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Literature summary extracted from

  • Liu, N.; Wu, L.; Feng, J.; Sheng, X.; Li, J.; Chen, X.; Li, J.; Liu, W.; Zhou, J.; Wu, Q.; Zhu, D.
    Crystal structures and catalytic mechanism of L-erythro-3,5-diaminohexanoate dehydrogenase and rational engineering for asymmetric synthesis of beta-amino acids (2021), Angew. Chem. Int. Ed. Engl., 60, 10203-10210 .
    View publication on PubMed

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
1.4.1.B2 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

EC Number Protein Variants Comment Organism
1.4.1.B2 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
1.4.1.B2 D177A 0.15% of wild-type activity towards L-erythro-3,5-diaminohexanoate Candidatus Cloacimonas acidaminovorans
1.4.1.B2 D177E 7% of wild-type activity towards L-erythro-3,5-diaminohexanoate Candidatus Cloacimonas acidaminovorans
1.4.1.B2 D177H 0.1% of wild-type activity towards L-erythro-3,5-diaminohexanoate Candidatus Cloacimonas acidaminovorans
1.4.1.B2 D177K almost complete loss of activity towards L-erythro-3,5-diaminohexanoate Candidatus Cloacimonas acidaminovorans
1.4.1.B2 D177N 0.15% of wild-type activity towards L-erythro-3,5-diaminohexanoate Candidatus Cloacimonas acidaminovorans
1.4.1.B2 D177R 0.5% of wild-type activity towards L-erythro-3,5-diaminohexanoate Candidatus Cloacimonas acidaminovorans
1.4.1.B2 D49A loss of activity towards L-erythro-3,5-diaminohexanoate Candidatus Cloacimonas acidaminovorans
1.4.1.B2 D49E 0.1% of wild-type activity towards L-erythro-3,5-diaminohexanoate Candidatus Cloacimonas acidaminovorans
1.4.1.B2 D49N less than 0.1% of wild-type activity towards L-erythro-3,5-diaminohexanoate Candidatus Cloacimonas acidaminovorans
1.4.1.B2 E310G mutant shows improved activity towards substrate (R)-beta-homomethionine Candidatus Cloacimonas acidaminovorans
1.4.1.B2 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
1.4.1.B2 E310G/G323S mutant shows improved activity towards substrate (R)-beta-homomethionine Candidatus Cloacimonas acidaminovorans
1.4.1.B2 H328A 71% of wild-type activity towards L-erythro-3,5-diaminohexanoate Candidatus Cloacimonas acidaminovorans
1.4.1.B2 S125A less than 0.1% of wild-type activity towards L-erythro-3,5-diaminohexanoate Candidatus Cloacimonas acidaminovorans
1.4.1.B2 S125T 6.5% of wild-type activity towards L-erythro-3,5-diaminohexanoate Candidatus Cloacimonas acidaminovorans
1.4.1.B2 S50A 85% of wild-type activity towards L-erythro-3,5-diaminohexanoate Candidatus Cloacimonas acidaminovorans
1.4.1.B2 S50T 0.8% of wild-type activity towards L-erythro-3,5-diaminohexanoate Candidatus Cloacimonas acidaminovorans

Organism

EC Number Organism UniProt Comment Textmining
1.4.1.B2 Candidatus Cloacimonas acidaminovorans B0VJ11
-
-
1.4.1.B2 Candidatus Cloacimonas acidaminovorans Evry B0VJ11
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
1.4.1.B2 (R)-beta-homomethionine + H2O + NADP+
-
 Candidatus Cloacimonas acidaminovorans ? + NH3 + NADPH + H+
-
 ?
1.4.1.B2 (R)-beta-homomethionine + H2O + NADP+
-
 Candidatus Cloacimonas acidaminovorans Evry ? + NH3 + NADPH + H+
-
 ?
1.4.1.B2 L-erythro-3,5-diaminohexanoate + H2O + NADP+
-
 Candidatus Cloacimonas acidaminovorans (S)-5-amino-3-oxohexanoate + NH3 + NADPH + H+
-
 ?
1.4.1.B2 L-erythro-3,5-diaminohexanoate + H2O + NADP+
-
 Candidatus Cloacimonas acidaminovorans Evry (S)-5-amino-3-oxohexanoate + NH3 + NADPH + H+
-
 ?

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
1.4.1.B2 11
-
-
 Candidatus Cloacimonas acidaminovorans

pH Range

EC Number pH Minimum pH Maximum Comment Organism
1.4.1.B2 9
-
 oxidative deamination activity increases rapidly under alkaline conditions from pH 9.0 on Candidatus Cloacimonas acidaminovorans

General Information

EC Number General Information Comment Organism
1.4.1.B2 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