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Literature summary extracted from

  • Rocco, C.J.; Wetterhorn, K.M.; Garvey, G.S.; Rayment, I.; Escalante-Semerena, J.C.
    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 .
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

EC Number Cloned (Comment) Organism
4.2.1.79 gene mmgE, the mother cell metabolic gene (mmg) operon encodes homologues from the methylcitric acid cycle Bacillus subtilis
4.2.1.79 gene prpD, the mother cell metabolic gene (mmg) operon encodes homologues from the methylcitric acid cycle Escherichia coli
4.2.1.79 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
4.2.1.117 gene acnD, the sequence of prp genes is prpR-prpB-prpC-acnD-prpF, functional recombinant coexpression of the genes acnD and prpF from Shewanella oneidensis in Salmonella enterica strain DELTAprpD, recombinant expression of His-tagged enzyme from gene acnD in Escherichia coli strain BL21(DE3) Shewanella oneidensis

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
5.2.1.B4 hanging drop vapor diffusion method, high-resolution three-dimensional crystal structures of mutant enzyme K73E in complex with trans-aconitate or malonate provides insights into the mechanism of catalysis of the wild-type protein Shewanella oneidensis

Protein Variants

EC Number Protein Variants Comment Organism
4.2.1.79 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
5.2.1.B4 C107A protein containing the C107A substitution is not overproduced and could not be purified Shewanella oneidensis
5.2.1.B4 C107S inactive mutant enzyme Shewanella oneidensis
5.2.1.B4 K73A protein containing the K73A substitution is not overproduced and could not be purified Shewanella oneidensis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4.2.1.79 (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate Escherichia coli
-
 (Z)-but-2-ene-1,2,3-tricarboxylate + H2O
-
 ?
4.2.1.79 (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate Bacillus subtilis
-
 (Z)-but-2-ene-1,2,3-tricarboxylate + H2O
-
 ?
4.2.1.79 (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate Salmonella enterica subsp. enterica serovar Typhimurium
-
 (Z)-but-2-ene-1,2,3-tricarboxylate + H2O
-
 ?
4.2.1.79 (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate Bacillus subtilis 168
-
 (Z)-but-2-ene-1,2,3-tricarboxylate + H2O
-
 ?
4.2.1.79 (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
-
 ?
4.2.1.117 (2S,3S)-2-methylcitrate Shewanella oneidensis
-
 2-methyl-trans-aconitate + H2O
-
 ?
5.2.1.B4 (R)-4-methyl-cis-aconitate Shewanella oneidensis the enzyme is involved in catabolism of propionate via the AcnD-dependent 2-methylcitric acid cycle. The 2-methylcitric acid cycle is a common route of propionate catabolism in microorganisms 2-methyl-cis-aconitate
-
 ?
5.3.3.7 trans-Aconitate Shewanella oneidensis
-
 cis-Aconitate
-
 r

Organism

EC Number Organism UniProt Comment Textmining
4.2.1.79 Bacillus subtilis P45859
-
-
4.2.1.79 Bacillus subtilis 168 P45859
-
-
4.2.1.79 Escherichia coli P77243
-
-
4.2.1.79 Salmonella enterica subsp. enterica serovar Typhimurium P74840
-
-
4.2.1.79 Salmonella enterica subsp. enterica serovar Typhimurium LT2 / SGSC1412 / ATCC 700720 P74840
-
-
4.2.1.99 no activity in Shewanella oneidensis strain MR-1
-
 the absence of 2-methylisocitrate dehydratase, PrpD, is compensated by the activity of SoAcnD and SoPrpF, SoAcnD has 2-methylcitrate dehydratase (EC 4.2.1.79) activity and PrpF has aconitate isomerase (EC 5.3.3.7) activity
-
4.2.1.117 Shewanella oneidensis Q8EJW3
-
-
5.2.1.B4 Shewanella oneidensis Q8EJW4
-
-
5.3.3.7 Shewanella oneidensis Q8EJW4
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
4.2.1.79 recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography Salmonella enterica subsp. enterica serovar Typhimurium
4.2.1.117 recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography Shewanella oneidensis

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.2.1.79 (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate
-
 Escherichia coli (Z)-but-2-ene-1,2,3-tricarboxylate + H2O
-
 ?
4.2.1.79 (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate
-
 Bacillus subtilis (Z)-but-2-ene-1,2,3-tricarboxylate + H2O
-
 ?
4.2.1.79 (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate
-
 Salmonella enterica subsp. enterica serovar Typhimurium (Z)-but-2-ene-1,2,3-tricarboxylate + H2O
-
 ?
4.2.1.79 (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate
-
 Bacillus subtilis 168 (Z)-but-2-ene-1,2,3-tricarboxylate + H2O
-
 ?
4.2.1.79 (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
-
 ?
4.2.1.79 (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate
-
 Escherichia coli (E)-but-2-ene-1,2,3-tricarboxylate + H2O
-
 ?
4.2.1.79 (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate
-
 Bacillus subtilis (E)-but-2-ene-1,2,3-tricarboxylate + H2O
-
 ?
4.2.1.79 (2S,3S)-2-hydroxybutane-1,2,3-tricarboxylate
-
 Bacillus subtilis 168 (E)-but-2-ene-1,2,3-tricarboxylate + H2O
-
 ?
4.2.1.79 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 ?
-
 ?
4.2.1.79 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 ?
-
 ?
4.2.1.79 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 ?
-
 ?
4.2.1.117 (2S,3S)-2-methylcitrate
-
 Shewanella oneidensis 2-methyl-trans-aconitate + H2O
-
 ?
4.2.1.117 additional information AcnD has aconitase-like activity Shewanella oneidensis ?
-
 ?
5.2.1.B4 (R)-4-methyl-cis-aconitate
-
 Shewanella oneidensis 2-methyl-cis-aconitate
-
 ?
5.2.1.B4 (R)-4-methyl-cis-aconitate the enzyme is involved in catabolism of propionate via the AcnD-dependent 2-methylcitric acid cycle. The 2-methylcitric acid cycle is a common route of propionate catabolism in microorganisms Shewanella oneidensis 2-methyl-cis-aconitate
-
 ?
5.3.3.7 4-methyl-cis-aconitate
-
 Shewanella oneidensis 2-methyl-cis-aconitate
-
 r
5.3.3.7 trans-Aconitate
-
 Shewanella oneidensis cis-Aconitate
-
 r

Synonyms

EC Number Synonyms Comment Organism
4.2.1.79 mmgE
-
 Bacillus subtilis
4.2.1.79 PrpD
-
 Escherichia coli
4.2.1.79 PrpD
-
 Bacillus subtilis
4.2.1.79 PrpD
-
 Salmonella enterica subsp. enterica serovar Typhimurium
4.2.1.79 SePrpD
-
 Salmonella enterica subsp. enterica serovar Typhimurium
4.2.1.79 STM0370
-
 Salmonella enterica subsp. enterica serovar Typhimurium
4.2.1.117 AcnD
-
 Shewanella oneidensis
4.2.1.117 SO_0343
-
 Shewanella oneidensis
5.2.1.B4 2-methyl-aconitate isomerase
-
 Shewanella oneidensis
5.2.1.B4 PrpF protein
-
 Shewanella oneidensis
5.3.3.7 Aconitate isomerase
-
 Shewanella oneidensis
5.3.3.7 PrpF
-
 Shewanella oneidensis

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
4.2.1.79 25 37 assay at Escherichia coli
4.2.1.79 25 37 assay at Bacillus subtilis
4.2.1.79 25 37 assay at Salmonella enterica subsp. enterica serovar Typhimurium
4.2.1.117 25 37 assay at Shewanella oneidensis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
4.2.1.79 8
-
 assay at Escherichia coli
4.2.1.79 8
-
 assay at Bacillus subtilis
4.2.1.79 8
-
 assay at Salmonella enterica subsp. enterica serovar Typhimurium
4.2.1.117 8
-
 assay at Shewanella oneidensis

General Information

EC Number General Information Comment Organism
4.2.1.79 metabolism the enzyme is involved in the 2-methylcitric acid cycle, overview Escherichia coli
4.2.1.79 metabolism the enzyme is involved in the 2-methylcitric acid cycle, overview Salmonella enterica subsp. enterica serovar Typhimurium
4.2.1.79 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
4.2.1.79 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
4.2.1.79 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
4.2.1.79 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
4.2.1.117 metabolism the enzyme is involved in catabolism of propionate via the AcnD-dependent 2-methylcitric acid cycle. The 2-methylcitric acid cycle is a common route of propionate catabolism in microorganisms Shewanella oneidensis
4.2.1.117 metabolism the enzyme is involved in the 2-methylcitric acid cycle, overview Shewanella oneidensis
4.2.1.117 physiological function 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 from Salmonella enterica, which encodes 2-methylcitrate dehydratase, PrpD /EC 4.2.1.79. SoAcnD and SePrpD synthesize different methylaconitate isomers. The SoPrpF protein isomerizes the product of the AcnD reaction into the PrpD product (2-MCA), known substrate of the housekeeping aconitase. It is likely that 4-methylaconitate is the product of the AcnD enzyme. PrpF (SoPrpF) protein isomerizes the product of the SoAcnD dehydratase (putatively 4-methyl-cis-aconitate (4-MCA)) to 2-methyl-cis-aconitate (2-MCA). Thus,the role of SoPrpF in the 2-methylcitrate cycle (2-MCC) is to change the stereochemistry of the SoAcnD reaction product. AcnD and PrpF activities are necessary and sufficient to compensate for the lack of PrpD during growth with propionate of the strain of Salmonella enterica. 2-Methylcitrate is dehydrated by AcnD to 4-methyl-cis-aconitate, which is then isomerized to 2-methyl-cis-aconitate by PrpF, and rehydrated to 2-methylisocitrate by aconitases A and B Shewanella oneidensis
5.2.1.B4 metabolism the enzyme is involved in catabolism of propionate via the AcnD-dependent 2-methylcitric acid cycle. The 2-methylcitric acid cycle is a common route of propionate catabolism in microorganisms Shewanella oneidensis