Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:1902600 proton transmembrane transport	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic (IBA) annotation that subunit E of V-ATPase participates in proton transmembrane transport. This is the central biological process for the V-ATPase complex and is the core function of this subunit, which forms part of the EG peripheral stalk required for the rotary pumping mechanism. Reason: The V-ATPase, of which subunit E is an obligate structural component, hydrolyzes ATP to drive proton translocation across membranes. This IBA annotation correctly captures the core biological role of the gene product.
GO:0046961 proton-transporting ATPase activity, rotational mechanism	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic (IBA) annotation to the rotary proton-transporting ATPase molecular function. Subunit E does not itself hydrolyze ATP, but as part of the EG stator stalks it is an essential structural component of the holoenzyme that enables this activity; GO annotates subunits of the complex to the complex activity. Reason: Subunit E is required for the rotary mechanism by anchoring the catalytic head; annotating the subunit with the complex molecular function follows GO convention for obligate complex members and represents the core function.
GO:0033178 proton-transporting two-sector ATPase complex, catalytic domain	IEA GO_REF:0000002	ACCEPT	Summary: InterPro-based (IPR002842, V-ATPase V1 E subunit) annotation placing ATP6V1E2 in the catalytic (V1) domain of the two-sector ATPase complex. The V1 sector is the ATP-hydrolyzing catalytic domain of the V-ATPase, and subunit E is a component of it. Reason: Subunit E is part of the V1 (catalytic) sector of the V-ATPase, so this complex-membership annotation correctly captures the cellular-component context and is consistent with the curated complex membership documented in UniProt. Supporting Evidence: file:human/ATP6V1E2/ATP6V1E2-uniprot.txt The V1 complex consists of three catalytic AB heterodimers that form a heterohexamer, three peripheral stalks each consisting of EG heterodimers, one central rotor including subunits D and F, and the regulatory subunits C and H.
GO:0046961 proton-transporting ATPase activity, rotational mechanism	IEA GO_REF:0000120	MARK AS OVER ANNOTATED	Summary: Electronic (IEA) annotation to the rotary proton-transporting ATPase activity, duplicating the more authoritative IBA annotation of the same term. Reason: This IEA annotation is redundant with the IBA annotation to the identical term (GO:0046961). The IBA version is retained as the representative core annotation; the duplicate IEA adds no information.
GO:1902600 proton transmembrane transport	IEA GO_REF:0000002	MARK AS OVER ANNOTATED	Summary: InterPro-based electronic (IEA) annotation to proton transmembrane transport, duplicating the more authoritative IBA annotation of the same term. Reason: This IEA annotation is redundant with the IBA annotation to the identical term (GO:1902600). The IBA version is retained as the representative core annotation; the duplicate IEA adds no information.
GO:0005515 protein binding	IPI PMID:21516116 Next-generation sequencing to generate interactome datasets.	MARK AS OVER ANNOTATED	Summary: High-throughput next-generation-sequencing interactome screen reporting a binary interaction (with ATP6V1G1, O75348). The E-G interaction is biologically expected since the V1 peripheral stalk is an E-G heterodimer, but the bare 'protein binding' term is uninformative as a molecular-function statement. Reason: GO:0005515 'protein binding' conveys no specific functional information. The underlying E-G heterodimer relationship is already captured by the V1-complex membership annotation (GO:0033178).
GO:0005515 protein binding	IPI PMID:25416956 A proteome-scale map of the human interactome network.	MARK AS OVER ANNOTATED	Summary: Proteome-scale binary interactome map (Rolland et al.) reporting interactions (with ATP6V1G1, O75348, and BBLN, Q9BUW7) from a high-throughput yeast two-hybrid screen. Bare 'protein binding' is uninformative. Reason: GO:0005515 'protein binding' conveys no specific molecular function. The meaningful E-G interaction is already represented by complex-membership annotations.
GO:0005515 protein binding	IPI PMID:30021884 Histone Interaction Landscapes Visualized by Crosslinking Ma...	MARK AS OVER ANNOTATED	Summary: Crosslinking mass-spectrometry study of histone interaction landscapes in intact nuclei, reporting an interaction with ATP6V1G1 (O75348) as part of a large-scale dataset. Bare 'protein binding' is uninformative and the study is not focused on ATP6V1E2 function. Reason: GO:0005515 'protein binding' conveys no specific molecular function and derives from a high-throughput dataset unrelated to the specific role of this subunit.
GO:0005515 protein binding	IPI PMID:32296183 A reference map of the human binary protein interactome.	MARK AS OVER ANNOTATED	Summary: HuRI reference binary interactome (Luck et al.) reporting interactions (with RASSF10 A6NK89, ATP6V1G1 O75348, ATP6V1G2 O95670, and MESD Q14696) from a high-throughput yeast two-hybrid screen. Bare 'protein binding' is uninformative. Reason: GO:0005515 'protein binding' conveys no specific molecular function. The E-G interactions (ATP6V1G1/G2) reflect expected V1 stalk architecture already captured by complex-membership annotations.
GO:0005515 protein binding	IPI PMID:40205054 Multimodal cell maps as a foundation for structural and func...	MARK AS OVER ANNOTATED	Summary: Multimodal cell-mapping study (Schaffer et al.) reporting an interaction with ATP6V1G2 (O95670) from a high-throughput dataset. Bare 'protein binding' is uninformative as a molecular-function statement. Reason: GO:0005515 'protein binding' conveys no specific molecular function. The E-G interaction is already represented by complex-membership annotations.
GO:0001669 acrosomal vesicle	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Ensembl-orthology electronic annotation transferred from mouse Atp6v1e2 (Q9D593) placing the protein in the acrosomal vesicle. The acrosome is a lysosome-related organelle in sperm, and V-ATPase-mediated acidification there is biologically plausible for this testis/sperm-enriched isoform, but the localization has not been directly demonstrated for the human protein. Reason: Plausible and consistent with the testis/sperm-enriched expression of ATP6V1E2, but supported only by orthology-based IEA without direct human experimental evidence; retained as a non-core localization.
GO:0016241 regulation of macroautophagy	NAS PMID:22982048 Lipofuscin is formed independently of macroautophagy and lys...	MARK AS OVER ANNOTATED	Summary: NAS (non-traceable author statement) annotation derived from a study of lipofuscin formation in stress-induced senescent fibroblasts. The paper concerns macroautophagy and lysosomal activity in fibroblasts and does not study the testis-specific ATP6V1E2 isoform. Any V-ATPase role in autophagy is an indirect downstream consequence of lysosomal acidification. Reason: The annotation is NAS without a traceable experimental link to this isoform; macroautophagy regulation is not a core function of this testis-restricted V1 stalk subunit and is at best an indirect consequence of organelle acidification.
GO:0005829 cytosol	TAS Reactome:R-HSA-1222516	KEEP AS NON CORE	Summary: Reactome reaction-level TAS annotation to cytosol. The V1 sector is cytoplasmic/peripheral, so 'cytosol' is defensible, but it is a coarse location that fails to capture the V-ATPase-complex / organelle-membrane functional context. Reason: Defensible but coarse; the V1 subunit is peripheral/cytoplasmic, yet the functionally informative location is the V-ATPase complex on intracellular membranes. Retained as non-core.
GO:0005829 cytosol	TAS Reactome:R-HSA-5252133	KEEP AS NON CORE	Summary: Reactome reaction-level TAS annotation to cytosol, duplicating other Reactome cytosol annotations for this gene. Reason: Defensible but coarse and redundant with other Reactome cytosol annotations; the informative location is the V-ATPase complex on membranes.
GO:0005829 cytosol	TAS Reactome:R-HSA-74723	KEEP AS NON CORE	Summary: Reactome reaction-level TAS annotation to cytosol, duplicating other Reactome cytosol annotations for this gene. Reason: Defensible but coarse and redundant with other Reactome cytosol annotations; the informative location is the V-ATPase complex on membranes.
GO:0005829 cytosol	TAS Reactome:R-HSA-917841	KEEP AS NON CORE	Summary: Reactome reaction-level TAS annotation to cytosol, duplicating other Reactome cytosol annotations for this gene. Reason: Defensible but coarse and redundant with other Reactome cytosol annotations; the informative location is the V-ATPase complex on membranes.
GO:0005829 cytosol	TAS Reactome:R-HSA-9639286	KEEP AS NON CORE	Summary: Reactome reaction-level TAS annotation to cytosol, duplicating other Reactome cytosol annotations for this gene. Reason: Defensible but coarse and redundant with other Reactome cytosol annotations; the informative location is the V-ATPase complex on membranes.
GO:0005829 cytosol	TAS Reactome:R-HSA-9640167	KEEP AS NON CORE	Summary: Reactome reaction-level TAS annotation to cytosol, duplicating other Reactome cytosol annotations for this gene. Reason: Defensible but coarse and redundant with other Reactome cytosol annotations; the informative location is the V-ATPase complex on membranes.
GO:0005829 cytosol	TAS Reactome:R-HSA-9640168	KEEP AS NON CORE	Summary: Reactome reaction-level TAS annotation to cytosol, duplicating other Reactome cytosol annotations for this gene. Reason: Defensible but coarse and redundant with other Reactome cytosol annotations; the informative location is the V-ATPase complex on membranes.
GO:0005829 cytosol	TAS Reactome:R-HSA-9640175	KEEP AS NON CORE	Summary: Reactome reaction-level TAS annotation to cytosol, duplicating other Reactome cytosol annotations for this gene. Reason: Defensible but coarse and redundant with other Reactome cytosol annotations; the informative location is the V-ATPase complex on membranes.
GO:0005829 cytosol	TAS Reactome:R-HSA-9640195	KEEP AS NON CORE	Summary: Reactome reaction-level TAS annotation to cytosol, duplicating other Reactome cytosol annotations for this gene. Reason: Defensible but coarse and redundant with other Reactome cytosol annotations; the informative location is the V-ATPase complex on membranes.
GO:0005829 cytosol	TAS Reactome:R-HSA-9645598	KEEP AS NON CORE	Summary: Reactome reaction-level TAS annotation to cytosol, duplicating other Reactome cytosol annotations for this gene. Reason: Defensible but coarse and redundant with other Reactome cytosol annotations; the informative location is the V-ATPase complex on membranes.
GO:0005829 cytosol	TAS Reactome:R-HSA-9645608	KEEP AS NON CORE	Summary: Reactome reaction-level TAS annotation to cytosol, duplicating other Reactome cytosol annotations for this gene. Reason: Defensible but coarse and redundant with other Reactome cytosol annotations; the informative location is the V-ATPase complex on membranes.
GO:0005829 cytosol	TAS Reactome:R-HSA-9646468	KEEP AS NON CORE	Summary: Reactome reaction-level TAS annotation to cytosol, duplicating other Reactome cytosol annotations for this gene. Reason: Defensible but coarse and redundant with other Reactome cytosol annotations; the informative location is the V-ATPase complex on membranes.

Core Functions

Structural component of the V1 peripheral (stator) stalk of the vacuolar H(+)-ATPase, forming an EG heterodimer that anchors the (AB)3 catalytic head and enables ATP hydrolysis-driven rotary proton transport

Molecular Function:

proton-transporting ATPase activity, rotational mechanism

Directly Involved In:

proton transmembrane transport

In Complex:

proton-transporting two-sector ATPase complex, catalytic domain

Supporting Evidence:

file:human/ATP6V1E2/ATP6V1E2-uniprot.txt
The V1 complex consists of three catalytic AB heterodimers that form a heterohexamer, three peripheral stalks each consisting of EG heterodimers, one central rotor including subunits D and F, and the regulatory subunits C and H.

References

GO_REF:0000002

Gene Ontology annotation through association of InterPro records with GO terms

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000107

Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:12036578

A human gene, ATP6E1, encoding a testis-specific isoform of H(+)-ATPase subunit E.

ATP6V1E2 (ATP6E1) encodes a testis-specific isoform of the V-ATPase subunit E, distinct from the ubiquitous ATP6V1E1 paralog.

PMID:21516116

Next-generation sequencing to generate interactome datasets.

PMID:22982048

Lipofuscin is formed independently of macroautophagy and lysosomal activity in stress-induced prematurely senescent human fibroblasts.

PMID:25416956

A proteome-scale map of the human interactome network.

PMID:30021884

Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei.

PMID:32296183

A reference map of the human binary protein interactome.

PMID:40205054

Multimodal cell maps as a foundation for structural and functional genomics.

Reactome:R-HSA-1222516

Intraphagosomal pH is lowered to 5 by V-ATPase

Reactome:R-HSA-5252133

ATP6AP1 binds V-ATPase

Reactome:R-HSA-74723

Endosome acidification

Reactome:R-HSA-917841

Acidification of Tf:TfR1 containing endosome

Reactome:R-HSA-9639286

RRAGC,D exchanges GTP for GDP

Reactome:R-HSA-9640167

RRAGA,B exchanges GDP for GTP

Reactome:R-HSA-9640168

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

Reactome:R-HSA-9640175

v-ATPase:Ragulator:RagA,B:GDP:RagC,D:GDP binds SLC38A9:Arginine

Reactome:R-HSA-9640195

RRAGA,B hydrolyzes GTP

Reactome:R-HSA-9645598

RRAGC,D hydrolyzes GTP

Reactome:R-HSA-9645608

v-ATPase:Ragulator:RRAGA,B:GTP:RRAGC,D:GDP binds mTORC1

Reactome:R-HSA-9646468

mTORC1 binds RHEB:GTP

Suggested Experiments

Experiment: Immunolocalization (and immuno-EM) of ATP6V1E2 in human/mouse testis and spermatozoa to confirm acrosomal-vesicle localization and distinguish it from ATP6V1E1.

Experiment: Reconstitution or co-immunoprecipitation assays to test EG heterodimer formation of ATP6V1E2 with ATP6V1G1/G2 and incorporation into an assembled, ATP-hydrolyzing V-ATPase complex.

Experiment: Generation and phenotyping of an Atp6v1e2 knockout (sperm count, motility, acrosome reaction, acrosomal pH, fertility) to define its in vivo role.

Deep Research

Falcon

(ATP6V1E2-deep-research-falcon.md)

Comprehensive Research Report on ATP6V1E2 (V-type proton ATPase subunit E2) Falcon

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Comprehensive Research Report on ATP6V1E2 (V-type proton ATPase subunit E2)

Gene Identity and Protein Family

ATP6V1E2 (UniProt: Q96A05) encodes V-type proton ATPase subunit E2, a structural component of the vacuolar H+-ATPase (V-ATPase) multi-subunit complex in Homo sapiens. The protein belongs to the V-ATPase E subunit family, and represents one of two E-subunit isoforms in mammals (E1 and E2) that show tissue-specific expression patterns (song2020theemergingroles pages 3-5). The V-ATPase is an evolutionarily conserved ATP-driven rotary proton pump structurally related to mitochondrial F-type ATP synthases, though it exclusively functions in ATP hydrolysis-driven proton translocation rather than ATP synthesis (eaton2021theh+atpase(vatpase) pages 1-5, chen2022thevatpasesin pages 1-2).

Structural Architecture and Primary Function

Overall V-ATPase Structure

The V-ATPase is a large multisubunit complex (~830 kDa) composed of two major domains: a cytosolic V1 domain responsible for ATP hydrolysis, and a membrane-embedded V0 domain that forms the proton translocation pore (eaton2021theh+atpase(vatpase) pages 1-5, song2020theemergingroles pages 1-2). Recent high-resolution cryo-electron microscopy structures of mammalian V-ATPases have revealed the complex architecture at near-atomic resolution (2.9-3.9 Å), enabling detailed understanding of subunit organization and mechanism (wang2020structuresofa pages 1-3, wang2020structuresofa pages 3-5).

The V1 domain contains subunits A3, B3, C, D, E3, F, G3, and H, while the V0 domain comprises subunits a, c9-10, c″, d, e, ATP6AP1 (Ac45), ATP6AP2 (prorenin receptor), and in some species RNAseK/f (wang2020structuresofa pages 1-3, wang2020structuresofa pages 3-5). The ATP:proton stoichiometry is 3:10, meaning three ATP molecules are hydrolyzed for every ten protons translocated, establishing a maximum transmembrane proton-motive force of ~180 mV or ~3 pH units (abbas2020structureofvatpase pages 4-5).

Role of Subunit E in the V-ATPase Complex

ATP6V1E2 encodes the E2 isoform of subunit E, which is a critical structural element of the peripheral stalks in the V1 domain. The V-ATPase contains three peripheral stalks, each composed of E-G heterodimers that connect the catalytic A3B3 hexamer head to the membrane-embedded V0 domain and the N-terminal domain of subunit a (wang2020structuresofa pages 3-5, wang2020structuresofa pages 5-7).

Structurally, the E subunit features:
- N-terminal domain (NTD): Forms long, curved coiled-coils with subunit G that extend from the V1 collar to the A3B3 head
- C-terminal domain (CTD): Adopts a compact configuration that directly engages B subunits in the catalytic hexamer (wang2020structuresofa pages 3-5)

The three peripheral stalks (PS-1, PS-2, PS-3) adopt different curvatures despite identical sequences, reflecting intrinsic structural plasticity that accommodates tilting and twisting of the A3B3 head during ATP binding and hydrolysis (wang2020structuresofa pages 3-5). This flexibility is essential for coupling the conformational precession of the catalytic head to rotation of the central stalk (D-F subunits) and ultimately to proton pumping through V0 (wang2020structuresofa pages 5-7).

The E subunit does not directly participate in ATP hydrolysis—the catalytic sites are located at the A-B interfaces in the hexamer. Instead, the E-G peripheral stalks form a stator apparatus that prevents rotation of the A3B3 head and associated V0 subunits (a, e, d), allowing the central D-F-d-c-ring rotor to turn relative to the stationary components (wang2020structuresofa pages 3-5, wang2020structuresofa pages 5-7).

Enzymatic Mechanism

The V-ATPase operates through a rotary catalytic mechanism:

ATP hydrolysis occurs at three catalytic sites in the A3B3 hexamer, cycling through ATP-bound, ADP-bound (post-hydrolysis), and empty conformations (abbas2020structureofvatpase pages 4-5)
This conformational precession drives rotation of the central stalk (D-F subunits) and the attached c-ring in the V0 domain (wang2020structuresofa pages 5-7)
As the c-ring rotates relative to subunit a, protons are abstracted from the cytoplasmic half-channel, carried by conserved glutamate residues on c-ring subunits through the lipid bilayer, and released into the luminal half-channel (abbas2020structureofvatpase pages 4-5)
Critical residues in subunit a (e.g., Arg741 in human a1) facilitate proton transfer by forming transient salt bridges with c-ring glutamates (abbas2020structureofvatpase pages 4-5)

The peripheral stalks containing subunit E ensure that ATP hydrolysis energy is efficiently converted to proton transport by maintaining mechanical coupling between the V1 and V0 domains (wang2020structuresofa pages 3-5).

Subcellular Localization

V-ATPases containing E subunits are localized to multiple intracellular membranes and, in specialized cells, to the plasma membrane (eaton2021theh+atpase(vatpase) pages 1-5). The primary subcellular locations include:

Intracellular Organelles

Lysosomes: V-ATPase is the primary proton pump maintaining acidic lysosomal pH (~4.5-5.0), essential for activating hydrolytic enzymes and protein degradation (song2020theemergingroles pages 1-2, song2020theemergingroles pages 3-5)
Endosomes (early and late): Progressive acidification along the endocytic pathway supports cargo sorting and receptor recycling (song2020theemergingroles pages 3-5)
Trans-Golgi Network (TGN): V-ATPase acidification is required for proper vesicle trafficking and delivery of cell wall/membrane components (seidel2022theplantvatpase pages 1-2, song2020theemergingroles pages 3-5)
Synaptic vesicles: In neurons, V-ATPase establishes the electrochemical proton gradient necessary for neurotransmitter loading (abbas2020structureofvatpase pages 1-2, kosmidis2022regulationofthe pages 1-3, song2020theemergingroles pages 3-5)
Secretory granules: Present in neuroendocrine cells for granule acidification and regulated secretion (song2020theemergingroles pages 3-5)

Specialized Plasma Membrane Localization

In certain differentiated cell types, V-ATPase is targeted to the plasma membrane for extracellular acidification:
- Osteoclasts (bone resorption)
- Kidney intercalated cells (acid secretion)
- Epididymal cells (sperm maturation)
- Inner ear cells (endolymph pH regulation) (eaton2021theh+atpase(vatpase) pages 1-5, eaton2021theh+atpase(vatpase) pages 5-9)

ATP6V1E2-Specific Localization

Recent evidence specifically implicates ATP6V1E2 in:
- Neuronal synaptic vesicles: ATP6V1E2 was downregulated in a homocysteine-induced neurotoxicity model affecting the synaptic vesicle cycle, suggesting a critical role in this compartment (wang2025theinvolvementof pages 1-2)
- Sperm acrosomes: ATP6V1E2 function is required for proper acrosomal acidification, essential for the acrosome reaction and fertilization (chavez2024cytosolicandacrosomal pages 1-2)

Biological Processes and Signaling Pathways

Core Biological Functions

1. pH Homeostasis and Organelle Acidification

The primary function of V-ATPase is establishing and maintaining acidic pH in intracellular compartments. Each organelle maintains a characteristic luminal pH: ER (~7.1), cis-Golgi (~6.8), TGN (~6.3), late endosomes (~5.3), and lysosomes (~5.2) (seidel2022theplantvatpase pages 1-2). This pH gradient is essential for:
- Activation of pH-dependent enzymes
- Protein folding and quality control
- Coupled ion/metabolite transport
- Receptor-ligand dissociation (eaton2021theh+atpase(vatpase) pages 1-5, song2020theemergingroles pages 1-2)

2. Autophagy and Lysosomal Degradation

V-ATPase-mediated lysosomal acidification is critical for autophagy, the cellular self-digestion pathway. Proper acidification activates lysosomal proteases, lipases, and nucleases that degrade autophagic cargo. V-ATPase dysfunction leads to:
- Impaired autophagosome-lysosome fusion
- Reduced hydrolase activity
- Accumulation of undegraded substrates
- Cellular stress and death (song2020theemergingroles pages 1-2, indrawinata2023structuralandfunctional pages 1-2)

Mutations in V-ATPase subunits, particularly in the a1 isoform (ATP6V0A1), cause severe neurodevelopmental disorders characterized by lysosomal and autophagic dysfunction, including developmental and epileptic encephalopathies (indrawinata2023structuralandfunctional pages 1-2).

3. Synaptic Vesicle Loading and Neurotransmission

In neurons, V-ATPase plays an indispensable role in synaptic vesicle function. The electrochemical proton gradient (both ΔpH and Δψ) drives secondary active transporters that load neurotransmitters into synaptic vesicles:
- Glutamate uptake relies primarily on electrical potential (Δψ)
- Monoamines (dopamine, serotonin, norepinephrine) utilize primarily the pH gradient (ΔpH)
- Acetylcholine and GABA depend on both components (song2020theemergingroles pages 3-5)

Recent evidence directly links ATP6V1E2 to this process: in a homocysteine neurotoxicity model, atp6v1e2 was one of four genes (along with snap25, cplx1, slc32a1) related to the synaptic vesicle cycle that showed decreased expression, correlating with neuronal apoptosis and synaptic dysfunction (wang2025theinvolvementof pages 1-2). This study employed microarray analysis followed by RT-qPCR and western blot validation in mouse neuroblastoma N2a cells and rat hippocampal tissues, providing direct experimental evidence for ATP6V1E2's role in synaptic function.

4. Endocytosis and Membrane Trafficking

V-ATPase activity is essential for endocytic trafficking and receptor-mediated endocytosis. Acidification of endosomes promotes:
- Ligand-receptor dissociation
- Cargo sorting
- Vesicle maturation along the endocytic pathway
- Recycling vs. degradative pathway decisions (eaton2021theh+atpase(vatpase) pages 1-5, song2020theemergingroles pages 3-5)

Defective V-ATPase activity disrupts membrane trafficking, protein processing, and secretory pathway function, with consequences for nutrient uptake, signal transduction, and pathogen defense (song2020theemergingroles pages 1-2, seidel2022theplantvatpase pages 1-2).

Signaling and Metabolic Pathways

mTORC1 and AMPK Nutrient Sensing

V-ATPase serves as a central component of the lysosomal nutrient-sensing platform that regulates mTORC1 (mechanistic target of rapamycin complex 1) and AMPK (AMP-activated protein kinase) signaling (chen2024vatpaseincancer pages 1-3, eaton2021theh+atpase(vatpase) pages 1-5, song2020theemergingroles pages 1-2).

Amino acid sensing: Under amino acid-replete conditions, the Ragulator complex (LAMTOR1-5) associated with V-ATPase recruits mTORC1 to the lysosomal surface for activation. V-ATPase activity is required for this process, though the precise mechanism involves both pH-dependent and pH-independent functions (song2020theemergingroles pages 3-5).

Glucose sensing: V-ATPase participates in the lysosomal glucose-sensing pathway that activates AMPK independently of AMP/ADP ratios. When intracellular glucose and fructose-1,6-bisphosphate (FBP) levels fall:
1. Aldolase dissociates from V-ATPase
2. V-ATPase activity is inhibited
3. AXIN-LKB1 complex is recruited to the lysosome via V-ATPase/Ragulator
4. LKB1 phosphorylates and activates AMPK (qu2023lithocholicacidtargets pages 1-5, eaton2021theh+atpase(vatpase) pages 1-5)

A recent mechanistic study (2023) demonstrated that lithocholic acid (LCA), a bile acid accumulated during calorie restriction, enhances sirtuin activity to deacetylate the V1E1 subunit of V-ATPase at residues K52, K99, and K191. This deacetylation inhibits V-ATPase, triggering AMPK activation via the lysosomal glucose-sensing pathway and mediating benefits of calorie restriction (qu2023lithocholicacidtargets pages 1-5). While this study focused on the E1 isoform rather than ATP6V1E2 directly, it establishes that E-subunit post-translational modifications represent an important regulatory mechanism for V-ATPase activity and cellular metabolism.

Wnt and Notch Signaling

ATP6AP2 (prorenin receptor), an accessory V-ATPase subunit, participates in Wnt signaling pathways during stem cell self-renewal and embryonic development. V-ATPase activity is also implicated in Notch signaling through effects on endosomal pH and receptor processing (chen2024vatpaseincancer pages 1-3, indrawinata2023structuralandfunctional pages 1-2).

Reproductive Cell Function

ATP6V1E2 plays a specific role in mammalian sperm acrosomal acidification. A comprehensive 2024 review on cytosolic and acrosomal pH regulation in mammalian sperm states that "ATP6V1E2 function, acrosomal acidification was affected, indicating that this isoform of the V-ATPase" is critical for maintaining the acidic acrosomal pH necessary for the acrosome reaction required for fertilization (chavez2024cytosolicandacrosomal pages 1-2). This represents one of the few tissue-specific functions directly attributed to ATP6V1E2 rather than V-ATPase broadly.

High-Altitude Adaptation

An emerging area of research links ATP6V1E2 genetic variation to hypoxia adaptation. A 2026 study in Tibetan populations identified the ATP6V1E2 rs896210 single nucleotide polymorphism as significantly associated with susceptibility to high-altitude polycythemia (HAPC), a maladaptive response to chronic hypoxia characterized by excessive red blood cell production (ran2026associationbetweenepas1 pages 1-6). The study suggests ATP6V1E2 may synergistically interact with EPAS1 (HIF-2α) polymorphisms in regulating erythropoiesis under hypoxic conditions, though the mechanistic basis requires further investigation.

Regulation of V-ATPase Activity

V-ATPase activity is regulated through multiple mechanisms that may involve the E subunit:

1. Reversible Assembly/Disassembly

In yeast and some mammalian contexts, V-ATPase can reversibly dissociate into V1 and V0 domains in response to glucose deprivation or other stresses. Dissociated domains are inactive—V1 loses ATPase activity and V0 becomes impermeable to protons, preventing futile ATP hydrolysis and proton leakage (eaton2021theh+atpase(vatpase) pages 5-9, song2020theemergingroles pages 3-5). However, this regulatory mechanism appears less prominent in mammalian cells compared to yeast, and may not occur in autotrophic plant cells (seidel2022theplantvatpase pages 1-2).

2. Post-Translational Modifications

As demonstrated in the LCA-sirtuin pathway study, V1E1 acetylation status regulates V-ATPase activity. Deacetylation at K52, K99, and K191 inhibits the enzyme, coupling V-ATPase to cellular metabolic state (qu2023lithocholicacidtargets pages 1-5). Disulfide bond formation between cysteine residues in subunit E can also modulate activity in plant V-ATPases (song2020theemergingroles pages 3-5).

3. Subunit Isoform Composition

The existence of two E-subunit isoforms (E1 and E2) allows tissue- and organelle-specific regulation. Different isoform combinations may confer distinct regulatory properties, localization signals, or interacting partners, though the specific functional differences between E1 and E2 remain incompletely characterized (song2020theemergingroles pages 3-5).

4. Lipid Environment and Protein Interactions

Recent structural studies reveal that V-ATPase interacts extensively with ordered phospholipids and cholesterol, particularly within the c-ring and at subunit interfaces. These lipid interactions stabilize the complex and may modulate activity (wang2020structuresofa pages 9-10). Additionally, V-ATPase associates with regulatory proteins including 14-3-3 proteins in plants and the RAVE complex in yeast (eaton2021theh+atpase(vatpase) pages 5-9, seidel2022theplantvatpase pages 1-2).

Experimental Evidence and Structural Insights

High-Resolution Structural Studies

Major advances in understanding V-ATPase structure come from cryo-EM studies:

Abbas et al. (2020) determined structures of rat brain V-ATPase at 3.6-3.9 Å resolution, revealing subunit organization including the E1 isoform in peripheral stalks and defining the ATP:H+ ratio as 3:10 (abbas2020structureofvatpase pages 1-2, abbas2020structureofvatpase pages 4-5)
Wang et al. (2020) reported human V-ATPase structures at 2.9-3.1 Å resolution, building complete atomic models including three peripheral stalks with E subunits (E1 isoform) and revealing extensive interactions with glycans and lipids (wang2020structuresofa pages 1-3, wang2020structuresofa pages 3-5, wang2020structuresofa pages 9-10)

These structures show that E subunits form elongated coiled-coils at their N-termini that extend ~100 Å from the V1 collar to the A3B3 head, with compact C-terminal domains that make specific contacts with B subunits. The three peripheral stalks adopt different overall conformations to accommodate the precession of the catalytic head during ATP hydrolysis (wang2020structuresofa pages 3-5, wang2020structuresofa pages 5-7).

Functional and Disease Studies

Neurotoxicity model (Wang et al., 2025): Microarray analysis in homocysteine-treated mouse neuroblastoma cells identified atp6v1e2 among four synaptic-vesicle-cycle genes with decreased expression. RT-qPCR and western blot confirmed downregulation at both mRNA and protein levels, correlating with neuronal apoptosis, LDH leakage, synaptic structural impairment, and depressive-like symptoms in treated rats (wang2025theinvolvementof pages 1-2). This provides direct experimental evidence linking ATP6V1E2 to neuronal health and synaptic function.

Calorie restriction pathway (Qu et al., 2023): Proteomic analysis of SIRT1-interacting proteins identified TULP3 as an LCA receptor that activates sirtuins to deacetylate V1E1 at K52, K99, and K191. Muscle-specific expression of a deacetylation-mimicking 3KR mutant of V1E1 activated AMPK and rejuvenated aged mouse muscles. LCA administration extended lifespan and healthspan in nematodes and flies in a manner dependent on TULP3 homologs (qu2023lithocholicacidtargets pages 1-5).

Sperm function (Chávez et al., 2024): Functional studies showed that ATP6V1E2 is required for proper acrosomal acidification in mammalian sperm, with loss of function affecting the acrosome reaction necessary for fertilization (chavez2024cytosolicandacrosomal pages 1-2).

Genetic association (Ran et al., 2026): Case-control study (78 HAPC patients, 85 controls) in Tibetan populations identified ATP6V1E2 rs896210 polymorphism as associated with HAPC susceptibility, with evidence for synergistic effects with EPAS1 polymorphisms (ran2026associationbetweenepas1 pages 1-6).

Disease Relevance

While ATP6V1E2-specific disease mutations are not well-documented, mutations in other V-ATPase subunits cause severe disorders:

ATP6V0A1 (a1 subunit) mutations cause developmental and epileptic encephalopathies with lysosomal dysfunction (indrawinata2023structuralandfunctional pages 1-2)
ATP6V1A mutations cause lysosomal homeostasis disorders with epilepsy and neurodegeneration (indrawinata2023structuralandfunctional pages 1-2)
V-ATPase dysfunction is implicated in neurodegenerative diseases (Alzheimer's, Parkinson's), cancer metastasis, osteopetrosis, and renal tubular acidosis (chen2024vatpaseincancer pages 1-3, song2020theemergingroles pages 1-2, chen2022thevatpasesin pages 1-2)

Summary and Knowledge Gaps

Category	Finding	Evidence / detail	Citation
Gene identity	ATP6V1E2 is the human gene for V-type proton ATPase subunit E2; it belongs to the V-ATPase E subunit family and corresponds to one of two mammalian E-subunit isoforms (E1/E2).	Literature on V-ATPase recognizes two E-subunit isoforms in higher eukaryotes; ATP6V1E2 is specifically the E2 isoform and should be distinguished from the more commonly studied E1 isoform in structural datasets.	(song2020theemergingroles pages 3-5, ran2026associationbetweenepas1 pages 1-6)
Protein complex context	ATP6V1E2 encodes a V1-sector structural subunit of the V-ATPase, not the catalytic ATP-hydrolyzing active site itself.	The V-ATPase is composed of a cytosolic V1 domain that hydrolyzes ATP and a membrane V0 domain that translocates protons. Subunit E is a V1 component.	(eaton2021theh+atpase(vatpase) pages 1-5, song2020theemergingroles pages 1-2, chen2022thevatpasesin pages 1-2)
Protein structure	Subunit E is part of the peripheral stalk(s) of V-ATPase and forms E–G heterodimers that connect the catalytic head to the membrane sector.	Cryo-EM structures of human V-ATPase show three peripheral stalks; each contains subunits E and G, with long coiled-coil N-termini and compact C-terminal regions that engage the catalytic head.	(wang2020structuresofa pages 3-5, abbas2020structureofvatpase pages 4-5)
Structural role	The E subunit helps stabilize the stator apparatus and mechanically couples ATP hydrolysis in V1 to proton pumping in V0.	Structural analysis shows E/G stalks link the A3B3 catalytic hexamer to collar/stator elements and accommodate conformational changes during rotary catalysis.	(wang2020structuresofa pages 3-5, wang2020structuresofa pages 5-7)
Primary biochemical function	ATP6V1E2 contributes to an enzyme complex whose overall reaction is ATP hydrolysis-driven proton transport across organellar or plasma membranes.	V-ATPase uses ATP hydrolysis in V1 to drive rotation and proton translocation through V0, generating electrochemical proton gradients and organelle acidification.	(wang2020structuresofa pages 1-3, eaton2021theh+atpase(vatpase) pages 1-5, chen2022thevatpasesin pages 1-2)
Substrate specificity	The relevant transported substrate for the holoenzyme is H+ (protons); ATP is the energy source. ATP6V1E2 itself is not the proton pore but supports the proton pump mechanism.	Reviews and structures consistently define V-ATPase as a proton pump that acidifies vesicles/organelles and, in some cells, the extracellular space.	(chen2024vatpaseincancer pages 1-3, eaton2021theh+atpase(vatpase) pages 1-5, song2020theemergingroles pages 1-2)
Subcellular localization	V-ATPases containing E subunits function on lysosomes, endosomes, Golgi/TGN, secretory granules, and synaptic vesicles; in specialized cells they can also localize to the plasma membrane.	V-ATPase is broadly distributed across acidic organelles and plasma membrane domains specialized for extracellular acidification.	(eaton2021theh+atpase(vatpase) pages 1-5, song2020theemergingroles pages 1-2, indrawinata2023structuralandfunctional pages 1-2, song2020theemergingroles pages 3-5)
Cellular site most relevant to ATP6V1E2	Available recent evidence particularly links ATP6V1E2 to neuronal/synaptic vesicle function and sperm acrosomal acidification.	ATP6V1E2 expression was reduced in a synaptic-vesicle-cycle neurotoxicity model; a sperm pH-regulation review cites ATP6V1E2 as important for acrosomal acidification.	(wang2025theinvolvementof pages 1-2, chavez2024cytosolicandacrosomal pages 1-2)
Core biological process	Organelle acidification / pH homeostasis	V-ATPase is the primary proton pump establishing acidic luminal pH in lysosomes and other endomembrane compartments.	(eaton2021theh+atpase(vatpase) pages 1-5, song2020theemergingroles pages 1-2, song2020theemergingroles pages 3-5)
Core biological process	Synaptic vesicle acidification and neurotransmitter loading	In neurons, V-ATPase-generated proton gradients energize loading of neurotransmitters into synaptic vesicles.	(abbas2020structureofvatpase pages 1-2, kosmidis2022regulationofthe pages 1-3, song2020theemergingroles pages 3-5)
Core biological process	Endocytosis, membrane trafficking, protein processing, and degradation	Acidification by V-ATPase supports endocytic trafficking, lysosomal proteolysis, and secretory/endosomal pathway function.	(eaton2021theh+atpase(vatpase) pages 1-5, song2020theemergingroles pages 1-2, seidel2022theplantvatpase pages 1-2)
Core biological process	Autophagy / lysosomal clearance	V-ATPase dysfunction perturbs lysosomal pH and impairs autophagic degradation, a major theme in disease studies of the complex.	(song2020theemergingroles pages 1-2, indrawinata2023structuralandfunctional pages 1-2, chen2022thevatpasesin pages 1-2)
Signaling pathway relevance	mTORC1 and AMPK nutrient/energy sensing	V-ATPase serves as part of a lysosomal signaling platform for amino-acid sensing and AMPK/mTORC1 regulation.	(chen2024vatpaseincancer pages 1-3, eaton2021theh+atpase(vatpase) pages 1-5, song2020theemergingroles pages 1-2)
Recent regulation finding (2023)	V-ATPase V1E1 can be regulated by sirtuin-dependent deacetylation at K52/K99/K191 in a calorie-restriction/LCA–TULP3–AMPK pathway.	Although demonstrated for the E1 isoform rather than ATP6V1E2 directly, this provides mechanistic evidence that E-subunit post-translational regulation can modulate V-ATPase activity.	(qu2023lithocholicacidtargets pages 1-5)
Recent functional association (2024)	ATP6V1E2 is implicated in mammalian sperm acrosomal pH regulation.	A 2024 review states that impaired ATP6V1E2 function affects acrosomal acidification, linking the isoform to reproductive cell physiology.	(chavez2024cytosolicandacrosomal pages 1-2)
Recent disease-model evidence (2025)	atp6v1e2 was downregulated in a homocysteine-induced neurotoxicity model associated with the synaptic vesicle cycle.	Microarray plus RT-qPCR and western blot validation identified atp6v1e2 among four synaptic-vesicle-related genes reduced in treated N2a cells.	(wang2025theinvolvementof pages 1-2)
Human genetics / population association	ATP6V1E2 rs896210 has been reported as associated with high-altitude polycythemia susceptibility in a Tibetan cohort.	This is a recent association study and suggests possible links to hypoxia adaptation, but functional validation remains limited.	(ran2026associationbetweenepas1 pages 1-6)
Strength of evidence	Direct ATP6V1E2-specific mechanistic literature is limited compared with the broader V-ATPase field.	Most precise mechanistic evidence comes from whole-complex V-ATPase structural/functional studies or from the E1 isoform; ATP6V1E2-specific conclusions are therefore partly inferred from conserved family function.	(wang2020structuresofa pages 1-3, wang2020structuresofa pages 3-5, song2020theemergingroles pages 3-5)

Table: This table summarizes verified identity, structure, localization, function, pathways, and recent research findings for human ATP6V1E2. It emphasizes where evidence is direct for ATP6V1E2 versus inferred from broader V-ATPase and E-subunit studies.

ATP6V1E2 encodes a structural component of the V1 peripheral stalk that is essential for V-ATPase function in proton pumping across intracellular and specialized plasma membranes. The protein contributes to a rotary mechanoenzyme that couples ATP hydrolysis to proton translocation, establishing pH gradients critical for autophagy, endocytosis, neurotransmitter loading, protein processing, and metabolic signaling.

Recent research (2024-2025) has specifically implicated ATP6V1E2 in neuronal synaptic vesicle function, sperm acrosomal acidification, and potentially high-altitude adaptation. Regulation of the E subunit by acetylation/deacetylation links V-ATPase to metabolic pathways including calorie restriction and AMPK signaling.

Important limitations: Direct ATP6V1E2-specific mechanistic studies remain limited compared to the broader V-ATPase literature. Most structural and functional insights are derived from studies of the related E1 isoform or from whole-complex analyses. The functional differences between E1 and E2 isoforms, their tissue-specific expression patterns, and the consequences of selective E2 deficiency require further investigation. Additionally, while genetic associations with HAPC are intriguing, the mechanistic basis for ATP6V1E2's role in hypoxia adaptation remains to be elucidated.

References

(song2020theemergingroles pages 3-5): Qiaoyun Song, Bo Meng, Haidong Xu, and Zixu Mao. The emerging roles of vacuolar-type atpase-dependent lysosomal acidification in neurodegenerative diseases. Translational Neurodegeneration, May 2020. URL: https://doi.org/10.1186/s40035-020-00196-0, doi:10.1186/s40035-020-00196-0. This article has 255 citations and is from a domain leading peer-reviewed journal.
(eaton2021theh+atpase(vatpase) pages 1-5): Amity F. Eaton, Maria Merkulova, and Dennis Brown. The h⁺-atpase (v-atpase): from proton pump to signaling complex in health and disease. Mar 2021. URL: https://doi.org/10.1152/ajpcell.00442.2020, doi:10.1152/ajpcell.00442.2020. This article has 188 citations.
(chen2022thevatpasesin pages 1-2): Fangquan Chen, Rui Kang, Jiao Liu, and Daolin Tang. The v-atpases in cancer and cell death. Cancer Gene Therapy, 29:1529-1541, May 2022. URL: https://doi.org/10.1038/s41417-022-00477-y, doi:10.1038/s41417-022-00477-y. This article has 129 citations and is from a peer-reviewed journal.
(song2020theemergingroles pages 1-2): Qiaoyun Song, Bo Meng, Haidong Xu, and Zixu Mao. The emerging roles of vacuolar-type atpase-dependent lysosomal acidification in neurodegenerative diseases. Translational Neurodegeneration, May 2020. URL: https://doi.org/10.1186/s40035-020-00196-0, doi:10.1186/s40035-020-00196-0. This article has 255 citations and is from a domain leading peer-reviewed journal.
(wang2020structuresofa pages 1-3): Longfei Wang, Di Wu, Carol V. Robinson, Hao Wu, and Tian-Min Fu. Structures of a complete human v-atpase reveal mechanisms of its assembly. Molecular Cell, 80:501-511.e3, Nov 2020. URL: https://doi.org/10.1016/j.molcel.2020.09.029, doi:10.1016/j.molcel.2020.09.029. This article has 184 citations and is from a highest quality peer-reviewed journal.
(wang2020structuresofa pages 3-5): Longfei Wang, Di Wu, Carol V. Robinson, Hao Wu, and Tian-Min Fu. Structures of a complete human v-atpase reveal mechanisms of its assembly. Molecular Cell, 80:501-511.e3, Nov 2020. URL: https://doi.org/10.1016/j.molcel.2020.09.029, doi:10.1016/j.molcel.2020.09.029. This article has 184 citations and is from a highest quality peer-reviewed journal.
(abbas2020structureofvatpase pages 4-5): Yazan M. Abbas, Di Wu, Stephanie A. Bueler, Carol V. Robinson, and John L. Rubinstein. Structure of v-atpase from the mammalian brain. Mar 2020. URL: https://doi.org/10.1126/science.aaz2924, doi:10.1126/science.aaz2924. This article has 278 citations and is from a highest quality peer-reviewed journal.
(wang2020structuresofa pages 5-7): Longfei Wang, Di Wu, Carol V. Robinson, Hao Wu, and Tian-Min Fu. Structures of a complete human v-atpase reveal mechanisms of its assembly. Molecular Cell, 80:501-511.e3, Nov 2020. URL: https://doi.org/10.1016/j.molcel.2020.09.029, doi:10.1016/j.molcel.2020.09.029. This article has 184 citations and is from a highest quality peer-reviewed journal.
(seidel2022theplantvatpase pages 1-2): Thorsten Seidel. The plant v-atpase. Frontiers in Plant Science, Jun 2022. URL: https://doi.org/10.3389/fpls.2022.931777, doi:10.3389/fpls.2022.931777. This article has 60 citations.
(abbas2020structureofvatpase pages 1-2): Yazan M. Abbas, Di Wu, Stephanie A. Bueler, Carol V. Robinson, and John L. Rubinstein. Structure of v-atpase from the mammalian brain. Mar 2020. URL: https://doi.org/10.1126/science.aaz2924, doi:10.1126/science.aaz2924. This article has 278 citations and is from a highest quality peer-reviewed journal.
(kosmidis2022regulationofthe pages 1-3): Eleftherios Kosmidis, Christopher G. Shuttle, Julia Preobraschenski, Marcelo Ganzella, Peter J. Johnson, Salome Veshaguri, Jesper Holmkvist, Mads P. Møller, Orestis Marantos, Frank Marcoline, Michael Grabe, Jesper L. Pedersen, Reinhard Jahn, and Dimitrios Stamou. Regulation of the mammalian-brain v-atpase through ultraslow mode-switching. Nov 2022. URL: https://doi.org/10.1038/s41586-022-05472-9, doi:10.1038/s41586-022-05472-9. This article has 39 citations and is from a highest quality peer-reviewed journal.
(eaton2021theh+atpase(vatpase) pages 5-9): Amity F. Eaton, Maria Merkulova, and Dennis Brown. The h⁺-atpase (v-atpase): from proton pump to signaling complex in health and disease. Mar 2021. URL: https://doi.org/10.1152/ajpcell.00442.2020, doi:10.1152/ajpcell.00442.2020. This article has 188 citations.
(wang2025theinvolvementof pages 1-2): Meng Wang, Xiaoshan Liang, Keqing Jin, Yinyue Liu, Suhui Luo, Qiang Zhang, Xuan Wang, Zhiping Dong, and Xumei zhang. The involvement of the synaptic vesicle cycle in homocysteine induced neurotoxicity in vitro and in vivo. Scientific Reports, May 2025. URL: https://doi.org/10.1038/s41598-025-98306-3, doi:10.1038/s41598-025-98306-3. This article has 3 citations and is from a peer-reviewed journal.
(chavez2024cytosolicandacrosomal pages 1-2): Julio C. Chávez, Gabriela Carrasquel-Martínez, Sandra Hernández-Garduño, Arturo Matamoros Volante, Claudia L. Treviño, Takuya Nishigaki, and Alberto Darszon. Cytosolic and acrosomal ph regulation in mammalian sperm. Cells, 13:865, May 2024. URL: https://doi.org/10.3390/cells13100865, doi:10.3390/cells13100865. This article has 15 citations.
(indrawinata2023structuralandfunctional pages 1-2): Karen Indrawinata, Peter Argiropoulos, and Shuzo Sugita. Structural and functional understanding of disease-associated mutations in v-atpase subunit a1 and other isoforms. Frontiers in Molecular Neuroscience, Jul 2023. URL: https://doi.org/10.3389/fnmol.2023.1135015, doi:10.3389/fnmol.2023.1135015. This article has 16 citations.
(chen2024vatpaseincancer pages 1-3): Tingting Chen, Xiaotan Lin, Shuo Lu, and Bo Li. V-atpase in cancer: mechanistic insights and therapeutic potentials. Cell Communication and Signaling : CCS, Dec 2024. URL: https://doi.org/10.1186/s12964-024-01998-9, doi:10.1186/s12964-024-01998-9. This article has 25 citations.
(qu2023lithocholicacidtargets pages 1-5): Qi Qu, Yan Chen, Yu Wang, Shating Long, Weiche Wang, Heng-Ye Yang, Jianfeng Wu, Mengqi Li, Xiao Tian, Xiaoyan Wei, Yan-Hui Liu, Shengrong Xu, Chunyan Yang, Zhenhua Wu, Xi Huang, Changchuan Xie, Yaying Wu, Zheni Xu, Cixiong Zhang, Baoding Zhang, Jin-Wei Feng, Junjie Chen, Liyun Lin, ZK Xie, Beibei Sun, Yong Yu, Hai-Long Piao, Xiao-Song Xie, Xianming Deng, Chen-Song Zhang, and Sheng-Cai Lin. Lithocholic acid targets tulp3 to activate sirtuins and ampk to retard ageing. bioRxiv, Dec 2023. URL: https://doi.org/10.1101/2023.12.07.570558, doi:10.1101/2023.12.07.570558. This article has 0 citations.
(ran2026associationbetweenepas1 pages 1-6): Lirong Ran, Yongjie Li, Ziyi Chen, Dongwei Liao, Guangming Wang, and Yuanyuan Zhang. Association between epas1 and atp6v1e2 polymorphisms and susceptibility to high altitude polycythemia in chinese tibetan population. MedRxiv, Jul 2026. URL: https://doi.org/10.1101/2025.07.11.25331345, doi:10.1101/2025.07.11.25331345. This article has 1 citations.
(wang2020structuresofa pages 9-10): Longfei Wang, Di Wu, Carol V. Robinson, Hao Wu, and Tian-Min Fu. Structures of a complete human v-atpase reveal mechanisms of its assembly. Molecular Cell, 80:501-511.e3, Nov 2020. URL: https://doi.org/10.1016/j.molcel.2020.09.029, doi:10.1016/j.molcel.2020.09.029. This article has 184 citations and is from a highest quality peer-reviewed journal.

📚 Additional Documentation

Notes

(ATP6V1E2-notes.md)

ATP6V1E2 (V-type proton ATPase subunit E 2) — curation notes

UniProt: Q96A05 (VATE2_HUMAN). 226 aa. Gene HGNC:18125, chromosome 2.
Synonyms: ATP6E1, ATP6EL2, ATP6V1EL2.

Identity and core function

ATP6V1E2 is one of two human paralogs encoding the "E" subunit of the V1 (peripheral,
cytoplasmic) sector of the vacuolar-type H(+)-ATPase (V-ATPase). The ubiquitously
expressed paralog is ATP6V1E1; ATP6V1E2 is the testis/sperm-restricted isoform
PMID:12036578. UniProt records TISSUE SPECIFICITY: "Testis specific"
[file:human/ATP6V1E2/ATP6V1E2-uniprot.txt "TISSUE SPECIFICITY: Testis specific. {ECO:0000269|PubMed:12036578}"].
Human Protein Atlas: "Tissue enriched (testis)"; Bgee: "Expressed in sperm and 140 other
cell types or tissues".

The V-ATPase is a rotary proton pump composed of a peripheral V1 complex that hydrolyzes
ATP and a membrane-integral V0 complex that translocates protons
[file:human/ATP6V1E2/ATP6V1E2-uniprot.txt "Subunit of the V1 complex of vacuolar(H+)-ATPase
(V-ATPase) ... a peripheral complex (V1) that hydrolyzes ATP and a membrane integral
complex (V0) that translocates protons"]. The V1 complex contains three catalytic AB
heterodimers forming a heterohexamer, three peripheral stalks each consisting of EG
heterodimers, one central rotor (subunits D and F), and regulatory subunits C and H
[file:human/ATP6V1E2/ATP6V1E2-uniprot.txt "The V1 complex consists of three catalytic AB
heterodimers ... three peripheral stalks each consisting of EG heterodimers, one central
rotor including subunits D and F, and the regulatory subunits C and H"].

Subunit E thus functions as part of the EG peripheral (stator) stalks that hold the (AB)3
catalytic head fixed against the torque produced when the central DF rotor turns during
ATP-hydrolysis-driven proton pumping. Its core molecular role is as a structural V1
peripheral-stalk component enabling rotary, ATP-driven proton transport. Family:
"Belongs to the V-ATPase E subunit family"
[file:human/ATP6V1E2/ATP6V1E2-uniprot.txt "SIMILARITY: Belongs to the V-ATPase E subunit family"].

Localization

V-ATPase acidifies and maintains the pH of intracellular compartments and, in some cell
types, is targeted to the plasma membrane to acidify the extracellular environment
[file:human/ATP6V1E2/ATP6V1E2-uniprot.txt "responsible for acidifying and maintaining the
pH of intracellular compartments and ... targeted to the plasma membrane, where it is
responsible for acidifying the extracellular environment"]. For the testis-enriched E2
isoform the acrosome (a lysosome-related organelle in sperm) is a biologically plausible
site of action; GOA carries an Ensembl-orthology IEA "acrosomal vesicle" (GO:0001669)
annotation transferred from mouse Atp6v1e2 (UniProtKB:Q9D593).

Interactions (GOA "protein binding" IPI annotations)

All GO:0005515 (protein binding) IPI annotations derive from high-throughput screens and
provide no specific functional information beyond confirming participation in PPIs:
- PMID:21516116 (Stitch-seq NGS interactome): with ATP6V1G1 (O75348).
- PMID:25416956 (Rolland et al., proteome-scale interactome): with ATP6V1G1 (O75348), BBLN (Q9BUW7).
- PMID:30021884 (histone crosslinking MS in nuclei): with ATP6V1G1 (O75348).
- PMID:32296183 (Luck et al. HuRI reference interactome): with RASSF10 (A6NK89), ATP6V1G1 (O75348), ATP6V1G2 (O95670), MESD (Q14696).
- PMID:40205054 (Schaffer et al. multimodal cell maps): with ATP6V1G2 (O95670).

Notably, UniProt INTERACTION lists curated interactions with ATP6V1G1 (NbExp=12) and
ATP6V1G2 (NbExp=7) [file:human/ATP6V1E2/ATP6V1E2-uniprot.txt "Q96A05; O75348: ATP6V1G1;
NbExp=12 ... Q96A05; O95670: ATP6V1G2; NbExp=7"]. These E–G interactions are biologically
meaningful: the V1 peripheral stalk is an E–G heterodimer, so the E2–G interactions
recapitulate the expected stator architecture. However, the bare GO:0005515 annotations
are uninformative as molecular-function statements and should be marked as over-annotated.

regulation of macroautophagy (GO:0016241, NAS, PMID:22982048)

PMID:22982048 (Höhn et al., lipofuscin formation in senescent fibroblasts) is an NAS
(non-traceable author statement) annotation by ParkinsonsUK-UCL. The paper concerns
lipofuscin formation and macroautophagy/lysosomal activity in fibroblasts and does not
specifically study ATP6V1E2 (the testis-specific isoform). Any V-ATPase role in autophagy
is mediated by lysosomal acidification and is a downstream/indirect consequence, not a
core function of this testis-restricted subunit. NAS without a traceable experimental
link to this isoform — mark as over-annotated.

Cytosol (GO:0005829, TAS Reactome x12)

Twelve identical TAS GO:0005829 (cytosol) annotations from Reactome reaction-level
records. The V1 sector is cytosolic/peripheral, so "cytosol" is defensible but is a coarse
location that does not capture the functional V-ATPase-complex / organelle-membrane
context. Keep as non-core.

Summary of recommended actions

ACCEPT: proton transmembrane transport (GO:1902600, IBA); proton-transporting ATPase
activity, rotational mechanism (GO:0046961, IBA); V1 sector / two-sector ATPase
catalytic-domain membership (GO:0033178, part_of).
MARK_AS_OVER_ANNOTATED for redundant IEA duplicates of the IBA terms (GO:0046961,
GO:1902600 IEA) — keep the IBA versions as the representative core annotations.
MARK_AS_OVER_ANNOTATED: all GO:0005515 protein binding (high-throughput PPI).
MARK_AS_OVER_ANNOTATED: GO:0016241 regulation of macroautophagy (NAS, not specific).
KEEP_AS_NON_CORE: GO:0001669 acrosomal vesicle (ortholog IEA, plausible for testis
isoform but unverified in human); GO:0005829 cytosol (TAS, coarse).

Falcon deep research synthesis (2026-06-21)

Falcon deep research has now completed (file:human/ATP6V1E2/ATP6V1E2-deep-research-falcon.md,
29 citations). It corroborates the testis-restricted E-paralog identity above and
adds a genuinely ATP6V1E2-specific function; no change to annotation calls.

Core confirmed. E2 is a paralog of the E subunit forming the EG peripheral
stalks (stator) of V1 — structural/regulatory, not catalytic; testis/sperm-
restricted vs ubiquitous E1.
Tissue-specific function — sperm acrosomal acidification (Chavez 2024). Loss
of ATP6V1E2 function impairs acrosomal acidification, required for the
acrosome reaction and fertilization — one of the few functions attributed
specifically to E2 rather than V-ATPase broadly. This supports an acrosomal/
reproductive functional context for E2 (the molecular function remains the E
peripheral-stalk role; the BP/CC context is sperm acrosome).
Other (non-core) leads: downregulation in a homocysteine neurotoxicity /
synaptic-vesicle-cycle model (Wang 2025); a Tibetan-population SNP (rs896210)
associated with high-altitude polycythemia, possibly synergizing with EPAS1/
HIF-2α (Ran 2026) — preliminary genetic-association context, not a function call.

Net: no change to calls — E2 is the testis/sperm-restricted E peripheral-stalk
paralog supporting V-ATPase assembly and (notably) acrosomal acidification.

Pn Notes

(ATP6V1E2-pn-notes.md)

ATP6V1E2 PN Consistency Notes

Generated: 2026-06-18
Project: PROTEOSTASIS
Scope: PN consistency rereview against local AIGR review and available deep-research artifacts
UniProt: Q96A05
AIGR review status: COMPLETE
Review batch: proteostasis-batch-2026-06-07
Batch change status: added

Source Files Checked

AIGR review YAML: present - genes/human/ATP6V1E2/ATP6V1E2-ai-review.yaml
AIGR review HTML: present - genes/human/ATP6V1E2/ATP6V1E2-ai-review.html
Gene notes: present - genes/human/ATP6V1E2/ATP6V1E2-notes.md
GOA TSV: present - genes/human/ATP6V1E2/ATP6V1E2-goa.tsv
UniProt record: present - genes/human/ATP6V1E2/ATP6V1E2-uniprot.txt
PN dossier: projects/PROTEOSTASIS/reports/phase1_dossiers/ATP6V1E2.md
PN consistency section: projects/PROTEOSTASIS/reports/phase1_dossiers/_sections/ATP6V1E2.md
PN projection report: projects/PROTEOSTASIS/reports/pn_projection/pn_projected_gene_go_summary.tsv
PN mapping audit: projects/PROTEOSTASIS/reports/pn_mapping_audit/current_mapping_scrutiny.tsv

Deep Research Files

No *-deep-research*.md file found in this gene directory.

AIGR Review Snapshot

Description: ATP6V1E2 encodes the testis/sperm-enriched isoform of subunit E of the peripheral V1 sector of the vacuolar-type H(+)-ATPase (V-ATPase), a rotary proton pump. The V-ATPase comprises a cytoplasmic V1 complex that hydrolyzes ATP and a membrane-integral V0 complex that translocates protons across the membrane. Within V1, subunit E pairs with subunit G to form the EG heterodimers that constitute the three peripheral (stator) stalks. These stalks hold the (AB)3 catalytic head stationary against the torque generated when the central D/F rotor turns, coupling ATP hydrolysis in V1 to proton translocation through V0. ATP6V1E2 is the tissue-restricted paralog of the ubiquitously expressed ATP6V1E1; it is enriched in testis and sperm, where a V-ATPase containing this subunit is plausibly associated with the acrosome (a lysosome-related organelle). Its core molecular role is as a structural V1 peripheral-stalk component that enables ATP hydrolysis-driven, rotary proton transport, contributing to acidification of intracellular compartments.
Existing/core annotation action counts: ACCEPT: 3; KEEP_AS_NON_CORE: 13; MARK_AS_OVER_ANNOTATED: 8

PN Consistency Summary

Consistency: CONFLICT on compartment. Review/notes establish E2 as the testis/sperm-enriched subunit-E paralog forming EG peripheral stalks; its plausible specialized compartment is the acrosome (acrosomal vesicle, GO:0001669, KEEP_AS_NON_CORE, orthology IEA) — a lysosome-related organelle, not the lysosome. The review carries no lysosomal annotation and MARKs_AS_OVER_ANNOTATED the macroautophagy NAS and five bare protein-binding IPIs. PN places E2 under "lysosomal v-ATPase" and projects lysosomal lumen acidification — mismatched to the sperm/acrosome biology. PN Notes template ("pumps protons into the lysosome") mis-frames this isoform.
PN story / NEW pressure: PN's lysosomal lumen acidification (new_to_goa) OVER-REACHES for E2. GO:0046612/GO:0007042 verified real but wrong specialization; the evidenced organelle is acrosome (lysosome-related, not lysosome). E2 lacks direct human localization evidence at all (acrosome is IEA-only). Lysosomal projection should NOT be propagated; if anything, an acrosome/lysosome-related-organelle framing is the honest one, but evidence is orthology-only.
Evidence alignment: No overlap. PN cites generic reviews; review cites E2-specific PMID:12036578 (testis-specific isoform) plus high-throughput interactome PMIDs (all over-annotated). Review better-targeted to the gene.
Verdict: OVER-REACH — PN lysosomal projection wrong-compartment for this testis/acrosome isoform (and acrosome itself is IEA-only). Recommended edits: [MAP] exempt ATP6V1E2 from lysosomal-acidification/lysosomal-V1 projection; restrict to vacuolar/catalytic V1 complex terms; keep acrosome as non-core.

Full Consistency Review

UniProt: Q96A05 · batch: proteostasis-batch-2026-06-07 · review status: COMPLETE
PN placement: two ALP leaves "V1 lysosomal v-ATPase proton pump component" (Nutrient sensing; Lysosomal acidification). PN-node mapping: leaf→GO:0046612 lysosomal V1 domain (more_specific_than_existing_goa); leaf→GO:0033176 V-type ATPase complex (new_to_goa); type→GO:0007042 lysosomal lumen acidification (new_to_goa).
Consistency: CONFLICT on compartment. Review/notes establish E2 as the testis/sperm-enriched subunit-E paralog forming EG peripheral stalks; its plausible specialized compartment is the acrosome (acrosomal vesicle, GO:0001669, KEEP_AS_NON_CORE, orthology IEA) — a lysosome-related organelle, not the lysosome. The review carries no lysosomal annotation and MARKs_AS_OVER_ANNOTATED the macroautophagy NAS and five bare protein-binding IPIs. PN places E2 under "lysosomal v-ATPase" and projects lysosomal lumen acidification — mismatched to the sperm/acrosome biology. PN Notes template ("pumps protons into the lysosome") mis-frames this isoform.
PN story / NEW pressure: PN's lysosomal lumen acidification (new_to_goa) OVER-REACHES for E2. GO:0046612/GO:0007042 verified real but wrong specialization; the evidenced organelle is acrosome (lysosome-related, not lysosome). E2 lacks direct human localization evidence at all (acrosome is IEA-only). Lysosomal projection should NOT be propagated; if anything, an acrosome/lysosome-related-organelle framing is the honest one, but evidence is orthology-only.
Mapping strategy: Like B1/G3, E2 is a tissue-restricted isoform whose specialized compartment is not the lysosome (TOMM20/HSPA8/RAB7A "too broad" precedent applies). [MAP] flag E2 as an exception to lysosomal projection; safe target is the generic catalytic/V1 complex term (GO:0033178, already in review). Acrosome remains non-core/IEA.
Evidence alignment: No overlap. PN cites generic reviews; review cites E2-specific PMID:12036578 (testis-specific isoform) plus high-throughput interactome PMIDs (all over-annotated). Review better-targeted to the gene.
Verdict: OVER-REACH — PN lysosomal projection wrong-compartment for this testis/acrosome isoform (and acrosome itself is IEA-only). Recommended edits: [MAP] exempt ATP6V1E2 from lysosomal-acidification/lysosomal-V1 projection; restrict to vacuolar/catalytic V1 complex terms; keep acrosome as non-core.

PN Dossier Context

review_batch: proteostasis-batch-2026-06-07
review_yaml: genes/human/ATP6V1E2/ATP6V1E2-ai-review.yaml
PN workbook rows: 2

PN row 1: Autophagy-Lysosome Pathway | Pre-initiation autophagy signaling | mTORC1 pathway, upstream | Nutrient sensing | V1 lysosomal v-ATPase proton pump component

UniProt: Q96A05
In branches: ALP
Notes: Subunit of the V1 (cytosolic) component of the lysosomal v-ATPase. The V0 and V1 components of the v-ATPase assemble during amino acid starvation creating the active v-ATPase that pumps protons into the lysosome for acidification. The v-ATPase also engages in amino acid-dependent interactions with the Ragulator complex. In the presence of amino acids, the v-ATPase-Ragulator complex undergoes a conformational change that results in Ragulator exerting its GEF activity on RAGA/B.
PN references (titles):
- Regulation of mTORC1 by amino acids - ScienceDirect
- Cells | Free Full-Text | SEA and GATOR 10 Years Later | HTML (mdpi.com)
- Eukaryotic V-ATPase: Novel structural findings and functional insights - ScienceDirect
- The emerging roles of vacuolar-type ATPase-dependent Lysosomal acidification in neurodegenerative diseases | Translational Neurodegeneration | Full Text (biomedcentral.com)
PN-node mapping records (path + ancestors):
- [subtype] Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|mTORC1 pathway, upstream|Nutrient sensing|V1 lysosomal v-ATPase proton pump component
  status=mapped scope=ok_for_propagation_to_go GO=[GO:0046612 lysosomal proton-transporting V-type ATPase, V1 domain]
  rationale: This PN leaf is restricted to V1-sector lysosomal V-ATPase components. The GO lysosomal V1-domain component term is the direct target.
- [type] Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|mTORC1 pathway, upstream|Nutrient sensing
  status=no_mapping scope= GO=[]
  rationale: Reviewed as a contextual PN role. The label is useful for curator triage, but by itself does not support a universal GO assertion for all member genes beyond curated ancestor or child mappings.
- [group] Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|mTORC1 pathway, upstream
  status=no_mapping scope= GO=[]
  rationale: Reviewed as a broad PN taxonomy container. The descendants mix components, regulators, context labels, and mechanistic leaves, so propagation should come only from narrower curated nodes.
- [class] Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling
  status=context_only scope=too_broad_to_propagate GO=[GO:0010506 regulation of autophagy]
  rationale: This class organizes upstream signaling inputs to autophagy initiation. Because the subtree contains generic insulin, AMPK, mTORC1, nutrient-sensing, and miscellaneous signaling components, class-level propagation to regulation of autophagy would over-annotate many genes.
- [branch] Autophagy-Lysosome Pathway
  status=no_mapping scope= GO=[]
  rationale: Reviewed as the top-level PN branch. It is a project taxonomy umbrella rather than a direct GO assertion; all propagation must come from manually curated child nodes.

PN row 2: Autophagy-Lysosome Pathway | Lysosomal catabolism | Regulation of lysosomal environment | Lysosomal acidification | V1 lysosomal v-ATPase proton pump component

UniProt: Q96A05
In branches: ALP
Notes: Subunit of the V1 (cytosolic) component of the lysosomal v-ATPase. The V0 and V1 components of the v-ATPase assemble during amino acid starvation creating the active v-ATPase that pumps protons into the lysosome for acidification. The v-ATPase also engages in amino acid-dependent interactions with the Ragulator complex. In the presence of amino acids, the v-ATPase-Ragulator complex undergoes a conformational change that results in Ragulator exerting its GEF activity on RAGA/B.
PN references (titles):
- Regulation of mTORC1 by amino acids - ScienceDirect
- Cells | Free Full-Text | SEA and GATOR 10 Years Later | HTML (mdpi.com)
- Eukaryotic V-ATPase: Novel structural findings and functional insights - ScienceDirect
- The emerging roles of vacuolar-type ATPase-dependent Lysosomal acidification in neurodegenerative diseases | Translational Neurodegeneration | Full Text (biomedcentral.com)
PN-node mapping records (path + ancestors):
- [subtype] Autophagy-Lysosome Pathway|Lysosomal catabolism|Regulation of lysosomal environment|Lysosomal acidification|V1 lysosomal v-ATPase proton pump component
  status=mapped scope=ok_for_propagation_to_go GO=[GO:0033176 proton-transporting V-type ATPase complex]
  rationale: This PN subtype denotes the V1-sector component of the lysosomal V-ATPase. In the current GO cache, the broader V-type ATPase complex is the safest validated target for this component role.
- [type] Autophagy-Lysosome Pathway|Lysosomal catabolism|Regulation of lysosomal environment|Lysosomal acidification
  status=mapped scope=ok_for_propagation_to_go GO=[GO:0007042 lysosomal lumen acidification]
  rationale: This PN group directly names the lysosomal acidification mechanism. Propagation to the GO lysosomal lumen acidification term is an exact mechanistic match.
- [group] Autophagy-Lysosome Pathway|Lysosomal catabolism|Regulation of lysosomal environment
  status=no_mapping scope= GO=[]
  rationale: Reviewed as a broad PN taxonomy container. The descendants mix components, regulators, context labels, and mechanistic leaves, so propagation should come only from narrower curated nodes.
- [class] Autophagy-Lysosome Pathway|Lysosomal catabolism
  status=no_mapping scope= GO=[]
  rationale: Reviewed as a broad lysosomal-degradation container. The subtree includes carbohydrate, lipid, protein, nuclease, phosphatase, sulfatase, and environment-regulation roles, so mapping should occur at the enzyme or process subtype level.
- [branch] Autophagy-Lysosome Pathway
  status=no_mapping scope= GO=[]
  rationale: Reviewed as the top-level PN branch. It is a project taxonomy umbrella rather than a direct GO assertion; all propagation must come from manually curated child nodes.

Projected GO annotations (3)

GO:0046612 lysosomal proton-transporting V-type ATPase, V1 domain | scope=ok_for_propagation_to_go | goa_status=more_specific_than_existing_goa | from=Autophagy-Lysosome Pathway|Pre-initiation autophagy signaling|mTORC1 pathway, upstream|Nutrient sensing|V1 lysosomal v-ATPase proton pump component
GO:0007042 lysosomal lumen acidification | scope=ok_for_propagation_to_go | goa_status=new_to_goa | from=Autophagy-Lysosome Pathway|Lysosomal catabolism|Regulation of lysosomal environment|Lysosomal acidification
GO:0033176 proton-transporting V-type ATPase complex | scope=ok_for_propagation_to_go | goa_status=new_to_goa | from=Autophagy-Lysosome Pathway|Lysosomal catabolism|Regulation of lysosomal environment|Lysosomal acidification|V1 lysosomal v-ATPase proton pump component

Note

This file is generated from the current PROTEOSTASIS phase-1 dossier and local gene-review artifacts. Edit the source review, PN mapping, or dossier rather than this generated note when correcting the underlying curation.

📄 View Raw YAML

id: Q96A05
gene_symbol: ATP6V1E2
product_type: PROTEIN
status: COMPLETE
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: ATP6V1E2 encodes the testis/sperm-enriched isoform of subunit E of the
  peripheral V1 sector of the vacuolar-type H(+)-ATPase (V-ATPase), a rotary proton
  pump. The V-ATPase comprises a cytoplasmic V1 complex that hydrolyzes ATP and a
  membrane-integral V0 complex that translocates protons across the membrane. Within
  V1, subunit E pairs with subunit G to form the EG heterodimers that constitute the
  three peripheral (stator) stalks. These stalks hold the (AB)3 catalytic head
  stationary against the torque generated when the central D/F rotor turns, coupling
  ATP hydrolysis in V1 to proton translocation through V0. ATP6V1E2 is the
  tissue-restricted paralog of the ubiquitously expressed ATP6V1E1; it is enriched
  in testis and sperm, where a V-ATPase containing this subunit is plausibly
  associated with the acrosome (a lysosome-related organelle). Its core molecular
  role is as a structural V1 peripheral-stalk component that enables ATP
  hydrolysis-driven, rotary proton transport, contributing to acidification of
  intracellular compartments.
existing_annotations:
- term:
    id: GO:1902600
    label: proton transmembrane transport
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: involved_in
  review:
    summary: Phylogenetic (IBA) annotation that subunit E of V-ATPase participates
      in proton transmembrane transport. This is the central biological process for
      the V-ATPase complex and is the core function of this subunit, which forms part
      of the EG peripheral stalk required for the rotary pumping mechanism.
    action: ACCEPT
    reason: The V-ATPase, of which subunit E is an obligate structural component,
      hydrolyzes ATP to drive proton translocation across membranes. This IBA
      annotation correctly captures the core biological role of the gene product.
- term:
    id: GO:0046961
    label: proton-transporting ATPase activity, rotational mechanism
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  qualifier: enables
  review:
    summary: Phylogenetic (IBA) annotation to the rotary proton-transporting ATPase
      molecular function. Subunit E does not itself hydrolyze ATP, but as part of
      the EG stator stalks it is an essential structural component of the holoenzyme
      that enables this activity; GO annotates subunits of the complex to the
      complex activity.
    action: ACCEPT
    reason: Subunit E is required for the rotary mechanism by anchoring the catalytic
      head; annotating the subunit with the complex molecular function follows GO
      convention for obligate complex members and represents the core function.
- term:
    id: GO:0033178
    label: proton-transporting two-sector ATPase complex, catalytic domain
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: part_of
  review:
    summary: InterPro-based (IPR002842, V-ATPase V1 E subunit) annotation placing
      ATP6V1E2 in the catalytic (V1) domain of the two-sector ATPase complex. The
      V1 sector is the ATP-hydrolyzing catalytic domain of the V-ATPase, and subunit
      E is a component of it.
    action: ACCEPT
    reason: Subunit E is part of the V1 (catalytic) sector of the V-ATPase, so this
      complex-membership annotation correctly captures the cellular-component context
      and is consistent with the curated complex membership documented in UniProt.
    supported_by:
    - reference_id: file:human/ATP6V1E2/ATP6V1E2-uniprot.txt
      supporting_text: The V1 complex consists of three catalytic AB heterodimers
        that form a heterohexamer, three peripheral stalks each consisting of EG
        heterodimers, one central rotor including subunits D and F, and the
        regulatory subunits C and H.
- term:
    id: GO:0046961
    label: proton-transporting ATPase activity, rotational mechanism
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  qualifier: enables
  review:
    summary: Electronic (IEA) annotation to the rotary proton-transporting ATPase
      activity, duplicating the more authoritative IBA annotation of the same term.
    action: MARK_AS_OVER_ANNOTATED
    reason: This IEA annotation is redundant with the IBA annotation to the identical
      term (GO:0046961). The IBA version is retained as the representative core
      annotation; the duplicate IEA adds no information.
- term:
    id: GO:1902600
    label: proton transmembrane transport
  evidence_type: IEA
  original_reference_id: GO_REF:0000002
  qualifier: involved_in
  review:
    summary: InterPro-based electronic (IEA) annotation to proton transmembrane
      transport, duplicating the more authoritative IBA annotation of the same term.
    action: MARK_AS_OVER_ANNOTATED
    reason: This IEA annotation is redundant with the IBA annotation to the identical
      term (GO:1902600). The IBA version is retained as the representative core
      annotation; the duplicate IEA adds no information.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21516116
  qualifier: enables
  review:
    summary: High-throughput next-generation-sequencing interactome screen reporting
      a binary interaction (with ATP6V1G1, O75348). The E-G interaction is
      biologically expected since the V1 peripheral stalk is an E-G heterodimer, but
      the bare 'protein binding' term is uninformative as a molecular-function
      statement.
    action: MARK_AS_OVER_ANNOTATED
    reason: GO:0005515 'protein binding' conveys no specific functional information.
      The underlying E-G heterodimer relationship is already captured by the
      V1-complex membership annotation (GO:0033178).
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25416956
  qualifier: enables
  review:
    summary: Proteome-scale binary interactome map (Rolland et al.) reporting
      interactions (with ATP6V1G1, O75348, and BBLN, Q9BUW7) from a high-throughput
      yeast two-hybrid screen. Bare 'protein binding' is uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: GO:0005515 'protein binding' conveys no specific molecular function. The
      meaningful E-G interaction is already represented by complex-membership
      annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:30021884
  qualifier: enables
  review:
    summary: Crosslinking mass-spectrometry study of histone interaction landscapes
      in intact nuclei, reporting an interaction with ATP6V1G1 (O75348) as part of a
      large-scale dataset. Bare 'protein binding' is uninformative and the study is
      not focused on ATP6V1E2 function.
    action: MARK_AS_OVER_ANNOTATED
    reason: GO:0005515 'protein binding' conveys no specific molecular function and
      derives from a high-throughput dataset unrelated to the specific role of this
      subunit.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  qualifier: enables
  review:
    summary: HuRI reference binary interactome (Luck et al.) reporting interactions
      (with RASSF10 A6NK89, ATP6V1G1 O75348, ATP6V1G2 O95670, and MESD Q14696) from
      a high-throughput yeast two-hybrid screen. Bare 'protein binding' is
      uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: GO:0005515 'protein binding' conveys no specific molecular function. The
      E-G interactions (ATP6V1G1/G2) reflect expected V1 stalk architecture already
      captured by complex-membership annotations.
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:40205054
  qualifier: enables
  review:
    summary: Multimodal cell-mapping study (Schaffer et al.) reporting an interaction
      with ATP6V1G2 (O95670) from a high-throughput dataset. Bare 'protein binding'
      is uninformative as a molecular-function statement.
    action: MARK_AS_OVER_ANNOTATED
    reason: GO:0005515 'protein binding' conveys no specific molecular function. The
      E-G interaction is already represented by complex-membership annotations.
- term:
    id: GO:0001669
    label: acrosomal vesicle
  evidence_type: IEA
  original_reference_id: GO_REF:0000107
  qualifier: located_in
  review:
    summary: Ensembl-orthology electronic annotation transferred from mouse Atp6v1e2
      (Q9D593) placing the protein in the acrosomal vesicle. The acrosome is a
      lysosome-related organelle in sperm, and V-ATPase-mediated acidification there
      is biologically plausible for this testis/sperm-enriched isoform, but the
      localization has not been directly demonstrated for the human protein.
    action: KEEP_AS_NON_CORE
    reason: Plausible and consistent with the testis/sperm-enriched expression of
      ATP6V1E2, but supported only by orthology-based IEA without direct human
      experimental evidence; retained as a non-core localization.
- term:
    id: GO:0016241
    label: regulation of macroautophagy
  evidence_type: NAS
  original_reference_id: PMID:22982048
  qualifier: involved_in
  review:
    summary: NAS (non-traceable author statement) annotation derived from a study of
      lipofuscin formation in stress-induced senescent fibroblasts. The paper
      concerns macroautophagy and lysosomal activity in fibroblasts and does not
      study the testis-specific ATP6V1E2 isoform. Any V-ATPase role in autophagy is
      an indirect downstream consequence of lysosomal acidification.
    action: MARK_AS_OVER_ANNOTATED
    reason: The annotation is NAS without a traceable experimental link to this
      isoform; macroautophagy regulation is not a core function of this
      testis-restricted V1 stalk subunit and is at best an indirect consequence of
      organelle acidification.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-1222516
  qualifier: located_in
  review:
    summary: Reactome reaction-level TAS annotation to cytosol. The V1 sector is
      cytoplasmic/peripheral, so 'cytosol' is defensible, but it is a coarse location
      that fails to capture the V-ATPase-complex / organelle-membrane functional
      context.
    action: KEEP_AS_NON_CORE
    reason: Defensible but coarse; the V1 subunit is peripheral/cytoplasmic, yet the
      functionally informative location is the V-ATPase complex on intracellular
      membranes. Retained as non-core.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-5252133
  qualifier: located_in
  review:
    summary: Reactome reaction-level TAS annotation to cytosol, duplicating other
      Reactome cytosol annotations for this gene.
    action: KEEP_AS_NON_CORE
    reason: Defensible but coarse and redundant with other Reactome cytosol
      annotations; the informative location is the V-ATPase complex on membranes.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-74723
  qualifier: located_in
  review:
    summary: Reactome reaction-level TAS annotation to cytosol, duplicating other
      Reactome cytosol annotations for this gene.
    action: KEEP_AS_NON_CORE
    reason: Defensible but coarse and redundant with other Reactome cytosol
      annotations; the informative location is the V-ATPase complex on membranes.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-917841
  qualifier: located_in
  review:
    summary: Reactome reaction-level TAS annotation to cytosol, duplicating other
      Reactome cytosol annotations for this gene.
    action: KEEP_AS_NON_CORE
    reason: Defensible but coarse and redundant with other Reactome cytosol
      annotations; the informative location is the V-ATPase complex on membranes.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9639286
  qualifier: located_in
  review:
    summary: Reactome reaction-level TAS annotation to cytosol, duplicating other
      Reactome cytosol annotations for this gene.
    action: KEEP_AS_NON_CORE
    reason: Defensible but coarse and redundant with other Reactome cytosol
      annotations; the informative location is the V-ATPase complex on membranes.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9640167
  qualifier: located_in
  review:
    summary: Reactome reaction-level TAS annotation to cytosol, duplicating other
      Reactome cytosol annotations for this gene.
    action: KEEP_AS_NON_CORE
    reason: Defensible but coarse and redundant with other Reactome cytosol
      annotations; the informative location is the V-ATPase complex on membranes.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9640168
  qualifier: located_in
  review:
    summary: Reactome reaction-level TAS annotation to cytosol, duplicating other
      Reactome cytosol annotations for this gene.
    action: KEEP_AS_NON_CORE
    reason: Defensible but coarse and redundant with other Reactome cytosol
      annotations; the informative location is the V-ATPase complex on membranes.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9640175
  qualifier: located_in
  review:
    summary: Reactome reaction-level TAS annotation to cytosol, duplicating other
      Reactome cytosol annotations for this gene.
    action: KEEP_AS_NON_CORE
    reason: Defensible but coarse and redundant with other Reactome cytosol
      annotations; the informative location is the V-ATPase complex on membranes.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9640195
  qualifier: located_in
  review:
    summary: Reactome reaction-level TAS annotation to cytosol, duplicating other
      Reactome cytosol annotations for this gene.
    action: KEEP_AS_NON_CORE
    reason: Defensible but coarse and redundant with other Reactome cytosol
      annotations; the informative location is the V-ATPase complex on membranes.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9645598
  qualifier: located_in
  review:
    summary: Reactome reaction-level TAS annotation to cytosol, duplicating other
      Reactome cytosol annotations for this gene.
    action: KEEP_AS_NON_CORE
    reason: Defensible but coarse and redundant with other Reactome cytosol
      annotations; the informative location is the V-ATPase complex on membranes.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9645608
  qualifier: located_in
  review:
    summary: Reactome reaction-level TAS annotation to cytosol, duplicating other
      Reactome cytosol annotations for this gene.
    action: KEEP_AS_NON_CORE
    reason: Defensible but coarse and redundant with other Reactome cytosol
      annotations; the informative location is the V-ATPase complex on membranes.
- term:
    id: GO:0005829
    label: cytosol
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9646468
  qualifier: located_in
  review:
    summary: Reactome reaction-level TAS annotation to cytosol, duplicating other
      Reactome cytosol annotations for this gene.
    action: KEEP_AS_NON_CORE
    reason: Defensible but coarse and redundant with other Reactome cytosol
      annotations; the informative location is the V-ATPase complex on membranes.
core_functions:
- description: Structural component of the V1 peripheral (stator) stalk of the
    vacuolar H(+)-ATPase, forming an EG heterodimer that anchors the (AB)3 catalytic
    head and enables ATP hydrolysis-driven rotary proton transport
  supported_by:
  - reference_id: file:human/ATP6V1E2/ATP6V1E2-uniprot.txt
    supporting_text: The V1 complex consists of three catalytic AB heterodimers that
      form a heterohexamer, three peripheral stalks each consisting of EG
      heterodimers, one central rotor including subunits D and F, and the regulatory
      subunits C and H.
  molecular_function:
    id: GO:0046961
    label: proton-transporting ATPase activity, rotational mechanism
  directly_involved_in:
  - id: GO:1902600
    label: proton transmembrane transport
  in_complex:
    id: GO:0033178
    label: proton-transporting two-sector ATPase complex, catalytic domain
proposed_new_terms: []
suggested_questions:
- question: Is the V-ATPase complex containing ATP6V1E2 specifically localized to the sperm acrosome, and does it acidify the acrosomal lumen during spermatogenesis or the acrosome reaction?
- question: Does ATP6V1E2 functionally substitute for ATP6V1E1 within the same V-ATPase holoenzyme in testis, or do the two paralogs assemble into distinct, tissue-specific V-ATPase populations?
- question: Does loss of ATP6V1E2 cause a male-fertility or sperm-function phenotype distinct from that of the ubiquitous ATP6V1E1?
suggested_experiments:
- description: Immunolocalization (and immuno-EM) of ATP6V1E2 in human/mouse testis and spermatozoa to confirm acrosomal-vesicle localization and distinguish it from ATP6V1E1.
- description: Reconstitution or co-immunoprecipitation assays to test EG heterodimer formation of ATP6V1E2 with ATP6V1G1/G2 and incorporation into an assembled, ATP-hydrolyzing V-ATPase complex.
- description: Generation and phenotyping of an Atp6v1e2 knockout (sperm count, motility, acrosome reaction, acrosomal pH, fertility) to define its in vivo role.
references:
- id: GO_REF:0000002
  title: Gene Ontology annotation through association of InterPro records with GO
    terms
  findings: []
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF: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:12036578
  title: A human gene, ATP6E1, encoding a testis-specific isoform of H(+)-ATPase subunit
    E.
  findings:
  - statement: ATP6V1E2 (ATP6E1) encodes a testis-specific isoform of the V-ATPase
      subunit E, distinct from the ubiquitous ATP6V1E1 paralog.
    reference_section_type: ABSTRACT
- id: PMID:21516116
  title: Next-generation sequencing to generate interactome datasets.
  findings: []
- id: PMID:22982048
  title: Lipofuscin is formed independently of macroautophagy and lysosomal activity
    in stress-induced prematurely senescent human fibroblasts.
  findings: []
- id: PMID:25416956
  title: A proteome-scale map of the human interactome network.
  findings: []
- id: PMID:30021884
  title: Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry
    in Intact Cell Nuclei.
  findings: []
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
  findings: []
- id: PMID:40205054
  title: Multimodal cell maps as a foundation for structural and functional genomics.
  findings: []
- 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-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: []

ATP6V1E2

Gene Description

Existing Annotations Review

Core Functions

Structural component of the V1 peripheral (stator) stalk of the vacuolar H(+)-ATPase, forming an EG heterodimer that anchors the (AB)3 catalytic head and enables ATP hydrolysis-driven rotary proton transport

References

Suggested Questions for Experts

Suggested Experiments

Deep Research

Falcon

Comprehensive Research Report on ATP6V1E2 (V-type proton ATPase subunit E2)

Gene Identity and Protein Family

Structural Architecture and Primary Function

Overall V-ATPase Structure

Role of Subunit E in the V-ATPase Complex

Enzymatic Mechanism

Subcellular Localization

Intracellular Organelles

Specialized Plasma Membrane Localization

ATP6V1E2-Specific Localization

Biological Processes and Signaling Pathways

Core Biological Functions

1. pH Homeostasis and Organelle Acidification

2. Autophagy and Lysosomal Degradation

3. Synaptic Vesicle Loading and Neurotransmission

4. Endocytosis and Membrane Trafficking

Signaling and Metabolic Pathways

mTORC1 and AMPK Nutrient Sensing

Wnt and Notch Signaling

Reproductive Cell Function

High-Altitude Adaptation

Regulation of V-ATPase Activity

1. Reversible Assembly/Disassembly

2. Post-Translational Modifications

3. Subunit Isoform Composition

4. Lipid Environment and Protein Interactions

Experimental Evidence and Structural Insights

High-Resolution Structural Studies

Functional and Disease Studies

Disease Relevance

Summary and Knowledge Gaps

📚 Additional Documentation

Notes

ATP6V1E2 (V-type proton ATPase subunit E 2) — curation notes

Identity and core function

Localization

Interactions (GOA "protein binding" IPI annotations)

regulation of macroautophagy (GO:0016241, NAS, PMID:22982048)

Cytosol (GO:0005829, TAS Reactome x12)

Summary of recommended actions

Falcon deep research synthesis (2026-06-21)

Pn Notes

ATP6V1E2 PN Consistency Notes

Source Files Checked

Deep Research Files

AIGR Review Snapshot

PN Consistency Summary

Full Consistency Review

PN Dossier Context

PN row 1: Autophagy-Lysosome Pathway | Pre-initiation autophagy signaling | mTORC1 pathway, upstream | Nutrient sensing | V1 lysosomal v-ATPase proton pump component

PN row 2: Autophagy-Lysosome Pathway | Lysosomal catabolism | Regulation of lysosomal environment | Lysosomal acidification | V1 lysosomal v-ATPase proton pump component

Projected GO annotations (3)

Note

📄 View Raw YAML