› 4ksj

X-ray diffraction
1.6Å resolution

Crystal structure of the OTU domain of Gumby/Fam105B at 1.6 angstrom

Released:
DOI: 10.2210/pdb4ksj/pdb
PDB entry 4ksj coloured by chain, front view.
PDB entry 4ksj coloured by chain, side view.
PDB entry 4ksj coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
The linear ubiquitin-specific deubiquitinase gumby regulates angiogenesis.
Rivkin E, Almeida SM, Ceccarelli DF, Juang YC, MacLean TA, Srikumar T, Huang H, Dunham WH, Fukumura R, Xie G, Gondo Y, Raught B, Gingras AC, Sicheri F, Cordes SP
Nature 498 318-24 (2013)
PMID: 23708998

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:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188378 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin thioesterase otulin Chain: A
Molecule details ›
Chain: A
Length: 276 amino acids
Theoretical weight: 32.5 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q96BN8 (Residues: 79-352; Coverage: 78%)
Gene names: FAM105B, OTULIN
Sequence domains: Peptidase family C101

Ligands and Environments

2 bound ligands:
Ligand BME 1 x BME
Ligand GOL 2 x GOL
1 modified residue:
Ligand MSE 9 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Spacegroup: P212121
Unit cell:
a: 43.35Å b: 71.82Å c: 94.2Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.18 0.215
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

78 review citations

Breaking the chains: deubiquitylating enzyme specificity begets function.
Clague et al. (2019)
77 more

3 mentions without citation

The linear ubiquitin-specific deubiquitinase gumby regulates angiogenesis.
Rivkin et al. (2013)
2 more