Nucleic acid polymerases

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 Janusz M Bujnicki International Institute of Molecular and Cell Biology Laboratory of Bioinformatics and Protein Engineering Trojdena 02-109 Warsaw Poland For further volumes: http://www.springer.com/series/881 ThiS is a FM Blank Page Katsuhiko S Murakami • Michael A Trakselis Editors Nucleic Acid Polymerases Editors Katsuhiko S Murakami Dept of Biochem and Mol Biology The Pennsylvania State University University Park Pennsylvania USA Michael A Trakselis Department of Chemistry University of Pittsburgh Pittsburgh Pennsylvania USA ISSN 0933-1891 ISSN 1869-2486 (electronic) ISBN 978-3-642-39795-0 ISBN 978-3-642-39796-7 (eBook) DOI 10.1007/978-3-642-39796-7 Springer Heidelberg New York Dordrecht London © Springer-Verlag Berlin Heidelberg 2014 This work is subject to copyright All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed Exempted from this legal reservation are brief excerpts in connection with reviews or scholarly analysis or material supplied specifically for the purpose of being entered and executed on a computer system, for exclusive use by the purchaser of the work Duplication of this publication or parts thereof is permitted only under the provisions of the Copyright Law of the Publisher’s location, in its current version, and permission for use must always be obtained from Springer Permissions for use may be obtained through RightsLink at the Copyright Clearance Center Violations are liable to prosecution under the respective Copyright Law The use of general descriptive names, registered names, trademarks, service marks, etc in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use While the advice and information in this book are believed to be true and accurate at the date of publication, neither the authors nor the editors nor the publisher can accept any legal responsibility for any errors or omissions that may be made The publisher makes no warranty, express or implied, with respect to the material contained herein Printed on acid-free paper Springer is part of Springer Science+Business Media (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 RNA polymerases are most noted for their active roles in controlling gene expression during transcription but can also be utilized in self-replicating ribozymes and viral replication Although the general sequence homology, structural architecture, and mechanism are conserved, they have evolved to incorporate deoxynucleotides (dNTPs) or ribonucleotides (rNTPs) explicitly Various nucleic acid polymerases have specificities for RNA or DNA templates, incorporate dNTPs 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 dogma of life This book provides a catalog and description of the multitude of polymerases (both DNA and RNA) that contribute to genomic replication, maintenance, and gene expression Evolution has resulted in tremendously efficient enzymes capable of repeated extremely rapid syntheses that have captivated researchers’ interests for 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 health and disease, and current and future biotechnology applications Nucleic acid polymerases are fascinating on a number of levels, yet still continue to surprise us with novel modes of action revealed through ongoing and future studies described within this volume We wish to thank all the authors for their specific expertise and willingness to participate in this comprehensive review of nucleic acid polymerases We are also 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 line of research We believe this book will be useful for a wide range of researchers in both the early and later stages of their careers We would be thrilled if this volume becomes the go-to resource for nucleic acid polymerase structure, function, and mechanism for years to come Pittsburgh, PA University Park, PA Michael A Trakselis Katsuhiko S Murakami Contents Introduction to Nucleic Acid Polymerases: Families, Themes, and Mechanisms Michael A Trakselis and Katsuhiko S Murakami Eukaryotic Replicative DNA Polymerases Erin Walsh and Kristin A Eckert 17 DNA Repair Polymerases Robert W Sobol 43 Eukaryotic Y-Family Polymerases: A Biochemical and Structural Perspective John M Pryor, Lynne M Dieckman, Elizabeth M Boehm, and M Todd Washington 85 DNA Polymerases That Perform Template-Independent DNA Synthesis 109 Anthony J Berdis Archaeal DNA Polymerases: Enzymatic Abilities, Coordination, and Unique Properties 139 Michael A Trakselis and Robert J Bauer Engineered DNA Polymerases 163 Roberto Laos, Ryan W Shaw, and Steven A Benner Reverse Transcriptases 189 Stuart F.J Le Grice and Marcin Nowotny Telomerase: A Eukaryotic DNA Polymerase Specialized in Telomeric Repeat Synthesis 215 Andrew F Brown, Joshua D Podlevsky, and Julian J.-L Chen 10 Bacteriophage RNA Polymerases 237 Ritwika S Basu and Katsuhiko S Murakami vii viii Contents 11 Mitochondrial DNA and RNA Polymerases 251 Y Whitney Yin 12 Eukaryotic RNA Polymerase II 277 David A Bushnell and Roger D Kornberg 13 Plant Multisubunit RNA Polymerases IV and V 289 Thomas S Ream, Jeremy R Haag, and Craig S Pikaard 14 Structure, Dynamics, and Fidelity of RNA-Dependent RNA Polymerases 309 David D Boehr, Jamie J Arnold, Ibrahim M Moustafa, and Craig E Cameron Index 335 Chapter Introduction to Nucleic Acid Polymerases: Families, Themes, and Mechanisms Michael A Trakselis and Katsuhiko S Murakami Keywords Polymerase • Mechanism • Structure • Function • Catalysis Abbreviations CPD E coli FDX FILS kDa pol Pol I RdRp Rif rRNA TLS UV XPD Cyclobutane pyrimidine dimers Escherichia coli Fidaxomicin Facial dysmorphism, immunodeficiency, livedo, and short statures Kilodaltons Polymerase E coli DNA polymerase I RNA-dependent RNA polymerase Rifampicin Ribosomal RNA Translesion synthesis Ultraviolet light Xeroderma pigmentosum M.A Trakselis (*) Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA e-mail: mtraksel@pitt.edu K.S Murakami (*) Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA The Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA e-mail: kum14@psu.edu K.S Murakami and M.A Trakselis (eds.), Nucleic Acid Polymerases, Nucleic Acids and Molecular Biology 30, DOI 10.1007/978-3-642-39796-7_1, © Springer-Verlag Berlin Heidelberg 2014 14 Structure, Dynamics, and Fidelity of RNA-Dependent RNA Polymerases 327 Arnold JJ, Cameron CE (2000) Poliovirus RNA-dependent RNA polymerase (3D(pol)) Assembly of stable, elongation-competent complexes by using a symmetrical primer-template substrate (sym/sub) J Biol Chem 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the virulence of 2009 pandemic H1N1 influenza virus in mice PLoS One 7(3): e33383 doi:10.1371/journal.pone.0033383, PONE-D-11-15459 [pii] Index A α-amanitin, 284 Archaeal DNA polymerases crenarchaeal B-family PolB1, 141–143 PolB2, 143 PolB3, 144 D-family, 145–146 vs eukaryotes, 140 euryarchaeal B-family, 144–145 PriSL primase, 149 proliferating cell nuclear antigen (PCNA) B-family polymerases, 150 complexation, 150, 151 D-family polymerases, 150 lesion bypass polymerases, 151–152 PCNA-interacting peptide (PIP) box, 150 replication and repair, coordination oligomeric DNA polymerase complexes, 152–153 participation, 155–156 thermodynamic DNA polymerase selection, 153–154 uracil read-ahead function, 155 Y-family error rate, 146–147 lesion bypass, 147–148 pyrophosphorolysis, 148–149 steric gate, 148 structural similarity, 146–147 Archaeal Y-family lesion bypass polymerase, 146–149 Artificially expanded genetic information systems (AEGIS), 177–178 B Bacteriophage RNA polymerases (RNAPs) N4 vRNAP characterization, 246 nucleotidyl transfer reaction, 247–249 structure, 246–247 unique hairpin promoter DNA recognition, 247 transcription elongation nucleotide addition cycle, 243–245 promoter release and processivity, 241–243 transition to elongation complex, 243 T7 RNAP promoter binding, 238–240 transcript initiation, 240–241 Base excision repair (BER) pathway backup DNA polymerases, 52–53 damage sources, 47 DNA polymerase β DNA damaging agents, 49 mouse embryonic fibroblasts, 50 mouse knockout, 51 posttranslational modification, 50 somatic/germline mutations, 51 structural and functional details, 48, 49 DNA polymerase γ MYH-mediated repair, 52 nonhomologous end joining, 51–52 oxidative damage, 52 long-patch BER, 47, 48 mitochondria, 258–259 mitochondrial BER, 53–54 short-patch BER, 47, 48 K.S Murakami and M.A Trakselis (eds.), Nucleic Acid Polymerases, Nucleic Acids and Molecular Biology 30, DOI 10.1007/978-3-642-39796-7, © Springer-Verlag Berlin Heidelberg 2014 335 336 B-family DNA replication polymerases crenarchaeal PolB1, 141–143 PolB2, 143 PolB3, 144 euryarchaeal, 144–145 BRCA1 C-terminal (BRCT) domain, 88, 89, 98 Bridge helix, 283 C Cap snatching, 315–316 Cognate lesions, 86–87 Compartmentalized self-replication (CSR) artificially expanded genetic information systems (AEGIS), 177–178 DNA polymerases, 179–181 history, 177 laboratory applications, 177 PCR amplification, 177, 178 Taq polymerase, heterotachous sites, 182, 183 Z:P pair, 178, 182 Crenarchaeal B-family DNA replication polymerases, 141–144 C-terminal extension (CTE), 219, 220 D D-family polymerases (PolD), archaeal-specific, 145–146 Directed evolution genetic diversity, 168, 169 genotype-phenotype linkage compartmentalized self-replication (CSR), 177–182 phage display, 182–183 screening, 176 library creation and protein sequence space, 168–170 unguided library creation, 171–172 DNA interstrand cross-links (ICLs), 63–65 DNA lesions, 87 DNA polymerases classification and function RNA-dependent, 4–5 single catalytic subunit, 2–4 conserved structures, 7–9 domain, RTs error rate, 199–200 HIV-1 RT, 197–199 low-processivity, 200 polymerization rate, 199 Index engineered (see Engineered DNA polymerases) template-dependent DNA synthesis, 110, 111 template-independent DNA synthesis double-strand breaks, 112 nonhomologous end joining, 113–114 pol β and λ, 112 pol μ, 112 primary amino acid sequence information, 123 TdT (see Terminal deoxynucleotidyl transferase (TdT)) DNA repair polymerases BER pathway (see Base excision repair (BER) pathway) double-strand break repair (see Double-strand break repair) interstrand cross-links repair, 63–64 mismatch repair pathway DNA metabolism, 62 DNA polymerase delta, 62–63 DNA replication fidelity improvement, 62 replicative polymerases δ and ε, 63 nucleotide excision repair pathway Pol δ and Pol ε, 59–61 Pol κ, 61 sub-pathways, 59 repair pathways, 46 Double-strand break repair homologous recombination pathway, 58–59 nonhomologous end joining (NHEJ) pathway DNA polymerase μ, 56 DNA polymerase β, 57–58 DNA polymerase λ, 56–57 NHEJ functioning mechanism, 54, 55 terminal deoxynucleotidyltransferase (TdT), 57 E Engineered DNA polymerases direct design fused polymerases, 166–167 guided modifications, 165–166 genotype–phenotype linkage compartmentalized self-replication (CSR), 177–182 phage display, 182–183 screening, 176 literature, 183–184 Index polymerase chain reaction (PCR), 164 protein engineering methods directed evolution, 168–172 gene shuffling/molecular breeding, 172–174 neutral drift libraries, 175–176 reconstructing evolutionary adaptive paths (REAP) approach, 174–175 Taq polymerase (Taq pol I), 164 Error-prone PCR (ePCR), 171 Eukaryotic replicative DNA polymerases composition, 19 DNA polymerase δ DNA substrates partitioning, 24 DNA synthesis, 23 high DNA synthesis fidelity, 24 homozygous mutations, 22 intrinsic kinetic properties, 24 mammalian Pol δ, 21–22 nucleotide misincorporation, 24–25 posttranslational regulation, 21–22 Schizosaccharomyces pombe, 22 structure, 22 DNA polymerase ε base substitution error rates, 27 chromosomal replication, 26 high fidelity, 27 immunodepletion, 26 vs Pol δ, 26 posttranslational regulation, 27–28 structure, 25–26 future aspects, 32 polymerase α-primase catalytic activities, 19 chromosomal replication, 18 moderately accurate polymerase, 20–21 posttranslational regulation, 21 p49 subunit, 19, 20 short RNA-DNA primers synthesis, 20 structure, 18 replication fork cell cycle checkpoint responses, 30–32 leading and lagging strands, 28–30 replication initiation, 28 Eukaryotic RNA polymerase II See Yeast RNA pol II Euryarchaeal B-family DNA replication polymerases, 144–145 F Fialuridine (1-(2-deoxy-2-fluoro-b-Darabinofuranosyl)-5-iodouracil (FIAU), 261–262 337 Fork loop, 283 Fused polymerases, 166–167 G Gene shuffling history, 172, 173 laboratory applications, 173–174 natural evolution, 173 Genotype–phenotype linkage compartmentalized self-replication (CSR) artificially expanded genetic information systems (AEGIS), 177–178 DNA polymerases, 179–181 history, 177 laboratory applications, 177 PCR amplification, 177, 178 Taq polymerase, heterotachous sites, 182, 183 Z:P pair, 178, 182 phage display, 182–183 screening, 176 H HIV-1 RT error rate, 199–200 nonnucleoside RT inhibitors (NNRTIs), 200 p51 subunit, 196 RNase H, 203–206 structure, 197–198 termination mechanism, 194 I Insertion in fingers domain (IFD), 220 L Library creation, directed evolution protein sequence space, 168–170 unguided, 171–172 Lid loop, 283 Long-patch BER (LP-BER), 47, 48, 258 M Minus-strand ssRNA viruses, 315–316 Mismatch repair (MMR) pathway DNA metabolism, 62 DNA polymerase delta, 62–63 DNA replication fidelity improvement, 62 replicative polymerases δ and ε, 63 338 Mitochondria DNA replication asymmetrical synthesis mechanism, 252–254 conventional mode, 252 displacement mode, 252 fungi, 254 human mitochondrial DNA, 252, 253 pol γ (see Polmerase γ holoenzyme) oxidative phosphorylation, 252 RNA transcription gene expression, ATP, 269 gene structure, 264–265 HMG proteins, 266 Mtf1, 266 mtRNAP, 267, 268 oxidative mtDNA damage, 269 promoter-specific transcription, 267 Rpo41, 265–266, 268 TFAM, 266 TFB1M and TFBM2, 266, 267 T7 RNAP, 267 Molecular breeding See Gene shuffling N Neutral drift libraries, 175–176 Nonhomologous end joining (NHEJ) pathway base excision repair (BER) pathway, 51–52 double-strand break repair DNA polymerase μ, 56 DNA polymerase β, 57–58 DNA polymerase λ, 56–57 NHEJ functioning mechanism, 54, 55 terminal deoxynucleotidyltransferase (TdT), 57 template-independent DNA synthesis, 113–114 Non-LTR retrotransposition mechanism, 195 Nucleic acid polymerases classification and function DNA polymerase, 2–5 RNA polymerase, 5–6 conserved structures DNA polymerase, 7–9 RNA polymerase, 10 discovery, family members, 2, future applications, 12–13 implications, disease/therapy, 11–12 Index Nucleoside/nucleotide reverse transcriptase inhibitors (NRTIs) clinical manifestations, 259 drug toxicity, 260, 261 HIV and HBV, 260–262 Nucleotide addition cycle nucleoside triphosphates (NTPs), 243 substrate loading, catalytic site, 244 substrate selection, pre-insertion site, 244 translocation, 245 Nucleotide excision repair (NER) pathway DNA polymerases Pol δ and Pol ε, 59–61 Pol κ, 61 sub-pathways, 59 N4 vRNAP characterization, 246 nucleotidyl transfer reaction, 247–249 structure, 246–247 unique hairpin promoter DNA recognition, 247 P PCNA-interacting peptide (PIP) box, 150 Phage display, 182–183 Plus-sense single stranded (ss) RNA viruses, 315 Poliovirus (PV) RdRp catalytic mechanism, 320–322 crystal structures, 318–320 dynamics Gly64Ser substitution, 322–325 MD simulations, 323, 325 NMR and mutational studies, 326 role of, 324 structure–function paradigm, 326 X-ray crystallography, 323, 324 kinetic mechanism chemistry, 317–318 nucleotide addition cycle, 316–317 pre-chemistry conformational change, 317–320 symmetrical primer–template RNA substrate, 316 structural differences, 316 viral pathogenesis and virulence, 322 Polmerase γ holoenzyme in mitochondrial DNA repair, 258–259 mutations Alpers syndrome, 263–264 MELAS, 264 Index oxidative damage, 264 progressive external ophthalmoplegia, 263 NRTIs clinical manifestations, 259 drug toxicity, 260, 261 HIV and HBV, 260–262 pol γA AID subdomain, 254–255 vs bacteriophage T7 DNA polymerase, 255–256 enzymatic activities, 253 IP subdomain, 254 vs pol γB, 257 pol γB interaction, 255 spacer domain, 254 pol γB functions, 253–254 Pol γA–distal Pol γB monomer, 257–258 processivity, 256–257 species-dependent variation, 257 Polymerase-associated domain (PAD), 87, 88, 91, 92 Posttranslational regulation DNA polymerase δ, 21–22 DNA polymerase ε, 27–28 polymerase α-primase, 21 PriSL primase, 149 Proliferating cell nuclear antigen (PCNA) B-family polymerases, 150 complexation, 150, 151 D-family polymerases, 150 DNA polymerase δ, 23 lesion bypass polymerases, 151–152 PCNA-interacting peptide (PIP) box, 150 Y-family polymerase interaction ubiquitin-modified PCNA, 98–99 umodified PCNA, 96–98 Protein engineering method directed evolution library creation and protein sequence space, 168–170 unguided library creation, 171–172 gene shuffling/molecular breeding history, 172, 173 laboratory applications, 173–174 natural evolution, 173 neutral drift libraries, 175–176 reconstructing evolutionary adaptive paths (REAP) approach, 174–175 339 R Reconstructing evolutionary adaptive paths (REAP) approach, 174–175 Replication factor C (RFC), 23 Retrotransposition mechanism, non-LTR elements See Non-LTR retrotransposition mechanism Retrotransposons, 190 Reverse transcriptases (RTs) connection and RNase H domains cellular types, 201 metal ion-assisted catalysis, 203 nucleic acid substrate, 203–204 phosphate-binding pocket, 202–203 definition, 190 DNA polymerase domain error rate, 199–200 HIV-1 RT, 197–199 low-processivity, 200 polymerization rate, 199 non-LTR retrotransposition mechanism, 195 retrotransposons, 190 retroviruses, 190 substrate binding and coordination, 204–206 subunit organization alpharetroviruses, 196 monomeric and dimeric, 196–197 TERT, 219–220 viral DNA synthesis, LTR elements central termination, 194–195 polypurine tract-primed (+) strand DNA synthesis, 193 (-) strand strong-stop DNA synthesis and strand transfer, 193 tRNA-primed (-) DNA synthesis, 191, 193 tRNA primer removal and (+) strand DNA transfer, 193–194 Rev1-interacting region (RIR), 89, 101 Ribonucleoprotein (RNP) core composition, 217 evolutionary aspects, 224–225 RNA-dependent DNA polymerase, 4–5 RNA-dependent RNA polymerase (RdRp) antiviral therapies, 311 biophysical techniques, 311–312 catalytic mechanism, 320–322 conformational changes, 311 dynamics 340 Gly64Ser substitution, 322–325 MD simulations, 323, 325 NMR and mutational studies, 326 role of, 324 structure–function paradigm, 326 X-ray crystallography, 323, 324 internal protein motions, 311 intrinsic genetic variation, 311 kinetic mechanism chemistry, 317–318 nucleotide addition cycle, 316–317 pre-chemistry conformational change, 317–320 symmetrical primer–template RNA substrate, 316 nucleotide incorporation fidelity, 310–311 structural architecture domains, 312 initiation mechanisms, 312–314 motifs and functional importance, 312, 314 structural differences dsRNA viruses, 316 minus-strand ssRNA viruses, 315–316 plus-sense single stranded (ss), 315 viral pathogenesis and virulence, 322, 323 RNA polymerase classification and function, 5–6 conserved structures, 10 RNase H domains cellular types, 201 metal ion-assisted catalysis, 203 nucleic acid substrate, 203–204 phosphate-binding pocket, 202–203 Rudder loop, 283 S Short-patch BER, 47, 48 Single-nucleotide BER (SN-BER), 258 Solvent deuterium kinetic isotope effects (SDKIE), 317–318 T Taq polymerase (Taq pol I) DNA polymerase I, 164, 165 fused polymerase, 166–167 heterotachous sites, 182, 183 TATA-binding protein 214 (TBP), 285, 286 Telomerase anticancer therapeutics, 229–230 catalytic cycle, 217, 218 mechanism Index duplex binding, 229 duplex dissociation, 227 nucleotide addition, 225–227 strand separation, 228 template realignment, 229 ribonucleoprotein (RNP) core composition, 217 evolutionary aspects, 224–225 telomerase reverse transcriptase (TERT) C-terminal extension (CTE), 219, 220 reverse transcriptase (RT), 219–220 telomerase essential N-terminal (TEN), 218, 219 telomerase RNA-binding domain (TRBD), 219 telomerase RNA (TR) conserved core, 221, 222 H/ACA domain, 223 pseudoknot and stem-loop moiety, 221–222 template boundary element (TBE), 223 yeast and filamentous fungi, 222–224 telomeres, 216 Telomerase essential N-terminal (TEN), 218, 219 Telomerase reverse transcriptase (TERT) C-terminal extension (CTE), 219, 220 reverse transcriptases (RTs), 219–220 telomerase essential N-terminal (TEN), 218, 219 telomerase RNA-binding domain (TRBD), 219 Telomerase RNA (TR) conserved core, 221, 222 H/ACA domain, 223 pseudoknot and stem-loop moiety, 221–222 template boundary element (TBE), 223 yeast and filamentous fungus, 222–224 Telomerase RNA-binding domain (TRBD), 219 Telomeres, 216 Template-dependent DNA synthesis, 110, 111 Template-independent DNA synthesis DNA polymerases double-strand breaks, 112 nonhomologous end joining, 113–114 pol β and λ, 112 pol μ, 112 primary amino acid sequence information, 123 TdT (see Terminal deoxynucleotidyl transferase (TdT)) Index double-strand breaks, 112 primary amino acid sequence information, 123 Terminal deoxynucleotidyl transferase (TdT) biochemical applications, 130 cancer acute lymphocytic leukemia, 127 anticancer agents, 127–128 chronic lymphocytic leukemia, 127 3-Eth-5-NIdR, 128–129 merkel cell carcinoma, 129–130 5-nitroindolyl-20 -deoxynucleoside triphosphate, 128 prognosis and survival, 127 enzymatic properties of, 119–120 kinetic mechanism conformational changes, 121 ordered substrate binding, 120 product release, 120–121 regulation of PCNA interaction, 127 posttranslational regulation, 126 protein–protein interactions, 126–127 sources and purification, 118–119 tertiary structure amino acids, 126 crystal structure, 123, 124 metal ions, 123 subdomains, 124, 125 Transcription elongation, RNAPs nucleotide addition cycle nucleoside triphosphates (NTPs), 243 substrate loading, catalytic site, 244 substrate selection, pre-insertion site, 244 translocation, 245 promoter release and processivity N-terminal domain (NTD), 241 RNA exit channel formation, 241, 243 transition to elongation complex, 243 Translesion synthesis (TLS), 86 T7 RNAP promoter binding, 238–240 transcript initiation, 240–241 U Ubiquitin-binding motif (UBM), 89, 98 Ubiquitin-binding zinc finger (UBZ), 89, 99 Ubiquitin-modified PCNA, 98–99 Unmodified PCNA, 96–98 341 V Viral DNA synthesis and reverse transcription central termination, 194–195 polypurine tract-primed (+) strand DNA synthesis, 193 () strand strong-stop DNA synthesis and strand transfer, 193 tRNA-primed () DNA synthesis, 191, 193 tRNA primer removal and (+) strand DNA transfer, 193–194 Virion protein genome (VPg), 315 W Werner syndrome protein (WRN), 25 X X-family DNA polymerases template-independent DNA synthesis nonhomologous end joining, 113–114 pol β and λ, 112 pol μ, 112 primary amino acid sequence information, 123 TdT (see Terminal deoxynucleotidyl transferase (TdT)) V(D)J recombination, 115–117 Y Yeast RNA pol II electron density map, 278 synchrotrons, 278 ten-subunit pol II, yeast, 278, 279 transcribing complex α-amanitin, 284 bridge helix, 283 DNA-RNA hybrid, 279, 280 fork loop, 283 magnesium ions and NTP entry site, 280 pol II-TFIIB complex, 284–286 post-translocation complex, 280 pre-translocation complex, 280 Rpb4 and Rpb7 subunits, 283–284 rudder and lid loop, 283 structure, 279 tailed template, 278 trigger loop, 280–282 342 Y-family polymerases catalytic activity core regions and active sites, 92 DNA polymerase η, 90–91 DNA polymerase ι, 91, 93 DNA polymerase κ, 93–94 Rev1, 95–96 cognate lesions, 86–87 DNA lesions, 87 interactions DNA polymerase η, 100–101 protein–protein interactions, 100 Rev1, 101–102 ubiquitin-modified PCNA, 98–99 unmodified PCNA, 96–98 Index lesion bypass error rate, 146–147 lesion bypass, 147–148 PCNA, 151–152 pyrophosphorolysis, 148–149 steric gate, 148 structural similarity, 146–147 structures of BRCA1 C-terminal domain, 88 C-terminal regions, 87–88 domains, 87 full-length Y-family polymerases, 89–90 translesion synthesis, 86