Structures of Thermophilic and Mesophilic Adenylate Kinases from the Genus Methanococcus

• Published in: Journal of molecular biology Vol. 330; no. 5; pp. 1087 - 1099
• Main Authors: Criswell, Angela R., Bae, Euiyoung, Stec, Boguslaw, Konisky, Jordan, Phillips Jr, George N.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 25.07.2003
• Subjects: Adenosine Monophosphate - chemistry; adenylate kinase; Adenylate Kinase - chemistry; Amino Acid Sequence; Arginine - chemistry; Binding Sites; Crystallography, X-Ray; DNA Mutational Analysis; Escherichia coli - metabolism; Hydrogen Bonding; Ligands; Lysine - chemistry; Methanococcus; Methanococcus - enzymology; Methanococcus thermolithotrophicus; Methanococcus voltae; Models, Chemical; Models, Molecular; Molecular Sequence Data; phosphate-binding loop; Plasmids - metabolism; Protein Binding; Protein Conformation; Protein Structure, Tertiary; protein thermostability; Sequence Homology, Amino Acid; Temperature; X-ray crystallography; AKvol, adenylate kinase from Methanococcus voltae; AKeco, adenylate kinase from Escherichia coli; Ap5A, P 1,P 5-di(adenosine-5′) pentaphosphate; AKign, adenylate kinase from Methanococcus igneus; phosphate-binding loop; NMP, nucleoside monophosphate; AKjan, adenylate kinase from Methanococcus jannaschii; adenylate kinase; X-ray crystallography; AMPPNP, 5′-adenylylimidodiphosphate; AKsac, adenylate kinase from Sulfolobus acidocaldarius; Methanococcus; protein thermostability; AKthe, adenylate kinase from Methanococcus thermolithotrophicus; AK, adenylate kinase; RMSD, root-mean-square deviation
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/S0022-2836(03)00655-7

The crystal structures of adenylate kinases from the thermophile Methanococcus thermolithotrophicus and the mesophile Methanococcus voltae have been solved to resolutions of 2.8 Å and 2.5 Å, respectively. The structures of the enzymes are similar to that of the adenylate kinase from archaeal Sulfolobus acidocaldarius in many respects such as the extended central β-sheets, the short LID domain, and the trimeric state. The analysis of unligated and AMP-bound subunits of M. voltae suggests that movements of two mobile domains are not independent of each other. The methanococcal structures are examined with respect to their lack of the “invariant” Lys residue within the phosphate-binding loop, and two Arg residues in the LID domain are proposed as substituting residues based on their conservation among archaeal adenylate kinases and mobility within the structures. Since S. acidocaldarius adenylate kinase has the invariant Lys residue as well as the two Arg residues, its phosphate-binding loop is examined and compared with those of other adenylate kinases. On the basis of the comparison and other available biochemical data, the unusual conformation of the Lys residue in S. acidocaldarius adenylate kinase is explained. Despite possessing 78% sequence identity, the methanococcal enzymes exhibit significantly different thermal stabilities. To study the determinants of thermostability, several structural features including salt-links, hydrogen bonds, packing density, surface to volume ratio and buried surface area are compared between the enzymes. From their difference in apolar buried surface area, hydrophobic interaction is proposed to be a basis for the disparate thermostabilities, and the corresponding free energy difference is also estimated. Results of previous mutational studies are interpreted in terms of the crystal structures, and support the importance of hydrophobic interactions in thermostability.