Dynamic allostery drives acetyl-CoA-mediated activation of Mycobacterium tuberculosis isocitrate lyase 2

Mycobacterium tuberculosis isocitrate lyase 2 (ICL2) is an allosterically regulated enzyme that enables the bacterium to survive on non-glycolytic substrates during infection. Previous studies showed that ICL2 is allosterically regulated by acetyl-CoA and its analogues but the molecular mechanism underpinning this regulation is unknown. Here, we use protein NMR, crystallography, molecular dynamics, and mutagenesis studies to show that two unique structural features of ICL2, its C-terminal domain and a unique helical substructure on its N-terminal catalytic domain, play important roles in the enzyme’s allostery. In particular, we found that the binding of acetyl-CoA promotes the dimerisation of the C-terminal domain and disrupts its interactions with the unique helical substructure on the N-terminal domain. This leads to conformational changes in the ICL2 enzyme that induces activation. Taken together, our findings reveal, for the first time, how the binding of acetyl-CoA, which is not an ICL2 substrate, induces ICL2 activation. By extension, the work also identifies a novel allosteric mechanism controlling M. tuberculosis metabolism that is amenable to therapeutic manipulation.