- EMDB-25502: Yeast Lon (PIM1) with endogenous substrate -
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Basic information
Entry
Database: EMDB / ID: EMD-25502
Title
Yeast Lon (PIM1) with endogenous substrate
Map data
Sample
Complex: Cryo-EM structure of yeast Lon (PIM1) in complex with endogenous substrate
Protein or peptide: Lon protease homolog, mitochondrial
Protein or peptide: endogenous substrate
Ligand: ADENOSINE-5'-TRIPHOSPHATE
Ligand: MAGNESIUM ION
Ligand: ADENOSINE-5'-DIPHOSPHATE
Function / homology
Function and homology information
regulation of mitochondrial DNA metabolic process / oxidation-dependent protein catabolic process / mitochondrial respiratory chain complex assembly / endopeptidase La / mitochondrial DNA metabolic process / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein complex assembly / mitochondrion organization / protein folding ...regulation of mitochondrial DNA metabolic process / oxidation-dependent protein catabolic process / mitochondrial respiratory chain complex assembly / endopeptidase La / mitochondrial DNA metabolic process / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / chaperone-mediated protein complex assembly / mitochondrion organization / protein folding / single-stranded DNA binding / cellular response to oxidative stress / response to heat / sequence-specific DNA binding / mitochondrial matrix / serine-type endopeptidase activity / ATP hydrolysis activity / mitochondrion / ATP binding Similarity search - Function
Lon protease homologue, chloroplastic/mitochondrial / Lon protease, bacterial/eukaryotic-type / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Lon N-terminal domain profile. / Lon protease, N-terminal domain ...Lon protease homologue, chloroplastic/mitochondrial / Lon protease, bacterial/eukaryotic-type / Peptidase S16, active site / ATP-dependent serine proteases, lon family, serine active site. / Lon proteolytic domain profile. / Peptidase S16, Lon proteolytic domain / Lon protease / Lon protease (S16) C-terminal proteolytic domain / Lon N-terminal domain profile. / Lon protease, N-terminal domain / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase Similarity search - Domain/homology
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)
United States
Citation
Journal: J Biol Chem / Year: 2022 Title: Cryo-EM structure of hexameric yeast Lon protease (PIM1) highlights the importance of conserved structural elements. Authors: Jie Yang / Albert S Song / R Luke Wiseman / Gabriel C Lander / Abstract: Lon protease is a conserved ATP-dependent serine protease composed of an AAA+ domain that mechanically unfolds substrates and a serine protease domain that degrades these unfolded substrates. In ...Lon protease is a conserved ATP-dependent serine protease composed of an AAA+ domain that mechanically unfolds substrates and a serine protease domain that degrades these unfolded substrates. In yeast, dysregulation of Lon protease (PIM1) attenuates lifespan and leads to gross mitochondrial morphological perturbations. Although structures of the bacterial and human Lon protease reveal a hexameric assembly, yeast PIM1 was speculated to form a heptameric assembly and is uniquely characterized by a ∼50-residue insertion between the ATPase and protease domains. To further understand the yeast-specific properties of PIM1, we determined a high-resolution cryo-electron microscopy structure of PIM1 in a substrate-translocating state. Here, we reveal that PIM1 forms a hexamer, conserved with that of bacterial and human Lon proteases, wherein the ATPase domains form a canonical closed spiral that enables pore loop residues to translocate substrates to the protease chamber. In the substrate-translocating state, PIM1 protease domains form a planar protease chamber in an active conformation and are uniquely characterized by a ∼15-residue C-terminal extension. These additional C-terminal residues form an α-helix located along the base of the protease domain. Finally, we did not observe density for the yeast-specific insertion between the ATPase and protease domains, likely due to high conformational flexibility. Biochemical studies to investigate the insertion using constructs that truncated or replaced the insertion with a glycine-serine linker suggest that the yeast-specific insertion is dispensable for PIM1's enzymatic function. Altogether, our structural and biochemical studies highlight unique components of PIM1 machinery and demonstrate evolutionary conservation of Lon protease function.
History
Deposition
Nov 24, 2021
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Header (metadata) release
Jan 12, 2022
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Map release
Jan 12, 2022
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Update
Jul 27, 2022
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Current status
Jul 27, 2022
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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