2-Pyrimidinone as a probe for studying the EcoRII DNA methyltransferase- substrate interaction

European Journal of Biochemistry

Volumn 271, Issue 12, 2004, Pages 2391-2399

  Subach, Oksana M ^a   Khoroshaev, Anton V ^a   Gerasimov, Dmitrii N ^a   Baskunov, Vladimir B ^a   Shchyolkina, Anna K ^b   Gromova, Elizaveta S ^a  

^a MOSCOW STATE UNIVERSITY   (Russian Federation)

^b ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

Author keywords

2 pyrimidinone; C5 cytosine DNA methyltransferase; DNA recognition; Inhibition; M.EcoRII

Indexed keywords

2 PYRIMIDINONE; AMIDE; BASE; CYTOSINE; CYTOSINE DERIVATIVE; DNA; DNA METHYLTRANSFERASE; FUNCTIONAL GROUP; METHYL GROUP; PYRIMIDINE; PYRIMIDINONE DERIVATIVE; S ADENOSYLMETHIONINE; THYMINE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; DNA BINDING; DNA DENATURATION; DNA DETERMINATION; DNA METHYLATION; ENZYME INHIBITION; ENZYME SUBSTRATE; GENETIC STABILITY; INHIBITION KINETICS; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; PROTON TRANSPORT; SEQUENCE ANALYSIS; THERMAL ANALYSIS;

CYTOSINE; DNA; MOLECULAR STRUCTURE; NUCLEIC ACID DENATURATION; PROTEIN BINDING; PYRIMIDINONES; SITE-SPECIFIC DNA METHYLTRANSFERASE (CYTOSINE-SPECIFIC); THERMODYNAMICS; THYMINE;

ESCHERICHIA COLI;

EID: 3042615203     PISSN: 00142956     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1432-1033.2004.04158.x     Document Type: Article

References (28)

1. Chen, L., MacMillan, A.M., Chang, W., Ezaz-Nikpay, K., Lane, W. & Verdine, G.L. (1991) Direct identification of the active-site nucleophile in a DNA (cytosine-5)methyltransferase. Biochemistry 30, 11018-11025.
2. Jeltsch, A. (2002) Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. Chembiochem. 3, 274-293.
3. Santi, D.V., Garrett, C.E. & Barr, P.J. (1983) On the mechanism of inhibition of DNA-cytosine methyltransferases by cytosine analogs. Cell 33, 9-10.
4. Klimasauskas, S., Kumar, S., Roberts, R.J. & Cheng, X. (1994) HhaI methyltransferase flips its target base out of the DNA helix. Cell 76, 357-369.
5. Gabbara, S. & Bhagwat, A. (1995) The mechanism of inhibition of DNA (cytosine-5-)-methyltransferases by 5-azacytosine is likely involve methyl transfer to the inhibitor. Biochem. J. 307, 87-92.
6. Zhou, L., Cheng, X., Connoly, B.A., Dickman, M.J., Hurd, P.J. & Hornby, D.P. (2002) Zebularine: a novel DNA methylation inhibitor that forms a covalent complex with DNA methyltransferases. J. Mol. Biol. 321, 591-599.
7. Hurd, P.J., Whitmarsh, A.J., Baldwin, G.S., Kelly, S.M., Waltho, J.P., Price, N.C., Connoly, B.A. & Hornby, D.P. (1999) Mechanism-based inhibition of C5-cytosine DNA methyltransferases by 2-H pyrimidinone. J. Mol. Biol. 286, 389-401.
8. Taylor, C., Ford, K., Connoly, B.A. & Hornby, D.P. (1993) Determination of the order of substrate addition to MspI DNA methyltransferase using a novel mechanism-based inhibitor. Biochem. J. 291, 493-504.
9. Baldwin, G.S., Kelly, S.M., Price, N.C., Wilson, G.W., Connoly, B.A., Artymiuk, P.J. & Hornby, D.P. (1994) Ligand-induced conformational states of the cytosine-specific DNA methyltransferase M.HgaI-2. J. Mol. Biol. 235, 545-553.
10. Driscoll, J.S., Marquez, V.E., Plowman, J., Liu, P.S., Kelley, J.A. & Barchi, J.J. Jr (1991) Antitumor properties of 2 (1H) -pyrimidinone riboside (zebularine) and its fluorinated analogues. J. Med. Chem. 34, 3280-3284.
11. Friedman, S. & Ansari, N. (1992) Binding of the EcoRII methyltransferase to 5-fluorocytosine-containing DNA. Isolation of a bound peptide. Nucleic Acids Res. 20, 3241-3248.
12. Wyszynski, M.W., Gabbara, S., Kubareva, E.A., Romanova, E.A., Oretskaya, T.S., Gromova, E.S., Shabarova, Z.A. & Bhagwat, A.S. (1993) The cysteine conserved among DNA cytosine methylases is required for methyl transfer, but not for specific DNA binding. Nucleic Acids Res. 21, 295-301.
13. Kiss, A., Posfai, G., Zsurka, G., Rasko, T. & 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.
14. Babkina, O.V., Evstafieva, A.G., Chichkova, N.V., Vartapetian, A.B., Müller, S., Baskunov, V.B., Petrauskene, O.V., Kochetkov, S.N. & Gromova, E.S. (2000) Recombinant components of the EcoRII restriction- modification system. Ability of restriction endonucleases to interact with DNA-RNA duplexes. Mol Biol. (Russ.) 34, 1065-1073.
15. Zhou, Y. & Ts'o, P.O. (1996) Solid-phase synthesis of oligo-2-pyrimidinone-2′-deoxyribonucleotides and oligo-2-pyrimidinone- 2′-deoxyriboside methylphosphonates. Nucleic Acids Res. 24, 2652-2659.
16. Gowher, H. & Jeltsch, A. (2000) Molecular enzymology of the EcoRV DNA-(Adenine-N(6)-methyltransferase: kinetics of DNA binding and bending, kinetic mechanism and linear diffusion of the enzyme on DNA. J. Mol. Biol. 303, 93-110.
17. Brennan, C.A., Van Cleve, M.D. & Gumport, R.I. (1986) The effects of base analogue substitutions on the methylation by the EcoRI modification methylase of octadeoxyribonucleotides containing modified EcoRI recognition sequences. J. Biol. Chem. 261, 7279-7286.
18. Connolly, B.A. & Newman, P.C. (1989) Synthesis and properties of oligonucleotides containing 4-thiothymidine, 5-methyl-2-pyrimidinone-1-β-D- (2′-deoxyriboside) and 2-thiothymidine. Nucleic Acids Res. 17, 4957-4974.
19. Gildea, B. & McLaughlin, L.W. (1989) The synthesis of 2-pyrimidinone nucleosides and their incorporation into oligodeoxynucleotides. Nucleic Acids Res. 17, 2261-2281.
20. Rappaport, H.P. (1988) The 6-thioguanine/5-methyl-2-pyrimidinone base pair. Nucleic Acids Res. 16, 7253-7267.
21. Kaluzhny, D.N., Mikhailov, S.N., Efimtseva, E.V., Borisova, O.F., Florentiev, V.L., Shchyolkina, A.K. & Jovin, T.M. (2003) Fluorescent 2-pyrimidinone nucleoside in parallel-stranded DNA. Nucleosides Nucleotides Nucleic Acids 22, 1499-1503.
22. Karyagina, A., Shilov, I., Tashlitskii, V., Khodoun, M., Vasil'ev, S., Lau, P.C.K. & Nikolskaya, I. (1997) Specific binding of SsoII DNA methyltransferase to its promoter region provides the regulation of SsoII restriction-modification gene expression. Nucleic Acids Res. 25, 2114-2120.
23. Scatchard, G. (1949) The attraction of proteins for small molecules and ions. Ann. NY Acad. Sci. 51, 660-672.
24. Aiken, C.R. & Gumport, R.I. (1991) Base analogs in study of restriction enzyme-DNA interactions. Methods Enzymol. 208, 433-457.
25. Ford, K., Taylor, C., Connolly, B. & Hornby, D.P. (1993) Effects of co-factor and deoxycytidine substituted oligonucleotides upon sequence-specific interactions between MspI DNA methyltransferase and DNA. J. Mol. Biol. 230, 779-786.
26. Cheng, X. & Roberts, R.J. (2001) AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res. 29, 3784-3795.
27. Osterman, D.G., DePillis, G.D., Wu, J.C., Matsuda, A. & Santi, D.V. (1988) 5-fluorocytosine in DNA is a mechanism-based inhibitor of HhaI methylase. Biochemistry 27, 5204-5210.
28. Sharath, A.N., Weinhold, E. & Bhagwat, A.S. (2000) Reviving a dead enzyme: cytosine deaminations promoted by an inactive DNA methyltransferase and S-adenosylmethyonine analogue. Biochemistry 39, 14611-14616.