The structure of DdrB from Deinococcus: A new fold for single-stranded DNA binding proteins

Nucleic Acids Research

Volumn 38, Issue 10, 2010, Pages 3432-3440

  Sugiman Marangos, Seiji ^a   Junop, Murray S ^a  

^a MCMASTER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; PROTEIN DDRB; SINGLE STRANDED DNA; UNCLASSIFIED DRUG; DNA BINDING PROTEIN; ESCHERICHIA COLI PROTEIN; SSB PROTEIN, E COLI;

ARTICLE; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DEINOCOCCUS; DNA BINDING; DNA DAMAGE; GENE FUNCTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PURIFICATION; PROTEIN STRUCTURE; SINGLE STRANDED DNA BREAK; STRUCTURE ANALYSIS; UPREGULATION; CHEMICAL STRUCTURE; CHEMISTRY; METABOLISM; PROTEIN CONFORMATION; PROTEIN FOLDING; X RAY CRYSTALLOGRAPHY;

DEINOCOCCUS;

BACTERIAL PROTEINS; CRYSTALLOGRAPHY, X-RAY; DEINOCOCCUS; DNA DAMAGE; DNA, SINGLE-STRANDED; DNA-BINDING PROTEINS; ESCHERICHIA COLI PROTEINS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 77953326057     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq036     Document Type: Article

References (36)

1. Pardo, B., Gomez-Gonzalez, B. and Aguilera, A. (2009) DNA repair in mammalian cells: DNA double-strand break repair: How to fix a broken relationship. Cell Mol. Life Sci., 66, 1039-1056.
2. Zahradka, K., Slade, D., Bailone, A., Sommer, S., Averbeck, D., Petranovic, M., Lindner, A.B. and Radman, M. (2006) Reassembly of shattered chromosomes in Deinococcus radiodurans. Nature, 443, 569-573.
3. Anderson, A.W., Nordan, H.C., Cain, R.F., Parish, G. and Duggan, D. (1956) Studies on a radioresistant Micrococcus. I. Isolation, morphology, cultural characteristics and resistance to gamma radiation. Food Technol., 10, 575-578.
4. Daly, M.J., Gaidamakova, E.K., Matrosova, V.Y., Vasilenko, A., Zhai, M., Venkateswaran, A., Hess, M., Omelchenko, M.V., Kostandarithes, H.M., Makarova, K.S. et al. (2004) Accumulation of Mn(II) in Deinococcus radiodurans facilitates gamma-radiation resistance. Science, 306, 1025-1028.
5. Daly, M.J., Gaidamakova, E.K., Matrosova, V.Y., Vasilenko, A., Zhai, M., Leapman, R.D., Lai, B., Ravel, B., Li, S.M., Kemner, K.M. et al. (2007) Protein oxidation implicated as the primary determinant of bacterial radioresistance. PLoS Biol., 5, e92.
6. Makarova, K.S., Omelchenko, M.V., Gaidamakova, E.K., Matrosova, V.Y., Vasilenko, A., Zhai, M., Lapidus, A., Copeland, A., Kim, E., Land, M. et al. (2007) Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks. PLoS ONE, 2, e955.
7. Slade, D., Lindner, A.B., Paul, G. and Radman, M. (2009) Recombination and replication in DNA repair of heavily irradiated Deinococcus radiodurans. Cell, 136, 1044-1055.
8. Tanaka, M., Earl, A.M., Howell, H.A., Park, M.J., Eisen, J.A., Peterson, S.N. and Battista, J.R. (2004) Analysis of Deinococcus radiodurans's transcriptional response to ionizing radiation and desiccation reveals novel proteins that contribute to extreme radioresistance. Genetics, 168, 21-33.
9. Dean, C.J., Little, J.G. and Serianni, R.W. (1970) The control of post irradiation DNA breakdown in Micrococcus radiodurans. Biochem. Biophys. Res. Commun., 39, 126-134.
10. Liu, Y., Zhou, J., Omelchenko, M.V., Beliaev, A.S., Venkateswaran, A., Stair, J., Wu, L., Thompson, D.K., Xu, D., Rogozin, I.B. et al. (2003) Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc. Natl Acad. Sci. USA, 100, 4191-4196.
11. Norais, C.A., Chitteni-Pattu, S., Wood, E.A., Inman, R.B. and Cox, M.M. (2009) DdrB protein, an alternative Deinococcus radiodurans SSB induced by ionizing radiation. J. Biol. Chem., 284, 21402-21411.
12. Pestryakov, P.E. and Lavrik, O.I. (2008) Mechanisms of single-stranded DNA-binding protein functioning in cellular DNA metabolism. Biochemistry, 73, 1388-1404.
13. Otwinowski, Z. and Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. In Carter, C.W.J. and Sweet, R.M. (eds), Methods in Enzymology: Macromolecular Crystallography, Part A, Vol. 276. Academic Press, New York, pp. 307-326.
14. Adams, P.D., Grosse-Kunstleve, R.W., Hung, L.W., Ioerger, T.R., McCoy, A.J., Moriarty, N.W., Read, R.J., Sacchettini, J.C., Sauter, N.K. and Terwilliger, T.C. (2002) PHENIX: Building new software for automated crystallographic structure determination. Acta Crystallogr. D Biol. Crystallogr., 58, 1948-1954.
15. Emsley, P. and Cowtan, K. (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr., 60, 2126-2132.
16. Lee, B. and Richards, F.M. (1971) The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol., 55, 379-400.
17. Saff, E. and Kuijlaars, A. (1997) Distributing many points on a sphere. Math. Intell., 19, 5-11.
18. Kabsch, W. (1976) A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A, 32, 922-923.
19. Weiner, J.H., Bertsch, L.L. and Kornberg, A. (1975) The deoxyribonucleic acid unwinding protein of Escherichia coli. Properties and functions in replication. J. Biol. Chem., 250, 1972-1980.
20. Jones, D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292, 195-202.
21. McGuffin, L.J., Bryson, K. and Jones, D.T. (2000) The PSIPRED protein structure prediction server. Bioinformatics, 16, 404-405.
22. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
23. Sancar, A., Williams, K.R., Chase, J.W. and Rupp, W.D. (1981) Sequences of the SSB gene and protein. Proc. Natl Acad. Sci. USA, 78, 4274-4278.
24. Curth, U., Genschel, J., Urbanke, C. and Greipel, J. (1996) In vitro and in vivo function of the C-terminus of Escherichia coli single-stranded DNA binding protein. Nucleic Acids Res., 24, 2706-2711.
25. Zhu, Z.Y. and Karlin, S. (1996) Clusters of charged residues in protein three-dimensional structures. Proc. Natl Acad. Sci. USA, 93, 8350-8355.
26. Theobald, D.L., Mitton-Fry, R.M. and Wuttke, D.S. (2003) Nucleic acid recognition by OB-fold proteins. Annu. Rev. Biophys. Biomol. Struct., 32, 115-133.
27. Suhrer, S.J., Wiederstein, M., Gruber, M. and Sippl, M.J. (2009) COPS-a novel workbench for explorations in fold space. Nucleic Acids Res., 37, W539-W544.
28. Holm, L., Kaariainen, S., Rosenstrom, P. and Schenkel, A. (2008) Searching protein structure databases with DaliLite v.3. Bioinformatics, 24, 2780-2781.
29. Yang, J.M. and Tung, C.H. (2006) Protein structure database search and evolutionary classification. Nucleic Acids Res., 34, 3646-3659.
30. Kawabata, T. (2003) MATRAS: a program for protein 3D structure comparison. Nucleic Acids Res., 31, 3367-3369.
31. Raghunathan, S., Kozlov, A.G., Lohman, T.M. and Waksman, G. (2000) Structure of the DNA binding domain of E. coli SSB bound to ssDNA. Nat. Struct. Biol., 7, 648-652.
32. Bailey, S., Wing, R.A. and Steitz, T.A. (2006) The structure of T. aquaticus DNA polymerase III is distinct from eukaryotic replicative DNA polymerases. Cell, 126, 893-904.
33. Gulbis, J.M., Kelman, Z., Hurwitz, J., O'Donnell, M. and Kuriyan, J. (1996) Structure of the C-terminal region of p21(WAF1/CIP1) complexed with human PCNA. Cell, 87, 297-306.
34. Kong, X.P., Onrust, R., O'Donnell, M. and Kuriyan, J. (1992) Three-dimensional structure of the beta subunit of E. coli DNA polymerase III holoenzyme: A sliding DNA clamp. Cell, 69, 425-437.
35. Patel, S.S. and Picha, K.M. (2000) Structure and function of hexameric helicases. Annu. Rev. Biochem., 69, 651-697.
36. Song, L., Hobaugh, M.R., Shustak, C., Cheley, S., Bayley, H. and Gouaux, J.E. (1996) Structure of Staphylococcal alpha-hemolysin, a heptameric transmembrane pore. Science, 274, 1859-1866.