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
2011
An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine
Su D, Lieberman A, Lang BF, Simonović M, Söll D, Ling J. An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine. Nucleic Acids Research 2011, 39: 4866-4874. PMID: 21321019, PMCID: PMC3113583, DOI: 10.1093/nar/gkr073.Peer-Reviewed Original ResearchConceptsCUN codonsYeast mitochondriaGenetic codeAlloacceptor tRNA gene recruitmentComprehensive phylogenetic analysisStandard genetic codeThreonyl-tRNA synthetaseHistidyl-tRNA synthetaseGene recruitmentEvolutionary originPhylogenetic analysisRecoding eventBiochemical experimentsFirst nucleotideAnticodon loopMST1CodonFirst clear exampleYeastMitochondriaThreonineSynthetaseCandida albicansGenomeClear example
2010
Mutations Disrupting Selenocysteine Formation Cause Progressive Cerebello-Cerebral Atrophy
Agamy O, Zeev B, Lev D, Marcus B, Fine D, Su D, Narkis G, Ofir R, Hoffmann C, Leshinsky-Silver E, Flusser H, Sivan S, Söll D, Lerman-Sagie T, Birk OS. Mutations Disrupting Selenocysteine Formation Cause Progressive Cerebello-Cerebral Atrophy. American Journal Of Human Genetics 2010, 87: 538-544. PMID: 20920667, PMCID: PMC2948803, DOI: 10.1016/j.ajhg.2010.09.007.Peer-Reviewed Original Research
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
2001
Protein 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
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
1997
Archaeal-type lysyl-tRNA synthetase in the Lyme disease spirochete Borrelia burgdorferi
Ibba M, Bono J, Rosa P, Söll D. Archaeal-type lysyl-tRNA synthetase in the Lyme disease spirochete Borrelia burgdorferi. Proceedings Of The National Academy Of Sciences Of The United States Of America 1997, 94: 14383-14388. PMID: 9405621, PMCID: PMC24988, DOI: 10.1073/pnas.94.26.14383.Peer-Reviewed Original ResearchConceptsLysyl-tRNA synthetasesLysyl-tRNA synthetaseOpen reading frameReading frameAminoacyl-tRNA synthetasesLyme disease spirochete Borrelia burgdorferiGroup of enzymesLysyl-tRNA synthetase activityAmino acid levelsBacterial pathogen Borrelia burgdorferiArchaeal kingdomHeterologous expressionProtein biosynthesisGenomic sequencesMRNA translationPathogen Borrelia burgdorferiSignificant similarityLysyl-tRNASynthetasesB. burgdorferiBorrelia burgdorferiEscherichia coliEukaryaSpirochete Borrelia burgdorferiPathogenic spirochetesA Euryarchaeal Lysyl-tRNA Synthetase: Resemblance to Class I Synthetases
Ibba M, Morgan S, Curnow A, Pridmore D, Vothknecht U, Gardner W, Lin W, Woese C, Söll D. A Euryarchaeal Lysyl-tRNA Synthetase: Resemblance to Class I Synthetases. Science 1997, 278: 1119-1122. PMID: 9353192, DOI: 10.1126/science.278.5340.1119.Peer-Reviewed Original ResearchConceptsClass I aminoacyl-tRNA synthetaseCrenarchaeote Sulfolobus solfataricusDinucleotide-binding domainAminoacyl-tRNA synthetasesAmino acid motifsAmino acid sequenceAminoacyl-tRNA synthetaseLysyl-tRNA synthetaseClass II synthetasesEuryarchaeal genomesUnassigned functionMethanococcus jannaschiiMethanococcus maripaludisLysRS proteinsReading frameSulfolobus solfataricusAcid motifAcid sequenceSuch organismsMethanobacterium thermoautotrophicumLysRSProteinSynthetasesSynthetaseRNA synthetaseDefining 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
1994
A 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