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Volumn 39, Issue 9, 2011, Pages 3771-3780

Direct observation of cytosine flipping and covalent catalysis in a DNA methyltransferase

Author keywords

[No Author keywords available]

Indexed keywords

DNA (CYTOSINE 5) METHYLTRANSFERASE; DNA METHYLTRANSFERASE;

EID: 79956001873     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1329     Document Type: Article
Times cited : (36)

References (36)
  • 2
    • 0028010888 scopus 로고
    • Hhal methyltransferase flips its target base out of the DNA helix
    • DOI 10.1016/0092-8674(94)90342-5
    • 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. (Pubitemid 24046697)
    • (1994) Cell , vol.76 , Issue.2 , pp. 357-369
    • Klimasauskas, S.1    Kumar, S.2    Roberts, R.J.3    Cheng, X.4
  • 3
    • 0023176797 scopus 로고
    • Kinetic and catalytic mechanism of HhaI methyltransferase
    • Wu, J.C. and Santi, D.V. (1987) Kinetic and catalytic mechanism of HhaI methyltransferase. J. Biol. Chem., 262, 4778-4786. (Pubitemid 17102852)
    • (1987) Journal of Biological Chemistry , vol.262 , Issue.10 , pp. 4778-4786
    • Wu, J.C.1    Santi, D.V.2
  • 4
    • 0028990179 scopus 로고
    • M.HhaI binds tightly to substrates containing mismatches at the target base
    • 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.
    • (1995) Nucleic Acids Res. , vol.23 , pp. 1388-1395
    • Klimasauskas, S.1    Roberts, R.J.2
  • 5
    • 0242444679 scopus 로고    scopus 로고
    • Dynamic modes of the flipped-out cytosine during Hhal methyltransferase-DNA interactions in solution
    • DOI 10.1093/emboj/17.1.317
    • Klimasauskas, S., Szyperski, T., Serva, S. and Wü thrich, K. (1998) Dynamic modes of the flipped-out cytosine during HhaI methyltransferase-DNA interactions in solution. EMBO J., 17, 317-324. (Pubitemid 28041072)
    • (1998) EMBO Journal , vol.17 , Issue.1 , pp. 317-324
    • Klimasauskas, S.1    Szyperski, T.2    Serva, S.3    Wuthrich, K.4
  • 6
    • 0034694685 scopus 로고    scopus 로고
    • Use of oligodeoxyribonucleotides with conformationally constrained abasic sugar targets to probe the mechanism of base flipping by hhaI DNA (cytosine C5)-methyltransferase
    • DOI 10.1021/ja001989s
    • Wang, P., Brank, A.S., Banavali, N.K., Nicklaus, M.C., Marquez, V.E., Christman, J.K. and MacKerell, A.D. (2000) Use of oligodeoxyribonucleotides with conformationally constrained abasic sugar targets to probe the mechanism of base flipping by HhaI DNA (cytosine C5)-methyltransferase. J. Am. Chem. Soc., 122, 12422-12434. (Pubitemid 32049422)
    • (2000) Journal of the American Chemical Society , vol.122 , Issue.50 , pp. 12422-12434
    • Wang, P.1    Brank, A.S.2    Banavali, N.K.3    Nicklaus, M.C.4    Marquez, V.E.5    Christman, J.K.6    Mackerell Jr., A.D.7
  • 7
    • 0035877609 scopus 로고    scopus 로고
    • The mechanism of DNA cytosine-5 methylation. Kinetic and mutational dissection of HhaI methyltransferase
    • Vilkaitis, G., Merkiene, E., Serva, S., Weinhold, E. and Klimasauskas, S. (2001) The mechanism of DNA cytosine-5 methylation. Kinetic and mutational dissection of HhaI methyltransferase. J. Biol. Chem., 276, 20924-20934.
    • (2001) J. Biol. Chem. , vol.276 , pp. 20924-20934
    • Vilkaitis, G.1    Merkiene, E.2    Serva, S.3    Weinhold, E.4    Klimasauskas, S.5
  • 8
    • 2942562870 scopus 로고    scopus 로고
    • HhaI DNA methyltransferase uses the protruding Gln237 for active flipping of its target cytosine
    • DOI 10.1016/j.str.2004.04.007, PII S0969212604001479
    • Daujotyte, D., Serva, S., Vilkaitis, G., Merkiene, E., Venclovas, C. and Klimasauskas, S. (2004) HhaI DNA methyltransferase uses the protruding Gln237 for active flipping of its target cytosine. Structure, 12, 1047-1055. (Pubitemid 38748776)
    • (2004) Structure , vol.12 , Issue.6 , pp. 1047-1055
    • Daujotyte, D.1    Serva, S.2    Vilkaitis, G.3    Merkiene, E.4    Venclovas, C.5    Klimasauskas, S.6
  • 9
    • 4444243400 scopus 로고    scopus 로고
    • The mechanism of target base attack in DNA cytosine carbon 5 methylation
    • DOI 10.1021/bi0496743
    • Svedruzic, Z.M. and Reich, N.O. (2004) The mechanism of target base attack in DNA cytosine carbon 5 methylation. Biochemistry, 43, 11460-11473. (Pubitemid 39186967)
    • (2004) Biochemistry , vol.43 , Issue.36 , pp. 11460-11473
    • Svedruzic, Z.M.1    Reich, N.O.2
  • 10
    • 3242714355 scopus 로고    scopus 로고
    • Caught in the act: Visualization of an intermediate in the DNA base-flipping pathway induced by Hhal methyltransferase
    • DOI 10.1093/nar/gkh701
    • Horton, J.R., Ratner, G., Banavali, N.K., Huang, N., Choi, Y., Maier, M.A., Marquez, V.E., MacKerell, A.D. and Cheng, X. (2004) Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase. Nucleic Acids Res., 32, 3877-3886. (Pubitemid 39199080)
    • (2004) Nucleic Acids Research , vol.32 , Issue.13 , pp. 3877-3886
    • Horton, J.R.1    Ratner, G.2    Banavali, N.K.3    Huang, N.4    Choi, Y.5    Maier, M.A.6    Marquez, V.E.7    MacKerell Jr., A.D.8    Cheng, X.9
  • 11
    • 13744261785 scopus 로고    scopus 로고
    • Probing a rate-limiting step by mutational perturbation of AdoMet binding in the Hhal methyltransferase
    • DOI 10.1093/nar/gki175
    • Merkiene, E. and Klimasauskas, S. (2005) Probing a rate-limiting step by mutational perturbation of AdoMet binding in the HhaI methyltransferase. Nucleic Acids Res., 33, 307-315. (Pubitemid 40276952)
    • (2005) Nucleic Acids Research , vol.33 , Issue.1 , pp. 307-315
    • Merkiene, E.1    Klimasauskas, S.2
  • 12
    • 0034624023 scopus 로고    scopus 로고
    • Functional roles of the conserved threonine 250 in the target recognition domain of HhaI DNA methyltransferase
    • 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. (Pubitemid 32009207)
    • (2000) Journal of Biological Chemistry , vol.275 , Issue.49 , pp. 38722-38730
    • Vilkaitis, G.1    Dong, A.2    Weinhold, E.3    Cheng, X.4    Klimasauskas, S.5
  • 13
    • 33845971526 scopus 로고    scopus 로고
    • Observing an induced-fit mechanism during sequence-specific DNA methylation
    • DOI 10.1074/jbc.M607538200
    • Estabrook, R.A. and Reich, N. (2006) Observing an induced-fit mechanism during sequence-specific DNA methylation. J. Biol. Chem., 281, 37205-37214. (Pubitemid 46042190)
    • (2006) Journal of Biological Chemistry , vol.281 , Issue.48 , pp. 37205-37214
    • Estabrook, R.A.1    Reich, N.2
  • 14
    • 69249150442 scopus 로고    scopus 로고
    • Coupling sequence-specific recognition to DNA modification
    • Estabrook, R.A., Nguyen, T.T., Fera, N. and Reich, N.O. (2009) Coupling sequence-specific recognition to DNA modification. J. Biol. Chem., 284, 22690-22696.
    • (2009) J. Biol. Chem. , vol.284 , pp. 22690-22696
    • Estabrook, R.A.1    Nguyen, T.T.2    Fera, N.3    Reich, N.O.4
  • 16
    • 0025035727 scopus 로고
    • Genetic and sequence organization of the mcrBC locus of Escherichia coli K-12
    • Dila, D., Sutherland, E., Moran, L., Slatko, B. and Raleigh, E.A. (1990) Genetic and sequence organization of the mcrBC locus of Escherichia coli K-12. J. Bacteriol., 172, 4888-4900. (Pubitemid 20281934)
    • (1990) Journal of Bacteriology , vol.172 , Issue.9 , pp. 4888-4900
    • Dila, D.1    Sutherland, E.2    Moran, L.3    Slatko, B.4    Raleigh, E.A.5
  • 17
    • 0029902679 scopus 로고    scopus 로고
    • Program DYNAFIT for the analysis of enzyme kinetic data: Application to HIV proteinase
    • DOI 10.1006/abio.1996.0238
    • Kuzmic, P. (1996) Program DYNAFIT for the analysis of enzyme kinetic data: application to HIV proteinase. Anal. Biochem., 237, 260-273. (Pubitemid 26177089)
    • (1996) Analytical Biochemistry , vol.237 , Issue.2 , pp. 260-273
    • Kuzmic, P.1
  • 20
    • 0017015847 scopus 로고
    • Double modification of cytidine residues in DNA
    • Ulanov, B.P., Matorina, T.I. and Emanuel, N.M. (1976) Double modification of cytidine residues in DNA. Mol. Biol., 10, 1211-1220.
    • (1976) Mol. Biol. , vol.10 , pp. 1211-1220
    • Ulanov, B.P.1    Matorina, T.I.2    Emanuel, N.M.3
  • 21
    • 0023718544 scopus 로고
    • 5-Fluorocytosine in DNA is a mechanism-based inhibitor of HhaI methylase
    • Osterman, D.G., DePillis, G.D., Wu, J.C., Matsuda, A. and Santi, D.V. (1988) 5-Fluorocytosine in DNA is a mechanism-based inhibitor of HhaI methylase. Biochemistry, 27, 5204-5210.
    • (1988) Biochemistry , vol.27 , pp. 5204-5210
    • Osterman, D.G.1    Depillis, G.D.2    Wu, J.C.3    Matsuda, A.4    Santi, D.V.5
  • 22
    • 0027318633 scopus 로고
    • The DNA binding affinity of HhaI methylase is increased by a single amino acid substitution in the catalytic center
    • Mi, S. and Roberts, R.J. (1993) The DNA binding affinity of HhaI methylase is increased by a single amino acid substitution in the catalytic center. Nucleic Acids Res., 21, 2459-2464. (Pubitemid 23180826)
    • (1993) Nucleic Acids Research , vol.21 , Issue.10 , pp. 2459-2464
    • Mi, S.1    Roberts, R.J.2
  • 23
    • 0018359137 scopus 로고
    • Evidence from ultraviolet absorbance measurements for a codon-induced conformational change in lysine tRNA from Escherichia coli
    • Mö ller, A., Wild, U., Riesner, D. and Gassen, H.G. (1979) Evidence from ultraviolet absorbance measurements for a codon-induced conformational change in lysine tRNA from Escherichia coli. Proc. Natl Acad. Sci. USA, 76, 3266-32701.
    • (1979) Proc. Natl Acad. Sci. USA , vol.76 , pp. 3266-32701
    • Möller, A.1
  • 25
    • 0033555454 scopus 로고    scopus 로고
    • Electron transfer between bases in double helical DNA
    • Kelley, S.O. and Barton, J.K. (1999) Electron transfer between bases in double helical DNA. Science, 283, 375-381.
    • (1999) Science , vol.283 , pp. 375-381
    • Kelley, S.O.1    Barton, J.K.2
  • 26
    • 0014725117 scopus 로고
    • Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxyoligonucleolides
    • Cantor, C.R., Warshaw, M.M. and Shapiro, H. (1970) Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxyoligonucleolides. Biopolymers, 9, 1059-1077.
    • (1970) Biopolymers , vol.9 , pp. 1059-1077
    • Cantor, C.R.1    Warshaw, M.M.2    Shapiro, H.3
  • 27
    • 17444453249 scopus 로고    scopus 로고
    • Revised UV extinction coefficients for nucleoside-5'-monophosphates and unpaired DNA and RNA
    • Cavaluzzi, M.J. and Borer, P.N. (2004) Revised UV extinction coefficients for nucleoside-5'-monophosphates and unpaired DNA and RNA. Nucleic Acids Res., 32, e13.
    • (2004) Nucleic Acids Res. , vol.32
    • Cavaluzzi, M.J.1    Borer, P.N.2
  • 28
    • 0024804759 scopus 로고
    • Absorbance melting curves of RNA
    • DOI 10.1016/0076-6879(89)80108-9
    • Puglisi, J.D. and Tinoco, I. (1989) Absorbance melting curves of RNA. Methods Enzymol., 180, 304-325. (Pubitemid 20039582)
    • (1989) Methods in Enzymology , vol.180 , pp. 304-325
    • Puglisi, J.D.1    Tinoco Jr., I.2
  • 29
    • 0038401523 scopus 로고
    • Spectrophotometric studies of nucleic acid derivatives and related compounds as a function of pH. II. Natural and synthetic pyrimidine nucleosides
    • Fox, J.J. and Shugar, D. (1952) Spectrophotometric studies of nucleic acid derivatives and related compounds as a function of pH. II. Natural and synthetic pyrimidine nucleosides. Biochim. Biophys. Acta, 9, 369-384.
    • (1952) Biochim. Biophys. Acta , vol.9 , pp. 369-384
    • Fox, J.J.1    Shugar, D.2
  • 30
    • 79956042694 scopus 로고    scopus 로고
    • M·HhaI and M·EcoRI: Paradigms for understanding the conformational mechanisms of DNA methyltransferases
    • Grosjean, H. (ed.) Landes Bioscience, Austin TX, USA
    • Reich, N.O. and Coffin, S.R. (2009) M·HhaI and M·EcoRI: paradigms for understanding the conformational mechanisms of DNA methyltransferases. In Grosjean, H. (ed.), DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution, Vol. 6. Landes Bioscience, Austin TX, USA, pp. 47-57.
    • (2009) DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution , vol.6 , pp. 47-57
    • Reich, N.O.1    Coffin, S.R.2
  • 31
    • 79956021252 scopus 로고    scopus 로고
    • Mechanism and evolution of DNA recognition by DNA-(adenine N6)-methyltransferases from the EcoDam family
    • Grosjean, H. (ed.) Landes Bioscience, Austin TX, USA
    • Jeltsch, A. and Jurkowski, T.P. (2009) Mechanism and evolution of DNA recognition by DNA-(adenine N6)-methyltransferases from the EcoDam family. In Grosjean, H. (ed.), DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution, Vol. 7. Landes Bioscience, Austin TX, USA, pp. 98-108.
    • (2009) DNA and RNA Modification Enzymes: Structure, Mechanism, Function and Evolution , vol.7 , pp. 98-108
    • Jeltsch, A.1    Jurkowski, T.P.2
  • 32
    • 0032145158 scopus 로고    scopus 로고
    • Chemical display of thymine residues flipped out by DNA methyltransferases
    • Serva, S., Weinhold, E., Roberts, R.J. and Klimasauskas, S. (1998) Chemical display of thymine residues flipped out by DNA methyltransferases. Nucleic Acids Res., 26, 3473-3479.
    • (1998) Nucleic Acids Res. , vol.26 , pp. 3473-3479
    • Serva, S.1    Weinhold, E.2    Roberts, R.J.3    Klimasauskas, S.4
  • 34
    • 0030789978 scopus 로고    scopus 로고
    • DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by Hhal methyltransferase
    • DOI 10.1093/nar/25.14.2773
    • Kumar, S., Horton, J.R., Jones, G.D., Walker, R.T., Roberts, R.J. and Cheng, X. (1997) DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferase. Nucleic Acids Res., 25, 2773-2783. (Pubitemid 27299791)
    • (1997) Nucleic Acids Research , vol.25 , Issue.14 , pp. 2773-2783
    • Kumar, S.1    Horton, J.R.2    Jones, G.D.3    Walker, R.T.4    Roberts, R.J.5    Cheng, X.6
  • 35
    • 77954383792 scopus 로고    scopus 로고
    • Mechanism of DNA methylation: The double role of DNA as a substrate and as a cofactor
    • Zangi, R., Arrieta, A. and Cossio, F.P. (2010) Mechanism of DNA methylation: the double role of DNA as a substrate and as a cofactor. J. Mol. Biol., 400, 632-644.
    • (2010) J. Mol. Biol. , vol.400 , pp. 632-644
    • Zangi, R.1    Arrieta, A.2    Cossio, F.P.3
  • 36
    • 33646566359 scopus 로고    scopus 로고
    • The mechanism of M.HhaI DNA C5 cytosine methyltransferase enzyme: A quantum mechanics/ molecular mechanics approach
    • Zhang, X. and Bruice, T. (2006) The mechanism of M.HhaI DNA C5 cytosine methyltransferase enzyme: a quantum mechanics/ molecular mechanics approach. Proc. Natl Acad. Sci. USA, 103, 6148-6153.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 6148-6153
    • Zhang, X.1    Bruice, T.2


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