8J9R

Crystal structure of UBR box of YIFS-UBR4

Summary for 8J9R

• Entry DOI: 10.2210/pdb8j9r/pdb
• Descriptor: E3 ubiquitin-protein ligase UBR4, ZINC ION (3 entities in total)
• Functional Keywords: e3 ligase, ubr box, ligase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 8619.05

Authors

Jeong, D.-E.,Kim, S.-J.,Shin, H.-C. (deposition date: 2023-05-04, release date: 2023-12-06, Last modification date: 2023-12-13)

Primary citation

Jeong, D.E.,Lee, H.S.,Ku, B.,Kim, C.H.,Kim, S.J.,Shin, H.C.
Insights into the recognition mechanism in the UBR box of UBR4 for its specific substrates.
Commun Biol, 6:1214-1214, 2023

PubMed Abstract: The N-end rule pathway is a proteolytic system involving the destabilization of N-terminal amino acids, known as N-degrons, which are recognized by N-recognins. Dysregulation of the N-end rule pathway results in the accumulation of undesired proteins, causing various diseases. The E3 ligases of the UBR subfamily recognize and degrade N-degrons through the ubiquitin-proteasome system. Herein, we investigated UBR4, which has a distinct mechanism for recognizing type-2 N-degrons. Structural analysis revealed that the UBR box of UBR4 differs from other UBR boxes in the N-degron binding sites. It recognizes type-2 N-terminal amino acids containing an aromatic ring and type-1 N-terminal arginine through two phenylalanines on its hydrophobic surface. We also characterized the binding mechanism for the second ligand residue. This is the report on the structural basis underlying the recognition of type-2 N-degrons by the UBR box with implications for understanding the N-end rule pathway.

PubMed: 38030679
DOI: 10.1038/s42003-023-05602-7

Experimental method

X-RAY DIFFRACTION (1.65 Å)