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.
The Protein Expertise Platform (PEP) at the Umeå University is acknowledged for providing reagents for protein production, and M. Lindberg at PEP is appreciated for preparation of plasmids. We acknowledge MAX IV Laboratory (Lund, Sweden) for time on BioMAX and DESY (Hamburg, Germany) for time on PETRA-3. All NMR experiments were performed at the Swedish NMR Center at Umeå University. We also acknowledge the Swedish National Infrastructure for Computing (SNIC) at the High Performance Computing Center North (HPC2N) and the National Energy Research Scientific Computing Center (NERSC) for computational resources.