rabelomycin

naturalproductmech:mibig-ec6ca029f7 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	JJOLHRYZQSDLSA-IBGZPJMESA-N
SMILES	C[C@@]1(O)CC(=O)C2=C3C(=O)C4=C(C(O)=CC=C4)C(=O)C3=C(O)C=C2C1
Stereochemistry	fully defined
Cross-references	npatlas:NPA019619, pubchem:443810

Filing pathway

Polyketides — 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 pks, saccharide, from MIBiG.

Producer organisms 3

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. PGA64 NCBITaxon:161235	BGC_CORRELATED	mibig:BGC0000262	PMID:12654660
uncultured bacterium BAC AB649/1850 NCBITaxon:1037453	SOURCE_ASSERTION	mibig:BGC0000223	PMID:20690632
Micromonospora rosaria NCBITaxon:47874	SOURCE_ASSERTION	mibig:BGC0001904	DOI:10.1021/acs.orglett.5b02683

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 olivaceus NCBITaxon:47716	LOTUS	DOI:10.7164/ANTIBIOTICS.23.437

Biosynthetic gene clusters 3

Accession	Host	Locus evidence	Genome
mibig:BGC0000262	Streptomyces sp. PGA64 NCBITaxon:161235	CLUSTER_DEMONSTRATED	genbank:AY034378.2
mibig:BGC0000223	uncultured bacterium BAC AB649/1850 NCBITaxon:1037453	CLUSTER_DEMONSTRATED	genbank:HM193369.1
mibig:BGC0001904	Micromonospora rosaria NCBITaxon:47874	CLUSTER_UNSTATED	genbank:KT726162.1

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	PgaY/PgaF and PgaL angucyclinone cyclization module		ungrounded → ungrounded	DOI:10.1128/AAC.47.4.1291-1296.2003

Step 1: This partial pathway entry captures two exact Streptomyces sp. PGA64 cyclization/aromatization proteins from the demonstrated BGC0000262 angucycline locus. The exact nascent polyketide intermediate and the final oxidation from the UWM6 branch toward rabelomycin are left unexpanded, so the module rather than a single substrate-to-product reaction is curated. Exact S-configured product assignment has not been established by the new stereochemistry audit; retain this proposed module subject to curator-rabelomycin-absolute-configuration, not as independent stereochemical proof.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 5 nodes, 4 edges

Partial Streptomyces sp. PGA64 rabelomycin biosynthesis graph for the BGC0000262 PgaY/PgaF and PgaL cyclization/aromatization proteins. Applicability to the exact S-configured owner remains under review in curator-rabelomycin-absolute-configuration; the shared compound name is not stereochemical proof.

Subject	Predicate	Object	Notes	Evidence
nascent angucycline polyketide	is cyclized toward	angucyclinone cyclization/aromatization	This edge deliberately leaves the exact nascent polyketide intermediate ungrounded; MIBiG and GenBank support the named cyclization genes in the exact rabelomycin-producing cluster, not a fully resolved intermediate structure.	DOI:10.1128/AAC.47.4.1291-1296.2003 https://mibig.secondarymetabolites.org/repository/BGC0000262.5/index.html reference DOI:10.1128/AAC.47.4.1291-1296.2003 evidence type PRIMARY_EXPERIMENT snippet Engineering anthracycline biosynthesis toward angucyclines. notes Metsa-Ketela et al. engineered early polyketide assembly toward angucycline products with Streptomyces sp. PGA64 genes; MIBiG cites this paper for the exact BGC0000262 rabelomycin row. reference https://mibig.secondarymetabolites.org/repository/BGC0000262.5/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes MIBiG BGC0000262.5 lists rabelomycin as a Streptomyces sp. PGA64 product of the AY034378.2 locus and marks the locus with enzymatic-assay, heterologous-expression, and gene-expression-correlated support.
PgaY/PgaF angucyclinone cyclase	participates in	angucyclinone cyclization/aromatization	MIBiG annotates AAK57524.1 as pgaF, while GenBank AY034378.2 annotates the same coding sequence as PgaY, an angucyclinone cyclase.	DOI:10.1128/AAC.47.4.1291-1296.2003 https://mibig.secondarymetabolites.org/repository/BGC0000262.5/index.html https://www.ncbi.nlm.nih.gov/protein/AAK57524.1 https://www.uniprot.org/uniprotkb/Q93LY5 reference DOI:10.1128/AAC.47.4.1291-1296.2003 evidence type PRIMARY_EXPERIMENT snippet Engineering anthracycline biosynthesis toward angucyclines. notes Metsa-Ketela et al. engineered early polyketide assembly toward angucycline products with Streptomyces sp. PGA64 genes; MIBiG cites this paper for the exact BGC0000262 rabelomycin row. reference https://mibig.secondarymetabolites.org/repository/BGC0000262.5/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes MIBiG BGC0000262.5 lists rabelomycin as a Streptomyces sp. PGA64 product of the AY034378.2 locus and marks the locus with enzymatic-assay, heterologous-expression, and gene-expression-correlated support. reference https://www.ncbi.nlm.nih.gov/protein/AAK57524.1 evidence type DATABASE_ASSERTION snippet angucyclinone cyclase retrieved on 2026-09-28 notes NCBI GenPept AAK57524.1 is the 109 aa Streptomyces sp. PGA64 angucyclinone cyclase encoded on AY034378.2. MIBiG names the same protein pgaF; the GenBank product label is PgaY. reference https://www.uniprot.org/uniprotkb/Q93LY5 evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes UniProtKB:Q93LY5 is the unreviewed 109 aa Streptomyces sp. PGA64 entry that cross-references EMBL AY034378 with ProteinId AAK57524.1.
PgaL cyclase/aromatase	participates in	angucyclinone cyclization/aromatization	NCBI GenBank AY034378.2 annotates PgaL/AAK57529.1 as a cyclase/aromatase in the PGA64 angucycline locus.	DOI:10.1128/AAC.47.4.1291-1296.2003 https://mibig.secondarymetabolites.org/repository/BGC0000262.5/index.html https://www.ncbi.nlm.nih.gov/protein/AAK57529.1 https://www.uniprot.org/uniprotkb/Q93LY0 reference DOI:10.1128/AAC.47.4.1291-1296.2003 evidence type PRIMARY_EXPERIMENT snippet Engineering anthracycline biosynthesis toward angucyclines. notes Metsa-Ketela et al. engineered early polyketide assembly toward angucycline products with Streptomyces sp. PGA64 genes; MIBiG cites this paper for the exact BGC0000262 rabelomycin row. reference https://mibig.secondarymetabolites.org/repository/BGC0000262.5/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes MIBiG BGC0000262.5 lists rabelomycin as a Streptomyces sp. PGA64 product of the AY034378.2 locus and marks the locus with enzymatic-assay, heterologous-expression, and gene-expression-correlated support. reference https://www.ncbi.nlm.nih.gov/protein/AAK57529.1 evidence type DATABASE_ASSERTION snippet cyclase/aromatase retrieved on 2026-09-28 notes NCBI GenPept AAK57529.1 is the 314 aa Streptomyces sp. PGA64 PgaL cyclase/aromatase encoded on AY034378.2. reference https://www.uniprot.org/uniprotkb/Q93LY0 evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes UniProtKB:Q93LY0 is the unreviewed 314 aa Streptomyces sp. PGA64 entry that cross-references EMBL AY034378 with ProteinId AAK57529.1.
angucyclinone cyclization/aromatization	supports biosynthesis of	rabelomycin	The graph captures the cyclization branch of the demonstrated BGC0000262 locus and leaves the unresolved rabelomycin-proximal oxidation as future curation. The compound endpoint follows the imported MIBiG identity; it is not independent evidence that the experimental product has the owner's S configuration. See curator-rabelomycin-absolute-configuration before extending or transferring this edge.	DOI:10.1128/AAC.47.4.1291-1296.2003 https://mibig.secondarymetabolites.org/repository/BGC0000262.5/index.html reference DOI:10.1128/AAC.47.4.1291-1296.2003 evidence type PRIMARY_EXPERIMENT snippet Engineering anthracycline biosynthesis toward angucyclines. notes Metsa-Ketela et al. engineered early polyketide assembly toward angucycline products with Streptomyces sp. PGA64 genes; MIBiG cites this paper for the exact BGC0000262 rabelomycin row. reference https://mibig.secondarymetabolites.org/repository/BGC0000262.5/index.html evidence type DATABASE_ASSERTION retrieved on 2026-09-28 notes MIBiG BGC0000262.5 lists rabelomycin as a Streptomyces sp. PGA64 product of the AY034378.2 locus and marks the locus with enzymatic-assay, heterologous-expression, and gene-expression-correlated support.

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

Explore across X-Mech

AntibioticMech (rabelomycin) ↗ MediaIngredientMech (naturalproductmech:mibig-ec6ca029f7) ↗ TaxonMech: Streptomyces sp. PGA64 (NCBITaxon:161235) ↗ TaxonMech: uncultured bacterium BAC AB649/1850 (NCBITaxon:1037453) ↗ TaxonMech: Micromonospora rosaria (NCBITaxon:47874) ↗ PathwayMech (mibig:BGC0000262) ↗ PathwayMech (mibig:BGC0000223) ↗ PathwayMech (mibig:BGC0001904) ↗

Open questions 1

curator-rabelomycin-absolute-configuration — Which absolute configuration is supported for each rabelomycin source claim, and do the existing pathway and candidate protein graphs apply to this S-configured owner?

Provenance

Source concept	Source	Version
BGC0000262	MIBIG	5
BGC0000223	MIBIG	5
BGC0001904	MIBIG	2

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