Springer Handbook of Enzymes: Class 2 Transferases EC 2.7.11.17-2.8 PDF
Preview Springer Handbook of Enzymes: Class 2 Transferases EC 2.7.11.17-2.8
Springer Handbook of Enzymes Supplement Volume S4 Dietmar Schomburg and Ida Schomburg (Eds.) Springer Handbook of Enzymes Supplement Volume S4 Class 2 Transferases EC 2.7.11.17–2.8 coedited by Antje Chang Second Edition 1 3 Professor Dietmar Schomburg TechnicalUniversityBraunschweig e-mail: [email protected] Bioinformatics & Systems Biology Langer Kamp 19b Dr. Ida Schomburg 38106 Braunschweig e-mail: [email protected] Germany Dr. Antje Chang e-mail: [email protected] Library of Congress Control Number: applied for ISBN 978-3-540-85700-6 2nd Edition Springer Berlin Heidelberg New York The first edition was published as the “Enzyme Handbook, edited by D. and I.Schomburg”. Thisworkissubjecttocopyright.Allrightsarereserved,whetherthewholeorpartofthematerialis concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting,reproductiononmicrofilmorinanyotherway,andstorageindatabanks.Duplication ofthispublicationorpartsthereofispermittedonlyundertheprovisionsoftheGermanCopyright LawofSeptember9,1965,initscurrentversion,andpermissionforusemustalwaysbeobtained fromSpringer.ViolationsareliabletoprosecutionundertheGermanCopyrightLaw. SpringerisapartofSpringerScience+BusinessMedia springer.com #Springer-VerlagBerlinHeidelberg2009 PrintedinGermany Theuseofgeneraldescriptivenames,registerednames,etc.inthispublicationdoesnotimply,even intheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotectivelaws andregulationsandfreeforgeneraluse. Thepublishercannotassumeanylegalresponsibilityforgivendata,especiallyasfarasdirectionsfor theuseandthehandlingofchemicalsandbiologicalmaterialareconcerned.Thisinformationcanbe obtainedfromtheinstructionsonsafelaboratorypracticeandfromthemanufacturersofchemicals andlaboratoryequipment. Coverdesign:ErichKirchner,Heidelberg Typesetting:medionetPublishingServicesLtd.,Berlin Printedonacid-freepaper 2/3141m-543210 Preface Today, as the full information about the genome is becoming available for a rapidly increasing number of organisms and transcriptome and proteome analysesarebeginningtoprovideuswithamuchwiderimageofproteinregu- lationandfunction,itisobviousthattherearelimitationstoourabilitytoaccess functionaldata for the geneproducts –theproteinsand,inparticular,foren- zymes. Those data are inherently very difficult to collect, interpret and stan- dardizeastheyarewidelydistributedamongjournalsfromdifferentfieldsand areoftensubjectto experimentalconditions.Nevertheless asystematiccollec- tionisessentialforourinterpretationofgenomeinformationandmoresofor applicationsofthisknowledgeinthefieldsofmedicine,agriculture,etc.Progress onenzymeimmobilisation,enzymeproduction,enzymeinhibition,coenzyme regenerationandenzymeengineeringhasopenedupfascinatingnewfieldsfor thepotentialapplicationofenzymesinawiderangeofdifferentareas. ThedevelopmentoftheenzymedatainformationsystemBRENDAwasstartedin 1987 at the German National Research Centre for Biotechnology in Braun- schweig(GBF),continuedattheUniversityofColognefrom1996to2007,and then returned to Braunschweig, to the Technical University, Institute of Bio- informatics & Systems Biology. The present book “Springer Handbookof En- zymes”representstheprintedversionofthisdatabank.Theinformationsystem hasbeendevelopedintoafullmetabolicdatabase. The enzymes in this Handbook are arranged according to the Enzyme Com- mission list of enzymes. Some 5,000 “different” enzymes are covered. Fre- quently enzymes with very different properties are included under the same EC-number.Althoughweintendtogivearepresentativeoverviewonthechar- acteristicsandvariabilityofeachenzyme,theHandbookisnotacompendium. Thereaderwillhavetogototheprimaryliteratureformoredetailedinforma- tion.Naturallyit isnotpossibletocoverallthenumerousliteraturereferences foreachenzyme(forsomeenzymesupto40,000)ifthedatarepresentationisto beconciseasisintended. Itshouldbementionedherethatthedatahavebeenextractedfromtheliterature andcriticallyevaluatedbyqualified scientists.Ontheotherhand,theoriginal authors’ nomenclatureforenzyme formsand subunits is retained. Inorder to keepthetablesconcise,redundantinformationisavoidedasfaraspossible(e.g. if K values are measured inthe presence of an obvious cosubstrate, only the m nameofthecosubstrateisgiveninparenthesesasacommentarywithoutrefer- encetoitsspecificrole). Theauthorsaregratefultothefollowingbiologistsandchemistsforinvaluable helpinthecompilationofdata:CorneliaMunarettoandDr.AntjeChang. Braunschweig Spring2009 DietmarSchomburg,IdaSchomburg VII List of Abbreviations A adenine Ac acetyl ADP adenosine5’-diphosphate Ala alanine All allose Alt altrose AMP adenosine5’-monophosphate Ara arabinose Arg arginine Asn asparagine Asp asparticacid ATP adenosine5’-triphosphate Bicine N,N’-bis(2-hydroxyethyl)glycine C cytosine cal calorie CDP cytidine5’-diphosphate CDTA trans-1,2-diaminocyclohexane-N,N,N,N-tetraaceticacid CMP cytidine5’-monophosphate CoA coenzymeA CTP cytidine5’-triphosphate Cys cysteine d deoxy- d- (andl-)prefixesindicatingconfiguration DFP diisopropylfluorophosphate DNA deoxyribonucleicacid DPN diphosphopyridiniumnucleotide(nowNAD+) DTNB 5,5’-dithiobis(2-nitrobenzoate) DTT dithiothreitol(i.e.Cleland’sreagent) EC numberofenzymeinEnzymeCommission’ssystem E.coli Escherichiacoli EDTA ethylenediaminetetraacetate EGTA ethyleneglycolbis(-aminoethylether)tetraacetate ER endoplasmicreticulum Et ethyl EXAFS extendedX-rayabsorptionfinestructure FAD flavin-adeninedinucleotide FMN flavinmononucleotide(riboflavin5’-monophosphate) Fru fructose Fuc fucose G guanine Gal galactose IX ListofAbbreviations GDP guanosine5’-diphosphate Glc glucose GlcN glucosamine GlcNAc N-acetylglucosamine Gln glutamine Glu glutamicacid Gly glycine GMP guanosine5’-monophosphate GSH glutathione GSSG oxidizedglutathione GTP guanosine5’-triphosphate Gul gulose h hour H4 tetrahydro HEPES 4-(2-hydroxyethyl)-1-piperazineethanesulfonicacid His histidine HPLC highperformanceliquidchromatography Hyl hydroxylysine Hyp hydroxyproline IAA iodoacetamide IC50 50%inhibitoryconcentration Ig immunoglobulin Ile isoleucine Ido idose IDP inosine5’-diphosphate IMP inosine5’-monophosphate ITP inosine5’-triphosphate K Michaelisconstant m l- (andd-)prefixesindicatingconfiguration Leu leucine Lys lysine Lyx lyxose M mol/l mM millimol/l m- meta- Man mannose MES 2-(N-morpholino)ethanesulfonate Met methionine min minute MOPS 3-(N-morpholino)propanesulfonate Mur muramicacid MW molecularweight NAD+ nicotinamide-adeninedinucleotide NADH reducedNAD NADP+ NADphosphate NADPH reducedNADP NAD(P)H indicateseitherNADHorNADPH X ListofAbbreviations NBS N-bromosuccinimide NDP nucleoside5’-diphosphate NEM N-ethylmaleimide Neu neuraminicacid NMN nicotinamidemononucleotide NMP nucleoside5’-monophosphate NTP nucleoside5’-triphosphate o- ortho- Orn ornithine p- para- PBS phosphate-bufferedsaline PCMB p-chloromercuribenzoate PEP phosphoenolpyruvate pH -log10[H+] Ph phenyl Phe phenylalanine PHMB p-hydroxymercuribenzoate PIXE proton-inducedX-rayemission PMSF phenylmethane-sulfonylfluoride p-NPP p-nitrophenylphosphate Pro proline (cid:2) Q factorforthechangeinreactionratefora10 Ctemperatureincrease 10 Rha rhamnose Rib ribose RNA ribonucleicacid mRNA messengerRNA rRNA ribosomalRNA tRNA transferRNA Sar N-methylglycine(sarcosine) SDS-PAGE sodiumdodecylsulfatepolyacrylamidegelelectrophoresis Ser serine T thymine t timeforhalf-completionofreaction H Tal talose TDP thymidine5’-diphosphate TEA triethanolamine Thr threonine TLCK Na-p-tosyl-l-lysinechloromethylketone T meltingtemperature m TMP thymidine5’-monophosphate Tos- tosyl-(p-toluenesulfonyl-) TPN triphosphopyridiniumnucleotide(nowNADP+) Tris tris(hydroxymethyl)-aminomethane Trp tryptophan TTP thymidine5’-triphosphate Tyr tyrosine U uridine XI ListofAbbreviations U/mg mmol/(mg*min) UDP uridine5’-diphosphate UMP uridine5’-monophosphate UTP uridine5’-triphosphate Val valine Xaa symbolforanaminoacidofunknownconstitutioninpeptideformula XAS X-rayabsorptionspectroscopy Xyl xylose XII Index of Recommended Enzyme Names EC-No. RecommendedName Page 2.7.11.27 [acetyl-CoAcarboxylase]kinase . . . . . . . . . . . . . . . . . 326 2.8.2.33 N-acetylgalactosamine4-sulfate6-O-sulfotransferase . . . . . . . . 489 2.7.11.17 Ca2+/calmodulin-dependentproteinkinase . . . . . . . . . . . . 1 2.7.11.22 cyclin-dependentkinase. . . . . . . . . . . . . . . . . . . . . 156 2.7.12.1 dual-specificitykinase . . . . . . . . . . . . . . . . . . . . . 372 2.7.11.20 elongationfactor2kinase. . . . . . . . . . . . . . . . . . . . 126 2.8.2.34 glycochenodeoxycholatesulfotransferase . . . . . . . . . . . . . 495 2.7.13.3 histidinekinase . . . . . . . . . . . . . . . . . . . . . . . . 420 2.7.11.31 [hydroxymethylglutaryl-CoAreductase(NADPH)]kinase . . . . . . 355 2.8.1.8 lipoylsynthase. . . . . . . . . . . . . . . . . . . . . . . . . 478 2.7.11.29 low-density-lipoproteinreceptorkinase . . . . . . . . . . . . . . 337 2.7.11.24 mitogen-activatedproteinkinase. . . . . . . . . . . . . . . . . 233 2.7.12.2 mitogen-activatedproteinkinasekinase. . . . . . . . . . . . . . 392 2.7.11.25 mitogen-activatedproteinkinasekinasekinase. . . . . . . . . . . 278 2.7.11.18 myosin-light-chainkinase. . . . . . . . . . . . . . . . . . . . 54 2.8.2.31 petromyzonolsulfotransferase . . . . . . . . . . . . . . . . . . 482 2.7.11.19 phosphorylasekinase. . . . . . . . . . . . . . . . . . . . . . 89 2.7.11.21 polokinase . . . . . . . . . . . . . . . . . . . . . . . . . . 134 2.7.13.1 protein-histidinepros-kinase . . . . . . . . . . . . . . . . . . 414 2.7.13.2 protein-histidinetele-kinase. . . . . . . . . . . . . . . . . . . 418 2.7.11.30 receptorproteinserine/threoninekinase . . . . . . . . . . . . . 340 2.7.11.23 [RNA-polymerase]-subunitkinase . . . . . . . . . . . . . . . . 220 2.8.2.32 scymnolsulfotransferase . . . . . . . . . . . . . . . . . . . . 484 2.7.11.26 t-proteinkinase . . . . . . . . . . . . . . . . . . . . . . . . 303 2.7.99.1 triphosphate-proteinphosphotransferase . . . . . . . . . . . . . 475 2.7.11.28 tropomyosinkinase. . . . . . . . . . . . . . . . . . . . . . . 333 XIII Description of Data Fields Allinformationexceptthenomenclatureoftheenzymes(whichisbasedonthe recommendationsoftheNomenclatureCommitteeofIUBMB(InternationalUn- ionofBiochemistryandMolecularBiology)andIUPAC(InternationalUnionof PureandAppliedChemistry)isextractedfromoriginalliterature(orreviewsfor verywellcharacterizedenzymes).Thequalityandreliabilityofthedatadepends onthemethodofdetermination,andforolderliteratureonthetechniquesavail- ableatthattime.ThisisespeciallytrueforthefieldsMolecularWeightandSub- units. Thegeneralstructureofthefieldsis:Information–Organism–Commentary– Literature Theinformationcanbefoundintheformofnumericalvalues(temperature,pH, K etc.)orastext(cofactors,inhibitorsetc.). m SometimesdataareclassifiedasAdditionalInformation.Hereyoumayfinddata thatcannotberecalculatedtotheunitsrequiredforafieldoralsogeneralinfor- mationbeingvalidforallvalues.Forexample,forInhibitors,AdditionalInforma- tionmaycontainalistofcompoundsthatarenotinhibitory. The detailed structure and contents of each field is described below. If one of thesefieldsismissingforaparticularenzyme,thismeansthatforthisfield,no dataareavailable. 1 Nomenclature ECnumber The number is as given by the IUBMB, classes of enzymes and subclasses definedaccordingtothereactioncatalyzed. Systematicname ThisisthenameasgivenbytheIUBMB/IUPACNomenclatureCommittee Recommendedname ThisisthenameasgivenbytheIUBMB/IUPACNomenclatureCommittee Synonyms Synonymswhicharefoundinotherdatabasesorintheliterature,abbrevia- tions,namesofcommerciallyavailableproducts.Ifidenticalnamesarefre- quentlyusedfordifferentenzymes,thesewillbementionedhere,crossrefer- encesaregiven.IfanotherECnumberhasbeenincludedinthisentry,it is mentionedhere. XV
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