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Information on EC 2.7.1.35 - pyridoxal kinase
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2.7.1.35 pyridoxal kinaseIUBMB Comments
Pyridoxine, pyridoxamine and various derivatives can also act as acceptors.
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Word Map
- 2.7.1.35
- 5'-phosphate
-
vitamers
- pyridoxal-5'-phosphate
-
4-pyridoxic
-
plp-dependent
- ribokinase
- medicine
- synthesis
- agriculture
- drug development
The enzyme appears in viruses and cellular organisms
Synonyms
ePL kinase, ePL kinase 1, hPL kinase, HPLK, kinase (phosphorylating), pyridoxal, kinase, pyridoxal (phosphorylating), LdPdxK, PdxK, pdxY, PKH, 
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SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
ePL kinase
-
two different forms encoded by genes PdxK and PdxY yielding kinase 1 and kinase 2, low activity of kinase 2 suggests that this kinase originally has another substrate but can also utilize pyridoxal
kinase (phosphorylating), pyridoxal
-
-
-
-
kinase, pyridoxal (phosphorylating)
-
-
-
-
LdPdxK
PdxK
PL kinase
PLK
Plk1
PM kinase
-
-
-
-
PN kinase
-
-
-
-
PN/PL/PM kinase
-
-
-
-
pyridoxal 5-phosphate-kinase
-
-
-
-
pyridoxal kinase
pyridoxal kinase PKL
pyridoxal kinase-like protein SOS4
-
-
-
-
pyridoxal phosphokinase
-
-
-
-
pyridoxamine kinase
-
-
-
-
pyridoxine kinase
-
-
-
-
pyridoxine/pyridoxal/pyridoxamine kinase
-
-
-
-
SAV0580
Sos4
vitamin B6 kinase
-
-
-
-
PL kinase
-
-
-
-
PLK
-
-
-
-
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 SOURCE
PATHWAYS
BRENDA
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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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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'-O-methylpyridoxine
ADP + 4'-O-methylpyridoxine 5'-phosphate
-
-
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine
ADP + 4-amino-5-phosphomethyl-2-methylpyrimidine
ATP + methyl (1S)-1-[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate
ADP + methyl (1S)-1-[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate 5'-phosphate
-
-
-
?
ATP + methyl N-[[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]methyl]histidinate
ADP + methyl N-[[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]methyl]histidinate 5'-phosphate
-
-
-
?
ATP + methyl N-[[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]methyl]tryptophanate
ADP + methyl N-[[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]methyl]tryptophanate 5'-phosphate
-
-
-
?
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 + 4-deoxypyridoxine
ADP + 4-deoxypyridoxine 5'-phosphate
-
-
-
-
?
ATP + ginkgotoxin
?
ginkgotoxin (from leaves of Ginkgo biloba) acts as pseudo-substrate for pyridoxal kinase with a Km value of 0.0297 mM
-
-
?
ATP + ginkgotoxin
?
ginkgotoxin (from leaves of Ginkgo biloba) acts as pseudo-substrate for pyridoxal kinase with a Km value of 0.0297 mM
-
-
?
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
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
-
-
-
?
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
preferred substrate
-
-
?
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
-
-
-
?
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
-
-
-
?
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
?
-
pyridoxal kinase catalyzes the forward reactions with pyridoxal, pyridoxamine, and pyridoxine, while pyridoxal phosphotase (PL phosphatase, PDXP, EC 3.1.3.74) catalyzes the reverse reaction of dephophorylation
-
-
-
additional information
?
-
-
pyridoxal kinase catalyzes the forward reactions with pyridoxal, pyridoxamine, and pyridoxine, while pyridoxal phosphotase (PL phosphatase, PDXP, EC 3.1.3.74) catalyzes the reverse reaction of dephophorylation
-
-
-
additional information
?
-
docking analysis of potent antimalarials to the enzyme, molecular docking indicates potential binding modes of methyl (1S)-1-[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate, methyl N-[[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]methyl]tryptophanate, and methyl N-[[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]methyl]histidinate as substrates of PfPdxK. PfPdxK is strongly implicated in the phosphorylation of methyl (1S)-1-[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]-2,3,4,9-tetrahydro-1H-pyrido[3,4-b]indole-3-carboxylate, methyl N-[[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]methyl]tryptophanate, and methyl N-[[3-hydroxy-5-(hydroxymethyl)-2-methylpyridin-4-yl]methyl]histidinate into their active forms
-
-
-
additional information
?
-
substrate binding strutures analysis from cyrstal structure of the enzyme-ligand complex, overview. ATP is covalently attached to Lys233 via a Schiff base linkage. In StPLK, the alpha-phosphate of ADP interacts with Ser201, Thr235, and nearby water molecule. The beta-phosphate of ADP interacts with Gly236, Asn164, one Mg2+ ion, and a few water molecules. Pyridoxal is covalently attached to an active site lysine residue (Lys233) forming a Schiff base, as well as to ADP, and a Mg2+ ion. Active site structure. Structure comparisons with other pyridoxal kinases from other species
-
-
-
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 SUBSTRATE
NATURAL 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 + 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
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
-
-
-
?
ATP + pyridoxine
ADP + pyridoxine 5'-phosphate
-
-
-
?
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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+
-
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+
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+
affinity to pyridoxal and ATP is increased manifold in the presence of K+ compared to Na+, 2.5fold increase of activity
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
K+
-
Km: 8.9 mM. Monovalent cation required, activation in the order of decreasing efficiency: K+, Rb+, NH4+
Mg2+
-
divalent cation required, activation of the recombinant enzyme in the order of decreasing efficiency: Zn2+, Co2+, Mn2+, Mg2+, Ca2+
Mg2+
-
cations activate in decreasing order of efficiency: Co2+, Mn2+, Mg2+, Zn2+, Cu2+, Ni2+, Fe2+
Mg2+
required, Mg2+ ion can be located near the bound phosphate, it is coordinated with O3 of the ADP beta-phosphate and four water molecules
Mn2+
-
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+
Na+
-
increases maximal velocity and affinity for ATP, but decreases affinity for pyridoxal
Na+
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, activation of the recombinant enzyme in the order of decreasing efficiency: Zn2+, Co2+, Mn2+, Mg2+, Ca2+. Optimum at about 0.1 mM Zn2+
Zn2+
-
divalent cation required, optimal concentration is 0.33 mM. Zn2+ is superior to Mg2+ below the optimum concentration of 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
-
the presence of 100 mM NaCl does not alter the potassium activation profile
additional information
Li+, Cs+, and Rb+ show no significant activity enhancement
additional information
-
Li+, Cs+, and Rb+ show no significant activity enhancement
additional information
the enzyme requires a metal cofactor, very low activity with Li+, Na+, K+, Rb+ and Cs+. Cobalt gives more activity when compared to that of Zn2+, Ca2+, Cu2+ and Ni2+. Cu2+ shows the least enzyme activity. Order of metal ions with increasing effect on enzyme activity is as follows: Co2+, Zn2+, Mn2+, Mg2+, Fe2+, Ca2+, Ni2+, Cu2+
additional information
-
the enzyme requires a metal cofactor, very low activity with Li+, Na+, K+, Rb+ and Cs+. Cobalt gives more activity when compared to that of Zn2+, Ca2+, Cu2+ and Ni2+. Cu2+ shows the least enzyme activity. Order of metal ions with increasing effect on enzyme activity is as follows: Co2+, Zn2+, Mn2+, Mg2+, Fe2+, Ca2+, Ni2+, Cu2+
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INHIBITOR
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
ADP
at high concentrations, product inhibition
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
pyridoxal
at high concentrations, substrate inhibition
pyridoxal 5'-phosphate
at high concentrations, product 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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DISEASE
TITLE OF PUBLICATION
LINK TO PUBMED
Anemia, Sideroblastic
Erythrocyte pyridoxine kinase levels in patients with sideroblastic anemia.
Anemia, Sideroblastic
Isoniazid inhibits human erythroid 5-aminolevulinate synthase: Molecular mechanism and tolerance study with four X-linked protoporphyria patients.
Carcinoma
Effects of vitamin B6 metabolism on oncogenesis, tumor progression and therapeutic responses.
Carcinoma, Non-Small-Cell Lung
Effects of vitamin B6 metabolism on oncogenesis, tumor progression and therapeutic responses.
Carcinoma, Non-Small-Cell Lung
Negative prognostic value of high levels of intracellular poly(ADP-ribose) in non-small cell lung cancer.
Down Syndrome
Expression of cystathionine beta-synthase, pyridoxal kinase, and ES1 protein homolog (mitochondrial precursor) in fetal Down syndrome brain.
Leishmaniasis, Visceral
Evaluation of Leishmania infantum pyridoxal kinase protein for the diagnosis of human and canine visceral leishmaniasis.
Leishmaniasis, Visceral
Leishmania infantum pyridoxal kinase evaluated in a recombinant protein and DNA vaccine to protects against visceral leishmaniasis.
Lung Neoplasms
Negative prognostic value of high levels of intracellular poly(ADP-ribose) in non-small cell lung cancer.
Lymphopenia
Inhibition of human pyridoxal kinase by 2-acetyl-4-((1R,2S,3R)-1,2,3,4-tetrahydroxybutyl)imidazole (THI).
Malaria
The antimalarial drugs chloroquine and primaquine inhibit pyridoxal kinase, an essential enzyme for vitamin B6 production.
Ovarian Neoplasms
[Pyridoxal kinase (PDXK) promotes the proliferation of serous ovarian cancer cells and is associated with poor prognosis].
Parkinson Disease
A loss of Pdxk model of Parkinson disease in Drosophila can be suppressed by Buffy.
Parkinson Disease
Single-cell expression profiling of dopaminergic neurons combined with association analysis identifies pyridoxal kinase as Parkinson's disease gene.
pyridoxal kinase deficiency
Apparent pyridoxine transport mutants of Escherichia coli with pyridoxal kinase deficiency.
Seizures
Changes in pyridoxal kinase immunoreactivity in the gerbil hippocampus following spontaneous seizure.
Seizures
Correlative changes of pyridoxal kinase pyridoxal-5'-phosphate and glutamate decarboxylase in brain, during drug-induced convulsions.
Seizures
Seizure susceptibility in the developing mouse and its relationship to glutamate decarboxylase and pyridoxal phosphate in brain.
Seizures
Vigabatrin inhibits pyridoxine-5'-phosphate oxidase, not pyridoxal kinase in the hippocampus of seizure prone gerbils.
Stomach Neoplasms
The differential proteome profile of stomach cancer: identification of the biomarker candidates.
Vitamin B 6 Deficiency
Evidence of a theophylline-induced vitamin B6 deficiency caused by noncompetitive inhibition of pyridoxal kinase.
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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
0.1
ATP
with pyridoxal, pH 6.6, 37°C
0.12
ATP
with pyridoxamine, pH 8.5, 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
0.044
pyridoxal
pH 6.6, 37°C
0.0441
pyridoxal
in 70 mM potassium phosphate (pH 5.5), 0.5 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
0.06
pyridoxamine
pH 8.5, 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
additional information
additional information
steady-state kinetics
-
additional information
additional information
Michaelis-Menten kinetics
-
additional information
additional information
-
Michaelis-Menten kinetics
-
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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
0.097
ATP
with pyridoxamine, pH 8.5, 37°C
0.107
ATP
with pyridoxal, pH 6.6, 37°C
106
ginkgotoxin
-
recombinant enzyme, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C
0.107
pyridoxal
pH 6.6, 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
1.35
pyridoxal
in 70 mM potassium phosphate (pH 5.5), 0.5 mM ZnCl2, at 37°C
131
pyridoxal
-
recombinant enzyme, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C
0.097
pyridoxamine
pH 8.5, 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
0.000254
pyridoxine
-
recombinant enzyme, apparent value, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C
0.81
ATP
with pyridoxamine, pH 8.5, 37°C
1.07
ATP
with pyridoxal, pH 6.6, 37°C
0.0009
pyridoxal
-
recombinant enzyme, apparent value, in HEPES/MgCl2 pH 7.4, 0.15 mM ZnCl2, at 37°C
2.43
pyridoxal
pH 6.6, 37°C
30.6
pyridoxal
in 70 mM potassium phosphate (pH 5.5), 0.5 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
1.62
pyridoxamine
pH 8.5, 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
1.8
crude enzyme, in 70 mM potassium phosphate (pH 5.5), 0.5 mM ZnCl2, at 37°C
1847
purified recombinant His-tagged wild-type enzyme, pH 7.2, 37°C
additional information
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.5 - 6
6.2 - 6.6
with substrate pyridoxal
6.5
8.5
8.5
with substrate pyridoxamine
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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
37
50
55
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TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25 - 42
maximal activity at 42°C, 80% of maximal activity at 37°C, 50% at 25°C, purified recombinant enzyme
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pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.3
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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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
brenda
-
from CA1 region, strong immunoreactivity
brenda
-
regions CA1, CA2/3 and dentate gyrus, increased enzyme activity detected 12-24 h after ischemia
brenda
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
splice variant SOS4.1 (but not SOS4.2) is localized in chloroplasts
brenda
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
physiological function
additional information
evolution
PdxK belongs to ribokinase enzyme family in which either cysteine or aspartate act as catalytic residue for its activity. The known catalytic mechanism of ribokinase family and for PdxK is the in line displacement mechanism in which hydroxyl group of the substrate is activated by a catalytic base (aspartate) of the enzyme, to make the nucleophilic attack on the gamma-phosphate group of ATP. The active site residues Leu43, Ser47, Ile52, Arg56, Asn87 and Thr227 present in LdPdxK are replaced with Phe43, Thr47, Try52, Val56, Arg86 and Val231 in mammalian PdxKs
evolution
pyridoxine/pyridoxal kinase (PdxK) belongs to the ribokinase family and is involved in the vitamin B6 salvage pathway by phosphorylating pyridoxal (PL) into an active form. In the human malaria parasite, Plasmodium falciparum, PfPdxK functions to salvage vitamin B6 from both itself and its host
evolution
-
PdxK belongs to ribokinase enzyme family in which either cysteine or aspartate act as catalytic residue for its activity. The known catalytic mechanism of ribokinase family and for PdxK is the in line displacement mechanism in which hydroxyl group of the substrate is activated by a catalytic base (aspartate) of the enzyme, to make the nucleophilic attack on the gamma-phosphate group of ATP. The active site residues Leu43, Ser47, Ile52, Arg56, Asn87 and Thr227 present in LdPdxK are replaced with Phe43, Thr47, Try52, Val56, Arg86 and Val231 in mammalian PdxKs
-
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
malfunction
in Drosophila, mutations in the dPdxk gene cause chromosome aberrations (CABs) and increased glucose content in larval hemolymph. The phenotype is rescued by the expression of wild-type human PDXK enzyme, although not by human PDXK mutants D87H, V128I, H246Q, and A243G
malfunction
the four PDXK human variants, D87H, V128I, H246Q, and A243Gf D87H, V128I, H246Q and A243G proteins show reduced catalytic activity and/or reduced affinity for PLP precursors. Although these variants are rare in population and carried in heterozygous condition, it is suggested that in certain metabolic contexts and diseases in which PLP levels are reduced, the presence of these PDXK variants might threaten genome integrity and increase cancer risk
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
physiological function
biotransformation of pyridoxal to pyridoxal 5'-phosphate (PLP) by pyridoxal kinase (pdxY) supports cadaverine production in Escherichia coli. PLP is an essential cofactor of lysine decarboxylase and the major bottleneck in the cadaverine biosynthesis pathway
physiological function
in eukaryotes, pyridoxal kinase (PDXK) acts in vitamin B6 salvage pathway to produce pyridoxal 5'-phosphate (PLP), the active form of the vitamin, which is implicated in numerous crucial metabolic reactions. PDXK converts PLP precursors such as pyridoxal (PL), pyridoxamine (PM) and pyridoxine (PN) taken from food into PLP, PMP and PNP, respectively. PNPO catalyzes the oxidation of PMP and PNP into PLP. PLP performs many functions by working as coenzyme for a wide number of enzymes which control amino acid, lipid and carbohydrate metabolism
physiological function
in eukaryotes, pyridoxal kinase (PDXK) acts in vitamin B6 salvage pathway to produce pyridoxal 5'-phosphate (PLP), the active form of the vitamin, which is implicated in numerous crucial metabolic reactions. PDXK converts PLP precursors such as pyridoxal (PL), pyridoxamine (PM) and pyridoxine (PN) taken from food into PLP, PMP and PNP, respectively. PNPO catalyzes the oxidation of PMP and PNP into PLP. PLP performs many functions by working as coenzyme for a wide number of enzymes which control amino acid, lipid and carbohydrate metabolism
physiological function
pyridoxal kinase (PdxK) is an important enzyme of the vitamin B6 salvage pathway which is required for phosphorylation of B6 vitamers
physiological function
pyridoxine/pyridoxal kinase (PdxK) belongs to the ribokinase family and is involved in the vitamin B6 salvage pathway by phosphorylating pyridoxal (PL) into an active form. In the human malaria parasite, Plasmodium falciparum, PfPdxK functions to salvage vitamin B6 from both itself and its host
physiological function
the enzyme pyridoxal kinase (PdxK) catalyzes the conversion of pyridoxal to pyridoxal 5'-phosphate (PLP) using ATP as the cosubstrate. The product PLP plays a key role in several biological processes such as transamination, decarboxylation and deamination
physiological function
vitamin B6 enters the cells after hydrolysis of the phosphorylated forms by the membrane-bound tissue non-specific alkaline phosphatase (TNSALP, EC 3.1.3.1). Once inside the cells, pyridoxal kinase (PL kinase, PDXK, EC 2.7.1.35) phosphorylates the hydroxymethyl group of PL, PN and PM to their respective 5'-phosphate forms
physiological function
-
pyridoxal kinase (PdxK) is an important enzyme of the vitamin B6 salvage pathway which is required for phosphorylation of B6 vitamers
-
physiological function
-
the enzyme pyridoxal kinase (PdxK) catalyzes the conversion of pyridoxal to pyridoxal 5'-phosphate (PLP) using ATP as the cosubstrate. The product PLP plays a key role in several biological processes such as transamination, decarboxylation and deamination
-
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
additional information
a FIxxIIxL motif at the C-terminus of the disordered repeat motif (XNXH)m that is implicated in binding the WD40 domain and may provide temporal control of PfPdxK through an interaction with a E3 ligase complex. Molecular docking and modelling, overview. Binding structure of AMP-PNP with PdxK
additional information
analysis of the binding structures of substrates and products from PdxK-ligand crystal structures, overview
additional information
-
analysis of the binding structures of substrates and products from PdxK-ligand crystal structures, overview
additional information
comparison of the structure of apo StPLK with its ligand-bound forms
additional information
in silico analysis of the human and parasite PdxK structure revealing significant differences in the active site region, LdPdxK homology modeling using pyridoxal kinase from Trypanosoma brucei (PDB ID 3ZS7) as a template, molecular dynamics and molecular docking, overview
additional information
-
in silico analysis of the human and parasite PdxK structure revealing significant differences in the active site region, LdPdxK homology modeling using pyridoxal kinase from Trypanosoma brucei (PDB ID 3ZS7) as a template, molecular dynamics and molecular docking, overview
additional information
-
in silico analysis of the human and parasite PdxK structure revealing significant differences in the active site region, LdPdxK homology modeling using pyridoxal kinase from Trypanosoma brucei (PDB ID 3ZS7) as a template, molecular dynamics and molecular docking, overview
-
additional information
-
analysis of the binding structures of substrates and products from PdxK-ligand crystal structures, overview
-
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PDB
SCOP
CATH
UNIPROT
ORGANISM