mitochondrial Lon protease complex

cellstructuremech:mitochondrial_lon_protease_complex · Other · Multiprotein complex · Proposed

An oligomeric mitochondrial matrix protease assembly built from Lon-family subunits that combine AAA+ ATPase and serine-protease domains to process protein substrates. [DOI:10.1016/j.jbc.2022.101694]

Figure 1: cryo-EM-derived atomic-model views of recombinant yeast Pim1, showing the six-subunit ATPase/protease assembly and substrate-engaging pore. This is a structural model visualization, not a raw micrograph or in situ image. OTHER · *Saccharomyces cerevisiae* (`NCBITaxon:4932`) · Jie Yang, Albert S. Song, R. Luke Wiseman, Gabriel C. Lander; CC BY, via PubMed Central · CC_BY_4_0 · source: PMC PMC8913295.1 fig1 · `DOI:10.1016/j.jbc.2022.101694`

Part of: mitochondrial matrix (GO:0005759)

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Components

Component	Type	Part of / acts on	Grounding	Genes	Stoichiometry	Essential	Role
Lon protease homologue, chloroplastic/mitochondrial	Protein	part of	`InterPro:IPR027503`	PIM1, LON			Lon-family ATPase/serine-protease subunit class represented by yeast Pim1 in the mitochondrial oligomer. The family label also includes chloroplastic homologues; those are not mitochondrial examples here. `DOI:10.1016/j.jbc.2022.101694` Results and Figure 1 resolve six recombinant yeast Pim1 subunits in a substrate-bound assembly. Mature N-terminally His-tagged protein was expressed in bacteria, not imaged in native yeast mitochondria. `InterPro:IPR027503` Native InterPro entry verifies this whole-protein family and its exact label; the source family is broader than its mitochondrial member curated here.

Organism-specific protein examples

Named proteins in which each component's role was established, with the organism the evidence comes from. The component above is the taxon-agnostic family; these are the specific entries behind it.

Lon protease homologue, chloroplastic/mitochondrial

Accession	Protein	Gene	Organism	Entry
`UniProtKB:P36775`	Lon protease homolog, mitochondrial	PIM1	Saccharomyces cerevisiae S288C (`NCBITaxon:559292`)	REVIEWED
Role and evidence (1 reference) Reviewed reference sequence for the yeast mitochondrial Lon subunit, not an identifier for the entire oligomer. `UniProtKB:P36775` Native reviewed record verifies the gene aliases PIM1/LON, loci YBL022C/YBL0440, matrix localization, organism and InterPro assignment.

Canonical examples

NCBITaxon:4932 Saccharomyces cerevisiae — Oligomeric Pim1 was isolated from mitochondria after overexpression in yeast. Its historical seven-subunit interpretation is retained as a preparation-specific conflict, not a fixed copy count. [DOI:10.1073/pnas.96.12.6787]
NCBITaxon:559292 Saccharomyces cerevisiae S288C — Reference-sequence organism, also assigned to the yeast protein entity in PDB 7SXO. The 2022 recombinant expression host was E. coli; this annotation does not establish an in situ S288C experiment. [UniProtKB:P36775]

Functions

ATP-dependent peptidase activity GO:0004176 — Protein-substrate degradation by the mitochondrial Lon assembly; the curated intervention assay uses purified recombinant yeast protein and beta-casein.
- UniProtKB:P36775 Reviewed enzyme annotation supports ATP-dependent proteolysis and mitochondrial matrix localization.
- DOI:10.1016/j.jbc.2022.101694 Figure 3C and Methods assay beta-casein degradation in 5 mM ATP at 37 C. This assay does not independently measure ATP hydrolysis coupling or identify a physiological yeast substrate.

Mechanism graphs

Yeast Pim1 assembly and proteolysis interventions (FUNCTION)

Structural membership and mutant effects on purified-protein beta-casein degradation.

Subject	Predicate	Object	Evidence
Lon protease homologue, chloroplastic/mitochondrial	forms	mitochondrial Lon protease complex	`DOI:10.1016/j.jbc.2022.101694` Figure 1 and structural Results identify a six-Pim1 assembly in the recombinant substrate-bound preparation; this does not settle all native oligomeric states.
mitochondrial Lon protease complex	catalyzes	ATP-dependent peptidase activity	`DOI:10.1016/j.jbc.2022.101694` Figure 3C WT control degrades beta-casein under the specified ATP-containing assay conditions. ATP coupling is supported separately by the reviewed enzyme annotation. `UniProtKB:P36775` Reviewed ATP-dependent enzyme annotation.
Pim1 S1015A substitution	impairs	ATP-dependent peptidase activity	`DOI:10.1016/j.jbc.2022.101694` Figure 3C uses S1015A as the protease-inactive control; loss of activity alone does not establish loss of assembly.
Pim1 charged-insertion deletion	retains assayed activity	ATP-dependent peptidase activity	`DOI:10.1016/j.jbc.2022.101694` PIM1-INSdel retains near-WT beta-casein degradation in Figure 3C. No native yeast or broad substrate-dispensability claim is inferred.
Pim1 charged-insertion GS-linker replacement	retains assayed activity	ATP-dependent peptidase activity	`DOI:10.1016/j.jbc.2022.101694` PIM1-GSlink retains near-WT beta-casein degradation in Figure 3C. This separates this assay from proposed recruitment or DNA-binding roles of the insertion.

Discussions

INTERPRETATION (RESOLVED): Distinguish the mitochondrial oligomer from its protein subunit, substrates and related proteases. Pim1 is a single gene product but forms a structurally resolved oligomer. The InterPro family includes chloroplastic proteins; matrix Lon is distinct from membrane-anchored i-AAA and m-AAA complexes.
CURATION_TODO (OPEN): Reconcile historical seven-subunit and modern six-subunit Pim1 preparations without assuming a universal native oligomer. The 1999 study interpreted a seven-subunit ring from mass measurements and electron microscopy of C-terminally His-tagged protein overexpressed in yeast and purified from mitochondria, including cross-linked preparations. The 2022 structure instead resolves six subunits of mature N-terminally His-tagged yeast protein expressed in bacteria and frozen with ATPgammaS and copurified substrate.
INTERPRETATION (RESOLVED): Resolve the paper's inconsistent structural accessions against native archives. The primary Data availability section lists EMD-25505 and PDB 7XSO. Native matching records are EMD-25502 and PDB 7SXO; each cites the exact Pim1 publication and crosslinks the other.
CURATION_TODO (OPEN): Reconcile publication and archive detail differences before asserting exact substrate or construct boundaries. The article describes a nine-residue polyalanine substrate model, whereas the native PDB entity is a 12-residue unknown sequence. The paper reports approximately 3.21 angstrom resolution versus the archive's 3.3 angstrom. Methods begin the construct at Met182 while the figure schematic labels 181, and Figure 1's pore-loop residue notation is internally inconsistent.
CURATION_TODO (OPEN): Test the insertion and C-terminal extension with physiological substrates or binding partners. The insertion mutants retain beta-casein degradation in vitro, but that does not establish native dispensability. Substrate/adaptor recruitment, DNA binding, peptide exit and a requirement for substrate in hexamerization are hypotheses in the inspected study. The C-terminal Results heading is stronger than the supporting experiments and Discussion.

Datasets

Cryo-EM structure of substrate-translocating S. cerevisiae Lon (PIM1) (PDB:7SXO) · OTHER · STRUCTURAL_IMAGING
Organism: Saccharomyces cerevisiae S288C (NCBITaxon:559292) · Platform: Single-particle cryo-EM
Assembly 1 contains six Pim1 chains A-F and an additional substrate chain G. Its global A6B1 heptameric annotation counts substrate, not seven Pim1 subunits. The model annotates four ATP and two ADP molecules; this is distinct from ATPgammaS used in preparation.
Native entry, polymer entities and assembly inspected. Entity 1 maps to UniProt P36775 and taxon 559292. Entity 2 is a 12-residue unknown-sequence substrate annotated to the E. coli host, but its biological identity is not established. No coordinates are hosted; construct mass and map resolution are not canonical biological properties.
- https://www.rcsb.org/structure/7SXO Native archive crosslinks EMD-25502 and matches the primary title, authors, DOI and PMID. Archive resolution is 3.3 angstrom; the paper reports approximately 3.21 angstrom.
Cryo-EM structure of substrate-translocating S. cerevisiae Lon (PIM1) (EMDB:EMD-25502) · OTHER · STRUCTURAL_IMAGING
Organism: Saccharomyces cerevisiae (NCBITaxon:4932) · Platform: Talos Arctica at 200 kV with a Gatan K2 detector
Native archive reports 3.3 angstrom resolution and links the yeast Pim1 atomic model. This is a purified recombinant preparation, not an in situ mitochondrial image.
Full native XML header SHA-256 621e50e914f5184d6f0d6cb5903e4e525221f3dfd703fccc9145befeb9270793. No map is copied into the repository.
- https://www.ebi.ac.uk/emdb/EMD-25502 Released archive metadata independently matches the primary DOI, PMID, title, authors and PDB 7SXO.

Evidence

DOI:10.1016/j.jbc.2022.101694 Yang and colleagues (2022), PMID 35143841, PMC8913295.1. Results, Discussion, Methods, Data availability, all main-figure captions and actual Figures 1-3 inspected. This record uses the yeast experiments, not bacterial or human comparison structures as yeast evidence.
DOI:10.1073/pnas.96.12.6787 Stahlberg and colleagues (1999), PMID 10359790. Publisher main text and figure captions inspected. Mitochondrial isolation supports native compartment assignment; the historical oligomer interpretation remains explicitly unresolved.
UniProtKB:P36775 Reviewed native protein record independently supports mitochondrial matrix location.
GO:1905368 Verified active cellular-component term peptidase complex supplies a broader is-a parent, not exact identity.
GO:0005759 Verified active cellular-component term mitochondrial matrix supplies compartment parthood, not an is-a relationship.

Curation history

2026-10-05T01:44:41Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-10-05T01:52:54Z codex · EXPANDED_RECORD — Added yeast-scoped protein-family and reference-sequence grounding, assay-bounded causal edges, verified structural datasets, a CC BY 4.0 figure, and explicit oligomer/source-provenance conflicts.

Source: data/structures/other/mitochondrial_lon_protease_complex.yaml