BRENDA - Enzyme Database

Structural insight into substrate selection and catalysis of lipid phosphate phosphatase PgpB in the cell membrane

Tong, S.; Lin, Y.; Lu, S.; Wang, M.; Bogdanov, M.; Zheng, L.; J. Biol. Chem. 291, 18342-18352 (2016)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
3.1.3.27
pgpB gene is cloned into the pET22b vector (Novagen) to generate the C-terminal His6-tagged protein. Mutants were generated using standard site-directed mutagenesis. The PgpB wild type and mutant proteins are expressed in Escherichia coli strain C41(DE3)
Escherichia coli
Crystallization (Commentary)
EC Number
Crystallization
Organism
3.1.3.27
vapor diffusion method, the structure is determined at 3.2 A resolution
Escherichia coli
Engineering
EC Number
Amino acid exchange
Commentary
Organism
3.1.3.27
D211A
mutant enzyme retains 50% activity
Escherichia coli
3.1.3.27
H163A
mutation increases hydrolysis of 1,2-dipalmitoryl-sn-glycero-3-[phospho-rac-(1'-(3'-phospho)glycerol)] by 50%
Escherichia coli
3.1.3.27
K93A
the mutant enzyme shows complete activity loss for lysophosphatidic acid and (2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate, whereas it retains full activity for phosphatidic acid and gains 40% more activity toward phosphatidylglycerol phosphate compared with wild type enzyme
Escherichia coli
3.1.3.27
K93A/K97A
the mutant enzyme shows complete activity loss for lysophosphatidic acid and (2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate, whereas it retains full activity for phosphatidic acid and gained 40% more activity toward phosphatidylglycerol phosphate compared with wild type enzyme
Escherichia coli
3.1.3.27
K93T
mutant enzyme with significantly improved activity for lysophosphatidic acid, (2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate, and phosphatidic acid by 2.5- or 3.4-fold but not for 1,2-dipalmitoryl-sn-glycero-3-[phospho-rac-(1'-(3'-phospho)glycerol)]
Escherichia coli
3.1.3.27
K93T/K97A
the mutant enzyme loses all activity for lysophosphatidic acid or (2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate, but retains 50% activity for phosphatidic acid or 1,2-dipalmitoryl-sn-glycero-3-[phospho-rac-(1'-(3'-phospho)glycerol)]
Escherichia coli
3.1.3.27
K97A
the mutant enzyme shows complete activity loss for lysophosphatidic acid and (2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate, whereas it retains full activity for phosphatidic acid and gained 40% more activity toward phosphatidylglycerol phosphate compared with wild type enzyme
Escherichia coli
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
3.1.3.27
orthovanadate
-
Escherichia coli
3.1.3.27
phosphatidylethanolamine
3 mM, 70% inhibition. competitive
Escherichia coli
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
3.1.3.27
0.108
-
1-(9Z-octadecenoyl)-sn-glycero-3-phosphate
pH 7.5, 23°C
Escherichia coli
3.1.3.27
5.052
-
1-hexanoyl-sn-glycero-3-phosphate
pH 7.5, 23°C
Escherichia coli
Localization
EC Number
Localization
Commentary
Organism
GeneOntology No.
Textmining
3.1.3.27
membrane
integral membrane protein
Escherichia coli
16020
-
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
3.1.3.27
Escherichia coli
P0A924
-
-
3.1.3.27
Escherichia coli K12
P0A924
-
-
Purification (Commentary)
EC Number
Commentary
Organism
3.1.3.27
-
Escherichia coli
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3.1.3.27
(2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate + H2O
-
751064
Escherichia coli
?
-
-
-
?
3.1.3.27
(2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate + H2O
-
751064
Escherichia coli K12
?
-
-
-
?
3.1.3.27
1,2-dihexadecanoyl-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli
1,2-dihexadecanoyl-sn-glycerol + phosphate
-
-
-
?
3.1.3.27
1,2-dihexadecanoyl-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli K12
1,2-dihexadecanoyl-sn-glycerol + phosphate
-
-
-
?
3.1.3.27
1,2-dipalmitoyl-sn-glycero-3-[phospho-rac-(1'-(3'-phospho)glycerol)] + H2O
-
751064
Escherichia coli
? + phosphate
-
-
-
?
3.1.3.27
1,2-dipalmitoyl-sn-glycero-3-[phospho-rac-(1'-(3'-phospho)glycerol)] + H2O
-
751064
Escherichia coli K12
? + phosphate
-
-
-
?
3.1.3.27
1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli
1-(9Z-octadecenoyl)-sn-glycerol + phosphate
-
-
-
?
3.1.3.27
1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli K12
1-(9Z-octadecenoyl)-sn-glycerol + phosphate
-
-
-
?
3.1.3.27
1-hexanoyl-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli
1-hexanoyl-sn-glycerol + phosphate
-
-
-
?
3.1.3.27
1-hexanoyl-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli K12
1-hexanoyl-sn-glycerol + phosphate
-
-
-
?
Ki Value [mM]
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
3.1.3.27
2.7
-
phosphatidylethanolamine
pH 7.5, 23°C
Escherichia coli
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
3.1.3.27
pgpB gene is cloned into the pET22b vector (Novagen) to generate the C-terminal His6-tagged protein. Mutants were generated using standard site-directed mutagenesis. The PgpB wild type and mutant proteins are expressed in Escherichia coli strain C41(DE3)
Escherichia coli
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
3.1.3.27
vapor diffusion method, the structure is determined at 3.2 A resolution
Escherichia coli
Engineering (protein specific)
EC Number
Amino acid exchange
Commentary
Organism
3.1.3.27
D211A
mutant enzyme retains 50% activity
Escherichia coli
3.1.3.27
H163A
mutation increases hydrolysis of 1,2-dipalmitoryl-sn-glycero-3-[phospho-rac-(1'-(3'-phospho)glycerol)] by 50%
Escherichia coli
3.1.3.27
K93A
the mutant enzyme shows complete activity loss for lysophosphatidic acid and (2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate, whereas it retains full activity for phosphatidic acid and gains 40% more activity toward phosphatidylglycerol phosphate compared with wild type enzyme
Escherichia coli
3.1.3.27
K93A/K97A
the mutant enzyme shows complete activity loss for lysophosphatidic acid and (2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate, whereas it retains full activity for phosphatidic acid and gained 40% more activity toward phosphatidylglycerol phosphate compared with wild type enzyme
Escherichia coli
3.1.3.27
K93T
mutant enzyme with significantly improved activity for lysophosphatidic acid, (2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate, and phosphatidic acid by 2.5- or 3.4-fold but not for 1,2-dipalmitoryl-sn-glycero-3-[phospho-rac-(1'-(3'-phospho)glycerol)]
Escherichia coli
3.1.3.27
K93T/K97A
the mutant enzyme loses all activity for lysophosphatidic acid or (2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate, but retains 50% activity for phosphatidic acid or 1,2-dipalmitoryl-sn-glycero-3-[phospho-rac-(1'-(3'-phospho)glycerol)]
Escherichia coli
3.1.3.27
K97A
the mutant enzyme shows complete activity loss for lysophosphatidic acid and (2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate, whereas it retains full activity for phosphatidic acid and gained 40% more activity toward phosphatidylglycerol phosphate compared with wild type enzyme
Escherichia coli
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
3.1.3.27
orthovanadate
-
Escherichia coli
3.1.3.27
phosphatidylethanolamine
3 mM, 70% inhibition. competitive
Escherichia coli
Ki Value [mM] (protein specific)
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
3.1.3.27
2.7
-
phosphatidylethanolamine
pH 7.5, 23°C
Escherichia coli
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
3.1.3.27
0.108
-
1-(9Z-octadecenoyl)-sn-glycero-3-phosphate
pH 7.5, 23°C
Escherichia coli
3.1.3.27
5.052
-
1-hexanoyl-sn-glycero-3-phosphate
pH 7.5, 23°C
Escherichia coli
Localization (protein specific)
EC Number
Localization
Commentary
Organism
GeneOntology No.
Textmining
3.1.3.27
membrane
integral membrane protein
Escherichia coli
16020
-
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
3.1.3.27
-
Escherichia coli
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3.1.3.27
(2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate + H2O
-
751064
Escherichia coli
?
-
-
-
?
3.1.3.27
(2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate + H2O
-
751064
Escherichia coli K12
?
-
-
-
?
3.1.3.27
1,2-dihexadecanoyl-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli
1,2-dihexadecanoyl-sn-glycerol + phosphate
-
-
-
?
3.1.3.27
1,2-dihexadecanoyl-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli K12
1,2-dihexadecanoyl-sn-glycerol + phosphate
-
-
-
?
3.1.3.27
1,2-dipalmitoyl-sn-glycero-3-[phospho-rac-(1'-(3'-phospho)glycerol)] + H2O
-
751064
Escherichia coli
? + phosphate
-
-
-
?
3.1.3.27
1,2-dipalmitoyl-sn-glycero-3-[phospho-rac-(1'-(3'-phospho)glycerol)] + H2O
-
751064
Escherichia coli K12
? + phosphate
-
-
-
?
3.1.3.27
1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli
1-(9Z-octadecenoyl)-sn-glycerol + phosphate
-
-
-
?
3.1.3.27
1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli K12
1-(9Z-octadecenoyl)-sn-glycerol + phosphate
-
-
-
?
3.1.3.27
1-hexanoyl-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli
1-hexanoyl-sn-glycerol + phosphate
-
-
-
?
3.1.3.27
1-hexanoyl-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli K12
1-hexanoyl-sn-glycerol + phosphate
-
-
-
?