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. 1997 Sep 15;25(18):3605–3614. doi: 10.1093/nar/25.18.3605

The integrase family of tyrosine recombinases: evolution of a conserved active site domain.

D Esposito 1, J J Scocca 1
PMCID: PMC146934  PMID: 9278480

Abstract

The integrases are a diverse family of tyrosine recombinases which rearrange DNA duplexes by means of conservative site-specific recombination reactions. Members of this family, of which the well-studied lambda Int protein is the prototype, were previously found to share four strongly conserved residues, including an active site tyrosine directly involved in transesterification. However, few additional sequence similarities were found in the original group of 27 proteins. We have now identified a total of 81 members of the integrase family deposited in the databases. Alignment and comparisons of these sequences combined with an evolutionary analysis aided in identifying broader sequence similarities and clarifying the possible functions of these conserved residues. This analysis showed that members of the family aggregate into subfamilies which are consistent with their biological roles; these subfamilies have significant levels of sequence similarity beyond the four residues previously identified. It was also possible to map the location of conserved residues onto the available crystal structures; most of the conserved residues cluster in the predicted active site cleft. In addition, these results offer clues into an apparent discrepancy between the mechanisms of different subfamilies of integrases.

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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. Abremski K., Hoess R. Bacteriophage P1 site-specific recombination. Purification and properties of the Cre recombinase protein. J Biol Chem. 1984 Feb 10;259(3):1509–1514. [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. 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]
  6. Blakely G. W., Sherratt D. J. Cis and trans in site-specific recombination. Mol Microbiol. 1996 Apr;20(1):234–237. doi: 10.1111/j.1365-2958.1996.tb02505.x. [DOI] [PubMed] [Google Scholar]
  7. Bushman W., Thompson J. F., Vargas L., Landy A. Control of directionality in lambda site specific recombination. Science. 1985 Nov 22;230(4728):906–911. doi: 10.1126/science.2932798. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Craig N. L. The mechanism of conservative site-specific recombination. Annu Rev Genet. 1988;22:77–105. doi: 10.1146/annurev.ge.22.120188.000453. [DOI] [PubMed] [Google Scholar]
  9. Dixon J. E., Shaikh A. C., Sadowski P. D. The Flp recombinase cleaves Holliday junctions in trans. Mol Microbiol. 1995 Nov;18(3):449–458. doi: 10.1111/j.1365-2958.1995.mmi_18030449.x. [DOI] [PubMed] [Google Scholar]
  10. Dorgai L., Yagil E., Weisberg R. A. Identifying determinants of recombination specificity: construction and characterization of mutant bacteriophage integrases. J Mol Biol. 1995 Sep 15;252(2):178–188. doi: 10.1006/jmbi.1995.0486. [DOI] [PubMed] [Google Scholar]
  11. Esposito D., Fitzmaurice W. P., Benjamin R. C., Goodman S. D., Waldman A. S., Scocca J. J. The complete nucleotide sequence of bacteriophage HP1 DNA. Nucleic Acids Res. 1996 Jun 15;24(12):2360–2368. doi: 10.1093/nar/24.12.2360. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Esposito D., Scocca J. J. Purification and characterization of HP1 Cox and definition of its role in controlling the direction of site-specific recombination. J Biol Chem. 1997 Mar 28;272(13):8660–8670. doi: 10.1074/jbc.272.13.8660. [DOI] [PubMed] [Google Scholar]
  13. Friesen H., Sadowski P. D. Mutagenesis of a conserved region of the gene encoding the FLP recombinase of Saccharomyces cerevisiae. A role for arginine 191 in binding and ligation. J Mol Biol. 1992 May 20;225(2):313–326. doi: 10.1016/0022-2836(92)90924-9. [DOI] [PubMed] [Google Scholar]
  14. Hakimi J. M., Scocca J. J. Binding sites for bacteriophage HP1 integrase on its DNA substrates. J Biol Chem. 1994 Aug 19;269(33):21340–21345. [PubMed] [Google Scholar]
  15. 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]
  16. Han Y. W., Gumport R. I., Gardner J. F. Mapping the functional domains of bacteriophage lambda integrase protein. J Mol Biol. 1994 Jan 21;235(3):908–925. doi: 10.1006/jmbi.1994.1048. [DOI] [PubMed] [Google Scholar]
  17. 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]
  18. 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]
  19. Kulpa J., Dixon J. E., Pan G., Sadowski P. D. Mutations of the FLP recombinase gene that cause a deficiency in DNA bending and strand cleavage. J Biol Chem. 1993 Jan 15;268(2):1101–1108. [PubMed] [Google Scholar]
  20. 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]
  21. Landy A. Dynamic, structural, and regulatory aspects of lambda site-specific recombination. Annu Rev Biochem. 1989;58:913–949. doi: 10.1146/annurev.bi.58.070189.004405. [DOI] [PubMed] [Google Scholar]
  22. Le Marrec C., Moreau S., Loury S., Blanco C., Trautwetter A. Genetic characterization of site-specific integration functions of phi AAU2 infecting "Arthrobacter aureus" C70. J Bacteriol. 1996 Apr;178(7):1996–2004. doi: 10.1128/jb.178.7.1996-2004.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lee M. H., Hatfull G. F. Mycobacteriophage L5 integrase-mediated site-specific integration in vitro. J Bacteriol. 1993 Nov;175(21):6836–6841. doi: 10.1128/jb.175.21.6836-6841.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. McClain M. S., Blomfield I. C., Eisenstein B. I. Roles of fimB and fimE in site-specific DNA inversion associated with phase variation of type 1 fimbriae in Escherichia coli. J Bacteriol. 1991 Sep;173(17):5308–5314. doi: 10.1128/jb.173.17.5308-5314.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Moitoso de Vargas L., Pargellis C. A., Hasan N. M., Bushman E. W., Landy A. Autonomous DNA binding domains of lambda integrase recognize two different sequence families. Cell. 1988 Sep 23;54(7):923–929. doi: 10.1016/0092-8674(88)90107-9. [DOI] [PubMed] [Google Scholar]
  26. 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]
  27. 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]
  28. Parsons R. L., Prasad P. V., Harshey R. M., Jayaram M. Step-arrest mutants of FLP recombinase: implications for the catalytic mechanism of DNA recombination. Mol Cell Biol. 1988 Aug;8(8):3303–3310. doi: 10.1128/mcb.8.8.3303. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Shaikh A. C., Sadowski P. D. The Cre recombinase cleaves the lox site in trans. J Biol Chem. 1997 Feb 28;272(9):5695–5702. doi: 10.1074/jbc.272.9.5695. [DOI] [PubMed] [Google Scholar]
  30. Waldman A. S., Fitzmaurice W. P., Scocca J. J. Integration of the bacteriophage HP1c1 genome into the Haemophilus influenzae Rd chromosome in the lysogenic state. J Bacteriol. 1986 Jan;165(1):297–300. doi: 10.1128/jb.165.1.297-300.1986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Yagil E., Dorgai L., Weisberg R. A. Identifying determinants of recombination specificity: construction and characterization of chimeric bacteriophage integrases. J Mol Biol. 1995 Sep 15;252(2):163–177. doi: 10.1006/jmbi.1995.0485. [DOI] [PubMed] [Google Scholar]
  32. Yu A., Bertani L. E., Haggård-Ljungquist E. Control of prophage integration and excision in bacteriophage P2: nucleotide sequences of the int gene and att sites. Gene. 1989 Aug 1;80(1):1–11. doi: 10.1016/0378-1119(89)90244-8. [DOI] [PubMed] [Google Scholar]
  33. Yu A., Haggård-Ljungquist E. Characterization of the binding sites of two proteins involved in the bacteriophage P2 site-specific recombination system. J Bacteriol. 1993 Mar;175(5):1239–1249. doi: 10.1128/jb.175.5.1239-1249.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]

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