Schematic diagram of UbL–UBA domain-containing proteins. The domain structures of yeast Rad23 (accession number NP_010877), human hHR23A (NP_005044) and hHR23B (NP_002865), yeast Dsk2 (P48510), human hPlic-1 (Ubiquilin) (AAD49751), yeast Ddi1 (NP_011070), mouse CIP75 (UBIN) (NP_277068), human A1Up (NP_064516), human KPC2 (NP_057256), human NUB1 (NP_057202) and NUB1L (AAO14547), and human p62 (NP_003891) are shown. The UbL–UBA family of proteins contains an N-terminal UbL domain (or the structurally similar PB1 domain for p62), one or more C-terminal UBA domain(s), and a variable central region (yeast Ddi1 contains a central RVP domain). For family members with multiple UBA domains, the most N-terminal UBA domain is referred to as UBA1 in the text, and additional UBA domains are referred to as UBA2 and UBA3

Model for the mechanism of UbL–UBA function in proteasomal degradation. a Intramolecular and intermolecular interactions between UbL and UBA domains. The UbL and UBA domains within the same protein can interact. They can also interact in either homoor heterodimeric fashion when present in separate proteins. b Under “resting”’ conditions, the UbL–UBA protein may reside in a conformation that is not amenable to binding to the proteasomal proteins or ubiquitinated substrates through UbL–UBA interactions (either intramolecular or intermolecular homo- or heterodimers). Upon induction of more favorable conditions (such as increased levels of ubiquitinated proteins), the UbL or UBA domains bind to the proteasome or the ubiquitinated target substrates, which causes a conformational change in the UbL–UBA protein and disruption of the intramolecular UbL–UBA interaction, for example. This allows the other domain to be able to bind as well, thereby creating a complex containing the UbL–UBA shuttle protein, the ubiquitinated target substrate, and the proteasome, which may facilitate the proteasomal degradation of the target protein. This sequence of events may occur for misfolded or damaged ER-localized proteins that are subject to ERAD. c Excessively high levels of the UbL–UBA proteins may exert a dominant negative effect (similar to expressing only one domain), where ubiquitinated substrates are bound by the UBA domain and proteasomal receptors are bound by the UbL domain of different proteins, depending on relative affinities. This would result in a sequestering effect that diminishes the ability of a single UbL– UBA protein to bind the target substrate and the proteasome simultaneously, as occurs in the model described in (b). d Conversely, the loss of UbL–UBA proteins would remove the necessary shuttle factor required to carry the target protein to the proteasome