Metal-ion dependence of the active-site conformation of the translesion DNA polymerase Dpo4 from Sulfolobus solfataricus

Acta Crystallographica Section F: Structural Biology and Crystallization Communications

Volumn 66, Issue 9, 2010, Pages 1013-1018

  Irimia, Adriana ^a,b   Loukachevitch, Lioudmila V ^a   Eoff, Robert L ^a   Guengerich, F Peter ^a   Egli, Martin ^a  

^a VANDERBILT UNIVERSITY   (United States)

^b SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

calcium; Dpo4 DNA polymerase; magnesium; protein DNA interactions

Indexed keywords

CALCIUM; DIVALENT CATION; DNA DIRECTED DNA POLYMERASE BETA; MAGNESIUM;

ARTICLE; BIOCATALYSIS; CHEMICAL STRUCTURE; CHEMISTRY; ENZYME ACTIVE SITE; ENZYMOLOGY; METABOLISM; PROTEIN BINDING; STRUCTURAL HOMOLOGY; SULFOLOBUS SOLFATARICUS; X RAY CRYSTALLOGRAPHY;

BIOCATALYSIS; CALCIUM; CATALYTIC DOMAIN; CATIONS, DIVALENT; CRYSTALLOGRAPHY, X-RAY; DNA POLYMERASE BETA; MAGNESIUM; MODELS, MOLECULAR; PROTEIN BINDING; STRUCTURAL HOMOLOGY, PROTEIN; SULFOLOBUS SOLFATARICUS;

SULFOLOBUS SOLFATARICUS;

EID: 77956529179     PISSN: 17443091     EISSN: 17443091     Source Type: Journal    
DOI: 10.1107/S1744309110029374     Document Type: Article

References (33)

1. Boudsocq, F., Iwai, S., Hanaoka, F. & Woodgate, R. (2001). Nucleic Acids Res. 29, 4607-4616.
2. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T. & Warren, G. L. (1998). Acta Cryst. D54, 905-921.
3. Cambillau, C. & Roussel, A. (1997). TURBO-FRODO, version OpenGL.1. University Aix-Marseille II, Marseille, France.
4. Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.
5. DeLano, W. L. (2002). PyMOL Molecular Viewer. DeLano Scientific, San Carlos, California, USA.
6. Eoff, R. L., Angel, K. C., Egli, M. & Guengerich, F. P. (2007). J. Biol. Chem. 282, 13573-13584.
7. Eoff, R. L., Egli, M. & Guengerich, F. P. (2010). The Chemical Biology of DNA Damage, edited by N. E. Geacintov & S. Broyde, pp. 299-330. Weinheim: Wiley-VCH.
8. Eoff, R. L., Irimia, A., Angel, K. C., Egli, M. & Guengerich, F. P. (2007). J. Biol. Chem. 282, 19831-19843.
9. Eoff, R. L., Irimia, A., Egli, M. & Guengerich, F. P. (2007). J. Biol. Chem. 282, 1456-1467.
10. Eoff, R. L., Stafford, J., Szekely, J., Rizzo, C. J., Egli, M., Guengerich, F. P. & Marnett, L. J. (2009). Biochemistry, 48, 7079-7088.
11. Fiala, K. A. & Suo, Z. (2004). Biochemistry, 43, 2116-2125.
12. French, S. & Wilson, K. (1978). Acta Cryst. A34, 517-525.
13. Guengerich, F. P. (2006). Chem. Rev. 106, 420-452.
14. Irimia, A., Eoff, R. L., Guengerich, F. P. & Egli, M. (2009). J. Biol. Chem. 284, 22467-22480.
15. Irimia, A., Eoff, R. L., Pallan, P. S., Guengerich, F. P. & Egli, M. (2007). J. Biol. Chem. 282, 36421-36433.
16. Irimia, A., Zang, H., Loukachevitch, L. V., Eoff, R. L., Guengerich, F. P. & Egli, M. (2006). Biochemistry, 45, 5949-5956.
17. Ling, H., Boudsocq, F., Plosky, B. S., Woodgate, R. & Yang, W. (2003). Nature (London), 424, 1083-1087.
18. Ling, H., Boudsocq, F., Woodgate, R. & Yang, W. (2001). Cell, 107, 91-102.
19. Ling, H., Boudsocq, F., Woodgate, R. & Yang, W. (2004). Mol. Cell, 13, 751-762.
20. Ling, H., Sayer, J. M., Plosky, B. S., Yagi, H., Boudsocq, F., Woodgate, R., Jerina, D. M. & Yang,W. (2004). Proc. Natl Acad. Sci. USA, 101, 2265-2269.
21. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J. (2007). J. Appl. Cryst. 40, 658-674.
22. Otwinowski, Z. & Minor, W. (1997). Methods Enzymol. 276, 307-326.
23. Prakash, S., Johnson, R. E. & Prakash, L. (2005). Annu. Rev. Biochem. 74, 317-353.
24. Rechkoblit, O., Kolbanovskiy, A., Malinina, L., Geacintov, N. E., Broyde, S. & Patel, D. J. (2010). Nature Struct. Mol. Biol. 17, 379-388.
25. Rechkoblit, O., Malinina, L., Cheng, Y., Kuryavyi, V., Broyde, S., Geacintov, N. E. & Patel, D. J. (2006). PLoS Biol. 4, 25-42.
26. Trincao, J., Johnson, R. E.,Wolfle,W. T., Escalante, C. R., Prakash, S., Prakash, L. & Aggarwal, A. K. (2004). Nature Struct. Mol. Biol. 11, 457-462.
27. Vaisman, A., Ling, H., Woodgate, R. & Yang, W. (2005). EMBO J. 24, 2957-2967.
28. Wang, Y., Musser, S., Saleh, S., Marnett, L. J., Egli, M. & Stone, M. P. (2008). Biochemistry, 47, 7322-7334.
29. Yang,W. & Woodgate, R. (2007). Proc. Natl Acad. Sci. USA, 104, 15591-15598.
30. Zang, H., Goodenough, A. K., Choi, J.-Y., Irimia, A., Loukachevitch, L. V., Kozekov, I. D., Angel, K. C., Rizzo, C. J., Egli,M. & Guengerich, F. P. (2005). J. Biol. Chem. 280, 29750-29764.
31. Zang, H., Irimia, A., Choi, J.-Y., Angel, K. C., Loukachevitch, L. V., Egli, M. & Guengerich, F. P. (2006). J. Biol. Chem. 281, 2358-2372.
32. Zhang, H., Eoff, R. L., Kozekov, I. D., Rizzo, C. J., Egli, M. & Guengerich, F. P. (2009a). J. Biol. Chem. 284, 3563-3576.
33. Zhang, H., Eoff, R. L., Kozekov, I. D., Rizzo, C. J., Egli, M. & Guengerich, F. P. (2009b). J. Biol. Chem. 284, 17687-17699.