Structure of an archaeal TYW1, the enzyme catalyzing the second step of wye-base biosynthesis

Acta Crystallographica Section D: Biological Crystallography

Volumn 63, Issue 10, 2007, Pages 1059-1068

  Goto Ito, Sakurako ^a,b   Ishii, Ryohei ^b   Ito, Takuhiro ^a,b   Shibata, Rie ^b   Fusatomi, Emiko ^b   Sekine, Shun Ichi ^a,b   Bessho, Yoshitaka ^b   Yokoyama, Shigeyuki ^a,b  

^a UNIVERSITY OF TOKYO   (Japan)

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

Author keywords

Radical AdoMet; RNA modification; TRNA; TYW1; Wye base

Indexed keywords

ARCHAEAL PROTEIN; ENZYME; IRON SULFUR PROTEIN; NUCLEOSIDE; UNCLASSIFIED DRUG; WYBUTOSINE;

AMINO ACID SEQUENCE; ARCHAEBACTERIUM; ARTICLE; BINDING SITE; CATALYSIS; CHEMISTRY; CONFORMATION; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; PYROCOCCUS HORIKOSHII; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY; X RAY CRYSTALLOGRAPHY;

AMINO ACID SEQUENCE; ARCHAEA; ARCHAEAL PROTEINS; BINDING SITES; CATALYSIS; CRYSTALLOGRAPHY, X-RAY; ENZYMES; IRON-SULFUR PROTEINS; MOLECULAR CONFORMATION; MOLECULAR SEQUENCE DATA; NUCLEOSIDES; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PYROCOCCUS HORIKOSHII; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY, AMINO ACID;

ARCHAEA; EUKARYOTA; PYROCOCCUS HORIKOSHII; SACCHAROMYCES CEREVISIAE;

EID: 34748889928     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444907040668     Document Type: Article

References (31)

1. Adams, P. D., Pannu, N. S., Read, R. J. & Brünger, A. T. (1997). Proc. Natl Acad. Sci. USA, 94, 5018-5023.
2. Berkovitch, F., Nicolet, Y., Wan, J. T., Jarrett, J. T. & Drennan, C. L. (2004). Science, 303, 76-79.
3. Blobstein, S. H., Grunberger, D., Weinstein, I. B. & Nakanishi, K. (1973). Biochemistry, 12, 188-193.
4. Grosjean, H. (2005). Editor. Fine-Tuning of RNA Modifications and Editing. Berlin/Heidelberg: Springer-Verlag.
5. Hanzelmann, P. & Schindelin, H. (2004). Proc. Natl Acad. Sci. USA, 101, 12870-12875.
6. Hatfield, D., Feng, Y. X., Lee, B. J., Rein, A., Levin, J. G. & Oroszlan, S. (1989). Virology, 173, 736-742.
7. Konevega, A. L., Soboleva, N. G., Makhno, V. I., Semenkov, Y. P., Wintermeyer, W., Rodnina, M. V. & Katunin, V. I. (2004). RNA, 10, 90-101.
8. Kuchino, Y., Borek, E., Grunberger, D., Mushinski, J. F. & Nishimura, S. (1982). Nucleic Acids Res. 10, 6421-6432.
9. La Fortelle, E. de & Bricogne, G. (1997). Methods Enzymol. 276, 472-494.
10. Layer, G., Heinz, D. W., Jahn, D. & Schubert, W. D. (2004). Curr. Opin. Chem. Biol. 8, 468-476.
11. Layer, G., Moser, J., Heinz, D. W., Jahn, D. & Schubert, W. D. (2003). EMBO J. 22, 6214-6224.
12. Lepore, B. W., Ruzicka, F. J., Frey, P. A. & Ringe, D. (2005). Proc. Natl Acad. Sci. USA, 102, 13819-13824.
13. Li, J., Esberg, B., Curran, J. F. & Bjork, G. R. (1997). J. Mol. Biol. 271, 209-221.
14. McCloskey, J. A., Graham, D. E., Zhou, S., Crain, P. F., Ibba, M., Konisky, J., Soll, D. & Olsen, G. J. (2001). Nucleic Acids Res. 29, 4699-4706.
15. Motorin, Y. & Grosjean, H. (2001). Encyclopedia of Life Sciences, pp. 1-9. New York: Wiley.
16. Murphy, F. V. IV, Ramakrishnan, V., Malkiewicz, A. & Agris, P. F. (2004). Nature Struct. Mol. Biol. 11, 1186-1191.
17. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
18. Nicholls, A., Sharp, K. A. & Honig, B. (1991). Proteins, 11, 281-296.
19. Noma, A., Kirino, Y., Ikeuchi, Y. & Suzuki, T. (2006). EMBO J. 25, 2142-2154.
20. Noon, K. R., Guymon, R., Crain, P. F., McCloskey, J. A., Thomm, M., Lim, J. & Cavicchioli, R. (2003). J. Bacteriol. 185, 5483-5490.
21. Otwinowski, Z. & Minor, W. (1997). Methods Enzymol. 276, 307-326.
22. Schneider, T. R. & Sheldrick, G. M. (2002). Acta Cryst. D58, 1772-1779.
23. Smith, C., Schmidt, P. G., Petsch, J. & Agris, P. F. (1985). Biochemistry, 24, 1434-1440.
24. Terwilliger, T. C. (2000). Acta Cryst. D56, 965-972.
25. Ugulava, N. B., Gibney, B. R. & Jarrett, J. T. (2001). Biochemistry, 40, 8343-8351.
26. Urbonavicius, J., Qian, Q., Durand, J. M., Hagervall, T. G. & Bjork, G. R. (2001). EMBO J. 20, 4863-4873.
27. Vagin, A. & Teplyakov, A. (1997). J. Appl. Cryst. 30, 1022-1025.
28. Vonrhein, C., Blanc, E., Roversi, P. & Bricogne, G. (2006). Macromolecular Crystallography Protocols, Vol. 2, Structure Determination, edited by S. Doublié, pp. 215-230. Totowa, NJ, USA: Humana Press.
29. Waas, W. F., de Crecy-Lagard, V. & Schimmel, P. (2005). J. Biol. Chem. 280, 37616-37622.
30. Yarian, C., Townsend, H., Czestkowski, W., Sochacka, E., Malkiewicz, A. J., Guenther, R., Miskiewicz, A. & Agris, P. F. (2002). J. Biol. Chem. 277, 16391-16395.
31. Zhou, S., Sitaramaiah, D., Noon, K. R., Guymon, R., Hashizume, T. & McCloskey, J. A. (2004). Bioorg. Chem. 32, 82-91.