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(−)-geosmin

CHEBI:46702 EXACT SEEDED

What these status tags mean

Curation status describes a workflow state. SEEDED means the record entered through the source-seeding workflow; it does not imply that no later curation occurred. PROPOSED marks an addition awaiting review; REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record. These are workflow decisions, not independently verified human review. Agent-assisted contributions may appear in the record history.

Grounding describes the identifier mapping: EXACT uses an ontology identity asserted by the source; MINTED keeps a local identifier when no defensible ontology identity is available; REVIEW_NEEDED flags an exact structure whose ontology identity needs adjudication. The grounding note retains any unresolved alternatives. These tags do not establish the strength of producer or activity evidence.

The (−)-stereoisomer of geosmin, having 4S,4aS,8aR configuration.

Structure

Standard InChIKeyJLPUXFOGCDVKGO-TUAOUCFPSA-N
SMILESC[C@H]1CCC[C@@]2([C@@]1(CCCC2)O)C
Stereochemistryfully defined

Filing pathway

Terpenoids — computed by NPClassifier npclassifier.gnps2.org@2026-09-07, which is why it is pinned rather than recomputed. The gene cluster's asserted class is terpene, from MIBiG.

Producer organisms 1

A claim that this taxon makes the compound. The basis says what the evidence addressed — a knockout and a database assertion are not the same claim.

TaxonBasisClusterEvidence
Streptomyces coelicolor A3(2)
NCBITaxon:100226		 SOURCE_ASSERTION mibig:BGC0001181 DOI:10.1038/s41564-020-0697-x

Occurrences 25

Somebody found the compound in this organism and cited it. That is not a claim that the organism makes it, and nothing here promotes one to the other.

TaxonSourceReference
Coffea arabica
NCBITaxon:13443		 LOTUS DOI:10.1007/S002170100305
Cortinarius herculeus
NCBITaxon:1586124		 LOTUS DOI:10.1080/00275514.1999.12060999
Cortinarius herculeus
NCBITaxon:1586124		 LOTUS DOI:10.2307/3761199
Beta vulgaris
NCBITaxon:161934		 LOTUS DOI:10.1021/JF60204A059
Oscillatoria brevis
NCBITaxon:177969		 LOTUS DOI:10.1007/BF00416598
Cystoderma amianthinum
NCBITaxon:182063		 LOTUS DOI:10.1080/00275514.1999.12060999
Cystoderma amianthinum
NCBITaxon:182063		 LOTUS DOI:10.2307/3761199
Streptomyces
NCBITaxon:1883		 LOTUS DOI:10.1016/J.YMBEN.2018.09.004
Streptomyces albidoflavus
NCBITaxon:1886		 LOTUS DOI:10.1007/S10295-013-1383-2
Streptomyces albidoflavus
NCBITaxon:1886		 LOTUS DOI:10.1016/B978-0-12-404634-4.00014-0
Streptomyces albidoflavus
NCBITaxon:1886		 LOTUS DOI:10.1021/JA062669X
Streptomyces albidoflavus
NCBITaxon:1886		 LOTUS DOI:10.1038/NCHEMBIO.2007.29
Streptomyces albidoflavus
NCBITaxon:1886		 LOTUS DOI:10.1371/JOURNAL.PONE.0060665
Streptomyces albidoflavus
NCBITaxon:1886		 LOTUS DOI:10.7164/ANTIBIOTICS.47.434
Streptomyces coelicolor
NCBITaxon:1902		 LOTUS DOI:10.1007/S10295-013-1383-2
Streptomyces coelicolor
NCBITaxon:1902		 LOTUS DOI:10.1016/B978-0-12-404634-4.00014-0
Streptomyces coelicolor
NCBITaxon:1902		 LOTUS DOI:10.1021/JA062669X
Streptomyces coelicolor
NCBITaxon:1902		 LOTUS DOI:10.1038/NCHEMBIO.2007.29
Streptomyces coelicolor
NCBITaxon:1902		 LOTUS DOI:10.1371/JOURNAL.PONE.0060665
Streptomyces griseus
NCBITaxon:1911		 LOTUS DOI:10.1111/J.1365-2672.1992.TB01818.X
Streptomyces tendae
NCBITaxon:1932		 LOTUS DOI:10.1021/JF00013A023
Streptomyces tendae
NCBITaxon:1932		 LOTUS DOI:10.1128/AEM.57.12.3429-3432.1991
Streptomyces halstedii
NCBITaxon:1944		 LOTUS DOI:10.1038/SJ.JIM.7000121
Streptomyces avermitilis
NCBITaxon:33903		 LOTUS DOI:10.1007/BF02932133
Streptomyces avermitilis
NCBITaxon:33903		 LOTUS DOI:10.1038/JA.2006.66

Biosynthetic gene clusters 1

AccessionHostLocus evidenceGenome
mibig:BGC0001181 Streptomyces coelicolor A3(2)
NCBITaxon:100226 		CLUSTER_UNSTATED genbank:AL645882.2

A locus claim and a taxon claim are different questions. Heterologous expression settles the first and leaves the second where the isolation report left it.

Biosynthesis curated

Written by a curator with claim-level evidence on each step; not derived from a source. This is what the rest of the record exists to support.

StepEnzymeReactionSubstrate → productEvidence
1 Cyc2 germacradienol/germacrene D synthase
UniProtKB:Q9X839		 RHEA:22436 CHEBI:175763 → CHEBI:46734 DOI:10.1073/pnas.0337625100
2 Cyc2 geosmin synthase
UniProtKB:Q9X839		 RHEA:30371 CHEBI:46734 → CHEBI:46702 DOI:10.1038/nchembio.2007.29

Step 1: The N-terminal domain of bifunctional Cyc2 cyclizes (2E,6E)-farnesyl diphosphate to germacradienol, the sesquiterpene alcohol intermediate in geosmin biosynthesis.

Step 2: The C-terminal domain of bifunctional Cyc2 converts germacradienol to (−)-geosmin.

Mechanism & Biosynthesis Overview

PRODUCERS & OCCURRENCE 1 producer (0 causal) 25 cited occurrences BIOSYNTHETIC LOCUS 1 gene cluster 2 curated pathway steps NATURAL PRODUCT (−)-geosmin CHEBI:46702 Terpenoids TARGETS & BIOACTIVITY 0 molecular targets 0 bioactivities · 1 graph

Causal graph — biosynthesis 4 nodes, 4 edges

Partial Streptomyces coelicolor geosmin biosynthesis graph for bifunctional Cyc2 conversion of farnesyl diphosphate to (−)-geosmin through germacradienol.

SubjectPredicateObjectNotesEvidence
(2E,6E)-farnesyl diphosphate is cyclized by Cyc2
DOI:10.1073/pnas.0337625100
  • reference
    DOI:10.1073/pnas.0337625100
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    Expression and mechanistic analysis of a germacradienol synthase
    notes
    UniProtKB:Q9X839 resolves to the Streptomyces coelicolor A3(2) cyc2/SCO6073 gene product, maps to EMBL AL939126 protein CAB41566.1, and annotates RHEA:22436 for formation of the germacradienol geosmin intermediate.
Cyc2 forms germacradienol
DOI:10.1073/pnas.0337625100
  • reference
    DOI:10.1073/pnas.0337625100
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    Expression and mechanistic analysis of a germacradienol synthase
    notes
    UniProtKB:Q9X839 resolves to the Streptomyces coelicolor A3(2) cyc2/SCO6073 gene product, maps to EMBL AL939126 protein CAB41566.1, and annotates RHEA:22436 for formation of the germacradienol geosmin intermediate.
germacradienol is converted by Cyc2
DOI:10.1038/nchembio.2007.29
  • reference
    DOI:10.1038/nchembio.2007.29
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    the bifunctional geosmin synthase mechanism
    notes
    UniProtKB:Q9X839 resolves to the Streptomyces coelicolor A3(2) cyc2/SCO6073 gene product; the domain-resolved study showed that the N-terminal domain forms germacradienol and that the C-terminal domain catalyzes the RHEA:30371 germacradienol-to-geosmin reaction.
Cyc2 forms (−)-geosmin
DOI:10.1038/nchembio.2007.29
  • reference
    DOI:10.1038/nchembio.2007.29
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    the bifunctional geosmin synthase mechanism
    notes
    UniProtKB:Q9X839 resolves to the Streptomyces coelicolor A3(2) cyc2/SCO6073 gene product; the domain-resolved study showed that the N-terminal domain forms germacradienol and that the C-terminal domain catalyzes the RHEA:30371 germacradienol-to-geosmin reaction.

Every edge carries its own citation; an uncited edge is refused by the corpus tests.

Explore across X-Mech

AntibioticMech ((−)-geosmin) ↗ MediaIngredientMech (CHEBI:46702) ↗ TaxonMech: Streptomyces coelicolor A3(2) (NCBITaxon:100226) ↗ PathwayMech (mibig:BGC0001181) ↗

Provenance

Source conceptSourceVersion
BGC0001181MIBIG4
CHEBI:46702CHEBI3-star

This page is generated from data/natural_products/terpenoids/geosmin.yaml, which is generated from the committed inventories. Neither is edited by hand.