2012
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
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 Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase
Xia S, Wang M, Blaha G, Konigsberg WH, Wang J. Structural Insights into Complete Metal Ion Coordination from Ternary Complexes of B Family RB69 DNA Polymerase. Biochemistry 2011, 50: 9114-9124. PMID: 21923197, PMCID: PMC3760225, DOI: 10.1021/bi201260h.Peer-Reviewed Original ResearchConceptsMetal ionsBond formationHydroxyl groupsCoordination bond lengthsMetal ion coordinationΑ-phosphateB-siteTernary complexMetal ion ACoordination complexesIon coordinationBond lengthsCoordination octahedraIon APhosphorus atomIonic radiusSimultaneous coordinationPhosphodiester bond formationIonsNucleotidyl transferStructural insightsComplexesPyrophosphate product
2010
Substitution of Ala for Tyr567 in RB69 DNA Polymerase Allows dAMP and dGMP To Be Inserted opposite Guanidinohydantoin,
Beckman J, Wang M, Blaha G, Wang J, Konigsberg WH. Substitution of Ala for Tyr567 in RB69 DNA Polymerase Allows dAMP and dGMP To Be Inserted opposite Guanidinohydantoin,. Biochemistry 2010, 49: 8554-8563. PMID: 20795733, PMCID: PMC3755731, DOI: 10.1021/bi100913v.Peer-Reviewed Original ResearchSubstitution 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
2006
The 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
Base 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
Pre-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
2002
The 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