2022
Structural Insights into Binding of Remdesivir Triphosphate within the Replication–Transcription Complex of SARS-CoV‑2
Wang J, Shi Y, Reiss K, Maschietto F, Lolis E, Konigsberg WH, Lisi GP, Batista VS. Structural Insights into Binding of Remdesivir Triphosphate within the Replication–Transcription Complex of SARS-CoV‑2. Biochemistry 2022, 61: 1966-1973. PMID: 36044776, PMCID: PMC9469760, DOI: 10.1021/acs.biochem.2c00341.Peer-Reviewed Original ResearchConceptsReplication-transcription complexStructural basisCryo-EM structureAdenosine monophosphateRemdesivir triphosphateStructural insightsDuplex productsPrimer extensionNucleotide selectivityBase pairsNucleotide incorporationIncoming substrateRibosyl moietyActive complexSARS-CoV-2 inhibitorsNew detailed informationTriphosphateComplexesMolecular dynamics simulationsAdenosine triphosphate
2021
Identification of Mg2+ ions next to nucleotides in cryo‐EM maps using electrostatic potential maps
Wang J, Natchiar SK, Moore PB, Klaholz BP. Identification of Mg2+ ions next to nucleotides in cryo‐EM maps using electrostatic potential maps. Acta Crystallographica Section D, Structural Biology 2021, 77: 534-539. PMID: 33825713, PMCID: PMC8025889, DOI: 10.1107/s2059798321001893.Peer-Reviewed Original Research
2018
Structural 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 hydrolysisSubunitsUnwindingNucleotidesDNASsDNAHelicasesHelicaseStructural Basis for Differential Insertion Kinetics of dNMPs Opposite a Difluorotoluene Nucleotide Residue
Xia S, Eom SH, Konigsberg WH, Wang J. Structural Basis for Differential Insertion Kinetics of dNMPs Opposite a Difluorotoluene Nucleotide Residue. Biochemistry 2012, 51: 1476-1485. PMID: 22304682, PMCID: PMC3292180, DOI: 10.1021/bi2016487.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
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 orientationComplexesEnzymeTerminus
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