Insights into the evolution of allosteric properties. The NADH binding site of hexameric type II citrate synthases

Biochemistry

Volumn 42, Issue 19, 2003, Pages 5555-5565

  Maurus, Robert ^a   Nguyen, Nham T ^a   Stokell, David J ^b   Ayed, Ayeda ^b   Hultin, Philip G ^b   Duckworth, Harry W ^b   Brayer, Gary D ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF MANITOBA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

CONFORMATIONS; DIMERS; ENZYMES; ESCHERICHIA COLI;

ALLOSTERIC PROPERTIES;

BIOCHEMISTRY;

CITRATE SYNTHASE; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE;

ALLOSTERISM; ARTICLE; BINDING SITE; ENZYME BINDING; ENZYME KINETICS; ENZYME STRUCTURE; ESCHERICHIA COLI; GRAM NEGATIVE BACTERIUM; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

ALLOSTERIC REGULATION; ALLOSTERIC SITE; AMINO ACID SEQUENCE; CITRATE (SI)-SYNTHASE; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; ESCHERICHIA COLI; EVOLUTION, MOLECULAR; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NAD; PROTEIN CONFORMATION; PROTEIN STRUCTURE, QUATERNARY; SEQUENCE HOMOLOGY, AMINO ACID; VARIATION (GENETICS);

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; NEGIBACTERIA;

EID: 0038629285     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi020622s     Document Type: Article

References (74)

1. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., and Bourne, P. E. (2000) Nucleic Acids Res. 28, 235-242.
2. Nguyen, N. T., Maurus, R., Stokell, D. J., Ayed, A., Duckworth, H. W., and Brayer, G. D. (2001) Biochemistry 40, 13177-13187.
3. Remington, S., Wiegand, G., and Huber, R. (1982) J. Mol. Biol. 158, 111-152.
4. Wiegand, G., and Remington, S. J. (1986) Annu. Rev. Biophys. Biophys. Chem. 15, 97-117.
5. Remington, S. J. (1992) Curr. Top. Cell. Regul. 33, 209-229.
6. Russell, R. J., Hough, D. W., Danson, M. J., and Taylor, G. L. (1994) Structure 2, 1157-1167.
7. Russell, R. J., Ferguson, J. M., Hough, D. W., Danson, M. J., and Taylor, G. L. (1997) Biochemistry 36, 9983-9994.
8. Russell, R. J., Gerike, U., Danson. M. J., Hough, D. W., and Taylor, G. L. (1998) Structure 6, 351-361.
9. Weitzman, P. D. J. (1966) Biochim. Biophys. Acta 128, 213-215.
10. Weitzman, P. D. J. (1966) Biochem. J. 101, 44c-45c.
11. Weitzman, P. D. J. (1981) Adv. Microbiol. Physiol. 22, 185-244.
12. Weitzman, P. D. J., and Jones, D. (1968) Nature 219, 270-272.
13. Weitzman, P. D. J., and Dunmore, P. (1969) Biochim. Biophys. Acta 171, 198-200.
14. Duckworth, H. W., and Tong, E. K. (1976) Biochemistry 15, 108-114.
15. Ner, S. S., Bhayana, V., Bell, A. W., Giles, I. G., Duckworth, H. W., and Bloxham, D. P. (1983) Biochemistry 22, 5243-5249.
16. Monod, J., Wyman, J., and Changeux, J.-P. (1965) J. Mol. Biol. 12, 88-118.
17. Pereira, D. S., Donald, L. J., Hosfield, D. J., and Duckworth, H. W. (1994) J. Biol. Chem. 269, 412-417.
18. Ayed, A., and Duckworth, H. W. (1999) Protein Sci. 8, 1116-1126.
19. Ayed, A., Krutchinsky, A., Ens, W., Standing, K. G., and Duckworth, H. W. (1998) Rapid Commun. Mass Spectrom. 12, 339-344.
20. Otwinowski, Z., and Minor, W. (1997) Methods Enzymol. 276, 307-326.
21. Collaborative Computational Project Number 4 (1994) Acta Crystallogr. D50, 760-763.
22. Yeates, T. O. (1997) Methods Enzymol. 267, 344-358.
23. Brunger, 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., and Warren, G. L. (1998) Acta Crystallogr. D54, 905-921.
24. Jones, T. A., Zhou, J.-Y., Cowan, S. W., and Kjeldgaard, M. (1991) Acta Crystallogr. A47, 110-119.
25. Luzzati, P. V. (1952) Acta Crystallogr. 5, 802-810.
26. Eklund, H. (1989) Biochem. Soc. Trans. 17, 293-296.
27. Eklund, H., Samama, J.-P., Wallen, L., Brändén, C.-I., Aakeson, A., and Jones, T. A. (1981) J. Mol. Biol. 146, 561-587.
28. Parthasarathy, R., and Fridey, S. M. (1984) Science 226, 969-971.
29. Reddy, B. S., Saenger, W., Mühlegger, K., and Weimann, G. (1981) J. Am. Chem. Soc. 103, 907-914.
30. Stura, E. A., Zanotti, G., Babu, Y. S., Sansom, M. S., Stuart, D. I., Wilson, K. S., Johnson, L. N., and Van de Werve, G. (1983) J. Mol. Biol. 170, 529-565.
31. Ko, T. P., Day, J., Malkin, A. J., and McPherson, A. (1999) Acta Crystallogr. D55, 1383-1394.
32. Mesecar, A. D., Stoddard, B. L., and Koshland, D. E., Jr. (1997) Science 277, 202-2066.
33. Eklund, H., and Brändén, C.-I. (1987) in Pyridine nucleotide coenzymes: Chemical, biochemical and medical aspects. (Dolphin, D., Avramovic, O., and Poulson, R., Eds.) pp 51-98, John Wiley and Sons, New York.
34. Danson, M. J., and Weitzman, P. D. J. (1973) Biochem. J. 135, 513-524.
35. Anderson, D. H., and Duckworth, H. W. (1988) J. Biol. Chem. 263, 2163-2169.
36. Talgoy, M. M., and Duckworth, H. W. (1979) Can. J. Biochem. 57, 385-395.
37. Donald, L. J., Crane, B. R., Anderson, D. H., and Duckworth, H. W. (1991) J. Biol. Chem. 266, 20709-20713.
38. Zauhar, R. J., Colbert, C. L., Morgan, R. S., and Welsh, W. J. (2000) Biopolymers 53, 233-248.
39. Weitzman, P. D. J., and Danson, M. J. (1976) Curr. Top. Cell. Regul. 10, 161-204.
40. Kraulis, P. J. (1991) J. Appl. Crystallogr. 24, 946-950.
41. Merritt, E. A., and Bacon, D. J. (1997) Methods Enzymol. 277, 505-524.
42. Nicholls, A., Sharp, K. A., and Honig, B. (1991) Proteins: Struct., Funct., Genet. 11, 281-296.
43. Fukaya, M., Takemura, H., Okumura, H., Kawamura, Y., Horinouchi, S., and Beppu, T. (1990) J. Bacteriol. 172, 2096-2104.
44. Donald, L. J., and Duckworth, H. W. (1987) Biochem. Cell Biol. 65, 930-939.
45. Norman, A. F., Regnery, R., Jameson, P., Greene, C., and Krause, D. C. (1995) J. Clin. Microbiol. 33, 1797-1803.
46. Heinzen, R. A., Frazier, M. E., and Mallavia, L. P. (1991) Gene 109, 63-69.
47. Nierman, W. C., Feldblyum, T. V., Laub, M. T., Paulsen, I. T., Nelson, K. E., Eisen, J., Heidelberg, J. F., Alley, M. R. K., Ohta, N., Maddock, J. R., Potocka, I., Nelson, W. C., Newton, A., Stephens, C., Phadke, N. D., Ely, B., DeBoy, R. T., Dodson, R. J., Durkin, A. S., Gwinn, M. L., Haft, D. H., Kolonay, J. F., Smit, J., Craven, M., Khouri, H., Shetty, J., Berry, K., Utterback, T., Tran, K., Wolf, A., Vamathevan, J., Ermolaeva, M., White, O., Salzberg, S. L., Venter, J. C., Shapiro, L., and Fraser, C. M. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 4136-4141.
48. Parkhill, J., Wren, B. W., Mungall, K., Ketley, J. M., Churcher, C., Basham, D., Chillingworth, T., Davies, R. M., Feltwell, T., Holroyd, S., Jagels, K., Karlyshev, A., Moule, S., Pallen, M. J., Penn, C. W., Quail, M., Rajandream, M. A., Rutherford, K. M., VanVliet, A., Whitehead, S., and Bartell, B. G. (2000) Nature 403, 665-668.
49. Tomb, J. F., White, O., Kerlavage, A. R., Clayton, R. A., Sutton, G. G., Fleischmann, R. D., Ketchum, K. A., Klenk, H. P., Gill, S., Dougherty, B. A., Nelson, K., Quackenbush, J., Zhou, L., Kirkness, E. F., Peterson, S., Loftus, B., Richardson, D., Dodson, R., Khalak, H. G., Glodek, A., McKenney, K., Fitzegerald, L. M., Lee, N., Adams, M. D., Hickey, E. K., Berg, D. E., Gocayne, J. D., Utterback, T. R., Peterson, J. D., Kelley, J. M., Cotton, M. D., Weidman, J. M., Fujii, C., Bowman, C., Watthey, L., Wallin, E., Hayes, W. S., Borodovsky, M., Karp, P. D., Smith, H. O., Fraser, C. M., and Venter, J. C. (1997) Nature 388, 539-547.
50. Kaneko, T., Nakamura, Y., Sato, S., Asamizu, E., Kato, T., Sasamoto, S., Watanabe, A., Idesawa, K., Ishikawa, A., Kawashima, K., Kimura, T., Kishida, Y., Kiyokawa, C., Kohara, M., Matsumoto, M., Matsuno, A., Mochizuki, Y., Nakayama, S., Nakazaki, N., Shimpo, S., Sugimoto, M., Takeuchi, C., Yamada, M., and Tabata, S. (2000) DNA Res. 7, 331-338.
51. Parkhill, J., Achtman, M., James, K. D., Bentley, S. D., Churcher, C., Klee, S. R., Morelli, G., Basham, D., Brown, D., Chillingworth, T., Davies, R. M., Davis, P., Devlin, K., Feltwell, T., Hamlin, N., Holroyd, S., Jagels, K., Leather, S., Moule, S., Mungall, K., Quail, M. A., Rajandream, M. A., Rutherford, K. M., Simmonds, M., Skelton, J., Whitehead, S., Spratt, B. G., and Barrell, B. G. (2000) Nature 404, 502-506.
52. Donald, L. J., Molgat, G. F., and Duckworth, H. W. (1989) J. Bacteriol. 171, 5542-5550.
53. May, B. J., Zhang, Q., Li, L., Paustian, M. L., Whittam, T. S., and Kapur, V. S. (2001) Proc. Natl. Acad. Sci. U.S.A. 98, 3460-3465.
54. Wood, D. O., Atkinson, W. H., Sikorski, R. S., and Winkler, H. H. (1987) J. Bacteriol. 155, 412-416.
55. Pardo, M. A., Lagunez, J., Miranda, J., and Martinez, E. (1994) Mol. Microbiol. 11, 315-321.
56. Mortimer, M. W., McDermott, T. R., York, G. M., Walker, G. C., and Kahn, M. L. (1999) J. Bacteriol. 181, 7608-7613.
57. McClelland, M., Sanderson, K. E., Spieth, J., Clifton, S. W., Latreille, P., Courtney, L., Porwollik, S., Ali, J., Dante, M., Du, F., Hou, S., Layman, D., Leonard, S., Nguyen, C., Scott, K., Holmes, A., Grewal, N., Mulvaney, E., Ryan, E., Sun, H., Florea, L., Miller, W., Stoneking, T., Nhan, M., Waterston, R., and Wilson, R. K. (2001) Nature 413, 852-856.
58. Heidelberg, J. F., Eisen, J. A., Nelson, W. C., Clayton, R. A., Gwinn, M. L., Dodson, R. J., Haft, D. H., Hickey, E. K., Peterson, J. D., Umayam, L., Gill, S. R., Nelson, K. E., Read, T. D., Tettelin, H., Richardson, D., Ermolaeva, M. D., Vamathevan, J., Bass, S., Qin, H., Dragoi, I., Sellers, P., McDonald, L., Utterback, T., Fleishmann, R. D., Nierman, W. C., and White, O. (2000) Nature 406, 477-483.
59. da Silva, A. C., Ferro, J. A., Reinach, F. C., Farah, C. S., Furlan, L. R., Quaggio, R. B., Monteiro-Vitorello, C. B., Van Sluys, M. A., Almeida, N. F., Alves, L. M., do Amaral, A. M., Bertolini, M. C., Camargo, L. E., Camarotte, G., Cannavan, F., Cardozo, J., Chambergo, F., Ciapina, L. P., Cicarelli, R. M., Coutinho, L. L., Cursino-Santos, J. R., El-Dorry, H., Faria, J. B., Ferreira, A. J., Ferreira, R. C., Ferro, M. I., Formighieri, E. F., Franco, M. C., Greggio, C. C., Gruber, A., Katsuyama, A. M., Kishi, L. T., Leite, R. P., Lemos, E. G., Lemos, M. V., Locali, E. C., Machado, M. A., Madeira, A. M., Martinez-Rossi, N. M., Martins, E. C., Meidanis, J., Menck, C. F., Miyaki, C. Y., Moon, D. H., Moreira, L. M., Novo, M. T., Okura, V. K., Oliveira, M. C., Oliveira, V. R., Pereira, H. A., Rossi, A., Sena, J. A., Silva, C., de Souza, R. F., Spinola, L. A., Takita, M. A., Tamura, R. E., Teixeira, E. C., Tezza, R. I., Trindade dos Santos, M., Truffi, D., Tsai, S. M., White, F. F., Setubal, J. C., and Kitajima, J. P. (2002) Nature 417, 459-463.
60. Simpson, A. J., Reinach, F. C., Arruda, P., Abreu, F. A., Acencio, M., Alvarenga, R., Alves, L. M., Araya, J. E., Baia, G. S., Baptista, C. S., Barros, M. H., Bonaccorsi, E. D., Bordin, S., Bove, J. M., Briones, M. R., Bueno, M. R., Camargo, A. A., Camargo, L. E., Carraro, D. M., Carrer, H., Colauto, N. B., Colombo, C., Costa, F. F., Costa, M. C., Costa-Neto, C. M., Coutinho, L. L., Cristofani, M., Dias-Neto, E., Docena, C., El-Dorry, H., Facincani, A. P., Ferreira, A. J., Ferreira, V. C., Ferro, J. A., Fraga, J. S., Franca, S. C., Franco, M. C., Frohme, M., Furlan, L. R., Garnier, M., Goldman, G. H., Goldman, M. H., Gomes, S. L., Gruber, A., Ho, P. L., Hoheisel, J. D., Junqueira, M. L., Kemper, E. L., Kitajima, J. P., and Marino, C. (2000) Nature 406, 151-157.
61. Rault-Leonardon, M., Atkinson, M. A., Slaughter, C. A., Moomaw, C. R., and Srere, P. A. (1995) Biochemistry 34, 257-263.
62. Heinzen, R. A., and Mallavia, L. P. (1987) Infect. Immun. 55, 848-855.
63. Sievers, M., Stockli, M., and Teuber, M. (1997) FEMS Microbiol. Lett. 146, 53-58.
64. Swissa, M., and Benziman, M. (1976) Biochem. J. 153, 173-179.
65. Pitson, S. M., Mendz, G. L., Srinivasan, S., and Hazell, S. L. (1999) Eur. J. Biochem. 260, 258-267.
66. Colby, J., and Zatman, L. J. (1975) Biochem. J. 150, 141-144.
67. Tabrett, C. A., and Copeland, L. (2000) Arch. Microbiol. 173, 42-48.
68. Belova, L. L., Sokolov, A. P., Morgunov, I. G., and Trotsenko, Yu. A. (1997) Biochemistry (Moscow) 62, 71-76.
69. Mothes, G., Rivera, I. S., and Babel, W. (1996) Arch. Microbiol. 166, 405-410.
70. Eidels, L., and Preiss, J. (1970) J. Biol. Chem. 245, 2937-2945.
71. Henderson, R. A., and Jones, C. W. (1997) Arch. Microbiol. 168, 486-492.
72. Phibbs, P. V., and Winkler, H. H. (1982) J. Bacteriol. 149, 718-725.
73. Massarini, E., Higa, A. I., and Cazzulo, J. J. (1976) Experientia 32, 426-428.
74. Borriss, R., and Ohmann, E. (1972) Biochem. Physiol. Pflanz. 163, 328-333.