› 2y6e

X-ray diffraction
2.4Å resolution

Structure of the D1D2 domain of USP4, the conserved catalytic domain

Released:
DOI: 10.2210/pdb2y6e/pdb
PDB entry 2y6e coloured by chain, front view.
PDB entry 2y6e coloured by chain, side view.
PDB entry 2y6e coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The DUSP-Ubl domain of USP4 enhances its catalytic efficiency by promoting ubiquitin exchange.
Clerici M, Luna-Vargas MP, Faesen AC, Sixma TK
Nat Commun 5 5399 (2014)
PMID: 25404403

Function and Biology Details

Reaction catalysed: 
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-171536 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin carboxyl-terminal hydrolase 4 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 367 amino acids
Theoretical weight: 42.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13107 (Residues: 296-490, 765-932; Coverage: 38%)
Gene names: UNP, UNPH, USP4
Sequence domains: Ubiquitin carboxyl-terminal hydrolase
Structure domains: Cysteine proteinases

Ligands and Environments

2 bound ligands:
Ligand ZN 6 x ZN
Ligand SO4 2 x SO4
1 modified residue:
Ligand CME 6 x CME

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-2
Spacegroup: P212121
Unit cell:
a: 110.5Å b: 151.03Å c: 178.67Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.178 0.21
Expression system: Escherichia coli

Quick links

Citations

12 review citations

USP7: Structure, substrate specificity, and inhibition.
Pozhidaeva et al. (2019)
11 more

13 mentions without citation

Molecular basis of USP7 inhibition by selective small-molecule inhibitors.
Turnbull et al. (2017)
12 more