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Literature summary for 5.4.3.5 extracted from
- Role of histidine 225 in adenosylcobalamin-dependent ornithine 4,5-aminomutase (2012), Bioorg. Chem., 40, 39-47.
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| recombinant expression of wild-type and mutant enzymes | Acetoanaerobium sticklandii |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| H225A | site-directed mutagenesis | Acetoanaerobium sticklandii |
| H225Q | site-directed mutagenesis | Acetoanaerobium sticklandii |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| 2,4-diaminobutyric acid | - |
Acetoanaerobium sticklandii |  |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| additional information | - |
additional information | Michaelis-Menten kinetics | Acetoanaerobium sticklandii | |
| 0.14 | - |
D-ornithine | recombinant mutant H225A, pH 8.5, 25°C | Acetoanaerobium sticklandii | |
| 0.19 | - |
D-ornithine | recombinant wild-type, pH 8.5, 25°C | Acetoanaerobium sticklandii | |
| 0.453 | - |
D-ornithine | recombinant mutant H225Q, pH 8.5, 25°C | Acetoanaerobium sticklandii | |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Co2+ | in the paramagnetic Co2+ metal center of the cob(II)alamin cofactor | Acetoanaerobium sticklandii | |
Molecular Weight [Da]
| Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|
| 12800 | - |
2 * 12800, subunit OraS + 2 * 82900, subunit OraE, alpha2beta2 | Acetoanaerobium sticklandii |
| 82900 | - |
2 * 12800, subunit OraS + 2 * 82900, subunit OraE, alpha2beta2 | Acetoanaerobium sticklandii |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| D-ornithine | Acetoanaerobium sticklandii | - |
(2R,4S)-2,4-diaminopentanoate | - |
? | |
| D-ornithine | Acetoanaerobium sticklandii DSM 519 | - |
(2R,4S)-2,4-diaminopentanoate | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Acetoanaerobium sticklandii | E3PY95 | beta-subunit | - |
| Acetoanaerobium sticklandii | E3PY96 | alpha-subunit | - |
| Acetoanaerobium sticklandii DSM 519 | E3PY95 | beta-subunit | - |
| Acetoanaerobium sticklandii DSM 519 | E3PY96 | alpha-subunit | - |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| D-ornithine = (2R,4S)-2,4-diaminopentanoate | radical-based catalysis that is initiated and propagated by the enzyme's adenosylcobalamin and pyridoxal 5'-phosphate cofactors. Following transaldimination, the Co-C bond of adenosylcobalamin undergoes homolytic rupture, generating a highly reactive carbon-centered 5'-deoxyadenosyl radical and cob(II)alamin. The 5'-deoxyadenosyl radical abstracts the C4 hydrogen atom from the D-ornithinyl-pyridoxal 5'-phosphate aldimine producing a substrate radical, which undergoes internal addition to the imine N to form an aziridylcarbinyl-pyridoxal 5'-phosphate radical adduct. Ring opening leads to formation of a product-like radical intermediate 3, which reabstracts a hydrogen atom from 5'-deoxyadenosine. Adenosylcobalamin is reformed with geminate recombination between the 5'-deoxyadenosyl radical and cob(II)alamin. Release of product from pyridoxal 5'-phosphate completes the catalytic cycle | Acetoanaerobium sticklandii | |
| D-ornithine = (2R,4S)-2,4-diaminopentanoate | radical-based catalysis that is initiated and propagated by the enzyme's adenosylcobalamin and pyridoxal 5'-phosphate cofactors. Following transaldimination, the Co-C bond of adenosylcobalamin undergoes homolytic rupture, generating a highly reactive carbon-centered 5'-deoxyadenosyl radical and cob(II)alamin. The 5'-deoxyadenosyl radical abstracts the C4 hydrogen atom from the D-ornithinylpyridoxal 5'-phosphate aldimine producing a substrate radical, which undergoes internal addition to the imine N to form an aziridylcarbinyl-pyridoxal 5'-phosphate radical adduct. Ring opening leads to formation of a product-like radical intermediate 3, which reabstracts a hydrogen atom from 5'-deoxyadenosine. Adenosylcobalamin is reformed with geminate recombination between the 5'-deoxyadenosyl radical and cob(II)alamin. Release of product from pyridoxal 5'-phosphate completes the catalytic cycle | Acetoanaerobium sticklandii |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| D-ornithine | - |
Acetoanaerobium sticklandii | (2R,4S)-2,4-diaminopentanoate | - |
? | |
| D-ornithine | the 1,2-amino shift performed by the enzyme is considered energetically challenging as it involves breakage of chemically inert C-H and C-N bonds. OAM overcomes this thermodynamic barrier with radical-based catalysis that is initiated and propagated by the enzyme's adenosylcobalamin and pyridoxal 5'-phosphate cofactors, conformational change upon substrate binding, overview | Acetoanaerobium sticklandii | (2R,4S)-2,4-diaminopentanoate | - |
? | |
| D-ornithine | the 1,2-amino shift performed by the enzyme is considered energetically challenging as it involves breakage of chemically inert CH and CN bonds. OAM overcomes this thermodynamic barrier with radical-based catalysis that is initiated and propagated by the enzyme's adenosylcobalamin and pyridoxal 5'-phosphate cofactors, conformational change upon substrate binding, overview | Acetoanaerobium sticklandii | (2R,4S)-2,4-diaminopentanoate | - |
? | |
| D-ornithine | - |
Acetoanaerobium sticklandii DSM 519 | (2R,4S)-2,4-diaminopentanoate | - |
? | |
| D-ornithine | the 1,2-amino shift performed by the enzyme is considered energetically challenging as it involves breakage of chemically inert CH and CN bonds. OAM overcomes this thermodynamic barrier with radical-based catalysis that is initiated and propagated by the enzyme's adenosylcobalamin and pyridoxal 5'-phosphate cofactors, conformational change upon substrate binding, overview | Acetoanaerobium sticklandii DSM 519 | (2R,4S)-2,4-diaminopentanoate | - |
? | |
| D-ornithine | the 1,2-amino shift performed by the enzyme is considered energetically challenging as it involves breakage of chemically inert C-H and C-N bonds. OAM overcomes this thermodynamic barrier with radical-based catalysis that is initiated and propagated by the enzyme's adenosylcobalamin and pyridoxal 5'-phosphate cofactors, conformational change upon substrate binding, overview | Acetoanaerobium sticklandii DSM 519 | (2R,4S)-2,4-diaminopentanoate | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| tetramer | 2 * 12800, subunit OraS + 2 * 82900, subunit OraE, alpha2beta2 | Acetoanaerobium sticklandii |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| adenosylcobalamin-dependent ornithine 4,5-aminomutase | - |
Acetoanaerobium sticklandii |
| OAM | - |
Acetoanaerobium sticklandii |
| ornithine 4,5-aminomutase | - |
Acetoanaerobium sticklandii |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 25 | - |
assay at | Acetoanaerobium sticklandii |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.3 | - |
D-ornithine | recombinant mutant H225A, pH 8.5, 25°C | Acetoanaerobium sticklandii | |
| 1 | - |
D-ornithine | recombinant mutant H225Q, pH 8.5, 25°C | Acetoanaerobium sticklandii | |
| 2.9 | - |
D-ornithine | recombinant wild-type, pH 8.5, 25°C | Acetoanaerobium sticklandii | |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 8.5 | - |
assay at | Acetoanaerobium sticklandii |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| adenosylcobalamin | paramagnetic Co2+ metal center of the cob(II)alamin cofactor | Acetoanaerobium sticklandii | |
| pyridoxal 5'-phosphate | covalently bound via a Schiff base (imine) to Lys629 | Acetoanaerobium sticklandii | |
Ki Value [mM]
| Ki Value [mM] | Ki Value maximum [mM] | Inhibitor | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.0046 | - |
2,4-diaminobutyric acid | recombinant wild-type, pH 8.5, 25°C | Acetoanaerobium sticklandii | |
| 0.095 | - |
2,4-diaminobutyric acid | recombinant mutant H225A, pH 8.5, 25°C | Acetoanaerobium sticklandii | |
| 0.098 | - |
2,4-diaminobutyric acid | recombinant mutant H225Q, pH 8.5, 25°C | Acetoanaerobium sticklandii | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| metabolism | the enzyme catalyzes the second step in the oxidative breakdown of the amino acid, converting D-ornithine to 2,4-diaminopentanoic acid | Acetoanaerobium sticklandii |
kcat/KM [mM/s]
| kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 2.2 | - |
D-ornithine | recombinant mutant H225A, pH 8.5, 25°C | Acetoanaerobium sticklandii | |
| 2.2 | - |
D-ornithine | recombinant mutant H225Q, pH 8.5, 25°C | Acetoanaerobium sticklandii | |
| 15.2 | - |
D-ornithine | recombinant wild-type, pH 8.5, 25°C | Acetoanaerobium sticklandii | |
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Release 2023.1 (January 2023)
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