BRENDA - Enzyme Database
show all sequences of 3.1.3.27

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)
Commentary
Organism
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)
Crystallization
Organism
vapor diffusion method, the structure is determined at 3.2 A resolution
Escherichia coli
Engineering
Amino acid exchange
Commentary
Organism
D211A
mutant enzyme retains 50% activity
Escherichia coli
H163A
mutation increases hydrolysis of 1,2-dipalmitoryl-sn-glycero-3-[phospho-rac-(1'-(3'-phospho)glycerol)] by 50%
Escherichia coli
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
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
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
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
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
Inhibitors
Commentary
Organism
Structure
orthovanadate
-
Escherichia coli
phosphatidylethanolamine
3 mM, 70% inhibition. competitive
Escherichia coli
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.108
-
1-(9Z-octadecenoyl)-sn-glycero-3-phosphate
pH 7.5, 23°C
Escherichia coli
5.052
-
1-hexanoyl-sn-glycero-3-phosphate
pH 7.5, 23°C
Escherichia coli
Localization
Localization
Commentary
Organism
GeneOntology No.
Textmining
membrane
integral membrane protein
Escherichia coli
16020
-
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli
P0A924
-
-
Escherichia coli K12
P0A924
-
-
Purification (Commentary)
Commentary
Organism
-
Escherichia coli
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
(2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate + H2O
-
751064
Escherichia coli
?
-
-
-
?
(2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate + H2O
-
751064
Escherichia coli K12
?
-
-
-
?
1,2-dihexadecanoyl-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli
1,2-dihexadecanoyl-sn-glycerol + phosphate
-
-
-
?
1,2-dihexadecanoyl-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli K12
1,2-dihexadecanoyl-sn-glycerol + phosphate
-
-
-
?
1,2-dipalmitoyl-sn-glycero-3-[phospho-rac-(1'-(3'-phospho)glycerol)] + H2O
-
751064
Escherichia coli
? + phosphate
-
-
-
?
1,2-dipalmitoyl-sn-glycero-3-[phospho-rac-(1'-(3'-phospho)glycerol)] + H2O
-
751064
Escherichia coli K12
? + phosphate
-
-
-
?
1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli
1-(9Z-octadecenoyl)-sn-glycerol + phosphate
-
-
-
?
1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli K12
1-(9Z-octadecenoyl)-sn-glycerol + phosphate
-
-
-
?
1-hexanoyl-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli
1-hexanoyl-sn-glycerol + phosphate
-
-
-
?
1-hexanoyl-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli K12
1-hexanoyl-sn-glycerol + phosphate
-
-
-
?
Ki Value [mM]
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
2.7
-
phosphatidylethanolamine
pH 7.5, 23°C
Escherichia coli
Cloned(Commentary) (protein specific)
Commentary
Organism
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)
Crystallization
Organism
vapor diffusion method, the structure is determined at 3.2 A resolution
Escherichia coli
Engineering (protein specific)
Amino acid exchange
Commentary
Organism
D211A
mutant enzyme retains 50% activity
Escherichia coli
H163A
mutation increases hydrolysis of 1,2-dipalmitoryl-sn-glycero-3-[phospho-rac-(1'-(3'-phospho)glycerol)] by 50%
Escherichia coli
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
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
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
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
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)
Inhibitors
Commentary
Organism
Structure
orthovanadate
-
Escherichia coli
phosphatidylethanolamine
3 mM, 70% inhibition. competitive
Escherichia coli
Ki Value [mM] (protein specific)
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
2.7
-
phosphatidylethanolamine
pH 7.5, 23°C
Escherichia coli
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.108
-
1-(9Z-octadecenoyl)-sn-glycero-3-phosphate
pH 7.5, 23°C
Escherichia coli
5.052
-
1-hexanoyl-sn-glycero-3-phosphate
pH 7.5, 23°C
Escherichia coli
Localization (protein specific)
Localization
Commentary
Organism
GeneOntology No.
Textmining
membrane
integral membrane protein
Escherichia coli
16020
-
Purification (Commentary) (protein specific)
Commentary
Organism
-
Escherichia coli
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
(2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate + H2O
-
751064
Escherichia coli
?
-
-
-
?
(2S,3R,4E)-2-aminooctadec-4-ene-1,3-diol-1-phosphate + H2O
-
751064
Escherichia coli K12
?
-
-
-
?
1,2-dihexadecanoyl-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli
1,2-dihexadecanoyl-sn-glycerol + phosphate
-
-
-
?
1,2-dihexadecanoyl-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli K12
1,2-dihexadecanoyl-sn-glycerol + phosphate
-
-
-
?
1,2-dipalmitoyl-sn-glycero-3-[phospho-rac-(1'-(3'-phospho)glycerol)] + H2O
-
751064
Escherichia coli
? + phosphate
-
-
-
?
1,2-dipalmitoyl-sn-glycero-3-[phospho-rac-(1'-(3'-phospho)glycerol)] + H2O
-
751064
Escherichia coli K12
? + phosphate
-
-
-
?
1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli
1-(9Z-octadecenoyl)-sn-glycerol + phosphate
-
-
-
?
1-(9Z-octadecenoyl)-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli K12
1-(9Z-octadecenoyl)-sn-glycerol + phosphate
-
-
-
?
1-hexanoyl-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli
1-hexanoyl-sn-glycerol + phosphate
-
-
-
?
1-hexanoyl-sn-glycero-3-phosphate + H2O
-
751064
Escherichia coli K12
1-hexanoyl-sn-glycerol + phosphate
-
-
-
?
Other publictions for EC 3.1.3.27
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
749968
Lin
Phosphatidylglycerophosphate ...
Arabidopsis thaliana
Biochim. Biophys. Acta
1863
563-575
2018
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-
-
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1
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7
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2
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2
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1
3
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-
746083
Zhou
Identification and characteri ...
Arabidopsis thaliana
Plant J.
89
221-234
2017
1
-
-
-
1
-
1
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1
1
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5
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5
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1
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1
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1
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1
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1
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5
-
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1
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1
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1
1
-
-
-
750277
Ghachi
Crystal structure and biochem ...
Bacillus subtilis 168, Bacillus subtilis
Cell. Mol. Life Sci.
74
2319-2332
2017
-
-
-
1
6
-
-
-
1
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2
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4
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8
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1
6
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1
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4
-
8
-
-
-
-
-
-
-
-
-
-
1
1
-
-
-
751064
Tong
Structural insight into subst ...
Escherichia coli, Escherichia coli K12
J. Biol. Chem.
291
18342-18352
2016
-
-
1
1
7
-
2
2
1
-
-
-
-
2
-
-
1
-
-
-
-
-
10
-
-
-
-
-
-
-
-
-
1
-
-
-
-
1
-
1
7
-
-
2
1
2
1
-
-
-
-
-
-
1
-
-
-
-
10
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
730834
Fan
Crystal structure of lipid pho ...
Escherichia coli, Escherichia coli B / ATCC 11303
Proc. Natl. Acad. Sci. USA
111
7636-7640
2014
-
-
1
1
16
1
-
1
1
-
1
2
-
4
-
-
1
-
-
-
-
-
10
1
-
-
1
1
-
-
-
-
-
-
-
-
-
1
-
1
16
1
-
-
-
1
1
-
1
2
-
-
-
1
-
-
-
-
10
1
-
-
1
1
-
-
-
-
-
-
-
-
-
-
730029
Teh
Identification of a mammalian- ...
Rhodopirellula baltica
J. Biol. Chem.
288
5176-5185
2013
-
-
1
-
-
-
-
-
-
-
-
1
-
6
-
-
1
-
-
-
-
-
2
-
-
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1
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-
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-
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1
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1
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1
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-
-
-
2
-
-
-
-
-
1
-
-
-
-
1
1
-
-
-
682404
Wu
Impaired photosynthesis in pho ...
Anabaena sp., Anabaena sp. PCC 7120
Plant Physiol.
141
1274-1283
2006
-
-
-
-
-
-
-
-
-
-
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-
22
-
-
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-
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-
2
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-
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-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
682752
Kumaran
Crystal structure of phosphati ...
Listeria monocytogenes
Proteins
64
851-862
2006
-
-
1
1
-
-
-
-
-
2
-
-
-
2
-
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-
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-
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-
-
1
1
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1
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1
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2
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-
-
1
1
-
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-
-
-
-
-
-
-
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-
-
-
-
94807
Griebau
Biosynthesis of phosphatidylgl ...
Vigna radiata
Plant Physiol.
105
1269-1274
1994
1
-
-
-
-
-
4
1
1
1
-
1
-
1
-
-
-
-
-
1
1
-
2
-
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-
-
-
1
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1
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4
-
1
1
1
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1
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1
1
-
2
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
94808
Cao
Stimulation of phosphatidylgly ...
Rattus sp.
Lipids
29
475-480
1994
2
-
-
-
-
2
2
-
1
-
-
1
-
2
-
-
-
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-
1
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2
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2
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2
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2
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1
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1
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1
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2
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-
94809
Dowhan
Phosphatidylglycerophosphate p ...
Escherichia coli
Methods Enzymol.
209
224-230
1992
-
-
-
-
-
5
1
1
2
1
-
1
-
1
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-
-
-
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-
4
-
2
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-
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1
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5
-
1
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1
2
1
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1
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4
-
2
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1
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94810
Funk
The pgpA and pgpB genes of Esc ...
Escherichia coli
J. Bacteriol.
174
205-213
1992
1
-
1
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3
4
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2
1
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1
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1
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3
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2
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1
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1
-
1
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3
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4
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2
1
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1
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3
-
2
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1
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-
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-
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-
94811
Kelly
Characterization and regulatio ...
Saccharomyces cerevisiae
Biochim. Biophys. Acta
1046
144-150
1990
1
-
-
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-
3
3
1
2
2
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1
-
2
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-
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1
-
2
-
1
-
-
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1
-
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1
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-
-
-
3
-
3
-
1
2
2
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1
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1
-
2
-
1
-
-
-
1
-
-
-
-
-
-
-
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-
94812
Chiu
An improved preparation of pho ...
Streptococcus sanguinis
Biochim. Biophys. Acta
876
167-169
1986
-
1
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-
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1
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1
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1
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2
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1
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1
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1
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2
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-
4778
Cain
Localization of phospholipid b ...
Escherichia coli
J. Biol. Chem.
259
942-948
1984
-
-
1
-
-
-
-
-
1
-
-
1
-
2
-
-
-
-
-
-
2
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
1
-
-
1
-
-
-
-
-
-
2
-
2
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
94814
Icho
Multiple genes for membrane-bo ...
Rattus sp.
J. Bacteriol.
153
722-730
1983
3
-
-
-
-
1
13
1
1
-
-
1
-
2
-
-
1
-
-
1
1
2
2
-
-
-
-
-
1
-
-
-
-
-
-
3
-
-
-
-
-
1
-
13
-
1
1
-
-
1
-
-
-
1
-
1
1
2
2
-
-
-
-
-
1
-
-
-
-
-
-
-
-
-
4768
Dutt
Intracellular distribution of ...
Escherichia coli, Klebsiella aerogenes, Micrococcus cerificans, Salmonella enterica subsp. enterica serovar Typhimurium, Serratia marcescens
J. Bacteriol.
132
159-165
1977
-
-
-
-
-
-
-
-
-
-
-
5
-
5
-
-
-
-
-
-
-
-
10
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
5
-
-
-
-
-
-
-
-
10
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
94816
Lipton
Phosphatidyl glycerol phosphat ...
Mesocricetus auratus, Rattus sp.
Biochem. Biophys. Res. Commun.
73
300-305
1976
-
-
-
-
-
-
1
-
-
-
-
2
-
2
-
-
-
-
-
1
-
-
4
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
1
-
-
-
-
-
2
-
-
-
-
-
1
-
-
4
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
94817
Larson
Phosphatidylglycerol biosynthe ...
Bacillus licheniformis
Biochemistry
15
974-979
1976
1
-
-
-
-
1
1
1
2
1
-
1
-
2
-
-
1
-
-
-
1
1
2
-
-
-
-
-
-
1
-
-
-
-
-
1
-
-
-
-
-
1
-
1
-
1
2
1
-
1
-
-
-
1
-
-
1
1
2
-
-
-
-
-
-
1
-
-
-
-
-
-
-
-
94818
Chang
Phosphatidyl glycerophosphate ...
Escherichia coli
J. Lipid Res.
8
456-462
1967
3
-
-
-
-
2
7
1
-
1
-
1
1
1
-
-
1
-
-
-
1
1
2
-
-
-
-
-
1
1
1
-
-
-
-
3
-
-
-
-
-
2
-
7
-
1
-
1
-
1
1
-
-
1
-
-
1
1
2
-
-
-
-
-
1
1
1
-
-
-
-
-
-
-