The integrase family of recombinases: Organization and function of the active site

Molecular Microbiology

Volumn 33, Issue 3, 1999, Pages 449-456

  Grainge, Ian ^a   Jayaram, Makkuni ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA TOPOISOMERASE; INTEGRASE; NUCLEASE; RECOMBINASE; DNA POLYMERASE; INTEGRON INTEGRASE INTI1;

CRYSTAL STRUCTURE; DNA CLEAVAGE; DNA RECOMBINATION; ENZYME ACTIVE SITE; ENZYME CONFORMATION; ENZYME MECHANISM; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN FAMILY; REVIEW; STRUCTURE ACTIVITY RELATION; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; GENETIC RECOMBINATION; HUMAN; PROTEIN CONFORMATION;

EUKARYOTA;

BINDING SITES; DNA NUCLEOTIDYLTRANSFERASES; DNA TOPOISOMERASES, TYPE I; HUMANS; INTEGRASES; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; RECOMBINASES; RECOMBINATION, GENETIC;

EID: 0032589787     PISSN: 0950382X     EISSN: None     Source Type: Journal    
DOI: 10.1046/j.1365-2958.1999.01493.x     Document Type: Review

References (38)

1. Aldaz, H., Schuster, E., and Baker, T.A. (1996) The interwoven architecture of the Mu transposase couples DNA synapsis to catalysis. Cell 85: 257-269.
2. Arciszewska, L.K., and Sherratt, D.J. (1995) Xer site-specific recombination in vitro. EMBO J 14: 2112-2120.
3. Arciszewska, L.K., Grainge, I., and Sherratt, D.J. (1995) Effects of Holliday junction position on Xer-mediated recombination in vitro. EMBO J 14: 2651-2660.
4. Cheng, C., Kussie, P., Pavletich, N., and Shuman, S. (1998) Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases. Cell 92: 841-850.
5. Esposito, D., and Scocca, J.J. (1997) The integrase family of tyrosine recombinases: evolution of a conserved active site domain. Nucleic Acids Res 25: 3605-3614.
6. Fersht, A. (1984) Enzyme Structure and Function. New York: Freeman Press, pp. 426-434.
7. Gopaul, D.N., Guo, F., and Van Duyne, G.D. (1998) Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination. EMBO J 17: 4175-4187.
8. 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.
9. Guo, F., Gopaul, D.N., and van Duyne, G.D. (1999) Asymmetric DNA-bending in the Cre-loxP site-specific recombination synapse. Proc Natl Acad Sci USA (in press).
10. 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.
11. Hickman, A.B., Waniger, S., Scocca, J.J., and Dyda, F. (1997) Molecular organisation in site-specific recombination: the catalytic domain of HP1 integrase at 2.7 Å resolution. Cell 89: 227-237.
12. Jo, K., and Topal, M.D. (1998) Step-wise DNA relaxation and decatenation by Nael-43K. Nucleic Acids Res 26: 2380-2384.
13. 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.
14. Landy, A. (1993) Mechanistic and structural complexity in the site-specific recombination pathways of Int and FLP. Curr Opin Genet Dev 3: 699-707.
15. Lee, J., Grainge, I., and Jayaram, M. (1999) Wild type Flp recombinase cleaves in trans. EMBO J 18: 784-791.
16. Lee, J., and Jayaram, M. (1995) Role of partner homology in DNA recombination. Complementary base pairing orients the 5′-hydroxyl for strand joining during Flp site-specific recombination. J Biol Chem 270: 4042-4052.
17. Lee, J., and Jayaram, M. (1997) A tetramer of Flp silences the trimers within it during resolution of a Holliday junction substrate. Genes Dev 11: 2438-2447.
18. Lee, J., Tonozuka, T., and Jayaram, M. (1997) Mechanism of active site exclusion in a site-specific recombinase: role of the DNA substrate in conferring half-of-the-sites activity. Genes Dev 11: 3061-3071.
19. Namgoong, S.Y., and Harshey, R.M. (1998) The same two monomers within a MuA tetramer provide the DDE domains for the strand cleavage and strand transfer steps of transposition. EMBO J 17: 3775-3785.
20. Nash, H.A. (1996) Site-specific recombination: integration, excision, resolution and inversion of defined DNA segments. In Escherichia coli and Salmonella: Cellular and Molecular Biology, Vol. 2. Neidhart, F.C., et al. (eds). Washington, DC: American Society of Microbiology Press, pp. 2363-2376.
21. Nash, H.A. (1998) Topological nuts and bolts. Science 279: 1490-1491.
22. Nunes-Duby, S.E., Tirumalai, R.S., Dorgai, L., Yagil, E., Weisberg, R.A., and Landy, A. (1994) Lambda integrase cleaves DNA in cis. EMBO J 13: 4421-4430.
23. Nunes-Duby, S.E., Azaro, M., and Landy, A. (1995) Swapping DNA strands and sensing homology without branch migration in lambda site-specific recombination. Curr Biol 5: 139-148.
24. Nunes-Duby, S.E., Tirumalai, R.S., Kwon, H.J., Ellenberger, T., and Landy, A. (1998) Similarities and differences among 105 members of the Int family of site-specific recombinases. Nucleic Acids Res 26: 391-406.
25. Redinbo, M.R., Stewart, L., Kuhn, P., Champoux, J.J., and Hol, W.G. (1998) Crystal structures of human topoisomerase I in covalent and noncovalent complexes with DNA. Science 279: 1504-1513.
26. Sadowski, P.D. (1993) Site-specific genetic recombination: hops, flips, and flops. FASEB J 7: 760-767.
27. Savilahti, H., and Mizuuchi, K. (1996) Mu transpositional recombination: donor DNA cleavage and strand transfer in trans by the Mu transposase. Cell 85: 271-280.
28. Sekiguchi, J., and Shuman, S. (1997) Site-specific ribonuclease activity of eukaryotic DNA topoisomerase I. Mol Cell 1: 89-97.
29. Shaikh, A.C., and Sadowski, P.D. (1997) The Cre recombinase cleaves the lox site in trans. J Biol Chem 272: 5695-5702.
30. Sherratt, D.J., and Wigley, D.B. (1998) Conserved themes but novel activities in recombinases and topoisomerases. Cell 93: 149-152.
31. Sherratt, D.J., Arciszewska, L.K., Blakely, G., Colloms, S., Grant, K., Leslie, N., et al. (1995) Site-specific recombination and circular chromosome segregation. Phil Trans R Soc Lond B Biol Sci 347: 37-42.
32. Stewart, L., Redinbo, M.R., Qiu, X., Hol, W.G., and Champoux, J.J. (1998) A model for the mechanism of human topoisomerase I. Science 279: 1534-1541.
33. 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.
34. Viswanathan, M., Dower, K.W., and Lovett, S.T. (1998) Identification of a potent DNase activity associated with RNaseT of Escherichia coli. J Biol Chem 273: 35126-35131.
35. Voziyanov, Y., Pathania, S., and Jayaram, M. (1999) A general model for site-specific recombination by the integrase family recombinases. Nucleic Acids Res 27: 930-941.
36. 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.
37. Wittschieben, J., Peterson, B.O., and Shuman, S. (1998). Replacement of the active site tyrosine of vaccinia DNA topoisomerase by glutamate, cysteine or histidine converts the enzyme into a site-specific endonuclease. Nucleic Acids Res 26: 490-496.
38. Xu, C.J., Grainge, I., Lee, J., Harshey, R.M., and Jayaram, M. (1998) Unveiling two distinct ribonuclease activities and a topoisomerase activity in a site-specific DNA recombinase. Mol Cell 1: 729-739.