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PMID: 8127644 Published · ppublish English Comparative Study Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S. Review

The DNA (cytosine-5) methyltransferases.

Nucleic acids research ·Vol. 22 ·No. 1 ·1994-01-11 ·Pages 1-10

Kumar S, Cheng X, Klimasauskas S, Mi S, Posfai J, Roberts RJ, Wilson GG

Abstract

The m5C-MTases form a closely-knit family of enzymes in which common amino acid sequence motifs almost certainly translate into common structural and functional elements. These common elements are located predominantly in a single structural domain that performs the chemistry of the reaction. Sequence-specific DNA recognition is accomplished by a separate domain that contains recognition elements not seen in other structures. This, combined with the novel and unexpected mechanistic feature of trapping a base out of the DNA helix, makes the m5C-MTases an intriguing class of enzymes for further study. The reaction pathway has suddenly become more complicated because of the base-flipping and much remains to be learned about the DNA recognition elements in the family members for which structural information is not yet available.

MeSH Terms
Amino Acid Sequence DNA-Cytosine Methylases/chemistry Models, Molecular Molecular Sequence Data Protein Structure, Tertiary S-Adenosylmethionine/metabolism Sequence Alignment Sequence Homology, Amino Acid Substrate Specificity
Chemicals
S-Adenosylmethionine DNA-Cytosine Methylases
Authors & Affiliations
7 authors, click to expand affiliations / ORCID
Kumar S
New England Biolabs, Beverly, MA 01915.
Cheng X
Klimasauskas S
Mi S
Posfai J
Roberts R J
Wilson G G
References (82)
82 references, click to expand
  1. Cloning and characterization of the genes encoding the MspI restriction modification system.
    Nucleic Acids Res. 1989 Apr 25;17(8):3001-11 PMID: 2471145
  2. Nucleotide sequence of the dcm locus of Escherichia coli K12.
    Nucleic Acids Res. 1989 Jul 25;17(14):5844 PMID: 2527357
  3. Sequence of the D-aspartyl/L-isoaspartyl protein methyltransferase from human erythrocytes. Common sequence motifs for protein, DNA, RNA, and small molecule S-adenosylmethionine-dependent methyltransferases.
    J Biol Chem. 1989 Nov 25;264(33):20131-9 PMID: 2684970
  4. Agmenellum quadruplicatum M.AquI, a novel modification methylase.
    J Bacteriol. 1990 Jan;172(1):266-72 PMID: 2104605
  5. Cloning and nucleotide sequences of the BanI restriction-modification genes in Bacillus aneurinolyticus.
    J Biochem. 1990 Apr;107(4):645-9 PMID: 2358438
  6. The HgaI restriction-modification system contains two cytosine methylase genes responsible for modification of different DNA strands.
    J Biol Chem. 1991 Jul 25;266(21):13952-7 PMID: 1856224
  7. Cloning and nucleotide sequence of the genes coding for the Sau96I restriction and modification enzymes.
    Nucleic Acids Res. 1990 Aug 25;18(16):4659-64 PMID: 2204026
  8. 5-Methylcytosine as an endogenous mutagen in the human LDL receptor and p53 genes.
    Science. 1990 Sep 14;249(4974):1288-90 PMID: 1697983
  9. Cloning, expression and characterization of the Sau3AI restriction and modification genes in Staphylococcus carnosus TM300.
    Gene. 1990 Sep 28;94(1):37-43 PMID: 2227451
  10. Cloning and characterization of two tandemly arranged DNA methyltransferase genes of Neisseria lactamica: an adenine-specific M.NlaIII and a cytosine-type methylase.
    Mol Gen Genet. 1990 Oct;224(1):101-10 PMID: 2277628
  11. Identification of a highly conserved domain in the EcoRII methyltransferase which can be photolabeled with S-adenosyl-L-[methyl-3H]methionine. Evidence for UV-induced transmethylation of cysteine 186.
    J Biol Chem. 1991 Feb 15;266(5):2937-45 PMID: 1993667
  12. Stepwise cloning and molecular characterization of the HgiDI restriction-modification system from Herpetosiphon giganteus Hpa2.
    Nucleic Acids Res. 1991 Mar 11;19(5):1049-56 PMID: 2020544
  13. Instability of a 550-base pair DNA segment and abnormal methylation in fragile X syndrome.
    Science. 1991 May 24;252(5009):1097-102 PMID: 2031184
  14. Organization of restriction-modification systems.
    Nucleic Acids Res. 1991 May 25;19(10):2539-66 PMID: 2041731
  15. M.H2I, a multispecific 5C-DNA methyltransferase encoded by Bacillus amyloliquefaciens phage H2.
    Gene. 1991 Apr;100:213-8 PMID: 2055471
  16. Isolation and genetic structure of the AvaII isoschizomeric restriction-modification system HgiBI from Herpetosiphon giganteus Hpg5: M.HgiBI reveals high homology to M.BanI.
    Nucleic Acids Res. 1991 Jun 25;19(12):3207-11 PMID: 2062638
  17. Cloning and molecular characterization of the HgiCI restriction/modification system from Herpetosiphon giganteus Hpg9 reveals high similarity to BanI.
    Eur J Biochem. 1991 Dec 18;202(3):1247-56 PMID: 1662609
  18. A gene required for very short patch repair in Escherichia coli is adjacent to the DNA cytosine methylase gene.
    J Bacteriol. 1990 Aug;172(8):4214-21 PMID: 2198248
  19. 'Pseudo' domains in phage-encoded DNA methyltransferases.
    Nature. 1991 Aug 15;352(6336):645-8 PMID: 1865925
  20. Complementation by detached parts of GGCC-specific DNA methyltransferases.
    Nucleic Acids Res. 1991 Sep 25;19(18):4843-7 PMID: 1923753
  21. Direct identification of the active-site nucleophile in a DNA (cytosine-5)-methyltransferase.
    Biochemistry. 1991 Nov 19;30(46):11018-25 PMID: 1932026
  22. Cloning, sequence and characterization of m5C-methyltransferase-encoding gene, hgiDIIM (GTCGAC), from Herpetosiphon giganteus strain Hpa2.
    Gene. 1991 Sep 30;106(1):87-92 PMID: 1937045
  23. A structural taxonomy of DNA-binding domains.
    Nature. 1991 Oct 24;353(6346):715-9 PMID: 1944532
  24. The sequence specificity domain of cytosine-C5 methylases.
    Nucleic Acids Res. 1991 Nov 25;19(22):6183-90 PMID: 1659688
  25. Substitutions of a cysteine conserved among DNA cytosine methylases result in a variety of phenotypes.
    Nucleic Acids Res. 1992 Jan 25;20(2):319-26 PMID: 1371346
  26. The mouse DNA methyltransferase 5'-region. A unique housekeeping gene promoter.
    J Biol Chem. 1992 Apr 15;267(11):7368-77 PMID: 1559980
  27. A single amino acid change restores DNA cytosine methyltransferase activity in a cloned chlorella virus pseudogene.
    Nucleic Acids Res. 1992 Apr 11;20(7):1637-42 PMID: 1579454
  28. Mechanisms and biological effects of mismatch repair.
    Annu Rev Genet. 1991;25:229-53 PMID: 1812808
  29. Restriction and modification systems.
    Annu Rev Genet. 1991;25:585-627 PMID: 1812816
  30. Isolation and characterization of the cDNA encoding human DNA methyltransferase.
    Nucleic Acids Res. 1992 May 11;20(9):2287-91 PMID: 1594447
  31. Mutation of asparagine 229 to aspartate in thymidylate synthase converts the enzyme to a deoxycytidylate methylase.
    Biochemistry. 1992 Jun 9;31(22):5100-4 PMID: 1606134
  32. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality.
    Cell. 1992 Jun 12;69(6):915-26 PMID: 1606615
  33. Construction of a Neisseria gonorrhoeae MS11 derivative deficient in NgoMI restriction and modification.
    J Bacteriol. 1992 Aug;174(15):4899-906 PMID: 1321116
  34. Stepwise cloning and genetic organization of the seemingly unclonable HgiCII restriction-modification system from Herpetosiphon giganteus strain Hpg9, using PCR technique.
    Gene. 1992 Aug 1;117(1):15-22 PMID: 1644308
  35. Sequence motifs characteristic of DNA[cytosine-N4]methyltransferases: similarity to adenine and cytosine-C5 DNA-methylases.
    Nucleic Acids Res. 1989 Dec 11;17(23):9823-32 PMID: 2690010
  36. DNA methylation: evolution of a bacterial immune function into a regulator of gene expression and genome structure in higher eukaryotes.
    Philos Trans R Soc Lond B Biol Sci. 1990 Jan 30;326(1235):179-87 PMID: 1968655
  37. Cloning, characterization, and expression in Escherichia coli of the gene coding for the CpG DNA methylase from Spiroplasma sp. strain MQ1(M.SssI).
    Nucleic Acids Res. 1990 Mar 11;18(5):1145-52 PMID: 2181400
  38. The amino acid sequence of the CCGG recognizing DNA methyltransferase M.BsuFI: implications for the analysis of sequence recognition by cytosine DNA methyltransferases.
    EMBO J. 1990 Apr;9(4):1007-13 PMID: 2108858
  39. Cloning and characterization of the HpaII methylase gene.
    Nucleic Acids Res. 1990 Mar 25;18(6):1377-83 PMID: 2183189
  40. Cloning and sequencing the cytosine methyltransferase gene M. CviJI from Chlorella virus IL-3A.
    Virology. 1990 May;176(1):16-24 PMID: 2158687
  41. Characterization of the archaeal, plasmid-encoded type II restriction-modification system MthTI from Methanobacterium thermoformicicum THF: homology to the bacterial NgoPII system from Neisseria gonorrhoeae.
    J Bacteriol. 1992 Sep;174(17):5719-26 PMID: 1512204
  42. Purification, crystallization, and preliminary X-ray diffraction analysis of an M.HhaI-AdoMet complex.
    Biochemistry. 1992 Sep 15;31(36):8648-53 PMID: 1390649
  43. How M.MspI and M.HpaII decide which base to methylate.
    Nucleic Acids Res. 1992 Sep 25;20(18):4811-6 PMID: 1408795
  44. Roles of Cys148 and Asp179 in catalysis by deoxycytidylate hydroxymethylase from bacteriophage T4 examined by site-directed mutagenesis.
    Biochemistry. 1992 Oct 27;31(42):10315-21 PMID: 1420151
  45. A targeting sequence directs DNA methyltransferase to sites of DNA replication in mammalian nuclei.
    Cell. 1992 Nov 27;71(5):865-73 PMID: 1423634
  46. High plasticity of multispecific DNA methyltransferases in the region carrying DNA target recognizing enzyme modules.
    EMBO J. 1992 Dec;11(12):4445-50 PMID: 1425579
  47. Methylation of DNA in prokaryotes.
    EXS. 1993;64:39-108 PMID: 8380352
  48. Analysis of the nucleotide and derived amino acid sequences of the SsoII restriction endonuclease and methyltransferase.
    Gene. 1993 Feb 14;124(1):13-9 PMID: 7916706
  49. The cysteine conserved among DNA cytosine methylases is required for methyl transfer, but not for specific DNA binding.
    Nucleic Acids Res. 1993 Jan 25;21(2):295-301 PMID: 8441637
  50. Sequence-specific and mechanism-based crosslinking of Dcm DNA cytosine-C5 methyltransferase of E. coli K-12 to synthetic oligonucleotides containing 5-fluoro-2'-deoxycytidine.
    Nucleic Acids Res. 1993 Jan 25;21(2):303-9 PMID: 8441638
  51. The M.AluI DNA-(cytosine C5)-methyltransferase has an unusually large, partially dispensable, variable region.
    Nucleic Acids Res. 1993 Feb 25;21(4):905-11 PMID: 8451189
  52. ScrFI restriction-modification system of Lactococcus lactis subsp. cremoris UC503: cloning and characterization of two ScrFI methylase genes.
    Appl Environ Microbiol. 1993 Mar;59(3):777-85 PMID: 8481004
  53. Isolation and identification by sequence homology of a putative cytosine methyltransferase from Arabidopsis thaliana.
    Nucleic Acids Res. 1993 May 25;21(10):2383-8 PMID: 8389441
  54. High frequency mutagenesis by a DNA methyltransferase.
    Cell. 1992 Dec 24;71(7):1073-80 PMID: 1473145
  55. The DNA binding affinity of HhaI methylase is increased by a single amino acid substitution in the catalytic center.
    Nucleic Acids Res. 1993 May 25;21(10):2459-64 PMID: 8506140
  56. Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine.
    Cell. 1993 Jul 30;74(2):299-307 PMID: 8343957
  57. Letter: A suggested nomenclature for bacterial host modification and restriction systems and their enzymes.
    J Mol Biol. 1973 Dec 15;81(3):419-23 PMID: 4588280
  58. Chemical and biological evolution of nucleotide-binding protein.
    Nature. 1974 Jul 19;250(463):194-9 PMID: 4368490
  59. A specific endonuclease from Haemophilus haemolyticus.
    J Mol Biol. 1976 May 5;103(1):199-208 PMID: 1085372
  60. Structure of the Bacillus sphaericus R modification methylase gene.
    J Mol Biol. 1983 Nov 5;170(3):597-610 PMID: 6313947
  61. Restriction and modification in Bacillus subtilis: nucleotide sequence, functional organization and product of the DNA methyltransferase gene of bacteriophage SPR.
    Gene. 1984 Jul-Aug;29(1-2):51-61 PMID: 6092231
  62. Structure of the gene coding for the sequence-specific DNA-methyltransferase of the B. subtilis phage SPR.
    Nucleic Acids Res. 1984 Dec 11;12(23):9039-49 PMID: 6096817
  63. Nucleotide sequence of the BsuRI restriction-modification system.
    Nucleic Acids Res. 1985 Sep 25;13(18):6403-21 PMID: 2997708
  64. Prediction of the occurrence of the ADP-binding beta alpha beta-fold in proteins, using an amino acid sequence fingerprint.
    J Mol Biol. 1986 Jan 5;187(1):101-7 PMID: 3959077
  65. DNA methyltransferase genes of Bacillus subtilis phages: comparison of their nucleotide sequences.
    Gene. 1986;42(1):89-96 PMID: 3087819
  66. Nucleotide sequence and expression of the gene encoding the EcoRII modification enzyme.
    Nucleic Acids Res. 1987 Jan 12;15(1):313-32 PMID: 3029675
  67. Cloning, sequencing, in vivo promoter mapping, and expression in Escherichia coli of the gene for the HhaI methyltransferase.
    J Biol Chem. 1987 Apr 5;262(10):4770-7 PMID: 3549710
  68. Kinetic and catalytic mechanism of HhaI methyltransferase.
    J Biol Chem. 1987 Apr 5;262(10):4778-86 PMID: 3558369
  69. Organization of multispecific DNA methyltransferases encoded by temperate Bacillus subtilis phages.
    EMBO J. 1987 Apr;6(4):1137-42 PMID: 3109889
  70. Nucleotide sequence of the DdeI restriction-modification system and characterization of the methylase protein.
    Nucleic Acids Res. 1987 Oct 26;15(20):8249-66 PMID: 2823226
  71. Construction and use of chimeric SPR/phi 3T DNA methyltransferases in the definition of sequence recognizing enzyme regions.
    EMBO J. 1987 Nov;6(11):3543-9 PMID: 2828032
  72. The CpG dinucleotide and human genetic disease.
    Hum Genet. 1988 Feb;78(2):151-5 PMID: 3338800
  73. Catalytic mechanism and inhibition of tRNA (uracil-5-)methyltransferase: evidence for covalent catalysis.
    Biochemistry. 1987 Dec 29;26(26):8599-606 PMID: 3327525
  74. Cloning and complete nucleotide sequences of the type II restriction-modification genes of Salmonella infantis.
    J Bacteriol. 1988 Jun;170(6):2527-32 PMID: 2836359
  75. Sequence analysis of the NgoPII methyltransferase gene from Neisseria gonorrhoeae P9: homologies with other enzymes recognizing the sequence 5'-GGCC-3'.
    Nucleic Acids Res. 1988 May 25;16(10):4369-87 PMID: 2837733
  76. Chimeric multispecific DNA methyltransferases with novel combinations of target recognition.
    Nucleic Acids Res. 1988 Jul 25;16(14A):6649-58 PMID: 3041380
  77. Sequential order of target-recognizing domains in multispecific DNA-methyltransferases.
    EMBO J. 1988 Aug;7(8):2601-9 PMID: 3142766
  78. Cloning and sequencing of a cDNA encoding DNA methyltransferase of mouse cells. The carboxyl-terminal domain of the mammalian enzymes is related to bacterial restriction methyltransferases.
    J Mol Biol. 1988 Oct 20;203(4):971-83 PMID: 3210246
  79. Cloning and structure of the BepI modification methylase.
    Nucleic Acids Res. 1989 Feb 11;17(3):1077-88 PMID: 2784204
  80. Cytosine-specific type II DNA methyltransferases. A conserved enzyme core with variable target-recognizing domains.
    J Mol Biol. 1989 Mar 20;206(2):305-12 PMID: 2716049
  81. Predictive motifs derived from cytosine methyltransferases.
    Nucleic Acids Res. 1989 Apr 11;17(7):2421-35 PMID: 2717398
  82. Cloning and analysis of the HaeIII and HaeII methyltransferase genes.
    Gene. 1988 Dec 25;74(1):45-50 PMID: 3248732
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/22.1.1
Published
1994-01-11
Pages
1-10
Language
English
Region
England
NLM ID
0411011
PMCID
PMC307737
Subset
IM
Grants
NIGMS NIH HHS · GM 15262 · United States
NIGMS NIH HHS · GM 49245 · United States
NIGMS NIH HHS · GM46127 · United States
External Links
PubMed source DOI: 10.1093/nar/22.1.1 PMC Full Text View journal details
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