AFG3L2 is a mitochondrial inner-membrane AAA+ zinc protease whose catalytic domains face the matrix. It assembles into homohexameric m-AAA proteases and heteromeric complexes with SPG7/paraplegin. ATP hydrolysis powers substrate unfolding and translocation into a proteolytic chamber. AFG3L2 removes unassembled or aberrant mitochondrial proteins, including nascent membrane proteins, and can carry out limited precursor processing. Human enzyme studies demonstrate maturation of a recombinant MRPL32 precursor, and expression in yeast supports AFG3L2 self-maturation and SPG7/paraplegin maturation; cellular studies implicate AFG3L2 in OMA1 and PINK1 processing. Regulated turnover of EMRE, SLC25A39, SLC25A45 and TMBIM5 connects its protease activity to calcium uptake, mitochondrial metabolite homeostasis and membrane stress. AFG3L2 dysfunction causes neurological disorders including dominant spinocerebellar ataxia and recessive spastic ataxia.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0034982 mitochondrial protein processing | IBA GO_REF:0000033 | ACCEPT | Summary: Conserved mitochondrial substrate maturation is supported by human AFG3L2 biochemistry. Reason: The PAINT ancestral assertion at PTN000554085 is consistent with maturation of a human MRPL32 precursor by engineered human AFG3L2 (PMID:29932645). Human self evidence in the descendant list is legitimate experimental grounding, not circularity. The assay is biochemical precursor processing; it does not establish that loss of this reaction explains every human mitoribosome phenotype. Independent human-protein expression in yeast also supports AFG3L2 self-maturation and SPG7/paraplegin maturation (PMID:30252181, Figure 3C-D); construct and host limits are recorded in the reference assessment. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000554085 SUPPORTS TRANSFER The ancestral assertion is consistent with human experimental evidence described above. No tree/alignment reconstruction was performed; descendant count and target self evidence are not treated as failures. Supporting Evidence: PMID:29932645 conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form |
| GO:0005745 m-AAA complex | IBA GO_REF:0000033 | ACCEPT | Summary: AFG3L2 is a conserved catalytic subunit of the mitochondrial m-AAA complex. Reason: PAINT node PTN000554085 is supported on the human target by AFG3L2–SPG7 coassembly (PMID:14623864), purified human complexes (PMID:19748354), and an engineered human homohexamer structure (PMID:31327635). Different species have different subunit repertoires, but these human data support the complex assignment. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000554085 SUPPORTS TRANSFER The ancestral assertion is consistent with human experimental evidence described above. No tree/alignment reconstruction was performed; descendant count and target self evidence are not treated as failures. Supporting Evidence: PMID:31327635 The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7) PMID:14623864 paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane |
| GO:0004222 metalloendopeptidase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Human AFG3L2 retains the ancestral zinc-dependent endopeptidase activity. Reason: The PTN008683692 inference agrees with peptide-cleavage assays and active-site mutagenesis in human AFG3L2 (PMID:29932645; PMID:31327635). Both SPG7 and human AFG3L2 experimental descendants can ground the ancestral assertion; no loss of catalytic capacity in the target is evident. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN008683692 SUPPORTS TRANSFER The ancestral assertion is consistent with human experimental evidence described above. No tree/alignment reconstruction was performed; descendant count and target self evidence are not treated as failures. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0004176 ATP-dependent peptidase activity | IEA GO_REF:0000002 | ACCEPT | Summary: AFG3L2 couples ATP use to protein-substrate degradation. Reason: The supplied InterPro assignments match an experimentally active AAA+ metalloprotease. Human enzyme assays demonstrate ATP-fueled substrate unfolding and degradation (PMID:29932645; PMID:31327635), supporting the integrated peptidase activity. Short unstructured peptide cleavage need not itself require ATP. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR000642 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. InterPro:IPR005936 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. InterPro:IPR011546 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. InterPro:IPR037219 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. PMID:19748354 we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes |
| GO:0004222 metalloendopeptidase activity | IEA GO_REF:0000002 | ACCEPT | Summary: The metalloprotease domain catalyses internal peptide-bond cleavage. Reason: The InterPro domain inference agrees with the human zinc-protease active site, peptide assays and proteolytic-site mutations (PMID:29932645; PMID:31327635). This is catalytic evidence rather than domain presence alone. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR000642 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. InterPro:IPR005936 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. InterPro:IPR011546 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. InterPro:IPR037219 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: ATP binds the AAA+ motor domain of AFG3L2. Reason: The InterPro ATPase signatures are consistent with nucleotide-bound human structures and Walker-motif experiments (PMID:19748354; PMID:31327635). Retain this true substrate-binding property as ancillary to the more informative ATP-dependent protease and ATP-hydrolysis activities. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: InterPro:IPR000642 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. InterPro:IPR003959 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. InterPro:IPR003960 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. InterPro:IPR011546 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. InterPro:IPR037219 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. Supporting Evidence: PMID:19748354 we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes PMID:31327635 ATP-dependent translocation to unfold and degrade targeted proteins |
| GO:0005743 mitochondrial inner membrane | IEA GO_REF:0000120 | ACCEPT | Summary: AFG3L2 is anchored in the mitochondrial inner membrane. Reason: The combined mouse-ortholog and UniProt subcellular-location sources agree with direct human mitoplast fractionation and alkaline extraction (PMID:14623864). Matrix-facing catalytic domains do not make the full-length protein a soluble matrix protein. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:Q8JZQ2 SUPPORTS TRANSFER Verified mouse Afg3l2 donor (MGI sequence record Q8JZQ2). Conserved enzyme architecture and independent human evidence support the scoped transfer; precursor autoprocessing is specifically grounded in mouse PMID:19656850 where relevant. ensembl:ENSMUSP00000025408 SUPPORTS TRANSFER The supplied Compara protein accompanies the mouse Afg3l2 donor. The evidence assessment is term-specific above; the complete current Ensembl gene tree was not reconstructed. UniProtKB-SubCell:SL-0168 SUPPORTS TRANSFER The supplied source mapping agrees with the experimentally established activity or subcellular location described above. Supporting Evidence: PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane |
| GO:0006508 proteolysis | IEA GO_REF:0000120 | MODIFY | Summary: AFG3L2 catalyses mitochondrial protein degradation. Reason: The combined ARBA/InterPro assertion of proteolysis is biologically sound. Mitochondrial protein catabolism specifies the established compartment and degradative role, supported by human substrate-turnover studies (PMID:37917749; PMID:38157846). Productive precursor maturation is represented separately. Propagation Review Root cause: NO FAILURE CORE Sources checked: ARBA:ARBA00026291 UNRESOLVED The rule identifier is preserved; its internal conditions were not recovered. The annotation judgment uses independent human evidence stated above. InterPro:IPR000642 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. InterPro:IPR037219 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. Proposed replacements: mitochondrial protein catabolic process Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0008270 zinc ion binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: The proteolytic active site uses zinc. Reason: The supplied InterPro metalloprotease-domain inference agrees with the zinc-containing human AFG3L2 active site (PMID:31327635). Retain metal binding as an ancillary chemical property; the catalytic activity is the more informative core assignment. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: InterPro:IPR011546 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0016020 membrane | IEA GO_REF:0000002 | ACCEPT | Summary: AFG3L2 is a membrane protein. Reason: The InterPro membrane assignment agrees with the native transmembrane architecture and direct human membrane extraction in PMID:14623864. Membrane anchoring is part of the core protease organization, so the broad assertion is retained as ACCEPT at its source resolution. The more precise inner-membrane location in the core summary includes this membrane association; different CC granularity alone does not make it non-core. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR005936 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. InterPro:IPR011546 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. Supporting Evidence: PMID:31327635 m- and i-AAA proteases, which are tethered to the mitochondrial inner membrane (IM), but expose their enzymatic domains to the matrix and intermembrane spaces (IMS), respectively PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane |
| GO:0016887 ATP hydrolysis activity | IEA GO_REF:0000120 | ACCEPT | Summary: AFG3L2 hydrolyses ATP to power substrate handling. Reason: The combined AAA-domain and RHEA:13065 inference agrees with direct ATPase measurements on purified human homo- and hetero-oligomeric complexes (PMID:19748354) and engineered human enzyme (PMID:31327635). ATP hydrolysis drives unfolding/translocation; it is not the chemical hydrolysis of the peptide bond. Propagation Review Root cause: NO FAILURE CORE Sources checked: InterPro:IPR003959 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. InterPro:IPR003960 SUPPORTS TRANSFER The supplied domain/signature supports the stated biochemical class; independent human activity or topology evidence is described above. RHEA:13065 SUPPORTS TRANSFER The supplied source mapping agrees with the experimentally established activity or subcellular location described above. Supporting Evidence: PMID:19748354 we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes PMID:31327635 ATP-dependent translocation to unfold and degrade targeted proteins |
| GO:0005515 protein binding | IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ... | REMOVE | Summary: The reported interaction does not specify an additional informative AFG3L2 molecular function. Reason: The original study is a neurodegenerative-disease interaction map using complementary interaction assays; the seeded partner is HTT/P42858. Its externally recovered main text does not supply a target-pair mechanistic function for AFG3L2. Remove the generic protein-binding term as uninformative; this is not a claim that the interaction is false. No specific replacement molecular function is established by this interaction evidence alone. |
| GO:0005745 m-AAA complex | IEA GO_REF:0000120 | ACCEPT | Summary: Human AFG3L2 forms m-AAA protease complexes. Reason: The ARBA and mouse Afg3l2 sources support a conserved complex component. Independent human AFG3L2–SPG7 coimmunoprecipitation and homohexamer biochemistry substantiate the assignment (PMID:14623864; PMID:19748354). The internal ARBA conditions were not recovered. Propagation Review Root cause: NO FAILURE CORE Sources checked: ARBA:ARBA00088390 UNRESOLVED The rule identifier is preserved; its internal conditions were not recovered. The annotation judgment uses independent human evidence stated above. UniProtKB:Q8JZQ2 SUPPORTS TRANSFER Verified mouse Afg3l2 donor (MGI sequence record Q8JZQ2). Conserved enzyme architecture and independent human evidence support the scoped transfer; precursor autoprocessing is specifically grounded in mouse PMID:19656850 where relevant. ensembl:ENSMUSP00000025408 SUPPORTS TRANSFER The supplied Compara protein accompanies the mouse Afg3l2 donor. The evidence assessment is term-specific above; the complete current Ensembl gene tree was not reconstructed. Supporting Evidence: PMID:31327635 The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7) PMID:14623864 paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane |
| GO:0008237 metallopeptidase activity | IEA GO_REF:0000107 | MODIFY | Summary: AFG3L2 is specifically a metalloendopeptidase. Reason: The mouse-ortholog inference of metallopeptidase activity is consistent with the conserved catalytic domain, and human substrate cleavage establishes internal proteolysis (PMID:29932645). Metalloendopeptidase activity is the supported refinement. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:Q8JZQ2 SUPPORTS TRANSFER Verified mouse Afg3l2 donor (MGI sequence record Q8JZQ2). Conserved enzyme architecture and independent human evidence support the scoped transfer; precursor autoprocessing is specifically grounded in mouse PMID:19656850 where relevant. ensembl:ENSMUSP00000025408 SUPPORTS TRANSFER The supplied Compara protein accompanies the mouse Afg3l2 donor. The evidence assessment is term-specific above; the complete current Ensembl gene tree was not reconstructed. Proposed replacements: metalloendopeptidase activity Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0016485 protein processing | IEA GO_REF:0000107 | MODIFY | Summary: AFG3L2 matures mitochondrial protein precursors. Reason: The Compara mouse Afg3l2 source is consistent with conserved mitochondrial precursor processing. Independent human MRPL32-precursor biochemistry (PMID:29932645) supports the mitochondrial refinement, without transferring every murine substrate or assembly phenotype. Independent human-protein expression in yeast also supports AFG3L2 self-maturation and SPG7/paraplegin maturation (PMID:30252181, Figure 3C-D); construct and host limits are recorded in the reference assessment. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:Q8JZQ2 SUPPORTS TRANSFER Verified mouse Afg3l2 donor (MGI sequence record Q8JZQ2). Conserved enzyme architecture and independent human evidence support the scoped transfer; precursor autoprocessing is specifically grounded in mouse PMID:19656850 where relevant. ensembl:ENSMUSP00000025408 SUPPORTS TRANSFER The supplied Compara protein accompanies the mouse Afg3l2 donor. The evidence assessment is term-specific above; the complete current Ensembl gene tree was not reconstructed. Proposed replacements: mitochondrial protein processing Supporting Evidence: PMID:29932645 conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form |
| GO:0016540 protein autoprocessing | IEA GO_REF:0000107 | ACCEPT | Summary: AFG3L2 catalyzes precursor self-maturation as part of m-AAA protease biogenesis. Reason: The mouse Q8JZQ2 donor is grounded in the MGI-linked PMID:19656850 precursor-processing experiments. Independent human-protein evidence in PMID:30252181 Figure 3C shows precursor accumulation for the protease-inactive E575Q control and R468C variant, supporting autocatalytic maturation. These experiments express human AFG3L2 in m-AAA-deficient yeast, not native human cells. Self-maturation is a direct proteolytic contribution to the conserved enzyme function; human evidence corroborates rather than replaces the mouse donor chain. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:Q8JZQ2 SUPPORTS TRANSFER Mouse Afg3l2 Q8JZQ2 is the original donor; its MGI autoprocessing annotation is experimentally grounded by PMID:19656850. Human AFG3L2 self-maturation in yeast is independently supported by PMID:30252181, with no transfer of mouse Afg3l1 as an active human paralog. ensembl:ENSMUSP00000025408 SUPPORTS TRANSFER The supplied Compara protein accompanies the mouse Afg3l2 donor. The evidence assessment is term-specific above; the complete current Ensembl gene tree was not reconstructed. Supporting Evidence: PMID:19656850 The mitochondrial processing peptidase MPP generates an intermediate form of Afg3l2 that is matured autocatalytically. file:human/AFG3L2/AFG3L2-uniprot.txt autocatalytic proteolytic processing to generate the proteolytically |
| GO:0051604 protein maturation | IEA GO_REF:0000120 | MODIFY | Summary: Proteolytic maturation by AFG3L2 occurs in mitochondria. Reason: The combined ARBA and mouse-ortholog maturation inference agrees with human precursor-processing biochemistry (PMID:29932645). Mitochondrial protein processing specifies the proteolytic step and compartment; the internal ARBA rule conditions remain unexamined. Independent human-protein expression in yeast also supports AFG3L2 self-maturation and SPG7/paraplegin maturation (PMID:30252181, Figure 3C-D); construct and host limits are recorded in the reference assessment. Propagation Review Root cause: NO FAILURE CORE Sources checked: ARBA:ARBA00026902 UNRESOLVED The rule identifier is preserved; its internal conditions were not recovered. The annotation judgment uses independent human evidence stated above. UniProtKB:Q8JZQ2 SUPPORTS TRANSFER Verified mouse Afg3l2 donor (MGI sequence record Q8JZQ2). Conserved enzyme architecture and independent human evidence support the scoped transfer; precursor autoprocessing is specifically grounded in mouse PMID:19656850 where relevant. ensembl:ENSMUSP00000025408 SUPPORTS TRANSFER The supplied Compara protein accompanies the mouse Afg3l2 donor. The evidence assessment is term-specific above; the complete current Ensembl gene tree was not reconstructed. Proposed replacements: mitochondrial protein processing Supporting Evidence: PMID:29932645 conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form |
| GO:0110097 regulation of calcium import into the mitochondrion | IEA GO_REF:0000107 | KEEP AS NON CORE | Summary: AFG3L2 regulates mitochondrial calcium uptake through EMRE turnover. Reason: The Compara mouse Afg3l2 inference is mechanistically plausible because human AFG3L2 depletion also stabilizes EMRE (PMID:28396416). Retain this substrate-specific regulatory outcome as non-core alongside the general protease function. The supported step is proteolysis of the channel regulator, not calcium permeation by AFG3L2. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: UniProtKB:Q8JZQ2 SUPPORTS TRANSFER Verified mouse Afg3l2 donor (MGI sequence record Q8JZQ2). Conserved enzyme architecture and independent human evidence support the scoped transfer; precursor autoprocessing is specifically grounded in mouse PMID:19656850 where relevant. ensembl:ENSMUSP00000025408 SUPPORTS TRANSFER The supplied Compara protein accompanies the mouse Afg3l2 donor. The evidence assessment is term-specific above; the complete current Ensembl gene tree was not reconstructed. Supporting Evidence: PMID:27642048 the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU PMID:28396416 mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis |
| GO:0005739 mitochondrion | IDA GO_REF:0000052 | ACCEPT | Summary: AFG3L2 resides in mitochondria. Reason: GO_REF:0000052 denotes curated immunofluorescence, supporting mitochondrial residence at this source’s resolution. The core mitochondrial location is independently established; separate inner-membrane annotations carry the finer topology. Supporting Evidence: PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane |
| GO:0004222 metalloendopeptidase activity | IMP PMID:41075794 SLC25A45 is required for mitochondrial uptake of methylated ... | ACCEPT | Summary: AFG3L2 protease activity controls SLC25A45 turnover. Reason: In the original study, AFG3L2 siRNA increased SLC25A45-FLAG abundance and slowed turnover; AFG3L2 knockout also caused accumulation (PMID:41075794, Figure 2 and Figure S6). This perturbation supports the established enzyme activity. It is not a purified AFG3L2–SLC25A45 cleavage assay. Supporting Evidence: PMID:41075794 SLC25A45-FLAG levels only increased in cells treated with siRNA targeting AFG3L2 PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0034982 mitochondrial protein processing | IMP PMID:41075794 SLC25A45 is required for mitochondrial uptake of methylated ... | MODIFY | Summary: The SLC25A45 experiment measures mitochondrial substrate degradation. Reason: PMID:41075794 reports increased abundance and blunted turnover after AFG3L2 depletion, rather than production of a mature functional SLC25A45 fragment. GO:0034982 descends from protein processing, whose definition specifies maturation. Mitochondrial protein catabolic process fits the actual experiment; AFG3L2 precursor-maturation capacity remains supported independently by PMID:29932645. Proposed replacements: mitochondrial protein catabolic process Supporting Evidence: PMID:41075794 SLC25A45-FLAG levels only increased in cells treated with siRNA targeting AFG3L2 |
| GO:0005743 mitochondrial inner membrane | IDA PMID:31327635 Unique Structural Features of the Mitochondrial AAA+ Proteas... | ACCEPT | Summary: AFG3L2 acts at the matrix face of the inner membrane. Reason: PMID:31327635 describes this topology, but its cryo-EM construct lacks the native membrane domain and is not a localization experiment on intact full-length protein. The original localization assignment is independently supported by human fractionation in PMID:14623864. Supporting Evidence: PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane |
| GO:0005745 m-AAA complex | IPI PMID:31327635 Unique Structural Features of the Mitochondrial AAA+ Proteas... | ACCEPT | Summary: AFG3L2 subunits assemble into an m-AAA homohexamer. Reason: The original study resolves a substrate-bound human catalytic-core homohexamer stabilized by catalytic-site mutations. This establishes subunit assembly in the engineered construct; earlier full-length human complex studies independently support physiological m-AAA membership (PMID:14623864; PMID:19748354). Supporting Evidence: PMID:31327635 The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7) PMID:14623864 paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane |
| GO:0034982 mitochondrial protein processing | IDA PMID:31327635 Unique Structural Features of the Mitochondrial AAA+ Proteas... | ACCEPT | Summary: AFG3L2 supports mitochondrial precursor processing as well as degradation. Reason: The original structural paper establishes substrate translocation and cleavage using engineered catalytic-core constructs and model substrates; it cites prior precursor-processing work. Retain the curated processing assignment with direct independent support from human MRPL32-precursor maturation in PMID:29932645, rather than treating a degradation assay alone as proof of productive maturation. Independent human-protein expression in yeast also supports AFG3L2 self-maturation and SPG7/paraplegin maturation (PMID:30252181, Figure 3C-D); construct and host limits are recorded in the reference assessment. Supporting Evidence: PMID:29932645 conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | ACCEPT | Summary: AFG3L2 resides in mitochondria. Reason: PMID:34800366 uses quantitative mitochondrial enrichment and proteomic classification. The target-specific supplementary measurement was not recovered in the cached body, but mitochondrial residence is directly established independently by PMID:10395799 and PMID:14623864. Accept with curator deference; do not attribute an inner-membrane topology assay to this source. Supporting Evidence: PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane |
| GO:0141164 mitochondrial protein quality control | IDA PMID:26504172 Quality control of mitochondrial protein synthesis is requir... | ACCEPT | Summary: AFG3L2 limits proteotoxic accumulation during mitochondrial protein synthesis. Reason: PMID:26504172 shows altered nascent-chain abundance after AFG3L2 depletion and suppression of actinonin effects by AFG3L2 overexpression. Five-day knockdown did not reduce large mitoribosomal-subunit assembly or monosome formation. These data support protein quality control without assigning all effects to MRPL32 maturation. Supporting Evidence: PMID:26504172 The mitochondrial m-AAA protease subunit AFG3L2 is critical to this surveillance mechanism |
| GO:0141164 mitochondrial protein quality control | IDA PMID:30683687 Mitochondrial stress response triggered by defects in protei... | ACCEPT | Summary: AFG3L2 protects mitochondria from nascent-chain proteotoxic stress. Reason: PMID:30683687 shows that inhibiting mitochondrial translation suppresses OMA1/OPA1 and later mitoribosome phenotypes after AFG3L2 depletion. This temporal and rescue evidence supports quality control of newly synthesized proteins. OMA1 performs the downstream OPA1 cleavage. Supporting Evidence: PMID:30683687 Responsive quality control mechanisms are needed to ensure that aberrant protein synthesis does not disrupt mitochondrial function. |
| GO:0141164 mitochondrial protein quality control | IDA PMID:34718584 Translation of MT-ATP6 pathogenic variants reveals distinct ... | ACCEPT | Summary: AFG3L2 removes mitochondrial nascent chains that fail membrane insertion. Reason: In PMID:34718584, combined AFG3L2/OXA1L depletion prevents rapid loss of newly synthesized MT-ATP6 and MT-CO2 seen after OXA1L depletion alone. This is direct substrate-quality-control evidence in human cultured fibroblasts, not merely a respiratory phenotype. Supporting Evidence: PMID:34718584 defects in the OXA1L-mediated insertion of MT-ATP6 nascent chains into the mitochondrial inner membrane are rapidly resolved by the AFG3L2 protease complex |
| GO:0004222 metalloendopeptidase activity | IDA PMID:29545505 m-AAA and i-AAA complexes coordinate to regulate OMA1, the s... | ACCEPT | Summary: AFG3L2 participates in proteolytic maturation of OMA1. Reason: The original abstract explicitly identifies AFG3L2-dependent conversion of 60 kDa pre-pro-OMA1 into a 40 kDa form by N-terminal cleavage (PMID:29545505). The full study was not recovered, so retain the established enzyme annotation with curator deference and independent human catalytic evidence. OPA1 cleavage downstream is mediated by OMA1/YME1L1. Supporting Evidence: PMID:29545505 we identify AFG3L2 [matrix (m)-AAA complex] as the major protease mediating this event PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0004222 metalloendopeptidase activity | IDA PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ... | ACCEPT | Summary: The m-AAA protease degrades unassembled EMRE. Reason: The original abstract links AFG3L2-containing m-AAA proteases to EMRE degradation and calcium control (PMID:27642048); it foregrounds a mouse neuronal interactome and does not resolve each human construct assay. Independent human EMRE turnover experiments in PMID:28396416 and AFG3L2 biochemistry support the catalytic assignment. Supporting Evidence: PMID:27642048 the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0004222 metalloendopeptidase activity | IDA PMID:28396416 Proteolytic control of the mitochondrial calcium uniporter c... | ACCEPT | Summary: AFG3L2 proteolysis eliminates excess EMRE in human cells. Reason: The externally read full PMID:28396416 shows that AFG3L2 depletion slows EMRE turnover in MCU-knockout HEK293 cells, with independent shRNAs and isolated-mitochondria ATP-dependence experiments. These experiments support substrate proteolysis, while the enzyme-class assignment also rests on established AFG3L2 chemistry. Supporting Evidence: PMID:28396416 mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis. PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0005743 mitochondrial inner membrane | IDA PMID:37917749 Autoregulatory control of mitochondrial glutathione homeosta... | ACCEPT | Summary: AFG3L2 encounters the matrix-facing loop of inner-membrane SLC25A39. Reason: PMID:37917749 shows substrate association with a trapped AFG3L2 ATPase mutant and loss of regulation after removing the SLC25A39 matrix loop. This is consistent with matrix-facing proteolysis by an inner-membrane enzyme; full-length AFG3L2 topology is independently supported by PMID:14623864. Supporting Evidence: PMID:37917749 Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2. PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane |
| GO:0005745 m-AAA complex | IDA PMID:28396416 Proteolytic control of the mitochondrial calcium uniporter c... | ACCEPT | Summary: AFG3L2 belongs to the m-AAA protease machinery degrading EMRE. Reason: The original full study distinguishes AFG3L2 homohexamers from AFG3L2–SPG7 heterohexamers and tests the effects of depleting each subunit on EMRE turnover (PMID:28396416). Complex membership is also established independently by human coassembly and structural studies. Supporting Evidence: PMID:28396416 mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis. PMID:31327635 The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7) PMID:14623864 paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane |
| GO:0110097 regulation of calcium import into the mitochondrion | IDA PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ... | KEEP AS NON CORE | Summary: Proteolytic control of EMRE abundance regulates calcium uptake. Reason: PMID:27642048 explicitly reports accumulation of unregulated MCU–EMRE channels after m-AAA loss. This substrate-specific regulatory role is supported independently in human cells by PMID:28396416; retain it as non-core. The original study’s inaccessible detailed assays are not reconstructed from its mouse-neuron abstract. Supporting Evidence: PMID:27642048 the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU PMID:28396416 mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis |
| GO:0110097 regulation of calcium import into the mitochondrion | IDA PMID:28396416 Proteolytic control of the mitochondrial calcium uniporter c... | KEEP AS NON CORE | Summary: AFG3L2-mediated EMRE degradation controls uniporter assembly and calcium uptake. Reason: The full PMID:28396416 establishes rapid unassembled-EMRE turnover and tests protease-resistant EMRE. In HEK293 cells, excess resistant EMRE alone did not produce detectable low-calcium uptake when MICU1 was sufficient; deregulated uptake depended on gatekeeper limitation. Retain the context-dependent regulation as non-core. Supporting Evidence: PMID:27642048 the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU PMID:28396416 mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis |
| GO:0004222 metalloendopeptidase activity | IDA PMID:37917749 Autoregulatory control of mitochondrial glutathione homeosta... | ACCEPT | Summary: AFG3L2 catalysis controls SLC25A39 degradation. Reason: PMID:37917749 combines a mitochondrial-protease CRISPR screen, AFG3L2 loss, substrate stabilization, and trapping with ATPase-mutant AFG3L2. SPG7 is dispensable in this setting. The data support AFG3L2 proteolysis rather than assigning glutathione transport or iron-sulfur sensing to the protease. Supporting Evidence: PMID:37917749 Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2. PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0004222 metalloendopeptidase activity | IDA PMID:38157846 Dual regulation of SLC25A39 by AFG3L2 and iron controls mito... | ACCEPT | Summary: AFG3L2 degrades the mitochondrial glutathione carrier SLC25A39. Reason: PMID:38157846 combines coimmunoprecipitation proteomics and targeted knockout: AFG3L2 loss strongly stabilizes endogenous and tagged SLC25A39 without increasing its mRNA. Substrate-loop experiments and independent AFG3L2 biochemistry support the enzyme assignment. Supporting Evidence: PMID:38157846 Co-immunoprecipitation mass spectrometry and CRISPR knockout (KO) in mammalian cells identified that mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1. PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0005743 mitochondrial inner membrane | TAS PMID:31327635 Unique Structural Features of the Mitochondrial AAA+ Proteas... | ACCEPT | Summary: The structural study describes the established inner-membrane m-AAA topology. Reason: This TAS row captures the source’s stated location. Its membrane-truncated structural construct does not independently locate the native membrane anchor; direct human fractionation in PMID:14623864 supports that topology. Supporting Evidence: PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane |
| GO:0030163 protein catabolic process | IDA PMID:37917749 Autoregulatory control of mitochondrial glutathione homeosta... | MODIFY | Summary: AFG3L2 degrades mitochondrial SLC25A39. Reason: The original PMID:37917749 directly links AFG3L2 loss to stabilization of the mitochondrial carrier. Mitochondrial protein catabolic process captures the substrate compartment more precisely than generic protein catabolism. Proposed replacements: mitochondrial protein catabolic process Supporting Evidence: PMID:37917749 Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2. PMID:38157846 mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1 |
| GO:0030163 protein catabolic process | IDA PMID:38157846 Dual regulation of SLC25A39 by AFG3L2 and iron controls mito... | MODIFY | Summary: AFG3L2 controls SLC25A39 turnover within mitochondria. Reason: PMID:38157846 places the proteolytic control at the carrier’s matrix-exposed loop and shows stabilization after AFG3L2 knockout. The mitochondrial catabolic term is a supported refinement of the original broad process. Proposed replacements: mitochondrial protein catabolic process Supporting Evidence: PMID:37917749 Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2. PMID:38157846 mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1 |
| GO:0072753 cellular response to glutathione | IDA PMID:37917749 Autoregulatory control of mitochondrial glutathione homeosta... | KEEP AS NON CORE | Summary: AFG3L2-dependent carrier turnover responds to glutathione availability. Reason: PMID:37917749 shows that GSH depletion reduces AFG3L2–SLC25A39 association and suppresses carrier turnover. AFG3L2 performs the responsive proteolytic step, whereas SLC25A39 mediates import and substrate-associated sensing. Retain this particular feedback response as non-core. Supporting Evidence: PMID:37917749 Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2. PMID:38157846 mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1 |
| GO:0072753 cellular response to glutathione | IDA PMID:38157846 Dual regulation of SLC25A39 by AFG3L2 and iron controls mito... | KEEP AS NON CORE | Summary: Glutathione depletion changes AFG3L2-mediated SLC25A39 degradation. Reason: PMID:38157846 shows that AFG3L2 knockout stabilizes the carrier and eliminates its normal response to GSH-biosynthesis inhibition. This supports the response annotation as a substrate-specific consequence of proteolysis, not direct GSH binding by AFG3L2. Supporting Evidence: PMID:37917749 Under physiological conditions, SLC25A39 is rapidly degraded by mitochondrial protease AFG3L2. PMID:38157846 mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1 |
| GO:0004222 metalloendopeptidase activity | IDA PMID:19748354 An intersubunit signaling network coordinates ATP hydrolysis... | ACCEPT | Summary: Human m-AAA protease complexes are proteolytically active. Reason: PMID:19748354 uses human AFG3L2 and SPG7 expressed in yeast, plus purified complexes, to test motor coordination and protease function. MrpL32 and Ccp1 processing in that experiment concerns yeast substrates; independent human-enzyme assays in PMID:29932645 establish catalytic activity without a species-transfer assumption. Supporting Evidence: PMID:19748354 DHFR- and his-tagged AFG3L2 assembled stochastically regardless of the presence of mutations in his-tagged subunits PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0004222 metalloendopeptidase activity | IDA PMID:29932645 Dissecting Substrate Specificities of the Mitochondrial AFG3... | ACCEPT | Summary: Human AFG3L2 cleaves protein substrates and short peptides. Reason: PMID:29932645 directly assays an engineered soluble, hexamerized human protease. Protein degradation is ATP-fueled, whereas a short accessible peptide can be cleaved without ATP. This supports endopeptidase activity without requiring every peptide-cleavage event to use the unfolding motor. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0004222 metalloendopeptidase activity | IDA PMID:31327635 Unique Structural Features of the Mitochondrial AAA+ Proteas... | ACCEPT | Summary: The human AFG3L2 protease active site catalyses peptide cleavage. Reason: PMID:31327635 combines substrate-bound structural density with peptide-cleavage and protein-degradation assays. The cryo-EM particle contains inactivating mutations; the catalytic conclusion is supported by the separate active-enzyme experiments, not cleavage in the trapped particle. Supporting Evidence: PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0005745 m-AAA complex | IDA PMID:19748354 An intersubunit signaling network coordinates ATP hydrolysis... | ACCEPT | Summary: Purified human AFG3L2 forms homo- and hetero-oligomeric m-AAA complexes. Reason: PMID:19748354 coexpresses human subunits in yeast, purifies complexes and measures intersubunit ATPase effects. Tagged wild-type and mutant AFG3L2 copurification directly supports complex assembly in that system. Supporting Evidence: PMID:19748354 DHFR- and his-tagged AFG3L2 assembled stochastically regardless of the presence of mutations in his-tagged subunits PMID:31327635 The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7) PMID:14623864 paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane |
| GO:0005745 m-AAA complex | IDA PMID:31327635 Unique Structural Features of the Mitochondrial AAA+ Proteas... | ACCEPT | Summary: Engineered human AFG3L2 catalytic cores assemble into a six-subunit m-AAA ring. Reason: PMID:31327635 resolves the homohexameric protease ring and ATPase spiral. The membrane domain is truncated and active-site mutations stabilize the cryo-EM particle; independent full-length human coassembly supports physiological complex membership. Supporting Evidence: PMID:31327635 The human m-AAA protease assembles as homohexamers of AFG3L2 subunits or heterohexamers comprising AFG3L2 subunits and subunits of the closely related homolog paraplegin (SPG7) PMID:14623864 paraplegin coassembles with a homologous protein, AFG3L2, in the mitochondrial inner membrane |
| GO:0016887 ATP hydrolysis activity | IDA PMID:19748354 An intersubunit signaling network coordinates ATP hydrolysis... | ACCEPT | Summary: AFG3L2 ATPase sites coordinate ATP hydrolysis across subunits. Reason: PMID:19748354 measures ATPase activity in purified human AFG3L2 homo- and SPG7-containing hetero-oligomers expressed in yeast. Walker A and Walker B mutations have distinct effects, directly supporting the hydrolysis activity and its intersubunit regulation. Supporting Evidence: PMID:19748354 we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes PMID:31327635 ATP-dependent translocation to unfold and degrade targeted proteins |
| GO:0016887 ATP hydrolysis activity | IDA PMID:31327635 Unique Structural Features of the Mitochondrial AAA+ Proteas... | ACCEPT | Summary: AFG3L2 hydrolyses ATP during substrate handling. Reason: PMID:31327635 reports coupled-enzyme ATPase assays on engineered hexameric human AFG3L2 and compares effects on ATP hydrolysis and substrate degradation. These active-enzyme assays, rather than the ATPase-inactive cryo-EM particle, establish the activity. Supporting Evidence: PMID:19748354 we demonstrate coordinated ATP hydrolysis within m-AAA protease ring complexes PMID:31327635 ATP-dependent translocation to unfold and degrade targeted proteins |
| GO:0051604 protein maturation | IDA PMID:29932645 Dissecting Substrate Specificities of the Mitochondrial AFG3... | MODIFY | Summary: Human AFG3L2 matures a recombinant MRPL32 precursor. Reason: PMID:29932645 uses a soluble, coiled-coil-hexamerized human enzyme and a human MRPL32 precursor lacking its first 30 residues; mass spectrometry identifies the processed product. The mitochondrial processing term describes this specific reaction. This does not establish its quantitative contribution to native human ribosome assembly. Proposed replacements: mitochondrial protein processing Supporting Evidence: PMID:29932645 conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form |
| GO:0005515 protein binding | IPI PMID:35912435 Regulation of mitochondrial proteostasis by the proton gradi... | REMOVE | Summary: The reported interaction does not specify an additional informative AFG3L2 molecular function. Reason: PMID:35912435 directly recovers TMBIM5 in AFG3L2 precipitates and studies its inhibitory regulation of the protease. The binding result does not make AFG3L2 a transporter or establish a separate adaptor activity. Remove the generic protein-binding term as uninformative; this is not a claim that the interaction is false. No specific replacement molecular function is established by this interaction evidence alone. Supporting Evidence: PMID:35912435 Besides these expected interactors, TMBIM5 (also known as GHITM or MICS1) was highly enriched in AFG3L2 precipitates |
| GO:0006508 proteolysis | IDA PMID:35912435 Regulation of mitochondrial proteostasis by the proton gradi... | MODIFY | Summary: AFG3L2 mediates regulated degradation of mitochondrial proteins. Reason: PMID:35912435 identifies TMBIM5 as an interactor and inhibitor of AFG3L2; under hyperpolarizing conditions, AFG3L2 depletion slows TMBIM5 turnover. The authors allow contributions from other peptidases. Mitochondrial protein catabolism is the supported refinement, without transferring TMBIM5 calcium/proton exchange to AFG3L2. Proposed replacements: mitochondrial protein catabolic process Supporting Evidence: PMID:35912435 Downregulation of AFG3L2 slowed degradation and stabilized TMBIM5 in the presence of oligomycin PMID:35912435 Besides these expected interactors, TMBIM5 (also known as GHITM or MICS1) was highly enriched in AFG3L2 precipitates PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0004222 metalloendopeptidase activity | IDA PMID:22354088 Mitochondrial processing peptidase regulates PINK1 processin... | ACCEPT | Summary: AFG3L2 contributes to PINK1 proteolytic processing. Reason: Externally recovered Results in PMID:22354088 show AFG3L2 knockdown alters PINK1 cleavage-fragment abundance while mitochondrial membrane potential is maintained. The paper infers direct participation but does not reconstitute cleavage with purified AFG3L2. Retain the established metalloendopeptidase assignment with independent catalytic support from PMID:29932645. Supporting Evidence: PMID:22354088 Using an unbiased RNA-mediated interference (RNAi)-based screen, we identified four mitochondrial proteases, mitochondrial processing peptidase (MPP), presenilin-associated rhomboid-like protease (PARL), m-AAA and ClpXP, involved in PINK1 degradation. PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0005739 mitochondrion | IDA PMID:22354088 Mitochondrial processing peptidase regulates PINK1 processin... | ACCEPT | Summary: AFG3L2 resides in mitochondria. Reason: The original PINK1 study analyzes AFG3L2-dependent processing in mitochondrial fractions and supports mitochondrial residence (PMID:22354088). Retain this source-level localization; independent inner-membrane assertions provide more detailed topology. Supporting Evidence: PMID:22354088 Using an unbiased RNA-mediated interference (RNAi)-based screen, we identified four mitochondrial proteases, mitochondrial processing peptidase (MPP), presenilin-associated rhomboid-like protease (PARL), m-AAA and ClpXP, involved in PINK1 degradation. |
| GO:0033619 membrane protein proteolysis | IDA PMID:22354088 Mitochondrial processing peptidase regulates PINK1 processin... | ACCEPT | Summary: AFG3L2 contributes to proteolysis of membrane-associated PINK1. Reason: The full externally recovered Results of PMID:22354088 show reduced accumulation of a 52 kDa PINK1 fragment and increased upstream cleavage intermediates after AFG3L2 silencing. Membrane-potential controls reduce the indirect-depolarization explanation. The evidence supports participation in membrane-associated proteolysis, without establishing the purified enzyme’s precise cleavage site. Supporting Evidence: PMID:22354088 we identified four mitochondrial proteases, mitochondrial processing peptidase (MPP), presenilin-associated rhomboid-like protease (PARL), m-AAA and ClpXP, involved in PINK1 degradation PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins |
| GO:0005515 protein binding | IPI PMID:26387735 SPG7 Is an Essential and Conserved Component of the Mitochon... | REMOVE | Summary: The reported interaction does not specify an additional informative AFG3L2 molecular function. Reason: PMID:26387735 reports AFG3L2 coprecipitation with SPG7 in cotransfected COS-7 cells. This physical association is independently supported by PMID:14623864 and is distinct from the paper’s broader permeability-transition interpretation. Remove the generic protein-binding term as uninformative; this is not a claim that the interaction is false. No specific replacement molecular function is established by this interaction evidence alone. Supporting Evidence: PMID:14623864 To explore a potential physical interaction between paraplegin and AFG3L2, we performed coimmunoprecipitation studies in HEK293. PMID:26387735 HA antibody immunoprecipitated a known SPG7 binding partner AFG3L2 |
| GO:0005743 mitochondrial inner membrane | ISS GO_REF:0000024 | ACCEPT | Summary: Inner-membrane localization is conserved between mouse and human AFG3L2. Reason: The ISS donor Q8JZQ2 is mouse Afg3l2. Human mitoplast fractionation and alkaline extraction directly support the same localization (PMID:14623864), so this transfer does not rest solely on sequence similarity. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:Q8JZQ2 SUPPORTS TRANSFER Verified mouse Afg3l2 donor (MGI sequence record Q8JZQ2). Conserved enzyme architecture and independent human evidence support the scoped transfer; precursor autoprocessing is specifically grounded in mouse PMID:19656850 where relevant. Supporting Evidence: PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane |
| GO:0016485 protein processing | ISS GO_REF:0000024 | MODIFY | Summary: Conserved AFG3L2 precursor processing occurs in mitochondria. Reason: The mouse Q8JZQ2 source is consistent with mitochondrial processing, and independent human MRPL32-precursor assays support the more precise term (PMID:29932645). The refinement does not assume that all mouse substrates or processing dependencies are identical in human cells. Independent human-protein expression in yeast also supports AFG3L2 self-maturation and SPG7/paraplegin maturation (PMID:30252181, Figure 3C-D); construct and host limits are recorded in the reference assessment. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:Q8JZQ2 SUPPORTS TRANSFER Verified mouse Afg3l2 donor (MGI sequence record Q8JZQ2). Conserved enzyme architecture and independent human evidence support the scoped transfer; precursor autoprocessing is specifically grounded in mouse PMID:19656850 where relevant. Proposed replacements: mitochondrial protein processing Supporting Evidence: PMID:29932645 conserved residues within the presequence of the mitochondrial ribosomal protein, MrpL32, target the subunit to the protease for processing into a mature form |
| GO:0016540 protein autoprocessing | ISS GO_REF:0000024 | ACCEPT | Summary: AFG3L2 catalyzes precursor self-maturation as part of m-AAA protease biogenesis. Reason: The mouse Q8JZQ2 donor is grounded in the MGI-linked PMID:19656850 precursor-processing experiments. Independent human-protein evidence in PMID:30252181 Figure 3C shows precursor accumulation for the protease-inactive E575Q control and R468C variant, supporting autocatalytic maturation. These experiments express human AFG3L2 in m-AAA-deficient yeast, not native human cells. Self-maturation is a direct proteolytic contribution to the conserved enzyme function; human evidence corroborates rather than replaces the mouse donor chain. Propagation Review Root cause: NO FAILURE CORE Sources checked: UniProtKB:Q8JZQ2 SUPPORTS TRANSFER Mouse Afg3l2 Q8JZQ2 is the original donor; its MGI autoprocessing annotation is experimentally grounded by PMID:19656850. Human AFG3L2 self-maturation in yeast is independently supported by PMID:30252181, with no transfer of mouse Afg3l1 as an active human paralog. Supporting Evidence: PMID:19656850 The mitochondrial processing peptidase MPP generates an intermediate form of Afg3l2 that is matured autocatalytically. file:human/AFG3L2/AFG3L2-uniprot.txt autocatalytic proteolytic processing to generate the proteolytically |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-8949649 | ACCEPT | Summary: The Reactome event places the m-AAA machinery at the mitochondrial inner membrane. Reason: The cached event "PMPCA:PMPCB cleaves the transit peptide of proSMDT1 (proEMRE)" is consistent with the established location of AFG3L2. Independent human fractionation in PMID:14623864 substantiates membrane residence. The transit-peptide cleavage in this event is performed by PMPCA/PMPCB; AFG3L2 participates in the surrounding EMRE proteostasis machinery. Supporting Evidence: PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-8949659 | ACCEPT | Summary: The Reactome event places the m-AAA machinery at the mitochondrial inner membrane. Reason: The cached event "AFG3L2 (m-AAA protease) degrades SMDT1 that is not assembled in MCU" is consistent with the established location of AFG3L2. Independent human fractionation in PMID:14623864 substantiates membrane residence. Supporting Evidence: PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-8949661 | ACCEPT | Summary: The Reactome event places the m-AAA machinery at the mitochondrial inner membrane. Reason: The cached event "C2orf47:AFG3L2 binds the transit peptide of SMDT1" is consistent with the established location of AFG3L2. Independent human fractionation in PMID:14623864 substantiates membrane residence. The cached phrase placing the complex in the matrix is interpreted in light of direct membrane anchoring: its catalytic face is matrix exposed. Supporting Evidence: PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-9838627 | ACCEPT | Summary: The Reactome event places the m-AAA machinery at the mitochondrial inner membrane. Reason: The cached event "AFG3L2 binds mitochondrial inner membrane proteins" is consistent with the established location of AFG3L2. Independent human fractionation in PMID:14623864 substantiates membrane residence. Supporting Evidence: PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-9839053 | ACCEPT | Summary: The Reactome event places the m-AAA machinery at the mitochondrial inner membrane. Reason: The cached event "AFG3L2:SPG7 binds SMDT1 (EMRE)" is consistent with the established location of AFG3L2. Independent human fractionation in PMID:14623864 substantiates membrane residence. Supporting Evidence: PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-9839059 | ACCEPT | Summary: The Reactome event places the m-AAA machinery at the mitochondrial inner membrane. Reason: The cached event "AFG3L2:SPG7 degrades SMDT1 (EMRE)" is consistent with the established location of AFG3L2. Independent human fractionation in PMID:14623864 substantiates membrane residence. Supporting Evidence: PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-9839105 | ACCEPT | Summary: The Reactome event places the m-AAA machinery at the mitochondrial inner membrane. Reason: The cached event "AFG3L2 degrades mitochondrial matrix proteins" is consistent with the established location of AFG3L2. Independent human fractionation in PMID:14623864 substantiates membrane residence. Matrix substrates are accessible to matrix-facing catalytic domains without requiring a soluble matrix pool. Supporting Evidence: PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-9839113 | ACCEPT | Summary: The Reactome event places the m-AAA machinery at the mitochondrial inner membrane. Reason: The cached event "AFG3L2 degrades mitochondrial inner membrane proteins" is consistent with the established location of AFG3L2. Independent human fractionation in PMID:14623864 substantiates membrane residence. Supporting Evidence: PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane |
| GO:0005743 mitochondrial inner membrane | TAS Reactome:R-HSA-9839149 | ACCEPT | Summary: The Reactome event places the m-AAA machinery at the mitochondrial inner membrane. Reason: The cached event "AFG3L2 binds mitochondrial matrix proteins" is consistent with the established location of AFG3L2. Independent human fractionation in PMID:14623864 substantiates membrane residence. Matrix substrates are accessible to matrix-facing catalytic domains without requiring a soluble matrix pool. Supporting Evidence: PMID:14623864 Paraplegin and AFG3L2 were recovered from the membrane fraction, indicating that both are integral proteins of the mitochondrial inner membrane |
| GO:0005515 protein binding | IPI PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ... | REMOVE | Summary: Generic protein binding does not specify the function of this reported interaction. Reason: The PMID:27642048 abstract establishes m-AAA–MAIP1 complex and EMRE-turnover context, but the exact seeded human MAIP1/Q8WWC4 pair and construct-specific assays remain unresolved because the full study was not recovered. Remove the generic protein-binding term as uninformative; this does not reject the interaction or infer a wrong-species assignment from the mouse-neuron abstract. The source-access limit prevents choosing a mechanistic molecular-function replacement. Supporting Evidence: PMID:27642048 MAIP1 assists biogenesis of the MCU subunit EMRE, the m-AAA protease degrades non-assembled EMRE PMID:27642048 the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU |
| GO:0005515 protein binding | IPI PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ... | REMOVE | Summary: Generic protein binding does not specify the function of this reported interaction. Reason: The PMID:27642048 abstract establishes m-AAA–MAIP1 complex and EMRE-turnover context, but the exact seeded human EMRE/SMDT1/Q9H4I9 pair and construct-specific assays remain unresolved because the full study was not recovered. Remove the generic protein-binding term as uninformative; this does not reject the interaction or infer a wrong-species assignment from the mouse-neuron abstract. The source-access limit prevents choosing a mechanistic molecular-function replacement. Supporting Evidence: PMID:27642048 MAIP1 assists biogenesis of the MCU subunit EMRE, the m-AAA protease degrades non-assembled EMRE PMID:27642048 the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU |
| GO:0006508 proteolysis | IMP PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ... | MODIFY | Summary: AFG3L2 degrades unassembled EMRE. Reason: The original PMID:27642048 abstract explicitly describes EMRE degradation by m-AAA protease. Independent human-cell experiments in PMID:28396416 support that substrate-turnover mechanism. Mitochondrial protein catabolism captures the compartment and degradative step. Proposed replacements: mitochondrial protein catabolic process Supporting Evidence: PMID:27642048 the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0007409 axonogenesis | IMP PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ... | UNDECIDED | Summary: The precise axonogenesis experiment remains unresolved. Reason: PMID:27642048 is available as an abstract describing neuronal calcium overload and death, but its full axon-development assay was not recovered. The 2019 structural paper’s general introduction cites other axonal studies and cannot replace this source-specific evidence. Retain the IMP assertion as UNDECIDED rather than claiming that the developmental phenotype is necessarily indirect or that the curator misassigned it. Supporting Evidence: PMID:27642048 Together, our results explain neuronal loss in m-AAA protease deficiency by deregulated mitochondrial Ca2+ homeostasis. |
| GO:0008237 metallopeptidase activity | IMP PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ... | MODIFY | Summary: The EMRE proteolysis result is consistent with AFG3L2 endopeptidase activity. Reason: PMID:27642048 supplies substrate-turnover evidence; human enzyme biochemistry and structure in PMID:29932645 and PMID:31327635 establish internal peptide-bond cleavage. Metalloendopeptidase activity is therefore more precise than the broad metallopeptidase term. Proposed replacements: metalloendopeptidase activity Supporting Evidence: PMID:27642048 the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU PMID:31327635 structure identifies multiple specialized structural features that integrate with conserved motifs required for ATP-dependent translocation to unfold and degrade targeted proteins PMID:29932645 Human AFG3L2 is a compartmental AAA+ protease that performs ATP-fueled degradation at the matrix face of the inner mitochondrial membrane. |
| GO:0036444 calcium import into the mitochondrion | IMP PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ... | MODIFY | Summary: AFG3L2 regulates mitochondrial calcium import by proteolytic control of EMRE. Reason: AFG3L2 performs the proteolytic step controlling uniporter composition; the original abstract reports excess ungated MCU–EMRE channels after protease loss (PMID:27642048). The specific regulatory replacement is supported independently by human experiments (PMID:28396416) and cached GO-CAM 65c57c3400001115. The rationale is the established regulatory mechanism, not a general rule that only channel proteins participate in transport. Proposed replacements: regulation of calcium import into the mitochondrion Supporting Evidence: PMID:27642048 the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU PMID:28396416 mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis |
| GO:0051560 mitochondrial calcium ion homeostasis | IMP PMID:27642048 The m-AAA Protease Associated with Neurodegeneration Limits ... | KEEP AS NON CORE | Summary: Proteolysis of EMRE contributes to mitochondrial calcium homeostasis. Reason: PMID:27642048 links loss of m-AAA protease to mitochondrial calcium overload and neuronal death; independent human EMRE-turnover and flux experiments support the mechanism (PMID:28396416). Retain this substrate-specific homeostatic role as non-core alongside the general protease function. Supporting Evidence: PMID:27642048 the m-AAA protease degrades non-assembled EMRE and ensures efficient assembly of gatekeeper subunits with MCU PMID:28396416 mitochondrial mAAA proteases AFG3L2 and SPG7 rapidly degrade unassembled EMRE using the energy of ATP hydrolysis |
| GO:0005515 protein binding | IPI PMID:14623864 Loss of m-AAA protease in mitochondria causes complex I defi... | REMOVE | Summary: The reported interaction does not specify an additional informative AFG3L2 molecular function. Reason: PMID:14623864 directly demonstrates reciprocal AFG3L2–SPG7 coimmunoprecipitation and high-mass complex formation in human cells. Complex membership is captured by existing m-AAA component annotations. Remove the generic protein-binding term as uninformative; this is not a claim that the interaction is false. No specific replacement molecular function is established by this interaction evidence alone. Supporting Evidence: PMID:14623864 To explore a potential physical interaction between paraplegin and AFG3L2, we performed coimmunoprecipitation studies in HEK293. PMID:26387735 HA antibody immunoprecipitated a known SPG7 binding partner AFG3L2 |
| GO:0005739 mitochondrion | TAS PMID:10395799 Identification and characterization of AFG3L2, a novel parap... | ACCEPT | Summary: AFG3L2 resides in mitochondria. Reason: The original human characterization explicitly reports mitochondrial immunofluorescence (PMID:10395799). This directly supports the broad compartment and is core localization. Separate inner-membrane assertions represent later biochemical precision. Supporting Evidence: PMID:10395799 Immunofluorescence studies revealed that AFG3L2 and paraplegin share a similar expression pattern and the same subcellular localization, the mitochondrial compartment. |
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Download this section (compressed HTML)Q: Which native human precursor-processing reactions require AFG3L2 directly, and how do they differ from substrate degradation or secondary mitochondrial stress responses?
Q: How do AFG3L2 homohexamers and SPG7-containing heterohexamers select regulatory substrates in different human cell types?
Q: How should one integrated m-AAA protease activity be represented with both ATP-dependent peptidase activity (GO:0004176) and metalloendopeptidase activity (GO:0004222), while preserving the distinction between ATP-driven protein translocation and short-peptide cleavage that can occur without ATP?
Experiment: Combine pulse-chase proteomics in AFG3L2 knockout/rescue cells with degron-mutant substrate panels for SLC25A39, SLC25A45, EMRE, and TMBIM5, measuring substrate half-life, AFG3L2 association, and mitochondrial metabolite or calcium readouts.
Hypothesis: AFG3L2 substrates can be prioritized by matrix-exposed degrons and metabolite-sensitive conformational states rather than by generic inner-membrane localization alone.
Type: proteomics and targeted substrate-turnover assays
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