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Literature summary for 5.4.3.3 extracted from
- Large-scale domain motions and pyridoxal-5-phosphate assisted radical catalysis in coenzyme B12-dependent aminomutases (2014), Int. J. Mol. Sci., 15, 3064-3087.
Activating Compound
| Activating Compound | Comment | Organism | Structure |
|---|---|---|---|
| ATP | is an allosteric regulator | Acetoanaerobium sticklandii |  |
| ATP | is an allosteric regulator | Porphyromonas gingivalis | |
| additional information | presence of enzyme component E2 in the assay mixture induces ATP to activate enzyme component E1 allosterically | Acetoanaerobium sticklandii | |
| additional information | presence of enzyme component E2 in the assay mixture induces ATP to activate enzyme component E1 allosterically | Porphyromonas gingivalis |
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| enzyme expression in Escherichia coli | Acetoanaerobium sticklandii |
| enzyme expression in Escherichia coli | Porphyromonas gingivalis |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| crystal structure analysis | Acetoanaerobium sticklandii |
KM Value [mM]
| KM Value [mM] | KM Value Maximum [mM] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.02 | - |
D-Lysine | pH and temperature not specified in the publication | Acetoanaerobium sticklandii | |
| 8.7 | - |
(3S)-3,6-diaminohexanoate | pH and temperature not specified in the publication | Acetoanaerobium sticklandii | |
| 20 | - |
(3R)-3,6-diaminohexanoate | pH and temperature not specified in the publication | Acetoanaerobium sticklandii | |
Molecular Weight [Da]
| Molecular Weight [Da] | Molecular Weight Maximum [Da] | Comment | Organism |
|---|---|---|---|
| 55000 | - |
2 * 55000, alpha-subunit + 2 * 300000, beta-subunit, alpha2beta2 | Acetoanaerobium sticklandii |
| 55000 | - |
2 * 55000, alpha-subunit + 2 * 300000, beta-subunit, alpha2beta2 | Porphyromonas gingivalis |
| 300000 | - |
2 * 55000, alpha-subunit + 2 * 300000, beta-subunit, alpha2beta2 | Acetoanaerobium sticklandii |
| 300000 | - |
2 * 55000, alpha-subunit + 2 * 300000, beta-subunit, alpha2beta2 | Porphyromonas gingivalis |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| (3S)-3,6-diaminohexanoate | Acetoanaerobium sticklandii | - |
(3S,5S)-3,5-diaminohexanoate | - |
r | |
| (3S)-3,6-diaminohexanoate | Porphyromonas gingivalis | - |
(3S,5S)-3,5-diaminohexanoate | - |
r | |
| D-lysine | Acetoanaerobium sticklandii | - |
2,5-diaminohexanoate | - |
r | |
| D-lysine | Porphyromonas gingivalis | - |
2,5-diaminohexanoate | - |
r | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Acetoanaerobium sticklandii | - |
- |
- |
| Porphyromonas gingivalis | - |
- |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
| recombinant enzyme from Escherichia coli | Acetoanaerobium sticklandii |
| recombinant enzyme from Escherichia coli | Porphyromonas gingivalis |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| (3S)-3,6-diaminohexanoate = (3S,5S)-3,5-diaminohexanoate | catalytic mechanism, overview | Acetoanaerobium sticklandii | |
| (3S)-3,6-diaminohexanoate = (3S,5S)-3,5-diaminohexanoate | catalytic mechanism, overview | Porphyromonas gingivalis | |
| D-lysine = (2R,5S)-2,5-diaminohexanoate | catalytic mechanism, overview | Acetoanaerobium sticklandii | |
| D-lysine = (2R,5S)-2,5-diaminohexanoate | catalytic mechanism, overview | Porphyromonas gingivalis |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| (3R)-3,6-diaminohexanoate | - |
Acetoanaerobium sticklandii | (3R,5S)-3,5-diaminohexanoate | - |
r | |
| (3S)-3,6-diaminohexanoate | - |
Acetoanaerobium sticklandii | (3S,5S)-3,5-diaminohexanoate | - |
r | |
| (3S)-3,6-diaminohexanoate | - |
Porphyromonas gingivalis | (3S,5S)-3,5-diaminohexanoate | - |
r | |
| D-lysine | - |
Acetoanaerobium sticklandii | 2,5-diaminohexanoate | - |
r | |
| D-lysine | - |
Porphyromonas gingivalis | 2,5-diaminohexanoate | - |
r | |
| additional information | the enzyme can accept D-lysine and L-beta-lysine. The enzyme employs radical generating capability of coenzyme B12, i.e. 5'-deoxyadenosylcobalamin, and ability of pyridoxal 5'-phosphate, i.e. vitamin B6, to stabilize high-energy intermediates for performing challenging 1,2-amino rearrangements between adjacent carbons | Acetoanaerobium sticklandii | ? | - |
? | |
| additional information | the enzyme can accept D-lysine and L-beta-lysine. The enzyme employs radical generating capability of coenzyme B12, i.e. 5'-deoxyadenosylcobalamin, and ability of pyridoxal 5'-phosphate, i.e. vitamin B6, to stabilize high-energy intermediates for performing challenging 1,2-amino rearrangements between adjacent carbons | Porphyromonas gingivalis | ? | - |
? | |
| additional information | the enzyme can accept D-lysine and L-beta-lysine. The enzyme employs radical generating capability of coenzyme B12, i.e. 5'-deoxyadenosylcobalamin, and ability of pyridoxal 5'-phosphate, i.e.vitamin B6, to stabilize high-energy intermediates for performing challenging 1,2-amino rearrangements between adjacent carbons | Porphyromonas gingivalis | ? | - |
? | |
| additional information | the enzyme can accept D-lysine, L-lysine, and L-beta-lysine. The enzyme employs radical generating capability of coenzyme B12, i.e. 5'-deoxyadenosylcobalamin, and ability of pyridoxal-5'-phosphate, i.e.vitamin B6, to stabilize high-energy intermediates for performing challenging 1,2-amino rearrangements between adjacent carbons | Acetoanaerobium sticklandii | ? | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| More | the enzyme comprises two protein components, the core enzyme E1 and an auxiliary activating protein E2. E1 is a 170 kDa heterotetramer composed of 55 kDa alpha-subunits and 30 kDa beta-subunits and formulated as alpha2beta2, whereas the molecular mass of E2 is about 80 kDa. E2 shows dAdoCbl synthetase activity when isolated separately. A large-scale domain movement is required for interconversion between the catalytically inactive open form and the catalytically active closed form | Acetoanaerobium sticklandii |
| More | the enzyme comprises two protein components, the core enzyme E1 and an auxiliary activating protein E2. E1 is a 170 kDa heterotetramer composed of 55 kDa alpha-subunits and 30 kDa beta-subunits and formulated as alpha2beta2, whereas the molecular mass of E2 is about 80 kDa. E2 shows dAdoCbl synthetase activity when isolated separately. A large-scale domain movement is required for interconversion between the catalytically inactive open form and the catalytically active closed form | Porphyromonas gingivalis |
| tetramer | 2 * 55000, alpha-subunit + 2 * 300000, beta-subunit, alpha2beta2 | Acetoanaerobium sticklandii |
| tetramer | 2 * 55000, alpha-subunit + 2 * 300000, beta-subunit, alpha2beta2 | Porphyromonas gingivalis |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| 5,6-LAM | - |
Acetoanaerobium sticklandii |
| 5,6-LAM | - |
Porphyromonas gingivalis |
| lysine 5,6-aminomutase | - |
Acetoanaerobium sticklandii |
| lysine 5,6-aminomutase | - |
Porphyromonas gingivalis |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| 5'-deoxyadenosylcobalamin | shows ability to produce highly reactive 5'-deoxyadenosyl radical in enzymatic environments | Porphyromonas gingivalis | |
| 5'-deoxyadenosylcobalamin | shows ability to produce highly reactive 5'-deoxyadenosyl radical in enzymatic environments, situated in the Rossmann domain in the crystal structure, and separated from pyridoxal 5'-phosphate | Acetoanaerobium sticklandii | |
| 5'-deoxyadenosylcobalamin | shows ability to produce highly reactive 5'-deoxyadenosyl radical in enzymatic environments, situated in the Rossmann domain in the crystal structure, and separated from pyridoxal-5'-phosphate | Acetoanaerobium sticklandii | |
| pyridoxal 5'-phosphate | stabilizes high-energy intermediates for performing challenging 1,2-amino rearrangements between adjacent carbons | Porphyromonas gingivalis | |
| pyridoxal 5'-phosphate | stabilizes high-energy intermediates for performing challenging 1,2-amino rearrangements between adjacent carbons, bound at the top of the TIM barrel domain and separated from 5'-deoxyadenosylcobalamin, binding site structure involving residues Tyr263, Asn299, Arg184, Arg268, Ser189, Gly187, Gln188, and Ser189, overview | Acetoanaerobium sticklandii | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | the enzyme belongs to the class III dAdoCbl-dependent isomerase family | Acetoanaerobium sticklandii |
| evolution | the enzyme belongs to the class III dAdoCbl-dependent isomerase family | Porphyromonas gingivalis |
| metabolism | the enzyme participates in the second step of the fermentation pathway of lysine in which lysine is converted to acetic acid, ammonia and butyric acid | Acetoanaerobium sticklandii |
| metabolism | the enzyme participates in the second step of the fermentation pathway of lysine in which lysine is converted to acetic acid, ammonia and butyric acid | Porphyromonas gingivalis |
| additional information | a large-scale domain movement is required for interconversion between the catalytically inactive open form and the catalytically active closed form. The recombinant enzyme (KamDE) containing only E1 is active, but is subjected to suicide inactivation with the substrate | Porphyromonas gingivalis |
| additional information | active site structure, overview. A large-scale domain movement is required for interconversion between the catalytically inactive open form and the catalytically active closed form. The recombinant enzyme (KamDE) containing only E1 is active, but is subjected to suicide inactivation with the substrate. Modeling of the closed conformation of the enzyme, domain motions, overview | Acetoanaerobium sticklandii |
kcat/KM [mM/s]
| kcat/KM Value [1/mMs-1] | kcat/KM Value Maximum [1/mMs-1] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.0004 | - |
(3R)-3,6-diaminohexanoate | pH and temperature not specified in the publication | Acetoanaerobium sticklandii | |
| 0.48 | - |
(3S)-3,6-diaminohexanoate | pH and temperature not specified in the publication | Acetoanaerobium sticklandii | |
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