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Literature summary for 2.7.4.7 extracted from
- A strictly monofunctional bacterial hydroxymethylpyrimidine phosphate kinase precludes damaging errors in thiamin biosynthesis (2017), Biochem. J., 474, 2887-2895 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene thiD2, functional complementation of an Escherichia coli DELTAthiD knockout mutant strain, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21-CodonPlus (DE3)-RIPL | Campylobacter concisus |
| gene thiD2, functional complementation of an Escherichia coli DELTAthiD knockout mutant strain, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21-CodonPlus (DE3)-RIPL | Sulfurimonas denitrificans |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| additional information | complementation of the Escherichia coli DELTA thiD knockout mutant is possible by heterologous expression of gene ThiD2. Strains expressing a standalone ThiD2 protein are 10fold more resistant than wild-type against bacimethrin toxicity. ThiD2 genes confer resistance to bacimethrin | Campylobacter concisus |
| additional information | complementation of the Escherichia coli DELTA thiD knockout mutant is possible by heterologous expression of gene ThiD2. Strains expressing a standalone ThiD2 protein are 10fold more resistant than wild-type against bacimethrin toxicity. ThiD2 genes confer resistance to bacimethrin | Sulfurimonas denitrificans |
| additional information | construction of a thiD knockout mutant strain, complementation of the Escherichia coli DELTA thiD knockout mutant is possible by heterologous expression of gene ThiD2, ThiD2 proteins catalyze phosphorylation of HMP monophosphate, but not of HMP or its toxic analogues and damage products such as bacimethrin and 5-(hydroxymethyl)-2-methylpyrimidin-4-ol. As strictly monofunctional HMP monophosphate kinases (EC 2.7.4.7), ThiD2 proteins eliminate a potentially fatal vulnerability of canonical ThiD, at the cost of the ability to reclaim HMP formed by thiamin turnover | Escherichia coli |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.00232 | - |
4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine | pH 7.5, temperature not specified in the publication, recombinant enzyme ThiD | Escherichia coli |  |
| 0.00512 | - |
4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine | pH 7.5, temperature not specified in the publication, recombinant enzyme ThiD2 | Sulfurimonas denitrificans | |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Mg2+ | required | Escherichia coli | |
| Mg2+ | required | Campylobacter concisus | |
| Mg2+ | required | Sulfurimonas denitrificans | |
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 | Escherichia coli | - |
ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine | - |
? | |
| ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine | Campylobacter concisus | - |
ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine | - |
? | |
| ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine | Sulfurimonas denitrificans | - |
ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine | - |
? | |
| ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine | Sulfurimonas denitrificans DSM 1251 | - |
ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine | - |
? | |
| ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine | Campylobacter concisus 13826 | - |
ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine | - |
? | |
| ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine | Sulfurimonas denitrificans ATCC 33889 | - |
ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Campylobacter concisus | A7ZG21 | - |
- |
| Campylobacter concisus 13826 | A7ZG21 | - |
- |
| Escherichia coli | P76422 | - |
- |
| Escherichia coli BW25113 | P76422 | - |
- |
| Sulfurimonas denitrificans | Q30NV2 | i.e. Thiomicrospira denitrificans strain ATCC 33889 / DSM 1251 | - |
| Sulfurimonas denitrificans ATCC 33889 | Q30NV2 | i.e. Thiomicrospira denitrificans strain ATCC 33889 / DSM 1251 | - |
| Sulfurimonas denitrificans DSM 1251 | Q30NV2 | i.e. Thiomicrospira denitrificans strain ATCC 33889 / DSM 1251 | - |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant His-tagged enzyme from Escherichia coli strain BL21-CodonPlus (DE3)-RIPL by nickel affinity chromatography and desalting gel filtration | Campylobacter concisus |
| recombinant His-tagged enzyme from Escherichia coli strain BL21-CodonPlus (DE3)-RIPL by nickel affinity chromatography and desalting gel filtration | Sulfurimonas denitrificans |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine | - |
Escherichia coli | ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine | - |
? | |
| ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine | - |
Campylobacter concisus | ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine | - |
? | |
| ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine | - |
Sulfurimonas denitrificans | ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine | - |
? | |
| ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine | - |
Sulfurimonas denitrificans DSM 1251 | ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine | - |
? | |
| ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine | - |
Campylobacter concisus 13826 | ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine | - |
? | |
| ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine | - |
Sulfurimonas denitrificans ATCC 33889 | ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine | - |
? | |
| additional information | the enzyme performs double phosphorylation on 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) | Escherichia coli | ? | - |
- |
|
| additional information | the enzyme performs double phosphorylation on 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) | Campylobacter concisus | ? | - |
- |
|
| additional information | the enzyme performs double phosphorylation on 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) | Sulfurimonas denitrificans | ? | - |
- |
|
| additional information | the enzyme performs double phosphorylation on 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) | Sulfurimonas denitrificans DSM 1251 | ? | - |
- |
|
| additional information | the enzyme performs double phosphorylation on 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) | Campylobacter concisus 13826 | ? | - |
- |
|
| additional information | the enzyme performs double phosphorylation on 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) | Sulfurimonas denitrificans ATCC 33889 | ? | - |
- |
|
| additional information | the enzyme performs double phosphorylation on 4-amino-5-hydroxymethyl-2-methylpyrimidine (HMP) | Escherichia coli BW25113 | ? | - |
- |
|
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| CCC13826_0338 | locus name | Campylobacter concisus |
| CcThiD2 | - |
Campylobacter concisus |
| HMP-P kinase | - |
Escherichia coli |
| HMP-P kinase | - |
Campylobacter concisus |
| HMP-P kinase | - |
Sulfurimonas denitrificans |
| hydroxymethylpyrimidine phosphate kinase | - |
Escherichia coli |
| hydroxymethylpyrimidine phosphate kinase | - |
Campylobacter concisus |
| hydroxymethylpyrimidine phosphate kinase | - |
Sulfurimonas denitrificans |
| More | see also EC 2.7.1.49 | Escherichia coli |
| Suden_2055 | locus name | Sulfurimonas denitrificans |
| TdThiD2 | - |
Sulfurimonas denitrificans |
| thiamine phosphate synthase | UniProt | Campylobacter concisus |
| ThiD | - |
Escherichia coli |
| ThiD2 | - |
Campylobacter concisus |
| ThiD2 | - |
Sulfurimonas denitrificans |
| ThiD2 domain-containing protein | UniProt | Sulfurimonas denitrificans |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.011 | - |
4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine | pH 7.5, temperature not specified in the publication, recombinant enzyme ThiD2 | Sulfurimonas denitrificans | |
| 0.034 | - |
4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine | pH 7.5, temperature not specified in the publication, recombinant enzyme ThiD | Escherichia coli | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 7.5 | - |
assay at | Escherichia coli |
| 7.5 | - |
assay at | Campylobacter concisus |
| 7.5 | - |
assay at | Sulfurimonas denitrificans |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | ThiD is a member of the ribokinase family, but differs from other members in catalyzing two consecutive phosphorylations. The other members of the family catalyze only the phosphorylation of a hydroxymethyl group to give a monophosphate, i.e. the equivalent of the HMP kinase reaction. The HMP kinase activity of ThiD is hence presumably ancestral and the HMP-P kinase activity is an evolutionary novelty | Escherichia coli |
| metabolism | the enzyme takes part in the bacterial thiamin biosynthesis and salvage pathways, overview | Escherichia coli |
| metabolism | the enzyme takes part in the bacterial thiamin biosynthesis and salvage pathways, overview | Campylobacter concisus |
| metabolism | the enzyme takes part in the bacterial thiamin biosynthesis and salvage pathways, overview | Sulfurimonas denitrificans |
| physiological function | the bifunctional canonical kinase (ThiD) that converts the thiamin biosynthesis intermediate hydroxymethylpyrimidine (HMP) monophosphate into the diphosphate (EC 2.7.4.7) can also very efficiently convert free HMP into the monophosphate (EC 2.7.1.49) in prokaryotes, plants, and fungi. This HMP kinase activity enables salvage of HMP, but it is not substrate-specific and so allows toxic HMP analogues and damage products to infiltrate the thiamin biosynthesis pathway | Escherichia coli |
| physiological function | ThiD2 proteins catalyze phosphorylation of HMP monophosphate, but not of HMP or its toxic analogues and damage products such as bacimethrin and 5-(hydroxymethyl)-2-methylpyrimidin-4-ol. As strictly monofunctional HMP monophosphate kinases (EC 2.7.4.7), ThiD2 proteins eliminate a potentially fatal vulnerability of canonical ThiD, at the cost of the ability to reclaim HMP formed by thiamin turnover. ThiD2 genes confer resistance to bacimethrin | Campylobacter concisus |
| physiological function | ThiD2 proteins catalyze phosphorylation of HMP monophosphate, but not of HMP or its toxic analogues and damage products such as bacimethrin and 5-(hydroxymethyl)-2-methylpyrimidin-4-ol. As strictly monofunctional HMP monophosphate kinases (EC 2.7.4.7), ThiD2 proteins eliminate a potentially fatal vulnerability of canonical ThiD, at the cost of the ability to reclaim HMP formed by thiamin turnover. ThiD2 genes confer resistance to bacimethrin | Sulfurimonas denitrificans |
kcat/KM [mM/s]
| kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 2.15 | - |
4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine | pH 7.5, temperature not specified in the publication, recombinant enzyme ThiD2 | Sulfurimonas denitrificans | |
| 14.66 | - |
4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine | pH 7.5, temperature not specified in the publication, recombinant enzyme ThiD | Escherichia coli | |
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