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this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.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 PEX1 (UniProt O43933) — Functional Annotation and Current Research

0. Target verification (gene/protein identity)

The target is human PEX1 (UniProt O43933), a peroxisomal AAA+ ATPase/peroxin-1 that forms a heterohexameric ATPase with PEX6 and is tethered to the peroxisomal membrane via PEX26 (mammals). This identity (PEX1/PEX6/PEX26 “receptor export module/exportomer”), the AAA+ ATPase family/domain architecture, and the peroxisome-import context are explicitly treated in human-focused sources and cross-species mechanistic literature used below. (judy2022insightsintothe pages 16-18, judy2022insightsintothe pages 1-3, pandey2024molecularinteractionsof pages 22-26, pandey2024molecularinteractionsof pages 1-9)

Table: A comprehensive overview of the human PEX1 protein (UniProt O43933), detailing its role as a peroxisomal AAA+ ATPase in receptor recycling, its assembly into the PEX1-PEX6-PEX26 exportomer, and its significance in Zellweger Spectrum Disorders (ZSD).

1. Key concepts and definitions (current understanding)

1.1 Peroxisomal matrix protein import cycle (context for PEX1 function)

Peroxisomes import many matrix enzymes post-translationally, including folded and oligomeric cargos, using cytosolic receptors and a docking/translocation system at the peroxisomal membrane. A current review model describes: (i) cargo recognition by Pex5 (PTS1) or Pex7 (PTS2), (ii) docking at membrane components including Pex13/Pex14, (iii) cargo translocation/release through a transient and dynamic pore-like assembly, and then (iv) receptor ubiquitination and recycling driven by AAA ATPases. (rudowitz2023importandquality pages 4-5, pedrosa2019amechanisticperspective pages 1-3)

A visual schematic of this import/recycling cycle (including the Pex1–Pex6 extraction step) is shown in Rudowitz & Erdmann 2023, Fig. 2A, where Step 6 depicts extraction of the ubiquitinated receptor by the Pex1–Pex6 AAA ATPase, followed by deubiquitination and reuse. (rudowitz2023importandquality media 4f856393)

1.2 What PEX1 is (molecular function)

PEX1 is not a metabolic enzyme for small molecules; it is an AAA+ ATPase that functions as a mechanochemical unfoldase/extractor. Its primary cellular role is to “reset” the peroxisomal import machinery by powering receptor recycling (rather than powering the translocation step itself). (pedrosa2019amechanisticperspective pages 1-3)

1.3 The Receptor Export Module (REM)/exportomer

PEX1 and PEX6 form the ATP-dependent Receptor Export Module (REM) (also termed exportomer in parts of the literature) that is tethered to the peroxisomal membrane by a membrane anchor (human PEX26; yeast Pex15). (pedrosa2019amechanisticperspective pages 1-3, judy2022insightsintothe pages 1-3)

1.4 Substrate specificity: the physiological substrate is ubiquitinated PEX5

The canonical physiological substrate is the matrix protein import receptor PEX5, after it becomes monoubiquitinated on a conserved N-terminal cysteine (Cys11 in mammals). PEX1/PEX6 extract this membrane-associated, ubiquitinated receptor back to the cytosol to enable subsequent rounds of import. (pedrosa2018peroxisomalmonoubiquitinatedpex5 pages 1-2, pandey2024molecularinteractionsof pages 16-20)

Importantly, mechanistic evidence supports that Ub-PEX5 can directly interact with both PEX1 and PEX6 via its ubiquitin moiety, and that the PEX5 polypeptide is unfolded during ATP-dependent extraction, consistent with a threading/unfoldase mechanism. (pedrosa2018peroxisomalmonoubiquitinatedpex5 pages 1-2)

2. Molecular mechanism and pathways (authoritative evidence)

2.1 Stepwise mechanism: docking/translocation → ubiquitination → ATPase extraction

A mechanistic summary across reviews and primary literature supports:

1. PEX5 delivers folded matrix cargo to the peroxisomal docking/translocation module (DTM) (involving PEX13/PEX14 and additional factors), where cargo release occurs. (rudowitz2023importandquality pages 4-5, pedrosa2019amechanisticperspective pages 1-3)
2. PEX5 is monoubiquitinated (E1/E2/E3 machinery including peroxisomal RING peroxins) as a prerequisite for recycling. (rudowitz2023importandquality pages 4-5, pedrosa2019amechanisticperspective pages 1-3)
3. The PEX1–PEX6 AAA+ ATPase then extracts the ubiquitinated receptor from the membrane in an ATP-driven process. (rudowitz2023importandquality pages 4-5, rudowitz2023importandquality media 4f856393)
4. The receptor is then deubiquitinated and reused; defects can route receptors to proteasomal degradation. (rudowitz2023importandquality pages 4-5)

2.2 How ATP hydrolysis is coupled to mechanical work (AAA+ unfoldase model)

PEX1/PEX6 is a Type II AAA+ motor that couples ATP hydrolysis to mechanical threading through a central pore, engaging substrates via conserved pore loops and pulling polypeptides through the channel to unfold/extract them. (ali2023thepex6n1 pages 1-3, gardner2018theperoxisomalaaaatpase pages 1-2)

Domain-level specialization is supported by both reviews and mechanistic work:
- Both PEX1 and PEX6 contain D1 and D2 AAA domains, but D1 is described as degenerate/inactive for hydrolysis, while D2 contains the canonical residues for ATP binding/hydrolysis. (pandey2024molecularinteractionsof pages 22-26, judy2022insightsintothea pages 6-8)
- Functional/mutational evidence emphasizes that ATP hydrolysis critical for motor activity maps strongly to the D2 ring, particularly Pex6/PEX6 D2 in several systems. (judy2022insightsintothea pages 8-9, judy2022insightsintothea pages 6-8)

3. Recent developments and latest research (prioritizing 2023–2024)

3.1 2023–2024 updates to peroxisomal import models (relevant to PEX1 function)

Recent reviews emphasized increasingly “nuclear pore-like” concepts for the docking/translocation step, including intrinsically disordered regions (IDRs) and repeat-rich segments in components such as PEX13, and continued debate about the transient pore architecture—while maintaining the core model in which ubiquitination and PEX1/PEX6 extraction reset the system. (rudowitz2023importandquality pages 4-5, kumar2024theperoxisomean pages 9-10)

3.2 2024 structural/mechanistic advance: N-domain/cofactor interactions that enable membrane recruitment and assembly

Ali et al. (JBC 2024; published Jan 2024; https://doi.org/10.1016/j.jbc.2023.105504) report that the Pex6 N1 domain is structurally conserved and required for binding the peroxisomal membrane tether (Pex15; the functional analog of mammalian PEX26-dependent recruitment) and for stable assembly with Pex1. Notably, an ATPase-active complex lacking this domain can be defective in vivo, separating recruitment/cofactor functions from basal ATPase activity. (ali2024then1domain pages 1-2)

3.3 2023 cryo-EM structures: substrate engagement by the Pex1/Pex6 motor

Rüttermann et al. (bioRxiv 2023; https://doi.org/10.1101/2022.11.19.517173) report cryo-EM structures of Pex1/Pex6 bound to an endogenous substrate in the central pore, supporting the staircase pore-loop engagement model and showing unique hetero-interfaces that coordinate mechanical force propagation; the D1 ring is catalytically inactive yet undergoes coupled conformational changes. These data strengthen the mechanistic analogy to other AAA+ threading motors and provide a structural basis for how defects in PEX1/PEX6 might impair receptor export. (ruttermann2023structureofthe pages 1-5, ruttermann2023structureofthe pages 9-13)

3.4 Human-focused mechanistic work in 2024: PEX1/PEX6 interactions and the common PEX1-G843D allele

A 2024 dissertation focused on the human PEX1/PEX6 complex describes REM composition (PEX1/PEX6/PEX26), domain architecture (D1/D2), and clinical relevance of PEX1-G843D, consistent with the human gene/protein target identity and disease focus. (pandey2024molecularinteractionsof pages 22-26, pandey2024molecularinteractionsof pages 1-9)

4. Current applications and real-world implementations

4.1 Clinical genetics and diagnostics for PEX1-mediated disease

PEX1 variants are a major cause of peroxisome biogenesis disorders, including Zellweger spectrum disorder (ZSD). Clinical diagnosis commonly uses:
- Genetic testing (e.g., exome sequencing or targeted PEX gene panels) to identify biallelic pathogenic PEX1 variants. (karuntu2024systematicstudyof pages 1-4, khan2024geneticinvestigationson pages 9-10)
- Biochemical markers of peroxisomal dysfunction in blood/plasma, including very-long-chain fatty acids (VLCFAs), phytanic/pristanic acids, C27 bile acid intermediates, and plasmalogen deficiency. (karuntu2024systematicstudyof pages 1-4, jiang2025modellingperoxisomaldisorders pages 6-8)

A real-world diagnostic pitfall is that mild PEX1-related disease may initially present with isolated hearing loss, risking misclassification as non-syndromic deafness or Usher syndrome until genomic testing and/or biochemical findings clarify the diagnosis. (khan2024geneticinvestigationson pages 9-10)

4.2 Phenotyping, monitoring, and multidisciplinary care

A 2024 cohort focusing on ophthalmology in PEX1-ZSD underscores the need for multidisciplinary evaluation and follow-up (metabolic pediatrics, neurology, genetics), reflecting the multisystem nature of ZSD (eye, hearing, liver, neurologic involvement). (karuntu2024systematicstudyof pages 12-13, karuntu2024systematicstudyof pages 1-4)

Monitoring in practice can include retinal imaging and functional testing such as BCVA, perimetry, microperimetry, SD-OCT, FAF, and ERG, to document retinopathy that can resemble retinitis pigmentosa. (karuntu2024systematicstudyof pages 1-4, karuntu2024systematicstudyof pages 5-6)

4.3 Example of an applied intervention (symptom-targeted)

In Karuntu et al. 2024 (Apr 2024; https://doi.org/10.1080/13816810.2024.2330389), two patients with PEX1-mediated ZSD received acetazolamide for intraretinal fluid/cystoid changes (reported doses 500 mg/day and 750 mg/day), exemplifying real-world management of ocular complications even in the absence of disease-modifying therapy. (karuntu2024systematicstudyof pages 5-6)

5. Relevant statistics and data (recent studies)

5.1 2024 PEX1-ZSD ophthalmology cohort (quantitative natural history features)

Karuntu et al. 2024 report a cross-sectional cohort of 10 patients from six families, predominantly carrying the common hypomorphic allele PEX1 c.2528G>A (p.Gly843Asp):
- Genotype distribution: 9/10 homozygous p.Gly843Asp; 1/10 compound heterozygous p.Gly843Asp + a frameshift allele (p.Ile700TyrfsTer42). (karuntu2024systematicstudyof pages 1-4)
- Age and onset: median age 22.6 years (IQR 15.9–29.9), symptom onset median 6 months (IQR 1.9–8.3). (karuntu2024systematicstudyof pages 1-4)
- Presenting features: hearing loss in 7/10 vs nyctalopia/reduced acuity in 3/10 at presentation. (karuntu2024systematicstudyof pages 1-4)
- Vision outcomes: median BCVA 0.8 logMAR (IQR 0.6–0.9) reported stable over 10.8 years. (karuntu2024systematicstudyof pages 1-4)
- Imaging abnormalities: SD-OCT abnormalities in all nine imaged patients, including central cystoid fluid and photoreceptor layer disruption (ELM/EZ). (karuntu2024systematicstudyof pages 5-6)

5.2 Mechanistic statistics for the AAA motor (biophysical efficiency)

Mechanistic review evidence suggests Pex1/Pex6 can display ATP-use efficiencies higher than strict hand-over-hand predictions (e.g., estimates on residues unfolded per ATP), implying non-sequential/probabilistic hydrolysis or other coupling features; such analyses provide quantitative constraints on models for how ATP hydrolysis powers extraction/unfolding. (judy2022insightsintothea pages 8-9)

6. Expert opinions and analysis (authoritative synthesis)

6.1 Consensus mechanism: PEX1 is a “reset” ATPase, not the translocation motor

An authoritative mechanistic viewpoint emphasizes that the peroxisomal system is unusual among protein-translocation systems in that ATP hydrolysis is used chiefly to reset components—specifically by exporting ubiquitinated receptors—rather than to directly power import across the membrane. (pedrosa2019amechanisticperspective pages 1-3)

6.2 Open questions highlighted in recent literature

Even with strong consensus on the REM role, multiple authoritative sources highlight remaining uncertainties that are active research areas:
- The precise architecture and dynamics of the docking/translocation step (e.g., contributions of flexible IDRs and hydrogel-like behavior). (rudowitz2023importandquality pages 4-5, kumar2024theperoxisomean pages 9-10)
- Which components besides Ub-PEX5 may be physiologic substrates or co-substrates (and how ubiquitination modulates substrate engagement). (judy2022insightsintothe pages 16-18)
- The detailed coordination of ATP hydrolysis across the heterohexamer (including asymmetry between PEX1 and PEX6 catalytic contributions). (judy2022insightsintothea pages 8-9, judy2022insightsintothe pages 16-18)

7. Source list (URLs and publication dates)

Key cited recent sources:
- Rudowitz & Erdmann. Import and quality control of peroxisomal proteins. Journal of Cell Science, Aug 2023. https://doi.org/10.1242/jcs.260999 (rudowitz2023importandquality pages 4-5, rudowitz2023importandquality media 4f856393)
- Kumar et al. The peroxisome: an update on mysteries 3.0. Histochemistry and Cell Biology, Jan 2024. https://doi.org/10.1007/s00418-023-02259-5 (kumar2024theperoxisomean pages 9-10)
- Ali et al. The N1 domain of the peroxisomal AAA-ATPase Pex6 is required for Pex15 binding and proper assembly with Pex1. Journal of Biological Chemistry, Jan 2024. https://doi.org/10.1016/j.jbc.2023.105504 (ali2024then1domain pages 1-2)
- Karuntu et al. Systematic study of ophthalmological findings in 10 patients with PEX1-mediated Zellweger spectrum disorder. Ophthalmic Genetics, Apr 2024. https://doi.org/10.1080/13816810.2024.2330389 (karuntu2024systematicstudyof pages 1-4, karuntu2024systematicstudyof pages 5-6)
- Khan et al. Genetic investigations on singleton school aged children reveal novel variants and new candidate genes for hearing loss. Scientific Reports, Sep 2024. https://doi.org/10.1038/s41598-024-71407-1 (khan2024geneticinvestigationson pages 9-10)

Foundational mechanistic sources (supporting core function):
- Pedrosa et al. Peroxisomal monoubiquitinated PEX5 interacts with the AAA ATPases PEX1 and PEX6 and is unfolded during its dislocation into the cytosol. JBC, Jul 2018. https://doi.org/10.1074/jbc.ra118.003669 (pedrosa2018peroxisomalmonoubiquitinatedpex5 pages 1-2)
- Pedrosa et al. A mechanistic perspective on PEX1 and PEX6… IJMS, Oct 2019. https://doi.org/10.3390/ijms20215246 (pedrosa2019amechanisticperspective pages 1-3)
- Judy et al. Insights into the structure and function of the Pex1/Pex6 AAA-ATPase… Cells, Jun 2022. https://doi.org/10.3390/cells11132067 (judy2022insightsintothea pages 8-9, judy2022insightsintothe pages 8-9)

8. Summary (functional annotation)

Human PEX1 encodes a peroxisomal AAA+ ATPase that—together with PEX6 and membrane tether PEX26—forms the REM/exportomer required for receptor recycling in peroxisomal matrix protein import. The key biochemical “substrate specificity” is for ubiquitinated PEX5, which is mechanically extracted/unfolded in an ATP-dependent threading process, thereby resetting the import machinery for additional rounds of matrix enzyme import. This pathway is central to peroxisome biogenesis and homeostasis, and pathogenic variants in PEX1 cause PEX1-mediated Zellweger spectrum disorder, with recent 2024 cohort data providing genotype distributions (notably the common p.Gly843Asp allele) and quantifiable visual and multisystem phenotypes relevant to diagnosis, monitoring, and future trial readiness. (pedrosa2018peroxisomalmonoubiquitinatedpex5 pages 1-2, rudowitz2023importandquality pages 4-5, karuntu2024systematicstudyof pages 1-4)

References

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Citations

1. pedrosa2019amechanisticperspective pages 1-3
2. rudowitz2023importandquality pages 4-5
3. khan2024geneticinvestigationson pages 9-10
4. karuntu2024systematicstudyof pages 5-6
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