DNA-repair enzymes

Current Opinion in Structural Biology

Volumn 7, Issue 1, 1997, Pages 103-109

  Vassylyev, Dmitry G ^a   Morikawa, Kosuke ^b  

^a ADVANCED TELECOMMUNICATIONS RESEARCH INSTITUTE INTERNATIONAL   (Japan)

^b BIOMOL ENG RESEARCH INSTITUTE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ENDONUCLEASE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE;

CRYSTAL STRUCTURE; DNA BINDING; DNA REPAIR; EXCISION REPAIR; PRIORITY JOURNAL; REVIEW;

EID: 0031056091     PISSN: 0959440X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-440X(97)80013-9     Document Type: Article

References (49)

1. Friedberg EC, Walker GC, Siede W. Spontaneous alterations of and damage to DNA. DNA Repair and Mutagenesis. 1995;2-19 ASM Press, Washington DC.
2. Lehman AR. Nucleotide excision repair and the link with transcription. Trends Biochem Sci. 20:1995;402-405.
3. Kolodner RD. Mismatch repair: mechanisms and relationship to cancer susceptibility. Trends Biochem Sci. 20:1995;397-401.
4. Friedberg EC, Walker GC, Siede W. Mismatch repair. DNA Repair and Mutagenesis. 1995;367-405 ASM Press, Washington.
5. Latham KA, Lloyd RS. T4 endonuclease V: perspectives on catalysis. Wallace S, Houten BV, Kow YW. DNA Damage. 1994;181-197 New York Academy of Sciences, New York.
6. Vassylyev DG, Kashiwagi T, Mikami Y, Ariyoshi M, Iwai S, Ohtsuka E, Morikawa K. Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition. of outstanding interest Cell. 83:1995;773-782 The crystal structure of an inactive mutant of T4 endo V in complex with a cognate DNA substrate refined to 2.75 Å resolution is reported. Implications for the mechanisms of damage recognition and catalytic reaction at the molecular level are discussed.
7. Morikawa K, Ariyoshi M, Vassylyev DG, Matsumoto O, Katayanagi K, Ohtsuka E. Crystal structure of a pyrimidine dimer-specific excision enzyme from bacteriophage T4: refinement at 1.45 Å resolution and X-ray analysis of the three active site mutants. J Mol Biol. 249:1995;360-375.
8. Kemmink J, Boelens R, Koning TMG, Kaptein R, Van der Marel GA, Van Boom JH. Conformational changes in the oligonucleotide duplex d(GCGTTGCG)d(CGCAACGC) induced by formation of cis-syn thymine dimer. Eur J Biochem. 162:1987;37-43.
9. 1H NMR study of the exchangeable protons of the duplex d(GCGTTGCG)d(CGCAACGC) containing a thymine dimer. Nucleic Acids Res. 15:1987;4645-4653.
10. 1H NMR assignment and melting temperature study of cis-syn and trans-syn thymine dimer containing duplex of d(GCTATTATGC)·d(GCATAATACG). Biochemistry. 29:1990;8858-8866.
11. Lee BJ, Sakashita H, Ohkubo T, Ikehara M, Doi T, Morikawa K, Kyogoku Y, Osafune T, Iwai S, Ohtsuka E. Nuclear magnetic resonance study of the interaction of T4 endonuclease V with DNA. Biochemistry. 33:1994;57-64.
12. Bremier LH, Lindahl T. A DNA glycosylase from Escherichia coli that releases free urea from polydeoxyribonucleotide containing fragments of base residues. Nucleic Acids Res. 8:1980;6199-6211.
13. Katcher HL, Wallace SS. Characterization of the Escherichia coli X-ray endonuclease, endonuclease III. Biochemistry. 22:1983;4071-4081.
14. Bremier LH, Lindahl T. DNA glycosylase activities for thymine residues damaged by ring saturation, fragmentation, or ring contraction are functions of endonuclease III in Escherichia coli. J Biol Chem. 259:1984;5543-5548.
15. Boorstein RJ, Hilbert TP, Cadet J, Cunningham RP, Teebor GW. UV-induced pyrimidine hydrates in DNA are repaired by bacterial and mammalian DNA glycosylase activities. Biochemistry. 28:1989;6164-6170.
16. 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. 32:1993;12105-12111.
17. Hatahet Z, Kow YW, Purmal AA, Cunningham RP, Wallace SS. New substrates for old enzymes, 5-hydroxy-2'-deoxycytidine and 5-hydroxy-2'-deoxyuridine are substrates for Escherichia coli endonuclease III and formamidopyrimidine DNA N-glycosylase, while 5-hydroxy-2'-deoxyuridine is a substrate for uracil DNA N-glycosylase. J Biol Chem. 269:1994;18814-18820.
18. Kow YW, Wallace SS. Mechanism of action of Escherichia coli endonuclease III. Biochemistry. 26:1987;8200-8206.
19. Thayer MM, Ahern H, Xing D, Cunningham RP, Tainer JA. Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure. of outstanding interest EMBO J. 14:1995;4108-4120 On the basis of the high-resolution crystal structure and a mutational analysis of the enzyme, the authors propose a structural basis for endo III - DNA binding and catalysis, involving two novel HhH and FCL DNA-binding motifs.
20. Kuo C-F, McRee DE, Fisher CL, O'Hadley SF, Cunningham RP, Tainer JA. Atomic structure of the DNA repair [4Fe - 4S] enzyme endonuclease III. Science. 258:1992;434-440.
21. Thomas L, Yang C-H, Goldthwait DA. Two DNA glycosylases in Escherichia coli which release primarily 3-methyladenine. Biochem J. 21:1982;1162-1169.
22. McCarthy TV, Karran P, Lindahl T. Inducible repair of O-alkylated DNA pyrimidines in Escherichia coli. EMBO J. 3:1984;545-550.
23. 2,3-ethenoguanine from chloracetaldehyde-treated DNA by Escherichia coli 3-methyladenine DNA glycosylase II. Proc Natl Acad Sci USA. 89:1992;9331-9334.
24. Bjelland S, Birkeland N-K, Benneche T, Volden G, Seeberg E. DNA glycosylase activities for thymine residues oxidized in the methyl group are functions of AlkA in Escherichia coli. J Biol Chem. 269:1994;30489-30495.
25. Saparbaev M, Laval J. Excision of hypoxanthine from DNA containing dIMP residues by the Escherichia coli, yeast, rat and human alkylpurine DNA glycosylases. Proc Natl Acad Sci USA. 91:1994;5873-5877.
26. 6-ethenoadenine when present in DNA. Nucleic Acids Res. 23:1995;3750-3755.
27. Yamagata Y, Kato M, Odawara K, Tokuno Y, Nakashima Y, Matsushima N, Yasumura K, Tomita K, Ihara K, Fujii Y, et al. Three-dimensional structure of a DNA repair enzyme, 3-methyladenine DNA glycosylase II, from Escherichia coli. of outstanding interest Cell. 86:1996;311-319 The structural analysis of AlkA at 2.3 Å resolution reveal that the 3D structures of the DNA-binding and catalytic domains are similar to those of two domains of endo III. The major catalytic residue, Asp238, determined by mutational analysis, is located in the cavity on the interface between the two domains. A tentative model of the enzyme - DNA complex is proposed.
28. Labahn J, Scharer OD, Long A, Ezaz-Nikpay K, Verdine GL, Ellenberger TE. Structural basis for the excision repair of alkylation-damaged DNA. of outstanding interest Cell. 86:1996;321-329 The crystal structure of the DNA repair enzyme AlkA refined to 1.8 Å resolution is presented. The significance of Asp238 in catalysis was confirmed by mutagenesis studies. The binding site for the alkylated bases is proposed to reside in a large hydrophobic cleft that is mostly occupied by aromatic residues.
29. Nikolov DB, Hu SH, Lin J, Gasch A, Hoffman A, Horikoshi M, Ohua NH, Roeder RG, Burley SK. Crystal structure of TFIID TATA box-binding protein. Nature. 360:1992;40-46.
30. Michaels ML, Tchou J, Grollman AP, Miller JH. A repair system for 8-oxo-7,8-dihydrodeoxyguanine. Biochemistry. 31:1992;10964-10968.
31. Tsai-Wu J-J, Liu H-F, Lu A-L. Escherichia coli MutY protein has both N-glycosylase and apurinic/apyrimidinic endonuclease activities on C and A-G mispairs. Proc Natl Acad Sci USA. 89:1992;8779-8783.
32. Hilbert P, Boorstein RJ, Kung HC, Bolton PH, Xing D, Cunningham RP, Teebor GW. 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. 35:1996;2505-2511.
33. Nash HM, Bruner SD, Scharer OD, Kawate T, Addona TA, Spooner E, Lane WS, Verdine GL. Cloning of a yeast 8-oxoguanine DNA glycosylase reveals the existence of a base-excision DNA-repair protein superfamily. of special interest Curr Biol. 6:1996;968-980 The yeast DNA glycosylase (Ogg1) specific to 8-oxoguanine is suggested to be closely related in 3D structure to endo III. The sequence motif shared between Ogg1, endo III, and AlkA was found in a number of other enzymes. This finding led to the proposal of a structural superfamily of DNA repair enzymes.
34. Seeberg E, Eide L, Bjoras M. The base excision repair pathway. Trends Biochem Sci. 20:1995;391-397.
35. Slupphaug G, Eftedal I, Kavli B, Bharati S, Helle NM, Haug T, Levine DW, Krokan HE. Properties of recombinant human uracil-DNA glycosylase from the UNG-gene and evidence that UNG-gene encodes the major uracil-DNA glycosylase. Biochemistry. 34:1995;128-138.
36. Savva R, McAuley-Hecht K, Brown T, Pearl L. The structural basis of specific base-excision repair by uracil-DNA glycosylase. of special interest Nature. 373:1995;487-493 The high-resolution crystal structures of UDG from herpes simplex virus, both in its free form and in complexes with a trinucleotide and uracil, reveal a new protein fold and allow the authors to propose mechanisms of DNA binding and catalysis.
37. Mol CD, Arvai AS, Slupphaug G, Kavli B, Alseth I, Krokan HE, Tainer JA. Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis. of special interest Cell. 80:1995;869-878 The crystal structures of the free form of glycosylase and its complex with 6-aminouracil, in combination with a mutational analysis, reveal the uracil-binding site, the catalytic residues, and the positively charged groove that is involved in DNA binding. The mechanism of the catalytic reaction is proposed.
38. Mol CD, Arvai AS, Sanderson RJ, Slupphaug G, Kavli B, Mosbaugh DW, Krokan HE, Tainer JA. Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: protein mimicry of DNA. of special interest Cell. 82:1995;701-708 The atomic structure of the complex of hUDG with a protein inhibitor, UGI, has been refined to 1.9 Å resolution. UGI was shown to bind to the DNA-binding loop of the hUDG, and to form no contacts with the uracil-binding pocket. A specific role in DNA binding is proposed for Leu272 of UDG.
39. Savva R, Pearl L. Nucleotide mimicry in the crystal structure of the uracil-DNA glycosylase-uracil glycosylase inhibitor protein complex. of special interest Nat Struct Biol. 373:1995;752-757 The crystal structure of HSV-1UDG in complex with a protein inhibitor (UGI) shows that UGI directly mimics the enzyme - DNA interactions observed in the HSV-1UDG - trinucleotide complex. UGI is shown to block access to the active site of the enzyme but to form no contacts within the uracil-binding pocket.
40. Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA. Structure of human uracil-DNA glycosylase bound to DNA shows a nucleotide flipping mechanism. of outstanding interest Nature. 384:1996;87-92 The structure of hUDG(Leu272→Arg/Asp 145→Asn) - DNA directly reveals the DNA - binding mechanism of hUDG and its cognate DNA substrate. The mutation Leu272→Arg abolishes the release of the product DNA from the protein but does not affect the glycosylase activity of the enzyme, so that the uracil in the complex is cleaved from the sugar moiety.
41. Klimasauskas S, Kumar S, Roberts RJ, Cheng X. Hha1 methyltransferase flips its target base out of the DNA duplex. Cell. 76:1994;357-369.
42. Sancar A. Structure and function of DNA photolyase. Biochemistry. 33:1994;2-9.
43. Park H-W, Kim S-T, Sancar A, Deisenhofer J. Crystal structure of DNA photolyase from Escherichia coli. of outstanding interest Science. 268:1995;1866-1872 The high resolution (2.3 Å) crystal structure of DNA photolyase complexed with its light-harvesting, MTF, and catalytic, FAD, cofactors is reported. The binding site for PD is determined and a mechanism of photoreactivation through electron transfer between FAD and PD is proposed.
44. Demple B, Harrison L. Repair of oxidative damage to DNA: enzymology and biology. Annu Rev Biochem. 63:1994;915-948.
45. 2+ and dCMP leaads to proposals of enzymatic and DNA-binding mechanisms.
46. Rice P, Craigie R, Davies DR. Retroviral integrases and their cousins. Curr Opin Struct Biol. 6:1996;76-83.
47. Scharer O, Verdine GL. A designed inhibitor of base-excision DNA repair. J Am Chem Soc. 117:1995;10781-10782.
48. Jones TA, Zou JY, Cowan SW, Kjeldgaard M. An improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst A. 47:1991;110-119.
49. 6-methylguanine-DNA methyltransferase from E. coli. EMBO J. 13:1994;1495-1501.