› 7jru

X-ray diffraction
2.21Å resolution

Phospholipase D engineered mutant bound to phosphatidic acid (8 hour soak)

Released:
DOI: 10.2210/pdb7jru/pdb
PDB entry 7jru coloured by chain, front view.
PDB entry 7jru coloured by chain, side view.
PDB entry 7jru coloured by chain, top view.
Source organism: Streptomyces antibioticus
Primary publication:
Structures of an engineered phospholipase D with specificity for secondary alcohol transphosphatidylation: insights into plasticity of substrate binding and activation.
Samantha A, Damnjanović J, Iwasaki Y, Nakano H, Vrielink A
OpenAccess logo Biochem J 478 1749-1767 (2021)
PMID: 33843991

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176073 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phospholipase D Chain: A
Molecule details ›
Chain: A
Length: 509 amino acids
Theoretical weight: 54 KDa
Source organism: Streptomyces antibioticus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q53728 (Residues: 48-556; Coverage: 100%)
Sequence domains: PLD-like domain

Ligands and Environments

3 bound ligands:
Ligand MES 1 x MES
Ligand GOL 1 x GOL
Ligand VHY 1 x VHY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: AUSTRALIAN SYNCHROTRON BEAMLINE MX1
Spacegroup: P212121
Unit cell:
a: 58.581Å b: 84.434Å c: 99.068Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.178 0.178 0.239
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Activity-based directed evolution of a membrane editor in mammalian cells.
Tei et al. (2023)
1 more