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 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    4UYO, 4UXW, 4UXX, 4UXZ

  • 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 ...

    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
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIACYLGLYCEROL KINASE A, B, C130Escherichia coli K-12Mutation(s): 4 
Gene Names: dgkA, b4042, JW4002
EC: 2.7.1.107
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL		Sub Group: 
Phosphotransferases		Protein: 
DgkA diacylglycerol kinase (DAGK) Δ4 mutant with bound monoacylglycerol (9.9 MAG) and ACP
Find proteins for P0ABN1 (Escherichia coli (strain K12))
Explore P0ABN1 
Go to UniProtKB:  P0ABN1
Protein Feature View
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  • Reference Sequence
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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View more in-depth experimental data

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