3ZE3

Crystal structure of the integral membrane diacylglycerol kinase - delta7


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1038/nature12179
  • Primary Citation of Related Structures:  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 ba ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIACYLGLYCEROL KINASE
A, B, C, D, E, F
130Escherichia coli (strain K12)Gene Names: dgkA
EC: 2.7.1.107
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Phosphotransferases
Protein: 
DgkA diacylglycerol kinase (DAGK)
Find proteins for P0ABN1 (Escherichia coli (strain K12))
Go to UniProtKB:  P0ABN1
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
78M
Query on 78M

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A, D
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
7.8 MONOACYLGLYCEROL
C18 H34 O4
BJMLBVHMHXYQFS-JJEJIETFSA-N
 Ligand Interaction
ZN
Query on ZN

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D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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E, F
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
78N
Query on 78N

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Download CCD File 
A, B, C
(2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
7.8 MONOACYLGLYCEROL (2R)
C18 H34 O4
BJMLBVHMHXYQFS-XZVRFQMRSA-N
 Ligand Interaction
ACT
Query on ACT

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D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
FLC
Query on FLC

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D
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.060α = 90.00
b = 91.540β = 90.00
c = 143.650γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
SHELXphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-05-29
    Type: Database references
  • Version 1.2: 2013-06-05
    Type: Database references