Crystal structure of the site-specific recombinase, XerD

EMBO Journal

Volumn 16, Issue 17, 1997, Pages 5178-5187

  Subramanya, Hosahalli S ^a   Arciszewska, Lidia K ^a   Baker, Rachel A ^a   Bird, Louise E ^a   Sherratt, David J ^a   Wigley, Dale B ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

DNA binding; Recombination mechanism; Site specific recombinase; XerD structure

Indexed keywords

RECOMBINASE;

ALPHA HELIX; ARTICLE; CARBOXY TERMINAL SEQUENCE; CHROMOSOME; CRYSTAL STRUCTURE; DNA STRUCTURE; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; ESCHERICHIA COLI; GENETIC CONSERVATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BINDING SITES; COMPUTER SIMULATION; CRYSTALLOGRAPHY, X-RAY; DNA NUCLEOTIDYLTRANSFERASES; DNA-BINDING PROTEINS; INTEGRASES; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; RECOMBINASES; RECOMBINATION, GENETIC; SEQUENCE HOMOLOGY, AMINO ACID; SURFACE PROPERTIES;

ESCHERICHIA COLI;

EID: 0030817595     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/16.17.5178     Document Type: Article

References (56)

1. Abremski, K.E. and Hoess, R.H. (1992) Evidence for the second conserved arginine residue in the integrase family of recombination proteins. Protein Engng, 5, 87-91.
2. Argos, P. et al. (1986) The integrase family of site-specific recombinases: regional similarities and global diversity. EMBO J., 5, 433-440.
3. Arciszewska, L.K. and Sherratt, D.J. (1995) Xer site-specific recombination in vitro. EMBO J., 14, 2112-2120.
4. Arciszewska, L.K., Grainge, I. and Sherratt, D.J. (1997) Action of site-specific recombinases XerC and XerD on tethered Holliday junctions. EMBO J., 16, 3731-3743.
5. Blake, J.A.R., Ganguly, N. and Sherratt, D.J. (1997) DNA sequence of recombinase-binding sites can determine Xer site-specific recombination outcome. Mol. Microbiol., 23, 387-398.
6. Blakely, G.W. and Sherratt, D.J. (1994) Interactions of the site-specific recombinases XerC and XerD with the recombination site dif. Nucleic Acids Res., 22, 5613-5620.
7. Blakely, G.W. and Sherratt, D.J. (1996a) Determinants of selectivity in Xer site-specific recombination. Genes Dev., 10, 762-773.
8. Blakely, G.W. and Sherratt, D.J. (1996b) Cis and trans in site-specific recombination. Mol. Microbiol., 20, 234-237.
9. Blakely, G.W., Colloms, S.D., May, G., Burke, M. and Sherratt, D.J. (1991) Escherichia coli XerC recombinase is required for chromosomal segregation at cell division. New Biol., 3, 789-798.
10. Blakely, G.W., May, G., McCulloch, R., Arciszewska, L., Burke, M., Lovett, S. and Sherratt, D.J. (1993) Two related recombinases are required for site-specific recombination at dif and cer in Escherichia coli K12. Cell, 75, 351-361.
11. Blakely, G.W., Davidson, A.O. and Sherratt, D.J. (1997) Binding and cleavage of nicked substrates by site-specific recombinases XerC and XerD. J. Mol. Biol., 265, 30-39.
12. Brennan, R.G. and Matthews, B.W. (1989) The helix-turn-helix DNA binding motif. J. Biol. Chem., 264, 1903-1906.
13. Brünger, A.T. (1992) The free R-value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature, 355, 472-474.
14. Carson, M. (1991) Ribbons 2.0. J. Appl. Crystallogr., 24, 958-961.
15. Chen, J.-W., Evans, B.R., Yang, S.-H., Teplow, D.B. and Jayaram, M. (1991) Domain of a yeast site-specific recombinase (Flp) that recognizes its target site. Proc. Natl Acad. Sci. USA, 88, 5944-5948.
16. Chen, J.-W., Evans, B.R., Yang, S.-H., Araki, H., Oshima, Y. and Jayaram, M. (1992a) Functional analysis of box I mutations in yeast site-specific recombinases Flp and R: pairwise complementation with recombinase variants lacking the active-site tyrosine. Mol. Cell Biol., 12, 3757-3765.
17. Chen, J.-W., Lee, J. and Jayaram, M. (1992b) DNA cleavage in trans by the active site tyrosine during Flp recombination: switching protein partners before exchanging strands. Cell. 69, 647-658.
18. Collaborative Computing Project No. 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr., D50, 760-763.
19. Colloms, D.S., McCulloch, R., Grant, K., Neilson, L. and Sherratt, D.J. (1996) Xer-mediated site-specific recombination in vitro. EMBO J., 15, 1172-1181.
20. Colloms, S.D., Bath, J. and Sherratt, D.J. (1997) Topology of Xer mediated site-specific recombination at psi and cer. Cell, 88, 855-864.
21. 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., in press.
22. Evans, B.R., Chen, J.W., Parsons, R.L., Bauer, T.K., Teplow, D.B. and Jayaram, M. (1990) Identification of the active-site tyrosine of FLP recombinase. J. Biol. Chem., 265, 18504-18510.
23. Friesen, H. and Sadowski, P.D. (1992) Mutagenesis of a conserved region of the gene encoding the FLP recombinase of Saccharomyces cerevisiae. J. Mol. Biol., 225, 313-326.
24. Han, Y.W., Gumport, R.I. and Gardner, J.F. (1993) Complementation of bacteriophage lambda integrase mutants: evidence for an intersubunit active site. EMBO J., 12, 4577-4584.
25. Hayes, F. and Sherratt, D.J. (1997) Recombinase binding specificity at the chromosome dimer resolution site dif of Escherichia coli. J. Mol. Biol., 266, 525-537.
26. Hayes, F., Lubetzki, S. and Sherratt, D.J. (1997) Salmonella typhimurium specifies a circular chromosome dimer resolution system which is homologous to the Xer site-specific recombination system in Escerichia coli. Gene, in press.
27. Hickman, A.B., Waninger, W., Scocca, J. and Dyda, F. (1997) Molecular organisation in site-specific recombination: the catalytic domain of bacteriophage HP1 integrase at 2.7 Å resolution. Cell. 89, 227-237
28. 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., 216, 873-882.
29. Jayaram, M. (1997) The cis-trans paradox of integrase. Science, 276, 49-51.
30. Jayaram, M. and Lee, J. (1995) Return to sobriety after the catalytic party. Trends Genet., 11, 432-433.
31. Kwon, H.J., Tirumalai, R., Landy, A. and Ellenberger, T. (1997) Flexibility in DNA recombination: structure of the lambda integrase catalytic core. Science, 276, 126-131.
32. Landy, A. (1993) Mechanistic and structural complexity in the site-specific recombination pathways of Int and Flp. Curr. Opin. Genet. Dev., 3, 699-707.
33. Laskowski, R.A., MacArthur, M.W., Moss, D.S. and Thornton, J.M. (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crysrallogr., 26, 283-291.
34. Lee, J., Serre, M.-C. Yang, S.-W., Whang, I., Araki, H., Oshima, Y. and Jayaram, M. (1992) Functional analysis of Box II mutations in yeast site-specific recombinase Flp and R. J. Mol. Biol., 228, 1091-1103.
35. Lee, J., Whang, I., Lee, J. and Jayaram, M. (1994) Directed protein replacement in recombination full sites reveals trans-horizontal DNA cleavage by Flp recombinase. EMBO J., 13, 5346-5354.
36. Leslie, N. and Sherratt, D.J. (1995) Site-specific recombination in the replication terminus region of Escherichia coli: functional replacement of dif. EMBO J., 14, 1561-1570.
37. Moitoso de Vargas, L., Pargellis, C.A., Hasan, N.M., Bushman, E.W. and Landy, A. (1988) Autonomous DNA binding domains of X integrase recognize two different sequence families. Cell, 54, 923-929.
38. Nash, H.A. (1996) Site-specific recombination: integration, excision, resolution and inversion of defined DNA segments. In Neidhardt, F.C. et al. (eds), Escherichia coli and Salmonella: Cellular and Molecular Biology. ASM Press, Washington, DC, pp. 2363-2376.
39. Nicholls, A. and Honig, B.J. (1991) A rapid finite-difference algoritim, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J. Comput. Chem., 12, 435-445.
40. Nunes-Düby, S.E., Tirumalai, R.S., Dorgai, L., Yagil, E., Weisberg, R.A. and Landy, A. (1994) λ Integrase cleaves DNA in cis. EMBO J., 13, 4421-4430.
41. Otwinowski, Z. (1993) Data Collection and Processing. SERC Daresbury DL/SC1/R34, 56-62.
42. Pan, G. and Sadowski, P.D. (1992) Ligation activity of Flp recombinase. J. Biol. Chem., 267, 12397-12399.
43. Pan, G. and Sadowski, P.D (1993) Identification of the functional domains of the FLP recombinase. J. Biol. Chem., 268, 22546-22551.
44. 2- and COOH-terminal domains of the FLP recombinase with the FLP recognition target sequence. J. Biol. Chem., 269, 10940-10945.
45. Panigrahi, G.B., Beatty, L.G. and Sadowski, P.D. (1992) The FLP protein contacts both major and minor grooves of its recognition target sequence. Nucleic Acids Res., 20, 5927-5935.
46. Pargellis, C.A., Nunes-Düby, S.E., Moitoso de Vargas, L. and Landy, A. (1988) Suicide recombination substrates yield covalent λ integrase-DNA complexes and lead to identification of the active-site tyrosine. J. Biol Chem., 263, 7678-7685.
47. Roussel, A. and Cambillau, C. (1989) TURBO-FRODO. In Silicon Graphics Geometry Partner Directory. Silicon Graphics, Mountain View, CA, pp. 77-78.
48. Sadowski, P.D. (1995) The FIp recombinase of the 2μm plasmid of Saccharomyces cerevisiae. Prog. Nucleic Acid Res. Mol. Biol., 51, 53-89.
49. Schultz, S.C., Shields, G.C. and Steitz, T.A. (1991) Crystal structure of a CAP-DNA complex: the DNA is bent by 90°. Science, 253, 1001-1007.
50. 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.
51. Sherratt, D.J., Arciszewska, L.K., Blakely, G., Colloms, S., Grant, K., Leslie, N. and McCulloch, R. (1995) Site-specific recombination and circular chromosome segregation. Philos. Trans. R. Soc. Lond. B., 347, 37-42.
52. Spiers, A. and Sherratt, D.J. (1997) Relating primary structure to function in the Escherichia coli XerD site-specific recombinase. Mol. Microbiol. 24, 1071-1082.
53. Stark, W.M. and Boocock, M.R. (1995a) Topological selectivity in site-specific recombination. In Sherratt, D.J. (ed.), Mobile Genetic Elements. IRL Press at Oxford University Press, pp. 101-129.
54. Stark, W.M. and Boocock, M.R. (1995b) Gatecrashers at the catalytic party. Trends Genet., 11, 121-123.
55. Stark, W.M., Boocock, M.R. and Sherratt, D.J. (1992) Catalysis by site-specific recombinases. Trends Genet., 8, 432-439.
56. Tecklenburg, M., Naumer, A., Nagapan, O. and Kuempel, P.L. (1995) The dif resolvase locus of the Escherichia coli chromosome can be replaced by a 33-bp sequence, but function depends on location. Proc. Natl Acad. Sci. USA, 92, 1352-1356.