Structural conservation of the isolated zinc site in archaeal zinc- containing ferredoxins as revealed by x-ray absorption spectroscopic analysis and its evolutionary implications

Journal of Biological Chemistry

Volumn 274, Issue 33, 1999, Pages 23160-23168

  Cosper, Nathaniel J ^a   Stålhandske, Christina M V ^a   Iwasaki, Hideo ^b   Oshima, Tairo ^c   Scott, Robert A ^a   Iwasaki, Toshio ^d  

^a UNIVERSITY OF GEORGIA   (United States)

^b NAGOYA UNIVERSITY   (Japan)

^c TOKYO UNIVERSITY OF PHARMACY AND LIFE SCIENCES   (Japan)

^d NIPPON MEDICAL SCHOOL   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; FERREDOXIN;

ARTICLE; EVOLUTION; GENE LOCUS; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SPECTROSCOPY; THERMOPLASMA ACIDOPHILUM; X RAY ANALYSIS;

AMINO ACID SEQUENCE; ARCHAEA; BASE SEQUENCE; DNA, ARCHAEAL; EVOLUTION, MOLECULAR; FERREDOXINS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PROTEIN CONFORMATION; SEQUENCE HOMOLOGY, AMINO ACID; SPECTRUM ANALYSIS; X-RAYS; ZINC;

ARCHAEA; BACTERIA (MICROORGANISMS); SULFOLOBUS SP.; THERMOPLASMA ACIDOPHILUM;

EID: 0039778012     PISSN: 00219258     EISSN: None     Source Type: Journal    
DOI: 10.1074/jbc.274.33.23160     Document Type: Article

References (71)

1. Woese, C. R., Kandler, O., and Wheelis, M. L. (1990) Proc. Natl. Acad. Sci. U. S. A. 87, 4576-4579
2. Olsen, G. J., Woese, C. R., and Overbeek, R. (1994) J. Bacteriol. 176, 1-6
3. Stetter, K. O. (1995) ASM News 61, 285-290
4. Kerscher, L., and Oesterhelt, D. (1977) FEBS Lett. 83, 197-201
5. Kerscher, L., and Oesterhelt, D. (1982) Trends Biochem. Sci. 7, 371-374
6. Iwasaki, T., Wakagi, T., Isogai, Y., Tanaka, K., Iizuka, T., and Oshima, T. (1994) J. Biol. Chem. 269, 29444-29450
7. Iwasaki, T., Wakagi, T., and Oshima, T. (1995) J. Biol. Chem. 270, 17878-17883
8. Kerscher, L., Nowitzki, S., and Oesterhelt, D. (1982) Eur. J. Biochem. 128, 223-230
9. Zhang, Q., Iwasaki, T., Wakagi, T., and Oshima, T. (1996) J. Biochem. 120, 587-599
10. Wakabayashi, S., Fujimoto, N., Wada, K., Matsubara, H., Keracher, L., and Oesterhelt, D. (1983) FEBS Lett. 162, 21-24
11. Minami, Y., Wakabayashi, S., Wada, K., Matsubara, H., Kerscher, L., and Oesterhelt, D. (1985) J. Biochem. (Tokyo) 97, 745-753
12. Teixeira, M., Batista, R., Campos, A. P., Gomes, C., Mendes, J., Pacheco, I., Anemüller, S., and Hagen, W. R. (1995) Eur. J. Biochem. 227, 322-327
13. Wakagi, T., Fujii, T., and Oshima, T. (1996) Biochem. Biophys. Res. Commun. 225, 489-493
14. Iwasaki, T., Suzuki, T., Kon, T., Imai, T., Urushiyama, A., Ohmori, D., and Oshima, T. (1997) J. Biol. Chem. 272, 3453-3458
15. Iwasaki, T., and Oshima, T. (1997) FEBS Lett. 417, 223-226
16. Fujii, T., Hata, Y., Wakagi, T., Tanaka, N., and Oshima, T. (1996) Nat. Struct. Biol. 3, 834-837
17. Darland, G., Brock, T. D., and Conti, S. F. (1970) Science 170, 1416-1418
18. Belly, R. T., Bohlool, B. B., and Brock, T. D. (1973) Ann. N. Y. Acad. Sci. 225, 94-107
19. Ree, H. K., Cao, K., Thurlow, D. L., and Zimmermann, R. A. (1989) Can. J. Microbiol. 35, 124-133
20. Yasuda, M., Oyaizu, H., Yamagishi, A., and Oshima, T. (1995) Appl. Environ. Microbiol. 61, 3482-3485
21. Gärtner, P. (1991) Eur. J. Biochem. 200, 215-222
22. Scott, R. A. (1985) Methods Enzymol. 117, 414-459
23. Iwasaki, T., Matsuura, K., and Oshima, T. (1995) J. Biol. Chem. 270, 30881-30892
24. Sambrook, J., Fritsch, E. F., and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual, 2nd Ed., Cold Spring Harbor Laboratory Press, Plain-view, NY
25. Worley, K. C., Wiese, B. A., and Smith, R. F. (1995) Genome Res. 5, 173-184
26. Thompson, J. D., Gibson, T. J., Plewniak, F., Jeanmougin, F., and Higgins, D. G. (1997) Nucleic Acids Res. 25, 4876-4882
27. Cosper, N. J., Stȧlhandske, C. M. V., Saari, R. E., Hausinger, R. P., and Scott, R. A. (1999) J. Biol. Inorg. Chem. 4, 122-129
28. Zabinsky, S. I., Rehr, J. J., Ankudinov, A., Albers, R. C., and Eller, M. J. (1995) Phys. Rev. B 52, 2995
29. Harrocks, W. D., Holmquist, J. N. I. B., and Thompson, J. S. (1980) J. Inorg. Biochem. 12, 131
30. Bear, C. A., Duggan, K. A., and Freeman, H. C. (1975) Acta Crystallogr. Sec. B 31, 2713
31. Bult, C. J., White, O., Olsen, G. J., Zhou, L., Fleischmann, R. D., Sutton, G. G., Blake, J. A., FitzGerald, L. M., Clayton, R. A., Gocayne, J. D., Kerlavage, A. R., Dougherty, B. A., Tomb, J.-F., Adams, M. D., Reich, C. I., Overbeek, R., Kirkness, E. F., Weinstock, K. G., Merrick, J. M., Glodek, A., Scott, J. L., Geoghagen, N. S. M., Weidman, J. F., Fuhrmann, J. L., Nguyen, D., Utterback, T. R., Kelley, J. M., Peterson, J. D., Sadow, P. W., Hanna, M. C., Cotton, M. D., Roberts, K. M., Hurst, M. A., Kaine, B. P., Borodovsky, M., Klenk, H.-P., Fraser, C. M., Smith, H. O., Woese, C. R., and Venter, J. C. (1996) Science 273, 1058-1073
32. Smith, D. R., Doucette-Stamm, L. A., Deloughery, C., Lee, H., Dubois, J., Aldredge, T., Bashirzadeh, R., Blakely, D., Cook, R., Gilbert, K., Harrison, D., Hoang, L., Keagle, P., Lumm, W., Pothier, B., Qiu, D., Spadafora, R., Vicaire, R., Wang, Y., Wierzbowski, J., Gibson, R., Jiwani, N., Caruso, A., Bush, D., Safer, H., Patwell, D., Prabhakar, S., McDougall, S., Shimer, G., Goyal, A., Pietrovski, S., Church, G. M., Daniels, C. J., Mao, J.-I., Rice, P., Nolling, J., and Reeve, J. N. (1997) J. Bacteriol. 179, 7135-7155
33. Kawarabayasi, Y., Sawada, M., Horikawa, H., Haikawa, Y., Hino, Y., Yamamoto, S., Sekine, M., Baba, S., Kosugi, H., Hosoyama, A., Nagai, Y., Sakai, M., Ogura, K., Otsuka, R., Nakazawa, H., Takamiya, M., Ohfuku, Y., Funahashi, T., Tanaka, T., Kudoh, Y., Yamazaki, J., Kushida, N., Oguchi, A., Aoki, K., Yoshizawa, T., Nakamura, Y., Robb, F. T., Horikoshi, K., Masuchi, Y., Shizuya, H., and Kikuchi, H. (1998) DNA Res. 5, 147-155
34. Klenk, H.-P., Clayton, R. A., Tomb, J.-F., White, O., Nelson, K. E., Ketchum, K. A., Dodson, R. J., Gwinn, M., Hickey, E. K., Peterson, J. D., Richardson, D. L., Kerlavage, A. R., Graham, D. E., Kyrpides, N. C., Fleischmann, R. D., Quackenbush, J., Lee, N. H., Sutton, G. G., Gill, S., Kirkness, E. F., Dougherty, B. A., McKenney, K., Adams, M. D., Loftus, B., Venter, J. C., Peterson, S., Reich, C. I., McNeil, L. K., Badger, J. H., Glodek, A., Zhou, L., Overbeek, R., Gocayne, J. D., Weidman, J. F., McDonald, L., Utterback, T., Cotton, M. D., Spriggs, T., Artiach, P., Kaine, B. P., Sykes, S. M., Sadow, P. W., D'Andrea, K. P., Bowman, C., Fujii, C., Garland, S. A., Mason, T. M., Olsen, G. J., Fraser, C. M., Smith, H. O., Woese, C. R., and Venter, J. C. (1997) Nature 390, 364-370
35. Deckert, G., Warren, P. V., Gaasterland, T., Young, W. G., Lenox, A. L., Graham, D. E., Overbeek, R., Snead, M. A., Keller, M., Aujay, M., Huber, R., Feldman, R. A., Short, J. M., Olsen, G. J., and Swanson, R. V. (1998) Nature 392, 353-358
36. Hain, J., Reiter, W.-D., Hüdepohl, U., and Zillig, W. (1992) Nucleic Acids Res. 20, 5423-5428
37. Reiter, W.-D., Palm, P., and Zillig, W. (1988) Nucleic Acids Res. 16, 2445-2459
38. Wiedmann, B., Sakai, H., Davis, T. A., and Wiedmann, M. (1994) Nature 370, 434-440
39. Shi, X., Parthun, M. R., and Jaehning, J. A. (1995) Gene (Amst.) 165, 199-202
40. George, R., Beddoe, T., Landl, K., and Lithgow, T. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 2296-2301
41. Yotov, W. V., Moreau, A., and St-Arnaud, R. (1998) Mol. Cell. Biol. 18, 1303-1311
42. Wang, S., Sakai, H., and Wiedmann, M. (1995) J. Cell Biol. 130, 519-528
43. Lauring, B., Kreibich, G., and Weidmann, M. (1995) Proc. Natl. Acad. Sci. U. S. A. 92, 9435-9439
44. Powers, T., and Walter, P. (1996) Curr. Biol. 6, 331-338
45. Yue, D., Maizels, N., and Weiner, A. M. (1996) RNA 2, 895-908
46. Shi, P. Y., Maizels, N., and Weiner, A. M. (1998) EMBO J. 17, 3197-3206
47. Thurlow, D. L., Pulido, G. M., and Millar, K. J. (1997) J. Mol. Evol. 44, 686-689
48. Jacquamet, L., Aberdam, D., Adrait, A., Hazeman, J.-L., Latour, J.-M., and Michaud-Soret, I. (1998) Biochemistry 37, 2564-2571
49. Clark-Baldwin, K., Tierney, D. L., Govindaswamy, N., Gruff, E. S., Kim, C., Berg, J., Koch, S. A., and Penner-Hahn, J. E. (1998) J. Am. Chem. Soc. 120, 8401-8409
50. Westre, T. E., Kennepohl, P., Dewitt, J. G., Hedman, B., Hodgson, K. O., and Solomon, E. I. (1997) J. Am. Chem. Soc. 119, 6297-6314
51. Roe, A. L., Schneider, D. J., Mayer, R. J., Pyrz, J. W., Widom, J., and Que, L. (1984) J. Am. Chem. Soc. 108, 1676-1681
52. Randall, C. R., Shu, L., Chiou, Y.-M., Hagen, K. S., Ito, M., Kitajima, N., Lachicotte, R. J., Zang, Y., and Que, L. (1995) Inorg. Chem. 34, 1036-1039
53. Bentrop, D., Bertini, I., Luchinat, C., Mendes, J., Piccioli, M., and Teixeira, M. (1996) Eur. J. Biochem. 236, 92-99
54. Bertini, I., Dikiy, A., Luchinat, C., Macinai, R., Viezzoli, M. S., and Vincenzini, M. (1997) Biochemistry 36, 3570-3579
55. Sato, S., Nakazawa, K., Hon-nami, K., and Oshima, T. (1981) Biochim. Biophys. Acta 668, 277-289
56. Bruschi, M., and Guerleaquin, F. (1988) FEMS Microbiol. Rev. 64, 155-176
57. Cammack, R. (1992) Adv. Inorg. Chem. 38, 281-322
58. Matsubara, H., and Saeki, K. (1992) Adv. Inorg. Chem. 38, 223-280
59. Golbeck, J. H. (1994) in Advances in Photosynthesis: The Molecular Biology of Cyanobacteria (Bryant, D. A., ed) pp. 319-360, Kluwer Academic Publishers, Dordrecht, The Netherlands
60. Krauss, N., Schubert, W. D., Klukas, O., Fromme, P., Witt, H. T., and Saenger, W. (1996) Nat. Struct. Biol. 3, 965-973
61. Bentrop, D., Bertini, I., Luchinat, C., Nitschke, W., and Muhlenhoff, U. (1997) Biochemistry 38, 13629-13637
62. Schubert, W. D., Klukas, O., Krauss, N., Saenger, W., Fromme, P., and Witt, H. T. (1997) J. Mol. Biol. 272, 741-769
63. Breton, J. L., Duff, J. L. C., Butt, J. N., Armstrong, F. A., George, S. J., Pétillot, Y., Forest, E., Schäfer, G., and Thomson, A. J. (1995) Eur. J. Biochem. 233, 937-946
64. Adams, M. W. W. (1993) Annu. Rev. Microbiol. 47, 627-658
65. Adams, M. W. W. (1994) FEMS Microbiol. Rev. 15, 261-277
66. Brereton, P. S., Verhagen, M. F. J. M., Zhou, Z. H., and Adams, M. W. W. (1998) Biochemistry 37, 7351-7362
67. Kerscher, L., Oesterhelt, D., Cammack, R., and Hall, D. O. (1976) Eur. J. Biochem. 71, 101-108
68. Pfeifer, F., Griffig, J., and Oesterhelt, D. (1993) Mol. Gen. Genet. 289, 66-71
69. Moll, R., and Schäfer, G. (1988) FEBS Lett. 232, 359-363
70. Lübben, M. (1995) Biochim. Biophys. Acta 1229, 1-22
71. Schäfer, G. (1996) Biochim. Biophys. Acta 1277, 163-200