A specificity switch in selected Cre recombinase variants is mediated by macromolecular plasticity and water

Chemistry and Biology

Volumn 10, Issue 11, 2003, Pages 1085-1094

  Baldwin, Enoch P ^a   Martin, Shelley S ^a   Abel, Jonas ^b   Gelato, Kathy A ^a   Kim, Hanseong ^a   Schultz, Peter G ^c   Santoro, Stephen W ^c,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Yolo Co Reg Opportunity Program   (United States)

^c SCRIPPS RESEARCH INSTITUTE   (United States)

^d HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0345531145     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2003.10.015     Document Type: Article

References (39)

1. Sternberg N. Bacteriophage P1 site-specific recombination. III. Strand exchange during recombination at lox sites. J. Mol. Biol. 150:1981;603-608.
2. Hoess R.H., Abremski K. Mechanism of strand cleavage and exchange in the Cre-lox site-specific recombination system. J. Mol. Biol. 181:1985;351-362.
3. Cheng C., Kussie P., Pavletich N., Shuman S. Conservation of structure and mechanism between eukaryotic topoisomerase I and site-specific recombinases. Cell. 92:1998;841-850.
4. Nunes-Duby S.E., Kwon H.J., Tirumalai R.S., Ellenberger T., Landy A. Similarities and differences among 105 members of the Int family of site-specific recombinases. Nucleic Acids Res. 26:1998;391-406.
5. Sherratt D.J., Wigley D.B. Conserved themes but novel activities in recombinases and topoisomerases. Cell. 93:1998;149-152.
6. Abremski K., Hoess R., Sternberg N. Studies on the properties of P1 site-specific recombination. evidence for topologically unlinked products following recombination Cell. 32:1983;1301-1311.
7. Hoess R.H., Ziese M., Sternberg N. P1 site-specific recombination. nucleotide sequence of the recombining sites Proc. Natl. Acad. Sci. USA. 79:1982;3398-3402.
8. Abremski K., Hoess R. Bacteriophage P1 site-specific recombination. Purification and properties of the Cre recombinase protein. J. Biol. Chem. 259:1984;1509-1514.
9. Nagy A. Cre recombinase. the universal reagent for genome tailoring Genesis. 26:2000;99-109.
10. Guo F., Gopaul D.N., van Duyne G.D. Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature. 389:1997;40-46.
11. Van Duyne G.D. A structural view of cre-loxp site-specific recombination. Annu. Rev. Biophys. Biomol. Struct. 30:2001;87-104.
12. Hoess R., Wierzbicki A., Abremski K. Isolation and characterization of intermediates in site-specific recombination. Proc. Natl. Acad. Sci. USA. 84:1987;6840-6844.
13. Hartung M., Kisters-Woike B. Cre mutants with altered DNA binding properties. J. Biol. Chem. 273:1998;22884-22891.
14. Martin S.S., Chu V.C., Baldwin E.P. Modulation of active complex assembly and turnover rate by protein-DNA interactions in Cre-LoxP recombination. Biochemistry. 42:2003;6814-6826.
15. Lee G., Saito I. Role of nucleotide sequences of loxP spacer region in Cre-mediated recombination. Gene. 216:1998;55-65.
16. Hoess R.H., Wierzbicki A., Abremski K. The role of the loxP spacer region in P1 site-specific recombination. Nucleic Acids Res. 14:1986;2287-2300.
17. Thyagarajan B., Guimaraes M.J., Groth A.C., Calos M.P. Mammalian genomes contain active recombinase recognition sites. Gene. 244:2000;47-54.
18. Buchholz F., Stewart A.F. Alteration of Cre recombinase site specificity by substrate-linked protein evolution. Nat. Biotechnol. 19:2001;1047-1052.
19. Santoro S.W., Schultz P.G. Directed evolution of the site specificity of Cre recombinase. Proc. Natl. Acad. Sci. USA. 99:2002;4185-4190.
20. Wolfe S.A., Grant R.A., Elrod-Erickson M., Pabo C.O. Beyond the "recognition code" structures of two Cys2His2 zinc finger/TATA box complexes Structure. 9:2001;717-723.
21. Elrod-Erickson M., Benson T.E., Pabo C.O. High-resolution structures of variant Zif268-DNA complexes. implications for understanding zinc finger-DNA recognition Structure. 6:1998;451-464.
22. 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.
23. Martin S.S., Pulido E., Chu V.C., Lechner T.S., Baldwin E.P. The order of strand exchanges in Cre-LoxP recombination and its basis suggested by the crystal structure of a Cre-LoxP Holliday junction complex. J. Mol. Biol. 319:2002;107-127.
24. Miller J.C., Pabo C.O. Rearrangement of side-chains in a Zif268 mutant highlights the complexities of zinc finger-DNA recognition. J. Mol. Biol. 313:2001;309-315.
25. Luscombe N.M., Laskowski R.A., Thornton J.M. Amino acid-base interactions. a three-dimensional analysis of protein-DNA interactions at an atomic level Nucleic Acids Res. 29:2001;2860-2874.
26. McClarin J.A., Frederick C.A., Wang B.C., Greene P., Boyer H.W., Grable J., Rosenberg J.M. Structure of the DNA-Eco RI endonuclease recognition complex at 3 Å resolution. Science. 234:1986;1526-1541.
27. Voziyanov Y., Konieczka J.H., Stewart A.F., Jayaram M. Stepwise manipulation of DNA specificity in Flp recombinase. progressively adapting Flp to individual and combinatorial mutations in its target site J. Mol. Biol. 326:2003;65-76.
28. Hegde R.S., Grossman S.R., Laimins L.A., Sigler P.B. Crystal structure at 1.7 A of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target. Nature. 359:1992;505-512.
29. Pingoud A., Jeltsch A. Structure and function of type II restriction endonucleases. Nucleic Acids Res. 29:2001;3705-3727.
30. Yagil E., Dorgai L., Weisberg R.A. Identifying determinants of recombination specificity. construction and characterization of chimeric bacteriophage integrases J. Mol. Biol. 252:1995;163-177.
31. Rufer A.W., Sauer B. Non-contact positions impose site-selectivity on Cre recombinase. Nucleic Acids Res. 30:2002;2764-2771.
32. Otwinowski Z., Schevitz R.W., Zhang R.G., Lawson C.L., Joachimiak A., Marmorstein R.Q., Luisi B.F., Sigler P.B. Crystal structure of trp repressor/operator complex at atomic resolution. Nature. 335:1988;321-329.
33. Woda J., Schneider B., Patel K., Mistry K., Berman H.M. An analysis of the relationship between hydration and protein-DNA interactions. Biophys. J. 75:1998;2170-2177.
34. Woods K.C., Martin S.S., Chu V.C., Baldwin E.P. Quasi-equivalence in site-specific recombinase structure and function. crystal structure and activity of trimeric Cre recombinase bound to a three-way Lox DNA junction J. Mol. Biol. 313:2001;49-69.
35. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
36. Tronrud D. TNT refinement package. Methods Enzymol. 277:1997;306-319.
37. CCP4 Collaborative Computational Project Number 4) The CCP4 suite. programs for protein crystallography Acta Crystallogr. D. 50:1994;760-763.
38. Tronrud D. Knowledge-based B-factor restraints for the refinement of proteins. J. Appl. Crystallogr. 29:1996;100-104.
39. Engh R., Huber R. Accurate bond and angle parameters for X-ray protein structure refinement. Acta Crystallogr. A. 47:1991;392-400.