Solution structures of spinach acyl carrier protein with decanoate and stearate

Biochemistry

Volumn 45, Issue 16, 2006, Pages 5217-5227

  Zornetzer, Gregory A ^a   Fox, Brian G ^a   Markley, John L ^a,b  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b Department of Biochemistry ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; FATTY ACIDS; MOLECULAR STRUCTURE; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; TOPOLOGY;

DECANOATES; DOCKING PROTOCOLS; PHOSPHOPANTETHEINE PROSTHETIC GROUPS; STEARATES;

PROTEINS;

ACYL CARRIER PROTEIN; DECANOIC ACID; FATTY ACID; PANTETHEINE PHOSPHATE; STEARIC ACID;

ARTICLE; BINDING SITE; FATTY ACID METABOLISM; NONHUMAN; NUCLEAR OVERHAUSER EFFECT; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN LIPID INTERACTION; PROTEIN STRUCTURE; SPINACH;

ACYL CARRIER PROTEIN; BINDING SITES; DECANOATES; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PANTETHEINE; PROTEIN STRUCTURE, QUATERNARY; SERINE; SOLUTIONS; SPINACIA OLERACEA; STEARATES;

SPINACIA OLERACEA;

EID: 33645968397     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi052062d     Document Type: Article

References (51)

1. Magnuson, K., Jackowski, S., Rock, C. O., and Cronan, J. E., Jr. (1993) Regulation of fatty acid biosynthesis in Escherlchia colt, Microbiol. Rev. 57, 522-542.
2. Issartel, J., Koronakis, V., and Hughes, C. (1991) Activation of Escherichia-coli prohaemolysin to the mature toxin by acyl carrier protein-dependent fatty acylation, Nature 351, 759-761.
3. Rumley, M., Therisod, H., Weissborn, A., and Kennedy, E. (1992) Mechanisms of regulation of the biosynthesis of membrane-derived oligosaccharides in Escherichia coli, J. Biol. Chem. 267, 11806-11810.
4. Therisod, H., Weissborn, A., and Kennedy, E. (1986) An essential function for acyl carrier protein in the biosynthesis of membrane-derived oligosaccharides of Escherichia coli, Proc. Natl. Acad. Sci. U.S.A. 83, 7236-7240.
5. Shen, B., Summers, R. G., Gramajo, H., Bibb, M. J., and Hutchinson, C. R. (1992) Purification and characterization of the acyl carrier protein of the Streptomyces glaucescens tetracenomycin C polyketide synthase, J. Bacteriol. 174, 3818-3821.
6. Summers, R. G., Ali, A., Shen, B., Wessel, W. A., and Hutchinson, C. R. (1995) Malonyl-coenzyme A:acyl carrier protein acyltransferase of Streptomyces glaucescens: A possible link between fatty acid and polyketide biosynthesis, Biochemistry 34, 9389-9402.
7. 13C-labelling studies, J. Am. Chem. Soc. 116, 2637-2638.
8. Rusnak, F., Sakaitani, M., Drueckhammer, D., Reichert, J., and Walsh, C. T. (1991) Biosynthesis of the Escherichia coli siderophore enterobactin: Sequence of the entF gene, expression and purification of EntF, and analysis of covalent phosphopantetheine, Biochemistry 30, 2916-2927.
9. 9 desaturase, Biochemistry 38, 12833-12840.
10. 9- desaturase: Substrate binding and comparison to ribonucleotide reductase, J. Am. Chem. Soc. 121, 2770-2783.
11. 9 desaturase: Oxidase reactivity during single turnover and implications for the mechanism of desaturation, Biochemistry 37, 14664-14671.
12. 9 stearoyl-acyl carrier protein desaturase from castor seed and its relationship to other di-iron proteins, EMBO J. 15, 4081-4092.
13. Haas, J. A., and Fox, B. G. (2002) Fluorescence anisotropy studies of enzyme-substrate complex formation in stearoyl-ACP desaturase, Biochemistry 41, 14472-14481.
14. Cronan, J, E., Jr. (1982) Molecular properties of short chain acyl thioesters of acyl carrier protein, J. Biol. Chem. 257, 5013-5017.
15. Mayo, K. H., and Prestegard, J. H. (1985) Acyl carrier protein from Escherichia coli. Structural characterization of short-chain acylated acyl carrier proteins by NTMR, Biochemistry 24, 7834-7838.
16. 1H heteronuclear nuclear Overhauser effect studies of the acyl chain-binding site of acyl carrier protein, J. Biol. Chem. 262, 8963-8965.
17. Roujeinikova, A., Baldock, C., Simon, W. J., Gilroy, J., Baker, P. J., Stuitje, A. R., Rice, D. W., Slabas, A. R., and Rafferty, J. B. (2002) X-ray crystallographic studies on butyryl-ACP reveal flexibility of the structure around a putative acyl chain binding site, Structure 10, 825-835.
18. Rock, C. O., and Garwin, J. L. (1979) Preparative enzymatic synthesis and hydrophobic chromatography of acyl-acyl carrier protein, J. Biol. Chem. 254, 7123-7128.
19. Zornetzer, G. A., White, R. D., Markley, J. L., and Fox, B. G. (2005) Preparation of isotopically labeled spinach acyl-acyl carrier protein for NMR structural studies, Protein Expression Purif. (in press).
20. Broadwater, J. A., and Fox, B. G. (1999) Spinach holo-acyl carrier protein: Overproduction and phosphopantetheinylation in Escherichia coli BL21(DE3), in vitro acylation, and enzymatic desaturation of histidine-tagged isoform I, Protein Expression Purif. 15, 314-326.
21. α chemical shifts and protein backbone conformation, J. Am. Chem. Soc. 119, 8070-8075.
22. Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe: A multidimensional spectral processing system based on UNIX pipes, J. Biomol. NMR 6, 277-293.
23. Goddard, T. D., and Kneller, D. G. (2003) SPARKY 3, University of California, San Francisco.
24. Eghbalnia, H. R., Bahrami, A., Wang, L., Assadi, A., and Markley, J. L. (2005) Probabilistic identification of spin systems and their assignments including coil-helix inference as output (PISTA-CHIO), J. Biomol. NMR 32, 219-233.
25. Cornilescu, G., Delaglio, F., and Bax, A. (1999) Protein backbone angle constraints from searching a database for chemical shift and sequence homology, J. Biomol. NMR 13, 289-302.
26. Herrmann, T., Guntert, P., and Wuthrich, K. (2002) Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA, J. Mol. Biol. 319, 209-227.
27. Guntert, P., Mumenthaler, C., and Wuthrich, K. (1997) Torsion angle dynamics for NMR structure calculation with the new program DYANA, J. Mol. Biol. 273, 283-298.
28. Ogura, K., Terasawa, H., and Inagaki, F. (1996) An improved doubled-tuned and isotope-filtered pulse scheme based on a pulsed field gradient and a wide-band inversion shaped pulse, J. Biomol. NMR 8, 492-498.
29. 31P CPMG-correlated experiments for the assignment of nucleic acids, J. Am. Chem. Soc. 123, 11306-11307.
30. Schwieters, C. D., Kuszewski, J. J., Tjandra, N., and Clore, G. M. (2003) The Xplor-NIH NMR molecular structure determination package, J. Magn. Reson. 160, 65-73.
31. Weber, H. P., Craven, B. M., Sawzik, P., and McMullan, R. K. (1991) Crystal structure and thermal vibrations of cholesteryl acetate from neutron diffraction at 123 and 20 K, Acta Crystallogr. B47, 116-127.
32. Shankland, N., Florence, A. J., and Wilson, C. C. (1997) Single-crystal neutron diffraction analysis of anion-cation interactions in perdeuteroacetylcholine bromide at 100 K, Acta Crystallogr. B53, 176-180.
33. Adams, R. D., Huang, M., and Huang, W. (1997) Catalytic ring opening of β-propiothiolactones by dirhenium and dimanganese carbonyl complexes, Organometallics 16, 4479-4485.
34. Kleywegt, G. J., and Jones, T. A. (1998) Databases in protein crystallography, Acta Crystallogr. D54, 1119-1131.
35. Kuszewski, J., Gronenborn, A. M., and Clore, G. M. (1996) Improving the quality of NMR and crystallographic protein structures by means of a conformational database potential derived from structure databases, Protein Sci. 5, 1067-1080.
36. Kuszewski, J., Gronenborn, A. M., and Clore, G. M. (1997) Improvements and extensions in the conformational database potential for the refinement of NMR and X-ray structures of proteins and nucleic acids, J. Magn. Reson. 125, 171-177.
37. Kuszewski, J., and Clore, G. M. (2000) Sources of and solutions to problems in the refinement of protein NMR structures against torsion angle potentials of mean force, J. Magn. Reson. 146, 249-254.
38. Dominguez, C., Boelens, R., and Bonvin, A. M. J. J. (2003) HADDOCK: A protein-protein docking approach based on biochemical or biophysical information, J. Am. Chem. Soc. 125, 1731-1737.
39. Liang, I., Edelsbrunner, H., and Woodward, C. (1998) Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications forligand design, Protein Sci. 7, 1884-1897.
40. Binkowski, T. A., Naghibzadeh, S., and Liang, J. (2003) CASTp: computed atlas of surface topography of proteins, Nucleic Acids Res. 31, 3352-3355.
41. Li, Q., Khosla, C., Puglisi, J. D., and Liu, C. W. (2003) Solution structure and backbone dynamics of the holo form of the frenolicin acyl carrier protein, Biochemistry 42, 4648-4657.
42. Kim, Y., and Prestegard, J. H. (1990) Demonstration of a conformational equilibrium in acyl carrier protein from spinach using rotating frame nuclear magnetic resonance spectroscopy, J. Am. Chem. Soc. 112, 3707-3709.
43. Oswood, M. C., Kim, Y., Ohlrogge, J. B., and Prestegard, J. H. (1997) Structural homology of spinach acyl carrier protein and Escherichia coli acyl carrier protein based on NMR data, Proteins 27, 131-143.
44. Holm, L., and Park, J. (2000) DaliLite workbench for protein structure comparison, Bioinformatics 16, 566-567.
45. Xu, G. Y., Tam, A., Lin, L., Hixon, J., Fritz, C. C., and Powers, R. (2001) Solution structure of B. subtilis acyl carrier protein, Structure 9, 277-287.
46. Wong, H. C., Liu, G., Zhang, Y., Rock, C. O., and Zheng, J. (2002) The solution structure of acyl carrier protein from Mycobacterium tuberculosis, J. Biol. Chem. 277, 15874-15880.
47. Findlow, S. C., Winsor, C., Simpson, T. J., Crosby, J., and Crump, M. P. (2003) Solution structure and dynamics of oxytetracycline polyketide synthase acyl carrier protein from Streptomyces rimosus, Biochemistry 42, 8423-8433.
48. Kim, Y., and Prestegard, J. H. (1990) Refinement of the NMR structures for acyl carrier protein with scalar coupling data, Proteins 8, 377-385.
49. Kim, Y., and Prestegard, J. H. (1989) A dynamic model for the structure of acyl carrier protein in solution, Biochemistry 28, 8792-8797.
50. Pedretti, A., Villa, L., and Vistoli, G. (2002) VEGA: A versatile program to convert, handle and visualize molecular structure on Windows-based PCs, J. Mol. Graphics Modell. 21, 47-49.
51. Heath, R. J., and Rock, C. O. (1996) Inhibition of β-ketoacylacyl carrier protein synthase III (FabH) by acyl-acyl carrier protein in Escherichia coli, J. Biol. Chem. 271, 10996-11000.