7OWE

Odinarchaeota Adenylate kinase (OdinAK) in complex with inhibitor Ap5a

Summary for 7OWE

• Entry DOI: 10.2210/pdb7owe/pdb
• Descriptor: Adenylate kinase, BIS(ADENOSINE)-5'-PENTAPHOSPHATE (2 entities in total)
• Functional Keywords: phosphotransferase, odinarchaeota adenylate kinase, ap5a, transferase
• Biological source: Candidatus Odinarchaeota archaeon LCB_4
• Total number of polymer chains: 6
• Total formula weight: 142799.30

Authors

Grundstrom, C.,Aberg-Zingmark, E.,Verma, A.,Wolf-Watz, M.,Sauer, U.H.,Sauer-Eriksson, A.E. (deposition date: 2021-06-18, release date: 2022-09-28, Last modification date: 2024-01-31)

Primary citation

Verma, A.,Aberg-Zingmark, E.,Sparrman, T.,Mushtaq, A.U.,Rogne, P.,Grundstrom, C.,Berntsson, R.,Sauer, U.H.,Backman, L.,Nam, K.,Sauer-Eriksson, E.,Wolf-Watz, M.
Insights into the evolution of enzymatic specificity and catalysis: From Asgard archaea to human adenylate kinases.
Sci Adv, 8:eabm4089-eabm4089, 2022

PubMed Abstract: 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 (OdinAK). 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 F 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.

PubMed: 36332013
DOI: 10.1126/sciadv.abm4089

Experimental method

X-RAY DIFFRACTION (2.75 Å)