β-Oxidation of unsaturated fatty acids poses a problem since the location of a cis-bond can prevent the formation of a trans-Δ bond which is essential for continuation of β-Oxidation as this conformation is ideal for enzyme catalysis. This is handled by additional two enzymes, Enoyl CoA isomerase and 2,4 Dienoyl CoA reductase.
β-oxidation occurs normally until the acyl CoA (because of the presence of a double bond) is not an appropriate substrate for acyl CoA dehydrogenase, or enoyl CoA hydratase:
* If the acyl CoA contains a cis-Δ bond, then cis-Δ-Enoyl CoA isomerase will convert the bond to a trans-Δ bond, which is a regular substrate.
* If the acyl CoA contains a cis-Δ double bond, then its dehydrogenation yields a 2,4-dienoyl intermediate, which is not a substrate for enoyl CoA hydratase. However, the enzyme 2,4 Dienoyl CoA reductase reduces the intermediate, using NADPH, into trans-Δ-enoyl CoA. This compound is converted into a suitable intermediate by 3,2-Enoyl CoA isomerase and β-Oxidation continues.