3NIM

The structure of UBR box (RRAA)

Summary for 3NIM

• Entry DOI: 10.2210/pdb3nim/pdb
• Related: 3NIH 3NII 3NIJ 3NIK 3NIL 3NIN 3NIS 3NIT
• Descriptor: E3 ubiquitin-protein ligase UBR1, Peptide RRAA, ZINC ION, ... (4 entities in total)
• Functional Keywords: e3 ubiquitin ligase, ubr box, zinc-binding protein, n-end rule, ligase, metal binding protein
• Biological source: Saccharomyces cerevisiae (Baker's yeast); More
• Total number of polymer chains: 5
• Total formula weight: 38205.04

Authors

Choi, W.S.,Jeong, B.-C.,Lee, M.-R.,Song, H.K. (deposition date: 2010-06-16, release date: 2010-09-15, Last modification date: 2023-11-01)

Primary citation

Choi, W.S.,Jeong, B.-C.,Joo, Y.J.,Lee, M.-R.,Kim, J.,Eck, M.J.,Song, H.K.
Structural basis for the recognition of N-end rule substrates by the UBR box of ubiquitin ligases
Nat.Struct.Mol.Biol., 17:1175-1181, 2010

PubMed Abstract: The N-end rule pathway is a regulated proteolytic system that targets proteins containing destabilizing N-terminal residues (N-degrons) for ubiquitination and proteasomal degradation in eukaryotes. The N-degrons of type 1 substrates contain an N-terminal basic residue that is recognized by the UBR box domain of the E3 ubiquitin ligase UBR1. We describe structures of the UBR box of Saccharomyces cerevisiae UBR1 alone and in complex with N-degron peptides, including that of the cohesin subunit Scc1, which is cleaved and targeted for degradation at the metaphase-anaphase transition. The structures reveal a previously unknown protein fold that is stabilized by a novel binuclear zinc center. N-terminal arginine, lysine or histidine side chains of the N-degron are coordinated in a multispecific binding pocket. Unexpectedly, the structures together with our in vitro biochemical and in vivo pulse-chase analyses reveal a previously unknown modulation of binding specificity by the residue at position 2 of the N-degron.

PubMed: 20835240
DOI: 10.1038/nsmb.1907

Experimental method

X-RAY DIFFRACTION (2 Å)