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HNH Endonucleases

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Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 16))

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References

  • Aravind L, Makarova KS, Koonin EV (2000) Holliday junction resolvases and related nucleases: identification of new families, phyletic distribution and evolutionary trajectories. Nucleic Acids Res 28:3417–3432

    Article  PubMed  CAS  Google Scholar 

  • Bujnicki JM, Radlinska M, Rychlewski L (2000) Atomic model of the 5-methylcytosine-specific restriction enzyme McrA reveals an atypical zinc finger and structural similarity to ββαMe endonucleases. Mol Microbiol 37:1280–1281

    Article  PubMed  CAS  Google Scholar 

  • Bujnicki JM, Radlinska M, Rychlewski L (2001) Polyphyletic evolution of type II restriction enzymes revisited: two independent sources of second-hand folds revealed. Trends Biochem Sci 26:9–11

    Article  PubMed  CAS  Google Scholar 

  • Changela A, Chen K, Xue Y, Holschen J, Outten CE, O’Halloran TV, Mondragon A (2003) Molecular basis of metal-ion selectivity and zeptomolar sensitivity by CueR. Science 301:1383–1387

    Article  PubMed  CAS  Google Scholar 

  • Cowan JA (1998) Metal activation of enzymes in nucleic acid biochemistry. Chem Rev 98:1067–1088

    Article  PubMed  CAS  Google Scholar 

  • Dalgaard JZ, Klar AJ, Moser MJ, Holley WR, Chatterjee A, Mian IS (1997) Statistical modeling and analysis of the LAGLIDADG family of site-specific endonucleases and identification of an intein that encodes a site-specific endonuclease of the HNH family. Nucleic Acids Res 25:4626–4638

    Article  PubMed  CAS  Google Scholar 

  • Datta S, Larkin C, Schildbach JF (2003) Structural insights into single-stranded DNA binding and cleavage by F factor TraI. Structure 11:1369–1379

    Article  PubMed  CAS  Google Scholar 

  • Drouin M, Lucas P, Otis C, Lemieux C, Turmel M (2000) Biochemical characterization of I-CmoeI reveals that this H-N-H homing endonuclease shares functional similarities with H-N-H colicins. Nucleic Acids Res 28:4566–4872

    Article  PubMed  CAS  Google Scholar 

  • Eddy SR, Gold L (1991) The phage T4 nrdB intron: a deletion mutant of a version found in the wild. Genes Dev 5:1032–1041

    PubMed  CAS  Google Scholar 

  • Friedhoff P, Franke I, Krause KL, Pingoud A (1999) Cleavage experiments with deoxythymidine 3′,5′-bis-(p-nitrophenyl phosphate) suggest that the homing endonuclease I-PpoI follows the same mechanism of phosphodiester bond hydrolysis as the non-specific Serratia nuclease. FEBS Lett 443:209–214

    Article  PubMed  CAS  Google Scholar 

  • Galburt EA, Chevalier B, Tang W, Jurica MS, Flick KE, Monnat RJ Jr, Stoddard BL (1999) A novel endonuclease mechanism directly visualized for I-PpoI. Nat Struct Biol 6:1096–1099

    Article  PubMed  CAS  Google Scholar 

  • Galburt EA, Stoddard BL (2002) Catalytic mechanisms of restriction and homing endonucleases. Biochemistry 41:13851–13860

    Article  PubMed  CAS  Google Scholar 

  • Galburt EA, Chadsey MS, Jurica MS, Chevalier BS, Erho D, Tang W, Monnat RJ Jr, Stoddard BL (2000) Conformational changes and cleavage by the homing endonuclease I-PpoI: a critical role for a leucine residue in the active site. J Mol Biol 300:877–887

    Article  PubMed  CAS  Google Scholar 

  • Goodrich-Blair H, Shub DA (1996) Beyond homing: competition between intron endonucleases confers a selective advantage on flanking genetic markers. Cell 84:211–221

    PubMed  CAS  Google Scholar 

  • Gorbalenya AE (1994) Self-splicing group I and group II introns encode homologous (putative) DNA endonucleases of a new family. Protein Sci 3:1117–1120

    Article  PubMed  CAS  Google Scholar 

  • Grishin NV (2001) Treble clef finger — a functionally diverse zinc-binding structural motif. Nucleic Acids Res 29:1703–1714

    PubMed  CAS  Google Scholar 

  • Hosfield DJ, Guan Y, Haas BJ, Cunningham RP, Tainer JA (1999) Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell 98:397–408

    Article  PubMed  CAS  Google Scholar 

  • Hsia KC, Chak KF, Liang PH, Cheng YS, Ku WY, Yuan HS (2004) DNA binding and degradation by the HNH protein ColE7. Structure 12:205–214

    Article  PubMed  Google Scholar 

  • James R, Penfold CN, Moore GR, Kleanthous C (2002) Killing of E. coli cells by E group nuclease colicins. Biochimie 84:381–389

    Article  PubMed  CAS  Google Scholar 

  • Keeble AH, Hemmings AM, James R, Moore GR, Kleanthous C (2002) Multistep binding of transition metals to the H-N-H endonuclease toxin colicin E9. Biochemistry 41:10234–10244

    Article  PubMed  CAS  Google Scholar 

  • Kleanthous C, Kuhlmann UC, Pommer AJ, Ferguson N, Radford SE, Moore GR, James R, Hemmings AM (1999) Structural and mechanistic basis of immunity toward endonuclease colicins. Nat Struct Biol 6:243–252

    Article  PubMed  CAS  Google Scholar 

  • Ko TP, Liao CC, Ku WY, Chak KF, Yuan HS (1999) The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein. Structure 7:91–102

    Article  PubMed  CAS  Google Scholar 

  • Ku WY, Liu YW, Hsu YC, Liao CC, Liang PH, Yuan HS, Chak KF (2002) The zinc ion in the HNH motif of the endonuclease domain of colicin E7 is not required for DNA binding but is essential for DNA hydrolysis. Nucleic Acids Res 30:1670–1678

    Article  PubMed  CAS  Google Scholar 

  • Kühlmann UC, Moore GR, James R, Kleanthous C, Hemmings AM (1999) Structural parsimony in endonuclease active sites: should the number of homing endonuclease families be redefined? FEBS Lett 463:1–2

    PubMed  Google Scholar 

  • Li CL, Hor LI, Chang ZF, Tsai LC, Yang WZ, Yuan HS (2003) DNA binding and cleavage by the periplasmic nuclease Vvn: a novel structure with a known active site. EMBO J 22:4014–4025

    PubMed  CAS  Google Scholar 

  • Malik HS, Henikoff S (2000) Dual recognition-incision enzymes might be involved in mismatch repair and meiosis. Trends Biochem Sci 25:414–418

    PubMed  CAS  Google Scholar 

  • Mannino SJ, Jenkins CL, Raines RT (1999) Chemical mechanism of DNA cleavage by the homing endonuclease I-PpoI. Biochemistry 36:16178–16186

    Google Scholar 

  • Maté MJ, Kleanthous C (2004) Structure-based analysis of the metal-dependent mechanism of H-N-H endonucleases. J Biol Chem 279:34763–34769

    PubMed  Google Scholar 

  • Miller MD, Cai J, Krause KL (1999) The active site of Serratia endonuclease contains a conserved magnesium-water cluster. J Mol Biol 288:975–987

    Article  PubMed  CAS  Google Scholar 

  • Pommer AJ, Wallis R, Moore GR, James R, Kleanthous C (1998) Enzymological characterization of the nuclease domain from the bacterial toxin colicin E9 from Escherichia coli. Biochem J 334:387–392

    PubMed  CAS  Google Scholar 

  • Pommer AJ, Kuhlmann UC, Cooper A, Hemmings AM, Moore GR, James R, Kleanthous C (1999) Homing in on the role of transition metals in the HNH motif of colicin endonucleases. J Biol Chem 274:27153–27160

    Article  PubMed  CAS  Google Scholar 

  • Pommer AJ, Cal S, Keeble AH, Walker D, Evans SJ, Kuhlmann UC, Cooper A, Connolly BA, Hemmings AM, Moore GR, James R, Kleanthous C (2001) Mechanism and cleavage specificity of the HNH endonuclease colicin E9. J Mol Biol 314:735–749

    Article  PubMed  CAS  Google Scholar 

  • Raaijmakers H, Toro I, Birkenbihl R, Kemper B, Suck D (2001) Conformational flexibility in T4 endonuclease VII revealed by crystallography: implications for substrate binding and cleavage. J Mol Biol 308:311–323

    Article  PubMed  CAS  Google Scholar 

  • San Filippo J, Lambowitz AM (2002) Characterization of the C-terminal DNA-binding/DNA endonuclease region of a group II intron-encoded protein. J Mol Biol 324:933–951

    Article  PubMed  CAS  Google Scholar 

  • Shen BW, Landthaler M, Shub DA, Stoddard BL (2004) DNA binding and cleavage by the HNH homing endonuclease I-HmuI. J Mol Biol 342:43–56

    Article  PubMed  CAS  Google Scholar 

  • Shub DA, Goodrich-Blair H, Eddy SR (1994) Amino acid sequence motif of group I intron endonucleases is conserved in open reading frames of group II introns. Trends Biochem Sci 19:402–404

    Article  PubMed  CAS  Google Scholar 

  • Sitbon E, Pietrokovski S (2003) New types of conserved sequence domains in DNA-binding regions of homing endonucleases. Trends Biochem Sci 28:473–477

    Article  PubMed  CAS  Google Scholar 

  • Walker DC, Georgiou T, Pommer AJ, Walker D, Moore GR, Kleanthous C, James R (2002) Mutagenic scan of the H-N-H motif of colicin E9: implications for the mechanistic enzymology of colicins, homing enzymes and apoptotic endonucleases. Nucleic Acids Res 30:3225–3234

    PubMed  CAS  Google Scholar 

  • Widlak P, Garrard WT (2001) Ionic and cofactor requirements for the activity of the apoptotic endonuclease DFF40/CAD. Mol Cell Biochem 218:125–130

    Article  PubMed  CAS  Google Scholar 

  • Widlak P, Li P, Wang X, Garrard WT (2000) Cleavage preferences of the apoptotic endonuclease DFF40 (caspase-activated DNase or nuclease) on naked DNA and chromatin substrates. J Biol Chem 275:8226–8232

    Article  PubMed  CAS  Google Scholar 

  • Wittmayer PK, Raines RT (1996) Substrate binding and turnover by the highly specific IPpoI endonuclease. Biochemistry 35:1076–1083

    Article  PubMed  CAS  Google Scholar 

  • Woo EJ, Kim YG, Kim MS, Han WD, Shin S, Robinson H, Park SY, Oh BH (2004) Structural mechanism for inactivation and activation of CAD/DFF40 in the apoptotic pathway. Mol Cell 14:531–539

    Article  PubMed  CAS  Google Scholar 

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Keeble, A.H., Maté, M.J., Kleanthous, C. (2005). HNH Endonucleases. In: Belfort, M., Wood, D.W., Stoddard, B.L., Derbyshire, V. (eds) Homing Endonucleases and Inteins. Nucleic Acids and Molecular Biology, vol 16. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-29474-0_4

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