Journal Of Biological Chemistry 1972, 247: 4975-4981. PMID: 4341532, DOI: 10.1016/s0021-9258(19)44926-0.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAmino Acyl-tRNA SynthetasesCarbon IsotopesCatalysisCentrifugation, Density GradientDiphosphatesDrug StabilityEscherichia coliGlutamatesHot TemperatureHydrogen-Ion ConcentrationKineticsLeucineMagnesiumPhosphorus IsotopesProtein BindingRNA, TransferSpectrometry, FluorescenceValineConceptsGlutamyl-transfer ribonucleic acid synthetaseEscherichia coli IITransfer ribonucleic acidTRNA-GluTRNA-ValTRNA-LeuCognate tRNABiological specificityRibonucleic acidPure enzymeEnzymeSimilar Km valuesComplex formationGradient centrifugationSynthetaseKm valuesFluorescence-quenching studiesTRNAIsoacceptorsComplexesFluorescence quenching studiesHeat inactivationInactivationLeuGluGlutamyl Transfer Ribonucleic Acid Synthetase of Escherichia coli III. INFLUENCE OF THE 46K PROTEIN ON THE AFFINITY OF THE 56K GLUTAMYL TRANSFER RIBONUCLEIC ACID SYNTHETASE FOR ITS SUBSTRATES
Lapointe J, Söll D. Glutamyl Transfer Ribonucleic Acid Synthetase of Escherichia coli III. INFLUENCE OF THE 46K PROTEIN ON THE AFFINITY OF THE 56K GLUTAMYL TRANSFER RIBONUCLEIC ACID SYNTHETASE FOR ITS SUBSTRATES. Journal Of Biological Chemistry 1972, 247: 4982-4985. PMID: 4560497, DOI: 10.1016/s0021-9258(19)44927-2.Peer-Reviewed Original Research
1971
A Comparative Study of the Interactions of Escherichia coli Leucyl-, Seryl-, and Valyl-Transfer Ribonucleic Acid Synthetases with Their Cognate Transfer Ribonucleic Acids
Myers G, Blank H, Söll D. A Comparative Study of the Interactions of Escherichia coli Leucyl-, Seryl-, and Valyl-Transfer Ribonucleic Acid Synthetases with Their Cognate Transfer Ribonucleic Acids. Journal Of Biological Chemistry 1971, 246: 4955-4964. PMID: 4936720, DOI: 10.1016/s0021-9258(18)61956-8.Peer-Reviewed Original ResearchConceptsEscherichia coli KSeryl-tRNA synthetaseLeucyl-tRNA synthetaseRibonucleic acidTransfer ribonucleic acidValyl-tRNA synthetaseTRNA recognitionColi KSynthetase-tRNA complexIsoacceptorsAmino acidsEquilibrium binding studiesPing-pong typeTRNASynthetaseEnzymeKm valuesSubstrate inhibitionBasic similaritiesBinding studiesSerylAcidATPSame bufferSequence
1970
The Interaction of Seryl and of Leucyl Transfer Ribonucleic Acid Synthetases with Their Cognate Transfer Ribonucleic Acids
Knowles J, Katze J, Konigsberg W, Söll D. The Interaction of Seryl and of Leucyl Transfer Ribonucleic Acid Synthetases with Their Cognate Transfer Ribonucleic Acids. Journal Of Biological Chemistry 1970, 245: 1407-1415. PMID: 4910800, DOI: 10.1016/s0021-9258(18)63251-x.Peer-Reviewed Original ResearchConceptsSeryl-tRNA synthetaseTransfer ribonucleic acidComplex formationTransfer RNA speciesLeucyl-tRNA synthetaseRibonucleic acidRNA speciesCognate tRNAEscherichia coliSynthetaseDensity gradient centrifugationTRNAStable complexesHigh saltGradient centrifugationSpeciesGel filtrationComplexesSerylColiATPEnzymeAcidSerFormation