4UYO

Structure of delta7-DgkA in 7.9 MAG by serial femtosecond crystatallography to 2.18 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Ternary Structure Reveals Mechanism of a Membrane Diacylglycerol Kinase.

Li, D.Stansfeld, P.J.Sansom, M.S.P.Keogh, A.Vogeley, L.Howe, N.Lyons, J.A.Aragao, D.Fromme, P.Fromme, R.Basu, S.Grotjohann, I.Kupitz, C.Rendek, K.Weierstall, U.Zatsepin, N.A.Cherezov, V.Liu, W.Bandaru, S.English, N.J.Gati, C.Barty, A.Yefanov, O.Chapman, H.N.Diederichs, K.Messerschmidt, M.Boutet, S.Williams, G.J.Marvin Seibert, M.Caffrey, M.

(2015) Nat.Commun. 6: 10140

  • DOI: 10.1038/ncomms10140
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available ...

    Diacylglycerol kinase catalyses the ATP-dependent conversion of diacylglycerol to phosphatidic acid in the plasma membrane of Escherichia coli. The small size of this integral membrane trimer, which has 121 residues per subunit, means that available protein must be used economically to craft three catalytic and substrate-binding sites centred about the membrane/cytosol interface. How nature has accomplished this extraordinary feat is revealed here in a crystal structure of the kinase captured as a ternary complex with bound lipid substrate and an ATP analogue. Residues, identified as essential for activity by mutagenesis, decorate the active site and are rationalized by the ternary structure. The γ-phosphate of the ATP analogue is positioned for direct transfer to the primary hydroxyl of the lipid whose acyl chain is in the membrane. A catalytic mechanism for this unique enzyme is proposed. The active site architecture shows clear evidence of having arisen by convergent evolution.


    Organizational Affiliation

    SFI Strategic Research Cluster in Solar Energy Conversion, School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland.,School of Medicine and School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland.,Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, California 94025, USA.,Department of Chemistry, Bridge Institute, University of Southern California, Los Angeles, California 90089, USA.,Center for Free Electron Laser Science, Deutsches Elektronen-Synchrotron, 22607 Hamburg, Germany.,Department of Biology, University of Konstanz, Box 647, D-78457 Konstanz, Germany.,School of Molecular Sciences and Center for Applied Structural Discovery at the Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.,Department of Physics, Arizona State University, Tempe, Arizona 85287, USA.,Department of Physics, University of Hamburg, 22761 Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIACYLGLYCEROL KINASE-DELTA 7
A, B, C, D, E, F
130Escherichia coli (strain K12)Mutation(s): 7 
Gene Names: dgkA
EC: 2.7.1.107
Membrane protein
mpstruc
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
79N
Query on 79N

Download SDF File 
Download CCD File 
A, B, C, D
(2S)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate
C19 H36 O4
OWGMAJRKMYGYBQ-LPADLIQXSA-N
 Ligand Interaction
FLC
Query on FLC

Download SDF File 
Download CCD File 
D
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
79M
Query on 79M

Download SDF File 
Download CCD File 
B, D, F
(2R)-2,3-dihydroxypropyl (7Z)-hexadec-7-enoate
[(2R)-2,3-bis(oxidanyl)propyl] (Z)-hexadec-7-enoate
C19 H36 O4
OWGMAJRKMYGYBQ-HJCTWCACSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 75.300α = 90.00
b = 91.800β = 90.00
c = 141.700γ = 90.00
Software Package:
Software NamePurpose
CrystFELdata reduction
PHENIXrefinement
PHASERphasing
CrystFELdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2016-01-13
    Type: Database references
  • Version 1.2: 2018-01-17
    Type: Data collection
  • Version 1.3: 2018-11-14
    Type: Data collection
  • Version 1.4: 2019-03-06
    Type: Data collection, Experimental preparation
  • Version 1.5: 2019-05-08
    Type: Data collection, Experimental preparation