Structure and catalytic mechanism of methylisocitrate lyase, a potential drug target against Coxiella burnetii

We present a comprehensive investigation into the catalytic mechanism of methylisocitrate lyase, a potential drug target candidate against the zoonotic pathogen Coxiella burnetii, the causative agent of Q fever and a federal select agent. Current treatment regimens are prolonged, often with incomplete clearance of the pathogen. We utilized a structure-based bioinformatics pipeline to identify methylisocitrate lyase as a candidate therapeutic target against C. burnetii from a list of essential genes. WT C. burnetii methylisocitrate lyase has a k_cat of 13.8 s^-1 (compared to 105 s^-1 for Salmonella enterica), and isocitrate inhibits with a K_I of 11 mM. We have determined the previously uncharacterized substrate-bound structure of this enzyme family, alongside product and inhibitor-bound structures. These structures of WT enzyme reveal that in the active state the catalytic C118 is positioned 2.98 Å from O5 of methylisocitrate and Arg152 moves toward the substrate relative to the inhibitor bound structure. Analysis of structure-based mutants reveals that Arg152 and Glu110 are both essential for catalysis. We suggest that Arg152 acts as the catalytic base that initiates the methylisocitrate lyase reaction. These results deepen our understanding of the catalytic mechanism of methylisocitrate lyase and could aid the development of new therapeutics against C. burnetii.