Structure and mechanism of DNA polymerases

Abbotts, 1988, Expression of human DNA polymerase β in Escherichia coli and characterization of the recombinant enzyme, Biochemistry, 27, 901, 10.1021/bi00403a010 Ahn, 1997, DNA polymerase β: Structure‐fidelity relationship from pre‐steady‐state kinetic analyses of all possible correct and incorrect base pairs for wild type and R283A mutant, Biochemistry, 36, 1100, 10.1021/bi961653o Andricioaei, 2004, Dependence of DNA polymerase replication rate on external forces: A model based on molecular dynamics simulations, Biophys. J., 87, 1478, 10.1529/biophysj.103.039313 Astatke, 1995, Deoxynucleoside triphosphate and pyrophosphate binding sites in the catalytically competent ternary complex for the polymerase reaction catalyzed by DNA polymerase I (Klenow fragment), J. Biol. Chem., 270, 1945, 10.1074/jbc.270.4.1945 Basu, 1987, Identification and amino acid sequence of the deoxynucleoside triphosphate binding site in Escherichia coli DNA polymerase I, Biochemistry, 26, 1704, 10.1021/bi00380a032 Beese, 1993, Structure of DNA polymerase I Klenow fragment bound to duplex DNA, Science, 260, 352, 10.1126/science.8469987 Beese, 1993, Crystal structures of the Klenow fragment of DNA polymerase I complexed with deoxynucleoside triphosphate and pyrophosphate, Biochemistry, 32, 14095, 10.1021/bi00214a004 Bork, 1997, A superFamily of conserved domains in DNA damage‐responsive cell cycle checkpoint proteins, FASEB J., 11, 68, 10.1096/fasebj.11.1.9034168 Boudsocq, 2001, Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): An archaeal DNA polymerase with lesion‐bypass properties akin to eukaryotic pol η, Nucleic Acids Res., 15, 4607, 10.1093/nar/29.22.4607 Braithwaite, 1993, Compilation, alignment, and phylogenetic relationships of DNA polymerases, Nucleic Acids Res., 21, 787, 10.1093/nar/21.4.787 Bruskov, 1979, On molecular mechanisms of nucleic acid synthesis. Fidelity aspects: 2. Contribution of protein‐nucleotide recognition, J. Theor. Biol., 78, 29, 10.1016/0022-5193(79)90323-0 Burgers, 2001, Eukaryotic DNA polymerases: Proposal for a revised nomenclature, J. Biol. Chem., 276, 43487, 10.1074/jbc.R100056200 Cann, 1998, A heterodimeric DNA polymerase: Evidence that members of Euryarchaeota possess a distinct DNA polymerase, Proc. Natl. Acad. Sci. USA, 95, 14250, 10.1073/pnas.95.24.14250 Capson, 1992, Kinetic characterization of the polymerase and exonuclease activities of the gene 43 protein of bacteriophage T4, Biochemistry, 31, 10984, 10.1021/bi00160a007 Carroll, 1991, A mutant of DNA polymerase I (Klenow Fragment) with reduced fidelity, Biochemistry, 30, 804, 10.1021/bi00217a034 Dahlberg, 1991, Kinetic mechanism of DNA polymerase I (Klenow fragment): Identification of a second conformational change and evaluation of the internal equilibrium constant, Biochemistry, 30, 4835, 10.1021/bi00234a002 Das, 2004, The crystal structure of the monomeric reverse transcriptase from Moloney murine leukemia virus, Structure, 12, 819, 10.1016/j.str.2004.02.032 Delarue, 1990, An attempt to unify the structure of polymerases, Protein Eng., 3, 461, 10.1093/protein/3.6.461 Dianov, 2003, Repair of abasic sites in DNA, Mutat. Res., 531, 157, 10.1016/j.mrfmmm.2003.09.003 Ding, 1998, Structure and functional implications of the polymerase active site region in a complex of HIV‐1 RT with a double‐stranded DNA template‐primer and an antibody Fab fragment at 2.8 Å resolution, J. Mol. Biol., 284, 1095, 10.1006/jmbi.1998.2208 Ding, 1995, Structure of HIV‐1 RT/TIBO R 86183 complex reveals similarity in the binding of diverse nonnucleoside inhibitors, Nat. Struct. Biol., 2, 407, 10.1038/nsb0595-407 Ding, 1995, Structure of HIV‐1 reverse transcriptase in a complex with the non‐nucleoside inhibitor alpha‐APA R 95845 at 2.8 Å resolution, Structure, 3, 365, 10.1016/S0969-2126(01)00168-X Divita, 1995, Dimerization kinetics of HIV‐1 and HIV‐2 reverse transcriptase: A two step process, J. Mol. Biol., 245, 508, 10.1006/jmbi.1994.0042 Divita, 1995, Conformational stability of dimeric HIV‐1 and HIV‐2 reverse transcriptases, Biochemistry, 34, 16337, 10.1021/bi00050a014 Dominguez, 2000, DNA polymerase μ (Pol μ), homologous to TdT, could act as a DNA mutator in eukaryotic cells, EMBO J., 19, 1731, 10.1093/emboj/19.7.1731 Dong, 1993, Mutational studies of human DNA polymerase α: Identification of residues critical for deoxynucleotide binding and misinsertion fidelity of DNA synthesis, J. Biol. Chem., 268, 24163, 10.1016/S0021-9258(20)80506-7 Donlin, 1991, Kinetic partitioning between the exonuclease and polymerase sites in DNA error correction, Biochemistry, 30, 538, 10.1021/bi00216a031 Doublie, 1998, Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution, Nature, 391, 251, 10.1038/34593 Dunlap, 2002, Use of 2‐aminopurine and tryptophan fluorescence as probes in kinetic analyses of DNA polymerase β, Biochemistry, 41, 11226, 10.1021/bi025837g Echols, 1991, Fidelity mechanism in DNA replication, Annu. Rev. Biochem., 60, 477, 10.1146/annurev.bi.60.070191.002401 Eger, 1992, Minimal kinetic mechanism for misincorporation by DNA polymerase I (Klenow fragment), Biochemistry, 31, 9227, 10.1021/bi00153a016 Engel, 1978, D(M6ATP) as a probe of the fidelity of base incorporation into polynucleotides by Escherichia coli DNA polymerase I, J. Biol. Chem., 253, 935, 10.1016/S0021-9258(17)38194-2 Eom, 1996, Structure of Taq ploymerase with DNA at the polymerase active site, Nature, 382, 278, 10.1038/382278a0 Esnouf, 1995, Mechanism of inhibition of HIV‐1 reverse transcriptase by non‐nucleoside inhibitors, Nat. Struct. Biol., 2, 303, 10.1038/nsb0495-303 Fiala, 2004, Mechanism of DNA polymerization catalyzed by Sulfolobus solfataricus P2 DNA polymerase IV, Biochemistry, 43, 2116, 10.1021/bi035746z Fiala, 2004, Pre‐steady‐state kinetic studies of the fidelity of Sulfolobus solfataricus P2 DNA polymerase IV, Biochemistry, 43, 2106, 10.1021/bi0357457 Franklin, 2001, Structure of the replicating complex of a pol α Family DNA polymerase, Cell, 105, 657, 10.1016/S0092-8674(01)00367-1 Freemont, 1988, Cocrystal structure of an editing complex of Klenow fragment with DNA, Proc. Natl. Acad. Sci. USA, 85, 8924, 10.1073/pnas.85.23.8924 Frey, 1995, The nucleotide analog 2‐aminopurine as a spectroscopic probe of nucleotide incorporation by the Klenow fragment of Escherichia coli polymerase I and bacteriophage T4 DNA polymerase, Biochemistry, 34, 9185, 10.1021/bi00028a031 Friedberg, 2000, The many faces of DNA polymerases: Strategies for mutagenesis and for mutational avoidance, Proc. Natl. Acad. Sci. USA, 97, 5681, 10.1073/pnas.120152397 Friedberg, 1999, Novel DNA polymerases offer clues to the molecular basis of mutagenesis, Cell, 98, 413, 10.1016/S0092-8674(00)81970-4 Garcia‐Diaz, 2000, DNA polymerase λ (Pol λ), a novel eukaryotic DNA polymerase with a potential role in meiosis, J. Mol. Biol., 301, 851, 10.1006/jmbi.2000.4005 Gillin, 1976, Control of mutation frequency by bacteriophage T4 DNA polymerase: II. Accuracy of nucleotide selection by the L88 mutator, CB120 antimutator, and wild type phage T4 DNA polymerases, J. Biol. Chem., 251, 5225, 10.1016/S0021-9258(17)33150-2 Goodman, 2000, Sloppier copier DNA polymerases involved in genome repair, Curr. Opin. Genet. Dev., 10, 162, 10.1016/S0959-437X(00)00057-5 Gotte, 1999, HIV‐1 reverse transcription: A brief overview focused on structure‐function relationships among molecules involved in initiation of the reaction, Arch. Biochem. Biophys., 365, 199, 10.1006/abbi.1999.1209 Greider, 1985, Identification of a specific telomere terminal transferase activity in Tetrahymena extracts, Cell, 43, 405, 10.1016/0092-8674(85)90170-9 Greider, 1989, A telomeric sequence in the RNA of Tetrahymena telomerase required for telomere repeat synthesis, Nature, 337, 331, 10.1038/337331a0 Guajardo, 1997, A model for the mechanism of polymerase translocation, J. Mol. Biol., 265, 8, 10.1006/jmbi.1996.0707 Hashimoto, 2001, Crystal structure of DNA polymerase from hyperthermophilic archaeon Pyrococcus kodakaraensis KOD1, J. Mol. Biol., 306, 469, 10.1006/jmbi.2000.4403 Hogg, 2004, Crystallographic snapshots of a replicative DNA polymerase encountering an abasic site, EMBO J., 23, 1483, 10.1038/sj.emboj.7600150 Hopfner, 1999, Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius, Proc. Natl. Acad. Sci. USA, 96, 3600, 10.1073/pnas.96.7.3600 Hsieh, 1993, Kinetic mechanism of the DNA‐dependent DNA polymerase activity of human immunodeficiency virus reverse transcriptase, J. Biol. Chem., 268, 24607, 10.1016/S0021-9258(19)74509-8 Hsiou, 1996, Structure of unliganded HIV‐1 reverse transcriptase at 2.7 Å resolution: Implications of conformational changes for polymerization and inhibition mechanisms, Structure, 4, 853, 10.1016/S0969-2126(96)00091-3 Huang, 1998, Structure of a covalently trapped catalytic complex of HIV‐1 reverse transcriptase: Implications for drug resistance, Science, 282, 1669, 10.1126/science.282.5394.1669 Ito, 1991, Compilation and alignment of DNA polymerase sequences, Nucl. Acids Res., 19, 4045, 10.1093/nar/19.15.4045 Jacobo‐Molina, 1993, Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double‐stranded DNA at 3.0 Å resolution shows bent DNA, Proc. Natl. Acad. Sci. USA, 90, 6320, 10.1073/pnas.90.13.6320 Jaeger, 1998, The structure of HIV‐1 reverse transcriptase complexed with an RNA pseudoknot inhibitor, EMBO J., 17, 4535, 10.1093/emboj/17.15.4535 Jezewska, 2002, Dynamics of gapped DNA recognition by human polymerase β, J. Biol. Chem., 277, 20316, 10.1074/jbc.M200918200 Jezewska, 2001, Energetics and specificity of Rat DNA polymerase β interactions with template‐primer and gapped DNA substrates, J. Biol. Chem., 276, 16123, 10.1074/jbc.M010434200 Jezewska, 2001, Interactions of the 8‐kDa domain of rat DNA polymerase β with DNA, Biochemistry, 40, 3295, 10.1021/bi002749s Johnson, 1999, Bridging the gap: A family of novel DNA polymerases that replicate faulty DNA, Proc. Natl. Acad. Sci. USA, 96, 12224, 10.1073/pnas.96.22.12224 Joyce, 1994, Function and structure relationships in DNA polymerases, Annu. Rev. Biochem., 63, 777, 10.1146/annurev.bi.63.070194.004021 Kati, 1992, Mechanism and fidelity of HIV reverse transcriptase, J. Biol. Chem., 267, 25988, 10.1016/S0021-9258(18)35706-5 Kelman, 1995, DNA polymerase III holoenzyme: Structure and function of a chromosomal replicating machine, Ann. Rev. Biochem., 64, 171, 10.1146/annurev.bi.64.070195.001131 Kensch, 2000, Temperature‐dependent equilibrium between the open and closed conformation of the p66 subunit of HIV‐1 reverse transcriptase revealed by site‐directed spin labelling, J. Mol. Biol., 301, 1029, 10.1006/jmbi.2000.3998 Kiefer, 1998, Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal, Nature, 391, 304, 10.1038/34693 Kim, 2003, Rapid segmental and subdomain motions of DNA polymerase β, J. Biol. Chem., 278, 5072, 10.1074/jbc.M208472200 Kim, 1995, Crystal structure of Thermus aquaticus DNA polymerase, Nature, 376, 612, 10.1038/376612a0 Klenow, 1970, Proteolytic cleavage of DNA polymerase from Escherichia coli B into an exonuclease unit and a polymerase unit, FEBS Lett., 6, 25, 10.1016/0014-5793(70)80032-1 Kohlstaedt, 1992, Crystal structure at 3.5 A resolution of HIV‐1 reverse transcriptase complexed with an inhibitor, Science, 256, 1783, 10.1126/science.1377403 Kornberg, 1980 Kornberg, 1992 Kornberg, 1956, Enzymic synthesis of deoxyribonucleic acid, Biochim. Biophys. Acta, 21, 197, 10.1016/0006-3002(56)90127-5 Korolev, 1995, Crystal structure of the large fragment of Thermus aquaticus DNA polymerase I at 2.5 A resolution: Structural basis for thermostability, Proc. Natl. Acad. Sci. USA, 92, 9264, 10.1073/pnas.92.20.9264 Krahn, 2003, Structure of DNA polymerase β with the mutagenic DNA lesion 8‐oxodeoxyguanine reveals structural insights into its coding potential, Structure, 11, 121, 10.1016/S0969-2126(02)00930-9 Kraynov, 1997, DNA polymerase β: Analysis of the contributions of tyrosine‐271 and asparagine‐279 to substrate specificity and fidelity of DNA replication by pre‐steady‐state kinetics, Biochem. J., 323, 103, 10.1042/bj3230103 Kuchta, 1988, Kinetic mechanism whereby DNA polymerase I (Klenow) replicates DNA with high fidelity, Biochemistry, 27, 6716, 10.1021/bi00418a012 Kuchta, 1987, Kinetic mechanism of DNA polymerase I (Klenow), Biochemistry, 26, 8410, 10.1021/bi00399a057 Kumar, 1990, Identification and properties of the catalytic domain of mammalian DNA polymerase β, Biochemistry, 29, 7156, 10.1021/bi00483a002 Lehman, 1958, Enzymatic synthesis of deoxyribonucleic acid: V. Chemical composition of enzymatically synthesized deoxyribonucleic acid, Proc. Natl. Acad. Sci. USA, 44, 1191, 10.1073/pnas.44.12.1191 Li, 2004, Nucleotide insertion opposite a cis‐syn thymine dimer by a replicative DNA polymerase from bacteriophage T7, Nat. Struct. Mol. Biol., 11, 784, 10.1038/nsmb792 Li, 1998, Crystal structures of the Klenow fragment of Thermus aquaticus DNA polymerase I complexed with deoxyribonucleoside triphosphates, Protein Sci., 7, 1116, 10.1002/pro.5560070505 Li, 1998, Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: Structural basis for nucleotide incorporation, EMBO J., 17, 7514, 10.1093/emboj/17.24.7514 Li, 2001, Crystal structures of a ddATP‐, ddTTP‐, ddCTP‐, and ddGTP‐trapped ternary complex of Klentaq1: Insights into the nucleotide incorporation and selectivity, Protein Sci., 10, 1225, 10.1110/ps.250101 Li, 2001, Structural studies of the Klentaq1 DNA polymerase, Curr. Organic Chem., 5, 871, 10.2174/1385272013375067 Lin, 1994, Isolation, characterization, and kinetic properties of truncated forms of T4 DNA polymerase that exhibit 3′‐5′ exonuclease activity, J. Biol. Chem., 269, 19286, 10.1016/S0021-9258(17)32165-8 Ling, 2003, Replication of a cis‐syn thymine dimer at atomic resolution, Nature, 424, 1083, 10.1038/nature01919 Ling, 2001, Crystal structure of a Y‐Family DNA polymerase in action: A mechanism for error‐prone and lesion‐bypass replication, Cell, 107, 91, 10.1016/S0092-8674(01)00515-3 Ling, 2004, Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase, Proc. Natl. Acad. Sci. USA, 101, 2265, 10.1073/pnas.0308332100 Loeb, 1982, Fidelity of DNA synthesis, Ann. Rev. Biochem., 52, 429, 10.1146/annurev.bi.51.070182.002241 Lu, 2004, Closing of the fingers domain generates motor forces in the HIV reverse transcriptase, J. Biol. Chem., 279, 54529, 10.1074/jbc.M407193200 Madrid, 1999, Major subdomain rearrangement in HIV‐1 reverse transcriptase simulated by molecular dynamics, Proteins, 35, 332, 10.1002/(SICI)1097-0134(19990515)35:3<332::AID-PROT7>3.0.CO;2-R Maier, 2000, Replication by a single DNA polymerase of a stretched single‐stranded DNA, Proc. Natl. Acad. Sci. USA, 97, 12002, 10.1073/pnas.97.22.12002 Martins, 1994, Genetic identification and nucleotide sequence of the DNA polymerase gene of African swine fever virus, Nucleic Acids Res., 22, 208, 10.1093/nar/22.2.208 Matsumoto, 1991, Repair of a synthetic abasic site involves concerted reactions of DNA synthesis followed by excision and ligation, Mol. Cell. Biol., 11, 4441, 10.1128/MCB.11.9.4441 Matsumoto, 1995, Excision of deoxyribose phosphate residues by DNA polymerase β during DNA repair, Science, 269, 699, 10.1126/science.7624801 Nair, 2004, Replication by human DNA polymerase‐ι occurs by Hoogsteen base‐pairing, Nature, 430, 377, 10.1038/nature02692 Ollis, 1985, Structure of large fragment of Escherichia coli DNA polymerase I complexed with dTMP, Nature, 313, 762, 10.1038/313762a0 Pata, 2004, Structure of HIV‐1 reverse transcriptase bound to an inhibitor active against mutant reverse transcriptases resistant to other nonnucleoside inhibitors, Proc. Natl. Acad. Sci. USA, 101, 10548, 10.1073/pnas.0404151101 Patel, 1991, Pre‐steady‐state kinetic analysis of processive DNA replication including complete characterization of an exonuclease‐deficient mutant, Biochemistry, 30, 511, 10.1021/bi00216a029 Pavlov, 1994, Binding specificity of T4 DNA polymerase to RNA, J. Biol. Chem., 269, 12968, 10.1016/S0021-9258(18)99970-9 Pelletier, 1994, Structures of ternary complexes of rat DNA polymerase β, a DNA template‐primer, and ddCTP, Science, 264, 1891, 10.1126/science.7516580 Pelletier, 1996, Crystal structures of human DNA polymerase β complexed with DNA: Implications for catalytic mechanism, processivity, and fidelity, Biochemistry, 35, 12742, 10.1021/bi952955d Petruska, 1986, Comparison of nucleotide interactions in water, proteins, and vacuum: Model for DNA polymerase fidelity, Proc. Natl. Acad. Sci. USA, 83, 1559, 10.1073/pnas.83.6.1559 Prasad, 1993, Yeast open reading frame YCR14C encodes a DNA β‐polymerase‐like enzyme, Nucl. Acids Res., 21, 5301, 10.1093/nar/21.23.5301 Purohit, 2003, Use of 2‐aminopurine fluorescence to examine conformational changes during nucleotide incorporation by DNA polymerase I (Klenow fragment), Biochemistry, 42, 10200, 10.1021/bi0341206 Rajendran, 1998, Human DNA polymerase β recognizes single‐stranded DNA using two different binding modes, J. Biol. Chem., 273, 31021, 10.1074/jbc.273.47.31021 Rajendran, 2001, Recognition of template‐primer and gapped DNA substrates by the human DNA polymerase β, J. Mol. Biol., 308, 477, 10.1006/jmbi.2001.4571 Ren, 2002, Structure of HIV‐2 reverse transcriptase at 2.35‐Å resolution and the mechanism of resistance to non‐nucleoside inhibitors, Proc. Natl. Acad. Sci. USA, 99, 14410, 10.1073/pnas.222366699 Ren, 1995, High resolution structures of HIV‐1 RT from four RT‐inhibitor complexes, Nat. Struct. Biol., 2, 293, 10.1038/nsb0495-293 Ren, 1998, Crystal structures of HIV‐1 reverse transcriptase in complex with carboxanilide derivatives, Biochemistry, 37, 14394, 10.1021/bi981309m Ren, 2004, Crystal structures of HIV‐1 reverse transcriptases mutated at codons 100, 106 and 108 and mechanisms of resistance to non‐nucleoside inhibitors, J. Mol. Biol., 336, 569, 10.1016/j.jmb.2003.12.055 Rittinger, 1995, Human immunodeficiency virus reverse transcriptase substrate‐induced conformational changes and the mechanism of inhibition by nonnucleoside inhibitors, Proc. Natl. Acad. Sci. USA, 92, 8046, 10.1073/pnas.92.17.8046 Rodgers, 1995, The structure of unliganded reverse transcriptase from the human immunodeficiency virus type 1, Proc. Natl. Acad. Sci. USA, 92, 1222, 10.1073/pnas.92.4.1222 Rodriguez, 2000, Crystal structure of a pol α Family DNA polymerase from the hyperthermophilic archaeon Thermococcus sp. 9 degrees N‐7, J. Mol. Biol., 299, 447, 10.1006/jmbi.2000.3728 Roth, 1985, Purification and characterization of murine retroviral reverse transcriptase expressed in Escherichia coli, J. Biol. Chem., 260, 9326, 10.1016/S0021-9258(17)39369-9 Rothwell, 2003, Multiparameter single‐molecule fluorescence spectroscopy reveals heterogeneity of HIV‐1 reverse transcriptase:primer/template complexes, Proc. Natl. Acad. Sci. USA, 100, 1655, 10.1073/pnas.0434003100 Sarafianos, 2002, Structures of HIV‐1 reverse transcriptase with pre‐ and post‐translocation AZTMP‐terminated DNA, EMBO J., 21, 6614, 10.1093/emboj/cdf637 Sarafianos, 2001, Crystal structure of HIV‐1 reverse transcriptase in complex with a polypurine tract RNA:DNA, EMBO J., 20, 1449, 10.1093/emboj/20.6.1449 Sawaya, 1994, Crystal structure of rat DNA polymerase β: Evidence for a common polymerase mechanism, Science, 264, 1930, 10.1126/science.7516581 Sawaya, 1997, Crystal structures of human DNA polymerase β complexed with gapped and nicked DNA: Evidence for an induced fit mechanism, Biochemistry, 36, 11205, 10.1021/bi9703812 Shah, 2003, Variants of DNA polymerase β extend mispaired DNA due to increased affinity for nucleotide substrate, Biochemistry, 42, 10709, 10.1021/bi034885d Silvian, 2001, Crystal structure of a DinB Family error‐prone DNA polymerase from Sulfolobus solfataricus, Nat. Struct. Biol., 8, 984, 10.1038/nsb1101-984 Sloane, 1988, The fidelity of base selection by the polymerase subunit of DNA polymerase III holoenzyme, Nucleic Acids Res., 16, 6465, 10.1093/nar/16.14.6465 Sluis‐Cremer, 2000, Molecular mechanisms of HIV‐1 resistance to nucleoside reverse transcriptase inhibitors (NRTIs), Cell Mol. Life Sci., 57, 1408, 10.1007/PL00000626 Smerdon, 1994, Structure of the binding site for nonnucleoside inhibitors of the reverse transcriptase of human immunodeficiency virus type 1, Proc. Natl. Acad. Sci. USA, 91, 3911, 10.1073/pnas.91.9.3911 Steitz, 1993, DNA‐ and RNA‐dependent DNA polymerases, Curr. Opin. Struct. Biol., 3, 31, 10.1016/0959-440X(93)90198-T Steitz, 1994, A unified polymerase mechanism for nonhomologous DNA and RNA polymerases, Science, 266, 2022, 10.1126/science.7528445 Steitz, 1998, A mechanism for all polymerases, Nature, 391, 231, 10.1038/34542 Suzuki, 1996, Random mutagenesis of Thermus aquaticus DNA polymerase I: Concordance of immutable sites in vivo with the crystal structure, Proc. Natl. Acad. Sci. USA, 93, 9670, 10.1073/pnas.93.18.9670 Tabor, 1987, Escherichia coli thioredoxin confers processivity on the DNA polymerase activity of the gene 5 protein of bacteriophage T7, J. Biol. Chem., 262, 16212, 10.1016/S0021-9258(18)47718-6 Topal, 1980, Molecular basis for substitution mutations: Effect of primer terminal and template residues on nucleotide selection by phage T4 DNA polymerase in vitro, J. Biol. Chem., 255, 11717, 10.1016/S0021-9258(19)70193-8 Trincao, 2001, Structure of the catalytic core of S. cerevisiae DNA polymerase η: Implications for translesion DNA synthesis, Mol. Cell, 8, 417, 10.1016/S1097-2765(01)00306-9 Tuerk, 1990, Autogenous translational operator recognized by bacteriophage T4 DNA polymerase, J. Mol. Biol., 213, 749, 10.1016/S0022-2836(05)80261-X Uemori, 1997, A novel DNA polymerase in the hyperthermophilic acrhaeon, Pyrococcus furiosus: Gene cloning, expression and characterization, Genes to Cell, 2, 499, 10.1046/j.1365-2443.1997.1380336.x Uljon, 2004, Crystal structure of the catalytic core of human DNA polymerase κ, Structure, 12, 1395, 10.1016/j.str.2004.05.011 Vande Berg, 2001, DNA structure and aspartate 276 influence nucleotide binding to human DNA polymerase β. Implication for the identity of the rate‐limiting conformational change, J. Biol. Chem., 276, 3408, 10.1074/jbc.M002884200 Wang, 1997, Evolution of RNA‐binding specificity in T4 DNA polymerase, J. Biol. Chem., 272, 17703, 10.1074/jbc.272.28.17703 Wang, 1997, Crystal structure of a pol α Family replication DNA polymerase from bacteriophage RB69, Cell, 89, 1087, 10.1016/S0092-8674(00)80296-2 Washington, 2001, Yeast DNA polymerase η utilizes an induced‐fit mechanism of nucleotide incorporation, Cell, 107, 917, 10.1016/S0092-8674(01)00613-4 Watson, 1953, Genetical implications of the structure of deoxyribonucleic acid, Nature, 171, 964, 10.1038/171964b0 Watson, 1953, Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid, Nature, 171, 737, 10.1038/171737a0 Werneburg, 1996, DNA polymerase β: Pre‐steady‐state kinetic analysis and roles of arginine–283 in catalysis and fidelity, Biochemistry, 35, 7041, 10.1021/bi9527202 Wöhrl, 1999, J. Mol. Biol., 292, 333, 10.1006/jmbi.1999.3057 Wong, 1991, An induced‐fit kinetic mechanism for DNA replication fidelity: Direct measurement by single‐turnover kinetics, Biochemistry, 30, 526, 10.1021/bi00216a030 Woodgate, 1999, A plethora of lesion‐replicating DNA polymerases, Genes Dev., 13, 2191, 10.1101/gad.13.17.2191 Wuite, 2000, Single‐molecule studies of the effect of template tension on T7 DNA polymerase activity, Nature, 404, 103, 10.1038/35003614 Yang, 2002, Correlation of the kinetics of finger domain mutants in RB69 DNA polymerase with its structure, Biochemistry, 41, 2526, 10.1021/bi0119924 Yang, 2004, Critical role of magnesium ions in DNA polymerase β's closing and active site assembly, J. Am. Chem. Soc., 126, 8441, 10.1021/ja049412o Yang, 2002, Polymerase β simulations suggest that Arg258 rotation is a slow step rather than large subdomain motions per se, J. Mol. Biol., 317, 651, 10.1006/jmbi.2002.5450 Yang, 2003, Damage repair DNA polymerases Y, Curr. Opin. Struct. Biol., 13, 23, 10.1016/S0959-440X(02)00003-9 Zhao, 1999, Crystal structure of an archaebacterial DNA polymerase, Structure Fold Des., 7, 1189, 10.1016/S0969-2126(00)80053-2 Zhong, 1997, DNA polymerase β: Multiple conformational changes in the mechanism of catalysis, Biochemistry, 36, 11891, 10.1021/bi963181j Zhou, 2001, Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain, Mol. Cell, 8, 427, 10.1016/S1097-2765(01)00310-0