Catechol 1,2-dioxygenase (catA-I, EC 1.13.11.1) catalyzes the intradiol (ortho) ring cleavage of catechol to cis,cis-muconate using non-heme Fe(III) as cofactor. This is the first committed step (step 1/3) in the catechol branch of the beta-ketoadipate pathway, which degrades aromatic compounds such as benzoate via catechol to TCA cycle intermediates. P. putida KT2440 has a paralog catA-II (PP_3166, Q88I35); catA-I (PP_3713) is the primary enzyme in the cat regulon. The enzyme belongs to the intradiol ring-cleavage dioxygenase family (PANTHER: PTHR33711, InterPro: IPR012801).
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003824 catalytic activity | IEA GO_REF:0000002 | MODIFY | Summary: GO:0003824 (catalytic activity) is the top-level molecular function term for any enzyme. CatA has a well-defined specific catalytic activity: catechol 1,2-dioxygenase (EC 1.13.11.1, GO:0018576), which is already annotated. This general parent term adds no information beyond what GO:0018576 provides. Reason: This annotation from InterPro IPR000627 maps to the overly general catalytic activity term. The specific activity GO:0018576 (catechol 1,2-dioxygenase activity) is already annotated and correctly captures the enzymatic function: catechol + O2 = cis,cis-muconate (Rhea:RHEA:23852). The general term should be replaced with the specific one. Proposed replacements: catechol 1,2-dioxygenase activity Supporting Evidence: GO_REF:0000002 InterPro:IPR000627 (Intradiol_dOase_C) maps to catalytic activity, but the more specific catechol 1,2-dioxygenase activity term is available and already annotated via GO_REF:0000120. |
| GO:0005506 iron ion binding | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: GO:0005506 (iron ion binding) is a general term covering both Fe(II) and Fe(III) binding. Intradiol dioxygenases including catechol 1,2-dioxygenase specifically use Fe(III) as the catalytic metal. The more specific term GO:0008199 (ferric iron binding) is already annotated for this protein. This general parent term is redundant. Reason: The enzyme uses non-heme Fe(III) as cofactor (UniProt cofactor annotation: Fe(3+), ChEBI:CHEBI:29034). The more specific GO:0008199 (ferric iron binding) is already present. While iron ion binding is not incorrect, it is a less informative parent of the already-annotated ferric iron binding term and represents an over-annotation. The InterPro domains IPR007535, IPR012801, and IPR015889 that source this annotation are all intradiol dioxygenase domains that use Fe(III) specifically. Supporting Evidence: file:PSEPK/catA/catA-notes.md Non-heme Fe(III) is the catalytic metal [conserved iron-coordinating residues: Tyr, His by homology to characterized intradiol dioxygenases] |
| GO:0008199 ferric iron binding | IEA GO_REF:0000002 | ACCEPT | Summary: GO:0008199 (ferric iron binding) correctly captures the Fe(III) requirement of intradiol dioxygenases. The UniProt cofactor annotation explicitly states Fe(3+) (ChEBI:CHEBI:29034). The structural basis for Fe(III) coordination in this enzyme family involves conserved Tyr and His residues forming a pentacoordinate iron center, as demonstrated in the related hydroxyquinol 1,2-dioxygenase PnpC from P. putida DLL-E4 (PMID:30446218). Reason: Ferric iron binding is the correct and specific molecular function for the cofactor requirement of catechol 1,2-dioxygenase. The enzyme uses Fe(III) in a non-heme iron center for intradiol ring cleavage. This is well-established for the entire intradiol dioxygenase family and confirmed by the UniProt cofactor annotation (Fe(3+), ChEBI:29034). Supporting Evidence: file:PSEPK/catA/catA-uniprot.txt COFACTOR: Name=Fe(3+); Xref=ChEBI:CHEBI:29034; Evidence={ECO:0000256|ARBA:ARBA00001965} file:PSEPK/catA/catA-notes.md Crystal structure of related hydroxyquinol 1,2-dioxygenase PnpC from P. putida DLL-E4 shows conserved Fe(III) pentacoordination by Tyr160, Tyr194, His218, His220 |
| GO:0009712 catechol-containing compound metabolic process | IEA GO_REF:0000002 | MODIFY | Summary: GO:0009712 (catechol-containing compound metabolic process) is a general parent of GO:0019614 (catechol-containing compound catabolic process), which is already annotated. CatA functions specifically in catabolism (degradation) of catechol, not in biosynthesis or other metabolic transformations of catechol-containing compounds. Reason: The enzyme catalyzes degradation (ring cleavage) of catechol, which is specifically a catabolic process. The more specific child term GO:0019614 (catechol-containing compound catabolic process) is already annotated and more accurately represents the biological role. This general metabolic process term should be replaced with the catabolic term. Proposed replacements: catechol-containing compound catabolic process Supporting Evidence: file:PSEPK/catA/catA-uniprot.txt PATHWAY: Aromatic compound metabolism; beta-ketoadipate pathway; 5-oxo-4,5-dihydro-2-furylacetate from catechol: step 1/3. file:PSEPK/catA/catA-notes.md The beta-ketoadipate pathway (ortho-cleavage pathway) degrades aromatic compounds (benzoate, p-hydroxybenzoate) through catechol or protocatechuate as central intermediates. |
| GO:0016702 oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: GO:0016702 is a broad grouping term for dioxygenase activities. It is an ancestor of GO:0018576 (catechol 1,2-dioxygenase activity), which is already annotated. While not incorrect, it provides no additional information beyond what the specific term conveys. Reason: This is a parent class of GO:0018576 (catechol 1,2-dioxygenase activity) which is already annotated. The specific term fully subsumes this general oxidoreductase classification. The IEA mapping from InterPro IPR015889 (intradiol dioxygenase core) is too general when the precise enzymatic activity is known and already annotated. Supporting Evidence: file:PSEPK/catA/catA-uniprot.txt CATALYTIC ACTIVITY: Reaction=catechol + O2 = cis,cis-muconate + 2 H(+); Xref=Rhea:RHEA:23852, ChEBI:CHEBI:15378, ChEBI:CHEBI:15379, ChEBI:CHEBI:18135, ChEBI:CHEBI:32379; EC=1.13.11.1 |
| GO:0018576 catechol 1,2-dioxygenase activity | IEA GO_REF:0000120 | ACCEPT | Summary: GO:0018576 (catechol 1,2-dioxygenase activity) is the correct and specific molecular function term for this enzyme. It catalyzes catechol + O2 = cis,cis-muconate (EC 1.13.11.1, Rhea:RHEA:23852). This is well-supported by the UniProt EC assignment, the gene name (catA = catechol 1,2-dioxygenase), InterPro domain matches (IPR012801, catechol dioxygenase probable; IPR007535, catechol dioxygenase N-terminal), and the TIGRFAMs hit (TIGR02439, catechol_proteo). The P. putida KT2440 genome paper (PMID:12534463) identifies this locus as part of the cat regulon. Reason: This is the core molecular function of catA. The enzyme is named for this activity, has EC 1.13.11.1 assignment, matches the catechol dioxygenase- specific InterPro domain IPR012801 and TIGRFAMs family TIGR02439 (catechol_proteo), and the catalytic reaction is annotated in UniProt (Rhea:RHEA:23852). Multiple lines of evidence converge on this being the correct and specific function. Supporting Evidence: file:PSEPK/catA/catA-uniprot.txt RecName: Full=catechol 1,2-dioxygenase; EC=1.13.11.1 file:PSEPK/catA/catA-uniprot.txt CATALYTIC ACTIVITY: Reaction=catechol + O2 = cis,cis-muconate + 2 H(+); Xref=Rhea:RHEA:23852 PMID:12534463 Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440 [genome paper identifying cat regulon genes] file:PSEPK/catA/catA-deep-research-falcon.md CatA (PP_3713) is the dominant catechol-processing enzyme in KT2440. Intradiol dioxygenases catalyze ortho cleavage and contain Fe(III) in the active site. A typical intradiol dioxygenase architecture comprises ~300-aa subunits with an N-terminal dimerization domain and catalytic domain, and an Fe(III) coordination sphere involving two histidines and two tyrosines plus water/hydroxide. |
| GO:0019614 catechol-containing compound catabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: GO:0019614 (catechol-containing compound catabolic process) correctly captures the biological process in which catA participates. The enzyme catalyzes the ring cleavage of catechol as part of aromatic compound degradation via the beta-ketoadipate pathway. This is the appropriate level of specificity for the catabolic process annotation. Reason: CatA catalyzes the first step of catechol degradation in the beta-ketoadipate pathway, converting catechol to cis,cis-muconate. This is definitionally a catechol-containing compound catabolic process. The term is at the right level of specificity - more specific than the general metabolic process (GO:0009712) and complementary to the pathway term (GO:0042952). Supporting Evidence: file:PSEPK/catA/catA-uniprot.txt PATHWAY: Aromatic compound metabolism; beta-ketoadipate pathway; 5-oxo-4,5-dihydro-2-furylacetate from catechol: step 1/3. file:PSEPK/catA/catA-notes.md Catechol 1,2-dioxygenase catalyzes the intradiol (ortho) ring cleavage of catechol to cis,cis-muconate. This is step 1/3 in the beta-ketoadipate pathway converting catechol to 5-oxo-4,5-dihydro-2-furylacetate. |
| GO:0042952 beta-ketoadipate pathway | IEA GO_REF:0000041 | ACCEPT | Summary: GO:0042952 (beta-ketoadipate pathway) correctly places catA in its pathway context. The beta-ketoadipate (ortho-cleavage) pathway degrades aromatic compounds through catechol or protocatechuate intermediates. CatA catalyzes step 1/3 of the catechol branch (catechol to cis,cis-muconate). This is confirmed by the UniPathway cross-reference (UPA00157, UER00258) and the UniProt pathway annotation. Reason: The beta-ketoadipate pathway is the primary biological pathway in which catA operates. The UniProt record explicitly annotates this pathway membership (UniPathway UPA00157), and the P. putida KT2440 genome identifies catA as part of the cat regulon for the beta-ketoadipate pathway. The cat operon regulation by CatR with cis,cis-muconate as inducer further confirms this pathway assignment. Supporting Evidence: file:PSEPK/catA/catA-uniprot.txt PATHWAY: Aromatic compound metabolism; beta-ketoadipate pathway; 5-oxo-4,5-dihydro-2-furylacetate from catechol: step 1/3. file:PSEPK/catA/catA-notes.md The beta-ketoadipate pathway (ortho-cleavage pathway) degrades aromatic compounds (benzoate, p-hydroxybenzoate) through catechol or protocatechuate as central intermediates. In P. putida KT2440: Benzoate -> catechol (via benABCD), Catechol -> cis,cis-muconate (catA, this gene) |
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