› 4pqt

X-ray diffraction
2.05Å resolution

Insights into the mechanism of deubiquitination by JAMM deubiquitinases from co-crystal structures of enzyme with substrate and product

Released:
DOI: 10.2210/pdb4pqt/pdb
PDB entry 4pqt coloured by chain, front view.
PDB entry 4pqt coloured by chain, side view.
PDB entry 4pqt 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

Assemblies composition:
monomeric
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-165047 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
AMSH-like protease sst2 Chain: A
Molecule details ›
Chain: A
Length: 197 amino acids
Theoretical weight: 21.94 KDa
Source organism: Schizosaccharomyces pombe 972h-
Expression system: Escherichia coli
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
Protein UBBP4 Chain: B
Molecule details ›
Chain: B
Length: 81 amino acids
Theoretical weight: 8.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-D
Spacegroup: P21
Unit cell:
a: 42.413Å b: 58.003Å c: 56.189Å
α: 90° β: 108.97° γ: 90°
R-values:
R R work R free
0.204 0.202 0.252
Expression system: Escherichia coli

Quick links

Citations

14 review citations

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

2 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)
1 more