2014
Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme
Eiler D, Wang J, Steitz TA. Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme. Proceedings Of The National Academy Of Sciences Of The United States Of America 2014, 111: 13028-13033. PMID: 25157168, PMCID: PMC4246988, DOI: 10.1073/pnas.1414571111.Peer-Reviewed Original ResearchStructural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix
Brown JA, Bulkley D, Wang J, Valenstein ML, Yario TA, Steitz TA, Steitz JA. Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix. Nature Structural & Molecular Biology 2014, 21: 633-640. PMID: 24952594, PMCID: PMC4096706, DOI: 10.1038/nsmb.2844.Peer-Reviewed Original ResearchMeSH KeywordsBase PairingBase SequenceCrystallography, X-RayHumansHydrogen BondingMolecular Sequence DataNucleic Acid ConformationRNA StabilityRNA, Long Noncoding
2013
Crystal structure of glycoprotein E2 from bovine viral diarrhea virus
Li Y, Wang J, Kanai R, Modis Y. Crystal structure of glycoprotein E2 from bovine viral diarrhea virus. Proceedings Of The National Academy Of Sciences Of The United States Of America 2013, 110: 6805-6810. PMID: 23569276, PMCID: PMC3637714, DOI: 10.1073/pnas.1300524110.Peer-Reviewed Original ResearchConceptsBovine viral diarrhea virus (BVDV) E2C-terminal motifHost cell cytoplasmImportant animal pathogenMembrane fusion mechanismIg-like domainsUnique protein architectureOuter lipid envelopeProtein architectureAnimal pathogensFusion apparatusStructure of E2New foldCellular membranesBovine viral diarrhea virusAromatic residuesViral diarrhea virusCell cytoplasmLipid envelopeDisulfide bondsCell entryDiarrhea virusMajor global health threatCrystal structureFusion mechanism
2011
Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures
Xia S, Wang M, Lee HR, Sinha A, Blaha G, Christian T, Wang J, Konigsberg W. Variation in Mutation Rates Caused by RB69pol Fidelity Mutants Can Be Rationalized on the Basis of Their Kinetic Behavior and Crystal Structures. Journal Of Molecular Biology 2011, 406: 558-570. PMID: 21216248, PMCID: PMC3059800, DOI: 10.1016/j.jmb.2010.12.033.Peer-Reviewed Original ResearchConceptsDouble mutantMutation rateAmino acid residuesRB69 DNA polymeraseSingle mutantsMutable sequencesPocket mutantsMutantsAcid residuesState kinetic parametersPrimer extensionT4 phageFidelity mutantsNucleotide residuesIncoming dNTPsDNA polymeraseReversion assayTernary complexComplementary strandCrystal structureResiduesBase selectivityPocketPolymeraseMisincorporation
2009
Tertiary architecture of the Oceanobacillus iheyensis group II intron
Toor N, Keating KS, Fedorova O, Rajashankar K, Wang J, Pyle AM. Tertiary architecture of the Oceanobacillus iheyensis group II intron. RNA 2009, 16: 57-69. PMID: 19952115, PMCID: PMC2802037, DOI: 10.1261/rna.1844010.Peer-Reviewed Original ResearchMeSH KeywordsBacillusBase SequenceCrystallography, X-RayIntronsModels, MolecularMolecular Sequence DataNucleic Acid ConformationRNA SplicingRNA, BacterialRNA, CatalyticConceptsGroup II intronsPotential evolutionary relationshipsGroup II intron structureGroup IIC intronIntron structureEvolutionary relationshipsEukaryotic spliceosomeInteraction networksRNA moleculesIntronsTertiary structural organizationGenetic studiesRibose zipperRNA foldingTertiary interactionsLarge ribozymesInteraction nodesStructural organizationTertiary architectureEukaryotesSpliceosomeGene therapyGenomeZipperFolding
2008
Mechanism of Inhibition of Human Immunodeficiency Virus Type 1 Reverse Transcriptase by a Stavudine Analogue, 4′-Ethynyl Stavudine Triphosphate
Yang G, Wang J, Cheng Y, Dutschman GE, Tanaka H, Baba M, Cheng YC. Mechanism of Inhibition of Human Immunodeficiency Virus Type 1 Reverse Transcriptase by a Stavudine Analogue, 4′-Ethynyl Stavudine Triphosphate. Antimicrobial Agents And Chemotherapy 2008, 52: 2035-2042. PMID: 18391035, PMCID: PMC2415781, DOI: 10.1128/aac.00083-08.Peer-Reviewed Original ResearchConceptsM184V mutantNucleoside reverse transcriptase inhibitorHuman immunodeficiency virus type 1Immunodeficiency virus type 1Human immunodeficiency virus type 1 reverse transcriptaseReverse transcriptase inhibitorType 1 reverse transcriptaseVirus type 1Mechanism of inhibitionHIV-1 RTWild-type RTStavudine triphosphateTranscriptase inhibitorD4TD4TTPType 1WT RTMutant RTsReverse transcriptase
2007
Crystal structure of Bacillus subtilis CodW, a noncanonical HslV‐like peptidase with an impaired catalytic apparatus
Rho S, Park HH, Kang GB, Im YJ, Kang MS, Lim BK, Seong IS, Seol J, Chung CH, Wang J, Eom SH. Crystal structure of Bacillus subtilis CodW, a noncanonical HslV‐like peptidase with an impaired catalytic apparatus. Proteins Structure Function And Bioinformatics 2007, 71: 1020-1026. PMID: 17979190, DOI: 10.1002/prot.21758.Peer-Reviewed Original Research
2005
Role of the GYVG Pore Motif of HslU ATPase in Protein Unfolding and Translocation for Degradation by HslV Peptidase*
Park E, Rho YM, Koh OJ, Ahn SW, Seong IS, Song JJ, Bang O, Seol JH, Wang J, Eom SH, Chung CH. Role of the GYVG Pore Motif of HslU ATPase in Protein Unfolding and Translocation for Degradation by HslV Peptidase*. Journal Of Biological Chemistry 2005, 280: 22892-22898. PMID: 15849200, DOI: 10.1074/jbc.m500035200.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAmino Acid MotifsAmino Acid SequenceCaseinsChromatographyCross-Linking ReagentsDose-Response Relationship, DrugElectrophoresis, Polyacrylamide GelEndopeptidase ClpEscherichia coliEscherichia coli ProteinsGlycineHydrolysisModels, BiologicalModels, MolecularMolecular Sequence DataMutagenesisMutagenesis, Site-DirectedMutationPeptidesProtein BindingProtein DenaturationProtein FoldingProtein TransportSequence Homology, Amino AcidTemperatureConceptsHslU ATPasePore motifHslVU complexHslV peptidaseCentral poreATP-dependent proteaseProtein unfoldingProteolytic active sitesHslU hexamerProteolytic chamberHslV dodecamerUnfolded proteinsHslV.HslUGly residueTranslocation processAmino acidsDegradation of caseinMotifProteinATP cleavageSame structural featuresATPase activityTranslocationATPaseA specific subdomain in φ29 DNA polymerase confers both processivity and strand-displacement capacity
Rodríguez I, Lázaro JM, Blanco L, Kamtekar S, Berman AJ, Wang J, Steitz TA, Salas M, de Vega M. A specific subdomain in φ29 DNA polymerase confers both processivity and strand-displacement capacity. Proceedings Of The National Academy Of Sciences Of The United States Of America 2005, 102: 6407-6412. PMID: 15845765, PMCID: PMC1088371, DOI: 10.1073/pnas.0500597102.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBacteriophage T4DNADNA PrimersDNA ReplicationDNA-Directed DNA PolymeraseElectrophoretic Mobility Shift AssayExodeoxyribonucleasesModels, MolecularMolecular Sequence DataMutagenesis, Site-DirectedProtein ConformationProtein Structure, TertiarySequence AlignmentTemplates, GeneticConceptsDNA polymerasePhi29 DNA polymeraseProtein-primed DNA polymerasesStrand-displacement capacityMutant DNA polymerasesΦ29 DNA polymeraseRecent crystallographic studiesDNA binding capacityAsp-398Deletion mutantsStructural insightsSpecific insertionProcessivityPolymeraseStrand displacementFunctional roleAmino acidsPalm subdomainSpecific subdomainsBiochemical analysisDNA synthesisCritical roleRegion 2Crystallographic studiesIntrinsic capacity
2004
Crystal structure of a group I intron splicing intermediate
Adams PL, Stahley MR, Gill ML, Kosek AB, Wang J, Strobel SA. Crystal structure of a group I intron splicing intermediate. RNA 2004, 10: 1867-1887. PMID: 15547134, PMCID: PMC1370676, DOI: 10.1261/rna.7140504.Peer-Reviewed Original ResearchCrystal structure of a self-splicing group I intron with both exons
Adams PL, Stahley MR, Kosek AB, Wang J, Strobel SA. Crystal structure of a self-splicing group I intron with both exons. Nature 2004, 430: 45-50. PMID: 15175762, DOI: 10.1038/nature02642.Peer-Reviewed Original Research
2003
Crystal Structures of an Archaeal Class I CCA-Adding Enzyme and Its Nucleotide Complexes
Xiong Y, Li F, Wang J, Weiner AM, Steitz TA. Crystal Structures of an Archaeal Class I CCA-Adding Enzyme and Its Nucleotide Complexes. Molecular Cell 2003, 12: 1165-1172. PMID: 14636575, DOI: 10.1016/s1097-2765(03)00440-4.Peer-Reviewed Original ResearchConceptsCCA-adding enzymeClass I CCA-adding enzymeCrystal structureClose evolutionary relationshipAddition of CCAChemical modificationAmino acid sequenceElectrostatic charge distributionNucleic acid templateEvolutionary relationshipsImmature tRNAsCharge distributionDomain architectureNucleotide complexesArcheoglobus fulgidusEnzyme classesTail domainAcid sequenceEnzyme bindsPolymerase domainTRNARelative orientationComplexesEnzymeTerminusCrystal structure of a transcription factor IIIB core interface ternary complex
Juo ZS, Kassavetis GA, Wang J, Geiduschek EP, Sigler PB. Crystal structure of a transcription factor IIIB core interface ternary complex. Nature 2003, 422: 534-539. PMID: 12660736, DOI: 10.1038/nature01534.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBase SequenceBinding SitesCrystallography, X-RayDNA, FungalFungal ProteinsGenes, FungalHydrogen BondingMacromolecular SubstancesModels, MolecularMolecular Sequence DataNucleic Acid ConformationPromoter Regions, GeneticProtein Structure, TertiaryProtein SubunitsRNA, Small NuclearSaccharomyces cerevisiae ProteinsStatic ElectricitySubstrate SpecificityTATA-Box Binding ProteinTranscription Factor TFIIIBConceptsTranscription factor IIIBGeneral transcription factor TFIIBDomain IIÅ resolution crystal structureTranscription factor TFIIBOpen initiation complexRegion of TBPTFIIB-related factorAmino-terminal halfCarboxy-terminal halfTernary complexResolution crystal structureRegulated transcriptionPromoter DNASequence similarityInitiation complexRNA polymeraseBase pairsBdp1Brf1Essential rolePolymerasePrimary interfaceCrystal structureResidue 435
2002
Crystal Structures of the Bacillus stearothermophilus CCA-Adding Enzyme and Its Complexes with ATP or CTP
Li F, Xiong Y, Wang J, Cho HD, Tomita K, Weiner AM, Steitz TA. Crystal Structures of the Bacillus stearothermophilus CCA-Adding Enzyme and Its Complexes with ATP or CTP. Cell 2002, 111: 815-824. PMID: 12526808, DOI: 10.1016/s0092-8674(02)01115-7.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAmino Acid MotifsAmino Acid SequenceCrystallography, X-RayCytidine TriphosphateDimerizationDNA Polymerase betaGeobacillus stearothermophilusModels, MolecularMolecular Sequence DataProtein FoldingProtein Structure, TertiaryRNA NucleotidyltransferasesSequence Homology, Amino AcidConceptsCCA-adding enzymeResolution crystal structureDNA polymerase betaImmature tRNAsNew proteinsBase specificityNucleic acid templateBacillus stearothermophilusPalm domainPolymerase betaIncoming ATPTRNAATPTerminusSubunitsCrystal structureActive siteAdditional structural featuresEnzymeCTPStructural featuresComplexesImportant componentTailDomainCrystal Structure of d-Hydantoinase from Bacillus stearothermophilus: Insight into the Stereochemistry of Enantioselectivity † , ‡
Cheon YH, Kim HS, Han KH, Abendroth J, Niefind K, Schomburg D, Wang J, Kim Y. Crystal Structure of d-Hydantoinase from Bacillus stearothermophilus: Insight into the Stereochemistry of Enantioselectivity † , ‡. Biochemistry 2002, 41: 9410-9417. PMID: 12135362, DOI: 10.1021/bi0201567.Peer-Reviewed Original ResearchConceptsD-hydantoinaseExocyclic substituentsTIM-barrel foldStriking structural similarityApo crystal structureSubstrate recognitionBarrel foldCatalytic chemistryStructural comparisonSide-chain precursorBacillus stearothermophilusCrystal structureAmino acidsStructural similarityDihydroorotaseHydantoinsStereochemistrySubstituentsEnantioselectivityEnzymeStereospecific hydrolysisHydrolysisStructureChemistryHydantoinaseThe C-terminal Tails of HslU ATPase Act as a Molecular Switch for Activation of HslV Peptidase*
Seong IS, Kang MS, Choi MK, Lee JW, Koh OJ, Wang J, Eom SH, Chung CH. The C-terminal Tails of HslU ATPase Act as a Molecular Switch for Activation of HslV Peptidase*. Journal Of Biological Chemistry 2002, 277: 25976-25982. PMID: 12011053, DOI: 10.1074/jbc.m202793200.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphatasesAmino Acid SequenceAmino Acid SubstitutionATP-Dependent ProteasesBinding SitesElectrophoresis, Polyacrylamide GelEndopeptidasesEnzyme ActivationHeat-Shock ProteinsModels, MolecularMolecular Sequence DataMutagenesis, Site-DirectedProtein ConformationSerine EndopeptidasesStructure-Activity RelationshipConceptsC-terminal tailHslV peptidaseHslVU complexC-terminusHexameric ringMolecular switchATP-dependent proteaseC-terminal 10 residuesAmino acidsProteolytic active sitesDodecamer consistingHslU hexamerHslU ATPaseTail peptideAxial poreATPase actsPolypeptide substratesSubstrate entryS proteasomeHslUCentral poreTerminusHslVPeptidaseCritical role
1997
The Structure of ClpP at 2.3 Å Resolution Suggests a Model for ATP-Dependent Proteolysis
Wang J, Hartling J, Flanagan J. The Structure of ClpP at 2.3 Å Resolution Suggests a Model for ATP-Dependent Proteolysis. Cell 1997, 91: 447-456. PMID: 9390554, DOI: 10.1016/s0092-8674(00)80431-6.Peer-Reviewed Original Research
1996
The 2.4 Å crystal structure of the bacterial chaperonin GroEL complexed with ATPγS
Boisvert D, Wang J, Otwinowski Z, Norwich A, Sigler P. The 2.4 Å crystal structure of the bacterial chaperonin GroEL complexed with ATPγS. Nature Structural & Molecular Biology 1996, 3: 170-177. PMID: 8564544, DOI: 10.1038/nsb0296-170.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAmino Acid SequenceBinding SitesChaperonin 60Crystallography, X-RayMagnesiumModels, MolecularMolecular Sequence DataProtein ConformationCrystal Structures of an NH2-Terminal Fragment of T4 DNA Polymerase and Its Complexes with Single-Stranded DNA and with Divalent Metal Ions †
Wang J, Yu P, Lin T, Konigsberg W, Steitz T. Crystal Structures of an NH2-Terminal Fragment of T4 DNA Polymerase and Its Complexes with Single-Stranded DNA and with Divalent Metal Ions †. Biochemistry 1996, 35: 8110-8119. PMID: 8679562, DOI: 10.1021/bi960178r.Peer-Reviewed Original ResearchConceptsT4 DNA polymeraseDNA polymeraseExonuclease domainKlenow fragmentExonuclease active siteActive site regionCrystallographic R-factorTranslational regulationMinimal sequence identityMetal ion cofactorsSequence identityActive siteNH2-terminal fragmentNH2-terminalSite regionDivalent metal ion cofactorCarboxylate residuesPolymeraseIon cofactorScissile phosphateEquivalent positionsResidue formsProteinSeparate domainsCrystal structure
1995
Crystal structure of Thermus aquaticus DNA polymerase
Kim Y, Eom S, Wang J, Lee D, Suh S, Steitz T. Crystal structure of Thermus aquaticus DNA polymerase. Nature 1995, 376: 612-616. PMID: 7637814, DOI: 10.1038/376612a0.Peer-Reviewed Original ResearchConceptsActive site