The 2.7-Angstrom Crystal Structure of a 194-kDa Homodimeric Fragment of the 6-deoxyerythronolide B Synthase

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2006 Jul 18

PMID 16844787

Citations 120

Authors

Yinyan Tang

Chu-Young Kim

Irimpan I Mathews

David E Cane

Chaitan Khosla

Affiliations

Soon will be listed here.

Abstract

The x-ray crystal structure of a 194-kDa fragment from module 5 of the 6-deoxyerythronolide B synthase has been solved at 2.7 Angstrom resolution. Each subunit of the homodimeric protein contains a full-length ketosynthase (KS) and acyl transferase (AT) domain as well as three flanking "linkers." The linkers are structurally well defined and contribute extensively to intersubunit or interdomain interactions, frequently by means of multiple highly conserved residues. The crystal structure also reveals that the active site residue Cys-199 of the KS domain is separated from the active site residue Ser-642 of the AT domain by approximately 80 Angstrom. This distance is too large to be covered simply by alternative positioning of a statically anchored, fully extended phosphopantetheine arm of the acyl carrier protein domain from module 5. Thus, substantial domain reorganization appears necessary for the acyl carrier protein to interact successively with both the AT and the KS domains of this prototypical polyketide synthase module. The 2.7-Angstrom KS-AT structure is fully consistent with a recently reported lower resolution, 4.5-Angstrom model of fatty acid synthase structure, and emphasizes the close biochemical and structural similarity between polyketide synthase and fatty acid synthase enzymology.

Citing Articles

Molecular Basis for Short-Chain Thioester Hydrolysis by Acyl Hydrolases in -Acyltransferase Polyketide Synthases.

Fage C, Passmore M, Tatman B, Smith H, Jian X, Dissanayake U JACS Au. 2025; 5(1):144-157.

PMID: 39886563 PMC: 11775670. DOI: 10.1021/jacsau.4c00837.

Chemical biology research in RIKEN NPDepo aimed at agricultural applications.

Osada H Proc Jpn Acad Ser B Phys Biol Sci. 2025; 101(1):8-31.

PMID: 39805590 PMC: 11808203. DOI: 10.2183/pjab.101.003.

Mutagenesis Supports AlphaFold Prediction of How Modular Polyketide Synthase Acyl Carrier Proteins Dock With Downstream Ketosynthases.

Hirsch M, Desai R, Annaswamy S, Keatinge-Clay A Proteins. 2024; 92(12):1375-1384.

PMID: 39078105 PMC: 11543512. DOI: 10.1002/prot.26733.

Insights into docking in megasynthases from the investigation of the toblerol -AT polyketide synthase: many α-helical means to an end.

Scat S, Weissman K, Chagot B RSC Chem Biol. 2024; 5(7):669-683.

PMID: 38966669 PMC: 11221535. DOI: 10.1039/d4cb00075g.

Programmed Iteration Controls the Assembly of the Nonanoic Acid Side Chain of the Antibiotic Mupirocin.

Winter A, Rowe M, Weir A, Akter N, Mbatha S, Walker P Angew Chem Weinheim Bergstr Ger. 2024; 134(50):e202212393.

PMID: 38505625 PMC: 10947060. DOI: 10.1002/ange.202212393.

References

Moche M, Schneider G, Edwards P, Dehesh K, Lindqvist Y . Structure of the complex between the antibiotic cerulenin and its target, beta-ketoacyl-acyl carrier protein synthase. J Biol Chem. 1999; 274(10):6031-4. DOI: 10.1074/jbc.274.10.6031. View

Gokhale R, Tsuji S, Cane D, Khosla C . Dissecting and exploiting intermodular communication in polyketide synthases. Science. 1999; 284(5413):482-5. DOI: 10.1126/science.284.5413.482. View

Ranganathan A, Timoney M, Bycroft M, Cortes J, Thomas I, Wilkinson B . Knowledge-based design of bimodular and trimodular polyketide synthases based on domain and module swaps: a route to simple statin analogues. Chem Biol. 1999; 6(10):731-41. DOI: 10.1016/s1074-5521(00)80020-4. View

OLSEN J, Kadziola A, von Wettstein-Knowles P, Lindquist Y, Larsen S . The X-ray crystal structure of beta-ketoacyl [acyl carrier protein] synthase I. FEBS Lett. 1999; 460(1):46-52. DOI: 10.1016/s0014-5793(99)01303-4. View

Davies C, Heath R, White S, Rock C . The 1.8 A crystal structure and active-site architecture of beta-ketoacyl-acyl carrier protein synthase III (FabH) from escherichia coli. Structure. 2000; 8(2):185-95. DOI: 10.1016/s0969-2126(00)00094-0. View

Lau J, Cane D, Khosla C . Substrate specificity of the loading didomain of the erythromycin polyketide synthase. Biochemistry. 2000; 39(34):10514-20. DOI: 10.1021/bi000602v. View

Chirala S, Jayakumar A, Gu Z, WAKIL S . Human fatty acid synthase: role of interdomain in the formation of catalytically active synthase dimer. Proc Natl Acad Sci U S A. 2001; 98(6):3104-8. PMC: 30614. DOI: 10.1073/pnas.051635998. View

Tsuji S, Wu N, Khosla C . Intermodular communication in polyketide synthases: comparing the role of protein-protein interactions to those in other multidomain proteins. Biochemistry. 2001; 40(8):2317-25. DOI: 10.1021/bi002462v. View

Tsuji S, Cane D, Khosla C . Selective protein-protein interactions direct channeling of intermediates between polyketide synthase modules. Biochemistry. 2001; 40(8):2326-31. DOI: 10.1021/bi002463n. View

10.

Reeves C, Murli S, Ashley G, Piagentini M, Hutchinson C, McDaniel R . Alteration of the substrate specificity of a modular polyketide synthase acyltransferase domain through site-specific mutations. Biochemistry. 2001; 40(51):15464-70. DOI: 10.1021/bi015864r. View

11.

Schneider T, Sheldrick G . Substructure solution with SHELXD. Acta Crystallogr D Biol Crystallogr. 2002; 58(Pt 10 Pt 2):1772-9. DOI: 10.1107/s0907444902011678. View

12.

Milne J, Shi D, Rosenthal P, Sunshine J, Domingo G, Wu X . Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: a multifunctional catalytic machine. EMBO J. 2002; 21(21):5587-98. PMC: 131071. DOI: 10.1093/emboj/cdf574. View

13.

Pan H, Tsai S, Meadows E, Miercke L, Keatinge-Clay A, OConnell J . Crystal structure of the priming beta-ketosynthase from the R1128 polyketide biosynthetic pathway. Structure. 2002; 10(11):1559-68. DOI: 10.1016/s0969-2126(02)00889-4. View

14.

Terwilliger T . Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr D Biol Crystallogr. 2002; 59(Pt 1):38-44. PMC: 2745878. DOI: 10.1107/s0907444902018036. View

15.

Keatinge-Clay A, Shelat A, Savage D, Tsai S, Miercke L, OConnell 3rd J . Catalysis, specificity, and ACP docking site of Streptomyces coelicolor malonyl-CoA:ACP transacylase. Structure. 2003; 11(2):147-54. DOI: 10.1016/s0969-2126(03)00004-2. View

16.

Kumar P, Li Q, Cane D, Khosla C . Intermodular communication in modular polyketide synthases: structural and mutational analysis of linker mediated protein-protein recognition. J Am Chem Soc. 2003; 125(14):4097-102. DOI: 10.1021/ja0297537. View

17.

Hans M, Hornung A, Dziarnowski A, Cane D, Khosla C . Mechanistic analysis of acyl transferase domain exchange in polyketide synthase modules. J Am Chem Soc. 2003; 125(18):5366-74. DOI: 10.1021/ja029539i. View

18.

Broadhurst R, Nietlispach D, Wheatcroft M, Leadlay P, Weissman K . The structure of docking domains in modular polyketide synthases. Chem Biol. 2003; 10(8):723-31. DOI: 10.1016/s1074-5521(03)00156-x. View

19.

Evans J, Huddler D, Hilgers M, Romanchuk G, Matthews R, Ludwig M . Structures of the N-terminal modules imply large domain motions during catalysis by methionine synthase. Proc Natl Acad Sci U S A. 2004; 101(11):3729-36. PMC: 374312. DOI: 10.1073/pnas.0308082100. View

20.

Walsh C . Polyketide and nonribosomal peptide antibiotics: modularity and versatility. Science. 2004; 303(5665):1805-10. DOI: 10.1126/science.1094318. View