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nargenicin A1

naturalproductmech:mibig-6437746e58 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 InChIKeyYEUSSARNQQYBKH-KFIBIINQSA-N
SMILESO=C2O[C@H]([C@H](O)C)[C@@H](\C=C(/C)[C@]51O[C@H]4[C@H](\C=C/[C@@H]1C[C@@H]2OC)[C@H]5[C@H](O)[C@H]([C@H]4OC(=O)c3ccc[nH]3)C)C
Stereochemistryfully defined
Cross-referencespubchem:6326334

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, 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
Nocardia argentinensis
NCBITaxon:1311812		 SOURCE_ASSERTION mibig:BGC0002024 PMID:30867595
Nocardia argentinensis
NCBITaxon:1311812		 SOURCE_ASSERTION mibig:BGC0002024 PMID:30867595

Occurrences 0

None cited.

Biosynthetic gene clusters 2

AccessionHostLocus evidenceGenome
mibig:BGC0002024 Nocardia argentinensis
NCBITaxon:1311812 		CLUSTER_UNSTATED genbank:MH544245.1
mibig:BGC0002024 Nocardia argentinensis
NCBITaxon:1311812 		CLUSTER_UNSTATED genbank:MH544245.1

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.

Mechanism & Biosynthesis Overview

PRODUCERS & OCCURRENCE 2 producers (0 causal) 0 cited occurrences BIOSYNTHETIC LOCUS 2 gene clusters 0 curated pathway steps NATURAL PRODUCT nargenicin A1 naturalproductmech:mibig-6437746e58 Polyketides TARGETS & BIOACTIVITY 0 molecular targets 0 bioactivities · 2 graphs

Causal graph — biosynthesis 4 nodes, 4 edges

NgnO1/NgnO2 evidence in two explicitly separated contexts: primary-text-reported paired activity on related streptoseomycin-pathway intermediates, and inferred native participation in nargenicin A1 biosynthesis. The proteins are canonical ATCC31306 parents with native CDS and GenPept identity verified. No mature-nargenicin reaction, nargenicin genetic necessity, exact historical tagged construct, physical Ngn heterodimer, or Ntf structural/ligand transfer is asserted. No MITE reaction model is adopted. This is not full-record REVIEWED sign-off.

SubjectPredicateObjectNotesEvidence
NgnO1, native ATCC 31306 parent is_required_partner_in_reported_assay_for Reported paired conversion of related-pathway mixture 6/7 to product 8 Both Ngn gene products were needed in the reported two-protein assay under its tested conditions. Numbers6/7 and8 are local to the cited2021 study and refer to related streptoseomycin-pathway compounds, not to mature nargenicin A1. The mixture experiment does not independently prove turnover of each isolated component, and the proposed transient products12/12b were not fully structure-elucidated. No exact SMILES, reaction order, catalytic site allocation, physical heterodimer or in-vivo native necessity is asserted. NtfO1/NtfO2 crystallography and FMN docking concern different proteins and are not transferred to these nodes.
DOI:10.1038/s41467-021-22395-7
https://www.ncbi.nlm.nih.gov/protein/AXG22411.1
https://rest.uniprot.org/uniparc/UPI0010059CF8.json
  • reference
    DOI:10.1038/s41467-021-22395-7
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-07
    notes
    Results: In vitro characterization of NgnO1-NgnO2 as hydroxylase; Fig.3 caption; Methods: Gene expression and protein purification and In vitro assay of NgnO1, NgnO2, NgnO1-NgnO2. The main text reports ATCC31306 genes expressed in E. coli, a paired assay with related streptoseomycin-pathway mixture6/7 and observed product8, and single-protein controls without detected conversion. Full main text inspected via NCBI BioC/PMC8027225; figure pixels and supplementary construct/assay data were not inspected. This is not a purified mature-nargenicin-forming assay.
    snippet
    NgnO1 or NgnO2 alone has no effects on 6/7
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AXG22411.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Native NgnO1 reference from Nocardia argentinensis ATCC31306/taxon1311812, 310aa. Gene name, strain and MH544245.1 coded_by mapping identify the canonical parent, not a completely reconstructed historical tagged assay construct. Family/product annotations are not independent proof of the specific reaction. Gene/species and exact GenPept-xref UniProtKB searches returned no entries on2026-10-07; this is not global absence and no homolog was selected.
  • reference
    https://rest.uniprot.org/uniparc/UPI0010059CF8.json
    evidence type
    DATABASE_ASSERTION
    notes
    UniParc UPI0010059CF8 (310 aa) links active EMBL AXG22411.1 (Nocardia argentinensis, taxon 1311812, gene ngnO1) and inactive UniProtKB/TrEMBL A0A3S7PZJ5, with zero active UniProtKB cross-references.
    retrieved on
    2026-10-30
NgnO1, native ATCC 31306 parent is_inferred_paired_oxidation_participant_in_biosynthesis_of nargenicin A1 Explicit native-pathway inference from the source-named ngn locus, canonical native gene identity and the measured paired activity on related-pathway intermediates. This is not direct observation of nargenicin formation, a nargenicin gene-deletion/complementation phenotype, or a precise native substrate/product assignment. The partner is also required in the reported related-pathway assay; neither individual enzyme is asserted to form the mature owner. Producer and BGC evidence grades remain unchanged.
DOI:10.1038/s41467-021-22395-7
https://www.ncbi.nlm.nih.gov/protein/AXG22411.1
https://www.ncbi.nlm.nih.gov/nuccore/MH544245.1
https://dl.secondarymetabolites.org/mibig/mibig_json_4.0.tar.gz
https://rest.uniprot.org/uniparc/UPI0010059CF8.json
  • reference
    DOI:10.1038/s41467-021-22395-7
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-07
    notes
    The introduction compares stm and ngn loci; the Results and Methods test the ATCC31306 NgnO1/NgnO2 pair in a related streptoseomycin-pathway context. Native nargenicin participation here is explicitly inferred, not a newly inspected direct native phenotype. Supplementary gene/construct tables and primary structure drawings were not inspected; no exact native reaction is claimed.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AXG22411.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Native NgnO1 reference from Nocardia argentinensis ATCC31306/taxon1311812, 310aa. Gene name, strain and MH544245.1 coded_by mapping identify the canonical parent, not a completely reconstructed historical tagged assay construct. Family/product annotations are not independent proof of the specific reaction. Gene/species and exact GenPept-xref UniProtKB searches returned no entries on2026-10-07; this is not global absence and no homolog was selected.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/MH544245.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-07
    notes
    Complete native CDS at forward52982..53914, 933nt, table11/codon1 translates to the exact 310-aa GenPeptAXG22411.1 reference; independent coded_by coordinates/strand/DNA and strain qualifiers agree. MH544245.1 is a69359bp nargenicin cluster deposit, not a complete genome. This identity check does not prove function by gene neighborhood alone.
  • reference
    https://dl.secondarymetabolites.org/mibig/mibig_json_4.0.tar.gz
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-06
    notes
    Adopted MIBiG4.0 archive SHA256 986f1a69fb5eeb84fd7c0175ae921304c22fd5f8ed04c96d8c1c0c95a145837b, BGC0002024v3 member inspected2026-10-07. Its two compound rows share the exact owner SMILES, locusMH544245.1 and taxon1311812. No NgnO1/O2 gene-function or locus evidence is supplied by this entry. It anchors the source compound/locus assertion only, not the experimental function or producer-grade upgrade.
  • reference
    https://rest.uniprot.org/uniparc/UPI0010059CF8.json
    evidence type
    DATABASE_ASSERTION
    notes
    UniParc UPI0010059CF8 (310 aa) links active EMBL AXG22411.1 (Nocardia argentinensis, taxon 1311812, gene ngnO1) and inactive UniProtKB/TrEMBL A0A3S7PZJ5, with zero active UniProtKB cross-references.
    retrieved on
    2026-10-30
NgnO2, native ATCC 31306 parent is_required_partner_in_reported_assay_for Reported paired conversion of related-pathway mixture 6/7 to product 8 Both Ngn gene products were needed in the reported two-protein assay under its tested conditions. Numbers6/7 and8 are local to the cited2021 study and refer to related streptoseomycin-pathway compounds, not to mature nargenicin A1. The mixture experiment does not independently prove turnover of each isolated component, and the proposed transient products12/12b were not fully structure-elucidated. No exact SMILES, reaction order, catalytic site allocation, physical heterodimer or in-vivo native necessity is asserted. NtfO1/NtfO2 crystallography and FMN docking concern different proteins and are not transferred to these nodes.
DOI:10.1038/s41467-021-22395-7
https://www.ncbi.nlm.nih.gov/protein/AXG22410.1
https://rest.uniprot.org/uniparc/UPI00100575B1.json
  • reference
    DOI:10.1038/s41467-021-22395-7
    evidence type
    PRIMARY_EXPERIMENT
    retrieved on
    2026-10-07
    notes
    Results: In vitro characterization of NgnO1-NgnO2 as hydroxylase; Fig.3 caption; Methods: Gene expression and protein purification and In vitro assay of NgnO1, NgnO2, NgnO1-NgnO2. The main text reports ATCC31306 genes expressed in E. coli, a paired assay with related streptoseomycin-pathway mixture6/7 and observed product8, and single-protein controls without detected conversion. Full main text inspected via NCBI BioC/PMC8027225; figure pixels and supplementary construct/assay data were not inspected. This is not a purified mature-nargenicin-forming assay.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AXG22410.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Native NgnO2 reference from Nocardia argentinensis ATCC31306/taxon1311812, 421aa. Gene name, strain and MH544245.1 coded_by mapping identify the canonical parent, not a completely reconstructed historical tagged assay construct. Family/product annotations are not independent proof of the specific reaction. Gene/species and exact GenPept-xref UniProtKB searches returned no entries on2026-10-07; this is not global absence and no homolog was selected.
  • reference
    https://rest.uniprot.org/uniparc/UPI00100575B1.json
    evidence type
    DATABASE_ASSERTION
    notes
    UniParc UPI00100575B1 (421 aa) links active EMBL AXG22410.1 (Nocardia argentinensis, taxon 1311812, gene ngnO2) and inactive UniProtKB/TrEMBL A0A3S7PZG8, with zero active UniProtKB cross-references.
    retrieved on
    2026-10-30
NgnO2, native ATCC 31306 parent is_inferred_paired_oxidation_participant_in_biosynthesis_of nargenicin A1 Explicit native-pathway inference from the source-named ngn locus, canonical native gene identity and the measured paired activity on related-pathway intermediates. This is not direct observation of nargenicin formation, a nargenicin gene-deletion/complementation phenotype, or a precise native substrate/product assignment. The partner is also required in the reported related-pathway assay; neither individual enzyme is asserted to form the mature owner. Producer and BGC evidence grades remain unchanged.
DOI:10.1038/s41467-021-22395-7
https://www.ncbi.nlm.nih.gov/protein/AXG22410.1
https://www.ncbi.nlm.nih.gov/nuccore/MH544245.1
https://dl.secondarymetabolites.org/mibig/mibig_json_4.0.tar.gz
https://rest.uniprot.org/uniparc/UPI00100575B1.json
  • reference
    DOI:10.1038/s41467-021-22395-7
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-07
    notes
    The introduction compares stm and ngn loci; the Results and Methods test the ATCC31306 NgnO1/NgnO2 pair in a related streptoseomycin-pathway context. Native nargenicin participation here is explicitly inferred, not a newly inspected direct native phenotype. Supplementary gene/construct tables and primary structure drawings were not inspected; no exact native reaction is claimed.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AXG22410.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Native NgnO2 reference from Nocardia argentinensis ATCC31306/taxon1311812, 421aa. Gene name, strain and MH544245.1 coded_by mapping identify the canonical parent, not a completely reconstructed historical tagged assay construct. Family/product annotations are not independent proof of the specific reaction. Gene/species and exact GenPept-xref UniProtKB searches returned no entries on2026-10-07; this is not global absence and no homolog was selected.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/MH544245.1
    evidence type
    CURATOR_INFERENCE
    retrieved on
    2026-10-07
    notes
    Complete native CDS at forward51720..52985, 1266nt, table11/codon1 translates to the exact 421-aa GenPeptAXG22410.1 reference; independent coded_by coordinates/strand/DNA and strain qualifiers agree. MH544245.1 is a69359bp nargenicin cluster deposit, not a complete genome. This identity check does not prove function by gene neighborhood alone.
  • reference
    https://dl.secondarymetabolites.org/mibig/mibig_json_4.0.tar.gz
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-06
    notes
    Adopted MIBiG4.0 archive SHA256 986f1a69fb5eeb84fd7c0175ae921304c22fd5f8ed04c96d8c1c0c95a145837b, BGC0002024v3 member inspected2026-10-07. Its two compound rows share the exact owner SMILES, locusMH544245.1 and taxon1311812. No NgnO1/O2 gene-function or locus evidence is supplied by this entry. It anchors the source compound/locus assertion only, not the experimental function or producer-grade upgrade.
  • reference
    https://rest.uniprot.org/uniparc/UPI00100575B1.json
    evidence type
    DATABASE_ASSERTION
    notes
    UniParc UPI00100575B1 (421 aa) links active EMBL AXG22410.1 (Nocardia argentinensis, taxon 1311812, gene ngnO2) and inactive UniProtKB/TrEMBL A0A3S7PZG8, with zero active UniProtKB cross-references.
    retrieved on
    2026-10-30

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

Causal graph — biosynthesis 2 nodes, 1 edge

Qualified database assignment of NgnD as a putative cyclase in nargenicin biosynthesis. The canonical ATCC 31306 protein is grounded independently of the longer PDB construct. This graph does not assert an inspected native knockout, an exact intermediate reaction, a demonstrated solution dimer, or direct production of mature nargenicin A1.

SubjectPredicateObjectNotesEvidence
NgnD, native ATCC 31306 parent (putative cyclase) is_database_assigned_putative_cyclase_in_biosynthesis_of nargenicin A1 Database-level pathway-role assertion only. The pinned MITE row gives a tentative bispericyclase assignment and links this exact GenPept reference to BGC0002024. Its knockout evidence code was not independently verified in the inaccessible 2020 paper, whose abstract names a different strain; no native ATCC 31306 knockout phenotype is transferred. MITE models are C22H34O4 intermediates, distinct from the C28H37NO8 owner even without stereochemistry, and its product has undefined centres. No exact native substrate/product pair, specific cycloaddition outcome or mature-owner-forming reaction is adopted. PDB biological-assembly annotation is not solution stoichiometry evidence.
https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000113.json
https://www.rcsb.org/structure/6A5F
https://www.ncbi.nlm.nih.gov/protein/AXG22404.1
https://www.ncbi.nlm.nih.gov/nuccore/MH544245.1
https://dl.secondarymetabolites.org/mibig/mibig_json_4.0.tar.gz
https://rest.uniprot.org/uniparc/UPI001005A892.json
  • reference
    https://github.com/mite-standard/mite_data/blob/6eacd913b2036376031072f69cbb33908f132998/mite_data/data/MITE0000113.json
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-06
    snippet
    [6+4] cycloaddition; NgnD acts likely similar to a bispericyclase
    notes
    MITE0000113 version 2, inspected 2026-10-07; archive member and Git blob verified at the cited commit. The row names NgnD, GenPept AXG22404.1, UniParc UPI001005A892 and MIBiG BGC0002024. Preserve the source's tentative wording. Neither its reaction model nor its knockout evidence code is promoted to an independently inspected primary experiment.
  • reference
    https://www.rcsb.org/structure/6A5F
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Independent PDB deposit DOI:10.2210/pdb6A5F/pdb names NgnD and a nargenicin-pathway cyclase. Polymer entity 1/chains A and B contain the exact 152-aa native sequence followed by 13 additional C-terminal residues; the origin of that extension is not reconstructed from the inaccessible paper. The 2.05-Angstrom model covers native positions 2-152, with residue 1 and the whole extension unmodeled. The source strain taxon 1311813 has species ancestor 1311812 in the inspected RCSB lineage. Author/PISA dimeric assembly annotation explicitly has experimental_support none; no physical assembly node is adopted. Structural identity does not establish the exact catalytic reaction.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AXG22404.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    Canonical native NgnD, Nocardia argentinensis ATCC 31306, 152 aa; source strain and gene agree. The full reverse-strand MH544245.1 CDS at 5198..5656 is 459 nt, table 11/codon 1, and translates identically to GenPept and UniParc UPI001005A892. Independent coded_by coordinates, strand and DNA agree. UniParc marks A0A3S7PZF0 inactive; the bounded current exact-gene/taxon or GenPept-xref UniProtKB query returned no entries. No homolog or same-sequence protein from another strain was substituted. Family annotation alone does not prove cyclase function.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/MH544245.1
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-07
    notes
    MH544245.1 is the complete 69,359-bp nargenicin cluster deposit, not a complete genome. It establishes native gene identity and source context, not experimental function from neighborhood alone.
  • reference
    https://dl.secondarymetabolites.org/mibig/mibig_json_4.0.tar.gz
    evidence type
    DATABASE_ASSERTION
    retrieved on
    2026-10-06
    notes
    Adopted MIBiG 4.0 archive SHA256 986f1a69fb5eeb84fd7c0175ae921304c22fd5f8ed04c96d8c1c0c95a145837b; BGC0002024 version 3 inspected 2026-10-07. Both compound rows share the exact owner SMILES, source taxon 1311812 and locus MH544245.1. This is a compound/locus anchor only: the entry supplies no NgnD gene-function evidence and does not support a producer or cluster evidence-grade upgrade.
  • reference
    https://rest.uniprot.org/uniparc/UPI001005A892.json
    evidence type
    DATABASE_ASSERTION
    notes
    UniParc UPI001005A892 (152 aa) links active EMBL AXG22404.1 (Nocardia argentinensis, taxon 1311812, gene ngnD) and inactive UniProtKB/TrEMBL A0A3S7PZF0, with zero active UniProtKB cross-references.
    retrieved on
    2026-10-30

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

Explore across X-Mech

AntibioticMech (nargenicin A1) ↗ MediaIngredientMech (naturalproductmech:mibig-6437746e58) ↗ TaxonMech: Nocardia argentinensis (NCBITaxon:1311812) ↗ TaxonMech: Nocardia argentinensis (NCBITaxon:1311812) ↗ PathwayMech (mibig:BGC0002024) ↗ PathwayMech (mibig:BGC0002024) ↗

Provenance

Source conceptSourceVersion
BGC0002024MIBIG3
BGC0002024MIBIG3

This page is generated from data/natural_products/polyketides/nargenicin-a1.yaml, which is generated from the committed inventories. Neither is edited by hand.