b-Oxidation of amino acyl coenzyme A (acyl-CoA) species in mammalian peroxisomes can occur via either multifunctional enzyme type 1 (MFE-1) or type 2 (MFE-2), both of which catalyze the hydration of trans-2-enoylCoA and the dehydrogenation of 3-hydroxyacyl-CoA, but with opposite chiral speci®city. MFE-2 has a modular organization of three domains. The function of the C-terminal domain of the mammalian MFE-2, which shows similarity with sterol carrier protein type 2 (SCP-2), is unclear. Here, the structure of the SCP-2-like domain comprising amino acid residues 618-736 of human MFE-2 (dÁhÁSCP-2L) was solved at 1.75 A Ê resolution in complex with Triton X-100, an analog of a lipid molecule. This is the ®rst reported structure of an MFE-2 domain. The dÁhÁSCP-2L has an a/b-fold consisting of ®ve b-strands and ®ve a-helices; the overall architecture resembles the rabbit and human SCP-2 structures. However, the structure of dÁhÁSCP-2L shows a hydrophobic tunnel that traverses the protein, which is occupied by an ordered Triton X-100 molecule. The tunnel is large enough to accommodate molecules such as straight-chain and branched-chain fatty acyl-CoAs and bile acid intermediates. Large empty apolar cavities are observed near the exit of the tunnel and between the helices C and D. In addition, the C-terminal peroxisomal targeting signal is ordered in the structure and solventexposed, which is not the case with unliganded rabbit SCP-2, supporting the hypothesis of a ligand-assisted targeting mechanism.