The NMR structure of the p62 PB1 domain, a key protein in autophagy and NF-κB signaling pathway

Abstract

In eukaryotic cells, proteins are degraded via two main pathways; One is the ubiquitin-proteasome system that degrades short-lived proteins, and the other is autophagy that degrades long-lived proteins and damaged organelles (Noda et al. 2009). The p62, also called ZIP (PKC-finteracting protein) or sequestosome 1, plays a crucial role in these protein degradation pathways (Sumimoto et al. 2007). In autophagy, polyubiquitinated aggregated proteins and damaged organelles are enclosed by the isolation membrane, eventually enwrapped by the autophagosome. The autophagosome is fused with the vacuole/lysosome and its inner content is delivered and then degraded. The p62, initially identified as a protein that binds to the SH2 domain of the tyrosine kinase Lck, functions as a receptor protein for aberrant proteins. It contains a PB1 domain at its N terminus, followed by a ZZ-type zinc-finger motif, a LC3 interacting region, and a UBA domain at its C-terminus (Geetha and Wooten 2002). The p62 interacts with ubiquitin through the UBA domain, and self-assembles through the PB1 domain to form large protein aggregates (Bjorkoy et al. 2005). The p62 also binds the autophagy adaptor LC3 through the WXXL motif in the LC3 interacting region (Noda et al. 2008). Defects in autophagy cause accumulation of protein aggregates that contain ubiquitin and p62, leading to severe liver damage such as steatohepatitis and hepatocellular carcinomas, and neurodegenerative diseases such as Parkinson’s disease, Alzheimer disease, and Huntington’s disease (Zatloukal et al. 2002). A recent study indicated that the oligomerization through the PB1 domain was important not only in the assembly of the targets, but also in the interaction with LC3 (Bjorkoy et al. 2005). In the ubiqutin-proteasome system, p62 acts as a shuttling factor that transports ubiquitinated proteins to the proteasome, by interaction through the PB1 domain with the proteasome subunits, S5a and Rpt1 (Seibenhener et al. 2004; Geetha et al. 2008). The p62 also works as a key factor in cell signal transduction. In the NF-jB signaling pathway, p62 controls osteoclastogenesis, T-cell differentiation, and tumor progression, via the PB1–PB1 interaction with PKCf (Geetha and Wooten 2002). Further, p62 controls adipogenesis and obesity via the interaction with ERK (Moscat et al. 2006), and apoptosis via ubiquitinated Caspase 8 (Jin et al. 2009). The p62 PB1 domain plays a variety of physiological roles, both through the PB1–PB1 interaction, and through ‘‘non-canonical’’ PB1 mediated interactions with proteins lacking the PB1 domain, such as S5a, Rpt1, ERK, and LCK. Thus, p62 PB1 can be expected to have characteristic features not common to other PB1 domains whose structures have been solved. The PB1 domain is classified into three types, type I, type II, and type I/II (Hirano et al. 2004). Type I contains a motif of 28 amino acid residues with highly conserved acidic and hydrophobic residues named the OPCA motif. Type II contains a conserved lysine residue on the side opposite to the OPCA motif. Type I/II contains the OPCA motif and the conserved lysine residue, and thus can selfinteract in a front-to-back topology. The p62 PB1 contains both the OPCA motif and the conserved lysine residue and T. Saio Graduate School of Life Science, Hokkaido University, Sapporo 001-0021, Japan