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Literature summary extracted from

  • Li, D.; Lyons, J.A.; Pye, V.E.; Vogeley, L.; Aragao, D.; Kenyon, C.P.; Shah, S.T.; Doherty, C.; Aherne, M.; Caffrey, M.
    Crystal structure of the integral membrane diacylglycerol kinase (2013), Nature, 497, 521-524.
    View publication on PubMedView publication on EuropePMC

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
2.7.1.107 purified recombinanz wild-type and DELTA4 and DELTA7 mutant enzymes in complex with lipid substrate and ATP, 20°C, X-ray diffraction structure determination and analysis at 2.05 A resolution, structure mmodeling. The kinase adopts a functional form in the crystal. Domain swapping, a key feature of the solution form, is not observed in the crystal structures. Crystals of mutant DELTA7 DgkA are soaked with the ATP analogue, adenylylmethylenediphosphate (Mg2+-AMPPCP). This causes the crystals to dissolve. Additional soaking with ATP, ADP, AMP, ATP?S, AMPPNP and dATP but not with GTP, CTP, UTP or TTP leads to crystal dissolution Escherichia coli

Protein Variants

EC Number Protein Variants Comment Organism
2.7.1.107 additional information construction of a thermostabilized DELTA4 (4 changes relative to wild-type) form of DgkA using the DELTA7 structure, overview Escherichia coli

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
2.7.1.107 cell envelope
-
 Escherichia coli 30313
-
2.7.1.107 membrane the enzyme is an integral membrane protein Escherichia coli 16020
-

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.7.1.107 Mg2+ required Escherichia coli
2.7.1.107 Zn2+ required Escherichia coli

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.7.1.107 ATP + 1,2-diacyl-sn-glycerol Escherichia coli
-
 ADP + 1,2-diacyl-sn-glycerol 3-phosphate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.7.1.107 Escherichia coli P0ABN1 gene dgkA
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.7.1.107 ATP + 1,2-diacyl-sn-glycerol
-
 Escherichia coli ADP + 1,2-diacyl-sn-glycerol 3-phosphate
-
 ?

Subunits

EC Number Subunits Comment Organism
2.7.1.107 homotrimer a homotrimeric enzyme with three transmembrane helices and an N-terminal amphiphilic helix per monomer. Bound lipid substrate and docked ATP identify the putative active site which is of the composite, shared site type. Each subunit within a trimer forms a bundle of 3 transmembrane helices. The three subunits are arranged around an approximate 3-fold symmetry axis that passes through the center of the trimer normal to the membrane plane, enzyme structure analysis, overview Escherichia coli

Synonyms

EC Number Synonyms Comment Organism
2.7.1.107 DGKA
-
 Escherichia coli

Cofactor

EC Number Cofactor Comment Organism Structure
2.7.1.107 ATP
-
 Escherichia coli

General Information

EC Number General Information Comment Organism
2.7.1.107 evolution DgkA is a unique kinase with a distinctive active site. It has no recognizable nucleotide sequence or structural binding motifs Escherichia coli
2.7.1.107 additional information DgkA catalyzes phosphoryl transfer expected to take place at a polar/apolar interface Escherichia coli
2.7.1.107 physiological function diacylglycerol kinase catalyzes 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 Escherichia coli