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Literature summary for 2.7.4.26 extracted from
- Improving the catalytic activity of isopentenyl phosphate kinase through protein coevolution analysis (2016), Sci. Rep., 6, 24117.
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene ipk, recombinant expression of His-tagged codon-optimized wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) | Methanocaldococcus jannaschii |
| gene ipk, recombinant expression of His-tagged codon-optimized wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) | Thermoplasma acidophilum |
| gene ipk, recombinant expression of His-tagged codon-optimized wild-type and mutant enzymes in Escherichia coli strain BL21(DE3) | Methanothermobacter thermautotrophicus |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| A53V | site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme, the mutant shows increased activity compared to the wild-type enzyme | Thermoplasma acidophilum |
| G44A | site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme | Thermoplasma acidophilum |
| G45A | site-directed mutagenesis, the mutant shows increased activity compared to the wild-type enzyme | Thermoplasma acidophilum |
| G49A | site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme | Thermoplasma acidophilum |
| I140V | site-directed mutagenesis, the mutant shows highly increased activity compared to the wild-type enzyme | Thermoplasma acidophilum |
| K204A | site-directed mutagenesis, the mutant shows highly increased activity compared to the wild-type enzyme | Thermoplasma acidophilum |
| K204G | site-directed mutagenesis, the mutant shows increased activity compared to the wild-type enzyme | Thermoplasma acidophilum |
| additional information | analysis and evaluation of a method of rational design that is able to identify desired mutants by analyzing the coevolution of protein sequence, use for evolving an archaeal isopentenyl phosphate kinase that can convert dimethylallyl alcohol into precursor of isoprenoids, overview. Site-directed mutagenesis of sites idetified as coevolved in the IPK family proteins | Thermoplasma acidophilum |
| V130A | site-directed mutagenesis, the mutant shows increased activity compared to the wild-type enzyme | Thermoplasma acidophilum |
| V73I | site-directed mutagenesis, the mutant shows highly increased activity compared to the wild-type enzyme | Thermoplasma acidophilum |
| V73I/K204G | site-directed mutagenesis, the mutant shows highly increased activity compared to the wild-type enzyme | Thermoplasma acidophilum |
| V73I/Y141V | site-directed mutagenesis, the mutant shows highly increased activity compared to the wild-type enzyme | Thermoplasma acidophilum |
| V73I/Y141V/K204G | site-directed mutagenesis, the mutant shows highly increased activity compared to the wild-type enzyme | Thermoplasma acidophilum |
| V73T | site-directed mutagenesis, the mutant shows increased activity compared to the wild-type enzyme | Thermoplasma acidophilum |
| Y141L | site-directed mutagenesis, the mutant shows increased activity compared to the wild-type enzyme | Thermoplasma acidophilum |
| Y141V | site-directed mutagenesis, the mutant shows highly increased activity compared to the wild-type enzyme | Thermoplasma acidophilum |
| Y141V/K204G | site-directed mutagenesis, the mutant shows highly increased activity compared to the wild-type enzyme | Thermoplasma acidophilum |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Mg2+ | required | Methanocaldococcus jannaschii |  |
| Mg2+ | required | Thermoplasma acidophilum | |
| Mg2+ | required | Methanothermobacter thermautotrophicus | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + dimethylallyl phosphate | Methanocaldococcus jannaschii | - |
ADP + dimethylallyl diphosphate | - |
? | |
| ATP + dimethylallyl phosphate | Thermoplasma acidophilum | - |
ADP + dimethylallyl diphosphate | - |
? | |
| ATP + dimethylallyl phosphate | Methanothermobacter thermautotrophicus | - |
ADP + dimethylallyl diphosphate | - |
? | |
| ATP + dimethylallyl phosphate | Methanothermobacter thermautotrophicus DSM 1053 | - |
ADP + dimethylallyl diphosphate | - |
? | |
| ATP + dimethylallyl phosphate | Methanocaldococcus jannaschii DSM 2661 | - |
ADP + dimethylallyl diphosphate | - |
? | |
| ATP + isopentenyl phosphate | Methanocaldococcus jannaschii | - |
ADP + isopentenyl diphosphate | - |
? | |
| ATP + isopentenyl phosphate | Thermoplasma acidophilum | - |
ADP + isopentenyl diphosphate | - |
? | |
| ATP + isopentenyl phosphate | Methanothermobacter thermautotrophicus | - |
ADP + isopentenyl diphosphate | - |
? | |
| ATP + isopentenyl phosphate | Methanothermobacter thermautotrophicus DSM 1053 | - |
ADP + isopentenyl diphosphate | - |
? | |
| ATP + isopentenyl phosphate | Methanocaldococcus jannaschii DSM 2661 | - |
ADP + isopentenyl diphosphate | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Methanocaldococcus jannaschii | Q60352 | gene ipk | - |
| Methanocaldococcus jannaschii DSM 2661 | Q60352 | gene ipk | - |
| Methanothermobacter thermautotrophicus | O26153 | gene ipk | - |
| Methanothermobacter thermautotrophicus DSM 1053 | O26153 | gene ipk | - |
| Thermoplasma acidophilum | Q9HLX1 | gene ipk | - |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, dialysis, and ultrafiltration | Methanocaldococcus jannaschii |
| recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, dialysis, and ultrafiltration | Thermoplasma acidophilum |
| recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, dialysis, and ultrafiltration | Methanothermobacter thermautotrophicus |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + dimethylallyl alcohol | molecular docking analysis indicates that dimethylallyl alcohol is a substrate for the archaeal IPK, although with low activity for the wild-type. The mutant enzymes show increased activity with dimethylallyl alcohol as substrate | Thermoplasma acidophilum | ADP + dimethylallyl phosphate | - |
? | |
| ATP + dimethylallyl alcohol | molecular docking analysis indicates that dimethylallyl alcohol is a substrate for the archaeal IPK, although with low activity for the wild-type. The mutant enzymes show increased activity with dimethylallyl alcohol as substrate | Methanothermobacter thermautotrophicus | ADP + dimethylallyl phosphate | - |
? | |
| ATP + dimethylallyl alcohol | molecular docking analysis indicates that dimethylallyl alcohol is a substrate for the archaeal IPK, although with low activity for thwild-type. The mutant enzymes show increased activity with dimethylallyl alcohol as substrate | Methanocaldococcus jannaschii | ADP + dimethylallyl phosphate | - |
? | |
| ATP + dimethylallyl alcohol | molecular docking analysis indicates that dimethylallyl alcohol is a substrate for the archaeal IPK, although with low activity for the wild-type. The mutant enzymes show increased activity with dimethylallyl alcohol as substrate | Methanothermobacter thermautotrophicus DSM 1053 | ADP + dimethylallyl phosphate | - |
? | |
| ATP + dimethylallyl alcohol | molecular docking analysis indicates that dimethylallyl alcohol is a substrate for the archaeal IPK, although with low activity for thwild-type. The mutant enzymes show increased activity with dimethylallyl alcohol as substrate | Methanocaldococcus jannaschii DSM 2661 | ADP + dimethylallyl phosphate | - |
? | |
| ATP + dimethylallyl phosphate | - |
Methanocaldococcus jannaschii | ADP + dimethylallyl diphosphate | - |
? | |
| ATP + dimethylallyl phosphate | - |
Thermoplasma acidophilum | ADP + dimethylallyl diphosphate | - |
? | |
| ATP + dimethylallyl phosphate | - |
Methanothermobacter thermautotrophicus | ADP + dimethylallyl diphosphate | - |
? | |
| ATP + dimethylallyl phosphate | - |
Methanothermobacter thermautotrophicus DSM 1053 | ADP + dimethylallyl diphosphate | - |
? | |
| ATP + dimethylallyl phosphate | - |
Methanocaldococcus jannaschii DSM 2661 | ADP + dimethylallyl diphosphate | - |
? | |
| ATP + isopentenyl phosphate | - |
Methanocaldococcus jannaschii | ADP + isopentenyl diphosphate | - |
? | |
| ATP + isopentenyl phosphate | - |
Thermoplasma acidophilum | ADP + isopentenyl diphosphate | - |
? | |
| ATP + isopentenyl phosphate | - |
Methanothermobacter thermautotrophicus | ADP + isopentenyl diphosphate | - |
? | |
| ATP + isopentenyl phosphate | - |
Methanothermobacter thermautotrophicus DSM 1053 | ADP + isopentenyl diphosphate | - |
? | |
| ATP + isopentenyl phosphate | - |
Methanocaldococcus jannaschii DSM 2661 | ADP + isopentenyl diphosphate | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| IPK | - |
Methanocaldococcus jannaschii |
| IPK | - |
Thermoplasma acidophilum |
| IPK | - |
Methanothermobacter thermautotrophicus |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 37 | - |
assay at | Methanocaldococcus jannaschii |
| 37 | - |
assay at | Thermoplasma acidophilum |
| 37 | - |
assay at | Methanothermobacter thermautotrophicus |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 8 | - |
assay at | Methanocaldococcus jannaschii |
| 8 | - |
assay at | Thermoplasma acidophilum |
| 8 | - |
assay at | Methanothermobacter thermautotrophicus |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| ATP | - |
Methanocaldococcus jannaschii | |
| ATP | - |
Thermoplasma acidophilum | |
| ATP | - |
Methanothermobacter thermautotrophicus | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| metabolism | the enzyme is involved in the mevalonate pathway forming the building blocks for isoprenoid biosynthesis, overview | Methanocaldococcus jannaschii |
| metabolism | the enzyme is involved in the mevalonate pathway forming the building blocks for isoprenoid biosynthesis, overview | Thermoplasma acidophilum |
| metabolism | the enzyme is involved in the mevalonate pathway forming the building blocks for isoprenoid biosynthesis, overview | Methanothermobacter thermautotrophicus |
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