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. 1997 Sep 1;16(17):5178–5187. doi: 10.1093/emboj/16.17.5178

Crystal structure of the site-specific recombinase, XerD.

H S Subramanya 1, L K Arciszewska 1, R A Baker 1, L E Bird 1, D J Sherratt 1, D B Wigley 1
PMCID: PMC1170150  PMID: 9311978

Abstract

The structure of the site-specific recombinase, XerD, that functions in circular chromosome separation, has been solved at 2.5 A resolution and reveals that the protein comprises two domains. The C-terminal domain contains two conserved sequence motifs that are located in similar positions in the structures of XerD, lambda and HP1 integrases. However, the extreme C-terminal regions of the three proteins, containing the active site tyrosine, are very different. In XerD, the arrangement of active site residues supports a cis cleavage mechanism. Biochemical evidence for DNA bending is encompassed in a model that accommodates extensive biochemical and genetic data, and in which the DNA is wrapped around an alpha-helix in a manner similar to that observed for CAP complexed with DNA.

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Selected References

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  1. Abremski K. E., Hoess R. H. Evidence for a second conserved arginine residue in the integrase family of recombination proteins. Protein Eng. 1992 Jan;5(1):87–91. doi: 10.1093/protein/5.1.87. [DOI] [PubMed] [Google Scholar]
  2. Arciszewska L. K., Grainge I., Sherratt D. J. Action of site-specific recombinases XerC and XerD on tethered Holliday junctions. EMBO J. 1997 Jun 16;16(12):3731–3743. doi: 10.1093/emboj/16.12.3731. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Arciszewska L. K., Sherratt D. J. Xer site-specific recombination in vitro. EMBO J. 1995 May 1;14(9):2112–2120. doi: 10.1002/j.1460-2075.1995.tb07203.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Argos P., Landy A., Abremski K., Egan J. B., Haggard-Ljungquist E., Hoess R. H., Kahn M. L., Kalionis B., Narayana S. V., Pierson L. S., 3rd The integrase family of site-specific recombinases: regional similarities and global diversity. EMBO J. 1986 Feb;5(2):433–440. doi: 10.1002/j.1460-2075.1986.tb04229.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Blake J. A., Ganguly N., Sherratt D. J. DNA sequence of recombinase-binding sites can determine Xer site-specific recombination outcome. Mol Microbiol. 1997 Jan;23(2):387–398. doi: 10.1046/j.1365-2958.1997.2261600.x. [DOI] [PubMed] [Google Scholar]
  6. Blakely G. W., Davidson A. O., Sherratt D. J. Binding and cleavage of nicked substrates by site-specific recombinases XerC and XerD. J Mol Biol. 1997 Jan 10;265(1):30–39. doi: 10.1006/jmbi.1996.0709. [DOI] [PubMed] [Google Scholar]
  7. Blakely G., Colloms S., May G., Burke M., Sherratt D. Escherichia coli XerC recombinase is required for chromosomal segregation at cell division. New Biol. 1991 Aug;3(8):789–798. [PubMed] [Google Scholar]
  8. Blakely G., May G., McCulloch R., Arciszewska L. K., Burke M., Lovett S. T., Sherratt D. J. Two related recombinases are required for site-specific recombination at dif and cer in E. coli K12. Cell. 1993 Oct 22;75(2):351–361. doi: 10.1016/0092-8674(93)80076-q. [DOI] [PubMed] [Google Scholar]
  9. Brennan R. G., Matthews B. W. The helix-turn-helix DNA binding motif. J Biol Chem. 1989 Feb 5;264(4):1903–1906. [PubMed] [Google Scholar]
  10. Chen J. W., Evans B. R., Yang S. H., Araki H., Oshima Y., Jayaram M. 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. 1992 Sep;12(9):3757–3765. doi: 10.1128/mcb.12.9.3757. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Chen J. W., Evans B. R., Yang S. H., Teplow D. B., Jayaram M. Domain of a yeast site-specific recombinase (Flp) that recognizes its target site. Proc Natl Acad Sci U S A. 1991 Jul 15;88(14):5944–5948. doi: 10.1073/pnas.88.14.5944. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Chen J. W., Lee J., Jayaram M. DNA cleavage in trans by the active site tyrosine during Flp recombination: switching protein partners before exchanging strands. Cell. 1992 May 15;69(4):647–658. doi: 10.1016/0092-8674(92)90228-5. [DOI] [PubMed] [Google Scholar]
  13. Colloms S. D., Bath J., Sherratt D. J. Topological selectivity in Xer site-specific recombination. Cell. 1997 Mar 21;88(6):855–864. doi: 10.1016/s0092-8674(00)81931-5. [DOI] [PubMed] [Google Scholar]
  14. Han Y. W., Gumport R. I., Gardner J. F. Complementation of bacteriophage lambda integrase mutants: evidence for an intersubunit active site. EMBO J. 1993 Dec;12(12):4577–4584. doi: 10.1002/j.1460-2075.1993.tb06146.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hayes F., Sherratt D. J. Recombinase binding specificity at the chromosome dimer resolution site dif of Escherichia coli. J Mol Biol. 1997 Feb 28;266(3):525–537. doi: 10.1006/jmbi.1996.0828. [DOI] [PubMed] [Google Scholar]
  16. Hickman A. B., Waninger S., Scocca J. J., Dyda F. Molecular organization in site-specific recombination: the catalytic domain of bacteriophage HP1 integrase at 2.7 A resolution. Cell. 1997 Apr 18;89(2):227–237. doi: 10.1016/s0092-8674(00)80202-0. [DOI] [PubMed] [Google Scholar]
  17. Jayaram M. The cis-trans paradox of integrase. Science. 1997 Apr 4;276(5309):49–51. doi: 10.1126/science.276.5309.49. [DOI] [PubMed] [Google Scholar]
  18. Kwon H. J., Tirumalai R., Landy A., Ellenberger T. Flexibility in DNA recombination: structure of the lambda integrase catalytic core. Science. 1997 Apr 4;276(5309):126–131. doi: 10.1126/science.276.5309.126. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Lee J., Serre M. C., Yang S. H., Whang I., Araki H., Oshima Y., Jayaram M. Functional analysis of Box II mutations in yeast site-specific recombinases Flp and R. Significance of amino acid conservation within the Int family and the yeast sub-family. J Mol Biol. 1992 Dec 20;228(4):1091–1103. doi: 10.1016/0022-2836(92)90317-d. [DOI] [PubMed] [Google Scholar]
  20. Lee J., Whang I., Lee J., Jayaram M. Directed protein replacement in recombination full sites reveals trans-horizontal DNA cleavage by Flp recombinase. EMBO J. 1994 Nov 15;13(22):5346–5354. doi: 10.1002/j.1460-2075.1994.tb06869.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Nunes-Düby S. E., Tirumalai R. S., Dorgai L., Yagil E., Weisberg R. A., Landy A. Lambda integrase cleaves DNA in cis. EMBO J. 1994 Sep 15;13(18):4421–4430. doi: 10.1002/j.1460-2075.1994.tb06762.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Pan G., Sadowski P. D. Identification of the functional domains of the FLP recombinase. Separation of the nonspecific and specific DNA-binding, cleavage, and ligation domains. J Biol Chem. 1993 Oct 25;268(30):22546–22551. [PubMed] [Google Scholar]
  23. Pan G., Sadowski P. D. Ligation activity of FLP recombinase. The strand ligation activity of a site-specific recombinase using an activated DNA substrate. J Biol Chem. 1992 Jun 25;267(18):12397–12399. [PubMed] [Google Scholar]
  24. Panigrahi G. B., Sadowski P. D. Interaction of the NH2- and COOH-terminal domains of the FLP recombinase with the FLP recognition target sequence. J Biol Chem. 1994 Apr 8;269(14):10940–10945. [PubMed] [Google Scholar]
  25. Pargellis C. A., Nunes-Düby S. E., de Vargas L. M., Landy A. Suicide recombination substrates yield covalent lambda integrase-DNA complexes and lead to identification of the active site tyrosine. J Biol Chem. 1988 Jun 5;263(16):7678–7685. [PubMed] [Google Scholar]
  26. Sheldrick G. M., Dauter Z., Wilson K. S., Hope H., Sieker L. C. The application of direct methods and Patterson interpretation to high-resolution native protein data. Acta Crystallogr D Biol Crystallogr. 1993 Jan 1;49(Pt 1):18–23. doi: 10.1107/S0907444992007364. [DOI] [PubMed] [Google Scholar]
  27. Sherratt D. J., Arciszewska L. K., Blakely G., Colloms S., Grant K., Leslie N., McCulloch R. Site-specific recombination and circular chromosome segregation. Philos Trans R Soc Lond B Biol Sci. 1995 Jan 30;347(1319):37–42. doi: 10.1098/rstb.1995.0006. [DOI] [PubMed] [Google Scholar]
  28. Spiers A. J., Sherratt D. J. Relating primary structure to function in the Escherichia coli XerD site-specific recombinase. Mol Microbiol. 1997 Jun;24(5):1071–1082. doi: 10.1046/j.1365-2958.1997.4171784.x. [DOI] [PubMed] [Google Scholar]
  29. Stark W. M., Boocock M. R. Gatecrashers at the catalytic party. Trends Genet. 1995 Apr;11(4):121–123. doi: 10.1016/s0168-9525(00)89016-2. [DOI] [PubMed] [Google Scholar]
  30. Stark W. M., Boocock M. R., Sherratt D. J. Catalysis by site-specific recombinases. Trends Genet. 1992 Dec;8(12):432–439. [PubMed] [Google Scholar]

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