› 2ik6

X-ray diffraction
1.8Å resolution

Yeast inorganic pyrophosphatase variant D120E with magnesium and phosphate

Released:
DOI: 10.2210/pdb2ik6/pdb
PDB entry 2ik6 coloured by chain, front view.
PDB entry 2ik6 coloured by chain, side view.
PDB entry 2ik6 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
A complete structural description of the catalytic cycle of yeast pyrophosphatase.
Oksanen E, Ahonen AK, Tuominen H, Tuominen V, Lahti R, Goldman A, Heikinheimo P
Biochemistry 46 1228-39 (2007)
PMID: 17260952

Function and Biology Details

Reaction catalysed: 
Diphosphate + H(2)O = 2 phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-133603 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Inorganic pyrophosphatase Chains: A, B
Molecule details ›
Chains: A, B
Length: 286 amino acids
Theoretical weight: 32.24 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli
UniProt:
  • Canonical: P00817 (Residues: 2-287; Coverage: 100%)
Gene names: IPP1, PPA, PPA1, YBR011C, YBR0202
Sequence domains: Inorganic pyrophosphatase
Structure domains: Inorganic pyrophosphatase

Ligands and Environments

3 bound ligands:
Ligand MG 5 x MG
Ligand PO4 2 x PO4
Ligand MPD 1 x MPD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P21
Unit cell:
a: 51.654Å b: 93.191Å c: 69.379Å
α: 90° β: 99.62° γ: 90°
R-values:
R R work R free
0.168 0.167 0.203
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Evolution of acidocalcisomes and their role in polyphosphate storage and osmoregulation in eukaryotic microbes.
Docampo et al. (2010)
2 more

1 mention without citation

Crystal Structure of Inorganic Pyrophosphatase From Schistosoma japonicum Reveals the Mechanism of Chemicals and Substrate Inhibition.
Wu et al. (2021)