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Literature summary extracted from

  • Le, S.B.; Heggeset, T.M.B.; Haugen, T.; Naerdal, I.; Brautaset, T.
    6-Phosphofructokinase and ribulose-5-phosphate 3-epimerase in methylotrophic Bacillus methanolicus ribulose monophosphate cycle (2017), Appl. Microbiol. Biotechnol., 101, 4185-4200 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.7.1.11 expression in Escherichia coli Bacillus methanolicus
5.1.3.1 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
5.1.3.1 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
5.1.3.1 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
5.1.3.22 expression in Escherichia coli Bacillus methanolicus

Inhibitors

EC Number Inhibitors Comment Organism Structure
5.1.3.1 Co2+ causes over 80% inhibition at 5 mM; causes over 80% inhibition at 5 mM; causes over 80% inhibition at 5 mM Bacillus methanolicus
5.1.3.1 Mg2+ causes only slight inhibition at 5 mM; causes only slight inhibition at 5 mM; causes only slight inhibition at 5 mM Bacillus methanolicus
5.1.3.1 Mn2+ causes 20% inhibition at 5 mM; causes 20% inhibition at 5 mM; causes 20% inhibition at 5 mM Bacillus methanolicus
5.1.3.1 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
5.1.3.1 Zn2+ causes complete inhibition at 5 mM; causes complete inhibition at 5 mM; causes complete inhibition at 5 mM Bacillus methanolicus

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
2.7.1.11 0.38
-
 ATP strain PB1, Pfk2, pH 9.0, 30°C Bacillus methanolicus
2.7.1.11 0.39
-
 ATP strain MGA3, Pfk2, pH 9.0, 30°C Bacillus methanolicus
2.7.1.11 0.61
-
 D-fructose 6-phosphate strain MGA3, Pfk2, pH 9.0, 30°C Bacillus methanolicus
2.7.1.11 0.79
-
 D-fructose 6-phosphate strain PB1, Pfk2, pH 9.0, 30°C Bacillus methanolicus
2.7.1.11 0.82
-
 ATP strain MGA3, Pfk1, pH 9.0, 30°C Bacillus methanolicus
2.7.1.11 0.94
-
 D-fructose 6-phosphate strain MGA3, Pfk1, pH 9.0, 30°C Bacillus methanolicus
5.1.3.1 additional information
-
 additional information Michaelis-Menten kinetics Bacillus methanolicus
5.1.3.1 0.056
-
 D-ribulose 5-phosphate recombinant enzyme, pH 7.7, 25°C Bacillus methanolicus
5.1.3.1 0.058
-
 D-ribulose 5-phosphate recombinant enzyme, pH 7.7, 25°C Bacillus methanolicus
5.1.3.1 0.075
-
 D-ribulose 5-phosphate recombinant enzyme, pH 7.7, 25°C Bacillus methanolicus

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.7.1.11 Mg2+ stimulates Bacillus methanolicus
2.7.1.11 Mn2+ stimulates Bacillus methanolicus
5.1.3.22 Mg2+ stimulates Bacillus methanolicus
5.1.3.22 Mn2+ stimulates Bacillus methanolicus

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.7.1.11 ATP + D-fructose 6-phosphate Bacillus methanolicus the enzyme is involved in the ribulose monophosphate cycle ADP + D-fructose 1,6-bisphosphate
-
 ?
2.7.1.11 ATP + D-fructose 6-phosphate Bacillus methanolicus PB1 the enzyme is involved in the ribulose monophosphate cycle ADP + D-fructose 1,6-bisphosphate
-
 ?
2.7.1.11 ATP + D-fructose 6-phosphate Bacillus methanolicus MGA3 the enzyme is involved in the ribulose monophosphate cycle ADP + D-fructose 1,6-bisphosphate
-
 ?
5.1.3.1 D-Ribulose 5-phosphate Bacillus methanolicus
-
 D-Xylulose 5-phosphate
-
 r
5.1.3.1 D-Ribulose 5-phosphate Bacillus methanolicus MGA3 / ATCC53907
-
 D-Xylulose 5-phosphate
-
 r
5.1.3.1 D-Ribulose 5-phosphate Bacillus methanolicus PB1 / NCIMB13113
-
 D-Xylulose 5-phosphate
-
 r
5.1.3.1 D-Ribulose 5-phosphate Bacillus methanolicus PB1
-
 D-Xylulose 5-phosphate
-
 r
5.1.3.22 L-ribulose 5-phosphate Bacillus methanolicus the enzyme is involved in the ribulose monophosphate cycle L-xylulose 5-phosphate
-
 ?
5.1.3.22 L-ribulose 5-phosphate Bacillus methanolicus PB1 / NCIMB13113 the enzyme is involved in the ribulose monophosphate cycle L-xylulose 5-phosphate
-
 ?
5.1.3.22 L-ribulose 5-phosphate Bacillus methanolicus PB1 the enzyme is involved in the ribulose monophosphate cycle L-xylulose 5-phosphate
-
 ?
5.1.3.22 L-ribulose 5-phosphate Bacillus methanolicus MGA3 the enzyme is involved in the ribulose monophosphate cycle L-xylulose 5-phosphate
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.7.1.11 Bacillus methanolicus
-
-
-
2.7.1.11 Bacillus methanolicus I3DYB8 strain PB1, pfk2
-
2.7.1.11 Bacillus methanolicus MGA3
-
-
-
2.7.1.11 Bacillus methanolicus PB1
-
-
-
2.7.1.11 Bacillus methanolicus PB1 I3DYB8 strain PB1, pfk2
-
5.1.3.1 Bacillus methanolicus I3DTN4
-
-
5.1.3.1 Bacillus methanolicus I3DTP3
-
-
5.1.3.1 Bacillus methanolicus I3DZ65
-
-
5.1.3.1 Bacillus methanolicus MGA3 / ATCC53907 I3DTN4
-
-
5.1.3.1 Bacillus methanolicus MGA3 / ATCC53907 I3DZ65
-
-
5.1.3.1 Bacillus methanolicus PB1 / NCIMB13113 I3DTP3
-
-
5.1.3.22 Bacillus methanolicus
-
-
-
5.1.3.22 Bacillus methanolicus I3DTP3
-
-
5.1.3.22 Bacillus methanolicus MGA3
-
-
-
5.1.3.22 Bacillus methanolicus PB1 I3DTP3
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
2.7.1.11
-
 Bacillus methanolicus
5.1.3.1 recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and diaylsis Bacillus methanolicus
5.1.3.22
-
 Bacillus methanolicus

Source Tissue

EC Number Source Tissue Comment Organism Textmining
5.1.3.1 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)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.7.1.11 ATP + D-fructose 6-phosphate
-
 Bacillus methanolicus ADP + D-fructose 1,6-bisphosphate
-
 ?
2.7.1.11 ATP + D-fructose 6-phosphate the enzyme is involved in the ribulose monophosphate cycle Bacillus methanolicus ADP + D-fructose 1,6-bisphosphate
-
 ?
2.7.1.11 ATP + D-fructose 6-phosphate
-
 Bacillus methanolicus PB1 ADP + D-fructose 1,6-bisphosphate
-
 ?
2.7.1.11 ATP + D-fructose 6-phosphate the enzyme is involved in the ribulose monophosphate cycle Bacillus methanolicus PB1 ADP + D-fructose 1,6-bisphosphate
-
 ?
2.7.1.11 ATP + D-fructose 6-phosphate
-
 Bacillus methanolicus MGA3 ADP + D-fructose 1,6-bisphosphate
-
 ?
2.7.1.11 ATP + D-fructose 6-phosphate the enzyme is involved in the ribulose monophosphate cycle Bacillus methanolicus MGA3 ADP + D-fructose 1,6-bisphosphate
-
 ?
5.1.3.1 D-Ribulose 5-phosphate
-
 Bacillus methanolicus D-Xylulose 5-phosphate
-
 r
5.1.3.1 D-Ribulose 5-phosphate
-
 Bacillus methanolicus MGA3 / ATCC53907 D-Xylulose 5-phosphate
-
 r
5.1.3.1 D-Ribulose 5-phosphate
-
 Bacillus methanolicus PB1 / NCIMB13113 D-Xylulose 5-phosphate
-
 r
5.1.3.1 D-Ribulose 5-phosphate
-
 Bacillus methanolicus PB1 D-Xylulose 5-phosphate
-
 r
5.1.3.22 L-ribulose 5-phosphate
-
 Bacillus methanolicus L-xylulose 5-phosphate
-
 ?
5.1.3.22 L-ribulose 5-phosphate the enzyme is involved in the ribulose monophosphate cycle Bacillus methanolicus L-xylulose 5-phosphate
-
 ?
5.1.3.22 L-ribulose 5-phosphate
-
 Bacillus methanolicus PB1 / NCIMB13113 L-xylulose 5-phosphate
-
 ?
5.1.3.22 L-ribulose 5-phosphate the enzyme is involved in the ribulose monophosphate cycle Bacillus methanolicus PB1 / NCIMB13113 L-xylulose 5-phosphate
-
 ?
5.1.3.22 L-ribulose 5-phosphate
-
 Bacillus methanolicus PB1 L-xylulose 5-phosphate
-
 ?
5.1.3.22 L-ribulose 5-phosphate the enzyme is involved in the ribulose monophosphate cycle Bacillus methanolicus PB1 L-xylulose 5-phosphate
-
 ?
5.1.3.22 L-ribulose 5-phosphate
-
 Bacillus methanolicus MGA3 L-xylulose 5-phosphate
-
 ?
5.1.3.22 L-ribulose 5-phosphate the enzyme is involved in the ribulose monophosphate cycle Bacillus methanolicus MGA3 L-xylulose 5-phosphate
-
 ?

Subunits

EC Number Subunits Comment Organism
2.7.1.11 octamer active both as octamer and as tetramer Bacillus methanolicus
2.7.1.11 tetramer active both as octamer and as tetramer Bacillus methanolicus
5.1.3.1 hexamer
-
 Bacillus methanolicus
5.1.3.22 hexamer
-
 Bacillus methanolicus

Synonyms

EC Number Synonyms Comment Organism
2.7.1.11 PFK
-
 Bacillus methanolicus
2.7.1.11 PFK1 wild-type strain MGA3, encoded on plasmid pBM19 Bacillus methanolicus
2.7.1.11 PFK1 wild-type strain PB1, encoded on plasmid pBM20 Bacillus methanolicus
2.7.1.11 PFK2 wild-type strain MGA3, chromosomal enzyme Bacillus methanolicus
2.7.1.11 PFK2 wild-type strain PB1, chromosomal enzyme Bacillus methanolicus
5.1.3.1 D-ribulose-5-phosphate-3-epimerase
-
 Bacillus methanolicus
5.1.3.1 RPE
-
 Bacillus methanolicus
5.1.3.1 rpe1
-
 Bacillus methanolicus
5.1.3.1 rpe1-MGA3
-
 Bacillus methanolicus
5.1.3.1 rpe1-PB1
-
 Bacillus methanolicus
5.1.3.1 rpe2
-
 Bacillus methanolicus
5.1.3.1 rpe2-MGA3
-
 Bacillus methanolicus
5.1.3.1 rpeC
-
 Bacillus methanolicus
5.1.3.1 rpeP
-
 Bacillus methanolicus
5.1.3.22 ribulose-5-phosphate 3-epimerase
-
 Bacillus methanolicus
5.1.3.22 RPE
-
 Bacillus methanolicus
5.1.3.22 rpe1 wild-type strain MGA3, encoded on plasmid pBM19 Bacillus methanolicus
5.1.3.22 rpe1 wild-type strain PB1, encoded on plasmid pBM20 Bacillus methanolicus
5.1.3.22 rpe2 wild-type strain MGA3, chromosomal enzyme Bacillus methanolicus

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
5.1.3.1 25
-
 assay at Bacillus methanolicus

Temperature Stability [°C]

EC Number Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
5.1.3.1 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
5.1.3.1 27
-
 purified recombinant His-tagged RPE2-MGA3 is completely stable at 27°C after 2 h Bacillus methanolicus
5.1.3.1 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
5.1.3.1 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
5.1.3.1 37
-
 purified recombinant His-tagged RPE2-MGA3 retains 95% activity after 2 h Bacillus methanolicus
5.1.3.1 50
-
 purified recombinant His-tagged RPE2-MGA3 retains 90% activity after 2 h Bacillus methanolicus
5.1.3.1 65
-
 purified recombinant His-tagged RPE2-MGA3 retains 20% activity after 2 h Bacillus methanolicus
5.1.3.1 80
-
 purified recombinant His-tagged RPE2-MGA3 retains below 5% activity after 2 h Bacillus methanolicus

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
5.1.3.1 7.7
-
 assay at Bacillus methanolicus

Expression

EC Number Organism Comment Expression
2.7.1.11 Bacillus methanolicus transcription of the plasmid-encoded gene is 10fold to 15fold upregulated in cells growing on methanol compared to mannitol, while the chromosomal gene is transcribed at similar levels under both conditions up
5.1.3.1 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
5.1.3.1 Bacillus methanolicus transcription of the plasmid-encoded gene is 10-15fold upregulated in cells growing on methanol compared to mannitol up
5.1.3.1 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
5.1.3.22 Bacillus methanolicus transcription of the plasmid-encoded genes is 10fold to 15fold upregulated in cells growing on methanol compared to mannitol, while the chromosomal genes are transcribed at similar levels under both conditions up

General Information

EC Number General Information Comment Organism
2.7.1.11 physiological function the enzyme is involved in the ribulose monophosphate cycle Bacillus methanolicus
5.1.3.1 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
5.1.3.1 evolution Bacillus methanolicus wild-type strain PB1 possesses one putative rpe gene encoded on plasmid pBM20 (rpe1-PB1) Bacillus methanolicus
5.1.3.1 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
5.1.3.1 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
5.1.3.22 physiological function the enzyme is involved in the ribulose monophosphate cycle Bacillus methanolicus