id: Q9Y5K8 gene_symbol: ATP6V1D product_type: PROTEIN status: COMPLETE taxon: id: NCBITaxon:9606 label: Homo sapiens description: ATP6V1D encodes the D subunit (28 kDa) of the V1 peripheral sector of the vacuolar-type H+-ATPase (V-ATPase). Subunit D forms the central rotor of V1 together with subunit F; ATP hydrolysis by the catalytic A3B3 hexamer drives rotation of the D-F stalk, which is mechanically coupled to the V0 proteolipid c-ring to translocate protons across organelle membranes. The human V-ATPase complex is responsible for acidifying lysosomes, endosomes, the Golgi apparatus, and other intracellular compartments, and in specialized cell types for extracellular acidification at the plasma membrane. Beyond proton pumping, the V1 D subunit directly contacts the Ragulator scaffold on lysosomes, and V-ATPase activity is required for amino acid-sensitive mTORC1 activation via an inside-out signaling mechanism. ATP6V1D additionally interacts with SNX10 and localizes to the centrosome and cilium base, where the V-ATPase is required for ciliogenesis. The protein is ubiquitously expressed in human tissues. existing_annotations: - term: id: GO:0033176 label: proton-transporting V-type ATPase complex evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: part_of review: summary: Phylogenetic inference that ATP6V1D is part of the V-type ATPase complex. Confirmed by cryo-EM structure and biochemical data. action: ACCEPT reason: The D subunit is a core structural and functional component of the V1 sector of the V-type ATPase complex. Multiple lines of evidence including cryo-EM (PMID:33065002) and biochemical pulldowns (PMID:18752060) confirm complex membership. supported_by: - reference_id: PMID:33065002 supporting_text: Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V1 complex for ATP hydrolysis and a membrane-embedded Vo complex for proton transfer. reference_section_type: ABSTRACT - reference_id: file:human/ATP6V1D/ATP6V1D-uniprot.txt supporting_text: Subunit of the V1 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that translocates protons reference_section_type: DATABASE_ENTRY - term: id: GO:0007035 label: vacuolar acidification evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: involved_in review: summary: Phylogenetic inference that ATP6V1D participates in vacuolar acidification. Well-supported by the established role of V-ATPase in acidifying intracellular compartments. action: ACCEPT reason: The V-ATPase is the primary driver of organellar acidification in eukaryotes, and subunit D is a core structural component essential for complex function. Vacuolar acidification is the core biological process. supported_by: - reference_id: PMID:33065002 supporting_text: Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V1 complex for ATP hydrolysis and a membrane-embedded Vo complex for proton transfer. They play important roles in acidification of intracellular vesicles, organelles, and the extracellular milieu in eukaryotes. reference_section_type: ABSTRACT - reference_id: PMID:32001091 supporting_text: V-ATPases are membrane-embedded protein complexes that function as ATP hydrolysis-driven proton pumps. V-ATPases are the primary source of organellar acidification in all eukaryotes, making them essential for many fundamental cellular processes. reference_section_type: ABSTRACT - term: id: GO:0046961 label: proton-transporting ATPase activity, rotational mechanism evidence_type: IBA original_reference_id: GO_REF:0000033 qualifier: contributes_to review: summary: Phylogenetic inference that subunit D contributes to proton-transporting ATPase activity via rotational mechanism. Supported by the established central rotor function of subunit D in the rotary mechanism. action: ACCEPT reason: Subunit D is a core structural component of the V1 central rotor that directly participates in the rotary mechanism. The contributes_to qualifier is appropriate since this is a complex-level activity. supported_by: - reference_id: PMID:18752060 supporting_text: Energy from this reaction drives the rotation of a central stalk consisting of V1 subunits D and F and this is coupled to rotation of the V0 proteolipid ring made up of c, c′ and c″. reference_section_type: INTRODUCTION - reference_id: PMID:33065002 supporting_text: Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V1 complex for ATP hydrolysis and a membrane-embedded Vo complex for proton transfer. reference_section_type: ABSTRACT - term: id: GO:0005765 label: lysosomal membrane evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in review: summary: UniProt subcellular location vocabulary mapping. Well-supported by multiple independent HDA and IDA lysosomal membrane annotations. action: ACCEPT reason: Lysosomal membrane is the primary functional location of the V-ATPase complex. Supported by HDA proteomics (PMID:17897319) and IDA data (PMID:22053050). - term: id: GO:0005813 label: centrosome evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in review: summary: UniProt subcellular location vocabulary mapping based on the centrosome localization reported in PMID:21844891. action: KEEP_AS_NON_CORE reason: Centrosome localization of ATP6V1D (via SNX10 interaction) is supported by IDA evidence (PMID:21844891) but represents a secondary ciliogenesis-related function rather than the core lysosomal proton-pumping role. supported_by: - reference_id: PMID:21844891 supporting_text: SNX10 interacts with V-ATPase complex and targets it to the centrosome where ciliogenesis is initiated. reference_section_type: ABSTRACT - term: id: GO:0005929 label: cilium evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in review: summary: UniProt subcellular location vocabulary mapping based on cilium localization reported in PMID:21844891. action: KEEP_AS_NON_CORE reason: Cilium localization is supported by IDA evidence but represents a secondary ciliogenesis-related function. The V-ATPase participates in ciliogenesis via vesicular trafficking to the cilium base. supported_by: - reference_id: PMID:21844891 supporting_text: Like SNX10, V-ATPase regulates ciliogenesis in vitro and in vivo and does so synergistically with SNX10. We further discover that SNX10 and V-ATPase regulate the ciliary trafficking of Rab8a, which is a critical regulator of ciliary membrane extension. reference_section_type: ABSTRACT - term: id: GO:0016020 label: membrane evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in review: summary: Generic membrane localization from UniProt vocabulary mapping. The V1 D subunit associates with the cytoplasmic face of membranes as part of the V-ATPase complex. action: MARK_AS_OVER_ANNOTATED reason: The generic membrane term is subsumed by the more specific lysosomal membrane, Golgi membrane, and endosome membrane annotations. The IDA annotation from PMID:18752060 (membrane) is more specific in context and provides better granularity. - term: id: GO:0030665 label: clathrin-coated vesicle membrane evidence_type: IEA original_reference_id: GO_REF:0000044 qualifier: located_in review: summary: UniProt subcellular location vocabulary mapping based on ortholog data. V-ATPase functions on clathrin-coated vesicles for endocytic pathway acidification. action: KEEP_AS_NON_CORE reason: The clathrin-coated vesicle membrane localization is consistent with V-ATPase's broad role in acidifying endocytic vesicles, but is not the primary functional context for this subunit. - term: id: GO:0046961 label: proton-transporting ATPase activity, rotational mechanism evidence_type: IEA original_reference_id: GO_REF:0000002 qualifier: enables review: summary: InterPro-based annotation. The enables qualifier for the whole-complex activity is somewhat imprecise for a structural subunit, but the rotational ATPase activity is the core molecular function. action: ACCEPT reason: The proton-transporting ATPase activity via rotational mechanism is the core molecular function of the complex in which ATP6V1D is an indispensable structural component. The IBA annotation with contributes_to is more precise, but this IEA is consistent. - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:25416956 qualifier: enables review: summary: Generic protein binding from a large-scale human interactome proteome map. Not informative for the specific function of ATP6V1D. action: MARK_AS_OVER_ANNOTATED reason: Protein binding is uninformative for this V-ATPase subunit. A high-throughput interactome map does not establish a meaningful GO annotation for ATP6V1D core function. - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:32296183 qualifier: enables review: summary: Generic protein binding from a reference human binary protein interactome map. High-throughput; not informative. action: MARK_AS_OVER_ANNOTATED reason: Protein binding from high-throughput interactome studies lacks specificity and is not useful for understanding ATP6V1D function. - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:33961781 qualifier: enables review: summary: Generic protein binding from a dual proteome-scale interactome network study. High-throughput; not informative. action: MARK_AS_OVER_ANNOTATED reason: High-throughput interactome data should not be used to assert generic protein binding as a meaningful function for a structural V-ATPase subunit. - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:35271311 qualifier: enables review: summary: Generic protein binding from the OpenCell endogenous tagging study. High-throughput; not informative for core function. action: MARK_AS_OVER_ANNOTATED reason: Protein binding is uninformative for ATP6V1D; these high-throughput interaction data points do not reveal specific biological function. - term: id: GO:0015078 label: proton transmembrane transporter activity evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: contributes_to review: summary: Ensembl ortholog-transfer annotation. Proton transmembrane transporter activity is the molecular function of the V-ATPase complex; subunit D contributes via the rotary mechanism. action: ACCEPT reason: This is an appropriate annotation for a core V-ATPase structural subunit. The contributes_to qualifier correctly acknowledges that the molecular function belongs to the whole complex. - term: id: GO:0033176 label: proton-transporting V-type ATPase complex evidence_type: IEA original_reference_id: GO_REF:0000120 qualifier: part_of review: summary: Automated IEA annotation consistent with the IBA and IDA evidence for complex membership. action: ACCEPT reason: Redundant with IBA but consistent with cryo-EM structural evidence. - term: id: GO:0097401 label: synaptic vesicle lumen acidification evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: involved_in review: summary: Ensembl ortholog-transfer annotation for synaptic vesicle lumen acidification. V-ATPase acidifies synaptic vesicles to enable neurotransmitter loading. However, there is no direct evidence that the ubiquitous D subunit specifically functions in neuronal synaptic vesicles as opposed to other organelles. action: KEEP_AS_NON_CORE reason: Synaptic vesicle lumen acidification is a legitimate biological process in which V-ATPase participates; the D subunit is a ubiquitously expressed component that would be present in neuronal V-ATPase complexes. However, this is a non-core context relative to lysosomal/endosomal function. - term: id: GO:0098850 label: extrinsic component of synaptic vesicle membrane evidence_type: IEA original_reference_id: GO_REF:0000107 qualifier: is_active_in review: summary: Ensembl ortholog-transfer annotation placing the D subunit on synaptic vesicle membrane. The V1 peripheral sector is an extrinsic component of vesicle membranes. action: KEEP_AS_NON_CORE reason: Supported by the V-ATPase's role in synaptic vesicle acidification, but this is non-core relative to the primary lysosomal/endosomal acidification function. - term: id: GO:0071230 label: cellular response to amino acid stimulus evidence_type: IDA original_reference_id: PMID:22053050 qualifier: involved_in review: summary: Direct evidence from Zoncu et al. (2011) showing the V-ATPase (specifically the V1 domain including subunit D) is required for mTORC1 activation in response to amino acids. The V1 D subunit directly contacts the Ragulator complex, and amino acids regulate this interaction. action: ACCEPT reason: The V-ATPase's role in amino acid sensing for mTORC1 is a genuine secondary function with direct experimental evidence. Subunit D specifically interacts with Ragulator p18 and p14 in vitro. This is well-supported functional biology beyond simple proton pumping. supported_by: - reference_id: PMID:22053050 supporting_text: the v-ATPase engages in extensive amino acid-sensitive interactions with the Ragulator, a scaffolding complex that anchors the Rag GTPases to the lysosome. In a cell-free system, ATP hydrolysis by the v-ATPase was necessary for amino acids to regulate the v-ATPase-Ragulator interaction and promote mTORC1 translocation. reference_section_type: ABSTRACT - reference_id: PMID:22053050 supporting_text: the V1 component D with p18 and, to a lesser degree, with p14 (Fig. 3D). No direct interactions were detected between the Rag GTPases and purified v-ATPase subunits reference_section_type: RESULTS - term: id: GO:0160124 label: guanyl nucleotide exchange factor activator activity evidence_type: IDA original_reference_id: PMID:22053050 qualifier: contributes_to review: summary: The V-ATPase contributes to GEF activator activity in the context of Ragulator-mediated Rag GTPase nucleotide exchange during amino acid signaling to mTORC1. The mechanistic link is that V-ATPase activity (ATP hydrolysis-driven rotation) is required to activate Ragulator as a GEF activator complex. action: KEEP_AS_NON_CORE reason: This annotation reflects a genuine but secondary function of the V-ATPase complex in mTORC1 signaling. It is mechanistically supported but is not the primary proton-pump function of the complex. supported_by: - reference_id: PMID:22053050 supporting_text: amino acids activate the Rag guanosine triphosphatases (GTPases), which promote the translocation of mTORC1 to the lysosomal surface, the site of mTORC1 activation. We found that the vacuolar H(+)-adenosine triphosphatase ATPase (v-ATPase) is necessary for amino acids to activate mTORC1. reference_section_type: ABSTRACT - term: id: GO:0005765 label: lysosomal membrane evidence_type: IDA original_reference_id: PMID:22053050 qualifier: is_active_in review: summary: Direct experimental evidence from the Zoncu et al. (2011) study shows the V-ATPase is active at the lysosomal membrane for both proton pumping and amino acid-sensitive mTORC1 signaling. action: ACCEPT reason: Lysosomal membrane is the primary site of V-ATPase function, and this IDA annotation from a key mechanistic study is well-supported. supported_by: - reference_id: PMID:22053050 supporting_text: the v-ATPase engages in extensive amino acid-sensitive interactions with the Ragulator, a scaffolding complex that anchors the Rag GTPases to the lysosome. reference_section_type: ABSTRACT - term: id: GO:0046611 label: lysosomal proton-transporting V-type ATPase complex evidence_type: IDA original_reference_id: PMID:22053050 qualifier: part_of review: summary: Direct evidence from the Zoncu et al. (2011) study showing the V-ATPase complex on lysosomes; subunit D is part of this complex. action: ACCEPT reason: Well-supported by both the amino acid sensing study (PMID:22053050) and the structural data (PMID:33065002). supported_by: - reference_id: PMID:22053050 supporting_text: the v-ATPase engages in extensive amino acid-sensitive interactions with the Ragulator, a scaffolding complex that anchors the Rag GTPases to the lysosome. reference_section_type: ABSTRACT - term: id: GO:1904263 label: positive regulation of TORC1 signaling evidence_type: IDA original_reference_id: PMID:22053050 qualifier: involved_in review: summary: The V-ATPase is required for positive regulation of mTORC1 signaling by amino acids. Subunit D directly contacts Ragulator, and ATP hydrolysis is required for mTORC1 activation. This is a genuine secondary function. action: KEEP_AS_NON_CORE reason: Positive regulation of TORC1 signaling is supported and real but is a secondary function of the V-ATPase complex, not the primary proton-pumping role. supported_by: - reference_id: PMID:22053050 supporting_text: ATP hydrolysis and the associated rotation of the v-ATPase appear to be essential to relay an amino acid signal from the lysosomal lumen to the Rag GTPases, whereas the capacity of the v-ATPase to set up the lysosomal proton gradient is dispensable. reference_section_type: RESULTS - term: id: GO:0005886 label: plasma membrane evidence_type: IDA original_reference_id: GO_REF:0000052 qualifier: located_in review: summary: Immunofluorescence-based annotation. V-ATPase can be targeted to the plasma membrane in specialized cell types for extracellular acidification. action: KEEP_AS_NON_CORE reason: Plasma membrane localization of V-ATPase is real in specialized contexts (osteoclasts, kidney intercalated cells, tumor cells) but is not the primary site of function for this ubiquitously expressed subunit. - term: id: GO:0000139 label: Golgi membrane evidence_type: NAS original_reference_id: PMID:32001091 qualifier: located_in review: summary: NAS from V-ATPase review (Vasanthakumar and Rubinstein 2020). V-ATPase acidifies the Golgi apparatus, and the D subunit is present as part of the complex. action: ACCEPT reason: Golgi membrane localization is a well-established aspect of V-ATPase biology; Golgi acidification is required for proper glycosylation and protein trafficking. - term: id: GO:0005765 label: lysosomal membrane evidence_type: NAS original_reference_id: PMID:32001091 qualifier: located_in review: summary: NAS from V-ATPase review. Consistent with multiple other lysosomal membrane annotations. action: ACCEPT reason: Core localization supported by multiple evidence types. - term: id: GO:0005886 label: plasma membrane evidence_type: NAS original_reference_id: PMID:32001091 qualifier: located_in review: summary: NAS from V-ATPase review. action: KEEP_AS_NON_CORE reason: Plasma membrane localization of V-ATPase is real in specialized contexts but is not the primary site for the ubiquitous D subunit. - term: id: GO:0007035 label: vacuolar acidification evidence_type: NAS original_reference_id: PMID:32001091 qualifier: involved_in review: summary: NAS from V-ATPase review. Consistent with core V-ATPase function. action: ACCEPT reason: Vacuolar acidification is the core biological process of V-ATPase. - term: id: GO:0007042 label: lysosomal lumen acidification evidence_type: NAS original_reference_id: PMID:32001091 qualifier: involved_in review: summary: NAS from V-ATPase review. Lysosomal lumen acidification is a specific, well-established aspect of V-ATPase function that is more precise than the broader vacuolar acidification term. action: ACCEPT reason: Lysosomal lumen acidification is a core function of the V-ATPase. - term: id: GO:0007042 label: lysosomal lumen acidification evidence_type: NAS original_reference_id: PMID:33065002 qualifier: involved_in review: summary: NAS from the structural study (Wang et al. 2020). Consistent with the established role of V-ATPase in lysosomal acidification. action: ACCEPT reason: Supported by extensive V-ATPase biology. - term: id: GO:0010008 label: endosome membrane evidence_type: NAS original_reference_id: PMID:32001091 qualifier: located_in review: summary: NAS from V-ATPase review. V-ATPase acidifies endosomes; the D subunit is present as part of the complex. action: ACCEPT reason: Endosome membrane is an established location for V-ATPase function in the endocytic pathway. - term: id: GO:0016020 label: membrane evidence_type: IDA original_reference_id: PMID:33065002 qualifier: located_in review: summary: IDA from the human V-ATPase structural study (cryo-EM). The D subunit is part of the membrane-associated V-ATPase complex on the cytoplasmic face of membranes. action: MARK_AS_OVER_ANNOTATED reason: The generic membrane annotation is subsumed by the more specific lysosomal membrane, Golgi membrane, and endosome membrane annotations. - term: id: GO:0033176 label: proton-transporting V-type ATPase complex evidence_type: NAS original_reference_id: PMID:33065002 qualifier: part_of review: summary: NAS from the structural study. Consistent with IDA from PMID:18752060 and IBA annotation. action: ACCEPT reason: Well-supported complex membership. - term: id: GO:0048388 label: endosomal lumen acidification evidence_type: NAS original_reference_id: PMID:32001091 qualifier: involved_in review: summary: NAS from V-ATPase review. Endosomal lumen acidification by V-ATPase is a core function. action: ACCEPT reason: Core function of V-ATPase in the endocytic pathway. - term: id: GO:0051452 label: intracellular pH reduction evidence_type: NAS original_reference_id: PMID:32001091 qualifier: involved_in review: summary: NAS from V-ATPase review. Intracellular pH reduction is a core outcome of V-ATPase activity. This term is somewhat redundant with the more specific acidification terms. action: MARK_AS_OVER_ANNOTATED reason: The intracellular pH reduction term is a less specific way to describe the same function captured by the more precise lysosomal/endosomal/Golgi lumen acidification annotations. Redundant and non-specific. - term: id: GO:0061795 label: Golgi lumen acidification evidence_type: NAS original_reference_id: PMID:32001091 qualifier: involved_in review: summary: NAS from V-ATPase review. V-ATPase acidifies the Golgi lumen, which is important for glycosylation and protein sorting. action: ACCEPT reason: Core function of V-ATPase in Golgi biology. - term: id: GO:1902600 label: proton transmembrane transport evidence_type: NAS original_reference_id: PMID:33065002 qualifier: involved_in review: summary: NAS from the structural study. Proton transmembrane transport is the core molecular process performed by V-ATPase. action: ACCEPT reason: Core biological process of V-ATPase. - term: id: GO:0000221 label: vacuolar proton-transporting V-type ATPase, V1 domain evidence_type: ISS original_reference_id: GO_REF:0000024 qualifier: part_of review: summary: Ortholog-based annotation placing the D subunit in the V1 domain. Confirmed by human cryo-EM structural data. action: ACCEPT reason: The D subunit is a defining structural component of the V1 domain, confirmed by cryo-EM. supported_by: - reference_id: PMID:33065002 supporting_text: Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V1 complex for ATP hydrolysis and a membrane-embedded Vo complex for proton transfer. reference_section_type: ABSTRACT - term: id: GO:0005886 label: plasma membrane evidence_type: TAS original_reference_id: Reactome:R-HSA-6799350 qualifier: located_in review: summary: Reactome TAS annotation placing ATP6V1D in specific granule membrane of neutrophils. V-ATPase is present in neutrophil granules. action: KEEP_AS_NON_CORE reason: Neutrophil-specific granule function is a non-core context for this ubiquitous subunit. - term: id: GO:0035579 label: specific granule membrane evidence_type: TAS original_reference_id: Reactome:R-HSA-6799350 qualifier: located_in review: summary: Reactome TAS annotation for V-ATPase in neutrophil specific granule membrane. action: KEEP_AS_NON_CORE reason: Neutrophil-specific context; non-core for this ubiquitous subunit. - term: id: GO:0016241 label: regulation of macroautophagy evidence_type: NAS original_reference_id: PMID:22982048 qualifier: involved_in review: summary: NAS from a study on lipofuscin and macroautophagy (PMID:22982048). V-ATPase is required for lysosomal acidification, which is necessary for autophagosome-lysosome fusion and degradation. However, this is an indirect effect rather than a specific regulatory function. action: MARK_AS_OVER_ANNOTATED reason: Regulation of macroautophagy is an indirect consequence of V-ATPase's role in lysosomal acidification. The annotation overstates the specificity; the core function is lysosomal proton pumping, not macroautophagy regulation per se. - term: id: GO:0033176 label: proton-transporting V-type ATPase complex evidence_type: IDA original_reference_id: PMID:18752060 qualifier: part_of review: summary: Direct experimental evidence from Smith et al. (2008) demonstrating that human D subunit co-purifies with V-ATPase complex and directly interacts with central stalk components. action: ACCEPT reason: The most specific experimental evidence for complex membership. Pulldown experiments demonstrated direct D-F and D-d subunit interactions. supported_by: - reference_id: PMID:18752060 supporting_text: each can pull down the central stalk's D and F subunits from human kidney membrane, and in vitro studies using D and F further showed that the interactions between these proteins and the d subunit is direct. reference_section_type: ABSTRACT - term: id: GO:0070062 label: extracellular exosome evidence_type: HDA original_reference_id: PMID:19199708 qualifier: located_in review: summary: High-throughput proteomics detection of ATP6V1D in parotid gland exosomes. V-ATPase subunits can co-purify with exosomes due to membrane association. action: MARK_AS_OVER_ANNOTATED reason: Exosome detection by proteomics likely reflects membrane co-purification rather than a specific function of subunit D in exosomes. This is a non-core, likely artifactual localization for a primarily lysosomal/endosomal subunit. - term: id: GO:0070062 label: extracellular exosome evidence_type: HDA original_reference_id: PMID:19056867 qualifier: located_in review: summary: High-throughput proteomics detection in urinary exosomes. Same reasoning as the parotid gland exosome annotation. action: MARK_AS_OVER_ANNOTATED reason: Urinary exosome proteomics detection likely reflects lysosomal membrane co-purification; not a specific function. - term: id: GO:0005765 label: lysosomal membrane evidence_type: HDA original_reference_id: PMID:17897319 qualifier: located_in review: summary: Lysosomal membrane proteomics study detected ATP6V1D, confirming its lysosomal membrane localization. action: ACCEPT reason: This direct proteomics evidence for lysosomal membrane localization is consistent with the established biology of V-ATPase. - term: id: GO:0061512 label: protein localization to cilium evidence_type: IMP original_reference_id: PMID:21844891 qualifier: involved_in review: summary: The V-ATPase (including subunit D via SNX10 interaction) is required for proper localization of proteins to the cilium. V-ATPase knockout disrupts Rab8a ciliary trafficking. action: KEEP_AS_NON_CORE reason: This is a genuine secondary function of the V-ATPase involving subunit D, but it is not the core lysosomal acidification function. supported_by: - reference_id: PMID:21844891 supporting_text: SNX10 and V-ATPase regulate the ciliary trafficking of Rab8a, which is a critical regulator of ciliary membrane extension. reference_section_type: ABSTRACT - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:21844891 qualifier: enables review: summary: The interaction detected in PMID:21844891 is the specific SNX10-V-ATPase interaction; however, the annotation is recorded as generic protein binding rather than the informative SNX10 interaction. action: MARK_AS_OVER_ANNOTATED reason: Protein binding is uninformative; the underlying interaction with SNX10 is more informative. The generic protein binding term should be replaced if a more specific term exists. As no specific SNX10-binding GO term exists, this is best flagged as over-annotated. - term: id: GO:0005813 label: centrosome evidence_type: IDA original_reference_id: PMID:21844891 qualifier: colocalizes_with review: summary: Direct experimental evidence (IDA) showing ATP6V1D colocalizes with centrosome marker proteins, mediated by SNX10 interaction that targets V-ATPase to the centrosome. action: KEEP_AS_NON_CORE reason: Centrosome colocalization is experimentally supported but is a secondary ciliogenesis-related function. supported_by: - reference_id: PMID:21844891 supporting_text: SNX10 interacts with V-ATPase complex and targets it to the centrosome where ciliogenesis is initiated. reference_section_type: ABSTRACT - term: id: GO:0005929 label: cilium evidence_type: IDA original_reference_id: PMID:21844891 qualifier: colocalizes_with review: summary: Direct evidence that V-ATPase (including D subunit) colocalizes with cilium. action: KEEP_AS_NON_CORE reason: Secondary ciliogenesis function. - term: id: GO:0060271 label: cilium assembly evidence_type: IMP original_reference_id: PMID:21844891 qualifier: involved_in review: summary: V-ATPase loss-of-function (through V-ATPase subunit knockdown including components targeting D subunit's complex) impairs cilium assembly in vitro and in vivo. action: KEEP_AS_NON_CORE reason: Cilium assembly is a genuine secondary function of the V-ATPase complex, supported by IMP evidence, but is not the primary lysosomal acidification role. supported_by: - reference_id: PMID:21844891 supporting_text: V-ATPase regulates ciliogenesis in vitro and in vivo and does so synergistically with SNX10. reference_section_type: ABSTRACT - term: id: GO:0005829 label: cytosol evidence_type: TAS original_reference_id: Reactome:R-HSA-1222516 qualifier: located_in review: summary: Reactome TAS annotation placing ATP6V1D in cytosol, consistent with the V1 domain being a peripheral complex on the cytoplasmic face of membranes. action: KEEP_AS_NON_CORE reason: The V1 peripheral sector, including subunit D, is present in the cytosol as a soluble complex during regulated disassembly from V0. - term: id: GO:0005829 label: cytosol evidence_type: TAS original_reference_id: Reactome:R-HSA-5252133 qualifier: located_in review: summary: Additional Reactome TAS annotation for cytosol localization. action: KEEP_AS_NON_CORE reason: Same reasoning as above; the V1 domain can exist in cytosol. - term: id: GO:0005829 label: cytosol evidence_type: TAS original_reference_id: Reactome:R-HSA-74723 qualifier: located_in review: summary: Reactome TAS annotation for cytosol. action: KEEP_AS_NON_CORE reason: Consistent with V1 domain biology. - term: id: GO:0005829 label: cytosol evidence_type: TAS original_reference_id: Reactome:R-HSA-917841 qualifier: located_in review: summary: Reactome TAS annotation for cytosol. action: KEEP_AS_NON_CORE reason: Consistent with V1 domain biology. - term: id: GO:0005829 label: cytosol evidence_type: TAS original_reference_id: Reactome:R-HSA-9639286 qualifier: located_in review: summary: Reactome TAS annotation for cytosol in RRAG-related pathway context. action: KEEP_AS_NON_CORE reason: V-ATPase participates in mTORC1 signaling on lysosomal surface, with V1 components accessible from cytosol. - term: id: GO:0005829 label: cytosol evidence_type: TAS original_reference_id: Reactome:R-HSA-9640167 qualifier: located_in review: summary: Reactome TAS annotation for cytosol. action: KEEP_AS_NON_CORE reason: Consistent. - term: id: GO:0005829 label: cytosol evidence_type: TAS original_reference_id: Reactome:R-HSA-9640168 qualifier: located_in review: summary: Reactome TAS annotation for cytosol. action: KEEP_AS_NON_CORE reason: Consistent. - term: id: GO:0005829 label: cytosol evidence_type: TAS original_reference_id: Reactome:R-HSA-9640175 qualifier: located_in review: summary: Reactome TAS annotation for cytosol. action: KEEP_AS_NON_CORE reason: Consistent. - term: id: GO:0005829 label: cytosol evidence_type: TAS original_reference_id: Reactome:R-HSA-9640195 qualifier: located_in review: summary: Reactome TAS annotation for cytosol. action: KEEP_AS_NON_CORE reason: Consistent. - term: id: GO:0005829 label: cytosol evidence_type: TAS original_reference_id: Reactome:R-HSA-9645598 qualifier: located_in review: summary: Reactome TAS annotation for cytosol. action: KEEP_AS_NON_CORE reason: Consistent. - term: id: GO:0005829 label: cytosol evidence_type: TAS original_reference_id: Reactome:R-HSA-9645608 qualifier: located_in review: summary: Reactome TAS annotation for cytosol. action: KEEP_AS_NON_CORE reason: Consistent. - term: id: GO:0005829 label: cytosol evidence_type: TAS original_reference_id: Reactome:R-HSA-9646468 qualifier: located_in review: summary: Reactome TAS annotation for cytosol. action: KEEP_AS_NON_CORE reason: Consistent. - term: id: GO:0005515 label: protein binding evidence_type: IPI original_reference_id: PMID:18752060 qualifier: enables review: summary: The IPI protein binding annotation from PMID:18752060 reflects specific interactions of subunit D with the V0 d subunit and with subunit F, which are mechanistically important. However, the generic protein binding term is less informative than the established subunit interactions. action: MARK_AS_OVER_ANNOTATED reason: The specific interactions (D-F central stalk; D-d1/d2 rotor junction) are more meaningful than a generic protein binding annotation. No specific binding term exists for the D-F or D-d interactions, but protein binding is uninformative here. - term: id: GO:0016020 label: membrane evidence_type: IDA original_reference_id: PMID:18752060 qualifier: located_in review: summary: IDA from Smith et al. (2008) showing D subunit in membrane preparations. The D subunit is a peripheral membrane protein on the cytoplasmic face. action: MARK_AS_OVER_ANNOTATED reason: The generic membrane annotation is subsumed by the more specific lysosomal membrane and other organelle membrane annotations. references: - id: GO_REF:0000002 title: Gene Ontology annotation through association of InterPro records with GO terms findings: [] - id: GO_REF:0000024 title: Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity findings: [] - id: GO_REF:0000033 title: Annotation inferences using phylogenetic trees findings: [] - id: GO_REF:0000044 title: Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt findings: [] - id: GO_REF:0000052 title: Gene Ontology annotation based on curation of immunofluorescence data findings: [] - id: GO_REF:0000107 title: Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara findings: [] - id: GO_REF:0000120 title: Combined Automated Annotation using Multiple IEA Methods findings: [] - id: PMID:17897319 title: Integral and associated lysosomal membrane proteins. findings: - statement: ATP6V1D detected in lysosomal membrane proteomics study. - id: PMID:18752060 title: The d subunit plays a central role in human vacuolar H(+)-ATPases. findings: - statement: Human V-ATPase D subunit directly interacts with d1, d2, and F subunits, forming the central stalk of V1. - id: PMID:19056867 title: Large-scale proteomics and phosphoproteomics of urinary exosomes. findings: - statement: ATP6V1D detected in urinary exosomes by mass spectrometry. - id: PMID:19199708 title: Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). findings: - statement: ATP6V1D detected in parotid gland exosome proteome. - id: PMID:21844891 title: A SNX10/V-ATPase pathway regulates ciliogenesis in vitro and in vivo. findings: - statement: V-ATPase (including D subunit) interacts with SNX10 and localizes to centrosome and cilium; required for ciliogenesis and ciliary Rab8a trafficking. - id: PMID:22053050 title: mTORC1 senses lysosomal amino acids through an inside-out mechanism that requires the vacuolar H(+)-ATPase. findings: - statement: V-ATPase D subunit directly interacts with Ragulator (p18/p14) on lysosomes; ATP hydrolysis by V-ATPase required for amino acid-induced mTORC1 activation. - id: PMID:22982048 title: Lipofuscin is formed independently of macroautophagy and lysosomal activity in stress-induced prematurely senescent human fibroblasts. findings: - statement: V-ATPase (via lysosomal acidification) broadly required for macroautophagy. - id: PMID:25416956 title: A proteome-scale map of the human interactome network. findings: - statement: ATP6V1D detected in high-throughput interactome study. - id: PMID:32001091 title: Structure and Roles of V-type ATPases. findings: - statement: Comprehensive review of V-ATPase structure, function, and disease relevance. - id: PMID:32296183 title: A reference map of the human binary protein interactome. findings: - statement: ATP6V1D detected in binary interactome map. - id: PMID:33065002 title: Structures of a Complete Human V-ATPase Reveal Mechanisms of Its Assembly. findings: - statement: Cryo-EM structures of complete human V-ATPase at 2.9 A; D subunit identified as central rotor component with subunit F. - id: PMID:33961781 title: Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. findings: - statement: ATP6V1D detected in proteome-scale interactome study. - id: PMID:35271311 title: 'OpenCell: Endogenous tagging for the cartography of human cellular organization.' findings: - statement: ATP6V1D localization mapped by endogenous tagging. - id: Reactome:R-HSA-1222516 title: Intraphagosomal pH is lowered to 5 by V-ATPase findings: [] - id: Reactome:R-HSA-5252133 title: ATP6AP1 binds V-ATPase findings: [] - id: Reactome:R-HSA-6799350 title: Exocytosis of specific granule membrane proteins findings: [] - id: Reactome:R-HSA-74723 title: Endosome acidification findings: [] - id: Reactome:R-HSA-917841 title: Acidification of Tf:TfR1 containing endosome findings: [] - id: Reactome:R-HSA-9639286 title: RRAGC,D exchanges GTP for GDP findings: [] - id: Reactome:R-HSA-9640167 title: RRAGA,B exchanges GDP for GTP findings: [] - id: Reactome:R-HSA-9640168 title: v-ATPase:Ragulator:RRAGA,B:GTP:RRAGC,D:GDP:SLC38A9:Arginine dissociates yielding v-ATPase:Ragulator:RRAGA,B:GTP:RRAGC,D:GDP and SLC38A9:Arginine findings: [] - id: Reactome:R-HSA-9640175 title: v-ATPase:Ragulator:RagA,B:GDP:RagC,D:GDP binds SLC38A9:Arginine findings: [] - id: Reactome:R-HSA-9640195 title: RRAGA,B hydrolyzes GTP findings: [] - id: Reactome:R-HSA-9645598 title: RRAGC,D hydrolyzes GTP findings: [] - id: Reactome:R-HSA-9645608 title: v-ATPase:Ragulator:RRAGA,B:GTP:RRAGC,D:GDP binds mTORC1 findings: [] - id: Reactome:R-HSA-9646468 title: mTORC1 binds RHEB:GTP findings: [] core_functions: - description: Central rotor component of the V1 sector of the vacuolar-type H+-ATPase (V-ATPase). Subunit D, together with subunit F, forms the central stalk that transmits ATP hydrolysis energy from the catalytic A3B3 hexamer to rotate the V0 proteolipid ring, enabling proton translocation across organelle membranes. Primary role is in acidification of lysosomes, endosomes, and the Golgi apparatus. contributes_to_molecular_function: id: GO:0046961 label: proton-transporting ATPase activity, rotational mechanism directly_involved_in: - id: GO:0007042 label: lysosomal lumen acidification - id: GO:0048388 label: endosomal lumen acidification - id: GO:0061795 label: Golgi lumen acidification locations: - id: GO:0005765 label: lysosomal membrane supported_by: - reference_id: PMID:33065002 supporting_text: Vesicular- or vacuolar-type adenosine triphosphatases (V-ATPases) are ATP-driven proton pumps comprised of a cytoplasmic V1 complex for ATP hydrolysis and a membrane-embedded Vo complex for proton transfer. reference_section_type: ABSTRACT - reference_id: PMID:18752060 supporting_text: Energy from this reaction drives the rotation of a central stalk consisting of V1 subunits D and F and this is coupled to rotation of the V0 proteolipid ring made up of c, c′ and c″. reference_section_type: INTRODUCTION - description: Secondary role in mTORC1 amino acid sensing. The D subunit directly contacts the Ragulator scaffold (p18/p14) on lysosomes, and V-ATPase ATP hydrolysis is required upstream of Rag GTPase activation for mTORC1 translocation to lysosomes in response to amino acids. directly_involved_in: - id: GO:1904263 label: positive regulation of TORC1 signaling - id: GO:0071230 label: cellular response to amino acid stimulus locations: - id: GO:0005765 label: lysosomal membrane supported_by: - reference_id: PMID:22053050 supporting_text: the V1 component D with p18 and, to a lesser degree, with p14 (Fig. 3D). No direct interactions were detected between the Rag GTPases and purified v-ATPase subunits reference_section_type: RESULTS - description: Secondary role in ciliogenesis. Via interaction with SNX10, the V-ATPase (including subunit D) is targeted to the centrosome and cilium base, where it regulates ciliary trafficking of Rab8a and cilium assembly. directly_involved_in: - id: GO:0060271 label: cilium assembly locations: - id: GO:0005813 label: centrosome supported_by: - reference_id: PMID:21844891 supporting_text: V-ATPase regulates ciliogenesis in vitro and in vivo and does so synergistically with SNX10. reference_section_type: ABSTRACT suggested_questions: - question: Is the role of subunit D in the Ragulator interaction specific to this subunit, or shared by other V1 subunits? What is the structural basis of D-Ragulator binding? experts: [] - question: Do disease-causing mutations in V-ATPase subunits affect the D-F central stalk interactions, and if so, does this impair ciliogenesis in addition to acidification? experts: [] - question: What is the mechanism by which SNX10-V-ATPase targeting to the centrosome promotes ciliogenesis? Is this dependent on V-ATPase proton-pumping activity or structural interactions? experts: [] suggested_experiments: - hypothesis: The D subunit directly contacts Ragulator at the lysosomal surface and this interface can be structurally defined. description: Cryo-EM structure determination of the V-ATPase-Ragulator complex to define the D subunit contact interface with p18 and p14, and to identify amino acid-dependent conformational changes. experiment_type: structural biology - hypothesis: The D-Ragulator contact can be uncoupled from proton pumping by targeted mutations. description: Engineer separation-of-function mutations in ATP6V1D that disrupt the Ragulator interaction without affecting V-ATPase proton pumping activity, then test mTORC1 activation in response to amino acids. experiment_type: mutagenesis and functional assay - hypothesis: V-ATPase targeting to the centrosome by SNX10 is required for ciliogenesis and occurs during a specific window of ciliation initiation. description: Time-lapse imaging of fluorescently tagged V-ATPase-SNX10 complex during ciliation initiation; test whether V-ATPase proton-pumping activity or only its structural association with SNX10 is required for ciliogenesis. experiment_type: live cell imaging and genetic rescue