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Information on EC 2.7.1.169 - pantoate kinase and Organism(s) Thermococcus kodakarensis and UniProt Accession Q5JHF1

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EC Tree
IUBMB Comments
The conversion of (R)-pantoate to (R)-4'-phosphopantothenate is part of the pathway leading to biosynthesis of 4'-phosphopantetheine, an essential cofactor of coenzyme A and acyl-carrier protein. In bacteria and eukaryotes this conversion is performed by condensation with beta-alanine, followed by phosphorylation (EC 6.3.2.1 and EC 2.7.1.33, respectively). In archaea the order of these two steps is reversed, and phosphorylation precedes condensation with beta-alanine.
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Thermococcus kodakarensis
UNIPROT: Q5JHF1
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The taxonomic range for the selected organisms is: Thermococcus kodakarensis
The expected taxonomic range for this enzyme is: Archaea, Bacteria
Synonyms
pantoate kinase, mhun_0831, cog1829, more
PATHWAY SOURCE
PATHWAYS
-
-
SYSTEMATIC NAME
IUBMB Comments
ATP:(R)-pantoate 4-phosphotransferase
The conversion of (R)-pantoate to (R)-4'-phosphopantothenate is part of the pathway leading to biosynthesis of 4'-phosphopantetheine, an essential cofactor of coenzyme A and acyl-carrier protein. In bacteria and eukaryotes this conversion is performed by condensation with beta-alanine, followed by phosphorylation (EC 6.3.2.1 and EC 2.7.1.33, respectively). In archaea the order of these two steps is reversed, and phosphorylation precedes condensation with beta-alanine.
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
ATP + (R)-pantoate
ADP + (R)-4-phosphopantoate
show the reaction diagram
-
-
-
?
ATP + pantoate
ADP + 4-phosphopantoate
show the reaction diagram
ATP + pantothenate
ADP + 4'-phosphopantothenate
show the reaction diagram
kcat/Km value with pantoate as a substrate is over 7fold higher than that observed with pantothenate
-
-
?
CTP + pantoate
CDP + 4-phosphopantoate
show the reaction diagram
-
-
-
?
GTP + pantoate
GDP + 4-phosphopantoate
show the reaction diagram
-
-
-
?
UTP + pantoate
UDP + 4-phosphopantoate
show the reaction diagram
-
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
ATP + (R)-pantoate
ADP + (R)-4-phosphopantoate
show the reaction diagram
-
-
-
?
ATP + pantoate
ADP + 4-phosphopantoate
show the reaction diagram
-
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
ATP
the electron density for the adenosine moiety of ATP is very weak, which most likely relates to its broad nucleotide specificity. The triphosphate moiety of ATP is surrounded by the lycine-rich loop of motif II (P96NGYGFGNSAG106). The magnesium ion can interact with oxygen atoms of beta- and gamma-phosphates, and with the O5' atom of ATP which bridges the adenosine and the triphosphate groups
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
K+
moderate stimulation, optimum at 10 mM
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
CoA
no inhibition in presence of 0.1 mM CoA, activity decrases by 20% in presence of 1 mM CoA
Pantoate
substrate inhibition
additional information
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.32 - 0.47
ATP
0.34
CTP
pH 7.5, 42°C
0.43
GTP
pH 7.5, 42°C
1.2 - 2.92
Pantoate
1.3
pantothenate
42°C
0.17
UTP
pH 7.5, 42°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.48
ATP
0.47
CTP
pH 7.5, 42°C
0.32
GTP
pH 7.5, 42°C
1.56 - 2.82
Pantoate
0.21
pantothenate
42°C
1.11
UTP
pH 7.5, 42°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.2 - 3.1
ATP
1.4
CTP
pH 7.5, 42°C
0.74
GTP
pH 7.5, 42°C
0.17
pantothenate
42°C
6.5
UTP
pH 7.5, 42°C
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
9.75
Pantoate
pH 7.5, 42°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
the deletion mutant strain grows well in media supplemented with 1 mM CoA. The deletion mutant strain could not grow at all in the absence of CoA
metabolism
the CoA biosynthesis pathway involves reactions that convert pantoate to 4'-phosphopantothenate. For this conversion, bacteria/eukaryotes commonly use two enzymes, pantothenate synthetase (PS) and pantothenate kinase (PanK). In the PS/PanK pathway, pantoate and beta-alanine are first condensed to form pantothenate by the reaction of PS, and then pantothenate is phosphorylated to generate 40-phosphopantothenate by the reaction of PanK
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
32748
2 * 32748, calculated from sequence
34000
2 * 34000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant enzyme in apoform or in complex with ATP and a magnesium ion, mixing of 5-10 mg/ml protein in 50 mM Tris-HCl, pH 7.5, with 18%-20% PEG 8000 solutions containing 200 mM calcium acetate and 100 mM MES, pH 6.0, as a precipitant, 1-2 weeks, 20°C, X-ray diffraction structure determination and analysis at 2.5-2.7 A resolution, single isomorphous replacement (SIR) method using derivative data of K2Pt (NO2)4 collected at 3.0 A resolution, modeling. In TkPoK/ATP, the adenine ring of the ATP is not included in the crystal structure, because its electron density is very poor
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D143
residue is the base responsible for proton abstraction from the pantoate hydroxy group
E134A
residue is involved in binding with Mg2+
H131A
residue is involved in pantoate recognition. 77% of wild-type activity in presence of 6 mM pantoate and 4 mM ATP
R155A
residue is involved in pantoate recognition and plays an important role in catalysis
S104A
residue is involved in binding with phosphate
S28A
residue is involved in pantoate recognition. 3.7% of wild-type activity in presence of 6 mM pantoate and 4 mM ATP
T186A
residue is involved in pantoate recognition and plays an important role in catalysis. Thr186 is involved in dimer assambly
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Thermococcus kodakarensis
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Yokooji, Y.; Tomita, H.; Atomi, H.; Imanaka, T.
Pantoate kinase and phosphopantothenate synthetase, two novel enzymes necessary for CoA biosynthesis in the archaea
J. Biol. Chem.
284
28137-28145
2009
Thermococcus kodakarensis (Q5JHF1), Thermococcus kodakarensis
Manually annotated by BRENDA team
Tomita, H.; Yokooji, Y.; Ishibashi, T.; Imanaka, T.; Atomi, H.
Biochemical characterization of pantoate kinase, a novel enzyme necessary for coenzyme A biosynthesis in the Archaea
J. Bacteriol.
194
5434-5443
2012
Thermococcus kodakarensis (Q5JHF1), Thermococcus kodakarensis
Manually annotated by BRENDA team
Kita, A.; Kishimoto, A.; Shimosaka, T.; Tomita, H.; Yokooji, Y.; Imanaka, T.; Atomi, H.; Miki, K.
Crystal structure of pantoate kinase from Thermococcus kodakarensis
Proteins
88
718-724
2020
Thermococcus kodakarensis (Q5JHF1), Thermococcus kodakarensis, Thermococcus kodakarensis JCM 12380 (Q5JHF1), Thermococcus kodakarensis ATCC BAA-918 (Q5JHF1)
Manually annotated by BRENDA team