How is Modification of the DNA Substrate Recognized by the Pull Restriction Endonuclease?

Biological Chemistry Hoppe-Seyler

Volumn 379, Issue 4-5, 1998, Pages 451-458

  Horton, John R ^a   Cheng, Xiaodong ^a   Bonventre, Joseph ^b  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NEW ENGLAND BIOLABS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DNA; IODINE DERIVATIVE; RESTRICTION ENDONUCLEASE; WATER;

CONFERENCE PAPER; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DNA CLEAVAGE; DNA MODIFICATION; ENZYME SUBSTRATE COMPLEX; HYDROGEN BOND; IODINATION; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DNA INTERACTION;

CRYSTALLOGRAPHY, X-RAY; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; DNA; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PROTEIN CONFORMATION; SUBSTRATE SPECIFICITY; WATER;

EID: 0031971246     PISSN: 01773593     EISSN: None     Source Type: Journal    
DOI: 10.1515/bchm.1998.379.4-5.451     Document Type: Article

References (31)

1. Adams, G. M., and Blumenthal, R. M. (1995). Genepi/t/IIW: a possible modulator of PvuW endonuclease subunit association. Gene 757,193–199.
2. Aggarwal, A. K. (1995). Structure and function of restriction endonucleases. Curr. Opin. Struct. Biol. 5,11–19.
3. Anderson, J. E. (1993). Restriction endonucleases and modification methylases. Curr. Opin. Struct. Biol. 3,24–30.
4. Athanasiadis, A., Vlassi, M., Kotsifaki, D., Tucker, P. A., Wilson, K. S., and Kokkinidis, M. (1994). Crystal structure of Pvu\I endonuclease reveals extensive structural homologies to EcoRV. Nat. Struct. Biol. 7,469–475.
5. Balendiran, K., Bonventre, J., Knott, R., Jack, W., Benner, J., Schildkraut, I., and Anderson, J. E. (1994). Expression, purification, and crystallization of restriction endonuclease PvuW with DNA containing its recognition site. Proteins: Structure Function Genet. 79,77–79.
6. Blumenthal, R. M., Gregory, S. A., and Cooperider, J. S. (1985). Cloning of a restriction-modification system from Proteus vulgaris and its use in analyzing a methylase-sensitive phenotype in Escherichia coli. J. Bacteriol. 764,501–509.
7. Brünger, A. T. (1992). XPLOR, A System for X-ray Crystallography and NMR, Version 3.1 (New Haven, CT, USA: Yale University Press).
8. Butkus, V., Klimasauskas, S., Petrauskiene, L., Maneliene, Z., Lebionka, A., and Janulaitis, A. (1987). Interaction oM/ul, Cfr6\ and PvuW restriction-modification enzymes with substrates containing either N4-methylcytosine or 5-methylcytosine. Biochim. Biophys. Acta 909,201–207.
9. Cheng, X., Balendiran, K., Schildkraut, I., and Anderson, J. E. (1994). Structure of Pwvll endonuclease with cognate DNA. EMBOJ. 73,3927–3935.
10. Ehbrecht, H. J., Pingoud, A., Urbanke, C., Maass, G., and Gualerzi, C. (1985). Linear diffusion of restriction endonucleases on DNA. J. Biol. Chem. 260,6160–6166.
11. Fujii, S., Wang, A. H. J., van der Marel, G., van Boom, J. H., and Rich, A. (1982). Molecular structure of (m5dC-dG)3i the role of the methyl group on 5-methylcytosine in stabilizing Z-DNA, Nucleic Acids Res. 10,7879–7892.
12. Gingeras, T. R., Greenough, L., Schildkraut, I., and Roberts, R. J. (1981). Two new restriction endonucleases from Proteus vulgaris. Nucleic Acids Res. 9,4525–4536.
13. Jeltsch, A., Alves, J., Maass, G., and Pingoud, A. (1992). On the catalytic mechanism of EcoRI and EcoRV. A detailed proposal based on biochemical results, structural data and molecular modelling. FEBS Lett. 304,4–8.
14. Jeltsch, A., Pleckaityte, M., Selent, U., Wolfes, H., Siksnys, V., and Pingoud, A. (1995). Evidence for substrate-assisted catalysis in the DNA cleavage of several restriction endonucleases. Gene 757,157–162.
15. Jen-Jacobsen, L., Engler, L. E., Lesser, D. R., Kurpiewski, M. R., Yee, C., and McVerry, B. (1996). Structural adaptations in the interaction of EcoRI endonuclease with methylated GAATTC sites. EMBO J. 75,2870–2882.
16. Jones, T. A., Zou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991). Improved methods for binding protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47,110–119.
17. Kostrewa, D., and Winkler, F. K. (1995). Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 resolution. Biochemistry 34,683–696.
18. Kovall, R., and Matthews, B. W. (1997). Toroidal structure of lambda-exonuclease. Science 277,1824–1827.
19. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structure coordinates. J. Appl. Cryst. A42.140–149.
20. McClelland, M., Nelson, M., and Raschke, E. (1994). Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases. Nucleic Acids Res. 22, 3640–3659.
21. Nastri, H. G., Evans, P. D., Walker, I. H., and Riggs, P. D. (1997). Catalytic and DNA binding properties of PvuW restriction endonuclease mutants. J. Biol. Chem. 272,25761–25767.
22. Nelson, P. S., Papas, T. S., Schweinfest, C. W. (1993). Restriction endonuclease cleavage of 5-methyl-deoxycytosine hemimethylated DNA at high enzyme-to-substrate ratios. Nucleic Acids Res. 27,681–686.
23. Otwinowski, Z., and Minor, W. (1997). Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326.
24. Pauling, L. (1960). The Nature of the Chemical Bond (Ithaca, New York: Cornell University Press).
25. Pingoud, A., and Jeltsch, A. (1997). Recognition and cleavage of DNA by type-ll restriction endonucleases. Eur. J. Biochem. 246,1–22.
26. Rhodes, D., Schwabe, J. W., Chapman, L., and Fairall, L. (1996). Towards an understanding of protein-DNA recognition. Philos. Trans. R. Soc. Lond. B Biol. Sci. 357,501–509.
27. Rice, M. R., Calvin-Koons, M. D., and Blumenthal, R. M. (1995). The PvuW (CAGCTG) endonuclease binds to and cleaves CAG5mCTG sites. FASEB J. 9, A1400.
28. Robinson, C. R., and Sligar, S. G. (1995). Heterogeneity in molecular recognition by restriction endonucleases: osmotic and hydrostatic pressure effects on BamH\, PvuW, and EcoRV specificity. Proc. Natl. Acad. Sci. USA 92,3444–3448.
29. Schwabe, J. W. (1997). The role of water in protein-DNA interactions. Curr. Opin. Struct. Biol. 7,126–134.
30. Tao, T., and Blumenthal, R. M. (1992). Sequence and characterization of pvullR, the PvuW endonuclease gene, and of pvuIIC, its regulatory gene. J. Bacteriol. 7 74,3395–3408.
31. Winkler, F. K., Banner, D. W., Oefner, C., Tsernoglou, D., Brown, R. S., Heathman, S. P., Bryan, R. K., Martin, P. D., Petratos, K., and Wiison, K. S. (1993). The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 72,1781–1795.