In biochemistry terms, it catalyses the chemical reaction that converts (S)-methylmalonyl-CoA to the (R) form:[3][4] Methylmalonyl CoA epimerase plays an important role in the catabolism of fatty acids with odd-length carbon chains.

In the catabolism of even-chain saturated fatty acids, the β-oxidation pathway breaks down fatty acyl-CoA molecules in repeated sequences of four reactions to yield one acetyl CoA per repeated sequence.

Methylmalonyl CoA epimerase then catalyzes the rearrangement of (S)-methylmalonyl-CoA to the (R) form in a reaction that uses a vitamin B12 cofactor and a resonance-stabilized carbanion intermediate.

Mutations in the MCEE gene causes methymalonyl-CoA epimerase deficiency (MCEED),[5] a rare autosomal recessive inborn error of metabolism in amino acid metabolisms involving branched-chain amino acids valine, leucine, and isoleucine.

Patients with MCEED may present with life-threatening neonatal metabolic acidosis, hyperammonemia, feeding difficulties, and coma.