2013
Prechemistry Nucleotide Selection Checkpoints in the Reaction Pathway of DNA Polymerase I and Roles of Glu710 and Tyr766
Bermek O, Grindley N, Joyce C. Prechemistry Nucleotide Selection Checkpoints in the Reaction Pathway of DNA Polymerase I and Roles of Glu710 and Tyr766. Biochemistry 2013, 52: 6258-6274. PMID: 23937394, PMCID: PMC3770053, DOI: 10.1021/bi400837k.Peer-Reviewed Original ResearchConceptsFidelity checkpointDNA polymerase IPolymerase IHigh-fidelity DNA polymeraseMutator allelesCheckpoint functionMutator polymeraseIncorrect base pairsSelection checkpointDNA templateConformational changesSubstrate poolBase pairsDNA polymeraseComplementary nucleotidesCheckpointNoncomplementary nucleotidesTemplating baseFinger closingPolymeraseDNTPsNucleotidesCorrect incomingPathwayWeak binding
2000
Identification of Genes Encoding Exported Mycobacterium tuberculosis Proteins Using a Tn552′phoA In Vitro Transposition System
Braunstein M, Griffin T, Kriakov J, Friedman S, Grindley N, Jacobs W. Identification of Genes Encoding Exported Mycobacterium tuberculosis Proteins Using a Tn552′phoA In Vitro Transposition System. Journal Of Bacteriology 2000, 182: 2732-2740. PMID: 10781540, PMCID: PMC101980, DOI: 10.1128/jb.182.10.2732-2740.2000.Peer-Reviewed Original ResearchMeSH KeywordsAlkaline PhosphataseAmino Acid SequenceArtificial Gene FusionBacterial ProteinsBiological TransportCosmidsCyclin-Dependent KinasesDNA Transposable ElementsDNA, BacterialGenes, BacterialGenomic LibraryMolecular Sequence DataMutagenesis, InsertionalMycobacterium tuberculosisPlasmidsReplication OriginConceptsProtective immunityM. tuberculosisMycobacterium tuberculosis pathogenesisImmune responseTuberculosis pathogenesisMycobacterium tuberculosis proteinsM. tuberculosis databaseTuberculosisTuberculosis databasePathogenesisTuberculosis proteinsImmunityEnvelope-associated proteinsM. smegmatisProteinPeptides
1998
How E. coli DNA polymerase I (klenow fragment) distinguishes between deoxy- and dideoxynucleotides11Edited by A. R Fersht
Astatke M, Grindley N, Joyce C. How E. coli DNA polymerase I (klenow fragment) distinguishes between deoxy- and dideoxynucleotides11Edited by A. R Fersht. Journal Of Molecular Biology 1998, 278: 147-165. PMID: 9571040, DOI: 10.1006/jmbi.1998.1672.Peer-Reviewed Original ResearchConceptsMutant derivativesWild-type Klenow fragmentKlenow fragmentTernary complexAmino acid residuesE. coli DNA polymerase IIncorporation of dNTPsDNA polymerase IDNTP ternary complexPolymerase IAcid residuesPhosphoryl transferState kinetic parametersConformational changesNatural substratePositions 762DNA polymeraseEnzyme DNAKlenow fragment DNA polymeraseDNTPsIncoming dNTPDNTPSide chain resultsRibose moietyDideoxynucleotides
1997
Biochemical and mutational studies of the 5′-3′ exonuclease of DNA polymerase I of Escherichia coli11Edited by A. R. Fersht
Xu Y, Derbyshire V, Ng K, Sun X, Grindley N, Joyce C. Biochemical and mutational studies of the 5′-3′ exonuclease of DNA polymerase I of Escherichia coli11Edited by A. R. Fersht. Journal Of Molecular Biology 1997, 268: 284-302. PMID: 9159471, DOI: 10.1006/jmbi.1997.0967.Peer-Reviewed Original Research
1995
The tyrosine‐6 hydroxyl of γδ resolvase is not required for the DNA cleavage and rejoining reactions
Leschziner A, Boocock M, Grindley N. The tyrosine‐6 hydroxyl of γδ resolvase is not required for the DNA cleavage and rejoining reactions. Molecular Microbiology 1995, 15: 865-870. PMID: 7596288, DOI: 10.1111/j.1365-2958.1995.tb02356.x.Peer-Reviewed Original ResearchDeoxynucleoside Triphosphate and Pyrophosphate Binding Sites in the Catalytically Competent Ternary Complex for the Polymerase Reaction Catalyzed by DNA Polymerase I (Klenow Fragment) (∗)
Astatke M, Grindley N, Joyce C. Deoxynucleoside Triphosphate and Pyrophosphate Binding Sites in the Catalytically Competent Ternary Complex for the Polymerase Reaction Catalyzed by DNA Polymerase I (Klenow Fragment) (∗). Journal Of Biological Chemistry 1995, 270: 1945-1954. PMID: 7829532, DOI: 10.1074/jbc.270.4.1945.Peer-Reviewed Original ResearchAmino Acid SequenceBacteriaBase SequenceBinding SitesConserved SequenceDeoxyribonucleotidesDiphosphatesDNA Polymerase IDNA PrimersKineticsMacromolecular SubstancesModels, MolecularMolecular Sequence DataMutagenesis, Site-DirectedOligodeoxyribonucleotidesPoint MutationPolymerase Chain ReactionProtein Structure, SecondarySaccharomyces cerevisiaeSequence Homology, Amino Acid
1991
The 3′‐5′ exonuclease of DNA polymerase I of Escherichia coli: contribution of each amino acid at the active site to the reaction.
Derbyshire V, Grindley N, Joyce C. The 3′‐5′ exonuclease of DNA polymerase I of Escherichia coli: contribution of each amino acid at the active site to the reaction. The EMBO Journal 1991, 10: 17-24. PMID: 1989882, PMCID: PMC452606, DOI: 10.1002/j.1460-2075.1991.tb07916.x.Peer-Reviewed Original ResearchConceptsActive siteMetal ionsEnzyme-bound metal ionSide chainsExonuclease reactionDivalent metal ionsAmino acid side chainsCarboxylate side chainAcid side chainsHydroxide ionMetal ligandsNucleophilic attackIonsTerminal phosphodiester bondPhosphodiester bondReactionExonuclease active siteActivity resultsKlenow fragmentDuplex DNA substratesCatalysisChainCarboxylateTerminal baseSubstrate
1990
Cooperativity mutants of the γδ resolvase identify an essential interdimer interaction
Hughes R, Hatfull G, Rice P, Steitz T, Grindley N. Cooperativity mutants of the γδ resolvase identify an essential interdimer interaction. Cell 1990, 63: 1331-1338. PMID: 2175679, DOI: 10.1016/0092-8674(90)90428-h.Peer-Reviewed Original ResearchConceptsProtein-protein interactionsHigher-order protein-protein interactionsCooperativity mutantsSite-specific recombinaseGamma delta resolvaseMutant phenotypeResolvase mutantsNucleoprotein complexesCrystallographic tetramersResolvase dimersΓδ resolvaseResolvaseCooperative bindingMutantsDNARecombinationSide chainsRecombinaseProteinInteractionCointegrate intermediatePhenotypeRecombination reactionBindingTetramerIdentification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I from Escherichia coli.
Polesky A, Steitz T, Grindley N, Joyce C. Identification of residues critical for the polymerase activity of the Klenow fragment of DNA polymerase I from Escherichia coli. Journal Of Biological Chemistry 1990, 265: 14579-14591. PMID: 2201688, DOI: 10.1016/s0021-9258(18)77342-0.Peer-Reviewed Original ResearchConceptsCluster of residuesIdentification of residuesSite-directed mutagenesisActive site residuesAmino acid residuesFuture mutational studiesImportant active site residuesDNA-binding propertiesActive site regionDNA polymerase IGenetic screenPosition 849Polymerase active siteMutant proteinsDNA substratesMutational studiesPolymerase IBiochemical experimentsSite residuesAcid residuesSite regionEscherichia coliPolymerase activityMutationsPolymerase reaction
1989
Preparation of heavy-atom derivatives using site-directed mutagenesis Introduction of cysteine residues into γδ resolvase
Hatfull G, Sanderson M, Freemont P, Raccuia P, Grindley N, Steitz T. Preparation of heavy-atom derivatives using site-directed mutagenesis Introduction of cysteine residues into γδ resolvase. Journal Of Molecular Biology 1989, 208: 661-667. PMID: 2553982, DOI: 10.1016/0022-2836(89)90156-3.Peer-Reviewed Original ResearchThe 43 residue DNA binding domain of γδ resolvase binds adjacent major and minor grooves of DNA
Rimphanitchayakit V, Hatfull G, Grindley N. The 43 residue DNA binding domain of γδ resolvase binds adjacent major and minor grooves of DNA. Nucleic Acids Research 1989, 17: 1035-1050. PMID: 2537948, PMCID: PMC331720, DOI: 10.1093/nar/17.3.1035.Peer-Reviewed Original Research
1986
Analysis of gamma delta resolvase mutants in vitro: evidence for an interaction between serine-10 of resolvase and site I of res.
Hatfull G, Grindley N. Analysis of gamma delta resolvase mutants in vitro: evidence for an interaction between serine-10 of resolvase and site I of res. Proceedings Of The National Academy Of Sciences Of The United States Of America 1986, 83: 5429-5433. PMID: 3016704, PMCID: PMC386300, DOI: 10.1073/pnas.83.15.5429.Peer-Reviewed Original ResearchConceptsSerine 10Resolvase mutantsRecombinational activitySite-specific recombination proteinsProtein-DNA complexesPosition 10Site-specific recombinationRecombination proteinsActive site serineMutant proteinsRecombinational crossover pointMutantsResolvaseRecombinational sitesLeucine changeSerineSite ICysteine changeGel electrophoresisSpecific defectsComplex formationCointegrate moleculeTransposon gamma deltaProteinDNA
1984
Cleavage of the site-specific recombination protein gamma delta resolvase: the smaller of two fragments binds DNA specifically.
Abdel-Meguid S, Grindley N, Templeton N, Steitz T. Cleavage of the site-specific recombination protein gamma delta resolvase: the smaller of two fragments binds DNA specifically. Proceedings Of The National Academy Of Sciences Of The United States Of America 1984, 81: 2001-2005. PMID: 6326096, PMCID: PMC345424, DOI: 10.1073/pnas.81.7.2001.Peer-Reviewed Original Research
1982
Nucleotide sequence of the Escherichia coli polA gene and primary structure of DNA polymerase I.
Joyce C, Kelley W, Grindley N. Nucleotide sequence of the Escherichia coli polA gene and primary structure of DNA polymerase I. Journal Of Biological Chemistry 1982, 257: 1958-1964. PMID: 6276402, DOI: 10.1016/s0021-9258(19)68132-9.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceBase SequenceDNA Restriction EnzymesEscherichia coliGenesPeptide FragmentsPlasmidsConceptsDNA polymerase IPolymerase INucleotide sequencePolA geneKilobase pair regionProtein chemical dataAmino acid sequenceWild-type alleleResidues 342Sequence comparisonDNA polymerase I.Polymerase moleculesDNA sequencesResidue 323Acid sequencePair regionPolA1 mutationPolymerase I.Primary structureBase pairsType alleleMild proteolysisGenesActive fragmentSequence