Localization | Comment | Organism | GeneOntology No. | Textmining |
---|---|---|---|---|
membrane | the enzyme is an integral membrane protein | Escherichia coli | 16020 | - |
Metals/Ions | Comment | Organism | Structure |
---|---|---|---|
Mg2+ | required | Escherichia coli |
Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
---|---|---|---|---|---|---|
ATP + 1,2-diacyl-sn-glycerol | Escherichia coli | - |
ADP + 1,2-diacyl-sn-glycerol 3-phosphate | - |
? |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Escherichia coli | P0ABN1 | - |
- |
Reaction | Comment | Organism | Reaction ID |
---|---|---|---|
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 |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
ATP + 1,2-diacyl-sn-glycerol | - |
Escherichia coli | ADP + 1,2-diacyl-sn-glycerol 3-phosphate | - |
? | |
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 | - |
? | |
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 | - |
? | |
additional information | DgkA also has ATPase activity which is about 25% of its kinase activity | Escherichia coli | ? | - |
? |
Subunits | Comment | Organism |
---|---|---|
trimer | optimized structures of the reactant, transition state and product with Mg2+ coordination, overview | Escherichia coli |
Synonyms | Comment | Organism |
---|---|---|
DGKA | - |
Escherichia coli |
Cofactor | Comment | Organism | Structure |
---|---|---|---|
ATP | - |
Escherichia coli |
General Information | Comment | Organism |
---|---|---|
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 |
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 |