Deep Mutational Scanning of FDX1 Identifies Key Structural Determinants of Lipoylation and Cuproptosis

Abstract Cuproptosis is a recently described form of regulated cell death triggered by ionophore-induced copper (Cu) overload in mitochondria. It is critically dependent on ferredoxin 1 (FDX1), a mitochondrial reductase that facilitates cuproptosis by reducing ionophore-bound Cu(II) to Cu(I) thereby triggering its release, and by promoting mitochondrial protein lipoylation, which is directly targeted by the released Cu to drive cell death. Despite the pivotal role of FDX1 in cuproptosis, the structural determinants underlying its distinct functions remain unclear. To address this, we performed deep mutational scanning (DMS) of FDX1 and identified two conserved, solvent-exposed residues—D136 and D139—on its third alpha helix (α-helix 3) that are critical for both FDX1-mediated cuproptosis and lipoylation. Charge-reversal mutations at these positions abolished FDX1’s ability to induce cuproptosis and support lipoylation in cells, despite retaining full enzymatic activity in vitro. Guided by structural and genomic analyses, we further identified dihydrolipoamide dehydrogenase (DLD), the E3 subunit of lipoylated complexes as an alternative FDX1 reductase both in cells and in vitro. Together, these findings establish the acidic α-helix 3 of FDX1 as a critical interface for its upstream regulation and suggest that FDX1’s roles in cuproptosis and in lipoylation are both structurally and functionally linked.