8W1J

Crystal Structure of a fatty acid decarboxylase from Corynebacterium lipophiloflavum in complex with palmitic acid

Summary for 8W1J

• Entry DOI: 10.2210/pdb8w1j/pdb
• Related: 8VWK 8W1K
• Descriptor: Fatty acid decarboxylase, CHLORIDE ION, PROTOPORPHYRIN IX CONTAINING FE, ... (8 entities in total)
• Functional Keywords: p450, oxidoreductase
• Biological source: Corynebacterium lipophiloflavum
• Total number of polymer chains: 3
• Total formula weight: 151657.22

Authors

Generoso, W.C.,Miyamoto, R.Y.,Murakami, M.T.,Zanphorlin, L.M. (deposition date: 2024-02-16, release date: 2024-12-04, Last modification date: 2025-04-02)

Primary citation

Generoso, W.C.,Alvarenga, A.H.S.,Simoes, I.T.,Miyamoto, R.Y.,Melo, R.R.,Guilherme, E.P.X.,Mandelli, F.,Santos, C.A.,Prata, R.,Santos, C.R.D.,Colombari, F.M.,Morais, M.A.B.,Pimentel Fernandes, R.,Persinoti, G.F.,Murakami, M.T.,Zanphorlin, L.M.
Coordinated conformational changes in P450 decarboxylases enable hydrocarbons production from renewable feedstocks.
Nat Commun, 16:945-945, 2025

PubMed Abstract: Fatty acid peroxygenases have emerged as promising biocatalysts for hydrocarbon biosynthesis due to their ability to perform C-C scission, producing olefins - key building blocks for sustainable materials and fuels. These enzymes operate through non-canonical and complex mechanisms that yield a bifurcated chemoselectivity between hydroxylation and decarboxylation. In this study, we elucidate structural features in P450 decarboxylases that enable the catalysis of unsaturated substrates, expanding the mechanistic pathways for decarboxylation reaction. Combining X-ray crystallography, molecular dynamics simulations, and machine learning, we have identified intricate molecular rearrangements within the active site that enable the Cβ atom of the substrate to approach the heme iron, thereby promoting oleate decarboxylation. Furthermore, we demonstrate that the absence of the aromatic residue in the Phe-His-Arg triad preserves chemoselectivity for alkenes, providing a distinct perspective on the molecular determinants of decarboxylation activity. Ultimately, these findings enable the sustainable production of biohydrocarbons from industrial feedstocks.

PubMed: 39843428
DOI: 10.1038/s41467-025-56256-4

Experimental method

X-RAY DIFFRACTION (1.8 Å)