2022
Structural Basis for Reduced Dynamics of Three Engineered HNH Endonuclease Lys-to-Ala Mutants for the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Associated 9 (CRISPR/Cas9) Enzyme
Wang J, Skeens E, Arantes PR, Maschietto F, Allen B, Kyro GW, Lisi GP, Palermo G, Batista VS. Structural Basis for Reduced Dynamics of Three Engineered HNH Endonuclease Lys-to-Ala Mutants for the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Associated 9 (CRISPR/Cas9) Enzyme. Biochemistry 2022, 61: 785-794. PMID: 35420793, PMCID: PMC9069930, DOI: 10.1021/acs.biochem.2c00127.Peer-Reviewed Original ResearchConceptsShort palindromic repeatsSubstrate specificityPalindromic repeatsAla mutantWT enzymeRNA-binding domainAssociated 9 (Cas9) systemForeign DNA sequencesDNA strandsWild-type enzymeDouble-strand breaksEnhanced substrate specificityHNH active siteDynamics of proteinsType II immunityCas9 proteinDNA substratesDNA sequencesStructural basisMutantsAla substitutionDistinct conformationsSingle LysCatalytic siteEnzyme
2016
Different Divalent Cations Alter the Kinetics and Fidelity of DNA Polymerases*
Vashishtha AK, Wang J, Konigsberg WH. Different Divalent Cations Alter the Kinetics and Fidelity of DNA Polymerases*. Journal Of Biological Chemistry 2016, 291: 20869-20875. PMID: 27462081, PMCID: PMC5076500, DOI: 10.1074/jbc.r116.742494.Peer-Reviewed Original ResearchConceptsMetal ionsWater moleculesTransfer reactionsDifferent divalent cationsOctahedral coordination geometryB metal ionsThird metal ionDifferent metal ionsAttacking water moleculeDivalent metal ionsNucleotidyl transfer reactionPhosphoryl transfer reactionsNon-bridging oxygen atomsOctahedral complexesCoordination geometryCarboxyl oxygenDivalent cationsOxygen atomsSixth ligandHydroxyl groupsTransition stateEffective nucleophilePhosphorous atomsIonsB-site
2012
DNA Mismatch Synthesis Complexes Provide Insights into Base Selectivity of a B Family DNA Polymerase
Xia S, Wang J, Konigsberg WH. DNA Mismatch Synthesis Complexes Provide Insights into Base Selectivity of a B Family DNA Polymerase. Journal Of The American Chemical Society 2012, 135: 193-202. PMID: 23214497, PMCID: PMC3760218, DOI: 10.1021/ja3079048.Peer-Reviewed Original ResearchContribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA
Xia S, Vashishtha A, Bulkley D, Eom SH, Wang J, Konigsberg WH. Contribution of Partial Charge Interactions and Base Stacking to the Efficiency of Primer Extension at and beyond Abasic Sites in DNA. Biochemistry 2012, 51: 4922-4931. PMID: 22630605, PMCID: PMC3426629, DOI: 10.1021/bi300296q.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 ResearchStructural 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
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
Hoogsteen base-pairing in DNA replication?
Wang J. Hoogsteen base-pairing in DNA replication? Nature 2005, 437: e6-e7. PMID: 16163299, DOI: 10.1038/nature04199.Peer-Reviewed Original ResearchA specific subdomain in φ29 DNA polymerase confers both processivity and strand-displacement capacity
Rodríguez I, Lázaro JM, Blanco L, Kamtekar S, Berman AJ, Wang J, Steitz TA, Salas M, de Vega M. A specific subdomain in φ29 DNA polymerase confers both processivity and strand-displacement capacity. Proceedings Of The National Academy Of Sciences Of The United States Of America 2005, 102: 6407-6412. PMID: 15845765, PMCID: PMC1088371, DOI: 10.1073/pnas.0500597102.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBacteriophage T4DNADNA PrimersDNA ReplicationDNA-Directed DNA PolymeraseElectrophoretic Mobility Shift AssayExodeoxyribonucleasesModels, MolecularMolecular Sequence DataMutagenesis, Site-DirectedProtein ConformationProtein Structure, TertiarySequence AlignmentTemplates, GeneticConceptsDNA polymerasePhi29 DNA polymeraseProtein-primed DNA polymerasesStrand-displacement capacityMutant DNA polymerasesΦ29 DNA polymeraseRecent crystallographic studiesDNA binding capacityAsp-398Deletion mutantsStructural insightsSpecific insertionProcessivityPolymeraseStrand displacementFunctional roleAmino acidsPalm subdomainSpecific subdomainsBiochemical analysisDNA synthesisCritical roleRegion 2Crystallographic studiesIntrinsic capacity
1996
Structure of Taq polymerase with DNA at the polymerase active site
Eom S, Wang J, Steitz T. Structure of Taq polymerase with DNA at the polymerase active site. Nature 1996, 382: 278-281. PMID: 8717047, DOI: 10.1038/382278a0.Peer-Reviewed Original ResearchConceptsDuplex DNADNA polymeraseEnded duplex DNAKlenow fragmentBlunt-end terminiActive-site cleftEscherichia coli DNA polymerase IProtein side chainsDNA polymerase ICo-crystal structurePolymerase active siteTaq polymeraseWide minor groovePol ICommon binding sitePolymerase IPolymerase domainExonuclease domainPolymerase cleftThermus aquaticusPolymeraseDNAPolymerase siteMinor grooveExonuclease site
1994
Structural basis of asymmetry in the human immunodeficiency virus type 1 reverse transcriptase heterodimer.
Wang J, Smerdon S, Jäger J, Kohlstaedt L, Rice P, Friedman J, Steitz T. Structural basis of asymmetry in the human immunodeficiency virus type 1 reverse transcriptase heterodimer. Proceedings Of The National Academy Of Sciences Of The United States Of America 1994, 91: 7242-7246. PMID: 7518928, PMCID: PMC44375, DOI: 10.1073/pnas.91.15.7242.Peer-Reviewed Original Research