shikimate degradation II
MetaCyc:PWY-6419
The MetaCyc shikimate degradation II pathway oxidizes shikimate with NAD+ to 3-dehydroshikimate and dehydrates it to protocatechuate in two reactions. This route is distinct from PQQ-dependent shikimate degradation I and the three-step quinate degradation II route. Strain R growth, uptake and gene-expression evidence is distinguished from ATCC 13032 QsuD and ATCC 13869 QsuB enzyme assays. Native database taxon associations do not establish shikimate uptake or growth in every strain.
- Pathway type
- aromatic compound catabolism
- Organism scope
Pathway network
39 nodes · 32 asserted directed edges
Arrows show recorded subject → object relationships, not necessarily metabolic flow. Select a node for details or an arrow for evidence. Scroll, zoom or find a node to explore.
- Reaction / activity
- Chemical / cofactor
- Protein / complex
- Other participant
- Cell / process context
- Taxon
- Pathway
- Solid arrow: mechanistic relation
- Dashed arrow: membership, location or cofactor relation
Components and activities
| Node | Kind or role | Source direction |
|---|---|---|
Corynebacterium glutamicumNCBITaxon:1718 | taxon | |
Corynebacterium glutamicum RNCBITaxon:340322 | taxon | |
shikimateCHEBI:36208 | small molecule | |
3-dehydroshikimateCHEBI:16630 | small molecule | |
3,4-dihydroxybenzoateCHEBI:36241 | small molecule | |
waterCHEBI:15377 | small molecule | |
hydronCHEBI:15378 | small molecule | |
NAD(1-)CHEBI:57540 | small molecule | |
NADH(2-)CHEBI:57945 | small molecule | |
magnesium(2+)CHEBI:18420 | cofactor | |
manganese(2+)CHEBI:29035 | cofactor | |
chorismate(2-)CHEBI:29748 | small molecule | |
cobalt(2+)CHEBI:48828 | cofactor | |
plasma membraneGO:0005886 | cellular component | |
cgR_0492KEGG:cgt:cgR_0492 | gene | |
cgR_0495KEGG:cgt:cgR_0495 | gene | |
cgR_2523KEGG:cgt:cgR_2523 | gene | |
quinate/shikimate dehydrogenaseMetaCyc:CPLX-7981 | complex | |
qsuBMetaCyc:G-11737 | gene | |
4-hydroxyphenylpyruvate dioxygenase [Corynebacterium glutamicum]NCBIProtein:ANU32720.1 | protein | |
hypothetical protein cgR_0491 [Corynebacterium glutamicum R]NCBIProtein:BAF53458.1 | protein | |
hypothetical protein cgR_0493 [Corynebacterium glutamicum R]NCBIProtein:BAF53460.1 | protein | |
Quinate/shikimate dehydrogenase (NAD(+))UniProtKB:A4QB65 | protein | |
Shikimate transporterUniProtKB:A4QH18 | protein | |
HTH-type transcriptional regulator ShiRUniProtKB:A4QH19 | protein | |
Quinate/shikimate dehydrogenase (NAD(+))UniProtKB:Q9X5C9 | protein | |
shikimate + NAD(+) => 3-dehydroshikimate + NADH + H(+)RHEA:17742 | molecular activity | left to right |
3-dehydroshikimate => 3,4-dihydroxybenzoate + H2ORHEA:24849 | molecular activity | left to right |
protocatechuate catabolic process, ortho-cleavageGO:0019618 | pathway |
Mechanistic edges
| Subject | Predicate and description | Object | Evidence |
|---|---|---|---|
MetaCyc:PWY-6419 | part_of Native database organism context. Strain R physiological evidence and other strain-specific enzyme assays remain separately scoped. | Corynebacterium glutamicumNCBITaxon:1718 |
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MetaCyc:PWY-6419 | part_of Native database organism context. Strain R physiological evidence and other strain-specific enzyme assays remain separately scoped. | Corynebacterium glutamicum RNCBITaxon:340322 |
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shikimate + NAD(+) => 3-dehydroshikimate + NADH + H(+)RHEA:17742 | part_of One of the two formal pathway reactions; the complete molecular equation agrees with the selected Rhea direction. | MetaCyc:PWY-6419 |
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shikimateCHEBI:36208 | consumes Selected catabolic orientation; complete reaction sides and atom/charge balance were compared. | shikimate + NAD(+) => 3-dehydroshikimate + NADH + H(+)RHEA:17742 |
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NAD(1-)CHEBI:57540 | consumes Selected catabolic orientation; complete reaction sides and atom/charge balance were compared. | shikimate + NAD(+) => 3-dehydroshikimate + NADH + H(+)RHEA:17742 |
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shikimate + NAD(+) => 3-dehydroshikimate + NADH + H(+)RHEA:17742 | produces Selected catabolic orientation; complete reaction sides and atom/charge balance were compared. | 3-dehydroshikimateCHEBI:16630 |
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shikimate + NAD(+) => 3-dehydroshikimate + NADH + H(+)RHEA:17742 | produces Selected catabolic orientation; complete reaction sides and atom/charge balance were compared. | NADH(2-)CHEBI:57945 |
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shikimate + NAD(+) => 3-dehydroshikimate + NADH + H(+)RHEA:17742 | produces Selected catabolic orientation; complete reaction sides and atom/charge balance were compared. | hydronCHEBI:15378 |
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3-dehydroshikimate => 3,4-dihydroxybenzoate + H2ORHEA:24849 | part_of One of the two formal pathway reactions; the complete molecular equation agrees with the selected Rhea direction. | MetaCyc:PWY-6419 |
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3-dehydroshikimateCHEBI:16630 | consumes Selected catabolic orientation; complete reaction sides and atom/charge balance were compared. | 3-dehydroshikimate => 3,4-dihydroxybenzoate + H2ORHEA:24849 |
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3-dehydroshikimate => 3,4-dihydroxybenzoate + H2ORHEA:24849 | produces Selected catabolic orientation; complete reaction sides and atom/charge balance were compared. | 3,4-dihydroxybenzoateCHEBI:36241 |
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3-dehydroshikimate => 3,4-dihydroxybenzoate + H2ORHEA:24849 | produces Selected catabolic orientation; complete reaction sides and atom/charge balance were compared. | waterCHEBI:15377 |
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shikimate + NAD(+) => 3-dehydroshikimate + NADH + H(+)RHEA:17742 | precedes Native ordering connects oxidation to the terminal dehydration. | 3-dehydroshikimate => 3,4-dihydroxybenzoate + H2ORHEA:24849 |
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Quinate/shikimate dehydrogenase (NAD(+))UniProtKB:Q9X5C9 | part_of The native QsuD complex contains two identical ATCC 13032 subunits; composition is not independent catalytic attribution to the monomer. | quinate/shikimate dehydrogenaseMetaCyc:CPLX-7981 |
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quinate/shikimate dehydrogenaseMetaCyc:CPLX-7981experimental construct: Recombinant ATCC 13032 QsuD homodimer preparation. The associated 2NLO structural sample has a 19-residue N-terminal extension containing His6; cleavage state across all kinetic preparations was not independently verified. Qualification evidence
| catalyzes QsuD catalyzes NAD-dependent shikimate oxidation. Native substrate Km is 46.6 mM. The curated complex comment reports NAD preference and >300-fold lower turnover with NADP; preference is not complete absence of NADP activity. The root chemistry audit verifies exact RXN-20484/RHEA:17742 molecular equivalence. | shikimate + NAD(+) => 3-dehydroshikimate + NADH + H(+)RHEA:17742 |
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hypothetical protein cgR_0493 [Corynebacterium glutamicum R]NCBIProtein:BAF53460.1 | enables The R-strain QsuB role is inferred from operon membership, sequence similarity and induction in the 2009 evidence. No purified R-QsuB assay is claimed; the ATCC 13869 QsuB assay is a different protein/strain context. | 3-dehydroshikimate => 3,4-dihydroxybenzoate + H2ORHEA:24849 |
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Shikimate transporterUniProtKB:A4QH18 | located_in Issuing UniProt places the R-strain ShiA protein at the cell membrane; the separate multipass topology prediction remains an inference, not an independently demonstrated topology. This is location of the transporter rather than location of the full catabolic pathway. | plasma membraneGO:0005886 |
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3-dehydroshikimate => 3,4-dihydroxybenzoate + H2ORHEA:24849 | provides_input_for The terminal dehydration supplies protocatechuate to the explicitly linked downstream ortho-cleavage pathway. This interface does not add the downstream reactions as formal shikimate-II members or assert whole-route activity in every downstream-pathway organism. | protocatechuate catabolic process, ortho-cleavageGO:0019618 |
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quinate/shikimate dehydrogenaseMetaCyc:CPLX-7981experimental construct: Recombinant ATCC 13032 Cgl0424 homodimer from pNHIS-QSDH in E. coli BL21, initially N-terminal His-tagged. Methods describe AcTEV cleavage verified by mass spectrometry to check tag effects; individual kinetic-table rows do not identify cleavage state. Deposited native-length sequence does not prove removal. Qualification evidence
| catalyzes Recombinant ATCC 13032 Cgl0424 oxidizes shikimate with NAD+ in vitro. Quinate has greater apparent catalytic efficiency. NADP+ turnover was not detected under the 2013 assay conditions; this differs from the low residual activity reported by the older native annotation and does not establish universal NADP exclusion. | shikimate + NAD(+) => 3-dehydroshikimate + NADH + H(+)RHEA:17742 |
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Quinate/shikimate dehydrogenase (NAD(+))UniProtKB:A4QB65 | enables C. glutamicum R qsuD disruption blocks shikimate growth and complementation restores it. This supports the genetically assigned first oxidation step, not a purified R-protein kinetics measurement. The 2013 supplement independently shows complementation in 50 mM shikimate BT medium. | shikimate + NAD(+) => 3-dehydroshikimate + NADH + H(+)RHEA:17742 |
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chorismate(2-)CHEBI:29748 | activates Chorismate changes the R-strain QsuR promoter footprint in vitro in a concentration-dependent manner; genetic pathway perturbations support transcriptional activation. Quinate and shikimate are not established direct ligands by these experiments. | hypothetical protein cgR_0491 [Corynebacterium glutamicum R]NCBIProtein:BAF53458.1experimental construct: N-terminal His6-tagged R-strain QsuR from pCRF206/pColdI, expressed in E. coli BL21. Gel filtration suggests a homotetramer; the qualified protein endpoint denotes this assay preparation without minting a separate assembly identifier. Qualification evidence
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hypothetical protein cgR_0491 [Corynebacterium glutamicum R]NCBIProtein:BAF53458.1 | activates R-strain QsuR increases qsuA transcription as part of the qsuABCD operon during shikimate growth, supported by qsuR disruption and complementation. This targets the gene, not direct enzyme activation. Residual induction in the qsuR mutant shows QsuR is not the only regulator. | cgR_0492KEGG:cgt:cgR_0492 |
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hypothetical protein cgR_0491 [Corynebacterium glutamicum R]NCBIProtein:BAF53458.1 | activates R-strain QsuR increases qsuB transcription as part of the qsuABCD operon during shikimate growth, supported by qsuR disruption and complementation. This targets the gene, not direct enzyme activation. Residual induction in the qsuR mutant shows QsuR is not the only regulator. | qsuBMetaCyc:G-11737 |
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hypothetical protein cgR_0491 [Corynebacterium glutamicum R]NCBIProtein:BAF53458.1 | activates R-strain QsuR increases qsuD transcription as part of the qsuABCD operon during shikimate growth, supported by qsuR disruption and complementation. This targets the gene, not direct enzyme activation. Residual induction in the qsuR mutant shows QsuR is not the only regulator. | cgR_0495KEGG:cgt:cgR_0495 |
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4-hydroxyphenylpyruvate dioxygenase [Corynebacterium glutamicum]NCBIProtein:ANU32720.1experimental construct: C-terminal His6-tagged full-length QsuB from C. glutamicum 2256/ATCC 13869; pET22b-qsuB expressed in E. coli BL21(DE3). Tag placement is inferred from inspected P4 tail and CDS alignment, not merely vector name. No separately deposited complete assay-clone sequence was inspected. Qualification evidence
| catalyzes ATCC 13869 full-length His-tagged QsuB DHS-to-PCA reaction; spectrophotometry plus supplementary HPLC product comparison. Source gene matches issuing ATCC 13869 CDS and P3/P4/P5 primer boundaries. | 3-dehydroshikimate => 3,4-dihydroxybenzoate + H2ORHEA:24849 |
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4-hydroxyphenylpyruvate dioxygenase [Corynebacterium glutamicum]NCBIProtein:ANU32720.1experimental construct: C-terminal His6-tagged full-length QsuB from C. glutamicum 2256/ATCC 13869; pET22b-qsuB expressed in E. coli BL21(DE3). Tag placement is inferred from inspected P4 tail and CDS alignment, not merely vector name. No separately deposited complete assay-clone sequence was inspected. Qualification evidence
| has_cofactor In vitro alternative metal support: Co > Mg > Mn, 10 mM metal screen; pH 7.5. This is not evidence of unique physiological metal requirement. | cobalt(2+)CHEBI:48828 |
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4-hydroxyphenylpyruvate dioxygenase [Corynebacterium glutamicum]NCBIProtein:ANU32720.1experimental construct: C-terminal His6-tagged full-length QsuB from C. glutamicum 2256/ATCC 13869; pET22b-qsuB expressed in E. coli BL21(DE3). Tag placement is inferred from inspected P4 tail and CDS alignment, not merely vector name. No separately deposited complete assay-clone sequence was inspected. Qualification evidence
| has_cofactor In vitro alternative metal support: Co > Mg > Mn, 10 mM metal screen; pH 7.5. This is not evidence of unique physiological metal requirement. | magnesium(2+)CHEBI:18420 |
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4-hydroxyphenylpyruvate dioxygenase [Corynebacterium glutamicum]NCBIProtein:ANU32720.1experimental construct: C-terminal His6-tagged full-length QsuB from C. glutamicum 2256/ATCC 13869; pET22b-qsuB expressed in E. coli BL21(DE3). Tag placement is inferred from inspected P4 tail and CDS alignment, not merely vector name. No separately deposited complete assay-clone sequence was inspected. Qualification evidence
| has_cofactor In vitro alternative metal support: Co > Mg > Mn, 10 mM metal screen; pH 7.5. This is not evidence of unique physiological metal requirement. | manganese(2+)CHEBI:29035 |
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3,4-dihydroxybenzoateCHEBI:36241 | inhibits PCA (3,4-DHBA) causes mixed inhibition of full-length C-terminal His6 QsuB in vitro. The Methods and Fig. 7 caption report different inhibitor concentrations; no numeric range is adopted. Truncated N-QsuB shows a different inhibition pattern. | 4-hydroxyphenylpyruvate dioxygenase [Corynebacterium glutamicum]NCBIProtein:ANU32720.1experimental construct: C-terminal His6-tagged full-length QsuB from C. glutamicum 2256/ATCC 13869; pET22b-qsuB expressed in E. coli BL21(DE3). Tag placement is inferred from inspected P4 tail and CDS alignment, not merely vector name. No separately deposited complete assay-clone sequence was inspected. Qualification evidence
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3-dehydroshikimateCHEBI:16630 | inhibits High DHS concentrations inhibit the full-length His6-tagged QsuB preparation in vitro. Activity falls beyond about 3 mM substrate; HPLC confirmation addressed absorbance interference above 4 mM. This is concentration-dependent substrate inhibition, not inhibition at every DHS concentration. | 4-hydroxyphenylpyruvate dioxygenase [Corynebacterium glutamicum]NCBIProtein:ANU32720.1experimental construct: C-terminal His6-tagged full-length QsuB from C. glutamicum 2256/ATCC 13869; pET22b-qsuB expressed in E. coli BL21(DE3). Tag placement is inferred from inspected P4 tail and CDS alignment, not merely vector name. No separately deposited complete assay-clone sequence was inspected. Qualification evidence
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Shikimate transporterUniProtKB:A4QH18 | enables C. glutamicum R ShiA/cgR_2523 supports shikimate uptake for the pathway. Loss of shiA blocks shikimate growth and extracellular consumption; uptake increases in a shiA-expressing strain. QsuA/cgR_0492 is a distinct gene. Primary abstract scope does not establish proton coupling or transport stoichiometry. | MetaCyc:PWY-6419 |
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HTH-type transcriptional regulator ShiRUniProtKB:A4QH19 | activates R-strain ShiR/cgR_2524 increases shiA transcription in shikimate-containing cultures; disrupting shiR reduces induction. This is gene-expression control. The inspected primary abstract does not establish direct shikimate binding to ShiR or the construct used for the separately annotated promoter-binding assay. | cgR_2523KEGG:cgt:cgR_2523 |
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References
MetaCyc:PWY-6419MetaCyc native object PWY-6419 (source version: MetaCyc 27.0)MetaCyc:SHIKIMATEMetaCyc native object SHIKIMATE (source version: MetaCyc 27.0)MetaCyc:3-DEHYDRO-SHIKIMATEMetaCyc native object 3-DEHYDRO-SHIKIMATE (source version: MetaCyc 27.0)MetaCyc:3-4-DIHYDROXYBENZOATEMetaCyc native object 3-4-DIHYDROXYBENZOATE (source version: MetaCyc 27.0)MetaCyc:WATERMetaCyc native object WATER (source version: MetaCyc 27.0)MetaCyc:PROTONMetaCyc native object PROTON (source version: MetaCyc 27.0)MetaCyc:NADMetaCyc native object NAD (source version: MetaCyc 27.0)MetaCyc:NADHMetaCyc native object NADH (source version: MetaCyc 27.0)MetaCyc:RXN-20484MetaCyc native object RXN-20484 (source version: MetaCyc 27.0)RHEA:17742Rhea equation RHEA:17742 (source version: Rhea 142 RDF; canonical label from pinned Rhea 139)MetaCyc:DHSHIKIMATE-DEHYDRO-RXNMetaCyc native object DHSHIKIMATE-DEHYDRO-RXN (source version: MetaCyc 27.0)RHEA:24849Rhea equation RHEA:24849 (source version: Rhea 142 RDF; canonical label from pinned Rhea 139)GO:0019618Gene Ontology: protocatechuate catabolic process, ortho-cleavage (source version: GO 2026-07-26; complete uncompressed semantic SQL database)UniProtKB:Q9X5C9UniProt Q9X5C9, ATCC 13032 QsuD (source version: entry version 166; last annotation update 2026-09-02)MetaCyc:CPLX-7981MetaCyc CPLX-7981 complete native object (source version: 27.0)MetaCyc:MONOMER-15330MetaCyc MONOMER-15330 complete native object (source version: 27.0)MetaCyc:G-11733MetaCyc G-11733 complete native object (source version: 27.0)DOI:10.2210/pdb2nlo/pdbPDB 2NLO polymer entity 1, ATCC 13032 QsuD structural sample (source version: RCSB JSON retrieved 2026-10-14)MetaCyc:ENZRXN-17383MetaCyc ENZRXN-17383 complete native object (source version: 27.0)MetaCyc:MONOMER-15334MetaCyc MONOMER-15334 complete native object (source version: 27.0)MetaCyc:ENZRXN-17385MetaCyc ENZRXN-17385 complete native object (source version: 27.0)MetaCyc:G-11737MetaCyc G-11737 complete native object (source version: 27.0)UniProtKB:A4QH18UniProt A4QH18, strain R shikimate transporter ShiA (source version: entry version 89; last annotation update 2026-09-02)MetaCyc:PROTOCATECHUATE-ORTHO-CLEAVAGE-PWYMetaCyc PROTOCATECHUATE-ORTHO-CLEAVAGE-PWY complete native object (source version: 27.0)PMID:19376919Regulation of expression of genes involved in quinate and shikimate utilization in Corynebacterium glutamicum. (source version: Full text inspected; retrieved 2026-10-14. Hash binds the PMC primary abstract and scan-index HTML; scan pages are separately hash-bound in the source manifest.)PMID:24674055Chorismate-dependent transcriptional regulation of quinate/shikimate utilization genes by LysR-type transcriptional regulator QsuR in Corynebacterium glutamicum: carbon flow control at metabolic branch point. (source version: Full-text web transcript inspected; retrieved 2026-10-14.)PMID:32822353Characterization of the Corynebacterium glutamicum dehydroshikimate dehydratase QsuB and its potential for microbial production of protocatechuic acid. (source version: Full text inspected; retrieved 2026-10-14.)PMID:23929881Enzyme-substrate complexes of the quinate/shikimate dehydrogenase from Corynebacterium glutamicum enable new insights in substrate and cofactor binding, specificity, and discrimination. (source version: 2013 article; full Results, Discussion, Methods and Table 1 text inspected through preserved DESY and author-uploaded web transcripts. Original article PDF and visual Table 1 unavailable. Hash binds the complete returned Methods transcript; other transcripts are linked in the source manifest.)PMID:23306642Characterization of shikimate dehydrogenase homologues of Corynebacterium glutamicum. (source version: 2013 primary abstract and all six pages of public supplementary PDF inspected visually; main article full text unavailable. Hash binds EuropePMC core primary abstract; supplement separately hash-bound.)PMID:25406451Identification and expression analysis of a gene encoding a shikimate transporter of Corynebacterium glutamicum. (source version: 2015 primary abstract inspected; the public publisher full-text endpoint returned HTTP 403. Hash binds the EuropePMC core primary abstract. UniProt annotations are cited separately as structured evidence.)UniProtKB:A4QH19UniProt A4QH19 reviewed protein entry (source version: Entry version 99; sequence version 1. First public date: 2022-10-12; last annotation update: 2026-09-02; last sequence update: 2007-05-15.)
Curation history
- codex
- CREATE — Add the NAD-dependent shikimate degradation II mechanism
Created MetaCyc:PWY-6419 with two formal reactions, exact chemical mappings, strain-specific enzyme and regulatory evidence, and the existing GO:0019618 downstream interface. The author evidence dossier retains complete source bindings, duplicate checks including ignored and hidden files, construct limitations, native annotation corrections and all selected identifiers. Full repository gates and independent scientific review follow this initial curation event; this event does not claim completed review or source exhaustion.
- CREATE — Add the NAD-dependent shikimate degradation II mechanism
- codex
- EDIT — Correct downstream pathway typing and source-version presentation
Applied three independently reviewed findings from 20261014T205746Z-shikimate-ii-initial-independent-scientific-review, 20261014T205748Z-shikimate-ii-integration-initial. GO:0019618 now has the explicit downstream pathway category. Six source-version descriptions now use readable prose while retaining the same dates, versions, access limits and source hashes. All mechanistic edges, evidence, other nodes and authority snapshots are unchanged. Generated pages and exports will be rebuilt and final gates and successor dispositions follow this correction.
- EDIT — Correct downstream pathway typing and source-version presentation