- Phytanic acid is first attached to CoA to form phytanoyl-CoA.
- Phytanoyl-CoA is oxidized by phytanoyl-CoA dioxygenase, in a process using Fe2+ and O2, to yield 2-hydroxyphytanoyl-CoA.
- 2-hydroxyphytanoyl-CoA is cleaved by 2-hydroxyphytanoyl-CoA lyase in a TPP-dependent reaction to form pristanal and formyl-CoA (in turn later broken down into formate and eventually CO2).
- Pristanal is oxidized by aldehyde dehydrogenase to form pristanic acid (which can then undergo beta-oxidation).
(Propionyl-CoA is released as a result of beta oxidation when the beta carbon is substituted)
Enzymatic deficiency in alpha-oxidation (most frequently in phytanoyl-CoA dioxygenase) leads to Refsum's disease, in which the accumulation of phytanic acid and its derivatives leads to neurological damage. Other disorders of peroxisome biogenesis also prevent alpha-oxidation from occurring.