Structure and function in the uracil-DNA glycosylase superfamily

Mutation Research - DNA Repair

Volumn 460, Issue 3-4, 2000, Pages 165-181

  Pearl, Laurence H ^a  

^a INSTITUTE OF CANCER RESEARCH   (United Kingdom)

Author keywords

SMUG; Transition mutations; Uracil DNA glycosylase

Indexed keywords

URACIL DNA GLYCOSYLTRANSFERASE;

CATALYSIS; DNA REPAIR; ENZYME ANALYSIS; ENZYME CONFORMATION; ENZYME STRUCTURE; ENZYME SUBSTRATE; GENE MUTATION; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN FAMILY; REVIEW;

EID: 0034734383     PISSN: 09218777     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0921-8777(00)00025-2     Document Type: Article

References (37)

1. Lindahl T. An N-glycosidase from Escherichia coli that releases free uracil from DNA containing deaminated cytosine residues. Proc. Natl. Acad. Sci. U. S. A. 71:1974;3649-3653.
2. Savva R., McAuley-Hecht K., Brown T., Pearl L.H. The structural basis of specific base-excision repair by uracil-DNA glycosylase. Nature. 373:1995;487-493.
3. Mol C.D., Arvai A.S., Slupphaug G., Kavli B., Alseth I., Krokan H.E., Tainer J.A. Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis. Cell. 80:1995;869-878.
4. Slupphaug G., Mol C.D., Kavli B., Arvai A.S., Krokan H.E., Tainer J.A. A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. Nature. 384:1996;87-91.
5. Parikh S.S., Mol C.D., Slupphaug G., Bharati S., Krokan H.E., Tainer J.A. Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA. EMBO J. 17:1998;5214-5226.
6. Xiao G.Y., Tordova M., Jagadeesh J., Drohat A.C., Stivers J.T., Gilliland G.L. Crystal structure of Escherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: structure and glycosylase mechanism revisited. Proteins: Struct. Funct. Genet. 35:1999;13-24.
7. Klimasauskas S., Kumar S., Roberts R.J., Cheng X.D. Hhal methyltransferase flips its target base out of the DNA helix. Cell. 76:1994;357-369.
8. Klimasauskas S., Szyperski T., Serva S., Wuthrich K. Dynamic modes of the flipped-out cytosine during HhaI methyltransferase-DNA interactions in solution. EMBO J. 17:1998;317-324.
9. Panayotou G., Brown T., Barlow T., Pearl L.H., Savva R. Direct measurement of the substrate preference of uracil-DNA glycosylase. J. Biol. Chem. 273:1998;45-50.
10. Von Hippel P.H., Berg O.G. Facilitated target location in biological systems. J. Biol. Chem. 264:1989;675-678.
11. Sirover M.A. New insights into an old protein: the functional diversity of mammalian glyceraldehyde-3-phosphate dehydrogenase. Biochim. Biophys. Acta, Protein Struct. Mol. Enzymol. 1432:1999;159-184.
12. Goodyear N., Murthy J.N., Soldin S.J. The 37 kDa immunophilin has uracil DNA glycosylase but not rotamase activity. Clin. Biochem. 30:1997;497-499.
13. Wang Z., Mosbaugh D.W. Uracil-DNA glycosylase inhibitor gene of bacteriophage PBS2 encodes a binding protein specific for uracil-DNA glycosylase. J. Biol. Chem. 264:1989;1163-1171.
14. Nedderman P., Jiricny J. The purification of a mismatch-specific thymine-DNA glycosylase from HeLa cells. J. Biol. Chem. 268:1993;21218-21224.
15. Nedderman P., Jiricny J. Efficient removal of uracil from G-U mispairs by the mismatch-specific thymine DNA glycosylase from HeLa-cells. Proc. Natl. Acad. Sci. U. S. A. 91:1994;1642-1646.
16. Gallinari P., Jiricny J. A new class of uracil-DNA glycosylases related to human thymine-DNA glycosylase. Nature. 383:1996;735-738.
17. Barrett T.E., Savva R., Panayotou G., Barlow T., Brown T., Jiricny J., Pearl L.H. Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions. Cell. 92:1998;117-129.
18. Dodson M.L., Michaels M.L., Lloyd R.S. Unified catalytic mechanism for DNA glycosylases. J. Biol. Chem. 269:1994;32709-32712.
19. Schärer O.D., Kawate T., Gallinari P., Jiricny J., Verdine G.L. Investigation of the mechanisms of DNA binding of the human G/T glycosylase using designed inhibitors. Proc. Natl. Acad. Sci. U. S. A. 94:1997;4878-4883.
20. Barrett T.E., Schärer O.D., Savva R., Brown T., Jiricny J., Verdine G.L., Pearl L.H. Crystal structure of a thwarted mismatch DNA glycosylase DNA repair complex. EMBO J. 18:1999;6599-6609.
21. 4-ethenocytosine, a highly mutagenic adduct, is a primary substrate for Escherichia coli double-stranded uracil-DNA glycosylase and human mismatch-specific thymine-DNA glycosylase. Proc. Natl. Acad. Sci. U. S. A. 95:1998;8508-8513.
22. 6-ethenoadenosine formation, mutagenicity and murine tumor-induction as indicators of the generation of an electrophilic epoxide metabolite of the closely related carcinogens ethyl carbamate (urethane) and vinyl carbamate. Carcinogenesis. 11:1990;463-473.
23. 32P postlabeling. Carcinogenesis. 16:1995;613-617.
24. Chung F.L., Chen H.J.C., Nath R.G. Lipid peroxidation as a potential endogenous source for the formation of exocyclic DNA adducts. Carcinogenesis. 17:1996;2105-2111.
25. 4-ethenocytosine and the G/T mismatch. Proc. Natl. Acad. Sci. U. S. A. 95:1998;13561-13566.
26. 4-ethenocytosine from DNA. J. Biol. Chem. 274:1999;31034-31038.
27. Hendrich B., Hardeland U., Ng H.-H., Jiricny J., Bird A. The thymine glycosylase MBD4 can bind to the product of deamination at methylated CpG sites. Nature. 401:1999;301-304.
28. Haushalter K.A., Stukenberg P.T., Kirschner M.W., Verdine G.L. Identification of a new uracil-DNA glycosylase family by expression cloning using synthetic inhibitors. Curr. Biol. 9:1999;174-185.
29. Drohat A.C., Xiao G.Y., Tordova M., Jagadeesh J., Pankiewicz K.W., Watanabe K.A., Gilliland G.L., Stivers J.T. Heteronuclear NMR and crystallographic studies of wild-type and H187Q Escherichia coli uracil DNA glycosylase: electrophilic catalysis of uracil expulsion by a neutral histidine 187. Biochemistry. 38:1999;11876-11886.
30. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search program. Nucleic Acids Res. 25:1997;3389-3402.
31. Kelley L.A., Maccallum R., Sternberg M.J.E. Recognition of remote protein homologies using three-dimensional information to generate a position specific scoring matrix in the program 3D-PSSM. Istrail S., Pevzner P., Waterman M. RECOMB 99, Proceedings of the Third Annual Conference on Computational Molecular Biology. 1999;218-225 The Association for Computing Machinery, New York.
32. Sandigursky M., Franklin W.A. Thermostable uracil-DNA glycosylase from Thermotoga maritima, a member of a novel class of DNA repair enzymes. Curr. Biol. 9:1999;531-534.
33. Koulis A., Cowan D.A., Pearl L.H., Savva R. Uracil-DNA glycosylase activities in hyperthermophilic micro-organisms. FEMS Microbiol. Lett. 143:1996;267-271.
34. Scarlato V., Gargano S. The DNA polymerase-encoding gene of Bacillus subtilis bacteriophage SPO1. Gene. 118:1992;109-113.
35. Greagg M.A., Fogg M.J., Panayotou G., Evans S.J., Connolly B.A., Pearl L.H. A read-ahead function in archaeal DNA polymerases detects pro-mutagenic template-strand uracil. Proc. Natl. Acad. Sci. U. S. A. 96:1999;9045-9050.
36. Hopfner K.-P., Eichinger A., Engh R.A., Laue F., Ankenbauer W., Huber R., Angerer B. Crystal structure of a thermostable type B DNA polymerase from Thermococcus gorgonarius. Proc. Natl. Acad. Sci. U. S. A. 96:1998;3600-3605.
37. Nash H., Bruner S.D., Schärer O.D., Kawate T., Addona T.A., Spooner E., Lane W.S., Verdine G.L. Cloning of a yeast 8-oxoguanine DNA glycosylase reveals the existence of a base-excision repair protein superfamily. Curr. Biol. 6:1996;968-980.