Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease

Nature Structural Biology

Volumn 6, Issue 3, 1999, Pages 269-277

  Martin, Amy M ^a   Sam, My D ^a   Reich, Norbert O ^a   Perona, John J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RESTRICTION ENDONUCLEASE;

ARTICLE; CRYSTAL STRUCTURE; DNA CLEAVAGE; ENZYME ACTIVE SITE; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN DNA BINDING;

BASE SEQUENCE; CALCIUM; CRYSTALLOGRAPHY, X-RAY; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DIMERIZATION; DNA; HYDROLYSIS; KINETICS; MOLECULAR STRUCTURE; PROTEIN CONFORMATION; SUBSTRATE SPECIFICITY; THERMODYNAMICS;

EID: 0032972857     PISSN: 10728368     EISSN: None     Source Type: Journal    
DOI: 10.1038/6707     Document Type: Article

References (13)

1. Rhodes, D., Schwabe, J.W., Chapman, L. & Fairall, L. Towards an understanding of protein-DNA recognition. Phil. Trans. Royal Soc. B351, 501-509 (1996).
2. Seeman, N.C., Rosenberg, J.M. & Rich, A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl. Acad. Sci. USA 73, 804-808 (1976).
3. Otwinowski, Z. et al. Crystal structure of trp repressor/operator complex at atomic resolution. Nature 335, 321-329 (1988).
4. Koudelka, G.B., Harrison, S.C. & Ptashne, M. Effect of noncontacted bases on the affinity of 434 operator for 434 repressor and Cro. Nature 326, 886-888 (1987).
5. Rosenberg, J.M. Structure and function of restriction endonucleases. Curr. Opin. Struct. Biol. 1, 104-113 (1991).
6. Lesser, D.R., Kurpiewski, M.R., Waters, T., Connolly, B.A. & Jen-Jacobson L. Facilitated distortion of the DNA site enhances EcoRl endonuclease-DNA recognition. Proc. Natl. Acad. Sci. USA 90, 7548-7552 (1993).
7. Draper, D.E. Protein-DNA complexes: the cost of recognition. Proc. Natl. Acad. Sci. USA 90, 7429-7430 (1993).
8. Jen-Jacobson, L. Structural-perturbation approaches to thermodynamics of site-specific protein-DNA interactions. Meth. Enz. 259, 305-344 (1995).
9. Schildkraut, I., Banner, C.D.B., Rhodes, C.S. & Parekh, S. The cleavage site for the restriction enzyme EcoRV is 5′-GAT/ATC-3′. Gene 27, 327-329 (1984).
10. Roberts, R.J. & Halford, S.E. In Nucleases (eds Linn, S.M., Lloyd, R.S. & Roberts. R.J.) 35-88 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York; 1993).
11. Vipond, I.B. & Halford, S.E. Structure-function correlation for the EcoRV restriction enzyme: from non-specific binding to specific DNA cleavage. Mol. Microbiol. 9, 225-231 (1993).
12. Engler, L.E., Welch, K.K. & Jen-Jacobson, L. Specific binding by EcoRV endonuclease to its DNA recognition site GATATC. J. Mol. Biol. 269, 82-101 (1997).
13. Winkler, F.K. et al. The crystal structure of the EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 12, 1781-1795 (1993).