Homology modeling of four Y-family, lesion-bypass DNA polymerases: The case that E. coli Pol IV and human Pol κ are orthologs, and E. coli Pol V and human Pol η are orthologs

Journal of Molecular Graphics and Modelling

Volumn 25, Issue 1, 2006, Pages 87-102

  Lee, Chiu Hong ^a   Chandani, Sushil ^b   Loechler, Edward L ^b  

^a HARVARD UNIVERSITY   (United States)

^b Boston University   (United States)

Author keywords

Adducts; Cancer; DNA polymerase; Genotoxins; Lesion; Mutations; Pol eta; Pol IV; Pol kappa; Pol V

Indexed keywords

ADDUCTS; DNA POLYMERASE; GENOTOXINS; MUTATIONS; POL ETA; POL IV; POL KAPPA; POL V;

BIOSYNTHESIS; CARCINOGENS; CONFORMATIONS; DNA; ESCHERICHIA COLI; PROTEINS; TUMORS;

ENZYME KINETICS;

AMINO ACID; BENZO[A]PYRENE; CARCINOGEN; DNA POLYMERASE; MUTAGENIC AGENT; POL PROTEIN;

ARTICLE; COMPARATIVE STUDY; CONFORMATION; CORRELATION ANALYSIS; DNA DAMAGE; DNA SEQUENCE; ENVIRONMENT; ESCHERICHIA COLI; EVOLUTION; HUMAN; MOLECULAR DYNAMICS; MUTAGENESIS; MUTATION; NONHUMAN; ORTHOLOGY; PRIORITY JOURNAL; RADIATION; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; SUBSTITUTION REACTION; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; DNA DAMAGE; DNA POLYMERASE BETA; DNA-DIRECTED DNA POLYMERASE; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; HUMANS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; STRUCTURAL HOMOLOGY, PROTEIN;

ESCHERICHIA COLI;

EID: 33747889221     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2005.10.009     Document Type: Article

References (110)

1. Bebenek K., and Kunkel T.A. Functions of eukaryotic DNA polymerases. Adv. Prot. Chem. 69 (2004) 137-165
2. Goodman M.F. Error-prone repair DNA polymerases in prokaryotes and eukaryotes. Annu. Rev. Biochem. 71 (2002) 17-50
3. Hubscher U., Maga G., and Spadari S. Eukaryotic DNA polymerases. Annu. Rev. Biochem. 71 (2002) 133-163
4. Rattray A.J., and Strathern J.N. Error-prone DNA polymerases: when making a mistake is the only way to get ahead. Annu. Rev. Genet. 37 (2003) 31-66
5. Ohmori H., Friedberg E.C., Fuchs R.P., Goodman M.F., Hanaoka F., Hinkle D., Kunkel T.A., Lawrence C.W., Livneh Z., Nohmi T., Prakash L., Prakash S., Todo T., Walker G.C., Wang Z., and Woodgate R. The Y-family of DNA polymerases. Mol. Cell. 8 (2001) 7-8
6. Boudsocq F., Ling H., Yang W., and Woodgate R. Structure-based interpretation of missense mutations in Y-family DNA polymerases and their implications for polymerase function and lesion bypass. DNA Repair (Amst.) 1 (2002) 343-358
7. Friedberg E.C., Wagner R., and Radman M. Specialized DNA polymerases, cellular survival, and the genesis of mutations. Science 296 (2002) 1627-1630
8. Friedberg E.C. Why do cells have multiple error-prone DNA polymerases?. Environ. Mol. Mutagen. 38 (2001) 105-110
9. Wang Z. Translesion synthesis by the UmuC family of DNA polymerases. Mutat. Res. 486 (2001) 59-70
10. Johnson R.E., Washington M.T., Prakash S., and Prakash L. Bridging the gap: a family of novel DNA polymerases that replicate faulty DNA. Proc. Natl. Acad. Sci. U.S.A. 96 (1999) 12224-12226
11. Pages V., and Fuchs R.P. How DNA lesions are turned into mutations within cells?. Oncogene 21 (2002) 8957-8966
12. Yang W. Damage repair DNA polymerases Y. Curr. Opin. Struct. Biol. 13 (2003) 23-30
13. Burgers P.M., Koonin E.V., Bruford E., Blanco L., Burtis K.C., Christman M.F., Copeland W.C., Friedberg E.C., Hanaoka F., Hinkle D.C., Lawrence C.W., Nakanishi M., Ohmori H., Prakash L., Prakash S., Reynaud C.A., Sugino A., Todo T., Wang Z., Weill J.C., and Woodgate R. Eukaryotic DNA polymerases: proposal for a revised nomenclature. J. Biol. Chem. 276 (2001) 43487-43490
14. Ohmori H., Friedberg E.C., Fuchs R.P., Goodman M.F., Hanaoka F., Hinkle D., Kunkel T.A., Lawrence C.W., Livneh Z., Nohmi T., Prakash L., Prakash S., Todo T., Walker G.C., Wang Z., and Woodgate R. The Y-family of DNA polymerases. Mol. Cell. 8 (2001) 7-8
15. Masutani C., Kusumoto R., Yamada A., Dohmae N., Yokoi M., Yuasa M., Araki M., Iwai S., Takio K., and Hanaoka F. The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase eta. Nature 399 (1999) 700-704
16. Johnson R.E., Prakash S., and Prakash L. Efficient bypass of a thymine-thymine dimer by yeast DNA polymerase, Poleta. Science 283 (1999) 1001-1004
17. Johnson R.E., Kondratick C.M., Prakash S., and Prakash L. hRAD30 mutations in the variant form of xeroderma pigmentosum. Science 285 (1999) 263-265
18. Washington M.T., Johnson R.E., Prakash S., and Prakash L. Fidelity and processivity of Saccharomyces cerevisiae DNA polymerase eta. J. Biol. Chem. 274 (1999) 36835-36838
19. Washington M.T., Johnson R.E., Prakash S., and Prakash L. Accuracy of thymine-thymine dimer bypass by Saccharomyces cerevisiae DNA polymerase eta. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 3094-3099
20. Johnson R.E., Washington M.T., Prakash S., and Prakash L. Fidelity of human DNA polymerase eta. J. Biol. Chem. 275 (2000) 7447-7450
21. 6-dA lesions catalyzed by DNA bypass polymerases. J. Biol. Chem. 277 (2002) 30488-30494
22. Suzuki N., Ohashi E., Kolbanovskiy A., Geacintov N.E., Grollman A.P., Ohmori H., and Shibutani S. Translesion synthesis by human DNA polymerase kappa on a DNA template containing a single stereoisomer of dG-(+)- or dG-(-)-anti-N(2)-BPDE (7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene). Biochemistry 41 (2002) 6100-6106
23. 2-dG lesion catalyzed by the Y-family polymerase pol kappa. Biochemistry 42 (2003) 2456-2466
24. Zhang Y., Wu X., Guo D., Rechkoblit O., and Wang Z. Activities of human DNA polymerase kappa in response to the major benzo[a]pyrene DNA adduct: error-free lesion bypass and extension synthesis from opposite the lesion. DNA Repair (Amst.) 1 (2002) 559-569
25. Ogi T., Shinkai Y., Tanaka K., and Ohmori H. Polkappa protects mammalian cells against the lethal and mutagenic effects of benzo[a]pyrene. Proc. Natl. Acad. Sci. U.S.A. 99 (2002) 15548-15553
26. Avkin S., Goldsmith M., Velasco-Miguel S., Geacintov N., Friedberg E.C., and Livneh Z. Quantitative analysis of translesion DNA synthesis across a benzo[a]pyrene-guanine adduct in mammalian cells: the role of DNA polymerase kappa. J. Biol. Chem. 279 (2004) 53298-53305
27. Zhou B.L., Pata J.D., and Steitz T.A. Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain. Mol. Cell. 8 (2001) 427-437
28. Ling H., Boudsocq F., Woodgate R., and Yang W. Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell 107 (2001) 91-102
29. Ling H., Boudsocq F., Plosky B.S., Woodgate R., and Yang W. Replication of a cis-syn thymine dimer at atomic resolution. Nature 424 (2003) 1083-1087
30. Ling H., Sayer J.M., Plosky B.S., Yagi H., Boudsocq F., Woodgate R., Jerina D.M., and Yang W. Crystal structure of a benzo[a]pyrene diol epoxide adduct in a ternary complex with a DNA polymerase. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 2265-2269
31. Ling H., Boudsocq F., Woodgate R., and Yang W. Snapshots of replication through an abasic lesion; structural basis for base substitutions and frameshifts. Mol. Cell. 13 (2004) 751-762
32. Trincao J., Johnson R.E., Wolfle W.T., Escalante C.R., Prakash S., Prakash L., and Aggarwal A.K. Dpo4 is hindered in extending a G.T mismatch by a reverse wobble. Nat. Struct. Mol. Biol. 11 (2004) 457-462
33. Trincao J., Johnson R.E., Escalante C.R., Prakash S., Prakash L., and Aggarwal A.K. Structure of the catalytic core of S. cerevisiae DNA polymerase eta: implications for translesion DNA synthesis. Mol. Cell. 8 (2001) 417-426
34. Nair D.T., Johnson R.E., Prakash S., Prakash L., and Aggarwal A.K. Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing. Nature 430 (2004) 377-380
35. Uljon S.N., Johnson R.E., Edwards T.A., Prakash S., Prakash L., and Aggarwal A.K. Crystal structure of the catalytic core of human DNA polymerase kappa. Structure (Camb.) 12 (2004) 1395-1404
36. Washington M.T., Helquist S.A., Kool E.T., Prakash L., and Prakash S. Requirement of Watson-Crick hydrogen bonding for DNA synthesis by yeast DNA polymerase eta. Mol. Cell. Biol. 23 (2003) 5107-5112
37. Washington M.T., Prakash L., and Prakash S. Mechanism of nucleotide incorporation opposite a thymine-thymine dimer by yeast DNA polymerase eta. Proc. Natl. Acad. Sci. U.S.A. 100 (2003) 12093-12098
38. 2-dG adduct when studied in a 5′-TGT sequence in Escherichia coli. DNA Repair 3 (2004) 323-334
39. Harvey R.G. Polycyclic Aromatic Hydrocarbons: Chemistry and Cancer (1997), Wiley-VCH Inc., New York
40. Phillips D.H. Fifty years of benzo[a]pyrene. Nature 303 (1983) 468-472
41. Singer B., and Grunberger D. Molecular Biology of Mutagens and Carcinogens (1983), Plenum Press, New York
42. Conney A.H. Induction of microsomal enzymes by foreign chemicals and carcinogens by polycyclic aromatic hydrocarbons. Cancer Res. 42 (1982) 4875-4917
43. Dipple A. Polycyclic aromatic hydrocarbon carcinogens. In: Harvey R.G. (Ed). Polycyclic Aromatic Hydrocarbons and Carcinogenesis (1985), American Chemical Society Press, Washington, DC 1-17
44. Jones P.W. Polynuclear aromatic hydrocarbons. In: Bowman M.G. (Ed). Handbook of Carcinogens and Hazardous Substances (1982), Marcel Dekker Inc., New York 573-639
45. Grasso P. Carcinogens in food. In: Searle C.E. (Ed). Chemical Carcinogens. second ed. (1984), ACS Monograph 182, Amreican Chemical Society Press, Washington DC 1205-1239
46. Samet J.M., DeMarini D.M., and Malling H.V. Do airborne particles induce heritable mutations?. Science 304 (2004) 971-972
47. Balmain A., and Brown K. Oncogene activation in chemical carcinogenesis. Adv. Cancer Res. 51 (1988) 147-182
48. Hall M., and Grover P.L. In: Cooper G.S., and Grover P.L. (Eds). Handbook of Experimental Pharmacology, vol. 94/1 Chemical Carcinogenesis and Mutagenesis (1990), Springer-Verlag, Heidelberg 327-372
49. Ruggeri B.A., Bauer B., Zhang S.-Y., and Klein-Szanto A.J.P. Murine squamous cell carcinoma cell lines produced by a complete carcinogenesis protocol with benzo[a]pyrene exhibit characteristic p53 mutations and the absence of H-ras and cyl1/cyclin D1 abnormalities. Carcinogenesis 15 (1994) 6113-1619
50. Chakravarti D., Pelling J., Cavalieri E.L., and Rogan E.G. Relating aromatic hydrocarbon-induced DNA adducts and the c-H-ras mutations in mouse skin papillomas: the role of apurinic sites. Proc. Natl. Acad. Sci. U.S.A. 92 (1995) 10422-10426
51. Chen L., Devanesan R., Higginbotham S., Ariese F., Jankowiak R., Small G.J., Rogan E.G., and Cavalieri E. Expanded analysis of benzo[a]pyrene-DNA adducts formed in vitro and in mouse skin: their significance in tumor initiation. Chem. Res. Toxicol. 9 (1996) 897-903
52. Chakravarti D., Mailander P., Franzen J., Higginbotham S., Cavalieri E.L., and Rogan E.G. Detection of dibenzo[a,l]pyrene-induced H-ras codon 61 mutant genes in preneoplastic SENCAR mouse skin using a new PCR-RFLP method. Oncogene 16 (1998) 3203-3210
53. Chakravarti D., Mailander P.C., Cavalieri E.L., and Rogan E.G. Evidence that error-prone DNA repair converts dibenzo[a,l]pyrene-induced depurinating lesions into mutations: formation, clonal proliferation and regression of initiated cells carrying H-ras oncogene mutations in early preneoplasia. Mutat. Res. 456 (2000) 17-32
54. Pfeifer G.P., and Hainaut P. On the origin of G → T transversions in lung cancer. Mutat. Res. 526 (2003) 39-43
55. Eisenstadt E., Warren A.J., Porter J., Atkins D., and Miller J.H. Carcinogenic epoxides of benzo[a]pyrene and cyclopenta[cd]pyrene induce base substitutions via specific transversions. Proc. Natl. Acad. Sci. U.S.A. 82 (1982) 1945-1949
56. Yang J.L., Maher V.M., and McCormick J.J. Kinds of mutations formed when a human shuttle vector containing adducts of (+/-)-7beta,8alpha-dihydroxy-9alpha,10alpha-epoxy-7,8,9,10- dihydrobenzo[a]pyrene replicates in human cells. Proc. Natl. Acad. Sci. U.S.A. 84 (1987) 3787-3791
57. Bernelot-Moens C., Glickman B.W., and Gordon A.J.E. Induction of specific frameshift and base substitution events by benzo[a]pyrene diol epoxide in excision-repair-deficient Escherichia coli. Carcinogenesis 11 (1990) 781-785
58. Yang J.-L., Chen R.-H., Maher V.M., and McCormick J.J. Kinds and locations of mutations induced by (+/-)-7beta, 8alpha-dihydroxy-9alpha, 10alpha-epoxy-7,8,9,10-dihydrobenzo[a]pyrene in the coding region of the hypoxanthine (guanine) phosphoribosyltransferase gene in diploid human fibroblasts. Carcinogenesis 12 (1990) 71-75
59. Carothers A.M., and Grunberger D. DNA base changes in benzo[a]pyrene diol epoxide-induced dihydrofolate reductase mutants of Chinese hampster ovary cells. Carcinogenesis 11 (1990) 189-192
60. Rodriguez H., and Loechler E.L. Mutational spectra of the (+)-anti-diol epoxide of senzo[a]pyrene in a supF gene of an Escherichia coli plasmid: DNA sequence context influences hotspots mutational specficity and the extent of SOS enhancement of mutagenesis. Carcinogenesis 14 (1993) 373-383
61. Rodriguez H., and Loechler E.L. Mutagenesis by the (+)-anti-diol epoxide of benzo[a]pyrene: what controls mutagenic specificity?. Biochemistry 32 (1993) 373-383
62. Wei S.J., Chang R.L., Wong C.Q., Cui X.X., Dandamudi N., Lu Y.P., Merkler K.A., Sayer J.M., Conney A.H., and Jerina D.M. The ratio of deoxyadenosine to deoxyguanosine adducts formed by (+)-(7R,8S,9S,10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene in purified calf thymus DNA and DNA in V-79 cells is independent of dose. Int. J. Oncol. 14 (1999) 509-513
63. Schiltz M., Cui X.X., Lu Y.P., Yagi H., Jerina D.M., Zdzienicka M.Z., Chang R.L., Conney A.H., and Wei S.J. Characterization of the mutational profile of (+)-7R,8S-dihydroxy-9S, 10R-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene at the hypoxanthine (guanine) phosphoribosyltransferase gene in repair-deficient Chinese hamster V-H1 cells. Carcinogenesis 20 (1999) 2279-2286
64. 2-Gua when studied in an Escherichia coli plasmid using site-directed methods. Carcinogenesis 13 (1992) 1415-1425
65. 2-dG adduct of (+)-anti-B[a]PDE induces G → A mutations in a 5′-AGA-3′ sequence context. Carcinogenesis 20 (1999) 261-268
66. Lenne-Samuel N., Janel-Bintz R., Kolbanovskiy A., Geacintov N.E., and Fuchs R.P. The processing of a benzo(a)pyrene adduct into a frameshift or a base substitution mutation requires a different set of genes in Escherichia coli. Mol. Microbiol. 38 (2000) 299-307
67. Napolitano R., Janel-Bintz R., Wagner J., and Fuchs R.P. All three SOS-inducible DNA polymerases (Pol II Pol IV and Pol V) are involved in induced mutagenesis. EMBO J. 19 (2000) 6259-6265
68. Napolitano R.L., Lambert I.B., and Fuchs R.P. SOS factors involved in translesion synthesis. Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 5733-5738
69. Becherel O.J., and Fuchs R.P. Mechanism of DNA polymerase II-mediated frameshift mutagenesis. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 8566-8571
70. Wagner J., Etienne H., Janel-Bintz R., and Fuchs R.P. Genetics of mutagenesis in E. coli: various combinations of translesion polymerases (Pol II IV and V) deal with lesion/sequence context diversity. DNA Repair 1 (2002) 159-167
71. Chiapperino D., Kroth H., Kramarczuk I.H., Sayer J.M., Masutani C., Hanaoka F., Jerina D.M., and Cheh A.M. Preferential misincorporation of purine nucleotides by human DNA polymerase eta opposite benzo[a]pyrene 7,8-diol, 9, 10-epoxide deoxyguanosine adducts. J. Biol. Chem. 277 (2002) 11765-11771
72. Zhang Y., Wu X., Guo D., Rechkoblit O., Geacintov N.E., and Wang Z. Two-step error-prone bypass of the (+)- and (-)-trans-anti-BPDE-N(2)-dG adducts by human DNA polymerases eta and kappa. Mutat. Res. 510 (2002) 23-35
73. Zhang Y., Yuan F., Wu X., Rechkoblit O., Taylor J.S., Geacintov N.E., and Wang Z. Error-prone lesion bypass by human DNA polymerase eta. Nucleic Acids Res. 28 (2000) 4717-4724
74. Shen X., Sayer J.M., Kroth H., Ponten I., O'Donnell M., Woodgate R., Jerina D.M., and Goodman M.F. Efficiency and accuracy of SOS-induced DNA polymerases replicating benzo[a]pyrene-7,8-diol 9,10-epoxide A and G adducts. J. Biol. Chem. 277 (2002) 5265-5274
75. Insight II, Version 98.0, Accelyrs Inc., San Diego, 1998.
76. Nilsson L., and Karplus M. Empirical energy functions for energy minimization and dynamics of nucleic acids. J. Comp. Chem. 7 (1986) 591-616
77. MacKerell Jr. A.D., Banavali N., and Foloppe N. Development and current status of the CHARMM force field for nucleic acids. Biopolymers 56 (2001) 257-265
78. 2-dG adduct using free energy perturbation techniques to assess energy differences for two conformations in two sequence contexts. Chem. Res. Toxicol. 18 (2005) 1108-1123
79. Doublie S., Tabor S., Long A.M., Richardson C.C., and Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Nature 391 (1998) 251-258
80. Bowie J.U., Lüthy R., and Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253 (1991) 164-170
81. Eisenberg D., Wesson M., and Yamashita M. Interpretation of protein folding and binding with atomic solvation parameters. Chem. Scr. 29A (1989) 217-221
82. Gribskov M., McLachlan A.D., and Eisenberg D. Profile analysis: detection of distantly related proteins. Proc. Natl. Acad. Sci. U.S.A. 84 (1987) 4355-4358
83. Gribskov M., Lüthy R., and Eisenberg D. Profile analysis. Methods Enzymol. 183 (1990) 146-159
84. Fujii S., Gasser V., and Fuchs R.P. The biochemical requirements of DNA polymerase V-mediated translesion synthesis revisited. J. Mol. Biol. 341 (2004) 405-417
85. Fujii S., and Fuchs R.P. Defining the position of the switches between replicative and bypass DNA polymerases. EMBO J. 23 (2004) 4342-4352
86. Tang M., Pham P., Shen X., Taylor J.S., O'Donnell M., Woodgate R., and Goodman M.F. Roles of E. coli DNA polymerases IV and V in lesion-targeted and untargeted SOS mutagenesis. Nature 404 (2000) 1014-1018
87. Lee J.H., Hwang G.S., and Choi B.S. Solution structure of a DNA decamer duplex containing the stable 3′ T.G base pair of the pyrimidine(6-4)pyrimidone photoproduct [(6-4) adduct]: implications for the highly specific 3′ T → C transition of the (6-4) adduct. Proc. Natl. Acad. Sci. U.S.A. 96 (1999) 6632-6636
88. Napolitano R., Janel-Bintz R., Wagner J., and Fuchs R.P. All three SOS-inducible DNA polymerases (Pol II Pol IV and Pol V) are involved in induced mutagenesis. EMBO J. 19 (2000) 6259-6265
89. Wagner J., Etienne H., Janel-Bintz R., and Fuchs R.P. Genetics of mutagenesis in E. coli: various combinations of translesion polymerases (Pol II, IV and V) deal with lesion/sequence context diversity. DNA Repair 1 (2002) 159-167
90. Napolitano R.L., Lambert I.B., and Fuchs R.P. SOS factors involved in translesion synthesis. Proc. Natl. Acad. Sci. U.S.A. 94 (1997) 5733-5738
91. Becherel O.J., and Fuchs R.P. Mechanism of DNA polymerase II-mediated frameshift mutagenesis. Proc. Natl. Acad. Sci. U.S.A. 98 (2001) 8566-8571
92. Strauss B.S. The "A" rule revisited: polymerases as determinants of mutational specificity. DNA Repair 1 (2002) 125-135
93. Loechler E.L. Mechanism by Which Aflatoxins and Other Bulky Carcinogens Induce Mutations. The Toxicology of Aflatoxins: Human Health, Veterinary and Agricultural Significance (Eaton and Groopman) (1994), Academic Press, Orlando pp. 149-178 (Chapter 8)
94. Brash D.E., and Haseltine W.A. UV-induced mutation hotspots occur at DNA damage hotspots. Nature 298 (1982) 189-192
95. Masutani C., Kusumoto R., Iwai S., and Hanaoka F. Mechanisms of accurate translesion synthesis by human DNA polymerase eta. EMBO J. 19 (2000) 3100-3109
96. Cordonnier A.M., Lehmann A.R., and Fuchs R.P. Impaired translesion synthesis in xeroderma pigmentosum variant extracts. Mol. Cell. Biol. 19 (1999) 2206-2211
97. Zhang Y., Yuan F., Wu X., Rechkoblit O., Taylor J.S., Geacintov N.E., and Wang Z. Error-prone lesion bypass by human DNA polymerase eta. Nucleic Acids Res. 28 (2000) 4717-4724
98. Yuan F., Zhang Y., Rajpal D.K., Wu X., Guo D., Wang M., Taylor J.S., and Wang Z. Specificity of DNA lesion bypass by the yeast DNA polymerase eta. J. Biol. Chem. 275 (2000) 8233-8239
99. Yu S.L., Johnson R.E., Prakash S., and Prakash L. Requirement of DNA polymerase eta for error-free bypass of UV-induced CC and TC photoproducts. Mol. Cell. Biol. 21 (2001) 185-188
100. Suzuki N., Ohashi E., Hayashi K., Ohmori H., Grollman A.P., and Shibutani S. Translesional synthesis past acetylaminofluorene-derived DNA adducts catalyzed by human DNA polymerase kappa and Escherichia coli DNA polymerase IV. Biochemistry 40 (2001) 15176-15183
101. Ohashi E., Ogi T., Kusumoto R., Iwai S., Masutani C., Hanaoka F., and Ohmori H. Error-prone bypass of certain DNA lesions by the human DNA polymerase kappa. Genes Dev. 14 (2000) 1589-1594
102. Zhang Y., Yuan F., Wu X., Wang M., Rechkoblit O., Taylor J.S., Geacintov N.E., and Wang Z. Error-free and error-prone lesion bypass by human DNA polymerase kappa in vitro. Nucleic Acids 28 (2000) 4138-4146
103. Gerlach V.L., Feaver W.J., Fischhaber P.L., and Friedberg E.C. Purification and characterization of pol kappa, a DNA polymerase encoded by the human DINB1 gene. J. Biol. Chem. 276 (2001) 92-98
104. Johnson R.E., Prakash S., and Prakash L. The human DINB1 gene encodes the DNA polymerase Poltheta. Proc. Natl. Acad. Sci. U.S.A. 97 (2000) 3838-3843
105. Ohashi E., Bebenek K., Matsuda T., Feaver W.J., Gerlach V.L., Friedberg E.C., Ohmori H., and Kunkel T.A. Fidelity and processivity of DNA synthesis by DNA polymerase kappa, the product of the human DINB1 gene. J. Biol. Chem. 275 (2000) 39678-39684
106. Ohashi E., Ogi T., Kusumoto R., Iwai S., Masutani C., Hanaoka F., and Ohmori H. Error-prone bypass of certain DNA lesions by the human DNA polymerase kappa. Genes Dev. 14 (2000) 1589-1594
107. Zhang Y., Yuan F., Wu X., Rechkoblit O., Taylor J.S., Geacintov N.E., and Wang Z. Error-prone lesion bypass by human DNA polymerase eta. Nucleic Acids Res. 28 (2000) 4717-4724
108. Prevelige Jr. P., and Fasman G. In: Fasman G. (Ed). Prediction of Protein Structure and the Principles of Protein Conformation (1989), Plenum, New York 391-416 (Chapter 9)
109. Garnier J., and Robson B. In: Fasman G. (Ed). Prediction of Protein Structure and the Principles of Protein Conformation (1989), Plenum, New York 417-465 (Chapter 10)
110. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680