The structure of a yeast RNA-editing deaminase provides insight into the fold and function of activation-induced deaminase and APOBEC-1

Proceedings of the National Academy of Sciences of the United States of America

Volumn 101, Issue 21, 2004, Pages 8114-8119

  Xie, Kefang ^a   Sowden, Mark P ^a   Dance, Geoffrey S C ^a,b   Torelli, Andrew T ^a   Smith, Harold C ^a   Wedekind, Joseph E ^a  

^a UNIVERSITY OF ROCHESTER SCHOOL OF MEDICINE AND DENTISTRY   (United States)

^b Genzyme Europe Research   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

APOLIPOPROTEIN B; APOLIPOPROTEIN B EDITING CATALYTIC SUBUNIT 1; DEAMINASE; FUNGAL RNA; NUCLEOSIDE; PROTEIN SUBUNIT; RNA; SINGLE STRANDED DNA; TRANS ACTING FACTOR; UNCLASSIFIED DRUG;

ARTICLE; CRYSTAL STRUCTURE; DIMERIZATION; ENZYME ACTIVATION; ENZYME ACTIVE SITE; ENZYME SUBSTRATE; MOLECULAR MODEL; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN RNA BINDING; PYRIMIDINE METABOLISM; RNA EDITING;

BINDING SITES; CRYSTALLOGRAPHY, X-RAY; CYTIDINE DEAMINASE; HUMANS; IMMUNOGLOBULIN M; MODELS, MOLECULAR; MUTATION; PROTEIN CONFORMATION; PROTEIN FOLDING; RNA EDITING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SYNDROME;

MAMMALIA;

EID: 2542542827     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0400493101     Document Type: Article

References (54)

1. Manis, J. P., Tian, M. & Alt, F. W. (2002) Trends Immunol. 23, 31-39.
2. Flajnik, M. F. (2002) Nat. Rev. Immunol. 2, 688-698.
3. Muramatsu, M., Kinoshita, K., Fagarasan, S., Yamada, S., Shinkai, Y. & Honjo, T. (2000) Cell 102, 553-563.
4. Harris, R. S., Sale, J. E., Petersen-Mahrt, S. K. & Neuberger, M. S. (2002) Curr. Biol. 12, 435-438.
5. Arakawa, H., Hauschild, J. & Buerstedde, J. M. (2002) Science 295, 1301-1306.
6. Rada, C., Jarvis, J. M. & Milstein, C. (2002) Proc. Natl. Acad. Sci. USA 99, 7003-7008.
7. Martin, A., Bardwell, P. D., Woo, C. J., Fan, M., Shulman, M. J. & Scharff, M. D. (2002) Nature 415, 802-806.
8. Yoshikawa, K., Okazaki, I. M., Eto, T., Kinoshita, K., Muramatsu, M., Nagaoka, H. & Honjo, T. (2002) Science 296, 2033-2036.
9. Faili, A., Aoufouchi, S., Gueranger, Q., Zober, C., Leon, A., Bertocci, B., Weill, J. C. & Reynaud, C. A. (2002) Nat. Immunol. 3, 815-821.
10. Okazaki, I. M., Kinoshita, K., Muramatsu, M., Yoshikawa, K. & Honjo, T. (2002) Nature 416, 340-345.
11. Revy, P., Muto, T., Levy, Y., Geissmann, F., Plebani, A., Sanal, O., Catalan, N., Forveille, M., Dufourcq-Labelouse, R., Gennery, A., et al. (2000) Cell 102, 565-575.
12. Petersen-Mahrt, S. K., Harris, R. S. & Neuberger, M. S. (2002) Nature 418, 99-103.
13. Imai, K., Slupphaug, G., Lee, W. I., Revy, P., Nonoyama, S., Catalan, N., Yel, L., Forveille, M., Kavli, B., Krokan, H. E., et al. (2003) Nat. Immunol. 4, 1023-1028.
14. Rada, C., Williams, G. T., Nilsen, H., Barnes, D. E., Lindahl, T. & Neuberger, M. S. (2002) Curr. Biol. 12, 1748-1755.
15. Dickerson, S. K., Market, E., Besmer, E. & Papavasiliou, F. N. (2003) J. Exp. Med. 197, 1291-1296.
16. Bransteitter, R., Pham, P., Scharff, M. D. & Goodman, M. F. (2003) Proc. Natl. Acad. Sci. USA 100, 4102-4107.
17. Martin, A. & Scharff, M. D. (2002) Proc. Natl. Acad. Sci. USA 99, 12304-12308.
18. Ramiro, A. R., Stavropoulos, P., Jankovic, M. & Nussenzweig, M. C. (2003) Nat. Immunol. 4, 452-456.
19. Sohail, A., Klapacz, J., Samaranayake, M., Ullah, A. & Bhagwat, A. S. (2003) Nucleic Acids Res. 31, 2990-2994.
20. Bass, B. L. (2002) Annu. Rev. Biochem. 71, 817-846.
21. Wedekind, J. E., Dance, G. S., Sowden, M. P. & Smith, H. C. (2003) Trends Genet. 19, 207-216.
22. Doi, T., Kinoshita, K., Ikegawa, M., Muramatsu, M. & Honjo, T. (2003) Proc. Natl. Acad. Sci. USA 100, 2634-2638.
23. Dance, G. S., Beemiller, P., Yang, Y., Mater, D. V., Mian, I. S. & Smith, H. C. (2001) Nuleic Acids Res. 29, 1772-1780.
24. Otwinowski, Z. & Minor, W. (1997) Methods Enzymol. 276, 307-326.
25. Terwilliger, T. C. (1997) Methods Enzymol. 276, 530-537.
26. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard. (1991) Acta Crystallogr. A 47, 110-119.
27. 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., et al. (1998) Acta Crystallogr. D 54, 905-921.
28. Betts, L., Xiang, S., Short, S. A., Wolfenden, R. & Carter, C. W., Jr. (1994) J. Mol. Biol. 235, 635-656.
29. Johansson, E., Mejlhede, N., Neuhard, J. & Larsen, S. (2002) Biochemistry 41, 2563-2570.
30. Ko, T. P., Lin, J. J., Hu, C. Y., Hsu, Y. H., Wang, A. H. & Liaw, S. H. (2003) J. Biol. Chem. 278, 19111-19117.
31. Xiang, S., Short, S. A., Wolfenden, R. & Carter, C. W., Jr. (1996) Biochemistry 35, 1335-1341.
32. Sowden, M., Hamm, J. K. & Smith, H. C. (1996) J. Biol. Chem. 271, 3011-3017.
33. Kurtz, J. E., Exinger, F., Erbs, P. & Jund, R. (1999) Curr. Genet. 36, 130-136.
34. Mian, I. S., Moser, M. J., Holley, W. R. & Chatterjee, A. (1998) J. Comput. Biol. 5, 57-72.
35. Zaim, J. & Kierzek, A. M. (2003) Nat. Immunol. 4, 1153-1154.
36. Ta, V. T., Nagaoka, H., Catalan, N., Durandy, A., Fischer, A., Imai, K., Nonoyama, S., Tashiro, J., Ikegawa, M., Ito, S., et al. (2003) Nat. Immunol. 4, 843-848.
37. Rost, B. (1999) Protein Eng. 12, 85-94.
38. Marti-Renom, M. A., Stuart, A. C., Fiser, A., Sanchez, R., Melo, F. & Sali, A. (2000) Annu. Rev. Biophys. Biomol. Struct. 29, 291-325.
39. Chothia, C. & Lesk, A. M. (1986) EMBO J. 5, 823-826.
40. Navaratnam, N., Bhattacharya, S., Fujino, T., Patel, D., Jarmuz, A. L. & Scott, J. (1995) Cell 81, 187-195.
41. Sheehy, A. M., Gaddis, N. C., Choi, J. D. & Malim, M. H. (2002) Nature 418, 646-650.
42. Lau, P. P., Zhu, H. J., Baldini, A., Charnsangavej, C. & Chan, L. (1994) Proc. Natl. Acad. Sci. USA 91, 8522-8526.
43. Oka, K., Kobayashi, K., Sullivan, M., Martinez, J., Teng, B. B., Ishimura-Oka, K. & Chan, L. (1997) J. Biol. Chem. 272, 1456-1460.
44. Gerber, A. P. & Keller, W. (2001) Trends Biochem. Sci. 26, 376-384.
45. Navaratnam, N., Fujino, T., Bayliss, J., Jarmuz, A., How, A., Richardson, N., Somasekaram, A., Bhattacharya, S., Carter, C. & Scott, J. (1998) J. Mol. Biol. 275, 695-714.
46. Smith, H. C. (1993) in Seminars in Cell Biology, ed. Stuart, K. (Saunders Scientific, London), Vol. 4, pp. 267-278.
47. Harris, R. S., Petersen-Mahrt, S. K. & Neuberger, M. S. (2002) Mol. Cell 10, 1247-1253.
48. Anant, S. & Davidson, N. O. (2000) Mol. Cell. Biol. 20, 1982-1992.
49. Mehta, A., Kinter, M. T., Sherman, N. E. & Driscoll, D. M. (2000) Mol. Cell. Biol. 20, 1846-1854.
50. Mehta, A. & Driscoll, D. M. (2002) RNA 8, 69-82.
51. Muramatsu, M., Sankaranand, V. S., Anant, S., Sugai, M., Kinoshita, K., Davidson, N. O. & Honjo, T. (1999) J. Biol. Chem. 274, 18470-18476.
52. Eto, T., Kinoshita, K., Yoshikawa, K., Muramatsu, M. & Honjo, T. (2003) Proc. Natl. Acad. Sci. USA 100, 12895-12898.
53. Ito, S., Nagaoka, H., Shinkura, R., Begum, M., Muramatsu, M., Nakata, M. & Honjo, T. (2004) Proc. Natl. Acad. Sci. USA 101, 1975-1908.
54. Esnouf, R. M. (1999) Acta Crystallogr. D 55, 938-940.