Identification of the citrate-binding site of human ATP-citrate lyase using X-ray crystallography

Journal of Biological Chemistry

Volumn 285, Issue 35, 2010, Pages 27418-27428

  Sun, Tianjun ^a,b   Hayakawa, Koto ^a   Bateman, Katherine S ^a   Fraser, Marie E ^a  

^a UNIVERSITY OF CALGARY   (Canada)

^b UNIVERSITY OF ALBERTA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ACETYL-COA; ACYL-COA SYNTHETASE; AMINO ACID PROTEINS; ATP-BINDING SITE; ATP-CITRATE LYASE; CARBOXYL GROUPS; CATALYTIC MECHANISMS; CYTOPLASMIC ENZYMES; ENERGY METABOLISM; IN-SITU; NUCLEOTIDE-BINDING SITES; SALT BRIDGES; STEREOSPECIFICITY; SYNTHETASES; TWO DOMAINS;

AMINO ACIDS; CARBOHYDRATES; CARBOXYLATION; CRYSTAL STRUCTURE; CRYSTALS; FATTY ACIDS; HYDROGEN BONDS; METABOLISM; ORGANIC ACIDS; PROTEOLYSIS; SUBSTRATES; X RAY CRYSTALLOGRAPHY;

BINDING ENERGY;

ADENOSINE TRIPHOSPHATE CITRATE LYASE; CARBOXYL GROUP; CITRIC ACID; HYDROXYL GROUP; TARTARIC ACID;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CONTROLLED STUDY; CRYSTAL STRUCTURE; DISSOCIATION CONSTANT; DISULFIDE BOND; ENTHALPY; ENZYME CONFORMATION; ENZYME STRUCTURE; ENZYME SUBSTRATE; ENZYME SUBSTRATE COMPLEX; HYDROGEN BOND; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; SEQUENCE ALIGNMENT; STEREOSPECIFICITY; X RAY CRYSTALLOGRAPHY; X RAY DIFFRACTION;

ADENOSINE TRIPHOSPHATE; ATP CITRATE (PRO-S)-LYASE; BINDING SITES; CATALYSIS; COENZYME A; CRYSTALLOGRAPHY, X-RAY; CYTOPLASM; HUMANS; STRUCTURE-ACTIVITY RELATIONSHIP; TARTRATES;

EID: 77956244445     PISSN: 00219258     EISSN: 1083351X     Source Type: Journal    
DOI: 10.1074/jbc.M109.078667     Document Type: Article

References (62)

1. Srere, P. A., and Lipmann, F. (1953) J. Am. Chem. Soc. 75, 4874
2. Wellen, K. E., Hatzivassiliou, G., Sachdeva, U. M., Bui, T. V., Cross, J. R., and Thompson, C. B. (2009) Science 324, 1076-1080
3. Beigneux, A. P., Kosinski, C., Gavino, B., Horton, J. D., Skarnes, W. C., and Young, S. G. (2004) J. Biol. Chem. 279, 9557-9564
4. Kaufman, S. (1953) Fed. Proc. 12, 704-708
5. Cottam, G. L., and Srere, P. A. (1969) Arch. Biochem. Biophys. 130, 304-311
6. Inoue, H., Suzuki, F., Tanioka, H., and Takeda, Y. (1967) Biochem. Biophys. Res. Commun. 26, 602-608
7. Wells, T. N. (1991) Eur. J. Biochem. 199, 163-168
8. Sánchez, L. B., Galperin, M. Y., and Müller, M. (2000) J. Biol. Chem. 275, 5794-5803
9. Wolodko, W. T., Fraser, M. E., James, M. N., and Bridger, W. A. (1994) J. Biol. Chem. 269, 10883-10890
10. Murzin, A. G. (1996) Curr. Opin. Struct. Biol. 6, 386-394
11. Joyce, M. A., Fraser, M. E., Brownie, E. R., James, M. N., Bridger, W. A., and Wolodko, W. T. (1999) Biochemistry 38, 7273-7283
12. Joyce, M. A., Fraser, M. E., James, M. N., Bridger, W. A., and Wolodko, W. T. (2000) Biochemistry 39, 17-25
13. Fraser, M. E., James, M. N., Bridger, W. A., and Wolodko, W. T. (2000) J. Mol. Biol. 299, 1325-1339
14. Fraser, M. E., Hayakawa, K., Hume, M. S., Ryan, D. G., and Brownie, E. R. (2006) J. Biol. Chem. 281, 11058-11065
15. Elshourbagy, N. A., Near, J. C., Kmetz, P. J., Wells, T. N., Groot, P. H., Saxty, B. A., Hughes, S. A., Franklin, M., and Gloger, I. S. (1992) Eur. J. Biochem. 204, 491-499
16. Pierce, M. W., Palmer, J. L., Keutmann, H. T., and Avruch, J. (1981) J. Biol. Chem. 256, 8867-8870
17. Ramakrishna, S., D'Angelo, G., and Benjamin, W. B. (1990) Biochemistry 29, 7617-7624
18. Berwick, D. C., Hers, I., Heesom, K. J., Moule, S. K., and Tavare, J. M. (2002) J. Biol. Chem. 277, 33895-33900
19. Altschul, S. F., Madden, T. L., Schäffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997) Nucleic Acids Res. 25, 3389-3402
20. Groot, P. H., Pearce, N. J., and Gribble, A. D. (2003) Curr. Med. Chem. Immun. Endocrin. Metab. Agents 3, 211-217
21. Clapham, J. C., and Arch, J. R. (2007) Diabetes Obes. Metab. 9, 259-275
22. Bauer, D. E., Hatzivassiliou, G., Zhao, F., Andreadis, C., and Thompson, C. B. (2005) Oncogene 24, 6314-6322
23. Hatzivassiliou, G., Zhao, F., Bauer, D. E., Andreadis, C., Shaw, A. N., Dhanak, D., Hingorani, S. R., Tuveson, D. A., and Thompson, C. B. (2005) Cancer Cell 8, 311-321
24. Garber, K. (2006) Science 312, 1158-1159
25. Migita, T., Narita, T., Nomura, K., Miyagi, E., Inazuka, F., Matsuura, M., Ushijima, M., Mashima, T., Seimiya, H., Satoh, Y., Okumura, S., Nakagawa, K., and Ishikawa, Y. (2008) Cancer Res. 68, 8547-8554
26. Potapova, I. A., El-Maghrabi, M. R., Doronin, S. V., and Benjamin, W. B. (2000) Biochemistry 39, 1169-1179
27. Sambrook, J., and Russell, D. W. (2001) Molecular Cloning: A Laboratory Manual, 3rd Ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
28. Deng, J., Davies, D. R., Wisedchaisri, G., Wu, M., Hol, W. G., and Mehlin, C. (2004) Acta Crystallogr. D Biol. Crystallogr. 60, 203-204
29. Dong, A., Xu, X., Edwards, A. M., Chang, C., Chruszcz, M., Cuff, M., Cymborowski, M., Di Leo, R., Egorova, O., Evdokimova, E., Filippova, E., Gu, J., Guthrie, J., Ignatchenko, A., Joachimiak, A., Klostermann, N., Kim, Y., Korniyenko, Y., Minor, W., Que, Q., Savchenko, A., Skarina, T., Tan, K., Yakunin, A., Yee, A., Yim, V., Zhang, R., Zheng, H., Akutsu, M., Arrowsmith, C., Avvakumov, G. V., Bochkarev, A., Dahlgren, L. G., Dhe-Paganon, S., Dimov, S., Dombrovski, L., Finerty, P., Jr., Flodin, S., Flores, A., Graslund, S., Hammerstrom, M., Herman, M. D., Hong, B. S., Hui, R., Johansson, I., Liu, Y., Nilsson, M., Nedyalkova, L., Nordlund, P., Nyman, T., Min, J., Ouyang, H., Park, H. W., Qi, C., Rabeh, W., Shen, L., Shen, Y., Sukumard, D., Tempel, W., Tong, Y., Tresagues, L., Vedadi, M., Walker, J. R., Weigelt, J., Welin, M., Wu, H., Xiao, T., Zeng, H., and Zhu, H. (2007) Nat. Methods 4, 1019-1021
30. Traini, M., Gooley, A. A., Ou, K., Wilkins, M. R., Tonella, L., Sanchez, J. C., Hochstrasser, D. F., and Williams, K. L. (1998) Electrophoresis 19, 1941-1949
31. Bateman, K. S., Brownie, E. R., Wolodko, W. T., and Fraser, M. E. (2002) Biochemistry 41, 14455-14462
32. Doublié, S. (1997) Methods Enzymol. 276, 523-530
33. Holton, J., and Alber, T. (2004) Proc. Natl. Acad. Sci. U.S.A. 101, 1537-1542
34. Leslie, A. G. (1992) Joint CCP4 + ESF-EAMCB Newsletter on Protein Crystallography, No. 26
35. Collaborative Computational Project, No. 4 (1994) Acta Crystallogr. Sect. D 50, 760-763
36. Matthews, B. W. (1968) J. Mol. Biol. 33, 491-497
37. Kantardjieff, K. A., and Rupp, B. (2003) Protein Sci. 12, 1865-1871
38. Adams, P. D., Afonine, P. V., Bunkoczi, G., Chen, V. B., Davis, I. W., Echols, N., Headd, J. J., Hung, L.-W., Kapral, G. J., Grosse-Kunstleve, R. W., McCoy, A. J., Moriarty, N. W., Oeffner, R., Read, R. J., Richardson, D. C., Richardson, J. S., Terwilliger, T. C., and Zwart, P. H. (2010) Acta Crystallogr. D Biol. Crystallogr. 66, 213-221
39. McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C., and Read, R. J. (2005) Acta Crystallogr. D Biol. Crystallogr. 61, 458-464
40. 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
41. Emsley, P., Lohkamp, B., Scott, W. G., and Cowtan, K. (2010) Acta Crystallogr. D Biol. Crystallogr. 66, 486-501
42. Laskowski, R. A., MacArthur, M. W., Moss, D. S., and Thornton, J. M. (1993) J. Appl. Crystallogr. 26, 283-291
43. Davis, I. W., Leaver-Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., Murray, L. W., Arendall, W. B., 3rd, Snoeyink, J., Richardson, J. S., and Richardson, D. C. (2007) Nucleic Acids Res. 35, W375-W383, web server issue
44. Guex, N., and Peitsch, M. C. (1997) Electrophoresis 18, 2714-2723
45. Jones, T. A., Zou, J.-Y., Cowan, S. W., and Kjeldgaard, M. (1991) Acta Crystallogr. A 47, 110-119
46. Inoue, H., Suzuki, F., Fukunishi, K., Adachi, K., and Takeda, Y. (1966) J. Biochem. 60, 543-553
47. Clauser, K. R., Baker, P., and Burlingame, A. L. (1999) Anal. Chem. 71, 2871-2882
48. Hanson, K. R. (1966) J. Am. Chem. Soc. 88, 2731-2742
49. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J., and Higgins, D. G. (2007) Bioinformatics 23, 2947-2948
50. Deleted in proof
51. Deleted in proof
52. Fatland, B. L., Ke, J., Anderson, M. D., Mentzen, W. I., Cui, L. W., Allred, C. C., Johnston, J. L., Nikolau, B. J., and Wurtele, E. S. (2002) Plant Physiol. 130, 740-756
53. Kim, W., and Tabita, F. R. (2006) J. Bacteriol. 188, 6544-6552
54. Singh, M., Richards, E. G., Mukherjee, A., and Srere, P. A. (1976) J. Biol. Chem. 251, 5242-5250
55. Rao, S. T., and Rossmann, M. G. (1973) J. Mol. Biol. 76, 241-256
56. Dalle-Donne, I., Rossi, R., Colombo, G., Giustarini, D., and Milzani, A. (2009) Trends Biochem. Sci. 34, 85-96
57. Srere, P. A., and Bhaduri, A. (1964) J. Biol. Chem. 239, 714-718
58. Aoshima, M., Ishii, M., and Igarashi, Y. (2004) Mol. Microbiol. 52, 751-761
59. Fraser, M. E., James, M. N., Bridger, W. A., and Wolodko, W. T. (1999) J. Mol. Biol. 285, 1633-1653
60. Sanadi, D. R., Gibson, D. M., Ayengar, P., and Jacob, M. (1956) J. Biol. Chem. 218, 505-520
61. Weitzman, P. D. J. (1981) Adv. Microb. Physiol. 22, 185-244
62. DeLano, W. L. (2002) The PyMOL Molecular Graphics System, DeLano Scientific LLC, San Carlos, CA