Visualizing Adenylate Kinase Catalysis Through the X-ray Lens

Abstract

∗ Conformational dynamics of Adenylate kinase is a key to understand the catalysis of this enzyme: a phosphoryl transfer reaction. Adenylate kinases maintain the level of nucleotides by transferring a phosphoryl group from ATP to AMP, which results in 2 ADPs in equilibrium. The active site locates where the ATP-lid and AMP-lid meet on top of the core domain. It has been proposed that various kinds of conformational stages exist by opening and closing the ATP- and the AMP-lids. However, only 4 characteristic types of structures so far have been reported: Open (without substrates, both lids open), Closed (with inhibitor, both lids closed), the AMP domain closed (with AMP, ATP-lid open without substrate) and the ATP domain closed (mutant Adkyst with ATP, AMP-lid open without substrate). We have determined crystal structures of AquifexAdenylate kinases with various substrates at high resolution up to 1.24 Å revealing conformational substates that include 1) a quasi-opened ATP-lid structure with substrates bound to both lids; 2) different conformations of substrates coinciding with movement of essential arginine residues; 3) a partially occupied metaphosphate intermediate structure. ∗ From these snapshots we suggest the role of arginine side chains in the active site with respect to the phosphoryl transfer step. By linking a series of these structures, we visualize the choreography of adenylate kinase catalysis in crystallographic view. NMR experiments characterizing the dynamics between these substates buttress our mechanistic interpretation of the x-ray snapshots.