Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation

Abstract

SnoaL belongs to a family of small polyketide cyclases, which catalyse ring closure steps in the biosynthesis of polyketide antibiotics produced in Streptomyces. Several of these antibiotics are among the most used anti-cancer drugs currently in use. The crystal structure of SnoaL, involved in nogalamycin biosynthesis, with a bound product, has been determined to 1.35 Å resolution. The fold of the subunit can be described as a distorted a þ b barrel, and the ligand is bound in the hydrophobic interior of the barrel. The 3D structure and site-directed mutagenesis experiments reveal that the mechanism of the intramolecular aldol condensation catalysed by SnoaL is different from that of the classical aldolases, which employ covalent Schiff base formation or a metal ion cofactor. The invariant residue Asp121 acts as an acid/base catalyst during the reaction. Stabilisation of the enol(ate) intermediate is mainly achieved by the delocalisation of the electron pair over the extended p system of the substrate. These polyketide cyclases thus form of family of enzymes with a unique catalytic strategy for aldol condensation.

Isolation, Characterization, and Heterologous Expression of the Biosynthesis Gene Cluster for the Antitumor Anthracycline Steffimycin

“…In the biosynthesis of nogalamycin and daunorubicin, at least three activities are required to transform nogalonic acid to nogalaviketone or aklanonic acid to aklaviketone. The C-10 carboxyl-methyl transferases SnoaC/DnrC (17,29), the nogalonic-aklanonic acid methyl ester cyclases SnoaL/DnrD (51,20), and homologues of ActVI-ORFA, SnoO/DpsH, with an unclear function (17,16), are required for cyclization (Fig. 5).…”

The polyketide cyclase RemF from Streptomyces resistomycificus contains an unusual octahedral zinc binding site

“…The SnoaL type catalyzes ring closure by internal aldol condensation using acid/base chemistry [8,9]. Albeit very different in three-dimensional structure to SnoaL the tetracenomycin aromatase/cyclase also catalyzes ring closure using acid/ base chemistry [10].…”

Identification of olivetolic acid cyclase from Cannabis sativa reveals a unique catalytic route to plant polyketides

“…A type II aldolase mechanism involving a metal ion can be excluded because 10 mM EDTA was not inhibitory. A mechanism for OAC is suggested by the base-catalyzed aldol condensations of Streptomyces cyclases, which involve enolate intermediates (22,32,33).…”