› 4msm

X-ray diffraction
1.74Å resolution

Crystal structure of Schizosaccharomyces pombe AMSH-like protease sst2 E286A mutant bound to ubiquitin

Released:
DOI: 10.2210/pdb4msm/pdb
PDB entry 4msm coloured by chain, front view.
PDB entry 4msm coloured by chain, side view.
PDB entry 4msm 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 dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-143407 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
AMSH-like protease sst2 Chains: A, C
Molecule details ›
Chains: A, C
Length: 197 amino acids
Theoretical weight: 21.92 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9P371 (Residues: 245-435; Coverage: 44%)
Gene names: SPAC19B12.10, sst2
Sequence domains: JAB1/Mov34/MPN/PAD-1 ubiquitin protease
Structure domains: Cytidine Deaminase, domain 2
Ubiquitin Chains: B, D
Molecule details ›
Chains: B, D
Length: 81 amino acids
Theoretical weight: 8.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand EDO 10 x EDO
Ligand PO4 2 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P212121
Unit cell:
a: 57.017Å b: 95.322Å c: 112.944Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.195 0.225
Expression system: Escherichia coli BL21

Quick links

Citations

14 review citations

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

2 mentions without citation

Atomic structure of the 26S proteasome lid reveals the mechanism of deubiquitinase inhibition.
Dambacher et al. (2016)
1 more