3VP7

Crystal structure of the beta-alpha repeated, autophagy-specific (BARA) domain of Vps30/Atg6

Summary for 3VP7

• Entry DOI: 10.2210/pdb3vp7/pdb
• Descriptor: Vacuolar protein sorting-associated protein 30 (2 entities in total)
• Functional Keywords: targeting, pi3-kinase complex i, pre-autophagosomal structure, protein transport
• Biological source: Saccharomyces cerevisiae (Baker's yeast)
• Cellular location: Endosome membrane; Peripheral membrane protein: Q02948
• Total number of polymer chains: 1
• Total formula weight: 24681.16

Authors

Noda, N.N.,Kobayashi, T.,Adachi, W.,Fujioka, Y.,Ohsumi, Y.,Inagaki, F. (deposition date: 2012-02-28, release date: 2012-03-14, Last modification date: 2023-10-18)

Primary citation

Noda, N.N.,Kobayashi, T.,Adachi, W.,Fujioka, Y.,Ohsumi, Y.,Inagaki, F.
Structure of the novel C-terminal domain of vacuolar protein sorting 30/autophagy-related protein 6 and its specific role in autophagy.
J.Biol.Chem., 287:16256-16266, 2012

PubMed Abstract: 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.

PubMed: 22437838
DOI: 10.1074/jbc.M112.348250

Experimental method

X-RAY DIFFRACTION (2.3 Å)