One form, crystallized in the presence of transition state analog components, revealed bound nucleotide, while the other was substrate-free. The two structures are similar to each other and more similar to the substrate-free forms of homologs than to the substrate-bound forms of the other phosphagen kinases. An active site specificity loop (309 - 317) that is disordered in substrate-free structures of homologs, and is known from the NMR of arginine kinase to be inherently dynamic, is resolved in both lombricine kinase structures, providing an improved basis for understanding the loop dynamics. Phosphagen kinases undergo a segmented closing on substrate-binding, but the lombricine kinase ADP complex is in the open form more typical of substrate-free homologs. Through comparison to prior complexes of intermediate structure, a correlation is revealed between overall enzyme conformation and the substrate interactions of His(178). Comparative modeling provides a rationale for the more relaxed specificity of the kinases whose natural substrates are among the larger of the phosphagen substrates.
The full article is available online in The Journal of Biological Chemistry and is free to access.