shikimate degradation I

MetaCyc:SHIKIMATEDEG-PWY

The two-step MetaCyc 27.0 shikimate degradation I definition converts shikimate through 3-dehydroshikimate to protocatechuate. The initial oxidation retains the source-defined quinone and quinol classes, with PQQ as a separate enzyme cofactor. This is distinct from the NAD-dependent shikimate II route and the three-step quinate I route. Enzyme and regulatory evidence retains organism, preparation and inference scope; the record does not assert a purified two-enzyme reconstruction for every source-listed organism.

Pathway type
aromatic compound catabolism
Organism scope

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Pathway network

28 nodes · 31 asserted directed edges

Arrows show recorded subject → object relationships, not necessarily metabolic flow. Select a node for details or an arrow for evidence. Scroll, zoom or find a node to explore.

Pathway network: shikimate degradation I 28 nodes · 31 asserted directed edges. Every arrow links to its evidence table row; nodes link to their component details. Isolated declared components are retained. MetaCyc:SHIKIMATEDEG-PWY — part_of → NCBITaxon:62977; Native pathway species context; individual enzyme evidence retains its strain and preparation scope.; Evidence: MetaCyc:SHIKIMATEDEG-PWYpart of MetaCyc:SHIKIMATEDEG-PWY — part_of → NCBITaxon:471; Historical A. calcoaceticus LMD 79.41 context: Table 1 reports shikimate growth of the wild type and impaired growth of PQQ-biosynthesis mutants. The paragraph above Table 1 describes rescue by added PQQ, while Methods reports identification using API 20 NE. This context is distinct from ADP1 and does not assert modern retyping of the historical isolate or purification of its complete route.; Evidence: MetaCyc:SHIKIMATEDEG-PWY, PMID:3044290part of MetaCyc:SHIKIMATEDEG-PWY — part_of → NCBITaxon:442; Native G. oxydans oxidative-enzyme context, including IFO3244 preparations. This does not assert shikimate-supported growth, complete mineralization, or a purified two-step reconstruction.; Evidence: MetaCyc:SHIKIMATEDEG-PWYpart of MetaCyc:SHIKIMATE-PQQ-RXN — part_of → MetaCyc:SHIKIMATEDEG-PWY; One of the two explicit native pathway members; the native reaction direction is preserved.; Evidence: MetaCyc:SHIKIMATEDEG-PWYpart of CHEBI:36208 — consumes → MetaCyc:SHIKIMATE-PQQ-RXN; Selected catabolic pathway orientation.; Evidence: MetaCyc:SHIKIMATE-PQQ-RXN, MetaCyc:SHIKIMATEconsumes MetaCyc:Quinones — consumes → MetaCyc:SHIKIMATE-PQQ-RXN; Selected catabolic pathway orientation. Native generic quinone class; this does not establish specificity for every class member or a measured physiological quinone.; Evidence: MetaCyc:SHIKIMATE-PQQ-RXNconsumes MetaCyc:SHIKIMATE-PQQ-RXN — produces → CHEBI:16630; Selected catabolic pathway orientation.; Evidence: MetaCyc:SHIKIMATE-PQQ-RXN, MetaCyc:3-DEHYDRO-SHIKIMATEproduces MetaCyc:SHIKIMATE-PQQ-RXN — produces → MetaCyc:Reduced-Quinones; Selected catabolic pathway orientation. Native generic quinone class; this does not establish specificity for every class member or a measured physiological quinone.; Evidence: MetaCyc:SHIKIMATE-PQQ-RXNproduces RHEA:24849 — part_of → MetaCyc:SHIKIMATEDEG-PWY; One of the two explicit native pathway members; the native reaction direction is preserved.; Evidence: MetaCyc:SHIKIMATEDEG-PWYpart of CHEBI:16630 — consumes → RHEA:24849; Selected catabolic pathway orientation.; Evidence: MetaCyc:DHSHIKIMATE-DEHYDRO-RXN, MetaCyc:3-DEHYDRO-SHIKIMATE, RHEA:24849consumes RHEA:24849 — produces → CHEBI:36241; Selected catabolic pathway orientation.; Evidence: MetaCyc:DHSHIKIMATE-DEHYDRO-RXN, MetaCyc:3-4-DIHYDROXYBENZOATE, RHEA:24849produces RHEA:24849 — produces → CHEBI:15377; Selected catabolic pathway orientation.; Evidence: MetaCyc:DHSHIKIMATE-DEHYDRO-RXN, MetaCyc:WATER, RHEA:24849produces MetaCyc:SHIKIMATE-PQQ-RXN — precedes → RHEA:24849; Native pathway reaction ordering selects forward catabolic progression.; Evidence: MetaCyc:SHIKIMATEDEG-PWYprecedes UniProtKB:Q59086 — catalyzes → MetaCyc:SHIKIMATE-PQQ-RXN; Native ADP1 QuiA shikimate activity is supported by pathway and genetic evidence. The native purified-protein code and kinetics cite Acinetobacter SA1/AC3 preparations; those measurements are not assigned to ADP1. The source groups the reaction as quinone-dependent oxidation without establishing use of every quinone.; Evidence: MetaCyc:ENZRXN-11861, MetaCyc:MONOMER-28catalyzes UniProtKB:Q59086 — part_of → NCBITaxon:62977; ADP1 source protein context; strain-specific activity and preparation limits remain on the catalytic edge.; Evidence: MetaCyc:MONOMER-28, MetaCyc:MONOMER-28part of UniProtKB:Q43922 — catalyzes → RHEA:24849; subject experimental construct: ADP1 genomic quiC expressed in E. coli DH5α(pZR564), a 2.0 kb HindIII insert; crude-extract assay. No protein tag reported or expressed termini measured. Text/Table 1 disagree on pBSK versus pBKS vector label.; Evidence PMID:7592351: pZR564 contains the open reading frame; DHS dehydration is supported by cloned quiC activity and native genetic phenotypes. The native protein comment incorrectly labels the assay as DHQ dehydration; no numeric activity is copied.; Evidence: MetaCyc:ENZRXN-38, MetaCyc:MONOMER-37catalyzes UniProtKB:Q43922 — part_of → NCBITaxon:62977; ADP1 source protein context; the catalytic experiment used the qualified recombinant crude-extract preparation.; Evidence: MetaCyc:MONOMER-37, MetaCyc:MONOMER-37part of MetaCyc:MONOMER-1 — catalyzes → RHEA:24849; subject molecular state: Native IFO3244 partially purified cytoplasmic enzyme fraction; DHS-dehydratase activity eluted separately from DQD on DEAE-Sephadex A-50. Exact protein sequence, termini and oligomeric state are unresolved.; Evidence PMID:14586099: DSA dehydratase was separated from DQD; Native IFO3244 DHS-dehydratase activity was separated from DQD and detected with a coupled qualitative protocatechuate assay. Exact gene and sequence identity remain unresolved.; Evidence: MetaCyc:ENZRXN-3catalyzes MetaCyc:MONOMER-1 — part_of → NCBITaxon:442; Source protein taxon context; this partially purified IFO3244 activity is not a sequence identity or full-route reconstruction for every strain.; Evidence: MetaCyc:MONOMER-1part of UniProtKB:Q59086 — has_cofactor → CHEBI:58442; PQQ is a prosthetic cofactor, distinct from the net electron-accepting quinone. The native assignment is independently supported by current ADP1 UniProt annotation; SA1/AC3 or LMD79.41 biochemical tests are not transferred to ADP1.; Evidence: MetaCyc:ENZRXN-11861, MetaCyc:MONOMER-28, UniProtKB:Q59086has cofactor MetaCyc:MONOMER-1 — located_in → GO:0005737; subject molecular state: Native IFO3244 partially purified cytoplasmic enzyme fraction; DHS-dehydratase activity eluted separately from DQD on DEAE-Sephadex A-50. Exact protein sequence, termini and oligomeric state are unresolved.; Evidence PMID:14586099: DSA dehydratase was separated from DQD; Recovery in the cytoplasmic fraction supports this preparation context without establishing exclusive localization of a sequence-defined enzyme.; Evidence: MetaCyc:ENZRXN-3located in MetaCyc:MONOMER-67 — catalyzes → MetaCyc:SHIKIMATE-PQQ-RXN; subject molecular state: Native IFO3244 membrane holo-QDH preparation; SDS bands approximately 65 and 21 kDa may reflect proteolysis of one polypeptide. Exact cleavage and whole-protein sequence are unresolved.; Evidence PMID:15598527: could be the result of proteolysis of single polypeptide; The inspected native ENZRXN-68 comment reports shikimate activity at 25% of the quinate rate and ferricyanide as the most efficient artificial acceptor, citing PMID:15598527. Its formal reaction slot is quinate oxidation. The shikimate claim is curated-source evidence; the 2004 full paper was unavailable. No physiological quinone specificity is inferred from the artificial-acceptor result.; Evidence: MetaCyc:ENZRXN-68catalyzes MetaCyc:MONOMER-67 — part_of → NCBITaxon:442; Native G. oxydans protein context; the cited preparation is IFO3244. This does not establish sequence identity or shikimate-supported growth for every strain.; Evidence: MetaCyc:MONOMER-67part of MetaCyc:MONOMER-67 — located_in → GO:0016020; subject molecular state: Native IFO3244 purified holo-QDH preparation; exact proteolytic cleavage state is unresolved.; Evidence MetaCyc:MONOMER-67: The native QDH protein comment describes a purified holoenzyme with 65/21 kDa SDS bands suggested to arise by proteolysis. (/ptools-xml/Protein[@frameid="MONOMER-67"]/comment); Native source and the inspected primary abstract describe membrane-bound IFO3244 QDH. This broad location does not establish exact orientation or an obligate respiratory assembly.; Evidence: MetaCyc:MONOMER-67located in UniProtKB:Q59086 — located_in → GO:0016020; The reviewed UniProt membrane annotation uses ECO:0000305 curator inference. The five membrane segments proposed in the 1994 study are hydropathy predictions, not direct topology measurements.; Evidence: UniProtKB:Q59086, MetaCyc:MONOMER-28located in UniProtKB:O83046 — part_of → NCBITaxon:62977; Reviewed ADP1 PcaU context; the initiating methionine is uncertain between Met1 and Met5, so no exact tested N terminus is assumed.; Evidence: UniProtKB:O83046part of MetaCyc:MONOMER-67 — has_cofactor → CHEBI:58442; subject molecular state: Native IFO3244 purified holo-QDH preparation; exact proteolytic cleavage state is unresolved.; Evidence MetaCyc:MONOMER-67: The native QDH protein comment describes a purified holoenzyme with 65/21 kDa SDS bands suggested to arise by proteolysis. (/ptools-xml/Protein[@frameid="MONOMER-67"]/comment); PQQ is bound as a prosthetic group; it is not consumed as the quinone electron acceptor. The full 2004 body remains unread.; Evidence: PMID:15598527has cofactor UniProtKB:O83046 — regulates → MetaCyc:G-27; PcaU controls quiA transcript abundance in ADP1 under protocatechuate induction. Northern analysis of ADP331 with a 552 bp pcaU deletion showed reduced transcript abundance and loss of inducer dependence relative to wild-type ADP1. The quiA signal was 25% of the induced wild-type level. The 442 bp quiA probe measures the target directly. This is transcriptional control inferred from genetic perturbation. Constitutive quiAp remains active independently of PcaU.; Evidence: PMID:15691962, MetaCyc:G-27regulates CHEBI:36241 — regulates → MetaCyc:G-27; Protocatechuate induces ADP1 quiA expression through the regulated pca-qui transcription system. Addition of 2 mM protocatechuate to cells growing on 20 mM pyruvate produced stronger Northern signals after 15 min. The pcaU deletion removed inducer dependence. The 442 bp quiA probe measures the target directly. No direct metabolite–PcaU binding is asserted.; Evidence: PMID:15691962, MetaCyc:G-27regulates UniProtKB:O83046 — regulates → MetaCyc:G-36; PcaU controls quiC transcript abundance in ADP1 under protocatechuate induction. Northern analysis of ADP331 with a 552 bp pcaU deletion showed reduced transcript abundance and loss of inducer dependence relative to wild-type ADP1. The shared quiC–quiX probe signal was 14% of the induced wild-type level. Target assignment is at the operon level: the 1,522 bp probe spans quiC and quiX and is called the quiX probe in the paper. Isolated quiC promoter activity was not measured. This is transcriptional control inferred from genetic perturbation. Constitutive quiAp remains active independently of PcaU.; Evidence: PMID:15691962, MetaCyc:G-36regulates CHEBI:36241 — regulates → MetaCyc:G-36; Protocatechuate induces ADP1 quiC expression through the regulated pca-qui transcription system. Addition of 2 mM protocatechuate to cells growing on 20 mM pyruvate produced stronger Northern signals after 15 min. The pcaU deletion removed inducer dependence. Target assignment is at the operon level: the 1,522 bp probe spans quiC and quiX and is called the quiX probe in the paper. Isolated quiC promoter activity was not measured. No direct metabolite–PcaU binding is asserted.; Evidence: PMID:15691962, MetaCyc:G-36regulates shikimate; CHEBI:36208; Declared type: small_molecule small molecule shikimate 3-dehydroshikimate; CHEBI:16630; Declared type: small_molecule small molecule 3-dehydroshikimate 3,4-dihydroxybenzoate; CHEBI:36241; Declared type: small_molecule small molecule 3,4-dihydroxybenzoate water; CHEBI:15377; Declared type: small_molecule small molecule water a quinone; MetaCyc:Quinones; Declared type: chemical_entity chemical entity a quinone a quinol; MetaCyc:Reduced-Quinones; Declared type: chemical_entity chemical entity a quinol Quinate/shikimate dehydrogenase (quinone); UniProtKB:Q59086; Declared type: protein protein Quinate/shikimate dehydrogenase (quinone) 3-dehydroshikimate dehydratase; UniProtKB:Q43922; Declared type: protein protein 3-dehydroshikimate dehydratase dehydroshikimate dehydratase; MetaCyc:MONOMER-1; Declared type: protein protein dehydroshikimate dehydratase quinate dehydrogenase; MetaCyc:MONOMER-67; Declared type: protein protein quinate dehydrogenase Pca operon regulatory protein; UniProtKB:O83046; Declared type: protein protein Pca operon regulatory protein quiA; MetaCyc:G-27; Declared type: gene gene quiA quiC; MetaCyc:G-36; Declared type: gene gene quiC pyrroloquinoline quinone(3-); CHEBI:58442; Declared type: cofactor cofactor pyrroloquinoline quinone(3-) membrane; GO:0016020; Declared type: cellular_component cellular component membrane cytoplasm; GO:0005737; Declared type: cellular_component cellular component cytoplasm shikimate oxidation with a quinone; MetaCyc:SHIKIMATE-PQQ-RXN; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity shikimate oxidation with a quinone 3-dehydroshikimate => 3,4-dihydroxybenzoate + H2O; RHEA:24849; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity 3-dehydroshikimate => 3,4-dihydroxybenzoate + H2O Acinetobacter baylyi ADP1; NCBITaxon:62977; Declared type: taxon taxon Acinetobacter baylyi ADP1 Acinetobacter calcoaceticus; NCBITaxon:471; Declared type: taxon taxon Acinetobacter calcoaceticus Gluconobacter oxydans; NCBITaxon:442; Declared type: taxon taxon Gluconobacter oxydans shikimate degradation I; MetaCyc:SHIKIMATEDEG-PWY; Declared type: pathway pathway shikimate degradation I 3-dehydroshikimate dehydratase; UniProtKB:Q43922; Declared type: protein; experimental construct: ADP1 genomic quiC expressed in E. coli DH5α(pZR564), a 2.0 kb HindIII insert; crude-extract assay. No protein tag reported or expressed termini measured. Text/Table 1 disagree on pBSK versus pBKS vector label.; Evidence PMID:7592351: pZR564 contains the open reading frame experimental construct 3-dehydroshikimate dehydratase [experimental construct: ADP1 genomic quiC expressed in E. coli DH5α(pZR564), a 2.0 kb HindIII insert; crude- extract assay.…] dehydroshikimate dehydratase; MetaCyc:MONOMER-1; Declared type: protein; molecular state: Native IFO3244 partially purified cytoplasmic enzyme fraction; DHS-dehydratase activity eluted separately from DQD on DEAE-Sephadex A-50. Exact protein sequence, termini and oligomeric state are unresolved.; Evidence PMID:14586099: DSA dehydratase was separated from DQD molecular state dehydroshikimate dehydratase [molecular state: Native IFO3244 partially purified cytoplasmic enzyme fraction; DHS-dehydratase activity eluted…] dehydroshikimate dehydratase; MetaCyc:MONOMER-1; Declared type: protein; molecular state: Native IFO3244 partially purified cytoplasmic enzyme fraction; DHS-dehydratase activity eluted separately from DQD on DEAE-Sephadex A-50. Exact protein sequence, termini and oligomeric state are unresolved.; Evidence PMID:14586099: DSA dehydratase was separated from DQD molecular state dehydroshikimate dehydratase [molecular state: Native IFO3244 partially purified cytoplasmic enzyme fraction; DHS-dehydratase activity eluted…] quinate dehydrogenase; MetaCyc:MONOMER-67; Declared type: protein; molecular state: Native IFO3244 membrane holo-QDH preparation; SDS bands approximately 65 and 21 kDa may reflect proteolysis of one polypeptide. Exact cleavage and whole-protein sequence are unresolved.; Evidence PMID:15598527: could be the result of proteolysis of single polypeptide molecular state quinate dehydrogenase [molecular state: Native IFO3244 membrane holo-QDH preparation; SDS bands approximately 65 and 21 kDa may reflect…] quinate dehydrogenase; MetaCyc:MONOMER-67; Declared type: protein; molecular state: Native IFO3244 purified holo-QDH preparation; exact proteolytic cleavage state is unresolved.; Evidence MetaCyc:MONOMER-67: The native QDH protein comment describes a purified holoenzyme with 65/21 kDa SDS bands suggested to arise by proteolysis. (/ptools-xml/Protein[@frameid="MONOMER-67"]/comment) molecular state quinate dehydrogenase [molecular state: Native IFO3244 purified holo-QDH preparation; exact proteolytic cleavage state is unresolved.] quinate dehydrogenase; MetaCyc:MONOMER-67; Declared type: protein; molecular state: Native IFO3244 purified holo-QDH preparation; exact proteolytic cleavage state is unresolved.; Evidence MetaCyc:MONOMER-67: The native QDH protein comment describes a purified holoenzyme with 65/21 kDa SDS bands suggested to arise by proteolysis. (/ptools-xml/Protein[@frameid="MONOMER-67"]/comment) molecular state quinate dehydrogenase [molecular state: Native IFO3244 purified holo-QDH preparation; exact proteolytic cleavage state is unresolved.]

Components and activities

Declared biological components and source reaction directions
NodeKind or roleSource direction
Acinetobacter baylyi ADP1
NCBITaxon:62977		taxon
Acinetobacter calcoaceticus
NCBITaxon:471		taxon
Gluconobacter oxydans
NCBITaxon:442		taxon
shikimate
CHEBI:36208		small molecule
3-dehydroshikimate
CHEBI:16630		small molecule
3,4-dihydroxybenzoate
CHEBI:36241		small molecule
water
CHEBI:15377		small molecule
a quinone
MetaCyc:Quinones		chemical entity
a quinol
MetaCyc:Reduced-Quinones		chemical entity
Quinate/shikimate dehydrogenase (quinone)
UniProtKB:Q59086		protein
3-dehydroshikimate dehydratase
UniProtKB:Q43922		protein
dehydroshikimate dehydratase
MetaCyc:MONOMER-1		protein
quinate dehydrogenase
MetaCyc:MONOMER-67		protein
Pca operon regulatory protein
UniProtKB:O83046		protein
quiA
MetaCyc:G-27		gene
quiC
MetaCyc:G-36		gene
pyrroloquinoline quinone(3-)
CHEBI:58442		cofactor
membrane
GO:0016020		cellular component
cytoplasm
GO:0005737		cellular component
shikimate oxidation with a quinone
MetaCyc:SHIKIMATE-PQQ-RXN		molecular activityleft to right
3-dehydroshikimate => 3,4-dihydroxybenzoate + H2O
RHEA:24849		molecular activityleft to right

Mechanistic edges

Mechanistic edges and their cited evidence
SubjectPredicate and descriptionObjectEvidence
MetaCyc:SHIKIMATEDEG-PWYpart_of

Native pathway species context; individual enzyme evidence retains its strain and preparation scope.

Acinetobacter baylyi ADP1
NCBITaxon:62977
  • MetaCyc:SHIKIMATEDEG-PWY

    Source assertion: The native pathway species slot lists TAX-62977; this is a source-listed organism context.

    Source location/ptools-xml/Pathway[@frameid="SHIKIMATEDEG-PWY"]/species/Organism[@frameid="TAX-62977"]
MetaCyc:SHIKIMATEDEG-PWYpart_of

Historical A. calcoaceticus LMD 79.41 context: Table 1 reports shikimate growth of the wild type and impaired growth of PQQ-biosynthesis mutants. The paragraph above Table 1 describes rescue by added PQQ, while Methods reports identification using API 20 NE. This context is distinct from ADP1 and does not assert modern retyping of the historical isolate or purification of its complete route.

Acinetobacter calcoaceticus
NCBITaxon:471
  • MetaCyc:SHIKIMATEDEG-PWY

    Source assertion: The native pathway species slot lists TAX-471; this is a source-listed organism context.

    Source location/ptools-xml/Pathway[@frameid="SHIKIMATEDEG-PWY"]/species/Organism[@frameid="TAX-471"]
  • PMID:3044290

    Source assertion: Table 1 records shikimate growth for wild-type LMD 79.41, no shikimate growth for the PQQ-biosynthesis mutants M7, 82.43 and 1347, and delayed or weak growth for several mutants under the tested PQQ-free conditions.

    Source locationAuthorized author reprint in the 1988 van Kleef dissertation: Chapter V, printed p. 85 (PDF page 94), Table 1, shikimate columns.
MetaCyc:SHIKIMATEDEG-PWYpart_of

Native G. oxydans oxidative-enzyme context, including IFO3244 preparations. This does not assert shikimate-supported growth, complete mineralization, or a purified two-step reconstruction.

Gluconobacter oxydans
NCBITaxon:442
  • MetaCyc:SHIKIMATEDEG-PWY

    Source assertion: The native pathway species slot lists TAX-442; this is a source-listed organism context.

    Source location/ptools-xml/Pathway[@frameid="SHIKIMATEDEG-PWY"]/species/Organism[@frameid="TAX-442"]
shikimate oxidation with a quinone
MetaCyc:SHIKIMATE-PQQ-RXN		part_of

One of the two explicit native pathway members; the native reaction direction is preserved.

MetaCyc:SHIKIMATEDEG-PWY
  • MetaCyc:SHIKIMATEDEG-PWY

    Source assertion: The reaction-list includes SHIKIMATE-PQQ-RXN and the selected pathway layout is L2R.

    Source location/ptools-xml/Pathway[@frameid="SHIKIMATEDEG-PWY"]/reaction-list|reaction-layout[Reaction/@frameid="SHIKIMATE-PQQ-RXN"]
shikimate
CHEBI:36208		consumes

Selected catabolic pathway orientation.

shikimate oxidation with a quinone
MetaCyc:SHIKIMATE-PQQ-RXN
  • MetaCyc:SHIKIMATE-PQQ-RXN

    Source assertion: The native left side contains SHIKIMATE. No explicit coefficient is supplied.

    Source location/ptools-xml/Reaction[@frameid="SHIKIMATE-PQQ-RXN"]/left/Compound[@frameid="SHIKIMATE"]
  • MetaCyc:SHIKIMATE

    Source assertion: The native compound links CHEBI:36208; its complete InChI agrees with the selected ChEBI molecular identity.

    Source location/ptools-xml/Compound[@frameid="SHIKIMATE"] /dblink[dblink-db="CHEBI"]|inchi
a quinone
MetaCyc:Quinones		consumes

Selected catabolic pathway orientation. Native generic quinone class; this does not establish specificity for every class member or a measured physiological quinone.

shikimate oxidation with a quinone
MetaCyc:SHIKIMATE-PQQ-RXN
  • MetaCyc:SHIKIMATE-PQQ-RXN

    Source assertion: The native left side contains Quinones. No explicit coefficient is supplied.

    Source location/ptools-xml/Reaction[@frameid="SHIKIMATE-PQQ-RXN"]/left/Compound[@frameid="Quinones"]
shikimate oxidation with a quinone
MetaCyc:SHIKIMATE-PQQ-RXN		produces

Selected catabolic pathway orientation.

3-dehydroshikimate
CHEBI:16630
  • MetaCyc:SHIKIMATE-PQQ-RXN

    Source assertion: The native right side contains 3-DEHYDRO-SHIKIMATE. No explicit coefficient is supplied.

    Source location/ptools-xml/Reaction[@frameid="SHIKIMATE-PQQ-RXN"]/right/Compound[@frameid="3-DEHYDRO-SHIKIMATE"]
  • MetaCyc:3-DEHYDRO-SHIKIMATE

    Source assertion: The native compound links CHEBI:16630; its complete InChI agrees with the selected ChEBI molecular identity.

    Source location/ptools-xml/Compound[@frameid="3-DEHYDRO-SHIKIMATE"] /dblink[dblink-db="CHEBI"]|inchi
shikimate oxidation with a quinone
MetaCyc:SHIKIMATE-PQQ-RXN		produces

Selected catabolic pathway orientation. Native generic quinone class; this does not establish specificity for every class member or a measured physiological quinone.

a quinol
MetaCyc:Reduced-Quinones
  • MetaCyc:SHIKIMATE-PQQ-RXN

    Source assertion: The native right side contains Reduced-Quinones. No explicit coefficient is supplied.

    Source location/ptools-xml/Reaction[@frameid="SHIKIMATE-PQQ-RXN"]/right/Compound[@frameid="Reduced-Quinones"]
3-dehydroshikimate => 3,4-dihydroxybenzoate + H2O
RHEA:24849		part_of

One of the two explicit native pathway members; the native reaction direction is preserved.

MetaCyc:SHIKIMATEDEG-PWY
  • MetaCyc:SHIKIMATEDEG-PWY

    Source assertion: The reaction-list includes DHSHIKIMATE-DEHYDRO-RXN and the selected pathway layout is L2R.

    Source location/ptools-xml/Pathway[@frameid="SHIKIMATEDEG-PWY"]/reaction-list|reaction-layout[Reaction/@frameid="DHSHIKIMATE-DEHYDRO-RXN"]
3-dehydroshikimate
CHEBI:16630		consumes

Selected catabolic pathway orientation.

3-dehydroshikimate => 3,4-dihydroxybenzoate + H2O
RHEA:24849
  • MetaCyc:DHSHIKIMATE-DEHYDRO-RXN

    Source assertion: The native left side contains 3-DEHYDRO-SHIKIMATE. No explicit coefficient is supplied.

    Source location/ptools-xml/Reaction[@frameid="DHSHIKIMATE-DEHYDRO-RXN"]/left/Compound[@frameid="3-DEHYDRO-SHIKIMATE"]
  • MetaCyc:3-DEHYDRO-SHIKIMATE

    Source assertion: The native compound links CHEBI:16630; its complete InChI agrees with the selected ChEBI molecular identity.

    Source location/ptools-xml/Compound[@frameid="3-DEHYDRO-SHIKIMATE"] /dblink[dblink-db="CHEBI"]|inchi
  • RHEA:24849

    Source assertion: RHEA:24849 left side contains CHEBI:16630 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/24848_L rh:contains1 http://rdf.rhea-db.org/Participant_24848_compound_3489; http://rdf.rhea-db.org/Participant_24848_compound_3489 rh:compound http://rdf.rhea-db.org/Compound_3489
3-dehydroshikimate => 3,4-dihydroxybenzoate + H2O
RHEA:24849		produces

Selected catabolic pathway orientation.

3,4-dihydroxybenzoate
CHEBI:36241
  • MetaCyc:DHSHIKIMATE-DEHYDRO-RXN

    Source assertion: The native right side contains 3-4-DIHYDROXYBENZOATE. No explicit coefficient is supplied.

    Source location/ptools-xml/Reaction[@frameid="DHSHIKIMATE-DEHYDRO-RXN"]/right/Compound[@frameid="3-4-DIHYDROXYBENZOATE"]
  • MetaCyc:3-4-DIHYDROXYBENZOATE

    Source assertion: The native compound links CHEBI:36241; its complete InChI agrees with the selected ChEBI molecular identity.

    Source location/ptools-xml/Compound[@frameid="3-4-DIHYDROXYBENZOATE"] /dblink[dblink-db="CHEBI"]|inchi
  • RHEA:24849

    Source assertion: RHEA:24849 right side contains CHEBI:36241 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/24848_R rh:contains1 http://rdf.rhea-db.org/Participant_24848_compound_3099; http://rdf.rhea-db.org/Participant_24848_compound_3099 rh:compound http://rdf.rhea-db.org/Compound_3099
3-dehydroshikimate => 3,4-dihydroxybenzoate + H2O
RHEA:24849		produces

Selected catabolic pathway orientation.

water
CHEBI:15377
  • MetaCyc:DHSHIKIMATE-DEHYDRO-RXN

    Source assertion: The native right side contains WATER. No explicit coefficient is supplied.

    Source location/ptools-xml/Reaction[@frameid="DHSHIKIMATE-DEHYDRO-RXN"]/right/Compound[@frameid="WATER"]
  • MetaCyc:WATER

    Source assertion: The native compound links CHEBI:15377; its complete InChI agrees with the selected ChEBI molecular identity.

    Source location/ptools-xml/Compound[@frameid="WATER"] /dblink[dblink-db="CHEBI"]|inchi
  • RHEA:24849

    Source assertion: RHEA:24849 right side contains CHEBI:15377 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/24848_R rh:contains1 http://rdf.rhea-db.org/Participant_24848_compound_1283; http://rdf.rhea-db.org/Participant_24848_compound_1283 rh:compound http://rdf.rhea-db.org/Compound_1283
shikimate oxidation with a quinone
MetaCyc:SHIKIMATE-PQQ-RXN		precedes

Native pathway reaction ordering selects forward catabolic progression.

3-dehydroshikimate => 3,4-dihydroxybenzoate + H2O
RHEA:24849
  • MetaCyc:SHIKIMATEDEG-PWY

    Source assertion: SHIKIMATE-PQQ-RXN is a predecessor of DHSHIKIMATE-DEHYDRO-RXN.

    Source location/ptools-xml/Pathway[@frameid="SHIKIMATEDEG-PWY"]/reaction-ordering[Reaction/@frameid="DHSHIKIMATE-DEHYDRO-RXN"]/predecessor-reactions
Quinate/shikimate dehydrogenase (quinone)
UniProtKB:Q59086		catalyzes

Native ADP1 QuiA shikimate activity is supported by pathway and genetic evidence. The native purified-protein code and kinetics cite Acinetobacter SA1/AC3 preparations; those measurements are not assigned to ADP1. The source groups the reaction as quinone-dependent oxidation without establishing use of every quinone.

shikimate oxidation with a quinone
MetaCyc:SHIKIMATE-PQQ-RXN
  • MetaCyc:ENZRXN-11861

    Source assertion: ENZRXN-11861 explicitly joins native enzyme MONOMER-28 to SHIKIMATE-PQQ-RXN.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-11861"]/enzyme | /ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-11861"]/reaction
  • MetaCyc:MONOMER-28

    Source assertion: The native protein MONOMER-28 carries a UniProt cross-reference to Q59086.

    Source location/ptools-xml/Protein[@frameid="MONOMER-28"]/dblink[dblink-db="UNIPROT"]
Quinate/shikimate dehydrogenase (quinone)
UniProtKB:Q59086		part_of

ADP1 source protein context; strain-specific activity and preparation limits remain on the catalytic edge.

Acinetobacter baylyi ADP1
NCBITaxon:62977
  • MetaCyc:MONOMER-28

    Source assertion: The native protein species slot identifies NCBI Taxonomy 62977; this is the source enzyme context, not full-route reconstruction in a single strain.

    Source location/ptools-xml/Protein[@frameid="MONOMER-28"]/species
  • MetaCyc:MONOMER-28

    Source assertion: The native protein MONOMER-28 carries a UniProt cross-reference to Q59086.

    Source location/ptools-xml/Protein[@frameid="MONOMER-28"]/dblink[dblink-db="UNIPROT"]
3-dehydroshikimate dehydratase
UniProtKB:Q43922

experimental construct: ADP1 genomic quiC expressed in E. coli DH5α(pZR564), a 2.0 kb HindIII insert; crude-extract assay. No protein tag reported or expressed termini measured. Text/Table 1 disagree on pBSK versus pBKS vector label.

Qualification evidence
catalyzes

DHS dehydration is supported by cloned quiC activity and native genetic phenotypes. The native protein comment incorrectly labels the assay as DHQ dehydration; no numeric activity is copied.

3-dehydroshikimate => 3,4-dihydroxybenzoate + H2O
RHEA:24849
  • MetaCyc:ENZRXN-38

    Source assertion: ENZRXN-38 explicitly joins native enzyme MONOMER-37 to DHSHIKIMATE-DEHYDRO-RXN.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-38"]/enzyme | /ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-38"]/reaction
  • MetaCyc:MONOMER-37

    Source assertion: The native protein MONOMER-37 carries a UniProt cross-reference to Q43922.

    Source location/ptools-xml/Protein[@frameid="MONOMER-37"]/dblink[dblink-db="UNIPROT"]
3-dehydroshikimate dehydratase
UniProtKB:Q43922		part_of

ADP1 source protein context; the catalytic experiment used the qualified recombinant crude-extract preparation.

Acinetobacter baylyi ADP1
NCBITaxon:62977
  • MetaCyc:MONOMER-37

    Source assertion: The native protein species slot identifies NCBI Taxonomy 62977; this is the source enzyme context, not full-route reconstruction in a single strain.

    Source location/ptools-xml/Protein[@frameid="MONOMER-37"]/species
  • MetaCyc:MONOMER-37

    Source assertion: The native protein MONOMER-37 carries a UniProt cross-reference to Q43922.

    Source location/ptools-xml/Protein[@frameid="MONOMER-37"]/dblink[dblink-db="UNIPROT"]
dehydroshikimate dehydratase
MetaCyc:MONOMER-1

molecular state: Native IFO3244 partially purified cytoplasmic enzyme fraction; DHS-dehydratase activity eluted separately from DQD on DEAE-Sephadex A-50. Exact protein sequence, termini and oligomeric state are unresolved.

Qualification evidence
catalyzes

Native IFO3244 DHS-dehydratase activity was separated from DQD and detected with a coupled qualitative protocatechuate assay. Exact gene and sequence identity remain unresolved.

3-dehydroshikimate => 3,4-dihydroxybenzoate + H2O
RHEA:24849
  • MetaCyc:ENZRXN-3

    Source assertion: ENZRXN-3 explicitly joins native enzyme MONOMER-1 to DHSHIKIMATE-DEHYDRO-RXN.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-3"]/enzyme | /ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-3"]/reaction
dehydroshikimate dehydratase
MetaCyc:MONOMER-1		part_of

Source protein taxon context; this partially purified IFO3244 activity is not a sequence identity or full-route reconstruction for every strain.

Gluconobacter oxydans
NCBITaxon:442
  • MetaCyc:MONOMER-1

    Source assertion: The native protein species slot identifies NCBI Taxonomy 442; this is the source enzyme context, not full-route reconstruction in a single strain.

    Source location/ptools-xml/Protein[@frameid="MONOMER-1"]/species
Quinate/shikimate dehydrogenase (quinone)
UniProtKB:Q59086		has_cofactor

PQQ is a prosthetic cofactor, distinct from the net electron-accepting quinone. The native assignment is independently supported by current ADP1 UniProt annotation; SA1/AC3 or LMD79.41 biochemical tests are not transferred to ADP1.

pyrroloquinoline quinone(3-)
CHEBI:58442
  • MetaCyc:ENZRXN-11861

    Source assertion: The QuiA shikimate activity record associates PQQ with enzyme MONOMER-28 as a cofactor. PQQ is distinct from the separately consumed quinone acceptor class.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-11861"]/enzyme | /ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-11861"]/cofactor
  • MetaCyc:MONOMER-28

    Source assertion: The native protein MONOMER-28 carries a UniProt cross-reference to Q59086.

    Source location/ptools-xml/Protein[@frameid="MONOMER-28"]/dblink[dblink-db="UNIPROT"]
  • UniProtKB:Q59086

    Source assertion: Q59086 COFACTOR comment identifies pyrroloquinoline quinone with ChEBI:58442.

    Source location$.comments[3].cofactors[0]
dehydroshikimate dehydratase
MetaCyc:MONOMER-1

molecular state: Native IFO3244 partially purified cytoplasmic enzyme fraction; DHS-dehydratase activity eluted separately from DQD on DEAE-Sephadex A-50. Exact protein sequence, termini and oligomeric state are unresolved.

Qualification evidence
located_in

Recovery in the cytoplasmic fraction supports this preparation context without establishing exclusive localization of a sequence-defined enzyme.

cytoplasm
GO:0005737
  • MetaCyc:ENZRXN-3

    Source assertion: The native activity comment reports partial purification of G. oxydans dehydroshikimate dehydratase from the cytoplasmic fraction.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-3"]/comment
quinate dehydrogenase
MetaCyc:MONOMER-67

molecular state: Native IFO3244 membrane holo-QDH preparation; SDS bands approximately 65 and 21 kDa may reflect proteolysis of one polypeptide. Exact cleavage and whole-protein sequence are unresolved.

Qualification evidence
  • PMID:15598527
    could be the result of proteolysis of single polypeptide
catalyzes

The inspected native ENZRXN-68 comment reports shikimate activity at 25% of the quinate rate and ferricyanide as the most efficient artificial acceptor, citing PMID:15598527. Its formal reaction slot is quinate oxidation. The shikimate claim is curated-source evidence; the 2004 full paper was unavailable. No physiological quinone specificity is inferred from the artificial-acceptor result.

shikimate oxidation with a quinone
MetaCyc:SHIKIMATE-PQQ-RXN
  • MetaCyc:ENZRXN-68

    Source assertion: The native G. oxydans QDH activity comment reports shikimate activity at 25% of the quinate rate and identifies ferricyanide as the most efficient artificial acceptor.

    Source location/ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-68"]/enzyme | /ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-68"]/comment | /ptools-xml/Enzymatic-Reaction[@frameid="ENZRXN-68"]/evidence
quinate dehydrogenase
MetaCyc:MONOMER-67		part_of

Native G. oxydans protein context; the cited preparation is IFO3244. This does not establish sequence identity or shikimate-supported growth for every strain.

Gluconobacter oxydans
NCBITaxon:442
  • MetaCyc:MONOMER-67

    Source assertion: The native protein species slot identifies G. oxydans; the linked PMID 15598527 title identifies the IFO3244 preparation.

    Source location/ptools-xml/Protein[@frameid="MONOMER-67"]/species | /ptools-xml/Protein[@frameid="MONOMER-67"]/molecular-weight-exp/citation/Publication/title
quinate dehydrogenase
MetaCyc:MONOMER-67

molecular state: Native IFO3244 purified holo-QDH preparation; exact proteolytic cleavage state is unresolved.

Qualification evidence
  • MetaCyc:MONOMER-67

    Source assertion: The native QDH protein comment describes a purified holoenzyme with 65/21 kDa SDS bands suggested to arise by proteolysis.

    Source location/ptools-xml/Protein[@frameid="MONOMER-67"]/comment
located_in

Native source and the inspected primary abstract describe membrane-bound IFO3244 QDH. This broad location does not establish exact orientation or an obligate respiratory assembly.

membrane
GO:0016020
  • MetaCyc:MONOMER-67

    Source assertion: The native G. oxydans protein has membrane location and cellular-component annotation GO:0016020.

    Source location/ptools-xml/Protein[@frameid="MONOMER-67"]/location | /ptools-xml/Protein[@frameid="MONOMER-67"]/has-go-term
Quinate/shikimate dehydrogenase (quinone)
UniProtKB:Q59086		located_in

The reviewed UniProt membrane annotation uses ECO:0000305 curator inference. The five membrane segments proposed in the 1994 study are hydropathy predictions, not direct topology measurements.

membrane
GO:0016020
  • UniProtKB:Q59086

    Source assertion: The reviewed ADP1 QuiA entry annotates cell-membrane location and multipass topology with ECO:0000305 curator inference.

    Source location$.comments[?(@.commentType=="SUBCELLULAR LOCATION")].subcellularLocations
  • MetaCyc:MONOMER-28

    Source assertion: The native protein MONOMER-28 carries a UniProt cross-reference to Q59086.

    Source location/ptools-xml/Protein[@frameid="MONOMER-28"]/dblink[dblink-db="UNIPROT"]
Pca operon regulatory protein
UniProtKB:O83046		part_of

Reviewed ADP1 PcaU context; the initiating methionine is uncertain between Met1 and Met5, so no exact tested N terminus is assumed.

Acinetobacter baylyi ADP1
NCBITaxon:62977
  • UniProtKB:O83046

    Source assertion: The reviewed PcaU entry identifies gene pcaU, locus ACIAD1702 and Acinetobacter baylyi ADP1 (NCBI Taxonomy 62977).

    Source location$.primaryAccession|$.genes|$.organism
quinate dehydrogenase
MetaCyc:MONOMER-67

molecular state: Native IFO3244 purified holo-QDH preparation; exact proteolytic cleavage state is unresolved.

Qualification evidence
  • MetaCyc:MONOMER-67

    Source assertion: The native QDH protein comment describes a purified holoenzyme with 65/21 kDa SDS bands suggested to arise by proteolysis.

    Source location/ptools-xml/Protein[@frameid="MONOMER-67"]/comment
has_cofactor

PQQ is bound as a prosthetic group; it is not consumed as the quinone electron acceptor. The full 2004 body remains unread.

pyrroloquinoline quinone(3-)
CHEBI:58442
  • PMID:15598527
    containing pyrroloquinoline quinone (PQQ) as the prosthetic group
Pca operon regulatory protein
UniProtKB:O83046		regulates

PcaU controls quiA transcript abundance in ADP1 under protocatechuate induction. Northern analysis of ADP331 with a 552 bp pcaU deletion showed reduced transcript abundance and loss of inducer dependence relative to wild-type ADP1. The quiA signal was 25% of the induced wild-type level. The 442 bp quiA probe measures the target directly. This is transcriptional control inferred from genetic perturbation. Constitutive quiAp remains active independently of PcaU.

quiA
MetaCyc:G-27
  • PMID:15691962
    much less abundant
    Source locationPMC546756 #sec16, first paragraph; probe definitions in #sec6.
  • MetaCyc:G-27

    Source assertion: The native gene G-27 has common-name quiA and the corresponding ADP1 protein product.

    Source location/ptools-xml/Gene[@frameid="G-27"]/common-name|product
3,4-dihydroxybenzoate
CHEBI:36241		regulates

Protocatechuate induces ADP1 quiA expression through the regulated pca-qui transcription system. Addition of 2 mM protocatechuate to cells growing on 20 mM pyruvate produced stronger Northern signals after 15 min. The pcaU deletion removed inducer dependence. The 442 bp quiA probe measures the target directly. No direct metabolite–PcaU binding is asserted.

quiA
MetaCyc:G-27
  • PMID:15691962
    reflecting the induction of expression by protocatechuate
    Source locationPMC546756 #sec14, first paragraph; probe definitions in #sec6.
  • MetaCyc:G-27

    Source assertion: The native gene G-27 has common-name quiA and the corresponding ADP1 protein product.

    Source location/ptools-xml/Gene[@frameid="G-27"]/common-name|product
Pca operon regulatory protein
UniProtKB:O83046		regulates

PcaU controls quiC transcript abundance in ADP1 under protocatechuate induction. Northern analysis of ADP331 with a 552 bp pcaU deletion showed reduced transcript abundance and loss of inducer dependence relative to wild-type ADP1. The shared quiC–quiX probe signal was 14% of the induced wild-type level. Target assignment is at the operon level: the 1,522 bp probe spans quiC and quiX and is called the quiX probe in the paper. Isolated quiC promoter activity was not measured. This is transcriptional control inferred from genetic perturbation. Constitutive quiAp remains active independently of PcaU.

quiC
MetaCyc:G-36
  • PMID:15691962
    much less abundant
    Source locationPMC546756 #sec16, first paragraph; probe definitions in #sec6.
  • MetaCyc:G-36

    Source assertion: The native gene G-36 has common-name quiC and the corresponding ADP1 protein product.

    Source location/ptools-xml/Gene[@frameid="G-36"]/common-name|product
3,4-dihydroxybenzoate
CHEBI:36241		regulates

Protocatechuate induces ADP1 quiC expression through the regulated pca-qui transcription system. Addition of 2 mM protocatechuate to cells growing on 20 mM pyruvate produced stronger Northern signals after 15 min. The pcaU deletion removed inducer dependence. Target assignment is at the operon level: the 1,522 bp probe spans quiC and quiX and is called the quiX probe in the paper. Isolated quiC promoter activity was not measured. No direct metabolite–PcaU binding is asserted.

quiC
MetaCyc:G-36
  • PMID:15691962
    reflecting the induction of expression by protocatechuate
    Source locationPMC546756 #sec14, first paragraph; probe definitions in #sec6.
  • MetaCyc:G-36

    Source assertion: The native gene G-36 has common-name quiC and the corresponding ADP1 protein product.

    Source location/ptools-xml/Gene[@frameid="G-36"]/common-name|product

References

Curation history