› 6afx

X-ray diffraction
2.3Å resolution

Proton pyrophosphatase - E225A

Released:
DOI: 10.2210/pdb6afx/pdb
PDB entry 6afx coloured by chain, front view.
PDB entry 6afx coloured by chain, side view.
PDB entry 6afx coloured by chain, top view.
Source organism: Vigna radiata var. radiata
Primary publication:
Roles of the Hydrophobic Gate and Exit Channel in Vigna radiata Pyrophosphatase Ion Translocation.
Tsai JY, Tang KZ, Li KM, Hsu BL, Chiang YW, Goldman A, Sun YJ
J Mol Biol 431 1619-1632 (2019)
PMID: 30878480

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
Molecule details ›
Chains: A, B
Length: 766 amino acids
Theoretical weight: 80.03 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

4 bound ligands:
Ligand PO4 4 x PO4
Ligand MG 10 x MG
Ligand K 2 x K
Ligand 1PG 7 x 1PG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSRRC BEAMLINE TPS 05A
Spacegroup: C2
Unit cell:
a: 217.197Å b: 88.321Å c: 158.843Å
α: 90° β: 125.14° γ: 90°
R-values:
R R work R free
0.166 0.165 0.199
Expression system: Saccharomyces cerevisiae

Quick links

Citations

5 review citations

Plant Proton Pumps and Cytosolic pH-Homeostasis.
Cosse et al. (2021)
4 more

2 mentions without citation

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