2010
mip1 containing mutations associated with mitochondrial disease causes mutagenesis and depletion of mtDNA in Saccharomyces cerevisiae
Stumpf J, Bailey C, Spell D, Stillwagon M, Anderson K, Copeland W. mip1 containing mutations associated with mitochondrial disease causes mutagenesis and depletion of mtDNA in Saccharomyces cerevisiae. Human Molecular Genetics 2010, 19: 2123-2133. PMID: 20185557, PMCID: PMC2865372, DOI: 10.1093/hmg/ddq089.Peer-Reviewed Original ResearchConceptsMitochondrial dysfunctionHuman pol gammaSaccharomyces cerevisiae orthologAssociated with mitochondrial diseasesDecreased polymerase activityAtaxia-neuropathy syndromeDepletion of mtDNADNA polymerase gammaDisease-associated mutationsMutations in vivoIncreased nucleotide poolOrthologous human mutationMtDNA replication defectsMtDNA mutagenesisMtDNA replicationProgressive external ophthalmoplegiaSaccharomyces cerevisiaeMutant strainMutant enzymesPol gammaHuman orthologPolymerase gammaConserved regionMtDNA depletionMtDNA
2009
Role of Loop−Loop Interactions in Coordinating Motions and Enzymatic Function in Triosephosphate Isomerase
Wang Y, Berlow RB, Loria JP. Role of Loop−Loop Interactions in Coordinating Motions and Enzymatic Function in Triosephosphate Isomerase. Biochemistry 2009, 48: 4548-4556. PMID: 19348462, PMCID: PMC2713366, DOI: 10.1021/bi9002887.Peer-Reviewed Original ResearchConceptsLoop 7Triosephosphate isomeraseLoop 6Chicken triosephosphate isomeraseC-terminal hingeActive site loopActive site loop motionArchaeal homologueEnzyme triosephosphate isomeraseMutant enzymesEnzymatic functionProtein sequencesBiological functionsSite loopEnzymatic activityFold lossTemperature-dependent NMR experimentsLoop motionModel systemIsomeraseSequenceActive siteEnzymeEnzymatic reactionsMutants
2002
F0 Cysteine, bCys21, in the Escherichia coli ATP Synthase Is Involved in Regulation of Potassium Uptake and Molecular Hydrogen Production in Anaerobic Conditions
Mnatsakanyan N, Bagramyan K, Vassilian A, Nakamoto RK, Trchounian A. F0 Cysteine, bCys21, in the Escherichia coli ATP Synthase Is Involved in Regulation of Potassium Uptake and Molecular Hydrogen Production in Anaerobic Conditions. Bioscience Reports 2002, 22: 421-430. PMID: 12516783, DOI: 10.1023/a:1020918125453.Peer-Reviewed Original ResearchConceptsEscherichia coli ATP synthaseATP synthaseMembrane vesiclesMolecular hydrogen productionATP-dependent increaseF0 sectorF1 sectorAnaerobic conditionsCysteine replacementMutant enzymesFermentative conditionsATP hydrolysisSingle cysteineAccessible thiol groupsPotassium uptakeWhole cellsB subunitCysteineVesiclesSynthaseThiol groupsCellsProtoplastsSubunitsUptake
2001
A DNA Polymerase β Mutator Mutant with Reduced Nucleotide Discrimination and Increased Protein Stability † , ‡
Shah A, Conn D, Li S, Capaldi A, Jäger J, Sweasy J. A DNA Polymerase β Mutator Mutant with Reduced Nucleotide Discrimination and Increased Protein Stability † , ‡. Biochemistry 2001, 40: 11372-11381. PMID: 11560485, DOI: 10.1021/bi010755y.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SubstitutionBase SequenceDeoxyribonucleotidesDNA Mutational AnalysisDNA Polymerase betaDNA, BacterialEnzyme StabilityEscherichia coliFrameshift MutationGene LibraryGenotypeHot TemperatureKineticsModels, ChemicalModels, MolecularMolecular Sequence DataMutationNucleic Acid ConformationPoint MutationProtein ConformationProtein DenaturationSimplexvirusSubstrate SpecificityThermodynamicsThymidine KinaseUreaConceptsNucleotide discriminationPol betaIncreased Protein StabilityVivo genetic screenHydrophobic amino acid residuesDeoxynucleoside triphosphate substratesProtein conformational changesAmino acid residuesC-terminal portionWild-type pol betaDNA synthesis fidelityPhosphodiester bond formationGenetic screenDNA polymerase betaSubstrate discriminationMutator mutantsGround-state bindingHigh mutation frequencyPolymerase structureProtein stabilityMutant enzymesStructural basisTransient-state kinetic methodsAcid residuesMutator activity
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 enzymeA 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 ResearchConceptsUnnatural 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
1996
HIV-1 Reverse Transcriptase Resistance to Nonnucleoside Inhibitors †
Spence R, Anderson K, Johnson K. HIV-1 Reverse Transcriptase Resistance to Nonnucleoside Inhibitors †. Biochemistry 1996, 35: 1054-1063. PMID: 8547241, DOI: 10.1021/bi952058+.Peer-Reviewed Original ResearchConceptsMutant enzymesPre-steady-state techniquesSingle nucleotide incorporationWild-type complexMaximum incorporation rateNucleotide incorporationEnzyme complexDuplex DNAAffinity 2Cysteine mutationsTwo-step bindingWild-typeConformational changesDecreased affinityEnzymePresence of nevirapineInhibitor resistanceMutationsIncorporation rateY181C mutationWild-type RTReverse transcriptaseHIV-1NevirapineY181CHomologous Expression and Purification of Mutants of an Essential Protein by Reverse Epitope-Tagging
Thomann H, Ibba M, Hong K, Söll D. Homologous Expression and Purification of Mutants of an Essential Protein by Reverse Epitope-Tagging. Bio/Technology 1996, 14: 50-55. PMID: 9636312, DOI: 10.1038/nbt0196-50.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseMutant enzymesEssential enzymeGlutaminyl-tRNA synthetasesWild-type proteinExtrachromosomal genetic elementsEpitope taggingEssential proteinsMutant proteinsHomologous expressionReporter epitopeCell-free extractsGenetic elementsNormal phenotypeBiochemical studiesEnzymatic activityEnzymeProteinSynthetaseProtein contaminationExpressionPurificationMutantsSynthetasesNovel strategy
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 substrateAminoacylationCrystal structure of the K12M/G15A triosephosphate isomerase double mutant and electrostatic analysis of the active site.
Joseph-McCarthy D, Lolis E, Komives E, Petsko G. Crystal structure of the K12M/G15A triosephosphate isomerase double mutant and electrostatic analysis of the active site. Biochemistry 1994, 33: 2815-23. PMID: 8130194, DOI: 10.1021/bi00176a010.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBase SequenceBinding SitesCrystallizationCrystallography, X-RayDNA PrimersLigandsModels, MolecularMolecular Sequence DataMutagenesis, Site-DirectedPoint MutationProtein FoldingProtein Structure, SecondaryRecombinant ProteinsSaccharomyces cerevisiaeTriose-Phosphate IsomeraseX-Ray DiffractionConceptsMutant enzymesSubstrate-binding loopActive-site LysLys-12Wild-type enzymeMet side chainsActive siteEnzyme-inhibitor complexThree-dimensional structureMutant structuresWild typeTriosephosphate isomeraseDianionic substrateEnzymeSame crystal formCrystal structureMET mutationsSide chainsIsomeraseSitesCrystal formsMutationsPhosphoglycolohydroxamateMethionineFunctional communication in the recognition of tRNA by Escherichia coli glutaminyl-tRNA synthetase.
Rogers M, Adachi T, Inokuchi H, Söll D. Functional communication in the recognition of tRNA by Escherichia coli glutaminyl-tRNA synthetase. Proceedings Of The National Academy Of Sciences Of The United States Of America 1994, 91: 291-295. PMID: 7506418, PMCID: PMC42933, DOI: 10.1073/pnas.91.1.291.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAmino Acyl-tRNA SynthetasesAnticodonBacterial ProteinsEscherichia coliGenes, SuppressorModels, MolecularMolecular Sequence DataMutagenesis, Site-DirectedProtein Structure, TertiaryRNA, BacterialRNA, TransferStructure-Activity RelationshipSubstrate SpecificityTransfer RNA AminoacylationConceptsEscherichia coli glutaminyl-tRNA synthetaseGlutaminyl-tRNA synthetaseLys-317Genetic selectionOpal suppressorMutant enzymesWild-type GlnRSAsp-235Anticodon-binding domainSingle amino acid changeSite-directed mutagenesisNumber of mutantsAmino acid changesRecognition of tRNAGlnR mutantAnticodon recognitionAdditional mutantsGln mutantGlnRMutantsAcid changesBase pairsSpecificity constantAminoacylationTRNA
1993
Acceptor end binding domain interactions ensure correct aminoacylation of transfer RNA.
Weygand-Durasević I, Schwob E, Söll D. Acceptor end binding domain interactions ensure correct aminoacylation of transfer RNA. Proceedings Of The National Academy Of Sciences Of The United States Of America 1993, 90: 2010-2014. PMID: 7680483, PMCID: PMC46010, DOI: 10.1073/pnas.90.5.2010.Peer-Reviewed Original ResearchConceptsAmber suppressor tRNASuppressor tRNAEscherichia coli glutaminyl-tRNA synthetaseAcceptor stemAccuracy of aminoacylationGlutaminyl-tRNA synthetaseWild-type enzymeNoncognate complexGlnR mutantTRNA specificityArg-130Amber mutationTransfer RNASuch mutantsMutant enzymesCritical residuesDomain contributesDomain interactionsRecognition specificityTRNAGlu-131MutantsNoncognate tRNAsGlnRCorrect aminoacylation
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
1984
Misaminoacylation by glutaminyl-tRNA synthetase: relaxed specificity in wild-type and mutant enzymes.
Hoben P, Uemura H, Yamao F, Cheung A, Swanson R, Sumner-Smith M, Söll D. Misaminoacylation by glutaminyl-tRNA synthetase: relaxed specificity in wild-type and mutant enzymes. The FASEB Journal 1984, 43: 2972-6. PMID: 6389180.Peer-Reviewed Original ResearchConceptsGlutaminyl-tRNA synthetaseMutant enzymesWild-type GlnRSAmino-terminal halfAmino acid sequenceAmino acid changesStructural gene mutationsTranslational controlTRNA speciesRelaxed specificityGene sequencesAcid sequenceGlnRRegulation mechanismAcid changesMonomeric polypeptideAmino acidsEnzymeTRNATyrSynthetaseMutationsGene mutationsGlutamineSequenceMisaminoacylation
1977
Suppression of a defective alanyl-tRNA synthetase in Escherichia coli: A compensatory mutation to high alanine affinity
Theall G, Low K, Söll D. Suppression of a defective alanyl-tRNA synthetase in Escherichia coli: A compensatory mutation to high alanine affinity. Molecular Genetics And Genomics 1977, 156: 221-227. PMID: 340903, DOI: 10.1007/bf00283495.Peer-Reviewed Original ResearchConceptsTemperature-resistant revertantsAlanyl-tRNA synthetaseResistant revertantsE. coli mapWild-type enzymeRibosomal proteinsStructural geneGene mapsSynthetase mutantsMutant enzymesParental enzymeCompensatory mutationsTemperature-sensitive characterEscherichia coliAdditional mutationsEnzymeRevertantsSynthetaseMutationsKm valuesAlanineRecAMutantsGenesAffinity
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