Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45063.99 
• Atom Count: 2754 
• Residue Count: 390 
• Unique protein chains: 1

4UXW

Structure of delta4-DgkA-apo in 9.9 MAG

• DOI: 10.2210/pdb4UXW/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli
• Mutation(s): 4 


• Deposited: 2014-08-27 Released: 2015-09-30 
• Deposition Author(s): Li, D., Pye, V.E., Aragao, D., Caffrey, M.

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Experimental Data Snapshot

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

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

• PubMed: 26673816 
• DOI: 10.1038/ncomms10140
• Primary Citation of Related Structures:  
  4UXZ, 4UXX, 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DIACYLGLYCEROL KINASE	A, B, C	130	Escherichia coli (strain K12)	Mutation(s): 4  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
OLC	A, B, C	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate 1-Oleoyl-R-glycerol C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
NA	C	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
NO3	C	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
MPD	B	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.15 Å
• R-Value Free: 0.268 
• R-Value Work: 0.224 
• Space Group: P 3₁ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 72.800	α = 90.00
b = 72.800	β = 90.00
c = 199.320	γ = 120.00

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing
XSCALE	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2014-08-27 
• Released Date: 2015-09-30 
• Deposition Author(s): Li, D., Pye, V.E., Aragao, D., Caffrey, M.

Revision History 

• Version 1.0: 2015-09-30
  Type: Initial release
• Version 1.1: 2016-01-13
  Type: Database references
• Version 1.2: 2019-03-06
  Type: Data collection, Experimental preparation, Other
• Version 1.3: 2019-04-03
  Type: Data collection, Experimental preparation