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), which triggers 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 residues, D136 and D139, on α-helix 3 that are critical for both FDX1-mediated lipoylation and cuproptosis. Charge-reversal mutations at these positions abolished FDX1 ability to support lipoylation and induce cuproptosis 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 α-helix 3 of FDX1 as a critical interface for its upstream regulation and suggest that FDX1 roles in lipoylation and cuproptosis are both structurally and functionally linked.