The UBR Domain of Plant Ubr1 Homolog PRT6 Accommodates Basic and Hydrophobic Amino Termini for Substrate Recognition

Abstract

N-degrons are amino-terminal degradation signals. Non-acetylated first residues with bulky side chains were the first discovered N-degrons. In yeast, their ability to destabilize a protein depends on ubiquitin ligase Ubr1, which has a binding site for basic first residues, the UBR box, and one for hydrophobic first residues, the N domain. We investigated PRT6, the Arabidopsis homolog of Ubr1, by expression in a yeast strain devoid of Ubr1. Phylogenetic analysis and structure prediction indicate that PRT6 lacks the N domain and thus should not accept hydrophobic N-degrons. However, we show that PRT6 mediates the turnover of proteins with Leu, Phe, Tyr and Trp as the first residue. By functional analysis in the heterologous host, we show that the PRT6 UBR box can accommodate these N-degrons. The data indicate a surprising evolutionary flexibility of the UBR box that may also be found in UBR box proteins of other organisms.

Keywords: N-degron pathway; UBR box; synthetic biology; ubiquitin ligase.