AdoMet-dependent methylation, DNA methyltransferases and base flipping

Nucleic Acids Research

Volumn 29, Issue 18, 2001, Pages 3784-3795

  Cheng, Xiaodong ^a   Roberts, Richard J ^b  

^a EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b NEW ENGLAND BIOLABS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; CATECHOL; DNA; DNA METHYLTRANSFERASE; DOUBLE STRANDED DNA; GLYCINE; LYSINE; METHYLTRANSFERASE; NITROGEN; NUCLEIC ACID BASE; NUCLEOTIDE; OXYGEN; PROTEIN; PROTEIN ARGININE METHYLTRANSFERASE; PROTEIN METHYLTRANSFERASE; RNA; RNA METHYLTRANSFERASE; S ADENOSYLMETHIONINE;

ARTICLE; BASE MISPAIRING; BETA SHEET; CATALYSIS; CHEMICAL BOND; CONTROLLED STUDY; DNA DAMAGE; DNA METHYLATION; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBSTRATE; EUKARYOTE; EXCISION REPAIR; HUMAN; MACROMOLECULE; MOLECULAR SIZE; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN FOLDING; ROTATION; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

EID: 0035883736     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/29.18.3784     Document Type: Article

References (135)

1. Enzymatic Reaction Mechanisms
2. REBASE-restriction enzymes and methylases
3. Bacterial DNA methyltransferases
4. Cloning of a mammalian DNA methyltransferase
5. A candidate mammalian DNA methyltransferase related to pmt 1p of fission yeast
6. Dnmt2 is not required for de novo and maintenance methylation of viral DNA in embryonic stem cells
7. Cloning and analysis of a novel human putative DNA methyltransferase
8. Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases
9. Eukaryotic DNA methyltransferases
10. Methylation-induced repression-belts, braces, and chromatin
11. The DNA methyltransferases of mammals
12. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a
13. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality
14. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development
15. Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development
16. Developmental abnormalities and epimutations associated with DNA hypomethylation mutations
17. Demethylation-induced developmental pleiotropy in Arabidopsis
18. Functions for DNA methylation in vertebrates
19. X-chromosome inactivation and cell memory
20. Establishment of imprinted methylation patterns during development
21. DNA methylation: A molecular lock
22. Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene
23. The Dnmt3b DNA methyltransferase gene is mutated in the ICF immunodeficiency syndrome
24. HhaI methyltransferase flips its target base out of the DNA helix
25. Crystal structure of the conserved core of protein arginine methyltransferase PRMT3
26. Crystal structure of protein isoaspartyl methyltransferase: A catalyst for protein repair
27. Structure and evolution of AdoMet-dependent methyltransferases
28. S-adenosylmethionine-dependent methylation in Saccharomyces cerevisiae. Identification of a novel protein arginine methyltransferase
29. Crystal structure of a fibrillarin homologue from Methanococcus jannaschii, a hyperthermophile, at 1.6 Å resolution
30. Sno storm in the nucleolus: New roles for myriad small RNPs
31. Crystal structure and functional analysis of a hypothetical protein, Mj0882, from Methanococcus jannascha
32. Hypothetical proteins from Haemophilus influenzae: Two new structures implying methyltransferase function
33. tRNA Methyltransferases
34. Depression of adenosylmethionine content of Escherichia coli by thioglycerol
35. Cleavage and methylation of DNA by the restriction endonuclease HinfIII isolated from Haemophilus influenzae Rf
36. Purification, crystallization, and preliminary X-ray diffraction analysis of an M.HhaI-AdoMet complex
37. Sequence-specific binding of DNA by the EcoRV restriction and modification enzymes with nucleic acids and cofactor analogues
38. The structure and oligomerization of the yeast arginine methyltransferase, Hmt1
39. Predictive motifs derived from cytosine methyltransferases
40. Cytosine-specific type II DNA methyltransferases. A conserved enzyme core with variable target-recognizing domains
41. Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes
42. Universal catalytic domain structure of AdoMet-dependent methyltransferases
43. Structure of PvuII DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein told assignment
44. Structure of RsrI methyltransferase, a member of the N6-adenine β class of DNA methyltransferases
45. Circular permutations in the molecular evolution of DNA methyltransferase
46. Crystal structure of the DpnM DNA adenine methyltransferase from the DpnII restriction system of Streptococcus pneumoniac bound to S-adenosylmethionine
47. Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base
48. Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA
49. Crystal structure of a G: T/U mismatch-specific DNA glycosylase: Mismatch recognition by complementary-strand interactions
50. Crystal structure of a thwarted mismatch glycosylase DNA repair complex
51. Crystal structure of a human alkylbase DNA repair enzyme complexed to DNA: Mechanisms for nucleotide flipping and base excision
52. DNA bending and a flip-out mechanism for base excision by the helix-hairpin-helix DNA glycosylase, Escherichia coli AlkA
53. Base flipping
54. HhaI binds tightly to substrates containing mismatches at the target base
55. HhaI and HpaII DNA methyltransferases bind DNA mismatches, methylate uracil and block DNA repair
56. Fluorescence studies of nucleotides and polynucleotides. I. Formycin, 2-aminopurine riboside, 2,6-diaminopurine riboside, and their derivatives
57. Targeted base stacking disruption by the EcoRI DNA methyltransferase
58. Direct real time observation of base flipping by the EcoRI DNA methyltransferase
59. 2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases
60. Binding of EcoP15I DNA methyltransferase to DNA reveals a large structural distortion within the recognition sequence
61. 2-Aminopurine fluorescence studies of base stacking interactions at abasic sites in DNA: Metal-ion and base sequence effects
62. Molecular enzymology of the EcoRV DNA-(adenine-N6)-methyltransferase: Kinetics of DNA binding and bending, kinetic mechanism and linear diffusion of the enzyme on DNA
63. Substrate binding in vitro and kinetics of RsrI [N6-adenine] DNA methyltransferase
64. The crystal structure of HaeIII methyltransferase covalently complexed to DNA: An extrahelical cytosine and rearranged base pairing
65. Structure of the N6-adenine DNA methyltransferase M. TaqI in complex with a cofactor analog
66. A Taq attack displaces bases
67. Functional insights from the structure of the 30S ribosomal subunit and its interactions with antibiotics
68. Crystal structure of an initiation factor bound to the 30S ribosomal subunit
69. Mechanistic link between DNA methyltransferases and DNA repair enzymes by base flipping
70. Active and alkylated human AGT structures: A novel zinc site, inhibitor and extrahelical base binding
71. A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA
72. Kinetic mechanism of damage site recognition and uracil flipping by Escherichia coli uracil DNA glycosylase
73. Direct measurement of the substrate preference of uracil-DNA glycosylase
74. Structural basis for recognition and repair of the endogenous mutagen 8-oxoguanine in DNA
75. Novel DNA binding motifs in the DNA repair enzyme endonuclease III crystal structure
76. MutY catalytic core, mutant and bound adenine structures define specificity for DNA repair enzyme superfamily
77. Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8
78. Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: Structural basis for damaged DNA recognition
79. Structure of the DNA repair enzyme endonuclease IV and its DNA complex: Double-nucleotide flipping at abasic sites and three-metal-ion catalysis
80. DNA-bound structures and mutants reveal abasic DNA binding by APE1 DNA repair and coordination
81. Structure and function of the multifunctional DNA-repair enzyme exonuclease III
82. A specific endonuclease from Haemophilus haemolyticus
83. Dynamic modes of the flipped-out cytosine during HhaI methyltransferase-DNA interactions in solution
84. Chemical display of thymine residues flipped out by DNA methyltransferases
85. Active site dynamics of HhaI methyltransferase: Insights from computer simulation
86. Protein-modulated DNA electron transfer
87. Reconciling structure and function in HhaI DNA cytosine-C-5 methyltransferase
88. Functional analysis of Gln-237 mutants of HhaI methyltransferase
89. Functional roles of the conserved Threonine-250 in the target recognition domain of HhaI DNA methyltransferase
90. Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine
91. Structure of a binary complex of HhaI methyltransferase with S-adenosyl-L-methionine formed in the presence of a short non-specific DNA oligonucleotide
92. Enzymatic C5-cytosine methylation of DNA: Mechanistic implications of new crystal structures for HhaI methyltransferase-DNA-AdoHcy complexes
93. A structural basis for the preferential binding of hemimethylated DNA by HhaI DNA methyltransferase
94. DNA containing 4′-thio-2′-deoxycytidine inhibits methylation by HhaI methyltransferase
95. Mechanism of inhibition of DNA-(cytosine C5) methyltransferases by oligodeoxyribonucleotides containing 5, 6-dihydro-5-azacytosine
96. Three-dimensional structure of the adenine-specific DNA methyltransferase M. TaqI in complex with the cofactor S-adenosylmethionine
97. Inhibition of EcoRI DNA methylase with cofactor analogs
98. Sequence-specific DNA binding by the MspI DNA methyltransferase
99. Mutational separation of DNA binding from catalysis in a DNA cytosine methyltransferase
100. Recombinant human DNA (cytosine-5) methyltransferase. I. Expression, purification, and comparison of de novo and maintenance methylation
101. DNA methylation as a target for drug design
102. On the mechanism of inhibition of DNA-cytosine methyltransferases by cytosine analogs
103. 5-Fluorocytosine in DNA is a mechanism-based inhibitor of HhaI methylase
104. Covalent bond formation between a DNA-cytosine methyltransferase and DNA containing 5-azacytosine
105. 5C DNA methyl transferases use different cysteine residues as catalysts
106. Kinetic and catalytic mechanism of HhaI methyltransferase
107. Biological implications of the mechanism of action of human DNA (cytosine-5) methyltransferase
108. DNA distortion and base flipping by the EcoRV DNA methyltransferase
109. Lack of correlation between binding of EcoRII methylase to DNA duplexes containing mismatches and the promotion of C to T mutations
110. Interaction of the phage T4 Dam DNA-(N6-adenine) methyltransferase with oligonucleotides containing native or modified (defective) recognition sites
111. Interaction of the type I methyltransferase M. EcoR124I with modified DNA substrates: Sequence discrimination and base flipping
112. Kinetic mechanism of cytosine DNA methyltransferase MspI
113. Murine DNA (cytosine-5)-methyltransferase: Steady-state and substrate trapping analyses of the kinetic mechanism
114. Contribution of facilitated diffusion and processive catalysis to enzyme efficiency: Implications for the EcoRI restriction-modification system
115. A cell cycle-regulated adenine DNA methyltransferase from Caulobacter crescentus processively methylates GANTC sites on hemimethylated DNA
116. Cloning, over-expression and the catalytic properties of the EcoP15 modification methylase from Escherichia coli
117. Kinetic characterization of the EcaI methyltransferase
118. Differential binding of S-adenosylmethionine, S-adenosylhomocysteine and sinefungin to the adenine-specific DNA methyltransferase M. Taq1
119. Structure of human DNMT2, an enigmatic DNA methyltransferase homolog that displays denaturant-resistant binding to DNA
120. Crystal structure of the chemotaxis receptor methyltransferase CheR suggests a conserved structural motif for binding S-adenosylmethionine
121. Chemotaxis receptor recognition by methyltransferase CheR
122. The 1.85 Å structure of vaccinia protein VP39: A bifunctional enzyme that participates in the modification of both mRNA ends
123. Specific protein recognition of an mRNA cap through its alkylated base
124. Structural basis for sequence non-specific recognition of 5′-capped mRNA by a cap modifying enzyme
125. mRNA cap recognition: Dominant role of enhanced stacking interactions between methylated bases and protein aromatic side chains
126. Solution structure of an rRNA methyltransferase (ErmAM) that confers macrolide-lincosamide-streptogramin antibiotic resistance
127. Crystal structure of ErmC′, an rRNA methyltransferase which mediates antibiotic resistance in bacteria
128. The 2.2 Å structure of the rRNA methyltransferase ermC' and its complexes with cofactor and cofactor analogs: Implications for the reation mechanism
129. RNA methylation under heat shock control
130. Crystal structure of catechol O-methyltransferase
131. Crystal structure of glycine N-methyltransferase from rat liver
132. Mechanisms for auto-inhibition and forced product release in glycine N-methyltransferase: Crystal structures of wild-type, mutant R175K and S-adenosylhomocysteine-bound R175K enzymes
133. Structures of two natural product methyltransferases reveal the basis for substrate specificity in plant O-methyltransferases
134. Uracil-DNA glycosylase-DNA substrate and product structures: Conformational strain promotes catalytic efficiency by coupled stereoelectronic effects