-
2
-
-
0028010888
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
15
-
-
0038576427
-
Solubility engineering of the HhaI methyltransferase
-
Daujotyte, D., Vilkaitis, G., Manelyte, L., Skalicky, J., Szyperski, T. and Klimasauskas, S. (2003) Solubility engineering of the HhaI methyltransferase. Protein Eng., 16, 295-301. (Pubitemid 36605012)
-
(2003)
Protein Engineering
, vol.16
, Issue.4
, pp. 295-301
-
-
Daujotyte, D.1
Vilkaitis, G.2
Manelyte, L.3
Skalicky, J.4
Szyperski, T.5
Klimasauskas, S.6
-
16
-
-
0025035727
-
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
-
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
-
18
-
-
0016016547
-
Some dihydro-cytidines and -isocytidines
-
Skaric, V., Gaspert, B., Hohniec, M. and Ladan, G. (1974) Some dihydro-cytidines and -isocytidines. J. Chem. Soc. Perkin., I, 267-271.
-
(1974)
J. Chem. Soc. Perkin.
, vol.1
, pp. 267-271
-
-
Skaric, V.1
Gaspert, B.2
Hohniec, M.3
Ladan, G.4
-
19
-
-
0015986774
-
Modification of cytidine residues with a bisulfite-O-methylhydroxylamine mixture
-
Sverdlov, E.D., Monastyrskaya, G.S., Guskova, L.I., Levitan, T.L., Sheichenko, V.I. and Budowsky, E.I. (1974) Modification of cytidine residues with a bisulfite-O-methylhydroxylamine mixture. Biochim. Biophys. Acta, 340, 153-165.
-
(1974)
Biochim. Biophys. Acta
, vol.340
, pp. 153-165
-
-
Sverdlov, E.D.1
Monastyrskaya, G.S.2
Guskova, L.I.3
Levitan, T.L.4
Sheichenko, V.I.5
Budowsky, E.I.6
-
20
-
-
0017015847
-
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
-
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
-
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
-
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
-
24
-
-
0033575095
-
Protein-Modulated DNA electron transfer
-
DOI 10.1021/ja9900813
-
Rajski, S.R., Kumar, S., Roberts, R.J. and Barton, J.K. (1999) Protein-modulated DNA electron transfer. J. Am. Chem. Soc., 121, 5615-5616. (Pubitemid 29293000)
-
(1999)
Journal of the American Chemical Society
, vol.121
, Issue.23
, pp. 5615-5616
-
-
Rajski, S.R.1
Kumar, S.2
Roberts, R.J.3
Barton, J.K.4
-
25
-
-
0033555454
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
33
-
-
0037422594
-
Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase
-
DOI 10.1073/pnas.0135427100
-
Huang, N., Banavali, N.K. and MacKerell, A.D. (2003) Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase. Proc. Natl Acad. Sci. USA, 100, 68-73. (Pubitemid 36078031)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.1
, pp. 68-73
-
-
Huang, N.1
Banavali, N.K.2
MacKerell Jr., A.D.3
-
34
-
-
0030789978
-
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
-
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
-
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
|