4AMM: Crystal Structure Of The Acyltransferase Domain Of The Iterative Polyketide Synthase In Enediyne Biosynthesis Reveals The Molecular Basis Of Substrate Specificity

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 A resolution unveils a alpha/beta 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 alpha/beta 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 alpha-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.
PDB ID: 4AMMDownload
MMDB ID: 99892
PDB Deposition Date: 2012/3/13
Updated in MMDB: 2012/08
Experimental Method:
x-ray diffraction
Resolution: 1.4  Å
Source Organism:
Similar Structures:
Biological Unit for 4AMM: monomeric; determined by author and by software (PISA)
Molecular Components in 4AMM
Label Count Molecule
Protein (1 molecule)
Molecule annotation
Chemical (1 molecule)
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Citing MMDB