2012
Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment
Ling J, Peterson KM, Simonović I, Cho C, Söll D, Simonović M. Yeast mitochondrial threonyl-tRNA synthetase recognizes tRNA isoacceptors by distinct mechanisms and promotes CUN codon reassignment. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 3281-3286. PMID: 22343532, PMCID: PMC3295322, DOI: 10.1073/pnas.1200109109.Peer-Reviewed Original ResearchMeSH KeywordsAeropyrumAmino Acid SequenceAnticodonCatalytic DomainCodonCrystallography, X-RayEscherichia coliEvolution, MolecularLeucineMitochondriaModels, MolecularMolecular Sequence DataProtein ConformationProtein Structure, TertiaryRNA EditingRNA, Transfer, Amino AcylSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsSequence AlignmentSpecies SpecificityStaphylococcus aureusSubstrate SpecificityThreonineThreonine-tRNA LigaseConceptsThreonyl-tRNA synthetaseAnticodon loopAnticodon sequenceEscherichia coli ThrRSSet of tRNAsDistinct recognition mechanismsAnticodon-binding domainAminoacyl-tRNA synthetasesCUN codonsDetailed structural comparisonCodon reassignmentYeast mitochondriaGenetic codeTRNA isoacceptorsSaccharomyces cerevisiaeIsoacceptor tRNAsEditing domainTRNAMST1Anticodon tripletStructural comparisonNatural tRNAAmino acidsDistinct mechanismsRecognition mechanism
2009
The Human SepSecS-tRNASec Complex Reveals the Mechanism of Selenocysteine Formation
Palioura S, Sherrer RL, Steitz TA, Söll D, Simonović M. The Human SepSecS-tRNASec Complex Reveals the Mechanism of Selenocysteine Formation. Science 2009, 325: 321-325. PMID: 19608919, PMCID: PMC2857584, DOI: 10.1126/science.1173755.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acyl-tRNA SynthetasesBase SequenceBiocatalysisCatalytic DomainCrystallography, X-RayHumansHydrogen BondingModels, MolecularMolecular Sequence DataNucleic Acid ConformationPhosphatesPhosphoserineProtein ConformationProtein MultimerizationProtein Structure, SecondaryRNA, Transfer, Amino Acid-SpecificRNA, Transfer, Amino AcylSelenocysteineConceptsTransfer RNASelenocysteine formationSelenocysteinyl-tRNA synthaseCognate transfer RNAEnzyme active siteTRNA bindingActive siteConformational changesEnzyme assaysAmino acidsFree phosphoserinePhosphoserineSepSecSFinal stepSelenocysteineBiosynthesisComplexesRNAMechanismBindsCrystal structureSynthaseBindingFormationAssays
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
A Mutant Escherichia coli Tyrosyl-tRNA Synthetase Utilizes the Unnatural Amino Acid Azatyrosine More Efficiently than Tyrosine*
Hamano-Takaku F, Iwama T, Saito-Yano S, Takaku K, Monden Y, Kitabatake M, Söll D, Nishimura S. A Mutant Escherichia coli Tyrosyl-tRNA Synthetase Utilizes the Unnatural Amino Acid Azatyrosine More Efficiently than Tyrosine*. Journal Of Biological Chemistry 2000, 275: 40324-40328. PMID: 11006270, DOI: 10.1074/jbc.m003696200.Peer-Reviewed Original ResearchMeSH KeywordsAlanineBase SequenceDNA PrimersEscherichia coliGenes, BacterialModels, MolecularMutagenesisPlasmidsProtein ConformationTyrosineTyrosine-tRNA LigaseConceptsUnnatural amino acidsTyrosyl-tRNA synthetaseEscherichia coli tyrosyl-tRNA synthetasePosition 130Amino acidsVivo protein biosynthesisE. coli cellsAminoacyl-tRNA formationSingle point mutationTyrRS mutantsCellular proteinsProtein biosynthesisTYR geneMutant enzymesPlasmid libraryReplacement of phenylalanineColi cellsImmense potentialNormal phenotypeEfficient productionPoint mutationsTyrRSProteinPolymerase chain reaction techniqueSynthetase
1998
C‐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 Research
1997
When protein engineering confronts the tRNA world
Schimmel P, Söll D. When protein engineering confronts the tRNA world. Proceedings Of The National Academy Of Sciences Of The United States Of America 1997, 94: 10007-10009. PMID: 9294151, PMCID: PMC33764, DOI: 10.1073/pnas.94.19.10007.Peer-Reviewed Original ResearchDefining 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
Glutaminyl‐tRNA synthetase: from genetics to molecular recognition
Ibba M, Hong K, Söll D. Glutaminyl‐tRNA synthetase: from genetics to molecular recognition. Genes To Cells 1996, 1: 421-427. PMID: 9078373, DOI: 10.1046/j.1365-2443.1996.d01-255.x.Peer-Reviewed Original ResearchConceptsEscherichia coli glutaminyl-tRNA synthetaseMajority of tRNAsCorrect amino acidGlutaminyl-tRNA synthetaseAminoacyl-tRNA synthetasesSequence-specific interactionsAmino acid recognitionEfficiency of aminoacylationGenetic codeTRNA selectionGlnRTRNAAmino acidsNoncognate tRNAsCellular viabilityStructural studiesMolecular recognitionSynthetasesAminoacylationComplex displaysGeneticsSynthetaseGlutamineMechanismViabilityAminoacyl-tRNA Synthetases Optimize Both Cognate tRNA Recognition and Discrimination against Noncognate tRNAs †
Sherman J, Söll D. Aminoacyl-tRNA Synthetases Optimize Both Cognate tRNA Recognition and Discrimination against Noncognate tRNAs †. Biochemistry 1996, 35: 601-607. PMID: 8555233, DOI: 10.1021/bi951602b.Peer-Reviewed Original ResearchConceptsTRNA recognitionNoncognate tRNAsEscherichia coli glutaminyl-tRNA synthetaseWild-type GlnRSGlutaminyl-tRNA synthetaseAminoacyl-tRNA synthetasesNucleic acid interactionsGlutamine tRNAFirst base pairMutational analysisSpecific proteinsTRNAGlnRSequence preferenceMutantsBase pairsAcid interactionsDecreased affinityVivoTRNAGlnAffinitySynthetasesProteinSynthetaseCrystal structure
1995
Substrate 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
1993
Selectivity and specificity in the recognition of tRNA by E coli glutaminyl-tRNA synthetase
Rogers M, Weygand-Durašević I, Schwob E, Sherman J, Rogers K, Adachi T, Inokuchi H, Söll D. Selectivity and specificity in the recognition of tRNA by E coli glutaminyl-tRNA synthetase. Biochimie 1993, 75: 1083-1090. PMID: 8199243, DOI: 10.1016/0300-9084(93)90007-f.Peer-Reviewed Original ResearchConceptsOpal suppressor tRNAGlutaminyl-tRNA synthetaseAcceptor stem recognitionSuppressor tRNAEscherichia coli glutaminyl-tRNA synthetaseGenetic selectionAmber suppressor tRNAExtensive mutational analysisRecognition of tRNARNA contactsTRNA transcriptsRelaxed specificityMutational analysisTRNAGlnRAcceptor stemExtensive proteinIndividual functional groupsMutantsSpecific recognitionAnticodonAminoacylationSynthetaseIdentity elementSynthetases
1992
Recognition of bases in Escherichia coli tRNA(Gln) by glutaminyl‐tRNA synthetase: a complete identity set.
Hayase Y, Jahn M, Rogers M, Sylvers L, Koizumi M, Inoue H, Ohtsuka E, Söll D. Recognition of bases in Escherichia coli tRNA(Gln) by glutaminyl‐tRNA synthetase: a complete identity set. The EMBO Journal 1992, 11: 4159-4165. PMID: 1396597, PMCID: PMC556926, DOI: 10.1002/j.1460-2075.1992.tb05509.x.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseRecognition of basesSet of tRNAsEscherichia coliCognate aminoacyl-tRNA synthetasesAminoacyl-tRNA synthetasesCorrect aminoacylationRecombinant RNA technologySet of nucleotidesNumber of mutantsGlutamine identityTRNA genesTRNA discriminationTransfer RNAExcellent systemGlnRFunctional importanceSingle deletionSpecific contactsRNA technologyBase changesSpecificity constantAminoacylationSpecific guanosineMutants
1990
The accuracy of aminoacylation — ensuring the fidelity of the genetic code
Söll D. The accuracy of aminoacylation — ensuring the fidelity of the genetic code. Cellular And Molecular Life Sciences 1990, 46: 1089-1096. PMID: 2253707, DOI: 10.1007/bf01936918.Peer-Reviewed Original ResearchConceptsAccuracy of aminoacylationTransfer RNA speciesAminoacyl-tRNA synthetasesMessenger RNA codonRNA speciesProtein biosynthesisGenetic codeProtein interactionsParticular tRNATRNACorrect attachmentBiophysical techniquesRNA codonsAmino acidsSynthetasesSpecific recognitionProper interactionAnticodonBiosynthesisCodonAminoacylationNucleotidesSpeciesEnzymeIdentity element
1983
The structure and regulation of Escherichia coli glutaminyl-tRNA synthetase.
Cheung A, Hoben P, Inokuchi H, Ozeki H, Sumner-Smith M, Swanson R, Uemura H, Yamao F, Söll D. The structure and regulation of Escherichia coli glutaminyl-tRNA synthetase. Nucleic Acids Symposium Series 1983, 221-2. PMID: 6364044.Peer-Reviewed Original Research
1979
Aminoacyl-tRNA Synthetases: General Features and Recognition of Transfer RNAs
Schimmel P, Söll D. Aminoacyl-tRNA Synthetases: General Features and Recognition of Transfer RNAs. Annual Review Of Biochemistry 1979, 48: 601-648. PMID: 382994, DOI: 10.1146/annurev.bi.48.070179.003125.Peer-Reviewed Original Research
1974
Nuclear magnetic resonance studies of protein-nucleic acid interactions II. The E. coli tRNAGlu complex with glutamyl-tRNA synthetase
Shulman R, Hilbers C, Söll D, Yang S. Nuclear magnetic resonance studies of protein-nucleic acid interactions II. The E. coli tRNAGlu complex with glutamyl-tRNA synthetase. Journal Of Molecular Biology 1974, 90: 609-611. PMID: 4615173, DOI: 10.1016/0022-2836(74)90238-1.Peer-Reviewed Original Research
1972
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
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