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.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0033615 mitochondrial proton-transporting ATP synthase complex assembly | IBA GO_REF:0000033 | ACCEPT | Summary: Conserved ATP23-family biology supports a core role in mitochondrial ATP synthase Fo-sector assembly. 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. Supporting Evidence: PMID:17135290 Atp23p, in addition to its processing activity, must provide another important function in F O assembly PMID:17135290 Atp23p may, therefore, also be a chaperone, which in conjunction with Atp10p mediates the association of subunit 6 with the subunit 9 ring. PMID:17135288 Atp23 promotes the association of mature Atp6 with Atp9 oligomers PMID:29440398 This intermediate provides the template for insertion of ATP6 and ATP8 |
| GO:0034982 mitochondrial protein processing | IBA GO_REF:0000033 | ACCEPT | Summary: ATP23-family proteins process mitochondrial Atp6/subunit 6 in yeast; this supports mitochondrial protein processing while the direct human substrate remains unresolved. 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. Supporting Evidence: PMID:17135290 Atp23p is a mitochondrial protease that removes the 10-residue-long N-terminal prepeptide of the subunit 6 precursor PMID:17135288 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. file:human/ATP23/ATP23-uniprot.txt InterPro; IPR019165; Peptidase_M76_ATP23. |
| GO:0004222 metalloendopeptidase activity | IEA GO_REF:0000002 | ACCEPT | Summary: The metalloendopeptidase activity annotation is supported by the conserved M76 domain and yeast ATP23 active-site evidence. 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. Supporting Evidence: PMID:17135290 It has an HEXXH motif previously shown to be part of the active sites of metalloproteases including zinc proteases PMID:17135290 Substitution of the essential glutamic acid by glutamine prevents cleavage of the N-terminal prepeptide file:human/ATP23/ATP23-uniprot.txt InterPro; IPR019165; Peptidase_M76_ATP23. file:human/ATP23/ATP23-uniprot.txt GO; GO:0004222; F:metalloendopeptidase activity; IEA:InterPro. |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: The generic binary-interactome protein-binding annotation is true at most as high-throughput interaction context and is not informative for ATP23 function. 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. Supporting Evidence: PMID:32296183 To map the reference interactome, we performed nine screens of Space III, followed by pairwise verification by quadruplicate retesting and sequence confirmation. file:human/ATP23/ATP23-uniprot.txt GO; GO:0004222; F:metalloendopeptidase activity; IEA:InterPro. |
| GO:0005515 protein binding | IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ... | MARK AS OVER ANNOTATED | Summary: The neurodegenerative-disease interactome annotation is too generic and not a mechanistic ATP23 molecular-function term. 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. Supporting Evidence: PMID:32814053 Interactome maps are valuable resources to elucidate protein function and disease mechanisms. file:human/ATP23/ATP23-uniprot.txt GO; GO:0004222; F:metalloendopeptidase activity; IEA:InterPro. |
| GO:0005829 cytosol | IDA GO_REF:0000052 | KEEP AS NON CORE | Summary: Cytosol is a broad HPA location and should not define ATP23's core cellular site. 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. Supporting Evidence: file:human/ATP23/ATP23-uniprot.txt GO; GO:0005829; C:cytosol; IDA:HPA. PMID:34800366 We defined a human mitochondrial high-confidence proteome (MitoCoP) of 1,134 protein-coding genes |
| GO:0005886 plasma membrane | IDA GO_REF:0000052 | REMOVE | Summary: Plasma membrane localization is not supported by ATP23's conserved mitochondrial protease/assembly-factor biology. 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. Supporting Evidence: file:human/ATP23/ATP23-uniprot.txt GO; GO:0005886; C:plasma membrane; IDA:HPA. PMID:34800366 We defined a human mitochondrial high-confidence proteome (MitoCoP) of 1,134 protein-coding genes PMID:17135290 Atp23p is associated with the mitochondrial inner membrane and is conserved from yeast to humans. |
| GO:0030054 cell junction | IDA GO_REF:0000052 | REMOVE | Summary: Cell junction localization is not supported by ATP23's mitochondrial protease/assembly factor evidence. 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. Supporting Evidence: file:human/ATP23/ATP23-uniprot.txt GO; GO:0030054; C:cell junction; IDA:HPA. PMID:34800366 We defined a human mitochondrial high-confidence proteome (MitoCoP) of 1,134 protein-coding genes PMID:17135290 Atp23p is associated with the mitochondrial inner membrane and is conserved from yeast to humans. |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | ACCEPT | Summary: Mitochondrion is the best-supported broad cellular location for ATP23. 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. Supporting Evidence: PMID:34800366 We defined a human mitochondrial high-confidence proteome (MitoCoP) of 1,134 protein-coding genes file:human/ATP23/ATP23-uniprot.txt GO; GO:0005739; C:mitochondrion; HTP:FlyBase. PMID:17135290 Atp23p is associated with the mitochondrial inner membrane and is conserved from yeast to humans. PMID:17135288 conserved metallopeptidase present in the intermembrane space, termed Atp23 |
| GO:0004677 DNA-dependent protein kinase activity | TAS PMID:10219089 Isolation of Ku70-binding proteins (KUBs). | REMOVE | Summary: The Ku70-binding paper does not show ATP23/KUB3 has DNA-dependent protein kinase activity. 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. Supporting Evidence: PMID:10219089 We isolated Ku70-binding proteins (KUB1-KUB4) using yeast two-hybrid analyses. PMID:10219089 The role of apoJ/XIP8 in ionizing radiation resistance/sensitivity is under investigation. file:human/ATP23/ATP23-uniprot.txt GO; GO:0004222; F:metalloendopeptidase activity; IEA:InterPro. |
| GO:0005958 DNA-dependent protein kinase-DNA ligase 4 complex | NAS PMID:10219089 Isolation of Ku70-binding proteins (KUBs). | REMOVE | Summary: Ku70 binding does not demonstrate ATP23/KUB3 membership in a DNA-PK-DNA ligase IV complex. 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. Supporting Evidence: PMID:10219089 We isolated Ku70-binding proteins (KUB1-KUB4) using yeast two-hybrid analyses. PMID:10219089 KUB3 with Ku70 were confirmed by co-immunoprecipitation analyses file:human/ATP23/ATP23-uniprot.txt GO; GO:0004222; F:metalloendopeptidase activity; IEA:InterPro. |
| GO:0006303 double-strand break repair via nonhomologous end joining | TAS PMID:10219089 Isolation of Ku70-binding proteins (KUBs). | REMOVE | Summary: The original KUB3/Ku70 paper is insufficient for annotating ATP23 to NHEJ. 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. Supporting Evidence: PMID:10219089 We isolated Ku70-binding proteins (KUB1-KUB4) using yeast two-hybrid analyses. PMID:10219089 The role of apoJ/XIP8 in ionizing radiation resistance/sensitivity is under investigation. file:human/ATP23/ATP23-deep-research-falcon.md 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. |
| GO:0005758 mitochondrial intermembrane space | ISO PMID:17135288 Prohibitins interact genetically with Atp23, a novel process... | NEW | Summary: Add as a conservative PN-supported location candidate, based on ATP23-family intermembrane-space topology evidence. 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. Supporting Evidence: PMID:17135288 conserved metallopeptidase present in the intermembrane space, termed Atp23 PMID:17135290 Atp23p is associated with the inner membrane in an orientation such that the C-terminus faces the intermembrane space. file:human/ATP23/ATP23-notes.md 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. |
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Download this section (compressed HTML)Q: 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?
Q: Has endogenous human ATP23 been directly localized by submitochondrial fractionation or protease-protection assays to the intermembrane-space face of the inner membrane?
Q: 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?
Experiment: 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.
Hypothesis: Human ATP23 is an inner-membrane/intermembrane-space ATP synthase assembly factor.
Type: subcellular localization/topology assay
Experiment: 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.
Hypothesis: Human ATP23 supports ATP synthase membrane-domain assembly through conserved M76-family catalytic and non-catalytic functions.
Type: loss-of-function and catalytic-mutant rescue
Experiment: 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.
Hypothesis: The reported KUB3/Ku70 interaction does not define the main ATP23 gene-product function.
Type: interaction and DNA-repair assay
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