DNA mimicry by proteins and the control of enzymatic activity on DNA

Trends in Biotechnology

Volumn 24, Issue 8, 2006, Pages 378-382

  Dryden, David T F ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CELLS; ELECTROSTATICS; ENZYME INHIBITION; ENZYME KINETICS; PROTEINS;

CELL CYCLES; CONTROL PROTEINS; DNA-BINDING PROTEINS;

DNA;

DNA;

AFFINITY CHROMATOGRAPHY; BINDING SITE; DNA DETERMINATION; DNA SEQUENCE; ENZYME ACTIVITY; MOLECULAR MIMICRY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DNA INTERACTION; PROTEIN EXPRESSION; PROTEIN STRUCTURE; REVIEW;

DNA; DNA RESTRICTION ENZYMES; DNA-BINDING PROTEINS; ENZYME ACTIVATION; MOLECULAR MIMICRY;

EID: 33745930556     PISSN: 01677799     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.tibtech.2006.06.004     Document Type: Review

References (50)

1. Muller-Hill B. The lac operon: a short history of a genetic paradigm (1996), Walter de Gruyter
2. Ptashne M. A Genetic Switch: Phage Lambda Revisited. 3rd edition (2004), Cold Spring Harbor Laboratory Press
3. Klose R.J., and Bird A.P. Genomic DNA methylation: the mark and its mediators. Trends Biochem. Sci. 31 (2006) 89-97
4. Hughes K.T., and Mathee K. The anti-sigma factors. Annu. Rev. Microbiol. 52 (1998) 231-286
5. Campbell E.A., et al. Crystal structure of Escherichia coli sigmaE with the cytoplasmic domain of its anti-sigma RseA. Mol. Cell 11 (2003) 1067-1078
6. Mol C.D., et al. Crystal structure of human uracil-DNA glycosylase in complex with a protein inhibitor: protein mimicry of DNA. Cell 82 (1995) 701-708
7. Savva R., and Pearl L.H. Nucleotide mimicry in the crystal structure of the uracil-DNA glycosylase-uracil glycosylase inhibitor protein complex. Nat. Struct. Biol. 2 (1995) 752-757
8. Sanderson R.J., and Mosbaugh D.W. Identification of specific carboxyl groups on uracil-DNA glycosylase inhibitor protein that are required for activity. J. Biol. Chem. 271 (1996) 29170-29181
9. Putnam C.D., et al. Protein mimicry of DNA from crystal structures of the uracil-DNA glycosylase inhibitor protein and its complex with Escherichia coli uracil-DNA glycosylase. J. Mol. Biol. 287 (1999) 331-346
10. Atanasiu C., et al. Interaction of the ocr gene 0.3 protein of bacteriophage T7 with EcoKI restriction/modification enzyme. Nucleic Acids Res. 30 (2002) 3936-3944
11. Walkinshaw M.D., et al. Structure of Ocr from bacteriophage T7, a protein that mimics B-form DNA. Mol. Cell 9 (2002) 187-194
12. Su T.-J., et al. DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping. Nucleic Acids Res. 33 (2005) 3235-3244
13. Belogurov A.A., and Delver E.P. A motif conserved among the type I restriction-modification enzymes and antirestriction proteins: a possible basis for mechanism of action of plasmid-encoded antirestriction functions. Nucleic Acids Res. 23 (1995) 785-787
14. Zavil'gel'skii G.B. Antirestriction. Mol. Biol. (Mosk). 34 (2000) 854-862
15. Wilkins B.M. Plasmid promiscuity: meeting the challenge of DNA immigration control. Environ. Microbiol. 4 (2002) 495-500
16. Parsons L.M., et al. Solution structure of the highly acidic protein HI1450 from Haemophilus influenzae, a putative double-stranded DNA mimic. Proteins 54 (2004) 375-383
17. Parsons L.M., et al. HU-alpha binds to the putative double-stranded DNA mimic HI1450 from Haemophilus influenzae. Protein Sci. 14 (2005) 1684-1687
18. Hegde S.S., et al. A fluoroquinolone resistance protein from Mycobacterium tuberculosis that mimics DNA. Science 308 (2005) 1480-1483
19. Liu D., et al. Solution structure of a TBP-TAF(II)230 complex: protein mimicry of the minor groove surface of the TATA box unwound by TBP. Cell 94 (1998) 573-583
20. Ratner D. The interaction of bacterial and phage proteins with immobilized Escherichia coli RNA polymerase. J. Mol. Biol. 88 (1974) 373-383
21. Ramirez B.E., et al. Solution structure of DinI provides insight into its mode of RecA inactivation. Protein Sci. 9 (2000) 2161-2169
22. Voloshin O.N., et al. A model for the abrogation of the SOS response by an SOS protein: a negatively charged helix in DinI mimics DNA in its interaction with RecA. Genes Dev. 15 (2001) 415-427
23. Yoshimasu M., et al. An NMR study on the interaction of Escherichia coli DinI with RecA-ssDNA complexes. Nucleic Acids Res. 31 (2003) 1735-1743
24. Lusetti S.L., et al. The DinI protein stabilizes RecA protein filaments. J. Biol. Chem. 279 (2004) 30037-30046
25. Bochkareva E., et al. Single-stranded DNA mimicry in the p53 transactivation domain interaction with replication protein A. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 15412-15417
26. Goodsell D.S. Recognition in action: DNA mimicry. J. Mol. Recognit. 18 (2005) 427-430
27. Putnam C.D., and Tainer J.A. Protein mimicry of DNA and pathway regulation. DNA Repair 4 (2005) 1410-1420
28. Tock M.R., and Dryden D.T.F. The biology of restriction and anti-restriction. Curr. Opin. Microbiol. 8 (2005) 466-472
29. Dryden D.T.F., and Tock M.R. DNA mimicry by proteins. Biochem. Soc. Trans. 34 (2006) 317-319
30. Vetting M.W., et al. Pentapeptide repeat proteins. Biochemistry 45 (2006) 1-10
31. Susskind M.M., and Botstein D. Molecular genetics of bacteriophage P22. Microbiol. Rev. 42 (1978) 385-413
32. Prell H.H., and Harvey A.M. P22 antirepressor protein prevents in vivo recA-dependent proteolysis of P22 repressor. Mol. Gen. Genet. 190 (1983) 427-431
33. Heinzel T., et al. C1 repressor of phage P1 is inactivated by noncovalent binding of P1 Coi protein. J. Biol. Chem. 267 (1992) 4183-4188
34. Velleman M., et al. The Bof protein of bacteriophage P1 exerts its modulating function by formation of a ternary complex with operator DNA and C1 repressor. J. Biol. Chem. 267 (1992) 12174-12181
35. Riedel H.D., et al. The antirepressor of phage P1. Isolation and interaction with the C1 repressor of P1 and P7. FEBS Lett. 334 (1993) 165-169
36. Liu T., et al. The E protein of satellite phage P4 acts as an anti-repressor by binding to the C protein of helper phage P2. Mol. Microbiol. 30 (1998) 1041-1050
37. Shearwin K.E., et al. The Tum protein of coliphage 186 is an antirepressor. J. Biol. Chem. 273 (1998) 5708-5715
38. Liu T., and Haggard-Ljungquist E. The transcriptional switch of bacteriophage Wφ{symbol}, a P2-related but heteroimmune coliphage. J. Virol. 73 (1999) 9816-9826
39. Ravin N.V., et al. The anti-immunity system of phage-plasmid N15: identification of the antirepressor gene and its control by a small processed RNA. Mol. Microbiol. 34 (1999) 980-994
40. Eriksson S.K., et al. Interacting interfaces of the P4 antirepressor E and the P2 immunity repressor C. Mol. Microbiol. 36 (2000) 1148-1155
41. Calisto B.M., et al. Crystal structure of a putative type I restriction-modification S subunit from Mycoplasma genitalium. J. Mol. Biol. 351 (2005) 749-762
42. Kim J.S., et al. Crystal structure of DNA sequence specificity subunit of a type I restriction-modification enzyme and its functional implications. Proc. Natl. Acad. Sci. U. S. A. 102 (2005) 3248-3253
43. Cerdeno-Tarraga A.M., et al. Extensive DNA inversions in the B. fragilis genome control variable gene expression. Science 307 (2005) 1463-1465
44. Tran J.H., and Jacoby G.A. Mechanism of plasmid-mediated quinolone resistance. Proc. Natl. Acad. Sci. U. S. A. 99 (2002) 5638-5642
45. Li X.Z. Quinolone resistance in bacteria: emphasis on plasmid-mediated mechanisms. Int. J. Antimicrob. Agents 25 (2005) 453-463
46. Dunn J.J., et al. Amino acid sequence of the gene 0.3 protein of bacteriophage T7 and nucleotide sequence of its mRNA. J. Biol. Chem. 256 (1981) 2579-2585
47. Mark K.K., and Studier F.W. Purification of the gene 0.3 protein of bacteriophage T7, an inhibitor of the DNA restriction system of Escherichia coli. J. Biol. Chem. 256 (1981) 2573-2578
48. Murray N.E. Type I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle). Microbiol. Mol. Biol. Rev. 64 (2000) 412-434
49. Loenen W.A. Tracking EcoKI and DNA fifty years on: a golden story full of surprises. Nucleic Acids Res. 31 (2003) 7059-7069
50. Roberts R.J., et al. REBASE-restriction enzymes and DNA methyltransferases. Nucleic Acids Res. 33 (2005) D230-D232