Catalyzes reduction of trans-2-enoyl-CoA to acyl-CoA, an important step in the fatty acid biosynthesis pathway, which is performed in mitochondria under anaerobiosis. Preferably catalyzes the reduction of short chain length substrates such as crotonyl-CoA ((2E)-butenoyl-CoA) and (2E)-hexenoyl-CoA. Can use both NADH and NADPH as electron donor, with 2-3-fold higher specific activities for NADH relative to NADPH. Originally thought to contribute to wax ester production under anaerobic conditions (PubMed:15569691). Later shown to be dispensable for wax ester production under anaerobic conditions, but involved in the greening process (chlorophyll synthesis and/or chloroplast development) (PubMed:30650145). a 2,3-saturated acyl-CoA + NAD(+) = a (2E)-enoyl-CoA + H(+) + NADH butanoyl-CoA + NAD(+) = (2E)-butenoyl-CoA + H(+) + NADH hexanoyl-CoA + NAD(+) = (2E)-hexenoyl-CoA + H(+) + NADH a (2E)-enoyl-CoA + H(+) + NADPH = a 2,3-saturated acyl-CoA + NADP(+) butanoyl-CoA + NADP(+) = (2E)-butenoyl-CoA + H(+) + NADPH (2E)-hexenoyl-CoA + H(+) + NADPH = hexanoyl-CoA + NADP(+) Lipid metabolism; fatty acid metabolism. Monomer. Expressed under aerobic and anaerobic conditions. The N-terminus is blocked. Severe bleaching phenotype concomitant with negligible levels of chlorophylls and glycolipids. The levels of alanine, glycine, tryptophan, and arginine, as well as those for glycerophospholipids were highly impacted in the mutant under anaerobic conditions. Euglena gracilis exhibits the metabolic behavior of a plant in the light and of an animal in the dark. Belongs to the TER reductase family.