› 4nql

X-ray diffraction
2.3Å resolution

The crystal structure of the DUB domain of AMSH orthologue, Sst2 from S. pombe, in complex with lysine 63-linked diubiquitin

Released:
DOI: 10.2210/pdb4nql/pdb
PDB entry 4nql coloured by chain, front view.
PDB entry 4nql coloured by chain, side view.
PDB entry 4nql coloured by chain, top view.
Source organisms:
Primary publication:
Insights into the mechanism of deubiquitination by JAMM deubiquitinases from cocrystal structures of the enzyme with the substrate and product.
Shrestha RK, Ronau JA, Davies CW, Guenette RG, Strieter ER, Paul LN, Das C
Biochemistry 53 3199-217 (2014)
PMID: 24787148

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
AMSH-like protease sst2 Chain: A
Molecule details ›
Chain: A
Length: 221 amino acids
Theoretical weight: 24.66 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9P371 (Residues: 221-435; Coverage: 49%)
Gene names: SPAC19B12.10, sst2
Sequence domains: JAB1/Mov34/MPN/PAD-1 ubiquitin protease
Structure domains: Cytidine Deaminase, domain 2
Ubiquitin Chain: B
Molecule details ›
Chain: B
Length: 76 amino acids
Theoretical weight: 8.6 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P0CG50 (Residues: 609-684; Coverage: 10%)
Gene name: Ubc
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Ubiquitin Chain: C
Molecule details ›
Chain: C
Length: 77 amino acids
Theoretical weight: 8.69 KDa
Source organism: Mus musculus
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P0CG50 (Residues: 609-684; Coverage: 10%)
Gene name: Ubc
Sequence domains: Ubiquitin family

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand EDO 7 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P212121
Unit cell:
a: 49.489Å b: 56.74Å c: 135.11Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.213 0.263
Expression system: Escherichia coli BL21

Quick links

Citations

14 review citations

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

5 mentions without citation

Insights into the mechanism of deubiquitination by JAMM deubiquitinases from cocrystal structures of the enzyme with the substrate and product.
Shrestha et al. (2014)
4 more