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Enzyme Nomenclature
Information on EC 2.7.1.35 - pyridoxal kinase
for references in articles please use BRENDA:EC2.7.1.35
Word Map on EC 2.7.1.35
- 2.7.1.35
- 5'-phosphate
-
vitamers
- pyridoxal-5'-phosphate
-
plp-dependent
-
4-pyridoxic
- agriculture
- medicine
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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria
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EC NUMBER 
COMMENTARY 
2.7.1.35
-
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RECOMMENDED NAME
GeneOntology No.
pyridoxal kinase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ATP + pyridoxal = ADP + pyridoxal 5'-phosphate
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
phospho group transfer
-
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
ATP:pyridoxal 5'-phosphotransferase
Pyridoxine, pyridoxamine and various derivatives can also act as acceptors.
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CAS REGISTRY NUMBER
COMMENTARY
9026-42-0
-
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
-
root growth of a sos4 mutant is significantly decreased when grown on either 100 mM or 200 mM sucrose as compared to root growth on10 mM sucrose. The sos4 mutant plant accumulates phytoglycogen
physiological function
additional information
-
experimental resurrection of the last common ancestor of the hydroxymethyl pyrimidine kinase group based on comparison of hydroxymethyl pyrimidine and pyridoxal kinases. Probably the last common ancestor was not able to use pyridoxal under physiological conditions. The pyridoxal kinase activity present in the current bifunctional enzymes must have appeared in a convergent event independently of the pyridoxal kinase activity of pdxY and pdxK genes. Substrate pyridoxal is 8-times less preferred than the phosphorylation of hydroxymethyl pyrimidine by the last ancestor
physiological function
-
pyridoxal kinase is a key enzyme in the metabolism of vitamin B6
physiological function
-
the enzyme is essential for growth of Trypanosoma brucei in vitro and for infectivity in mice
physiological function
-
the SOS4 pyridoxal kinase is required for maintenance of vitamin B6-mediated processes in chloroplasts. SOS4 is required for maintenance of phosphorylated B6 vitamer concentrations in chloroplasts
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine
ADP + 4-amino-5-phosphomethyl-2-methylpyrimidine
methyl (1S)-1-[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]-2,3,4,9-tetrahydro-1H-beta-carboline-3-carboxylate + ATP
methyl (1S)-1-[3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl]-2,3,4,9-tetrahydro-1H-beta-carboline-3-carboxylate + ADP
-
-
very probably: methyl (1S)-1-[3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl]-2,3,4,9-tetrahydro-1H-beta-carboline-3-carboxylate is an inhibitor of Plasmodium falciparum ornithine decarboxylase
-
?
methyl N-[[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]methyl]histidinate + ATP
methyl N-([3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl]methyl)histidinate + ADP
-
-
methyl N-([3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl]methyl)histidinate is an inhibitor of Plasmodium falciparum ornithine decarboxylase: IC50 = 0.058 mM
-
?
methyl N-[[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]methyl]tryptophanate + ATP
methyl N-([3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl]methyl)tryptophanate + ADP
-
-
methyl N-([3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl]methyl)tryptophanate is an inhibitor of Plasmodium falciparum ornithine decarboxylase: IC50 = 0.064 mM
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine
ADP + 4-amino-5-phosphomethyl-2-methylpyrimidine
-
-
-
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine
ADP + 4-amino-5-phosphomethyl-2-methylpyrimidine
reaction of EC 2.7.1.49
-
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine
ADP + 4-amino-5-phosphomethyl-2-methylpyrimidine
reaction of EC 2.7.1.49
-
-
?
ATP + 4-deoxypyridoxine
ADP + 4-deoxypyridoxine 5'-phosphate
-
-
-
-
?
ATP + omega-methylpyridoxal
ADP + omega-methylpyridoxal 5'-phosphate
-
-
-
-
?
ATP + omega-methylpyridoxal
ADP + omega-methylpyridoxal 5'-phosphate
-
-
-
-
?
ATP + omega-methylpyridoxal
ADP + omega-methylpyridoxal 5'-phosphate
-
-
-
-
?
ATP + omega-methylpyridoxal
ADP + omega-methylpyridoxal 5'-phosphate
-
-
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
the SOS4 gene encodes a pyridoxal kinase that functions upstream of ethylene and auxin in root hair development, SOS4 is required for the initiation and tip growth of root hairs
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
generates the active form of vitamin B6, which serves as cofactor for many enzymes
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
the pdxY gene encodes a novel pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate biosynthesis. The pyridoxal kinase PdxY and the pyridoxine/pyridoxal/pyridoxamine kinase PdxK are the only physiologically important B6 vitamer kinases in Escherichia coli and their function is confined to the pyridoxal 5'-phosphate salvage pathway
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
generates the active form of vitamin B6, which serves as cofactor for many enzymes
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
-
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
generates the active form of vitamin B6, which serves as cofactor for many enzymes
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
generates the active form of vitamin B6, which serves as cofactor for many enzymes, increased enzyme activity detected 12-24 h after ischemia, pyridoxal 5'-phosphate essential for the synthesis of some neurotransmitters
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
key enzyme in transformation of vitamin B6 to pyridoxal 5'-phosphate. Pyridoxal 5'-phosphate is the crucial cofactor required by numerous enzymes involved in the metabolism of amino acids and the synthesis of many neurotransmitters
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
generates the active form of vitamin B6, which serves as cofactor for many enzymes
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
generates the active form of vitamin B6, which serves as cofactor for many enzymes
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
generates the active form of vitamin B6, which serves as cofactor for many enzymes
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
important enzyme involved in bioactivation of vitamin B6
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
generates the active form of vitamin B6, which serves as cofactor for many enzymes, interaction of pyridoxal kinase with pyridoxal 5'-phosphate dependent enzymes seems to be important for providing sufficient amounts of enzyme cofactor
-
-
?
ATP + pyridoxamine
ADP + pyridoxamine 5'-phosphate
-
-
-
-
?
ATP + pyridoxamine
ADP + pyridoxamine 5'-phosphate
-
33% of the activity with pyridoxal
-
-
?
ATP + pyridoxamine
ADP + pyridoxamine 5'-phosphate
-
not a substrate of the purified enzyme
-
-
-
ATP + pyridoxamine
ADP + pyridoxamine 5'-phosphate
-
study of substrate-enzyme interaction between immobilized pyridoxamine and recombinant porcine pyridoxal kinase using surface plasmon resonance biosensor
-
-
?
ATP + pyridoxine
ADP + pyridoxine 5'-phosphate
-
40% of the activity with pyridoxal
-
-
?
ATP + pyridoxine
ADP + pyridoxine 5'-phosphate
-
-
-
?
ATP + pyridoxine
ADP + pyridoxine 5'-phosphate
-
46% of the activity with pyridoxal
-
-
?
additional information
?
-
-
the enzyme possesses also a 4-amino-5-hydroxymethyl-2-methylpyrimidine kinase activity
-
-
-
additional information
?
-
the reactive Cys110 residue in the lid region forms a hemithioactetal intermediate with the 4'-aldehyde of pyridoxal. This hemithioacetal, in concert with the catalytic Cys214, increases the nucleophilicity of the pyridoxal 5'-OH group for the inline displacement reaction with the gamma-phosphate of ATP
-
-
-
additional information
?
-
-
the reactive Cys110 residue in the lid region forms a hemithioactetal intermediate with the 4'-aldehyde of pyridoxal. This hemithioacetal, in concert with the catalytic Cys214, increases the nucleophilicity of the pyridoxal 5'-OH group for the inline displacement reaction with the gamma-phosphate of ATP
-
-
-
additional information
?
-
the reactive Cys110 residue in the lid region forms a hemithioactetal intermediate with the 4'-aldehyde of pyridoxal. This hemithioacetal, in concert with the catalytic Cys214, increases the nucleophilicity of the pyridoxal 5'-OH group for the inline displacement reaction with the gamma-phosphate of ATP
-
-
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
the SOS4 gene encodes a pyridoxal kinase that functions upstream of ethylene and auxin in root hair development, SOS4 is required for the initiation and tip growth of root hairs
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
generates the active form of vitamin B6, which serves as cofactor for many enzymes
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
the pdxY gene encodes a novel pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate biosynthesis. The pyridoxal kinase PdxY and the pyridoxine/pyridoxal/pyridoxamine kinase PdxK are the only physiologically important B6 vitamer kinases in Escherichia coli and their function is confined to the pyridoxal 5'-phosphate salvage pathway
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
generates the active form of vitamin B6, which serves as cofactor for many enzymes
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
O00764
generates the active form of vitamin B6, which serves as cofactor for many enzymes
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
generates the active form of vitamin B6, which serves as cofactor for many enzymes, increased enzyme activity detected 12-24 h after ischemia, pyridoxal 5'-phosphate essential for the synthesis of some neurotransmitters
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
key enzyme in transformation of vitamin B6 to pyridoxal 5'-phosphate. Pyridoxal 5'-phosphate is the crucial cofactor required by numerous enzymes involved in the metabolism of amino acids and the synthesis of many neurotransmitters
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
generates the active form of vitamin B6, which serves as cofactor for many enzymes
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
P82197
generates the active form of vitamin B6, which serves as cofactor for many enzymes
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
generates the active form of vitamin B6, which serves as cofactor for many enzymes
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
important enzyme involved in bioactivation of vitamin B6
-
-
?
ATP + pyridoxal
ADP + pyridoxal 5'-phosphate
-
generates the active form of vitamin B6, which serves as cofactor for many enzymes, interaction of pyridoxal kinase with pyridoxal 5'-phosphate dependent enzymes seems to be important for providing sufficient amounts of enzyme cofactor
-
-
?
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
Co2+
Cu2+
Fe2+
K+
Li+
-
poor activator which seems to modify the enzymatic mechanism from a random to an ordered sequential pattern with ATP bound before pyridoxal. Km: 37 mM
Mg2+
Mn2+
Na+
Ni2+
Rb+
-
Km: 5.3 mM. Monovalent cation required, activation in the order of decreasing efficiency: K+, Rb+, NH4+
Zn2+
additional information
Ca2+
-
divalent cation required, activation of the recombinant enzyme in the order of decreasing efficiency: Zn2+, Co2+, Mn2+, Mg2+, Ca2+
Co2+
-
cations activate in decreasing order of efficiency: Co2+, Mn2+, Mg2+, Zn2+, Cu2+, Ni2+, Fe2+
Co2+
-
divalent cation required, activation of the recombinant enzyme in the order of decreasing efficiency: Zn2+, Co2+, Mn2+, Mg2+, Ca2+
Cu2+
-
cations activate in decreasing order of efficiency: Co2+, Mn2+, Mg2+, Zn2+, Cu2+, Ni2+, Fe2+
Fe2+
-
cations activate in decreaseing order of efficiency: Co2+, Mn2+, Mg2+, Zn2+, Cu2+, Ni2+, Fe2+
K+
-
when only triethanolamine is present as the cation, K+ is an activator of the enzyme
K+
-
in the absence of any potassium ion, the activity is less than 5% of the maximum activity
K+
-
most effective monovalent cation in activation. Improves both affinity for the substrates and maximal velocity. Km: 35 mM
K+
-
activation. Affinity for ATP and pyridoxal is increased severalfold in presence of K+ compared with Na+, but the maximal activity of the Na+ form is more than double the activity of the K+ form; affinity to pyridoxal and ATP is increased manifold in the presence of K+ compared to Na+, 2.5fold increase of activity
K+
-
Km: 8.9 mM. Monovalent cation required, activation in the order of decreasing efficiency: K+, Rb+, NH4+
Mg2+
-
cations activate in decreasing order of efficiency: Co2+, Mn2+, Mg2+, Zn2+, Cu2+, Ni2+, Fe2+
Mg2+
-
divalent cation required, activation of the recombinant enzyme in the order of decreasing efficiency: Zn2+, Co2+, Mn2+, Mg2+, Ca2+
Mn2+
-
cations activate in decreasing order of efficiency: Co2+, Mn2+, Mg2+, Zn2+, Cu2+, Ni2+, Fe2+
Mn2+
-
divalent cation required, activation of the recombinant enzyme in the order of decreasing efficiency: Zn2+, Co2+, Mn2+, Mg2+, Ca2+
Na+
-
increases maximal velocity and affinity for ATP, but decreases affinity for pyridoxal
Na+
-
6fold increase of activity; activation. Affinity for ATP and pyridoxal is increased severalfold in presence of K+ compared with Na+, but the maximal activity of the Na+ form is more than double the activity of the K+ form
Ni2+
-
cations activate in decreasing order of efficiency: Co2+, Mn2+, Mg2+, Zn2+, Cu2+, Ni2+, Fe2+
Zn2+
-
Zn2+ is the most effective cation for catalysis under saturating substrate concentrations
Zn2+
-
cations activate in decreasing order of efficiency: Co2+, Mn2+, Mg2+, Zn2+, Cu2+, Ni2+, Fe2+
Zn2+
-
divalent cation required, optimal concentration is 0.33 mM. Zn2+ is superior to Mg2+ below the optimum concentration of Zn2+
Zn2+
-
divalent cation required, activation of the recombinant enzyme in the order of decreasing efficiency: Zn2+, Co2+, Mn2+, Mg2+, Ca2+. Optimum at about 0.1 mM Zn2+
Zn2+
-
activator at low concentrations (0.019 mM optimal concentration), most effective divalent cation for catalysis
Zn2+
-
the enzyme requires divalent cations for activity. At 0.08 mM the cations activate in order of decreasing efficiency: Mn2+, Zn2+, Mg2+. At 0.4 mM the cations activate in the order of decreasing efficiency: Mn2+, Zn2+, Mg2+
additional information
-
the presence of 100 mM NaCl does not alter the potassium activation profile
additional information
-
Li+, Cs+, and Rb+ show no significant activity enhancement; no singnificant activity with Li+, Cs+, Rb+
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
4'-O-methylpyridoxine
-
i.e. ginkgotoxin. Treatment leads to temporarily reduced pyridoxal phosphate formation in vitro and possibly in vivo
5-dimethylaminonaphthalene-1-sulfonyl-4-aminobutyrate
-
competitive with respect to pyridoxal
5-hydroxytryptamine
-
0.5 mM, 11% inhibition of activity with pyridoxine, 81% inhibition of activity with pyridoxal
cycloserine
-
0.1 mM, inhibits activity with pyridoxal, but not with pyridoxamine as substrate, 42% inhibition
D-penicillamine
-
0.1 mM, inhibits activity with pyridoxal, but not with pyridoxamine as substrate, 20% inhibition
Isoniazid
-
0.1 mM, inhibits activity with pyridoxal, but not with pyridoxamine as substrate, 81% inhibition
levodopa
-
0.1 mM, inhibits activity with pyridoxal, but not with pyridoxamine as substrate, 16% inhibition
muzolimine
-
0.1 mM, inhibits activity with pyridoxal, but not with pyridoxamine as substrate, 27% inhibition
NADH
-
0.5 mM, 14% inhibition of activity with pyridoxine, 11% inhibition of activity with pyridoxal
picolinate
-
0.5 mM, 95% inhibition of activity with pyridoxine, 97% inhibition of activity with pyridoxal
progabide
-
0.1 mM, inhibits using either pyridoxamine or pyridoxal as substrate
quinolinate
-
0.5 mM, 82% inhibition of activity with pyridoxine, 82% inhibition of activity with pyridoxal
rugulactone
selectively modifies the enzyme not at the active site cysteine, but on a remote cysteine residue
Thiamphenicol
-
0.1 mM, inhibits activity with pyridoxal, but not with pyridoxamine as substrate, 31% inhibition
xanthurenate
-
0.5 mM, 19% inhibition of activity with pyridoxine, 18% inhibition of activity with pyridoxal
dopamine
-
0.1 mM, inhibits activity with pyridoxal, but not with pyridoxamine as substrate, 52% inhibition
theophylline
-
0.1 mM, inhibits using either pyridoxamine or pyridoxal as substrate, 86% inhibition of reaction with pyridoxal, 88% inhibition of reaction with pyridoxamine
tryptamine
-
no inhibition of activity with pyridoxine, 72% inhibition of activity with pyridoxal
additional information
-
ATP4- and HATP3- do not affect the enzyme activity. Free Mg2+ does not inhibit enzyme activity
-
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
NH4+
-
Km: 3.7 mM. Monovalent cation required, activation in the order of decreasing efficiency: K+, Rb+, NH4+
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0216
4'-deoxypyridoxine
-
in 70 mM potassium phosphate buffer, pH 6.2; pH 6.2, 37°C
1.85
4-Amino-5-hydroxymethyl-2-methylpyrimidine
mutant C110A, pH not specified in the publication, temperature not specified in the publication
1.99
4-Amino-5-hydroxymethyl-2-methylpyrimidine
wild-type, pH not specified in the publication, temperature not specified in the publication
0.025
ATP
-
in the presence of K+, and in complex with Mg2+; presence of 40 mM Na+, pH 7.3, 37°C
0.5
ATP
-
in the presence of Na+, and in complex with Mg2+; presence of 40 mM Na+, pH 7.3, 37°C
0.0466
ginkgotoxin
-
recombinant enzyme, apparent value, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C
0.00165
pyridoxal
-
recombinant enzyme, apparent value, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C
0.038
pyridoxal
-
recombinant enzyme, apparent value, in 70 mM potassium phosphate pH 7.0, 0.15 mM ZnCl2, at 37°C
0.111
pyridoxal
wild-type, pH not specified in the publication, temperature not specified in the publication
0.26
pyridoxal
mutant C214D, pH not specified in the publication, temperature not specified in the publication
0.0594
pyridoxamine
-
recombinant enzyme, apparent value, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C
0.048
pyridoxine
-
recombinant enzyme, apparent value, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C
1.51
pyridoxine
mutant C110A, pH not specified in the publication, temperature not specified in the publication
2.07
pyridoxine
wild-type, pH not specified in the publication, temperature not specified in the publication
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.044
4-Amino-5-hydroxymethyl-2-methylpyrimidine
mutant C110A, pH not specified in the publication, temperature not specified in the publication
0.045
4-Amino-5-hydroxymethyl-2-methylpyrimidine
wild-type, pH not specified in the publication, temperature not specified in the publication
106
ginkgotoxin
-
recombinant enzyme, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C
0.165
pyridoxal
wild-type, pH not specified in the publication, temperature not specified in the publication
0.328
pyridoxal
mutant C214D, pH not specified in the publication, temperature not specified in the publication
131
pyridoxal
-
recombinant enzyme, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C
127
pyridoxamine
-
recombinant enzyme, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C
0.015
pyridoxine
mutant C110A, pH not specified in the publication, temperature not specified in the publication
0.016
pyridoxine
wild-type, pH not specified in the publication, temperature not specified in the publication
122
pyridoxine
-
recombinant enzyme, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.000228
ginkgotoxin
-
recombinant enzyme, apparent value, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C
0.000214
pyridoxamine
-
recombinant enzyme, apparent value, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C
0.000254
pyridoxine
-
recombinant enzyme, apparent value, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C
0.0009
pyridoxal
-
recombinant enzyme, apparent value, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1.54
Mg2+
-
recombinant enzyme, apparent value, in 70 mM potassium phosphate pH 7.0, 0.15 mM ZnCl2, at 37°C
0.0398
Zn2+
-
recombinant enzyme, apparent value, in 70 mM potassium phosphate pH 7.0, 0.15 mM ZnCl2, at 37°C
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IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.0125
0.02
-
substrate: methyl N-[[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]methyl]tryptophanate
0.03
0.038
-
substrate: methyl (1S)-1-[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]-2,3,4,9-tetrahydro-1H-beta-carboline-3-carboxylate
0.05
0.064
-
substrate: methyl N-[[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]methyl]histidinate
0.07
-
crude enzyme, in 70 mM potassium phosphate (pH 5.5), 0.5 mM ZnCl2, at 37°C
0.112
additional information
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.5 - 6
6.5
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
4.5 - 8.5
-
the enzyme is inactive below pH 4.5. Enzyme activity decreases slowly above pH 6.0, to approximately 35% at pH 8.5
4.7 - 5.3
-
pH 4.7: about 60% of maximal activity, pH 5.3: about 40% of maximal activity
5 - 5.7
-
pH 5.0: about 90% of maximal activity, pH 5.7: about 45% of maximal activity
5 - 8
-
pH 5.0: about 70% of maximal activity, pH 8.0: about 50% of maximal activity
6 - 7
-
pH 6.0: about 50% of maximal activity, pH 7.0: about 50% of maximal activity
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
50
55
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.3
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
-
dentate granule cell. Pyridoxal kinase immunoreactivity is not increased after induction of long-term potentiation and not involved in increase in the efficiency of high frequency stimulus-induced potentiation of populations spike amplitude when compared with saline-, or Tat-protein-treated animals
-
regions CA1, CA2/3 and dentate gyrus, increased enzyme activity detected 12-24 h after ischemia
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
splice variant SOS4.1 (but not SOS4.2) is localized in chloroplasts
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Burkholderia multivorans (strain ATCC 17616 / 249)
Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
Lactobacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
35000
37000
40000
57200
-
2 * 57200, calculated from the deduced amino acid sequence, 2 * 58000, SDS-PAGE, native mass by gel filtration
58000
-
2 * 57200, calculated from the deduced amino acid sequence, 2 * 58000, SDS-PAGE, native mass by gel filtration
80000
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
homodimer
monomer
dimer
-
2 * 57200, calculated from the deduced amino acid sequence, 2 * 58000, SDS-PAGE, native mass by gel filtration
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
hanging drop vapour diffusion method using 28% PEG 4000, 0.17 M sodium acetate trihydrate, and 0.1 M Tris-HCl (pH 8.5)
-
with 28% (w/v) PEG 4000, 0.17 M sodium acetate trihydrate, 0.1 M Tris-HCl (pH 8.5) as the precipitant in the presence of 10 mM ADP and 10 mM MgCl
-
hanging drop vapour diffusion method using 20 mM potassium phosphate, pH 7.5, 5 mM beta-mercaptoethanol, 0.2 mM EDTA, and 21% PEG 4K, 100 mM Tris-HCl, pH 8.5, 200 mM Na acetate, 40 mM MgSO4, and 10% glycerol
-
hanging drop vapour diffusion method using 0.1 mM Tris-HCl pH 8.0, 1.8 M NH4Ac, and 3% glycol
-
hanging drop vapour diffusion method using 100 mM Tris-HCl pH 8.0 and 50% 2-methyl-2,4-pentanediol; unliganded enzyme and in complex with MgATP, diffraction to 2.0 and 2.2 A rsolution, respectively. both Structures show similar open conformations. Mg2+ and Na+ act in tandem to anchor the ATP at the active site, which itself acts as a sink to bind several molecules of 2-methyl-2,4-pentanediol
-
in complex with ginkgotoxin and theophylline, hanging drop vapor diffusion method, using 48-50% (w/v) 2-methyl-1,3 propanediol as precipitant, at 22°C
-
crystallized in the orthorhombic form using the hanging-drop vapour-diffusion method with sodium citrate as the precipitant, crystals are transferred into a soaking liquid without citrate and two-heavy-atom derivatives are prepared
-
crystals are grown in the presence of 100 mM potassium phosphate, pH 7.2, and 120 mM ammonium sulfate and crystals grown in the presence of 600 mM potassium phosphate, pH 7.2, and in the absence of ammonium sulfate. The crystals are quite stable to X-rays and diffract at 2.2 A resolution
-
hanging drop vapor diffusion method in complex with adenosine 5-(beta, gamma-methylenetriphosphate)-pyridoxamine, ADP-pyriodoxal 5-phosphate, and ADP
-
hanging drop vapor diffusion method, in complex with (R)-roscovitine and N6-methyl-(R)-roscovitine
sitting drop vapor diffusion method, using 0.1 M Tris, pH 8.5, 1 M LiCl2, and 15% (w/v) PEG 6000
native protein and in complex with its substrates to 1.4?1.85 A resolution. The protein shows a typical ribokinase fold with a central large beta-sheet consisting of nine strands, flanked by three and five structurally conserved alpha-helices
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
3 M guanidine hydrochloride, enzyme loses more than 90% of the alpha-helix content
-
if instead of the phosphate buffer an acetate buffer is used, enzymatic activity is reduced to 74% and almost no activity is recorded when a citrate buffer is used
-
the enzyme is digested by chymotrypsin to proteolytic fragments of 24000 Da and 16000 Da
-
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80°C, 20 mM phosphate buffer, pH 7.3, stable for at least some weeks
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Ni-NTA agarose column chromatography
Ni-NTA agarose column chromatography and HiLoad 26/60 Superdex 200 gel filtration
-
Ni-NTA column chromatography and Mono Q column chromatography
Phenyl ToyoPearl 650S column chromatography and Hi-Load Superdex 200 column gel filtration
-
recombinant enzyme
TMAE column chromatography, Phenyl Sepharose column chromatography, and hydroxyapatite column chromatography
-
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli Rosetta (DE3)pLysS cells; expression in Escherichia coli
-
expression in Escherichia coli
kinase 1 and 2 expressed in Escherichia coli HMS174(DE3), kinase 2 additionally expressed as His-tag fusion protein
-
recombinant enzyme is overexpressed in Escherichia coli as a fusion protein with maltose binding protein
-
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
expression patterns show that the gene is involved in abiotic stress and phytohormone regulation; expression patterns show that the gene is involved in abiotic stress and phytohormone regulation
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
K229Q
C124A
the mutant shows about 2fold increased catalytic efficiency compared to the wild type enzyme
C124A
-
the mutant shows about 2fold increased catalytic efficiency compared to the wild type enzyme
-
C110A
residue C110 is mandatory for pyridoxal, but not for pyridoxine, or 4-amino-5-hydroxymethyl-2-methylpyrimidine turnover
C214A
mutant does not turn over pyridoxal, pyridoxine, or 4-amino-5-hydroxymethyl-2-methylpyrimidine. Residue C214 acts as the catalytic base in the phosphorylation reaction
C110A
-
residue C110 is mandatory for pyridoxal, but not for pyridoxine, or 4-amino-5-hydroxymethyl-2-methylpyrimidine turnover
-
C214A
-
mutant does not turn over pyridoxal, pyridoxine, or 4-amino-5-hydroxymethyl-2-methylpyrimidine. Residue C214 acts as the catalytic base in the phosphorylation reaction
-
additional information
plants lacking enzyme activity display chlorosis and reduced plant size, and hypersensitivity to NaCl and sucrose. Mutant has higher level of pyridoxine, pyridoxamine, and pyridoxal 5'-phosphate. Mutant shows higher activity of pyridoxine/pyridoxamine 5'-phosphate oxidase as well as of the vitamin B6 de novo pathway enzyme Pdx1 and increased total vitamin B6 levels
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Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
the enzyme which has lost more than 90% of the alpha-helix content after treatment with 3 M guanidine hydrochloride regains more than 90% of the original catalytic activity after overnight dialysis against 10 mM potassium phosphate, pH 7 at 4°C
-
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
agriculture
plants lacking enzyme activity display chlorosis and reduced plant size, and hypersensitivity to NaCl and sucrose. Mutant has higher level of pyridoxine, pyridoxamine, and pyridoxal 5'-phosphate. Mutant shows higher activity of pyridoxine/pyridoxamine 5'-phosphate oxidase as well as of the vitamin B6 de novo pathway enzyme Pdx1 and increased total vitamin B6 levels
medicine
medicine
-
ingestion of 4'-O-methylpyridoxine, i.e. ginkgotoxin, triggers epileptic convulsions and other neuronal symptoms. 4'-O-Methylpyridoxine is an competitive inhibitor of pyridoxal kinase and leads to temporarily reduced pyridoxal phosphate formation in vitro and possibly in vivo
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LINKS TO OTHER DATABASES (specific for EC-Number 2.7.1.35)
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