Identification of the incednine biosynthetic gene cluster: characterization of novel β-glutamate-β-decarboxylase IdnL3

Abstract

A biosynthetic gene cluster for the 24-membered macrolactam antibiotic incednine was identified from the producer strain, Streptomyces sp. ML694-90F3. Among the putative incednine biosynthetic enzymes, a novel pyridoxal 5'-phosphate (PLP)-dependent β-glutamate-β-decarboxylase, IdnL3, was functionally characterized in vitro by demonstrating its (S)-3-aminobutyrate-forming activity with β-glutamate in the presence of PLP. Because (S)-3-aminobutyrate is known for the direct precursor of incednine, this enzyme supplies the unique β-amino acid starter unit. The identified gene cluster encodes five characteristic β-amino acid carrying enzymes, consisting of a pathway-specific ATP-dependent ligase, a discrete acyl carrier protein (ACP), β-aminoacyl-ACP β-amino group-protecting ATP-dependent ligase, dipeptidyl-ACP:PKS-loading ACP dipeptidyltransferase and a terminal amino acid peptidase, which are completely conserved in β-amino acid-containing macrolactam biosynthetic gene clusters. Overall, a plausible biosynthetic pathway for incednine was proposed.

The many roles of glutamate in metabolism

“…4) is produced through a different route. The gene cluster was found to encode a glutamate 2,3-aminomutase and a decarboxylase [79]. The presence of these genes suggests glutamate is transformed to γ-glutamate by the aminomutase, which is then converted to 3-aminobutyrate by the decarboxylase, a route that was confirmed by labeling studies [78].…”

The Crystal Structure of the Adenylation Enzyme VinN Reveals a Unique β-Amino Acid Recognition Mechanism

“…In many cases, adenylation enzymes that activate ␤-amino acids are involved in their biosynthetic pathways (13)(14)(15)(16)(17)(18)(19)(20)(21)(22)(23)(24). Similar to ␣-amino acid-activating enzymes, the interaction with the ␤-amino group and the carboxylate group should be important for ␤-amino acid-activating enzymes to fix the substrate orientation.…”

Characterization of Heronamide Biosynthesis Reveals a Tailoring Hydroxylase and Indicates Migrated Double Bonds

“…[3] Recently,w er eported heronamides D-F (1-3), [4] whose side chains are two carbons shorter than those of 4-6,f rom the deep-sea-derived Streptomyces sp. [1] Well-studied examples include vicenistatin (a b-aminoisobutyrates tarter unit), [7] incednine (a baminobutyrate starter unit), [8] and hitachimycin (an S-b-phenylalanines tarter unit). [5] Although displaying no antibiotic or anticancera ctivity, [2,4] heronamides were initially found to elicit unexpected effects on cell morphology, [2] and were recently shown to have unique membrane-bindinga bilities.…”

“…[6] Recent characterization of an umber of bPM biosynthetic gene clusters has revealed ac ommon strategy of using av ariety of b-aminoa cids as starteru nits in type Ip olyketide synthase (PKS) pathways. [1] Well-studied examples include vicenistatin (a b-aminoisobutyrates tarter unit), [7] incednine (a baminobutyrate starter unit), [8] and hitachimycin (an S-b-phenylalanines tarter unit). [9] In structurala nalogy to heronamides, as ide chain of six or eight carbons is also present in the other bPMs (Scheme 1), such as BE-14106 (7), ML-449 (8), cremimycin (9), and aureoverticilactam (10).…”

“…[1] Well-studied examples include vicenistatin (a b-aminoisobutyrates tarter unit), [7] incednine (a baminobutyrate starter unit), [8] and hitachimycin (an S-b-phenylalanines tarter unit). [9] In structurala nalogy to heronamides, as ide chain of six or eight carbons is also present in the other bPMs (Scheme 1), such as BE-14106 (7), ML-449 (8), cremimycin (9), and aureoverticilactam (10). The biosynthetic gene clusters of BE-14106 (7)a nd ML-449 (8)h ave been decipheredb y Zotchev and co-workers.…”