II shares structural elements with other members of the carnitine acyltransferase protein family.[8] The crystal structure of rat CPT II was recently elucidated by Hsiao et al.[9] The human homolog of the CPT II enzyme shows 82.2% amino acid sequence homology with the rat protein.[10] Significant structural and functional information about CPT II has thus been derived from the crystallographic studies with the rat protein.
In addition to similarities shared by the acyltransferases, CPT II also contains a distinct insertion of 30 residues in the amino domain that forms a relatively hydrophobic protrusion composed of two alpha helices and a small anti-parallel beta sheet.[9] It has been proposed that this segment mediates the association of CPT II with the inner mitochondrial membrane.[9] Moreover, the insert might also facilitate the shuttling of palmitoylcarnitines directly into the active site of CPT II after translocation across the inner membrane by virtue of its juxtaposition to the active site tunnel of the enzyme.