Role of active site tyrosines in dynamic aspects of DNA binding by AP endonuclease

DNA Repair

Volumn 6, Issue 3, 2007, Pages 374-382

  Melo, Luisa F ^a   Mundle, Sophia T ^a   Fattal, Michael H ^a   O'Regan, N Edel ^a   Strauss, Phyllis R ^a  

^a NORTHEASTERN UNIVERSITY   (United States)

Author keywords

AP endonuclease; APE1; Apex; Base excision repair; DNA binding; EMSA; Kinetics; Tyrosine

Indexed keywords

DNA (APURINIC OR APYRIMIDINIC SITE) LYASE; HYDROXYL GROUP; TYROSINE;

ARTICLE; CATALYSIS; CONTROLLED STUDY; DNA BINDING; DNA CLEAVAGE; ENZYME ACTIVITY; ENZYME METABOLISM; GEL MOBILITY SHIFT ASSAY; HUMAN; MOLECULAR DYNAMICS; PRIORITY JOURNAL;

BINDING SITES; DNA; DNA REPAIR; DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE; ELECTROPHORETIC MOBILITY SHIFT ASSAY; HUMANS; KINETICS; TIME FACTORS; TYROSINE;

EID: 33847258902     PISSN: 15687864     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dnarep.2006.11.004     Document Type: Article

References (52)

1. Barzilay G., Walker L.J., Robson C.N., and Hickson I.D. Site-directed mutagenesis of the human DNA repair enzyme HAP1: identification of residues important for AP endonuclease and RNase H activity. Nucleic Acids Res. 23 (1995) 1544
2. Beloglazova N.G., Kirpota O.O., Starostin K.V., Ishchenko A.A., Yamkovoy V.I., et al. 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 (2004) 5134
3. Bennett S.E., Sanderson R.J., and Mosbaugh D.W. Processivity of Escherichia coli and rat liver mitochondrial uracil-DNA glycosylase is affected by NaCl concentration. Biochemistry 34 (1995) 6109
4. Brent T.P. Purification and characterization of human endonucleases specific for damaged DNA. Analysis of lesions induced by ultraviolet or X-radiation. Biochim. Biophys. Acta 454 (1976) 172
5. Carey D.C., and Strauss P.R. Human apurinic/apyrimidinic endonuclease is processive. Biochemistry 38 (1999) 16553
6. Chaudhry M.A., and Weinfeld M. Reactivity of human apurinic/apyrimidinic endonuclease and Escherichia coli exonuclease III with bistranded abasic sites in DNA. J. Biol. Chem. 272 (1997) 15650
7. David S.S., and Williams S.D. Chemistry of glycosylases and endonucleases involved in base-excision repair. Chem. Rev. 98 (1998) 1221
8. Demple B., and Harrison L. Repair of oxidative damage to DNA: enzymology and biology. Annu. Rev. Biochem. 63 (1994) 915
9. Demple B., Herman T., and Chen D.S. 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. U.S.A. 88 (1991) 11450
10. Doetsch P.W., and Cunningham R.P. The enzymology of apurinic/apyrimidinic endonucleases. Mutat. Res. 236 (1990) 173
11. Erzberger J.P., Barsky D., Scharer O.D., Colvin M.E., and Wilson III D.M. Elements in abasic site recognition by the major human and Escherichia coli apurinic/apyrimidinic endonucleases. Nucleic Acids Res. 26 (1998) 2771
12. Fersht A. Structure and Mechanism in Protein Science (1999), WH Freeman, New York
13. Friedberg E.C., Walker G.C., Siede W., Wood R.D., Schultz R.A., and Ellenberger T. DNA Repair and Mutagenesis (2006), ASM Press, Washington, DC 1118 pp
14. Gangurde R., Kaushik N., Singh K., and Modak M.J. A carboxylate triad is essential for the polymerase activity of Escherichia coli DNA polymerase I (Klenow fragment). Presence of two functional triads at the catalytic center. J. Biol. Chem. 275 (2000) 19685
15. Garner M.M., and Revzin A. A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res. 9 (1981) 3047
16. Henis Y.I., and Levitzki A. An analysis on the slope of Scatchard plots. Eur. J. Biochem. 71 (1976) 529
17. Izumi T., Henner W.D., and Mitra S. Negative regulation of the major human AP-endonuclease, a multifunctional protein. Biochemistry 35 (1996) 14679
18. Kan H.Y., Pissios P., Chambaz J., and Zannis V.I. DNA binding specificity and transactivation properties of SREBP-2 bound to multiple sites on the human apoA-II promoter. Nucleic Acids Res. 27 (1999) 1104
19. Kane C.M., and Linn S. Purification and characterization of an apurinic/apyrimidinic endonuclease from HeLa cells. J. Biol. Chem. 256 (1981) 3405
20. Klotz I.M., and Hunston D.L. Protein affinities for small molecules: conceptions and misconceptions. Arch. Biochem. Biophys. 193 (1979) 314
21. m. Nucleic Acids Res. 5 (1978) 951
22. Kuhnlein U., Penhoet E.E., and Linn S. An altered apurinic DNA endonuclease activity in group A and group D xeroderma pigmentosum fibroblasts. Proc. Natl. Acad. Sci. U.S.A. 73 (1976) 1169
23. Lindahl T. Instability and decay of the primary structure of DNA. Nature 362 (1993) 709
24. Lindahl T. DNA lesions generated in vivo by reactive oxygen species, their accumulation and repair. In: Dizdaroglu M. (Ed). DNA Damage and Repair: Oxygen Radical Effects, Cellular Protection and Biological Consequences (1999), Plenum Press, New York
25. Lindahl T., and Barnes D.E. Repair of endogenous DNA damage. Cold Spring Harb. Symp. Quant. Biol. 65 (2000) 127
26. Linsley W.S., Penhoet E.E., and Linn S. Human endonuclease specific for apurinic/apyrimidinic sites in DNA. Partial purification and characterization of multiple forms from placenta. J. Biol. Chem. 252 (1977) 1235
27. Lucas J.A., Masuda Y., Bennett R.A., Strauss N.S., and Strauss P.R. Single-turnover analysis of mutant human apurinic/apyrimidinic endonuclease. Biochemistry 38 (1999) 4958
28. Masuda Y., Bennett R.A., and Demple B. Dynamics of the interaction of human apurinic endonuclease (Ape1) with its substrate and product. J. Biol. Chem. 273 (1998) 30352
29. Masuda Y., Bennett R.A., and Demple B. Rapid dissociation of human apurinic endonuclease (Ape1) from incised DNA induced by magnesium. J. Biol. Chem. 273 (1998) 30360
30. McCullough A.K., Dodson M.L., and Lloyd R.S. Initiation of base excision repair: glycosylase mechanisms and structures. Annu. Rev. Biochem. 68 (1999) 255
31. McCullough A.K., Sanchez A., Dodson M.L., Marapaka P., Taylor J.S., and Lloyd R.S. The reaction mechanism of DNA glycosylase/AP lyases at abasic sites. Biochemistry 40 (2001) 561
32. McKenzie J.A., and Strauss P.R. Oligonucleotides with bistranded abasic sites interfere with substrate binding and catalysis by human apurinic/apyrimidinic endonuclease. Biochemistry 40 (2001) 13254
33. Mol C.D., Izumi T., Mitra S., and Tainer J.A. DNA-bound structures and mutants reveal abasic DNA binding by APE1 and DNA repair coordination [corrected]. Nature 403 (2000) 451
34. Mosbaugh D.W., and Linn S. Further characterization of human fibroblast apurinic/apyrimidinic DNA endonucleases. The definition of two mechanistic classes of enzyme. J. Biol. Chem. 255 (1980) 11743
35. Mundle S.T., Fattal M., Melo L.M., and Strauss P.R. A novel mechanism for human AP endonuclease 1. DNA Repair (Amst) 3 (2004) 1447
36. Nakamura J., and Swenberg J.A. Endogenous apurinic/apyrimidinic sites in genomic DNA of mammalian tissues. Cancer Res 59 (1999) 2522
37. Nardone G., George J., and Chirikjian J.G. Differences in the kinetic properties of BamHI endonuclease and methylase with linear DNA substrates. J. Biol. Chem. 261 (1986) 12128
38. Nguyen L.H., Barsky D., Erzberger J.P., and Wilson III D.M. Mapping the protein-DNA interface and the metal-binding site of the major human apurinic/apyrimidinic endonuclease. J. Mol. Biol. 298 (2000) 447
39. Pollock R., and Treisman R. A sensitive method for the determination of protein-DNA binding specificities. Nucleic Acids Res. 18 (1990) 6197
40. Robson C.N., and Hickson I.D. Isolation of cDNA clones encoding a human apurinic/apyrimidinic endonuclease that corrects DNA repair and mutagenesis defects in E. coli xth (exonuclease III) mutants. Nucleic Acids Res. 19 (1991) 5519
41. Sambrook Ja.R., and David W. Molecular Cloning (2001), Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New Yok
42. Seki S., Hatsushika M., Watanabe S., Akiyama K., Nagao K., and Tsutsui K. cDNA cloning, sequencing, expression and possible domain structure of human APEX nuclease homologous to Escherichia coli exonuclease III. Biochim. Biophys. Acta 1131 (1992) 287
43. Strauss P.R., Beard W.A., Patterson T.A., and Wilson S.H. Substrate binding by human apurinic/apyrimidinic endonuclease indicates a Briggs-Haldane mechanism. J. Biol. Chem. 272 (1997) 1302
44. Strauss P.R., and O'Regan N.E. Abasic site repair in higher eukaryotes. DNA Damage Repair (2001) 43
45. Terry B.J., Jack W.E., and Modrich P. Facilitated diffusion during catalysis by EcoRI endonuclease. Nonspecific interactions in EcoRI catalysis. J. Biol. Chem. 260 (1985) 13130
46. Weston K. Extension of the DNA binding consensus of the chicken c-Myb and v-Myb proteins. Nucleic Acids Res. 20 (1992) 3043
47. Wilson III D.M., Takeshita M., and Demple B. Abasic site binding by the human apurinic endonuclease, Ape, and determination of the DNA contact sites. Nucleic Acids Res. 25 (1997) 933
48. Wilstermann A.M., and Osheroff N. Stabilization of eukaryotic topoisomerase II-DNA cleavage complexes. Curr. Top. Med. Chem. 3 (2003) 321
49. Xanthoudakis S., and Curran T. Identification and characterization of Ref-1, a nuclear protein that facilitates AP-1 DNA-binding activity. Embo J. 11 (1992) 653
50. Xanthoudakis S., Miao G., Wang F., Pan Y.C., and Curran T. Redox activation of Fos-Jun DNA binding activity is mediated by a DNA repair enzyme. Embo J. 11 (1992) 3323
51. Yajko D.M., and Weiss B. Mutations simultaneously affecting endonuclease II and exonuclease III in Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 72 (1975) 688
52. Yu S.L., Lee S.K., Johnson R.E., Prakash L., and Prakash S. The stalling of transcription at abasic sites is highly mutagenic. Mol. Cell. Biol. 23 (2003) 382