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Information on EC 3.1.3.74 - pyridoxal phosphatase and Organism(s) Homo sapiens and UniProt Accession Q8TCD6

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EC Tree
     3 Hydrolases
         3.1 Acting on ester bonds
             3.1.3 Phosphoric-monoester hydrolases
                3.1.3.74 pyridoxal phosphatase
IUBMB Comments
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.
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Homo sapiens
UNIPROT: Q8TCD6 not found.
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Word Map
The taxonomic range for the selected organisms is: Homo sapiens
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
plpp/cin, plp phosphatase, pyridoxal phosphatase, pyridoxal phosphate phosphatase, plpase, pyridoxine phosphate phosphatase, pyridoxal-5'-phosphate phosphatase, pyridoxal-5'-phosphate phosphatase/chronophin, pnp phosphatase, pyridoxine 5'-phosphate phosphatase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
PLP phosphatase
-
-
pyridoxal phosphatase
-
pyridoxal phosphate phosphatase
-
pyridoxal-5'-phosphate phosphatase
pyridoxal-specific 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 SOURCE
PATHWAYS
-
-, -
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
-
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
-
-
-
-
?
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
-
-
-
-
?
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
-
-
-
-
?
N-(5'-phospho-4'-pyridoxyl)phenylalanine + H2O
4'-pyridoxylphenylalanine + phosphate
show the reaction diagram
-
much higher catalytic efficiency than with pyridoxine 5’-phosphate
-
-
?
p-nitrophenyl phosphate + H2O
p-nitrophenol + phosphate
show the reaction diagram
-
slow hydrolysis
-
-
?
pyridoxal 5'-phosphate + H2O
pyridoxal + phosphate
show the reaction diagram
pyridoxal 5'phosphate + H2O
pyridoxal + phosphate
show the reaction diagram
-
-
-
?
pyridoxal-5'-phosphate + H2O
pyridoxal + phosphate
show the reaction diagram
pyridoxamine 5'-phosphate + H2O
pyridoxamine + phosphate
show the reaction diagram
pyridoxine 5'-phosphate + H2O
pyridoxine + phosphate
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
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
-
enzyme probably plays an important role in the hydrolysis of pyridoxal 5’-phosphate to pyridoxal in erythrocytes, may be important in the regulation of pyridoxal 5’-phosphate concentration
-
-
?
pyridoxal 5'phosphate + H2O
pyridoxal + phosphate
show the reaction diagram
-
-
-
?
pyridoxal-5'-phosphate + H2O
pyridoxal + phosphate
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
CaCl2
-
enzyme has 17% as much activity with 1 mM CaCl2 than with MgCl2
Co2+
-
similar activation as by Mg2+ and Ni2+, kinetics
Cu2+
-
enzyme has 4% as much activity with 1 mM Cu2+ than with MgCl2
Ni2+
-
similar activation as by Mg2+ and Co2+, kinetics
Zn2+
-
activates somewhat at low concentrations, inhibits at higher concentrations
additional information
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2,2'-dithiodipyridine
-
0.005 mM, 50% inhibition
2-ethyl-5-phenylisoxazolium-3'-sulfonate
4,4'-dithiodipyridine
-
0.005 mM, 50% inhibition
4-pyridoxic acid 5'-phosphate
-
very effective inhibitor, 0.02 mM, 50% inhibition of pyridoxine 5’-phosphate hydrolysis
5,5'-dithiobis(2-nitrobenzoate)
5,5'-dithiobis(2-nitrobenzoic acid)
-
50 nM, 50% inhibition, incorporation of 1 mol per mol of subunit leads to complete inactivation, phosphate or dithiothreitol protects
Ca2+
-
competitive inhibition versus Mg2+, noncompetitive versus substrate
Cd2+
-
-
Cu2+
-
-
cysteine
-
-
diethyldicarbonate
disulfide reagent
-
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
-
EDTA
-
0.2 mM, complete inhibition in the absence of Mg2+, 50% inhibition in the presence of 1 mM Mg2+
Fe2+
-
-
fluoride
-
2 mM, 50% inhibition
iodoacetamide
-
weak
iodoacetate
Mn2+
-
inhibits above 0.05 mM, activates below 0.05 mM
molybdate
N-(5'-phospho-4'-pyridoxyl)ethanolamine
-
0.05 mM, 12% inhibition
N-(5'-phospho-4'-pyridoxyl)glycine
-
0.05 mM, 32% inhibition
N-(5'-phospho-4'-pyridoxyl)phenylalanine
-
0.05 mM, 51% inhibition
N-ethylmaleimide
p-chloromercuribenzoate
p-nitrophenyl phosphate
-
poor, 4 mM, 50% inhibition of pyridoxine 5’-phosphate hydrolysis
Pb2+
-
-
Phenyl phosphate
-
very poor inhibitor of pyridoxine 5’-phosphate hydrolysis
Phenylglyoxal
phosphate
pyridoxal
-
weak, 11 mM, 50% inhibition of hydrolysis of pyridoxal 5’-phosphate or pyridoxine 5’-phosphate
pyridoxal 5'-phosphate
-
very effective inhibitor, 0.03 mM, 50% inhibition of pyridoxine 5’-phosphate hydrolysis
pyridoxamine 5'-phosphate
-
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
-
0.05 mM, 45% inhibition
Tetranitromethane
-
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
-
a variety of thiol-specific reagents inactivate in a time- and concentration-dependent manner, pyridoxal phosphate or phosphate protects
-
additional information
-
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
-
pH 7.4, 37°C
0.0786
N-(5'-phospho-4'-pyridoxyl)ethanolamine
-
pH 7.4, 37°C
0.0143
N-(5'-phospho-4'-pyridoxyl)glycine
-
pH 7.4, 37°C
0.00824
N-(5'-phospho-4'-pyridoxyl)phenylalanine
-
pH 7.4, 37°C
0.00129 - 0.0025
pyridoxal 5'-phosphate
0.034 - 0.0806
pyridoxamine 5'-phosphate
0.0043 - 0.0434
pyridoxine 5'-phosphate
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.52
pyridoxal 5'-phosphate
pH 7.4, 37°C, recombinant enzyme
0.45
pyridoxamine 5'-phosphate
pH 7.4, 37°C, recombinant enzyme
1.25
pyridoxine 5'-phosphate
pH 7.4, 37°C, recombinant enzyme
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00638
Ca2+
-
-
0.00348
molybdate
-
-
0.22 - 0.8
phosphate
additional information
additional information
-
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.575
-
pH 7.4, 37°C
5.3
-
pH 7.4, 37°C
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 6.5
-
-
additional information
-
alkaline and acid pyridoxal phosphate phosphatase, not identical with alkaline and acid phosphatase
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22
-
assay at, inhibition studies
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6
sequence calculation
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
high expression
Manually annotated by BRENDA team
-
polymorphonuclear
Manually annotated by BRENDA team
-
-
Manually annotated by BRENDA team
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
-
-
Manually annotated by BRENDA team
additional information
-
subcellular localization in polymorphonuclear leukocytes
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
PDXP transgenic mice have immature spines with small heads, while PDXP knockout mice have gigantic spines. PDXP transgenic mice exhibit enhanced synaptic plasticity, while knockout mice show abnormal synaptic plasticity. PDXP also enhances N-methyl-D-aspartate receptor (GluN) functionality by regulating the coupling of GluN2A with interacting proteins, particularly postsynaptic density-95
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
PHOP2_HUMAN
241
0
27769
Swiss-Prot
other Location (Reliability: 3)
PLPP_HUMAN
296
0
31698
Swiss-Prot
other Location (Reliability: 4)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25000
SDS-PAGE, Western blot (rabbit anti-histidine polyclonal antibody)
31698
2 * 31698, sequence calculation, 2 * 32000, recombinant enzyme, SDS-PAGE
32000
33000
60000
gel filtration, recombinant enzyme
64000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 9
-
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
-
recombinant PEP-1-PLPP fusion protein transduced into PC12 cells is stable for 36 h
ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ethanol
-
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
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
168000fold
-
51000fold
-
70fold
-
9.6fold, recombinant enzyme
by Ni2+ column
Ni-affinity chromatography
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
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
cDNA, from brain, expression in Escherichia coli M15/pRER4, sequencing, ORF is located on chromosome 22q12.3, genomic organization
cloned into plasmid pET15b, expression in Escherichi coli BL21 (DE3) as His-tag fusion protein
-
His-tag fusion, expression in Escherichia coli
into pET15b vector and expressed in Escherichia coli BL21(DE3)
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)
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
lactoferrin activates expression of PDXP, which significantly up-regulates the synthesis of vitamin B6 and the phosphoinositide 3-kinase/serine/threonine-protein kinase/extracellular regulated protein kinases 1/2 pathway
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
drug development
transduction of the PEP-1-PLPP fusion protein into cells would be useful as therapeutic agent for various disorders related to this enzyme and vitamin B6
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Gao, G.J.; Fonda, M.L.
Evidence for a phosphoenzyme intermediate formed during catalysis by pyridoxal phosphatase from human erythrocytes
Arch. Biochem. Biophys.
313
166-172
1994
Homo sapiens
Manually annotated by BRENDA team
Fonda, M.L.; Zhang, Y.N.
Kinetic mechanism and divalent metal activation of human erythrocyte pyridoxal phosphatase
Arch. Biochem. Biophys.
320
345-352
1995
Homo sapiens
Manually annotated by BRENDA team
Smith, G.P.; Peters, T.J.
Subcellular localization and properties of pyridoxal phosphate phosphatases of human polymorphonuclear leukocytes and their relationship to acid and alkaline phosphatase
Biochim. Biophys. Acta
661
287-294
1981
Homo sapiens
Manually annotated by BRENDA team
Fonda, M.L.
Purification and characterization of vitamin B6-phosphate phosphatase from human erythrocytes
J. Biol. Chem.
267
15978-15983
1992
Homo sapiens
Manually annotated by BRENDA team
Gao, G.J.; Fonda, M.L.
Kinetic analysis and chemical modification of vitamin B6 phosphatase from human erythrocytes
J. Biol. Chem.
269
7163-7168
1994
Homo sapiens
Manually annotated by BRENDA team
Gao, G.J.; Fonda, M.L.
Identification of an essential cysteine residue in pyridoxal phosphatase from human erythrocytes
J. Biol. Chem.
269
8234-8239
1994
Homo sapiens
Manually annotated by BRENDA team
Jang, Y.M.; Kim, D.W.; Kang, T.C.; Won, M.H.; Baek, N.I.; Moon, B.J.; Choi, S.Y.; Kwon, O.S.
Human pyridoxal phosphatase. Molecular cloning, functional expression, and tissue distribution
J. Biol. Chem.
278
50040-50046
2003
Homo sapiens (Q96GD0), Homo sapiens, Mus musculus (P60487), Mus musculus
Manually annotated by BRENDA team
Saraswathi, S.; Bachhawat, B.K.
Phosphatases from human brain. I. Purification and properties of pyridoxal phosphate phosphatase
J. Neurochem.
10
127-133
1963
Homo sapiens
Manually annotated by BRENDA team
Boe, A.S.; Bredholt, G.; Knappskog, P.M.; Storstein, A.; Vedeler, C.A.; Husebye, E.S.
Pyridoxal phosphatase is a novel cancer autoantigen in the central nervous system
Br. J. Cancer
91
1508-1514
2004
Homo sapiens (Q96GD0), Homo sapiens
Manually annotated by BRENDA team
Kim, D.W.; Eum, W.S.; Choi, H.S.; Kim, S.Y.; An, J.J.; Lee, S.H.; Sohn, E.J.; Hwang, S.I.; Kwon, O.S.; Kang, T.C.; Won, M.H.; Cho, S.W.; Lee, K.S.; Park, J.; Choi, S.Y.
Human brain pyridoxal-5'-phosphate phosphatase: production and characterization of monoclonal antibodies
J. Biochem. Mol. Biol.
38
703-708
2005
Bos taurus, Brachylagus idahoensis, Canis lupus familiaris, Felis catus, Gallus gallus, Homo sapiens, Mus musculus, Rattus norvegicus, Sus scrofa
Manually annotated by BRENDA team
Afjehi-Sadat, L.; Yang, J.W.; Pollak, A.; Kim, D.W.; Choi, S.Y.; Lubec, G.
Structural and functional analysis of hypothetical proteins in mouse hippocampus from two-dimensional gel electrophoresis
J. Proteome Res.
6
711-723
2007
Homo sapiens (Q96GD0), Mus musculus (Q8CHP8), Mus musculus
Manually annotated by BRENDA team
Lee, Y.P.; Kim, D.W.; Lee, M.J.; Jeong, M.S.; Kim, S.Y.; Lee, S.H.; Jang, S.H.; Park, J.; Kang, T.C.; Won, M.H.; Cho, S.W.; Kwon, O.S.; Eum, W.S.; Choi, S.Y.
Human brain pyridoxal-5-phosphate phosphatase (PLPP):protein transduction of PEP-1-PLPP into PC12 cells
BMB Rep.
41
408-413
2008
Homo sapiens (Q96GD0), Homo sapiens
Manually annotated by BRENDA team
Li, H.; Wang, Y.; Yang, H.; Liu, L.; Wang, J.; Zheng, N.
Lactoferrin induces the synthesis of vitamin B6 and protects HUVEC functions by activating PDXP and the PI3K/AKT/ERK1/2 pathway
Int. J. Mol. Sci.
20
587
2019
Homo sapiens (Q96GD0)
Manually annotated by BRENDA team
Kim, J.E.; Kim, Y.J.; Lee, D.S.; Kim, J.Y.; Ko, A.R.; Hyun, H.W.; Kim, M.J.; Kang, T.C.
PLPP/CIN regulates bidirectional synaptic plasticity via GluN2A interaction with postsynaptic proteins
Sci. Rep.
6
26576
2016
Homo sapiens (Q96GD0)
Manually annotated by BRENDA team