Promiscuous isomerase that catalyzes epimerization of both ethylmalonyl-CoA and methylmalonyl-CoA. Has thus a dual role in the ethylmalonyl-CoA pathway for acetyl-CoA assimilation required for R.sphaeroides growth on acetate as sole carbon source. (2R)-ethylmalonyl-CoA = (2S)-ethylmalonyl-CoA (R)-methylmalonyl-CoA = (S)-methylmalonyl-CoA Can use Co(2+) or Mn(2+) as cofactor, but Mg(2+) and Ni(2+) cannot support enzymatic activity. Belongs to the methylmalonyl-CoA epimerase family.