Structural basis for thermostability and identification of potential active site residues for adenylate kinases from the archaeal genus Methanococcus

Sequence comparisons of highly related archaeal adenylate kinases (AKs) from the mesophilic Methanococcus voltae, the moderate thermophile Methanococcus thermolithotrophicus, and two extreme thermophiles Methanococcus igneus and Methanococcus jannaschii, allow identification of interactions responsible for the large variation in temperatures for optimal catalytic activity and thermostabilities observed for these proteins. The tertiary structures of the methanococcal AKs have been predicted by using homology modeling to further investigate the potential role of specific interactions on thermal stability and activity. The alignments for the methanococcal AKs have been generated by using an energy-based sequence- structure threading procedure against high-resolution crystal structures of eukaryotic, eubacterial, and mitochondrial adenylate and uridylate (UK) kinases. From these alignments, full atomic model structures have been produced using the program MODELLER. The final structures allow identification of potential active site interactions and place a polyproline region near the active site, both of which are unique to the archaeal AKs. Based on these model structures, the additional polar residues present in the thermophiles could contribute four additional salt bridges and a higher negative surface charge. Since only one of these possible salt bridges is interior, they do not appear significantly to the thermal stability. Instead, our model structures indicate that a larger and moro hydrophobic core, due to a specific increase in aliphatic amino acid content and aliphatic side chain volume, in the thermophilic AKs is responsible for increased thermal stability.