2011
Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase
O’Donoghue P, Sheppard K, Nureki O, Söll D. Rational design of an evolutionary precursor of glutaminyl-tRNA synthetase. Proceedings Of The National Academy Of Sciences Of The United States Of America 2011, 108: 20485-20490. PMID: 22158897, PMCID: PMC3251134, DOI: 10.1073/pnas.1117294108.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAmino Acyl-tRNA SynthetasesBase SequenceCodonEscherichia coliEvolution, MolecularGenetic EngineeringKineticsMethanobacteriaceaeModels, MolecularMolecular ConformationMolecular Sequence DataNucleic Acid ConformationPhylogenyProtein Structure, SecondarySequence Homology, Amino AcidConceptsGlutaminyl-tRNA synthetaseAminoacyl-tRNA synthetasesGenetic code engineeringAmino acidsDomains of lifeMost aminoacyl-tRNA synthetasesGlutamyl-tRNA synthetaseCanonical amino acidsBacterial GlnRSTRNA specificityTRNA pairsParticular codonsEvolutionary precursorBiochemical characterizationStem loopGlnRAdditional codonsCAA codonCodonProtein synthesisCAG codonEscherichia coliSpecific enzymesCatalytic preferenceSynthetase
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
2001
Conserved amino acids near the carboxy terminus of bacterial tyrosyl‐tRNA synthetase are involved in tRNA and Tyr‐AMP binding
Salazar J, Zuñiga R, Lefimil C, Söll D, Orellana O. Conserved amino acids near the carboxy terminus of bacterial tyrosyl‐tRNA synthetase are involved in tRNA and Tyr‐AMP binding. FEBS Letters 2001, 491: 257-260. PMID: 11240138, DOI: 10.1016/s0014-5793(01)02214-1.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine MonophosphateBacterial ProteinsCloning, MolecularConserved SequenceDimerizationEscherichia coliGammaproteobacteriaGene ExpressionGenetic Complementation TestGeobacillus stearothermophilusMutagenesis, Site-DirectedRNA, TransferSequence Homology, Amino AcidStructure-Activity RelationshipTyrosineTyrosine-tRNA LigaseConceptsBacterial tyrosyl-tRNA synthetasesBacterial tyrosyl tRNA synthetaseConserved amino acidsAmino acidsAmino acid identityAmino-terminal regionActive site domainCarboxy-terminal segmentTyrosyl-tRNA synthetasesTyrosyl-tRNA synthetaseAcid identityLargest subfamilyCarboxy terminusSite domainTRNA bindingEnzyme functionTyr-AMPTRNATyrRSResiduesEquivalent roleBindingH306S356K395Protein phosphatase 2A: identification in Oryza sativa of the gene encoding the regulatory A subunit
Yu S, Lei H, Chang W, Söll D, Hong G. Protein phosphatase 2A: identification in Oryza sativa of the gene encoding the regulatory A subunit. Plant Molecular Biology 2001, 45: 107-112. PMID: 11247601, DOI: 10.1023/a:1006472722500.Peer-Reviewed Original ResearchConceptsProtein phosphatase 2AAmino acid identitySouthern blot analysisRice genomePP2A proteinPhosphatase 2ABAC libraryRegulatory subunitOryza sativaNicotiana tabacumAcid identityCDNA libraryBp cDNASingle copyGenomic DNAGenesBlot analysisRice proteinRepeat unitsSubunitsProteinArabidopsisIntronsGenomeRPA1
2000
Ancient 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 site
1999
Mutations in a new Arabidopsis cyclophilin disrupt its interaction with protein phosphatase 2A
Jackson K, Söll D. Mutations in a new Arabidopsis cyclophilin disrupt its interaction with protein phosphatase 2A. Molecular Genetics And Genomics 1999, 262: 830-838. PMID: 10628867, DOI: 10.1007/s004380051147.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceArabidopsisMolecular Sequence DataMutationPeptidylprolyl IsomerasePhenotypePhosphoprotein PhosphatasesProtein BindingProtein Phosphatase 2Sequence Homology, Amino AcidConceptsProtein phosphatase 2APhosphatase 2AHeterotrimeric protein phosphatase 2ARegulatory subunit AProtein phosphatase 2BMultiple signaling pathwaysAuxin transportPhosphatase 2BPP2A activityAntisense transcriptsResponse pathwaysArabidopsis extractsGene productsN-terminusRoot growthSubunit ASignaling pathwaysNovel cyclophilinCyclophilinArabidopsisAltered formsTranscriptsMutationsPathwayEukaryotesCysteinyl‐tRNA formation: the last puzzle of aminoacyl‐tRNA synthesis
Li T, Graham D, Stathopoulos C, Haney P, Kim H, Vothknecht U, Kitabatake M, Hong K, Eggertsson G, Curnow A, Lin W, Celic I, Whitman W, Söll D. Cysteinyl‐tRNA formation: the last puzzle of aminoacyl‐tRNA synthesis. FEBS Letters 1999, 462: 302-306. PMID: 10622715, DOI: 10.1016/s0014-5793(99)01550-1.Peer-Reviewed Original ResearchConceptsLateral gene transferAminoacyl-tRNA synthesisCysteinyl-tRNA synthetaseEscherichia coli cysteinyl-tRNA synthetaseMolecular phylogenyPyrococcus sppMethanococcus jannaschiiMethanococcus maripaludisM. maripaludisMethanogenic archaeaMethanosarcina sppGene transferCysRSMethanosarcina barkeriGenesSpecific relativeLast puzzleSppOrthologsArchaeaPhylogenyJannaschiiMutantsLineagesOrganisms
1998
Sequence Divergence of Seryl-tRNA Synthetases in Archaea
Kim H, Vothknecht U, Hedderich R, Celic I, Söll D. Sequence Divergence of Seryl-tRNA Synthetases in Archaea. Journal Of Bacteriology 1998, 180: 6446-6449. PMID: 9851985, PMCID: PMC107743, DOI: 10.1128/jb.180.24.6446-6449.1998.Peer-Reviewed Original ResearchConceptsOpen reading frameM. thermoautotrophicumRelevant open reading frameSeryl-tRNA synthetasesCys-tRNACysCanonical cysteinyl-tRNA synthetaseGel shift experimentsCysteinyl-tRNA synthetaseN-terminal peptide sequenceEscherichia coli tRNASequence divergenceDirect aminoacylationM. jannaschiiMethanococcus jannaschiiGenomic sequencesReading frameSer geneHomologous tRNAsGenomic dataMethanogenic archaeaMethanobacterium thermoautotrophicumShift experimentsEnzymatic propertiesArchaeaSerineC‐terminal truncation of yeast SerRS is toxic for Saccharomyces cerevisiae due to altered mechanism of substrate recognition
Lenhard B, Prætorius-Ibba M, Filipic S, Söll D, Weygand-Durasevic I. C‐terminal truncation of yeast SerRS is toxic for Saccharomyces cerevisiae due to altered mechanism of substrate recognition. FEBS Letters 1998, 439: 235-240. PMID: 9845329, DOI: 10.1016/s0014-5793(98)01376-3.Peer-Reviewed Original ResearchMaize mitochondrial seryl-tRNA synthetase recognizes Escherichia coli tRNASer in vivo and in vitro
Rokov J, Söll D, Weygand-Durašević I. Maize mitochondrial seryl-tRNA synthetase recognizes Escherichia coli tRNASer in vivo and in vitro. Plant Molecular Biology 1998, 38: 497-502. PMID: 9747857, DOI: 10.1023/a:1006088516228.Peer-Reviewed Original ResearchConceptsSeryl-tRNA synthetaseMitochondrial seryl-tRNA synthetasePutative mature proteinSeryl-tRNA synthetasesEscherichia coliStructure/function relationshipsMature proteinGene sequencesMutant strainSignificant similarityFunctional identityN-terminalYeast tRNAMitochondrial functionFunction relationshipsProteinPoor substrateSynthetaseColiSynthetasesTRNAVivoCDNAMaizeEnzyme
1997
Glu-tRNAGln amidotransferase: A novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation
Curnow A, Hong K, Yuan R, Kim S, Martins O, Winkler W, Henkin T, Söll D. Glu-tRNAGln amidotransferase: A novel heterotrimeric enzyme required for correct decoding of glutamine codons during translation. Proceedings Of The National Academy Of Sciences Of The United States Of America 1997, 94: 11819-11826. PMID: 9342321, PMCID: PMC23611, DOI: 10.1073/pnas.94.22.11819.Peer-Reviewed Original ResearchConceptsTranscriptional unitsGln-tRNAGlnGram-positive eubacteriaHeterotrimeric enzymeGlu-tRNAGlnTranslational apparatusHeterotrimeric proteinGlutamine codonB. subtilisAmidotransferaseSynthetase activityOnly pathwayEnzymeGlutamylEssential componentArchaeaTransamidationEubacteriaOperonCyanobacteriaGATCOrganellesCodonGenesGATAA nuclear genetic lesion affecting Saccharomyces cerevisiae mitochondrial translation is complemented by a homologous Bacillus gene
Kim S, Stange-Thomann N, Martins O, Hong K, Söll D, Fox T. A nuclear genetic lesion affecting Saccharomyces cerevisiae mitochondrial translation is complemented by a homologous Bacillus gene. Journal Of Bacteriology 1997, 179: 5625-5627. PMID: 9287027, PMCID: PMC179443, DOI: 10.1128/jb.179.17.5625-5627.1997.Peer-Reviewed Original ResearchMeSH KeywordsBacillus subtilisDNA, FungalDNA, MitochondrialFungal ProteinsGenes, BacterialMitochondrial ProteinsMolecular Sequence DataProtein BiosynthesisRecombinant Fusion ProteinsSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence Analysis, DNASequence Homology, Amino AcidTransaminasesTranscription Factors
1996
Lactobacillus bulgaricus asparagine synthetase and asparaginyl-tRNA synthetase: coregulation by transcription antitermination?
Kim S, Germond J, Pridmore D, Söll D. Lactobacillus bulgaricus asparagine synthetase and asparaginyl-tRNA synthetase: coregulation by transcription antitermination? Journal Of Bacteriology 1996, 178: 2459-2461. PMID: 8636057, PMCID: PMC177964, DOI: 10.1128/jb.178.8.2459-2461.1996.Peer-Reviewed Original ResearchAmino Acid SequenceAmino Acyl-tRNA SynthetasesAspartate-Ammonia LigaseAspartate-tRNA LigaseBase SequenceGene Expression Regulation, BacterialGenes, BacterialGenetic Complementation TestLactobacillusMolecular Sequence DataNucleic Acid ConformationRNA, Transfer, Amino AcylSequence Homology, Amino AcidTerminator Regions, GeneticTranscription, GeneticThe C-terminal Extension of Yeast Seryl-tRNA Synthetase Affects Stability of the Enzyme and Its Substrate Affinity (*)
Weygand-Durasevic I, Lenhard B, Filipic S, Söll D. The C-terminal Extension of Yeast Seryl-tRNA Synthetase Affects Stability of the Enzyme and Its Substrate Affinity (*). Journal Of Biological Chemistry 1996, 271: 2455-2461. PMID: 8576207, DOI: 10.1074/jbc.271.5.2455.Peer-Reviewed Original ResearchEscherichia 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
1994
Light regulation of chlorophyll biosynthesis at the level of 5-aminolevulinate formation in Arabidopsis.
Ilag L, Kumar A, Söll D. Light regulation of chlorophyll biosynthesis at the level of 5-aminolevulinate formation in Arabidopsis. The Plant Cell 1994, 6: 265-275. PMID: 7908550, PMCID: PMC160432, DOI: 10.1105/tpc.6.2.265.Peer-Reviewed Original ResearchMeSH KeywordsAldehyde OxidoreductasesAmino Acid SequenceAminolevulinic AcidArabidopsisChlorophyllChloroplastsEscherichia coliGene Expression RegulationGenes, PlantGlutamatesGlutamic AcidIntramolecular TransferasesIsomerasesLightMolecular Sequence DataPromoter Regions, GeneticRNA, Transfer, GluSequence Homology, Amino AcidSequence Homology, Nucleic AcidTranscription, GeneticConceptsC5 pathwayAmino acid sequenceHemA proteinChlorophyll biosynthesisGlu-tRNAALA formationAcid sequenceRNA gel blot analysisDeduced amino acid sequenceGlu-tRNA reductaseChloroplasts of plantsGel blot analysisArabidopsis genesFunctional complementationShort intronsCorresponding genesTranscriptional controlFlower tissuesLight regulationExtensive homologyFirst enzymeUniversal precursorReductase geneChlorophyll formationSecond enzymeA Lactobacillus nifS-like gene suppresses an Escherichia coli transaminase B mutation
Leong-Morgenthaler P, Oliver S, Hottinger H, Söll D. A Lactobacillus nifS-like gene suppresses an Escherichia coli transaminase B mutation. Biochimie 1994, 76: 45-49. PMID: 8031904, DOI: 10.1016/0300-9084(94)90061-2.Peer-Reviewed Original ResearchConceptsNifS-like genesNifS-like proteinsNif gene productsNif proteinsNif genesGene productsNitrogen-fixing bacteriaGroup of enzymesRemarkable sequence homologyCysteine desulfuraseSequence conservationEfficient nitrogen fixationLeucine auxotrophyTransaminase BDiverse functionsSequence homologyNitrogen fixationEscherichia coli strainsProtein productsMetabolic pathwaysAzotobacter vinelandiiGenesB mutationsProteinDissimilar mutations
1993
Two members of the ERabp gene family are expressed differentially in reproductive organs but to similar levels in the coleoptile of maize
Hesse T, Garbers C, Brzobohaty B, Kreimer G, Söll D, Melkonian M, Schell J, Palme K. Two members of the ERabp gene family are expressed differentially in reproductive organs but to similar levels in the coleoptile of maize. Plant Molecular Biology 1993, 23: 57-66. PMID: 8219056, DOI: 10.1007/bf00021419.Peer-Reviewed Original ResearchConceptsC-terminal KDEL motifExpression patternsN-terminal hydrophobic leader sequenceColeoptiles of maizePrimary amino acid sequenceFemale flower partsHydrophobic leader sequenceAmino acid sequencePotential glycosylation sitesGene familyFlower organsKDEL motifProtein familyCDNA clonesLeader sequenceMaize seedlingsAcid sequenceGlycosylation sitesPrimary leavesFlower partsGenesLaser scanning microscopyRetention of proteinsReproductive organsNew memberMolecular analysis of three maize 22 kDa auxin‐binding protein genes — transient promoter expression and regulatory regions
Schwob E, Choi S, Simmons C, Migliaccio F, Ilag L, Hesse T, Palme K, Söll D. Molecular analysis of three maize 22 kDa auxin‐binding protein genes — transient promoter expression and regulatory regions. The Plant Journal 1993, 4: 423-432. PMID: 7693132, DOI: 10.1046/j.1365-313x.1993.04030423.x.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBase SequenceDNA, ComplementaryGene ExpressionGenes, PlantGenes, RegulatorGenes, ReporterIndoleacetic AcidsMolecular Sequence DataPlant Growth RegulatorsPlant ProteinsPromoter Regions, GeneticReceptors, Cell SurfaceRestriction MappingRNASequence DeletionSequence Homology, Amino AcidSequence Homology, Nucleic AcidTissue DistributionZea maysConceptsZm-ERabp1C-terminal KDEL sequenceSmall gene familyMolecular analysisPromoter deletion analysisMaize leaf protoplastsAuxin-binding proteinGene expression systemNegative regulatory sequencesPrimer extension analysisAuxin-binding siteGene-specific oligonucleotide probesTwofold higher expressionTransit peptideGene familySignal peptideLeaf protoplastsRegulatory sequencesTranscription startDeletion analysisTranscription factorsRegulatory regionsTATA boxKDEL sequencePromoter expressionSPL1-1, a Saccharomyces cerevisiae mutation affecting tRNA splicing
Kolman C, Söll D. SPL1-1, a Saccharomyces cerevisiae mutation affecting tRNA splicing. Journal Of Bacteriology 1993, 175: 1433-1442. PMID: 8444805, PMCID: PMC193230, DOI: 10.1128/jb.175.5.1433-1442.1993.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBase SequenceBlotting, NorthernIntronsMolecular Sequence DataMutationNucleic Acid ConformationRNA Processing, Post-TranscriptionalRNA SplicingRNA, FungalRNA, TransferSaccharomyces cerevisiaeSequence Homology, Amino AcidSequence Homology, Nucleic AcidTranscription, GeneticConceptsTRNA genesSaccharomyces cerevisiae genesMature suppressor tRNASuppressor tRNA geneOpen reading frameSaccharomyces cerevisiae mutationsCerevisiae genesTRNA splicingSuppression phenotypeTRNA processingChromosome IIIGenetic approachesSuppressor tRNAReading frameGenetic analysisNorthern analysisMutant selectionMutantsNonsense mutationGenesMutationsLEU2Cell levelIncreased synthesisNFS1