Functional mapping of the EcoRV DNA methyltransferase by random mutagenesis and screening for catalytically inactive mutants

Biological Chemistry

Volumn 379, Issue 4-5, 1998, Pages 475-480

  Friedrich, Tatjana ^a   Roth, Markus ^a   Helm Kruse, Sabine ^a   Jeltsch, Albert ^a  

^a JUSTUS LIEBIG UNIVERSITY   (Germany)

Author keywords

Adenine N6 methyltransferase; DNA modification; Protein nucleic acid interaction; Restriction modification system; Structure prediction

Indexed keywords

ADENINE; DNA; DNA METHYLTRANSFERASE; HYBRID PROTEIN; MUTANT PROTEIN;

BINDING SITE; CONFERENCE PAPER; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME PURIFICATION; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; MUTAGENESIS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN DNA BINDING;

EID: 0031970825     PISSN: 14316730     EISSN: None     Source Type: Journal    
DOI: 10.1515/bchm.1998.379.4-5.475     Document Type: Conference Paper

References (31)

1. Ahmad, I., and Rao, D.N. (1996a). Chemistry and biology of DNA methyltransferases. Crit. Rev. Biochem. Mol. Biol. 37, 361-380.
2. Ahmad, I., and Rao, D.N. (1996b). Functional analysis of conserved motifs in EcoP15I DNA methyltransferase. J. Mol. Biol. 259, 229-240.
3. Allan, B.W., and Reich, N.O. (1996). Targeted base stacking disruption by the EcoRI DNA methyltransferase. Biochemistry 35, 14757-14762.
4. Bougueleret, L., Schwarzstein, M., Tsugita, A., and Zabeau, M. (1984). Characterization of the genes coding for the EcoRV restriction and modification system of Escherichia coli. Nucl. Acids Res. 12, 3659-3677.
5. Cal, S., and Connolly, B.A. (1997). DNA distortion and base flipping by the EcoRV DNA methyltransferase. J. Biol. Chem. 272, 490-496.
6. Cheng, X., Kumar, S., Posfai, J., Pflugrath, J.W., and Roberts, R.J. (1993). Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine. Cell 74, 299-307.
7. Cheng, X. (1995). Structure and function of DNA methyltransferases. Annu. Rev. Biophys. Biomol. Struct. 24, 293-318.
8. Gong, W., O'Gara, M., Blumenthal, R.M., and Cheng, X. (1997). Structure of PvuII DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Res. 25, 2702-2715.
9. Guschlbauer, W. (1988). The DNA and S-adenosylmethionine-binding regions of EcoDam and related methyltransferases. Gene 74, 211-214.
10. Jeltsch, A., Sobotta, T., and Pingoud, A. (1996). Structure prediction of the EcoRV DNA methyltransferase based on mutant profiling, secondary structure analysis, comparison with known structures of methyltransferases and isolation of catalytically inactive single mutants. Protein Eng. 9, 413-423.
11. 6 methyltransferase. J. Mol. Biol., in press.
12. Klimasauskas, S., Kumar, S., Roberts, R.J., and Cheng, X. (1994). HhaI methyltransferase flips its target base out of the DNA helix. Cell 76, 357-369.
13. Klimasauskas, S., and Roberts, R.J. (1995a). M.HhaI binds tightly to substrates containing mismatches at the target base. Nucleic Acids Res. 23, 1388-1395.
14. Klimasauskas, S., and Roberts, R.J. (1995b). Disruption of the target G-C base-pair by the HhaI methyltransferase. Gene 157, 163-164.
15. Labahn, J., Granzin, J., Schluckebier, G., Robinson, D.P., Jack, W.E., Schildkraut, I., and Saenger, W. (1994). Three-dimensional structure of the adenine-specific DNA methyltransferase M.TaqI in complex with the cofactor S-adenosylmethionine. Proc. Natl. Acad. Sci. USA 91, 10957-10961.
16. Lauster, R., Kriebardis, A., and Guschlbauer, W. (1987). The GATATC-modification enzyme EcoRV is closely related to the GATC-recognizing methyltransferases DpnII and dam from E. coli and phage T4. FEBS Lett. 220, 167-176.
17. Malone, T., Blumenthal, R.M., and Cheng, X. (1995). Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyl-transferases, and suggests a catalytic mechanism for these enzymes. J. Mol. Biol. 253, 618-632.
18. 6-adenine] methyltransferase (dam) of bacteriophage T4. Nucl. Acids Res. 17, 8149-8157.
19. Noyer-Weidner, M., and Trautner, T.A. (1993). Methylation of DNA in prokaryotes. In: DNA Methylation: Molecular Biology and Biological Significance (J.P. Jost, H.P. Saluz, eds.), (Basel, Switzerland: Birkhäuser Verlag) pp. 40-108.
20. Nwosu, V. U., Connolly, B.A., Halford, S.E., and Garnett, J. (1988). The cloning, purification and characterization of the EcoRV modification methylase. Nucl. Acids Res. 16, 3705-3720.
21. O'Gara, M., Klimasauskas, S., Roberts, R.J., and Cheng, X. (1996a). Enzymatic C5-cytosine methylation of DNA: Mechanistic implications of new crystal structures for HhaI methyltransferase-DNA-AdoHcy complexes. J. Mol. Biol. 261, 634-1645.
22. O'Gara, M., Roberts, R.J., and Cheng, X. (1996b). A structural basis for the preferential binding of hemimethylated DNA by HhaI DNAmethyltransferase. J. Mol. Biol. 263, 597-606.
23. Pace, C.N., Vajdos, F., Fee, L., Grimsley, G., and Gray, T. (1995). How to measure and predict a molar absorption coefficient of a protein. Prot. Sci. 4, 2411-2423.
24. Reinisch, K. M., Chen, L., Verdine, G.L., and Lipscomb, W.N. (1995). The crystal structure of HaeIII methyltransferase covalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell 82, 143-153.
25. Schluckebier, G., O'Gara, M., Saenger, W., and Cheng, X. (1995a). Universal catalytic domain structure of AdoMet-dependent methyltransferases. J. Mol. Biol. 247, 16-20.
26. 6-adenine-methyltransferase. Gene 157, 131-134.
27. Schluckebier, G., Kozak, M., Bleimling, N., Weinhold, E., and Saenger, W. (1997). Differential binding of S-adenosylmethionine, S-adenosylhomocysteine and sinefungin to the adenine-specific DNA methyltransferase M.TaqI. J. Mol. Biol. 265, 56-67.
28. Spee, J.H., de Vos, W.M., and Kuipers, O.P. (1993). Efficient random mutagenesis method with adjustable mutation frequency by use of PCR and dITR Nucl. Acids Res. 21, 777-778.
29. Wende, W., Stahl, F. and Pingoud, A. (1996). The production and characterization of artificial heterodimers of the restriction endonuclease EcoRV. Biol. Chem. 377, 625-632.
30. Willcock, D. F., Dryden, D.T.F., and Murray, N.E. (1994). A mutational analysis of the two motifs common to adenine methyltransferases. EMBO J. 13, 3902-3908.
31. Yang, A. S., Shen, J.-C., Zingg, J.-M., Mi, S., and Jones, P.A. (1995). HhaI and HpaII DNA methyltransferases bind DNA mismatches, methylate uracil and block DNA repair. Nucleic Acids Res. 23, 1380-1387.