2010
Structure of an archaeal non-discriminating glutamyl-tRNA synthetase: a missing link in the evolution of Gln-tRNAGln formation
Nureki O, O’Donoghue P, Watanabe N, Ohmori A, Oshikane H, Araiso Y, Sheppard K, Söll D, Ishitani R. Structure of an archaeal non-discriminating glutamyl-tRNA synthetase: a missing link in the evolution of Gln-tRNAGln formation. Nucleic Acids Research 2010, 38: 7286-7297. PMID: 20601684, PMCID: PMC2978374, DOI: 10.1093/nar/gkq605.Peer-Reviewed Original ResearchConceptsNon-discriminating glutamyl-tRNA synthetaseGlutamyl-tRNA synthetaseND-GluRSEscherichia coli GlnRSFormation of GlnCognate tRNA moleculesGlutaminyl-tRNA synthetaseAnticodon-binding domainEvolutionary predecessorPhylogenetic analysisGenetic codeMolecular basisTRNA moleculesRecognition pocketGlnRGenetic encodingAmino acidsSpecific ligationStructural determinantsKey eventsSynthetaseGluPromiscuous recognitionGluRGln
2008
Characterization 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
2004
Cys-tRNACys formation and cysteine biosynthesis in methanogenic archaea: two faces of the same problem?
Ambrogelly A, Kamtekar S, Sauerwald A, Ruan B, Tumbula-Hansen D, Kennedy D, Ahel I, Söll D. Cys-tRNACys formation and cysteine biosynthesis in methanogenic archaea: two faces of the same problem? Cellular And Molecular Life Sciences 2004, 61: 2437-2445. PMID: 15526152, DOI: 10.1007/s00018-004-4194-9.Peer-Reviewed Original ResearchConceptsMethanogenic archaeaCysteine biosynthesisCellular translation machineryAminoacyl-tRNA synthesisCanonical cysteinyl-tRNA synthetaseAminoacyl-tRNA synthetasesCysteinyl-tRNA synthetaseRecognizable genesTranslation machineryGenome sequenceArchaeaBiosynthesisEssential componentSynthetasesTRNARibosomesGenesMachineryOrganismsSynthetasePossible linkSequenceFormation
2000
Methanococcus jannaschii Prolyl-Cysteinyl-tRNA Synthetase Possesses Overlapping Amino Acid Binding Sites †
Stathopoulos C, Jacquin-Becker C, Becker H, Li T, Ambrogelly A, Longman R, Söll D. Methanococcus jannaschii Prolyl-Cysteinyl-tRNA Synthetase Possesses Overlapping Amino Acid Binding Sites †. Biochemistry 2000, 40: 46-52. PMID: 11141055, DOI: 10.1021/bi002108x.Peer-Reviewed Original ResearchConceptsAmino acidsTRNA synthetaseProtein translation apparatusCysteinyl-tRNA synthetase activityCognate tRNA speciesSite-directed mutagenesisAmino acid activationAbsence of tRNAAmino acid residuesSynthetase activityTranslation apparatusMethanococcus jannaschiiTRNA speciesCysteine activationUnusual enzymeDifferent amino acidsMutant enzymesCysteine bindingProline bindingProlyl-tRNA synthetase activityAcid residuesAminoacyl-tRNAPosition 103Single enzymeAncient Adaptation of the Active Site of Tryptophanyl-tRNA Synthetase for Tryptophan Binding †
Ibba M, Stange-Thomann N, Kitabatake M, Ali K, Söll I, Carter, C, Michael Ibba, and, Söll D. Ancient Adaptation of the Active Site of Tryptophanyl-tRNA Synthetase for Tryptophan Binding †. Biochemistry 2000, 39: 13136-13143. PMID: 11052665, DOI: 10.1021/bi001512t.Peer-Reviewed Original ResearchMeSH KeywordsAcylationAnimalsBacillus subtilisBacterial ProteinsBinding SitesCattleDiphosphatesDNA Mutational AnalysisDNA, BacterialEvolution, MolecularGeobacillus stearothermophilusHumansKineticsMiceMutagenesis, Site-DirectedProtein BindingRabbitsRNA, Transfer, TrpSequence Homology, Amino AcidTryptophanTryptophan-tRNA LigaseTyrosineConceptsAmino acid specificityActive site residuesTyrosyl-tRNA synthetasesTryptophanyl-tRNA synthetaseAncient adaptationAnalogous residuesGlu side chainsTryptophan replacementHomologous positionsSystematic mutationAromatic side chainsTrpRSTryptophan recognitionBacillus stearothermophilusSide chainsTryptophan bindingTyrRSResiduesCommon originCompetitive inhibitorMutationsTrp bindingMechanistic supportCatalytic efficiencyActive siteOne Polypeptide with Two Aminoacyl-tRNA Synthetase Activities
Stathopoulos C, Li T, Longman R, Vothknecht U, Becker H, Ibba M, Söll D. One Polypeptide with Two Aminoacyl-tRNA Synthetase Activities. Science 2000, 287: 479-482. PMID: 10642548, DOI: 10.1126/science.287.5452.479.Peer-Reviewed Original ResearchConceptsProlyl-tRNA synthetaseProtein synthesisCysteinyl-tRNA synthetase activityAmino-terminal sequenceSynthetase activityAminoacyl-tRNA synthetase activityCertain archaeaEvolutionary originMethanococcus jannaschiiGenome sequenceSubstrate specificityGenetic analysisSuch organismsMessenger RNARNA synthetasesSynthetaseSequenceArchaeaJannaschiiSynthetasesRNAOrganismsPolypeptideProlylProtein
1999
Transfer RNA identity contributes to transition state stabilization during aminoacyl-tRNA synthesis
Ibba M, Sever S, Praetorius-Ibba M, Söll D. Transfer RNA identity contributes to transition state stabilization during aminoacyl-tRNA synthesis. Nucleic Acids Research 1999, 27: 3631-3637. PMID: 10471730, PMCID: PMC148616, DOI: 10.1093/nar/27.18.3631.Peer-Reviewed Original Research
1998
Retracing the evolution of amino acid specificity in glutaminyl‐tRNA synthetase
Hong K, Ibba M, Söll D. Retracing the evolution of amino acid specificity in glutaminyl‐tRNA synthetase. FEBS Letters 1998, 434: 149-154. PMID: 9738468, DOI: 10.1016/s0014-5793(98)00968-5.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseTranslational error rateMolecular phylogenetic studiesAmino acid specificityGlutamyl-tRNA synthetaseFirst biochemical evidenceCellular growth ratePhe-90Phylogenetic studiesSynthetase mutantsTyr-240SynthetaseBiochemical evidenceVivo expressionGenesGlutamic acidActive siteGrowth rateMisacylationMutantsMutagenesisDuplicationDiversificationResiduesKey stepMajor Identity Element of Glutamine tRNAs from Bacillus subtilis and Escherichia coli in the Reaction with B. subtilis Glutamyl-tRNA Synthetase
Kim S, Söll D. Major Identity Element of Glutamine tRNAs from Bacillus subtilis and Escherichia coli in the Reaction with B. subtilis Glutamyl-tRNA Synthetase. Molecules And Cells 1998, 8: 459-465. PMID: 9749534, DOI: 10.1016/s1016-8478(23)13451-0.Peer-Reviewed Original ResearchThe Terminal Adenosine of tRNAGln Mediates tRNA-Dependent Amino Acid Recognition by Glutaminyl-tRNA Synthetase †
Liu J, Ibba M, Hong K, Söll D. The Terminal Adenosine of tRNAGln Mediates tRNA-Dependent Amino Acid Recognition by Glutaminyl-tRNA Synthetase †. Biochemistry 1998, 37: 9836-9842. PMID: 9657697, DOI: 10.1021/bi980704+.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseAmino acid recognitionEscherichia coli glutaminyl-tRNA synthetaseSequence-specific interactionsDouble-mutant cycle analysisAmino acid glutamineMutant cycle analysisApparent affinityConservative replacementsNonconservative replacementGlutamine bindingKcat/KmTyr211Biochemical studiesNoncognate tRNAsTerminal adenosineSynthetaseGlutamineSpecific interactionsCycle analysisKmAsp66AffinityTRNADramatic decrease
1997
Defining the Active Site of Yeast Seryl-tRNA Synthetase MUTATIONS IN MOTIF 2 LOOP RESIDUES AFFECT tRNA-DEPENDENT AMINO ACID RECOGNITION*
Lenhard B, Filipić S, Landeka I, Škrtić I, Söll D, Weygand-Durašević I. Defining the Active Site of Yeast Seryl-tRNA Synthetase MUTATIONS IN MOTIF 2 LOOP RESIDUES AFFECT tRNA-DEPENDENT AMINO ACID RECOGNITION*. Journal Of Biological Chemistry 1997, 272: 1136-1141. PMID: 8995413, DOI: 10.1074/jbc.272.2.1136.Peer-Reviewed Original ResearchConceptsMotif 2 loopAmino acid recognitionSeryl-tRNA synthetaseClass II aminoacyl-tRNA synthetasesSeryl-tRNA synthetasesYeast seryl-tRNA synthetaseAmino acidsLoss of complementationAminoacyl-tRNA synthetasesActive sitePresence of tRNASteady-state kinetic analysisProkaryotic counterpartsYeast enzymeElevated Km valuesNull allelesConformational changesTRNAAcceptor endSynthetasesGenesATPStructural dataStructural studiesSerine
1996
Interactions between tRNA identity nucleotides and their recognition sites in glutaminyl-tRNA synthetase determine the cognate amino acid affinity of the enzyme.
Ibba M, Hong K, Sherman J, Sever S, Söll D. Interactions between tRNA identity nucleotides and their recognition sites in glutaminyl-tRNA synthetase determine the cognate amino acid affinity of the enzyme. Proceedings Of The National Academy Of Sciences Of The United States Of America 1996, 93: 6953-6958. PMID: 8692925, PMCID: PMC38915, DOI: 10.1073/pnas.93.14.6953.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acyl-tRNA SynthetasesAnimalsBase SequenceBinding SitesCalorimetryCloning, MolecularConsensus SequenceEscherichia coliHumansKineticsModels, StructuralMolecular Sequence DataNucleic Acid ConformationProtein FoldingRecombinant ProteinsRNA, Transfer, GlnSequence Homology, Nucleic AcidConceptsGlutaminyl-tRNA synthetaseAmino acid affinityAmino acid recognitionEscherichia coli glutaminyl-tRNA synthetaseBase pairsIdentity nucleotidesProtein-RNA interactionsDiscriminator baseE. coli tryptophanyl-tRNA synthetaseAminoacyl-tRNA synthetasesSequence-specific interactionsAcid affinityRecognition sitesAbility of tRNATryptophanyl-tRNA synthetaseTRNA specificityNoncognate substratesTranslational fidelityTRNA recognitionBiochemical functionsRNA recognitionCognate tRNATRNAMajor binding siteNoncognate tRNAsTransfer 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 roleGlnTRNAGlnEscherichia coli Tryptophanyl-tRNA Synthetase Mutants Selected for Tryptophan Auxotrophy Implicate the Dimer Interface in Optimizing Amino Acid Binding †
Sever S, Rogers K, Rogers M, Carter C, Söll D. Escherichia coli Tryptophanyl-tRNA Synthetase Mutants Selected for Tryptophan Auxotrophy Implicate the Dimer Interface in Optimizing Amino Acid Binding †. Biochemistry 1996, 35: 32-40. PMID: 8555191, DOI: 10.1021/bi952103d.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBacillus subtilisBase SequenceBinding SitesCloning, MolecularDNA PrimersEscherichia coliGenes, BacterialGeobacillus stearothermophilusHaemophilus influenzaeKineticsMacromolecular SubstancesModels, MolecularMolecular Sequence DataPolymerase Chain ReactionProtein FoldingProtein Structure, SecondaryRecombinant ProteinsRestriction MappingSequence Homology, Amino AcidTryptophanTryptophan-tRNA LigaseConceptsTryptophanyl-tRNA synthetaseDimer interfaceClass I aminoacyl-tRNA synthetasesAminoacyl-tRNA synthetasesAmino acid bindingAmino acid activationActive siteSteady-state kinetic analysisSynthetase mutantsRossmann foldApparent KmKMSKS loopTrp lociProtein structureTrpR proteinTryptophan auxotrophDimeric enzymeAuxotrophic strainsBacillus stearothermophilusAcid bindingEscherichia coliOptimal catalysisAminoacyl adenylatesMutantsMutations
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 ResearchSubstrate selection by aminoacyl-tRNA synthetases.
Ibba M, Thomann H, Hong K, Sherman J, Weygand-Durasevic I, Sever S, Stange-Thomann N, Praetorius M, Söll D. Substrate selection by aminoacyl-tRNA synthetases. Nucleic Acids Symposium Series 1995, 40-2. PMID: 8643392.Peer-Reviewed Original Research
1994
Connecting Anticodon Recognition with the Active Site of Escherichia coli Glutaminyl-tRNA Synthetase
Weygand-Duraševic I, Rogers M, Söll D. Connecting Anticodon Recognition with the Active Site of Escherichia coli Glutaminyl-tRNA Synthetase. Journal Of Molecular Biology 1994, 240: 111-118. PMID: 8027995, DOI: 10.1006/jmbi.1994.1425.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseAnticodon recognitionMutant enzymesEscherichia coli glutaminyl-tRNA synthetaseOpal suppressor tRNASpecificity constantMutant gene productsWild-type enzymeAmino acid loopExtensive conformational changesActive siteNumber of mutationsSuppressor tRNAGene productsGlnRPathways of communicationSaturation mutagenesisTRNAAcceptor stemAcid loopGenetic selectionConformational changesAnticodonPoor substrateAminoacylation
1993
Selection of a ‘minimal’ glutaminyl‐tRNA synthetase and the evolution of class I synthetases.
Schwob E, Söll D. Selection of a ‘minimal’ glutaminyl‐tRNA synthetase and the evolution of class I synthetases. The EMBO Journal 1993, 12: 5201-5208. PMID: 7505222, PMCID: PMC413784, DOI: 10.1002/j.1460-2075.1993.tb06215.x.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acyl-tRNA SynthetasesBacterial ProteinsBase SequenceBinding SitesBiological EvolutionEscherichia coliModels, MolecularMolecular Sequence DataMutagenesis, Site-DirectedProtein Structure, TertiaryRNA, BacterialRNA, Transfer, GlnRNA, Transfer, SerStructure-Activity RelationshipTransfer RNA AminoacylationConceptsGlutaminyl-tRNA synthetaseAminoacyl-tRNA synthetasesEscherichia coli glutaminyl-tRNA synthetaseClass I aminoacyl-tRNA synthetasesNew recognition specificitiesNon-catalytic domainSubstrate recognition propertiesNon-cognate tRNAsRecognition of tRNACommon ancestorSequence motifsAmber suppressorGenetic codeTRNA substratesCatalytic coreGlnRTRNARecognition specificityDistinct domainsEnzymatic activityElaborate relationshipSynthetasesSpecific roleClass ISynthetase
1991
Mutant enzymes and tRNAs as probes of the glutaminyl-tRNA synthetase: tRNAGln interaction
Enlisch-Peters S, Conley J, Plumbridge J, Leptak C, Söll D, Rogers M. Mutant enzymes and tRNAs as probes of the glutaminyl-tRNA synthetase: tRNAGln interaction. Biochimie 1991, 73: 1501-1508. PMID: 1725262, DOI: 10.1016/0300-9084(91)90184-3.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseEscherichia coli glutaminyl-tRNA synthetaseClass I aminoacyl-tRNA synthetaseTemperature-sensitive phenotypeAminoacyl-tRNA synthetaseTemperature-sensitive mutantGlutamine identityThree-dimensional structureMutant enzymesGlnRMutantsTerminal adenosineAminoacylation reactionExchange activitySynthetaseMutationsSubsequent assaysPseudorevertantsGlutaminylationTRNAAminoacylationGenesNucleotidesSpeciesColi