5TDC

Crystal structure of the human UBR-box domain from UBR1 in complex with monomethylated arginine peptide.

Summary for 5TDC

• Entry DOI: 10.2210/pdb5tdc/pdb
• Related: 5TDA 5TDB 5TDD
• Descriptor: E3 ubiquitin-protein ligase UBR1, NMM-ILE-PHE-SER peptide, ZINC ION, ... (5 entities in total)
• Functional Keywords: ubr-box, n-end rule, n-degron, monomethylated arginine, ligase
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 4
• Total formula weight: 18298.63

Authors

Kozlov, G.,Munoz-Escobar, J.,Matta-Camacho, E.,Gehring, K. (deposition date: 2016-09-19, release date: 2017-03-22, Last modification date: 2023-10-04)

Primary citation

Munoz-Escobar, J.,Matta-Camacho, E.,Cho, C.,Kozlov, G.,Gehring, K.
Bound Waters Mediate Binding of Diverse Substrates to a Ubiquitin Ligase.
Structure, 25:719-729.e3, 2017

PubMed Abstract: The N-end rule pathway controls the half-life of proteins based on their N-terminal residue. Positively charged type 1 N-degrons are recognized by a negatively charged pocket on the Zn finger named the UBR box. Here, we show that the UBR box is rigid, but bound water molecules in the pocket provide the structural plasticity required to bind different positively charged amino acids. Ultra-high-resolution crystal structures of arginine, histidine, and methylated arginine reveal that water molecules mediate the binding of N-degron peptides. Using a high-throughput binding assay and isothermal titration calorimetry, we demonstrate that the UBR box is able to bind methylated arginine and lysine peptides with high affinity and measure the preference for hydrophobic residues in the second position in the N-degron peptide. Finally, we show that the V122L mutation present in Johanson-Blizzard syndrome patients changes the specificity for the second position due to occlusion of the secondary pocket.

PubMed: 28392261
DOI: 10.1016/j.str.2017.03.004

Experimental method

X-RAY DIFFRACTION (1.607 Å)