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 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 | Comment | Organism | Structure |
---|---|---|---|
Mg2+ | required | Salmonella enterica subsp. enterica serovar Typhimurium | |
Mg2+ | required | Thermus thermophilus |
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 | 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 (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 | 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 | 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 | 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 | 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 Maximum [°C] | Comment | Organism |
---|---|---|---|
25 | - |
assay at | Salmonella enterica subsp. enterica serovar Typhimurium |
25 | - |
assay at | Thermus thermophilus |
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 Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
7 | - |
assay at | Salmonella enterica subsp. enterica serovar Typhimurium |
7 | - |
assay at | Thermus thermophilus |
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 |