Crystal structure of the β-subunit of acyl-CoA carboxylase: Structure-based engineering of substrate specificity

Biochemistry

Volumn 43, Issue 44, 2004, Pages 14027-14036

  Diacovich, Lautaro ^a   Mitchell, Deborah Lynn ^c   Pham, Huy ^c   Gago, Gabriela ^a   Melgar, Melrose Mendoza ^c   Khosla, Chaitan ^b   Gramajo, Hugo ^a   Tsai, Shiou Chuan ^c  

^a UNIVERSIDAD NACIONAL DE ROSARIO   (Argentina)

^b STANFORD UNIVERSITY   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACYLATION; BIOMEDICAL ENGINEERING; CATALYSIS; DIMERS; HYDROPHOBICITY; SUBSTRATES;

HEXAMERS; THERAPEUTIC PROPERTY;

CRYSTAL STRUCTURE;

ACETYL COENZYME A CARBOXYLASE; ACETYL COENZYME A CARBOXYLASE BETA; BIOTIN; PROPIONYL COENZYME A; PROPIONYL COENZYME A CARBOXYLASE; UNCLASSIFIED DRUG;

ARTICLE; BINDING SITE; CATALYSIS; CRYSTAL STRUCTURE; ENZYME SPECIFICITY; ENZYME STABILITY; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SEQUENCE ALIGNMENT;

ACETYL COENZYME A; ACYL COENZYME A; AMINO ACID SEQUENCE; BINDING SITES; CARBON-CARBON LIGASES; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; ELECTROSTATICS; METHYLMALONYL-COA DECARBOXYLASE; MOLECULAR SEQUENCE DATA; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN SUBUNITS; PROTEIN TRANSPORT; STREPTOMYCES COELICOLOR; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; SURFACE PROPERTIES;

STREPTOMYCES; STREPTOMYCES COELICOLOR;

EID: 8344220571     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi049065v     Document Type: Article

References (34)

1. Dakshinamurti, K., and Chauhan, J. (1988) Regulation of biotin enzymes, Annu. Rev. Nutr. 8, 211-233.
2. Cronan, J. E., Jr., and Waldrop, G. L. (2002) Multi-subunit acetyl-CoA carboxylases, Prog. Lipid Res. 41, 407-435.
3. Cane, D. E., Walsh, C. T., and Khosla, C. (1998) Harnessing the biosynthetic code: combinations, permutations, and mutations, Science 282, 63-68.
4. Milgraum, L. Z., Witters, L. A., Pasternack, G. R., and Kuhajda, F. P. (1997) Enzymes of the fatty acid synthesis pathway are highly expressed in in situ breast carcinoma, Clin. Cancer Res. 3, 2115-2120.
5. Pacheco-Alvarez, D., Solorzano-Vargas, R. S., and Del Rio, A. L. (2002) Biotin in metabolism and its relationship to human disease, Arch. Med. Res. 33, 439-447.
6. Witters, L. A., Widmer, J., King, A. N., Fassihi, K., and Kuhajda, F. (1994) Identification of human acetyl-CoA carboxylase isozymes in tissue and in breast cancer cells, Int. J. Biochem. 26, 589-594.
7. Mandrup, S., Loftus, T. M., MacDougald, O. A., Kuhajda, F. P., and Lane, M. D. (1997) Obese gene expression at in vivo levels by fat pads derived from s.c. implanted 3T3-F442A preadipocytes, Proc. Natl. Acad. Sci. U.S.A. 94, 4300-4305.
8. Pizer, E. S., Thupari, J., Han, W. F., Pinn, M. L., Chrest, F. J., Frehywot, G. L., Townsend, C. A., and Kuhajda, F. P. (2000) Malonyl-coenzyme-A is a potential mediator of cytotoxicity induced by fatty-acid synthase inhibition in human breast cancer cells and xenografts, Cancer Res. 60, 213-218.
9. Levert, K. L., Waldrop, G. L., and Stephens, J. M. (2002) A biotin analog inhibits acetyl-CoA carboxylase activity and adipogenesis, J. Biol. Chem. 277, 16347-16350.
10. Diacovich, L., Peiru, S., Kurth, D., Rodriguez, E., Podesta, F., Khosla, C., and Gramajo, H. (2002) Kinetic and structural analysis of a new group of Acyl-CoA carboxylases found in Streptomyces coelicolor A3(2), J. Biol. Chem. 277, 31228-31236.
11. Haase, F. C., Beegen, H., and Allen, S. H. (1984) Propionyl-coenzyme A carboxylase of Mycobacterium smegmatis. An electron microscopic study, Eur. J. Biochem. 140, 147-151.
12. Hunaiti, A. R., and Kolattukudy, P. E. (1982) Isolation and characterization of an acyl-coenzyme A carboxylase from an erythromycin- producing Streptomyces erythreus, Arch. Biochem. Biophys. 216, 362-371.
13. Kimura, Y., Kojyo, T., Kimura, I., and Sato, M. (1998) Propionyl-CoA carboxylase of Myxococcus xanthus: catalytic properties and function in developing cells, Arch. Microbiol. 170, 179-184.
14. Rodriguez, E., Banchio, C., Diacovich, L., Bibb, M. J., and Gramajo, H. (2001) Role of an essential acyl coenzyme A carboxylase in the primary and secondary metabolism of Streptomyces coelicolor A3(2), Appl. Environ. Microbiol. 67, 4166-4176.
15. Rodriguez, E., and Gramajo, H. (1999) Genetic and biochemical characterization of the α and β components of a propionyl-CoA carboxylase complex of Streptomyces coelicolor A3(2), Microbiology 145 (Part 11), 3109-3119.
16. Pfeifer, B. A., Admiraal, S. J., Gramajo, H., Cane, D. E., and Khosla, C. (2001) Biosynthesis of complex polyketides in a metabolically engineered strain of E. coli, Science 291, 1790-1792.
17. Jitrapakdee, S., and Wallace, J. C. (2003) The biotin enzyme family: conserved structural motifs and domain rearrangements, Curr. Protein Pept. Sci. 4, 217-229.
18. Zhang, H., Yang, Z., Shen, Y., and Tong, L. (2003) Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase, Science 299, 2064-2067.
19. Wendt, K. S., Schall, I., Huber, R., Buckel, W., and Jacob, U. (2003) Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase, EMBO J. 22, 3493-3502.
20. Hall, P. R., Wang, Y. F., Rivera-Hainaj, R. E., Zheng, X., Pustai-Carey, M., Carey, P. R., and Yee, V. C. (2003) Transcarboxylase 12S crystal structure: hexamer assembly and substrate binding to a multienzyme core, EMBO J. 22, 2334-2347.
21. Holden, H. M., Henning, M. M., Haller, T., and Gerlt, J. A. (2001) The crotonase superfamily: divergently related enzymes that catalyze different reactions involving acyl coenzyme a thioesters, Acc. Chem. Res. 34, 145-157.
22. Benning, M. M., Taylor, K. L., Liu, R. Q., Yang, G., Xiang, H., Wesenberg, G., Dunaway-Mariano, D., and Holden, H. M. (1996) Structure of 4-chlorobenzoyl coenzyme A dehalogenase determined to 1.8 Å resolution: an enzyme catalyst generated via adaptive mutation, Biochemistry 35, 8103-8109.
23. Benning, M. M., Haller, T., Gerlt, J. A., and Holden, H. M. (2000) New reactions in the crotonase superfamily: structure of methylmalonyl CoA decarboxylase from Escherichia coli, Biochemistry 39, 4630-4639.
24. Bahnson, B. J., Anderson, V. E., and Petsko, G. A. (2002) Structural mechanism of enoyl-CoA hydratase: three atoms from a single water are added in either an E1cb stepwise or concerted fashion, Biochemistry 41, 2621-2629.
25. Modis, Y., Filppula, S. A., Novikov, D. K., Norledge, B., Hiltunen, J. K., and Wierenga, R. K. (1998) The crystal structure of dienoyl-CoA isomerase at 1.5 Å resolution reveals the importance of aspartate and glutamate side chains for catalysis, Structure 6, 957-970.
26. Otwinoswski, Z., and Minor, W. (1997) Processing of X-ray Diffraction Data Collected in Oscillation Mode, Methods Enzymol. 276, 307-326.
27. 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) Crystallography & NMR system: A new software suite for macromolecular structure determination, Acta Crystallogr. D54 (Part 5), 905-921.
28. Schwede, T., Kopp, J., Guex, N., and Peitsch, M. C. (2003) SWISS-MODEL: An automated protein homology-modeling server, Nucleic Acids Res. 31, 3381-3385.
29. Knowles, J. R. (1989) The mechanism of biotin-dependent enzymes, Annu. Rev. Biochem. 58, 195-221.
30. Lindqvist, Y., and Schneider, G. (1996) Protein-biotin interactions, Curr. Opin. Struct. Biol. 6, 798-803.
31. Yong-Biao, J., Islam, M. N., Sueda, S., and Kondo, H. (2004) Identification of the catalytic residues involved in the carboxyl transfer of pyruvate carboxylase, Biochemistry 43, 5912-5920.
32. Cronan, J. E., Jr. (2001) The biotinyl domain of Escherichia coli acetyl-CoA carboxylase. Evidence that the "thumb" structure is essential and that the domain functions as a dimer, J. Biol. Chem. 276, 37355-37364.
33. Smith, G. R., and Sternberg, M. J. (2003) Evaluation of the 3D-Dock protein docking suite in rounds 1 and 2 of the CAPRI blind trial, Proteins 52, 74-79.
34. Blanchard, C. Z., and Waldrop, G. L. (1998) Overexpression and kinetic characterization of the carboxyltransferase component of acetyl-CoA carboxylase, J. Biol. Chem. 273, 19140-19145.