Identification and functional characterization of NAD(P)+ -dependent meso-diaminopimelate dehydrogenase from Numidum massiliense

Abstract

meso-Diaminopimelate dehydrogenase (meso-DAPDH) catalyzes the reversible NADP⁺ -dependent oxidative deamination of meso-2,6-diaminopimelate (meso-DAP) to produce l-2-amino-6-oxopimelate. Moreover, d-amino acid dehydrogenase (d-AADHs) derived from protein-engineered meso-DAPDH is useful for one-step synthesis of d-amino acids with high optical purity. Here, we report the identification and functional characterization of a novel NAD(P)⁺ -dependent meso-DAPDH from Numidum massiliense (NmDAPDH). After the gene encoding the putative NmDAPDH was expressed in recombinant Escherichia coli cells, the enzyme was purified 4.0-fold to homogeneity from the crude extract through five purification steps. Although the previously known meso-DAPDHs use only NADP⁺ as a coenzyme, NmDAPDH was able to use both NADP⁺ and NAD⁺ as coenzymes. When NADP⁺ was used as a coenzyme, NmDAPDH exhibited an approximately 2 times higher k_cat /K_m value toward meso-DAP than that of meso-DAPDH from Symbiobacterium thermophilum (StDAPDH). NmDAPDH also catalyzed the reductive amination of corresponding 2-oxo acids to produce acidic d-amino acids such as d-aspartate and d-glutamate. The optimum pH and temperature for the oxidative deamination of meso-DAP were about 10.5 and 75°C, respectively. Like StDAPDH, NmDAPDH exhibited high stability: it retained more than 75% of its activity after 30 min at 60°C (pH 7.2) or at pHs ranging from 5.5 to 13.0 (50°C). Alignment of the amino acid sequences of NmDAPDH and the known meso-DAPDHs suggested NmDAPDH has a hexameric structure. Given its specificity for both NADP⁺ and NAD⁺ , high stability, and a broad range of reductive amination activity toward 2-oxo acids, NmDAPDH appears to offer advantages for engineering a more effective d-AADH.

Keywords: NAD(P)+-dependent; Numidum massiliense; d-Amino acid; meso-Diaminopimelate; meso-Diaminopimelate dehydrogenase.