Investigating the target recognition of DNA cytosine-5 methyltransferase Hhal by library selection using in vitro compartmentalisation

Nucleic Acids Research

Volumn 30, Issue 22, 2002, Pages 4937-4944

  Lee, Yin Fai ^a   Tawfik, Dan S ^a,b   Griffiths, Andrew D ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

^b WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CYTOSINE; DNA; DNA (CYTOSINE 5) METHYLTRANSFERASE; GLYCINE; GUANINE; SERINE; TYROSINE;

BASE PAIRING; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLOGRAPHY; DNA METHYLATION; EMULSION; ENZYME ACTIVITY; ENZYME MECHANISM; GENE LIBRARY; GENE MUTATION; GENE SEQUENCE; GENETIC CODE; IN VITRO STUDY; MOLECULAR CLONING; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN DOMAIN; PROTEIN TARGETING; RANDOMIZATION; REVIEW; RNA TRANSLATION; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; WILD TYPE;

EID: 0037112614     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Review

References (34)

1. Fersht, A. (1999) Structure and Mechanism in Protein Science. W.H. Freeman and Co., New York, NY.
2. Cunningham, B.C. and Wells, J.A. (1989) High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. Science, 244, 1081-1085.
3. Fernandez, M.R., Biosca, J.A., Torres, D., Crosas, B. and Pares, X. (1999) A double residue substitution in the coenzyme-binding site accounts for the different kinetic properties between yeast and human formaldehyde dehydrogenases. J. Biol. Chem., 274, 37869-37875.
4. Clackson, T. and Wells, J.A. (1994) In vitro selection from protein and peptide libraries. Trends Biotechnol., 12, 173-184.
5. Wahler, D. and Reymond, J.L. (2001) Novel methods for biocatalyst screening. Curr. Opin. Chem. Biol., 5, 152-158.
6. Griffiths, A.D. and Tawfik, D.S. (2000) Man-made enzymes-from design to in vitro compartmentalisation. Curr. Opin. Biotechnol., 11, 338-353.
7. Pluckthun, A., Schaffitzel, C., Hanes, J. and Jermutus, L. (2000) In vitro selection and evolution of proteins. Adv. Protein Chem., 55, 367-403.
8. Fastrez, J. (1997) In vivo versus in vitro screening or selection for catalytic activity in enzymes and abzymes. Mol. Biotechnol., 7, 37-55.
9. Tawfik, D.S. and Griffiths, A.D. (1998) Man-made cell-like compartments for molecular evolution. Nat. Biotechnol., 16, 652-656.
10. Ghadessy, F.J., Ong, J.L. and Holliger, P. (2001) Directed evolution of polymerase function by compartmentalized self-replication. Proc. Natl Acad. Sci. USA, 98, 4552-4557.
11. Dryden, D.T.F. (1999) Bacterial DNA methyltransferases. In Cheng, X. and Blumenthal, R.M. (eds), S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions. World Scientific, Singapore, pp. 283-340.
12. Vertino, P.M. (1999) Eukaryotic DNA methyltransferases. In Cheng, X. and Blumenthal, R.M. (eds), S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions. World Scientific, Singapore, pp. 341-372.
13. Laird, P.W. and Jaenisch, R. (1996) The role of DNA methylation in cancer genetic and epigenetics. Annu. Rev. Genet., 30, 441-464.
14. Schmutte, C. and Jones, P.A. (1998) Involvement of DNA methylation in human carcinogenesis. Biol. Chem., 379, 377-388.
15. 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.
16. 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.
17. Schluckebier, G., O'Gara, M., Saenger, W. and Cheng, X. (1995) Universal catalytic domain structure of AdoMet-dependent methyltransferases. J. Mol. Biol., 247, 16-20.
18. Cheng, X. and Blumenthal, R.M. (1999) S-Adenosylmethionine-dependent Methyltransferases: Structures and Functions. World Scientific, Singapore.
19. Kumar, S., Cheng, X., Klimasauskas, S., Mi, S., Posfai, J., Roberts, R.J. and Wilson, G.G. (1994) The DNA (cytosine-5) methyltransferases. Nucleic Acids Res., 22, 1-10.
20. Reinisch, K.M., Chen, L., Verdine, G.L. and Lipscomb, W.N. (1995) The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell, 82, 143-153.
21. Caserta, M., Zacharias, W., Nwankwo, D., Wilson, G.G. and Wells, R.D. (1987) Cloning, sequencing, in vivo promoter mapping and expression in Escherichia coli of the gene for the HhaI methyltransferase. J. Biol. Chem., 262, 4770-4777.
22. Paulin, R., Grigg, G.W., Davey, M.W. and Piper, A.A. (1998) Urea improves efficiency of bisulphite-mediated sequencing of 5′-methylcytosine in genomic DNA. Nucleic Acids Res., 26, 5009-5010.
23. Ramachandran, G.N. and Sasiskharan, V. (1968) Conformation of polypeptides and proteins. Adv. Protein Chem., 23, 283-437.
24. Allen, F.H., Bird, C.M., Rowland, R.S. and Raithby, P.R. (1997) Hydrogen-bond acceptor and donor properties of divalent sulfur (Y-S-Z and R-S-H). Acta Crystallogr., B53, 696-701.
25. Vilkaitis, G., Dong, A., Weinhold, E., Cheng, X. and Klimasauskas, S. (2000) Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase. J. Biol. Chem., 275, 38722-38730.
26. Lange, C., Wild, C. and Trautner, T.A. (1996) Identification of a subdomain within DNA-(cytosine-C5)-methyltransferases responsible for the recognition of the 5′ part of their DNA target. EMBO J., 15, 1443-1450.
27. Cheng, X. and Blumenthal, R.M. (1996) Finding a basis for flipping bases. Structure, 4, 639-645.
28. Szomolanyi, E., Kiss, A. and Venetianer, P. (1980) Cloning the modification methylase gene of Bacillus sphaericus R in Escherichia coli. Gene, 10, 219-225.
29. Kiss, A., Posfai, G., Zsurka, G., Rasko, T. and Venetianer, P. (2001) Role of DNA minor groove interactions in substrate recognition by the M.SinI and M.EcoRII DNA (cytosine-5) methyltransferases. Nucleic Acids Res., 29, 3188-3194.
30. Vilkaitis, G., Lubys, A., Merkiene, E., Timinskas, A., Janulaitis, A. and Klimasauskas, S. (2002) Circular permutation of DNA cytosine-N4 methyltransferases: in vivo coexistence in the BcnI system and in vitro probing by hybrid formation. Nucleic Acids Res., 30, 1547-1557.
31. Wu, J.C. and Santi, D.V. (1987) Kinetic and catalytic mechanism of HhaI methyltransferase. J. Biol. Chem., 262, 4778-4786.
32. Mi, S., Alonso, D. and Roberts, R.J. (1995) Functional analysis of Gln-237 mutants of HhaI methyltransferase. Nucleic Acids Res., 23, 620-627.
33. O'Gara, M., Klimasauskas, S., Roberts, R.J. and Cheng, X. (1996) Enzymatic C5-cytosine methylation of DNA: mechanistic implications of new crystal structures for HhaL methyltransferase-DNA-AdoHcy complexes. J. Mol. Biol., 261, 634-645.
34. Klimasauskas, S., Szyperski, T., Serva, S. and Wuthrich, K. (1998) Dynamic modes of the flipped-out cytosine during HhaI methyltransferase-DNA interactions in solution. EMBO J., 17, 317-324.