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Literature summary extracted from

  • Jiang, Y.; Tan, H.; Zheng, J.; Li, X.; Chen, G.; Jia, Z.
    Phosphoryl transfer reaction catalyzed by membrane diacylglycerol kinase: a theoretical mechanism study (2015), Phys. Chem. Chem. Phys., 17, 25228-25234.
    View publication on PubMed

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
2.7.1.107 membrane the enzyme is an integral membrane protein Escherichia coli 16020
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Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.7.1.107 Mg2+ 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
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 ADP + 1,2-diacyl-sn-glycerol 3-phosphate
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 ?

Organism

EC Number Organism UniProt Comment Textmining
2.7.1.107 Escherichia coli P0ABN1
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Reaction

EC Number Reaction Comment Organism Reaction ID
2.7.1.107 ATP + 1,2-diacyl-sn-glycerol = ADP + 1,2-diacyl-sn-glycerol 3-phosphate analysis of the catalytic kinase mechanism molecular dynamics and quantum mechanics calculations, and density functional theory calculations, overview. The active site is relatively open and able to accommodate ligands in multiple orientations, suggesting that the optimization of binding orientations and conformational changes occurs prior to actual phosphoryl transfer Escherichia coli
a

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
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 Escherichia coli ADP + 1,2-diacyl-sn-glycerol 3-phosphate
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 ?
2.7.1.107 ATP + 1,2-diacyl-sn-glycerol enzyme DgkA primarily recognizes diacylglycerol in the glycerol backbone and ester linkages but not the fatty acyl group Escherichia coli ADP + 1,2-diacyl-sn-glycerol 3-phosphate
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 ?
2.7.1.107 ATP + 1,2-dioleoylglycerol modeling of lipid substrate binding, involving residues Arg9, Ser17, Ser98 and Glu69, overview Escherichia coli ADP + 1,2-dioleoylglycerol 3-phospate
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 ?
2.7.1.107 additional information DgkA also has ATPase activity which is about 25% of its kinase activity Escherichia coli ?
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 ?

Subunits

EC Number Subunits Comment Organism
2.7.1.107 trimer optimized structures of the reactant, transition state and product with Mg2+ coordination, overview Escherichia coli

Synonyms

EC Number Synonyms Comment Organism
2.7.1.107 DGKA
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 Escherichia coli

Cofactor

EC Number Cofactor Comment Organism Structure
2.7.1.107 ATP
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 Escherichia coli

General Information

EC Number General Information Comment Organism
2.7.1.107 evolution as the smallest kinase known, it shares no sequence homology with conventional kinases and possesses a distinct trimer structure. The phosphorylation reaction of diacylglycerol kinase features the same phosphoryl transfer mechanism as other kinases, despite its unique structural properties. DgkA appears to be an evolutionarily optimized enzyme and its chemical reaction rate approaches the substrate diffusion-controlled rate limit Escherichia coli
2.7.1.107 additional information 1,2-dioctanoylglycerol is first docked into the active site of the crystal structure of DgkA, PDB ID 3ZE5, followed by construction of a ternary complex model by docking co-factor ATP and substrate 1,2-dioctanoylglycerol into the active site of DgkA. The complex of DgkA is optimized and equilibrated by molecular dynamics simulation in the lipid bilayer. The phosphotransfer reaction catalyzed by DgkA is then investigated through the hybrid density functional theory method B3LYP. Important role of the surface helix in the active site formation Escherichia coli