Journal:Acta Cryst F:S2053230X19002863

Functional and structural characterization of IdnL7, an adenylation enzyme involved in incednine biosynthesis

Jolanta Cieślak, Akimasa Miyanaga, Makoto Takaishi, Fumitaka Kudo, Tadashi Eguchi ^[1]

Molecular Tour
Adenylation enzymes are responsible for the selective incorporation of an appropriate carboxylate building block in the biosynthesis of nonribosomal peptides and related natural products. The substrate specificity of adenylation enzymes dictates the chemical structure of natural products. Understanding how adenylation enzymes recognize their own substrates is important for engineering biosynthetic pathways to produce novel compounds for drug discovery.

This paper describes the biochemical and structural analyses of adenylation enzyme IdnL7 involved in the biosynthesis of macrolactam antibiotic incednine. IdnL7 shows a broad substrate specificity for several small L-amino acids such as L-alanine and glycine. To obtain mechanistic insights into the substrate recognition of IdnL7, we determined the crystal structure of IdnL7 in complex with a reaction intermediate analog. IdnL7 has Cys217, Ala285 and Thr318 at the substrate binding pocket. These residues likely enable to accommodate various small L-amino acids as a substrate. This structural observation expands our understanding of the structure-function relationships of adenylation enzymes.

. The overall structure consists of the N-terminal domain (pink) and the C-terminal domain (magenta). IdnL7 consists of two domains: a large N-terminal domain (Met1–Gly413) and a smaller C-terminal domain (Gln420–Leu522) (Fig. 3B). Both domains are connected by a flexible hinge region (Arg414–Leu419), which allows for the rotation of the C-terminal domain during the two catalytic reaction steps. The N-terminal domain forms a five-layered αβαβα-sandwich fold, whereas the C-terminal domain comprises three helices with one two-stranded and one three-stranded antiparallel β-sheet. The C-terminal domain is arranged in the adenylation conformation in relation to the N-terminal domain.

References

1. ↑ Cieslak J, Miyanaga A, Takaishi M, Kudo F, Eguchi T. Functional and structural characterization of IdnL7, an adenylation enzyme involved in incednine biosynthesis. Acta Crystallogr F Struct Biol Commun. 2019 Apr 1;75(Pt 4):299-306. doi:, 10.1107/S2053230X19002863. Epub 2019 Apr 2. PMID:30950831 doi:http://dx.doi.org/10.1107/S2053230X19002863