› 2gfo

X-ray diffraction
2Å resolution

Structure of the Catalytic Domain of Human Ubiquitin Carboxyl-terminal Hydrolase 8

Released:
DOI: 10.2210/pdb2gfo/pdb
PDB entry 2gfo coloured by chain, front view.
PDB entry 2gfo coloured by chain, side view.
PDB entry 2gfo coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Amino-terminal dimerization, NRDP1-rhodanese interaction, and inhibited catalytic domain conformation of the ubiquitin-specific protease 8 (USP8).
Avvakumov GV, Walker JR, Xue S, Finerty PJ, Mackenzie F, Newman EM, Dhe-Paganon S
J Biol Chem 281 38061-70 (2006)
PMID: 17035239

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 domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154190 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin carboxyl-terminal hydrolase 8 Chain: A
Molecule details ›
Chain: A
Length: 396 amino acids
Theoretical weight: 45.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P40818 (Residues: 734-1110; Coverage: 34%)
Gene names: KIAA0055, UBPY, USP8
Sequence domains: Ubiquitin carboxyl-terminal hydrolase
Structure domains: Cysteine proteinases

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
1 modified residue:
Ligand MSE 5 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: P61
Unit cell:
a: 67.173Å b: 67.173Å c: 194.458Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.171 0.168 0.21
Expression system: Escherichia coli BL21

Quick links

Citations

36 review citations

Breaking the chains: structure and function of the deubiquitinases.
Komander et al. (2009)
35 more

14 mentions without citation

Regulation of proteolysis by human deubiquitinating enzymes.
Eletr et al. (2014)
13 more