Trapping the dynamic acyl carrier protein in fatty acid biosynthesis

Nature

Volumn 505, Issue 7483, 2014, Pages 427-431

  Nguyen, Chi ^a   Haushalter, Robert W ^b   Lee, D John ^b   Markwick, Phineus R L ^b,c,d   Bruegger, Joel ^a   Caldara Festin, Grace ^a   Finzel, Kara ^b   Jackson, David R ^a   Ishikawa, Fumihiro ^b   O'Dowd, Bing ^b   McCammon, J Andrew ^b,d   Opella, Stanley J ^b   Tsai, Shiou Chuan ^a   Burkart, Michael D ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACYL CARRIER PROTEIN; ARGININE; BACTERIAL ENZYME; FABA PROTEIN; FATTY ACID; HOMODIMER; HYDROLYASE; PANTETHEINE PHOSPHATE; UNCLASSIFIED DRUG;

CANCER; CRYSTAL STRUCTURE; ENZYME ACTIVITY; FATTY ACID; INFECTIOUS DISEASE; LIPID; MAGNETIC PROPERTY; METABOLISM; OBESITY; PROTEIN; RESOLUTION; STABILIZATION;

ARTICLE; BINDING SITE; COMPLEX FORMATION; COVALENT BOND; CRYSTAL STRUCTURE; FATTY ACID SYNTHESIS; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN CROSS LINKING; PROTEIN STRUCTURE;

ACYL CARRIER PROTEIN; BINDING SITES; CATALYTIC DOMAIN; CROSS-LINKING REAGENTS; CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; FATTY ACID SYNTHASE, TYPE II; FATTY ACIDS; HISTIDINE; HYDRO-LYASES; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEIN INTERACTION MAPS;

ESCHERICHIA COLI;

EID: 84892573703     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature12810     Document Type: Article

References (30)

1. Chan, D. I. & Vogel, H. J. Current understanding of fatty acid biosynthesis and the acyl carrier protein. Biochem. J. 430, 1-19 (2010)
2. Rock, C. O. & Cronan, J. E., Jr. Acyl carrier protein from Escherichia coli. Methods Enzymol. 71, 341-351 (1981)
3. Crosby, J. & Crump, M. P. The structural role of the carrier protein-active controller or passive carrier. Nat. Prod. Rep. 29, 1111-1137 (2012)
4. Magnuson, K., Jackowski, S., Rock, C. O. & Cronan, J. E., Jr. Regulation of fatty acid biosynthesis in Escherichia coli. Microbiol. Rev. 57, 522-542 (1993)
5. Joshi, A. K., Witkowski, A., Berman, H. A., Zhang, L.&Smith, S. Effect ofmodification of the length and flexibility of the acyl carrier protein-thioesterase interdomain linker on functionality of the animal fatty acid synthase. Biochemistry 44, 4100-4107 (2005)
6. Issartel, J. P., Koronakis, V. & Hughes, C. Activation of Escherichia coli prohaemolysin to the mature toxin by acyl carrier protein-dependent fatty acylation. Nature 351, 759-761 (1991)
7. Agarwal, V., Lin, S., Lukk, T., Nair, S. K. & Cronan, J. E., Jr. Structure of the enzymeacyl carrier protein (ACP) substrate gatekeeper complex required for biotin synthesis. Proc. Natl Acad. Sci. USA 109, 17406-17411 (2012)
8. Anderson, M. S., Bulawa, C. E. & Raetz, C. R. The biosynthesis of gram-negative endotoxin. Formation of lipid A precursors from UDP-GlcNAc in extracts of Escherichia coli. J. Biol. Chem. 260, 15536-15541 (1985)
9. Jordan, S. W. & Cronan, J. E., Jr. A new metabolic link. The acyl carrier protein of lipid synthesis donates lipoic acid to the pyruvate dehydrogenase complex in Escherichia coli and mitochondria. J. Biol. Chem. 272, 17903-17906 (1997)
10. Lu, Y. J. et al. Acyl-phosphates initiatemembrane phospholipid synthesis in Grampositive pathogens. Mol. Cell 23, 765-772 (2006)
11. Roujeinikova, A. et al. Crystallizationand preliminary X-ray crystallographic studies on acyl-(acyl carrier protein) from Escherichia coli. Acta Crystallogr. D 58, 330-332 (2002)
12. Leibundgut, M., Jenni, S., Frick, C. & Ban, N. Structural basis for substrate delivery by acyl carrier protein in the yeast fatty acid synthase. Science 316, 288-290 (2007)
13. Roujeinikova, A. et al. Structural studies of fatty acyl-(acyl carrier protein) thioesters reveal a hydrophobic binding cavity that can expand to fit longer substrates. J.Mol. Biol. 365, 135-145 (2007)
14. Meier, J. L.& Burkart, M. D. The chemical biology ofmodular biosynthetic enzymes. Chem. Soc. Rev. 38, 2012-2045 (2009)
15. Ishikawa, F., Haushalter, R. W. & Burkart, M. D. Dehydratase-specific probes for fatty acid and polyketide synthases. J. Am. Chem. Soc. 134, 769-772 (2012)
16. Endo, K., Helmkamp, G. M. Jr & Bloch, K. Mode of inhibition of b-hydroxydecanoyl thioester dehydrase by 3-decynoyl-N-acetylcysteamine. J. Biol. Chem. 245, 4293-4296 (1970)
17. Leesong, M., Henderson, B. S., Gillig, J. R., Schwab, J. M. & Smith, J. L. Structure of a dehydratase-isomerase from the bacterial pathway for biosynthesis of unsaturated fatty acids: two catalytic activities in one active site. Structure 4, 253-264 (1996)
18. Zhuang, Z. et al. Divergence of function in the hot dog fold enzymesuperfamily: the bacterial thioesterase YciA. Biochemistry 47, 2789-2796 (2008)
19. Moynié, L. et al. Structural insights into the mechanism and inhibition of the b-hydroxydecanoyl-acyl carrier protein dehydratase from Pseudomonas aeruginosa. J. Mol. Biol. 425, 365-377 (2013)
20. Guy, J. E. et al. Remote control of regioselectivity in acyl-acyl carrier proteindesaturases. Proc. Natl Acad. Sci. USA 108, 16594-16599 (2011)
21. Parris, K. D. et al. Crystal structures of substrate binding to Bacillus subtilis holo- (acyl carrier protein) synthase reveal a novel trimeric arrangement of molecules resulting in three active sites. Structure 8, 883-895 (2000)
22. Cryle, M. J. & Schlichting, I. Structural insights from a P450 Carrier Protein complex reveal how specificity is achieved in the P450(BioI) ACP complex. Proc. Natl Acad. Sci. USA 105, 15696-15701 (2008)
23. Babu, M. et al. Structure of a SLC26 anion transporter STAS domain in complex with acyl carrier protein: implications for E. coli YchM in fatty acid metabolism. Structure 18, 1450-1462 (2010)
24. Qiu, X. & Janson, C. A. Structure of apo acyl carrier protein and a proposal to engineer protein crystallization through metal ions. Acta Crystallogr. D 60, 1545-1554 (2004)
25. Salzmann, M., Pervushin, K., Wider, G., Senn, H. & Wuthrich, K. TROSY in tripleresonance experiments: newperspectives for sequentialNMRassignment of large proteins. Proc. Natl Acad. Sci. USA 95, 13585-13590 (1998)
26. Hansen, M. R., Mueller, L. & Pardi, A. Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions. Nature Struct. Biol. 5, 1065-1074 (1998)
27. Markwick, P. R. L. & McCammon, J. A. Studying functional dynamics in biomolecules using accelerated molecular dynamics. Phys. Chem. Chem. Phys. 13, 20053-20065 (2011)
28. Markwick, P. R. et al. Toward a unified representation of protein structural dynamics in solution. J. Am. Chem. Soc. 131, 16968-16975 (2009)
29. Frueh, D. P. et al. Dynamic thiolation-thioesterase structure of a non-ribosomal peptide synthetase. Nature 454, 903-906 (2008)
30. Alekseyev, V. Y., Liu, C. W., Cane, D. E., Puglisi, J. D. & Khosla, C. Solution structure and proposed domain-domain recognition interface of an acyl carrier protein domain from a modular polyketide synthase. Protein Sci. 16, 2093-2107 (2007).