Revisiting the structure of UBR box from human UBR6

Eukaryotic N-degron pathways are proteolytic systems with the ability to recognize specific N-terminal residues of substrate proteins, which are essential parts of their degradation signals. Domains, referred to as UBR boxes, of several E3 ubiquitin ligases can recognize basic N-terminal residues as N-degrons. UBR6 is among the seven mammalian UBR family proteins containing the UBR box domain. However, the recognition of basic type-1 N-degrons by UBR6 is still not well understood. The crystal structure of the UBR box from human UBR6 revealed zinc-mediated dimerization, a structural feature distinct from other monomeric UBR boxes. Furthermore, its folding pattern differed from that of the UBR fold, although the sequences aligned well with those of other UBR boxes. In this study, we re-determined the structure of the UBR box from human UBR6 to investigate whether the unusual domain-swapped dimer was structurally relevant. The newly determined UBR box of UBR6 at 1.5 Å resolution was a monomer with a classical UBR fold. Our structure was compared with previously reported structures of UBR boxes, and its structural features were further analyzed using N-degron binding assays.