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Literature summary extracted from
- Assimilation of aromatic compounds by Comamonas testosteroni: characterization and spreadability of protocatechuate 4,5-cleavage pathway in bacteria (2013), Appl. Microbiol. Biotechnol., 97, 6031-6041.
Cloned(Commentary)
| EC Number | Cloned (Comment) | Organism |
|---|---|---|
| 4.1.3.B3 | gene pmdF, orf CtCNB1_2744, DNA and amino acid sequence determination and analysis, genetic organization, phylogenetic analysis, expression in Escherichia coli | Comamonas testosteroni |
| 4.2.1.83 | gene pmdE | Comamonas testosteroni |
| 4.2.1.83 | gene pmdE, expression of wild-type and mutants in Escherichia coli | Comamonas testosteroni |
Protein Variants
| EC Number | Protein Variants | Comment | Organism |
|---|---|---|---|
| 4.1.3.B3 | additional information | gene disruption and complementation of genes pmdE, pmdF, and pmdU in Comamonas testosteroni wild-type and mutants, overview | Comamonas testosteroni |
| 4.2.1.83 | additional information | generation of several pmdE gene truncated mutants, lacking residues 6 to 226, 32 to 296, or 105 to 215, overview. A pmdE knock out mutant loses the ability to grow on vanillate, 3-hydroxybenzoate, and 4-hydroxybenzoate as carbon sources. This ability to grow on vanillate, 3-hydroxybenzoate, and 4-hydroxybenzoate is restored by genetic complementation | Comamonas testosteroni |
Natural Substrates/ Products (Substrates)
| EC Number | Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 4.1.3.B3 | 4-carboxy-4-hydroxy-2-oxoadipate | Comamonas testosteroni | - |
oxaloacetate + pyruvate | - |
? |  |
| 4.1.3.B3 | 4-carboxy-4-hydroxy-2-oxoadipate | Comamonas testosteroni CNB-1 | - |
oxaloacetate + pyruvate | - |
? | |
| 4.1.3.B3 | additional information | Comamonas testosteroni | the bifunctional enzyme PmdF shows obvious aldolase activity when 4-carboxy-4-hydroxy-2-oxoadipate is used as substrate and obvious oxalacetate decarboxylase activity when oxaloacetate is used as substrate | ? | - |
? | |
| 4.1.3.B3 | additional information | Comamonas testosteroni CNB-1 | the bifunctional enzyme PmdF shows obvious aldolase activity when 4-carboxy-4-hydroxy-2-oxoadipate is used as substrate and obvious oxalacetate decarboxylase activity when oxaloacetate is used as substrate | ? | - |
? | |
| 5.3.2.8 | (2E)-2-(2-methylprop-2-en-1-ylidene)-4-oxopentanedioic acid | Comamonas testosteroni | - |
(2Z,4E)-2-hydroxy-4-(2-methylprop-2-en-1-ylidene)pent-2-enedioic acid | - |
? | |
| 5.3.2.8 | (2E)-2-(2-methylprop-2-en-1-ylidene)-4-oxopentanedioic acid | Comamonas testosteroni CNB-1 | - |
(2Z,4E)-2-hydroxy-4-(2-methylprop-2-en-1-ylidene)pent-2-enedioic acid | - |
? | |
Organism
| EC Number | Organism | UniProt | Comment | Textmining |
|---|---|---|---|---|
| 4.1.3.B3 | Comamonas testosteroni | Q93PS8 | gene pmdF | - |
| 4.1.3.B3 | Comamonas testosteroni CNB-1 | Q93PS8 | gene pmdF | - |
| 4.2.1.83 | Comamonas testosteroni | D0IZN8 | gene pmdE | - |
| 4.2.1.83 | Comamonas testosteroni | Q93PS9 | gene pmdE | - |
| 4.2.1.83 | Comamonas testosteroni CNB-1 | Q93PS9 | gene pmdE | - |
| 4.2.1.83 | Comamonas testosteroni CNB-2 | D0IZN8 | gene pmdE | - |
| 5.3.2.8 | Comamonas testosteroni | - |
- |
- |
| 5.3.2.8 | Comamonas testosteroni CNB-1 | - |
- |
- |
Purification (Commentary)
| EC Number | Purification (Comment) | Organism |
|---|---|---|
| 4.1.3.B3 | recombinant enzyme from Escherichia coli | Comamonas testosteroni |
Source Tissue
| EC Number | Source Tissue | Comment | Organism | Textmining |
|---|---|---|---|---|
| 4.1.3.B3 | additional information | strain CNB-1 grows on phenol, gentisate, vanillate, 3-hydroxybenzoate, and 4-hydroxybenzoate as carbon and energy sources | Comamonas testosteroni | - |
| 4.2.1.83 | culture condition:3-hydroxybenzoate-grown cell | - |
Comamonas testosteroni | - |
| 4.2.1.83 | culture condition:4-hydroxybenzoate-grown cell | - |
Comamonas testosteroni | - |
| 4.2.1.83 | culture condition:gentisate-grown cell | - |
Comamonas testosteroni | - |
| 4.2.1.83 | culture condition:phenol-grown cell | - |
Comamonas testosteroni | - |
| 4.2.1.83 | culture condition:vanillate-grown cell | - |
Comamonas testosteroni | - |
| 4.2.1.83 | additional information | strain CNB-1 grows on phenol, gentisate, vanillate, 3-hydroxybenzoate, and 4-hydroxybenzoate as carbon and energy sources, but does not grow on resorcinol, 2,4-dihydroxybenzoate, 4-cresol, and phenylacetate | Comamonas testosteroni | - |
Substrates and Products (Substrate)
| EC Number | Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|---|
| 4.1.3.B3 | 4-carboxy-4-hydroxy-2-oxoadipate | - |
Comamonas testosteroni | oxaloacetate + pyruvate | - |
? | |
| 4.1.3.B3 | 4-carboxy-4-hydroxy-2-oxoadipate | - |
Comamonas testosteroni CNB-1 | oxaloacetate + pyruvate | - |
? | |
| 4.1.3.B3 | additional information | the bifunctional enzyme PmdF shows obvious aldolase activity when 4-carboxy-4-hydroxy-2-oxoadipate is used as substrate and obvious oxalacetate decarboxylase activity when oxaloacetate is used as substrate | Comamonas testosteroni | ? | - |
? | |
| 4.1.3.B3 | additional information | the bifunctional enzyme PmdF shows obvious aldolase activity when 4-carboxy-4-hydroxy-2-oxoadipate is used as substrate and obvious oxalacetate decarboxylase activity when oxaloacetate is used as substrate | Comamonas testosteroni CNB-1 | ? | - |
? | |
| 4.2.1.83 | 2-hydroxy-4-carboxy-hexa-2,4-dienedioate | 4-oxalomesaconate hydratase uses only enol-OMA as substrate | Comamonas testosteroni | 4-carboxy-4-hydroxy-2-oxoadipate + H2O | - |
? | |
| 4.2.1.83 | 2-hydroxy-4-carboxy-hexa-2,4-dienedioate | 4-oxalomesaconate hydratase uses only enol-OMA as substrate | Comamonas testosteroni CNB-2 | 4-carboxy-4-hydroxy-2-oxoadipate + H2O | - |
? | |
| 4.2.1.83 | 2-hydroxy-4-carboxy-hexa-2,4-dienedioate | 4-oxalomesaconate hydratase uses only enol-OMA as substrate | Comamonas testosteroni CNB-1 | 4-carboxy-4-hydroxy-2-oxoadipate + H2O | - |
? | |
| 5.3.2.8 | (2E)-2-(2-methylprop-2-en-1-ylidene)-4-oxopentanedioic acid | - |
Comamonas testosteroni | (2Z,4E)-2-hydroxy-4-(2-methylprop-2-en-1-ylidene)pent-2-enedioic acid | - |
? | |
| 5.3.2.8 | (2E)-2-(2-methylprop-2-en-1-ylidene)-4-oxopentanedioic acid | - |
Comamonas testosteroni CNB-1 | (2Z,4E)-2-hydroxy-4-(2-methylprop-2-en-1-ylidene)pent-2-enedioic acid | - |
? | |
| 5.3.2.8 | 4-chloronitrobenzene | - |
Comamonas testosteroni | ? | - |
? | |
| 5.3.2.8 | 4-chloronitrobenzene | - |
Comamonas testosteroni CNB-1 | ? | - |
? | |
Synonyms
| EC Number | Synonyms | Comment | Organism |
|---|---|---|---|
| 4.1.3.B3 | 4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase | - |
Comamonas testosteroni |
| 4.1.3.B3 | CHA aldolase | - |
Comamonas testosteroni |
| 4.1.3.B3 | PmdF | - |
Comamonas testosteroni |
| 4.2.1.83 | OMA | - |
Comamonas testosteroni |
| 4.2.1.83 | PmdE | - |
Comamonas testosteroni |
| 5.3.2.8 | OMA tautomerase | - |
Comamonas testosteroni |
| 5.3.2.8 | pmdU | - |
Comamonas testosteroni |
Temperature Optimum [°C]
| EC Number | Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|---|
| 4.1.3.B3 | 22 | - |
assay at room temperature | Comamonas testosteroni |
| 4.2.1.83 | 22 | - |
assay at room temperature | Comamonas testosteroni |
pH Optimum
| EC Number | pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|---|
| 4.2.1.83 | 7 | - |
assay at, about | Comamonas testosteroni |
pI Value
| EC Number | Organism | Comment | pI Value Maximum | pI Value |
|---|---|---|---|---|
| 4.2.1.83 | Comamonas testosteroni | sequence calculation | - |
5.81 |
| 4.2.1.83 | Comamonas testosteroni | isoelectric focusing | - |
6.23 |
General Information
| EC Number | General Information | Comment | Organism |
|---|---|---|---|
| 4.1.3.B3 | evolution | the protocatechuate 4,5-cleavage pathway is mainly distributed in alpha- and beta-proteobacteria, gene clusters of protocatechuate 4,5-cleavage pathway in strain CNB-1 and other bacterial strains, genotyping and phylogenetic analysis, overview. Two types of genetic organization/cluster are recognized for PCA 4,5-cleavage pathway: The Sphingobium-type gene cluster constitutes several transcriptional units. The Comamonas-Pseudomonas type constitutes only one transcriptional unit | Comamonas testosteroni |
| 4.1.3.B3 | metabolism | the enzyme catalyzes the last step of the protocatechuate 4,5-cleavage pathway. Vanillate, 3-hydroxybenzoate, and 4-hydroxybenzoate are degraded via protocatechuate 4,5-cleavage pathway | Comamonas testosteroni |
| 4.2.1.83 | evolution | comparison of gene clusters of the protocatechuate 4,5-cleavage pathway in bacterial strains, overview | Comamonas testosteroni |
| 4.2.1.83 | malfunction | a pmdE knock out mutant loses the ability to grow on vanillate, 3-hydroxybenzoate, and 4-hydroxybenzoate as carbon sources. This ability to grow on vanillate, 3-hydroxybenzoate, and 4-hydroxybenzoate is restored by genetic complementation | Comamonas testosteroni |
| 4.2.1.83 | metabolism | the enzyme is active in the protocatechuate 4,5-cleavage pathway. Gene pmdU encodes an 4-oxalomesaconate tautomerase and catalyzes conversion of 4-oxalomesaconate-keto into 4-oxalomesaconate-enol, which is the only substrate of 4-oxalomesaconate hydratase. Pathway overview | Comamonas testosteroni |
| 4.2.1.83 | physiological function | the enzyme in strain CNB-1 is essential for growth on phenol, gentisate, vanillate, 3-hydroxybenzoate, and 4-hydroxybenzoate as carbon and energy sources | Comamonas testosteroni |
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