2DYM

The crystal structure of Saccharomyces cerevisiae Atg5- Atg16(1-46) complex

Summary for 2DYM

• Entry DOI: 10.2210/pdb2dym/pdb
• Related: 2DYO
• Descriptor: Autophagy protein 5, Autophagy protein 16 (3 entities in total)
• Functional Keywords: ubiquitin-fold, herix-bundle, protein turnover-protein turnover complex, protein turnover/protein turnover
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Cellular location: Cytoplasm: Q12380; Vacuole (Potential): Q03818
• Total number of polymer chains: 8
• Total formula weight: 157449.34

Authors

Matsushita, M.,Suzuki, N.N.,Inagaki, F. (deposition date: 2006-09-15, release date: 2006-12-26, Last modification date: 2024-03-13)

Primary citation

Matsushita, M.,Suzuki, N.N.,Obara, K.,Fujioka, Y.,Ohsumi, Y.,Inagaki, F.
Structure of Atg5.Atg16, a complex essential for autophagy
J.Biol.Chem., 282:6763-6772, 2007

PubMed Abstract: Atg5 is covalently modified with a ubiquitin-like modifier, Atg12, and the Atg12-Atg5 conjugate further forms a complex with the multimeric protein Atg16. The Atg12-Atg5.Atg16 multimeric complex plays an essential role in autophagy, the bulk degradation system conserved in all eukaryotes. We have reported here the crystal structure of Atg5 complexed with the N-terminal region of Atg16 at 1.97A resolution. Atg5 comprises two ubiquitin-like domains that flank a helix-rich domain. The N-terminal region of Atg16 has a helical structure and is bound to the groove formed by these three domains. In vitro analysis showed that Arg-35 and Phe-46 of Atg16 are crucial for the interaction. Atg16, with a mutation at these residues, failed to localize to the pre-autophagosomal structure and could not restore autophagy in Atg16-deficient yeast strains. Furthermore, these Atg16 mutants could not restore a severe reduction in the formation of the Atg8-phosphatidylethanolamine conjugate, another essential factor for autophagy, in Atg16-deficient strains under starvation conditions. These results taken together suggest that the direct interaction between Atg5 and Atg16 is crucial to the performance of their roles in autophagy.

PubMed: 17192262
DOI: 10.1074/jbc.M609876200

Experimental method

X-RAY DIFFRACTION (2.2 Å)