Existing Annotations Review

GO Term	Evidence	Action	Reason
GO:0005778 peroxisomal membrane	IBA GO_REF:0000033	ACCEPT	Summary: PEX3 is a well-established integral peroxisomal membrane protein. IBA annotation is phylogenetically supported and consistent with extensive experimental evidence from multiple species. PEX3 has two transmembrane domains and localizes to the peroxisomal membrane in human cells (PMID:10430017, PMID:9657383). Reason: Core localization of PEX3. Peroxisomal membrane localization is confirmed by immunofluorescence in multiple studies and by UniProt topology annotation showing transmembrane helices at residues 16-36 and 117-140. Supporting Evidence: PMID:10430017 H sPEX3 is an integral peroxisomal membrane protein with the N-terminus inside the peroxisome and the C-terminus facing the cytoplasm PMID:9657383 human Pex3p is localized at the peroxisome
GO:0030674 protein-macromolecule adaptor activity	IBA GO_REF:0000033	ACCEPT	Summary: PEX3 functions as a membrane-anchored docking/adaptor for PEX19, bridging the cytosolic PEX19-PMP cargo complex to the peroxisomal membrane. This adaptor activity is well supported by structural (PMID:21102411) and functional (PMID:15007061) studies. The IBA annotation captures the molecular function at an appropriate level of specificity. Reason: PEX3 serves as a docking receptor/adaptor for PEX19 at the peroxisomal membrane, enabling PMP insertion. This is the core molecular function of PEX3. The term protein-macromolecule adaptor activity is appropriate as PEX3 bridges PEX19-cargo complexes to the membrane. Supporting Evidence: PMID:15007061 PEX3 is required for PEX19 to dock at peroxisomes, interacts specifically with the docking domain of PEX19, and is required for recruitment of the PEX19 docking domain to peroxisomes PMID:21102411 The interaction between Pex3p, which resides on the peroxisomal membrane, and Pex19p, which resides in the cytosol, is crucial for peroxisome formation and the post-translational targeting of peroxisomal membrane proteins
GO:0045046 protein import into peroxisome membrane	IBA GO_REF:0000033	ACCEPT	Summary: PEX3 is essential for the import of class I peroxisomal membrane proteins. Transient depletion of PEX3 specifically abrogates class I PMP import without affecting class II PMP import or matrix protein import (PMID:15007061). IBA annotation is phylogenetically well-supported and captures the core biological process. Reason: This is the central biological process function of PEX3. Fang et al. (2004) demonstrated that PEX3 depletion by RNAi specifically blocks class I PMP import, establishing PEX3 as essential for this process. Supporting Evidence: PMID:15007061 transient inhibition of PEX3 abrogates class I PMP import but has no effect on class II PMP import or peroxisomal matrix protein import
GO:0005778 peroxisomal membrane	IEA GO_REF:0000120	ACCEPT	Summary: Automated annotation of PEX3 to peroxisomal membrane. Consistent with the IBA and IDA annotations for the same term and well supported experimentally. Reason: Redundant with IBA and IDA annotations but correctly reflects the established localization. IEA annotations at this level are acceptable when confirmed by other evidence. Supporting Evidence: PMID:10430017 H sPEX3 is an integral peroxisomal membrane protein with the N-terminus inside the peroxisome and the C-terminus facing the cytoplasm
GO:0007031 peroxisome organization	IEA GO_REF:0000120	ACCEPT	Summary: Automated annotation of PEX3 to peroxisome organization. PEX3 is essential for peroxisome membrane biogenesis and thus for overall peroxisome organization. This is consistent with IMP annotations from multiple publications. Reason: Peroxisome organization is a parent term that encompasses peroxisome biogenesis. PEX3 is essential for peroxisome membrane assembly and cells lacking PEX3 have no detectable peroxisomes. The IEA is consistent with experimental evidence. Supporting Evidence: PMID:10958759 Expression of wild-type PEX3 in the mutant cell lines restored peroxisomal biogenesis, whereas transfection of mutated PEX3 cDNA did not
GO:0005515 protein binding	IPI PMID:10704444 PEX19 binds multiple peroxisomal membrane proteins, is predo...	MODIFY	Summary: Sacksteder et al. (2000) demonstrated that PEX19 binds multiple PMPs including PEX3, using two-hybrid and blot overlay assays. The interaction with PEX19 is the core molecular function of PEX3. However, 'protein binding' is too generic -- the IBA annotation for protein-macromolecule adaptor activity better captures this function. Reason: The PEX3-PEX19 interaction is real and well-documented, but 'protein binding' is uninformative. The more specific term 'protein-macromolecule adaptor activity' (GO:0030674) already captures this function. This annotation should be replaced with the more informative term. Proposed replacements: protein-macromolecule adaptor activity Supporting Evidence: PMID:10704444 PEX19 binds a broad spectrum of PMPs, displays saturable PMP binding, and interacts with regions of PMPs required for their targeting to peroxisomes
GO:0005515 protein binding	IPI PMID:12096124 Analysis of mammalian peroxin interactions using a non-trans...	MODIFY	Summary: Fransen et al. (2002) used a bacterial two-hybrid system to analyze interactions among mammalian peroxins and confirmed PEX3-PEX19 interaction. This is a focused peroxin interaction study, not a generic high-throughput screen. The interaction is specific and well-characterized. Reason: The PEX3-PEX19 interaction documented here reflects PEX3's adaptor/docking function. 'Protein binding' is uninformative; this should be replaced with the more specific adaptor activity term. Proposed replacements: protein-macromolecule adaptor activity Supporting Evidence: PMID:12096124 we report a detailed interaction map of these peroxins
GO:0005515 protein binding	IPI PMID:16189514 Towards a proteome-scale map of the human protein-protein in...	MARK AS OVER ANNOTATED	Summary: Rual et al. (2005) is a large-scale proteome-wide yeast two-hybrid screen. While PEX3 interactions detected here may include PEX19, this is a high-throughput study and the generic 'protein binding' term provides no functional insight. Reason: High-throughput interactome screen. 'Protein binding' from a proteome-scale Y2H screen provides no specific functional information about PEX3. The meaningful interactions (PEX19, PEX16) are already captured by more specific annotations. Supporting Evidence: PMID:16189514 Towards a proteome-scale map of the human protein-protein interaction network
GO:0005515 protein binding	IPI PMID:16280322 In vitro transport of membrane proteins to peroxisomes by sh...	MODIFY	Summary: Matsuzono and Fujiki (2006) developed an in vitro cell-free PMP transport system and showed that PEX19 complexes with PMPs bind to PEX3 in vitro, and that PEX19 translocates PMPs to peroxisomes in a PEX3-dependent manner. This is a focused mechanistic study of the PEX3-PEX19 docking interaction. Reason: This study specifically demonstrates the PEX3-PEX19 docking interaction in the context of PMP transport. 'Protein binding' should be replaced with the more informative adaptor activity term. Proposed replacements: protein-macromolecule adaptor activity Supporting Evidence: PMID:16280322 Pex19p translocates the membrane peroxins from the cytosol to peroxisomes in an ATP- and Pex3p-dependent manner and then shuttles back to the cytosol
GO:0005515 protein binding	IPI PMID:21102411 Structural basis for docking of peroxisomal membrane protein...	MODIFY	Summary: Sato et al. (2010) solved the crystal structure of the PEX3-PEX19 complex (2.50 A), revealing the structural basis of the docking interaction. The PEX19 peptide forms an alpha-helix at the apex of the PEX3 spheroid. This is a definitive structural characterization of the core PEX3 function. Reason: This landmark structural study defines the PEX3-PEX19 docking interface at atomic resolution. 'Protein binding' does not capture the specificity of this interaction. The adaptor activity term is more appropriate. Proposed replacements: protein-macromolecule adaptor activity Supporting Evidence: PMID:21102411 we present the three-dimensional structure of the complex between a cytosolic domain of Pex3p and the binding-region peptide of Pex19p
GO:0005515 protein binding	IPI PMID:25416956 A proteome-scale map of the human interactome network.	MARK AS OVER ANNOTATED	Summary: Rolland et al. (2014) is a proteome-scale interactome mapping study. Generic high-throughput protein binding annotation for PEX3 is uninformative. Reason: High-throughput interactome screen. 'Protein binding' from this study does not add specific functional information about PEX3 beyond what is already captured by more informative terms. Supporting Evidence: PMID:25416956 A proteome-scale map of the human interactome network
GO:0005515 protein binding	IPI PMID:25502805 A massively parallel pipeline to clone DNA variants and exam...	MARK AS OVER ANNOTATED	Summary: Wei et al. (2014) is a massively parallel pipeline for cloning DNA variants and examining molecular phenotypes. High-throughput study providing generic protein binding annotation. Reason: High-throughput methodology study. 'Protein binding' annotation from this pipeline is uninformative for PEX3 functional annotation. Supporting Evidence: PMID:25502805 A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations
GO:0005515 protein binding	IPI PMID:27107012 Pooled-matrix protein interaction screens using Barcode Fusi...	MARK AS OVER ANNOTATED	Summary: Yachie et al. (2016) used Barcode Fusion Genetics for pooled-matrix protein interaction screens. High-throughput interaction data providing generic protein binding. Reason: High-throughput interactome screen. Generic 'protein binding' is uninformative for PEX3. Supporting Evidence: PMID:27107012 Pooled-matrix protein interaction screens using Barcode Fusion Genetics
GO:0005515 protein binding	IPI PMID:28514442 Architecture of the human interactome defines protein commun...	MARK AS OVER ANNOTATED	Summary: Huttlin et al. (2017) is a large-scale interactome mapping study defining protein communities and disease networks. High-throughput data. Reason: High-throughput interactome mapping. Generic 'protein binding' adds no specific insight into PEX3 function. Supporting Evidence: PMID:28514442 Architecture of the human interactome defines protein communities and disease networks
GO:0005515 protein binding	IPI PMID:29997244 LuTHy: a double-readout bioluminescence-based two-hybrid tec...	MARK AS OVER ANNOTATED	Summary: Wehr et al. (2019) developed LuTHy, a bioluminescence-based two-hybrid technology for mapping protein-protein interactions. Methodological study providing generic protein binding data. Reason: Method-development/high-throughput study. 'Protein binding' is uninformative for PEX3 function. Supporting Evidence: PMID:29997244 LuTHy: a double-readout bioluminescence-based two-hybrid technology for quantitative mapping of protein-protein interactions in mammalian cells
GO:0005515 protein binding	IPI PMID:31467278 Maximizing binary interactome mapping with a minimal number ...	MARK AS OVER ANNOTATED	Summary: Choi et al. (2019) is a study on maximizing binary interactome mapping efficiency. High-throughput methodology study. Reason: High-throughput interactome methodology study. 'Protein binding' is uninformative. Supporting Evidence: PMID:31467278 Maximizing binary interactome mapping with a minimal number of assays
GO:0005515 protein binding	IPI PMID:31515488 Extensive disruption of protein interactions by genetic vari...	MARK AS OVER ANNOTATED	Summary: Sahni et al. (2019) studied disruption of protein interactions by genetic variants. High-throughput interactome study. Reason: High-throughput variant-interaction study. 'Protein binding' is uninformative for PEX3. Supporting Evidence: PMID:31515488 Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations
GO:0005515 protein binding	IPI PMID:32296183 A reference map of the human binary protein interactome.	MARK AS OVER ANNOTATED	Summary: Luck et al. (2020) is a reference map of the human binary protein interactome. Large-scale high-throughput study. Reason: High-throughput interactome reference map. 'Protein binding' is uninformative for PEX3. Supporting Evidence: PMID:32296183 A reference map of the human binary protein interactome
GO:0005515 protein binding	IPI PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative ...	MARK AS OVER ANNOTATED	Summary: Haenig et al. (2020) studied interactome mapping of neurodegenerative disease proteins. High-throughput interaction study. Reason: High-throughput interactome mapping. 'Protein binding' is uninformative for PEX3. Supporting Evidence: PMID:32814053 Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains
GO:0005515 protein binding	IPI PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling...	MARK AS OVER ANNOTATED	Summary: Huttlin et al. (2021) mapped dual proteome-scale networks revealing cell-specific remodeling. High-throughput interactome study. Reason: High-throughput interactome mapping. 'Protein binding' is uninformative for PEX3. Supporting Evidence: PMID:33961781 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome
GO:0005515 protein binding	IPI PMID:35271311 OpenCell: Endogenous tagging for the cartography of human ce...	MARK AS OVER ANNOTATED	Summary: Cho et al. (2022) is the OpenCell project using endogenous tagging for cellular organization cartography. High-throughput proteomics/imaging study. Reason: High-throughput cellular organization mapping. 'Protein binding' is uninformative for PEX3. Supporting Evidence: PMID:35271311 OpenCell: Endogenous tagging for the cartography of human cellular organization
GO:0005515 protein binding	IPI PMID:37398436 AI-guided pipeline for protein-protein interaction drug disc...	MARK AS OVER ANNOTATED	Summary: Duran-Frigola et al. (2023) used AI-guided pipeline for PPI drug discovery, focusing on SARS-CoV-2. High-throughput/computational study. Reason: AI-guided drug discovery pipeline. 'Protein binding' is uninformative for PEX3 function. Supporting Evidence: PMID:37398436 AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor
GO:0005515 protein binding	IPI PMID:38225382 Systematic discovery of protein interaction interfaces using...	MARK AS OVER ANNOTATED	Summary: Humphreys et al. (2024) used AlphaFold for systematic discovery of protein interaction interfaces. Computational/high-throughput study. Reason: Computational high-throughput interaction interface study. 'Protein binding' is uninformative. Supporting Evidence: PMID:38225382 Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation
GO:0005515 protein binding	IPI PMID:40205054 Multimodal cell maps as a foundation for structural and func...	MARK AS OVER ANNOTATED	Summary: Huttlin et al. (2025) is a multimodal cell maps study for structural and functional genomics. High-throughput study. Reason: High-throughput multimodal cellular mapping. 'Protein binding' is uninformative for PEX3. Supporting Evidence: PMID:40205054 Multimodal cell maps as a foundation for structural and functional genomics
GO:0005777 peroxisome	IDA GO_REF:0000052	ACCEPT	Summary: PEX3 localization to peroxisomes confirmed by immunofluorescence-based curation (GO_REF:0000052). This is consistent with extensive literature showing PEX3 at the peroxisomal membrane. However, the more specific term 'peroxisomal membrane' (GO:0005778) is also annotated and is more informative. Reason: Correct localization, albeit less specific than peroxisomal membrane. Peroxisome is a valid parent localization term and the IDA evidence from immunofluorescence curation is appropriate. Supporting Evidence: PMID:10430017 H sPEX3 is an integral peroxisomal membrane protein with the N-terminus inside the peroxisome and the C-terminus facing the cytoplasm
GO:0016020 membrane	HDA PMID:19946888 Defining the membrane proteome of NK cells.	ACCEPT	Summary: Ghosh et al. (2010) defined the membrane proteome of NK cells by mass spectrometry and detected PEX3 in the membrane fraction. The term 'membrane' is extremely generic for an established integral peroxisomal membrane protein. Reason: While very generic, this HDA annotation from a proteomics study is not incorrect -- PEX3 is indeed an integral membrane protein. More specific peroxisomal membrane annotations exist. This is acceptable as a broad localization annotation from high-throughput data. Supporting Evidence: PMID:19946888 Defining the membrane proteome of NK cells
GO:0005515 protein binding	IPI PMID:18174172 Characterization of the interaction between recombinant huma...	MODIFY	Summary: Sato et al. (2008) characterized the PEX3-PEX19 interaction in detail using recombinant proteins, determining a KD of 3.4 nM and identifying Trp-104 as a critical binding residue. This is a focused mechanistic study of the core PEX3-PEX19 docking interaction. Reason: This study specifically characterizes the PEX3-PEX19 docking interaction at the biochemical level. 'Protein binding' should be replaced with the more informative adaptor activity term. Proposed replacements: protein-macromolecule adaptor activity Supporting Evidence: PMID:18174172 the wild-type and the W104A and W104F mutants showed K(D) values of 3.4 nm, 1080 nm, and 66.2 nm, respectively
GO:0007031 peroxisome organization	IMP PMID:18174172 Characterization of the interaction between recombinant huma...	ACCEPT	Summary: Sato et al. (2008) showed that PEX3 Trp-104 mutations that disrupted PEX19 binding also impaired peroxisome restoring activity in pex3-deficient cells, demonstrating that the PEX3-PEX19 interaction is required for peroxisome organization. Reason: IMP evidence from mutational analysis showing that disrupting the PEX3-PEX19 interface impairs peroxisome biogenesis. This directly supports PEX3's role in peroxisome organization. Supporting Evidence: PMID:18174172 The affinity differences with mutation affected their peroxisome restoring activities in pex3 ZPG208 cells
GO:0005783 endoplasmic reticulum	IDA PMID:21768384 Sec16B is involved in the endoplasmic reticulum export of th...	KEEP AS NON CORE	Summary: Yonekawa et al. (2011) showed that when Sec16B is overexpressed, PEX3 and PEX16 are redistributed from peroxisomes to ER membranes, and that Sec16B knockdown suppresses PEX3 expression. This indicates PEX3 transits through the ER during peroxisome biogenesis. Reason: PEX3 transits through the ER during de novo peroxisome biogenesis, but the ER is not its primary steady-state location. The peroxisomal membrane is the core localization. ER localization represents a transient intermediate in the biogenesis pathway. Supporting Evidence: PMID:21768384 Concomitant with the overexpression of Sec16B, peroxisomal membrane biogenesis factors peroxin 3 (Pex3) and Pex16 were redistributed from peroxisomes to Sec16B-positive ER membranes
GO:0032991 protein-containing complex	IDA PMID:18174172 Characterization of the interaction between recombinant huma...	MARK AS OVER ANNOTATED	Summary: Sato et al. (2008) demonstrated that PEX3 and PEX19 form a 1:1 monomeric complex by gel filtration chromatography. PEX3 exists in a complex with PEX19. However, 'protein-containing complex' is extremely generic and uninformative. Reason: While PEX3 does form a complex with PEX19, the term 'protein-containing complex' is too generic to be informative. The complex formation is better captured by the adaptor activity and peroxisome organization annotations. Supporting Evidence: PMID:18174172 Gel filtration chromatography analyses and intrinsic tryptophan fluorescence titrations revealed that a one-to-one complex is formed between monomeric Pex3p and monomeric Pex19p
GO:0005778 peroxisomal membrane	HDA PMID:21525035 PEX14 is required for microtubule-based peroxisome motility ...	ACCEPT	Summary: Bharti et al. (2011) isolated native peroxisomal membrane protein complexes from human cells using PEX14 as bait and identified PEX3 as a constituent of peroxisomal membrane complexes by mass spectrometry. This confirms PEX3 peroxisomal membrane localization via proteomics. Reason: HDA evidence from native peroxisomal membrane complex isolation confirms PEX3 at the peroxisomal membrane, consistent with all other localization data. Supporting Evidence: PMID:21525035 almost all known human peroxins involved in protein import were identified as constituents of the PEX14 complexes
GO:0007031 peroxisome organization	IMP PMID:19479899 Pex3p-dependent peroxisomal biogenesis initiates in the endo...	ACCEPT	Summary: Toro et al. (2009) showed that Pex3p-GFP expressed in PEX3-deficient ZS cells (MR cell line) localizes first to the ER and then to newly formed peroxisomes, demonstrating PEX3 drives de novo peroxisome biogenesis from the ER. Reason: IMP evidence showing PEX3 expression restores peroxisome formation in PEX3-deficient Zellweger cells, directly demonstrating PEX3's essential role in peroxisome organization. Supporting Evidence: PMID:19479899 Pex3p-GFP expressed in a new ZS cell line (MR), which lacks peroxisomes due to a mutation in the PEX3 gene, localizes first in the ER and subsequently in newly formed peroxisomes
GO:0005783 endoplasmic reticulum	IDA PMID:19479899 Pex3p-dependent peroxisomal biogenesis initiates in the endo...	KEEP AS NON CORE	Summary: Toro et al. (2009) demonstrated by fluorescence microscopy that Pex3p-GFP localizes to the ER before redistributing to newly formed peroxisomes. An artificial N-glycosylation site confirmed ER targeting. This is the first demonstration of PEX3 ER transit in mammalian cells. Reason: PEX3 transits through the ER during de novo peroxisome biogenesis, as directly observed by Toro et al. However, the ER is a transient intermediate, not the primary steady-state localization. Supporting Evidence: PMID:19479899 Pex3p bearing an artificial N-glycosylation site shows an electrophoretic shift indicative of ER targeting while en route to preformed peroxisomes in normal fibroblast
GO:0032994 protein-lipid complex	IDA PMID:19715730 The cytosolic domain of PEX3, a protein involved in the biog...	UNDECIDED	Summary: Pinto et al. (2009) showed that recombinant PEX3 cytosolic domain interacts with liposomes causing their flocculation or partial solubilization. This suggests a protein-lipid complex formation. However, this is an in vitro observation with recombinant protein and its physiological relevance is uncertain. Reason: The lipid interaction was observed in vitro with recombinant protein. While potentially relevant to PEX3's membrane insertion function, the physiological significance of a PEX3-lipid complex is not established. The study itself notes that the implications need further investigation. Supporting Evidence: PMID:19715730 this recombinant protein actually precipitates when incubated with mild detergents, suggesting that this domain of PEX3 interacts with amphipathic molecules
GO:0005515 protein binding	IPI PMID:19715730 The cytosolic domain of PEX3, a protein involved in the biog...	MARK AS OVER ANNOTATED	Summary: Pinto et al. (2009) is primarily about PEX3 lipid binding, not protein-protein interactions. Any protein binding observation in this context is secondary and the generic term is uninformative. Reason: This paper focuses on PEX3 lipid binding. 'Protein binding' annotation from this study is tangential and uninformative. Supporting Evidence: PMID:19715730 The cytosolic domain of PEX3, a protein involved in the biogenesis of peroxisomes, binds membrane lipids
GO:0008289 lipid binding	IDA PMID:19715730 The cytosolic domain of PEX3, a protein involved in the biog...	KEEP AS NON CORE	Summary: Pinto et al. (2009) demonstrated that recombinant PEX3 cytosolic domain binds liposomes strongly, causing flocculation or partial solubilization. This is an in vitro finding. Lipid binding may relate to PEX3's role in membrane insertion of PMPs but the physiological relevance is not firmly established. Reason: The lipid binding activity was demonstrated in vitro and may reflect PEX3's membrane-associated function. However, lipid binding is not the primary characterized function of PEX3 (which is PEX19 docking/adaptor activity). This is a potential secondary activity. Supporting Evidence: PMID:19715730 we tested this recombinant protein in lipid-binding assays and found that it interacts strongly with liposomes inducing their flocculation or even partial solubilization
GO:0005778 peroxisomal membrane	TAS Reactome:R-HSA-382613	ACCEPT	Summary: Reactome pathway annotation for PEX3 involvement in docking of ABCD1/D2/D3 (ABC transporters) to the peroxisomal membrane via PEX19. This is consistent with PEX3's role as the membrane docking factor for the PEX19-PMP import pathway. Reason: Reactome correctly places PEX3 at the peroxisomal membrane in the context of ABC transporter PMP import. This is well supported by the established PEX3-PEX19 docking model. Supporting Evidence: PMID:15007061 PEX3 is required for PEX19 to dock at peroxisomes
GO:0005778 peroxisomal membrane	TAS Reactome:R-HSA-9603775	ACCEPT	Summary: Reactome pathway annotation for PEX3:PEX19:class I PMP complex dissociation at the peroxisomal membrane. This correctly places PEX3 at the peroxisomal membrane during PMP release. Reason: Reactome correctly represents PEX3 at the peroxisomal membrane during the PMP insertion cycle. Supporting Evidence: PMID:15007061 PEX3 is also sufficient to dock PEX19 at heterologous organelles
GO:0005778 peroxisomal membrane	TAS Reactome:R-HSA-9603784	ACCEPT	Summary: Reactome pathway annotation for PEX19:class I PMP binding to PEX3 at the peroxisomal membrane. This correctly represents the docking step. Reason: Reactome correctly represents PEX3 at the peroxisomal membrane during PEX19:PMP docking. Supporting Evidence: PMID:15007061 PEX3 is required for PEX19 to dock at peroxisomes, interacts specifically with the docking domain of PEX19
GO:0005778 peroxisomal membrane	IDA PMID:10430017 Identification and characterization of the human peroxin PEX...	ACCEPT	Summary: Soukupova et al. (1999) identified and characterized human PEX3 as an integral peroxisomal membrane protein using N- and C-terminal tags and immunofluorescence microscopy. The N-terminus is inside the peroxisome and the C-terminus faces the cytoplasm. Reason: Primary experimental evidence for PEX3 peroxisomal membrane localization by immunofluorescence. This is one of the foundational characterization studies of human PEX3. Supporting Evidence: PMID:10430017 H sPEX3 is an integral peroxisomal membrane protein with the N-terminus inside the peroxisome and the C-terminus facing the cytoplasm
GO:0005778 peroxisomal membrane	IDA PMID:9657383 Cloning and characterization of the gene encoding the human ...	ACCEPT	Summary: Kammerer et al. (1998) cloned human PEX3 and showed by transfection of epitope-tagged constructs and immunofluorescence that PEX3 is localized at the peroxisome. The N-terminal 40 amino acids were sufficient for peroxisomal targeting. Reason: Original cloning and characterization of human PEX3 confirming peroxisomal localization. One of the first studies establishing PEX3 at the peroxisomal membrane. Supporting Evidence: PMID:9657383 human Pex3p is localized at the peroxisome. The N-terminal 40 amino acids were revealed to be sufficient to target a GFP reporter protein to the peroxisome
GO:0007031 peroxisome organization	IMP PMID:10958759 Defective peroxisome membrane synthesis due to mutations in ...	ACCEPT	Summary: Muntau et al. (2000) demonstrated that homozygous PEX3 mutations in two Zellweger syndrome patients (complementation group G) cause complete loss of peroxisomal membrane structures. Expression of wild-type PEX3 restored peroxisomal biogenesis, confirming PEX3 is required for peroxisome organization. Reason: Definitive human genetic and complementation evidence that PEX3 is essential for peroxisome organization. Loss of PEX3 causes absence of detectable peroxisomes; re-expression restores them. Supporting Evidence: PMID:10958759 Two patients assigned to complementation group G who had not been linked previously to a specific gene defect were confirmed as displaying a cellular phenotype characterized by a lack of even residual peroxisomal membrane structures PMID:10958759 Expression of wild-type PEX3 in the mutant cell lines restored peroxisomal biogenesis, whereas transfection of mutated PEX3 cDNA did not
GO:0045046 protein import into peroxisome membrane	IMP PMID:15007061 PEX3 functions as a PEX19 docking factor in the import of cl...	ACCEPT	Summary: Fang et al. (2004) demonstrated using PEX3 RNAi in human fibroblasts that PEX3 depletion specifically abrogates class I PMP import without affecting class II PMP import or matrix protein import. PEX3 is both necessary and sufficient for PEX19 docking at peroxisomes. Reason: This is the key study establishing PEX3 as the PEX19 docking factor essential for class I PMP import. The IMP evidence from RNAi knockdown is strong and specific. Supporting Evidence: PMID:15007061 transient inhibition of PEX3 abrogates class I PMP import but has no effect on class II PMP import or peroxisomal matrix protein import PMID:15007061 PEX3 is required for PEX19 to dock at peroxisomes, interacts specifically with the docking domain of PEX19, and is required for recruitment of the PEX19 docking domain to peroxisomes. PEX3 is also sufficient to dock PEX19 at heterologous organelles
GO:0005777 peroxisome	IMP PMID:12924628 The interaction between human PEX3 and PEX19 characterized b...	ACCEPT	Summary: Muntau et al. (2003) used FRET analysis to visualize the PEX3-PEX19 interaction in living cells and confirmed the peroxisome as the main intracellular site of this interaction. PEX3 expression in PEX3-deficient cells restored import-competent peroxisomes. Reason: FRET analysis directly demonstrates PEX3 localization to peroxisomes and shows the PEX3-PEX19 interaction occurs primarily at peroxisomes. Consistent with all other localization data. Supporting Evidence: PMID:12924628 the peroxisome was identified to be the main intracellular site of the PEX3-PEX19 interaction
GO:0007031 peroxisome organization	IMP PMID:12924628 The interaction between human PEX3 and PEX19 characterized b...	ACCEPT	Summary: Muntau et al. (2003) showed that transfection of tagged PEX3 into PEX3-deficient human fibroblasts from Zellweger patients led to reformation of import-competent peroxisomes, providing IMP evidence for PEX3's role in peroxisome organization. Reason: Complementation of PEX3-deficient cells restoring peroxisome biogenesis is direct IMP evidence for PEX3's role in peroxisome organization. Supporting Evidence: PMID:12924628 Functionality of the fusion proteins was shown by transfection of human PEX3- and PEX19-deficient fibroblasts from Zellweger patients with tagged versions of PEX3 and PEX19. This led to reformation of import-competent peroxisomes in both cell lines previously lacking detectable peroxisomal membrane structures
GO:0005515 protein binding	IPI PMID:11883941 Two splice variants of human PEX19 exhibit distinct function...	MODIFY	Summary: Mayerhofer et al. (2002) studied two PEX19 splice variants and showed both interact with full-length PEX3 by in vitro protein interaction studies. This is a focused peroxin interaction study, not a generic high-throughput screen. Reason: The PEX19-PEX3 interaction documented here reflects PEX3's adaptor/docking function. 'Protein binding' should be replaced with the more informative adaptor activity term. Proposed replacements: protein-macromolecule adaptor activity Supporting Evidence: PMID:11883941 Both interact with peroxisomal ABC transporters (ALDP, ALDRP, PMP70) and with full-length PEX3 as shown by in vitro protein interaction studies
GO:0005777 peroxisome	IDA PMID:9922452 Peroxisome synthesis in the absence of preexisting peroxisom...	ACCEPT	Summary: South and Gould (1999) studied peroxisome synthesis in the absence of preexisting peroxisomes in PEX16-deficient cells. While this study primarily focuses on PEX16, PEX3 is contextualized as one of the few peroxins required for peroxisome membrane synthesis. The IDA for PEX3 peroxisome localization from this study may be indirect. Reason: PEX3 is mentioned as a peroxisomal protein in this study. The localization is well established from other sources, and this annotation is consistent with the overall body of evidence. Supporting Evidence: PMID:9922452 other human PMPs, including PEX3myc (Kammerer et al., 1998), PEX10myc (Warren et al., 1998)

References

GO_REF:0000033

Annotation inferences using phylogenetic trees

GO_REF:0000052

Gene Ontology annotation based on curation of immunofluorescence data

GO_REF:0000120

Combined Automated Annotation using Multiple IEA Methods

PMID:10430017

Identification and characterization of the human peroxin PEX3.

PEX3 is an integral peroxisomal membrane protein with N-terminus inside peroxisome and C-terminus facing cytoplasm
PEX19 interacts with PEX3 in mammalian two-hybrid assay
N-terminal 33 amino acids are necessary and sufficient for peroxisomal targeting

PMID:10704444

PEX19 binds multiple peroxisomal membrane proteins, is predominantly cytoplasmic, and is required for peroxisome membrane synthesis.

PEX19 binds a broad spectrum of PMPs including PEX3
PEX19 is predominantly cytoplasmic with a minor peroxisomal pool
Loss of PEX19 results in PMP degradation or mislocalization

PMID:10958759

Defective peroxisome membrane synthesis due to mutations in human PEX3 causes Zellweger syndrome, complementation group G.

Homozygous PEX3 mutations cause Zellweger syndrome with complete absence of peroxisomal membrane structures
Wild-type PEX3 expression restores peroxisomal biogenesis in mutant cells
PEX3 is established as a key factor in early human peroxisome synthesis

PMID:11883941

Two splice variants of human PEX19 exhibit distinct functions in peroxisomal assembly.

Both PEX19 splice variants interact with full-length PEX3
PEX19 domain structure is linked to specific interaction capabilities

PMID:12096124

Analysis of mammalian peroxin interactions using a non-transcription-based bacterial two-hybrid assay.

Detailed peroxin interaction map confirms PEX3-PEX19 interaction
PEX19 farnesylation enhances affinity for some peroxins

PMID:12924628

The interaction between human PEX3 and PEX19 characterized by fluorescence resonance energy transfer (FRET) analysis.

FRET demonstrates PEX3-PEX19 interaction occurs primarily at peroxisomes
Tagged PEX3 restores peroxisome biogenesis in PEX3-deficient Zellweger cells

PMID:15007061

PEX3 functions as a PEX19 docking factor in the import of class I peroxisomal membrane proteins.

PEX3 is the membrane docking factor for PEX19
PEX3 depletion specifically blocks class I PMP import
PEX3 is sufficient to dock PEX19 at heterologous organelles
Conserved motif aa120-136 of PEX3 is essential for PEX19 binding

PMID:16189514

Towards a proteome-scale map of the human protein-protein interaction network.

PMID:16280322

In vitro transport of membrane proteins to peroxisomes by shuttling receptor Pex19p.

PEX19 translocates PMPs to peroxisomes in an ATP- and PEX3-dependent manner
PEX19-PMP complexes bind to PEX3 in vitro

PMID:18174172

Characterization of the interaction between recombinant human peroxin Pex3p and Pex19p: identification of TRP-104 IN Pex3p as a critical residue for the interaction.

PEX3-PEX19 form a 1:1 complex with KD of 3.4 nM
Trp-104 of PEX3 is critical for PEX19 binding
PEX19 binding mutations impair peroxisome restoring activity

PMID:19479899

Pex3p-dependent peroxisomal biogenesis initiates in the endoplasmic reticulum of human fibroblasts.

PEX3 transits through the ER before reaching peroxisomes during de novo biogenesis
PEX3 requires PEX16 for ER localization
PEX3 can drive peroxisome biogenesis from the ER

PMID:19715730

The cytosolic domain of PEX3, a protein involved in the biogenesis of peroxisomes, binds membrane lipids.

Recombinant PEX3 cytosolic domain binds liposomes
PEX3 interacts with amphipathic molecules

PMID:19946888

Defining the membrane proteome of NK cells.

PEX3 detected in membrane fraction of NK cells by mass spectrometry

PMID:21102411

Structural basis for docking of peroxisomal membrane protein carrier Pex19p onto its receptor Pex3p.

Crystal structure of PEX3-PEX19 complex at 2.50 A resolution
PEX3 has a novel twisted six-helix bundle fold
PEX19 binds at apex of PEX3 via an alpha-helix with leucine triad motif

PMID:21525035

PEX14 is required for microtubule-based peroxisome motility in human cells.

PEX3 identified as constituent of native PEX14 peroxisomal membrane complexes

PMID:21768384

Sec16B is involved in the endoplasmic reticulum export of the peroxisomal membrane biogenesis factor peroxin 16 (Pex16) in mammalian cells.

PEX3 redistributes to ER when Sec16B is overexpressed
Sec16B knockdown suppresses PEX3 expression

PMID:25416956

A proteome-scale map of the human interactome network.

PMID:25502805

A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations.

PMID:27107012

Pooled-matrix protein interaction screens using Barcode Fusion Genetics.

PMID:28514442

Architecture of the human interactome defines protein communities and disease networks.

PMID:29997244

LuTHy: a double-readout bioluminescence-based two-hybrid technology for quantitative mapping of protein-protein interactions in mammalian cells.

PMID:31467278

Maximizing binary interactome mapping with a minimal number of assays.

PMID:31515488

Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations.

PMID:32296183

A reference map of the human binary protein interactome.

PMID:32814053

Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation in Affected Brains.

PMID:33961781

Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.

PMID:35271311

OpenCell: Endogenous tagging for the cartography of human cellular organization.

PMID:37398436

AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor.

PMID:38225382

Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation.

PMID:40205054

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

PMID:9657383

Cloning and characterization of the gene encoding the human peroxisomal assembly protein Pex3p.

First cloning of human PEX3
PEX3 localized to peroxisomes by immunofluorescence
N-terminal 40 amino acids sufficient for targeting

PMID:9922452

Peroxisome synthesis in the absence of preexisting peroxisomes.

PEX3, PEX16, PEX19 are involved in peroxisome membrane synthesis
Peroxisomes can form de novo

Reactome:R-HSA-382613

PEX-19 docks ABCD1/D2/D3 to peroximal membrane

Reactome:R-HSA-9603775

PEX3:PEX19:class I PMP dissociates

Reactome:R-HSA-9603784

PEX19:class I PMP binds PEX3

Deep Research

Falcon

(PEX3-deep-research-falcon.md)

Research Report: Human **PEX3** (UniProt **P56589**) — Functional Annotation, Mechanism, and Translational Relevance Falcon Edison Scientific Literature 44 citations 2026-03-05T04:21:55.291719

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.

Research Report: Human PEX3 (UniProt P56589) — Functional Annotation, Mechanism, and Translational Relevance

0) Target verification (critical disambiguation)

The literature synthesized here pertains to human PEX3 (UniProt P56589), annotated as Peroxisomal biogenesis factor 3 / Peroxin-3, an integral peroxisomal membrane protein required for peroxisome membrane biogenesis, and a key docking factor for PEX19. Multiple sources explicitly study PEX3 in human cells/patient fibroblasts and in mammalian systems, and align with the peroxin-3 family function and domains described in UniProt. (fang2004pex3functionsas pages 2-3, matsuzaki2008theperoxisomalmembrane pages 2-4, theodoulou2013peroxisomemembraneproteins pages 4-6)

1) Key concepts and definitions (current understanding)

1.1 Peroxisome biogenesis and “peroxins”

Peroxisomes are single-membrane organelles with essential roles in lipid metabolism and redox homeostasis; disruption of peroxisomal function causes severe inherited metabolic disorders. Reviews emphasize that peroxisome biogenesis and protein import are mediated by peroxins (PEX proteins). (rudowitz2023importandquality pages 2-3)

1.2 PEX3: primary molecular role

PEX3 is best understood as a peroxisomal membrane docking factor for PEX19, thereby enabling import/insertion of a major class of peroxisomal membrane proteins (PMPs). In a foundational human-cell study, PEX3 was shown to be necessary and sufficient to dock PEX19 at membranes, and disruption of the PEX19-binding site on PEX3 prevented PEX19 recruitment and abolished PEX3 function in PMP import. (fang2004pex3functionsas pages 7-8, fang2004pex3functionsas pages 2-3)

1.3 PEX19 and PEX16 (core partners and pathway context)

PEX19 is a cytosolic chaperone/receptor for newly synthesized PMPs. Mechanistic reviews highlight that PEX19 binds PMP membrane targeting signals (mPTS) to shield hydrophobic segments from degradation and delivers cargo to membranes by docking to PEX3; PEX16 in mammals supports recruitment/trafficking steps and can function as a docking factor for the PEX3–PEX19 complex. (rudowitz2023importandquality pages 2-3)

1.4 Class I vs. Class II peroxisomal membrane proteins (concept)

PEX3 is commonly discussed as part of the PEX19-dependent pathway for class I PMPs, while PEX3 itself is often described as a class II PMP with partially distinct targeting logic (including ER involvement in some models). (fujiki2006importofperoxisomal pages 3-5, giannopoulou2016towardsthemolecular pages 3-4)

2) Protein function, mechanism, and subcellular localization

2.1 Localization and requirement for peroxisomes in human cells

In human cells, loss of PEX3 produces a severe “peroxisome absent” phenotype: human (and yeast) cells lacking PEX3 are described as devoid of detectable peroxisomes, with rapid degradation of many PMPs and mislocalization of others. In human fibroblasts treated with PEX3 siRNAs, PEX3 becomes undetectable on peroxisomes by immunofluorescence within days, supporting its peroxisomal membrane localization and requirement for organelle maintenance. (fang2004pex3functionsas pages 2-3)

2.2 Docking interaction with PEX19: structural basis

Structural evidence supports the docking model: a human PEX3 soluble region forms a twisted six-helix bundle with a hydrophobic cavity that binds a helix from PEX19; mutational/binding/complementation studies in human fibroblasts have been used to validate functional relevance of the interaction. (theodoulou2013peroxisomemembraneproteins pages 4-6)

Figure-based evidence: crystal-structure panels show the 3D PEX3–PEX19 complex and residue-level interface features that implement docking, with the PEX3 N-terminus indicated as membrane-bound. (sato2010structuralbasisfor media 7d1bd89a, sato2010structuralbasisfor media d01a8113)

2.3 PEX3 trafficking and the PEX16-dependent import of full-length PEX3 (mammalian evidence)

A mammalian cell study showed newly synthesized PEX3 forms soluble cytosolic complexes with PEX19 that are competent for peroxisomal targeting; PEX16 functions as a membrane receptor/docking site for PEX3–PEX19 complexes in this context. PEX19 knockdown selectively blocks peroxisomal targeting of full-length PEX3, supporting a PEX19/PEX16-dependent import route for PEX3 itself. (matsuzaki2008theperoxisomalmembrane pages 2-4, matsuzaki2008theperoxisomalmembrane pages 1-2)

2.4 Quantitative mechanistic data: stabilization and affinity

PEX19 stabilizes PEX3: PEX3 apparent half-life was ~6 h with PEX19 coexpression vs ~2 h without PEX19, indicating a chaperone/stabilization role for PEX19 on newly synthesized full-length PEX3. (matsuzaki2008theperoxisomalmembrane pages 2-4)
PEX19 lipidation increases cargo affinity: A 2023 review reports that PEX19 farnesylation causes a conformational change leading to a ~10-fold increase in cargo affinity. (rudowitz2023importandquality pages 2-3)

3) Biological processes and pathways involving PEX3

3.1 Peroxisomal membrane protein insertion and organelle biogenesis

PEX3 is central to pathways that establish/maintain the peroxisomal membrane proteome. The dominant model is that cytosolic PEX19–PMP complexes dock at membrane PEX3 and release PMPs into the peroxisomal membrane, enabling organelle formation and maturation. (fang2004pex3functionsas pages 7-8, costa2023theperoxisomalredox pages 31-34)

3.2 De novo biogenesis models and ER involvement

Reviews describe unresolved aspects of how peroxisomes form “de novo,” including routes involving the ER and pre-peroxisomal vesicles and how PEX3/PEX19/PEX16 coordinate insertion and trafficking steps. PEX3 has been discussed as anchoring into membranes with sequence features consistent with ER translocation machinery involvement in vertebrates, and PEX16 is described as an ER receptor for PEX3 in some models while also participating in docking at mature peroxisomes. (giannopoulou2016towardsthemolecular pages 3-4)

3.3 Additional/non-canonical roles (emerging)

While PEX3 is canonically a peroxisome biogenesis factor, recent mammalian studies explore broader functions and contexts:
- In mouse heart, cardiomyocyte-specific Pex3 knockout disturbed redox homeostasis and impaired regenerative repair after injury, with mechanistic links to plasmalogen metabolism and AKT/GSK3β signaling via ITGB3 plasma membrane localization. (sun2024pex3promotesregenerative pages 1-2)
- In melanoma therapy resistance, repressing PEX3 compromised peroxisome biogenesis and rewired lipid metabolism (ceramide/UGCG axis), sensitizing tumors to MAPK inhibitors. (huang2023peroxisomedisruptionalters pages 1-2)

4) Recent developments (prioritizing 2023–2024)

4.1 2024: Live-cell imaging probes for peroxisomes validated in PEX3-deficient patient cells

A 2024 Nature Communications study developed improved fluorescent fatty-acid–based probes (PeroxiSPY650/555) enabling fast, non-cytotoxic peroxisome staining in live mammalian cells, and demonstrated their ability to diagnose peroxisome abnormalities in CRISPR/Cas9 PBD models and patient-derived cell lines, including PEX3-deficient patient fibroblasts that lack peroxisomal compartments. This represents a practical assay advance for research and potentially for diagnostic workflows in specialized settings. (korotkova2024fluorescentfattyacid pages 1-2)

Publication details: May 2024; https://doi.org/10.1038/s41467-024-48679-2 (korotkova2024fluorescentfattyacid pages 1-2)

4.2 2023: Targeting PEX3 in cancer metabolism and therapy resistance; PEX3–PEX19 inhibitor

A 2023 Journal of Clinical Investigation study found that compromising peroxisome biogenesis by repressing PEX3 potentiated MAPK-targeted therapy via ceramide induction and identified a small-molecule inhibitor of the PEX3–PEX19 interaction that showed efficacy in combination therapy in preclinical melanoma models. This is a notable translational development because it directly targets the PEX3 docking function. (huang2023peroxisomedisruptionalters pages 1-2)

Publication details: Oct 2023; https://doi.org/10.1172/jci166644 (huang2023peroxisomedisruptionalters pages 1-2)

4.3 2023: Updated expert synthesis on import and quality control

A 2023 Journal of Cell Science review reframed peroxisomal protein import and quality control, emphasizing PEX19’s chaperone features, PEX3-mediated membrane delivery, PEX16’s roles in mammals, and alternative origins for pre-peroxisomal vesicles. This review is an authoritative “expert opinion” synthesis relevant for functional annotation of PEX3. (rudowitz2023importandquality pages 2-3)

Publication details: Aug 2023; https://doi.org/10.1242/jcs.260999 (rudowitz2023importandquality pages 2-3)

4.4 2024: Clinical genetics/prenatal diagnostic interpretation of PEX3 deletion risk

A 2024 Diagnostics prenatal report illustrates real-world genomic testing interpretation when a fetal chromosomal finding includes PEX3 deletion. The paper provides explicit ZSD context and highlights implementation issues: array CGH can detect ~5% additional pathogenic CNVs beyond karyotype and informs counseling. (villa2024cytogeneticallybalancedreciprocal pages 1-2, villa2024cytogeneticallybalancedreciprocal pages 2-4)

Publication details: Aug 2024; https://doi.org/10.3390/diagnostics14161732 (villa2024cytogeneticallybalancedreciprocal pages 1-2)

5) Current applications and real-world implementations

5.1 Clinical genetics: Zellweger spectrum disorder (ZSD) association and prenatal counseling

PEX3 is associated with peroxisome biogenesis disorders / Zellweger syndrome spectrum with biallelic inheritance in disease knowledgebases. (OpenTargets Search: -PEX3)

A 2024 prenatal diagnostic case report shows how detection of a fetal CNV including PEX3 triggers ZSD risk assessment and counseling. The report provides concrete implementation notes: array CGH adds ~5% yield beyond karyotype and biochemical tests on amniotic fluid can be done but have limited sensitivity; gene sequencing is challenged by VUS burden, limiting prenatal actionability in some settings. (villa2024cytogeneticallybalancedreciprocal pages 2-4)

5.2 Cellular diagnostics / functional assays in patient-derived cells

The 2024 PeroxiSPY probes offer a practical laboratory assay to visualize peroxisomes in live cells, including patient-derived PEX3-deficient fibroblasts. This supports research-grade diagnosis/phenotyping of peroxisomal abnormalities and may complement genetic testing in specialized labs. (korotkova2024fluorescentfattyacid pages 1-2)

5.3 Drug discovery: pathway inhibition via PEX3–PEX19 docking disruption

The melanoma study illustrates a real-world translational direction: designing inhibitors of the PEX3–PEX19 interaction to disrupt peroxisome biogenesis in tumors and sensitize to targeted therapies. (huang2023peroxisomedisruptionalters pages 1-2)

6) Expert opinions and analysis (authoritative interpretations)

6.1 Mechanistic consensus and remaining uncertainties

Expert reviews converge that PEX3 and PEX19 are “early peroxins” for peroxisomal membrane protein targeting and insertion, but emphasize that mechanistic details (direct insertion vs ER-vesicle models; relative contributions across contexts) remain disputed and may differ by organism/cell state. (rudowitz2023importandquality pages 2-3, giannopoulou2016towardsthemolecular pages 3-4)

6.2 Systems-level implications

The 2023 review highlights that peroxisomal import is tightly linked to quality control pathways and that defects in import can trigger secondary responses (e.g., removal pathways), reinforcing why PEX3 loss produces systemic phenotypes beyond a single pathway. (rudowitz2023importandquality pages 2-3)

7) Relevant statistics and quantitative data (recent studies and key classic measurements)

7.1 Human disease statistics (2024 clinical genetics report)

From a 2024 prenatal diagnostic genetics analysis:
- PEX3 pathogenic variants estimated to account for ~0.7% of Zellweger syndrome cases. (villa2024cytogeneticallybalancedreciprocal pages 2-4)
- Using ZS incidence ~1/133,000 and estimated PEX3 carrier frequency ~1/1820, a fetus with a paternal PEX3 deletion had a theoretical ZS risk of ~1/3640 (0.03%). (villa2024cytogeneticallybalancedreciprocal pages 2-4)
- Reported constraint metrics suggested heterozygous PEX3 loss is unlikely to be strongly deleterious (Decipher HI 27.6%; pLI 0.02), consistent with recessive disease logic. (villa2024cytogeneticallybalancedreciprocal pages 2-4)

7.2 Quantitative cell biology measurements (PEX3/PEX19/PEX16 pathway)

PEX3 stability: PEX19 coexpression increased PEX3 half-life from ~2 h to ~6 h. (matsuzaki2008theperoxisomalmembrane pages 2-4)
PEX19 cargo affinity: PEX19 farnesylation produces ~10-fold increased cargo affinity. (rudowitz2023importandquality pages 2-3)

7.3 Quantitative proteomics with PEX3 depletion in human cells

A label-free MS study of PEX3-depleted HeLa cells quantified 6488 proteins, achieved ~85% knockdown, and identified 13 significantly decreased proteins (none increased) under FDR-adjusted p<0.05. This provides a quantitative view of downstream proteome sensitivity to PEX3 depletion under the tested conditions. (zimmermann2021quantitativeproteomicsand pages 6-8)

7.4 Quantitative oncology model outcomes (PEX3 perturbation)

In a melanoma model study, screening 80 clones yielded 2 single-allele Pex3+/– clones (2/80). In vivo, after MAPK inhibitor treatment, tumors showed a rapid decrease in volume within 48 h in Pex3+/– arms (when treated at ~200 mm3 tumor size). (huang2023peroxisomedisruptionalters pages 1-2)

8) Consolidated functional annotation (high-confidence summary)

Gene/protein: PEX3 (UniProt P56589) encodes an integral peroxisomal membrane peroxin required for peroxisome membrane biogenesis.

Primary function: PEX3 is a docking factor for the cytosolic PMP chaperone/receptor PEX19, enabling recruitment of PEX19–PMP complexes and thereby facilitating insertion of major classes of peroxisomal membrane proteins. (fang2004pex3functionsas pages 2-3, fang2004pex3functionsas pages 7-8, rudowitz2023importandquality pages 2-3)

Localization: peroxisomal membrane; N-terminal membrane anchor with a cytosolic domain that structurally accommodates PEX19 docking via a helical interface. (theodoulou2013peroxisomemembraneproteins pages 4-6, sato2010structuralbasisfor media 7d1bd89a)

Key partners: PEX19 (direct docking and chaperone complex), PEX16 (mammalian receptor/docking support for PEX3 trafficking and/or PEX3–PEX19 docking, depending on model). (matsuzaki2008theperoxisomalmembrane pages 2-4, rudowitz2023importandquality pages 2-3)

Human disease: biallelic pathogenic variants cause Zellweger spectrum/peroxisome biogenesis disorders; prenatal genomic detection of PEX3 CNVs can be incorporated into risk assessment and counseling. (OpenTargets Search: -PEX3, villa2024cytogeneticallybalancedreciprocal pages 2-4)

Translational directions (2023–2024): new live-cell diagnostic probes validated in PEX3-deficient patient fibroblasts (PeroxiSPY), and oncology drug-discovery strategies targeting the PEX3–PEX19 interaction to modulate peroxisome biogenesis in tumors. (korotkova2024fluorescentfattyacid pages 1-2, huang2023peroxisomedisruptionalters pages 1-2)

Summary Table (synthesis)

Aspect	Current Understanding	Key Evidence (Paper + Year)	Quantitative/Data Notes	URL/DOI
Molecular Function	Essential membrane docking factor for PEX19; mediates insertion of Class I Peroxisomal Membrane Proteins (PMPs) and de novo peroxisome biogenesis.	Fang et al. (2004); Rudowitz & Erdmann (2023)	Essential for class I PMP import; depletion leads to rapid PMP degradation.	10.1083/jcb.200311131; 10.1242/jcs.260999
Localization & Topology	Integral peroxisomal membrane protein; cytosolic C-terminal domain forms a six-helix bundle for PEX19 binding; N-terminal membrane anchor.	Sato et al. (2010); Theodoulou et al. (2013)	Crystallography of human PEX3 (residues 26-373) complexed with PEX19 peptide.	10.1038/emboj.2010.293; 10.1042/bj20130078
Core Interactions	Directly binds PEX19 (chaperone); recruits PEX19-PMP complexes. PEX16 is required for PEX3 targeting/stability in mammals.	Matsuzaki & Fujiki (2008); Schmidt et al. (2012)	PEX19 binding increases PEX3 half-life from ~2h to ~6h in mammalian cells.	10.1083/jcb.200806062; 10.1111/j.1600-0854.2012.01380.x
Disease Association	Biallelic loss-of-function mutations cause Zellweger Spectrum Disorders (ZSD); associated with severe peroxisome biogenesis defects.	Villa et al. (2024); Open Targets (2025)	PEX3 mutations account for ~0.7% of Zellweger syndrome cases; carrier freq ~1/1820.	10.3390/diagnostics14161732; Open Targets
Therapeutic Target	Inhibition of PEX3–PEX19 interaction sensitizes melanoma cells to MAPK inhibitors by inducing ceramides.	Huang et al. (2023)	Small-molecule inhibitors of PEX3-PEX19 interaction demonstrated in preclinical models.	10.1172/jci166644
Diagnostics	PEX3 deficiency detectable in patient fibroblasts via specific fluorescent fatty acid probes (e.g., PeroxiSPY).	Korotkova et al. (2024)	Validated in CRISPR/Cas9 PEX3-deficient cells and patient-derived lines.	10.1038/s41467-024-48679-2

Table: Overview of human PEX3 function, interactions, and clinical relevance based on recent and foundational literature.

Visual evidence (structure/topology)

Crystal structure and docking interface of the PEX3–PEX19 complex are shown in Sato et al. figures retrieved here. (sato2010structuralbasisfor media 7d1bd89a, sato2010structuralbasisfor media d01a8113)

References

(fang2004pex3functionsas pages 2-3): Yi Fang, James C. Morrell, Jacob M. Jones, and Stephen J. Gould. Pex3 functions as a pex19 docking factor in the import of class i peroxisomal membrane proteins. The Journal of Cell Biology, 164:863-875, Mar 2004. URL: https://doi.org/10.1083/jcb.200311131, doi:10.1083/jcb.200311131. This article has 347 citations.
(matsuzaki2008theperoxisomalmembrane pages 2-4): Takashi Matsuzaki and Yukio Fujiki. The peroxisomal membrane protein import receptor pex3p is directly transported to peroxisomes by a novel pex19p- and pex16p-dependent pathway. The Journal of Cell Biology, 183(7):1275-1286, Dec 2008. URL: https://doi.org/10.1083/jcb.200806062, doi:10.1083/jcb.200806062. This article has 200 citations.
(theodoulou2013peroxisomemembraneproteins pages 4-6): Frederica L. Theodoulou, Kristin Bernhardt, Nicole Linka, and Alison Baker. Peroxisome membrane proteins: multiple trafficking routes and multiple functions? The Biochemical journal, 451 3:345-52, May 2013. URL: https://doi.org/10.1042/bj20130078, doi:10.1042/bj20130078. This article has 78 citations.
(rudowitz2023importandquality pages 2-3): Markus Rudowitz and Ralf Erdmann. Import and quality control of peroxisomal proteins. Journal of cell science, Aug 2023. URL: https://doi.org/10.1242/jcs.260999, doi:10.1242/jcs.260999. This article has 16 citations and is from a domain leading peer-reviewed journal.
(fang2004pex3functionsas pages 7-8): Yi Fang, James C. Morrell, Jacob M. Jones, and Stephen J. Gould. Pex3 functions as a pex19 docking factor in the import of class i peroxisomal membrane proteins. The Journal of Cell Biology, 164:863-875, Mar 2004. URL: https://doi.org/10.1083/jcb.200311131, doi:10.1083/jcb.200311131. This article has 347 citations.
(fujiki2006importofperoxisomal pages 3-5): Yukio Fujiki, Yuji Matsuzono, Takashi Matsuzaki, and Marc Fransen. Import of peroxisomal membrane proteins: the interplay of pex3p- and pex19p-mediated interactions. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research, 1763(12):1639-1646, Dec 2006. URL: https://doi.org/10.1016/j.bbamcr.2006.09.030, doi:10.1016/j.bbamcr.2006.09.030. This article has 173 citations and is from a peer-reviewed journal.
(giannopoulou2016towardsthemolecular pages 3-4): Evdokia-Anastasia Giannopoulou, Leonidas Emmanouilidis, Michael Sattler, Gabriele Dodt, and Matthias Wilmanns. Towards the molecular mechanism of the integration of peroxisomal membrane proteins☆. Biochimica et Biophysica Acta, 1863:863-869, May 2016. URL: https://doi.org/10.1016/j.bbamcr.2015.09.031, doi:10.1016/j.bbamcr.2015.09.031. This article has 39 citations.
(sato2010structuralbasisfor media 7d1bd89a): Yasuhiko Sato, Hiroyuki Shibata, Toru Nakatsu, Hiroaki Nakano, Yoshinori Kashiwayama, Tsuneo Imanaka, and Hiroaki Kato. Structural basis for docking of peroxisomal membrane protein carrier pex19p onto its receptor pex3p. The EMBO Journal, 29:4083-4093, Dec 2010. URL: https://doi.org/10.1038/emboj.2010.293, doi:10.1038/emboj.2010.293. This article has 82 citations.
(sato2010structuralbasisfor media d01a8113): Yasuhiko Sato, Hiroyuki Shibata, Toru Nakatsu, Hiroaki Nakano, Yoshinori Kashiwayama, Tsuneo Imanaka, and Hiroaki Kato. Structural basis for docking of peroxisomal membrane protein carrier pex19p onto its receptor pex3p. The EMBO Journal, 29:4083-4093, Dec 2010. URL: https://doi.org/10.1038/emboj.2010.293, doi:10.1038/emboj.2010.293. This article has 82 citations.
(matsuzaki2008theperoxisomalmembrane pages 1-2): Takashi Matsuzaki and Yukio Fujiki. The peroxisomal membrane protein import receptor pex3p is directly transported to peroxisomes by a novel pex19p- and pex16p-dependent pathway. The Journal of Cell Biology, 183(7):1275-1286, Dec 2008. URL: https://doi.org/10.1083/jcb.200806062, doi:10.1083/jcb.200806062. This article has 200 citations.
(costa2023theperoxisomalredox pages 31-34): C Figueiredo Costa and M Fransen. The peroxisomal redox orchestra: new melodies of old molecular players. Unknown journal, 2023.
(sun2024pex3promotesregenerative pages 1-2): Jia-Teng Sun, Zi-Mu Wang, Liu-Hua Zhou, Tong-Tong Yang, Di Zhao, Yu-Lin Bao, Si-Bo Wang, Ling-Feng Gu, Jia-Wen Chen, Tian-Kai Shan, Tian-Wen Wei, Hao Wang, Qi-Ming Wang, Xiang-Qing Kong, Li-Ping Xie, Ai-Hua Gu, Yang Zhao, Feng Chen, Yong Ji, Yi-Qiang Cui, and Lian-Sheng Wang. Pex3 promotes regenerative repair after myocardial injury in mice through facilitating plasma membrane localization of itgb3. Communications Biology, Jul 2024. URL: https://doi.org/10.1038/s42003-024-06483-0, doi:10.1038/s42003-024-06483-0. This article has 8 citations and is from a peer-reviewed journal.
(huang2023peroxisomedisruptionalters pages 1-2): Fan Huang, Feiyang Cai, Michael S. Dahabieh, Kshemaka Gunawardena, Ali Talebi, Jonas Dehairs, Farah El-Turk, Jae Yeon Park, Mengqi Li, Christophe Goncalves, Natascha Gagnon, Jie Su, Judith H. LaPierre, Perrine Gaub, Jean-Sébastien Joyal, John J. Mitchell, Johannes V. Swinnen, Wilson H. Miller, and Sonia V. del Rincón. Peroxisome disruption alters lipid metabolism and potentiates antitumor response with mapk-targeted therapy in melanoma. Journal of Clinical Investigation, Oct 2023. URL: https://doi.org/10.1172/jci166644, doi:10.1172/jci166644. This article has 32 citations and is from a highest quality peer-reviewed journal.
(korotkova2024fluorescentfattyacid pages 1-2): Daria Korotkova, Anya Borisyuk, Anthony Guihur, Manon Bardyn, Fabien Kuttler, Luc Reymond, Milena Schuhmacher, and Triana Amen. Fluorescent fatty acid conjugates for live cell imaging of peroxisomes. Nature Communications, May 2024. URL: https://doi.org/10.1038/s41467-024-48679-2, doi:10.1038/s41467-024-48679-2. This article has 22 citations and is from a highest quality peer-reviewed journal.
(villa2024cytogeneticallybalancedreciprocal pages 1-2): Nicoletta Villa, Serena Redaelli, Stefania Farina, Elena Sala, Francesca Crosti, Sabrina Cozzolino, Maria Verderio, Leda Dalprà, Gaia Roversi, Angela Bentivegna, Giovanni Cazzaniga, Marialuisa Lavitrano, and Donatella Conconi. Cytogenetically balanced reciprocal translocation could hide molecular genomic unbalances: implications for foetal phenotype correlation. Diagnostics, 14:1732, Aug 2024. URL: https://doi.org/10.3390/diagnostics14161732, doi:10.3390/diagnostics14161732. This article has 0 citations.
(villa2024cytogeneticallybalancedreciprocal pages 2-4): Nicoletta Villa, Serena Redaelli, Stefania Farina, Elena Sala, Francesca Crosti, Sabrina Cozzolino, Maria Verderio, Leda Dalprà, Gaia Roversi, Angela Bentivegna, Giovanni Cazzaniga, Marialuisa Lavitrano, and Donatella Conconi. Cytogenetically balanced reciprocal translocation could hide molecular genomic unbalances: implications for foetal phenotype correlation. Diagnostics, 14:1732, Aug 2024. URL: https://doi.org/10.3390/diagnostics14161732, doi:10.3390/diagnostics14161732. This article has 0 citations.
(OpenTargets Search: -PEX3): Open Targets Query (-PEX3, 5 results). Buniello, A. et al. (2025). Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery. Nucleic Acids Research.
(zimmermann2021quantitativeproteomicsand pages 6-8): Richard Zimmermann, Sven Lang, Monika Lerner, Friedrich G Förster, Duy Nguyen, Volkard Helms, and Bianca Schrul. Quantitative proteomics and differential protein abundance analysis after depletion of pex3 from human cells identifies additional aspects of protein targeting to the er. International Journal of Molecular Sciences, Nov 2021. URL: https://doi.org/10.20944/preprints202111.0414.v1, doi:10.20944/preprints202111.0414.v1. This article has 14 citations.

Citations

rudowitz2023importandquality pages 2-3
theodoulou2013peroxisomemembraneproteins pages 4-6
matsuzaki2008theperoxisomalmembrane pages 2-4
giannopoulou2016towardsthemolecular pages 3-4
huang2023peroxisomedisruptionalters pages 1-2
korotkova2024fluorescentfattyacid pages 1-2
villa2024cytogeneticallybalancedreciprocal pages 1-2
villa2024cytogeneticallybalancedreciprocal pages 2-4
zimmermann2021quantitativeproteomicsand pages 6-8
fujiki2006importofperoxisomal pages 3-5
matsuzaki2008theperoxisomalmembrane pages 1-2
costa2023theperoxisomalredox pages 31-34
10.1083/jcb.200311131
10.1242/jcs.260999
10.1038/emboj.2010.293
10.1042/bj20130078
10.1083/jcb.200806062
10.1111/j.1600-0854.2012.01380.x
10.3390/diagnostics14161732
Open Targets
10.1172/jci166644
10.1038/s41467-024-48679-2
https://doi.org/10.1038/s41467-024-48679-2
https://doi.org/10.1172/jci166644
https://doi.org/10.1242/jcs.260999
https://doi.org/10.3390/diagnostics14161732
https://doi.org/10.1083/jcb.200311131
https://doi.org/10.1038/emboj.2010.293
https://doi.org/10.1042/bj20130078
https://doi.org/10.1083/jcb.200806062
https://doi.org/10.1111/j.1600-0854.2012.01380.x
https://platform.opentargets.org/
https://doi.org/10.1083/jcb.200311131,
https://doi.org/10.1083/jcb.200806062,
https://doi.org/10.1042/bj20130078,
https://doi.org/10.1242/jcs.260999,
https://doi.org/10.1016/j.bbamcr.2006.09.030,
https://doi.org/10.1016/j.bbamcr.2015.09.031,
https://doi.org/10.1038/emboj.2010.293,
https://doi.org/10.1038/s42003-024-06483-0,
https://doi.org/10.1172/jci166644,
https://doi.org/10.1038/s41467-024-48679-2,
https://doi.org/10.3390/diagnostics14161732,
https://doi.org/10.20944/preprints202111.0414.v1,

📄 View Raw YAML

id: P56589
gene_symbol: PEX3
product_type: PROTEIN
status: IN_PROGRESS
taxon:
  id: NCBITaxon:9606
  label: Homo sapiens
description: PEX3 (Peroxisomal biogenesis factor 3 / Peroxin-3) is an integral peroxisomal membrane protein that serves as
  the membrane-anchored docking receptor for the cytosolic PEX19-PMP (peroxisomal membrane protein) chaperone/receptor complex.
  PEX3 is essential for peroxisome membrane biogenesis -- cells lacking PEX3 are devoid of detectable peroxisomes entirely.
  PEX3 recruits PEX19-bound class I PMPs to the peroxisomal membrane for insertion. The cytosolic domain of PEX3 forms a twisted
  six-helix bundle that binds an N-terminal helix of PEX19 at a hydrophobic interface. PEX3 also transits through the ER during
  de novo peroxisome biogenesis. Biallelic loss-of-function mutations in PEX3 cause Zellweger spectrum disorders (complementation
  group 12/G).
existing_annotations:
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: PEX3 is a well-established integral peroxisomal membrane protein. IBA annotation is phylogenetically supported
      and consistent with extensive experimental evidence from multiple species. PEX3 has two transmembrane domains and localizes
      to the peroxisomal membrane in human cells (PMID:10430017, PMID:9657383).
    action: ACCEPT
    reason: Core localization of PEX3. Peroxisomal membrane localization is confirmed by immunofluorescence in multiple studies
      and by UniProt topology annotation showing transmembrane helices at residues 16-36 and 117-140.
    supported_by:
    - reference_id: PMID:10430017
      supporting_text: "H sPEX3 is an integral peroxisomal membrane protein with the N-terminus inside the peroxisome and the C-terminus facing the cytoplasm"
    - reference_id: PMID:9657383
      supporting_text: "human Pex3p is localized at the peroxisome"
- term:
    id: GO:0030674
    label: protein-macromolecule adaptor activity
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: PEX3 functions as a membrane-anchored docking/adaptor for PEX19, bridging the cytosolic PEX19-PMP cargo complex
      to the peroxisomal membrane. This adaptor activity is well supported by structural (PMID:21102411) and functional (PMID:15007061)
      studies. The IBA annotation captures the molecular function at an appropriate level of specificity.
    action: ACCEPT
    reason: PEX3 serves as a docking receptor/adaptor for PEX19 at the peroxisomal membrane, enabling PMP insertion. This
      is the core molecular function of PEX3. The term protein-macromolecule adaptor activity is appropriate as PEX3 bridges
      PEX19-cargo complexes to the membrane.
    supported_by:
    - reference_id: PMID:15007061
      supporting_text: PEX3 is required for PEX19 to dock at peroxisomes, interacts specifically with the docking domain of
        PEX19, and is required for recruitment of the PEX19 docking domain to peroxisomes
    - reference_id: PMID:21102411
      supporting_text: The interaction between Pex3p, which resides on the peroxisomal membrane, and Pex19p, which resides
        in the cytosol, is crucial for peroxisome formation and the post-translational targeting of peroxisomal membrane proteins
- term:
    id: GO:0045046
    label: protein import into peroxisome membrane
  evidence_type: IBA
  original_reference_id: GO_REF:0000033
  review:
    summary: PEX3 is essential for the import of class I peroxisomal membrane proteins. Transient depletion of PEX3 specifically
      abrogates class I PMP import without affecting class II PMP import or matrix protein import (PMID:15007061). IBA annotation
      is phylogenetically well-supported and captures the core biological process.
    action: ACCEPT
    reason: This is the central biological process function of PEX3. Fang et al. (2004) demonstrated that PEX3 depletion by
      RNAi specifically blocks class I PMP import, establishing PEX3 as essential for this process.
    supported_by:
    - reference_id: PMID:15007061
      supporting_text: transient inhibition of PEX3 abrogates class I PMP import but has no effect on class II PMP import
        or peroxisomal matrix protein import
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: Automated annotation of PEX3 to peroxisomal membrane. Consistent with the IBA and IDA annotations for the same
      term and well supported experimentally.
    action: ACCEPT
    reason: Redundant with IBA and IDA annotations but correctly reflects the established localization. IEA annotations at
      this level are acceptable when confirmed by other evidence.
    supported_by:
    - reference_id: PMID:10430017
      supporting_text: "H sPEX3 is an integral peroxisomal membrane protein with the N-terminus inside the peroxisome and the C-terminus facing the cytoplasm"
- term:
    id: GO:0007031
    label: peroxisome organization
  evidence_type: IEA
  original_reference_id: GO_REF:0000120
  review:
    summary: Automated annotation of PEX3 to peroxisome organization. PEX3 is essential for peroxisome membrane biogenesis
      and thus for overall peroxisome organization. This is consistent with IMP annotations from multiple publications.
    action: ACCEPT
    reason: Peroxisome organization is a parent term that encompasses peroxisome biogenesis. PEX3 is essential for peroxisome
      membrane assembly and cells lacking PEX3 have no detectable peroxisomes. The IEA is consistent with experimental evidence.
    supported_by:
    - reference_id: PMID:10958759
      supporting_text: Expression of wild-type PEX3 in the mutant cell lines restored peroxisomal biogenesis, whereas transfection
        of mutated PEX3 cDNA did not
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:10704444
  review:
    summary: Sacksteder et al. (2000) demonstrated that PEX19 binds multiple PMPs including PEX3, using two-hybrid and blot
      overlay assays. The interaction with PEX19 is the core molecular function of PEX3. However, 'protein binding' is too
      generic -- the IBA annotation for protein-macromolecule adaptor activity better captures this function.
    action: MODIFY
    reason: The PEX3-PEX19 interaction is real and well-documented, but 'protein binding' is uninformative. The more specific
      term 'protein-macromolecule adaptor activity' (GO:0030674) already captures this function. This annotation should be
      replaced with the more informative term.
    proposed_replacement_terms:
    - id: GO:0030674
      label: protein-macromolecule adaptor activity
    supported_by:
    - reference_id: PMID:10704444
      supporting_text: PEX19 binds a broad spectrum of PMPs, displays saturable PMP binding, and interacts with regions of
        PMPs required for their targeting to peroxisomes
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:12096124
  review:
    summary: Fransen et al. (2002) used a bacterial two-hybrid system to analyze interactions among mammalian peroxins and
      confirmed PEX3-PEX19 interaction. This is a focused peroxin interaction study, not a generic high-throughput screen.
      The interaction is specific and well-characterized.
    action: MODIFY
    reason: The PEX3-PEX19 interaction documented here reflects PEX3's adaptor/docking function. 'Protein binding' is uninformative;
      this should be replaced with the more specific adaptor activity term.
    proposed_replacement_terms:
    - id: GO:0030674
      label: protein-macromolecule adaptor activity
    supported_by:
    - reference_id: PMID:12096124
      supporting_text: we report a detailed interaction map of these peroxins
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16189514
  review:
    summary: Rual et al. (2005) is a large-scale proteome-wide yeast two-hybrid screen. While PEX3 interactions detected here
      may include PEX19, this is a high-throughput study and the generic 'protein binding' term provides no functional insight.
    action: MARK_AS_OVER_ANNOTATED
    reason: High-throughput interactome screen. 'Protein binding' from a proteome-scale Y2H screen provides no specific functional
      information about PEX3. The meaningful interactions (PEX19, PEX16) are already captured by more specific annotations.
    supported_by:
    - reference_id: PMID:16189514
      supporting_text: Towards a proteome-scale map of the human protein-protein interaction network
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:16280322
  review:
    summary: Matsuzono and Fujiki (2006) developed an in vitro cell-free PMP transport system and showed that PEX19 complexes
      with PMPs bind to PEX3 in vitro, and that PEX19 translocates PMPs to peroxisomes in a PEX3-dependent manner. This is
      a focused mechanistic study of the PEX3-PEX19 docking interaction.
    action: MODIFY
    reason: This study specifically demonstrates the PEX3-PEX19 docking interaction in the context of PMP transport. 'Protein
      binding' should be replaced with the more informative adaptor activity term.
    proposed_replacement_terms:
    - id: GO:0030674
      label: protein-macromolecule adaptor activity
    supported_by:
    - reference_id: PMID:16280322
      supporting_text: Pex19p translocates the membrane peroxins from the cytosol to peroxisomes in an ATP- and Pex3p-dependent
        manner and then shuttles back to the cytosol
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:21102411
  review:
    summary: Sato et al. (2010) solved the crystal structure of the PEX3-PEX19 complex (2.50 A), revealing the structural
      basis of the docking interaction. The PEX19 peptide forms an alpha-helix at the apex of the PEX3 spheroid. This is a
      definitive structural characterization of the core PEX3 function.
    action: MODIFY
    reason: This landmark structural study defines the PEX3-PEX19 docking interface at atomic resolution. 'Protein binding'
      does not capture the specificity of this interaction. The adaptor activity term is more appropriate.
    proposed_replacement_terms:
    - id: GO:0030674
      label: protein-macromolecule adaptor activity
    supported_by:
    - reference_id: PMID:21102411
      supporting_text: we present the three-dimensional structure of the complex between a cytosolic domain of Pex3p and the
        binding-region peptide of Pex19p
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25416956
  review:
    summary: Rolland et al. (2014) is a proteome-scale interactome mapping study. Generic high-throughput protein binding
      annotation for PEX3 is uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: High-throughput interactome screen. 'Protein binding' from this study does not add specific functional information
      about PEX3 beyond what is already captured by more informative terms.
    supported_by:
    - reference_id: PMID:25416956
      supporting_text: A proteome-scale map of the human interactome network
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:25502805
  review:
    summary: Wei et al. (2014) is a massively parallel pipeline for cloning DNA variants and examining molecular phenotypes.
      High-throughput study providing generic protein binding annotation.
    action: MARK_AS_OVER_ANNOTATED
    reason: High-throughput methodology study. 'Protein binding' annotation from this pipeline is uninformative for PEX3 functional
      annotation.
    supported_by:
    - reference_id: PMID:25502805
      supporting_text: A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease
        mutations
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:27107012
  review:
    summary: Yachie et al. (2016) used Barcode Fusion Genetics for pooled-matrix protein interaction screens. High-throughput
      interaction data providing generic protein binding.
    action: MARK_AS_OVER_ANNOTATED
    reason: High-throughput interactome screen. Generic 'protein binding' is uninformative for PEX3.
    supported_by:
    - reference_id: PMID:27107012
      supporting_text: Pooled-matrix protein interaction screens using Barcode Fusion Genetics
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:28514442
  review:
    summary: Huttlin et al. (2017) is a large-scale interactome mapping study defining protein communities and disease networks.
      High-throughput data.
    action: MARK_AS_OVER_ANNOTATED
    reason: High-throughput interactome mapping. Generic 'protein binding' adds no specific insight into PEX3 function.
    supported_by:
    - reference_id: PMID:28514442
      supporting_text: Architecture of the human interactome defines protein communities and disease networks
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:29997244
  review:
    summary: Wehr et al. (2019) developed LuTHy, a bioluminescence-based two-hybrid technology for mapping protein-protein
      interactions. Methodological study providing generic protein binding data.
    action: MARK_AS_OVER_ANNOTATED
    reason: Method-development/high-throughput study. 'Protein binding' is uninformative for PEX3 function.
    supported_by:
    - reference_id: PMID:29997244
      supporting_text: 'LuTHy: a double-readout bioluminescence-based two-hybrid technology for quantitative mapping of protein-protein
        interactions in mammalian cells'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:31467278
  review:
    summary: Choi et al. (2019) is a study on maximizing binary interactome mapping efficiency. High-throughput methodology
      study.
    action: MARK_AS_OVER_ANNOTATED
    reason: High-throughput interactome methodology study. 'Protein binding' is uninformative.
    supported_by:
    - reference_id: PMID:31467278
      supporting_text: Maximizing binary interactome mapping with a minimal number of assays
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:31515488
  review:
    summary: Sahni et al. (2019) studied disruption of protein interactions by genetic variants. High-throughput interactome
      study.
    action: MARK_AS_OVER_ANNOTATED
    reason: High-throughput variant-interaction study. 'Protein binding' is uninformative for PEX3.
    supported_by:
    - reference_id: PMID:31515488
      supporting_text: Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum
        in human populations
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32296183
  review:
    summary: Luck et al. (2020) is a reference map of the human binary protein interactome. Large-scale high-throughput study.
    action: MARK_AS_OVER_ANNOTATED
    reason: High-throughput interactome reference map. 'Protein binding' is uninformative for PEX3.
    supported_by:
    - reference_id: PMID:32296183
      supporting_text: A reference map of the human binary protein interactome
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:32814053
  review:
    summary: Haenig et al. (2020) studied interactome mapping of neurodegenerative disease proteins. High-throughput interaction
      study.
    action: MARK_AS_OVER_ANNOTATED
    reason: High-throughput interactome mapping. 'Protein binding' is uninformative for PEX3.
    supported_by:
    - reference_id: PMID:32814053
      supporting_text: Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread
        Protein Aggregation in Affected Brains
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:33961781
  review:
    summary: Huttlin et al. (2021) mapped dual proteome-scale networks revealing cell-specific remodeling. High-throughput
      interactome study.
    action: MARK_AS_OVER_ANNOTATED
    reason: High-throughput interactome mapping. 'Protein binding' is uninformative for PEX3.
    supported_by:
    - reference_id: PMID:33961781
      supporting_text: Dual proteome-scale networks reveal cell-specific remodeling of the human interactome
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:35271311
  review:
    summary: Cho et al. (2022) is the OpenCell project using endogenous tagging for cellular organization cartography. High-throughput
      proteomics/imaging study.
    action: MARK_AS_OVER_ANNOTATED
    reason: High-throughput cellular organization mapping. 'Protein binding' is uninformative for PEX3.
    supported_by:
    - reference_id: PMID:35271311
      supporting_text: 'OpenCell: Endogenous tagging for the cartography of human cellular organization'
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:37398436
  review:
    summary: Duran-Frigola et al. (2023) used AI-guided pipeline for PPI drug discovery, focusing on SARS-CoV-2. High-throughput/computational
      study.
    action: MARK_AS_OVER_ANNOTATED
    reason: AI-guided drug discovery pipeline. 'Protein binding' is uninformative for PEX3 function.
    supported_by:
    - reference_id: PMID:37398436
      supporting_text: AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:38225382
  review:
    summary: Humphreys et al. (2024) used AlphaFold for systematic discovery of protein interaction interfaces. Computational/high-throughput
      study.
    action: MARK_AS_OVER_ANNOTATED
    reason: Computational high-throughput interaction interface study. 'Protein binding' is uninformative.
    supported_by:
    - reference_id: PMID:38225382
      supporting_text: Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:40205054
  review:
    summary: Huttlin et al. (2025) is a multimodal cell maps study for structural and functional genomics. High-throughput
      study.
    action: MARK_AS_OVER_ANNOTATED
    reason: High-throughput multimodal cellular mapping. 'Protein binding' is uninformative for PEX3.
    supported_by:
    - reference_id: PMID:40205054
      supporting_text: Multimodal cell maps as a foundation for structural and functional genomics
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: GO_REF:0000052
  review:
    summary: PEX3 localization to peroxisomes confirmed by immunofluorescence-based curation (GO_REF:0000052). This is consistent
      with extensive literature showing PEX3 at the peroxisomal membrane. However, the more specific term 'peroxisomal membrane'
      (GO:0005778) is also annotated and is more informative.
    action: ACCEPT
    reason: Correct localization, albeit less specific than peroxisomal membrane. Peroxisome is a valid parent localization
      term and the IDA evidence from immunofluorescence curation is appropriate.
    supported_by:
    - reference_id: PMID:10430017
      supporting_text: "H sPEX3 is an integral peroxisomal membrane protein with the N-terminus inside the peroxisome and the C-terminus facing the cytoplasm"
- term:
    id: GO:0016020
    label: membrane
  evidence_type: HDA
  original_reference_id: PMID:19946888
  review:
    summary: Ghosh et al. (2010) defined the membrane proteome of NK cells by mass spectrometry and detected PEX3 in the membrane
      fraction. The term 'membrane' is extremely generic for an established integral peroxisomal membrane protein.
    action: ACCEPT
    reason: While very generic, this HDA annotation from a proteomics study is not incorrect -- PEX3 is indeed an integral
      membrane protein. More specific peroxisomal membrane annotations exist. This is acceptable as a broad localization annotation
      from high-throughput data.
    supported_by:
    - reference_id: PMID:19946888
      supporting_text: Defining the membrane proteome of NK cells
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:18174172
  review:
    summary: Sato et al. (2008) characterized the PEX3-PEX19 interaction in detail using recombinant proteins, determining
      a KD of 3.4 nM and identifying Trp-104 as a critical binding residue. This is a focused mechanistic study of the core
      PEX3-PEX19 docking interaction.
    action: MODIFY
    reason: This study specifically characterizes the PEX3-PEX19 docking interaction at the biochemical level. 'Protein binding'
      should be replaced with the more informative adaptor activity term.
    proposed_replacement_terms:
    - id: GO:0030674
      label: protein-macromolecule adaptor activity
    supported_by:
    - reference_id: PMID:18174172
      supporting_text: the wild-type and the W104A and W104F mutants showed K(D) values of 3.4 nm, 1080 nm, and 66.2 nm, respectively
- term:
    id: GO:0007031
    label: peroxisome organization
  evidence_type: IMP
  original_reference_id: PMID:18174172
  review:
    summary: Sato et al. (2008) showed that PEX3 Trp-104 mutations that disrupted PEX19 binding also impaired peroxisome restoring
      activity in pex3-deficient cells, demonstrating that the PEX3-PEX19 interaction is required for peroxisome organization.
    action: ACCEPT
    reason: IMP evidence from mutational analysis showing that disrupting the PEX3-PEX19 interface impairs peroxisome biogenesis.
      This directly supports PEX3's role in peroxisome organization.
    supported_by:
    - reference_id: PMID:18174172
      supporting_text: The affinity differences with mutation affected their peroxisome restoring activities in pex3 ZPG208
        cells
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IDA
  original_reference_id: PMID:21768384
  review:
    summary: Yonekawa et al. (2011) showed that when Sec16B is overexpressed, PEX3 and PEX16 are redistributed from peroxisomes
      to ER membranes, and that Sec16B knockdown suppresses PEX3 expression. This indicates PEX3 transits through the ER during
      peroxisome biogenesis.
    action: KEEP_AS_NON_CORE
    reason: PEX3 transits through the ER during de novo peroxisome biogenesis, but the ER is not its primary steady-state
      location. The peroxisomal membrane is the core localization. ER localization represents a transient intermediate in
      the biogenesis pathway.
    supported_by:
    - reference_id: PMID:21768384
      supporting_text: Concomitant with the overexpression of Sec16B, peroxisomal membrane biogenesis factors peroxin 3 (Pex3)
        and Pex16 were redistributed from peroxisomes to Sec16B-positive ER membranes
- term:
    id: GO:0032991
    label: protein-containing complex
  evidence_type: IDA
  original_reference_id: PMID:18174172
  review:
    summary: Sato et al. (2008) demonstrated that PEX3 and PEX19 form a 1:1 monomeric complex by gel filtration chromatography.
      PEX3 exists in a complex with PEX19. However, 'protein-containing complex' is extremely generic and uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: While PEX3 does form a complex with PEX19, the term 'protein-containing complex' is too generic to be informative.
      The complex formation is better captured by the adaptor activity and peroxisome organization annotations.
    supported_by:
    - reference_id: PMID:18174172
      supporting_text: Gel filtration chromatography analyses and intrinsic tryptophan fluorescence titrations revealed that
        a one-to-one complex is formed between monomeric Pex3p and monomeric Pex19p
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: HDA
  original_reference_id: PMID:21525035
  review:
    summary: Bharti et al. (2011) isolated native peroxisomal membrane protein complexes from human cells using PEX14 as bait
      and identified PEX3 as a constituent of peroxisomal membrane complexes by mass spectrometry. This confirms PEX3 peroxisomal
      membrane localization via proteomics.
    action: ACCEPT
    reason: HDA evidence from native peroxisomal membrane complex isolation confirms PEX3 at the peroxisomal membrane, consistent
      with all other localization data.
    supported_by:
    - reference_id: PMID:21525035
      supporting_text: almost all known human peroxins involved in protein import were identified as constituents of the PEX14
        complexes
- term:
    id: GO:0007031
    label: peroxisome organization
  evidence_type: IMP
  original_reference_id: PMID:19479899
  review:
    summary: Toro et al. (2009) showed that Pex3p-GFP expressed in PEX3-deficient ZS cells (MR cell line) localizes first
      to the ER and then to newly formed peroxisomes, demonstrating PEX3 drives de novo peroxisome biogenesis from the ER.
    action: ACCEPT
    reason: IMP evidence showing PEX3 expression restores peroxisome formation in PEX3-deficient Zellweger cells, directly
      demonstrating PEX3's essential role in peroxisome organization.
    supported_by:
    - reference_id: PMID:19479899
      supporting_text: Pex3p-GFP expressed in a new ZS cell line (MR), which lacks peroxisomes due to a mutation in the PEX3
        gene, localizes first in the ER and subsequently in newly formed peroxisomes
- term:
    id: GO:0005783
    label: endoplasmic reticulum
  evidence_type: IDA
  original_reference_id: PMID:19479899
  review:
    summary: Toro et al. (2009) demonstrated by fluorescence microscopy that Pex3p-GFP localizes to the ER before redistributing
      to newly formed peroxisomes. An artificial N-glycosylation site confirmed ER targeting. This is the first demonstration
      of PEX3 ER transit in mammalian cells.
    action: KEEP_AS_NON_CORE
    reason: PEX3 transits through the ER during de novo peroxisome biogenesis, as directly observed by Toro et al. However,
      the ER is a transient intermediate, not the primary steady-state localization.
    supported_by:
    - reference_id: PMID:19479899
      supporting_text: Pex3p bearing an artificial N-glycosylation site shows an electrophoretic shift indicative of ER targeting
        while en route to preformed peroxisomes in normal fibroblast
- term:
    id: GO:0032994
    label: protein-lipid complex
  evidence_type: IDA
  original_reference_id: PMID:19715730
  review:
    summary: Pinto et al. (2009) showed that recombinant PEX3 cytosolic domain interacts with liposomes causing their flocculation
      or partial solubilization. This suggests a protein-lipid complex formation. However, this is an in vitro observation
      with recombinant protein and its physiological relevance is uncertain.
    action: UNDECIDED
    reason: The lipid interaction was observed in vitro with recombinant protein. While potentially relevant to PEX3's membrane
      insertion function, the physiological significance of a PEX3-lipid complex is not established. The study itself notes
      that the implications need further investigation.
    supported_by:
    - reference_id: PMID:19715730
      supporting_text: this recombinant protein actually precipitates when incubated with mild detergents, suggesting that
        this domain of PEX3 interacts with amphipathic molecules
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:19715730
  review:
    summary: Pinto et al. (2009) is primarily about PEX3 lipid binding, not protein-protein interactions. Any protein binding
      observation in this context is secondary and the generic term is uninformative.
    action: MARK_AS_OVER_ANNOTATED
    reason: This paper focuses on PEX3 lipid binding. 'Protein binding' annotation from this study is tangential and uninformative.
    supported_by:
    - reference_id: PMID:19715730
      supporting_text: The cytosolic domain of PEX3, a protein involved in the biogenesis of peroxisomes, binds membrane lipids
- term:
    id: GO:0008289
    label: lipid binding
  evidence_type: IDA
  original_reference_id: PMID:19715730
  review:
    summary: Pinto et al. (2009) demonstrated that recombinant PEX3 cytosolic domain binds liposomes strongly, causing flocculation
      or partial solubilization. This is an in vitro finding. Lipid binding may relate to PEX3's role in membrane insertion
      of PMPs but the physiological relevance is not firmly established.
    action: KEEP_AS_NON_CORE
    reason: The lipid binding activity was demonstrated in vitro and may reflect PEX3's membrane-associated function. However,
      lipid binding is not the primary characterized function of PEX3 (which is PEX19 docking/adaptor activity). This is a
      potential secondary activity.
    supported_by:
    - reference_id: PMID:19715730
      supporting_text: we tested this recombinant protein in lipid-binding assays and found that it interacts strongly with
        liposomes inducing their flocculation or even partial solubilization
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-382613
  review:
    summary: Reactome pathway annotation for PEX3 involvement in docking of ABCD1/D2/D3 (ABC transporters) to the peroxisomal
      membrane via PEX19. This is consistent with PEX3's role as the membrane docking factor for the PEX19-PMP import pathway.
    action: ACCEPT
    reason: Reactome correctly places PEX3 at the peroxisomal membrane in the context of ABC transporter PMP import. This
      is well supported by the established PEX3-PEX19 docking model.
    supported_by:
    - reference_id: PMID:15007061
      supporting_text: PEX3 is required for PEX19 to dock at peroxisomes
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9603775
  review:
    summary: Reactome pathway annotation for PEX3:PEX19:class I PMP complex dissociation at the peroxisomal membrane. This
      correctly places PEX3 at the peroxisomal membrane during PMP release.
    action: ACCEPT
    reason: Reactome correctly represents PEX3 at the peroxisomal membrane during the PMP insertion cycle.
    supported_by:
    - reference_id: PMID:15007061
      supporting_text: PEX3 is also sufficient to dock PEX19 at heterologous organelles
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: TAS
  original_reference_id: Reactome:R-HSA-9603784
  review:
    summary: Reactome pathway annotation for PEX19:class I PMP binding to PEX3 at the peroxisomal membrane. This correctly
      represents the docking step.
    action: ACCEPT
    reason: Reactome correctly represents PEX3 at the peroxisomal membrane during PEX19:PMP docking.
    supported_by:
    - reference_id: PMID:15007061
      supporting_text: PEX3 is required for PEX19 to dock at peroxisomes, interacts specifically with the docking domain of
        PEX19
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: IDA
  original_reference_id: PMID:10430017
  review:
    summary: Soukupova et al. (1999) identified and characterized human PEX3 as an integral peroxisomal membrane protein using
      N- and C-terminal tags and immunofluorescence microscopy. The N-terminus is inside the peroxisome and the C-terminus
      faces the cytoplasm.
    action: ACCEPT
    reason: Primary experimental evidence for PEX3 peroxisomal membrane localization by immunofluorescence. This is one of
      the foundational characterization studies of human PEX3.
    supported_by:
    - reference_id: PMID:10430017
      supporting_text: "H sPEX3 is an integral peroxisomal membrane protein with the N-terminus inside the peroxisome and the C-terminus facing the cytoplasm"
- term:
    id: GO:0005778
    label: peroxisomal membrane
  evidence_type: IDA
  original_reference_id: PMID:9657383
  review:
    summary: Kammerer et al. (1998) cloned human PEX3 and showed by transfection of epitope-tagged constructs and immunofluorescence
      that PEX3 is localized at the peroxisome. The N-terminal 40 amino acids were sufficient for peroxisomal targeting.
    action: ACCEPT
    reason: Original cloning and characterization of human PEX3 confirming peroxisomal localization. One of the first studies
      establishing PEX3 at the peroxisomal membrane.
    supported_by:
    - reference_id: PMID:9657383
      supporting_text: human Pex3p is localized at the peroxisome. The N-terminal 40 amino acids were revealed to be sufficient
        to target a GFP reporter protein to the peroxisome
- term:
    id: GO:0007031
    label: peroxisome organization
  evidence_type: IMP
  original_reference_id: PMID:10958759
  review:
    summary: Muntau et al. (2000) demonstrated that homozygous PEX3 mutations in two Zellweger syndrome patients (complementation
      group G) cause complete loss of peroxisomal membrane structures. Expression of wild-type PEX3 restored peroxisomal biogenesis,
      confirming PEX3 is required for peroxisome organization.
    action: ACCEPT
    reason: Definitive human genetic and complementation evidence that PEX3 is essential for peroxisome organization. Loss
      of PEX3 causes absence of detectable peroxisomes; re-expression restores them.
    supported_by:
    - reference_id: PMID:10958759
      supporting_text: Two patients assigned to complementation group G who had not been linked previously to a specific gene
        defect were confirmed as displaying a cellular phenotype characterized by a lack of even residual peroxisomal membrane
        structures
    - reference_id: PMID:10958759
      supporting_text: Expression of wild-type PEX3 in the mutant cell lines restored peroxisomal biogenesis, whereas transfection
        of mutated PEX3 cDNA did not
- term:
    id: GO:0045046
    label: protein import into peroxisome membrane
  evidence_type: IMP
  original_reference_id: PMID:15007061
  review:
    summary: Fang et al. (2004) demonstrated using PEX3 RNAi in human fibroblasts that PEX3 depletion specifically abrogates
      class I PMP import without affecting class II PMP import or matrix protein import. PEX3 is both necessary and sufficient
      for PEX19 docking at peroxisomes.
    action: ACCEPT
    reason: This is the key study establishing PEX3 as the PEX19 docking factor essential for class I PMP import. The IMP
      evidence from RNAi knockdown is strong and specific.
    supported_by:
    - reference_id: PMID:15007061
      supporting_text: transient inhibition of PEX3 abrogates class I PMP import but has no effect on class II PMP import
        or peroxisomal matrix protein import
    - reference_id: PMID:15007061
      supporting_text: PEX3 is required for PEX19 to dock at peroxisomes, interacts specifically with the docking domain of
        PEX19, and is required for recruitment of the PEX19 docking domain to peroxisomes. PEX3 is also sufficient to dock
        PEX19 at heterologous organelles
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IMP
  original_reference_id: PMID:12924628
  review:
    summary: Muntau et al. (2003) used FRET analysis to visualize the PEX3-PEX19 interaction in living cells and confirmed
      the peroxisome as the main intracellular site of this interaction. PEX3 expression in PEX3-deficient cells restored
      import-competent peroxisomes.
    action: ACCEPT
    reason: FRET analysis directly demonstrates PEX3 localization to peroxisomes and shows the PEX3-PEX19 interaction occurs
      primarily at peroxisomes. Consistent with all other localization data.
    supported_by:
    - reference_id: PMID:12924628
      supporting_text: the peroxisome was identified to be the main intracellular site of the PEX3-PEX19 interaction
- term:
    id: GO:0007031
    label: peroxisome organization
  evidence_type: IMP
  original_reference_id: PMID:12924628
  review:
    summary: Muntau et al. (2003) showed that transfection of tagged PEX3 into PEX3-deficient human fibroblasts from Zellweger
      patients led to reformation of import-competent peroxisomes, providing IMP evidence for PEX3's role in peroxisome organization.
    action: ACCEPT
    reason: Complementation of PEX3-deficient cells restoring peroxisome biogenesis is direct IMP evidence for PEX3's role
      in peroxisome organization.
    supported_by:
    - reference_id: PMID:12924628
      supporting_text: Functionality of the fusion proteins was shown by transfection of human PEX3- and PEX19-deficient fibroblasts
        from Zellweger patients with tagged versions of PEX3 and PEX19. This led to reformation of import-competent peroxisomes
        in both cell lines previously lacking detectable peroxisomal membrane structures
- term:
    id: GO:0005515
    label: protein binding
  evidence_type: IPI
  original_reference_id: PMID:11883941
  review:
    summary: Mayerhofer et al. (2002) studied two PEX19 splice variants and showed both interact with full-length PEX3 by
      in vitro protein interaction studies. This is a focused peroxin interaction study, not a generic high-throughput screen.
    action: MODIFY
    reason: The PEX19-PEX3 interaction documented here reflects PEX3's adaptor/docking function. 'Protein binding' should
      be replaced with the more informative adaptor activity term.
    proposed_replacement_terms:
    - id: GO:0030674
      label: protein-macromolecule adaptor activity
    supported_by:
    - reference_id: PMID:11883941
      supporting_text: Both interact with peroxisomal ABC transporters (ALDP, ALDRP, PMP70) and with full-length PEX3 as shown
        by in vitro protein interaction studies
- term:
    id: GO:0005777
    label: peroxisome
  evidence_type: IDA
  original_reference_id: PMID:9922452
  review:
    summary: South and Gould (1999) studied peroxisome synthesis in the absence of preexisting peroxisomes in PEX16-deficient
      cells. While this study primarily focuses on PEX16, PEX3 is contextualized as one of the few peroxins required for peroxisome
      membrane synthesis. The IDA for PEX3 peroxisome localization from this study may be indirect.
    action: ACCEPT
    reason: PEX3 is mentioned as a peroxisomal protein in this study. The localization is well established from other sources,
      and this annotation is consistent with the overall body of evidence.
    supported_by:
    - reference_id: PMID:9922452
      supporting_text: "other human PMPs, including PEX3myc (Kammerer et al., 1998), PEX10myc (Warren et al., 1998)"
references:
- id: GO_REF:0000033
  title: Annotation inferences using phylogenetic trees
  findings: []
- id: GO_REF:0000052
  title: Gene Ontology annotation based on curation of immunofluorescence data
  findings: []
- id: GO_REF:0000120
  title: Combined Automated Annotation using Multiple IEA Methods
  findings: []
- id: PMID:10430017
  title: Identification and characterization of the human peroxin PEX3.
  findings:
  - statement: PEX3 is an integral peroxisomal membrane protein with N-terminus inside peroxisome and C-terminus facing cytoplasm
  - statement: PEX19 interacts with PEX3 in mammalian two-hybrid assay
  - statement: N-terminal 33 amino acids are necessary and sufficient for peroxisomal targeting
- id: PMID:10704444
  title: PEX19 binds multiple peroxisomal membrane proteins, is predominantly cytoplasmic, and is required for peroxisome
    membrane synthesis.
  findings:
  - statement: PEX19 binds a broad spectrum of PMPs including PEX3
  - statement: PEX19 is predominantly cytoplasmic with a minor peroxisomal pool
  - statement: Loss of PEX19 results in PMP degradation or mislocalization
- id: PMID:10958759
  title: Defective peroxisome membrane synthesis due to mutations in human PEX3 causes Zellweger syndrome, complementation
    group G.
  findings:
  - statement: Homozygous PEX3 mutations cause Zellweger syndrome with complete absence of peroxisomal membrane structures
  - statement: Wild-type PEX3 expression restores peroxisomal biogenesis in mutant cells
  - statement: PEX3 is established as a key factor in early human peroxisome synthesis
- id: PMID:11883941
  title: Two splice variants of human PEX19 exhibit distinct functions in peroxisomal assembly.
  findings:
  - statement: Both PEX19 splice variants interact with full-length PEX3
  - statement: PEX19 domain structure is linked to specific interaction capabilities
- id: PMID:12096124
  title: Analysis of mammalian peroxin interactions using a non-transcription-based bacterial two-hybrid assay.
  findings:
  - statement: Detailed peroxin interaction map confirms PEX3-PEX19 interaction
  - statement: PEX19 farnesylation enhances affinity for some peroxins
- id: PMID:12924628
  title: The interaction between human PEX3 and PEX19 characterized by fluorescence resonance energy transfer (FRET) analysis.
  findings:
  - statement: FRET demonstrates PEX3-PEX19 interaction occurs primarily at peroxisomes
  - statement: Tagged PEX3 restores peroxisome biogenesis in PEX3-deficient Zellweger cells
- id: PMID:15007061
  title: PEX3 functions as a PEX19 docking factor in the import of class I peroxisomal membrane proteins.
  findings:
  - statement: PEX3 is the membrane docking factor for PEX19
  - statement: PEX3 depletion specifically blocks class I PMP import
  - statement: PEX3 is sufficient to dock PEX19 at heterologous organelles
  - statement: Conserved motif aa120-136 of PEX3 is essential for PEX19 binding
- id: PMID:16189514
  title: Towards a proteome-scale map of the human protein-protein interaction network.
  findings: []
- id: PMID:16280322
  title: In vitro transport of membrane proteins to peroxisomes by shuttling receptor Pex19p.
  findings:
  - statement: PEX19 translocates PMPs to peroxisomes in an ATP- and PEX3-dependent manner
  - statement: PEX19-PMP complexes bind to PEX3 in vitro
- id: PMID:18174172
  title: 'Characterization of the interaction between recombinant human peroxin Pex3p and Pex19p: identification of TRP-104
    IN Pex3p as a critical residue for the interaction.'
  findings:
  - statement: PEX3-PEX19 form a 1:1 complex with KD of 3.4 nM
  - statement: Trp-104 of PEX3 is critical for PEX19 binding
  - statement: PEX19 binding mutations impair peroxisome restoring activity
- id: PMID:19479899
  title: Pex3p-dependent peroxisomal biogenesis initiates in the endoplasmic reticulum of human fibroblasts.
  findings:
  - statement: PEX3 transits through the ER before reaching peroxisomes during de novo biogenesis
  - statement: PEX3 requires PEX16 for ER localization
  - statement: PEX3 can drive peroxisome biogenesis from the ER
- id: PMID:19715730
  title: The cytosolic domain of PEX3, a protein involved in the biogenesis of peroxisomes, binds membrane lipids.
  findings:
  - statement: Recombinant PEX3 cytosolic domain binds liposomes
  - statement: PEX3 interacts with amphipathic molecules
- id: PMID:19946888
  title: Defining the membrane proteome of NK cells.
  findings:
  - statement: PEX3 detected in membrane fraction of NK cells by mass spectrometry
- id: PMID:21102411
  title: Structural basis for docking of peroxisomal membrane protein carrier Pex19p onto its receptor Pex3p.
  findings:
  - statement: Crystal structure of PEX3-PEX19 complex at 2.50 A resolution
  - statement: PEX3 has a novel twisted six-helix bundle fold
  - statement: PEX19 binds at apex of PEX3 via an alpha-helix with leucine triad motif
- id: PMID:21525035
  title: PEX14 is required for microtubule-based peroxisome motility in human cells.
  findings:
  - statement: PEX3 identified as constituent of native PEX14 peroxisomal membrane complexes
- id: PMID:21768384
  title: Sec16B is involved in the endoplasmic reticulum export of the peroxisomal membrane biogenesis factor peroxin 16 (Pex16)
    in mammalian cells.
  findings:
  - statement: PEX3 redistributes to ER when Sec16B is overexpressed
  - statement: Sec16B knockdown suppresses PEX3 expression
- id: PMID:25416956
  title: A proteome-scale map of the human interactome network.
  findings: []
- id: PMID:25502805
  title: A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations.
  findings: []
- id: PMID:27107012
  title: Pooled-matrix protein interaction screens using Barcode Fusion Genetics.
  findings: []
- id: PMID:28514442
  title: Architecture of the human interactome defines protein communities and disease networks.
  findings: []
- id: PMID:29997244
  title: 'LuTHy: a double-readout bioluminescence-based two-hybrid technology for quantitative mapping of protein-protein
    interactions in mammalian cells.'
  findings: []
- id: PMID:31467278
  title: Maximizing binary interactome mapping with a minimal number of assays.
  findings: []
- id: PMID:31515488
  title: Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations.
  findings: []
- id: PMID:32296183
  title: A reference map of the human binary protein interactome.
  findings: []
- id: PMID:32814053
  title: Interactome Mapping Provides a Network of Neurodegenerative Disease Proteins and Uncovers Widespread Protein Aggregation
    in Affected Brains.
  findings: []
- id: PMID:33961781
  title: Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
  findings: []
- id: PMID:35271311
  title: 'OpenCell: Endogenous tagging for the cartography of human cellular organization.'
  findings: []
- id: PMID:37398436
  title: AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor.
  findings: []
- id: PMID:38225382
  title: Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation.
  findings: []
- id: PMID:40205054
  title: Multimodal cell maps as a foundation for structural and functional genomics.
  findings: []
- id: PMID:9657383
  title: Cloning and characterization of the gene encoding the human peroxisomal assembly protein Pex3p.
  findings:
  - statement: First cloning of human PEX3
  - statement: PEX3 localized to peroxisomes by immunofluorescence
  - statement: N-terminal 40 amino acids sufficient for targeting
- id: PMID:9922452
  title: Peroxisome synthesis in the absence of preexisting peroxisomes.
  findings:
  - statement: PEX3, PEX16, PEX19 are involved in peroxisome membrane synthesis
  - statement: Peroxisomes can form de novo
- id: Reactome:R-HSA-382613
  title: PEX-19 docks ABCD1/D2/D3 to peroximal membrane
  findings: []
- id: Reactome:R-HSA-9603775
  title: PEX3:PEX19:class I PMP dissociates
  findings: []
- id: Reactome:R-HSA-9603784
  title: PEX19:class I PMP binds PEX3
  findings: []

PEX3

Gene Description

Existing Annotations Review

References

Deep Research

Falcon

Research Report: Human PEX3 (UniProt P56589) — Functional Annotation, Mechanism, and Translational Relevance

0) Target verification (critical disambiguation)

1) Key concepts and definitions (current understanding)

1.1 Peroxisome biogenesis and “peroxins”

1.2 PEX3: primary molecular role

1.3 PEX19 and PEX16 (core partners and pathway context)

1.4 Class I vs. Class II peroxisomal membrane proteins (concept)

2) Protein function, mechanism, and subcellular localization

2.1 Localization and requirement for peroxisomes in human cells

2.2 Docking interaction with PEX19: structural basis

2.3 PEX3 trafficking and the PEX16-dependent import of full-length PEX3 (mammalian evidence)

2.4 Quantitative mechanistic data: stabilization and affinity

3) Biological processes and pathways involving PEX3

3.1 Peroxisomal membrane protein insertion and organelle biogenesis

3.2 De novo biogenesis models and ER involvement

3.3 Additional/non-canonical roles (emerging)

4) Recent developments (prioritizing 2023–2024)

4.1 2024: Live-cell imaging probes for peroxisomes validated in PEX3-deficient patient cells

4.2 2023: Targeting PEX3 in cancer metabolism and therapy resistance; PEX3–PEX19 inhibitor

4.3 2023: Updated expert synthesis on import and quality control

4.4 2024: Clinical genetics/prenatal diagnostic interpretation of PEX3 deletion risk

5) Current applications and real-world implementations

5.1 Clinical genetics: Zellweger spectrum disorder (ZSD) association and prenatal counseling

5.2 Cellular diagnostics / functional assays in patient-derived cells

5.3 Drug discovery: pathway inhibition via PEX3–PEX19 docking disruption

6) Expert opinions and analysis (authoritative interpretations)

6.1 Mechanistic consensus and remaining uncertainties

6.2 Systems-level implications

7) Relevant statistics and quantitative data (recent studies and key classic measurements)

7.1 Human disease statistics (2024 clinical genetics report)

7.2 Quantitative cell biology measurements (PEX3/PEX19/PEX16 pathway)

7.3 Quantitative proteomics with PEX3 depletion in human cells

7.4 Quantitative oncology model outcomes (PEX3 perturbation)

8) Consolidated functional annotation (high-confidence summary)

Summary Table (synthesis)

Visual evidence (structure/topology)

Citations

📄 View Raw YAML