Information on EC 3.1.3.3 - phosphoserine phosphatase

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

EC NUMBER
COMMENTARY hide
3.1.3.3
-
RECOMMENDED NAME
GeneOntology No.
phosphoserine phosphatase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
O-phospho-L(or D)-serine + H2O = L(or D)-serine + phosphate
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Biosynthesis of antibiotics
-
-
Glycine, serine and threonine metabolism
-
-
L-serine biosynthesis
-
-
Metabolic pathways
-
-
Methane metabolism
-
-
Microbial metabolism in diverse environments
-
-
serine metabolism
-
-
SYSTEMATIC NAME
IUBMB Comments
O-phosphoserine phosphohydrolase
-
CAS REGISTRY NUMBER
COMMENTARY hide
9025-73-4
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Mus musculus C57BL/6
C57BL/6
UniProt
Manually annotated by BRENDA team
isoform SerB2
UniProt
Manually annotated by BRENDA team
isoform SerB2
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
ATCC14921
-
-
Manually annotated by BRENDA team
ATCC14921
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
physiological function
-
the embryo-lethal phenotype of isoform psp1 mutants can be complemented with PSP1 cDNA under the control of Pro35S. However, this construct is poorly expressed in the anther tapetum, and does not complement mutant fertility. Microspore development in psp1.1/psp1.1 mutants expressing Pro35S:PSP1 arrest at the polarized stage. The tapetum from these lines displays delayed and irregular development. In addition to embryo death and male sterility, conditional psp1 mutants display a short-root phenotype, which is reverted in the presence of serine
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
4-nitrophenylphosphate + H2O
4-nitrophenol + phosphate
show the reaction diagram
-
-
-
?
beta-glycerophosphate + H2O
glycerol + phosphate
show the reaction diagram
-
-
-
?
D-fructose 6-phosphate + H2O
D-fructose + phosphate
show the reaction diagram
-
-
-
?
D-phosphoserine + H2O
D-Ser + phosphate
show the reaction diagram
DL-phosphoserine + H2O
DL-Ser + phosphate
show the reaction diagram
glycerinaldehyde-3-phosphate-dehydrogenase + H2O
?
show the reaction diagram
-
-
-
-
?
heat-shock protein 90 + H2O
?
show the reaction diagram
-
-
-
-
?
L-3-phosphoserine + H2O
L-serine + phosphate
show the reaction diagram
L-O-phospho-serine + H2O
L-serine + phosphate
show the reaction diagram
-
-
-
?
L-O-phosphoserine + H2O
L-serine + phosphate
show the reaction diagram
L-phosphoserine + H2O
L-Ser + phosphate
show the reaction diagram
L-phosphoserine + H2O
L-serine + phosphate
show the reaction diagram
O-phospho-L-serine + H2O
L-serine + phosphate
show the reaction diagram
O-phospho-L-tyrosine + H2O
L-Tyr + phosphate
show the reaction diagram
p-nitrophenyl phosphate + H2O
p-nitrophenol + phosphate
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
L-3-phosphoserine + H2O
L-serine + phosphate
show the reaction diagram
L-O-phosphoserine + H2O
L-serine + phosphate
show the reaction diagram
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enzyme is responsible for the third and final step of the L-serine biosynthetic pathway
-
?
O-phospho-L-serine + H2O
L-serine + phosphate
show the reaction diagram
additional information
?
-
-
the enzyme may play a role in altered neuronal function in Alzheimers disease via enhancing glutamate-induced neurotoxicity by D-serine and the IL-11 receptor system
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Al3+
-
at near-physiological ratios of aluminum to magnesium, aluminum can dominate over magnesium in the enzyme-metal fluoride inhibitory TSA complexes, aluminium is the more likely origin of some of the physiological effects of fluoride
Cu2+
-
activation
Fe2+
-
can substitute for Mg2+ in activation
Ni2+
-
can substitute for Mg2+ in activation
Zn2+
-
can substitute for Mg2+ in activation
additional information
no divalent metal ion required; no divalent metal ion required
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3-(1-pyridinio)-1-propanesulfonate
-
-
BeF3-
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at 50C, the hydrolytic activity of is markedly inhibited (more than 95%) in the presence of both BeCl2 and NaF. The latter is provided at concentrations that yield predominantly BeF3- in situ. Either BeCl2 or NaF alone has a much smaller inhibitory effect (35 or 20%, respectively). Similar inhibition by BeF3- is observed at room temperature or at 70C
Cd2+
-
-
chlorpromazine
-
-
Clorobiocin
displays bactericidal activity and kills intracellular bacteria in a dose-dependent manner, highly specific in the ability to inhibit isoform SerB2 in comparison with human phosphoserine phosphatase
Cu2+
-
-
D-2-amino-3-phosphonopropionic acid
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-
D-alanine
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-
D-serine
DL-2-amino-3-phosphonopropionic acid
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DL-2-Amino-4-phosphonobutyric acid
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Glycerophosphorylcholine
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glycine
hexadecylphosphocholine
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iodoacetate
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L-2-amino-3-phosphonopropionic acid
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L-alanine
L-serine
Mn2+
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N-ethylmaleimide
okadaic acid
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p-chloromercuribenzoate
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p-chloromercuriphenylsulfanate
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-
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phosphonoalanine
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phosphorylcholine
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-
rosaniline
displays bactericidal activity and kills intracellular bacteria in a dose-dependent manner
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sodium orthovanadate
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Trifluorperazine
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-
vanadate
-
-
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Chlordiazepoxide
-
activation
diazepam
-
activation
Sucrose
-
activation
Triton X-100
presence of 0.01% Triton X-100 enhances isoform SerB2 activity by 15-20%
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.1 - 4.2
D-phosphoserine
0.05 - 0.11
DL-phosphoserine
3.5
L-3-phosphoserine
-
0.02 - 20
L-phosphoserine
0.117
L-phosphothreonine
-
at 30C, in 50 mM Tris (pH 7.5), with 5 mM MgCl2
0.047
L-phosphotyrosine
-
at 30C, in 50 mM Tris (pH 7.5), with 5 mM MgCl2
0.081 - 0.181
O-phospho-L-serine
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.508 - 804
L-phosphoserine
0.0004
L-phosphothreonine
Porphyromonas gingivalis
-
at 30C, in 50 mM Tris (pH 7.5), with 5 mM MgCl2
0.00003
L-phosphotyrosine
Porphyromonas gingivalis
-
at 30C, in 50 mM Tris (pH 7.5), with 5 mM MgCl2
0.0073 - 0.182
O-phospho-L-serine
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.24 - 98
L-phosphoserine
0.00159 - 1.81
O-phospho-L-serine
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0168
Clorobiocin
Mycobacterium tuberculosis
O53289
pH 7.4, 37C
0.67
DL-2-amino-3-phosphonopropionic acid
Mycobacterium tuberculosis
O53289
pH 7.4, 37C
-
4.4
EDTA
Porphyromonas gingivalis
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at 30C, in 50 mM Tris (pH 7.5), with 5 mM MgCl2
1.3
Na3VO4
Porphyromonas gingivalis
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at 30C, in 50 mM Tris (pH 7.5), with 5 mM MgCl2
5.9
NaF
Porphyromonas gingivalis
-
at 30C, in 50 mM Tris (pH 7.5), with 5 mM MgCl2
0.005
okadaic acid
Porphyromonas gingivalis
-
IC50: above 0.005 mM, at 30C, in 50 mM Tris (pH 7.5), with 5 mM MgCl2
0.0315
rosaniline
Mycobacterium tuberculosis
O53289
pH 7.4, 37C
-
0.458
sodium orthovanadate
Mycobacterium tuberculosis
O53289
pH 7.4, 37C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.018
-
-
0.13
-
-
5.3
substrate L-O-phosphoserine, presence of 1 mM Mn2+
17.3
substrate L-O-phosphoserine, presence of 5 mM Mg2+
28
substrate L-phosphoserine, pH 8.0, 70C
58
substrate L-phosphoserine, pH 8.0, 70C
additional information
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aluminum fluoride transition state analogs (TSA) complexes analyzed, NMR spectra indicated, pH titration, chemical shifts of the 19F NMR resonances not markedly affected by pH
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 6.6
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-
5.6 - 6.6
-
-
5.8 - 6.2
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unassociated enzyme form
6 - 6.4
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associated enzyme form
6.5 - 7
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.4 - 9.2
-
fluoride chemical shifts constant throughout the pH range examined
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
60 - 75
60C: about 50% of maximal activity, 75C: about 75% of maximal activity
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
enzyme plays a crucial role in embry, pollen and root development
Manually annotated by BRENDA team
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-
Manually annotated by BRENDA team
-
enzyme plays a crucial role in embry, pollen and root development
Manually annotated by BRENDA team
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-
Manually annotated by BRENDA team
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highly induced in squamous cell carcinoma
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
-
cytoplasmic protein in keratinocytes that primarily localizes to endosomes
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Bacillus subtilis (strain 168)
Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6)
Hydrogenobacter thermophilus (strain DSM 6534 / IAM 12695 / TK-6)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Mycobacterium avium (strain 104)
Mycobacterium avium (strain 104)
Mycobacterium avium (strain 104)
Mycobacterium avium (strain 104)
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Thermococcus onnurineus (strain NA1)
Thermococcus onnurineus (strain NA1)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
47000
-
mouse, gel filtration
65000
-
bovine, gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop vapour-diffusion method. A resolution of 1.53 A provides a detailed model of the active site in a completely open conformation and the water molecules bound to it
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hanging-drop vapour diffusion method
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hanging-drop vapour-diffusion method
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replacement of sixfold coordinated Mg2+ in active site by Ca2+ results in sevenfold coordinated metal ion, explaining the inhibitory effect of Ca2+
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apo-form and in complex with its substrate L-phosphoserine, to 1.5 A and 1.8 A resolution, respectively. In the crystal structure of the enzyme-substrate complex, oxygen atoms of the carboxyl group of L-phosphoserine form hydrogen bonds with main-chain amides of Gln21 and Gly22, and Nepsilon2 of Gln21, and partly form a hydrogen or an ionic bond withNepsilon2 of His85. The nitrogen atom of amino group of L-phosphoserine forms a hydrogen or an ionic bond with oxygen atoms of the side-chain carboxyl group of Glu82, and forms hydrogen bonds with Nepsilon2 of His85 and Ogamma1 of Thr15
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two diffraction data sets with resolution ranges of 45.0-2.50 and 45.0-1.50 A. The space group of the crystal is orthorhombic P212121, with unit-cell parameters a = 49.8, b = 73.6, c = 124.3 A
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crystals are grown by using the hanging drop vapor diffusion method with seeding.1.5 A resolution the X-ray crystal structure of the complex of BeF3 2 with phosphoserine phosphatase. The structure is comparable to that of a phosphoenzyme intermediate: BeF3- is bound to Asp11 with the tetrahedral geometry of a phosphoryl group, is coordinated to Mg2+, and is bound to residues surrounding the active site that are conserved in the haloacid dehalogenase (HAD) superfamily
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hanging-drop vapor-diffusion method, crystal structure determined at 1.8 A resolution
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high-resolution, 1.5-1.9 A structures which define the open state prior to substrate binding, the complex with phosphoserine substrate bound, and the complex with AlF3, a transition-state analog for the phospho-transfer steps in the reaction
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construction of a homology model and molecular docking of O-phospho-L-serine. Residues Asp185, Ser273, Lys-318, and Asp-341 are part of the substrate binding pocket. Val186 and Ser188 might also interact with O-phospho-L-serine
hanging-drop vapour diffsuion method
-
sitting drop method at 18 C, crystal structure of the enzyme at 1.8 A resolution
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
extremely unstable
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-9C, stable for several months
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
BioLogic DuoFlow chromatography system loaded with an IMAC column
-
partially
partially, copurifies with serine phosphotransferase
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) Gold pLysS and in HEK-293 cell
expressed in Escherichia coli strain DH5alpha
-
expression in Escherichia coli
expression in Escherichia coli; expression in Escherichia coli
expression in Eschericia coli
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
highly induced in squamous cell carcinoma
-
in liver in response to a low protein diet
in MDA-MB-231(SA) cell
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E29D
-
less than 5% of the activity of wild-type enzyme with L-phosphoserine as substrate
E29Q
-
inactive mutant enzyme
N133A
-
about 25% of the activity of wild-type enzyme with L-phosphoserine as substrate
N133D
-
about 130% of the activity of wild-type enzyme with L-phosphoserine as substrate
R202A
-
inactive mutant enzyme
R202K
-
less than 5% of the activity of wild-type enzyme with L-phosphoserine as substrate
R65A
-
inactive mutant enzyme
R65K
-
inactive mutant enzyme
S23A
-
about 50% of the activity of wild-type enzyme with L-phosphoserine as substrate
S23T
-
about 20% of the activity of wild-type enzyme with L-phosphoserine as substrate
T182S
-
about 5% of the activity of wild-type enzyme with L-phosphoserine as substrate
T182V
-
about 75% of the activity of wild-type enzyme with L-phosphoserine as substrate
delI211
-
50fold decrease in catalytic efficiency
delVal2-I211
-
400fold decrease in catalytic efficiency
H85A
-
almost complete loss of activity
H9A
-
almost complete loss of activity
delI211
-
50fold decrease in catalytic efficiency
-
delVal2-I211
-
400fold decrease in catalytic efficiency
-
H85A
-
almost complete loss of activity
-
H9A
-
almost complete loss of activity
-
D185G
complete loss of activity
D341G
about 10% residual activity, no change in secondary structure compared to wild-type
K318E
complete loss of activity
S188A
activity similar to wild-type
S273A
about 30% residual activity, no change in secondary structure compared to wild-type
V186Q
about 55% residual activity
D185G
-
complete loss of activity
-
D341G
-
about 10% residual activity, no change in secondary structure compared to wild-type
-
K318E
-
complete loss of activity
-
S188A
-
activity similar to wild-type
-
S273A
-
about 30% residual activity, no change in secondary structure compared to wild-type
-
D198N
-
9% activity of the wild type enzyme
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
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