Solution Structure of the Ubiquitin-associated (UBA) Domain of Human Autophagy Receptor NBR1 and Its Interaction with Ubiquitin and Polyubiquitin

Abstract

Background:The autophagic receptor NBR1 is commonly found in ubiquitin-positive inclusions in neurodegenerative diseases. Results: Molecular recognition of ubiquitin and polyubiquitin by NBR1 is described. Conclusion:The ubiquitin-associated domain of NBR1 shows unexpectedly high affinity for monoubiquitin but lacks polyubiquitin linkage specificity. Significance: NBR1 may be highly efficient at forming intracellular inclusions with ubiquitylated proteins via non-linkagespecific association with ubiquitin.

DNA-Damage-Inducible 1 Protein (Ddi1) Contains an Uncharacteristic Ubiquitin-like Domain that Binds Ubiquitin

“…In Ddi1UBA, the most perturbed residues are clustered around Gly402, located in the loop between helices 1 and 2, Glu420 and Ala423 in helix 3, and Phe427 at the C terminus (Fig 4D–E). The analysis of NMR titration curves from this titration yielded the dissociation constant K d of 150 ± 16 μM (Fig 4C, F), which is in the typical K d range (4–500 μM) reported for interactions between monomeric Ub and other UBA domains (Ohno et al, 2005; Raasi et al, 2005; Trempe et al, 2005; Varadan et al, 2005; Walinda et al, 2014; Zhang et al, 2008). Based on the CSP data from Ub:Ddi1UBA titrations, complemented with intermolecular distance constraints derived using site-directed paramagnetic spin-labeling (Fig S5), we generated a structural model of the Ub:Ddi1UBA complex using biomolecular docking program HADDOCK (de Vries et al, 2010).…”

Autophagic degradation of the androgen receptor mediated by increased phosphorylation of p62 suppresses apoptosis in hypoxia

“…The autophagy adaptor protein NBR1 also has a C-terminal UBA domain [53], and the NBR1 UBA domain binds to ubiquitin with higher affinity (K D = 3-4 μM) compared to the p62 UBA domain (K D = 540-750 μM) in vitro [49,54]. The difference in ubiquitin affinity is attributed to structural differences of the UBA domains in each protein.…”

“…The UBA domain contains the evolutionarily conserved MGF motif, and the charge of the amino acid residue immediately upstream of the MGF motif plays a crucial role in the interaction with ubiquitin [53]. Among UBA domains in the SMART database, 42% have a negatively charged amino acid residue at the position in front of the MGF motif, and the corresponding amino acid of NBR1 is the negatively charged at glutamic acid 926 [53]. In contrast, at the equivalent site of p62, serine 403 is uncharged.…”

The receptor proteins: pivotal roles in selective autophagy

“…Due to the high architectural similarity between NBR1 and p62, both p62 and NBR1 have been reported to act cooperatively to target polyubiquitylated aggregates and whole organelles, including peroxisomes, to be selectively degraded [48,49]. Unexpectedly, Walinda et al [50] found that NBR1 differs from p62 in its UBA structure and accordingly in its interaction with ubiquitin. These differences result in a much higher affinity of NBR1 for ubiquitin than p62.…”