Enzyme - Wikipedia

Enzymes are proteins that act as biological catalysts (biocatalysts). Catalysts accelerate chemical reactions. The molecules upon which enzymes may act are ... Enzyme FromWikipedia,thefreeencyclopedia Jumptonavigation Jumptosearch Largebiologicalmoleculethatactsasacatalyst "Biocatalyst"redirectshere.Fortheuseofnaturalcatalystsinorganicchemistry,seeBiocatalysis. Theenzymeglucosidaseconvertsthesugarmaltoseintotwoglucosesugars.Activesiteresiduesinred,maltosesubstrateinblack,andNADcofactorinyellow.(PDB:1OBB​) PartofaseriesonBiochemistryChemistryoflife Index Outline History Keycomponents Biomolecules Enzymes Geneexpression Metabolism Listofbiochemists Biochemist Listofbiochemists Glossaries Glossaryofbiology Glossaryofchemistry  Categoryvte Enzymes(/ˈɛnzaɪmz/)areproteinsthatactasbiologicalcatalysts(biocatalysts).Catalystsacceleratechemicalreactions.Themoleculesuponwhichenzymesmayactarecalledsubstrates,andtheenzymeconvertsthesubstratesintodifferentmoleculesknownasproducts.Almostallmetabolicprocessesinthecellneedenzymecatalysisinordertooccuratratesfastenoughtosustainlife.[1]: 8.1 Metabolicpathwaysdependuponenzymestocatalyzeindividualsteps.Thestudyofenzymesiscalledenzymologyandthefieldofpseudoenzymeanalysisrecognizesthatduringevolution,someenzymeshavelosttheabilitytocarryoutbiologicalcatalysis,whichisoftenreflectedintheiraminoacidsequencesandunusual'pseudocatalytic'properties.[2][3] Enzymesareknowntocatalyzemorethan5,000biochemicalreactiontypes.[4]OtherbiocatalystsarecatalyticRNAmolecules,calledribozymes.Enzymes'specificitycomesfromtheiruniquethree-dimensionalstructures. Likeallcatalysts,enzymesincreasethereactionratebyloweringitsactivationenergy.Someenzymescanmaketheirconversionofsubstratetoproductoccurmanymillionsoftimesfaster.Anextremeexampleisorotidine5'-phosphatedecarboxylase,whichallowsareactionthatwouldotherwisetakemillionsofyearstooccurinmilliseconds.[5][6]Chemically,enzymesarelikeanycatalystandarenotconsumedinchemicalreactions,nordotheyaltertheequilibriumofareaction.Enzymesdifferfrommostothercatalystsbybeingmuchmorespecific.Enzymeactivitycanbeaffectedbyothermolecules:inhibitorsaremoleculesthatdecreaseenzymeactivity,andactivatorsaremoleculesthatincreaseactivity.Manytherapeuticdrugsandpoisonsareenzymeinhibitors.Anenzyme'sactivitydecreasesmarkedlyoutsideitsoptimaltemperatureandpH,andmanyenzymesare(permanently)denaturedwhenexposedtoexcessiveheat,losingtheirstructureandcatalyticproperties. Someenzymesareusedcommercially,forexample,inthesynthesisofantibiotics.Somehouseholdproductsuseenzymestospeedupchemicalreactions:enzymesinbiologicalwashingpowdersbreakdownprotein,starchorfatstainsonclothes,andenzymesinmeattenderizerbreakdownproteinsintosmallermolecules,makingthemeateasiertochew. Contents 1Etymologyandhistory 2Classificationandnomenclature 3Structure 4Mechanism 4.1Substratebinding 4.1.1"Lockandkey"model 4.1.2Inducedfitmodel 4.2Catalysis 4.3Dynamics 4.4Substratepresentation 4.5Allostericmodulation 5Cofactors 5.1Coenzymes 6Thermodynamics 7Kinetics 8Inhibition 8.1Typesofinhibition 8.1.1Competitive 8.1.2Non-competitive 8.1.3Uncompetitive 8.1.4Mixed 8.1.5Irreversible 8.2Functionsofinhibitors 9Factorsaffectingenzymeactivity 10Biologicalfunction 10.1Metabolism 10.2Controlofactivity 10.2.1Regulation 10.2.2Post-translationalmodification 10.2.3Quantity 10.2.4Subcellulardistribution 10.2.5Organspecialization 10.3Involvementindisease 11Evolution 12Industrialapplications 13Seealso 13.1Enzymedatabases 14References 15Furtherreading 15.1General 15.2Etymologyandhistory 15.3Enzymestructureandmechanism 15.4Kineticsandinhibition Etymologyandhistory EduardBuchner Bythelate17thandearly18thcenturies,thedigestionofmeatbystomachsecretions[7]andtheconversionofstarchtosugarsbyplantextractsandsalivawereknownbutthemechanismsbywhichtheseoccurredhadnotbeenidentified.[8] FrenchchemistAnselmePayenwasthefirsttodiscoveranenzyme,diastase,in1833.[9]Afewdecadeslater,whenstudyingthefermentationofsugartoalcoholbyyeast,LouisPasteurconcludedthatthisfermentationwascausedbyavitalforcecontainedwithintheyeastcellscalled"ferments",whichwerethoughttofunctiononlywithinlivingorganisms.Hewrotethat"alcoholicfermentationisanactcorrelatedwiththelifeandorganizationoftheyeastcells,notwiththedeathorputrefactionofthecells."[10] In1877,GermanphysiologistWilhelmKühne(1837–1900)firstusedthetermenzyme,whichcomesfromGreekἔνζυμον,"leavened"or"inyeast",todescribethisprocess.[11]Thewordenzymewasusedlatertorefertononlivingsubstancessuchaspepsin,andthewordfermentwasusedtorefertochemicalactivityproducedbylivingorganisms.[12] EduardBuchnersubmittedhisfirstpaperonthestudyofyeastextractsin1897.InaseriesofexperimentsattheUniversityofBerlin,hefoundthatsugarwasfermentedbyyeastextractsevenwhentherewerenolivingyeastcellsinthemixture.[13]Henamedtheenzymethatbroughtaboutthefermentationofsucrose"zymase".[14]In1907,hereceivedtheNobelPrizeinChemistryfor"hisdiscoveryofcell-freefermentation".FollowingBuchner'sexample,enzymesareusuallynamedaccordingtothereactiontheycarryout:thesuffix-aseiscombinedwiththenameofthesubstrate(e.g.,lactaseistheenzymethatcleaveslactose)ortothetypeofreaction(e.g.,DNApolymeraseformsDNApolymers).[15] Thebiochemicalidentityofenzymeswasstillunknownintheearly1900s.Manyscientistsobservedthatenzymaticactivitywasassociatedwithproteins,butothers(suchasNobellaureateRichardWillstätter)arguedthatproteinsweremerelycarriersforthetrueenzymesandthatproteinspersewereincapableofcatalysis.[16]In1926,JamesB.Sumnershowedthattheenzymeureasewasapureproteinandcrystallizedit;hedidlikewisefortheenzymecatalasein1937.TheconclusionthatpureproteinscanbeenzymeswasdefinitivelydemonstratedbyJohnHowardNorthropandWendellMeredithStanley,whoworkedonthedigestiveenzymespepsin(1930),trypsinandchymotrypsin.Thesethreescientistswereawardedthe1946NobelPrizeinChemistry.[17] Thediscoverythatenzymescouldbecrystallizedeventuallyallowedtheirstructurestobesolvedbyx-raycrystallography.Thiswasfirstdoneforlysozyme,anenzymefoundintears,salivaandeggwhitesthatdigeststhecoatingofsomebacteria;thestructurewassolvedbyagroupledbyDavidChiltonPhillipsandpublishedin1965.[18]Thishigh-resolutionstructureoflysozymemarkedthebeginningofthefieldofstructuralbiologyandtheefforttounderstandhowenzymesworkatanatomiclevelofdetail.[19] Classificationandnomenclature Enzymescanbeclassifiedbytwomaincriteria:eitheraminoacidsequencesimilarity(andthusevolutionaryrelationship)orenzymaticactivity. Enzymeactivity.Anenzyme'snameisoftenderivedfromitssubstrateorthechemicalreactionitcatalyzes,withthewordendingin-ase.[1]: 8.1.3 Examplesarelactase,alcoholdehydrogenaseandDNApolymerase.Differentenzymesthatcatalyzethesamechemicalreactionarecalledisozymes.[1]: 10.3  TheInternationalUnionofBiochemistryandMolecularBiologyhavedevelopedanomenclatureforenzymes,theECnumbers(for"EnzymeCommission").Eachenzymeisdescribedby"EC"followedbyasequenceoffournumberswhichrepresentthehierarchyofenzymaticactivity(fromverygeneraltoveryspecific).Thatis,thefirstnumberbroadlyclassifiestheenzymebasedonitsmechanismwhiletheotherdigitsaddmoreandmorespecificity.[20] Thetop-levelclassificationis: EC1,Oxidoreductases:catalyzeoxidation/reductionreactions EC2,Transferases:transferafunctionalgroup(e.g.amethylorphosphategroup) EC3,Hydrolases:catalyzethehydrolysisofvariousbonds EC4,Lyases:cleavevariousbondsbymeansotherthanhydrolysisandoxidation EC5,Isomerases:catalyzeisomerizationchangeswithinasinglemolecule EC6,Ligases:jointwomoleculeswithcovalentbonds. EC7,Translocases:catalyzethemovementofionsormoleculesacrossmembranes,ortheirseparationwithinmembranes. Thesesectionsaresubdividedbyotherfeaturessuchasthesubstrate,products,andchemicalmechanism.Anenzymeisfullyspecifiedbyfournumericaldesignations.Forexample,hexokinase(EC2.7.1.1)isatransferase(EC2)thataddsaphosphategroup(EC2.7)toahexosesugar,amoleculecontaininganalcoholgroup(EC2.7.1).[21] Sequencesimilarity.ECcategoriesdonotreflectsequencesimilarity.Forinstance,twoligasesofthesameECnumberthatcatalyzeexactlythesamereactioncanhavecompletelydifferentsequences.Independentoftheirfunction,enzymes,likeanyotherproteins,havebeenclassifiedbytheirsequencesimilarityintonumerousfamilies.ThesefamilieshavebeendocumentedindozensofdifferentproteinandproteinfamilydatabasessuchasPfam.[22] Structure Enzymeactivityinitiallyincreaseswithtemperature(Q10coefficient)untiltheenzyme'sstructureunfolds(denaturation),leadingtoanoptimalrateofreactionatanintermediatetemperature. Seealso:Proteinstructure Enzymesaregenerallyglobularproteins,actingaloneorinlargercomplexes.Thesequenceoftheaminoacidsspecifiesthestructurewhichinturndeterminesthecatalyticactivityoftheenzyme.[23]Althoughstructuredeterminesfunction,anovelenzymaticactivitycannotyetbepredictedfromstructurealone.[24]Enzymestructuresunfold(denature)whenheatedorexposedtochemicaldenaturantsandthisdisruptiontothestructuretypicallycausesalossofactivity.[25]Enzymedenaturationisnormallylinkedtotemperaturesaboveaspecies'normallevel;asaresult,enzymesfrombacterialivinginvolcanicenvironmentssuchashotspringsareprizedbyindustrialusersfortheirabilitytofunctionathightemperatures,allowingenzyme-catalysedreactionstobeoperatedataveryhighrate. Enzymesareusuallymuchlargerthantheirsubstrates.Sizesrangefromjust62aminoacidresidues,forthemonomerof4-oxalocrotonatetautomerase,[26]toover2,500residuesintheanimalfattyacidsynthase.[27]Onlyasmallportionoftheirstructure(around2–4aminoacids)isdirectlyinvolvedincatalysis:thecatalyticsite.[28]Thiscatalyticsiteislocatednexttooneormorebindingsiteswhereresiduesorientthesubstrates.Thecatalyticsiteandbindingsitetogethercomposetheenzyme'sactivesite.Theremainingmajorityoftheenzymestructureservestomaintainthepreciseorientationanddynamicsoftheactivesite.[29] Insomeenzymes,noaminoacidsaredirectlyinvolvedincatalysis;instead,theenzymecontainssitestobindandorientcatalyticcofactors.[29]Enzymestructuresmayalsocontainallostericsiteswherethebindingofasmallmoleculecausesaconformationalchangethatincreasesordecreasesactivity.[30] AsmallnumberofRNA-basedbiologicalcatalystscalledribozymesexist,whichagaincanactaloneorincomplexwithproteins.ThemostcommonoftheseistheribosomewhichisacomplexofproteinandcatalyticRNAcomponents.[1]: 2.2  Mechanism Organisationofenzymestructureandlysozymeexample.Bindingsitesinblue,catalyticsiteinredandpeptidoglycansubstrateinblack.(PDB:9LYZ​) Substratebinding Enzymesmustbindtheirsubstratesbeforetheycancatalyseanychemicalreaction.Enzymesareusuallyveryspecificastowhatsubstratestheybindandthenthechemicalreactioncatalysed.Specificityisachievedbybindingpocketswithcomplementaryshape,chargeandhydrophilic/hydrophobiccharacteristicstothesubstrates.Enzymescanthereforedistinguishbetweenverysimilarsubstratemoleculestobechemoselective,regioselectiveandstereospecific.[31] Someoftheenzymesshowingthehighestspecificityandaccuracyareinvolvedinthecopyingandexpressionofthegenome.Someoftheseenzymeshave"proof-reading"mechanisms.Here,anenzymesuchasDNApolymerasecatalyzesareactioninafirststepandthenchecksthattheproductiscorrectinasecondstep.[32]Thistwo-stepprocessresultsinaverageerrorratesoflessthan1errorin100millionreactionsinhigh-fidelitymammalianpolymerases.[1]: 5.3.1 SimilarproofreadingmechanismsarealsofoundinRNApolymerase,[33]aminoacyltRNAsynthetases[34]andribosomes.[35] Conversely,someenzymesdisplayenzymepromiscuity,havingbroadspecificityandactingonarangeofdifferentphysiologicallyrelevantsubstrates.Manyenzymespossesssmallsideactivitieswhicharosefortuitously(i.e.neutrally),whichmaybethestartingpointfortheevolutionaryselectionofanewfunction.[36][37] Enzymechangesshapebyinducedfituponsubstratebindingtoformenzyme-substratecomplex.Hexokinasehasalargeinducedfitmotionthatclosesoverthesubstratesadenosinetriphosphateandxylose.Bindingsitesinblue,substratesinblackandMg2+cofactorinyellow.(PDB:2E2N​,2E2Q​) "Lockandkey"model Toexplaintheobservedspecificityofenzymes,in1894EmilFischerproposedthatboththeenzymeandthesubstratepossessspecificcomplementarygeometricshapesthatfitexactlyintooneanother.[38]Thisisoftenreferredtoas"thelockandkey"model.[1]: 8.3.2 Thisearlymodelexplainsenzymespecificity,butfailstoexplainthestabilizationofthetransitionstatethatenzymesachieve.[39] Inducedfitmodel In1958,DanielKoshlandsuggestedamodificationtothelockandkeymodel:sinceenzymesareratherflexiblestructures,theactivesiteiscontinuouslyreshapedbyinteractionswiththesubstrateasthesubstrateinteractswiththeenzyme.[40]Asaresult,thesubstratedoesnotsimplybindtoarigidactivesite;theaminoacidside-chainsthatmakeuptheactivesitearemoldedintotheprecisepositionsthatenabletheenzymetoperformitscatalyticfunction.Insomecases,suchasglycosidases,thesubstratemoleculealsochangesshapeslightlyasitenterstheactivesite.[41]Theactivesitecontinuestochangeuntilthesubstrateiscompletelybound,atwhichpointthefinalshapeandchargedistributionisdetermined.[42] Inducedfitmayenhancethefidelityofmolecularrecognitioninthepresenceofcompetitionandnoiseviatheconformationalproofreadingmechanism.[43] Catalysis Seealso:EnzymecatalysisandTransitionstatetheory Enzymescanacceleratereactionsinseveralways,allofwhichlowertheactivationenergy(ΔG‡,Gibbsfreeenergy)[44] Bystabilizingthetransitionstate: Creatinganenvironmentwithachargedistributioncomplementarytothatofthetransitionstatetoloweritsenergy[45] Byprovidinganalternativereactionpathway: Temporarilyreactingwiththesubstrate,formingacovalentintermediatetoprovidealowerenergytransitionstate[46] Bydestabilisingthesubstrategroundstate: Distortingboundsubstrate(s)intotheirtransitionstateformtoreducetheenergyrequiredtoreachthetransitionstate[47] Byorientingthesubstratesintoaproductivearrangementtoreducethereactionentropychange[48](thecontributionofthismechanismtocatalysisisrelativelysmall)[49] Enzymesmayuseseveralofthesemechanismssimultaneously.Forexample,proteasessuchastrypsinperformcovalentcatalysisusingacatalytictriad,stabilisechargebuild-uponthetransitionstatesusinganoxyanionhole,completehydrolysisusinganorientedwatersubstrate.[50] Dynamics Seealso:Proteindynamics Enzymesarenotrigid,staticstructures;insteadtheyhavecomplexinternaldynamicmotions–thatis,movementsofpartsoftheenzyme'sstructuresuchasindividualaminoacidresidues,groupsofresiduesformingaproteinlooporunitofsecondarystructure,orevenanentireproteindomain.Thesemotionsgiverisetoaconformationalensembleofslightlydifferentstructuresthatinterconvertwithoneanotheratequilibrium.Differentstateswithinthisensemblemaybeassociatedwithdifferentaspectsofanenzyme'sfunction.Forexample,differentconformationsoftheenzymedihydrofolatereductaseareassociatedwiththesubstratebinding,catalysis,cofactorrelease,andproductreleasestepsofthecatalyticcycle,[51]consistentwithcatalyticresonancetheory. Substratepresentation Substratepresentationisaprocesswheretheenzymeissequesteredawayfromitssubstrate.Enzymescanbesequesteredtotheplasmamembraneawayfromasubstrateinthenucleusorcytosol.Orwithinthemembrane,anenzymecanbesequesteredintolipidraftsawayfromitssubstrateinthedisorderedregion.Whentheenzymeisreleaseditmixeswithitssubstrate.Alternatively,theenzymecanbesequesterednearitssubstratetoactivatetheenzyme.Forexample,theenzymecanbesolubleanduponactivationbindtoalipidintheplasmamembraneandthenactuponmoleculesintheplasmamembrane. Allostericmodulation Mainarticle:Allostericregulation Allostericsitesarepocketsontheenzyme,distinctfromtheactivesite,thatbindtomoleculesinthecellularenvironment.Thesemoleculesthencauseachangeintheconformationordynamicsoftheenzymethatistransducedtotheactivesiteandthusaffectsthereactionrateoftheenzyme.[52]Inthisway,allostericinteractionscaneitherinhibitoractivateenzymes.Allostericinteractionswithmetabolitesupstreamordownstreaminanenzyme'smetabolicpathwaycausefeedbackregulation,alteringtheactivityoftheenzymeaccordingtothefluxthroughtherestofthepathway.[53] Cofactors Chemicalstructureforthiaminepyrophosphateandproteinstructureoftransketolase.Thiaminepyrophosphatecofactorinyellowandxylulose5-phosphatesubstrateinblack.(PDB:4KXV​) Mainarticle:Cofactor(biochemistry) Someenzymesdonotneedadditionalcomponentstoshowfullactivity.Othersrequirenon-proteinmoleculescalledcofactorstobeboundforactivity.[54]Cofactorscanbeeitherinorganic(e.g.,metalionsandiron–sulfurclusters)ororganiccompounds(e.g.,flavinandheme).Thesecofactorsservemanypurposes;forinstance,metalionscanhelpinstabilizingnucleophilicspecieswithintheactivesite.[55]Organiccofactorscanbeeithercoenzymes,whicharereleasedfromtheenzyme'sactivesiteduringthereaction,orprostheticgroups,whicharetightlyboundtoanenzyme.Organicprostheticgroupscanbecovalentlybound(e.g.,biotininenzymessuchaspyruvatecarboxylase).[56] Anexampleofanenzymethatcontainsacofactoriscarbonicanhydrase,whichusesazinccofactorboundaspartofitsactivesite.[57]Thesetightlyboundionsormoleculesareusuallyfoundintheactivesiteandareinvolvedincatalysis.[1]: 8.1.1 Forexample,flavinandhemecofactorsareofteninvolvedinredoxreactions.[1]: 17  Enzymesthatrequireacofactorbutdonothaveoneboundarecalledapoenzymesorapoproteins.Anenzymetogetherwiththecofactor(s)requiredforactivityiscalledaholoenzyme(orhaloenzyme).Thetermholoenzymecanalsobeappliedtoenzymesthatcontainmultipleproteinsubunits,suchastheDNApolymerases;heretheholoenzymeisthecompletecomplexcontainingallthesubunitsneededforactivity.[1]: 8.1.1  Coenzymes Coenzymesaresmallorganicmoleculesthatcanbelooselyortightlyboundtoanenzyme.Coenzymestransportchemicalgroupsfromoneenzymetoanother.[58]ExamplesincludeNADH,NADPHandadenosinetriphosphate(ATP).Somecoenzymes,suchasflavinmononucleotide(FMN),flavinadeninedinucleotide(FAD),thiaminepyrophosphate(TPP),andtetrahydrofolate(THF),arederivedfromvitamins.Thesecoenzymescannotbesynthesizedbythebodydenovoandcloselyrelatedcompounds(vitamins)mustbeacquiredfromthediet.Thechemicalgroupscarriedinclude: thehydrideion(H−),carriedbyNADorNADP+ thephosphategroup,carriedbyadenosinetriphosphate theacetylgroup,carriedbycoenzymeA formyl,methenylormethylgroups,carriedbyfolicacidand themethylgroup,carriedbyS-adenosylmethionine[58] Sincecoenzymesarechemicallychangedasaconsequenceofenzymeaction,itisusefultoconsidercoenzymestobeaspecialclassofsubstrates,orsecondsubstrates,whicharecommontomanydifferentenzymes.Forexample,about1000enzymesareknowntousethecoenzymeNADH.[59] Coenzymesareusuallycontinuouslyregeneratedandtheirconcentrationsmaintainedatasteadylevelinsidethecell.Forexample,NADPHisregeneratedthroughthepentosephosphatepathwayandS-adenosylmethioninebymethionineadenosyltransferase.Thiscontinuousregenerationmeansthatsmallamountsofcoenzymescanbeusedveryintensively.Forexample,thehumanbodyturnsoveritsownweightinATPeachday.[60] Thermodynamics Theenergiesofthestagesofachemicalreaction.Uncatalysed(dashedline),substratesneedalotofactivationenergytoreachatransitionstate,whichthendecaysintolower-energyproducts.Whenenzymecatalysed(solidline),theenzymebindsthesubstrates(ES),thenstabilizesthetransitionstate(ES‡)toreducetheactivationenergyrequiredtoproduceproducts(EP)whicharefinallyreleased. Mainarticles:Activationenergy,Thermodynamicequilibrium,andChemicalequilibrium Aswithallcatalysts,enzymesdonotalterthepositionofthechemicalequilibriumofthereaction.Inthepresenceofanenzyme,thereactionrunsinthesamedirectionasitwouldwithouttheenzyme,justmorequickly.[1]: 8.2.3 Forexample,carbonicanhydrasecatalyzesitsreactionineitherdirectiondependingontheconcentrationofitsreactants:[61] CO 2 + H 2 O → Carbonicanhydrase H 2 CO 3 {\displaystyle{\ce{CO2{}+H2O->[{\text{Carbonicanhydrase}}]H2CO3}}} (intissues;highCO2concentration)         (1) CO 2 + H 2 O ← Carbonicanhydrase H 2 CO 3 {\displaystyle{\ce{CO2{}+H2O