homogentisate catabolic process
GO:1902000
The complete three-step central homogentisate pathway in Pseudomonas putida strain U converts homogentisate through 4-maleylacetoacetate and 4-fumarylacetoacetate to fumarate and acetoacetate. HmgA, HmgC and HmgB act in that chemical order. Strain U gene disruptions and cluster complementation support pathway function; HmgB and HmgC assignments also depend on sequence-based functional interpretation, rather than purified strain U enzyme assays. The deposited strain U sequences identify the three proteins precisely. The selected boundary starts at homogentisate and ends at fumarate plus acetoacetate; upstream phenylalanine, tyrosine and hydroxyphenylacetate routes are outside this record. HmgA assembly and iron binding, HmgB metal annotations, and protein localization retain their computational evidence limits. The related KT2440 enzyme experiments and expression context are not treated as direct strain U measurements.
- Pathway type
- homogentisate degradation
- Organism scope
Pathway network
19 nodes · 24 asserted directed edges
Arrows show recorded subject → object relationships, not necessarily metabolic flow. Select a node for details or an arrow for evidence. Scroll, zoom or find a node to explore.
- Reaction / activity
- Chemical / cofactor
- Protein / complex
- Cell / process context
- Pathway
- Solid arrow: mechanistic relation
- Dashed arrow: membership, location or cofactor relation
Components and activities
| Node | Kind or role | Source direction |
|---|---|---|
Pseudomonas putidaNCBITaxon:303 | taxon | |
homogentisateCHEBI:16169 | small molecule | |
dioxygenCHEBI:15379 | small molecule | |
4-maleylacetoacetateCHEBI:17105 | small molecule | |
hydronCHEBI:15378 | small molecule | |
4-fumarylacetoacetate(2-)CHEBI:18034 | small molecule | |
waterCHEBI:15377 | small molecule | |
acetoacetateCHEBI:13705 | small molecule | |
fumarate(2-)CHEBI:29806 | small molecule | |
iron cationCHEBI:24875 | cofactor | |
calcium(2+)CHEBI:29108 | cofactor | |
magnesium(2+)CHEBI:18420 | cofactor | |
Homogentisate 1,2-dioxygenaseUniProtKB:Q6EMI9 | protein | |
Maleylacetoacetate isomeraseUniProtKB:Q6EMI7 | protein | |
fumarylacetoacetaseUniProtKB:Q6EMI8 | protein | |
cytoplasmGO:0005737 | cellular component | |
homogentisate + O2 => 4-maleylacetoacetate + H(+)RHEA:15450 | molecular activity | left to right |
4-maleylacetoacetate => 4-fumarylacetoacetateRHEA:14818 | molecular activity | left to right |
4-fumarylacetoacetate + H2O => acetoacetate + fumarate + H(+)RHEA:10245 | molecular activity | left to right |
Mechanistic edges
| Subject | Predicate and description | Object | Evidence |
|---|---|---|---|
homogentisateCHEBI:16169 | consumes | homogentisate + O2 => 4-maleylacetoacetate + H(+)RHEA:15450 |
|
dioxygenCHEBI:15379 | consumes | homogentisate + O2 => 4-maleylacetoacetate + H(+)RHEA:15450 |
|
homogentisate + O2 => 4-maleylacetoacetate + H(+)RHEA:15450 | produces | 4-maleylacetoacetateCHEBI:17105 |
|
homogentisate + O2 => 4-maleylacetoacetate + H(+)RHEA:15450 | produces | hydronCHEBI:15378 |
|
4-maleylacetoacetateCHEBI:17105 | consumes | 4-maleylacetoacetate => 4-fumarylacetoacetateRHEA:14818 |
|
4-maleylacetoacetate => 4-fumarylacetoacetateRHEA:14818 | produces | 4-fumarylacetoacetate(2-)CHEBI:18034 |
|
4-fumarylacetoacetate(2-)CHEBI:18034 | consumes | 4-fumarylacetoacetate + H2O => acetoacetate + fumarate + H(+)RHEA:10245 |
|
waterCHEBI:15377 | consumes | 4-fumarylacetoacetate + H2O => acetoacetate + fumarate + H(+)RHEA:10245 |
|
4-fumarylacetoacetate + H2O => acetoacetate + fumarate + H(+)RHEA:10245 | produces | acetoacetateCHEBI:13705 |
|
4-fumarylacetoacetate + H2O => acetoacetate + fumarate + H(+)RHEA:10245 | produces | fumarate(2-)CHEBI:29806 |
|
4-fumarylacetoacetate + H2O => acetoacetate + fumarate + H(+)RHEA:10245 | produces | hydronCHEBI:15378 |
|
Homogentisate 1,2-dioxygenaseUniProtKB:Q6EMI9 | enables Functional gene-product assignment from the native study and exact deposited sequence; no isolated-monomer catalytic unit is asserted. The strain U hexamer annotation is inferred by HAMAP; KT2440 structural experiments are separate. | homogentisate + O2 => 4-maleylacetoacetate + H(+)RHEA:15450 |
|
Maleylacetoacetate isomeraseUniProtKB:Q6EMI7 | enables Functional gene-product assignment from the native study and exact deposited sequence; no isolated-monomer catalytic unit is asserted. The UniProt entry is unreviewed; the primary evidence is genetics and sequence-based functional assignment, not a purified-enzyme assay of this strain U protein. | 4-maleylacetoacetate => 4-fumarylacetoacetateRHEA:14818 |
|
fumarylacetoacetaseUniProtKB:Q6EMI8 | enables Functional gene-product assignment from the native study and exact deposited sequence; no isolated-monomer catalytic unit is asserted. The UniProt entry is unreviewed; the primary evidence is genetics and sequence-based functional assignment, not a purified-enzyme assay of this strain U protein. | 4-fumarylacetoacetate + H2O => acetoacetate + fumarate + H(+)RHEA:10245 |
|
homogentisate + O2 => 4-maleylacetoacetate + H(+)RHEA:15450 | part_of | GO:1902000 |
|
4-maleylacetoacetate => 4-fumarylacetoacetateRHEA:14818 | part_of | GO:1902000 |
|
4-fumarylacetoacetate + H2O => acetoacetate + fumarate + H(+)RHEA:10245 | part_of | GO:1902000 |
|
homogentisate + O2 => 4-maleylacetoacetate + H(+)RHEA:15450 | provides_input_for Direct material connection by the exact shared intermediate and the primary pathway figure; gene order hmgABC is not used as reaction order. | 4-maleylacetoacetate => 4-fumarylacetoacetateRHEA:14818 |
|
4-maleylacetoacetate => 4-fumarylacetoacetateRHEA:14818 | provides_input_for Direct material connection by the exact shared intermediate and the primary pathway figure; gene order hmgABC is not used as reaction order. | 4-fumarylacetoacetate + H2O => acetoacetate + fumarate + H(+)RHEA:10245 |
|
Homogentisate 1,2-dioxygenaseUniProtKB:Q6EMI9 | has_cofactor Inferred strain U annotation. The broad iron-cation identifier does not assert a measured oxidation state or occupancy for this protein. | iron cationCHEBI:24875 |
|
fumarylacetoacetaseUniProtKB:Q6EMI8 | has_cofactor Automatic family-level cofactor annotation, not a strain U binding or activity measurement. The separate Ca and Mg annotations do not establish simultaneous requirements or physiological occupancy. | calcium(2+)CHEBI:29108 |
|
fumarylacetoacetaseUniProtKB:Q6EMI8 | has_cofactor Automatic family-level cofactor annotation, not a strain U binding or activity measurement. The separate Ca and Mg annotations do not establish simultaneous requirements or physiological occupancy. | magnesium(2+)CHEBI:18420 |
|
Homogentisate 1,2-dioxygenaseUniProtKB:Q6EMI9 | located_in Electronic localization annotation; not a direct localization experiment or a claim of exclusive residence. | cytoplasmGO:0005737 |
|
Maleylacetoacetate isomeraseUniProtKB:Q6EMI7 | located_in Electronic localization annotation; not a direct localization experiment or a claim of exclusive residence. | cytoplasmGO:0005737 |
|
References
GO:1902000Gene Ontology homogentisate catabolic process (source version: QuickGO response retrieved 2026-10-11)PMID:15262943The homogentisate pathway: a central catabolic pathway involved in the degradation of L-phenylalanine, L-tyrosine, and 3-hydroxyphenylacetate in Pseudomonas putida. (source version: Journal of Bacteriology 186:5062-5077 (2004); complete 16-page primary PDF, relevant figure, methods and results inspected)UniProtKB:Q6EMI9UniProtKB reviewed (Swiss-Prot) Q6EMI9: native sequence, function and annotation evidence (source version: Native four-entry AY168855 response; Q6EMI9 entry version 76, sequence version 1, annotation updated 2026-01-28)UniProtKB:Q6EMI7UniProtKB unreviewed (TrEMBL) Q6EMI7: native sequence, function and annotation evidence (source version: Native four-entry AY168855 response; Q6EMI7 entry version 79, sequence version 1, annotation updated 2026-09-02)UniProtKB:Q6EMI8UniProtKB unreviewed (TrEMBL) Q6EMI8: native sequence, function and annotation evidence (source version: Native four-entry AY168855 response; Q6EMI8 entry version 72, sequence version 1, annotation updated 2026-09-02)RHEA:15450Rhea directed reaction 15450 (source version: Rhea release 142; complete RDF, exact native triples projected in author dossier)RHEA:14818Rhea directed reaction 14818 (source version: Rhea release 142; complete RDF, exact native triples projected in author dossier)RHEA:10245Rhea directed reaction 10245 (source version: Rhea release 142; complete RDF, exact native triples projected in author dossier)
Curation history
- Codex
- CREATE — Add the complete three-reaction homogentisate catabolic pathway.
Curated exact GO:1902000 for Pseudomonas putida strain U, with deposited sequences linked to HmgA, HmgB and HmgC. Preserved strain U versus KT2440 evidence, unreviewed protein annotation limits, and the boundary distinct from broader tyrosine degradation. Source and duplicate-search dossiers are retained in research/pathway_additions/2026-10-11-next-pathways. Shared identifier authorities, generated pages, validation and independent reviews are recorded separately.
- CREATE — Add the complete three-reaction homogentisate catabolic pathway.