PEX39 (peroxisomal biogenesis factor 39, formerly C6orf226) is a small (101-residue) cytosolic peroxin of the type 2 peroxisomal targeting signal (PTS2) protein import pathway. It is built around a DUF5572/KPWE module and its most conserved feature, an (R/K)PWE motif, is shared with the N terminus of the peroxisomal membrane protein PEX13. PEX39 binds the PTS2 receptor PEX7 with nanomolar affinity through this motif while its N-terminal region wraps onto the receptor, clamping PEX7 onto PTS2-bearing cargo such as phytanoyl-CoA 2-hydroxylase (PHYH), alkyl-dihydroxyacetone phosphate synthase (AGPS) and peroxisomal thiolase (ACAA1) and stabilizing an interaction that is otherwise weak. The PEX39-PEX7 interaction is deliberately labile: at the peroxisomal membrane PEX39 is displaced by the competing KPWE motif of PEX13, handing the loaded receptor to the docking/translocation machinery. PEX39 acts only on the PTS2 branch of matrix protein import and has no effect on PTS1 cargo. Loss of PEX39 causes accumulation of unprocessed PTS2 precursors in the cytosol in both yeast and human cells, and excess PEX39 is also inhibitory, so the protein is normally kept at low abundance. The gene is conserved from budding yeast (Yjr012c/Pex39) to human, and the presence of PEX39 across eukaryotes tracks the presence of the PEX13 KPWE motif.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005829 cytosol | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic transfer of the UniProt subcellular-location annotation, which is itself based on the 2025 experimental fractionation. Reason: Correct and is the compartment in which PEX39 acts; PEX39 loads PEX7 with PTS2 cargo in the cytosol before the complex reaches the peroxisomal membrane. Supporting Evidence: PMID:40739340 whereas cellular fractionation revealed that endogenous HsPEX39 is cytosolic |
| GO:0005515 protein binding | IPI PMID:25416956 A proteome-scale map of the human interactome network. | REMOVE | Summary: Bare protein binding from a large-scale binary interactome screen (partners O95273, P61978, Q6A162, Q8IYF3, Q92624), none of which has a known role in peroxisomal biology. Reason: Per project curation guidance, protein binding carries no functional information. These high-throughput partners are also not corroborated by the focused biochemistry in PMID:40739340, which defines PEX7 as the functionally relevant partner. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:29892012 An interactome perturbation framework prioritizes damaging m... | REMOVE | Summary: Bare protein binding from an interactome-perturbation screen (partner P61978). Reason: Uninformative as a molecular function; no peroxisomal context. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:31515488 Extensive disruption of protein interactions by genetic vari... | REMOVE | Summary: Bare protein binding from a population-variant interaction screen (partner O95273). Reason: Uninformative as a molecular function; no peroxisomal context. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0005515 protein binding | IPI PMID:32296183 A reference map of the human binary protein interactome. | REMOVE | Summary: Bare protein binding from the HuRI binary interactome (partner Q92624). Reason: Uninformative as a molecular function; no peroxisomal context. No more informative molecular function is supportable from this evidence, so the row is removed rather than rewritten. Removal does not imply the reported interaction is false. |
| GO:0016560 protein import into peroxisome matrix, docking | IMP PMID:40739340 PEX39 facilitates the peroxisomal import of PTS2-containing ... | ACCEPT | Summary: CRISPR knockout of PEX39 in two human cell lines caused accumulation of precursor PHYH in the cytosolic fraction and loss of mature PHYH from the organellar fraction; the equivalent PTS2 import defect was seen in Scpex39-delta yeast. Reason: Correct participation in PTS2 matrix import, and the docking sub-process is a defensible placement because PEX39's mechanistic contribution ends exactly at the membrane, where its KPWE motif is exchanged for the competing KPWE motif of PEX13 and the loaded receptor is handed to the docking/translocation module. The caveat worth recording is that the measured phenotype is failure of PTS2 import as a whole (GO:0016558, the parent), and that a large part of PEX39's work - clamping PEX7 onto cargo - happens in the cytosol upstream of docking; GO currently has no child term for receptor cargo loading. Supporting Evidence: PMID:40739340 Importantly, cellular fractionation revealed that HsPEX39 loss led to an accumulation of precursor PHYH in the cytosolic fraction and a decrease of mature PHYH in the organellar fraction, thus demonstrating impaired import of PTS2-containing proteins PMID:40739340 These results suggest that PEX39 must dissociate from PEX7 to allow PEX7 to bind the N terminus of PEX13 at the peroxisome, a handover mechanism that would be facilitated if the PEX39–PEX7 interaction were labile. |
| GO:0000268 peroxisome signal sequence receptor activity | IDA PMID:40739340 PEX39 facilitates the peroxisomal import of PTS2-containing ... | MODIFY | Summary: The 2025 paper is correctly cited and PEX39 is genuinely a PTS2-pathway factor, but this particular term asserts more than the paper shows. GO defines GO:0000268 as "Binding to a peroxisomal targeting sequence"; the same paper reports that PEX39 on its own does not bind a PTS2 cargo protein at all. PEX39 binds PEX7 through its KPWE motif and clamps the receptor onto cargo, which is co-receptor behaviour rather than receptor behaviour. Reason: The essence is sound and the annotation must not be discarded - PEX39 is an experimentally demonstrated component of PTS2 receptor function. What is wrong is the choice of the receptor term. Native PAGE shows PEX39 cannot form a complex with PHYH alone, so an independent PTS2-binding activity is not established (a direct PEX39-PTS2 contact is predicted by AlphaFold and is consistent with the N-terminal truncation data, but was never measured as a separate binding event). GO:0140597 protein carrier chaperone (renamed "protein carrier activity" in current GO; "Directly binding to a protein and delivering it either to an acceptor molecule or to a specific location") describes what was actually demonstrated - high-affinity binding of PEX7 and its delivery to PEX13 - and is the term the budding-yeast PTS2 co-receptor Pex21 (UniProtKB:P50091) already carries with IDA evidence, so the change keeps PEX39 consistent with existing GO treatment of PTS2 co-receptors. GO:0030674 protein-macromolecule adaptor activity would be a defensible alternative for the clamping step alone. Proposed replacements: protein carrier chaperone Supporting Evidence: PMID:40739340 HsPEX39 could not complex with either PEX5 or PHYH alone, per native PAGE PMID:40739340 Collectively, our data indicate that PEX39 stabilizes the interaction between PEX7 and PTS2-containing proteins, thereby providing a mechanism by which PEX39 facilitates the import of PTS2-containing proteins. PMID:40739340 Because of the labile nature of the PEX39–PEX7 interaction via the (R/K)PWE motif, PEX39 can now be exchanged with the PEX13 N terminus, which also contains a KPWE motif (steps 4 and 5), thus handing PEX7 over from PEX39 to PEX13. |
| GO:0005515 protein binding | IPI PMID:40739340 PEX39 facilitates the peroxisomal import of PTS2-containing ... | MODIFY | Summary: This is the functionally central interaction of the protein - PEX39 with PEX7 (WITH UniProtKB:O00628), mapped to the KPWE motif and measured in the nanomolar range - but it is recorded under the uninformative bare protein binding term. Reason: Not because the interaction is doubtful; it is the best-supported fact about PEX39. Bare protein binding simply does not express it. The interaction is captured instead by the molecular-function annotation (GO:0140597, proposed above) and by the core function below. Project rules require a single action per GO term, so this shares the action applied to the four high-throughput protein binding rows. Replaced by GO:0140597 protein carrier chaperone, which states what the interaction accomplishes. Proposed replacements: protein carrier chaperone Supporting Evidence: PMID:40739340 PEX39 and PEX13, a peroxisomal membrane translocon protein, both possess an (R/K)PWE motif necessary for PEX7 binding. PMID:40739340 HsPEX39(4A) could not interact with PEX7 and failed to stabilize the interaction between PEX7 and the PTS2-containing protein PHYH |
| GO:0005829 cytosol | IDA PMID:40739340 PEX39 facilitates the peroxisomal import of PTS2-containing ... | ACCEPT | Summary: Cell fractionation of human cells places endogenous PEX39 in the cytosol; the yeast orthologue fused to mNeonGreen distributes between cytosol and peroxisomes. Reason: Core location, and the compartment where the PEX7 cargo-loading step occurs. Supporting Evidence: PMID:40739340 whereas cellular fractionation revealed that endogenous HsPEX39 is cytosolic |
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Download this section (compressed HTML)Q: Does PEX39 contact the PTS2 nonapeptide directly, as the AlphaFold model of the PEX7-PEX39-PHYH(1-24) complex predicts, or does its N-terminal region stabilize the PEX7 binding groove without touching the signal? This decides whether PEX39 should ever carry GO:0000268 peroxisome signal sequence receptor activity in addition to a carrier or adaptor term.
Suggested experts: Walter W. Chen, Jorge E. Azevedo, Bettina Warscheid
Q: How do PEX39 and PEX5L, the established human PTS2 co-receptor, act in sequence? Both are present in the same in vitro PEX7-PHYH-PEX39-PEX5 species, and PEX5(179-266) is predicted to displace the N-terminal portion of PEX39 while leaving the KPWE contact intact - is PEX39 required for PEX5L loading, or a parallel stabilizer?
Suggested experts: Tony A. Rodrigues, Jorge E. Azevedo
Q: Are PEX39 variants a cause or a modifier of human peroxisomal disease? Loss of PEX39 impairs but does not abolish PTS2 import, so PEX39 would be expected to produce a mild, PTS2-restricted phenotype rather than a Zellweger-spectrum presentation.
Suggested experts: Hans R. Waterham
Experiment: Site-specific photo-crosslinking from within a PTS2 peptide (or from PEX39 residues predicted to contact it, e.g. L21) in reconstituted PEX7-cargo-PEX39 complexes, followed by mass spectrometric identification of the crosslinked partner. A positive PEX39-PTS2 crosslink that is lost in the PEX39 N-terminal truncation would establish direct signal binding.
Hypothesis: The N-terminal region of PEX39 makes direct physical contact with the PTS2 nonapeptide of cargo bound to PEX7.
Type: site-specific photo-crosslinking with MS readout
Experiment: Titrate PEX39 expression across a wide range in PEX39-knockout human cells using a dose-controlled promoter, and quantify the mature/precursor ratio of PHYH, AGPS and ACAA1 by immunoblot at each level, to establish whether import efficiency is a narrow optimum and where endogenous PEX39 sits on that curve.
Hypothesis: PEX39 abundance is a rate-limiting parameter of PTS2 import, since both its loss and its overexpression impair import.
Type: dose-response complementation with quantitative import readout
Experiment: Knock out PEX39 in patient-derived fibroblasts carrying hypomorphic PEX7 alleles (rhizomelic chondrodysplasia punctata type 1) and matched controls, and measure plasmalogen synthesis, phytanic acid alpha-oxidation and PTS2 precursor processing. This tests the modifier hypothesis directly in a human genetic background.
Hypothesis: PEX39 is dispensable for PTS1 import but required for the residual PTS2 import seen in hypomorphic PEX7 patient backgrounds.
Type: genetic interaction test in patient fibroblasts
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