Information on EC 3.1.4.46 - glycerophosphodiester phosphodiesterase

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The enzyme appears in viruses and cellular organisms

EC NUMBER
COMMENTARY hide
3.1.4.46
-
RECOMMENDED NAME
GeneOntology No.
glycerophosphodiester phosphodiesterase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
a glycerophosphodiester + H2O = a primary alcohol + sn-glycerol 3-phosphate
show the reaction diagram
broad specificity; broad specificity for glycerophosphodiesters, glycerophosphocholine, glycerophosphoethanolamine, glycerophosphoglycerol and bis(glycerophospho)-glycerol are hydrolysed
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-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of carboxylic diester
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
glycerophosphodiester degradation
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phospholipid remodeling (phosphatidylethanolamine, yeast)
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degradation of sugar alcohols
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Glycerophospholipid metabolism
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SYSTEMATIC NAME
IUBMB Comments
glycerophosphodiester glycerophosphohydrolase
Broad specificity for glycerophosphodiesters; glycerophosphocholine, glycerophosphoethanolamine, glycerophosphoglycerol and bis(glycerophospho)-glycerol are hydrolysed.
CAS REGISTRY NUMBER
COMMENTARY hide
86280-59-3
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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-
-
Manually annotated by BRENDA team
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UniProt
Manually annotated by BRENDA team
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Swissprot
Manually annotated by BRENDA team
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Swissprot
Manually annotated by BRENDA team
fragment
TrEMBL
Manually annotated by BRENDA team
relapsing fever spirochetes have enzymic activity while Lyme disease spirochetes have not
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-
Manually annotated by BRENDA team
nontypeable Haemophilus influenzae
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-
Manually annotated by BRENDA team
two isozymes
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-
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
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F4HG94
UniProt
Manually annotated by BRENDA team
MPN420 or GlpQ; gene glpQ, the genome encodes two potential enzymes (MPN420 or GlpQ, and MPN566), although only GlpQ is functional
UniProt
Manually annotated by BRENDA team
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-
-
Manually annotated by BRENDA team
constitutive enzyme
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
metabolism
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the isozyme GDPD5 is a glycerophosphodiester phosphodiesterase that likely participates in regulating choline phospholipid metabolism in breast cancer, which possibly occurs in cooperation with choline kinase alpha and phosphatidylcholine-specific phospholipase D1
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
bis(glycerophospho)glycerol + H2O
?
show the reaction diagram
low activity
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-
?
bis(glycerophospho)glycerol + H2O
sn-gycerol 3-phosphate + ?
show the reaction diagram
bis(p-nitrophenyl) phosphate + H2O
p-nitrophenyl phosphate + p-nitrophenol
show the reaction diagram
-
-
-
-
?
cardiolipin + H2O
?
show the reaction diagram
low activity
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-
?
cyclic sn-2,3-phosphoglycerol + H2O
?
show the reaction diagram
-
-
-
-
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demeton + H2O
?
show the reaction diagram
-
-
-
-
?
ethyl p-nitrophenyl phosphate + H2O
p-nitrophenol + ethyl phosphate
show the reaction diagram
-
-
-
-
?
glycerophosphocholine + H2O
choline + glycerol-3-phosphate
show the reaction diagram
-
-
-
-
?
glycerophosphocholine + H2O
sn-glycerol 3-phosphate + choline
show the reaction diagram
glycerophosphodiester + H2O
glycerol 3-phosphate + alcohol
show the reaction diagram
glycerophosphodiester + H2O
sn-glycerol 3-phosphate + alcohol
show the reaction diagram
glycerophosphoethanolamine + H2O
sn-glycerol 3-phosphate + ethanolamine
show the reaction diagram
glycerophosphoglycerol + H2O
sn-glycerol 3-phosphate + glycerol
show the reaction diagram
glycerophosphoinositol + H2O
?
show the reaction diagram
glycerophosphoinositol + H2O
sn-glycerol 3-phosphate + inositol
show the reaction diagram
-
-
-
-
?
glycerophosphorylcholine + H2O
sn-glycerol 3-phosphate + choline
show the reaction diagram
-
-
-
?
glycerophosphoserine + H2O
?
show the reaction diagram
glycerophosphoserine + H2O
sn-glycerol 3-phosphate + serine
show the reaction diagram
-
-
-
-
?
L-alpha-glycerophosphocholine + H2O
choline + sn-glycerol-3-phosphate
show the reaction diagram
L-alpha-glycerophosphorylcholine + H2O
sn-glycerol 3-phosphate + choline
show the reaction diagram
-
-
-
-
?
p-nitrophenyl phosphate + H2O
p-nitrophenol + phosphate
show the reaction diagram
-
-
-
-
?
paraoxon + H2O
?
show the reaction diagram
-
-
-
-
?
sn-glycero-3-phospho-L-serine
L-serine + sn-glycerol 3-phosphate
show the reaction diagram
-
-
-
?
sn-glycero-3-phosphocholine + H2O
choline + sn-glycerol 3-phosphate
show the reaction diagram
sn-glycero-3-phosphoethanolamine + H2O
ethanolamine + sn-glycerol 3-phosphate
show the reaction diagram
sn-glycero-3-phosphoglycerol + H2O
glycerol + sn-glycerol 3-phosphate
show the reaction diagram
sn-glycero-3-phosphoinositol + H2O
inositol + sn-glycerol 3-phosphate
show the reaction diagram
sn-glycero-3-phosphoserine
serine + sn-glycerol 3-phosphate
show the reaction diagram
-
-
-
-
?
additional information
?
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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
glycerophosphocholine + H2O
choline + glycerol-3-phosphate
show the reaction diagram
-
-
-
-
?
glycerophosphocholine + H2O
sn-glycerol 3-phosphate + choline
show the reaction diagram
glycerophosphodiester + H2O
glycerol 3-phosphate + alcohol
show the reaction diagram
glycerophosphodiester + H2O
sn-glycerol 3-phosphate + alcohol
show the reaction diagram
glycerophosphoethanolamine + H2O
sn-glycerol 3-phosphate + ethanolamine
show the reaction diagram
glycerophosphoglycerol + H2O
sn-glycerol 3-phosphate + glycerol
show the reaction diagram
-
-
-
-
?
glycerophosphoinositol + H2O
sn-glycerol 3-phosphate + inositol
show the reaction diagram
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-
-
-
?
glycerophosphoserine + H2O
sn-glycerol 3-phosphate + serine
show the reaction diagram
-
-
-
-
?
L-alpha-glycerophosphocholine + H2O
choline + sn-glycerol-3-phosphate
show the reaction diagram
sn-glycero-3-phosphocholine + H2O
choline + sn-glycerol 3-phosphate
show the reaction diagram
sn-glycero-3-phosphoethanolamine + H2O
ethanolamine + sn-glycerol 3-phosphate
show the reaction diagram
sn-glycero-3-phosphoglycerol + H2O
glycerol + sn-glycerol 3-phosphate
show the reaction diagram
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isozyme At-GDPD1
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?
sn-glycero-3-phosphoinositol + H2O
inositol + sn-glycerol 3-phosphate
show the reaction diagram
Q8WTR4, Q9NPB8
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?
additional information
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Cu2+
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40% inhibition at 5 mM
Fe2+
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90% inhibition at 0.1 mM
glycerophosphoethanolamine
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Mg2+
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4 mM
Mn2+
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4 mM
p-nitrophenyl phosphate
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phosphate
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hydrolysis of p-nitrophenyl phosphate, competitive
Zn2+
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40% inhibition at 5 mM
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.6
bis(glycerophospho)glycerol
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25C, pH 9.0
3.5 - 7
bis(p-nitrophenyl phosphate)
0.12 - 3.95
bis(p-nitrophenyl) phosphate
0.036 - 2
glycerophosphocholine
0.2 - 0.22
glycerophosphoethanolamine
0.2 - 0.62
glycerophosphoglycerol
0.39
glycerophosphoinositol
0.66
glycerophosphoserine
0.12 - 49
p-nitrophenyl phosphate
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.176 - 2.78
bis(p-nitrophenyl phosphate)
1.4 - 2
bis(p-nitrophenyl) phosphate
3.2
glycerophosphocholine
1.1
glycerophosphoethanolamine
3.3
glycerophosphoglycerol
1.8
glycerophosphoinositol
2.8
glycerophosphoserine
0.24 - 6.4
p-nitrophenyl phosphate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0498 - 0.4
bis(p-nitrophenyl phosphate)
1.6
glycerophosphocholine
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4.8
glycerophosphoethanolamine
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5.4
glycerophosphoglycerol
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4.7
glycerophosphoinositol
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4.2
glycerophosphoserine
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0.006 - 16.4
p-nitrophenyl phosphate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.04
glycerophosphoethanolamine
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30C
0.078
p-nitrophenyl phosphate
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
31
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substrate paraoxon, 22C, pH 5.0
120
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substrate demeton, 22C, pH 8.0; substrate paraoxon, 22C, pH 8.0
2600
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substrate demeton, 22C, pH 5.0
additional information
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activity increases after proteolytic digestion with trypsin
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4 - 10
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.64
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calculated from the deduced amino acid sequence
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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the isozyme GDPD5 is significantly overexpressed in highly malignant estrogen receptor negative compared to weakly malignant estrogen receptor positive human breast cancer cells and breast tumors from patients, GDPD5 expression in tumors and correlation to choline containing metabolite levels, overview
Manually annotated by BRENDA team
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weak signal
Manually annotated by BRENDA team
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osteoblast-like cells
Manually annotated by BRENDA team
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nonmalignant human mammary epithelial cells
Manually annotated by BRENDA team
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estrogen-sensitive weakly metastatic human breast cancer cells
Manually annotated by BRENDA team
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estrogen-independent highly metastatic human breast cancer cells
Manually annotated by BRENDA team
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skeletal muscle
Manually annotated by BRENDA team
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expression of GDE2 is significantly upregulated during neuronal differentiation by retinoic acid treatment hippocampus
Manually annotated by BRENDA team
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low level
Manually annotated by BRENDA team
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
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plastid-localized isozyme AtGDPD1
Manually annotated by BRENDA team
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enzyme co-localizes with actin cytoskeleton
Manually annotated by BRENDA team
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isozymes GlpQ1-3 are secreted
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Manually annotated by BRENDA team
additional information
PDB
SCOP
CATH
ORGANISM
UNIPROT
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Cytophaga hutchinsonii (strain ATCC 33406 / NCIMB 9469)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Staphylococcus aureus (strain Newman)
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
17500
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x * 17500, SDS-PAGE
25570
calculated, residues 1-222
27300
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6 * 27300, crystal structure analysis; x * 27300, gel filtration experiments with an estimated molecular weight of approximately 160000 Da indicates a higher number of monomers than found in crystals
36200
x * 36200, calculated from cDNA
39000
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x * 39000, SDS-PAGE
40000
-
x * 40000, periplasmic enzyme, SDS-PAGE
45000
x * 45000, deduced from gene sequence
55000
-
x * 55000, SDS-PAGE
61000
-
x * 61000, deduced from gene sequence
68600
-
x * 68600, calculated from the deduced amino acid sequence
68910
-
calculated from cDNA sequence
69000
-
x * 69000, SDS-PAGE
138000
160000
-
a molecular weight of approximately 160000 Da estimated by gel filtration
280000
-
gel filtration
3083993
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2 * 3083993, calculated from the deduced amino acid sequence, crystal structure analysis
additional information
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nucleotide sequence
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
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2 * 3083993, calculated from the deduced amino acid sequence, crystal structure analysis; 2 * 31000, SDS-PAGE, crystal structure analysis
hexamer
trimer
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3 * 31000, SDS-PAGE
additional information
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
glycoprotein
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lipoprotein
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystal structure analysis
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sitting drop vapor diffusion method
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crystal structure of the Thermoanaerobacter tengcongensis (ttGDPD) at 1.91 A resolution is reported, with a calcium ion and glycerol as a substrate mimic coordinated at this calcium ion (PDB entry 2pz0). The ttGDPD dimer with an intermolecular disulfide bridge and two hydrogen bonds is considered as the potential functional unit
crystal structure analysis
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sitting drop vapor diffusion method, best crystallization results when apo-GpdQ is used, crystals with bound Zn2+ and Co2+
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crystal structure analysis of the TM1621 protein
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nanodroplet vapour diffusion method, 40% PEG-600 and 0.1 M 2-(cyclohexylamino)ethane sulfonic acid, pH 9.6, MAD with 1.6 A resolution
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ion exchange chromatography, hydroxyapatite chromatography, gel filtration
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ion-exchange chromatography (DEAE), hydrophobic interaction chromatography (Phenyl Sepharose), gel filtration
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metal chelate affinity resin
partial
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recombinant protein
recombinant protein using His-tag
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sonication, centrifugation, dialysis against PBS
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using Ni-NTA chromatography and gel filtration
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
13 potential homologues are identified and subdivided into two groups: the first comprising proteins with only one GP-PDE domain or canonical type A enzymes, AtGDPD1-6, and the second including proteins with two putative GP-PDE domains, type B enzymes AtGDPDL1-7
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336 amino acids
complete coding sequence by using genomic DNA of strain FR64B, 334 amino acids
constitutive enzyme, transgenic enzyme expression can complement the enzyme UgpQ in a gene ugpQ-deleted strain of Escherichia coli
expressed as His-tag fusion protein in Escherichia coli TOP10 cells
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expressed in Escherichia coli BL21(DE3)
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expressed in Escherichia coli DH5alpha
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expressin of Myc-tagged vectors in COS-7 cells
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expression in Escherichia coli DL41 with His-Tag
GDE2, maps to 11q13.4-13.5, and contains 17 exons and 16 introns, overexpression of a the tagged GDE2 in COS-7, HEK-293cells, and in HeLa cell endoplasmic reticulum, as well as at the plasma membrane, depending on cell confluence, with a predominant plasma-membrane localization in confluent
gene glpQ, phylogenetic analysis; gene ugpQ, phylogenetic analysis
gene gpdQ, DNA and amino acid seuence determination and analysis
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gene YPL110c; gene YPL206c
generation of an 86-028NP-derived NTHI strain that expresses an hpd/glpQ promoter-driven luciferase reporter from the vector pKMLN-01, hpd/glpQ is expressed in an operon with glpT
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isolation of cDNAs encoding GDE2 and GDE6, cloned by using mouse brain cDNA libraries, expression in Escherichia coli JM109
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protein in Escherichia coli BL21(DE3)
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the genome encodes seven genes, glpQ1-3 and ugpQ1-4
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YqiK is regulated by the same operon yqiHIK as other hydrolytic enzymes
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
expression of the UgpQ protein is significantly induced in phosphate-starved wild-type Escherichia coli
GDE2 up-regulation upon retinoic-acid treatment
high-salinity growth conditions induce the up-regulation of the transcription of the operon yqiHIK encoding the enzyme
increased enzyme expression in microarray studies under low-phosphate conditions
osmotic stress conditions resulting from high salt concentrations cause a decrease in the sioyzme GDE2 mRNA half-life, with the consequent lowering of GDE2 protein levels and a decrease in glycero-3-phosphocholine hydrolysis in transgenic murine mIMCD3 cells
PhoP-dependent upregulation in response to phosphate shiftdown; PhoP-dependent upregulation in response to phosphate shiftdown
salt and osmotic stress induce up-regulation of AtGDPDL genes, while AtGDPDs genes are up-regulated by inorganic phosphate deprivation
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the isozymes are induced by phosphate deprivation
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
N80A
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ligand of the metal ion
medicine
-
GP-PDE plays a role in the regulation of cytoskeletal modification
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
diagnostics
the enzyme is used for the serological diagnosis of patients with tick-borne relapsing fever because the presence of antibodies against this spirochete has been detected upon infection, and for the setting-up of molecular and serologic techniques for the diagnosis of relapsing fever borreliosis
drug development
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the enzyme might be a promising target for anti-malaria drug development
environmental protection
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the enzyme might be useful in the bioremediation of soil, through the detoxification of organophosphate pesticides and products of the degradation of nerve agents
medicine
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