3ZE5

Crystal structure of the integral membrane diacylglycerol kinase - delta4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.6 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: 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DIACYLGLYCEROL KINASE
A, B, C
130Escherichia coli K-12Mutation(s): 4 
EC: 2.7.1.107
Membrane Entity: Yes 
UniProt
Find proteins for P0ABN1 (Escherichia coli (strain K12))
Explore P0ABN1 
Go to UniProtKB:  P0ABN1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0ABN1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.234 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.74α = 90
b = 72.74β = 90
c = 198.99γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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, Other, Structure summary
  • Version 1.6: 2024-02-07
    Changes: Data collection, Refinement description