› 5gpj

X-ray diffraction
3.5Å resolution

Crystal Structure of Proton-Pumping Pyrophosphatase

Released:
DOI: 10.2210/pdb5gpj/pdb
PDB entry 5gpj coloured by chain, front view.
PDB entry 5gpj coloured by chain, side view.
PDB entry 5gpj coloured by chain, top view.
Source organism: Vigna radiata var. radiata
Primary publication:
Membrane pyrophosphatases from Thermotoga maritima and Vigna radiata suggest a conserved coupling mechanism.
Li KM, Wilkinson C, Kellosalo J, Tsai JY, Kajander T, Jeuken LJ, Sun YJ, Goldman A
Nat Commun 7 13596 (2016)
PMID: 27922000

Function and Biology Details

Reaction catalysed: 
Diphosphate + H(2)O + H(+)(Side 1) = 2 phosphate + H(+)(Side 2)
Biochemical function:
Biological process:
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-149335 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Pyrophosphate-energized vacuolar membrane proton pump Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 774 amino acids
Theoretical weight: 81.1 KDa
Source organism: Vigna radiata var. radiata
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: P21616 (Residues: 1-766; Coverage: 100%)
Sequence domains: Inorganic H+ pyrophosphatase

Ligands and Environments

2 bound ligands:
Ligand PO4 4 x PO4
Ligand MG 8 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE BL15A1
Spacegroup: C2
Unit cell:
a: 225.703Å b: 81.637Å c: 264.845Å
α: 90° β: 92.87° γ: 90°
R-values:
R R work R free
0.23 0.226 0.304
Expression system: Saccharomyces cerevisiae

Quick links

Citations

3 review citations

Biochemical, Structural and Physiological Characteristics of Vacuolar H+-Pyrophosphatase.
Segami et al. (2018)
2 more

5 mentions without citation

The Function of Membrane Integral Pyrophosphatases From Whole Organism to Single Molecule.
Holmes et al. (2019)
4 more