Affinage

ATP6V1D

V-type proton ATPase subunit D · UniProt Q9Y5K8

Round 2 corrected
Length
247 aa
Mass
28.3 kDa
Annotated
2026-04-28
44 papers in source corpus 5 papers cited in narrative 5 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

ATP6V1D encodes the D subunit of the V1 catalytic sector of the vacuolar H+-ATPase (V-ATPase), functioning as an essential structural component required for V1 assembly onto the Vo membrane sector and for ATP hydrolysis-driven proton pumping that acidifies lysosomes and vacuoles (PMID:7831318, PMID:7797485). Beyond canonical acidification, ATP6V1D maintains autophagic flux in hepatocellular carcinoma cells by promoting ESCRT-III complex assembly through enhancement of the CHMP4B–IST1 interaction, thereby facilitating autophagosome–lysosome fusion and sustaining cancer cell stemness (PMID:39316516). In macrophages, ATP6V1D-dependent lysosomal acidification activates hydrolytic enzymes required for degradation of intracellular Toxoplasma gondii, acting additively with GIMAP-mediated lysosome translocation to restrict parasite growth (PMID:41972776).

Mechanistic history

Synthesis pass · year-by-year structured walk · 4 steps
  1. 1995 High

    Identification of subunit D as an integral, essential component of the V1 sector resolved how the catalytic domain achieves its stoichiometric assembly and established its requirement for V-ATPase-dependent vacuolar acidification.

    Evidence Protein sequencing of bovine chromaffin granule V-ATPase, cDNA cloning, yeast VMA8 disruption with quinacrine acidification assay and complementation rescue (PMID:7831318); independent yeast gene disruption with ATPase activity assay and immunoblot/density gradient fractionation showing V1 failure to associate with vacuolar membranes (PMID:7797485)

    PMID:7797485 PMID:7831318

    Open questions at the time
    • Atomic-resolution structure of subunit D within the V1 complex was not determined
    • Mechanism by which subunit D nucleates V1 assembly onto Vo was not defined
    • Mammalian loss-of-function data were lacking
  2. 2001 Medium

    Cloning and chromosomal mapping of the mouse ortholog, together with deep evolutionary conservation analysis, established that subunit D is under strong purifying selection, consistent with an indispensable role across eukaryotes.

    Evidence cDNA cloning, chromosomal mapping to mouse chromosome 12 (syntenic with human 14q24), phylogenetic analysis

    PMID:11435709

    Open questions at the time
    • No functional perturbation was performed in mammalian cells
    • Tissue-specific expression or regulation was not characterized
  3. 2024 High

    Discovery that ATP6V1D sustains autophagic flux not only through lysosomal acidification but also by promoting CHMP4B–IST1 interaction and ESCRT-III assembly for autophagosome–lysosome fusion revealed a non-canonical, acidification-independent arm of V-ATPase subunit function in cancer stemness.

    Evidence CRISPR-Cas9 metabolic knockout screen in HCC cells, shRNA knockdown, co-immunoprecipitation of CHMP4B–IST1, immunofluorescence, in vitro and in vivo tumor models, epistasis via CHMP4B/IST1 silencing

    PMID:39316516

    Open questions at the time
    • Direct physical interaction between ATP6V1D and the CHMP4B–IST1 complex was not shown; the mechanism of enhancement is unclear
    • Whether the ESCRT-III-promoting function operates outside of HCC or cancer contexts is untested
    • Structural basis for subunit D engagement with ESCRT machinery is unknown
  4. 2026 High

    Demonstration that ATP6V1D-dependent lysosomal acidification is required for macrophage killing of intracellular Toxoplasma gondii, acting additively with GIMAP-mediated lysosome translocation, established a cell-autonomous innate immune role for the V-ATPase D subunit.

    Evidence CRISPR/Cas9 knockout in rat NR8383 macrophages, lysosomal acidification assays, intracellular parasite growth quantification, genetic epistasis with GIMAP5/6 overexpression

    PMID:41972776

    Open questions at the time
    • Whether this innate immune role extends to human macrophages or other intracellular pathogens is untested
    • The molecular interface between ATP6V1D loss and impaired hydrolytic enzyme activation has not been dissected

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key unresolved questions include the structural basis of subunit D within the assembled mammalian V-ATPase, the direct molecular mechanism by which ATP6V1D promotes ESCRT-III assembly independently of acidification, and whether ATP6V1D mutations cause human Mendelian disease.
  • No high-resolution structure of mammalian V-ATPase with subunit D resolved in mechanistic detail
  • No direct binding interface mapped between ATP6V1D and ESCRT-III components
  • No human genetic disease attributed to ATP6V1D loss-of-function

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 2 GO:0140657 ATP-dependent activity 2
Localization
GO:0005764 lysosome 2 GO:0005773 vacuole 2
Pathway
R-HSA-382551 Transport of small molecules 3 R-HSA-168256 Immune System 1 R-HSA-9612973 Autophagy 1
Partners
CHMP4BGIMAP5GIMAP6IST1
Complex memberships
V-ATPase (V1 sector)

Evidence

Reading pass · 5 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1995 Subunit D of bovine V-ATPase (ATP6V1D) was identified by partial proteolysis and amino acid sequencing of chromaffin granule V-ATPase. A cDNA encoding a 247-amino acid protein (MW ~28 kDa) was cloned. The yeast ortholog VMA8 shares 55% identity, and deletion of VMA8 abolished V-ATPase activity and vacuolar acidification (loss of quinacrine accumulation), establishing subunit D as an integral and essential subunit of the V1 catalytic sector. Structural analysis suggested analogy to the gamma subunit of F-ATPases. Protein sequencing, cDNA cloning, yeast gene disruption (null mutant), quinacrine fluorescence assay for vacuolar acidification, complementation rescue Proceedings of the National Academy of Sciences of the United States of America High 7831318
1995 Yeast VMA8 (ATP6V1D ortholog) encodes the 32-kDa V1 subunit of V-ATPase. Disruption of VMA8 resulted in complete loss of V-ATPase ATPase activity in vacuolar membranes. Immunoblot and density gradient fractionation showed that in vma8Δ cells, V1 subunits failed to associate with the vacuolar membrane while Vo subunits remained stable there, demonstrating that subunit D is required for assembly of the V1 sector onto the membrane. Vma8p was found only in the fully assembled V-ATPase and could not assemble onto vacuolar membranes in the absence of other V1 subunits. Gene disruption, ATPase activity assay on isolated vacuolar membranes, immunoblot analysis, density gradient fractionation The Journal of biological chemistry High 7797485
2001 The mouse V-ATPase subunit D gene (Atp6m, ortholog of human ATP6V1D) was cloned and mapped to chromosome 12 in a region syntenic with human chromosome 14q24. Evolutionary analysis across multiple species showed that subunit D is highly conserved and under strong negative selection, consistent with an essential, multi-functional role in V-ATPase-dependent cellular processes including pH regulation, vesicular transport, endocytosis, secretion, and apoptosis. cDNA cloning, chromosomal mapping, evolutionary/phylogenetic analysis Cytogenetics and cell genetics Medium 11435709
2024 ATP6V1D was identified as a key metabolic regulator of hepatocellular carcinoma (HCC) stemness via a metabolic CRISPR-Cas9 knockout screen. Mechanistically, ATP6V1D maintains autophagic flux by two mechanisms: (1) promoting lysosomal acidification, and (2) enhancing the interaction between CHMP4B and IST1 to foster ESCRT-III complex assembly, thereby facilitating autophagosome-lysosome fusion. Knockdown of ATP6V1D inhibited HCC stemness and malignant progression in vitro and in vivo. Silencing CHMP4B or IST1 phenocopied ATP6V1D loss. CRISPR-Cas9 knockout screen, shRNA knockdown, co-immunoprecipitation (co-IP), immunofluorescence, in vitro and in vivo tumor models, autophagic flux assays Autophagy High 39316516
2026 ATP6V1D (lysosomal V-ATPase subunit D) is upregulated in T. gondii-resistant Lewis rats in response to infection. CRISPR/Cas9 disruption of ATP6V1D in rat macrophages (NR8383) impaired v-ATPase function, leading to defective lysosomal acidification and increased intracellular T. gondii growth. Overexpression of GIMAP5 or GIMAP6 in ATP6V1D-knockout cells still reduced parasite growth (2.5- to 5-fold), but less robustly than in wild-type cells, establishing that ATP6V1D and GIMAPs act additively: GIMAPs drive lysosome translocation to the parasitophorous vacuole membrane while ATP6V1D enables lysosomal acidification to activate hydrolytic enzymes for parasite degradation. CRISPR/Cas9 knockout, transgene overexpression, lysosomal acidification assays, intracellular parasite growth quantification, genetic epistasis Microbiology spectrum High 41972776

Source papers

Stage 0 corpus · 44 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2011 mTORC1 senses lysosomal amino acids through an inside-out mechanism that requires the vacuolar H(+)-ATPase. Science (New York, N.Y.) 1323 22053050
2015 The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 1118 26186194
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2015 A human interactome in three quantitative dimensions organized by stoichiometries and abundances. Cell 1015 26496610
2014 A proteome-scale map of the human interactome network. Cell 977 25416956
2002 The vacuolar (H+)-ATPases--nature's most versatile proton pumps. Nature reviews. Molecular cell biology 961 11836511
2020 A reference map of the human binary protein interactome. Nature 849 32296183
2003 Complete sequencing and characterization of 21,243 full-length human cDNAs. Nature genetics 754 14702039
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2012 A census of human soluble protein complexes. Cell 689 22939629
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2008 Large-scale proteomics and phosphoproteomics of urinary exosomes. Journal of the American Society of Nephrology : JASN 607 19056867
1997 Structure, function and regulation of the vacuolar (H+)-ATPase. Annual review of cell and developmental biology 488 9442887
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2022 OpenCell: Endogenous tagging for the cartography of human cellular organization. Science (New York, N.Y.) 432 35271311
2005 Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome research 409 16344560
2015 Panorama of ancient metazoan macromolecular complexes. Nature 407 26344197
1996 Normalization and subtraction: two approaches to facilitate gene discovery. Genome research 401 8889548
1999 Vacuolar and plasma membrane proton-adenosinetriphosphatases. Physiological reviews 348 10221984
2007 Coupling of rotation and catalysis in F(1)-ATPase revealed by single-molecule imaging and manipulation. Cell 307 17662945
1999 Structure and properties of the vacuolar (H+)-ATPases. The Journal of biological chemistry 252 10224039
2009 Proteomic analysis of human parotid gland exosomes by multidimensional protein identification technology (MudPIT). Journal of proteome research 237 19199708
2007 hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Genomics 222 17207965
2017 Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification. Nature communications 221 28524877
1999 Animal plasma membrane energization by proton-motive V-ATPases. BioEssays : news and reviews in molecular, cellular and developmental biology 206 10440860
2018 An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations. Nature communications 201 29568061
1997 The vacuolar H+-ATPase: a universal proton pump of eukaryotes. The Biochemical journal 199 9210392
1986 Receptor-mediated endocytosis: the intracellular journey of transferrin and its receptor. Biochimie 169 2874839
2020 Structure and Roles of V-type ATPases. Trends in biochemical sciences 168 32001091
1995 A bovine cDNA and a yeast gene (VMA8) encoding the subunit D of the vacuolar H(+)-ATPase. Proceedings of the National Academy of Sciences of the United States of America 78 7831318
2000 Quinupristin/dalfopristin-resistant enterococci of the satA (vatD) and satG (vatE) genotypes from different ecological origins in Germany. Microbial drug resistance (Larchmont, N.Y.) 57 10868806
2002 Crystal structure of Vat(D): an acetyltransferase that inactivates streptogramin group A antibiotics. Biochemistry 52 11841212
1995 VMA8 encodes a 32-kDa V1 subunit of the Saccharomyces cerevisiae vacuolar H(+)-ATPase required for function and assembly of the enzyme complex. The Journal of biological chemistry 48 7797485
2001 Indication of transposition of a mobile DNA element containing the vat(D) and erm(B) genes in Enterococcus faecium. Antimicrobial agents and chemotherapy 27 11600385
2013 Role of periplasmic binding proteins, FatB and VatD, in the vulnibactin utilization system of Vibrio vulnificus M2799. Microbial pathogenesis 9 24135791
2024 ATP6V1D drives hepatocellular carcinoma stemness and progression via both lysosome acidification-dependent and -independent mechanisms. Autophagy 5 39316516
2001 cDNA cloning, chromosomal localization and evolutionary analysis of mouse vacuolar ATPase subunit D, Atp6m. Cytogenetics and cell genetics 4 11435709
2025 Arabidopsis phospholipase Dζ2 facilitates vacuolar acidification and autophagy under phosphorus starvation by interacting with VATD. Cell reports 1 40668679
2015 Expression, purification, crystallization and X-ray crystallographic analysis of the periplasmic binding protein VatD from Vibrio vulnificus M2799. Acta crystallographica. Section F, Structural biology communications 1 26249703
2026 Synergy between upregulated small GTPase immunity-associated proteins and lysosomal ATP6V1D in restricting intracellular Toxoplasma growth. Microbiology spectrum 0 41972776
2025 Association and functional study of ATP6V1D and GPHN gene polymorphisms with depression in Chinese population. World journal of psychiatry 0 40309610
2025 Detection of a streptogramin A O-acetyltransferase gene (vatD) in the chromosome of Clostridium botulinum isolated from infants in the United States. Applied and environmental microbiology 0 40693774
2025 Differential Expression of ATP6V1D and Its Diagnostic Potential in IgA Nephropathy. Current medical science 0 40911183