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PDBsum entry 1mht

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protein dna_rna ligands links
Transferase/DNA PDB id
1mht
Jmol
Contents
Protein chain
327 a.a. *
DNA/RNA
Ligands
SAH
* Residue conservation analysis
PDB id:
1mht
Name: Transferase/DNA
Title: Covalent ternary structure of hhai methyltransferase, DNA and s-adenosyl-l-homocysteine
Structure: DNA (5'-d(p Gp Ap Tp Ap Gp (C36) p Gp Cp Tp Ap Tp C)-3'). Chain: b. Engineered: yes. DNA (5'-d( Tp Gp Ap Tp Ap Gp (C36) p Gp Cp Tp Ap Tp C)-3'). Chain: c. Engineered: yes. Protein (hhai methyltransferase).
Source: Synthetic: yes. Haemophilus haemolyticus. Organism_taxid: 726
Biol. unit: Nonamer (from PQS)
Resolution:
2.60Å     R-factor:   0.174    
Authors: X.Cheng
Key ref:
S.Klimasauskas et al. (1994). HhaI methyltransferase flips its target base out of the DNA helix. Cell, 76, 357-369. PubMed id: 8293469 DOI: 10.1016/0092-8674(94)90342-5
Date:
08-Dec-94     Release date:   03-Jun-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P05102  (MTH1_HAEPH) -  Modification methylase HhaI
Seq:
Struc:
327 a.a.
327 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.1.1.37  - Dna (cytosine-5-)-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: S-adenosyl-L-methionine + DNA = S-adenosyl-L-homocysteine + DNA containing 5-methylcytosine
S-adenosyl-L-methionine
+ DNA
=
S-adenosyl-L-homocysteine
Bound ligand (Het Group name = SAH)
corresponds exactly
+ DNA containing 5-methylcytosine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     C-5 methylation of cytosine   4 terms 
  Biochemical function     transferase activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1016/0092-8674(94)90342-5 Cell 76:357-369 (1994)
PubMed id: 8293469  
 
 
HhaI methyltransferase flips its target base out of the DNA helix.
S.Klimasauskas, S.Kumar, R.J.Roberts, X.Cheng.
 
  ABSTRACT  
 
The crystal structure has been determined at 2.8 A resolution for a chemically-trapped covalent reaction intermediate between the HhaI DNA cytosine-5-methyltransferase, S-adenosyl-L-homocysteine, and a duplex 13-mer DNA oligonucleotide containing methylated 5-fluorocytosine at its target. The DNA is located in a cleft between the two domains of the protein and has the characteristic conformation of B-form DNA, except for a disrupted G-C base pair that contains the target cytosine. The cytosine residue has swung completely out of the DNA helix and is positioned in the active site, which itself has undergone a large conformational change. The DNA is contacted from both the major and the minor grooves, but almost all base-specific interactions between the enzyme and the recognition bases occur in the major groove, through two glycine-rich loops from the small domain. The structure suggests how the active nucleophile reaches its target, directly supports the proposed mechanism for cytosine-5 DNA methylation, and illustrates a novel mode of sequence-specific DNA recognition.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Schematic Representation of the Reaction Pathway Based on the mechanism proposed by Wu and Santi (1985).
Figure 8.
Figure 8. Schematic Representation Showing the Specific Base and Phosphate Contacts between M. Hhl and DNA
 
  The above figures are reprinted by permission from Cell Press: Cell (1994, 76, 357-369) copyright 1994.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20960567 D.Renčiuk, J.Kypr, and M.Vorlíčková (2011).
CGG repeats associated with fragile X chromosome form left-handed Z-DNA structure.
  Biopolymers, 95, 174-181.  
21163962 J.Song, O.Rechkoblit, T.H.Bestor, and D.J.Patel (2011).
Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation.
  Science, 331, 1036-1040.
PDB codes: 3pt6 3pt9 3pta
21350155 L.A.Godley, and A.Mondragón (2011).
Molecular biology. Preference by exclusion.
  Science, 331, 1017-1018.  
20861000 M.Firczuk, M.Wojciechowski, H.Czapinska, and M.Bochtler (2011).
DNA intercalation without flipping in the specific ThaI-DNA complex.
  Nucleic Acids Res, 39, 744-754.
PDB code: 3ndh
20615081 N.A.Cherepanova, A.A.Ivanov, D.V.Maltseva, A.S.Minero, A.V.Gromyko, S.A.Streltsov, A.L.Zhuze, and E.S.Gromova (2011).
Dimeric bisbenzimidazoles inhibit the DNA methylation catalyzed by the murine Dnmt3a catalytic domain.
  J Enzyme Inhib Med Chem, 26, 295-300.  
21245034 R.Gerasimaite, E.Merkiene, and S.Klimasauskas (2011).
Direct observation of cytosine flipping and covalent catalysis in a DNA methyltransferase.
  Nucleic Acids Res, 39, 3771-3780.  
19938008 A.Granzhan, E.Largy, N.Saettel, and M.P.Teulade-Fichou (2010).
Macrocyclic DNA-mismatch-binding ligands: structural determinants of selectivity.
  Chemistry, 16, 878-889.  
20550934 E.Yakubovskaya, E.Mejia, J.Byrnes, E.Hambardjieva, and M.Garcia-Diaz (2010).
Helix unwinding and base flipping enable human MTERF1 to terminate mitochondrial transcription.
  Cell, 141, 982-993.
PDB codes: 3mva 3mvb
20939822 F.Xu, C.Mao, Y.Ding, C.Rui, L.Wu, A.Shi, H.Zhang, L.Zhang, and Z.Xu (2010).
Molecular and enzymatic profiles of mammalian DNA methyltransferases: structures and targets for drugs.
  Curr Med Chem, 17, 4052-4071.  
20033464 J.A.Castelán-Vega, A.Jiménez-Alberto, and R.M.Ribas-Aparicio (2010).
Homology modeling and molecular dynamics simulations of HgiDII methyltransferase in complex with DNA and S-adenosyl-methionine: catalytic mechanism and interactions with DNA.
  J Mol Model, 16, 1213-1222.  
20142834 J.A.Law, and S.E.Jacobsen (2010).
Establishing, maintaining and modifying DNA methylation patterns in plants and animals.
  Nat Rev Genet, 11, 204-220.  
20507910 L.Shen, G.Gao, Y.Zhang, H.Zhang, Z.Ye, S.Huang, J.Huang, and J.Kang (2010).
A single amino acid substitution confers enhanced methylation activity of mammalian Dnmt3b on chromatin DNA.
  Nucleic Acids Res, 38, 6054-6064.  
20186448 M.M.Rodriguez-Ramos, and J.J.Wilker (2010).
Metal-bipyridine complexes in DNA backbones and effects on thermal stability.
  J Biol Inorg Chem, 15, 629-639.  
20151717 M.N.Kinde-Carson, C.Ferguson, N.A.Oyler, G.S.Harbison, and G.A.Meints (2010).
Solid state 2H NMR analysis of furanose ring dynamics in DNA containing uracil.
  J Phys Chem B, 114, 3285-3293.  
21077830 N.A.Cherepanova, A.L.Zhuze, and E.S.Gromova (2010).
Inhibition of murine DNA methyltransferase Dnmt3a by DNA duplexes containing pyrimidine-2(1H)-one.
  Biochemistry (Mosc), 75, 1115-1125.  
20820727 S.S.Jaffer, P.Ghosh, A.Das, and P.Purkayastha (2010).
Opening of DNA double helix at room temperature: Application of alpha-cyclodextrin self-aggregates.
  Nanoscale, 2, 1420-1422.  
20184512 U.K.Madhusoodanan, and D.N.Rao (2010).
Diversity of DNA methyltransferases that recognize asymmetric target sequences.
  Crit Rev Biochem Mol Biol, 45, 125-145.  
20423306 Y.Li, and T.O.Tollefsbol (2010).
Impact on DNA methylation in cancer prevention and therapy by bioactive dietary components.
  Curr Med Chem, 17, 2141-2151.  
19298824 A.Alian, A.DeGiovanni, S.L.Griner, J.S.Finer-Moore, and R.M.Stroud (2009).
Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome.
  J Mol Biol, 388, 785-800.
PDB code: 3dh3
19129216 C.Frauer, and H.Leonhardt (2009).
A versatile non-radioactive assay for DNA methyltransferase activity and DNA binding.
  Nucleic Acids Res, 37, e22.  
19278652 C.Tu, J.E.Tropea, B.P.Austin, D.L.Court, D.S.Waugh, and X.Ji (2009).
Structural basis for binding of RNA and cofactor by a KsgA methyltransferase.
  Structure, 17, 374-385.
PDB codes: 3ftc 3ftd 3fte 3ftf
19465399 D.Kim, S.Reddy, D.Y.Kim, A.Rich, S.Lee, K.K.Kim, and Y.G.Kim (2009).
Base extrusion is found at helical junctions between right- and left-handed forms of DNA and RNA.
  Nucleic Acids Res, 37, 4353-4359.  
19453271 E.G.Malygin, A.A.Evdokimov, and S.Hattman (2009).
Dimeric/oligomeric DNA methyltransferases: an unfinished story.
  Biol Chem, 390, 835-844.  
19586933 G.L.Randall, L.Zechiedrich, and B.M.Pettitt (2009).
In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form.
  Nucleic Acids Res, 37, 5568-5577.  
19233205 G.Nimrod, A.Szilágyi, C.Leslie, and N.Ben-Tal (2009).
Identification of DNA-binding proteins using structural, electrostatic and evolutionary features.
  J Mol Biol, 387, 1040-1053.  
19077538 H.Hashimoto, J.R.Horton, X.Zhang, and X.Cheng (2009).
UHRF1, a modular multi-domain protein, regulates replication-coupled crosstalk between DNA methylation and histone modifications.
  Epigenetics, 4, 8.
PDB codes: 3f8i 3f8j 3fde
19436759 N.K.Banavali, and A.D.Mackerell (2009).
Characterizing structural transitions using localized free energy landscape analysis.
  PLoS ONE, 4, e5525.  
19916931 O.V.Kirsanova, N.A.Cherepanova, and E.S.Gromova (2009).
Inhibition of C5-cytosine-DNA-methyltransferases.
  Biochemistry (Mosc), 74, 1175-1186.  
19497854 R.A.Estabrook, T.T.Nguyen, N.Fera, and N.O.Reich (2009).
Coupling sequence-specific recognition to DNA modification.
  J Biol Chem, 284, 22690-22696.  
19783820 R.Gerasimaite, G.Vilkaitis, and S.Klimasauskas (2009).
A directed evolution design of a GCG-specific DNA hemimethylase.
  Nucleic Acids Res, 37, 7332-7341.  
19740769 R.K.Neely, G.Tamulaitis, K.Chen, M.Kubala, V.Siksnys, and A.C.Jones (2009).
Time-resolved fluorescence studies of nucleotide flipping by restriction enzymes.
  Nucleic Acids Res, 37, 6859-6870.  
19222038 S.Warncke, A.Gégout, and T.Carell (2009).
Phosphorothioation of oligonucleotides strongly influences the inhibition of bacterial (M.HhaI) and human (Dnmt1) DNA methyltransferases.
  Chembiochem, 10, 728-734.  
19351663 T.C.Petrossian, and S.G.Clarke (2009).
Multiple Motif Scanning to identify methyltransferases from the yeast proteome.
  Mol Cell Proteomics, 8, 1516-1526.  
19430486 Z.Liutkeviciute, G.Lukinavicius, V.Masevicius, D.Daujotyte, and S.Klimasauskas (2009).
Cytosine-5-methyltransferases add aldehydes to DNA.
  Nat Chem Biol, 5, 400-402.  
18281210 A.D.Mackerell, and L.Nilsson (2008).
Molecular dynamics simulations of nucleic acid-protein complexes.
  Curr Opin Struct Biol, 18, 194-199.  
18836494 A.Jeltsch (2008).
Reading and writing DNA methylation.
  Nat Struct Mol Biol, 15, 1003-1004.  
18385156 B.Youngblood, E.Bonnist, D.T.Dryden, A.C.Jones, and N.O.Reich (2008).
Differential stabilization of reaction intermediates: specificity checkpoints for M.EcoRI revealed by transient fluorescence and fluorescence lifetime studies.
  Nucleic Acids Res, 36, 2917-2925.  
18450817 D.Daujotyte, Z.Liutkeviciūte, G.Tamulaitis, and S.Klimasauskas (2008).
Chemical mapping of cytosines enzymatically flipped out of the DNA helix.
  Nucleic Acids Res, 36, e57.  
18844399 D.Echodu, G.Goobes, Z.Shajani, K.Pederson, G.Meints, G.Varani, and G.Drobny (2008).
Furanose dynamics in the HhaI methyltransferase target DNA studied by solution and solid-state NMR relaxation.
  J Phys Chem B, 112, 13934-13944.  
18755835 E.Purta, K.H.Kaminska, J.M.Kasprzak, J.M.Bujnicki, and S.Douthwaite (2008).
YbeA is the m3Psi methyltransferase RlmH that targets nucleotide 1915 in 23S rRNA.
  RNA, 14, 2234-2244.  
18849437 E.Tímár, P.Venetianer, and A.Kiss (2008).
In vivo DNA protection by relaxed-specificity SinI DNA methyltransferase variants.
  J Bacteriol, 190, 8003-8008.  
17977734 F.H.Schmidt, M.Hüben, B.Gider, F.Renault, M.P.Teulade-Fichou, and E.Weinhold (2008).
Sequence-specific Methyltransferase-Induced Labelling (SMILing) of plasmid DNA for studying cell transfection.
  Bioorg Med Chem, 16, 40-48.  
18820295 G.Tamulaitis, M.Zaremba, R.H.Szczepanowski, M.Bochtler, and V.Siksnys (2008).
How PspGI, catalytic domain of EcoRII and Ecl18kI acquire specificities for different DNA targets.
  Nucleic Acids Res, 36, 6101-6108.  
18772889 G.V.Avvakumov, J.R.Walker, S.Xue, Y.Li, S.Duan, C.Bronner, C.H.Arrowsmith, and S.Dhe-Paganon (2008).
Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1.
  Nature, 455, 822-825.
PDB codes: 3bi7 3clz
18772888 H.Hashimoto, J.R.Horton, X.Zhang, M.Bostick, S.E.Jacobsen, and X.Cheng (2008).
The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix.
  Nature, 455, 826-829.
PDB codes: 2zo0 2zo1 2zo2
18353991 J.Hu, A.Ma, and A.R.Dinner (2008).
A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT.
  Proc Natl Acad Sci U S A, 105, 4615-4620.  
18000994 J.T.Stivers (2008).
Extrahelical damaged base recognition by DNA glycosylase enzymes.
  Chemistry, 14, 786-793.  
18772891 K.Arita, M.Ariyoshi, H.Tochio, Y.Nakamura, and M.Shirakawa (2008).
Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism.
  Nature, 455, 818-821.
PDB codes: 2zkd 2zke 2zkf 2zkg
18086248 K.Yang, and R.J.Stanley (2008).
The extent of DNA deformation in DNA photolyase-substrate complexes: a solution state fluorescence study.
  Photochem Photobiol, 84, 741-749.  
18219418 L.L.O'Neil, and O.Wiest (2008).
Sequence dependence in base flipping: experimental and computational studies.
  Org Biomol Chem, 6, 485-492.  
18718929 M.A.Carpenter, and A.S.Bhagwat (2008).
DNA base flipping by both members of the PspGI restriction-modification system.
  Nucleic Acids Res, 36, 5417-5425.  
18658249 M.Bahr, V.Gabelica, A.Granzhan, M.P.Teulade-Fichou, and E.Weinhold (2008).
Selective recognition of pyrimidine-pyrimidine DNA mismatches by distance-constrained macrocyclic bis-intercalators.
  Nucleic Acids Res, 36, 5000-5012.  
18304803 M.Orozco, A.Noy, and A.Pérez (2008).
Recent advances in the study of nucleic acid flexibility by molecular dynamics.
  Curr Opin Struct Biol, 18, 185-193.  
18829716 R.H.Szczepanowski, M.A.Carpenter, H.Czapinska, M.Zaremba, G.Tamulaitis, V.Siksnys, A.S.Bhagwat, and M.Bochtler (2008).
Central base pair flipping and discrimination by PspGI.
  Nucleic Acids Res, 36, 6109-6117.  
18479503 R.K.Neely, and R.J.Roberts (2008).
The BsaHI restriction-modification system: cloning, sequencing and analysis of conserved motifs.
  BMC Mol Biol, 9, 48.  
18384044 S.Goto-Ito, T.Ito, R.Ishii, Y.Muto, Y.Bessho, and S.Yokoyama (2008).
Crystal structure of archaeal tRNA(m(1)G37)methyltransferase aTrm5.
  Proteins, 72, 1274-1289.
PDB code: 2yx1
18246412 S.K.Patra, A.Patra, F.Rizzi, T.C.Ghosh, and S.Bettuzzi (2008).
Demethylation of (Cytosine-5-C-methyl) DNA and regulation of transcription in the epigenetic pathways of cancer development.
  Cancer Metastasis Rev, 27, 315-334.  
18060563 T.Latham, N.Gilbert, and B.Ramsahoye (2008).
DNA methylation in mouse embryonic stem cells and development.
  Cell Tissue Res, 331, 31-55.  
18567810 T.P.Jurkowski, M.Meusburger, S.Phalke, M.Helm, W.Nellen, G.Reuter, and A.Jeltsch (2008).
Human DNMT2 methylates tRNA(Asp) molecules using a DNA methyltransferase-like catalytic mechanism.
  RNA, 14, 1663-1670.  
18334209 X.Cheng, and R.M.Blumenthal (2008).
Mammalian DNA methyltransferases: a structural perspective.
  Structure, 16, 341-350.  
17182629 A.E.Smith, and K.G.Ford (2007).
Specific targeting of cytosine methylation to DNA sequences in vivo.
  Nucleic Acids Res, 35, 740-754.  
17338633 A.N.Mak, W.T.Fung, K.P.Kong, A.W.Poon, S.M.Ngai, and P.C.Shaw (2007).
Characterization of the large subunit of EcoHK31I methyltransferase by structural modeling and mutagenesis.
  Biol Chem, 388, 265-271.  
17496048 B.Bouvier, and H.Grubmüller (2007).
A molecular dynamics study of slow base flipping in DNA using conformational flooding.
  Biophys J, 93, 770-786.  
17507378 D.J.Baker, G.Wuenschell, L.Xia, J.Termini, S.E.Bates, A.D.Riggs, and T.R.O'Connor (2007).
Nucleotide excision repair eliminates unique DNA-protein cross-links from mammalian cells.
  J Biol Chem, 282, 22592-22604.  
17713477 D.Jia, R.Z.Jurkowska, X.Zhang, A.Jeltsch, and X.Cheng (2007).
Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation.
  Nature, 449, 248-251.
PDB code: 2qrv
  17183163 E.G.Kapetaniou, D.Kotsifaki, M.Providaki, M.Rina, V.Bouriotis, and M.Kokkinidis (2007).
Purification, crystallization and preliminary X-ray analysis of the BseCI DNA methyltransferase from Bacillus stearothermophilus in complex with its cognate DNA.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 12-14.  
17617640 G.Tamulaitis, M.Zaremba, R.H.Szczepanowski, M.Bochtler, and V.Siksnys (2007).
Nucleotide flipping by restriction enzymes analyzed by 2-aminopurine steady-state fluorescence.
  Nucleic Acids Res, 35, 4792-4799.  
17412704 J.Bischerour, and R.Chalmers (2007).
Base-flipping dynamics in a DNA hairpin processing reaction.
  Nucleic Acids Res, 35, 2584-2595.  
17914173 J.Nakonieczna, J.W.Zmijewski, B.Banecki, and A.J.Podhajska (2007).
Binding of MmeI restriction-modification enzyme to its specific recognition sequence is stimulated by S-adenosyl-L-methionine.
  Mol Biotechnol, 37, 127-135.  
17576694 L.Schermelleh, A.Haemmer, F.Spada, N.Rösing, D.Meilinger, U.Rothbauer, M.C.Cardoso, and H.Leonhardt (2007).
Dynamics of Dnmt1 interaction with the replication machinery and its role in postreplicative maintenance of DNA methylation.
  Nucleic Acids Res, 35, 4301-4312.  
17388812 O.M.Subach, D.V.Maltseva, A.Shastry, A.Kolbanovskiy, S.Klimasauskas, N.E.Geacintov, and E.S.Gromova (2007).
The stereochemistry of benzo[a]pyrene-2'-deoxyguanosine adducts affects DNA methylation by SssI and HhaI DNA methyltransferases.
  FEBS J, 274, 2121-2134.  
17687327 S.K.Ooi, C.Qiu, E.Bernstein, K.Li, D.Jia, Z.Yang, H.Erdjument-Bromage, P.Tempst, S.P.Lin, C.D.Allis, X.Cheng, and T.H.Bestor (2007).
DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA.
  Nature, 448, 714-717.
PDB codes: 2pv0 2pvc
17284456 S.L.Reichow, T.Hamma, A.R.Ferré-D'Amaré, and G.Varani (2007).
The structure and function of small nucleolar ribonucleoproteins.
  Nucleic Acids Res, 35, 1452-1464.  
17292915 W.Xie, C.Zhou, and R.H.Huang (2007).
Structure of tRNA dimethylallyltransferase: RNA modification through a channel.
  J Mol Biol, 367, 872-881.
PDB codes: 3crm 3crq 3crr
16485345 C.B.Yoo, and P.A.Jones (2006).
Epigenetic therapy of cancer: past, present and future.
  Nat Rev Drug Discov, 5, 37-50.  
16408089 C.Dalhoff, G.Lukinavicius, S.Klimasăuskas, and E.Weinhold (2006).
Direct transfer of extended groups from synthetic cofactors by DNA methyltransferases.
  Nat Chem Biol, 2, 31-32.  
16641988 D.MacDonald, G.Demarre, M.Bouvier, D.Mazel, and D.N.Gopaul (2006).
Structural basis for broad DNA-specificity in integron recombination.
  Nature, 440, 1157-1162.
PDB code: 2a3v
16524590 J.R.Horton, K.Liebert, M.Bekes, A.Jeltsch, and X.Cheng (2006).
Structure and substrate recognition of the Escherichia coli DNA adenine methyltransferase.
  J Mol Biol, 358, 559-570.
PDB code: 2g1p
16473850 J.R.Horton, X.Zhang, R.Maunus, Z.Yang, G.G.Wilson, R.J.Roberts, and X.Cheng (2006).
DNA nicking by HinP1I endonuclease: bending, base flipping and minor groove expansion.
  Nucleic Acids Res, 34, 939-948.
PDB codes: 2fkc 2fkh 2fl3 2flc
16282443 L.Armstrong, M.Lako, W.Dean, and M.Stojkovic (2006).
Epigenetic modification is central to genome reprogramming in somatic cell nuclear transfer.
  Stem Cells, 24, 805-814.  
16998239 M.A.Kastenholz, T.U.Schwartz, and P.H.Hünenberger (2006).
The transition between the B and Z conformations of DNA investigated by targeted molecular dynamics simulations with explicit solvation.
  Biophys J, 91, 2976-2990.  
16628220 M.Bochtler, R.H.Szczepanowski, G.Tamulaitis, S.Grazulis, H.Czapinska, E.Manakova, and V.Siksnys (2006).
Nucleotide flips determine the specificity of the Ecl18kI restriction endonuclease.
  EMBO J, 25, 2219-2229.
PDB codes: 2fqz 2gb7
16885288 M.Watanabe, H.Yuzawa, N.Handa, and I.Kobayashi (2006).
Hyperthermophilic DNA methyltransferase M.PabI from the archaeon Pyrococcus abyssi.
  Appl Environ Microbiol, 72, 5367-5375.  
16771353 N.K.Banavali, N.Huang, and A.D.MacKerell (2006).
Conserved patterns in backbone torsional changes allow for single base flipping from duplex DNA with minimal distortion of the double helix.
  J Phys Chem B, 110, 10997-11004.  
17005571 R.A.Estabrook, and N.Reich (2006).
Observing an induced-fit mechanism during sequence-specific DNA methylation.
  J Biol Chem, 281, 37205-37214.  
16768442 T.Christian, C.Evilia, and Y.M.Hou (2006).
Catalysis by the second class of tRNA(m1G37) methyl transferase requires a conserved proline.
  Biochemistry, 45, 7463-7473.  
15653631 E.Merkiene, and S.Klimasauskas (2005).
Probing a rate-limiting step by mutational perturbation of AdoMet binding in the HhaI methyltransferase.
  Nucleic Acids Res, 33, 307-315.  
16047360 F.R.Wibowo, C.Rauch, M.Trieb, and K.R.Liedl (2005).
M.TaqI facilitates the base flipping via an unusual DNA backbone conformation.
  Biopolymers, 79, 128-138.  
16236720 J.Luo, and T.C.Bruice (2005).
Low-frequency normal mode in DNA HhaI methyltransferase and motions of residues involved in the base flipping.
  Proc Natl Acad Sci U S A, 102, 16194-16198.  
15882618 J.R.Horton, K.Liebert, S.Hattman, A.Jeltsch, and X.Cheng (2005).
Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase.
  Cell, 121, 349-361.
PDB codes: 1yf3 1yfj 1yfl
15811914 K.Hart, B.Nyström, M.Ohman, and L.Nilsson (2005).
Molecular dynamics simulations and free energy calculations of base flipping in dsRNA.
  RNA, 11, 609-618.  
16179918 K.Schuebel, and S.Baylin (2005).
In living color: DNA methyltransferase caught in the act.
  Nat Methods, 2, 736-738.  
15558546 M.Radlinska, A.Kondrzycka-Dada, A.Piekarowicz, and J.M.Bujnicki (2005).
Identification of amino acids important for target recognition by the DNA:m5C methyltransferase M.NgoPII by alanine-scanning mutagenesis of residues at the protein-DNA interface.
  Proteins, 58, 263-270.  
15657135 R.A.Estabrook, J.Luo, M.M.Purdy, V.Sharma, P.Weakliem, T.C.Bruice, and N.O.Reich (2005).
Statistical coevolution analysis and molecular dynamics: identification of amino acid pairs essential for catalysis.
  Proc Natl Acad Sci U S A, 102, 994-999.  
16340006 R.K.Neely, D.Daujotyte, S.Grazulis, S.W.Magennis, D.T.Dryden, S.Klimasauskas, and A.C.Jones (2005).
Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes.
  Nucleic Acids Res, 33, 6953-6960.
PDB codes: 2c7o 2c7p 2c7q 2c7r
16237447 S.C.Ha, K.Lowenhaupt, A.Rich, Y.G.Kim, and K.K.Kim (2005).
Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases.
  Nature, 437, 1183-1186.
PDB code: 2acj
15948708 S.Hattman (2005).
DNA-[adenine] methylation in lower eukaryotes.
  Biochemistry (Mosc), 70, 550-558.  
16246913 T.Shevchuk, L.Kretzner, K.Munson, J.Axume, J.Clark, O.V.Dyachenko, M.Caudill, Y.Buryanov, and S.S.Smith (2005).
Transgene-induced CCWGG methylation does not alter CG methylation patterning in human kidney cells.
  Nucleic Acids Res, 33, 6124-6136.  
15766524 T.T.Lee, S.Agarwalla, and R.M.Stroud (2005).
A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function.
  Cell, 120, 599-611.
PDB code: 2bh2
16097936 Y.I.Buryanov, and T.V.Shevchuk (2005).
DNA methyltransferases and structural-functional specificity of eukaryotic DNA modification.
  Biochemistry (Mosc), 70, 730-742.  
15195996 A.Dong, L.Zhou, X.Zhang, S.Stickel, R.J.Roberts, and X.Cheng (2004).
Structure of the Q237W mutant of HhaI DNA methyltransferase: an insight into protein-protein interactions.
  Biol Chem, 385, 373-379.
PDB code: 1svu
15210696 B.B.Hopkins, and N.O.Reich (2004).
Simultaneous DNA binding, bending, and base flipping: evidence for a novel M.EcoRI methyltransferase-DNA complex.
  J Biol Chem, 279, 37049-37060.  
15274924 D.Daujotyte, S.Serva, G.Vilkaitis, E.Merkiene, C.Venclovas, and S.Klimasauskas (2004).
HhaI DNA methyltransferase uses the protruding Gln237 for active flipping of its target cytosine.
  Structure, 12, 1047-1055.  
15221026 D.S.Daniels, T.T.Woo, K.X.Luu, D.M.Noll, N.D.Clarke, A.E.Pegg, and J.A.Tainer (2004).
DNA binding and nucleotide flipping by the human DNA repair protein AGT.
  Nat Struct Mol Biol, 11, 714-720.
PDB codes: 1t38 1t39
15375145 J.Hager, B.L.Staker, and U.Jakob (2004).
Substrate binding analysis of the 23S rRNA methyltransferase RrmJ.
  J Bacteriol, 186, 6634-6642.  
15121902 J.M.Bujnicki, M.Feder, C.L.Ayres, and K.L.Redman (2004).
Sequence-structure-function studies of tRNA:m5C methyltransferase Trm4p and its relationship to DNA:m5C and RNA:m5U methyltransferases.
  Nucleic Acids Res, 32, 2453-2463.  
15273274 J.R.Horton, G.Ratner, N.K.Banavali, N.Huang, Y.Choi, M.A.Maier, V.E.Marquez, A.D.MacKerell, and X.Cheng (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.
PDB code: 1skm
15292170 K.Sawada, Z.Yang, J.R.Horton, R.E.Collins, X.Zhang, and X.Cheng (2004).
Structure of the conserved core of the yeast Dot1p, a nucleosomal histone H3 lysine 79 methyltransferase.
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PDB code: 1u2z
15102449 M.Steiniger-White, I.Rayment, and W.S.Reznikoff (2004).
Structure/function insights into Tn5 transposition.
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PDB code: 1mus
15155847 N.B.Edfeldt, E.A.Harwood, S.T.Sigurdsson, P.B.Hopkins, and B.R.Reid (2004).
Solution structure of a nitrous acid induced DNA interstrand cross-link.
  Nucleic Acids Res, 32, 2785-2794.
PDB codes: 1s9n 1s9o
14704346 N.Fujikawa, H.Kurumizaka, O.Nureki, Y.Tanaka, M.Yamazoe, S.Hiraga, and S.Yokoyama (2004).
Structural and biochemical analyses of hemimethylated DNA binding by the SeqA protein.
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PDB codes: 1iu3 1j3e
15182354 O.M.Subach, A.V.Khoroshaev, D.N.Gerasimov, V.B.Baskunov, A.K.Shchyolkina, and E.S.Gromova (2004).
2-Pyrimidinone as a probe for studying the EcoRII DNA methyltransferase-substrate interaction.
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15143064 R.A.Estabrook, R.Lipson, B.Hopkins, and N.Reich (2004).
The coupling of tight DNA binding and base flipping: identification of a conserved structural motif in base flipping enzymes.
  J Biol Chem, 279, 31419-31428.  
15570069 S.H.Chan, Z.Zhu, J.L.Van Etten, and S.Y.Xu (2004).
Cloning of CviPII nicking and modification system from chlorella virus NYs-1 and application of Nt.CviPII in random DNA amplification.
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15107490 T.J.Su, B.A.Connolly, C.Darlington, R.Mallin, and D.T.Dryden (2004).
Unusual 2-aminopurine fluorescence from a complex of DNA and the EcoKI methyltransferase.
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15169780 T.Torizawa, T.Ueda, S.Kuramitsu, K.Hitomi, T.Todo, S.Iwai, K.Morikawa, and I.Shimada (2004).
Investigation of the cyclobutane pyrimidine dimer (CPD) photolyase DNA recognition mechanism by NMR analyses.
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15280508 V.V.Zinoviev, S.I.Yakishchik, A.A.Evdokimov, E.G.Malygin, and S.Hattman (2004).
Symmetry elements in DNA structure important for recognition/methylation by DNA [amino]-methyltransferases.
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15223314 Z.Yang, L.Shipman, M.Zhang, B.P.Anton, R.J.Roberts, and X.Cheng (2004).
Structural characterization and comparative phylogenetic analysis of Escherichia coli HemK, a protein (N5)-glutamine methyltransferase.
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PDB code: 1t43
14661275 A.David, N.Bleimling, C.Beuck, J.M.Lehn, E.Weinhold, and M.P.Teulade-Fichou (2003).
DNA mismatch-specific base flipping by a bisacridine macrocycle.
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12732637 C.B.Thomas, R.D.Scavetta, R.I.Gumport, and M.E.Churchill (2003).
Structures of liganded and unliganded RsrI N6-adenine DNA methyltransferase: a distinct orientation for active cofactor binding.
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PDB codes: 1nw5 1nw6 1nw7 1nw8
12824489 D.J.Miller, N.Ouellette, E.Evdokimova, A.Savchenko, A.Edwards, and W.F.Anderson (2003).
Crystal complexes of a predicted S-adenosylmethionine-dependent methyltransferase reveal a typical AdoMet binding domain and a substrate recognition domain.
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PDB codes: 1m6y 1n2x
12893823 E.G.Malygin, W.M.Lindstrom, V.V.Zinoviev, A.A.Evdokimov, S.L.Schlagman, N.O.Reich, and S.Hattman (2003).
Bacteriophage T4Dam (DNA-(adenine-N6)-methyltransferase): evidence for two distinct stages of methylation under single turnover conditions.
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12595551 E.Giudice, P.Várnai, and R.Lavery (2003).
Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations.
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14522053 E.M.Duguid, Y.Mishina, and C.He (2003).
How do DNA repair proteins locate potential base lesions? a chemical crosslinking method to investigate O6-alkylguanine-DNA alkyltransferases.
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14527324 G.L.Verdine, and D.P.Norman (2003).
Covalent trapping of protein-DNA complexes.
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12907723 G.Natrajan, M.H.Lamers, J.H.Enzlin, H.H.Winterwerp, A.Perrakis, and T.K.Sixma (2003).
Structures of Escherichia coli DNA mismatch repair enzyme MutS in complex with different mismatches: a common recognition mode for diverse substrates.
  Nucleic Acids Res, 31, 4814-4821.
PDB codes: 1oh5 1oh6 1oh7 1oh8
12773376 H.J.Ahn, H.W.Kim, H.J.Yoon, B.I.Lee, S.W.Suh, and J.K.Yang (2003).
Crystal structure of tRNA(m1G37)methyltransferase: insights into tRNA recognition.
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PDB codes: 1uaj 1uak 1ual 1uam
12741815 H.L.Schubert, J.D.Phillips, and C.P.Hill (2003).
Structures along the catalytic pathway of PrmC/HemK, an N5-glutamine AdoMet-dependent methyltransferase.
  Biochemistry, 42, 5592-5599.
PDB codes: 1nv8 1nv9
12826405 H.L.Schubert, R.M.Blumenthal, and X.Cheng (2003).
Many paths to methyltransfer: a chronicle of convergence.
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12562799 H.Pinarbasi, E.Pinarbasi, and D.P.Hornby (2003).
The small subunit of M. AquI is responsible for sequence-specific DNA recognition and binding in the absence of the catalytic domain.
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14527954 J.Kindrachuk, J.Parent, G.F.Davies, M.Dinsmore, S.Attah-Poku, and S.Napper (2003).
Overexpression of L-isoaspartate O-methyltransferase in Escherichia coli increases heat shock survival by a mechanism independent of methyltransferase activity.
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12954781 J.Osipiuk, M.A.Walsh, and A.Joachimiak (2003).
Crystal structure of MboIIA methyltransferase.
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PDB code: 1g60
14515373 K.Bastard, A.Thureau, R.Lavery, and C.Prévost (2003).
Docking macromolecules with flexible segments.
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12506195 N.Huang, N.K.Banavali, and A.D.MacKerell (2003).
Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.
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14656444 P.G.Foster, C.R.Nunes, P.Greene, D.Moustakas, and R.M.Stroud (2003).
The first structure of an RNA m5C methyltransferase, Fmu, provides insight into catalytic mechanism and specific binding of RNA substrate.
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PDB codes: 1sqf 1sqg
14751833 V.E.Marquez, R.Eritja, J.A.Kelley, D.Vanbemmel, and J.K.Christman (2003).
Potent inhibition of HhaI DNA methylase by the aglycon of 2-(1H)-pyrimidinone riboside (zebularine) at the GCGC recognition domain.
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12501249 V.V.Zinoviev, A.A.Evdokimov, E.G.Malygin, S.L.Schlagman, and S.Hattman (2003).
Bacteriophage T4 Dam DNA-(N6-adenine)-methyltransferase. Processivity and orientation to the methylation target.
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12937411 Z.Yang, J.R.Horton, L.Zhou, X.J.Zhang, A.Dong, X.Zhang, S.L.Schlagman, V.Kossykh, S.Hattman, and X.Cheng (2003).
Structure of the bacteriophage T4 DNA adenine methyltransferase.
  Nat Struct Biol, 10, 849-855.
PDB codes: 1q0s 1q0t
11933228 A.Jeltsch (2002).
Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases.
  Chembiochem, 3, 274-293.  
12202767 A.R.McNamara, P.J.Hurd, A.E.Smith, and K.G.Ford (2002).
Characterisation of site-biased DNA methyltransferases: specificity, affinity and subsite relationships.
  Nucleic Acids Res, 30, 3818-3830.  
11805107 B.Ason, and W.S.Reznikoff (2002).
Mutational analysis of the base flipping event found in Tn5 transposition.
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11729191 C.P.Swaminathan, U.T.Sankpal, D.N.Rao, and A.Surolia (2002).
Water-assisted dual mode cofactor recognition by HhaI DNA methyltransferase.
  J Biol Chem, 277, 4042-4049.  
12056895 G.D.Markham, P.O.Norrby, and C.W.Bock (2002).
S-adenosylmethionine conformations in solution and in protein complexes: conformational influences of the sulfonium group.
  Biochemistry, 41, 7636-7646.  
11814334 G.S.Laco, J.R.Collins, B.T.Luke, H.Kroth, J.M.Sayer, D.M.Jerina, and Y.Pommier (2002).
Human topoisomerase I inhibition: docking camptothecin and derivatives into a structure-based active site model.
  Biochemistry, 41, 1428-1435.  
11907039 I.Wong, A.J.Lundquist, A.S.Bernards, and D.W.Mosbaugh (2002).
Presteady-state analysis of a single catalytic turnover by Escherichia coli uracil-DNA glycosylase reveals a "pinch-pull-push" mechanism.
  J Biol Chem, 277, 19424-19432.  
12142288 J.Goodrich, and S.Tweedie (2002).
Remembrance of things past: chromatin remodeling in plant development.
  Annu Rev Cell Dev Biol, 18, 707-746.  
11929612 J.M.Bujnicki, and L.Rychlewski (2002).
RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited--bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure.
  BMC Bioinformatics, 3, 10.  
11959553 K.A.Farrow, D.Lyras, G.Polekhina, K.Koutsis, M.W.Parker, and J.I.Rood (2002).
Identification of essential residues in the Erm(B) rRNA methyltransferase of Clostridium perfringens.
  Antimicrob Agents Chemother, 46, 1253-1261.  
12206775 L.Zhou, X.Cheng, B.A.Connolly, M.J.Dickman, P.J.Hurd, and D.P.Hornby (2002).
Zebularine: a novel DNA methylation inhibitor that forms a covalent complex with DNA methyltransferases.
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PDB code: 1m0e
12222679 M.Shiraishi, A.J.Oates, and T.Sekiya (2002).
An overview of the analysis of DNA methylation in mammalian genomes.
  Biol Chem, 383, 893-906.  
12490708 P.Várnai, D.Djuranovic, R.Lavery, and B.Hartmann (2002).
Alpha/gamma transitions in the B-DNA backbone.
  Nucleic Acids Res, 30, 5398-5406.  
12011426 S.H.Chou, K.H.Chin, and F.M.Chen (2002).
Looped out and perpendicular: deformation of Watson-Crick base pair associated with actinomycin D binding.
  Proc Natl Acad Sci U S A, 99, 6625-6630.
PDB code: 1l1v
  15130839 T.D.Schneider (2002).
Consensus sequence Zen.
  Appl Bioinformatics, 1, 111-119.  
11821381 T.Yokochi, and K.D.Robertson (2002).
Preferential methylation of unmethylated DNA by Mammalian de novo DNA methyltransferase Dnmt3a.
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12177302 U.Aapola, I.Liiv, and P.Peterson (2002).
Imprinting regulator DNMT3L is a transcriptional repressor associated with histone deacetylase activity.
  Nucleic Acids Res, 30, 3602-3608.  
12060679 U.T.Sankpal, and D.N.Rao (2002).
Mutational analysis of conserved residues in HhaI DNA methyltransferase.
  Nucleic Acids Res, 30, 2628-2638.  
11839295 X.Cheng, and R.M.Blumenthal (2002).
Cytosines do it, thymines do it, even pseudouridines do it--base flipping by an enzyme that acts on RNA.
  Structure, 10, 127-129.  
12433997 Y.F.Lee, D.S.Tawfik, and A.D.Griffiths (2002).
Investigating the target recognition of DNA cytosine-5 methyltransferase HhaI by library selection using in vitro compartmentalisation.
  Nucleic Acids Res, 30, 4937-4944.  
12220189 Y.L.Jiang, and J.T.Stivers (2002).
Mutational analysis of the base-flipping mechanism of uracil DNA glycosylase.
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11139614 A.Dong, J.A.Yoder, X.Zhang, L.Zhou, T.H.Bestor, and X.Cheng (2001).
Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistant binding to DNA.
  Nucleic Acids Res, 29, 439-448.
PDB code: 1g55
11405235 A.Jeltsch (2001).
The cytosine N4-methyltransferase M.PvuII also modifies adenine residues.
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11470876 A.Kiss, G.Pósfai, G.Zsurka, T.Raskó, and P.Venetianer (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.  
11266551 A.V.Matveyev, K.T.Young, A.Meng, and J.Elhai (2001).
DNA methyltransferases of the cyanobacterium Anabaena PCC 7120.
  Nucleic Acids Res, 29, 1491-1506.  
11779468 C.Hoang, and A.R.Ferré-D'Amaré (2001).
Cocrystal structure of a tRNA Psi55 pseudouridine synthase: nucleotide flipping by an RNA-modifying enzyme.
  Cell, 107, 929-939.
PDB code: 1k8w
11376154 E.G.Malygin, A.A.Evdokimov, V.V.Zinoviev, L.G.Ovechkina, W.M.Lindstrom, N.O.Reich, S.L.Schlagman, and S.Hattman (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.  
11483533 E.Kouzminova, and E.U.Selker (2001).
dim-2 encodes a DNA methyltransferase responsible for all known cytosine methylation in Neurospora.
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11208790 G.Macintyre, C.V.Atwood, and C.G.Cupples (2001).
Lowering S-adenosylmethionine levels in Escherichia coli modulates C-to-T transition mutations.
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11732917 J.C.Delaney, and J.M.Essigmann (2001).
Effect of sequence context on O(6)-methylguanine repair and replication in vivo.
  Biochemistry, 40, 14968-14975.  
11713319 K.Lepikhov, A.Tchernov, L.Zheleznaja, N.Matvienko, J.Walter, and T.A.Trautner (2001).
Characterization of the type IV restriction modification system BspLU11III from Bacillus sp. LU11.
  Nucleic Acids Res, 29, 4691-4698.  
11329623 M.Blank, and R.Goodman (2001).
Electromagnetic initiation of transcription at specific DNA sites.
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11423420 M.Feig, M.Zacharias, and B.M.Pettitt (2001).
Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations.
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11551826 M.Franchina, J.Hooper, and P.H.Kay (2001).
Five novel alternatively spliced transcripts of DNA (cytosine-5) methyltransferase 2 in human peripheral blood leukocytes.
  Int J Biochem Cell Biol, 33, 1104-1115.  
11470870 M.Roth, and A.Jeltsch (2001).
Changing the target base specificity of the EcoRV DNA methyltransferase by rational de novo protein-design.
  Nucleic Acids Res, 29, 3137-3144.  
11223884 O.D.Schärer, and J.Jiricny (2001).
Recent progress in the biology, chemistry and structural biology of DNA glycosylases.
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11726698 T.D.Schneider (2001).
Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation.
  Nucleic Acids Res, 29, 4881-4891.  
11557810 X.Cheng, and R.J.Roberts (2001).
AdoMet-dependent methylation, DNA methyltransferases and base flipping.
  Nucleic Acids Res, 29, 3784-3795.  
11087417 A.N.Sharath, E.Weinhold, and A.S.Bhagwat (2000).
Reviving a dead enzyme: cytosine deaminations promoted by an inactive DNA methyltransferase and an S-adenosylmethionine analogue.
  Biochemistry, 39, 14611-14616.  
11112526 D.L.Wong, and N.O.Reich (2000).
Identification of tyrosine 204 as the photo-cross-linking site in the DNA-EcoRI DNA methyltransferase complex by electrospray ionization mass spectrometry.
  Biochemistry, 39, 15410-15417.  
10654930 H.Wang, D.Boisvert, K.K.Kim, R.Kim, and S.H.Kim (2000).
Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 A resolution.
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PDB code: 1fbn
10606635 J.E.Wibley, A.E.Pegg, and P.C.Moody (2000).
Crystal structure of the human O(6)-alkylguanine-DNA alkyltransferase.
  Nucleic Acids Res, 28, 393-401.
PDB code: 1qnt
10839821 N.E.Murray (2000).
Type I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle).
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  11104519 N.M.Luscombe, S.E.Austin, H.M.Berman, and J.M.Thornton (2000).
An overview of the structures of protein-DNA complexes.
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11015203 O.M.Stephens, H.Y.Yi-Brunozzi, and P.A.Beal (2000).
Analysis of the RNA-editing reaction of ADAR2 with structural and fluorescent analogues of the GluR-B R/G editing site.
  Biochemistry, 39, 12243-12251.  
11000262 P.E.Verdemato, J.A.Brannigan, C.Damblon, F.Zuccotto, P.C.Moody, and L.Y.Lian (2000).
DNA-binding mechanism of the Escherichia coli Ada O(6)-alkylguanine-DNA alkyltransferase.
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11024175 R.D.Scavetta, C.B.Thomas, M.A.Walsh, S.Szegedi, A.Joachimiak, R.I.Gumport, and M.E.Churchill (2000).
Structure of RsrI methyltransferase, a member of the N6-adenine beta class of DNA methyltransferases.
  Nucleic Acids Res, 28, 3950-3961.
PDB code: 1eg2
10790376 S.Pradhan, and R.J.Roberts (2000).
Hybrid mouse-prokaryotic DNA (cytosine-5) methyltransferases retain the specificity of the parental C-terminal domain.
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11024176 S.S.Szegedi, N.O.Reich, and R.I.Gumport (2000).
Substrate binding in vitro and kinetics of RsrI [N6-adenine] DNA methyltransferase.
  Nucleic Acids Res, 28, 3962-3971.  
10642186 S.Wärmländer, A.Sen, and M.Leijon (2000).
Imino proton exchange in DNA catalyzed by ammonia and trimethylamine: evidence for a secondary long-lived open state of the base pair.
  Biochemistry, 39, 607-615.  
10931923 T.Raskó, C.Finta, and A.Kiss (2000).
DNA bending induced by DNA (cytosine-5) methyltransferases.
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10671528 W.M.Lindstrom, J.Flynn, and N.O.Reich (2000).
Reconciling structure and function in HhaI DNA cytosine-C-5 methyltransferase.
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10781108 X.Cao, N.M.Springer, M.G.Muszynski, R.L.Phillips, S.Kaeppler, and S.E.Jacobsen (2000).
Conserved plant genes with similarity to mammalian de novo DNA methyltransferases.
  Proc Natl Acad Sci U S A, 97, 4979-4984.  
10995470 Y.Pommier, G.S.Laco, G.Kohlhagen, J.M.Sayer, H.Kroth, and D.M.Jerina (2000).
Position-specific trapping of topoisomerase I-DNA cleavage complexes by intercalated benzo[a]- pyrene diol epoxide adducts at the 6-amino group of adenine.
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11088571 Y.Z.Chen, V.Mohan, and R.H.Griffey (2000).
Spontaneous base flipping in DNA and its possible role in methyltransferase binding.
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10551869 A.Bacolla, S.Pradhan, R.J.Roberts, and R.D.Wells (1999).
Recombinant human DNA (cytosine-5) methyltransferase. II. Steady-state kinetics reveal allosteric activation by methylated dna.
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10391886 A.Jeltsch, F.Christ, M.Fatemi, and M.Roth (1999).
On the substrate specificity of DNA methyltransferases. adenine-N6 DNA methyltransferases also modify cytosine residues at position N4.
  J Biol Chem, 274, 19538-19544.  
10467137 A.Shekhtman, L.McNaughton, R.P.Cunningham, and S.M.Baxter (1999).
Identification of the Archaeoglobus fulgidus endonuclease III DNA interaction surface using heteronuclear NMR methods.
  Structure, 7, 919-930.  
10329711 B.Holz, N.Dank, J.E.Eickhoff, G.Lipps, G.Krauss, and E.Weinhold (1999).
Identification of the binding site for the extrahelical target base in N6-adenine DNA methyltransferases by photo-cross-linking with duplex oligodeoxyribonucleotides containing 5-iodouracil at the target position.
  J Biol Chem, 274, 15066-15072.  
10220317 B.W.Allan, N.O.Reich, and J.M.Beechem (1999).
Measurement of the absolute temporal coupling between DNA binding and base flipping.
  Biochemistry, 38, 5308-5314.  
10383435 B.W.Allan, R.Garcia, K.Maegley, J.Mort, D.Wong, W.Lindstrom, J.M.Beechem, and N.O.Reich (1999).
DNA bending by EcoRI DNA methyltransferase accelerates base flipping but compromises specificity.
  J Biol Chem, 274, 19269-19275.  
10518532 D.M.van Aalten, D.A.Erlanson, G.L.Verdine, and L.Joshua-Tor (1999).
A structural snapshot of base-pair opening in DNA.
  Proc Natl Acad Sci U S A, 96, 11809-11814.
PDB code: 1cw9
9931007 H.Pues, N.Bleimling, B.Holz, J.Wölcke, and E.Weinhold (1999).
Functional roles of the conserved aromatic amino acid residues at position 108 (motif IV) and position 196 (motif VIII) in base flipping and catalysis by the N6-adenine DNA methyltransferase from Thermus aquaticus.
  Biochemistry, 38, 1426-1434.  
9893991 J.T.Stivers, K.W.Pankiewicz, and K.A.Watanabe (1999).
Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase.
  Biochemistry, 38, 952-963.  
10026283 K.Nadassy, S.J.Wodak, and J.Janin (1999).
Structural features of protein-nucleic acid recognition sites.
  Biochemistry, 38, 1999-2017.  
10651285 M.Radlinska, J.M.Bujnicki, and A.Piekarowicz (1999).
Structural characterization of two tandemly arranged DNA methyltransferase genes from Neisseria gonorrhoeae MS11: N4-cytosine specific M.NgoMXV and nonfunctional 5-cytosine-type M.NgoMorf2P.
  Proteins, 37, 717-728.  
10518555 M.S.Hung, N.Karthikeyan, B.Huang, H.C.Koo, J.Kiger, and C.J.Shen (1999).
Drosophila proteins related to vertebrate DNA (5-cytosine) methyltransferases.
  Proc Natl Acad Sci U S A, 96, 11940-11945.  
9917068 M.Sette, R.Spurio, P.van Tilborg, C.O.Gualerzi, and R.Boelens (1999).
Identification of the ribosome binding sites of translation initiation factor IF3 by multidimensional heteronuclear NMR spectroscopy.
  RNA, 5, 82-92.  
10619018 R.C.Gupta, E.Folta-Stogniew, S.O'Malley, M.Takahashi, and C.M.Radding (1999).
Rapid exchange of A:T base pairs is essential for recognition of DNA homology by human Rad51 recombination protein.
  Mol Cell, 4, 705-714.  
10454610 R.Reid, P.J.Greene, and D.V.Santi (1999).
Exposition of a family of RNA m(5)C methyltransferases from searching genomic and proteomic sequences.
  Nucleic Acids Res, 27, 3138-3145.  
  10593256 S.Kumar, B.Ma, C.J.Tsai, H.Wolfson, and R.Nussinov (1999).
Folding funnels and conformational transitions via hinge-bending motions.
  Cell Biochem Biophys, 31, 141-164.  
10551868 S.Pradhan, A.Bacolla, R.D.Wells, and R.J.Roberts (1999).
Recombinant human DNA (cytosine-5) methyltransferase. I. Expression, purification, and comparison of de novo and maintenance methylation.
  J Biol Chem, 274, 33002-33010.  
10369689 S.Sethmann, P.Ceglowski, J.Willert, R.Iwanicka-Nowicka, T.A.Trautner, and J.Walter (1999).
M.(phi)BssHII, a novel cytosine-C5-DNA-methyltransferase with target-recognizing domains at separated locations of the enzyme.
  EMBO J, 18, 3502-3508.  
10066749 U.Dornberger, M.Leijon, and H.Fritzsche (1999).
High base pair opening rates in tracts of GC base pairs.
  J Biol Chem, 274, 6957-6962.  
10445884 Y.Motorin, and H.Grosjean (1999).
Multisite-specific tRNA:m5C-methyltransferase (Trm4) in yeast Saccharomyces cerevisiae: identification of the gene and substrate specificity of the enzyme.
  RNA, 5, 1105-1118.  
9461471 B.Holz, S.Klimasauskas, S.Serva, and E.Weinhold (1998).
2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases.
  Nucleic Acids Res, 26, 1076-1083.  
9442083 B.W.Allan, J.M.Beechem, W.M.Lindstrom, and N.O.Reich (1998).
Direct real time observation of base flipping by the EcoRI DNA methyltransferase.
  J Biol Chem, 273, 2368-2373.  
  9628328 C.Schmutte, and P.A.Jones (1998).
Involvement of DNA methylation in human carcinogenesis.
  Biol Chem, 379, 377-388.  
9726812 D.C.Liebler, A.E.Aust, G.L.Wilson, and E.S.Copeland (1998).
Reactive oxidants from nitric oxide, oxidants and cellular signalling, and repair of oxidative DNA damage: a Chemical Pathology Study Section workshop.
  Mol Carcinog, 22, 209-220.  
9454602 D.Carotti, S.Funiciello, F.Palitti, and R.Strom (1998).
Influence of pre-existing methylation on the de novo activity of eukaryotic DNA methyltransferase.
  Biochemistry, 37, 1101-1108.  
9585521 D.E.Bussiere, S.W.Muchmore, C.G.Dealwis, G.Schluckebier, V.L.Nienaber, R.P.Edalji, K.A.Walter, U.S.Ladror, T.F.Holzman, and C.Abad-Zapatero (1998).
Crystal structure of ErmC', an rRNA methyltransferase which mediates antibiotic resistance in bacteria.
  Biochemistry, 37, 7103-7112.
PDB code: 2erc
9421528 D.L.Wong, J.G.Pavlovich, and N.O.Reich (1998).
Electrospray ionization mass spectrometric characterization of photocrosslinked DNA-EcoRI DNA methyltransferase complexes.
  Nucleic Acids Res, 26, 645-649.  
9730810 D.O.Zharkov, and A.P.Grollman (1998).
MutY DNA glycosylase: base release and intermediate complex formation.
  Biochemistry, 37, 12384-12394.  
9751641 D.P.Hornby, and G.C.Ford (1998).
Protein-mediated base flipping.
  Curr Opin Biotechnol, 9, 354-358.  
  9811640 D.P.Twomey, L.L.McKay, and D.J.O'Sullivan (1998).
Molecular characterization of the Lactococcus lactis LlaKR2I restriction-modification system and effect of an IS982 element positioned between the restriction and modification genes.
  J Bacteriol, 180, 5844-5854.  
15012234 E.J.Finnegan, R.K.Genger, W.J.Peacock, and E.S.Dennis (1998).
DNA METHYLATION IN PLANTS.
  Annu Rev Plant Physiol Plant Mol Biol, 49, 223-247.  
9417045 G.Panayotou, T.Brown, T.Barlow, L.H.Pearl, and R.Savva (1998).
Direct measurement of the substrate preference of uracil-DNA glycosylase.
  J Biol Chem, 273, 45-50.  
9790680 J.Flynn, and N.Reich (1998).
Murine DNA (cytosine-5-)-methyltransferase: steady-state and substrate trapping analyses of the kinetic mechanism.
  Biochemistry, 37, 15162-15169.  
9461472 K.Stankevicius, A.Lubys, A.Timinskas, D.Vaitkevicius, and A.Janulaitis (1998).
Cloning and analysis of the four genes coding for Bpu10I restriction-modification enzymes.
  Nucleic Acids Res, 26, 1084-1091.  
9783745 M.O'Gara, J.R.Horton, R.J.Roberts, and X.Cheng (1998).
Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base.
  Nat Struct Biol, 5, 872-877.
PDB codes: 7mht 8mht 9mht
9843515 M.O'Neill, D.T.Dryden, and N.E.Murray (1998).
Localization of a protein-DNA interface by random mutagenesis.
  EMBO J, 17, 7118-7127.  
9651316 M.Roth, S.Helm-Kruse, T.Friedrich, and A.Jeltsch (1998).
Functional roles of conserved amino acid residues in DNA methyltransferases investigated by site-directed mutagenesis of the EcoRV adenine-N6-methyltransferase.
  J Biol Chem, 273, 17333-17342.  
9862809 P.H.Tran, Z.R.Korszun, S.Cerritelli, S.S.Springhorn, and S.A.Lacks (1998).
Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of streptococcus pneumoniae bound to S-adenosylmethionine.
  Structure, 6, 1563-1575.
PDB code: 2dpm
9759487 R.J.Roberts, and X.Cheng (1998).
Base flipping.
  Annu Rev Biochem, 67, 181-198.  
  9584105 S.Henikoff, and L.Comai (1998).
A DNA methyltransferase homolog with a chromodomain exists in multiple polymorphic forms in Arabidopsis.
  Genetics, 149, 307-318.  
9427765 S.Klimasauskas, T.Szyperski, S.Serva, and K.Wüthrich (1998).
Dynamic modes of the flipped-out cytosine during HhaI methyltransferase-DNA interactions in solution.
  EMBO J, 17, 317-324.  
  9628345 S.Saha, I.Ahmad, Y.V.Reddy, V.Krishnamurthy, and D.N.Rao (1998).
Functional analysis of conserved motifs in type III restriction-modification enzymes.
  Biol Chem, 379, 511-517.  
9671807 S.Serva, E.Weinhold, R.J.Roberts, and S.Klimasauskas (1998).
Chemical display of thymine residues flipped out by DNA methyltransferases.
  Nucleic Acids Res, 26, 3473-3479.  
  9628340 T.Friedrich, M.Roth, S.Helm-Kruse, and A.Jeltsch (1998).
Functional mapping of the EcoRV DNA methyltransferase by random mutagenesis and screening for catalytically inactive mutants.
  Biol Chem, 379, 475-480.  
9115372 A.K.Dubey, and S.K.Bhattacharya (1997).
Angle and locus of the bend induced by the msp I DNA methyltransferase in a sequence-specific complex with DNA.
  Nucleic Acids Res, 25, 2025-2029.  
9341165 A.K.McCullough, M.L.Dodson, O.D.Schärer, and R.S.Lloyd (1997).
The role of base flipping in damage recognition and catalysis by T4 endonuclease V.
  J Biol Chem, 272, 27210-27217.  
9428703 A.S.Kamath-Loeb, A.Hizi, J.Tabone, M.S.Solomon, and L.A.Loeb (1997).
Inefficient repair of RNA x DNA hybrids.
  Eur J Biochem, 250, 492-501.  
9405430 A.T.Ferguson, P.M.Vertino, J.R.Spitzner, S.B.Baylin, M.T.Muller, and N.E.Davidson (1997).
Role of estrogen receptor gene demethylation and DNA methyltransferase.DNA adduct formation in 5-aza-2'deoxycytidine-induced cytotoxicity in human breast cancer cells.
  J Biol Chem, 272, 32260-32266.  
9207033 C.Finta, and A.Kiss (1997).
Footprint analysis of the bsp RI DNA methyltransferase-DNA interaction.
  Nucleic Acids Res, 25, 2841-2846.  
9032058 D.G.Vassylyev, and K.Morikawa (1997).
DNA-repair enzymes.
  Curr Opin Struct Biol, 7, 103-109.  
9358163 D.Meierhans, M.Sieber, and R.K.Allemann (1997).
High affinity binding of MEF-2C correlates with DNA bending.
  Nucleic Acids Res, 25, 4537-4544.  
9336474 E.G.Malygin, N.A.Petrov, Y.A.Gorbunov, V.G.Kossykh, and S.Hattman (1997).
Interaction of the phage T4 Dam DNA-[N6-adenine] methyltransferase with oligonucleotides containing native or modified (defective) recognition sites.
  Nucleic Acids Res, 25, 4393-4399.  
9398832 G.L.Xu, and T.H.Bestor (1997).
Cytosine methylation targetted to pre-determined sequences.
  Nat Genet, 17, 376-378.  
9204874 G.M.Adams, and R.M.Blumenthal (1997).
The PvuII DNA (cytosine-N4)-methyltransferase comprises two trypsin-defined domains, each of which binds a molecule of S-adenosyl-L-methionine.
  Biochemistry, 36, 8284-8292.  
9278491 H.Kong, and C.L.Smith (1997).
Substrate DNA and cofactor regulate the activities of a multi-functional restriction-modification enzyme, BcgI.
  Nucleic Acids Res, 25, 3687-3692.  
  9371633 J.Sekiguchi, and S.Shuman (1997).
Nick sensing by vaccinia virus DNA ligase requires a 5' phosphate at the nick and occupancy of the adenylate binding site on the enzyme.
  J Virol, 71, 9679-9684.  
9399916 K.D.Robertson, and P.A.Jones (1997).
Dynamic interrelationships between DNA replication, methylation, and repair.
  Am J Hum Genet, 61, 1220-1224.  
9079656 K.Goodtzova, S.Kanugula, S.Edara, G.T.Pauly, R.C.Moschel, and A.E.Pegg (1997).
Repair of O6-benzylguanine by the Escherichia coli Ada and Ogt and the human O6-alkylguanine-DNA alkyltransferases.
  J Biol Chem, 272, 8332-8339.  
9084861 M.Blank, and R.Goodman (1997).
Do electromagnetic fields interact directly with DNA?
  Bioelectromagnetics, 18, 111-115.  
9327396 M.J.Guille, and G.G.Kneale (1997).
Methods for the analysis of DNA-protein interactions.
  Mol Biotechnol, 8, 35-52.  
9113112 M.L.Gonzalgo, and P.A.Jones (1997).
Mutagenic and epigenetic effects of DNA methylation.
  Mutat Res, 386, 107-118.  
9288926 M.O'Gara, G.M.Adams, W.Gong, R.Kobayashi, R.M.Blumenthal, and X.Cheng (1997).
Expression, purification, mass spectrometry, crystallization and multiwavelength anomalous diffraction of selenomethionyl PvuII DNA methyltransferase (cytosine-N4-specific).
  Eur J Biochem, 247, 1009-1018.  
9218422 M.Oda, K.Furukawa, K.Ogata, A.Sarai, S.Ishii, Y.Nishimura, and H.Nakamura (1997).
Investigation of the pyrimidine preference by the c-Myb DNA-binding domain at the initial base of the consensus sequence.
  J Biol Chem, 272, 17966-17971.  
9171083 N.V.Kumar, and U.Varshney (1997).
Contrasting effects of single stranded DNA binding protein on the activity of uracil DNA glycosylase from Escherichia coli towards different DNA substrates.
  Nucleic Acids Res, 25, 2336-2343.  
9144158 O.D.Schärer, T.Kawate, P.Gallinari, J.Jiricny, and G.L.Verdine (1997).
Investigation of the mechanisms of DNA binding of the human G/T glycosylase using designed inhibitors.
  Proc Natl Acad Sci U S A, 94, 4878-4883.  
  9444478 P.A.Bullock (1997).
The initiation of simian virus 40 DNA replication in vitro.
  Crit Rev Biochem Mol Biol, 32, 503-568.  
9122155 P.A.Jones, and M.L.Gonzalgo (1997).
Altered DNA methylation and genome instability: a new pathway to cancer?
  Proc Natl Acad Sci U S A, 94, 2103-2105.  
9108149 P.H.Thorpe, D.Ternent, and N.E.Murray (1997).
The specificity of sty SKI, a type I restriction enzyme, implies a structure with rotational symmetry.
  Nucleic Acids Res, 25, 1694-1700.  
9287157 R.C.Manuel, and R.S.Lloyd (1997).
Cloning, overexpression, and biochemical characterization of the catalytic domain of MutY.
  Biochemistry, 36, 11140-11152.  
9782776 R.E.Dickerson, and T.K.Chiu (1997).
Helix bending as a factor in protein/DNA recognition.
  Biopolymers, 44, 361-403.  
9352585 R.O.Pieper (1997).
Understanding and manipulating O6-methylguanine-DNA methyltransferase expression.
  Pharmacol Ther, 74, 285-297.  
8994613 R.S.Keyes, E.V.Bobst, Y.Y.Cao, and A.M.Bobst (1997).
Overall and internal dynamics of DNA as monitored by five-atom-tethered spin labels.
  Biophys J, 72, 282-290.  
9354758 R.S.Lloyd, and X.Cheng (1997).
Mechanistic link between DNA methyltransferases and DNA repair enzymes by base flipping.
  Biopolymers, 44, 139-151.  
8995288 S.Cal, and B.A.Connolly (1997).
DNA distortion and base flipping by the EcoRV DNA methyltransferase. A study using interference at dA and T bases and modified deoxynucleosides.
  J Biol Chem, 272, 490-496.  
9115443 S.Djordjevic, and A.M.Stock (1997).
Crystal structure of the chemotaxis receptor methyltransferase CheR suggests a conserved structural motif for binding S-adenosylmethionine.
  Structure, 5, 545-558.
PDB code: 1af7
9207024 S.Kumar, J.R.Horton, G.D.Jones, R.T.Walker, R.J.Roberts, and X.Cheng (1997).
DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferase.
  Nucleic Acids Res, 25, 2773-2783.
PDB code: 6mht
9358180 S.Pradhan, D.Talbot, M.Sha, J.Benner, L.Hornstra, E.Li, R.Jaenisch, and R.J.Roberts (1997).
Baculovirus-mediated expression and characterization of the full-length murine DNA methyltransferase.
  Nucleic Acids Res, 25, 4666-4673.  
9122165 S.S.Smith, L.Niu, D.J.Baker, J.A.Wendel, S.E.Kane, and D.S.Joy (1997).
Nucleoprotein-based nanoscale assembly.
  Proc Natl Acad Sci U S A, 94, 2162-2167.  
9254696 S.S.Sturrock, and D.T.Dryden (1997).
A prediction of the amino acids and structures involved in DNA recognition by type I DNA restriction and modification enzymes.
  Nucleic Acids Res, 25, 3408-3414.  
9321648 S.Xu, J.Xiao, J.Posfai, R.Maunus, and J.Benner (1997).
Cloning of the BssHII restriction-modification system in Escherichia coli : BssHII methyltransferase contains circularly permuted cytosine-5 methyltransferase motifs.
  Nucleic Acids Res, 25, 3991-3994.  
9207015 W.Gong, M.O'Gara, R.M.Blumenthal, and X.Cheng (1997).
Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment.
  Nucleic Acids Res, 25, 2702-2715.
PDB code: 1boo
9405473 X.Zhao, J.Liu, D.S.Hsu, S.Zhao, J.S.Taylor, and A.Sancar (1997).
Reaction mechanism of (6-4) photolyase.
  J Biol Chem, 272, 32580-32590.  
8612277 A.E.Hodel, P.D.Gershon, X.Shi, and F.A.Quiocho (1996).
The 1.85 A structure of vaccinia protein VP39: a bifunctional enzyme that participates in the modification of both mRNA ends.
  Cell, 85, 247-256.
PDB code: 1vpt
8919860 A.Jeltsch, and A.Pingoud (1996).
Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems.
  J Mol Evol, 42, 91-96.  
8942637 B.W.Allan, and N.O.Reich (1996).
Targeted base stacking disruption by the EcoRI DNA methyltransferase.
  Biochemistry, 35, 14757-14762.  
  8635477 C.Lange, C.Wild, and T.A.Trautner (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.  
  8597892 C.T.Denny (1996).
Gene rearrangements in Ewing's sarcoma.
  Cancer Invest, 14, 83-88.  
8794746 D.Carotti, S.Funiciello, P.Lavia, P.Caiafa, and R.Strom (1996).
Different effects of histone H1 on de novo DNA methylation in vitro depend on both the DNA base composition and the DNA methyltransferase.
  Biochemistry, 35, 11660-11667.  
8994964 D.G.Vassylyev, and K.Morikawa (1996).
Precluding uracil from DNA.
  Structure, 4, 1381-1385.  
9016653 D.R.Mernagh, and G.G.Kneale (1996).
High resolution footprinting of a type I methyltransferase reveals a large structural distortion within the DNA recognition site.
  Nucleic Acids Res, 24, 4853-4858.  
8650230 F.C.Christians, and L.A.Loeb (1996).
Novel human DNA alkyltransferases obtained by random substitution and genetic selection in bacteria.
  Proc Natl Acad Sci U S A, 93, 6124-6128.  
8807872 H.C.Nelson, and T.H.Bestor (1996).
Base eversion and shuffling by DNA methyltransferases.
  Chem Biol, 3, 419-423.  
8653795 H.S.Subramanya, A.J.Doherty, S.R.Ashford, and D.B.Wigley (1996).
Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7.
  Cell, 85, 607-615.
PDB code: 1a0i
8679635 H.Thorogood, T.R.Waters, A.W.Parker, C.W.Wharton, and B.A.Connolly (1996).
Resonance Raman spectroscopy of 4-thiothymidine and oligodeoxynucleotides containing this base both free in solution and bound to the restriction endonuclease EcoRV.
  Biochemistry, 35, 8723-8733.  
  8994802 I.Ahmad, and D.N.Rao (1996).
Chemistry and biology of DNA methyltransferases.
  Crit Rev Biochem Mol Biol, 31, 361-380.  
8652507 J.Flynn, J.F.Glickman, and N.O.Reich (1996).
Murine DNA cytosine-C5 methyltransferase: pre-steady- and steady-state kinetic analysis with regulatory DNA sequences.
  Biochemistry, 35, 7308-7315.  
8774911 J.M.Zingg, J.C.Shen, A.S.Yang, H.Rapoport, and P.A.Jones (1996).
Methylation inhibitors can increase the rate of cytosine deamination by (cytosine-5)-DNA methyltransferase.
  Nucleic Acids Res, 24, 3267-3275.  
8611496 J.S.Finer-Moore, L.Liu, C.E.Schafmeister, D.L.Birdsall, T.Mau, D.V.Santi, and R.M.Stroud (1996).
Partitioning roles of side chains in affinity, orientation, and catalysis with structures for mutant complexes: asparagine-229 in thymidylate synthase.
  Biochemistry, 35, 5125-5136.
PDB codes: 1nja 1njb 1njc 1njd 1nje
8702632 J.Sekiguchi, and S.Shuman (1996).
Covalent DNA binding by vaccinia topoisomerase results in unpairing of the thymine base 5' of the scissile bond.
  J Biol Chem, 271, 19436-19442.  
8608116 L.A.Lipscomb, F.X.Zhou, S.R.Presnell, R.J.Woo, M.E.Peek, R.R.Plaskon, and L.D.Williams (1996).
Structure of DNA-porphyrin complex.
  Biochemistry, 35, 2818-2823.
PDB code: 231d
8952480 M.G.Fried, S.Kanugula, J.L.Bromberg, and A.E.Pegg (1996).
DNA binding mechanism of O6-alkylguanine-DNA alkyltransferase: stoichiometry and effects of DNA base composition and secondary structure on complex stability.
  Biochemistry, 35, 15295-15301.  
  8947052 M.P.Kladde, M.Xu, and R.T.Simpson (1996).
Direct study of DNA-protein interactions in repressed and active chromatin in living cells.
  EMBO J, 15, 6290-6300.  
9238641 M.Suzuki, F.C.Christians, B.Kim, A.Skandalis, M.E.Black, and L.A.Loeb (1996).
Tolerance of different proteins for amino acid diversity.
  Mol Divers, 2, 111-118.  
8804109 M.Szyf (1996).
The DNA methylation machinery as a target for anticancer therapy.
  Pharmacol Ther, 70, 1.  
8855952 N.V.Bulychev, C.V.Varaprasad, G.Dormán, J.H.Miller, M.Eisenberg, A.P.Grollman, and F.Johnson (1996).
Substrate specificity of Escherichia coli MutY protein.
  Biochemistry, 35, 13147-13156.  
8982461 P.W.Laird, and R.Jaenisch (1996).
The role of DNA methylation in cancer genetic and epigenetics.
  Annu Rev Genet, 30, 441-464.  
8945517 Q.Feng, J.V.Moran, H.H.Kazazian, and J.D.Boeke (1996).
Human L1 retrotransposon encodes a conserved endonuclease required for retrotransposition.
  Cell, 87, 905-916.  
8755524 R.A.Garcia, C.J.Bustamante, and N.O.Reich (1996).
Sequence-specific recognition of cytosine C5 and adenine N6 DNA methyltransferases requires different deformations of DNA.
  Proc Natl Acad Sci U S A, 93, 7618-7622.  
8557624 S.Cal, and B.A.Connolly (1996).
The EcoRV modification methylase causes considerable bending of DNA upon binding to its recognition sequence GATATC.
  J Biol Chem, 271, 1008-1015.  
  8635476 T.A.Trautner, B.Pawlek, B.Behrens, and J.Willert (1996).
Exact size and organization of DNA target-recognizing domains of multispecific DNA-(cytosine-C5)-methyltransferases.
  EMBO J, 15, 1434-1442.  
8688422 T.Bentin, and P.E.Nielsen (1996).
Enhanced peptide nucleic acid binding to supercoiled DNA: possible implications for DNA "breathing" dynamics.
  Biochemistry, 35, 8863-8869.  
8940189 T.Davis-Smyth, R.C.Duncan, T.Zheng, G.Michelotti, and D.Levens (1996).
The far upstream element-binding proteins comprise an ancient family of single-strand DNA-binding transactivators.
  J Biol Chem, 271, 31679-31687.  
8805547 X.Cheng, and R.M.Blumenthal (1996).
Finding a basis for flipping bases.
  Structure, 4, 639-645.  
7739896 A.Chen, L.M.Powell, D.T.Dryden, N.E.Murray, and T.Brown (1995).
Tyrosine 27 of the specificity polypeptide of EcoKI can be UV crosslinked to a bromodeoxyuridine-substituted DNA target sequence.
  Nucleic Acids Res, 23, 1177-1183.  
7753629 A.S.Yang, J.C.Shen, J.M.Zingg, S.Mi, and P.A.Jones (1995).
HhaI and HpaII DNA methyltransferases bind DNA mismatches, methylate uracil and block DNA repair.
  Nucleic Acids Res, 23, 1380-1387.  
7583113 B.Demple (1995).
Enzyme structures. DNA repair flips out.
  Curr Biol, 5, 719-721.  
7697717 C.D.Mol, A.S.Arvai, G.Slupphaug, B.Kavli, I.Alseth, H.E.Krokan, and J.A.Tainer (1995).
Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis.
  Cell, 80, 869-878.  
7671300 C.D.Mol, A.S.Arvai, R.J.Sanderson, G.Slupphaug, B.Kavli, H.E.Krokan, D.W.Mosbaugh, and J.A.Tainer (1995).
Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: protein mimicry of DNA.
  Cell, 82, 701-708.
PDB code: 1ugh
8846216 C.M.Nunn, and S.Neidle (1995).
The structure of chain-linked DNA as a possible model for the transcription bubble.
  Nat Struct Biol, 2, 1060-1061.  
9383473 C.R.Allerson, and G.L.Verdine (1995).
Synthesis and biochemical evaluation of RNA containing an intrahelical disulfide crosslink.
  Chem Biol, 2, 667-675.  
7862522 C.R.Wilkinson, R.Bartlett, P.Nurse, and A.P.Bird (1995).
The fission yeast gene pmt1+ encodes a DNA methyltransferase homologue.
  Nucleic Acids Res, 23, 203-210.  
8521494 D.G.Vassylyev, T.Kashiwagi, Y.Mikami, M.Ariyoshi, S.Iwai, E.Ohtsuka, and K.Morikawa (1995).
Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition.
  Cell, 83, 773-782.
PDB code: 1vas
7552723 D.T.Dryden, S.S.Sturrock, and M.Winter (1995).
Structural modelling of a type I DNA methyltransferase.
  Nat Struct Biol, 2, 632-635.  
7540055 G.Siligardi, and A.F.Drake (1995).
The importance of extended conformations and, in particular, the PII conformation for the molecular recognition of peptides.
  Biopolymers, 37, 281-292.  
7773744 J.A.Tainer, M.M.Thayer, and R.P.Cunningham (1995).
DNA repair proteins.
  Curr Opin Struct Biol, 5, 20-26.  
7501446 J.C.Shen, J.M.Zingg, A.S.Yang, C.Schmutte, and P.A.Jones (1995).
A mutant HpaII methyltransferase functions as a mutator enzyme.
  Nucleic Acids Res, 23, 4275-4282.  
7697713 J.E.Cleaver, and S.K.Layher (1995).
If the shoe fits": clues on structural recognition of DNA damage.
  Cell, 80, 825-827.  
7638194 J.K.Christman, G.Sheikhnejad, C.J.Marasco, and J.R.Sufrin (1995).
5-Methyl-2'-deoxycytidine in single-stranded DNA can act in cis to signal de novo DNA methylation.
  Proc Natl Acad Sci U S A, 92, 7347-7351.  
7870574 K.F.Lee, K.M.Kam, and P.C.Shaw (1995).
A bacterial methyltransferase M.EcoHK311 requires two proteins for in vitro methylation.
  Nucleic Acids Res, 23, 103-108.  
7606780 K.M.Reinisch, L.Chen, G.L.Verdine, and W.N.Lipscomb (1995).
The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing.
  Cell, 82, 143-153.
PDB code: 1dct
8533156 L.H.Pearl, and R.Savva (1995).
DNA repair in three dimensions.
  Trends Biochem Sci, 20, 421-426.  
7731811 L.M.Powell, and N.E.Murray (1995).
S-adenosyl methionine alters the DNA contacts of the EcoKI methyltransferase.
  Nucleic Acids Res, 23, 967-974.  
  7862132 M.A.O'Connell, S.Krause, M.Higuchi, J.J.Hsuan, N.F.Totty, A.Jenny, and W.Keller (1995).
Cloning of cDNAs encoding mammalian double-stranded RNA-specific adenosine deaminase.
  Mol Cell Biol, 15, 1389-1397.  
  7664751 M.M.Thayer, H.Ahern, D.Xing, R.P.Cunningham, and J.A.Tainer (1995).
Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure.
  EMBO J, 14, 4108-4120.
PDB code: 2abk
7735832 M.S.Chapman, and M.G.Rossmann (1995).
Single-stranded DNA-protein interactions in canine parvovirus.
  Structure, 3, 151-162.
PDB code: 3dpv
7479880 N.Spink, C.M.Nunn, J.Vojtechovsky, H.M.Berman, and S.Neidle (1995).
Crystal structure of a DNA decamer showing a novel pseudo four-way helix-helix junction.
  Proc Natl Acad Sci U S A, 92, 10767-10771.
PDB code: 237d
7476180 P.L.deHaseth, and J.D.Helmann (1995).
Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA.
  Mol Microbiol, 16, 817-824.  
7606789 R.J.Roberts (1995).
On base flipping.
  Cell, 82, 9.  
7748164 R.L.Adams (1995).
Eukaryotic DNA methyltransferases--structure and function.
  Bioessays, 17, 139-145.  
7753630 S.Klimasauskas, and R.J.Roberts (1995).
M.HhaI binds tightly to substrates containing mismatches at the target base.
  Nucleic Acids Res, 23, 1388-1395.  
  7768854 S.Kulakauskas, A.Lubys, and S.D.Ehrlich (1995).
DNA restriction-modification systems mediate plasmid maintenance.
  J Bacteriol, 177, 3451-3454.  
9383436 T.Ellenberger (1995).
Pocketing the difference: structures of uracil excision repair proteins.
  Chem Biol, 2, 351-354.  
7761473 X.Chen, S.V.Mariappan, P.Catasti, R.Ratliff, R.K.Moyzis, A.Laayoun, S.S.Smith, E.M.Bradbury, and G.Gupta (1995).
Hairpins are formed by the single DNA strands of the fragile X triplet repeats: structure and biological implications.
  Proc Natl Acad Sci U S A, 92, 5199-5203.  
7773746 X.Cheng (1995).
DNA modification by methyltransferases.
  Curr Opin Struct Biol, 5, 4.  
  7527340 A.G.Polson, and B.L.Bass (1994).
Preferential selection of adenosines for modification by double-stranded RNA adenosine deaminase.
  EMBO J, 13, 5701-5711.  
  8070417 D.F.Willcock, D.T.Dryden, and N.E.Murray (1994).
A mutational analysis of the two motifs common to adenine methyltransferases.
  EMBO J, 13, 3902-3908.  
7922330 D.Suck (1994).
DNA-protein interactions. Flip out and modify.
  Curr Biol, 4, 252-255.  
8081744 F.K.Winkler (1994).
DNA totally flipped-out by methylase.
  Structure, 2, 79-83.  
7889321 G.King, and N.E.Murray (1994).
Restriction enzymes in cells, not eppendorfs.
  Trends Microbiol, 2, 465-469.  
8293456 G.L.Verdine (1994).
The flip side of DNA methylation.
  Cell, 76, 197-200.  
7971279 J.Gopal, M.J.Yebra, and A.S.Bhagwat (1994).
DsaV methyltransferase and its isoschizomers contain a conserved segment that is similar to the segment in Hhai methyltransferase that is in contact with DNA bases.
  Nucleic Acids Res, 22, 4482-4488.  
7971991 J.Labahn, J.Granzin, G.Schluckebier, D.P.Robinson, W.E.Jack, I.Schildkraut, and W.Saenger (1994).
Three-dimensional structure of the adenine-specific DNA methyltransferase M.Taq I in complex with the cofactor S-adenosylmethionine.
  Proc Natl Acad Sci U S A, 91, 10957-10961.
PDB code: 1adm
7816625 K.Matsuo, J.Silke, K.Gramatikoff, and W.Schaffner (1994).
The CpG-specific methylase SssI has topoisomerase activity in the presence of Mg2+.
  Nucleic Acids Res, 22, 5354-5359.  
8065896 L.Szilák, C.Finta, A.Patthy, P.Venetianer, and A.Kiss (1994).
Self-methylation of BspRI DNA-methyltransferase.
  Nucleic Acids Res, 22, 2876-2881.  
7812717 L.W.Hardy, D.F.Pacitti, and E.Nalivaika (1994).
Use of a purified heterodimer to test negative cooperativity as the basis of substrate inactivation of Escherichia coli thymidylate synthase (Asn177-->Asp).
  Structure, 2, 833-838.  
7816649 M.Noyer-Weidner, J.Walter, P.A.Terschüren, S.Chai, and T.A.Trautner (1994).
M.phi 3TII: a new monospecific DNA (cytosine-C5) methyltransferase with pronounced amino acid sequence similarity to a family of adenine-N6-DNA-methyltransferases.
  Nucleic Acids Res, 22, 5517-5523.  
7937131 M.Noyer-Weidner, J.Walter, P.A.Terschüren, S.Chai, and T.A.Trautner (1994).
M.phi 3TII: a new monospecific DNA (cytosine-C5) methyltransferase with pronounced amino acid sequence similarity to a family of adenine-N6-DNA-methyltransferases.
  Nucleic Acids Res, 22, 4066-4072.  
7527544 R.Jüttermann, E.Li, and R.Jaenisch (1994).
Toxicity of 5-aza-2'-deoxycytidine to mammalian cells is mediated primarily by covalent trapping of DNA methyltransferase rather than DNA demethylation.
  Proc Natl Acad Sci U S A, 91, 11797-11801.  
7833450 R.J.Roberts (1994).
An amazing distortion in DNA induced by a methyltransferase.
  Biosci Rep, 14, 103-117.  
7917329 T.H.Bestor, and G.L.Verdine (1994).
DNA methyltransferases.
  Curr Opin Cell Biol, 6, 380-389.  
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