yatakemycin

naturalproductmech:mibig-a2b558b44b MINTED SEEDED

Grounding review: No 3-star ChEBI entry shares this structure, so the record keeps a content-hashed identifier.

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	CJTUMLYXLYEBOO-UHFFFAOYSA-N
SMILES	COC1=CC2=C(NC(=C2)C(=O)N2CC3CC33C4=C(NC(=C4)C(=O)N4CCC5=C6C=C(NC6=C(OC)C(O)=C45)SC(C)=O)C(=O)C=C23)C=C1O
Stereochemistry	undefined stereocentres — the InChIKey does not distinguish this compound from its stereoisomers
Cross-references	npatlas:NPA01250, pubchem:11721692

Filing pathway

Alkaloids — 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 nrps, 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.

Taxon	Basis	Cluster	Evidence
Streptomyces sp. TP-A2060 NCBITaxon:991125	SOURCE_ASSERTION	mibig:BGC0000466	PMID:22612591

Occurrences 1

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
Streptomyces NCBITaxon:1883	LOTUS	DOI:10.7164/ANTIBIOTICS.56.107

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000466	Streptomyces sp. TP-A2060 NCBITaxon:991125	CLUSTER_UNSTATED	genbank:JF429418.1

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.

Step	Enzyme	Reaction	Substrate → product	Evidence
1	YtkW SAM-dependent methyltransferase UniProtKB:I3NN71		ungrounded → ungrounded	DOI:10.1002/anie.202522109

Step 1: YtkW S-methylates the thiocarboxylic acid moiety of a yatakemycin subunit A intermediate. This single-step partial pathway leaves YtkG/YtkF sulfur transfer and the remaining assembly of the YTM scaffold uncurated.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 3 nodes, 2 edges

Partial Streptomyces sp. TP-A2060 yatakemycin biosynthesis graph for YtkW S-methylation of a thiocarboxylic-acid-bearing subunit A intermediate.

Subject	Predicate	Object	Notes	Evidence
thiocarboxylated yatakemycin subunit A intermediate	is S-methylated by	YtkW SAM-dependent methyltransferase	MITE records YtkW as the SAM-dependent enzyme for S-methylation of a thiocarboxylic acid moiety in yatakemycin subunit A.	DOI:10.1002/anie.202522109 https://mite.lisc.univie.ac.at/repository/MITE0000458 https://mibig.secondarymetabolites.org/repository/BGC0000466.5/BGC0000466.gbk https://www.uniprot.org/uniprotkb/I3NN71 https://www.ncbi.nlm.nih.gov/protein/ADZ13559.1 reference DOI:10.1002/anie.202522109 evidence type PRIMARY_EXPERIMENT snippet catalytic mechanism of YtkW notes Feng et al. functionally characterized ytkG/F/W in yatakemycin biosynthesis; MITE curates the YtkW S-methyltransferase reaction as an in vitro assay from this primary article. reference https://mite.lisc.univie.ac.at/repository/MITE0000458 evidence type DATABASE_ASSERTION snippet S-methylation on thiocarboxylic acid moiety of subunit A of yatakemycin retrieved on 2026-10-01 notes MITE0000458 is an active YtkW entry for S-methylation of a thiocarboxylic acid on yatakemycin subunit A; it links UniProtKB:I3NN71, GenPept ADZ13559.1, MIBiG BGC0000466 and the Feng et al. DOI. reference https://mibig.secondarymetabolites.org/repository/BGC0000466.5/BGC0000466.gbk evidence type DATABASE_ASSERTION snippet protein_id="ADZ13559.1" retrieved on 2026-10-01 notes MIBiG BGC0000466.5 places ADZ13559.1 in the active Streptomyces sp. TP-A2060 yatakemycin cluster as the YtkW methyltransferase CDS. reference https://www.uniprot.org/uniprotkb/I3NN71 evidence type DATABASE_ASSERTION snippet SubName: Full=YtkW retrieved on 2026-10-01 notes Current unreviewed UniProtKB:I3NN71 resolves as a 209 aa Streptomyces sp. TP-A2060 YtkW protein and cross-references EMBL JF429418 protein ADZ13559.1. reference https://www.ncbi.nlm.nih.gov/protein/ADZ13559.1 evidence type DATABASE_ASSERTION snippet YtkW [Streptomyces sp. TP-A2060] retrieved on 2026-10-01 notes GenPept ADZ13559.1 is the 209 aa Streptomyces sp. TP-A2060 YtkW protein encoded by JF429418.1:29692..30321.
YtkW SAM-dependent methyltransferase	forms	S-methyl thioester yatakemycin subunit A intermediate	This graph stops at the S-methyl thioester subunit A intermediate because later yatakemycin scaffold assembly steps are not curated here.	DOI:10.1002/anie.202522109 https://mite.lisc.univie.ac.at/repository/MITE0000458 https://mibig.secondarymetabolites.org/repository/BGC0000466.5/BGC0000466.gbk https://www.uniprot.org/uniprotkb/I3NN71 https://www.ncbi.nlm.nih.gov/protein/ADZ13559.1 reference DOI:10.1002/anie.202522109 evidence type PRIMARY_EXPERIMENT snippet catalytic mechanism of YtkW notes Feng et al. functionally characterized ytkG/F/W in yatakemycin biosynthesis; MITE curates the YtkW S-methyltransferase reaction as an in vitro assay from this primary article. reference https://mite.lisc.univie.ac.at/repository/MITE0000458 evidence type DATABASE_ASSERTION snippet S-methylation on thiocarboxylic acid moiety of subunit A of yatakemycin retrieved on 2026-10-01 notes MITE0000458 is an active YtkW entry for S-methylation of a thiocarboxylic acid on yatakemycin subunit A; it links UniProtKB:I3NN71, GenPept ADZ13559.1, MIBiG BGC0000466 and the Feng et al. DOI. reference https://mibig.secondarymetabolites.org/repository/BGC0000466.5/BGC0000466.gbk evidence type DATABASE_ASSERTION snippet protein_id="ADZ13559.1" retrieved on 2026-10-01 notes MIBiG BGC0000466.5 places ADZ13559.1 in the active Streptomyces sp. TP-A2060 yatakemycin cluster as the YtkW methyltransferase CDS. reference https://www.uniprot.org/uniprotkb/I3NN71 evidence type DATABASE_ASSERTION snippet SubName: Full=YtkW retrieved on 2026-10-01 notes Current unreviewed UniProtKB:I3NN71 resolves as a 209 aa Streptomyces sp. TP-A2060 YtkW protein and cross-references EMBL JF429418 protein ADZ13559.1. reference https://www.ncbi.nlm.nih.gov/protein/ADZ13559.1 evidence type DATABASE_ASSERTION snippet YtkW [Streptomyces sp. TP-A2060] retrieved on 2026-10-01 notes GenPept ADZ13559.1 is the 209 aa Streptomyces sp. TP-A2060 YtkW protein encoded by JF429418.1:29692..30321.

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

Explore across X-Mech

AntibioticMech (yatakemycin) ↗ MediaIngredientMech (naturalproductmech:mibig-a2b558b44b) ↗ TaxonMech: Streptomyces sp. TP-A2060 (NCBITaxon:991125) ↗ PathwayMech (mibig:BGC0000466) ↗

Provenance

Source concept	Source	Version
BGC0000466	MIBIG	5

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