Identification and molecular characterization of a metagenome-derived L-lysine decarboxylase gene from subtropical soil microorganisms

<div><p>L-lysine decarboxylase (LDC, EC 4.1.1.18) is a key enzyme in the decarboxylation of L-lysine to 1,5-pentanediamine and efficiently contributes significance to biosynthetic capability. Metagenomic technology is a shortcut approach used to obtain new genes from uncultured microorganisms. In this study, a subtropical soil metagenomic library was constructed, and a putative LDC gene named <i>ldc1E</i> was isolated by function-based screening strategy through the indication of pH change by L-lysine decarboxylation. Amino acid sequence comparison and homology modeling indicated the close relation between Ldc1E and other putative LDCs. Multiple sequence alignment analysis revealed that Ldc1E contained a highly conserved motif Ser-X-His-Lys (Pxl), and molecular docking results showed that this motif was located in the active site and could combine with the cofactor pyridoxal 5′-phosphate. The <i>ldc1E</i> gene was subcloned into the pET-30a(+) vector and highly expressed in <i>Escherichia coli</i> BL21 (DE3) pLysS. The recombinant protein was purified to homogeneity. The maximum activity of Ldc1E occurred at pH 6.5 and 40°C using L-lysine monohydrochloride as the substrate. Recombinant Ldc1E had apparent <i>K</i>_m, <i>k</i>_cat, and <i>k</i>_cat/<i>K</i>_m values of 1.08±0.16 mM, 5.09±0.63 s⁻¹, and 4.73×10³ s⁻¹ M⁻¹, respectively. The specific activity of Ldc1E was 1.53±0.06 U mg⁻¹ protein. Identifying a metagenome-derived LDC gene provided a rational reference for further gene modifications in industrial applications.</p>