AT2433-A1

naturalproductmech:mibig-6c1bd93a9d 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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	CGQSZYLXZOKJEJ-VYCQBBBDSA-N
SMILES	CN[C@H]1CO[C@H](C[C@@H]1O)OC[C@H]1O[C@H]([C@H](O)[C@@H](O)[C@@H]1OC)N1C2=C3NC4=C(C=CC=C4)C3=C3C(=O)N(C)C(=O)C3=C2C2=C1C(Cl)=CC=C2
Stereochemistry	fully defined
Cross-references	npatlas:NPA011993

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 other, 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
Actinomadura melliaura NCBITaxon:360723	SOURCE_ASSERTION	mibig:BGC0000809	PMID:16873021

Occurrences 2

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
Actinomadura melliaura NCBITaxon:360723	LOTUS	DOI:10.1021/ACS.JNATPROD.5B00429
Actinomadura melliaura NCBITaxon:360723	LOTUS	DOI:10.7164/ANTIBIOTICS.42.1547

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000809	Actinomadura melliaura NCBITaxon:360723	CLUSTER_UNSTATED	genbank:DQ297453.1

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

Causal graph — biosynthesis 2 nodes, 1 edge

Cofactor binding by the AT2433-cluster protein AtmC; partial biochemical evidence, not a demonstrated complete AT2433-A1 pathway or an assay of the finished compound's bioactivity.

Subject	Predicate	Object	Notes	Evidence
AtmC recombinant assay construct	binds	FAD	Table 2: AtmC ITC Kd = 73 +/- 28 nM, five experiments. Rosetta 2(DE3) pLysS expression, Ni-affinity purification and deflavination with 2 M KBr/2 M urea preceded ITC in 150 mM NaCl, 25 mM HEPES pH 7.5, 10% glycerol. Cofactor binding does not establish the substrate, elementary chemistry, or AT2433-A1 formation.	DOI:10.1016/j.chembiol.2012.05.016 https://ars.els-cdn.com/content/image/1-s2.0-S1074552112001809-mmc1.pdf https://www.uniprot.org/uniprotkb/Q0H2X3 reference DOI:10.1016/j.chembiol.2012.05.016 evidence type PRIMARY_EXPERIMENT snippet purifies with bound FAD notes Table 2: reported uncertainty retained without assigning an unstated SD/SEM statistic. reference https://ars.els-cdn.com/content/image/1-s2.0-S1074552112001809-mmc1.pdf evidence type PRIMARY_EXPERIMENT notes Fig. S2D and caption: ITC at 25 C. SI p. 19: Actinomadura melliaura atmC cloned into pET28a; canonical identifier excludes its affinity tag. reference https://www.uniprot.org/uniprotkb/Q0H2X3 evidence type DATABASE_ASSERTION notes The 534-aa canonical atC sequence, taxon 360723, exactly matches DQ297453.1 CDS ABC02791.1 from A. melliaura SCC 1655 and SI Fig. S1 AtmC. The forward primer targets the CDS start; the reverse primer targets downstream genomic sequence, retaining the native stop. This is the record's BGC0000809 locus, not an unrelated fungal atmC homolog. retrieved on 2026-10-03

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

Causal graph — biosynthesis 11 nodes, 10 edges

Sequential in-vitro assays of three AT2433-cluster sugar enzymes; partial aminopentose-precursor evidence shared by AT2433 congeners, including AT2433-A1. Neither a finished aminopentose donor nor AT2433-A1 was made in these assays.

Subject	Predicate	Object	Notes	Evidence
TDP-alpha-D-glucose (2-T)	is_substrate_for	AtmS8 glucose oxidation assay		DOI:10.1002/cbic.201500365 reference DOI:10.1002/cbic.201500365 evidence type PRIMARY_EXPERIMENT notes Figure 1A/B and AtmS8 experimental section.
AtmS8 N-terminal His6 construct	catalyzes	AtmS8 glucose oxidation assay	Genomic PCR; pET28a, E. coli BL21(DE3), N-terminal His6. 10 uM AtmS8, 2 mM TDP-glucose and 6 mM NAD+ at 30 C; pyruvate/LDH NAD+ regeneration. NMR/HPLC reported about 97% conversion after 16 h; enzyme-omission controls showed no reaction.	DOI:10.1002/cbic.201500365 https://www.uniprot.org/uniprotkb/Q0H2W3 reference DOI:10.1002/cbic.201500365 evidence type PRIMARY_EXPERIMENT notes Figure 1A/B and AtmS8 experimental section. snippet No reaction was observed via NMR or HPLC in controls lacking AtmS8. reference https://www.uniprot.org/uniprotkb/Q0H2W3 evidence type DATABASE_ASSERTION notes Canonical atS8, 450 aa, NCBITaxon:360723, exactly matches GenBank DQ297453.1 CDS ABC02801.1 from Actinomadura melliaura SCC 1655, the BGC0000809 locus in this record. Translation was checked with the CDS genetic code and initiator convention. The identifier denotes the native parent, not its affinity tag. retrieved on 2026-10-03
AtmS8 glucose oxidation assay	produces	TDP-alpha-D-glucuronic acid (3-T)		DOI:10.1002/cbic.201500365 reference DOI:10.1002/cbic.201500365 evidence type PRIMARY_EXPERIMENT notes Figure 1A/B and AtmS8 experimental section.
TDP-alpha-D-glucuronic acid (3-T)	is_substrate_for	AtmS9 glucuronate decarboxylation assay		DOI:10.1002/cbic.201500365 reference DOI:10.1002/cbic.201500365 evidence type PRIMARY_EXPERIMENT notes Figure 2A and AtmS9 experimental section.
AtmS9 N-terminal His6 construct	catalyzes	AtmS9 glucuronate decarboxylation assay	Same genomic-PCR expression strategy as AtmS8. Adding 15 uM AtmS9 after AtmS8 completion gave quantitative 4-T formation in 15 h at 30 C (NMR/HPLC); enzyme-omission controls showed no reaction. The paper also reports reduced xylose nucleotide after longer incubations (>24 h, 37 C), so 4-T is not an exclusive product under all conditions.	DOI:10.1002/cbic.201500365 https://www.uniprot.org/uniprotkb/Q0H2W2 reference DOI:10.1002/cbic.201500365 evidence type PRIMARY_EXPERIMENT notes Figure 2A and AtmS9 experimental section. snippet quantitative conversion reference https://www.uniprot.org/uniprotkb/Q0H2W2 evidence type DATABASE_ASSERTION notes Canonical atS9, 329 aa, NCBITaxon:360723, exactly matches GenBank DQ297453.1 CDS ABC02802.1 from Actinomadura melliaura SCC 1655, the BGC0000809 locus in this record. Translation was checked with the CDS genetic code and initiator convention. The identifier denotes the native parent, not its affinity tag. retrieved on 2026-10-03
AtmS9 glucuronate decarboxylation assay	produces	TDP-4-keto-alpha-D-xylose (4-T)		DOI:10.1002/cbic.201500365 reference DOI:10.1002/cbic.201500365 evidence type PRIMARY_EXPERIMENT notes Figure 2A and AtmS9 experimental section.
TDP-4-keto-alpha-D-xylose (4-T)	is_substrate_for	AtmS14 addition to 4-T: degradation readout		DOI:10.1002/cbic.201500365 reference DOI:10.1002/cbic.201500365 evidence type PRIMARY_EXPERIMENT notes Figure 3 and AtmS14 experimental section.
AtmS14 synthetic-gene His6 construct	enables_observed_degradation_in	AtmS14 addition to 4-T: degradation readout	pUC57 codon-optimized synthetic gene subcloned into pET28a; N-terminal His6, E. coli BL21(DE3). The main paper identifies the parent; the supplemental synthetic sequence was not retrievable and was not independently verified. Adding 14 uM AtmS14 after AtmS9 completion yielded 6 and TDP within 6 h at 30 C (NMR/HPLC). Proposed 2,3-dehydration intermediate TDP-2-deoxy-4-keto-alpha-D-pentos-2-ene (5-T) was not isolated; these are degradation products, not a demonstrated finished sugar donor or direct two-product enzymatic reaction.	DOI:10.1002/cbic.201500365 https://www.uniprot.org/uniprotkb/Q0H2W5 reference DOI:10.1002/cbic.201500365 evidence type PRIMARY_EXPERIMENT notes Figure 3 and AtmS14 experimental section. snippet two new products reference https://www.uniprot.org/uniprotkb/Q0H2W5 evidence type DATABASE_ASSERTION notes Canonical atS14, 483 aa, NCBITaxon:360723, exactly matches GenBank DQ297453.1 CDS ABC02799.1 from Actinomadura melliaura SCC 1655, the BGC0000809 locus in this record. Translation was checked with the CDS genetic code and initiator convention. The identifier denotes the native parent, not its affinity tag. retrieved on 2026-10-03
AtmS14 addition to 4-T: degradation readout	yields_observed_product	3-hydroxy-4H-pyran-4-one (6; pyromicomic acid)		DOI:10.1002/cbic.201500365 reference DOI:10.1002/cbic.201500365 evidence type PRIMARY_EXPERIMENT notes Figure 3 and AtmS14 experimental section.
AtmS14 addition to 4-T: degradation readout	yields_observed_product	TDP		DOI:10.1002/cbic.201500365 reference DOI:10.1002/cbic.201500365 evidence type PRIMARY_EXPERIMENT notes Figure 3 and AtmS14 experimental section.

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

Causal graph — biosynthesis 3 nodes, 2 edges

Structural evidence for the AT2433-cluster putative sugar aminotransferase AtmS13. Dimer and PLP-adduct observations do not establish native-substrate turnover, substrate stereochemistry, or completed AT2433-A1 biosynthesis.

Subject	Predicate	Object	Notes	Evidence
AtmS13 SeMet construct (4ZWV; cleaved tag)	is_subunit_of	AtmS13 homodimer in 4ZWV	1.50-A X-ray structure of SeMet protein expressed from pMCSG68 in E. coli BL21(DE3)-Gold. TEV removal of the StrepII/His6 tag leaves SNA before the native parent. The two-subunit crystal assembly is structural evidence, not an in-vivo assembly assay. The separate 3.00-A structure 4XAU used non-SeMet, pET28a N-His6 protein with a different 20-residue N-terminal extension.	DOI:10.1002/prot.24844 https://www.uniprot.org/uniprotkb/Q0H2X1 https://www.rcsb.org/structure/4ZWV reference DOI:10.1002/prot.24844 evidence type PRIMARY_EXPERIMENT notes Figure 2A and Overall Structure section. snippet representing the formation of a dimer reference https://www.uniprot.org/uniprotkb/Q0H2X1 evidence type DATABASE_ASSERTION notes Canonical atS13, 369 aa, NCBITaxon:360723, exactly matches GenBank DQ297453.1 CDS ABC02793.1 from Actinomadura melliaura SCC 1655, the BGC0000809 locus in this record. Translation was checked with the CDS genetic code and initiator convention. The identifier denotes the native parent, not its affinity tag. retrieved on 2026-10-03 reference https://www.rcsb.org/structure/4ZWV evidence type DATABASE_ASSERTION notes Deposited canonical entity sequence is SNA plus all 369 residues of Q0H2X1. SIFTS maps the complete native parent; assembly 1 is author/PISA-assigned dimeric. retrieved on 2026-10-03
AtmS13 SeMet construct (4ZWV; cleaved tag)	forms_covalent_internal_aldimine_with	Pyridoxal 5-phosphate (PLP)	Crystallized with 1 mM PLP. The 4ZWV Lys187-PLP adduct occurs in both subunits, with two alternate PLP orientations refined at 0.50 occupancy each. This is cofactor-adduct evidence, not an aminopentose transamination assay.	DOI:10.1002/prot.24844 https://files.rcsb.org/download/4ZWV.cif reference DOI:10.1002/prot.24844 evidence type PRIMARY_EXPERIMENT notes Table 1, Figure 2B and Cofactor Binding Site section. snippet Both subunits contain a covalent PLP internal aldimine reference https://files.rcsb.org/download/4ZWV.cif evidence type DATABASE_ASSERTION notes Chains A and B: modified residue LLP has label_seq_id 190 and auth_seq_id 187, matching native Q0H2X1 Lys187. The three-residue prefix is not part of native numbering. retrieved on 2026-10-03

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

Explore across X-Mech

AntibioticMech (AT2433-A1) ↗ MediaIngredientMech (naturalproductmech:mibig-6c1bd93a9d) ↗ TaxonMech: Actinomadura melliaura (NCBITaxon:360723) ↗ PathwayMech (mibig:BGC0000809) ↗

Provenance

Source concept	Source	Version
BGC0000809	MIBIG	3

This page is generated from data/natural_products/alkaloids/at2433-a1.yaml, which is generated from the committed inventories. Neither is edited by hand.