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 roleBindingH306S356K395
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
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 step
1988
Site-directed mutagenesis to fine-tune enzyme specificity
Uemura H, Rogers M, Swanson R, Watson L, Söll D. Site-directed mutagenesis to fine-tune enzyme specificity. Protein Engineering Design And Selection 1988, 2: 293-296. PMID: 3150543, DOI: 10.1093/protein/2.4.293.Peer-Reviewed Original ResearchConceptsOligonucleotide-directed mutagenesisEscherichia coli glutaminyl-tRNA synthetaseGenetic selectionGlutaminyl-tRNA synthetaseAmino acid replacementsSite-directed mutagenesisAcid replacementsEnzyme specificitySingle residueMutagenesisSide chainsRepulsive charge-charge interactionsSpecific recognitionCharge-charge interactionsNucleic acidsMutantsProteinSupFSynthetaseResiduesGlutamineSelection
1985
Heptapeptide repeat structure of a wheat γ-gliadin
Scheets K, Rafalski J, Hedgcoth C, Söll D. Heptapeptide repeat structure of a wheat γ-gliadin. Plant Science 1985, 37: 221-225. DOI: 10.1016/0304-4211(85)90008-2.Peer-Reviewed Original Research
1982
19 Nucleotide Modification in RNA
Kline L, Söll D. 19 Nucleotide Modification in RNA. The Enzymes 1982, 15: 567-582. DOI: 10.1016/s1874-6047(08)60291-7.Peer-Reviewed Original ResearchRNA base modificationsAnticodon of tRNAComplex nucleotidesNucleotide modificationsAdenosine modificationsEnzymatic modificationRNA chainsBase modificationsEnzymatic stepsAdenosine residuesUracil residuesNucleotidesRNABiochemical evidenceEnzymeModifying groupUracil nucleotidesResiduesGuanine structureFirst positionTRNAAnticodonGeneticsTranscriptsModificationGenes for tRNA 5Lys from Drosophila melanogaster
DeFranco D, Burke K, Hayashi S, Tener G, Miller R, Söll D. Genes for tRNA 5Lys from Drosophila melanogaster. Nucleic Acids Research 1982, 10: 5799-5808. PMID: 6292853, PMCID: PMC320931, DOI: 10.1093/nar/10.19.5799.Peer-Reviewed Original Research
1972
N6 - (Δ2 - Isopentenyl) Adenosine: Biosynthesis in vitro in transfer RNA by an enzyme purified from Eschericha coli
Bartz J, Söll D. N6 - (Δ2 - Isopentenyl) Adenosine: Biosynthesis in vitro in transfer RNA by an enzyme purified from Eschericha coli. Biochimie 1972, 54: 31-39. PMID: 4346747, DOI: 10.1016/s0300-9084(72)80035-x.Peer-Reviewed Original Research
1970
In Vitro Biosynthesis of Pseudouridine at the Polynucleotide Level by an Enzyme Extract from Escherichia coli
Johnson L, Söll D. In Vitro Biosynthesis of Pseudouridine at the Polynucleotide Level by an Enzyme Extract from Escherichia coli. Proceedings Of The National Academy Of Sciences Of The United States Of America 1970, 67: 943-950. PMID: 4943184, PMCID: PMC283296, DOI: 10.1073/pnas.67.2.943.Peer-Reviewed Original ResearchConceptsE. coli RNA polymeraseRNA transcription productsColi RNA polymeraseConversion of uridineE. coli extractsTRNA genesRNA polymerasePolynucleotide levelUridine residuesTranscription productsVitro BiosynthesisMycoplasma spEscherichia coliLambda DNARNADNAMacromolecular levelEnzyme extractBiosynthesisGenesPolymerasePseudouridineSpColiResiduesN6-(Δ2-isopentenyl)adenosine: Biosynthesis in vitro in transfer RNA by an enzyme purified from escherichia coli
Bartz J, Kline L, Söll D. N6-(Δ2-isopentenyl)adenosine: Biosynthesis in vitro in transfer RNA by an enzyme purified from escherichia coli. Biochemical And Biophysical Research Communications 1970, 40: 1481-1487. PMID: 4326583, DOI: 10.1016/0006-291x(70)90035-5.Peer-Reviewed Original ResearchMeSH KeywordsAdenineAdenine NucleotidesAlkenesAnimalsCentrifugation, Density GradientChromatography, PaperColiphagesEscherichia coliHydrogen-Ion ConcentrationHydrolysisLiverMolecular WeightMycoplasmaNucleosidesOrganophosphorus CompoundsPhosphoric AcidsPolynucleotidesPotassium PermanganateRatsRNA, BacterialRNA, TransferRNA, ViralTransferases