Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases

Cell

Volumn 92, Issue 6, 1998, Pages 841-850

  Cheng, Chonghui ^a   Kussie, Paul ^a   Pavletich, Nikola ^a   Shuman, Stewart ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA TOPOISOMERASE; RECOMBINASE;

AMINO ACID SEQUENCE; ARTICLE; ENZYME STRUCTURE; EUKARYOTE; GENETIC CONSERVATION; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; STRUCTURE ACTIVITY RELATION;

EUKARYOTA; SACCHAROMYCES CEREVISIAE; VACCINIA;

EID: 0032549763     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(00)81411-7     Document Type: Article

References (54)

1. Abremski, K., Wierzbicki, A., Frommer, B., and Hoess, R.H. (1986). Bacteriophage P1 Cre-loxP site-specific recombination: site-specific DNA topoisomerase activity of the Cre recombination protein. J. Biol. Chem. 261, 391-396.
2. Brunger, A.T. (1991). X-PLOR, a system for crystallography and NMR. Version 3.0. (New Haven, CT: Yale University Press).
3. Caron, P.R., and Wang, J.C. (1994). Alignment of primary sequences of DNA topoisomerases. Adv. Pharmacol. 29B, 271-297.
4. Cheng, C., Wang, L.K., Sekiguchi, J., and Shuman, S. (1997). Mutational analysis of 39 residues of vaccinia DNA topoisomerase identifies Lys-220, Arg-223, and Asn-228 as important for covalent catalysis. J. Biol. Chem. 272, 8263-8269.
5. Cornet, F., Hallet, B., and Sherratt, D.J. (1997). Xer recombination in Escherichia coli: site-specific DNA topoisomerase activity of the XerC and XerD recombinases. J. Biol. Chem. 272, 21927-21931.
6. Eng, W., Pandit, S.D., and Sternglanz, R. (1989). Mapping of the active site tyrosine of eukaryotic DNA topoisomerase I. J. Biol. Chem. 262, 13373-13376.
7. Guo, F., Gopaul, D.N., and Van Duyne, G.D. (1997). Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature 389, 40-46.
8. Gupta, M., Fujimori, A., and Pommier, Y. (1995). Eukaryotic DNA topoisomerases I. Biochim. Biophys. Acta 1262, 1-14.
9. Han, Y.W., Gumport, R.I., and Gardner, J.F. (1993). Complementation of bacteriophage lambda integrase mutants. EMBO J. 12, 4577-4584.
10. Hickman, A.B., Waninger, S., Scocca, J.J, and Dyda, F. (1997). Molecular organization in site-specific recombination: the catalytic domain of bacteriophage HP1 integrase at 2.7 Å resolution. Cell 89, 227-237.
11. Hoess, R., Abremski, K., Irwin, S., Kendall, M., and Mack, A. (1990). DNA specificity of the Cre recombinase resides in the 25 kDa carboxyl domain of the protein. J. Mol. Biol. 276, 873-882.
12. Holm, L., and Sander, C. (1993). Protein structure comparison by alignment of distant matrices. J. Mol. Biol. 233, 123-138.
13. Jaxel, C., Capranico, G., Kerrigan, D., Kohn, K.W., and Pommier, Y. (1991). Effect of local DNA sequence on topoisomerase I cleavage in the presence or absence of camptothecin. J. Biol. Chem. 266, 20418-20423.
14. Jensen, A.D., and Svejstrup, J.Q. (1996). Purification and characterization of human topoisomerase I mutants. Eur. J. Biochem. 236, 389-394.
15. Jones, T.A., Zou, J.Y., Cowan, S.W., and Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Cryst. A47, 110-119.
16. Kikuchi, Y., and Nash, H.A. (1979). Nicking-closing activity associated with bacteriophage λ int gene product. Proc. Natl. Acad. Sci. USA 76, 3760-3764.
17. Kraulis, P. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crtystallogr. 24, 946-950.
18. Krogh, S., Mortensen, U.H., Westergaard, O., and Bonven, B.J. (1991). Eukaryotic topoisomerase I-DNA interecation is stabilized by helix curvature. Nucleic Acids Res. 19, 1235-1241.
19. Kwon, H.J., Tirumalai, R., Landy, A., and Ellenberger, T. (1997). Flexibility in DNA recombination: structure of lambda integrase catalytic core. Science 276, 126-131.
20. Lee, J., and Jayaram, M. (1993). Mechanism of site-specific recombination: logic of assembling recombinase catalytic site from fractional active sites. J. Biol. Chem. 268, 17564-17579.
21. Lue, N., Sharma, A., Mondragon, A., and Wang, J.C. (1995). A 26 kDa yeast DNA topoisomerase I fragment: crystallographic structure and mechanistic implications. Structure 3, 1315-1322.
22. Lynn, R.M., Bjornsti, M., Caron, P.R., and Wang, J.C. (1989). Peptide sequencing and site-directed mutagenesis identify tyrosine-727 as the active site tyrosine of Saccharomyces cerevisiae DNA topoisomerase I. Proc. Natl. Acad. Sci. USA 86, 3559-3563.
23. Morham, S.G., and Shuman, S. (1990). Phenotypic selection and characterization of mutant alleles of a eukaryotic DNA topoisomerase I. Genes Dev. 4, 515-524.
24. Morham, S.G., and Shuman, S. (1992). Covalent and noncovalent DNA binding by mutants of vaccinia DNA topoisomerase I. J. Biol. Chem. 267, 15984-15992.
25. Parsons, R.L., Prasad, P.V., Harshey, R.M., and Jayaram, M. (1988). Step-arrest mutants of FLP recombinase: implications for the catalytic mechanism of DNA recombination. Mol. Cell. Biol. 8, 3303-3310.
26. Parsons, R.L., Evans, B.R., Zheng, L., and Jayaram, M. (1990). Functional analysis of Arg-308 mutants of Flp recombinase: possible role of Arg-308 in coupling substrate binding to catalysis. J. Biol. Chem. 265, 4527-4533.
27. Petersen, B.Ø., and Shuman, S. (1997). Histidine-265 is important for covalent catalysis by vaccinia topoisomerase and is conserved in all eukaryotic type I enzymes. J. Biol. Chem. 272, 3891-3896.
28. Petersen, B.Ø., Wittschieben, J., and Shuman, S. (1996). Mutations within a conserved region of vaccinia topoisomerase affect the cleavage-religation equilibrium. J. Mol. Biol. 263, 181-195.
29. Petersen, B.Ø., Hall, R.L., Moyer R.W., and Shuman, S. (1997). Characterization of a DNA topoisomerase encoded by Amsacta moorei entomopoxvirus. Virology 230, 197-206.
30. Rothenberg, M.L. (1997). Topoisomerase I inhibitors: review and update. Ann. Oncology 8, 837-855.
31. Sekiguchi, J., and Shuman, S. (1994). Vaccinia topoisomerase binds circumferentially to DNA. J. Biol. Chem. 269, 31731-31734.
32. Sekiguchi, J., and Shuman, S. (1995). Proteolytic footprinting of vaccinia topoisomerase I bound to DNA. J. Biol. Chem. 270, 11636-11645.
33. Sekiguchi, J., and Shuman, S. (1996a). Identification of contacts between topoisomerase I and its target DNA by site-specific cross-linking. EMBO J. 15, 3448-3457.
34. Sekiguchi, J., and Shuman, S. (1996b). Covalent DNA binding by vaccinia topoisomerase results in unpairing of the thymine base 5′ of the scissile bond. J. Biol. Chem. 271, 19436-19442.
35. Sekiguchi, J., and Shuman, S. (1997). Mutational analysis of vaccinia virus topoisomerase identifies residues involved in DNA binding. Nucleic Acids Res. 25, 3649-3656.
36. Sekiguchi, J., Seeman, N.C., and Shuman, S. (1996). Resolution of Holliday junctions by eukaryotic DNA topoisomerase I. Proc. Natl Acad. Sci. USA 93, 785-789.
37. Sharma, A., Hanai, R., and Mondragon, A. (1994). Crystal structure of the amino-terminal fragment of vaccinia virus DNA topoisomerase I at 1.6 Å resolution. Structure 2, 767-777.
38. Sheldrick, G.M., Dauter, Z., Wilson, K.S., Hope, H., and Sieker, L.C. (1993). The application of direct methods and Patterson interpretation to high resolution protein data. Acta Crystallogr. D49, 18-23.
39. Shuman, S. (1989). Vaccinia DNA topoisomerase I promotes illegitimate recombination in Escherichia coli. Proc. Natl. Acad. Sci. USA 86, 3489-3493.
40. Shuman, S. (1991a). Site-specific interaction of vaccinia virus DNA topoisomerase I with duplex DNA: minimal DNA substrate for strand cleavage in vitro. J. Biol. Chem. 266, 11372-11379.
41. Shuman, S. (1991b). Recombination mediated by vaccinia DNA topoisomerase I in Escherichia coli is sequence specific. Proc. Natl. Acad. Sci. USA 88, 10104-10108.
42. Shuman, S., and Prescott, J. (1990). Specific DNA cleavage and binding by vaccinia virus DNA topoisomerase I. J. Biol. Chem. 265, 17826-17836.
43. Shuman, S., and Turner, J. (1993). Site-specific interaction of vaccinia virus topoisomerase I with base and sugar moieties in duplex DNA. J. Biol. Chem. 268, 18943-18950.
44. Shuman, S., Kane, E.M., and Morham, S.G. (1989). Mapping the active site tyrosine of vaccinia virus DNA topoisomerase I. Proc. Natl. Acad. Sci. USA 86, 9793-9797.
45. Shuman, S., Bear, D.G., and Sekiguchi, J. (1997). Intramolecular synapsis of duplex DNA by vaccinia topoisomerase. EMBO J. 16, 6584-6589.
46. Stivers, J.T., Shuman, S., and Mildvan, A.S. (1994). Vaccinia DNA topoisomerase I: single-turnover and steady-state kinetic analysis of the DNA strand cleavage and ligation reactions. Biochemistry 33, 327-339.
47. Subramanya, H.S., Arciszewska, L.K., Baker, R.A., Bird, L.E., Sherratt, D.J., and Wigley D.B. (1997). Crystal structure of the site-specific recombinase XerD. EMBO J. 16, 5178-5187.
48. Tirumalai, R.S., Healey, E., and Landy, A. (1997). Proc. Natl. Acad. Sci. USA 94, 6104-6109.
49. Wang, J.C. (1996). DNA topoisomerases. Annu. Rev. Biochem. 65, 635-692.
50. Wang, L.K., and Shuman, S. (1997). Deletions at the carboxyl terminus of vaccinia DNA topoisomerase affect DNA binding and enhance distributivity in DNA relaxation. Biochemistry 36, 3909-3916.
51. Wang, L.K., Wittschieben, J., and Shuman, S. (1997). Mutational analysis of 26 residues of vaccinia DNA topoisomerase identifies Ser-204 as important for DNA binding and cleavage. Biochemistry 36, 7944-7950.
52. Wittschieben, J., and Shuman, S. (1994). Mutational analysis of vaccinia virus DNA topoisomerase defines amino acid residues essential for covalent catalysis. J. Biol. Chem. 269, 29978-29983.
53. Wittschieben, J., and Shuman, S. (1997). Mechanism of DNA transesterification by vaccinia topoisomerase: catalytic contributions of essential residues Arg-130, Gly-132, Tyr-136, and Lys-167. Nucleic Acids Res. 25, 3001-3008.
54. Yang, W., and Mizuuchi, K. (1997). Site-specific recombination in plane view. Structure 5, 1401-1406.