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Literature summary for 5.1.3.1 extracted from
- 6-Phosphofructokinase and ribulose-5-phosphate 3-epimerase in methylotrophic Bacillus methanolicus ribulose monophosphate cycle (2017), Appl. Microbiol. Biotechnol., 101, 4185-4200 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene rpe1 or rpeP is plasmid-encoded in Bacillus methanolicus strain MGA3, DNA and amino acid sequence determination and analysis, genomic organization, sequence comparisons and phylogenetic tree, real-time PCR enzyme expression analysis, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) | Bacillus methanolicus |
| gene rpe1 or rpeP is plasmid-encoded in Bacillus methanolicus strain PB1, DNA and amino acid sequence determination and analysis, genomic organization, sequence comparisons and phylogenetic tree, real-time PCR enzyme expression analysis, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) | Bacillus methanolicus |
| gene rpe2 or rpeC is encoded on the chromosome in Bacillus methanolicus strain MGA3, DNA and amino acid sequence determination and analysis, genomic organization, sequence comparisons and phylogenetic tree, real-time PCR enzyme expression analysis, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) | Bacillus methanolicus |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| Co2+ | causes over 80% inhibition at 5 mM; causes over 80% inhibition at 5 mM; causes over 80% inhibition at 5 mM | Bacillus methanolicus |  |
| Mg2+ | causes only slight inhibition at 5 mM; causes only slight inhibition at 5 mM; causes only slight inhibition at 5 mM | Bacillus methanolicus | |
| Mn2+ | causes 20% inhibition at 5 mM; causes 20% inhibition at 5 mM; causes 20% inhibition at 5 mM | Bacillus methanolicus | |
| additional information | EDTA does not affect the enzyme at 5 mM; EDTA does not affect the enzyme at 5 mM; EDTA does not affect the enzyme at 5 mM | Bacillus methanolicus | |
| Zn2+ | causes complete inhibition at 5 mM; causes complete inhibition at 5 mM; causes complete inhibition at 5 mM | Bacillus methanolicus | |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| additional information | - |
additional information | Michaelis-Menten kinetics | Bacillus methanolicus | |
| 0.056 | - |
D-ribulose 5-phosphate | recombinant enzyme, pH 7.7, 25°C | Bacillus methanolicus | |
| 0.058 | - |
D-ribulose 5-phosphate | recombinant enzyme, pH 7.7, 25°C | Bacillus methanolicus | |
| 0.075 | - |
D-ribulose 5-phosphate | recombinant enzyme, pH 7.7, 25°C | Bacillus methanolicus | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| D-Ribulose 5-phosphate | Bacillus methanolicus | - |
D-Xylulose 5-phosphate | - |
r | |
| D-Ribulose 5-phosphate | Bacillus methanolicus MGA3 / ATCC53907 | - |
D-Xylulose 5-phosphate | - |
r | |
| D-Ribulose 5-phosphate | Bacillus methanolicus PB1 / NCIMB13113 | - |
D-Xylulose 5-phosphate | - |
r | |
| D-Ribulose 5-phosphate | Bacillus methanolicus PB1 | - |
D-Xylulose 5-phosphate | - |
r | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Bacillus methanolicus | I3DTN4 | - |
- |
| Bacillus methanolicus | I3DTP3 | - |
- |
| Bacillus methanolicus | I3DZ65 | - |
- |
| Bacillus methanolicus MGA3 / ATCC53907 | I3DTN4 | - |
- |
| Bacillus methanolicus MGA3 / ATCC53907 | I3DZ65 | - |
- |
| Bacillus methanolicus PB1 / NCIMB13113 | I3DTP3 | - |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and diaylsis | Bacillus methanolicus |
Source Tissue
| Source Tissue | Comment | Organism | Textmining |
|---|---|---|---|
| additional information | Bacillus methanolicus has a growth optimum at 50°C and uses the ribulose monophosphate (RuMP) cycle for methanol assimilation | Bacillus methanolicus | - |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| D-Ribulose 5-phosphate | - |
Bacillus methanolicus | D-Xylulose 5-phosphate | - |
r | |
| D-Ribulose 5-phosphate | - |
Bacillus methanolicus MGA3 / ATCC53907 | D-Xylulose 5-phosphate | - |
r | |
| D-Ribulose 5-phosphate | - |
Bacillus methanolicus PB1 / NCIMB13113 | D-Xylulose 5-phosphate | - |
r | |
| D-Ribulose 5-phosphate | - |
Bacillus methanolicus PB1 | D-Xylulose 5-phosphate | - |
r | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| hexamer | - |
Bacillus methanolicus |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| D-ribulose-5-phosphate-3-epimerase | - |
Bacillus methanolicus |
| RPE | - |
Bacillus methanolicus |
| rpe1 | - |
Bacillus methanolicus |
| rpe1-MGA3 | - |
Bacillus methanolicus |
| rpe1-PB1 | - |
Bacillus methanolicus |
| rpe2 | - |
Bacillus methanolicus |
| rpe2-MGA3 | - |
Bacillus methanolicus |
| rpeC | - |
Bacillus methanolicus |
| rpeP | - |
Bacillus methanolicus |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 25 | - |
assay at | Bacillus methanolicus |
Temperature Stability [°C]
| Temperature Stability Minimum [°C] | Temperature Stability Maximum [°C] | Comment | Organism |
|---|---|---|---|
| additional information | - |
presence of ribulose 5-phosphate reduces the melting temperatures of the RPE enzymes significantly by up to 10°C, while addition of Mg2+ has no effect on RPE thermostability | Bacillus methanolicus |
| 27 | - |
purified recombinant His-tagged RPE2-MGA3 is completely stable at 27°C after 2 h | Bacillus methanolicus |
| 27 | 80 | after 2 h, purified recombinant His-tagged RPE1-MGA3 is completely stable at up to 65°C, and retains 60% activity at 80°C | Bacillus methanolicus |
| 27 | 80 | after 2 h, purified recombinant His-tagged RPE1-PB1 is completely stable at up to 65°C, with slightly reduced activity at 27°C, and about 70% reduced activity at 80°C | Bacillus methanolicus |
| 37 | - |
purified recombinant His-tagged RPE2-MGA3 retains 95% activity after 2 h | Bacillus methanolicus |
| 50 | - |
purified recombinant His-tagged RPE2-MGA3 retains 90% activity after 2 h | Bacillus methanolicus |
| 65 | - |
purified recombinant His-tagged RPE2-MGA3 retains 20% activity after 2 h | Bacillus methanolicus |
| 80 | - |
purified recombinant His-tagged RPE2-MGA3 retains below 5% activity after 2 h | Bacillus methanolicus |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 7.7 | - |
assay at | Bacillus methanolicus |
Expression
| Organism | Comment | Expression |
|---|---|---|
| Bacillus methanolicus | transcription of the plasmid-encoded gene is 10-15fold upregulated in cells growing on methanol compared to mannitol, while the chromosomal gene is transcribed at similar levels under both conditions | additional information |
| Bacillus methanolicus | transcription of the plasmid-encoded gene is 10-15fold upregulated in cells growing on methanol compared to mannitol | up |
| Bacillus methanolicus | transcription of the plasmid-encoded gene is 10-15fold upregulated in cells growing on methanol compared to mannitol, while the chromosomal gene is transcribed at similar levels under both conditions | up |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | Bacillus methanolicus wild-type strain MGA3 possesses two putative rpe genes encoded on plasmid pBM19 (rpe1-MGA3) and on the chromosome (rpe2-MGA3). The Rpe2-MGA3 enzyme shows a 2fold lower Vmax and a significantly reduced thermostability compared to the Rpe1 protein | Bacillus methanolicus |
| evolution | Bacillus methanolicus wild-type strain PB1 possesses one putative rpe gene encoded on plasmid pBM20 (rpe1-PB1) | Bacillus methanolicus |
| metabolism | D-ribulose-5-phosphate-3-epimerase (RPE) is involved in the ribulose monophosphate (RuMP) cycle in Bacillus methanolicus. Strains MGA3 and PB1 exert alternative solutions to plasmid-dependent methylotrophy, including genetic organization, regulation, and biochemistry of RuMP cycle enzymes, overview | Bacillus methanolicus |
| physiological function | Bacillus methanolicus uses the ribulose monophosphate (RuMP) cycle for methanol assimilation involving the enzyme D-ribulose-5-phosphate-3-epimerase (RPE). RPE catalyses the interconversion between D-xylulose-5-phosphate and D-ribulose-5-phosphate, which is the pentose precursor for nucleotide synthesis. In addition to the RuMP cycle, it is involved in the pentose phosphate pathway (PPP). It is presumably not essential for the metabolism of glucose or mannitol | Bacillus methanolicus |
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