Structure of the Novel C-terminal Domain of Vacuolar Protein Sorting 30/Autophagy-related Protein 6 and Its Specific Role in Autophagy

• Published in: The Journal of biological chemistry 2012-05, Vol.287 (20), p.16256-16266
• Main Authors: Noda, Nobuo N., Kobayashi, Takafumi, Adachi, Wakana, Fujioka, Yuko, Ohsumi, Yoshinori, Inagaki, Fuyuhiko
• Format: Article
• Language: English
• Subjects: Atg6; Autophagy; Autophagy - physiology; Beclin 1; Crystal Structure; Crystallography; Crystallography, X-Ray; Membrane Proteins - chemistry; Membrane Proteins - genetics; Membrane Proteins - metabolism; Microtubule-Associated Proteins - chemistry; Microtubule-Associated Proteins - genetics; Microtubule-Associated Proteins - metabolism; Phosphatidylinositol 3-Kinase; Protein Folding; Protein Structure and Folding; Protein Structure, Secondary; Protein Structure, Tertiary; Protein Transport - physiology; Saccharomyces cerevisiae - chemistry; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; Structural Biology; Vacuolar Protein Sorting; Vps30
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M112.348250

Vacuolar protein sorting 30 (Vps30)/autophagy-related protein 6 (Atg6) is a common component of two distinct phosphatidylinositol 3-kinase complexes. In complex I, Atg14 links Vps30 to Vps34 lipid kinase and exerts its specific role in autophagy, whereas in complex II, Vps38 links Vps30 to Vps34 and plays a crucial role in vacuolar protein sorting. However, the molecular role of Vps30 in each pathway remains unclear. Here, we report the crystal structure of the carboxyl-terminal domain of Vps30. The structure is a novel globular fold comprised of three β-sheet-α-helix repeats. Truncation analyses showed that the domain is dispensable for the construction of both complexes, but is specifically required for autophagy through the targeting of complex I to the pre-autophagosomal structure. Thus, the domain is named the β-α repeated, autophagy-specific (BARA) domain. On the other hand, the N-terminal region of Vps30 was shown to be specifically required for vacuolar protein sorting. These structural and functional investigations of Vps30 domains, which are also conserved in the mammalian ortholog, Beclin 1, will form the basis for studying the molecular functions of this protein family in various biological processes. Vps30/Atg6 is responsible for both autophagy and vacuolar protein sorting. Structure of the Vps30 BARA domain was determined and its function was characterized. BARA domain has a unique fold and is specifically required for autophagy. This study will be a basis for elucidating the various functions of Vps30 homologs.