ATP13A3

Summary: ATP binding is the more informative nucleotide-binding assignment.

Reason: The P-type ATPase nucleotide-binding machinery uses ATP. Refine the broad nucleotide-binding term to the existing ATP-binding term; this does not propose an additional activity or a new source annotation.

Proposed replacements: ATP binding

Summary: ATP binding is part of the P-type transport cycle.

Reason: The conserved P-type ATPase architecture and human ATP13A3 autophosphorylation observations support ATP binding. Autophosphorylation in PMID29505581 was variable across preparations; do not substitute the more extensive controls on other family members for ATP13A3-specific measurements.

Summary: The inherited calcium-homeostasis assertion remains unresolved for ATP13A3.

Reason: The PAINT export records a non-negated calcium-homeostasis IBD at PANTHER:PTN000643505, and this IBA asserts that ATP13A3 inherits that ancestral function. The open biological question is retention of a calcium-homeostatic role in the ATP13A3 branch, not whether an IBA exists or has descendant evidence. Available target experiments establish polyamine transport without excluding an accompanying indirect calcium role, while the underlying descendant source PMID:22186024 is abstract-only here. No decisive target-specific loss or divergence was established. Retain UNDECIDED rather than infer an error from donor count, annotation date or incomplete reconstruction of the tree/MSA.

Summary: Polyamine transport is the central ATP13A3 activity.

Reason: Human ATP13A3 restored cellular polyamine-probe uptake in mutant CHO cells, whereas the D498N mutant did not; knockdown supplied complementary evidence. The polyamine IBA is consistent with this target-specific evidence. ATP13A3 appearing among its own WITH/FROM sources is expected when its experimental evidence helped place the ancestral assertion.

Summary: Retain polyamine transport while correcting the ABC mechanism.

Reason: The ARBA assignment has a mechanistic mismatch. The current term belongs to the ABC transporter lineage, whose definition specifies ABC nucleotide-binding/transmembrane architecture. ATP13A3 is a P5B-type ATPase. The supported substrate-transport function is retained using the existing mechanism-neutral polyamine transporter term, while the P-type mechanism is represented by its separate existing annotation. Preserve the original source ID and evidence code.

Proposed replacements: polyamine transmembrane transporter activity

Summary: The experimental putrescine-uptake result does not establish an ABC transporter.

Reason: The original source is preserved. Human WT ATP13A3, unlike the D498N mutant, restored putrescine-probe uptake in hamster CHO cells. The current ABC-type term imposes an incompatible transporter architecture. Its non-ABC putrescine-transporter parent preserves the directly supported substrate specificity; the separate existing P-type annotations retain the mechanism. Cellular uptake does not establish purified-protein kinetics or direct plasma-membrane flux.

Proposed replacements: putrescine transmembrane transporter activity

Summary: The reaction mapping should not impose an ABC mechanism on ATP13A3.

Reason: The Rhea/EC mapping captures ATP-linked putrescine movement but its current GO term also imposes ABC architecture. Use the non-ABC putrescine transporter term, retaining the original electronic source and Rhea/EC objects. This preserves putrescine specificity while the existing P-type annotations represent the mechanism.

Proposed replacements: putrescine transmembrane transporter activity

Summary: P-type ion transport is compatible with transport of charged polyamines.

Reason: Unlike the separate monoatomic-cation term, GO:0015662 is not restricted to single-atom ions. Polyamines are charged organic solutes, so their transport does not contradict this broad P-type ion assignment. The P-type architecture and cellular catalytic-mutant evidence support the mechanism.

Summary: Putrescine transport is supported independently of the problematic ABC parent assignment.

Reason: Human ATP13A3 complementation and knockdown changed BODIPY-putrescine uptake in CHO cells. The upstream ABC-mechanism mapping requires correction, but the putrescine-transport process itself is supported. Whole-cell uptake does not specify direct transport across the plasma membrane.

Summary: Retain the original broad membrane localization without imposing an endosomal compartment on the proteomics result.

Reason: The original HDA assertion is a membrane-proteomics annotation from PMID19946888. Its complete cached abstract describes the YTS membrane preparation, but the ATP13A3 target entry and compartment-specific evidence were not inspected. Broad membrane association is independently established by human ATP13A3 imaging in PMID29505581, so retain the source annotation with curatorial deference as non-core. Do not replace this HDA term using another study: the independently supported recycling-endosome location already has its own IDA and electronic rows.

Summary: The domain signatures establish membrane association without selecting an endosomal compartment.

Reason: The IPR001757/IPR006544 P-type ATPase signatures support the broad membrane assignment. Retain this accurate architectural property as non-core. Recycling-endosome localization has separate IDA and subcellular-vocabulary annotations; those independent experiments do not make this domain mapping compartment-specific.

Summary: ATP hydrolysis is a component of the transport cycle.

Reason: ATP hydrolysis powers the same P-type polyamine transport cycle. Retain it as a biochemical facet of that core, not a separate uncoupled ATPase function. The conserved fold, variable ATP13A3 phosphoenzyme signal and loss of cellular rescue by D498N support the mechanism; purified ATP13A3 turnover kinetics and transport stoichiometry were not measured in these experiments.

Summary: Remove the over-specific electronic monoatomic-cation mapping while retaining the existing P-type and polyamine annotations.

Reason: The InterPro mapping assigns a monoatomic-cation substrate class to ATP13A3, whereas the target-specific experiments establish transport of organic polyamines and P-type ATPase function. GO:0019829 explicitly inherits monoatomic-cation transporter terms; GO:0015662 instead targets ions without that single-atom restriction. The latter P-type term is already present from the identical GO_REF:0000002 / InterPro:IPR047821 source, so a replacement would duplicate that source assertion. Remove this over-propagated substrate classification rather than manufacture a redundant replacement. This is a judgment about the electronic mapping, not an experimental claim that every possible additional substrate has been excluded.

Summary: Early endosomal localization is a supported component of the endosomal distribution.

Reason: The ATP13A2-focused paper also directly assays tagged human ATP13A3 in HeLa cells. Its early-endosomal RAB5 overlap supports this location, although recycling-endosomal overlap is stronger. Retain early endosome membrane as part of the distribution associated with the same uptake route, without claiming equal abundance across compartments or a direct isolated-compartment flux assay. PMID33310703 provides complementary endocytosis and endosomal-cargo evidence, while citing PMID29505581 for ATP13A3 protein localization; it is not treated as an independent protein-localization assay.

Summary: The early-endosome mapping agrees with direct human ATP13A3 localization.

Reason: The UniProt vocabulary mapping agrees with direct human ATP13A3 imaging. Early endosomal membrane is a supported location of the same endosomal transport system, with the strongest observed pool in recycling endosomes. The concise core lists the principal location; that does not exclude this additional supported pool. PMID33310703 provides complementary endocytosis and endosomal-cargo evidence, while citing PMID29505581 for ATP13A3 protein localization; it is not treated as an independent protein-localization assay.

Summary: Late endosomal localization is compatible with a secondary ATP13A3 pool.

Reason: The PAINT location inference is consistent with human ATP13A3 overlap with late-endosomal markers. Recycling-endosomal localization predominated in the direct study. Retain the secondary compartment without arguing against the IBA because ATP13A3 appears among its experimental sources.

Summary: The study directly observes a lesser late-endosomal ATP13A3 pool.

Reason: Human ATP13A3 constructs were studied despite the ATP13A2-focused title. RAB7 and endogenous late endosomal/lysosomal markers overlapped with ATP13A3 to a lesser extent than recycling-endosomal markers. Preserve the source IDA without claiming universal restriction to one compartment.

Summary: The electronic late-endosome assignment agrees with direct localization evidence.

Reason: Retain the secondary late-endosomal pool supported by human ATP13A3 localization experiments. This location is compatible with, but less prominent than, the recycling-endosomal pool.

Summary: Recycling endosomal membrane is the best-supported principal location.

Reason: The study directly examined tagged human ATP13A3 in HeLa cells. Its strongest overlap was with RAB11-positive recycling endosomes; N- and C-terminal tags gave similar distributions. This is evidence from an expression system, not proof of identical endogenous localization in every tissue. PMID33310703 provides complementary endocytosis and endosomal-cargo evidence, while citing PMID29505581 for ATP13A3 protein localization; it is not treated as an independent protein-localization assay.

Summary: The recycling-endosome mapping is corroborated by direct human ATP13A3 imaging.

Reason: The vocabulary mapping agrees with the principal compartment reported in PMID29505581. Retain it as a core location while keeping the expression-system boundary explicit. PMID33310703 provides complementary endocytosis and endosomal-cargo evidence, while citing PMID29505581 for ATP13A3 protein localization; it is not treated as an independent protein-localization assay.

Summary: Remove the monoatomic-cation process inferred from the unsupported monoatomic molecular-function mapping.

Reason: This GO_REF:0000108 assertion follows GO:0019829. Its monoatomic substrate restriction is not supported by the ATP13A3 polyamine experiments, and the upstream electronic mapping is removed in this audit. GO:0034220 is also explicitly monoatomic ion transmembrane transport, so it would preserve the same mismatch. A polyamine-process replacement would switch to independent evidence rather than repair this automatic inference, and that process already has a separate supported IBA. Preserve both original source objects while removing this inherited electronic overreach; this does not exclude an untested additional ATP13A3 substrate.

Summary: The P-type transport mechanism is supported, with a cellular-assay boundary.

Reason: Human WT ATP13A3 restored uptake whereas the D498N catalytic mutant did not. Together with P5B architecture and ATP13A3 autophosphorylation observations in PMID29505581, this supports the P-type mechanism. The cited cellular rescue is not a purified-protein flux or phosphorylation-stoichiometry assay.

Summary: The P-type domain inference agrees with target-specific functional evidence.

Reason: Retain the P-type transporter annotation supported by conserved architecture and human ATP13A3 cellular rescue/localization studies. It describes the mechanism of the same polyamine transport activity, not a second core function.

Summary: ATP13A3 contributes directly to polyamine transmembrane transport.

Reason: Cellular complementation, knockdown and polyamine-probe experiments support a direct transport role consistent with the ancestral inference. Endocytosis-inhibition and endosomal-retention experiments support an endosomal-release model; they do not resolve purified-protein kinetics or prove direct plasma-membrane flux.