UV damage endonuclease employs a novel dual-dinucleotide flipping mechanism to recognize different DNA lesions

Nucleic Acids Research

Volumn 41, Issue 2, 2013, Pages 1363-1371

  Meulenbroek, Elisabeth M ^a   Cane, Caroline Peron ^a   Jala, Isabelle ^a   Iwai, Shigenori ^b   Moolenaar, Geri F ^a   Goosen, Nora ^a   Pannu, Navraj S ^a  

^a LEIDEN UNIVERSITY   (Netherlands)

^b OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; ENDONUCLEASE; HYDROXYL GROUP; METAL ION; PURINE; PYRIMIDINE; UNCLASSIFIED DRUG; UV DAMAGE ENDONUCLEASE;

ARTICLE; CATALYSIS; CONTROLLED STUDY; DNA DAMAGE; DNA HELIX; DNA REPAIR; DNA STRUCTURE; DUAL DINUCLEOTIDE FLIPPING; ENZYME ACTIVITY; ENZYME STRUCTURE; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; RADIATION INJURY; STRUCTURE ANALYSIS; SULFOLOBUS ACIDOCALDARIUS; ULTRAVIOLET RADIATION;

AMINO ACID SEQUENCE; DNA; DNA DAMAGE; DNA REPAIR ENZYMES; ENDODEOXYRIBONUCLEASES; METALS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PYRIMIDINE DIMERS; SEQUENCE ALIGNMENT; SULFOLOBUS ACIDOCALDARIUS;

SULFOLOBUS ACIDOCALDARIUS;

EID: 84875432306     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1127     Document Type: Article

References (23)

1. Daniels, D.S., Woo, T.T., Luu, K.X., Noll, D.M., Clarke, N.D., Pegg, A.E. and Tainer, J.A. (2004) DNA binding and nucleotide flipping by the human DNA repair protein AGT. Nat. Struct. Mol. Biol, 11, 714-720. (Pubitemid 39014496)
2. Maul, M.J., Barends, T.R.M., Glas, A.F., Cryle, M.J., Domratcheva, T., Schneider, S., Schlichting, I. and Carell, T. (2008) Crystal structure and mechanism of a DNA (6-4) photolyase. Angew. Chem. Int. Ed. Engl, 47, 10076-10080.
3. Parikh, S.S., Walcher, G., Jones, G.D., Slupphaug, G., Krokan, H.E., Blackburn, M. and Tainer, J.A. (2000) Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects. Proc. Natl Acad. Sci. USA, 97, 5083-5088. (Pubitemid 30313675)
4. Vassylyev, D.G., Kashiwagi, T., Mikami, Y., Arlyoshi, M., Iwai, S., Ohtsuka, E. and Morikawa, K. (1995) Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition. Cell, 83, 773-782.
5. Min, J.H. and Pavletich, N.P. (2007) Recognition of DNA damage by the Rad4 nucleotide excision repair protein. Nature, 449, 570-576.
6. Bowman, K.K., Sidik, K., Smith, C.A., Taylor, J.S., Doetsch, P.W. and Freyer, G.A. (1994) A new ATP-independent DNA endonuclease from Schizosaccharomyces pombe that recognizes cyclobutane pyrimidine dimers and 6-4 photoproducts. Nucleic Acids Res., 22, 3026-3032. (Pubitemid 24260631)
7. Avery, A.M., Kaur, B., Taylor, J., Mello, J.A., Essigmann, J.M. and Doetsch, P.W. (1999) Substrate specificity of ultraviolet DNA endonuclease (UVDE/Uve1p) from Schizosaccharomyces pombe. Nucleic Acids Res., 27, 2256-2264. (Pubitemid 29245642)
8. Paspaleva, K., Moolenaar, G.F. and Goosen, N. (2009) Damage recognition by UV damage endonuclease from Schizosaccharomyces pombe. DNA Repair, 8, 600-611.
9. Paspaleva, K., Thomassen, E., Pannu, N.S., Iwai, S., Moolenaar, G.F., Goosen, N. and Abrahams, J.P. (2007) Crystal structure of the DNA repair enzyme ultraviolet damage endonuclease. Structure, 15, 1316-1324. (Pubitemid 47539156)
10. Iwai, S. (2006) Chemical synthesis of oligonucleotides containing damaged bases for biological studies. Nucleosides Nucleotides Nucleic Acids, 25, 561-582. (Pubitemid 44264722)
11. Verhoeven, E.E., Van Kesteren, M., Turner, J.J., Van der Maarel, G.A., Van Boom, J.H., Moolenaar, G.F. and Goosen, N. (2002) The C-terminal region of Escherichia coli UvrC contributes to the flexibility of the UvrABC nucleotide excision repair system. Nucleic Acids Res., 30, 2492-2500. (Pubitemid 34619002)
12. Leslie, A.G. (1999) Integration of macromolecular diffraction data. Acta Crystallogr, D55, 1696-1702. (Pubitemid 29504424)
13. Evans, P. (2006) Scaling and assessment of data quality. Acta Crystallogr., D62, 72-82.
14. Winn, M.D., Ballard, C.C., Cowtan, K.D., Dodson, E.J., Emsley, P., Evans, P.R., Keegan, R.M., Krissinel, E.B., Leslie, A.G., McCoy, A. et al. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr., D67, 235-242.
15. Perrakis, A., Morris, R. and Lamzin, V.S. (1999) Automated protein model building combined with iterative structure refinement. Nat. Struct. Biol., 6, 458-463. (Pubitemid 29218016)
16. Murshudov, G.N., Skubak, P., Lebedev, A.A., Pannu, N.S., Steiner, R.A., Nicholls, R.A., Winn, M.D., Long, F. and Vagin, A.A. (2011) REFMAC5 for the refinement of macro-molecular crystal structures. Acta Crystallogr., D67, 355-367.
17. Emsley, P., Lohkamp, B., Scott, W.G. and Cowtan, K. (2010) Features and development of Coot. Acta Crystallogr., D66, 486-501.
18. Theobald, D.L. and Wuttke, D.S. (2006) THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures. Bioinformatics, 22, 2171-2172. (Pubitemid 44390914)
19. Thompson, K.E., Wang, Y., Madej, T. and Bryant, S.H. (2009) Improving protein structure similarity searches using domain boundaries based on conserved sequence information. BMC Struct. Biol., 19, 33.
20. Potterton, L., McNicholas, S., Krissinel, E., Gruber, J., Cowtan, K., Emsley, P., Murshudov, G.N., Cohen, S., Perrakis, A. and Noble, M. (2004) Developments in the CCP4 molecular graphics project. Acta Crystallogr., D60, 2288-2294. (Pubitemid 41742782)
21. Hosfield, D.J., Guan, Y., Haas, B.J., Cunningham, R.P. and Tainer, J.A. (1999) Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell, 98, 397-408. (Pubitemid 29380574)
22. Kim, J.K. and Choi, B.S. (1995) The solution structure of DNA duplex-decamer containing the (6-4) photoproduct of thymidylyl (30!50) thymidine by NMR and relaxation matrix refinement. Eur. J. Biochem, 228, 849-854.
23. Davis, I.W., Leaver-Fay, A., Chen, V.B., Block, J.N., Kapral, G.J., Wang, X., Murray, L.W., Arendall, W.B., Snoeyink, J., Richardson, J.S. et al. (2007) MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res., 35, 375-383.