5YEC

Crystal structure of Atg7CTD-Atg8-MgATP complex in form II

Summary for 5YEC

• Entry DOI: 10.2210/pdb5yec/pdb
• Descriptor: Ubiquitin-like modifier-activating enzyme ATG7, Autophagy-related protein 8, ZINC ION, ... (6 entities in total)
• Functional Keywords: autophagy, e1 enzyme, ubiquitin-like protein, metal binding protein, protein transport-metal binding protein complex, protein transport/metal binding protein
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast); More
• Cellular location: Cytoplasm: P38862; Cytoplasmic vesicle, cvt vesicle membrane; Lipid-anchor: P38182
• Total number of polymer chains: 4
• Total formula weight: 104999.24

Authors

Yamaguchi, M.,Satoo, K.,Noda, N.N. (deposition date: 2017-09-16, release date: 2018-03-28, Last modification date: 2024-03-27)

Primary citation

Yamaguchi, M.,Satoo, K.,Suzuki, H.,Fujioka, Y.,Ohsumi, Y.,Inagaki, F.,Noda, N.N.
Atg7 Activates an Autophagy-Essential Ubiquitin-like Protein Atg8 through Multi-Step Recognition.
J. Mol. Biol., 430:249-257, 2018

PubMed Abstract: Atg8 is a unique ubiquitin-like protein that is covalently conjugated with a phosphatidylethanolamine through reactions similar to ubiquitination and plays essential roles in autophagy. Atg7 is the E1 enzyme for Atg8, and it activates the C-terminal Gly116 of Atg8 using ATP. Here, we report the crystal structure of Atg8 bound to the C-terminal domain of Atg7 in an unprecedented mode. Atg8 neither contacts with the central β-sheet nor binds to the catalytic site of Atg7, both of which were observed in previously reported Atg7-Atg8 structures. Instead, Atg8 binds to the C-terminal α-helix and crossover loop, thereby changing the autoinhibited conformation of the crossover loop observed in the free Atg7 structure into a short helix and a disordered loop. Mutational analyses suggested that this interaction mode is important for the activation reaction. We propose that Atg7 recognizes Atg8 through multiple steps, which would be necessary to induce a conformational change in Atg7 that is optimal for the activation reaction.

PubMed: 29237558
DOI: 10.1016/j.jmb.2017.12.002

Experimental method

X-RAY DIFFRACTION (2.147 Å)