Arm sequences contribute to the architecture and catalytic function of a λ integrase-Holliday junction complex

Molecular Cell

Volumn 11, Issue 3, 2003, Pages 783-794

  Radman Livaja, Marta ^a   Shaw, Christine ^b   Azaro, Marco ^c   Biswas, Tapan ^b   Ellenberger, Tom ^b   Landy, Arthur ^a  

^a BROWN UNIVERSITY   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c RUTGERS CANCER INSTITUTE OF NEW JERSEY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA INTEGRASE; INTEGRASE; M PROTEIN; PROTEIN INT; UNCLASSIFIED DRUG;

ARTICLE; ENZYME ACTIVITY; GENE SEQUENCE; HOLLIDAY JUNCTION; NUCLEOTIDE REPEAT; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN STRUCTURE;

EID: 0344806949     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1097-2765(03)00111-4     Document Type: Article

References (39)

1. Arciszewska L.K., Grainge I., Sherratt D.J. Action of site-specific recombinases XerC and XerD on tethered Holliday junctions. EMBO J. 16:1997;3731-3743.
2. Azaro M.A., Landy A. The isomeric preference of Holliday junctions influences resolution bias by λ integrase. EMBO J. 16:1997;3744-3755.
3. Azaro M.A., Landy A. λ Int and the λ Int family. Craig N.L., Craigie R., Gellert M., Lambowitz A. Mobile DNA II. 2002;ASM Press, Washington, DC. 118-148.pp.
4. Campbell A.M. Episomes. Caspari E.W., Thoday J.M. Advances in Genetics. 1962;Academic Press, New York. 101-145.pp.
5. Chen Y., Narendra U., Iype L.E., Cox M.M., Rice P.A. Crystal structure of a Flp recombinase-Holliday junction complex. assembly of an active oligomer by helix swapping Mol. Cell. 6:2000;885-897.
6. Christ N., Dröge P. Alterations in the directionality of λ site-specific recombination catalyzed by mutant integrases in vivo. J. Mol. Biol. 288:1998;825-836.
7. Clegg R.M. Fluorescence resonance energy transfer and nucleic acids. Methods Enzymol. 211:1992;353-388.
8. Dorgai L., Yagil E., Weisberg R.A. Identifying determinants of recombination specificity. construction and characterization of mutant bacteriophage integrases J. Mol. Biol. 252:1995;178-188.
9. Franz B., Landy A. The Holliday junction intermediates of λ integrative and excisive recombination respond differently to the bending proteins, IHF, and Xis. EMBO J. 14:1995;397-406.
10. Gopaul D.N., Guo F., Van Duyne G.D. Structure of the Holliday junction intermediate in Cre-loxP site-specific recombination. EMBO J. 17:1998;4175-4187.
11. Grainge I., Jayaram M. The integrase family of recombinase. organization and function of the active site Mol. Microbiol. 33:1999;449-456.
12. Hallet B., Arciszewska L.K., Sherratt D.J. Reciprocal control of catalysis by the tyrosine recombinases XerC and XerD. an enzymatic switch in site-specific recombination Mol. Cell. 4:1999;949-959.
13. Holliday R. A mechanism for gene conversion in fungi. Genet. Res. 5:1964;282-304.
14. Kikuchi Y., Nash H.A. Nicking-closing activity associated with bacteriophage λ int gene product. Proc. Natl. Acad. Sci. USA. 76:1979;3760-3764.
15. Kim S.-H., Landy A. λ Int protein bridges between higher order complexes at two distant chromosomal loci attL and attR. Science. 256:1992;198-203.
16. Kitts P.A., Nash H.A. An intermediate in the phage λ site-specific recombination reaction is revealed by phosphorothioate substitution in DNA. Nucleic Acids Res. 16:1988;6839-6856.
17. Lilley D.M.J. Structues of helical junctions in nucleic acids. Q. Rev. Biophys. 33:2000;109-159.
18. Miick S.M., Fee R.S., Millar D.P., Chazin W.J. Crossover isomer bias is the primary sequence-dependent property of immobilized Holliday junctions. Proc. Natl. Acad. Sci. USA. 94:1997;9080-9084.
19. Moitoso de Vargas L., Pargellis C.A., Hasan N.M., Bushman E.W., Landy A. Autonomous DNA binding domains of λ integrase recognize different sequence families. Cell. 54:1988;923-929.
20. Moitoso de Vargas L., Kim S., Landy A. DNA looping generated by the DNA-bending protein IHF and the two domains of λ integrase. Science. 244:1989;1457-1461.
21. Nash H.A. Purification of bactriophage λ Int protein. Nature. 247:1974;543-545.
22. Numrych T.E., Gumport R.I., Gardner J.F. A comparison of the effects of single-base and triple-base changes in the integrase arm-type binding sites on the site-specific recombination of bacteriophage λ Nucleic Acids Res. 18:1990;3953-3959.
23. Nunes-Düby S.E., Matsumoto L., Landy A. Site-specific recombination intermediates trapped with suicide substrates. Cell. 50:1987;779-788.
24. Nunes-Düby S.E., Tirumalai R.S., Dorgai L., Yagil R., Weisberg R., Landy A. λ integrase cleaves DNA in cis. EMBO J. 13:1994;4421-4430.
25. Nunes-Düby S., Azaro M., Landy A. Swapping DNA strands and sensing homology without branch migration in λ site-specific recombination. Curr. Biol. 5:1995;139-148.
26. Nunes-Düby S.E., Yu D., Landy A. Sensing homology at the strand swapping step in λ excisive recombination. J. Mol. Biol. 272:1997;493-508.
27. Richet E., Abcarian P., Nash H.A. Synapsis of attachment sites during λ integrative recombination involves capture of a naked DNA by a protein-DNA complex. Cell. 52:1988;9-17.
28. Sarkar D., Radman-Livaja M., Landy A. The small DNA binding domain of λ Int is a context-sensitive modulator of recombinase functions. EMBO J. 20:2001;1203-1212.
29. Sarkar D., Azaro M.A., Aihara H., Papagiannis C., Tirumalai R.S., Nunes-Düby S.E., Johnson R.C., Ellenberger T., Landy A. Differential affinity and cooperativity functions of the amino-terminal 70 residues of λ integrase. J. Mol. Biol. 324:2002;775-789.
30. Sekiguchi J., Cheng C., Shuman S. Kinetic analysis of DNA and RNA strand transfer reactions catalyzed by vaccinia topoisomerase. J. Biol. Chem. 272:1997;15721-15728.
31. Sherratt D.J., Wigley D.B. Conserved themes but novel activities in recombinases and topoisomerases. Cell. 93:1998;149-152.
32. Thompson J.F., Landy A. Empirical estimation of protein-induced DNA bending angles. Applications to λ site-specific recombination complexes Nucleic Acids Res. 16:1988;9687-9705.
33. Thompson J.F., Moitoso de Vargas L., Skinner S.E., Landy A. Protein-protein interactions in a higher-order structure direct λ site-specific recombination. J. Mol. Biol. 195:1987;481-493.
34. Thompson J.F., Snyder U.K., Landy A. Helical repeat dependence of λ integrative recombination. role of the P1 and H1 protein binding sites Proc. Natl. Acad. Sci. USA. 85:1988;6323-6327.
35. Van Duyne G.D. A structural view of cre-loxP site-specific recombination. Annu. Rev. Biophys. Biomol. Struct. 30:2001;87-104.
36. Wojciak J.M., Connolly K.M., Clubb R.T. NMR structure of the Tn916 integrase-DNA complex. Nat. Struct. Biol. 6:1999;366-373.
37. Wojciak J.M., Sarkar D., Landy A., Clubb R.T. Arm site binding by the λ integrase protein. solution structure and functional characterization of its amino-terminal domain Proc. Natl. Acad. Sci. USA. 99:2002;3434-3439.
38. Wu Z., Gumport R.I., Gardner J.F. Defining the structural and functional roles of the carboxyl region of the bacteriophage λ excisionase (Xis) protein. J. Mol. Biol. 281:1998;651-661.
39. Zhu X.-D., Pan G., Luetke K., Sadowski P.D. Homology requirements for ligation and strand exchange by the FLP recombinase. J. Biol. Chem. 270:1995;11646-11653.