2024
Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels
Flesher D, Liu J, Wang J, Gisriel C, Yang K, Batista V, Debus R, Brudvig G. Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels. Journal Of Biological Chemistry 2024, 300: 107475. PMID: 38879008, PMCID: PMC11294709, DOI: 10.1016/j.jbc.2024.107475.Peer-Reviewed Original ResearchOxygen-evolving complexPhotosystem II active sitePhotosystem IIJahn-Teller distortionPhotosystem II complexD1-Asp170Jahn-TellerResolution cryo-EM structureMutation-induced structural changesCryo-EM structureMagnetic propertiesD1 subunitActive siteOxygenic photosynthesisMutagenesis studiesLight-driven water oxidationSpectroscopic propertiesStructural basisSpectroscopic dataAmino acidsWater oxidation mechanismPhotosystemMutationsMutation-induced shiftWater oxidation
2023
Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning
Kapuścińska K, Dukała Z, Doha M, Ansari E, Wang J, Brudvig G, Brooks B, Amin M. Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning. Journal Of Chemical Information And Modeling 2023, 64: 2586-2593. PMID: 38054243, DOI: 10.1021/acs.jcim.3c01564.Peer-Reviewed Original ResearchOxidation stateMetal ionsActive siteCambridge Crystallographic Data CentreMetal oxidation stateElectron transfer reactionsStandard reduction potentialLower oxidation statesX-ray crystallographyCoordination chemistryCryogenic electron microscopyMetal clustersTransfer reactionsReaction mechanismReduction potentialXFEL crystallographyMetalloproteinsAppropriate experimental conditionsSmall moleculesCrystallographySmall compoundsSpecific reactionElectron microscopyRemarkable efficiencyMetals
2021
High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803
Gisriel CJ, Wang J, Liu J, Flesher DA, Reiss KM, Huang HL, Yang KR, Armstrong WH, Gunner MR, Batista VS, Debus RJ, Brudvig GW. High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 119: e2116765118. PMID: 34937700, PMCID: PMC8740770, DOI: 10.1073/pnas.2116765118.Peer-Reviewed Original ResearchConceptsCryo-electron microscopy structurePCC 6803Photosystem IIWater oxidationMicroscopy structureMesophilic cyanobacteriumHigh-resolution cryo-electron microscopy structuresOxygen-evolving photosystem IILight-driven water oxidationCyanobacterial photosystem IIHigh-resolution structuresD1 subunitPSII structureSynechocystis spLarge water channelsGenetic manipulationC-terminusBiophysical dataActive siteCyanobacteriumSpStructural pictureSubunitsOxidationWater channels
2017
Determination of chemical identity and occupancy from experimental density maps
Wang J. Determination of chemical identity and occupancy from experimental density maps. Protein Science 2017, 27: 411-420. PMID: 29027293, PMCID: PMC5775170, DOI: 10.1002/pro.3325.Peer-Reviewed Original ResearchConceptsCharge densityFourier transformElectrostatic potentialExperimental charge densitySolvent moleculesAtomic B-factorsElectron densityBasic electronic propertiesESP mapsProtein α-helixChemical identityActive siteElectronic propertiesLarge macromolecular complexesExperimental density mapsDensity mapsMoleculesVitreous iceMacromolecular complexesΑ-helixSmall protein subunitESP valuesTransformStructure factorSupercomplexes
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 insightStrandsLigaseMutagenesisBidentate and tridentate metal‐ion coordination states within ternary complexes of RB69 DNA polymerase
Xia S, Eom SH, Konigsberg WH, Wang J. Bidentate and tridentate metal‐ion coordination states within ternary complexes of RB69 DNA polymerase. Protein Science 2012, 21: 447-451. PMID: 22238207, PMCID: PMC3375444, DOI: 10.1002/pro.2026.Peer-Reviewed Original ResearchConceptsCoordination complexesMetal ionsCoordination stateSecond metal ionMetal ion coordinationDivalent metal ionsTernary complexTridentate coordinationBond formationPhosphorus atomActive siteRelevant conformationsStructural studiesSelectivity mechanismIonsTriphosphate tailComplexesRB69 DNA polymeraseÅ resolutionBase selectivityGround stateSubstrate alignmentPolymerase active siteCatalysisCoordination
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
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
2002
Crystal Structures of the Bacillus stearothermophilus CCA-Adding Enzyme and Its Complexes with ATP or CTP
Li F, Xiong Y, Wang J, Cho HD, Tomita K, Weiner AM, Steitz TA. Crystal Structures of the Bacillus stearothermophilus CCA-Adding Enzyme and Its Complexes with ATP or CTP. Cell 2002, 111: 815-824. PMID: 12526808, DOI: 10.1016/s0092-8674(02)01115-7.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAmino Acid MotifsAmino Acid SequenceCrystallography, X-RayCytidine TriphosphateDimerizationDNA Polymerase betaGeobacillus stearothermophilusModels, MolecularMolecular Sequence DataProtein FoldingProtein Structure, TertiaryRNA NucleotidyltransferasesSequence Homology, Amino AcidConceptsCCA-adding enzymeResolution crystal structureDNA polymerase betaImmature tRNAsNew proteinsBase specificityNucleic acid templateBacillus stearothermophilusPalm domainPolymerase betaIncoming ATPTRNAATPTerminusSubunitsCrystal structureActive siteAdditional structural featuresEnzymeCTPStructural featuresComplexesImportant componentTailDomain
2000
Sulfolobus shibatae CCA-adding enzyme forms a tetramer upon binding two tRNA molecules: a scrunching-shuttling model of CCA specificity1 1Edited by T. Richmond
Li F, Wang J, Steitz T. Sulfolobus shibatae CCA-adding enzyme forms a tetramer upon binding two tRNA molecules: a scrunching-shuttling model of CCA specificity1 1Edited by T. Richmond. Journal Of Molecular Biology 2000, 304: 483-492. PMID: 11090289, DOI: 10.1006/jmbi.2000.4189.Peer-Reviewed Original ResearchConceptsActive siteMulti-angle laser lightSmall-angle X-ray scatteringSize exclusion chromatographyX-ray scatteringFurther dimerizationExclusion chromatographyMoleculesDimeric enzymeC basesOligomerization stateTetramerTransfer RNA moleculesLaser lightTRNA moleculesRNA moleculesMonomersPrimer strandChromatographyEnzymeDimersHigh specificityBindingCCA-adding enzymeDimerization
1998
Crystal Structure Determination ofEscherichia coliClpP Starting from an EM-Derived Mask
Wang J, Hartling J, Flanagan J. Crystal Structure Determination ofEscherichia coliClpP Starting from an EM-Derived Mask. Journal Of Structural Biology 1998, 124: 151-163. PMID: 10049803, DOI: 10.1006/jsbi.1998.4058.Peer-Reviewed Original ResearchConceptsATP-dependent proteolytic complexEscherichia coli ClpPATP-dependent proteaseProteolytic active sitesEvolutionary convergenceClpP structureHeptameric ringsProteolytic complexIntracellular proteolysisProteolytic componentBiophysical techniquesClpPSmall-angle X-rayX-ray crystallographyX-ray crystal structureStriking exampleMatrix refinementActive siteProteaseStructure determinationHslVOverall architectureProteasomeStructural levelElectron microscopy
1996
Crystal 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
1995
Crystal structure of Thermus aquaticus DNA polymerase
Kim Y, Eom S, Wang J, Lee D, Suh S, Steitz T. Crystal structure of Thermus aquaticus DNA polymerase. Nature 1995, 376: 612-616. PMID: 7637814, DOI: 10.1038/376612a0.Peer-Reviewed Original Research