› 3ze3

X-ray diffraction
2.05Å resolution

Crystal structure of the integral membrane diacylglycerol kinase - delta7

Released:
DOI: 10.2210/pdb3ze3/pdb
PDB entry 3ze3 coloured by chain, front view.
PDB entry 3ze3 coloured by chain, side view.
PDB entry 3ze3 coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
Crystal structure of the integral membrane diacylglycerol kinase.
Li D, Lyons JA, Pye VE, Vogeley L, Aragão D, Kenyon CP, Shah ST, Doherty C, Aherne M, Caffrey M
Nature 497 521-4 (2013)
PMID: 23676677

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 analysis Details

Assembly composition:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-142184 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Diacylglycerol kinase Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 130 amino acids
Theoretical weight: 14.2 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0ABN1 (Residues: 2-122; Coverage: 99%)
Gene names: JW4002, b4042, dgk, dgkA
Sequence domains: Prokaryotic diacylglycerol kinase
Structure domains: Helix Hairpins

Ligands and Environments

6 bound ligands:
Ligand 78N 7 x 78N
Ligand 78M 6 x 78M
Ligand ZN 1 x ZN
Ligand FLC 1 x FLC
Ligand ACT 1 x ACT
Ligand NA 2 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P212121
Unit cell:
a: 75.06Å b: 91.54Å c: 143.65Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.197 0.196 0.217
Expression system: Escherichia coli

Quick links

Citations

15 review citations

Deciphering the metabolism of undecaprenyl-phosphate: the bacterial cell-wall unit carrier at the membrane frontier.
Manat et al. (2014)
14 more

11 mentions without citation

A comprehensive review of the lipid cubic phase or in meso method for crystallizing membrane and soluble proteins and complexes.
Caffrey M. (2015)
10 more