Limits...
Structure of the novel C-terminal domain of vacuolar protein sorting 30/autophagy-related protein 6 and its specific role in autophagy.

Noda NN, Kobayashi T, Adachi W, Fujioka Y, Ohsumi Y, Inagaki F - J. Biol. Chem. (2012)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Microbial Chemistry, Tokyo, Tokyo 141-0021, Japan. nn@bikaken.or.jp

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.

Show MeSH
Domain architecture of Vps30 and sequence alignment with homologues.A, domain architecture of Vps30. B, sequence alignment of the C-terminal region of Vps30/Beclin 1 homologues. Perfectly conserved residues are shaded black, and residues conserved as hydrophobic are shaded gray. The secondary structural elements of BARA are shown above the alignment. HsBec1, Homo sapiens Beclin 1; At, Arabidopsis thaliana; Dm, Drosophila melanogaster.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3351336&req=5

Figure 2: Domain architecture of Vps30 and sequence alignment with homologues.A, domain architecture of Vps30. B, sequence alignment of the C-terminal region of Vps30/Beclin 1 homologues. Perfectly conserved residues are shaded black, and residues conserved as hydrophobic are shaded gray. The secondary structural elements of BARA are shown above the alignment. HsBec1, Homo sapiens Beclin 1; At, Arabidopsis thaliana; Dm, Drosophila melanogaster.

Mentions: Sequence alignment of Vps30 with its higher eukaryote homologues (Beclin 1) shows that the C-terminal region is highly conserved among them (Fig. 2B). The Beclin 1 ECD corresponds to residues 297–390 of Vps30, which comprise the C-terminal portion of the predicted coiled-coil, repeat 1, and the N-terminal portion of repeat 2. The region C-terminal to the ECD is also conserved, especially the residues constituting the secondary structures of repeat 3 (Fig. 2B). Most of the hydrophobic residues contributing to the interaction among the three subdomains in Fig. 1D are conserved (Fig. 2B). These observations suggest that the three-repeat architecture of the C-terminal region of Vps30 is conserved among Vps30/Beclin 1 homologues. On the basis of its unique β-sheet-α-helix repeat and its functional significance in autophagy described below, the C-terminal region is named the BARA domain. Comparison of the BARA structure with the PDB data base using the DALI search engine (41) revealed that the three-repeat architecture of BARA, namely a three-helix bundle surrounded by three β-sheets, is novel.


Structure of the novel C-terminal domain of vacuolar protein sorting 30/autophagy-related protein 6 and its specific role in autophagy.

Noda NN, Kobayashi T, Adachi W, Fujioka Y, Ohsumi Y, Inagaki F - J. Biol. Chem. (2012)

Domain architecture of Vps30 and sequence alignment with homologues.A, domain architecture of Vps30. B, sequence alignment of the C-terminal region of Vps30/Beclin 1 homologues. Perfectly conserved residues are shaded black, and residues conserved as hydrophobic are shaded gray. The secondary structural elements of BARA are shown above the alignment. HsBec1, Homo sapiens Beclin 1; At, Arabidopsis thaliana; Dm, Drosophila melanogaster.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3351336&req=5

Figure 2: Domain architecture of Vps30 and sequence alignment with homologues.A, domain architecture of Vps30. B, sequence alignment of the C-terminal region of Vps30/Beclin 1 homologues. Perfectly conserved residues are shaded black, and residues conserved as hydrophobic are shaded gray. The secondary structural elements of BARA are shown above the alignment. HsBec1, Homo sapiens Beclin 1; At, Arabidopsis thaliana; Dm, Drosophila melanogaster.
Mentions: Sequence alignment of Vps30 with its higher eukaryote homologues (Beclin 1) shows that the C-terminal region is highly conserved among them (Fig. 2B). The Beclin 1 ECD corresponds to residues 297–390 of Vps30, which comprise the C-terminal portion of the predicted coiled-coil, repeat 1, and the N-terminal portion of repeat 2. The region C-terminal to the ECD is also conserved, especially the residues constituting the secondary structures of repeat 3 (Fig. 2B). Most of the hydrophobic residues contributing to the interaction among the three subdomains in Fig. 1D are conserved (Fig. 2B). These observations suggest that the three-repeat architecture of the C-terminal region of Vps30 is conserved among Vps30/Beclin 1 homologues. On the basis of its unique β-sheet-α-helix repeat and its functional significance in autophagy described below, the C-terminal region is named the BARA domain. Comparison of the BARA structure with the PDB data base using the DALI search engine (41) revealed that the three-repeat architecture of BARA, namely a three-helix bundle surrounded by three β-sheets, is novel.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Institute of Microbial Chemistry, Tokyo, Tokyo 141-0021, Japan. nn@bikaken.or.jp

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.

Show MeSH