2012
Active site residues critical for flavin binding and 5,6‐dimethylbenzimidazole biosynthesis in the flavin destructase enzyme BluB
Yu T, Mok K, Kennedy K, Valton J, Anderson K, Walker G, Taga M. Active site residues critical for flavin binding and 5,6‐dimethylbenzimidazole biosynthesis in the flavin destructase enzyme BluB. Protein Science 2012, 21: 839-849. PMID: 22528544, PMCID: PMC3403419, DOI: 10.1002/pro.2068.Peer-Reviewed Original ResearchConceptsConserved residuesFlavin mononucleotideReduced catalytic functionPurified mutant proteinsBacterium Sinorhizobium melilotiActive site residuesReduced flavin mononucleotideFlavin isoalloxazine ringCatalytic residuesMutant proteinsFlavin bindingDMB synthesisStructure-function relationshipsActive siteEnzyme familyGenetic screeningSite residuesMutant formsLower axial ligandBound flavinCatalytic functionMutantsEnzyme assaysIsoalloxazine ringBluB
2003
Detection and characterization of enzyme intermediates: utility of rapid chemical quench methodology and single enzyme turnover experiments
Anderson K. Detection and characterization of enzyme intermediates: utility of rapid chemical quench methodology and single enzyme turnover experiments. 2003, 19-48. DOI: 10.1093/oso/9780198524946.003.0002.Peer-Reviewed Original ResearchEnzyme active siteEnzyme intermediateProtein structure-function studiesSteady-state kinetic studiesStructure-function studiesTransient kinetic approachActive siteMolecule of substrateEnzyme catalysisQuenching methodologyEnzymeTurnover experimentsTransient kinetic techniquesStructure-based drug designEnzyme Transition StatesDrug designMechanistic informationKinetic techniquesSubstrate(sMillisecond time scaleProteinSitesPathwayKinetic studiesIntermediate
2002
The Kinetic Mechanism of the Human Bifunctional Enzyme ATIC (5-Amino-4-imidazolecarboxamide Ribonucleotide Transformylase/Inosine 5′-Monophosphate Cyclohydrolase) A SURPRISING LACK OF SUBSTRATE CHANNELING*
Bulock K, Beardsley G, Anderson K. The Kinetic Mechanism of the Human Bifunctional Enzyme ATIC (5-Amino-4-imidazolecarboxamide Ribonucleotide Transformylase/Inosine 5′-Monophosphate Cyclohydrolase) A SURPRISING LACK OF SUBSTRATE CHANNELING*. Journal Of Biological Chemistry 2002, 277: 22168-22174. PMID: 11948179, DOI: 10.1074/jbc.m111964200.Peer-Reviewed Original ResearchConceptsCyclohydrolase reactionProduction of inosine monophosphateRelease of tetrahydrofolateSteady-state kinetic techniquesStopped-flow absorbanceBifunctional enzymeActive siteBifunctional proteinSubstrate channelingInosine 5'-monophosphateCyclohydrolaseEnzymatic activityChemotherapeutic targetEnzyme reaction pathwayInosine monophosphateKinetic mechanismFormyltransferaseProteinEnzymeKinetic analysisPathwayKinetic advantageKinetic evidenceKinetic techniquesRibonucleotides
2000
Energetics of S-Adenosylmethionine Synthetase Catalysis †
McQueney M, Anderson K, Markham G. Energetics of S-Adenosylmethionine Synthetase Catalysis †. Biochemistry 2000, 39: 4443-4454. PMID: 10757994, DOI: 10.1021/bi992876s.Peer-Reviewed Original ResearchMeSH KeywordsAdenosine TriphosphateAmino Acid SequenceBinding SitesCatalysisComputer SimulationDiphosphatesEscherichia coliFluorescenceHydrolysisIsomerismKineticsLigandsMethionineMethionine AdenosyltransferaseOxygenOxygen IsotopesPhosphatesPolyphosphatesS-AdenosylmethionineSolventsThermodynamicsTitrimetryWaterConceptsFree energy profilesSubstrate bindingLoop movementEnergy profilesFormation of AdoMetS-adenosylmethionineChemical interconversion stepPre-steady-state kineticsS-adenosylmethionine synthetaseProduct releaseP(i) complexEquilibrium binding measurementsEnzyme-catalyzed reactionsAdoMet formationBiological alkylating agentsConcentration of substrateFormation reactionCrystallographic studiesEnzyme turnoverEquilibrium constantsCatalyze formationRate constantsInterconversion stepActive siteBinding energy
1999
Crystallographic Studies of Phosphonate-Based α-Reaction Transition-State Analogues Complexed to Tryptophan Synthase † , ‡
Sachpatzidis A, Dealwis C, Lubetsky J, Liang P, Anderson K, Lolis E. Crystallographic Studies of Phosphonate-Based α-Reaction Transition-State Analogues Complexed to Tryptophan Synthase † , ‡. Biochemistry 1999, 38: 12665-12674. PMID: 10504236, DOI: 10.1021/bi9907734.Peer-Reviewed Original ResearchConceptsTransition stateShort hydrogen bondsTryptophan synthaseHigh conformational flexibilityTetrahedral transition stateTransition state analogueMechanism of catalysisEnzyme-inhibitor complexStructure-based approachPhosphonate oxygenIndole-3-glycerol phosphateHydroxyl oxygenHydrogen bondsSulfur atomsActive siteC3 atomC2 atomCrystal structureConformational flexibilityCrystallographic studiesInhibitor bindingConformation changeAtomsNew herbicidesGlu-49
1998
Substrate Channeling and Domain−Domain Interactions in Bifunctional Thymidylate Synthase−Dihydrofolate Reductase †
Liang P, Anderson K. Substrate Channeling and Domain−Domain Interactions in Bifunctional Thymidylate Synthase−Dihydrofolate Reductase †. Biochemistry 1998, 37: 12195-12205. PMID: 9724533, DOI: 10.1021/bi9803168.Peer-Reviewed Original ResearchConceptsDHFR active siteActive siteTS active siteCrystal structureTransient kinetic analysisEnzyme active siteBifunctional TS-DHFRProtein surfaceTS-DHFRKinetics of substrateReductase enzymeSingle polypeptide chainKinetic analysisDihydrofolateThymidylate synthasePolypeptide chainSubstrateEnzymeStructureDomain-domain interactionsSpecies of protozoaInteractionKineticsL. majorChain
1997
Detection and Identification of Transient Enzyme Intermediates Using Rapid Mixing, Pulsed-Flow Electrospray Mass Spectrometry †
Paiva A, Tilton R, Crooks G, Huang L, Anderson K. Detection and Identification of Transient Enzyme Intermediates Using Rapid Mixing, Pulsed-Flow Electrospray Mass Spectrometry †. Biochemistry 1997, 36: 15472-15476. PMID: 9398276, DOI: 10.1021/bi971883i.Peer-Reviewed Original ResearchConceptsTetrahedral intermediateElectrospray ionization ion trap mass spectrometerIon trap mass spectrometerNegative ion mass spectraElectrospray ionization mass spectrometryCollision-induced dissociationEnzyme intermediateIon mass spectraTrap mass spectrometerIonization mass spectrometryEnzyme reaction intermediatesElectrospray ionizationDaughter ionsSubsecond time scaleEnzyme active siteReaction intermediatesAtomic mass unitsMass spectraMass spectrometerChemical quench studiesQuenching studiesMass spectrometryRapid mixing deviceQuenching methodActive sitePre-Steady-State Kinetic Analysis of the Trichodiene Synthase Reaction Pathway †
Cane D, Chiu H, Liang P, Anderson K. Pre-Steady-State Kinetic Analysis of the Trichodiene Synthase Reaction Pathway †. Biochemistry 1997, 36: 8332-8339. PMID: 9204880, DOI: 10.1021/bi963018o.Peer-Reviewed Original ResearchConceptsChemical catalysisReaction pathwaysRapid chemical quench methodsActive siteSteady-state catalytic rateSingle turnover reactionsRate constant kcatEnzyme active siteNerolidyl diphosphateDeuterium isotope effectSingle-turnover experimentsSingle turnover rateState kinetic analysisTurnover reactionsDetection limitCatalytic rateOverall reactionSteady-state releaseIsotope effectRate-limiting stepState kineticsCatalysisReactionQuench methodSynthase reaction
1995
Reevaluating glyphosate as a transition-state inhibitor of EPSP synthase: identification of an EPSP synthase.EPSP.glyphosate ternary complex.
Sammons R, Gruys K, Anderson K, Johnson K, Sikorski J. Reevaluating glyphosate as a transition-state inhibitor of EPSP synthase: identification of an EPSP synthase.EPSP.glyphosate ternary complex. Biochemistry 1995, 34: 6433-40. PMID: 7756274, DOI: 10.1021/bi00019a024.Peer-Reviewed Original ResearchConceptsEPSP synthaseTernary complexShikimate 3-phosphateSteady-state kineticsEnzyme active siteTransition-state analogSubstrate turnoverSynthase reactionTransition-state inhibitorsEnzymeAssociated with PEPUncompetitive inhibitorBinding resultsSynthaseActive siteFluorescence titration experimentsShikimateOxonium ionsTurnoverInteraction of glyphosateTitration experiments
1991
Structure and topological symmetry of the glyphosate target 5-enolpyruvylshikimate-3-phosphate synthase: a distinctive protein fold.
Stallings W, Abdel-Meguid S, Lim L, Shieh H, Dayringer H, Leimgruber N, Stegeman R, Anderson K, Sikorski J, Padgette S, Kishore G. Structure and topological symmetry of the glyphosate target 5-enolpyruvylshikimate-3-phosphate synthase: a distinctive protein fold. Proceedings Of The National Academy Of Sciences Of The United States Of America 1991, 88: 5046-5050. PMID: 11607190, PMCID: PMC51804, DOI: 10.1073/pnas.88.11.5046.Peer-Reviewed Original ResearchThree-dimensional structureSynthesis of aromatic amino acidsProtein-folding unitTwo-domain structureBinding of substratesPolypeptide backbone chainFour-stranded sheetFolding unitsGlobular domainSequence alterationsBeta-sheetEscherichia coliElectron density mapsBroad-spectrum herbicide glyphosateAromatic amino acidsApproximate dyadAmino acidsHelixProteinActive siteLinear sequenceEnzymeSequenceCrystallographic techniquesPseudo-symmetrySerine modulates substrate channeling in tryptophan synthase. A novel intersubunit triggering mechanism
Anderson K, Miles E, Johnson K. Serine modulates substrate channeling in tryptophan synthase. A novel intersubunit triggering mechanism. Journal Of Biological Chemistry 1991, 266: 8020-8033. PMID: 1902468, DOI: 10.1016/s0021-9258(18)92934-0.Peer-Reviewed Original ResearchConceptsIndole-3-glycerol phosphateTryptophan synthaseProtein conformationAlpha 2 beta 2 complexReaction of serineAbsence of serineBeta siteFormation of tryptophanAlpha siteSteady-state turnoverActive siteAccumulation of indoleAlpha reactionSubstitution of cysteineSubstrate channelingBeta reactionBeta subunitMetabolic intermediatesSerineAlpha subunitQuench-flowProtein fluorescenceTurnover experimentsProteinTryptophan release
1990
"Kinetic competence" of the 5-enolpyruvoylshikimate-3-phosphate synthase tetrahedral intermediate.
Anderson K, Johnson K. "Kinetic competence" of the 5-enolpyruvoylshikimate-3-phosphate synthase tetrahedral intermediate. Journal Of Biological Chemistry 1990, 265: 5567-5572. PMID: 2180929, DOI: 10.1016/s0021-9258(19)39398-6.Peer-Reviewed Original ResearchObservation by 13C NMR of the EPSP synthase tetrahedral intermediate bound to the enzyme active site.
Anderson K, Sammons R, Leo G, Sikorski J, Benesi A, Johnson K. Observation by 13C NMR of the EPSP synthase tetrahedral intermediate bound to the enzyme active site. Biochemistry 1990, 29: 1460-5. PMID: 2334707, DOI: 10.1021/bi00458a017.Peer-Reviewed Original ResearchConceptsEnzyme active siteTetrahedral intermediateFormation of pyruvateActive siteEnzyme sitesComparison of quenchingReaction of enzymeTime of incubationTetrahedral centerCompound giving riseReaction pathwaysEnzymatic hydrolysisPeak assignmentsEnzymeNMR experimentsTernary complexNMR measurementsSide productsRate of formationSpectroscopic probesLong time of incubationNMRSpeciesTriethylamineCovalent adducts