6KGI

RLGS-yUbr1 Ubr box

Summary for 6KGI

• Entry DOI: 10.2210/pdb6kgi/pdb
• Descriptor: E3 ubiquitin-protein ligase UBR1, ZINC ION (3 entities in total)
• Functional Keywords: ubr1, ubr box, ligase
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
• Total number of polymer chains: 1
• Total formula weight: 9875.11

Authors

Heo, J.,Kwon, D.H.,Kim, L.,Song, H.K. (deposition date: 2019-07-11, release date: 2020-01-22, Last modification date: 2023-11-22)

Primary citation

Kim, L.,Kwon, D.H.,Heo, J.,Park, M.R.,Song, H.K.
Use of the LC3B-fusion technique for biochemical and structural studies of proteins involved in the N-degron pathway.
J.Biol.Chem., 295:2590-2600, 2020

PubMed Abstract: The N-degron pathway, formerly the N-end rule pathway, is a protein degradation process that determines the half-life of proteins based on their N-terminal residues. In contrast to the well-established studies over decades, studies of this pathway, including biochemical characterization and high-resolution structures, are relatively limited. In this study, we have developed a unique fusion technique using microtubule-associated protein 1A/1B light chain 3B, a key marker protein of autophagy, to tag the N terminus of the proteins involved in the N-degron pathway, which enables high yield of homogeneous target proteins with variable N-terminal residues for diverse biochemical studies including enzymatic and binding assays and substrate identification. Intriguingly, crystallization showed a markedly enhanced probability, even for the N-degron complexes. To validate our results, we determined the structures of select proteins in the N-degron pathway and compared them with the Protein Data Bank-deposited proteins. Furthermore, several biochemical applications of this technique were introduced. Therefore, this technique can be used as a general tool for the study of the N-degron pathway.

PubMed: 31919097
DOI: 10.1074/jbc.RA119.010912

Experimental method

X-RAY DIFFRACTION (1.04 Å)