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)
|
The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.
You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.
We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.
We are interested in where in or outside the cell the gene product carries out its function.
We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.
Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.
The target protein CatA-I (PP_3713) in Pseudomonas putida KT2440 is a catechol 1,2-dioxygenase (C1,2O; EC 1.13.11.1) that catalyzes intradiol (ortho) ring cleavage of catechol → cis,cis-muconate, a central step in the benzoate/catechol (ben/cat) branch of the β-ketoadipate pathway that funnels aromatic carbon to succinyl-CoA and acetyl-CoA. Direct genetic and biochemical evidence shows CatA (PP_3713) provides the bulk of C1,2O capacity in KT2440, while a paralog CatA2 (PP_3166) contributes less under typical conditions but becomes important at high catechol load as a “safety valve”. (jimenez2014asecondchromosomal pages 1-4, jimenez2014asecondchromosomal pages 4-7)
KT2440 encodes two catA-type catechol 1,2-dioxygenases:
* catA / CatA (PP_3713): canonical chromosomal enzyme; dominant activity. (jimenez2014asecondchromosomal pages 1-4, jimenez2014asecondchromosomal pages 4-7)
* catA2 / CatA2 (PP_3166): second chromosomal copy downstream of the ben operon; functional C1,2O, proposed as a safety valve at high catechol. (jimenez2014asecondchromosomal pages 1-4, jimenez2014asecondchromosomal pages 4-7)
Because the question targets Q88GK8 = PP_3713, this report focuses on CatA (PP_3713), referencing CatA2 only where it informs CatA’s physiological context.
Catechol 1,2-dioxygenases are intradiol aromatic ring-cleaving enzymes that perform ortho cleavage between the two hydroxylated carbons of catechol to yield cis,cis-muconate (muconic acid) (terminology varies by protonation state). For KT2440 CatA, this is described as ortho cleavage of catechol → cis,cis-muconate. (jimenez2014asecondchromosomal pages 1-4, jimenez2002genomicanalysisof pages 5-6)
In KT2440, benzoate is converted to catechol via the ben genes, and catechol is processed via the cat genes (including catA) as part of the chromosome-encoded ortho/β-ketoadipate route to central metabolism. (jimenez2014asecondchromosomal pages 1-4, jimenez2014asecondchromosomal pages 18-22)
A key regulatory architecture is:
* BenR and XylS respond to benzoate (inducing ben-related functions). (jimenez2014asecondchromosomal pages 18-22)
* CatR responds to cis,cis-muconate and induces the cat operon (catBCA and related genes). (jimenez2014asecondchromosomal pages 18-22, duuren2011generationofa pages 8-9)
A CatR mutation can prevent cat operon induction and alter muconate accumulation phenotypes. (duuren2011generationofa pages 8-9)
Primary function: Catechol 1,2-dioxygenase CatA (PP_3713) catalyzes the ring cleavage of catechol to cis,cis-muconate, measured by product formation at 260 nm in enzymatic assays. (jimenez2014asecondchromosomal pages 1-4, jimenez2014asecondchromosomal pages 12-15)
Kinetic comparisons in KT2440 show CatA is a high-capacity, high-affinity enzyme relative to CatA2:
* CatA (PP_3713): apparent Km ~1.3 ± 0.2 µM, Vmax ~6.6 ± 0.3 µmol·min⁻¹·mg⁻¹. (jimenez2014asecondchromosomal pages 4-7)
* CatA2 (PP_3166): apparent Km ~7.4 ± 1.4 µM, Vmax ~0.3 ± 0.1 µmol·min⁻¹·mg⁻¹. (jimenez2014asecondchromosomal pages 4-7)
These kinetics support a model where CatA2 contributes disproportionately when catechol is high (CatA saturation). (jimenez2014asecondchromosomal pages 4-7)
Both KT2440 enzymes cleave catechol most efficiently; substituted catechols are accepted with reduced activity. Reported relative activities include:
* 4-methylcatechol: CatA 44%, CatA2 59%
* 3-methylcatechol: CatA 5%, CatA2 7%
* 4-chlorocatechol: CatA 1.7%, CatA2 5%
* Protocatechuate: CatA <1%, CatA2 not detected (n.d.)
(jimenez2014asecondchromosomal pages 35-37)
In KT2440 during benzoate use, CatA is estimated to process >95% of benzoate-derived catechol flux, with CatA2 contributing <5% under standard conditions. (jimenez2014asecondchromosomal pages 4-7)
Direct subcellular localization experiments (e.g., fluorescence tagging) were not retrieved in the present evidence set. However, multiple independent lines support intracellular/soluble (cytosolic) localization consistent with canonical intradiol dioxygenases:
* CatA/CatA2 activity is assayed from crude cell extracts obtained after cell lysis, indicating an intracellular soluble enzyme fraction. (jimenez2014asecondchromosomal pages 12-15)
* CatA/CatA2 were expressed and recovered as soluble proteins for biochemical assays in heterologous expression contexts, consistent with soluble cytosolic enzymes rather than secreted/periplasmic proteins. (jimenez2014asecondchromosomal pages 4-7)
Deletion analysis in KT2440 shows:
* ΔcatA2: no detectable growth phenotype under tested benzoate conditions. (jimenez2014asecondchromosomal pages 4-7)
* ΔcatA: significantly delayed growth on benzoate; reduced C1,2O activity. (jimenez2014asecondchromosomal pages 4-7)
* ΔcatA ΔcatA2: no detectable C1,2O activity and inability to grow on 5 mM benzoate; catechol accumulation visible as dark/brown pigments. (jimenez2014asecondchromosomal pages 4-7, jimenez2014asecondchromosomal pages 1-4)
Measured crude-extract activities strongly support CatA dominance:
* WT: 1.2 ± 0.2 µmol·min⁻¹·mg⁻¹
* ΔcatA2: 0.96 ± 0.07
* ΔcatA: 0.08 ± 0.02
(jimenez2014asecondchromosomal pages 4-7)
A biosensor-based intracellular catechol assay indicates that while wild type can remove intracellular catechol even at high benzoate, strains lacking CatA2 accumulate catechol above roughly ~1 mM benzoate, consistent with CatA saturation and CatA2 engagement. (jimenez2014asecondchromosomal pages 4-7)
Although no structure or metal-cofactor measurements for KT2440 CatA (PP_3713) were retrieved directly, 2024 literature summarizes consensus for intradiol catechol 1,2-dioxygenases:
* Intradiol dioxygenases catalyze ortho cleavage and contain Fe(III) in the active site. (davletgildeeva2024bioremediationofpolycyclic pages 14-16)
* Mechanistic proposals include Fe(III)-assisted substrate activation (iron(II)-semiquinone formation), reaction with O2 to a peroxide/hydroperoxide intermediate, and rearrangement steps leading to muconic products. (lister2024…codeexpansion pages 23-28, lister2024…codeexpansion pages 17-23)
* A typical intradiol dioxygenase architecture comprises ~300-aa subunits with an N-terminal dimerization domain and catalytic domain, and an Fe(III) coordination sphere commonly involving two histidines and two tyrosines plus water/hydroxide. (lister2024…codeexpansion pages 23-28)
Given that KT2440 CatA is explicitly classified as an intradiol dioxygenase and is ~311 aa, these family-level properties are a reasonable mechanistic framing but should be treated as inference from family membership, not KT2440-specific measurement. (jimenez2002genomicanalysisof pages 5-6, lister2024…codeexpansion pages 23-28)
Aromatic catabolic genes in KT2440 include a canonical cat cluster and a second catA-like gene within the ben cluster. Early genome-scale analysis identified both catA and catA2 annotated as catechol 1,2-dioxygenases, with catA2 located in the benzoate (ben) cluster. (jimenez2002genomicanalysisof pages 5-6)
CatR is a LysR-type regulator that divergently induces cat genes in response to cis,cis-muconate; a point mutation in catR can abolish cat operon induction, altering catechol processing capacity and enabling muconate accumulation phenotypes. (duuren2011generationofa pages 8-9)
CatA (PP_3713) is a central control point because it sits at the catechol node, which is both a toxicity hotspot and an industrial platform-chemical precursor node.
An applied metabolic engineering strategy is to knock out catA and catA2 to prevent catechol cleavage and accumulate catechol from benzoate/aromatic streams:
* On sodium benzoate, ΔcatA showed transient catechol accumulation and 27.47% molar catechol yield; ΔcatAΔcatA2 improved to 57.68% molar yield with stable accumulation, while growth rates decreased from 0.27 h⁻¹ (WT) to 0.22 h⁻¹ (ΔcatA) and 0.18 h⁻¹ (ΔcatAΔcatA2). (upadhyay2022engineeredpseudomonasputida pages 5-7)
These data demonstrate CatA’s role as the primary sink preventing catechol accumulation and underscore why it is a primary engineering target.
Industrial biotechnology perspectives identify the catechol → muconate step (CatA/C1,2O) as critical for improving catechol tolerance and muconate productivity. One reported approach is introducing an extra copy of catA2 under the native Pcat promoter to increase catechol 1,2-dioxygenase activity, improving catechol tolerance and degradation. (weimer2020industrialbiotechnologyof pages 11-12)
Process-level metrics cited for engineered P. putida systems include:
* 64.2 g·L⁻¹ cis,cis-muconate produced from catechol via fed-batch strategies that address energy limitation, and a stated kilogram-scale pilot with 98% product purity. (weimer2020industrialbiotechnologyof pages 11-12)
These values indicate real-world scaling and provide context for why CatA-level control is industrially important.
A 2023 high-impact study engineered Pseudomonas putida for plastic upcycling and muconate production with explicit manipulation of the catRBCA region:
* A knockout of the catRBCA cluster was used to eliminate muconate utilization in one engineered strain background. (bao2023engineeringmicrobialdivision pages 9-10)
* A separate construct deleted catRBC and inserted a Ptac promoter upstream of catA (placing catA under a strong/inducible promoter) to increase catechol 1,2-dioxygenase expression and drive catechol → muconate. (bao2023engineeringmicrobialdivision pages 9-10)
* In a division-of-labor consortium, the system produced 33.28 ± 1.34 mM (4.73 ± 0.19 g·L⁻¹) cis,cis-muconic acid, reported as a 2.84-fold improvement over a comparator fermentation. (bao2023engineeringmicrobialdivision pages 8-9)
This is a concrete, recent (2023) example of direct catA locus engineering for muconate as a product from plastic-derived feedstocks.
A structured summary of the most relevant kinetics/activities/substrate specificity and engineering phenotypes is provided below.
| Metric | CatA / catA-I (PP_3713) | CatA2 (PP_3166) | Notes / citation |
|---|---|---|---|
| Apparent Km for catechol | 1.3 ± 0.2 µM | 7.4 ± 1.4 µM | Purified/overexpressed enzymes; CatA has higher apparent affinity for catechol (jimenez2014asecondchromosomal pages 4-7) |
| Apparent Vmax for catechol | 6.6 ± 0.3 µmol·min⁻¹·mg⁻¹ | 0.3 ± 0.1 µmol·min⁻¹·mg⁻¹ | Jiménez et al. 2014 kinetic comparison (jimenez2014asecondchromosomal pages 4-7) |
| Relative activity on catechol | 100% | 100% | Substrate specificity benchmark (jimenez2014asecondchromosomal pages 35-37, jimenez2014asecondchromosomal pages 31-35) |
| Relative activity on 4-methylcatechol | 44% | 59% | CatA2 somewhat higher than CatA (jimenez2014asecondchromosomal pages 35-37, jimenez2014asecondchromosomal pages 31-35) |
| Relative activity on 3-methylcatechol | 5% | 7% | Low activity for both enzymes (jimenez2014asecondchromosomal pages 35-37, jimenez2014asecondchromosomal pages 31-35) |
| Relative activity on 4-chlorocatechol | 1.7% | 5% | Very low activity; CatA2 higher than CatA (jimenez2014asecondchromosomal pages 35-37) |
| Relative activity on protocatechuate | <1% | n.d. | Trace/undetectable under conditions tested (jimenez2014asecondchromosomal pages 35-37) |
| Crude extract C1,2O activity in WT background | 1.2 ± 0.2 µmol·min⁻¹·mg⁻¹ | — | Whole-cell extract from KT2440 wild type; reflects total chromosomal activity dominated by CatA (jimenez2014asecondchromosomal pages 4-7) |
| Crude extract C1,2O activity in ΔcatA2 mutant | 0.96 ± 0.07 µmol·min⁻¹·mg⁻¹ | — | Little loss versus WT, consistent with minor CatA2 contribution under standard conditions (jimenez2014asecondchromosomal pages 4-7) |
| Crude extract C1,2O activity in ΔcatA mutant | 0.08 ± 0.02 µmol·min⁻¹·mg⁻¹ | — | Residual activity attributable mainly to CatA2 (jimenez2014asecondchromosomal pages 4-7) |
| Contribution to benzoate-derived catechol processing | >95% | <5% | Estimated in vivo division of labor during benzoate catabolism (jimenez2014asecondchromosomal pages 4-7) |
| Additional CatA2 kinetics from independent study | — | Km = 0.0010 mM; Vmax ≈ 0.4 M·min⁻¹·mg⁻¹; IC50 (cis,cis-muconate) = 0.1392 mM; Ki = 0.0028 mM | Heterologous characterization in van Duuren et al. 2011; reported units/format as given in source (duuren2011generationofa pages 8-9) |
| Growth rate on sodium benzoate (engineered strains) | WT: 0.27 h⁻¹; ΔcatA: 0.22 h⁻¹ | ΔcatAΔcatA2: 0.18 h⁻¹ | Upadhyay et al. 2022, relevant for physiological impact of deleting catechol-cleavage capacity (upadhyay2022engineeredpseudomonasputida pages 5-7) |
| Catechol accumulation / yield on sodium benzoate (engineered strains) | ΔcatA: 27.47 mol% yield; max catechol accumulation 0.202 g/g at ~8 h | ΔcatAΔcatA2: 57.68 mol% yield; stable catechol accumulation 0.507 g/g | Upadhyay et al. 2022; useful application metric showing why CatA/CatA2 are engineering targets (upadhyay2022engineeredpseudomonasputida pages 5-7) |
Table: This table compiles the main quantitative biochemical and physiological data for the two catechol 1,2-dioxygenases in Pseudomonas putida KT2440. It is useful for comparing the dominant housekeeping enzyme CatA/catA-I (PP_3713) with the secondary paralog CatA2 (PP_3166) in terms of affinity, activity, substrate scope, and engineering consequences.
Figure-level evidence supporting pathway context and substrate specificity was retrieved from the key KT2440 CatA/CatA2 study:
* ben/cat pathway and genetic context figure (jimenez2014asecondchromosomal media 370bf556)
* substrate specificity table for CatA vs CatA2 (jimenez2014asecondchromosomal media 3b231231)
References
(jimenez2014asecondchromosomal pages 1-4): Jose I. Jiménez, Danilo Pérez‐Pantoja, Max Chavarría, Eduardo Díaz, and Víctor de Lorenzo. A second chromosomal copy of the cata gene endows pseudomonas putida mt-2 with an enzymatic safety valve for excess of catechol. Environmental microbiology, 16 6:1767-78, Jun 2014. URL: https://doi.org/10.1111/1462-2920.12361, doi:10.1111/1462-2920.12361. This article has 53 citations and is from a domain leading peer-reviewed journal.
(jimenez2014asecondchromosomal pages 4-7): Jose I. Jiménez, Danilo Pérez‐Pantoja, Max Chavarría, Eduardo Díaz, and Víctor de Lorenzo. A second chromosomal copy of the cata gene endows pseudomonas putida mt-2 with an enzymatic safety valve for excess of catechol. Environmental microbiology, 16 6:1767-78, Jun 2014. URL: https://doi.org/10.1111/1462-2920.12361, doi:10.1111/1462-2920.12361. This article has 53 citations and is from a domain leading peer-reviewed journal.
(jimenez2002genomicanalysisof pages 5-6): José Ignacio Jiménez, Baltasar Miñambres, José Luis García, and Eduardo Díaz. Genomic analysis of the aromatic catabolic pathways from pseudomonas putida kt2440. Environmental microbiology, 4 12:824-41, Dec 2002. URL: https://doi.org/10.1046/j.1462-2920.2002.00370.x, doi:10.1046/j.1462-2920.2002.00370.x. This article has 688 citations and is from a domain leading peer-reviewed journal.
(jimenez2014asecondchromosomal pages 18-22): Jose I. Jiménez, Danilo Pérez‐Pantoja, Max Chavarría, Eduardo Díaz, and Víctor de Lorenzo. A second chromosomal copy of the cata gene endows pseudomonas putida mt-2 with an enzymatic safety valve for excess of catechol. Environmental microbiology, 16 6:1767-78, Jun 2014. URL: https://doi.org/10.1111/1462-2920.12361, doi:10.1111/1462-2920.12361. This article has 53 citations and is from a domain leading peer-reviewed journal.
(duuren2011generationofa pages 8-9): J.B.J.H. van Duuren, D. Wijte, Audrey Leprince, Bianka Karge, Jacek Puchałka, Jan Wery, V.A.P. Martins dos Santos, Gerrit Eggink, and A. Mars. Generation of a catr deficient mutant of p. putida kt2440 that produces cis, cis-muconate from benzoate at high rate and yield. Journal of biotechnology, 156 3:163-72, Dec 2011. URL: https://doi.org/10.1016/j.jbiotec.2011.08.030, doi:10.1016/j.jbiotec.2011.08.030. This article has 67 citations and is from a peer-reviewed journal.
(jimenez2014asecondchromosomal pages 12-15): Jose I. Jiménez, Danilo Pérez‐Pantoja, Max Chavarría, Eduardo Díaz, and Víctor de Lorenzo. A second chromosomal copy of the cata gene endows pseudomonas putida mt-2 with an enzymatic safety valve for excess of catechol. Environmental microbiology, 16 6:1767-78, Jun 2014. URL: https://doi.org/10.1111/1462-2920.12361, doi:10.1111/1462-2920.12361. This article has 53 citations and is from a domain leading peer-reviewed journal.
(jimenez2014asecondchromosomal pages 35-37): Jose I. Jiménez, Danilo Pérez‐Pantoja, Max Chavarría, Eduardo Díaz, and Víctor de Lorenzo. A second chromosomal copy of the cata gene endows pseudomonas putida mt-2 with an enzymatic safety valve for excess of catechol. Environmental microbiology, 16 6:1767-78, Jun 2014. URL: https://doi.org/10.1111/1462-2920.12361, doi:10.1111/1462-2920.12361. This article has 53 citations and is from a domain leading peer-reviewed journal.
(davletgildeeva2024bioremediationofpolycyclic pages 14-16): Anastasiia T. Davletgildeeva and Nikita A. Kuznetsov. Bioremediation of polycyclic aromatic hydrocarbons by means of bacteria and bacterial enzymes. Sep 2024. URL: https://doi.org/10.3390/microorganisms12091814, doi:10.3390/microorganisms12091814. This article has 34 citations.
(lister2024…codeexpansion pages 23-28): J Lister. … code expansion and rational disulfide bond design to engineer improved activity and (thermo) stability of rhodococcus opacus catechol 1, 2-dioxygenase. Unknown journal, 2024.
(lister2024…codeexpansion pages 17-23): J Lister. … code expansion and rational disulfide bond design to engineer improved activity and (thermo) stability of rhodococcus opacus catechol 1, 2-dioxygenase. Unknown journal, 2024.
(upadhyay2022engineeredpseudomonasputida pages 5-7): Priya Upadhyay and Arvind Lali. Engineered pseudomonas putida for biosynthesis of catechol from lignin-derived model compounds and biomass hydrolysate. Preparative Biochemistry & Biotechnology, 52:80-88, Apr 2022. URL: https://doi.org/10.1080/10826068.2021.1910960, doi:10.1080/10826068.2021.1910960. This article has 11 citations and is from a peer-reviewed journal.
(weimer2020industrialbiotechnologyof pages 11-12): Anna Weimer, Michael Kohlstedt, Daniel C. Volke, Pablo I. Nikel, and Christoph Wittmann. Industrial biotechnology of pseudomonas putida: advances and prospects. Applied Microbiology and Biotechnology, 104:7745-7766, Aug 2020. URL: https://doi.org/10.1007/s00253-020-10811-9, doi:10.1007/s00253-020-10811-9. This article has 336 citations and is from a domain leading peer-reviewed journal.
(bao2023engineeringmicrobialdivision pages 9-10): Teng Bao, Yuanchao Qian, Yongping Xin, James J. Collins, and Ting Lu. Engineering microbial division of labor for plastic upcycling. Nature Communications, Sep 2023. URL: https://doi.org/10.1038/s41467-023-40777-x, doi:10.1038/s41467-023-40777-x. This article has 123 citations and is from a highest quality peer-reviewed journal.
(bao2023engineeringmicrobialdivision pages 8-9): Teng Bao, Yuanchao Qian, Yongping Xin, James J. Collins, and Ting Lu. Engineering microbial division of labor for plastic upcycling. Nature Communications, Sep 2023. URL: https://doi.org/10.1038/s41467-023-40777-x, doi:10.1038/s41467-023-40777-x. This article has 123 citations and is from a highest quality peer-reviewed journal.
(sitompul2024improvinginhibitoranda pages 51-54): SN Sitompul. Improving inhibitor and glycerol tolerance of cupriavidus necator h16 via adaptive laboratory evolution (ale). Unknown journal, 2024.
(jimenez2014asecondchromosomal pages 31-35): Jose I. Jiménez, Danilo Pérez‐Pantoja, Max Chavarría, Eduardo Díaz, and Víctor de Lorenzo. A second chromosomal copy of the cata gene endows pseudomonas putida mt-2 with an enzymatic safety valve for excess of catechol. Environmental microbiology, 16 6:1767-78, Jun 2014. URL: https://doi.org/10.1111/1462-2920.12361, doi:10.1111/1462-2920.12361. This article has 53 citations and is from a domain leading peer-reviewed journal.
(jimenez2014asecondchromosomal media 370bf556): Jose I. Jiménez, Danilo Pérez‐Pantoja, Max Chavarría, Eduardo Díaz, and Víctor de Lorenzo. A second chromosomal copy of the cata gene endows pseudomonas putida mt-2 with an enzymatic safety valve for excess of catechol. Environmental microbiology, 16 6:1767-78, Jun 2014. URL: https://doi.org/10.1111/1462-2920.12361, doi:10.1111/1462-2920.12361. This article has 53 citations and is from a domain leading peer-reviewed journal.
(jimenez2014asecondchromosomal media 3b231231): Jose I. Jiménez, Danilo Pérez‐Pantoja, Max Chavarría, Eduardo Díaz, and Víctor de Lorenzo. A second chromosomal copy of the cata gene endows pseudomonas putida mt-2 with an enzymatic safety valve for excess of catechol. Environmental microbiology, 16 6:1767-78, Jun 2014. URL: https://doi.org/10.1111/1462-2920.12361, doi:10.1111/1462-2920.12361. This article has 53 citations and is from a domain leading peer-reviewed journal.
Catechol 1,2-dioxygenase catalyzes the intradiol (ortho) ring cleavage of catechol to cis,cis-muconate:
catechol + O2 -> cis,cis-muconate + 2H+
This is step 1/3 in the beta-ketoadipate pathway converting catechol to 5-oxo-4,5-dihydro-2-furylacetate PMID:12534463.
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)
- cis,cis-muconate -> muconolactone (catB, muconate cycloisomerase)
- muconolactone -> beta-ketoadipate enol-lactone (catC, muconolactone isomerase)
P. putida KT2440 has a second catechol 1,2-dioxygenase (catA-II, Q88I35, 304 aa). catA-I (PP_3713) is considered the primary enzyme in the beta-ketoadipate/cat pathway context.
Exported on March 22, 2026 at 02:33 AM
Organism: Pseudomonas putida
Sequence:
MTVKISHTADIQAFFNRVAGLDHAEGNPRFKQIILRVLQDTARLIEDLEITEDEFWHAVDYLNRLGGRNEAGLLAAGLGIEHFLDLLQDAKDAEAGLGGGTPRTIEGPLYVAGAPLAQGEARMDDGTDPGVVMFLQGQVFDADGKPLAGATVDLWHANTQGTYSYFDSTQSEFNLRRRIITDAEGRYRARSIVPSGYGCDPQGPTQECLDLLGRHGQRPAHVHFFISAPGHRHLTTQINFAGDKYLWDDFAYATRDGLIGELRFVEDAAAARDRGVQGERFAELSFDFRLQGAKSPDAEARSHRPRALQEG
I begin with the InterPro architecture. The sequence is covered end-to-end by IPR015889 (Intradiol ring-cleavage dioxygenase, core homologous superfamily, residues 1–311), establishing a classic ferric-heme fold that binds and activates O2 for intradiol aromatic ring scission. Within this scaffold, two family-level signatures reinforce the enzyme class: IPR012801 (Catechol 1,2-dioxygenase, proteobacteria family, residues 8–291) and IPR050770 (Intradiol Ring-Cleavage Dioxygenase family, residues 21–295). The architecture resolves into two functional lobes: an N-terminal catalytic module IPR007535 (Catechol dioxygenase, N-terminal domain, residues 27–96) followed by IPR000627 (Intradiol ring-cleavage dioxygenase, C-terminal domain, residues 105–292). This bipartite arrangement is typical of soluble bacterial catechol/ intradiol dioxygenases, where the N-terminus helps coordinate the ferric cofactor and shape the substrate pocket, and the C-terminus completes the oxygenase barrel and substrate channel.
This domain ensemble dictates molecular function. The intradiol dioxygenase core and proteobacterial catechol 1,2-dioxygenase signatures specify a non-heme Fe(III)-dependent dioxygenase that incorporates both atoms of molecular oxygen into a catecholic substrate via intradiol cleavage chemistry. That chemistry defines dioxygenase activity and inherently requires heme/iron cofactor binding. Thus, the primary molecular function is dioxygenase catalysis (GO:0051213), supported by a heme-binding catalytic core and consistent with iron-dependent oxygenation.
From function to process, intradiol dioxygenation of catechols is a central step in aromatic compound catabolism. The explicit proteobacterial catechol 1,2-dioxygenase family mark ties the enzyme to the aerobic degradation routes of catechol and related intermediates, funneling diverse ring-containing aromatics toward central metabolism. This places the enzyme squarely in aromatic compound catabolic pathways, i.e., the biological process of breaking down aromatic molecules.
Cellular location follows from the soluble, non-membranous architecture. The absence of signal peptides or transmembrane segments in this soluble oxygenase fold, together with the cytosolic nature of catechol/ intradiol pathways in Gram-negative bacteria, indicates a cytoplasmic enzyme. This aligns with a soluble, intracellular localization where substrate pools and downstream enzymes are accessible.
Mechanistically, the N-terminal dioxygenase domain and the C-terminal barrel assemble a ferric-heme center that polarizes and activates O2 for intradiol cleavage of catechol to form cis,cis-muconate. The iron center and adjacent residues enforce catechol binding and concerted O–O scission. In vivo, this enzyme likely operates downstream of catechol-forming steps and upstream of muconate-cleavage enzymes, creating a metabolic node that couples oxygenation to ring fission. I therefore hypothesize transient assemblies with catechol-forming enzymes and muconate-processing enzymes to channel intermediates efficiently in the cytoplasm of Pseudomonas putida.
A soluble bacterial oxygenase that catalyzes intradiol cleavage of catecholic substrates as part of aerobic aromatic breakdown. It uses a non-heme iron–heme catalytic core to incorporate molecular oxygen into catechol, producing ring-opened muconate intermediates that feed into central metabolism. Operating as a cytoplasmic enzyme, it likely forms transient assemblies with adjacent steps in the pathway to streamline the flow of aromatic intermediates.
Involved in the degradation of aromatic compounds.
IPR015889, homologous_superfamily) — residues 1-311IPR012801, family) — residues 8-291IPR050770, family) — residues 21-295IPR007535, domain) — residues 27-96IPR000627, domain) — residues 105-292Molecular Function: molecular_function (GO:0003674), binding (GO:0005488), catalytic activity (GO:0003824), sulfur compound binding (GO:1901681), ion binding (GO:0043167), oxidoreductase activity (GO:0016491), cation binding (GO:0043169), dioxygenase activity (GO:0051213), oxidoreductase activity, acting on single donors with incorporation of molecular oxygen (GO:0016701), oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702), metal ion binding (GO:0046872), transition metal ion binding (GO:0046914), iron ion binding (GO:0005506)
Biological Process: biological_process (GO:0008150), metabolic process (GO:0008152), cellular process (GO:0009987), catabolic process (GO:0009056), cellular metabolic process (GO:0044237), organic substance metabolic process (GO:0071704), organic substance catabolic process (GO:1901575), organic hydroxy compound metabolic process (GO:1901615), cellular aromatic compound metabolic process (GO:0006725), organic cyclic compound metabolic process (GO:1901360), aromatic compound catabolic process (GO:0019439), phenol-containing compound metabolic process (GO:0018958), organic cyclic compound catabolic process (GO:1901361)
Cellular Component: cellular_component (GO:0005575), cellular anatomical entity (GO:0110165), cytoplasm (GO:0005737), intracellular anatomical structure (GO:0005622)
Generated by BioReason
Source: catA-bioreason-rl-predictions.md
The BioReason functional summary describes catA as:
A soluble bacterial oxygenase that catalyzes intradiol cleavage of catecholic substrates as part of aerobic aromatic breakdown. It uses a non-heme iron-heme catalytic core to incorporate molecular oxygen into catechol, producing ring-opened muconate intermediates that feed into central metabolism. Operating as a cytoplasmic enzyme, it likely forms transient assemblies with adjacent steps in the pathway to streamline the flow of aromatic intermediates.
This is a largely accurate summary. The core function is correctly identified:
- Intradiol ring cleavage of catechol
- Aerobic aromatic compound degradation
- Production of cis,cis-muconate
- Cytoplasmic localization
- Non-heme iron cofactor
One notable error: the summary mentions "non-heme iron-heme catalytic core," which is self-contradictory. Catechol 1,2-dioxygenase uses a non-heme Fe(III) cofactor, not heme. The thinking trace also refers to a "ferric-heme fold" and "ferric-heme center," which is incorrect terminology for an intradiol dioxygenase. This appears to be a confusion between heme-dependent and non-heme iron-dependent oxygenases.
Other minor gaps:
- Does not specify the enzyme as catechol 1,2-dioxygenase (EC 1.13.11.1)
- Does not place it in the beta-ketoadipate pathway specifically
- Does not mention the paralog catA-II (PP_3166) in KT2440
- The "transient assemblies with adjacent steps" hypothesis is reasonable but unsubstantiated
Comparison with interpro2go:
The curated review's interpro2go annotations include catalytic activity (GO:0003824, noted as too general), oxidoreductase activity (GO:0016491, accepted), iron ion binding (GO:0005506, accepted), and catechol 1,2-dioxygenase activity (GO:0018576, accepted as the specific correct annotation). BioReason's functional summary captures the dioxygenase activity at an appropriate level of specificity. The model correctly identifies the intradiol ring-cleavage dioxygenase family from InterPro, which is essentially recapitulating what interpro2go provides. The narrative adds pathway context (aromatic compound degradation) that goes modestly beyond interpro2go.
The trace correctly identifies all five InterPro domains and reasons well from domain architecture to catalytic function. The "heme" terminology is a consistent error throughout the trace. The mention of "muconate-processing enzymes" as downstream partners is appropriate for the beta-ketoadipate pathway.
id: Q88GK8
gene_symbol: catA
product_type: PROTEIN
status: DRAFT
taxon:
id: NCBITaxon:160488
label: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950
/ KT2440)
description: >-
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).
existing_annotations:
- term:
id: GO:0003824
label: catalytic activity
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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.
action: MODIFY
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_replacement_terms:
- id: GO:0018576
label: catechol 1,2-dioxygenase activity
supported_by:
- reference_id: GO_REF:0000002
supporting_text: >-
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.
- term:
id: GO:0005506
label: iron ion binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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.
action: MARK_AS_OVER_ANNOTATED
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.
supported_by:
- reference_id: file:PSEPK/catA/catA-notes.md
supporting_text: >-
Non-heme Fe(III) is the catalytic metal [conserved iron-coordinating
residues: Tyr, His by homology to characterized intradiol dioxygenases]
- term:
id: GO:0008199
label: ferric iron binding
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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).
action: ACCEPT
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).
supported_by:
- reference_id: file:PSEPK/catA/catA-uniprot.txt
supporting_text: >-
COFACTOR: Name=Fe(3+); Xref=ChEBI:CHEBI:29034;
Evidence={ECO:0000256|ARBA:ARBA00001965}
- reference_id: file:PSEPK/catA/catA-notes.md
supporting_text: >-
Crystal structure of related hydroxyquinol 1,2-dioxygenase PnpC from
P. putida DLL-E4 shows conserved Fe(III) pentacoordination by Tyr160,
Tyr194, His218, His220
- term:
id: GO:0009712
label: catechol-containing compound metabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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.
action: MODIFY
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_replacement_terms:
- id: GO:0019614
label: catechol-containing compound catabolic process
supported_by:
- reference_id: file:PSEPK/catA/catA-uniprot.txt
supporting_text: >-
PATHWAY: Aromatic compound metabolism; beta-ketoadipate pathway;
5-oxo-4,5-dihydro-2-furylacetate from catechol: step 1/3.
- reference_id: file:PSEPK/catA/catA-notes.md
supporting_text: >-
The beta-ketoadipate pathway (ortho-cleavage pathway) degrades aromatic
compounds (benzoate, p-hydroxybenzoate) through catechol or
protocatechuate as central intermediates.
- term:
id: GO:0016702
label: oxidoreductase activity, acting on single donors with incorporation of
molecular oxygen, incorporation of two atoms of oxygen
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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.
action: MARK_AS_OVER_ANNOTATED
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.
supported_by:
- reference_id: file:PSEPK/catA/catA-uniprot.txt
supporting_text: >-
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
- term:
id: GO:0018576
label: catechol 1,2-dioxygenase activity
evidence_type: IEA
original_reference_id: GO_REF:0000120
review:
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.
action: ACCEPT
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.
supported_by:
- reference_id: file:PSEPK/catA/catA-uniprot.txt
supporting_text: >-
RecName: Full=catechol 1,2-dioxygenase; EC=1.13.11.1
- reference_id: file:PSEPK/catA/catA-uniprot.txt
supporting_text: >-
CATALYTIC ACTIVITY: Reaction=catechol + O2 = cis,cis-muconate + 2
H(+); Xref=Rhea:RHEA:23852
- reference_id: PMID:12534463
supporting_text: >-
Complete genome sequence and comparative analysis of the metabolically
versatile Pseudomonas putida KT2440 [genome paper identifying cat
regulon genes]
- reference_id: file:PSEPK/catA/catA-deep-research-falcon.md
supporting_text: >-
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.
- term:
id: GO:0019614
label: catechol-containing compound catabolic process
evidence_type: IEA
original_reference_id: GO_REF:0000002
review:
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.
action: ACCEPT
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).
supported_by:
- reference_id: file:PSEPK/catA/catA-uniprot.txt
supporting_text: >-
PATHWAY: Aromatic compound metabolism; beta-ketoadipate pathway;
5-oxo-4,5-dihydro-2-furylacetate from catechol: step 1/3.
- reference_id: file:PSEPK/catA/catA-notes.md
supporting_text: >-
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.
- term:
id: GO:0042952
label: beta-ketoadipate pathway
evidence_type: IEA
original_reference_id: GO_REF:0000041
review:
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.
action: ACCEPT
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.
supported_by:
- reference_id: file:PSEPK/catA/catA-uniprot.txt
supporting_text: >-
PATHWAY: Aromatic compound metabolism; beta-ketoadipate pathway;
5-oxo-4,5-dihydro-2-furylacetate from catechol: step 1/3.
- reference_id: file:PSEPK/catA/catA-notes.md
supporting_text: >-
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)
references:
- id: GO_REF:0000002
title: Gene Ontology annotation through association of InterPro records with GO
terms
findings: []
- id: GO_REF:0000041
title: Gene Ontology annotation based on UniPathway vocabulary mapping
findings: []
- id: GO_REF:0000120
title: Combined Automated Annotation using Multiple IEA Methods
findings: []
- id: PMID:12534463
title: Complete genome sequence and comparative analysis of the metabolically
versatile Pseudomonas putida KT2440
findings:
- statement: >-
The P. putida KT2440 genome encodes genes for aromatic compound
degradation pathways including the beta-ketoadipate pathway via the cat
regulon.
supporting_text: >-
Pseudomonas putida is a metabolically versatile saprophytic soil
bacterium... Sequence analysis of the 6.18 Mb genome of strain KT2440
reveals diverse transport and metabolic systems.
- id: PMID:24341396
title: >-
A second chromosomal copy of the catA gene endows Pseudomonas putida mt-2
with an enzymatic safety valve for excess of catechol
findings:
- statement: >-
CatA is the dominant catechol 1,2-dioxygenase in P. putida, with CatA2
serving as a metabolic safety valve for excess catechol at high
concentrations. Induction of the ortho pathway by benzoate in KT2440
leads to catechol surplus counteracted by CatA2.
supporting_text: >-
The data consistently indicated that induction of the ortho pathway by
benzoate plasmid-less strain P. putida KT2440 led to catechol surplus,
the toxicity of which at high concentrations being counteracted by CatA2.
- statement: >-
P. putida mt-2 has a second chromosomal copy of the catA gene (catA2)
located downstream of the ben operon encoding an additional catechol
1,2-dioxygenase.
supporting_text: >-
P. putida mt-2 has a second chromosomal copy of the catA gene (named
catA2) located downstream of the ben operon that encodes an additional
catechol-1,2-dioxygenase.
- id: PMID:12534466
title: >-
Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida
KT2440
findings:
- statement: >-
KT2440 has catechol (cat genes) and protocatechuate (pca genes) branches
of the beta-ketoadipate pathway, plus homogentisate and phenylacetate
pathways for aromatic compound catabolism.
supporting_text: >-
predicted the existence of at least four main pathways for the catabolism
of central aromatic intermediates, that is, the protocatechuate (pca
genes) and catechol (cat genes) branches of the beta-ketoadipate
pathway, the homogentisate pathway (hmg/fah/mai genes) and the
phenylacetate pathway (pha genes).
- id: PMID:21906639
title: >-
Generation of a catR deficient mutant of P. putida KT2440 that produces
cis, cis-muconate from benzoate at high rate and yield
findings:
- statement: >-
CatR is the transcriptional regulator of the cat operon. A point
mutation in the DNA binding domain of catR abolishes cat operon
induction. The ben operon contains PP_3166 (catA2), a second catechol
1,2-dioxygenase.
supporting_text: >-
Transcriptome analysis showed that the cat operon was not induced in
P. putida KT2440-JD1 in the presence of 5mM benzoate, due to a point
mutation in the highly conserved DNA binding domain of the
transcriptional regulator (catR) of the cat operon. The ben operon was
highly expressed in the presence of benzoate in the mutant and its
parental strain. This operon contains PP_3166 (catA2), which was shown
to be a second catechol 1,2-dioxygenase besides catA.
core_functions:
- description: >-
Catechol 1,2-dioxygenase catalyzes the intradiol (ortho) ring cleavage of
catechol to cis,cis-muconate using non-heme Fe(III), the first step of
the catechol branch of the beta-ketoadipate pathway for aromatic compound
degradation.
molecular_function:
id: GO:0018576
label: catechol 1,2-dioxygenase activity
directly_involved_in:
- id: GO:0019614
label: catechol-containing compound catabolic process
- id: GO:0042952
label: beta-ketoadipate pathway
supported_by:
- reference_id: file:PSEPK/catA/catA-uniprot.txt
supporting_text: >-
CATALYTIC ACTIVITY: Reaction=catechol + O2 = cis,cis-muconate + 2
H(+); Xref=Rhea:RHEA:23852; EC=1.13.11.1
- reference_id: file:PSEPK/catA/catA-uniprot.txt
supporting_text: >-
PATHWAY: Aromatic compound metabolism; beta-ketoadipate pathway;
5-oxo-4,5-dihydro-2-furylacetate from catechol: step 1/3.
- reference_id: PMID:12534463
supporting_text: >-
Complete genome sequence and comparative analysis of the metabolically
versatile Pseudomonas putida KT2440 [genome paper identifying cat
regulon genes]