Peroxisomal matrix proteins were extracted from the highly purified peroxisomes with sodium pyrophosphate, and the membranes were sedimented by high speed centrifugation. Biochemical marker enzyme analyses revealed a quantitative release of a number of well-known peroxisomal matrix proteins from the purified peroxisomes. In contrast, carnitine medium/long chain acyltransferase activity, assayed with decanoyl-CoA and palmitoyl-CoA as substrates, was equally distributed in the membrane and the matrix fractions. The matrix and the membrane enzyme activities were differentially affected by a number of detergents. The enzyme in the membrane fraction showed higher malonyl-CoA sensitivity compared to the enzyme in the matrix fraction. The enzyme(s) from the purified peroxisomes or the peroxisomal membranes was quantitatively solubilized by sodium cholate, and the cholate-solubilized enzyme retained malonyl-CoA sensitivity. The membrane enzyme was separated from the matrix enzyme by hydroxylapatite column chromatography. The separation of the membrane enzyme or the matrix enzyme by hydroxylapatite column chromatography resulted in loss of malonyl-CoA sensitivity. The partially purified membrane and the matrix enzymes showed broad substrate specificity, and the highest enzyme activities for both were observed with decanoyl-CoA. In contrast to the matrix enzyme, the membrane enzyme was strongly inhibited by high concentrations (> or = 50 microM) of acyl-CoAs (> 10 carbons in length). The matrix enzyme showed a 2.5-fold lower Km for carnitine compared to the membrane enzyme. The catalytic properties of the partially purified matrix enzyme appear to be similar to the well-characterized peroxisomal carnitine octanoyltransferase, though we find highest activity with decanoyl-CoA rather than octanoyl-CoA as a substrate. The data presented clearly indicate that the membrane and the matrix enzyme activities are due to different proteins.