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Literature summary for 5.4.3.3 extracted from
- The molecular mechanism of the open-closed protein conformational cycle transitions and coupled substrate binding, activation and product release events in lysine 5,6-aminomutase (2016), Chem. Commun. (Camb.), 52, 6399-6402 .
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| D298A | site-directed mutagenesis, the mutation of the alpha-subunit | Acetoanaerobium sticklandii |
|
| D298N | site-directed mutagenesis, the mutation of the alpha-subunit reduces the enzymatic activity in converting D-lysine into D-2,5-diaminohexanoic acid | Acetoanaerobium sticklandii |
| K370A | site-directed mutagenesis, the mutation of the alpha-subunit reduces the enzymatic activity in converting D-lysine into D-2,5-diaminohexanoic acid | Acetoanaerobium sticklandii |
| K370Q | site-directed mutagenesis, the mutation of the alpha-subunit reduces the enzymatic activity in converting D-lysine into D-2,5-diaminohexanoic acid | Acetoanaerobium sticklandii |
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 |  |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Acetoanaerobium sticklandii | E3PRJ5 AND E3PRJ4 | alpha- and beta-subunits | - |
Reaction
| Reaction | Comment | Organism | Reaction ID |
|---|---|---|---|
| (3S)-3,6-diaminohexanoate = (3S,5S)-3,5-diaminohexanoate | in the first step of the proposed catalytic cycle the enzyme accepts the substrate in the open state. Substrate interactions with the active site residues initiate an external aldimine formation with PLP breaking the pyridoxal 5'-phosphate-lys144beta internal aldimine, which results in two simultaneous events: (1) the domain motion brings dAdoCbl close to the pyridoxal 5'-phosphate-substrate adduct and locks the enzyme in the catalytically active closed state and (2) cleavage of the Co-C bond of dAdoCbl generates the 5'-deoxyadenosyl radical and cob(II)alamin. Hydrogen abstraction by 5'-deoxyadenosyl radical from the substrate generates deoxyadenosine and the substrate related radical that undergoes radical isomerization via a hypothetical azacyclopropylcarbinyl radical to afford the product related radical. Hydrogen abstraction by the product related radical from deoxyadenosine generates the product-pyridoxal 5'-phosphate adduct and 5'-deoxyadenosyl radical. Finally, transition from the closed state to open state occurs, which allows the release of the product and reformation of dAdoCbl and the internal aldimine | Acetoanaerobium sticklandii |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| (3S)-3,6-diaminohexanoate | - |
Acetoanaerobium sticklandii | (3S,5S)-3,5-diaminohexanoate | - |
r | |
| D-lysine | - |
Acetoanaerobium sticklandii | 2,5-diaminohexanoate | - |
r | |
| additional information | lysine 5,6-aminomutase, 5,6-LAM, catalyzes the reversible amino shift between C6 and C5 of D-lysine and L-beta-lysine. 5,6-LAM is a 5'-deoxyadenosylcobalamin and pyridoxal 5'-phosphate co-dependent radical enzyme, molecular mechanism of the open-closed protein conformational cycle transitions and coupled substrate binding, activation and product release events in lysine 5,6-aminomutase, overview | Acetoanaerobium sticklandii | ? | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| heterotetramer | alpha2beta2, subunits alpha and beta are encoded by genes kamD and kamE | Acetoanaerobium sticklandii |
| More | the beta-Rossmann subunit binds dAdoCbl in a base-off mode with the axial 5,6-dimethylbenzimidazole ligand displaced by His133beta. The alpha-triosephosphate isomerase barrel binds pyridoxal 5'-phosphate, which is also covalently bound as a Schiff base (internal aldimine) to Lys144beta, forming a cross-link between the subunits. The distance between dAdoCbl and pyridoxal 5'-phosphate is 24 A. This configuration represents the open state of the enzyme | Acetoanaerobium sticklandii |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| 5,6-LAM | - |
Acetoanaerobium sticklandii |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| 5'-deoxyadenosylcobalamin | - |
Acetoanaerobium sticklandii | |
| additional information | lysine 5,6-aminomutase is a 5'-deoxyadenosylcobalamin and pyridoxal 5'-phosphate co-dependent radical enzyme | Acetoanaerobium sticklandii | |
| pyridoxal 5'-phosphate | - |
Acetoanaerobium sticklandii | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| malfunction | the D298N, D298A, K370Q, and K370A variants of the alpha-subunits abolish the enzymatic activity in converting D-lysine into D-2,5-diaminohexanoic acid | Acetoanaerobium sticklandii |
| additional information | both Asp298alpha and Lys370alpha are functionally important residues in enzyme 5,6-LAM | Acetoanaerobium sticklandii |
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