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Literature summary for 3.1.4.4 extracted from
- Phospholipase D as a catalyst: application in phospholipid synthesis, molecular structure and protein engineering (2013), J. Biosci. Bioeng., 116, 271-280.
Application
| Application | Comment | Organism |
|---|---|---|
| synthesis | phospholipase D is a useful enzyme for its transphosphatidylation activity, which enables the enzymatic synthesis of various phospholipids, natural and unnatural phospholipids, and phospholipids with a functional head group, detailed overview | Actinomadura sp. |
| synthesis | phospholipase D is a useful enzyme for its transphosphatidylation activity, which enables the enzymatic synthesis of various phospholipids, natural and unnatural phospholipids, and phospholipids with a functional head group, detailed overview | Streptomyces cinnamoneus |
| synthesis | phospholipase D is a useful enzyme for its transphosphatidylation activity, which enables the enzymatic synthesis of various phospholipids, natural and unnatural phospholipids, and phospholipids with a functional head group, detailed overview | Streptomyces chromofuscus |
| synthesis | phospholipase D is a useful enzyme for its transphosphatidylation activity, which enables the enzymatic synthesis of various phospholipids, natural and unnatural phospholipids, and phospholipids with a functional head group, detailed overview | Homo sapiens |
| synthesis | phospholipase D is a useful enzyme for its transphosphatidylation activity, which enables the enzymatic synthesis of various phospholipids, natural and unnatural phospholipids, and phospholipids with a functional head group, detailed overview | Streptomyces antibioticus |
| synthesis | phospholipase D is a useful enzyme for its transphosphatidylation activity, which enables the enzymatic synthesis of various phospholipids, natural and unnatural phospholipids, and phospholipids with a functional head group, detailed overview | Brassica oleracea |
| synthesis | phospholipase D is a useful enzyme for its transphosphatidylation activity, which enables the enzymatic synthesis of various phospholipids, natural and unnatural phospholipids, and phospholipids with a functional head group, detailed overview | Saccharomyces cerevisiae |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| tertiary structure and structure comparison | Streptomyces antibioticus |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| G215S | site-directed mutagenesis of the GG/GS motifs resulting in a several fold enhancement in transphosphatidylation activity | Streptomyces cinnamoneus |
| G216S | site-directed mutagenesis of the GG/GS motifs resulting in a several fold enhancement in transphosphatidylation activity | Streptomyces cinnamoneus |
| G216S/S489G | site-directed mutagenesis of the GG/GS motifs resulting in a several fold enhancement in transphosphatidylation activity | Streptomyces cinnamoneus |
| H168 | inactive mutant | Streptomyces antibioticus |
| additional information | protein engineering to create enzyme variants that can synthesize phosphatidylinositol from phosphatidylcholine and myo-inositol by transphosphatidylation by site-directed saturation mutagenesis at positions suspected to be involved in substrate recognition, namely Trp187, Tyr191 and Tyr385, high-throughput screening. Three variants (187D/191Y/385R, 187A/191Y/385R and 187M/191Y/385R) selectively produced 1(3)-phosphatidylinositol over the other phosphatidylinositol isomers | Streptomyces antibioticus |
| additional information | targeted mutations in the GG/GS motifs reveal its influence on both enzymatic activity and stability, a remarkable, 9-27 fold enhancement in transphosphatidylation activity is observed in the mutants | Streptomyces cinnamoneus |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Actinomadura sp. | - |
- |
- |
| Actinomadura sp. 362 | - |
- |
- |
| Brassica oleracea | O82549 | - |
- |
| Homo sapiens | Q13393 | - |
- |
| Saccharomyces cerevisiae | P36126 | - |
- |
| Saccharomyces cerevisiae ATCC 204508 | P36126 | - |
- |
| Streptomyces antibioticus | Q53728 | - |
- |
| Streptomyces chromofuscus | - |
- |
- |
| Streptomyces cinnamoneus | - |
- |
- |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| a phosphatidylcholine + H2O = choline + a phosphatidate | mode of substrate binding, the catalysis proceeds via two-step reaction with the formation of phosphatidyl-enzyme intermediate. Both of the two catalytic His residues are critical in the reaction course, where one acts as a nucleophile, while the other functions as a general acid/base, reaction cycle overview | Streptomyces chromofuscus | |
| a phosphatidylcholine + H2O = choline + a phosphatidate | mode of substrate binding, the catalysis proceeds via two-step reaction with the formation of phosphatidyl-enzyme intermediate. Both of the two catalytic His residues are critical in the reaction course, where one acts as a nucleophile, while the other functions as a general acid/base, reaction cycle overview | Streptomyces antibioticus | |
| a phosphatidylcholine + H2O = choline + a phosphatidate | the catalysis proceeds via two-step reaction with the formation of phosphatidyl-enzyme intermediate. Both of the two catalytic His residues are critical in the reaction course, where one acts as a nucleophile, while the other functions as a general acid/base, reaction cycle overview | Actinomadura sp. | |
| a phosphatidylcholine + H2O = choline + a phosphatidate | the catalysis proceeds via two-step reaction with the formation of phosphatidyl-enzyme intermediate. Both of the two catalytic His residues are critical in the reaction course, where one acts as a nucleophile, while the other functions as a general acid/base, reaction cycle overview | Streptomyces cinnamoneus | |
| a phosphatidylcholine + H2O = choline + a phosphatidate | the catalysis proceeds via two-step reaction with the formation of phosphatidyl-enzyme intermediate. Both of the two catalytic His residues are critical in the reaction course, where one acts as a nucleophile, while the other functions as a general acid/base, reaction cycle overview | Homo sapiens | |
| a phosphatidylcholine + H2O = choline + a phosphatidate | the catalysis proceeds via two-step reaction with the formation of phosphatidyl-enzyme intermediate. Both of the two catalytic His residues are critical in the reaction course, where one acts as a nucleophile, while the other functions as a general acid/base, reaction cycle overview | Brassica oleracea | |
| a phosphatidylcholine + H2O = choline + a phosphatidate | the catalysis proceeds via two-step reaction with the formation of phosphatidyl-enzyme intermediate. Both of the two catalytic His residues are critical in the reaction course, where one acts as a nucleophile, while the other functions as a general acid/base, reaction cycle overview | Saccharomyces cerevisiae |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | transphosphatidylation reaction is typically carried out in a bi-phase system consisting of a water-immiscible organic solvent (e.g., diethylether, ethylacetate) containing phospholipids and an aqueous solution of enzyme and acceptor compounds (e.g., ethanolamine, glycerol, serine) | Actinomadura sp. | ? | - |
? |  |
| additional information | transphosphatidylation reaction is typically carried out in a bi-phase system consisting of a water-immiscible organic solvent (e.g., diethylether, ethylacetate) containing phospholipids and an aqueous solution of enzyme and acceptor compounds (e.g., ethanolamine, glycerol, serine) | Homo sapiens | ? | - |
? | |
| additional information | transphosphatidylation reaction is typically carried out in a bi-phase system consisting of a water-immiscible organic solvent (e.g., diethylether, ethylacetate) containing phospholipids and an aqueous solution of enzyme and acceptor compounds (e.g., ethanolamine, glycerol, serine) | Saccharomyces cerevisiae | ? | - |
? | |
| additional information | transphosphatidylation reaction is typically carried out in a bi-phase system consisting of a water-immiscible organic solvent (e.g., diethylether, ethylacetate) containing phospholipids and an aqueous solution of enzyme and acceptor compounds (e.g., ethanolamine, glycerol, serine). Transphosphatidylation with L- and D-serine gives phosphatidyl-L- and D-serine, respectively. Synthesis of phosphatidylinositol by bacterial enzyme is unsuccessful is likely the low affinity of the enzyme toward myo-inositol, a bulky molecule causing steric hindrances in the active site | Streptomyces cinnamoneus | ? | - |
? | |
| additional information | transphosphatidylation reaction is typically carried out in a bi-phase system consisting of a water-immiscible organic solvent (e.g., diethylether, ethylacetate) containing phospholipids and an aqueous solution of enzyme and acceptor compounds (e.g., ethanolamine, glycerol, serine). Transphosphatidylation with L- and D-serine gives phosphatidyl-L- and D-serine, respectively. Synthesis of phosphatidylinositol by bacterial enzyme is unsuccessful is likely the low affinity of the enzyme toward myo-inositol, a bulky molecule causing steric hindrances in the active site | Streptomyces chromofuscus | ? | - |
? | |
| additional information | transphosphatidylation reaction is typically carried out in a bi-phase system consisting of a water-immiscible organic solvent (e.g., diethylether, ethylacetate) containing phospholipids and an aqueous solution of enzyme and acceptor compounds (e.g., ethanolamine, glycerol, serine). Transphosphatidylation with L- and D-serine gives phosphatidyl-L- and D-serine, respectively. Synthesis of phosphatidylinositol by bacterial enzyme is unsuccessful is likely the low affinity of the enzyme toward myo-inositol, a bulky molecule causing steric hindrances in the active site | Streptomyces antibioticus | ? | - |
? | |
| additional information | transphosphatidylation reaction is typically carried out in a bi-phase system consisting of a water-immiscible organic solvent (e.g., diethylether, ethylacetate) containing phospholipids and an aqueous solution of enzyme and acceptor compounds (e.g., ethanolamine, glycerol, serine). Transphosphatidylation with L-serine gives phosphatidyl-L-serine, no activity with D-serine | Brassica oleracea | ? | - |
? | |
| additional information | transphosphatidylation reaction is typically carried out in a bi-phase system consisting of a water-immiscible organic solvent (e.g., diethylether, ethylacetate) containing phospholipids and an aqueous solution of enzyme and acceptor compounds (e.g., ethanolamine, glycerol, serine) | Saccharomyces cerevisiae ATCC 204508 | ? | - |
? | |
| additional information | transphosphatidylation reaction is typically carried out in a bi-phase system consisting of a water-immiscible organic solvent (e.g., diethylether, ethylacetate) containing phospholipids and an aqueous solution of enzyme and acceptor compounds (e.g., ethanolamine, glycerol, serine) | Actinomadura sp. 362 | ? | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| PLD | - |
Actinomadura sp. |
| PLD | - |
Streptomyces cinnamoneus |
| PLD | - |
Streptomyces chromofuscus |
| PLD | - |
Homo sapiens |
| PLD | - |
Streptomyces antibioticus |
| PLD | - |
Brassica oleracea |
| PLD | - |
Saccharomyces cerevisiae |
| PLD1 | - |
Homo sapiens |
| PLDalpha1 | - |
Brassica oleracea |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | the enzyme belongs to the PLD superfamily, PLD superfamily members share a common core structure, and a common catalytic mechanism | Streptomyces antibioticus |
| evolution | the enzyme belongs to the PLD superfamily, PLD superfamily members share a common core structure, and thereby, a common catalytic mechanism | Actinomadura sp. |
| evolution | the enzyme belongs to the PLD superfamily, PLD superfamily members share a common core structure, and thereby, a common catalytic mechanism | Streptomyces cinnamoneus |
| evolution | the enzyme belongs to the PLD superfamily, PLD superfamily members share a common core structure, and thereby, a common catalytic mechanism | Streptomyces chromofuscus |
| evolution | the enzyme belongs to the PLD superfamily, PLD superfamily members share a common core structure, and thereby, a common catalytic mechanism | Homo sapiens |
| evolution | the enzyme belongs to the PLD superfamily, PLD superfamily members share a common core structure, and thereby, a common catalytic mechanism | Brassica oleracea |
| evolution | the enzyme belongs to the PLD superfamily, PLD superfamily members share a common core structure, and thereby, a common catalytic mechanism | Saccharomyces cerevisiae |
| additional information | change of the PLD structure upon phospholipid binding, conformational change of the gate-like structure formed by the two loops around Y126 and G381, residues, W187, Y191 and Y385 are responsible for head group specificity, structure overview | Streptomyces antibioticus |
| additional information | the conserved glycine-glycine (GG) and glycine-serine (GS) motifs, especially the Ser residue, in the Streptoverticillium cinnamoneum enzyme are essential in affecting transphosphatidylation activity. The motifs are located seven residues downstream of the HKD motifs, in a close proximity to the catalytic histidines. The GG/GS motifs are suggested to maintain local conformation of the active site by positioning the catalytic His through the hydrogen bond network | Streptomyces cinnamoneus |
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