Information on EC 3.1.4.2 - glycerophosphocholine phosphodiesterase

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria

EC NUMBER
COMMENTARY hide
3.1.4.2
-
RECOMMENDED NAME
GeneOntology No.
glycerophosphocholine phosphodiesterase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
sn-glycero-3-phosphocholine + H2O = choline + sn-glycerol 3-phosphate
show the reaction diagram
also acts on sn-glycero 3-phosphoethanolamine
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of phosphoric ester
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
phosphatidylcholine resynthesis via glycerophosphocholine
-
-
phospholipid remodeling (phosphatidylethanolamine, yeast)
-
-
Glycerophospholipid metabolism
-
-
SYSTEMATIC NAME
IUBMB Comments
sn-glycero-3-phosphocholine glycerophosphohydrolase
Also acts on sn-glycero-3-phosphoethanolamine.
CAS REGISTRY NUMBER
COMMENTARY hide
9025-85-8
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
phosphate-starved
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
found in all 127 Haemophilus influenzae strains, including encapsulated serotypes a-f and NT Haemophilus influenzae strains, number of Protein D molecules is estimated to be 2800 molecules per bacterial cell
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-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
gene glpQ
-
-
Manually annotated by BRENDA team
rabbit
-
-
Manually annotated by BRENDA team
inositol-starved
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
-
the Arabidopsis GDPD family can be classified into canonical GDPD (AtGDPD1-6) and GDPD-like (AtGDPDL1-7) subfamilies
malfunction
metabolism
-
the GDPD-mediated lipid metabolic pathway may be involved in release of phosphate from phospholipids during phosphate starvation
physiological function
additional information
-
a second glycerophosphodiesterase enzyme, MPN566, is catalytically inactive and its deletion does not cause an altered phenotype
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
1,2,2-trimethylpropyl methylphosphonate + H2O
3,3-dimethylbutan-2-ol + methylphosphonate
show the reaction diagram
-
-
-
-
ir
4-nitrophenyl ethylphosphonate + H2O
4-nitrophenyl + ethylphosphonate
show the reaction diagram
-
-
-
-
ir
4-nitrophenyl methylphosphonate + H2O
4-nitrophenyl + methylphosphonate
show the reaction diagram
-
-
-
-
ir
4-nitrophenyl phenyl phosphate + H2O
4-nitrophenol + phenyl phosphate
show the reaction diagram
-
-
-
-
ir
4-nitrophenyl phenyl phosphonate + H2O
4-nitrophenol + phenyl phosphonate
show the reaction diagram
-
-
-
-
ir
4-nitrophenylphosphate + H2O
4-nitrophenol + phosphate
show the reaction diagram
-
-
-
-
ir
bis(4-nitrophenyl) phosphate + H2O
4-nitrophenol + phosphate
show the reaction diagram
-
-
-
-
ir
bis(p-nitro-phenyl)phosphate + H2O
?
show the reaction diagram
-
-
-
-
?
diethyl phosphate + H2O
ethanol + ethyl phosphate
show the reaction diagram
-
-
-
-
ir
dimethyl 4-nitrophenyl phosphate + H2O
?
show the reaction diagram
-
-
-
-
ir
dimethyl phosphate + H2O
methanol + methyl phosphate
show the reaction diagram
-
-
-
-
ir
ethyl 4-nitrophenyl phosphate + H2O
4-nitrophenol + ethyl phosphate
show the reaction diagram
-
-
-
-
ir
ethyl demeton S
?
show the reaction diagram
-
-
-
-
-
ethyl methyl 4-nitrophenyl phosphate + H2O
?
show the reaction diagram
-
-
-
-
ir
ethyl methylphosphonate + H2O
ethanol + methylphosphonate
show the reaction diagram
-
-
-
-
ir
glycero-3-phosphoethanolamine + H2O
sn-glycerol-3-phosphate + ethanolamine
show the reaction diagram
glycerophosphocholine + H2O
glycerol 1,2-cyclic phosphate + choline
show the reaction diagram
glycerophosphocholine + H2O
sn-glycerol 3-phosphate + choline
show the reaction diagram
-
-
-
-
?
glycerophosphoethanolamine + H2O
?
show the reaction diagram
glycerophosphoethanolamine + H2O
glycerol 1,2-cyclic phosphate + ethanolamine
show the reaction diagram
glycerophosphoglycerol + H2O
glycerol + glycerol 3-phosphate
show the reaction diagram
-
-
-
?
glycerophosphoinositol + H2O
inositol + glycerol 3-phosphate
show the reaction diagram
glycerophosphoserine + H2O
L-serine + glycerol 3-phosphate
show the reaction diagram
-
-
-
?
glycerophosphoserine + H2O
serine + glycerol 3-phosphate
show the reaction diagram
-
-
-
?
isobutyl methylphosphonate + H2O
isobutanol + methylphosphonate
show the reaction diagram
-
-
-
-
ir
isopropyl 4-nitrophenyl phosphate + H2O
4-nitrophenol + isopropyl phosphate
show the reaction diagram
-
-
-
-
ir
isopropyl methylphosphonate + H2O
isopropanol + methylphosphonate
show the reaction diagram
-
-
-
-
ir
methyl 4-nitrophenyl phosphate + H2O
4-nitrophenol + methyl phosphate
show the reaction diagram
-
-
-
-
ir
O-ethyl S-[2-(ethylsulfanyl)ethyl] hydrogen thiophosphate + H2O
?
show the reaction diagram
-
-
-
-
ir
p-nitrophenylphosphocholine + H2O
p-nitrophenol + phosphocholine
show the reaction diagram
-
-
single enzyme utilizing both glycerophosphocholine and p-nitrophenylphosphocholine as substrates
?
paraoxon + H2O
4-nitrophenol + diethyl phosphate
show the reaction diagram
-
-
-
-
ir
phenyl methylphosphonate + H2O
phenol + methylphosphonate
show the reaction diagram
-
-
-
-
ir
polyglycerophosphate + H2O
glycerol + sn-glycerol 3-phosphate
show the reaction diagram
-
exhibits a structural requirement for phosphodiester bonds between adjacent glycerol units
-
?
S-[2-(ethylsulfanyl)ethyl] O,O-dimethyl thiophosphate + H2O
?
show the reaction diagram
-
-
-
-
ir
S-[2-(ethylsulfanyl)ethyl] O-methyl hydrogen thiophosphate + H2O
?
show the reaction diagram
-
-
-
-
ir
S-[2-[bis(1-methylethyl)amino]ethyl] O-ethyl hydrogen thiophosphate + H2O
?
show the reaction diagram
-
-
-
-
ir
sn-glycero 3-phosphorylcholine + H2O
?
show the reaction diagram
sn-glycero 3-phosphorylcholine + H2O
sn-glycerol 3-phosphate + choline
show the reaction diagram
sn-glycero 3-phosphorylethanolamine + H2O
?
show the reaction diagram
sn-glycero 3-phosphorylethanolamine + H2O
sn-glycerol 3-phosphate + ethanolamine
show the reaction diagram
sn-glycero-3-phosphocholine + H2O
choline + sn-glycerol 3-phosphate
show the reaction diagram
sn-glycero-3-phosphocholine + H2O
sn-glycerol 3-phosphate + choline
show the reaction diagram
-
-
-
-
?
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
glycero-3-phosphoethanolamine + H2O
sn-glycerol-3-phosphate + ethanolamine
show the reaction diagram
-
hydrolysis of the 3'-5' phosphodiester bond
-
-
?
sn-glycero 3-phosphorylcholine + H2O
?
show the reaction diagram
sn-glycero 3-phosphorylethanolamine + H2O
?
show the reaction diagram
sn-glycero-3-phosphocholine + H2O
choline + sn-glycerol 3-phosphate
show the reaction diagram
sn-glycero-3-phosphocholine + H2O
sn-glycerol 3-phosphate + choline
show the reaction diagram
-
-
-
-
?
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Cd2+
-
fully restored activity if chelating agents used
Ni2+
-
restore activity if EDTA or EGTA used
Sr2+
-
restore activity if metal-binding agents used
additional information
-
no activation by Ca2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-[5-Amino-2-(4-fluoro-phenyl)-6-oxo-6H-pyrimidin-1-yl]-N-(1-benzyl-2-oxo-2-thiazol-2-yl-ethyl)-acetamide
-
-
Ca2+
-
no activity with
Cd2+
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-
choline
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-
citrate
-
24% inhibition at 6 mM
Co2+
-
no activity with
diphenylphosphate
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15% inhibition at 5 mM
ethanolamine
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glycero 3-phosphorylethanolamine
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45% inhibition of choline formation in equimolar ratio to glycerophosphorylcholine
glycerophosphocholine
-
competitive inhibition
glycerophosphoethanolamine
heparin
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70% inhibition at 0.02 mg/ml
L-alpha-glycerol 3-phosphate
metal-binding agents
-
complete inhibition by EDTA and EGTA, EDDA inhibits competitve, urea and increasing temperature potentiate inhibitory effect by EDTA
-
Mg2+
-
90% inhibition at 1 mM
Mn2+
-
90% inhibition at 1 mM
N,N-dimethylethanolamine
-
-
N-ethylmaleimide
N-Methylethanolamine
-
-
nafoxidine
-
complete inhibition
p-chloromercuribenzoate
-
at 0.1 mM, about 25% inhibition
phosphate
tryptic digested cell walls
-
derived from various gram-positive bacteria and murein-sacculi from E. coli, 60% inhibition
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
17beta-estradiol
-
only in uterine responsive for estradiol
activator protein 18.5 kDa
-
2fold increase of activation, co-purified with the enzyme
-
Ca2+
-
-
Calmodulin
-
activation, source: bovine
Cu2+
-
-
Mg2+
-
-
Zn2+
-
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.4
4-nitrophenyl ethylphosphonate
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-
1.3
4-nitrophenyl methylphosphonate
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-
1.8
4-nitrophenyl phenyl phosphate
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-
13
4-nitrophenyl phenyl phosphonate
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-
0.9
bis(4-nitrophenyl) phosphate
-
-
0.5
diethyl phosphate
-
-
0.06
dimethyl phosphate
-
-
0.9
ethyl 4-nitrophenyl phosphate
-
-
0.74
ethyl methylphosphonate
-
-
0.23 - 0.65
glycerophosphocholine
0.24
glycerophosphoethanolamine
-
-
0.35
glycerophosphoglycerol
-
-
1
glycerophosphoinositol
-
-
2.5
Glycerophosphorylcholine
-
-
1.2
glycerophosphorylethanolamine
-
-
0.59
glycerophosphoserine
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-
3.3
isobutyl methylphosphonate
-
-
6.5
isopropyl 4-nitrophenyl phosphate
-
-
19
isopropyl methylphosphonate
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-
2.6
methyl 4-nitrophenyl phosphate
-
-
0.22
p-nitrophenylphosphocholine
-
-
0.6 - 5.7
sn-glycero 3-phosphocholine
0.31 - 1.2
sn-glycero 3-phosphorylcholine
-
2.5
sn-glycero 3-phosphorylethanolamine
-
-
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.5
4-nitrophenyl ethylphosphonate
-
-
1.6
4-nitrophenyl methylphosphonate
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-
4
4-nitrophenyl phenyl phosphate
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-
2.8
4-nitrophenyl phenyl phosphonate
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-
6
bis(4-nitrophenyl) phosphate
-
-
0.0074
diethyl phosphate
-
-
0.005
dimethyl phosphate
-
-
2
ethyl 4-nitrophenyl phosphate
-
-
0.0012
ethyl methylphosphonate
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-
0.001
isobutyl methylphosphonate
-
-
1
isopropyl 4-nitrophenyl phosphate
-
-
0.001
isopropyl methylphosphonate
-
-
7.3
methyl 4-nitrophenyl phosphate
-
-
0.0012
O-ethyl S-[2-(ethylsulfanyl)ethyl] hydrogen thiophosphate
-
-
0.0031
phenyl methylphosphonate
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-
1.1
S-[2-[bis(1-methylethyl)amino]ethyl] O-ethyl hydrogen thiophosphate
-
-
220
sn-glycero 3-phosphorylcholine
-
-
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.04
2-[5-Amino-2-(4-fluoro-phenyl)-6-oxo-6H-pyrimidin-1-yl]-N-(1-benzyl-2-oxo-2-thiazol-2-yl-ethyl)-acetamide
-
glycerophosphoethanolamine pH 6.0, 30C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.005
-
-
0.006
-
-
0.046
-
in renal medulla
0.089
-
in renal cortex
0.096
-
for glycero 3-phosphocholine hydrolysis
0.1
-
proestrous fluid purification
0.195
-
freezing and thawing increases specific activity
0.598
-
for p-nitrophenylphosphocholine hydrolysis
0.763
-
in vitro synthesis and purification of the enzyme
2
-
purified recombinant His-tagged GDE5, substrate is glycerophosphoethanolamine, pH 7.4, 37C
2.19
-
partially purified enzyme
4.57
-
0.55 M activator protein added
5.72
-
1.1 M activator protein added
325
-
90% homogenity
additional information
-
enzymatic activity similar to that of GlpQ (glycerophosphodiester phosphodiesterase, EC 3.1.4.44) of Escherichia coli
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.4
-
assay at
7.8
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using two-step assay
8 - 8.6
-
-
8.5 - 9
-
-
8.5
-
-
8.9
-
-
9
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in glycine/NaOH buffer, above pH 9.0 in glycylglycine/NaOH buffer
9.3
-
-
10
-
for glycerophosporylcholine hydrolysis
11
-
for p-nitrophenylphosphocholine hydrolysis
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.7 - 9
-
less than 50% activity below pH6 6.7 and above pH 9.0
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
-
assay at
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.45
-
theoretical value
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
the cells show a 2-4fold activation of glycerophosphocholine-phosphodiesterase compared to control cells
Manually annotated by BRENDA team
-
low activity
Manually annotated by BRENDA team
-
considerable activity
Manually annotated by BRENDA team
-
-
Manually annotated by BRENDA team
-
highest activity
Manually annotated by BRENDA team
-
PAP-HT25 renal medullary epithelial cells
Manually annotated by BRENDA team
-
cultured retinal microcapillary pericytes, high enzymic activity
Manually annotated by BRENDA team
-
-
Manually annotated by BRENDA team
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
abundance of GPX-PDE2 protein is substantially greater in cell wall extracts of Pi-deficient plants as compared with Pi-sufficient plants
Manually annotated by BRENDA team
-
outer membrane-anchored lipoprotein
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
14000
-
SDS-PAGE and native PAGE analysis
30000
-
SDS-PAGE and native PAGE analysis
30800
-
monomer
31000
-
determined by SDS-PAGE
40000
-
SDS-PAGE analysis
41820
-
calculated from DNA sequence encoding Protein D (346 amino acids), SDS-PAGE, Western Blot
70000
-
gel filtration chromatography
72000
-
sucrose density gradient centrifugation, SDS-PAGE analysis
75000
-
native PAGE analysis
81000
-
x * 81000, recombinant His6-tagged enzyme, SDS-PAGE
105000
-
gel filtration
185700
-
electrospray ionisation mass spectrometry, under non-denaturing conditions, consistent with calculated mass of hexamer
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
-
three dimers stabilized by an inter-chain disulfide bond, alpha/beta-sandwich
monomer
-
1* 14000, SDS-PAGE
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
side-chain modification
-
N-acetylglucosamine, N-acetylgalactosamine
additional information
-
acylation of Protein D determines its hydrophobicity
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
in complex with Zn and Co as well as without metals in apo-form
-
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
-
10% inactivation after 5 min
ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Acetone
-
90% v/v, 50% loss of activity
Ethanol
-
90% v/v, 80% loss of activity
isopropanol
-
90% v/v, 24% loss of activity
Methanol
-
70% v/v, complete denaturation
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-75C, 25 mM Tris-HCl pH 7.4, 0.1 mM DTT, 10% glycerol, several months
-
room temperature, 0.02 M Tris-HCl pH 7.5, 24 h
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
34-fold purification
-
37-fold purification
-
60-fold purification
-
80-99fold purification
-
gel filtration
-
N-terminally Strep-tagged enzymes
-
partial
partial 20-fold purification
-
partial, 17-fold purification
-
recombinant C-terminally His6-tagged enzyme from Spodoptera frugiperda Sf9 cells by nickel affinity chromatography and gel filtration
-
size exclusion column, anion-exchange column
-
to homogenity
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
expression of C-terminally His6-tagged enzyme in Spodoptera frugiperda Sf9 cells
-
genes glpQ and mpn566, expression of N-terminally Strep-tagged enzymes
-
GPX-PDE1 and GPX-PDE2, DNA and amino acid sequence determination and analysis, phylogenetic tree, expression GST-tagged GPX-PDE2
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
AtGDPDs but not AtGDPDLs are up-regulated by phosphate starvation
-
transcripts of GPX-PDE2 accumulated to about 15fold higher in photosynthate-deprived plants than normal light/dark plants, and the stimulation is displayed in both roots and leaves
-
when plants are deprived of light by dark treatment for 24h, GPX-PDE1 transcripts in Pi-deficient roots are reversibly decreased by about 70% compared with under normal light/dark conditions. The expression level of GPX-PDE1 in leaf tissue is not affected
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biotechnology
-
efficient selection system for the identification of phosphotriesterase mutants with enhanced catalytic properties for selected organophosphate substrates
diagnostics
-
increased enzyme activity due to altered phosphatidylcholine metabolism in epithelial ovarian cancer cells can serve as diagnostic marker, overview
drug development
-
possible vaccination, Protein D is immunogenic in human. Vaccine containing polysaccharides from 7 serotypes (each conjugated to CRM197, a nontoxic mutant of diphtheria toxin that is an immunogenically inactive carrier) shows high efficacy in young children. Experiments with rats: vaccination with Protein D induces high levels of serum IgG and IgA antibodies and significant bactericidal activity against homologous and heterologous strains (rat middle ear clearance model, rat pulmonary clearance model). Pronounced activity of Protein D antibodies is shown in the chinchilla acute otitis media model