id: Q9Y6H3 gene_symbol: ATP23 product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:9606 label: Homo sapiens description: >- ATP23 encodes a conserved M76-family metalloprotease homolog associated with mitochondria. The ATP23 family is best characterized as a mitochondrial inner-membrane/intermembrane-space factor for ATP synthase biogenesis: yeast Atp23 processes the mitochondrially encoded Atp6/subunit 6 precursor and also promotes Fo-sector assembly independently of proteolysis. Human ATP23 carries the conserved metalloprotease features and is detected in human mitochondrial proteome datasets, but its direct mammalian substrate and submitochondrial topology remain less fully characterized. Older KUB3/XRCC6BP1 literature describes Ku70 binding, but the strongest functional model for UniProt Q9Y6H3 is mitochondrial ATP synthase assembly and mitochondrial protein processing rather than DNA repair. existing_annotations: - term: id: GO:0033615 label: mitochondrial proton-transporting ATP synthase complex assembly evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in review: summary: Conserved ATP23-family biology supports a core role in mitochondrial ATP synthase Fo-sector assembly. action: ACCEPT reason: >- Accept as core. The strongest mechanistic evidence comes from yeast Atp23, where ATP23 mutants impair Fo assembly and protease-inactive Atp23 still supports functional ATPase assembly, separating the assembly-factor role from proteolytic processing. Human ATP synthase assembly literature establishes the ATP6/ATP8 membrane-domain assembly context, while ATP23-specific human substrate data remain limited. additional_reference_ids: - PMID:17135290 - PMID:17135288 - PMID:29440398 - file:human/ATP23/ATP23-deep-research-falcon.md supported_by: - &zeng_dual reference_id: PMID:17135290 supporting_text: Atp23p, in addition to its processing activity, must provide another important function in F O assembly - &zeng_chaperone reference_id: PMID:17135290 supporting_text: Atp23p may, therefore, also be a chaperone, which in conjunction with Atp10p mediates the association of subunit 6 with the subunit 9 ring. - &osman_dual reference_id: PMID:17135288 supporting_text: Atp23 promotes the association of mature Atp6 with Atp9 oligomers - &he_context reference_id: PMID:29440398 supporting_text: This intermediate provides the template for insertion of ATP6 and ATP8 - term: id: GO:0034982 label: mitochondrial protein processing evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in review: summary: ATP23-family proteins process mitochondrial Atp6/subunit 6 in yeast; this supports mitochondrial protein processing while the direct human substrate remains unresolved. action: ACCEPT reason: >- Accept, with the caveat that the precise human cleavage substrate is not established. Yeast Atp23 removes the N-terminal prepeptide from the mitochondrial ATP synthase subunit 6 precursor, and human ATP23 retains the conserved M76/metalloprotease signature. Because mammalian ATP6 lacks the same yeast presequence, this term should be interpreted as conserved ATP23-family mitochondrial protein-processing biology rather than a demonstrated human ATP6 cleavage event. additional_reference_ids: - PMID:17135290 - PMID:17135288 - file:human/ATP23/ATP23-uniprot.txt - file:human/ATP23/ATP23-deep-research-falcon.md supported_by: - &zeng_processing reference_id: PMID:17135290 supporting_text: Atp23p is a mitochondrial protease that removes the 10-residue-long N-terminal prepeptide of the subunit 6 precursor - &osman_processing reference_id: PMID:17135288 supporting_text: Atp23 serves as a processing peptidase and mediates the maturation of the mitochondrial-encoded F(O)-subunit Atp6 after its insertion into the inner membrane. - &uniprot_m76 reference_id: file:human/ATP23/ATP23-uniprot.txt supporting_text: InterPro; IPR019165; Peptidase_M76_ATP23. - term: id: GO:0004222 label: metalloendopeptidase activity evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables review: summary: The metalloendopeptidase activity annotation is supported by the conserved M76 domain and yeast ATP23 active-site evidence. action: ACCEPT reason: >- Accept as core molecular function. Human ATP23 has the Peptidase_M76_ATP23 InterPro/Pfam signatures and conserved metal-binding/catalytic features; yeast mutagenesis shows that the HEXXH active-site glutamate is required for cleavage of the Atp6 precursor. additional_reference_ids: - PMID:17135290 - file:human/ATP23/ATP23-uniprot.txt supported_by: - &zeng_active_site reference_id: PMID:17135290 supporting_text: It has an HEXXH motif previously shown to be part of the active sites of metalloproteases including zinc proteases - &zeng_cleavage reference_id: PMID:17135290 supporting_text: Substitution of the essential glutamic acid by glutamine prevents cleavage of the N-terminal prepeptide - *uniprot_m76 - &uniprot_metallo reference_id: file:human/ATP23/ATP23-uniprot.txt supporting_text: GO; GO:0004222; F:metalloendopeptidase activity; IEA:InterPro. - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:32296183 qualifier: enables review: summary: The generic binary-interactome protein-binding annotation is true at most as high-throughput interaction context and is not informative for ATP23 function. action: MARK_AS_OVER_ANNOTATED reason: >- Mark as over-annotated. The source is a broad human binary interactome map rather than ATP23-focused functional evidence. For ATP23, the informative molecular function is metalloendopeptidase activity and the informative process is ATP synthase assembly/protein processing; generic protein binding should not be treated as a core function. additional_reference_ids: - PMID:17135290 - file:human/ATP23/ATP23-uniprot.txt supported_by: - reference_id: PMID:32296183 supporting_text: To map the reference interactome, we performed nine screens of Space III, followed by pairwise verification by quadruplicate retesting and sequence confirmation. - *uniprot_metallo - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:32814053 qualifier: enables review: summary: The neurodegenerative-disease interactome annotation is too generic and not a mechanistic ATP23 molecular-function term. action: MARK_AS_OVER_ANNOTATED reason: >- Mark as over-annotated. The publication reports systematic interaction mapping and aggregation network resources, not a specific ATP23 activity. The ATP23 review should emphasize metalloendopeptidase/ATP synthase assembly biology rather than the uninformative parent term protein binding. additional_reference_ids: - PMID:17135290 - file:human/ATP23/ATP23-uniprot.txt supported_by: - reference_id: PMID:32814053 supporting_text: Interactome maps are valuable resources to elucidate protein function and disease mechanisms. - *uniprot_metallo - term: id: GO:0005829 label: cytosol evidence_type: IDA original_reference_id: GO_REF:0000052 qualifier: located_in review: summary: Cytosol is a broad HPA location and should not define ATP23's core cellular site. action: KEEP_AS_NON_CORE reason: >- Keep as non-core. HPA-derived cytosol staining may reflect a non-mitochondrial pool or precursor/background signal, but the coherent ATP23-family model and independent mitochondrial proteome evidence point to mitochondrial localization as the functional location. additional_reference_ids: - PMID:34800366 - file:human/ATP23/ATP23-uniprot.txt supported_by: - &uniprot_cytosol reference_id: file:human/ATP23/ATP23-uniprot.txt supporting_text: GO; GO:0005829; C:cytosol; IDA:HPA. - &mitocop reference_id: PMID:34800366 supporting_text: We defined a human mitochondrial high-confidence proteome (MitoCoP) of 1,134 protein-coding genes - term: id: GO:0005886 label: plasma membrane evidence_type: IDA original_reference_id: GO_REF:0000052 qualifier: located_in review: summary: Plasma membrane localization is not supported by ATP23's conserved mitochondrial protease/assembly-factor biology. action: REMOVE reason: >- Remove. This HPA-derived cellular-component annotation conflicts with stronger ATP23-family and mitochondrial proteome evidence, and there is no functional literature placing ATP23 at the plasma membrane. additional_reference_ids: - PMID:34800366 - PMID:17135290 - file:human/ATP23/ATP23-uniprot.txt supported_by: - reference_id: file:human/ATP23/ATP23-uniprot.txt supporting_text: GO; GO:0005886; C:plasma membrane; IDA:HPA. - *mitocop - &zeng_inner_membrane reference_id: PMID:17135290 supporting_text: Atp23p is associated with the mitochondrial inner membrane and is conserved from yeast to humans. - term: id: GO:0030054 label: cell junction evidence_type: IDA original_reference_id: GO_REF:0000052 qualifier: located_in review: summary: Cell junction localization is not supported by ATP23's mitochondrial protease/assembly factor evidence. action: REMOVE reason: >- Remove. This HPA-derived location is not corroborated by UniProt functional features, ATP23 orthology, or mitochondrial proteome evidence, and it is not connected to any supported ATP23 biological role. additional_reference_ids: - PMID:34800366 - PMID:17135290 - file:human/ATP23/ATP23-uniprot.txt supported_by: - reference_id: file:human/ATP23/ATP23-uniprot.txt supporting_text: GO; GO:0030054; C:cell junction; IDA:HPA. - *mitocop - *zeng_inner_membrane - term: id: GO:0005739 label: mitochondrion evidence_type: HTP original_reference_id: PMID:34800366 qualifier: located_in review: summary: Mitochondrion is the best-supported broad cellular location for ATP23. action: ACCEPT reason: >- Accept. The human MitoCoP study defines a high-confidence mitochondrial proteome from multiple proteomics/importomics approaches, and ATP23's protein name, M76 family membership, and yeast ortholog evidence all support mitochondrial localization. additional_reference_ids: - PMID:17135290 - PMID:17135288 - file:human/ATP23/ATP23-uniprot.txt supported_by: - *mitocop - &uniprot_mito reference_id: file:human/ATP23/ATP23-uniprot.txt supporting_text: GO; GO:0005739; C:mitochondrion; HTP:FlyBase. - *zeng_inner_membrane - &osman_ims reference_id: PMID:17135288 supporting_text: conserved metallopeptidase present in the intermembrane space, termed Atp23 - term: id: GO:0004677 label: DNA-dependent protein kinase activity evidence_type: TAS original_reference_id: PMID:10219089 qualifier: enables review: summary: The Ku70-binding paper does not show ATP23/KUB3 has DNA-dependent protein kinase activity. action: REMOVE reason: >- Remove. The original publication describes DNA-PK as a separate repair kinase and reports isolation of Ku70-binding proteins, including KUB3. It does not establish KUB3/ATP23 as the catalytic DNA-dependent protein kinase, and this annotation conflicts with the supported metalloprotease/mitochondrial assembly model. additional_reference_ids: - file:human/ATP23/ATP23-deep-research-falcon.md - file:human/ATP23/ATP23-uniprot.txt supported_by: - &kub3_abstract reference_id: PMID:10219089 supporting_text: We isolated Ku70-binding proteins (KUB1-KUB4) using yeast two-hybrid analyses. - &kub3_role_under_investigation reference_id: PMID:10219089 supporting_text: The role of apoJ/XIP8 in ionizing radiation resistance/sensitivity is under investigation. - *uniprot_metallo - term: id: GO:0005958 label: DNA-dependent protein kinase-DNA ligase 4 complex evidence_type: NAS original_reference_id: PMID:10219089 qualifier: part_of review: summary: Ku70 binding does not demonstrate ATP23/KUB3 membership in a DNA-PK-DNA ligase IV complex. action: REMOVE reason: >- Remove. The cited abstract indicates that KUB3 interacts with Ku70, but does not place KUB3 in the DNA-PK-DNA ligase IV complex. The assignment appears to over-interpret an alias-linked interaction report and is not part of the conserved ATP23 mitochondrial function. additional_reference_ids: - file:human/ATP23/ATP23-deep-research-falcon.md - file:human/ATP23/ATP23-uniprot.txt supported_by: - *kub3_abstract - reference_id: PMID:10219089 supporting_text: KUB3 with Ku70 were confirmed by co-immunoprecipitation analyses - *uniprot_metallo - term: id: GO:0006303 label: double-strand break repair via nonhomologous end joining evidence_type: TAS original_reference_id: PMID:10219089 qualifier: involved_in review: summary: The original KUB3/Ku70 paper is insufficient for annotating ATP23 to NHEJ. action: REMOVE reason: >- Remove. The paper frames DNA-PK/Ku as NHEJ machinery but reports KUB3 primarily as a Ku70-binding clone; it does not demonstrate that ATP23 is a NHEJ effector. Later Falcon review also flags KUB3/XRCC6BP1 DNA-repair literature as alias-linked and functionally distinct from the better-supported mitochondrial ATP23 model. additional_reference_ids: - file:human/ATP23/ATP23-deep-research-falcon.md - file:human/ATP23/ATP23-uniprot.txt supported_by: - *kub3_abstract - *kub3_role_under_investigation - &falcon_alias_caution reference_id: file:human/ATP23/ATP23-deep-research-falcon.md supporting_text: Any functional annotation must explicitly separate (i) robust mitochondrial Atp23 ortholog biology from (ii) KUB3/XRCC6BP1 nuclear DNA-repair reports until mapping is confirmed by a source that links these identifiers directly. - term: id: GO:0005758 label: mitochondrial intermembrane space evidence_type: ISO original_reference_id: PMID:17135288 qualifier: located_in review: summary: Add as a conservative PN-supported location candidate, based on ATP23-family intermembrane-space topology evidence. action: NEW reason: >- Add as a conservative cellular-component annotation. The PN projection places ATP23 in the intermembrane-space-protease bucket and proposes the compartmental term rather than a shared enzymatic/process term. Ortholog evidence supports Atp23 as an intermembrane-space/inner-membrane protein, but this should be treated as sequence-orthology/topology inference for human ATP23 rather than direct human submitochondrial fractionation. additional_reference_ids: - PMID:17135290 - file:human/ATP23/ATP23-notes.md supported_by: - *osman_ims - reference_id: PMID:17135290 supporting_text: Atp23p is associated with the inner membrane in an orientation such that the C-terminus faces the intermembrane space. - reference_id: file:human/ATP23/ATP23-notes.md supporting_text: 'PN projection review: ATP23 is listed in the PN intermembrane-space-protease bucket with candidate GO:0005758; this is acceptable as a conservative, compartmental location only when supported by ATP23 family topology evidence.' references: - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: [] - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: [] - id: GO_REF:0000052 title: Gene Ontology annotation based on curation of immunofluorescence data findings: [] - id: PMID:10219089 title: Isolation of Ku70-binding proteins (KUBs). findings: [] - id: PMID:17135290 title: The metalloprotease encoded by ATP23 has a dual function in processing and assembly of subunit 6 of mitochondrial ATPase. findings: [] - id: PMID:17135288 title: Prohibitins interact genetically with Atp23, a novel processing peptidase and chaperone for the F1Fo-ATP synthase. findings: [] - id: PMID:29440398 title: Assembly of the membrane domain of ATP synthase in human mitochondria. findings: [] - id: PMID:32296183 title: A reference map of the human binary protein interactome. findings: [] - id: PMID:32814053 title: Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains. findings: [] - id: PMID:34800366 title: Quantitative high-confidence human mitochondrial proteome and its dynamics in cellular context. findings: [] - id: PMID:38906862 title: Enhancing mitochondrial proteolysis alleviates alpha-synuclein-mediated cellular toxicity. findings: [] - id: file:human/ATP23/ATP23-uniprot.txt title: UniProtKB record for human ATP23 findings: [] - id: file:human/ATP23/ATP23-deep-research-falcon.md title: Falcon deep research report for ATP23 findings: [] - id: file:human/ATP23/ATP23-notes.md title: ATP23 PN review notes findings: [] core_functions: - molecular_function: id: GO:0004222 label: metalloendopeptidase activity description: >- ATP23 is best represented as a conserved mitochondrial M76 metalloprotease and ATP synthase assembly factor. Yeast Atp23 cleaves the Atp6/subunit 6 precursor and also promotes Atp6 association with the Atp9 ring independently of proteolysis; human ATP23 is inferred to share this mitochondrial ATP synthase biogenesis/protein-processing role, although the direct human substrate and cleavage event remain unresolved. directly_involved_in: - id: GO:0033615 label: mitochondrial proton-transporting ATP synthase complex assembly - id: GO:0034982 label: mitochondrial protein processing locations: - id: GO:0005739 label: mitochondrion - id: GO:0005758 label: mitochondrial intermembrane space supported_by: - *zeng_processing - *zeng_chaperone - *osman_dual - *uniprot_m76 - *mitocop proposed_new_terms: [] suggested_questions: - question: >- What is the direct mammalian substrate, if any, for human ATP23 proteolytic activity, given that mammalian ATP6 does not have the same yeast Atp6 N-terminal presequence? experts: [] - question: >- Has endogenous human ATP23 been directly localized by submitochondrial fractionation or protease-protection assays to the intermembrane-space face of the inner membrane? experts: [] - question: >- Should the historical KUB3/XRCC6BP1 Ku70-binding literature remain linked to ATP23 functional annotation, or should DNA-repair GO annotations be retired as alias-driven over-interpretation? experts: [] suggested_experiments: - hypothesis: Human ATP23 is an inner-membrane/intermembrane-space ATP synthase assembly factor. description: >- Endogenously tag ATP23 in human cells and test submitochondrial localization by mitochondrial fractionation, alkaline extraction, and protease-protection assays with outer- and inner-membrane permeabilization controls. experiment_type: subcellular localization/topology assay - hypothesis: Human ATP23 supports ATP synthase membrane-domain assembly through conserved M76-family catalytic and non-catalytic functions. description: >- Generate ATP23 knockout or knockdown human cells and rescue with wild-type and catalytic-site mutant ATP23; assay ATP synthase assembly by BN-PAGE, complex V activity, ATP6/ATP8 stability, and oxidative phosphorylation phenotypes. experiment_type: loss-of-function and catalytic-mutant rescue - hypothesis: The reported KUB3/Ku70 interaction does not define the main ATP23 gene-product function. description: >- Re-test Ku70 interaction and NHEJ phenotypes using sequence-verified ATP23 constructs, endogenous ATP23 perturbation, and rescue variants that distinguish mitochondrial targeting/topology from any nuclear pool. experiment_type: interaction and DNA-repair assay