2018
Crystallographic evidence for two‐metal‐ion catalysis in human pol η
Wang J, Smithline ZB. Crystallographic evidence for two‐metal‐ion catalysis in human pol η. Protein Science 2018, 28: 439-447. PMID: 30368948, PMCID: PMC6319759, DOI: 10.1002/pro.3541.Peer-Reviewed Original ResearchMeSH KeywordsBinding SitesCatalysisCrystallography, X-RayDNA-Directed DNA PolymeraseHumansMagnesiumModels, MolecularConceptsMetal ionsProduct pyrophosphateChemical reactionsTwo-metal-ion catalysisTwo-metal-ion catalytic mechanismThird metal ionPhosphoryl transfer reactionsTransfer reactionsCrystallographic dataCatalytic mechanismCrystal structureCrystallographic evidenceHuman Pol ηMeal ionsIonsHuman polymerase ηCatalysisReactionComplexesSubPyrophosphateBindingProductsDNA polymeraseCrystals
2017
Structural insights into the oligomerization of FtsH periplasmic domain from Thermotoga maritima
An JY, Sharif H, Kang GB, Park KJ, Lee JG, Lee S, Jin MS, Song JJ, Wang J, Eom SH. Structural insights into the oligomerization of FtsH periplasmic domain from Thermotoga maritima. Biochemical And Biophysical Research Communications 2017, 495: 1201-1207. PMID: 29180014, DOI: 10.1016/j.bbrc.2017.11.158.Peer-Reviewed Original ResearchConceptsPeriplasmic domainMisfolded membrane proteinsATP-dependent proteaseMembrane protein complexesResolution crystal structureHydrophobic membrane environmentMembrane homeostasisProtein complexesMembrane proteinsTransmembrane proteinMembrane environmentThermotoga maritimaStructural insightsFtsHProtease domainToxic proteinsProteinOligomerizationHigh energetic barrierDomainTranslocatesEnergetic barrierMaritimaHomeostasisCrystal structure
2016
S3 State of the O2‑Evolving Complex of Photosystem II: Insights from QM/MM, EXAFS, and Femtosecond X‑ray Diffraction
Askerka M, Wang J, Vinyard DJ, Brudvig GW, Batista VS. S3 State of the O2‑Evolving Complex of Photosystem II: Insights from QM/MM, EXAFS, and Femtosecond X‑ray Diffraction. Biochemistry 2016, 55: 981-984. PMID: 26849148, DOI: 10.1021/acs.biochem.6b00041.Peer-Reviewed Original ResearchConceptsExtended X-ray absorption fine structureFemtosecond x-ray diffractionX-ray diffractionOxygen-evolving complexS3 stateHybrid quantum mechanics/molecular mechanics (QM/MM) methodX-ray absorption fine structureQuantum mechanics/molecular mechanics methodsAbsorption fine structureQM/MMPhotosystem IIMolecular mechanics methodElectron paramagnetic resonanceWater ligandsS3 transitionAmmonia bindingParamagnetic resonanceFine structureMechanics methodDiffractionComplexesStateResonanceLigandsMn4
2015
Crystallographic study of a MATE transporter presents a difficult case in structure determination with low‐resolution, anisotropic data and crystal twinning
Symersky J, Guo Y, Wang J, Lu M. Crystallographic study of a MATE transporter presents a difficult case in structure determination with low‐resolution, anisotropic data and crystal twinning. Acta Crystallographica Section D, Structural Biology 2015, 71: 2287-2296. PMID: 26527145, PMCID: PMC4631480, DOI: 10.1107/s1399004715016995.Peer-Reviewed Original Research
2012
Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3′-terminal phosphate and 5′-OH
Englert M, Xia S, Okada C, Nakamura A, Tanavde V, Yao M, Eom SH, Konigsberg WH, Söll D, Wang J. Structural and mechanistic insights into guanylylation of RNA-splicing ligase RtcB joining RNA between 3′-terminal phosphate and 5′-OH. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: 15235-15240. PMID: 22949672, PMCID: PMC3458315, DOI: 10.1073/pnas.1213795109.Peer-Reviewed Original ResearchConceptsRNA substratesRNA strandRNA phosphate backboneRNA endExtensive mutagenesisSecond RNA substrateKey residuesLigation pathwayBiochemical experimentsOverall ligationRNA ligaseGuanylylationRtcBMechanistic insightsGTP/Critical rolePhosphate backboneGMPActive siteCyclic phosphateDependent reactionDetailed insightStrandsLigaseMutagenesisUsing a Fluorescent Cytosine Analogue tCo To Probe the Effect of the Y567 to Ala Substitution on the Preinsertion Steps of dNMP Incorporation by RB69 DNA Polymerase
Xia S, Beckman J, Wang J, Konigsberg WH. Using a Fluorescent Cytosine Analogue tCo To Probe the Effect of the Y567 to Ala Substitution on the Preinsertion Steps of dNMP Incorporation by RB69 DNA Polymerase. Biochemistry 2012, 51: 4609-4617. PMID: 22616982, PMCID: PMC3437246, DOI: 10.1021/bi300241m.Peer-Reviewed Original ResearchProbing Minor Groove Hydrogen Bonding Interactions between RB69 DNA Polymerase and DNA
Xia S, Christian TD, Wang J, Konigsberg WH. Probing Minor Groove Hydrogen Bonding Interactions between RB69 DNA Polymerase and DNA. Biochemistry 2012, 51: 4343-4353. PMID: 22571765, PMCID: PMC3374494, DOI: 10.1021/bi300416z.Peer-Reviewed Original Research
2011
Structural Basis of Cooperative Ligand Binding by the Glycine Riboswitch
Butler EB, Xiong Y, Wang J, Strobel SA. Structural Basis of Cooperative Ligand Binding by the Glycine Riboswitch. Cell Chemical Biology 2011, 18: 293-298. PMID: 21439473, PMCID: PMC3076126, DOI: 10.1016/j.chembiol.2011.01.013.Peer-Reviewed Original ResearchMeSH KeywordsAptamers, NucleotideBinding SitesGene Expression RegulationGlycineLigandsNucleic Acid ConformationRiboswitchRNAConceptsGlycine riboswitchStructural basisGene expressionÅ crystal structureTandem riboswitchesCooperative ligand bindingRiboswitchLigand bindingTandem pairMinor contactsBinding sitesAmino acid ligandsCooperative recognitionExpressionExtensive networkOperonFusobacterium nucleatumAptamerCrystal structureGlycine binding siteBindingLigandsInteractionAcid ligands
2010
Substitution of Ala for Tyr567 in RB69 DNA Polymerase Allows dAMP To Be Inserted opposite 7,8-Dihydro-8-oxoguanine,
Beckman J, Wang M, Blaha G, Wang J, Konigsberg WH. Substitution of Ala for Tyr567 in RB69 DNA Polymerase Allows dAMP To Be Inserted opposite 7,8-Dihydro-8-oxoguanine,. Biochemistry 2010, 49: 4116-4125. PMID: 20411947, PMCID: PMC2882254, DOI: 10.1021/bi100102s.Peer-Reviewed Original Research
2009
Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding
Sharma H, Yu S, Kong J, Wang J, Steitz TA. Structure of apo-CAP reveals that large conformational changes are necessary for DNA binding. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 16604-16609. PMID: 19805344, PMCID: PMC2745332, DOI: 10.1073/pnas.0908380106.Peer-Reviewed Original ResearchConceptsColi catabolite gene activator proteinEscherichia coli catabolite gene activator proteinCatabolite gene activator proteinC-helixConformational changesGene activator proteinDNA binding domainsDNA recognition helixEarlier biochemical dataLarge conformational changesSpecific DNA sequencesBinding of cAMPRecognition helixActivator proteinDNA sequencesDNA bindingBinding domainsActive DNAWT structureInactive formInactive structureBiochemical dataDifferent conformationsBindingConformation
2007
Structural Metals in the Group I Intron: A Ribozyme with a Multiple Metal Ion Core
Stahley MR, Adams PL, Wang J, Strobel SA. Structural Metals in the Group I Intron: A Ribozyme with a Multiple Metal Ion Core. Journal Of Molecular Biology 2007, 372: 89-102. PMID: 17612557, PMCID: PMC2071931, DOI: 10.1016/j.jmb.2007.06.026.Peer-Reviewed Original Research
2006
The ϕ29 DNA polymerase:protein‐primer structure suggests a model for the initiation to elongation transition
Kamtekar S, Berman AJ, Wang J, Lázaro JM, de Vega M, Blanco L, Salas M, Steitz TA. The ϕ29 DNA polymerase:protein‐primer structure suggests a model for the initiation to elongation transition. The EMBO Journal 2006, 25: 1335-1343. PMID: 16511564, PMCID: PMC1422159, DOI: 10.1038/sj.emboj.7601027.Peer-Reviewed Original ResearchConceptsTerminal proteinDNA polymeraseDNA synthesisPrime replicationLinear chromosomesElongation transitionϕ29 DNA polymeraseBacteriophage genomesProtein movesBacteriophage phi29Resolution structureDuplex productsElongation phaseBinding cleftThird domainPolymeraseTemplate DNADuplex DNAPrimer strandSerine hydroxylProteinAbsolute requirementDNAActive siteDomainThe L561A Substitution in the Nascent Base-Pair Binding Pocket of RB69 DNA Polymerase Reduces Base Discrimination †
Zhang H, Rhee C, Bebenek A, Drake JW, Wang J, Konigsberg W. The L561A Substitution in the Nascent Base-Pair Binding Pocket of RB69 DNA Polymerase Reduces Base Discrimination †. Biochemistry 2006, 45: 2211-2220. PMID: 16475809, PMCID: PMC3373012, DOI: 10.1021/bi052099y.Peer-Reviewed Original Research
2005
Hoogsteen base-pairing in DNA replication?
Wang J. Hoogsteen base-pairing in DNA replication? Nature 2005, 437: e6-e7. PMID: 16163299, DOI: 10.1038/nature04199.Peer-Reviewed Original ResearchBase Selectivity Is Impaired by Mutants that Perturb Hydrogen Bonding Networks in the RB69 DNA Polymerase Active Site †
Yang G, Wang J, Konigsberg W. Base Selectivity Is Impaired by Mutants that Perturb Hydrogen Bonding Networks in the RB69 DNA Polymerase Active Site †. Biochemistry 2005, 44: 3338-3346. PMID: 15736944, DOI: 10.1021/bi047921x.Peer-Reviewed Original ResearchMeSH KeywordsAlanineAmino Acid SubstitutionBase Pair MismatchBinding SitesDeoxyadenine NucleotidesDeoxycytosine NucleotidesDeoxyguanine NucleotidesDNA-Directed DNA PolymeraseEnterobacterHydrogen BondingKineticsNucleotidesPhenylalanineSubstrate SpecificityThymine NucleotidesTolueneTyrosineViral ProteinsConceptsRB69 polRapid chemical quenchHydrogen bonding networkSet of mutantsStopped-flow fluorescencePutative conformational changesPhosphoryl transfer reactionsPolymerase active siteRB69 DNA polymeraseDNA polymerase active siteChemical quenchMolecular basisBonding networkNoncomplementary dNTPsMutantsTransfer reactionsExo enzymesState kinetic parametersConformational changesMismatched basesActive siteExo formCrystal structureDNA polymeraseNucleoside triphosphates
2004
Insights into Strand Displacement and Processivity from the Crystal Structure of the Protein-Primed DNA Polymerase of Bacteriophage φ29
Kamtekar S, Berman AJ, Wang J, Lázaro JM, de Vega M, Blanco L, Salas M, Steitz TA. Insights into Strand Displacement and Processivity from the Crystal Structure of the Protein-Primed DNA Polymerase of Bacteriophage φ29. Molecular Cell 2004, 16: 609-618. PMID: 15546620, DOI: 10.1016/j.molcel.2004.10.019.Peer-Reviewed Original ResearchConceptsDNA polymerasePhi29 DNA polymeraseT7 RNA polymeraseB-family polymerasesSpecific serinePriming proteinPolymerase active sitePhage phi29RNA polymerasePhage genomeSpecificity loopNontemplate strandStrand displacement activityFirst nucleotideHomology modelingSequence insertionHigh processivityProtein primerB familyPolymeraseDuplex DNATemplate DNAProcessivityProteinDNACrystal 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 ResearchThe structure of a ribosomal protein S8/spc operon mRNA complex
Merianos HJ, Wang J, Moore PB. The structure of a ribosomal protein S8/spc operon mRNA complex. RNA 2004, 10: 954-964. PMID: 15146079, PMCID: PMC1370587, DOI: 10.1261/rna.7030704.Peer-Reviewed Original ResearchMeSH KeywordsBase SequenceBinding SitesCrystallography, X-RayEscherichia coliEscherichia coli ProteinsGenes, BacterialLigandsMacromolecular SubstancesModels, MolecularNucleic Acid ConformationOperonProtein BiosynthesisRibosomal ProteinsRNA, BacterialRNA, MessengerSpecies SpecificityStatic ElectricityConceptsSpc operon mRNAOperon mRNARibosomal protein cistronsSmall ribosomal subunitRibosomal initiation complexResolution crystal structureProtein synthesis resultsSpc operonAutogenous regulationTranslational repressionInitiation complexOwn mRNARibosomal subunitS8 bindingSequence differencesCistronInternal sequencesMRNAGenesConformational similarityBindingComplexesRetroregulationRRNAsOperonThe Activity of Selected RB69 DNA Polymerase Mutants Can Be Restored by Manganese Ions: The Existence of Alternative Metal Ion Ligands Used during the Polymerization Cycle †
Zakharova E, Wang J, Konigsberg W. The Activity of Selected RB69 DNA Polymerase Mutants Can Be Restored by Manganese Ions: The Existence of Alternative Metal Ion Ligands Used during the Polymerization Cycle †. Biochemistry 2004, 43: 6587-6595. PMID: 15157091, DOI: 10.1021/bi049615p.Peer-Reviewed Original ResearchConceptsMetal ionsRapid chemical quench techniquesB metal ionsMetal ion ligandsMetal ion dependenceNucleotidyl transfer reactionState kinetic analysisTransfer reactionsIon ligandsActive centersCrystal structureSide chainsManganese ionsCatalytic sitePolymerization cyclesIonsIon dependenceAlternative ligandsRB69 DNA Polymerase MutantsLigandsConformational changesPol complexPhosphoryl transferKinetic analysisComplexes
2003
Domain Motions in GroEL upon Binding of an Oligopeptide
Wang J, Chen L. Domain Motions in GroEL upon Binding of an Oligopeptide. Journal Of Molecular Biology 2003, 334: 489-499. PMID: 14623189, DOI: 10.1016/j.jmb.2003.09.074.Peer-Reviewed Original Research