Journal:Acta Cryst F:S2053230X19002863
From Proteopedia
Functional and structural characterization of IdnL7, an adenylation enzyme involved in incednine biosynthesisJolanta Cieślak, Akimasa Miyanaga, Makoto Takaishi, Fumitaka Kudo, Tadashi Eguchi [1] Molecular Tour 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 of IdnL7 consists of two domains: a large (Met1–Gly413; in pink) and a smaller (Gln420–Leu522; in magenta). Both domains are connected by a (Arg414–Leu419), which allows for the rotation of the C-terminal domain during the two catalytic reaction steps. The N-terminal domain forms a , whereas the C-terminal domain comprises . The C-terminal domain is arranged in the adenylation conformation in relation to the N-terminal domain. . The L-Ala-SA molecule and residues involved in interactions with the ligand are shown as cyan and pink ball-and-sticks, respectively. Red balls represent the positions of water molecules. White dashed lines indicate hydrogen bonding. The adenine moiety is buried in a hydrophobic pocket that is lined by on the other side. This architecture stabilizes the purine base by hydrophobic and van der Waals interactions. Additionally, the . Several water molecules participate in direct interactions with the sulfamoyladenosine moiety. . The through hydrogen bonds. The ribose . The . The binding site of the amino acyl moiety includes two charged residues, , which are oriented to make contact with the amino and carboxy groups, respectively. The α-amino group of the L-alanyl moiety is involved in two salt bridge interactions (2.9 Å and 3.1 Å) with the side-chain of , and two hydrogen bonds (2.9 Å and 2.7 Å) with the backbone oxygen atoms of . References
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