title: Crystal structure of the acyltransferase domain of the iterative polyketide synthase in enediyne biosynthesis.
abstract: Biosynthesis of the enediyne natural product dynemicin in Micromonospora chersina is initiated by DynE8, a highly reducing iterative type I polyketide synthase that assembles polyketide intermediates from the acetate units derived solely from malonyl-CoA. To understand the substrate specificity and the evolutionary relationship between the acyltransferase (AT) domains of DynE8, fatty acid synthase, and modular polyketide synthases, we overexpressed a 44-kDa fragment of DynE8 (hereafter named AT(DYN10)) encompassing its entire AT domain and the adjacent linker domain. The crystal structure at 1.4 Å resolution unveils a α/β hydrolase and a ferredoxin-like subdomain with the Ser-His catalytic dyad located in the cleft between the two subdomains. The linker domain also adopts a α/β fold abutting the AT catalytic domain. Co-crystallization with malonyl-CoA yielded a malonyl-enzyme covalent complex that most likely represents the acyl-enzyme intermediate. The structure explains the preference for malonyl-CoA with a conserved arginine orienting the carboxylate group of malonate and several nonpolar residues that preclude α-alkyl malonyl-CoA binding. Co-crystallization with acetyl-CoA revealed two noncovalently bound acetates generated by the enzymatic hydrolysis of acetyl-CoA that acts as an inhibitor for DynE8. This suggests that the AT domain can upload the acyl groups from either malonyl-CoA or acetyl-CoA onto the catalytic Ser(651) residue. However, although the malonyl group can be transferred to the acyl carrier protein domain, transfer of the acetyl group to the acyl carrier protein domain is suppressed. Local structural differences may account for the different stability of the acyl-enzyme intermediates.
authors.affiliation: School of Biological Sciences, Nanyang Technological University, Singapore 637551.
authors.forename: Chong Wai
authors.initials: CW
authors.lastname: Liew
authors.forename: Martina
authors.initials: M
authors.lastname: Nilsson
authors.forename: Ming Wei
authors.initials: MW
authors.lastname: Chen
authors.forename: Huihua
authors.initials: H
authors.lastname: Sun
authors.forename: Tobias
authors.initials: T
authors.lastname: Cornvik
authors.forename: Zhao-Xun
authors.initials: ZX
authors.lastname: Liang
authors.forename: Julien
authors.initials: J
authors.lastname: Lescar
mesh_terms: D000105:Acetyl Coenzyme A / Q000378:metabolism; D000217:Acyltransferases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D020816:Amino Acid Motifs; D000900:Anti-Bacterial Agents / Q000737:chemistry; D020134:Catalytic Domain; D003001:Cloning, Molecular; D003461:Crystallography; D053281:Enediynes / Q000378:metabolism*; D005990:Glycerol / Q000737:chemistry; D008847:Micromonospora / Q000201:enzymology* / Q000235:genetics; D048630:Polyketide Synthases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
chemical_list: D000900:Anti-Bacterial Agents; D053281:Enediynes; D000105:Acetyl Coenzyme A; D048630:Polyketide Synthases; D000217:Acyltransferases; D005990:Glycerol