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Literature summary for 4.2.1.79 extracted from
- The PrpF protein of Shewanella oneidensis MR-1 catalyzes the isomerization of 2-methyl-cis-aconitate during the catabolism of propionate via the AcnD-dependent 2-methylcitric acid cycle (2017), PLoS ONE, 12, e0188130 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| gene mmgE, the mother cell metabolic gene (mmg) operon encodes homologues from the methylcitric acid cycle | Bacillus subtilis |
| gene prpD, the mother cell metabolic gene (mmg) operon encodes homologues from the methylcitric acid cycle | Escherichia coli |
| gene prpD, the sequence of prp genes is prpR-prpB-prpC-prpD-prpE, recombinant expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) | Salmonella enterica subsp. enterica serovar Typhimurium |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| additional information | construction of enzyme-deficient DELTA prpD mutant. The two genes acnD and prpF, encoding 2-methylcitrate dehydratase (AcnD, EC 4.2.1.117) and 2-methyl-aconitate isomerase (SoPrpF, EC 5.3.3.-) from Shewanella oneidensis together can replace gene prpD in Salmonella enterica. SoAcnD and SePrpD synthesize different methylaconitate isomers | Salmonella enterica subsp. enterica serovar Typhimurium |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate | Escherichia coli | - |
(Z)-but-2-ene-1,2,3-tricarboxylate + H2O | - |
? |  |
| (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate | Bacillus subtilis | - |
(Z)-but-2-ene-1,2,3-tricarboxylate + H2O | - |
? | |
| (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate | Salmonella enterica subsp. enterica serovar Typhimurium | - |
(Z)-but-2-ene-1,2,3-tricarboxylate + H2O | - |
? | |
| (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate | Bacillus subtilis 168 | - |
(Z)-but-2-ene-1,2,3-tricarboxylate + H2O | - |
? | |
| (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate | Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720 | - |
(Z)-but-2-ene-1,2,3-tricarboxylate + H2O | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Bacillus subtilis | P45859 | - |
- |
| Bacillus subtilis 168 | P45859 | - |
- |
| Escherichia coli | P77243 | - |
- |
| Salmonella enterica subsp. enterica serovar Typhimurium | P74840 | - |
- |
| Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720 | P74840 | - |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography | Salmonella enterica subsp. enterica serovar Typhimurium |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate | - |
Escherichia coli | (Z)-but-2-ene-1,2,3-tricarboxylate + H2O | - |
? | |
| (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate | - |
Bacillus subtilis | (Z)-but-2-ene-1,2,3-tricarboxylate + H2O | - |
? | |
| (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate | - |
Salmonella enterica subsp. enterica serovar Typhimurium | (Z)-but-2-ene-1,2,3-tricarboxylate + H2O | - |
? | |
| (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate | - |
Bacillus subtilis 168 | (Z)-but-2-ene-1,2,3-tricarboxylate + H2O | - |
? | |
| (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate | - |
Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720 | (Z)-but-2-ene-1,2,3-tricarboxylate + H2O | - |
? | |
| (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate | - |
Escherichia coli | (E)-but-2-ene-1,2,3-tricarboxylate + H2O | - |
? | |
| (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate | - |
Bacillus subtilis | (E)-but-2-ene-1,2,3-tricarboxylate + H2O | - |
? | |
| (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate | - |
Bacillus subtilis 168 | (E)-but-2-ene-1,2,3-tricarboxylate + H2O | - |
? | |
| additional information | the MmgE enzyme is not a stereospecific 2-methylcitrate dehydratase because it can dehydrate at least two of the four diastereomers of 2-methylcitrate to yield either (E)-2-methylaconitate or (Z)-2-methylaconitate, but the physiological pathways proceed via (Z)-2-methylaconitate, which serves as the substrate for the citB enzyme in the synthesis of 2-methylisocitrate | Bacillus subtilis | ? | - |
? | |
| additional information | the PrpD enzyme from Escherichia coli is not a stereospecific 2-methylcitrate dehydratase because it can dehydrate at least two of the four diastereomers of 2-methylcitrate to yield either (E)-2-methylaconitate or (Z)-2-methylaconitate, but the physiological pathways proceed via (Z)-2-methylaconitate, which serves as the substrate for the citB enzyme in the synthesis of 2-methylisocitrate | Escherichia coli | ? | - |
? | |
| additional information | the MmgE enzyme is not a stereospecific 2-methylcitrate dehydratase because it can dehydrate at least two of the four diastereomers of 2-methylcitrate to yield either (E)-2-methylaconitate or (Z)-2-methylaconitate, but the physiological pathways proceed via (Z)-2-methylaconitate, which serves as the substrate for the citB enzyme in the synthesis of 2-methylisocitrate | Bacillus subtilis 168 | ? | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| mmgE | - |
Bacillus subtilis |
| PrpD | - |
Escherichia coli |
| PrpD | - |
Bacillus subtilis |
| PrpD | - |
Salmonella enterica subsp. enterica serovar Typhimurium |
| SePrpD | - |
Salmonella enterica subsp. enterica serovar Typhimurium |
| STM0370 | - |
Salmonella enterica subsp. enterica serovar Typhimurium |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 25 | 37 | assay at | Escherichia coli |
| 25 | 37 | assay at | Bacillus subtilis |
| 25 | 37 | assay at | Salmonella enterica subsp. enterica serovar Typhimurium |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 8 | - |
assay at | Escherichia coli |
| 8 | - |
assay at | Bacillus subtilis |
| 8 | - |
assay at | Salmonella enterica subsp. enterica serovar Typhimurium |
General Information
| General Information | Comment | Organism |
|---|---|---|
| metabolism | the enzyme is involved in the 2-methylcitric acid cycle, overview | Escherichia coli |
| metabolism | the enzyme is involved in the 2-methylcitric acid cycle, overview | Salmonella enterica subsp. enterica serovar Typhimurium |
| metabolism | the enzyme is involved in the 2-methylcitric acid cycle, overview. The three genes, mmgDE and yqiQ (mmgF), provide three of the five steps of the methylcitric acid cycle, encoded in the mmg operon. The fourth step can be supplied by citB (aconitase), and the fifth probably missing step, the propionyl-CoA synthetase, is probably skipped because the beta-oxidation of methyl-branched fatty acids by the enzymes encoded by mmgABC produce propionyl-CoA. The 2-methylisocitrate produced by CitB is converted to pyruvate and succinate by the enzyme YqiQ(MmgF) | Bacillus subtilis |
| additional information | construction of enzyme-deficient DELTA prpD mutant. The two genes acnD and prpF, encoding 2-methylcitrate dehydratase (AcnD, EC 4.2.1.117) and 2-methyl-aconitate isomerase (SoPrpF, EC 5.3.3.-) from Shewanella oneidensis together can replace gene prpD in Salmonella enterica. SoAcnD and SePrpD synthesize different methylaconitate isomers. The SoPrpF protein isomerizes the product of the AcnD reaction into the PrpD product. Mutant SoPrpF variants with substitutions of residues K73 or C107 fail to support growth with propionate as the sole source of carbon and energy | Salmonella enterica subsp. enterica serovar Typhimurium |
| physiological function | the MmgE enzyme is not a stereospecific 2-methylcitrate dehydratase because it can dehydrate at least two of the four diastereomers of 2-methylcitrate to yield either (E)-2-methylaconitate or (Z)-2-methylaconitate, but the physiological pathways proceed via (Z)-2-methylaconitate, which serves as the substrate for the citB enzyme in the synthesis of 2-methylisocitrate | Bacillus subtilis |
| physiological function | the PrpD enzyme from Escherichia coli is not a stereospecific 2-methylcitrate dehydratase because it can dehydrate at least two of the four diastereomers of 2-methylcitrate to yield either (E)-2-methylaconitate or (Z)-2-methylaconitate, but the physiological pathways proceed via (Z)-2-methylaconitate, which serves as the substrate for the citB enzyme in the synthesis of 2-methylisocitrate | Escherichia coli |
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