› 2qiz

X-ray diffraction
2.56Å resolution

Structure of the yeast U-box-containing ubiquitin ligase Ufd2p

Released:
DOI: 10.2210/pdb2qiz/pdb
PDB entry 2qiz coloured by chain, front view.
PDB entry 2qiz coloured by chain, side view.
PDB entry 2qiz coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Structure and function of the yeast U-box-containing ubiquitin ligase Ufd2p.
Tu D, Li W, Ye Y, Brunger AT
Proc Natl Acad Sci U S A 104 15599-606 (2007)
PMID: 17890322

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-157116 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
E4 ubiquitin-protein ligase UFD2 Chain: A
Molecule details ›
Chain: A
Length: 982 amino acids
Theoretical weight: 112.23 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P54860 (Residues: 1-961; Coverage: 100%)
Gene names: D1255, UFD2, YDL190C
Sequence domains:
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)

Ligands and Environments

1 bound ligand:
Ligand K 1 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL11-1
Spacegroup: P212121
Unit cell:
a: 65.502Å b: 122.989Å c: 176.411Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.226 0.221 0.276
Expression system: Escherichia coli

Quick links

Citations

14 review citations

Structural insights into the catalysis and regulation of E3 ubiquitin ligases.
Buetow et al. (2016)
13 more

9 mentions without citation

The UNC-45 myosin chaperone: from worms to flies to vertebrates.
Lee et al. (2014)
8 more