2024
Composition Heterogeneity of Metal Ions Bound at the Oxygen-Evolving Center of Photosystem II in Living Cells
Wang J. Composition Heterogeneity of Metal Ions Bound at the Oxygen-Evolving Center of Photosystem II in Living Cells. Biochemistry 2024, 63: 1963-1968. PMID: 39037205, DOI: 10.1021/acs.biochem.4c00261.Peer-Reviewed Original ResearchConceptsX-ray free-electron lasersStructure of photosystem IIOxygen-evolving centerPhotosystem IICrystal structure of photosystem IIFree-electron laserPhotosystem II dimersPhotosystem ILight-harvesting complexesCryo-electron tomographyMetal ionsPSII samplesCryo-electron microscopyCryo-ETDimeric core complexesCryo-EMMetal ion cofactorsLiving cellsCrystal structureCryo-electronCryo-EM structureMetal-ion occupancyIon occupancySpectroscopic interpretationAsymmetric environment
2022
Glycerol binding at the narrow channel of photosystem II stabilizes the low-spin S2 state of the oxygen-evolving complex
Flesher DA, Liu J, Wiwczar JM, Reiss K, Yang KR, Wang J, Askerka M, Gisriel CJ, Batista VS, Brudvig GW. Glycerol binding at the narrow channel of photosystem II stabilizes the low-spin S2 state of the oxygen-evolving complex. Photosynthesis Research 2022, 152: 167-175. PMID: 35322325, PMCID: PMC9427693, DOI: 10.1007/s11120-022-00911-0.Peer-Reviewed Original ResearchConceptsOxygen-evolving complexHydrogen bond networkS2 stateEPR signalPhotosystem II cyclesX-ray crystal structureRelative stabilityState EPR signalsD1-Asp61Water oxidationCatalytic intermediatesPhotochemical oxidationEPR spectraGlycerol moleculesCrystal structureCyanobacterial PSIIMultiline signalState SiPhotosystem IIOxidationRelative intensitiesComplexesEffect of glycerolExperimental conditionsStability
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 relevanceHeterogeneous Composition of Oxygen-Evolving Complexes in Crystal Structures of Dark-Adapted Photosystem II
Wang J, Gisriel CJ, Reiss K, Huang HL, Armstrong WH, Brudvig GW, Batista VS. Heterogeneous Composition of Oxygen-Evolving Complexes in Crystal Structures of Dark-Adapted Photosystem II. Biochemistry 2021, 60: 3374-3384. PMID: 34714055, DOI: 10.1021/acs.biochem.1c00611.Peer-Reviewed Original ResearchConceptsOxygen-evolving complexMetal ionsPhotosystem IIElectron density peakIndividual metal ionsElectron density distributionNumber of electronsPSII dimersMetal centerWater oxidationOxidation stateElectron numberHomodimeric protein complexElectronsCrystal structurePSII structureDensity distributionDensity peaksComplexesRedox stateIonsDimersMonomersPeakOxidation
2019
Visualization of H atoms in the X‐ray crystal structure of photoactive yellow protein: Does it contain low‐barrier hydrogen bonds?
Wang J. Visualization of H atoms in the X‐ray crystal structure of photoactive yellow protein: Does it contain low‐barrier hydrogen bonds? Protein Science 2019, 28: 1966-1972. PMID: 31441173, PMCID: PMC6798185, DOI: 10.1002/pro.3716.Peer-Reviewed Original ResearchConceptsPhotoactive yellow proteinLow-barrier hydrogen bondH atomsYellow proteinResidual electron density mapsNeutron structureAtomsO bond angleO distancesO atomsHydrogen bondsElectron density mapsBond anglesDensity mapsX-ray structureCrystal structureResolution X-ray structureStructureBondsX-ray crystal structureCrystallographic identification of spontaneous oxidation intermediates and products of protein sulfhydryl groups
Wang J. Crystallographic identification of spontaneous oxidation intermediates and products of protein sulfhydryl groups. Protein Science 2019, 28: 472-477. PMID: 30592103, PMCID: PMC6371210, DOI: 10.1002/pro.3568.Peer-Reviewed Original ResearchConceptsLys side chainsSide chainsO bridgesChemical identificationCrystal structureElectron density featuresCross-linking speciesCys side chainDirect chemical identificationProtein crystal structuresMass spectrometric analysisOxidation intermediatesCys-245Primary aminesMethylene groupCrystallographic identificationSpectrometric analysisDehydration mechanismLys-158Protein sulfhydryl groupsSulfhydryl groupsProtein structureChainCHCys residues
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 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 structureChlorophyll a with a farnesyl tail in thermophilic cyanobacteria
Wiwczar JM, LaFountain AM, Wang J, Frank HA, Brudvig GW. Chlorophyll a with a farnesyl tail in thermophilic cyanobacteria. Photosynthesis Research 2017, 134: 175-182. PMID: 28741056, PMCID: PMC5832022, DOI: 10.1007/s11120-017-0425-4.Peer-Reviewed Original ResearchConceptsThermophilic cyanobacteriaPhotosystem IIMajor light-harvesting pigmentOxygenic photosynthetic organismsLight-harvesting pigmentsÅ crystal structurePhotosynthetic organismsFarnesyl tailCyanobacteriaIsoprene unitsSpecific ChlSmall populationPhytyl tailElectron density mapsTailChlMass spectrometryOrganismsCofactorDensity mapsCrystal structureHigh-performance liquid chromatographyExperimental evidencePigmentsLiquid chromatography
2014
Structural 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 Research
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
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 ResearchConceptsGlycine riboswitchStructural basisGene expressionÅ crystal structureTandem riboswitchesCooperative ligand bindingRiboswitchLigand bindingTandem pairMinor contactsBinding sitesAmino acid ligandsCooperative recognitionExpressionExtensive networkOperonFusobacterium nucleatumAptamerCrystal structureGlycine binding siteBindingLigandsInteractionAcid ligandsVariation 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
2010
Crystal structure of a designed tetratricopeptide repeat module in complex with its peptide ligand
Cortajarena AL, Wang J, Regan L. Crystal structure of a designed tetratricopeptide repeat module in complex with its peptide ligand. The FEBS Journal 2010, 277: 1058-1066. PMID: 20089039, DOI: 10.1111/j.1742-4658.2009.07549.x.Peer-Reviewed Original ResearchConceptsTPR domainC-terminusKey protein-protein interactionsTetratricopeptide repeat modulesChaperone heat shock proteinProtein-protein interactionsHeat shock responseHeat shock proteinsTPR proteinsChaperone functionTPR unitsProtein domainsNew packing arrangementRepeat modulesMolecular basisPeptide ligandsShock proteinsShock responseHsp90Terminal residuesX-ray crystal structureProteinCrystal structureDomainTetratricopeptide
2009
Structures of RB69 DNA polymerase ternary complexes reveal multiple modes of metal ion coordination to correct incoming dNTPs
Wang M, Konigsberg W, Steitz T, Wang J. Structures of RB69 DNA polymerase ternary complexes reveal multiple modes of metal ion coordination to correct incoming dNTPs. The FASEB Journal 2009, 23: 482.1-482.1. DOI: 10.1096/fasebj.23.1_supplement.482.1.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
Visualizing a Circadian Clock Protein Crystal Structure of KaiC and Functional Insights
Pattanayek R, Wang J, Mori T, Xu Y, Johnson CH, Egli M. Visualizing a Circadian Clock Protein Crystal Structure of KaiC and Functional Insights. Molecular Cell 2004, 15: 375-388. PMID: 15304218, DOI: 10.1016/j.molcel.2004.07.013.Peer-Reviewed Original ResearchConceptsClock protein complexesAuto-phosphorylation siteGlobal gene expressionCircadian biological clockHomohexameric complexEvolutionary relationshipsProtein complexesCircadian clockworkATP bindingFunctional insightsCircadian proteinsKaiCProtein crystal structuresCentral poreGene expressionMolecular componentsBiochemical mechanismsBiological clockCrystal structureDouble donutComplex formationProteinCircadian rhythmicityMutationsCyanobacteriaThe 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
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