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Literature summary extracted from

  • Matsumoto, Y.; Kashiwabara, N.; Oyama, T.; Murayama, K.; Matsumoto, H.; Sakasegawa, S.; Sugimori, D.
    Molecular cloning, heterologous expression, and enzymatic characterization of lysoplasmalogen-specific phospholipase D from Thermocrispum sp. (2016), FEBS Open Bio, 6, 1113-1130 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.1.4.2 expressed in Escherichia coli Shuffle T7 cells Thermocrispum sp. RD004668
3.3.2.2 expression in Escherichia coli Thermocrispum sp. RD004668

Protein Variants

EC Number Protein Variants Comment Organism
3.1.4.2 A55D the enzyme activity of the mutant is remarkably decreased compared with that of wild type enzyme Thermocrispum sp. RD004668
3.1.4.2 A55N the enzyme activity of the mutant is remarkably decreased compared with that of wild type enzyme Thermocrispum sp. RD004668
3.1.4.2 E175A inactive Thermocrispum sp. RD004668
3.1.4.2 F211A the enzyme activity of the mutant is remarkably decreased compared with that of wild type enzyme Thermocrispum sp. RD004668
3.1.4.2 N56D the enzyme activity of the mutant is remarkably decreased compared with that of wild type enzyme Thermocrispum sp. RD004668
3.1.4.2 N56Q the enzyme activity of the mutant is remarkably decreased compared with that of wild type enzyme Thermocrispum sp. RD004668
3.3.2.2 A55D 47% of wild-type activity with substrate choline lysoplasmalogen Thermocrispum sp. RD004668
3.3.2.2 A55N 51.6% of wild-type activity with substrate choline lysoplasmalogen Thermocrispum sp. RD004668
3.3.2.2 F211A 20.0% of wild-type activity with substrate choline lysoplasmalogen Thermocrispum sp. RD004668
3.3.2.2 N56D 8.4% of wild-type activity with substrate choline lysoplasmalogen Thermocrispum sp. RD004668
3.3.2.2 N56Q 55.2% of wild-type activity with substrate choline lysoplasmalogen Thermocrispum sp. RD004668

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.1.4.2 1-stearoyl-2-hydroxy-sn-glycero-3-phosphate 89.8% residual activity at 4 mM Thermocrispum sp. RD004668
3.1.4.2 Al3+ inhibited by more than 5 mM Al3+ Thermocrispum sp. RD004668
3.1.4.2 EDTA complete inhibition at 2 mM Thermocrispum sp. RD004668
3.1.4.2 L-alpha-lysophosphatidylcholine 60.7% residual activity at 4 mM Thermocrispum sp. RD004668
3.1.4.2 L-alpha-lysophosphatidylethanolamine 50.9% residual activity at 4 mM Thermocrispum sp. RD004668
3.1.4.2 Mg2+ 5.4% residual activity at 2 mM Thermocrispum sp. RD004668
3.1.4.2 additional information glycerophosphocholine, CDP-choline, dithiothreitol, 2-mercaptoethanol, iodoacetamide, and phenylmethylsulfonyl fluoride have no effect on enzyme activity Thermocrispum sp. RD004668
3.1.4.2 Triton X-100 about 30% residual activity at 0.1% (v/v) Thermocrispum sp. RD004668

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.1.4.2 0.0132
-
 choline lysoplasmalogen at pH 8.0 and 50°C Thermocrispum sp. RD004668
3.3.2.2 0.0132
-
 choline lysoplasmalogen pH 8.0, 50°C Thermocrispum sp. RD004668

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.1.4.2 Al3+ the enzyme is activated in the presence of Al3+ Thermocrispum sp. RD004668
3.1.4.2 Ca2+ the enzyme is activated in the presence of 0.5-10 mM Ca2+ Thermocrispum sp. RD004668

Organism

EC Number Organism UniProt Comment Textmining
3.1.4.2 Thermocrispum sp. RD004668 A0A0U4VTN7
-
-
3.3.2.2 Thermocrispum sp. RD004668 A0A0U4VTN7
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
3.1.4.2 ammonium sulfate precipitation, Resource Iso column chromatography, Mono Q column chromatography, PPG-600M column chromatography, Giga Cap Q-650M column chromatography, and Superdex 200 gel filtration Thermocrispum sp. RD004668

Specific Activity [micromol/min/mg]

EC Number Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
3.3.2.2 345
-
 pH 8.0, 50°C Thermocrispum sp. RD004668

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.1.4.2 choline lysoplasmalogen + H2O preferred substrate, i.e. 1-O-1'-(Z)-octadecenyl-2-hydroxy-sn-glycero-3-phosphocholine Thermocrispum sp. RD004668 choline + 1-(1-alkenyl)-sn-glycero-3-phosphate
-
 ?
3.1.4.2 ethanolamine lysoplasmalogen + H2O modest activity, i.e. 1-O-1'-(Z)-octadecenyl-2-hydroxy-sn-glycero-3-phosphoethanolamine Thermocrispum sp. RD004668 ethanolamine + 1-(1-alkenyl)-sn-glycero-3-phosphate
-
 ?
3.3.2.2 choline lysoplasmalogen + H2O preferred substrate Thermocrispum sp. RD004668 ? + glycerophospho-choline
-
 ?
3.3.2.2 ethanolamine lysoplasmalogen + H2O 6.5% of the activity with choline lysoplasmalogen Thermocrispum sp. RD004668 ? + glycerophospho-ethanolamine
-
 ?
3.3.2.2 additional information no substrates: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, sphingomyelin, choline plasmalogen, ethanolamine plasmalogen Thermocrispum sp. RD004668 ?
-
 ?

Subunits

EC Number Subunits Comment Organism
3.1.4.2 ? x * 33452, calculated from amino acid sequence Thermocrispum sp. RD004668

Synonyms

EC Number Synonyms Comment Organism
3.1.4.2 LyPls-PLD
-
 Thermocrispum sp. RD004668
3.1.4.2 LyPls-specific PLD
-
 Thermocrispum sp. RD004668
3.1.4.2 lysoplasmalogen-specific phospholipase D
-
 Thermocrispum sp. RD004668
3.3.2.2 LyPls-PLD
-
 Thermocrispum sp. RD004668
3.3.2.2 lysoplasmalogenase
-
 Thermocrispum sp. RD004668

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.1.4.2 50
-
-
 Thermocrispum sp. RD004668
3.3.2.2 50
-
-
 Thermocrispum sp. RD004668

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
3.1.4.2 4 37 the enzyme is stable between 4 and 37°C for 60 min at pH 8.0 Thermocrispum sp. RD004668

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.1.4.2 70.6
-
 choline lysoplasmalogen at pH 8.0 and 50°C Thermocrispum sp. RD004668
3.3.2.2 70.6
-
 choline lysoplasmalogen pH 8.0, 50°C Thermocrispum sp. RD004668

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.1.4.2 8
-
-
 Thermocrispum sp. RD004668
3.3.2.2 8
-
-
 Thermocrispum sp. RD004668

pH Stability

EC Number pH Stability pH Stability Maximum Comment Organism
3.1.4.2 4.1 9.8 enzyme activity is maintained between pH 4.1 and 9.8 at 4°C for 4 h Thermocrispum sp. RD004668

pI Value

EC Number Organism Comment pI Value Maximum pI Value
3.1.4.2 Thermocrispum sp. RD004668 calculated from amino acid sequence
-
 5.6