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Literature summary for 1.5.99.B4 extracted from
- Characterization of flavin-containing opine dehydrogenase from bacteria (2015), PLoS ONE, 10, e0138434 .
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| PpOdhB, PpOdhC, and PpOdhA genes in the PpOdhABC gene cluster, the genes encoding the beta-, gamma-, and alpha-subunits are arranged in tandem on the bacterial genome, genetic structure overview, and amino acid sequence determination, analysis, and comparisons, genetic structure, phylogenetic analysis, recombinant expression as N-terminally His6-tagged proteins in Escherichia coli strain BL21(DE3), recombinant expression of the PpOdhABC gene cluster in Pseudomonas putida | Pseudomonas putida |
| the gene cluster from Bradyrhizobium japonicum consists of genes OdhB1-C-A-B2, from which two proteins, OdhAB1C and OdhAB2C, appear through the assembly of each beta-subunit together with common alpha- and gamma-subunits, and amino acid sequence determination, analysis, and comparisons, genetic structure, phylogenetic analysis, recombinant expression as N-terminally His6-tagged proteins in Escherichia coli strain BL21(DE3), recombinant expression of the PpOdhABC gene cluster in Pseudomonas putida | Bradyrhizobium japonicum |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| L-arginine | substrate inhibition | Bradyrhizobium japonicum |  |
| L-lysine | - |
Bradyrhizobium japonicum | |
| L-ornithine | - |
Bradyrhizobium japonicum | |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.0078 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with 2,6-dichloroindophenol, recombinant His6-tagged enzyme | Pseudomonas putida | |
| 0.077 | - |
N2-(D-1,3-dicarboxypropyl)-L-arginine | pH 9.0, 30°C, with nitroblue tetrazolium (NBT) together with phenazine methosulfate, recombinant His6-tagged enzyme | Pseudomonas putida | |
| 0.127 | - |
N2-(D-1,3-dicarboxypropyl)-L-arginine | pH 9.0, 30°C, with 4-iodonitrotetrazolium violet (INT) together with phenazine methosulfate, recombinant His6-tagged enzyme | Pseudomonas putida | |
| 0.379 | - |
N2-(D-1,3-dicarboxypropyl)-L-arginine | pH 9.0, 30°C, with cytochrome c, recombinant His6-tagged enzyme | Pseudomonas putida | |
| 0.379 | - |
N2-(D-1,3-dicarboxypropyl)-L-arginine | pH 9.0, 30°C, with ferricyanide, recombinant His6-tagged enzyme | Pseudomonas putida | |
| 0.476 | - |
N2-(D-1,3-dicarboxypropyl)-L-arginine | pH 9.0, 30°C, with 2,6-dichloroindophenol, recombinant His6-tagged enzyme | Pseudomonas putida | |
| 1.29 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with nitroblue tetrazolium (NBT) together with phenazine methosulfate, recombinant His6-tagged enzyme | Bradyrhizobium japonicum | |
| 3.54 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with cytochrome c, recombinant His6-tagged enzyme | Bradyrhizobium japonicum | |
| 4.81 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with 2,6-dichloroindophenol, recombinant His6-tagged enzyme | Bradyrhizobium japonicum | |
| 6.52 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with ferricyanide, recombinant His6-tagged enzyme | Bradyrhizobium japonicum | |
| 12.9 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with 4-iodonitrotetrazolium violet (INT) together with phenazine methosulfate, recombinant His6-tagged enzyme | Bradyrhizobium japonicum | |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Fe2+ | in iron-sufur clusters, [4Fe-4S] and [2Fe-2S], overview | Pseudomonas putida | |
| Fe2+ | in iron-sufur clusters, [4Fe-4S] and [2Fe-2S], overview | Bradyrhizobium japonicum | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| N2-(D-1,3-dicarboxypropyl)-L-arginine + FAD + H2O | Pseudomonas putida | i.e. nopaline | L-arginine + 2-oxoglutarate + FADH2 | - |
? | |
| N2-(D-1,3-dicarboxypropyl)-L-arginine + FAD + H2O | Pseudomonas putida KT 2240 | i.e. nopaline | L-arginine + 2-oxoglutarate + FADH2 | - |
? | |
| N2-(D-1-carboxyethyl)-L-arginine + FAD + H2O | Pseudomonas putida | i.e. D-octopine | L-arginine + pyruvate + FADH2 | - |
? | |
| N2-(D-1-carboxyethyl)-L-arginine + FAD + H2O | Bradyrhizobium japonicum | i.e. D-octopine | L-arginine + pyruvate + FADH2 | - |
? | |
| N2-(D-1-carboxyethyl)-L-arginine + FAD + H2O | Bradyrhizobium japonicum USDA110 | i.e. D-octopine | L-arginine + pyruvate + FADH2 | - |
? | |
| N2-(D-1-carboxyethyl)-L-arginine + FAD + H2O | Pseudomonas putida KT 2240 | i.e. D-octopine | L-arginine + pyruvate + FADH2 | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Bradyrhizobium japonicum | Q89E96 AND Q89E94 AND Q89E97 | subunits BjOdhA (bll7191 or ooxA), BjOdhB1 (bll7193), and BjOdhB2 (bll7190 or soxB) | - |
| Bradyrhizobium japonicum USDA110 | Q89E96 AND Q89E94 AND Q89E97 | subunits BjOdhA (bll7191 or ooxA), BjOdhB1 (bll7193), and BjOdhB2 (bll7190 or soxB) | - |
| Pseudomonas putida | Q88EK6 AND Q88EK5 | subunits alpha and beta; isolated from soil | - |
| Pseudomonas putida KT 2240 | Q88EK6 AND Q88EK5 | subunits alpha and beta; isolated from soil | - |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, ultrafiltration, dialysis, and gel filtration | Pseudomonas putida |
| recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, ultrafiltration, dialysis, and gel filtration | Bradyrhizobium japonicum |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | analysis of specificity of electron acceptors using 2,6-dichloroindophenol, 4-iodonitrotetrazolium violet (INT) or nitroblue tetrazolium (NBT) together with phenazine methosulfate (PMS) (electron-transfer intermediate), ferricyanide, horse heart cytochrome c, and NAD(P)+ | Pseudomonas putida | ? | - |
? | |
| additional information | analysis of specificity of electron acceptors using 2,6-dichloroindophenol, 4-iodonitrotetrazolium violet (INT) or nitroblue tetrazolium (NBT) together with phenazine methosulfate (PMS) (electron-transfer intermediate), ferricyanide, horse heart cytochrome c, and NAD(P)+. Enzyme BjOdhAB2C and BjOdhAB1C both function as octopine-specific OpnDH, poor activity with nopaline | Bradyrhizobium japonicum | ? | - |
? | |
| additional information | analysis of specificity of electron acceptors using 2,6-dichloroindophenol, 4-iodonitrotetrazolium violet (INT) or nitroblue tetrazolium (NBT) together with phenazine methosulfate (PMS) (electron-transfer intermediate), ferricyanide, horse heart cytochrome c, and NAD(P)+. Enzyme BjOdhAB2C and BjOdhAB1C both function as octopine-specific OpnDH, poor activity with nopaline | Bradyrhizobium japonicum USDA110 | ? | - |
? | |
| additional information | analysis of specificity of electron acceptors using 2,6-dichloroindophenol, 4-iodonitrotetrazolium violet (INT) or nitroblue tetrazolium (NBT) together with phenazine methosulfate (PMS) (electron-transfer intermediate), ferricyanide, horse heart cytochrome c, and NAD(P)+ | Pseudomonas putida KT 2240 | ? | - |
? | |
| N2-(D-1,3-dicarboxypropyl)-L-arginine + FAD + H2O | i.e. nopaline | Pseudomonas putida | L-arginine + 2-oxoglutarate + FADH2 | - |
? | |
| N2-(D-1,3-dicarboxypropyl)-L-arginine + FAD + H2O | i.e. nopaline | Pseudomonas putida KT 2240 | L-arginine + 2-oxoglutarate + FADH2 | - |
? | |
| N2-(D-1-carboxyethyl)-L-arginine + FAD + H2O | i.e. D-octopine | Pseudomonas putida | L-arginine + pyruvate + FADH2 | - |
? | |
| N2-(D-1-carboxyethyl)-L-arginine + FAD + H2O | i.e. D-octopine | Bradyrhizobium japonicum | L-arginine + pyruvate + FADH2 | - |
? | |
| N2-(D-1-carboxyethyl)-L-arginine + FAD + H2O | i.e. D-octopine | Bradyrhizobium japonicum USDA110 | L-arginine + pyruvate + FADH2 | - |
? | |
| N2-(D-1-carboxyethyl)-L-arginine + FAD + H2O | i.e. D-octopine | Pseudomonas putida KT 2240 | L-arginine + pyruvate + FADH2 | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| heterododecamer | alpha4beta4gamma4 | Bradyrhizobium japonicum |
| heterododecamer | alpha4beta4gamma4, 4 * 42000, beta-subunit, + 4 * 9000, gamma-subunit, + 4 * 45000, alpha-subunit, SDS-PAGE | Pseudomonas putida |
| More | BjOdhB1 and BjOdhB2 both assemble with common alpha- and gamma-subunits, and function as the same octopine dehydrogenase. Most of the purified BjOdhAB2C exists as alpha4beta4gamma4 as determined by gel-filtration, while BjOdhB1 is clearly dominant in purified BjOdhAB1C, thereby confirming that the molar ratio of FAD:FMN of the former (1.8:1.0) is similar to that of PpOdhABC. The gene cluster from Bradyrhizobium japonicum consists of genes OdhB1-C-A-B2, from which two proteins, OdhAB1C and OdhAB2C, appear through the assembly of each beta-subunit together with common alpha- and gamma-subunits, overview. A poor phylogenetic relationship exists between OdhB1 and OdhB2 in spite of them both functioning as octopine dehydrogenases, which provided clear evidence for the acquisition of novel functions by subunit exchange | Bradyrhizobium japonicum |
| More | PpOpnDH (alpha4beta4gamma4) contained 2 FAD (alpha- and beta-subunits), 1 FMN (between the alpha- and beta-subunits), and 1 [2Fe-2S] iron-sulfur cluster (gamma-subunit) within the structural unit of alphabetagamma. The beta- and alpha-subunit are both necessary for substrate binding, but the beta-subunit functions as a catalytic subunit by itself | Pseudomonas putida |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| BjOpnDH | - |
Bradyrhizobium japonicum |
| bll7190 | - |
Bradyrhizobium japonicum |
| bll7191 | - |
Bradyrhizobium japonicum |
| bll7192 | - |
Bradyrhizobium japonicum |
| bll7193 | - |
Bradyrhizobium japonicum |
| flavin-containing opine dehydrogenase | - |
Pseudomonas putida |
| flavin-containing opine dehydrogenase | - |
Bradyrhizobium japonicum |
| Nox/Oox-like protein | - |
Pseudomonas putida |
| Nox/Oox-like protein | - |
Bradyrhizobium japonicum |
| OdhA | - |
Pseudomonas putida |
| odhB | - |
Pseudomonas putida |
| odhC | - |
Pseudomonas putida |
| ooxA | - |
Bradyrhizobium japonicum |
| OpnDH | - |
Pseudomonas putida |
| OpnDH | - |
Bradyrhizobium japonicum |
| SoxB | - |
Bradyrhizobium japonicum |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 30 | - |
assay at | Pseudomonas putida |
| 30 | - |
assay at | Bradyrhizobium japonicum |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.093 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with nitroblue tetrazolium (NBT) together with phenazine methosulfate, recombinant His6-tagged enzyme | Bradyrhizobium japonicum | |
| 0.098 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with 2,6-dichloroindophenol, recombinant His6-tagged enzyme | Bradyrhizobium japonicum | |
| 0.173 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with cytochrome c, recombinant His6-tagged enzyme | Bradyrhizobium japonicum | |
| 0.21 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with 4-iodonitrotetrazolium violet (INT) together with phenazine methosulfate, recombinant His6-tagged enzyme | Bradyrhizobium japonicum | |
| 0.252 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with ferricyanide, recombinant His6-tagged enzyme | Bradyrhizobium japonicum | |
| 2.3 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with 2,6-dichloroindophenol, recombinant His6-tagged enzyme | Pseudomonas putida | |
| 17.33 | - |
N2-(D-1,3-dicarboxypropyl)-L-arginine | pH 9.0, 30°C, with ferricyanide, recombinant His6-tagged enzyme | Pseudomonas putida | |
| 23.17 | - |
N2-(D-1,3-dicarboxypropyl)-L-arginine | pH 9.0, 30°C, with nitroblue tetrazolium (NBT) together with phenazine methosulfate, recombinant His6-tagged enzyme | Pseudomonas putida | |
| 91.5 | - |
N2-(D-1,3-dicarboxypropyl)-L-arginine | pH 9.0, 30°C, with 4-iodonitrotetrazolium violet (INT) together with phenazine methosulfate, recombinant His6-tagged enzyme | Pseudomonas putida | |
| 298.67 | - |
N2-(D-1,3-dicarboxypropyl)-L-arginine | pH 9.0, 30°C, with cytochrome c, recombinant His6-tagged enzyme | Pseudomonas putida | |
| 315 | - |
N2-(D-1,3-dicarboxypropyl)-L-arginine | pH 9.0, 30°C, with 2,6-dichloroindophenol, recombinant His6-tagged enzyme | Pseudomonas putida | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| additional information | - |
pH optimum of BjOdhAB2C and BjOdhAB1C, overview | Bradyrhizobium japonicum |
| 9 | - |
assay at | Pseudomonas putida |
| 9 | - |
assay at | Bradyrhizobium japonicum |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| FAD | - |
Pseudomonas putida | |
| FAD | - |
Bradyrhizobium japonicum | |
| FMN | - |
Bradyrhizobium japonicum | |
| FMN | required for activity, the gamma-subunit has no effect on the binding of FMN | Pseudomonas putida | |
| additional information | electron acceptor specificities of BjOdhAB2C and BjOdhAB1C, overview | Bradyrhizobium japonicum | |
| [2Fe-2S]-center | [4Fe-4S] and [2Fe-2S] clusters bind to two different types of [Fe-S] binding sites in the gamma- and alpha-subunits, respectively. Cysteine residues C380, C382, C415, and C420 coordinate with the [Fe-S] clusters. The [2Fe-2S] cluster is important for structural folding and enzyme catalysis | Pseudomonas putida | |
| [2Fe-2S]-center | [4Fe-4S] and [2Fe-2S] clusters bind to two different types of [Fe-S] binding sites in the gamma- and alpha-subunits, respectively. The [2Fe-2S] cluster is important for structural folding and enzyme catalysis | Bradyrhizobium japonicum | |
| [4Fe-4S]-center | [4Fe-4S] and [2Fe-2S] clusters bind to two different types of [Fe-S] binding sites in the gamma- and alpha-subunits, respectively | Bradyrhizobium japonicum | |
| [4Fe-4S]-center | [4Fe-4S] and [2Fe-2S] clusters bind to two different types of [Fe-S] binding sites in the gamma- and alpha-subunits, respectively. Cysteine residues C56, C61, C64, and C77 coordinate with the [Fe-S] clusters | Pseudomonas putida | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | opine dehydrogenase (OpnDH) belongs to a group of so-called dye-linked dehydrogenases that catalyze the oxidation of various organic acids, amino acids, and alcohols in the presence of an artificial electron acceptor, such as 2,6-dichloroindophenol, in which FAD and/or FMN is commonly contained as a prosthetic group(s). This enzyme is phylogenetically related to hydrogen cyanide synthase, EC 1.4.99.5, from bacteria, D-hydroxyproline dehydrogenase from bacteria, and L-proline dehydrogenase, EC 1.5.5.2, from archaea. In contrast to Agrobacterium species, PpOpnDH and BjOpnDH genes are located on the chromosome. Flavin-containing OpnDH (the beta-subunit) belongs to the D-amino acid oxidase (DAD) superfamily (pfam01266). An ancestor of this protein family may inherently possess FMN between the alpha- and beta-subunits, and OpnDHtype-1 and OpnDHtype-2 may have acquired the same substrate specificity independently, convergent evolution of OpnDH | Bradyrhizobium japonicum |
| evolution | opine dehydrogenase (OpnDH) belongs to a group of so-called dye-linked dehydrogenases that catalyze the oxidation of various organic acids, amino acids, and alcohols in the presence of an artificial electron acceptor, such as 2,6-dichloroindophenol, in which FAD and/or FMN is commonly contained as a prosthetic group(s). This enzyme is phylogenetically related to hydrogen cyanide synthase, EC 1.4.99.5, from bacteria, D-hydroxyproline dehydrogenase from bacteria, and L-proline dehydrogenase, EC 1.5.5.2, from archaea. In contrast to Agrobacterium species, PpOpnDH and BjOpnDH, genes are located on the chromosome. Pseudomonas putida strain KT2440 very recently acquired this ability by horizontal gene transfer (not plasmid transfer). Convergent evolution of OpnDH | Pseudomonas putida |
| additional information | a poor phylogenetic relationship exists between OdhB1 and OdhB2 in spite of them both functioning as octopine dehydrogenases, which provided clear evidence for the acquisition of novel functions by subunit exchange | Bradyrhizobium japonicum |
| additional information | the beta-subunit functions as a catalytic subunit by itself | Pseudomonas putida |
| physiological function | a potential physiological role in opine catabolism may be limited to (active) BjOpnDH2 because the OdhA and OdhC proteins preferentially associate with OdhB2 over OdhB1 | Bradyrhizobium japonicum |
kcat/KM [mM/s]
| kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.0163 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with 4-iodonitrotetrazolium violet (INT) together with phenazine methosulfate, recombinant His6-tagged enzyme | Bradyrhizobium japonicum | |
| 0.0203 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with 2,6-dichloroindophenol, recombinant His6-tagged enzyme | Bradyrhizobium japonicum | |
| 0.0387 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with ferricyanide, recombinant His6-tagged enzyme | Bradyrhizobium japonicum | |
| 0.0489 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with cytochrome c, recombinant His6-tagged enzyme | Bradyrhizobium japonicum | |
| 0.0721 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with nitroblue tetrazolium (NBT) together with phenazine methosulfate, recombinant His6-tagged enzyme | Bradyrhizobium japonicum | |
| 45.73 | - |
N2-(D-1,3-dicarboxypropyl)-L-arginine | pH 9.0, 30°C, with ferricyanide, recombinant His6-tagged enzyme | Pseudomonas putida | |
| 294.87 | - |
N2-(D-1-carboxyethyl)-L-arginine | pH 9.0, 30°C, with 2,6-dichloroindophenol, recombinant His6-tagged enzyme | Pseudomonas putida | |
| 300.9 | - |
N2-(D-1,3-dicarboxypropyl)-L-arginine | pH 9.0, 30°C, with nitroblue tetrazolium (NBT) together with phenazine methosulfate, recombinant His6-tagged enzyme | Pseudomonas putida | |
| 661.77 | - |
N2-(D-1,3-dicarboxypropyl)-L-arginine | pH 9.0, 30°C, with 2,6-dichloroindophenol, recombinant His6-tagged enzyme | Pseudomonas putida | |
| 720.47 | - |
N2-(D-1,3-dicarboxypropyl)-L-arginine | pH 9.0, 30°C, with 4-iodonitrotetrazolium violet (INT) together with phenazine methosulfate, recombinant His6-tagged enzyme | Pseudomonas putida | |
| 788.05 | - |
N2-(D-1,3-dicarboxypropyl)-L-arginine | pH 9.0, 30°C, with cytochrome c, recombinant His6-tagged enzyme | Pseudomonas putida | |
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