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Literature summary for 2.7.1.47 extracted from
- Molecular identification of D-ribulokinase in budding yeast and mammals (2017), J. Biol. Chem., 292, 1005-1028 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene FGGY, sequence comparisons and phylogenetic tree, recombinant expression of N-terminally His-tagged FGGY in Escherichia coli | Homo sapiens |
| gene YDR109C, sequence comparisons and phylogenetic tree, recombinant expression of N-terminally His-tagged Ydr109c in Escherichia coli | Saccharomyces cerevisiae |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| additional information | generation of human FGGY deletion mutant HEK293 cells, when ribitol is added to the cultivation medium, FGGY silencing leads to ribulose accumulation | Homo sapiens |
| additional information | untargeted metabolomics analysis of an Saccharomyces cerevisiae deletion mutant of YDR109C reveals ribulose as one of the metabolites with the most significantly changed intracellular concentration as compared with a wild-type strain. Effect of YDR109C deletion on metabolite level other than ribulose and ribitol, overview | Saccharomyces cerevisiae |
General Stability
| General Stability | Organism |
|---|---|
| the human recombinant His-tagged FGGY protein is, unlike its yeast homologue, very stable | Homo sapiens |
| the yeast recombinant His-tagged Ydr109c protein is, unlike its human homologue, very unstable | Saccharomyces cerevisiae |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| additional information | - |
additional information | Michaelis-Menten kinetics | Saccharomyces cerevisiae | |
| 0.097 | - |
D-ribulose | pH 7.1, 30°C, recombinant enzyme | Homo sapiens |  |
| 0.217 | - |
D-ribulose | pH 7.1, 30°C, recombinant enzyme | Saccharomyces cerevisiae | |
| 1.468 | - |
ribitol | pH 7.1, 30°C, recombinant enzyme | Homo sapiens | |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Mg2+ | required | Saccharomyces cerevisiae | |
| Mg2+ | required | Homo sapiens | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + D-ribulose | Saccharomyces cerevisiae | - |
ADP + D-ribulose 5-phosphate | - |
? | |
| ATP + D-ribulose | Homo sapiens | - |
ADP + D-ribulose 5-phosphate | - |
? | |
| ATP + D-ribulose | Saccharomyces cerevisiae ATCC 204508 | - |
ADP + D-ribulose 5-phosphate | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Homo sapiens | Q96C11 | - |
- |
| Saccharomyces cerevisiae | Q04585 | - |
- |
| Saccharomyces cerevisiae ATCC 204508 | Q04585 | - |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant N-terminally His-tagged FGGY from Escherichia coli by nickel affinity chromatography | Homo sapiens |
| recombinant N-terminally His-tagged Ydr109c from Escherichia coli by nickel affinity chromatography | Saccharomyces cerevisiae |
Source Tissue
| Source Tissue | Comment | Organism | Textmining |
|---|---|---|---|
| HEK-293 cell | - |
Homo sapiens | - |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + D-ribulose | - |
Saccharomyces cerevisiae | ADP + D-ribulose 5-phosphate | - |
? | |
| ATP + D-ribulose | - |
Homo sapiens | ADP + D-ribulose 5-phosphate | - |
? | |
| ATP + D-ribulose | - |
Saccharomyces cerevisiae ATCC 204508 | ADP + D-ribulose 5-phosphate | - |
? | |
| ATP + L-ribulose | 8% activity compared to D-ribulose | Homo sapiens | ADP + L-ribulose 5-phosphate | - |
? | |
| ATP + ribitol | 21% activity compared to D-ribulose | Homo sapiens | ADP + ribitol phosphate | - |
? | |
| additional information | the FGGY protein shows a clear substrate preference for D-ribulose over a range of other sugars and sugar derivatives tested, including L-ribulose. Recombinant human FGGY protein specifically converts D-ribulose to D-ribulose 5-phosphate in the presence of ATP. No or poor activity with D-xylulose, L-xylulose, D-glucose, arabitol, erythritol, L-arabinose, D-arabinose, D-ribose, glycerol, D-ribulose 5-phosphate, gluconate, 2-deoxy-D-ribose, D-lyxose, D-ribose 5-phosphate, D-mannitol, and D-ribose 1-phosphate | Homo sapiens | ? | - |
- |
|
| additional information | the Ydr109c protein shows a clear specificity for D-ribulose over a range of other sugars and sugar derivatives tested, including L-ribulose. Recombinant yeast Ydr109c specifically converts D-ribulose to D-ribulose 5-phosphate in the presence of ATP. No activity with L-ribulose, ribitol, D-xylulose, L-xylulose, D-glucose, arabitol, erythritol, L-arabinose, D-arabinose, D-ribose, glycerol, D-ribulose 5-phosphate, gluconate, 2-deoxy-D-ribose, D-lyxose, D-ribose 5-phosphate, D-mannitol, and D-ribose 1-phosphate | Saccharomyces cerevisiae | ? | - |
- |
|
| additional information | the Ydr109c protein shows a clear specificity for D-ribulose over a range of other sugars and sugar derivatives tested, including L-ribulose. Recombinant yeast Ydr109c specifically converts D-ribulose to D-ribulose 5-phosphate in the presence of ATP. No activity with L-ribulose, ribitol, D-xylulose, L-xylulose, D-glucose, arabitol, erythritol, L-arabinose, D-arabinose, D-ribose, glycerol, D-ribulose 5-phosphate, gluconate, 2-deoxy-D-ribose, D-lyxose, D-ribose 5-phosphate, D-mannitol, and D-ribose 1-phosphate | Saccharomyces cerevisiae ATCC 204508 | ? | - |
- |
|
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| ? | x * 63700, recombinant His-tagged FGGY, SDS-PAGE | Homo sapiens |
| ? | x * 82800, recombinant His-tagged Ydr109c, SDS-PAGE | Saccharomyces cerevisiae |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| FGGY | - |
Homo sapiens |
| Ydr109c protein | - |
Saccharomyces cerevisiae |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 30 | - |
assay at | Saccharomyces cerevisiae |
| 30 | - |
assay at | Homo sapiens |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 7.1 | - |
assay at | Saccharomyces cerevisiae |
| 7.1 | - |
assay at | Homo sapiens |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | the enzyme belongs to the broadly conserved FGGY family of carbohydrate kinases. Yeast Ydr109c and human FGGY are homologues of a proteobacterial D-ribulokinase involved in ribitol metabolism | Saccharomyces cerevisiae |
| evolution | the enzyme belongs to the broadly conserved FGGY family of carbohydrate kinases. Yeast Ydr109c and human FGGY are homologues of a proteobacterial D-ribulokinase involved in ribitol metabolism | Homo sapiens |
| malfunction | in human FGGY deletion mutant HEK293 cells, ribulose can only be detected when ribitol is added to the cultivation medium. Under this condition, FGGY silencing leads to ribulose accumulation | Homo sapiens |
| malfunction | untargeted metabolomics analysis of an Saccharomyces cerevisiae deletion mutant of YDR109C reveals ribulose as one of the metabolites with the most significantly changed intracellular concentration as compared with a wild-type strain | Saccharomyces cerevisiae |
| additional information | the enzyme contains a 5-residue D-ribulokinase signature motif (TCSLV). Structural homology modeling of human D-ribulokinase and definition of a D-ribulokinase signature motif, using template structures from PDB entries 3GG4 chain A and 3L0Q chain A, respectively, of Yersinia pseudotuberculosis D-ribulokinase | Homo sapiens |
| additional information | the enzyme contains a 5-residue D-ribulokinase signature motif (TCSLV). Structural homology modeling of yeast D-ribulokinase and definition of a D-ribulokinase signature motif, using template structures from PDB entries 3GG4 chain A and 3L0Q chain A, respectively, of Yersinia pseudotuberculosis D-ribulokinase | Saccharomyces cerevisiae |
| physiological function | the FGGY protein might act as a metabolite repair enzyme, serving to re-phosphorylate free D-ribulose generated by promiscuous phosphatases from D-ribulose 5-phosphate | Homo sapiens |
| physiological function | the Ydr109c protein might act as a metabolite repair enzyme, serving to re-phosphorylate free D-ribulose generated by promiscuous phosphatases from D-ribulose 5-phosphate | Saccharomyces cerevisiae |
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