Mitochondrial Lon protease couples substrate translocation to proteolytic activation

Abstract

Human LonP1 is an ATP-dependent mitochondrial protease that degrades damaged or redundant proteins. Indiscriminate proteolysis by LonP1 is limited through tight coordination of substrate recognition, unfolding, translocation and catalytic cleavage, yet the role of ATP hydrolysis in these individual steps remains unclear. Here, we show that LonP1 binds substrates and cleaves peptide bonds without ATP hydrolysis, whereas degradation of folded proteins strictly depends on ATP-driven unfolding and translocation. Initial substrate binding opens a closed ADP-bound resting state, enabling nucleotide exchange and stimulating ATPase activity. The opening also increases accessibility of the proteolytic chamber, modestly enhancing peptidase activity. Maximal peptidase activity is observed in a transition-state mimic stabilised by ADP{middle dot}AlF, in which substrate is engaged within the translocation channel. Cryo-EM analysis reveals that in this state the proteolytic active sites are no longer occluded, linking ATP-driven substrate translocation to full proteolytic activation. Together, these findings reveal how LonP1 prevents indiscriminate proteolysis during substrate selection by ensuring that efficient proteolysis occurs only in substrate-translocating states. Model of the conformational landscape and functional cycle of LonP1Schematic overview of LonP1 states and their inter-conversion. State transitions are modulated by substrate, nucleotide occupancy, temperature, and inhibitors. Key distinguishing features include the presence or absence of the lateral gap, nucleotide state, substrate engagement within the A-tunnel, and the handedness of the ATPase (A) domains. Additional indicators include the compactness of the proteolytic (P) domain and the presence of substrate density within the N-terminal (N) domain or at the coiled-coil domain (CCD) as well as the position of a loop within the catalytic centre. The depicted cryo-EM structures represent a model of a continuous conformational landscape and correspond to the closest matching biological states and positions within the reaction cycle, but may also capture transient intermediates or conformations stabilised by experimental conditions. The shown atomic models correspond to the states highlighted in larger font (R-state: PDB 7NGL; P1-state: PDB 7NFY; P2-state: PDB 7NGC; closed LonP1-ADP-substrate: PDB 9CC1). O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=118 SRC="FIGDIR/small/733973v1_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@62128forg.highwire.dtl.DTLVardef@b0a5faorg.highwire.dtl.DTLVardef@160ea7forg.highwire.dtl.DTLVardef@1c35e82_HPS_FORMAT_FIGEXP M_FIG C_FIG