4UXW

Structure of delta4-DgkA-apo in 9.9 MAG


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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: https://doi.org/10.1038/ncomms10140
  • Primary Citation of Related Structures:  
    4UXW, 4UXX, 4UXZ, 4UYO

  • 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 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

    School of Medicine and School of Biochemistry and Immunology, 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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
G [auth B]
H [auth B]
K [auth C]
D [auth A],
E [auth A],
G [auth B],
H [auth B],
K [auth C],
L [auth C]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
F [auth B](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
I [auth C]NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
J [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.8α = 90
b = 72.8β = 90
c = 199.32γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-30
    Type: Initial release
  • Version 1.1: 2016-01-13
    Changes: Database references
  • Version 1.2: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-04-03
    Changes: Data collection, Experimental preparation
  • Version 1.4: 2023-03-29
    Changes: Database references, Derived calculations, Other, Structure summary
  • Version 1.5: 2024-02-07
    Changes: Data collection, Refinement description