Decoding allosteric communication pathways in protein lysine acetyltransferase

In bacteria, protein lysine acetylation circuits can control core processes such as carbon metabolism. In E. coli, cyclic adenosine monophosphate (cAMP) controls the transcription level and activity of protein lysine acetyltransferase (PAT). The M. tuberculosis PatA (Mt-PatA) resides in two different conformations; the activated state and autoinhibited state. However, the mechanism of cAMP allosteric regulation of Mt-PatA remains mysterious. Here, we performed extensive all-atom molecular dynamics (MD) simulations (three independent run for each system) and built a residue-residue dynamic correlation network to show how cAMP mediates allosteric activation. cAMP binds at the regulatory site in the regulatory domain, which is 32 Å away from the catalytic site. An extensive conformational restructuring relieves autoinhibition caused by a molecular Lid (residues 161-203) that shelters the substrate-binding surface. In the activated state, the regulatory domain rotates (~40°) around Ser144, which links both domains. Rotation removes the C-terminus from the cAMP site and relieves the autoinhibited state. Also, the molecular Lid refolds and creates an activator binding site. A conserved residue, His173, was mutated into Lys in the Lid, and during an MD trajectory of the activated state, positioned itself near an acetyl donor molecule in the catalytic domain, suggesting a direct mechanism for acetylation. This study describes the allosteric framework for Mt-PatA and prerequisite intermediate states that permit long-distance signal transmission.