Functions as an auxiliary enzyme in the beta-oxidation of unsaturated fatty acids with double bonds at even carbon positions. Catalyzes the NADPH-dependent reduction of the C4-C5 double bond of the acyl chain of 2,4-dienoyl-CoA to yield 2-trans-enoyl-CoA (PubMed:9346310, PubMed:6363415). Acts on both isomers, 2-trans,4-cis- and 2-trans,4-trans-decadienoyl-CoA, with almost equal efficiency (PubMed:6363415). Is not active with NADH instead of NADPH (PubMed:6363415). Does not show cis->trans isomerase activity (PubMed:10933894). a 4,5-saturated-(2E)-enoyl-CoA + NADP(+) = a (2E,4E)-dienoyl-CoA + H(+) + NADPH a (2E,4Z)-dienoyl-CoA + H(+) + NADPH = a 4,5-saturated-(2E)-enoyl-CoA + NADP(+) (2E)-decenoyl-CoA + NADP(+) = (2E,4E)-decadienoyl-CoA + H(+) + NADPH (2E)-decenoyl-CoA + NADP(+) = (2E,4Z)-decadienoyl-CoA + H(+) + NADPH Is non-competitively inhibited by NADH. kcat is 16 sec(-1) for the NADPH-reduction of (2E,4E)-decadienoyl-CoA. Lipid metabolism; fatty acid beta-oxidation. Monomer. Induced when cells are grown on oleate as sole carbon source. Repressed by glucose. Is composed of three domains: an N-terminal TIM barrel (residues 1-368) which binds FMN, the 4Fe-4S cluster, and the substrate; a flavodoxin-like fold (residues 369-467 and 626-671) which binds FAD; and an NADP(H)-binding domain (residues 468-625). The overall reaction mechanism can be divided into three stages: initially, reduction of FAD by NADPH, then electron transfer from FAD to FMN via the 4Fe-4S cluster, and finally reduction of substrate. In the N-terminal section; belongs to the NADH:flavin oxidoreductase/NADH oxidase family.