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PMID: 9254696 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

A prediction of the amino acids and structures involved in DNA recognition by type I DNA restriction and modification enzymes.

Nucleic acids research ·Vol. 25 ·No. 17 ·1997-09-01 ·Pages 3408-14

Sturrock SS, Dryden DT

Abstract

The S subunits of type I DNA restriction/modification enzymes are responsible for recognising the DNA target sequence for the enzyme. They contain two domains of approximately 150 amino acids, each of which is responsible for recognising one half of the bipartite asymmetric target. In the absence of any known tertiary structure for type I enzymes or recognisable DNA recognition motifs in the highly variable amino acid sequences of the S subunits, it has previously not been possible to predict which amino acids are responsible for sequence recognition. Using a combination of sequence alignment and secondary structure prediction methods to analyse the sequences of S subunits, we predict that all of the 51 known target recognition domains (TRDs) have the same tertiary structure. Furthermore, this structure is similar to the structure of the TRD of the C5-cytosine methyltransferase, Hha I, which recognises its DNA target via interactions with two short polypeptide loops and a beta strand. Our results predict the location of these sequence recognition structures within the TRDs of all type I S subunits.

MeSH Terms
Amino Acid Sequence Binding Sites Crystallization DNA/chemistry,metabolism DNA Methylation Deoxyribonucleases, Type I Site-Specific/chemistry,metabolism Deoxyribonucleases, Type II Site-Specific/chemistry,metabolism Models, Molecular Molecular Sequence Data Protein Structure, Secondary Sequence Alignment Structure-Activity Relationship Substrate Specificity
Chemicals
DNA Deoxyribonucleases, Type I Site-Specific Deoxyribonucleases, Type II Site-Specific GCGC-specific type II deoxyribonucleases
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Sturrock S S
Institute of Cell and Molecular Biology, The King's Buildings, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JR, UK.
Dryden D T
References (66)
66 references, click to expand
  1. Basis for changes in DNA recognition by the EcoR124 and EcoR124/3 type I DNA restriction and modification enzymes.
    J Mol Biol. 1989 Jan 5;205(1):115-25 PMID: 2784505
  2. Conservation of organization in the specificity polypeptides of two families of type I restriction enzymes.
    J Mol Biol. 1989 Oct 5;209(3):335-44 PMID: 2585490
  3. The X-ray structure of the DNA-binding domain from the Saccharomyces cerevisiae cell-cycle transcription factor Mbp1 at 2.1 A resolution.
    J Mol Biol. 1997 Sep 12;272(1):1-8 PMID: 9299332
  4. A third family of allelic hsd genes in Salmonella enterica: sequence comparisons with related proteins identify conserved regions implicated in restriction of DNA.
    Mol Microbiol. 1996 Nov;22(3):437-47 PMID: 8939428
  5. Agmenellum quadruplicatum M.AquI, a novel modification methylase.
    J Bacteriol. 1990 Jan;172(1):266-72 PMID: 2104605
  6. Recognition of unusual DNA structures by human DNA (cytosine-5)methyltransferase.
    J Mol Biol. 1991 Jan 5;217(1):39-51 PMID: 1988679
  7. A structural taxonomy of DNA-binding domains.
    Nature. 1991 Oct 24;353(6346):715-9 PMID: 1944532
  8. Recombination of constant and variable modules alters DNA sequence recognition by type IC restriction-modification enzymes.
    EMBO J. 1992 Jan;11(1):233-40 PMID: 1740108
  9. Restriction and modification systems.
    Annu Rev Genet. 1991;25:585-627 PMID: 1812816
  10. Roles of selection and recombination in the evolution of type I restriction-modification systems in enterobacteria.
    Proc Natl Acad Sci U S A. 1992 Oct 15;89(20):9836-40 PMID: 1409708
  11. How clonal are bacteria?
    Proc Natl Acad Sci U S A. 1993 May 15;90(10):4384-8 PMID: 8506277
  12. Biology of DNA restriction.
    Microbiol Rev. 1993 Jun;57(2):434-50 PMID: 8336674
  13. Crystal structure of the HhaI DNA methyltransferase complexed with S-adenosyl-L-methionine.
    Cell. 1993 Jul 30;74(2):299-307 PMID: 8343957
  14. Prediction of protein secondary structure at better than 70% accuracy.
    J Mol Biol. 1993 Jul 20;232(2):584-99 PMID: 8345525
  15. Conservation of motifs within the unusually variable polypeptide sequences of type I restriction and modification enzymes.
    Mol Microbiol. 1993 Jul;9(1):133-43 PMID: 8412658
  16. Macroevolution by transposition: drastic modification of DNA recognition by a type I restriction enzyme following Tn5 transposition.
    EMBO J. 1993 Dec;12(12):4585-91 PMID: 8223468
  17. A deletion mutant of the type IC restriction endonuclease EcoR1241 expressing a novel DNA specificity.
    Nucleic Acids Res. 1993 Sep 25;21(19):4435-43 PMID: 8233776
  18. HhaI methyltransferase flips its target base out of the DNA helix.
    Cell. 1994 Jan 28;76(2):357-69 PMID: 8293469
  19. The domains of a type I DNA methyltransferase. Interactions and role in recognition of DNA methylation.
    J Mol Biol. 1994 Mar 4;236(4):1011-21 PMID: 8120883
  20. The Escherichia coli prr region encodes a functional type IC DNA restriction system closely integrated with an anticodon nuclease gene.
    J Mol Biol. 1994 Apr 1;237(3):266-74 PMID: 8145241
  21. PHD--an automatic mail server for protein secondary structure prediction.
    Comput Appl Biosci. 1994 Feb;10(1):53-60 PMID: 8193956
  22. A symmetrical model for the domain structure of type I DNA methyltransferases.
    J Mol Biol. 1994 Oct 14;243(1):1-5 PMID: 7932730
  23. Regulation of a restriction and modification system via DNA inversion in Mycoplasma pulmonis.
    Mol Microbiol. 1994 May;12(4):547-60 PMID: 7934878
  24. 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. 1994 Nov 8;91(23):10957-61 PMID: 7971991
  25. A bacterial methyltransferase M.EcoHK311 requires two proteins for in vitro methylation.
    Nucleic Acids Res. 1995 Jan 11;23(1):103-8 PMID: 7870574
  26. Restriction enzymes in cells, not eppendorfs.
    Trends Microbiol. 1994 Dec;2(12):465-9 PMID: 7889321
  27. Tyrosine 27 of the specificity polypeptide of EcoKI can be UV crosslinked to a bromodeoxyuridine-substituted DNA target sequence.
    Nucleic Acids Res. 1995 Apr 11;23(7):1177-83 PMID: 7739896
  28. HhaI and HpaII DNA methyltransferases bind DNA mismatches, methylate uracil and block DNA repair.
    Nucleic Acids Res. 1995 Apr 25;23(8):1380-7 PMID: 7753629
  29. M.HhaI binds tightly to substrates containing mismatches at the target base.
    Nucleic Acids Res. 1995 Apr 25;23(8):1388-95 PMID: 7753630
  30. The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing.
    Cell. 1995 Jul 14;82(1):143-53 PMID: 7606780
  31. On base flipping.
    Cell. 1995 Jul 14;82(1):9-12 PMID: 7606789
  32. A model for DNA binding and enzyme action derived from crystallographic studies of the TaqI N6-adenine-methyltransferase.
    Gene. 1995 May 19;157(1-2):131-4 PMID: 7607476
  33. BsuCI, a type-I restriction-modification system in Bacillus subtilis.
    Gene. 1995 May 19;157(1-2):59 PMID: 7607526
  34. Probing the domain structure of the type IC DNA methyltransferase M.EcoR124I by limited proteolysis.
    J Mol Biol. 1995 Jul 7;250(2):181-90 PMID: 7608969
  35. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
    Science. 1995 Jul 28;269(5223):496-512 PMID: 7542800
  36. Structural modelling of a type I DNA methyltransferase.
    Nat Struct Biol. 1995 Aug;2(8):632-5 PMID: 7552723
  37. Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes.
    J Mol Biol. 1995 Nov 3;253(4):618-32 PMID: 7473738
  38. The diversity of alleles at the hsd locus in natural populations of Escherichia coli.
    Genetics. 1995 Aug;140(4):1187-97 PMID: 7498762
  39. Surface labelling of the type I methyltransferase M.EcoR124I reveals lysine residues critical for DNA binding.
    J Mol Biol. 1996 Apr 26;258(1):62-73 PMID: 8613993
  40. Identification of a subdomain within DNA-(cytosine-C5)-methyltransferases responsible for the recognition of the 5' part of their DNA target.
    EMBO J. 1996 Mar 15;15(6):1443-50 PMID: 8635477
  41. Nucleotide sequence of the recognition site for the restriction-modification enzyme of Escherichia coli B.
    Proc Natl Acad Sci U S A. 1978 May;75(5):2266-70 PMID: 353810
  42. Recognition site of Escherichia coli B restriction enzyme on phi XsB1 and simian virus 40 DNAs: an interrupted sequence.
    Proc Natl Acad Sci U S A. 1978 May;75(5):2271-5 PMID: 209460
  43. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii.
    Science. 1996 Aug 23;273(5278):1058-73 PMID: 8688087
  44. Finding a basis for flipping bases.
    Structure. 1996 Jun 15;4(6):639-45 PMID: 8805547
  45. Generation of new DNA binding specificity by truncation of the type IC EcoDXXI hsdS gene.
    EMBO J. 1996 Sep 2;15(17):4775-83 PMID: 8887569
  46. Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems.
    J Mol Evol. 1996 Feb;42(2):91-6 PMID: 8919860
  47. The restriction-modification system of Pasteurella haemolytica is a member of a new family of type I enzymes.
    Gene. 1996 Oct 31;178(1-2):89-96 PMID: 8921897
  48. Physical basis of a protein-DNA recognition code.
    Curr Opin Struct Biol. 1997 Feb;7(1):117-25 PMID: 9032060
  49. The type IC hsd loci of the enterobacteria are flanked by DNA with high homology to the phage P1 genome: implications for the evolution and spread of DNA restriction systems.
    Mol Microbiol. 1997 Feb;23(4):729-36 PMID: 9157244
  50. The specificity of sty SKI, a type I restriction enzyme, implies a structure with rotational symmetry.
    Nucleic Acids Res. 1997 May 1;25(9):1694-700 PMID: 9108149
  51. Nucleotide sequence of the recognition site of the B-specific restriction modification system in E. coli.
    Mol Gen Genet. 1979 Jan 11;168(3):331-35 PMID: 374993
  52. The nucleotide sequence recognized by the Escherichia coli K12 restriction and modification enzymes.
    J Mol Biol. 1979 May 15;130(2):191-209 PMID: 381674
  53. Identification of common molecular subsequences.
    J Mol Biol. 1981 Mar 25;147(1):195-7 PMID: 7265238
  54. Sequence diversity among related genes for recognition of specific targets in DNA molecules.
    J Mol Biol. 1983 May 5;166(1):1-19 PMID: 6304321
  55. The nucleotide recognized by the Escherichia coli A restriction and modification enzyme.
    Nucleic Acids Res. 1984 Jan 25;12(2):887-99 PMID: 6320124
  56. The EcoA restriction and modification system of Escherichia coli 15T-: enzyme structure and DNA recognition sequence.
    EMBO J. 1984 Mar;3(3):575-9 PMID: 6325176
  57. Genetic recombination can generate altered restriction specificity.
    Proc Natl Acad Sci U S A. 1984 Oct;81(19):6095-9 PMID: 6091134
  58. The nucleotide sequence recognised by the Escherichia coli D type I restriction and modification enzyme.
    Nucleic Acids Res. 1985 Jan 25;13(2):389-99 PMID: 2987794
  59. Evidence for a repeating domain in type I restriction enzymes.
    EMBO J. 1985 May;4(5):1351-5 PMID: 2988943
  60. Two type I restriction enzymes from Salmonella species. Purification and DNA recognition sequences.
    J Mol Biol. 1985 Apr 20;182(4):579-87 PMID: 2989535
  61. Two DNA recognition domains of the specificity polypeptides of a family of type I restriction enzymes.
    Proc Natl Acad Sci U S A. 1986 Dec;83(24):9368-72 PMID: 3025838
  62. DNA recognition by a new family of type I restriction enzymes: a unique relationship between two different DNA specificities.
    EMBO J. 1987 May;6(5):1493-7 PMID: 3038525
  63. Reassortment of DNA recognition domains and the evolution of new specificities.
    Mol Microbiol. 1987 Jul;1(1):13-22 PMID: 2838725
  64. Sequential order of target-recognizing domains in multispecific DNA-methyltransferases.
    EMBO J. 1988 Aug;7(8):2601-9 PMID: 3142766
  65. Conservation of complex DNA recognition domains between families of restriction enzymes.
    Cell. 1989 Jan 13;56(1):103-9 PMID: 2642743
  66. Frequency-dependent selection in bacterial populations.
    Philos Trans R Soc Lond B Biol Sci. 1988 Jul 6;319(1196):459-72 PMID: 2905487
Article Info
Journal
Nucleic acids research
Abbr.
Nucleic Acids Res
ISSN
0305-1048
DOI
10.1093/nar/25.17.3408
Published
1997-09-01
Pages
3408-14
Language
English
Region
England
NLM ID
0411011
PMCID
PMC146914
Subset
IM
External Links
PubMed source DOI: 10.1093/nar/25.17.3408 PMC Full Text View journal details
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