NDUFA9 (NADH:ubiquinone oxidoreductase subunit A9; also called the 39 kDa subunit, CI-39kD) is an accessory (supernumerary) subunit of mitochondrial respiratory Complex I (NADH:ubiquinone oxidoreductase). It sits at the junction between the peripheral (matrix) arm and the membrane arm, near the Q-module, and adopts a short-chain dehydrogenase/reductase (SDR) NAD(P)-binding Rossmann-like fold. NDUFA9 binds a structural NADPH dinucleotide cofactor that is not turned over catalytically; the subunit itself is not part of the electron-transfer wire and does not carry a redox-active Fe-S cluster. Its role is structural: it stabilises the Q-module/junction and is required for proper assembly of a functional Complex I. Through Complex I it contributes to mitochondrial electron transport from NADH to ubiquinone and hence to oxidative phosphorylation. The mature protein (after cleavage of a mitochondrial targeting presequence) resides in the mitochondrial inner membrane as an integral component of Complex I. Biallelic loss-of-function variants cause mitochondrial Complex I deficiency (nuclear type 26 / MC1DN26), a severe mitochondrial disease with phenotypes including Leigh syndrome and neonatally fatal encephalopathy.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetic (IBA) localization of NDUFA9 to the mitochondrion. NDUFA9 is a nucleus-encoded Complex I subunit with a cleaved N-terminal mitochondrial targeting presequence and is a bona fide mitochondrial protein. Correct but generic; the more informative location is the mitochondrial inner membrane (GO:0005743), where the mature protein resides as part of Complex I. Reason: Accurate compartment assignment but superseded in specificity by the inner-membrane and respiratory-chain-complex-I annotations. Retained as non-core supporting localization. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Accessory subunit of the mitochondrial membrane respiratory |
| GO:0006744 ubiquinone biosynthetic process | IBA GO_REF:0000033 | REMOVE | Summary: Phylogenetic (IBA) annotation to ubiquinone biosynthetic process. This is incorrect for NDUFA9. Complex I uses ubiquinone as an electron acceptor and reduces it to ubiquinol; it does not synthesize ubiquinone (that pathway is carried out by the COQ enzymes). NDUFA9 is a non-catalytic accessory subunit and has no role in ubiquinone biosynthesis. The IBA propagation likely conflated "acts on ubiquinone" with "makes ubiquinone". Reason: Biologically wrong process. NDUFA9/Complex I reduces ubiquinone as part of electron transport (GO:0006120), and does not participate in ubiquinone biosynthesis. No literature supports a biosynthetic role. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION Sources checked: PomBase:SPCC1840.09 Fission yeast Complex I-related family member; the biosynthetic-process term conflates acting on ubiquinone with synthesizing it. SGD:S000004281 Budding yeast family source in the same IBA propagation. Supporting Evidence: PMID:9878551 the transport of electrons from NADH to ubiquinone, which is |
| GO:0044877 protein-containing complex binding | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Phylogenetic (IBA) annotation to protein-containing complex binding. NDUFA9 is a constitutive subunit of Complex I rather than an external ligand that binds a complex; the informative statement is that it is part_of respiratory chain complex I (GO:0045271). "protein-containing complex binding" is uninformative here and does not capture its structural role. Reason: Not wrong in the trivial sense (it contacts other Complex I subunits), but it is over-annotation of a subunit that is a stable constituent of the complex. Its role is better represented as part_of Complex I (GO:0045271) and structural molecule activity. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000252522 Family node from which the generic "protein-containing complex binding" MF was propagated; for a constitutive subunit, part_of Complex I is the informative statement rather than binding the complex. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Complex I is composed of 45 different subunits. |
| GO:0005759 mitochondrial matrix | IEA GO_REF:0000044 | MARK AS OVER ANNOTATED | Summary: IEA subcellular-location mapping to mitochondrial matrix, mirroring the UniProt SUBCELLULAR LOCATION annotation (Mitochondrion matrix, ECO:0000305 from PubMed:12611891). NDUFA9 is part of Complex I, which is embedded in the inner membrane with its accessory subunits (including NDUFA9 at the peripheral-arm/membrane-arm junction) facing the matrix; structural data place it as an integral part of the inner-membrane-bound complex. The inner-membrane annotation (GO:0005743) is the more accurate location. Reason: Historically-derived "matrix" call reflecting the matrix-facing peripheral arm, but NDUFA9 is a bound subunit of the inner-membrane Complex I. The IDA/IEA inner-membrane annotations (GO:0005743) are preferred; matrix is kept as over-annotated rather than removed since UniProt still records it. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Mitochondrion matrix |
| GO:1902600 proton transmembrane transport | IEA GO_REF:0000108 | MARK AS OVER ANNOTATED | Summary: IEA inferred by inter-ontology logical inference from the molecular-function annotation GO:0008137 (NADH dehydrogenase (ubiquinone) activity), which links to proton translocation. Complex I as a whole couples NADH:ubiquinone oxidoreduction to proton pumping across the inner membrane, but this activity is a property of the intact enzyme (driven by the membrane-arm ND subunits), not of the non-catalytic accessory subunit NDUFA9. The inference is only as valid as the GO:0008137 annotation it derives from, which is itself an over-annotation for NDUFA9. Reason: Complex-level proton transport should not be propagated to a structural accessory subunit that does not perform catalysis or proton translocation. Inherited from the questionable GO:0008137 annotation; better captured at the level of the ND core subunits. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt chain NADH dehydrogenase (Complex I), that is believed not to be |
| GO:0005515 protein binding | IPI PMID:17500595 Huntingtin interacting proteins are genetic modifiers of neu... | MARK AS OVER ANNOTATED | Summary: IPI protein binding with huntingtin (HTT, UniProtKB:P42858) from a high-throughput screen for huntingtin-interacting proteins. This is a bare "protein binding" term that conveys no specific molecular function, and the interaction is from a broad interactome/modifier study rather than a characterized NDUFA9 function. UniProt records the HTT interaction in its INTERACTION section. Reason: Uninformative "protein binding"; per curation policy such IPIs are marked as over-annotated rather than removed. The interaction is real per the interactome data but does not define NDUFA9's core function. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Q16795; P42858: HTT; |
| GO:0005515 protein binding | IPI PMID:19103604 hNOA1 interacts with complex I and DAP3 and regulates mitoch... | MARK AS OVER ANNOTATED | Summary: IPI protein binding with NOA1 (hNOA1, UniProtKB:Q8NC60), a mitochondrial GTPase that co-purifies with Complex I. The paper reports that hNOA1 interacts with Complex I and regulates Complex I-dependent respiration; NDUFA9 was identified among the interacting Complex I subunits. This is a bare "protein binding" term. Reason: Uninformative "protein binding". The NOA1-Complex I association is biologically plausible but the term does not describe a molecular function of NDUFA9; marked over-annotated per policy. Supporting Evidence: PMID:19103604 hNOA1 interacts with both file:human/NDUFA9/NDUFA9-uniprot.txt Q16795; Q8NC60: NOA1; |
| GO:0005515 protein binding | IPI PMID:22309213 Identification of a molecular component of the mitochondrial... | MARK AS OVER ANNOTATED | Summary: IPI protein binding with BLOC1S1/GCN5L1 (UniProtKB:P78537). This study identified GCN5L1/BLOC1S1 as a mitochondrial acetyltransferase-programme component; UniProt records that NDUFA9 interacts with BLOC1S1 and that BLOC1S1 is required for NDUFA9 acetylation. This is a bare "protein binding" term. Reason: Uninformative "protein binding". The BLOC1S1 interaction relates to acetylation of NDUFA9 rather than to a molecular function it enables; marked over-annotated per policy. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Interacts with BLOC1S1 (PubMed:22309213). Interacts |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: IPI protein binding from the HuRI human binary interactome map (yeast two-hybrid). Two rows derive from this reference; this one pairs NDUFA9 with CYSRT1 (UniProtKB:A8MQ03), a keratin-associated/cysteine-rich protein. Y2H-derived binary interactions with non-mitochondrial keratin-family proteins are commonly spurious/non-physiological for a matrix-facing Complex I subunit. Bare "protein binding" term. Reason: Uninformative "protein binding" from a large-scale binary screen; the CYSRT1 pairing has no evident biological relevance to NDUFA9's mitochondrial role. Marked over-annotated per policy rather than removed. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Q16795; A8MQ03: CYSRT1; |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | MARK AS OVER ANNOTATED | Summary: Second IPI from the HuRI binary interactome (PMID:32296183), pairing NDUFA9 with KRTAP6-2 (UniProtKB:Q3LI66), a keratin-associated protein. As with the CYSRT1 pairing, this is a large-scale Y2H binary interaction with a non-mitochondrial keratin-family protein and is likely non-physiological. Bare "protein binding" term. Reason: Uninformative "protein binding" from a high-throughput binary screen; the KRTAP6-2 pairing lacks biological relevance to NDUFA9's Complex I function. Marked over-annotated per policy. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Q16795; Q3LI66: KRTAP6-2; |
| GO:0005515 protein binding | IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ... | MARK AS OVER ANNOTATED | Summary: IPI protein binding with huntingtin (HTT, UniProtKB:P42858 per GOA WITH/FROM) from a neurodegenerative-disease interactome mapping study. This is another bare "protein binding" annotation; the interaction with huntingtin (HTT, P42858) is already captured (PMID:17500595) and is recorded in the UniProt INTERACTION section. Reason: Uninformative "protein binding" from a disease-interactome screen; redundant with the HTT interaction and not indicative of a molecular function. Marked over-annotated per policy. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Q16795; P42858: HTT; |
| GO:0005743 mitochondrial inner membrane | IEA GO_REF:0000107 | ACCEPT | Summary: IEA orthology transfer (Ensembl Compara, from mouse Q9DC69) placing NDUFA9 at the mitochondrial inner membrane. This is the correct anatomical location for a Complex I subunit and is independently supported by the ComplexPortal IDA (GO:0005743, PMID:28844695). NDUFA9 is an integral part of the inner-membrane-embedded Complex I. Reason: Accurate and specific location, concordant with experimental (IDA) and structural evidence for Complex I in the inner mitochondrial membrane. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Accessory subunit of the mitochondrial membrane respiratory |
| GO:0045271 respiratory chain complex I | IEA GO_REF:0000107 | ACCEPT | Summary: IEA orthology transfer (Ensembl Compara, from mouse Q9DC69) that NDUFA9 is part of respiratory chain complex I. This is the defining, well-established structural membership of NDUFA9 and is corroborated by multiple IDA annotations (PMID:12611891, 17209039, 27626371, 31536960, 9878551) and cryo-EM structures. Reason: Core structural annotation. NDUFA9 is an accessory subunit of Complex I; membership is supported by immunopurification, proteomics and structural studies. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Complex I is composed of 45 different subunits. |
| GO:0005743 mitochondrial inner membrane | IDA PMID:28844695 Architecture of Human Mitochondrial Respiratory Megacomplex ... | ACCEPT | Summary: IDA (ComplexPortal) localization to mitochondrial inner membrane, from the cryo-EM structure of the human respiratory megacomplex I2III2IV2, in which NDUFA9 is assigned as an individual subunit of Complex I within the inner membrane. This is the correct, specific anatomical location. Reason: Directly supported by structural determination of Complex I in the respiratory (super)complex; the most accurate location term for NDUFA9. Supporting Evidence: PMID:28844695 precise assignment of individual subunits of |
| GO:0009060 aerobic respiration | NAS PMID:30030361 Assembly of mammalian oxidative phosphorylation complexes I-... | KEEP AS NON CORE | Summary: NAS (ComplexPortal) annotation to aerobic respiration, based on Complex I's role as the entry point of the OXPHOS electron transport chain. As a subunit of Complex I, NDUFA9 participates in aerobic respiration. This is a high-level process term; the more precise process for NDUFA9's contribution is mitochondrial electron transport, NADH to ubiquinone (GO:0006120). Reason: Correct but broad; NDUFA9 contributes to aerobic respiration only via its structural role in Complex I. Retained as non-core; the specific electron transport process term is core. Supporting Evidence: PMID:30030361 'supernumerary' subunits that play essential roles in assembly, regulation |
| GO:0042776 proton motive force-driven mitochondrial ATP synthesis | NAS PMID:30030361 Assembly of mammalian oxidative phosphorylation complexes I-... | MARK AS OVER ANNOTATED | Summary: NAS (ComplexPortal) annotation to proton motive force-driven mitochondrial ATP synthesis. Complex I generates part of the proton-motive force that drives ATP synthase, but ATP synthesis is performed by Complex V; NDUFA9 as a non-catalytic accessory subunit contributes only indirectly and distally to this process. This is an over-broad process for a structural subunit. Reason: Downstream/complex-level process not directly enabled by NDUFA9. Its contribution is limited to structural stabilization of Complex I, upstream of ATP synthesis; better captured by GO:0006120. Supporting Evidence: PMID:30030361 'supernumerary' subunits that play essential roles in assembly, regulation |
| GO:0045271 respiratory chain complex I | IPI PMID:28844695 Architecture of Human Mitochondrial Respiratory Megacomplex ... | ACCEPT | Summary: IPI (ComplexPortal) evidence that NDUFA9 is part_of respiratory chain complex I, from the cryo-EM megacomplex structure in which NDUFA9 is resolved as an individual Complex I subunit. Core, well-supported structural membership. Reason: Structural evidence directly places NDUFA9 within Complex I; a defining component annotation. Supporting Evidence: PMID:28844695 precise assignment of individual subunits of |
| GO:0005739 mitochondrion | HTP PMID:34800366 Quantitative high-confidence human mitochondrial proteome an... | KEEP AS NON CORE | Summary: High-throughput (HTP) proteomics localization to mitochondrion, from a quantitative high-confidence human mitochondrial proteome study. Consistent with NDUFA9 being a mitochondrial Complex I subunit, though generic relative to the inner-membrane/Complex I annotations. Reason: Correct but non-specific compartment; superseded by the inner-membrane and Complex I localizations. Retained as supporting non-core evidence. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Accessory subunit of the mitochondrial membrane respiratory |
| GO:0045271 respiratory chain complex I | IDA PMID:12611891 The subunit composition of the human NADH dehydrogenase obta... | ACCEPT | Summary: IDA that NDUFA9 (the 39 kDa subunit) is part of Complex I, from one-step immunopurification of human NADH dehydrogenase and mass spectrometry identification of its subunits. NDUFA9 is identified as one of the human Complex I polypeptides. Core structural annotation. Reason: Direct experimental identification of NDUFA9 as a Complex I subunit by immunopurification/MS. Supporting Evidence: PMID:12611891 isolating this multisubunit |
| GO:0045271 respiratory chain complex I | IDA PMID:17209039 Identification of mitochondrial complex I assembly intermedi... | ACCEPT | Summary: IDA that NDUFA9 is part of Complex I, from a study tracing tagged NDUFS3 to define stepwise Complex I assembly intermediates; NDUFA9 is detected in Complex I subcomplexes. Supports both structural membership and involvement in the assembly pathway. Reason: Experimental identification of NDUFA9 within assembling Complex I; consistent with its role in Complex I biogenesis. Supporting Evidence: PMID:17209039 stepwise assembly of CI |
| GO:0045271 respiratory chain complex I | IDA PMID:27626371 Accessory subunits are integral for assembly and function of... | ACCEPT | Summary: IDA that NDUFA9 is part of Complex I, from the systematic gene-editing study of human Complex I accessory subunits. Knockout cell lines showed that most accessory subunits (including NDUFA9) are strictly required for assembly of a functional complex, and loss of a subunit destabilizes co-module subunits. Establishes NDUFA9 both as a component and as functionally required. Reason: Direct experimental demonstration that NDUFA9 is an integral, functionally important accessory subunit of Complex I. Supporting Evidence: PMID:27626371 25 subunits are strictly PMID:27626371 affects the stability of other subunits residing in the same |
| GO:0045271 respiratory chain complex I | IDA PMID:31536960 Rewiring of the Human Mitochondrial Interactome during Neuro... | ACCEPT | Summary: IDA that NDUFA9 is part of Complex I, from the human mitochondrial interactome study during neuronal reprogramming; NDUFA9 is detected in complexes with other Complex I (FS3, FS7), Complex III and Complex IV subunits within respirasome-containing assemblies. Supports Complex I membership. Reason: Interactome/proteomics evidence placing NDUFA9 within Complex I and the respiratory supercomplex; concordant structural membership. Supporting Evidence: PMID:31536960 NDUFA9, FS3, FS7) |
| GO:0045271 respiratory chain complex I | IDA PMID:9878551 cDNA of eight nuclear encoded subunits of NADH:ubiquinone ox... | ACCEPT | Summary: IDA that NDUFA9 is part of Complex I, from the cDNA characterization of the nuclear-encoded human Complex I subunits, which places these subunits (including the 39 kDa/NDUFA9 subunit) within the inner-membrane NADH:ubiquinone oxidoreductase. Supports structural membership. Reason: Establishes NDUFA9 as a characterized nuclear-encoded subunit of human Complex I located in the inner mitochondrial membrane. Supporting Evidence: PMID:9878551 multiprotein complex located in the inner mitochondrial membrane |
| GO:0005515 protein binding | IPI PMID:31536960 Rewiring of the Human Mitochondrial Interactome during Neuro... | MARK AS OVER ANNOTATED | Summary: IPI protein binding with RAB5IF (UniProtKB:Q9BUV8) identified in the mitochondrial interactome study; UniProt records that NDUFA9 interacts with RAB5IF. This is a bare "protein binding" term that does not describe a molecular function of NDUFA9. Reason: Uninformative "protein binding" from interactome mapping; marked over-annotated per policy rather than removed. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Interacts with RAB5IF (PubMed:31536960). |
| GO:0044877 protein-containing complex binding | IDA PMID:23209302 KIF14 negatively regulates Rap1a-Radil signaling during brea... | MARK AS OVER ANNOTATED | Summary: IDA (MGI) protein-containing complex binding. The cited reference (PMID:23209302) concerns KIF14 regulation of Rap1a-Radil signaling in breast cancer; the cached full text does not mention NDUFA9, so the basis of this IDA could not be verified here. The term is uninformative for NDUFA9, whose relevant "complex" relationship is being a constitutive part_of Complex I (GO:0045271) rather than binding an external complex. Reason: Uninformative complex-binding term; NDUFA9's role is as a stable Complex I subunit. Marked over-annotated rather than removed (the underlying experimental support could not be verified, as the cached full text of PMID:23209302 does not mention NDUFA9; it presumably rests on supplementary data, and an MGI IDA should not be overruled on that basis). Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Complex I is composed of 45 different subunits. |
| GO:0005515 protein binding | IPI PMID:28985504 CLOCK Acetylates ASS1 to Drive Circadian Rhythm of Ureagenes... | MARK AS OVER ANNOTATED | Summary: IPI protein binding with CLOCK (UniProtKB:O15516). UniProt records that NDUFA9 interacts with CLOCK and is acetylated by CLOCK in a circadian manner. This is a bare "protein binding" term; the interaction relates to post-translational acetylation of NDUFA9 rather than a molecular function it enables. Reason: Uninformative "protein binding"; the CLOCK interaction underlies circadian acetylation of NDUFA9 but the MF term itself is uninformative. Marked over-annotated per policy. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Interacts with CLOCK (PubMed:28985504). |
| GO:0007623 circadian rhythm | IDA PMID:28985504 CLOCK Acetylates ASS1 to Drive Circadian Rhythm of Ureagenes... | MARK AS OVER ANNOTATED | Summary: IDA involvement in circadian rhythm, based on the finding that NDUFA9 is acetylated by CLOCK in a circadian manner (UniProt PTM, PubMed:28985504). The evidence establishes that NDUFA9 is a circadian-regulated target (an output/substrate of the clock), not that NDUFA9 is a component of the circadian oscillator or regulates rhythmicity. "involved_in circadian rhythm" over-reads a PTM observation. Reason: NDUFA9 is a substrate of circadian CLOCK-mediated acetylation, i.e. a downstream target rather than a functional participant in generating circadian rhythm. Peripheral to its core Complex I role and an over-read of the acetylation data. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Acetylated by CLOCK in a circadian manner |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-163217 | MARK AS OVER ANNOTATED | Summary: Reactome TAS localization to mitochondrial matrix for the Complex I reaction "Complex I oxidises NADH to NAD+, reduces CoQ to CoQH2". As with the other matrix annotations, NDUFA9 is a subunit of inner-membrane Complex I whose peripheral arm faces the matrix; the more precise location is the mitochondrial inner membrane (GO:0005743). Reason: Matrix call reflects the matrix-facing catalytic module of Complex I but NDUFA9 is an inner-membrane-associated subunit; inner-membrane annotations are preferred. One of several redundant Reactome matrix annotations. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Mitochondrion matrix |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-6799178 | MARK AS OVER ANNOTATED | Summary: Reactome TAS matrix localization associated with a Complex I biogenesis reaction. Redundant with the other matrix annotations; NDUFA9 is an inner-membrane Complex I subunit and GO:0005743 is the preferred location. Reason: Redundant Reactome matrix annotation for an inner-membrane subunit; kept as over-annotated in favor of the inner-membrane location. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Mitochondrion matrix |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-6799179 | MARK AS OVER ANNOTATED | Summary: Reactome TAS matrix localization associated with a Complex I biogenesis reaction. Redundant with the other matrix annotations; NDUFA9 is an inner-membrane Complex I subunit and GO:0005743 is the preferred location. Reason: Redundant Reactome matrix annotation for an inner-membrane subunit; kept as over-annotated in favor of the inner-membrane location. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Mitochondrion matrix |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-6799191 | MARK AS OVER ANNOTATED | Summary: Reactome TAS matrix localization associated with a Complex I biogenesis reaction. Redundant with the other matrix annotations; NDUFA9 is an inner-membrane Complex I subunit and GO:0005743 is the preferred location. Reason: Redundant Reactome matrix annotation for an inner-membrane subunit; kept as over-annotated in favor of the inner-membrane location. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Mitochondrion matrix |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-6799196 | MARK AS OVER ANNOTATED | Summary: Reactome TAS matrix localization associated with a Complex I biogenesis reaction. Redundant with the other matrix annotations; NDUFA9 is an inner-membrane Complex I subunit and GO:0005743 is the preferred location. Reason: Redundant Reactome matrix annotation for an inner-membrane subunit; kept as over-annotated in favor of the inner-membrane location. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Mitochondrion matrix |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-6799197 | MARK AS OVER ANNOTATED | Summary: Reactome TAS matrix localization associated with a Complex I biogenesis reaction. Redundant with the other matrix annotations; NDUFA9 is an inner-membrane Complex I subunit and GO:0005743 is the preferred location. Reason: Redundant Reactome matrix annotation for an inner-membrane subunit; kept as over-annotated in favor of the inner-membrane location. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Mitochondrion matrix |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-6799202 | MARK AS OVER ANNOTATED | Summary: Reactome TAS matrix localization associated with a Complex I biogenesis reaction. Redundant with the other matrix annotations; NDUFA9 is an inner-membrane Complex I subunit and GO:0005743 is the preferred location. Reason: Redundant Reactome matrix annotation for an inner-membrane subunit; kept as over-annotated in favor of the inner-membrane location. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Mitochondrion matrix |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-6799203 | MARK AS OVER ANNOTATED | Summary: Reactome TAS matrix localization associated with a Complex I biogenesis reaction. Redundant with the other matrix annotations; NDUFA9 is an inner-membrane Complex I subunit and GO:0005743 is the preferred location. Reason: Redundant Reactome matrix annotation for an inner-membrane subunit; kept as over-annotated in favor of the inner-membrane location. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Mitochondrion matrix |
| GO:0005759 mitochondrial matrix | TAS Reactome:R-HSA-6800868 | MARK AS OVER ANNOTATED | Summary: Reactome TAS matrix localization associated with a Complex I biogenesis reaction ("NDUF subunits bind to form the IP subcomplex"). Redundant with the other matrix annotations; NDUFA9 is an inner-membrane Complex I subunit and GO:0005743 is the preferred location. Reason: Redundant Reactome matrix annotation for an inner-membrane subunit; kept as over-annotated in favor of the inner-membrane location. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Mitochondrion matrix |
| GO:0005634 nucleus | HDA PMID:21630459 Proteomic characterization of the human sperm nucleus. | REMOVE | Summary: HDA nucleus localization from a proteomic characterization of the human sperm nucleus. NDUFA9 is a mitochondrial Complex I subunit with an N-terminal mitochondrial targeting sequence and no known nuclear function; its detection in a sperm-nucleus proteome most likely reflects mitochondrial/contaminating material rather than a genuine nuclear localization. Reason: Nuclear localization is not supported for this mitochondrial inner-membrane Complex I subunit and is inconsistent with its targeting sequence and structural role. Likely a proteomic contaminant/artifact; no functional nuclear role is described. Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt Accessory subunit of the mitochondrial membrane respiratory |
| GO:0005759 mitochondrial matrix | IDA PMID:8486360 Construction and evaluation of a hncDNA library of human 12p... | MARK AS OVER ANNOTATED | Summary: IDA (UniProt) mitochondrial matrix localization, from the cDNA characterization identifying this transcript as the human homologue of the bovine 39-kDa nuclear-encoded NADH:ubiquinone oxidoreductase subunit. This is the historical UniProt matrix call for NDUFA9. As above, the matrix location reflects the matrix-facing peripheral arm; the inner membrane (GO:0005743) is the more precise location for this Complex I subunit. Reason: Retained matrix annotation for the inner-membrane Complex I subunit; the inner-membrane location terms are preferred. Kept as over-annotated in line with UniProt's recorded subcellular location. Supporting Evidence: PMID:8486360 human homologue of the bovine 39-kDa nuclear-encoded |
| GO:0003954 NADH dehydrogenase activity | IMP PMID:11112787 Human complex I defects can be resolved by monoclonal antibo... | MODIFY | Summary: IMP annotation of NADH dehydrogenase activity, from a study using monoclonal antibodies (including one against the 39 kDa/NDUFA9 subunit) to distinguish catalytic versus assembly defects in Complex I deficiency. The measured NADH dehydrogenase activity is a property of the intact Complex I holoenzyme, and UniProt explicitly states NDUFA9 is an accessory subunit "believed not to be involved in catalysis". Attributing the catalytic MF directly to NDUFA9 over-reads the complex-level assay. Reason: NDUFA9 is non-catalytic; the redox activity belongs to the core (Q-module/N- module) subunits, not this accessory subunit. NDUFA9's contribution to the assay is structural (its loss disrupts assembly and thereby activity), so the informative MF is structural molecule activity, with the process captured by GO:0006120. The catalytic MF should not be assigned to NDUFA9. Proposed replacements: structural molecule activity Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt chain NADH dehydrogenase (Complex I), that is believed not to be PMID:11112787 distinguish catalytic versus assembly |
| GO:0006120 mitochondrial electron transport, NADH to ubiquinone | NAS PMID:9878551 cDNA of eight nuclear encoded subunits of NADH:ubiquinone ox... | ACCEPT | Summary: NAS involvement in mitochondrial electron transport, NADH to ubiquinone. As a required accessory subunit of Complex I (NADH:ubiquinone oxidoreductase), whose main function is the transport of electrons from NADH to ubiquinone, NDUFA9 is properly annotated to this process. This is the core biological process for NDUFA9's contribution to respiration. Reason: Correct and appropriately specific process term. NDUFA9 contributes to NADH-to-ubiquinone electron transport via its structural role in Complex I; this is its core biological-process annotation. Supporting Evidence: PMID:9878551 the transport of electrons from NADH to ubiquinone, which is |
| GO:0008137 NADH dehydrogenase (ubiquinone) activity | NAS PMID:9878551 cDNA of eight nuclear encoded subunits of NADH:ubiquinone ox... | MODIFY | Summary: NAS annotation of NADH dehydrogenase (ubiquinone) activity, propagated to NDUFA9 as a Complex I subunit. This catalytic MF is a property of the intact Complex I holoenzyme, not of the non-catalytic accessory subunit NDUFA9, which UniProt states is "believed not to be involved in catalysis". Reason: Catalytic activity of the whole complex should not be assigned to a structural accessory subunit. NDUFA9's role is structural; replace with structural molecule activity. The process-level contribution is captured by GO:0006120. Proposed replacements: structural molecule activity Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt chain NADH dehydrogenase (Complex I), that is believed not to be |
| GO:0031966 mitochondrial membrane | IDA PMID:17209039 Identification of mitochondrial complex I assembly intermedi... | MODIFY | Summary: IDA mitochondrial membrane localization, from the study tracing Complex I assembly intermediates. Correct but less specific than mitochondrial inner membrane (GO:0005743), which is the precise compartment for Complex I. Reason: Correct membrane localization but insufficiently specific; NDUFA9 resides in the mitochondrial inner membrane as part of Complex I. Replace/generalize to the more precise inner-membrane term. Proposed replacements: mitochondrial inner membrane Supporting Evidence: PMID:17209039 stepwise assembly of CI |
| GO:0003954 NADH dehydrogenase activity | NAS PMID:8486360 Construction and evaluation of a hncDNA library of human 12p... | MODIFY | Summary: NAS annotation of NADH dehydrogenase activity from the original cDNA identification of NDUFA9 as the human homologue of the bovine 39-kDa Complex I subunit. As with the other catalytic MF annotations, this reflects the activity of the whole complex; NDUFA9 itself is non-catalytic. Reason: Redundant catalytic MF assigned to a non-catalytic accessory subunit; replace with structural molecule activity. Duplicate of the IMP GO:0003954 annotation (PMID:11112787). Proposed replacements: structural molecule activity Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt chain NADH dehydrogenase (Complex I), that is believed not to be |
| GO:0006814 sodium ion transport | NAS PMID:8486360 Construction and evaluation of a hncDNA library of human 12p... | REMOVE | Summary: NAS annotation to sodium ion transport. This is incorrect for human NDUFA9/Complex I. Mammalian mitochondrial Complex I is a proton-pumping NADH:ubiquinone oxidoreductase; it does not transport sodium. Na+-translocating NADH:quinone oxidoreductases (Na+-NQR) are a distinct bacterial enzyme family. The annotation appears to be a legacy mis-assignment. Reason: No evidence that human NDUFA9 or human Complex I transports sodium; the coupling ion for mammalian Complex I is the proton, not Na+. Biologically wrong process. Supporting Evidence: PMID:9878551 translocation of protons from the mitochondrial matrix to the |
| GO:0008137 NADH dehydrogenase (ubiquinone) activity | NAS PMID:8486360 Construction and evaluation of a hncDNA library of human 12p... | MODIFY | Summary: NAS annotation of NADH dehydrogenase (ubiquinone) activity from the original cDNA identification of NDUFA9. Duplicate of the GO:0008137 NAS annotation (PMID:9878551); this catalytic MF belongs to the holoenzyme, not the non-catalytic accessory subunit NDUFA9. Reason: Catalytic MF assigned to a structural accessory subunit; replace with structural molecule activity. Redundant with the other GO:0008137 annotation. Proposed replacements: structural molecule activity Supporting Evidence: file:human/NDUFA9/NDUFA9-uniprot.txt chain NADH dehydrogenase (Complex I), that is believed not to be |
| GO:0032981 mitochondrial respiratory chain complex I assembly | IMP PMID:27626371 Accessory subunits are integral for assembly and function of... | NEW | Summary: Proposed new annotation. NDUFA9 is required for proper assembly of a functional Complex I: gene-editing knockout studies show that most accessory subunits, including NDUFA9, are strictly required for assembly of a functional complex, and loss of a subunit destabilizes co-module subunits. UniProt states NDUFA9 is "Required for proper complex I assembly", and pathogenic NDUFA9 variants cause a Complex I assembly defect with accumulation of assembly intermediates. This process is not currently in the GOA set but is strongly supported. Reason: Captures NDUFA9's core biological role (assembly/stabilization of Complex I), which is better supported than the catalytic MF annotations and complements the electron-transport process term. Supporting Evidence: PMID:27626371 25 subunits are strictly file:human/NDUFA9/NDUFA9-uniprot.txt involved in catalysis. Required for proper complex I assembly |
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Download this section (compressed HTML)Q: Is the NAD(P)H dinucleotide bound by the NDUFA9 Rossmann fold purely structural, or does its redox state act as a regulatory sensor that tunes Complex I stability or the active/deactive transition?
Q: Do the CLOCK-dependent acetylation sites on NDUFA9 alter Complex I assembly, stability or activity, or are they functionally silent marks?
Q: Which NDUFA9 missense variants found in MC1DN26 patients act by destabilising the Q-module junction versus by impairing cofactor binding, and does this distinction predict clinical severity?
Experiment: Generate NDUFA9 knockout cells reconstituted with wild-type NDUFA9 or with Rossmann-fold point mutants predicted to abolish dinucleotide binding, then compare Complex I assembly by blue native PAGE and complexome profiling, NADH:ubiquinone oxidoreductase activity, and thermal stability of the isolated complex.
Hypothesis: The NAD(P)H dinucleotide bound by the NDUFA9 Rossmann fold is a structural cofactor whose binding is required for Q-module stabilisation rather than for any redox chemistry. Note that UniProt Q16795 instead records FAD as the cofactor ("Binds 1 FAD per subunit"), so the identity of the bound dinucleotide is itself part of what this experiment should settle.
Type: structure-function mutagenesis with blue native PAGE and enzyme assay
Experiment: Map endogenous NDUFA9 acetylation sites by targeted mass spectrometry, then express acetyl-null (K to R) and acetyl-mimetic (K to Q) NDUFA9 variants in NDUFA9 knockout cells and measure Complex I assembly intermediates, holoenzyme levels, oxygen consumption rate and supercomplex distribution.
Hypothesis: Acetylation of NDUFA9 modulates Complex I assembly or activity.
Type: site-directed PTM mimetic analysis with respirometry
Experiment: Introduce patient-derived NDUFA9 missense variants into an isogenic knockout background and determine the resulting Complex I structures by cryo-EM alongside quantitative complexome profiling, to localise the assembly block and correlate structural destabilisation with residual enzymatic activity.
Hypothesis: Patient NDUFA9 variants cause disease through destabilisation of the Q-module junction of Complex I.
Type: cryo-EM and complexome profiling of variant knock-in cells
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