RPE65

Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0003834 beta-carotene 15,15'-dioxygenase activity	IBA GO_REF:0000033	MARK AS OVER ANNOTATED	Summary: Family-level phylogenetic (IBA) inference of beta-carotene 15,15'-dioxygenase activity. This is the activity of the paralogous carotenoid oxygenase BCO1/BCMO1, not RPE65. RPE65 is a non-oxygenase member of the family that isomerizes all-trans-retinyl esters rather than symmetrically cleaving beta-carotene, and it does not incorporate molecular oxygen. This is an over-annotation propagated from the family tree. Reason: RPE65 is an isomerohydrolase, not a dioxygenase; the beta-carotene cleavage activity belongs to the BCO1 branch of the carotenoid oxygenase family. UniProt places RPE65 in the carotenoid oxygenase family but annotates only isomerohydrolase activity, not dioxygenase activity. Propagation Review Root cause: PROPAGATION BAD Failure modes: WRONG ORTHOLOG OR PARALOG Supporting Evidence: file:human/RPE65/RPE65-uniprot.txt Belongs to the carotenoid oxygenase family.
GO:0052885 all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic (IBA) annotation of the core isomerohydrolase activity of RPE65. This is the primary, well-established molecular function of RPE65 and is independently supported by human experimental data (IDA/EXP, PMID:25112876, PMID:29659842). Represents the core function of the gene. Supporting Evidence: PMID:25112876 RPE65 is the retinoid isomerohydrolase that converts all-trans-retinyl ester to
GO:0042574 retinal metabolic process	IBA GO_REF:0000033	ACCEPT	Summary: Phylogenetic (IBA) annotation to retinal metabolic process. RPE65 regenerates 11-cis-retinol, the immediate precursor of the visual chromophore 11-cis-retinal, so participation in retinal metabolism is well supported. A correct process annotation reflecting the biological output of the core enzymatic function.
GO:1901827 zeaxanthin biosynthetic process	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: Phylogenetic (IBA) annotation to zeaxanthin biosynthetic process, reflecting the secondary lutein-to-meso-zeaxanthin isomerase activity of RPE65 (PMID:28874556). This is a genuine but non-core, eye-specific carotenoid metabolic role. Supporting Evidence: PMID:28874556 culture leads to the production of meso-zeaxanthin from lutein.
GO:0050251 retinol isomerase activity	IBA GO_REF:0000033	KEEP AS NON CORE	Summary: Phylogenetic (IBA) annotation to the parent retinol isomerase activity. This is correct but less precise than the substrate-specific isomerohydrolase terms (GO:0052885/GO:0052884) that better capture the coupled ester-hydrolysis and trans-to-cis isomerization RPE65 performs. Kept as a broader, valid MF. Reason: Correct general activity but superseded by the more specific isomerohydrolase terms already annotated; retained as a valid broader function.
GO:0001523 retinoid metabolic process	IEA GO_REF:0000117	ACCEPT	Summary: ARBA (IEA) annotation to retinoid metabolic process. RPE65 is a central retinoid-cycle enzyme, so this is correct and consistent with the IDA and TAS annotations to the same term. A valid, if general, process annotation.
GO:0005737 cytoplasm	IEA GO_REF:0000120	KEEP AS NON CORE	Summary: Combined-IEA annotation to cytoplasm, consistent with UniProt's "Cytoplasm" localization for the soluble (unpalmitoylated) form. Correct but very general; the informative localization is the ER/microsomal membrane of the RPE. Supporting Evidence: file:human/RPE65/RPE65-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm
GO:0005886 plasma membrane	IEA GO_REF:0000120	MARK AS OVER ANNOTATED	Summary: Combined-IEA annotation to plasma membrane. RPE65 is membrane-associated via a palmitoyl lipid anchor, but its physiological membrane compartment in RPE cells is the smooth ER / microsomal membrane, not the plasma membrane. This electronic call is imprecise; the ER-membrane IDA (GO:0005789) is preferred. Reason: RPE65 associates with intracellular (microsomal/ER) membranes as a peripheral, palmitoyl-anchored protein; plasma-membrane localization is not the established compartment.
GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	IEA GO_REF:0000002	REMOVE	Summary: InterPro2GO (IEA) annotation to dioxygenase activity from the carotenoid oxygenase domain signature. RPE65 does not incorporate molecular oxygen and is not a dioxygenase; it is an isomerohydrolase. This is a clearly incorrect electronic annotation driven by the family-level domain mapping. Reason: RPE65 catalyzes ester hydrolysis and trans-cis isomerization, not oxygen incorporation. The dioxygenase activity is characteristic of BCO1/BCO2 paralogs, not RPE65. Wrong-branch IEA.
GO:0052884 all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity	IEA GO_REF:0000116	ACCEPT	Summary: Rhea-based (IEA) annotation of the palmitate-specific isomerohydrolase reaction (RHEA:31775). This is the specific substrate variant of the core RPE65 activity and is independently confirmed by human IDA (PMID:25112876). Represents a core function.
GO:0120254 olefinic compound metabolic process	IEA GO_REF:0000117	MARK AS OVER ANNOTATED	Summary: ARBA (IEA) annotation to the very generic "olefinic compound metabolic process". While retinoids and carotenoids are technically olefinic (polyene) compounds, this grandparent-level term adds no functional specificity beyond the retinoid/retinal metabolic process annotations already present. Reason: Uninformatively broad; the specific retinoid/retinal metabolic process and zeaxanthin biosynthesis terms already capture RPE65's substrate metabolism.
GO:0005515 protein binding	IPI PMID:28514442 Architecture of the human interactome defines protein commun...	MARK AS OVER ANNOTATED	Summary: High-throughput AP-MS (BioPlex 2.0) IPI annotation. The interactor (IntAct WITH/FROM) is CCT6B (Q92526), a CCT/TRiC chaperonin subunit, most consistent with chaperonin-assisted folding rather than a functionally specific partnership. Bare "protein binding" is uninformative about molecular function. Reason: Generic protein-binding term from a proteome-scale AP-MS screen with a chaperonin prey; provides no specific functional insight. Retained (not removed) per policy on IPI protein-binding annotations.
GO:0005515 protein binding	IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling...	MARK AS OVER ANNOTATED	Summary: Second high-throughput AP-MS (BioPlex 3.0) IPI annotation, again reporting the RPE65-CCT6B (Q92526) chaperonin co-purification. Bare "protein binding" is uninformative; the biologically meaningful interaction for RPE65 is with MYO7A (light-dependent transport), not captured here. Reason: Generic protein-binding term from a proteome-scale AP-MS screen with a chaperonin prey; provides no specific functional insight. Retained (not removed) per policy on IPI protein-binding annotations.
GO:0003407 neural retina development	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Ensembl orthology (IEA) transfer from a rodent ortholog. RPE65 supports photoreceptor maintenance through chromophore supply, and its loss causes early-onset retinal dystrophy, so a developmental/maintenance association is plausible but peripheral to the core enzymatic function.
GO:0005634 nucleus	IEA GO_REF:0000107	REMOVE	Summary: Ensembl orthology (IEA) transfer placing RPE65 in the nucleus. This is implausible for a palmitoyl-anchored, microsomal/ER-membrane isomerohydrolase of the visual cycle and is not supported by any experimental data for RPE65. Likely an erroneous orthology transfer. Reason: No experimental or biological basis for nuclear localization of RPE65; contradicts its established membrane-associated, ER/microsomal localization. Wrong-compartment IEA.
GO:0007623 circadian rhythm	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Ensembl orthology (IEA) transfer to circadian rhythm. Visual-cycle activity can influence light-dependent physiology, but a direct circadian role for RPE65 is not established in human; this is a peripheral orthology-transferred process.
GO:0009416 response to light stimulus	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Ensembl orthology (IEA) transfer to response to light stimulus. Consistent with RPE65's light-dependent intracellular translocation (via MYO7A) and its role in regenerating chromophore after photobleaching, but not a core molecular function.
GO:0042572 retinol metabolic process	IEA GO_REF:0000107	ACCEPT	Summary: Ensembl orthology (IEA) transfer to retinol metabolic process. RPE65 produces 11-cis-retinol and, in its soluble form, binds all-trans-retinol (vitamin A), so involvement in retinol metabolism is well supported and consistent with the broader retinoid metabolic process annotations.
GO:0042574 retinal metabolic process	IEA GO_REF:0000107	ACCEPT	Summary: Ensembl orthology (IEA) annotation to retinal metabolic process, duplicating the IBA annotation to the same term. Correct: RPE65 regenerates the immediate precursor of 11-cis-retinal.
GO:0043010 camera-type eye development	IEA GO_REF:0000107	KEEP AS NON CORE	Summary: Ensembl orthology (IEA) transfer to camera-type eye development. RPE65 is required for normal photoreceptor function and its loss causes retinal degeneration, but a direct role in eye morphogenesis is not established; this is a peripheral, phenotype-associated process rather than a core function.
GO:0044297 cell body	IEA GO_REF:0000107	MARK AS OVER ANNOTATED	Summary: Ensembl orthology (IEA) transfer to the generic component "cell body". This is uninformative for RPE65, whose functionally relevant localization is the RPE ER/microsomal membrane. Not supported as a meaningful localization. Reason: Non-specific cellular-component transfer that does not reflect RPE65's established membrane localization; uninformative.
GO:0052885 all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity	IEA GO_REF:0000120	ACCEPT	Summary: Combined-IEA annotation of the core isomerohydrolase activity (duplicates the IBA, ISS, and EXP annotations to the same term). Correct core molecular function.
GO:0001523 retinoid metabolic process	TAS Reactome:R-HSA-2453902	ACCEPT	Summary: Reactome TAS annotation to retinoid metabolic process, based on the curated canonical retinoid (visual) cycle pathway. Correct and consistent with the IDA and IEA annotations to the same term.
GO:0005737 cytoplasm	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: ISS annotation to cytoplasm transferred from an ortholog, consistent with the soluble unpalmitoylated form of RPE65. Correct but general; kept as non-core relative to the specific ER-membrane localization.
GO:0005886 plasma membrane	EXP PMID:19049981 Identification of a novel palmitylation site essential for m...	MARK AS OVER ANNOTATED	Summary: Experimental (subcellular fractionation / immunocytochemistry) evidence that RPE65 is membrane-associated via Cys-112 palmitoylation (PMID:19049981). The assay establishes lipid-anchored membrane association; assigning this specifically to the plasma membrane is likely an over-interpretation, since RPE65's functional compartment is the microsomal/ER membrane. Marked over-annotated with respect to the plasma-membrane compartment specificity (experimental annotation not removed; the underlying membrane-association finding is sound). Reason: Experimental support is for palmitoyl-anchored membrane association generally; the plasma-membrane compartment specificity is weak, whereas RPE65's functional compartment is the ER/microsomal membrane. Not removed (experimental evidence). Supporting Evidence: PMID:19049981 intact enzymatic activity similar to that of wtRPE65, whereas C112A lost its
GO:0052885 all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity	EXP PMID:29659842 Insights into the pathogenesis of dominant retinitis pigment...	ACCEPT	Summary: Experimental (EXP) annotation of the core isomerohydrolase / trans-cis isomerase activity from the D477G study, which measured retinoid isomerase activity. Directly supports the primary molecular function of RPE65. Supporting Evidence: PMID:29659842 RPE65 is the essential trans-cis isomerase of the classical retinoid (visual)
GO:0052884 all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity	TAS Reactome:R-HSA-2453833	ACCEPT	Summary: Reactome TAS annotation of the palmitate-specific isomerohydrolase reaction, matching the curated "RPE65 isomero-hydrolyses atREs to 11cROL" reaction. Correct core molecular function.
GO:0001523 retinoid metabolic process	IDA PMID:25112876 Identification of key residues determining isomerohydrolase ...	ACCEPT	Summary: IDA annotation to retinoid metabolic process from the human RPE65 isomerohydrolase characterization (in vitro assay, HPLC retinoid analysis). Correct and directly experimentally grounded. Supporting Evidence: PMID:25112876 RPE65 is the retinoid isomerohydrolase that converts all-trans-retinyl ester to
GO:0052884 all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity	IDA PMID:25112876 Identification of key residues determining isomerohydrolase ...	ACCEPT	Summary: Direct experimental (IDA) evidence for the palmitate-specific isomerohydrolase activity of human RPE65 (KM 0.35 uM for all-trans-retinyl palmitate). This is a core molecular function of RPE65. Supporting Evidence: PMID:25112876 RPE65 is the retinoid isomerohydrolase that converts all-trans-retinyl ester to
GO:0005789 endoplasmic reticulum membrane	IDA PMID:29659842 Insights into the pathogenesis of dominant retinitis pigment...	ACCEPT	Summary: Direct experimental (IDA) localization of RPE65 to the endoplasmic reticulum membrane. This is the functionally relevant compartment for the visual-cycle isomerohydrolase (the RPE smooth ER / microsomal membrane) and is the most informative localization annotation for RPE65.
GO:0016853 isomerase activity	IDA PMID:28874556 RPE65 has an additional function as the lutein to meso-zeaxa...	MARK AS OVER ANNOTATED	Summary: IDA annotation to the generic "isomerase activity" from the lutein-to-meso-zeaxanthin study (PMID:28874556). The experiment demonstrates a specific carotenoid cis-trans isomerase (lutein to meso-zeaxanthin) activity; the bare parent term is under-specific. Reason: "Isomerase activity" is a high-level parent term. The experimentally demonstrated activity is the specific lutein-to-meso-zeaxanthin (carotenoid) isomerase; the generic term is uninformative. The primary retinoid isomerohydrolase activity is captured by GO:0052885/GO:0052884. Supporting Evidence: PMID:28874556 is also the isomerase enzyme responsible for the
GO:1901827 zeaxanthin biosynthetic process	IDA PMID:28874556 RPE65 has an additional function as the lutein to meso-zeaxa...	KEEP AS NON CORE	Summary: IDA annotation to zeaxanthin biosynthetic process, directly supported by the demonstration that RPE65 produces meso-zeaxanthin from lutein (PMID:28874556). A genuine but non-core, eye-specific carotenoid metabolic role. Supporting Evidence: PMID:28874556 culture leads to the production of meso-zeaxanthin from lutein.
GO:0052885 all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity	ISS GO_REF:0000024	ACCEPT	Summary: ISS annotation of the core isomerohydrolase activity transferred from bovine RPE65 (Q28175). Correct core molecular function, redundant with the IBA, IEA, and EXP annotations to the same term.
GO:0001786 phosphatidylserine binding	ISS GO_REF:0000024	MARK AS OVER ANNOTATED	Summary: ISS annotation to phosphatidylserine binding transferred from bovine RPE65. RPE65 is peripherally membrane-associated via a palmitoyl anchor, and its established physiological ligands are retinoids/retinyl esters. Specific phosphatidylserine-headgroup binding is not an established RPE65 molecular function; this is a weakly supported lipid-binding transfer. Reason: No experimental support in human; likely reflects generic membrane-lipid affinity rather than a specific, biologically meaningful phosphatidylserine-binding function.
GO:0016020 membrane	ISS GO_REF:0000024	KEEP AS NON CORE	Summary: ISS annotation to the generic "membrane" component, consistent with RPE65's palmitoyl-anchored membrane association. Correct but non-specific; the ER-membrane IDA (GO:0005789) is the informative localization.
GO:0031210 phosphatidylcholine binding	ISS GO_REF:0000024	MARK AS OVER ANNOTATED	Summary: ISS annotation to phosphatidylcholine binding transferred from bovine RPE65. As with the other phospholipid-binding ISS transfers, this is not an established human RPE65 molecular function and likely reflects generic membrane affinity rather than specific headgroup recognition. Reason: No experimental support in human; not among the established functions (retinoid isomerohydrolase / carotenoid isomerase / iron binding). Over-annotation.
GO:1901612 cardiolipin binding	ISS GO_REF:0000024	MARK AS OVER ANNOTATED	Summary: ISS annotation to cardiolipin binding transferred from bovine RPE65. Cardiolipin is essentially mitochondria-restricted, whereas RPE65 resides on the ER/microsomal membrane and is not a mitochondrial protein; a specific cardiolipin-binding function is implausible and unsupported experimentally. Reason: Biologically implausible for an ER-membrane isomerohydrolase; no experimental support. Over-annotation from ortholog transfer.
GO:0001895 retina homeostasis	IMP PMID:15557452 A homozygosity-based search for mutations in patients with a...	KEEP AS NON CORE	Summary: IMP annotation to retina homeostasis based on the RPE65 R515W mutation identified in an autosomal recessive retinitis pigmentosa patient (PMID:15557452). RPE65 loss-of-function causes progressive retinal degeneration, so a role in retinal homeostasis is supported, though it is a downstream physiological consequence of the core enzymatic function rather than a molecular activity. Supporting Evidence: PMID:15557452 The other was a mutation in RPE65 (c.1543C-->T, R515W), which is known to cause
GO:0050908 detection of light stimulus involved in visual perception	IMP PMID:15557452 A homozygosity-based search for mutations in patients with a...	KEEP AS NON CORE	Summary: IMP annotation to detection of light stimulus involved in visual perception, based on the disease phenotype of the RPE65 R515W mutation (PMID:15557452). RPE65 is required to regenerate the chromophore that enables phototransduction, so this is a supported downstream visual-perception process. Kept as non-core relative to the isomerohydrolase molecular function and the general visual perception term. Supporting Evidence: PMID:15557452 The other was a mutation in RPE65 (c.1543C-->T, R515W), which is known to cause
GO:0005886 plasma membrane	TAS Reactome:R-HSA-2453833	MARK AS OVER ANNOTATED	Summary: Reactome TAS annotation to plasma membrane. As with the IEA plasma-membrane call, RPE65 functions on the RPE microsomal/ER membrane rather than the plasma membrane; the Reactome reaction models RPE65 at the RPE membrane generically. Imprecise compartment assignment. Reason: RPE65's established functional compartment is the ER/microsomal membrane, not the plasma membrane; the specific plasma-membrane localization is not well supported.
GO:0006776 vitamin A metabolic process	TAS PMID:9326941 Mutations in RPE65 cause autosomal recessive childhood-onset...	ACCEPT	Summary: TAS annotation to vitamin A metabolic process. RPE65 is central to the RPE/photoreceptor vitamin-A (retinoid) cycle, binding all-trans-retinol (vitamin A) in its soluble form and regenerating 11-cis-retinoids. A correct process annotation. Supporting Evidence: PMID:9326941 an important role in the RPE/photoreceptor vitamin-A cycle is
GO:0007601 visual perception	TAS PMID:9326941 Mutations in RPE65 cause autosomal recessive childhood-onset...	ACCEPT	Summary: TAS annotation to visual perception. RPE65 is indispensable for regenerating the visual chromophore for both rods and cones, and its loss causes severe visual impairment (LCA/RP). A well-supported core biological process for this gene.

Gene Description

Existing Annotations Review

Core Functions

Retinoid isomerohydrolase of the visual (retinoid) cycle: hydrolyzes all-trans-retinyl esters and couples this to trans-to-cis isomerization, forming 11-cis-retinol, the precursor of the 11-cis-retinal chromophore.

Palmitate-specific isomerohydrolase activity: hydrolyzes all-trans-retinyl palmitate (with coupled isomerization) to yield 11-cis-retinol, the physiologically dominant retinyl-ester substrate of RPE65.

Binds the catalytic Fe(2+) cofactor required for isomerohydrolase activity (coordinated by conserved histidine residues His-180/His-241/His-313/His-527).

Central enzymatic step of the retinoid (visual) cycle, regenerating 11-cis-retinoids that reconstitute rod and cone visual pigments; underlies visual perception.

Secondary, eye-specific carotenoid isomerase activity: converts lutein to meso-zeaxanthin, producing an ocular macular carotenoid (non-core).

References

📚 Additional Documentation

Notes

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