Translocation-independent dimerization of the EcoKI endonuclease visualized by atomic force microscopy

Biophysical Journal

Volumn 79, Issue 1, 2000, Pages 479-484

  Berge, Torunn ^a   Ellis, Darren J ^a   Dryden, David T F ^b   Edwardson, J Michael ^a   Henderson, Robert M ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; ENDONUCLEASE;

ARTICLE; ATOMIC FORCE MICROSCOPY; DIMERIZATION; DNA SEQUENCE; ENZYME ACTIVITY; ENZYME ANALYSIS; ENZYME BINDING; NONHUMAN; PROTEIN DNA BINDING;

BACTERIA (MICROORGANISMS);

EID: 0033918211     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0006-3495(00)76309-0     Document Type: Article

References (32)

1. Bickle, T. A. 1993 The ATP-dependent restriction endonucleases. In Nucleases. E. M. Linn, R. S. Lloyd, and R. J. Roberts, editors. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY. 89-109.
2. Bickle, T. A., C. Brack, and R. Yuan. 1978. ATP-induced conformational changes in the restriction endonuclease from Escherichia coli K-12. Proc. Natl. Acad. Sci. USA. 75:3099-3103.
3. Bickle, T. A., and D. H. Kruger. 1993. Biology of DNA restriction. Microbiol. Rev. 57:434-450.
4. Davies, G. P., I. Martin, S. S. Sturrock, A. Cronshaw, N. E. Murray, and D. T. F. Dryden. 1999. On the structure and operation of type I restriction enzymes. J. Mol. Biol. 290:565-579.
5. Davies, G. P., L. M. Powell, J. L. Webb, L. P. Cooper, and N. E. Murray. 1998 EcoKI with an amino acid substitution in any one of seven DEAD-box motifs has impaired ATPase and endonuclease activities. Nucleic Acids Res. 26:4828-4836.
6. Dreier, J., M. P. MacWilliams, and T. A. Bickle. 1996. DNA cleavage by the type IC restriction-modification enzyme EcoR124II. J. Mol. Biol. 264:722-733.
7. Dryden, D. T. F., L. P. Cooper, P. H. Thorpe, and O. Byron. 1997. The in vitro assembly of the EcoKI type I DNA restriction/modification enzyme and its in vivo implications. Biochemistry. 36:1065-1076.
8. Dryden, D. T. F., S. S. Sturrock, and M. Winter. 1995. Structural modelling of a type I DNA methyltransferase. Nature Struct. Biol. 2:632-635.
9. Edstrom, R. D., M. H. Meinke, R. Yang, X. Yang, V. Elings and D. F. Evans. 1990 Direct visualization of phosphorylase-phosphorylase kinase complexes by scanning tunneling and atomic force microscopy. Biophys. J. 58:1437-1448.
10. Ellis, D. J., D. T. F. Dryden, T. Berge, J. M. Edwardson, and R. M. Henderson. 1999. Direct observation of DNA translocation and cleavage by atomic force microscopy. Nature Struct. Biol. 6:15-17.
11. Embleton, M. L., S. A. Williams, M. A. Watson, and S. E. Halford. 1999. Specificity from the synapsis of DNA elements by the SfiI endonuclease. J. Mol. Biol. 289:785-797.
12. Endlich, B., and S. Linn. 1985. The DNA restriction endonuclease of Escherichia coli B. II. Further studies of the structure of DNA intermediates and products. J. Biol. Chem. 260:5729-5738.
13. Janscak, P., M. P. MacWilliams, U. Sandmeier, V. Nagaraja, and T. A. Bickle. 1999. DNA translocation blockage, a general mechanism of cleavage site selection by type I restriction enzymes. EMBO J. 18: 2638-2647.
14. King, G., and N. E. Murray. 1994. Restriction enzymes in cells, not Eppendorfs. Trends Microbiol. 2:465-469.
15. Kong, H., and C. L. Smith. 1998. Does BcgI, a unique restriction endonuclease, require two recognition sites for cleavage? Biol. Chem. 379: 605-609.
16. Meisel, A., P. Mackeldanz, T. A. Bickle, D. H. Kruger, and C. Schroeder. 1995 Type III restriction endonucleases translocate DNA in a reaction driven by recognition site-specific ATP hydrolysis. EMBO J. 14: 2958-2966.
17. Modrich, P. 1979. Structures and mechanisms of DNA restriction and modification enzymes. Q. Rev. Biophys. 12:316-369.
18. Powell, L. M., D. T. F. Dryden, and N. E. Murray. 1998. Sequence-specific DNA binding by EcoKI, a type IA DNA restriction enzyme. J. Mol. Biol. 283:963-976.
19. Reuter, M., D. Kupper, A. Meisel, C. Schroeder, and D. H. Krueger. 1998. Cooperative binding properties of restriction endonuclease EcoRII with DNA recognition sites. J. Biol. Chem. 273:8294-8300.
20. Rippe, K., P. H. von Hippel, and J. Langowski. 1995. Action at a distance: DNA-looping and initiation of transcription. Trends Biochem. Sci. 20: 500-506.
21. Rosamund, J., B. Endlich, and S. Linn. 1979. Electron microscopic studies of the mechanism of action of the restriction endonuclease of Escherichia coli B. J. Mol. Biol. 129:619-635.
22. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
23. Schneider, S. W., G. Folprecht, G. Krohne, and H. Oberleithner. 1995. Immunolocalization of lamins and nuclear pore complex proteins by atomic force microscopy. Pflügers Arch. 430:795-801.
24. Schneider, S. W., J. Lärmer, R. M. Henderson, and H. Oberleithner. 1998. Molecular weights of individual proteins correlate with molecular volumes measured by atomic force microscopy. Pflügers Arch. 435: 362-367.
25. Shulman, M. J. 1974. Model for wandering restriction enzymes. Nature. 384:379-383.
26. Studier, F. W., and P. K. Bandyopadhyay. 1988. Model for how type I restriction enzymes select cleavage sites in DNA. Proc. Natl. Acad. Sci. USA. 85:4677-4681.
27. Sturrock, S. S., and D. T. F. Dryden. 1997. A prediction of the amino acids and structures involved in DNA recognition by type I DNA restriction and modification enzymes. Nucleic Acids Res. 25:3408-3414.
28. Szczelkun, M. D., P. Janscak, K. Firman, and S. E. Halford. 1997. Selection of non-specific cleavage sites by the type IC restriction endonuclease EcoR124I. J. Mol. Biol. 271:112-123.
29. Topal, M. D., R. J. Thresher, M. Conrad, and J. Griffith. 1991. NaeI endonuclease binding to pBR322 DNA induces looping. Biochemistry. 30:2006-2010.
30. Webb, J. L., G. King, D. Ternent, A. J. B. Titheradge, and N. E. Murray. 1996. Restriction by EcoKI is enhanced by cooperative interactions between target sequences and is dependent on DEAD box motifs. EMBO J. 15:2003-2009.
31. Yuan, R. 1981. Structure and mechanism of multifunctional restriction endonucleases. Annu. Rev. Biochem. 50:285-315.
32. Yuan, R., D. L. Hamilton, and J. Burckhardt. 1980. DNA translocation by the restriction enzyme from E. coli K. Cell. 20:237-244.