Affinage

PEX12

Peroxisome assembly protein 12 · UniProt O00623

Length
359 aa
Mass
40.8 kDa
Annotated
2026-04-29
16 papers in source corpus 6 papers cited in narrative 7 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

PEX12 is an integral peroxisomal membrane protein with a RING finger E3 ubiquitin ligase domain that is essential for peroxisomal matrix protein import. It contains two transmembrane segments and a cytosol-facing C-terminal RING domain that directly binds the PTS1 import receptor PEX5 and the partner RING peroxin PEX10; this interaction occurs independently of PEX5 cargo recognition and acts downstream of PEX5 docking at the peroxisomal membrane (PMID:9632816, PMID:10562279, PMID:12456682). As part of the PEX2/PEX10/PEX12 E3 ligase complex, PEX12 catalyzes Pex4(Ubc10)-dependent monoubiquitination of PEX5, which is required for receptor recycling and sustained rounds of matrix protein import (PMID:19687296). Loss-of-function mutations in PEX12 cause peroxisome biogenesis disorder (complementation group 3), as demonstrated by restoration of peroxisomal protein import upon PEX12 expression in patient fibroblasts (PMID:9090384).

Mechanistic history

Synthesis pass · year-by-year structured walk · 5 steps
  1. 1997 High

    Establishing that PEX12 is a peroxisomal membrane protein whose loss causes a human peroxisome biogenesis disorder answered the question of which gene underlies PBD complementation group 3 and linked PEX12 directly to matrix protein import.

    Evidence Functional complementation of patient fibroblasts, subcellular fractionation, and mutation analysis

    PMID:9090384

    Open questions at the time
    • Molecular mechanism by which PEX12 supports import was unknown
    • Topology and domain architecture uncharacterized
  2. 1998 High

    Determination of PEX12 membrane topology and identification of its RING finger domain established the structural framework needed to understand its mechanistic role, showing that both cytoplasmic regions are functionally essential.

    Evidence Epitope-tagged topology analysis, truncation and site-directed mutagenesis with functional complementation in CHO mutant cells

    PMID:9632816

    Open questions at the time
    • Binding partners of the RING domain were unknown
    • Enzymatic activity of the RING domain not yet tested
  3. 1999 High

    Demonstration that the PEX12 RING domain directly binds both PEX5 and PEX10, and that PEX12 acts downstream of receptor docking, placed PEX12 at a post-docking step in the import cycle and identified its key interaction partners.

    Evidence Two-hybrid, co-immunoprecipitation, blot overlay, genetic suppression, and PEX5 fractionation in loss-of-function cell lines

    PMID:10562279

    Open questions at the time
    • Whether PEX12 interaction with PEX5 requires cargo binding was unresolved
    • Catalytic function of PEX12 not yet demonstrated
  4. 2002 Medium

    Showing that PEX12 binds the PTS1-binding domain of PEX5 without altering cargo recognition kinetics established that PEX12–PEX5 interaction is independent of cargo loading, separating receptor engagement from cargo release.

    Evidence Fluorescence anisotropy binding assay with purified recombinant proteins in vitro

    PMID:12456682

    Open questions at the time
    • In vitro binding only; in vivo significance of cargo-independent interaction not directly tested
    • No enzymatic assay performed
  5. 2009 High

    Reconstitution of PEX12-dependent monoubiquitination of PEX5 via the Pex4/Ubc10 conjugating enzyme identified PEX12 as the E3 ligase responsible for receptor recycling, providing the central enzymatic mechanism of the import cycle.

    Evidence In vitro ubiquitination reconstitution with purified components, RING mutagenesis, and yeast genetics

    PMID:19687296

    Open questions at the time
    • Relative contributions of PEX2, PEX10, and PEX12 RING domains within the complex were not fully resolved
    • Structural basis of the trimeric E3 complex unknown
    • Whether mammalian PEX12 uses the same E2 enzyme not directly shown

Open questions

Synthesis pass · forward-looking unresolved questions
  • A high-resolution structural understanding of the mammalian PEX2/PEX10/PEX12 complex and the mechanism by which cargo translocation is coupled to PEX5 ubiquitination and recycling remains to be established.
  • No atomic structure of the mammalian PEX12-containing E3 complex
  • Mechanism coupling cargo release to PEX5 ubiquitination is unclear
  • Regulation of PEX12 ligase activity in vivo is unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016874 ligase activity 1 GO:0140096 catalytic activity, acting on a protein 1
Localization
GO:0043226 organelle 2
Pathway
R-HSA-9609507 Protein localization 3 R-HSA-1852241 Organelle biogenesis and maintenance 2 R-HSA-392499 Metabolism of proteins 1
Partners
PEX10PEX4PEX5
Complex memberships
PEX2/PEX10/PEX12 E3 ligase complex

Evidence

Reading pass · 7 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1997 Human PEX12 localizes to the peroxisome membrane and is essential for peroxisomal matrix protein import; expression of PEX12 restored peroxisomal protein import in fibroblasts from PBD complement group 3 patients. Subcellular fractionation, functional complementation in patient fibroblasts, mutation analysis Nature genetics High 9090384
1998 PEX12 is an integral peroxisomal membrane protein with two transmembrane segments and a cytosol-facing C-terminal RING finger (zinc finger) domain; both the N- and C-terminal cytoplasmic regions are essential for biological function. Epitope-tagged expression, topology analysis, truncation and site-directed mutagenesis, functional complementation in CHO mutant cells Molecular and cellular biology High 9632816
1999 The zinc RING domain of PEX12 directly binds both PEX5 (the PTS1 import receptor) and PEX10 (another peroxisomal membrane protein); a patient missense mutation S320F in the zinc-binding domain reduces these interactions, and overexpression of PEX5 or PEX10 suppresses this mutation. Two-hybrid assay, blot overlay, co-immunoprecipitation, genetic epistasis (suppressor overexpression) The Journal of cell biology High 10562279
1999 Loss of PEX12 or PEX10 does not reduce the docking of PEX5 to peroxisomes, demonstrating that PEX12 acts downstream of receptor docking in the matrix protein import pathway. Loss-of-function cell lines, subcellular fractionation/PEX5 association assay The Journal of cell biology High 10562279
2002 The PEX12 zinc RING domain interacts with the PTS1-binding domain of PEX5 but does not alter the kinetics of PEX5-PTS1 binding, indicating PEX12 interacts with PEX5 independently of cargo recognition. Fluorescence anisotropy binding assay with purified recombinant proteins The Journal of biological chemistry Medium 12456682
2009 Pex12 (yeast ortholog) functions as an E3 ubiquitin-protein isopeptide ligase (RING peroxin) and specifically facilitates Pex4 (Ubc10)-dependent monoubiquitination of the import receptor Pex5, which is required for receptor recycling. In vitro ubiquitination assay, mutagenesis, yeast genetics Molecular and cellular biology High 19687296
2025 The yeast Pex2/Pex10/Pex12 complex functions as an E3-ubiquitin ligase module; Pex8 interacts with the N-terminal domain of Pex5 via a HEAT repeat array and promotes assembly with the Pex2/Pex10/Pex12 complex to initiate receptor recycling after cargo translocation. Cryo-EM structure, in vitro binding assays, mutagenesis, peroxisomal import functional assays in yeast bioRxivpreprint Medium bio_10.1101_2025.08.30.673231

Source papers

Stage 0 corpus · 16 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2009 Pex2 and pex12 function as protein-ubiquitin ligases in peroxisomal protein import. Molecular and cellular biology 162 19687296
1997 Isolation of the human PEX12 gene, mutated in group 3 of the peroxisome biogenesis disorders. Nature genetics 123 9090384
1999 PEX12 interacts with PEX5 and PEX10 and acts downstream of receptor docking in peroxisomal matrix protein import. The Journal of cell biology 115 10562279
1998 PEX12, the pathogenic gene of group III Zellweger syndrome: cDNA cloning by functional complementation on a CHO cell mutant, patient analysis, and characterization of PEX12p. Molecular and cellular biology 92 9632816
2005 The Arabidopsis PEX12 gene is required for peroxisome biogenesis and is essential for development. Plant physiology 83 16113209
2006 The Arabidopsis pex12 and pex13 mutants are defective in both PTS1- and PTS2-dependent protein transport to peroxisomes. The Plant journal : for cell and molecular biology 68 16813573
2010 Different functions of the C3HC4 zinc RING finger peroxins PEX10, PEX2, and PEX12 in peroxisome formation and matrix protein import. Proceedings of the National Academy of Sciences of the United States of America 47 20679226
2006 Identification of novel mutations in PEX2, PEX6, PEX10, PEX12, and PEX13 in Zellweger spectrum patients. Human mutation 39 17041890
2005 Identification and characterization of three peroxins--PEX6, PEX10 and PEX12--involved in glycosome biogenesis in Trypanosoma brucei. Biochimica et biophysica acta 37 16388862
2007 A novel PEX12 mutation identified as the cause of a peroxisomal biogenesis disorder with mild clinical phenotype, mild biochemical abnormalities in fibroblasts and a mosaic catalase immunofluorescence pattern, even at 40 degrees C. Journal of human genetics 32 17534573
2002 PEX5 binds the PTS1 independently of Hsp70 and the peroxin PEX12. The Journal of biological chemistry 30 12456682
2004 Novel mutations in the PEX12 gene of patients with a peroxisome biogenesis disorder. European journal of human genetics : EJHG 16 14571262
2016 Effect of l-Arginine in One Patient with Peroxisome Biogenesis Disorder due to PEX12 Deficiency. Neuropediatrics 5 26947510
2015 A novel mutation in the PEX12 gene causing a peroxisomal biogenesis disorder. Molecular biology reports 5 26094004
2025 Evaluation of Antimicrobial Activity of Novel Chimeric M-PEX12 Peptide Against Acinetobacter baumannii. Iranian journal of pharmaceutical research : IJPR 2 40718457
2020 A founder mutation in PEX12 among Egyptian patients in peroxisomal biogenesis disorder. Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology 2 33123925