peroxisomal matrix

GO:0005782 · Membrane organelle · Subcellular region · Proposed

The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase. [GO:0005782]

Synonyms: peroxisomal lumen

Part of: peroxisome (GO:0005777)

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Taxonomic distribution

• NCBITaxon:4932 Saccharomyces cerevisiae — COMMON: Saccharomyces cerevisiae peroxisomes contain a matrix compartment that houses fatty-acid beta-oxidation enzymes. [DOI:10.1093/femsyr/fow038]

Canonical examples

• NCBITaxon:4932 Saccharomyces cerevisiae — Budding-yeast model for import of nuclear-encoded, targeting-signal-bearing metabolic enzymes into the peroxisomal matrix. [DOI:10.1016/j.bbamcr.2015.09.008]

Functions

• fatty acid beta-oxidation GO:0006635 — The peroxisomal matrix compartmentalizes enzymes for fatty-acid beta-oxidation in yeasts.
  • DOI:10.1093/femsyr/fow038 Sibirny 2016 reviewed fatty-acid beta-oxidation as a major metabolic function of yeast peroxisomes.

Related pathways

• fatty acid oxidation pathway (gomodel:YeastPathways_YEAST-FAO-PWY) — SITE_OF; target taxon NCBITaxon:559292.

  This applies to the peroxisomal beta-oxidation reactions in the budding-yeast exemplar. The target is the S288C pathway model; activation and auxiliary reactions are not all asserted to occur in the matrix.

  Basis: Existing matrix beta-oxidation function reviewed against the organism-scoped pathway; no new protein example or strain-specific experiment is asserted.. PathwayMech revision: d8ec2b69f7a4c615aecddff80498fef1e1fab0ce.

  • DOI:10.1093/femsyr/fow038 Sibirny 2016 reviews the beta-oxidation role and matrix-soluble enzymes of yeast peroxisomes. Abstract read through Europe PMC on 2026-10-05; matrix localization is already curated on this structure.

Mechanism graphs

Peroxisomal matrix topology (FUNCTION)

The peroxisomal matrix is the internal peroxisome compartment enclosed by the peroxisomal membrane.

Discussions

• INTERPRETATION (RESOLVED): Keep the peroxisomal membrane as the boundary of the peroxisomal matrix rather than as a matrix component. GO:0005782 denotes the volume contained within peroxisome membranes, whereas GO:0005778 denotes the lipid bilayer surrounding a peroxisome.

Evidence

• GO:0005782 Gene Ontology cellular-component term for peroxisomal matrix.
• GO:0031907 Gene Ontology cellular-component parent term for microbody lumen.
• GO:0005777 Gene Ontology cellular-component term for the containing peroxisome.
• GO:0005778 Gene Ontology cellular-component term for the peroxisomal membrane that encloses the matrix.
• GO:0006635 Gene Ontology biological-process term for fatty acid beta-oxidation.
• DOI:10.1093/femsyr/fow038 Sibirny 2016, Yeast peroxisomes: structure, functions and biotechnological opportunities, FEMS Yeast Research.
• DOI:10.1016/j.bbamcr.2015.09.008 Yuan, Veenhuis and van der Klei 2016, The birth of yeast peroxisomes, Biochimica et Biophysica Acta - Molecular Cell Research.

Curation history

• 2026-09-15T05:01:39Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
• 2026-09-15T05:02:42Z codex · EXPANDED_RECORD — Added exact GO synonymy, microbody-lumen parentage, peroxisome parthood, Saccharomyces scope, a matrix beta-oxidation function, GO/DOI evidence, a nonmechanistic matrix-topology graph, and a resolved boundary interpretation.
• 2026-09-15T05:12:40Z codex · REVIEW_FIX — Addressed issues #932 and #933 by removing import-only evidence from the beta-oxidation function and grounding the fatty acid beta-oxidation function and graph node to GO:0006635.
• 2026-10-05T17:45:01Z codex · ADD_PATHWAY_LINK — Added an evidence-backed, organism-scoped PathwayMech link with a full source commit and explicit relation limits.

Source: data/structures/membrane_organelle/peroxisomal_matrix.yaml