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Literature summary for 2.7.1.49 extracted from

  • Cea, P.A.; Araya, G.; Vallejos, G.; Recabarren, R.; Alzate-Morales, J.; Babul, J.; Guixe, V.; Castro-Fernandez, V.
    Characterization of hydroxymethylpyrimidine phosphate kinase from mesophilic and thermophilic bacteria and structural insights into their differential thermal stability (2020), Arch. Biochem. Biophys., 688, 108389 .
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
gene thiD, phylogenetic tree, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) Salmonella enterica subsp. enterica serovar Typhimurium
gene thiD, phylogenetic tree, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) Thermus thermophilus

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information kinetic analysis, Michaelis-Menten model, ordered sequential kinetic mechanism Salmonella enterica subsp. enterica serovar Typhimurium
additional information
-
additional information kinetic analysis, Michaelis-Menten model, ordered sequential kinetic mechanism Thermus thermophilus
0.01
-
4-Amino-5-hydroxymethyl-2-methylpyrimidine pH 8.0, 25°C Thermus thermophilus
0.017
-
4-Amino-5-hydroxymethyl-2-methylpyrimidine pH 8.0, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
0.7
-
ATP pH 8.0, 25°C Thermus thermophilus
0.74
-
ATP pH 8.0, 25°C Salmonella enterica subsp. enterica serovar Typhimurium
0.74
-
ATP pH 7.0, 25°C, recombinant enzyme, MgATP Salmonella enterica subsp. enterica serovar Typhimurium
17
-
4-Amino-5-hydroxymethyl-2-methylpyrimidine pH 7.0, 25°C, recombinant enzyme Salmonella enterica subsp. enterica serovar Typhimurium

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required Salmonella enterica subsp. enterica serovar Typhimurium
Mg2+ required Thermus thermophilus

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine Salmonella enterica subsp. enterica serovar Typhimurium
-
ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine Thermus thermophilus
-
ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine Salmonella enterica subsp. enterica serovar Typhimurium SGSC1412
-
ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720
-
ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine Thermus thermophilus DSM 579
-
ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine Thermus thermophilus ATCC 27634
-
ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine Salmonella enterica subsp. enterica serovar Typhimurium
-
ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine Thermus thermophilus
-
ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine Salmonella enterica subsp. enterica serovar Typhimurium the enzyme catalyzes an essential step for the biosynthesis of thiamin pyrophosphate ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine Thermus thermophilus the enzyme catalyzes an essential step for the biosynthesis of thiamin pyrophosphate ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine Salmonella enterica subsp. enterica serovar Typhimurium SGSC1412
-
ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine Salmonella enterica subsp. enterica serovar Typhimurium SGSC1412 the enzyme catalyzes an essential step for the biosynthesis of thiamin pyrophosphate ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720
-
ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720 the enzyme catalyzes an essential step for the biosynthesis of thiamin pyrophosphate ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine Thermus thermophilus DSM 579
-
ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine Thermus thermophilus DSM 579 the enzyme catalyzes an essential step for the biosynthesis of thiamin pyrophosphate ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine Thermus thermophilus ATCC 27634
-
ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine Thermus thermophilus ATCC 27634 the enzyme catalyzes an essential step for the biosynthesis of thiamin pyrophosphate ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?

Organism

Organism UniProt Comment Textmining
Salmonella enterica subsp. enterica serovar Typhimurium P55882
-
-
Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720 P55882
-
-
Salmonella enterica subsp. enterica serovar Typhimurium SGSC1412 P55882
-
-
Thermus thermophilus Q5SKG3
-
-
Thermus thermophilus ATCC 27634 Q5SKG3
-
-
Thermus thermophilus DSM 579 Q5SKG3
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and dialysis Salmonella enterica subsp. enterica serovar Typhimurium
recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and dialysis Thermus thermophilus

Reaction

Reaction Comment Organism Reaction ID
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine = ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine ordered sequential mechanism Salmonella enterica subsp. enterica serovar Typhimurium
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine = ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine ordered sequential mechanism Thermus thermophilus

Storage Stability

Storage Stability Organism
-80°C, 25 mM Tris-HCl (pH 8.0) and 100 mM arginine, 20% glycerol, stable for months Salmonella enterica subsp. enterica serovar Typhimurium
-80°C, in the presence of 25 mM Tris-HCl, pH 8.0, and 100 mM arginine the protein remains stable for hours. The addition of 20% glycerol maintains the protein stable for months. Purified StHMPPK is highly unstable at room temperature, with a strong trend to aggregate formation. Salmonella enterica subsp. enterica serovar Typhimurium
-80°C, the addition of 20% glycerol maintains the protein stable for months, for purified TtHMPPK, optimal storage conditions include 25 mM Tris-HCl, pH 8.0, and 300 mM NaCl Thermus thermophilus

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
Salmonella enterica subsp. enterica serovar Typhimurium ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
Thermus thermophilus ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine reaction of EC 2.7.4.7 Salmonella enterica subsp. enterica serovar Typhimurium ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine reaction of EC 2.7.4.7 Thermus thermophilus ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
Salmonella enterica subsp. enterica serovar Typhimurium SGSC1412 ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine reaction of EC 2.7.4.7 Salmonella enterica subsp. enterica serovar Typhimurium SGSC1412 ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720 ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine reaction of EC 2.7.4.7 Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720 ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
Thermus thermophilus DSM 579 ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine reaction of EC 2.7.4.7 Thermus thermophilus DSM 579 ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
Thermus thermophilus ATCC 27634 ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine reaction of EC 2.7.4.7 Thermus thermophilus ATCC 27634 ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine
-
Salmonella enterica subsp. enterica serovar Typhimurium ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine
-
Thermus thermophilus ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine the enzyme catalyzes an essential step for the biosynthesis of thiamin pyrophosphate Salmonella enterica subsp. enterica serovar Typhimurium ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine the enzyme catalyzes an essential step for the biosynthesis of thiamin pyrophosphate Thermus thermophilus ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine
-
Salmonella enterica subsp. enterica serovar Typhimurium SGSC1412 ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine the enzyme catalyzes an essential step for the biosynthesis of thiamin pyrophosphate Salmonella enterica subsp. enterica serovar Typhimurium SGSC1412 ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine
-
Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720 ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine the enzyme catalyzes an essential step for the biosynthesis of thiamin pyrophosphate Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720 ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine
-
Thermus thermophilus DSM 579 ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine the enzyme catalyzes an essential step for the biosynthesis of thiamin pyrophosphate Thermus thermophilus DSM 579 ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine
-
Thermus thermophilus ATCC 27634 ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
ATP + 4-amino-5-hydroxymethyl-2-methylpyrimidine the enzyme catalyzes an essential step for the biosynthesis of thiamin pyrophosphate Thermus thermophilus ATCC 27634 ADP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine
-
?
additional information the enzyme performs double phosphorylation on 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP), it is specific for HMP and does not use pyridoxal-like molecules (pyridoxal (PL), pyridoxine (PN) and pyridoxamine (PM)) as substrates Salmonella enterica subsp. enterica serovar Typhimurium ?
-
-
additional information the enzyme performs double phosphorylation on 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP), it is specific for HMP and does not use pyridoxal-like molecules (pyridoxal (PL), pyridoxine (PN) and pyridoxamine (PM)) as substrates Thermus thermophilus ?
-
-
additional information the enzyme performs double phosphorylation on 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP), it is specific for HMP and does not use pyridoxal-like molecules (pyridoxal (PL), pyridoxine (PN) and pyridoxamine (PM)) as substrates Salmonella enterica subsp. enterica serovar Typhimurium SGSC1412 ?
-
-
additional information the enzyme performs double phosphorylation on 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP), it is specific for HMP and does not use pyridoxal-like molecules (pyridoxal (PL), pyridoxine (PN) and pyridoxamine (PM)) as substrates Salmonella enterica subsp. enterica serovar Typhimurium ATCC 700720 ?
-
-
additional information the enzyme performs double phosphorylation on 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP), it is specific for HMP and does not use pyridoxal-like molecules (pyridoxal (PL), pyridoxine (PN) and pyridoxamine (PM)) as substrates Thermus thermophilus DSM 579 ?
-
-
additional information the enzyme performs double phosphorylation on 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP), it is specific for HMP and does not use pyridoxal-like molecules (pyridoxal (PL), pyridoxine (PN) and pyridoxamine (PM)) as substrates Thermus thermophilus ATCC 27634 ?
-
-

Synonyms

Synonyms Comment Organism
HMP kinase
-
Salmonella enterica subsp. enterica serovar Typhimurium
HMP kinase
-
Thermus thermophilus
HMPK
-
Salmonella enterica subsp. enterica serovar Typhimurium
HMPK
-
Thermus thermophilus
HMPPK
-
Salmonella enterica subsp. enterica serovar Typhimurium
HMPPK
-
Thermus thermophilus
hydroxymethylpyrimidine phosphate kinase
-
Salmonella enterica subsp. enterica serovar Typhimurium
hydroxymethylpyrimidine phosphate kinase
-
Thermus thermophilus
More see also EC 2.7.4.7 Salmonella enterica subsp. enterica serovar Typhimurium
More see also EC 2.7.4.7 Thermus thermophilus
StHMPPK
-
Salmonella enterica subsp. enterica serovar Typhimurium
ThiD
-
Salmonella enterica subsp. enterica serovar Typhimurium
ThiD
-
Thermus thermophilus
TTHA0680 locus name Thermus thermophilus
TtHMPPK
-
Thermus thermophilus

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
25
-
assay at Salmonella enterica subsp. enterica serovar Typhimurium
25
-
assay at Thermus thermophilus

Temperature Stability [°C]

Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
50.1
-
Tm-value Salmonella enterica subsp. enterica serovar Typhimurium
50.1
-
average Tm observerd for TtHMPPK is 50.1°C Salmonella enterica subsp. enterica serovar Typhimurium
83.1
-
Tm-value Thermus thermophilus
83.1
-
average Tm observerd for TtHMPPK is 83.1°C Thermus thermophilus

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7
-
assay at Salmonella enterica subsp. enterica serovar Typhimurium
7
-
assay at Thermus thermophilus

General Information

General Information Comment Organism
metabolism the salvage of HMP is accomplished by its phosphorylation to HMP-P by the HMP kinase activity (HMPK) Salmonella enterica subsp. enterica serovar Typhimurium
metabolism the salvage of HMP is accomplished by its phosphorylation to HMP-P by the HMP kinase activity (HMPK) Thermus thermophilus
additional information molecular dynamics simulation shows that Salmonella typhimurium StHMPPK and Thermus thermophilus TtHMPPK have striking differences in their conformational flexibility, which can be correlated with the hydrophobic packing and electrostatic interaction network given mainly by salt bridge bonds, but interestingly not by the number of hydrogen bond interactions as reported for other thermophilic enzymes, stucture comparisons, all-atom explicit solvent molecular dynamics simulation of StHMPPK and TtHMPPK, overview Salmonella enterica subsp. enterica serovar Typhimurium
additional information molecular dynamics simulation shows that Salmonella typhimurium StHMPPK and Thermus thermophilus TtHMPPK have striking differences in their conformational flexibility, which can be correlated with the hydrophobic packing and electrostatic interaction network given mainly by salt bridge bonds, but interestingly not by the number of hydrogen bond interactions as reported for other thermophilic enzymes, stucture comparisons, all-atom explicit solvent molecular dynamics simulation of StHMPPK and TtHMPPK, overview Thermus thermophilus
physiological function the hydroxymethylpyrimidine phosphate kinases (HMPPK) encoded by the thiD gene are involved in the thiamine biosynthesis pathway, can perform two consecutive phosphorylations of 4-amino-5-hydroxymethyl-2-methyl pyrimidine (HMP) and are found in thermophilic and mesophilic bacteria. The enzyme StHMPPK is able to catalyze two related reactions in consecutive steps, besides the phosphorylation of HMP to give HMP-P, the same enzyme catalyzes the phosphorylation of its reaction product to generate hydroxymethylpyrimidine pyrophosphate (HMPPK, EC 2.7.4.7) being this last reaction an essential step for the biosynthesis of thiamin diphosphate Salmonella enterica subsp. enterica serovar Typhimurium
physiological function the hydroxymethylpyrimidine phosphate kinases (HMPPK) encoded by the thiD gene are involved in the thiamine biosynthesis pathway, can perform two consecutive phosphorylations of 4-amino-5-hydroxymethyl-2-methyl pyrimidine (HMP) and are found in thermophilic and mesophilic bacteria. The enzyme TtHMPPK is able to catalyze two related reactions in consecutive steps, besides the phosphorylation of HMP to give HMP-P, the same enzyme catalyzes the phosphorylation of its reaction product to generate hydroxymethylpyrimidine pyrophosphate (HMPPK, EC 2.7.4.7) being this last reaction an essential step for the biosynthesis of thiamin diphosphate Thermus thermophilus
physiological function the enzyme catalyzes an essential step for the biosynthesis of thiamin pyrophosphate Salmonella enterica subsp. enterica serovar Typhimurium
physiological function the enzyme catalyzes an essential step for the biosynthesis of thiamin pyrophosphate Thermus thermophilus