Crystallization (Comment) | Organism |
---|---|
structures of 3,5-DAHDH in apo form, complexed with cofactor NADPH, and of variant E310G/A314Y in complex with NADPH. The overall monomeric structure of 3,5-DAHDH is composed of an N-terminal catalytic domain (Domain I) and a C-terminal cofactor-binding domain (Domain II) separating by a deep cleft | Candidatus Cloacimonas acidaminovorans |
Protein Variants | Comment | Organism |
---|---|---|
A179S/E310G/G323S/H328N | mutant exhibited an about 200 times enhanced activity towards substrate (R)-beta-homomethionine compared to mutant E310G and increased activities with (S)-beta-homolysine, (S)-beta-aminobutyric acid, (R)-beta-phenylalanine, (S)-beta-homophenylalanine | Candidatus Cloacimonas acidaminovorans |
D177A | 0.15% of wild-type activity towards L-erythro-3,5-diaminohexanoate | Candidatus Cloacimonas acidaminovorans |
D177E | 7% of wild-type activity towards L-erythro-3,5-diaminohexanoate | Candidatus Cloacimonas acidaminovorans |
D177H | 0.1% of wild-type activity towards L-erythro-3,5-diaminohexanoate | Candidatus Cloacimonas acidaminovorans |
D177K | almost complete loss of activity towards L-erythro-3,5-diaminohexanoate | Candidatus Cloacimonas acidaminovorans |
D177N | 0.15% of wild-type activity towards L-erythro-3,5-diaminohexanoate | Candidatus Cloacimonas acidaminovorans |
D177R | 0.5% of wild-type activity towards L-erythro-3,5-diaminohexanoate | Candidatus Cloacimonas acidaminovorans |
D49A | loss of activity towards L-erythro-3,5-diaminohexanoate | Candidatus Cloacimonas acidaminovorans |
D49E | 0.1% of wild-type activity towards L-erythro-3,5-diaminohexanoate | Candidatus Cloacimonas acidaminovorans |
D49N | less than 0.1% of wild-type activity towards L-erythro-3,5-diaminohexanoate | Candidatus Cloacimonas acidaminovorans |
E310G | mutant shows improved activity towards substrate (R)-beta-homomethionine | Candidatus Cloacimonas acidaminovorans |
E310G/A314Y | mutation E310G destroys the hydrogen bond interaction with the amide group of NADPH observed in the wild-type structure. Mutant shows improved activity towards substrate (R)-beta-homomethionine | Candidatus Cloacimonas acidaminovorans |
E310G/G323S | mutant shows improved activity towards substrate (R)-beta-homomethionine | Candidatus Cloacimonas acidaminovorans |
H328A | 71% of wild-type activity towards L-erythro-3,5-diaminohexanoate | Candidatus Cloacimonas acidaminovorans |
S125A | less than 0.1% of wild-type activity towards L-erythro-3,5-diaminohexanoate | Candidatus Cloacimonas acidaminovorans |
S125T | 6.5% of wild-type activity towards L-erythro-3,5-diaminohexanoate | Candidatus Cloacimonas acidaminovorans |
S50A | 85% of wild-type activity towards L-erythro-3,5-diaminohexanoate | Candidatus Cloacimonas acidaminovorans |
S50T | 0.8% of wild-type activity towards L-erythro-3,5-diaminohexanoate | Candidatus Cloacimonas acidaminovorans |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Candidatus Cloacimonas acidaminovorans | B0VJ11 | - |
- |
Candidatus Cloacimonas acidaminovorans Evry | B0VJ11 | - |
- |
Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
---|---|---|---|---|---|---|
(R)-beta-homomethionine + H2O + NADP+ | - |
Candidatus Cloacimonas acidaminovorans | ? + NH3 + NADPH + H+ | - |
? | |
(R)-beta-homomethionine + H2O + NADP+ | - |
Candidatus Cloacimonas acidaminovorans Evry | ? + NH3 + NADPH + H+ | - |
? | |
L-erythro-3,5-diaminohexanoate + H2O + NADP+ | - |
Candidatus Cloacimonas acidaminovorans | (S)-5-amino-3-oxohexanoate + NH3 + NADPH + H+ | - |
? | |
L-erythro-3,5-diaminohexanoate + H2O + NADP+ | - |
Candidatus Cloacimonas acidaminovorans Evry | (S)-5-amino-3-oxohexanoate + NH3 + NADPH + H+ | - |
? |
pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
11 | - |
- |
Candidatus Cloacimonas acidaminovorans |
pH Minimum | pH Maximum | Comment | Organism |
---|---|---|---|
9 | - |
oxidative deamination activity increases rapidly under alkaline conditions from pH 9.0 on | Candidatus Cloacimonas acidaminovorans |
General Information | Comment | Organism |
---|---|---|
metabolism | in the proposed mechanism, the catalytic cycle starts with the hydride transfer from C3 of L-erythro-3,5-diaminohexanoate to C4 of NADP+ with a barrier of 18.8 kcal/mol. The generated iminium intermediate (Int1) is 1.8 kcal/mol lower than the ternary complex E:DAH. In the next hydration step, both the deprotonated C5-amino group of L-erythro-3,5-diaminohexanoate and D177 can be the catalytic base to activate the water molecule that attacks the electrophilic carbon of Int1. The barrier is 8.3 kcal/mol or 12.4 kcal/mol relative to Int1 for the pathways with C5-amino group or D177, respectively. For the former pathway, after the formation of hydrated intermediate (Int2), a proton transfer takes place from the protonated C5-amino group to D177 via the newly formed hydroxyl group with a barrier of 10.7 kcal/mol relative to Int1, arriving at the same intermediate (Int3) as the latter pathway. Then, a proton transfer from D177 to C3-amino group results in intermediate Int4 with -0.1 kcal/mol energy, in which the protonated amino group can be significantly stabilized by the carboxylate groups of D49 and D177. Finally, the products are formed by the C-N bond cleavage, concurrently with intramolecular proton transfer from the C3-hydroxyl group to the C5-amine | Candidatus Cloacimonas acidaminovorans |