› 4z2z

X-ray diffraction
1.8Å resolution

New crystal structure of yeast Ddi1 aspartyl protease reveals substrate engagement mode

Released:
DOI: 10.2210/pdb4z2z/pdb
PDB entry 4z2z coloured by chain, front view.
PDB entry 4z2z coloured by chain, side view.
PDB entry 4z2z coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family.
Trempe JF, Šašková KG, Sivá M, Ratcliffe CD, Veverka V, Hoegl A, Ménade M, Feng X, Shenker S, Svoboda M, Kožíšek M, Konvalinka J, Gehring K
Sci Rep 6 33671 (2016)
PMID: 27646017

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-154022 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
DNA damage-inducible protein 1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 146 amino acids
Theoretical weight: 16.33 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P40087 (Residues: 185-325; Coverage: 33%)
Gene names: DDI1, VSM1, YER143W
Sequence domains: gag-polyprotein putative aspartyl protease
Structure domains: Acid Proteases

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P212121
Unit cell:
a: 41.515Å b: 50.051Å c: 131.562Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.184 0.183 0.213
Expression system: Escherichia coli K-12

Quick links

Citations

3 review citations

DNA-protein crosslink proteases in genome stability.
Ruggiano et al. (2021)
2 more

5 mentions without citation

Structural studies of the yeast DNA damage-inducible protein Ddi1 reveal domain architecture of this eukaryotic protein family.
Trempe et al. (2016)
4 more