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<i>Meso</i>-diaminopimelate dehydrogenase (<i>meso</i>-DAPDH) from <i>Corynebacterium glutamicum</i> ATCC13032 (CgDAPDH) is a type I <i>meso</i>-DAPDH that shows obvious preference toward <i>meso</i>-diaminopimelate (<i>meso</i>-DAP) and exhibits almost no amination activity toward 2-keto acids. There are seven distinct conserved insertions and deletions (indels) between type I and type II <i>meso</i>-DAPDH. The current functional analysis of indels is not comprehensive in <i>meso</i>-DAPDH. Continuing from our previous work on these indels, we first examined the functions of the other indels shown as insertion residues in type I CgDAPDH. Alanine mutations in M216, T240, K289, and Q290 lost at least 40% of their activity, highlighting the importance of these four sites in CgDAPDH. Molecular dynamic analysis indicated that the four non-active sites altered the dynamic network of interactions within the protein. Subsequently, these four sites together with the previously identified indel-related residues R180, L176, and H193 were targeted by site-saturation mutagenesis to improve the amination ability of CgDAPDH toward pyruvic acid. The most significant improvement was observed with the mutant CgL176R, which showed a six-fold increase toward pyruvic acid in <i>k</i>_cat/<i>K</i>_m compared to wild-type CgDAPDH. Overall, our study provides new hotspots and ideas for the subsequent protein engineering of CgDAPDH, which may also be applied to other <i>meso</i>-DAPDHs.