The structure of the human AGT protein bound to DNA and its implications for damage detection

Journal of Molecular Biology

Volumn 350, Issue 4, 2005, Pages 657-666

  Duguid, Erica M ^a   Rice, Phoebe A ^b   He, Chuan ^a  

^a UNIVERSITY OF CHICAGO   (United States)

^b Department of Biochemistry and Molecular Biology ^*  (United States)

Author keywords

Damage detection; DNA repair; Human AGT

Indexed keywords

CYTOSINE; DNA; DOUBLE STRANDED DNA; O ALKYLGUANINE DNA ALKYLTRANSFERASE; THYMINE; TRANSFERASE; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CRYSTAL STRUCTURE; DNA DAMAGE; ENZYME ACTIVE SITE; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN MODIFICATION; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; WILD TYPE; X RAY ANALYSIS;

EID: 20544455000     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.05.028     Document Type: Article

References (58)

1. E.C. Friedberg, G.C. Walker, and W. Siede DNA Repair and Mutagenesis 1995 ASM Press Washington, DC
2. R.D. Wood, M. Mitchell, J. Sgouros, and T. Lindahl Human DNA repair genes Science 291 2001 1284 1289
3. T. Lindahl, B. Sedgewick, M. Sekiguchi, and Y. Nakabeppu Regulation and expression of the adaptive response to alkylating agents Annu. Rev. Biochem. 57 1988 133 157
4. B. Sedgwick, P. Robins, N. Totty, and T. Lindahl Functional domains and methyl acceptor sites of the Escherichia coli Ada protein J. Biol. Chem. 263 1988 4430 4433
5. P.Ø. Falnes, R.F. Johansen, and E. Seeberg AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli Nature 419 2002 178 182
6. S. Trewick, T.F. Henshaw, R.P. Hausinger, T. Lindahl, and B. Sedgwick Oxidative demethylation by Escherichia coli AlkB directly reverts DNA damage Nature 419 2002 174 178
7. B. Sedgwick Repairing DNA-methylation damage Nature Rev. Mol. Cell Biol. 5 2004 148 157
8. 6-methylguanine-DNA methyltransferase in cell survivial, mutagenesis, and carcinogenesis Mutat. Res. 145 1985 1 16
9. 6-alkylguanine-DNA alkyltransferase: regulation and importance in response to alkylating carcinogenic and therapeutic agents Cancer Res. 50 1990 6119 6129
10. S. Mitra, and B. Kaina Regulation of repair of alkylation damage in mammalian genomes Prog. Nucl. Acid Res. Mol. Biol. 44 1993 109 142
11. 6-alkylguanine by alkyltransferases Mutat. Res. 462 2000 83 100
12. S.A. Kyrtopoulos, L.M. Anderson, S.K. Chhabra, V.L. Souliotis, V. Pletsa, C. Valavanis, and P. Georgiadis DNA adducts and the mechanism of carcinogenesis and cytotoxicity of methylating agents of environmental and clinical significance Cancer Detect. Prev. 21 1997 391 405
13. S.A. Kyrtopoulos DNA adducts in humans after exposure to methylating agents Mutat. Res. 405 1998 135 143
14. 6-alkylguanine-DNA alkyltransferase: role in carcinogenesis and chemotherapy BioEssays 24 2002 255 266
15. 6-methylguanine DNA-methyltransferase in other organisms Mutat. Res. 512 2002 67 84
16. J.A. Eisen, and P.C. Hanawalt A phylogenomic study of DNA repair genes, proteins, and processes Mutat. Res. 435 1999 171 213
17. 6-methylguanine- DNA methyltransferases J. Biol. Chem. 269 1994 730 733
18. 4-alkylthymine following exposure to methylating and ethylating hepatocarcinogens Carcinogenesis 6 1985 625 629
19. B. Singer O-Alkyl pyrimidines in mutagenesis and carcinogenesis: occurrence and significance Cancer Res. 46 1986 4879 4885
20. 6-benzylguanine Biochem. J. 298 1994 231 235
21. 6-alkylguanine-DNA alkyltransferases J. Biol. Chem. 272 1997 8332 8339
22. 6-benzylguanine Biochemistry 32 1993 11998 12006
23. S.L. Gerson Clinical relevance of MGMT in the treatment of cancer J. Clin. Oncol. 20 2002 2388 2399
24. 6-Benzylguanine and its role in chemotherapy Clin. Cancer Res. 3 1997 837 847
25. 6-benzylguanine in oligodeoxyribonucleotides J. Biol. Chem. 273 1998 10863 10867
26. 6-alkylguanine-DNA alkyltransferase Cancer Res. 54 1994 5123 5130
27. D.S. Daniels, C.D. Mol, A.S. Arvai, S. Kanugula, A.E. Pegg, and J.A. Tainer Active and alkylated human AGT structures: a novel zinc site, inhibitor and extrahelical base binding EMBO J. 19 2000 1719 1730
28. 6-alkylguanine-DNA alkyltransferase Biochemistry 42 2003 980 990
29. a and high reactivity of cysteine 145 Biochemistry 42 2003 10965 10970
30. 6-alkylguanine-DNA alkyltransferase Nucl. Acids Res. 28 2000 393 401
31. G.L. Verdine, and S.D. Bruner How do DNA repair proteins locate damaged bases in the genome? Chem. Biol. 4 1997 329 334
32. G.L. Verdine The flip side of DNA methylation Cell 76 1994 197 200
33. S. Klimasauskas, S. Kumar, S.J. Roberts, and X. Cheng HhaI methyltransferase flips its target base out of the DNA helix Cell 76 1994 357 369
34. K.M. Reinisch, L. Chen, G.L. Verdine, and W.N. Lipscomb The crystal structure of HaeIII methyltransferase covalently complexed to DNA: an extrahelical cytosine and rearranged base-pairing Cell 82 1995 143 153
35. G. Slupphaug, C.D. Mol, B. Kavil, A.S. Arvai, H.E. Krokan, and J.A. Tainer A nucleotide-flipping mechanism from the structure of human uracil DNA glycosylase bound to DNA Nature 384 1996 87 92
36. J. Labahn, O.D. Scharer, A. Long, K. Ezaz-Nikpay, G.L. Verdine, and T.E. Ellenberger Structurral basis for the excision repair of alkylation-damaged DNA Cell 86 1996 321 329
37. Y. Yamagata, S. Fujii, M. Kato, K. Odawara, Y. Tokuno, and Y. Nakashima Three-dimensional structure of a DNA repair enzyme 3-methyladenine DNA glycosylase II, from Escherichia coli Cell 86 1996 311 319
38. R. Roberts, and X. Cheng Base flipping Annu. Rev. Biochem. 67 1998 181 198
39. D.P. Hornby, and G.C. Ford Protein-mediated base flipping Curr. Opin. Biotechnol. 9 1998 354 358
40. S.D. Bruner, D.P.G. Norman, and G.L. Verdine Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA Nature 403 2000 859 866
41. J.C. Fromme, A. Banerjee, S.J. Huang, and G.L. Verdine Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase Nature 427 2003 652 656
42. S.S. David, and S.D. Williams Chemistry of glycosylases and endonucleases involved in base-excision repair Chem. Rev. 98 1998 1221 1261
43. 6-alkylguanine-DNA alkyltransferases Chem. Biol. 10 2003 827 835
44. D.S. Daniels, T.T. Woo, K.X. Luu, D.M. Noll, N.D. Clarke, A.E. Pegg, and J.A. Tainer DNA binding and nucleotide flipping by the human DNA repair protein AGT Nature Struct. Biol. Mol. Biol. 11 2004 714 720
45. 6-methylguanine in DNA with Michaelis-Menten-like kinetics Chem. Res. Toxicol. 16 2003 1405 1409
46. X.-J. Lu, and W.K. Olsen 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures Nucl. Acids Res. 31 2003 5108 5121
47. A. Banerjee, W. Yang, M. Karplus, and G.L. Verdine Structure of a repair enzyme interrogating undamaged DNA elucidated recognition of damaged DNA Nature 434 2005 612 618
48. B.K. Kay, M.P. Williamson, and M. Sudol The importance of being proline: the interaction of proline-rich motifs in signaling proteins with their cognate domains FASEB J. 14 2000 231 241
49. S. Jones, and J.M. Thorton Prediction of protein-protein interaction sites using patch analysis J. Mol. Biol. 272 1997 121 132
50. J.J. Rasimas, A.E. Pegg, and M.G. Fried DNA-binding mechanism of O6-alkylguanine-DNA alkyltransferase. Effects of protein and DNA alkylation on complex stability J. Biol. Chem. 278 2003 7973 7980
51. C. Cao, Y.L. Jiang, J.T. Stivers, and F. Song Dynamic openning of DNA during the enzymatic search for a damaged base Nature Struct. Biol. Mol. Biol. 11 2004 1230 1236
52. D.J. Krosky, F.P. Schwarz, and J.T. Stivers Linear free engery correlation for enzyme base flipping: how do damaged base-pairs faciliate specific recognition? Biochemistry 43 2004 4188 4195
53. Y. Mishina, and C. He Probing the structure and function of the Escherichia coli DNA alkylation repair AlkB protein through chemical cross-linking J. Am. Chem. Soc. 125 2003 8730 8731
54. S.S. Parikh, C.D. Mol, G. Slupphaug, S. Bharati, H.E. Krokan, and J.A. Tainer Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA EMBO J. 17 1998 5214 5226
55. A.M. MacMillan, and G.L. Verdine Synthesis of functionally tethered oligonucleotides by the convertible nucleoside approach J. Org. Chem. 55 1990 5931 5933
56. A.M. MacMillan, and G.L. Verdine Engineering tethered DNA molecules by the convertible nucleoside approach Tetrahedron 14 1991 2603 2616
57. 4-(dimethylamino)-5-methylcytosine and 4-thiothymine J. Org. Chem. 57 1992 3839 3845
58. Z.M.W. Otwinowski Processing of X-ray diffraction data collected in oscillation mode Methods Enzymol. 276 1996 307 326