› 2qv7

X-ray diffraction
2.3Å resolution

Crystal Structure of Diacylglycerol Kinase DgkB in complex with ADP and Mg

Released:
DOI: 10.2210/pdb2qv7/pdb
PDB entry 2qv7 coloured by chain, front view.
PDB entry 2qv7 coloured by chain, side view.
PDB entry 2qv7 coloured by chain, top view.
Source organism: Staphylococcus aureus
Primary publication:
Analysis of the Staphylococcus aureus DgkB structure reveals a common catalytic mechanism for the soluble diacylglycerol kinases.
Miller DJ, Jerga A, Rock CO, White SW
Structure 16 1036-46 (2008)
PMID: 18611377

Function and Biology Details

Reaction catalysed: 
ATP + 1,2-diacyl-sn-glycerol = ADP + 1,2-diacyl-sn-glycerol 3-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-179662 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Diacylglycerol kinase Chain: A
Molecule details ›
Chain: A
Length: 337 amino acids
Theoretical weight: 37.9 KDa
Source organism: Staphylococcus aureus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6GFF9 (Residues: 1-315; Coverage: 100%)
Gene names: SAR1989, dagK, dgkB
Sequence domains:
Structure domains:

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand ADP 1 x ADP
1 modified residue:
Ligand MSE 11 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P42212
Unit cell:
a: 123.76Å b: 123.76Å c: 47.68Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.206 0.246
Expression system: Escherichia coli

Quick links

Citations

12 review citations

Regulation of sphingosine kinase and sphingolipid signaling.
Pitson SM. (2011)
11 more

11 mentions without citation

The Blueprint of a Minimal Cell: MiniBacillus.
Reuß et al. (2016)
10 more