Insights into links between autophagy and the ubiquitin system from the structure of LC3B bound to the LIR motif from the E3 ligase NEDD4

Abstract

Members of the LC3/GABARAP family of ubiquitin-like proteins function during autophagy by serving as membrane linked protein-binding platforms. Their C-termini are physically attached to membranes through covalent linkage to primary amines on lipids such as phosphatidylethanolamine, while their ubiquitin-like fold domains bind "LIR" (LC3-Interacting Region) sequences found within an extraordinarily diverse array of proteins including regulators of autophagy, adaptors that recruit ubiquitinated cargoes to be degraded, and even proteins controlling processes at membranes that are not associated with autophagy. Recently, LC3/GABARAP proteins were found to bind the ubiquitin E3 ligase NEDD4 to influence ubiquitination associated with autophagy in human cell lines. Here, we use purified recombinant proteins to define LC3B interactions with a specific LIR sequence from NEDD4, present a crystal structure showing atomic details of the interaction, and show that LC3B-binding can steer intrinsic NEDD4 E3 ligase activity. The data provide detailed molecular insights underlying recruitment of an E3 ubiquitin ligase to phagophores during autophagy.

Astrocytes and neurons produce distinct types of polyglucosan bodies in Lafora disease

“…The direct binding of p62 to LC3 and GABARAP family proteins, that serves as membrane linked protein-binding platforms (Qiu et al, 2017), allows p62 to guide ubiquitinated proteins to autophagosomes and to autophagic processes (Isakson et al, 2013). Moreover, p62 is also related to secretory autophagy, in which the content of the autophagosome is extruded from the cell (Ponpuak et al, 2016).…”

“…The direct binding of p62 to LC3 and GABARAP family proteins, that serves as membrane linked protein-binding platforms (Qiu, Zheng, Wu, & Schulman, 2017), allows p62 to guide ubiquitinated proteins to autophagosomes and to autophagic processes (Isakson et al, 2013).…”

Regulation of the Tumor-Suppressor BECLIN 1 by Distinct Ubiquitination Cascades

“…The interaction of NEDD4 to LC3 stimulates the E3 ligase activity of NEDD4 and ubiquitinated LC3 species can be detected. However, future work will clarify whether this ubiquitination represents an enhancing or self-limiting effect on starvation induced autophagy [ 106 , 107 ].…”

The conformational and mutational landscape of the ubiquitin-like marker for the autophagosome formation in cancer

“…Several three-dimensional (3D) structures of LC3B have been solved by X-ray or NMR in the free state (Kouno et al, 2005;Rogov et al, 2013) or in complex with different biological partners (Ichimura et al, 2008;Jemal et al, 2011;Kuang et al, 2016b;Kwon et al, 2017;Lv et al, 2016;McEwan et al, 2015;Olsvik et al, 2015;Qiu et al, 2017;Rogov et al, 2017Rogov et al, , 2013Stadel et al, 2015;Suzuki et al, 2014;Yang et al, 2017). This provides a valuable source of information for investigations using biomolecular simulations and other structural computational methods of both the LC3B wild-type and its mutated variant.…”