7LY5

Proteolyzed crystal structure of the bacillamide NRPS, BmdB, in complex with the oxidase BmdC

Summary for 7LY5

• Entry DOI: 10.2210/pdb7ly5/pdb
• Descriptor: BmdC, oxidase, BmdB, Bacillamide NRPS, FLAVIN MONONUCLEOTIDE, ... (4 entities in total)
• Functional Keywords: nonribosomal peptide synthetases, bacillamide, flavoprotein, biosynthetic protein, biosynthetic protein-oxidoreductase complex, biosynthetic protein/oxidoreductase
• Biological source: Thermoactinomyces vulgaris; More
• Total number of polymer chains: 2
• Total formula weight: 55735.20

Authors

Fortinez, C.M.,Schmeing, T.M. (deposition date: 2021-03-05, release date: 2022-02-02, Last modification date: 2024-04-03)

Primary citation

Fortinez, C.M.,Bloudoff, K.,Harrigan, C.,Sharon, I.,Strauss, M.,Schmeing, T.M.
Structures and function of a tailoring oxidase in complex with a nonribosomal peptide synthetase module.
Nat Commun, 13:548-548, 2022

PubMed Abstract: Nonribosomal peptide synthetases (NRPSs) are large modular enzymes that synthesize secondary metabolites and natural product therapeutics. Most NRPS biosynthetic pathways include an NRPS and additional proteins that introduce chemical modifications before, during or after assembly-line synthesis. The bacillamide biosynthetic pathway is a common, three-protein system, with a decarboxylase that prepares an NRPS substrate, an NRPS, and an oxidase. Here, the pathway is reconstituted in vitro. The oxidase is shown to perform dehydrogenation of the thiazoline in the peptide intermediate while it is covalently attached to the NRPS, as the penultimate step in bacillamide D synthesis. Structural analysis of the oxidase reveals a dimeric, two-lobed architecture with a remnant RiPP recognition element and a dramatic wrapping loop. The oxidase forms a stable complex with the NRPS and dimerizes it. We visualized co-complexes of the oxidase bound to the elongation module of the NRPS using X-ray crystallography and cryo-EM. The three active sites (for adenylation, condensation/cyclization, and oxidation) form an elegant arc to facilitate substrate delivery. The structures enabled a proof-of-principle bioengineering experiment in which the BmdC oxidase domain is embedded into the NRPS.

PubMed: 35087027
DOI: 10.1038/s41467-022-28221-y

Experimental method

X-RAY DIFFRACTION (2.5 Å)