Ether phospholipids are essential constituents of eukaryotic cell membranes. Rhizomelic chondrodysplasia punctata type 3 is a severe peroxisomal disorder caused by inborn deficiency of alkyldihydroxyacetonephosphate synthase (ADPS). The enzyme carries out the most characteristic step in ether phospholipid biosynthesis: formation of the ether bond.

ADPS consists of a FAD-binding domain spanning residues 94-315 and 543-587, a cap domain comprising residues 316-542, and an N-terminal domain consisting of residues 9-93. This third domain has not been found in other members of the vanillyl-alcohol oxidase family and consists of a beta sheet and helix alpha-1, named the "gating helix" since it is involved in substrate tunnel closure. The gating helix is relevant in product release and substrate binding. The helix is part of the positively charged patch on the protein surface that likely interacts with the membrane.

This superfamily entry is represented by the cap domain and the N-terminal domain which contains the gating helix.

DOI:10.1016/j.str.2007.04.009,INTERPRO:IPR004113,PFAM:PF02913