Atomic mechanism of ATP versus GTP selectivity in a small kinase
Dr. Per Rogne, Senior research engineer at Department of Chemistry, Umeå University, Sweden
Adenylate kinase is an essential housekeeping enzyme that controls the energy balance in the cell by catalysing the reversible phosphorylation of adenylate mono phosphate (AMP), using adenylate tri phosphate (ATP) as phosphoryl donor. If the phosphoryl donor, ATP, is replaced by the analog guanosine tri phosphate (GTP) the activity is reduced by two orders of magnitude. Both ATP and GTP are present in similar concentrations in the cells 3 mM and 0.5 mM for ATP and GTP respectively. However, ATP and GTP have very different roles in the cell, ATP is the principal energy carrier in the cell while GTP has specific roles in many signalling pathways. Hence, the selectivity of Adk is very important in order to protect the intracellular pool of GTP.
By an investigation combining NMR, X-ray crystallography, and organic synthesis we have been able to determine the molecular basis for the ATP over GTP selectivity of Adk. We have shown that Adk binds GTP, almost as strong as ATP. However, it binds in a catalytically inhibited conformation. ATP binding, on the other hand, binds in a conformation that induces a large, activating conformational change in Adk. Furthermore, the binding surfaces that mediates both the productive ATP binding and the unproductive GTP binding consists, in part, of the same amino acid residues. By synthesising new ATP analogs we were also able to pinpoint one single interaction between the adenosine moiety of ATP and the backbone of the enzyme that is essential for the difference in ATP and GTP binding conformations.
Our findings are likely of a general nature since, for example, all families of human protein kinases shares the same vital interaction between ATP and the backbone of the protein that we have investigated.
Reference: Rogne P, et al. (2018). Proc Nat Acad Sci 115(12):3012-3017.