The crystal structures of adenylate kinases from the mesophile Methanococcus voltae (37°C) and the thermophile M. thermolithotrophicus (65°C) have been solved to 2.5 A resolution using molecular replacement methods. These adenylate kinases share 78% primary sequence identity, yet exhibit significantly different thermal stabilities and optimal activity ranges. Analyses of these archaeal structures reveal possible details regarding their disparate thermostabilities. In this study, we perform a comparative structural analysis of the mesophilic and thermophilic adenylate kinases and draw four general conclusions. First, we find correlation between thermostability and ionic interactions and identify a unique ionic network in the thermophilic enzyme. Second, we find beta-branched residues incorporated within alpha-helices of the thermophilic enzyme with significantly greater frequency. Third, we find examples of tighter packing within the CORE domain of the thermophilic enzyme. Last, most of the mutations in the thermophile occur very near the surface resulting in greater negative surface potential. In additional to the comparative thermostability study, we also analyze these two methanococcal structures with respect to their apparent lack of an essential lysine residue, which is present within the P-loop of previously characterized adenylate kinases. Previous modeling experiments proposed that, if protonated, His92 could participate in a similar manner as the lysine residue present in homologous adenylate kinases. From our investigation, we conclude that, as in the case of the homologous Sulfolobus acidocaldarius adenylate kinase structure, His92 is involved in interactions with the terminal phosphate group of AMP. Structural alignments of Methanococcus and homologous enzymes demonstrate that Gly14 is structurally equivalent to Lys14, indicating that an amino acid outside of the canonical P-loop must compensate for the essential lysine deficiency. We propose that this compensatory role is filled either by Arg138 or Arg140, each of which are LID domain residues conserved among the archaeal enzymes.