Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 89.67 kDa 
• Atom Count: 5,042 
• Modelled Residue Count: 583 
• Deposited Residue Count: 780 
• Unique protein chains: 1

 3ZE3

Crystal structure of the integral membrane diacylglycerol kinase - delta7

• PDB DOI:  https://doi.org/10.2210/pdb3ZE3/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2012-12-03 Released: 2013-05-22 
• Deposition Author(s): Li, D., Pye, V.E., Lyons, J.A., Vogeley, L., Aragao, D., Caffrey, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.217 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 

Literature

Crystal Structure of the Integral Membrane Diacylglycerol Kinase.

Li, D., Lyons, J.A., Pye, V.E., Vogeley, L., Aragao, D., Kenyon, C.P., Shah, S.T.A., Doherty, C., Aherne, M., Caffrey, M.

(2013) Nature 497: 521

• PubMed: 23676677 
• DOI: https://doi.org/10.1038/nature12179
• Primary Citation of Related Structures:  
  3ZE3, 3ZE4, 3ZE5


• PubMed Abstract: 
  

Diacylglycerol kinase catalyses the ATP-dependent phosphorylation of diacylglycerol to phosphatidic acid for use in shuttling water-soluble components to membrane-derived oligosaccharide and lipopolysaccharide in the cell envelope of Gram-negative bacteria. For half a century, this 121-residue kinase has served as a model for investigating membrane protein enzymology, folding, assembly and stability. Here we present crystal structures for three functional forms of this unique and paradigmatic kinase, one of which is wild type. These reveal a homo-trimeric enzyme with three transmembrane helices and an amino-terminal amphiphilic helix per monomer. Bound lipid substrate and docked ATP identify the putative active site that is of the composite, shared site type. The crystal structures rationalize extensive biochemical and biophysical data on the enzyme. They are, however, at variance with a published solution NMR model in that domain swapping, a key feature of the solution form, is not observed in the crystal structures.

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Organizational Affiliation: 

School of Biochemistry and Immunology & School of Medicine, Trinity College Dublin, Dublin 2, Ireland.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIACYLGLYCEROL KINASE	A, B, C, D, E, F	130	Escherichia coli K-12	Mutation(s): 7  Gene Names: dgkA, dgk, b4042, JW4002 EC: 2.7.1.107 Membrane Entity: Yes
UniProt
Find proteins for P0ABN1 (Escherichia coli (strain K12)) Explore P0ABN1  Go to UniProtKB:  P0ABN1

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
78M	J [auth A], K [auth A], S [auth D], T [auth D], U [auth D], V [auth D]	(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE C18 H34 O4 BJMLBVHMHXYQFS-JJEJIETFSA-N
78N	G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth C], O [auth C]	(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE C18 H34 O4 BJMLBVHMHXYQFS-XZVRFQMRSA-N
FLC	Q [auth D]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
ZN	P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	R [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	W [auth E], X [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 0.217 
• R-Value Work: 0.196 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.06	α = 90
b = 91.54	β = 90
c = 143.65	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-05-22 
Deposition Author(s): Li, D., Pye, V.E., Lyons, J.A., Vogeley, L., Aragao, D., Caffrey, M.

Revision History  

• Version 1.0: 2013-05-22
  Type: Initial release
  
• Version 1.1: 2013-05-29
  Changes: Database references
• Version 1.2: 2013-06-05
  Changes: Database references
• Version 1.3: 2019-03-06
  Changes: Data collection, Experimental preparation, Other
• Version 1.4: 2019-04-03
  Changes: Data collection, Experimental preparation
• Version 1.5: 2023-03-29
  Changes: Database references, Derived calculations, Other, Structure summary