The Crystal Structure of Atg3, an Autophagy-related Ubiquitin Carrier Protein (E2) Enzyme that Mediates Atg8 Lipidation

• Published in: The Journal of biological chemistry 2007-03, Vol.282 (11), p.8036-8043
• Main Authors: Yamada, Yuya, Suzuki, Nobuo N., Hanada, Takao, Ichimura, Yoshinobu, Kumeta, Hiroyuki, Fujioka, Yuko, Ohsumi, Yoshinori, Inagaki, Fuyuhiko
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Autophagy; Autophagy-Related Protein 7; Autophagy-Related Protein 8 Family; Autophagy-Related Proteins; Catalytic Domain; Crystallography, X-Ray; Glutathione Transferase - metabolism; Microtubule-Associated Proteins - chemistry; Models, Molecular; Molecular Sequence Data; Protein Binding; Protein Conformation; Protein Structure, Secondary; Saccharomyces cerevisiae; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - metabolism; Sequence Homology, Amino Acid; Ubiquitin-Conjugating Enzymes - chemistry
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M611473200

Atg3 is an E2-like enzyme that catalyzes the conjugation of Atg8 and phosphatidylethanolamine (PE). The Atg8-PE conjugate is essential for autophagy, which is the bulk degradation process of cytoplasmic components by the vacuolar/lysosomal system. We report here the crystal structure of Saccharomyces cerevisiae Atg3 at 2.5-Aå resolution. Atg3 has an α/β-fold, and its core region is topologically similar to canonical E2 enzymes. Atg3 has two regions inserted in the core region, one of which consists of ∼80 residues and has a random coil structure in solution and another with a long α-helical structure that protrudes from the core region as far as 30Aå.In vivo and in vitro analyses suggested that the former region is responsible for binding Atg7, an E1-like enzyme, and that the latter is responsible for binding Atg8. A sulfate ion was bound near the catalytic cysteine of Atg3, suggesting a possible binding site for the phosphate moiety of PE. The structure of Atg3 provides a molecular basis for understanding the unique lipidation reaction that Atg3 carries out.