Protein-mediated base flipping

Current Opinion in Biotechnology

Volumn 9, Issue 4, 1998, Pages 354-358

  Hornby, David P ^a   Ford, Geoffrey C ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOSINE; DNA METHYLTRANSFERASE;

CATALYSIS; CHEMICAL MODIFICATION; CRYSTALLOGRAPHY; DNA CONFORMATION; DNA PROTEIN COMPLEX; MOLECULAR INTERACTION; MOLECULAR STABILITY; NUCLEIC ACID BASE SUBSTITUTION; PRIORITY JOURNAL; REVIEW;

EID: 0032146154     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0958-1669(98)80007-4     Document Type: Article

References (37)

1. Harnson SC, Aggarwal AK. DNA recognition by proteins with the helix-turn-helix motif. Ann Rev Biochem. 59:1990;933-969.
2. Rafferty JB, Sedelnikova SE, Hargreaves D, Artymiuk PJ, Baker PJ, Sharples GJ, Mahdi AA, Lloyd RG, Rice DW. Crystal structure of DNA recombination protein RuvA and a model for its binding to the Holliday junction. Science. 274:1996;415-421.
3. Cheng X, Kumar S, Klimasauskas S, Roberts RJ. Crystal structure of the Hhal DNA methyltransferase. Cell. 82:1995;9-12.
4. Klimasauskas S, Kumar S, Roberts RJ, Cheng X. Hhal methyltransferase flips its target base out of the DNA helix. Cell. 76:1994;357-369.
5. Roberts RJ. On base flipping. Cell. 82:1995;9-12.
6. Winkler FK. DNA totally flipped-out by methylase. Structure. 2:1994;79-83.
7. Vordine GL. The flip side of DNA methylation. Cell. 76:1994;197-200.
8. Cheng X. DNA modification by methyltransferase. Curr Opin Struct Biol. 5:1995;4-10.
9. Nelson HC, Bestor T. Base eversion and shuffling by DNA methyltransferase. Chem Biol. 3:1996;419-423.
10. Gong W, O'Gara M, Blumenthal RM, Cheng X. Structure of pvu II DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Res. 25:1997;2702-2715.
11. Renisch KM, Chen L, Verdine GL, Lipscomb WN. The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing. Cell. 82:1995;143-153.
12. Savva R, McAuley-Hecht K, Brown T, Pearl L. The structural basis of specific base-excision repair uracil-DNA glycosylase. Nature. 373:1995;487-493.
13. Slupphaug G, Mol CD, Kavli B, Arvai AS, Krokan HE, Tainer JA. A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature. 384:1996;87-92.
14. Barrett TE, Savva R, Panayotou G, Barlow T, Brown T, Jiricny J, Pearl LH. Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions. Cell. 92:1998;117-129.
15. Vassylyev DG, Kashiwagi T, Mikami Y, Ariyoshi M, Iwai S, Ohtsuka E, Morikawa K. Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition. Cell. 83:1995;773-782.
16. Trautner TA, Pawlek B, Behrens B, Willert J. Exact size and organization of DNA target-recognizing domains of multispecific DNA-(cytosine-C5)-methyltransferase. EMBO J. 15:1996;1434-1442.
17. Smith SS, Hardy TA, Baker DJ. Human DNA (cytosine-5)methyltransferase selectively methylates duplex DNA containing mispairs. Nucleic Acids Res. 15:1987;6899-6916.
18. Klimasauskas S, Roberts RJ. M.HhaI binds tightly to substrates containing mismatches at the target base. Nucleic Acids Res. 23:1995;1388-1395.
19. Allan BW, Beechem JM, Lindstrom WM, Reich NO. Direct real time observation of base flipping by the EcoRI DNA methyltransferase. J Biol Chem. 273:1998;2368-2373.
20. Allan BW, Reich NO. Targeted base stacking disruption by the EcoRI DNA methyltransferase. Biochemistry. 35:1996;14757-14762.
21. McCullough AK, Dodson ML, Scharer OD, Lloyd RS. The role of base flipping in damage recognition and catalysis by T4 endonuclease V. J Biol Chem. 272:1997;27210-27217.
22. Holz B, Klimasauskas S, Serva S, Weinhold E. 2-aminopurine as a fluorescent probe for DNA base flipping by methyltransferase. Nucleic Acids Res. 26:1998;1076-1083.
23. Jeltsch A, Friedrich T, Roth M. Kinetics of methylation and binding of DNA by the EcoRV adenine-N6 methyltransferase. J Mol Biol. 275:1998;747-758.
24. Cal S, Connolly BA. 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. 272:1997;490-496.
25. Klimasauskas S, Szyperski T, Serva S, Wüthrich K. Dynamic modes of the flipped-out cytosine during HhaI methyltransferase - DNA interactions in solution. EMBO J. 17:1998;317-324.
26. Baldwin GS, Kelly SM, Price NC, Wilson GW, Connolly BA, Artymiuk PJ, Hornby DP. Ligand-induced conformational states of the cytosine-specific DNA methyltransferase M.HgaI-2. J Mol Biol. 235:1994;545-553.
27. Hornby DP, Whitmarsh A, Pinarbasi H, Kelly SM, Price NC, Shore P, Baldwin GS, Waltho J. The DNA recognition subunit of a DNA methyltransferase is predominantly a molten globule in the absence of DNA. FEBS Lett. 355:1994;57-60.
28. Burley SK. The TATA box binding protein. Curr Opin Struct Biol. 6:1996;69-75.
29. Zhang Y, Nelson M, Van Etten JL. A single amino acid change restores DNA cytosine methyltransferase activity in a cloned chlorella virus pseudogene. Nucleic Acids Res. 20:1992;1637-1642.
30. Wilkinson CR, Bartlett R, Nurse P, Bird AP. The fission yeast gene pmt1+ encodes a DNA methyltransferase homologue. Nucleic Acid Res. 23:1995;203-210.
31. Pinarbasi E, Elliott J, Hornby DP. Activation of a yeast pseudo DNA methyltransferase by deletion of a single amino acid. J Mol Biol. 257:1996;804-813.
32. Malagnac F, Wendel B, Goyon C, Faugeron G, Zickler D, Rossignol JL, Noyer-Weidner M, Vollmayr P, Trautner TA, Walter J. A gene essential for de novo methylation and development in Ascobolus reveals a novel type of eukaryotic DNA methyltransferase structure. Cell. 91:1997;281-290.
33. Yoder JA, Bestor TH. A candidate mammalian DNA methyltransferase related to pmt1 p of fission yeast. Hum Mol Genet. 7:1998;279-284.
34. Ferrin TE, Huang CC, Jarvis LE, Langridge R. The MIDAS display system. J Mol Graphics. 6:1988;13-27.
35. Huang CC, Petterson EF, Klein TE, Ferrin TE, Langridge R. Conic: a fast renderer for space-filling molecules with shadows. J Mol Graphics. 9:1991;230-236.
36. Abola EE, Bernstein FC, Bryant SH, Koetzle TF, Weng J. Protein Data Bank. Allen FH, Bergerhoff G, Sievers R. Crystallographic Databases-Information Content, Software Systems, Scientific Applications. 1987;107-132 Commission of the International Union of Crystallography, Data Bonn/Cambridge/Chester.
37. Bernstein FC, Koetzle TF, Williams GJ, Meyer BEF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol. 112:1977;535-542.