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Crystallographic Studies of Proteins Involved in Recombinational Repair and Excision Repair

  • Chapter
DNA Repair

Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 12))

Abstract

DNA repair is a very complicated phenomenon that is inseparable from replication and transcription. However, it may be roughly divided into recombinational repair relevant to SOS response and excision repair for the elimination of lesions produced by radiation exposure or by chemical modification. Both of these processes involve various protein factors and enzymes acting on the DNA. These proteins essentially interact with DNA through the recognition of unique conformations around damaged moieties or of four-way junctions at the points of strand exchange. In this respect, they are distinct from other well-characterized DNA binding proteins, such as transcriptional regulatory factors, the functions of which rely upon the specific recognition of base sequences. Thus, a major focus in cell biology and medical sciences is to fully understand the structural basis for the maintenance of genetic information.

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References

  • Ariyoshi M, Vassylyev DG, Fujishima A, Iwasaki H, Shinagawa H, Morikawa K (1994a) Preliminary crystallographic study of Escherichia coli RuvC protein: an endonuclease specific for Holliday junctions. J Mol Biol 241: 281–282

    Article  CAS  PubMed  Google Scholar 

  • Ariyoshi M, Vassylyev DG, Iwasaki H, Shinagawa H, Morikawa K (1994b) Atomic structure of the RuvC resolvase: a Holliday junction-specific endonuclease from E. coli. Cell 78: 1063–1072

    Article  CAS  PubMed  Google Scholar 

  • Bennett RJ, West SC (1995a) RuvC protein resolves Holliday junctions via cleavage of the continuous (noncrossover) strands. Proc Natl Acad Sci USA 92: 5635–5639

    Article  CAS  PubMed  Google Scholar 

  • Bennett RJ, West SC (1995b) Structural analysis of the RuvC Holliday junction complex reveals an unfolded junction. J Mol Biol 252: 213–226

    Article  CAS  PubMed  Google Scholar 

  • Bennett RJ, Dunderdale HJ, West SC (1993) Resolution of Holliday junctions by RuvC resolvase: cleavage specificity and DNA distortion. Cell 74: 1021–1031

    Article  CAS  PubMed  Google Scholar 

  • Bochkarev A, Pfuetzner RA, Edwards AM, Frappier L (1997) Structure of the singlestranded-DNA-binding domain of replication protein A bound to DNA. Nature 385: 176–181

    Article  CAS  PubMed  Google Scholar 

  • Bujacz C, Jaskolski M, Alexandratos J, Wlodawer A, Markel G, Katz RA, Skalka AM (1995) High-resolution structure of the catalytic domain of avian sarcoma integrase. J Mol Biol 253: 333–346

    Article  CAS  PubMed  Google Scholar 

  • Bujacz C, Jaskolski M, Alexandratos J, Wlodawer A, Markel G, Katz RA, Skalka AM (1996) The catalytic domain of avian sarcoma virus integrase: conformation of the active-site residues in the presence of divalent cations. Structure 4: 89–96

    Article  CAS  PubMed  Google Scholar 

  • Cheng X, Kumar S, Posfai J, Pflugrath JW, Roberts RJ (1993) Crystal structure of the Hhal DNA methyltransferase complexed with S-adenosyl-L-methionine. Cell 74: 299–307

    Article  CAS  PubMed  Google Scholar 

  • Dodson ML, Lloyd RS (1989) Structure-function studies of the T4 endonuclease V repair enzyme. Mutat Res 218: 49–65

    CAS  PubMed  Google Scholar 

  • Dodson ML, Schrock RD III, Lloyd RS (1993) Evidence for an imino intermediate in the T4 endonuclease V reaction. Biochemistry 32: 8284–8290

    Article  CAS  PubMed  Google Scholar 

  • Doherty JA, Serpell LC, Ponting CP (1996) The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA. Nucleic Acids Res 24: 88–2497

    Google Scholar 

  • Doi T, Recktenwald A, Karaki Y, Kikuchi M, Morikawa K, Ikehara M, Inaoka T, Hori N, Ohtsuka E (1992) Role of the basic amino acid cluster and Glu-23 in pyrimidine dimer glycosylase activity of T4 endonuclease V Proc Natl Acad Sci USA 89: 9420–9424

    Article  CAS  PubMed  Google Scholar 

  • Dunderdale HJ, Benson FE, Parsons CA, Sharpies GJ, Lloyd RG, West SC (1991) Formation and resolution of recombination intermediates by E. coli RecA and RuvC proteins. Nature 354: 506–510

    Article  CAS  PubMed  Google Scholar 

  • Dyda F, Hickman AB, Jenkins TM, Engelman A, Craigie R, Davies DR (1994) Crystal structure of the catalytic domain of HIV-1 integrase: similarity to other polynucleotidyl transferases. Science 266: 1981–1986

    Article  CAS  PubMed  Google Scholar 

  • Eggleston AK, Mitchell AH, West SC (1997) In vitro reconsititution of the late steps of genetic recombination in E. Coli. Cell 89: 607–617

    Article  CAS  PubMed  Google Scholar 

  • Holliday R (1964) A mechanism for gene conversion in fungi. Genet Res Camb 5: 282–304

    Article  Google Scholar 

  • Iwai S, Maeda M, Shirai M, Shimada Y, Osafune T, Murata T, Ohtsuka E (1995) Reaction mechanism of T4 endonuclease V determined by analysis using modified oligonucleotide duplexes. Biochemistry 34: 4601–4609

    Article  CAS  PubMed  Google Scholar 

  • Iwasaki H, Takahagi M, Shiba T, Nakata A, Shinagawa H (1991) Escherichia coli RuvC protein is an endonuclease that resolves the Holliday structure. EMBO J 10: 4381–4389

    CAS  PubMed  Google Scholar 

  • Iwasaki H, Takahagi M, Nakata A, Shinagawa H (1992) Escherichia coli RuvA and RuvB proteins specifically interact with Holliday junctions and promote branch migration. Genes Dev 6: 2214–2220

    Article  CAS  PubMed  Google Scholar 

  • Kashiwagi T, Denis J, Mitsuru H, Katayanagi K, Kanaya S, Morikawa K (1996) Proposal for new catalytic roles for two invariant residues in Escherichia coli ribonuclease HI. Protein Engin 9: 857–867

    Article  CAS  Google Scholar 

  • Katayanagi K, Miyagawa M, Ishikawa M, Matsushima M, Kanaya S, Ikehara M, Matsuzaki T, Morikawa K (1990) Three-dimensional structure of ribonuclease H from E. coll Nature 347: 306–309

    Article  CAS  PubMed  Google Scholar 

  • Katayanagi K, Miyagawa M, Matsushima M, Ishikawa M, Kanaya S, Nakamura H, Ikehara M, Matsuzaki T, Morikawa K (1992) Structural details of ribonuclease H from Escherichia coli as refined to an atomic resolution. J Mol Biol 223: 1029–1052

    Article  CAS  PubMed  Google Scholar 

  • Katayanagi K, Okumura M, Morikawa K (1993) Crystal sturcture of Escherichia coli Rnase HI in complex with Mg2+ at 2.8 Ã… resolution: proof for a single Mg2+-binding site. Proteins: Struct Funct Genet 17: 337–346

    Article  CAS  Google Scholar 

  • Kemmink J, Boelens R, Koning TMG, Kaptein R, van der Marel GA, van Boom JH (1987a) Conformational changes in the oligonucleotide duplex d(GCGTTGCG). d(CGCAACGC) induced by formation of a cis-syn thymine dimer. Eur J Biochem 162: 37–43

    Article  CAS  PubMed  Google Scholar 

  • Kemmink J, Boelens R, Koning T, van der Marel GA, van Boom JH, Kaptein R (1987b) 1H NMR study of the exchangeable protons of the duplex d(GCGTTGCG)d(CGCAACGC) containing a thymine photodimer. Nucleic Acids Res 15: 4645–4653

    Article  CAS  PubMed  Google Scholar 

  • Kilmasaukas S, Kumar S, Roberts RJ, Cheng X (1994) Hhal methyltransferase flips its target base out of DNA helix. Cell 76: 357–369

    Article  Google Scholar 

  • Latham KA, Manuel RC, Lloyd RS (1995) The interaction of T4 endonuclease V E23Q mutant with thymine dimer-and tetrahydrofuran-containing DNA. J Bacteriol 177: 5166–5168

    CAS  PubMed  Google Scholar 

  • Lee BJ, Sakashita H, Ohkubo T, Ikehara M, Doi T, Morikawa K, Kyogoku Y, Osafune T, Iwai S, Ohtsuka E (1994) Nuclear magnetic resonance study of the interaction of T4 endonuclease V with DNA. Biochemistry 33: 57–64

    Article  CAS  PubMed  Google Scholar 

  • Loll PJ, Lattman EE (1989) The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 Ã…. Proteins: Struct Funct Gen 5: 183–201

    Article  CAS  Google Scholar 

  • Manuel RC, Latham KA, Dodson ML, Lloyd RS (1995) Involvement of glutamic acid 23 in the catalytic mechanism of T4 endonuclease V. J Biol Chem 270: 2652–2661

    Article  CAS  PubMed  Google Scholar 

  • Miaskiewicz K, Miller J, Cooney M, Osman R (1996) Computational simulations of DNA distortions by a cis-syn-cyclobutane thymine dimer lesion. J Am Chem Soc 118: 9156–9163

    Article  CAS  Google Scholar 

  • Mizuuchi K (1997) Polynucleotidyl transfer reaction in site-specific DNA recombination. Gene Cells 2: 1–12

    Article  CAS  Google Scholar 

  • Morikawa K, Tsujimoto M, Ikehara M, Inaoka T, Ohtsuka E (1988) Preliminary crystallographic study of pyrimidine dimer-specific excision-repair enzyme from bacteriophage T4. J Mol Biol 202: 683–684

    Article  CAS  PubMed  Google Scholar 

  • Morikawa K, Matsumoto O, Tsujimoto M, Katayanagi K, Ariyoshi M, Doi T, Ikehara M, Inaoka T, Ohtsuka E (1992) X-ray structure of T4 endonuclease V: an excision repair enzyme specific for a pyrimidine dimer. Science 256: 523–526

    Article  CAS  PubMed  Google Scholar 

  • Morikawa K, Ariyoshi M, Vassylyev DG, Matsumoto O, Katayanagi K, Ohtsuka E (1995) Crystal structure of a pyrimidine dimer-specific excision repair enzyme from bacteriophage T4: refinement at 1.45 Ã… and X-ray analysis of three active site mutants. J Mol Biol 249: 360–375

    Article  CAS  PubMed  Google Scholar 

  • Murzin AG (1993) OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J 12: 861–867

    CAS  PubMed  Google Scholar 

  • Nishino T, Ariyoshi M, Iwasaki H, Shinagawa H, Morikawa K (1998) Functional analyses of the domain structure in the Holliday junction binding protein RuvA. Structure 6: 11–21

    Article  CAS  PubMed  Google Scholar 

  • Osman R, Luo N, Miaskiewicz K, Miller L (1995) Structure/function relationships at early times. In: Fuciarelli AF, Zimbrick JD (eds) Radiation damage in DNA. Battelle Press, Columbus, Ohio pp 323–330

    Google Scholar 

  • Rafferty JB, Sedelnikova SE, Hargreaves DH, Artymiuk PJ, Baker PJ, Sharpies GJ, Mahdi AA, Lloyd RG, Rice DW (1996) Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction. Science 274: 415–421

    Article  CAS  PubMed  Google Scholar 

  • Rice P, Mizuuchi K (1995) Structure of the bacteriophage Mu transposase core: a common structural motif for DNA transposition and retroviral integration. Cell 82: 209–220

    Article  CAS  PubMed  Google Scholar 

  • Ruff M, Krishnaswamy S, Boeglin M, Poterszman A, Mitschler A, Podjarny A, Rees B, Thiery JC, Moras D (1991) ClassII aminoacyl transfer RNA synthetase: crystal structure of yeast aspartyl-tRNA synthetase complexed with tRNAAsp. Science 252: 1682–1689

    Article  CAS  PubMed  Google Scholar 

  • Saito A, Iwasaki H, Ariyoshi M, Morikawa K, Shinagawa H (1995) Identification of four acidic amino acids that constitute the catalytic center of the RuvC Holliday junction resolvase. Proc Natl Acad Sci USA 92: 7470–7474

    Article  CAS  PubMed  Google Scholar 

  • Schrock RD III, Lloyd RS (1991) Reductive methylation of the amino terminus of endonuclease V eradicates catalytic activities. J Biol Chem 266: 17631–17639

    CAS  PubMed  Google Scholar 

  • Sedelnikova SE, Rafferty JB, Hargreaves D, Mahdi AA, Lloyd RG, Rice DW (1997) Crystallization of E. coli RuvA gives insights into the symmetry of a Holliday junction/protein complex. Acta Crystallogr D53: 122–124

    CAS  Google Scholar 

  • Shamoo Y, Friedman AM, Parsons MR, Konigsberg WH, Steitz TA (1995) Crystal structure of a replication fork single-stranded DNA binding protein (T4 gp32) complexed to DNA. Nature 376: 362–366

    Article  CAS  PubMed  Google Scholar 

  • Shida T, Hiroshi I, Atsushi S, Yoshimasa Kyogoku Shinagawa H (1996) Analysis of substrate specificity of the RuvC Holliday junction resolvase with synthetic Holliday junctions. J Biol Chem 271: 26105–26109

    Article  CAS  PubMed  Google Scholar 

  • Shinagawa H, Iwasaki H (1996) Processing the Holliday junction in homologous recombination. Trends Biochem Sci 21: 107–111

    CAS  PubMed  Google Scholar 

  • Slupphaug G, Mol CD, Kavil B, Arvai AS, Krokan HE, Tainer JA (1997) Structure of human uracil-DNA glycosylase bound to DNA shows a nucleotide flipping mechanism. Nature 384: 87–92

    Article  Google Scholar 

  • Tsaneva IR, Muller B, West SC (1992) ATP-dependent branch migration of Holliday junctions promoted by the RuvA and RuvB proteins of E. coli. Cell 69: 1171–1180

    Article  CAS  PubMed  Google Scholar 

  • Tsaneva IR, Muller B, West SC (1993) The RuvA and RuvB proteins Escherichia coli exhibit DNA helicase activity in vitro. Proc Natl Acad Sci USA 90: 1315–1319

    Article  CAS  PubMed  Google Scholar 

  • Vassylyev DG, Morikawa K (1997) DNA-repair enzymes. Curr Opin Struct Biol 7: 103–109

    Article  CAS  PubMed  Google Scholar 

  • Vassylyev DG, Kashiwagi T, Mileami Y, Aviyoshi M, Iwai S, Ohtsuka E, Movikawa K (1995) Atomic model of a pyrimidine dimer excisior repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition. Cell 83: 773–782

    Article  CAS  PubMed  Google Scholar 

  • von Kitzing E, Lilley MJ, Dieksmann S (1990) The sterochemistry of a four-way DNA junction: a theoretical study. Nucl Acids Res 18: 2671–2683

    Article  Google Scholar 

  • West SC (1996) The RuvABC proteins and Holliday junction processing in Escherichia coli. J Bacteriol 178: 1237–1241

    CAS  PubMed  Google Scholar 

  • Whitby MC, Bolt EL, Chan SN, Lloyd RG (1997) Interaction between RuvA and RuvC at Holliday junctions: inhibition of junction cleavage and formation of a RuvA-RuvC-DNA complex. J Mol Biol 264: 878–890

    Article  Google Scholar 

  • Yang C, Curth U, Urbanke C, Kang C (1997) Crystal structure of human mitochondrial single-stranded DNA binding protein at 2.4 A resolution. Nat Struct Biol 4: 152–157

    Article  Google Scholar 

  • Yang W, Steitz TA (1995) Recombining the structures of HIV integrase, RuvC and RNaseH. Structure 3: 131–134

    Article  CAS  PubMed  Google Scholar 

  • Yu X, West SC, Egelman EH (1997) Structure and subunit composition of the RuvAB-Holliday junction complex. J Mol Biol 266: 217–222

    Article  CAS  PubMed  Google Scholar 

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© 1998 Springer-Verlag Berlin Heidelberg

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Morikawa, K. (1998). Crystallographic Studies of Proteins Involved in Recombinational Repair and Excision Repair. In: Eckstein, F., Lilley, D.M.J. (eds) DNA Repair. Nucleic Acids and Molecular Biology, vol 12. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-48770-5_12

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  • DOI: https://doi.org/10.1007/978-3-642-48770-5_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-48772-9

  • Online ISBN: 978-3-642-48770-5

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