{"gene":"PEX6","run_date":"2026-04-29T11:37:58","timeline":{"discoveries":[{"year":1996,"finding":"PEX6 (PXAAA1/PAF-2) encodes a cytoplasmic AAA-family ATPase required for peroxisomal protein import; substitution of the conserved lysine in the ATPase domain abolishes biological activity, and PEX6 is required for stability of the PTS1 receptor (Pxr1p/PEX5).","method":"Functional complementation in patient fibroblasts, ATPase domain mutagenesis (K→R), Western blot for PTS1 receptor stability","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1–2 — active-site mutagenesis plus functional complementation, replicated by independent group same year","pmids":["8670792"],"is_preprint":false},{"year":1996,"finding":"Human PEX6 (PAF-2) restores peroxisome assembly in fibroblasts from complementation group C Zellweger patients, confirming its essential role in peroxisome biogenesis.","method":"Functional complementation by cDNA transfection in patient-derived CHO and Zellweger fibroblasts","journal":"American journal of human genetics","confidence":"High","confidence_rationale":"Tier 2 — clean complementation assay, independently replicated across two papers same year","pmids":["8940266"],"is_preprint":false},{"year":1998,"finding":"PEX1 and PEX6 physically interact to form a complex essential for peroxisome biogenesis; overexpression of one suppresses loss-of-function alleles of the other in an allele-specific manner; the PEX1 G843D disease mutation attenuates the PEX1–PEX6 interaction.","method":"Yeast two-hybrid assay, in vitro binding (pulldown), allele-specific genetic suppression","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1–2 — genetic epistasis plus in vitro physical interaction, replicated across methods in one study","pmids":["9671729"],"is_preprint":false},{"year":2002,"finding":"In PEX6-deficient CHO cells, peroxisomal ghosts are complex double-membraned structures; upon complementation with PEX6 cDNA, these structures become import-competent and are converted into functional peroxisomes, establishing PEX6's role in enabling matrix protein import into pre-existing membrane structures.","method":"Genetic complementation, immunofluorescence microscopy, electron microscopy, GFP-PTS1 reporter, biochemical fractionation","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal imaging and biochemical methods in a single study","pmids":["11854424"],"is_preprint":false},{"year":2011,"finding":"AWP1/ZFAND6 interacts with PEX6 AAA ATPase (but not with PEX1–PEX6 complexes) and preferentially binds cysteine-monoubiquitinated PEX5 via its A20 zinc-finger domain; AWP1 stimulates PEX5 export from peroxisomes and is required for PTS1-protein import.","method":"In vitro Pex5 export assay, Co-IP, antibody inhibition, RNAi knockdown, PEX5 stability assay","journal":"Traffic (Copenhagen, Denmark)","confidence":"High","confidence_rationale":"Tier 2 — reciprocal binding assays plus functional in vitro export assay with multiple orthogonal approaches","pmids":["21980954"],"is_preprint":false},{"year":2015,"finding":"Cryo-EM structures of the Pex1/Pex6 complex reveal an unprecedented heterohexameric double ring in which Pex1 and Pex6 alternate; the N-terminal D1 ring is catalytically inactive and symmetric, while the C-terminal D2 ring is active and asymmetric; the N1 domain of Pex1 is mobile, suggesting coordinated subunit activity analogous to p97/NSF.","method":"Cryo-electron microscopy, computational domain fitting, Monte Carlo modeling with energy minimization","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 — cryo-EM structure with computational modeling validated against known AAA+ homologs","pmids":["26170309"],"is_preprint":false},{"year":2018,"finding":"The yeast Pex1/Pex6 complex is a protein translocase that unfolds its substrate Pex15 by processive threading through the central pore in a pore-loop-dependent and ATP-hydrolysis-dependent manner; Pex15 binds the N-terminal domains of Pex6 before its disordered C-terminal region engages the pore loops; Pex15 also directly binds the cargo receptor Pex5, linking Pex1/Pex6 to the import machinery.","method":"In vitro unfolding/translocation assay, cryo-EM of Pex1/Pex6–Pex15 complex, pulldown/binding assays, ATPase mutagenesis","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 — reconstituted in vitro translocase activity plus cryo-EM structure plus mutagenesis, multiple orthogonal approaches","pmids":["29321502"],"is_preprint":false},{"year":2018,"finding":"DTM-embedded monoubiquitinated PEX5 (Ub-PEX5) interacts directly with both PEX1 and PEX6 through its ubiquitin moiety, and the PEX5 polypeptide chain is globally unfolded during ATP-dependent extraction, establishing monoubiquitinated PEX5 as a bona fide substrate of the PEX1–PEX6 complex.","method":"Cell-free in vitro Pex5 export system, photoaffinity cross-linking, protein PEGylation assay","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 — reconstituted cell-free system with photoaffinity cross-linking and PEGylation as orthogonal unfolding readout","pmids":["29884772"],"is_preprint":false},{"year":2023,"finding":"CryoEM structures of S. cerevisiae Pex1/Pex6 with an endogenous substrate trapped in the D2 pore reveal that pairs of Pex1/Pex6 D2 subdomains engage substrate via a staircase of pore-1 loops; the inactive D1 ring undergoes ATP-hydrolysis-driven conformational changes; a 'twin-seam' Pex1/Pex6(D2) heterodimer disengages from the staircase to drive substrate translocation.","method":"Cryo-EM with endogenous substrate trapping, structural analysis of pore-loop contacts","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 1 — high-resolution cryo-EM with substrate-engaged complex revealing translocation mechanism","pmids":["37741838"],"is_preprint":false},{"year":2023,"finding":"The N1 domain of Pex6 mediates binding to the peroxisomal membrane tether Pex15 and to an extended loop from the D2 ATPase domain of Pex1 that stabilizes the Pex1/Pex6 heterohexamer; deletion of Pex6 N1 abolishes in vivo peroxisome function despite retaining ATPase activity in vitro.","method":"X-ray crystallography of isolated Pex6 N1 domain, cryo-EM of Pex1/Pex6, AlphaFold2 modeling, biochemical pulldown assays, in vivo complementation","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 — crystal structure plus cryo-EM plus biochemical binding assays plus in vivo functional test","pmids":["38036174"],"is_preprint":false},{"year":2014,"finding":"In S. cerevisiae, deficiency of the exportomer subunits Pex1, Pex6, and Pex15 causes enhanced pexophagy via the Atg36 receptor and Atg11 scaffold; accumulation of ubiquitinated peroxin receptors at the peroxisomal membrane does not, by itself, trigger pexophagy in yeast, as shown by genetic epistasis.","method":"Genetic deletion analysis (pex1Δ, atg1Δ, atg36 mutants), fluorescence microscopy of phagophore assembly sites, epistasis analysis","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 — clean genetic epistasis with imaging, single lab study","pmids":["24657987"],"is_preprint":false},{"year":2015,"finding":"PEX6 localizes to cilia of retinal photoreceptor cells and to the apical extensions of secretory ameloblasts and odontoblasts in mice, linking peroxisome biogenesis to photoreceptor ciliary function.","method":"Immunofluorescence microscopy in mouse tissues (retina, ameloblasts, odontoblasts)","journal":"Human mutation","confidence":"Medium","confidence_rationale":"Tier 3 — direct localization by immunofluorescence, single study, functional link inferred from patient phenotype","pmids":["26593283"],"is_preprint":false},{"year":2007,"finding":"In S. cerevisiae, extra copies of PEX6 suppress mitochondrial aging defects in an atp2 mutant by improving import kinetics of Atp2p into mitochondria, restoring normal mitochondrial inheritance; this function requires ATP binding and/or hydrolysis activity of Pex6p.","method":"Multicopy suppressor screen, mitochondrial protein import assay, ATPase mutant analysis, daughter-cell mitochondrial inheritance assay","journal":"Aging cell","confidence":"Medium","confidence_rationale":"Tier 2 — suppressor screen with biochemical follow-up, single lab","pmids":["17465979"],"is_preprint":false},{"year":2026,"finding":"Pex6 (together with ubiquitination of Pex5) regulates reversible ATP-dependent topological remodeling of the Pex14 N-terminal domain at the peroxisomal membrane: normally the Pex14 N terminus faces the lumen, but loss of Pex6 or Pex26, or inhibition of AAA+ ATPases, exposes it to the cytoplasm; blocking ubiquitin activation prevents this reorientation, linking Pex5 ubiquitination and Pex6-mediated extraction to structural reorganization of the docking–translocation complex.","method":"Immunofluorescence microscopy, protease protection assay, pharmacological inhibition of AAA+ ATPases (NEM), ubiquitin inhibitor (MLN-7243), Pex6/Pex26 knockdown/knockout","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 — multiple orthogonal biochemical and cell-biological approaches, single recent study","pmids":["41581879"],"is_preprint":false},{"year":2003,"finding":"In Hansenula polymorpha, a point mutation in the first AAA module of Pex6p (G737E) combined with a secondary mutation in the second AAA domain (R1000G) creates a cold-sensitive conditional allele, demonstrating that both AAA cassettes contribute functionally to peroxisome biogenesis.","method":"UV mutagenesis, intragenic suppressor analysis, sequencing, electron microscopy of peroxisomes","journal":"FEMS yeast research","confidence":"Low","confidence_rationale":"Tier 3 — single lab, single genetic approach in a non-standard yeast model","pmids":["14613878"],"is_preprint":false}],"current_model":"PEX6 is a cytoplasmic AAA+ ATPase that hetero-hexamerizes with PEX1 (alternating subunits in a double ring) and is recruited to the peroxisomal membrane via the tail-anchored tether PEX15/PEX26; the active D2 ring processively threads and unfolds monoubiquitinated PEX5 through its central pore using a staircase of pore-1 loops, thereby extracting PEX5 from the docking–translocation module and recycling it to the cytosol for further rounds of peroxisomal matrix protein import, while also dynamically remodeling the topology of the Pex14 docking component in an ATP- and ubiquitination-dependent manner."},"narrative":{"teleology":[{"year":1996,"claim":"Identification of PEX6 as a cytoplasmic AAA ATPase essential for peroxisome biogenesis and PTS1-receptor stability established the molecular identity of the gene defective in Zellweger complementation group C.","evidence":"Functional complementation in Zellweger patient fibroblasts and CHO cells, ATPase domain K→R mutagenesis, Western blot for PEX5 stability","pmids":["8670792","8940266"],"confidence":"High","gaps":["Whether PEX6 acts alone or requires a partner ATPase was unknown","The substrate of PEX6's ATPase activity was not identified","How PEX6 is recruited to peroxisomes was not determined"]},{"year":1998,"claim":"Demonstrating that PEX1 and PEX6 physically interact and that disease mutations weaken this interaction established the functional ATPase complex and explained genotype–phenotype relationships in peroxisome biogenesis disorders.","evidence":"Yeast two-hybrid, in vitro pulldown, allele-specific genetic suppression between PEX1 and PEX6","pmids":["9671729"],"confidence":"High","gaps":["Stoichiometry and architecture of the PEX1–PEX6 complex were unknown","The direct substrate of the complex had not been identified"]},{"year":2002,"claim":"Showing that PEX6 converts import-incompetent peroxisomal ghost membranes into functional peroxisomes demonstrated that PEX6 acts downstream of membrane assembly to enable matrix protein translocation.","evidence":"EM and immunofluorescence of PEX6-deficient CHO cells before and after complementation, GFP-PTS1 reporter","pmids":["11854424"],"confidence":"High","gaps":["The step at which PEX6 acts in the import cycle (receptor docking, translocation, or recycling) was not resolved","Whether PEX6 acts on PEX5 directly or indirectly was unclear"]},{"year":2011,"claim":"Identification of AWP1/ZFAND6 as a PEX6-binding cofactor that recognizes monoubiquitinated PEX5 and stimulates its export linked PEX6 function specifically to ubiquitin-dependent receptor recycling.","evidence":"Co-IP, in vitro PEX5 export assay, RNAi knockdown, antibody inhibition","pmids":["21980954"],"confidence":"High","gaps":["Whether AWP1 is essential in vivo or merely enhances export efficiency was not resolved","The mechanism by which AWP1 cooperates with the PEX1–PEX6 ATPase was not determined"]},{"year":2014,"claim":"Demonstrating that loss of Pex1/Pex6/Pex15 triggers enhanced pexophagy via Atg36 revealed that the exportomer's activity protects peroxisomes from autophagic degradation, explaining the peroxisome-loss phenotype in mutant cells.","evidence":"Genetic epistasis with atg1Δ and atg36 mutants, fluorescence microscopy in S. cerevisiae","pmids":["24657987"],"confidence":"Medium","gaps":["The pexophagy signal generated by exportomer deficiency was not molecularly defined","Whether this pexophagy mechanism is conserved in mammals was not tested"]},{"year":2015,"claim":"Cryo-EM structures revealed the unprecedented alternating PEX1–PEX6 heterohexameric double-ring architecture with a catalytically inactive D1 ring and an active asymmetric D2 ring, providing the structural framework for understanding substrate processing.","evidence":"Cryo-EM of the S. cerevisiae Pex1/Pex6 complex, computational domain fitting","pmids":["26170309"],"confidence":"High","gaps":["No substrate was captured in the pore, so the translocation mechanism remained hypothetical","How the complex engages the peroxisomal membrane was not structurally resolved"]},{"year":2018,"claim":"Reconstituted translocase activity and cryo-EM of substrate-engaged complexes established that PEX1/PEX6 is a processive protein unfoldase that threads substrates through its D2 pore via pore-loop contacts, with monoubiquitinated PEX5 as its bona fide physiological substrate.","evidence":"In vitro unfolding/translocation assay with Pex15, cryo-EM of Pex1/Pex6–Pex15 complex, cell-free PEX5 export with photoaffinity cross-linking and PEGylation unfolding readout","pmids":["29321502","29884772"],"confidence":"High","gaps":["The step-by-step nucleotide cycle driving translocation was not resolved","Whether PEX5 and PEX15 are threaded by the same or distinct mechanisms was unclear"]},{"year":2023,"claim":"High-resolution cryo-EM with endogenous substrate trapped in the pore revealed the twin-seam translocation mechanism and showed that the PEX6 N1 domain serves dual roles as membrane tether anchor and hexamer stabilizer, completing the structural model of the translocase.","evidence":"Cryo-EM with endogenous substrate trapping, X-ray crystallography of Pex6 N1, in vivo complementation of N1 deletion","pmids":["37741838","38036174"],"confidence":"High","gaps":["The identity of the endogenous substrate trapped in the pore was not determined","Structural basis of how PEX26 (mammalian tether) engages PEX6 N1 awaits high-resolution data","How the twin-seam mechanism coordinates with ubiquitin recognition is not resolved"]},{"year":2026,"claim":"Demonstrating that PEX6 and PEX5 ubiquitination jointly drive reversible topological remodeling of the PEX14 docking complex established that receptor extraction is mechanistically coupled to structural reorganization of the translocation channel.","evidence":"Protease protection assay, immunofluorescence, pharmacological AAA+ inhibition (NEM), ubiquitin inhibitor MLN-7243, PEX6/PEX26 knockdown","pmids":["41581879"],"confidence":"Medium","gaps":["Whether PEX14 remodeling is a cause or consequence of PEX5 extraction is not distinguished","The structural basis for PEX14 topology change at the membrane is unknown","Single study; independent confirmation is needed"]},{"year":null,"claim":"The precise nucleotide-driven conformational cycle that couples ATP hydrolysis in the D2 ring to stepwise substrate translocation, and how ubiquitin on PEX5 is recognized and processed during threading, remain structurally unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No time-resolved or single-molecule measurements of the translocation cycle exist","Structural basis of ubiquitin recognition by the PEX1–PEX6 pore is unknown","Role of the catalytically inactive D1 ring in allosteric regulation of translocation is not mechanistically defined"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140657","term_label":"ATP-dependent activity","supporting_discovery_ids":[0,5,6,7,8]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,6,8]},{"term_id":"GO:0044183","term_label":"protein folding chaperone","supporting_discovery_ids":[6,7,8]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0]},{"term_id":"GO:0005777","term_label":"peroxisome","supporting_discovery_ids":[3,9]},{"term_id":"GO:0005929","term_label":"cilium","supporting_discovery_ids":[11]}],"pathway":[{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,1,3,5,6]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[10]},{"term_id":"R-HSA-9609507","term_label":"Protein localization","supporting_discovery_ids":[6,7,13]}],"complexes":["PEX1–PEX6 heterohexamer"],"partners":["PEX1","PEX15","PEX26","PEX5","PEX14","AWP1"],"other_free_text":[]},"mechanistic_narrative":"PEX6 is a AAA+ ATPase that functions as an essential component of the peroxisomal matrix protein import machinery by powering the extraction and recycling of the cargo receptor PEX5 from the peroxisomal membrane. PEX6 forms an alternating heterohexameric double-ring complex with PEX1 in which the C-terminal D2 ring is catalytically active and processively threads monoubiquitinated PEX5 through its central pore via a staircase of pore-1 loops, globally unfolding the substrate during ATP-dependent extraction [PMID:29321502, PMID:37741838, PMID:29884772]. The N1 domain of PEX6 mediates recruitment to the peroxisomal membrane through binding the tail-anchored tether PEX15 (yeast)/PEX26 (mammals) and simultaneously stabilizes the PEX1–PEX6 hexamer by contacting an extended loop from the PEX1 D2 domain [PMID:38036174, PMID:26170309]. Loss of PEX6 function underlies peroxisome biogenesis disorders including Zellweger syndrome (complementation group C), and PEX6-dependent extraction of ubiquitinated PEX5 is coupled to dynamic topological remodeling of the PEX14 docking complex at the peroxisomal membrane [PMID:8940266, PMID:41581879]."},"prefetch_data":{"uniprot":{"accession":"Q13608","full_name":"Peroxisomal ATPase PEX6","aliases":["Peroxin-6","Peroxisomal biogenesis factor 6","Peroxisomal-type ATPase 1","Peroxisome assembly factor 2","PAF-2"],"length_aa":980,"mass_kda":104.1,"function":"Component of the PEX1-PEX6 AAA ATPase complex, a protein dislocase complex that mediates the ATP-dependent extraction of the PEX5 receptor from peroxisomal membranes, an essential step for PEX5 recycling (PubMed:16314507, PubMed:16854980, PubMed:21362118, PubMed:29884772). Specifically recognizes PEX5 monoubiquitinated at 'Cys-11', and pulls it out of the peroxisome lumen through the PEX2-PEX10-PEX12 retrotranslocation channel (PubMed:29884772). Extraction by the PEX1-PEX6 AAA ATPase complex is accompanied by unfolding of the TPR repeats and release of bound cargo from PEX5 (PubMed:29884772)","subcellular_location":"Cytoplasm, cytosol; Peroxisome membrane; Cell projection, cilium, photoreceptor outer segment","url":"https://www.uniprot.org/uniprotkb/Q13608/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PEX6","classification":"Not Classified","n_dependent_lines":187,"n_total_lines":1208,"dependency_fraction":0.15480132450331127},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/PEX6","total_profiled":1310},"omim":[{"mim_id":"619518","title":"MUSCULAR DYSTROPHY, CONGENITAL HEARING LOSS, AND OVARIAN INSUFFICIENCY SYNDROME; MDHLO","url":"https://www.omim.org/entry/619518"},{"mim_id":"616617","title":"HEIMLER SYNDROME 2; HMLR2","url":"https://www.omim.org/entry/616617"},{"mim_id":"614885","title":"PEROXISOME BIOGENESIS DISORDER 11B; PBD11B","url":"https://www.omim.org/entry/614885"},{"mim_id":"614870","title":"PEROXISOME BIOGENESIS DISORDER 6A (ZELLWEGER); PBD6A","url":"https://www.omim.org/entry/614870"},{"mim_id":"614863","title":"PEROXISOME BIOGENESIS DISORDER 4B; PBD4B","url":"https://www.omim.org/entry/614863"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Golgi apparatus","reliability":"Approved"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"pancreas","ntpm":71.9}],"url":"https://www.proteinatlas.org/search/PEX6"},"hgnc":{"alias_symbol":["PXAAA1","PAF-2"],"prev_symbol":[]},"alphafold":{"accession":"Q13608","domains":[{"cath_id":"-","chopping":"1-62_69-106","consensus_level":"medium","plddt":33.2914,"start":1,"end":106},{"cath_id":"2.40.40.20","chopping":"191-294","consensus_level":"medium","plddt":63.0966,"start":191,"end":294},{"cath_id":"3.10.330.10","chopping":"319-414","consensus_level":"medium","plddt":75.9725,"start":319,"end":414},{"cath_id":"3.40.50.300","chopping":"437-591","consensus_level":"high","plddt":79.9297,"start":437,"end":591},{"cath_id":"1.10.8.60","chopping":"597-654_671-690","consensus_level":"medium","plddt":84.5042,"start":597,"end":690},{"cath_id":"3.40.50.300","chopping":"696-868","consensus_level":"high","plddt":82.4492,"start":696,"end":868},{"cath_id":"1.10.8.60","chopping":"875-961","consensus_level":"high","plddt":87.7785,"start":875,"end":961}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13608","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q13608-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q13608-F1-predicted_aligned_error_v6.png","plddt_mean":69.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PEX6","jax_strain_url":"https://www.jax.org/strain/search?query=PEX6"},"sequence":{"accession":"Q13608","fasta_url":"https://rest.uniprot.org/uniprotkb/Q13608.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q13608/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q13608"}},"corpus_meta":[{"pmid":"8670792","id":"PMC_8670792","title":"The peroxisome biogenesis disorder group 4 gene, PXAAA1, encodes a cytoplasmic ATPase required for stability of the PTS1 receptor.","date":"1996","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/8670792","citation_count":165,"is_preprint":false},{"pmid":"9671729","id":"PMC_9671729","title":"Disruption of a PEX1-PEX6 interaction is the most common cause of the neurologic disorders Zellweger syndrome, neonatal adrenoleukodystrophy, and infantile Refsum disease.","date":"1998","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/9671729","citation_count":105,"is_preprint":false},{"pmid":"8940266","id":"PMC_8940266","title":"Human peroxisome assembly factor-2 (PAF-2): a gene responsible for group C peroxisome biogenesis disorder in humans.","date":"1996","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/8940266","citation_count":96,"is_preprint":false},{"pmid":"21487094","id":"PMC_21487094","title":"Arabidopsis ABERRANT PEROXISOME MORPHOLOGY9 is a peroxin that recruits the PEX1-PEX6 complex to peroxisomes.","date":"2011","source":"The Plant cell","url":"https://pubmed.ncbi.nlm.nih.gov/21487094","citation_count":73,"is_preprint":false},{"pmid":"26170309","id":"PMC_26170309","title":"Unique double-ring structure of the peroxisomal Pex1/Pex6 ATPase complex revealed by cryo-electron microscopy.","date":"2015","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/26170309","citation_count":68,"is_preprint":false},{"pmid":"11873320","id":"PMC_11873320","title":"A PEX6-defective peroxisomal biogenesis disorder with severe phenotype in an infant, versus mild phenotype resembling Usher syndrome in the affected parents.","date":"2002","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/11873320","citation_count":59,"is_preprint":false},{"pmid":"24657987","id":"PMC_24657987","title":"Deficiency of the exportomer components Pex1, Pex6, and Pex15 causes enhanced pexophagy in Saccharomyces cerevisiae.","date":"2014","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/24657987","citation_count":57,"is_preprint":false},{"pmid":"29321502","id":"PMC_29321502","title":"The peroxisomal AAA-ATPase Pex1/Pex6 unfolds substrates by processive threading.","date":"2018","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/29321502","citation_count":52,"is_preprint":false},{"pmid":"17544464","id":"PMC_17544464","title":"Jasmonate biosynthesis in Arabidopsis thaliana requires peroxisomal beta-oxidation enzymes--additional proof by properties of pex6 and aim1.","date":"2007","source":"Phytochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/17544464","citation_count":47,"is_preprint":false},{"pmid":"21980954","id":"PMC_21980954","title":"AWP1/ZFAND6 functions in Pex5 export by interacting with cys-monoubiquitinated Pex5 and Pex6 AAA ATPase.","date":"2011","source":"Traffic (Copenhagen, Denmark)","url":"https://pubmed.ncbi.nlm.nih.gov/21980954","citation_count":46,"is_preprint":false},{"pmid":"29220678","id":"PMC_29220678","title":"Allelic Expression Imbalance Promoting a Mutant PEX6 Allele Causes Zellweger Spectrum Disorder.","date":"2017","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/29220678","citation_count":41,"is_preprint":false},{"pmid":"29884772","id":"PMC_29884772","title":"Peroxisomal monoubiquitinated PEX5 interacts with the AAA ATPases PEX1 and PEX6 and is unfolded during its dislocation into the cytosol.","date":"2018","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/29884772","citation_count":39,"is_preprint":false},{"pmid":"17041890","id":"PMC_17041890","title":"Identification of novel mutations in PEX2, PEX6, PEX10, PEX12, and PEX13 in Zellweger spectrum patients.","date":"2006","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/17041890","citation_count":39,"is_preprint":false},{"pmid":"16388862","id":"PMC_16388862","title":"Identification and characterization of three peroxins--PEX6, PEX10 and PEX12--involved in glycosome biogenesis in Trypanosoma brucei.","date":"2005","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/16388862","citation_count":37,"is_preprint":false},{"pmid":"26593283","id":"PMC_26593283","title":"PEX6 is Expressed in Photoreceptor Cilia and Mutated in Deafblindness with Enamel Dysplasia and Microcephaly.","date":"2015","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/26593283","citation_count":34,"is_preprint":false},{"pmid":"19877282","id":"PMC_19877282","title":"Spectrum of PEX6 mutations in Zellweger syndrome spectrum patients.","date":"2010","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/19877282","citation_count":32,"is_preprint":false},{"pmid":"22894767","id":"PMC_22894767","title":"A founder mutation in the PEX6 gene is responsible for increased incidence of Zellweger syndrome in a French Canadian population.","date":"2012","source":"BMC medical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/22894767","citation_count":32,"is_preprint":false},{"pmid":"10408779","id":"PMC_10408779","title":"Genomic structure and identification of 11 novel mutations of the PEX6 (peroxisome assembly factor-2) gene in patients with peroxisome biogenesis disorders.","date":"1999","source":"Human mutation","url":"https://pubmed.ncbi.nlm.nih.gov/10408779","citation_count":25,"is_preprint":false},{"pmid":"17465979","id":"PMC_17465979","title":"A novel role of peroxin PEX6: suppression of aging defects in mitochondria.","date":"2007","source":"Aging cell","url":"https://pubmed.ncbi.nlm.nih.gov/17465979","citation_count":24,"is_preprint":false},{"pmid":"11854424","id":"PMC_11854424","title":"Peroxisomes are formed from complex membrane structures in PEX6-deficient CHO cells upon genetic complementation.","date":"2002","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/11854424","citation_count":23,"is_preprint":false},{"pmid":"28430524","id":"PMC_28430524","title":"miRNA-Related Polymorphisms in miR-423 (rs6505162) and PEX6 (rs1129186) and Risk of Esophageal Squamous Cell Carcinoma in an Iranian Cohort.","date":"2017","source":"Genetic testing and molecular biomarkers","url":"https://pubmed.ncbi.nlm.nih.gov/28430524","citation_count":23,"is_preprint":false},{"pmid":"31374812","id":"PMC_31374812","title":"Structural Mapping of Missense Mutations in the Pex1/Pex6 Complex.","date":"2019","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/31374812","citation_count":20,"is_preprint":false},{"pmid":"11004248","id":"PMC_11004248","title":"Temperature-sensitive mutation of PEX6 in peroxisome biogenesis disorders in complementation group C (CG-C): comparative study of PEX6 and PEX1.","date":"2000","source":"Pediatric research","url":"https://pubmed.ncbi.nlm.nih.gov/11004248","citation_count":19,"is_preprint":false},{"pmid":"28600347","id":"PMC_28600347","title":"The PEX1 ATPase Stabilizes PEX6 and Plays Essential Roles in Peroxisome Biology.","date":"2017","source":"Plant physiology","url":"https://pubmed.ncbi.nlm.nih.gov/28600347","citation_count":17,"is_preprint":false},{"pmid":"29555730","id":"PMC_29555730","title":"A pex1 missense mutation improves peroxisome function in a subset of Arabidopsis pex6 mutants without restoring PEX5 recycling.","date":"2018","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/29555730","citation_count":17,"is_preprint":false},{"pmid":"25079577","id":"PMC_25079577","title":"Late-onset Zellweger spectrum disorder caused by PEX6 mutations mimicking X-linked adrenoleukodystrophy.","date":"2014","source":"Pediatric neurology","url":"https://pubmed.ncbi.nlm.nih.gov/25079577","citation_count":17,"is_preprint":false},{"pmid":"28742939","id":"PMC_28742939","title":"Disparate peroxisome-related defects in Arabidopsis pex6 and pex26 mutants link peroxisomal retrotranslocation and oil body utilization.","date":"2017","source":"The Plant journal : for cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/28742939","citation_count":16,"is_preprint":false},{"pmid":"37741838","id":"PMC_37741838","title":"Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate.","date":"2023","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/37741838","citation_count":15,"is_preprint":false},{"pmid":"29676688","id":"PMC_29676688","title":"Ophthalmic manifestations of Heimler syndrome due to PEX6 mutations.","date":"2018","source":"Ophthalmic genetics","url":"https://pubmed.ncbi.nlm.nih.gov/29676688","citation_count":15,"is_preprint":false},{"pmid":"29047053","id":"PMC_29047053","title":"Mild Zellweger syndrome due to a novel PEX6 mutation: correlation between clinical phenotype and in silico prediction of variant pathogenicity.","date":"2017","source":"Journal of applied genetics","url":"https://pubmed.ncbi.nlm.nih.gov/29047053","citation_count":13,"is_preprint":false},{"pmid":"31652724","id":"PMC_31652724","title":"A Mechanistic Perspective on PEX1 and PEX6, Two AAA+ Proteins of the Peroxisomal Protein Import Machinery.","date":"2019","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/31652724","citation_count":12,"is_preprint":false},{"pmid":"32214787","id":"PMC_32214787","title":"Exome sequencing identifies PEX6 mutations in three cases diagnosed with Retinitis Pigmentosa and hearing impairment.","date":"2020","source":"Molecular vision","url":"https://pubmed.ncbi.nlm.nih.gov/32214787","citation_count":8,"is_preprint":false},{"pmid":"36249295","id":"PMC_36249295","title":"PEX6 Mutations in Peroxisomal Biogenesis Disorders: An Usher Syndrome Mimic.","date":"2021","source":"Ophthalmology science","url":"https://pubmed.ncbi.nlm.nih.gov/36249295","citation_count":8,"is_preprint":false},{"pmid":"31555682","id":"PMC_31555682","title":"Two novel mutations of PEX6 in one Chinese Zellweger spectrum disorder and their clinical characteristics.","date":"2019","source":"Annals of translational medicine","url":"https://pubmed.ncbi.nlm.nih.gov/31555682","citation_count":7,"is_preprint":false},{"pmid":"34631344","id":"PMC_34631344","title":"RNAi-mediated silencing of PEX6 and GAS1 genes of Fusarium oxysporum f. sp. lycopersici confers resistance against Fusarium wilt in tomato.","date":"2021","source":"3 Biotech","url":"https://pubmed.ncbi.nlm.nih.gov/34631344","citation_count":6,"is_preprint":false},{"pmid":"38036174","id":"PMC_38036174","title":"The N1 domain of the peroxisomal AAA-ATPase Pex6 is required for Pex15 binding and proper assembly with Pex1.","date":"2023","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/38036174","citation_count":5,"is_preprint":false},{"pmid":"11389979","id":"PMC_11389979","title":"Identification and characterisation of PEX6 orthologues from plants.","date":"2001","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/11389979","citation_count":5,"is_preprint":false},{"pmid":"36980088","id":"PMC_36980088","title":"PEX6 Mutation in a Child with Infantile Refsum Disease-A Case Report and Literature Review.","date":"2023","source":"Children (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/36980088","citation_count":3,"is_preprint":false},{"pmid":"28033303","id":"PMC_28033303","title":"Strong cis-acting expression quantitative trait loci for the genes encoding SNHG5 and PEX6.","date":"2016","source":"Medicine","url":"https://pubmed.ncbi.nlm.nih.gov/28033303","citation_count":3,"is_preprint":false},{"pmid":"37842507","id":"PMC_37842507","title":"Zellweger's Syndrome With PEX6 Gene Mutation in Mixteco Neonates Due to Possible Founder Effect.","date":"2023","source":"Cureus","url":"https://pubmed.ncbi.nlm.nih.gov/37842507","citation_count":1,"is_preprint":false},{"pmid":"39013483","id":"PMC_39013483","title":"A novel splice variant in intron 10 of PEX6 is associated with Zellweger Syndrome in a Chinese neonate.","date":"2024","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/39013483","citation_count":1,"is_preprint":false},{"pmid":"14613878","id":"PMC_14613878","title":"Identification of intragenic mutations in the Hansenula polymorpha PEX6 gene that affect peroxisome biogenesis and methylotrophic growth.","date":"2003","source":"FEMS yeast research","url":"https://pubmed.ncbi.nlm.nih.gov/14613878","citation_count":1,"is_preprint":false},{"pmid":"41581879","id":"PMC_41581879","title":"Pex6 and ubiquitination regulate topological remodeling of the peroxisomal membrane protein Pex14.","date":"2026","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/41581879","citation_count":0,"is_preprint":false},{"pmid":"37745580","id":"PMC_37745580","title":"The Pex6 N1 domain is required for Pex15 binding and proper assembly with Pex1.","date":"2023","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/37745580","citation_count":0,"is_preprint":false},{"pmid":"41787707","id":"PMC_41787707","title":"Unraveling PEX6: insights into very-long-chain fatty acid levels and peroxisome biogenesis disorders in pediatric populations.","date":"2026","source":"Annals of pediatric endocrinology & metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/41787707","citation_count":0,"is_preprint":false},{"pmid":"36952198","id":"PMC_36952198","title":"Purification of a Recombinant Human PEX1/PEX6 AAA+ ATPase Complex from HEK293TT Cells.","date":"2023","source":"Methods in molecular biology (Clifton, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/36952198","citation_count":0,"is_preprint":false},{"pmid":"38154976","id":"PMC_38154976","title":"[Zellweger syndrome caused by PEX6 gene variation in 2 cases and literature review].","date":"2024","source":"Zhonghua er ke za zhi = Chinese journal of pediatrics","url":"https://pubmed.ncbi.nlm.nih.gov/38154976","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.10.03.680009","title":"Identification of small molecule inhibitors of <i>Trypanosoma</i> PEX15– PEX6 interaction","date":"2025-10-04","source":"bioRxiv","url":"https://doi.org/10.1101/2025.10.03.680009","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.10.14.682039","title":"<i>ATAD1</i> Overexpression Enhances Mitochondrial and Peroxisomal Function in Zellweger Syndrome Disorder Models","date":"2025-10-15","source":"bioRxiv","url":"https://doi.org/10.1101/2025.10.14.682039","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.12.10.627778","title":"PEX1<sup>G843D</sup>remains functional in peroxisome biogenesis but is rapidly degraded by the proteasome","date":"2024-12-13","source":"bioRxiv","url":"https://doi.org/10.1101/2024.12.10.627778","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.08.01.25332822","title":"Genetically determined platelet traits impact stroke risk through multiple mechanisms and cell types","date":"2025-08-05","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.01.25332822","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.11.06.622258","title":"Complementation of a human disease phenotype in vitro by intercellular mRNA transfer","date":"2024-11-06","source":"bioRxiv","url":"https://doi.org/10.1101/2024.11.06.622258","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2024.12.20.629653","title":"Single Cell Transcriptomic Modelling of the Fallopian Tube Epithelium Identifies Cellular Specialisation, Novel Differentiation Trajectories, and Gene Network Associations with Ectopic Pregnancy","date":"2024-12-20","source":"bioRxiv","url":"https://doi.org/10.1101/2024.12.20.629653","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":27524,"output_tokens":3653,"usd":0.068683},"stage2":{"model":"claude-opus-4-6","input_tokens":7079,"output_tokens":2867,"usd":0.160605},"total_usd":0.229288,"stage1_batch_id":"msgbatch_012ZiiCUBfB62NCTQd4Bk1Jo","stage2_batch_id":"msgbatch_01Xuqq9aUHoQouS7UVGZNStZ","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1996,\n      \"finding\": \"PEX6 (PXAAA1/PAF-2) encodes a cytoplasmic AAA-family ATPase required for peroxisomal protein import; substitution of the conserved lysine in the ATPase domain abolishes biological activity, and PEX6 is required for stability of the PTS1 receptor (Pxr1p/PEX5).\",\n      \"method\": \"Functional complementation in patient fibroblasts, ATPase domain mutagenesis (K→R), Western blot for PTS1 receptor stability\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — active-site mutagenesis plus functional complementation, replicated by independent group same year\",\n      \"pmids\": [\"8670792\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Human PEX6 (PAF-2) restores peroxisome assembly in fibroblasts from complementation group C Zellweger patients, confirming its essential role in peroxisome biogenesis.\",\n      \"method\": \"Functional complementation by cDNA transfection in patient-derived CHO and Zellweger fibroblasts\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — clean complementation assay, independently replicated across two papers same year\",\n      \"pmids\": [\"8940266\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1998,\n      \"finding\": \"PEX1 and PEX6 physically interact to form a complex essential for peroxisome biogenesis; overexpression of one suppresses loss-of-function alleles of the other in an allele-specific manner; the PEX1 G843D disease mutation attenuates the PEX1–PEX6 interaction.\",\n      \"method\": \"Yeast two-hybrid assay, in vitro binding (pulldown), allele-specific genetic suppression\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — genetic epistasis plus in vitro physical interaction, replicated across methods in one study\",\n      \"pmids\": [\"9671729\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"In PEX6-deficient CHO cells, peroxisomal ghosts are complex double-membraned structures; upon complementation with PEX6 cDNA, these structures become import-competent and are converted into functional peroxisomes, establishing PEX6's role in enabling matrix protein import into pre-existing membrane structures.\",\n      \"method\": \"Genetic complementation, immunofluorescence microscopy, electron microscopy, GFP-PTS1 reporter, biochemical fractionation\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal imaging and biochemical methods in a single study\",\n      \"pmids\": [\"11854424\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"AWP1/ZFAND6 interacts with PEX6 AAA ATPase (but not with PEX1–PEX6 complexes) and preferentially binds cysteine-monoubiquitinated PEX5 via its A20 zinc-finger domain; AWP1 stimulates PEX5 export from peroxisomes and is required for PTS1-protein import.\",\n      \"method\": \"In vitro Pex5 export assay, Co-IP, antibody inhibition, RNAi knockdown, PEX5 stability assay\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal binding assays plus functional in vitro export assay with multiple orthogonal approaches\",\n      \"pmids\": [\"21980954\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Cryo-EM structures of the Pex1/Pex6 complex reveal an unprecedented heterohexameric double ring in which Pex1 and Pex6 alternate; the N-terminal D1 ring is catalytically inactive and symmetric, while the C-terminal D2 ring is active and asymmetric; the N1 domain of Pex1 is mobile, suggesting coordinated subunit activity analogous to p97/NSF.\",\n      \"method\": \"Cryo-electron microscopy, computational domain fitting, Monte Carlo modeling with energy minimization\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — cryo-EM structure with computational modeling validated against known AAA+ homologs\",\n      \"pmids\": [\"26170309\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"The yeast Pex1/Pex6 complex is a protein translocase that unfolds its substrate Pex15 by processive threading through the central pore in a pore-loop-dependent and ATP-hydrolysis-dependent manner; Pex15 binds the N-terminal domains of Pex6 before its disordered C-terminal region engages the pore loops; Pex15 also directly binds the cargo receptor Pex5, linking Pex1/Pex6 to the import machinery.\",\n      \"method\": \"In vitro unfolding/translocation assay, cryo-EM of Pex1/Pex6–Pex15 complex, pulldown/binding assays, ATPase mutagenesis\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — reconstituted in vitro translocase activity plus cryo-EM structure plus mutagenesis, multiple orthogonal approaches\",\n      \"pmids\": [\"29321502\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"DTM-embedded monoubiquitinated PEX5 (Ub-PEX5) interacts directly with both PEX1 and PEX6 through its ubiquitin moiety, and the PEX5 polypeptide chain is globally unfolded during ATP-dependent extraction, establishing monoubiquitinated PEX5 as a bona fide substrate of the PEX1–PEX6 complex.\",\n      \"method\": \"Cell-free in vitro Pex5 export system, photoaffinity cross-linking, protein PEGylation assay\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — reconstituted cell-free system with photoaffinity cross-linking and PEGylation as orthogonal unfolding readout\",\n      \"pmids\": [\"29884772\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"CryoEM structures of S. cerevisiae Pex1/Pex6 with an endogenous substrate trapped in the D2 pore reveal that pairs of Pex1/Pex6 D2 subdomains engage substrate via a staircase of pore-1 loops; the inactive D1 ring undergoes ATP-hydrolysis-driven conformational changes; a 'twin-seam' Pex1/Pex6(D2) heterodimer disengages from the staircase to drive substrate translocation.\",\n      \"method\": \"Cryo-EM with endogenous substrate trapping, structural analysis of pore-loop contacts\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — high-resolution cryo-EM with substrate-engaged complex revealing translocation mechanism\",\n      \"pmids\": [\"37741838\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"The N1 domain of Pex6 mediates binding to the peroxisomal membrane tether Pex15 and to an extended loop from the D2 ATPase domain of Pex1 that stabilizes the Pex1/Pex6 heterohexamer; deletion of Pex6 N1 abolishes in vivo peroxisome function despite retaining ATPase activity in vitro.\",\n      \"method\": \"X-ray crystallography of isolated Pex6 N1 domain, cryo-EM of Pex1/Pex6, AlphaFold2 modeling, biochemical pulldown assays, in vivo complementation\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — crystal structure plus cryo-EM plus biochemical binding assays plus in vivo functional test\",\n      \"pmids\": [\"38036174\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"In S. cerevisiae, deficiency of the exportomer subunits Pex1, Pex6, and Pex15 causes enhanced pexophagy via the Atg36 receptor and Atg11 scaffold; accumulation of ubiquitinated peroxin receptors at the peroxisomal membrane does not, by itself, trigger pexophagy in yeast, as shown by genetic epistasis.\",\n      \"method\": \"Genetic deletion analysis (pex1Δ, atg1Δ, atg36 mutants), fluorescence microscopy of phagophore assembly sites, epistasis analysis\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — clean genetic epistasis with imaging, single lab study\",\n      \"pmids\": [\"24657987\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"PEX6 localizes to cilia of retinal photoreceptor cells and to the apical extensions of secretory ameloblasts and odontoblasts in mice, linking peroxisome biogenesis to photoreceptor ciliary function.\",\n      \"method\": \"Immunofluorescence microscopy in mouse tissues (retina, ameloblasts, odontoblasts)\",\n      \"journal\": \"Human mutation\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — direct localization by immunofluorescence, single study, functional link inferred from patient phenotype\",\n      \"pmids\": [\"26593283\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"In S. cerevisiae, extra copies of PEX6 suppress mitochondrial aging defects in an atp2 mutant by improving import kinetics of Atp2p into mitochondria, restoring normal mitochondrial inheritance; this function requires ATP binding and/or hydrolysis activity of Pex6p.\",\n      \"method\": \"Multicopy suppressor screen, mitochondrial protein import assay, ATPase mutant analysis, daughter-cell mitochondrial inheritance assay\",\n      \"journal\": \"Aging cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — suppressor screen with biochemical follow-up, single lab\",\n      \"pmids\": [\"17465979\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Pex6 (together with ubiquitination of Pex5) regulates reversible ATP-dependent topological remodeling of the Pex14 N-terminal domain at the peroxisomal membrane: normally the Pex14 N terminus faces the lumen, but loss of Pex6 or Pex26, or inhibition of AAA+ ATPases, exposes it to the cytoplasm; blocking ubiquitin activation prevents this reorientation, linking Pex5 ubiquitination and Pex6-mediated extraction to structural reorganization of the docking–translocation complex.\",\n      \"method\": \"Immunofluorescence microscopy, protease protection assay, pharmacological inhibition of AAA+ ATPases (NEM), ubiquitin inhibitor (MLN-7243), Pex6/Pex26 knockdown/knockout\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal biochemical and cell-biological approaches, single recent study\",\n      \"pmids\": [\"41581879\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"In Hansenula polymorpha, a point mutation in the first AAA module of Pex6p (G737E) combined with a secondary mutation in the second AAA domain (R1000G) creates a cold-sensitive conditional allele, demonstrating that both AAA cassettes contribute functionally to peroxisome biogenesis.\",\n      \"method\": \"UV mutagenesis, intragenic suppressor analysis, sequencing, electron microscopy of peroxisomes\",\n      \"journal\": \"FEMS yeast research\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — single lab, single genetic approach in a non-standard yeast model\",\n      \"pmids\": [\"14613878\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PEX6 is a cytoplasmic AAA+ ATPase that hetero-hexamerizes with PEX1 (alternating subunits in a double ring) and is recruited to the peroxisomal membrane via the tail-anchored tether PEX15/PEX26; the active D2 ring processively threads and unfolds monoubiquitinated PEX5 through its central pore using a staircase of pore-1 loops, thereby extracting PEX5 from the docking–translocation module and recycling it to the cytosol for further rounds of peroxisomal matrix protein import, while also dynamically remodeling the topology of the Pex14 docking component in an ATP- and ubiquitination-dependent manner.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"PEX6 is a AAA+ ATPase that functions as an essential component of the peroxisomal matrix protein import machinery by powering the extraction and recycling of the cargo receptor PEX5 from the peroxisomal membrane. PEX6 forms an alternating heterohexameric double-ring complex with PEX1 in which the C-terminal D2 ring is catalytically active and processively threads monoubiquitinated PEX5 through its central pore via a staircase of pore-1 loops, globally unfolding the substrate during ATP-dependent extraction [PMID:29321502, PMID:37741838, PMID:29884772]. The N1 domain of PEX6 mediates recruitment to the peroxisomal membrane through binding the tail-anchored tether PEX15 (yeast)/PEX26 (mammals) and simultaneously stabilizes the PEX1–PEX6 hexamer by contacting an extended loop from the PEX1 D2 domain [PMID:38036174, PMID:26170309]. Loss of PEX6 function underlies peroxisome biogenesis disorders including Zellweger syndrome (complementation group C), and PEX6-dependent extraction of ubiquitinated PEX5 is coupled to dynamic topological remodeling of the PEX14 docking complex at the peroxisomal membrane [PMID:8940266, PMID:41581879].\",\n  \"teleology\": [\n    {\n      \"year\": 1996,\n      \"claim\": \"Identification of PEX6 as a cytoplasmic AAA ATPase essential for peroxisome biogenesis and PTS1-receptor stability established the molecular identity of the gene defective in Zellweger complementation group C.\",\n      \"evidence\": \"Functional complementation in Zellweger patient fibroblasts and CHO cells, ATPase domain K→R mutagenesis, Western blot for PEX5 stability\",\n      \"pmids\": [\"8670792\", \"8940266\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether PEX6 acts alone or requires a partner ATPase was unknown\",\n        \"The substrate of PEX6's ATPase activity was not identified\",\n        \"How PEX6 is recruited to peroxisomes was not determined\"\n      ]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Demonstrating that PEX1 and PEX6 physically interact and that disease mutations weaken this interaction established the functional ATPase complex and explained genotype–phenotype relationships in peroxisome biogenesis disorders.\",\n      \"evidence\": \"Yeast two-hybrid, in vitro pulldown, allele-specific genetic suppression between PEX1 and PEX6\",\n      \"pmids\": [\"9671729\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Stoichiometry and architecture of the PEX1–PEX6 complex were unknown\",\n        \"The direct substrate of the complex had not been identified\"\n      ]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Showing that PEX6 converts import-incompetent peroxisomal ghost membranes into functional peroxisomes demonstrated that PEX6 acts downstream of membrane assembly to enable matrix protein translocation.\",\n      \"evidence\": \"EM and immunofluorescence of PEX6-deficient CHO cells before and after complementation, GFP-PTS1 reporter\",\n      \"pmids\": [\"11854424\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The step at which PEX6 acts in the import cycle (receptor docking, translocation, or recycling) was not resolved\",\n        \"Whether PEX6 acts on PEX5 directly or indirectly was unclear\"\n      ]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Identification of AWP1/ZFAND6 as a PEX6-binding cofactor that recognizes monoubiquitinated PEX5 and stimulates its export linked PEX6 function specifically to ubiquitin-dependent receptor recycling.\",\n      \"evidence\": \"Co-IP, in vitro PEX5 export assay, RNAi knockdown, antibody inhibition\",\n      \"pmids\": [\"21980954\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Whether AWP1 is essential in vivo or merely enhances export efficiency was not resolved\",\n        \"The mechanism by which AWP1 cooperates with the PEX1–PEX6 ATPase was not determined\"\n      ]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Demonstrating that loss of Pex1/Pex6/Pex15 triggers enhanced pexophagy via Atg36 revealed that the exportomer's activity protects peroxisomes from autophagic degradation, explaining the peroxisome-loss phenotype in mutant cells.\",\n      \"evidence\": \"Genetic epistasis with atg1Δ and atg36 mutants, fluorescence microscopy in S. cerevisiae\",\n      \"pmids\": [\"24657987\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"The pexophagy signal generated by exportomer deficiency was not molecularly defined\",\n        \"Whether this pexophagy mechanism is conserved in mammals was not tested\"\n      ]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Cryo-EM structures revealed the unprecedented alternating PEX1–PEX6 heterohexameric double-ring architecture with a catalytically inactive D1 ring and an active asymmetric D2 ring, providing the structural framework for understanding substrate processing.\",\n      \"evidence\": \"Cryo-EM of the S. cerevisiae Pex1/Pex6 complex, computational domain fitting\",\n      \"pmids\": [\"26170309\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No substrate was captured in the pore, so the translocation mechanism remained hypothetical\",\n        \"How the complex engages the peroxisomal membrane was not structurally resolved\"\n      ]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Reconstituted translocase activity and cryo-EM of substrate-engaged complexes established that PEX1/PEX6 is a processive protein unfoldase that threads substrates through its D2 pore via pore-loop contacts, with monoubiquitinated PEX5 as its bona fide physiological substrate.\",\n      \"evidence\": \"In vitro unfolding/translocation assay with Pex15, cryo-EM of Pex1/Pex6–Pex15 complex, cell-free PEX5 export with photoaffinity cross-linking and PEGylation unfolding readout\",\n      \"pmids\": [\"29321502\", \"29884772\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The step-by-step nucleotide cycle driving translocation was not resolved\",\n        \"Whether PEX5 and PEX15 are threaded by the same or distinct mechanisms was unclear\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"High-resolution cryo-EM with endogenous substrate trapped in the pore revealed the twin-seam translocation mechanism and showed that the PEX6 N1 domain serves dual roles as membrane tether anchor and hexamer stabilizer, completing the structural model of the translocase.\",\n      \"evidence\": \"Cryo-EM with endogenous substrate trapping, X-ray crystallography of Pex6 N1, in vivo complementation of N1 deletion\",\n      \"pmids\": [\"37741838\", \"38036174\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The identity of the endogenous substrate trapped in the pore was not determined\",\n        \"Structural basis of how PEX26 (mammalian tether) engages PEX6 N1 awaits high-resolution data\",\n        \"How the twin-seam mechanism coordinates with ubiquitin recognition is not resolved\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Demonstrating that PEX6 and PEX5 ubiquitination jointly drive reversible topological remodeling of the PEX14 docking complex established that receptor extraction is mechanistically coupled to structural reorganization of the translocation channel.\",\n      \"evidence\": \"Protease protection assay, immunofluorescence, pharmacological AAA+ inhibition (NEM), ubiquitin inhibitor MLN-7243, PEX6/PEX26 knockdown\",\n      \"pmids\": [\"41581879\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether PEX14 remodeling is a cause or consequence of PEX5 extraction is not distinguished\",\n        \"The structural basis for PEX14 topology change at the membrane is unknown\",\n        \"Single study; independent confirmation is needed\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The precise nucleotide-driven conformational cycle that couples ATP hydrolysis in the D2 ring to stepwise substrate translocation, and how ubiquitin on PEX5 is recognized and processed during threading, remain structurally unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No time-resolved or single-molecule measurements of the translocation cycle exist\",\n        \"Structural basis of ubiquitin recognition by the PEX1–PEX6 pore is unknown\",\n        \"Role of the catalytically inactive D1 ring in allosteric regulation of translocation is not mechanistically defined\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140657\", \"supporting_discovery_ids\": [0, 5, 6, 7, 8]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 6, 8]},\n      {\"term_id\": \"GO:0044183\", \"supporting_discovery_ids\": [6, 7, 8]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0005777\", \"supporting_discovery_ids\": [3, 9]},\n      {\"term_id\": \"GO:0005929\", \"supporting_discovery_ids\": [11]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 1, 3, 5, 6]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [10]},\n      {\"term_id\": \"R-HSA-9609507\", \"supporting_discovery_ids\": [6, 7, 13]}\n    ],\n    \"complexes\": [\n      \"PEX1–PEX6 heterohexamer\"\n    ],\n    \"partners\": [\n      \"PEX1\",\n      \"PEX15\",\n      \"PEX26\",\n      \"PEX5\",\n      \"PEX14\",\n      \"AWP1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}