Structural insights into butyryl-CoA dehydrogenase and its modeled complex with electron transferring flavoprotein from Faecalibacterium prausnitzii L2-6

Faecalibacterium prausnitzii is a predominant anaerobic bacterium in the human gut microbiome, contributing to host intestinal health through butyrate production and anti-inflammatory effects. The L2-6 strain serves as a representative model for genomic and metabolic research, with high potential for therapeutic modulation of the gut microbiota. Butyrate biosynthesis in this organism proceeds through the butyryl-CoA dehydrogenase (BCD) and electron transferring flavoprotein (Etf) system, which is a key enzymatic step linking fatty acid metabolism and redox equilibrium. So far, structural information on F. prausnitzii BCD has been lacking, limiting our mechanistic comprehension of its catalytic cycle. Here, we report the crystal structures of F. prausnitzii L2-6 BCD in both apo and FAD-bound states. The catalytic glutamate is positioned approximately 8.0 Å from the FAD isoalloxazine ring, suggesting that crotonyl-CoA likely enters through the space between E373 and the re-face of FAD. To compare the structure with other species, we obtained a modeling structure of BCD and Etf complexes in the Fp L2-6 strain. Comparative analysis with structurally characterized BCDs and Etf complexes from other butyrate-producing species reveals that F. prausnitzii L2-6 follows a similar electron transfer and catalytic cycle, reinforcing its role in energy conservation and redox balance under anaerobic conditions. These findings deepen our molecular understanding of butyrate metabolism in F. prausnitzii, with broader implications for host-microbiome interactions. Furthermore, the structural framework provided here can serve as a basis for future studies aiming to modulate butyrate production across strains, potentially informing the development of microbiome-based therapeutics.