linamarin

CHEBI:16441 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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.

Structure

Standard InChIKey	QLTCHMYAEJEXBT-ZEBDFXRSSA-N
SMILES	CC(C)(C#N)O[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O)O)O
Stereochemistry	fully defined

Filing pathway

Amino acids and peptides — 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 other, from MIBiG.

Producer organisms 2

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.

Taxon	Basis	Cluster	Evidence
Lotus japonicus NCBITaxon:34305	SOURCE_ASSERTION	mibig:BGC0001316	DOI:10.3923/ijcr.2020.18.27
Manihot esculenta NCBITaxon:3983	SOURCE_ASSERTION	mibig:BGC0001318	PMID:21707799

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.

Taxon	Source	Reference
Osteospermum ecklonis NCBITaxon:1053381	LOTUS	DOI:10.1016/S0031-9422(00)86154-3
Lotus arenarius NCBITaxon:118906	LOTUS	DOI:10.1016/S0031-9422(00)86154-3
Hevea pauciflora NCBITaxon:1318717	LOTUS	DOI:10.1016/0031-9422(91)83601-G
Hevea pauciflora NCBITaxon:1318717	LOTUS	DOI:10.1016/S0031-9422(00)81211-X
Hevea spruceana NCBITaxon:1318718	LOTUS	DOI:10.1016/S0031-9422(00)81211-X
Passiflora pendens NCBITaxon:1341377	LOTUS	DOI:10.1016/0031-9422(86)88016-5
Passiflora pendens NCBITaxon:1341377	LOTUS	DOI:10.1016/S0031-9422(01)00485-X
Passiflora foetida NCBITaxon:159421	LOTUS	DOI:10.1016/S0031-9422(01)00485-X
Passiflora foetida NCBITaxon:159421	LOTUS	DOI:10.1016/S0031-9422(98)80070-8
Passiflora morifolia NCBITaxon:159435	LOTUS	DOI:10.1016/0031-9422(86)88016-5
Passiflora morifolia NCBITaxon:159435	LOTUS	DOI:10.1016/0031-9422(92)80427-G
Passiflora morifolia NCBITaxon:159435	LOTUS	DOI:10.1016/0031-9422(96)00065-9
Passiflora morifolia NCBITaxon:159435	LOTUS	DOI:10.1016/S0031-9422(01)00485-X
Passiflora morifolia NCBITaxon:159435	LOTUS	DOI:10.1055/S-2007-971239
Lotus arabicus NCBITaxon:181260	LOTUS	DOI:10.1016/S0031-9422(00)86154-3
Lotus creticus NCBITaxon:181267	LOTUS	DOI:10.1016/0031-9422(90)89077-M
Lotus creticus NCBITaxon:181267	LOTUS	DOI:10.1016/S0031-9422(00)86154-3
Lotus edulis NCBITaxon:181270	LOTUS	DOI:10.1016/S0031-9422(00)86154-3
Lotus maroccanus NCBITaxon:181276	LOTUS	DOI:10.1016/S0031-9422(00)86154-3
Lotus parviflorus NCBITaxon:181280	LOTUS	DOI:10.1016/S0031-9422(00)86154-3
Passiflora subpeltata NCBITaxon:1822414	LOTUS	DOI:10.1016/0031-9422(89)85023-X
Acacia aroma NCBITaxon:207708	LOTUS	DOI:10.1016/0305-1978(83)90023-6
Passiflora adenopoda NCBITaxon:237834	LOTUS	DOI:10.1016/0031-9422(86)88016-5
Passiflora adenopoda NCBITaxon:237834	LOTUS	DOI:10.1016/S0031-9422(01)00485-X
Hevea camargoana NCBITaxon:2733477	LOTUS	DOI:10.1016/0031-9422(91)83601-G

Biosynthetic gene clusters 2

Accession	Host	Locus evidence	Genome
mibig:BGC0001316	Lotus japonicus NCBITaxon:34305	CLUSTER_UNSTATED	genbank:MIBIG.BGC0001316.1
mibig:BGC0001318	Manihot esculenta NCBITaxon:3983	CLUSTER_UNSTATED	genbank:MIBIG.BGC0001318.1

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.

#	Enzyme	Reaction	Substrate → product	Evidence
1	UGT85K4 linamarin synthase 1 UniProtKB:G3FIN8	RHEA:20009	CHEBI:15348 + CHEBI:58885 → CHEBI:16441 + CHEBI:58223 + CHEBI:15378	DOI:10.1111/j.1365-313X.2011.04695.x
2	UGT85K5 linamarin synthase 2 UniProtKB:G3FIN9	RHEA:20009	CHEBI:15348 + CHEBI:58885 → CHEBI:16441 + CHEBI:58223 + CHEBI:15378	DOI:10.1111/j.1365-313X.2011.04695.x

Entry 1: UGT85K4 is one of two Manihot esculenta paralogs biochemically shown to glucosylate acetone cyanohydrin with UDP-glucose to form linamarin. The two entries are unnumbered to avoid implying an order between the UGT85K4 and UGT85K5 alternatives. Seeded BGC0001318 is Manihot esculenta but has only placeholder genome coordinates, so the exact grounding used here is the JF727883 cDNA characterized by Kannangara et al., not a resolved MIBiG CDS.

Entry 2: UGT85K5 is one of two Manihot esculenta paralogs biochemically shown to glucosylate acetone cyanohydrin with UDP-glucose to form linamarin. The two entries are unnumbered to avoid implying an order between the UGT85K4 and UGT85K5 alternatives. Seeded BGC0001318 is Manihot esculenta but has only placeholder genome coordinates, so the exact grounding used here is the JF727884 cDNA characterized by Kannangara et al., not a resolved MIBiG CDS.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 4 nodes, 4 edges

Partial Manihot esculenta linamarin biosynthesis graph for the parallel UGT85K4- and UGT85K5-catalyzed terminal acetone-cyanohydrin glucosylation reactions.

Subject	Predicate	Object	Notes	Evidence
2-hydroxy-2-methylpropanenitrile	is glucosylated by	UGT85K4 linamarin synthase 1	UGT85K4 glucosylates acetone cyanohydrin in the Manihot linamarin-forming reaction.	DOI:10.1111/j.1365-313X.2011.04695.x https://www.uniprot.org/uniprotkb/G3FIN8 https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv reference DOI:10.1111/j.1365-313X.2011.04695.x evidence type PRIMARY_EXPERIMENT snippet Recombinant UGT85K4 and UGT85K5 produced in Escherichia coli were able to glucosylate acetone cyanohydrin notes Kannangara et al. isolated full-length Manihot esculenta UGT85K4 and UGT85K5 cDNAs, expressed both enzymes in E. coli, identified linamarin among the cyanogenic-glucoside products of radiolabeled UDP-glucose assays, and showed that their transcripts and proteins co-localize with the upstream CYP79D and CYP71E paralogs. reference https://www.uniprot.org/uniprotkb/G3FIN8 evidence type DATABASE_ASSERTION snippet Able to glucosylate acetone cyanohydrin and 2-hydroxy-2-methylbutyronitrile, forming linamarin and lotaustralin retrieved on 2026-09-30 notes Reviewed UniProtKB:G3FIN8 is the 483 aa Manihot esculenta linamarin synthase 1, gene UGT85K4, cross-references EMBL JF727883 protein AEO45781.1, and annotates EC 2.4.1.63 and RHEA:20009 from PMID:21736650. reference https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes The Rhea Swiss-Prot mapping links the linamarin synthase reaction RHEA:20009 to UniProtKB:G3FIN8 and UniProtKB:G3FIN9.
UGT85K4 linamarin synthase 1	forms	linamarin	UGT85K4 forms linamarin by transferring glucose from UDP-glucose to acetone cyanohydrin.	DOI:10.1111/j.1365-313X.2011.04695.x https://www.uniprot.org/uniprotkb/G3FIN8 https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv reference DOI:10.1111/j.1365-313X.2011.04695.x evidence type PRIMARY_EXPERIMENT snippet Recombinant UGT85K4 and UGT85K5 produced in Escherichia coli were able to glucosylate acetone cyanohydrin notes Kannangara et al. isolated full-length Manihot esculenta UGT85K4 and UGT85K5 cDNAs, expressed both enzymes in E. coli, identified linamarin among the cyanogenic-glucoside products of radiolabeled UDP-glucose assays, and showed that their transcripts and proteins co-localize with the upstream CYP79D and CYP71E paralogs. reference https://www.uniprot.org/uniprotkb/G3FIN8 evidence type DATABASE_ASSERTION snippet Able to glucosylate acetone cyanohydrin and 2-hydroxy-2-methylbutyronitrile, forming linamarin and lotaustralin retrieved on 2026-09-30 notes Reviewed UniProtKB:G3FIN8 is the 483 aa Manihot esculenta linamarin synthase 1, gene UGT85K4, cross-references EMBL JF727883 protein AEO45781.1, and annotates EC 2.4.1.63 and RHEA:20009 from PMID:21736650. reference https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes The Rhea Swiss-Prot mapping links the linamarin synthase reaction RHEA:20009 to UniProtKB:G3FIN8 and UniProtKB:G3FIN9.
2-hydroxy-2-methylpropanenitrile	is glucosylated by	UGT85K5 linamarin synthase 2	UGT85K5 glucosylates acetone cyanohydrin in the Manihot linamarin-forming reaction.	DOI:10.1111/j.1365-313X.2011.04695.x https://www.uniprot.org/uniprotkb/G3FIN9 https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv reference DOI:10.1111/j.1365-313X.2011.04695.x evidence type PRIMARY_EXPERIMENT snippet Recombinant UGT85K4 and UGT85K5 produced in Escherichia coli were able to glucosylate acetone cyanohydrin notes Kannangara et al. isolated full-length Manihot esculenta UGT85K4 and UGT85K5 cDNAs, expressed both enzymes in E. coli, identified linamarin among the cyanogenic-glucoside products of radiolabeled UDP-glucose assays, and showed that their transcripts and proteins co-localize with the upstream CYP79D and CYP71E paralogs. reference https://www.uniprot.org/uniprotkb/G3FIN9 evidence type DATABASE_ASSERTION snippet Able to glucosylate acetone cyanohydrin and 2-hydroxy-2-methylbutyronitrile, forming linamarin and lotaustralin retrieved on 2026-09-30 notes Reviewed UniProtKB:G3FIN9 is the 483 aa Manihot esculenta linamarin synthase 2, gene UGT85K5, cross-references EMBL JF727884 protein AEO45782.1, and annotates EC 2.4.1.63 and RHEA:20009 from PMID:21736650. reference https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes The Rhea Swiss-Prot mapping links the linamarin synthase reaction RHEA:20009 to UniProtKB:G3FIN8 and UniProtKB:G3FIN9.
UGT85K5 linamarin synthase 2	forms	linamarin	UGT85K5 forms linamarin by transferring glucose from UDP-glucose to acetone cyanohydrin.	DOI:10.1111/j.1365-313X.2011.04695.x https://www.uniprot.org/uniprotkb/G3FIN9 https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv reference DOI:10.1111/j.1365-313X.2011.04695.x evidence type PRIMARY_EXPERIMENT snippet Recombinant UGT85K4 and UGT85K5 produced in Escherichia coli were able to glucosylate acetone cyanohydrin notes Kannangara et al. isolated full-length Manihot esculenta UGT85K4 and UGT85K5 cDNAs, expressed both enzymes in E. coli, identified linamarin among the cyanogenic-glucoside products of radiolabeled UDP-glucose assays, and showed that their transcripts and proteins co-localize with the upstream CYP79D and CYP71E paralogs. reference https://www.uniprot.org/uniprotkb/G3FIN9 evidence type DATABASE_ASSERTION snippet Able to glucosylate acetone cyanohydrin and 2-hydroxy-2-methylbutyronitrile, forming linamarin and lotaustralin retrieved on 2026-09-30 notes Reviewed UniProtKB:G3FIN9 is the 483 aa Manihot esculenta linamarin synthase 2, gene UGT85K5, cross-references EMBL JF727884 protein AEO45782.1, and annotates EC 2.4.1.63 and RHEA:20009 from PMID:21736650. reference https://ftp.expasy.org/databases/rhea/tsv/rhea2uniprot_sprot.tsv evidence type DATABASE_ASSERTION retrieved on 2026-09-30 notes The Rhea Swiss-Prot mapping links the linamarin synthase reaction RHEA:20009 to UniProtKB:G3FIN8 and UniProtKB:G3FIN9.

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

Explore across X-Mech

AntibioticMech (linamarin) ↗ MediaIngredientMech (CHEBI:16441) ↗ TaxonMech: Lotus japonicus (NCBITaxon:34305) ↗ TaxonMech: Manihot esculenta (NCBITaxon:3983) ↗ PathwayMech (mibig:BGC0001316) ↗ PathwayMech (mibig:BGC0001318) ↗

Open questions 1

shared-structure — This structure is reported by more than one MIBiG entry: BGC0001316, BGC0001318. Confirm they describe the same compound rather than an upstream cross-reference error.

Provenance

Source concept	Source	Version
BGC0001316	MIBIG	4
BGC0001318	MIBIG	4
CHEBI:16441	CHEBI	3-star

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