Information on EC 2.7.4.7 - phosphomethylpyrimidine kinase

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

EC NUMBER
COMMENTARY
2.7.4.7
-
RECOMMENDED NAME
GeneOntology No.
phosphomethylpyrimidine kinase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
ATP + (4-amino-2-methylpyrimidin-5-yl)methyl phosphate = ADP + (4-amino-2-methylpyrimidin-5-yl)methyl diphosphate
show the reaction diagram
proposed reaction mechanism
-
ATP + (4-amino-2-methylpyrimidin-5-yl)methyl phosphate = ADP + (4-amino-2-methylpyrimidin-5-yl)methyl diphosphate
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
phospho group transfer
-
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis
-
4-amino-2-methyl-5-phosphomethylpyrimidine biosynthesis (yeast)
-
hydroxymethylpyrimidine salvage
-
Metabolic pathways
-
thiamin formation from pyrithiamine and oxythiamine (yeast)
-
Thiamine metabolism
-
SYSTEMATIC NAME
IUBMB Comments
ATP:(4-amino-2-methylpyrimidin-5-yl)methyl-phosphate phosphotransferase
-
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
2-methyl-4-amino-5-hydroxymethylpyrimidine monophosphate kinase
-
-
HMP-P kinase
-
-
HMP-P kinase
-
-
HMP-P kinase
Saccharomyces cerevisiae YPH500
-
-
-
hydroxymethylpyrimidine phosphokinase
-
-
-
-
kinase, phosphomethylpyrimidine (phosphorylating)
-
-
-
-
Thi20p protein
-
-
Thi20p protein
Saccharomyces cerevisiae YPH500
-
-
-
Thi21p protein
-
-
CAS REGISTRY NUMBER
COMMENTARY
37278-18-5
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
bifunctional hydroxymethylpyrimidine/phosphomethylpyrimidine kinase
SwissProt
Manually annotated by BRENDA team
trifunctional enzyme EC 3.5.99.2/EC 2.7.1.49/EC 2.7.4.7
SwissProt
Manually annotated by BRENDA team
trifunctional enzyme: EC 3.5.99.2/EC 2.7.1.49/EC 2.7.4.7
SwissProt
Manually annotated by BRENDA team
bifunctional hydroxymethylpyrimidine/phosphomethylpyrimidine kinase
UniProt
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + (4-amino-2-methylpyrimidin-5-yl)methyl phosphate
ADP + (4-amino-2-methylpyrimidin-5-yl)methyl diphosphate
show the reaction diagram
Q08224
-
-
-
?
ATP + 2-methyl-4-amino-5-hydroxymethylpyrimidine
ADP + 2-methyl-4-amino-5-phosphomethylpyrimidine
show the reaction diagram
-
-
-
?
ATP + 2-methyl-4-amino-5-hydroxymethylpyrimidine
ADP + 2-methyl-4-amino-5-phosphomethylpyrimidine
show the reaction diagram
-
-
-
?
ATP + 2-methyl-4-amino-5-hydroxymethylpyrimidine
ADP + 2-methyl-4-amino-5-phosphomethylpyrimidine
show the reaction diagram
-
involved in thiamine biosynthesis
-
-
ATP + 2-methyl-4-amino-5-phosphomethylpyrimidine
ADP + 2-methyl-4-amino-5-diphosphomethylpyrimidine
show the reaction diagram
-
-
-
?
ATP + 2-methyl-4-amino-5-phosphomethylpyrimidine
ADP + 2-methyl-4-amino-5-diphosphomethylpyrimidine
show the reaction diagram
-
-
-
?
ATP + 2-methyl-4-amino-5-phosphomethylpyrimidine
ADP + 2-methyl-4-amino-5-diphosphomethylpyrimidine
show the reaction diagram
-
specific for ATP
product demonstrated in crude extract
?
ATP + 2-methyl-4-amino-5-phosphomethylpyrimidine
ADP + 2-methyl-4-amino-5-diphosphomethylpyrimidine
show the reaction diagram
-, O48881
enzyme has both 2-methyl-4-amino-5-hydroxymethylpyrimidine phosphate kinase and thiamin-phosphate diphosphatase activities
-
?
ATP + 2-methyl-4-amino-5-phosphomethylpyrimidine
ADP + 2-methyl-4-amino-5-diphosphomethylpyrimidine
show the reaction diagram
-, O48881
enzyme has both 2-methyl-4-amino-5-hydroxymethylpyrimidine phosphate kinase and thiamin-phosphate diphosphatase activities, involved in thiamine biosynthesis
-
?
ATP + 4-amino-2-methyl-phosphomethylpyrimidine
ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine
show the reaction diagram
-
enzyme is required for thiamin biosynthesis, the Thi20p protein has a greater ability than the Thi21p protein to catalyze the reaction
-
-
?
ATP + 4-amino-2-methyl-phosphomethylpyrimidine
ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine
show the reaction diagram
Saccharomyces cerevisiae YPH500
-
enzyme is required for thiamin biosynthesis, the Thi20p protein has a greater ability than the Thi21p protein to catalyze the reaction
-
-
?
additional information
?
-
Q08224
Thi20p is involved in thiamine synthesis from pyrithiamin and oxythiamin
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + (4-amino-2-methylpyrimidin-5-yl)methyl phosphate
ADP + (4-amino-2-methylpyrimidin-5-yl)methyl diphosphate
show the reaction diagram
Q08224
-
-
-
?
ATP + 2-methyl-4-amino-5-hydroxymethylpyrimidine
ADP + 2-methyl-4-amino-5-phosphomethylpyrimidine
show the reaction diagram
-
involved in thiamine biosynthesis
-
-
ATP + 2-methyl-4-amino-5-phosphomethylpyrimidine
ADP + 2-methyl-4-amino-5-diphosphomethylpyrimidine
show the reaction diagram
-
-
-
?
ATP + 2-methyl-4-amino-5-phosphomethylpyrimidine
ADP + 2-methyl-4-amino-5-diphosphomethylpyrimidine
show the reaction diagram
-
specific for ATP
product demonstrated in crude extract
?
ATP + 2-methyl-4-amino-5-phosphomethylpyrimidine
ADP + 2-methyl-4-amino-5-diphosphomethylpyrimidine
show the reaction diagram
-, O48881
enzyme has both 2-methyl-4-amino-5-hydroxymethylpyrimidine phosphate kinase and thiamin-phosphate diphosphatase activities, involved in thiamine biosynthesis
-
?
ATP + 4-amino-2-methyl-phosphomethylpyrimidine
ADP + 4-amino-2-methyl-5-diphosphomethylpyrimidine
show the reaction diagram
Saccharomyces cerevisiae, Saccharomyces cerevisiae YPH500
-
enzyme is required for thiamin biosynthesis
-
-
?
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Mg2+
-
required for activity
Mn2+
-
may substitute for Mg2+
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
(6R)-6-[(2E)-4-oxo-6-phenylhex-2-en-1-yl]-5,6-dihydro-2H-pyran-2-one
P66915
lactone isolated from Cryptocarya rugulosa, covalent inhibition
-
(6R)-6-[(2E)-6-(4-ethynylphenyl)-4-oxohex-2-en-1-yl]-5,6-dihydro-2H-pyran-2-one
P66915
derivative of a lactone isolated from Cryptocarya rugulosa, covalent inhibition
-
(6S)-6-[(2E)-6-(4-ethynylphenyl)-4-oxohex-2-en-1-yl]tetrahydro-2H-pyran-2-one
P66915
derivative of a lactone isolated from Cryptocarya rugulosa, covalent inhibition
-
p-hydroxymercuribenzoate
-
1 mM, complete inhibition
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.15
-
2-methyl-4-amino-5-hydroxymethylpyrimidine
-
pH 8.0, 25C, recombinant ThiD
0.023
-
2-methyl-4-amino-5-hydroxymethylpyrimidine phosphate
-
pH 8.0, 25C, recombinant ThiD
0.193
-
ATP
-
pH 8.0, 25C, recombinant ThiD
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.0867
-
2-methyl-4-amino-5-hydroxymethylpyrimidine
-
pH 8.0, 25C, recombinant ThiD
0.07
-
2-methyl-4-amino-5-hydroxymethylpyrimidine phosphate
-
pH 8.0, 25C, recombinant ThiD
0.07
-
ATP
-
pH 8.0, 25C, recombinant ThiD
IC50 VALUE [mM]
IC50 VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.025
-
(6R)-6-[(2E)-4-oxo-6-phenylhex-2-en-1-yl]-5,6-dihydro-2H-pyran-2-one
P66915
pH not specified in the publication, temperature not specified in the publication
-
0.014
-
(6R)-6-[(2E)-6-(4-ethynylphenyl)-4-oxohex-2-en-1-yl]-5,6-dihydro-2H-pyran-2-one
P66915
pH not specified in the publication, temperature not specified in the publication
-
0.032
-
(6S)-6-[(2E)-6-(4-ethynylphenyl)-4-oxohex-2-en-1-yl]tetrahydro-2H-pyran-2-one
P66915
pH not specified in the publication, temperature not specified in the publication
-
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.5
-
Q08224
assay at
8
-
Q08224
assay at
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
32
-
Q08224
assay at
37
-
Q08224
assay at
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-, O48881
putative plastid target signal in BTH1 suggests plastidic localization
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
Clostridium difficile (strain 630)
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
tetramer
-
4 * 31232, deduced from nucleotide sequence; 4 * 33000, SDS-PAGE
additional information
-, O48881
enzyme has 2 distinct domains related to TMP-PPase and HMP-P kinase activities
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
to 2.7 A resolution. Enzyme is composed of a ThiD-like N-terminal domain that catalyzes the phosphorylation of 4-amino-5-hydroxymethyl-2-methylpyrimidine and 4-amino-5-hydroxymethyl-2-methylpyrimidine phosphate and a TenA-like C-terminal domain with thiaminase activity. The structure reveals an overall dimeric organization in which N-terminal domains and C-terminal domains form ThiD-like and TenA-like local dimers. A relatively flexible linker region composed of a loop and a short helix joins the two domains. This linker region and a flexible N-terminal extension occupy the interface between the ThiD-like and TenA-like dimers. The N-terminal extension is composed of a single beta-strand that packs against and extends the length of the internal beta-sheet of the ThiD-like domain and a short alpha-helix
Q08224
hanging drop vapor diffusion, 6 mg/ml HMPP kinase, hanging drops contain 0.002 mL protein solution and 0.002 ml reservoir solution, crystal without HMP are obtained using a reservoir solution containing 1.35 M MgSO4, 150 mM MES, pH 7.0, crystals with HMP are obtained with 1.4 M MgSO4 and 150 M MES, crystals of native HMP-P kinase diffract to 2.3 A resolution
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
his-tagged recombinant ThiD
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
cloning of BTH1 cDNA in Escherichia coli
-, O48881
overexpression of ThiD in Escherichia coli
-
expression in Escherichia coli
-
overexpression in Escherichia coli
Q08224