Defining the functional footprint for recognition and repair of deaminated DNA

Nucleic Acids Research

Volumn 40, Issue 22, 2012, Pages 11638-11647

  Baldwin, Michael R ^a   O'Brien, Patrick J ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALKYLADENINE DNA GLYCOSYLTRANSFERASE; DNA (APURINIC OR APYRIMIDINIC SITE) LYASE; DNA GLYCOSYLTRANSFERASE; OLIGONUCLEOTIDE; UNCLASSIFIED DRUG;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CATALYSIS; CRYSTAL STRUCTURE; DEAMINATION; DNA FOOTPRINTING; ENZYME ACTIVATION; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME METABOLISM; ENZYME SUBSTRATE COMPLEX; EXCISION REPAIR; HUMAN; PRIORITY JOURNAL;

BINDING SITES; DEAMINATION; DNA; DNA DAMAGE; DNA GLYCOSYLASES; DNA REPAIR; DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; HUMANS; OLIGONUCLEOTIDES; PROTEIN FOOTPRINTING;

EID: 84871251700     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks952     Document Type: Article

References (42)

1. Lindahl, T. (1993) Instability and decay of the primary structure of DNA. Nature, 362, 709-715.
2. Myrnes, B., Guddal, P. H. and Krokan, H. (1982) Metabolism of dITP in HeLa cell extracts, incorporation into DNA by isolated nuclei and release of hypoxanthine from DNA by a hypoxanthine-DNA glycosylase activity. Nucleic Acids Res., 10, 3693-3701.
3. Dianov, G. and Lindahl, T. (1991) Preferential recognition of I. T base-pairs in the initiation of excision-repair by hypoxanthine-DNA glycosylase. Nucleic Acids Res., 19, 3829-3833.
4. Lindahl, T. and Nyberg, B. (1974) Heat-induced deamination of cytosine residues in deoxyribonucleic acid. Biochemistry, 13, 3405-3410.
5. Saparbaev, M. and Laval, J. (1994) Excision of hypoxanthine from DNA containing dIMP residues by the Escherichia coli, yeast, rat, and human alkylpurine DNA glycosylases. Proc. Natl Acad. Sci. USA, 91, 5873-5877.
6. Hitchcock, T. M., Dong, L., Connor, E. E., Meira, L. B., Samson, L. D., Wyatt, M. D. and Cao, W. (2004) Oxanine DNA glycosylase activity from mammalian alkyladenine glycosylase. J. Biol. Chem., 279, 38177-38183.
7. Wuenschell, G. E., O'Connor, T. R. and Termini, J. (2003) Stability, miscoding potential, and repair of 20-deoxyxanthosine in DNA: implications for nitric oxide-induced mutagenesis. Biochemistry, 42, 3608-3616.
8. Dong, L., Meira, L. B., Hazra, T. K., Samson, L. D. and Cao, W. (2008) Oxanine DNA glycosylase activities in mammalian systems. DNA Repair, 7, 128-134.
9. Lau, A. Y., Scharer, O. D., Samson, L., Verdine, G. L. and Ellenberger, T. (1998) Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision. Cell, 95, 249-258.
10. Lau, A. Y., Wyatt, M. D., Glassner, B. J., Samson, L. D. and Ellenberger, T. (2000) Molecular basis for discriminating between normal and damaged bases by the human alkyladenine glycosylase, AAG. Proc. Natl Acad. Sci. USA, 97, 13573-13578.
11. Lingaraju, G. M., Davis, C. A., Setser, J. W., Samson, L. D. and Drennan, C. L. (2011) Structural basis for the inhibition of human alkyladenine DNA glycosylase (AAG) by 3, N4-ethenocytosine-containing DNA. J. Biol. Chem., 286, 13205-13213.
12. O'Brien, P. J. and Ellenberger, T. (2004) Dissecting the broad substrate specificity of human 3-methyladenine-DNA glycosylase. J. Biol. Chem., 279, 9750-9757.
13. Setser, J. W., Lingaraju, G. M., Davis, C. A., Samson, L. D. and Drennan, C. L. (2012) Searching for DNA lesions: structural evidence for lower-and higher-affinity DNA binding conformations of human alkyladenine DNA glycosylase. Biochemistry, 51, 382-390.
14. Baldwin, M. R. and O'Brien, P. J. (2010) Nonspecific DNA binding and coordination of the first two steps of base excision repair. Biochemistry, 49, 7879-7891.
15. Mol, C. D., Izumi, T., Mitra, S. and Tainer, J. A. (2000) DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected]. Nature, 403, 451-456.
16. Fitzgerald, M. E. and Drohat, A. C. (2008) Coordinating the initial steps of base excision repair. Apurinic/apyrimidinic endonuclease 1 actively stimulates thymine DNA glycosylase by disrupting the product complex. J. Biol. Chem., 283, 32680-32690.
17. Waters, T. R., Gallinari, P., Jiricny, J. and Swann, P. F. (1999) Human thymine DNA glycosylase binds to apurinic sites in DNA but is displaced by human apurinic endonuclease 1. J. Biol. Chem., 274, 67-74.
18. Hill, J. W., Hazra, T. K., Izumi, T. and Mitra, S. (2001) Stimulation of human 8-oxoguanine-DNA glycosylase by AP-endonuclease: potential coordination of the initial steps in base excision repair. Nucleic Acids Res., 29, 430-438.
19. Marenstein, D. R., Chan, M. K., Altamirano, A., Basu, A. K., Boorstein, R. J., Cunningham, R. P. and Teebor, G. W. (2003) Substrate specificity of human endonuclease III (hNTH1). Effect of human APE1 on hNTH1 activity. J. Biol. Chem., 278, 9005-9012.
20. Hegde, M. L., Hazra, T. K. and Mitra, S. (2010) Functions of disordered regions in mammalian early base excision repair proteins. Cell. Mol. Life Sci., 67, 3573-3587.
21. Ward, J. J., Sodhi, J. S., McGuffin, L. J., Buxton, B. F. and Jones, D. T. (2004) Prediction and functional analysis of native disorder in proteins from the three kingdoms of life. J. Mol. Biol., 337, 635-645.
22. Dyson, H. J. and Wright, P. E. (2005) Intrinsically unstructured proteins and their functions. Nat. Rev. Mol. Cell Biol., 6, 197-208.
23. O'Brien, P. J. and Ellenberger, T. (2003) Human alkyladenine DNA glycosylase uses acid-base catalysis for selective excision of damaged purines. Biochemistry, 42, 12418-12429.
24. Beernink, P. T., Segelke, B. W., Hadi, M. Z., Erzberger, J. P., Wilson, D. M. 3rd and Rupp, B. (2001) Two divalent metal ions in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1: implications for the catalytic mechanism. J. Mol. Biol., 307, 1023-1034.
25. Strauss, P. R. and Holt, C. M. (1998) Domain mapping of human apurinic/apyrimidinic endonuclease. Structural and functional evidence for a disordered amino terminus and a tight globular carboxyl domain. J. Biol. Chem., 273, 14435-14441.
26. Izumi, T. and Mitra, S. (1998) Deletion analysis of human AP-endonuclease: minimum sequence required for the endonuclease activity. Carcinogenesis, 19, 525-527.
27. Baldwin, M. R. and O'Brien, P. J. (2009) Human AP endonuclease 1 stimulates multiple-turnover base excision by alkyladenine DNA glycosylase. Biochemistry, 48, 6022-6033.
28. Fersht, A. (1999) Structure and Mechanism in Protein Science. W. H. Freeman, New York.
29. Hedglin, M. and O'Brien, P. J. (2008) Human alkyladenine DNA glycosylase employs a processive search for DNA damage. Biochemistry, 47, 11434-11445.
30. Maher, R. L. and Bloom, L. B. (2007) Pre-steady-state kinetic characterization of the AP endonuclease activity of human AP endonuclease 1. J. Biol. Chem., 282, 30577-30585.
31. Roy, R., Biswas, T., Hazra, T. K., Roy, G., Grabowski, D. T., Izumi, T., Srinivasan, G. and Mitra, S. (1998) Specific interaction of wild-type and truncated mouse N-methylpurine-DNA glycosylase with ethenoadenine-containing DNA. Biochemistry, 37, 580-589.
32. Miao, F., Bouziane, M. and O'Connor, T. R. (1998) Interaction of the recombinant human methylpurine-DNA glycosylase (MPG protein) with oligodeoxyribonucleotides containing either hypoxanthine or abasic sites. Nucleic Acids Res., 26, 4034-4041.
33. Nguyen, L. H., Barsky, D., Erzberger, J. P. and Wilson, D. M. 3rd. (2000) Mapping the protein-DNA interface and the metal-binding site of the major human apurinic/apyrimidinic endonuclease. J. Mol. Biol., 298, 447-459.
34. Nevinsky, G. A. (2011) Structural, thermodynamic, and kinetic basis for the activities of some nucleic acid repair enzymes. J. Mol. Recognit., 24, 656-677.
35. Beloglazova, N. G., Kirpota, O. O., Starostin, K. V., Ishchenko, A. A., Yamkovoy, V. I., Zharkov, D. O., Douglas, K. T. and Nevinsky, G. A. (2004) Thermodynamic, kinetic and structural basis for recognition and repair of abasic sites in DNA by apurinic/apyrimidinic endonuclease from human placenta. Nucleic Acids Res., 32, 4134-5146.
36. Yu, E., Gaucher, S. P. and Hadi, M. Z. (2010) Probing conformational changes in Ape1 during the progression of base excision repair. Biochemistry, 49, 3786-3796.
37. Hirao, I., Nishimura, Y., Tagawa, Y., Watanabe, K. and Miura, K. (1992) Extraordinarily stable mini-hairpins: electrophoretical and thermal properties of the various sequence variants of d(GCGAA AGC) and their effect on DNA sequencing. Nucleic Acids Res., 20, 3891-3896.
38. Santini, G. P., Cognet, J. A., Xu, D., Singarapu, K. K. and Herve du Penhoat, C. (2009) Nucleic acid folding determined by mesoscale modeling and NMR spectroscopy: solution structure of d(GCGA AAGC). J. Phys. Chem. B, 113, 6881-6893.
39. Antao, V. P., Lai, S. Y. and Tinoco, I. Jr. (1991) A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res., 19, 5901-5905.
40. Ng, P. S. and Bergstrom, D. E. (2004) Protein-DNA footprinting by endcapped duplex oligodeoxyribonucleotides. Nucleic Acids Res., 32, e107.
41. Ng, P. S., Pingle, M. R., Balasundarum, G., Friedman, A., Zu, X. and Bergstrom, D. E. (2003) Endcaps for stabilizing short DNA duplexes. Nucleosides Nucleotides Nucleic Acids, 22, 1635-1637.
42. Goujon, M., McWilliam, H., Li, W., Valentin, F., Squizzato, S., Paern, J. and Lopez, R. (2010) A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res., 38, W695-W699.