Nucleic Acid Polymerases PDF
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Nucleic Acids and Molecular Biology 30 Katsuhiko S. Murakami Michael A. Trakselis Editors Nucleic Acid Polymerases Nucleic Acids and Molecular Biology Volume 30 Series Editor JanuszM. Bujnicki International InstituteofMolecular and Cell Biology Laboratory ofBioinformatics and Protein Engineering Trojdena 4 02-109 Warsaw Poland For furthervolumes: http://www.springer.com/series/881 ThiSisaFMBlankPage Katsuhiko S. Murakami (cid:129) Michael A. Trakselis Editors Nucleic Acid Polymerases Editors KatsuhikoS.Murakami MichaelA.Trakselis Dept.ofBiochem.andMol.Biology DepartmentofChemistry ThePennsylvaniaStateUniversity UniversityofPittsburgh UniversityPark Pittsburgh Pennsylvania Pennsylvania USA USA ISSN0933-1891 ISSN1869-2486(electronic) ISBN978-3-642-39795-0 ISBN978-3-642-39796-7(eBook) DOI10.1007/978-3-642-39796-7 SpringerHeidelbergNewYorkDordrechtLondon ©Springer-VerlagBerlinHeidelberg2014 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpart of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation,broadcasting,reproductiononmicrofilmsorinanyotherphysicalway,andtransmissionor informationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilar methodologynowknownorhereafterdeveloped.Exemptedfromthislegalreservationarebriefexcerpts inconnectionwithreviewsorscholarlyanalysisormaterialsuppliedspecificallyforthepurposeofbeing enteredandexecutedonacomputersystem,forexclusiveusebythepurchaserofthework.Duplication ofthispublicationorpartsthereofispermittedonlyundertheprovisionsoftheCopyrightLawofthe Publisher’s location, in its current version, and permission for use must always be obtained from Springer.PermissionsforusemaybeobtainedthroughRightsLinkattheCopyrightClearanceCenter. ViolationsareliabletoprosecutionundertherespectiveCopyrightLaw. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publicationdoesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexempt fromtherelevantprotectivelawsandregulationsandthereforefreeforgeneraluse. While the advice and information in this book are believed to be true and accurate at the date of publication,neithertheauthorsnortheeditorsnorthepublishercanacceptanylegalresponsibilityfor anyerrorsoromissionsthatmaybemade.Thepublishermakesnowarranty,expressorimplied,with respecttothematerialcontainedherein. Printedonacid-freepaper SpringerispartofSpringerScience+BusinessMedia(www.springer.com) Preface More than any other class of enzymes, nucleic acid polymerases are directly responsible for an overabundance of enzymatic, regulatory, and maintenance activities in the cell. DNA polymerases accurately replicate copies of genomes in all forms of life as well as have specialized roles in DNA repair and immune response.RNApolymerasesaremostnotedfortheiractiverolesincontrollinggene expression during transcription but can also be utilized in self-replicating ribozymes and viral replication. Although the general sequence homology, struc- turalarchitecture,andmechanismareconserved,theyhaveevolvedtoincorporate deoxynucleotides (dNTPs) or ribonucleotides (rNTPs) explicitly. Various nucleic acidpolymeraseshavespecificitiesforRNAorDNAtemplates,incorporatedNTPs or rNTPs, and can be template dependent or independent. Here, we provide examples on the latest understanding of each class of nucleic acid polymerase, their structural and kinetic mechanisms, and their respective roles in the central dogmaoflife. This book provides a catalog and description of the multitude of polymerases (both DNA and RNA) that contribute to genomic replication, maintenance, and geneexpression.Evolutionhasresultedintremendouslyefficientenzymescapable ofrepeatedextremelyrapidsynthesesthathavecaptivatedresearchers’interestsfor decades. We are inspired by work that started over 60 years ago and is actively pursued today for a fundamental understanding of life, contributions to human healthanddisease,andcurrentandfuturebiotechnologyapplications.Nucleicacid polymerasesarefascinatingonanumberoflevels,yetstillcontinuetosurpriseus withnovelmodesofactionrevealedthroughongoingandfuturestudiesdescribed withinthisvolume. We wish to thank all the authors for their specific expertise and willingness to participateinthiscomprehensivereviewofnucleicacidpolymerases.Wearealso grateful to the many investigators before us (including our research mentors: Stephen Benkovic and Akira Ishihama) who began and continue this important v vi Preface lineofresearch.Webelievethisbookwillbeusefulforawiderangeofresearchers in both the early and later stages of their careers. We would be thrilled if this volumebecomesthego-toresourcefornucleicacidpolymerasestructure,function, andmechanismforyearstocome. Pittsburgh,PA MichaelA.Trakselis UniversityPark,PA KatsuhikoS.Murakami Contents 1 IntroductiontoNucleicAcidPolymerases:Families,Themes, andMechanisms. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 MichaelA.TrakselisandKatsuhikoS.Murakami 2 EukaryoticReplicativeDNAPolymerases. . . . . . . . . . . . . . . . . . . 17 ErinWalshandKristinA.Eckert 3 DNARepairPolymerases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43 RobertW.Sobol 4 EukaryoticY-FamilyPolymerases:ABiochemicaland StructuralPerspective. . . . . .. . . . .. . . . . .. . . . . .. . . . .. . . . . .. 85 JohnM.Pryor,LynneM.Dieckman,ElizabethM.Boehm, andM.ToddWashington 5 DNAPolymerasesThatPerformTemplate-IndependentDNA Synthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 109 AnthonyJ.Berdis 6 ArchaealDNAPolymerases:EnzymaticAbilities,Coordination, andUniqueProperties. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139 MichaelA.TrakselisandRobertJ.Bauer 7 EngineeredDNAPolymerases. . . . . . . . . . . . . . . . . . . . . . . . . . . . 163 RobertoLaos,RyanW.Shaw,andStevenA.Benner 8 ReverseTranscriptases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189 StuartF.J.LeGriceandMarcinNowotny 9 Telomerase:AEukaryoticDNAPolymeraseSpecialized inTelomericRepeatSynthesis. . . . . . . . . . . . . . . . . . . . . . . . . . . . 215 AndrewF.Brown,JoshuaD.Podlevsky,andJulianJ.-L.Chen 10 BacteriophageRNAPolymerases. . . . . . . . . . . . . . . . . . . . . . . . . . 237 RitwikaS.BasuandKatsuhikoS.Murakami vii viii Contents 11 MitochondrialDNAandRNAPolymerases. . . . . . . . . . . . . . . . . . 251 Y.WhitneyYin 12 EukaryoticRNAPolymeraseII. . . . . . . . . . . . . . . . . . . . . . . . . . . 277 DavidA.BushnellandRogerD.Kornberg 13 PlantMultisubunitRNAPolymerasesIVandV. . . . . . . . . . . . . . . 289 ThomasS.Ream,JeremyR.Haag,andCraigS.Pikaard 14 Structure,Dynamics,andFidelityofRNA-Dependent RNAPolymerases. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 309 DavidD.Boehr,JamieJ.Arnold,IbrahimM.Moustafa, andCraigE.Cameron Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 335 Chapter 1 Introduction to Nucleic Acid Polymerases: Families, Themes, and Mechanisms MichaelA.TrakselisandKatsuhikoS.Murakami Keywords Polymerase(cid:129)Mechanism(cid:129)Structure(cid:129)Function(cid:129)Catalysis Abbreviations CPD Cyclobutanepyrimidinedimers E.coli Escherichiacoli FDX Fidaxomicin FILS Facialdysmorphism,immunodeficiency,livedo,andshortstatures kDa Kilodaltons pol Polymerase PolI E.coliDNApolymeraseI RdRp RNA-dependentRNApolymerase Rif Rifampicin rRNA RibosomalRNA TLS Translesionsynthesis UV Ultravioletlight XPD Xerodermapigmentosum M.A.Trakselis(*) DepartmentofChemistry,UniversityofPittsburgh,Pittsburgh,PA15260,USA e-mail:[email protected] K.S.Murakami(*) DepartmentofBiochemistryandMolecularBiology,PennsylvaniaStateUniversity, UniversityPark,PA16802,USA TheCenterforRNAMolecularBiology,PennsylvaniaStateUniversity,UniversityPark, PA16802,USA e-mail:[email protected] K.S.MurakamiandM.A.Trakselis(eds.),NucleicAcidPolymerases,NucleicAcids 1 andMolecularBiology30,DOI10.1007/978-3-642-39796-7_1, ©Springer-VerlagBerlinHeidelberg2014
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