Symmetry elements in DNA structure important for recognition/methylation by DNA [amino]-methyltransferases

Nucleic Acids Research

Volumn 32, Issue 13, 2004, Pages 3930-3934

  Zinoviev, Victor V ^b   Yakishchik, S I ^b   Evdokimov, Alexey A ^b   Malygin, Ernst G ^b   Hattman, Stanley ^a  

^a UNIVERSITY OF ROCHESTER   (United States)

^b STATE RESEARCH CENTER OF VIROLOGY AND BIOTECHNOLOGY VECTOR   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

ADENINE; BACTERIOPHAGE DNA; CYTOSINE; DNA ADENINE METHYLTRANSFERASE; DNA METHYLTRANSFERASE; DOUBLE STRANDED DNA; GUANINE; PALINDROMIC DNA; THYMINE; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE; AMINE; DNA; DNA MODIFICATION METHYLASE BAMHI; OLIGODEOXYRIBONUCLEOTIDE; SITE SPECIFIC DNA METHYLTRANSFERASE (ADENINE SPECIFIC); SITE SPECIFIC DNA METHYLTRANSFERASE (CYTOSINE SPECIFIC);

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; BACTERIOPHAGE T4; CONTROLLED STUDY; DNA DETERMINATION; DNA INTEGRATION; DNA METHYLATION; DNA PROTEIN COMPLEX; DNA SEQUENCE; DNA STRUCTURE; ENZYME ACTIVE SITE; ENZYME ACTIVITY; GENE DELETION; GENE DISRUPTION; MOLECULAR RECOGNITION; NONHUMAN; NUCLEIC ACID ANALYSIS; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN TARGETING; SEQUENCE ALIGNMENT; THEORETICAL STUDY; CHEMISTRY; COMPARATIVE STUDY; ENZYME SPECIFICITY; KINETICS; METABOLISM;

AMINES; BASE SEQUENCE; DNA; DNA METHYLATION; KINETICS; OLIGODEOXYRIBONUCLEOTIDES; SITE-SPECIFIC DNA METHYLTRANSFERASE (CYTOSINE-SPECIFIC); SITE-SPECIFIC DNA-METHYLTRANSFERASE (ADENINE-SPECIFIC); SUBSTRATE SPECIFICITY;

EID: 3242668857     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh712     Document Type: Article

References (26)

1. Barras,F. and Marinus,M.G. (1989) The great GATC: DNA methylation in E. coli. Trends Genet., 5, 139-143.
2. Cheng,X. (1995) Structure and function of DNA methyltransferases. Annu. Rev. Biophys. Biomol. Struct., 24, 293-318.
3. Wu,J.C. and Santi,D.V. (1987) Kinetic and catalytic mechanism of HhaI methyltransferase. J. Biol. Chem., 262, 4778-4786.
4. Malone,Th., Blumenthal,R.M. and Cheng,X. (1995) Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes. J. Mol. Biol., 253, 618-632.
5. Jeltsch,A. (2002) Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. Chembiochem, 3, 274-293.
6. 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.
7. 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.
8. Goedecke,K., Pignot,M., Goody,R.S., Scheidig,A.J. and Weinhold,E. (2001) Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog. Nature Struct. Biol., 8, 121-125.
9. Yang,Z., Horton,J.R., Zhou,L., Zhang,X.J., Dong,A., Zhang,X., Schlagman,S.L., Kossykh,V., Hattman,S. and Cheng,X. (2003) Structure of the bacteriophage T4 DNA adenine methyltransferase. Nature Struct. Biol., 10, 849-855.
10. Dryden,D.T. (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.
11. Thielking,V., Dubois,S., Eritja,R. and Guschlbauer,W. (1997) Dam methyltransferase from Escherichia coli: kinetic studies using modified DNA oligomers: nonmethylated substrates. Biol. Chem., 378, 407-415.
12. Buryanov,Ya.I., Zinoviev,V.V., Gorbunov,Yu.A., Tuzikov,F.V., Rechkunova,N.I., Malygin,E.G. and Bayev,A.A. (1988) Interaction of the EcoDam methyltransferase with synthetic oligodeoxyribonucleotides. Gene, 74, 67-69.
13. Zinoviev,V.V., Evdokimov,A.A., Gorbunov,Yu.A., Malygin,E.G., Kossykh,V.G. and Hattman,S. (1998) Phage T4 DNA [N6-adenine] methyltransferase: kinetic studies using oligonucleotides containing native or modified recognition sites. Biol. Chem., 379, 481-488.
14. Malygin,E.G. and Zinoviev,V.V. (1989) Studies on the role of symmetry in the specific recognition of natural and synthetic DNA by type II restriction and modification enzymes. Sov. Sci. Rev. D. Physiochem. Biol., 9, 87-142.
15. Malygin,E.G., Evdokimov,A.A., Zinoviev,V.V., Ovechkina,L.G., Lindstrom,W.M., Reich,N.O., Schlagman,S.L. and Hattman,S.M. (2001) A dual role for substrate S-adenosyl-L-methionine in the methylation reaction with bacteriophage T4 Dam DNA-[N6-adenine]-methyltransferase. Nucleic Acids Res., 29, 2361-2369.
16. Modrich,P. (1982) Studies on sequence recognition by type II restriction and modification enzymes. CRC Crit. Rev. Biochem., 13, 287-323.
17. Kossykh,V.G., Schlagman,S.L. and Hattman,S.M. (1993) Conserved sequence motif DPPY in region IV of the phage T4 Dam DNA-[N6-adenine]-methyltransferase is important for S-adenosyl-L-methionine binding. Nucleic Acids Res., 21, 4659-4662.
18. Hattman,S., Keister,T. and Gottehrer,A. (1978) Sequence specificity of DNA methylases from Bacillus amyloliquefaciens and Bacillus brevis. J. Mol. Biol., 124, 701-711.
19. Kossykh,V.G., Schlagman,S.L. and Hattman,S.M. (1995) Phage T4 DNA [N6-adenine]-methyltransferase: overexpression, purification and characterization. J. Biol. Chem., 270, 14389-14393.
20. Seeman,N.C., Rosenberg,J.M. and Rich,A. (1976) Sequence-specific recognition of double helical nucleic acids by proteins. Proc. Natl Acad. Sci. USA, 73, 804-808.
21. Renbaum,P. and Razin,A. (1995) Interaction of M.SssI and M.HhaI with single-base mismatched oligodeoxynucleotide duplexes. Gene, 157, 177-179.
22. Klimasauskas,S. and Roberts,R.J. (1995) M.HhaI binds tightly to substrates containing mismatches at the target base. Nucleic Acids Res., 23, 1388-1395.
23. Szczelkun,M.D., Jones,H. and Connolly,B.A. (1995) Probing the protein-DNA interface of the EcoRV modification methyltransferase bound to its recognition sequence, GATATC. Biochemistry, 34, 10734-10743.
24. Basak,S. and Nagaraja,V. (2001) A versatile in vivo footprinting technique using 1,10-phenanthroline-copper complex to study important cellular processes. Nucleic Acids Res., 29, e105.
25. Papavassiliou,A.G. (1995) Chemical nucleases as probes for studying DNA-protein interactions. Biochem. J., 305 (Pt 2), 345-357.
26. Gromova,E.S. and Khoroshaev,A.V. (2003) Prokaryotic DNA methyltransferases: the structure and the mechanism of interaction with DNA. Mol. Biol., 37, 300-314.