› 7auu

X-ray diffraction
2.45Å resolution

Yeast Diphosphoinositol Polyphosphate Phosphohydrolase DDP1-nose mutant in complex with InsP6

Released:
DOI: 10.2210/pdb7auu/pdb
PDB entry 7auu coloured by chain, front view.
PDB entry 7auu coloured by chain, side view.
PDB entry 7auu coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Multiple substrate recognition by yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase through phosphate clamping.
Márquez-Moñino MÁ, Ortega-García R, Shipton ML, Franco-Echevarría E, Riley AM, Sanz-Aparicio J, Potter BVL, González B
Sci Adv 7 (2021)
PMID: 33893105

Function and Biology Details

Reactions catalysed: 
Polyphosphate + n H(2)O = (n+1) oligophosphate
Diphospho-myo-inositol polyphosphate + H(2)O = myo-inositol polyphosphate + phosphate
P(1),P(5)-bis(5'-adenosyl)pentaphosphate + H(2)O = adenosine 5'-tetraphosphate + AMP
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-189183 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Diphosphoinositol polyphosphate phosphohydrolase DDP1 Chain: A
Molecule details ›
Chain: A
Length: 171 amino acids
Theoretical weight: 19.19 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: Q99321 (Residues: 1-103, 127-188; Coverage: 88%)
Gene names: DDP1, O3575, YOR163W
Sequence domains: NUDIX domain

Ligands and Environments

2 bound ligands:
Ligand IHP 1 x IHP
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALBA BEAMLINE XALOC
Spacegroup: P3221
Unit cell:
a: 62.12Å b: 62.12Å c: 92.472Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.208 0.206 0.255
Expression system: Escherichia coli

Quick links

Citations

7 citation in other articles

Cleavage-Polyadenylation Factor Cft1 and SPX Domain Proteins Are Agents of Inositol Pyrophosphate Toxicosis in Fission Yeast.
Schwer et al. (2022)
6 more

1 mention without citation

Multiple substrate recognition by yeast diadenosine and diphosphoinositol polyphosphate phosphohydrolase through phosphate clamping.
Márquez-Moñino et al. (2021)