Functional Studies on an Indel Loop between the Subtypes of meso-Diaminopimelate Dehydrogenase

Divergent evolution exists in the meso-diaminopimelate dehydrogenase (meso-DAPDH) family. Taking meso-DAPDH from Corynebacterium glutamicium ATCC13032 (CgDAPDH) and Symbiobacterium thermophilum IAM14863 (StDAPDH) as examples, the two subtypes differ in terms of their amination ability toward 2-keto acids. The significant structural difference between these two subtypes is an indel loop containing 16 amino acid residues, which exists in CgDAPDH. However, the function of the indel loop has still not been reported to date. Herein, mutagenesis, including loop insertion, loop deletion, and alanine replacement, and molecular dynamics were employed to investigate the function of the loop in CgDAPDH and the evolution of meso-DAPDH. We unveiled the pivotal role of the indel loop during the catalytic cycle of CgDAPDH, especially the R180 residue. The hydrogen-bond interactions formed between R180 and E262 maintain the correct conformation of the catalytic cavity and the catalytic H152 residue. In addition, the indel loop forms a closed hydrogen-bond network with the upstream L176 and downstream H193 residues, which stabilizes the hydrogen-bond network formed by the amino acid side chains throughout the entire protein. Our results demonstrate that the indel loop is not the driving force for the divergent evolution of meso-DAPDH. However, the indel loop affects the release pathway for meso-DAP and pyruvic acid and, more significantly, the release of meso-DAP. Overall, we have identified the importance of the indel loop in CgDAPDH and have excluded its role in the divergent evolution of the meso-DAPDH family.

Automated summary

This study reveals the existence of divergent evolution in the meso-diaminopimelate dehydrogenase (meso-DAPDH) family and investigates the function of an indel loop in CgDAPDH. The results demonstrate that the indel loop plays a crucial role in the catalytic cycle of CgDAPDH, maintaining the correct conformation of the protein and stabilizing the hydrogen-bond network. However, it is not the driving force for the divergent evolution of the meso-DAPDH family.