PDBsum entry 3nim

Metal binding protein

PDB id: 3nim

Contents

Protein chains

82 a.a. *

Ligands

ARG-ARG-ALA-ALA

Metals

_ZN ×12

Waters ×255

* Residue conservation analysis

PDB id:

3nim

Name:

Metal binding protein

Title:

The structure of ubr box (rraa)

Structure:

E3 ubiquitin-protein ligase ubr1. Chain: a, b, d, f. Fragment: ubr-type domain, residues 115-194. Synonym: n-recognin-1, n-end-recognizing protein. Engineered: yes. Other_details: ubr box. Peptide rraa. Chain: x. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Other_details: chemical synthesis

Resolution:

2.00Å R-factor: 0.193 R-free: 0.240

Authors:

W.S.Choi,B.-C.Jeong,M.-R.Lee,H.K.Song

Key ref:

W.S.Choi et al. (2010). Structural basis for the recognition of N-end rule substrates by the UBR box of ubiquitin ligases. Nat Struct Biol, 17, 1175-1181. PubMed id: 20835240

Date:

16-Jun-10 Release date: 15-Sep-10

Protein chains

P19812  (UBR1_YEAST) -  E3 ubiquitin-protein ligase UBR1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1950 a.a.

Struc: 82 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.2.3.2.27 - RING-type E3 ubiquitin transferase.
• Reaction: S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N₆- ubiquitinyl-[acceptor protein]-L-lysine

Nat Struct Biol 17:1175-1181 (2010)

PubMed id: 20835240

Structural basis for the recognition of N-end rule substrates by the UBR box of ubiquitin ligases.

W.S.Choi, B.C.Jeong, Y.J.Joo, M.R.Lee, J.Kim, M.J.Eck, H.K.Song.

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.