FIGURE 1.

Structure of the NBD of the P. furiosus SMC protein in complex with Ap₅A (Protein Data Bank code 3KTA) (19). A, one adenosine moiety of Ap₅A (A1), the adjacent three phosphates, and a Mg²⁺ ion (orange sphere) are bound like Mg-ATP in complex with this SMC-NBD (71). The P-loop (Walker A motif) plays an essential role in phosphate group binding. The Q-loop and the position of the side chain of its conserved glutamine (Gln-145 of SMC) in relationship to the second adenosine moiety of Ap₅A (A2) are depicted in green. The side-chain oxygen, which participates in Mg²⁺ coordination, is depicted in red, and the nitrogen is shown in blue. B, close-up view. The Q-loop glutamine side chain and the Ap₅A molecule are shown in a space-filling representation to illustrate how the second adenosine moiety of Ap₅A (A2) stacks onto the glutamine side chain. Water molecules contained in the crystal structure are not shown. C, several hydrogen bonds (yellow dotted lines) between Gln-145, the second adenosine moiety of Ap₅A, and three water molecules (W1, W2, and W3; red spheres) are thought to confer specific recognition of adenine (19). Water-mediated base specificity has previously been observed in other nucleotide monophosphate kinases (85, 86).