Structural insights into pink-eyed dilution protein (Oca2)

• Published in: Bioscience reports 2023-07, Vol.43 (7), p.1
• Main Authors: Mesdaghi, Shahram, Murphy, David L, Simpkin, Adam J, Rigden, Daniel J
• Format: Article
• Language: English
• Subjects: Albinism; Albinism, Oculocutaneous - genetics; Asparagine; Binding sites; Bioinformatics; Deep learning; Dilution; Endoplasmic reticulum; Glycosylation; Gold; Golgi apparatus; Homology; Humans; Inverted repeat; Melanosomes; Membrane Transport Proteins - genetics; Modelling; Molecular Bases of Health & Disease; Mutation; Proteins; Scaffolds; Sequence analysis; Sodium; Standard scores; Structural Biology; Structure-function relationships; Topology
• ISSN: 0144-8463; 1573-4935
• DOI: 10.1042/BSR20230060

Recent innovations in computational structural biology have opened an opportunity to revise our current understanding of the structure and function of clinically important proteins. This study centres on human Oca2 which is located on mature melanosomal membranes. Mutations of Oca2 can result in a form of oculocutanous albinism, which is the most prevalent and visually identifiable form of albinism. Sequence analysis predicts Oca2 to be a member of the SLC13 transporter family, but it has not been classified into any existing SLC families. The modelling of Oca2 with AlphaFold2 and other advanced methods show that, like SLC13 members, it consists of a scaffold and transport domain and displays a pseudo inverted repeat topology that includes re-entrant loops. This finding contradicts the prevailing consensus view of its topology. In addition to the scaffold and transport domains, the presence of a cryptic GOLD domain is revealed that is likely responsible for its trafficking from the endoplasmic reticulum to the Golgi prior to localisation at the melanosomes. The GOLD domain harbours some known glycosylation sites. Analysis of the putative ligand binding site of the model shows the presence of highly conserved key asparagine residues that suggest Oca2 may be a Na+/dicarboxylate symporter. Known critical pathogenic mutations map to structural features present in the repeat regions that form the transport domain. Exploiting the AlphaFold2 multimeric modelling protocol in combination with conventional homology modelling allowed the building of plausible homodimers in both inward- and outward-facing conformations, supporting an elevator-type transport mechanism.