A Newly Determined Member of the meso -Diaminopimelate Dehydrogenase Family with a Broad Substrate Spectrum

meso -Diaminopimelate dehydrogenase (meso -DAPDH) fromSymbiobacterium thermophilum (StDAPDH) is the first member of themeso -DAPDH family known to catalyze the asymmetric reductive amination of 2-keto acids to produced -amino acids. It is important to understand the catalytic mechanisms of StDAPDH and other enzymes in this family. In this study, based on an evolutionary analysis and examination of catalytic activity, themeso -DAPDH enzymes can be divided into two types. Type I showed highly preferable activity towardmeso -diaminopimelate (meso -DAP), and type II exhibited obviously reversible amination activity with a broad substrate spectrum. StDAPDH belongs to type II. A quaternary structure analysis revealed that insertions/deletions (indels) and a loss of quaternary structure resulted in divergence among members of themeso -DAPDH family. A structure alignment of StDAPDH with a representative of type I, themeso -DAPDH fromCorynebacterium glutamicum (CgDAPDH), indicated that they had the same folding. Based on sequence and conservation analyses, two amino acid residues of StDAPDH, R35 and R71, were found to be highly conserved within type II while also distinct from each other between the subtypes. Site mutagenesis studies identified R71 as a substrate preference-related residue of StDAPDH, which may serve as an indicator of the amination preference of type II. These results deepen the present understanding of themeso -DAPDH family and provide a solid foundation for the discovery and engineering ofmeso -DAPDH ford -amino acid biosynthesis.IMPORTANCE Thel -form of amino acids is typically more abundant than thed -form. However, thed -form has many important pharmaceutical applications.meso -Diaminopimelate dehydrogenase (meso -DAPDH) fromSymbiobacterium thermophilum (StDAPDH) was the first member ofmeso -DAPDH known to catalyze the amination of 2-keto acids to produced -amino acids. Accordingly, we analyzed the evolution ofmeso -DAPDH proteins and found that they form two groups, i.e., type I proteins, which show high preference towardmeso -diaminopimelate (meso -DAP), and type II proteins, which show a broad substrate spectrum. We examined the differences in sequence, ternary structure, and quaternary structure to determine the mechanisms underlying the functional differences between the type I and type II lineages. These results will facilitate the identification of additionalmeso -DAPDHs and may provide guidance to protein engineering studies ford -amino acid biosynthesis.