Molecular recognition between ketosynthase and acyl carrier protein domains of the 6-deoxyerythronolide B synthase

Proceedings of the National Academy of Sciences of the United States of America

Volumn 107, Issue 51, 2010, Pages 22066-22071

  Kapur, Shiven ^a   Chen, Alice Y ^b   Cane, David E ^a   Khosla, Chaitan ^a,b,c  

^a STANFORD UNIVERSITY   (United States)

^b Stanford University   (United States)

^c BROWN UNIVERSITY   (United States)

Author keywords

Assembly line enzymes; Polyketide synthase; Protein protein interactions

Indexed keywords

6 DEOXYERYTHRONOLIDE B SYNTHASE; ACYL CARRIER PROTEIN; EPITOPE; ERYTHRONOLIDE DERIVATIVE; KETOSYNTHASE; PEPTIDE SYNTHASE; POLYKETIDE SYNTHASE; SYNTHETASE; UNCLASSIFIED DRUG;

ARTICLE; CATALYSIS; ENZYMOLOGY; EXPERIMENTAL DESIGN; MUTAGENESIS; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN INTERACTION;

ACYL CARRIER PROTEIN; BACTERIAL PROTEINS; ERYTHROMYCIN; POLYKETIDE SYNTHASES; PROTEIN STRUCTURE, TERTIARY;

EID: 78650660868     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1014081107     Document Type: Article

References (44)

1. Khosla C, Tang Y, Chen AY, Schnarr NA, Cane DE (2007) Structure and mechanism of the 6-deoxyerythronolide B synthase. Annu Rev Biochem 76:195-221.
2. Weissman KJ, Leadlay PF (2005) Combinatorial biosynthesis of reduced polyketides. Nat Rev Microbiol 3:925-936.
3. Wenzel SC, Muller R (2005) Formation of novel secondary metabolites by bacterial multimodular assembly lines: Deviations from textbook biosynthetic logic. Curr Opin Chem Biol 9:447-458.
4. McDaniel R, Welch M, Hutchinson CR (2005) Genetic approaches to polyketide antibiotics. 1. Chem Rev 105:543-558.
5. Hill AM (2006) The biosynthesis, molecular genetics, and enzymology of the polyke-tide-derived metabolites. Nat Prod Rep 23:256-320.
6. Fischbach MA, Walsh CT (2006) Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: Logic, machinery, and mechanisms. Chem Rev 106:3468-3496.
7. Wu N, Tsuji SY, Cane DE, Khosla C (2001) Assessing the balance between protein-protein interactions and enzyme-substrate interactions in the channeling of intermediates between polyketide synthase modules. J Am Chem Soc 123:6465-6474.
8. Wu N, Cane DE, Khosla C (2002) Quantitative analysis of the relative contributions of donoracyl carrierproteins, acceptorketosynthases, andlinkerregionstointermodular transfer of intermediates in hybrid polyketide synthases. Biochemistry 41:5056-5066.
9. Chen AY, Schnarr NA, Kim CY, Cane DE, Khosla C (2006) Extender unit and acyl carrier protein specificity of ketosynthase domains of the 6-deoxyerythronolide B synthase. J Am Chem Soc 128:3067-3074.
10. Kim CY, et al. (2004) Reconstituting modular activity from separated domains of 6-deoxyerythronolide B synthase. Biochemistry 43:13892-13898.
11. Weissman KJ, Muller R (2008) Protein-protein interactions in multienzyme mega-synthetases. ChemBioChem 9:826-848.
12. Zhang YM, Marrakchi H, White SW, Rock CO (2003) The application of computational methods to explore the diversity and structure of bacterial fatty acid synthase. J Lipid Res 44:1-10.
13. Weissman KJ, Hong H, Popovic B, Meersman F (2006) Evidence for a protein-protein interaction motif on an acyl carrier protein domain from a modular polyketide synthase. Chem Biol 13:625-636.
14. Parris KD, et al. (2000) 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.
15. Zhang YM, et al. (2001) Identification and analysis of the acyl carrier protein (ACP) docking site on beta-ketoacyl-ACP synthase III. J Biol Chem 276:8231-8238.
16. Zhang YM, Wu B, Zheng J, Rock CO (2003) Key residues responsible for acyl carrier protein and beta-ketoacyl-acyl carrier protein reductase (FabG) interaction. J Biol Chem 278:52935-52943.
17. Rafi S, et al. (2006) Structure of acyl carrier protein bound to FabI, the FASII enoyl reductase from Escherichia coli. J Biol Chem 281:39285-39293.
18. Leibundgut M, Jenni S, Frick C, Ban N (2007) Structural basis for substrate deliveryby acyl carrier protein in the yeast fatty acid synthase. Science 316:288-290.
19. Alekseyev VY, Liu CW, Cane DE, Puglisi JD, Khosla C (2007) Solution structure and proposeddomain domain recognition interfaceofan acyl carrierprotein domain from a modular polyketide synthase. Protein Sci 16:2093-2107.
20. Tang Y, KimCY, Mathews II, Cane DE, Khosla C (2006) The 2.7-angstromcrystal structure of a 194-kDa homodimeric fragment of the 6-deoxyerythronolide B synthase. Proc Natl Acad Sci USA 103:11124-11129.
21. Wong FT, Chen AY, Cane DE, Khosla C (2010) Protein-protein recognition between acyltransferases and acyl carrier proteins in multimodular polyketide synthases. Biochemistry 49:95-102.
22. Kapur S, et al. (2008) Mechanism based protein crosslinking of domains from the 6-deoxyerythronolide B synthase. Bioorg Med Chem Lett 18:3034-3038.
23. Wu S, Skolnick J, Zhang Y (2007) Ab initio modeling of small proteins by iterative TASSER simulations. BMC Biol 5:17.
24. Zhang Y (2008) I-TASSER server for protein 3D structure prediction. BMC Bioinformatics 9:40.
25. Tang Y, Lee TS, Kobayashi S, Khosla C (2003) Ketosynthases in the initiation and elongation modules of aromatic polyketide synthases have orthogonal acyl carrier protein specificity. Biochemistry 42:6588-6595.
26. Duhovny D, Nussinov R, Wolfson HJ (2002) Proceedings of the Second International Workshop, WABI2002 Rome, Italy, September 17-21, 2002. Lecture Notes in Computer Science, eds R Guigó and D Gusfield (Springer, Berlin), 2452, pp 185-200.
27. Schneidman-Duhovny D, Inbar Y, Nussinov R, Wolfson HJ (2005) PatchDock and Symm-Dock: Servers for rigid and symmetric docking. Nucleic Acids Res 33:W363-367.
28. Andrusier N, Nussinov R, Wolfson HJ (2007) FireDock: Fast interaction refinement in molecular docking. Proteins 69:139-159.
29. Mashiach E, Schneidman-Duhovny D, Andrusier N, Nussinov R, Wolfson HJ (2008) FireDock: A web server for fast interaction refinement in molecular docking. Nucleic Acids Res 36:W229-232.
30. Kao CM, Pieper R, Cane DE, Khosla C (1996) Evidence for two catalytically independent clusters of active sites in a functional modular polyketide synthase. Biochemistry 35:12363-12368.
31. Ploskon E, et al. (2008) A mammalian type I fatty acid synthase acyl carrier protein domain does not sequester acyl chains. J Biol Chem 283:518-528.
32. Maier T, Leibundgut M, Ban N (2008) The crystal structure of a mammalian fatty acid synthase. Science 321:1315-1322.
33. Tanovic A, Samel SA, Essen L-O, Marahiel MA (2008) Crystal structure of the termination module of a nonribosomal peptide synthetase. Science 321:659-663.
34. Koglin A, et al. (2008) Structural basis for the selectivity of the external thioesterase of the surfactin synthetase. Nature 454:907-911.
35. Frueh DP, et al. (2008) Dynamic thiolation-thioesterase structure of a non-ribosomal peptide synthetase. Nature 454:903-906.
36. Gokhale RS, Tsuji SY, Cane DE, Khosla C (1999) Dissecting and exploiting intermodular communication in polyketide synthases. Science 284:482-485.
37. Sieber SA, et al. (2002) Evidence for a monomeric structure of nonribosomal peptide synthetases. Chem Biol 9:997-1008.
38. Tang Y, Chen AY, Kim CY, Cane DE, Khosla C (2007) Structural and mechanistic analysis of protein interactionsin module3 ofthe6- deoxyerythronolideB synthase. Chem Biol 14:931-943.
39. Tran L, Broadhurst RW, Tosin M, Cavalli A, Weissman KJ (2010) Insights into protein-protein and enzyme-substrate interactions in modular polyketide synthases. Chem Biol 17:705-716.
40. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Electrostatics of nanosystems: Application to microtubules and the ribosome. Proc Natl Acad Sci USA 98:10037-10041.
41. Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA (2004) PDB2PQR: An automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32:W665-667.
42. Dolinsky TJ, et al. (2007) PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic Acids Res 35:W522-525.
43. Li H, Robertson AD, Jensen JH (2005) Very fast empirical prediction and rationalization of protein pKa values. Proteins 61:704-721. (Pubitemid 41753142)
44. DeLano W (2002) The PyMOL User's Manual (DeLano Scientific, San Carlos, CA).