Molecular Recognition Strategies I: One Enzyme-One Substrate Motifs

  • Hanspeter Naegeli
Part of the Molecular Biology Intelligence Unit book series (MBIU)


To store the genetic information and serve as the genetic link between generations, the nucleotide sequence of DNA must be faithfully maintained despite the numerous physical or chemical insults discussed in the previous chapter. To that end, all organisms from bacteria to mammals are endowed with DNA repair mechanisms, and even some viral genomes carry their own DNA repair enzymes.


Excision Repair Nucleotide Excision Repair Pyrimidine Dimer Cyclobutane Pyrimidine Dimer Active Site Pocket 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. 1.
    Sancar A. Mechanisms of DNA excision repair. Science 1994; 266:1954–1956.CrossRefGoogle Scholar
  2. 2.
    Wood RD. DNA repair in eukaryotes. Annu Rev Biochem 1996; 65:135–167.CrossRefGoogle Scholar
  3. 3.
    Modrich P. Mechanisms and biological effects of mismatch repair. Annu Rev Genet 1991; 25:229–253.CrossRefGoogle Scholar
  4. 4.
    Friedberg EC, Walker GC, Siede W. DNA Repair and Mutagenesis. Washington, D.C.: American Society for Microbiology, 1995.Google Scholar
  5. 5.
    Park H-W, Kim S-T, Sancar A et al. Crystal structure of DNA photolyase from Escherichia coli. Science 1995; 268:1866–1872.CrossRefGoogle Scholar
  6. 6.
    Mol CD, Arvai AS, Slupphaug G et al. Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis. Cell 1995; 80:869–878.CrossRefGoogle Scholar
  7. 7.
    Sun B, Latham KA, Dodson ML et al. Studies on the catalytic mechanism of five DNA glycosylases. J Biol Chem 1995; 270:19501–19508.CrossRefGoogle Scholar
  8. 8.
    Demple B, Harrison L. Repair of oxidative damage to DNA: enzymology and biology. Annu Rev Biochem 1994; 63:915–948.CrossRefGoogle Scholar
  9. 9.
    Sancar A, Sancar GB. DNA repair enzymes. Annu Rev Biochem 1988; 57:29–67.CrossRefGoogle Scholar
  10. 10.
    Pegg AE, Byers TL. Repair of DNA containing O 6-alkylguanine. FASEB J 1992; 6:2302–2310.Google Scholar
  11. 11.
    Setlow P. I will survive: protecting and repairing spore DNA. J Bacteriol 1992; 174:2737–2741.Google Scholar
  12. 12.
    Tang M-s, Nazimiec ME, Doisy RP et al. Repair of helix-stabilizing anthramycin-N2 guanine DNA adducts by UVRA and UVRB proteins. J Mol Biol 1991; 220:855–866.CrossRefGoogle Scholar
  13. 13.
    Lindahl T, Sedgwick B, Sekiguchi M et al. Regulation and expression of the adaptive response to alkylating agents. Annu Rev Biochem 1988; 57:133–157.CrossRefGoogle Scholar
  14. 14.
    Mitra S, Kaina B. Regulation of repair of alkylation damage in mammalian genomes. Progr Nucleic Acid Res Mol Biol 1993; 44:109–142.CrossRefGoogle Scholar
  15. 15.
    Pegg AE, Dolan ME, Moschel RC. Structure, function, and inhibition of O 6-alkylguanine-DNA alkyltransferase. Progr Nucleic Acid Res Mol Biol 1995; 51:167–223.CrossRefGoogle Scholar
  16. 16.
    Zak P, Kleibl K, Laval F. Repair of O 6-methylguanine and O4-methylthymine by the human and rat O 6-methylguanine-DNA methyltransferase. J Biol Chem 1994; 269:730–733.Google Scholar
  17. 17.
    Moore MH, Gulbis JM, Dodson EJ et al. Crystal structure of a suicidal DNA repair protein: the Ada O 6-methylguanine-DNA methyltransferase from E. coli. EMBO J 1994; 13:1495–1501.Google Scholar
  18. 18.
    Kanugula S, Goodtzova K, Edara S et al. Alteration of arginine-128 to alanine abolishes the ability of human O 6-alkylguanine-DNA alkyltransferase to repair methylated DNA but has no effect on its reaction with O 6-benzylguanine. Biochemistry 1995; 34:7113–7119.CrossRefGoogle Scholar
  19. 19.
    Goodtzova K, Crone TM, Pegg AE. Activation of O 6-alkyltransferase by DNA. Biochemistry 1994; 33:8385–8390.CrossRefGoogle Scholar
  20. 20.
    Takahashi, Sakumi K, Sekiguchi M. Interaction of Ada protein with DNA examined by fluorescence anisotropy of the protein. Biochemistry 1990; 29:3431–3436.CrossRefGoogle Scholar
  21. 21.
    Chan CL, Wu Z, Ciardelli T et al. Kinetic and DNA-binding properties of recombinant human O 6-methylguanine-DNA methyltransferase. Arch Biochem Biophys 1993; 300:193–200.CrossRefGoogle Scholar
  22. 22.
    Hearst JE. The structure of photolyase: using photon energy for DNA repair. Science 1995; 268:1859–1859.CrossRefGoogle Scholar
  23. 23.
    Li YF, Kim ST, Sancar A. Evidence for lack of DNA photoreactivating enzyme in humans. Proc Natl Acad Sci USA 1993; 90:4389–4393.CrossRefGoogle Scholar
  24. 24.
    Kim ST, Sancar A. Photochemistry, photophysics, and mechanism of pyrimidine dimer repair by DNA photolyase. Photochem Photobiol 1993; 57:895–904.CrossRefGoogle Scholar
  25. 25.
    Cook, J.S. Photoreactivation in animal cells. Photophysiology 1970; 5:191–213.Google Scholar
  26. 26.
    Sutherland BM, Bennett PV. Human white blood cells contain cyclobutyl pyrimidine dimer photolyase. Proc Natl Acad Sci USA 1995; 92:9732–9736.CrossRefGoogle Scholar
  27. 27.
    Sancar GB, Smith FW, Sancar A. Binding of Escherichia coli DNA photolyase to UV-irradiated DNA. Biochemistry 1985; 24:1849–1855.CrossRefGoogle Scholar
  28. 28.
    Husain I, Sancar A. Binding of E. coli DNA photolyase to a defined substrate containing a single T<>T dimer. Nuclei Acids Res 1987; 15:1109–1120.CrossRefGoogle Scholar
  29. 29.
    Kim ST, Sancar A. Effect of base, pentose, and phosphodiester backbone structures on binding and repair of pyrimidine dimers by Escherichia coli DNA photolyase. Biochemistry 1991; 30:8623–8630.CrossRefGoogle Scholar
  30. 30.
    Baer ME, Sancar GB. The role of conserved amino acids in substrate binding and discrimination by photolyase. J Biol Chem 1993; 268:16717–16724.Google Scholar
  31. 31.
    Todo T, Takemori H, Ryo H et al. A new photoreactivating enzyme that specifically repairs ultraviolet light-induced (6-4) photoproducts. Nature 1993; 361:371–374.CrossRefGoogle Scholar
  32. 32.
    Todo T, Ryo H, Yamamoto K et al. Similarity among the Drosophila (6-4)photolyase, a human photolyase homolog, and the DNA photolyase-bluelight photoreceptor family. Science 1996; 272:109–112.CrossRefGoogle Scholar
  33. 33.
    Dianov G, Price A, Lindahl T. Generation of single-nucleotide repair patches following excision of uracil residues from DNA. Mol Cell Biol 1992; 12:1605–1612.Google Scholar
  34. 34.
    Lindahl T. New class of enzymes acting on damaged DNA. Nature 1976; 259:64–66.CrossRefGoogle Scholar
  35. 35.
    Jiricny J. Colon cancer and DNA repair: have mismatches met their match? Trends Genet 1994; 10:164–168.CrossRefGoogle Scholar
  36. 36.
    Lindahl T. DNA repair enzymes. Annu Rev Biochem 1982; 51:61–87.CrossRefGoogle Scholar
  37. 37.
    Kow YW, Wallace SS. Mechanism of action of Escherichia coli endonuclease III. Biochemistry 1987; 26:8200–8206.CrossRefGoogle Scholar
  38. 38.
    Lindahl T. An N-glycosidase from Escherichia coli that releases free uracil from DNA containing deaminated cytosine residues. Proc Natl Acad Sci USA 1974; 71:3649–3653.CrossRefGoogle Scholar
  39. 39.
    Friedberg EC, Ganesan AK, Minton K. N-Glycosidase activity in extracts of Bacillus subtilis and its inhibition after infection with bacteriophage PBS2. J Virol 1975; 16:315–321.Google Scholar
  40. 40.
    O’Connor TR, Laval J. Physical association of the 2,6-diamino-4-hydroxy-5N-formamidopyrimidine-DNA glycosylase of Escherichia coli and an activity nicking DNA at apurinic/apyrimidinic sites. Proc Natl Acad Sci USA 1989; 86:5222–5226.CrossRefGoogle Scholar
  41. 41.
    Radman, M. An endonuclease from Escherichia coli that introduces single polynucleotide chain scissions in ultravioletirradiated DNA. J Biol Chem 1976; 251:1438–1445.Google Scholar
  42. 42.
    Friedberg EC, King JJ. Endonucleolytic cleavage of UV-irradiated DNA controlled by the V + gene in phage T4. Biochem Biophys Res Commun 1969; 37:646–651.CrossRefGoogle Scholar
  43. 43.
    Loeb LA, Preston BD. Mutagenesis by apurinic/apyrimidinic sites. Annu Rev Genet 1986; 20:201–230.CrossRefGoogle Scholar
  44. 44.
    Demple B, Herman T, Chem D. Cloning and expression of APE, the cDNA encoding the major human apurinic endonuclease: definition of a family of DNA repair enzymes. Proc Natl Acad Sci USA 1991; 88:11450–11454.CrossRefGoogle Scholar
  45. 45.
    Robson CN, Hickson ID. Isolation of cDNA clones encoding a human apurinic/apyrimidinic endonuclease that corrects DNA repair and mutagenesis defects in Escherichia coli xth (exonuclease III) mutants. Nucleic Acids Res 1991; 19:5519–5523.CrossRefGoogle Scholar
  46. 46.
    Seki S, Akiyama K, Watanabe S et al. A mouse DNA repair enzyme (APEX nuclease) having exonuclease and apurinic/ apyrimidinic endonuclease activities: purification and characterization. Biochim Biophys Acta 1992; 1079:57–64.CrossRefGoogle Scholar
  47. 47.
    Xanthoudakis S, Miao G, Wang F et al. Redox activation of Fos-Jun DNA binding activity is mediated by a DNA repair enzyme. EMBO J 1992; 11:3323–3335.Google Scholar
  48. 48.
    Demple B, Johnson A, Fung D. Exonuclease III and endonuclease IV remove 3′ blocks from DNA synthesis primers in H2O2-damaged Escherichia coli. Proc Natl Acad Sci USA 1986; 83:7731–7735.CrossRefGoogle Scholar
  49. 49.
    Graves RJ, Felzenszwalk I, Laval J et al. Excision of 5′-terminal deoxyribose phosphate from damaged DNA is catalyzed by the Fpg protein of Escherichia coli. J Biol Chem 1992; 267:1442914435.Google Scholar
  50. 50.
    Dianov G, Sedgwick B, Graham D et al. Release of 5′-terminal deoxyribose-phosphate residues from incised abasic sites in DNA by the Escherichia coli RecJ protein. Nucleic Acids Res 1994; 22:993–998.CrossRefGoogle Scholar
  51. 51.
    Sobol RB, Horton JK, Kühn R et al. Requirement of mammalian DNA polymerase-β in base-excision repair. Nature 1996; 379:183–186.CrossRefGoogle Scholar
  52. 52.
    Matsumoto Y, Kim K. Excision of deoxyribose phosphate residues by DNA polymerase β during DNA repair. Science 1995; 269:699–702.CrossRefGoogle Scholar
  53. 53.
    Prigent C, Satoh MS, Daly G et al. Aberrant DNA repair and DNA replication due to an inherited enzymatic defect in human DNA ligase I. Mol Cell Biol 1994; 14:310–317.Google Scholar
  54. 54.
    Caldecott KW, Tucker JD, Stanker LH et al. Characterization of the XRCC1-DNA ligase III complex in vitro and its absence from mutant hamster cells. Nucleic Acids Res 1995; 23:4836–4843.CrossRefGoogle Scholar
  55. 55.
    Lindahl T. An N-glycosydase from Escherichia coli that releases free uracil from DNA containing deaminated cytosine residues. Proc Natl Acad Sci USA 1974; 71:3649–3653.CrossRefGoogle Scholar
  56. 56.
    Olsen LC, Aasland R, Wittwer CU et al. Molecular cloning of a human uracil-DNA glycosylase, a highly conserved DNA repair enzyme. EMBO J 1989; 8:3121–3125.Google Scholar
  57. 57.
    Upton C, Stuart DT, McFadden G. Identification of a poxvirus gene encoding a uracil DNA glycosylase. Proc Natl Acad Sci USA 1993; 90:4518–4522.CrossRefGoogle Scholar
  58. 58.
    Gallinari P, Jiricny J. A new class of uracil-DNA glycosylases related to human thymine-DNA glycosylases. Nature 1996; 383:735–738.CrossRefGoogle Scholar
  59. 59.
    Hatahet Z, Kow YW, Purmal AA et al. New substrates for old enzymes. 5-Hydroxy-2′-deoxycytidine and 5-hydroxy-2′-deoxyuridine are substrates for Escherichia coli endonuclease III and form-amidopyrimidine DNA N-glycosylase, while 5-hydroxy-2′-deoxyuridine is a substrate for uracil DNA N-glycosylase. J Biol Chem 1994; 269:18814–18820.Google Scholar
  60. 60.
    Zastawny TH, Doetsch PW, Dizdaroglu M. A novel activity of E. coli uracil DNA N-glycosylase: excision of isodialuric acid (5,6-dihydroxyuracil), a major product of oxidative DNA damage, from DNA. FEBS Lett 1995; 364:255–258.CrossRefGoogle Scholar
  61. 61.
    Dizdaroglu M, Karakaya A, Jaruga P et al. Novel activities of human uracil-DNA N-glycosylase for cytosine-derived products of oxidative DNA damage. Nucleic Acids Res 1996; 24:418–422.CrossRefGoogle Scholar
  62. 62.
    Sawa R, McAuley-Hecht K, Brown T et al. The structural basis of specific baseexcision repair by uracil-DNA glycosylase. Nature 1995; 373:487–493.CrossRefGoogle Scholar
  63. 63.
    Kavli B, Slupphaug G, Mol CD et al. Excision of cytosine and thymine from DNA by mutants of human uracil-DNA glycosylase. EMBO J 1996; 15:3442–3447.Google Scholar
  64. 64.
    Slupphaug G, Mol CD, Kavli B et al. A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature 1996; 386:87–92.CrossRefGoogle Scholar
  65. 65.
    Slupphaug G, Eftedal I, Kavli B et al. Properties of a recombinant human uracil-DNA glycosylase from the UNG-gene and evidence that the UNG-gene encodes the major uracil-DNA glycosylase. Biochemistry 1995; 34:128–138.CrossRefGoogle Scholar
  66. 66.
    Verri A, Mazzarello P, Spadari S et al. Uracil-DNA glycosylases preferentially excise mispaired uracil. Biochem J 1992; 287:1007–1010.Google Scholar
  67. 67.
    Rould MA, Perona JJ, Soil D et al. Structure of an E. coli glutamyl-tRNA synthetase complexed with tRNAGln and ATP at 2.8 Å resolution: implications for tRNA discrimination. Science 1989; 246:1135–1142.CrossRefGoogle Scholar
  68. 68.
    Yasuda S, Sekiguchi M. T4 endonuclease involved in repair of DNA. Proc Natl Acad USA 1970; 67:1839–1845.CrossRefGoogle Scholar
  69. 69.
    McMillan S, Edenberg HJ, Radany EH et al. denV gene of bacteriophage T4 codes for both pyrimidine dimer-DNA glycosylase and apyrimidinic endonuclease activities. J Virol 1981; 40:211–223.Google Scholar
  70. 70.
    Dodson ML, Michaels ML, Lloyd RS. Unified catalytic mechanism for DNA glycosylase. J Biol Chem 1994; 269:32709–32712.Google Scholar
  71. 71.
    Grafstrom RH, Park L, Grossman L. Enzymatic repair of pyrimidine dimer-containing DNA. A 5′ dimer DNA glycosylase: 3′-apyrimidinic endonuclease mechanism from Micrococcus luteus. J Biol Chem 1982; 257:13465–13474.Google Scholar
  72. 72.
    Hamilton KK, Kim PM, Doetsch PW. A eukaryotic DNA glycosylase/lyase recognizing ultraviolet light-induced pyrimidine dimers. Nature 1992; 356:725–728.CrossRefGoogle Scholar
  73. 73.
    Morikava K, Matsumoto O, Tsujimoto M et al. X-ray structure of T4 endonuclease V: an excision repair enzyme specific for a pyrimidine dimer. Science 1992; 256:523–526.CrossRefGoogle Scholar
  74. 74.
    Morikava K. DNA repair enzymes. Curr Opin Struct Biol 1993; 3:17–24.CrossRefGoogle Scholar
  75. 75.
    Morikava K, Ariyoshi M, Vassylyev D et al. Crystal structure of a pyrimidine dimer-specific excision repair enzyme from bacteriophage T4: refinement at 1.45 Å resolution and X-ray analysis of the three active site mutants. J Mol Biol 1995; 249:360–375.CrossRefGoogle Scholar
  76. 76.
    Doi T, Recktenwald A, Karaki Y et al. Role of the basic amino acid cluster and Glu-23 in pyrimidine dimer glycosylase activity of T4 endonuclease V. Proc Natl Acad Sci USA 1992; 89:9420–9424.CrossRefGoogle Scholar
  77. 77.
    Schrock RD, Lloyd RS. Reductive methylation of the amino terminus of endonuclease V eradicates catalytic activities. J Biol Chem 1991; 266:17631–17639.Google Scholar
  78. 78.
    Schrock RD, Lloyd RS. Site-directed mutagenesis of the NH2 terminus of T4 endonuclease V. J Biol Chem 1993; 268:880–886.Google Scholar
  79. 79.
    Vassylyev DG, Kashiwagi T, Mikami Y et al. Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition. Cell 1995; 83:773–782.CrossRefGoogle Scholar
  80. 80.
    Iwai S, Maeda M, Shimada Y et al. Endonuclease V from bacteriophage T4 interacts with its substrate in the minor groove. Biochemistry 1994; 33:5581–5588.CrossRefGoogle Scholar
  81. 81.
    Inaoka T, Ishida M, Ohtsuka E. Affinity of single-or double-stranded oligodeoxyribonucleotides containing a thymine photodimer for T4 endonuclease V. J Biol Chem 1989; 264:2609–2614.Google Scholar
  82. 82.
    Kemmink J, Boelens R, Koning T et al. 1H NMR study of the exchangeable protons of the duplex d(GCGTTGCG)-d(CGCAACGC) containing a thymine photodimer. Nucleic Acids Res 1987; 15:4645–4653.CrossRefGoogle Scholar
  83. 83.
    Taylor J-S, Garrett DS, Brockie IR et al. 1H NMR assignment and melting temperature study of cis-syn and trans-syn thymine dimer containing duplexes of d(CGTATTATGC) d(GCATAATACG). Biochemistry 1990; 29:8858–8866.CrossRefGoogle Scholar
  84. 84.
    Breimer L, Lindahl T. A DNA glycosylase from Escherichia coli that releases free urea from a polydeoxyribonucleotide containing fragments of base residues. Nucleic Acids Res 1980; 8:6199–6211.CrossRefGoogle Scholar
  85. 85.
    Katcher HL, Wallace SS. Characterization of the Escherichia coli X-ray endonuclease, endonuclease III. Biochemistry 1983; 22:4071–4081.CrossRefGoogle Scholar
  86. 86.
    Boorstein RJ, Hubert TP, Cadet J et al. UV-induced pyrimidine hydrates in DNA are repaired by bacterial and mammalian DNA glycosylase activity. Biochemistry 1989; 28:6164–6170.CrossRefGoogle Scholar
  87. 87.
    Dizdaroglu M, Laval J, Boiteux S. Substrate specificity of the Escherichia coli endonuclease III: excision of thymine-and cytosine-derived lesions in DNA produced by radiation-generated free radicals. Biochemistry 1993; 32:12105–12111.CrossRefGoogle Scholar
  88. 88.
    Strniste GF, Wallace SS. Endonucleolytic incision of x-irradiated deoxyribonucleic acid by extracts of Escherichia coli. Proc Natl Acad Sci USA 1975; 72:1997–2001.CrossRefGoogle Scholar
  89. 89.
    Gates FT, Linn S. Endonuclease from Escherichia coli that acts specifically upon duplex DNA damaged by ultraviolet light, osmium tetroxide, acid, or x-rays. I Biol Chem 1977; 252:2802–2807.Google Scholar
  90. 90.
    Bailly V, Verly WG. Escherichia coli endonuclease III is not an endonuclease but a β-elimination catalyst. Biochem J 1987; 242:565–572.Google Scholar
  91. 91.
    Kim J, Linn S. The mechanism of action of E. coli endonuclease III and T4 UV endonuclease (endonuclease V) at AP sites. Nucleic Acids Res 1988; 16:1135–1141.CrossRefGoogle Scholar
  92. 92.
    Mazumder A, Gerlt JA, Absalon MJ et al. Stereochemical studies of the β-elimina-tion reactions at aldehydic abasic sites in DNA: endonuclease III from Escherichia coliy sodium hydroxide and Lys-Trp-Lys. Biochemistry 1991; 30:1119–1126.CrossRefGoogle Scholar
  93. 93.
    Kuo C-F, McRee DE, Fisher CL et al. Atomic structure of the DNA repair [4Fe-4S] enzyme endonuclease III. Science 1992; 258:434–440.CrossRefGoogle Scholar
  94. 94.
    Kuo C-F, McRee DE, Cunningham RP et al. Crystallization and crystallographic characterization of the ironsulfur-containing enzyme endonuclease III from Escherichia coli. J Mol Biol 1992; 227:347–351.CrossRefGoogle Scholar
  95. 95.
    Thayer MM, Ahern H, Xing D et al. Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure. EMBO J 1995; 14:4108–4120.Google Scholar
  96. 96.
    Ohlendorf DH, Anderson WF, Fisher RG et al. The molecular basis of DNA-protein recognition inferred from the structure of cro repressor. Nature 1982; 298:718–723.CrossRefGoogle Scholar
  97. 97.
    O’Handley S, Scholes CP, Cunningham RP. Endonuclease III interactions with DNA substrates. 1. Binding and footprinting studies with oligonucleotides containing a reduced apyrimidinic site. Biochemistry 1995; 34:2528–2536.CrossRefGoogle Scholar
  98. 98.
    Hilbert TP, Boorstein RJ, Kung HC et al. Purification of a mammalian homologue of Escherichia coli endonuclease III: identification of a bovine pyrimidine hydrate-thymine glycol DNA-glycosylase/AP lyase by irreversible cross linking to a thymine glycol-containing oligodeoxynucleotide. Biochemistry 1996; 35:2505–2511.CrossRefGoogle Scholar
  99. 99.
    Mattes WB, Lee C-S, Laval J et al. Excision of DNA adducts of nitrogen mustards by bacterial and mammalian 3-methyladenine-DNA glycosylases. Carcinogenesis 1996; 17:643–648.CrossRefGoogle Scholar
  100. 100.
    Nakabeppu Y, Kondo H, Sekiguchi M. Cloning and characterization of the AlkA gene of Escherichia coli that encodes 3-methyladenine DNA glycosylase II. J Biol Chem 1984; 259:13723–13729.Google Scholar
  101. 101.
    Saparbaev M, Kleibl K, Laval J. Escherichia coli, Saccharomyces cerevisiae, rat, and human 3-methyladenine DNA glycosylases repair 1,N 6-ethenoadenine when present in DNA. Nucleic Acids Res 1995; 23:3750–3755.CrossRefGoogle Scholar
  102. 102.
    Seeberg E, Eide L, Bjoras M. The baseexcision repair pathway. Trends Biochem Sci 1995; 20:391–397.CrossRefGoogle Scholar
  103. 103.
    Thomas L, Yang C-H, Goldthwait DA. Two DNA glycosylases in Escherichia coli which release primarily 3-methyladenine. Biochemistry 1982; 21:1162–1169.CrossRefGoogle Scholar
  104. 104.
    Yamagata Y, Kato M, Odawara et al. Three-dimensional structure of a DNA repair enzyme, 3-methyladenine DNA glycosylase II, from Escherichia coli. Cell 1996; 86:311–319.CrossRefGoogle Scholar
  105. 105.
    Labahn J, Schärer OD, Long A et al. Structural basis for the excision repair of alkylation-damaged DNA. Cell 1996; 86:321–329.CrossRefGoogle Scholar
  106. 106.
    Ishida T, Doi M, Ueda H et al. Specific ring stacking interaction on the tryptophan-7-methylguanine system: comparative crystallographic studies of indole derivatives-7-methylguanine base, nucleoside, and nucleotide complexes. J Am Chem Soc 1988; 110:2286–2294.CrossRefGoogle Scholar
  107. 107.
    Boiteux S, Bichara M, Fuchs RP et al. Excision of the imidazole ring-opened form of N-2-aminofluorene-C(8)-guanine adduct in poly(dG-dC) by Escherichia coli formamidopyrimidine-DNA glycosylase. Carcinogenesis 1989; 10:1905–1909.CrossRefGoogle Scholar
  108. 108.
    Chetsanga CJ, Lindahl T. Release of 7-methylguanine residues whose imidazole rings have been opened from damaged DNA by a DNA glycosylase from Escherichia coli. Nucleic Acids Res 1979; 6:3673–3683.CrossRefGoogle Scholar
  109. 109.
    Bessho T, Roy R, Yamamoto K et al. Repair of 8-hydroxyguanine in DNA by mammalian N-methylpurine-DNA glycosylase. Proc Natl Acad Sci USA 1993; 90:8901–8904.CrossRefGoogle Scholar
  110. 110.
    Tchou J, Kasai H, Shibutani S et al. 8-Oxoguanine (8-hydroxyguanine) DNA glycosylase and its substrate specificity. Proc Natl Acad Sci USA 1991; 88:4690–4694.CrossRefGoogle Scholar
  111. 111.
    Chetsanga CJ, Frenette GP. Excision of aflatoxin B1-imidazole ring opened guanine adducts from DNA by formamidopyrimidine-DNA glycosylase. Carcinogenesis 1983; 4:997–1000.CrossRefGoogle Scholar
  112. 112.
    Laval J, Boiteux S, O’Connor TR. Physiological properties and repair of apurinic/ apyrimidinic sites and imidazole ringopened guanines in DNA. Mutat Res 1990; 233:73–79.CrossRefGoogle Scholar
  113. 113.
    Tchou J, Grollman AP. Repair of DNA containing the oxidatively-damaged base, 8-oxoguanine. Mutat Res 1993; 299:277–287.CrossRefGoogle Scholar
  114. 114.
    O’Connor TR, Graves RJ, de Murcia G et al. Fpg protein of Escherichia coli is a zinc finger protein whose cysteine residues have a structural and/or functional role. J Biol Chem 1993; 268:9063–9070.Google Scholar
  115. 115.
    Tchou J, Michaels ML, Miller JH et al. Function of the zinc finger in Escherichia coli Fpg protein. J Biol Chem 1993; 268:26738–26744.Google Scholar
  116. 116.
    Castaing B, Boiteux S, Zelwer C. DNA containing a chemically reduced apurinic site is a high affinity ligand for the Escherichia coli formamidopyrimidine-DNA glycosylase. Nucleic Acids Res 1993; 21:2899–2905.CrossRefGoogle Scholar
  117. 117.
    Tchou J, Bodepudi V, Shibutani S et al. Substrate specificity of Fpg protein. J Biol Chem 1994; 269:15318–15324.Google Scholar
  118. 118.
    Riggs AD, Bourgeois S, Cohn M. The 1ac repressor-operator interaction. J Mol Biol 1970; 53:401–417.CrossRefGoogle Scholar
  119. 119.
    Berg OG, Winter RB, von Hippel PH. How do genome-regulatory proteins locate their DNA target sites? Trends Biochem Sci 1982; 7:52–55.CrossRefGoogle Scholar
  120. 120.
    Ehbrecht H-J, Pingoud A, Urbanke C et al. Linear diffusion of restriction endonucleases on DNA. J Biol Chem 1985; 260:6160–6166.Google Scholar
  121. 121.
    Singer P, Wu C-W. Promoter search by Escherichia coli RNA polymerase on a circular DNA template. J Biol Chem 1987; 262:14178–14189.Google Scholar
  122. 122.
    Ganesan AK, Seawell P, Lewis RJ et al. Processivity of T4 endonuclease V is sensitive to NaCl concentration. Biochemistry 1986; 25:5751–5755.CrossRefGoogle Scholar
  123. 123.
    Gruskin EA, Lloyd RS. The DNA scanning mechanism of T4 endonuclease V: effect of NaCl concentration on processive nicking activity. J Biol Chem 1986; 261:9607–9613.Google Scholar
  124. 124.
    Gruskin EA, Lloyd RS. Molecular analysis of plasmid DNA repair within UV-irradiated Escherichia coli. I: T4 endonuclease V-initiated excision repair. J Biol Chem 1988; 263:12728–12737.Google Scholar
  125. 125.
    Hamilton RW, Lloyd RS. Modulation of the DNA scanning activity of the Micrococcus luteus UV endonuclease. J Biol Chem 1989; 264:17422–17427.Google Scholar
  126. 126.
    Higley M, Lloyd RS. Processivity of uracil DNA glycosylase. Mutat Res 1993; 294:109–116.CrossRefGoogle Scholar
  127. 127.
    Berg OG, Winter RB, von Hippel PH. Diffusion-driven mechanisms of protein translocation on nucleic acids. Biochemistry 1981; 20:6929–6948.CrossRefGoogle Scholar
  128. 128.
    Lloyd RS, Dodson ML, Gruskin EA et al. T4 endonuclease V promotes the formation of multimeric DNA structures. Mutat Res 1987; 183:109–115.CrossRefGoogle Scholar
  129. 129.
    Grossman L, Thiagalingam S. Nucleotide excision repair, a tracking mechanism in search of damage. J Biol Chem 1993; 268:16871–16874.Google Scholar

Copyright information

© R.G. Landes Company 1997

Authors and Affiliations

  • Hanspeter Naegeli
    • 1
  1. 1.Institute of Pharmacology and ToxicologyUniversity of Zürich-TierspitalZürichSwitzerland

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