komodoquinone B

CHEBI:167002 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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.

A member of the class of tetracenequinones that is 7,8,9,10-tetrahydrotetracene-5,12-dione carrying hydroxy groups at positions 1, 6, 8S, 10S and 11 and a methyl group at position 8S. It is the aglycone of komodoquinone A which was isolated from the marine bacterium Streptomyces sp. KS3.

Structure

Standard InChIKey	SFRTWZQYMRMOOJ-OVWNDWIMSA-N
SMILES	C[C@]1(C[C@@H](C2=C(C3=C(C(=C2C1)O)C(=O)C4=C(C3=O)C(=CC=C4)O)O)O)O
Stereochemistry	fully defined
Cross-references	npatlas:NPA019430

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 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
Streptomyces erythrochromogenes NCBITaxon:285574	SOURCE_ASSERTION	mibig:BGC0001851	DOI:10.1021/acschembio.9b00238
Streptomyces sp. NRRL S-378 NCBITaxon:1463904	SOURCE_ASSERTION	mibig:BGC0001852	DOI:10.1021/acschembio.9b00238

Occurrences 3

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:10.1021/NP030212K
Streptomyces NCBITaxon:1883	LOTUS	DOI:10.1248/CPB.51.1402
Streptomyces sp. NCBITaxon:1931	CHEBI	PMID:14646317

Biosynthetic gene clusters 2

Accession	Host	Locus evidence	Genome
mibig:BGC0001851	Streptomyces erythrochromogenes NCBITaxon:285574	CLUSTER_DEMONSTRATED	genbank:NZ_JNZG01000006.1
mibig:BGC0001852	Streptomyces sp. NRRL S-378 NCBITaxon:1463904	CLUSTER_DEMONSTRATED	genbank:NZ_JOBX01000002.1

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	EamK 10-decarboxylase UniProtKB:A0ABZ1Q8A7		ungrounded → ungrounded	DOI:10.1021/acschembio.9b00238

Step 1: This curates S. erythrochromogenes NRRL B-2112 IO28_RS0104785/eamK, encoded in BGC0001851 as RefSeq WP_245240010.1, as an assayed 10-decarboxylase that contributes to komodoquinone B aglycone formation. The native substrate of the decarboxylation branch is left unexpanded.

Mechanism & Biosynthesis Overview

Causal graph — biosynthesis 3 nodes, 2 edges

Partial S. erythrochromogenes komodoquinone B biosynthesis graph for the EamK-catalyzed anthracycline 10-decarboxylation branch.

Subject	Predicate	Object	Notes	Evidence
EamK 10-decarboxylase	catalyzes	anthracycline 10-decarboxylation	Grocholski et al. assayed EamK with 10-carboxylated anthracycline substrates generated by 15-methylesterases and observed 10-decarboxylated products. This edge is scoped to the decarboxylation chemistry and does not assert the exact native substrate.	DOI:10.1021/acschembio.9b00238 mibig:BGC0001851 https://www.uniprot.org/uniprotkb/A0ABZ1Q8A7 https://www.ncbi.nlm.nih.gov/protein/WP_245240010.1 https://www.ncbi.nlm.nih.gov/nuccore/NZ_JNZG01000006.1 reference DOI:10.1021/acschembio.9b00238 evidence type PRIMARY_EXPERIMENT snippet able to fully convert the substrate notes Grocholski et al. assayed S. erythrochromogenes NRRL B-2112 EamK in vitro as an anthracycline 10-decarboxylase and then isolated komodoquinone B from S. erythrochromogenes NRRL B-2112 and Streptomyces sp. NRRL S-378. reference mibig:BGC0001851 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet 10-decarboxylase notes MIBiG BGC0001851 version 4 names komodoquinone B as the exact product of the S. erythrochromogenes NRRL B-2112 type II PKS cluster and annotates IO28_RS0104785/eamK as a 10-decarboxylase encoded on NZ_JNZG01000006.1. reference https://www.uniprot.org/uniprotkb/A0ABZ1Q8A7 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet Methyltransferase notes Unreviewed UniProtKB:A0ABZ1Q8A7 is a 368 aa S. erythrochromogenes entry whose sequence matches the RefSeq WP_245240010.1 product of the BGC0001851 IO28_RS0104785/eamK locus. reference https://www.ncbi.nlm.nih.gov/protein/WP_245240010.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet methyltransferase notes NCBI RefSeq WP_245240010.1 is the 368 aa S. erythrochromogenes protein encoded by the IO28_RS0104785 CDS in the BGC0001851 locus. reference https://www.ncbi.nlm.nih.gov/nuccore/NZ_JNZG01000006.1 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet Streptomyces erythrochromogenes strain NRRL B-2112 notes RefSeq NZ_JNZG01000006.1 contains IO28_RS0104785 at 201890..202996 and encodes WP_245240010.1.
anthracycline 10-decarboxylation	contributes to	komodoquinone B	Komodoquinone B isolated from the two exact MIBiG source strains is the 10-decarboxylated aglycone product of highly similar anthracycline BGC0001851 and BGC0001852 clusters.	DOI:10.1021/acschembio.9b00238 mibig:BGC0001851 mibig:BGC0001852 reference DOI:10.1021/acschembio.9b00238 evidence type PRIMARY_EXPERIMENT snippet able to fully convert the substrate notes Grocholski et al. assayed S. erythrochromogenes NRRL B-2112 EamK in vitro as an anthracycline 10-decarboxylase and then isolated komodoquinone B from S. erythrochromogenes NRRL B-2112 and Streptomyces sp. NRRL S-378. reference mibig:BGC0001851 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 snippet 10-decarboxylase notes MIBiG BGC0001851 version 4 names komodoquinone B as the exact product of the S. erythrochromogenes NRRL B-2112 type II PKS cluster and annotates IO28_RS0104785/eamK as a 10-decarboxylase encoded on NZ_JNZG01000006.1. reference mibig:BGC0001852 evidence type DATABASE_ASSERTION retrieved on 2026-09-27 notes MIBiG BGC0001852 version 4 names komodoquinone B as the exact product of the Streptomyces sp. NRRL S-378 type II PKS and saccharide cluster on NZ_JOBX01000002.1.

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

Explore across X-Mech

AntibioticMech (komodoquinone B) ↗ MediaIngredientMech (CHEBI:167002) ↗ TaxonMech: Streptomyces erythrochromogenes (NCBITaxon:285574) ↗ TaxonMech: Streptomyces sp. NRRL S-378 (NCBITaxon:1463904) ↗ PathwayMech (mibig:BGC0001851) ↗ PathwayMech (mibig:BGC0001852) ↗

Provenance

Source concept	Source	Version
BGC0001851	MIBIG	4
BGC0001852	MIBIG	4
CHEBI:167002	CHEBI	3-star

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