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 ResearchConceptsMetal ionsProduct pyrophosphateChemical reactionsTwo-metal-ion catalysisTwo-metal-ion catalytic mechanismThird metal ionPhosphoryl transfer reactionsTransfer reactionsCrystallographic dataCatalytic mechanismCrystal structureCrystallographic evidenceHuman Pol ηMeal ionsIonsHuman polymerase ηCatalysisReactionComplexesSubPyrophosphateBindingProductsDNA polymeraseCrystalsStructural and biochemical insights into inhibition of human primase by citrate
Lee JG, Park KR, An JY, Kang JY, Shen H, Wang J, Eom SH. Structural and biochemical insights into inhibition of human primase by citrate. Biochemical And Biophysical Research Communications 2018, 507: 383-388. PMID: 30446220, DOI: 10.1016/j.bbrc.2018.11.047.Peer-Reviewed Original ResearchConceptsDNA replicationSmall catalytic subunitShort RNA segmentReplicative DNA polymerasesPhosphate binding siteMammalian chromosomesReplication forksCatalytic subunitAccessory subunitsBiochemical insightsOkazaki fragmentsRNA primersKey regulatorRNA segmentsBacterial enzymesHuman primasePrimaseDNA templateBase pairsDNA polymeraseInactive formDNA strandsBinding sitesPolymeraseSubunits
2012
The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation
Itsathitphaisarn O, Wing RA, Eliason WK, Wang J, Steitz TA. The Hexameric Helicase DnaB Adopts a Nonplanar Conformation during Translocation. Cell 2012, 151: 267-277. PMID: 23022319, PMCID: PMC3597440, DOI: 10.1016/j.cell.2012.09.014.Peer-Reviewed Original ResearchConceptsTranslocation mechanismParental duplex DNAReplicative DNA helicaseNucleotides of ssDNAC-terminal domainDNA helicaseDnaB hexamerHelicase DnaBNTP hydrolysisNascent DNAStructural insightsQuaternary structureDNA templateDuplex DNADNA polymeraseDnaBTranslocationSequential hydrolysisSubunitsUnwindingNucleotidesDNASsDNAHelicasesHelicase
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
RB69 DNA Polymerase Mutants with Expanded Nascent Base-Pair-Binding Pockets Are Highly Efficient but Have Reduced Base Selectivity
Zhang H, Beckman J, Wang J, Konigsberg W. RB69 DNA Polymerase Mutants with Expanded Nascent Base-Pair-Binding Pockets Are Highly Efficient but Have Reduced Base Selectivity. Biochemistry 2009, 48: 6940-6950. PMID: 19522539, PMCID: PMC2847438, DOI: 10.1021/bi900422b.Peer-Reviewed Original ResearchConceptsBase pairsCorrect base pairReplicative DNA polymerasesRB69 polRB69 DNA Polymerase MutantsNascent base pairDouble mutantSingle mutantsTriple mutantNumber of substitutionsWild typeMutantsBacteriophage RB69DNA polymerase mutantsPolymerase mutantsDNA polymeraseBinding pocketsNegative selectionDNA polRapid incorporationCatalytic centerLow incorporation efficiencyG mutationSulfolobus solfataricus Dpo4Base discrimination
2008
Structural basis for base discrimination by RB69 DNA polymerase
Wang M, Klimenko D, Steitz T, Wang J. Structural basis for base discrimination by RB69 DNA polymerase. The FASEB Journal 2008, 22: 593.2-593.2. DOI: 10.1096/fasebj.22.1_supplement.593.2.Peer-Reviewed Original ResearchTriple mutantApo formStructural basisBase pairsDNA polymeraseReplicative DNA polymerasesWild-type enzymeTernary complexTemplating baseHelix PBase selectivityNascent base pairRB69 DNA polymeraseBase discriminationWild-type PolType enzymeMismatched base pairsMutantsPol mutantsRB69 polPolymeraseComplexesS565Y416Pol
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 siteDomain
2005
A 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 capacityBase 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 A, Wang J, Lázaro J, de Vega M, Blanco L, Salas M, Steitz T. Insights into Strand Displacement and Processivity from the Crystal Structure of the Protein-Primed DNA Polymerase of Bacteriophage φ29. Molecular Cell 2004, 16: 1035-1036. DOI: 10.1016/j.molcel.2004.12.006.Peer-Reviewed Original ResearchDNA polymeraseInsights 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 DNAProcessivityProteinDNAPre-Steady-State Kinetics of RB69 DNA Polymerase and Its Exo Domain Mutants: Effect of pH and Thiophosphoryl Linkages on 3‘−5‘ Exonuclease Activity †
Wang C, Zakharova E, Li J, Joyce C, Wang J, Konigsberg W. Pre-Steady-State Kinetics of RB69 DNA Polymerase and Its Exo Domain Mutants: Effect of pH and Thiophosphoryl Linkages on 3‘−5‘ Exonuclease Activity †. Biochemistry 2004, 43: 3853-3861. PMID: 15049692, DOI: 10.1021/bi0302292.Peer-Reviewed Original ResearchMeSH KeywordsAlanineAmino Acid SubstitutionBacteriophage T4Base Pair MismatchDNA Polymerase IDNA-Directed DNA PolymeraseEnzyme ActivationExodeoxyribonucleasesGlutamineHydrogen-Ion ConcentrationKineticsMutagenesis, Site-DirectedPhosphatesPhosphorylationProtein Structure, TertiaryRNA EditingSubstrate SpecificityThionucleotidesT-PhagesViral ProteinsConceptsRate-determining stepDivalent metal ionsPH-activity profileB family replicative DNA polymerasesChemical stepMetal ionsSingle-turnover conditionsWild-type enzymeEffects of pHKlenow fragmentB-family DNA polymerasesFamily DNA polymerasesState kineticsDNA polymeraseThree-dimensional structureDomain mutantsExonuclease reactionExonuclease activityPhosphorothioate linkagesPhi29 DNA polymeraseElemental effectsReplicative DNA polymerasesRepair DNA polymerasesExo activityCatalysis
2001
Structure of the Replicating Complex of a Pol α Family DNA Polymerase
Franklin M, Wang J, Steitz T. Structure of the Replicating Complex of a Pol α Family DNA Polymerase. Cell 2001, 105: 657-667. PMID: 11389835, DOI: 10.1016/s0092-8674(01)00367-1.Peer-Reviewed Original ResearchConceptsAlpha familyDNA polymeraseResolution crystal structureTernary complex structureApo-protein structurePrimer-template DNAMinor groove interactionsFamily DNA polymerasesFamily polymerasesRB69 DNA polymerasePol IFidelity mechanismsPrimer 3' terminusPrimer extensionPolymeraseGroove interactionsDNA motionTerminusDNA orientationFamilyDNADegrees rotationCrystal structureComplex structureDTTP
1996
Structure of Taq polymerase with DNA at the polymerase active site
Eom S, Wang J, Steitz T. Structure of Taq polymerase with DNA at the polymerase active site. Nature 1996, 382: 278-281. PMID: 8717047, DOI: 10.1038/382278a0.Peer-Reviewed Original ResearchConceptsDuplex DNADNA polymeraseEnded duplex DNAKlenow fragmentBlunt-end terminiActive-site cleftEscherichia coli DNA polymerase IProtein side chainsDNA polymerase ICo-crystal structurePolymerase active siteTaq polymeraseWide minor groovePol ICommon binding sitePolymerase IPolymerase domainExonuclease domainPolymerase cleftThermus aquaticusPolymeraseDNAPolymerase siteMinor grooveExonuclease siteCrystal 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