2021
Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69
Park J, Youn HS, An JY, Lee Y, Eom SH, Wang J. Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69. Frontiers In Molecular Biosciences 2021, 8: 704813. PMID: 34869578, PMCID: PMC8639217, DOI: 10.3389/fmolb.2021.704813.Peer-Reviewed Original ResearchDivalent metal ionsMetal ionsT duplexSecond divalent metal ionSingle divalent metal ionDimeric complexCrystal structureTernary complex structureBinary complexIonsSpecific interactionsTernary complexDimeric formAdditional conformational changesComplexesInitial bindingDNA complexesConformational changesNew binaryClosed ternary complexRB69polDNTP-binding pocketStructurePolymerizationBiological relevanceStructural analyses of an RNA stability element interacting with poly(A)
Torabi SF, Chen YL, Zhang K, Wang J, DeGregorio SJ, Vaidya AT, Su Z, Pabit SA, Chiu W, Pollack L, Steitz JA. Structural analyses of an RNA stability element interacting with poly(A). Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2026656118. PMID: 33785601, PMCID: PMC8040590, DOI: 10.1073/pnas.2026656118.Peer-Reviewed Original ResearchConceptsRNA stability elementCis-acting RNA elementsGlobal conformational changesRich internal loopCryo-electron microscopyRice transposable elementsDiverse genomesDouble-helical regionsSmall-angle X-ray scatteringEne motifTransposable elementsGlobal structural changesRNA interactionsRNA stabilityBioinformatics studiesRNA elementsStability elementShort helixConformational changesDecay pathwaysInternal loopBiochemical structureTriplex structureBindingMotif
2019
Thermodynamics of the S 2 -to-S 3 state transition of the oxygen-evolving complex of photosystem II
Amin M, Kaur D, Yang KR, Wang J, Mohamed Z, Brudvig GW, Gunner MR, Batista V. Thermodynamics of the S 2 -to-S 3 state transition of the oxygen-evolving complex of photosystem II. Physical Chemistry Chemical Physics 2019, 21: 20840-20848. PMID: 31517382, DOI: 10.1039/c9cp02308a.Peer-Reviewed Original ResearchConceptsOxygen-evolving complexD1-E189Water/hydroxide moleculeOxygen evolution reactionWater/hydroxidePhotosystem IIVan der WaalsRedox isomersAdditional hydroxideHydroxide moleculeCatalytic intermediatesElectrostatic interactionsProton lossCoordination shellDer WaalsSerial femtosecond crystallographyHydroxide additionHydroxideConformational changesFree electron laser measurementXFEL structureAdditional oxygenMn4IntermediatesFemtosecond crystallography
2013
Calcium-dependent conformational transition of calmodulin determined by Fourier transform infrared spectroscopy
Yu T, Wu G, Yang H, Wang J, Yu S. Calcium-dependent conformational transition of calmodulin determined by Fourier transform infrared spectroscopy. International Journal Of Biological Macromolecules 2013, 56: 57-61. PMID: 23403030, DOI: 10.1016/j.ijbiomac.2013.02.004.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
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
Nucleotide-dependent domain motions within rings of the RecA/AAA+ superfamily
Wang J. Nucleotide-dependent domain motions within rings of the RecA/AAA+ superfamily. Journal Of Structural Biology 2004, 148: 259-267. PMID: 15522774, DOI: 10.1016/j.jsb.2004.07.003.Peer-Reviewed Original ResearchConceptsNucleotide-dependent conformational changesT7 DNA helicaseImportant biological functionsMechanochemical motorOligomeric ringsDNA helicaseBiological functionsF1-ATPaseConformational changesDomain motionProteinMechanistic workForce generationHslUHelicaseFoldsChemical energyATPFamilyRing structureDomainMembersThe 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
The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases
Kamtekar S, Kennedy WD, Wang J, Stathopoulos C, Söll D, Steitz TA. The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases. Proceedings Of The National Academy Of Sciences Of The United States Of America 2003, 100: 1673-1678. PMID: 12578991, PMCID: PMC149891, DOI: 10.1073/pnas.0437911100.Peer-Reviewed Original ResearchConceptsLigand-free conformationCognate amino acidAmino acidsRecent biochemical experimentsProlyl-tRNA synthetasesCysteinyl-tRNA synthetaseProlyl-tRNA synthetaseActive site pocketMethanocaldococcus jannaschiiMethanopyrus kandleriMethanothermobacter thermautotrophicusCognate tRNAEssential enzymeApo formStructural basisBiochemical experimentsAminoacyl-adenylate analoguesHomology modelingConformational changesProtein synthesisTRNAProRSAdenylate complexNanomolar affinitySynthetase