› 1v0w

X-ray diffraction
1.35Å resolution

Phospholipase D from Streptomyces sp. strain PMF soaked with the substrate dibutyrylphosphatidylcholine.

Released:
DOI: 10.2210/pdb1v0w/pdb
PDB entry 1v0w coloured by chain, front view.
PDB entry 1v0w coloured by chain, side view.
PDB entry 1v0w coloured by chain, top view.
Source organism: Streptomyces sp. PMF
Primary publication:
The reaction mechanism of phospholipase D from Streptomyces sp. strain PMF. Snapshots along the reaction pathway reveal a pentacoordinate reaction intermediate and an unexpected final product.
Leiros I, McSweeney S, Hough E
J Mol Biol 339 805-20 (2004)
PMID: 15165852

Function and Biology Details

Reaction catalysed: 
A phosphatidylcholine + H(2)O = choline + a phosphatidate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-160844 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
PLD phosphodiesterase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 506 amino acids
Theoretical weight: 54.06 KDa
Source organism: Streptomyces sp. PMF
UniProt:
  • Canonical: P84147 (Residues: 1-506; Coverage: 100%)
Sequence domains: PLD-like domain
Structure domains: Endonuclease Chain A

Ligands and Environments

1 bound ligand:
Ligand PO3 1 x PO3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM1A
Spacegroup: P21
Unit cell:
a: 57.227Å b: 56.37Å c: 68.631Å
α: 90° β: 93.69° γ: 90°
R-values:
R R work R free
0.162 0.161 0.186

Quick links

Citations

7 review citations

Bacterial Sphingomyelinases and Phospholipases as Virulence Factors.
Flores-Díaz et al. (2016)
6 more

7 mentions without citation

Phospholipase D: enzymology, functionality, and chemical modulation.
Selvy et al. (2011)
6 more