9PRR

X-ray crystal structure of Streptomyces cacaoi PolF in complex with iron and L-isoleucine

Summary for 9PRR

• Entry DOI: 10.2210/pdb9prr/pdb
• Related: 9MRI
• Descriptor: PolF, GLYCEROL, FE (II) ION, ... (6 entities in total)
• Functional Keywords: polyoximic acid, diiron cofactor, biosynthesis, cyclization, heme-oxygenase-like diiron enzyme, biosynthetic protein, oxidoreductase
• Biological source: Streptomyces cacaoi
• Total number of polymer chains: 6
• Total formula weight: 183106.05

Authors

Blancas Cortez, J.J.,Boal, A.K. (deposition date: 2025-07-24, release date: 2025-10-15, Last modification date: 2025-11-05)

Primary citation

Du, Y.,Thanapipatsiri, A.,Blancas Cortez, J.J.,Salas-Sola, X.E.,Lin, C.Y.,Boal, A.K.,Krebs, C.,Bollinger Jr., J.M.,Yokoyama, K.
Azetidine amino acid biosynthesis by non-haem iron-dependent enzymes.
Nat.Chem., 2025

PubMed Abstract: Azetidine, a four-membered aza-cycle, is a crucial structure in many bioactive compounds and drugs. However, their biosynthesis is frequently enigmatic. Here we report the mechanism of azetidine amino acid (polyoximic acid) biosynthesis in the polyoxin antifungal pathway. Genetic, enzymological and structural experiments revealed that PolF is a member of haem-oxygenase-like dimetal oxidase and/or oxygenase (HDO) superfamily, and this enzyme alone is sufficient for the transformation of L-isoleucine (L-Ile) and L-valine to their azetidine derivatives via a 3,4-desaturated intermediate. Mechanistic studies of PolF suggested that a μ-peroxo-Fe(III) intermediate is directly responsible for the unactivated C-H bond cleavage, and the post-H-abstraction reactions, including the C-N bond formation, probably proceed through radical mechanisms. We also found that PolE, a member of the DUF6421 family, is an Fe and pterin-dependent oxidase that catalyses the desaturation of L-Ile, assisting PolF by increasing the flux of L-Ile desaturation. The results provide important insights into azetidine biosynthesis and the catalytic mechanisms of HDO enzymes in general.

PubMed: 41120677
DOI: 10.1038/s41557-025-01958-x

Experimental method

X-RAY DIFFRACTION (2.06 Å)