NaturalProductMech

Browse · Alkaloids · xiamycin A

xiamycin A

naturalproductmech:mibig-9f978c0043 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 InChIKeyXUTJPVCJXVRRLB-SKWRMQMOSA-N
SMILES[H][C@@]12CCC3=C(C=C4C(NC5=C4C=CC=C5)=C3)[C@@]1(C)CC[C@H](O)[C@@]2(C)C(O)=O
Stereochemistryfully defined
Cross-referencesnpatlas:NPA012008, pubchem:38358410

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 terpene, 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.

TaxonBasisClusterEvidence
Streptomyces sp. HKI0576
NCBITaxon:995841		 BGC_CHARACTERIZED mibig:BGC0000665 DOI:10.1016/j.bmcl.2010.09.010
Streptomyces sp. SCSIO 02999
NCBITaxon:1194094		 BGC_CHARACTERIZED mibig:BGC0000666 PMID:22591327

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.

TaxonSourceReference
Streptomyces xinghaiensis
NCBITaxon:1038928		 LOTUS DOI:10.1007/S00253-018-9337-2
Streptomyces
NCBITaxon:1883		 LOTUS DOI:10.1016/J.BMCL.2010.09.010
Streptomyces olivaceus
NCBITaxon:47716		 LOTUS DOI:10.3390/MD17100593

Biosynthetic gene clusters 2

AccessionHostLocus evidenceGenome
mibig:BGC0000665 Streptomyces sp. HKI0576
NCBITaxon:995841 		CLUSTER_DEMONSTRATED genbank:HE815466.1
mibig:BGC0000666 Streptomyces sp. SCSIO 02999
NCBITaxon:1194094 		CLUSTER_DEMONSTRATED genbank:JQ812811.1

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.

StepEnzymeReactionSubstrate → productEvidence
1 XiaI
UniProtKB:I3VFB9		 naturalproductmech:mibig-cb4ddd98d8 → naturalproductmech:mibig-9f978c0043 DOI:10.1021/ja303004g

Step 1: This deliberately curates only the Streptomyces sp. SCSIO 02999 XiaI oxidative cyclization of indosespene to xiamycin A; upstream formation of indosespene and parallel oxiamycin tailoring remain uncurated.

Mechanism & Biosynthesis Overview

PRODUCERS & OCCURRENCE 2 producers (2 causal) 3 cited occurrences BIOSYNTHETIC LOCUS 2 gene clusters 1 curated pathway step NATURAL PRODUCT xiamycin A naturalproductmech:mibig-9f978c0043 Alkaloids TARGETS & BIOACTIVITY 0 molecular targets 0 bioactivities · 1 graph

Causal graph — biosynthesis 3 nodes, 2 edges

Partial Streptomyces sp. SCSIO 02999 xiamycin A biosynthesis graph for the XiaI-catalyzed oxidative cyclization of indosespene.

SubjectPredicateObjectNotesEvidence
indosespene is oxidatively cyclized by XiaI
DOI:10.1021/ja303004g
https://www.uniprot.org/uniprotkb/I3VFB9
https://www.ncbi.nlm.nih.gov/protein/AFK78075.1
  • reference
    DOI:10.1021/ja303004g
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    the flavin dependent oxygenase XiaI was biochemically characterized in vitro to convert indosespene to XMA
    notes
    Li et al. identified the Streptomyces sp. SCSIO 02999 xiamycin/oxiamycin cluster and biochemically assigned XiaI to the indosespene-to-xiamycin A oxidative cyclization.
  • reference
    https://www.uniprot.org/uniprotkb/I3VFB9
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    notes
    UniProtKB:I3VFB9 resolves XiaI to the unreviewed Streptomyces sp. SCSIO 02999 protein and cross-references EMBL JQ812811 protein AFK78075.1.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AFK78075.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    notes
    NCBI GenPept AFK78075.1 is the JQ812811.1 XiaI coding sequence from the Streptomyces sp. SCSIO 02999 xiamycin/oxiamycin gene cluster.
XiaI forms xiamycin A This is a single curated tailoring step; upstream indosespene formation and the alternative oxiamycin branch remain uncurated.
DOI:10.1021/ja303004g
https://www.uniprot.org/uniprotkb/I3VFB9
https://www.ncbi.nlm.nih.gov/protein/AFK78075.1
  • reference
    DOI:10.1021/ja303004g
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    the flavin dependent oxygenase XiaI was biochemically characterized in vitro to convert indosespene to XMA
    notes
    Li et al. identified the Streptomyces sp. SCSIO 02999 xiamycin/oxiamycin cluster and biochemically assigned XiaI to the indosespene-to-xiamycin A oxidative cyclization.
  • reference
    https://www.uniprot.org/uniprotkb/I3VFB9
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    notes
    UniProtKB:I3VFB9 resolves XiaI to the unreviewed Streptomyces sp. SCSIO 02999 protein and cross-references EMBL JQ812811 protein AFK78075.1.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AFK78075.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-09-27
    notes
    NCBI GenPept AFK78075.1 is the JQ812811.1 XiaI coding sequence from the Streptomyces sp. SCSIO 02999 xiamycin/oxiamycin gene cluster.

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

Explore across X-Mech

AntibioticMech (xiamycin A) ↗ MediaIngredientMech (naturalproductmech:mibig-9f978c0043) ↗ TaxonMech: Streptomyces sp. HKI0576 (NCBITaxon:995841) ↗ TaxonMech: Streptomyces sp. SCSIO 02999 (NCBITaxon:1194094) ↗ PathwayMech (mibig:BGC0000665) ↗ PathwayMech (mibig:BGC0000666) ↗

Open questions 1

shared-structure — This structure is reported by more than one MIBiG entry: BGC0000665, BGC0000666. Confirm they describe the same compound rather than an upstream cross-reference error.

Provenance

Source conceptSourceVersion
BGC0000665MIBIG5
BGC0000666MIBIG5

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