Replication of a cis-syn thymine dimer at atomic resolution

Nature

Volumn 424, Issue 6952, 2003, Pages 1083-1087

  Ling, Hong ^a   Boudsocq, François ^b,c   Plosky, Brian S ^b   Woodgate, Roger ^b   Yang, Wei ^a  

^a NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^b EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT   (United States)

^c CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYSIS; CHEMICAL BONDS; CRYSTAL STRUCTURE; DNA; SKIN; TUMORS; ULTRAVIOLET RADIATION;

SKIN CANCER;

DIMERS;

ADENOSINE TRIPHOSPHATE DERIVATIVE; CYCLOBUTANE DERIVATIVE; CYCLOBUTANE PYRIMIDINE DIMER; DIMER; DNA POLYMERASE; DOUBLE STRANDED DNA; PHOSPHORUS 32; PYRIMIDINE DERIVATIVE; THYMINE; UNCLASSIFIED DRUG;

BIOLOGY; DNA;

ARTICLE; CANCER SUSCEPTIBILITY; CRYSTAL STRUCTURE; DNA REPAIR; DNA REPLICATION; ENZYME STRUCTURE; GENE MUTATION; GENETIC PREDISPOSITION; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN STRUCTURE; SACCHAROMYCES CEREVISIAE; SKIN CANCER; ULTRAVIOLET IRRADIATION; XERODERMA PIGMENTOSUM; YEAST;

AMINO ACID SEQUENCE; ARCHAEAL PROTEINS; BASE PAIRING; BASE SEQUENCE; BINDING SITES; CRYSTALLIZATION; DNA DAMAGE; DNA REPLICATION; DNA-DIRECTED DNA POLYMERASE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PYRIMIDINE DIMERS; SACCHAROMYCES CEREVISIAE; SOLUTIONS; STRUCTURE-ACTIVITY RELATIONSHIP; SULFOLOBUS; TEMPLATES, GENETIC;

ARCHAEA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE;

EID: 0041864009     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/nature01919     Document Type: Article

References (30)

1. Ravanat, J. L., Douki, T. & Cadet, J. Direct and indirect effects of UV radiation on DNA and its components. J. Photochem. Photobiol. B 63, 88-102 (2001).
2. Masutani, C., Kusumoto, R., Iwai, S. & Hanaoka, F. Mechanisms of accurate translesion synthesis by human DNA polymerase η. EMBO J. 19, 3100-3109 (2000).
3. Johnson, R. E., Washington, M. T., Prakash, S. & Prakash, L. Fidelity of human DNA polymerase η. J. Biol. Chem. 275, 7447-7450 (2000).
4. Lehmann, A. R. Replication of damaged DNA in mammalian cells: new solutions to an old problem. Mutat. Res. 509, 23-34 (2002).
5. Masutani, C. et al. The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase. Nature 399, 700-704 (1999).
6. Johnson, R. E., Kondratick, C. M., Prakash, S. & Prakash, L. hRAD30 mutations in the variant form of xeroderma pigmentosum. Science 285, 263-265 (1999).
7. Thoma, F. Light and dark in chromatin repair: repair of UV-induced DNA lesions by photolyase and nucleotide excision repair. EMBO J. 18, 6585-6598 (1999).
8. Hoeijmakers, J. H. Genome maintenance mechanisms for preventing cancer. Nature 411, 366-374 (2001).
9. Ohmori, H. et al. The Y-family of DNA polymerases. Mol. Cell 8, 7-8 (2001).
10. Yang, W. Damage repair DNA polymerases Y. Curr. Opin. Struct. Biol. 13, 23-30 (2003).
11. Ling, H., Boudsocq, F., Woodgate, R. & Yang, W. Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell 107, 91-102 (2001).
12. Boudsocq, F., Iwai, S., Hanaoka, F. & Woodgate, R. Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4): an archaeal DNA polymerase with properties akin to eukaryotic Pol η. Nucleic Acids Res. 29, 4607-4616 (2001).
13. Patel, P. H., Suzuki, M., Adman, E., Shinkai, A. & Loeb, L. A. Prokaryotic DNA polymerase I: evolution, structure, and "base flipping" mechanism for nucleotide selection. J. Mol. Biol. 308, 823-837 (2001).
14. Glick, E., Vigna, K. L. & Loeb, L. A. Mutations in human DNA polymerase η motif II alter bypass of DNA lesions. EMBO J. 20, 7303-7312 (2001).
15. Park, I. Y. & Choi, B. S. NMR investigation of echinomycin binding to d(ACGTTAACGT)2: Hoogsteen versus Watson-Crick A.T base pairing between echinomycin binding sites. J. Biochem. (Tokyo) 118, 989-995 (1995).
16. Aishima, J. et al. A Hoogsteen base pair embedded in undistorted B-DNA. Nucleic Acids Res. 30, 5244-5252 (2002).
17. Patikoglou, G. A. et al. TATA element recognition by the TATA box-binding protein has been conserved throughout evolution. Genes Dev. 13, 3217-3230 (1999).
18. Bunting, K. A. et al. Crystal structure of the Escherichia coli dcm very-short-patch DNA repair endonuclease bound to its reaction product-site in a DNA superhelix. Nucleic Acids Res. 31, 1633-1639 (2003).
19. Park, H. et al. Crystal structure of a DNA decamer containing a cis-syn thymine dimer. Proc. Natl Acad. Sci. USA 99, 15965-15970 (2002).
20. Zhang, H. & Siede, W. UV-induced T → C transition at a TT photoproduct site is dependent on Saccharomyces cerevisiae polymerase η in vivo. Nucleic Acids Res. 30, 1262-1267 (2002).
21. Szekeres, E. S. Jr, Woodgate, R. & Lawrence, C. W. Substitution ofmucAB or rumAB for umuDC alters the relative frequencies of the two classes of mutations induced by a site-specific T-T cyclobutane dimer and the efficiency of translesion DNA synthesis. J. Bacteriol. 178, 2559-2563 (1996).
22. Trincao, J. et al. Structure of the catalytic core of S. cerevisiae DNA polymerase II: implications for translesion DNA synthesis. Mol. Cell 8, 417-426 (2001).
23. Washington, M. T., Prakash, L., Prakash, S. & Yeast, D. N. A. polymerase η utilizes an induced-fit mechanism of nucleotide incorporation. Cell 107, 917-927 (2001).
24. Zhou, B. L., Pata, J. D. & Steitz, T. A. Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain. Mol. Cell 8, 427-437 (2001).
25. Silvian, L. F., Toth, E. A., Pham, P., Goodman, M. F. & Ellenberger, T. Crystal structure of a DinB family error-prone DNA polymerase from Sulfolobus solfataricus. Nature Struct. Biol. 8, 984-989 (2001).
26. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307-326 (1997).
27. Brünger, A. T. et al. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905-921 (1998).
28. Jones, T. A., Zou, J.-Y. & Cowan, S. W. Improved methods for building models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110-119 (1991).
29. Vassylyev, D. G. et al. Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition. Cell 83, 773-782 (1995).
30. Cohen, G. E. ALIGN: a program to superimpose protein coordinates. J. Appl. Crystallogr. 30, 1160-1161 (1997).