Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases

Enzymatic catalysis is critically dependent on selectivity, active site architecture, and dynamics. To contribute insights into the interplay of these properties, we established an approach with NMR, crystallography, and MD simulations focused on the ubiquitous phosphotransferase adenylate kinase (AK) isolated from Odinarchaeota (OdinAK). Odinarchaeota belongs to the Asgard archaeal phylum that is believed to be the closest known ancestor to eukaryotes. We show that OdinAK is a hyperthermophilic trimer that, contrary to other AK family members, can use all NTPs for its phosphorylation reaction. Crystallographic structures of OdinAK-NTP complexes revealed a universal NTP-binding motif, while 19F NMR experiments uncovered a conserved and rate-limiting dynamic signature. As a consequence of trimerization, the active site of OdinAK was found to be lacking a critical catalytic residue and is therefore considered to be atypical. On the basis of discovered relationships with human monomeric homologs, our findings are discussed in terms of evolution of enzymatic substrate specificity and cold adaptation.

Automated summary

Enzymatic catalysis relies on selectivity, active site architecture, and dynamics, which were investigated in this study using NMR, crystallography, and MD simulations on the phosphotransferase adenylate kinase (AK) from Odinarchaeota (OdinAK). OdinAK, a hyperthermophilic trimer, was found to use all NTPs for phosphorylation reaction, unlike other AK family members. Crystallographic structures revealed a common NTP-binding motif, while 19F NMR experiments showed a conserved and rate-limiting dynamic signature. The trimeric form of OdinAK lacked a critical catalytic residue in its active site, making it atypical. The findings provide insights into the evolution of enzymatic substrate specificity and cold adaptation through comparisons with human monomeric homologs.