Information on EC 3.1.3.74 - pyridoxal phosphatase

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

EC NUMBER
COMMENTARY hide
3.1.3.74
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RECOMMENDED NAME
GeneOntology No.
pyridoxal phosphatase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
pyridoxal 5'-phosphate + H2O = pyridoxal + phosphate
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of phosphoric ester
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
pyridoxal 5'-phosphate salvage II (plants)
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Vitamin B6 metabolism
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Metabolic pathways
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SYSTEMATIC NAME
IUBMB Comments
pyridoxal-5'-phosphate phosphohydrolase
Requires Mg2+. This enzyme is specific for phosphorylated vitamin B6 compounds: it acts not only on pyridoxal phosphate (PLP), but also on pyridoxine phosphate (PNP), pyridoxamine phosphate (PMP), 4-pyridoxic acid phosphate and 4-deoxypyridoxine phosphate. This reaction can also be carried out by EC 3.1.3.1 (alkaline phosphatase) and EC 3.1.3.2 (acid phosphatase), but these enzymes have very broad substrate specificities.
CAS REGISTRY NUMBER
COMMENTARY hide
9076-92-0
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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-
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
4-deoxypyridoxine 5'-phosphate + H2O
4-deoxypyridoxine + phosphate
show the reaction diagram
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-
-
-
?
4-pyridoxic acid 5'-phosphate + H2O
4-pyridoxic acid + phosphate
show the reaction diagram
N-(5'-phospho-4'-pyridoxyl)benzylamine + H2O
4'-pyridoxylbenzylamine + phosphate
show the reaction diagram
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-
-
-
?
N-(5'-phospho-4'-pyridoxyl)ethanolamine + H2O
4'-pyridoxylethanolamine + phosphate
show the reaction diagram
-
-
-
-
?
N-(5'-phospho-4'-pyridoxyl)glycine + H2O
4'-pyridoxylglycine + phosphate
show the reaction diagram
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-
-
-
?
N-(5'-phospho-4'-pyridoxyl)phenylalanine + H2O
4'-pyridoxylphenylalanine + phosphate
show the reaction diagram
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much higher catalytic efficiency than with pyridoxine 5’-phosphate
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-
?
p-nitrophenyl phosphate + H2O
p-nitrophenol + phosphate
show the reaction diagram
p-nitrophenyl-phosphate + H2O
p-nitrophenol + phosphate
show the reaction diagram
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-
-
-
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pyridoxal 5'-phosphate + H2O
pyridoxal + phosphate
show the reaction diagram
pyridoxal 5'phosphate + H2O
pyridoxal + phosphate
show the reaction diagram
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-
-
-
?
pyridoxal-5'-phosphate + H2O
pyridoxal + phosphate
show the reaction diagram
pyridoxamine 5'-phosphate + H2O
pyridoxamine + phosphate
show the reaction diagram
pyridoxine 5'-phosphate + H2O
pyridoxal + phosphate
show the reaction diagram
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-
-
?
pyridoxine 5'-phosphate + H2O
pyridoxine + phosphate
show the reaction diagram
pyridoxine phosphate + H2O
pyridoxine + phosphate
show the reaction diagram
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-
-
-
?
pyridoxine-5'-phosphate + H2O
pyridoxine + phosphate
show the reaction diagram
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-
-
-
?
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
pyridoxal 5'-phosphate + H2O
pyridoxal + phosphate
show the reaction diagram
pyridoxal 5'phosphate + H2O
pyridoxal + phosphate
show the reaction diagram
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-
-
-
-
pyridoxal-5'-phosphate + H2O
pyridoxal + phosphate
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
CaCl2
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enzyme has 17% as much activity with 1 mM CaCl2 than with MgCl2
Cu2+
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enzyme has 4% as much activity with 1 mM Cu2+ than with MgCl2
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2,2'-dithiodipyridine
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0.005 mM, 50% inhibition
2-ethyl-5-phenylisoxazolium-3'-sulfonate
4,4'-dithiodipyridine
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0.005 mM, 50% inhibition
4-pyridoxic acid 5'-phosphate
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very effective inhibitor, 0.02 mM, 50% inhibition of pyridoxine 5’-phosphate hydrolysis
5,5'-dithiobis(2-nitrobenzoate)
5,5'-dithiobis(2-nitrobenzoic acid)
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50 nM, 50% inhibition, incorporation of 1 mol per mol of subunit leads to complete inactivation, phosphate or dithiothreitol protects
Ca2+
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competitive inhibition versus Mg2+, noncompetitive versus substrate
Cd2+
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Cu2+
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cysteine
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diethyldicarbonate
disulfide reagent
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reactivation by excess dithiothreitol, inactivation is due to formation of a mixed disulfide between the reagent and a free cysteinyl residue at or near the active site of enzyme
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EDTA
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0.2 mM, complete inhibition in the absence of Mg2+, 50% inhibition in the presence of 1 mM Mg2+
Fe2+
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fluoride
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2 mM, 50% inhibition
iodacetate
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52% inhibition at 5 mM
iodoacetamide
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weak
iodoacetate
KH2PO4
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56% inhibition at 5 mM
levamisole
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26% inhibtion at 5 mM
molybdate
N-(5'-phospho-4'-pyridoxyl)ethanolamine
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0.05 mM, 12% inhibition
N-(5'-phospho-4'-pyridoxyl)glycine
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0.05 mM, 32% inhibition
N-(5'-phospho-4'-pyridoxyl)phenylalanine
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0.05 mM, 51% inhibition
N-ethylmaleimide
NaF
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24% inhibition at 5 mM
p-chloromercuribenzoate
p-nitrophenyl phosphate
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poor, 4 mM, 50% inhibition of pyridoxine 5’-phosphate hydrolysis
Pb2+
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Phenyl phosphate
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very poor inhibitor of pyridoxine 5’-phosphate hydrolysis
Phenylglyoxal
phosphate
pyridoxal
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weak, 11 mM, 50% inhibition of hydrolysis of pyridoxal 5’-phosphate or pyridoxine 5’-phosphate
pyridoxal 5'-phosphate
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very effective inhibitor, 0.03 mM, 50% inhibition of pyridoxine 5’-phosphate hydrolysis
pyridoxamine 5'-phosphate
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0.5 mM, 50% inhibition of pyridoxine 5’-phosphate hydrolysis, less effective than pyridoxal 5’-phosphate or 4-pyridoxic acid 5’-phosphate
pyridoxine 5'-phosphate
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0.05 mM, 45% inhibition
Sodium molybdate
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79% inhibition at 5 mM
Tetranitromethane
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inactivates in a time-dependent manner, 10 mM, 70% inhibition in the absence of pyridoxal 5’-phosphate and 30% in the presence of 0.15 mM pyridoxal 5’-phosphate
thiol-specific reagent
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a variety of thiol-specific reagents inactivate in a time- and concentration-dependent manner, pyridoxal phosphate or phosphate protects
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additional information
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
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the presence of glucose in the growth medium increases the amount of pyridoxal phosphate phosphatase compared with pyridoxamine oxidase activity
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00112 - 0.00255
4-pyridoxic acid 5'-phosphate
0.0635
N-(5'-phospho-4'-pyridoxyl)benzylamine
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pH 7.4, 37°C
0.0786
N-(5'-phospho-4'-pyridoxyl)ethanolamine
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pH 7.4, 37°C
0.0143
N-(5'-phospho-4'-pyridoxyl)glycine
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pH 7.4, 37°C
0.00824
N-(5'-phospho-4'-pyridoxyl)phenylalanine
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pH 7.4, 37°C
0.00129 - 0.33
pyridoxal 5'-phosphate
0.33 - 0.385
pyridoxal-5'-phosphate
0.034 - 0.0806
pyridoxamine 5'-phosphate
0.0043 - 0.0434
pyridoxine 5'-phosphate
0.385
pyridoxine-5'-phosphate
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1 mM MnCl2, 50 mM Tris-HCl pH 7.0
additional information
additional information
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.52 - 19.4
pyridoxal 5'-phosphate
19
pyridoxal-5'-phosphate
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5 mM CoCl2, 1 mM dithiothreitol, 50 mM Tris/maleate pH 5.0, 37°C
0.45
pyridoxamine 5'-phosphate
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pH 7.4, 37°C, recombinant enzyme
1.25
pyridoxine 5'-phosphate
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pH 7.4, 37°C, recombinant enzyme
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00638
Ca2+
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0.00348
molybdate
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0.22 - 0.8
phosphate
additional information
additional information
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.575
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pH 7.4, 37°C
5.3
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pH 7.4, 37°C
7
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5 mM CoCl2, 1 mM dithiothreitol, 50 mM Tris/maleate pH 5.0, 37°C; purified enzyme
20
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5 mM CoCl2, 1 mM dithiothreitol, 50 mM Tris/maleate pH 5.0, 37°C
42
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1 mM MnCl2, 50 mM Tris-HCl pH 7.0
105
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1 mM MnCl2, 50 mM Tris-HCl pH 7.0
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 6.5
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additional information
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alkaline and acid pyridoxal phosphate phosphatase, not identical with alkaline and acid phosphatase
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22
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assay at, inhibition studies
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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high expression
Manually annotated by BRENDA team
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high expression
Manually annotated by BRENDA team
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polymorphonuclear
Manually annotated by BRENDA team
additional information
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mRNA is differentially expressed in a tissue-specific manner, tissue distribution
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
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Manually annotated by BRENDA team
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25000
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SDS-PAGE, Western blot (rabbit anti-histidine polyclonal antibody)
26470
sequence analysis
29000
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gel filtration
31512
x * 31512, sequence calculation
31698
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2 * 31698, sequence calculation, 2 * 32000, recombinant enzyme, SDS-PAGE
45000
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2 * 45000, gel filtration compared to deduced molecular weight from sequence; 2 * 45000, SDS-PAGE
60000
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gel filtration, recombinant enzyme
90000
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 31512, sequence calculation
monomer
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1 * 29000, SDS-PAGE
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 9
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60 min, no loss of activity
655966
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
purified enzyme is unstable at low protein concentration, 0.002% Triton X-100 stabilizes, enzyme is unstable to freezing in the absence of glycerol
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recombinant PEP-1-PLPP fusion protein transduced into PC12 cells is stable for 36 h
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ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ethanol
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10%, no effect on enzyme activity
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, storage at concentrations of 0.3 mg/ml or greater, 30 mM phosphate, at least 6 months, stable
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
168000fold
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5 chromatography steps to homogeneity
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51000fold
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70fold
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9.6fold, recombinant enzyme
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by gel filtration; one chromatography step to homogeneity
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by Ni2+ column
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lysed by French Press Cell and by sonication in binding buffer (5 mM imidazole, 500 mM NaCl, and 20 mMTris-HCl, pH 7.9)., Ni2+-IDA column, desalting with PD10 column
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Ni-affinity chromatography
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sonication of cells in binding buffer (5 mM imidazole, 0.5 M NaCl, 20 mM Tris-HCl, pH 7.9), centrifugation, Ni2+-nitrilotriacetic acid Sepharose affinity column, salt removed with PD10 column
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cDNA, from brain, expression in Escherichia coli M15/pRER4, sequencing, ORF is located on chromosome 22q12.3, genomic organization
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cloned into plasmid pET15b, expression in Escherichi coli BL21 (DE3) as His-tag fusion protein
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expression in Escherichia coli HMS174(DE3); yzgd gene subcloned from plasmid pAN13, ligated into plasmid pET11b, transformed into Escherichia coli DH5alpha for storage and Escherichia coli HMS174(DE3) for expression
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full-length cDNA, from brain, sequencing, ORF is located on chromosome 15.E1, genomic organization
getting Tat-PLPP/CIN: amplification of PLPP/CIN via PCR and inserted into pGEM-T vector, subcloned into pET15b, transformation of BL21 Escherichia coli. getting PLPP: cDNA of PLPP amplified via PCR and cloned into pET15b, transformation of Escherichia coli JM109 (DE3). experiments with Sprague-Dawley (SD) rats (7 weeks old). The effect of PNP treatment on PLPP/CIN immunoreactivity in the rat hippocampus: vitamin B6 may not be directly involved in ADF/cofilin-mediated F-actin depolymerization in normal condition. Up-regulation of PLPP/CIN expression following status epilepticus may play an important role in the formation of epileptic hippocampus. Hippocampal excitability following transduction of Tat-PLPP/CIN: F-actin depolymerization induced by over-expression of PLPP/CIN may increase excitability ratio in the hippocampus via postsynaptic changes, not via impaired GABAergic inhibition (immunohistochemistry, optical density, enzyme activity, electrophysiological analysis)
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getting Tat-PLPP/CIN: amplification of PLPP/CIN via PCR and inserted into pGEM-T vector, subcloned into pET15b, transformation of BL21 Escherichia coli. getting PLPP: cDNA of PLPP amplified via PCR and cloned into pET15b, transformation of Escherichia coli JM109 (DE3). investigation whether expression of PLPP/CIN is altered following long-term potentiation (LTP) induction and whether Tat-PLPP/CIN transduction affects LTP induction in the rat Sprague-Dawley. PLPP/CIN immunoreactivity is decreased in dentate granule cells after induction of LTP (induction: stimulating electrode for high frequency stimulation and recording electrode). Tat-PLPP/CIN transduction (20 and 200 microg/kg) decreased the efficiency of high frequency stimulus-induced potentiation of populations spike amplitude as compared to saline or Tat-protein-treated animals. PLPP/CIN protein level shows inverse correlation with phosphorylated ADF/cofilin levels and F-actin content (immunohistochemistry). conclusion: PLPP/CIN-mediated actin dynamics may play important role in changes of morphological properties (dendritic spine reorganization) of the hippocampus in LTP.
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His-tag fusion, expression in Escherichia coli
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into pCRII-TOPO vector, 0.86 kb SmaI fragment from TOPOpdxP ligated into the SmaI site of pKK223-3, overexpression in Escherichia coli JM109. Overexpression in Sinorhizobium meliloti IFO 14782 recombinant with pVKPtacpdxP
into pET15b vector and expressed in Escherichia coli BL21(DE3)
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PLPP gene fused with a PEP-1 peptide (PEP-1-PLPP) and 6His-tag and cloned into pET-15b. Expression in Escherichia coli BL21 (DE3) transduced into PC12 cells at various times and concentrations to evaluate the transduction ability (analyzed by Western blotting, fluorescence labeled). PLP concentration in cells PC12 cells changed by transduced PEP-1-PLPP fusion protein (spectroscopic measurement)
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D12N
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complete loss of activity, the corresponding Asp residue is part of the active site in other HAD superfamily members; complete loss of PLPase activity
E324Q
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no difference in the expression, solubility or PLPase activity between the mutant or the wild-type enzyme
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
drug development
additional information
hypothetical protein Q8CHP8 shows 44-47% sequence identity to pyridoxal phosphate phosphatase
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