› 5k16

X-ray diffraction
2.6Å resolution

Crystal structure of free Ubiquitin-specific protease 12

Released:
DOI: 10.2210/pdb5k16/pdb
PDB entry 5k16 coloured by chain, front view.
PDB entry 5k16 coloured by chain, side view.
PDB entry 5k16 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Allosteric Activation of Ubiquitin-Specific Proteases by β-Propeller Proteins UAF1 and WDR20.
Li H, Lim KS, Kim H, Hinds TR, Jo U, Mao H, Weller CE, Sun J, Chatterjee C, D'Andrea AD, Zheng N
Mol Cell 63 249-260 (2016)
PMID: 27373336

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:
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-130888 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ubiquitin carboxyl-terminal hydrolase 12 Chains: A, B
Molecule details ›
Chains: A, B
Length: 355 amino acids
Theoretical weight: 41.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: O75317 (Residues: 16-370; Coverage: 96%)
Gene names: UBH1, USP12, USP12L1
Sequence domains: Ubiquitin carboxyl-terminal hydrolase
Structure domains: Cysteine proteinases

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Spacegroup: P212121
Unit cell:
a: 52.396Å b: 109.636Å c: 134.193Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.193 0.19 0.246
Expression system: Escherichia coli K-12

Quick links

Citations

7 review citations

Mechanisms of Deubiquitinase Specificity and Regulation.
Mevissen et al. (2017)
6 more

7 mentions without citation

Molecular Mechanisms of DUBs Regulation in Signaling and Disease.
Li et al. (2021)
6 more