protocatechuate degradation III (para-cleavage pathway)

MetaCyc:PWY-6336

The complete five-step protocatechuate 2,3-cleavage route in Paenibacillus sp. JJ-1b proceeds through the Z,Z carboxysemialdehyde, hydroxymuconate semialdehyde, hydroxymuconate and oxalocrotonate to the Z-enol hydroxypentadienoate. It connects to the separate downstream degradation pathway. The five individual recombinant enzymes are assayed as crude extracts; their endpoint qualifications retain construct uncertainty. The historical native dioxygenase assembly and iron annotation remain distinct from those recombinant preparations. Spontaneous intermediate conversion is compatible with enzyme acceleration. NAD is the selected reaction coenzyme; lower NADP-supported PraB activity is retained separately. Upstream 4-hydroxybenzoate conversion and the downstream three-enzyme module are outside the internal five-step boundary.

Pathway type
aromatic compound catabolism
Organism scope

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Pathway network

41 nodes · 46 asserted directed edges

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Pathway network: protocatechuate degradation III (para-cleavage pathway) 41 nodes · 46 asserted directed edges. Every arrow links to its evidence table row; nodes link to their component details. Isolated declared components are retained. MetaCyc:RXN-10882 — part_of → MetaCyc:PWY-6336; Member of the five-step protocatechuate 2,3-cleavage route.; Evidence: MetaCyc:PWY-6336part of CHEBI:36241 — consumes → MetaCyc:RXN-10882; Coefficient 1 in the selected pathway flux.; Evidence: MetaCyc:RXN-10882consumes CHEBI:15379 — consumes → MetaCyc:RXN-10882; Coefficient 1 in the selected pathway flux.; Evidence: MetaCyc:RXN-10882consumes MetaCyc:RXN-10882 — produces → MetaCyc:CPD-14966; Coefficient 1 in the selected pathway flux. Explicit member/layout Z,Z source frame retained; narrative hyperlink CPD-11842 is the distinct E,Z stereoisomer.; Evidence: MetaCyc:RXN-10882produces MetaCyc:RXN-10882 — produces → CHEBI:15378; Coefficient 1 in the selected pathway flux.; Evidence: MetaCyc:RXN-10882produces MetaCyc:RXN-10883 — part_of → MetaCyc:PWY-6336; Member of the five-step protocatechuate 2,3-cleavage route. Native spontaneous=true allows uncatalyzed background; this does not negate experimentally accelerated PraH catalysis.; Evidence: MetaCyc:PWY-6336part of MetaCyc:CPD-14966 — consumes → MetaCyc:RXN-10883; Coefficient 1 in the selected pathway flux. Explicit member/layout Z,Z source frame retained; narrative hyperlink CPD-11842 is the distinct E,Z stereoisomer.; Evidence: MetaCyc:RXN-10883consumes CHEBI:15378 — consumes → MetaCyc:RXN-10883; Coefficient 1 in the selected pathway flux.; Evidence: MetaCyc:RXN-10883consumes MetaCyc:RXN-10883 — produces → CHEBI:71198; Coefficient 1 in the selected pathway flux.; Evidence: MetaCyc:RXN-10883produces MetaCyc:RXN-10883 — produces → CHEBI:16526; Coefficient 1 in the selected pathway flux.; Evidence: MetaCyc:RXN-10883produces RHEA:34220 — part_of → MetaCyc:PWY-6336; Member of the five-step protocatechuate 2,3-cleavage route.; Evidence: MetaCyc:PWY-6336, RHEA:34220part of CHEBI:71198 — consumes → RHEA:34220; Coefficient 1 in the selected pathway flux.; Evidence: RHEA:34220, MetaCyc:RXN-8527consumes CHEBI:15377 — consumes → RHEA:34220; Coefficient 1 in the selected pathway flux.; Evidence: RHEA:34220, MetaCyc:RXN-8527consumes CHEBI:57540 — consumes → RHEA:34220; Coefficient 1 in the selected pathway flux.; Evidence: RHEA:34220, MetaCyc:RXN-8527consumes RHEA:34220 — produces → CHEBI:28080; Coefficient 1 in the selected pathway flux.; Evidence: RHEA:34220, MetaCyc:RXN-8527produces RHEA:34220 — produces → CHEBI:57945; Coefficient 1 in the selected pathway flux.; Evidence: RHEA:34220, MetaCyc:RXN-8527produces RHEA:34220 — produces → CHEBI:15378; Coefficient 2 in the selected pathway flux.; Evidence: RHEA:34220, MetaCyc:RXN-8527produces RHEA:33432 — part_of → MetaCyc:PWY-6336; Member of the five-step protocatechuate 2,3-cleavage route. Native reaction is REVERSIBLE; this graph selects its degradative flux. Native Rhea32214 xref has different stereoisomers; the exact equation is RHEA33432.; Evidence: MetaCyc:PWY-6336, RHEA:33432part of CHEBI:28080 — consumes → RHEA:33432; Coefficient 1 in the selected pathway flux.; Evidence: RHEA:33432, MetaCyc:RXN-8529consumes RHEA:33432 — produces → CHEBI:64908; Coefficient 1 in the selected pathway flux.; Evidence: RHEA:33432, MetaCyc:RXN-8529produces MetaCyc:4.1.1.77-RXN — part_of → MetaCyc:PWY-6336; Member of the five-step protocatechuate 2,3-cleavage route.; Evidence: MetaCyc:PWY-6336part of CHEBI:64908 — consumes → MetaCyc:4.1.1.77-RXN; Coefficient 1 in the selected pathway flux.; Evidence: MetaCyc:4.1.1.77-RXNconsumes CHEBI:15378 — consumes → MetaCyc:4.1.1.77-RXN; Coefficient 1 in the selected pathway flux.; Evidence: MetaCyc:4.1.1.77-RXNconsumes MetaCyc:4.1.1.77-RXN — produces → CHEBI:67152; Coefficient 1 in the selected pathway flux. The immediate Z-enol is retained. RHEA24261 instead produces the keto tautomer CHEBI11641; it is not an exact replacement.; Evidence: MetaCyc:4.1.1.77-RXNproduces MetaCyc:4.1.1.77-RXN — produces → CHEBI:16526; Coefficient 1 in the selected pathway flux.; Evidence: MetaCyc:4.1.1.77-RXNproduces MetaCyc:RXN-10882 — provides_input_for → MetaCyc:RXN-10883; Direct transfer through the same exact intermediate MetaCyc:CPD-14966.; Evidence: MetaCyc:RXN-10882, MetaCyc:RXN-10883provides input for MetaCyc:RXN-10883 — provides_input_for → RHEA:34220; Direct transfer through the same exact intermediate CHEBI:71198.; Evidence: MetaCyc:RXN-10883, MetaCyc:RXN-8527provides input for RHEA:34220 — provides_input_for → RHEA:33432; Direct transfer through the same exact intermediate CHEBI:28080.; Evidence: MetaCyc:RXN-8527, MetaCyc:RXN-8529provides input for RHEA:33432 — provides_input_for → MetaCyc:4.1.1.77-RXN; Direct transfer through the same exact intermediate CHEBI:64908.; Evidence: MetaCyc:RXN-8529, MetaCyc:4.1.1.77-RXNprovides input for MetaCyc:4.1.1.77-RXN — provides_input_for → MetaCyc:PWY-5162; The terminal Z-enol supplies the separately identified downstream pathway. Its first reaction is selected R2L and consumes this exact enol; downstream reactions are outside the five-step record boundary.; Evidence: MetaCyc:PWY-6336, MetaCyc:PWY-5162, MetaCyc:2-OXOPENT-4-ENOATE-HYDRATASE-RXNprovides input for MetaCyc:CPLX-7915 — has_part → UniProtKB:C4TP01; Native MetaCyc complex model has four PraA subunits. Historical native enzyme was reported tetrameric, but its 35.5-kDa subunit estimate differs from the 266-aa recombinant sequence; this does not establish exact sequence identity of the historical preparation or measure oligomerization of the 2009 recombinant construct.; Evidence: MetaCyc:CPLX-7915, MetaCyc:MONOMER-15106has part MetaCyc:CPLX-7915 — has_cofactor → CHEBI:29033; Fe2+ is a source-supported cofactor of the historical native protocatechuate 2,3-dioxygenase, reported at one atom per subunit. The native database associates this property with CPLX-7915; the 2009 recombinant assembly and its metal occupancy were not measured by this evidence.; Evidence: MetaCyc:ENZRXN-16910, MetaCyc:CPLX-7915has cofactor CHEBI:64755 — inhibits → MetaCyc:CPLX-7915; Native database assertion of an in-vitro inhibitor of the purified-enzyme activity, citing Wolgel and Lipscomb 1990. Concentration and inhibition mechanism are not given in the structured object; no physiological regulatory role or metal requirement is inferred. Chemical ionization follows the source-normalized compound, not measured assay protonation.; Evidence: MetaCyc:REG-12850inhibits CHEBI:25548 — inhibits → MetaCyc:CPLX-7915; Native database assertion of an in-vitro inhibitor of the purified-enzyme activity, citing Wolgel and Lipscomb 1990. Concentration and inhibition mechanism are not given in the structured object; no physiological regulatory role or metal requirement is inferred. Chemical ionization follows the source-normalized compound, not measured assay protonation.; Evidence: MetaCyc:REG-12851inhibits MetaCyc:CPLX-7915 — catalyzes → MetaCyc:RXN-10882; The native database model assigns protocatechuate 2,3-cleavage activity to CPLX-7915 with native-host purified-protein evidence from 1990/1993. This is the curated historical enzyme assignment; it does not directly establish that the historical 35.5-kDa subunit preparation had the complete 2009 C4TP01 sequence or that the recombinant construct had the same assembly.; Evidence: MetaCyc:ENZRXN-16910catalyzes UniProtKB:C4TP01 — catalyzes → MetaCyc:RXN-10882; subject experimental construct: Recombinant praA product from pETA23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.; Evidence PMID:19717587: Table 1 identifies pETA23 as a pET21a(+) expression plasmid carrying praA; the study uses BL21(DE3) for expression. (PMC2795304 HTML section#t1, pETA23 and BL21(DE3) rows; section#sec6); PraA recombinant crude-extract assay supports the initial ring cleavage. Its product subsequently decarboxylates spontaneously; PraA is not assigned the separate decarboxylation reaction. Exact chemical stereochemistry follows the native reaction and chemical objects.; Evidence: PMID:19717587, MetaCyc:MONOMER-15106catalyzes UniProtKB:C4TP08 — catalyzes → MetaCyc:RXN-10883; subject experimental construct: Recombinant PraH from pETH23 in E. coli BL21(DE3), assayed as crude extract. The selected MYDVH start matches deposited C4TP08; it is not a demonstrated native truncation. Exact terminal sequence and tag state remain unresolved.; Evidence PMID:19717587: Table 1 identifies pETH23 as a pET21a(+) expression plasmid carrying praH; the study uses BL21(DE3) for expression. (PMC2795304 HTML section#t1, pETH23 and BL21(DE3) rows; section#sec6); PraH accelerates conversion of the unstable initial cleavage intermediate to hydroxymuconate semialdehyde. Spontaneous conversion on a longer timescale remains supported; this edge does not claim that the enzyme is strictly required for all conversion.; Evidence: PMID:19717587, MetaCyc:MONOMER-15107, MetaCyc:ENZRXN-16911catalyzes UniProtKB:C4TP02 — catalyzes → RHEA:34220; subject experimental construct: Recombinant praB product from pETB23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.; Evidence PMID:19717587: Table 1 identifies pETB23 as a pET21a(+) expression plasmid carrying praB; the study uses BL21(DE3) for expression. (PMC2795304 HTML section#t1, pETB23 and BL21(DE3) rows; section#sec6); PraB recombinant crude-extract assay supports NAD-dependent semialdehyde oxidation. NADP also supports lower activity in the same study; neither reaction membership nor the selected NAD equation establishes exclusive physiological coenzyme use.; Evidence: PMID:19717587, MetaCyc:MONOMER-15108, MetaCyc:ENZRXN-16912catalyzes UniProtKB:C4TP07 — catalyzes → RHEA:33432; subject experimental construct: Recombinant praC product from pETC23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.; Evidence PMID:19717587: Table 1 identifies pETC23 as a pET21a(+) expression plasmid carrying praC; the study uses BL21(DE3) for expression. (PMC2795304 HTML section#t1, pETC23 and BL21(DE3) rows; section#sec6); PraC accelerates hydroxymuconate tautomerization. The native reaction is reversible and its comment also describes slow aqueous conversion; the pathway selects the forward flux. The exact Rhea equation is 33432; the native 32214 cross-reference has different stereoisomers.; Evidence: PMID:19717587, MetaCyc:MONOMER-15109, MetaCyc:ENZRXN-16913catalyzes UniProtKB:C4TP06 — catalyzes → MetaCyc:4.1.1.77-RXN; subject experimental construct: Recombinant praD product from pC4D23 (pColdIV) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.; Evidence PMID:19717587: Table 1 identifies pC4D23 as a pColdIV expression plasmid carrying praD; the study uses BL21(DE3) for expression. (PMC2795304 HTML section#t1, pC4D23 and BL21(DE3) rows; section#sec6); PraD recombinant crude-extract assay supports oxalocrotonate decarboxylation to hydroxypentadienoate. The assay included 500 micromolar MgSO4, which alone does not prove a physiological magnesium requirement. The enol product is preserved, rather than substituted by its keto tautomer.; Evidence: PMID:19717587, MetaCyc:MONOMER-15110, MetaCyc:ENZRXN-16914catalyzes UniProtKB:C4TP02 — has_cofactor → CHEBI:57540; subject experimental construct: Recombinant praB product from pETB23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.; Evidence PMID:19717587: Table 1 identifies pETB23 as a pET21a(+) expression plasmid carrying praB; the study uses BL21(DE3) for expression. (PMC2795304 HTML section#t1, pETB23 and BL21(DE3) rows; section#sec6); Recombinant crude PraB uses NAD+ in the HMS dehydrogenase assay (1.19±0.07U/mg). NADP+ also supports activity at approximately one-eleventh this rate, so this is preference rather than exclusivity. Chemical ionization is the curated ChEBI normalization, not measured assay protonation.; Evidence: PMID:19717587has cofactor UniProtKB:C4TP02 — has_cofactor → CHEBI:58349; subject experimental construct: Recombinant praB product from pETB23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.; Evidence PMID:19717587: Table 1 identifies pETB23 as a pET21a(+) expression plasmid carrying praB; the study uses BL21(DE3) for expression. (PMC2795304 HTML section#t1, pETB23 and BL21(DE3) rows; section#sec6); Recombinant crude PraB supports a lower HMS dehydrogenase activity with NADP+ (0.113±0.009U/mg) than with NAD+ (1.19±0.07U/mg). This in-vitro alternative does not establish the dominant physiological coenzyme. Chemical ionization is the curated ChEBI normalization, not measured assay protonation.; Evidence: PMID:19717587has cofactor CHEBI:16240 — inhibits → MetaCyc:CPLX-7915; The 1993 abstract reports in-vitro inactivation of purified native JJ1b protocatechuate 2,3-dioxygenase by hydrogen peroxide among Fe2+-oxidizing reagents. This is an assay perturbation of the historical native preparation, not physiological regulation or a 2009 recombinant-sequence claim. No dose or exact damaged-site occupancy is asserted.; Evidence: PMID:8392511, PMID:8392511, MetaCyc:CPLX-7915inhibits CHEBI:22651 — activates → MetaCyc:CPLX-7915; object molecular state: Historical purified native JJ1b 2,3-PCD after inactivation by hydrogen peroxide, as described among the oxidizing treatments in the 1993 abstract. This qualifier restricts the recovery claim to inactive enzyme; the source does not resolve damage sites, metal-state occupancy, dose or a separate treatment-specific recovery protocol.; Evidence PMID:8392511: inactivated (PubmedArticleSet/PubmedArticle/MedlineCitation/Article/Abstract/AbstractText; sentence beginning The enzyme was inactivated); Evidence MetaCyc:CPLX-7915: The native complex annotation describes purification from JJ-1b and a later native homotetramer characterization citing PMID:8392511; this maps the historical preparation to CPLX-7915 without proving its complete 2009 protein sequence. (/ptools-xml/Protein[@frameid="CPLX-7915"]/comment); Ascorbate restores activity to the historical purified native enzyme after oxidative inactivation, including the reported hydrogen peroxide treatment. The abstract attributes recovery to reduction of the iron. This edge claims recovery of the qualified inactive preparation, not stimulation of untreated enzyme; stereochemistry of the ascorbate reagent is not specified.; Evidence: PMID:8392511, PMID:8392511, MetaCyc:CPLX-7915activates CHEBI:30060 — inhibits → MetaCyc:CPLX-7915; The 1993 abstract reports in-vitro inactivation of purified native JJ1b protocatechuate 2,3-dioxygenase by potassium ferricyanide among Fe2+-oxidizing reagents. This is an assay perturbation of the historical native preparation, not physiological regulation or a 2009 recombinant-sequence claim. No dose or exact damaged-site occupancy is asserted.; Evidence: PMID:8392511, PMID:8392511, MetaCyc:CPLX-7915inhibits CHEBI:22651 — activates → MetaCyc:CPLX-7915; object molecular state: Historical purified native JJ1b 2,3-PCD after inactivation by potassium ferricyanide, as described among the oxidizing treatments in the 1993 abstract. This qualifier restricts the recovery claim to inactive enzyme; the source does not resolve damage sites, metal-state occupancy, dose or a separate treatment-specific recovery protocol.; Evidence PMID:8392511: inactivated (PubmedArticleSet/PubmedArticle/MedlineCitation/Article/Abstract/AbstractText; sentence beginning The enzyme was inactivated); Evidence MetaCyc:CPLX-7915: The native complex annotation describes purification from JJ-1b and a later native homotetramer characterization citing PMID:8392511; this maps the historical preparation to CPLX-7915 without proving its complete 2009 protein sequence. (/ptools-xml/Protein[@frameid="CPLX-7915"]/comment); Ascorbate restores activity to the historical purified native enzyme after oxidative inactivation, including the reported potassium ferricyanide treatment. The abstract attributes recovery to reduction of the iron. This edge claims recovery of the qualified inactive preparation, not stimulation of untreated enzyme; stereochemistry of the ascorbate reagent is not specified.; Evidence: PMID:8392511, PMID:8392511, MetaCyc:CPLX-7915activates 3,4-dihydroxybenzoate; CHEBI:36241; Declared type: small_molecule small molecule 3,4-dihydroxybenzoate carbon dioxide; CHEBI:16526; Declared type: small_molecule small molecule carbon dioxide (2Z,4E)-2-hydroxymuconate(2-); CHEBI:28080; Declared type: small_molecule small molecule (2Z,4E)-2-hydroxymuconate(2- ) (2Z)-2-hydroxypenta-2,4-dienoate; CHEBI:67152; Declared type: small_molecule small molecule (2Z)-2-hydroxypenta-2,4- dienoate (2Z,4Z)-2-hydroxy-5-carboxymuconate-6-semialdehyde; MetaCyc:CPD-14966; Declared type: small_molecule small molecule (2Z,4Z)-2-hydroxy-5- carboxymuconate-6- semialdehyde (3E)-2-oxohex-3-enedioate; CHEBI:64908; Declared type: small_molecule small molecule (3E)-2-oxohex-3-enedioate (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate; CHEBI:71198; Declared type: small_molecule small molecule (2Z,4E)-2-hydroxy-6-oxohexa- 2,4-dienoate NAD(1-); CHEBI:57540; Declared type: cofactor cofactor NAD(1-) NADH(2-); CHEBI:57945; Declared type: small_molecule small molecule NADH(2-) dioxygen; CHEBI:15379; Declared type: small_molecule small molecule dioxygen hydron; CHEBI:15378; Declared type: small_molecule small molecule hydron water; CHEBI:15377; Declared type: small_molecule small molecule water protocatechuate 2,3-dioxygenase; MetaCyc:CPLX-7915; Declared type: complex complex protocatechuate 2,3-dioxygenase iron(2+); CHEBI:29033; Declared type: cofactor cofactor iron(2+) EDTA(2-); CHEBI:64755; Declared type: small_molecule small molecule EDTA(2-) nitrilotriacetate(3-); CHEBI:25548; Declared type: small_molecule small molecule nitrilotriacetate(3-) Protocatechuate 2,3-dioxygenase; UniProtKB:C4TP01; Declared type: protein protein Protocatechuate 2,3-dioxygenase 5-carboxy-2-hydroxymuconate-6-semialdehyde decarboxylase; UniProtKB:C4TP08; Declared type: protein protein 5-carboxy-2-hydroxymuconate- 6-semialdehyde decarboxylase 2-hydroxymuconate-6-semialdehyde dehydrogenase; UniProtKB:C4TP02; Declared type: protein protein 2-hydroxymuconate-6- semialdehyde dehydrogenase Tautomerase; UniProtKB:C4TP07; Declared type: protein protein Tautomerase 4-oxalocrotonate decarboxylase; UniProtKB:C4TP06; Declared type: protein protein 4-oxalocrotonate decarboxylase NADP(3-); CHEBI:58349; Declared type: cofactor cofactor NADP(3-) hydrogen peroxide; CHEBI:16240; Declared type: small_molecule small molecule hydrogen peroxide potassium hexacyanoferrate(3-); CHEBI:30060; Declared type: small_molecule small molecule potassium hexacyanoferrate(3-) ascorbate; CHEBI:22651; Declared type: chemical_entity chemical entity ascorbate protocatechuate 2,3-ring cleavage; MetaCyc:RXN-10882; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity protocatechuate 2,3-ring cleavage 5-carboxy-2-hydroxymuconate semialdehyde decarboxylation; MetaCyc:RXN-10883; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity 5-carboxy-2-hydroxymuconate semialdehyde decarboxylation (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + NAD(+) + H2O => (2Z,4E)-2-hydroxyhexa-2,4-dienedioate + NADH + 2 H(+); RHEA:34220; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity (2Z,4E)-2-hydroxy-6-oxohexa- 2,4-dienoate + NAD(+) + H2O => (2Z,4E)-2-hydroxyhexa- 2,4-dienedioate + NADH + 2 H(+) (2Z,4E)-2-hydroxyhexa-2,4-dienedioate => (3E)-2-oxohex-3-enedioate; RHEA:33432; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity (2Z,4E)-2-hydroxyhexa-2,4- dienedioate => (3E)-2-oxohex-3-enedioate 4-oxalocrotonate decarboxylation to the Z-enol; MetaCyc:4.1.1.77-RXN; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity 4-oxalocrotonate decarboxylation to the Z-enol 2-hydroxypenta-2,4-dienoate degradation; MetaCyc:PWY-5162; Declared type: pathway pathway 2-hydroxypenta-2,4-dienoate degradation protocatechuate degradation III (para-cleavage pathway); MetaCyc:PWY-6336; Declared type: pathway pathway protocatechuate degradation III (para-cleavage pathway) Protocatechuate 2,3-dioxygenase; UniProtKB:C4TP01; Declared type: protein; experimental construct: Recombinant praA product from pETA23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.; Evidence PMID:19717587: Table 1 identifies pETA23 as a pET21a(+) expression plasmid carrying praA; the study uses BL21(DE3) for expression. (PMC2795304 HTML section#t1, pETA23 and BL21(DE3) rows; section#sec6) experimental construct Protocatechuate 2,3-dioxygenase [experimental construct: Recombinant praA product from pETA23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as…] 5-carboxy-2-hydroxymuconate-6-semialdehyde decarboxylase; UniProtKB:C4TP08; Declared type: protein; experimental construct: Recombinant PraH from pETH23 in E. coli BL21(DE3), assayed as crude extract. The selected MYDVH start matches deposited C4TP08; it is not a demonstrated native truncation. Exact terminal sequence and tag state remain unresolved.; Evidence PMID:19717587: Table 1 identifies pETH23 as a pET21a(+) expression plasmid carrying praH; the study uses BL21(DE3) for expression. (PMC2795304 HTML section#t1, pETH23 and BL21(DE3) rows; section#sec6) experimental construct 5-carboxy-2-hydroxymuconate- 6-semialdehyde decarboxylase [experimental construct: Recombinant PraH from pETH23 in E. coli BL21(DE3), assayed as crude extract. The selected MYDVH…] 2-hydroxymuconate-6-semialdehyde dehydrogenase; UniProtKB:C4TP02; Declared type: protein; experimental construct: Recombinant praB product from pETB23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.; Evidence PMID:19717587: Table 1 identifies pETB23 as a pET21a(+) expression plasmid carrying praB; the study uses BL21(DE3) for expression. (PMC2795304 HTML section#t1, pETB23 and BL21(DE3) rows; section#sec6) experimental construct 2-hydroxymuconate-6- semialdehyde dehydrogenase [experimental construct: Recombinant praB product from pETB23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as…] Tautomerase; UniProtKB:C4TP07; Declared type: protein; experimental construct: Recombinant praC product from pETC23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.; Evidence PMID:19717587: Table 1 identifies pETC23 as a pET21a(+) expression plasmid carrying praC; the study uses BL21(DE3) for expression. (PMC2795304 HTML section#t1, pETC23 and BL21(DE3) rows; section#sec6) experimental construct Tautomerase [experimental construct: Recombinant praC product from pETC23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as…] 4-oxalocrotonate decarboxylase; UniProtKB:C4TP06; Declared type: protein; experimental construct: Recombinant praD product from pC4D23 (pColdIV) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.; Evidence PMID:19717587: Table 1 identifies pC4D23 as a pColdIV expression plasmid carrying praD; the study uses BL21(DE3) for expression. (PMC2795304 HTML section#t1, pC4D23 and BL21(DE3) rows; section#sec6) experimental construct 4-oxalocrotonate decarboxylase [experimental construct: Recombinant praD product from pC4D23 (pColdIV) expressed in E. coli BL21(DE3) and assayed as crude…] 2-hydroxymuconate-6-semialdehyde dehydrogenase; UniProtKB:C4TP02; Declared type: protein; experimental construct: Recombinant praB product from pETB23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.; Evidence PMID:19717587: Table 1 identifies pETB23 as a pET21a(+) expression plasmid carrying praB; the study uses BL21(DE3) for expression. (PMC2795304 HTML section#t1, pETB23 and BL21(DE3) rows; section#sec6) experimental construct 2-hydroxymuconate-6- semialdehyde dehydrogenase [experimental construct: Recombinant praB product from pETB23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as…] 2-hydroxymuconate-6-semialdehyde dehydrogenase; UniProtKB:C4TP02; Declared type: protein; experimental construct: Recombinant praB product from pETB23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.; Evidence PMID:19717587: Table 1 identifies pETB23 as a pET21a(+) expression plasmid carrying praB; the study uses BL21(DE3) for expression. (PMC2795304 HTML section#t1, pETB23 and BL21(DE3) rows; section#sec6) experimental construct 2-hydroxymuconate-6- semialdehyde dehydrogenase [experimental construct: Recombinant praB product from pETB23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as…] protocatechuate 2,3-dioxygenase; MetaCyc:CPLX-7915; Declared type: complex; molecular state: Historical purified native JJ1b 2,3-PCD after inactivation by hydrogen peroxide, as described among the oxidizing treatments in the 1993 abstract. This qualifier restricts the recovery claim to inactive enzyme; the source does not resolve damage sites, metal-state occupancy, dose or a separate treatment-specific recovery protocol.; Evidence PMID:8392511: inactivated (PubmedArticleSet/PubmedArticle/MedlineCitation/Article/Abstract/AbstractText; sentence beginning The enzyme was inactivated); Evidence MetaCyc:CPLX-7915: The native complex annotation describes purification from JJ-1b and a later native homotetramer characterization citing PMID:8392511; this maps the historical preparation to CPLX-7915 without proving its complete 2009 protein sequence. (/ptools-xml/Protein[@frameid="CPLX-7915"]/comment) molecular state protocatechuate 2,3-dioxygenase [molecular state: Historical purified native JJ1b 2,3-PCD after inactivation by hydrogen peroxide, as described among…] protocatechuate 2,3-dioxygenase; MetaCyc:CPLX-7915; Declared type: complex; molecular state: Historical purified native JJ1b 2,3-PCD after inactivation by potassium ferricyanide, as described among the oxidizing treatments in the 1993 abstract. This qualifier restricts the recovery claim to inactive enzyme; the source does not resolve damage sites, metal-state occupancy, dose or a separate treatment-specific recovery protocol.; Evidence PMID:8392511: inactivated (PubmedArticleSet/PubmedArticle/MedlineCitation/Article/Abstract/AbstractText; sentence beginning The enzyme was inactivated); Evidence MetaCyc:CPLX-7915: The native complex annotation describes purification from JJ-1b and a later native homotetramer characterization citing PMID:8392511; this maps the historical preparation to CPLX-7915 without proving its complete 2009 protein sequence. (/ptools-xml/Protein[@frameid="CPLX-7915"]/comment) molecular state protocatechuate 2,3-dioxygenase [molecular state: Historical purified native JJ1b 2,3-PCD after inactivation by potassium ferricyanide, as described…]

Components and activities

Declared biological components and source reaction directions
NodeKind or roleSource direction
Paenibacillus sp. JJ-1b
NCBITaxon:649508		taxon
3,4-dihydroxybenzoate
CHEBI:36241		small molecule
carbon dioxide
CHEBI:16526		small molecule
(2Z,4E)-2-hydroxymuconate(2-)
CHEBI:28080		small molecule
(2Z)-2-hydroxypenta-2,4-dienoate
CHEBI:67152		small molecule
(2Z,4Z)-2-hydroxy-5-carboxymuconate-6-semialdehyde
MetaCyc:CPD-14966		small molecule
(3E)-2-oxohex-3-enedioate
CHEBI:64908		small molecule
(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate
CHEBI:71198		small molecule
NAD(1-)
CHEBI:57540		cofactor
NADH(2-)
CHEBI:57945		small molecule
dioxygen
CHEBI:15379		small molecule
hydron
CHEBI:15378		small molecule
water
CHEBI:15377		small molecule
protocatechuate 2,3-dioxygenase
MetaCyc:CPLX-7915		complex
iron(2+)
CHEBI:29033		cofactor
EDTA(2-)
CHEBI:64755		small molecule
nitrilotriacetate(3-)
CHEBI:25548		small molecule
Protocatechuate 2,3-dioxygenase
UniProtKB:C4TP01		protein
5-carboxy-2-hydroxymuconate-6-semialdehyde decarboxylase
UniProtKB:C4TP08		protein
2-hydroxymuconate-6-semialdehyde dehydrogenase
UniProtKB:C4TP02		protein
Tautomerase
UniProtKB:C4TP07		protein
4-oxalocrotonate decarboxylase
UniProtKB:C4TP06		protein
NADP(3-)
CHEBI:58349		cofactor
hydrogen peroxide
CHEBI:16240		small molecule
potassium hexacyanoferrate(3-)
CHEBI:30060		small molecule
ascorbate
CHEBI:22651		chemical entity
protocatechuate 2,3-ring cleavage
MetaCyc:RXN-10882		molecular activityleft to right
5-carboxy-2-hydroxymuconate semialdehyde decarboxylation
MetaCyc:RXN-10883		molecular activityleft to right
(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + NAD(+) + H2O => (2Z,4E)-2-hydroxyhexa-2,4-dienedioate + NADH + 2 H(+)
RHEA:34220		molecular activityleft to right
(2Z,4E)-2-hydroxyhexa-2,4-dienedioate => (3E)-2-oxohex-3-enedioate
RHEA:33432		molecular activityleft to right
4-oxalocrotonate decarboxylation to the Z-enol
MetaCyc:4.1.1.77-RXN		molecular activityleft to right
2-hydroxypenta-2,4-dienoate degradation
MetaCyc:PWY-5162		pathway

Mechanistic edges

Mechanistic edges and their cited evidence
SubjectPredicate and descriptionObjectEvidence
protocatechuate 2,3-ring cleavage
MetaCyc:RXN-10882		part_of

Member of the five-step protocatechuate 2,3-cleavage route.

MetaCyc:PWY-6336
  • MetaCyc:PWY-6336

    Source assertion: The complete native pathway lists MetaCyc:RXN-10882 as a member and selects L2R flux.

    Source location/ptools-xml/Pathway/reaction-list/Reaction[@frameid='RXN-10882']; /ptools-xml/Pathway/reaction-layout[Reaction/@frameid='RXN-10882']
3,4-dihydroxybenzoate
CHEBI:36241		consumes

Coefficient 1 in the selected pathway flux.

protocatechuate 2,3-ring cleavage
MetaCyc:RXN-10882
  • MetaCyc:RXN-10882

    Source assertion: The complete native reaction left side contains 3-4-DIHYDROXYBENZOATE with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='RXN-10882']/left[Compound/@frameid='3-4-DIHYDROXYBENZOATE']
dioxygen
CHEBI:15379		consumes

Coefficient 1 in the selected pathway flux.

protocatechuate 2,3-ring cleavage
MetaCyc:RXN-10882
  • MetaCyc:RXN-10882

    Source assertion: The complete native reaction left side contains OXYGEN-MOLECULE with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='RXN-10882']/left[Compound/@frameid='OXYGEN-MOLECULE']
protocatechuate 2,3-ring cleavage
MetaCyc:RXN-10882		produces

Coefficient 1 in the selected pathway flux. Explicit member/layout Z,Z source frame retained; narrative hyperlink CPD-11842 is the distinct E,Z stereoisomer.

(2Z,4Z)-2-hydroxy-5-carboxymuconate-6-semialdehyde
MetaCyc:CPD-14966
  • MetaCyc:RXN-10882

    Source assertion: The complete native reaction right side contains CPD-14966 with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='RXN-10882']/right[Compound/@frameid='CPD-14966']
protocatechuate 2,3-ring cleavage
MetaCyc:RXN-10882		produces

Coefficient 1 in the selected pathway flux.

hydron
CHEBI:15378
  • MetaCyc:RXN-10882

    Source assertion: The complete native reaction right side contains PROTON with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='RXN-10882']/right[Compound/@frameid='PROTON']
5-carboxy-2-hydroxymuconate semialdehyde decarboxylation
MetaCyc:RXN-10883		part_of

Member of the five-step protocatechuate 2,3-cleavage route. Native spontaneous=true allows uncatalyzed background; this does not negate experimentally accelerated PraH catalysis.

MetaCyc:PWY-6336
  • MetaCyc:PWY-6336

    Source assertion: The complete native pathway lists MetaCyc:RXN-10883 as a member and selects L2R flux.

    Source location/ptools-xml/Pathway/reaction-list/Reaction[@frameid='RXN-10883']; /ptools-xml/Pathway/reaction-layout[Reaction/@frameid='RXN-10883']
(2Z,4Z)-2-hydroxy-5-carboxymuconate-6-semialdehyde
MetaCyc:CPD-14966		consumes

Coefficient 1 in the selected pathway flux. Explicit member/layout Z,Z source frame retained; narrative hyperlink CPD-11842 is the distinct E,Z stereoisomer.

5-carboxy-2-hydroxymuconate semialdehyde decarboxylation
MetaCyc:RXN-10883
  • MetaCyc:RXN-10883

    Source assertion: The complete native reaction left side contains CPD-14966 with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='RXN-10883']/left[Compound/@frameid='CPD-14966']
hydron
CHEBI:15378		consumes

Coefficient 1 in the selected pathway flux.

5-carboxy-2-hydroxymuconate semialdehyde decarboxylation
MetaCyc:RXN-10883
  • MetaCyc:RXN-10883

    Source assertion: The complete native reaction left side contains PROTON with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='RXN-10883']/left[Compound/@frameid='PROTON']
5-carboxy-2-hydroxymuconate semialdehyde decarboxylation
MetaCyc:RXN-10883		produces

Coefficient 1 in the selected pathway flux.

(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate
CHEBI:71198
  • MetaCyc:RXN-10883

    Source assertion: The complete native reaction right side contains HYDROXYMUCONATE-SALD with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='RXN-10883']/right[Compound/@frameid='HYDROXYMUCONATE-SALD']
5-carboxy-2-hydroxymuconate semialdehyde decarboxylation
MetaCyc:RXN-10883		produces

Coefficient 1 in the selected pathway flux.

carbon dioxide
CHEBI:16526
  • MetaCyc:RXN-10883

    Source assertion: The complete native reaction right side contains CARBON-DIOXIDE with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='RXN-10883']/right[Compound/@frameid='CARBON-DIOXIDE']
(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + NAD(+) + H2O => (2Z,4E)-2-hydroxyhexa-2,4-dienedioate + NADH + 2 H(+)
RHEA:34220		part_of

Member of the five-step protocatechuate 2,3-cleavage route.

MetaCyc:PWY-6336
  • MetaCyc:PWY-6336

    Source assertion: The complete native pathway lists MetaCyc:RXN-8527 as a member and selects L2R flux.

    Source location/ptools-xml/Pathway/reaction-list/Reaction[@frameid='RXN-8527']; /ptools-xml/Pathway/reaction-layout[Reaction/@frameid='RXN-8527']
  • RHEA:34220

    Source assertion: The complete issuing reaction sides exactly match the native substrates, products, coefficients and selected flux.

    Source locationAggregate rdf:Description rdf:about=http://rdf.rhea-db.org/34220
(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate
CHEBI:71198		consumes

Coefficient 1 in the selected pathway flux.

(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + NAD(+) + H2O => (2Z,4E)-2-hydroxyhexa-2,4-dienedioate + NADH + 2 H(+)
RHEA:34220
  • RHEA:34220

    Source assertion: RHEA:34220 places CHEBI:71198 on its substrates side with coefficient 1.

    Source locationAggregate rdf:Description: http://rdf.rhea-db.org/34220 rh:substrates http://rdf.rhea-db.org/34219_L -> http://rdf.rhea-db.org/34219_L rh:contains1 http://rdf.rhea-db.org/Participant_34219_compound_7622 -> http://rdf.rhea-db.org/Participant_34219_compound_7622 rh:compound http://rdf.rhea-db.org/Compound_7622 -> http://rdf.rhea-db.org/Compound_7622 rh:chebi http://purl.obolibrary.org/obo/CHEBI_71198
  • MetaCyc:RXN-8527

    Source assertion: The complete native reaction left side contains HYDROXYMUCONATE-SALD with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='RXN-8527']/left[Compound/@frameid='HYDROXYMUCONATE-SALD']
water
CHEBI:15377		consumes

Coefficient 1 in the selected pathway flux.

(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + NAD(+) + H2O => (2Z,4E)-2-hydroxyhexa-2,4-dienedioate + NADH + 2 H(+)
RHEA:34220
  • RHEA:34220

    Source assertion: RHEA:34220 places CHEBI:15377 on its substrates side with coefficient 1.

    Source locationAggregate rdf:Description: http://rdf.rhea-db.org/34220 rh:substrates http://rdf.rhea-db.org/34219_L -> http://rdf.rhea-db.org/34219_L rh:contains1 http://rdf.rhea-db.org/Participant_34219_compound_1283 -> http://rdf.rhea-db.org/Participant_34219_compound_1283 rh:compound http://rdf.rhea-db.org/Compound_1283 -> http://rdf.rhea-db.org/Compound_1283 rh:chebi http://purl.obolibrary.org/obo/CHEBI_15377
  • MetaCyc:RXN-8527

    Source assertion: The complete native reaction left side contains WATER with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='RXN-8527']/left[Compound/@frameid='WATER']
NAD(1-)
CHEBI:57540		consumes

Coefficient 1 in the selected pathway flux.

(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + NAD(+) + H2O => (2Z,4E)-2-hydroxyhexa-2,4-dienedioate + NADH + 2 H(+)
RHEA:34220
  • RHEA:34220

    Source assertion: RHEA:34220 places CHEBI:57540 on its substrates side with coefficient 1.

    Source locationAggregate rdf:Description: http://rdf.rhea-db.org/34220 rh:substrates http://rdf.rhea-db.org/34219_L -> http://rdf.rhea-db.org/34219_L rh:contains1 http://rdf.rhea-db.org/Participant_34219_compound_3484 -> http://rdf.rhea-db.org/Participant_34219_compound_3484 rh:compound http://rdf.rhea-db.org/Compound_3484 -> http://rdf.rhea-db.org/Compound_3484 rh:chebi http://purl.obolibrary.org/obo/CHEBI_57540
  • MetaCyc:RXN-8527

    Source assertion: The complete native reaction left side contains NAD with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='RXN-8527']/left[Compound/@frameid='NAD']
(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + NAD(+) + H2O => (2Z,4E)-2-hydroxyhexa-2,4-dienedioate + NADH + 2 H(+)
RHEA:34220		produces

Coefficient 1 in the selected pathway flux.

(2Z,4E)-2-hydroxymuconate(2-)
CHEBI:28080
  • RHEA:34220

    Source assertion: RHEA:34220 places CHEBI:28080 on its products side with coefficient 1.

    Source locationAggregate rdf:Description: http://rdf.rhea-db.org/34220 rh:products http://rdf.rhea-db.org/34219_R -> http://rdf.rhea-db.org/34219_R rh:contains1 http://rdf.rhea-db.org/Participant_34219_compound_7273 -> http://rdf.rhea-db.org/Participant_34219_compound_7273 rh:compound http://rdf.rhea-db.org/Compound_7273 -> http://rdf.rhea-db.org/Compound_7273 rh:chebi http://purl.obolibrary.org/obo/CHEBI_28080
  • MetaCyc:RXN-8527

    Source assertion: The complete native reaction right side contains CPD-13339 with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='RXN-8527']/right[Compound/@frameid='CPD-13339']
(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + NAD(+) + H2O => (2Z,4E)-2-hydroxyhexa-2,4-dienedioate + NADH + 2 H(+)
RHEA:34220		produces

Coefficient 1 in the selected pathway flux.

NADH(2-)
CHEBI:57945
  • RHEA:34220

    Source assertion: RHEA:34220 places CHEBI:57945 on its products side with coefficient 1.

    Source locationAggregate rdf:Description: http://rdf.rhea-db.org/34220 rh:products http://rdf.rhea-db.org/34219_R -> http://rdf.rhea-db.org/34219_R rh:contains1 http://rdf.rhea-db.org/Participant_34219_compound_1650 -> http://rdf.rhea-db.org/Participant_34219_compound_1650 rh:compound http://rdf.rhea-db.org/Compound_1650 -> http://rdf.rhea-db.org/Compound_1650 rh:chebi http://purl.obolibrary.org/obo/CHEBI_57945
  • MetaCyc:RXN-8527

    Source assertion: The complete native reaction right side contains NADH with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='RXN-8527']/right[Compound/@frameid='NADH']
(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + NAD(+) + H2O => (2Z,4E)-2-hydroxyhexa-2,4-dienedioate + NADH + 2 H(+)
RHEA:34220		produces

Coefficient 2 in the selected pathway flux.

hydron
CHEBI:15378
  • RHEA:34220

    Source assertion: RHEA:34220 places CHEBI:15378 on its products side with coefficient 2.

    Source locationAggregate rdf:Description: http://rdf.rhea-db.org/34220 rh:products http://rdf.rhea-db.org/34219_R -> http://rdf.rhea-db.org/34219_R rh:contains2 http://rdf.rhea-db.org/Participant_34219_compound_3249 -> http://rdf.rhea-db.org/Participant_34219_compound_3249 rh:compound http://rdf.rhea-db.org/Compound_3249 -> http://rdf.rhea-db.org/Compound_3249 rh:chebi http://purl.obolibrary.org/obo/CHEBI_15378
  • MetaCyc:RXN-8527

    Source assertion: The complete native reaction right side contains PROTON with coefficient 2.

    Source location/ptools-xml/Reaction[@frameid='RXN-8527']/right[Compound/@frameid='PROTON']
(2Z,4E)-2-hydroxyhexa-2,4-dienedioate => (3E)-2-oxohex-3-enedioate
RHEA:33432		part_of

Member of the five-step protocatechuate 2,3-cleavage route. Native reaction is REVERSIBLE; this graph selects its degradative flux. Native Rhea32214 xref has different stereoisomers; the exact equation is RHEA33432.

MetaCyc:PWY-6336
  • MetaCyc:PWY-6336

    Source assertion: The complete native pathway lists MetaCyc:RXN-8529 as a member and selects L2R flux.

    Source location/ptools-xml/Pathway/reaction-list/Reaction[@frameid='RXN-8529']; /ptools-xml/Pathway/reaction-layout[Reaction/@frameid='RXN-8529']
  • RHEA:33432

    Source assertion: The complete issuing reaction sides exactly match the native substrates, products, coefficients and selected flux.

    Source locationAggregate rdf:Description rdf:about=http://rdf.rhea-db.org/33432
(2Z,4E)-2-hydroxymuconate(2-)
CHEBI:28080		consumes

Coefficient 1 in the selected pathway flux.

(2Z,4E)-2-hydroxyhexa-2,4-dienedioate => (3E)-2-oxohex-3-enedioate
RHEA:33432
  • RHEA:33432

    Source assertion: RHEA:33432 places CHEBI:28080 on its substrates side with coefficient 1.

    Source locationAggregate rdf:Description: http://rdf.rhea-db.org/33432 rh:substrates http://rdf.rhea-db.org/33431_L -> http://rdf.rhea-db.org/33431_L rh:contains1 http://rdf.rhea-db.org/Participant_33431_compound_7273 -> http://rdf.rhea-db.org/Participant_33431_compound_7273 rh:compound http://rdf.rhea-db.org/Compound_7273 -> http://rdf.rhea-db.org/Compound_7273 rh:chebi http://purl.obolibrary.org/obo/CHEBI_28080
  • MetaCyc:RXN-8529

    Source assertion: The complete native reaction left side contains CPD-13339 with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='RXN-8529']/left[Compound/@frameid='CPD-13339']
(2Z,4E)-2-hydroxyhexa-2,4-dienedioate => (3E)-2-oxohex-3-enedioate
RHEA:33432		produces

Coefficient 1 in the selected pathway flux.

(3E)-2-oxohex-3-enedioate
CHEBI:64908
  • RHEA:33432

    Source assertion: RHEA:33432 places CHEBI:64908 on its products side with coefficient 1.

    Source locationAggregate rdf:Description: http://rdf.rhea-db.org/33432 rh:products http://rdf.rhea-db.org/33431_R -> http://rdf.rhea-db.org/33431_R rh:contains1 http://rdf.rhea-db.org/Participant_33431_compound_7274 -> http://rdf.rhea-db.org/Participant_33431_compound_7274 rh:compound http://rdf.rhea-db.org/Compound_7274 -> http://rdf.rhea-db.org/Compound_7274 rh:chebi http://purl.obolibrary.org/obo/CHEBI_64908
  • MetaCyc:RXN-8529

    Source assertion: The complete native reaction right side contains CPD-8742 with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='RXN-8529']/right[Compound/@frameid='CPD-8742']
4-oxalocrotonate decarboxylation to the Z-enol
MetaCyc:4.1.1.77-RXN		part_of

Member of the five-step protocatechuate 2,3-cleavage route.

MetaCyc:PWY-6336
  • MetaCyc:PWY-6336

    Source assertion: The complete native pathway lists MetaCyc:4.1.1.77-RXN as a member and selects L2R flux.

    Source location/ptools-xml/Pathway/reaction-list/Reaction[@frameid='4.1.1.77-RXN']; /ptools-xml/Pathway/reaction-layout[Reaction/@frameid='4.1.1.77-RXN']
(3E)-2-oxohex-3-enedioate
CHEBI:64908		consumes

Coefficient 1 in the selected pathway flux.

4-oxalocrotonate decarboxylation to the Z-enol
MetaCyc:4.1.1.77-RXN
  • MetaCyc:4.1.1.77-RXN

    Source assertion: The complete native reaction left side contains CPD-8742 with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='4.1.1.77-RXN']/left[Compound/@frameid='CPD-8742']
hydron
CHEBI:15378		consumes

Coefficient 1 in the selected pathway flux.

4-oxalocrotonate decarboxylation to the Z-enol
MetaCyc:4.1.1.77-RXN
  • MetaCyc:4.1.1.77-RXN

    Source assertion: The complete native reaction left side contains PROTON with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='4.1.1.77-RXN']/left[Compound/@frameid='PROTON']
4-oxalocrotonate decarboxylation to the Z-enol
MetaCyc:4.1.1.77-RXN		produces

Coefficient 1 in the selected pathway flux. The immediate Z-enol is retained. RHEA24261 instead produces the keto tautomer CHEBI11641; it is not an exact replacement.

(2Z)-2-hydroxypenta-2,4-dienoate
CHEBI:67152
  • MetaCyc:4.1.1.77-RXN

    Source assertion: The complete native reaction right side contains CPD-14447 with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='4.1.1.77-RXN']/right[Compound/@frameid='CPD-14447']
4-oxalocrotonate decarboxylation to the Z-enol
MetaCyc:4.1.1.77-RXN		produces

Coefficient 1 in the selected pathway flux.

carbon dioxide
CHEBI:16526
  • MetaCyc:4.1.1.77-RXN

    Source assertion: The complete native reaction right side contains CARBON-DIOXIDE with coefficient 1.

    Source location/ptools-xml/Reaction[@frameid='4.1.1.77-RXN']/right[Compound/@frameid='CARBON-DIOXIDE']
protocatechuate 2,3-ring cleavage
MetaCyc:RXN-10882		provides_input_for

Direct transfer through the same exact intermediate MetaCyc:CPD-14966.

5-carboxy-2-hydroxymuconate semialdehyde decarboxylation
MetaCyc:RXN-10883
  • MetaCyc:RXN-10882

    Source assertion: The native reaction produces CPD-14966.

    Source location/ptools-xml/Reaction/right[Compound/@frameid='CPD-14966']
  • MetaCyc:RXN-10883

    Source assertion: The next native reaction consumes the same CPD-14966.

    Source location/ptools-xml/Reaction/left[Compound/@frameid='CPD-14966']
5-carboxy-2-hydroxymuconate semialdehyde decarboxylation
MetaCyc:RXN-10883		provides_input_for

Direct transfer through the same exact intermediate CHEBI:71198.

(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + NAD(+) + H2O => (2Z,4E)-2-hydroxyhexa-2,4-dienedioate + NADH + 2 H(+)
RHEA:34220
  • MetaCyc:RXN-10883

    Source assertion: The native reaction produces HYDROXYMUCONATE-SALD.

    Source location/ptools-xml/Reaction/right[Compound/@frameid='HYDROXYMUCONATE-SALD']
  • MetaCyc:RXN-8527

    Source assertion: The next native reaction consumes the same HYDROXYMUCONATE-SALD.

    Source location/ptools-xml/Reaction/left[Compound/@frameid='HYDROXYMUCONATE-SALD']
(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + NAD(+) + H2O => (2Z,4E)-2-hydroxyhexa-2,4-dienedioate + NADH + 2 H(+)
RHEA:34220		provides_input_for

Direct transfer through the same exact intermediate CHEBI:28080.

(2Z,4E)-2-hydroxyhexa-2,4-dienedioate => (3E)-2-oxohex-3-enedioate
RHEA:33432
  • MetaCyc:RXN-8527

    Source assertion: The native reaction produces CPD-13339.

    Source location/ptools-xml/Reaction/right[Compound/@frameid='CPD-13339']
  • MetaCyc:RXN-8529

    Source assertion: The next native reaction consumes the same CPD-13339.

    Source location/ptools-xml/Reaction/left[Compound/@frameid='CPD-13339']
(2Z,4E)-2-hydroxyhexa-2,4-dienedioate => (3E)-2-oxohex-3-enedioate
RHEA:33432		provides_input_for

Direct transfer through the same exact intermediate CHEBI:64908.

4-oxalocrotonate decarboxylation to the Z-enol
MetaCyc:4.1.1.77-RXN
  • MetaCyc:RXN-8529

    Source assertion: The native reaction produces CPD-8742.

    Source location/ptools-xml/Reaction/right[Compound/@frameid='CPD-8742']
  • MetaCyc:4.1.1.77-RXN

    Source assertion: The next native reaction consumes the same CPD-8742.

    Source location/ptools-xml/Reaction/left[Compound/@frameid='CPD-8742']
4-oxalocrotonate decarboxylation to the Z-enol
MetaCyc:4.1.1.77-RXN		provides_input_for

The terminal Z-enol supplies the separately identified downstream pathway. Its first reaction is selected R2L and consumes this exact enol; downstream reactions are outside the five-step record boundary.

2-hydroxypenta-2,4-dienoate degradation
MetaCyc:PWY-5162
  • MetaCyc:PWY-6336

    Source assertion: The native pathway links terminal CPD-14447 to PWY-5162.

    Source location/ptools-xml/Pathway/pathway-link[Compound/@frameid='CPD-14447']/link-target/Pathway[@frameid='PWY-5162']
  • MetaCyc:PWY-5162

    Source assertion: PWY-5162 selects R2L flux through 2-OXOPENT-4-ENOATE-HYDRATASE-RXN, using right-primary CPD-14447.

    Source location/ptools-xml/Pathway/reaction-layout[Reaction/@frameid='2-OXOPENT-4-ENOATE-HYDRATASE-RXN']
  • MetaCyc:2-OXOPENT-4-ENOATE-HYDRATASE-RXN

    Source assertion: The complete written right side contains CPD-14447 and WATER; R2L consumes the exact Z-enol.

    Source location/ptools-xml/Reaction/right
protocatechuate 2,3-dioxygenase
MetaCyc:CPLX-7915		has_part

Native MetaCyc complex model has four PraA subunits. Historical native enzyme was reported tetrameric, but its 35.5-kDa subunit estimate differs from the 266-aa recombinant sequence; this does not establish exact sequence identity of the historical preparation or measure oligomerization of the 2009 recombinant construct.

Protocatechuate 2,3-dioxygenase
UniProtKB:C4TP01
  • MetaCyc:CPLX-7915

    Source assertion: The native complex component is MONOMER-15106 with coefficient 4.

    Source location/ptools-xml/Protein/component[Protein/@frameid='MONOMER-15106']/coefficient
  • MetaCyc:MONOMER-15106

    Source assertion: MONOMER-15106 is explicitly unified to UniProt C4TP01.

    Source location/ptools-xml/Protein/dblink[dblink-db='UNIPROT']
protocatechuate 2,3-dioxygenase
MetaCyc:CPLX-7915		has_cofactor

Fe2+ is a source-supported cofactor of the historical native protocatechuate 2,3-dioxygenase, reported at one atom per subunit. The native database associates this property with CPLX-7915; the 2009 recombinant assembly and its metal occupancy were not measured by this evidence.

iron(2+)
CHEBI:29033
  • MetaCyc:ENZRXN-16910

    Source assertion: ENZRXN-16910 lists FE+2 as a cofactor, cites PMID:8392511, and identifies CPLX-7915 as its enzyme.

    Source location/ptools-xml/Enzymatic-Reaction/cofactor; enzyme
  • MetaCyc:CPLX-7915

    Source assertion: The native annotation reports Fe2+ dependence and one iron atom per monomer, citing the 1993 characterization.

    Source location/ptools-xml/Protein/comment
EDTA(2-)
CHEBI:64755		inhibits

Native database assertion of an in-vitro inhibitor of the purified-enzyme activity, citing Wolgel and Lipscomb 1990. Concentration and inhibition mechanism are not given in the structured object; no physiological regulatory role or metal requirement is inferred. Chemical ionization follows the source-normalized compound, not measured assay protonation.

protocatechuate 2,3-dioxygenase
MetaCyc:CPLX-7915
  • MetaCyc:REG-12850

    Source assertion: The native regulation object assigns mode minus to EDTA acting on ENZRXN-16910/CPLX-7915; its citation is PMID:2280722 and mechanism is OTHER.

    Source location/ptools-xml/Regulation/mode; regulator; regulated-entity; citation; mechanism
nitrilotriacetate(3-)
CHEBI:25548		inhibits

Native database assertion of an in-vitro inhibitor of the purified-enzyme activity, citing Wolgel and Lipscomb 1990. Concentration and inhibition mechanism are not given in the structured object; no physiological regulatory role or metal requirement is inferred. Chemical ionization follows the source-normalized compound, not measured assay protonation.

protocatechuate 2,3-dioxygenase
MetaCyc:CPLX-7915
  • MetaCyc:REG-12851

    Source assertion: The native regulation object assigns mode minus to CPD-10188 acting on ENZRXN-16910/CPLX-7915; its citation is PMID:2280722 and mechanism is OTHER.

    Source location/ptools-xml/Regulation/mode; regulator; regulated-entity; citation; mechanism
protocatechuate 2,3-dioxygenase
MetaCyc:CPLX-7915		catalyzes

The native database model assigns protocatechuate 2,3-cleavage activity to CPLX-7915 with native-host purified-protein evidence from 1990/1993. This is the curated historical enzyme assignment; it does not directly establish that the historical 35.5-kDa subunit preparation had the complete 2009 C4TP01 sequence or that the recombinant construct had the same assembly.

protocatechuate 2,3-ring cleavage
MetaCyc:RXN-10882
  • MetaCyc:ENZRXN-16910

    Source assertion: ENZRXN-16910 assigns CPLX-7915 to RXN-10882. Separate EV-EXP-IDA-PURIFIED-PROTEIN-NH evidence cites PMID:2280722 and PMID:8392511; the 2009 heterologous assay is not the basis of this native-preparation claim.

    Source location/ptools-xml/Enzymatic-Reaction/enzyme; reaction; evidence[Evidence-Code/@frameid='EV-EXP-IDA-PURIFIED-PROTEIN-NH']
Protocatechuate 2,3-dioxygenase
UniProtKB:C4TP01

experimental construct: Recombinant praA product from pETA23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.

Qualification evidence
  • PMID:19717587

    Source assertion: Table 1 identifies pETA23 as a pET21a(+) expression plasmid carrying praA; the study uses BL21(DE3) for expression.

    Source locationPMC2795304 HTML section#t1, pETA23 and BL21(DE3) rows; section#sec6
catalyzes

PraA recombinant crude-extract assay supports the initial ring cleavage. Its product subsequently decarboxylates spontaneously; PraA is not assigned the separate decarboxylation reaction. Exact chemical stereochemistry follows the native reaction and chemical objects.

protocatechuate 2,3-ring cleavage
MetaCyc:RXN-10882
  • PMID:19717587

    Source assertion: Figure 2A records the PCA substrate spectrum changing to a product peak at 350 nm in the crude PraA assay; panel B records the later 350-to-375 nm change. The initial cleavage product precedes spontaneous decarboxylation.

    Source locationPMC2795304 HTML figure#f2, panelsA–B and caption; source rasterfigure-2.jpg
  • MetaCyc:MONOMER-15106

    Source assertion: The native protein object explicitly links MONOMER-15106 to UniProt C4TP01.

    Source location/ptools-xml/Protein/dblink[dblink-db='UNIPROT']
5-carboxy-2-hydroxymuconate-6-semialdehyde decarboxylase
UniProtKB:C4TP08

experimental construct: Recombinant PraH from pETH23 in E. coli BL21(DE3), assayed as crude extract. The selected MYDVH start matches deposited C4TP08; it is not a demonstrated native truncation. Exact terminal sequence and tag state remain unresolved.

Qualification evidence
  • PMID:19717587

    Source assertion: Table 1 identifies pETH23 as a pET21a(+) expression plasmid carrying praH; the study uses BL21(DE3) for expression.

    Source locationPMC2795304 HTML section#t1, pETH23 and BL21(DE3) rows; section#sec6
catalyzes

PraH accelerates conversion of the unstable initial cleavage intermediate to hydroxymuconate semialdehyde. Spontaneous conversion on a longer timescale remains supported; this edge does not claim that the enzyme is strictly required for all conversion.

5-carboxy-2-hydroxymuconate semialdehyde decarboxylation
MetaCyc:RXN-10883
  • PMID:19717587
    praH encodes 5CHMS decarboxylase
    Source locationPMC2795304 HTML section#sec21
  • MetaCyc:MONOMER-15107

    Source assertion: The native protein object explicitly links MONOMER-15107 to UniProt C4TP08.

    Source location/ptools-xml/Protein/dblink[dblink-db='UNIPROT']
  • MetaCyc:ENZRXN-16911

    Source assertion: The complete native enzymatic-reaction object assigns MONOMER-15107 to RXN-10883. Heterologous-assay evidence includes PMID:19717587; primary construct details must remain on affected assay endpoints.

    Source location/ptools-xml/Enzymatic-Reaction/enzyme; reaction; evidence
2-hydroxymuconate-6-semialdehyde dehydrogenase
UniProtKB:C4TP02

experimental construct: Recombinant praB product from pETB23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.

Qualification evidence
  • PMID:19717587

    Source assertion: Table 1 identifies pETB23 as a pET21a(+) expression plasmid carrying praB; the study uses BL21(DE3) for expression.

    Source locationPMC2795304 HTML section#t1, pETB23 and BL21(DE3) rows; section#sec6
catalyzes

PraB recombinant crude-extract assay supports NAD-dependent semialdehyde oxidation. NADP also supports lower activity in the same study; neither reaction membership nor the selected NAD equation establishes exclusive physiological coenzyme use.

(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate + NAD(+) + H2O => (2Z,4E)-2-hydroxyhexa-2,4-dienedioate + NADH + 2 H(+)
RHEA:34220
  • PMID:19717587
    praB encodes HMS dehydrogenase
    Source locationPMC2795304 HTML section#sec22
  • MetaCyc:MONOMER-15108

    Source assertion: The native protein object explicitly links MONOMER-15108 to UniProt C4TP02.

    Source location/ptools-xml/Protein/dblink[dblink-db='UNIPROT']
  • MetaCyc:ENZRXN-16912

    Source assertion: The complete native enzymatic-reaction object assigns MONOMER-15108 to RXN-8527. Heterologous-assay evidence includes PMID:19717587; primary construct details must remain on affected assay endpoints.

    Source location/ptools-xml/Enzymatic-Reaction/enzyme; reaction; evidence
Tautomerase
UniProtKB:C4TP07

experimental construct: Recombinant praC product from pETC23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.

Qualification evidence
  • PMID:19717587

    Source assertion: Table 1 identifies pETC23 as a pET21a(+) expression plasmid carrying praC; the study uses BL21(DE3) for expression.

    Source locationPMC2795304 HTML section#t1, pETC23 and BL21(DE3) rows; section#sec6
catalyzes

PraC accelerates hydroxymuconate tautomerization. The native reaction is reversible and its comment also describes slow aqueous conversion; the pathway selects the forward flux. The exact Rhea equation is 33432; the native 32214 cross-reference has different stereoisomers.

(2Z,4E)-2-hydroxyhexa-2,4-dienedioate => (3E)-2-oxohex-3-enedioate
RHEA:33432
  • PMID:19717587
    tautomerization catalyzed by PraC
    Source locationPMC2795304 HTML section#sec22
  • MetaCyc:MONOMER-15109

    Source assertion: The native protein object explicitly links MONOMER-15109 to UniProt C4TP07.

    Source location/ptools-xml/Protein/dblink[dblink-db='UNIPROT']
  • MetaCyc:ENZRXN-16913

    Source assertion: The complete native enzymatic-reaction object assigns MONOMER-15109 to RXN-8529. Heterologous-assay evidence includes PMID:19717587; primary construct details must remain on affected assay endpoints.

    Source location/ptools-xml/Enzymatic-Reaction/enzyme; reaction; evidence
4-oxalocrotonate decarboxylase
UniProtKB:C4TP06

experimental construct: Recombinant praD product from pC4D23 (pColdIV) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.

Qualification evidence
  • PMID:19717587

    Source assertion: Table 1 identifies pC4D23 as a pColdIV expression plasmid carrying praD; the study uses BL21(DE3) for expression.

    Source locationPMC2795304 HTML section#t1, pC4D23 and BL21(DE3) rows; section#sec6
catalyzes

PraD recombinant crude-extract assay supports oxalocrotonate decarboxylation to hydroxypentadienoate. The assay included 500 micromolar MgSO4, which alone does not prove a physiological magnesium requirement. The enol product is preserved, rather than substituted by its keto tautomer.

4-oxalocrotonate decarboxylation to the Z-enol
MetaCyc:4.1.1.77-RXN
  • PMID:19717587
    decarboxylation of OCA to produce HPD
    Source locationPMC2795304 HTML section#sec22
  • MetaCyc:MONOMER-15110

    Source assertion: The native protein object explicitly links MONOMER-15110 to UniProt C4TP06.

    Source location/ptools-xml/Protein/dblink[dblink-db='UNIPROT']
  • MetaCyc:ENZRXN-16914

    Source assertion: The complete native enzymatic-reaction object assigns MONOMER-15110 to 4.1.1.77-RXN. Heterologous-assay evidence includes PMID:19717587; primary construct details must remain on affected assay endpoints.

    Source location/ptools-xml/Enzymatic-Reaction/enzyme; reaction; evidence
2-hydroxymuconate-6-semialdehyde dehydrogenase
UniProtKB:C4TP02

experimental construct: Recombinant praB product from pETB23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.

Qualification evidence
  • PMID:19717587

    Source assertion: Table 1 identifies pETB23 as a pET21a(+) expression plasmid carrying praB; the study uses BL21(DE3) for expression.

    Source locationPMC2795304 HTML section#t1, pETB23 and BL21(DE3) rows; section#sec6
has_cofactor

Recombinant crude PraB uses NAD+ in the HMS dehydrogenase assay (1.19±0.07U/mg). NADP+ also supports activity at approximately one-eleventh this rate, so this is preference rather than exclusivity. Chemical ionization is the curated ChEBI normalization, not measured assay protonation.

NAD(1-)
CHEBI:57540
  • PMID:19717587
    in the presence of NAD+
    Source locationPMC2795304 HTML section#sec22, second paragraph, comparative HMS dehydrogenase activities
2-hydroxymuconate-6-semialdehyde dehydrogenase
UniProtKB:C4TP02

experimental construct: Recombinant praB product from pETB23 (pET21a(+)) expressed in E. coli BL21(DE3) and assayed as crude extract. Exact terminal sequence and tag state were not independently resolved from the unavailable primer supplement.

Qualification evidence
  • PMID:19717587

    Source assertion: Table 1 identifies pETB23 as a pET21a(+) expression plasmid carrying praB; the study uses BL21(DE3) for expression.

    Source locationPMC2795304 HTML section#t1, pETB23 and BL21(DE3) rows; section#sec6
has_cofactor

Recombinant crude PraB supports a lower HMS dehydrogenase activity with NADP+ (0.113±0.009U/mg) than with NAD+ (1.19±0.07U/mg). This in-vitro alternative does not establish the dominant physiological coenzyme. Chemical ionization is the curated ChEBI normalization, not measured assay protonation.

NADP(3-)
CHEBI:58349
  • PMID:19717587
    with NADP+
    Source locationPMC2795304 HTML section#sec22, second paragraph, comparative HMS dehydrogenase activities
hydrogen peroxide
CHEBI:16240		inhibits

The 1993 abstract reports in-vitro inactivation of purified native JJ1b protocatechuate 2,3-dioxygenase by hydrogen peroxide among Fe2+-oxidizing reagents. This is an assay perturbation of the historical native preparation, not physiological regulation or a 2009 recombinant-sequence claim. No dose or exact damaged-site occupancy is asserted.

protocatechuate 2,3-dioxygenase
MetaCyc:CPLX-7915
  • PMID:8392511
    enzyme was inactivated
    Source locationPubmedArticleSet/PubmedArticle/MedlineCitation/Article/Abstract/AbstractText; sentence beginning The enzyme was inactivated
  • PMID:8392511
    H2O2
    Source locationPubmedArticleSet/PubmedArticle/MedlineCitation/Article/Abstract/AbstractText; sentence beginning The enzyme was inactivated
  • MetaCyc:CPLX-7915

    Source assertion: The native complex annotation describes purification from JJ-1b and a later native homotetramer characterization citing PMID:8392511; this maps the historical preparation to CPLX-7915 without proving its complete 2009 protein sequence.

    Source location/ptools-xml/Protein[@frameid="CPLX-7915"]/comment
ascorbate
CHEBI:22651		activates

Ascorbate restores activity to the historical purified native enzyme after oxidative inactivation, including the reported hydrogen peroxide treatment. The abstract attributes recovery to reduction of the iron. This edge claims recovery of the qualified inactive preparation, not stimulation of untreated enzyme; stereochemistry of the ascorbate reagent is not specified.

protocatechuate 2,3-dioxygenase
MetaCyc:CPLX-7915

molecular state: Historical purified native JJ1b 2,3-PCD after inactivation by hydrogen peroxide, as described among the oxidizing treatments in the 1993 abstract. This qualifier restricts the recovery claim to inactive enzyme; the source does not resolve damage sites, metal-state occupancy, dose or a separate treatment-specific recovery protocol.

Qualification evidence
  • PMID:8392511
    inactivated
    Source locationPubmedArticleSet/PubmedArticle/MedlineCitation/Article/Abstract/AbstractText; sentence beginning The enzyme was inactivated
  • MetaCyc:CPLX-7915

    Source assertion: The native complex annotation describes purification from JJ-1b and a later native homotetramer characterization citing PMID:8392511; this maps the historical preparation to CPLX-7915 without proving its complete 2009 protein sequence.

    Source location/ptools-xml/Protein[@frameid="CPLX-7915"]/comment
  • PMID:8392511
    full activity was restored
    Source locationPubmedArticleSet/PubmedArticle/MedlineCitation/Article/Abstract/AbstractText; sentence beginning The enzyme was inactivated
  • PMID:8392511
    by ascorbate
    Source locationPubmedArticleSet/PubmedArticle/MedlineCitation/Article/Abstract/AbstractText; sentence beginning The enzyme was inactivated
  • MetaCyc:CPLX-7915

    Source assertion: The native complex annotation describes purification from JJ-1b and a later native homotetramer characterization citing PMID:8392511; this maps the historical preparation to CPLX-7915 without proving its complete 2009 protein sequence.

    Source location/ptools-xml/Protein[@frameid="CPLX-7915"]/comment
potassium hexacyanoferrate(3-)
CHEBI:30060		inhibits

The 1993 abstract reports in-vitro inactivation of purified native JJ1b protocatechuate 2,3-dioxygenase by potassium ferricyanide among Fe2+-oxidizing reagents. This is an assay perturbation of the historical native preparation, not physiological regulation or a 2009 recombinant-sequence claim. No dose or exact damaged-site occupancy is asserted.

protocatechuate 2,3-dioxygenase
MetaCyc:CPLX-7915
  • PMID:8392511
    enzyme was inactivated
    Source locationPubmedArticleSet/PubmedArticle/MedlineCitation/Article/Abstract/AbstractText; sentence beginning The enzyme was inactivated
  • PMID:8392511
    K3FE(CN)6
    Source locationPubmedArticleSet/PubmedArticle/MedlineCitation/Article/Abstract/AbstractText; sentence beginning The enzyme was inactivated
  • MetaCyc:CPLX-7915

    Source assertion: The native complex annotation describes purification from JJ-1b and a later native homotetramer characterization citing PMID:8392511; this maps the historical preparation to CPLX-7915 without proving its complete 2009 protein sequence.

    Source location/ptools-xml/Protein[@frameid="CPLX-7915"]/comment
ascorbate
CHEBI:22651		activates

Ascorbate restores activity to the historical purified native enzyme after oxidative inactivation, including the reported potassium ferricyanide treatment. The abstract attributes recovery to reduction of the iron. This edge claims recovery of the qualified inactive preparation, not stimulation of untreated enzyme; stereochemistry of the ascorbate reagent is not specified.

protocatechuate 2,3-dioxygenase
MetaCyc:CPLX-7915

molecular state: Historical purified native JJ1b 2,3-PCD after inactivation by potassium ferricyanide, as described among the oxidizing treatments in the 1993 abstract. This qualifier restricts the recovery claim to inactive enzyme; the source does not resolve damage sites, metal-state occupancy, dose or a separate treatment-specific recovery protocol.

Qualification evidence
  • PMID:8392511
    inactivated
    Source locationPubmedArticleSet/PubmedArticle/MedlineCitation/Article/Abstract/AbstractText; sentence beginning The enzyme was inactivated
  • MetaCyc:CPLX-7915

    Source assertion: The native complex annotation describes purification from JJ-1b and a later native homotetramer characterization citing PMID:8392511; this maps the historical preparation to CPLX-7915 without proving its complete 2009 protein sequence.

    Source location/ptools-xml/Protein[@frameid="CPLX-7915"]/comment
  • PMID:8392511
    full activity was restored
    Source locationPubmedArticleSet/PubmedArticle/MedlineCitation/Article/Abstract/AbstractText; sentence beginning The enzyme was inactivated
  • PMID:8392511
    by ascorbate
    Source locationPubmedArticleSet/PubmedArticle/MedlineCitation/Article/Abstract/AbstractText; sentence beginning The enzyme was inactivated
  • MetaCyc:CPLX-7915

    Source assertion: The native complex annotation describes purification from JJ-1b and a later native homotetramer characterization citing PMID:8392511; this maps the historical preparation to CPLX-7915 without proving its complete 2009 protein sequence.

    Source location/ptools-xml/Protein[@frameid="CPLX-7915"]/comment

References

Curation history