Structure of the autophagic E2 enzyme Atg10

Abstract

Autophagy is a regulated degradation pathway that plays a critical role in all eukaryotic life cycles. One interesting feature of the core autophagic process, autophagosome formation, is similar to ubiquitination. One of two autophagic E2 enzymes, Atg10, interacts with Atg7 to receive Atg12, a ubiquitin-like molecule, and is also involved in the Atg12-Atg5 conjugation reaction. To date, no information on the interaction between Atg10 and Atg7 has been reported, although structural information is available pertaining to the individual components. Here, the crystal structure of Atg10 from Saccharomyces cerevisiae is described at 2.7 Å resolution. A significant improvement of the diffraction limit by heavy-atom derivatization was essential for structure determination. The core fold of yeast Atg10 is well conserved compared with those of Atg3 and other E2 enzymes. In contrast to other E2 enzymes, however, the autophagic E2 enzymes Atg3 and Atg10 possess insertion regions in the middle of the core fold and may be involved in protein function. The missing segment, which was termed the `FR-region', in Atg10 may be important for interaction with the E1 enzyme Atg7. This study provides a framework for understanding the E2 conjugation reaction in autophagy.

Dynamic regulation of macroautophagy by distinctive ubiquitin-like proteins

“…The E2 active site regions display a range of conformations or are not visible in some crystals, raising the possibility of active site malleability being important for different reactions, such as receiving the cognate UBL from Atg7 and subsequent ligation 70,71,73-75 . Comparison of free and Atg7-bound structures reveals dramatic reorientation of the E2 active sites.…”

“…( b ) Conformational variability of the active site region of autophagy E2 enzymes. For Atg3 and Atg10 from S. cerevisiae , the active site and other structural regions are dramatically reoriented upon binding to Atg7, although the crystal structure of isolated Atg10 from K. marxianus appears closer to the active conformation 70,71,73-75 . ( c ) Crystal structure of human ATG3 (cyan)-ATG12 (orange)–ATG5 (green)-ATG16L1 N-terminal domain (purple)1 79 .…”

Atomistic Autophagy: The Structures of Cellular Self-Digestion

“…The detailed basis for Atg12 transfer from Atg10 to Atg5 remains unknown. Nonetheless, clues have been provided by NMR, mutagenesis, and crosslinking to identify Atg10 and Atg5 residues involved in their interaction (Hong et al, 2012; Matsushita et al, 2007; Yamaguchi et al, 2012). Mapping important residues suggests that Atg5 binds the concave surface surrounding Atg10’s active site (Yamaguchi et al, 2012).…”

“…Structures of K. marxianus Atg10 (cyan) and human Atg12 (lime)~Atg5 (blue)-Atg16 (magenta) (Hong et al, 2012; Noda et al, 2013; Otomo et al, 2013; Yamaguchi et al, 2012). Arrow highlights the Atg3 cysteine, from which Atg12 is transferred, to the Atg5 target.…”

Insights into autophagosome maturation revealed by the structures of ATG5 with its interacting partners

“…13,26,[36][37][38][39][40][41][42][43][44] Despite this, however, autophagosome maturation is still poorly understood and the recently discovered TECPR1 protein is one of the few factors identified to date that mediates the fusion of autophagosomes and lysosomes. 21,22 TECPR1 was initially characterized in association with TRAPP vesicle-tethering, the CCT chaperonin, and the ATG12-ATG5-ATG16L1 complex by extensive proteomic analysis, suggesting its involvement in phagophore elongation and autophagosome assembly.…”